Mercurial > repos > marcel > caddsuite_linux_x86_64
changeset 3:ff6df146c0d5
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/AntitargetRescorer Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,4 @@ +#!/bin/bash + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/AntitargetRescorer.bin "$@"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/AutoModel Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,4 @@ +#!/bin/bash + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/AutoModel.bin "$@"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/BindingDBCleaner Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,4 @@ +#!/bin/bash + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/BindingDBCleaner.bin "$@"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/CADDSuite-description.txt Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,60 @@ +This package contains tools belonging to +CADDSuite: A flexible and open framework for Computer-Aided Drug Design + +There are tools for the following tasks: + +Get Data: + - CombiLibGenerator: generate R-group decorated ligands + - DBExporter: fetch (filtered) molecules from DB + +Preparation of input: + - PDBCutter: separate ligand and receptor + - ProteinProtonator: protonate protein structures + - BindingDBCleaner: fix data from bindingdb.org + - EvenSplit: generate splits w/ equal property range + - PropertyModifier: modify property tags + - LigandFileSplitter: split molecule files + - Ligand3DGenerator: generate 3D coordinates for small molecules + +Structure checks and evaluations: + - ProteinCheck: evaluate protein quality + - LigCheck: chemical sanity check for ligands + +QuEasy (QSAR): + - InputReader: read molecules and generate features + - ModelCreator: create a QSAR model + - FeatureSelector: automatically select features of a QSAR model + - Validator: evaluate quality of a QSAR model + - MolPredictor: predict molecule activities with QSAR model + - AutoModel: automatically find best QSAR model + +Docking: + - WaterFinder: find strongly bound water molecules + - SpatialConstraintDefiner: define spatial constraint + - ConstraintsFinder: find strongly interacting residues + - PocketDetector: detect ligand binding pocket + - GridBuilder: precalculate grids for docking + - IMeedyDock: run Iterative Multi-Greedy Docking + +Rescoring: + - SimpleRescorer: rescore docking results + - TaGRes-train: Target-specific Grid-Rescoring, training + - TaGRes: Target-specific Grid-Rescoring + - AntitargetRescoring: rescore w/ respect to antitarget + +Analysis: + - ScoreAnalyzer: generate ROC or enrichment plots + - SimilarityAnalyzer: analyze similarity between two molecule sets + - PropertyPlotter: plot molecule properties + - RMSDCalculator: calculate RMSD between conformations + - VendorFinder: search vendors for compounds + +Convert, combine and store: + - DockResultMerger: merge docking output files and/or filter them + - MolCombine: combine molecular files + - DBImporter: import molecules into DB + - Converter: interconvert molecular file-formats + - MolDepict: generate structure diagrams + - VendorFinder: search vendors for compounds + +For more information about an individual tool, please call the tool without any parameters (or with '-help').
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/CombiLibGenerator Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,4 @@ +#!/bin/bash + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/CombiLibGenerator.bin "$@"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/ConstraintsFinder Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,4 @@ +#!/bin/bash + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/ConstraintsFinder.bin "$@"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/Converter Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,4 @@ +#!/bin/bash + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/Converter.bin "$@"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/DBExporter Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,4 @@ +#!/bin/bash + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/DBExporter.bin "$@"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/DBImporter Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,4 @@ +#!/bin/bash + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/DBImporter.bin "$@"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/DockResultMerger Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,4 @@ +#!/bin/bash + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/DockResultMerger.bin "$@"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/EvenSplit Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,4 @@ +#!/bin/bash + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/EvenSplit.bin "$@"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/FeatureSelector Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,4 @@ +#!/bin/bash + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/FeatureSelector.bin "$@"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/GalaxyConfigGenerator Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,4 @@ +#!/bin/bash + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/GalaxyConfigGenerator.bin "$@"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/GridBuilder Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,4 @@ +#!/bin/bash + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/GridBuilder.bin "$@"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/IMGDock Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,4 @@ +#!/bin/bash + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/IMGDock.bin "$@"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/InputPartitioner Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,4 @@ +#!/bin/bash + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/InputPartitioner.bin "$@"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/InputReader Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,4 @@ +#!/bin/bash + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/InputReader.bin "$@"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/InteractionConstraintDefiner Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,4 @@ +#!/bin/bash + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/InteractionConstraintDefiner.bin "$@"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/LigCheck Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,4 @@ +#!/bin/bash + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/LigCheck.bin "$@"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/Ligand3DGenerator Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,4 @@ +#!/bin/bash + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/Ligand3DGenerator.bin "$@"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/LigandFileSplitter Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,4 @@ +#!/bin/bash + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/LigandFileSplitter.bin "$@"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/ModelCreator Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,4 @@ +#!/bin/bash + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/ModelCreator.bin "$@"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/MolCombine Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,4 @@ +#!/bin/bash + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/MolCombine.bin "$@"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/MolDepict Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,4 @@ +#!/bin/bash + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/MolDepict.bin "$@"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/MolFilter Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,4 @@ +#!/bin/bash + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/MolFilter.bin "$@"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/MolPredictor Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,4 @@ +#!/bin/bash + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/MolPredictor.bin "$@"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/PDBCutter Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,4 @@ +#!/bin/bash + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/PDBCutter.bin "$@"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/PDBDownload Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,4 @@ +#!/bin/bash + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/PDBDownload.bin "$@"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/PartialChargesCopy Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,4 @@ +#!/bin/bash + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/PartialChargesCopy.bin "$@"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/PocketDetector Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,4 @@ +#!/bin/bash + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/PocketDetector.bin "$@"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/Predictor Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,4 @@ +#!/bin/bash + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/Predictor.bin "$@"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/PropertyModifier Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,4 @@ +#!/bin/bash + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/PropertyModifier.bin "$@"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/PropertyPlotter Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,4 @@ +#!/bin/bash + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/PropertyPlotter.bin "$@"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/ProteinCheck Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,4 @@ +#!/bin/bash + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/ProteinCheck.bin "$@"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/ProteinProtonator Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,4 @@ +#!/bin/bash + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/ProteinProtonator.bin "$@"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/QuEasyRun Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,4 @@ +#!/bin/bash + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/QuEasyRun.bin "$@"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/README Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,41 @@ +----------------------------------------------------------------------- + CADDSuite - A flexible and open framework and workflow system + for computer-aided drug design +----------------------------------------------------------------------- + +This package contains all tools belonging to CADDSuite. +For an overview over the contained tools, please see CADDSuite-description.txt. +After extraction the package, you can directly start the applications using the startup-scripts in the base-folder. + +For more information about an individual tool, please call the tool without any parameters (or with '-h'). + + + +-------------------------------------------------------------------- +Instructions for integration of CADDSuite into the workflow-system +Galaxy (http://getgalaxy.org) +-------------------------------------------------------------------- + + +In order to install CADDSuite into your Galaxy installation, please to the following: + +Let's assume $galaxybase is the base-folder of your Galaxy installation. +If you don't have a galaxy-installation yet, download a version from http://getgalaxy.org and follow the installation instructions shown there first. + + +-- Extract the CADDSuite archive into a new folder $galaxybase/tools/CADDSuite, or extract it somewhere else and create a link named $galaxybase/tools/CADDSuite that points to this destination. + +After this, you need to copy a few files that you find in the galaxyconfig/ subfolder of this archive to the destinations specified below: + +-- Copy tool_conf.xml and datatypes_conf.xml to $galaxybase if you want to setup your Galaxy instance for exclusive use of CADDSuite, or copy the contents of those files into the files already existing in $galaxybase if you want to keep using tools that came along with the Galaxy installation. + +-- Copy molFiles.py, confFiles.py and countResidues.sh to $galaxybase/lib/galaxy/datatypes/ + +-- Add "#import molFiles, confFiles.py" to the beginning of the file $galaxybase/lib/galaxy/datatypes/registry.py + + + +Last but not least, restart Galaxy. +All CADDSuite tools should now appear in your Galaxy webinterface. + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/RMSDCalculator Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,4 @@ +#!/bin/bash + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/RMSDCalculator.bin "$@"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/ScoreAnalyzer Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,4 @@ +#!/bin/bash + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/ScoreAnalyzer.bin "$@"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/SideChainGridBuilder Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,4 @@ +#!/bin/bash + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/SideChainGridBuilder.bin "$@"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/SimilarityAnalyzer Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,4 @@ +#!/bin/bash + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/SimilarityAnalyzer.bin "$@"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/SimpleRescorer Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,4 @@ +#!/bin/bash + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/SimpleRescorer.bin "$@"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/SpatialConstraintDefiner Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,4 @@ +#!/bin/bash + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/SpatialConstraintDefiner.bin "$@"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/TaGRes Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,4 @@ +#!/bin/bash + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/TaGRes.bin "$@"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/TaGRes-train Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,4 @@ +#!/bin/bash + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/TaGRes-train.bin "$@"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/Validator Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,4 @@ +#!/bin/bash + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/Validator.bin "$@"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/VendorFinder Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,4 @@ +#!/bin/bash + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/VendorFinder.bin "$@"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/WaterFinder Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,4 @@ +#!/bin/bash + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/WaterFinder.bin "$@"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/changelog.txt Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,46 @@ +Version 0.94, 06-27-2011: + - Fixed tool-startup script for pathes containing whitespaces + - New tool SpatialConstraintDefiner + - New tool InteractionConstraintDefiner + - Removed superficial pathes from startup-script + - Slight change in ParamFile format (i.e. the files written with -write_par) + - Renamed IMeedyDock to IMGDock + +Version 0.93, 05-30-2011: + - Split Rescorer into 3 tools: SimpleRescorer, TaGRes-train, TaGRes (Target-Specific Grid-Rescoring) + - Allow to optionally specify output filenames to LigandFileSplitter + - Fixed creation of galaxy-scripts for tools with inputfile-lists + - Fixed creation of galaxy-scripts for Converter and DockResultMerger + - Automatically create and add all files necessary for integration of CADDSuite into Galaxy to the makeself archive + - New tool MolFilter + - Fixed some gnuplot issues + - Added PDBDownload tool + - Slight change of format of ParamFile + - Added some missing tool-manuals + - Disable B-factor check for hydrogens in ProteinCheck + - Added safeguards to several tools + - Automatically delete existing hydrogens from BALL-system before protonation is done by ProteinProtonator + - Fixed reading of mulitple ScoreGridSets (for cases when no ini-file is used) + - Simplified use of VendorFinder by allowing to set all db-parameters on the command-line (instead of using ini-file) + - Enhanced several tool manuals + - Let tools register their category (e.g. Preparation, Docking, etc.). Write and read information about this category to/from ParamFiles. + +Version 0.92, 05-17-2011: + - Speed-up of ob-mol generation + - Support build on Windows + - ProteinCheck now generates protein-quality report as pdf + - Added info about mandatory parameters and parameter-restrictions to parameter xml-file + - Simplified use of DBImporter+DBExporter by allowing to set all db-parameters on the command-line (instead of using ini-file) + - Simplified use of some other tools by merging several flags into one string-parameter that has restrictions. + - New tool MolDepict. It generates structure diagrams for small molecules by using openbabel's svg-writer and merges them to one pdf-file (3 on 5). + - Allow to create makeself-archive containing CADDSuite, all necessary contrib-libs, data-files and install-script + - Write information about supported file-formats to parameter xml-file + - new tool ProteinProtonator + - new tool Ligand3DGenerator + - new tool GalaxyConfigGenerator + - allow to open file that do not have an extension (by searching for format-specific keywords) + +Version 0.91, 04-12-2011: + - All tools now write a manual text to cout as well as to parameter xml-file (as generated by 'write_par) + +Version 0.9
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/Amber/amber96-docking.ini Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,1666 @@ +; This file contains parameter needed for nonbonded ScoringComponents. +; The parameters were converted from parm96.dat using amber2ini and all sections for bonded parameters were removed since are not needed for docking. +; Furthermore, lennard-jones and AtomType parameters for some metal ions were obtained from the sources indicated in the comment column and added to this file. + +[Options] +key:0 +@SCEE=1.2 +; please check the settings for SCEE! AMBER91/89a requires a value of 2.0 here! + + + + +[HydrophilicTypes] +; ignored +; +C H HO N NA NB NC N2 NT N2 N3 N* O OH OS P O2 + + +[HydrogenBonds] +ver:version key:I key:J value:A value:B +@unit_A=kcal/mol*A^12 +@unit_B=kcal/mol*A^10 +; +; +; Rev I J A B +; --- --- --- ---------- ---------- + 1.0 HW OW 0.0000 0.0000 + + +[AtomTypes] +value:ver key:type value:mass value:comment +@unit=g/mol +; +; +; Rev Type mass comment +; --- ---- ---------- ---------------------------------- + 1.0 BR 79.90000 "bromine" + 1.0 C 12.01000 "sp2 C carbonyl group " + 1.0 F 19.00000 "fluorine" + 1.0 I 126.90000 "iodine" + 1.0 H 1.00800 "H bonded to nitrogen atoms" + 1.0 IM 35.45000 "assumed to be Cl-" + 1.0 IP 22.99000 "assumed to be Na+" + 1.0 IB 131.00000 "'big ion w/ waters' for vacuum (Na+, 6H2O)" + 1.0 N 14.01000 "sp2 nitrogen in amide groups" + 1.0 O 16.00000 "carbonyl group oxygen" + 1.0 P 30.97000 "phosphate" + 1.0 S 32.06000 "sulphur in disulfide linkage" + 1.0 Cu 63.55000 "copper" + 1.0 Fe 55.00000 "iron" + 1.0 Li 6.94000 "lithium" + 1.0 K 39.10000 "potassium" + 1.0 Rb 85.47000 "rubidium" + 1.0 Cs 132.91000 "cesium" + ant Cl 35.450 "same as cl" + 2.0 Ca 40.08000 "calcium" + 1.0 Mg 24.30500 "magnesium" + ant Zn 65.4 "Zn2+, taken from parm99.dat (antechamber)" + + +[LennardJones] +ver:version key:I value:R value:epsilon +@unit_R=Angstrom +@unit_epsilon=kcal/mol +@format=RE +; +; +; Rev I R epsilon comment +; --- --- ---------- ---------- ------------------------- + 1.0 Ca 1.600000 0.100000 " calcium from parm91.dat" + 1.0 H 0.600000 0.015700 " !Ferguson base pair geom." + 1.0 O 1.661200 0.210000 " OPLS" + 1.0 C 1.908000 0.086000 " OPLS" + 1.0 N 1.824000 0.170000 " OPLS" + 1.0 S 2.000000 0.250000 " W. Cornell CH3SH and CH3SCH3 FEP's" + 1.0 P 2.100000 0.200000 " JCC,7,(1986),230;" + 1.0 IM 2.470000 0.100000 " Cl- Smith & Dang, JCP 1994,100:5,3757" + 1.0 IB 5.000000 0.100000 " solvated ion for vacuum approximation" + 1.0 Li 1.137000 0.018300 " Li+ Aqvist JPC 1990,94,8021. (adapted)" + 1.0 IP 1.868000 0.002770 " Na+ Aqvist JPC 1990,94,8021. (adapted)" + 1.0 K 2.658000 0.000328 " K+ Aqvist JPC 1990,94,8021. (adapted)" + 1.0 Rb 2.956000 0.000170 " Rb+ Aqvist JPC 1990,94,8021. (adapted)" + 1.0 Cs 3.395000 0.000081 " Cs+ Aqvist JPC 1990,94,8021. (adapted)" + 1.0 I 2.350000 0.400000 " JCC,7,(1986),230;" + 1.0 F 1.750000 0.061000 " Gough et al. JCC 13,(1992),963." + ant Cl 2.47 0.1 " Cl- Smith & Dang, JCP 1994,100:5,3757, taken from parm99.dat (antechamber)" + ant Zn 1.10 0.0125 " Zn2+, Merz,PAK, JACS,113,8262,(1991), taken from parm99.dat (antechamber)" + ant Mg 0.7926 0.8947 " Mg2+ Aqvist JPC 1990,94,8021.(adapted), taken from parm99.dat (antechamber)" +; ant Cl 1.9480 0.2650 "same as cl" +; 1.0 Mg 1.170000 0.100000 " magnesium from parm91.dat" + + +[ResidueImproperTorsions] +key:name +; +; +; res:atom +; ------------- + ALA:N + ALA:C + GLY:N + GLY:C + SER:N + SER:C + THR:N + THR:C + LEU:N + LEU:C + ILE:N + ILE:C + VAL:N + VAL:C + ASN:N + ASN:C + ASN:CG + ASN:ND2 + GLN:N + GLN:C + GLN:CD + GLN:NE2 + ARG:N + ARG:C + ARG:CZ + ARG:NE + ARG:NH1 + ARG:NH2 + HIS:N + HIS:C + HIS:ND1 + HIS:CD2 + HIS:CE1 + HIS:CG + HIS:N + HIS:C + HIS:NE2 + HIS:CD2 + HIS:CE1 + HIS:CG + HIS:N + HIS:C + HIS:ND1 + HIS:NE2 + HIS:CD2 + HIS:CE1 + HIS:CG + TRP:N + TRP:C + TRP:NE1 + TRP:CZ2 + TRP:CH2 + TRP:CZ3 + TRP:CE3 + TRP:CD1 + TRP:CG + PHE:N + PHE:C + PHE:CD2 + PHE:CE2 + PHE:CZ + PHE:CE1 + PHE:CD1 + PHE:CG + TYR:N + TYR:C + TYR:CD2 + TYR:CE2 + TYR:CE1 + TYR:CD1 + TYR:CG + TYR:CZ + GLU:N + GLU:C + GLU:CD + ASP:N + ASP:C + ASP:CG + LYS:N + LYS:C + LYN:N + LYN:C + PRO:C + PRO:N + CYS:N + CYS:C + CYM:N + CYM:C + CYS-S:N + CYS-S:C + MET:N + MET:C + ACE:C + NME:N + ASH:N + ASH:C + ASH:CG + GLH:N + GLH:C + GLH:CD + ALA-N:C + GLY-N:C + SER-N:C + THR-N:C + LEU-N:C + ILE-N:C + VAL-N:C + ASN-N:C + ASN-N:CG + ASN-N:ND2 + GLN-N:C + GLN-N:CD + GLN-N:NE2 + ARG-N:C + ARG-N:CZ + ARG-N:NE + ARG-N:NH1 + ARG-N:NH2 + HIS-N:C + HIS-N:ND1 + HIS-N:CD2 + HIS-N:CE1 + HIS-N:CG + HIS-N:C + HIS-N:NE2 + HIS-N:CD2 + HIS-N:CE1 + HIS-N:CG + HIS-N:C + HIS-N:ND1 + HIS-N:NE2 + HIS-N:CD2 + HIS-N:CE1 + HIS-N:CG + TRP-N:C + TRP-N:NE1 + TRP-N:CZ2 + TRP-N:CH2 + TRP-N:CZ3 + TRP-N:CE3 + TRP-N:CD1 + TRP-N:CG + PHE-N:C + PHE-N:CD2 + PHE-N:CE2 + PHE-N:CZ + PHE-N:CE1 + PHE-N:CD1 + PHE-N:CG + TYR-N:C + TYR-N:CD2 + TYR-N:CE2 + TYR-N:CE1 + TYR-N:CD1 + TYR-N:CG + TYR-N:CZ + GLU-N:C + GLU-N:CD + ASP-N:C + ASP-N:CG + LYS-N:C + PRO-N:C + CYS-N:C + CYS-NS:C + MET-N:C + ALA-C:N + ALA-C:C + GLY-C:N + GLY-C:C + SER-C:N + SER-C:C + THR-C:N + THR-C:C + LEU-C:N + LEU-C:C + ILE-C:N + ILE-C:C + VAL-C:N + VAL-C:C + ASN-C:N + ASN-C:C + ASN-C:CG + ASN-C:ND2 + GLN-C:N + GLN-C:C + GLN-C:CD + GLN-C:NE2 + ARG-C:N + ARG-C:C + ARG-C:CZ + ARG-C:NE + ARG-C:NH1 + ARG-C:NH2 + HIS-C:N + HIS-C:C + HIS-C:ND1 + HIS-C:CD2 + HIS-C:CE1 + HIS-C:CG + HIS-C:N + HIS-C:C + HIS-C:NE2 + HIS-C:CD2 + HIS-C:CE1 + HIS-C:CG + HIS-C:N + HIS-C:C + HIS-C:ND1 + HIS-C:NE2 + HIS-C:CD2 + HIS-C:CE1 + HIS-C:CG + TRP-C:N + TRP-C:C + TRP-C:NE1 + TRP-C:CZ2 + TRP-C:CH2 + TRP-C:CZ3 + TRP-C:CE3 + TRP-C:CD1 + TRP-C:CG + PHE-C:N + PHE-C:C + PHE-C:CD2 + PHE-C:CE2 + PHE-C:CZ + PHE-C:CE1 + PHE-C:CD1 + PHE-C:CG + TYR-C:N + TYR-C:C + TYR-C:CD2 + TYR-C:CE2 + TYR-C:CE1 + TYR-C:CD1 + TYR-C:CG + TYR-C:CZ + GLU-C:N + GLU-C:C + GLU-C:CD + ASP-C:N + ASP-C:C + ASP-C:CG + LYS-C:N + LYS-C:C + PRO-C:C + PRO-C:N + CYS-C:N + CYS-C:C + CYS-CS:N + CYS-CS:C + MET-C:N + MET-C:C + +[ChargesAndTypeNames] +ver:version key:name value:q value:type +@unit_q=e0 + 1.0 ALA:N -0.41570 N + 1.0 ALA:H 0.27190 H + 1.0 ALA:CA 0.03370 CT + 1.0 ALA:HA 0.08230 H1 + 1.0 ALA:CB -0.18250 CT + 1.0 ALA:1HB 0.06030 HC + 1.0 ALA:2HB 0.06030 HC + 1.0 ALA:3HB 0.06030 HC + 1.0 ALA:C 0.59730 C + 1.0 ALA:O -0.56790 O + 1.0 GLY:N -0.41570 N + 1.0 GLY:H 0.27190 H + 1.0 GLY:CA -0.02520 CT + 1.0 GLY:1HA 0.06980 H1 + 1.0 GLY:2HA 0.06980 H1 + 1.0 GLY:C 0.59730 C + 1.0 GLY:O -0.56790 O + 1.0 SER:N -0.41570 N + 1.0 SER:H 0.27190 H + 1.0 SER:CA -0.02490 CT + 1.0 SER:HA 0.08430 H1 + 1.0 SER:CB 0.21170 CT + 1.0 SER:1HB 0.03520 H1 + 1.0 SER:2HB 0.03520 H1 + 1.0 SER:OG -0.65460 OH + 1.0 SER:HG 0.42750 HO + 1.0 SER:C 0.59730 C + 1.0 SER:O -0.56790 O + 1.0 THR:N -0.41570 N + 1.0 THR:H 0.27190 H + 1.0 THR:CA -0.03890 CT + 1.0 THR:HA 0.10070 H1 + 1.0 THR:CB 0.36540 CT + 1.0 THR:HB 0.00430 H1 + 1.0 THR:CG2 -0.24380 CT + 1.0 THR:1HG2 0.06420 HC + 1.0 THR:2HG2 0.06420 HC + 1.0 THR:3HG2 0.06420 HC + 1.0 THR:OG1 -0.67610 OH + 1.0 THR:HG1 0.41020 HO + 1.0 THR:C 0.59730 C + 1.0 THR:O -0.56790 O + 1.0 LEU:N -0.41570 N + 1.0 LEU:H 0.27190 H + 1.0 LEU:CA -0.05180 CT + 1.0 LEU:HA 0.09220 H1 + 1.0 LEU:CB -0.11020 CT + 1.0 LEU:1HB 0.04570 HC + 1.0 LEU:2HB 0.04570 HC + 1.0 LEU:CG 0.35310 CT + 1.0 LEU:HG -0.03610 HC + 1.0 LEU:CD1 -0.41210 CT + 1.0 LEU:1HD1 0.10000 HC + 1.0 LEU:2HD1 0.10000 HC + 1.0 LEU:3HD1 0.10000 HC + 1.0 LEU:CD2 -0.41210 CT + 1.0 LEU:1HD2 0.10000 HC + 1.0 LEU:2HD2 0.10000 HC + 1.0 LEU:3HD2 0.10000 HC + 1.0 LEU:C 0.59730 C + 1.0 LEU:O -0.56790 O + 1.0 ILE:N -0.41570 N + 1.0 ILE:H 0.27190 H + 1.0 ILE:CA -0.05970 CT + 1.0 ILE:HA 0.08690 H1 + 1.0 ILE:CB 0.13030 CT + 1.0 ILE:HB 0.01870 HC + 1.0 ILE:CG2 -0.32040 CT + 1.0 ILE:1HG2 0.08820 HC + 1.0 ILE:2HG2 0.08820 HC + 1.0 ILE:3HG2 0.08820 HC + 1.0 ILE:CG1 -0.04300 CT + 1.0 ILE:1HG1 0.02360 HC + 1.0 ILE:2HG1 0.02360 HC + 1.0 ILE:CD1 -0.06600 CT + 1.0 ILE:1HD1 0.01860 HC + 1.0 ILE:2HD1 0.01860 HC + 1.0 ILE:3HD1 0.01860 HC + 1.0 ILE:C 0.59730 C + 1.0 ILE:O -0.56790 O + 1.0 VAL:N -0.41570 N + 1.0 VAL:H 0.27190 H + 1.0 VAL:CA -0.08750 CT + 1.0 VAL:HA 0.09690 H1 + 1.0 VAL:CB 0.29850 CT + 1.0 VAL:HB -0.02970 HC + 1.0 VAL:CG1 -0.31920 CT + 1.0 VAL:1HG1 0.07910 HC + 1.0 VAL:2HG1 0.07910 HC + 1.0 VAL:3HG1 0.07910 HC + 1.0 VAL:CG2 -0.31920 CT + 1.0 VAL:1HG2 0.07910 HC + 1.0 VAL:2HG2 0.07910 HC + 1.0 VAL:3HG2 0.07910 HC + 1.0 VAL:C 0.59730 C + 1.0 VAL:O -0.56790 O + 1.0 ASN:N -0.41570 N + 1.0 ASN:H 0.27190 H + 1.0 ASN:CA 0.01430 CT + 1.0 ASN:HA 0.10480 H1 + 1.0 ASN:CB -0.20410 CT + 1.0 ASN:1HB 0.07970 HC + 1.0 ASN:2HB 0.07970 HC + 1.0 ASN:CG 0.71300 C + 1.0 ASN:OD1 -0.59310 O + 1.0 ASN:ND2 -0.91910 N + 1.0 ASN:1HD2 0.41960 H + 1.0 ASN:2HD2 0.41960 H + 1.0 ASN:C 0.59730 C + 1.0 ASN:O -0.56790 O + 1.0 GLN:N -0.41570 N + 1.0 GLN:H 0.27190 H + 1.0 GLN:CA -0.00310 CT + 1.0 GLN:HA 0.08500 H1 + 1.0 GLN:CB -0.00360 CT + 1.0 GLN:1HB 0.01710 HC + 1.0 GLN:2HB 0.01710 HC + 1.0 GLN:CG -0.06450 CT + 1.0 GLN:1HG 0.03520 HC + 1.0 GLN:2HG 0.03520 HC + 1.0 GLN:CD 0.69510 C + 1.0 GLN:OE1 -0.60860 O + 1.0 GLN:NE2 -0.94070 N + 1.0 GLN:1HE2 0.42510 H + 1.0 GLN:2HE2 0.42510 H + 1.0 GLN:C 0.59730 C + 1.0 GLN:O -0.56790 O + 1.0 ARG:N -0.34790 N + 1.0 ARG:H 0.27470 H + 1.0 ARG:CA -0.26370 CT + 1.0 ARG:HA 0.15600 H1 + 1.0 ARG:CB -0.00070 CT + 1.0 ARG:1HB 0.03270 HC + 1.0 ARG:2HB 0.03270 HC + 1.0 ARG:CG 0.03900 CT + 1.0 ARG:1HG 0.02850 HC + 1.0 ARG:2HG 0.02850 HC + 1.0 ARG:CD 0.04860 CT + 1.0 ARG:1HD 0.06870 H1 + 1.0 ARG:2HD 0.06870 H1 + 1.0 ARG:NE -0.52950 N2 + 1.0 ARG:HE 0.34560 H + 1.0 ARG:CZ 0.80760 CA + 1.0 ARG:NH1 -0.86270 N2 + 1.0 ARG:1HH1 0.44780 H + 1.0 ARG:2HH1 0.44780 H + 1.0 ARG:NH2 -0.86270 N2 + 1.0 ARG:1HH2 0.44780 H + 1.0 ARG:2HH2 0.44780 H + 1.0 ARG:C 0.73410 C + 1.0 ARG:O -0.58940 O + 1.0 HIS:N -0.34790 N + 1.0 HIS:H 0.27470 H + 1.0 HIS:CA -0.13540 CT + 1.0 HIS:HA 0.12120 H1 + 1.0 HIS:CB -0.04140 CT + 1.0 HIS:1HB 0.08100 HC + 1.0 HIS:2HB 0.08100 HC + 1.0 HIS:CG -0.00120 CC + 1.0 HIS:ND1 -0.15130 NA + 1.0 HIS:HD1 0.38660 H + 1.0 HIS:CE1 -0.01700 CR + 1.0 HIS:HE1 0.26810 H5 + 1.0 HIS:NE2 -0.17180 NA + 1.0 HIS:CD2 -0.11410 CW + 1.0 HIS:HD2 0.23170 H4 + 1.0 HIS:C 0.73410 C + 1.0 HIS:O -0.58940 O + 1.0 HIS:N -0.34790 N + 1.0 HIS:H 0.27470 H + 1.0 HIS:CA -0.13540 CT + 1.0 HIS:HA 0.12120 H1 + 1.0 HIS:CB -0.04140 CT + 1.0 HIS:1HB 0.08100 HC + 1.0 HIS:2HB 0.08100 HC + 1.0 HIS:CG -0.00120 CC + 1.0 HIS:ND1 -0.15130 NA + 1.0 HIS:CE1 -0.01700 CR + 1.0 HIS:HE1 0.26810 H5 + 1.0 HIS:NE2 -0.17180 NA + 1.0 HIS:HE2 0.39110 H + 1.0 HIS:CD2 -0.11410 CW + 1.0 HIS:HD2 0.23170 H4 + 1.0 HIS:C 0.73410 C + 1.0 HIS:O -0.58940 O + 1.0 HIS:N -0.34790 N + 1.0 HIS:H 0.27470 H + 1.0 HIS:CA -0.13540 CT + 1.0 HIS:HA 0.12120 H1 + 1.0 HIS:CB -0.04140 CT + 1.0 HIS:1HB 0.08100 HC + 1.0 HIS:2HB 0.08100 HC + 1.0 HIS:CG -0.00120 CC + 1.0 HIS:ND1 -0.15130 NA + 1.0 HIS:HD1 0.38660 H + 1.0 HIS:CE1 -0.01700 CR + 1.0 HIS:HE1 0.26810 H5 + 1.0 HIS:NE2 -0.17180 NA + 1.0 HIS:HE2 0.39110 H + 1.0 HIS:CD2 -0.11410 CW + 1.0 HIS:HD2 0.23170 H4 + 1.0 HIS:C 0.73410 C + 1.0 HIS:O -0.58940 O + 1.0 TRP:N -0.41570 N + 1.0 TRP:H 0.27190 H + 1.0 TRP:CA -0.02750 CT + 1.0 TRP:HA 0.11230 H1 + 1.0 TRP:CB -0.00500 CT + 1.0 TRP:1HB 0.03390 HC + 1.0 TRP:2HB 0.03390 HC + 1.0 TRP:CG -0.14150 C* + 1.0 TRP:CD1 -0.16380 CW + 1.0 TRP:HD1 0.20620 H4 + 1.0 TRP:NE1 -0.34180 NA + 1.0 TRP:HE1 0.34120 H + 1.0 TRP:CE2 0.13800 CN + 1.0 TRP:CZ2 -0.26010 CA + 1.0 TRP:HZ2 0.15720 HA + 1.0 TRP:CH2 -0.11340 CA + 1.0 TRP:HH2 0.14170 HA + 1.0 TRP:CZ3 -0.19720 CA + 1.0 TRP:HZ3 0.14470 HA + 1.0 TRP:CE3 -0.23870 CA + 1.0 TRP:HE3 0.17000 HA + 1.0 TRP:CD2 0.12430 CB + 1.0 TRP:C 0.59730 C + 1.0 TRP:O -0.56790 O + 1.0 PHE:N -0.41570 N + 1.0 PHE:H 0.27190 H + 1.0 PHE:CA -0.00240 CT + 1.0 PHE:HA 0.09780 H1 + 1.0 PHE:CB -0.03430 CT + 1.0 PHE:1HB 0.02950 HC + 1.0 PHE:2HB 0.02950 HC + 1.0 PHE:CG 0.01180 CA + 1.0 PHE:CD1 -0.12560 CA + 1.0 PHE:HD1 0.13300 HA + 1.0 PHE:CE1 -0.17040 CA + 1.0 PHE:HE1 0.14300 HA + 1.0 PHE:CZ -0.10720 CA + 1.0 PHE:HZ 0.12970 HA + 1.0 PHE:CE2 -0.17040 CA + 1.0 PHE:HE2 0.14300 HA + 1.0 PHE:CD2 -0.12560 CA + 1.0 PHE:HD2 0.13300 HA + 1.0 PHE:C 0.59730 C + 1.0 PHE:O -0.56790 O + 1.0 TYR:N -0.41570 N + 1.0 TYR:H 0.27190 H + 1.0 TYR:CA -0.00140 CT + 1.0 TYR:HA 0.08760 H1 + 1.0 TYR:CB -0.01520 CT + 1.0 TYR:1HB 0.02950 HC + 1.0 TYR:2HB 0.02950 HC + 1.0 TYR:CG -0.00110 CA + 1.0 TYR:CD1 -0.19060 CA + 1.0 TYR:HD1 0.16990 HA + 1.0 TYR:CE1 -0.23410 CA + 1.0 TYR:HE1 0.16560 HA + 1.0 TYR:CZ 0.32260 C + 1.0 TYR:OH -0.55790 OH + 1.0 TYR:HH 0.39920 HO + 1.0 TYR:CE2 -0.23410 CA + 1.0 TYR:HE2 0.16560 HA + 1.0 TYR:CD2 -0.19060 CA + 1.0 TYR:HD2 0.16990 HA + 1.0 TYR:C 0.59730 C + 1.0 TYR:O -0.56790 O + 1.0 GLU:N -0.51630 N + 1.0 GLU:H 0.29360 H + 1.0 GLU:CA 0.03970 CT + 1.0 GLU:HA 0.11050 H1 + 1.0 GLU:CB 0.05600 CT + 1.0 GLU:1HB -0.01730 HC + 1.0 GLU:2HB -0.01730 HC + 1.0 GLU:CG 0.01360 CT + 1.0 GLU:1HG -0.04250 HC + 1.0 GLU:2HG -0.04250 HC + 1.0 GLU:CD 0.80540 C + 1.0 GLU:OE1 -0.81880 O2 + 1.0 GLU:OE2 -0.81880 O2 + 1.0 GLU:C 0.53660 C + 1.0 GLU:O -0.58190 O + 1.0 ASP:N -0.51630 N + 1.0 ASP:H 0.29360 H + 1.0 ASP:CA 0.03810 CT + 1.0 ASP:HA 0.08800 H1 + 1.0 ASP:CB -0.03030 CT + 1.0 ASP:1HB -0.01220 HC + 1.0 ASP:2HB -0.01220 HC + 1.0 ASP:CG 0.79940 C + 1.0 ASP:OD1 -0.80140 O2 + 1.0 ASP:OD2 -0.80140 O2 + 1.0 ASP:C 0.53660 C + 1.0 ASP:O -0.58190 O + 1.0 LYS:N -0.34790 N + 1.0 LYS:H 0.27470 H + 1.0 LYS:CA -0.24000 CT + 1.0 LYS:HA 0.14260 H1 + 1.0 LYS:CB -0.00940 CT + 1.0 LYS:1HB 0.03620 HC + 1.0 LYS:2HB 0.03620 HC + 1.0 LYS:CG 0.01870 CT + 1.0 LYS:1HG 0.01030 HC + 1.0 LYS:2HG 0.01030 HC + 1.0 LYS:CD -0.04790 CT + 1.0 LYS:1HD 0.06210 HC + 1.0 LYS:2HD 0.06210 HC + 1.0 LYS:CE -0.01430 CT + 1.0 LYS:1HE 0.11350 HP + 1.0 LYS:2HE 0.11350 HP + 1.0 LYS:NZ -0.38540 N3 + 1.0 LYS:1HZ 0.34000 H + 1.0 LYS:2HZ 0.34000 H + 1.0 LYS:3HZ 0.34000 H + 1.0 LYS:C 0.73410 C + 1.0 LYS:O -0.58940 O + 1.0 LYN:N -0.41570 N + 1.0 LYN:H 0.27190 H + 1.0 LYN:CA -0.07206 CT + 1.0 LYN:HA 0.09940 H1 + 1.0 LYN:CB -0.04845 CT + 1.0 LYN:HB2 0.03400 HC + 1.0 LYN:HB3 0.03400 HC + 1.0 LYN:CG 0.06612 CT + 1.0 LYN:HG2 0.01041 HC + 1.0 LYN:HG3 0.01041 HC + 1.0 LYN:CD -0.03768 CT + 1.0 LYN:HD2 0.01155 HC + 1.0 LYN:HD3 0.01155 HC + 1.0 LYN:CE 0.32604 CT + 1.0 LYN:HE2 -0.03358 HP + 1.0 LYN:HE3 -0.03358 HP + 1.0 LYN:NZ -1.03581 N3 + 1.0 LYN:HZ2 0.38604 H + 1.0 LYN:HZ3 0.38604 H + 1.0 LYN:C 0.59730 C + 1.0 LYN:O -0.56790 O + 1.0 PRO:N -0.25480 N + 1.0 PRO:CD 0.01920 CT + 1.0 PRO:1HD 0.03910 H1 + 1.0 PRO:2HD 0.03910 H1 + 1.0 PRO:CG 0.01890 CT + 1.0 PRO:1HG 0.02130 HC + 1.0 PRO:2HG 0.02130 HC + 1.0 PRO:CB -0.00700 CT + 1.0 PRO:1HB 0.02530 HC + 1.0 PRO:2HB 0.02530 HC + 1.0 PRO:CA -0.02660 CT + 1.0 PRO:HA 0.06410 H1 + 1.0 PRO:C 0.58960 C + 1.0 PRO:O -0.57480 O + 1.0 CYS:N -0.41570 N + 1.0 CYS:H 0.27190 H + 1.0 CYS:CA 0.02130 CT + 1.0 CYS:HA 0.11240 H1 + 1.0 CYS:CB -0.12310 CT + 1.0 CYS:1HB 0.11120 H1 + 1.0 CYS:2HB 0.11120 H1 + 1.0 CYS:SG -0.31190 SH + 1.0 CYS:HG 0.19330 HS + 1.0 CYS:C 0.59730 C + 1.0 CYS:O -0.56790 O + 1.0 CYM:N -0.46300 N + 1.0 CYM:HN 0.25200 H + 1.0 CYM:CA 0.03500 CT + 1.0 CYM:HA 0.04800 H1 + 1.0 CYM:CB -0.73600 CT + 1.0 CYM:HB3 0.24400 H1 + 1.0 CYM:HB2 0.24400 H1 + 1.0 CYM:SG -0.73600 SH + 1.0 CYM:C 0.61600 C + 1.0 CYM:O -0.50400 O + 1.0 CYS-S:N -0.41570 N + 1.0 CYS-S:H 0.27190 H + 1.0 CYS-S:CA 0.04290 CT + 1.0 CYS-S:HA 0.07660 H1 + 1.0 CYS-S:CB -0.07900 CT + 1.0 CYS-S:1HB 0.09100 H1 + 1.0 CYS-S:2HB 0.09100 H1 + 1.0 CYS-S:SG -0.10810 S + 1.0 CYS-S:C 0.59730 C + 1.0 CYS-S:O -0.56790 O + 1.0 MET:N -0.41570 N + 1.0 MET:H 0.27190 H + 1.0 MET:CA -0.02370 CT + 1.0 MET:HA 0.08800 H1 + 1.0 MET:CB 0.03420 CT + 1.0 MET:1HB 0.02410 HC + 1.0 MET:2HB 0.02410 HC + 1.0 MET:CG 0.00180 CT + 1.0 MET:1HG 0.04400 H1 + 1.0 MET:2HG 0.04400 H1 + 1.0 MET:SD -0.27370 S + 1.0 MET:CE -0.05360 CT + 1.0 MET:1HE 0.06840 H1 + 1.0 MET:2HE 0.06840 H1 + 1.0 MET:3HE 0.06840 H1 + 1.0 MET:C 0.59730 C + 1.0 MET:O -0.56790 O + 1.0 ACE:1HH3 0.11230 HC + 1.0 ACE:CH3 -0.36620 CT + 1.0 ACE:2HH3 0.11230 HC + 1.0 ACE:3HH3 0.11230 HC + 1.0 ACE:C 0.59720 C + 1.0 ACE:O -0.56790 O + 1.0 HOH:1H 0.41700 HW + 1.0 HOH:O -0.83400 OW + 1.0 HOH:2H 0.41700 HW + 1.0 HOH:H1 0.41700 HW + 1.0 HOH:O -0.83400 OW + 1.0 HOH:H2 0.41700 HW + 1.0 WAT:1H 0.41700 HW + 1.0 WAT:O -0.83400 OW + 1.0 WAT:2H 0.41700 HW + 1.0 ASH:N -0.41570 N + 1.0 ASH:H 0.27190 H + 1.0 ASH:CA 0.03410 CT + 1.0 ASH:HA 0.08640 H1 + 1.0 ASH:CB -0.03160 CT + 1.0 ASH:HB2 0.04880 HC + 1.0 ASH:HB3 0.04880 HC + 1.0 ASH:CG 0.64620 C + 1.0 ASH:OD1 -0.55540 O + 1.0 ASH:OD2 -0.63760 OH + 1.0 ASH:HD2 0.47470 HO + 1.0 ASH:C 0.59730 C + 1.0 ASH:O -0.56790 O + 1.0 GLH:N -0.41570 N + 1.0 GLH:H 0.27190 H + 1.0 GLH:CA 0.01450 CT + 1.0 GLH:HA 0.07790 H1 + 1.0 GLH:CB -0.00710 CT + 1.0 GLH:HB2 0.02560 HC + 1.0 GLH:HB3 0.02560 HC + 1.0 GLH:CG -0.01740 CT + 1.0 GLH:HG2 0.04300 HC + 1.0 GLH:HG3 0.04300 HC + 1.0 GLH:CD 0.68010 C + 1.0 GLH:OE1 -0.58380 O + 1.0 GLH:OE2 -0.65110 OH + 1.0 GLH:HE2 0.46410 HO + 1.0 GLH:C 0.59730 C + 1.0 GLH:O -0.56790 O + 1.0 CIP:NA+ 1.00000 IP + 1.0 CIM:CL- -1.00000 IM + 1.0 ALA-N:N 0.14140 N3 + 1.0 ALA-N:1H 0.19970 H + 1.0 ALA-N:2H 0.19970 H + 1.0 ALA-N:3H 0.19970 H + 1.0 ALA-N:CA 0.09620 CT + 1.0 ALA-N:HA 0.08890 HP + 1.0 ALA-N:CB -0.05970 CT + 1.0 ALA-N:1HB 0.03000 HC + 1.0 ALA-N:2HB 0.03000 HC + 1.0 ALA-N:3HB 0.03000 HC + 1.0 ALA-N:C 0.61630 C + 1.0 ALA-N:O -0.57220 O + 1.0 GLY-N:N 0.29430 N3 + 1.0 GLY-N:1H 0.16420 H + 1.0 GLY-N:2H 0.16420 H + 1.0 GLY-N:3H 0.16420 H + 1.0 GLY-N:CA -0.01000 CT + 1.0 GLY-N:1HA 0.08950 HP + 1.0 GLY-N:2HA 0.08950 HP + 1.0 GLY-N:C 0.61630 C + 1.0 GLY-N:O -0.57220 O + 1.0 SER-N:N 0.18490 N3 + 1.0 SER-N:1H 0.18980 H + 1.0 SER-N:2H 0.18980 H + 1.0 SER-N:3H 0.18980 H + 1.0 SER-N:CA 0.05670 CT + 1.0 SER-N:HA 0.07820 HP + 1.0 SER-N:CB 0.25960 CT + 1.0 SER-N:1HB 0.02730 H1 + 1.0 SER-N:2HB 0.02730 H1 + 1.0 SER-N:OG -0.67140 OH + 1.0 SER-N:HG 0.42390 HO + 1.0 SER-N:C 0.61630 C + 1.0 SER-N:O -0.57220 O + 1.0 THR-N:N 0.18120 N3 + 1.0 THR-N:1H 0.19340 H + 1.0 THR-N:2H 0.19340 H + 1.0 THR-N:3H 0.19340 H + 1.0 THR-N:CA 0.00340 CT + 1.0 THR-N:HA 0.10870 HP + 1.0 THR-N:CB 0.45140 CT + 1.0 THR-N:HB -0.03230 H1 + 1.0 THR-N:CG2 -0.25540 CT + 1.0 THR-N:1HG2 0.06270 HC + 1.0 THR-N:2HG2 0.06270 HC + 1.0 THR-N:3HG2 0.06270 HC + 1.0 THR-N:OG1 -0.67640 OH + 1.0 THR-N:HG1 0.40700 HO + 1.0 THR-N:C 0.61630 C + 1.0 THR-N:O -0.57220 O + 1.0 LEU-N:N 0.10100 N3 + 1.0 LEU-N:1H 0.21480 H + 1.0 LEU-N:2H 0.21480 H + 1.0 LEU-N:3H 0.21480 H + 1.0 LEU-N:CA 0.01040 CT + 1.0 LEU-N:HA 0.10530 HP + 1.0 LEU-N:CB -0.02440 CT + 1.0 LEU-N:1HB 0.02560 HC + 1.0 LEU-N:2HB 0.02560 HC + 1.0 LEU-N:CG 0.34210 CT + 1.0 LEU-N:HG -0.03800 HC + 1.0 LEU-N:CD1 -0.41060 CT + 1.0 LEU-N:1HD1 0.09800 HC + 1.0 LEU-N:2HD1 0.09800 HC + 1.0 LEU-N:3HD1 0.09800 HC + 1.0 LEU-N:CD2 -0.41040 CT + 1.0 LEU-N:1HD2 0.09800 HC + 1.0 LEU-N:2HD2 0.09800 HC + 1.0 LEU-N:3HD2 0.09800 HC + 1.0 LEU-N:C 0.61230 C + 1.0 LEU-N:O -0.57130 O + 1.0 ILE-N:N 0.03110 N3 + 1.0 ILE-N:1H 0.23290 H + 1.0 ILE-N:2H 0.23290 H + 1.0 ILE-N:3H 0.23290 H + 1.0 ILE-N:CA 0.02570 CT + 1.0 ILE-N:HA 0.10310 HP + 1.0 ILE-N:CB 0.18850 CT + 1.0 ILE-N:HB 0.02130 HC + 1.0 ILE-N:CG2 -0.37200 CT + 1.0 ILE-N:1HG2 0.09470 HC + 1.0 ILE-N:2HG2 0.09470 HC + 1.0 ILE-N:3HG2 0.09470 HC + 1.0 ILE-N:CG1 -0.03870 CT + 1.0 ILE-N:1HG1 0.02010 HC + 1.0 ILE-N:2HG1 0.02010 HC + 1.0 ILE-N:CD1 -0.09080 CT + 1.0 ILE-N:1HD1 0.02260 HC + 1.0 ILE-N:2HD1 0.02260 HC + 1.0 ILE-N:3HD1 0.02260 HC + 1.0 ILE-N:C 0.61230 C + 1.0 ILE-N:O -0.57130 O + 1.0 VAL-N:N 0.05770 N3 + 1.0 VAL-N:1H 0.22720 H + 1.0 VAL-N:2H 0.22720 H + 1.0 VAL-N:3H 0.22720 H + 1.0 VAL-N:CA -0.00540 CT + 1.0 VAL-N:HA 0.10930 HP + 1.0 VAL-N:CB 0.31960 CT + 1.0 VAL-N:HB -0.02210 HC + 1.0 VAL-N:CG1 -0.31290 CT + 1.0 VAL-N:1HG1 0.07350 HC + 1.0 VAL-N:2HG1 0.07350 HC + 1.0 VAL-N:3HG1 0.07350 HC + 1.0 VAL-N:CG2 -0.31290 CT + 1.0 VAL-N:1HG2 0.07350 HC + 1.0 VAL-N:2HG2 0.07350 HC + 1.0 VAL-N:3HG2 0.07350 HC + 1.0 VAL-N:C 0.61630 C + 1.0 VAL-N:O -0.57220 O + 1.0 ASN-N:N 0.18010 N3 + 1.0 ASN-N:1H 0.19210 H + 1.0 ASN-N:2H 0.19210 H + 1.0 ASN-N:3H 0.19210 H + 1.0 ASN-N:CA 0.03680 CT + 1.0 ASN-N:HA 0.12310 HP + 1.0 ASN-N:CB -0.02830 CT + 1.0 ASN-N:1HB 0.05150 HC + 1.0 ASN-N:2HB 0.05150 HC + 1.0 ASN-N:CG 0.58330 C + 1.0 ASN-N:OD1 -0.57440 O + 1.0 ASN-N:ND2 -0.86340 N + 1.0 ASN-N:1HD2 0.40970 H + 1.0 ASN-N:2HD2 0.40970 H + 1.0 ASN-N:C 0.61630 C + 1.0 ASN-N:O -0.57220 O + 1.0 GLN-N:N 0.14930 N3 + 1.0 GLN-N:1H 0.19960 H + 1.0 GLN-N:2H 0.19960 H + 1.0 GLN-N:3H 0.19960 H + 1.0 GLN-N:CA 0.05360 CT + 1.0 GLN-N:HA 0.10150 HP + 1.0 GLN-N:CB 0.06510 CT + 1.0 GLN-N:1HB 0.00500 HC + 1.0 GLN-N:2HB 0.00500 HC + 1.0 GLN-N:CG -0.09030 CT + 1.0 GLN-N:1HG 0.03310 HC + 1.0 GLN-N:2HG 0.03310 HC + 1.0 GLN-N:CD 0.73540 C + 1.0 GLN-N:OE1 -0.61330 O + 1.0 GLN-N:NE2 -1.00310 N + 1.0 GLN-N:1HE2 0.44290 H + 1.0 GLN-N:2HE2 0.44290 H + 1.0 GLN-N:C 0.61230 C + 1.0 GLN-N:O -0.57130 O + 1.0 ARG-N:N 0.13050 N3 + 1.0 ARG-N:1H 0.20830 H + 1.0 ARG-N:2H 0.20830 H + 1.0 ARG-N:3H 0.20830 H + 1.0 ARG-N:CA -0.02230 CT + 1.0 ARG-N:HA 0.12420 HP + 1.0 ARG-N:CB 0.01180 CT + 1.0 ARG-N:1HB 0.02260 HC + 1.0 ARG-N:2HB 0.02260 HC + 1.0 ARG-N:CG 0.02360 CT + 1.0 ARG-N:1HG 0.03090 HC + 1.0 ARG-N:2HG 0.03090 HC + 1.0 ARG-N:CD 0.09350 CT + 1.0 ARG-N:1HD 0.05270 H1 + 1.0 ARG-N:2HD 0.05270 H1 + 1.0 ARG-N:NE -0.56500 N2 + 1.0 ARG-N:HE 0.35920 H + 1.0 ARG-N:CZ 0.82810 CA + 1.0 ARG-N:NH1 -0.86930 N2 + 1.0 ARG-N:1HH1 0.44940 H + 1.0 ARG-N:2HH1 0.44940 H + 1.0 ARG-N:NH2 -0.86930 N2 + 1.0 ARG-N:1HH2 0.44940 H + 1.0 ARG-N:2HH2 0.44940 H + 1.0 ARG-N:C 0.72140 C + 1.0 ARG-N:O -0.60130 O + 1.0 HIS-N:N 0.25600 N3 + 1.0 HIS-N:1H 0.17040 H + 1.0 HIS-N:2H 0.17040 H + 1.0 HIS-N:3H 0.17040 H + 1.0 HIS-N:CA 0.05810 CT + 1.0 HIS-N:HA 0.10470 HP + 1.0 HIS-N:CB 0.04840 CT + 1.0 HIS-N:1HB 0.05310 HC + 1.0 HIS-N:2HB 0.05310 HC + 1.0 HIS-N:CG -0.02360 CC + 1.0 HIS-N:ND1 -0.15100 NA + 1.0 HIS-N:HD1 0.38210 H + 1.0 HIS-N:CE1 -0.00110 CR + 1.0 HIS-N:HE1 0.26450 H5 + 1.0 HIS-N:NE2 -0.17390 NA + 1.0 HIS-N:CD2 -0.14330 CW + 1.0 HIS-N:HD2 0.24950 H4 + 1.0 HIS-N:C 0.72140 C + 1.0 HIS-N:O -0.60130 O + 1.0 HIS-N:N 0.25600 N3 + 1.0 HIS-N:1H 0.17040 H + 1.0 HIS-N:2H 0.17040 H + 1.0 HIS-N:3H 0.17040 H + 1.0 HIS-N:CA 0.05810 CT + 1.0 HIS-N:HA 0.10470 HP + 1.0 HIS-N:CB 0.04840 CT + 1.0 HIS-N:1HB 0.05310 HC + 1.0 HIS-N:2HB 0.05310 HC + 1.0 HIS-N:CG -0.02360 CC + 1.0 HIS-N:ND1 -0.15100 NA + 1.0 HIS-N:CE1 -0.00110 CR + 1.0 HIS-N:HE1 0.26450 H5 + 1.0 HIS-N:NE2 -0.17390 NA + 1.0 HIS-N:HE2 0.39210 H + 1.0 HIS-N:CD2 -0.14330 CW + 1.0 HIS-N:HD2 0.24950 H4 + 1.0 HIS-N:C 0.72140 C + 1.0 HIS-N:O -0.60130 O + 1.0 HIS-N:N 0.25600 N3 + 1.0 HIS-N:1H 0.17040 H + 1.0 HIS-N:2H 0.17040 H + 1.0 HIS-N:3H 0.17040 H + 1.0 HIS-N:CA 0.05810 CT + 1.0 HIS-N:HA 0.10470 HP + 1.0 HIS-N:CB 0.04840 CT + 1.0 HIS-N:1HB 0.05310 HC + 1.0 HIS-N:2HB 0.05310 HC + 1.0 HIS-N:CG -0.02360 CC + 1.0 HIS-N:ND1 -0.15100 NA + 1.0 HIS-N:HD1 0.38210 H + 1.0 HIS-N:CE1 -0.00110 CR + 1.0 HIS-N:HE1 0.26450 H5 + 1.0 HIS-N:NE2 -0.17390 NA + 1.0 HIS-N:HE2 0.39210 H + 1.0 HIS-N:CD2 -0.14330 CW + 1.0 HIS-N:HD2 0.24950 H4 + 1.0 HIS-N:C 0.72140 C + 1.0 HIS-N:O -0.60130 O + 1.0 TRP-N:N 0.19130 N3 + 1.0 TRP-N:1H 0.18880 H + 1.0 TRP-N:2H 0.18880 H + 1.0 TRP-N:3H 0.18880 H + 1.0 TRP-N:CA 0.04210 CT + 1.0 TRP-N:HA 0.11620 HP + 1.0 TRP-N:CB 0.05430 CT + 1.0 TRP-N:1HB 0.02220 HC + 1.0 TRP-N:2HB 0.02220 HC + 1.0 TRP-N:CG -0.16540 C* + 1.0 TRP-N:CD1 -0.17880 CW + 1.0 TRP-N:HD1 0.21950 H4 + 1.0 TRP-N:NE1 -0.34440 NA + 1.0 TRP-N:HE1 0.34120 H + 1.0 TRP-N:CE2 0.15750 CN + 1.0 TRP-N:CZ2 -0.27100 CA + 1.0 TRP-N:HZ2 0.15890 HA + 1.0 TRP-N:CH2 -0.10800 CA + 1.0 TRP-N:HH2 0.14110 HA + 1.0 TRP-N:CZ3 -0.20340 CA + 1.0 TRP-N:HZ3 0.14580 HA + 1.0 TRP-N:CE3 -0.22650 CA + 1.0 TRP-N:HE3 0.16460 HA + 1.0 TRP-N:CD2 0.11320 CB + 1.0 TRP-N:C 0.61230 C + 1.0 TRP-N:O -0.57130 O + 1.0 PHE-N:N 0.17370 N3 + 1.0 PHE-N:1H 0.19210 H + 1.0 PHE-N:2H 0.19210 H + 1.0 PHE-N:3H 0.19210 H + 1.0 PHE-N:CA 0.07330 CT + 1.0 PHE-N:HA 0.10410 HP + 1.0 PHE-N:CB 0.03300 CT + 1.0 PHE-N:1HB 0.01040 HC + 1.0 PHE-N:2HB 0.01040 HC + 1.0 PHE-N:CG 0.00310 CA + 1.0 PHE-N:CD1 -0.13920 CA + 1.0 PHE-N:HD1 0.13740 HA + 1.0 PHE-N:CE1 -0.16020 CA + 1.0 PHE-N:HE1 0.14330 HA + 1.0 PHE-N:CZ -0.12080 CA + 1.0 PHE-N:HZ 0.13290 HA + 1.0 PHE-N:CE2 -0.16030 CA + 1.0 PHE-N:HE2 0.14330 HA + 1.0 PHE-N:CD2 -0.13910 CA + 1.0 PHE-N:HD2 0.13740 HA + 1.0 PHE-N:C 0.61230 C + 1.0 PHE-N:O -0.57130 O + 1.0 TYR-N:N 0.19400 N3 + 1.0 TYR-N:1H 0.18730 H + 1.0 TYR-N:2H 0.18730 H + 1.0 TYR-N:3H 0.18730 H + 1.0 TYR-N:CA 0.05700 CT + 1.0 TYR-N:HA 0.09830 HP + 1.0 TYR-N:CB 0.06590 CT + 1.0 TYR-N:1HB 0.01020 HC + 1.0 TYR-N:2HB 0.01020 HC + 1.0 TYR-N:CG -0.02050 CA + 1.0 TYR-N:CD1 -0.20020 CA + 1.0 TYR-N:HD1 0.17200 HA + 1.0 TYR-N:CE1 -0.22390 CA + 1.0 TYR-N:HE1 0.16500 HA + 1.0 TYR-N:CZ 0.31390 C + 1.0 TYR-N:OH -0.55780 OH + 1.0 TYR-N:HH 0.40010 HO + 1.0 TYR-N:CE2 -0.22390 CA + 1.0 TYR-N:HE2 0.16500 HA + 1.0 TYR-N:CD2 -0.20020 CA + 1.0 TYR-N:HD2 0.17200 HA + 1.0 TYR-N:C 0.61230 C + 1.0 TYR-N:O -0.57130 O + 1.0 GLU-N:N 0.00170 N3 + 1.0 GLU-N:1H 0.23910 H + 1.0 GLU-N:2H 0.23910 H + 1.0 GLU-N:3H 0.23910 H + 1.0 GLU-N:CA 0.05880 CT + 1.0 GLU-N:HA 0.12020 HP + 1.0 GLU-N:CB 0.09090 CT + 1.0 GLU-N:1HB -0.02320 HC + 1.0 GLU-N:2HB -0.02320 HC + 1.0 GLU-N:CG -0.02360 CT + 1.0 GLU-N:1HG -0.03150 HC + 1.0 GLU-N:2HG -0.03150 HC + 1.0 GLU-N:CD 0.80870 C + 1.0 GLU-N:OE1 -0.81890 O2 + 1.0 GLU-N:OE2 -0.81890 O2 + 1.0 GLU-N:C 0.56210 C + 1.0 GLU-N:O -0.58890 O + 1.0 ASP-N:N 0.07820 N3 + 1.0 ASP-N:1H 0.22000 H + 1.0 ASP-N:2H 0.22000 H + 1.0 ASP-N:3H 0.22000 H + 1.0 ASP-N:CA 0.02920 CT + 1.0 ASP-N:HA 0.11410 HP + 1.0 ASP-N:CB -0.02350 CT + 1.0 ASP-N:1HB -0.01690 HC + 1.0 ASP-N:2HB -0.01690 HC + 1.0 ASP-N:CG 0.81940 C + 1.0 ASP-N:OD1 -0.80840 O2 + 1.0 ASP-N:OD2 -0.80840 O2 + 1.0 ASP-N:C 0.56210 C + 1.0 ASP-N:O -0.58890 O + 1.0 LYS-N:N 0.09660 N3 + 1.0 LYS-N:1H 0.21650 H + 1.0 LYS-N:2H 0.21650 H + 1.0 LYS-N:3H 0.21650 H + 1.0 LYS-N:CA -0.00150 CT + 1.0 LYS-N:HA 0.11800 HP + 1.0 LYS-N:CB 0.02120 CT + 1.0 LYS-N:1HB 0.02830 HC + 1.0 LYS-N:2HB 0.02830 HC + 1.0 LYS-N:CG -0.00480 CT + 1.0 LYS-N:1HG 0.01210 HC + 1.0 LYS-N:2HG 0.01210 HC + 1.0 LYS-N:CD -0.06080 CT + 1.0 LYS-N:1HD 0.06330 HC + 1.0 LYS-N:2HD 0.06330 HC + 1.0 LYS-N:CE -0.01810 CT + 1.0 LYS-N:1HE 0.11710 HP + 1.0 LYS-N:2HE 0.11710 HP + 1.0 LYS-N:NZ -0.37640 N3 + 1.0 LYS-N:1HZ 0.33820 H + 1.0 LYS-N:2HZ 0.33820 H + 1.0 LYS-N:3HZ 0.33820 H + 1.0 LYS-N:C 0.72140 C + 1.0 LYS-N:O -0.60130 O + 1.0 PRO-N:N -0.20200 N3 + 1.0 PRO-N:1H 0.31200 H + 1.0 PRO-N:2H 0.31200 H + 1.0 PRO-N:3H 0.31200 H + 1.0 PRO-N:CD -0.01200 CT + 1.0 PRO-N:1HD 0.10000 HP + 1.0 PRO-N:2HD 0.10000 HP + 1.0 PRO-N:CG -0.12100 CT + 1.0 PRO-N:1HG 0.10000 HC + 1.0 PRO-N:2HG 0.10000 HC + 1.0 PRO-N:CB -0.11500 CT + 1.0 PRO-N:1HB 0.10000 HC + 1.0 PRO-N:2HB 0.10000 HC + 1.0 PRO-N:CA 0.10000 CT + 1.0 PRO-N:HA 0.10000 HP + 1.0 PRO-N:C 0.52600 C + 1.0 PRO-N:O -0.50000 O + 1.0 CYS-N:N 0.13250 N3 + 1.0 CYS-N:1H 0.20230 H + 1.0 CYS-N:2H 0.20230 H + 1.0 CYS-N:3H 0.20230 H + 1.0 CYS-N:CA 0.09270 CT + 1.0 CYS-N:HA 0.14110 HP + 1.0 CYS-N:CB -0.11950 CT + 1.0 CYS-N:1HB 0.11880 H1 + 1.0 CYS-N:2HB 0.11880 H1 + 1.0 CYS-N:SG -0.32980 SH + 1.0 CYS-N:HSG 0.19750 HS + 1.0 CYS-N:C 0.61230 C + 1.0 CYS-N:O -0.57130 O + 1.0 CYS-NS:N 0.20690 N3 + 1.0 CYS-NS:1H 0.18150 H + 1.0 CYS-NS:2H 0.18150 H + 1.0 CYS-NS:3H 0.18150 H + 1.0 CYS-NS:CA 0.10550 CT + 1.0 CYS-NS:HA 0.09220 HP + 1.0 CYS-NS:CB -0.02770 CT + 1.0 CYS-NS:1HB 0.06800 H1 + 1.0 CYS-NS:2HB 0.06800 H1 + 1.0 CYS-NS:SG -0.09840 S + 1.0 CYS-NS:C 0.61230 C + 1.0 CYS-NS:O -0.57130 O + 1.0 MET-N:N 0.15920 N3 + 1.0 MET-N:1H 0.19840 H + 1.0 MET-N:2H 0.19840 H + 1.0 MET-N:3H 0.19840 H + 1.0 MET-N:CA 0.02210 CT + 1.0 MET-N:HA 0.11160 HP + 1.0 MET-N:CB 0.08650 CT + 1.0 MET-N:1HB 0.01250 HC + 1.0 MET-N:2HB 0.01250 HC + 1.0 MET-N:CG 0.03340 CT + 1.0 MET-N:1HG 0.02920 H1 + 1.0 MET-N:2HG 0.02920 H1 + 1.0 MET-N:SD -0.27740 S + 1.0 MET-N:CE -0.03410 CT + 1.0 MET-N:1HE 0.05970 H1 + 1.0 MET-N:2HE 0.05970 H1 + 1.0 MET-N:3HE 0.05970 H1 + 1.0 MET-N:C 0.61230 C + 1.0 MET-N:O -0.57130 O + 1.0 ALA-C:N -0.38210 N + 1.0 ALA-C:H 0.26810 H + 1.0 ALA-C:CA -0.17470 CT + 1.0 ALA-C:HA 0.10670 H1 + 1.0 ALA-C:CB -0.20930 CT + 1.0 ALA-C:1HB 0.07640 HC + 1.0 ALA-C:2HB 0.07640 HC + 1.0 ALA-C:3HB 0.07640 HC + 1.0 ALA-C:C 0.77310 C + 1.0 ALA-C:O -0.80550 O2 + 1.0 ALA-C:OXT -0.80550 O2 + 1.0 GLY-C:N -0.38210 N + 1.0 GLY-C:H 0.26810 H + 1.0 GLY-C:CA -0.24930 CT + 1.0 GLY-C:1HA 0.10560 H1 + 1.0 GLY-C:2HA 0.10560 H1 + 1.0 GLY-C:C 0.72310 C + 1.0 GLY-C:O -0.78550 O2 + 1.0 GLY-C:OXT -0.78550 O2 + 1.0 SER-C:N -0.38210 N + 1.0 SER-C:H 0.26810 H + 1.0 SER-C:CA -0.27220 CT + 1.0 SER-C:HA 0.13040 H1 + 1.0 SER-C:CB 0.11230 CT + 1.0 SER-C:1HB 0.08130 H1 + 1.0 SER-C:2HB 0.08130 H1 + 1.0 SER-C:OG -0.65140 OH + 1.0 SER-C:HG 0.44740 HO + 1.0 SER-C:C 0.81130 C + 1.0 SER-C:O -0.81320 O2 + 1.0 SER-C:OXT -0.81320 O2 + 1.0 THR-C:N -0.38210 N + 1.0 THR-C:H 0.26810 H + 1.0 THR-C:CA -0.24200 CT + 1.0 THR-C:HA 0.12070 H1 + 1.0 THR-C:CB 0.30250 CT + 1.0 THR-C:HB 0.00780 H1 + 1.0 THR-C:CG2 -0.18530 CT + 1.0 THR-C:1HG2 0.05860 HC + 1.0 THR-C:2HG2 0.05860 HC + 1.0 THR-C:3HG2 0.05860 HC + 1.0 THR-C:OG1 -0.64960 OH + 1.0 THR-C:HG1 0.41190 HO + 1.0 THR-C:C 0.78100 C + 1.0 THR-C:O -0.80440 O2 + 1.0 THR-C:OXT -0.80440 O2 + 1.0 LEU-C:N -0.38210 N + 1.0 LEU-C:H 0.26810 H + 1.0 LEU-C:CA -0.28470 CT + 1.0 LEU-C:HA 0.13460 H1 + 1.0 LEU-C:CB -0.24690 CT + 1.0 LEU-C:1HB 0.09740 HC + 1.0 LEU-C:2HB 0.09740 HC + 1.0 LEU-C:CG 0.37060 CT + 1.0 LEU-C:HG -0.03740 HC + 1.0 LEU-C:CD1 -0.41630 CT + 1.0 LEU-C:1HD1 0.10380 HC + 1.0 LEU-C:2HD1 0.10380 HC + 1.0 LEU-C:3HD1 0.10380 HC + 1.0 LEU-C:CD2 -0.41630 CT + 1.0 LEU-C:1HD2 0.10380 HC + 1.0 LEU-C:2HD2 0.10380 HC + 1.0 LEU-C:3HD2 0.10380 HC + 1.0 LEU-C:C 0.83260 C + 1.0 LEU-C:O -0.81990 O2 + 1.0 LEU-C:OXT -0.81990 O2 + 1.0 ILE-C:N -0.38210 N + 1.0 ILE-C:H 0.26810 H + 1.0 ILE-C:CA -0.31000 CT + 1.0 ILE-C:HA 0.13750 H1 + 1.0 ILE-C:CB 0.03630 CT + 1.0 ILE-C:HB 0.07660 HC + 1.0 ILE-C:CG2 -0.34980 CT + 1.0 ILE-C:1HG2 0.10210 HC + 1.0 ILE-C:2HG2 0.10210 HC + 1.0 ILE-C:3HG2 0.10210 HC + 1.0 ILE-C:CG1 -0.03230 CT + 1.0 ILE-C:1HG1 0.03210 HC + 1.0 ILE-C:2HG1 0.03210 HC + 1.0 ILE-C:CD1 -0.06990 CT + 1.0 ILE-C:1HD1 0.01960 HC + 1.0 ILE-C:2HD1 0.01960 HC + 1.0 ILE-C:3HD1 0.01960 HC + 1.0 ILE-C:C 0.83430 C + 1.0 ILE-C:O -0.81900 O2 + 1.0 ILE-C:OXT -0.81900 O2 + 1.0 NME-C:N -0.41570 N + 1.0 NME-C:H 0.27190 H + 1.0 NME-C:CH3 -0.14900 CT + 1.0 NME-C:1HH3 0.09760 H1 + 1.0 NME-C:2HH3 0.09760 H1 + 1.0 NME-C:3HH3 0.09760 H1 + 1.0 VAL-C:N -0.38210 N + 1.0 VAL-C:H 0.26810 H + 1.0 VAL-C:CA -0.34380 CT + 1.0 VAL-C:HA 0.14380 H1 + 1.0 VAL-C:CB 0.19400 CT + 1.0 VAL-C:HB 0.03080 HC + 1.0 VAL-C:CG1 -0.30640 CT + 1.0 VAL-C:1HG1 0.08360 HC + 1.0 VAL-C:2HG1 0.08360 HC + 1.0 VAL-C:3HG1 0.08360 HC + 1.0 VAL-C:CG2 -0.30640 CT + 1.0 VAL-C:1HG2 0.08360 HC + 1.0 VAL-C:2HG2 0.08360 HC + 1.0 VAL-C:3HG2 0.08360 HC + 1.0 VAL-C:C 0.83500 C + 1.0 VAL-C:O -0.81730 O2 + 1.0 VAL-C:OXT -0.81730 O2 + 1.0 ASN-C:N -0.38210 N + 1.0 ASN-C:H 0.26810 H + 1.0 ASN-C:CA -0.20800 CT + 1.0 ASN-C:HA 0.13580 H1 + 1.0 ASN-C:CB -0.22990 CT + 1.0 ASN-C:1HB 0.10230 HC + 1.0 ASN-C:2HB 0.10230 HC + 1.0 ASN-C:CG 0.71530 C + 1.0 ASN-C:OD1 -0.60100 O + 1.0 ASN-C:ND2 -0.90840 N + 1.0 ASN-C:1HD2 0.41500 H + 1.0 ASN-C:2HD2 0.41500 H + 1.0 ASN-C:C 0.80500 C + 1.0 ASN-C:O -0.81470 O2 + 1.0 ASN-C:OXT -0.81470 O2 + 1.0 GLN-C:N -0.38210 N + 1.0 GLN-C:H 0.26810 H + 1.0 GLN-C:CA -0.22480 CT + 1.0 GLN-C:HA 0.12320 H1 + 1.0 GLN-C:CB -0.06640 CT + 1.0 GLN-C:1HB 0.04520 HC + 1.0 GLN-C:2HB 0.04520 HC + 1.0 GLN-C:CG -0.02100 CT + 1.0 GLN-C:1HG 0.02030 HC + 1.0 GLN-C:2HG 0.02030 HC + 1.0 GLN-C:CD 0.70930 C + 1.0 GLN-C:OE1 -0.60980 O + 1.0 GLN-C:NE2 -0.95740 N + 1.0 GLN-C:1HE2 0.43040 H + 1.0 GLN-C:2HE2 0.43040 H + 1.0 GLN-C:C 0.77750 C + 1.0 GLN-C:O -0.80420 O2 + 1.0 GLN-C:OXT -0.80420 O2 + 1.0 ARG-C:N -0.34810 N + 1.0 ARG-C:H 0.27640 H + 1.0 ARG-C:CA -0.30680 CT + 1.0 ARG-C:HA 0.14470 H1 + 1.0 ARG-C:CB -0.03740 CT + 1.0 ARG-C:1HB 0.03710 HC + 1.0 ARG-C:2HB 0.03710 HC + 1.0 ARG-C:CG 0.07440 CT + 1.0 ARG-C:1HG 0.01850 HC + 1.0 ARG-C:2HG 0.01850 HC + 1.0 ARG-C:CD 0.11140 CT + 1.0 ARG-C:1HD 0.04680 H1 + 1.0 ARG-C:2HD 0.04680 H1 + 1.0 ARG-C:NE -0.55640 N2 + 1.0 ARG-C:HE 0.34790 H + 1.0 ARG-C:CZ 0.83680 CA + 1.0 ARG-C:NH1 -0.87370 N2 + 1.0 ARG-C:1HH1 0.44930 H + 1.0 ARG-C:2HH1 0.44930 H + 1.0 ARG-C:NH2 -0.87370 N2 + 1.0 ARG-C:1HH2 0.44930 H + 1.0 ARG-C:2HH2 0.44930 H + 1.0 ARG-C:C 0.85570 C + 1.0 ARG-C:O -0.82660 O2 + 1.0 ARG-C:OXT -0.82660 O2 + 1.0 HIS-C:N -0.34810 N + 1.0 HIS-C:H 0.27640 H + 1.0 HIS-C:CA -0.14450 CT + 1.0 HIS-C:HA 0.11150 H1 + 1.0 HIS-C:CB -0.08000 CT + 1.0 HIS-C:1HB 0.08680 HC + 1.0 HIS-C:2HB 0.08680 HC + 1.0 HIS-C:CG 0.02980 CC + 1.0 HIS-C:ND1 -0.15010 NA + 1.0 HIS-C:HD1 0.38830 H + 1.0 HIS-C:CE1 -0.02510 CR + 1.0 HIS-C:HE1 0.26940 H5 + 1.0 HIS-C:NE2 -0.16830 NA + 1.0 HIS-C:CD2 -0.12560 CW + 1.0 HIS-C:HD2 0.23360 H4 + 1.0 HIS-C:C 0.80320 C + 1.0 HIS-C:O -0.81770 O2 + 1.0 HIS-C:OXT -0.81770 O2 + 1.0 HIS-C:N -0.34810 N + 1.0 HIS-C:H 0.27640 H + 1.0 HIS-C:CA -0.14450 CT + 1.0 HIS-C:HA 0.11150 H1 + 1.0 HIS-C:CB -0.08000 CT + 1.0 HIS-C:1HB 0.08680 HC + 1.0 HIS-C:2HB 0.08680 HC + 1.0 HIS-C:CG 0.02980 CC + 1.0 HIS-C:ND1 -0.15010 NA + 1.0 HIS-C:CE1 -0.02510 CR + 1.0 HIS-C:HE1 0.26940 H5 + 1.0 HIS-C:NE2 -0.16830 NA + 1.0 HIS-C:HE2 0.39130 H + 1.0 HIS-C:CD2 -0.12560 CW + 1.0 HIS-C:HD2 0.23360 H4 + 1.0 HIS-C:C 0.80320 C + 1.0 HIS-C:O -0.81770 O2 + 1.0 HIS-C:OXT -0.81770 O2 + 1.0 HIS-C:N -0.34810 N + 1.0 HIS-C:H 0.27640 H + 1.0 HIS-C:CA -0.14450 CT + 1.0 HIS-C:HA 0.11150 H1 + 1.0 HIS-C:CB -0.08000 CT + 1.0 HIS-C:1HB 0.08680 HC + 1.0 HIS-C:2HB 0.08680 HC + 1.0 HIS-C:CG 0.02980 CC + 1.0 HIS-C:ND1 -0.15010 NA + 1.0 HIS-C:HD1 0.38830 H + 1.0 HIS-C:CE1 -0.02510 CR + 1.0 HIS-C:HE1 0.26940 H5 + 1.0 HIS-C:NE2 -0.16830 NA + 1.0 HIS-C:HE2 0.39130 H + 1.0 HIS-C:CD2 -0.12560 CW + 1.0 HIS-C:HD2 0.23360 H4 + 1.0 HIS-C:C 0.80320 C + 1.0 HIS-C:O -0.81770 O2 + 1.0 HIS-C:OXT -0.81770 O2 + 1.0 TRP-C:N -0.38210 N + 1.0 TRP-C:H 0.26810 H + 1.0 TRP-C:CA -0.20840 CT + 1.0 TRP-C:HA 0.12720 H1 + 1.0 TRP-C:CB -0.07420 CT + 1.0 TRP-C:1HB 0.04970 HC + 1.0 TRP-C:2HB 0.04970 HC + 1.0 TRP-C:CG -0.07960 C* + 1.0 TRP-C:CD1 -0.18080 CW + 1.0 TRP-C:HD1 0.20430 H4 + 1.0 TRP-C:NE1 -0.33160 NA + 1.0 TRP-C:HE1 0.34130 H + 1.0 TRP-C:CE2 0.12220 CN + 1.0 TRP-C:CZ2 -0.25940 CA + 1.0 TRP-C:HZ2 0.15670 HA + 1.0 TRP-C:CH2 -0.10200 CA + 1.0 TRP-C:HH2 0.14010 HA + 1.0 TRP-C:CZ3 -0.22870 CA + 1.0 TRP-C:HZ3 0.15070 HA + 1.0 TRP-C:CE3 -0.18370 CA + 1.0 TRP-C:HE3 0.14910 HA + 1.0 TRP-C:CD2 0.10780 CB + 1.0 TRP-C:C 0.76580 C + 1.0 TRP-C:O -0.80110 O2 + 1.0 TRP-C:OXT -0.80110 O2 + 1.0 PHE-C:N -0.38210 N + 1.0 PHE-C:H 0.26810 H + 1.0 PHE-C:CA -0.18250 CT + 1.0 PHE-C:HA 0.10980 H1 + 1.0 PHE-C:CB -0.09590 CT + 1.0 PHE-C:1HB 0.04430 HC + 1.0 PHE-C:2HB 0.04430 HC + 1.0 PHE-C:CG 0.05520 CA + 1.0 PHE-C:CD1 -0.13000 CA + 1.0 PHE-C:HD1 0.14080 HA + 1.0 PHE-C:CE1 -0.18470 CA + 1.0 PHE-C:HE1 0.14610 HA + 1.0 PHE-C:CZ -0.09440 CA + 1.0 PHE-C:HZ 0.12800 HA + 1.0 PHE-C:CE2 -0.18470 CA + 1.0 PHE-C:HE2 0.14610 HA + 1.0 PHE-C:CD2 -0.13000 CA + 1.0 PHE-C:HD2 0.14080 HA + 1.0 PHE-C:C 0.76600 C + 1.0 PHE-C:O -0.80260 O2 + 1.0 PHE-C:OXT -0.80260 O2 + 1.0 TYR-C:N -0.38210 N + 1.0 TYR-C:H 0.26810 H + 1.0 TYR-C:CA -0.20150 CT + 1.0 TYR-C:HA 0.10920 H1 + 1.0 TYR-C:CB -0.07520 CT + 1.0 TYR-C:1HB 0.04900 HC + 1.0 TYR-C:2HB 0.04900 HC + 1.0 TYR-C:CG 0.02430 CA + 1.0 TYR-C:CD1 -0.19220 CA + 1.0 TYR-C:HD1 0.17800 HA + 1.0 TYR-C:CE1 -0.24580 CA + 1.0 TYR-C:HE1 0.16730 HA + 1.0 TYR-C:CZ 0.33950 C + 1.0 TYR-C:OH -0.56430 OH + 1.0 TYR-C:HH 0.40170 HO + 1.0 TYR-C:CE2 -0.24580 CA + 1.0 TYR-C:HE2 0.16730 HA + 1.0 TYR-C:CD2 -0.19220 CA + 1.0 TYR-C:HD2 0.17800 HA + 1.0 TYR-C:C 0.78170 C + 1.0 TYR-C:O -0.80700 O2 + 1.0 TYR-C:OXT -0.80700 O2 + 1.0 GLU-C:N -0.51920 N + 1.0 GLU-C:H 0.30550 H + 1.0 GLU-C:CA -0.20590 CT + 1.0 GLU-C:HA 0.13990 H1 + 1.0 GLU-C:CB 0.00710 CT + 1.0 GLU-C:1HB -0.00780 HC + 1.0 GLU-C:2HB -0.00780 HC + 1.0 GLU-C:CG 0.06750 CT + 1.0 GLU-C:1HG -0.05480 HC + 1.0 GLU-C:2HG -0.05480 HC + 1.0 GLU-C:CD 0.81830 C + 1.0 GLU-C:OE1 -0.82200 O2 + 1.0 GLU-C:OE2 -0.82200 O2 + 1.0 GLU-C:C 0.74200 C + 1.0 GLU-C:O -0.79300 O2 + 1.0 GLU-C:OXT -0.79300 O2 + 1.0 ASP-C:N -0.51920 N + 1.0 ASP-C:H 0.30550 H + 1.0 ASP-C:CA -0.18170 CT + 1.0 ASP-C:HA 0.10460 H1 + 1.0 ASP-C:CB -0.06770 CT + 1.0 ASP-C:1HB -0.02120 HC + 1.0 ASP-C:2HB -0.02120 HC + 1.0 ASP-C:CG 0.88510 C + 1.0 ASP-C:OD1 -0.81620 O2 + 1.0 ASP-C:OD2 -0.81620 O2 + 1.0 ASP-C:C 0.72560 C + 1.0 ASP-C:O -0.78870 O2 + 1.0 ASP-C:OXT -0.78870 O2 + 1.0 LYS-C:N -0.34810 N + 1.0 LYS-C:H 0.27640 H + 1.0 LYS-C:CA -0.29030 CT + 1.0 LYS-C:HA 0.14380 H1 + 1.0 LYS-C:CB -0.05380 CT + 1.0 LYS-C:1HB 0.04820 HC + 1.0 LYS-C:2HB 0.04820 HC + 1.0 LYS-C:CG 0.02270 CT + 1.0 LYS-C:1HG 0.01340 HC + 1.0 LYS-C:2HG 0.01340 HC + 1.0 LYS-C:CD -0.03920 CT + 1.0 LYS-C:1HD 0.06110 HC + 1.0 LYS-C:2HD 0.06110 HC + 1.0 LYS-C:CE -0.01760 CT + 1.0 LYS-C:1HE 0.11210 HP + 1.0 LYS-C:2HE 0.11210 HP + 1.0 LYS-C:NZ -0.37410 N3 + 1.0 LYS-C:1HZ 0.33740 H + 1.0 LYS-C:2HZ 0.33740 H + 1.0 LYS-C:3HZ 0.33740 H + 1.0 LYS-C:C 0.84880 C + 1.0 LYS-C:O -0.82520 O2 + 1.0 LYS-C:OXT -0.82520 O2 + 1.0 PRO-C:N -0.28020 N + 1.0 PRO-C:CD 0.04340 CT + 1.0 PRO-C:1HD 0.03310 H1 + 1.0 PRO-C:2HD 0.03310 H1 + 1.0 PRO-C:CG 0.04660 CT + 1.0 PRO-C:1HG 0.01720 HC + 1.0 PRO-C:2HG 0.01720 HC + 1.0 PRO-C:CB -0.05430 CT + 1.0 PRO-C:1HB 0.03810 HC + 1.0 PRO-C:2HB 0.03810 HC + 1.0 PRO-C:CA -0.13360 CT + 1.0 PRO-C:HA 0.07760 H1 + 1.0 PRO-C:C 0.66310 C + 1.0 PRO-C:O -0.76970 O2 + 1.0 PRO-C:OXT -0.76970 O2 + 1.0 CYS-C:N -0.38210 N + 1.0 CYS-C:H 0.26810 H + 1.0 CYS-C:CA -0.16350 CT + 1.0 CYS-C:HA 0.13960 H1 + 1.0 CYS-C:CB -0.19960 CT + 1.0 CYS-C:1HB 0.14370 H1 + 1.0 CYS-C:2HB 0.14370 H1 + 1.0 CYS-C:SG -0.31020 SH + 1.0 CYS-C:HSG 0.20680 HS + 1.0 CYS-C:C 0.74970 C + 1.0 CYS-C:O -0.79810 O2 + 1.0 CYS-C:OXT -0.79810 O2 + 1.0 CYS-CS:N -0.38210 N + 1.0 CYS-CS:H 0.26810 H + 1.0 CYS-CS:CA -0.13180 CT + 1.0 CYS-CS:HA 0.09380 H1 + 1.0 CYS-CS:CB -0.19430 CT + 1.0 CYS-CS:1HB 0.12280 H1 + 1.0 CYS-CS:2HB 0.12280 H1 + 1.0 CYS-CS:SG -0.05290 S + 1.0 CYS-CS:C 0.76180 C + 1.0 CYS-CS:O -0.80410 O2 + 1.0 CYS-CS:OXT -0.80410 O2 + 1.0 MET-C:N -0.38210 N + 1.0 MET-C:H 0.26810 H + 1.0 MET-C:CA -0.25970 CT + 1.0 MET-C:HA 0.12770 H1 + 1.0 MET-C:CB -0.02360 CT + 1.0 MET-C:1HB 0.04800 HC + 1.0 MET-C:2HB 0.04800 HC + 1.0 MET-C:CG 0.04920 CT + 1.0 MET-C:1HG 0.03170 H1 + 1.0 MET-C:2HG 0.03170 H1 + 1.0 MET-C:SD -0.26920 S + 1.0 MET-C:CE -0.03760 CT + 1.0 MET-C:1HE 0.06250 H1 + 1.0 MET-C:2HE 0.06250 H1 + 1.0 MET-C:3HE 0.06250 H1 + 1.0 MET-C:C 0.80130 C + 1.0 MET-C:O -0.81050 O2 + 1.0 MET-C:OXT -0.81050 O2 + 1.0 CA:CA 2.00000 C0 + 1.0 MG:MG 2.00000 MG + 1.0 CH4-M:C 0.00000 CT + 1.0 CH4-M:1H 0.00000 H1 + 1.0 CH4-M:2H 0.00000 H1 + 1.0 CH4-M:3H 0.00000 H1 + 1.0 CH4-M:4H 0.00000 H1 + 1.0 PCA:N -0.720984 N + 1.0 PCA:H 0.374677 H + 1.0 PCA:CA -0.025874 CT + 1.0 PCA:C 0.865161 C + 1.0 PCA:O -0.798202 O + 1.0 PCA:CB 0.114954 CT + 1.0 PCA:CG -0.126748 CT + 1.0 PCA:CD 0.770356 C + 1.0 PCA:OE -0.682912 O + 1.0 PCA:HA 0.039708 H1 + 1.0 PCA:1HB 0.000266 HC + 1.0 PCA:2HB -0.031861 HC + 1.0 PCA:1HG 0.034072 HC + 1.0 PCA:2HG 0.025655 HC + 1.0 PCA:OXT -0.838268 O + 1.0 PCA-N:N -0.720984 N + 1.0 PCA-N:H 0.374677 H + 1.0 PCA-N:CA -0.025874 CT + 1.0 PCA-N:C 0.865161 C + 1.0 PCA-N:O -0.798202 O + 1.0 PCA-N:CB 0.114954 CT + 1.0 PCA-N:CG -0.126748 CT + 1.0 PCA-N:CD 0.770356 C + 1.0 PCA-N:OE -0.682912 O + 1.0 PCA-N:HA 0.039708 H1 + 1.0 PCA-N:1HB 0.000266 HC + 1.0 PCA-N:2HB -0.031861 HC + 1.0 PCA-N:1HG 0.034072 HC + 1.0 PCA-N:2HG 0.025655 HC + 1.0 PCA-M:N -0.720984 N + 1.0 PCA-M:H 0.374677 H + 1.0 PCA-M:CA -0.025874 CT + 1.0 PCA-M:C 0.865161 C + 1.0 PCA-M:O -0.798202 O + 1.0 PCA-M:CB 0.114954 CT + 1.0 PCA-M:CG -0.126748 CT + 1.0 PCA-M:CD 0.770356 C + 1.0 PCA-M:OE -0.682912 O + 1.0 PCA-M:HA 0.039708 H1 + 1.0 PCA-M:1HB 0.000266 HC + 1.0 PCA-M:2HB -0.031861 HC + 1.0 PCA-M:1HG 0.034072 HC + 1.0 PCA-M:2HG 0.025655 HC + 1.0 PCA-M:OXT -0.838268 O
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/CMakeLists.txt Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,53 @@ +# 2008-03-15 + +set(to_install + aromatic.txt + atomtyp.txt + bondtyp.txt + element.txt + fragments.txt + gaff.dat + gaff.prm + ghemical.prm + isotope-small.txt + isotope.txt + logp.txt + MACCS.txt + mmff94.ff + mmff94s.ff + mmffang.par + mmffbndk.par + mmffbond.par + mmffchg.par + mmffdef.par + mmffdfsb.par + mmffoop.par + mmffpbci.par + mmffprop.par + mmffstbn.par + mmfftor.par + mmffvdw.par + mmffs_oop.par + mmffs_tor.par + mr.txt + patterns.txt + phmodel.txt + plugindefines.txt + psa.txt + qeq.txt + resdata.txt + ringtyp.txt + SMARTS_InteLigand.txt + space-groups.txt + superatom.txt + svgformat.script + torlib.txt + types.txt + UFF.prm +) + +if(NOT MSVC) + install(FILES ${to_install} DESTINATION share/openbabel/${BABEL_VERSION}) +else(NOT MSVC) + install(FILES ${to_install} DESTINATION bin/data) +endif(NOT MSVC)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/MACCS.txt Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,205 @@ +#Comments after SMARTS +# Extracted from RDKit Jul 2008 release (r747) Python/Chem/MACCSKeys.py +# +# Copyright (C) 2001-2006 greg Landrum and Rational Discovery LLC +# +# @@ All Rights Reserved @@ +# +#Redistribution and use in source and binary forms, with or without +#modification, are permitted provided that the following conditions are +#met: +# +# * Redistributions of source code must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# * Redistributions in binary form must reproduce the above +# copyright notice, this list of conditions and the following +# disclaimer in the documentation and/or other materials provided +# with the distribution. +# * Neither the name of Rational Discovery nor the names of its +# contributors may be used to endorse or promote products derived +# from this software without specific prior written permission. +# +#THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS +#"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT +#LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR +#A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT +#OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +#SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT +#LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, +#DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY +#THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +#(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +#OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +# these are SMARTS patterns corresponding to the MDL MACCS keys + 1:('?',0), # ISOTOPE + #2:('[#103,#104,#105,#106,#107,#106,#109,#110,#111,#112]',0), # ISOTOPE Not complete + 2:('[#103,#104]',0), # ISOTOPE Not complete + 3:('[Ge,As,Se,Sn,Sb,Te,Tl,Pb,Bi]',0), # Group IVa,Va,VIa Periods 4-6 (Ge...) *NOTE* spec wrong + 4:('[Ac,Th,Pa,U,Np,Pu,Am,Cm,Bk,Cf,Es,Fm,Md,No,Lr]',0), # actinide + 5:('[Sc,Ti,Y,Zr,Hf]',0), # Group IIIB,IVB (Sc...) *NOTE* spec wrong + 6:('[La,Ce,Pr,Nd,Pm,Sm,Eu,Gd,Tb,Dy,Ho,Er,Tm,Yb,Lu]',0), # Lanthanide + 7:('[V,Cr,Mn,Nb,Mo,Tc,Ta,W,Re]',0), # Group VB,VIB,VIIB (V...) *NOTE* spec wrong + 8:('[!C;!c;!#1]1~*~*~*~*1',0), # QAAA@1 + 9:('[Fe,Co,Ni,Ru,Rh,Pd,Os,Ir,Pt]',0), # Group VIII (Fe...) + 10:('[Be,Mg,Ca,Sr,Ba,Ra]',0), # Group IIa (Alkaline earth) + 11:('*1~*~*~*~*1',0), # 4M Ring *NOTE* Was '*1~*~*~*~1' This and 9 others changed by CM because OB didn't like it + 12:('[Cu,Zn,Ag,Cd,Au,Hg]',0), # Group IB,IIB (Cu..) + 13:('[O,o]~[N,n](~[C,c])~[C,c]',0), # ON(C)C + 14:('[S,s]-[S,s]',0), # S-S + 15:('[O,o]~[C,c](~[O,o])~[O,o]',0), # OC(O)O + 16:('[!C;!c;!#1]1~*~*~*1',0), # QAA@1 + 17:('[C,c]#[C,c]',0), #CTC + 18:('[B,Al,Ga,In,Tl]',0), # Group IIIA (B...) *NOTE* spec wrong + 19:('*1~*~*~*~*~*~*~*1',0), # 7M Ring + 20:('[Si]',0), #Si + 21:('[C,c]=[C,c](~[!C;!c;!#1])~[!C;!c;!#1]',0), # C=C(Q)Q + 22:('*1~*~*~*1',0), # 3M Ring + 23:('[N,n]~[C,c](~[O,o])~[O,o]',0), # NC(O)O + 24:('[N,n]-[O,o]',0), # N-O + 25:('[N,n]~[C,c](~[N,n])~[N,n]',0), # NC(N)N + 26:('[C,c]=;@[C,c](@*)@*',0), # C$=C($A)$A + 27:('[I]',0), # I + 28:('[!C;!c;!#1]~[CH2]~[!C;!c;!#1]',0), # QCH2Q + 29:('P',0),# P + 30:('[C,c]~[!C;!c;!#1](~[C,c])(~[C,c])~*',0), # CQ(C)(C)A + 31:('[!C;!c;!#1]~[F,Cl,Br,I]',0), # QX + 32:('[C,c]~[S,s]~[N,n]',0), # CSN + 33:('[N,n]~[S,s]',0), # NS + 34:('[CH2]=*',0), # CH2=A + 35:('[Li,Na,K,Rb,Cs,Fr]',0), # Group IA (Alkali Metal) + 36:('[$(S@*),$(s@*)]',0), # S Heterocycle + 37:('[N,n]~[C,c](~[O,o])~[N,n]',0), # NC(O)N + 38:('[N,n]~[C,c](~[C,c])~[N,n]',0), # NC(C)N + 39:('[O,o]~[S,s](~[O,o])~[O,o]',0), # OS(O)O + 40:('[S,s]-[O,o]',0), # S-O + 41:('[C,c]#[N,n]',0), # CTN + 42:('F',0), # F + 43:('[!C;!c;!#1;H,H2,H3,H4]~*~[!C;!c;!#1;H,H2,H3,H4]',0), # QHAQH FIX: possibly incomplete + 44:('?',0), # OTHER + 45:('[C,c]=[C,c]~[N,n]',0), # C=CN + 46:('Br',0), # BR + 47:('[S,s]~*~[N,n]',0), # SAN + 48:('[O,o]~[!C;!c;!#1](~[O,o])(~[O,o])~*',0), # OQ(O)O + 49:('[-,-2,-3,-4,+,+2,+3,+4]',0), # CHARGE FIX: possibly incomplete + 50:('[C,c]=[C,c](~[C,c])~[C,c]',0), # C=C(C)C + 51:('[C,c]~[S,s]~[O,o]',0), # CSO + 52:('[N,n]~[N,n]',0), # NN + 53:('[!#6;!#1;!H0]~*~*~*~[!#6;!#1;!H0]',0), # QHAAAQH FIX: possibly incomplete + 54:('[!#6;!#1;!H0]~*~*~[!#6;!#1;!H0]',0), # QHAAQH FIX: possibly incomplete + 55:('[O,o]~[S,s]~[O,o]',0), #OSO + 56:('[O,o]~[N,n](~[O,o])~[C,c]',0), # ON(O)C + 57:('[$(O@*),$(o@*)]',0), # O Heterocycle + 58:('[!C;!c;!#1]~[S,s]~[!C;!c;!#1]',0), # QSQ + 59:('[S,s]!:*:*',0), # Snot%A%A + 60:('[S,s]=[O,o]',0), # S=O + 61:('*~[S,s](~*)~*',0), # AS(A)A + 62:('*@*!@*@*',0), # A$!A$A + 63:('[N,n]=[O,o]',0), # N=O + 64:('*@*!@[S,s]',0), # A$A!S + 65:('[C,c]:[N,n]',0), # C%N + 66:('[C,c]~[C,c](~[C,c])(~[C,c])~*',0), # CC(C)(C)A + 67:('[!C;!c;!#1]~[S,s]',0), # QS + 68:('[!#6;!#1;!H0]~[!#6;!#1;!H0]',0), # QHQH FIX: possibly incomplete + 69:('[!C;!c;!#1]~[!#6;!#1;!H0]',0), # QQH FIX: possibly incomplete + 70:('[!C;!c;!#1]~[N,n]~[!C;!c;!#1]',0), # QNQ + 71:('[N,n]~[O,o]',0), # NO + 72:('[O,o]~*~*~[O,o]',0), # OAAO + 73:('[S,s]=*',0), # S=A + 74:('[CH3]~*~[CH3]',0), # CH3ACH3 + 75:('*!@[N,n]@*',0), # A!N$A + 76:('[C,c]=[C,c](~*)~*',0), # C=C(A)A + 77:('[N,n]~*~[N,n]',0), # NAN + 78:('[C,c]=[N,n]',0), # C=N + 79:('[N,n]~*~*~[N,n]',0), # NAAN + 80:('[N,n]~*~*~*~[N,n]',0), # NAAAN + 81:('[S,s]~*(~*)~*',0), # SA(A)A + 82:('*~[CH2]~[!#6;!#1;!H0]',0), # ACH2QH + 83:('[!C;!c;!#1]1~*~*~*~*~*1',0), # QAAAA@1 + 84:('[NH2]',0), #NH2 + 85:('[C,c]~[N,n](~[C,c])~[C,c]',0), # CN(C)C + 86:('[CH2][!C;!c;!#1][CH2]',0), # CH2QCH2 + 87:('[F,Cl,Br,I]!@*@*',0), # X!A$A + 88:('[S,s]',0), # S + 89:('[O,o]~*~*~*~[O,o]',0), # OAAAO + 90:('[!#6;!#1;!H0]~*~*~[CH2]~*',0), # QHAACH2A + 91:('[!#6;!#1;!H0]~*~*~*~[CH2]~*',0), # QHAAACH2A + 92:('[O,o]~[C,c](~[N,n])~[C,c]',0), # OC(N)C + 93:('[!C;!c;!#1]~[CH3]',0), # QCH3 + 94:('[!C;!c;!#1]~[N,n]',0), # QN + 95:('[N,n]~*~*~[O,o]',0), # NAAO + 96:('*1~*~*~*~*~*1',0), # 5 M ring + 97:('[N,n]~*~*~*~[O,o]',0), # NAAAO + 98:('[!C;!c;!#1]1~*~*~*~*~*~*1',0), # QAAAAA@1 + 99:('[C,c]=[C,c]',0), # C=C + 100:('*~[CH2]~[N,n]',0), # ACH2N + 101:('[r8,r9,r10,r11,r12]',0), # 8M Ring or larger FIX: This is not exhaustive and it appears that oelib doesn't do this right + 102:('[!C;!c;!#1]~[O,o]',0), # QO + 103:('Cl',0), # CL + 104:('[!#6;!#1;!H0]~*~[CH2]~*',0), # QHACH2A + 105:('[!C;!c;!#1]@*(@*)@*',0), # A$A($A)$A + 106:('[!C;!c;!#1]~*(~[!C;!c;!#1])~[!C;!c;!#1]',0), # QA(Q)Q + 107:('[F,Cl,Br,I]~*(~*)~*',0), # XA(A)A + 108:('[CH3]~*~*~*~[CH2]~*',0), # CH3AAACH2A + 109:('*~[CH2]~[O,o]',0), # ACH2O + 110:('[N,n]~[C,c]~[O,o]',0), # NCO + 111:('[N,n]~*~[CH2]~*',0), # NACH2A + 112:('*~*(~*)(~*)~*',0), # AA(A)(A)A + 113:('[O,o]!:*:*',0), # Onot%A%A + 114:('[CH3]~[CH2]~*',0), # CH3CH2A + 115:('[CH3]~*~[CH2]~*',0), # CH3ACH2A + 116:('[CH3]~*~*~[CH2]~*',0), # CH3AACH2A + 117:('[N,n]~*~[O,o]',0), # NAO + 118:('*~[CH2]~[CH2]~*',1), # ACH2CH2A > 1 + 119:('[N,n]=*',0), # N=A + 120:('[!C;!c;R]',1), # Heterocyclic atom > 1 + 121:('[$(N@*),$(n@*)]',0), # N Heterocycle + 122:('*~[N,n](~*)~*',0), # AN(A)A + 123:('[O,o]~[C,c]~[O,o]',0), # OCO + 124:('[!C;!c;!#1]~[!C;!c;!#1]',0), # QQ + 125:('?',0), # Aromatic Ring > 1 + 126:('*!@[O,o]!@*',0), # A!O!A + 127:('*@*!@[O,o]',1), # A$A!O > 1 + 128:('*~[CH2]~*~*~*~[CH2]~*',0), # ACH2AAACH2A + 129:('*~[CH2]~*~*~[CH2]~*',0), # ACH2AACH2A + 130:('[!C;!c;!#1]~[!C;!c;!#1]',1), # QQ > 1 (&...) + 131:('[!#6;!#1;!H0]',1), # QH > 1 + 132:('[O,o]~*~[CH2]~*',0), # OACH2A + 133:('*@*!:[N,n]',0), # A$A!N + 134:('[F,Cl,Br,I]',0), # X (HALOGEN) + 135:('[N,n]!:*:*',0), # Nnot%A%A + 136:('[O,o]=*',1), # O=A>1 FIX: maybe not right key + 137:('[!C;!c;R]',0), # Heterocycle + 138:('[!C;!c;!#1]~[CH2]~*',1), # QCH2A>1 (&...) + 139:('[OH,OH2,OH3]',0), # OH + 140:('[O,o]',3), # O > 3 + 141:('[CH3]',2), # CH3 > 2 + 142:('[N,n]',1), # N > 1 + 143:('*@*!@[O,o]',0), # A$A!O + 144:('*!:*:*!:*',0), # Anot%A%Anot%A + 145:('*1~*~*~*~*~*~*1',1), # 6M ring > 1 + 146:('[O,o]',2), # O > 2 + 147:('*~[CH2]~[CH2]~*',0), # ACH2CH2A + 148:('*~[!C;!c;!#1](~*)~*',0), # AQ(A)A + 149:('[CH3]',1), # CH3 > 1 + 150:('*!@*@*!@*',0), # A!A$A!A + 151:('[N!H0]',0), # NH + 152:('[O,o]~[C,c](~[C,c])~[C,c]',0), # OC(C)C + 153:('[!C;!c;!#1]~[CH2]~*',0), # QCH2A + 154:('[C,c]=[O,o]',0), # C=O + 155:('*!@[CH2]!@*',0), # A!CH2!A + 156:('[N,n]~*(~*)~*',0), # NA(A)A + 157:('[C,c]-[O,o]',0), # C-O + 158:('[C,c]-[N,n]',0), # C-N + 159:('[O,o]',1), # O>1 + 160:('[CH3]',0), #CH3 + 161:('[N,n]',0), # N + 162:('a',0), # Aromatic + 163:('*1~*~*~*~*~*~*1',0), # 6M Ring + 164:('[O,o]',0), # O + 165:('[R]',0), # Ring + 166:('?',0), # Fragments FIX: this should be (*).(*), but that doesn't work properly in oelib + +# Output with SMILES "CNO" +#> 24: N-O 68: QHQH 69: QQH 71: NO 93: QCH3 94: QN 102: QO +#124: QQ 131: QH > 1*2 139: OH 151: NH 158: C-N 160: CH3 161: N 164: O
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/Makefile Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,178 @@ +# CMAKE generated file: DO NOT EDIT! +# Generated by "Unix Makefiles" Generator, CMake Version 2.6 + +# Default target executed when no arguments are given to make. +default_target: all +.PHONY : default_target + +#============================================================================= +# Special targets provided by cmake. + +# Disable implicit rules so canoncical targets will work. +.SUFFIXES: + +# Remove some rules from gmake that .SUFFIXES does not remove. +SUFFIXES = + +.SUFFIXES: .hpux_make_needs_suffix_list + +# Suppress display of executed commands. +$(VERBOSE).SILENT: + +# A target that is always out of date. +cmake_force: +.PHONY : cmake_force + +#============================================================================= +# Set environment variables for the build. + +# The shell in which to execute make rules. +SHELL = /bin/sh + +# The 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/SMARTS_InteLigand.txt Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,983 @@ +# +# SMARTS Patterns for Functional Group Classification +# +# written by Christian Laggner +# Copyright 2005 Inte:Ligand Software-Entwicklungs und Consulting GmbH +# +# Released under the Lesser General Public License (LGPL license) +# see http://www.gnu.org/copyleft/lesser.html +# Modified from Version 221105 +##################################################################################################### + +# General Stuff: +# These patters were written in an attempt to represent the classification of organic compounds +# from the viewpoint of an organic chemist. +# They are often very restrictive. This may be generally a good thing, but it also takes some time +# for filtering/indexing large compound sets. +# For filtering undesired groups (in druglike compounds) one will want to have more general patterns +# (e.g. you don't want *any* halide of *any* acid, *neither* aldehyde *nor* formyl esters and amides, ...). +# + +# Part I: Carbon +# ============== + + +# I.1: Carbon-Carbon Bonds +# ------------------------ + +# I.1.1 Alkanes: + +Primary_carbon: [CX4H3][#6] + +Secondary_carbon: [CX4H2]([#6])[#6] + +Tertiary_carbon: [CX4H1]([#6])([#6])[#6] + +Quaternary_carbon: [CX4]([#6])([#6])([#6])[#6] + + +# I.1.2 C-C double and Triple Bonds + +Alkene: [CX3;$([H2]),$([H1][#6]),$(C([#6])[#6])]=[CX3;$([H2]),$([H1][#6]),$(C([#6])[#6])] +# sp2 C may be substituted only by C or H - +# does not hit ketenes and allenes, nor enamines, enols and the like + +Alkyne: [CX2]#[CX2] +# non-carbon substituents (e.g. alkynol ethers) are rather rare, thus no further discrimination + +Allene: [CX3]=[CX2]=[CX3] + + +# I.2: One Carbon-Hetero Bond +# --------------------------- + + +# I.2.1 Alkyl Halogenides + +Alkylchloride: [ClX1][CX4] +# will also hit chloromethylethers and the like, but no chloroalkenes, -alkynes or -aromats +# a more restrictive version can be obtained by modifying the Alcohol string. + +Alkylfluoride: [FX1][CX4] + +Alkylbromide: [BrX1][CX4] + +Alkyliodide: [IX1][CX4] + + +# I.2.2 Alcohols and Ethers + +Alcohol: [OX2H][CX4;!$(C([OX2H])[O,S,#7,#15])] +# nonspecific definition, no acetals, aminals, and the like + +Primary_alcohol: [OX2H][CX4H2;!$(C([OX2H])[O,S,#7,#15])] + +Secondary_alcohol: [OX2H][CX4H;!$(C([OX2H])[O,S,#7,#15])] + +Tertiary_alcohol: [OX2H][CX4D4;!$(C([OX2H])[O,S,#7,#15])] + +Dialkylether: [OX2]([CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])])[CX4;!$(C([OX2])[O,S,#7,#15])] +# no acetals and the like; no enolethers + +Dialkylthioether: [SX2]([CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])])[CX4;!$(C([OX2])[O,S,#7,#15])] +# no acetals and the like; no enolethers + +Alkylarylether: [OX2](c)[CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])] +# no acetals and the like; no enolethers + +Diarylether: [c][OX2][c] + +Alkylarylthioether: [SX2](c)[CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])] + +Diarylthioether: [c][SX2][c] + +Oxonium: [O+;!$([O]~[!#6]);!$([S]*~[#7,#8,#15,#16])] +# can't be aromatic, thus O and not #8 + +# I.2.3 Amines + +Amine: [NX3+0,NX4+;!$([N]~[!#6]);!$([N]*~[#7,#8,#15,#16])] +# hits all amines (prim/sec/tert/quart), including ammonium salts, also enamines, but not amides, imides, aminals, ... + +# the following amines include also the protonated forms + +Primary_aliph_amine: [NX3H2+0,NX4H3+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])] + +Secondary_aliph_amine: [NX3H1+0,NX4H2+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])] + +Tertiary_aliph_amine: [NX3H0+0,NX4H1+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])] + +Quaternary_aliph_ammonium: [NX4H0+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])] + +Primary_arom_amine: [NX3H2+0,NX4H3+]c + +Secondary_arom_amine: [NX3H1+0,NX4H2+;!$([N][!c]);!$([N]*~[#7,#8,#15,#16])] + +Tertiary_arom_amine: [NX3H0+0,NX4H1+;!$([N][!c]);!$([N]*~[#7,#8,#15,#16])] + +Quaternary_arom_ammonium: [NX4H0+;!$([N][!c]);!$([N]*~[#7,#8,#15,#16])] + +Secondary_mixed_amine: [NX3H1+0,NX4H2+;$([N]([c])[C]);!$([N]*~[#7,#8,#15,#16])] + +Tertiary_mixed_amine: [NX3H0+0,NX4H1+;$([N]([c])([C])[#6]);!$([N]*~[#7,#8,#15,#16])] + +Quaternary_mixed_ammonium: [NX4H0+;$([N]([c])([C])[#6][#6]);!$([N]*~[#7,#8,#15,#16])] + +Ammonium: [N+;!$([N]~[!#6]);!$(N=*);!$([N]*~[#7,#8,#15,#16])] +# only C and H substituents allowed. Quaternary or protonated amines +# NX4+ or Nv4+ is not recognized by Daylight's depictmatch if less than four C are present + + +# I.2.4 Others + +Alkylthiol: [SX2H][CX4;!$(C([SX2H])~[O,S,#7,#15])] + +Dialkylthioether: [SX2]([CX4;!$(C([SX2])[O,S,#7,#15,F,Cl,Br,I])])[CX4;!$(C([SX2])[O,S,#7,#15])] + +Alkylarylthioether: [SX2](c)[CX4;!$(C([SX2])[O,S,#7,#15])] + +Disulfide: [SX2D2][SX2D2] + +1,2-Aminoalcohol: [OX2H][CX4;!$(C([OX2H])[O,S,#7,#15,F,Cl,Br,I])][CX4;!$(C([N])[O,S,#7,#15])][NX3;!$(NC=[O,S,N])] +# does not hit alpha-amino acids, enaminoalcohols, 1,2-aminoacetals, o-aminophenols, etc. + +1,2-Diol: [OX2H][CX4;!$(C([OX2H])[O,S,#7,#15])][CX4;!$(C([OX2H])[O,S,#7,#15])][OX2H] +# does not hit alpha-hydroxy acids, enolalcohols, 1,2-hydroxyacetals, 1,2-diphenols, etc. + +1,1-Diol: [OX2H][CX4;!$(C([OX2H])([OX2H])[O,S,#7,#15])][OX2H] + +Hydroperoxide: [OX2H][OX2] +#does not neccessarily have to be connected to a carbon atom, includes also hydrotrioxides + +Peroxo: [OX2D2][OX2D2] + +Organolithium_compounds: [LiX1][#6,#14] + +Organomagnesium_compounds: [MgX2][#6,#14] +# not restricted to Grignard compounds, also dialkyl Mg + +Organometallic_compounds: [!#1;!#5;!#6;!#7;!#8;!#9;!#14;!#15;!#16;!#17;!#33;!#34;!#35;!#52;!#53;!#85]~[#6;!-] +# very general, includes all metals covalently bound to carbon + + +# I.3: Two Carbon-Hetero Bonds (Carbonyl and Derivatives) +# ---------------------------- + +# I.3.1 Double Bond to Hetero + +Aldehyde: [$([CX3H][#6]),$([CX3H2])]=[OX1] +# hits aldehydes including formaldehyde + +Ketone: [#6][CX3](=[OX1])[#6] +# does not include oxo-groups connected to a (hetero-) aromatic ring + +Thioaldehyde: [$([CX3H][#6]),$([CX3H2])]=[SX1] + +Thioketone: [#6][CX3](=[SX1])[#6] +# does not include thioxo-groups connected to a (hetero-) aromatic ring + +Imine: [NX2;$([N][#6]),$([NH]);!$([N][CX3]=[#7,#8,#15,#16])]=[CX3;$([CH2]),$([CH][#6]),$([C]([#6])[#6])] +# nitrogen is not part of an amidelike strukture, nor of an aromatic ring, but can be part of an aminal or similar + +Immonium: [NX3+;!$([N][!#6]);!$([N][CX3]=[#7,#8,#15,#16])] + +Oxime: [NX2](=[CX3;$([CH2]),$([CH][#6]),$([C]([#6])[#6])])[OX2H] + +Oximether: [NX2](=[CX3;$([CH2]),$([CH][#6]),$([C]([#6])[#6])])[OX2][#6;!$(C=[#7,#8])] +# ether, not ester or amide; does not hit isoxazole + + +# I.3.2. Two Single Bonds to Hetero + +Acetal: [OX2]([#6;!$(C=[O,S,N])])[CX4;!$(C(O)(O)[!#6])][OX2][#6;!$(C=[O,S,N])] +# does not hit hydroxy-methylesters, ketenacetals, hemiacetals, orthoesters, etc. + +Hemiacetal: [OX2H][CX4;!$(C(O)(O)[!#6])][OX2][#6;!$(C=[O,S,N])] + +Aminal: [NX3v3;!$(NC=[#7,#8,#15,#16])]([#6])[CX4;!$(C(N)(N)[!#6])][NX3v3;!$(NC=[#7,#8,#15,#16])][#6] +# Ns are not part of an amide or similar. v3 ist to exclude nitro and similar groups + +Hemiaminal: [NX3v3;!$(NC=[#7,#8,#15,#16])]([#6])[CX4;!$(C(N)(N)[!#6])][OX2H] + +Thioacetal: [SX2]([#6;!$(C=[O,S,N])])[CX4;!$(C(S)(S)[!#6])][SX2][#6;!$(C=[O,S,N])] + +Thiohemiacetal: [SX2]([#6;!$(C=[O,S,N])])[CX4;!$(C(S)(S)[!#6])][OX2H] + +Halogen_acetal_like: [NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1] +# hits chloromethylenethers and other reactive alkylating agents + +Acetal_like: [NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1,NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])] +# includes all of the above and other combinations (S-C-N, hydrates, ...), but still no aminomethylenesters and similar + +Halogenmethylen_ester_and_similar: [NX3v3,SX2,OX2;$(**=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1] +# also reactive alkylating agents. Acid does not have to be carboxylic acid, also S- and P-based acids allowed + +NOS_methylen_ester_and_similar: [NX3v3,SX2,OX2;$(**=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])] +# Same as above, but N,O or S instead of halogen. Ester/amide allowed only on one side + +Hetero_methylen_ester_and_similar: [NX3v3,SX2,OX2;$(**=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1,NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])] +# Combination of the last two patterns + +Cyanhydrine: [NX1]#[CX2][CX4;$([CH2]),$([CH]([CX2])[#6]),$(C([CX2])([#6])[#6])][OX2H] + + +# I.3.3 Single Bond to Hetero, C=C Double Bond (Enols and Similar) + +Chloroalkene: [ClX1][CX3]=[CX3] + +Fluoroalkene: [FX1][CX3]=[CX3] + +Bromoalkene: [BrX1][CX3]=[CX3] + +Iodoalkene: [IX1][CX3]=[CX3] + +Enol: [OX2H][CX3;$([H1]),$(C[#6])]=[CX3] +# no phenols + +Endiol: [OX2H][CX3;$([H1]),$(C[#6])]=[CX3;$([H1]),$(C[#6])][OX2H] +# no 1,2-diphenols, ketenacetals, ... + +Enolether: [OX2]([#6;!$(C=[N,O,S])])[CX3;$([H0][#6]),$([H1])]=[CX3] +# finds also endiodiethers, but not enolesters, no aromats + +Enolester: [OX2]([CX3]=[OX1])[#6X3;$([#6][#6]),$([H1])]=[#6X3;!$(C[OX2H])] + + +Enamine: [NX3;$([NH2][CX3]),$([NH1]([CX3])[#6]),$([N]([CX3])([#6])[#6]);!$([N]*=[#7,#8,#15,#16])][CX3;$([CH]),$([C][#6])]=[CX3] +# does not hit amines attached to aromatic rings, nor may the nitrogen be aromatic + +Thioenol: [SX2H][CX3;$([H1]),$(C[#6])]=[CX3] + +Thioenolether: [SX2]([#6;!$(C=[N,O,S])])[CX3;$(C[#6]),$([CH])]=[CX3] + + +# I.4: Three Carbon-Hetero Bonds (Carboxyl and Derivatives) +# ------------------------------ + +Acylchloride: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[ClX1] + +Acylfluoride: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[FX1] + +Acylbromide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[BrX1] + +Acyliodide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[IX1] + +Acylhalide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[FX1,ClX1,BrX1,IX1] +# all of the above + + +# The following contains all simple carboxylic combinations of O, N, S, & Hal - +# - acids, esters, amides, ... as well as a few extra cases (anhydride, hydrazide...) +# Cyclic structures (including aromats) like lactones, lactames, ... got their own +# definitions. Structures where both heteroatoms are part of an aromatic ring +# (oxazoles, imidazoles, ...) were excluded. + +Carboxylic_acid: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[$([OX2H]),$([OX1-])] +# includes carboxylate anions + +Carboxylic_ester: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[OX2][#6;!$(C=[O,N,S])] +# does not hit anhydrides or lactones + +Lactone: [#6][#6X3R](=[OX1])[#8X2][#6;!$(C=[O,N,S])] +# may also be aromatic + +Carboxylic_anhydride: [CX3;$([H0][#6]),$([H1])](=[OX1])[#8X2][CX3;$([H0][#6]),$([H1])](=[OX1]) +# anhydride formed by two carboxylic acids, no mixed anhydrides (e.g. between carboxylic acid and sulfuric acid); may be part of a ring, even aromatic + +Carboxylic_acid_derivative: [$([#6X3H0][#6]),$([#6X3H])](=[!#6])[!#6] +# includes most of the structures of I.4 and many more, also 1,3-heteroaromatics such as isoxazole + +Carbothioic_acid: [CX3;!R;$([C][#6]),$([CH]);$([C](=[OX1])[$([SX2H]),$([SX1-])]),$([C](=[SX1])[$([OX2H]),$([OX1-])])] +# hits both tautomeric forms, as well as anions + +Carbothioic_S_ester: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[SX2][#6;!$(C=[O,N,S])] + +Carbothioic_S_lactone: [#6][#6X3R](=[OX1])[#16X2][#6;!$(C=[O,N,S])] +# may also be aromatic + +Carbothioic_O_ester: [CX3;$([H0][#6]),$([H1])](=[SX1])[OX2][#6;!$(C=[O,N,S])] + +Carbothioic_O_lactone: [#6][#6X3R](=[SX1])[#8X2][#6;!$(C=[O,N,S])] + +Carbothioic_halide: [CX3;$([H0][#6]),$([H1])](=[SX1])[FX1,ClX1,BrX1,IX1] + +Carbodithioic_acid: [CX3;!R;$([C][#6]),$([CH]);$([C](=[SX1])[SX2H])] + +Carbodithioic_ester: [CX3;!R;$([C][#6]),$([CH]);$([C](=[SX1])[SX2][#6;!$(C=[O,N,S])])] + +Carbodithiolactone: [#6][#6X3R](=[SX1])[#16X2][#6;!$(C=[O,N,S])] + + +Amide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] +# does not hit lactames + +Primary_amide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[NX3H2] + +Secondary_amide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[#7X3H1][#6;!$(C=[O,N,S])] + +Tertiary_amide: [CX3;$([R0][#6]),$([H1R0])](=[OX1])[#7X3H0]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])] + +Lactam: [#6R][#6X3R](=[OX1])[#7X3;$([H1][#6;!$(C=[O,N,S])]),$([H0]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] +# cyclic amides, may also be aromatic + +Alkyl_imide: [#6X3;$([H0][#6]),$([H1])](=[OX1])[#7X3H0]([#6])[#6X3;$([H0][#6]),$([H1])](=[OX1]) +# may be part of a ring, even aromatic. only C allowed at central N. May also be triacyl amide + +N_hetero_imide: [#6X3;$([H0][#6]),$([H1])](=[OX1])[#7X3H0]([!#6])[#6X3;$([H0][#6]),$([H1])](=[OX1]) +# everything else than H or C at central N + +Imide_acidic: [#6X3;$([H0][#6]),$([H1])](=[OX1])[#7X3H1][#6X3;$([H0][#6]),$([H1])](=[OX1]) +# can be deprotonated + +Thioamide: [$([CX3;!R][#6]),$([CX3H;!R])](=[SX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] +# does not hit thiolactames + +Thiolactam: [#6R][#6X3R](=[SX1])[#7X3;$([H1][#6;!$(C=[O,N,S])]),$([H0]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] +# cyclic thioamides, may also be aromatic + + +Oximester: [#6X3;$([H0][#6]),$([H1])](=[OX1])[#8X2][#7X2]=,:[#6X3;$([H0]([#6])[#6]),$([H1][#6]),$([H2])] +# may also be part of a ring / aromatic + +Amidine: [NX3;!$(NC=[O,S])][CX3;$([CH]),$([C][#6])]=[NX2;!$(NC=[O,S])] +# only basic amidines, not as part of aromatic ring (e.g. imidazole) + +Hydroxamic_acid: [CX3;$([H0][#6]),$([H1])](=[OX1])[#7X3;$([H1]),$([H0][#6;!$(C=[O,N,S])])][$([OX2H]),$([OX1-])] + +Hydroxamic_acid_ester: [CX3;$([H0][#6]),$([H1])](=[OX1])[#7X3;$([H1]),$([H0][#6;!$(C=[O,N,S])])][OX2][#6;!$(C=[O,N,S])] +# does not hit anhydrides of carboxylic acids withs hydroxamic acids + + +Imidoacid: [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([OX2H]),$([OX1-])] +# not cyclic + +Imidoacid_cyclic: [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([OX2H]),$([OX1-])] +# the enamide-form of lactames. may be aromatic like 2-hydroxypyridine + +Imidoester: [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[OX2][#6;!$(C=[O,N,S])] +# esters of the above structures. no anhydrides. + +Imidolactone: [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[OX2][#6;!$(C=[O,N,S])] +# no oxazoles and similar + +Imidothioacid: [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([SX2H]),$([SX1-])] +# not cyclic + +Imidothioacid_cyclic: [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([SX2H]),$([SX1-])] +# the enamide-form of thiolactames. may be aromatic like 2-thiopyridine + +Imidothioester: [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[SX2][#6;!$(C=[O,N,S])] +# thioesters of the above structures. no anhydrides. + +Imidothiolactone: [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[SX2][#6;!$(C=[O,N,S])] +# no thioxazoles and similar + +Amidine: [#7X3v3;!$(N([#6X3]=[#7X2])C=[O,S])][CX3R0;$([H1]),$([H0][#6])]=[NX2v3;!$(N(=[#6X3][#7X3])C=[O,S])] +# only basic amidines, not substituted by carbonyl or thiocarbonyl, not as part of a ring + +Imidolactam: [#6][#6X3R;$([H0](=[NX2;!$(N(=[#6X3][#7X3])C=[O,S])])[#7X3;!$(N([#6X3]=[#7X2])C=[O,S])]),$([H0](-[NX3;!$(N([#6X3]=[#7X2])C=[O,S])])=,:[#7X2;!$(N(=[#6X3][#7X3])C=[O,S])])] +# one of the two C~N bonds is part of a ring (may be aromatic), but not both - thus no imidazole + +Imidoylhalide: [CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[FX1,ClX1,BrX1,IX1] +# not cyclic + +Imidoylhalide_cyclic: [#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[FX1,ClX1,BrX1,IX1] +# may also be aromatic + +# may be ring, aromatic, substituted with carbonyls, hetero, ... +# (everything else would get too complicated) + +Amidrazone: [$([$([#6X3][#6]),$([#6X3H])](=[#7X2v3])[#7X3v3][#7X3v3]),$([$([#6X3][#6]),$([#6X3H])]([#7X3v3])=[#7X2v3][#7X3v3])] +# hits both tautomers. as above, it may be ring, aromatic, substituted with carbonyls, hetero, ... + + +Alpha_aminoacid: [NX3,NX4+;!$([N]~[!#6]);!$([N]*~[#7,#8,#15,#16])][C][CX3](=[OX1])[OX2H,OX1-] +# N may be alkylated, but not part of an amide (as in peptides), ionic forms are included +# includes also non-natural aminoacids with double-bonded or two aliph./arom. substituents at alpha-C +# N may not be aromatic as in 1H-pyrrole-2-carboxylic acid + +Alpha_hydroxyacid: [OX2H][C][CX3](=[OX1])[OX2H,OX1-] + +Peptide_middle: [NX3;$([N][CX3](=[OX1])[C][NX3,NX4+])][C][CX3](=[OX1])[NX3;$([N][C][CX3](=[OX1])[NX3,OX2,OX1-])] +# finds peptidic structures which are neither C- nor N-terminal. Both neighbours must be amino-acids/peptides + +Peptide_C_term: [NX3;$([N][CX3](=[OX1])[C][NX3,NX4+])][C][CX3](=[OX1])[OX2H,OX1-] +# finds C-terminal amino acids + +Peptide_N_term: [NX3,NX4+;!$([N]~[!#6]);!$([N]*~[#7,#8,#15,#16])][C][CX3](=[OX1])[NX3;$([N][C][CX3](=[OX1])[NX3,OX2,OX1-])] +# finds N-terminal amino acids. As above, N may be substituted, but not part of an amide-bond. + + +Carboxylic_orthoester: [#6][OX2][CX4;$(C[#6]),$([CH])]([OX2][#6])[OX2][#6] +# hits also anhydride like struktures (e. g. HC(OMe)2-OC=O residues) + +Ketene: [CX3]=[CX2]=[OX1] + +Ketenacetal: [#7X2,#8X3,#16X2;$(*[#6,#14])][#6X3]([#7X2,#8X3,#16X2;$(*[#6,#14])])=[#6X3] +# includes aminals, silylacetals, ketenesters, etc. C=C DB is not aromatic, everything else may be + +Nitrile: [NX1]#[CX2] +# includes cyanhydrines + +Isonitrile: [CX1-]#[NX2+] + + +Vinylogous_carbonyl_or_carboxyl_derivative: [#6X3](=[OX1])[#6X3]=,:[#6X3][#7,#8,#16,F,Cl,Br,I] +# may be part of a ring, even aromatic + +Vinylogous_acid: [#6X3](=[OX1])[#6X3]=,:[#6X3][$([OX2H]),$([OX1-])] + +Vinylogous_ester: [#6X3](=[OX1])[#6X3]=,:[#6X3][#6;!$(C=[O,N,S])] + +Vinylogous_amide: [#6X3](=[OX1])[#6X3]=,:[#6X3][#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] + +Vinylogous_halide: [#6X3](=[OX1])[#6X3]=,:[#6X3][FX1,ClX1,BrX1,IX1] + + + +# I.5: Four Carbon-Hetero Bonds (Carbonic Acid and Derivatives) +# ----------------------------- + +Carbonic_acid_dieester: [#6;!$(C=[O,N,S])][#8X2][#6X3](=[OX1])[#8X2][#6;!$(C=[O,N,S])] +# may be part of a ring, even aromatic + +Carbonic_acid_esterhalide: [#6;!$(C=[O,N,S])][OX2;!R][CX3](=[OX1])[OX2][FX1,ClX1,BrX1,IX1] + +Carbonic_acid_monoester: [#6;!$(C=[O,N,S])][OX2;!R][CX3](=[OX1])[$([OX2H]),$([OX1-])] +# unstable + +Carbonic_acid_derivatives: [!#6][#6X3](=[!#6])[!#6] + + +Thiocarbonic_acid_dieester: [#6;!$(C=[O,N,S])][#8X2][#6X3](=[SX1])[#8X2][#6;!$(C=[O,N,S])] +# may be part of a ring, even aromatic + +Thiocarbonic_acid_esterhalide: [#6;!$(C=[O,N,S])][OX2;!R][CX3](=[SX1])[OX2][FX1,ClX1,BrX1,IX1] + +Thiocarbonic_acid_monoester: [#6;!$(C=[O,N,S])][OX2;!R][CX3](=[SX1])[$([OX2H]),$([OX1-])] + + +Urea:[#7X3;!$([#7][!#6])][#6X3](=[OX1])[#7X3;!$([#7][!#6])] +# no check whether part of imide, biuret, etc. Aromatic structures are only hit if +# both N share no double bonds, like in the dioxo-form of uracil + +Thiourea: [#7X3;!$([#7][!#6])][#6X3](=[SX1])[#7X3;!$([#7][!#6])] + +Isourea: [#7X2;!$([#7][!#6])]=,:[#6X3]([#8X2&!$([#8][!#6]),OX1-])[#7X3;!$([#7][!#6])] +# O may be substituted. no check whether further amide-like bonds are present. Aromatic +# structures are only hit if single bonded N shares no additional double bond, like in +# the 1-hydroxy-3-oxo form of uracil + +Isothiourea: [#7X2;!$([#7][!#6])]=,:[#6X3]([#16X2&!$([#16][!#6]),SX1-])[#7X3;!$([#7][!#6])] + +Guanidine: [N;v3X3,v4X4+][CX3](=[N;v3X2,v4X3+])[N;v3X3,v4X4+] +# also hits guanidinium salts. v3 and v4 to avoid nitroamidines + +Carbaminic_acid: [NX3]C(=[OX1])[O;X2H,X1-] +# quite unstable, unlikely to be found. Also hits salts + +Urethan: [#7X3][#6](=[OX1])[#8X2][#6] +# also hits when part of a ring, no check whether the last C is part of carbonyl + +Biuret: [#7X3][#6](=[OX1])[#7X3][#6](=[OX1])[#7X3] + +Semicarbazide: [#7X3][#7X3][#6X3]([#7X3;!$([#7][#7])])=[OX1] + +Carbazide: [#7X3][#7X3][#6X3]([#7X3][#7X3])=[OX1] + +Semicarbazone: [#7X2](=[#6])[#7X3][#6X3]([#7X3;!$([#7][#7])])=[OX1] + +Carbazone: [#7X2](=[#6])[#7X3][#6X3]([#7X3][#7X3])=[OX1] + +Thiosemicarbazide: [#7X3][#7X3][#6X3]([#7X3;!$([#7][#7])])=[SX1] + +Thiocarbazide: [#7X3][#7X3][#6X3]([#7X3][#7X3])=[SX1] + +Thiosemicarbazone: [#7X2](=[#6])[#7X3][#6X3]([#7X3;!$([#7][#7])])=[SX1] + +Thiocarbazone: [#7X2](=[#6])[#7X3][#6X3]([#7X3][#7X3])=[SX1] + + +Isocyanate: [NX2]=[CX2]=[OX1] + +Cyanate: [OX2][CX2]#[NX1] + +Isothiocyanate: [NX2]=[CX2]=[SX1] + +Thiocyanate: [SX2][CX2]#[NX1] + +Carbodiimide: [NX2]=[CX2]=[NX2] + +Orthocarbonic_derivatives: [CX4H0]([O,S,#7])([O,S,#7])([O,S,#7])[O,S,#7,F,Cl,Br,I] +# halogen allowed just once, to avoid mapping to -OCF3 and similar groups (much more +# stable as for example C(OCH3)4) + + +# I.6 Aromatics +# ------------- + +# I know that this classification is not very logical, arylamines are found under I.2 ... + +Phenol: [OX2H][c] + +1,2-Diphenol: [OX2H][c][c][OX2H] + +Arylchloride: [Cl][c] + +Arylfluoride: [F][c] + +Arylbromide: [Br][c] + +Aryliodide: [I][c] + +Arylthiol: [SX2H][c] + +Iminoarene: [c]=[NX2;$([H1]),$([H0][#6;!$([C]=[N,S,O])])] +# N may be substituted with H or C, but not carbonyl or similar +# aromatic atom is always C, not S or P (these are not planar when substituted) + +Oxoarene: [c]=[OX1] + +Thioarene: [c]=[SX1] + +Hetero_N_basic_H: [nX3H1+0] +# as in pyrole. uncharged to exclude pyridinium ions + +Hetero_N_basic_no_H: [nX3H0+0] +# as in N-methylpyrole. uncharged to exclude pyridinium ions + +Hetero_N_nonbasic: [nX2,nX3+] +# as in pyridine, pyridinium + +Hetero_O: [o] + +Hetero_S: [sX2] +# X2 because Daylight's depictmatch falsely describes C1=CS(=O)C=C1 as aromatic +# (is not planar because of lonepair at S) + +Heteroaromatic: [a;!c] + + +# Part II: N, S, P, Si, B +# ======================= + + +# II.1 Nitrogen +# ------------- + +Nitrite: [NX2](=[OX1])[O;$([X2]),$([X1-])] +# hits nitrous acid, its anion, esters, and other O-substituted derivatives + +Thionitrite: [SX2][NX2]=[OX1] + +Nitrate: [$([NX3](=[OX1])(=[OX1])[O;$([X2]),$([X1-])]),$([NX3+]([OX1-])(=[OX1])[O;$([X2]),$([X1-])])] +# hits nitric acid, its anion, esters, and other O-substituted derivatives + +Nitro: [$([NX3](=O)=O),$([NX3+](=O)[O-])][!#8] +# hits nitro groups attached to C,N, ... but not nitrates + +Nitroso: [NX2](=[OX1])[!#7;!#8] +# no nitrites, no nitrosamines + +Azide: [NX1]~[NX2]~[NX2,NX1] +# hits both mesomeric forms, also anion + +Acylazide: [CX3](=[OX1])[NX2]~[NX2]~[NX1] + +Diazo: [$([#6]=[NX2+]=[NX1-]),$([#6-]-[NX2+]#[NX1])] + +Diazonium: [#6][NX2+]#[NX1] + +Nitrosamine: [#7;!$(N*=O)][NX2]=[OX1] + +Nitrosamide: [NX2](=[OX1])N-*=O +# includes nitrososulfonamides + +N-Oxide: [$([#7+][OX1-]),$([#7v5]=[OX1]);!$([#7](~[O])~[O]);!$([#7]=[#7])] +# Hits both forms. Won't hit azoxy, nitro, nitroso, or nitrate. + + +Hydrazine: [NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])][NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])] +# no hydrazides + +Hydrazone: [NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])][NX2]=[#6] + +Hydroxylamine: [NX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6]);!$(NC=[O,N,S])][OX2;$([H1]),$(O[#6;!$(C=[N,O,S])])] +# no discrimination between O-, N-, and O,N-substitution + + +# II.2 Sulfur +# ----------- + +Sulfon: [$([SX4](=[OX1])(=[OX1])([#6])[#6]),$([SX4+2]([OX1-])([OX1-])([#6])[#6])] +# can't be aromatic, thus S and not #16 + +Sulfoxide: [$([SX3](=[OX1])([#6])[#6]),$([SX3+]([OX1-])([#6])[#6])] + +Sulfonium: [S+;!$([S]~[!#6]);!$([S]*~[#7,#8,#15,#16])] +# can't be aromatic, thus S and not #16 + +Sulfuric_acid: [SX4](=[OX1])(=[OX1])([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])] +# includes anions + +Sulfuric_monoester: [SX4](=[OX1])(=[OX1])([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])] + +Sulfuric_diester: [SX4](=[OX1])(=[OX1])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])] + +Sulfuric_monoamide: [SX4](=[OX1])(=[OX1])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[$([OX2H]),$([OX1-])] + +Sulfuric_diamide: [SX4](=[OX1])(=[OX1])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] + +Sulfuric_esteramide: [SX4](=[OX1])(=[OX1])([#7X3][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])] + +Sulfuric_derivative: [SX4D4](=[!#6])(=[!#6])([!#6])[!#6] +# everything else (would not be a "true" derivative of sulfuric acid, if one of the substituents were less electronegative +# than sulfur, but this should be very very rare, anyway) + + + +#### sulfurous acid and derivatives missing!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! + + + + +Sulfonic_acid: [SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[$([OX2H]),$([OX1-])] + +Sulfonamide: [SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] + +Sulfonic_ester: [SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[OX2][#6;!$(C=[O,N,S])] + +Sulfonic_halide: [SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[FX1,ClX1,BrX1,IX1] + +Sulfonic_derivative: [SX4;$([H1]),$([H0][#6])](=[!#6])(=[!#6])[!#6] +# includes all of the above and many more +# for comparison: this is what "all sulfonic derivatives but not the ones above" would look like: +# [$([SX4;$([H1]),$([H0][#6])](=[!#6])(=[!#6;!O])[!#6]),$([SX4;$([H1]),$([H0][#6])](=[OX1])(=[OX1])[!$([FX1,ClX1,BrX1,IX1]);!$([#6]);!$([OX2H]);!$([OX1-]);!$([OX2][#6;!$(C=[O,N,S])]);!$([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])])] + + +Sulfinic_acid: [SX3;$([H1]),$([H0][#6])](=[OX1])[$([OX2H]),$([OX1-])] + +Sulfinic_amide: [SX3;$([H1]),$([H0][#6])](=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] + +Sulfinic_ester: [SX3;$([H1]),$([H0][#6])](=[OX1])[OX2][#6;!$(C=[O,N,S])] + +Sulfinic_halide: [SX3;$([H1]),$([H0][#6])](=[OX1])[FX1,ClX1,BrX1,IX1] + +Sulfinic_derivative: [SX3;$([H1]),$([H0][#6])](=[!#6])[!#6] + +Sulfenic_acid: [SX2;$([H1]),$([H0][#6])][$([OX2H]),$([OX1-])] + +Sulfenic_amide: [SX2;$([H1]),$([H0][#6])][#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] + +Sulfenic_ester: [SX2;$([H1]),$([H0][#6])][OX2][#6;!$(C=[O,N,S])] + +Sulfenic_halide: [SX2;$([H1]),$([H0][#6])][FX1,ClX1,BrX1,IX1] + +Sulfenic_derivative: [SX2;$([H1]),$([H0][#6])][!#6] + + +# II.3 Phosphorous +# ---------------- + +Phosphine: [PX3;$([H3]),$([H2][#6]),$([H1]([#6])[#6]),$([H0]([#6])([#6])[#6])] +# similar to amine, but less restrictive: includes also amide- and aminal-analogues + +Phosphine_oxide: [PX4;$([H3]=[OX1]),$([H2](=[OX1])[#6]),$([H1](=[OX1])([#6])[#6]),$([H0](=[OX1])([#6])([#6])[#6])] + +Phosphonium: [P+;!$([P]~[!#6]);!$([P]*~[#7,#8,#15,#16])] +# similar to Ammonium + +Phosphorylen: [PX4;$([H3]=[CX3]),$([H2](=[CX3])[#6]),$([H1](=[CX3])([#6])[#6]),$([H0](=[CX3])([#6])([#6])[#6])] + + +# conventions for the following acids and derivatives: +# acids find protonated and deprotonated acids +# esters do not find mixed anhydrides ( ...P-O-C(=O)) +# derivatives: subtituents which go in place of the OH and =O are not H or C (may also be O, +# thus including acids and esters) + +Phosphonic_acid: [PX4;$([H1]),$([H0][#6])](=[OX1])([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])] +# includes anions + +Phosphonic_monoester: [PX4;$([H1]),$([H0][#6])](=[OX1])([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])] + +Phosphonic_diester: [PX4;$([H1]),$([H0][#6])](=[OX1])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])] + +Phosphonic_monoamide: [PX4;$([H1]),$([H0][#6])](=[OX1])([$([OX2H]),$([OX1-])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] + +Phosphonic_diamide: [PX4;$([H1]),$([H0][#6])](=[OX1])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] + +Phosphonic_esteramide: [PX4;$([H1]),$([H0][#6])](=[OX1])([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] + +Phosphonic_acid_derivative: [PX4;$([H1]),$([H0][#6])](=[!#6])([!#6])[!#6] +# all of the above and much more + + +Phosphoric_acid: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])] +# includes anions + +Phosphoric_monoester: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])] + +Phosphoric_diester: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])] + +Phosphoric_triester: [PX4D4](=[OX1])([OX2][#6;!$(C=[O,N,S])])([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])] + +Phosphoric_monoamide: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([$([OX2H]),$([OX1-])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] + +Phosphoric_diamide: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] + +Phosphoric_triamide: [PX4D4](=[OX1])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] + +Phosphoric_monoestermonoamide: [PX4D4](=[OX1])([$([OX2H]),$([OX1-])])([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] + +Phosphoric_diestermonoamide: [PX4D4](=[OX1])([OX2][#6;!$(C=[O,N,S])])([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] + +Phosphoric_monoesterdiamide: [PX4D4](=[OX1])([OX2][#6;!$(C=[O,N,S])])([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] + +Phosphoric_acid_derivative: [PX4D4](=[!#6])([!#6])([!#6])[!#6] + + +Phosphinic_acid: [PX4;$([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[OX1])[$([OX2H]),$([OX1-])] + +Phosphinic_ester: [PX4;$([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[OX1])[OX2][#6;!$(C=[O,N,S])] + +Phosphinic_amide: [PX4;$([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] + +Phosphinic_acid_derivative: [PX4;$([H2]),$([H1][#6]),$([H0]([#6])[#6])](=[!#6])[!#6] + + +Phosphonous_acid: [PX3;$([H1]),$([H0][#6])]([$([OX2H]),$([OX1-])])[$([OX2H]),$([OX1-])] + +Phosphonous_monoester: [PX3;$([H1]),$([H0][#6])]([$([OX2H]),$([OX1-])])[OX2][#6;!$(C=[O,N,S])] + +Phosphonous_diester: [PX3;$([H1]),$([H0][#6])]([OX2][#6;!$(C=[O,N,S])])[OX2][#6;!$(C=[O,N,S])] + +Phosphonous_monoamide: [PX3;$([H1]),$([H0][#6])]([$([OX2H]),$([OX1-])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] + +Phosphonous_diamide: [PX3;$([H1]),$([H0][#6])]([#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] + +Phosphonous_esteramide: [PX3;$([H1]),$([H0][#6])]([OX2][#6;!$(C=[O,N,S])])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] + +Phosphonous_derivatives: [PX3;$([D2]),$([D3][#6])]([!#6])[!#6] + + +Phosphinous_acid: [PX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6])][$([OX2H]),$([OX1-])] + +Phosphinous_ester: [PX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6])][OX2][#6;!$(C=[O,N,S])] + +Phosphinous_amide: [PX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6])][#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])] + +Phosphinous_derivatives: [PX3;$([H2]),$([H1][#6]),$([H0]([#6])[#6])][!#6] + + +# II.4 Silicon +# ------------ + +Quart_silane: [SiX4]([#6])([#6])([#6])[#6] +# four C-substituents. non-reactive, non-toxic, in experimental phase for drug development + +Non-quart_silane: [SiX4;$([H1]([#6])([#6])[#6]),$([H2]([#6])[#6]),$([H3][#6]),$([H4])] +# has 1-4 hydride(s), reactive. Daylight's depictmatch does not add hydrogens automatically to +# the free positions at Si, thus Hs had to be added implicitly + +Silylmonohalide: [SiX4]([FX1,ClX1,BrX1,IX1])([#6])([#6])[#6] +# reagents for inserting protection groups + +Het_trialkylsilane: [SiX4]([!#6])([#6])([#6])[#6] +# mostly acid-labile protection groups such as trimethylsilyl-ethers + +Dihet_dialkylsilane: [SiX4]([!#6])([!#6])([#6])[#6] + +Trihet_alkylsilane: [SiX4]([!#6])([!#6])([!#6])[#6] + +Silicic_acid_derivative: [SiX4]([!#6])([!#6])([!#6])[!#6] +# four substituent which are neither C nor H + + +# II.5 Boron +# ---------- + +Trialkylborane: [BX3]([#6])([#6])[#6] +# also carbonyls allowed + +Boric_acid_derivatives: [BX3]([!#6])([!#6])[!#6] +# includes acids, esters, amides, ... H-substituent at B is very rare. + +Boronic_acid_derivative: [BX3]([!#6])([!#6])[!#6] +# # includes acids, esters, amides, ... + +Borohydride: [BH1,BH2,BH3,BH4] +# at least one H attached to B + +Quaternary_boron: [BX4] +# mostly borates (negative charge), in complex with Lewis-base + + + +# Part III: Some Special Patterns +# =============================== + + +# III.1 Chains +# ------------ + +# some simple chains + + + +# III.2 Rings +# ----------- + +Aromatic: a + +Heterocyclic: [!#6;!R0] +# may be aromatic or not + +Epoxide: [OX2r3]1[#6r3][#6r3]1 +# toxic/reactive. may be annelated to aromat, but must not be aromatic itself (oxirane-2,3-dione) + +NH_aziridine: [NX3H1r3]1[#6r3][#6r3]1 +# toxic/reactive according to Maybridge's garbage filter + +Spiro: [D4R;$(*(@*)(@*)(@*)@*)] +# at least two different rings can be found which are sharing just one atom. +# these two rings can be connected by a third ring, so it matches also some +# bridged systems, like morphine + +Annelated_rings: [R;$(*(@*)(@*)@*);!$([R2;$(*(@*)(@*)(@*)@*)])]@[R;$(*(@*)(@*)@*);!$([R2;$(*(@*)(@*)(@*)@*)])] +# two different rings sharing exactly two atoms + +Bridged_rings: [R;$(*(@*)(@*)@*);!$([D4R;$(*(@*)(@*)(@*)@*)]);!$([R;$(*(@*)(@*)@*);!$([R2;$(*(@*)(@*)(@*)@*)])]@[R;$(*(@*)(@*)@*);!$([R2;$(*(@*)(@*)(@*)@*)])])] +# part of two or more rings, not spiro, not annelated -> finds bridgehead atoms, +# but only if they are not annelated at the same time - otherwise impossible (?) +# to distinguish from non-bridgehead annelated atoms + +# some basic ring-patterns (just size, no other information): + + + + + +# III.3 Sugars and Nucleosides/Nucleotides, Steroids +# -------------------------------------------------- + +# because of the large variety of sugar derivatives, different patterns can be applied. +# The choice of patterns and their combinations will depend on the contents of the database +# e.g. natural products, nucleoside analoges with modified sugars, ... as well as on the +# desired restriction + + +Sugar_pattern_1: [OX2;$([r5]1@C@C@C(O)@C1),$([r6]1@C@C@C(O)@C(O)@C1)] +# 5 or 6-membered ring containing one O and at least one (r5) or two (r6) oxygen-substituents. + +Sugar_pattern_2: [OX2;$([r5]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)] +# 5 or 6-membered ring containing one O and an acetal-like bond at postion 2. + +Sugar_pattern_combi: [OX2;$([r5]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C(O)@C1),$([r6]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C(O)@C(O)@C1)] +# combination of the two above + +Sugar_pattern_2_reducing: [OX2;$([r5]1@C(!@[OX2H1])@C@C@C1),$([r6]1@C(!@[OX2H1])@C@C@C@C1)] +# 5 or 6-membered cyclic hemi-acetal + +Sugar_pattern_2_alpha: [OX2;$([r5]1@[C@@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@[C@@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)] +# 5 or 6-membered cyclic hemi-acetal + +Sugar_pattern_2_beta: [OX2;$([r5]1@[C@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@[C@](!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)] +# 5 or 6-membered cyclic hemi-acetal + +##Poly_sugar_1: ([OX2;$([r5]1@C@C@C(O)@C1),$([r6]1@C@C@C(O)@C(O)@C1)].[OX2;$([r5]1@C@C@C(O)@C1),$([r6]1@C@C@C(O)@C(O)@C1)]) +# pattern1 occours more than once (in same molecule, but moieties don't have to be adjacent!) + +##Poly_sugar_2: ([OX2;$([r5]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)].[OX2;$([r5]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C1),$([r6]1@C(!@[OX2,NX3,SX2,FX1,ClX1,BrX1,IX1])@C@C@C@C1)]) +# pattern2 occours more than once (in same molecule, but moieties don't have to be adjacent!) + + +# III.4 Everything else... +# ------------------------ + +Conjugated_double_bond: *=*[*]=,#,:[*] + +Conjugated_tripple_bond: *#*[*]=,#,:[*] + +Cis_double_bond: */[D2]=[D2]\* +# only one single-bonded substituent on each DB-atom. no aromats. +# only found when character of DB is explicitely stated. + +Trans_double_bond: */[D2]=[D2]/* +# analog + +Mixed_anhydrides: [$(*=O),$([#16,#14,#5]),$([#7]([#6]=[OX1]))][#8X2][$(*=O),$([#16,#14,#5]),$([#7]([#6]=[OX1]))] +# should hits all combinations of two acids + +Halogen_on_hetero: [FX1,ClX1,BrX1,IX1][!#6] + +Halogen_multi_subst: [F,Cl,Br,I;!$([X1]);!$([X0-])] +# Halogen which is not mono-substituted nor an anion, e.g. chlorate. +# Most of these cases should be also filtered by Halogen_on_hetero. + +Trifluoromethyl: [FX1][CX4;!$([H0][Cl,Br,I]);!$([F][C]([F])([F])[F])]([FX1])([FX1]) +# C with three F attached, connected to anything which is not another halogen + +C_ONS_bond: [#6]~[#7,#8,#16] +# probably all drug-like molecules have at least one O, N, or S connected to a C -> nice filter + +## Mixture: (*).(*) +# two or more seperate parts, may also be salt +# component-level grouping is not yet supported in Open Babel Version 2.0 + + +Charged: [!+0] + +Anion: [-1,-2,-3,-4,-5,-6,-7] + +Kation: [+1,+2,+3,+4,+5,+6,+7] + +Salt: ([-1,-2,-3,-4,-5,-6,-7]).([+1,+2,+3,+4,+5,+6,+7]) +# two or more seperate components with opposite charges + +##Zwitterion: ([-1,-2,-3,-4,-5,-6,-7].[+1,+2,+3,+4,+5,+6,+7]) +# both negative and positive charges somewhere within the same molecule. + +1,3-Tautomerizable: [$([#7X2,OX1,SX1]=*[!H0;!$([a;!n])]),$([#7X3,OX2,SX2;!H0]*=*),$([#7X3,OX2,SX2;!H0]*:n)] +# 1,3 migration of H allowed. Includes keto/enol and amide/enamide. +# Aromatic rings must stay aromatic - no keto form of phenol + +1,5-Tautomerizable: [$([#7X2,OX1,SX1]=,:**=,:*[!H0;!$([a;!n])]),$([#7X3,OX2,SX2;!H0]*=**=*),$([#7X3,OX2,SX2;!H0]*=,:**:n)] + +Rotatable_bond: [!$(*#*)&!D1]-!@[!$(*#*)&!D1] +# taken from http://www.daylight.com/support/contrib/smarts/content.html + +Michael_acceptor: [CX3]=[CX3][$([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-])] +# the classical case: C=C near carbonyl, nitrile, nitro, or similar +# Oxo-heteroaromats and similar are not included. + +Dicarbodiazene: [CX3](=[OX1])[NX2]=[NX2][CX3](=[OX1]) +# Michael-like acceptor, see Mitsunobu reaction + +# H-Bond_donor: + +# H-Bond_acceptor: + +# Pos_ionizable: + +# Neg_ionizable: + +# Unlikely_ions: +# O+,N-,C+,C-, ... + +CH-acidic: [$([CX4;!$([H0]);!$(C[!#6;!$([P,S]=O);!$(N(~O)~O)])][$([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-]);!$(*[S,O,N;H1,H2]);!$([*+0][S,O;X1-])]),$([CX4;!$([H0])]1[CX3]=[CX3][CX3]=[CX3]1)] +# C-H alpha to carbony, nitro or similar, C is not double-bonded, only C, H, S,P=O and nitro substituents allowed. +# pentadiene is included. acids, their salts, prim./sec. amides, and imides are excluded. +# hits also CH-acidic_strong + +CH-acidic_strong: [CX4;!$([H0]);!$(C[!#6;!$([P,S]=O);!$(N(~O)~O)])]([$([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-]);!$(*[S,O,N;H1,H2]);!$([*+0][S,O;X1-])])[$([CX3]=[O,N,S]),$(C#[N]),$([S,P]=[OX1]),$([NX3]=O),$([NX3+](=O)[O-]);!$(*[S,O,N;H1,H2]);!$([*+0][S,O;X1-])] +# same as above (without pentadiene), but carbonyl or similar on two or three sides + +Chiral_center_specified: [$([*@](~*)(~*)(*)*),$([*@H](*)(*)*),$([*@](~*)(*)*),$([*@H](~*)~*)] +# Hits atoms with tetrahedral chirality, if chiral center is specified in the SMILES string +# depictmach does not find oxonium, sulfonium, or sulfoxides! + +# Chiral_center_unspecified: [$([*@?](~*)(~*)(*)*),$([*@?H](*)(*)*),$([*@?](~*)(*)*),$([*@?H](~*)~*)] +# Hits atoms with tetrahedral chirality, if chiral center is not specified in the SMILES string +# "@?" (unspecified chirality) is not yet supported in Open Babel Version 2.0 + \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/UFF.prm Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,274 @@ +# +# Open Babel file: UFF.prm +# +# Force field parameters for UFF, the Universal Force Field +# Used by OBForceField and OBUFFForceField +# +# J. Am. Chem. Soc. (1992) 114(25) p. 10024-10035. +# The parameters in this file are taken from the UFF implementation in RDKit +# http://rdkit.org/ +# +# Atom typing rules are based on UFF published atom descriptions +# atom [SMARTS] [atomtype] [description] +# These must be sorted according to the element and complexity +# of the type rule (i.e., generic rules first, more specific rules later) +# +# Parameters follow later +# param Atom r1 theta0 x1 D1 zeta Z1 Vi Uj Xi Hard Radius + +atom [#1] H_ Generic hydrogen +atom [#1D2] H_b Bridging hydrogen +atom [#2] He4+4 Helium +atom [#3] Li Lithium +atom [#4] Be3+2 Generic Be +atom [#5] B_2 Trigonal planar boron +atom [#5D4] B_3 Tetrahedral boron +atom [#6] C_3 Generic sp3 C +atom [C^2] C_2 sp2 non-aromatic C +atom [C^1] C_1 sp hybridized C +atom [c] C_R aromatic C +atom [#7] N_3 Generic sp3 N +atom [N^2] N_2 sp2 non-aromatic N +atom [N^1] N_1 sp hybridized N +atom [n] N_R aromatic N +atom [#8] O_3 generic, sp3 hybridized O +atom [#8][#14] O_3_z sp3 hybridized O for zeolites +atom [O^2] O_2 sp2 hybridized O +atom [O^1] O_1 sp hybridized O +atom [o] O_R aromatic O +atom [#9] F_ generic F +atom [#10] Ne4+4 +atom [#11] Na +atom [#12] Mg3+2 +atom [#13] Al3 +atom [#14] Si3 +#atom [#15] P_3+q Organometallic phosphine ligands +atom [#15] P_3+3 generic phosphorus +atom [#15D5] P_3+5 formal charge +5 +atom [#16] S_3+2 generic S +atom [#16+4] S_3+4 S+4 ( SO2 ) +atom [#16+6] S_3+6 S+6 ( SO3 / H2SO4 ) +atom [S^2] S_2 non-aromatic sp2 S +atom [s] S_R aromatic S +atom [#17] Cl +atom [#18] Ar4+4 +atom [#19] K_ +atom [#20] Ca6+2 +atom [#21] Sc3+3 +atom [#22] Ti6+4 generic Ti (6-valent) +atom [#22D3] Ti3+4 +atom [#23] V_3+5 +atom [#24] Cr6+3 +atom [#25] Mn6+2 +atom [#26] Fe6+2 generic Fe (6-valent) +atom [#26D3] Fe3+2 +atom [#27] Co6+3 +atom [#28] Ni4+2 +atom [#29] Cu3+1 +atom [#30] Zn3+2 +atom [#31] Ga3+3 +atom [#32] Ge3 +atom [#33] As3+3 +atom [#34] Se3+2 +atom [#35] Br +atom [#36] Kr4+4 +atom [#37] Rb +atom [#38] Sr6+2 +atom [#39] Y_3+3 +atom [#40] Zr3+4 +atom [#41] Nb3+5 +atom [#42] Mo6+6 generic Mo (6-valent) +atom [#42D3] Mo3+6 trivalent Mo +atom [#43] Tc6+5 +atom [#44] Ru6+2 +atom [#45] Rh6+3 +atom [#46] Pd4+2 +atom [#47] Ag1+1 +atom [#48] Cd3+2 +atom [#49] In3+3 +atom [#50] Sn3 +atom [#51] Sb3+3 +atom [#52] Te3+2 +atom [#53] I_ +atom [#54] Xe4+4 +atom [#55] Cs +atom [#56] Ba6+2 +atom [#57] La3+3 +atom [#58] Ce6+3 +atom [#59] Pr6+3 +atom [#60] Nd6+3 +atom [#61] Pm6+3 +atom [#62] Sm6+3 +atom [#63] Eu6+3 +atom [#64] Gd6+3 +atom [#65] Tb6+3 +atom [#66] Dy6+3 +atom [#67] Ho6+3 +atom [#68] Er6+3 +atom [#69] Tm6+3 +atom [#70] Yb6+3 +atom [#71] Lu6+3 +atom [#72] Hf3+4 +atom [#73] Ta3+5 +atom [#74] W_6+6 generic W (6-valent) +atom [#74D3+4] W_3+4 +atom [#74D3+6] W_3+6 +atom [#75] Re6+5 generic Re (6-valent) +atom [#75D3] Re3+7 trivalent Re +atom [#76] Os6+6 +atom [#77] Ir6+3 +atom [#78] Pt4+2 +atom [#79] Au4+3 +atom [#80] Hg1+2 +atom [#81] Tl3+3 +atom [#82] Pb3 +atom [#83] Bi3+3 +atom [#84] Po3+2 +atom [#85] At +atom [#86] Rn4+4 +atom [#87] Fr +atom [#88] Ra6+2 +atom [#89] Ac6+3 +atom [#90] Th6+4 +atom [#91] Pa6+4 +atom [#92] U_6+4 +atom [#93] Np6+4 +atom [#94] Pu6+4 +atom [#95] Am6+4 +atom [#96] Cm6+3 +atom [#97] Bk6+3 +atom [#98] Cf6+3 +atom [#99] Es6+3 +atom [#100] Fm6+3 +atom [#101] Md6+3 +atom [#102] No6+3 +atom [#103] Lw6+3 + +# Atom r1 theta0 x1 D1 zeta Z1 Vi Uj Xi Hard Radius +param H_ 0.354 180 2.886 0.044 12 0.712 0 0 4.528 6.9452 0.371 +param H_b 0.46 83.5 2.886 0.044 12 0.712 0 0 4.528 6.9452 0.371 +param He4+4 0.849 90 2.362 0.056 15.24 0.098 0 0 9.66 14.92 1.3 +param Li 1.336 180 2.451 0.025 12 1.026 0 2 3.006 2.386 1.557 +param Be3+2 1.074 109.47 2.745 0.085 12 1.565 0 2 4.877 4.443 1.24 +param B_3 0.838 109.47 4.083 0.18 12.052 1.755 0 2 5.11 4.75 0.822 +param B_2 0.828 120 4.083 0.18 12.052 1.755 0 2 5.11 4.75 0.822 +param C_3 0.757 109.47 3.851 0.105 12.73 1.912 2.119 2 5.343 5.063 0.759 +param C_R 0.729 120 3.851 0.105 12.73 1.912 0 2 5.343 5.063 0.759 +param C_2 0.732 120 3.851 0.105 12.73 1.912 0 2 5.343 5.063 0.759 +param C_1 0.706 180 3.851 0.105 12.73 1.912 0 2 5.343 5.063 0.759 +param N_3 0.7 106.7 3.66 0.069 13.407 2.544 0.45 2 6.899 5.88 0.715 +param N_R 0.699 120 3.66 0.069 13.407 2.544 0 2 6.899 5.88 0.715 +param N_2 0.685 111.2 3.66 0.069 13.407 2.544 0 2 6.899 5.88 0.715 +param N_1 0.656 180 3.66 0.069 13.407 2.544 0 2 6.899 5.88 0.715 +param O_3 0.658 104.51 3.5 0.06 14.085 2.3 0.018 2 8.741 6.682 0.669 +param O_3_z 0.528 146 3.5 0.06 14.085 2.3 0.018 2 8.741 6.682 0.669 +param O_R 0.68 110 3.5 0.06 14.085 2.3 0 2 8.741 6.682 0.669 +param O_2 0.634 120 3.5 0.06 14.085 2.3 0 2 8.741 6.682 0.669 +param O_1 0.639 180 3.5 0.06 14.085 2.3 0 2 8.741 6.682 0.669 +param F_ 0.668 180 3.364 0.05 14.762 1.735 0 2 10.874 7.474 0.706 +param Ne4+4 0.92 90 3.243 0.042 15.44 0.194 0 2 11.04 10.55 1.768 +param Na 1.539 180 2.983 0.03 12 1.081 0 1.25 2.843 2.296 2.085 +param Mg3+2 1.421 109.47 3.021 0.111 12 1.787 0 1.25 3.951 3.693 1.5 +param Al3 1.244 109.47 4.499 0.505 11.278 1.792 0 1.25 4.06 3.59 1.201 +param Si3 1.117 109.47 4.295 0.402 12.175 2.323 1.225 1.25 4.168 3.487 1.176 +param P_3+3 1.101 93.8 4.147 0.305 13.072 2.863 2.4 1.25 5.463 4 1.102 +param P_3+5 1.056 109.47 4.147 0.305 13.072 2.863 2.4 1.25 5.463 4 1.102 +param P_3+q 1.056 109.47 4.147 0.305 13.072 2.863 2.4 1.25 5.463 4 1.102 +param S_3+2 1.064 92.1 4.035 0.274 13.969 2.703 0.484 1.25 6.928 4.486 1.047 +param S_3+4 1.049 103.2 4.035 0.274 13.969 2.703 0.484 1.25 6.928 4.486 1.047 +param S_3+6 1.027 109.47 4.035 0.274 13.969 2.703 0.484 1.25 6.928 4.486 1.047 +param S_R 1.077 92.2 4.035 0.274 13.969 2.703 0 1.25 6.928 4.486 1.047 +param S_2 0.854 120 4.035 0.274 13.969 2.703 0 1.25 6.928 4.486 1.047 +param Cl 1.044 180 3.947 0.227 14.866 2.348 0 1.25 8.564 4.946 0.994 +param Ar4+4 1.032 90 3.868 0.185 15.763 0.3 0 1.25 9.465 6.355 2.108 +param K_ 1.953 180 3.812 0.035 12 1.165 0 0.7 2.421 1.92 2.586 +param Ca6+2 1.761 90 3.399 0.238 12 2.141 0 0.7 3.231 2.88 2 +param Sc3+3 1.513 109.47 3.295 0.019 12 2.592 0 0.7 3.395 3.08 1.75 +param Ti3+4 1.412 109.47 3.175 0.017 12 2.659 0 0.7 3.47 3.38 1.607 +param Ti6+4 1.412 90 3.175 0.017 12 2.659 0 0.7 3.47 3.38 1.607 +param V_3+5 1.402 109.47 3.144 0.016 12 2.679 0 0.7 3.65 3.41 1.47 +param Cr6+3 1.345 90 3.023 0.015 12 2.463 0 0.7 3.415 3.865 1.402 +param Mn6+2 1.382 90 2.961 0.013 12 2.43 0 0.7 3.325 4.105 1.533 +param Fe3+2 1.27 109.47 2.912 0.013 12 2.43 0 0.7 3.76 4.14 1.393 +param Fe6+2 1.335 90 2.912 0.013 12 2.43 0 0.7 3.76 4.14 1.393 +param Co6+3 1.241 90 2.872 0.014 12 2.43 0 0.7 4.105 4.175 1.406 +param Ni4+2 1.164 90 2.834 0.015 12 2.43 0 0.7 4.465 4.205 1.398 +param Cu3+1 1.302 109.47 3.495 0.005 12 1.756 0 0.7 4.2 4.22 1.434 +param Zn3+2 1.193 109.47 2.763 0.124 12 1.308 0 0.7 5.106 4.285 1.4 +param Ga3+3 1.26 109.47 4.383 0.415 11 1.821 0 0.7 3.641 3.16 1.211 +param Ge3 1.197 109.47 4.28 0.379 12 2.789 0.701 0.7 4.051 3.438 1.189 +param As3+3 1.211 92.1 4.23 0.309 13 2.864 1.5 0.7 5.188 3.809 1.204 +param Se3+2 1.19 90.6 4.205 0.291 14 2.764 0.335 0.7 6.428 4.131 1.224 +param Br 1.192 180 4.189 0.251 15 2.519 0 0.7 7.79 4.425 1.141 +param Kr4+4 1.147 90 4.141 0.22 16 0.452 0 0.7 8.505 5.715 2.27 +param Rb 2.26 180 4.114 0.04 12 1.592 0 0.2 2.331 1.846 2.77 +param Sr6+2 2.052 90 3.641 0.235 12 2.449 0 0.2 3.024 2.44 2.415 +param Y_3+3 1.698 109.47 3.345 0.072 12 3.257 0 0.2 3.83 2.81 1.998 +param Zr3+4 1.564 109.47 3.124 0.069 12 3.667 0 0.2 3.4 3.55 1.758 +param Nb3+5 1.473 109.47 3.165 0.059 12 3.618 0 0.2 3.55 3.38 1.603 +param Mo6+6 1.467 90 3.052 0.056 12 3.4 0 0.2 3.465 3.755 1.53 +param Mo3+6 1.484 109.47 3.052 0.056 12 3.4 0 0.2 3.465 3.755 1.53 +param Tc6+5 1.322 90 2.998 0.048 12 3.4 0 0.2 3.29 3.99 1.5 +param Ru6+2 1.478 90 2.963 0.056 12 3.4 0 0.2 3.575 4.015 1.5 +param Rh6+3 1.332 90 2.929 0.053 12 3.5 0 0.2 3.975 4.005 1.509 +param Pd4+2 1.338 90 2.899 0.048 12 3.21 0 0.2 4.32 4 1.544 +param Ag1+1 1.386 180 3.148 0.036 12 1.956 0 0.2 4.436 3.134 1.622 +param Cd3+2 1.403 109.47 2.848 0.228 12 1.65 0 0.2 5.034 3.957 1.6 +param In3+3 1.459 109.47 4.463 0.599 11 2.07 0 0.2 3.506 2.896 1.404 +param Sn3 1.398 109.47 4.392 0.567 12 2.961 0.199 0.2 3.987 3.124 1.354 +param Sb3+3 1.407 91.6 4.42 0.449 13 2.704 1.1 0.2 4.899 3.342 1.404 +param Te3+2 1.386 90.25 4.47 0.398 14 2.882 0.3 0.2 5.816 3.526 1.38 +param I_ 1.382 180 4.5 0.339 15 2.65 0 0.2 6.822 3.762 1.333 +param Xe4+4 1.267 90 4.404 0.332 12 0.556 0 0.2 7.595 4.975 2.459 +param Cs 2.57 180 4.517 0.045 12 1.573 0 0.1 2.183 1.711 2.984 +param Ba6+2 2.277 90 3.703 0.364 12 2.727 0 0.1 2.814 2.396 2.442 +param La3+3 1.943 109.47 3.522 0.017 12 3.3 0 0.1 2.8355 2.7415 2.071 +param Ce6+3 1.841 90 3.556 0.013 12 3.3 0 0.1 2.774 2.692 1.925 +param Pr6+3 1.823 90 3.606 0.01 12 3.3 0 0.1 2.858 2.564 2.007 +param Nd6+3 1.816 90 3.575 0.01 12 3.3 0 0.1 2.8685 2.6205 2.007 +param Pm6+3 1.801 90 3.547 0.009 12 3.3 0 0.1 2.881 2.673 2 +param Sm6+3 1.78 90 3.52 0.008 12 3.3 0 0.1 2.9115 2.7195 1.978 +param Eu6+3 1.771 90 3.493 0.008 12 3.3 0 0.1 2.8785 2.7875 2.227 +param Gd6+3 1.735 90 3.368 0.009 12 3.3 0 0.1 3.1665 2.9745 1.968 +param Tb6+3 1.732 90 3.451 0.007 12 3.3 0 0.1 3.018 2.834 1.954 +param Dy6+3 1.71 90 3.428 0.007 12 3.3 0 0.1 3.0555 2.8715 1.934 +param Ho6+3 1.696 90 3.409 0.007 12 3.416 0 0.1 3.127 2.891 1.925 +param Er6+3 1.673 90 3.391 0.007 12 3.3 0 0.1 3.1865 2.9145 1.915 +param Tm6+3 1.66 90 3.374 0.006 12 3.3 0 0.1 3.2514 2.9329 2 +param Yb6+3 1.637 90 3.355 0.228 12 2.618 0 0.1 3.2889 2.965 2.158 +param Lu6+3 1.671 90 3.64 0.041 12 3.271 0 0.1 2.9629 2.4629 1.896 +param Hf3+4 1.611 109.47 3.141 0.072 12 3.921 0 0.1 3.7 3.4 1.759 +param Ta3+5 1.511 109.47 3.17 0.081 12 4.075 0 0.1 5.1 2.85 1.605 +param W_6+6 1.392 90 3.069 0.067 12 3.7 0 0.1 4.63 3.31 1.538 +param W_3+4 1.526 109.47 3.069 0.067 12 3.7 0 0.1 4.63 3.31 1.538 +param W_3+6 1.38 109.47 3.069 0.067 12 3.7 0 0.1 4.63 3.31 1.538 +param Re6+5 1.372 90 2.954 0.066 12 3.7 0 0.1 3.96 3.92 1.6 +param Re3+7 1.314 109.47 2.954 0.066 12 3.7 0 0.1 3.96 3.92 1.6 +param Os6+6 1.372 90 3.12 0.037 12 3.7 0 0.1 5.14 3.63 1.7 +param Ir6+3 1.371 90 2.84 0.073 12 3.731 0 0.1 5 4 1.866 +param Pt4+2 1.364 90 2.754 0.08 12 3.382 0 0.1 4.79 4.43 1.557 +param Au4+3 1.262 90 3.293 0.039 12 2.625 0 0.1 4.894 2.586 1.618 +param Hg1+2 1.34 180 2.705 0.385 12 1.75 0 0.1 6.27 4.16 1.6 +param Tl3+3 1.518 120 4.347 0.68 11 2.068 0 0.1 3.2 2.9 1.53 +param Pb3 1.459 109.47 4.297 0.663 12 2.846 0.1 0.1 3.9 3.53 1.444 +param Bi3+3 1.512 90 4.37 0.518 13 2.47 1 0.1 4.69 3.74 1.514 +param Po3+2 1.5 90 4.709 0.325 14 2.33 0.3 0.1 4.21 4.21 1.48 +param At 1.545 180 4.75 0.284 15 2.24 0 0.1 4.75 4.75 1.47 +param Rn4+4 1.42 90 4.765 0.248 16 0.583 0 0.1 5.37 5.37 2.2 +param Fr 2.88 180 4.9 0.05 12 1.847 0 0 2 2 2.3 +param Ra6+2 2.512 90 3.677 0.404 12 2.92 0 0 2.843 2.434 2.2 +param Ac6+3 1.983 90 3.478 0.033 12 3.9 0 0 2.835 2.835 2.108 +param Th6+4 1.721 90 3.396 0.026 12 4.202 0 0 3.175 2.905 2.018 +param Pa6+4 1.711 90 3.424 0.022 12 3.9 0 0 2.985 2.905 1.8 +param U_6+4 1.684 90 3.395 0.022 12 3.9 0 0 3.341 2.853 1.713 +param Np6+4 1.666 90 3.424 0.019 12 3.9 0 0 3.549 2.717 1.8 +param Pu6+4 1.657 90 3.424 0.016 12 3.9 0 0 3.243 2.819 1.84 +param Am6+4 1.66 90 3.381 0.014 12 3.9 0 0 2.9895 3.0035 1.942 +param Cm6+3 1.801 90 3.326 0.013 12 3.9 0 0 2.8315 3.1895 1.9 +param Bk6+3 1.761 90 3.339 0.013 12 3.9 0 0 3.1935 3.0355 1.9 +param Cf6+3 1.75 90 3.313 0.013 12 3.9 0 0 3.197 3.101 1.9 +param Es6+3 1.724 90 3.299 0.012 12 3.9 0 0 3.333 3.089 1.9 +param Fm6+3 1.712 90 3.286 0.012 12 3.9 0 0 3.4 3.1 1.9 +param Md6+3 1.689 90 3.274 0.011 12 3.9 0 0 3.47 3.11 1.9 +param No6+3 1.679 90 3.248 0.011 12 3.9 0 0 3.475 3.175 1.9 +param Lw6+3 1.698 90 3.236 0.011 12 3.9 0 0 3.5 3.2 1.9
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/aromatic.h Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,43 @@ +/*************************************************************** +This file is part of the Open Babel project. +This is copyright under the GNU General Public License (GPL) +For more information, see <http://openbabel.org/> + +This file contains a binary representation of data tables + used by Open Babel. It is used as a fallback if the textual + data table is not found at runtime. It is not a normal header. +***************************************************************/ + + +#ifndef OB_AROMATIC_H +#define OB_AROMATIC_H + +namespace OpenBabel +{ +static const char AromaticData[] = { + 0x5B,0x23,0x36,0x72,0x44,0x32,0x5D,0x09,0x09,0x09,0x31,0x09,0x31,0x0A,0x5B, + 0x23,0x36,0x72,0x44,0x33,0x5D,0x7E,0x21,0x40,0x5B,0x23,0x38,0x5D,0x09,0x09, + 0x30,0x09,0x31,0x0A,0x5B,0x23,0x36,0x72,0x44,0x32,0x2B,0x2C,0x23,0x36,0x72, + 0x44,0x33,0x2B,0x5D,0x09,0x09,0x31,0x09,0x31,0x0A,0x5B,0x23,0x36,0x72,0x5D, + 0x3D,0x40,0x2A,0x09,0x09,0x31,0x09,0x31,0x0A,0x5B,0x23,0x36,0x72,0x44,0x33, + 0x5D,0x3D,0x21,0x40,0x2A,0x09,0x09,0x31,0x09,0x31,0x0A,0x5B,0x23,0x36,0x72, + 0x44,0x33,0x5D,0x3D,0x21,0x40,0x5B,0x21,0x23,0x36,0x5D,0x09,0x09,0x30,0x09, + 0x30,0x0A,0x5B,0x23,0x36,0x72,0x44,0x33,0x2D,0x5D,0x09,0x09,0x32,0x09,0x32, + 0x0A,0x5B,0x23,0x37,0x72,0x44,0x32,0x5D,0x09,0x09,0x09,0x31,0x09,0x32,0x0A, + 0x5B,0x23,0x37,0x72,0x44,0x33,0x5D,0x20,0x31,0x20,0x32,0x0A,0x5B,0x23,0x37, + 0x72,0x5D,0x28,0x2D,0x40,0x2A,0x29,0x2D,0x40,0x2A,0x20,0x09,0x09,0x31,0x09, + 0x32,0x0A,0x5B,0x23,0x37,0x72,0x44,0x32,0x5D,0x3D,0x40,0x2A,0x09,0x09,0x31, + 0x09,0x31,0x0A,0x5B,0x23,0x37,0x72,0x44,0x33,0x2B,0x5D,0x09,0x09,0x31,0x09, + 0x31,0x0A,0x5B,0x23,0x37,0x72,0x44,0x33,0x5D,0x3D,0x4F,0x09,0x09,0x31,0x09, + 0x31,0x0A,0x5B,0x23,0x37,0x72,0x44,0x32,0x2D,0x5D,0x09,0x09,0x32,0x09,0x32, + 0x0A,0x5B,0x23,0x38,0x72,0x5D,0x09,0x09,0x09,0x32,0x09,0x32,0x0A,0x5B,0x23, + 0x38,0x72,0x2B,0x5D,0x09,0x09,0x09,0x31,0x09,0x31,0x0A,0x5B,0x23,0x31,0x36, + 0x72,0x44,0x32,0x5D,0x09,0x09,0x32,0x09,0x32,0x0A,0x5B,0x23,0x31,0x36,0x72, + 0x44,0x32,0x2B,0x5D,0x09,0x09,0x31,0x09,0x31,0x0A,0x5B,0x23,0x31,0x36,0x72, + 0x44,0x33,0x5D,0x3D,0x21,0x40,0x4F,0x09,0x09,0x32,0x09,0x32,0x0A,0x5B,0x23, + 0x31,0x35,0x72,0x44,0x33,0x5D,0x09,0x09,0x32,0x09,0x32,0x0A,0x5B,0x23,0x33, + 0x34,0x72,0x44,0x32,0x5D,0x09,0x09,0x32,0x09,0x32,0x0A,0x00}; + +} // namespace OpenBabel +#endif // OB_AROMATIC_H +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/aromatic.txt Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,59 @@ +############################################################################## +# # +# Open Babel file: aromatic.txt # # # +# # +# Copyright (c) 1998-2001 by OpenEye Scientific Software, Inc. # +# Some portions Copyright (c) 2001-2005 Geoffrey R. Hutchison # +# Part of the Open Babel package, under the GNU General Public License (GPL)# +# # +# SMARTS patterns with minimum and maximum pi-electrons contributed to an # +# aromatic system (used by typer.cpp:OBAromaticTyper) # +# The LAST PATTERN MATCHED is used to assign values, so that patterns should # +# be ordered from more general to more specific # +# # +############################################################################## + +#PATTERN MIN MAX + +#carbon patterns +[#6rD2] 1 1 +# exo ketone or alcohol -- don't know which +[#6rD3]~!@[#8] 0 1 +[#6rD2+,#6rD3+] 1 1 +[#6r]=@* 1 1 +[#6rD3]=!@* 1 1 +# external double bonds to hetero atoms contribute no electrons to the +# aromatic systems -- quinoid systems are non-aromatic, e.g. 1,4-benzoquinone +[#6rD3]=!@[!#6] 0 0 +[#6rD3-] 2 2 + +#nitrogen patterns +[#7rD2] 1 2 +[#7rD3] 1 2 +[#7r](-@*)-@* 1 2 +[#7rD2]=@* 1 1 +[#7rD3+] 1 1 +[#7rD3]=O 1 1 +[#7rD2-] 2 2 + +#oxygen patterns +[#8r] 2 2 +[#8r+] 1 1 + +#sulfur patterns +[#16rD2] 2 2 +[#16rD2+] 1 1 +[#16rD3]=!@O 2 2 + +#other misc patterns +# Accounts Chem Res 1978 11 p. 153 +# phosphole, phosphabenzene (not v. aromatic) +[#15rD3] 2 2 +# selenophene +[#34rD2] 2 2 +# arsabenzene, etc. (*really* not v. aromatic) +#[#33rD3] 2 2 +# tellurophene, etc. (*really* not v. aromatic) +#[#52rD2] 2 2 +# stilbabenzene, etc. (very little aromatic character) +#[#51rD3] 2 2
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/atomtyp.h Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,306 @@ +/*************************************************************** +This file is part of the Open Babel project. +This is copyright under the GNU General Public License (GPL) +For more information, see <http://openbabel.org/> + +This file contains a binary representation of data tables + used by Open Babel. It is used as a fallback if the textual + data table is not found at runtime. It is not a normal header. +***************************************************************/ + + +#ifndef OB_ATOMTYP_H +#define OB_ATOMTYP_H + +namespace OpenBabel +{ +static const char AtomTypeData[] = { + 0x49,0x4E,0x54,0x48,0x59,0x42,0x20,0x5B,0x44,0x34,0x5D,0x20,0x33,0x20,0x23, + 0x61,0x6E,0x79,0x20,0x34,0x2D,0x76,0x61,0x6C,0x65,0x6E,0x74,0x20,0x61,0x74, + 0x6F,0x6D,0x20,0x2D,0x2D,0x20,0x74,0x65,0x74,0x72,0x61,0x68,0x65,0x64,0x72, + 0x61,0x6C,0x0A,0x49,0x4E,0x54,0x48,0x59,0x42,0x20,0x5B,0x44,0x35,0x5D,0x20, + 0x35,0x20,0x23,0x61,0x6E,0x79,0x20,0x35,0x2D,0x76,0x61,0x6C,0x65,0x6E,0x74, + 0x20,0x61,0x74,0x6F,0x6D,0x20,0x2D,0x2D,0x20,0x74,0x72,0x69,0x67,0x62,0x69, + 0x70,0x79,0x0A,0x49,0x4E,0x54,0x48,0x59,0x42,0x20,0x5B,0x44,0x36,0x5D,0x20, + 0x36,0x20,0x23,0x61,0x6E,0x79,0x20,0x36,0x2D,0x76,0x61,0x6C,0x65,0x6E,0x74, + 0x20,0x61,0x74,0x6F,0x6D,0x20,0x2D,0x2D,0x20,0x6F,0x63,0x74,0x0A,0x49,0x4E, + 0x54,0x48,0x59,0x42,0x20,0x5B,0x43,0x5D,0x20,0x33,0x20,0x23,0x73,0x70,0x33, + 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0x20,0x5B,0x23,0x31,0x35,0x3B,0x24,0x28,0x5B,0x23,0x31,0x35,0x44,0x34,0x5D, + 0x28,0x7E,0x5B,0x4F,0x44,0x31,0x5D,0x29,0x28,0x7E,0x5B,0x4F,0x44,0x31,0x5D, + 0x29,0x7E,0x5B,0x4F,0x44,0x31,0x5D,0x29,0x5D,0x20,0x50,0x61,0x63,0x0A,0x45, + 0x58,0x54,0x54,0x59,0x50,0x20,0x5B,0x23,0x31,0x35,0x3B,0x24,0x28,0x5B,0x23, + 0x31,0x35,0x44,0x33,0x5D,0x28,0x7E,0x5B,0x4F,0x44,0x31,0x5D,0x29,0x7E,0x5B, + 0x4F,0x44,0x31,0x5D,0x29,0x5D,0x20,0x50,0x61,0x63,0x0A,0x45,0x58,0x54,0x54, + 0x59,0x50,0x20,0x5B,0x23,0x31,0x36,0x5D,0x20,0x53,0x33,0x0A,0x45,0x58,0x54, + 0x54,0x59,0x50,0x20,0x5B,0x23,0x31,0x36,0x44,0x33,0x2B,0x2C,0x23,0x31,0x36, + 0x58,0x33,0x2B,0x5D,0x20,0x53,0x33,0x2B,0x0A,0x45,0x58,0x54,0x54,0x59,0x50, + 0x20,0x5B,0x23,0x31,0x36,0x3B,0x73,0x2C,0x24,0x28,0x5B,0x53,0x44,0x31,0x5D, + 0x3D,0x2A,0x29,0x5D,0x20,0x53,0x32,0x0A,0x45,0x58,0x54,0x54,0x59,0x50,0x20, + 0x5B,0x23,0x31,0x36,0x44,0x34,0x3B,0x24,0x28,0x53,0x28,0x3D,0x4F,0x29,0x28, + 0x3D,0x4F,0x29,0x29,0x5D,0x20,0x53,0x6F,0x32,0x0A,0x45,0x58,0x54,0x54,0x59, + 0x50,0x20,0x5B,0x23,0x31,0x36,0x44,0x33,0x3B,0x24,0x28,0x53,0x28,0x3D,0x4F, + 0x29,0x29,0x5D,0x20,0x53,0x6F,0x78,0x0A,0x45,0x58,0x54,0x54,0x59,0x50,0x20, + 0x5B,0x23,0x31,0x36,0x3B,0x24,0x28,0x5B,0x23,0x31,0x36,0x44,0x34,0x5D,0x28, + 0x7E,0x5B,0x4F,0x44,0x31,0x5D,0x29,0x28,0x7E,0x5B,0x4F,0x44,0x31,0x5D,0x29, + 0x7E,0x5B,0x4F,0x44,0x31,0x5D,0x29,0x5D,0x20,0x53,0x61,0x63,0x0A,0x45,0x58, + 0x54,0x54,0x59,0x50,0x20,0x5B,0x23,0x31,0x36,0x3B,0x24,0x28,0x5B,0x23,0x31, + 0x36,0x44,0x33,0x5D,0x28,0x7E,0x5B,0x4F,0x44,0x31,0x5D,0x29,0x7E,0x5B,0x4F, + 0x44,0x31,0x5D,0x29,0x5D,0x20,0x53,0x61,0x63,0x0A,0x45,0x58,0x54,0x54,0x59, + 0x50,0x20,0x5B,0x23,0x35,0x5D,0x20,0x42,0x32,0x0A,0x45,0x58,0x54,0x54,0x59, + 0x50,0x20,0x5B,0x23,0x35,0x44,0x34,0x5D,0x20,0x42,0x33,0x0A,0x00}; + +} // namespace OpenBabel +#endif // OB_ATOMTYP_H +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/atomtyp.txt Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,249 @@ +############################################################################## +# # +# Open Babel file: atomtyp.txt # +# # +# # +# Copyright (c) 1998-2001 by OpenEye Scientific Software, Inc. # +# Some portions Copyright (c) 2001-2008 Geoffrey R. Hutchison # +# Part of the Open Babel package, under the GNU General Public License (GPL)# +# # +# SMARTS patterns for atom typing (used by typer.cpp:OBAtomTyper) # +# # +# INTHYB: used to assign the internal hybridization values for atoms # +# IMPVAL: used to assign the implicit valence of an atom # +# EXTTYP: used to assign the external type of an atom for translation to # +# package specific types (i.e. Sybyl Mol2) # +# (these should correspond to INT type names in types.txt too.) # +# # +# The LAST PATTERN MATCHED is used to assign values with the corresponding # +# INTHYB, IMPVAL, and EXTTYP values. Additions to this file should be placed # +# in the EXTRA DEFINITIONS section (to separate from original patterns.) # +# # +############################################################################## + +INTHYB [D4] 3 #any 4-valent atom -- tetrahedral +INTHYB [D5] 5 #any 5-valent atom -- trigbipy +INTHYB [D6] 6 #any 6-valent atom -- oct +INTHYB [C] 3 #sp3 carbon +INTHYB [c,$(C=*)] 2 #sp2 carbon +# INTHYB [$([#6]([#8D1])[#8D1])] 2 # Commented out after PR#3089597 +INTHYB [$(C#*),$(C(=*)=*)] 1 #sp carbon + +INTHYB [N] 3 #sp3 nitrogen +INTHYB [n,$(N=*),$(N[#6,#7,#8]=,:,#*)] 2 #sp2 nitrogen +INTHYB [ND1,ND2,ND3]a 2 #sp2 nitrogen +INTHYB [$(N#*),$([ND2](=*)=*)] 1 #sp nitrogen + +INTHYB [O] 3 #sp3 oxygen +INTHYB [o,$(O=*),$(O[#6,#7,#8]=,:*)] 2 #sp2 oxygen +INTHYB [$([#8D1][#6][#8D1])] 2 #sp2 oxygen +INTHYB [$(O#*)] 1 #sp oxygen + +INTHYB [P] 3 #sp3 phosphorus +INTHYB [#15;$([PD1]=*)] 2 #sp2 phosphorus +INTHYB [PD5] 5 #sp3d phosphorus, as in PF5 +INTHYB [Pv5] 5 #sp3d phosphorus, as in H3PO4 +INTHYB [S] 3 #sp3 sulfur +INTHYB [#16;s,$([SD1]=*)] 2 #sp2 sulfur +INTHYB [SD6] 6 #sp3d2 sulfur, as in SF6 +INTHYB [B] 2 #sp2 boron +INTHYB [BD4] 3 #sp3 boron + +INTHYB [Al] 2 # typical sp2 Al (and family) +INTHYB [Ga] 2 +INTHYB [In] 2 +INTHYB [Tl] 2 +INTHYB [AlD4] 3 # sp3 Al +INTHYB [Si] 3 # sp3 Si (and family) +INTHYB [Ge] 3 +INTHYB [Sn] 3 +INTHYB [Pb] 3 +INTHYB [As] 3 # sp3 hybridization As (and family) +INTHYB [Sb] 3 +INTHYB [Bi] 3 + +INTHYB [se] 2 # aromatic sp2 Se +INTHYB [Se] 3 # sp3 hybridization Se (and family) +INTHYB [Te] 3 +INTHYB [Po] 3 + +INTHYB [Be] 1 # Alkaline earth, like sp hybrids +INTHYB [Mg] 1 +INTHYB [Ca] 1 +INTHYB [Sr] 1 +INTHYB [Ba] 1 +INTHYB [Ra] 1 + +#INTHYB [Pt] 4 # normally square planar +#INTHYB [Pd] 4 +#INTHYB [Cu] 4 +#INTHYB [Ag] 4 +#INTHYB [Au] 4 + +# +#IMPLICIT VALENCE RULES +# +#IMPVAL [#3,#11,#19,#37,#55,#87] 1 # Alkali metals +#IMPVAL [#4,#12,#20,#38,#56,#88] 2 # Alkaline earth + +IMPVAL [#5] 3 # Generic boron +IMPVAL [$([#6+]=*)] 2 +IMPVAL [$([#6+]#*)] 1 # just for InChI C2 + +IMPVAL [#6^3] 4 +IMPVAL [#6^2] 3 +IMPVAL [#6^1] 2 +IMPVAL [#6^3-] 3 +IMPVAL [#6^2-] 2 +IMPVAL [#6^1-] 1 # isocyanides, CO (valence=1, bond order=3) +IMPVAL [c+] 2 + +IMPVAL [N^3] 3 +IMPVAL [N^3+] 4 +IMPVAL [N^2] 3 +#IMPVAL [N^2-,N^3-] 2 +IMPVAL [ND1^1] 1 +IMPVAL [ND2^1] 2 +IMPVAL [$(N([OD1])*)] 3 +IMPVAL [$(NC=O)] 3 +#IMPVAL [$(n(c=O)c=O)] 3 # aromatic diimide +IMPVAL [$(N(~[OD1])~[OD1])] 3 +IMPVAL [$([Nr0]C=[Nr0])] 3 +IMPVAL [$(N=*)] 2 +#IMPVAL [$([Nr0]=C[Nr0])] 3 +IMPVAL [$([Nr0]=C[Nr0])] 2 +IMPVAL [$([N+r0]=C[Nr0])] 3 # patch from Steve Constable +IMPVAL [$([#7D1-]=*)] 1 +IMPVAL [N^1-] 1 # N2O [N-]=[N+]=O (valence=1, bondorder=2) +IMPVAL [N-] 2 +IMPVAL [n] 2 +IMPVAL [n-] 2 +IMPVAL [n+] 3 +IMPVAL [$([#7-]=*)] 1 +IMPVAL [$([#7+]#*)] 2 + +IMPVAL [$([#8+]#*)] 1 + +IMPVAL [#8] 2 # Generic O +IMPVAL [#8-] 1 +IMPVAL [#8-2] 0 +IMPVAL [#8+] 3 +IMPVAL [$([#8]=*)] 1 +IMPVAL [#8^1+] 1 # carbon monoxide + +IMPVAL [#9D0] 1 +IMPVAL [#9D0-] 0 #[F-] + +IMPVAL [#13] 3 # generic Al + +IMPVAL [#14] 4 # regular sp3 Si +IMPVAL [#14^2] 2 # silylenes +IMPVAL [$([#14]=*)] 3 # e.g., Si=O +IMPVAL [$([#14](=*)=*)] 0 # e.g., Si(=O)=O +IMPVAL [$([#14+]#*)] 1 # just for InChI Si2 +IMPVAL [$([#14-]#*)] 1 # just for InChI Si2 + +IMPVAL [#15D4] 4 +IMPVAL [#15D3] 3 +IMPVAL [#15D2] 3 +IMPVAL [#15D1^3] 3 +IMPVAL [#15D1^2] 3 +IMPVAL [#15D0] 3 +IMPVAL [$([#15]=[#6])] 2 +IMPVAL [pD2] 2 +IMPVAL [$([#15]=[#8])] 4 # phosphinate (double bond = one valence) +IMPVAL [$([#15](=[#8])=[#8])] 3 # metaphosphate (double bond = one valence) +IMPVAL [$([#15+](=[#8])([#8]))] 0 # R-P+O2 + +IMPVAL [#16] 2 #revised CM April 2008 +IMPVAL [$([#16D1]=*)] 1 +IMPVAL [$([#16D3](=O)(=O)-O)] 4 #e.g. O[S](=O)=O +IMPVAL [$([#16D2](=O)-O)] 3 # e.g. O[S]=O +IMPVAL [#16D1-] 1 + +IMPVAL [#17D0] 1 +IMPVAL [#17D0-] 0 #[Cl-] + +IMPVAL [#31] 3 +IMPVAL [#32] 4 + +IMPVAL [#33] 3 +IMPVAL [as] 3 + +IMPVAL [#34] 2 + +IMPVAL [#35D0] 1 +IMPVAL [#35D0-] 0 #[Br-] + +#IMPVAL [#49,#81] 3 # In, Tl, like Ga +#IMPVAL [#50,#82] 4 # Sn, Pb, like Ge +#IMPVAL [#51,#83] 3 # Sb, Bi, like As + +IMPVAL [#52] 2 +IMPVAL [#53D0] 1 +IMPVAL [#53D0-] 0 #[I-] + +# +#EXTERNAL TYPE RULES +# + +# Tinker OH hydrogens for MM2 +# Fixes PR# 1839274 +EXTTYP [#1][#8] HO + +EXTTYP [#7^3] N3 +EXTTYP [#7X4] N3+ +EXTTYP [#7^2] Npl +EXTTYP [#7^1] N1 +EXTTYP [$(N=*)] N2 +EXTTYP [$([Nr0]C(=[Nr0])[Nr0])] Ng+ +EXTTYP [$([Nr0]=C([Nr0])[Nr0])] Ng+ +EXTTYP [$([ND1]=C[ND1])] Ng+ +EXTTYP [$([ND1]C=[ND1])] Ng+ +EXTTYP [$(N(O)*)] Nox +EXTTYP [$(NC=[O,S])] Nam +EXTTYP [$(N(~[OD1])~[OD1])] Ntr +EXTTYP [n] Nar + +EXTTYP [#6^3] C3 +EXTTYP [#6^2] C2 +EXTTYP [$(C(=O)[OD1])] Cac +EXTTYP [c] Car +EXTTYP [#6^1] C1 +EXTTYP [#6+] C+ +EXTTYP [#6-] C- + +EXTTYP [#8^3] O3 +EXTTYP [#8^2] O2 +EXTTYP [$(Oa)] O2 +#The following 2 lines used for correct Sybyl atom typing +EXTTYP [$([OD2]C=[O,S])] O3 #ester oxygen +EXTTYP [$(Oa)] O3 #aromatic ether +EXTTYP [#8-] O- +EXTTYP [$([#8D1]~[#6^2]~[#8D1])] O.co2 + +EXTTYP [#15] P +EXTTYP [#15X4+] P3+ +EXTTYP [#15;$([#15D4](~[OD1])(~[OD1])~[OD1])] Pac +EXTTYP [#15;$([#15D3](~[OD1])~[OD1])] Pac + +EXTTYP [#16] S3 +EXTTYP [#16D3+,#16X3+] S3+ +EXTTYP [#16;s,$([SD1]=*)] S2 +EXTTYP [#16D4;$(S(=O)(=O))] So2 +EXTTYP [#16D3;$(S(=O))] Sox +EXTTYP [#16;$([#16D4](~[OD1])(~[OD1])~[OD1])] Sac +EXTTYP [#16;$([#16D3](~[OD1])~[OD1])] Sac + +EXTTYP [#5] B2 +EXTTYP [#5D4] B3 + +######################## Add Extra Definitions Here ########################## + +#INTHYB [U] 3 +#INTHYB [W] 3 +#INTHYB [Mo] 6 # for development +#INTHYB [Cr] 5 # for development + +############################# End Extra Definitions ########################## +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/babel_povray3.inc Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,1229 @@ +//Include for Babel +//Copyright (c) by Steffen Reith and Oliver Weichold 1996-2002 +// This program is free software; you can redistribute it and/or modify +// it under the terms of the GNU General Public License as published by +// the Free Software Foundation version 2 of the License. +//EMail: streit@streit.cc +//For chemical questions send mail to +//weichold@sas.upenn.edu + +//$Id: babel_povray3.inc 3895 2010-07-22 10:36:05Z baoilleach $ + +#include "colors.inc" +#include "metals.inc" + +//Do a ball and sticks model as default (nothing defined) +#ifndef (BAS) + #ifndef (SPF) + #ifndef (CST) + #declare BAS = true; + #declare SPF = false; + #declare CST = false; + #end + #end +#end + +//Default: No Ball and Sticks-model (if undefined) +#ifndef (BAS) + #declare BAS = false; +#end + +//Default: No Spacefill-model (if undefined) +#ifndef (SPF) + #declare SPF = false; +#end + +//Default: No capped sticks-model (if undefined) +#ifndef (CST) + #declare CST = false; +#end + +//Is a model (BAS, SPF or CST) selected ? +#if (!((BAS | SPF) | CST)) + + //Terminate parsing + #error "You have to select BAS (default), SPF or CST" + +#end + +//Select only one model +#if ((BAS & SPF) | ((BAS & CST) | (SPF & CST))) + + //Terminate parsing + #error "You have to select only one model-type" + +#end + +//Display copyright +#render "\n\n" +#render "\nbabel31.inc (C) 1996-2002 by\n" +#render "Oliver Weichold (weichold@sas.upenn.edu)\n" +#render "and Steffen Reith (streit@streit.cc)\n" +#render "\n\n" + +//TRANS mode off by default (only needed for transparent textures) +#ifndef (TRANS) +#declare TRANS = false; +#end + +#if (TRANS) +#include "glass.inc" +#end + +//Finishs for atoms (Nonmetals, Transmetals, Halfmetals and Metals) +#if (TRANS) + + #declare TransFinish = finish { + ambient 0.1 + diffuse 0.1 + specular 0.8 + reflection 0.1 + roughness 0.0003 + phong 1 phong_size 400 + } + + //Transparent finishs + #declare MetalFinish = finish {TransFinish} + #declare HalfMetalFinish = finish {TransFinish} + #declare NonMetalFinish = finish {TransFinish} + #declare TransMetalFinish = finish {TransFinish} + #declare Bond_0_Finish = finish {TransFinish} + #declare Bond_1_Finish = finish {TransFinish} + #declare Bond_2_Finish = finish {TransFinish} + #declare Bond_3_Finish = finish {TransFinish} + #declare Bond_4_Finish = finish {TransFinish} + #declare Bond_5_Finish = finish {TransFinish} + + //Filter values for transparent finishs + #declare MetalFilter = 1.00; + #declare HalfMetalFilter = 0.95; + #declare NonMetalFilter = 1.00; + #declare TransMetalFilter = 0.95; + #declare Bond_0_Filter = 0.00; + #declare Bond_1_Filter = 0.90; + #declare Bond_2_Filter = 0.90; + #declare Bond_3_Filter = 0.90; + #declare Bond_4_Filter = 0.90; + #declare Bond_5_Filter = 0.90; + +#else + + //Solid finishs + #declare MetalFinish = finish {F_MetalA} + #declare HalfMetalFinish = finish {F_MetalD} + #declare NonMetalFinish = finish { + + ambient 0.2 + diffuse 0.8 + brilliance 1.0 + phong 1.0 + phong_size 80 + reflection 0.25 + + } + #declare TransMetalFinish = finish {F_MetalD} + #declare Bond_0_Finish = finish {F_MetalC} + #declare Bond_1_Finish = finish {F_MetalC} + #declare Bond_2_Finish = finish {F_MetalC} + #declare Bond_3_Finish = finish {F_MetalC} + #declare Bond_4_Finish = finish {F_MetalC} + #declare Bond_5_Finish = finish {F_MetalC} + + //No additional filter (texture is not transparent) + #declare MetalFilter = 0.0; + #declare HalfMetalFilter = 0.0; + #declare NonMetalFilter = 0.0; + #declare TransMetalFilter = 0.0; + #declare Bond_0_Filter = 0.0; + #declare Bond_1_Filter = 0.0; + #declare Bond_2_Filter = 0.0; + #declare Bond_3_Filter = 0.0; + #declare Bond_4_Filter = 0.0; + #declare Bond_5_Filter = 0.0; + +#end + +//Thickness of Bonds (see Makro Bond_order) +#if (CST) + + // For capped-stick models you must use _one_ Bond_Thick ! + #declare Bond_Thick_0 = 0.1; + #declare Bond_Thick_1 = Bond_Thick_0; + #declare Bond_Thick_2 = Bond_Thick_0; + #declare Bond_Thick_3 = Bond_Thick_0; + #declare Bond_Thick_4 = Bond_Thick_0; + #declare Bond_Thick_5 = Bond_Thick_0; + +#else + + #declare Bond_Thick_0 = 0.1; + #declare Bond_Thick_1 = 0.1; + #declare Bond_Thick_2 = 0.1; + #declare Bond_Thick_3 = 0.1; + #declare Bond_Thick_4 = 0.1; + #declare Bond_Thick_5 = 0.1; + +#end + +//Colors for Bonds (see Makro Bond_order) +#declare Bond_0_Color = rgbf <1.00,0.725,0.275,Bond_0_Filter>; +#declare Bond_1_Color = rgbf <1.00,0.725,0.275,Bond_1_Filter>; +#declare Bond_2_Color = rgbf <1.00,0.725,0.275,Bond_2_Filter>; +#declare Bond_3_Color = rgbf <1.00,0.725,0.275,Bond_3_Filter>; +#declare Bond_4_Color = rgbf <1.00,0.725,0.275,Bond_4_Filter>; +#declare Bond_5_Color = rgbf <1.00,0.725,0.275,Bond_5_Filter>; + +#declare Bond_0_Color = rgbf <0.95,0.95,0.1,Bond_0_Filter>; +#declare Bond_1_Color = rgbf <0.95,0.95,0.1,Bond_1_Filter>; +#declare Bond_2_Color = rgbf <0.95,0.95,0.1,Bond_2_Filter>; +#declare Bond_3_Color = rgbf <0.95,0.95,0.1,Bond_3_Filter>; +#declare Bond_4_Color = rgbf <0.95,0.95,0.1,Bond_4_Filter>; +#declare Bond_5_Color = rgbf <0.95,0.95,0.1,Bond_5_Filter>; + +//The bond declarations +#declare bond_0 = cylinder { + <0,0,0> + <1,0,0> + Bond_Thick_0 + texture { + + pigment {color Bond_0_Color} + finish {Bond_0_Finish} + + } +#if (TRANS) + interior{ I_Glass} +#end + } +#declare bond_1 = cylinder { + <0,0,0> + <1,0,0> + Bond_Thick_1 + texture { + + pigment {color Bond_1_Color} + finish {Bond_1_Finish} + + } +#if (TRANS) + interior{ I_Glass} +#end + } +#declare bond_2 = cylinder { + <0,0,0> + <1,0,0> + Bond_Thick_2 + texture { + + pigment {color Bond_2_Color} + finish {Bond_2_Finish} + + } +#if (TRANS) + interior{ I_Glass} +#end + } +#declare bond_3 = cylinder { + <0,0,0> + <1,0,0> + Bond_Thick_3 + texture { + + pigment {color Bond_3_Color} + finish {Bond_3_Finish} + + } +#if (TRANS) + interior{ I_Glass} +#end + } +#declare bond_4 = cylinder { + <0,0,0> + <1,0,0> + Bond_Thick_4 + texture { + + pigment {color Bond_4_Color} + finish {Bond_4_Finish} + + } +#if (TRANS) + interior{ I_Glass} +#end + } +#declare bond_5 = cylinder { + <0,0,0> + <1,0,0> + Bond_Thick_5 + texture { + + pigment {color Bond_5_Color} + finish {Bond_5_Finish} + + } +#if (TRANS) + interior{ I_Glass} +#end + } + +//Generic definition of an atom +#if (BAS) +#render "\n\nCalculate a ball and sticks model of :" +#declare atom = sphere {<0,0,0>,0.6} +#end +#if (SPF) +#render "\n\nCalculate a spacefill model of :" +#declare atom = sphere {<0,0,0>,1.66} +#end +#if (CST) +#render "\n\nCalculate a capped sticks model of :" +#declare atom = sphere {<0,0,0>,1.0} +#end + +//For Povray 3.1 only +#version 3.1; + +//For capped sticks models we use Bond_Thick_0 for all atom radii +#if (CST) + + #declare Radius_C1 = Bond_Thick_0; + #declare Radius_C2 = Bond_Thick_0; + #declare Radius_C3 = Bond_Thick_0; + #declare Radius_H = Bond_Thick_0; + #declare Radius_D = Bond_Thick_0; + #declare Radius_O = Bond_Thick_0; + #declare Radius_N = Bond_Thick_0; + #declare Radius_S = Bond_Thick_0; + #declare Radius_P = Bond_Thick_0; + #declare Radius_F = Bond_Thick_0; + #declare Radius_Cl = Bond_Thick_0; + #declare Radius_Br = Bond_Thick_0; + #declare Radius_I = Bond_Thick_0; + + #declare Radius_Si = Bond_Thick_0; + #declare Radius_B = Bond_Thick_0; + #declare Radius_Ge = Bond_Thick_0; + #declare Radius_Se = Bond_Thick_0; + + #declare Radius_Ca = Bond_Thick_0; + #declare Radius_Ca2 = Bond_Thick_0; + #declare Radius_Sn = Bond_Thick_0; + #declare Radius_Sn2 = Bond_Thick_0; + #declare Radius_Sn4 = Bond_Thick_0; + #declare Radius_Pb = Bond_Thick_0; + #declare Radius_Pb2 = Bond_Thick_0; + #declare Radius_Pb4 = Bond_Thick_0; + #declare Radius_Te = Bond_Thick_0; + #declare Radius_Te4 = Bond_Thick_0; + #declare Radius_Te6 = Bond_Thick_0; + #declare Radius_Na = Bond_Thick_0; + #declare Radius_Na1 = Bond_Thick_0; + #declare Radius_K = Bond_Thick_0; + #declare Radius_K1 = Bond_Thick_0; + #declare Radius_Li = Bond_Thick_0; + #declare Radius_Li1 = Bond_Thick_0; + #declare Radius_Al = Bond_Thick_0; + #declare Radius_Al3 = Bond_Thick_0; + + #declare Radius_Mn = Bond_Thick_0; + #declare Radius_Mn2 = Bond_Thick_0; + #declare Radius_Mn3 = Bond_Thick_0; + #declare Radius_Mn4 = Bond_Thick_0; + #declare Radius_W = Bond_Thick_0; + #declare Radius_W4 = Bond_Thick_0; + #declare Radius_W6 = Bond_Thick_0; + #declare Radius_Fe = Bond_Thick_0; + #declare Radius_Fe2 = Bond_Thick_0; + #declare Radius_Fe3 = Bond_Thick_0; + #declare Radius_Pd = Bond_Thick_0; + #declare Radius_Pd2 = Bond_Thick_0; + #declare Radius_Pd4 = Bond_Thick_0; + #declare Radius_Ni = Bond_Thick_0; + #declare Radius_Ni2 = Bond_Thick_0; + #declare Radius_Ni3 = Bond_Thick_0; + #declare Radius_Cu = Bond_Thick_0; + #declare Radius_Cu1 = Bond_Thick_0; + #declare Radius_Cu2 = Bond_Thick_0; + #declare Radius_V = Bond_Thick_0; + #declare Radius_V2 = Bond_Thick_0; + #declare Radius_V3 = Bond_Thick_0; + #declare Radius_V4 = Bond_Thick_0; + #declare Radius_V5 = Bond_Thick_0; + #declare Radius_Zn = Bond_Thick_0; + #declare Radius_Zn2 = Bond_Thick_0; + +#else + + //Atom radii in A as published in J. Emsley, The Elements, + //Clarender Press, Oxford 1991 + + //All uncharged radii are kovalent. The values for Na and V are calculated + //from the atomic radius (10% less). + //We use the kovalent radii for the description of metal atoms. If you want to + //use ion radii, just replace the radius in the atom description. + //E.g., replace + // + //scale Radius_Zn + // + //by + // + //scale Radius_Zn2 + // + //for creating a sphere with the ion radius of Zn2+. + + #declare Radius_C1 = 0.770; + #declare Radius_C2 = 0.670; + #declare Radius_C3 = 0.600; + + #declare Radius_H = 0.370; + #declare Radius_D = 0.370; + #declare Radius_O = 0.660; + #declare Radius_N = 0.700; + #declare Radius_S = 1.040; + #declare Radius_P = 1.100; + #declare Radius_F = 0.580; + #declare Radius_Cl = 0.990; + #declare Radius_Br = 1.142; + #declare Radius_I = 1.330; + + #declare Radius_Si = 1.170; + #declare Radius_B = 0.880; + #declare Radius_Ge = 1.220; + #declare Radius_Se = 1.170; + + #declare Radius_Ca = 1.740; + #declare Radius_Ca2 = 1.060; + #declare Radius_Sn = 1.400; + #declare Radius_Sn2 = 0.930; + #declare Radius_Sn4 = 0.740; + #declare Radius_Pb = 1.540; + #declare Radius_Pb2 = 1.320; + #declare Radius_Pb4 = 0.890; + #declare Radius_Te = 1.370; + #declare Radius_Te4 = 0.970; + #declare Radius_Te6 = 0.560; + #declare Radius_Na = 1.380; + #declare Radius_Na1 = 0.980; + #declare Radius_K = 2.030; + #declare Radius_K1 = 1.330; + #declare Radius_Li = 1.230; + #declare Radius_Li1 = 0.780; + #declare Radius_Al = 1.250; + #declare Radius_Al3 = 0.570; + + #declare Radius_Mn = 1.170; + #declare Radius_Mn2 = 0.910; + #declare Radius_Mn3 = 0.700; + #declare Radius_Mn4 = 0.520; + #declare Radius_W = 1.300; + #declare Radius_W4 = 0.680; + #declare Radius_W6 = 0.620; + #declare Radius_Fe = 1.165; + #declare Radius_Fe2 = 0.820; + #declare Radius_Fe3 = 0.670; + #declare Radius_Pd = 1.280; + #declare Radius_Pd2 = 0.860; + #declare Radius_Pd4 = 0.640; + #declare Radius_Ni = 1.150; + #declare Radius_Ni2 = 0.780; + #declare Radius_Ni3 = 0.620; + #declare Radius_Cu = 1.170; + #declare Radius_Cu1 = 0.960; + #declare Radius_Cu2 = 0.720; + #declare Radius_V = 1.188; + #declare Radius_V2 = 0.720; + #declare Radius_V3 = 0.650; + #declare Radius_V4 = 0.610; + #declare Radius_V5 = 0.590; + #declare Radius_Zn = 1.250; + #declare Radius_Zn2 = 0.830; + +#end + +//Atom descriptions + +//Section: Nonmetals +#declare Color_C1 = rgbf <0.00,0.00,0.00,NonMetalFilter>; +#declare Atom_C1 = object { + + atom + scale Radius_C1 + texture { + + pigment {color Color_C1} + finish {NonMetalFinish} + + } +#if (TRANS) + interior{ I_Glass} +#end + + } +#declare Atom_C = Atom_C1 +#declare Atom_Cac = Atom_C1 +#declare Atom_Cbl = Atom_C1 +#declare Atom_Cmi = Atom_C1 +#declare Atom_Crad = Atom_C1 +#declare Atom_Cx = Atom_C1 +#declare Atom_Nr = Atom_C1 + +#declare Radius_Cac = Radius_C1; +#declare Radius_Cbl = Radius_C1; +#declare Radius_Cmi = Radius_C1; +#declare Radius_Crad = Radius_C1; +#declare Radius_Cx = Radius_C1; +#declare Radius_Nr = Radius_C1; + +#declare Color_C = Color_C1; +#declare Color_Cac = Color_C1; +#declare Color_Cbl = Color_C1; +#declare Color_Cmi = Color_C1; +#declare Color_Crad = Color_C1; +#declare Color_Cx = Color_C1; +#declare Color_Nr = Color_C1; + +#declare Color_C2 = rgbf <0.00,0.00,0.00,NonMetalFilter>; +#declare Atom_C2 = object { + + atom + scale Radius_C2 + texture { + + pigment {color Color_C2} + finish {NonMetalFinish} + + } +#if (TRANS) + interior{ I_Glass} +#end + } + +#declare Color_C3 = rgbf <0.00,0.00,0.00,NonMetalFilter>; +#declare Atom_C3 = object { + + atom + scale Radius_C3 + texture { + + pigment {color Color_C3} + finish {NonMetalFinish} + + } +#if (TRANS) + interior{ I_Glass} +#end + } +#declare Atom_Car = Atom_C3 +#declare Atom_Cpl = Atom_C3 +#declare Atom_Cx = Atom_C3 + +#declare Radius_Car = Radius_C3; +#declare Radius_Cpl = Radius_C3; +#declare Radius_Cx = Radius_C3; + +#declare Color_Car = Color_C3; +#declare Color_Cpl = Color_C3; +#declare Color_Cx = Color_C3; + +#declare Color_H = rgbf <1.00,1.00,1.00,NonMetalFilter>; +#declare Atom_H = object { + + atom + scale Radius_H + texture { + + pigment {color Color_H} + finish {NonMetalFinish} + + } +#if (TRANS) + interior{ I_Glass} +#end + } +#declare Atom_HC = Atom_H +#declare Atom_HO = Atom_H +#declare Atom_HN = Atom_H +#declare Atom_Hpl = Atom_H + +#declare Radius_HC = Radius_H; +#declare Radius_HO = Radius_H; +#declare Radius_HN = Radius_H; +#declare Radius_Hpl = Radius_H; + +#declare Color_HC = Color_H; +#declare Color_HO = Color_H; +#declare Color_HN = Color_H; +#declare Color_Hpl = Color_H; + +#declare Color_D = rgbf <0.85,0.85,0.95,NonMetalFilter>; +#declare Atom_D = object { + + atom + scale Radius_D + texture { + + pigment {color Color_D} + finish {NonMetalFinish} + + } +#if (TRANS) + interior{ I_Glass} +#end + } +#declare Atom_DC = Atom_D + +#declare Radius_DC = Radius_D; + +#declare Color_DC = Color_D; + +#declare Color_O = rgbf <1.00,0.00,0.00,NonMetalFilter>; +#declare Atom_O = object { + + atom + scale Radius_O + texture { + + pigment {color Color_O} + finish {NonMetalFinish} + + } +#if (TRANS) + interior{ I_Glass} +#end + } +#declare Atom_O3 = Atom_O +#declare Atom_O2 = Atom_O +#declare Atom_Omi = Atom_O +#declare Atom_OCO2 = Atom_O +#declare Atom_Oany = Atom_O +#declare Atom_Oco2 = Atom_O + +#declare Radius_O3 = Radius_O; +#declare Radius_O2 = Radius_O; +#declare Radius_Omi = Radius_O; +#declare Radius_OCO2 = Radius_O; +#declare Radius_Oany = Radius_O; +#declare Radius_Oco2 = Radius_O; + +#declare Color_O3 = Color_O; +#declare Color_O2 = Color_O; +#declare Color_Omi = Color_O; +#declare Color_OCO2 = Color_O; +#declare Color_Oany = Color_O; +#declare Color_Oco2 = Color_O; + +#declare Color_N = rgbf <0.14,0.42,0.56,NonMetalFilter>; +#declare Atom_N = object { + + atom + scale Radius_N + texture { + + pigment {color Color_N} + finish {NonMetalFinish} + + } +#if (TRANS) + interior{ I_Glass} +#end + } +#declare Atom_NPL3 = Atom_N +#declare Atom_N2 = Atom_N +#declare Atom_N4 = Atom_N +#declare Atom_N3 = Atom_N +#declare Atom_Npl = Atom_N +#declare Atom_N2pl = Atom_N +#declare Atom_Naz = Atom_N +#declare Atom_N1 = Atom_N +#declare Atom_Nox = Atom_N +#declare Atom_Ntr = Atom_N +#declare Atom_NC = Atom_N +#declare Atom_Nar = Atom_N +#declare Atom_Nam = Atom_N +#declare Atom_Ngpl = Atom_N +#declare Atom_N3pl = Atom_N +#declare Atom_Nany = Atom_N + +#declare Radius_NPL3 = Radius_N; +#declare Radius_N2 = Radius_N; +#declare Radius_N4 = Radius_N; +#declare Radius_N3 = Radius_N; +#declare Radius_Npl = Radius_N; +#declare Radius_N2pl = Radius_N; +#declare Radius_Naz = Radius_N; +#declare Radius_N1 = Radius_N; +#declare Radius_Nox = Radius_N; +#declare Radius_Ntr = Radius_N; +#declare Radius_NC = Radius_N; +#declare Radius_Nar = Radius_N; +#declare Radius_Nam = Radius_N; +#declare Radius_Ngpl = Radius_N; +#declare Radius_N3pl = Radius_N; +#declare Radius_Nany = Radius_N; + +#declare Color_NPL3 = Color_N; +#declare Color_N2 = Color_N; +#declare Color_N4 = Color_N; +#declare Color_N3 = Color_N; +#declare Color_Npl = Color_N; +#declare Color_N2pl = Color_N; +#declare Color_Naz = Color_N; +#declare Color_N1 = Color_N; +#declare Color_Nox = Color_N; +#declare Color_Ntr = Color_N; +#declare Color_NC = Color_N; +#declare Color_Nar = Color_N; +#declare Color_Nam = Color_N; +#declare Color_Ngpl = Color_N; +#declare Color_N3pl = Color_N; +#declare Color_Nany = Color_N; + +#declare Color_F = rgbf<1.00,1.00,0.88,NonMetalFilter>; +#declare Atom_F = object { + + atom + scale Radius_F + texture { + + pigment {color Color_F} + finish {NonMetalFinish} + + } +#if (TRANS) + interior{ I_Glass} +#end + } + +#declare Color_Cl = rgbf <0.20,0.80,0.20,NonMetalFilter>; +#declare Atom_Cl = object { + + atom + scale Radius_Cl + texture { + + pigment {color Color_Cl} + finish {NonMetalFinish} + + } +#if (TRANS) + interior{ I_Glass} +#end + } + +#declare Color_Br = rgbf <0.65,0.16,0.16,NonMetalFilter>; +#declare Atom_Br = object { + + atom + scale Radius_Br + texture { + + pigment {color Color_Br} + finish {NonMetalFinish} + + } +#if (TRANS) + interior{ I_Glass} +#end + } + +#declare Color_I = rgbf<0.58,0.44,0.86,NonMetalFilter>; +#declare Atom_I = object { + + atom + scale Radius_I + texture { + + pigment {color Color_I} + finish {NonMetalFinish} + + } +#if (TRANS) + interior{ I_Glass} +#end + } + +#declare Color_P = rgbf <1.00,0.50,0.00,NonMetalFilter>; +#declare Atom_P = object { + + atom + scale Radius_P + texture { + + pigment {color Color_P} + finish{NonMetalFinish} + + } +#if (TRANS) + interior{ I_Glass} +#end + } +#declare Atom_Pac = Atom_P +#declare Atom_P3 = Atom_P +#declare Atom_Pox = Atom_P +#declare Atom_P3pl = Atom_P + +#declare Radius_Pac = Radius_P; +#declare Radius_P3 = Radius_P; +#declare Radius_Pox = Radius_P; +#declare Radius_P3pl = Radius_P; + +#declare Color_Pac = Color_P; +#declare Color_P3 = Color_P; +#declare Color_Pox = Color_P; +#declare Color_P3pl = Color_P; + +#declare Color_S = rgbf <1.00,1.00,0.00,NonMetalFilter>; +#declare Atom_S = object { + + atom + scale Radius_S + texture { + + pigment {color Color_S} + finish {NonMetalFinish} + + } +#if (TRANS) + interior{ I_Glass} +#end + } +#declare Atom_S3pl = Atom_S +#declare Atom_S3 = Atom_S +#declare Atom_S2 = Atom_S +#declare Atom_Sac = Atom_S +#declare Atom_Sox = Atom_S +#declare Atom_Sany = Atom_S +#declare Atom_So = Atom_S + +#declare Radius_S3pl = Radius_S; +#declare Radius_S3 = Radius_S; +#declare Radius_S2 = Radius_S; +#declare Radius_Sac = Radius_S; +#declare Radius_Sox = Radius_S; +#declare Radius_Sany = Radius_S; +#declare Radius_So = Radius_S; + +#declare Color_S3pl = Color_S; +#declare Color_S3 = Color_S; +#declare Color_S2 = Color_S; +#declare Color_Sac = Color_S; +#declare Color_Sox = Color_S; +#declare Color_Sany = Color_S; +#declare Color_So = Color_S; + +//A special color for halfmetals +#declare HalfMetalColor = rgbf <0.6,0.6,0.85,HalfMetalFilter>; + +//Section: HalfMetals +#declare Color_B = rgbf <0,1.0,0,HalfMetalFilter>; +#declare Atom_B = object { + + atom + scale Radius_B + texture { + + pigment {color Color_B} + finish {HalfMetalFinish} + + } +#if (TRANS) + interior{ I_Glass} +#end + } +#declare Atom_Bac = Atom_B +#declare Atom_Box = Atom_B + +#declare Radius_Bac = Radius_B; +#declare Radius_Box = Radius_B; + +#declare Color_Bac = Color_B; +#declare Color_Box = Color_B; + +#declare Color_Si = HalfMetalColor; +#declare Atom_Si = object { + + atom + scale Radius_Si + texture { + + pigment {color Color_Si} + finish {HalfMetalFinish} + + } +#if (TRANS) + interior{ I_Glass} +#end + } + + +#declare Color_Ge = HalfMetalColor; +#declare Atom_Ge = object { + + atom + scale Radius_Ge + texture { + + pigment {color Color_Ge} + finish {HalfMetalFinish} + + } +#if (TRANS) + interior{ I_Glass} +#end + } +#declare Color_Se = HalfMetalColor; +#declare Atom_Se = object { + + atom + scale Radius_Se + texture { + + pigment {color Color_Se} + finish {HalfMetalFinish} + + } +#if (TRANS) + interior{ I_Glass} +#end + } + +//Metals +#declare Color_Metal = rgbf <0.94,0.93,0.90,MetalFilter>; + +#declare Color_Te = rgbf <0.6,0.6,0.6,MetalFilter>; +#declare Atom_Te = object { + + atom + scale Radius_Te + texture { + + pigment {color Color_Te} + finish {MetalFinish} + + } +#if (TRANS) + interior{ I_Glass} +#end + } + +#declare Color_Li = Color_Metal; +#declare Atom_Li = object { + + atom + scale Radius_Li + texture { + + pigment {color Color_Li} + finish {MetalFinish} + + } +#if (TRANS) + interior{ I_Glass} +#end + } + +#declare Color_Na = Color_Metal; +#declare Atom_Na = object { + + atom + scale Radius_Na + texture { + + pigment {color Color_Na} + finish {MetalFinish} + + } +#if (TRANS) + interior{ I_Glass} +#end + } + +#declare Color_K = Color_Metal; +#declare Atom_K = object { + + atom + scale Radius_K + texture { + + pigment {color Color_K} + finish {MetalFinish} + + } +#if (TRANS) + interior{ I_Glass} +#end + } + +#declare Color_Ca = Color_Metal; +#declare Atom_Ca = object { + + atom + scale Radius_Ca + texture { + + pigment {color Color_Ca} + finish {MetalFinish} + + } +#if (TRANS) + interior{ I_Glass} +#end + } + +#declare Color_Al = Color_Metal; +#declare Atom_Al = object { + + atom + scale Radius_Al + texture { + + pigment {color Color_Al} + finish {MetalFinish} + + } +#if (TRANS) + interior{ I_Glass} +#end + } + +#declare Color_Sn = Color_Metal; +#declare Atom_Sn = object { + + atom + scale Radius_Sn + texture { + + pigment {color Color_Sn} + finish {MetalFinish} + + } +#if (TRANS) + interior{ I_Glass} +#end + } + +#declare Color_Pb = Color_Metal; +#declare Atom_Pb = object { + + atom + scale Radius_Pb + texture { + + pigment {color Color_Pb} + finish {MetalFinish} + + } +#if (TRANS) + interior{ I_Glass} +#end + } + +//TransMetals +#declare Color_TransMetal = rgbf <0.94,0.93,0.90,TransMetalFilter>; + +#declare Color_W = Color_TransMetal; +#declare Atom_W = object { + + atom + scale Radius_W + texture { + + pigment {color Color_W} + finish {TransMetalFinish} + + } +#if (TRANS) + interior{ I_Glass} +#end + } + +#declare Color_Pd = Color_TransMetal; +#declare Atom_Pd = object { + + atom + scale Radius_Pd + texture { + + pigment {color Color_Pd} + finish {TransMetalFinish} + + } +#if (TRANS) + interior{ I_Glass} +#end + } + +#declare Color_Ni = Color_TransMetal; +#declare Atom_Ni = object { + + atom + scale Radius_Ni + texture { + + pigment {color Color_Ni} + finish {TransMetalFinish} + + } +#if (TRANS) + interior{ I_Glass} +#end + } + +#declare Color_Cu = rgbf <0.50,0.25,0.15,TransMetalFilter>; +#declare Atom_Cu = object { + + atom + scale Radius_Cu + + texture { + + pigment {color Color_Cu} + finish {TransMetalFinish} + + } +#if (TRANS) + interior{ I_Glass} +#end + } + +#declare Color_Mn = Color_TransMetal; +#declare Atom_Mn = object { + + atom + scale Radius_Mn + texture { + + pigment {color Color_Mn} + finish {TransMetalFinish} + + } +#if (TRANS) + interior{ I_Glass} +#end + } + +#declare Color_Fe = Color_TransMetal; +#declare Atom_Fe = object { + + atom + scale Radius_Fe + + texture { + + pigment {color Color_Fe} + finish {TransMetalFinish} + + } +#if (TRANS) + interior{ I_Glass} +#end + } + + +#declare Color_V = Color_TransMetal; +#declare Atom_V = object { + + atom + scale Radius_V + texture { + + pigment {color Color_V} + finish {TransMetalFinish} + + } +#if (TRANS) + interior{ I_Glass} +#end + } + +#declare Atom_V2 = object { + + atom + scale Radius_V2 + texture { + + pigment {color Color_V} + finish {TransMetalFinish} + + } +#if (TRANS) + interior{ I_Glass} +#end + } + +#declare Atom_V3 = object { + + atom + scale Radius_V3 + texture { + + pigment {color Color_V} + finish {TransMetalFinish} + + } +#if (TRANS) + interior{ I_Glass} +#end + } + +#declare Atom_V4 = object { + + atom + scale Radius_V4 + texture { + + pigment {color Color_V} + finish {TransMetalFinish} + + } +#if (TRANS) + interior{ I_Glass} +#end + } + +#declare Atom_V5 = object { + + atom + scale Radius_V5 + texture { + + pigment {color Color_V} + finish {TransMetalFinish} + + } +#if (TRANS) + interior{ I_Glass} +#end + } + + +#declare Color_Zn = Color_TransMetal; +#declare Atom_Zn = object { + + atom + scale Radius_Zn + texture { + + pigment {color Color_Zn} + finish {TransMetalFinish} + + } +#if (TRANS) + interior{ I_Glass} +#end + } + +#declare Atom_Zn2 = object { + + atom + scale Radius_Zn2 + texture { + + pigment {color Color_Zn} + finish {TransMetalFinish} + + } +#if (TRANS) + interior{ I_Glass} +#end + }
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/bin2hex.pl Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,144 @@ +#!/usr/bin/env perl +# bin2hex.pl + +######################################################################## +# Copyright (C) 2001 by OpenEye Scientific Software, Inc. +# Some portions Copyright (c) 2002 by Geoffrey R. Hutchison +# +# This file is part of the Open Babel project. +# For more information, see <http://openbabel.org/> +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation version 2 of the License. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +######################################################################## + + +# Autoflush STDOUT +#STDOUT->autoflush(1); +$| = 1; + +$argc = @ARGV; +if( $argc == 2 ) { + $filename = @ARGV[0]; + $arrayname = @ARGV[1]; + + $pos = index($filename,"."); + if( $pos > 0 ) { + $guard = uc(substr($filename,0,$pos)); + } else { + $guard = uc($filename); + } +} elsif( $argc == 3 ) { + $filename = @ARGV[0]; + $arrayname = @ARGV[1]; + $guard = @ARGV[2]; +} else { + print "usage: bin2hex.pl <binaryfile> <arrayname>\n\n"; + exit; +} + +$debug = 0; + +open(F,$filename) || die "Error: Unable to open binary file!\n"; + +if( !$debug ) { + print "/***************************************************************\n"; + print "This file is part of the Open Babel project.\n"; + print "This is copyright under the GNU General Public License (GPL)\n"; + print "For more information, see <http://openbabel.org/>\n\n"; + print "This file contains a binary representation of data tables\n"; + print " used by Open Babel. It is used as a fallback if the textual\n"; + print " data table is not found at runtime. It is not a normal header.\n"; + print "***************************************************************/\n"; + print "\n\n"; + + print "#ifndef OB_" . $guard . "_H\n"; + print "#define OB_" . $guard . "_H\n\n"; + print "namespace OpenBabel\n{\n"; + print "static const char " . $arrayname . "[] = {\n "; +} + +binmode(F); + +$col = 0; +$init = 0; +$ignore = 0; +$newline = 1; +$spacerun = 0; # collapse runs of spaces + +while( !eof(F) ) { + $ch = ord(getc(F)); + if( $ch == 13 ) { # ignore \r characters + $ch = 0; + } + + if ( $spacerun ) { + if ( $ch == 32 ) { + $ch = 0; + } else { + $spacerun = 0; + } + } elsif ( $ch == 32) { + $spacerun = 1; + } + + if( $ignore ) { + if( $ch == 10 ) { # found the \n after an '#' ignore comment + $ignore = 0; + } + $ch = 0; + } elsif( $newline ) { # just saw a \n -- do we see real text + if( $ch == 10 ) { + $ch = 0; + } elsif ( $ch == 35 ) { # ignore anything after a '#' until a \n + $ignore = 1; + $ch = 0; + } elsif( $ch == 32 ) { # space + $ch = 0; + } elsif( $ch == 9 ) { # tab + $ch = 0; + } elsif( $ch ) { # something else, so clear the blank-line boolean + $newline = 0; + } + } elsif( $ch == 10 ) { # set the blank-line detector + $newline = 1; + } + + if( $ch ) { + if( $debug ) { + print chr($ch); + } else { + if( $init ) { + print ","; + } else { + $init = 1; + } + if( $col >= 15 ) { + print "\n "; + $col = 0; + } + print sprintf("0x%02X",$ch); + $col++; + } + } +} + +if( !$debug ) { + if( $col >= 15 ) { + print ",\n0x00};\n\n"; + } else { + print ",0x00};\n\n"; + } + print "} // namespace OpenBabel\n"; + print "#endif // OB_" . $guard . "_H\n\n"; +} + +close(F); +exit; +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/bondtyp.h Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,132 @@ +/*************************************************************** +This file is part of the Open Babel project. +This is copyright under the GNU General Public License (GPL) +For more information, see <http://openbabel.org/> + +This file contains a binary representation of data tables + used by Open Babel. It is used as a fallback if the textual + data table is not found at runtime. It is not a normal header. +***************************************************************/ + + +#ifndef OB_BONDTYP_H +#define OB_BONDTYP_H + +namespace OpenBabel +{ +static const char BondTypeData[] = { + 0x2A,0x31,0x5B,0x23,0x36,0x5D,0x28,0x5B,0x23,0x37,0x44,0x33,0x5D,0x32,0x29, + 0x5B,0x23,0x36,0x5D,0x5B,0x23,0x36,0x5D,0x5B,0x23,0x36,0x5D,0x32,0x2A,0x5B, + 0x23,0x36,0x5D,0x28,0x5B,0x23,0x37,0x44,0x33,0x5D,0x33,0x29,0x5B,0x23,0x36, + 0x5D,0x5B,0x23,0x36,0x5D,0x5B,0x23,0x36,0x5D,0x33,0x2A,0x5B,0x23,0x36,0x5D, + 0x28,0x5B,0x23,0x37,0x44,0x33,0x5D,0x34,0x29,0x5B,0x23,0x36,0x5D,0x5B,0x23, + 0x36,0x5D,0x5B,0x23,0x36,0x5D,0x34,0x2A,0x5B,0x23,0x36,0x5D,0x28,0x5B,0x23, + 0x37,0x44,0x33,0x5D,0x35,0x29,0x5B,0x23,0x36,0x5D,0x5B,0x23,0x36,0x5D,0x5B, + 0x23,0x36,0x5D,0x35,0x31,0x09,0x30,0x20,0x31,0x20,0x32,0x20,0x31,0x20,0x32, + 0x20,0x31,0x20,0x31,0x20,0x33,0x20,0x31,0x20,0x33,0x20,0x34,0x20,0x32,0x20, + 0x34,0x20,0x35,0x20,0x31,0x20,0x35,0x20,0x32,0x20,0x31,0x20,0x35,0x20,0x36, + 0x20,0x32,0x20,0x36,0x20,0x37,0x20,0x31,0x20,0x37,0x20,0x38,0x20,0x32,0x20, + 0x37,0x20,0x39,0x20,0x31,0x20,0x39,0x20,0x31,0x30,0x20,0x32,0x20,0x31,0x30, + 0x20,0x31,0x31,0x20,0x31,0x20,0x31,0x31,0x20,0x38,0x20,0x31,0x20,0x31,0x31, + 0x20,0x31,0x32,0x20,0x32,0x20,0x31,0x32,0x20,0x31,0x33,0x20,0x31,0x20,0x31, + 0x33,0x20,0x31,0x34,0x20,0x31,0x20,0x31,0x33,0x20,0x31,0x35,0x20,0x32,0x20, + 0x31,0x35,0x20,0x31,0x36,0x20,0x31,0x20,0x31,0x36,0x20,0x31,0x37,0x20,0x32, + 0x20,0x31,0x37,0x20,0x31,0x34,0x20,0x31,0x20,0x31,0x37,0x20,0x31,0x38,0x20, + 0x31,0x20,0x31,0x38,0x20,0x31,0x39,0x20,0x32,0x20,0x31,0x39,0x20,0x32,0x30, + 0x20,0x31,0x20,0x31,0x39,0x20,0x32,0x31,0x20,0x31,0x20,0x32,0x31,0x20,0x32, + 0x32,0x20,0x32,0x20,0x32,0x32,0x20,0x32,0x33,0x20,0x31,0x20,0x32,0x33,0x20, + 0x32,0x30,0x20,0x32,0x0A,0x2A,0x31,0x5B,0x23,0x36,0x5D,0x28,0x5B,0x23,0x37, + 0x44,0x33,0x5D,0x32,0x29,0x5B,0x23,0x36,0x5D,0x5B,0x23,0x36,0x5D,0x5B,0x23, + 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0x36,0x5D,0x29,0x28,0x5B,0x23,0x31,0x2C,0x23,0x36,0x5D,0x29,0x5B,0x23,0x37, + 0x44,0x33,0x5E,0x32,0x3B,0x21,0x52,0x5D,0x28,0x5B,0x23,0x31,0x5D,0x29,0x5B, + 0x23,0x36,0x5D,0x09,0x30,0x20,0x31,0x20,0x31,0x20,0x30,0x20,0x32,0x20,0x31, + 0x20,0x30,0x20,0x33,0x20,0x32,0x20,0x33,0x20,0x34,0x20,0x31,0x20,0x33,0x20, + 0x35,0x20,0x31,0x0A,0x00}; + +} // namespace OpenBabel +#endif // OB_BONDTYP_H +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/bondtyp.txt Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,76 @@ +############################################################################## +# # +# Open Babel file: bondtyp.txt # +# # +# Copyright (c) 2002-2005 by Geoffrey R Hutchison # +# Part of the Open Babel package, under the GNU General Public License (GPL)# +# # +# Used by bondtyper.cpp::OBBondTyper (and thus OBMol::PerceiveBondOrders() # +# # +# List of functional groups with double, triple (etc.) bond orders # +# Pattern Atom1 Atom2 Bond Order (repeat as needed) # +# * = Any atom (for setting non-multiple bonds) # +# # +# NOTE: These are applied in order, first to last. # +# So it's generally better to have a long (specifc) SMARTS first. # +# (all bonds must be single bonds to match) # +# # +############################################################################## + +# Porphyrin / phthalocyanine (3 patterns for three separate bonding motifs) +# this one has explicit bonds to all four nitrogens (e.g., metal bond or hydrogens) +#0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 +*1[#6]([#7D3]2)[#6][#6][#6]2*[#6]([#7D3]3)[#6][#6][#6]3*[#6]([#7D3]4)[#6][#6][#6]4*[#6]([#7D3]5)[#6][#6][#6]51 0 1 2 1 2 1 1 3 1 3 4 2 4 5 1 5 2 1 5 6 2 6 7 1 7 8 2 7 9 1 9 10 2 10 11 1 11 8 1 11 12 2 12 13 1 13 14 1 13 15 2 15 16 1 16 17 2 17 14 1 17 18 1 18 19 2 19 20 1 19 21 1 21 22 2 22 23 1 23 20 2 + +# this one has explicit bonds to two nitrogens (12 and 14) +#0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 +*1[#6]([#7D3]2)[#6][#6][#6]2*[#6]([#7]3)[#6][#6][#6]3*[#6]([#7D3]4)[#6][#6][#6]4*[#6]([#7]5)[#6][#6][#6]51 0 1 2 1 2 1 1 3 1 3 4 2 4 5 1 5 2 1 5 6 2 6 7 1 7 8 2 7 9 1 9 10 2 10 11 1 11 8 1 11 12 2 12 13 1 13 14 1 13 15 2 15 16 1 16 17 2 17 14 1 17 18 1 18 19 2 19 20 1 19 21 1 21 22 2 22 23 1 23 20 2 + +# and this one doesn't have any explicit bonds to the nitrogens +#0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 +*1[#6]([#7]2)[#6][#6][#6]2*[#6]([#7]3)[#6][#6][#6]3*[#6]([#7]4)[#6][#6][#6]4*[#6]([#7]5)[#6][#6][#6]51 0 1 2 1 2 1 1 3 1 3 4 2 4 5 1 5 2 1 5 6 2 6 7 1 7 8 2 7 9 1 9 10 2 10 11 1 11 8 1 11 12 2 12 13 1 13 14 1 13 15 2 15 16 1 16 17 2 17 14 1 17 18 1 18 19 2 19 20 1 19 21 1 21 22 2 22 23 1 23 20 2 + +# Azide +[#7D2][#7D2^1][#7D1] 0 1 2 1 2 2 +# Nitro +[#8D1][#7D3^2]([#8D1])* 0 1 2 1 2 2 1 3 1 +# Sulphone +[#16D4]([#8D1])([#8D1])(*)(*) 0 1 2 0 2 2 0 3 1 0 4 1 +# Phosphone +[#15D4]([#8D1])(*)(*)(*) 0 1 2 0 2 1 0 3 1 0 4 1 + +# Carboxylic Acid, ester, etc. +[#6D3^2]([#8D1])([#8])* 0 1 2 0 2 1 0 3 1 +# Carbon dioxide +[#8D1][#6D2^1][#8D1] 0 1 2 1 2 2 +# Amide C(=O)N +[#6D3^2]([#8D1])([#7])* 0 1 2 0 2 1 0 3 1 +# Seleninic acid Se(=O)OH +[#34D3^2]([#8D1])([#8])* 0 1 2 0 2 1 0 3 1 +# Thioacid / Thioester C(=O)S +[#6D3^2]([#8D1])([#16])* 0 1 2 0 2 1 0 3 1 +# dithioacid / dithioester C(=S)S +[#6D3^2]([#16D1])([#16])* 0 1 2 0 2 1 0 3 1 +# thioamide C(=S)N +[#6D3^2]([#16D1])([#7])* 0 1 2 0 2 1 0 3 1 + +# allene C=C=C +# (this is problematic -- need to make sure the center carbon is sp) +[#6^2][#6D2^1][#6^2] 0 1 2 1 2 2 + +# guanidinium and amidine -C(=NH)NH2 without hydrogens +[#6D3^2;!R]([#7D1H0;!R])([#7;!R])* 0 1 2 0 2 1 0 3 1 +# and also with hydrogens +# (this can normally be figured out, but is needed to avoid matching the next SMARTS) +[#6D3^2;!R]([#7D2H1;!R])([#7;!R])* 0 1 2 0 2 1 0 3 1 +# and also with more hydrogens than normal (protonated) +[#6D3^2;!R]([#7D3H2;!R])([#7;!R])* 0 1 2 0 2 1 0 3 1 + +# Schiff base, protonated +[#6D3^2;!R]([#1,#6])([#1,#6])[#7D3^2;!R]([#1])[#6] 0 1 1 0 2 1 0 3 2 3 4 1 3 5 1 + +### other potential functional groups that may (or may not) be useful to add +# imidines ( N=C/N\C=N +# sulfoxides +# heme / porphyrin +# phthalocyanine
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/cmake_install.cmake Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,82 @@ +# Install script for directory: /share/opt/x86_64_sl5/openbabel-2.3.0/build/data + +# Set the install prefix +IF(NOT DEFINED CMAKE_INSTALL_PREFIX) + SET(CMAKE_INSTALL_PREFIX "/share/opt/x86_64_sl5/openbabel-2.3.0") +ENDIF(NOT DEFINED CMAKE_INSTALL_PREFIX) +STRING(REGEX REPLACE "/$" "" CMAKE_INSTALL_PREFIX "${CMAKE_INSTALL_PREFIX}") + +# Set the install configuration name. +IF(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME) + IF(BUILD_TYPE) + STRING(REGEX REPLACE "^[^A-Za-z0-9_]+" "" + CMAKE_INSTALL_CONFIG_NAME "${BUILD_TYPE}") + ELSE(BUILD_TYPE) + SET(CMAKE_INSTALL_CONFIG_NAME "Release") + ENDIF(BUILD_TYPE) + MESSAGE(STATUS "Install configuration: \"${CMAKE_INSTALL_CONFIG_NAME}\"") +ENDIF(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME) + +# Set the component getting installed. +IF(NOT CMAKE_INSTALL_COMPONENT) + IF(COMPONENT) + MESSAGE(STATUS "Install component: \"${COMPONENT}\"") + SET(CMAKE_INSTALL_COMPONENT "${COMPONENT}") + ELSE(COMPONENT) + SET(CMAKE_INSTALL_COMPONENT) + ENDIF(COMPONENT) +ENDIF(NOT CMAKE_INSTALL_COMPONENT) + +# Install shared libraries without execute permission? +IF(NOT DEFINED CMAKE_INSTALL_SO_NO_EXE) + SET(CMAKE_INSTALL_SO_NO_EXE "0") +ENDIF(NOT DEFINED CMAKE_INSTALL_SO_NO_EXE) + +IF(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified") + FILE(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/share/openbabel/2.3.0" TYPE FILE FILES + "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/aromatic.txt" + "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/atomtyp.txt" + "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/bondtyp.txt" + "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/element.txt" + "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/fragments.txt" + "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/gaff.dat" + "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/gaff.prm" + "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/ghemical.prm" + "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/isotope-small.txt" + "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/isotope.txt" + "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/logp.txt" + "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/MACCS.txt" + "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/mmff94.ff" + "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/mmff94s.ff" + "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/mmffang.par" + "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/mmffbndk.par" + "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/mmffbond.par" + "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/mmffchg.par" + "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/mmffdef.par" + "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/mmffdfsb.par" + "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/mmffoop.par" + "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/mmffpbci.par" + "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/mmffprop.par" + "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/mmffstbn.par" + "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/mmfftor.par" + "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/mmffvdw.par" + "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/mmffs_oop.par" + "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/mmffs_tor.par" + "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/mr.txt" + "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/patterns.txt" + "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/phmodel.txt" + "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/plugindefines.txt" + "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/psa.txt" + "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/qeq.txt" + "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/resdata.txt" + "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/ringtyp.txt" + "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/SMARTS_InteLigand.txt" + "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/space-groups.txt" + "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/superatom.txt" + "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/svgformat.script" + "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/torlib.txt" + "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/types.txt" + "/share/opt/x86_64_sl5/openbabel-2.3.0/build/data/UFF.prm" + ) +ENDIF(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified") +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/element.h Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,616 @@ +/*************************************************************** +This file is part of the Open Babel project. +This is copyright under the GNU General Public License (GPL) +For more information, see <http://openbabel.org/> + +This file contains a binary representation of data tables + used by Open Babel. It is used as a fallback if the textual + data table is not found at runtime. It is not a normal header. +***************************************************************/ + + +#ifndef OB_ELEMENT_H +#define OB_ELEMENT_H + +namespace OpenBabel +{ +static const char ElementData[] = { + 0x30,0x09,0x58,0x78,0x09,0x30,0x2E,0x30,0x30,0x09,0x30,0x2E,0x30,0x30,0x09, + 0x30,0x2E,0x30,0x30,0x09,0x30,0x2E,0x30,0x30,0x09,0x30,0x09,0x30,0x09,0x30, + 0x2E,0x30,0x30,0x09,0x30,0x09,0x30,0x09,0x30,0x2E,0x30,0x37,0x09,0x30,0x2E, + 0x35,0x30,0x09,0x30,0x2E,0x37,0x30,0x09,0x44,0x75,0x6D,0x6D,0x79,0x0A,0x31, + 0x09,0x48,0x09,0x32,0x2E,0x32,0x30,0x09,0x30,0x2E,0x33,0x31,0x09,0x30,0x2E, + 0x33,0x31,0x09,0x31,0x2E,0x31,0x30,0x09,0x31,0x09,0x31,0x2E,0x30,0x30,0x37, + 0x39,0x34,0x09,0x32,0x2E,0x32,0x30,0x09,0x31,0x33,0x2E,0x35,0x39,0x38,0x34, + 0x09,0x30,0x2E,0x37,0x35,0x34,0x32,0x30,0x33,0x37,0x35,0x09,0x30,0x2E,0x37, + 0x35,0x09,0x30,0x2E,0x37,0x35,0x09,0x30,0x2E,0x37,0x35,0x09,0x48,0x79,0x64, + 0x72,0x6F,0x67,0x65,0x6E,0x0A,0x32,0x09,0x48,0x65,0x09,0x30,0x2E,0x30,0x30, + 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/element.txt Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,153 @@ +############################################################################## +# # +# Open Babel file: element.txt # +# # +# Some portions Copyright (c) 2001-2009 Geoffrey R. Hutchison # +# Part of the Open Babel package, under the GNU General Public License (GPL)# +# # +# Created from the Blue Obelisk Cheminformatics Data Repository # +# Direct Source: http://www.blueobelisk.org/ # +# http://www.blueobelisk.org/repos/blueobelisk/elements.xml # +# (includes furhter bibliographic citation information) # +# # +# Allred and Rochow Electronegativity from: # +# http://www.hull.ac.uk/chemistry/electroneg.php?type=Allred-Rochow # +# # +# Columns represent: (used by data.cpp:OBElementTable and OBElement) # +# - atomic number (used as an index to the vector as well) # +# - elemental symbol # +# - Allred and Rochow electronegativity 0.0 if unknown # +# - covalent radii (in Angstrom) 1.6 if unknown # +# from http://dx.doi.org/10.1039/b801115j # +# - "bond order" radii -- ignored, but included for compatibility # +# - van der Waals radii (in Angstrom) 2.0 if unknown # +# from http://dx.doi.org/10.1021/jp8111556 # +# - maximum bond valence 6 if unknown # +# - IUPAC recommended atomic masses (in amu) # +# - Pauling electronegativity 0.0 if unknown # +# - ionization potential (in eV) 0.0 if unknown # +# - electron affinity (in eV) 0.0 if unknown # +# - RGB values (defaults for visualization) # +# - element name (in English) # +# # +############################################################################## +#Num Symb ARENeg RCov RBO RVdW MaxBnd Mass ElNeg. Ionization ElAffinity Red Green Blue Name +0 Xx 0.00 0.00 0.00 0.00 0 0 0.00 0 0 0.07 0.50 0.70 Dummy +1 H 2.20 0.31 0.31 1.10 1 1.00794 2.20 13.5984 0.75420375 0.75 0.75 0.75 Hydrogen +2 He 0.00 0.28 0.28 1.40 0 4.002602 0.00 24.5874 0 0.85 1.00 1.00 Helium +3 Li 0.97 1.28 1.28 1.81 1 6.941 0.98 5.3917 0.618049 0.80 0.50 1.00 Lithium +4 Be 1.47 0.96 0.96 1.53 2 9.012182 1.57 9.3227 0 0.76 1.00 0.00 Beryllium +5 B 2.01 0.84 0.84 1.92 4 10.811 2.04 8.298 0.279723 1.00 0.71 0.71 Boron +6 C 2.50 0.76 0.76 1.70 4 12.0107 2.55 11.2603 1.262118 0.40 0.40 0.40 Carbon +7 N 3.07 0.71 0.71 1.55 4 14.0067 3.04 14.5341 -0.07 0.05 0.05 1.00 Nitrogen +8 O 3.50 0.66 0.66 1.52 2 15.9994 3.44 13.6181 1.461112 1.00 0.05 0.05 Oxygen +9 F 4.10 0.57 0.57 1.47 1 18.9984032 3.98 17.4228 3.4011887 0.50 0.70 1.00 Fluorine +10 Ne 0.00 0.58 0.58 1.54 0 20.1797 0.00 21.5645 0 0.70 0.89 0.96 Neon +11 Na 1.01 1.66 1.66 2.27 1 22.98977 0.93 5.1391 0.547926 0.67 0.36 0.95 Sodium +12 Mg 1.23 1.41 1.41 1.73 2 24.3050 1.31 7.6462 0 0.54 1.00 0.00 Magnesium +13 Al 1.47 1.21 1.21 1.84 6 26.981538 1.61 5.9858 0.43283 0.75 0.65 0.65 Aluminium +14 Si 1.74 1.11 1.11 2.10 6 28.0855 1.90 8.1517 1.389521 0.50 0.60 0.60 Silicon +15 P 2.06 1.07 1.07 1.80 6 30.973761 2.19 10.4867 0.7465 1.00 0.50 0.00 Phosphorus +16 S 2.44 1.05 1.05 1.80 6 32.065 2.58 10.36 2.0771029 0.70 0.70 0.00 Sulfur +17 Cl 2.83 1.02 1.02 1.75 1 35.453 3.16 12.9676 3.612724 0.12 0.94 0.12 Chlorine +18 Ar 0.00 1.06 1.06 1.88 0 39.948 0.00 15.7596 0 0.50 0.82 0.89 Argon +19 K 0.91 2.03 2.03 2.75 1 39.0983 0.82 4.3407 0.501459 0.56 0.25 0.83 Potassium +20 Ca 1.04 1.76 1.76 2.31 2 40.078 1.00 6.1132 0.02455 0.24 1.00 0.00 Calcium +21 Sc 1.20 1.70 1.70 2.30 6 44.95591 1.36 6.5615 0.188 0.90 0.90 0.90 Scandium +22 Ti 1.32 1.60 1.60 2.15 6 47.867 1.54 6.8281 0.084 0.75 0.76 0.78 Titanium +23 V 1.45 1.53 1.53 2.05 6 50.9415 1.63 6.7462 0.525 0.65 0.65 0.67 Vanadium +24 Cr 1.56 1.39 1.39 2.05 6 51.9961 1.66 6.7665 0.67584 0.54 0.60 0.78 Chromium +25 Mn 1.60 1.39 1.39 2.05 8 54.938049 1.55 7.434 0 0.61 0.48 0.78 Manganese +26 Fe 1.64 1.32 1.32 2.05 6 55.845 1.83 7.9024 0.151 0.88 0.40 0.20 Iron +27 Co 1.70 1.26 1.26 2.00 6 58.9332 1.88 7.881 0.6633 0.94 0.56 0.63 Cobalt +28 Ni 1.75 1.24 1.24 2.00 6 58.6934 1.91 7.6398 1.15716 0.31 0.82 0.31 Nickel +29 Cu 1.75 1.32 1.32 2.00 6 63.546 1.90 7.7264 1.23578 0.78 0.50 0.20 Copper +30 Zn 1.66 1.22 1.22 2.10 6 65.38 1.65 9.3942 0 0.49 0.50 0.69 Zinc +31 Ga 1.82 1.22 1.22 1.87 3 69.723 1.81 5.9993 0.41 0.76 0.56 0.56 Gallium +32 Ge 2.02 1.20 1.20 2.11 4 72.64 2.01 7.8994 1.232712 0.40 0.56 0.56 Germanium +33 As 2.20 1.19 1.19 1.85 3 74.92160 2.18 9.7886 0.814 0.74 0.50 0.89 Arsenic +34 Se 2.48 1.20 1.20 1.90 2 78.96 2.55 9.7524 2.02067 1.00 0.63 0.00 Selenium +35 Br 2.74 1.20 1.20 1.83 1 79.904 2.96 11.8138 3.363588 0.65 0.16 0.16 Bromine +36 Kr 0.00 1.16 1.16 2.02 0 83.798 3.00 13.9996 0 0.36 0.72 0.82 Krypton +37 Rb 0.89 2.20 2.20 3.03 1 85.4678 0.82 4.1771 0.485916 0.44 0.18 0.69 Rubidium +38 Sr 0.99 1.95 1.95 2.49 2 87.62 0.95 5.6949 0.05206 0.00 1.00 0.00 Strontium +39 Y 1.11 1.90 1.90 2.40 6 88.90585 1.22 6.2173 0.307 0.58 1.00 1.00 Yttrium +40 Zr 1.22 1.75 1.75 2.30 6 91.224 1.33 6.6339 0.426 0.58 0.88 0.88 Zirconium +41 Nb 1.23 1.64 1.64 2.15 6 92.90638 1.60 6.7589 0.893 0.45 0.76 0.79 Niobium +42 Mo 1.30 1.54 1.54 2.10 6 95.96 2.16 7.0924 0.7472 0.33 0.71 0.71 Molybdenum +43 Tc 1.36 1.47 1.47 2.05 6 98 1.90 7.28 0.55 0.23 0.62 0.62 Technetium +44 Ru 1.42 1.46 1.46 2.05 6 101.07 2.20 7.3605 1.04638 0.14 0.56 0.56 Ruthenium +45 Rh 1.45 1.42 1.42 2.00 6 102.90550 2.28 7.4589 1.14289 0.04 0.49 0.55 Rhodium +46 Pd 1.35 1.39 1.39 2.05 6 106.42 2.20 8.3369 0.56214 0.00 0.41 0.52 Palladium +47 Ag 1.42 1.45 1.45 2.10 6 107.8682 1.93 7.5762 1.30447 0.88 0.88 1.00 Silver +48 Cd 1.46 1.44 1.44 2.20 6 112.411 1.69 8.9938 0 1.00 0.85 0.56 Cadmium +49 In 1.49 1.42 1.42 2.20 3 114.818 1.78 5.7864 0.404 0.65 0.46 0.45 Indium +50 Sn 1.72 1.39 1.39 1.93 4 118.701 1.96 7.3439 1.112066 0.40 0.50 0.50 Tin +51 Sb 1.82 1.39 1.39 2.17 3 121.760 2.05 8.6084 1.047401 0.62 0.39 0.71 Antimony +52 Te 2.01 1.38 1.38 2.06 2 127.60 2.10 9.0096 1.970875 0.83 0.48 0.00 Tellurium +53 I 2.21 1.39 1.39 1.98 1 126.90447 2.66 10.4513 3.059038 0.58 0.00 0.58 Iodine +54 Xe 0.00 1.40 1.40 2.16 0 131.293 2.60 12.1298 0 0.26 0.62 0.69 Xenon +55 Cs 0.86 2.44 2.44 3.43 1 132.90545 0.79 3.8939 0.471626 0.34 0.09 0.56 Caesium +56 Ba 0.97 2.15 2.15 2.68 2 137.327 0.89 5.2117 0.14462 0.00 0.79 0.00 Barium +57 La 1.08 2.07 2.07 2.50 12 138.9055 1.10 5.5769 0.47 0.44 0.83 1.00 Lanthanum +58 Ce 0.00 2.04 2.04 2.48 6 140.116 1.12 5.5387 0.5 1.00 1.00 0.78 Cerium +59 Pr 0.00 2.03 2.03 2.47 6 140.90765 1.13 5.473 0.5 0.85 1.00 0.78 Praseodymium +60 Nd 0.00 2.01 2.01 2.45 6 144.24 1.14 5.525 0.5 0.78 1.00 0.78 Neodymium +61 Pm 0.00 1.99 1.99 2.43 6 145 0.00 5.582 0.5 0.64 1.00 0.78 Promethium +62 Sm 0.00 1.98 1.98 2.42 6 150.36 1.17 5.6437 0.5 0.56 1.00 0.78 Samarium +63 Eu 0.00 1.98 1.98 2.40 6 151.964 0.00 5.6704 0.5 0.38 1.00 0.78 Europium +64 Gd 0.00 1.96 1.96 2.38 6 157.25 1.20 6.1498 0.5 0.27 1.00 0.78 Gadolinium +65 Tb 0.00 1.94 1.94 2.37 6 158.92534 0.00 5.8638 0.5 0.19 1.00 0.78 Terbium +66 Dy 0.00 1.92 1.92 2.35 6 162.500 1.22 5.9389 0.5 0.12 1.00 0.78 Dysprosium +67 Ho 0.00 1.92 1.92 2.33 6 164.93032 1.23 6.0215 0.5 0.00 1.00 0.61 Holmium +68 Er 0.00 1.89 1.89 2.32 6 167.259 1.24 6.1077 0.5 0.00 0.90 0.46 Erbium +69 Tm 0.00 1.90 1.90 2.30 6 168.93421 1.25 6.1843 0.5 0.00 0.83 0.32 Thulium +70 Yb 0.00 1.87 1.87 2.28 6 173.054 0.00 6.2542 0.5 0.00 0.75 0.22 Ytterbium +71 Lu 0.00 1.87 1.87 2.27 6 174.9668 1.27 5.4259 0.5 0.00 0.67 0.14 Lutetium +72 Hf 1.23 1.75 1.75 2.25 6 178.49 1.30 6.8251 0 0.30 0.76 1.00 Hafnium +73 Ta 1.33 1.70 1.70 2.20 6 180.9479 1.50 7.5496 0.322 0.30 0.65 1.00 Tantalum +74 W 1.40 1.62 1.62 2.10 6 183.84 2.36 7.864 0.815 0.13 0.58 0.84 Tungsten +75 Re 1.46 1.51 1.51 2.05 6 186.207 1.90 7.8335 0.15 0.15 0.49 0.67 Rhenium +76 Os 1.52 1.44 1.44 2.00 6 190.23 2.20 8.4382 1.0778 0.15 0.40 0.59 Osmium +77 Ir 1.55 1.41 1.41 2.00 6 192.217 2.20 8.967 1.56436 0.09 0.33 0.53 Iridium +78 Pt 1.44 1.36 1.36 2.05 6 195.078 2.28 8.9588 2.1251 0.96 0.93 0.82 Platinum +79 Au 1.42 1.36 1.36 2.10 6 196.96655 2.54 9.2255 2.30861 0.80 0.82 0.12 Gold +80 Hg 1.44 1.32 1.32 2.05 6 200.59 2.00 10.4375 0 0.71 0.71 0.76 Mercury +81 Tl 1.44 1.45 1.45 1.96 3 204.3833 1.62 6.1082 0.377 0.65 0.33 0.30 Thallium +82 Pb 1.55 1.46 1.46 2.02 4 207.2 2.33 7.4167 0.364 0.34 0.35 0.38 Lead +83 Bi 1.67 1.48 1.48 2.07 3 208.98040 2.02 7.2855 0.942363 0.62 0.31 0.71 Bismuth +84 Po 1.76 1.40 1.40 1.97 2 209 2.00 8.414 1.9 0.67 0.36 0.00 Polonium +85 At 1.90 1.50 1.50 2.02 1 210 2.20 0 2.8 0.46 0.31 0.27 Astatine +86 Rn 0.00 1.50 1.50 2.20 0 222 0.00 10.7485 0 0.26 0.51 0.59 Radon +87 Fr 0.00 2.60 2.60 3.48 1 223 0.70 4.0727 0 0.26 0.00 0.40 Francium +88 Ra 0.00 2.21 2.21 2.83 2 226 0.90 5.2784 0 0.00 0.49 0.00 Radium +89 Ac 0.00 2.15 2.15 2.00 6 227 1.10 5.17 0 0.44 0.67 0.98 Actinium +90 Th 0.00 2.06 2.06 2.40 6 232.0381 1.30 6.3067 0 0.00 0.73 1.00 Thorium +91 Pa 0.00 2.00 2.00 2.00 6 231.03588 1.50 5.89 0 0.00 0.63 1.00 Protactinium +92 U 0.00 1.96 1.96 2.30 6 238.02891 1.38 6.1941 0 0.00 0.56 1.00 Uranium +93 Np 0.00 1.90 1.90 2.00 6 237 1.36 6.2657 0 0.00 0.50 1.00 Neptunium +94 Pu 0.00 1.87 1.87 2.00 6 244 1.28 6.026 0 0.00 0.42 1.00 Plutonium +95 Am 0.00 1.80 1.80 2.00 6 243 1.30 5.9738 0 0.33 0.36 0.95 Americium +96 Cm 0.00 1.69 1.69 2.00 6 247 1.30 5.9914 0 0.47 0.36 0.89 Curium +97 Bk 0.00 1.60 1.60 2.00 6 247 1.30 6.1979 0 0.54 0.31 0.89 Berkelium +98 Cf 0.00 1.60 1.60 2.00 6 251 1.30 6.2817 0 0.63 0.21 0.83 Californium +99 Es 0.00 1.60 1.60 2.00 6 252 1.30 6.42 0 0.70 0.12 0.83 Einsteinium +100 Fm 0.00 1.60 1.60 2.00 6 257 1.30 6.5 0 0.70 0.12 0.73 Fermium +101 Md 0.00 1.60 1.60 2.00 6 258 1.30 6.58 0 0.70 0.05 0.65 Mendelevium +102 No 0.00 1.60 1.60 2.00 6 259 1.30 6.65 0 0.74 0.05 0.53 Nobelium +103 Lr 0.00 1.60 1.60 2.00 6 262 0.00 4.9 0 0.78 0.00 0.40 Lawrencium +104 Rf 0.00 1.60 1.60 2.00 6 267 0.00 6 0 0.80 0.00 0.35 Rutherfordium +105 Db 0.00 1.60 1.60 2.00 6 268 0.00 0 0 0.82 0.00 0.31 Dubnium +106 Sg 0.00 1.60 1.60 2.00 6 271 0.00 0 0 0.85 0.00 0.27 Seaborgium +107 Bh 0.00 1.60 1.60 2.00 6 272 0.00 0 0 0.88 0.00 0.22 Bohrium +108 Hs 0.00 1.60 1.60 2.00 6 270 0.00 0 0 0.90 0.00 0.18 Hassium +109 Mt 0.00 1.60 1.60 2.00 6 268 0.00 0 0 0.92 0.00 0.15 Meitnerium +110 Ds 0.00 1.60 1.60 2.00 6 281 0.00 0 0 0.93 0.00 0.14 Darmstadtium +111 Rg 0.00 1.60 1.60 2.00 6 280 0.00 0 0 0.94 0.00 0.13 Roentgenium +112 Cn 0.00 1.60 1.60 2.00 6 285 0.00 0 0 0.95 0.00 0.12 Copernicium +113 Uut 0.00 1.60 1.60 2.00 6 284 0.00 0 0 0.96 0.00 0.11 Ununtrium +114 Uuq 0.00 1.60 1.60 2.00 6 289 0.00 0 0 0.97 0.00 0.10 Ununquadium +115 Uup 0.00 1.60 1.60 2.00 6 288 0.00 0 0 0.98 0.00 0.09 Ununpentium +116 Uuh 0.00 1.60 1.60 2.00 6 293 0.00 0 0 0.99 0.00 0.08 Ununhexium +117 Uuh 0.00 1.60 1.60 2.00 6 294 0.00 0 0 0.99 0.00 0.07 Ununseptium +118 Uuh 0.00 1.60 1.60 2.00 6 294 0.00 0 0 0.99 0.00 0.06 Ununoctium
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/fragments.txt Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,33785 @@ +# +# Open Babel file: fragments.txt +# +# Copyright (c) 2007-2008 by Geoffrey R Hutchison +# Part of the Open Babel package, under the GNU General Public License (GPL) +# +# Fragments for OBBuilder coordinate generation +# These consist of a generic SMARTS pattern +# followed by the 3D coordinates of all heavy atoms +# +# Fragments are ordered by length of SMARTS pattern +# (i.e., most complicated will match first) +# +# This file contains ~1000 of the most common ring fragments +# from analysis over the NCI database and ZINC +# +# NCI: http://cactus.nci.nih.gov/ncidb2/download.html +# ZINC: http://zinc.docking.org/ +# +A1AA[A@@]2(AA1)A[A@H]1[A@H](A[A@@H]3[A@@H]1AA[A@H]1[A@@H]3AA[A@H]3AAAA[A@H]13)A2 + -6.211 -1.460 -0.030 + -5.943 -0.593 1.206 + -5.091 0.648 0.864 + -3.994 0.300 -0.169 + -4.538 -0.250 -1.367 + -5.898 -0.674 -1.321 + -3.111 1.535 -0.461 + -1.792 1.261 0.318 + -2.126 0.038 1.158 + -0.839 -0.820 1.272 + 0.215 0.187 0.788 + -0.505 0.862 -0.397 + 0.361 2.038 -0.842 + 1.787 1.544 -1.206 + 2.492 0.838 -0.023 + 1.643 -0.352 0.504 + 1.731 -1.601 -0.389 + 3.140 -1.884 -0.874 + 4.220 -1.079 -0.124 + 5.652 -1.521 -0.524 + 6.711 -0.431 -0.189 + 6.283 0.453 0.974 + 4.934 1.171 0.717 + 3.983 0.435 -0.283 + -3.106 -0.636 0.409 +A1A=A2AA3AA[A@@]45[A@@H]3A[A@@H]2[A@H]2[A@@H](A1)AAA(a1aaaaa51)[A@H]42 + -3.888 0.914 0.115 + -3.459 -0.469 0.519 + -2.450 -1.056 -0.087 + -1.962 -2.361 0.428 + -0.673 -2.830 -0.062 + 0.191 -3.047 1.144 + 0.602 -1.615 1.554 + 0.598 -0.812 0.219 + 0.084 -1.793 -0.806 + -0.800 -1.233 -1.901 + -1.848 -0.330 -1.263 + -1.065 0.868 -0.767 + -1.865 2.101 -0.431 + -2.873 1.838 0.542 + -0.974 3.251 0.020 + 0.403 2.844 0.453 + 0.828 1.570 0.379 + 2.076 1.022 0.182 + 3.313 1.677 0.144 + 4.435 0.913 -0.126 + 4.355 -0.449 -0.358 + 3.133 -1.117 -0.307 + 2.013 -0.363 -0.016 + -0.183 0.472 0.416 +A1AA[A@@H]2[A@H](A1)AA[A@H]1[A@@H]2AA[A@@H]2[A@H]1AA[A@@H]1AAA[A@@H]21 + -3.053 1.785 1.205 + -3.252 1.888 -0.289 + -3.572 0.529 -0.878 + -2.734 -0.643 -0.356 + -2.599 -0.629 1.153 + -2.102 0.714 1.691 + -1.649 -1.724 1.640 + -0.276 -1.515 1.004 + -0.364 -1.639 -0.513 + -1.409 -0.720 -1.105 + -0.879 0.699 -1.318 + 0.352 0.642 -2.224 + 1.470 -0.096 -1.492 + 1.030 -1.511 -1.133 + 2.052 -2.232 -0.252 + 2.597 -1.407 0.910 + 3.123 -0.085 0.382 + 3.542 0.917 1.473 + 3.414 2.288 0.758 + 2.384 2.093 -0.385 + 1.927 0.647 -0.270 +A1AA[A@@H]2[A@H](A1)AA[A@H]1[A@@H]2AA[A@@H]2[A@H]1AA[A@H]1AAA[A@@H]21 + 3.192 1.390 -1.579 + 3.326 1.929 -0.176 + 3.606 0.809 0.807 + 2.782 -0.467 0.617 + 2.739 -0.906 -0.833 + 2.271 0.207 -1.774 + 1.821 -2.114 -1.014 + 0.409 -1.749 -0.560 + 0.383 -1.369 0.915 + 1.409 -0.313 1.261 + 0.898 1.103 1.000 + -0.408 1.331 1.764 + -1.489 0.408 1.193 + -1.036 -1.032 1.362 + -2.064 -1.979 0.744 + -2.348 -1.673 -0.709 + -2.655 -0.233 -0.998 + -4.130 0.114 -0.711 + -4.114 1.655 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/gaff.dat Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,5169 @@ +AMBER General Force Field for organic mol., add. info. at the end (June, 2003) +c 12.01 0.616 Sp2 C carbonyl group +c1 12.01 0.360 Sp C +c2 12.01 0.360 Sp2 C +c3 12.01 0.878 Sp3 C +ca 12.01 0.360 Sp2 C in pure aromatic systems +cp 12.01 0.360 Head Sp2 C that connect two rings in biphenyl sys. +cq 12.01 0.360 Head Sp2 C that connect two rings in biphenyl sys. identical to cp +cc 12.01 0.360 Sp2 carbons in non-pure aromatic systems +cd 12.01 0.360 Sp2 carbons in non-pure aromatic systems, identical to cc +ce 12.01 0.360 Inner Sp2 carbons in conjugated systems +cf 12.01 0.360 Inner Sp2 carbons in conjugated systems, identical to ce +cg 12.01 0.360 Inner Sp carbons in conjugated systems +ch 12.01 0.360 Inner Sp carbons in conjugated systems, identical to cg +cx 12.01 0.360 Sp3 carbons in triangle systems +cy 12.01 0.360 Sp3 carbons in square systems +cu 12.01 0.360 Sp2 carbons in triangle systems +cv 12.01 0.360 Sp2 carbons in square systems +h1 1.008 0.135 H bonded to aliphatic carbon with 1 electrwd. group +h2 1.008 0.135 H bonded to aliphatic carbon with 2 electrwd. group +h3 1.008 0.135 H bonded to aliphatic carbon with 3 electrwd. group +h4 1.008 0.135 H bonded to non-sp3 carbon with 1 electrwd. group +h5 1.008 0.135 H bonded to non-sp3 carbon with 2 electrwd. group +ha 1.008 0.135 H bonded to aromatic carbon +hc 1.008 0.135 H bonded to aliphatic carbon without electrwd. group +hn 1.008 0.161 H bonded to nitrogen atoms +ho 1.008 0.135 Hydroxyl group +hp 1.008 0.135 H bonded to phosphate +hs 1.008 0.135 Hydrogen bonded to sulphur +hw 1.008 0.135 Hydrogen in water +hx 1.008 0.135 H bonded to C next to positively charged group +f 19.00 0.320 Fluorine +cl 35.45 1.910 Chlorine +br 79.90 2.880 Bromine +i 126.9 4.690 Iodine +n 14.01 0.530 Sp2 nitrogen in amide groups +n1 14.01 0.530 Sp N +n2 14.01 0.530 aliphatic Sp2 N with two connected atoms +n3 14.01 0.530 Sp3 N with three connected atoms +n4 14.01 0.530 Sp3 N with four connected atoms +na 14.01 0.530 Sp2 N with three connected atoms +nb 14.01 0.530 Sp2 N in pure aromatic systems +nc 14.01 0.530 Sp2 N in non-pure aromatic systems +nd 14.01 0.530 Sp2 N in non-pure aromatic systems, identical to nc +ne 14.01 0.530 Inner Sp2 N in conjugated systems +nf 14.01 0.530 Inner Sp2 N in conjugated systems, identical to ne +nh 14.01 0.530 Amine N connected one or more aromatic rings +no 14.01 0.530 Nitro N +o 16.00 0.434 Oxygen with one connected atom +oh 16.00 0.465 Oxygen in hydroxyl group +os 16.00 0.465 Ether and ester oxygen +ow 16.00 0.465 Oxygen in water +p2 30.97 1.538 Phosphate with two connected atoms +p3 30.97 1.538 Phosphate with three connected atoms, such as PH3 +p4 30.97 1.538 Phosphate with three connected atoms, such as O=P(CH3)2 +p5 30.97 1.538 Phosphate with four connected atoms, such as O=P(OH)3 +pb 30.97 1.538 Sp2 P in pure aromatic systems +pc 30.97 1.538 Sp2 P in non-pure aromatic systems +pd 30.97 1.538 Sp2 P in non-pure aromatic systems, identical to pc +pe 30.97 1.538 Inner Sp2 P in conjugated systems +pf 30.97 1.538 Inner Sp2 P in conjugated systems, identical to pe +px 30.97 1.538 Special p4 in conjugated systems +py 30.97 1.538 Special p5 in conjugated systems +s 32.06 2.900 S with one connected atom +s2 32.06 2.900 S with two connected atom, involved at least one double bond +s4 32.06 2.900 S with three connected atoms +s6 32.06 2.900 S with four connected atoms +sh 32.06 2.900 Sp3 S connected with hydrogen +ss 32.06 2.900 Sp3 S in thio-ester and thio-ether +sx 32.06 2.900 Special s4 in conjugated systems +sy 32.06 2.900 Special s6 in conjugated systems + +hn ho hs n na nc nd ne nf n2 n3 n4 o oh os ow sh ss +ow-hw 553.0 0.9572 TIP3P water +br-br 123.2 2.542 SOURCE1 4 0.0000 0.0000 +br-c 240.3 1.946 SOURCE2 2 0.0285 0.0285 +br-c1 352.7 1.787 SOURCE2 4 0.0022 0.0024 +br-c2 278.7 1.883 SOURCE1 31 0.0000 0.0000 +br-c3 229.5 1.966 SOURCE1 100 0.0000 0.0000 +br-ca 269.6 1.897 SOURCE1 127 0.0028 0.0058 +br-cx 261.4 1.910 SOURCE1 8 0.0000 0.0000 +br-i 142.4 2.671 SOURCE1 2 0.0245 0.0245 +br-n 320.2 1.873 SOURCE3 4 0.0037 0.0046 +br-n1 330.4 1.860 SOURCE0 1 +br-n2 219.0 2.038 SOURCE3 5 0.0956 0.1082 +br-n3 265.9 1.952 SOURCE3 2 0.0000 0.0000 +br-n4 282.4 1.926 SOURCE3 3 0.0012 0.0013 +br-na 237.3 2.002 SOURCE3 7 0.1938 0.2156 +br-nh 270.9 1.944 SOURCE3 1 0.0000 0.0000 +br-no 191.0 2.101 SOURCE3 1 0.0000 0.0000 +br-o 278.9 1.800 SOURCE0 1 +br-oh 237.2 1.866 SOURCE3 1 0.0000 0.0000 +br-os 225.6 1.887 SOURCE3 2 0.0000 0.0000 +br-p2 174.3 2.210 SOURCE3 9 0.0470 0.0510 +br-p3 167.0 2.231 SOURCE3 3 0.0096 0.0101 +br-p4 188.8 2.171 SOURCE0 1 +br-p5 179.3 2.196 SOURCE3 3 0.0094 0.0099 +br-s 170.6 2.220 SOURCE0 1 +br-s4 134.3 2.341 SOURCE3 1 0.0000 0.0000 +br-s6 172.7 2.214 SOURCE3 3 0.0417 0.0443 +br-sh 174.4 2.209 SOURCE3 1 0.0000 0.0000 +br-ss 176.6 2.203 SOURCE3 3 0.0033 0.0035 +c -c 290.1 1.550 SOURCE1 31 0.0080 0.0100 +c -c1 379.8 1.460 SOURCE0 1 +c -c2 449.9 1.406 SOURCE3 2 0.0370 0.0370 +c -c3 328.3 1.508 SOURCE1 2949 0.0049 0.0060 +c -ca 349.7 1.487 SOURCE1 480 0.0031 0.0055 +c -cc 377.4 1.462 SOURCE3 132 0.0165 0.0210 +c -cd 377.4 1.462 SOURCE3 132 0.0165 0.0210 +c -ce 363.8 1.474 SOURCE1 601 0.0091 0.0105 +c -cf 363.8 1.474 SOURCE1 601 0.0091 0.0105 +c -cg 389.3 1.452 SOURCE3 2 0.0000 0.0000 +c -ch 389.3 1.452 SOURCE3 2 same as c -cg +c -cl 293.5 1.766 SOURCE3 6 0.0235 0.0250 +c -cu 441.4 1.412 SOURCE2 1 0.0000 0.0000 +c -cx 350.8 1.486 SOURCE1 105 0.0000 0.0000 +c -cy 308.5 1.529 SOURCE1 18 0.0000 0.0000 +c -f 387.9 1.325 SOURCE2 6 0.0140 0.0147 +c -ha 325.1 1.101 SOURCE3 53 0.0078 0.0102 +c -i 198.9 2.209 SOURCE3 4 0.0332 0.0365 +c -n 478.2 1.345 SOURCE1 1235 0.0162 0.0215 +c -n2 374.6 1.420 SOURCE0 1 +c -n4 255.5 1.546 SOURCE3 4 0.0388 0.0388 +c -nc 438.8 1.371 SOURCE3 2 0.0108 0.0108 +c -nd 438.8 1.371 SOURCE3 2 same as c -nc +c -ne 388.0 1.409 SOURCE3 3 0.0088 0.0094 +c -nf 388.0 1.409 SOURCE3 3 same as c -ne +c -no 260.1 1.540 SOURCE0 1 +c -o 648.0 1.214 SOURCE1 3682 0.0134 0.0165 +c -oh 466.4 1.306 SOURCE1 271 0.0026 0.0041 +c -os 411.3 1.343 SOURCE1 1044 0.0114 0.0171 +c -p2 210.3 1.900 SOURCE0 1 +c -p3 219.0 1.883 SOURCE3 6 0.0094 0.0129 +c -p4 220.6 1.880 SOURCE0 1 +c -p5 225.9 1.870 SOURCE0 1 +c -pe 204.9 1.911 SOURCE3 3 0.0023 0.0025 +c -pf 204.9 1.911 SOURCE3 3 same as c -pe +c -px 208.3 1.904 SOURCE3 1 0.0000 0.0000 +c -py 227.6 1.867 SOURCE3 6 0.0141 0.0199 +c -s 328.9 1.675 SOURCE1 401 0.0077 0.0128 +c -s4 200.4 1.870 SOURCE0 1 +c -s6 200.4 1.870 SOURCE0 1 +c -sh 249.6 1.781 SOURCE3 6 0.0157 0.0171 +c -ss 261.9 1.762 SOURCE1 20 0.0000 0.0000 +c -sx 193.3 1.885 SOURCE3 5 0.0070 0.0088 +c -sy 202.8 1.865 SOURCE3 5 0.0063 0.0085 +c1-c1 986.2 1.181 SOURCE1 265 0.0022 0.0031 +c1-c2 625.0 1.307 SOURCE1 18 0.0000 0.0000 +c1-c3 368.3 1.470 SOURCE1 215 0.0013 0.0017 +c1-ca 404.1 1.440 SOURCE0 1 +c1-cg 845.8 1.222 SOURCE3 22 0.0074 0.0101 +c1-ch 845.8 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371.8 1.630 SOURCE1 14 0.0000 0.0000 +c1-s2 410.0 1.595 SOURCE3 1 0.0000 0.0000 +c1-s4 272.9 1.746 SOURCE3 2 0.0000 0.0000 +c1-s6 290.4 1.722 SOURCE3 2 0.0000 0.0000 +c1-sh 324.5 1.680 SOURCE0 1 +c1-ss 325.4 1.679 SOURCE1 10 0.0000 0.0000 +c2-c2 589.7 1.324 SOURCE1 974 0.0048 0.0096 +c2-c3 328.3 1.508 SOURCE1 2536 0.0016 0.0021 +c2-ca 357.2 1.480 SOURCE0 1 +c2-cc 522.6 1.360 SOURCE1 771 0.0152 0.0185 +c2-cd 522.6 1.360 SOURCE1 771 0.0152 0.0185 +c2-ce 560.5 1.339 SOURCE3 62 0.0085 0.0128 +c2-cf 560.5 1.339 SOURCE3 62 same as c2-ce +c2-cl 328.8 1.722 SOURCE1 163 0.0093 0.0098 +c2-cu 573.9 1.332 SOURCE2 1 0.0000 0.0000 +c2-cx 333.3 1.503 SOURCE2 1 0.0000 0.0000 +c2-cy 309.4 1.528 SOURCE2 1 0.0000 0.0000 +c2-f 368.7 1.340 SOURCE1 34 0.0000 0.0000 +c2-h4 348.6 1.084 SOURCE3 40 0.0037 0.0058 +c2-h5 357.5 1.078 SOURCE3 3 0.0061 0.0067 +c2-ha 344.3 1.087 SOURCE3 797 0.0030 0.0046 +c2-hc 344.3 1.087 SOURCE3 789 0.0030 0.0046 +c2-hx 350.1 1.083 SOURCE3 3 0.0008 0.0008 +c2-i 223.2 2.153 SOURCE3 2 0.0000 0.0000 +c2-n 390.5 1.407 SOURCE3 9 0.0109 0.0124 +c2-n1 546.0 1.306 SOURCE3 4 0.0161 0.0161 +c2-n2 581.1 1.288 SOURCE1 103 0.0095 0.0100 +c2-n3 486.3 1.340 SOURCE0 1 +c2-n4 309.1 1.482 SOURCE3 5 0.0047 0.0064 +c2-na 411.1 1.391 SOURCE3 31 0.0271 0.0289 +c2-nc 533.0 1.313 SOURCE1 99 0.0065 0.0095 +c2-nd 533.0 1.313 SOURCE1 99 same as c2-nc +c2-ne 597.7 1.280 SOURCE3 37 0.0090 0.0110 +c2-nf 597.7 1.280 SOURCE3 37 same as c2-ne +c2-nh 462.6 1.355 SOURCE3 38 0.0385 0.0413 +c2-no 327.6 1.463 SOURCE3 4 0.0013 0.0013 +c2-o 546.2 1.261 SOURCE3 4 0.0144 0.0144 +c2-oh 425.4 1.333 SOURCE1 53 0.0000 0.0000 +c2-os 392.6 1.357 SOURCE1 315 0.0088 0.0097 +c2-p2 375.9 1.670 SOURCE3 62 0.0078 0.0147 +c2-p3 246.6 1.834 SOURCE3 5 0.0041 0.0042 +c2-p4 254.0 1.822 SOURCE0 1 +c2-p5 255.2 1.820 SOURCE0 1 +c2-pe 355.3 1.691 SOURCE3 52 0.0318 0.0542 +c2-pf 355.3 1.691 SOURCE3 52 same as c2-pe +c2-s 281.5 1.734 SOURCE3 4 0.0034 0.0034 +c2-s2 393.1 1.610 SOURCE2 1 0.0000 0.0000 +c2-s4 263.2 1.760 SOURCE0 1 +c2-s6 263.2 1.760 SOURCE0 1 +c2-sh 255.3 1.772 SOURCE3 3 0.0068 0.0072 +c2-ss 280.0 1.736 SOURCE1 209 0.0135 0.0155 +c3-c3 303.1 1.535 SOURCE1 14664 0.0043 0.0048 +c3-ca 323.5 1.513 SOURCE1 1813 0.0000 0.0000 +c3-cc 337.3 1.499 SOURCE3 50 0.0059 0.0096 +c3-cd 337.3 1.499 SOURCE3 50 0.0059 0.0096 +c3-ce 331.3 1.505 SOURCE3 9 0.0019 0.0024 +c3-cf 331.3 1.505 SOURCE3 9 same as c3-ce +c3-cl 279.0 1.786 SOURCE1 267 0.0151 0.0194 +c3-cu 359.4 1.478 SOURCE1 7 0.0000 0.0000 +c3-cv 347.6 1.489 SOURCE1 11 0.0000 0.0000 +c3-cx 322.5 1.514 SOURCE1 712 0.0044 0.0045 +c3-cy 308.5 1.529 SOURCE1 376 0.0000 0.0000 +c3-f 363.8 1.344 SOURCE1 617 0.0241 0.0281 +c3-h1 335.9 1.093 SOURCE3 2175 0.0045 0.0082 +c3-h2 326.4 1.100 SOURCE3 66 0.0110 0.0280 +c3-h3 335.9 1.093 SOURCE2 1 0.0000 0.0000 +c3-hc 337.3 1.092 SOURCE3 2815 0.0040 0.0059 +c3-hx 338.7 1.091 SOURCE3 146 0.0023 0.0066 +c3-i 219.1 2.162 SOURCE1 15 0.0000 0.0000 +c3-n 330.6 1.460 SOURCE1 187 0.0065 0.0079 +c3-n1 325.1 1.470 SOURCE3 +c3-n2 313.8 1.477 SOURCE1 129 0.0136 0.0138 +c3-n3 320.6 1.470 SOURCE1 1678 0.0013 0.0017 +c3-n4 293.6 1.499 SOURCE1 1370 0.0000 0.0000 +c3-na 334.7 1.456 SOURCE3 23 0.0096 0.0119 +c3-nc 334.7 1.456 SOURCE3 9 0.0091 0.0109 +c3-nd 334.7 1.456 SOURCE3 9 same as c3-nc +c3-nh 332.7 1.458 SOURCE3 27 0.0067 0.0085 +c3-no 265.4 1.533 SOURCE1 83 0.0163 0.0212 +c3-o 422.6 1.335 SOURCE3 4 0.0100 0.0100 +c3-oh 314.1 1.426 SOURCE1 914 0.0110 0.0129 +c3-os 301.5 1.439 SOURCE1 3123 0.0112 0.0126 +c3-p2 234.3 1.855 SOURCE3 9 0.0100 0.0125 +c3-p3 240.6 1.844 SOURCE3 109 0.0091 0.0107 +c3-p4 247.2 1.833 SOURCE3 29 0.0091 0.0138 +c3-p5 259.7 1.813 SOURCE1 84 0.0000 0.0000 +c3-px 252.7 1.824 SOURCE3 28 0.0079 0.0098 +c3-py 259.7 1.813 SOURCE3 13 0.0144 0.0163 +c3-s 212.9 1.845 SOURCE3 4 0.0185 0.0185 +c3-s4 233.8 1.807 SOURCE1 139 0.0022 0.0023 +c3-s6 254.0 1.774 SOURCE1 118 0.0080 0.0103 +c3-sh 225.3 1.822 SOURCE3 12 0.0042 0.0051 +c3-ss 225.8 1.821 SOURCE1 358 0.0049 0.0075 +c3-sx 232.6 1.809 SOURCE3 30 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1.335 SOURCE1 25 0.0000 0.0000 +cv-cy 323.5 1.513 SOURCE1 50 0.0000 0.0000 +cv-ha 344.3 1.087 SOURCE3 2 0.0000 0.0000 +cx-cv 328.3 1.508 SOURCE1 2536 Same as +cx-cx 337.3 1.499 SOURCE1 1204 0.0159 0.0183 +cx-cy 321.5 1.515 SOURCE3 2 0.0000 0.0000 +cx-f 347.2 1.358 SOURCE2 3 0.0047 0.0050 +cx-h1 344.3 1.087 SOURCE3 10 0.0013 0.0017 +cx-h2 350.1 1.083 SOURCE3 2 0.0000 0.0000 +cx-hc 345.8 1.086 SOURCE3 44 0.0009 0.0011 +cx-n 315.7 1.475 SOURCE3 1 0.0000 0.0000 +cx-n2 309.1 1.482 SOURCE3 2 0.0000 0.0000 +cx-n3 318.7 1.472 SOURCE1 134 0.0000 0.0000 +cx-oh 387.4 1.361 SOURCE3 3 0.0017 0.0018 +cx-os 320.1 1.420 SOURCE3 7 0.0205 0.0222 +cx-p3 227.6 1.867 SOURCE2 1 0.0000 0.0000 +cx-s4 225.3 1.822 SOURCE2 1 0.0000 0.0000 +cx-s6 283.7 1.731 SOURCE2 1 0.0000 0.0000 +cx-ss 229.2 1.815 SOURCE2 1 0.0000 0.0000 +cy-cy 286.8 1.554 SOURCE1 742 0.0013 0.0041 +cy-h1 330.4 1.097 SOURCE3 17 0.0042 0.0058 +cy-hc 334.5 1.094 SOURCE3 63 0.0012 0.0014 +cy-n3 307.2 1.484 SOURCE1 21 0.0000 0.0000 +cy-oh 325.2 1.415 SOURCE3 2 0.0000 0.0000 +cy-os 280.7 1.462 SOURCE3 4 0.0101 0.0101 +f -n 391.7 1.397 SOURCE3 3 0.0106 0.0112 +f -n1 375.7 1.410 SOURCE0 1 +f -n2 337.5 1.444 SOURCE3 5 0.0292 0.0377 +f -n3 380.6 1.406 SOURCE1 9 0.0000 0.0000 +f -n4 526.8 1.308 SOURCE3 2 0.0000 0.0000 +f -na 374.5 1.411 SOURCE3 7 0.0537 0.0611 +f -nh 357.1 1.426 SOURCE3 3 0.0080 0.0085 +f -no 314.4 1.467 SOURCE2 1 0.0000 0.0000 +f -o 442.2 1.330 SOURCE0 1 +f -oh 305.4 1.444 SOURCE3 1 0.0000 0.0000 +f -os 326.2 1.423 SOURCE3 2 0.0000 0.0000 +f -p2 287.3 1.536 SOURCE3 7 0.1437 0.2054 +f -p3 254.5 1.578 SOURCE2 8 0.0093 0.0103 +f -p4 246.0 1.590 SOURCE0 1 +f -p5 253.8 1.579 SOURCE1 72 0.0000 0.0000 +f -s 233.3 1.660 SOURCE0 1 +f -s2 244.4 1.643 SOURCE2 1 0.0000 0.0000 +f -s4 282.4 1.591 SOURCE2 4 0.0065 0.0065 +f -s6 312.1 1.556 SOURCE2 5 0.0163 0.0220 +f -sh 240.4 1.649 SOURCE3 1 0.0000 0.0000 +f -ss 250.5 1.634 SOURCE3 3 0.0147 0.0156 +hn-n 410.2 1.009 SOURCE3 149 0.0089 0.0098 +hn-n1 455.1 0.986 SOURCE2 1 0.0000 0.0000 +hn-n2 375.5 1.029 SOURCE3 108 0.0070 0.0096 +hn-n3 394.1 1.018 SOURCE3 157 0.0063 0.0086 +hn-n4 369.0 1.033 SOURCE3 264 0.0054 0.0082 +hn-na 406.6 1.011 SOURCE3 46 0.0076 0.0107 +hn-nh 401.2 1.014 SOURCE3 209 0.0068 0.0091 +hn-no 385.6 1.023 SOURCE3 1 0.0000 0.0000 +ho-o 357.9 0.981 SOURCE3 1 0.0000 0.0000 +ho-oh 369.6 0.974 SOURCE3 367 0.0069 0.0105 +hp-p2 385.1 1.336 SOURCE3 87 0.1430 0.1706 +hp-p3 303.1 1.409 SOURCE3 101 0.0170 0.0617 +hp-p4 368.7 1.349 SOURCE3 17 0.1277 0.1577 +hp-p5 305.0 1.407 SOURCE3 7 0.0049 0.0062 +hs-s 286.4 1.353 SOURCE3 1 0.0000 0.0000 +hs-s4 266.4 1.375 SOURCE3 5 0.0004 0.0004 +hs-s6 280.8 1.359 SOURCE3 5 0.0012 0.0015 +hs-sh 302.2 1.337 SOURCE3 98 0.0150 0.0486 +i -i 109.2 2.917 SOURCE1 1 0.0000 0.0000 +i -n 278.3 2.098 SOURCE3 5 0.0153 0.0156 +i -n1 302.1 2.060 SOURCE0 1 +i -n2 182.6 2.304 SOURCE3 6 0.1010 0.1186 +i -n3 231.8 2.185 SOURCE3 3 0.0412 0.0437 +i -n4 246.6 2.155 SOURCE3 3 0.0158 0.0168 +i -na 260.5 2.129 SOURCE3 8 0.0838 0.1276 +i -nh 249.2 2.150 SOURCE3 1 0.0000 0.0000 +i -no 211.0 2.231 SOURCE3 1 0.0000 0.0000 +i -o 323.8 1.980 SOURCE0 1 +i -oh 247.9 2.101 SOURCE3 2 0.0000 0.0000 +i -os 233.6 2.129 SOURCE3 3 0.0138 0.0146 +i -p2 108.2 2.643 SOURCE3 6 0.0266 0.0297 +i -p3 123.6 2.566 SOURCE3 3 0.0015 0.0016 +i -p4 183.0 2.352 SOURCE3 4 0.2600 0.2600 +i -p5 117.3 2.596 SOURCE3 3 0.0135 0.0143 +i -s 175.1 2.430 SOURCE0 1 +i -s4 82.8 2.870 SOURCE0 1 +i -s6 82.8 2.870 SOURCE3 1 0.0000 0.0000 +i -sh 138.5 2.560 SOURCE0 1 +i -ss 135.9 2.571 SOURCE3 3 0.0061 0.0065 +n -n 469.7 1.390 SOURCE3 5 0.0035 0.0038 +n -n1 553.9 1.340 SOURCE0 1 +n -n2 499.7 1.371 SOURCE3 9 0.0164 0.0200 +n -n3 443.3 1.408 SOURCE3 5 0.0077 0.0087 +n -n4 410.8 1.432 SOURCE3 5 0.0096 0.0098 +n -na 486.8 1.379 SOURCE3 11 0.0052 0.0071 +n -nc 532.1 1.352 SOURCE3 4 0.0055 0.0058 +n -nd 532.1 1.352 SOURCE3 4 same as n -nc +n -nh 437.7 1.412 SOURCE3 4 0.0035 0.0037 +n -no 381.2 1.456 SOURCE3 4 0.0278 0.0327 +n -o 646.6 1.264 SOURCE3 9 0.0336 0.0381 +n -oh 395.4 1.410 SOURCE3 6 0.0078 0.0106 +n -os 372.3 1.429 SOURCE3 7 0.0364 0.0528 +n -p2 310.3 1.733 SOURCE3 8 0.0143 0.0217 +n -p3 282.2 1.770 SOURCE3 9 0.0102 0.0118 +n -p4 309.5 1.734 SOURCE3 1 0.0000 0.0000 +n -p5 327.0 1.713 SOURCE3 4 0.0084 0.0109 +n -pc 304.8 1.740 SOURCE3 3 0.0009 0.0010 +n -pd 304.8 1.740 SOURCE3 3 same as n -pc +n -s 247.5 1.767 SOURCE3 3 0.0011 0.0011 +n -s4 238.2 1.782 SOURCE3 4 0.0154 0.0214 +n -s6 270.8 1.732 SOURCE3 4 0.0177 0.0224 +n -sh 273.6 1.728 SOURCE3 4 0.0108 0.0128 +n -ss 281.6 1.717 SOURCE3 7 0.0120 0.0133 +n1-n1 1221.7 1.124 SOURCE1 19 0.0000 0.0000 +n1-n1 1365.7 1.100 SOURCE3 +n1-n2 857.4 1.216 SOURCE1 19 0.0000 0.0000 +n1-n3 535.7 1.350 SOURCE0 1 +n1-n4 518.2 1.360 SOURCE0 1 +n1-na 535.7 1.350 SOURCE0 1 +n1-nc 857.4 1.216 SOURCE1 38 0.0000 0.0000 +n1-nd 857.4 1.216 SOURCE1 38 0.0000 0.0000 +n1-ne 751.9 1.252 SOURCE2 1 0.0000 0.0000 +n1-nf 751.9 1.252 SOURCE2 1 same as n1-ne +n1-nh 553.9 1.340 SOURCE0 1 +n1-no 454.8 1.400 SOURCE0 1 +n1-o 617.5 1.277 SOURCE3 5 0.0340 0.0438 +n1-oh 569.8 1.300 SOURCE0 1 +n1-os 550.5 1.310 SOURCE0 1 +n1-p2 358.8 1.678 SOURCE3 2 0.0282 0.0282 +n1-p3 376.7 1.660 SOURCE0 1 +n1-p4 353.0 1.680 SOURCE3 +n1-p5 482.7 1.571 SOURCE1 132 0.0000 0.0000 +n1-s 328.7 1.659 SOURCE3 6 0.0693 0.0789 +n1-s2 604.3 1.449 SOURCE2 2 0.0010 0.0010 +n1-s4 336.8 1.650 SOURCE0 1 +n1-s6 670.3 1.416 SOURCE2 2 0.0000 0.0000 +n1-sh 376.1 1.610 SOURCE0 1 +n1-ss 376.1 1.610 SOURCE0 1 +n2-n2 702.7 1.271 SOURCE3 27 0.0228 0.0347 +n2-n3 574.8 1.329 SOURCE2 1 0.0000 0.0000 +n2-n4 200.8 1.679 SOURCE3 7 0.2778 0.3138 +n2-na 450.4 1.403 SOURCE3 14 0.0399 0.0575 +n2-nc 743.9 1.255 SOURCE1 13 same as n2-nd +n2-nd 743.9 1.255 SOURCE1 13 0.0000 0.0000 +n2-ne 685.5 1.278 SOURCE3 30 0.0224 0.0302 +n2-nf 685.5 1.278 SOURCE3 30 same as n2-ne +n2-nh 525.1 1.356 SOURCE3 22 0.0218 0.0300 +n2-no 231.9 1.626 SOURCE3 4 0.1591 0.1933 +n2-o 789.9 1.209 SOURCE3 20 0.0284 0.0344 +n2-oh 416.2 1.394 SOURCE1 67 0.0000 0.0000 +n2-os 400.5 1.406 SOURCE3 10 0.0120 0.0147 +n2-p2 438.3 1.605 SOURCE3 35 0.0392 0.0737 +n2-p3 286.5 1.764 SOURCE3 7 0.0320 0.0374 +n2-p4 317.7 1.724 SOURCE0 1 +n2-p5 445.8 1.599 SOURCE1 7 0.0000 0.0000 +n2-pe 527.9 1.540 SOURCE3 20 0.1112 0.1392 +n2-pf 527.9 1.540 SOURCE3 20 same as n2-pe +n2-s 458.1 1.541 SOURCE1 37 0.0000 0.0000 +n2-s2 499.0 1.512 SOURCE2 1 0.0000 0.0000 +n2-s4 376.1 1.610 SOURCE0 1 +n2-s6 468.9 1.533 SOURCE3 3 0.0144 0.0144 +n2-sh 266.6 1.738 SOURCE3 5 0.0405 0.0511 +n2-ss 331.4 1.656 SOURCE1 36 0.0000 0.0000 +n3-n3 383.6 1.454 SOURCE1 44 0.0000 0.0000 +n3-n4 434.9 1.414 SOURCE1 13 0.0000 0.0000 +n3-na 426.7 1.420 SOURCE1 68 0.0000 0.0000 +n3-nh 426.7 1.420 SOURCE1 68 0.0000 0.0000 +n3-no 394.5 1.445 SOURCE3 3 0.0196 0.0208 +n3-o 564.0 1.303 SOURCE3 4 0.1197 0.1217 +n3-oh 413.5 1.396 SOURCE1 28 0.0000 0.0000 +n3-os 359.6 1.440 SOURCE1 34 0.0301 0.0315 +n3-p2 366.6 1.670 SOURCE0 1 +n3-p3 312.8 1.730 SOURCE1 40 0.0000 0.0000 +n3-p4 341.1 1.697 SOURCE1 88 0.0000 0.0000 +n3-p5 373.6 1.663 SOURCE1 501 0.0033 0.0086 +n3-s 232.3 1.792 SOURCE3 3 0.0168 0.0178 +n3-s4 251.3 1.761 SOURCE3 6 0.0563 0.0766 +n3-s6 353.8 1.632 SOURCE1 99 0.0090 0.0136 +n3-sh 265.9 1.739 SOURCE3 3 0.0145 0.0154 +n3-ss 277.9 1.722 SOURCE3 5 0.0172 0.0207 +n4-n4 349.9 1.484 SOURCE3 4 0.0089 0.0089 +n4-na 407.0 1.435 SOURCE3 9 0.0242 0.0390 +n4-nh 369.7 1.466 SOURCE3 5 0.0097 0.0108 +n4-no 354.2 1.480 SOURCE0 1 +n4-o 463.6 1.361 SOURCE3 3 0.0039 0.0041 +n4-oh 408.2 1.400 SOURCE3 3 0.0108 0.0115 +n4-os 381.8 1.421 SOURCE3 5 0.0225 0.0249 +n4-p2 185.9 1.942 SOURCE3 10 0.0514 0.0643 +n4-p3 215.1 1.880 SOURCE3 5 0.0143 0.0146 +n4-p4 187.6 1.938 SOURCE3 1 0.0000 0.0000 +n4-p5 242.9 1.830 SOURCE3 5 0.0082 0.0087 +n4-py 204.2 1.902 SOURCE3 4 0.0000 0.0000 +n4-s 210.3 1.832 SOURCE3 3 0.0004 0.0004 +n4-s4 151.0 1.972 SOURCE3 3 0.0187 0.0198 +n4-s6 172.7 1.914 SOURCE3 5 0.0414 0.0432 +n4-sh 221.5 1.811 SOURCE3 3 0.0025 0.0027 +n4-ss 221.0 1.812 SOURCE3 5 0.0061 0.0064 +na-na 453.3 1.401 SOURCE1 40 0.0000 0.0000 +na-nc 535.7 1.350 SOURCE3 152 0.0117 0.0180 +na-nd 535.7 1.350 SOURCE3 152 0.0117 0.0180 +na-nh 453.3 1.401 SOURCE1 40 0.0000 0.0000 +na-no 401.9 1.439 SOURCE3 9 0.0241 0.0289 +na-o 644.3 1.265 SOURCE1 25 0.0345 0.0347 +na-oh 412.2 1.397 SOURCE3 9 0.0161 0.0217 +na-os 355.2 1.444 SOURCE3 45 0.0349 0.0423 +na-p2 297.8 1.749 SOURCE3 11 0.0164 0.0192 +na-p3 288.0 1.762 SOURCE3 8 0.0101 0.0113 +na-p4 492.4 1.564 SOURCE3 5 0.2116 0.2161 +na-p5 325.3 1.715 SOURCE3 11 0.0197 0.0238 +na-pc 311.1 1.732 SOURCE3 81 0.0124 0.0207 +na-pd 311.1 1.732 SOURCE3 81 same as na-pc +na-py 327.8 1.712 SOURCE3 2 0.0000 0.0000 +na-s 248.7 1.765 SOURCE3 8 0.0083 0.0095 +na-s4 231.7 1.793 SOURCE3 10 0.0316 0.0421 +na-s6 274.3 1.727 SOURCE3 10 0.0169 0.0201 +na-sh 278.6 1.721 SOURCE3 9 0.0101 0.0113 +na-ss 270.1 1.733 SOURCE3 38 0.0280 0.0412 +na-sy 274.3 1.727 SOURCE3 1 +nb-nb 550.2 1.342 SOURCE1 15 0.0307 0.0314 +nb-pb 461.1 1.587 SOURCE1 162 0.0076 0.0091 +nc-nc 486.8 1.379 SOURCE3 9 0.0145 0.0164 +nc-nd 602.9 1.315 SOURCE3 9 0.0205 0.0221 +nc-os 414.9 1.395 SOURCE1 46 0.0163 0.0188 +nc-ss 433.5 1.560 SOURCE1 74 0.0000 0.0000 +nc-sy 439.8 1.555 SOURCE3 2 +nd-nd 486.8 1.379 SOURCE3 9 0.0145 0.0164 +nd-nd 602.9 1.315 SOURCE3 9 same as nc-nd +nd-os 414.9 1.395 SOURCE1 46 0.0163 0.0188 +nd-ss 433.5 1.560 SOURCE1 74 0.0000 0.0000 +nd-sy 439.8 1.555 SOURCE3 2 +ne-ne 355.3 1.479 SOURCE3 19 0.0960 0.1705 +ne-nf 738.6 1.257 SOURCE3 1 0.0000 0.0000 +ne-o 736.4 1.228 SOURCE3 40 0.0207 0.0255 +ne-p2 493.9 1.563 SOURCE3 14 0.0950 0.1325 +ne-pe 327.8 1.712 SOURCE3 28 0.0848 0.1076 +ne-px 336.6 1.702 SOURCE3 11 0.0578 0.0883 +ne-py 320.2 1.721 SOURCE3 15 0.0497 0.0702 +ne-s 463.5 1.537 SOURCE3 22 0.1396 0.1708 +ne-sx 207.3 1.838 SOURCE3 7 0.0760 0.1060 +ne-sy 257.1 1.752 SOURCE3 7 0.0640 0.0814 +nf-nf 355.3 1.479 SOURCE3 19 same as ne-ne +nf-nf 738.6 1.257 SOURCE3 1 same as ne-nf +nf-o 736.4 1.228 SOURCE3 40 same as ne- o +nf-p2 493.9 1.563 SOURCE3 14 same as ne-p2 +nf-pf 327.8 1.712 SOURCE3 28 same as ne-pe +nf-px 336.6 1.702 SOURCE3 11 same as ne-px +nf-py 320.2 1.721 SOURCE3 15 same as ne-py +nf-s 463.5 1.537 SOURCE3 22 same as ne- s +nf-sx 207.3 1.838 SOURCE3 7 same as ne-sx +nf-sy 257.1 1.752 SOURCE3 7 same as ne-sy +nh-nh 453.3 1.401 SOURCE1 40 0.0000 0.0000 +nh-no 381.2 1.456 SOURCE3 4 0.0364 0.0370 +nh-o 596.2 1.287 SOURCE3 3 0.0424 0.0450 +nh-oh 359.6 1.440 SOURCE3 1 0.0000 0.0000 +nh-os 358.5 1.441 SOURCE3 3 0.0029 0.0031 +nh-p2 357.8 1.679 SOURCE3 17 0.0422 0.0872 +nh-p3 312.8 1.730 SOURCE3 3 0.0015 0.0016 +nh-p4 333.1 1.706 SOURCE3 3 0.0008 0.0008 +nh-p5 365.6 1.671 SOURCE3 3 0.0007 0.0007 +nh-s 237.0 1.784 SOURCE3 3 0.0072 0.0076 +nh-s4 259.1 1.749 SOURCE3 3 0.0192 0.0203 +nh-s6 300.0 1.693 SOURCE3 3 0.0036 0.0038 +nh-sh 288.3 1.708 SOURCE3 1 0.0000 0.0000 +nh-ss 288.3 1.708 SOURCE1 52 0.0015 0.0015 +nh-sy 324.2 1.664 SOURCE3 1 0.0000 0.0000 +no-no 138.3 1.824 SOURCE3 1 0.0000 0.0000 +no-o 761.2 1.219 SOURCE1 1838 0.0023 0.0049 +no-oh 400.5 1.406 SOURCE2 1 0.0000 0.0000 +no-os 320.8 1.477 SOURCE3 4 0.0526 0.0532 +no-p2 306.3 1.738 SOURCE3 10 0.2024 0.2231 +no-p3 234.7 1.844 SOURCE3 3 0.0005 0.0005 +no-p4 220.4 1.870 SOURCE3 3 0.0005 0.0006 +no-p5 240.5 1.834 SOURCE3 4 0.0019 0.0020 +no-s 263.8 1.742 SOURCE3 2 0.0000 0.0000 +no-s4 143.0 1.996 SOURCE3 3 0.0295 0.0313 +no-s6 149.6 1.976 SOURCE3 3 0.0490 0.0520 +no-sh 225.4 1.804 SOURCE3 1 0.0000 0.0000 +no-ss 212.4 1.828 SOURCE3 3 0.0230 0.0244 +o -o 384.3 1.430 SOURCE3 2 0.0500 0.0500 +o -oh 294.6 1.517 SOURCE3 2 0.0000 0.0000 +o -os 306.3 1.504 SOURCE3 3 0.0110 0.0117 +o -p2 449.7 1.508 SOURCE3 17 0.0167 0.0306 +o -p3 440.4 1.515 SOURCE3 35 0.0214 0.0297 +o -p4 456.4 1.503 SOURCE3 42 0.0343 0.0749 +o -p5 487.7 1.481 SOURCE1 263 0.0180 0.0205 +o -pe 432.6 1.521 SOURCE3 20 0.0138 0.0171 +o -pf 432.6 1.521 SOURCE3 20 same as o -pe +o -px 459.2 1.501 SOURCE3 37 0.0125 0.0160 +o -py 477.5 1.488 SOURCE3 63 0.0063 0.0091 +o -s 194.8 1.802 SOURCE3 2 0.0000 0.0000 +o -s2 333.6 1.599 SOURCE3 3 0.0666 0.0707 +o -s4 448.7 1.497 SOURCE1 90 0.0000 0.0000 +o -s6 541.1 1.436 SOURCE1 1038 0.0072 0.0128 +o -sh 328.0 1.605 SOURCE3 2 0.0000 0.0000 +o -ss 398.5 1.537 SOURCE3 3 0.0434 0.0501 +o -sx 434.2 1.508 SOURCE3 40 0.0083 0.0130 +o -sy 493.0 1.466 SOURCE3 92 0.0077 0.0114 +oh-oh 340.5 1.469 SOURCE3 1 0.0000 0.0000 +oh-os 342.6 1.467 SOURCE3 3 0.0065 0.0072 +oh-p2 316.8 1.630 SOURCE3 8 0.0600 0.0916 +oh-p3 278.8 1.677 SOURCE3 3 0.0140 0.0148 +oh-p4 307.4 1.641 SOURCE3 4 0.0092 0.0092 +oh-p5 321.2 1.625 SOURCE3 92 0.0293 0.0451 +oh-py 332.1 1.613 SOURCE3 79 0.0111 0.0138 +oh-s 190.0 1.812 SOURCE3 2 0.0000 0.0000 +oh-s4 274.3 1.670 SOURCE3 3 0.0173 0.0184 +oh-s6 344.1 1.588 SOURCE3 13 0.0072 0.0091 +oh-sh 258.6 1.692 SOURCE3 2 0.0003 0.0003 +oh-ss 265.6 1.682 SOURCE3 4 0.0131 0.0131 +oh-sy 302.6 1.634 SOURCE3 4 0.0153 0.0154 +os-os 343.6 1.466 SOURCE1 20 0.0047 0.0067 +os-p2 371.9 1.573 SOURCE1 16 0.0000 0.0000 +os-p3 272.2 1.686 SOURCE3 6 0.0141 0.0201 +os-p4 311.6 1.636 SOURCE3 4 0.0056 0.0057 +os-p5 342.5 1.602 SOURCE1 248 0.0332 0.0400 +os-py 328.5 1.617 SOURCE3 17 0.0082 0.0139 +os-s 195.8 1.800 SOURCE3 3 0.0049 0.0052 +os-s4 253.9 1.699 SOURCE3 8 0.0194 0.0223 +os-s6 355.0 1.577 SOURCE1 75 0.0019 0.0030 +os-sh 273.6 1.671 SOURCE3 3 0.0100 0.0106 +os-ss 250.5 1.704 SOURCE3 9 0.0241 0.0277 +os-sy 253.9 1.699 SOURCE3 1 0.0000 0.0000 +p2-p2 490.3 1.786 SOURCE3 25 0.3198 0.3488 +p2-p3 211.9 2.152 SOURCE3 9 0.1116 0.1777 +p2-p4 200.4 2.179 SOURCE0 1 +p2-p5 199.9 2.180 SOURCE0 1 +p2-pe 401.6 1.867 SOURCE3 16 0.3079 0.3571 +p2-pf 401.6 1.867 SOURCE3 16 same as p2-pe +p2-s 361.6 1.772 SOURCE3 26 0.2523 0.3014 +p2-s4 139.4 2.190 SOURCE0 1 +p2-s6 142.3 2.180 SOURCE0 1 +p2-sh 224.0 1.971 SOURCE3 10 0.2263 0.2829 +p2-ss 226.6 1.966 SOURCE3 10 0.2189 0.2739 +p3-p3 186.5 2.214 SOURCE1 41 0.0000 0.0000 +p3-p4 185.7 2.216 SOURCE3 3 0.0010 0.0011 +p3-p5 186.9 2.213 SOURCE3 9 0.0257 0.0265 +p3-s 179.7 2.070 SOURCE0 1 +p3-s4 173.2 2.087 SOURCE3 8 0.1935 0.2235 +p3-s6 176.9 2.077 SOURCE3 11 0.1085 0.1420 +p3-sh 157.3 2.132 SOURCE3 3 0.0073 0.0078 +p3-ss 161.0 2.121 SOURCE3 3 0.0056 0.0059 +p4-p4 273.1 2.034 SOURCE1 1 0.0000 0.0000 +p4-p5 178.0 2.237 SOURCE0 1 +p4-s 152.7 2.146 SOURCE3 5 0.0571 0.0601 +p4-s4 123.2 2.251 SOURCE0 1 +p4-s6 118.9 2.269 SOURCE0 1 +p4-sh 163.1 2.115 SOURCE3 4 0.0006 0.0008 +p4-ss 167.0 2.104 SOURCE3 4 0.0042 0.0044 +p5-p5 261.4 2.054 SOURCE1 1 0.0000 0.0000 +p5-s 250.8 1.922 SOURCE1 89 0.0097 0.0140 +p5-s4 191.9 2.040 SOURCE0 1 +p5-s6 191.9 2.040 SOURCE0 1 +p5-sh 175.0 2.082 SOURCE3 3 0.0033 0.0035 +p5-ss 164.8 2.110 SOURCE3 6 0.0379 0.0531 +pe-pe 240.7 2.092 SOURCE3 7 0.1280 0.1369 +pe-pf 260.8 2.055 SOURCE3 1 0.0000 0.0000 +pe-px 291.4 2.005 SOURCE3 12 0.2364 0.2609 +pe-py 278.6 2.025 SOURCE3 12 0.2453 0.2617 +pe-s 374.7 1.758 SOURCE3 31 0.2925 0.3197 +pe-sx 145.9 2.168 SOURCE3 9 0.1092 0.1743 +pe-sy 133.0 2.213 SOURCE3 6 0.0106 0.0127 +pf-pf 240.7 2.092 SOURCE3 7 same as pe-pe +pf-pf 260.8 2.055 SOURCE3 1 same as pe-pf +pf-px 291.4 2.005 SOURCE3 12 same as pe-px +pf-py 278.6 2.025 SOURCE3 12 same as pe-py +pf-s 374.7 1.758 SOURCE3 31 same as pe- s +pf-sx 145.9 2.168 SOURCE3 9 same as pe-sx +pf-sy 133.0 2.213 SOURCE3 6 same as pe-sy +px-py 192.3 2.199 SOURCE3 5 0.0221 0.0238 +px-sx 125.4 2.242 SOURCE3 3 0.0112 0.0119 +px-sy 123.7 2.249 SOURCE3 3 0.0256 0.0272 +py-py 197.5 2.186 SOURCE3 8 0.0110 0.0132 +py-sx 121.2 2.259 SOURCE3 7 0.0595 0.0603 +py-sy 141.7 2.182 SOURCE3 5 0.0044 0.0047 +s -s 169.0 2.030 SOURCE3 1 0.0000 0.0000 +s -s2 229.2 1.897 SOURCE1 5 0.0000 0.0000 +s -s4 152.8 2.076 SOURCE3 4 0.0345 0.0345 +s -s6 166.0 2.038 SOURCE3 3 0.0293 0.0311 +s -sh 142.0 2.110 SOURCE3 2 0.0000 0.0000 +s -ss 148.5 2.089 SOURCE3 1 0.0000 0.0000 +s4-s4 151.5 2.080 SOURCE0 1 +s4-s6 151.5 2.080 SOURCE0 1 +s4-sh 125.7 2.168 SOURCE3 3 0.0214 0.0227 +s4-ss 126.2 2.166 SOURCE3 5 0.0241 0.0247 +s6-s6 151.5 2.080 SOURCE0 1 +s6-sh 142.6 2.108 SOURCE3 3 0.0136 0.0144 +s6-ss 139.6 2.118 SOURCE3 5 0.0198 0.0209 +sh-sh 158.9 2.058 SOURCE2 1 0.0000 0.0000 +sh-ss 155.8 2.067 SOURCE3 3 0.0027 0.0029 +ss-ss 161.7 2.050 SOURCE1 225 0.0015 0.0015 +sx-sx 80.9 2.391 SOURCE3 3 0.0174 0.0185 +sx-sy 105.3 2.255 SOURCE3 5 0.0703 0.0737 +sy-sy 106.4 2.250 SOURCE3 3 0.0272 0.0289 + +hw-ow-hw 100. 104.52 TIP3P water +hw-hw-ow 0. 127.74 (found in crystallographic water with 3 bonds) +br-c -br 66.9 113.10 SOURCE0 1 +br-c -c3 63.3 110.74 SOURCE3 1 0.0000 0.0000 +br-c -o 63.2 121.46 SOURCE3 5 1.5866 1.6264 +c -c -c 62.3 111.68 SOURCE3 2 6.1226 6.1226 +c -c -c3 61.7 116.86 SOURCE3 5 0.1552 0.1653 +c -c -cc 64.0 111.67 SOURCE3 4 5.1992 5.5146 +c -c -cd 64.0 111.67 SOURCE3 4 5.1992 5.5146 +c -c -ha 44.8 115.43 SOURCE2 3 0.5556 0.6549 +c -c -hc 44.6 117.08 SOURCE0 1 +c -c -n 69.9 104.81 SOURCE3 2 0.0000 0.0000 +c -c -o 66.8 122.34 SOURCE3 24 2.7100 3.2125 +c -c -oh 68.2 113.23 SOURCE3 5 0.4643 0.5615 +c1-c -c1 65.1 115.32 SOURCE0 1 +c1-c -o 69.9 122.34 SOURCE0 1 +c2-c -c2 67.2 116.78 SOURCE0 1 +c2-c -ha 48.6 115.95 SOURCE0 1 +c2-c -o 72.8 119.12 SOURCE3 2 0.0000 0.0000 +c2-c -s 64.7 119.16 SOURCE3 2 0.0000 0.0000 +c3-c -c3 62.8 116.05 SOURCE3 11 0.9292 1.0986 +c3-c -ca 62.3 119.53 SOURCE3 3 0.4442 0.4712 +c3-c -cc 67.2 104.51 SOURCE3 1 0.0000 0.0000 +c3-c -cd 67.2 104.51 SOURCE3 1 same as c3-c -cc +c3-c -ce 63.2 117.28 SOURCE3 2 0.7766 0.7766 +c3-c -cf 63.2 117.28 SOURCE3 2 same as c3-c -ce +c3-c -cg 64.3 115.00 SOURCE2 1 0.0000 0.0000 +c3-c -ch 64.3 115.00 SOURCE2 1 same as c3-c -cg +c3-c -cl 58.2 111.99 SOURCE3 2 0.0125 0.0125 +c3-c -f 66.9 110.70 SOURCE2 1 0.0000 0.0000 +c3-c -ha 46.0 115.22 SOURCE3 15 0.2737 0.3181 +c3-c -i 56.9 112.94 SOURCE3 1 0.0000 0.0000 +c3-c -n 67.9 115.15 SOURCE3 153 1.9677 2.7443 +c3-c -n2 66.6 114.53 SOURCE0 1 +c3-c -n4 64.6 112.26 SOURCE3 2 0.0000 0.0000 +c3-c -ne 67.2 113.38 SOURCE3 1 0.0000 0.0000 +c3-c -nf 67.2 113.38 SOURCE3 1 same as c3-c -ne +c3-c -nh 68.2 113.58 SOURCE0 1 +c3-c -o 68.0 123.11 SOURCE3 267 2.2483 3.0977 +c3-c -oh 69.8 112.20 SOURCE3 14 1.4815 1.8324 +c3-c -os 69.3 111.96 SOURCE3 15 1.8520 2.3072 +c3-c -p3 74.5 116.42 SOURCE3 3 0.1217 0.1291 +c3-c -p5 74.2 118.90 SOURCE0 1 +c3-c -pe 74.2 114.85 SOURCE3 1 0.0000 0.0000 +c3-c -pf 74.2 114.85 SOURCE3 1 same as c3-c -pe +c3-c -px 74.2 115.60 SOURCE3 1 0.0000 0.0000 +c3-c -py 74.5 118.16 SOURCE3 3 1.0121 1.0735 +c3-c -s 62.0 123.73 SOURCE3 9 1.2078 1.4528 +c3-c -s4 59.6 114.79 SOURCE0 1 +c3-c -s6 59.7 114.72 SOURCE0 1 +c3-c -sh 62.0 114.21 SOURCE3 3 2.0662 2.3916 +c3-c -ss 62.4 114.32 SOURCE3 5 2.0411 2.7478 +c3-c -sx 59.5 113.97 SOURCE3 3 0.0575 0.0610 +c3-c -sy 59.9 114.28 SOURCE3 3 0.6921 0.7341 +ca-c -ca 62.8 119.53 SOURCE3 1 0.0000 0.0000 +ca-c -cc 64.8 114.09 SOURCE3 2 0.0000 0.0000 +ca-c -cd 64.8 114.09 SOURCE3 2 0.0000 0.0000 +ca-c -ha 46.8 114.12 SOURCE3 1 0.0000 0.0000 +ca-c -n 69.4 112.03 SOURCE3 3 5.1757 5.5118 +ca-c -o 68.7 123.44 SOURCE3 18 2.1221 2.5574 +ca-c -oh 69.5 115.46 SOURCE3 3 1.8325 2.0619 +ca-c -os 68.8 115.54 SOURCE3 5 2.1366 2.6708 +ca-c -s 62.2 124.28 SOURCE3 2 2.3863 2.3863 +ca-c -sh 61.1 118.63 SOURCE3 1 0.0000 0.0000 +cc-c -cc 65.3 114.45 SOURCE3 7 5.3959 6.2434 +cd-c -cd 65.3 114.45 SOURCE3 7 5.3959 6.2434 +cc-c -cd 65.7 112.79 SOURCE3 1 0.0000 0.0000 +cc-c -n 70.2 111.86 SOURCE3 36 1.6194 2.3407 +cd-c -n 70.2 111.86 SOURCE3 36 1.6194 2.3407 +cc-c -o 68.9 125.71 SOURCE3 66 1.9961 2.4784 +cd-c -o 68.9 125.71 SOURCE3 66 1.9961 2.4784 +cc-c -os 70.5 112.30 SOURCE3 6 2.3802 2.7842 +cd-c -os 70.5 112.30 SOURCE3 6 2.3802 2.7842 +cd-c -oh 71.5 111.59 SOURCE3 1 0.0000 0.0000 +cc-c -oh 71.5 111.59 SOURCE3 1 same as cd-c -oh +ce-c -ce 64.1 116.78 SOURCE3 1 0.0000 0.0000 +cf-c -cf 64.1 116.78 SOURCE3 1 same as ce-c -ce +ce-c -ha 46.9 115.22 SOURCE3 7 1.6044 2.4188 +cf-c -ha 46.9 115.22 SOURCE3 7 same as ce-c -ha +ce-c -n 68.9 115.01 SOURCE3 2 0.5478 0.5478 +cf-c -n 68.9 115.01 SOURCE3 2 same as ce-c -n +ce-c -o 69.3 122.92 SOURCE3 17 2.3941 3.5085 +cf-c -o 69.3 122.92 SOURCE3 17 2.3941 3.5085 +ce-c -oh 70.8 112.41 SOURCE3 3 0.3261 0.3261 +cf-c -oh 70.8 112.41 SOURCE3 3 0.3261 0.3261 +ce-c -s 64.1 117.80 SOURCE3 1 0.0000 0.0000 +cf-c -s 64.1 117.80 SOURCE3 1 same as ce-c -s +cg-c -cg 65.4 115.38 SOURCE3 1 0.0000 0.0000 +ch-c -ch 65.4 115.38 SOURCE3 1 same as cg-c -cg +cg-c -ha 47.8 113.90 SOURCE2 1 0.0000 0.0000 +ch-c -ha 47.8 113.90 SOURCE2 1 same as cg-c -ha +cg-c -o 70.2 122.31 SOURCE3 2 0.0000 0.0000 +ch-c -o 70.2 122.31 SOURCE3 2 same as cg-c -o +cl-c -cl 54.8 111.30 SOURCE2 1 0.0000 0.0000 +cl-c -f 59.0 112.00 SOURCE2 1 0.0000 0.0000 +cl-c -ha 40.4 109.90 SOURCE2 1 0.0000 0.0000 +cl-c -o 59.8 121.51 SOURCE3 6 1.5810 1.6987 +cl-c -s 56.7 127.60 SOURCE2 1 0.0000 0.0000 +cx-c -cx 85.4 64.60 SOURCE2 1 0.0000 0.0000 +cy-c -cy 70.1 90.55 SOURCE2 2 2.4500 2.4500 +cy-c -o 64.1 135.74 SOURCE3 4 2.0890 2.0890 +cy-c -os 74.8 94.37 SOURCE3 2 0.0000 0.0000 +f -c -f 72.2 107.35 SOURCE2 2 0.2500 0.2500 +f -c -h 51.5 109.90 SOURCE2 1 0.0000 0.0000 +f -c -o 73.2 123.44 SOURCE0 1 +f -c -s 63.4 124.00 SOURCE2 1 0.0000 0.0000 +h -c -o 53.1 127.30 SOURCE2 1 0.0000 0.0000 +ha-c -ha 37.9 115.61 SOURCE3 4 0.0329 0.0458 +ha-c -i 36.7 110.58 SOURCE3 1 0.0000 0.0000 +ha-c -n 52.4 112.37 SOURCE3 4 0.5562 0.6424 +ha-c -o 54.3 121.94 SOURCE3 51 1.7337 2.3235 +ha-c -oh 54.0 111.82 SOURCE3 4 1.9074 1.9375 +ha-c -os 53.2 110.34 SOURCE3 8 1.6046 1.9344 +ha-c -s 44.3 119.56 SOURCE3 3 0.7139 0.7586 +hc-c -hc 39.3 115.68 SOURCE0 1 +hc-c -n 51.1 120.00 SOURCE0 1 +hc-c -nh 52.5 112.70 SOURCE0 1 +hc-c -o 55.4 120.00 SOURCE0 1 +hc-c -oh 54.1 113.70 SOURCE0 1 +hc-c -os 52.9 113.58 SOURCE0 1 +i -c -i 59.8 116.45 SOURCE3 1 0.0000 0.0000 +i -c -o 55.5 122.02 SOURCE3 4 1.0210 1.2961 +n -c -n 75.4 111.70 SOURCE3 11 2.6976 3.1820 +n -c -nc 73.0 116.84 SOURCE3 2 0.8166 0.8166 +n -c -nd 73.0 116.84 SOURCE3 2 same as n -c -nc +n -c -o 75.8 122.03 SOURCE3 221 1.7197 2.3565 +n -c -os 74.7 115.25 SOURCE3 1 0.0000 0.0000 +n -c -s 65.7 123.88 SOURCE3 5 1.0157 1.2935 +n -c -ss 67.7 107.69 SOURCE3 1 0.0000 0.0000 +n2-c -n2 71.8 110.31 SOURCE0 1 +n2-c -na 70.7 118.60 SOURCE0 1 +n2-c -o 73.0 122.50 SOURCE0 1 +n3-c -n3 72.4 112.98 SOURCE0 1 +n3-c -o 74.1 122.26 SOURCE0 1 +n4-c -n4 64.7 114.64 SOURCE3 1 0.0000 0.0000 +n4-c -o 69.6 118.83 SOURCE3 4 3.8516 3.8516 +na-c -na 73.2 115.40 SOURCE0 1 +na-c -o 75.0 122.85 SOURCE0 1 +nc-c -o 73.9 125.29 SOURCE3 2 0.9029 0.9029 +nd-c -o 73.9 125.29 SOURCE3 2 same as nc-c -o +ne-c -ne 72.4 110.31 SOURCE3 1 0.0000 0.0000 +nf-c -nf 72.4 110.31 SOURCE3 1 same as ne-c -ne +ne-c -o 72.8 124.39 SOURCE3 3 0.6099 0.6469 +nf-c -o 72.8 124.39 SOURCE3 3 same as ne-c -o +nh-c -nh 75.2 110.98 SOURCE0 1 +nh-c -o 74.8 124.62 SOURCE0 1 +no-c -no 66.5 109.28 SOURCE0 1 +no-c -o 68.0 125.36 SOURCE0 1 +o -c -o 79.1 127.33 SOURCE3 14 3.9382 4.4102 +o -c -oh 77.4 122.88 SOURCE3 33 1.6641 2.1896 +o -c -os 76.2 122.43 SOURCE3 39 2.7251 3.2180 +o -c -p2 75.7 123.10 SOURCE0 1 +o -c -p3 77.1 120.79 SOURCE0 1 +o -c -pe 75.2 123.02 SOURCE3 3 0.1324 0.1404 +o -c -pf 75.2 123.02 SOURCE3 3 same as o -c -pe +o -c -px 76.7 119.10 SOURCE3 1 0.0000 0.0000 +o -c -py 77.8 120.52 SOURCE3 6 4.7048 6.3825 +o -c -s 68.2 120.44 SOURCE3 2 0.0000 0.0000 +o -c -s4 61.2 121.15 SOURCE0 1 +o -c -s6 61.7 119.45 SOURCE0 1 +o -c -sh 64.2 121.41 SOURCE3 4 1.2105 1.4052 +o -c -ss 64.6 122.29 SOURCE3 7 1.3372 1.9240 +o -c -sx 60.7 121.15 SOURCE3 5 3.5627 3.6452 +o -c -sy 61.9 119.32 SOURCE3 5 2.2318 2.4495 +oh-c -oh 78.9 110.56 SOURCE3 2 0.5498 0.5498 +oh-c -s 66.6 123.44 SOURCE3 1 0.0000 0.0000 +os-c -os 77.8 107.49 SOURCE3 1 0.0000 0.0000 +p2-c -p2 94.4 113.75 SOURCE0 1 +p3-c -p3 93.5 118.04 SOURCE3 1 0.0000 0.0000 +p3-c -py 107.5 90.08 SOURCE3 1 0.0000 0.0000 +p5-c -p5 92.0 123.76 SOURCE0 1 +pe-c -pe 93.9 113.77 SOURCE3 1 0.0000 0.0000 +pf-c -pf 93.9 113.77 SOURCE3 1 same as pe-c -pe +py-c -py 92.1 123.80 SOURCE3 1 0.0000 0.0000 +s -c -s 65.0 120.40 SOURCE3 2 1.2766 1.2766 +s -c -sh 62.5 121.94 SOURCE3 2 2.5846 2.5846 +s -c -ss 61.9 125.90 SOURCE3 1 0.0000 0.0000 +s4-c -s4 61.3 108.81 SOURCE0 1 +s6-c -s6 59.4 115.75 SOURCE0 1 +sh-c -sh 62.5 115.33 SOURCE3 1 0.0000 0.0000 +ss-c -ss 63.8 113.00 SOURCE3 1 0.0000 0.0000 +sx-c -sx 60.8 108.80 SOURCE3 1 0.0000 0.0000 +sy-c -sy 59.5 115.78 SOURCE3 1 0.0000 0.0000 +br-c1-c1 54.9 180.00 SOURCE3 1 0.0000 0.0000 +c -c1-c1 56.3 180.00 SOURCE0 1 +c1-c1-c1 64.4 180.00 SOURCE3 1 0.0000 0.0000 +c1-c1-c2 60.8 180.00 SOURCE3 2 0.0000 0.0000 +c1-c1-c3 56.4 177.99 SOURCE3 4 1.0065 1.1721 +c1-c1-ca 56.9 180.00 SOURCE0 1 +c1-c1-cl 51.4 180.00 SOURCE0 1 +c1-c1-f 61.0 180.00 SOURCE0 1 +c1-c1-ha 44.8 178.38 SOURCE3 41 1.6952 2.0683 +c1-c1-hc 44.7 180.00 SOURCE0 1 +c1-c1-i 49.8 180.00 SOURCE3 1 0.0000 0.0000 +c1-c1-n 62.1 177.18 SOURCE3 1 0.0000 0.0000 +c1-c1-n1 67.2 180.00 SOURCE0 1 +c1-c1-n2 65.2 180.00 SOURCE0 1 +c1-c1-n3 59.8 180.00 SOURCE0 1 +c1-c1-n4 59.1 179.56 SOURCE3 3 0.2919 0.3096 +c1-c1-na 61.2 176.75 SOURCE3 8 2.6227 2.9328 +c1-c1-nh 61.1 179.27 SOURCE3 3 0.2222 0.2357 +c1-c1-no 59.4 180.00 SOURCE3 3 0.0000 0.0000 +c1-c1-o 66.8 180.00 SOURCE3 1 0.0000 0.0000 +c1-c1-oh 62.7 176.65 SOURCE3 1 0.0000 0.0000 +c1-c1-os 62.8 176.42 SOURCE3 2 0.0000 0.0000 +c1-c1-p2 65.2 180.00 SOURCE0 1 +c1-c1-p3 66.4 169.63 SOURCE3 2 0.0000 0.0000 +c1-c1-p4 64.5 180.00 SOURCE0 1 +c1-c1-p5 66.5 176.17 SOURCE3 2 0.0000 0.0000 +c1-c1-s 55.7 179.97 SOURCE3 1 0.0000 0.0000 +c1-c1-s4 54.1 167.47 SOURCE3 2 0.0000 0.0000 +c1-c1-s6 53.7 174.38 SOURCE3 2 0.0000 0.0000 +c1-c1-sh 54.1 180.00 SOURCE0 1 +c1-c1-ss 55.2 173.22 SOURCE3 2 0.0000 0.0000 +c2-c1-c2 58.2 180.00 SOURCE3 1 0.0000 0.0000 +c2-c1-o 63.1 179.50 SOURCE2 1 0.0000 0.0000 +c2-c1-s2 56.7 172.98 SOURCE3 1 0.0000 0.0000 +c3-c1-n1 58.3 177.57 SOURCE2 3 2.3778 2.5773 +cg-c1-ha 44.0 177.41 SOURCE3 22 2.3752 2.4947 +ch-c1-ha 44.0 177.41 SOURCE3 22 same as cg-c1-ha +n1-c1-n1 93.2 102.01 SOURCE0 1 +n1-c1-n3 63.7 169.70 SOURCE2 1 0.0000 0.0000 +n1-c1-os 64.7 178.59 SOURCE3 1 0.0000 0.0000 +n1-c1-p3 67.7 171.20 SOURCE2 1 0.0000 0.0000 +n1-c1-ss 55.8 178.68 SOURCE3 1 0.0000 0.0000 +n2-c1-o 69.1 171.79 SOURCE3 2 0.3594 0.3594 +n2-c1-s 57.8 174.05 SOURCE3 2 0.1358 0.1358 +ne-c1-o 68.7 172.33 SOURCE3 1 0.0000 0.0000 +nf-c1-o 68.7 172.33 SOURCE3 1 same as ne-c1-o +br-c2-br 68.6 115.06 SOURCE3 1 0.0000 0.0000 +br-c2-c2 63.1 122.42 SOURCE3 3 0.0663 0.0703 +br-c2-ha 43.2 113.28 SOURCE3 1 0.0000 0.0000 +c -c2-c 66.6 118.88 SOURCE0 1 +c -c2-c2 67.9 120.70 SOURCE0 1 +c -c2-c3 63.9 119.70 SOURCE0 1 +c -c2-ha 47.7 121.33 SOURCE3 4 0.2462 0.2462 +c -c2-hc 48.0 119.70 SOURCE0 1 +c1-c2-c1 72.3 116.77 SOURCE0 1 +c1-c2-c2 70.3 121.62 SOURCE0 1 +c1-c2-c3 65.1 121.60 SOURCE2 2 1.0000 1.0000 +c1-c2-f 68.0 124.90 SOURCE2 1 0.0000 0.0000 +c1-c2-ha 50.4 121.37 SOURCE3 8 0.0055 0.0055 +c2-c2-c2 69.8 121.81 SOURCE3 10 0.3648 0.3843 +c2-c2-c3 64.3 123.42 SOURCE3 41 1.8126 2.6057 +c2-c2-ca 66.9 117.00 SOURCE0 1 +c2-c2-cc 70.2 117.21 SOURCE3 2 0.3418 0.3418 +c2-c2-cd 70.2 117.21 SOURCE3 2 same as c2-c2-cc +c2-c2-cl 58.4 122.79 SOURCE3 3 0.2303 0.2442 +c2-c2-cx 69.7 105.70 SOURCE2 1 0.0000 0.0000 +c2-c2-cy 69.7 103.30 SOURCE2 1 0.0000 0.0000 +c2-c2-f 67.8 124.01 SOURCE3 3 1.3603 1.4428 +c2-c2-h4 49.3 124.68 SOURCE3 39 3.2023 3.8280 +c2-c2-ha 50.0 120.94 SOURCE3 254 0.8639 1.3150 +c2-c2-hc 50.3 119.70 SOURCE0 1 +c2-c2-hx 49.0 126.45 SOURCE3 3 0.0207 0.0219 +c2-c2-i 56.3 121.03 SOURCE3 2 0.0000 0.0000 +c2-c2-n 68.8 123.45 SOURCE3 7 3.0021 4.5840 +c2-c2-n2 71.3 126.01 SOURCE3 1 0.0000 0.0000 +c2-c2-n3 70.3 124.55 SOURCE0 1 +c2-c2-n4 67.2 121.52 SOURCE3 5 1.2100 1.2656 +c2-c2-na 69.8 121.38 SOURCE3 26 5.2386 6.9463 +c2-c2-nh 69.8 124.99 SOURCE3 7 0.8702 0.9929 +c2-c2-no 67.6 121.89 SOURCE3 4 1.1592 1.1594 +c2-c2-o 71.0 130.89 SOURCE3 2 0.0201 0.0201 +c2-c2-oh 71.6 122.28 SOURCE3 4 0.5600 0.5600 +c2-c2-os 71.2 121.43 SOURCE3 26 4.0372 5.2559 +c2-c2-p2 84.7 115.10 SOURCE0 1 +c2-c2-p3 75.2 124.83 SOURCE3 5 2.0793 2.1222 +c2-c2-p4 77.2 119.76 SOURCE0 1 +c2-c2-p5 75.4 125.97 SOURCE0 1 +c2-c2-s 61.3 129.37 SOURCE3 2 0.0000 0.0000 +c2-c2-s4 62.9 119.84 SOURCE0 1 +c2-c2-s6 62.8 120.01 SOURCE0 1 +c2-c2-sh 61.0 125.70 SOURCE3 3 1.2624 1.3390 +c2-c2-ss 63.9 118.62 SOURCE3 18 3.5098 4.5127 +c3-c2-c3 62.7 116.52 SOURCE3 15 2.1251 3.1001 +c3-c2-cc 63.2 125.64 SOURCE3 1 0.0000 0.0000 +c3-c2-cd 63.2 125.64 SOURCE3 1 same as c3-c2-cc +c3-c2-ce 65.7 117.40 SOURCE2 2 8.2000 8.2000 +c3-c2-cf 65.7 117.40 SOURCE2 2 same as c3-c2-ce +c3-c2-h4 43.8 127.53 SOURCE3 1 0.0000 0.0000 +c3-c2-ha 45.7 117.30 SOURCE3 33 1.4120 1.7453 +c3-c2-hc 45.1 120.00 SOURCE0 1 +c3-c2-n2 67.1 121.24 SOURCE3 10 3.4840 4.3825 +c3-c2-na 65.0 122.54 SOURCE3 1 0.0000 0.0000 +c3-c2-ne 67.0 122.15 SOURCE3 4 0.2197 0.2197 +c3-c2-nf 67.0 122.15 SOURCE3 4 same as c3-c2-ne +c3-c2-nh 66.7 118.59 SOURCE3 6 1.7963 2.2622 +c3-c2-o 69.1 116.88 SOURCE3 2 0.0663 0.0663 +c3-c2-oh 67.4 118.81 SOURCE3 3 0.1564 0.1659 +c3-c2-p2 79.0 122.74 SOURCE3 2 0.0000 0.0000 +c3-c2-s 62.8 115.44 SOURCE3 2 0.0115 0.0115 +ca-c2-ca 63.5 117.88 SOURCE0 1 +ca-c2-hc 45.3 123.30 SOURCE0 1 +cc-c2-ha 49.1 120.76 SOURCE3 11 0.8455 1.4155 +cd-c2-ha 49.1 120.76 SOURCE3 11 0.8455 1.4155 +ce-c2-ha 49.6 121.19 SOURCE3 122 0.4300 0.5318 +cf-c2-ha 49.6 121.19 SOURCE3 122 same as ce-c2-ha +cl-c2-cl 55.3 114.77 SOURCE3 1 0.0000 0.0000 +cl-c2-ha 40.9 113.20 SOURCE3 1 0.0000 0.0000 +cx-c2-ha 44.3 125.40 SOURCE2 1 0.0000 0.0000 +f -c2-f 70.7 109.60 SOURCE2 2 0.6000 0.6000 +f -c2-ha 51.3 110.00 SOURCE2 1 0.0000 0.0000 +h4-c2-n 49.2 119.41 SOURCE3 1 0.0000 0.0000 +h4-c2-n2 53.3 116.67 SOURCE3 2 2.4512 2.4512 +h4-c2-na 50.4 116.25 SOURCE3 15 3.1414 3.7439 +h4-c2-os 52.2 113.70 SOURCE3 13 1.8718 2.0464 +h4-c2-ss 42.8 118.47 SOURCE3 9 2.2828 2.5335 +h5-c2-n2 52.0 123.09 SOURCE3 2 0.0000 0.0000 +h5-c2-na 48.3 126.39 SOURCE3 4 0.3299 0.3299 +ha-c2-ha 38.0 117.65 SOURCE3 349 1.0413 1.3426 +ha-c2-n 50.5 113.40 SOURCE3 4 0.9474 1.2182 +ha-c2-n1 51.8 120.76 SOURCE3 8 0.6630 0.6632 +ha-c2-n2 52.4 120.54 SOURCE3 92 0.8283 1.4571 +ha-c2-n3 52.4 113.54 SOURCE0 1 +ha-c2-na 51.2 112.42 SOURCE3 8 0.5805 0.6507 +ha-c2-ne 52.5 121.18 SOURCE3 68 0.5649 0.6824 +ha-c2-nf 52.5 121.18 SOURCE3 68 same as ha-c2-ne +ha-c2-nh 51.3 116.68 SOURCE3 13 2.3477 2.5734 +ha-c2-no 49.1 112.14 SOURCE3 2 0.0264 0.0264 +ha-c2-o 54.2 117.23 SOURCE3 2 0.0201 0.0201 +ha-c2-oh 52.3 116.18 SOURCE3 2 0.0000 0.0000 +ha-c2-os 52.4 112.69 SOURCE3 13 2.2236 2.5851 +ha-c2-p2 55.7 121.48 SOURCE3 122 0.3598 0.4329 +ha-c2-p3 52.0 114.31 SOURCE3 3 0.0000 0.0000 +ha-c2-p4 51.6 117.86 SOURCE0 1 +ha-c2-p5 51.2 120.10 SOURCE3 2 0.0000 0.0000 +ha-c2-pe 55.0 121.46 SOURCE3 104 0.5185 0.7821 +ha-c2-pf 55.0 121.46 SOURCE3 104 same as ha-c2-pe +ha-c2-s 43.4 115.70 SOURCE3 2 0.0000 0.0000 +ha-c2-s2 46.2 118.74 SOURCE3 2 0.0000 0.0000 +ha-c2-s4 42.8 115.30 SOURCE3 2 0.0000 0.0000 +ha-c2-s6 42.6 116.60 SOURCE3 2 0.0000 0.0000 +ha-c2-sh 43.2 111.74 SOURCE3 1 0.0000 0.0000 +ha-c2-ss 43.2 116.72 SOURCE3 7 2.0736 2.7543 +hc-c2-hc 37.8 118.92 SOURCE0 1 +hc-c2-n 50.3 114.04 SOURCE0 1 +hc-c2-n2 52.4 120.40 SOURCE0 1 +hc-c2-na 49.7 119.10 SOURCE0 1 +hc-c2-nh 52.0 113.36 SOURCE0 1 +hc-c2-no 49.1 112.12 SOURCE0 1 +hc-c2-oh 52.3 116.22 SOURCE0 1 +hc-c2-os 51.7 116.11 SOURCE0 1 +hc-c2-p3 51.4 117.19 SOURCE0 1 +hc-c2-p5 51.3 119.58 SOURCE0 1 +hc-c2-s4 42.7 116.12 SOURCE0 1 +hc-c2-s6 42.8 115.45 SOURCE0 1 +hc-c2-sh 42.4 115.63 SOURCE0 1 +hc-c2-ss 43.4 115.62 SOURCE0 1 +hn-c2-n4 11.9 112.74 SOURCE0 1 +hx-c2-n4 48.4 113.03 SOURCE3 3 0.3651 0.3873 +i -c2-i 61.0 117.94 SOURCE3 1 0.0000 0.0000 +n -c2-n 71.5 113.23 SOURCE3 1 0.0000 0.0000 +n -c2-n2 70.6 125.95 SOURCE3 2 5.0202 5.0202 +n -c2-na 74.6 105.42 SOURCE3 1 0.0000 0.0000 +n -c2-ss 67.4 109.31 SOURCE3 1 0.0000 0.0000 +n2-c2-n2 78.0 113.82 SOURCE3 1 0.0000 0.0000 +n2-c2-na 71.7 123.62 SOURCE3 1 0.0000 0.0000 +n2-c2-nh 72.6 124.27 SOURCE3 12 1.4852 2.4114 +n2-c2-oh 74.4 122.08 SOURCE3 1 0.0000 0.0000 +n2-c2-os 74.6 118.96 SOURCE3 2 1.1624 1.1624 +n2-c2-ss 62.9 129.77 SOURCE3 1 0.0000 0.0000 +n3-c2-n3 73.4 118.47 SOURCE0 1 +n4-c2-n4 67.7 113.93 SOURCE3 1 0.0000 0.0000 +na-c2-na 73.7 109.33 SOURCE3 3 2.8004 3.0187 +ne-c2-nh 73.3 122.72 SOURCE3 2 0.0000 0.0000 +nf-c2-nh 73.3 122.72 SOURCE3 2 same as ne-c2-nh +nh-c2-nh 72.9 117.50 SOURCE3 18 4.1761 4.7058 +no-c2-no 68.6 113.90 SOURCE3 1 0.0000 0.0000 +o -c2-o 77.9 121.69 SOURCE0 1 +o -c2-s 64.0 127.68 SOURCE3 2 0.0547 0.0547 +oh-c2-oh 76.0 114.33 SOURCE3 1 0.0000 0.0000 +os-c2-os 74.2 115.80 SOURCE3 1 0.0000 0.0000 +p2-c2-p2 100.6 129.80 SOURCE0 1 +p3-c2-p3 97.1 115.54 SOURCE3 1 0.0000 0.0000 +p5-c2-p5 95.3 121.85 SOURCE0 1 +s -c2-s 62.5 121.67 SOURCE0 1 +s4-c2-s4 61.9 120.32 SOURCE0 1 +s4-c2-s6 62.0 119.95 SOURCE0 1 +s6-c2-s6 62.0 119.97 SOURCE0 1 +sh-c2-sh 64.1 110.48 SOURCE3 1 0.0000 0.0000 +sh-c2-ss 62.7 117.82 SOURCE0 1 +ss-c2-ss 62.8 120.24 SOURCE3 1 0.0000 0.0000 +br-c3-br 66.6 111.75 SOURCE2 2 0.9500 0.9500 +br-c3-c1 62.8 111.80 SOURCE2 3 0.2000 0.2160 +br-c3-c3 63.0 109.25 SOURCE3 10 0.5567 0.5685 +br-c3-h1 43.1 103.04 SOURCE3 5 0.2592 0.3092 +br-c3-hc 42.4 106.50 SOURCE0 1 +c -c3-c 63.7 112.95 SOURCE3 3 2.9833 3.2539 +c -c3-c2 64.6 109.73 SOURCE3 3 5.3858 5.7300 +c -c3-c3 63.8 110.53 SOURCE3 62 1.7223 1.9636 +c -c3-ca 64.1 111.23 SOURCE3 2 0.0000 0.0000 +c -c3-h1 47.6 107.66 SOURCE3 66 1.2143 1.4015 +c -c3-hc 47.2 109.68 SOURCE3 614 0.4058 0.6426 +c -c3-hx 47.4 108.64 SOURCE3 1 0.0000 0.0000 +c -c3-n 66.7 111.56 SOURCE3 28 0.7771 1.7981 +c -c3-n3 65.8 113.91 SOURCE3 2 0.0000 0.0000 +c -c3-n4 65.8 111.54 SOURCE3 1 0.0000 0.0000 +c -c3-na 68.6 105.72 SOURCE3 2 2.6464 2.6464 +c -c3-oh 68.4 109.46 SOURCE3 2 1.1805 1.1805 +c -c3-os 68.0 109.82 SOURCE3 10 1.4728 2.0612 +c -c3-ss 61.7 111.58 SOURCE3 5 1.4553 1.9506 +c1-c3-c1 66.5 109.00 SOURCE2 1 0.0000 0.0000 +c1-c3-c3 64.2 111.59 SOURCE0 1 +c1-c3-cl 58.5 110.63 SOURCE2 3 1.1556 1.2257 +c1-c3-h1 49.1 105.97 SOURCE3 2 0.4303 0.4303 +c1-c3-hc 48.3 109.75 SOURCE3 12 0.7064 0.8436 +c1-c3-os 68.1 112.83 SOURCE3 2 0.4762 0.4762 +c2-c3-c2 64.6 109.71 SOURCE0 1 +c2-c3-c3 63.7 110.96 SOURCE3 12 2.5022 3.2903 +c2-c3-f 66.4 111.30 SOURCE2 2 0.4000 0.4000 +c2-c3-h1 47.0 110.46 SOURCE3 17 1.0324 1.1525 +c2-c3-hc 47.0 110.49 SOURCE3 159 0.5121 0.7479 +c2-c3-n3 66.5 111.47 SOURCE3 3 2.1065 2.2409 +c2-c3-oh 68.3 109.72 SOURCE3 2 1.8365 1.8365 +c2-c3-os 68.3 108.88 SOURCE3 2 1.3604 1.3604 +c2-c3-ss 63.6 104.97 SOURCE3 2 2.2248 2.2248 +c3-c3-c3 63.2 110.63 SOURCE3 507 1.7605 2.7845 +c3-c3-ca 62.5 114.61 SOURCE3 8 2.6906 2.7907 +c3-c3-cc 64.7 108.10 SOURCE3 5 4.5525 4.8691 +c3-c3-cd 64.7 108.10 SOURCE3 5 same as c3-c3-cc +c3-c3-cl 57.8 110.33 SOURCE3 20 0.9282 1.1495 +c3-c3-cx 65.6 104.10 SOURCE3 2 0.0000 0.0000 +c3-c3-cy 63.6 109.62 SOURCE3 5 1.6598 2.0747 +c3-c3-f 66.2 109.41 SOURCE3 18 0.9661 1.1878 +c3-c3-h1 46.4 110.07 SOURCE3 457 0.9255 1.1542 +c3-c3-h2 46.0 111.59 SOURCE3 8 0.7200 1.1217 +c3-c3-hc 46.4 110.05 SOURCE3 2092 0.5379 0.6991 +c3-c3-hx 46.0 111.74 SOURCE3 15 1.0925 1.2365 +c3-c3-i 58.5 110.96 SOURCE3 2 0.0000 0.0000 +c3-c3-n 65.9 112.13 SOURCE3 31 1.0775 2.0700 +c3-c3-n2 66.4 109.16 SOURCE3 8 1.3147 1.4079 +c3-c3-n3 66.2 110.38 SOURCE3 69 2.0699 2.9054 +c3-c3-n4 66.0 108.93 SOURCE3 11 2.7418 3.0139 +c3-c3-na 65.8 112.59 SOURCE3 4 2.2797 2.6730 +c3-c3-nh 66.6 109.78 SOURCE3 2 0.0333 0.0333 +c3-c3-oh 67.7 109.43 SOURCE3 48 0.9661 1.5023 +c3-c3-os 67.8 108.42 SOURCE3 122 1.0750 1.6759 +c3-c3-p5 77.0 114.24 SOURCE3 4 2.0849 2.5420 +c3-c3-s6 62.4 111.90 SOURCE3 2 1.7244 1.7244 +c3-c3-sh 61.5 111.09 SOURCE3 4 2.8882 2.8907 +c3-c3-ss 61.1 112.69 SOURCE3 24 2.0616 2.1842 +ca-c3-ca 63.6 112.47 SOURCE3 3 0.4951 0.5285 +ca-c3-cc 65.2 108.08 SOURCE3 8 3.1217 4.1083 +ca-c3-cd 65.2 108.08 SOURCE3 8 same as ca-c3-cc +ca-c3-h1 46.8 110.95 SOURCE3 12 0.8880 1.1170 +ca-c3-hc 47.0 110.15 SOURCE3 47 1.1349 1.2602 +ca-c3-n2 66.0 112.10 SOURCE3 1 0.0000 0.0000 +ca-c3-nc 68.2 106.51 SOURCE3 1 0.0000 0.0000 +ca-c3-nd 68.2 106.51 SOURCE3 1 same as ca-c3-nc +ca-c3-oh 67.2 112.97 SOURCE3 1 0.0000 0.0000 +ca-c3-os 67.7 110.51 SOURCE3 4 3.2176 3.2176 +cc-c3-cc 65.5 107.99 SOURCE3 10 5.0855 5.1937 +cd-c3-cd 65.5 107.99 SOURCE3 10 5.0855 5.1937 +cc-c3-cd 67.3 102.35 SOURCE3 1 0.0000 0.0000 +cc-c3-h1 47.0 111.62 SOURCE3 20 0.7861 1.0215 +cd-c3-h1 47.0 111.62 SOURCE3 20 0.7861 1.0215 +cc-c3-hc 47.2 110.86 SOURCE3 85 0.8792 1.0276 +cd-c3-hc 47.2 110.86 SOURCE3 85 0.8792 1.0276 +cc-c3-nc 68.4 107.04 SOURCE3 2 0.0000 0.0000 +cd-c3-nd 68.4 107.04 SOURCE3 2 same as cc-c3-nc +cc-c3-os 67.8 111.28 SOURCE3 7 2.5177 2.9265 +cd-c3-os 67.8 111.28 SOURCE3 7 same as cc-c3-os +cd-c3-sh 61.1 114.02 SOURCE3 1 0.0000 0.0000 +cc-c3-sh 61.1 114.02 SOURCE3 1 same as cd-c3-sh +ce-c3-hc 47.0 110.98 SOURCE3 27 0.1170 0.1559 +cf-c3-hc 47.0 110.98 SOURCE3 27 same as ce-c3-hc +cl-c3-cl 54.2 111.03 SOURCE2 6 0.9889 1.1324 +cl-c3-f 59.0 109.60 SOURCE2 3 0.3333 0.3742 +cl-c3-h1 40.7 105.93 SOURCE3 19 0.9624 1.1883 +cl-c3-hc 40.3 107.65 SOURCE2 2 2.2500 2.2500 +cx-c3-hc 46.7 111.35 SOURCE3 4 0.0000 0.0000 +cy-c3-hc 46.5 110.17 SOURCE3 16 0.5607 0.5693 +f -c3-f 71.3 107.16 SOURCE2 10 0.9600 1.1324 +f -c3-h1 51.6 107.85 SOURCE3 14 0.8579 0.9537 +f -c3-h2 51.4 108.41 SOURCE3 6 0.4791 0.5081 +f -c3-hc 51.3 108.92 SOURCE2 5 2.4272 3.0534 +f -c3-n2 69.2 110.40 SOURCE2 3 2.3333 2.6470 +h1-c3-h1 39.2 109.55 SOURCE3 1888 0.8483 1.1205 +h1-c3-n 49.8 109.32 SOURCE3 91 0.8246 1.0325 +h1-c3-n2 49.3 109.61 SOURCE3 63 0.7888 1.0452 +h1-c3-n3 49.4 109.92 SOURCE3 313 0.8219 1.1810 +h1-c3-na 49.9 109.45 SOURCE3 53 0.7716 0.9555 +h1-c3-nc 50.1 108.57 SOURCE3 6 0.0720 0.0764 +h1-c3-nd 50.1 108.57 SOURCE3 6 same as h1-c3-nc +h1-c3-nh 49.7 109.96 SOURCE3 70 0.4865 0.7000 +h1-c3-no 48.1 107.56 SOURCE3 3 0.0000 0.0000 +h1-c3-o 52.0 117.19 SOURCE3 6 0.0003 0.0003 +h1-c3-oh 51.0 109.88 SOURCE3 63 1.1555 1.3172 +h1-c3-os 50.8 108.82 SOURCE3 541 0.5769 0.8042 +h1-c3-s 41.2 112.60 SOURCE3 6 0.0026 0.0026 +h1-c3-s4 42.9 108.66 SOURCE3 201 0.2964 0.3834 +h1-c3-s6 43.9 108.11 SOURCE3 160 0.3521 0.5518 +h1-c3-sh 42.4 109.21 SOURCE3 22 1.0660 1.2028 +h1-c3-ss 42.4 109.34 SOURCE3 356 0.4558 0.6573 +h1-c3-sx 42.8 108.69 SOURCE3 90 0.2163 0.2749 +h1-c3-sy 43.7 108.09 SOURCE3 93 0.2266 0.2556 +h2-c3-h2 39.0 109.19 SOURCE3 29 1.8754 3.1352 +h2-c3-i 38.7 104.99 SOURCE3 2 0.0000 0.0000 +h2-c3-n 50.0 108.31 SOURCE3 4 0.0000 0.0000 +h2-c3-n2 49.1 110.22 SOURCE3 6 0.2011 0.2133 +h2-c3-n3 49.3 109.91 SOURCE3 4 0.0000 0.0000 +h2-c3-na 50.3 107.66 SOURCE3 6 1.2854 1.4096 +h2-c3-nc 49.8 109.47 SOURCE3 10 0.2445 0.3133 +h2-c3-nd 49.8 109.47 SOURCE3 10 same as h2-c3-nc +h2-c3-nh 49.5 110.80 SOURCE3 4 0.0000 0.0000 +h2-c3-no 47.8 108.69 SOURCE3 4 0.0000 0.0000 +h2-c3-o 53.8 108.97 SOURCE3 4 0.0000 0.0000 +h2-c3-oh 51.3 108.30 SOURCE3 6 0.5117 0.5715 +h2-c3-os 50.8 108.58 SOURCE3 44 0.9621 1.2773 +h2-c3-s 42.3 106.75 SOURCE3 4 0.0000 0.0000 +h2-c3-s4 42.9 108.58 SOURCE3 8 0.2408 0.2408 +h2-c3-s6 43.8 108.42 SOURCE3 4 0.0000 0.0000 +h2-c3-sh 42.7 107.87 SOURCE3 6 0.4125 0.4376 +h2-c3-ss 42.3 109.75 SOURCE3 10 0.2525 0.3442 +h3-c3-n3 50.1 106.77 SOURCE3 1 0.0000 0.0000 +h3-c3-nc 49.9 109.37 SOURCE3 1 0.0000 0.0000 +h3-c3-nd 49.9 109.37 SOURCE3 1 same as h3-c3-nc +h3-c3-nh 50.0 108.93 SOURCE3 1 0.0000 0.0000 +hc-c3-hc 39.4 108.35 SOURCE3 2380 0.7199 0.9006 +hc-c3-i 38.6 104.99 SOURCE0 1 +hc-c3-n 49.8 109.50 SOURCE0 1 +hc-c3-n2 49.3 109.50 SOURCE0 1 +hc-c3-n3 49.4 109.80 SOURCE2 5 1.5200 2.0070 +hc-c3-n4 49.0 107.90 SOURCE0 1 +hc-c3-na 49.9 109.50 SOURCE0 1 +hc-c3-nh 49.4 111.54 SOURCE0 1 +hc-c3-no 48.2 107.20 SOURCE2 1 0.0000 0.0000 +hc-c3-oh 51.1 109.50 SOURCE0 1 +hc-c3-os 50.9 108.70 SOURCE2 13 2.0769 2.3739 +hc-c3-p2 52.4 110.18 SOURCE3 25 0.3432 0.4057 +hc-c3-p3 52.7 110.14 SOURCE3 325 0.4003 0.5126 +hc-c3-p4 53.2 109.59 SOURCE3 87 0.2573 0.3196 +hc-c3-p5 53.8 109.64 SOURCE3 69 0.5787 0.8112 +hc-c3-px 53.5 109.74 SOURCE3 84 0.2586 0.3474 +hc-c3-py 53.9 109.54 SOURCE3 39 0.1670 0.1999 +hc-c3-s4 43.1 107.50 SOURCE2 1 0.0000 0.0000 +hc-c3-s6 43.8 108.20 SOURCE0 1 +hc-c3-sh 42.7 107.87 SOURCE2 3 1.9778 2.0981 +hc-c3-ss 42.5 108.76 SOURCE2 3 1.4244 1.6891 +hx-c3-hx 39.0 110.74 SOURCE3 137 0.3838 0.5531 +hx-c3-n4 49.0 107.91 SOURCE3 148 0.4013 0.5899 +i -c3-i 62.0 113.12 SOURCE3 1 0.0000 0.0000 +n -c3-n 68.8 113.81 SOURCE3 1 0.0000 0.0000 +n2-c3-n2 69.9 107.70 SOURCE3 1 0.0000 0.0000 +n2-c3-os 71.1 108.03 SOURCE3 1 0.0000 0.0000 +n3-c3-n3 69.3 110.48 SOURCE3 1 0.0000 0.0000 +n3-c3-nc 68.8 113.29 SOURCE3 1 0.0000 0.0000 +n3-c3-nd 68.8 113.29 SOURCE3 1 same as n3-c3-nc +n3-c3-nh 71.1 105.80 SOURCE3 1 0.0000 0.0000 +n4-c3-n4 67.1 113.32 SOURCE3 1 0.0000 0.0000 +na-c3-na 69.1 113.49 SOURCE3 1 0.0000 0.0000 +na-c3-os 71.2 109.19 SOURCE3 2 0.6009 0.6009 +nc-c3-nc 70.0 110.61 SOURCE3 1 0.0000 0.0000 +nd-c3-nd 70.0 110.61 SOURCE3 1 same as nc-c3-nc +nc-c3-nh 69.3 112.43 SOURCE3 1 0.0000 0.0000 +nd-c3-nh 69.3 112.43 SOURCE3 1 same as nc-c3-nh +nc-c3-os 69.3 115.41 SOURCE3 3 0.8415 1.0288 +nd-c3-os 69.3 115.41 SOURCE3 3 same as nc-c3-os +nh-c3-nh 71.4 105.87 SOURCE3 1 0.0000 0.0000 +no-c3-no 67.0 108.76 SOURCE3 1 0.0000 0.0000 +o -c3-o 73.4 122.30 SOURCE3 1 0.0000 0.0000 +oh-c3-oh 72.1 111.08 SOURCE3 1 0.0000 0.0000 +oh-c3-os 71.1 113.27 SOURCE3 1 0.0000 0.0000 +oh-c3-sh 63.3 115.46 SOURCE3 1 0.0000 0.0000 +os-c3-os 71.7 110.24 SOURCE3 17 1.6690 2.1340 +os-c3-ss 65.0 109.20 SOURCE3 1 0.0000 0.0000 +p2-c3-p2 98.2 110.48 SOURCE3 1 0.0000 0.0000 +p3-c3-p3 98.9 110.16 SOURCE3 1 0.0000 0.0000 +p5-c3-p5 97.9 116.24 SOURCE3 1 0.0000 0.0000 +s -c3-s 58.3 123.35 SOURCE3 1 0.0000 0.0000 +s4-c3-s4 62.4 112.29 SOURCE3 2 1.2724 1.2724 +s4-c3-s6 62.6 113.52 SOURCE0 1 +s6-c3-s6 63.7 111.75 SOURCE3 1 0.0000 0.0000 +sh-c3-sh 60.8 116.26 SOURCE3 1 0.0000 0.0000 +sh-c3-ss 62.3 110.73 SOURCE0 1 +ss-c3-ss 62.8 109.02 SOURCE3 2 0.2226 0.2226 +br-ca-br 67.3 117.60 SOURCE0 1 +br-ca-ca 63.5 118.13 SOURCE3 8 0.5232 0.6041 +c -ca-c 62.7 120.00 SOURCE0 1 +c -ca-c3 62.6 118.06 SOURCE0 1 +c -ca-ca 64.6 120.14 SOURCE3 40 0.3838 0.4788 +c -ca-ha 46.5 115.90 SOURCE0 1 +c -ca-hc 11.2 120.00 SOURCE0 1 +c -ca-nc 64.4 130.80 SOURCE0 1 +c -ca-nd 64.4 130.80 SOURCE0 1 same as c -ca-nc +c1-ca-c1 64.7 120.00 SOURCE0 1 +c1-ca-ca 65.9 120.00 SOURCE0 1 +c2-ca-c2 62.9 120.00 SOURCE0 1 +c2-ca-ca 64.7 120.60 SOURCE0 1 +c3-ca-c2 62.2 120.00 SOURCE0 1 +c3-ca-c3 62.4 116.80 SOURCE0 1 +c3-ca-ca 63.8 120.63 SOURCE3 60 0.5436 0.7175 +c3-ca-cp 63.7 120.63 SOURCE3 60 0.5436 0.7175 +c3-ca-cq 63.7 120.63 SOURCE3 60 0.5436 0.7175 +ca-ca-ca 67.2 119.97 SOURCE3 1969 0.1024 0.3480 +ca-ca-cc 66.0 120.10 SOURCE3 103 0.2645 0.3451 +ca-ca-cd 66.0 120.10 SOURCE3 103 0.2645 0.3451 +ca-ca-ce 64.9 120.66 SOURCE3 14 0.1371 0.1564 +ca-ca-cf 64.9 120.66 SOURCE3 14 same as ca-ca-ce +ca-ca-cg 65.9 120.05 SOURCE3 6 0.2260 0.2397 +ca-ca-ch 65.9 120.05 SOURCE3 6 same as ca-ca-cg +ca-ca-cl 58.4 119.90 SOURCE2 2 0.0000 0.0000 +ca-ca-cp 67.2 119.07 SOURCE3 14 2.0133 2.3077 +ca-ca-cq 67.2 119.07 SOURCE3 14 2.0133 2.3077 +ca-ca-cx 64.8 119.68 SOURCE3 2 0.0000 0.0000 +ca-ca-f 67.6 118.74 SOURCE3 2 0.0000 0.0000 +ca-ca-h4 48.2 121.09 SOURCE3 57 1.0923 1.4696 +ca-ca-ha 48.5 120.01 SOURCE3 2980 0.1509 0.2511 +ca-ca-i 58.6 118.47 SOURCE3 10 0.4657 0.6181 +ca-ca-n 68.0 119.89 SOURCE3 18 0.1731 0.2095 +ca-ca-n2 66.8 119.57 SOURCE0 1 +ca-ca-n3 18.5 121.19 SOURCE0 1 +ca-ca-n4 67.3 118.41 SOURCE3 6 0.1594 0.1691 +ca-ca-na 70.2 118.34 SOURCE3 54 2.1861 3.6168 +ca-ca-nb 69.2 122.63 SOURCE3 83 0.9345 1.1249 +ca-ca-nc 70.1 119.72 SOURCE3 22 2.1776 3.3994 +ca-ca-nd 70.1 119.72 SOURCE3 22 2.1776 3.3994 +ca-ca-ne 67.7 119.88 SOURCE3 24 0.2867 0.3637 +ca-ca-nf 67.7 119.88 SOURCE3 24 0.2867 0.3637 +ca-ca-nh 69.3 120.13 SOURCE3 193 0.4375 0.6341 +ca-ca-no 66.9 119.54 SOURCE3 10 1.0504 1.3187 +ca-ca-o 70.9 123.43 SOURCE3 4 0.0000 0.0000 +ca-ca-oh 69.8 119.94 SOURCE3 14 0.1421 0.1627 +ca-ca-os 69.8 119.20 SOURCE3 52 0.4006 0.5240 +ca-ca-p2 77.9 114.36 SOURCE0 1 +ca-ca-p3 76.3 120.73 SOURCE3 6 0.1200 0.1273 +ca-ca-p4 77.1 120.30 SOURCE0 1 +ca-ca-p5 77.6 119.98 SOURCE0 1 +ca-ca-pe 76.3 120.45 SOURCE3 20 0.2577 0.2719 +ca-ca-pf 76.3 120.45 SOURCE3 20 0.2577 0.2719 +ca-ca-px 76.4 120.53 SOURCE3 10 0.4207 0.4509 +ca-ca-py 77.4 119.98 SOURCE3 6 0.0632 0.0670 +ca-ca-s 62.2 122.55 SOURCE3 4 0.0000 0.0000 +ca-ca-s4 61.7 119.15 SOURCE0 1 +ca-ca-s6 62.5 119.11 SOURCE0 1 +ca-ca-sh 61.5 120.13 SOURCE3 4 0.0431 0.0431 +ca-ca-ss 62.0 119.93 SOURCE3 16 0.3295 0.3901 +ca-ca-sx 61.2 119.18 SOURCE3 6 0.0409 0.0434 +ca-ca-sy 61.6 119.89 SOURCE3 24 1.1928 1.8813 +cd-ca-nb 66.9 126.21 SOURCE3 1 0.0000 0.0000 +cc-ca-nb 66.9 126.21 SOURCE3 1 same as cd-ca-nb +cl-ca-cl 54.2 118.72 SOURCE0 1 +cp-ca-ha 48.0 121.08 SOURCE3 12 1.5789 1.7484 +cq-ca-ha 48.0 121.08 SOURCE3 12 1.5789 1.7484 +cp-ca-sy 63.9 111.18 SOURCE3 2 0.0000 0.0000 +cq-ca-sy 63.9 111.18 SOURCE3 2 0.0000 0.0000 +f -ca-f 68.1 117.50 SOURCE0 1 +h4-ca-n 49.5 116.02 SOURCE0 1 +h4-ca-na 51.9 114.65 SOURCE3 5 1.5115 1.5484 +h4-ca-nb 51.8 115.94 SOURCE3 52 0.5536 0.7370 +h4-ca-nc 51.5 118.36 SOURCE0 1 +h4-ca-nd 51.5 118.36 SOURCE0 1 same as h4-ca-nc +h4-ca-os 52.3 111.15 SOURCE0 1 +h4-ca-ss 42.4 116.19 SOURCE0 1 +h5-ca-nb 51.8 116.35 SOURCE3 30 0.4960 0.5545 +h5-ca-nc 50.7 122.11 SOURCE0 1 +h5-ca-nd 50.7 122.11 SOURCE0 1 same as h5-ca-nc +ha-ca-n2 48.1 116.00 SOURCE2 1 0.0000 0.0000 +ha-ca-p2 50.1 122.56 SOURCE0 1 +i -ca-i 62.3 119.28 SOURCE0 1 +n -ca-nc 69.7 123.86 SOURCE0 1 +n -ca-nd 69.7 123.86 SOURCE0 1 same as n -ca-nc +n -ca-nh 71.3 116.16 SOURCE0 1 +n2-ca-n2 66.5 120.00 SOURCE0 1 +n2-ca-na 69.2 119.60 SOURCE0 1 +n4-ca-n4 67.7 116.82 SOURCE0 1 +na-ca-na 74.5 113.32 SOURCE0 1 +na-ca-nb 70.2 128.56 SOURCE3 3 0.3052 0.3533 +nb-ca-nb 71.2 125.84 SOURCE3 17 2.5680 4.1190 +nb-ca-nd 71.1 126.50 SOURCE3 2 0.0000 0.0000 +nb-ca-nc 71.1 126.50 SOURCE3 2 same as nb-ca-nd +nb-ca-nh 72.6 118.96 SOURCE3 3 0.0580 0.0706 +nc-ca-nc 70.7 128.74 SOURCE0 1 +nd-ca-nd 70.7 128.74 SOURCE0 1 same as nc-ca-nc +nc-ca-nh 72.8 118.86 SOURCE0 1 +nd-ca-nh 72.8 118.86 SOURCE0 1 same as nc-ca-nh +nh-ca-nh 71.4 120.98 SOURCE0 1 +no-ca-no 67.4 117.14 SOURCE0 1 +o -ca-o 75.5 126.82 SOURCE0 1 +oh-ca-oh 72.6 120.00 SOURCE0 1 +os-ca-os 74.0 113.73 SOURCE0 1 +p2-ca-p2 94.5 121.20 SOURCE0 1 +p3-ca-p3 95.2 121.46 SOURCE0 1 +p5-ca-p5 97.3 120.00 SOURCE0 1 +s -ca-s 61.4 125.14 SOURCE0 1 +s4-ca-s4 65.0 105.81 SOURCE0 1 +s6-ca-s6 66.0 105.81 SOURCE0 1 +sh-ca-sh 61.0 120.24 SOURCE0 1 +ss-ca-ss 62.9 115.15 SOURCE0 1 +c -cc-c2 65.4 121.76 SOURCE3 1 0.0000 0.0000 +c -cd-c2 65.4 121.76 SOURCE3 1 same as c -cc-c2 +c -cc-c3 64.9 112.75 SOURCE3 4 0.2063 0.2063 +c -cd-c3 64.9 112.75 SOURCE3 4 0.2063 0.2063 +c -cc-ca 63.6 122.95 SOURCE3 1 0.0000 0.0000 +c -cd-ca 63.6 122.95 SOURCE3 1 same as c -cc-ca +c -cc-cc 63.7 122.69 SOURCE3 2 0.0000 0.0000 +c -cd-cd 63.7 122.69 SOURCE3 2 0.0000 0.0000 +c -cc-cd 65.7 119.92 SOURCE3 61 2.5574 3.8679 +c -cd-cc 65.7 119.92 SOURCE3 61 2.5574 3.8679 +c -cc-cl 57.8 121.79 SOURCE3 1 0.0000 0.0000 +c -cd-cl 57.8 121.79 SOURCE3 1 same as c -cc-cl +c -cc-ha 47.0 117.02 SOURCE3 56 1.2989 1.9713 +c -cd-ha 47.0 117.02 SOURCE3 56 1.2989 1.9713 +c -cc-n2 68.4 120.89 SOURCE3 1 0.0000 0.0000 +c -cd-n2 68.4 120.89 SOURCE3 1 same as c -cc-n2 +c -cc-nd 70.1 112.91 SOURCE3 1 0.0000 0.0000 +c -cd-nc 70.1 112.91 SOURCE3 1 same as c -cc-nd +c -cc-oh 68.5 118.74 SOURCE3 3 5.1845 5.1845 +c -cd-oh 68.5 118.74 SOURCE3 3 5.1845 5.1845 +c2-cc-c3 63.3 126.11 SOURCE3 2 0.0000 0.0000 +c2-cd-c3 63.3 126.11 SOURCE3 2 0.0000 0.0000 +c2-cc-ca 64.4 128.22 SOURCE3 1 0.0000 0.0000 +c2-cd-ca 64.4 128.22 SOURCE3 1 same as c2-cc-ca +c2-cc-cc 65.3 125.41 SOURCE3 3 2.0867 2.0867 +c2-cd-cd 65.3 125.41 SOURCE3 3 2.0867 2.0867 +c2-cc-cd 69.1 117.02 SOURCE3 2 0.0703 0.0703 +c2-cd-cc 69.1 117.02 SOURCE3 2 same as c2-cc-cd +c2-cc-ha 48.7 122.72 SOURCE3 2 0.0092 0.0092 +c2-cd-ha 48.7 122.72 SOURCE3 2 same as c2-cc-ha +c2-cc-n 67.7 126.90 SOURCE3 1 0.0000 0.0000 +c2-cd-n 67.7 126.90 SOURCE3 1 same as c2-cc-n +c2-cc-os 70.5 119.31 SOURCE3 2 2.2167 2.2167 +c2-cd-os 70.5 119.31 SOURCE3 2 same as c2-cc-os +c3-cc-ca 64.1 117.81 SOURCE3 8 9.2044 9.2060 +c3-cd-ca 64.1 117.81 SOURCE3 8 same as c3-cc-ca +c3-cc-cc 64.7 115.97 SOURCE3 4 2.7731 3.0507 +c3-cd-cd 64.7 115.97 SOURCE3 4 2.7731 3.0507 +c3-cc-cd 64.8 119.45 SOURCE3 35 7.1944 8.2040 +c3-cd-cc 64.8 119.45 SOURCE3 35 7.1944 8.2040 +c3-cc-cf 65.4 117.84 SOURCE3 1 0.0000 0.0000 +c3-cd-ce 65.4 117.84 SOURCE3 1 same as c3-cc-cf +c3-cc-ha 45.1 121.52 SOURCE3 32 2.8716 3.2091 +c3-cd-ha 45.1 121.52 SOURCE3 32 2.8716 3.2091 +c3-cc-n2 64.5 131.55 SOURCE3 1 0.0000 0.0000 +c3-cd-n2 64.5 131.55 SOURCE3 1 same as c3-cc-n2 +c3-cc-na 65.5 122.80 SOURCE3 4 0.4055 0.4308 +c3-cd-na 65.5 122.80 SOURCE3 4 0.4055 0.4308 +c3-cc-nc 65.8 121.44 SOURCE3 2 0.1912 0.1912 +c3-cd-nd 65.8 121.44 SOURCE3 2 same as c3-cc-nc +c3-cc-nd 66.4 121.96 SOURCE3 6 4.6612 4.8451 +c3-cd-nc 66.4 121.96 SOURCE3 6 4.6612 4.8451 +ca-cc-cc 67.7 111.04 SOURCE3 9 5.2494 7.9455 +ca-cd-cd 67.7 111.04 SOURCE3 9 5.2494 7.9455 +ca-cc-cd 68.2 113.51 SOURCE3 26 6.3054 7.4229 +ca-cd-cc 68.2 113.51 SOURCE3 26 6.3054 7.4229 +ca-cc-h4 45.6 128.66 SOURCE3 10 2.0866 3.1167 +ca-cd-h4 45.6 128.66 SOURCE3 10 2.0866 3.1167 +ca-cc-ha 46.4 124.04 SOURCE3 34 2.5190 3.6691 +ca-cd-ha 46.4 124.04 SOURCE3 34 2.5190 3.6691 +ca-cc-n 72.5 104.87 SOURCE3 1 0.0000 0.0000 +ca-cd-n 72.5 104.87 SOURCE3 1 same as ca-cc-n +ca-cc-nd 70.2 115.05 SOURCE3 6 3.7100 4.3938 +ca-cc-nc 70.2 115.05 SOURCE3 6 3.7100 4.3938 added by eajfpeters +ca-cd-nc 70.2 115.05 SOURCE3 6 3.7100 4.3938 +ca-cd-nc 70.2 115.05 SOURCE3 6 3.7100 4.3938 added by eajfpeters +ca-cc-os 69.5 116.24 SOURCE3 4 3.6507 5.0903 +ca-cd-os 69.5 116.24 SOURCE3 4 same as ca-cc-os +ca-cc-ss 64.9 111.09 SOURCE3 4 0.0000 0.0000 +ca-cd-ss 64.9 111.09 SOURCE3 4 same as ca-cc-ss +cc-cc-cc 67.9 110.70 SOURCE3 54 2.3111 3.4091 +cd-cd-cd 67.9 110.70 SOURCE3 54 2.3111 3.4091 +cc-cc-cd 68.2 114.19 SOURCE3 517 5.4334 6.5960 +cc-cd-cd 68.2 114.19 SOURCE3 517 5.4334 6.5960 +cc-cc-cf 65.6 123.92 SOURCE3 1 0.0000 0.0000 +cd-cd-ce 65.6 123.92 SOURCE3 1 same as cc-cc-cf +cc-cc-h4 45.6 129.47 SOURCE3 171 1.7718 2.2734 +cd-cd-h4 45.6 129.47 SOURCE3 171 1.7718 2.2734 +cc-cc-ha 46.6 123.74 SOURCE3 656 2.7165 3.3195 +cd-cd-ha 46.6 123.74 SOURCE3 656 2.7165 3.3195 +cc-cc-n 67.9 119.89 SOURCE3 36 0.1731 0.2095 +cd-cd-n 67.9 119.89 SOURCE3 36 0.1731 0.2095 +cc-cc-n2 69.3 121.15 SOURCE3 6 0.4642 0.4642 +cd-cd-n2 69.3 121.15 SOURCE3 6 0.4642 0.4642 +cc-cc-na 72.2 106.80 SOURCE3 33 0.4847 0.6297 +cd-cd-na 72.2 106.80 SOURCE3 33 same as cc-cc-na +cc-cc-nc 70.0 113.42 SOURCE3 4 1.1985 1.3957 +cd-cd-nd 70.0 113.42 SOURCE3 4 same as cc-cc-nc +cc-cc-nd 71.1 112.56 SOURCE3 141 3.3765 4.2871 +cd-cd-nc 71.1 112.56 SOURCE3 141 3.3765 4.2871 +cc-cc-os 68.4 120.43 SOURCE3 4 7.5873 8.6974 +cd-cd-os 68.4 120.43 SOURCE3 4 same as cc-cc-os +cc-cc-ss 63.8 115.02 SOURCE3 2 0.0000 0.0000 +cd-cd-ss 63.8 115.02 SOURCE3 2 0.0000 0.0000 +cd-cc-cd 69.3 115.51 SOURCE3 2 0.0000 0.0000 +cc-cd-cc 69.3 115.51 SOURCE3 2 0.0000 0.0000 +cd-cc-h4 47.2 129.11 SOURCE3 418 2.0265 3.1355 +cc-cd-h4 47.2 129.11 SOURCE3 418 2.0265 3.1355 +cd-cc-ha 48.4 122.89 SOURCE3 584 2.3225 2.9334 +cc-cd-ha 48.4 122.89 SOURCE3 584 2.3225 2.9334 +cd-cc-n 70.7 115.52 SOURCE3 52 1.0811 1.3322 +cc-cd-n 70.7 115.52 SOURCE3 52 1.0811 1.3322 +cd-cc-na 72.9 109.42 SOURCE3 265 1.3410 2.6051 +cc-cd-na 72.9 109.42 SOURCE3 265 1.3410 2.6051 +cd-cc-nc 71.0 114.98 SOURCE3 23 4.6219 5.3935 +cc-cd-nd 71.0 114.98 SOURCE3 23 4.6219 5.3935 +cd-cc-nh 68.4 125.04 SOURCE3 1 0.0000 0.0000 +cc-cd-nh 68.4 125.04 SOURCE3 1 same as cd-cc-nh +cd-cc-oh 68.8 126.44 SOURCE3 3 0.5018 0.5018 +cc-cd-oh 68.8 126.44 SOURCE3 3 0.5018 0.5018 +cd-cc-os 70.0 120.30 SOURCE3 64 3.4271 5.4354 +cc-cd-os 70.0 120.30 SOURCE3 64 3.4271 5.4354 +cd-cc-ss 63.6 118.17 SOURCE3 37 3.1217 5.1653 +cc-cd-ss 63.6 118.17 SOURCE3 37 3.1217 5.1653 +cl-cc-nd 59.8 125.30 SOURCE3 1 0.0000 0.0000 +cl-cd-nc 59.8 125.30 SOURCE3 1 same as cl-cc-nd +h4-cc-n 50.4 117.62 SOURCE3 53 0.6887 0.9721 +h4-cd-n 50.4 117.62 SOURCE3 53 0.6887 0.9721 +h4-cc-na 50.2 119.66 SOURCE3 294 0.9445 2.4702 +h4-cd-na 50.2 119.66 SOURCE3 294 0.9445 2.4702 +h4-cc-nc 50.0 120.03 SOURCE3 16 1.9828 2.3863 +h4-cd-nd 50.0 120.03 SOURCE3 16 1.9828 2.3863 +h4-cc-nd 51.4 119.11 SOURCE3 135 1.2486 1.6946 +h4-cd-nc 51.4 119.11 SOURCE3 135 1.2486 1.6946 +h4-cc-os 52.3 111.89 SOURCE3 61 1.5084 2.3500 +h4-cd-os 52.3 111.89 SOURCE3 61 1.5084 2.3500 +h4-cc-ss 43.0 117.75 SOURCE3 40 2.0527 3.1156 +h4-cd-ss 43.0 117.75 SOURCE3 40 2.0527 3.1156 +h5-cc-na 49.8 122.10 SOURCE3 16 1.2773 1.4626 +h5-cd-na 49.8 122.10 SOURCE3 16 1.2773 1.4626 +h5-cc-nc 49.3 123.70 SOURCE3 6 0.2952 0.3547 +h5-cd-nd 49.3 123.70 SOURCE3 6 0.2952 0.3547 +h5-cc-nd 50.1 125.38 SOURCE3 40 1.6952 2.2157 +h5-cd-nc 50.1 125.38 SOURCE3 40 1.6952 2.2157 +h5-cc-os 51.3 116.33 SOURCE3 12 2.1788 3.2919 +h5-cd-os 51.3 116.33 SOURCE3 12 2.1788 3.2919 +h5-cc-ss 42.2 122.00 SOURCE3 6 0.5719 0.7237 +h5-cd-ss 42.2 122.00 SOURCE3 6 0.5719 0.7237 +ha-cc-na 49.8 121.50 SOURCE2 1 0.0000 0.0000 +ha-cd-na 49.8 121.50 SOURCE2 1 same as ha-cc-na +ha-cc-nc 50.7 116.54 SOURCE3 5 1.4298 1.4482 +ha-cd-nd 50.7 116.54 SOURCE3 5 1.4298 1.4482 +ha-cc-nd 51.4 118.88 SOURCE3 20 2.6038 2.8923 +ha-cd-nc 51.4 118.88 SOURCE3 20 2.6038 2.8923 +ha-cc-os 52.5 110.86 SOURCE3 7 1.2407 1.3846 +ha-cd-os 52.5 110.86 SOURCE3 7 1.2407 1.3846 +ha-cc-ss 42.3 121.64 SOURCE2 5 1.0080 1.3276 +ha-cd-ss 42.3 121.64 SOURCE2 5 same as ha-cc-ss +n -cc-c 68.2 116.06 SOURCE3 1 0.0000 0.0000 +c -cd-n 68.2 116.06 SOURCE3 1 same as n -cc-c +n -cc-nh 72.2 117.01 SOURCE3 2 0.0000 0.0000 +n -cd-nh 72.2 117.01 SOURCE3 2 0.0000 0.0000 +na-cc-nc 69.7 125.32 SOURCE3 1 0.0000 0.0000 +na-cd-nd 69.7 125.32 SOURCE3 1 same as na-cc-nc +na-cc-nd 74.8 112.02 SOURCE3 17 1.9564 2.2434 +na-cd-nc 74.8 112.02 SOURCE3 17 1.9564 2.2434 +nc-cc-nd 72.5 118.69 SOURCE3 9 6.4647 6.6642 +nc-cd-nd 72.5 118.69 SOURCE3 9 6.4647 6.6642 +nc-cc-ss 64.6 119.86 SOURCE3 2 0.0000 0.0000 +nd-cd-ss 64.6 119.86 SOURCE3 2 same as nc-cc-ss +nd-cc-nh 72.4 120.11 SOURCE3 5 0.7833 0.9313 +nc-cd-nh 72.4 120.11 SOURCE3 5 0.7833 0.9313 +nd-cc-os 73.0 119.14 SOURCE3 16 7.0412 7.4096 +nc-cd-os 73.0 119.14 SOURCE3 16 7.0412 7.4096 +nd-cc-ss 66.5 114.51 SOURCE3 8 0.2795 0.3449 +nc-cd-ss 66.5 114.51 SOURCE3 8 0.2795 0.3449 +nh-cc-nh 72.9 115.96 SOURCE3 1 0.0000 0.0000 +nh-cd-nh 72.9 115.96 SOURCE3 1 same as nh-cc-nh +os-cc-ss 62.0 132.01 SOURCE3 1 0.0000 0.0000 +os-cd-ss 62.0 132.01 SOURCE3 1 same as os-cc-ss +ss-cc-ss 62.2 122.30 SOURCE3 2 0.0000 0.0000 +ss-cd-ss 62.2 122.30 SOURCE3 2 same as ss-cc-ss +c -cd-nd 64.3 130.80 SOURCE3 1 0.0000 0.0000 +c -cc-nc 64.3 130.80 SOURCE3 1 same as c -cd-nd +c3-cd-os 67.8 115.89 SOURCE3 1 0.0000 0.0000 +c3-cc-os 67.8 115.89 SOURCE3 1 same as c3-cd-os +cd-cd-nh 68.6 118.98 SOURCE3 1 0.0000 0.0000 +cc-cc-nh 68.6 118.98 SOURCE3 1 same as cd-cd-nh +cd-cd-pc 80.8 115.36 SOURCE3 84 3.0583 3.2889 +cc-cc-pd 80.8 115.36 SOURCE3 84 same as cd-cd-pc +ha-cd-pc 53.6 121.76 SOURCE3 84 2.0450 2.2216 +ha-cc-pd 53.6 121.76 SOURCE3 84 same as ha-cd-pc +n -cd-nc 70.9 123.86 SOURCE3 1 0.0000 0.0000 +n -cc-nd 70.9 123.86 SOURCE3 1 same as n -cd-nc +nd-cd-nh 73.9 111.94 SOURCE3 1 0.0000 0.0000 +nc-cc-nh 73.9 111.94 SOURCE3 1 same as nd-cd-nh +c -ce-c 63.5 118.85 SOURCE3 1 0.0000 0.0000 +c -cf-c 63.5 118.85 SOURCE3 1 same as c -ce-c +c -ce-c2 65.8 120.42 SOURCE3 13 1.3613 1.8877 +c -cf-c2 65.8 120.42 SOURCE3 13 same as c -ce-c2 +c -ce-c3 63.1 118.00 SOURCE3 4 2.0537 2.1860 +c -cf-c3 63.1 118.00 SOURCE3 4 same as c -ce-c3 +c -ce-cf 64.3 126.41 SOURCE3 2 5.7847 5.7847 +c -cf-ce 64.3 126.41 SOURCE3 2 same as c -ce-cf +c -ce-ha 46.6 117.26 SOURCE3 11 2.2096 2.7158 +c -cf-ha 46.6 117.26 SOURCE3 11 2.2096 2.7158 +c -ce-nh 66.7 122.76 SOURCE3 1 0.0000 0.0000 +c -cf-nh 66.7 122.76 SOURCE3 1 same as c -ce-nh +c2-ce-c3 64.3 122.89 SOURCE3 7 0.8750 1.0449 +c2-cf-c3 64.3 122.89 SOURCE3 7 same as c2-ce-c3 +c2-ce-ca 65.2 123.08 SOURCE3 6 2.1558 2.1589 +c2-cf-ca 65.2 123.08 SOURCE3 6 same as c2-ce-ca +c2-ce-ce 65.7 123.08 SOURCE3 12 0.5820 0.6518 +c2-cf-cf 65.7 123.08 SOURCE3 12 same as c2-ce-ce +c2-ce-cg 66.5 122.22 SOURCE3 3 0.7952 0.8434 +c2-cf-ch 66.5 122.22 SOURCE3 3 same as c2-ce-cg +c2-ce-ha 49.6 121.10 SOURCE3 46 1.8238 2.4054 +c2-cf-ha 49.6 121.10 SOURCE3 46 same as c2-ce-ha +c2-ce-n2 70.3 128.70 SOURCE3 1 0.0000 0.0000 +c2-cf-n2 70.3 128.70 SOURCE3 1 same as c2-ce-n2 +c2-ce-ne 69.7 118.32 SOURCE3 7 0.8179 1.0468 +c2-cf-nf 69.7 118.32 SOURCE3 7 same as c2-ce-ne +c2-ce-p2 77.9 118.24 SOURCE0 1 +c2-cf-p2 77.9 118.24 SOURCE0 1 same as c2-ce-p2 +c2-ce-pe 77.6 118.76 SOURCE3 8 2.1170 2.3984 +c2-cf-pf 77.6 118.76 SOURCE3 8 same as c2-ce-pe +c2-ce-px 77.2 119.72 SOURCE3 6 0.3888 0.5213 +c2-cf-px 77.2 119.72 SOURCE3 6 same as c2-ce-px +c2-ce-py 77.4 122.13 SOURCE3 5 3.0715 3.1367 +c2-cf-py 77.4 122.13 SOURCE3 5 same as c2-ce-py +c2-ce-sx 61.6 119.87 SOURCE3 5 0.6330 0.8557 +c2-cf-sx 61.6 119.87 SOURCE3 5 same as c2-ce-sx +c2-ce-sy 62.0 120.35 SOURCE3 5 0.4293 0.5401 +c2-cf-sy 62.0 120.35 SOURCE3 5 same as c2-ce-sy +c3-ce-ca 63.2 117.62 SOURCE3 1 0.0000 0.0000 +c3-cf-ca 63.2 117.62 SOURCE3 1 same as c3-ce-ca +c3-ce-ce 63.3 118.71 SOURCE3 4 1.3456 1.5974 +c3-cf-cf 63.3 118.71 SOURCE3 4 same as c3-ce-ce +c3-ce-n2 68.6 116.94 SOURCE3 2 0.0000 0.0000 +c3-cf-n2 68.6 116.94 SOURCE3 2 same as c3-ce-n2 +ca-ce-ca 63.8 117.93 SOURCE3 1 0.0000 0.0000 +ca-cf-ca 63.8 117.93 SOURCE3 1 same as ca-ce-ca +ca-ce-ha 46.7 116.87 SOURCE3 4 1.2172 1.4055 +ca-cf-ha 46.7 116.87 SOURCE3 4 same as ca-ce-ha +ca-ce-n2 68.5 120.72 SOURCE3 1 0.0000 0.0000 +ca-cf-n2 68.5 120.72 SOURCE3 1 same as ca-ce-n2 +ce-ce-ce 64.5 118.74 SOURCE3 1 0.0000 0.0000 +cf-cf-cf 64.5 118.74 SOURCE3 1 same as ce-ce-ce +ce-ce-ha 47.5 115.90 SOURCE3 12 0.3242 0.4670 +cf-cf-ha 47.5 115.90 SOURCE3 12 0.3242 0.4670 +ce-ce-n2 68.5 123.00 SOURCE3 2 0.0000 0.0000 +cf-cf-n2 68.5 123.00 SOURCE3 2 same as ce-ce-n2 +cf-ce-ha 50.6 116.11 SOURCE3 4 1.6696 1.6696 +ce-cf-ha 50.6 116.11 SOURCE3 4 1.6696 1.6696 +cg-ce-cg 66.0 116.75 SOURCE3 1 0.0000 0.0000 +ch-cf-ch 66.0 116.75 SOURCE3 1 same as cg-ce-cg +cg-ce-ha 47.8 117.00 SOURCE2 1 0.0000 0.0000 +ch-cf-ha 47.8 117.00 SOURCE2 1 same as cg-ce-ha +cg-ce-n1 69.3 119.50 SOURCE2 1 0.0000 0.0000 +ch-cf-n1 69.3 119.50 SOURCE2 1 same as cg-ce-n1 +ha-ce-n2 52.9 119.51 SOURCE3 2 0.4623 0.4623 +ha-cf-n2 52.9 119.51 SOURCE3 2 same as ha-ce-n2 +ha-ce-ne 49.2 118.59 SOURCE3 5 1.0130 1.1113 +ha-cf-nf 49.2 118.59 SOURCE3 5 same as ha-ce-ne +ha-ce-nh 52.1 114.99 SOURCE3 1 0.0000 0.0000 +ha-cf-nh 52.1 114.99 SOURCE3 1 same as ha-ce-nh +ha-ce-p2 51.4 120.11 SOURCE0 1 +ha-cf-p2 51.4 120.11 SOURCE0 1 same as ha-ce-p2 +ha-ce-pe 51.4 119.33 SOURCE3 6 0.7187 0.8966 +ha-cf-pf 51.4 119.33 SOURCE3 6 same as ha-ce-pe +ha-ce-px 51.7 117.90 SOURCE3 6 0.1568 0.1809 +ha-cf-px 51.7 117.90 SOURCE3 6 same as ha-ce-px +ha-ce-py 52.3 118.72 SOURCE3 3 0.2888 0.3064 +ha-cf-py 52.3 118.72 SOURCE3 3 same as ha-ce-py +ha-ce-sx 41.8 115.45 SOURCE3 3 0.6260 0.6640 +ha-cf-sx 41.8 115.45 SOURCE3 3 same as ha-ce-sx +ha-ce-sy 42.3 114.86 SOURCE3 3 0.4447 0.4717 +ha-cf-sy 42.3 114.86 SOURCE3 3 same as ha-ce-sy +ne-ce-ne 68.1 123.87 SOURCE3 1 0.0000 0.0000 +nf-cf-nf 68.1 123.87 SOURCE3 1 same as ne-ce-ne +pe-ce-pe 92.4 129.79 SOURCE3 1 0.0000 0.0000 +pf-cf-pf 92.4 129.79 SOURCE3 1 same as pe-ce-pe +py-ce-py 102.6 108.06 SOURCE3 1 0.0000 0.0000 +py-cf-py 102.6 108.06 SOURCE3 1 same as py-ce-py +sx-ce-sx 60.6 120.32 SOURCE3 1 0.0000 0.0000 +sx-cf-sx 60.6 120.32 SOURCE3 1 same as sx-ce-sx +sy-ce-sy 61.2 119.97 SOURCE3 1 0.0000 0.0000 +sy-cf-sy 61.2 119.97 SOURCE3 1 same as sy-ce-sy +c -cf-cc 63.9 126.07 SOURCE3 1 0.0000 0.0000 +c -ce-cd 63.9 126.07 SOURCE3 1 same as c -cf-cc +cc-cf-ha 49.3 119.16 SOURCE3 1 0.0000 0.0000 +cd-ce-ha 49.3 119.16 SOURCE3 1 same as cc-cf-ha +ce-cf-cf 63.8 130.92 SOURCE3 2 5.4656 5.4656 +ce-ce-cf 63.8 130.92 SOURCE3 2 same as ce-cf-cf +cf-cf-n1 66.6 127.15 SOURCE3 2 2.1936 2.1936 +ce-ce-n1 66.6 127.15 SOURCE3 2 same as cf-cf-n1 +ha-cf-n1 52.5 115.96 SOURCE3 2 3.5425 3.5425 +ha-ce-n1 52.5 115.96 SOURCE3 2 same as ha-cf-n1 +c -cg-c1 56.2 179.14 SOURCE3 2 0.0000 0.0000 +c -ch-c1 56.2 179.14 SOURCE3 2 same as c -cg-c1 +c1-cg-ca 56.4 180.00 SOURCE3 2 0.0000 0.0000 +c1-ch-ca 56.4 180.00 SOURCE3 2 same as c1-cg-ca +c1-cg-ce 56.9 178.32 SOURCE3 1 0.0000 0.0000 +c1-ch-cf 56.9 178.32 SOURCE3 1 same as c1-cg-ce +c1-cg-cg 58.1 180.00 SOURCE3 2 0.0000 0.0000 +c1-ch-ch 58.1 180.00 SOURCE3 2 same as c1-cg-cg +c1-cg-ne 61.7 170.02 SOURCE3 4 0.9102 1.1724 +c1-ch-nf 61.7 170.02 SOURCE3 4 same as c1-cg-ne +c1-cg-pe 71.8 173.29 SOURCE3 11 4.6016 4.9305 +c1-ch-pf 71.8 173.29 SOURCE3 11 same as c1-cg-pe +ca-cg-n1 58.8 180.00 SOURCE3 1 0.0000 0.0000 +ca-ch-n1 58.8 180.00 SOURCE3 1 same as ca-cg-n1 +ce-cg-n1 59.1 179.58 SOURCE3 2 0.0000 0.0000 +cf-ch-n1 59.1 179.58 SOURCE3 2 same as ce-cg-n1 +n1-cg-ne 63.4 176.17 SOURCE2 3 2.5556 3.0641 +n1-ch-nf 63.4 176.17 SOURCE2 3 same as n1-cg-ne +f -cl-f 0.0 87.50 SOURCE2 1 0.0000 0.0000 +ca-cp-ca 67.1 118.75 SOURCE3 4 0.0123 0.0123 +ca-cp-cp 62.6 127.01 SOURCE3 18 7.1022 7.1465 +ca-cp-nb 68.7 122.97 SOURCE3 2 0.0000 0.0000 +cp-cp-cp 72.2 90.00 SOURCE3 4 0.0000 0.0000 +cp-cp-nb 67.9 116.43 SOURCE3 2 0.0000 0.0000 +ca-cq-ca 67.1 118.75 SOURCE3 4 0.0123 0.0123 +ca-cq-cq 62.6 127.01 SOURCE3 18 7.1022 7.1465 +ca-cq-nb 68.7 122.97 SOURCE3 2 0.0000 0.0000 +cq-cq-cq 72.2 90.00 SOURCE3 4 0.0000 0.0000 +cq-cq-nb 67.9 116.43 SOURCE3 2 0.0000 0.0000 +c -cu-cu 95.0 62.60 SOURCE2 1 0.0000 0.0000 +cu-cu-cx 101.0 50.80 SOURCE2 1 0.0000 0.0000 +cu-cu-ha 46.1 147.73 SOURCE2 3 1.8889 2.0950 +cv-cv-cy 73.3 94.17 SOURCE3 2 0.0000 0.0000 +cv-cv-ha 47.3 133.70 SOURCE3 2 0.0000 0.0000 +cx-cv-cx 84.7 63.90 SOURCE2 1 0.0000 0.0000 +cy-cv-ha 42.9 132.14 SOURCE3 2 0.0000 0.0000 +c -cx-cx 72.6 88.75 SOURCE2 2 31.0500 31.0500 +c -cx-hc 46.0 118.50 SOURCE2 1 0.0000 0.0000 +c2-cx-hc 44.5 124.20 SOURCE2 2 0.0000 0.0000 +c3-cx-c3 61.5 120.00 SOURCE2 1 0.0000 0.0000 +c3-cx-cx 61.7 120.67 SOURCE3 4 0.0000 0.0000 +ca-cx-oh 69.3 112.93 SOURCE3 1 0.0000 0.0000 +ca-cx-os 66.5 118.12 SOURCE3 2 0.0000 0.0000 +cl-cx-cl 54.4 114.20 SOURCE2 1 0.0000 0.0000 +cl-cx-cx 56.9 118.70 SOURCE2 1 0.0000 0.0000 +cl-cx-h1 40.4 111.43 SOURCE3 1 0.0000 0.0000 +cl-cx-hc 39.6 115.80 SOURCE2 1 0.0000 0.0000 +cu-cx-cu 91.5 54.60 SOURCE2 1 0.0000 0.0000 +cx-cx-cx 85.3 63.75 SOURCE2 11 6.2810 11.0052 +cx-cx-cy 67.5 100.53 SOURCE3 4 0.0000 0.0000 +cx-cx-f 64.7 117.25 SOURCE3 2 0.0000 0.0000 +cx-cx-h1 45.5 119.66 SOURCE3 12 0.2763 0.4529 +cx-cx-hc 45.8 117.92 SOURCE3 92 0.7174 1.1927 +cx-cx-n3 65.3 116.30 SOURCE2 1 0.0000 0.0000 +cx-cx-os 93.3 59.41 SOURCE3 4 0.0000 0.0000 +cy-cx-hc 44.0 125.43 SOURCE3 2 0.0000 0.0000 +f -cx-f 70.6 106.90 SOURCE2 2 1.4000 1.4000 +f -cx-h1 50.3 111.68 SOURCE3 1 0.0000 0.0000 +f -cx-hc 50.2 112.30 SOURCE2 1 0.0000 0.0000 +h1-cx-h1 38.4 115.45 SOURCE3 4 0.0168 0.0168 +h1-cx-os 50.0 115.17 SOURCE3 8 0.0226 0.0226 +h2-cx-h2 37.9 119.43 SOURCE3 1 0.0000 0.0000 +h2-cx-n2 47.6 117.18 SOURCE3 4 0.0000 0.0000 +hc-cx-hc 38.6 114.47 SOURCE3 19 0.2816 0.3295 +hc-cx-os 50.3 114.10 SOURCE2 1 0.0000 0.0000 +n -cx-oh 69.2 119.75 SOURCE3 2 0.0000 0.0000 +n -cx-os 91.6 65.98 SOURCE3 1 0.0000 0.0000 +n2-cx-n2 102.1 50.16 SOURCE3 1 0.0000 0.0000 +oh-cx-oh 76.7 107.85 SOURCE3 1 0.0000 0.0000 +oh-cx-os 71.6 118.12 SOURCE3 4 1.3581 1.3581 +os-cx-os 93.3 66.95 SOURCE3 1 0.0000 0.0000 +c -cy-cy 71.4 85.95 SOURCE3 4 2.1019 2.1019 +c -cy-hc 45.7 113.85 SOURCE3 8 0.2067 0.2067 +c -cy-os 74.7 88.50 SOURCE2 1 0.0000 0.0000 +c2-cy-cy 66.1 100.40 SOURCE2 1 0.0000 0.0000 +c3-cy-cy 62.0 114.15 SOURCE3 12 5.4760 6.0450 +c3-cy-h1 46.6 109.66 SOURCE3 2 0.0000 0.0000 +c3-cy-hc 46.2 111.55 SOURCE3 5 0.5021 0.6276 +c3-cy-n3 65.3 112.92 SOURCE3 2 0.0000 0.0000 +cl-cy-cy 57.6 112.00 SOURCE3 2 0.0000 0.0000 +cl-cy-h1 41.0 106.59 SOURCE3 1 0.0000 0.0000 +cl-cy-hc 39.6 114.00 SOURCE2 1 0.0000 0.0000 +cv-cy-cy 71.8 85.83 SOURCE3 2 0.0000 0.0000 +cv-cy-hc 45.8 115.88 SOURCE3 4 0.0000 0.0000 +cx-cy-cy 66.1 101.23 SOURCE3 4 0.0000 0.0000 +cx-cy-hc 45.3 118.30 SOURCE2 3 5.4000 5.7799 +cy-cy-cy 70.2 87.61 SOURCE3 32 1.1419 1.5407 +cy-cy-h1 44.9 114.84 SOURCE3 20 1.8317 2.5651 +cy-cy-hc 44.8 115.14 SOURCE3 114 0.7232 0.8364 +cy-cy-n 64.9 112.13 SOURCE3 31 1.0775 2.0700 +cy-cy-n3 73.5 87.58 SOURCE3 4 0.6135 0.6135 +cy-cy-oh 66.0 114.19 SOURCE3 4 0.0000 0.0000 +cy-cy-os 72.9 91.10 SOURCE3 4 0.4160 0.4160 +h1-cy-h1 39.0 109.72 SOURCE3 6 0.7518 0.8087 +h1-cy-n3 48.2 113.36 SOURCE3 6 1.3680 1.4509 +h1-cy-oh 50.9 111.49 SOURCE3 2 0.0000 0.0000 +h1-cy-os 49.7 110.94 SOURCE3 8 0.6521 0.6522 +hc-cy-hc 39.2 109.04 SOURCE3 28 0.4802 0.5962 +ca-i -cl 0.0 90.21 SOURCE3 2 0.0000 0.0000 +ca-i -o 0.0 97.08 SOURCE3 5 0.1786 0.2233 +cl-i -cl 0.0 179.58 SOURCE3 1 0.0000 0.0000 +br-n -br 66.6 116.20 SOURCE3 1 0.0000 0.0000 +br-n -c 61.9 120.77 SOURCE3 5 2.1068 2.6390 +br-n -ca 62.1 118.19 SOURCE0 1 +br-n -cd 62.3 118.19 SOURCE3 1 0.0000 0.0000 +br-n -cc 62.3 118.19 SOURCE3 1 same as br-n -cd +c -n -c 67.4 119.63 SOURCE3 13 6.4901 7.0653 +c -n -c1 68.5 117.04 SOURCE3 1 0.0000 0.0000 +c -n -c2 65.1 122.15 SOURCE3 9 4.1277 5.1016 +c -n -c3 63.9 121.35 SOURCE3 54 1.7456 2.3808 +c -n -ca 64.3 123.71 SOURCE3 10 3.3441 3.8159 +c -n -cc 65.2 124.19 SOURCE3 57 1.8239 2.2262 +c -n -cd 65.2 124.19 SOURCE3 57 1.8239 2.2262 +c -n -cl 58.2 115.32 SOURCE3 3 0.5092 0.5401 +c -n -cx 65.9 112.77 SOURCE3 1 0.0000 0.0000 +c -n -f 68.3 108.63 SOURCE3 3 4.4109 4.6785 +c -n -hn 49.2 118.46 SOURCE3 157 1.8119 2.4094 +c -n -i 56.3 120.38 SOURCE3 5 1.6364 2.1600 +c -n -n 68.2 118.42 SOURCE3 10 2.3102 2.8922 +c -n -n2 68.1 120.59 SOURCE3 9 1.9051 3.2410 +c -n -n3 67.1 120.43 SOURCE3 5 0.9122 0.9481 +c -n -n4 68.8 112.32 SOURCE3 5 1.2355 1.2622 +c -n -na 68.2 119.20 SOURCE3 11 2.1211 2.3032 +c -n -nc 68.6 120.31 SOURCE3 4 1.9095 2.2197 +c -n -nd 68.6 120.31 SOURCE3 4 same as c -n -nc +c -n -nh 68.0 117.06 SOURCE3 4 0.4170 0.4454 +c -n -no 66.5 118.16 SOURCE3 4 4.5037 5.4870 +c -n -o 71.6 118.90 SOURCE3 9 4.4216 5.4085 +c -n -oh 69.5 113.39 SOURCE3 6 1.2395 1.3345 +c -n -os 69.1 113.14 SOURCE3 7 2.9643 3.0839 +c -n -p2 76.5 124.56 SOURCE3 8 2.7083 3.6907 +c -n -p3 75.8 122.54 SOURCE3 9 3.4441 4.4802 +c -n -p4 76.8 123.44 SOURCE3 1 0.0000 0.0000 +c -n -p5 78.3 121.27 SOURCE3 4 2.2442 2.6505 +c -n -pc 77.0 122.23 SOURCE3 3 2.7141 2.8787 +c -n -pd 77.0 122.23 SOURCE3 3 same as c -n -pc +c -n -s 59.0 126.55 SOURCE3 3 4.0857 4.3365 +c -n -s4 60.1 120.41 SOURCE3 4 2.6351 3.1760 +c -n -s6 61.7 119.57 SOURCE3 4 2.7801 3.2191 +c -n -sh 61.9 119.54 SOURCE3 4 1.5284 1.7681 +c -n -ss 62.0 120.37 SOURCE3 7 1.1024 1.4450 +c1-n -c1 73.5 102.69 SOURCE0 1 +c1-n -ca 65.9 118.88 SOURCE0 1 +c1-n -cd 67.0 118.88 SOURCE3 1 0.0000 0.0000 +c1-n -cc 67.0 118.88 SOURCE3 1 same as c1-n -cd +c2-n -c2 65.2 116.75 SOURCE3 1 0.0000 0.0000 +c2-n -c3 62.1 123.87 SOURCE3 1 0.0000 0.0000 +c2-n -ca 64.9 116.54 SOURCE0 1 +c2-n -cd 65.9 116.54 SOURCE3 1 0.0000 0.0000 +c2-n -cc 65.9 116.54 SOURCE3 1 same as c2-n -cd +c2-n -hn 47.4 117.86 SOURCE3 5 3.0657 3.7489 +c3-n -c3 64.0 112.62 SOURCE3 3 1.9371 2.0546 +c3-n -ca 62.4 121.15 SOURCE0 1 +c3-n -cc 63.3 121.17 SOURCE3 4 1.1758 1.2476 +c3-n -cd 63.3 121.17 SOURCE3 4 1.1758 1.2476 +c3-n -hn 46.0 116.78 SOURCE3 39 1.6197 2.1985 +ca-n -ca 64.5 116.80 SOURCE3 1 0.0000 0.0000 +ca-n -cd 65.0 118.42 SOURCE3 1 0.0000 0.0000 +ca-n -cc 65.0 118.42 SOURCE3 1 same as ca-n -cd +ca-n -cl 56.9 117.72 SOURCE0 1 +ca-n -f 64.6 114.92 SOURCE0 1 +ca-n -hn 47.6 114.59 SOURCE3 4 0.3352 0.3353 +ca-n -i 56.6 119.30 SOURCE0 1 +ca-n -n2 66.8 118.25 SOURCE3 1 0.0000 0.0000 +ca-n -n4 64.1 122.98 SOURCE0 1 +ca-n -na 66.8 117.57 SOURCE0 1 +ca-n -nc 68.8 113.03 SOURCE0 1 +ca-n -nd 68.8 113.03 SOURCE0 1 same as ca-n -nc +ca-n -nh 66.4 116.45 SOURCE0 1 +ca-n -p2 79.6 112.32 SOURCE0 1 +ca-n -p3 74.2 125.11 SOURCE0 1 +ca-n -s4 60.0 118.40 SOURCE0 1 +ca-n -s6 61.6 117.32 SOURCE0 1 +ca-n -ss 62.2 116.60 SOURCE0 1 +cc-n -cc 68.8 108.92 SOURCE3 11 0.2418 0.3167 +cd-n -cd 68.8 108.92 SOURCE3 11 same as cc-n -cc +cc-n -hn 47.5 121.52 SOURCE3 4 1.9166 1.9166 +cd-n -hn 47.5 121.52 SOURCE3 4 1.9166 1.9166 +cc-n -nc 69.9 113.03 SOURCE3 1 0.0000 0.0000 +cd-n -nd 69.9 113.03 SOURCE3 1 same as cc-n -nc +cd-n -cl 57.3 117.72 SOURCE3 1 0.0000 0.0000 +cc-n -cl 57.3 117.72 SOURCE3 1 same as cd-n -cl +cd-n -f 65.6 114.92 SOURCE3 1 0.0000 0.0000 +cc-n -f 65.6 114.92 SOURCE3 1 same as cd-n -f +cd-n -i 56.6 119.30 SOURCE3 1 0.0000 0.0000 +cc-n -i 56.6 119.30 SOURCE3 1 same as cd-n -i +cd-n -n 66.5 121.37 SOURCE3 1 0.0000 0.0000 +cc-n -n 66.5 121.37 SOURCE3 1 same as cd-n -n +cd-n -n2 70.1 110.87 SOURCE3 1 0.0000 0.0000 +cc-n -n2 70.1 110.87 SOURCE3 1 same as cd-n -n2 +cd-n -na 67.9 117.57 SOURCE3 1 0.0000 0.0000 +cc-n -na 67.9 117.57 SOURCE3 1 same as cd-n -na +cd-n -nh 67.1 117.52 SOURCE3 1 0.0000 0.0000 +cc-n -nh 67.1 117.52 SOURCE3 1 same as cd-n -nh +cd-n -no 66.4 115.92 SOURCE3 1 0.0000 0.0000 +cc-n -no 66.4 115.92 SOURCE3 1 same as cd-n -no +cd-n -o 70.1 120.54 SOURCE3 1 0.0000 0.0000 +cc-n -o 70.1 120.54 SOURCE3 1 same as cd-n -o +cd-n -oh 67.3 118.15 SOURCE3 1 0.0000 0.0000 +cc-n -oh 67.3 118.15 SOURCE3 1 same as cd-n -oh +cd-n -os 67.6 115.56 SOURCE3 1 0.0000 0.0000 +cc-n -os 67.6 115.56 SOURCE3 1 same as cd-n -os +cd-n -p2 80.2 112.32 SOURCE3 1 0.0000 0.0000 +cc-n -p2 80.2 112.32 SOURCE3 1 same as cd-n -p2 +cd-n -p3 74.7 125.11 SOURCE3 1 0.0000 0.0000 +cc-n -p3 74.7 125.11 SOURCE3 1 same as cd-n -p3 +cd-n -p5 77.9 121.00 SOURCE3 1 0.0000 0.0000 +cc-n -p5 77.9 121.00 SOURCE3 1 same as cd-n -p5 +cd-n -s 60.8 118.29 SOURCE3 1 0.0000 0.0000 +cc-n -s 60.8 118.29 SOURCE3 1 same as cd-n -s +cd-n -s4 60.3 118.40 SOURCE3 1 0.0000 0.0000 +cc-n -s4 60.3 118.40 SOURCE3 1 same as cd-n -s4 +cd-n -s6 62.0 117.32 SOURCE3 1 0.0000 0.0000 +cc-n -s6 62.0 117.32 SOURCE3 1 same as cd-n -s6 +cd-n -sh 61.6 119.13 SOURCE3 1 0.0000 0.0000 +cc-n -sh 61.6 119.13 SOURCE3 1 same as cd-n -sh +cd-n -ss 62.6 116.60 SOURCE3 2 1.8318 1.8318 +cc-n -ss 62.6 116.60 SOURCE3 2 same as cd-n -ss +cl-n -cl 54.3 111.69 SOURCE3 1 0.0000 0.0000 +cx-n -os 95.6 54.04 SOURCE3 1 0.0000 0.0000 +f -n -f 67.9 102.98 SOURCE3 1 0.0000 0.0000 +hn-n -hn 39.7 117.85 SOURCE3 15 1.8879 2.3694 +hn-n -i 36.1 117.24 SOURCE3 2 0.4435 0.4435 +hn-n -n 50.1 113.12 SOURCE3 7 2.2740 3.2954 +hn-n -n2 49.6 118.33 SOURCE3 5 2.0148 2.2377 +hn-n -n3 49.3 114.33 SOURCE3 3 2.6378 2.7978 +hn-n -n4 48.9 112.68 SOURCE3 3 1.8617 1.9746 +hn-n -na 50.4 113.55 SOURCE3 8 1.7554 1.9324 +hn-n -nh 49.6 112.41 SOURCE3 1 0.0000 0.0000 +hn-n -no 48.7 110.11 SOURCE3 1 0.0000 0.0000 +hn-n -o 53.8 116.32 SOURCE3 2 0.0175 0.0175 +hn-n -oh 50.7 109.21 SOURCE3 3 0.2949 0.3165 +hn-n -os 50.1 108.90 SOURCE3 3 0.5220 0.5537 +hn-n -p2 52.5 118.05 SOURCE3 7 2.5423 3.0564 +hn-n -p3 50.9 119.63 SOURCE3 2 0.0000 0.0000 +hn-n -p4 53.0 115.71 SOURCE3 1 0.0000 0.0000 +hn-n -p5 53.6 116.26 SOURCE3 3 0.6453 0.6845 +hn-n -s 41.1 114.92 SOURCE3 2 0.0260 0.0260 +hn-n -s4 41.2 112.46 SOURCE3 1 0.0000 0.0000 +hn-n -s6 42.5 112.68 SOURCE3 1 0.0000 0.0000 +hn-n -sh 42.2 114.91 SOURCE3 1 0.0000 0.0000 +hn-n -ss 42.4 115.60 SOURCE3 3 0.6047 0.6414 +i -n -i 60.7 118.20 SOURCE3 1 0.0000 0.0000 +n -n -n 69.9 114.62 SOURCE3 1 0.0000 0.0000 +n2-n -n2 70.2 116.89 SOURCE3 1 0.0000 0.0000 +n3-n -n3 68.0 117.94 SOURCE3 1 0.0000 0.0000 +n4-n -n4 68.4 112.69 SOURCE3 1 0.0000 0.0000 +na-n -na 69.6 117.38 SOURCE3 1 0.0000 0.0000 +nc-n -nc 71.3 116.41 SOURCE3 1 0.0000 0.0000 +nd-n -nd 71.3 116.41 SOURCE3 1 same as nc-n -nc +nc-n -p2 80.7 117.21 SOURCE0 1 +nd-n -p2 80.7 117.21 SOURCE0 1 same as nc-n -p2 +nc-n -pc 80.5 117.21 SOURCE3 1 0.0000 0.0000 +nd-n -pd 80.5 117.21 SOURCE3 1 same as nc-n -pc +nh-n -nh 68.6 115.18 SOURCE3 1 0.0000 0.0000 +no-n -no 68.5 108.66 SOURCE3 1 0.0000 0.0000 +o -n -o 73.4 128.61 SOURCE3 3 1.0018 1.0626 +oh-n -oh 72.0 107.26 SOURCE3 1 0.0000 0.0000 +os-n -os 71.3 106.53 SOURCE3 1 0.0000 0.0000 +p2-n -p2 98.0 119.62 SOURCE0 1 +p3-n -p3 100.7 108.73 SOURCE3 3 0.2443 0.2591 +p4-n -p4 102.8 108.55 SOURCE0 1 +p5-n -p5 108.5 99.99 SOURCE0 1 +pc-n -pc 97.6 119.62 SOURCE3 1 0.0000 0.0000 +pd-n -pd 97.6 119.62 SOURCE3 1 same as pc-n -pc +s -n -s 58.5 126.00 SOURCE0 1 +s4-n -s4 61.0 113.75 SOURCE3 1 0.0000 0.0000 +s6-n -s6 61.2 119.68 SOURCE3 1 0.0000 0.0000 +sh-n -sh 61.5 119.03 SOURCE3 1 0.0000 0.0000 +ss-n -ss 62.1 118.49 SOURCE3 1 0.0000 0.0000 +c2-n1-o 73.1 116.94 SOURCE3 2 0.0060 0.0060 +c2-n1-s 64.7 118.00 SOURCE3 2 0.0121 0.0121 +cf-n1-o 71.1 122.40 SOURCE3 1 0.0000 0.0000 +ce-n1-o 71.1 122.40 SOURCE3 1 same as cf-n1-o +cf-n1-s 64.8 117.34 SOURCE3 1 0.0000 0.0000 +ce-n1-s 64.8 117.34 SOURCE3 1 same as cf-n1-s +o -n1-p2 84.7 116.05 SOURCE3 1 0.0000 0.0000 +p2-n1-s 80.3 119.93 SOURCE3 1 0.0000 0.0000 +n1-n1-s 54.6 180.00 SOURCE3 1 0.0000 0.0000 +br-n2-br 63.9 106.60 SOURCE0 1 +br-n2-c2 59.1 112.40 SOURCE3 1 0.0000 0.0000 +br-n2-n2 61.1 110.42 SOURCE3 1 0.0000 0.0000 +br-n2-o 60.1 114.47 SOURCE3 1 0.0000 0.0000 +br-n2-p2 80.1 111.03 SOURCE3 1 0.0000 0.0000 +br-n2-s 62.4 115.78 SOURCE3 1 0.0000 0.0000 +c -n2-c 62.7 123.80 SOURCE0 1 +c -n2-c2 66.2 120.97 SOURCE0 1 +c -n2-ca 62.4 120.50 SOURCE0 1 +c1-n2-c1 74.4 121.10 SOURCE0 1 +c1-n2-c3 58.7 151.88 SOURCE3 4 13.3413 15.8282 +c1-n2-cl 55.4 118.80 SOURCE2 1 0.0000 0.0000 +c1-n2-hn 51.5 126.50 SOURCE2 3 6.6667 7.6267 +c1-n2-n2 76.8 113.40 SOURCE0 1 +c1-n2-o 79.2 113.59 SOURCE0 1 +c1-n2-p2 84.8 119.57 SOURCE0 1 +c1-n2-s 69.8 117.67 SOURCE0 1 +c2-n2-c2 70.8 118.18 SOURCE0 1 +c2-n2-c3 66.1 115.30 SOURCE3 8 2.6931 4.2940 +c2-n2-ca 65.0 119.94 SOURCE0 1 +c2-n2-cl 56.7 112.64 SOURCE3 1 0.0000 0.0000 +c2-n2-f 68.3 108.14 SOURCE3 1 0.0000 0.0000 +c2-n2-hn 52.6 110.33 SOURCE3 9 0.5299 0.6498 +c2-n2-i 51.9 114.74 SOURCE3 2 0.0139 0.0139 +c2-n2-n 70.4 117.24 SOURCE3 5 3.9916 5.0254 +c2-n2-n2 77.9 103.59 SOURCE3 2 0.0000 0.0000 +c2-n2-n3 71.3 118.14 SOURCE0 1 +c2-n2-n4 62.4 112.22 SOURCE3 3 0.0383 0.0406 +c2-n2-na 69.3 117.58 SOURCE3 8 1.3943 1.6671 +c2-n2-nh 70.7 117.61 SOURCE3 6 2.3364 3.2642 +c2-n2-no 64.2 111.54 SOURCE3 1 0.0000 0.0000 +c2-n2-o 75.5 116.94 SOURCE0 1 +c2-n2-oh 72.4 109.82 SOURCE3 4 0.5608 0.7131 +c2-n2-os 72.0 110.01 SOURCE3 5 3.1049 4.2241 +c2-n2-p2 85.0 116.00 SOURCE0 1 +c2-n2-p3 77.5 119.30 SOURCE3 3 2.6860 2.8489 +c2-n2-p4 79.3 118.77 SOURCE0 1 +c2-n2-s 68.7 118.00 SOURCE0 1 +c2-n2-s4 68.1 112.29 SOURCE0 1 +c2-n2-s6 69.4 116.24 SOURCE0 1 +c2-n2-sh 63.1 115.48 SOURCE3 1 0.0000 0.0000 +c2-n2-ss 65.0 118.04 SOURCE3 4 1.9749 2.2804 +c3-n2-c3 63.8 110.70 SOURCE0 1 +c3-n2-ca 60.6 123.20 SOURCE0 1 +c3-n2-hn 45.2 118.40 SOURCE0 1 +c3-n2-n1 68.9 115.38 SOURCE3 1 0.0000 0.0000 +c3-n2-n2 69.3 111.18 SOURCE3 7 0.3839 0.4349 +c3-n2-nh 68.1 109.99 SOURCE3 1 0.0000 0.0000 +c3-n2-o 70.3 112.40 SOURCE2 1 0.0000 0.0000 +c3-n2-p2 82.1 114.21 SOURCE3 2 2.2772 2.2772 +c3-n2-s 65.7 116.72 SOURCE3 1 0.0000 0.0000 +c3-n2-s6 66.7 113.84 SOURCE3 1 0.0000 0.0000 +ca-n2-ca 63.6 112.20 SOURCE0 1 +ca-n2-hn 45.1 120.00 SOURCE0 1 +ca-n2-n2 68.8 113.53 SOURCE0 1 +ca-n2-o 69.4 116.00 SOURCE2 1 0.0000 0.0000 +ca-n2-p2 80.9 118.11 SOURCE0 1 +ca-n2-s 64.9 120.11 SOURCE0 1 +cc-n2-hn 52.5 109.65 SOURCE3 3 0.0968 0.0968 +cd-n2-hn 52.5 109.65 SOURCE3 3 0.0968 0.0968 +cd-n2-cl 55.9 115.79 SOURCE3 1 0.0000 0.0000 +cc-n2-cl 55.9 115.79 SOURCE3 1 same as cd-n2-cl +ce-n2-hn 53.9 106.50 SOURCE3 1 0.0000 0.0000 +cf-n2-hn 53.9 106.50 SOURCE3 1 same as ce-n2-hn +ce-n2-nh 70.5 119.08 SOURCE3 2 0.0000 0.0000 +cf-n2-nh 70.5 119.08 SOURCE3 2 same as ce-n2-nh +ce-n2-o 77.4 112.16 SOURCE0 1 +cf-n2-o 77.4 112.16 SOURCE0 1 same as ce-n2-o +ce-n2-oh 72.6 109.87 SOURCE3 1 0.0000 0.0000 +cf-n2-oh 72.6 109.87 SOURCE3 1 same as ce-n2-oh +ce-n2-s 69.3 116.28 SOURCE0 1 +cf-n2-s 69.3 116.28 SOURCE0 1 same as ce-n2-s +cl-n2-n1 59.3 108.70 SOURCE2 1 0.0000 0.0000 +cl-n2-n2 58.7 110.47 SOURCE3 1 0.0000 0.0000 +cl-n2-o 58.2 114.03 SOURCE0 1 +cl-n2-p2 74.0 112.98 SOURCE3 1 0.0000 0.0000 +cl-n2-s 58.5 115.77 SOURCE3 1 0.0000 0.0000 +cx-n2-n2 90.5 64.92 SOURCE3 2 0.0000 0.0000 +f -n2-n2 68.3 114.60 SOURCE2 1 0.0000 0.0000 +f -n2-o 71.2 110.10 SOURCE2 1 0.0000 0.0000 +f -n2-p2 84.3 107.10 SOURCE3 1 0.0000 0.0000 +f -n2-s 67.1 110.73 SOURCE3 1 0.0000 0.0000 +hn-n2-hn 38.6 120.00 SOURCE0 1 +hn-n2-n1 55.3 114.10 SOURCE2 1 0.0000 0.0000 +hn-n2-n2 55.8 105.01 SOURCE3 19 1.1377 1.5183 +hn-n2-ne 54.7 108.56 SOURCE3 29 4.7084 5.5708 +hn-n2-nf 54.7 108.56 SOURCE3 29 same as hn-n2-ne +hn-n2-o 57.6 107.37 SOURCE3 1 0.0000 0.0000 +hn-n2-p2 58.6 112.09 SOURCE3 18 3.1633 4.0663 +hn-n2-p4 54.5 111.33 SOURCE3 1 0.0000 0.0000 +hn-n2-p5 56.3 122.34 SOURCE3 1 0.0000 0.0000 +hn-n2-pe 61.3 111.41 SOURCE3 20 3.8728 4.9895 +hn-n2-pf 61.3 111.41 SOURCE3 20 same as hn-n2-pe +hn-n2-s 49.1 108.17 SOURCE3 1 0.0000 0.0000 +hn-n2-s2 48.3 115.80 SOURCE2 1 0.0000 0.0000 +hn-n2-s4 46.3 111.21 SOURCE3 1 0.0000 0.0000 +hn-n2-s6 48.4 112.59 SOURCE3 2 0.0000 0.0000 +i -n2-n2 53.7 111.79 SOURCE3 1 0.0000 0.0000 +i -n2-o 52.3 116.82 SOURCE3 1 0.0000 0.0000 +i -n2-p2 72.3 113.26 SOURCE3 1 0.0000 0.0000 +i -n2-s 56.3 116.85 SOURCE3 1 0.0000 0.0000 +n -n2-n2 74.7 110.42 SOURCE3 1 0.0000 0.0000 +n -n2-o 76.2 111.38 SOURCE3 1 0.0000 0.0000 +n -n2-p2 85.2 117.30 SOURCE3 1 0.0000 0.0000 +n -n2-s 69.6 115.74 SOURCE3 1 0.0000 0.0000 +n2-n2-n1 79.0 180.00 dac: for azides +n2-n2-n2 78.2 109.49 SOURCE3 2 0.0000 0.0000 +n2-n2-n3 76.6 108.88 SOURCE0 1 +n2-n2-n4 65.8 106.45 SOURCE3 1 0.0000 0.0000 +n2-n2-na 73.1 112.23 SOURCE0 1 +n2-n2-nh 74.8 111.70 SOURCE3 5 0.2774 0.3475 +n2-n2-no 67.7 105.97 SOURCE3 1 0.0000 0.0000 +n2-n2-o 80.2 110.43 SOURCE0 1 +n2-n2-oh 74.0 111.51 SOURCE3 1 0.0000 0.0000 +n2-n2-os 74.7 108.38 SOURCE3 1 0.0000 0.0000 +n2-n2-p2 90.1 109.15 SOURCE0 1 +n2-n2-p3 81.7 113.05 SOURCE3 1 0.0000 0.0000 +n2-n2-p4 81.4 118.77 SOURCE0 1 +n2-n2-p5 89.8 110.46 SOURCE0 1 +n2-n2-s 71.2 115.91 SOURCE0 1 +n2-n2-s4 71.6 107.30 SOURCE0 1 +n2-n2-s6 73.0 111.25 SOURCE0 1 +n2-n2-sh 66.0 111.10 SOURCE3 1 0.0000 0.0000 +n2-n2-ss 68.5 112.14 SOURCE3 1 0.0000 0.0000 +n3-n2-n3 73.0 115.07 SOURCE0 1 +n3-n2-o 76.9 114.00 SOURCE2 1 0.0000 0.0000 +n3-n2-p2 86.7 115.34 SOURCE0 1 +n3-n2-s 70.0 117.13 SOURCE0 1 +n4-n2-n4 60.0 106.70 SOURCE0 1 +n4-n2-o 64.9 112.20 SOURCE3 1 0.0000 0.0000 +n4-n2-p2 79.5 113.07 SOURCE3 1 0.0000 0.0000 +n4-n2-s 62.4 118.50 SOURCE3 1 0.0000 0.0000 +na-n2-na 71.7 107.00 SOURCE0 1 +na-n2-o 74.5 113.09 SOURCE3 1 0.0000 0.0000 +na-n2-p2 83.9 119.16 SOURCE3 1 0.0000 0.0000 +na-n2-s 68.3 118.26 SOURCE3 1 0.0000 0.0000 +ne-n2-nh 74.7 111.38 SOURCE3 1 0.0000 0.0000 +nf-n2-nh 74.7 111.38 SOURCE3 1 same as ne-n2-nh +ne-n2-o 80.0 110.31 SOURCE0 1 +nf-n2-o 80.0 110.31 SOURCE0 1 same as ne-n2-o +ne-n2-s 71.0 116.22 SOURCE0 1 +nf-n2-s 71.0 116.22 SOURCE0 1 same as ne-n2-s +nh-n2-nh 69.7 121.20 SOURCE0 1 +nh-n2-o 76.2 112.96 SOURCE3 3 0.2935 0.3515 +nh-n2-p2 84.9 118.83 SOURCE3 2 0.1024 0.1024 +nh-n2-s 69.6 116.90 SOURCE3 2 0.2276 0.2276 +no-n2-no 62.8 103.70 SOURCE0 1 +no-n2-o 70.4 100.76 SOURCE3 1 0.0000 0.0000 +no-n2-p2 81.3 111.95 SOURCE3 1 0.0000 0.0000 +o -n2-o 81.0 115.37 SOURCE0 1 +o -n2-oh 75.6 112.15 SOURCE2 2 1.4500 1.4500 +o -n2-os 75.7 110.35 SOURCE3 2 0.0042 0.0042 +o -n2-p2 88.7 116.08 SOURCE0 1 +o -n2-p3 82.4 113.43 SOURCE3 1 0.0000 0.0000 +o -n2-p4 85.2 110.61 SOURCE0 1 +o -n2-p5 91.7 109.11 SOURCE0 1 +o -n2-pe 85.2 134.56 SOURCE0 1 +o -n2-pf 85.2 134.56 SOURCE0 1 same as o -n2-pe +o -n2-s 72.1 117.18 SOURCE0 1 +o -n2-s4 72.1 108.91 SOURCE0 1 +o -n2-s6 74.3 111.34 SOURCE0 1 +o -n2-sh 65.6 114.98 SOURCE3 1 0.0000 0.0000 +o -n2-ss 68.4 115.34 SOURCE3 1 0.0000 0.0000 +oh-n2-oh 74.8 101.70 SOURCE0 1 +oh-n2-p2 86.1 115.11 SOURCE3 1 0.0000 0.0000 +oh-n2-s 69.5 116.08 SOURCE3 1 0.0000 0.0000 +os-n2-os 71.3 110.29 SOURCE0 1 +os-n2-p2 87.7 110.20 SOURCE3 1 0.0000 0.0000 +os-n2-s 70.5 112.23 SOURCE3 1 0.0000 0.0000 +p2-n2-p2 107.1 116.80 SOURCE0 1 +p2-n2-p3 98.4 124.48 SOURCE3 1 0.0000 0.0000 +p2-n2-p4 98.3 128.37 SOURCE0 1 +p2-n2-p5 104.4 123.47 SOURCE0 1 +p2-n2-s 85.9 117.84 SOURCE0 1 +p2-n2-s4 86.3 112.10 SOURCE0 1 +p2-n2-s6 86.9 115.70 SOURCE0 1 +p2-n2-sh 80.4 118.45 SOURCE3 1 0.0000 0.0000 +p2-n2-ss 82.0 120.43 SOURCE3 1 0.0000 0.0000 +p3-n2-p3 96.0 120.40 SOURCE0 1 +p3-n2-s 80.1 120.86 SOURCE3 1 0.0000 0.0000 +p4-n2-s 77.8 131.84 SOURCE0 1 +p5-n2-p5 105.8 120.60 SOURCE0 1 +p5-n2-s 85.3 119.89 SOURCE0 1 +pe-n2-s 88.6 115.73 SOURCE0 1 +pf-n2-s 88.6 115.73 SOURCE0 1 same as pe-n2-s +s -n2-s 68.5 120.88 SOURCE0 1 +s -n2-s4 69.2 113.00 SOURCE0 1 +s -n2-s6 69.0 119.61 SOURCE0 1 +s -n2-sh 63.6 122.05 SOURCE3 1 0.0000 0.0000 +s -n2-ss 66.6 118.19 SOURCE3 1 0.0000 0.0000 +s4-n2-s4 66.0 119.18 SOURCE0 1 +s4-n2-s6 67.5 119.18 SOURCE0 1 +s6-n2-s6 69.3 119.18 SOURCE0 1 +sh-n2-sh 60.0 123.93 SOURCE0 1 +sh-n2-ss 61.3 123.93 SOURCE0 1 +ss-n2-ss 62.9 123.93 SOURCE0 1 +br-n3-br 66.5 107.15 SOURCE3 1 0.0000 0.0000 +br-n3-c3 62.7 106.93 SOURCE3 2 0.0000 0.0000 +c -n3-c 63.1 127.17 SOURCE0 1 +c1-n3-c1 64.1 123.34 SOURCE0 1 +c1-n3-f 68.2 104.70 SOURCE2 1 0.0000 0.0000 +c1-n3-hn 47.7 118.31 SOURCE0 1 +c1-n3-o 70.0 116.63 SOURCE0 1 +c2-n3-c2 66.2 124.68 SOURCE0 1 +c2-n3-hn 49.1 119.38 SOURCE0 1 +c3-n3-c3 64.0 110.90 SOURCE3 40 1.6285 2.3048 +c3-n3-ca 16.9 116.39 SOURCE0 1 +c3-n3-cl 58.1 107.23 SOURCE3 3 0.3463 0.3673 +c3-n3-cy 61.2 120.16 SOURCE3 2 0.0000 0.0000 +c3-n3-f 66.8 103.13 SOURCE3 2 0.0000 0.0000 +c3-n3-hn 47.1 109.92 SOURCE3 120 1.5757 2.2590 +c3-n3-i 57.0 108.48 SOURCE3 2 0.0000 0.0000 +c3-n3-n 67.2 109.97 SOURCE3 2 0.0000 0.0000 +c3-n3-n2 66.2 118.75 SOURCE2 2 2.6500 2.6500 +c3-n3-n3 66.8 108.15 SOURCE3 15 1.0563 1.3999 +c3-n3-n4 67.2 109.65 SOURCE3 3 0.1080 0.1146 +c3-n3-nh 67.4 108.44 SOURCE3 1 0.0000 0.0000 +c3-n3-no 66.0 111.27 SOURCE3 1 0.0000 0.0000 +c3-n3-o 68.7 113.31 SOURCE3 5 8.7272 8.9081 +c3-n3-oh 68.9 106.62 SOURCE3 4 0.1844 0.2167 +c3-n3-os 68.2 105.73 SOURCE3 4 0.3563 0.3760 +c3-n3-p3 75.8 121.93 SOURCE3 3 5.2806 5.6009 +c3-n3-p5 78.7 119.35 SOURCE3 4 0.9279 0.9604 +c3-n3-s 61.5 110.02 SOURCE3 1 0.0000 0.0000 +c3-n3-s4 61.4 112.91 SOURCE3 3 0.8469 0.8983 +c3-n3-s6 63.9 115.81 SOURCE3 3 0.5687 0.6032 +c3-n3-sh 62.1 112.70 SOURCE3 1 0.0000 0.0000 +c3-n3-ss 61.6 116.01 SOURCE3 3 1.1261 1.1944 +cl-n3-cl 53.8 108.28 SOURCE3 1 0.0000 0.0000 +cl-n3-hn 39.9 104.39 SOURCE3 2 0.0000 0.0000 +cl-n3-n3 59.6 107.65 SOURCE3 1 0.0000 0.0000 +cy-n3-cy 70.5 89.57 SOURCE3 2 0.2809 0.2809 +cy-n3-hn 45.7 114.80 SOURCE3 2 0.0000 0.0000 +f -n3-f 67.7 102.22 SOURCE2 4 0.6250 0.7562 +f -n3-hn 50.8 99.80 SOURCE2 1 0.0000 0.0000 +hn-n3-hn 41.3 107.13 SOURCE3 44 1.2683 1.9687 +hn-n3-i 35.4 109.98 SOURCE3 2 0.0000 0.0000 +hn-n3-n 51.0 106.57 SOURCE3 6 1.0152 1.0767 +hn-n3-n2 51.4 115.94 SOURCE0 1 +hn-n3-n3 50.2 103.98 SOURCE3 18 1.2193 1.8593 +hn-n3-n4 50.9 106.40 SOURCE3 5 0.5735 0.5863 +hn-n3-na 50.3 107.89 SOURCE0 1 +hn-n3-nh 50.4 107.39 SOURCE3 11 1.2116 1.6294 +hn-n3-no 50.3 104.78 SOURCE3 3 1.0489 1.1126 +hn-n3-o 53.1 113.32 SOURCE3 3 4.1430 4.3945 +hn-n3-oh 53.1 101.11 SOURCE3 4 0.9921 0.9921 +hn-n3-os 51.7 100.92 SOURCE3 6 0.6490 0.7295 +hn-n3-p2 54.2 120.26 SOURCE0 1 +hn-n3-p3 52.9 116.89 SOURCE3 9 3.4043 3.8816 +hn-n3-p4 55.0 113.05 SOURCE3 2 0.0000 0.0000 +hn-n3-p5 56.0 113.68 SOURCE3 6 1.9887 2.1781 +hn-n3-s 41.5 109.47 SOURCE0 1 +hn-n3-s4 42.5 108.93 SOURCE3 7 1.5575 1.7819 +hn-n3-s6 45.4 112.52 SOURCE3 9 3.3273 3.7049 +hn-n3-sh 43.1 108.67 SOURCE3 3 2.3593 2.5025 +hn-n3-ss 43.4 109.85 SOURCE3 5 1.8572 2.3215 +i -n3-i 60.0 111.27 SOURCE3 1 0.0000 0.0000 +n -n3-n 70.3 110.55 SOURCE3 1 0.0000 0.0000 +n2-n3-n2 71.8 118.73 SOURCE0 1 +n2-n3-o 74.1 114.91 SOURCE0 1 +n3-n3-n3 69.6 105.71 SOURCE3 3 0.3357 0.3561 +n4-n3-n4 69.0 113.48 SOURCE3 1 0.0000 0.0000 +n4-n3-nh 70.9 107.14 SOURCE0 1 +na-n3-na 69.2 112.00 SOURCE0 1 +nh-n3-nh 70.8 107.15 SOURCE3 1 0.0000 0.0000 +no-n3-no 67.0 115.26 SOURCE3 1 0.0000 0.0000 +o -n3-o 71.9 126.14 SOURCE0 1 +o -n3-p2 84.3 117.02 SOURCE0 1 +o -n3-p4 83.4 116.65 SOURCE0 1 +o -n3-s 62.0 119.81 SOURCE0 1 +o -n3-s4 64.6 114.09 SOURCE0 1 +o -n3-s6 68.8 113.80 SOURCE0 1 +oh-n3-oh 72.8 107.18 SOURCE3 1 0.0000 0.0000 +os-n3-os 70.8 106.52 SOURCE3 1 0.0000 0.0000 +p2-n3-p2 97.5 130.13 SOURCE0 1 +p3-n3-p3 98.6 118.74 SOURCE3 3 3.1825 3.3755 +p4-n3-p4 101.5 116.35 SOURCE0 1 +p5-n3-p5 102.2 119.42 SOURCE3 1 0.0000 0.0000 +s -n3-s 56.5 131.36 SOURCE3 1 0.0000 0.0000 +s4-n3-s4 60.1 120.02 SOURCE3 1 0.0000 0.0000 +s4-n3-s6 62.0 120.95 SOURCE0 1 +s6-n3-s6 63.3 126.13 SOURCE3 1 0.0000 0.0000 +sh-n3-sh 61.2 118.63 SOURCE3 1 0.0000 0.0000 +sh-n3-ss 61.3 119.67 SOURCE0 1 +ss-n3-ss 61.6 119.57 SOURCE3 1 0.0000 0.0000 +br-n4-br 65.1 114.82 SOURCE3 1 0.0000 0.0000 +br-n4-hn 41.4 108.44 SOURCE3 7 0.5572 0.5630 +c -n4-c 61.5 108.61 SOURCE3 1 0.0000 0.0000 +c -n4-hn 44.7 110.86 SOURCE3 10 0.9869 1.0073 +c1-n4-c1 65.5 113.87 SOURCE3 1 0.0000 0.0000 +c1-n4-hn 48.6 110.19 SOURCE3 7 1.0735 1.0847 +c2-n4-c2 63.0 112.58 SOURCE3 1 0.0000 0.0000 +c2-n4-h4 11.3 112.46 SOURCE0 1 +c2-n4-hn 46.4 111.36 SOURCE3 13 1.1254 1.2672 +c3-n4-c3 62.8 110.64 SOURCE3 13 1.0808 1.3060 +c3-n4-ca 63.0 112.41 SOURCE3 2 0.0000 0.0000 +c3-n4-cl 57.9 108.04 SOURCE3 3 0.0000 0.0000 +c3-n4-hn 46.2 110.11 SOURCE3 100 1.0473 1.3136 +c3-n4-n3 66.7 108.72 SOURCE3 2 0.0000 0.0000 +c3-n4-n4 63.7 114.07 SOURCE3 4 0.0000 0.0000 +c3-n4-nh 64.8 111.73 SOURCE3 1 0.0000 0.0000 +c3-n4-no 65.2 109.08 SOURCE3 1 0.0000 0.0000 +c3-n4-o 67.3 111.66 SOURCE3 1 0.0000 0.0000 +c3-n4-oh 65.9 113.73 SOURCE3 1 0.0000 0.0000 +c3-n4-os 67.4 107.42 SOURCE3 3 3.3865 3.5920 +c3-n4-p2 71.9 112.52 SOURCE3 1 0.0000 0.0000 +c3-n4-p3 74.4 110.73 SOURCE3 3 1.9878 2.1084 +c3-n4-p5 75.1 113.22 SOURCE3 3 0.3791 0.4021 +c3-n4-s 59.2 113.55 SOURCE3 1 0.0000 0.0000 +c3-n4-s4 57.2 108.23 SOURCE3 3 0.3955 0.4195 +c3-n4-s6 57.7 111.56 SOURCE3 3 1.7773 1.8851 +c3-n4-sh 59.1 115.81 SOURCE3 1 0.0000 0.0000 +c3-n4-ss 59.7 113.68 SOURCE3 3 1.0752 1.1405 +ca-n4-ca 63.2 114.48 SOURCE3 1 0.0000 0.0000 +ca-n4-hn 47.5 108.52 SOURCE3 5 0.9354 1.1693 +cl-n4-cl 52.7 114.91 SOURCE3 1 0.0000 0.0000 +cl-n4-hn 39.5 108.87 SOURCE3 7 0.7640 0.7719 +f -n4-f 70.5 109.05 SOURCE3 1 0.0000 0.0000 +f -n4-hn 51.7 108.39 SOURCE3 4 0.0000 0.0000 +hn-n4-hn 40.5 108.11 SOURCE3 208 1.1062 1.4126 +hn-n4-i 36.4 108.72 SOURCE3 7 1.2587 1.2717 +hn-n4-n 49.6 109.08 SOURCE3 13 1.3969 1.6047 +hn-n4-n2 42.3 109.68 SOURCE3 19 0.4842 0.6266 +hn-n4-n3 49.9 110.40 SOURCE3 11 0.6778 0.7307 +hn-n4-n4 48.1 108.66 SOURCE3 18 1.2886 1.2967 +hn-n4-na 49.4 109.38 SOURCE3 25 0.9072 1.0758 +hn-n4-nh 48.4 109.92 SOURCE3 12 0.5359 0.7304 +hn-n4-no 49.2 104.38 SOURCE3 2 0.0000 0.0000 +hn-n4-o 52.1 109.26 SOURCE3 6 1.9991 2.1203 +hn-n4-oh 51.1 108.09 SOURCE3 6 1.5771 1.6728 +hn-n4-os 50.2 109.39 SOURCE3 10 1.1420 1.4403 +hn-n4-p2 47.7 110.50 SOURCE3 25 1.0144 1.0664 +hn-n4-p3 49.7 109.89 SOURCE3 10 2.2397 2.3870 +hn-n4-p4 47.7 111.33 SOURCE3 3 0.0000 0.0000 +hn-n4-p5 51.3 110.00 SOURCE3 10 0.8162 1.0282 +hn-n4-py 47.4 117.89 SOURCE3 8 0.0000 0.0000 +hn-n4-s 41.1 106.89 SOURCE3 6 1.0159 1.0775 +hn-n4-s4 37.1 110.10 SOURCE3 6 0.7986 0.8471 +hn-n4-s6 38.6 108.94 SOURCE3 10 0.5598 0.5715 +hn-n4-sh 41.3 108.56 SOURCE3 6 0.8047 0.8535 +hn-n4-ss 41.1 109.17 SOURCE3 10 0.6521 0.8455 +i -n4-i 59.0 118.49 SOURCE3 1 0.0000 0.0000 +n -n4-n 66.7 118.62 SOURCE3 1 0.0000 0.0000 +n2-n4-n2 59.4 108.64 SOURCE3 1 0.0000 0.0000 +n3-n4-n3 69.8 111.07 SOURCE3 1 0.0000 0.0000 +n4-n4-n4 65.2 115.49 SOURCE3 1 0.0000 0.0000 +na-n4-na 66.3 119.60 SOURCE3 1 0.0000 0.0000 +nh-n4-nh 67.8 109.38 SOURCE3 1 0.0000 0.0000 +o -n4-o 70.3 120.97 SOURCE3 1 0.0000 0.0000 +oh-n4-oh 72.2 108.19 SOURCE3 1 0.0000 0.0000 +os-n4-os 72.5 104.40 SOURCE3 1 0.0000 0.0000 +p2-n4-p2 89.6 113.91 SOURCE3 2 0.0000 0.0000 +p3-n4-p3 89.7 121.38 SOURCE3 1 0.0000 0.0000 +p5-n4-p5 98.1 107.02 SOURCE3 1 0.0000 0.0000 +py-n4-py 116.9 69.79 SOURCE3 2 0.0000 0.0000 +s -n4-s 56.7 124.55 SOURCE3 1 0.0000 0.0000 +s4-n4-s4 54.8 115.43 SOURCE0 1 +s6-n4-s6 57.9 109.51 SOURCE3 1 0.0000 0.0000 +sh-n4-sh 60.4 112.59 SOURCE3 1 0.0000 0.0000 +ss-n4-ss 61.3 109.20 SOURCE3 1 0.0000 0.0000 +br-na-br 60.6 123.00 SOURCE0 1 +br-na-c2 63.6 100.48 SOURCE3 2 1.0536 1.0536 +br-na-ca 57.1 124.81 SOURCE0 1 +br-na-cc 57.2 124.62 SOURCE3 3 0.5042 0.5348 +br-na-cd 57.2 124.62 SOURCE3 3 same as br-na-cc +br-na-nc 59.9 119.42 SOURCE3 4 1.3872 1.6703 +br-na-nd 59.9 119.42 SOURCE3 4 same as br-na-nc +br-na-os 63.9 104.99 SOURCE3 1 0.0000 0.0000 +br-na-p2 75.9 121.01 SOURCE0 1 +br-na-pc 76.4 120.26 SOURCE3 3 2.0229 2.1456 +br-na-pd 76.4 120.26 SOURCE3 3 same as br-na-pc +br-na-ss 62.5 112.28 SOURCE3 1 0.0000 0.0000 +c -na-c 64.7 126.40 SOURCE0 1 +c -na-c2 64.3 125.09 SOURCE0 1 +c -na-c3 64.7 117.60 SOURCE0 1 +c -na-ca 65.3 125.20 SOURCE0 1 +c -na-hn 48.8 118.00 SOURCE0 1 +c -na-n 66.3 124.66 SOURCE0 1 +c1-na-c1 67.2 117.20 SOURCE0 1 +c1-na-c2 64.3 125.20 SOURCE0 1 +c1-na-ca 66.5 120.57 SOURCE0 1 +c1-na-cc 65.8 121.35 SOURCE3 6 0.6144 0.6517 +c1-na-cd 65.8 121.35 SOURCE3 6 0.6144 0.6517 +c1-na-nc 68.3 120.24 SOURCE3 4 1.3854 1.6849 +c1-na-nd 68.3 120.24 SOURCE3 4 same as c1-na-nc +c1-na-os 70.2 106.96 SOURCE3 2 0.0000 0.0000 +c1-na-p2 76.5 122.25 SOURCE0 1 +c1-na-pc 77.3 121.48 SOURCE3 3 2.0441 2.1681 +c1-na-pd 77.3 121.48 SOURCE3 3 same as c1-na-pc +c1-na-ss 61.9 118.30 SOURCE3 1 0.0000 0.0000 +c2-na-c2 67.8 110.37 SOURCE3 6 0.4285 0.5121 +c2-na-c3 64.2 117.20 SOURCE3 2 0.0000 0.0000 +c2-na-ca 66.2 119.26 SOURCE3 2 5.6375 5.6375 +c2-na-cc 64.0 125.75 SOURCE3 10 1.1039 1.5856 +c2-na-cd 64.0 125.75 SOURCE3 10 1.1039 1.5856 +c2-na-cl 58.8 101.01 SOURCE3 2 1.5799 1.5799 +c2-na-f 68.6 103.11 SOURCE3 1 0.0000 0.0000 +c2-na-hn 47.6 119.28 SOURCE3 14 6.5120 6.6027 +c2-na-i 59.0 106.74 SOURCE3 1 0.0000 0.0000 +c2-na-n 65.6 124.70 SOURCE0 1 +c2-na-n2 65.0 125.00 SOURCE0 1 +c2-na-n3 64.6 124.80 SOURCE0 1 +c2-na-n4 65.2 121.32 SOURCE0 1 +c2-na-na 65.1 124.60 SOURCE0 1 +c2-na-nc 67.6 119.95 SOURCE3 4 1.8044 1.8457 +c2-na-nd 67.6 119.95 SOURCE3 4 same as c2-na-nc +c2-na-nh 65.0 124.98 SOURCE0 1 +c2-na-no 64.3 124.20 SOURCE0 1 +c2-na-o 68.2 125.90 SOURCE0 1 +c2-na-oh 65.8 123.90 SOURCE0 1 +c2-na-os 68.5 110.33 SOURCE3 4 2.7760 3.2172 +c2-na-p2 76.2 122.14 SOURCE0 1 +c2-na-p3 74.6 126.10 SOURCE0 1 +c2-na-p4 81.6 125.00 SOURCE0 1 +c2-na-p5 76.4 125.10 SOURCE0 1 +c2-na-pc 77.0 121.56 SOURCE3 3 1.5323 1.6252 +c2-na-pd 77.0 121.56 SOURCE3 3 same as c2-na-pc +c2-na-s 58.9 125.80 SOURCE0 1 +c2-na-s4 58.4 124.90 SOURCE0 1 +c2-na-s6 60.2 124.40 SOURCE0 1 +c2-na-sh 60.2 125.10 SOURCE0 1 +c2-na-ss 62.3 115.53 SOURCE3 5 1.1554 1.4036 +c3-na-c3 60.7 125.59 SOURCE3 1 0.0000 0.0000 +c3-na-ca 63.1 124.36 SOURCE3 5 4.0243 4.2557 +c3-na-cc 62.6 125.09 SOURCE3 18 1.1830 1.2138 +c3-na-cd 62.6 125.09 SOURCE3 18 1.1830 1.2138 +c3-na-n2 68.7 106.67 SOURCE3 2 0.0000 0.0000 +c3-na-nc 65.7 120.46 SOURCE3 8 1.7737 2.1625 +c3-na-nd 65.7 120.46 SOURCE3 8 1.7737 2.1625 +c3-na-os 68.9 104.39 SOURCE3 3 1.1329 1.2017 +c3-na-p2 75.0 123.12 SOURCE0 1 +c3-na-pc 75.9 122.11 SOURCE3 3 2.6874 2.8504 +c3-na-pd 75.9 122.11 SOURCE3 3 same as c3-na-pc +c3-na-sh 63.4 110.28 SOURCE0 1 +c3-na-ss 62.9 110.87 SOURCE3 3 0.7788 0.8260 +ca-na-ca 67.1 119.80 SOURCE2 1 0.0000 0.0000 +ca-na-cc 68.5 113.15 SOURCE3 18 9.7983 9.8644 +ca-na-cd 68.5 113.15 SOURCE3 18 9.7983 9.8644 +ca-na-cl 53.2 124.79 SOURCE0 1 +ca-na-f 65.5 116.40 SOURCE0 1 +ca-na-hn 48.2 122.77 SOURCE3 13 5.8799 7.1074 +ca-na-i 55.2 121.62 SOURCE0 1 +ca-na-n 67.3 122.00 SOURCE0 1 +ca-na-n2 66.9 121.23 SOURCE0 1 +ca-na-n4 66.4 120.19 SOURCE0 1 +ca-na-na 66.3 123.76 SOURCE0 1 +ca-na-nc 69.3 117.85 SOURCE3 6 3.3298 3.6536 +ca-na-nd 69.3 117.85 SOURCE3 6 same as ca-na-nc +ca-na-nh 67.7 118.59 SOURCE0 1 +ca-na-o 70.9 120.68 SOURCE3 4 0.1702 0.1702 +ca-na-oh 66.7 124.08 SOURCE0 1 +ca-na-os 69.7 109.46 SOURCE3 1 0.0000 0.0000 +ca-na-p2 75.5 125.85 SOURCE0 1 +ca-na-p3 75.5 124.38 SOURCE0 1 +ca-na-p4 82.4 124.97 SOURCE0 1 +ca-na-p5 77.5 123.30 SOURCE0 1 +ca-na-pc 77.3 122.13 SOURCE3 3 2.1112 2.2393 +ca-na-pd 77.3 122.13 SOURCE3 3 same as ca-na-pc +ca-na-py 72.6 140.88 SOURCE3 2 0.0000 0.0000 +ca-na-s 59.3 125.64 SOURCE0 1 +ca-na-s4 60.6 117.23 SOURCE0 1 +ca-na-s6 61.6 120.69 SOURCE0 1 +ca-na-sh 60.5 125.44 SOURCE0 1 +ca-na-ss 62.4 116.60 SOURCE0 1 +cc-na-cc 68.9 109.90 SOURCE3 109 1.2152 1.5547 +cd-na-cd 68.9 109.90 SOURCE3 109 1.2152 1.5547 +cc-na-cd 63.9 128.01 SOURCE3 1 0.0000 0.0000 +cc-na-cl 53.1 124.61 SOURCE3 3 0.4910 0.5208 +cd-na-cl 53.1 124.61 SOURCE3 3 same as cc-na-cl +cc-na-f 64.6 118.03 SOURCE3 4 0.2905 0.3081 +cd-na-f 64.6 118.03 SOURCE3 4 0.2905 0.3081 +cc-na-hn 47.2 124.66 SOURCE3 38 4.3279 5.9689 +cd-na-hn 47.2 124.66 SOURCE3 38 4.3279 5.9689 +cc-na-i 54.3 125.70 SOURCE3 6 0.6256 0.7821 +cd-na-i 54.3 125.70 SOURCE3 6 0.6256 0.7821 +cc-na-n 66.5 123.19 SOURCE3 13 0.1564 0.3010 +cd-na-n 66.5 123.19 SOURCE3 13 0.1564 0.3010 +cc-na-n2 66.0 122.96 SOURCE3 15 0.5269 0.9350 +cd-na-n2 66.0 122.96 SOURCE3 15 0.5269 0.9350 +cc-na-n4 65.9 120.31 SOURCE3 10 3.0227 3.4394 +cd-na-n4 65.9 120.31 SOURCE3 10 3.0227 3.4394 +cc-na-na 65.9 123.43 SOURCE3 23 0.1445 0.2088 +cd-na-na 65.9 123.43 SOURCE3 23 0.1445 0.2088 +cc-na-nc 70.2 113.02 SOURCE3 38 1.6684 2.2867 +cd-na-nd 70.2 113.02 SOURCE3 38 1.6684 2.2867 +cc-na-nh 66.2 122.25 SOURCE3 19 0.1526 0.2010 +cd-na-nh 66.2 122.25 SOURCE3 19 0.1526 0.2010 +cc-na-no 65.4 121.78 SOURCE3 9 0.2814 0.3521 +cd-na-no 65.4 121.78 SOURCE3 9 0.2814 0.3521 +cc-na-o 69.0 125.21 SOURCE3 10 0.0087 0.0124 +cd-na-o 69.0 125.21 SOURCE3 10 0.0087 0.0124 +cc-na-oh 66.7 122.38 SOURCE3 10 0.1099 0.1570 +cd-na-oh 66.7 122.38 SOURCE3 10 0.1099 0.1570 +cc-na-os 67.3 115.74 SOURCE3 41 4.3528 5.4093 +cd-na-os 67.3 115.74 SOURCE3 41 4.3528 5.4093 +cc-na-p2 75.3 125.86 SOURCE3 14 1.2242 2.2993 +cd-na-p2 75.3 125.86 SOURCE3 14 1.2242 2.2993 +cc-na-p3 75.0 125.25 SOURCE3 8 0.1571 0.1998 +cd-na-p3 75.0 125.25 SOURCE3 8 0.1571 0.1998 +cc-na-p4 81.1 127.73 SOURCE3 7 3.1941 3.6077 +cd-na-p4 81.1 127.73 SOURCE3 7 same as cc-na-p4 +cc-na-p5 76.8 124.70 SOURCE3 13 0.8852 1.4225 +cd-na-p5 76.8 124.70 SOURCE3 13 0.8852 1.4225 +cc-na-s 59.1 125.66 SOURCE3 8 0.1504 0.1880 +cd-na-s 59.1 125.66 SOURCE3 8 0.1504 0.1880 +cc-na-s4 59.4 121.03 SOURCE3 10 0.4358 0.5589 +cd-na-s4 59.4 121.03 SOURCE3 10 0.4358 0.5589 +cc-na-s6 61.0 122.19 SOURCE3 10 0.7706 0.9634 +cd-na-s6 61.0 122.19 SOURCE3 10 0.7706 0.9634 +cc-na-sh 60.7 123.96 SOURCE3 10 0.2394 0.3424 +cd-na-sh 60.7 123.96 SOURCE3 10 0.2394 0.3424 +cc-na-ss 61.6 119.18 SOURCE3 36 4.3591 5.0538 +cd-na-ss 61.6 119.18 SOURCE3 36 4.3591 5.0538 +cl-na-cl 48.7 122.80 SOURCE0 1 +cl-na-nc 55.7 119.36 SOURCE3 4 1.4294 1.7128 +cl-na-nd 55.7 119.36 SOURCE3 4 same as cl-na-nc +cl-na-os 58.6 106.58 SOURCE3 1 0.0000 0.0000 +cl-na-p2 68.7 121.29 SOURCE0 1 +cl-na-pc 69.2 120.51 SOURCE3 3 2.0728 2.1985 +cl-na-pd 69.2 120.51 SOURCE3 3 same as cl-na-pc +cl-na-ss 56.7 111.91 SOURCE3 1 0.0000 0.0000 +f -na-f 62.2 120.20 SOURCE0 1 +f -na-nc 66.6 118.05 SOURCE3 4 1.5336 1.7931 +f -na-nd 66.6 118.05 SOURCE3 4 same as f -na-nc +f -na-os 69.2 103.86 SOURCE3 1 0.0000 0.0000 +f -na-p2 75.5 119.95 SOURCE0 1 +f -na-pc 76.4 119.10 SOURCE3 3 2.2596 2.3967 +f -na-pd 76.4 119.10 SOURCE3 3 same as f -na-pc +f -na-ss 63.3 108.01 SOURCE3 1 0.0000 0.0000 +hn-na-hn 39.8 116.80 SOURCE0 1 +hn-na-nc 50.0 119.61 SOURCE3 16 1.4674 1.8079 +hn-na-nd 50.0 119.61 SOURCE3 16 1.4674 1.8079 +hn-na-os 51.4 101.41 SOURCE3 7 2.1205 3.0814 +hn-na-p2 51.0 122.52 SOURCE0 1 +hn-na-pc 51.8 121.48 SOURCE3 3 2.7676 2.9355 +hn-na-pd 51.8 121.48 SOURCE3 3 same as hn-na-pc +hn-na-ss 42.2 113.95 SOURCE3 1 0.0000 0.0000 +i -na-i 58.3 124.20 SOURCE0 1 +i -na-nc 56.9 120.03 SOURCE3 4 1.6724 2.0032 +i -na-nd 56.9 120.03 SOURCE3 4 same as i -na-nc +i -na-os 59.9 109.91 SOURCE3 1 0.0000 0.0000 +i -na-p2 73.4 122.28 SOURCE0 1 +i -na-pc 73.8 121.40 SOURCE3 3 2.3347 2.4763 +i -na-pd 73.8 121.40 SOURCE3 3 same as i -na-pc +i -na-ss 59.0 118.40 SOURCE3 1 0.0000 0.0000 +n -na-n 67.8 123.80 SOURCE0 1 +n -na-nc 69.6 119.85 SOURCE3 4 1.3529 1.6156 +n -na-nd 69.6 119.85 SOURCE3 4 same as n -na-nc +n -na-os 72.3 104.71 SOURCE3 1 0.0000 0.0000 +n -na-p2 78.5 121.35 SOURCE0 1 +n -na-pc 79.3 120.64 SOURCE3 3 1.9015 2.0168 +n -na-pd 79.3 120.64 SOURCE3 3 same as n -na-pc +n -na-ss 63.8 116.10 SOURCE3 1 0.0000 0.0000 +n2-na-n2 68.6 116.71 SOURCE0 1 +n2-na-nc 68.9 119.96 SOURCE3 4 3.7508 4.5041 +n2-na-nd 68.9 119.96 SOURCE3 4 same as n2-na-nc +n2-na-os 69.6 111.53 SOURCE3 1 0.0000 0.0000 +n2-na-p2 77.1 124.88 SOURCE0 1 +n2-na-pc 78.2 123.18 SOURCE3 3 4.5205 4.7947 +n2-na-pd 78.2 123.18 SOURCE3 3 same as n2-na-pc +n2-na-ss 61.4 124.64 SOURCE3 1 0.0000 0.0000 +n3-na-n3 65.8 124.00 SOURCE0 1 +n4-na-n4 68.6 111.70 SOURCE0 1 +n4-na-nc 69.1 116.44 SOURCE3 4 3.4363 3.6604 +n4-na-nd 69.1 116.44 SOURCE3 4 same as n4-na-nc +n4-na-os 71.6 102.97 SOURCE3 1 0.0000 0.0000 +n4-na-p2 77.0 123.56 SOURCE0 1 +n4-na-pc 78.1 121.98 SOURCE3 3 4.2317 4.4884 +n4-na-pd 78.1 121.98 SOURCE3 3 same as n4-na-pc +na-na-na 66.8 123.60 SOURCE0 1 +na-na-nc 69.1 119.64 SOURCE3 4 1.4391 1.6920 +na-na-nd 69.1 119.64 SOURCE3 4 same as na-na-nc +na-na-os 70.2 109.47 SOURCE3 1 0.0000 0.0000 +na-na-p2 78.1 121.72 SOURCE0 1 +na-na-pc 78.9 120.91 SOURCE3 3 2.1716 2.3033 +na-na-pd 78.9 120.91 SOURCE3 3 same as na-na-pc +na-na-ss 63.5 116.50 SOURCE3 1 0.0000 0.0000 +nc-na-nc 71.2 117.08 SOURCE3 31 1.3370 1.8121 +nd-na-nd 71.2 117.08 SOURCE3 31 1.3370 1.8121 +nc-na-nh 68.8 120.55 SOURCE3 8 0.9372 1.1436 +nd-na-nh 68.8 120.55 SOURCE3 8 same as nc-na-nh +nc-na-no 68.2 119.15 SOURCE3 4 1.3563 1.6049 +nd-na-no 68.2 119.15 SOURCE3 4 same as nc-na-no +nc-na-o 72.0 122.79 SOURCE3 6 0.9658 1.3154 +nd-na-o 72.0 122.79 SOURCE3 6 same as nc-na-o +nc-na-oh 69.7 119.22 SOURCE3 4 1.4515 1.7201 +nd-na-oh 69.7 119.22 SOURCE3 4 same as nc-na-oh +nc-na-os 68.3 119.65 SOURCE3 4 1.2975 1.5019 +nd-na-os 68.3 119.65 SOURCE3 4 same as nc-na-os +nc-na-p2 79.2 119.99 SOURCE3 4 3.1175 3.6009 +nd-na-p2 79.2 119.99 SOURCE3 4 same as nc-na-p2 +nc-na-p3 78.7 120.07 SOURCE3 4 3.2166 3.7188 +nd-na-p3 78.7 120.07 SOURCE3 4 same as nc-na-p3 +nc-na-p4 86.2 119.77 SOURCE3 3 0.3532 0.3747 +nd-na-p4 86.2 119.77 SOURCE3 3 same as nc-na-p4 +nc-na-p5 80.8 118.95 SOURCE3 4 2.8603 3.1194 +nd-na-p5 80.8 118.95 SOURCE3 4 same as nc-na-p5 +nc-na-pc 80.3 118.66 SOURCE3 27 1.2284 1.5082 +nd-na-pd 80.3 118.66 SOURCE3 27 same as nc-na-pc +nc-na-s 61.6 122.26 SOURCE3 4 0.7754 0.9173 +nd-na-s 61.6 122.26 SOURCE3 4 same as nc-na-s +nc-na-s4 61.5 119.20 SOURCE3 4 1.9615 2.3841 +nd-na-s4 61.5 119.20 SOURCE3 4 same as nc-na-s4 +nc-na-s6 63.4 119.24 SOURCE3 4 1.8561 2.2262 +nd-na-s6 63.4 119.24 SOURCE3 4 same as nc-na-s6 +nc-na-sh 63.3 120.50 SOURCE3 4 1.2479 1.5016 +nd-na-sh 63.3 120.50 SOURCE3 4 same as nc-na-sh +nc-na-ss 62.9 120.50 SOURCE3 4 1.2895 1.5615 +nd-na-ss 62.9 120.50 SOURCE3 4 same as nc-na-ss +nh-na-nh 66.8 123.60 SOURCE0 1 +nh-na-os 69.6 111.37 SOURCE3 1 0.0000 0.0000 +nh-na-p2 78.3 120.86 SOURCE0 1 +nh-na-pc 79.1 120.38 SOURCE3 6 1.2708 1.3513 +nh-na-pd 79.1 120.38 SOURCE3 6 same as nh-na-pc +nh-na-ss 64.7 112.35 SOURCE3 2 5.2951 5.2951 +no-na-no 65.2 122.80 SOURCE0 1 +no-na-os 70.3 106.55 SOURCE3 1 0.0000 0.0000 +no-na-pc 78.6 120.11 SOURCE3 3 1.9631 2.0821 +no-na-pd 78.6 120.11 SOURCE3 3 same as no-na-pc +no-na-ss 63.5 114.95 SOURCE3 1 0.0000 0.0000 +o -na-o 74.0 126.20 SOURCE0 1 +o -na-os 70.8 118.39 SOURCE3 1 0.0000 0.0000 +o -na-p2 79.5 122.80 SOURCE0 1 +o -na-pc 80.4 122.34 SOURCE3 3 1.2169 1.2908 +o -na-pd 80.4 122.34 SOURCE3 3 same as o -na-pc +oh-na-oh 68.1 122.20 SOURCE0 1 +oh-na-p2 78.9 120.76 SOURCE0 1 +oh-na-pc 79.7 119.99 SOURCE3 3 2.0491 2.1734 +oh-na-pd 79.7 119.99 SOURCE3 3 same as oh-na-pc +oh-na-ss 64.9 113.04 SOURCE3 1 0.0000 0.0000 +os-na-os 71.3 104.45 SOURCE3 2 0.0983 0.0983 +os-na-p2 79.2 117.86 SOURCE3 1 0.0000 0.0000 +os-na-p3 83.6 104.70 SOURCE3 1 0.0000 0.0000 +os-na-p5 82.6 111.41 SOURCE3 1 0.0000 0.0000 +os-na-pc 79.1 119.91 SOURCE3 3 1.7915 1.9002 +os-na-pd 79.1 119.91 SOURCE3 3 same as os-na-pc +os-na-s4 64.8 105.88 SOURCE3 2 0.0000 0.0000 +os-na-s6 64.8 112.00 SOURCE3 2 0.0000 0.0000 +os-na-ss 65.3 109.64 SOURCE3 3 3.9028 4.1395 +p2-na-p2 96.6 120.91 SOURCE0 1 +p2-na-p3 94.7 124.80 SOURCE0 1 +p2-na-p5 96.3 123.99 SOURCE0 1 +p2-na-pc 97.2 120.72 SOURCE3 3 0.2270 0.2407 +p2-na-pd 97.2 120.72 SOURCE3 3 same as p2-na-pc +p2-na-s 75.7 121.85 SOURCE0 1 +p2-na-s4 74.9 122.47 SOURCE0 1 +p2-na-s6 76.3 122.50 SOURCE0 1 +p2-na-sh 76.7 121.75 SOURCE0 1 +p2-na-ss 76.4 121.88 SOURCE0 1 +p3-na-p3 93.7 126.60 SOURCE0 1 +p3-na-pc 95.8 123.32 SOURCE3 3 3.9391 4.1781 +p3-na-pd 95.8 123.32 SOURCE3 3 same as p3-na-pc +p5-na-p5 97.1 124.60 SOURCE0 1 +p5-na-pc 97.3 122.69 SOURCE3 3 3.4637 3.6738 +p5-na-pd 97.3 122.69 SOURCE3 3 same as p5-na-pc +p5-na-ss 78.2 118.52 SOURCE3 1 0.0000 0.0000 +pc-na-pc 97.6 120.78 SOURCE3 27 1.2682 1.6457 +pd-na-pd 97.6 120.78 SOURCE3 27 same as pc-na-pc +pc-na-s 76.2 121.47 SOURCE3 3 1.0058 1.0668 +pd-na-s 76.2 121.47 SOURCE3 3 same as pc-na-s +pc-na-s4 75.5 121.51 SOURCE3 3 2.5684 2.7242 +pd-na-s4 75.5 121.51 SOURCE3 3 same as pc-na-s4 +pc-na-s6 77.0 121.55 SOURCE3 3 2.5517 2.7065 +pd-na-s6 77.0 121.55 SOURCE3 3 same as pc-na-s6 +pc-na-sh 77.3 121.08 SOURCE3 3 1.7859 1.8942 +pd-na-sh 77.3 121.08 SOURCE3 3 same as pc-na-sh +pc-na-ss 77.0 121.20 SOURCE3 3 1.8191 1.9295 +pd-na-ss 77.0 121.20 SOURCE3 3 same as pc-na-ss +py-na-py 122.7 78.25 SOURCE3 1 0.0000 0.0000 +s -na-s 58.5 126.00 SOURCE0 1 +s -na-ss 62.5 112.49 SOURCE3 1 0.0000 0.0000 +s4-na-s4 58.1 124.20 SOURCE0 1 +s4-na-s6 62.0 112.86 SOURCE0 1 +s4-na-ss 62.2 111.92 SOURCE3 1 0.0000 0.0000 +s6-na-s6 60.5 123.20 SOURCE0 1 +s6-na-ss 61.4 119.10 SOURCE3 1 0.0000 0.0000 +sh-na-sh 60.4 124.60 SOURCE0 1 +sh-na-ss 61.6 118.79 SOURCE3 1 0.0000 0.0000 +ss-na-ss 62.9 113.24 SOURCE3 2 6.6084 6.6084 +sy-na-sy 60.5 123.20 SOURCE0 1 +ca-nb-ca 68.6 115.86 SOURCE3 46 0.9817 1.1645 +ca-nb-cp 68.0 117.04 SOURCE3 2 0.0000 0.0000 +ca-nb-cq 68.0 117.04 SOURCE3 2 0.0000 0.0000 +ca-nb-nb 69.4 118.89 SOURCE3 10 0.4394 0.6031 +nb-nb-nb 70.4 121.04 SOURCE3 1 0.0000 0.0000 +c -nc-ca 66.6 120.66 SOURCE0 1 +c -nd-ca 66.6 120.66 SOURCE0 1 same as c -nc-ca +c -nc-cd 67.0 119.25 SOURCE3 2 1.4095 1.4095 +c -nd-cc 67.0 119.25 SOURCE3 2 same as c -nc-cd +c3-nc-cd 67.6 109.51 SOURCE3 9 5.0602 5.4142 +c3-nd-cc 67.6 109.51 SOURCE3 9 same as c3-nc-cd +ca-nc-ca 70.7 109.95 SOURCE0 1 +ca-nd-ca 70.7 109.95 SOURCE0 1 same as ca-nc-ca +ca-nc-cc 71.1 108.82 SOURCE3 11 4.2211 5.0835 +ca-nd-cc 71.1 108.82 SOURCE3 11 4.2211 5.0835 added by eajfpeter +ca-nc-cd 71.1 108.82 SOURCE3 11 4.2211 5.0835 +ca-nd-cd 71.1 108.82 SOURCE3 11 4.2211 5.0835 added by eajfpeter +ca-nc-n 73.8 104.69 SOURCE0 1 +ca-nd-n 73.8 104.69 SOURCE0 1 same as ca-nc-n +ca-nc-na 74.1 104.16 SOURCE0 1 +ca-nd-na 74.1 104.16 SOURCE0 1 same as ca-nc-na +ca-nc-os 73.1 104.34 SOURCE3 1 0.0000 0.0000 +ca-nd-os 73.1 104.34 SOURCE3 1 same as ca-nc-os +ca-nc-ss 67.8 116.29 SOURCE0 1 +ca-nd-ss 67.8 116.29 SOURCE0 1 same as ca-nc-ss +cc-nc-cc 68.6 110.19 SOURCE3 1 0.0000 0.0000 +cd-nd-cd 68.6 110.19 SOURCE3 1 same as cc-nc-cc +cc-nc-cd 70.5 107.47 SOURCE3 26 4.9214 5.4053 +cc-nd-cd 70.5 107.47 SOURCE3 26 4.9214 5.4053 +cc-nc-na 73.4 102.97 SOURCE3 1 0.0000 0.0000 +cd-nd-na 73.4 102.97 SOURCE3 1 same as cc-nc-na +cc-nc-nd 72.5 107.94 SOURCE3 6 1.2473 1.4052 +cd-nd-nc 72.5 107.94 SOURCE3 6 1.2473 1.4052 +cd-nc-n 74.0 104.15 SOURCE3 4 1.8118 2.1512 +cc-nd-n 74.0 104.15 SOURCE3 4 same as cd-nc-n +cd-nc-na 74.2 103.73 SOURCE3 122 1.9430 2.3292 +cc-nd-na 74.2 103.73 SOURCE3 122 1.9430 2.3292 +cd-nc-nc 71.4 109.51 SOURCE3 15 3.8384 5.1636 +cc-nd-nd 71.4 109.51 SOURCE3 15 3.8384 5.1636 +cd-nc-os 72.2 106.99 SOURCE3 10 4.4186 4.6698 +cc-nd-os 72.2 106.99 SOURCE3 10 4.4186 4.6698 +cd-nc-ss 70.3 108.50 SOURCE3 4 0.6893 0.7311 +cc-nd-ss 70.3 108.50 SOURCE3 4 0.6893 0.7311 +na-nc-nd 76.0 105.47 SOURCE3 6 0.4926 0.6349 +na-nd-nc 76.0 105.47 SOURCE3 6 0.4926 0.6349 +nd-nc-os 74.4 107.22 SOURCE3 3 0.4201 0.4707 +nc-nd-os 74.4 107.22 SOURCE3 3 same as nd-nc-os +nc-nd-nd 73.2 111.15 SOURCE3 3 0.4213 0.4528 +nc-nc-nd 73.2 111.15 SOURCE3 3 same as nc-nd-nd +c -ne-c2 67.4 118.53 SOURCE3 3 3.0224 3.2058 +c -nf-c2 67.4 118.53 SOURCE3 3 same as c -ne-c2 +c1-ne-ca 62.9 137.74 SOURCE3 1 0.0000 0.0000 +c1-nf-ca 62.9 137.74 SOURCE3 1 same as c1-ne-ca +c1-ne-cg 64.4 140.00 SOURCE2 1 0.0000 0.0000 +c1-nf-ch 64.4 140.00 SOURCE2 1 same as c1-ne-cg +c2-ne-ca 66.7 118.67 SOURCE3 2 0.7082 0.7082 +c2-nf-ca 66.7 118.67 SOURCE3 2 same as c2-ne-ca +c2-ne-ce 67.3 118.17 SOURCE3 3 1.1667 1.2374 +c2-nf-cf 67.3 118.17 SOURCE3 3 same as c2-ne-ce +c2-ne-n2 74.6 113.31 SOURCE0 1 +c2-nf-n2 74.6 113.31 SOURCE0 1 same as c2-ne-n2 +c2-ne-ne 69.2 110.86 SOURCE3 7 3.2451 4.5874 +c2-nf-nf 69.2 110.86 SOURCE3 7 same as c2-ne-ne +c2-ne-p2 80.8 134.03 SOURCE0 1 +c2-nf-p2 80.8 134.03 SOURCE0 1 same as c2-ne-p2 +c2-ne-pe 79.2 120.52 SOURCE3 8 6.9715 8.1381 +c2-nf-pf 79.2 120.52 SOURCE3 8 same as c2-ne-pe +c2-ne-px 80.6 117.75 SOURCE3 5 0.8192 0.8581 +c2-nf-px 80.6 117.75 SOURCE3 5 same as c2-ne-px +c2-ne-py 80.1 117.04 SOURCE3 3 1.3574 1.4398 +c2-nf-py 80.1 117.04 SOURCE3 3 same as c2-ne-py +c2-ne-sx 61.0 111.98 SOURCE3 3 0.3856 0.4090 +c2-nf-sx 61.0 111.98 SOURCE3 3 same as c2-ne-sx +c2-ne-sy 62.9 114.81 SOURCE3 3 1.2186 1.2925 +c2-nf-sy 62.9 114.81 SOURCE3 3 same as c2-ne-sy +ca-ne-n2 70.0 113.11 SOURCE3 2 0.3839 0.3839 +ca-nf-n2 70.0 113.11 SOURCE3 2 same as ca-ne-n2 +ca-ne-nf 69.9 114.72 SOURCE3 2 0.0000 0.0000 +ca-nf-ne 69.9 114.72 SOURCE3 2 0.0000 0.0000 +ca-ne-o 71.1 113.96 SOURCE3 3 0.9256 1.1253 +ca-nf-o 71.1 113.96 SOURCE3 3 same as ca-ne-o +ca-ne-p2 83.1 118.09 SOURCE3 1 0.0000 0.0000 +ca-nf-p2 83.1 118.09 SOURCE3 1 same as ca-ne-p2 +ca-ne-s 65.8 120.11 SOURCE3 1 0.0000 0.0000 +ca-nf-s 65.8 120.11 SOURCE3 1 same as ca-ne-s +ce-ne-n2 71.2 111.19 SOURCE3 1 0.0000 0.0000 +cf-nf-n2 71.2 111.19 SOURCE3 1 same as ce-ne-n2 +ce-ne-o 72.3 112.16 SOURCE3 1 0.0000 0.0000 +cf-nf-o 72.3 112.16 SOURCE3 1 same as ce-ne-o +ce-ne-p2 83.8 117.02 SOURCE3 1 0.0000 0.0000 +cf-nf-p2 83.8 117.02 SOURCE3 1 same as ce-ne-p2 +ce-ne-s 67.1 116.28 SOURCE3 1 0.0000 0.0000 +cf-nf-s 67.1 116.28 SOURCE3 1 same as ce-ne-s +cg-ne-n1 70.6 120.20 SOURCE2 1 0.0000 0.0000 +ch-nf-n1 70.6 120.20 SOURCE2 1 same as cg-ne-n1 +cg-ne-n2 72.0 113.39 SOURCE3 1 0.0000 0.0000 +ch-nf-n2 72.0 113.39 SOURCE3 1 same as cg-ne-n2 +cg-ne-o 73.2 114.70 SOURCE2 1 0.0000 0.0000 +ch-nf-o 73.2 114.70 SOURCE2 1 same as cg-ne-o +cg-ne-p2 84.0 119.57 SOURCE3 1 0.0000 0.0000 +ch-nf-p2 84.0 119.57 SOURCE3 1 same as cg-ne-p2 +cg-ne-s 67.7 117.70 SOURCE3 1 0.0000 0.0000 +ch-nf-s 67.7 117.70 SOURCE3 1 same as cg-ne-s +n2-ne-n2 78.6 107.22 SOURCE0 1 +n2-nf-n2 78.6 107.22 SOURCE0 1 same as n2-ne-n2 +n2-ne-ne 70.9 110.72 SOURCE3 9 5.6539 6.1488 +n2-nf-nf 70.9 110.72 SOURCE3 9 same as n2-ne-ne +n2-ne-o 78.1 114.10 SOURCE3 1 0.0000 0.0000 +n2-nf-o 78.1 114.10 SOURCE3 1 same as n2-ne-o +n2-ne-p2 91.6 109.66 SOURCE0 1 +n2-nf-p2 91.6 109.66 SOURCE0 1 same as n2-ne-p2 +n2-ne-pe 84.2 112.15 SOURCE3 7 5.8874 6.5273 +n2-nf-pf 84.2 112.15 SOURCE3 7 same as n2-ne-pe +n2-ne-px 83.2 115.97 SOURCE3 3 1.8719 1.9854 +n2-nf-px 83.2 115.97 SOURCE3 3 same as n2-ne-px +n2-ne-py 82.9 114.60 SOURCE3 3 2.7587 2.9261 +n2-nf-py 82.9 114.60 SOURCE3 3 same as n2-ne-py +n2-ne-s 71.3 115.90 SOURCE3 1 0.0000 0.0000 +n2-nf-s 71.3 115.90 SOURCE3 1 same as n2-ne-s +n2-ne-sx 63.8 107.29 SOURCE3 1 0.0000 0.0000 +n2-nf-sx 63.8 107.29 SOURCE3 1 same as n2-ne-sx +n2-ne-sy 65.5 111.21 SOURCE3 1 0.0000 0.0000 +n2-nf-sy 65.5 111.21 SOURCE3 1 same as n2-ne-sy +ne-ne-o 72.3 110.45 SOURCE3 10 1.5341 1.8535 +nf-nf-o 72.3 110.45 SOURCE3 10 same as ne-ne-o +ne-ne-p2 85.3 114.39 SOURCE3 6 3.7554 4.0528 +nf-nf-p2 85.3 114.39 SOURCE3 6 same as ne-ne-p2 +ne-ne-s 67.6 115.95 SOURCE3 6 3.1034 3.4604 +nf-nf-s 67.6 115.95 SOURCE3 6 same as ne-ne-s +o -ne-o 76.9 124.09 SOURCE3 2 8.7534 8.7534 +o -nf-o 76.9 124.09 SOURCE3 2 same as o -ne-o +o -ne-pe 78.3 132.32 SOURCE3 11 22.7306 23.9559 +o -nf-pf 78.3 132.32 SOURCE3 11 same as o -ne-pe +o -ne-px 86.1 110.62 SOURCE3 1 0.0000 0.0000 +o -nf-px 86.1 110.62 SOURCE3 1 same as o -ne-px +o -ne-py 85.2 110.79 SOURCE3 4 1.6818 1.6818 +o -nf-py 85.2 110.79 SOURCE3 4 same as o -ne-py +o -ne-s 72.0 117.19 SOURCE3 2 0.0225 0.0225 +o -nf-s 72.0 117.19 SOURCE3 2 same as o -ne-s +o -ne-sx 63.8 108.92 SOURCE3 1 0.0000 0.0000 +o -nf-sx 63.8 108.92 SOURCE3 1 same as o -ne-sx +o -ne-sy 66.1 111.34 SOURCE3 1 0.0000 0.0000 +o -nf-sy 66.1 111.34 SOURCE3 1 same as o -ne-sy +p2-ne-pe 104.6 116.81 SOURCE3 1 0.0000 0.0000 +p2-nf-pf 104.6 116.81 SOURCE3 1 same as p2-ne-pe +p2-ne-px 100.1 128.35 SOURCE3 1 0.0000 0.0000 +p2-nf-px 100.1 128.35 SOURCE3 1 same as p2-ne-px +p2-ne-py 101.4 123.47 SOURCE3 1 0.0000 0.0000 +p2-nf-py 101.4 123.47 SOURCE3 1 same as p2-ne-py +p2-ne-sx 80.5 112.12 SOURCE3 1 0.0000 0.0000 +p2-nf-sx 80.5 112.12 SOURCE3 1 same as p2-ne-sx +p2-ne-sy 81.8 115.73 SOURCE3 1 0.0000 0.0000 +p2-nf-sy 81.8 115.73 SOURCE3 1 same as p2-ne-sy +pe-ne-s 83.5 115.73 SOURCE3 1 0.0000 0.0000 +pf-nf-s 83.5 115.73 SOURCE3 1 same as pe-ne-s +px-ne-s 78.5 131.84 SOURCE3 1 0.0000 0.0000 +px-nf-s 78.5 131.84 SOURCE3 1 same as px-ne-s +py-ne-s 83.1 116.18 SOURCE3 4 3.7135 3.7135 +py-nf-s 83.1 116.18 SOURCE3 4 same as py-ne-s +s -ne-s 68.6 120.87 SOURCE3 1 0.0000 0.0000 +s -nf-s 68.6 120.87 SOURCE3 1 same as s -ne-s +s -ne-sx 63.7 112.96 SOURCE3 1 0.0000 0.0000 +s -nf-sx 63.7 112.96 SOURCE3 1 same as s -ne-sx +s -ne-sy 63.9 119.63 SOURCE3 1 0.0000 0.0000 +s -nf-sy 63.9 119.63 SOURCE3 1 same as s -ne-sy +br-nh-br 67.1 106.27 SOURCE0 1 +br-nh-ca 62.0 111.88 SOURCE3 1 0.0000 0.0000 +br-nh-hn 42.1 101.56 SOURCE3 1 0.0000 0.0000 +c -nh-c 67.0 119.57 SOURCE0 1 +c -nh-ca 65.6 123.57 SOURCE0 1 +c -nh-hn 49.5 115.73 SOURCE0 1 +c -nh-n4 68.0 111.35 SOURCE0 1 +c1-nh-c1 67.7 116.98 SOURCE3 1 0.0000 0.0000 +c1-nh-ca 65.9 122.36 SOURCE3 3 1.1328 1.2016 +c1-nh-hn 49.0 118.07 SOURCE3 1 0.0000 0.0000 +c2-nh-c2 65.5 124.69 SOURCE3 1 0.0000 0.0000 +c2-nh-c3 63.2 123.71 SOURCE3 8 2.9758 3.5348 +c2-nh-ca 65.5 123.66 SOURCE3 3 0.9054 0.9603 +c2-nh-hn 49.0 117.94 SOURCE3 63 3.2395 3.5550 +c3-nh-c3 63.5 114.54 SOURCE3 4 4.3647 5.3186 +c3-nh-ca 64.6 117.77 SOURCE3 8 1.6597 1.7521 +c3-nh-cc 63.7 121.18 SOURCE3 1 0.0000 0.0000 +c3-nh-cd 63.7 121.18 SOURCE3 1 same as c3-nh-cc +c3-nh-hn 46.5 114.95 SOURCE3 19 1.8868 2.4787 +c3-nh-n2 67.9 112.35 SOURCE3 9 3.0433 4.0058 +c3-nh-p2 77.1 123.35 SOURCE3 1 0.0000 0.0000 +ca-nh-ca 64.3 127.46 SOURCE3 2 0.0002 0.0002 +ca-nh-cl 57.7 113.15 SOURCE3 1 0.0000 0.0000 +ca-nh-f 67.9 106.09 SOURCE3 3 1.0050 1.0660 +ca-nh-hn 49.6 113.79 SOURCE3 94 2.6056 3.1958 +ca-nh-i 55.5 117.83 SOURCE3 1 0.0000 0.0000 +ca-nh-n 68.8 112.95 SOURCE3 4 0.9096 1.0790 +ca-nh-n2 68.1 120.05 SOURCE3 8 2.5677 2.6934 +ca-nh-n3 68.2 114.21 SOURCE3 6 1.6106 2.2412 +ca-nh-n4 68.6 108.94 SOURCE3 5 0.6400 0.6562 +ca-nh-na 68.6 114.54 SOURCE3 8 0.6124 0.7807 +ca-nh-nh 68.5 114.87 SOURCE3 6 2.0206 2.1432 +ca-nh-no 67.3 113.92 SOURCE3 4 2.5876 2.9561 +ca-nh-o 69.6 121.92 SOURCE3 2 3.9630 3.9630 +ca-nh-oh 68.5 112.80 SOURCE3 1 0.0000 0.0000 +ca-nh-os 69.3 110.17 SOURCE3 3 0.6080 0.6448 +ca-nh-p2 78.0 125.27 SOURCE3 8 3.8796 5.1798 +ca-nh-p3 76.1 125.70 SOURCE3 3 5.4491 5.7796 +ca-nh-p4 77.4 124.01 SOURCE3 3 2.4334 2.5810 +ca-nh-p5 78.2 125.61 SOURCE3 3 0.4984 0.5287 +ca-nh-s 59.4 122.54 SOURCE3 3 2.5457 2.7001 +ca-nh-s4 62.1 115.62 SOURCE3 3 0.3238 0.3434 +ca-nh-s6 63.7 115.88 SOURCE3 3 0.6984 0.7407 +ca-nh-sh 61.8 121.41 SOURCE3 1 0.0000 0.0000 +ca-nh-ss 61.8 121.50 SOURCE3 3 2.4754 2.6255 +ca-nh-sy 64.0 117.74 SOURCE3 1 0.0000 0.0000 +cc-nh-hn 48.9 117.16 SOURCE3 11 2.3900 2.6137 +cd-nh-hn 48.9 117.16 SOURCE3 11 2.3900 2.6137 +ce-nh-hn 50.1 114.73 SOURCE3 1 0.0000 0.0000 +cf-nh-hn 50.1 114.73 SOURCE3 1 same as ce-nh-hn +ce-nh-o 68.2 129.43 SOURCE3 1 0.0000 0.0000 +cf-nh-o 68.2 129.43 SOURCE3 1 same as ce-nh-o +cl-nh-cl 54.4 106.60 SOURCE0 1 +cl-nh-hn 40.1 104.14 SOURCE3 1 0.0000 0.0000 +f -nh-f 66.9 101.70 SOURCE3 1 0.0000 0.0000 +f -nh-hn 49.8 101.23 SOURCE3 1 0.0000 0.0000 +hn-nh-hn 40.1 114.43 SOURCE3 56 3.1626 3.8013 +hn-nh-i 36.5 107.57 SOURCE3 1 0.0000 0.0000 +hn-nh-n 51.1 105.95 SOURCE3 4 0.4635 0.5421 +hn-nh-n2 50.7 115.14 SOURCE3 21 2.5438 3.0032 +hn-nh-n3 50.1 109.12 SOURCE3 5 2.1577 2.3680 +hn-nh-n4 49.7 104.40 SOURCE3 3 0.4767 0.5056 +hn-nh-na 50.9 107.91 SOURCE3 26 1.2007 1.5528 +hn-nh-nh 50.9 108.08 SOURCE3 4 3.3278 3.3278 +hn-nh-no 49.9 104.71 SOURCE3 2 1.4480 1.4480 +hn-nh-o 53.0 116.45 SOURCE3 2 0.6063 0.6063 +hn-nh-oh 51.1 103.15 SOURCE3 1 0.0000 0.0000 +hn-nh-os 50.7 104.76 SOURCE3 3 0.4604 0.4883 +hn-nh-p2 54.4 118.18 SOURCE3 21 3.2394 3.6927 +hn-nh-p3 53.1 116.19 SOURCE3 3 2.8792 3.0539 +hn-nh-p4 54.7 112.60 SOURCE3 3 0.7766 0.8237 +hn-nh-p5 55.3 115.26 SOURCE3 3 0.8644 0.9168 +hn-nh-s 40.8 114.37 SOURCE3 1 0.0000 0.0000 +hn-nh-s4 43.1 107.48 SOURCE3 3 1.3162 1.3960 +hn-nh-s6 44.8 106.95 SOURCE3 3 0.5772 0.6122 +hn-nh-sh 43.3 112.25 SOURCE3 1 0.0000 0.0000 +hn-nh-ss 43.0 113.89 SOURCE3 3 1.3228 1.4030 +hn-nh-sy 45.2 109.10 SOURCE3 1 0.0000 0.0000 +i -nh-i 59.8 115.82 SOURCE0 1 +n -nh-o 71.8 115.63 SOURCE0 1 +n2-nh-n2 70.8 117.50 SOURCE3 2 1.1907 1.1907 +n2-nh-n3 69.6 115.54 SOURCE3 1 0.0000 0.0000 +n2-nh-o 70.4 126.06 SOURCE3 1 0.0000 0.0000 +n3-nh-n3 69.5 110.98 SOURCE3 1 0.0000 0.0000 +n4-nh-n4 68.2 108.36 SOURCE3 1 0.0000 0.0000 +na-nh-na 70.1 112.01 SOURCE3 1 0.0000 0.0000 +nh-nh-nh 70.1 112.23 SOURCE3 1 0.0000 0.0000 +no-nh-no 68.6 108.55 SOURCE3 1 0.0000 0.0000 +o -nh-o 72.2 128.06 SOURCE0 1 +oh-nh-oh 70.9 106.27 SOURCE0 1 +os-nh-os 71.2 105.27 SOURCE0 1 +p2-nh-p2 98.1 127.33 SOURCE3 2 2.7857 2.7857 +p3-nh-p3 96.0 125.08 SOURCE0 1 +p5-nh-p5 104.7 112.76 SOURCE0 1 +s -nh-s 59.7 118.73 SOURCE3 1 0.0000 0.0000 +s4-nh-s4 62.6 112.39 SOURCE0 1 +s6-nh-s6 62.5 120.27 SOURCE0 1 +sh-nh-sh 62.3 119.00 SOURCE0 1 +ss-nh-ss 62.2 119.25 SOURCE0 1 +br-no-o 58.5 113.19 SOURCE3 2 0.0000 0.0000 +c -no-o 67.1 115.26 SOURCE0 1 +c1-no-o 71.3 116.63 SOURCE3 6 0.0000 0.0000 +c2-no-o 69.3 116.87 SOURCE3 8 0.4199 0.4200 +c3-no-o 67.0 116.56 SOURCE3 6 0.3733 0.3959 +ca-no-o 68.7 118.10 SOURCE3 10 0.8958 1.1524 +cl-no-o 57.3 115.08 SOURCE3 2 0.0000 0.0000 +hn-no-o 55.3 115.49 SOURCE3 2 0.0000 0.0000 +i -no-o 54.6 116.31 SOURCE3 2 0.0000 0.0000 +n -no-o 71.7 115.41 SOURCE3 8 0.3612 0.3748 +n2-no-o 65.8 115.10 SOURCE2 2 2.4000 2.4000 +n3-no-o 72.0 115.56 SOURCE3 6 0.6060 0.6427 +n4-no-o 72.9 109.00 SOURCE3 2 0.0000 0.0000 +na-no-o 72.2 115.49 SOURCE3 18 0.4677 0.5640 +nh-no-o 71.6 115.71 SOURCE3 8 0.4808 0.4811 +no-no-o 59.9 112.38 SOURCE3 4 0.0000 0.0000 +o -no-o 76.4 127.55 SOURCE3 89 2.7577 3.8475 +o -no-oh 74.1 114.70 SOURCE3 2 0.0000 0.0000 +o -no-os 71.8 114.01 SOURCE3 8 0.9760 0.9778 +o -no-p2 82.1 117.38 SOURCE3 20 0.6173 0.8083 +o -no-p3 77.7 116.78 SOURCE3 6 0.4648 0.4929 +o -no-p4 76.7 116.64 SOURCE3 6 0.0084 0.0089 +o -no-p5 78.2 116.69 SOURCE3 8 0.4507 0.4507 +o -no-s 64.0 119.81 SOURCE3 4 0.0042 0.0042 +o -no-s4 57.1 114.49 SOURCE3 6 0.5349 0.5674 +o -no-s6 57.8 114.39 SOURCE3 6 0.7836 0.8311 +o -no-sh 62.9 116.10 SOURCE3 2 0.0000 0.0000 +o -no-ss 62.3 115.58 SOURCE3 6 0.5525 0.5860 +br-oh-ho 42.2 101.60 SOURCE3 1 0.0000 0.0000 +c -oh-ho 51.2 107.37 SOURCE3 34 1.4300 1.6830 +c1-oh-ho 50.2 108.76 SOURCE3 1 0.0000 0.0000 +c2-oh-ho 49.9 108.98 SOURCE3 6 1.6080 2.2379 +c3-oh-ho 47.1 108.16 SOURCE3 42 1.1979 1.3034 +ca-oh-ho 48.9 109.47 SOURCE3 7 0.9655 1.0405 +cc-oh-ho 49.7 107.72 SOURCE3 3 1.0115 1.0115 +cd-oh-ho 49.7 107.72 SOURCE3 3 1.0115 1.0115 +cl-oh-ho 40.5 102.40 SOURCE2 1 0.0000 0.0000 +cx-oh-ho 49.6 106.17 SOURCE3 3 0.0608 0.0644 +cy-oh-ho 47.7 106.88 SOURCE3 2 0.0000 0.0000 +f -oh-ho 48.5 96.80 SOURCE2 1 0.0000 0.0000 +ho-oh-ho 41.9 104.80 SOURCE2 1 0.0000 0.0000 +ho-oh-i 35.7 107.98 SOURCE3 2 0.0000 0.0000 +ho-oh-n 50.5 101.03 SOURCE3 6 1.1335 1.4086 +ho-oh-n2 50.6 102.74 SOURCE3 9 1.5684 2.1286 +ho-oh-n3 50.6 102.33 SOURCE3 5 0.9483 1.2591 +ho-oh-n4 49.4 106.63 SOURCE3 3 0.2612 0.2770 +ho-oh-na 50.2 103.71 SOURCE3 9 1.0282 1.2590 +ho-oh-nh 49.3 101.78 SOURCE3 1 0.0000 0.0000 +ho-oh-no 50.3 102.17 SOURCE3 1 0.0000 0.0000 +ho-oh-o 47.3 100.87 SOURCE0 1 +ho-oh-oh 49.3 98.72 SOURCE3 2 0.0000 0.0000 +ho-oh-os 49.4 98.77 SOURCE3 3 0.6106 0.6830 +ho-oh-p2 55.9 109.45 SOURCE3 8 2.2353 3.3491 +ho-oh-p3 53.8 110.64 SOURCE3 3 0.4894 0.5191 +ho-oh-p4 55.3 110.19 SOURCE3 4 0.2049 0.2372 +ho-oh-p5 55.9 110.14 SOURCE3 92 2.0406 3.8033 +ho-oh-py 56.2 110.73 SOURCE3 79 1.5384 1.7835 +ho-oh-s 40.9 100.15 SOURCE3 2 0.0000 0.0000 +ho-oh-s4 43.6 106.31 SOURCE3 3 1.2438 1.3192 +ho-oh-s6 45.5 109.20 SOURCE3 13 0.1484 0.1856 +ho-oh-sh 43.0 106.24 SOURCE3 2 0.0661 0.0661 +ho-oh-ss 43.1 107.06 SOURCE3 4 0.9702 0.9967 +ho-oh-sy 44.7 106.11 SOURCE3 4 0.9258 1.1482 +br-os-br 65.1 110.63 SOURCE3 1 0.0000 0.0000 +c -os-c 64.0 122.65 SOURCE3 5 3.3752 3.5418 +c -os-c2 68.2 106.90 SOURCE2 1 0.0000 0.0000 +c -os-c3 63.6 115.14 SOURCE3 17 1.5416 1.8967 +c -os-ca 64.6 117.61 SOURCE3 2 2.1561 2.1561 +c -os-cc 64.2 119.62 SOURCE3 5 5.2421 6.0675 +c -os-cd 64.2 119.62 SOURCE3 5 5.2421 6.0675 +c -os-cy 70.9 91.10 SOURCE3 2 0.0155 0.0155 +c -os-oh 66.2 110.50 SOURCE3 1 0.0000 0.0000 +c -os-sy 61.9 113.49 SOURCE3 1 0.0000 0.0000 +c1-os-c1 67.0 115.02 SOURCE3 1 0.0000 0.0000 +c1-os-c3 64.5 113.39 SOURCE3 1 0.0000 0.0000 +c2-os-c2 66.0 113.14 SOURCE3 6 1.9475 2.1932 +c2-os-c3 64.2 112.09 SOURCE3 7 3.0925 4.1809 +c2-os-ca 65.4 113.59 SOURCE3 1 0.0000 0.0000 +c2-os-n2 64.9 118.13 SOURCE3 1 0.0000 0.0000 +c2-os-na 68.2 103.85 SOURCE3 4 0.6297 0.6297 +c2-os-os 68.3 102.77 SOURCE3 1 0.0000 0.0000 +c2-os-ss 63.1 108.13 SOURCE3 1 0.0000 0.0000 +c3-os-c3 62.1 113.41 SOURCE3 50 2.5452 3.0289 +c3-os-ca 62.4 117.60 SOURCE3 8 2.5372 2.9174 +c3-os-cc 63.1 115.18 SOURCE3 8 3.4925 3.8476 +c3-os-cd 63.1 115.18 SOURCE3 8 3.4925 3.8476 +c3-os-cl 56.2 110.50 SOURCE2 1 0.0000 0.0000 +c3-os-i 54.9 113.70 SOURCE3 1 0.0000 0.0000 +c3-os-n 65.3 108.57 SOURCE3 4 0.5159 0.6121 +c3-os-n2 65.9 108.12 SOURCE3 7 0.2643 0.3048 +c3-os-n3 65.3 107.69 SOURCE3 3 0.3554 0.3770 +c3-os-n4 64.9 110.50 SOURCE3 3 0.5116 0.5426 +c3-os-na 64.5 109.91 SOURCE3 9 1.1472 1.8268 +c3-os-nc 64.8 112.73 SOURCE3 2 1.0358 1.0358 +c3-os-nd 64.8 112.73 SOURCE3 2 same as c3-os-nc +c3-os-nh 65.4 107.26 SOURCE3 1 0.0000 0.0000 +c3-os-no 63.3 111.47 SOURCE3 2 1.6956 1.6956 +c3-os-o 65.6 103.00 SOURCE3 1 0.0000 0.0000 +c3-os-oh 65.7 105.42 SOURCE3 2 0.8087 0.8087 +c3-os-os 65.9 105.01 SOURCE3 7 0.5292 0.6328 +c3-os-p2 80.2 115.47 SOURCE3 8 1.7016 2.6374 +c3-os-p3 76.5 115.97 SOURCE3 3 0.3392 0.3597 +c3-os-p4 77.6 117.48 SOURCE3 4 0.3849 0.3850 +c3-os-p5 78.5 118.00 SOURCE3 31 1.0807 1.2882 +c3-os-py 78.1 117.80 SOURCE3 16 0.9119 0.9654 +c3-os-s 59.3 109.55 SOURCE3 1 0.0000 0.0000 +c3-os-s4 61.3 111.50 SOURCE3 6 1.2743 1.4240 +c3-os-s6 63.3 115.38 SOURCE3 2 2.2498 2.2498 +c3-os-sh 61.7 112.82 SOURCE3 1 0.0000 0.0000 +c3-os-ss 60.7 113.19 SOURCE3 3 0.2315 0.2455 +ca-os-ca 63.6 118.96 SOURCE3 3 1.2676 1.4055 +ca-os-cc 66.2 109.77 SOURCE3 6 3.8556 5.0326 +ca-os-cd 66.2 109.77 SOURCE3 6 3.8556 5.0326 +ca-os-n3 65.4 112.19 SOURCE3 1 0.0000 0.0000 +ca-os-na 66.5 108.24 SOURCE3 1 0.0000 0.0000 +ca-os-nc 66.1 113.68 SOURCE0 2 +ca-os-nd 66.1 113.68 SOURCE0 2 +cc-os-cc 66.5 109.17 SOURCE3 12 6.7381 7.2529 +cd-os-cd 66.5 109.17 SOURCE3 12 6.7381 7.2529 +cc-os-cd 62.7 122.99 SOURCE3 3 0.1438 0.1525 +cc-os-na 65.5 111.66 SOURCE3 28 3.6412 4.1343 +cd-os-na 65.5 111.66 SOURCE3 28 3.6412 4.1343 +cc-os-nc 68.1 107.23 SOURCE3 6 2.1966 2.7507 +cd-os-nd 68.1 107.23 SOURCE3 6 2.1966 2.7507 +cc-os-os 66.3 108.47 SOURCE3 2 0.0000 0.0000 +cd-os-os 66.3 108.47 SOURCE3 2 same as cc-os-os +cc-os-ss 59.9 119.59 SOURCE3 1 0.0000 0.0000 +cd-os-ss 59.9 119.59 SOURCE3 1 same as cc-os-ss +cl-os-cl 52.3 110.76 SOURCE3 2 0.0000 0.0000 +cx-os-cx 85.7 61.19 SOURCE3 2 0.0000 0.0000 +cx-os-n 88.4 59.99 SOURCE3 1 0.0000 0.0000 +cx-os-os 90.4 56.52 SOURCE3 2 0.0000 0.0000 +cy-os-cy 67.4 93.40 SOURCE2 2 1.4000 1.4000 +f -os-f 63.9 103.30 SOURCE2 1 0.0000 0.0000 +f -os-os 63.9 109.50 SOURCE2 1 0.0000 0.0000 +i -os-i 58.1 115.67 SOURCE3 1 0.0000 0.0000 +n -os-n 67.2 108.31 SOURCE3 1 0.0000 0.0000 +n2-os-n2 68.8 106.83 SOURCE3 1 0.0000 0.0000 +n3-os-n3 67.8 104.88 SOURCE3 1 0.0000 0.0000 +n4-os-n4 65.7 114.68 SOURCE3 1 0.0000 0.0000 +na-os-na 66.1 109.59 SOURCE3 1 0.0000 0.0000 +na-os-ss 64.7 104.34 SOURCE3 1 0.0000 0.0000 +nc-os-nc 68.2 110.40 SOURCE2 1 0.0000 0.0000 +nd-os-nd 68.2 110.40 SOURCE2 1 same as nc-os-nc +nc-os-ss 63.4 110.97 SOURCE3 1 0.0000 0.0000 +nd-os-ss 63.4 110.97 SOURCE3 1 same as nc-os-ss +nh-os-nh 66.6 108.29 SOURCE3 1 0.0000 0.0000 +no-os-no 64.0 111.86 SOURCE3 1 0.0000 0.0000 +o -os-o 62.8 114.68 SOURCE3 1 0.0000 0.0000 +p2-os-p2 103.6 120.02 SOURCE3 1 0.0000 0.0000 +p2-os-p5 108.3 107.86 SOURCE3 1 0.0000 0.0000 +p3-os-p3 96.2 121.22 SOURCE3 1 0.0000 0.0000 +p3-os-py 105.1 105.58 SOURCE3 1 0.0000 0.0000 +p5-os-p5 99.2 126.25 SOURCE3 1 0.0000 0.0000 +s -os-s 57.0 118.08 SOURCE3 1 0.0000 0.0000 +s4-os-s4 62.1 111.63 SOURCE3 1 0.0000 0.0000 +s6-os-s6 64.8 119.07 SOURCE3 2 0.4318 0.4318 +sh-os-sh 61.2 118.95 SOURCE3 1 0.0000 0.0000 +ss-os-ss 60.8 115.64 SOURCE3 1 0.0000 0.0000 +br-p2-br 40.7 108.60 SOURCE0 1 +br-p2-c2 39.4 102.32 SOURCE3 2 0.0146 0.0146 +br-p2-n2 40.4 103.33 SOURCE3 1 0.0000 0.0000 +br-p2-o 39.4 110.87 SOURCE3 1 0.0000 0.0000 +br-p2-p2 50.2 115.46 SOURCE3 4 6.8089 7.8622 +br-p2-s 40.6 110.52 SOURCE3 1 0.0000 0.0000 +c -p2-c 38.3 90.10 SOURCE0 1 +c -p2-c2 38.9 97.30 SOURCE0 1 +c1-p2-c1 39.2 99.04 SOURCE0 1 +c1-p2-c2 39.8 101.29 SOURCE0 1 +c1-p2-n2 41.4 101.79 SOURCE0 1 +c1-p2-o 41.3 107.62 SOURCE0 1 +c1-p2-p2 53.3 99.54 SOURCE0 1 +c1-p2-s 41.0 105.90 SOURCE0 1 +c2-p2-c2 40.4 104.50 SOURCE0 1 +c2-p2-c3 38.6 101.90 SOURCE3 4 0.0911 0.1132 +c2-p2-ca 38.8 101.95 SOURCE0 1 +c2-p2-cl 35.6 102.72 SOURCE3 2 0.0000 0.0000 +c2-p2-f 41.6 103.47 SOURCE3 2 0.0136 0.0136 +c2-p2-hp 30.1 97.19 SOURCE3 3 0.0204 0.0216 +c2-p2-i 33.9 101.94 SOURCE3 2 0.0368 0.0368 +c2-p2-n 40.9 103.28 SOURCE3 4 2.8675 3.3113 +c2-p2-n2 43.2 99.88 SOURCE0 1 +c2-p2-n3 42.0 101.80 SOURCE0 1 +c2-p2-n4 39.1 98.26 SOURCE3 6 0.1327 0.1522 +c2-p2-na 40.5 103.99 SOURCE3 8 1.4375 1.6834 +c2-p2-nh 41.2 105.17 SOURCE3 8 0.6846 0.8263 +c2-p2-no 41.9 97.97 SOURCE3 3 0.3936 0.4175 +c2-p2-o 41.5 115.16 SOURCE0 1 +c2-p2-oh 42.5 102.89 SOURCE3 3 0.7723 0.8191 +c2-p2-os 43.3 102.12 SOURCE3 4 0.7246 0.8783 +c2-p2-p2 54.7 99.56 SOURCE0 1 +c2-p2-p3 48.1 99.27 SOURCE3 4 1.1367 1.1590 +c2-p2-p4 48.2 96.94 SOURCE0 1 +c2-p2-p5 48.0 97.61 SOURCE0 1 +c2-p2-s 42.2 105.53 SOURCE0 1 +c2-p2-s4 38.3 95.15 SOURCE0 1 +c2-p2-s6 38.3 95.51 SOURCE0 1 +c2-p2-sh 40.2 101.49 SOURCE3 3 0.0053 0.0057 +c2-p2-ss 40.2 101.81 SOURCE3 4 0.5882 0.5883 +c3-p2-c3 37.4 99.30 SOURCE0 1 +c3-p2-n2 40.3 100.82 SOURCE3 1 0.0000 0.0000 +c3-p2-o 40.1 106.72 SOURCE3 1 0.0000 0.0000 +c3-p2-os 40.7 101.34 SOURCE3 1 0.0000 0.0000 +c3-p2-p2 51.8 100.48 SOURCE3 1 0.0000 0.0000 +c3-p2-s 40.0 105.68 SOURCE3 1 0.0000 0.0000 +ca-p2-ca 37.6 99.70 SOURCE0 1 +ca-p2-n 41.7 89.97 SOURCE0 1 +ca-p2-n2 40.5 100.82 SOURCE0 1 +ca-p2-na 41.7 89.21 SOURCE0 1 +ca-p2-o 40.3 106.88 SOURCE0 1 +ca-p2-s 39.8 107.93 SOURCE0 1 +ce-p2-o 40.6 107.44 SOURCE0 1 +cf-p2-o 40.6 107.44 SOURCE0 1 same as ce-p2-o +ce-p2-s 40.6 105.54 SOURCE0 1 +cf-p2-s 40.6 105.54 SOURCE0 1 same as ce-p2-s +cl-p2-cl 32.0 108.70 SOURCE0 1 +cl-p2-n2 36.7 103.38 SOURCE3 1 0.0000 0.0000 +cl-p2-o 36.0 110.57 SOURCE3 1 0.0000 0.0000 +cl-p2-p2 47.8 103.11 SOURCE3 1 0.0000 0.0000 +cl-p2-s 36.6 110.11 SOURCE3 1 0.0000 0.0000 +f -p2-f 42.2 107.10 SOURCE0 1 +f -p2-n2 43.6 103.57 SOURCE3 1 0.0000 0.0000 +f -p2-o 43.8 110.61 SOURCE3 1 0.0000 0.0000 +f -p2-p2 54.5 103.48 SOURCE3 1 0.0000 0.0000 +f -p2-s 41.2 114.71 SOURCE3 2 5.2794 5.2794 +hp-p2-hp 22.8 98.76 SOURCE0 1 +hp-p2-n1 31.1 95.18 SOURCE3 2 1.5708 1.5708 +hp-p2-n2 32.1 95.54 SOURCE3 19 3.3767 4.7352 +hp-p2-ne 31.9 100.10 SOURCE3 14 5.3381 6.1290 +hp-p2-nf 31.9 100.10 SOURCE3 14 same as hp-p2-ne +hp-p2-o 32.0 105.58 SOURCE3 1 0.0000 0.0000 +hp-p2-p2 38.2 101.88 SOURCE3 27 12.2440 12.9535 +hp-p2-p4 32.7 94.51 SOURCE3 1 0.0000 0.0000 +hp-p2-p5 33.7 89.07 SOURCE3 1 0.0000 0.0000 +hp-p2-pe 37.6 97.25 SOURCE3 16 7.5144 8.8916 +hp-p2-pf 37.6 97.25 SOURCE3 16 same as hp-p2-pe +hp-p2-s 30.3 102.52 SOURCE3 1 0.0000 0.0000 +hp-p2-s4 26.3 89.99 SOURCE3 1 0.0000 0.0000 +hp-p2-s6 26.7 88.13 SOURCE3 1 0.0000 0.0000 +i -p2-i 35.8 104.16 SOURCE0 1 +i -p2-n2 34.6 101.77 SOURCE3 1 0.0000 0.0000 +i -p2-o 33.3 109.51 SOURCE3 1 0.0000 0.0000 +i -p2-p2 46.2 102.63 SOURCE3 1 0.0000 0.0000 +i -p2-s 35.2 110.60 SOURCE3 1 0.0000 0.0000 +n -p2-n2 43.6 98.85 SOURCE3 1 0.0000 0.0000 +n -p2-o 43.5 105.08 SOURCE3 1 0.0000 0.0000 +n -p2-p2 54.5 102.12 SOURCE3 1 0.0000 0.0000 +n -p2-s 41.2 112.34 SOURCE3 1 0.0000 0.0000 +n2-p2-n2 45.6 98.00 SOURCE0 1 +n2-p2-n3 44.1 100.42 SOURCE0 1 +n2-p2-n4 41.5 93.42 SOURCE3 1 0.0000 0.0000 +n2-p2-na 42.6 102.03 SOURCE3 1 0.0000 0.0000 +n2-p2-nh 43.7 101.87 SOURCE3 2 0.8491 0.8491 +n2-p2-no 43.6 98.12 SOURCE3 1 0.0000 0.0000 +n2-p2-o 43.5 115.34 SOURCE0 1 +n2-p2-oh 43.0 109.72 SOURCE3 1 0.0000 0.0000 +n2-p2-os 45.4 102.29 SOURCE3 1 0.0000 0.0000 +n2-p2-p3 49.6 99.51 SOURCE3 1 0.0000 0.0000 +n2-p2-p4 48.5 101.73 SOURCE0 1 +n2-p2-p5 50.5 93.68 SOURCE0 1 +n2-p2-s 42.5 112.94 SOURCE0 1 +n2-p2-s4 38.9 97.83 SOURCE0 1 +n2-p2-s6 39.0 98.14 SOURCE0 1 +n2-p2-sh 41.8 100.82 SOURCE3 1 0.0000 0.0000 +n2-p2-ss 41.6 101.76 SOURCE3 1 0.0000 0.0000 +n3-p2-n3 42.1 106.30 SOURCE0 1 +n3-p2-o 44.2 106.83 SOURCE0 1 +n3-p2-p2 55.8 100.58 SOURCE0 1 +n3-p2-s 43.2 105.75 SOURCE0 1 +n4-p2-n4 39.6 88.80 SOURCE0 1 +n4-p2-o 40.7 101.36 SOURCE3 1 0.0000 0.0000 +n4-p2-p2 52.7 96.53 SOURCE3 1 0.0000 0.0000 +n4-p2-s 40.1 104.98 SOURCE3 1 0.0000 0.0000 +na-p2-na 40.2 106.10 SOURCE0 1 +na-p2-o 42.7 107.46 SOURCE3 1 0.0000 0.0000 +na-p2-s 41.8 108.15 SOURCE3 1 0.0000 0.0000 +ne-p2-o 45.7 107.71 SOURCE0 1 +nf-p2-o 45.7 107.71 SOURCE0 1 same as ne-p2-o +ne-p2-s 44.3 105.50 SOURCE0 1 +nf-p2-s 44.3 105.50 SOURCE0 1 same as ne-p2-s +nh-p2-nh 42.3 104.00 SOURCE0 1 +nh-p2-o 43.7 108.11 SOURCE3 2 0.6773 0.6773 +nh-p2-p2 53.8 107.73 SOURCE3 3 2.7661 3.1678 +nh-p2-s 42.3 109.62 SOURCE3 2 1.7725 1.7725 +no-p2-no 42.1 98.20 SOURCE0 1 +no-p2-o 43.4 104.87 SOURCE3 1 0.0000 0.0000 +no-p2-p2 52.7 108.57 SOURCE3 3 7.7424 8.2121 +no-p2-s 41.8 109.06 SOURCE3 2 5.4074 5.4074 +o -p2-o 44.4 119.96 SOURCE0 1 +o -p2-oh 44.3 110.46 SOURCE3 1 0.0000 0.0000 +o -p2-os 45.6 108.81 SOURCE3 1 0.0000 0.0000 +o -p2-p2 54.6 114.23 SOURCE0 1 +o -p2-p3 48.5 106.69 SOURCE3 1 0.0000 0.0000 +o -p2-p4 48.4 104.37 SOURCE0 1 +o -p2-p5 48.4 104.49 SOURCE0 1 +o -p2-pe 46.7 145.96 SOURCE0 1 +o -p2-pf 46.7 145.96 SOURCE0 1 same as o -p2-pe +o -p2-s 42.8 117.42 SOURCE0 1 +o -p2-s4 37.7 106.59 SOURCE0 1 +o -p2-s6 38.1 105.04 SOURCE0 1 +o -p2-sh 40.8 109.60 SOURCE3 1 0.0000 0.0000 +o -p2-ss 40.9 109.60 SOURCE3 1 0.0000 0.0000 +oh-p2-oh 45.0 100.10 SOURCE0 1 +oh-p2-p2 54.7 107.82 SOURCE3 2 2.6708 2.6708 +oh-p2-s 43.1 109.75 SOURCE3 1 0.0000 0.0000 +os-p2-os 47.0 98.30 SOURCE0 1 +os-p2-p2 57.1 101.46 SOURCE3 1 0.0000 0.0000 +os-p2-s 43.9 108.47 SOURCE3 3 1.6089 1.7065 +p2-p2-n2 57.6 97.40 SOURCE0 1 +p2-p2-p3 64.1 101.73 SOURCE3 1 0.0000 0.0000 +p2-p2-p4 63.4 101.98 SOURCE0 1 +p2-p2-p5 64.2 99.33 SOURCE0 1 +p2-p2-s 54.5 111.28 SOURCE0 1 +p2-p2-s4 51.5 95.73 SOURCE0 1 +p2-p2-s6 51.6 95.95 SOURCE0 1 +p2-p2-sh 50.8 113.94 SOURCE3 3 8.0148 8.5009 +p3-p2-p3 59.9 101.00 SOURCE0 1 +p3-p2-s 48.1 113.28 SOURCE3 2 6.7035 6.7035 +p4-p2-s 49.7 103.89 SOURCE0 1 +p5-p2-p5 62.8 89.40 SOURCE0 1 +p5-p2-s 50.4 101.21 SOURCE0 1 +pe-p2-s 54.5 106.35 SOURCE0 1 +pf-p2-s 54.5 106.35 SOURCE0 1 same as pe-p2-s +s -p2-s 44.2 106.60 SOURCE0 1 +s -p2-s4 38.9 105.29 SOURCE0 1 +s -p2-s6 38.7 106.93 SOURCE0 1 +s -p2-sh 40.8 110.73 SOURCE3 2 0.0232 0.0232 +s -p2-ss 40.3 114.14 SOURCE3 4 5.9162 5.9223 +s4-p2-s4 40.0 85.30 SOURCE0 1 +s6-p2-s6 37.4 98.20 SOURCE0 1 +sh-p2-sh 41.3 98.50 SOURCE0 1 +ss-p2-ss 41.6 97.90 SOURCE0 1 +br-p3-br 41.3 103.54 SOURCE3 1 0.0000 0.0000 +br-p3-hp 26.9 96.36 SOURCE3 4 0.6701 0.6701 +c -p3-c 36.5 100.90 SOURCE3 1 0.0000 0.0000 +c -p3-c3 37.6 97.06 SOURCE3 3 1.0833 1.1490 +c -p3-hp 27.1 96.55 SOURCE3 6 0.4924 0.5223 +c -p3-os 43.9 81.32 SOURCE3 1 0.0000 0.0000 +c1-p3-c1 38.5 100.50 SOURCE3 1 0.0000 0.0000 +c1-p3-f 40.7 96.90 SOURCE2 1 0.0000 0.0000 +c1-p3-hp 28.1 97.67 SOURCE3 2 0.0000 0.0000 +c2-p3-c2 37.3 101.77 SOURCE3 3 0.0000 0.0000 +c2-p3-hp 27.6 97.85 SOURCE3 4 0.0000 0.0000 +c3-p3-c3 37.5 99.66 SOURCE3 40 0.8383 0.9854 +c3-p3-ca 37.3 101.94 SOURCE3 2 0.0000 0.0000 +c3-p3-cl 35.7 99.89 SOURCE3 1 0.0000 0.0000 +c3-p3-f 39.7 97.80 SOURCE2 1 0.0000 0.0000 +c3-p3-hp 27.5 97.66 SOURCE3 9 0.2559 0.4096 +c3-p3-n 38.8 101.77 SOURCE3 12 2.2839 2.4449 +c3-p3-n2 39.9 96.55 SOURCE3 2 0.0000 0.0000 +c3-p3-n3 39.3 101.18 SOURCE3 10 1.7890 2.2338 +c3-p3-n4 38.6 96.94 SOURCE3 6 0.4540 0.4815 +c3-p3-na 39.2 100.17 SOURCE3 4 0.0554 0.0554 +c3-p3-nh 38.6 104.50 SOURCE3 2 0.0000 0.0000 +c3-p3-no 39.0 96.98 SOURCE3 2 0.0000 0.0000 +c3-p3-o 39.3 111.67 SOURCE3 28 3.9148 5.3387 +c3-p3-oh 40.6 98.21 SOURCE3 2 0.0000 0.0000 +c3-p3-os 40.2 99.53 SOURCE3 3 1.6667 1.7678 +c3-p3-p3 45.8 100.31 SOURCE3 18 2.0337 2.1836 +c3-p3-p5 45.6 100.90 SOURCE3 10 2.6003 2.7070 +c3-p3-s4 37.9 98.88 SOURCE3 8 5.3873 6.2235 +c3-p3-s6 37.6 101.18 SOURCE3 12 5.5239 6.4536 +c3-p3-sh 37.4 98.71 SOURCE3 2 0.0000 0.0000 +c3-p3-ss 37.4 99.37 SOURCE3 2 0.0000 0.0000 +ca-p3-ca 37.9 99.86 SOURCE3 1 0.0000 0.0000 +ca-p3-hp 27.7 97.50 SOURCE3 2 0.0000 0.0000 +cl-p3-cl 33.9 102.82 SOURCE3 1 0.0000 0.0000 +cl-p3-f 37.0 99.20 SOURCE2 1 0.0000 0.0000 +cl-p3-hp 25.7 96.30 SOURCE3 3 0.5848 0.6203 +cx-p3-hp 27.5 95.20 SOURCE2 1 0.0000 0.0000 +f -p3-f 43.1 97.40 SOURCE2 8 1.3750 1.6636 +f -p3-hp 30.6 96.41 SOURCE3 2 0.0000 0.0000 +f -p3-n3 41.9 100.60 SOURCE2 1 0.0000 0.0000 +f -p3-os 42.4 102.20 SOURCE2 1 0.0000 0.0000 +f -p3-p3 47.1 97.20 SOURCE2 1 0.0000 0.0000 +hp-p3-hp 22.0 95.52 SOURCE3 44 1.2944 2.4200 +hp-p3-i 23.4 96.19 SOURCE3 4 0.6454 0.6454 +hp-p3-n 29.5 95.15 SOURCE3 2 0.0000 0.0000 +hp-p3-n2 29.1 98.28 SOURCE3 10 1.6390 1.8860 +hp-p3-n3 30.1 94.46 SOURCE3 2 0.0000 0.0000 +hp-p3-n4 28.3 93.21 SOURCE3 2 0.0000 0.0000 +hp-p3-na 29.2 97.27 SOURCE3 12 0.7938 0.9318 +hp-p3-nh 30.2 94.10 SOURCE3 2 0.0000 0.0000 +hp-p3-no 28.8 93.06 SOURCE3 2 0.0000 0.0000 +hp-p3-o 32.0 101.02 SOURCE3 2 0.0000 0.0000 +hp-p3-oh 30.7 95.95 SOURCE3 2 0.0000 0.0000 +hp-p3-os 30.4 97.35 SOURCE3 6 2.6706 2.8326 +hp-p3-p2 32.4 99.11 SOURCE3 16 2.7761 4.3022 +hp-p3-p3 32.1 95.52 SOURCE3 4 0.0844 0.0844 +hp-p3-p4 32.0 95.95 SOURCE3 6 0.0461 0.0489 +hp-p3-p5 32.1 95.54 SOURCE3 2 0.0000 0.0000 +hp-p3-s4 26.9 95.49 SOURCE3 2 0.0000 0.0000 +hp-p3-s6 27.4 92.95 SOURCE3 2 0.0000 0.0000 +hp-p3-sh 26.5 94.21 SOURCE3 2 0.0000 0.0000 +hp-p3-ss 26.6 94.61 SOURCE3 2 0.0000 0.0000 +i -p3-i 36.6 105.25 SOURCE3 1 0.0000 0.0000 +n -p3-n 40.0 104.58 SOURCE0 1 +n -p3-o 42.8 104.99 SOURCE3 4 0.0000 0.0000 +n2-p3-n2 40.4 103.46 SOURCE3 1 0.0000 0.0000 +n3-p3-n3 39.3 113.80 SOURCE3 1 0.0000 0.0000 +n3-p3-o 43.0 107.10 SOURCE3 4 0.0000 0.0000 +n3-p3-oh 43.1 98.36 SOURCE0 1 +n4-p3-n4 38.5 100.53 SOURCE3 1 0.0000 0.0000 +na-p3-na 39.9 106.22 SOURCE0 1 +nh-p3-nh 40.1 109.11 SOURCE3 1 0.0000 0.0000 +no-p3-no 39.6 98.33 SOURCE3 1 0.0000 0.0000 +o -p3-o 43.8 122.18 SOURCE3 2 7.8556 7.8556 +o -p3-p3 45.1 116.74 SOURCE3 14 0.5266 0.7525 +o -p3-p5 47.0 107.62 SOURCE3 4 0.0000 0.0000 +o -p3-s4 38.6 110.70 SOURCE3 4 0.7259 0.7259 +o -p3-s6 39.5 106.66 SOURCE3 6 3.2072 3.4017 +oh-p3-oh 42.8 104.48 SOURCE3 1 0.0000 0.0000 +os-p3-os 42.1 106.65 SOURCE3 1 0.0000 0.0000 +p2-p3-p2 59.1 103.58 SOURCE3 1 0.0000 0.0000 +p3-p3-p3 57.0 105.31 SOURCE3 4 3.1059 3.5864 +p4-p3-p4 58.7 99.09 SOURCE0 1 +p5-p3-p5 58.8 99.10 SOURCE3 1 0.0000 0.0000 +s -p3-s 34.1 131.32 SOURCE0 1 +s4-p3-s4 39.1 98.26 SOURCE3 1 0.0000 0.0000 +s6-p3-s6 39.4 97.78 SOURCE3 1 0.0000 0.0000 +sh-p3-sh 36.6 107.58 SOURCE3 1 0.0000 0.0000 +ss-p3-ss 36.5 109.24 SOURCE3 1 0.0000 0.0000 +br-p4-br 41.1 110.41 SOURCE0 1 +br-p4-o 37.8 124.80 SOURCE0 1 +c2-p4-c2 37.1 104.21 SOURCE0 1 +c2-p4-hp 27.7 99.50 SOURCE3 2 0.0000 0.0000 +c2-p4-o 39.4 113.59 SOURCE0 1 +c3-p4-c3 37.2 102.55 SOURCE3 4 0.0192 0.0192 +c3-p4-n 39.0 103.26 SOURCE3 1 0.0000 0.0000 +c3-p4-n2 39.1 103.17 SOURCE0 1 +c3-p4-n3 39.5 102.37 SOURCE3 1 0.0000 0.0000 +c3-p4-n4 37.5 99.57 SOURCE3 1 0.0000 0.0000 +c3-p4-na 37.9 117.67 SOURCE3 5 18.6523 19.0404 +c3-p4-nh 39.3 102.79 SOURCE3 1 0.0000 0.0000 +c3-p4-no 38.2 99.80 SOURCE3 3 0.2028 0.2151 +c3-p4-o 38.8 116.44 SOURCE3 25 1.6284 2.6494 +c3-p4-oh 41.0 98.56 SOURCE3 2 0.4558 0.4558 +c3-p4-os 41.2 98.01 SOURCE3 2 0.0931 0.0931 +c3-p4-p2 44.4 109.27 SOURCE0 1 +c3-p4-p3 45.1 103.53 SOURCE3 1 0.0000 0.0000 +c3-p4-p4 48.1 102.12 SOURCE0 1 +c3-p4-p5 44.6 104.15 SOURCE0 1 +c3-p4-sh 37.4 100.17 SOURCE3 2 0.0815 0.0815 +c3-p4-ss 37.4 101.19 SOURCE0 1 +ca-p4-ca 36.8 107.77 SOURCE0 1 +ca-p4-o 40.0 111.64 SOURCE0 1 +cl-p4-cl 33.8 103.51 SOURCE3 1 0.0000 0.0000 +cl-p4-o 36.0 116.53 SOURCE3 2 0.0000 0.0000 +hp-p4-hp 22.6 99.21 SOURCE3 4 5.1252 6.4572 +hp-p4-o 31.4 109.35 SOURCE3 6 9.0789 10.8284 +hp-p4-p3 31.4 98.96 SOURCE3 4 0.0000 0.0000 +hp-p4-s 24.3 110.24 SOURCE3 4 4.1081 4.1081 +i -p4-i 38.5 113.22 SOURCE3 2 6.7916 6.7916 +i -p4-o 37.7 110.22 SOURCE3 4 9.7726 9.7726 +n -p4-o 41.0 117.99 SOURCE3 1 0.0000 0.0000 +n2-p4-n2 41.5 102.54 SOURCE0 1 +n2-p4-o 40.8 120.28 SOURCE0 1 +n3-p4-o 42.5 113.27 SOURCE3 1 0.0000 0.0000 +n4-p4-o 39.6 107.61 SOURCE3 1 0.0000 0.0000 +na-p4-o 45.2 110.60 SOURCE3 5 1.1626 1.3133 +nh-p4-nh 43.5 95.30 SOURCE3 1 0.0000 0.0000 +nh-p4-o 41.9 115.86 SOURCE3 3 3.0841 3.2712 +no-p4-o 39.4 114.69 SOURCE3 3 0.1008 0.1070 +o -p4-o 45.1 117.22 SOURCE3 6 2.7792 2.7792 +o -p4-oh 42.9 117.39 SOURCE3 4 0.9528 1.0083 +o -p4-os 43.1 116.67 SOURCE3 4 0.6527 0.6923 +o -p4-p2 44.9 121.35 SOURCE0 1 +o -p4-p3 45.6 114.00 SOURCE3 3 0.6282 0.6663 +o -p4-p4 48.8 116.43 SOURCE0 1 +o -p4-p5 46.0 109.76 SOURCE0 1 +o -p4-s 37.3 112.78 SOURCE3 2 0.0000 0.0000 +o -p4-s4 35.8 112.19 SOURCE0 1 +o -p4-s6 35.2 113.89 SOURCE0 1 +o -p4-sh 37.0 118.09 SOURCE0 1 +o -p4-ss 37.5 116.14 SOURCE3 4 0.9499 1.0636 +oh-p4-oh 45.7 95.71 SOURCE3 1 0.0000 0.0000 +os-p4-os 44.7 100.34 SOURCE3 1 0.0000 0.0000 +p2-p4-p2 56.5 110.71 SOURCE0 1 +p3-p4-p3 54.5 114.98 SOURCE3 1 0.0000 0.0000 +p4-p4-p4 61.4 107.38 SOURCE0 1 +p5-p4-p5 55.8 107.78 SOURCE0 1 +s -p4-s 36.5 106.30 SOURCE3 2 25.0119 25.0119 +s4-p4-s4 36.6 96.24 SOURCE0 1 +s6-p4-s6 35.2 102.36 SOURCE0 1 +sh-p4-sh 38.5 98.81 SOURCE3 1 0.0000 0.0000 +ss-p4-ss 37.6 104.41 SOURCE3 1 0.0000 0.0000 +br-p5-br 42.0 103.38 SOURCE3 1 0.0000 0.0000 +br-p5-o 39.0 114.65 SOURCE3 3 1.0286 1.0910 +br-p5-oh 40.9 102.92 SOURCE3 4 0.5468 0.5468 +c -p5-c 36.2 104.16 SOURCE0 1 +c -p5-o 38.7 113.88 SOURCE0 1 +c -p5-oh 39.9 102.12 SOURCE0 1 +c1-p5-c1 38.8 102.89 SOURCE3 1 0.0000 0.0000 +c1-p5-o 40.3 115.77 SOURCE3 2 0.0000 0.0000 +c1-p5-oh 41.4 102.79 SOURCE3 2 0.0000 0.0000 +c2-p5-c2 36.8 106.56 SOURCE0 1 +c2-p5-o 39.4 114.81 SOURCE0 1 +c2-p5-oh 40.7 101.69 SOURCE0 1 +c2-p5-os 40.6 103.34 SOURCE0 1 +c3-p5-c3 37.0 106.23 SOURCE3 14 2.4917 2.6389 +c3-p5-hp 26.9 104.49 SOURCE3 1 0.0000 0.0000 +c3-p5-n3 40.0 102.76 SOURCE3 1 0.0000 0.0000 +c3-p5-o 39.9 112.50 SOURCE3 23 4.1385 4.4203 +c3-p5-oh 40.8 101.56 SOURCE3 17 1.4803 2.1803 +c3-p5-os 40.6 103.83 SOURCE3 4 2.0564 2.3806 +c3-p5-p4 44.3 106.27 SOURCE0 1 +c3-p5-s 37.5 113.40 SOURCE3 4 1.7378 2.0067 +c3-p5-ss 37.0 103.76 SOURCE3 1 0.0000 0.0000 +ca-p5-ca 37.1 107.53 SOURCE0 1 +ca-p5-o 39.9 113.98 SOURCE0 1 +ca-p5-oh 41.0 101.77 SOURCE0 1 +ca-p5-os 40.9 103.75 SOURCE0 1 +cl-p5-cl 33.8 103.70 SOURCE2 1 0.0000 0.0000 +cl-p5-o 36.3 115.32 SOURCE3 2 0.0000 0.0000 +cl-p5-oh 37.9 102.44 SOURCE3 2 0.0000 0.0000 +f -p5-f 42.5 99.96 SOURCE2 4 0.7600 0.9197 +f -p5-o 42.3 116.75 SOURCE3 2 0.0000 0.0000 +f -p5-oh 43.3 101.98 SOURCE3 2 0.0000 0.0000 +f -p5-s 38.1 117.40 SOURCE2 1 0.0000 0.0000 +ho-p5-os 7.9 102.31 SOURCE0 1 +hp-p5-hp 21.4 101.09 SOURCE3 4 1.1290 1.3036 +hp-p5-o 30.2 116.58 SOURCE3 7 1.0523 1.3282 +hp-p5-oh 30.6 101.45 SOURCE3 5 0.7264 0.9084 +hp-p5-s 26.0 119.20 SOURCE2 1 0.0000 0.0000 +i -p5-i 35.9 107.17 SOURCE3 1 0.0000 0.0000 +i -p5-o 33.0 115.93 SOURCE3 3 0.0392 0.0415 +i -p5-oh 35.4 102.26 SOURCE3 4 1.9577 1.9577 +n -p5-n 41.7 103.09 SOURCE3 1 0.0000 0.0000 +n -p5-o 42.1 115.26 SOURCE3 4 1.4228 1.6532 +n -p5-oh 43.1 102.44 SOURCE3 4 0.0999 0.0999 +n -p5-os 43.8 100.48 SOURCE3 2 0.0000 0.0000 +n2-p5-n2 44.0 106.34 SOURCE0 1 +n2-p5-o 44.3 113.53 SOURCE0 1 +n2-p5-oh 44.7 102.40 SOURCE0 1 +n3-p5-n3 43.8 99.11 SOURCE3 1 0.0000 0.0000 +n3-p5-o 43.2 113.54 SOURCE3 7 5.0248 5.6747 +n3-p5-oh 43.4 104.18 SOURCE3 6 0.4123 0.4373 +n3-p5-os 44.9 98.88 SOURCE3 2 0.0000 0.0000 +n4-p5-n4 39.2 102.20 SOURCE3 1 0.0000 0.0000 +n4-p5-o 41.1 109.78 SOURCE3 5 2.6856 2.7519 +n4-p5-oh 42.2 98.48 SOURCE3 6 0.3869 0.4104 +n4-p5-os 43.3 94.55 SOURCE3 2 0.0000 0.0000 +na-p5-na 40.6 108.57 SOURCE3 1 0.0000 0.0000 +na-p5-o 42.4 113.43 SOURCE3 11 0.7963 0.8968 +na-p5-oh 43.1 102.07 SOURCE3 16 1.2552 1.4144 +na-p5-os 43.2 103.06 SOURCE3 4 0.7463 0.7463 +nh-p5-nh 43.5 99.51 SOURCE3 1 0.0000 0.0000 +nh-p5-o 42.1 118.91 SOURCE3 3 1.2480 1.3237 +nh-p5-oh 43.4 103.81 SOURCE3 2 0.0000 0.0000 +nh-p5-os 44.4 100.51 SOURCE3 2 0.0000 0.0000 +no-p5-no 40.4 95.68 SOURCE3 1 0.0000 0.0000 +no-p5-o 40.5 112.75 SOURCE3 4 3.3675 3.3684 +no-p5-oh 41.6 101.35 SOURCE3 2 0.0000 0.0000 +no-p5-os 41.7 101.70 SOURCE3 4 0.0565 0.0565 +o -p5-o 46.0 115.80 SOURCE3 17 4.6921 5.7902 +o -p5-oh 43.8 115.03 SOURCE3 86 3.5330 4.9414 +o -p5-os 44.0 116.09 SOURCE3 35 2.3321 3.2062 +o -p5-p2 46.2 114.60 SOURCE0 1 +o -p5-p3 45.4 115.48 SOURCE3 9 1.7451 2.1084 +o -p5-p4 45.1 114.66 SOURCE0 1 +o -p5-p5 49.1 113.44 SOURCE0 1 +o -p5-s 40.5 116.94 SOURCE3 3 2.7818 2.9506 +o -p5-s4 39.6 110.23 SOURCE0 1 +o -p5-s6 39.3 111.75 SOURCE0 1 +o -p5-sh 38.1 114.56 SOURCE3 3 1.6636 1.7645 +o -p5-ss 38.0 112.46 SOURCE3 6 2.2289 2.7392 +oh-p5-oh 44.6 102.45 SOURCE3 39 1.8849 2.4223 +oh-p5-os 44.9 102.37 SOURCE3 8 1.0873 1.5063 +oh-p5-p2 48.2 103.53 SOURCE0 1 +oh-p5-p3 47.5 103.83 SOURCE3 13 0.4174 0.4303 +oh-p5-p4 47.6 101.79 SOURCE0 1 +oh-p5-p5 51.4 100.45 SOURCE0 1 +oh-p5-s 42.2 102.88 SOURCE3 3 1.5127 1.6044 +oh-p5-s4 40.3 103.24 SOURCE0 1 +oh-p5-s6 40.7 101.48 SOURCE0 1 +oh-p5-sh 40.0 101.41 SOURCE3 2 0.0000 0.0000 +oh-p5-ss 39.0 104.33 SOURCE3 6 1.8962 2.0112 +os-p5-os 45.2 102.46 SOURCE3 16 2.7156 3.4477 +os-p5-p3 47.7 103.67 SOURCE3 2 0.0000 0.0000 +os-p5-p5 50.6 104.48 SOURCE0 1 +os-p5-s4 40.6 102.52 SOURCE0 1 +os-p5-s6 40.7 101.89 SOURCE0 1 +os-p5-sh 39.5 104.59 SOURCE3 2 0.0000 0.0000 +os-p5-ss 39.9 100.24 SOURCE3 3 5.9143 6.2730 +p2-p5-p2 57.4 107.14 SOURCE0 1 +p3-p5-p3 57.0 105.23 SOURCE3 3 4.8106 5.1024 +p4-p5-p4 57.4 101.62 SOURCE0 1 +p5-p5-p5 59.4 112.72 SOURCE0 1 +s -p5-s 39.4 114.13 SOURCE3 1 0.0000 0.0000 +s6-p5-s6 38.6 105.18 SOURCE0 1 +sh-p5-sh 38.0 104.56 SOURCE3 1 0.0000 0.0000 +sh-p5-ss 37.3 107.13 SOURCE0 1 +ss-p5-ss 36.6 109.61 SOURCE3 1 0.0000 0.0000 +cd-pc-n 42.8 90.80 SOURCE3 3 2.2084 2.3423 +cc-pd-n 42.8 90.80 SOURCE3 3 same as cd-pc-n +cd-pc-na 43.0 90.18 SOURCE3 81 2.4347 2.7619 +cc-pd-na 43.0 90.18 SOURCE3 81 same as cd-pc-na +c -pe-c2 38.6 97.30 SOURCE3 3 0.0316 0.0335 +c -pf-c2 38.6 97.30 SOURCE3 3 same as c -pe-c2 +c2-pe-ca 38.8 101.44 SOURCE3 3 0.6764 0.7177 +c2-pf-ca 38.8 101.44 SOURCE3 3 same as c2-pe-ca +c2-pe-ce 38.7 103.01 SOURCE3 4 1.4470 1.4470 +c2-pf-cf 38.7 103.01 SOURCE3 4 same as c2-pe-ce +c2-pe-cg 40.8 104.03 SOURCE3 3 3.6524 3.8740 +c2-pf-ch 40.8 104.03 SOURCE3 3 same as c2-pe-cg +c2-pe-n2 44.9 94.14 SOURCE0 1 +c2-pf-n2 44.9 94.14 SOURCE0 1 same as c2-pe-n2 +c2-pe-ne 41.8 98.70 SOURCE3 12 3.8876 5.3383 +c2-pf-nf 41.8 98.70 SOURCE3 12 same as c2-pe-ne +c2-pe-o 41.1 115.16 SOURCE3 2 0.0149 0.0149 +c2-pf-o 41.1 115.16 SOURCE3 2 same as c2-pe-o +c2-pe-p2 50.9 107.82 SOURCE0 1 +c2-pf-p2 50.9 107.82 SOURCE0 1 same as c2-pe-p2 +c2-pe-pe 48.2 102.99 SOURCE3 9 7.0590 8.2860 +c2-pf-pf 48.2 102.99 SOURCE3 9 same as c2-pe-pe +c2-pe-px 51.1 97.37 SOURCE3 4 0.5674 0.6655 +c2-pf-px 51.1 97.37 SOURCE3 4 same as c2-pe-px +c2-pe-py 50.9 96.71 SOURCE3 4 0.9336 1.2755 +c2-pf-py 50.9 96.71 SOURCE3 4 same as c2-pe-py +c2-pe-s 41.1 111.16 SOURCE3 2 0.0000 0.0000 +c2-pf-s 41.1 111.16 SOURCE3 2 same as c2-pe-s +c2-pe-sx 38.5 95.11 SOURCE3 4 0.2597 0.2676 +c2-pf-sx 38.5 95.11 SOURCE3 4 same as c2-pe-sx +c2-pe-sy 37.8 95.56 SOURCE3 2 0.0462 0.0462 +c2-pf-sy 37.8 95.56 SOURCE3 2 same as c2-pe-sy +ca-pe-n2 41.0 102.03 SOURCE3 1 0.0000 0.0000 +ca-pf-n2 41.0 102.03 SOURCE3 1 same as ca-pe-n2 +ca-pe-o 40.4 106.88 SOURCE3 2 0.0018 0.0018 +ca-pf-o 40.4 106.88 SOURCE3 2 same as ca-pe-o +ca-pe-p2 51.0 100.79 SOURCE3 1 0.0000 0.0000 +ca-pf-p2 51.0 100.79 SOURCE3 1 same as ca-pe-p2 +ca-pe-pf 48.4 99.70 SOURCE3 2 0.0000 0.0000 +ca-pf-pe 48.4 99.70 SOURCE3 2 0.0000 0.0000 +ca-pe-s 40.1 107.93 SOURCE3 1 0.0000 0.0000 +ca-pf-s 40.1 107.93 SOURCE3 1 same as ca-pe-s +ce-pe-n2 41.4 100.55 SOURCE3 1 0.0000 0.0000 +cf-pf-n2 41.4 100.55 SOURCE3 1 same as ce-pe-n2 +ce-pe-o 40.5 107.44 SOURCE3 1 0.0000 0.0000 +cf-pf-o 40.5 107.44 SOURCE3 1 same as ce-pe-o +ce-pe-p2 51.4 99.56 SOURCE3 1 0.0000 0.0000 +cf-pf-p2 51.4 99.56 SOURCE3 1 same as ce-pe-p2 +ce-pe-s 40.7 105.54 SOURCE3 1 0.0000 0.0000 +cf-pf-s 40.7 105.54 SOURCE3 1 same as ce-pe-s +cg-pe-n2 44.3 101.79 SOURCE3 1 0.0000 0.0000 +ch-pf-n2 44.3 101.79 SOURCE3 1 same as cg-pe-n2 +cg-pe-o 43.6 107.62 SOURCE3 1 0.0000 0.0000 +ch-pf-o 43.6 107.62 SOURCE3 1 same as cg-pe-o +cg-pe-p2 52.5 104.68 SOURCE3 2 5.1435 5.1435 +ch-pf-p2 52.5 104.68 SOURCE3 2 same as cg-pe-p2 +cg-pe-s 42.3 108.60 SOURCE3 4 2.6981 2.6981 +ch-pf-s 42.3 108.60 SOURCE3 4 same as cg-pe-s +n2-pe-n2 45.3 108.14 SOURCE0 1 +n2-pf-n2 45.3 108.14 SOURCE0 1 same as n2-pe-n2 +n2-pe-ne 42.9 106.80 SOURCE3 6 3.8963 4.5981 +n2-pf-nf 42.9 106.80 SOURCE3 6 same as n2-pe-ne +n2-pe-o 44.3 115.39 SOURCE3 1 0.0000 0.0000 +n2-pf-o 44.3 115.39 SOURCE3 1 same as n2-pe-o +n2-pe-p2 52.9 111.60 SOURCE0 1 +n2-pf-p2 52.9 111.60 SOURCE0 1 same as n2-pe-p2 +n2-pe-pe 48.7 109.40 SOURCE3 1 0.0000 0.0000 +n2-pf-pf 48.7 109.40 SOURCE3 1 same as n2-pe-pe +n2-pe-px 50.3 110.30 SOURCE3 3 5.7085 6.0548 +n2-pf-px 50.3 110.30 SOURCE3 3 same as n2-pe-px +n2-pe-py 54.1 93.68 SOURCE3 1 0.0000 0.0000 +n2-pf-py 54.1 93.68 SOURCE3 1 same as n2-pe-py +n2-pe-s 42.9 114.84 SOURCE3 3 3.4424 3.6512 +n2-pf-s 42.9 114.84 SOURCE3 3 same as n2-pe-s +n2-pe-sx 39.4 97.83 SOURCE3 1 0.0000 0.0000 +n2-pf-sx 39.4 97.83 SOURCE3 1 same as n2-pe-sx +n2-pe-sy 38.6 98.14 SOURCE3 1 0.0000 0.0000 +n2-pf-sy 38.6 98.14 SOURCE3 1 same as n2-pe-sy +ne-pe-o 42.7 110.24 SOURCE3 3 3.3676 3.8478 +nf-pf-o 42.7 110.24 SOURCE3 3 same as ne-pe-o +ne-pe-p2 52.8 104.48 SOURCE3 2 7.1207 7.1207 +nf-pf-p2 52.8 104.48 SOURCE3 2 same as ne-pe-p2 +ne-pe-s 42.2 109.19 SOURCE3 5 2.9509 3.6708 +nf-pf-s 42.2 109.19 SOURCE3 5 same as ne-pe-s +o -pe-o 44.0 119.96 SOURCE3 1 0.0000 0.0000 +o -pf-o 44.0 119.96 SOURCE3 1 same as o -pe-o +o -pe-p2 52.7 114.23 SOURCE3 1 0.0000 0.0000 +o -pf-p2 52.7 114.23 SOURCE3 1 same as o -pe-p2 +o -pe-pe 42.5 145.96 SOURCE3 1 0.0000 0.0000 +o -pf-pf 42.5 145.96 SOURCE3 1 same as o -pe-pe +o -pe-px 52.1 104.37 SOURCE3 1 0.0000 0.0000 +o -pf-px 52.1 104.37 SOURCE3 1 same as o -pe-px +o -pe-py 51.6 104.49 SOURCE3 1 0.0000 0.0000 +o -pf-py 51.6 104.49 SOURCE3 1 same as o -pe-py +o -pe-s 42.9 117.42 SOURCE3 2 0.0426 0.0426 +o -pf-s 42.9 117.42 SOURCE3 2 same as o -pe-s +o -pe-sx 38.0 106.59 SOURCE3 1 0.0000 0.0000 +o -pf-sx 38.0 106.59 SOURCE3 1 same as o -pe-sx +o -pe-sy 37.6 105.04 SOURCE3 1 0.0000 0.0000 +o -pf-sy 37.6 105.04 SOURCE3 1 same as o -pe-sy +p2-pe-pe 65.6 98.24 SOURCE3 1 0.0000 0.0000 +p2-pf-pf 65.6 98.24 SOURCE3 1 same as p2-pe-pe +p2-pe-px 64.1 108.28 SOURCE3 2 6.2959 6.2959 +p2-pf-px 64.1 108.28 SOURCE3 2 same as p2-pe-px +p2-pe-py 63.0 110.87 SOURCE3 3 7.6976 8.1645 +p2-pf-py 63.0 110.87 SOURCE3 3 same as p2-pe-py +p2-pe-s 53.4 111.28 SOURCE3 1 0.0000 0.0000 +p2-pf-s 53.4 111.28 SOURCE3 1 same as p2-pe-s +p2-pe-sx 51.3 95.73 SOURCE3 1 0.0000 0.0000 +p2-pf-sx 51.3 95.73 SOURCE3 1 same as p2-pe-sx +p2-pe-sy 50.5 95.95 SOURCE3 1 0.0000 0.0000 +p2-pf-sy 50.5 95.95 SOURCE3 1 same as p2-pe-sy +pe-pe-s 50.4 107.91 SOURCE3 2 1.5577 1.5577 +pf-pf-s 50.4 107.91 SOURCE3 2 same as pe-pe-s +px-pe-s 52.0 107.62 SOURCE3 2 3.7266 3.7266 +px-pf-s 52.0 107.62 SOURCE3 2 same as px-pe-s +py-pe-s 51.4 108.73 SOURCE3 3 5.0158 5.3201 +py-pf-s 51.4 108.73 SOURCE3 3 same as py-pe-s +s -pe-s 34.4 178.44 SOURCE3 1 0.0000 0.0000 +s -pf-s 34.4 178.44 SOURCE3 1 same as s -pe-s +s -pe-sx 38.7 108.32 SOURCE3 2 3.0318 3.0318 +s -pf-sx 38.7 108.32 SOURCE3 2 same as s -pe-sx +s -pe-sy 38.4 106.93 SOURCE3 1 0.0000 0.0000 +s -pf-sy 38.4 106.93 SOURCE3 1 same as s -pe-sy +c -px-c3 36.7 101.72 SOURCE3 1 0.0000 0.0000 +c -px-o 38.0 114.47 SOURCE3 1 0.0000 0.0000 +c3-px-ca 37.0 104.79 SOURCE3 1 0.0000 0.0000 +c3-px-ce 37.0 104.86 SOURCE3 4 0.5282 0.6354 +c3-px-cf 37.0 104.86 SOURCE3 4 same as c3-px-ce +c3-px-ne 39.5 102.46 SOURCE3 7 1.2108 1.8685 +c3-px-nf 39.5 102.46 SOURCE3 7 same as c3-px-ne +c3-px-o 39.4 113.68 SOURCE3 28 3.8637 4.8990 +c3-px-pe 47.8 105.73 SOURCE3 10 3.6317 4.4059 +c3-px-pf 47.8 105.73 SOURCE3 10 same as c3-px-pe +c3-px-py 45.5 103.11 SOURCE3 3 0.8183 0.8680 +c3-px-sx 36.1 99.55 SOURCE3 1 0.0000 0.0000 +c3-px-sy 35.3 103.41 SOURCE3 1 0.0000 0.0000 +ca-px-ca 37.1 104.15 SOURCE3 2 3.6168 3.6168 +ca-px-o 40.5 107.50 SOURCE3 5 5.5918 5.7355 +ce-px-ce 37.1 104.21 SOURCE3 1 0.0000 0.0000 +cf-px-cf 37.1 104.21 SOURCE3 1 same as ce-px-ce +ce-px-o 39.4 113.79 SOURCE3 6 0.3605 0.3877 +cf-px-o 39.4 113.79 SOURCE3 6 same as ce-px-o +ne-px-ne 41.9 103.22 SOURCE3 2 0.6807 0.6807 +nf-px-nf 41.9 103.22 SOURCE3 2 same as ne-px-ne +ne-px-o 42.3 114.13 SOURCE3 11 6.5928 8.9737 +nf-px-o 42.3 114.13 SOURCE3 11 same as ne-px-o +o -px-pe 49.4 116.50 SOURCE3 12 5.9082 8.2925 +o -px-pf 49.4 116.50 SOURCE3 12 same as o -px-pe +o -px-py 45.9 114.20 SOURCE3 5 1.2921 1.7165 +o -px-sx 35.8 112.81 SOURCE3 3 0.8296 0.8799 +o -px-sy 35.6 113.54 SOURCE3 3 0.4723 0.5010 +pe-px-pe 61.4 110.71 SOURCE3 1 0.0000 0.0000 +pf-px-pf 61.4 110.71 SOURCE3 1 same as pe-px-pe +py-px-py 56.7 107.78 SOURCE3 1 0.0000 0.0000 +sx-px-sx 36.8 96.24 SOURCE3 1 0.0000 0.0000 +sy-px-sy 35.5 102.36 SOURCE3 1 0.0000 0.0000 +c -py-c 36.2 104.20 SOURCE3 1 0.0000 0.0000 +c -py-c3 35.7 110.36 SOURCE3 1 0.0000 0.0000 +c -py-o 38.5 115.25 SOURCE3 6 1.8195 2.6519 +c -py-oh 40.0 102.14 SOURCE3 6 1.0044 1.0654 +c -py-os 41.3 95.74 SOURCE3 3 8.5794 9.0999 +c3-py-n4 37.3 103.83 SOURCE3 4 0.0000 0.0000 +c3-py-na 38.8 106.89 SOURCE3 2 0.0000 0.0000 +c3-py-o 38.9 117.87 SOURCE3 13 2.2138 2.3554 +c3-py-oh 41.2 100.16 SOURCE3 2 0.0000 0.0000 +c3-py-os 40.2 105.39 SOURCE3 1 0.0000 0.0000 +c3-py-px 44.9 106.27 SOURCE3 2 0.0000 0.0000 +c3-py-py 43.5 113.97 SOURCE3 10 1.4783 1.6346 +c3-py-sx 34.7 106.36 SOURCE3 4 0.0000 0.0000 +ca-py-ca 37.0 107.55 SOURCE3 1 0.0000 0.0000 +ca-py-o 39.8 113.98 SOURCE3 3 0.5006 0.5309 +ca-py-oh 41.1 101.78 SOURCE3 2 0.0000 0.0000 +ca-py-os 40.7 103.75 SOURCE3 2 0.0000 0.0000 +ce-py-ce 37.3 106.54 SOURCE3 1 0.0000 0.0000 +cf-py-cf 37.3 106.54 SOURCE3 1 same as ce-py-ce +ce-py-o 40.2 112.16 SOURCE3 5 3.1814 3.2594 +cf-py-o 40.2 112.16 SOURCE3 5 same as ce-py-o +ce-py-oh 40.6 104.77 SOURCE3 6 2.0602 2.1852 +cf-py-oh 40.6 104.77 SOURCE3 6 same as ce-py-oh +ce-py-os 40.8 103.34 SOURCE3 2 0.0000 0.0000 +cf-py-os 40.8 103.34 SOURCE3 2 same as ce-py-os +n4-py-o 38.8 115.58 SOURCE3 4 0.0000 0.0000 +n4-py-py 63.2 55.10 SOURCE3 4 0.0000 0.0000 +na-py-o 40.8 122.40 SOURCE3 2 0.0000 0.0000 +na-py-py 67.7 50.88 SOURCE3 2 0.0000 0.0000 +ne-py-ne 40.9 106.29 SOURCE3 1 0.0000 0.0000 +nf-py-nf 40.9 106.29 SOURCE3 1 same as ne-py-ne +ne-py-o 42.3 113.21 SOURCE3 15 3.5046 3.8894 +nf-py-o 42.3 113.21 SOURCE3 15 same as ne-py-o +ne-py-oh 42.6 104.70 SOURCE3 26 2.5109 2.7513 +nf-py-oh 42.6 104.70 SOURCE3 26 same as ne-py-oh +ne-py-os 43.3 101.33 SOURCE3 2 0.0000 0.0000 +nf-py-os 43.3 101.33 SOURCE3 2 same as ne-py-os +o -py-oh 43.7 116.14 SOURCE3 79 1.6546 2.1455 +o -py-os 43.6 116.79 SOURCE3 17 1.1002 1.3534 +o -py-pe 49.5 114.56 SOURCE3 12 2.8971 3.6114 +o -py-pf 49.5 114.56 SOURCE3 12 same as o -py-pe +o -py-px 46.5 111.37 SOURCE3 5 0.3464 0.3803 +o -py-py 45.0 120.43 SOURCE3 16 5.2423 6.0629 +o -py-sx 34.7 118.56 SOURCE3 7 6.2302 6.2976 +o -py-sy 37.0 111.71 SOURCE3 5 1.0701 1.1937 +oh-py-oh 45.1 101.78 SOURCE3 35 1.6164 2.2937 +oh-py-pe 51.0 104.84 SOURCE3 22 1.8517 2.0337 +oh-py-pf 51.0 104.84 SOURCE3 22 same as oh-py-pe +oh-py-px 47.7 104.30 SOURCE3 8 1.0656 1.2772 +oh-py-py 48.9 100.45 SOURCE3 6 0.0000 0.0000 +oh-py-sx 37.4 100.94 SOURCE3 4 0.0000 0.0000 +oh-py-sy 38.5 101.47 SOURCE3 6 0.2348 0.2490 +os-py-os 45.1 101.25 SOURCE3 8 1.4909 2.0860 +os-py-py 47.9 104.48 SOURCE3 4 0.0000 0.0000 +os-py-sx 36.9 103.86 SOURCE3 2 0.0000 0.0000 +os-py-sy 38.4 102.12 SOURCE3 2 0.0000 0.0000 +pe-py-pe 61.8 107.14 SOURCE3 1 0.0000 0.0000 +pf-py-pf 61.8 107.14 SOURCE3 1 same as pe-py-pe +py-py-py 55.8 112.70 SOURCE3 1 0.0000 0.0000 +py-py-sx 58.7 61.54 SOURCE3 4 0.0000 0.0000 +sy-py-sy 36.1 105.17 SOURCE3 1 0.0000 0.0000 +c1-s2-o 65.8 117.25 SOURCE3 1 0.0000 0.0000 +c2-s2-n2 68.7 110.84 SOURCE3 1 0.0000 0.0000 +c2-s2-o 66.2 114.70 SOURCE2 1 0.0000 0.0000 +cl-s2-n1 53.4 117.70 SOURCE2 1 0.0000 0.0000 +f -s2-n1 66.1 116.90 SOURCE2 1 0.0000 0.0000 +n2-s2-o 67.9 121.20 SOURCE2 2 0.8000 0.8000 +o -s2-o 68.0 116.17 SOURCE3 1 0.0000 0.0000 +o -s2-s 63.8 118.30 SOURCE2 1 0.0000 0.0000 +s -s2-s 63.5 115.04 SOURCE3 1 0.0000 0.0000 +br-s4-br 64.6 98.02 SOURCE0 1 +br-s4-c3 62.2 92.98 SOURCE3 1 0.0000 0.0000 +br-s4-o 59.2 112.07 SOURCE3 1 0.0000 0.0000 +c -s4-c 63.3 86.83 SOURCE0 1 +c -s4-c3 61.5 95.07 SOURCE0 1 +c -s4-o 64.0 106.17 SOURCE0 1 +c1-s4-c1 65.4 93.55 SOURCE3 1 0.0000 0.0000 +c1-s4-o 66.0 110.36 SOURCE3 2 0.0000 0.0000 +c2-s4-c2 62.0 102.29 SOURCE0 1 +c2-s4-c3 63.5 94.95 SOURCE0 1 +c2-s4-o 66.6 107.09 SOURCE0 1 +c3-s4-c3 62.1 96.82 SOURCE3 11 1.3798 1.5580 +c3-s4-ca 63.0 95.00 SOURCE0 1 +c3-s4-f 66.3 91.70 SOURCE3 1 0.0000 0.0000 +c3-s4-hs 46.5 90.60 SOURCE3 1 0.0000 0.0000 +c3-s4-i 52.9 90.53 SOURCE3 1 0.0000 0.0000 +c3-s4-n 64.3 96.07 SOURCE3 4 0.8172 1.0354 +c3-s4-n2 69.1 90.59 SOURCE0 1 +c3-s4-n3 65.2 94.49 SOURCE3 4 1.5239 1.5570 +c3-s4-n4 62.0 92.47 SOURCE3 1 0.0000 0.0000 +c3-s4-na 65.1 93.07 SOURCE3 10 1.5730 1.8813 +c3-s4-nh 64.5 97.08 SOURCE3 1 0.0000 0.0000 +c3-s4-no 62.5 89.53 SOURCE3 1 0.0000 0.0000 +c3-s4-o 65.6 106.21 SOURCE3 60 1.3147 2.0426 +c3-s4-oh 67.3 93.88 SOURCE3 1 0.0000 0.0000 +c3-s4-os 68.2 90.06 SOURCE3 4 0.3752 0.4484 +c3-s4-p2 76.4 94.37 SOURCE0 1 +c3-s4-p3 78.2 96.54 SOURCE3 4 1.1521 1.3634 +c3-s4-p4 73.7 97.40 SOURCE0 1 +c3-s4-p5 78.3 99.18 SOURCE0 1 +c3-s4-s 61.3 98.72 SOURCE3 2 0.0185 0.0185 +c3-s4-s4 64.3 89.50 SOURCE0 1 +c3-s4-s6 61.6 97.48 SOURCE0 1 +c3-s4-sh 60.7 94.66 SOURCE3 1 0.0000 0.0000 +c3-s4-ss 60.6 95.31 SOURCE3 3 1.3294 1.4101 +ca-s4-ca 63.3 95.21 SOURCE0 1 +ca-s4-o 66.0 106.63 SOURCE0 1 +cl-s4-cl 53.9 97.68 SOURCE3 1 0.0000 0.0000 +cl-s4-o 58.1 108.34 SOURCE3 2 0.0000 0.0000 +cx-s4-cx 86.7 48.80 SOURCE2 1 0.0000 0.0000 +cx-s4-o 64.1 110.00 SOURCE2 1 0.0000 0.0000 +f -s4-f 70.0 92.71 SOURCE2 3 0.1400 0.1490 +f -s4-o 70.1 106.81 SOURCE2 2 0.0100 0.0100 +f -s4-s 59.8 107.50 SOURCE2 1 0.0000 0.0000 +hn-s4-hs 10.2 86.99 SOURCE0 1 +hs-s4-hs 37.8 87.00 SOURCE3 2 0.0202 0.0202 +hs-s4-o 49.8 110.27 SOURCE3 5 0.1523 0.1908 +i -s4-i 54.4 97.29 SOURCE0 1 +i -s4-o 47.3 113.91 SOURCE3 1 0.0000 0.0000 +n -s4-n 68.0 91.30 SOURCE0 1 +n -s4-o 68.1 105.70 SOURCE3 4 1.5958 1.6857 +n2-s4-n2 75.8 90.17 SOURCE0 1 +n2-s4-o 72.1 107.57 SOURCE0 1 +n3-s4-n3 68.9 91.19 SOURCE3 1 0.0000 0.0000 +n3-s4-o 67.6 109.07 SOURCE3 6 1.7576 2.3605 +n4-s4-n4 60.4 94.61 SOURCE3 1 0.0000 0.0000 +n4-s4-o 63.2 104.91 SOURCE3 3 0.4120 0.4370 +na-s4-na 63.6 103.10 SOURCE0 1 +na-s4-o 66.5 109.75 SOURCE3 10 2.2612 2.6919 +nh-s4-nh 69.0 92.24 SOURCE3 1 0.0000 0.0000 +nh-s4-o 68.4 107.54 SOURCE3 3 0.0378 0.0401 +no-s4-no 63.6 83.40 SOURCE3 1 0.0000 0.0000 +no-s4-o 62.9 103.58 SOURCE3 3 1.4245 1.5109 +o -s4-o 74.4 110.61 SOURCE3 5 3.5677 3.6413 +o -s4-oh 71.3 106.38 SOURCE3 3 0.9318 0.9883 +o -s4-os 69.7 109.02 SOURCE3 8 1.3833 1.5005 +o -s4-p2 76.2 106.77 SOURCE0 1 +o -s4-p3 79.8 106.51 SOURCE3 8 2.6099 4.0943 +o -s4-p4 75.4 103.36 SOURCE0 1 +o -s4-p5 85.3 96.95 SOURCE0 1 +o -s4-s 61.7 112.22 SOURCE3 4 2.8682 2.8682 +o -s4-s4 63.8 104.55 SOURCE0 1 +o -s4-s6 64.3 102.84 SOURCE0 1 +o -s4-sh 60.6 107.51 SOURCE3 3 0.7081 0.7511 +o -s4-ss 60.1 109.49 SOURCE3 5 1.4035 1.8509 +oh-s4-oh 70.1 100.34 SOURCE0 1 +os-s4-os 71.3 93.68 SOURCE3 2 2.4166 2.4166 +p2-s4-p2 98.2 92.62 SOURCE0 1 +p3-s4-p3 101.4 95.71 SOURCE3 2 1.2239 1.2239 +p5-s4-p5 104.7 93.86 SOURCE0 1 +s -s4-s 59.9 108.08 SOURCE3 1 0.0000 0.0000 +s4-s4-s4 65.4 90.17 SOURCE0 1 +s4-s4-s6 65.4 90.17 SOURCE0 1 +s6-s4-s6 64.2 93.52 SOURCE0 1 +sh-s4-sh 58.8 102.76 SOURCE3 1 0.0000 0.0000 +sh-s4-ss 58.9 102.64 SOURCE0 1 +ss-s4-ss 61.1 95.47 SOURCE3 1 0.0000 0.0000 +br-s6-br 67.1 101.57 SOURCE3 1 0.0000 0.0000 +br-s6-c3 63.2 98.99 SOURCE3 1 0.0000 0.0000 +br-s6-f 63.1 100.60 SOURCE2 1 0.0000 0.0000 +br-s6-o 63.9 107.58 SOURCE3 6 0.2828 0.3000 +c -s6-c 59.1 99.82 SOURCE0 1 +c -s6-c3 60.1 101.24 SOURCE0 1 +c -s6-o 64.0 107.97 SOURCE0 1 +c -s6-os 64.4 102.12 SOURCE0 1 +c1-s6-c1 64.1 99.99 SOURCE3 1 0.0000 0.0000 +c1-s6-o 68.1 108.23 SOURCE3 4 0.0000 0.0000 +c2-s6-c2 61.9 102.75 SOURCE0 1 +c2-s6-c3 61.2 104.05 SOURCE0 1 +c2-s6-o 67.5 106.58 SOURCE0 1 +c3-s6-c3 61.4 102.83 SOURCE3 7 1.1315 1.2531 +c3-s6-ca 61.5 103.17 SOURCE0 1 +c3-s6-f 65.7 97.11 SOURCE3 1 0.0000 0.0000 +c3-s6-hs 44.9 100.62 SOURCE3 1 0.0000 0.0000 +c3-s6-i 50.8 97.74 SOURCE3 1 0.0000 0.0000 +c3-s6-n 63.5 102.97 SOURCE3 4 0.8504 0.8785 +c3-s6-n2 65.3 107.47 SOURCE3 3 0.1592 0.1689 +c3-s6-n3 65.2 102.92 SOURCE3 3 0.8719 0.9248 +c3-s6-n4 61.3 99.40 SOURCE3 3 0.4426 0.4695 +c3-s6-na 63.7 102.81 SOURCE3 10 2.6278 3.1256 +c3-s6-nh 64.8 101.13 SOURCE3 1 0.0000 0.0000 +c3-s6-no 60.1 99.57 SOURCE3 1 0.0000 0.0000 +c3-s6-o 66.6 108.32 SOURCE3 112 1.2779 1.8014 +c3-s6-oh 68.6 95.95 SOURCE3 1 0.0000 0.0000 +c3-s6-os 68.9 95.65 SOURCE3 4 1.0005 1.0632 +c3-s6-p2 72.5 106.47 SOURCE0 1 +c3-s6-p3 76.2 103.40 SOURCE3 3 0.8029 0.8516 +c3-s6-p4 71.1 104.12 SOURCE0 1 +c3-s6-p5 77.2 103.46 SOURCE0 1 +c3-s6-s 60.7 104.50 SOURCE3 1 0.0000 0.0000 +c3-s6-s4 61.8 98.10 SOURCE0 1 +c3-s6-s6 60.6 101.95 SOURCE0 1 +c3-s6-sh 60.1 101.84 SOURCE3 1 0.0000 0.0000 +c3-s6-ss 59.7 102.47 SOURCE3 3 1.6453 1.7451 +ca-s6-ca 61.8 103.08 SOURCE0 1 +ca-s6-o 67.3 107.49 SOURCE0 1 +cl-s6-cl 52.9 101.25 SOURCE3 1 0.0000 0.0000 +cl-s6-f 57.9 99.00 SOURCE2 1 0.0000 0.0000 +cl-s6-o 58.5 107.66 SOURCE3 4 0.0000 0.0000 +cx-s6-cx 86.2 54.70 SOURCE2 1 0.0000 0.0000 +f -s6-f 70.8 94.70 SOURCE2 3 0.9333 0.9899 +f -s6-o 72.4 106.48 SOURCE3 2 0.0000 0.0000 +hs-s6-hs 35.8 99.02 SOURCE3 2 0.0595 0.0595 +hs-s6-o 51.9 107.60 SOURCE3 10 0.0263 0.0343 +i -s6-i 53.9 99.25 SOURCE0 1 +i -s6-o 47.7 109.74 SOURCE3 2 0.0000 0.0000 +n -s6-n 65.5 104.16 SOURCE0 1 +n -s6-o 70.2 105.91 SOURCE3 8 0.2938 0.2953 +n2-s6-n2 76.1 98.61 SOURCE0 1 +n2-s6-o 72.6 116.41 SOURCE3 3 4.7923 5.0830 +n2-s6-oh 72.1 106.96 SOURCE3 2 0.0000 0.0000 +n2-s6-os 73.7 103.25 SOURCE0 1 +n3-s6-n3 69.5 104.28 SOURCE3 2 6.7537 6.7537 +n3-s6-o 72.9 106.80 SOURCE3 14 1.7070 1.7908 +n4-s6-n4 60.0 101.85 SOURCE3 1 0.0000 0.0000 +n4-s6-o 65.8 102.92 SOURCE3 10 1.5005 1.5434 +na-s6-na 67.7 98.04 SOURCE0 1 +na-s6-o 70.5 105.67 SOURCE3 20 0.6876 0.8019 +nh-s6-nh 70.4 94.56 SOURCE3 1 0.0000 0.0000 +nh-s6-o 70.3 109.12 SOURCE3 6 0.9009 0.9556 +no-s6-no 61.2 91.63 SOURCE3 1 0.0000 0.0000 +no-s6-o 62.7 107.43 SOURCE3 6 1.4608 1.5494 +o -s6-o 74.6 119.82 SOURCE3 84 4.1358 5.2345 +o -s6-oh 74.1 108.21 SOURCE3 18 0.5949 0.7437 +o -s6-os 74.6 107.84 SOURCE3 12 0.6328 0.7025 +o -s6-p2 76.6 106.61 SOURCE0 1 +o -s6-p3 80.2 107.07 SOURCE3 22 1.0007 1.0550 +o -s6-p4 73.9 105.67 SOURCE0 1 +o -s6-p5 81.7 106.64 SOURCE0 1 +o -s6-s 63.5 110.29 SOURCE3 6 2.1124 2.2405 +o -s6-s4 63.0 107.85 SOURCE0 1 +o -s6-s6 63.6 106.07 SOURCE0 1 +o -s6-sh 62.5 106.81 SOURCE3 6 0.5932 0.6292 +o -s6-ss 62.1 107.43 SOURCE3 10 1.0654 1.1423 +oh-s6-p2 75.1 109.67 SOURCE3 2 0.0000 0.0000 +oh-s6-oh 73.7 100.34 SOURCE3 6 0.0076 0.0076 +os-s6-os 74.8 98.70 SOURCE3 1 0.0000 0.0000 +p3-s6-p3 94.9 110.17 SOURCE3 4 5.3595 5.3678 +p5-s6-p5 99.2 104.49 SOURCE0 1 +s -s6-s 60.6 109.34 SOURCE3 1 0.0000 0.0000 +s4-s6-s4 61.5 101.99 SOURCE0 1 +s4-s6-s6 65.4 90.17 SOURCE0 1 +s6-s6-s6 61.1 103.29 SOURCE0 1 +sh-s6-sh 59.4 106.43 SOURCE3 1 0.0000 0.0000 +sh-s6-ss 60.4 102.64 SOURCE0 1 +ss-s6-ss 60.5 101.82 SOURCE3 1 0.0000 0.0000 +br-sh-hs 43.5 95.64 SOURCE3 1 0.0000 0.0000 +c -sh-hs 46.0 96.07 SOURCE3 6 0.9968 1.1164 +c2-sh-hs 46.2 95.94 SOURCE3 3 0.3373 0.3578 +c3-sh-hs 44.9 96.60 SOURCE3 12 0.6315 0.8009 +ca-sh-hs 45.7 96.61 SOURCE3 2 0.2867 0.2867 +f -sh-hs 48.1 96.50 SOURCE3 1 0.0000 0.0000 +hs-sh-hs 37.4 93.72 SOURCE3 3 0.4504 0.4777 +hs-sh-i 37.1 96.44 SOURCE3 1 0.0000 0.0000 +hs-sh-n 48.4 95.59 SOURCE3 4 3.3575 3.9065 +hs-sh-n2 48.1 95.82 SOURCE3 5 2.3697 3.1495 +hs-sh-n3 48.1 95.98 SOURCE3 3 1.1064 1.1735 +hs-sh-n4 47.1 93.13 SOURCE3 3 0.1579 0.1675 +hs-sh-na 48.1 97.38 SOURCE3 9 0.7962 1.0223 +hs-sh-nh 47.5 101.11 SOURCE3 1 0.0000 0.0000 +hs-sh-no 47.4 92.93 SOURCE3 1 0.0000 0.0000 +hs-sh-o 48.2 109.23 SOURCE3 2 0.0068 0.0068 +hs-sh-oh 48.7 98.64 SOURCE3 2 0.0605 0.0605 +hs-sh-os 49.3 98.15 SOURCE3 3 0.1566 0.1661 +hs-sh-p2 56.5 99.12 SOURCE3 10 4.3193 5.4110 +hs-sh-p3 53.1 95.81 SOURCE3 3 0.4144 0.4396 +hs-sh-p4 54.0 94.22 SOURCE3 4 0.7391 0.7605 +hs-sh-p5 54.8 94.52 SOURCE3 3 0.5269 0.5589 +hs-sh-s 40.9 102.87 SOURCE3 2 0.0000 0.0000 +hs-sh-s4 42.0 92.16 SOURCE3 3 1.5574 1.6519 +hs-sh-s6 42.9 93.83 SOURCE3 3 1.1843 1.2561 +hs-sh-sh 42.8 99.07 SOURCE3 2 0.0000 0.0000 +hs-sh-ss 42.6 99.17 SOURCE3 3 0.2316 0.2457 +br-ss-br 67.0 102.92 SOURCE3 1 0.0000 0.0000 +br-ss-c3 63.1 99.03 SOURCE3 1 0.0000 0.0000 +c -ss-c 62.2 101.40 SOURCE3 1 0.0000 0.0000 +c -ss-c2 65.6 92.43 SOURCE3 1 0.0000 0.0000 +c -ss-c3 61.5 100.29 SOURCE3 5 1.7050 2.2127 +c1-ss-c1 66.3 98.30 SOURCE2 1 0.0000 0.0000 +c1-ss-c3 62.9 99.90 SOURCE2 1 0.0000 0.0000 +c2-ss-c2 63.7 99.56 SOURCE3 1 0.0000 0.0000 +c2-ss-c3 63.4 95.73 SOURCE3 7 4.4315 4.6586 +c2-ss-n2 64.5 106.76 SOURCE3 1 0.0000 0.0000 +c2-ss-na 65.0 100.51 SOURCE3 6 6.4994 6.9702 +c2-ss-os 69.8 89.76 SOURCE3 1 0.0000 0.0000 +c2-ss-ss 64.8 92.26 SOURCE3 1 0.0000 0.0000 +c3-ss-c3 60.6 99.92 SOURCE3 14 1.4406 2.0723 +c3-ss-ca 61.3 100.62 SOURCE3 2 1.9639 1.9639 +c3-ss-cl 56.4 99.40 SOURCE2 1 0.0000 0.0000 +c3-ss-f 63.4 97.49 SOURCE3 1 0.0000 0.0000 +c3-ss-ha 11.1 96.50 SOURCE2 1 0.0000 0.0000 +c3-ss-i 56.0 100.00 SOURCE3 1 0.0000 0.0000 +c3-ss-n 63.7 100.30 SOURCE3 4 0.4972 0.6579 +c3-ss-n2 65.9 96.42 SOURCE3 5 1.1712 1.3604 +c3-ss-n3 64.1 98.83 SOURCE3 3 0.2742 0.2909 +c3-ss-n4 62.9 97.79 SOURCE3 3 0.1887 0.2002 +c3-ss-na 63.5 100.14 SOURCE3 12 1.3814 1.7415 +c3-ss-nh 63.7 100.63 SOURCE3 1 0.0000 0.0000 +c3-ss-no 62.4 98.62 SOURCE3 1 0.0000 0.0000 +c3-ss-o 64.7 106.60 SOURCE3 2 1.6714 1.6714 +c3-ss-oh 65.3 98.28 SOURCE3 2 1.4326 1.4326 +c3-ss-os 65.0 98.21 SOURCE3 4 1.4684 1.7097 +c3-ss-p2 80.2 98.41 SOURCE3 8 0.8438 0.9454 +c3-ss-p3 76.3 98.70 SOURCE3 3 0.0336 0.0356 +c3-ss-p4 76.9 98.16 SOURCE3 4 0.1322 0.1361 +c3-ss-p5 76.4 99.03 SOURCE3 3 0.5264 0.5584 +c3-ss-s 59.9 101.90 SOURCE3 1 0.0000 0.0000 +c3-ss-s4 60.1 96.37 SOURCE3 3 0.0190 0.0202 +c3-ss-s6 60.9 96.76 SOURCE3 3 1.4784 1.5680 +c3-ss-sh 60.4 101.93 SOURCE3 1 0.0000 0.0000 +c3-ss-ss 59.8 104.90 SOURCE3 25 3.6163 3.9326 +ca-ss-ca 62.4 99.92 SOURCE3 1 0.0000 0.0000 +ca-ss-cc 63.9 96.98 SOURCE3 2 0.0000 0.0000 +ca-ss-cd 63.9 96.98 SOURCE3 2 0.0000 0.0000 +ca-ss-cl 56.5 101.05 SOURCE3 1 0.0000 0.0000 +ca-ss-n 65.8 97.16 SOURCE0 1 +ca-ss-na 64.8 99.32 SOURCE0 1 +ca-ss-nc 69.2 94.76 SOURCE3 1 0.0000 0.0000 +ca-ss-nd 69.2 94.76 SOURCE3 1 same as ca-ss-nc +cc-ss-cc 67.0 89.91 SOURCE3 11 2.0978 2.2164 +cd-ss-cd 67.0 89.91 SOURCE3 11 2.0978 2.2164 +cc-ss-cd 61.2 107.91 SOURCE3 1 0.0000 0.0000 +cc-ss-nc 69.7 95.66 SOURCE3 3 0.0000 0.0000 +cd-ss-nd 69.7 95.66 SOURCE3 3 0.0000 0.0000 +cc-ss-os 66.5 98.81 SOURCE3 2 2.1583 2.1583 +cd-ss-os 66.5 98.81 SOURCE3 2 same as cc-ss-os +cc-ss-ss 61.5 102.46 SOURCE3 2 0.0000 0.0000 +cd-ss-ss 61.5 102.46 SOURCE3 2 same as cc-ss-ss +cd-ss-n 66.4 97.16 SOURCE3 1 0.0000 0.0000 +cc-ss-n 66.4 97.16 SOURCE3 1 same as cd-ss-n +cd-ss-na 65.4 99.33 SOURCE3 18 1.9415 2.5847 +cc-ss-na 65.4 99.33 SOURCE3 18 same as cd-ss-na +cl-ss-cl 52.4 103.37 SOURCE3 1 0.0000 0.0000 +cx-ss-cx 87.5 48.30 SOURCE2 1 0.0000 0.0000 +f -ss-f 66.2 98.30 SOURCE2 1 0.0000 0.0000 +f -ss-ss 59.9 108.30 SOURCE2 1 0.0000 0.0000 +i -ss-i 58.1 106.29 SOURCE3 1 0.0000 0.0000 +n -ss-n 66.4 103.10 SOURCE3 1 0.0000 0.0000 +n2-ss-n2 71.1 96.75 SOURCE3 1 0.0000 0.0000 +n3-ss-n3 66.5 102.34 SOURCE3 1 0.0000 0.0000 +n4-ss-n4 63.6 101.19 SOURCE3 1 0.0000 0.0000 +na-ss-na 65.9 102.81 SOURCE3 1 0.0000 0.0000 +nc-ss-nc 74.4 99.50 SOURCE2 1 0.0000 0.0000 +nd-ss-nd 74.4 99.50 SOURCE2 1 same as nc-ss-nc +nh-ss-nh 65.3 107.89 SOURCE3 1 0.0000 0.0000 +no-ss-no 61.4 106.43 SOURCE3 1 0.0000 0.0000 +o -ss-o 69.8 119.30 SOURCE2 1 0.0000 0.0000 +o -ss-p5 78.8 106.41 SOURCE3 1 0.0000 0.0000 +o -ss-s6 62.4 105.39 SOURCE0 1 +o -ss-ss 62.0 112.70 SOURCE2 1 0.0000 0.0000 +oh-ss-oh 68.2 104.25 SOURCE3 1 0.0000 0.0000 +os-ss-os 67.8 102.99 SOURCE3 1 0.0000 0.0000 +p2-ss-p2 105.5 99.52 SOURCE3 1 0.0000 0.0000 +p3-ss-p3 96.8 101.67 SOURCE0 1 +p5-ss-p5 103.5 89.83 SOURCE3 1 0.0000 0.0000 +s -ss-s 57.7 115.04 SOURCE0 1 +s4-ss-s4 60.9 96.08 SOURCE3 1 0.0000 0.0000 +s4-ss-s6 59.9 101.26 SOURCE0 1 +s6-ss-s6 60.5 101.81 SOURCE3 1 0.0000 0.0000 +sh-ss-sh 60.3 107.54 SOURCE3 1 0.0000 0.0000 +sh-ss-ss 60.8 106.53 SOURCE0 1 +ss-ss-ss 60.4 108.71 SOURCE3 1 0.0000 0.0000 +c -sx-c 62.8 86.85 SOURCE3 1 0.0000 0.0000 +c -sx-c3 62.0 92.71 SOURCE3 3 0.2918 0.3095 +c -sx-o 63.5 106.17 SOURCE3 5 0.8807 0.9477 +c3-sx-ca 62.6 95.00 SOURCE3 1 0.0000 0.0000 +c3-sx-ce 62.8 94.95 SOURCE3 3 0.0006 0.0007 +c3-sx-cf 62.8 94.95 SOURCE3 3 same as c3-sx-ce +c3-sx-ne 65.3 90.06 SOURCE3 5 1.4630 1.9627 +c3-sx-nf 65.3 90.06 SOURCE3 5 same as c3-sx-ne +c3-sx-o 64.9 107.88 SOURCE3 30 0.7662 0.8721 +c3-sx-pe 77.0 94.32 SOURCE3 7 0.5270 0.5547 +c3-sx-pf 77.0 94.32 SOURCE3 7 same as c3-sx-pe +c3-sx-px 74.3 96.46 SOURCE3 3 1.2587 1.3351 +c3-sx-py 74.1 95.67 SOURCE3 1 0.0000 0.0000 +c3-sx-sx 57.2 91.47 SOURCE3 4 1.9919 1.9919 +c3-sx-sy 58.7 95.47 SOURCE3 3 2.6797 2.8422 +ca-sx-ca 62.6 95.21 SOURCE3 1 0.0000 0.0000 +ca-sx-o 65.3 106.92 SOURCE3 3 0.3800 0.4031 +ce-sx-ce 63.0 94.96 SOURCE3 1 0.0000 0.0000 +cf-sx-cf 63.0 94.96 SOURCE3 1 same as ce-sx-ce +ce-sx-o 65.4 107.47 SOURCE3 5 0.3064 0.3128 +cf-sx-o 65.4 107.47 SOURCE3 5 same as ce-sx-o +ne-sx-ne 66.4 90.17 SOURCE3 1 0.0000 0.0000 +nf-sx-nf 66.4 90.17 SOURCE3 1 same as ne-sx-ne +ne-sx-o 65.4 109.20 SOURCE3 7 1.3979 1.4542 +nf-sx-o 65.4 109.20 SOURCE3 7 same as ne-sx-o +o -sx-pe 77.0 106.43 SOURCE3 9 2.1093 2.8345 +o -sx-pf 77.0 106.43 SOURCE3 9 same as o -sx-pe +o -sx-px 75.2 104.77 SOURCE3 3 1.8677 1.9810 +o -sx-py 73.1 109.13 SOURCE3 7 5.2928 5.6840 +o -sx-sx 55.7 104.65 SOURCE3 6 2.8778 3.0524 +o -sx-sy 59.4 103.41 SOURCE3 5 0.7671 0.9618 +pe-sx-pe 99.2 92.62 SOURCE3 1 0.0000 0.0000 +pf-sx-pf 99.2 92.62 SOURCE3 1 same as pe-sx-pe +py-sx-py 110.1 69.23 SOURCE3 3 16.4184 17.4143 +sx-sx-sx 58.6 84.90 SOURCE3 1 0.0000 0.0000 +sy-sx-sy 59.2 93.52 SOURCE3 1 0.0000 0.0000 +c -sy-c 59.2 99.81 SOURCE3 1 0.0000 0.0000 +c -sy-c3 60.1 101.25 SOURCE3 3 1.1172 1.1850 +c -sy-o 64.1 107.23 SOURCE3 10 0.8191 0.8425 +c3-sy-ca 60.9 103.17 SOURCE3 1 0.0000 0.0000 +c3-sy-ce 60.8 103.81 SOURCE3 3 0.3175 0.3368 +c3-sy-cf 60.8 103.81 SOURCE3 3 same as c3-sy-ce +c3-sy-ne 63.0 103.12 SOURCE3 5 3.6732 4.1882 +c3-sy-nf 63.0 103.12 SOURCE3 5 same as c3-sy-ne +c3-sy-o 66.0 108.48 SOURCE3 62 0.7297 0.8576 +c3-sy-pe 71.8 106.03 SOURCE3 6 2.3845 2.6117 +c3-sy-pf 71.8 106.03 SOURCE3 6 same as c3-sy-pe +c3-sy-px 71.7 103.62 SOURCE3 3 0.6673 0.7078 +c3-sy-py 73.5 103.39 SOURCE3 3 0.4302 0.4563 +c3-sy-sx 56.3 104.64 SOURCE3 3 4.3630 4.6276 +c3-sy-sy 57.4 100.78 SOURCE3 4 1.1633 1.1633 +ca-sy-ca 62.1 99.34 SOURCE3 3 4.9868 5.2893 +ca-sy-nh 65.2 100.83 SOURCE3 1 0.0000 0.0000 +ca-sy-o 65.8 108.73 SOURCE3 26 1.1018 1.2638 +ca-sy-oh 65.7 101.84 SOURCE3 4 0.9524 1.1069 +ca-sy-os 67.6 92.98 SOURCE3 1 0.0000 0.0000 +ce-sy-ce 61.1 102.78 SOURCE3 1 0.0000 0.0000 +cf-sy-cf 61.1 102.78 SOURCE3 1 same as ce-sy-ce +ce-sy-o 66.4 107.25 SOURCE3 10 0.5364 0.5477 +cf-sy-o 66.4 107.25 SOURCE3 10 same as ce-sy-o +na-sy-na 67.7 98.04 SOURCE0 1 +nc-sy-nc 75.2 98.04 SOURCE0 2 +nd-sy-nd 75.2 98.04 SOURCE0 2 +ne-sy-ne 66.6 98.62 SOURCE3 1 0.0000 0.0000 +nf-sy-nf 66.6 98.62 SOURCE3 1 same as ne-sy-ne +ne-sy-o 68.9 107.06 SOURCE3 14 2.1834 2.2705 +nf-sy-o 68.9 107.06 SOURCE3 14 same as ne-sy-o +nh-sy-o 70.9 108.46 SOURCE3 2 0.0000 0.0000 +o -sy-o 72.4 121.88 SOURCE3 46 0.7319 0.9495 +o -sy-oh 72.7 106.93 SOURCE3 8 0.6101 0.7424 +o -sy-os 70.6 107.62 SOURCE3 2 0.0000 0.0000 +o -sy-pe 75.4 106.90 SOURCE3 12 1.4233 1.4524 +o -sy-pf 75.4 106.90 SOURCE3 12 same as o -sy-pe +o -sy-px 74.4 106.17 SOURCE3 6 0.6656 0.7059 +o -sy-py 76.5 106.67 SOURCE3 10 0.6188 0.6478 +o -sy-sx 58.6 106.33 SOURCE3 10 1.9984 2.0456 +o -sy-sy 58.8 106.19 SOURCE3 12 0.1653 0.1754 +py-sy-py 92.8 104.49 SOURCE3 1 0.0000 0.0000 +sx-sy-sx 56.7 101.99 SOURCE3 1 0.0000 0.0000 +sy-sy-sy 56.5 103.29 SOURCE3 1 0.0000 0.0000 +br-n1-c1 51.1 180.00 HF/6-31G* +c1-n1-c1 64.9 179.92 HF/6-31G* +c1-n1-c2 60.2 177.73 HF/6-31G* +c1-n1-c3 59.9 180.00 HF/6-31G* +c1-n1-ca 59.9 179.99 HF/6-31G* +c1-n1-cl 50.1 179.95 HF/6-31G* +c1-n1-f 55.9 179.96 HF/6-31G* +c1-n1-hn 45.6 179.98 HF/6-31G* +c1-n1-i 46.2 179.95 HF/6-31G* +c1-n1-n1 66.9 180.00 HF/6-31G* +c1-n1-n2 65.7 171.56 HF/6-31G* +c1-n1-n3 60.7 175.59 HF/6-31G* +c1-n1-n4 59.7 179.69 HF/6-31G* +c1-n1-na 59.9 180.00 HF/6-31G* +c1-n1-nh 60.9 176.35 HF/6-31G* +c1-n1-o 62.6 179.95 HF/6-31G* +c1-n1-oh 62.9 174.31 HF/6-31G* +c1-n1-os 62.2 176.61 HF/6-31G* +c1-n1-p2 83.5 172.83 HF/6-31G* +c1-n1-p3 68.7 173.51 HF/6-31G* +c1-n1-p4 68.7 173.64 HF/6-31G* +c1-n1-p5 71.5 177.28 HF/6-31G* +c1-n1-s 53.3 179.99 HF/6-31G* +c1-n1-s2 60.3 178.11 HF/6-31G* +c1-n1-s4 55.2 169.60 HF/6-31G* +c1-n1-s6 61.8 175.92 HF/6-31G* +c1-n1-sh 55.7 174.25 HF/6-31G* +c1-n1-ss 55.4 176.06 HF/6-31G* +c1-ng-ng 51.9 179.97 HF/6-31G* +c2-c1-n1 63.1 180.00 HF/6-31G* +c2-c2-n1 71.7 122.98 HF/6-31G* +c2-n1-n1 61.6 180.00 HF/6-31G* +c2-n2-n1 75.5 115.09 HF/6-31G* +c2-na-n1 66.3 124.81 HF/6-31G* +c3-n1-n1 58.8 180.00 HF/6-31G* +c3-os-n1 66.3 113.50 HF/6-31G* +c3-ss-n1 65.9 98.44 HF/6-31G* +ca-ca-n1 63.4 118.50 HF/6-31G* +ca-n1-n1 59.0 180.00 HF/6-31G* +ca-nh-n1 69.4 117.13 HF/6-31G* +cl-n1-n1 51.4 179.94 HF/6-31G* +f -n1-n1 57.4 179.93 HF/6-31G* +h1-c3-n1 60.3 107.31 HF/6-31G* +hn-n1-n1 47.1 179.91 HF/6-31G* +hn-n3-n1 52.0 110.17 HF/6-31G* +hn-n4-n1 51.8 109.39 HF/6-31G* +hn-nh-n1 52.3 110.57 HF/6-31G* +ho-oh-n1 52.5 107.81 HF/6-31G* +hp-p3-n1 31.3 92.98 HF/6-31G* +hp-p4-n1 30.5 99.91 HF/6-31G* +hp-p5-n1 31.1 101.32 HF/6-31G* +hs-s4-n1 51.2 90.51 HF/6-31G* +hs-s6-n1 54.7 97.27 HF/6-31G* +hs-sh-n1 51.7 93.51 HF/6-31G* +i -n1-n1 47.3 179.94 HF/6-31G* +n1-n1-n1 69.0 179.97 HF/6-31G* +n1-n1-n2 67.7 171.57 HF/6-31G* +n1-n1-n3 62.5 175.09 HF/6-31G* +n1-n1-n4 61.3 179.91 HF/6-31G* +n1-n1-na 61.6 179.97 HF/6-31G* +n1-n1-nh 62.7 176.00 HF/6-31G* +n1-n1-o 64.4 179.94 HF/6-31G* +n1-n1-oh 64.8 173.77 HF/6-31G* +n1-n1-os 64.0 176.12 HF/6-31G* +n1-n1-p2 69.4 174.71 HF/6-31G* +n1-n1-p3 70.2 174.27 HF/6-31G* +n1-n1-s 54.6 179.96 HF/6-31G* +n1-n1-sh 57.0 175.07 HF/6-31G* +n1-n1-ss 56.9 175.61 HF/6-31G* +n1-p4-o 49.7 114.59 HF/6-31G* +n1-p5-o 44.7 113.78 HF/6-31G* +n1-s2-o 73.1 108.46 HF/6-31G* +n1-s4-o 70.2 110.09 HF/6-31G* +n1-s6-o 78.8 107.52 HF/6-31G* +n1-c1-n1 70.2 180.00 HF/6-31G* +n1-c2-n1 73.6 124.15 HF/6-31G* +n1-c3-n1 80.0 105.07 HF/6-31G* +n1-ca-n1 75.8 117.03 HF/6-31G* +n1-n2-n1 80.8 112.00 HF/6-31G* +n1-n3-n1 72.4 113.21 HF/6-31G* +n1-n4-n1 72.7 110.67 HF/6-31G* +n1-no-o 73.8 115.00 HF/6-31G* +n1-nh-n1 75.1 106.71 HF/6-31G* +n1-os-n1 70.3 117.79 HF/6-31G* +n1-ss-n1 73.1 96.96 HF/6-31G* +n1-s4-n1 72.4 94.02 HF/6-31G* +n1-s6-n1 83.7 95.52 HF/6-31G* +n1-p2-n1 46.5 86.22 HF/6-31G* +n1-p3-n1 45.9 90.44 HF/6-31G* +n1-p4-n1 43.5 100.61 HF/6-31G* +n1-p5-n1 45.8 101.55 HF/6-31G* +o -c1-o 69.3 180.00 Guess +c3-c1-c3 51.7 180.00 Guess +ca-c1-ca 52.8 180.00 Guess +f -c1-f 58.2 180.00 Guess +cl-c1-cl 46.6 180.00 Guess +br-c1-br 57.8 180.00 Guess +i -c1-i 53.4 180.00 Guess +s -c1-s 54.6 180.00 Guess +s2-c1-s2 55.8 180.00 Guess +s4-c1-s4 51.0 180.00 Guess +s6-c1-s6 51.7 180.00 Guess +sh-c1-sh 53.0 180.00 Guess +ss-c1-ss 53.0 180.00 Guess +oh-c1-oh 60.9 180.00 Guess +os-c1-os 61.0 180.00 Guess +p2-c1-p2 80.6 180.00 Guess +p3-c1-p3 79.7 180.00 Guess +p4-c1-p4 79.7 180.00 Guess +p5-c1-p5 81.4 180.00 Guess +n -c1-n 60.0 180.00 Guess +n2-c1-n2 66.0 180.00 Guess +n3-c1-n3 57.4 180.00 Guess +n4-c1-n4 56.3 180.00 Guess +nh-c1-nh 59.0 180.00 Guess +no-c1-no 56.8 180.00 Guess +na-c1-na 58.6 180.00 Guess +na-c1-na 58.6 180.00 Guess +na-c1-na 58.6 180.00 Guess + +X -c -c -X 4 1.200 180.000 2.000 +X -c -c1-X 2 0.000 180.000 2.000 +X -c -cg-X 2 0.000 180.000 2.000 same as X-c-c1-X +X -c -ch-X 2 0.000 180.000 2.000 +X -c -c2-X 4 8.700 180.000 2.000 intrpol.bsd.on C6H6 +X -c -cu-X 4 8.700 180.000 2.000 intrpol.bsd.on C6H6 +X -c -cv-X 4 8.700 180.000 2.000 intrpol.bsd.on C6H6 +X -c -ce-X 4 8.700 180.000 2.000 intrpol.bsd.on C6H6 +X -c -cf-X 4 8.700 180.000 2.000 intrpol.bsd.on C6H6 +X -c -c3-X 6 0.000 180.000 2.000 JCC, 7, (1986), 230 +X -c -cx-X 6 0.000 180.000 2.000 JCC, 7, (1986), 230 +X -c -cy-X 6 0.000 180.000 2.000 JCC, 7, (1986), 230 +X -c -ca-X 4 14.500 180.000 2.000 intrpol.bsd.on C6H6 +X -c -cc-X 4 11.500 180.000 2.000 statistic value +X -c -cd-X 4 11.500 180.000 2.000 statistic value +X -c -n -X 4 10.000 180.000 2.000 AA,NMA (no c-n3, c-n4, c-nh) +X -c -n2-X 2 8.300 180.000 2.000 double bond, same as X-c2-n2-X +X -c -nc-X 2 8.00 180.000 2.000 same as X-C-NC-X +X -c -nd-X 2 8.00 180.000 2.000 same as X-C-NC-X +X -c -ne-X 2 0.400 180.000 2.000 single bond +X -c -nf-X 2 0.400 180.000 2.000 single bond +X -c -na-X 4 5.800 180.000 -2.000 +X -c -na-X 4 1.400 180.000 4.000 +X -c -no-X 4 1.800 180.000 2.000 +X -c -oh-X 2 4.600 180.000 2.000 Junmei et al, 1999 +X -c -os-X 2 5.400 180.000 2.000 Junmei et al, 1999 +X -c -pc-X 2 4.000 180.000 2.000 estimated +X -c -p2-X 2 13.300 180.000 2.000 double bond, same as X-c2-p2-X +X -c -pc-X 2 4.000 180.000 2.000 estimated +X -c -pd-X 2 4.000 180.000 2.000 estimated +X -c -pe-X 2 0.000 180.000 2.000 single bond +X -c -pf-X 2 0.000 180.000 2.000 single bond +X -c -p3-X 4 6.200 180.000 2.000 +X -c -p4-X 4 5.400 180.000 2.000 +X -c -px-X 4 5.400 180.000 2.000 +X -c -p5-X 4 4.000 0.000 2.000 +X -c -py-X 4 4.000 0.000 2.000 +X -c -sh-X 2 4.500 180.000 2.000 +X -c -ss-X 2 6.200 180.000 2.000 +X -c -s4-X 4 0.800 180.000 2.000 +X -c -sx-X 4 0.800 180.000 2.000 +X -c -s6-X 6 3.000 0.000 2.000 +X -c -sy-X 6 3.000 0.000 2.000 +X -c1-c1-X 1 0.000 180.000 2.000 for both triple and single bonds +X -c1-cg-X 1 0.000 180.000 2.000 for both triple and single bonds +X -c1-ch-X 1 0.000 180.000 2.000 for both triple and single bonds +X -cg-cg-X 1 0.000 180.000 2.000 for both triple and single bonds +X -ch-ch-X 1 0.000 180.000 2.000 for both triple and single bonds +X -cg-ch-X 1 0.000 180.000 2.000 for both triple and single bonds +X -c1-c2-X 2 0.000 180.000 2.000 +X -c1-c3-X 3 0.000 180.000 2.000 +X -c1-ca-X 2 0.000 180.000 2.000 +X -c1-cb-X 2 0.000 180.000 2.000 +X -c1-cc-X 2 0.000 180.000 2.000 +X -c1-cd-X 2 0.000 180.000 2.000 +X -c1-ce-X 2 0.000 180.000 2.000 +X -c1-cf-X 2 0.000 180.000 2.000 +X -c1-cu-X 2 0.000 180.000 2.000 +X -c1-cv-X 2 0.000 180.000 2.000 +X -c1-cx-X 3 0.000 180.000 2.000 +X -c1-cy-X 3 0.000 180.000 2.000 +X -c1-n -X 2 0.000 180.000 2.000 +X -c1-n2-X 1 0.000 180.000 2.000 +X -c1-n3-X 2 0.000 180.000 2.000 +X -c1-n4-X 3 0.000 180.000 2.000 +X -c1-na-X 2 0.000 180.000 2.000 +X -c1-nb-X 2 0.000 180.000 2.000 +X -c1-nc-X 2 0.000 180.000 2.000 +X -c1-nd-X 2 0.000 180.000 2.000 +X -c1-ne-X 2 0.000 180.000 2.000 +X -c1-nf-X 2 0.000 180.000 2.000 +X -c1-nh-X 2 0.000 180.000 2.000 +X -c1-no-X 2 0.000 180.000 2.000 +X -c1-oh-X 1 0.000 180.000 2.000 +X -c1-os-X 1 0.000 180.000 2.000 +X -c1-p2-X 1 0.000 180.000 2.000 +X -c1-pb-X 1 0.000 180.000 2.000 +X -c1-pc-X 1 0.000 180.000 2.000 +X -c1-pd-X 1 0.000 180.000 2.000 +X -c1-pe-X 1 0.000 180.000 2.000 +X -c1-pf-X 1 0.000 180.000 2.000 +X -c1-p3-X 2 0.000 180.000 2.000 +X -c1-p4-X 2 0.000 180.000 2.000 +X -c1-px-X 2 0.000 180.000 2.000 +X -c1-p5-X 3 0.000 180.000 2.000 +X -c1-py-X 3 0.000 180.000 2.000 +X -c1-s2-X 1 0.000 180.000 2.000 +X -c1-sh-X 1 0.000 180.000 2.000 +X -c1-ss-X 1 0.000 180.000 2.000 +X -c1-s4-X 2 0.000 180.000 2.000 +X -c1-sx-X 2 0.000 180.000 2.000 +X -c1-s6-X 3 0.000 180.000 2.000 +X -c1-sy-X 3 0.000 180.000 2.000 +X -c2-c2-X 4 26.600 180.000 2.000 c2=c2 double bond, intrpol.bsd.on C6H6 +X -c2-ce-X 4 26.600 180.000 2.000 c2=c2 double bond, intrpol.bsd.on C6H6 +X -c2-cf-X 4 26.600 180.000 2.000 c2=c2 double bond, intrpol.bsd.on C6H6 +X -ce-cf-X 4 26.600 180.000 2.000 c2=c2 double bond, intrpol.bsd.on C6H6 +X -ce-ce-X 4 4.000 180.000 2.000 c2-c2 single bond, parm99 +X -cf-cf-X 4 4.000 180.000 2.000 c2-c2 single bond, parm99 +X -cc-cd-X 4 16.000 180.000 2.000 statistic value of parm94 +X -cc-cc-X 4 16.000 180.000 2.000 statistic value of parm94 +X -cd-cd-X 4 16.000 180.000 2.000 statistic value of parm94 +X -c2-c3-X 6 0.000 0.000 2.000 JCC,7,(1986),230 +X -c2-ca-X 4 10.200 180.000 2.000 intrpol.bsd.on C6H6 +X -c2-n -X 4 2.600 180.000 2.000 +X -c2-n2-X 2 8.300 180.000 2.000 double bond, parm99 +X -c2-ne-X 2 8.300 180.000 2.000 double bond, parm99 +X -c2-nf-X 2 8.300 180.000 2.000 double bond, parm99 +X -ce-ne-X 2 1.600 180.000 2.000 single bond +X -cf-nf-X 2 1.600 180.000 2.000 single bond +X -c2-nc-X 2 9.500 180.000 2.000 statistic value from parm94 +X -c2-nd-X 2 9.500 180.000 2.000 statistic value from parm94 +X -cc-nd-X 2 9.500 180.000 2.000 statistic value from parm94 +X -cd-nc-X 2 9.500 180.000 2.000 statistiv value from parm94 +X -cc-nc-X 2 9.500 180.000 2.000 statistic value from parm94 +X -cd-nd-X 2 9.500 180.000 2.000 statistiv value from parm94 +X -c2-n3-X 4 1.200 180.000 2.000 intrpol. +X -c2-n4-X 6 0.000 180.000 3.000 intrpol. +X -c2-na-X 4 2.500 180.000 2.000 +X -cc-na-X 4 6.800 180.000 2.000 statistic value from parm94 +X -cd-na-X 4 6.800 180.000 2.000 statistic value from parm94 +X -c2-nh-X 4 2.700 180.000 2.000 +X -c2-no-X 4 3.000 180.000 2.000 +X -c2-oh-X 2 2.100 180.000 2.000 parm99 +X -c2-os-X 2 2.100 180.000 2.000 parm99 +X -c2-p2-X 2 13.300 180.000 2.000 double bond +X -c2-pe-X 2 13.300 180.000 2.000 double bond +X -c2-pf-X 2 13.300 180.000 2.000 double bond +X -ce-pf-X 2 13.300 180.000 2.000 double bond +X -ce-pe-X 2 1.900 180.000 2.000 single bond +X -cf-pf-X 2 1.900 180.000 2.000 single bond +X -c2-pc-X 2 9.500 180.000 2.000 estimated +X -c2-pd-X 2 9.500 180.000 2.000 estimated +X -cc-pc-X 2 9.500 180.000 2.000 estimated +X -cc-pd-X 2 9.500 180.000 2.000 estimated +X -cd-pc-X 2 9.500 180.000 2.000 estimated +X -cd-pd-X 2 9.500 180.000 2.000 estimated +X -c2-p3-X 4 1.800 180.000 2.000 +X -c2-p4-X 4 26.600 180.000 2.000 c2=p4 double bond !!! +X -ce-p4-X 4 26.600 180.000 2.000 c2=p4 double bond !!! +X -cf-p4-X 4 26.600 180.000 2.000 c2=p4 double bond !!! +X -c2-px-X 4 1.300 0.000 2.000 +X -ce-px-X 4 1.300 0.000 2.000 +X -cf-px-X 4 1.300 0.000 2.000 +X -c2-p5-X 6 39.900 180.000 2.000 c2=p5 double bond !!! +X -ce-p5-X 6 39.900 180.000 2.000 c2=p5 double bond !!! +X -cf-p5-X 6 39.900 180.000 2.000 c2=p5 double bond !!! +X -c2-py-X 6 8.600 180.000 2.000 +X -ce-py-X 6 8.600 180.000 2.000 +X -cf-py-X 6 8.600 180.000 2.000 +X -c2-sh-X 2 1.000 180.000 2.000 +X -c2-ss-X 2 2.200 180.000 2.000 +X -c2-s4-X 4 26.600 180.000 2.000 c2=s4 double bond !!! +X -ce-s4-X 4 26.600 180.000 2.000 c2=s4 double bond !!! +X -cf-s4-X 4 26.600 180.000 2.000 c2=s4 double bond !!! +X -c2-sx-X 4 2.400 0.000 2.000 +X -ce-sx-X 4 2.400 0.000 2.000 +X -cf-sx-X 4 2.400 0.000 2.000 +X -c2-s6-X 6 39.900 180.000 2.000 c2=s6 double bond !!! +X -ce-s6-X 6 39.900 180.000 2.000 c2=s6 double bond !!! +X -cf-s6-X 6 39.900 180.000 2.000 c2=s6 double bond !!! +X -c2-sy-X 6 7.600 180.000 2.000 +X -ce-sy-X 6 7.600 180.000 2.000 +X -cf-sy-X 6 7.600 180.000 2.000 +X -c3-c3-X 9 1.400 0.000 3.000 JCC,7,(1986),230 +X -cx-cx-X 9 1.400 0.000 3.000 same as X-c3-c3-X +X -cy-cy-X 9 1.400 0.000 3.000 same as X-c3-c3-X +X -c3-ca-X 6 0.000 0.000 2.000 JCC,7,(1986),230 +X -c3-n -X 6 0.000 0.000 2.000 JCC,7,(1986),230 +X -cx-n -X 6 0.000 0.000 2.000 same as X-c3-n-X +X -cy-n -X 6 0.000 0.000 2.000 same as X-c3-n-X +X -c3-n2-X 6 0.000 0.000 3.000 JCC,7,(1986),230 +X -c3-ne-X 6 0.000 0.000 3.000 JCC,7,(1986),230 +X -c3-nf-X 6 0.000 0.000 3.000 JCC,7,(1986),230 +X -c3-n3-X 6 1.800 0.000 3.000 Junmei et al, 1999 +X -c3-n4-X 9 1.400 0.000 3.000 JCC,7,(1986),230 +X -c3-na-X 6 0.000 0.000 2.000 JCC,7,(1986),230 +X -c3-nh-X 6 0.000 0.000 2.000 JCC,7,(1986),230 +X -c3-no-X 6 0.000 0.000 2.000 JCC,7,(1986),230 +X -c3-oh-X 3 0.500 0.000 3.000 JCC,7,(1986),230 +X -c3-os-X 3 1.150 0.000 3.000 JCC,7,(1986),230 +X -c3-p2-X 3 0.800 180.000 2.000 +X -c3-pe-X 3 0.800 180.000 2.000 +X -c3-pf-X 3 0.800 180.000 2.000 +X -c3-p3-X 6 0.800 0.000 3.000 +X -c3-p4-X 6 0.800 0.000 3.000 +X -c3-px-X 6 0.800 0.000 3.000 +X -c3-p5-X 9 0.200 0.000 3.000 +X -c3-py-X 9 0.200 0.000 3.000 +X -c3-sh-X 3 0.750 0.000 3.000 JCC,7,(1986),230 +X -c3-ss-X 3 1.000 0.000 3.000 JCC,7,(1986),230 +X -c3-s4-X 6 1.200 0.000 3.000 +X -c3-sx-X 6 1.200 0.000 3.000 +X -c3-s6-X 9 1.300 0.000 3.000 +X -c3-sy-X 9 1.300 0.000 3.000 +X -c3-cc-X 6 0.000 0.000 3.000 same as X-c3-ca-X +X -c3-cd-X 6 0.000 0.000 3.000 same as X-c3-ca-X +X -ca-ca-X 4 14.500 180.000 2.000 intrpol.bsd.on C6H6 +X -ca-cc-X 4 14.500 180.000 2.000 added by EAJF Peters +X -ca-cp-X 4 14.500 180.000 2.000 intrpol.bsd.on C6H6 +X -ca-cq-X 4 14.500 180.000 2.000 intrpol.bsd.on C6H6 +X -cp-cp-X 4 4.000 180.000 2.000 estimated, intrpol. +X -cq-cq-X 4 4.000 180.000 2.000 estimated, intrpol. +X -ca-n -X 4 1.800 180.000 2.000 +X -ca-n2-X 2 0.000 180.000 3.000 +X -ca-ne-X 2 0.000 180.000 3.000 +X -ca-nf-X 2 0.000 180.000 3.000 +X -ca-n4-X 4 7.000 0.000 2.000 +X -ca-na-X 4 1.200 180.000 2.000 +X -ca-nb-X 2 9.60 180.0 2.000 same as X-CA-NC-X +X -ca-nc-X 2 9.60 180.0 2.000 same as X-CA-NC-X +X -ca-nd-X 2 9.60 180.0 2.000 same as X-CA-NC-X +X -ca-nh-X 4 4.200 180.000 2.000 +X -cc-nh-X 4 4.200 180.000 2.000 same as X-ca-nh-X +X -cd-nh-X 4 4.200 180.000 2.000 same as X-ca-nh-X +X -ca-no-X 4 2.400 180.000 2.000 +X -ca-oh-X 2 1.800 180.000 2.000 Junmei et al, 99 +X -ca-os-X 2 1.800 180.000 2.000 same as X-ca-oh-X +X -ca-p2-X 2 1.200 180.000 2.000 +X -ca-pe-X 2 1.200 180.000 2.000 same as X-ca-p2-X +X -ca-pf-X 2 1.200 180.000 2.000 same as X-ca-p2-X +X -ca-pc-X 2 9.600 180.000 2.000 estimated, intrpol +X -ca-pd-X 2 9.600 180.000 2.000 estimated, intrpol +X -ca-p3-X 4 0.000 180.000 2.000 +X -ca-p4-X 4 2.100 180.000 2.000 +X -ca-px-X 4 2.100 180.000 2.000 estimated, same as X-ca-p4-X +X -ca-p5-X 6 8.800 180.000 2.000 +X -ca-py-X 6 8.800 180.000 2.000 estimated, same as X-ca-p5-X +X -ca-sh-X 2 0.000 180.000 2.000 +X -ca-ss-X 2 0.800 180.000 2.000 +X -ca-s4-X 4 1.200 0.000 2.000 +X -ca-sx-X 4 1.200 0.000 2.000 estimated, same as X-ca-s4-X +X -ca-s6-X 6 7.800 180.000 2.000 +X -ca-sy-X 6 7.800 180.000 2.000 estimated, same as X-ca-s6-X +X -n -cc-X 4 6.600 180.000 2.000 statistic value from parm94 +X -n -cd-X 4 6.600 180.000 2.000 statistic value from parm94 +X -n -n -X 4 4.600 0.000 2.000 +X -n -n2-X 2 0.800 0.000 2.000 +X -n -ne-X 2 0.800 0.000 2.000 +X -n -nf-X 2 0.800 0.000 2.000 +X -n -n3-X 4 4.300 0.000 2.000 +X -n -n4-X 4 3.800 0.000 2.000 +X -n -na-X 4 2.800 0.000 2.000 +X -n -nc-X 2 9.600 180.000 2.000 estimated, intrpol. +X -n -nd-X 2 9.600 180.000 2.000 estimated, intrpol. +X -n -nh-X 4 4.400 0.000 2.000 +X -n -no-X 4 5.500 180.000 2.000 +X -n -oh-X 2 3.000 0.000 2.000 +X -n -os-X 2 2.200 0.000 2.000 +X -n -p2-X 2 2.000 180.000 2.000 +X -n -pe-X 2 2.000 180.000 2.000 +X -n -pf-X 2 9.600 180.000 2.000 estimated, intrpol. +X -n -pc-X 2 9.600 180.000 2.000 estimated, intrpol. +X -n -pd-X 2 2.000 180.000 2.000 +X -n -p3-X 4 9.000 0.000 2.000 +X -n -p4-X 4 1.300 0.000 2.000 +X -n -px-X 4 1.300 0.000 2.000 +X -n -p5-X 6 13.200 180.000 2.000 +X -n -py-X 6 13.200 180.000 2.000 +X -n -sh-X 2 2.200 0.000 2.000 +X -n -ss-X 2 3.000 0.000 2.000 +X -n -s4-X 4 6.000 0.000 3.000 +X -n -sx-X 4 6.000 0.000 3.000 +X -n -s6-X 6 6.600 180.000 2.000 +X -n -sy-X 6 6.600 180.000 2.000 +X -n1-c2-X 2 0.000 180.000 2.000 +X -n1-c3-X 3 0.000 180.000 2.000 +X -n1-ca-X 2 0.000 180.000 2.000 +X -n1-cb-X 2 0.000 180.000 2.000 +X -n1-cc-X 2 0.000 180.000 2.000 +X -n1-cd-X 2 0.000 180.000 2.000 +X -n1-ce-X 2 0.000 180.000 2.000 +X -n1-cf-X 2 0.000 180.000 2.000 +X -n1-cu-X 2 0.000 180.000 2.000 +X -n1-cv-X 2 0.000 180.000 2.000 +X -n1-cx-X 3 0.000 180.000 2.000 +X -n1-cy-X 3 0.000 180.000 2.000 +X -n1-n -X 2 0.000 180.000 2.000 +X -n1-n1-X 1 0.000 180.000 2.000 +X -n1-n2-X 1 0.000 180.000 2.000 +X -n1-n3-X 2 0.000 180.000 2.000 +X -n1-n4-X 3 0.000 180.000 2.000 +X -n1-na-X 2 0.000 180.000 2.000 +X -n1-nb-X 2 0.000 180.000 2.000 +X -n1-nc-X 2 0.000 180.000 2.000 +X -n1-nd-X 2 0.000 180.000 2.000 +X -n1-ne-X 2 0.000 180.000 2.000 +X -n1-nf-X 2 0.000 180.000 2.000 +X -n1-nh-X 2 0.000 180.000 2.000 +X -n1-no-X 2 0.000 180.000 2.000 +X -n1-oh-X 1 0.000 180.000 2.000 +X -n1-os-X 1 0.000 180.000 2.000 +X -n1-p2-X 1 0.000 180.000 2.000 +X -n1-pb-X 1 0.000 180.000 2.000 +X -n1-pc-X 1 0.000 180.000 2.000 +X -n1-pd-X 1 0.000 180.000 2.000 +X -n1-pe-X 1 0.000 180.000 2.000 +X -n1-pf-X 1 0.000 180.000 2.000 +X -n1-p3-X 2 0.000 180.000 2.000 +X -n1-p4-X 2 0.000 180.000 2.000 +X -n1-px-X 2 0.000 180.000 2.000 +X -n1-p5-X 3 0.000 180.000 2.000 +X -n1-py-X 3 0.000 180.000 2.000 +X -n1-s2-X 1 0.000 180.000 2.000 +X -n1-sh-X 1 0.000 180.000 2.000 +X -n1-ss-X 1 0.000 180.000 2.000 +X -n1-s4-X 2 0.000 180.000 2.000 +X -n1-sx-X 2 0.000 180.000 2.000 +X -n1-s6-X 3 0.000 180.000 2.000 +X -n1-sy-X 3 0.000 180.000 2.000 +X -n2-n2-X 1 3.000 180.000 -2.000 double bond +X -n2-n2-X 1 2.800 0.000 1.000 double bond +X -n2-ne-X 1 3.000 180.000 -2.000 double bond +X -n2-ne-X 1 2.800 0.000 1.000 double bond +X -n2-nf-X 1 3.000 180.000 -2.000 double bond +X -n2-nf-X 1 2.800 0.000 1.000 double bond +X -ne-nf-X 1 3.000 180.000 -2.000 double bond +X -ne-nf-X 1 2.800 0.000 1.000 double bond +X -ne-ne-X 1 1.200 180.000 2.000 single bond, intrpol +X -nf-nf-X 1 1.200 180.000 2.000 single bond, intrpol +X -nc-nc-X 1 4.000 180.000 2.000 estimated, intrpol +X -nd-nd-X 1 4.000 180.000 2.000 estimated, intrpol +X -nc-nd-X 1 4.000 180.000 2.000 estimated, intrpol +X -n2-nc-X 1 3.000 180.000 -2.000 same as X-n2-n2-X +X -n2-nc-X 1 2.800 0.000 1.000 +X -n2-nd-X 1 3.000 180.000 -2.000 same as X-n2-n2-X +X -n2-nd-X 1 2.800 0.000 1.000 +X -n2-n3-X 2 12.200 180.000 2.000 +X -ne-n3-X 2 12.200 180.000 2.000 +X -nf-n3-X 2 12.200 180.000 2.000 +X -n2-n4-X 3 24.000 180.000 2.000 +X -ne-n4-X 3 24.000 180.000 2.000 +X -nf-n4-X 3 24.000 180.000 2.000 +X -n2-na-X 2 3.400 180.000 2.000 +X -ne-na-X 2 3.400 180.000 2.000 +X -nf-na-X 2 3.400 180.000 2.000 +X -na-nc-X 2 9.600 180.000 2.000 estimated, intrpol. +X -na-nd-X 2 9.600 180.000 2.000 estimated, intrpol. +X -n2-nh-X 2 5.600 180.000 2.000 +X -ne-nh-X 2 5.600 180.000 2.000 +X -nf-nh-X 2 5.600 180.000 2.000 +X -n2-no-X 2 1.500 180.000 2.000 +X -ne-no-X 2 1.500 180.000 2.000 +X -nf-no-X 2 1.500 180.000 2.000 +X -n2-oh-X 1 3.200 180.000 2.000 +X -ne-oh-X 1 3.200 180.000 2.000 +X -nf-oh-X 1 3.200 180.000 2.000 +X -n2-os-X 1 3.000 180.000 2.000 +X -ne-os-X 1 3.000 180.000 2.000 +X -nf-os-X 1 3.000 180.000 2.000 +X -nc-os-X 1 4.800 180.000 2.000 estimated, intrpol. +X -nc-ss-X 1 4.800 180.000 2.000 estimated, intrpol. +X -n2-p2-X 1 5.400 180.000 2.000 estimated, intrpol. +X -n2-pe-X 1 5.400 180.000 2.000 estimated, intrpol. +X -n2-pf-X 1 5.400 180.000 2.000 estimated, intrpol. +X -ne-pf-X 1 5.400 180.000 2.000 estimated, intrpol. +X -n2-pc-X 1 5.400 180.000 2.000 estimated, intrpol. +X -n2-pd-X 1 5.400 180.000 2.000 estimated, intrpol. +X -nc-p2-X 1 5.400 180.000 2.000 estimated, intrpol. +X -nd-p2-X 1 5.400 180.000 2.000 estimated, intrpol. +X -nc-pc-X 1 6.600 180.000 2.000 estimated, intrpol. +X -nd-pd-X 1 6.600 180.000 2.000 estimated, intrpol. +X -nd-pc-X 1 6.600 180.000 2.000 estimated, intrpol. +X -nc-pd-X 1 6.600 180.000 2.000 estimated, intrpol. +X -ne-pe-X 1 0.600 0.000 1.000 single bond +X -nf-pf-X 1 0.600 0.000 1.000 single bond +X -n2-p3-X 2 4.200 180.000 2.000 +X -n2-p4-X 2 13.300 180.000 2.000 estimated !!! +X -ne-p4-X 2 13.300 180.000 2.000 estimated !!! +X -nf-p4-X 2 13.300 180.000 2.000 estimated !!! +X -n2-p5-X 3 20.000 180.000 2.000 estimated !!! +X -ne-p5-X 3 3.000 180.000 3.000 +X -nf-p5-X 3 3.000 180.000 3.000 +X -ne-px-X 3 3.000 180.000 3.000 +X -nf-px-X 3 3.000 180.000 3.000 +X -n2-sh-X 1 2.100 180.000 2.000 +X -ne-sh-X 1 2.100 180.000 2.000 +X -nf-sh-X 1 2.100 180.000 2.000 +X -n2-ss-X 1 2.800 180.000 -2.000 +X -n2-ss-X 1 1.300 180.000 1.000 +X -ne-ss-X 1 2.800 180.000 -2.000 +X -ne-ss-X 1 1.300 180.000 1.000 +X -nf-ss-X 1 2.800 180.000 -2.000 +X -nf-ss-X 1 1.300 180.000 1.000 +X -n2-s4-X 2 13.300 180.000 2.000 estimated !!! +X -ne-sx-X 2 3.000 180.000 3.000 +X -nf-sx-X 2 3.000 180.000 3.000 +X -n2-s6-X 3 20.000 180.000 2.000 estimated !!! +X -ne-sy-X 3 1.500 180.000 -3.000 +X -ne-sy-X 3 20.400 180.000 1.000 +X -nf-sy-X 3 1.500 180.000 -3.000 +X -nf-sy-X 3 20.400 180.000 1.000 +X -n3-n3-X 4 9.000 0.000 2.000 +X -n3-n4-X 6 1.500 0.000 3.000 +X -n3-na-X 4 6.400 0.000 2.000 +X -n3-nh-X 4 7.600 0.000 2.000 +X -n3-no-X 4 16.000 180.000 2.000 +X -n3-oh-X 1 2.200 0.000 2.000 +X -n3-os-X 1 1.800 0.000 2.000 +X -n3-p2-X 2 6.400 180.000 2.000 +X -n3-pe-X 2 6.400 180.000 2.000 +X -n3-pf-X 2 6.400 180.000 2.000 +X -n3-p3-X 4 9.400 0.000 2.000 +X -n3-p4-X 4 8.400 180.000 2.000 +X -n3-px-X 4 8.400 180.000 2.000 +X -n3-p5-X 6 18.000 180.000 2.000 +X -n3-py-X 6 18.000 180.000 2.000 +X -n3-sh-X 1 3.100 0.000 2.000 +X -n3-ss-X 1 2.600 0.000 2.000 +X -n3-s4-X 4 15.000 0.000 2.000 +X -n3-sx-X 4 15.000 0.000 2.000 +X -n3-s6-X 6 18.800 0.000 2.000 +X -n3-sy-X 6 18.800 0.000 2.000 +X -n4-n4-X 9 1.700 0.000 3.000 +X -n4-na-X 6 1.400 0.000 3.000 +X -n4-nh-X 6 1.100 0.000 3.000 +X -n4-no-X 6 0.500 180.000 3.000 +X -n4-oh-X 3 1.000 0.000 3.000 +X -n4-os-X 3 1.700 0.000 3.000 +X -n4-p2-X 3 0.500 180.000 3.000 +X -n4-pe-X 3 0.500 180.000 3.000 +X -n4-pf-X 3 0.500 180.000 3.000 +X -n4-p3-X 6 0.900 0.000 3.000 +X -n4-p4-X 4 0.200 0.000 3.000 +X -n4-px-X 4 0.200 0.000 3.000 +X -n4-p5-X 9 0.800 0.000 3.000 +X -n4-py-X 9 0.800 0.000 3.000 +X -n4-sh-X 3 2.000 0.000 3.000 +X -n4-ss-X 3 1.000 0.000 3.000 +X -n4-s4-X 6 1.700 0.000 3.000 +X -n4-sx-X 6 1.700 0.000 3.000 +X -n4-s6-X 9 1.200 0.000 3.000 +X -n4-sy-X 9 1.200 0.000 3.000 +X -na-na-X 4 3.600 0.000 2.000 +X -na-nh-X 4 4.800 0.000 2.000 +X -na-no-X 4 24.000 180.000 2.000 +X -na-oh-X 2 2.000 0.000 2.000 +X -na-os-X 2 1.300 0.000 2.000 +X -na-p2-X 1 1.000 180.000 2.000 +X -na-pe-X 1 1.000 180.000 2.000 +X -na-pf-X 1 1.000 180.000 2.000 +X -na-p3-X 4 5.800 0.000 2.000 +X -na-p4-X 4 4.400 0.000 3.000 +X -na-px-X 4 4.400 0.000 3.000 +X -na-p5-X 6 5.000 180.000 2.000 +X -na-py-X 6 5.000 180.000 2.000 +X -na-sh-X 2 3.600 0.000 2.000 +X -na-ss-X 2 15.600 0.000 2.000 +X -na-s4-X 4 4.200 0.000 2.000 +X -na-sx-X 4 4.200 0.000 2.000 +X -na-s6-X 6 22.000 180.000 2.000 +X -na-sy-X 6 22.000 180.000 2.000 +X -nh-nh-X 4 7.200 180.000 3.000 +X -nh-no-X 4 10.200 180.000 2.000 +X -nh-oh-X 2 3.000 0.000 2.000 +X -nh-os-X 2 3.000 0.000 1.000 +X -nh-p2-X 2 2.800 180.000 2.000 +X -nh-pe-X 2 2.800 180.000 2.000 +X -nh-pf-X 2 2.800 180.000 2.000 +X -nh-p3-X 4 9.400 0.000 2.000 +X -nh-p4-X 4 4.700 0.000 3.000 +X -nh-px-X 4 4.700 0.000 3.000 +X -nh-p5-X 6 4.800 0.000 2.000 +X -nh-py-X 6 4.800 0.000 2.000 +X -nh-sh-X 2 3.200 0.000 2.000 +X -nh-ss-X 2 4.200 0.000 2.000 +X -nh-s4-X 4 3.000 0.000 -2.000 +X -nh-s4-X 4 0.400 180.000 3.000 +X -nh-sx-X 4 3.000 0.000 -2.000 +X -nh-sx-X 4 0.400 180.000 3.000 +X -nh-s6-X 6 0.600 180.000 2.000 +X -nh-sy-X 6 0.600 180.000 2.000 +X -no-no-X 4 1.600 180.000 -4.000 +X -no-no-X 4 7.200 180.000 2.000 +X -no-oh-X 2 7.800 180.000 2.000 +X -no-os-X 2 6.000 180.000 2.000 +X -no-p2-X 1 0.300 180.000 2.000 +X -no-pe-X 1 0.300 180.000 2.000 +X -no-pf-X 1 0.300 180.000 2.000 +X -no-p3-X 4 7.600 180.000 2.000 +X -no-p4-X 4 2.300 180.000 2.000 +X -no-px-X 4 2.300 180.000 2.000 +X -no-p5-X 6 14.400 0.000 -2.000 +X -no-p5-X 6 2.400 0.000 3.000 +X -no-py-X 6 14.400 0.000 -2.000 +X -no-py-X 6 2.400 0.000 3.000 +X -no-sh-X 2 4.600 180.000 2.000 +X -no-ss-X 2 5.400 180.000 2.000 +X -no-s4-X 4 10.400 180.000 2.000 +X -no-sx-X 4 10.400 180.000 2.000 +X -no-s6-X 6 2.000 0.000 2.000 +X -no-sy-X 6 2.000 0.000 2.000 +X -oh-oh-X 1 1.600 0.000 2.000 +X -oh-os-X 1 1.600 0.000 2.000 +X -oh-p2-X 1 1.500 180.000 2.000 +X -oh-pe-X 1 1.500 180.000 2.000 +X -oh-pf-X 1 1.500 180.000 2.000 +X -oh-p3-X 2 0.800 180.000 3.000 +X -oh-p4-X 2 1.400 0.000 1.000 +X -oh-px-X 2 1.400 0.000 1.000 +X -oh-p5-X 3 1.600 0.000 3.000 +X -oh-py-X 3 1.600 0.000 3.000 +X -oh-sh-X 1 2.400 0.000 2.000 +X -oh-ss-X 1 2.400 0.000 2.000 +X -oh-s4-X 2 10.000 0.000 1.000 +X -oh-sx-X 2 10.000 0.000 1.000 +X -oh-s6-X 3 28.500 180.000 1.000 +X -oh-sy-X 3 28.500 180.000 1.000 +X -os-os-X 1 1.000 0.000 1.000 +X -os-ss-X 1 2.200 0.000 2.000 +X -os-sh-X 1 1.800 0.000 2.000 +X -os-s4-X 2 3.300 0.000 3.000 +X -os-sx-X 2 3.300 0.000 3.000 +X -os-s6-X 3 3.600 180.000 2.000 +X -os-sy-X 3 3.600 180.000 2.000 +X -os-p2-X 1 3.000 180.000 -2.000 +X -os-p2-X 1 2.000 180.000 1.000 +X -os-pe-X 1 3.000 180.000 -2.000 +X -os-pe-X 1 2.000 180.000 1.000 +X -os-pf-X 1 3.000 180.000 -2.000 +X -os-pf-X 1 2.000 180.000 1.000 +X -os-p3-X 2 4.400 0.000 2.000 +X -os-p4-X 2 2.100 180.000 2.000 +X -os-px-X 2 2.100 180.000 2.000 +X -os-p5-X 3 2.400 0.000 2.000 +X -os-py-X 3 2.400 0.000 2.000 +X -p2-p2-X 1 6.600 180.000 2.000 estimated, intrpol. +X -p2-pe-X 1 6.600 180.000 2.000 estimated, intrpol. +X -p2-pf-X 1 6.600 180.000 2.000 estimated, intrpol. +X -p2-pc-X 1 6.600 180.000 2.000 estimated, intrpol. +X -p2-pd-X 1 6.600 180.000 2.000 estimated, intrpol. +X -pe-pe-X 1 1.200 180.000 2.000 single bond +X -pf-pf-X 1 1.200 180.000 2.000 single bond +X -pc-pc-X 1 7.200 180.000 2.000 estimated, intrpol. +X -pd-pd-X 1 7.200 180.000 2.000 estimated, intrpol. +X -pc-pd-X 1 7.200 180.000 2.000 estimated, intrpol. +X -p2-p3-X 2 2.400 0.000 1.000 +X -pe-p3-X 2 2.400 0.000 1.000 +X -pf-p3-X 2 2.400 0.000 1.000 +X -p2-p4-X 2 13.300 180.000 2.000 estimated !!! +X -pe-px-X 2 4.900 0.000 2.000 +X -pf-px-X 2 4.900 0.000 2.000 +X -p2-p5-X 3 20.000 180.000 2.000 estimated !!! +X -pe-py-X 3 5.700 0.000 1.000 +X -pf-py-X 3 5.700 0.000 1.000 +X -p2-sh-X 1 1.400 180.000 2.000 +X -pe-sh-X 1 1.400 180.000 2.000 +X -pf-sh-X 1 1.400 180.000 2.000 +X -p2-ss-X 1 1.400 180.000 2.000 +X -pe-ss-X 1 1.400 180.000 2.000 +X -pf-ss-X 1 1.400 180.000 2.000 +X -p2-s4-X 2 13.300 180.000 2.000 estimated !!! +X -pe-sx-X 2 3.000 0.000 2.000 +X -pf-sx-X 2 3.000 0.000 2.000 +X -p2-s6-X 3 20.000 180.000 2.000 estimated !!! +X -pe-sy-X 3 1.200 180.000 3.000 +X -pf-sy-X 3 1.200 180.000 3.000 +X -p3-p3-X 4 2.000 0.000 3.000 +X -p3-p4-X 4 3.600 0.000 1.000 +X -p3-px-X 4 3.600 0.000 1.000 +X -p3-p5-X 6 11.000 180.000 2.000 +X -p3-py-X 6 11.000 180.000 2.000 +X -p3-sh-X 2 9.200 0.000 2.000 +X -p3-ss-X 2 2.300 0.000 3.000 +X -p3-ss-X 2 2.300 0.000 3.000 +X -p3-s4-X 4 15.400 0.000 2.000 +X -p3-sx-X 4 15.400 0.000 2.000 +X -p3-s6-X 6 1.600 0.000 3.000 +X -p3-sy-X 6 1.600 0.000 3.000 +X -p4-p4-X 4 26.600 180.000 2.000 estimated !!! +X -px-px-X 4 5.800 180.000 2.000 +X -p4-p5-X 6 39.900 180.000 2.000 estimated !!! +X -px-py-X 6 1.900 180.000 2.000 +X -p4-s4-X 4 26.600 180.000 2.000 estimated !!! +X -px-sx-X 4 3.400 0.000 1.000 +X -p4-s6-X 6 39.900 180.000 2.000 estimated !!! +X -px-sy-X 6 0.700 0.000 3.000 +X -p4-sh-X 2 0.500 180.000 1.000 +X -px-sh-X 2 0.500 180.000 1.000 +X -p4-ss-X 2 1.200 180.000 2.000 +X -px-ss-X 2 1.200 180.000 2.000 +X -p5-p5-X 9 60.000 180.000 2.000 estimated !!! +X -py-py-X 9 5.400 0.000 2.000 +X -p5-sh-X 3 0.900 0.000 3.000 +X -py-sh-X 3 0.900 0.000 3.000 +X -p5-ss-X 3 11.400 180.000 2.000 +X -py-ss-X 3 11.400 180.000 2.000 +X -p5-s4-X 6 40.000 180.000 2.000 estimated !!! +X -py-sx-X 6 1.600 0.000 3.000 +X -p5-s6-X 9 60.000 180.000 2.000 estimated !!! +X -py-sy-X 9 2.500 0.000 3.000 +X -sh-sh-X 1 5.600 0.000 3.000 +X -sh-ss-X 1 5.300 0.000 3.000 +X -sh-s4-X 2 1.400 0.000 3.000 +X -sh-sx-X 2 1.400 0.000 3.000 +X -sh-s6-X 3 14.000 180.000 2.000 +X -sh-sy-X 3 14.000 180.000 2.000 +X -ss-ss-X 1 0.000 0.000 3.000 +X -ss-s4-X 2 0.600 0.000 3.000 +X -ss-sx-X 2 0.600 0.000 3.000 +X -ss-s6-X 3 9.200 180.000 2.000 +X -ss-sy-X 3 9.200 180.000 2.000 +X -s4-s4-X 4 26.600 180.000 2.000 estimated !!! +X -sx-sx-X 4 2.500 0.000 3.000 +X -s4-s6-X 6 40.000 180.000 2.000 estimated !!! +X -sx-sy-X 6 26.000 180.000 2.000 +X -s6-s6-X 9 60.000 180.000 2.000 estimated !!! +X -sy-sy-X 9 1.400 180.000 2.000 +c3-c -sh-hs 1 2.250 180.000 -2.000 +c3-c -sh-hs 1 1.300 180.000 1.000 +c2-c2-ss-c3 1 1.100 180.000 -2.000 +c2-c2-ss-c3 1 0.700 180.000 3.000 +c2-c2-n -c 1 0.650 180.000 -2.000 +c2-c2-n -c 1 1.200 180.000 1.000 +c -n -p2-c2 1 1.000 180.000 -2.000 +c -n -p2-c2 1 1.900 180.000 1.000 +n -c3-c -n 1 1.700 180.000 -1. +n -c3-c -n 1 2.000 180.000 2. +c -n -c3-c 1 0.850 180.000 -2. +c -n -c3-c 1 0.800 0.000 1. +c3-c3-n -c 1 0.50 180.0 -4. phi,psi,parm94 +c3-c3-n -c 1 0.15 180.0 -3. phi,psi,parm94 +c3-c3-n -c 1 0.53 0.0 1. phi,psi,parm94 +c3-c3-c -n 1 0.100 0.0 -4. phi,psi,parm94 +c3-c3-c -n 1 0.07 0.0 2. phi,psi,parm94 +c2-ne-p5-o 1 2.30 0.0 1. phi,psi,parm94 +c2-nf-p5-o 1 2.30 0.0 1. phi,psi,parm94 +ce-ne-p5-o 1 2.30 0.0 1. phi,psi,parm94 +ce-nf-p5-o 1 2.30 0.0 1. phi,psi,parm94 +cf-ne-p5-o 1 2.30 0.0 1. phi,psi,parm94 +cf-nf-p5-o 1 2.30 0.0 1. phi,psi,parm94 +hn-n -c -o 1 2.50 180.0 -2. JCC,7,(1986),230 +hn-n -c -o 1 2.00 0.0 1. J.C.cistrans-NMA DE +c3-ss-ss-c3 1 3.50 0.0 -2. JCC,7,(1986),230 +c3-ss-ss-c3 1 0.60 0.0 3. JCC,7,(1986),230 +c3-n3-nh-ca 1 1.90 0.0 -2. +c3-n3-nh-ca 1 1.90 0.0 3. +c3-n3-p5-o 1 3.00 180.0 -2. +c3-n3-p5-o 1 2.30 0.0 3. +ca-nh-oh-ho 1 1.20 0.0 -1. +ca-nh-oh-ho 2 3.00 0.0 2. +oh-p5-os-c3 1 0.25 0.0 -3. JCC,7,(1986),230 +oh-p5-os-c3 1 1.20 0.0 2. gg> ene.631g*/mp2 +os-p5-os-c3 1 0.25 0.0 -3. JCC,7,(1986),230 +os-p5-os-c3 1 1.20 0.0 2. gg> ene.631g*/mp2 +h1-c3-c -o 1 0.80 0.0 -1. Junmei et al, 1999 +h1-c3-c -o 1 0.08 180.0 3. Junmei et al, 1999 +hc-c3-c -o 1 0.80 0.0 -1. Junmei et al, 1999 +hc-c3-c -o 1 0.08 180.0 3. Junmei et al, 1999 +hc-c3-c3-hc 1 0.15 0.0 3. Junmei et al, 1999 +hc-c3-c3-c3 1 0.16 0.0 3. Junmei et al, 1999 +hc-c3-c2-c2 1 0.38 180.0 -3. Junmei et al, 1999 +hc-c3-c2-c2 1 1.15 0.0 1. Junmei et al, 1999 +ho-oh-c3-c3 1 0.16 0.0 -3. Junmei et al, 1999 +ho-oh-c3-c3 1 0.25 0.0 1. Junmei et al, 1999 +ho-oh-c -o 1 2.30 180.0 -2. Junmei et al, 1999 +ho-oh-c -o 1 1.90 0.0 1. Junmei et al, 1999 +c2-c2-c -o 1 2.175 180.0 -2. Junmei et al, 1999 +c2-c2-c -o 1 0.30 0.0 3. Junmei et al, 1999 +c3-c2-c2-c3 1 6.65 180.0 -2. Junmei et al, 1999 +c3-c2-c2-c3 1 1.90 180.0 1. Junmei et al, 1999 +c3-c3-c3-c3 1 0.18 0.0 -3. Junmei et al, 1999 +c3-c3-c3-c3 1 0.25 180.0 -2. Junmei et al, 1999 +c3-c3-c3-c3 1 0.20 180.0 1. Junmei et al, 1999 +c3-c3-n3-c3 1 0.30 0.0 -3. Junmei et al, 1999 +c3-c3-n3-c3 1 0.48 180.0 2. Junmei et al, 1999 +c3-c3-os-c3 1 0.383 0.0 -3. +c3-c3-os-c3 1 0.1 180.0 2. +c3-c3-os-c 1 0.383 0.0 -3. Junmei et al, 1999 +c3-c3-os-c 1 0.80 180.0 1. Junmei et al, 1999 +c3-os-c3-os 1 0.10 0.0 -3. Junmei et al, 1999 +c3-os-c3-os 1 0.85 180.0 -2. Junmei et al, 1999 +c3-os-c3-os 1 1.35 180.0 1. Junmei et al, 1999 +c3-os-c3-na 1 0.383 0.0 -3. parm98.dat, TC,PC,PAK +c3-os-c3-na 1 0.65 0.0 2. Piotr et al. +o -c -os-c3 1 2.70 180.0 -2. Junmei et al, 1999 +o -c -os-c3 1 1.40 180.0 1. Junmei et al, 1999 +os-c3-na-c2 1 0.00 000.0 -2. parm98, TC,PC,PAK +os-c3-na-c2 1 2.50 0.0 1. parm98, TC,PC,PAK +os-c3-c3-os 1 0.144 0.0 -3. parm98, TC,PC,PAK +os-c3-c3-os 1 1.175 0.0 2. Piotr et al. +os-c3-c3-oh 1 0.144 0.0 -3. parm98, TC,PC,PAK +os-c3-c3-oh 1 1.175 0.0 2. parm98, TC,PC,PAK +oh-c3-c3-oh 1 0.144 0.0 -3. parm98, TC,PC,PAK +oh-c3-c3-oh 1 1.175 0.0 2. parm98, TC,PC,PAK +f -c3-c3-f 1 1.20 180.0 1. Junmei et al, 1999 +cl-c3-c3-cl 1 0.45 180.0 1. Junmei et al, 1999 +br-c3-c3-br 1 0.00 180.0 1. Junmei et al, 1999 +h1-c3-c3-os 1 0.25 0.0 1. Junmei et al, 1999 +h1-c3-c3-oh 1 0.25 0.0 1. Junmei et al, 1999 +h1-c3-c3-f 1 0.19 0.0 1. Junmei et al, 1999 +h1-c3-c3-cl 1 0.25 0.0 1. Junmei et al, 1999 +h1-c3-c3-br 1 0.55 0.0 1. Junmei et al, 1999 +hc-c3-c3-os 1 0.25 0.0 1. Junmei et al, 1999 +hc-c3-c3-oh 1 0.25 0.0 1. Junmei et al, 1999 +hc-c3-c3-f 1 0.19 0.0 1. Junmei et al, 1999 +hc-c3-c3-cl 1 0.25 0.0 1. Junmei et al, 1999 +hc-c3-c3-br 1 0.55 0.0 1. Junmei et al, 1999 + +X -o -c -o 1.1 180. 2. JCC,7,(1986),230 +X -X -c -o 10.5 180. 2. JCC,7,(1986),230 +X -X -ca-ha 1.1 180. 2. bsd.on C6H6 nmodes +X -X -n -hn 1.1 180. 2. JCC,7,(1986),230 +X -X -n2-hn 1.1 180. 2. JCC,7,(1986),230 +X -X -na-hn 1.1 180. 2. JCC,7,(1986),230 +X -c3-n -c3 1.1 180. 2. JCC,7,(1986),230 +X -n2-ca-n2 10.5 180. 2. JCC,7,(1986),230 +c -c2-c2-c3 1.1 180. 2. dac guess, 9/94 +c -ca-ca-c3 1.1 180. 2. dac guess, 9/94 +c -c3-n -hn 1.1 180. 2. Junmei et al.1999 +c -c3-n -o 1.1 180. 2. Junmei et al.1999 +c2-c2-na-c3 1.1 180. 2. +c2-c -c2-c3 1.1 180. 2. +c3-o -c -oh 1.1 180. 2. +c2-c3-c2-hc 1.1 180. 2. Junmei et al.1999 +c2-c3-ca-hc 1.1 180. 2. Junmei et al.1999 +c2-hc-c -o 1.1 180. 2. Junmei et al.1999 +c3-o -c -oh 1.1 180. 2. +c3-c2-c2-n2 1.1 180. 2. +c3-c2-c2-na 1.1 180. 2. +c3-ca-ca-n2 1.1 180. 2. +c3-ca-ca-na 1.1 180. 2. +ca-ca-ca-c2 1.1 180. 2. +ca-ca-ca-c3 1.1 180. 2. +ca-ca-ca-f 1.1 180. 2. Junmei et al.1999 +ca-ca-ca-cl 1.1 180. 2. Junmei et al.1999 +ca-ca-ca-br 1.1 180. 2. Junmei et al.1999 +ca-ca-ca-i 1.1 180. 2. Junmei et al.1999 +ca-ca-c -oh 1.1 180. 2. (not used in tyr!) +ca-ca-na-c3 1.1 180. 2. +ca-c -ca-c3 1.1 180. 2. +ca-hc-c -o 1.1 180. 2. Junmei et al.1999 +ca-n2-ca-n2 1.1 180. 2. dac, 10/94 +hc-o -c -oh 1.1 180. 2. Junmei et al.1999 +hc-o -c -os 1.1 180. 2. +n2-c2-ca-n2 1.1 180. 2. dac guess, 9/94 +n2-ca-ca-c3 1.1 180. 2. +n2-ca-ca-n2 1.1 180. 2. dac guess, 9/94 +na-ca-ca-c3 1.1 180. 2. +na-n2-ca-n2 1.1 180. 2. dac, 10/94 + + hw ow 0000. 0000. 4. flag for fast water + +n na n2 + +MOD4 RE + h1 1.3870 0.0157 Veenstra et al JCC,8,(1992),963 + h2 1.2870 0.0157 Veenstra et al JCC,8,(1992),963 + h3 1.1870 0.0157 Veenstra et al JCC,8,(1992),963 + h4 1.4090 0.0150 Spellmeyer, one electrowithdr. neighbor + h5 1.3590 0.0150 Spellmeyer, two electrowithdr. neighbor + ha 1.4590 0.0150 Spellmeyer + hc 1.4870 0.0157 OPLS + hn 0.6000 0.0157 !Ferguson base pair geom. + ho 0.0000 0.0000 OPLS Jorgensen, JACS,110,(1988),1657 + hp 0.6000 0.0157 same to hs (be careful !) + hs 0.6000 0.0157 W. Cornell CH3SH --> CH3OH FEP + hw 0.0000 0.0000 OPLS Jorgensen, JACS,110,(1988),1657 + hx 1.1000 0.0157 Veenstra et al JCC,8,(1992),963 + o 1.6612 0.2100 OPLS + oh 1.7210 0.2104 OPLS + os 1.6837 0.1700 OPLS ether + ow 1.7683 0.1520 TIP3P water model + c 1.9080 0.0860 OPLS + c1 1.9080 0.0860 cp C + c2 1.9080 0.0860 sp2 atom in the middle of C=CD-CD=C + c3 1.9080 0.1094 OPLS + ca 1.9080 0.0860 OPLS + cc 1.9080 0.0860 OPLS + cd 1.9080 0.0860 OPLS + ce 1.9080 0.0860 OPLS + cf 1.9080 0.0860 OPLS + cg 1.9080 0.0860 OPLS + ch 1.9080 0.0860 OPLS + cp 1.9080 0.0860 OPLS + cq 1.9080 0.0860 OPLS + cu 1.9080 0.0860 OPLS + cv 1.9080 0.0860 OPLS + cx 1.9080 0.0860 OPLS + cy 1.9080 0.0860 OPLS + n 1.8240 0.1700 OPLS + n1 1.8240 0.1700 OPLS + n2 1.8240 0.1700 OPLS + n3 1.8240 0.1700 OPLS + n4 1.8240 0.1700 OPLS + na 1.8240 0.1700 OPLS + nb 1.8240 0.1700 OPLS + nc 1.8240 0.1700 OPLS + nd 1.8240 0.1700 OPLS + ne 1.8240 0.1700 OPLS + nf 1.8240 0.1700 OPLS + nh 1.8240 0.1700 OPLS + no 1.8240 0.1700 OPLS + s 2.0000 0.2500 W. Cornell CH3SH and CH3SCH3 FEP's + s2 2.0000 0.2500 W. Cornell CH3SH and CH3SCH3 FEP's + s4 2.0000 0.2500 W. Cornell CH3SH and CH3SCH3 FEP's + s6 2.0000 0.2500 W. Cornell CH3SH and CH3SCH3 FEP's + sx 2.0000 0.2500 W. Cornell CH3SH and CH3SCH3 FEP's + sy 2.0000 0.2500 W. Cornell CH3SH and CH3SCH3 FEP's + sh 2.0000 0.2500 W. Cornell CH3SH and CH3SCH3 FEP's + ss 2.0000 0.2500 W. Cornell CH3SH and CH3SCH3 FEP's + p2 2.1000 0.2000 JCC,7,(1986),230; + p3 2.1000 0.2000 JCC,7,(1986),230; + p4 2.1000 0.2000 JCC,7,(1986),230; + p5 2.1000 0.2000 JCC,7,(1986),230; + pb 2.1000 0.2000 JCC,7,(1986),230; + px 2.1000 0.2000 JCC,7,(1986),230; + py 2.1000 0.2000 JCC,7,(1986),230; + f 1.75 0.061 Gough et al. JCC 13,(1992),963. + cl 1.948 0.265 Fox, JPCB,102,8070,(98),flex.mdl CHCl3 + br 2.22 0.320 Junmei + i 2.35 0.40 JCC,7,(1986),230; + +END + + + +---------------------------------------------------------------------------- + Miscellaneous + !!!! gaff is still in development, for some molecules, the current version + may have some problems. Please find the latest parameter file from + www.amber.ucsf.edu/antechamber.html + +(1) Parameters for p4 are not enough +(2) For bond lengty, bond angle and torsional angle parameters, hc and ha + are the generic names of aliphatic and aromatic hydrogen connected + to carbon, respectively. +(3) Defination priority of nitrogen: n>n3, n>n4, n>nh, n2>n, no>n, na>n + n4>nh +(5) Although the four atom types are same, maybe there are several different + parameters correspond to different bond types. You may need to use + additional atom types to apply them correctly (with antechamber package, + you can easily do this). +(4) Polarizabilities: mg2+ 0.120, f- 0.9743 +----------------------------------------------------------------------------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/gaff.prm Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,222 @@ +// +// Copyright (C) 2009 by Frank Peters <e.a.j.f.peters@tue.nl> +// +// This is a SMARTS template-file for GAFF-atom types +// +// It is attempted to obey the typing given in the "ATOMTYPE_GFF.DEF" +// file included with the antechamber package of amber10. +// There is no 1-to-1 correspondence between the ATD format and SMARTS. +// Therefore the current definitions need to be tested and possibly changed +// +// +// +// GAFF atomtypes defined using SMARTS +// [SMARTS] [atomtype id number] [description] +// must be sorted according to the ELEMENT and COMPLEXITY OF THE TYPERULE! +// +// Be careful lines do not exceed the maximum length of 80! + +atom [*] X +atom [#1X1] ha "other hydrogen e.g. on aromatic C" +atom [#1X1][CX4] hc "hydrogen on aliphatic C" +// "hydrogen on aliphatic C with 1 ewd" +atom [#1X1][CX4][#7,#8,#16,#17,#35,#53] h1 +// "hydrogen on aliphatic C with 2 ewd" +atom [#1X1][CX4]([#7,#8,#16,#17,#35,#53])[#7,#8,#16,#17,#35,#53] h2 +// "hydrogen on aliphatic C with 3 ewd" +atom [#1X1][CX4]([#7,#8,#16,#17,#35,#53])([#7,#8,#16,#17,#35,#53])[#7,#8] h3 +atom [#1X1][CX4]([#7,#8,#16,#17,#35,#53])([#7,#8,#16,#17,#35,#53])[#16,#17] h3 +atom [#1X1][CX4]([#7,#8,#16,#17,#35,#53])([#7,#8,#16,#17,#35,#53])[#35,#53] h3 +// "hydrogen on sp2 C with 1 ewd" +atom [#1X1][#6X3][#7,#8,#16,#17,#35,#53] h4 +// "hydrogen on sp2 C with 2 ewd" +atom [#1X1][#6X3]([#7,#8,#16,#17,#35,#53])[#7,#8,#16,#17,#35,#53] h5 +atom [#1X1][#6](N)(N)(N)N hx "" +atom [#1X1]O ho "hydrogen on oxygen" +atom [#1X1][Oh1] hw "hydrogen on water" +atom [#1X1]N hn "nitrogen" +atom [#1X1]S hs "sulphur" +atom [#1X1]P hp "phosphor" +atom [#6X4] c3 "other sp3 C" +atom [#6X4r3] cx "3-membered ring atom" +atom [#6X4r4] cy "4-membered ring atom" +atom [#6X3] c2 "other sp2 C" +atom [#6X3]=[O,S] c "C=O or C=S" +atom [#6X3](N)(N)N cz "" +atom [#6X3;R](=*)-*=* cc "inner sp2 C of conjugated ring systems" +atom [#6X3;R](=*)-*#* cc "inner sp2 C of conjugated ring systems" +atom [#6X3;R](#*)-*#* cc "inner sp2 C of conjugated ring systems" +atom [#6X3;!R](=*)-*=* ce "inner sp2 C of conjugated ring systems" +atom [#6X3;!R](#*)-*=* ce "inner sp2 C of conjugated ring systems" +atom [#6X3;!R](#*)-*#* ce "inner sp2 C of conjugated ring systems" +atom [cr6](c)(c)c cp "bridge aromatic c in byphenyl system" +atom [#6X3r3] cu "sp2 carbon in a 3-membered ring" +atom [#6X3r4] cv "sp2 carbon in a 4-membered ring" +atom [c] ca "pure aromatic atom" +atom [#6X2] c1 "other sp C" +atom [#6X2](=*)-*=* cg "sp C of conjugated system" +atom [#6X2](#*)-*=* cg "sp C of conjugated system" +atom [#6X2](#*)-*#* cg "sp C of conjugated system" +atom [#6X1] c1 "other sp C" + +atom [F]* f (-*) "general fluorine" +atom [Cl]* cl (-*) "general chlorine" +atom [Br]* br (-*) "general bromine" +atom [I]* i (-*) "general iodine" + +atom [#15X1] p2 "other sp2 P" +atom [#15X2] p2 "other sp2 P" +atom [#15X2;R](=*)-*=* pc "inner sp2 P of conjugated ring systems" +atom [#15X2;R](=*)-*#* pc "inner sp2 P of conjugated ring systems" +atom [#15X2;R](#*)-*#* pc "inner sp2 P of conjugated ring systems" +atom [#15X2;!R](=*)-*=* pe "inner sp2 P of conjugated chain system" +atom [#15X2;!R](=*)-*#* pe "inner sp2 P of conjugated chain system" +atom [#15X2;!R](#*)-*#* pe "inner sp2 P of conjugated chain system" +atom [#15;a] pb "aromatic P" +atom [#15X3] p3 "other sp3 P" +atom [#15X3](=*)-*=* px "sp2 P of conjugated system" +atom [#15X3](=*)-*#* px "sp2 P of conjugated system" +atom [#15X3]=[O,S] p4 "hypervalent P" +atom [#15X4] p5 "hypervalent P" +atom [#15X4](=*)-*=* py "P of conjugated system" +atom [#15X4](=*)-*#* py "P of conjugated system" +atom [#15X5] p5 "hypervalent P" +atom [#15X6] p5 "hypervalent P" + +atom [#7X1] n1 "sp1 N" + +atom [#7X2] n2 "sp2 N" +atom [#7X2](=*)=* n1 "sp1 N" +atom [#7X2](-*)#* n1 "sp1 N" +atom [#7X2;R](=*)-*=* nc "inner sp2 N of conjugated ring systems" +atom [#7X2;R](=*)-*#* nc "inner sp2 N of conjugated ring systems" +atom [#7X2;R](#*)-*#* nc "inner sp2 N of conjugated ring systems" +atom [#7X2;!R](=*)-*=* ne "inner sp2 N of conjugated chain system" +atom [#7X2;!R](=*)-*#* ne "inner sp2 N of conjugated chain system" +atom [#7X2;!R](#*)-*#* ne "inner sp2 N of conjugated chain system" +atom [nX2] nb "aromatic N" + +atom [#7X3] n3 "sp3 N" +atom [#7X3]a nh "amine N connected to aromatic ring" +atom [#7X3]=[CX3] nh "" +atom [#7X3]=[N2] nh "" +atom [#7X3]=[P2] nh "" +atom [#7X3]-[CX3]=[O,S] n "sp2 N in amides" +atom [#7X3](O)O no "N in nitro group" +atom [nX3] na "aromatic N" + +atom [#7X4] n4 "sp3 N" + +atom [OX1] o "sp2 O" +atom [OX2] os "sp3 O in esters and ethers" +atom [OX3] os "sp3 O in esters and ethers" +atom [OX2H] oh "sp3 O in hydroxyl group" +atom [OX3H] oh "sp3 O in hydroxyl group" + +atom [SX1] s "" +atom [SX2] ss "sp3 sulphur" +atom [SX2]=* s2 "sp2 sulphur" +atom [SX2]#* s2 "sp2 sulphur" +atom [SX2H] sh "sp3 S in thiol" +atom [SX3] s4 "hypervalent S" +atom [SX3](=*)-*=* sx "conjugated S" +atom [SX3](=*)-*#* sx "conjugated S" +atom [SX4] s6 "hypervalent S" +atom [SX4](=*)-*=* sy "conjugated S" +atom [SX4](=*)-*#* sy "conjugated S" +atom [SX5] s6 "hypervalent S" +atom [SX6] s6 "hypervalent S" + +atom [He] He "" +atom [Li] Li "" +atom [Be] Be "" +atom [B] B "" +atom [Ne] Ne "" +atom [Na] Na "" +atom [Mg] Mg "" +atom [Al] Al "" +atom [Si] Si "" +atom [Ar] Ar "" +atom [K] K "" +atom [Ca] Ca "" +atom [Sc] Sc "" +atom [Ti] Ti "" +atom [V] V "" +atom [Cr] Cr "" +atom [Mn] Mn "" +atom [Fe] Fe "" +atom [Co] Co "" +atom [Ni] Ni "" +atom [Cu] Cu "" +atom [Zn] Zn "" +atom [Ga] Ga "" +atom [Ge] Ge "" +atom [As] As "" +atom [Se] Se "" +atom [Kr] Kr "" +atom [Rb] Rb "" +atom [Sr] Sr "" +atom [Y] Y "" +atom [Zr] Zr "" +atom [Nb] Nb "" +atom [Mo] Mo "" +atom [Tc] Tc "" +atom [Ru] Ru "" +atom [Rh] Rh "" +atom [Pd] Pd "" +atom [Ag] Ag "" +atom [Cd] Cd "" +atom [In] In "" +atom [Sn] Sn "" +atom [Sb] Sb "" +atom [Te] Te "" +atom [Xe] Xe "" +atom [Cs] Cs "" +atom [Ba] Ba "" +atom [La] La "" +atom [Ce] Ce "" +atom [Pr] Pr "" +atom [Nd] Nd "" +atom [Pm] Pm "" +atom [Sm] Sm "" +atom [Eu] Eu "" +atom [Gd] Gd "" +atom [Tb] Tb "" +atom [Dy] Dy "" +atom [Ho] Ho "" +atom [Er] Er "" +atom [Tm] Tm "" +atom [Yb] Yb "" +atom [Lu] Lu "" +atom [Hf] Hf "" +atom [Ta] Ta "" +atom [W] W "" +atom [Re] Re "" +atom [Os] Os "" +atom [Ir] Ir "" +atom [Pt] Pt "" +atom [Au] Au "" +atom [Hg] Hg "" +atom [Tl] Tl "" +atom [Pb] Pb "" +atom [Bi] Bi "" +atom [Po] Po "" +atom [At] At "" +atom [Rn] Rn "" +atom [Fr] Fr "" +atom [Ra] Ra "" +atom [Ac] Ac "" +atom [Th] Th "" +atom [Pa] Pa "" +atom [U] U "" +atom [Np] Np "" +atom [Pu] Pu "" +atom [Am] Am "" +atom [Cm] Cm "" +atom [Bk] Bk "" +atom [Cf] Cf "" +atom [Es] Es "" +atom [Fm] Fm "" +atom [Md] Md "" +atom [No] No "" +atom [Lr] Lr ""
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/genheaders.sh Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,11 @@ +#!/bin/sh + +./bin2hex.pl aromatic.txt AromaticData >aromatic.h +./bin2hex.pl atomtyp.txt AtomTypeData >atomtyp.h +./bin2hex.pl bondtyp.txt BondTypeData >bondtyp.h +./bin2hex.pl element.txt ElementData >element.h +./bin2hex.pl isotope-small.txt IsotopeData ISOTOPE >isotope.h +./bin2hex.pl phmodel.txt PhModelData PHMODELDATA >phmodeldata.h +./bin2hex.pl resdata.txt ResidueData >resdata.h +./bin2hex.pl torlib.txt TorsionDefaults >torlib.h +./bin2hex.pl types.txt TypesData >types.h
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/ghemical.prm Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,476 @@ +// +// The parameters int his file are taken from ghemical. +// + +// atomtypes and typerules 09.05.2000 (based on Tripos 5.2 and MMFF94) +// [SMARTS] [atomtype id number] [typerule] [description] +// +// must be sorted according to the ELEMENT and COMPLEXITY OF THE TYPERULE!!! + +atom [*] FFFF +atom [#1] 0100 (-*) "general hydrogen" +atom [#6] 0600 (-*) "general sp3 carbon" +atom [#6]=* 0601 (=*) "general sp2 carbon" +atom [#6]#* 0602 (#*) "general sp carbon" +atom [#6](=*)=* 0602 (=*,=*) "allenic sp carbon" +atom [c] 0603 (~*,~*) "aromatic sp2 carbon" +//atom [#6^3r3] 0604 ([-*?*-]) "sp3 carbon in a 3-membered ring" +//atom [#6^3r4] 0605 ([-*?*?*-]) "sp3 carbon in a 4-membered ring" +atom [N] 0700 (-*) "general sp3 nitrogen" +atom [N]=* 0701 (=*) "general sp2 nitrogen" +atom [N]#* 0702 (#*) "general sp nitrogen" +atom [n] 0703 (~*,~*) "aromatic sp2 nitrogen" +atom [ND4] 0704 (-*,-*,-*,-*) "ammonium nitrogen" +atom [#7][C]=O 0705 (-C(=O)) "amide nitrogen" +atom [O] 0800 (-*) "general sp3 oxygen" +atom [O]=* 0801 (=*) "general sp2 oxygen" +atom [F]* 0900 (-*) "general fluorine" +atom [P] 0F00 (-*) "general sp3 phosphorus" +atom [S] 1000 (-*) "general sp3 sulphur" +atom [S]=* 1001 (=*) "general sp2 sulphur" +atom [S]=[#8] 1002 (=O) "sulfoxide sulphur" +atom [S](=O)=O 1003 (=O,=O) "sulfone sulphur" +atom [Cl]* 1100 (-*) "general chlorine" +atom [Br]* 2300 (-*) "general bromine" +atom [I]* 3500 (-*) "general iodine" + +// bond stretching parameters 09.05.2000 (based on Tripos 5.2 and MMFF94) +// [id #1] [id #2] [bondtype] [opt] [fc] +// +// wildcard atomtype is FFFF !!!!!!!!!!!!!!!!!!!!!!!!!!! +// wildcard atomtype is FFFF !!!!!!!!!!!!!!!!!!!!!!!!!!! +// wildcard atomtype is FFFF !!!!!!!!!!!!!!!!!!!!!!!!!!! +// +// parameters containing those should be left last since the first matching +// one is chosen. that is, choose normal parameters if there is any matching +// one, and take wildcarded one only if there is no better choice... +// +// [opt] = Å +// [fc] = kcal/(mol * Å^2) + +bond 0602 0602 T 1.204 1400.0 +bond 0602 0602 S 1.380 700.0 +bond 2300 0601 S 1.890 500.0 +bond 0602 0601 S 1.440 1340.0 +bond 0602 0601 D 1.440 1340.0 +bond 0601 0601 D 1.335 1340.0 +bond 0601 0601 S 1.470 700.0 +bond 0602 0600 S 1.458 640.0 +bond 0601 0600 S 1.501 639.0 +bond 0600 0600 S 1.540 633.6 +bond 2300 0603 S 1.850 500.0 +bond 0602 0603 S 1.440 1340.0 +bond 0601 0603 S 1.510 1340.0 +bond 0600 0603 S 1.525 640.0 +bond 0603 0603 C 1.395 1400.0 +bond 0603 0603 S 1.480 1000.0 +bond 0601 1100 S 1.750 520.0 +bond 0600 1100 S 1.767 600.0 +bond 0603 1100 S 1.750 513.4 +bond 0601 2300 S 1.850 520.0 +bond 0600 2300 S 1.867 600.0 +bond 0603 2300 S 1.850 513.4 +bond 0601 0900 S 1.330 1200.0 +bond 0600 0900 S 1.360 600.0 +bond 0603 0900 S 1.330 500.0 +bond 0602 0100 S 1.056 700.0 +bond 0601 0100 S 1.089 692.0 +bond 0600 0100 S 1.100 662.4 +bond 0603 0100 S 1.084 692.0 +bond 0600 3500 S 2.050 490.0 //added 20050225 +bond 0601 3500 S 2.050 490.0 //added 20050225 +bond 0602 3500 S 2.050 490.0 //added 20050225 +bond 0603 3500 S 2.050 490.0 +bond 0602 0702 T 1.158 1600.0 +bond 0602 0701 S 1.330 1300.0 +bond 0602 0701 D 1.330 1300.0 +bond 0601 0701 D 1.270 1305.9 +bond 0601 0701 S 1.444 1300.0 +bond 0600 0701 S 1.440 760.2 +bond 0603 0701 S 1.346 1305.9 +bond 0701 0701 D 1.346 1305.9 +bond 0701 0701 S 1.418 1300.0 +bond 0601 0700 S 1.330 1300.0 +bond 0600 0700 S 1.470 760.0 +bond 0603 0700 S 1.410 720.0 +bond 0100 0700 S 1.080 692.0 +bond 0601 0704 S 1.330 1300.0 +bond 0600 0704 S 1.470 760.0 +bond 0603 0704 S 1.410 720.0 +bond 0601 0705 S 1.345 870.1 +bond 0600 0705 S 1.450 677.6 +bond 0603 0705 S 1.416 1090.1 +bond 0100 0705 S 1.000 700.0 +bond 0701 0705 S 1.440 667.6 +bond 0705 0705 S 1.450 744.5 +bond 0603 0703 C 1.346 1305.9 +bond 0703 0703 C 1.330 1400.0 +bond 0601 0801 D 1.220 1555.2 +bond 0705 0801 S 1.240 1120.0 +bond 0705 0801 D 1.210 680.0 +bond 0601 0800 S 1.330 699.8 +bond 0600 0800 S 1.430 618.9 +bond 0603 0800 S 1.390 700.0 +bond 0100 0800 S 0.950 1007.5 +bond 0701 0800 S 1.405 1200.0 +bond 0705 0800 S 1.400 620.0 +bond 0800 0800 S 1.480 1172.2 +bond 0600 0F00 S 1.830 407.6 +bond 0801 0F00 S 1.490 1400.0 +bond 0801 0F00 D 1.490 1400.0 +bond 0800 0F00 S 1.600 800.0 +bond 0601 1001 D 1.710 400.0 +bond 0600 1001 S 1.800 381.6 +bond 0603 1001 S 1.740 700.0 +bond 0601 1000 S 1.780 360.0 +bond 0600 1000 S 1.817 381.6 +bond 0603 1000 S 1.770 360.0 +bond 0700 1000 S 1.625 360.0 +bond 0704 1000 S 1.625 360.0 +bond 0801 1000 D 1.450 600.0 +bond 1000 1000 S 2.030 600.0 +bond 0601 1002 S 1.710 360.0 +bond 0600 1002 S 1.800 381.6 +bond 0801 1002 D 1.450 600.0 +bond 0800 1002 S 1.500 600.0 +bond 0600 1003 S 1.800 381.6 +bond 0801 1003 D 1.450 600.0 +bond 0800 1003 S 1.500 600.0 +bond FFFF 0100 S 1.008 700.0 + +// angle bending parameters 09.05.2000 (based on Tripos 5.2 and MMFF94) +// [id #1] [id #2] [id #3] [bt12][bt23] [opt] [fc] +// +// ordering should be made similarly as in parameters1.txt!!!!!!! +// original Tripos 5.2 did not contain the bond types here at all... +// +// [opt] = deg +// [fc] = kcal/(mol * deg^2) + +angle 0602 0602 0601 ?? 180.0 0.040 +angle 0601 0602 0702 ?? 180.0 0.040 +angle 0600 0602 0702 ?? 180.0 0.040 +angle 0603 0602 0702 ?? 180.0 0.040 +angle 0702 0602 0800 ?? 180.0 0.040 +angle 2300 0601 2300 ?? 120.0 0.020 +angle 2300 0601 0601 ?? 120.0 0.036 +angle 0601 0601 0601 ?? 121.7 0.018 +angle 0602 0601 0600 ?? 120.0 0.024 +angle 0601 0601 0600 ?? 121.0 0.024 +angle 0600 0601 0600 ?? 116.4 0.046 +angle 0602 0601 0603 ?? 120.0 0.024 +angle 0601 0601 0603 ?? 120.0 0.026 +angle 0600 0601 0603 ?? 120.0 0.024 +angle 0603 0601 0603 ?? 120.0 0.024 +angle 0601 0601 1100 ?? 120.0 0.036 +angle 0603 0601 1100 ?? 120.0 0.036 +angle 1100 0601 1100 ?? 122.0 0.030 +angle 0601 0601 2300 ?? 120.0 0.036 +angle 0603 0601 2300 ?? 120.0 0.036 +angle 2300 0601 2300 ?? 122.0 0.030 +angle 0602 0601 0701 ?? 123.0 0.070 +angle 0601 0601 0701 ?? 120.0 0.024 +angle 0600 0601 0701 ?? 118.0 0.020 +angle 0603 0601 0701 ?? 120.0 0.040 +angle 0601 0601 0700 ?? 120.0 0.024 +angle 0600 0601 0700 ?? 118.0 0.040 +angle 0701 0601 0700 ?? 121.8 0.030 +angle 0700 0601 0700 ?? 116.4 0.030 +angle 0601 0601 0705 ?? 120.0 0.024 +angle 0600 0601 0705 ?? 117.0 0.020 +angle 0603 0601 0705 ?? 120.0 0.040 +angle 0701 0601 0705 ?? 123.0 0.070 +angle 0705 0601 0705 ?? 120.0 0.030 +angle 0602 0601 0801 ?? 120.0 0.060 +angle 0601 0601 0801 ?? 120.0 0.026 +angle 0600 0601 0801 ?? 120.0 0.026 +angle 0603 0601 0801 ?? 120.0 0.026 +angle 0700 0601 0801 ?? 120.0 0.026 +angle 0705 0601 0801 ?? 123.0 0.030 +angle 0601 0601 0800 ?? 120.0 0.072 +angle 0600 0601 0800 ?? 114.0 0.030 +angle 0603 0601 0800 ?? 120.0 0.030 +angle 0705 0601 0800 ?? 110.5 0.014 +angle 0801 0601 0800 ?? 120.0 0.030 +angle 0701 0601 1000 ?? 125.6 0.028 +angle 0705 0601 1000 ?? 111.5 0.030 +angle 0801 0601 1000 ?? 125.0 0.016 +angle 0601 0600 0601 ?? 109.5 0.018 +angle 0602 0600 0600 ?? 109.5 0.024 +angle 0601 0600 0600 ?? 109.5 0.018 +angle 0600 0600 0600 ?? 109.5 0.024 +angle 0601 0600 0603 ?? 109.5 0.018 +angle 0600 0600 0603 ?? 109.5 0.024 +angle 0603 0600 0603 ?? 109.5 0.018 +angle 0600 0600 1100 ?? 109.5 0.020 +angle 1100 0600 1100 ?? 109.5 0.020 +angle 0600 0600 2300 ?? 109.5 0.020 +angle 2300 0600 2300 ?? 109.5 0.020 +angle 0603 0600 0900 ?? 110.0 0.024 +angle 0900 0600 0900 ?? 109.5 0.040 +angle 0601 0600 0100 ?? 110.0 0.016 +angle 0100 0600 0100 ?? 109.5 0.024 +angle 0600 0600 0701 ?? 109.5 0.018 +angle 0601 0600 0700 ?? 109.5 0.018 +angle 0600 0600 0700 ?? 109.5 0.024 +angle 0603 0600 0700 ?? 109.5 0.018 +angle 0601 0600 0705 ?? 109.5 0.022 +angle 0600 0600 0705 ?? 109.5 0.018 +angle 0603 0600 0705 ?? 109.5 0.020 +angle 0100 0600 0705 ?? 110.0 0.020 +angle 0701 0600 0705 ?? 109.5 0.020 +angle 0705 0600 0705 ?? 109.5 0.040 +angle 0900 0600 0703 ?? 109.5 0.040 +angle 0601 0600 0800 ?? 109.5 0.022 +angle 0600 0600 0800 ?? 109.5 0.022 +angle 0603 0600 0800 ?? 109.5 0.018 +angle 0705 0600 0800 ?? 109.5 0.020 +angle 0800 0600 0800 ?? 109.5 0.020 +angle 0600 0600 0F00 ?? 112.0 0.014 +angle 0601 0600 1001 ?? 109.5 0.018 +angle 0600 0600 1001 ?? 109.5 0.018 +angle 0705 0600 1001 ?? 109.5 0.040 +angle 0601 0600 1000 ?? 107.8 0.018 +angle 0600 0600 1000 ?? 107.8 0.018 +angle 0603 0600 1000 ?? 107.8 0.018 +angle 0705 0600 1000 ?? 109.5 0.024 +angle 0800 0600 1000 ?? 107.8 0.020 +angle 2300 0603 0603 ?? 120.0 0.036 +angle 0601 0603 0603 ?? 120.0 0.024 +angle 0600 0603 0603 ?? 120.0 0.024 +angle 0603 0603 0603 ?? 120.0 0.024 +angle 0603 0603 1100 ?? 120.0 0.036 +angle 0603 0603 2300 ?? 120.0 0.036 +angle 0603 0603 0900 ?? 120.0 0.036 +angle 0603 0603 3500 ?? 120.0 0.036 +angle 0600 0603 0701 ?? 120.0 0.040 +angle 0603 0603 0701 ?? 120.0 0.040 +angle 0701 0603 0701 ?? 120.0 0.040 +angle 0603 0603 0700 ?? 120.0 0.062 +angle 0600 0603 0705 ?? 120.0 0.040 +angle 0603 0603 0705 ?? 120.0 0.062 +angle 0701 0603 0705 ?? 118.0 0.040 +angle 0705 0603 0705 ?? 120.0 0.030 +angle 0601 0603 0703 ?? 120.0 0.040 +angle 0600 0603 0703 ?? 120.0 0.040 +angle 0603 0603 0703 ?? 120.0 0.024 +angle 0705 0603 0703 ?? 118.0 0.040 +angle 0600 0603 0800 ?? 120.0 0.040 +angle 0603 0603 0800 ?? 120.0 0.062 +angle 0603 0603 1001 ?? 120.0 0.062 +angle 0603 0603 1000 ?? 120.0 0.062 +angle 0602 0701 0601 ?? 120.0 0.040 +angle 0601 0701 0601 ?? 123.0 0.080 +angle 0601 0701 0600 ?? 110.0 0.082 +angle 0601 0701 0603 ?? 123.0 0.080 +angle 0600 0701 0603 ?? 110.0 0.082 +angle 0603 0701 0603 ?? 120.0 0.040 +angle 0601 0701 0701 ?? 112.0 0.044 +angle 0600 0701 0701 ?? 118.0 0.040 +angle 0603 0701 0701 ?? 118.0 0.040 +angle 0601 0701 0705 ?? 120.0 0.044 +angle 0601 0701 0800 ?? 105.0 0.044 +angle 0601 0700 0600 ?? 110.0 0.040 +angle 0600 0700 0600 ?? 109.5 0.018 +angle 0600 0700 0603 ?? 118.0 0.040 +angle 0603 0700 0603 ?? 118.0 0.040 +angle 0600 0700 1001 ?? 109.5 0.040 +angle 0600 0704 0600 ?? 109.5 0.018 +angle 0601 0705 0601 ?? 120.0 0.018 +angle 0601 0705 0600 ?? 118.0 0.044 +angle 0600 0705 0600 ?? 122.0 0.040 +angle 0601 0705 0603 ?? 120.0 0.052 +angle 0600 0705 0603 ?? 118.0 0.044 +angle 0603 0705 0603 ?? 120.0 0.044 +angle 0601 0705 0100 ?? 119.0 0.016 +angle 0600 0705 0100 ?? 117.0 0.020 +angle 0601 0705 0701 ?? 120.0 0.018 +angle 0600 0705 0701 ?? 120.0 0.024 +angle 0603 0705 0701 ?? 109.5 0.044 +angle 0601 0705 0705 ?? 120.0 0.018 +angle 0600 0705 0705 ?? 120.0 0.024 +angle 0603 0705 0705 ?? 120.0 0.052 +angle 0601 0705 0801 ?? 120.0 0.024 +angle 0600 0705 0801 ?? 120.0 0.020 +angle 0603 0705 0801 ?? 120.0 0.024 +angle 0801 0705 0801 ?? 120.0 0.020 +angle 0603 0703 0603 ?? 120.0 0.040 +angle 0601 0800 0601 ?? 110.0 0.020 +angle 0601 0800 0600 ?? 109.5 0.044 +angle 0600 0800 0600 ?? 109.5 0.044 +angle 0601 0800 0603 ?? 110.0 0.020 +angle 0600 0800 0603 ?? 110.0 0.020 +angle 0603 0800 0603 ?? 110.0 0.020 +angle 0601 0800 0701 ?? 108.5 0.044 +angle 0600 0800 0800 ?? 103.9 0.094 +angle 0600 0800 0F00 ?? 120.0 0.010 +angle 0801 0F00 0801 ?? 109.5 0.020 +angle 0801 0F00 0800 ?? 109.5 0.020 +angle 0800 0F00 0800 ?? 109.5 0.020 +angle 0600 1001 0700 ?? 111.0 0.040 +angle 0603 1001 0700 ?? 111.0 0.040 +angle 0601 1000 0600 ?? 94.3 0.022 +angle 0600 1000 0600 ?? 98.0 0.020 +angle 0603 1000 0603 ?? 97.5 0.062 +angle 0603 1000 1000 ?? 102.9 0.060 +angle 0801 1003 0801 ?? 118.0 0.040 +angle FFFF 0601 0100 ?? 120.0 0.012 +angle FFFF 0600 0100 ?? 109.5 0.016 +angle FFFF 1002 0801 ?? 107.0 0.040 +angle FFFF 1003 0801 ?? 107.0 0.040 +angle FFFF 0602 FFFF ?? 180.0 0.040 +angle FFFF 0601 FFFF ?? 120.0 0.024 +angle FFFF 0600 FFFF ?? 109.5 0.020 +angle FFFF 0603 FFFF ?? 120.0 0.024 +angle FFFF 0702 FFFF ?? 180.0 0.080 +angle FFFF 0701 FFFF ?? 120.0 0.040 +angle FFFF 0700 FFFF ?? 109.5 0.040 +angle FFFF 0704 FFFF ?? 109.5 0.010 +angle FFFF 0705 FFFF ?? 120.0 0.020 +angle FFFF 0703 FFFF ?? 120.0 0.020 +angle FFFF 0800 FFFF ?? 109.5 0.020 +angle FFFF 0F00 FFFF ?? 109.5 0.020 +angle FFFF 1001 FFFF ?? 110.5 0.040 +angle FFFF 1000 FFFF ?? 97.0 0.020 + +// torsion parameters 09.05.2000 (based on Tripos 5.2 and MMFF94) +// [id #1] [id #2] [id #3] [id #4] [bt12][bt23][bt34] [k] [n] [s] +// +// ordering should be made similarly as in parameters1.txt!!!!!!! +// original Tripos 5.2 did not contain all these bond types here... +// +// [k] = kcal/mol (rotational barrier ???) + +torsion 0801 0601 0600 0600 ?S? 0.700 - 3.0 +torsion 0601 0600 0600 0601 ?S? 0.040 + 3.0 +torsion 0601 0600 0600 0600 ?S? 0.126 + 3.0 +torsion 0600 0600 0600 0600 ?S? 0.500 + 3.0 +torsion 0601 0601 0600 0601 ?S? 0.126 - 3.0 +torsion 0601 0601 0600 0100 ?S? 0.273 - 3.0 +torsion 0600 0601 0600 0601 ?S? 0.126 + 3.0 +torsion 0600 0601 0600 0600 ?S? 0.126 + 3.0 +torsion 0600 0601 0600 0100 ?S? 0.274 + 3.0 +torsion 0100 0601 0600 0601 ?S? 0.274 + 3.0 +torsion 0100 0601 0600 0600 ?S? 0.274 + 3.0 +torsion 0100 0601 0600 0100 ?S? 0.274 + 3.0 +torsion 0601 0601 0600 0600 ?S? 0.126 - 3.0 +torsion FFFF 0601 0600 0601 ?S? 0.126 + 3.0 +torsion FFFF 0601 0600 0600 ?S? 0.126 + 3.0 +torsion FFFF 0601 0600 0100 ?S? 0.274 + 3.0 +torsion FFFF 0600 0600 0100 ?S? 0.320 + 3.0 +torsion 0601 0601 0600 FFFF ?S? 0.126 - 3.0 +torsion 0600 0601 0600 FFFF ?S? 0.126 + 3.0 +torsion 0100 0601 0600 FFFF ?S? 0.274 + 3.0 +torsion FFFF 0602 0602 FFFF ?T? 0.000 + 1.0 +torsion FFFF 0602 0602 FFFF ?S? 0.000 + 1.0 +torsion FFFF 0602 0601 FFFF ?S? 0.000 + 1.0 +torsion FFFF 0602 0601 FFFF ?D? 0.000 + 1.0 +torsion FFFF 0601 0601 FFFF ?D? 12.500 - 2.0 +torsion FFFF 0601 0601 FFFF ?S? 1.424 - 2.0 +torsion FFFF 0602 0600 FFFF ?S? 0.000 + 1.0 +torsion FFFF 0601 0600 FFFF ?S? 0.120 - 3.0 +torsion FFFF 0600 0600 FFFF ?S? 0.200 + 3.0 +torsion FFFF 0602 0603 FFFF ?S? 0.000 + 1.0 +torsion FFFF 0601 0603 FFFF ?S? 1.600 - 2.0 +torsion FFFF 0600 0603 FFFF ?S? 0.120 - 3.0 +torsion FFFF 0603 0603 FFFF ?C? 2.000 - 2.0 +torsion FFFF 0603 0603 FFFF ?S? 0.600 - 2.0 +torsion FFFF 0602 0701 FFFF ?S? 0.000 + 1.0 +torsion FFFF 0602 0701 FFFF ?D? 0.000 + 1.0 +torsion FFFF 0601 0701 FFFF ?D? 12.000 - 2.0 +torsion FFFF 0601 0701 FFFF ?S? 12.000 - 2.0 +torsion FFFF 0600 0701 FFFF ?S? 0.400 - 3.0 +torsion FFFF 0603 0701 FFFF ?S? 1.600 - 2.0 +torsion FFFF 0701 0701 FFFF ?D? 1.600 - 2.0 +torsion FFFF 0701 0701 FFFF ?S? 1.600 - 2.0 +torsion FFFF 0601 0700 FFFF ?S? 0.120 - 3.0 +torsion FFFF 0600 0700 FFFF ?S? 0.200 + 3.0 +torsion FFFF 0603 0700 FFFF ?S? 0.120 - 3.0 +torsion FFFF 0700 0700 FFFF ?S? 0.200 + 3.0 +torsion FFFF 0601 0705 FFFF ?S? 6.460 - 2.0 +torsion FFFF 0600 0705 FFFF ?S? 0.200 + 3.0 +torsion FFFF 0603 0705 FFFF ?S? 1.600 - 2.0 +torsion FFFF 0701 0705 FFFF ?S? 1.600 - 2.0 +torsion FFFF 0700 0705 FFFF ?S? 0.120 - 3.0 +torsion FFFF 0705 0705 FFFF ?S? 1.600 - 2.0 +torsion FFFF 0603 0703 FFFF ?C? 1.600 - 2.0 +torsion FFFF 0601 0800 FFFF ?S? 5.800 - 2.0 +torsion FFFF 0600 0800 FFFF ?S? 1.200 + 3.0 +torsion FFFF 0603 0800 FFFF ?S? 1.200 - 2.0 +torsion FFFF 0701 0800 FFFF ?S? 1.000 + 2.0 +torsion FFFF 0700 0800 FFFF ?S? 0.200 + 3.0 +torsion FFFF 0601 0F00 FFFF ?S? 1.000 - 2.0 +torsion FFFF 0600 0F00 FFFF ?S? 0.400 + 3.0 +torsion FFFF 0603 0F00 FFFF ?S? 1.000 + 3.0 +torsion FFFF 0800 0F00 FFFF ?S? 0.400 + 3.0 +torsion FFFF 0601 1001 FFFF ?D? 1.000 - 2.0 +torsion FFFF 0600 1001 FFFF ?S? 0.400 + 3.0 +torsion FFFF 0603 1001 FFFF ?S? 1.000 + 3.0 +torsion FFFF 0700 1001 FFFF ?S? 0.400 + 3.0 +torsion FFFF 0601 1000 FFFF ?S? 1.000 - 2.0 +torsion FFFF 0600 1000 FFFF ?S? 0.400 + 3.0 +torsion FFFF 0603 1000 FFFF ?S? 1.000 + 3.0 +torsion FFFF 1000 1000 FFFF ?S? 4.000 + 3.0 + +// lenjon-parameters 09.05.2000 (based on Tripos 5.2 and MMFF94) +// [id] [r] [k] +// +// [r] = Å +// [k] = kcal/mol + +vdw 0100 1.50 0.042 +vdw 0600 1.70 0.107 +vdw 0601 1.70 0.107 +vdw 0602 1.70 0.107 +vdw 0603 1.70 0.107 +vdw 0604 1.70 0.107 +vdw 0605 1.70 0.107 +vdw 0700 1.55 0.095 +vdw 0701 1.55 0.095 +vdw 0702 1.55 0.095 +vdw 0703 1.55 0.095 +vdw 0704 1.55 0.095 +vdw 0705 1.55 0.095 +vdw 0800 1.52 0.116 +vdw 0801 1.52 0.116 +vdw 0900 1.47 0.109 +vdw 0F00 1.80 0.314 +vdw 1000 1.80 0.314 +vdw 1001 1.80 0.314 +vdw 1002 1.80 0.314 +vdw 1003 1.80 0.314 +vdw 1100 1.75 0.314 +vdw 2300 1.85 0.434 +vdw 3500 1.98 0.623 +vdw FFFF 1.50 0.042 + +// atomic charge parameters 09.05.2000 (based on Tripos 5.2 and MMFF94) +// [id #1] [id #2] [delta] +// +// THE NUMERICAL VALUES HERE ARE NOT PROPERLY CHECKED!!! +// +// sign of [delta] is inverted if order of atoms is switched... +// sign of [delta] is inverted if order of atoms is switched... +// sign of [delta] is inverted if order of atoms is switched... + +charge 0601 0100 S +0.100 +charge 0602 0100 S +0.200 +charge 0603 0100 S +0.100 +charge 0604 0100 S +0.050 +charge 0700 0100 S +0.100 +charge 0701 0100 S +0.200 +charge 0702 0100 S +0.250 +charge 0703 0100 S +0.250 +charge 0704 0100 S +0.200 +charge 0705 0100 S +0.150 +charge 0800 0100 S +0.250 +charge 0801 0601 D +0.100 +charge 0900 0100 S +0.500 +charge 0900 0600 S +0.125 +charge 1002 0801 D +0.200 +charge 1003 0801 D +0.200 +charge 1100 0600 S +0.150 +charge 2300 0600 S +0.175 +charge 3500 0600 S +0.200 + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/isotope-small.txt Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,141 @@ +############################################################################## +# # +# Open Babel file: isotope-small.txt # +# # +# Copyright (c) 2002-2003 by Geoffrey R. Hutchison # +# Part of the Open Babel package, under the GNU General Public License (GPL)# +# # +# Small isotope table with most frequently-used isotopes (as default data) # +# (GRH currently trimmed up to atomic # 40 and #100+) # +# Note that this is only used when data files are not available # +# and hence is not as likely to be updated frequently--it is hand-edited! # +# # +# This file has a series of lines, one for each element # +# (i.e. line 0 = neutron, line 1 = hydrogen, line 2 = helium, etc.) # +# Each line: Atomic #, 0 then exact mass of most abundant isotope # +# then a list of isotopes as int, float pairs corresponding to masses # +# # +# CAUTION: Masses have been zero-padded to 6 decimal places # +# (we don't currently have a math package that can deal with sig. fig.) # +# so trailing zeros may not be significant and/or useful # +# # +# Values are compiled from "The 1995 update to the atomic mass evaluation" # +# by G.Audi and A.H.Wapstra # +# Nuclear Physics A595 vol. 4 p.409-480, December 25, 1995. # +# as made available in the mass_rmd.mas95 file # +# # +# Currently: 110 lines (neutron, H to Mt) # +# (note that since element 0 often represents a dummy atom, the default # +# mass is 0 amu, *not* the mass of a neutron, accessible as isotope 1) # +# # +############################################################################## +0 0 0.000000 1 1.008664 +1 0 1.007825 1 1.007825 2 2.014101 3 3.016049 +2 0 4.002603 3 3.016029 4 4.002603 5 5.012220 6 6.018888 7 7.028030 8 8.033922 9 9.043820 10 10.052400 +3 0 7.016004 5 5.012540 6 6.015122 7 7.016004 8 8.022486 9 9.026789 10 10.035481 11 11.043796 +4 0 9.012182 6 6.019726 7 7.016929 8 8.005305 9 9.012182 10 10.013533 11 11.021658 12 12.026921 14 14.042820 +5 0 11.009305 7 7.029920 8 8.024606 9 9.013328 10 10.012937 11 11.009305 12 12.014352 13 13.017780 14 14.025404 15 15.031097 17 17.046930 19 19.063730 +6 0 12.000000 8 8.037675 9 9.031040 10 10.016853 11 11.011433 12 12.000000 13 13.003354 14 14.003241 15 15.010599 16 16.014701 17 17.022584 18 18.026760 19 19.035250 20 20.040320 +7 0 14.003074 12 12.018613 13 13.005738 14 14.003074 15 15.000108 16 16.006101 17 17.008450 18 18.014082 19 19.017027 20 20.023370 21 21.027090 22 22.034440 23 23.040510 +8 0 15.994914 12 12.034405 13 13.024810 14 14.008595 15 15.003065 16 15.994914 17 16.999131 18 17.999160 19 19.003579 20 20.004076 21 21.008655 22 22.009970 23 23.015690 24 24.020370 +9 0 18.998403 15 15.018010 16 16.011466 17 17.002095 18 18.000937 19 18.998403 20 19.999981 21 20.999948 22 22.002999 23 23.003570 24 24.008100 25 25.012090 26 26.019630 27 27.026890 +10 0 19.992440 16 16.025757 17 17.017700 18 18.005697 19 19.001879 20 19.992440 21 20.993846 22 21.991385 23 22.994467 24 23.993615 25 24.997790 26 26.000460 27 27.007620 28 28.012110 29 29.019350 +11 0 22.989769 19 19.013879 20 20.007348 21 20.997655 22 21.994436 23 22.989769 24 23.990963 25 24.989954 26 25.992590 27 26.994010 28 27.998890 29 29.002810 30 30.009230 31 31.013600 32 32.019650 33 33.027390 34 34.034900 35 35.044180 +12 0 23.985041 20 20.018863 21 21.011714 22 21.999574 23 22.994124 24 23.985041 25 24.985837 26 25.982593 27 26.984340 28 27.983876 29 28.988550 30 29.990460 31 30.996550 32 31.999150 33 33.005590 +13 0 26.981538 22 22.019520 23 23.007265 24 23.999941 25 24.990428 26 25.986891 27 26.981538 28 27.981910 29 28.980444 30 29.982960 31 30.983946 32 31.988120 33 32.990870 34 33.996930 35 34.999940 36 36.006350 +14 0 27.976926 22 22.034530 24 24.011546 25 25.004107 26 25.992330 27 26.986704 28 27.976926 29 28.976494 30 29.973770 31 30.975363 32 31.974148 33 32.978001 34 33.978576 35 34.984580 36 35.986690 37 36.993000 38 37.995980 39 39.002300 +15 0 30.973761 26 26.011780 27 26.999190 28 27.992312 29 28.981801 30 29.978313 31 30.973761 32 31.973907 33 32.971725 34 33.973636 35 34.973314 36 35.978260 37 36.979610 38 37.984470 39 38.986420 40 39.991050 41 40.994800 42 42.000090 +16 0 31.972070 27 27.018800 28 28.004370 29 28.996610 30 29.984903 31 30.979554 32 31.972070 33 32.971458 34 33.967866 35 34.969032 36 35.967080 37 36.971125 38 37.971163 39 38.975140 40 39.975470 41 40.980030 42 41.981490 43 42.986600 44 43.988320 +17 0 34.968852 31 30.992420 32 31.985689 33 32.977451 34 33.973761 35 34.968852 36 35.968306 37 36.965902 38 37.968010 39 38.968007 40 39.970420 41 40.970650 42 41.973170 43 42.974200 44 43.978540 45 44.979700 46 45.984120 47 46.987950 +18 0 39.962383 31 31.012130 32 31.997660 33 32.989930 34 33.980270 35 34.975256 36 35.967546 37 36.966775 38 37.962732 39 38.964313 40 39.962383 41 40.964500 42 41.963050 43 42.965670 44 43.965365 45 44.968090 46 45.968090 47 46.972190 +19 0 38.963706 35 34.988012 36 35.981293 37 36.973376 38 37.969080 39 38.963706 40 39.963998 41 40.961825 42 41.962403 43 42.960716 44 43.961560 45 44.960700 46 45.961976 47 46.961678 48 47.965513 49 48.967450 50 49.972780 51 50.976380 52 51.982610 53 52.987120 54 53.993990 +20 0 39.962591 35 35.004770 36 35.993090 37 36.985872 38 37.976319 39 38.970717 40 39.962591 41 40.962278 42 41.958618 43 42.958766 44 43.955481 45 44.956185 46 45.953692 47 46.954546 48 47.952534 49 48.955673 50 49.957518 51 50.961470 52 51.965100 53 52.970050 +21 0 44.955910 40 39.977964 41 40.969251 42 41.965516 43 42.961151 44 43.959403 45 44.955910 46 45.955170 47 46.952408 48 47.952235 49 48.950024 50 49.952187 51 50.953603 52 51.956650 53 52.959240 54 53.963000 55 54.967430 +22 0 47.947947 39 39.001320 40 39.990500 41 40.983130 42 41.973032 43 42.968523 44 43.959690 45 44.958124 46 45.952629 47 46.951763 48 47.947947 49 48.947870 50 49.944792 51 50.946616 52 51.946898 53 52.949730 54 53.950870 55 54.955120 56 55.957990 57 56.962900 58 57.966110 +23 0 50.943963 43 42.980650 44 43.974400 45 44.965782 46 45.960199 47 46.954906 48 47.952254 49 48.948516 50 49.947162 51 50.943963 52 51.944779 53 52.944343 54 53.946444 55 54.947240 56 55.950360 57 56.952360 58 57.956650 59 58.959300 60 59.964500 61 60.967410 +24 0 51.940511 43 42.997710 44 43.985470 45 44.979160 46 45.968362 47 46.962907 48 47.954036 49 48.951341 50 49.946049 51 50.944771 52 51.940511 53 52.940653 54 53.938884 55 54.940844 56 55.940645 57 56.943750 58 57.944250 59 58.948630 60 59.949730 61 60.954090 62 61.955800 63 62.961860 +25 0 54.938049 46 45.986720 47 46.976100 48 47.968870 49 48.959623 50 49.954244 51 50.948215 52 51.945570 53 52.941294 54 53.940363 55 54.938049 56 55.938909 57 56.938287 58 57.939990 59 58.940450 60 59.943190 61 60.944460 62 61.947970 63 62.949810 64 63.953730 65 64.956100 66 65.960820 +26 0 55.934942 46 46.000810 47 46.992890 48 47.980560 49 48.973610 50 49.962990 51 50.956825 52 51.948117 53 52.945312 54 53.939614 55 54.938298 56 55.934942 57 56.935398 58 57.933280 59 58.934880 60 59.934077 61 60.936749 62 61.936770 63 62.940120 64 63.940870 65 64.944940 66 65.945980 67 66.950000 68 67.952510 69 68.957700 +27 0 58.933200 50 49.981540 51 50.970720 52 51.963590 53 52.954225 54 53.948464 55 54.942003 56 55.939843 57 56.936296 58 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146.939840 148 147.937270 149 148.933790 150 149.933350 151 150.931681 152 151.931740 153 152.930195 154 153.930596 155 154.929079 156 155.929710 157 156.928190 158 157.928950 159 158.927709 160 159.928726 161 160.927852 162 161.929092 163 162.928730 164 163.930231 165 164.930319 166 165.932281 167 166.933126 168 167.935500 169 168.936868 170 169.939610 171 170.941460 172 171.944820 +68 0 165.930290 147 146.949310 148 147.944440 149 148.942170 150 149.937760 151 150.937460 152 151.935080 153 152.935093 154 153.932777 155 154.933200 156 155.931020 157 156.931950 158 157.929910 159 158.930681 160 159.929080 161 160.930001 162 161.928775 163 162.930029 164 163.929197 165 164.930723 166 165.930290 167 166.932045 168 167.932368 169 168.934588 170 169.935460 171 170.938026 172 171.939352 173 172.942400 174 173.944340 +69 0 168.934211 146 145.966500 147 146.961080 148 147.957550 149 148.952650 150 149.949670 151 150.945430 152 151.944300 153 152.942028 154 153.941420 155 154.939192 156 155.939010 157 156.936760 158 157.937000 159 158.934810 160 159.935090 161 160.933400 162 161.933970 163 162.932648 164 163.933451 165 164.932432 166 165.933553 167 166.932849 168 167.934170 169 168.934211 170 169.935798 171 170.936426 172 171.938396 173 172.939600 174 173.942160 175 174.943830 176 175.946990 +70 0 173.938858 151 150.955250 152 151.950170 153 152.949210 154 153.946240 155 154.945790 156 155.942850 157 156.942660 158 157.939858 159 158.940150 160 159.937560 161 160.937850 162 161.935750 163 162.936270 164 163.934520 165 164.935398 166 165.933880 167 166.934947 168 167.933894 169 168.935187 170 169.934759 171 170.936322 172 171.936377 173 172.938206 174 173.938858 175 174.941272 176 175.942568 177 176.945257 178 177.946643 179 178.950170 180 179.952330 +71 0 174.940767 150 149.972670 151 150.967150 152 151.963610 153 152.958690 154 153.957100 155 154.954230 156 155.952910 157 156.950102 158 157.949170 159 158.946620 160 159.946020 161 160.943540 162 161.943220 163 162.941200 164 163.941220 165 164.939610 166 165.939760 167 166.938310 168 167.938700 169 168.937649 170 169.938472 171 170.937910 172 171.939082 173 172.938927 174 173.940333 175 174.940767 176 175.942682 177 176.943755 178 177.945951 179 178.947324 180 179.949880 181 180.951970 182 181.955210 183 182.957570 +72 0 179.946548 154 153.964250 155 154.962760 156 155.959250 157 156.958130 158 157.954650 159 158.954000 160 159.950710 161 160.950330 162 161.947203 163 162.947060 164 163.944420 165 164.944540 166 165.942250 167 166.942600 168 167.940630 169 168.941160 170 169.939650 171 170.940490 172 171.939460 173 172.940650 174 173.940040 175 174.941503 176 175.941401 177 176.943220 178 177.943697 179 178.945815 180 179.946548 181 180.949099 182 181.950553 183 182.953530 184 183.955450 185 184.958780 +73 0 180.947996 156 155.971690 157 156.968150 158 157.966370 159 158.962910 160 159.961360 161 160.958370 162 161.957150 163 162.954320 164 163.953570 165 164.950820 166 165.950470 167 166.947970 168 167.947790 169 168.945920 170 169.946090 171 170.944460 172 171.944740 173 172.943540 174 173.944170 175 174.943650 176 175.944740 177 176.944472 178 177.945750 179 178.945934 180 179.947466 181 180.947996 182 181.950152 183 182.951373 184 183.954009 185 184.955559 186 185.958550 +74 0 183.950932 158 157.973940 159 158.972280 160 159.968370 161 160.967090 162 161.963340 163 162.962530 164 163.958980 165 164.958340 166 165.955020 167 166.954670 168 167.951860 169 168.951760 170 169.949290 171 170.949460 172 171.947420 173 172.947830 174 173.946160 175 174.946770 176 175.945590 177 176.946620 178 177.945850 179 178.947072 180 179.946706 181 180.948198 182 181.948206 183 182.950224 184 183.950932 185 184.953420 186 185.954362 187 186.957158 188 187.958487 189 188.961910 190 189.963180 +75 0 186.955750 160 159.981490 161 160.977660 162 161.975710 163 162.971970 164 163.970320 165 164.967050 166 165.965800 167 166.962560 168 167.961610 169 168.958830 170 169.958160 171 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174.981550 176 175.980270 177 176.977220 178 177.975980 179 178.973410 180 179.972400 181 180.969950 182 181.969620 183 182.967620 184 183.967470 185 184.965810 186 185.966000 187 186.964560 188 187.965090 189 188.963890 190 189.964699 191 190.963650 192 191.964810 193 192.964132 194 193.965339 195 194.965018 196 195.966551 197 196.966552 198 197.968225 199 198.968748 200 199.970720 201 200.971641 202 201.973790 203 202.975137 204 203.977710 205 204.979610 +80 0 201.970626 175 174.991410 176 175.987410 177 176.986340 178 177.982476 179 178.981780 180 179.978320 181 180.977810 182 181.974750 183 182.974560 184 183.971900 185 184.971980 186 185.969460 187 186.969790 188 187.967560 189 188.968130 190 189.966280 191 190.967060 192 191.965570 193 192.966644 194 193.965382 195 194.966640 196 195.965815 197 196.967195 198 197.966752 199 198.968262 200 199.968309 201 200.970285 202 201.970626 203 202.972857 204 203.973476 205 204.976056 206 205.977499 207 206.982580 208 207.985940 +81 0 204.974412 179 178.991470 182 181.985610 183 182.982700 184 183.981760 185 184.979100 186 185.978550 187 186.976170 188 187.975920 189 188.973690 190 189.973790 191 190.971890 192 191.972140 193 192.970550 194 193.971050 195 194.969650 196 195.970520 197 196.969540 198 197.970470 199 198.969810 200 199.970945 201 200.970804 202 201.972091 203 202.972329 204 203.973849 205 204.974412 206 205.976095 207 206.977408 208 207.982005 209 208.985349 210 209.990066 +82 0 207.976636 182 181.992676 183 182.991930 184 183.988200 185 184.987580 186 185.984300 187 186.984030 188 187.981060 189 188.980880 190 189.978180 191 190.978200 192 191.975760 193 192.976080 194 193.973970 195 194.974470 196 195.972710 197 196.973380 198 197.971980 199 198.972910 200 199.971816 201 200.972850 202 201.972144 203 202.973375 204 203.973029 205 204.974467 206 205.974449 207 206.975881 208 207.976636 209 208.981075 210 209.984173 211 210.988731 212 211.991887 213 212.996500 214 213.999798 +83 0 208.980383 187 186.993460 188 187.992170 189 188.989510 190 189.988520 191 190.986050 192 191.985370 193 192.983060 194 193.982750 195 194.980750 196 195.980610 197 196.978930 198 197.979020 199 198.977580 200 199.978140 201 200.976970 202 201.977670 203 202.976868 204 203.977805 205 204.977375 206 205.978483 207 206.978455 208 207.979727 209 208.980383 210 209.984105 211 210.987258 212 211.991272 213 212.994375 214 213.998699 215 215.001830 216 216.006200 +84 0 208.982416 192 191.991520 193 192.991100 194 193.988280 195 194.988050 196 195.985510 197 196.985570 198 197.983340 199 198.983600 200 199.981740 201 200.982210 202 201.980700 203 202.981410 204 203.980307 205 204.981170 206 205.980465 207 206.981578 208 207.981231 209 208.982416 210 209.982857 211 210.986637 212 211.988852 213 212.992843 214 213.995186 215 214.999415 216 216.001905 217 217.006250 218 218.008965 +85 0 209.987131 196 195.995700 197 196.993290 198 197.992750 199 198.990630 200 199.990290 201 200.988490 202 201.988450 203 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254 254.100170 255 255.101490 256 256.101180 257 257.103070 258 258.103570 259 259.105630 260 260.106430 261 261.108750 262 262.109920 263 263.112540 +105 0 262.114150 255 255.107400 257 257.107860 258 258.109440 259 259.109720 260 260.111430 261 261.112110 262 262.114150 263 263.115080 +106 0 263.118310 259 259.114650 260 260.114440 261 261.116200 263 263.118310 265 265.121070 266 266.121930 +107 0 264.124730 261 261.121800 262 262.123010 264 264.124730 +108 0 265.130000 263 263.128710 264 264.128410 265 265.130000 +109 0 268.138820 266 266.137940 268 268.138820
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/isotope.h Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,2551 @@ +/*************************************************************** +This file is part of the Open Babel project. +This is copyright under the GNU General Public License (GPL) +For more information, see <http://openbabel.org/> + +This file contains a binary representation of data tables + used by Open Babel. It is used as a fallback if the textual + data table is not found at runtime. It is not a normal header. +***************************************************************/ + + +#ifndef OB_ISOTOPE_H +#define OB_ISOTOPE_H + +namespace OpenBabel +{ +static const char IsotopeData[] = { + 0x30,0x20,0x30,0x20,0x30,0x2E,0x30,0x30,0x30,0x30,0x30,0x30,0x20,0x31,0x20, + 0x31,0x2E,0x30,0x30,0x38,0x36,0x36,0x34,0x0A,0x31,0x20,0x30,0x20,0x31,0x2E, + 0x30,0x30,0x37,0x38,0x32,0x35,0x20,0x31,0x20,0x31,0x2E,0x30,0x30,0x37,0x38, + 0x32,0x35,0x20,0x32,0x20,0x32,0x2E,0x30,0x31,0x34,0x31,0x30,0x31,0x20,0x33, + 0x20,0x33,0x2E,0x30,0x31,0x36,0x30,0x34,0x39,0x0A,0x32,0x20,0x30,0x20,0x34, + 0x2E,0x30,0x30,0x32,0x36,0x30,0x33,0x20,0x33,0x20,0x33,0x2E,0x30,0x31,0x36, + 0x30,0x32,0x39,0x20,0x34,0x20,0x34,0x2E,0x30,0x30,0x32,0x36,0x30,0x33,0x20, + 0x35,0x20,0x35,0x2E,0x30,0x31,0x32,0x32,0x32,0x30,0x20,0x36,0x20,0x36,0x2E, + 0x30,0x31,0x38,0x38,0x38,0x38,0x20,0x37,0x20,0x37,0x2E,0x30,0x32,0x38,0x30, + 0x33,0x30,0x20,0x38,0x20,0x38,0x2E,0x30,0x33,0x33,0x39,0x32,0x32,0x20,0x39, + 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0x30,0x37,0x20,0x30,0x20,0x32,0x36,0x34,0x2E,0x31,0x32,0x34,0x37,0x33,0x30, + 0x20,0x32,0x36,0x31,0x20,0x32,0x36,0x31,0x2E,0x31,0x32,0x31,0x38,0x30,0x30, + 0x20,0x32,0x36,0x32,0x20,0x32,0x36,0x32,0x2E,0x31,0x32,0x33,0x30,0x31,0x30, + 0x20,0x32,0x36,0x34,0x20,0x32,0x36,0x34,0x2E,0x31,0x32,0x34,0x37,0x33,0x30, + 0x0A,0x31,0x30,0x38,0x20,0x30,0x20,0x32,0x36,0x35,0x2E,0x31,0x33,0x30,0x30, + 0x30,0x30,0x20,0x32,0x36,0x33,0x20,0x32,0x36,0x33,0x2E,0x31,0x32,0x38,0x37, + 0x31,0x30,0x20,0x32,0x36,0x34,0x20,0x32,0x36,0x34,0x2E,0x31,0x32,0x38,0x34, + 0x31,0x30,0x20,0x32,0x36,0x35,0x20,0x32,0x36,0x35,0x2E,0x31,0x33,0x30,0x30, + 0x30,0x30,0x0A,0x31,0x30,0x39,0x20,0x30,0x20,0x32,0x36,0x38,0x2E,0x31,0x33, + 0x38,0x38,0x32,0x30,0x20,0x32,0x36,0x36,0x20,0x32,0x36,0x36,0x2E,0x31,0x33, + 0x37,0x39,0x34,0x30,0x20,0x32,0x36,0x38,0x20,0x32,0x36,0x38,0x2E,0x31,0x33, + 0x38,0x38,0x32,0x30,0x0A,0x00}; + +} // namespace OpenBabel +#endif // OB_ISOTOPE_H +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/isotope.txt Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,147 @@ +############################################################################## +# # +# Open Babel file: isotope.txt # +# # +# Copyright (c) 2002-2004 by Geoffrey R. Hutchison # +# Part of the Open Babel package, under the GNU General Public License (GPL)# +# # +# This file has a series of lines, one for each element # +# (i.e. line 0 = neutron, line 1 = hydrogen, line 2 = helium, etc.) # +# Each line: Atomic #, 0 then exact mass of most abundant isotope # +# then a list of isotopes as int, float pairs corresponding to masses # +# # +# CAUTION: Masses have been zero-padded to 9 decimal places # +# (we don't currently have a math package that can deal with sig. fig.) # +# so trailing zeros may not be significant and/or useful # +# # +# Values are compiled from: # +# "The Ame2003 atomic mass evaluation (II)" # +# by G.Audi, A.H.Wapstra and C.Thibault # +# Nuclear Physics A729 p. 337-676, December 22, 2003. # +# as made available in the mass.mas03round file # +# (these are values for publication) # +# # +# Currently: 110 lines (neutron, H to Mt) # +# (note that since element 0 often represents a dummy atom, the default # +# mass is 0 amu, *not* the mass of a neutron, accessible as isotope 1) # +# # +############################################################################## +0 0 0.000000000 1 1.008664915 +1 0 1.007825032 1 1.007825032 2 2.014101778 3 3.016049278 4 4.027810000 5 5.035310000 6 6.044940000 7 7.052750000 +2 0 4.002603254 3 3.016029319 4 4.002603254 5 5.012220000 6 6.018889100 7 7.028021000 8 8.033922000 9 9.043950000 10 10.052400000 +3 0 7.016004550 3 3.030780000 4 4.027190000 5 5.012540000 6 6.015122795 7 7.016004550 8 8.022487360 9 9.026789500 10 10.035481000 11 11.043798000 12 12.053780000 +4 0 9.012182200 5 5.040790000 6 6.019726000 7 7.016929830 8 8.005305100 9 9.012182200 10 10.013533800 11 11.021658000 12 12.026921000 13 13.035690000 14 14.042890000 15 15.053460000 16 16.061920000 +5 0 11.009305400 6 6.046810000 7 7.029920000 8 8.024607200 9 9.013328800 10 10.012937000 11 11.009305400 12 12.014352100 13 13.017780200 14 14.025404000 15 15.031103000 16 16.039810000 17 17.046990000 18 18.056170000 19 19.063730000 +6 0 12.000000000 8 8.037675000 9 9.031036700 10 10.016853200 11 11.011433600 12 12.000000000 13 13.003354838 14 14.003241989 15 15.010599300 16 16.014701000 17 17.022586000 18 18.026760000 19 19.034810000 20 20.040320000 21 21.049340000 22 22.057200000 +7 0 14.003074005 10 10.041650000 11 11.026090000 12 12.018613200 13 13.005738610 14 14.003074005 15 15.000108898 16 16.006101700 17 17.008450000 18 18.014079000 19 19.017029000 20 20.023370000 21 21.027110000 22 22.034390000 23 23.041220000 24 24.051040000 25 25.060660000 +8 0 15.994914620 12 12.034405000 13 13.024812000 14 14.008596250 15 15.003065600 16 15.994914620 17 16.999131700 18 17.999161000 19 19.003580000 20 20.004076700 21 21.008656000 22 22.009970000 23 23.015690000 24 24.020470000 25 25.029460000 26 26.038340000 27 27.048260000 28 28.057810000 +9 0 18.998403220 14 14.035060000 15 15.018010000 16 16.011466000 17 17.002095240 18 18.000938000 19 18.998403220 20 19.999981320 21 20.999949000 22 22.002999000 23 23.003570000 24 24.008120000 25 25.012100000 26 26.019620000 27 27.026760000 28 28.035670000 29 29.043260000 30 30.052500000 31 31.060430000 +10 0 19.992440175 16 16.025761000 17 17.017672000 18 18.005708200 19 19.001880200 20 19.992440175 21 20.993846680 22 21.991385114 23 22.994466900 24 23.993610800 25 24.997737000 26 26.000461000 27 27.007590000 28 28.012070000 29 29.019390000 30 30.024800000 31 31.033110000 32 32.040020000 33 33.049380000 34 34.057030000 +11 0 22.989769281 18 18.025970000 19 19.013877000 20 20.007351000 21 20.997655200 22 21.994436400 23 22.989769281 24 23.990962780 25 24.989954000 26 25.992633000 27 26.994077000 28 27.998938000 29 29.002861000 30 30.008976000 31 31.013590000 32 32.020470000 33 33.026720000 34 34.035170000 35 35.042490000 36 36.051480000 37 37.059340000 +12 0 23.985041700 19 19.035470000 20 20.018863000 21 21.011713000 22 21.999573800 23 22.994123700 24 23.985041700 25 24.985836920 26 25.982592929 27 26.984340590 28 27.983876800 29 28.988600000 30 29.990434000 31 30.996546000 32 31.998975000 33 33.005254000 34 34.009460000 35 35.017340000 36 36.023000000 37 37.031400000 38 38.037570000 39 39.046770000 40 40.053930000 +13 0 26.981538630 21 21.028040000 22 22.019520000 23 23.007267000 24 23.999938900 25 24.990428100 26 25.986891690 27 26.981538630 28 27.981910310 29 28.980445000 30 29.982960000 31 30.983947000 32 31.988120000 33 32.990840000 34 33.996850000 35 34.999860000 36 36.006210000 37 37.010680000 38 38.017230000 39 39.022970000 40 40.031450000 41 41.038330000 42 42.046890000 +14 0 27.976926532 22 22.034530000 23 23.025520000 24 24.011546000 25 25.004106000 26 25.992330000 27 26.986704910 28 27.976926532 29 28.976494700 30 29.973770170 31 30.975363230 32 31.974148080 33 32.978000000 34 33.978576000 35 34.984580000 36 35.986600000 37 36.992940000 38 37.995630000 39 39.002070000 40 40.005870000 41 41.014560000 42 42.019790000 43 43.028660000 44 44.035260000 +15 0 30.973761630 24 24.034350000 25 25.020260000 26 26.011780000 27 26.999230000 28 27.992315000 29 28.981800600 30 29.978313800 31 30.973761630 32 31.973907270 33 32.971725500 34 33.973636000 35 34.973314100 36 35.978260000 37 36.979610000 38 37.984160000 39 38.986180000 40 39.991300000 41 40.994340000 42 42.001010000 43 43.006190000 44 44.012990000 45 45.019220000 46 46.027380000 +16 0 31.972071000 26 26.027880000 27 27.018830000 28 28.004370000 29 28.996610000 30 29.984903000 31 30.979554700 32 31.972071000 33 32.971458760 34 33.967866900 35 34.969032160 36 35.967080760 37 36.971125570 38 37.971163000 39 38.975130000 40 39.975450000 41 40.979580000 42 41.981020000 43 42.987150000 44 43.990210000 45 44.996510000 46 46.000750000 47 47.008590000 48 48.014170000 49 49.023620000 +17 0 34.968852680 28 28.028510000 29 29.014110000 30 30.004770000 31 30.992410000 32 31.985690000 33 32.977451900 34 33.973762820 35 34.968852680 36 35.968306980 37 36.965902590 38 37.968010430 39 38.968008200 40 39.970420000 41 40.970680000 42 41.973250000 43 42.974050000 44 43.978280000 45 44.980290000 46 45.984210000 47 46.988710000 48 47.994950000 49 49.000320000 50 50.007840000 51 51.014490000 +18 0 39.962383123 30 30.021560000 31 31.012120000 32 31.997638000 33 32.989925700 34 33.980271200 35 34.975257600 36 35.967545106 37 36.966776320 38 37.962732400 39 38.964313000 40 39.962383123 41 40.964500600 42 41.963046000 43 42.965636000 44 43.964924000 45 44.968040000 46 45.968090000 47 46.972190000 48 47.974540000 49 48.980520000 50 49.984430000 51 50.991630000 52 51.996780000 53 53.004940000 +19 0 38.963706680 32 32.021920000 33 33.007260000 34 33.998410000 35 34.988010000 36 35.981292000 37 36.973375890 38 37.969081200 39 38.963706680 40 39.963998480 41 40.961825760 42 41.962402810 43 42.960716000 44 43.961560000 45 44.960699000 46 45.961977000 47 46.961678000 48 47.965514000 49 48.967450000 50 49.972780000 51 50.976380000 52 51.982610000 53 52.987120000 54 53.994200000 55 54.999710000 +20 0 39.962590980 34 34.014120000 35 35.004940000 36 35.993090000 37 36.985870000 38 37.976318000 39 38.970719700 40 39.962590980 41 40.962278060 42 41.958618010 43 42.958766600 44 43.955481800 45 44.956186600 46 45.953692600 47 46.954546000 48 47.952534000 49 48.955674000 50 49.957519000 51 50.961500000 52 51.965100000 53 52.970050000 54 53.974350000 55 54.980550000 56 55.985570000 57 56.992360000 +21 0 44.955911900 36 36.014920000 37 37.003050000 38 37.994700000 39 38.984790000 40 39.977967000 41 40.969251130 42 41.965516430 43 42.961150700 44 43.959402800 45 44.955911900 46 45.955171900 47 46.952407500 48 47.952231000 49 48.950024000 50 49.952188000 51 50.953603000 52 51.956680000 53 52.959610000 54 53.963260000 55 54.968240000 56 55.972870000 57 56.977790000 58 57.983710000 59 58.989220000 60 59.995710000 +22 0 47.947946300 38 38.009770000 39 39.001610000 40 39.990500000 41 40.983150000 42 41.973031000 43 42.968522000 44 43.959690100 45 44.958125600 46 45.952631600 47 46.951763100 48 47.947946300 49 48.947870000 50 49.944791200 51 50.946615000 52 51.946897000 53 52.949730000 54 53.951050000 55 54.955270000 56 55.958200000 57 56.963990000 58 57.966970000 59 58.972930000 60 59.976760000 61 60.983200000 62 61.987490000 63 62.994420000 +23 0 50.943959500 40 40.011090000 41 40.999780000 42 41.991230000 43 42.980650000 44 43.974110000 45 44.965776000 46 45.960200500 47 46.954908900 48 47.952253700 49 48.948516100 50 49.947158500 51 50.943959500 52 51.944775500 53 52.944338000 54 53.946440000 55 54.947230000 56 55.950530000 57 56.952560000 58 57.956830000 59 58.960210000 60 59.965030000 61 60.968480000 62 61.973780000 63 62.977550000 64 63.983470000 65 64.987920000 +24 0 51.940507500 42 42.006430000 43 42.997710000 44 43.985550000 45 44.979640000 46 45.968359000 47 46.962900000 48 47.954032000 49 48.951335700 50 49.946044200 51 50.944767400 52 51.940507500 53 52.940649400 54 53.938880400 55 54.940839700 56 55.940653100 57 56.943613000 58 57.944350000 59 58.948590000 60 59.950080000 61 60.954720000 62 61.956610000 63 62.961860000 64 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48.001760000 49 48.989720000 50 49.981540000 51 50.970720000 52 51.963590000 53 52.954219000 54 53.948459600 55 54.941999000 56 55.939839300 57 56.936291400 58 57.935752800 59 58.933195000 60 59.933817100 61 60.932475800 62 61.934051000 63 62.933612000 64 63.935810000 65 64.936478000 66 65.939760000 67 66.940890000 68 67.944870000 69 68.946320000 70 69.951000000 71 70.952900000 72 71.957810000 73 72.960240000 74 73.965380000 75 74.968330000 +28 0 57.935342900 48 48.019750000 49 49.009660000 50 49.995930000 51 50.987720000 52 51.975680000 53 52.968470000 54 53.957910000 55 54.951330000 56 55.942132000 57 56.939793500 58 57.935342900 59 58.934346700 60 59.930786400 61 60.931056000 62 61.928345100 63 62.929669400 64 63.927966000 65 64.930084300 66 65.929139300 67 66.931569000 68 67.931869000 69 68.935610000 70 69.936500000 71 70.940740000 72 71.942090000 73 72.946470000 74 73.948070000 75 74.952870000 76 75.955330000 77 76.960550000 78 77.963180000 +29 0 62.929597500 52 51.997180000 53 52.985550000 54 53.976710000 55 54.966050000 56 55.958560000 57 56.949211000 58 57.944538500 59 58.939498000 60 59.937365000 61 60.933457800 62 61.932584000 63 62.929597500 64 63.929764200 65 64.927789500 66 65.928868800 67 66.927730300 68 67.929610900 69 68.929429300 70 69.932392300 71 70.932676800 72 71.935820300 73 72.936675000 74 73.939875000 75 74.941900000 76 75.945275000 77 76.947850000 78 77.951960000 79 78.954560000 80 79.960870000 +30 0 63.929142000 54 53.992950000 55 54.983980000 56 55.972380000 57 56.964790000 58 57.954590000 59 58.949260000 60 59.941827000 61 60.939511000 62 61.934330000 63 62.933211000 64 63.929142000 65 64.929241000 66 65.926033000 67 66.927127000 68 67.924844000 69 68.926550000 70 69.925319000 71 70.927722000 72 71.926858000 73 72.929780000 74 73.929460000 75 74.932940000 76 75.933290000 77 76.936960000 78 77.938440000 79 78.942650000 80 79.944340000 81 80.950480000 82 81.954420000 83 82.961030000 +31 0 68.925573000 56 55.994910000 57 56.982930000 58 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237.052900000 238 238.053030000 239 239.054960000 240 240.055529000 241 241.057653000 242 242.058835000 243 243.061389000 244 244.062752000 245 245.065491000 246 246.067223000 247 247.070354000 248 248.072349000 249 249.075953000 250 250.078357000 251 251.082285000 252 252.084870000 +97 0 247.070307000 235 235.056580000 236 236.057330000 237 237.057000000 238 238.058280000 239 239.058280000 240 240.059760000 241 241.060230000 242 242.061980000 243 243.063008000 244 244.065181000 245 245.066361000 246 246.068670000 247 247.070307000 248 248.073090000 249 249.074986000 250 250.078317000 251 251.080760000 252 252.084310000 253 253.086880000 254 254.090600000 +98 0 251.079587000 237 237.062070000 238 238.061410000 239 239.062420000 240 240.062300000 241 241.063730000 242 242.063700000 243 243.065430000 244 244.066001000 245 245.068049000 246 246.068805000 247 247.071001000 248 248.072185000 249 249.074853000 250 250.076406000 251 251.079587000 252 252.081626000 253 253.085133000 254 254.087323000 255 255.091050000 256 256.093440000 +99 0 252.082980000 240 240.068920000 241 241.068540000 242 242.069750000 243 243.069550000 244 244.070880000 245 245.071320000 246 246.072900000 247 247.073660000 248 248.075470000 249 249.076410000 250 250.078610000 251 251.079992000 252 252.082980000 253 253.084824000 254 254.088022000 255 255.090273000 256 256.093600000 257 257.095980000 258 258.099520000 +100 0 257.095105000 242 242.073430000 243 243.074350000 244 244.074080000 245 245.075390000 246 246.075300000 247 247.076850000 248 248.077195000 249 249.079030000 250 250.079521000 251 251.081575000 252 252.082467000 253 253.085185000 254 254.086854000 255 255.089962000 256 256.091773000 257 257.095105000 258 258.097080000 259 259.100600000 260 260.102680000 +101 0 258.098431000 245 245.080830000 246 246.081890000 247 247.081640000 248 248.082820000 249 249.083010000 250 250.084420000 251 251.084840000 252 252.086560000 253 253.087280000 254 254.089660000 255 255.091083000 256 256.094060000 257 257.095541000 258 258.098431000 259 259.100510000 260 260.103650000 261 261.105720000 262 262.108870000 +102 0 259.101030000 248 248.086600000 249 249.087830000 250 250.087510000 251 251.089010000 252 252.088977000 253 253.090680000 254 254.090955000 255 255.093241000 256 256.094283000 257 257.096877000 258 258.098210000 259 259.101030000 260 260.102640000 261 261.105750000 262 262.107300000 263 263.110550000 264 264.112350000 +103 0 262.109630000 251 251.094360000 252 252.095370000 253 253.095210000 254 254.096450000 255 255.096680000 256 256.098630000 257 257.099560000 258 258.101810000 259 259.102900000 260 260.105500000 261 261.106880000 262 262.109630000 263 263.111290000 264 264.114040000 265 265.115840000 266 266.119310000 +104 0 261.108770000 253 253.100690000 254 254.100180000 255 255.101340000 256 256.101166000 257 257.102990000 258 258.103490000 259 259.105640000 260 260.106440000 261 261.108770000 262 262.109930000 263 263.112550000 264 264.113990000 265 265.116700000 266 266.117960000 267 267.121530000 268 268.123640000 +105 0 262.114080000 255 255.107400000 256 256.108130000 257 257.107720000 258 258.109230000 259 259.109610000 260 260.111300000 261 261.112060000 262 262.114080000 263 263.114990000 264 264.117400000 265 265.118600000 266 266.121030000 267 267.122380000 268 268.125450000 269 269.127460000 270 270.130710000 +106 0 263.118320000 258 258.113170000 259 259.114500000 260 260.114420000 261 261.116120000 262 262.116400000 263 263.118320000 264 264.118930000 265 265.121110000 266 266.122070000 267 267.124430000 268 268.125610000 269 269.128760000 270 270.130330000 271 271.133470000 272 272.135160000 273 273.138220000 +107 0 264.124600000 260 260.121970000 261 261.121660000 262 262.122890000 263 263.123040000 264 264.124600000 265 265.125150000 266 266.126940000 267 267.127650000 268 268.129760000 269 269.130690000 270 270.133620000 271 271.135180000 272 272.138030000 273 273.139620000 274 274.142440000 275 275.144250000 +108 0 265.130090000 263 263.128560000 264 264.128390000 265 265.130090000 266 266.130100000 267 267.131790000 268 268.132160000 269 269.134060000 270 270.134650000 271 271.137660000 272 272.139050000 273 273.141990000 274 274.143130000 275 275.145950000 276 276.147210000 277 277.149840000 +109 0 268.138730000 265 265.136150000 266 266.137300000 267 267.137310000 268 268.138730000 269 269.139060000 270 270.140660000 271 271.141140000 272 272.143740000 273 273.144910000 274 274.147490000 275 275.148650000 276 276.151160000 277 277.152420000 278 278.154810000 279 279.156190000 +110 0 281.162061 281 281.162061 +111 0 280.164473 280 280.164473 +112 0 285.174105 285 285.174105 +113 0 284.178080 284 284.178080 +114 0 289.187279 289 289.187279 +115 0 288.192492 288 288.192492 +116 0 292.199786 292 292.199786 +117 0 292.207550 291 291.206560 292 292.207550 +118 0 293.214670 293 293.214670
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/logp.txt Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,169 @@ +###################################################################### +# Copyright OELIB: OpenEye Scientific Software, Santa Fe, +# U.S.A., 1999,2000,2001 +# Copyright JOELIB/JOELib2: Dept. Computer Architecture, University of +# Tuebingen, Germany, 2001,2002,2003,2004,2005 +# Copyright JOELIB/JOELib2: ALTANA PHARMA AG, Konstanz, Germany, +# 2003,2004,2005 +# +# Authors: Stephen Jelfs +# Joerg Kurt Wegner, me@cheminformatics.eu +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation version 2 of the License. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +###################################################################### +# LopP Atomic Contributions +# ref. Wildman, S.A. and Crippen, G.M., J. Chem. Inf. Comput. Sci., +# 1999, 39, 868-873. +# Table below is adapted from above ref. +###################################################################### +;hydrogen +[*] 0.1125 +[#6] 0.123 +[#1] 0.123 +[O][CX4] -0.2677 +[O]c -0.2677 +[O][#5] -0.2677 +[O][#14] -0.2677 +[O][#15] -0.2677 +[O][#33] -0.2677 +[O][#50] -0.2677 +[#5] -0.2677 +[#14] -0.2677 +[#15] -0.2677 +[#16] -0.2677 +[#50] -0.2677 +[#7] 0.2142 +[O][#7] 0.2142 +[O]C=[#6] 0.298 +[O]C=[#7] 0.298 +[O]C=O 0.298 +[O]C=S 0.298 +[O]O 0.298 +[O]S 0.298 +;heavy +[*] 0 +[#6] 0.0813 +[CH4] 0.1441 +[CH3]C 0.1441 +[CH2](C)C 0.1441 +[CH](C)(C)C 0 +[C](C)(C)(C)C 0 +[CH3][O,N,F,Cl,Br,#15,#16,#53;!a] -0.2035 +[CH2X4][O,N,F,Cl,Br,#15,#16,#53;!a] -0.2035 +[CHX4][O,N,F,Cl,Br,#15,#16,#53;!a] -0.2051 +[CH0X4][O,N,F,Cl,Br,#15,#16,#53;!a] -0.2051 +[C]=[A!#6] -0.2783 +[CH2]=C 0.1551 +[CH1](=C)A 0.1551 +[CH0](=C)(A)A 0.1551 +[C](=C)=C 0.1551 +[CX2]#A 0.0017 +[CH3]c 0.0845 +[CH3][a!#6] -0.1444 +[CH2X4]a -0.0516 +[CHX4]a 0.1193 +[CH0X4]a -0.0967 +[c][#5,#14,#15,#33,#34,#50,#80] -0.5443 +[c][#9] 0 +[c][#17] 0.245 +[c][#35] 0.198 +[c][#53] 0 +[cH] 0.1581 +[c](:a)(:a):a 0.2955 +[c](:a)(:a)-a 0.2713 +[c](:a)(:a)-C 0.136 +[c](:a)(:a)-N 0.4619 +[c](:a)(:a)-O 0.5437 +[c](:a)(:a)-S 0.1893 +[c](:a)(:a)=C -0.8186 +[c](:a)(:a)=N -0.8186 +[c](:a)(:a)=O -0.8186 +[C](=C)(a)A 0.264 +[C](=C)(c)a 0.264 +[CH](=C)a 0.264 +[C]=c 0.264 +[CX4][!#6;!#7;!#8;!#9;!#15;!#16;!#17;!#35;!#53;!#1] 0.2148 +[#7] -0.4806 +[NH2+0]A -1.019 +[NH+0](A)A -0.7096 +[NH2+0]a -1.027 +[NH+0](A)a -0.5188 +[NH+0](a)a -0.5188 +[NH+0]=A 0.0839 +[NH+0]=a 0.0839 +[N+0](=A)A 0.1836 +[N+0](=A)a 0.1836 +[N+0](=a)A 0.1836 +[N+0](=a)a 0.1836 +[N+0](A)(A)A -0.3187 +[N+0](a)(A)A -0.4458 +[N+0](a)(a)A -0.4458 +[N+0](a)(a)a -0.4458 +[N+0]#A 0.01508 +[NH3+*] -1.95 +[NH2+*] -1.95 +[NH+*] -1.95 +[n+0] -0.3239 +[n+*] -1.119 +[NH0+*](A)(A)(A)A -0.3396 +[NH0+*](=A)(A)A -0.3396 +[NH0+*](=A)(A)a -0.3396 +[NH0+*](=[#6])=[#7] -0.3396 +[N+*]#A 0.2887 +[N-*] 0.2887 +[N+*](=[N-*])=N 0.2887 +[#8] -0.1188 +[o] 0.1552 +[OH] -0.2893 +[OH2] -0.2893 +[O](C)C -0.0684 +[OH0](C)[A!#6] -0.0684 +[OH0]([A!#6])[A!#6] -0.0684 +[O]([A;!#1])a -0.4195 +[O](a)a -0.4195 +[O]=[#8] 0.0335 +[O]=[#7] 0.0335 +[OX1-*][#7] 0.0335 +[OX1-*][#16] -0.3339 +[OX1-*][#15;#33;#43;#53] -1.189 +[O]=c 0.1788 +[O]=[CH]C -0.1526 +[O]=C(C)C -0.1526 +[O]=[CH0](C)[A;!6] -0.1526 +[O]=[CH]N -0.1526 +[O]=[CH]O -0.1526 +[O]=[CH2] -0.1526 +[O]=[CX2]=O -0.1526 +[O]=[CH]c 0.1129 +[O]=C(C)c 0.1129 +[O]=C(c)c 0.1129 +[O]=[CH0](c)[a!#6] 0.1129 +[O]=[CH0](c)[A!#6] 0.1129 +[O]=[CH0](C)[a!#6] 0.1129 +[O]=C([A!#6])[A!#6] 0.4833 +[O]=C([A!#6])[a!#6] 0.4833 +[O]=C([a!#6])[a!#6] 0.4833 +[O-1]C(=O) -1.326 +[#9-0] 0.4202 +[#17-0] 0.6895 +[#35-0] 0.8456 +[#53-0] 0.8857 +[#9-*] -2.996 +[#17-*] -2.996 +[#35-*] -2.996 +[#53-*] -2.996 +[#53+*] -2.996 +[#15] 0.8612 +[S-0] 0.6482 +[S-*] -0.0024 +[S+*] -0.0024 +[s] 0.6237 +[B,Si,Ga,Ge,As,Se,Sn,Te,Pb,Nc,Nr,Kr,Xe,Rn] -0.3808 +[Fe,Cu,Zn,Tc,Cd,Pt,Au,Hg] -0.0025
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/mm2.prm Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,2028 @@ + + ############################## + ## ## + ## Force Field Definition ## + ## ## + ############################## + + +forcefield MM2-1991 + +bondunit 71.94 +bond-cubic -2.0 +bond-quartic 1.25 !! keeps Ebond positive; not in "real" MM2 +angleunit 0.02191418 +angle-sextic 0.00000007 +strbndunit 2.51118 +mm2-strbnd +opbendunit 0.02191418 +torsionunit 0.5 +vdwtype BUCKINGHAM +radiusrule ARITHMETIC +radiustype R-MIN +radiussize RADIUS +epsilonrule GEOMETRIC +a-expterm 290000.0 +b-expterm 12.5 +c-expterm 2.25 +vdw-14-scale 1.0 +chg-14-scale 1.0 +dielectric 1.5 + + + ############################# + ## ## + ## Literature References ## + ## ## + ############################# + + +N. L. Allinger, "Conformational Analysis. 130. MM2. A Hydrocarbon +Force Field Utilizing V1 and V2 Torsional Terms", J. Am. Chem. Soc., +99, 8127-8134 (1977) + +J. T. Sprague, J. C. Tai, Y. Yuh and N. L. Allinger, "The MMP2 +Calculational Method", J. Comput. Chem., 8, 581-603 (1987) + +N. L. Allinger, R. A. Kok and M. R. Imam, "Hydrogen Bonding in MM2", +J. Comput. Chem., 9, 591-595 (1988) + +All parameters in this file are from the "MM2 (1991) Parameter Set", +as provided by Prof. N. L. Allinger, University of Georgia + + + ############################# + ## ## + ## Atom Type Definitions ## + ## ## + ############################# + + +atom 1 C "CSP3 ALKANE" 6 12.000 4 +atom 2 C "CSP2 ALKENE" 6 12.000 3 +atom 3 C "CSP2 CARBONYL" 6 12.000 3 +atom 4 C "CSP ALKYNE, C=C=O" 6 12.000 2 +atom 5 H "NONPOLAR HYDROGEN" 1 1.008 1 +atom 6 O "-O- ALCOHOL, ETHER" 8 15.995 4 +atom 7 O "=O CARBONYL" 8 15.995 1 +atom 8 N "NSP3" 7 14.003 4 +atom 9 N "NSP2 AMIDE" 7 14.003 3 +atom 10 N "NSP" 7 14.003 1 +atom 11 F "FLUORIDE" 9 18.998 1 +atom 12 Cl "CHLORIDE" 17 34.969 1 +atom 13 Br "BROMIDE" 35 78.918 1 +atom 14 I "IODIDE" 53 126.900 1 +atom 15 S "-S- SULFIDE" 16 31.972 2 +atom 16 S+ ">S+ SULFONIUM" 16 31.972 2 +atom 17 S ">S=O SULFOXIDE" 16 31.972 3 +atom 18 S ">SO2 SULFONE" 16 31.972 4 +atom 19 Si "SILANE" 14 27.977 4 +atom 20 Lp "LONE PAIR" 0 0.000 1 +atom 21 H "-OH ALCOHOL" 1 1.008 1 +atom 22 C "CYCLOPROPANE" 6 12.000 4 +atom 23 H "NH AMINE" 1 1.008 1 +atom 24 H "COOH CARBOXYL" 1 1.008 1 +atom 25 P ">P- PHOSPHINE" 15 30.994 3 +atom 26 B ">B- TRIGONAL" 5 11.009 3 +atom 27 B ">B< TETRAHEDRAL" 5 11.009 4 +atom 28 H "-H AMIDE, ENOL" 1 1.008 1 +atom 29 C* "CARBON RADICAL" 6 12.000 3 +atom 30 C+ "CARBONIUM ION" 6 12.000 3 +atom 31 Ge "GERMANIUM" 32 73.922 2 +atom 32 Sn "TIN" 50 117.902 2 +atom 33 Pb "LEAD (IV)" 82 207.977 4 +atom 34 Se "SELENIUM" 34 79.917 2 +atom 35 Te "TELLURIUM" 52 129.907 2 +atom 36 D "DEUTERIUM" 1 2.014 1 +atom 37 N "-N= AZO,PYRIDINE" 7 14.003 3 +atom 38 C "CSP2 CYCLOPROPENE" 6 12.000 3 +atom 39 N+ "NSP3 AMMONIUM" 7 14.003 4 +atom 40 N "NSP2 PYRROLE" 7 14.003 3 +atom 41 O "OSP2 FURAN" 8 15.995 3 +atom 42 S "SSP2 THIOPHENE" 16 31.972 2 +atom 43 N "-N=N-O AZOXY" 7 14.003 2 +atom 44 H "-SH THIOL" 1 1.008 1 +atom 45 N "AZIDE (CENTER-N)" 7 14.003 2 +atom 46 N "NO2 NITRO" 7 14.003 3 +atom 47 O "CARBOXYLATE" 8 15.995 1 +atom 48 H "AMMONIUM" 1 1.008 1 +atom 49 O "EPOXY" 8 15.995 4 +atom 50 C "BENZENE" 6 12.000 3 +atom 51 He "HELIUM" 2 4.003 0 +atom 52 Ne "NEON" 10 20.179 0 +atom 53 Ar "ARGON" 18 39.948 0 +atom 54 Kr "KRYPTON" 36 83.800 0 +atom 55 Xe "XENON" 54 131.300 0 +atom 59 Mg "MAGNESIUM" 12 24.301 0 +atom 60 P "PHOSPHORUS (V)" 15 30.994 4 +atom 61 Fe "IRON (II)" 26 55.847 0 +atom 62 Fe "IRON (III)" 26 55.847 0 +atom 63 Ni "NICKEL (II)" 27 58.710 0 +atom 64 Ni "NICKEL (III)" 27 58.710 0 +atom 65 Co "COBALT (II)" 28 58.933 0 +atom 66 Co "COBALT (III)" 28 58.933 0 +atom 69 O "AMINE OXIDE" 8 15.995 1 +atom 70 O "KETONIUM OXYGEN" 8 15.995 1 +atom 71 C "KETONIUM CARBON" 6 12.000 2 +atom 72 N "=N- IMINE, OXIME" 7 14.003 3 +atom 73 N+ "=N(+)- PYRIDINIUM" 7 14.003 3 +atom 74 N+ "=N(+)- IMMINIUM" 7 14.003 3 +atom 75 N "N-OH OXIME" 7 14.003 3 + + + ################################ + ## ## + ## Van der Waals Parameters ## + ## ## + ################################ + + +vdw 1 1.900 0.044 +vdw 2 1.940 0.044 +vdw 3 1.940 0.044 +vdw 4 1.940 0.044 +vdw 5 1.500 0.047 0.915 +vdw 6 1.740 0.050 +vdw 7 1.740 0.066 +vdw 8 1.820 0.055 +vdw 9 1.820 0.055 +vdw 10 1.820 0.055 +vdw 11 1.650 0.078 +vdw 12 2.030 0.240 +vdw 13 2.180 0.320 +vdw 14 2.320 0.424 +vdw 15 2.110 0.202 +vdw 16 2.110 0.202 +vdw 17 2.110 0.202 +vdw 18 2.110 0.202 +vdw 19 2.250 0.140 +vdw 20 1.200 0.016 +vdw 21 0.950 0.036 +vdw 22 1.900 0.044 +vdw 23 1.050 0.034 +vdw 24 0.900 0.015 +vdw 25 2.180 0.168 +vdw 26 1.980 0.034 +vdw 27 1.980 0.034 +vdw 28 0.900 0.015 +vdw 29 1.940 0.044 +vdw 30 1.940 0.044 +vdw 31 2.400 0.200 +vdw 32 2.550 0.270 +vdw 33 2.700 0.340 +vdw 34 2.250 0.276 +vdw 35 2.400 0.368 +vdw 36 1.497 0.047 0.915 +vdw 37 1.820 0.055 +vdw 38 1.940 0.044 +vdw 39 1.820 0.055 +vdw 40 1.820 0.055 +vdw 41 1.740 0.050 +vdw 42 2.110 0.202 +vdw 43 1.820 0.055 +vdw 44 0.000 0.000 +vdw 45 1.820 0.055 +vdw 46 1.820 0.055 +vdw 47 1.740 0.050 +vdw 48 0.900 0.015 +vdw 49 1.740 0.050 +vdw 50 1.940 0.044 +vdw 51 1.530 0.026 +vdw 52 1.600 0.090 +vdw 53 1.990 0.268 +vdw 54 2.150 0.358 +vdw 55 2.280 0.495 +vdw 59 2.200 0.015 +vdw 60 2.200 0.168 +vdw 61 2.200 0.020 +vdw 62 2.200 0.020 +vdw 63 2.200 0.020 +vdw 64 2.200 0.020 +vdw 65 2.200 0.020 +vdw 66 2.200 0.020 +vdw 69 1.820 0.059 +vdw 70 1.740 0.066 +vdw 71 1.940 0.056 +vdw 72 1.820 0.055 +vdw 73 1.820 0.055 +vdw 74 1.820 0.055 +vdw 75 1.820 0.055 + + + ##################################### + ## ## + ## Van der Waals Pair Parameters ## + ## ## + ##################################### + + +vdwpr 1 5 3.340 0.046 +vdwpr 1 36 3.337 0.046 +vdwpr 2 21 2.340 1.100 +vdwpr 2 23 2.340 0.400 +vdwpr 2 24 2.340 1.000 +vdwpr 2 28 2.340 1.000 +vdwpr 6 21 1.830 1.300 +vdwpr 6 23 1.830 0.600 +vdwpr 6 24 2.140 2.200 +vdwpr 6 28 2.140 2.400 +vdwpr 7 21 2.140 2.950 +vdwpr 7 23 2.140 0.400 +vdwpr 7 24 2.030 3.000 +vdwpr 7 28 2.030 3.000 +vdwpr 8 21 2.220 2.000 +vdwpr 8 23 2.220 0.400 +vdwpr 8 24 2.220 1.400 +vdwpr 8 28 2.220 1.000 +vdwpr 11 21 2.050 0.800 +vdwpr 11 23 2.050 0.200 +vdwpr 11 24 2.050 0.600 +vdwpr 11 28 2.050 0.400 +vdwpr 12 21 2.430 3.600 +vdwpr 12 23 2.430 0.200 +vdwpr 12 24 2.430 0.600 +vdwpr 12 28 2.430 0.400 +vdwpr 13 21 2.580 0.800 +vdwpr 13 23 2.580 0.200 +vdwpr 13 24 2.580 0.600 +vdwpr 13 28 2.580 0.400 +vdwpr 14 21 2.720 0.600 +vdwpr 14 23 2.720 0.400 +vdwpr 14 24 2.720 0.400 +vdwpr 14 28 2.720 0.200 +vdwpr 15 21 2.510 0.400 +vdwpr 15 23 2.510 0.200 +vdwpr 15 24 2.510 0.400 +vdwpr 15 28 2.510 0.200 + + + ################################## + ## ## + ## Bond Stretching Parameters ## + ## ## + ################################## + + +bond 1 1 4.400 1.523 +bond 1 2 4.400 1.497 +bond 1 3 4.400 1.509 +bond 1 4 5.200 1.470 +bond 1 5 4.600 1.113 +bond 1 6 5.360 1.402 +bond 1 8 5.100 1.438 +bond 1 9 3.520 1.437 +bond 1 11 5.100 1.392 +bond 1 12 3.230 1.795 +bond 1 13 2.300 1.949 +bond 1 14 2.200 2.149 +bond 1 15 3.213 1.815 +bond 1 16 3.213 1.816 +bond 1 17 3.213 1.805 +bond 1 18 3.213 1.784 +bond 1 19 2.970 1.880 +bond 1 22 4.400 1.502 +bond 1 25 2.910 1.856 +bond 1 29 4.400 1.497 +bond 1 31 2.700 1.950 +bond 1 32 2.124 2.147 +bond 1 33 1.900 2.242 +bond 1 34 2.680 1.948 +bond 1 35 2.700 2.140 +bond 1 36 4.600 1.108 +bond 1 37 3.950 1.470 +bond 1 38 4.400 1.497 +bond 1 39 5.100 1.499 +bond 1 41 5.360 1.414 +bond 1 43 3.950 1.488 +bond 1 46 7.000 1.498 +bond 1 50 4.400 1.497 +bond 1 70 3.000 1.480 +bond 1 71 4.400 1.509 +bond 1 72 3.950 1.470 +bond 2 2 9.600 1.337 +bond 2 3 9.600 1.351 +bond 2 4 9.900 1.313 +bond 2 5 4.600 1.101 +bond 2 6 6.000 1.355 +bond 2 8 6.320 1.377 +bond 2 9 5.000 1.410 +bond 2 11 5.400 1.320 +bond 2 12 3.400 1.719 +bond 2 13 2.500 1.881 +bond 2 14 2.480 2.075 +bond 2 19 3.500 1.865 +bond 2 22 4.400 1.467 +bond 2 25 2.910 1.828 +bond 2 37 11.090 1.260 +bond 2 38 9.600 1.336 +bond 2 40 11.090 1.266 +bond 2 41 10.000 1.225 +bond 2 42 6.471 1.459 +bond 2 46 5.050 1.463 +bond 2 72 11.090 1.260 +bond 3 3 9.600 1.415 +bond 3 5 4.600 1.113 +bond 3 6 5.050 1.338 +bond 3 7 10.800 1.208 +bond 3 9 6.400 1.385 +bond 3 22 4.400 1.447 +bond 3 36 4.600 1.130 +bond 3 72 11.090 1.280 +bond 4 4 15.600 1.212 +bond 4 5 5.900 1.090 +bond 4 10 17.730 1.158 +bond 5 15 3.800 1.345 +bond 5 16 3.800 1.346 +bond 5 17 3.800 1.346 +bond 5 18 3.800 1.346 +bond 5 19 2.720 1.489 +bond 5 22 4.600 1.086 +bond 5 25 3.330 1.437 +bond 5 29 4.600 1.101 +bond 5 31 2.570 1.530 +bond 5 32 2.229 1.696 +bond 5 33 1.894 1.775 +bond 5 34 3.170 1.472 +bond 5 35 2.850 1.670 +bond 5 38 4.600 1.072 +bond 5 71 4.600 1.113 +bond 6 6 3.950 1.428 +bond 6 19 5.500 1.626 +bond 6 20 4.600 0.600 +bond 6 21 4.600 0.942 +bond 6 24 7.200 0.972 +bond 6 25 2.900 1.615 +bond 6 28 7.200 0.972 +bond 7 17 5.000 1.480 +bond 7 18 8.412 1.450 +bond 7 43 10.800 1.268 +bond 7 46 7.500 1.220 +bond 8 8 5.600 1.381 +bond 8 20 6.100 0.600 +bond 8 23 6.100 1.020 +bond 9 18 6.100 1.660 +bond 9 28 5.900 1.022 +bond 15 15 3.100 2.024 +bond 19 19 1.850 2.332 +bond 19 22 3.500 1.860 +bond 20 37 6.100 0.600 +bond 20 41 4.600 0.600 +bond 20 72 6.100 0.600 +bond 22 22 4.400 1.474 +bond 22 38 4.400 1.488 +bond 22 46 4.350 1.477 +bond 23 37 5.240 1.022 +bond 23 40 6.100 1.050 +bond 23 72 5.240 1.022 +bond 28 41 7.200 0.972 +bond 33 33 0.980 2.891 +bond 37 37 10.720 1.248 +bond 37 40 11.000 1.230 +bond 37 43 10.720 1.257 +bond 38 38 9.600 1.303 +bond 39 48 6.100 1.045 +bond 50 50 8.065 1.392 +bond 70 71 10.000 1.236 + + + ########################################### + ## ## + ## Bond Stretching Parameters (4-Ring) ## + ## ## + ########################################### + + +bond4 22 22 4.400 1.528 + + + ########################################### + ## ## + ## Bond Stretching Parameters (3-Ring) ## + ## ## + ########################################### + + +bond3 22 22 4.400 1.503 +bond3 22 49 5.360 1.435 + + + ################################ + ## ## + ## Angle Bending Parameters ## + ## ## + ################################ + + +angle 1 1 1 0.450 109.470 109.510 109.500 +angle 1 1 2 0.450 109.470 109.510 109.500 +angle 1 1 3 0.450 107.800 109.900 110.000 +angle 1 1 4 0.450 109.470 112.400 109.000 +angle 1 1 5 0.360 109.390 109.410 110.000 +angle 1 1 6 0.700 107.500 107.700 107.400 +angle 1 1 8 0.570 109.470 108.800 109.500 +angle 1 1 9 0.500 109.280 110.780 109.280 +angle 1 1 11 0.650 109.500 107.500 109.500 +angle 1 1 12 0.560 108.200 0.000 0.000 +angle 1 1 13 0.630 108.200 0.000 0.000 +angle 1 1 14 0.490 108.900 0.000 0.000 +angle 1 1 15 0.550 109.000 107.000 106.500 +angle 1 1 16 0.420 107.800 0.000 0.000 +angle 1 1 17 0.420 106.000 0.000 0.000 +angle 1 1 18 0.420 102.000 0.000 0.000 +angle 1 1 19 0.400 109.000 110.900 112.700 +angle 1 1 22 0.450 112.400 112.400 112.400 +angle 1 1 25 0.480 111.500 0.000 0.000 +angle 1 1 29 0.450 110.000 0.000 0.000 +angle 1 1 31 0.640 110.500 0.000 0.000 +angle 1 1 32 0.560 110.200 0.000 0.000 +angle 1 1 33 0.300 110.200 0.000 0.000 +angle 1 1 34 0.500 108.200 0.000 0.000 +angle 1 1 35 0.450 108.200 0.000 0.000 +angle 1 1 36 0.360 109.390 109.410 110.000 +angle 1 1 37 0.380 110.740 0.000 0.000 +angle 1 1 39 0.570 103.500 102.700 103.900 +angle 1 1 41 0.700 107.500 0.000 0.000 +angle 1 1 43 0.380 104.640 0.000 0.000 +angle 1 1 46 0.600 106.000 106.800 106.800 +angle 1 1 50 0.450 109.470 109.510 109.500 +angle 1 1 70 0.700 104.000 0.000 0.000 +angle 1 1 71 0.450 107.800 109.900 110.000 +angle 2 1 2 0.450 109.470 109.510 109.500 +angle 2 1 3 0.470 109.470 110.510 110.200 +angle 2 1 4 0.470 109.470 110.510 110.200 +angle 2 1 5 0.360 109.390 109.410 110.000 +angle 2 1 6 0.700 109.500 0.000 0.000 +angle 2 1 8 1.045 110.740 0.000 0.000 +angle 2 1 9 0.500 109.800 0.000 0.000 +angle 2 1 11 0.650 109.000 0.000 0.000 +angle 2 1 12 0.560 109.500 0.000 0.000 +angle 2 1 15 0.420 107.800 107.800 109.500 +angle 2 1 16 0.420 107.800 0.000 0.000 +angle 2 1 19 0.500 109.500 110.500 113.000 +angle 2 1 22 0.450 112.400 0.000 0.000 +angle 2 1 36 0.360 109.390 109.410 110.000 +angle 2 1 37 0.380 110.510 0.000 0.000 +angle 2 1 39 1.045 110.740 0.000 0.000 +angle 2 1 43 0.380 110.510 0.000 0.000 +angle 3 1 3 0.470 109.470 110.510 110.200 +angle 3 1 5 0.370 107.900 108.800 109.470 +angle 3 1 6 0.700 109.500 0.000 0.000 +angle 3 1 8 1.045 110.740 0.000 0.000 +angle 3 1 9 0.820 109.800 111.100 109.800 +angle 3 1 11 0.650 109.200 0.000 0.000 +angle 3 1 12 0.560 109.800 0.000 0.000 +angle 3 1 13 0.630 109.100 0.000 0.000 +angle 3 1 14 0.490 108.900 0.000 0.000 +angle 3 1 15 0.420 107.800 0.000 0.000 +angle 3 1 16 0.420 107.800 0.000 0.000 +angle 3 1 36 0.370 108.800 108.800 109.470 +angle 4 1 4 0.470 109.470 110.510 110.200 +angle 4 1 5 0.360 109.390 109.410 110.000 +angle 5 1 5 0.320 109.400 109.000 109.470 +angle 5 1 6 0.540 106.700 106.700 106.700 +angle 5 1 8 0.500 108.800 0.000 0.000 +angle 5 1 9 0.420 109.000 0.000 0.000 +angle 5 1 11 0.490 110.500 0.000 0.000 +angle 5 1 12 0.530 106.900 0.000 0.000 +angle 5 1 13 0.440 106.500 0.000 0.000 +angle 5 1 14 0.540 106.400 0.000 0.000 +angle 5 1 15 0.360 112.000 112.000 109.300 +angle 5 1 16 0.300 108.200 0.000 0.000 +angle 5 1 17 0.384 108.600 0.000 0.000 +angle 5 1 18 0.384 108.600 0.000 0.000 +angle 5 1 19 0.320 108.600 110.800 107.000 +angle 5 1 22 0.360 109.410 109.410 109.410 +angle 5 1 25 0.360 111.000 0.000 0.000 +angle 5 1 29 0.360 110.000 0.000 0.000 +angle 5 1 31 0.449 110.400 0.000 0.000 +angle 5 1 32 0.350 112.000 0.000 0.000 +angle 5 1 33 0.100 109.500 0.000 0.000 +angle 5 1 34 0.330 110.500 0.000 0.000 +angle 5 1 35 0.300 110.500 0.000 0.000 +angle 5 1 36 0.320 109.400 109.000 109.470 +angle 5 1 37 0.480 107.500 0.000 0.000 +angle 5 1 39 0.500 108.800 0.000 0.000 +angle 5 1 41 0.540 106.700 0.000 0.000 +angle 5 1 43 0.480 107.500 0.000 0.000 +angle 5 1 46 0.480 109.000 0.000 0.000 +angle 5 1 50 0.360 109.390 109.410 110.000 +angle 5 1 70 0.350 102.800 0.000 0.000 +angle 5 1 71 0.370 107.900 108.800 109.500 +angle 5 1 72 0.480 107.500 0.000 0.000 +angle 6 1 6 0.460 99.900 97.000 102.200 +angle 6 1 12 0.560 108.500 0.000 0.000 +angle 6 1 71 0.700 103.000 0.000 0.000 +angle 8 1 8 1.045 110.740 0.000 0.000 +angle 8 1 39 1.045 110.740 0.000 0.000 +angle 9 1 15 0.580 107.000 108.000 114.800 +angle 9 1 36 0.420 109.000 0.000 0.000 +angle 11 1 11 1.070 107.100 0.000 0.000 +angle 11 1 12 1.075 110.400 0.000 0.000 +angle 11 1 13 1.024 109.400 0.000 0.000 +angle 12 1 12 1.080 111.700 0.000 0.000 +angle 12 1 13 1.030 110.700 0.000 0.000 +angle 13 1 13 0.980 109.700 0.000 0.000 +angle 15 1 15 0.420 116.200 0.000 0.000 +angle 19 1 19 0.400 115.500 0.000 0.000 +angle 22 1 22 0.450 112.000 0.000 105.000 +angle 22 1 37 0.380 110.200 0.000 0.000 +angle 22 1 43 0.380 110.200 0.000 0.000 +angle 36 1 36 0.320 109.400 109.000 109.470 +angle 36 1 50 0.360 109.390 109.410 110.000 +angle 50 1 50 0.450 109.470 109.510 109.500 +angle 1 2 1 0.450 117.200 0.000 0.000 +angle 1 2 2 0.550 121.400 122.000 0.000 +angle 1 2 3 0.380 121.000 0.000 0.000 +angle 1 2 4 0.470 122.000 0.000 0.000 +angle 1 2 5 0.360 118.200 0.000 0.000 +angle 1 2 6 0.500 120.000 0.000 0.000 +angle 1 2 19 0.400 120.000 0.000 0.000 +angle 1 2 37 0.550 115.100 125.300 0.000 +angle 2 2 2 0.430 120.000 0.000 0.000 +angle 2 2 3 0.600 114.600 117.600 0.000 +angle 2 2 5 0.360 120.000 120.500 0.000 +angle 2 2 6 0.700 124.300 0.000 0.000 +angle 2 2 8 0.616 123.000 124.000 0.000 +angle 2 2 9 0.500 118.000 0.000 0.000 +angle 2 2 11 0.650 121.000 0.000 0.000 +angle 2 2 12 0.550 118.800 0.000 0.000 +angle 2 2 13 0.450 118.100 0.000 0.000 +angle 2 2 14 0.410 118.800 0.000 0.000 +angle 2 2 19 0.400 122.500 120.500 0.000 +angle 2 2 22 0.550 121.000 0.000 0.000 +angle 2 2 25 0.380 120.000 0.000 0.000 +angle 2 2 37 0.430 120.000 123.500 0.000 +angle 2 2 40 0.430 120.000 119.000 0.000 +angle 2 2 41 0.600 120.000 118.100 0.000 +angle 2 2 42 0.380 119.000 0.000 0.000 +angle 2 2 46 0.600 113.500 0.000 0.000 +angle 2 2 72 0.430 120.000 123.500 0.000 +angle 3 2 5 0.240 120.000 0.000 0.000 +angle 4 2 5 0.360 121.100 121.600 0.000 +angle 5 2 5 0.320 119.000 0.000 0.000 +angle 5 2 6 0.540 116.400 0.000 0.000 +angle 5 2 8 0.540 119.000 0.000 0.000 +angle 5 2 9 0.300 109.000 0.000 0.000 +angle 5 2 11 0.450 120.000 0.000 0.000 +angle 5 2 12 0.450 112.600 0.000 0.000 +angle 5 2 13 0.460 112.100 0.000 0.000 +angle 5 2 14 0.450 112.600 0.000 0.000 +angle 5 2 19 0.240 118.400 0.000 0.000 +angle 5 2 22 0.360 118.200 0.000 0.000 +angle 5 2 37 0.360 116.500 120.500 0.000 +angle 5 2 38 0.360 120.000 0.000 0.000 +angle 5 2 40 0.400 113.500 0.000 0.000 +angle 5 2 41 0.450 108.000 0.000 0.000 +angle 5 2 42 0.400 120.000 0.000 0.000 +angle 5 2 46 0.260 119.000 0.000 0.000 +angle 5 2 72 0.360 116.500 120.500 0.000 +angle 9 2 9 0.400 120.000 0.000 0.000 +angle 12 2 41 0.500 105.000 0.000 0.000 +angle 13 2 41 0.500 104.000 0.000 0.000 +angle 14 2 41 0.500 107.000 0.000 0.000 +angle 19 2 19 0.400 120.000 0.000 0.000 +angle 37 2 37 0.400 120.000 127.000 0.000 +angle 37 2 40 0.400 126.000 126.000 0.000 +angle 1 3 1 0.400 116.600 0.000 0.000 +angle 1 3 2 0.400 115.000 0.000 0.000 +angle 1 3 3 0.600 114.000 0.000 0.000 +angle 1 3 5 0.370 116.400 0.000 0.000 +angle 1 3 6 0.650 107.100 0.000 0.000 +angle 1 3 7 0.460 122.500 0.000 0.000 +angle 1 3 9 0.660 116.500 0.000 0.000 +angle 1 3 72 0.550 116.800 0.000 0.000 +angle 2 3 2 0.600 112.000 0.000 0.000 +angle 2 3 3 0.480 120.000 0.000 0.000 +angle 2 3 5 0.400 113.500 0.000 0.000 +angle 2 3 6 0.700 124.300 0.000 0.000 +angle 2 3 7 0.460 123.000 0.000 0.000 +angle 2 3 9 99.000 120.000 0.000 0.000 +angle 2 3 72 0.690 120.400 0.000 0.000 +angle 3 3 5 0.400 112.000 0.000 0.000 +angle 3 3 7 0.430 119.000 0.000 0.000 +angle 3 3 36 0.400 112.500 0.000 0.000 +angle 5 3 5 0.360 118.200 0.000 0.000 +angle 5 3 6 0.650 105.900 0.000 0.000 +angle 5 3 7 0.370 120.300 0.000 0.000 +angle 5 3 9 0.300 109.000 0.000 0.000 +angle 5 3 72 0.660 119.500 0.000 0.000 +angle 6 3 7 0.800 122.000 0.000 0.000 +angle 7 3 9 0.670 124.300 0.000 0.000 +angle 7 3 22 0.460 122.500 0.000 0.000 +angle 7 3 36 0.370 120.000 0.000 0.000 +angle 9 3 9 0.500 120.000 0.000 0.000 +angle 1 4 4 0.200 180.000 0.000 0.000 +angle 1 4 10 0.325 180.000 0.000 0.000 +angle 2 4 2 0.400 180.000 0.000 0.000 +angle 2 4 4 0.470 180.000 0.000 0.000 +angle 4 4 5 0.360 180.000 0.000 0.000 +angle 1 6 1 0.770 106.800 0.000 0.000 +angle 1 6 2 0.770 110.800 0.000 0.000 +angle 1 6 3 0.600 109.900 0.000 0.000 +angle 1 6 6 0.635 98.700 0.000 0.000 +angle 1 6 19 0.400 114.600 0.000 0.000 +angle 1 6 20 0.350 105.160 0.000 0.000 +angle 1 6 21 0.350 106.900 0.000 0.000 +angle 1 6 25 0.770 116.000 0.000 0.000 +angle 2 6 20 0.350 103.260 0.000 0.000 +angle 2 6 25 0.800 118.000 0.000 0.000 +angle 2 6 28 0.350 108.000 0.000 0.000 +angle 3 6 20 0.350 105.160 0.000 0.000 +angle 3 6 24 0.300 106.100 0.000 0.000 +angle 6 6 20 0.350 103.260 0.000 0.000 +angle 6 6 21 0.511 98.440 0.000 0.000 +angle 19 6 19 0.150 145.700 0.000 0.000 +angle 19 6 20 0.350 97.500 0.000 0.000 +angle 20 6 20 0.240 131.000 0.000 0.000 +angle 20 6 21 0.240 101.010 0.000 0.000 +angle 20 6 24 0.240 101.000 0.000 0.000 +angle 20 6 25 0.350 105.000 0.000 0.000 +angle 20 6 28 0.240 101.100 0.000 0.000 +angle 21 6 21 0.400 104.500 0.000 0.000 +angle 21 6 21 0.630 105.000 0.000 0.000 +angle 1 8 1 0.630 107.700 0.000 0.000 +angle 1 8 2 0.698 107.000 0.000 0.000 +angle 1 8 8 0.740 105.500 0.000 0.000 +angle 1 8 20 0.500 109.200 0.000 0.000 +angle 1 8 23 0.500 109.470 0.000 0.000 +angle 2 8 20 0.350 87.000 0.000 0.000 +angle 2 8 23 0.527 109.500 0.000 0.000 +angle 8 8 20 0.350 109.000 0.000 0.000 +angle 8 8 23 0.430 103.200 0.000 0.000 +angle 20 8 20 0.587 106.820 0.000 0.000 +angle 20 8 23 0.500 108.000 0.000 0.000 +angle 23 8 23 0.500 104.500 0.000 0.000 +angle 1 9 1 0.760 126.000 0.000 0.000 +angle 1 9 2 0.630 119.900 0.000 0.000 +angle 1 9 3 0.760 119.900 0.000 0.000 +angle 1 9 18 0.300 110.000 0.000 0.000 +angle 1 9 28 0.440 124.000 0.000 0.000 +angle 2 9 2 0.400 107.000 0.000 0.000 +angle 2 9 3 0.600 115.000 0.000 0.000 +angle 2 9 28 0.500 110.000 0.000 0.000 +angle 3 9 3 0.500 125.000 0.000 0.000 +angle 3 9 28 0.420 119.000 0.000 0.000 +angle 18 9 28 0.300 122.000 0.000 0.000 +angle 28 9 28 0.320 123.000 0.000 0.000 +angle 1 15 1 0.720 96.300 0.000 0.000 +angle 1 15 5 0.480 96.000 0.000 0.000 +angle 1 15 15 1.168 102.900 0.000 0.000 +angle 5 15 15 0.400 91.200 0.000 0.000 +angle 1 16 1 0.500 94.300 0.000 0.000 +angle 1 16 5 0.400 94.000 0.000 0.000 +angle 1 17 1 0.720 93.000 0.000 0.000 +angle 1 17 7 0.597 106.000 0.000 0.000 +angle 1 18 1 0.720 102.000 0.000 0.000 +angle 1 18 7 0.597 107.700 0.000 0.000 +angle 1 18 9 0.800 103.000 0.000 0.000 +angle 5 18 7 0.560 101.500 0.000 0.000 +angle 5 18 9 0.600 98.000 0.000 0.000 +angle 7 18 7 0.900 116.600 0.000 0.000 +angle 7 18 9 1.700 108.000 0.000 0.000 +angle 1 19 1 0.480 110.800 110.400 108.500 +angle 1 19 2 0.400 110.200 0.000 0.000 +angle 1 19 5 0.460 109.300 107.000 110.200 +angle 1 19 6 0.350 108.500 0.000 0.000 +angle 1 19 19 0.750 110.000 0.000 0.000 +angle 2 19 2 0.600 109.500 0.000 0.000 +angle 2 19 5 0.240 109.500 0.000 0.000 +angle 2 19 19 0.400 110.200 0.000 0.000 +angle 5 19 5 0.380 104.500 108.700 109.500 +angle 5 19 6 0.350 109.500 0.000 0.000 +angle 5 19 19 0.378 111.000 111.000 111.000 +angle 5 19 22 0.460 110.200 0.000 0.000 +angle 6 19 6 0.450 113.500 0.000 0.000 +angle 19 19 19 0.350 111.300 110.800 110.000 +angle 1 22 1 0.450 120.000 0.000 0.000 +angle 1 22 5 0.360 123.500 0.000 0.000 +angle 1 22 22 0.600 118.200 118.200 0.000 +angle 1 22 49 0.560 115.000 0.000 0.000 +angle 2 22 2 0.450 120.000 0.000 0.000 +angle 2 22 5 0.360 123.500 0.000 0.000 +angle 2 22 22 0.600 118.200 0.000 0.000 +angle 2 22 49 0.560 115.000 0.000 0.000 +angle 3 22 5 0.360 123.500 123.500 123.500 +angle 5 22 5 0.320 120.600 0.000 0.000 +angle 5 22 19 0.240 123.500 0.000 0.000 +angle 5 22 22 0.360 124.500 119.700 0.000 +angle 5 22 38 0.360 124.500 119.700 0.000 +angle 5 22 46 0.050 114.000 0.000 0.000 +angle 5 22 49 0.430 113.000 0.000 0.000 +angle 19 22 22 0.530 117.500 0.000 0.000 +angle 22 22 22 0.350 119.140 120.700 0.000 +angle 22 22 46 0.700 117.000 117.000 117.000 +angle 1 25 1 0.576 96.000 0.000 0.000 +angle 1 25 2 0.480 92.500 0.000 0.000 +angle 1 25 5 0.480 95.000 0.000 0.000 +angle 2 25 2 0.480 93.200 0.000 0.000 +angle 5 25 5 0.438 93.400 0.000 0.000 +angle 6 25 6 0.450 99.500 0.000 0.000 +angle 1 29 1 0.450 120.000 0.000 0.000 +angle 1 29 5 0.360 120.000 0.000 0.000 +angle 5 29 5 0.320 120.000 0.000 0.000 +angle 1 31 1 0.490 110.000 0.000 0.000 +angle 1 31 5 0.352 109.500 0.000 0.000 +angle 5 31 5 0.216 109.000 0.000 0.000 +angle 1 32 1 0.320 107.000 0.000 0.000 +angle 1 32 5 0.227 110.500 0.000 0.000 +angle 5 32 5 0.132 109.500 0.000 0.000 +angle 1 33 1 0.100 109.500 0.000 0.000 +angle 1 33 5 0.100 109.500 0.000 0.000 +angle 1 33 33 0.100 109.500 0.000 0.000 +angle 5 33 5 0.100 109.500 0.000 0.000 +angle 1 34 1 0.500 94.800 0.000 0.000 +angle 1 34 5 0.430 94.500 0.000 0.000 +angle 1 35 1 0.590 95.050 0.000 0.000 +angle 1 35 5 0.390 94.600 0.000 0.000 +angle 1 37 2 0.550 108.000 0.000 0.000 +angle 1 37 20 0.350 120.000 0.000 0.000 +angle 1 37 37 0.690 106.500 0.000 0.000 +angle 1 37 43 0.570 99.100 0.000 0.000 +angle 2 37 2 0.430 115.000 0.000 0.000 +angle 2 37 20 0.500 122.500 0.000 0.000 +angle 2 37 23 0.500 110.000 0.000 0.000 +angle 2 37 37 0.400 107.500 0.000 0.000 +angle 2 37 40 0.430 115.000 0.000 0.000 +angle 20 37 23 0.500 127.500 0.000 0.000 +angle 20 37 37 0.350 120.000 0.000 0.000 +angle 20 37 40 0.500 122.500 0.000 0.000 +angle 20 37 43 0.350 120.000 0.000 0.000 +angle 23 37 37 0.400 103.500 0.000 0.000 +angle 1 38 22 0.450 117.200 0.000 0.000 +angle 2 38 22 0.550 137.000 0.000 0.000 +angle 5 38 22 0.360 146.000 0.000 0.000 +angle 5 38 38 0.360 146.000 0.000 0.000 +angle 1 39 1 0.630 108.600 111.200 115.400 +angle 1 39 48 0.500 109.470 0.000 0.000 +angle 48 39 48 0.500 104.500 0.000 0.000 +angle 2 40 2 0.430 124.000 124.000 0.000 +angle 2 40 23 0.360 118.000 0.000 0.000 +angle 2 40 37 0.430 124.000 124.000 0.000 +angle 23 40 37 0.360 113.000 0.000 0.000 +angle 1 41 2 0.770 113.600 0.000 0.000 +angle 1 41 20 0.350 124.200 0.000 0.000 +angle 2 41 2 0.870 113.950 0.000 0.000 +angle 2 41 20 0.350 122.200 0.000 0.000 +angle 2 41 28 0.360 109.000 0.000 0.000 +angle 20 41 28 0.360 128.800 0.000 0.000 +angle 2 42 2 0.680 98.500 0.000 0.000 +angle 1 43 7 0.570 120.400 0.000 0.000 +angle 1 43 37 0.380 114.000 0.000 0.000 +angle 7 43 37 0.380 125.000 0.000 0.000 +angle 1 46 7 0.594 115.830 0.000 0.000 +angle 2 46 7 0.800 115.000 0.000 0.000 +angle 7 46 7 0.600 128.600 0.000 0.000 +angle 7 46 22 0.594 111.000 0.000 0.000 +angle 20 49 20 0.240 131.000 0.000 0.000 +angle 20 49 22 0.350 103.000 0.000 0.000 +angle 1 50 1 0.450 117.200 0.000 0.000 +angle 1 50 5 0.360 118.200 0.000 0.000 +angle 1 50 50 0.550 121.400 122.000 120.000 +angle 5 50 5 0.320 119.000 0.000 0.000 +angle 5 50 50 0.360 120.000 120.500 0.000 +angle 50 50 50 0.430 120.000 0.000 0.000 +angle 1 70 71 0.800 116.000 0.000 0.000 +angle 1 71 1 0.400 116.600 0.000 0.000 +angle 1 71 5 0.370 116.400 0.000 0.000 +angle 1 71 70 0.520 113.000 116.500 0.000 +angle 5 71 5 0.440 122.400 0.000 0.000 +angle 5 71 70 0.360 111.000 117.000 0.000 +angle 1 72 3 0.550 111.000 0.000 0.000 +angle 1 72 20 0.350 120.000 0.000 0.000 +angle 2 72 3 0.570 115.000 0.000 0.000 +angle 2 72 20 0.500 122.500 0.000 0.000 +angle 3 72 20 0.550 112.500 0.000 0.000 +angle 3 72 23 0.550 110.000 0.000 0.000 +angle 20 72 23 0.500 127.500 0.000 0.000 + + + ######################################### + ## ## + ## Angle Bending Parameters (4-Ring) ## + ## ## + ######################################### + + +angle4 1 1 1 0.340 109.470 0.000 109.500 +angle4 1 1 1 0.290 0.000 109.510 0.000 +angle4 1 1 2 0.360 109.470 109.510 109.500 +angle4 1 1 3 0.340 107.800 109.900 111.000 +angle4 1 1 6 0.530 107.400 0.000 0.000 +angle4 1 1 8 0.320 108.800 0.000 0.000 +angle4 1 1 9 0.550 106.500 0.000 0.000 +angle4 1 1 15 0.500 106.500 106.500 105.800 +angle4 1 1 19 0.300 94.500 0.000 94.500 +angle4 1 1 22 0.340 0.000 112.300 112.300 +angle4 1 1 31 0.640 92.000 0.000 0.000 +angle4 1 1 37 0.350 110.740 0.000 0.000 +angle4 1 1 39 0.450 108.800 0.000 0.000 +angle4 1 1 43 0.350 110.740 0.000 0.000 +angle4 2 1 2 0.340 109.470 109.510 109.500 +angle4 1 2 1 0.220 117.200 0.000 0.000 +angle4 1 2 2 0.340 121.400 122.000 120.000 +angle4 2 2 2 0.340 120.000 0.000 0.000 +angle4 1 3 1 0.300 116.600 0.000 0.000 +angle4 1 3 6 0.480 106.500 0.000 0.000 +angle4 1 3 9 0.660 113.000 0.000 0.000 +angle4 1 3 11 0.490 88.000 0.000 0.000 +angle4 22 3 22 0.300 116.600 0.000 0.000 +angle4 1 6 1 0.580 106.800 0.000 0.000 +angle4 1 6 3 0.450 109.900 0.000 0.000 +angle4 1 8 1 0.470 107.700 0.000 0.000 +angle4 1 9 3 0.600 119.800 0.000 0.000 +angle4 1 15 1 0.650 96.500 0.000 0.000 +angle4 1 19 1 0.450 90.500 0.000 90.500 +angle4 1 22 22 0.340 0.000 119.300 0.000 +angle4 3 22 22 0.340 119.300 119.300 119.300 +angle4 22 22 22 0.450 112.500 98.000 0.000 +angle4 1 31 1 0.490 88.000 0.000 0.000 +angle4 1 37 37 0.620 106.500 0.000 0.000 +angle4 1 37 43 0.480 99.100 0.000 0.000 +angle4 1 39 1 0.380 107.700 0.000 0.000 +angle4 1 43 37 0.350 114.000 0.000 0.000 + + + ######################################### + ## ## + ## Angle Bending Parameters (3-Ring) ## + ## ## + ######################################### + + +angle3 22 22 22 0.450 55.800 60.000 60.000 +angle3 22 22 38 0.450 48.000 0.000 0.000 +angle3 22 22 49 0.560 59.300 0.000 0.000 +angle3 38 22 38 0.450 53.000 0.000 0.000 +angle3 22 38 22 0.400 67.000 0.000 0.000 +angle3 22 38 38 0.550 80.000 0.000 0.000 +angle3 22 49 22 0.620 61.400 0.000 0.000 + + + ############################### + ## ## + ## Stretch-Bend Parameters ## + ## ## + ############################### + + +strbnd 1 0.120 0.090 0.000 +strbnd 2 0.120 0.090 0.000 +strbnd 3 0.120 0.090 0.000 +strbnd 4 0.120 0.090 0.000 +strbnd 6 0.120 0.090 0.000 +strbnd 8 0.120 0.090 0.000 +strbnd 9 0.120 0.090 0.000 +strbnd 15 0.250 -0.400 0.000 +strbnd 16 0.250 -0.400 0.000 +strbnd 17 0.250 -0.400 0.000 +strbnd 18 0.250 -0.400 0.000 +strbnd 19 0.200 0.060 0.000 +strbnd 22 0.120 0.090 0.000 +strbnd 25 0.200 0.060 0.000 +strbnd 26 0.120 0.090 0.000 +strbnd 27 0.120 0.090 0.000 +strbnd 29 0.120 0.090 0.000 +strbnd 30 0.120 0.090 0.000 +strbnd 34 0.450 0.000 0.000 +strbnd 37 0.120 0.090 0.000 +strbnd 38 0.120 0.090 0.000 +strbnd 39 0.120 0.090 0.000 +strbnd 40 0.120 0.090 0.000 +strbnd 41 0.120 0.090 0.000 +strbnd 42 0.250 -0.400 0.000 +strbnd 43 0.120 0.090 0.000 +strbnd 45 0.120 0.090 0.000 +strbnd 46 0.120 0.090 0.000 +strbnd 49 0.120 0.090 0.000 +strbnd 50 0.120 0.090 0.000 +strbnd 60 0.200 0.060 0.000 +strbnd 71 0.120 0.090 0.000 +strbnd 72 0.120 0.090 0.000 + + + #################################### + ## ## + ## Out-of-Plane Bend Parameters ## + ## ## + #################################### + + +opbend 2 1 0.050 +opbend 2 2 0.050 +opbend 2 3 0.050 +opbend 2 4 0.050 +opbend 2 5 0.050 +opbend 2 6 0.050 +opbend 2 7 0.050 +opbend 2 8 0.050 +opbend 2 9 0.050 +opbend 2 11 0.050 +opbend 2 12 0.050 +opbend 2 13 0.050 +opbend 2 14 0.050 +opbend 2 19 0.050 +opbend 2 22 0.050 +opbend 2 25 0.500 +opbend 2 37 0.050 +opbend 2 38 0.050 +opbend 2 40 0.050 +opbend 2 41 0.050 +opbend 2 42 0.050 +opbend 2 46 0.200 +opbend 2 72 0.050 +opbend 3 1 0.800 +opbend 3 2 0.800 +opbend 3 3 0.900 +opbend 3 4 0.800 +opbend 3 5 0.800 +opbend 3 6 0.800 +opbend 3 7 0.800 +opbend 3 8 0.800 +opbend 3 9 0.800 +opbend 3 22 0.800 +opbend 3 36 0.800 +opbend 3 72 0.050 +opbend 9 1 0.050 +opbend 9 2 0.050 +opbend 9 3 0.050 +opbend 9 4 0.050 +opbend 9 6 0.050 +opbend 9 7 0.050 +opbend 9 8 0.050 +opbend 9 9 0.050 +opbend 9 18 0.050 +opbend 9 28 0.010 +opbend 29 1 0.150 +opbend 29 5 0.150 +opbend 30 1 0.050 +opbend 30 5 0.050 +opbend 37 1 0.050 +opbend 37 1 0.050 +opbend 37 2 0.050 +opbend 37 20 0.050 +opbend 37 20 0.050 +opbend 37 23 0.050 +opbend 37 23 0.050 +opbend 37 37 0.050 +opbend 37 37 0.050 +opbend 37 40 0.050 +opbend 37 43 0.050 +opbend 38 2 0.050 +opbend 38 5 0.050 +opbend 38 22 0.050 +opbend 38 38 0.050 +opbend 40 2 0.050 +opbend 40 23 0.050 +opbend 40 37 0.050 +opbend 41 1 0.050 +opbend 41 2 0.050 +opbend 41 20 0.050 +opbend 41 28 0.050 +opbend 43 1 0.050 +opbend 43 7 0.050 +opbend 43 37 0.050 +opbend 46 1 0.200 +opbend 46 2 0.200 +opbend 46 7 0.200 +opbend 46 22 0.200 +opbend 50 1 0.050 +opbend 50 5 0.050 +opbend 50 50 0.050 +opbend 71 1 0.800 +opbend 71 5 0.800 +opbend 71 70 1.569 +opbend 72 1 0.050 +opbend 72 2 0.050 +opbend 72 3 0.050 +opbend 72 20 0.050 +opbend 72 23 0.050 + + + ############################ + ## ## + ## Torsional Parameters ## + ## ## + ############################ + + +torsion 1 1 1 1 0.200 0.0 1 0.270 180.0 2 0.093 0.0 3 +torsion 1 1 1 2 0.170 0.0 1 0.270 180.0 2 0.093 0.0 3 +torsion 1 1 1 3 0.050 0.0 1 0.370 180.0 2 0.000 0.0 3 +torsion 1 1 1 4 0.200 0.0 1 -0.260 180.0 2 0.093 0.0 3 +torsion 1 1 1 5 0.000 0.0 1 0.000 180.0 2 0.267 0.0 3 +torsion 1 1 1 6 0.100 0.0 1 0.100 180.0 2 0.180 0.0 3 +torsion 1 1 1 8 0.100 0.0 1 0.400 180.0 2 0.500 0.0 3 +torsion 1 1 1 9 0.000 0.0 1 0.000 180.0 2 0.400 0.0 3 +torsion 1 1 1 11 0.000 0.0 1 -0.086 180.0 2 0.930 0.0 3 +torsion 1 1 1 12 0.000 0.0 1 -0.250 180.0 2 0.550 0.0 3 +torsion 1 1 1 13 0.000 0.0 1 -0.410 180.0 2 1.060 0.0 3 +torsion 1 1 1 14 0.000 0.0 1 -0.500 180.0 2 0.267 0.0 3 +torsion 1 1 1 15 0.140 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 1 1 1 16 0.000 0.0 1 0.000 180.0 2 0.483 0.0 3 +torsion 1 1 1 17 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 1 1 1 18 0.200 0.0 1 0.270 180.0 2 0.093 0.0 3 +torsion 1 1 1 19 0.000 0.0 1 0.000 180.0 2 0.500 0.0 3 +torsion 1 1 1 22 0.200 0.0 1 -0.200 180.0 2 0.600 0.0 3 +torsion 1 1 1 25 0.000 0.0 1 0.000 180.0 2 0.400 0.0 3 +torsion 1 1 1 29 0.170 0.0 1 0.270 180.0 2 0.093 0.0 3 +torsion 1 1 1 31 0.000 0.0 1 0.000 180.0 2 -0.065 0.0 3 +torsion 1 1 1 32 -0.083 0.0 1 -0.083 180.0 2 0.050 0.0 3 +torsion 1 1 1 33 0.000 0.0 1 -0.008 180.0 2 0.110 0.0 3 +torsion 1 1 1 34 0.140 0.0 1 0.000 180.0 2 0.100 0.0 3 +torsion 1 1 1 35 0.000 0.0 1 0.200 180.0 2 0.400 0.0 3 +torsion 1 1 1 36 0.000 0.0 1 0.000 180.0 2 0.267 0.0 3 +torsion 1 1 1 37 0.000 0.0 1 0.000 180.0 2 0.100 0.0 3 +torsion 1 1 1 39 0.100 0.0 1 0.400 180.0 2 0.500 0.0 3 +torsion 1 1 1 43 0.000 0.0 1 0.000 180.0 2 0.100 0.0 3 +torsion 1 1 1 46 0.000 0.0 1 0.000 180.0 2 0.800 0.0 3 +torsion 1 1 1 50 0.170 0.0 1 0.270 180.0 2 0.093 0.0 3 +torsion 1 1 1 70 0.129 0.0 1 -0.650 180.0 2 0.817 0.0 3 +torsion 1 1 1 71 0.050 0.0 1 0.370 180.0 2 0.000 0.0 3 +torsion 2 1 1 2 2.100 0.0 1 0.270 180.0 2 0.093 0.0 3 +torsion 2 1 1 3 0.000 0.0 1 0.000 180.0 2 0.180 0.0 3 +torsion 2 1 1 4 0.000 0.0 1 0.000 180.0 2 0.093 0.0 3 +torsion 2 1 1 5 0.000 0.0 1 0.000 180.0 2 0.500 0.0 3 +torsion 2 1 1 6 0.000 0.0 1 0.000 180.0 2 0.180 0.0 3 +torsion 2 1 1 8 0.000 0.0 1 0.000 180.0 2 0.180 0.0 3 +torsion 2 1 1 9 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 2 1 1 15 0.000 0.0 1 0.000 180.0 2 0.483 0.0 3 +torsion 2 1 1 16 0.000 0.0 1 0.000 180.0 2 0.483 0.0 3 +torsion 2 1 1 19 0.000 0.0 1 0.000 180.0 2 0.167 0.0 3 +torsion 2 1 1 36 0.000 0.0 1 0.000 180.0 2 0.500 0.0 3 +torsion 2 1 1 39 0.000 0.0 1 0.000 180.0 2 0.180 0.0 3 +torsion 3 1 1 3 0.000 0.0 1 0.000 180.0 2 0.180 0.0 3 +torsion 3 1 1 5 0.000 0.0 1 0.000 180.0 2 0.180 0.0 3 +torsion 3 1 1 6 0.000 0.0 1 0.000 180.0 2 0.180 0.0 3 +torsion 3 1 1 8 0.000 0.0 1 0.400 180.0 2 0.500 0.0 3 +torsion 3 1 1 9 0.000 0.0 1 0.000 180.0 2 0.180 0.0 3 +torsion 3 1 1 11 -1.000 0.0 1 0.000 180.0 2 0.200 0.0 3 +torsion 3 1 1 12 -0.585 0.0 1 0.000 180.0 2 0.200 0.0 3 +torsion 3 1 1 13 -0.465 0.0 1 0.000 180.0 2 0.200 0.0 3 +torsion 3 1 1 15 0.000 0.0 1 0.000 180.0 2 0.483 0.0 3 +torsion 3 1 1 16 0.000 0.0 1 0.000 180.0 2 0.483 0.0 3 +torsion 3 1 1 25 0.000 0.0 1 0.000 180.0 2 0.400 0.0 3 +torsion 3 1 1 36 0.000 0.0 1 0.000 180.0 2 0.180 0.0 3 +torsion 3 1 1 39 0.000 0.0 1 0.400 180.0 2 0.500 0.0 3 +torsion 4 1 1 4 1.000 0.0 1 0.000 180.0 2 0.093 0.0 3 +torsion 4 1 1 5 0.000 0.0 1 0.000 180.0 2 0.400 0.0 3 +torsion 4 1 1 6 0.000 0.0 1 -0.400 180.0 2 0.180 0.0 3 +torsion 5 1 1 5 0.000 0.0 1 0.000 180.0 2 0.237 0.0 3 +torsion 5 1 1 6 0.000 0.0 1 0.000 180.0 2 0.180 0.0 3 +torsion 5 1 1 8 -0.150 0.0 1 0.000 180.0 2 0.150 0.0 3 +torsion 5 1 1 9 0.000 0.0 1 0.000 180.0 2 0.400 0.0 3 +torsion 5 1 1 11 0.000 0.0 1 0.000 180.0 2 0.351 0.0 3 +torsion 5 1 1 12 0.000 0.0 1 0.000 180.0 2 0.406 0.0 3 +torsion 5 1 1 13 0.000 0.0 1 0.000 180.0 2 0.385 0.0 3 +torsion 5 1 1 14 0.000 0.0 1 0.000 180.0 2 0.267 0.0 3 +torsion 5 1 1 15 0.000 0.0 1 0.000 180.0 2 0.330 0.0 3 +torsion 5 1 1 16 0.000 0.0 1 0.000 180.0 2 0.483 0.0 3 +torsion 5 1 1 17 0.000 0.0 1 0.000 180.0 2 0.125 0.0 3 +torsion 5 1 1 18 0.000 0.0 1 0.000 180.0 2 0.125 0.0 3 +torsion 5 1 1 19 0.000 0.0 1 0.000 180.0 2 0.105 0.0 3 +torsion 5 1 1 22 0.000 0.0 1 0.000 180.0 2 0.167 0.0 3 +torsion 5 1 1 25 0.000 0.0 1 0.000 180.0 2 0.330 0.0 3 +torsion 5 1 1 29 0.000 0.0 1 0.000 180.0 2 0.100 0.0 3 +torsion 5 1 1 31 0.000 0.0 1 0.000 180.0 2 -0.065 0.0 3 +torsion 5 1 1 32 0.000 0.0 1 0.000 180.0 2 -0.155 0.0 3 +torsion 5 1 1 33 0.000 0.0 1 0.000 180.0 2 0.040 0.0 3 +torsion 5 1 1 34 0.000 0.0 1 0.000 180.0 2 0.280 0.0 3 +torsion 5 1 1 35 0.000 0.0 1 0.000 180.0 2 0.540 0.0 3 +torsion 5 1 1 36 0.000 0.0 1 0.000 180.0 2 0.237 0.0 3 +torsion 5 1 1 37 0.000 0.0 1 0.000 180.0 2 0.500 0.0 3 +torsion 5 1 1 39 -0.150 0.0 1 0.000 180.0 2 0.150 0.0 3 +torsion 5 1 1 41 0.000 0.0 1 0.000 180.0 2 0.180 0.0 3 +torsion 5 1 1 43 0.000 0.0 1 0.000 180.0 2 0.500 0.0 3 +torsion 5 1 1 46 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3 +torsion 5 1 1 50 0.000 0.0 1 0.000 180.0 2 0.500 0.0 3 +torsion 5 1 1 70 0.004 0.0 1 0.000 180.0 2 0.427 0.0 3 +torsion 5 1 1 71 0.000 0.0 1 0.000 180.0 2 0.180 0.0 3 +torsion 6 1 1 6 0.000 0.0 1 -0.600 180.0 2 0.300 0.0 3 +torsion 6 1 1 8 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 6 1 1 9 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 6 1 1 11 0.000 0.0 1 -1.400 180.0 2 0.180 0.0 3 +torsion 6 1 1 12 0.000 0.0 1 -1.400 180.0 2 0.180 0.0 3 +torsion 6 1 1 13 0.000 0.0 1 -1.400 180.0 2 0.180 0.0 3 +torsion 6 1 1 14 0.000 0.0 1 -1.400 180.0 2 0.180 0.0 3 +torsion 6 1 1 15 -0.800 0.0 1 0.900 180.0 2 -0.300 0.0 3 +torsion 6 1 1 17 -0.800 0.0 1 0.900 180.0 2 -0.300 0.0 3 +torsion 6 1 1 18 -0.800 0.0 1 0.000 180.0 2 -0.300 0.0 3 +torsion 6 1 1 39 0.000 0.0 1 -0.600 180.0 2 0.300 0.0 3 +torsion 6 1 1 70 -5.500 0.0 1 -2.500 180.0 2 2.000 0.0 3 +torsion 6 1 1 71 -7.225 0.0 1 0.000 180.0 2 0.740 0.0 3 +torsion 8 1 1 8 -0.400 0.0 1 -1.100 180.0 2 1.200 0.0 3 +torsion 8 1 1 9 1.170 0.0 1 -1.263 180.0 2 2.064 0.0 3 +torsion 9 1 1 9 0.000 0.0 1 0.000 180.0 2 -0.500 0.0 3 +torsion 9 1 1 15 -1.000 0.0 1 -0.300 180.0 2 0.400 0.0 3 +torsion 9 1 1 15 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 11 1 1 11 -0.100 0.0 1 -2.000 180.0 2 0.200 0.0 3 +torsion 11 1 1 12 0.000 0.0 1 0.000 180.0 2 0.253 0.0 3 +torsion 11 1 1 13 0.000 0.0 1 0.000 180.0 2 0.253 0.0 3 +torsion 12 1 1 12 -0.240 0.0 1 0.620 180.0 2 0.540 0.0 3 +torsion 12 1 1 13 0.000 0.0 1 0.000 180.0 2 0.267 0.0 3 +torsion 13 1 1 13 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 15 1 1 15 -0.800 0.0 1 0.900 180.0 2 -0.300 0.0 3 +torsion 15 1 1 17 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 17 1 1 17 0.000 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13 2 41 2 0.000 0.0 1 15.500 180.0 2 0.000 0.0 3 +torsion 13 2 41 20 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 14 2 41 2 0.000 0.0 1 15.500 180.0 2 0.000 0.0 3 +torsion 14 2 41 20 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 2 2 42 2 0.000 0.0 1 1.700 180.0 2 0.400 0.0 3 +torsion 5 2 42 2 0.000 0.0 1 1.700 180.0 2 0.000 0.0 3 +torsion 2 2 46 7 0.000 0.0 1 1.500 180.0 2 0.000 0.0 3 +torsion 5 2 46 7 0.000 0.0 1 1.300 180.0 2 0.000 0.0 3 +torsion 2 2 72 3 1.581 0.0 1 3.430 180.0 2 3.010 0.0 3 +torsion 2 2 72 20 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 5 2 72 3 0.000 0.0 1 10.000 180.0 2 0.000 0.0 3 +torsion 5 2 72 20 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 1 3 3 1 1.000 0.0 1 6.500 180.0 2 0.000 0.0 3 +torsion 1 3 3 5 0.000 0.0 1 5.200 180.0 2 0.000 0.0 3 +torsion 1 3 3 7 -1.000 0.0 1 6.500 180.0 2 0.000 0.0 3 +torsion 2 3 3 2 1.000 0.0 1 12.500 180.0 2 0.000 0.0 3 +torsion 2 3 3 5 0.000 0.0 1 5.000 180.0 2 0.000 0.0 3 +torsion 2 3 3 7 -0.700 0.0 1 12.500 180.0 2 0.000 0.0 3 +torsion 5 3 3 5 0.000 0.0 1 10.000 180.0 2 0.000 0.0 3 +torsion 5 3 3 7 -0.120 0.0 1 10.000 180.0 2 0.000 0.0 3 +torsion 5 3 3 36 0.000 0.0 1 10.000 180.0 2 0.000 0.0 3 +torsion 7 3 3 7 0.000 0.0 1 10.000 180.0 2 0.000 0.0 3 +torsion 7 3 3 36 -0.120 0.0 1 10.000 180.0 2 0.000 0.0 3 +torsion 36 3 3 36 0.000 0.0 1 10.000 180.0 2 0.000 0.0 3 +torsion 1 3 6 1 -2.500 0.0 1 1.390 180.0 2 0.000 0.0 3 +torsion 1 3 6 20 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 1 3 6 24 0.000 0.0 1 0.500 180.0 2 0.000 0.0 3 +torsion 2 3 6 1 3.530 0.0 1 2.300 180.0 2 -3.530 0.0 3 +torsion 5 3 6 1 0.000 0.0 1 0.880 180.0 2 0.000 0.0 3 +torsion 5 3 6 20 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 5 3 6 24 -0.770 0.0 1 0.850 180.0 2 0.000 0.0 3 +torsion 7 3 6 1 -1.660 0.0 1 8.980 180.0 2 0.000 0.0 3 +torsion 7 3 6 20 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 7 3 6 24 -3.285 0.0 1 5.600 180.0 2 0.000 0.0 3 +torsion 1 3 9 1 1.100 0.0 1 5.000 180.0 2 0.000 0.0 3 +torsion 1 3 9 2 -4.000 0.0 1 2.700 180.0 2 0.500 0.0 3 +torsion 1 3 9 3 -0.900 0.0 1 1.600 180.0 2 0.000 0.0 3 +torsion 1 3 9 28 0.000 0.0 1 5.000 180.0 2 0.000 0.0 3 +torsion 2 3 9 1 0.000 0.0 1 5.000 180.0 2 0.000 0.0 3 +torsion 5 3 9 1 0.000 0.0 1 5.000 180.0 2 0.000 0.0 3 +torsion 5 3 9 3 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 5 3 9 28 0.000 0.0 1 5.000 180.0 2 0.000 0.0 3 +torsion 7 3 9 1 0.000 0.0 1 5.000 180.0 2 0.000 0.0 3 +torsion 7 3 9 2 -0.600 0.0 1 4.200 180.0 2 0.000 0.0 3 +torsion 7 3 9 2 -3.100 0.0 1 2.900 180.0 2 0.000 0.0 3 +torsion 7 3 9 3 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 7 3 9 3 0.600 0.0 1 1.300 180.0 2 0.000 0.0 3 +torsion 7 3 9 28 1.100 0.0 1 5.000 180.0 2 0.000 0.0 3 +torsion 9 3 9 1 0.000 0.0 1 0.000 180.0 2 0.010 0.0 3 +torsion 9 3 9 2 2.400 0.0 1 2.500 180.0 2 0.000 0.0 3 +torsion 9 3 9 3 0.800 0.0 1 1.300 180.0 2 0.000 0.0 3 +torsion 9 3 9 28 0.000 0.0 1 1.000 180.0 2 0.000 0.0 3 +torsion 7 3 22 5 -0.167 0.0 1 0.000 180.0 2 -0.100 0.0 3 +torsion 7 3 22 22 -0.300 0.0 1 1.200 180.0 2 -0.350 0.0 3 +torsion 22 3 22 5 0.000 0.0 1 0.000 180.0 2 0.130 0.0 3 +torsion 1 3 72 1 -1.900 0.0 1 17.800 180.0 2 0.000 0.0 3 +torsion 1 3 72 20 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 1 3 72 23 -0.950 0.0 1 17.950 180.0 2 1.110 0.0 3 +torsion 2 3 72 1 -1.090 0.0 1 17.950 180.0 2 0.000 0.0 3 +torsion 2 3 72 2 1.150 0.0 1 15.250 180.0 2 0.000 0.0 3 +torsion 2 3 72 20 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 5 3 72 1 0.000 0.0 1 16.900 180.0 2 1.600 0.0 3 +torsion 5 3 72 2 0.000 0.0 1 14.150 180.0 2 -0.990 0.0 3 +torsion 5 3 72 5 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 5 3 72 5 0.000 0.0 1 16.000 180.0 2 1.600 0.0 3 +torsion 5 3 72 20 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 5 3 72 23 0.000 0.0 1 16.800 180.0 2 0.000 0.0 3 +torsion 1 4 4 2 0.000 0.0 1 0.001 180.0 2 0.000 0.0 3 +torsion 1 4 4 4 0.000 0.0 1 0.001 180.0 2 0.000 0.0 3 +torsion 2 4 4 2 0.000 0.0 1 0.001 180.0 2 0.000 0.0 3 +torsion 2 4 4 4 0.000 0.0 1 0.001 180.0 2 0.000 0.0 3 +torsion 2 4 4 5 0.000 0.0 1 0.001 180.0 2 0.000 0.0 3 +torsion 4 4 4 4 0.000 0.0 1 0.001 180.0 2 0.000 0.0 3 +torsion 1 6 6 1 2.095 0.0 1 -2.155 180.0 2 -0.113 0.0 3 +torsion 1 6 6 20 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 1 6 6 21 2.865 0.0 1 -2.305 180.0 2 0.505 0.0 3 +torsion 20 6 6 20 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 20 6 6 21 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 21 6 6 21 0.753 0.0 1 -1.202 180.0 2 -0.250 0.0 3 +torsion 1 6 19 1 0.000 0.0 1 0.000 180.0 2 0.230 0.0 3 +torsion 1 6 19 5 0.000 0.0 1 0.000 180.0 2 0.320 0.0 3 +torsion 1 6 19 6 0.000 0.0 1 0.000 180.0 2 0.150 0.0 3 +torsion 19 6 19 1 0.000 0.0 1 0.000 180.0 2 0.100 0.0 3 +torsion 19 6 19 5 0.000 0.0 1 0.000 180.0 2 0.100 0.0 3 +torsion 19 6 19 6 0.000 0.0 1 0.000 180.0 2 0.100 0.0 3 +torsion 20 6 19 1 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 20 6 19 5 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 20 6 19 6 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 1 6 25 6 0.000 0.0 1 0.000 180.0 2 0.400 0.0 3 +torsion 2 6 25 6 0.200 0.0 1 0.000 180.0 2 -0.300 0.0 3 +torsion 20 6 25 6 -0.300 0.0 1 1.200 180.0 2 -0.350 0.0 3 +torsion 1 8 8 1 0.900 0.0 1 -6.800 180.0 2 0.210 0.0 3 +torsion 1 8 8 20 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 1 8 8 23 2.000 0.0 1 -8.500 180.0 2 0.800 0.0 3 +torsion 8 8 8 23 0.025 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 20 8 8 20 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 20 8 8 23 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 23 8 8 23 1.800 0.0 1 -9.680 180.0 2 0.210 0.0 3 +torsion 1 9 18 1 -4.000 0.0 1 -3.000 180.0 2 -2.100 0.0 3 +torsion 1 9 18 7 -0.500 0.0 1 -1.000 180.0 2 0.000 0.0 3 +torsion 28 9 18 1 -0.500 0.0 1 -2.000 180.0 2 -4.000 0.0 3 +torsion 28 9 18 5 0.000 0.0 1 0.000 180.0 2 0.030 0.0 3 +torsion 28 9 18 7 0.000 0.0 1 0.000 180.0 2 0.060 0.0 3 +torsion 1 15 15 1 0.000 0.0 1 -7.000 180.0 2 0.467 0.0 3 +torsion 5 15 15 5 0.000 0.0 1 -7.000 180.0 2 0.000 0.0 3 +torsion 1 19 19 1 0.000 0.0 1 0.000 180.0 2 0.633 0.0 3 +torsion 1 19 19 2 0.170 0.0 1 0.270 180.0 2 0.093 0.0 3 +torsion 1 19 19 19 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3 +torsion 2 19 19 2 0.000 0.0 1 0.000 180.0 2 0.400 0.0 3 +torsion 2 19 19 5 0.000 0.0 1 0.000 180.0 2 0.450 0.0 3 +torsion 5 19 19 5 0.000 0.0 1 0.000 180.0 2 0.136 0.0 3 +torsion 5 19 19 19 0.000 0.0 1 0.000 180.0 2 0.070 0.0 3 +torsion 19 19 19 19 0.000 0.0 1 0.000 180.0 2 0.100 0.0 3 +torsion 5 19 22 5 0.000 0.0 1 0.000 180.0 2 0.500 0.0 3 +torsion 5 19 22 22 0.000 0.0 1 0.000 180.0 2 0.083 0.0 3 +torsion 1 22 22 1 0.200 0.0 1 0.270 180.0 2 0.240 0.0 3 +torsion 1 22 22 3 0.200 0.0 1 0.200 180.0 2 0.000 0.0 3 +torsion 1 22 22 5 0.000 0.0 1 0.000 180.0 2 0.120 0.0 3 +torsion 1 22 22 22 0.200 0.0 1 0.270 180.0 2 0.093 0.0 3 +torsion 1 22 22 49 0.000 0.0 1 0.000 180.0 2 0.530 0.0 3 +torsion 2 22 22 2 0.200 0.0 1 0.270 180.0 2 0.093 0.0 3 +torsion 2 22 22 5 0.000 0.0 1 0.000 180.0 2 0.120 0.0 3 +torsion 2 22 22 22 0.170 0.0 1 0.270 180.0 2 0.093 0.0 3 +torsion 2 22 22 49 0.000 0.0 1 0.000 180.0 2 0.530 0.0 3 +torsion 3 22 22 5 0.000 0.0 1 0.000 180.0 2 0.120 0.0 3 +torsion 3 22 22 22 0.200 0.0 1 0.200 180.0 2 0.000 0.0 3 +torsion 5 22 22 5 0.000 0.0 1 0.000 180.0 2 0.137 0.0 3 +torsion 5 22 22 19 0.000 0.0 1 0.000 180.0 2 0.120 0.0 3 +torsion 5 22 22 22 0.000 0.0 1 0.000 180.0 2 0.167 0.0 3 +torsion 5 22 22 38 0.000 0.0 1 2.000 180.0 2 0.500 0.0 3 +torsion 5 22 22 46 0.000 0.0 1 0.000 180.0 2 0.200 0.0 3 +torsion 5 22 22 49 0.000 0.0 1 0.000 180.0 2 0.530 0.0 3 +torsion 19 22 22 22 0.220 0.0 1 0.270 180.0 2 0.093 0.0 3 +torsion 22 22 22 22 -0.520 0.0 1 0.000 180.0 2 0.160 0.0 3 +torsion 22 22 22 46 0.000 0.0 1 0.000 180.0 2 0.167 0.0 3 +torsion 5 22 38 1 0.000 0.0 1 0.000 180.0 2 0.540 0.0 3 +torsion 5 22 38 2 0.000 0.0 1 0.000 180.0 2 -0.240 0.0 3 +torsion 5 22 38 5 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 5 22 38 22 0.000 0.0 1 2.000 180.0 2 0.540 0.0 3 +torsion 5 22 38 38 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 22 22 38 2 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 22 22 38 5 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 38 22 38 1 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3 +torsion 38 22 38 2 0.100 0.0 1 0.000 180.0 2 0.500 0.0 3 +torsion 38 22 38 5 0.000 0.0 1 0.000 180.0 2 0.600 0.0 3 +torsion 5 22 46 7 0.000 0.0 1 1.000 180.0 2 0.000 0.0 3 +torsion 22 22 46 7 0.000 0.0 1 2.000 180.0 2 0.000 0.0 3 +torsion 1 22 49 20 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 1 22 49 22 0.000 0.0 1 0.000 180.0 2 1.210 0.0 3 +torsion 2 22 49 20 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 2 22 49 22 0.000 0.0 1 0.000 180.0 2 1.210 0.0 3 +torsion 5 22 49 20 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 5 22 49 22 0.000 0.0 1 0.000 180.0 2 1.210 0.0 3 +torsion 22 22 49 20 0.000 0.0 1 0.000 180.0 2 0.000 0.0 3 +torsion 1 33 33 1 0.000 0.0 1 0.000 180.0 2 0.021 0.0 3 +torsion 1 37 37 1 -1.900 0.0 1 10.000 180.0 2 0.000 0.0 3 +torsion 1 37 37 20 0.000 0.0 1 10.000 180.0 2 0.000 0.0 3 +torsion 2 37 37 2 0.000 0.0 1 10.000 180.0 2 0.000 0.0 3 +torsion 2 37 37 20 0.000 0.0 1 10.000 180.0 2 0.000 0.0 3 +torsion 20 37 37 20 0.000 0.0 1 10.000 180.0 2 0.000 0.0 3 +torsion 20 37 37 23 0.000 0.0 1 10.000 180.0 2 0.000 0.0 3 +torsion 23 37 37 23 2.400 0.0 1 15.000 180.0 2 0.000 0.0 3 +torsion 2 37 40 2 0.000 0.0 1 10.000 180.0 2 0.000 0.0 3 +torsion 2 37 40 23 0.000 0.0 1 10.000 180.0 2 0.000 0.0 3 +torsion 20 37 40 2 0.000 0.0 1 10.000 180.0 2 0.000 0.0 3 +torsion 20 37 40 23 0.000 0.0 1 10.000 180.0 2 0.000 0.0 3 +torsion 1 37 43 1 -1.900 0.0 1 10.000 180.0 2 0.000 0.0 3 +torsion 1 37 43 7 -5.400 0.0 1 10.000 180.0 2 0.000 0.0 3 +torsion 20 37 43 1 0.000 0.0 1 10.000 180.0 2 0.000 0.0 3 +torsion 20 37 43 7 0.000 0.0 1 10.000 180.0 2 0.000 0.0 3 +torsion 1 38 38 22 -0.100 0.0 1 15.000 180.0 2 0.000 0.0 3 +torsion 5 38 38 5 0.000 0.0 1 15.000 180.0 2 0.000 0.0 3 +torsion 5 38 38 22 0.000 0.0 1 15.000 180.0 2 0.000 0.0 3 +torsion 1 50 50 1 -0.100 0.0 1 9.000 180.0 2 0.000 0.0 3 +torsion 1 50 50 5 0.000 0.0 1 9.000 180.0 2 0.000 0.0 3 +torsion 1 50 50 50 -0.270 0.0 1 9.000 180.0 2 0.000 0.0 3 +torsion 5 50 50 5 0.000 0.0 1 9.000 180.0 2 0.000 0.0 3 +torsion 5 50 50 50 0.000 0.0 1 5.405 180.0 2 -1.060 0.0 3 +torsion 50 50 50 50 -0.930 0.0 1 4.800 180.0 2 0.000 0.0 3 +torsion 1 70 71 1 0.000 0.0 1 10.560 180.0 2 0.000 0.0 3 +torsion 1 70 71 5 0.000 0.0 1 9.070 180.0 2 0.000 0.0 3 + + + ##################################### + ## ## + ## Torsional Parameters (4-Ring) ## + ## ## + ##################################### + + +torsion4 1 1 1 1 0.200 0.0 1 0.270 180.0 2 1.533 0.0 3 +torsion4 1 1 1 2 0.000 0.0 1 0.000 180.0 2 1.900 0.0 3 +torsion4 1 1 1 3 0.200 0.0 1 0.270 180.0 2 1.533 0.0 3 +torsion4 1 1 1 6 0.130 0.0 1 0.000 180.0 2 1.500 0.0 3 +torsion4 1 1 1 8 0.100 0.0 1 0.400 180.0 2 2.500 0.0 3 +torsion4 1 1 1 15 0.000 0.0 1 -0.100 180.0 2 1.100 0.0 3 +torsion4 1 1 1 19 0.100 0.0 1 0.000 180.0 2 0.900 0.0 3 +torsion4 1 1 1 31 0.000 0.0 1 0.000 180.0 2 -0.065 0.0 3 +torsion4 1 1 1 39 0.100 0.0 1 0.400 180.0 2 2.500 0.0 3 +torsion4 2 1 1 2 0.200 0.0 1 0.270 180.0 2 1.530 0.0 3 +torsion4 3 1 1 6 0.100 0.0 1 0.000 180.0 2 1.500 0.0 3 +torsion4 3 1 1 9 0.000 0.0 1 0.000 180.0 2 0.250 0.0 3 +torsion4 22 1 1 22 0.200 0.0 1 0.270 180.0 2 1.533 0.0 3 +torsion4 37 1 1 37 0.000 0.0 1 0.000 180.0 2 1.533 0.0 3 +torsion4 37 1 1 43 0.000 0.0 1 0.000 180.0 2 1.533 0.0 3 +torsion4 1 1 2 1 0.000 0.0 1 0.030 180.0 2 0.900 0.0 3 +torsion4 1 1 2 2 -0.700 0.0 1 0.240 180.0 2 0.060 0.0 3 +torsion4 2 1 2 1 0.000 0.0 1 0.000 180.0 2 0.300 0.0 3 +torsion4 2 1 2 2 0.000 0.0 1 0.000 180.0 2 0.600 0.0 3 +torsion4 1 1 3 1 0.550 0.0 1 -0.180 180.0 2 0.400 0.0 3 +torsion4 1 1 3 6 0.100 0.0 1 0.000 180.0 2 1.500 0.0 3 +torsion4 1 1 3 9 0.000 0.0 1 0.000 180.0 2 0.250 0.0 3 +torsion4 1 1 6 1 0.130 0.0 1 0.000 180.0 2 1.500 0.0 3 +torsion4 1 1 6 3 0.100 0.0 1 0.000 180.0 2 1.500 0.0 3 +torsion4 1 1 8 1 -0.200 0.0 1 0.730 180.0 2 2.500 0.0 3 +torsion4 1 1 9 3 0.000 0.0 1 0.000 180.0 2 0.250 0.0 3 +torsion4 1 1 15 1 0.000 0.0 1 -0.100 180.0 2 1.100 0.0 3 +torsion4 1 1 19 1 0.100 0.0 1 0.000 180.0 2 0.900 0.0 3 +torsion4 1 1 22 22 0.200 0.0 1 0.270 180.0 2 1.533 0.0 3 +torsion4 1 1 31 1 0.000 0.0 1 0.000 180.0 2 0.152 0.0 3 +torsion4 1 1 37 37 0.000 0.0 1 0.000 180.0 2 0.060 0.0 3 +torsion4 1 1 37 43 0.000 0.0 1 0.000 180.0 2 0.060 0.0 3 +torsion4 1 1 39 1 -0.200 0.0 1 0.730 180.0 2 2.500 0.0 3 +torsion4 1 2 2 1 -0.100 0.0 1 15.000 180.0 2 0.000 0.0 3 +torsion4 2 2 2 2 -0.930 0.0 1 15.000 180.0 2 0.000 0.0 3 +torsion4 1 3 6 1 -2.500 0.0 1 1.390 180.0 2 0.000 0.0 3 +torsion4 1 3 9 1 0.000 0.0 1 0.000 180.0 2 0.250 0.0 3 +torsion4 22 3 22 22 0.550 0.0 1 -0.180 180.0 2 0.400 0.0 3 +torsion4 1 22 22 1 0.200 0.0 1 0.270 180.0 2 2.500 0.0 3 +torsion4 1 22 22 22 0.200 0.0 1 0.270 180.0 2 1.533 0.0 3 +torsion4 3 22 22 22 0.200 0.0 1 0.270 180.0 2 1.533 0.0 3 +torsion4 22 22 22 22 6.070 0.0 1 0.000 180.0 2 -0.880 0.0 3 +torsion4 1 37 37 1 -1.900 0.0 1 10.000 180.0 2 0.000 0.0 3 +torsion4 1 37 43 1 -1.900 0.0 1 10.000 180.0 2 0.000 0.0 3 + + + ###################################### + ## ## + ## Torsional Parameters (Allenes) ## + ## ## + ###################################### + + +#torsion 1 2 2 1 0.000 0.0 1 -11.500 180.0 2 0.000 0.0 3 +#torsion 1 2 2 5 0.000 0.0 1 -11.500 180.0 2 0.000 0.0 3 +#torsion 5 2 2 5 0.050 0.0 1 -12.100 180.0 2 0.000 0.0 3 + + + ######################################## + ## ## + ## Atomic Partial Charge Parameters ## + ## ## + ######################################## + + +charge 16 1.000 +charge 30 1.000 +charge 39 1.000 +charge 47 -0.500 + + + ##################################### + ## ## + ## Bond Dipole Moment Parameters ## + ## ## + ##################################### + + +dipole 1 2 0.300 0.500 +dipole 1 3 0.300 0.500 +dipole 1 4 0.750 0.500 +dipole 1 6 0.440 0.500 +dipole 1 8 0.040 0.500 +dipole 1 9 1.470 0.500 +dipole 1 11 1.820 0.500 +dipole 1 12 1.940 0.500 +dipole 1 13 1.790 0.500 +dipole 1 14 1.300 0.500 +dipole 1 15 1.200 0.500 +dipole 1 16 1.200 0.500 +dipole 1 17 1.200 0.500 +dipole 1 18 1.200 0.500 +dipole 1 19 -0.600 0.500 +dipole 1 22 0.150 0.500 +dipole 1 25 0.830 0.500 +dipole 1 31 -0.550 0.500 +dipole 1 32 -0.650 0.500 +dipole 1 33 -0.500 0.500 +dipole 1 34 -1.100 0.500 +dipole 1 35 -1.000 0.500 +dipole 1 37 1.260 0.500 +dipole 1 38 0.300 0.500 +dipole 1 41 0.220 0.500 +dipole 1 43 1.260 0.500 +dipole 1 46 1.350 0.500 +dipole 1 50 0.300 0.500 +dipole 1 70 1.900 0.500 +dipole 1 71 0.300 0.500 +dipole 1 72 1.260 0.500 +dipole 2 6 0.001 0.500 +dipole 2 8 -0.400 0.500 +dipole 2 9 1.300 0.500 +dipole 2 11 1.480 0.500 +dipole 2 12 1.580 0.500 +dipole 2 13 1.560 0.500 +dipole 2 14 1.400 0.500 +dipole 2 19 -0.650 0.500 +dipole 2 22 -0.150 0.500 +dipole 2 25 1.040 0.500 +dipole 2 37 0.583 0.500 +dipole 2 40 0.870 0.500 +dipole 2 41 0.950 0.500 +dipole 2 42 1.925 0.500 +dipole 2 46 1.700 0.500 +dipole 2 72 0.583 0.500 +dipole 3 6 -0.200 0.500 +dipole 3 7 2.600 0.500 +dipole 3 9 -0.290 0.500 +dipole 3 11 1.480 0.500 +dipole 3 12 1.580 0.500 +dipole 3 13 1.560 0.500 +dipole 3 14 1.400 0.500 +dipole 3 22 0.300 0.500 +dipole 3 72 0.583 0.500 +dipole 4 10 3.400 0.500 +dipole 5 15 0.900 0.500 +dipole 5 25 0.500 0.500 +dipole 5 34 0.700 0.500 +dipole 5 35 0.800 0.500 +dipole 6 19 -0.400 0.500 +dipole 6 20 0.900 0.500 +dipole 6 21 -1.115 0.500 +dipole 6 24 -0.700 0.500 +dipole 6 25 0.970 0.500 +dipole 6 28 -0.700 0.500 +dipole 7 17 -3.030 0.500 +dipole 7 18 -2.930 0.500 +dipole 7 43 -2.600 0.500 +dipole 7 46 -2.530 0.500 +dipole 8 20 0.600 0.500 +dipole 8 23 -0.760 0.500 +dipole 9 18 0.800 0.500 +dipole 9 28 -1.310 0.500 +dipole 20 37 -0.600 0.500 +dipole 20 41 -0.750 0.500 +dipole 20 72 -0.600 0.500 +dipole 22 46 1.700 0.500 +dipole 23 37 0.600 0.500 +dipole 23 40 0.550 0.500 +dipole 23 72 0.600 0.500 +dipole 28 41 0.700 0.500 +dipole 37 40 0.300 0.500 +dipole 70 71 -2.800 0.500 + + + ############################################## + ## ## + ## Bond Dipole Moment Parameters (3-Ring) ## + ## ## + ############################################## + + +dipole3 22 49 0.735 0.500 + + + ########################################### + ## ## + ## Conjugated Pisystem Atom Parameters ## + ## ## + ########################################### + + +piatom 2 1.0 -11.160 11.134 +piatom 3 1.0 -11.160 11.134 +piatom 4 1.0 -11.160 11.134 +piatom 6 2.0 -17.600 19.342 +piatom 7 1.0 -17.210 14.520 +piatom 9 2.0 -13.145 17.210 +piatom 10 1.0 -14.120 12.340 +piatom 37 1.0 -14.120 12.340 +piatom 40 2.0 -13.145 17.210 +piatom 41 2.0 -17.600 19.342 +piatom 42 2.0 -15.800 11.920 +piatom 72 1.0 -14.120 12.340 + + + ########################################### + ## ## + ## Conjugated Pisystem Bond Parameters ## + ## ## + ########################################### + + +pibond 2 2 4.600 0.166 +pibond 2 3 4.600 0.166 +pibond 2 4 7.790 0.156 +pibond 2 37 10.880 0.196 +pibond 2 40 10.880 0.196 +pibond 2 41 5.440 0.196 +pibond 2 42 4.861 0.397 +pibond 2 72 10.880 0.196 +pibond 3 3 4.600 0.140 +pibond 3 4 4.600 0.166 +pibond 3 7 4.600 0.105 +pibond 3 72 10.880 0.196 +pibond 4 4 4.600 0.238 +pibond 37 37 10.500 0.170 +pibond 37 40 10.880 0.196
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/mmff94.ff Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,28 @@ +# +# MMFF94 paremeter files +# + +# atom properties +prop mmffprop.par +# fallback defs +def mmffdef.par +# bond stretching parameters +bond mmffbond.par +# angle bending parameters +ang mmffang.par +# empirical rule parameters (bond stretching) +bndk mmffbndk.par +# charge parameters +chg mmffchg.par +# empirical rule parameters (bend-stretch) +dfsb mmffdfsb.par +# out-of-plane parameters +oop mmffoop.par +# partial bond charge increments +pbci mmffpbci.par +# strech-bend parameters +stbn mmffstbn.par +# torsion parameters +tor mmfftor.par +# van der waals parameters +vdw mmffvdw.par
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/mmff94s.ff Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,28 @@ +# +# MMFF94 paremeter files +# + +# atom properties +prop mmffprop.par +# fallback defs +def mmffdef.par +# bond stretching parameters +bond mmffbond.par +# angle bending parameters +ang mmffang.par +# empirical rule parameters (bond stretching) +bndk mmffbndk.par +# charge parameters +chg mmffchg.par +# empirical rule parameters (bend-stretch) +dfsb mmffdfsb.par +# out-of-plane parameters +oop mmffs_oop.par +# partial bond charge increments +pbci mmffpbci.par +# strech-bend parameters +stbn mmffstbn.par +# torsion parameters +tor mmffs_tor.par +# van der waals parameters +vdw mmffvdw.par
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/mmffang.par Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,2354 @@ +* +* Copyright (c) Merck and Co., Inc., 1994 +* All Rights Reserved +* +* MMFF ANGLE PARAMETERS- Rev: 26-Oct-94 Source: MMFF94 +* C94 = CORE MMFF94 parameter - obtained from ab initio data +* X94 = EXTD MMFF94 parameter - fit to additional ab initio data +* E94 = theta0 from fit to X-ray data, ka from empirical rule +* #E94 = theta0 and ka both from empirical rules +* +* types ka theta0 Comment/origin +0 0 1 0 0.000 108.900 0:*-1-* MMFF94 DEF +0 1 1 1 0.851 109.608 C94 +0 1 1 2 0.736 109.445 C94 +0 1 1 3 0.777 107.517 C94 +0 1 1 4 1.006 110.265 E94 +0 1 1 5 0.636 110.549 C94 +0 1 1 6 0.992 108.133 C94 +0 1 1 8 0.777 108.290 C94 +0 1 1 9 1.136 108.194 E94 +0 1 1 10 1.050 109.960 C94 +0 1 1 11 1.225 108.313 C94 +0 1 1 12 1.056 108.679 C94 +0 1 1 13 1.078 106.820 E94 +0 1 1 14 0.980 109.945 E94 +0 1 1 15 0.743 107.397 C94 +0 1 1 17 1.089 108.578 E94 +0 1 1 18 1.093 109.315 E94 +0 1 1 19 0.755 115.436 E94 +0 1 1 20 1.021 108.659 E94 +0 1 1 22 1.001 110.125 E94 +0 1 1 25 0.803 112.356 X94 +0 1 1 26 0.833 109.879 E94 +0 1 1 34 1.179 106.493 C94 +0 1 1 37 0.756 108.617 C94 +0 1 1 39 0.927 109.170 C94 +0 1 1 40 1.130 108.678 E94 +0 1 1 41 0.330 98.422 C94 +0 1 1 43 1.135 108.019 E94 +0 1 1 45 1.197 105.028 E94 +0 1 1 54 1.173 106.424 E94 +0 1 1 55 1.150 107.604 E94 +0 1 1 56 1.199 110.371 C94 +0 1 1 57 1.012 109.900 E94 +0 1 1 58 1.179 106.327 E94 +0 1 1 61 1.125 109.311 E94 +0 1 1 63 1.006 110.058 E94 +0 1 1 64 0.988 111.064 E94 +0 1 1 67 1.216 104.557 E94 +0 1 1 68 1.018 107.195 C94 +0 1 1 73 1.160 104.658 E94 +0 1 1 78 1.012 109.850 E94 +0 1 1 80 0.947 113.327 E94 +0 1 1 81 1.108 109.837 E94 +0 2 1 2 1.113 111.453 C94 +0 2 1 3 0.667 104.829 C94 +0 2 1 4 1.022 109.873 E94 +0 2 1 5 0.632 110.292 C94 +0 2 1 6 1.074 108.699 C94 +0 2 1 8 0.884 111.553 C94 +0 2 1 9 1.118 109.577 E94 +0 2 1 10 1.160 107.963 E94 +0 2 1 11 1.192 110.419 E94 +0 2 1 12 1.070 109.410 E94 +0 2 1 15 1.078 109.560 E94 +0 2 1 17 1.077 109.434 E94 +0 2 1 18 1.188 105.110 E94 +0 2 1 20 1.053 107.448 E94 +0 2 1 22 0.942 114.020 E94 +0 2 1 25 0.893 106.815 E94 +0 2 1 26 1.029 99.065 E94 +0 2 1 34 1.066 111.817 E94 +0 2 1 37 0.985 111.446 E94 +0 2 1 39 1.124 109.513 E94 +0 2 1 40 1.149 108.270 E94 +0 2 1 45 1.232 103.978 E94 +0 2 1 63 0.935 114.692 E94 +0 2 1 67 1.224 104.687 E94 +0 3 1 3 0.974 111.746 E94 +0 3 1 4 1.019 109.850 E94 +0 3 1 5 0.650 108.385 C94 +0 3 1 6 0.528 104.112 C94 +0 3 1 8 1.197 105.837 E94 +0 3 1 9 1.201 105.535 E94 +0 3 1 10 0.634 102.655 C94 +0 3 1 11 1.189 110.328 E94 +0 3 1 12 1.136 106.064 E94 +0 3 1 13 1.147 103.645 E94 +0 3 1 14 1.048 106.404 E94 +0 3 1 15 1.125 107.192 E94 +0 3 1 17 1.092 108.602 E94 +0 3 1 18 1.120 108.119 E94 +0 3 1 20 0.969 111.830 E94 +0 3 1 22 0.999 110.522 E94 +0 3 1 26 0.742 116.555 E94 +0 3 1 34 1.141 107.871 E94 +0 3 1 37 1.011 109.833 E94 +0 3 1 39 1.136 108.751 E94 +0 3 1 40 1.174 106.941 E94 +0 3 1 41 1.033 108.216 E94 +0 3 1 45 1.221 104.281 E94 +0 3 1 63 1.069 107.077 E94 +0 3 1 64 1.028 109.186 E94 +0 3 1 81 1.167 107.327 E94 +0 4 1 4 0.954 114.186 E94 +0 4 1 5 0.615 111.417 X94 +0 4 1 6 1.273 109.977 E94 +0 4 1 8 1.099 111.063 E94 +0 4 1 9 1.187 106.750 E94 +0 4 1 10 1.117 110.488 E94 +0 4 1 13 1.021 110.047 E94 +0 4 1 15 1.028 112.432 E94 +0 4 1 18 1.187 105.351 E94 +0 4 1 22 1.174 102.556 E94 +0 4 1 26 0.853 108.999 E94 +0 4 1 34 1.148 108.160 E94 +0 4 1 37 0.993 111.424 E94 +0 5 1 5 0.516 108.836 C94 +0 5 1 6 0.781 108.577 C94 +0 5 1 8 0.653 110.297 C94 +0 5 1 9 0.733 109.894 C94 +0 5 1 10 0.740 107.646 C94 +0 5 1 11 0.875 107.897 C94 +0 5 1 12 0.698 108.162 C94 +0 5 1 13 0.613 106.049 E94 +0 5 1 14 0.508 113.019 E94 +0 5 1 15 0.576 109.609 C94 +0 5 1 17 0.634 107.944 X94 +0 5 1 18 0.663 106.855 X94 +0 5 1 19 0.450 113.195 X94 +0 5 1 20 0.706 111.000 C94 +0 5 1 22 0.618 110.380 E94 +0 5 1 25 0.487 109.486 X94 +0 5 1 26 0.466 111.172 X94 +0 5 1 34 0.872 106.224 C94 +0 5 1 35 0.644 125.663 X94 +0 5 1 37 0.627 109.491 C94 +0 5 1 39 0.811 106.299 C94 +0 5 1 40 0.719 109.870 C94 +0 5 1 41 0.525 108.904 C94 +0 5 1 43 0.692 109.083 X94 +0 5 1 45 0.741 105.197 X94 +0 5 1 46 0.719 106.735 X94 +0 5 1 54 0.874 106.973 C94 +0 5 1 55 0.861 108.507 C94 +0 5 1 56 0.814 108.223 C94 +0 5 1 57 0.626 110.420 E94 +0 5 1 58 0.750 105.481 E94 +0 5 1 61 0.710 109.227 X94 +0 5 1 62 0.655 113.035 X94 +0 5 1 63 0.621 110.467 E94 +0 5 1 64 0.622 110.457 E94 +0 5 1 67 0.732 106.474 E94 +0 5 1 68 0.748 103.817 C94 +0 5 1 72 0.547 116.576 X94 +0 5 1 73 0.633 107.153 X94 +0 5 1 78 0.640 109.078 E94 +0 5 1 80 0.684 105.144 E94 +0 5 1 81 0.721 107.870 E94 +0 6 1 6 1.156 111.368 C94 +0 6 1 8 1.333 112.223 E94 +0 6 1 9 1.224 116.950 E94 +0 6 1 10 1.432 108.568 E94 +0 6 1 11 1.593 106.900 E94 +0 6 1 15 1.273 112.012 E94 +0 6 1 17 1.348 108.655 E94 +0 6 1 19 0.906 117.214 E94 +0 6 1 20 1.293 108.202 E94 +0 6 1 22 1.287 108.913 E94 +0 6 1 25 1.171 103.598 E94 +0 6 1 26 0.888 118.433 E94 +0 6 1 34 1.257 114.975 E94 +0 6 1 37 0.878 107.978 C94 +0 6 1 39 1.485 106.464 E94 +0 6 1 40 1.371 110.779 E94 +0 6 1 41 1.333 106.467 E94 +0 6 1 45 1.523 104.438 E94 +0 6 1 57 1.308 108.467 E94 +0 6 1 63 1.351 106.535 E94 +0 6 1 64 1.238 111.308 E94 +0 8 1 8 1.203 110.856 E94 +0 8 1 9 1.133 114.080 E94 +0 8 1 10 1.258 108.683 E94 +0 8 1 12 1.217 107.251 E94 +0 8 1 15 1.120 112.356 E94 +0 8 1 20 1.116 109.353 E94 +0 8 1 25 1.143 98.698 E94 +0 8 1 34 1.138 113.412 E94 +0 8 1 37 1.090 110.992 E94 +0 8 1 39 1.364 104.193 E94 +0 8 1 40 0.964 123.962 E94 +0 8 1 41 1.234 103.868 E94 +0 8 1 43 1.137 113.596 E94 +0 8 1 45 1.583 96.139 E94 +0 8 1 57 1.038 114.266 E94 +0 8 1 63 1.104 110.598 E94 +0 8 1 64 1.156 108.127 E94 +0 9 1 10 1.209 110.720 E94 +0 9 1 12 1.173 109.152 E94 +0 9 1 15 1.024 117.465 E94 +0 9 1 25 1.060 102.432 E94 +0 9 1 37 1.077 111.565 E94 +0 9 1 40 1.084 116.728 E94 +0 9 1 80 1.163 107.509 E94 +0 10 1 10 1.191 111.995 E94 +0 10 1 15 1.161 110.502 E94 +0 10 1 17 1.269 105.509 E94 +0 10 1 20 1.220 104.838 E94 +0 10 1 22 1.132 109.262 E94 +0 10 1 25 1.015 104.822 E94 +0 10 1 37 1.107 110.423 E94 +0 10 1 40 1.264 108.536 E94 +0 10 1 41 1.087 110.961 E94 +0 10 1 57 1.268 103.622 E94 +0 11 1 11 1.638 106.081 C94 +0 11 1 15 1.254 109.517 E94 +0 11 1 20 1.243 107.637 E94 +0 11 1 25 1.244 97.532 E94 +0 11 1 34 1.338 108.669 E94 +0 11 1 35 1.556 110.367 E94 +0 11 1 37 1.151 112.278 E94 +0 11 1 41 1.301 105.053 E94 +0 11 1 45 1.550 100.991 E94 +0 11 1 73 1.303 106.569 E94 +0 11 1 75 0.884 114.378 E94 +0 12 1 12 1.096 110.422 C94 +0 12 1 15 1.146 111.064 E94 +0 12 1 18 1.299 104.827 E94 +0 12 1 19 0.932 108.971 E94 +0 12 1 20 1.081 108.605 E94 +0 12 1 22 1.097 108.028 E94 +0 12 1 25 0.989 106.118 E94 +0 12 1 37 1.076 109.030 E94 +0 12 1 39 1.150 110.359 E94 +0 12 1 45 1.353 101.430 E94 +0 12 1 63 1.071 109.474 E94 +0 12 1 64 1.093 108.338 E94 +0 13 1 13 1.093 111.645 E94 +0 13 1 20 1.084 106.534 E94 +0 13 1 22 1.068 107.469 E94 +0 13 1 45 1.305 101.383 E94 +0 14 1 20 1.021 107.718 E94 +0 15 1 15 1.147 111.896 E94 +0 15 1 25 1.059 103.308 E94 +0 15 1 34 1.222 107.318 E94 +0 15 1 37 1.051 110.959 E94 +0 15 1 40 1.149 111.005 E94 +0 15 1 41 1.263 100.981 E94 +0 15 1 63 1.060 110.596 E94 +0 15 1 64 1.059 110.703 E94 +0 15 1 73 1.289 105.029 E94 +0 17 1 37 1.065 110.049 E94 +0 18 1 20 1.121 107.960 E94 +0 18 1 22 1.283 101.125 E94 +0 18 1 37 1.203 104.390 E94 +0 18 1 45 1.287 105.273 E94 +0 18 1 64 1.093 109.683 E94 +0 19 1 54 0.772 119.506 E94 +0 20 1 20 1.229 99.084 E94 +0 20 1 37 1.052 107.428 E94 +0 20 1 45 1.169 106.335 E94 +0 22 1 22 0.990 111.226 E94 +0 22 1 25 0.885 107.293 E94 +0 22 1 34 1.045 112.940 E94 +0 22 1 37 1.037 108.586 E94 +0 22 1 45 1.182 106.181 E94 +0 25 1 25 0.551 127.138 E94 +0 25 1 34 0.779 119.271 E94 +0 25 1 37 0.784 113.945 E94 +0 25 1 40 1.062 102.417 E94 +0 25 1 58 0.916 110.234 E94 +0 26 1 26 0.625 118.700 E94 +0 34 1 34 1.216 109.167 E94 +0 34 1 37 1.075 111.275 E94 +0 34 1 41 1.048 112.238 E94 +0 34 1 63 1.077 111.412 E94 +0 34 1 73 1.142 110.240 E94 +0 37 1 37 0.986 111.315 E94 +0 37 1 40 1.129 109.188 E94 +0 37 1 43 1.074 111.478 E94 +0 37 1 45 1.259 102.800 E94 +0 37 1 57 0.981 112.047 E94 +0 37 1 64 1.175 102.239 E94 +0 37 1 68 1.100 109.983 E94 +0 37 1 78 1.005 110.638 E94 +0 37 1 81 1.176 107.040 E94 +0 39 1 39 1.260 108.547 E94 +0 40 1 40 1.182 112.005 E94 +0 40 1 55 1.322 105.786 E94 +0 40 1 63 1.032 114.505 E94 +0 40 1 64 1.000 116.376 E94 +0 41 1 41 1.082 105.400 E94 +0 41 1 63 1.061 107.112 E94 +0 41 1 81 1.093 110.553 E94 +0 45 1 45 1.391 102.088 E94 +0 0 2 0 0.000 119.400 0:*-2-* MMFF94 DEF +1 0 2 0 0.000 118.200 0:*-2-* MMFF94 DEF +2 0 2 0 0.000 120.800 2::*-2-* MMFF94 DEF +3 0 2 0 0.000 62.600 3::*-2-* MMFF94 DEF +6 0 2 0 0.000 60.500 6:*-2-* MMFF94 DEF +0 1 2 1 0.752 118.043 C94 +0 1 2 2 0.672 122.141 C94 +1 1 2 2 0.684 116.929 C94 +1 1 2 3 0.698 116.104 C94 +0 1 2 4 0.828 125.045 E94 +1 1 2 4 0.846 121.613 E94 +0 1 2 5 0.446 120.108 C94 +0 1 2 6 1.160 115.518 E94 +0 1 2 10 1.015 116.707 E94 +0 1 2 12 0.983 115.343 E94 +0 1 2 13 0.964 115.395 E94 +0 1 2 15 0.939 119.465 E94 +0 1 2 17 0.883 121.868 E94 +0 1 2 18 0.961 117.918 E94 +0 1 2 20 0.880 118.310 E94 +0 1 2 22 0.873 119.114 E94 +0 1 2 30 0.826 124.605 E94 +1 1 2 37 0.721 116.064 C94 +0 1 2 40 0.982 118.515 E94 +0 1 2 45 1.121 109.921 E94 +0 1 2 56 1.006 117.192 E94 +1 1 2 63 0.768 127.945 E94 +1 1 2 64 0.966 113.884 E94 +1 1 2 67 1.115 110.185 E94 +1 2 2 2 0.747 121.550 C94 +2 2 2 2 0.796 126.284 E94 +6 2 2 2 0.173 60.549 E94 +1 2 2 3 0.545 111.297 C94 +2 2 2 3 0.893 118.456 E94 +5 2 2 3 0.184 59.145 E94 +1 2 2 4 0.902 121.053 E94 +2 2 2 4 0.889 119.794 E94 +0 2 2 5 0.535 121.004 C94 +1 2 2 5 0.463 118.442 C94 +0 2 2 6 1.117 121.267 C94 +1 2 2 6 1.204 114.538 E94 +1 2 2 9 0.960 123.536 E94 +2 2 2 9 1.045 116.273 E94 +0 2 2 10 1.003 120.828 E94 +1 2 2 10 1.026 117.324 E94 +0 2 2 11 1.089 119.100 X94 +1 2 2 11 1.090 116.828 E94 +0 2 2 12 0.931 120.132 X94 +1 2 2 12 0.957 117.526 E94 +0 2 2 13 0.867 122.717 E94 +0 2 2 14 0.818 122.584 E94 +1 2 2 14 0.819 122.344 E94 +0 2 2 15 0.931 121.553 E94 +1 2 2 15 0.949 119.466 E94 +0 2 2 17 0.977 117.167 E94 +0 2 2 18 1.044 114.561 E94 +0 2 2 19 0.668 124.721 E94 +0 2 2 20 0.931 117.784 E94 +0 2 2 22 0.809 126.820 E94 +3 2 2 22 0.149 66.165 E94 +0 2 2 25 0.700 123.830 E94 +0 2 2 34 1.066 116.151 E94 +0 2 2 35 0.911 137.103 X94 +1 2 2 37 0.598 117.508 C94 +2 2 2 37 0.817 124.229 E94 +1 2 2 39 0.976 122.360 E94 +0 2 2 40 0.773 126.830 C94 +1 2 2 40 0.976 120.132 E94 +0 2 2 41 0.432 110.442 C94 +0 2 2 43 1.144 111.808 E94 +0 2 2 45 1.194 109.231 X94 +1 2 2 45 1.062 113.984 E94 +0 2 2 46 1.005 121.534 E94 +0 2 2 55 0.995 121.154 E94 +0 2 2 56 1.234 108.879 E94 +0 2 2 62 0.808 135.269 X94 +1 2 2 63 0.948 118.277 E94 +1 2 2 64 0.866 123.528 E94 +2 2 2 64 0.859 121.998 E94 +1 2 2 67 1.132 112.136 E94 +0 2 2 72 0.770 134.269 X94 +1 2 2 81 1.078 116.541 E94 +2 3 2 3 0.853 120.370 E94 +2 3 2 4 0.878 119.739 E94 +1 3 2 5 0.487 117.291 C94 +1 3 2 6 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115.350 C94 +1 2 3 6 0.932 106.510 C94 +1 2 3 7 0.936 122.623 C94 +1 2 3 9 0.831 122.253 C94 +2 2 3 9 1.120 111.408 E94 +1 2 3 10 1.042 111.721 C94 +1 2 3 12 0.901 120.769 E94 +1 2 3 15 1.057 112.105 E94 +1 2 3 16 0.881 124.850 E94 +1 2 3 22 0.969 113.027 E94 +1 2 3 25 0.853 109.794 E94 +2 2 3 37 0.973 112.935 E94 +2 2 3 39 1.197 107.592 E94 +1 2 3 40 0.910 123.437 E94 +1 2 3 43 1.105 111.169 E94 +1 2 3 53 1.082 114.032 E94 +1 2 3 54 1.012 118.588 E94 +1 2 3 55 1.186 107.278 E94 +1 2 3 56 1.151 108.909 E94 +2 2 3 63 0.918 116.947 E94 +2 2 3 64 1.033 110.084 E94 +1 2 3 67 1.022 117.597 E94 +2 3 3 3 0.822 121.775 E94 +8 3 3 3 1.280 89.965 E94 +1 3 3 5 0.943 113.762 C94 +1 3 3 6 0.935 103.030 C94 +1 3 3 7 0.919 117.024 C94 +1 3 3 9 1.050 115.704 E94 +1 3 3 10 1.129 110.421 E94 +1 3 3 12 1.053 111.492 E94 +1 3 3 15 1.390 97.562 E94 +1 3 3 16 1.092 111.888 E94 +1 3 3 20 0.977 110.910 E94 +1 3 3 22 1.010 110.295 E94 +8 3 3 30 1.353 87.789 E94 +2 3 3 37 0.932 114.949 E94 +2 3 3 39 1.237 105.384 E94 +1 3 3 40 1.003 117.124 E94 +1 3 3 41 0.790 124.361 E94 +1 3 3 45 0.919 121.023 E94 +1 3 3 53 1.170 109.169 E94 +2 3 3 63 0.981 112.685 E94 +2 3 3 64 0.880 118.840 E94 +1 3 3 67 1.119 111.860 E94 +1 4 3 6 1.269 111.750 E94 +1 4 3 7 1.126 120.852 E94 +1 4 3 9 1.192 109.833 E94 +2 4 3 37 0.964 114.081 E94 +0 5 3 5 0.594 116.699 C94 +0 5 3 6 0.819 108.253 C94 +0 5 3 7 0.670 123.439 C94 +0 5 3 9 0.623 119.491 C94 +1 5 3 9 0.638 117.168 E94 +0 5 3 10 0.874 111.761 C94 +0 5 3 16 0.522 124.405 E94 +1 5 3 37 0.564 116.400 E94 +0 5 3 40 0.959 111.684 C94 +0 5 3 53 0.644 118.000 #E94 +0 5 3 54 0.816 115.471 C94 +1 5 3 63 0.559 118.000 #E94 +1 5 3 64 0.566 117.000 #E94 +0 5 3 67 0.700 113.698 E94 +0 6 3 6 1.678 109.094 E94 +0 6 3 7 1.155 124.425 C94 +0 6 3 9 1.275 119.478 E94 +1 6 3 9 1.416 111.868 E94 +0 6 3 10 1.405 112.187 E94 +0 6 3 16 1.269 116.317 E94 +0 6 3 20 1.182 113.581 E94 +4 6 3 20 1.495 93.130 E94 +0 6 3 22 1.276 110.826 E94 +7 6 3 30 1.530 93.191 E94 +1 6 3 37 0.808 102.881 C94 +1 6 3 39 1.611 104.655 E94 +0 6 3 40 1.371 113.565 E94 +0 6 3 41 1.477 102.658 E94 +0 6 3 43 1.330 114.183 E94 +0 6 3 48 1.315 115.328 E94 +0 6 3 51 1.409 120.427 E94 +0 6 3 54 1.495 110.510 E94 +0 6 3 62 1.421 112.542 E94 +1 6 3 63 1.339 109.082 E94 +1 6 3 64 1.267 111.993 E94 +1 6 3 80 1.256 113.698 E94 +1 7 3 9 1.147 127.084 E94 +0 7 3 10 0.907 127.152 C94 +0 7 3 12 0.984 130.049 E94 +0 7 3 15 1.101 123.313 E94 +0 7 3 20 0.713 129.492 C94 +0 7 3 22 1.093 121.851 E94 +1 7 3 30 0.972 129.010 E94 +1 7 3 37 0.734 119.968 C94 +1 7 3 39 1.352 116.727 E94 +0 7 3 41 1.281 112.087 E94 +0 7 3 43 1.163 124.549 X94 +0 7 3 48 1.114 127.879 E94 +1 7 3 54 1.288 114.184 E94 +0 7 3 55 1.258 120.056 E94 +0 7 3 56 1.175 123.854 E94 +1 7 3 58 1.323 117.081 E94 +0 7 3 62 1.129 129.349 E94 +1 7 3 63 1.036 126.456 E94 +1 7 3 64 1.071 124.133 E94 +1 7 3 78 0.955 132.047 E94 +1 9 3 9 1.119 120.094 E94 +2 9 3 9 1.021 124.131 E94 +0 9 3 10 1.105 120.697 E94 +1 9 3 10 1.154 116.608 E94 +0 9 3 12 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105.875 X94 +0 1 6 63 1.449 109.545 E94 +0 1 6 64 1.512 106.848 E94 +0 2 6 2 1.354 113.339 E94 +0 2 6 3 0.671 98.438 C94 +0 2 6 18 1.365 117.169 E94 +0 2 6 25 1.025 120.078 E94 +0 2 6 29 0.816 105.727 C94 +0 2 6 37 1.418 110.694 E94 +0 2 6 57 1.341 114.785 E94 +0 3 6 3 1.455 110.067 E94 +0 3 6 4 1.409 112.404 E94 +0 3 6 8 1.648 105.872 E94 +0 3 6 10 1.596 108.437 E94 +0 3 6 18 1.274 121.468 E94 +0 3 6 19 1.019 119.840 E94 +0 3 6 20 1.379 111.381 E94 +4 3 6 20 1.748 91.216 E94 +0 3 6 22 1.328 113.491 E94 +0 3 6 24 0.583 111.948 C94 +0 3 6 25 1.006 121.410 E94 +0 3 6 29 0.876 111.417 E94 +0 3 6 37 0.614 95.300 C94 +0 3 6 64 1.424 111.483 E94 +0 4 6 18 1.423 115.233 E94 +0 6 6 21 1.362 95.697 E94 +0 8 6 21 0.832 99.409 C94 +0 9 6 21 1.115 101.592 E94 +0 10 6 21 0.923 99.688 C94 +0 18 6 18 1.334 125.242 E94 +0 18 6 33 0.812 115.364 X94 +0 18 6 37 1.429 114.473 E94 +0 18 6 39 1.558 114.152 E94 +0 18 6 43 1.710 108.479 E94 +0 19 6 19 0.642 141.096 E94 +0 19 6 21 0.597 118.204 X94 +0 19 6 37 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0:*-54-* MMFF94 DEF +1 0 54 0 0.000 115.700 1:*-54-* MMFF94 DEF +0 1 54 1 0.923 121.439 E94 +0 1 54 3 0.707 124.083 C94 +0 1 54 36 0.294 122.881 C94 +0 3 54 6 1.376 115.398 E94 +1 3 54 9 1.128 114.457 E94 +0 3 54 36 0.685 119.698 C94 +1 3 54 40 1.105 116.439 E94 +0 6 54 36 0.826 115.000 #E94 +0 9 54 40 1.195 123.403 E94 +0 36 54 36 0.300 113.943 C94 +0 0 55 0 0.000 120.800 0:*-55-* MMFF94 DEF +0 1 55 1 0.951 119.946 E94 +0 1 55 36 0.307 126.448 C94 +0 1 55 37 1.032 117.035 E94 +0 1 55 57 0.751 120.606 C94 +0 1 55 80 0.972 121.082 E94 +0 2 55 3 1.041 116.994 E94 +0 2 55 36 0.621 120.000 #E94 +0 2 55 57 1.047 118.847 E94 +0 3 55 9 1.053 121.298 E94 +0 3 55 36 0.567 124.000 #E94 +0 3 55 57 0.953 123.573 E94 +0 3 55 62 1.041 122.163 E94 +0 6 55 36 0.833 114.000 #E94 +0 6 55 57 1.408 112.958 E94 +0 8 55 36 0.656 122.000 #E94 +0 8 55 57 1.259 113.209 E94 +0 9 55 57 1.001 126.373 E94 +0 18 55 36 0.578 125.000 #E94 +0 18 55 57 1.054 122.320 E94 +0 36 55 36 0.355 117.729 C94 +0 36 55 37 0.623 120.405 E94 +0 36 55 41 0.485 134.689 E94 +0 36 55 57 0.663 119.499 C94 +0 36 55 64 0.632 118.000 #E94 +0 36 55 80 0.684 115.880 E94 +0 37 55 57 1.110 115.816 E94 +0 41 55 57 0.911 126.801 E94 +0 57 55 62 1.054 123.366 E94 +0 57 55 64 1.026 119.465 E94 +0 0 56 0 0.000 119.100 0:*-56-* MMFF94 DEF +0 1 56 36 0.472 123.585 C94 +0 1 56 57 0.774 119.267 C94 +0 2 56 9 1.181 116.311 E94 +0 2 56 36 0.582 124.037 E94 +0 2 56 57 1.029 118.607 E94 +0 3 56 36 0.585 121.521 E94 +0 3 56 57 0.885 126.567 E94 +0 8 56 36 0.785 111.009 E94 +0 8 56 57 1.288 110.357 E94 +0 9 56 36 0.683 120.258 E94 +0 9 56 57 1.186 115.661 E94 +0 36 56 36 0.450 117.534 C94 +0 36 56 37 0.602 120.000 #E94 +0 36 56 57 0.646 120.649 C94 +0 36 56 63 0.579 123.766 E94 +0 36 56 80 0.625 120.000 #E94 +0 37 56 57 1.058 115.912 E94 +0 57 56 63 1.019 118.915 E94 +0 0 57 0 0.000 120.900 0:*-57-* MMFF94 DEF +1 0 57 0 0.000 118.100 1:*-57-* MMFF94 DEF +0 1 57 55 1.017 117.865 E94 +1 3 57 55 1.085 115.034 E94 +0 5 57 55 0.674 116.747 C94 +0 6 57 55 1.279 119.257 E94 +1 9 57 55 0.980 128.143 E94 +0 12 57 55 1.058 118.327 E94 +0 15 57 55 0.983 123.646 E94 +0 25 57 55 0.790 122.889 E94 +1 37 57 55 0.967 121.379 E94 +0 55 57 55 0.855 126.476 C94 +1 55 57 63 1.016 118.800 E94 +1 55 57 64 1.039 117.166 E94 +0 56 57 56 1.342 120.010 C94 +0 0 58 0 0.000 119.000 0:*-58-* MMFF94 DEF +1 0 58 0 0.000 119.900 1:*-58-* MMFF94 DEF +0 1 58 37 1.003 119.236 E94 +0 1 58 64 0.961 121.070 E94 +1 3 58 37 0.983 121.506 E94 +0 6 58 37 1.371 114.370 E94 +0 18 58 37 1.005 120.665 E94 +0 36 58 37 0.650 118.713 E94 +0 36 58 63 0.650 118.000 #E94 +0 36 58 64 0.620 120.051 E94 +0 37 58 37 0.996 122.710 E94 +1 37 58 37 1.036 118.260 E94 +0 37 58 63 1.087 116.989 E94 +0 37 58 64 1.061 117.942 E94 +0 0 59 0 0.000 105.600 0:*-59-* MMFF94 DEF +0 63 59 63 1.273 106.313 C94 +0 63 59 65 1.750 107.755 C94 +0 63 59 78 1.713 101.179 E94 +0 63 59 80 1.599 105.341 E94 +0 65 59 65 1.754 107.683 E94 +0 65 59 78 1.644 107.142 E94 +0 65 59 82 1.864 103.624 E94 +0 0 61 0 0.000 180.000 0:*-61-* MMFF94 DEF +0 1 61 60 0.475 180.000 E94 +0 37 61 42 0.536 180.000 E94 +0 37 61 60 0.484 180.000 E94 +0 0 62 0 0.000 108.300 0:*-62-* MMFF94 DEF +0 1 62 18 1.316 109.273 X94 +0 2 62 23 0.817 105.542 X94 +0 3 62 3 1.318 106.821 E94 +0 3 62 18 1.311 111.144 E94 +0 3 62 55 1.528 102.414 E94 +0 9 62 18 1.515 107.660 E94 +0 18 62 37 1.229 114.618 E94 +0 18 62 41 1.366 108.722 E94 +0 18 62 63 1.427 106.284 E94 +0 18 62 64 1.317 110.366 E94 +0 0 63 0 0.000 123.300 0:*-63-* MMFF94 DEF +1 0 63 0 0.000 124.300 1:*-63-* MMFF94 DEF +0 1 63 39 0.935 121.832 E94 +0 1 63 44 0.902 122.101 E94 +0 1 63 59 1.175 115.253 E94 +0 1 63 64 0.737 131.378 E94 +0 1 63 66 0.865 127.610 E94 +1 2 63 39 1.027 117.864 E94 +1 2 63 59 0.987 127.524 E94 +1 2 63 64 0.730 133.818 E94 +1 2 63 66 0.828 132.383 E94 +1 3 63 39 0.900 125.395 E94 +1 3 63 44 0.935 120.481 E94 +1 3 63 59 1.158 117.219 E94 +1 3 63 64 0.766 130.065 E94 +1 3 63 66 0.950 123.049 E94 +1 4 63 44 0.848 126.602 E94 +1 4 63 59 1.211 114.804 E94 +1 4 63 64 0.795 127.817 E94 +0 5 63 39 0.617 121.127 C94 +0 5 63 44 0.393 126.141 C94 +0 5 63 59 0.784 114.076 C94 +0 5 63 64 0.577 131.721 C94 +0 5 63 66 0.643 125.134 C94 +0 5 63 78 0.482 130.000 #E94 +0 5 63 81 0.588 124.000 #E94 +0 6 63 39 1.234 120.509 E94 +0 6 63 59 1.564 113.514 E94 +0 6 63 64 0.951 131.301 E94 +1 9 63 39 1.068 121.741 E94 +1 9 63 44 0.963 124.598 E94 +1 9 63 64 0.804 134.237 E94 +1 9 63 66 0.912 133.020 E94 +0 10 63 39 1.084 120.356 E94 +0 10 63 44 1.112 115.732 E94 +0 10 63 59 1.307 116.218 E94 +0 10 63 64 0.867 128.750 E94 +0 10 63 66 0.981 127.617 E94 +0 12 63 39 1.111 114.439 E94 +0 12 63 44 1.035 119.321 E94 +0 12 63 64 0.838 126.226 E94 +0 12 63 66 0.980 122.280 E94 +0 15 63 39 1.064 117.958 E94 +0 15 63 44 0.952 125.654 E94 +0 15 63 64 0.813 129.284 E94 +0 15 63 66 0.962 124.490 E94 +0 18 63 44 1.110 116.077 E94 +0 18 63 64 0.740 135.028 E94 +0 19 63 39 0.647 132.369 E94 +0 19 63 64 0.517 141.986 E94 +0 25 63 39 0.597 139.439 E94 +0 25 63 66 0.776 122.699 E94 +0 35 63 59 1.351 124.475 E94 +0 35 63 64 0.808 145.098 E94 +0 37 63 39 1.011 132.046 C94 +1 37 63 39 0.934 123.481 E94 +0 37 63 44 0.764 133.930 E94 +1 37 63 44 0.915 121.637 E94 +0 37 63 59 1.041 124.836 E94 +1 37 63 59 1.214 114.211 E94 +0 37 63 64 0.679 122.881 C94 +1 37 63 64 0.742 131.784 E94 +0 37 63 66 0.742 140.668 E94 +1 37 63 66 0.871 128.130 E94 +0 38 63 39 1.022 124.814 E94 +0 38 63 64 0.910 126.513 E94 +0 39 63 39 0.910 131.461 E94 +1 39 63 39 1.105 119.174 E94 +0 39 63 40 1.112 119.261 E94 +1 39 63 44 1.144 114.126 E94 +0 39 63 45 1.166 115.115 E94 +1 39 63 57 0.931 123.222 E94 +0 39 63 58 1.042 123.231 E94 +1 39 63 63 0.949 122.353 E94 +0 39 63 64 0.813 107.255 C94 +1 39 63 64 0.943 123.441 E94 +0 39 63 66 1.012 110.865 C94 +1 39 63 66 1.095 120.834 E94 +0 40 63 44 0.943 125.881 E94 +0 40 63 59 1.298 117.078 E94 +0 40 63 64 0.845 130.865 E94 +0 40 63 66 0.940 130.926 E94 +0 44 63 45 1.125 114.633 E94 +0 44 63 56 1.030 120.178 E94 +0 44 63 62 0.991 122.899 E94 +1 44 63 63 0.894 123.341 E94 +0 44 63 64 0.853 108.480 C94 +0 44 63 66 0.854 114.516 C94 +0 44 63 72 0.915 129.129 E94 +0 44 63 78 1.217 106.254 E94 +0 44 63 81 1.278 108.400 E94 +0 45 63 59 1.467 108.824 E94 +0 45 63 64 0.940 122.725 E94 +0 45 63 66 1.164 116.157 E94 +0 56 63 66 0.875 134.888 E94 +1 57 63 66 0.945 123.246 E94 +0 58 63 64 0.965 122.522 E94 +0 59 63 64 1.035 110.108 C94 +0 59 63 66 1.181 115.592 C94 +0 62 63 66 0.976 128.662 E94 +1 63 63 64 0.776 129.499 E94 +1 63 63 66 0.929 124.689 E94 +0 66 63 72 0.911 129.610 E94 +0 0 64 0 0.000 121.400 0:*-64-* MMFF94 DEF +1 0 64 0 0.000 121.700 1:*-64-* MMFF94 DEF +0 1 64 63 0.776 128.041 E94 +0 1 64 64 0.766 128.061 E94 +0 1 64 65 0.963 120.640 E94 +0 1 64 66 0.952 120.685 E94 +0 1 64 81 1.050 114.735 E94 +0 1 64 82 1.013 117.414 E94 +1 2 64 63 0.861 122.947 E94 +1 2 64 64 0.816 125.433 E94 +1 2 64 65 0.907 125.781 E94 +1 2 64 66 1.010 118.540 E94 +1 2 64 82 0.923 124.473 E94 +1 3 64 63 0.828 124.890 E94 +1 3 64 64 0.774 128.286 E94 +1 3 64 65 0.973 120.954 E94 +1 3 64 66 0.949 121.821 E94 +1 3 64 81 0.995 118.754 E94 +1 4 64 63 0.845 123.889 E94 +1 4 64 64 0.804 126.131 E94 +1 4 64 65 1.036 117.401 E94 +1 4 64 66 1.010 118.254 E94 +0 5 64 63 0.501 126.170 C94 +0 5 64 64 0.546 127.405 C94 +0 5 64 65 0.664 118.412 C94 +0 5 64 66 0.699 120.478 C94 +0 5 64 78 0.482 127.331 E94 +0 5 64 81 0.605 120.000 #E94 +0 5 64 82 0.597 122.000 #E94 +0 6 64 63 1.112 120.985 E94 +0 6 64 64 1.043 123.922 E94 +0 6 64 65 1.348 115.506 E94 +0 6 64 66 1.156 123.890 E94 +1 9 64 64 0.959 120.924 E94 +1 9 64 65 1.098 119.529 E94 +1 9 64 66 1.013 123.743 E94 +0 10 64 63 0.937 123.695 E94 +0 10 64 64 0.893 125.735 E94 +0 10 64 65 1.016 124.788 E94 +0 10 64 66 1.065 121.125 E94 +0 12 64 63 0.845 126.259 E94 +0 12 64 64 0.869 124.058 E94 +0 12 64 65 1.020 120.198 E94 +0 12 64 66 0.971 122.900 E94 +0 13 64 63 0.845 123.004 E94 +0 13 64 64 0.883 120.111 E94 +0 15 64 63 0.870 124.581 E94 +0 15 64 64 0.882 123.309 E94 +0 15 64 65 1.008 121.049 E94 +0 15 64 66 0.990 121.826 E94 +0 18 64 65 1.065 118.404 E94 +0 18 64 66 1.067 118.002 E94 +0 37 64 63 0.906 117.966 C94 +0 37 64 64 0.854 136.087 C94 +1 37 64 64 0.772 128.673 E94 +0 37 64 65 0.799 134.844 E94 +1 37 64 65 0.942 122.866 E94 +0 37 64 66 0.845 130.337 E94 +0 37 64 78 0.706 135.432 E94 +0 37 64 81 0.917 124.856 E94 +0 37 64 82 0.946 123.684 E94 +1 37 64 82 1.000 119.086 E94 +0 38 64 63 0.988 121.242 E94 +0 38 64 64 0.858 129.014 E94 +0 38 64 65 0.989 127.335 E94 +0 38 64 66 1.022 124.454 E94 +0 39 64 64 1.086 114.312 E94 +0 39 64 65 1.060 122.481 E94 +1 39 64 65 1.204 114.188 E94 +1 39 64 66 1.170 115.157 E94 +0 40 64 63 0.948 123.538 E94 +0 40 64 64 0.928 123.853 E94 +0 40 64 65 0.958 129.125 E94 +0 40 64 81 1.035 123.154 E94 +0 40 64 82 1.183 115.934 E94 +0 43 64 63 0.885 126.749 E94 +0 43 64 64 0.898 124.876 E94 +0 43 64 65 1.024 123.706 E94 +0 43 64 66 1.017 123.409 E94 +0 45 64 63 0.981 120.063 E94 +0 45 64 64 0.921 123.014 E94 +0 45 64 65 1.276 110.521 E94 +0 45 64 66 1.199 113.371 E94 +0 55 64 64 0.907 124.405 E94 +0 55 64 65 1.002 125.220 E94 +1 57 64 65 1.020 117.950 E94 +1 57 64 66 0.959 121.017 E94 +0 58 64 63 1.075 115.646 E94 +0 58 64 64 0.815 131.812 E94 +0 58 64 66 0.978 126.562 E94 +0 62 64 64 0.885 126.560 E94 +0 62 64 65 1.073 121.703 E94 +0 63 64 64 0.866 108.239 C94 +1 63 64 64 0.827 124.584 E94 +0 63 64 66 1.038 111.621 C94 +0 63 64 78 1.172 105.176 E94 +0 63 64 81 1.164 110.895 E94 +0 63 64 82 1.395 101.902 E94 +0 64 64 64 0.967 115.037 E94 +0 64 64 65 0.916 113.570 C94 +1 64 64 66 1.003 118.067 E94 +0 64 64 78 1.194 103.479 E94 +0 64 64 82 1.210 108.553 E94 +0 65 64 66 1.055 115.369 C94 +0 65 64 81 1.168 116.240 E94 +0 66 64 66 0.932 129.624 E94 +0 0 65 0 0.000 104.500 0:*-65-* MMFF94 DEF +0 39 65 64 1.738 101.550 C94 +0 39 65 66 1.589 106.360 C94 +0 39 65 82 1.740 101.208 E94 +0 44 65 64 1.430 103.829 C94 +0 44 65 66 1.366 110.552 E94 +0 44 65 78 1.419 104.213 E94 +0 59 65 64 1.788 103.452 C94 +0 59 65 81 1.774 104.872 E94 +0 0 66 0 0.000 106.900 0:*-66-* MMFF94 DEF +0 63 66 64 1.206 103.779 C94 +0 63 66 66 1.406 106.735 C94 +0 63 66 78 1.339 105.365 E94 +0 63 66 81 1.408 106.806 E94 +0 64 66 65 1.709 107.658 C94 +0 65 66 66 1.932 111.306 C94 +0 0 67 0 0.000 119.900 0:*-67-* MMFF94 DEF +1 0 67 0 0.000 116.600 1:*-67-* MMFF94 DEF +0 1 67 3 0.982 120.683 E94 +0 1 67 9 1.178 115.581 E94 +0 1 67 32 1.233 119.589 E94 +0 1 67 67 1.257 111.574 E94 +1 2 67 32 1.118 126.320 E94 +1 2 67 67 1.231 113.438 E94 +0 3 67 23 0.567 128.000 #E94 +0 3 67 32 1.290 120.945 E94 +1 3 67 37 1.122 113.631 E94 +1 9 67 30 1.142 118.899 E94 +0 9 67 32 1.325 125.531 E94 +1 9 67 37 1.186 115.979 E94 +0 23 67 32 0.805 120.000 #E94 +1 30 67 32 1.370 114.854 E94 +1 32 67 37 1.240 120.019 E94 +0 32 67 67 1.504 117.327 E94 +1 37 67 67 1.310 110.017 E94 +0 0 68 0 0.000 108.800 0:*-68-* MMFF94 DEF +0 1 68 1 1.159 108.238 C94 +0 1 68 23 0.772 107.200 C94 +0 1 68 32 0.958 110.757 C94 +0 23 68 23 0.650 104.892 C94 +0 23 68 32 0.659 112.977 C94 +0 0 69 0 0.000 120.300 0:*-69-* MMFF94 DEF +0 32 69 37 1.123 121.777 C94 +0 32 69 38 1.486 117.217 E94 +0 37 69 37 1.223 116.447 C94 +0 38 69 38 1.122 125.930 E94 +0 31 70 31 0.658 103.978 C94 +0 0 73 0 0.000 106.600 0:*-73-* MMFF94 DEF +0 1 73 32 1.590 100.180 X94 +0 1 73 72 1.481 96.166 X94 +0 32 73 32 1.665 115.012 X94 +0 32 73 72 1.326 115.134 X94 +0 0 74 0 0.000 113.000 0:*-74-* MMFF94 DEF +0 3 74 7 1.357 113.010 X94 +0 0 75 0 0.000 94.900 0:*-75-* MMFF94 DEF +0 1 75 3 1.138 96.779 E94 +0 3 75 19 1.044 91.970 E94 +0 3 75 71 0.729 95.899 X94 +0 0 76 0 0.000 107.600 0:*-76-* MMFF94 DEF +0 76 76 76 1.434 109.889 X94 +0 76 76 78 1.493 103.519 X94 +0 78 76 78 1.235 109.421 E94 +0 0 77 0 0.000 109.500 0:*-77-* MMFF94 DEF +0 32 77 32 1.652 109.472 X94 +0 0 78 0 0.000 121.900 0:*-78-* MMFF94 DEF +1 0 78 0 0.000 126.100 1:*-78-* MMFF94 DEF +0 1 78 78 0.744 130.960 E94 +0 1 78 81 0.938 121.477 E94 +1 3 78 78 0.827 125.468 E94 +1 3 78 81 0.922 123.748 E94 +0 5 78 76 0.584 123.407 X94 +0 5 78 78 0.546 128.000 C94 +0 5 78 79 0.617 122.000 #E94 +0 5 78 81 0.542 109.881 C94 +1 9 78 78 0.863 129.501 E94 +1 9 78 81 0.991 125.857 E94 +0 37 78 76 0.770 137.282 E94 +0 37 78 78 0.803 128.249 E94 +0 37 78 81 0.864 128.714 E94 +0 38 78 78 0.844 130.617 E94 +0 38 78 81 1.023 123.532 E94 +0 39 78 64 0.734 138.714 E94 +0 39 78 78 1.202 109.426 E94 +0 40 78 76 0.930 130.150 E94 +0 40 78 78 0.778 135.746 E94 +0 40 78 81 1.058 121.251 E94 +0 44 78 63 0.677 141.902 E94 +0 44 78 64 0.663 142.589 E94 +0 44 78 66 0.816 134.701 E94 +0 44 78 78 1.089 111.702 E94 +0 45 78 76 1.199 114.467 E94 +0 45 78 78 0.915 125.050 E94 +0 45 78 81 1.216 112.926 E94 +0 59 78 64 0.963 128.471 E94 +0 59 78 65 1.097 128.375 E94 +0 59 78 78 1.443 105.916 E94 +0 63 78 64 0.942 117.779 E94 +0 64 78 65 0.835 131.530 E94 +0 64 78 78 1.038 111.834 E94 +0 66 78 78 1.030 118.376 E94 +0 76 78 76 1.245 113.179 X94 +0 76 78 78 1.159 111.900 E94 +0 78 78 78 1.336 99.459 E94 +0 78 78 81 1.302 105.130 C94 +0 79 78 81 1.217 114.792 E94 +0 0 79 0 0.000 103.400 0:*-79-* MMFF94 DEF +0 78 79 81 1.569 102.043 E94 +0 79 79 81 1.625 104.857 E94 +0 0 80 0 0.000 121.900 0:*-80-* MMFF94 DEF +1 0 80 0 0.000 128.200 1:*-80-* MMFF94 DEF +0 1 80 81 0.864 127.147 E94 +1 3 80 81 0.886 128.181 E94 +0 5 80 81 0.651 125.682 C94 +0 18 80 81 1.032 120.869 E94 +0 41 80 81 0.909 125.057 E94 +0 44 80 55 0.918 127.755 E94 +0 44 80 81 1.184 112.411 E94 +0 55 80 59 1.254 120.263 E94 +0 55 80 81 0.991 127.612 E94 +0 56 80 81 1.003 126.038 E94 +0 59 80 81 1.439 112.030 E94 +0 81 80 81 1.205 108.609 C94 +0 0 81 0 0.000 119.500 0:*-81-* MMFF94 DEF +0 1 81 63 0.996 120.129 E94 +0 1 81 64 0.978 119.970 E94 +0 1 81 78 0.879 126.535 E94 +0 1 81 79 1.144 116.113 E94 +0 1 81 80 0.895 126.324 E94 +1 2 81 78 0.927 125.080 E94 +1 2 81 80 0.895 128.399 E94 +1 9 81 78 1.015 124.270 E94 +1 9 81 80 1.106 120.028 E94 +0 36 81 64 0.522 130.295 E94 +0 36 81 66 0.583 128.738 E94 +0 36 81 78 0.578 124.658 C94 +0 36 81 80 0.575 124.787 C94 +0 37 81 64 0.929 122.408 E94 +1 37 81 64 0.983 119.722 E94 +0 37 81 65 1.184 114.158 E94 +1 37 81 65 1.281 110.477 E94 +1 37 81 78 0.884 126.208 E94 +1 37 81 80 0.940 123.333 E94 +0 63 81 64 1.115 114.945 E94 +0 64 81 65 1.075 122.099 E94 +0 64 81 80 1.143 113.176 E94 +0 66 81 80 1.067 122.250 E94 +0 78 81 80 0.957 110.556 C94 +0 79 81 80 1.379 107.936 E94 +0 32 82 59 1.666 114.660 E94 +0 32 82 64 1.075 131.706 E94 +0 32 82 65 1.238 129.293 E94 +0 59 82 64 1.563 105.660 E94 +0 64 82 65 1.281 112.955 E94 +$
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/mmffbndk.par Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,68 @@ +* +* Copyright (c) Merck and Co., Inc., 1994 +* All Rights Reserved +* +* MMFF BOND LENGTH, FORCE CONSTANT DEFAULT-RULE PARAMETERS +* C94 = Fitted to ab-initio derived core MMFF94 force constants +* E94 = Based on Herschberg/Laurie parameterization of Badger's rule +* +* species r0-ref kb-ref Source + 1 6 1.084 5.15 C94 + 1 7 1.001 7.35 C94 + 1 8 0.947 9.10 C94 + 1 9 0.92 10.6 E94 + 1 14 1.48 2.3 E94 + 1 15 1.415 2.95 C94 + 1 16 1.326 4.30 C94 + 1 17 1.28 4.3 E94 + 1 35 1.41 4.2 E94 + 1 53 1.60 2.7 E94 + 6 6 1.512 3.80 C94 + 6 7 1.439 4.55 C94 + 6 8 1.393 5.40 C94 + 6 9 1.353 6.20 C94 + 6 14 1.86 2.6 E94 + 6 15 1.84 2.7 E94 + 6 16 1.812 2.85 C94 + 6 17 1.781 2.75 C94 + 6 35 1.94 2.6 E94 + 6 53 2.16 1.4 E94 + 7 7 1.283 6.00 C94 + 7 8 1.333 5.90 C94 + 7 9 1.36 5.9 E94 + 7 14 1.74 3.7 E94 + 7 15 1.65 4.8 E94 + 7 16 1.674 3.75 C94 + 7 17 1.75 3.5 E94 + 7 35 1.90 2.9 E94 + 7 53 2.10 1.6 E94 + 8 8 1.48 3.6 E94 + 8 9 1.42 4.6 E94 + 8 14 1.63 5.2 E94 + 8 15 1.66 4.7 E94 + 8 16 1.470 9.90 C94 + 8 17 1.70 4.1 E94 + 8 35 1.85 3.4 E94 + 8 53 2.05 1.6 E94 + 9 14 1.57 6.4 E94 + 9 15 1.54 7.1 E94 + 9 16 1.55 6.9 E94 + 14 14 2.32 1.3 E94 + 14 15 2.25 1.5 E94 + 14 16 2.15 2.0 E94 + 14 17 2.02 3.1 E94 + 14 35 2.19 2.1 E94 + 14 53 2.44 1.5 E94 + 15 15 2.21 1.7 E94 + 15 16 2.10 2.4 E94 + 15 17 2.03 3.0 E94 + 15 35 2.21 2.0 E94 + 15 53 2.47 1.4 E94 + 16 16 2.052 2.50 C94 + 16 17 2.04 2.9 E94 + 16 35 2.24 1.9 E94 + 16 53 2.40 1.7 E94 + 17 17 1.99 3.5 E94 + 35 35 2.28 2.4 E94 + 53 53 2.67 1.6 E94 +$
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/mmffbond.par Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,507 @@ +* +* Copyright (c) Merck and Co., Inc., 1994 +* All Rights Reserved +* +* MMFF BOND PARAMETERS- Rev: 26-OCT-94 Source: MMFF94 +* C94 = CORE MMFF94 parameter - obtained from ab initio data +* X94 = EXTD MMFF94 parameter - fit to additional ab initio data +* E94 = r0 from fit to X-ray data, kb from empirical rule +* #C94 = r0 lies between C94 and E94 values, kb from empirical rule +* #X94 = r0 lies between X94 and E94 values, kb from empirical rule +* #E94 = r0 and k both from empirical rules +* +* types kb r0 Source +0 1 1 4.258 1.508 C94 +0 1 2 4.539 1.482 C94 +0 1 3 4.190 1.492 C94 +0 1 4 4.707 1.459 X94 +0 1 5 4.766 1.093 C94 +0 1 6 5.047 1.418 C94 +0 1 8 5.084 1.451 C94 +0 1 9 4.763 1.458 C94 +0 1 10 4.664 1.436 C94 +0 1 11 6.011 1.360 #C94 +0 1 12 2.974 1.773 C94 +0 1 13 2.529 1.949 E94 +0 1 14 1.706 2.090 E94 +0 1 15 2.893 1.805 C94 +0 1 17 2.841 1.813 X94 +0 1 18 3.258 1.772 X94 +0 1 19 2.866 1.830 #X94 +0 1 20 4.650 1.504 C94 +0 1 22 4.286 1.482 E94 +0 1 25 2.980 1.810 #X94 +0 1 26 2.790 1.830 #X94 +0 1 34 3.844 1.480 #C94 +0 1 35 7.915 1.307 X94 +0 1 37 4.957 1.486 C94 +0 1 39 6.114 1.445 C94 +0 1 40 4.922 1.446 C94 +0 1 41 3.830 1.510 #C94 +0 1 43 3.971 1.472 X94 +0 1 45 3.844 1.480 X94 +0 1 46 3.813 1.482 X94 +0 1 54 4.267 1.461 C94 +0 1 55 4.646 1.454 C94 +0 1 56 4.166 1.453 C94 +0 1 57 4.669 1.461 E94 +0 1 58 4.329 1.451 E94 +0 1 61 4.845 1.424 X94 +0 1 62 4.456 1.444 X94 +0 1 63 4.481 1.471 E94 +0 1 64 4.518 1.469 E94 +0 1 67 4.188 1.459 E94 +0 1 68 4.217 1.479 C94 +0 1 72 2.956 1.801 X94 +0 1 73 2.608 1.839 X94 +0 1 75 2.547 1.858 E94 +0 1 78 4.593 1.465 E94 +0 1 80 4.373 1.477 E94 +0 1 81 4.512 1.441 E94 +0 2 2 9.505 1.333 C94 +1 2 2 5.310 1.430 #C94 +1 2 3 4.565 1.468 C94 +0 2 4 9.538 1.297 E94 +1 2 4 5.657 1.415 E94 +0 2 5 5.170 1.083 C94 +0 2 6 5.520 1.373 C94 +1 2 9 6.385 1.360 E94 +0 2 10 6.329 1.362 E94 +0 2 11 6.283 1.350 #X94 +0 2 12 3.390 1.720 #X94 +0 2 13 3.413 1.854 E94 +0 2 14 2.062 2.025 E94 +0 2 15 3.896 1.720 E94 +0 2 17 3.247 1.773 E94 +0 2 18 3.789 1.728 E94 +0 2 19 3.052 1.811 E94 +0 2 20 4.593 1.465 E94 +0 2 22 4.926 1.448 E94 +0 2 25 3.750 1.742 E94 +0 2 30 8.166 1.331 E94 +0 2 34 5.207 1.407 E94 +0 2 35 10.343 1.250 #X94 +1 2 37 5.007 1.449 C94 +1 2 39 6.164 1.368 E94 +0 2 40 6.110 1.370 #C94 +0 2 41 3.746 1.505 C94 +0 2 43 4.928 1.420 E94 +0 2 45 4.725 1.430 #X94 +0 2 46 7.466 1.325 E94 +0 2 55 6.164 1.368 E94 +0 2 56 6.246 1.365 E94 +0 2 62 7.105 1.336 X94 +1 2 63 6.030 1.400 E94 +1 2 64 5.754 1.411 E94 +1 2 67 4.685 1.432 E94 +0 2 72 4.179 1.700 #X94 +1 2 81 6.357 1.361 E94 +1 3 3 4.418 1.489 C94 +1 3 4 5.135 1.438 E94 +0 3 5 4.650 1.101 C94 +0 3 6 5.801 1.355 C94 +0 3 7 12.950 1.222 C94 +0 3 9 10.077 1.290 C94 +1 3 9 6.273 1.364 E94 +0 3 10 5.829 1.369 C94 +0 3 11 6.570 1.340 E94 +0 3 12 3.449 1.715 E94 +0 3 15 3.536 1.748 E94 +0 3 16 4.735 1.665 E94 +0 3 17 2.888 1.808 E94 +0 3 18 3.394 1.760 E94 +0 3 20 3.298 1.530 C94 +0 3 22 4.593 1.465 E94 +0 3 25 3.164 1.792 E94 +1 3 30 4.481 1.471 E94 +0 3 35 11.012 1.237 E94 +1 3 37 4.488 1.457 C94 +1 3 39 5.978 1.375 E94 +0 3 40 6.110 1.370 #C94 +0 3 41 4.286 1.482 E94 +0 3 43 4.928 1.420 X94 +0 3 45 4.531 1.440 E94 +0 3 48 5.412 1.398 E94 +0 3 51 8.562 1.290 #X94 +0 3 53 7.637 1.320 #X94 +0 3 54 10.333 1.280 C94 +1 3 54 2.771 1.563 E94 +0 3 55 4.886 1.422 E94 +0 3 56 4.907 1.421 E94 +1 3 57 5.492 1.422 E94 +1 3 58 5.163 1.409 E94 +0 3 62 7.568 1.322 E94 +1 3 63 5.468 1.423 E94 +1 3 64 5.288 1.431 E94 +0 3 67 8.217 1.304 E94 +0 3 74 5.204 1.639 X94 +0 3 75 4.191 1.710 #X94 +1 3 78 5.705 1.413 E94 +1 3 80 6.719 1.375 E94 +0 4 4 15.206 1.200 #X94 +0 4 5 5.726 1.065 X94 +0 4 6 7.193 1.328 E94 +0 4 7 14.916 1.176 E94 +0 4 9 15.589 1.172 E94 +1 4 9 7.041 1.338 E94 +0 4 10 6.824 1.345 E94 +0 4 15 4.330 1.690 E94 +0 4 20 5.178 1.436 E94 +0 4 22 5.400 1.426 E94 +0 4 30 10.227 1.282 E94 +1 4 37 5.445 1.424 E94 +0 4 42 16.582 1.160 #X94 +0 4 43 6.947 1.341 E94 +1 4 63 5.633 1.416 E94 +1 4 64 5.492 1.422 E94 +0 5 19 2.254 1.485 X94 +0 5 20 4.852 1.093 C94 +0 5 22 5.191 1.082 C94 +0 5 30 5.176 1.086 C94 +0 5 37 5.306 1.084 C94 +0 5 41 3.256 1.144 C94 +0 5 57 5.633 1.076 C94 +0 5 63 5.531 1.080 C94 +0 5 64 5.506 1.080 C94 +0 5 78 5.506 1.080 C94 +0 5 80 5.633 1.076 C94 +0 6 6 4.088 1.449 E94 +0 6 8 5.059 1.450 C94 +0 6 9 4.491 1.395 E94 +0 6 10 5.982 1.410 C94 +0 6 15 4.757 1.661 E94 +0 6 17 5.779 1.608 E94 +0 6 18 5.326 1.630 #X94 +0 6 19 4.661 1.660 #X94 +0 6 20 5.623 1.433 C94 +0 6 21 7.794 0.972 C94 +0 6 22 4.556 1.433 E94 +0 6 24 7.403 0.981 C94 +0 6 25 5.243 1.630 #X94 +0 6 26 5.481 1.618 E94 +0 6 29 7.839 0.973 C94 +0 6 30 9.359 1.271 E94 +0 6 33 7.143 0.986 X94 +0 6 37 5.614 1.376 C94 +0 6 39 4.629 1.388 E94 +0 6 40 4.609 1.389 E94 +0 6 41 6.754 1.342 E94 +0 6 43 3.937 1.426 E94 +0 6 45 4.321 1.404 X94 +0 6 54 5.117 1.365 E94 +0 6 55 4.772 1.381 E94 +0 6 57 7.128 1.330 E94 +0 6 58 4.792 1.380 E94 +0 6 63 7.324 1.324 E94 +0 6 64 6.664 1.345 E94 +0 7 17 8.770 1.500 #X94 +0 7 46 9.329 1.235 X94 +0 7 74 9.129 1.490 #X94 +0 8 8 3.264 1.420 E94 +0 8 9 4.581 1.342 E94 +0 8 10 3.909 1.378 E94 +0 8 12 3.371 1.761 E94 +0 8 15 4.060 1.652 E94 +0 8 17 3.901 1.663 E94 +0 8 19 4.254 1.700 E94 +0 8 20 5.107 1.456 C94 +0 8 22 4.223 1.457 E94 +0 8 23 6.490 1.019 C94 +0 8 25 4.629 1.660 E94 +0 8 26 4.027 1.699 E94 +0 8 34 3.775 1.386 E94 +0 8 39 3.435 1.408 E94 +0 8 40 3.710 1.390 E94 +0 8 43 3.977 1.374 E94 +0 8 45 4.267 1.358 E94 +0 8 46 5.519 1.301 E94 +0 8 55 4.229 1.360 E94 +0 8 56 3.995 1.373 E94 +0 9 9 7.256 1.243 E94 +1 9 9 3.808 1.384 E94 +0 9 10 4.480 1.347 E94 +0 9 12 3.635 1.739 E94 +0 9 15 3.791 1.671 E94 +0 9 18 4.465 1.626 E94 +0 9 19 3.687 1.741 E94 +0 9 20 4.401 1.447 E94 +0 9 25 5.379 1.619 E94 +0 9 27 6.230 1.026 C94 +0 9 34 3.223 1.423 E94 +0 9 35 5.095 1.366 E94 +1 9 37 5.529 1.393 E94 +1 9 39 4.685 1.337 E94 +0 9 40 4.382 1.352 E94 +0 9 41 5.650 1.388 E94 +0 9 45 4.857 1.329 E94 +0 9 53 7.291 1.242 X94 +0 9 54 4.991 1.323 E94 +0 9 55 3.825 1.383 E94 +0 9 56 4.602 1.341 E94 +1 9 57 6.824 1.345 E94 +0 9 62 4.749 1.334 E94 +1 9 63 6.824 1.345 E94 +1 9 64 5.458 1.396 E94 +0 9 67 6.752 1.258 E94 +1 9 78 6.644 1.351 E94 +1 9 81 3.909 1.378 E94 +0 10 10 3.977 1.374 E94 +0 10 13 3.110 1.878 E94 +0 10 14 1.967 2.029 E94 +0 10 15 3.593 1.686 E94 +0 10 17 3.930 1.661 E94 +0 10 20 4.240 1.456 E94 +0 10 22 4.970 1.418 E94 +0 10 25 3.820 1.714 E94 +0 10 26 3.651 1.727 E94 +0 10 28 6.663 1.015 C94 +0 10 34 3.960 1.375 E94 +0 10 35 4.898 1.375 E94 +0 10 37 5.482 1.395 E94 +0 10 39 4.382 1.352 E94 +0 10 40 3.841 1.382 E94 +0 10 41 7.466 1.325 E94 +0 10 45 3.524 1.402 E94 +0 10 63 6.137 1.369 E94 +0 10 64 5.952 1.376 E94 +0 11 20 6.339 1.348 E94 +0 11 22 5.296 1.389 X94 +0 11 25 6.019 1.583 E94 +0 11 26 6.204 1.575 E94 +0 11 37 6.511 1.342 E94 +0 11 40 4.187 1.440 E94 +0 12 15 2.978 2.031 E94 +0 12 18 2.808 2.051 E94 +0 12 19 2.838 2.050 #X94 +0 12 20 2.859 1.751 C94 +0 12 22 3.056 1.750 #X94 +0 12 25 3.063 2.023 E94 +0 12 26 2.448 2.100 #X94 +0 12 37 3.378 1.721 E94 +0 12 40 3.737 1.731 E94 +0 12 57 3.714 1.694 E94 +0 12 63 3.413 1.718 E94 +0 12 64 3.649 1.699 E94 +0 13 20 2.767 1.920 E94 +0 13 22 2.928 1.902 E94 +0 13 37 3.031 1.891 E94 +0 13 64 3.031 1.891 E94 +0 14 20 0.884 2.332 E94 +0 14 37 1.781 2.075 E94 +0 15 15 2.531 2.050 C94 +0 15 18 2.214 2.094 E94 +0 15 19 2.022 2.146 E94 +0 15 20 2.757 1.822 E94 +0 15 22 3.802 1.727 E94 +0 15 25 2.319 2.112 E94 +0 15 26 2.359 2.106 E94 +0 15 30 3.750 1.731 E94 +0 15 37 3.565 1.765 C94 +0 15 40 3.859 1.666 E94 +0 15 43 3.221 1.717 E94 +0 15 57 3.993 1.713 E94 +0 15 63 3.724 1.733 E94 +0 15 64 3.548 1.747 E94 +0 15 71 4.014 1.341 C94 +0 17 20 2.397 1.865 E94 +0 17 22 2.566 1.844 E94 +0 17 37 3.098 1.787 E94 +0 17 43 4.900 1.601 E94 +0 18 20 3.172 1.780 E94 +0 18 22 2.757 1.822 E94 +0 18 32 10.748 1.450 #X94 +0 18 37 3.281 1.770 X94 +0 18 39 3.504 1.693 X94 +0 18 43 3.301 1.710 #X94 +0 18 48 6.186 1.540 X94 +0 18 55 4.432 1.628 E94 +0 18 58 2.568 1.783 E94 +0 18 62 5.510 1.570 #X94 +0 18 63 3.524 1.749 E94 +0 18 64 3.856 1.723 E94 +0 18 80 4.150 1.702 E94 +0 19 20 2.288 1.900 E94 +0 19 37 3.072 1.809 E94 +0 19 40 4.470 1.686 E94 +0 19 63 3.219 1.795 E94 +0 19 75 1.600 2.226 E94 +0 20 20 3.663 1.526 C94 +0 20 22 4.251 1.484 E94 +0 20 25 2.718 1.838 E94 +0 20 26 2.588 1.853 E94 +0 20 30 3.977 1.507 C94 +0 20 34 4.171 1.460 E94 +0 20 37 3.740 1.516 E94 +0 20 40 4.784 1.427 E94 +0 20 41 4.286 1.482 E94 +0 20 43 3.737 1.487 E94 +0 20 45 3.844 1.480 E94 +0 22 22 3.969 1.499 C94 +0 22 30 3.785 1.513 E94 +0 22 34 4.103 1.464 E94 +0 22 37 4.481 1.471 E94 +0 22 40 4.188 1.459 E94 +0 22 41 5.071 1.441 E94 +0 22 43 4.070 1.466 E94 +0 22 45 4.311 1.452 E94 +0 23 39 7.112 1.012 C94 +0 23 62 6.339 1.026 X94 +0 23 67 6.610 1.019 #E94 +0 23 68 5.899 1.038 C94 +0 25 25 1.514 2.253 E94 +0 25 32 8.296 1.510 #X94 +0 25 37 3.586 1.755 E94 +0 25 39 4.370 1.676 E94 +0 25 40 4.629 1.660 E94 +0 25 43 3.237 1.762 X94 +0 25 57 4.356 1.699 E94 +0 25 63 3.711 1.745 E94 +0 25 71 3.001 1.411 X94 +0 25 72 3.744 1.950 #X94 +0 26 26 1.414 2.279 E94 +0 26 34 3.395 1.748 E94 +0 26 37 3.207 1.788 E94 +0 26 40 4.870 1.646 E94 +0 26 71 2.959 1.415 C94 +0 28 40 6.576 1.018 C94 +0 28 43 6.265 1.028 X94 +0 28 48 6.413 1.024 X94 +0 30 30 9.579 1.343 C94 +1 30 30 5.355 1.428 E94 +0 30 40 8.447 1.298 E94 +1 30 67 5.274 1.404 E94 +0 31 70 7.880 0.969 C94 +0 32 41 9.756 1.261 C94 +0 32 45 9.420 1.233 X94 +0 32 67 7.926 1.269 E94 +0 32 68 4.398 1.348 C94 +0 32 69 6.098 1.261 C94 +0 32 73 8.427 1.510 #X94 +0 32 77 10.648 1.450 #X94 +0 32 82 8.594 1.252 E94 +0 34 36 6.163 1.028 C94 +0 34 37 4.347 1.450 E94 +0 34 43 4.401 1.351 E94 +0 35 37 9.767 1.262 E94 +0 35 63 12.760 1.207 E94 +0 36 54 6.529 1.022 C94 +0 36 55 6.744 1.014 C94 +0 36 56 6.490 1.017 C94 +0 36 58 6.610 1.019 #E94 +0 36 81 6.980 1.016 C94 +0 37 37 5.573 1.374 C94 +1 37 37 5.178 1.436 E94 +0 37 38 5.737 1.333 C94 +0 37 39 5.978 1.375 E94 +1 37 39 5.650 1.388 E94 +0 37 40 6.168 1.398 C94 +0 37 41 4.537 1.468 E94 +0 37 43 4.764 1.428 X94 +0 37 45 4.705 1.431 E94 +0 37 46 6.191 1.367 E94 +0 37 55 6.615 1.352 E94 +0 37 56 5.055 1.414 E94 +1 37 57 5.092 1.440 E94 +0 37 58 7.432 1.326 E94 +1 37 58 5.055 1.414 E94 +0 37 61 5.724 1.385 E94 +0 37 62 7.137 1.335 E94 +0 37 63 6.095 1.372 C94 +1 37 63 5.178 1.436 E94 +0 37 64 6.161 1.379 C94 +1 37 64 5.265 1.432 E94 +1 37 67 4.725 1.430 E94 +0 37 69 5.396 1.352 C94 +0 37 78 6.719 1.375 E94 +0 37 81 3.987 1.471 E94 +1 37 81 4.531 1.440 E94 +0 38 38 5.002 1.246 C94 +0 38 63 7.299 1.330 E94 +0 38 64 6.978 1.340 E94 +0 38 69 5.036 1.321 E94 +0 38 78 6.218 1.366 E94 +0 39 40 4.101 1.367 E94 +0 39 45 3.524 1.402 E94 +0 39 63 6.301 1.364 C94 +1 39 63 6.137 1.369 E94 +0 39 64 6.357 1.361 E94 +1 39 64 5.482 1.395 E94 +0 39 65 5.513 1.339 C94 +0 39 78 6.137 1.369 E94 +0 40 40 4.248 1.359 E94 +0 40 45 4.305 1.356 E94 +0 40 46 4.727 1.335 E94 +0 40 54 6.817 1.256 E94 +0 40 63 6.733 1.348 E94 +0 40 64 6.644 1.351 E94 +0 40 78 5.900 1.378 E94 +0 41 41 5.029 1.443 E94 +0 41 55 5.577 1.391 E94 +0 41 62 7.137 1.335 E94 +0 41 72 4.519 1.678 X94 +0 41 80 5.222 1.434 E94 +0 42 61 16.223 1.087 E94 +0 43 43 4.211 1.361 E94 +0 43 45 3.710 1.390 E94 +0 43 64 5.389 1.399 E94 +0 44 63 3.589 1.717 C94 +0 44 65 3.374 1.684 C94 +0 44 78 3.711 1.734 E94 +0 44 80 3.910 1.719 E94 +0 45 63 5.119 1.411 E94 +0 45 64 5.076 1.413 E94 +0 45 78 5.724 1.385 E94 +0 47 53 12.192 1.140 #X94 +0 49 50 6.812 0.991 C94 +0 51 52 7.100 0.987 X94 +0 55 57 7.227 1.319 C94 +0 55 62 3.977 1.374 E94 +0 55 64 5.529 1.393 E94 +0 55 80 7.500 1.324 E94 +0 56 57 4.137 1.383 C94 +0 56 63 5.900 1.378 E94 +0 56 80 6.470 1.357 E94 +1 57 63 5.400 1.426 E94 +1 57 64 5.135 1.438 E94 +0 58 63 6.794 1.346 E94 +0 58 64 6.164 1.368 E94 +0 59 63 5.787 1.360 C94 +0 59 65 4.756 1.388 C94 +0 59 78 6.127 1.364 E94 +0 59 80 7.064 1.332 E94 +0 59 82 3.855 1.431 E94 +0 60 61 15.749 1.170 #X94 +0 62 63 6.947 1.341 E94 +0 62 64 6.273 1.364 E94 +1 63 63 5.729 1.412 E94 +0 63 64 7.118 1.377 C94 +0 63 66 8.326 1.313 C94 +0 63 72 4.503 1.679 E94 +0 63 78 7.434 1.352 E94 +0 63 81 7.778 1.316 E94 +0 64 64 4.313 1.418 C94 +1 64 64 4.926 1.448 E94 +0 64 65 8.258 1.335 C94 +0 64 66 4.456 1.369 C94 +0 64 78 5.492 1.422 E94 +0 64 81 5.824 1.381 E94 +0 64 82 6.794 1.346 E94 +0 65 66 7.243 1.323 C94 +0 65 78 8.447 1.298 E94 +0 65 81 5.223 1.313 E94 +0 65 82 5.622 1.297 E94 +0 66 66 3.874 1.368 C94 +0 66 78 6.385 1.360 E94 +0 66 81 3.960 1.375 E94 +0 67 67 6.085 1.280 E94 +0 71 75 2.852 1.423 X94 +0 72 73 2.628 2.035 X94 +0 76 76 4.286 1.357 X94 +0 76 78 6.824 1.345 X94 +0 78 78 5.573 1.374 C94 +0 78 79 8.890 1.287 E94 +0 78 81 5.046 1.381 C94 +0 79 79 6.408 1.269 E94 +0 79 81 4.305 1.356 E94 +0 80 81 8.237 1.335 C94 +$
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/mmffchg.par Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,512 @@ +* +* Copyright (c) Merck and Co., Inc., 1994 +* All Rights Reserved +* +* MMFF BOND-CHARGE INCREMENTS - Rev: 26-OCT-94 Source: MMFF94 +* C94 - CORE MMFF94 parameter, obtained from fit to dipole moments +* #C94 - CORE MMFF94 parameter, either fixed or adjusted to fit +* HF/6-31G* interaction energies +* X94 - EXTD MMFF94 parameter, obtained from fit to dipole moments +* #X94 - EXTD MMFF94 parameter, fixed in the fit to dipole moments +* E94 - derived from partial bond charge increments (empirical rule) +* +* types bci Source +0 1 1 0.0000 #C94 +0 1 2 -0.1382 C94 +0 1 3 -0.0610 #C94 +0 1 4 -0.2000 #X94 +0 1 5 0.0000 #C94 +0 1 6 -0.2800 #C94 +0 1 8 -0.2700 #C94 +0 1 9 -0.2460 #C94 +0 1 10 -0.3001 C94 +0 1 11 -0.3400 #C94 +0 1 12 -0.2900 #C94 +0 1 13 -0.2300 #X94 +0 1 14 -0.1900 #X94 +0 1 15 -0.2300 #C94 +0 1 17 -0.1935 X94 +0 1 18 -0.1052 X94 +0 1 19 0.0805 X94 +0 1 20 0.0000 #C94 +0 1 22 -0.0950 E94 +0 1 25 0.0000 #X94 +0 1 26 -0.1669 X94 +0 1 34 -0.5030 C94 +0 1 35 -0.4274 X94 +0 1 37 -0.1435 C94 +0 1 39 -0.2556 C94 +0 1 40 -0.3691 C94 +0 1 41 0.1060 #C94 +0 1 43 -0.3557 X94 +0 1 45 -0.2402 X94 +0 1 46 -0.3332 X94 +0 1 54 -0.3461 C94 +0 1 55 -0.4895 C94 +0 1 56 -0.3276 C94 +0 1 57 -0.1050 E94 +0 1 58 -0.4880 E94 +0 1 61 -0.2657 X94 +0 1 62 -0.2000 #X94 +0 1 63 -0.1800 E94 +0 1 64 -0.1810 E94 +0 1 67 -0.0990 E94 +0 1 68 -0.2560 #C94 +0 1 72 -0.5500 #X94 +0 1 73 -0.0877 X94 +0 1 75 -0.2550 E94 +0 1 78 -0.1680 E94 +0 1 80 -0.1440 E94 +0 1 81 -0.5140 E94 +0 2 2 0.0000 #C94 +1 2 2 0.0000 #C94 +1 2 3 -0.0144 C94 +0 2 4 -0.0650 E94 +1 2 4 -0.0650 E94 +0 2 5 0.1500 #C94 +0 2 6 -0.0767 C94 +1 2 9 -0.1710 E94 +0 2 10 -0.1090 E94 +0 2 11 -0.1495 X94 +0 2 12 -0.1400 #X94 +0 2 13 -0.1100 #X94 +0 2 14 -0.0900 #X94 +0 2 15 -0.1010 E94 +0 2 17 -0.0560 E94 +0 2 18 0.0170 E94 +0 2 19 0.2290 E94 +0 2 20 0.1160 E94 +0 2 22 0.0400 E94 +0 2 25 0.1470 E94 +0 2 30 -0.0310 E94 +0 2 34 -0.3560 E94 +0 2 35 -0.3500 #X94 +1 2 37 0.0284 C94 +1 2 39 0.0310 E94 +0 2 40 -0.1000 #C94 +0 2 41 0.2500 #C94 +0 2 43 -0.1910 E94 +0 2 45 -0.2044 X94 +0 2 46 -0.2940 E94 +0 2 55 -0.3410 E94 +0 2 56 -0.3030 E94 +0 2 62 -0.0500 #X94 +1 2 63 -0.0450 E94 +1 2 64 -0.0460 E94 +1 2 67 0.0360 E94 +0 2 72 -0.4500 #X94 +1 2 81 -0.3790 E94 +1 3 3 0.0000 #C94 +1 3 4 -0.1050 E94 +0 3 5 0.0600 #C94 +0 3 6 -0.1500 #C94 +0 3 7 -0.5700 #C94 +0 3 9 -0.4500 #C94 +1 3 9 -0.2110 E94 +0 3 10 -0.0600 C94 +0 3 11 -0.2220 E94 +0 3 12 -0.2090 E94 +0 3 15 -0.1410 E94 +0 3 16 -0.3800 #X94 +0 3 17 -0.0960 E94 +0 3 18 -0.0230 E94 +0 3 20 0.0530 #C94 +0 3 22 0.0000 E94 +0 3 25 0.1070 E94 +1 3 30 -0.0710 E94 +0 3 35 -0.3610 E94 +1 3 37 0.0862 C94 +1 3 39 -0.0090 E94 +0 3 40 -0.0500 #C94 +0 3 41 0.1470 E94 +0 3 43 -0.2363 X94 +0 3 45 -0.1650 E94 +0 3 48 -0.4300 E94 +0 3 51 -0.9500 #X94 +0 3 53 -0.0134 X94 +0 3 54 -0.4000 #C94 +1 3 54 -0.3290 E94 +0 3 55 -0.3810 E94 +0 3 56 -0.3430 E94 +1 3 57 -0.0100 E94 +1 3 58 -0.3930 E94 +0 3 62 -0.0300 E94 +1 3 63 -0.0850 E94 +1 3 64 -0.0860 E94 +0 3 67 -0.0040 E94 +0 3 74 -0.3190 X94 +0 3 75 -0.2474 X94 +1 3 78 -0.0730 E94 +1 3 80 -0.0490 E94 +0 4 5 0.1770 E94 +0 4 6 -0.0430 E94 +0 4 7 -0.4870 E94 +0 4 9 -0.3000 E94 +1 4 9 -0.1060 E94 +0 4 10 -0.0440 E94 +0 4 15 -0.0360 E94 +0 4 20 0.1810 E94 +0 4 22 0.1050 E94 +0 4 30 0.0340 E94 +1 4 37 0.0730 E94 +0 4 40 -0.0640 E94 +0 4 42 -0.5571 X94 +0 4 43 -0.1260 E94 +1 4 63 0.0200 E94 +1 4 64 0.0190 E94 +0 5 19 0.2000 #X94 +0 5 20 0.0000 #C94 +0 5 22 -0.1000 #C94 +0 5 30 -0.1500 #C94 +0 5 37 -0.1500 #C94 +0 5 41 0.2203 C94 +0 5 57 -0.1500 #C94 +0 5 63 -0.1500 #C94 +0 5 64 -0.1500 #C94 +0 5 78 -0.1500 #C94 +0 5 80 -0.1500 #C94 +0 6 6 0.0000 #C94 +0 6 8 -0.1000 #C94 +0 6 9 -0.0630 E94 +0 6 10 0.0355 C94 +0 6 15 0.0070 E94 +0 6 17 0.0520 E94 +0 6 18 0.1837 X94 +0 6 19 0.2974 X94 +0 6 20 0.2579 C94 +0 6 21 0.4000 #C94 +0 6 22 0.1480 E94 +0 6 24 0.5000 #C94 +0 6 25 0.2712 X94 +0 6 26 0.1010 E94 +0 6 29 0.4500 #C94 +0 6 30 0.0770 E94 +0 6 33 0.5000 #X94 +0 6 37 0.0825 C94 +0 6 39 0.1390 E94 +0 6 40 -0.0210 E94 +0 6 41 0.2950 E94 +0 6 43 -0.0830 E94 +0 6 45 -0.0090 X94 +0 6 54 -0.1810 E94 +0 6 55 -0.2330 E94 +0 6 57 0.1380 E94 +0 6 58 -0.2450 E94 +0 6 63 0.0630 E94 +0 6 64 0.0620 E94 +0 7 17 0.5000 #X94 +0 7 46 0.1618 X94 +0 7 74 0.5000 #X94 +0 8 8 0.0000 #C94 +0 8 9 -0.0530 E94 +0 8 10 0.0090 E94 +0 8 12 -0.0510 E94 +0 8 15 0.0170 E94 +0 8 17 0.0620 E94 +0 8 19 0.3470 E94 +0 8 20 0.2096 C94 +0 8 22 0.1580 E94 +0 8 23 0.3600 #C94 +0 8 25 0.2679 X94 +0 8 26 0.1110 E94 +0 8 34 -0.2380 E94 +0 8 39 0.1490 E94 +0 8 40 -0.0110 E94 +0 8 43 -0.0730 E94 +0 8 45 -0.0070 E94 +0 8 46 -0.1760 E94 +0 8 55 -0.2230 E94 +0 8 56 -0.1850 E94 +0 9 9 0.0000 #C94 +0 9 10 0.0620 E94 +0 9 12 0.0020 E94 +0 9 15 0.0700 E94 +0 9 18 0.1880 E94 +0 9 19 0.4000 E94 +0 9 20 0.2870 E94 +0 9 25 0.3180 E94 +0 9 27 0.4000 #C94 +0 9 34 -0.1850 E94 +0 9 35 -0.1500 E94 +1 9 37 0.1790 E94 +1 9 39 0.2020 E94 +0 9 40 0.0420 E94 +0 9 41 0.3580 E94 +0 9 45 0.0460 E94 +0 9 53 0.3179 X94 +0 9 54 -0.1180 E94 +0 9 55 -0.1700 E94 +0 9 56 -0.1320 E94 +1 9 57 0.2010 E94 +0 9 62 0.1810 E94 +1 9 63 0.1260 E94 +1 9 64 0.1250 E94 +0 9 67 0.2070 E94 +1 9 78 0.1380 E94 +1 9 81 -0.2080 E94 +0 10 10 0.0000 #C94 +0 10 13 0.0060 E94 +0 10 14 0.0360 E94 +0 10 15 0.0080 E94 +0 10 17 0.0530 E94 +0 10 20 0.2250 E94 +0 10 22 0.1490 E94 +0 10 25 0.2560 E94 +0 10 26 0.1020 E94 +0 10 28 0.3700 #C94 +0 10 34 -0.2470 E94 +0 10 35 -0.2120 E94 +0 10 37 0.1170 E94 +0 10 39 0.1400 E94 +0 10 40 -0.0200 E94 +0 10 41 0.2960 E94 +0 10 45 -0.0160 E94 +0 10 63 0.0640 E94 +0 10 64 0.0630 E94 +0 11 20 0.2980 E94 +0 11 22 0.2317 X94 +0 11 25 0.3290 E94 +0 11 26 0.1750 E94 +0 11 37 0.1900 E94 +0 11 40 0.0530 E94 +0 12 15 0.0680 E94 +0 12 18 0.1860 E94 +0 12 19 0.3701 X94 +0 12 20 0.2900 #C94 +0 12 22 0.2273 X94 +0 12 25 0.3160 E94 +0 12 26 0.2112 X94 +0 12 37 0.1770 E94 +0 12 40 0.0400 E94 +0 12 57 0.1990 E94 +0 12 63 0.1240 E94 +0 12 64 0.1230 E94 +0 13 20 0.2190 E94 +0 13 22 0.1430 E94 +0 13 37 0.1110 E94 +0 13 64 0.0570 E94 +0 14 20 0.1890 E94 +0 14 37 0.0810 E94 +0 15 15 0.0000 #C94 +0 15 18 0.1180 E94 +0 15 19 0.3300 E94 +0 15 20 0.2170 E94 +0 15 22 0.1410 E94 +0 15 25 0.2480 E94 +0 15 26 0.0940 E94 +0 15 30 0.0700 E94 +0 15 37 0.1015 C94 +0 15 40 -0.0280 E94 +0 15 43 -0.0900 E94 +0 15 57 0.1310 E94 +0 15 63 0.0560 E94 +0 15 64 0.0550 E94 +0 15 71 0.1800 #C94 +0 16 16 0.0000 #C94 +0 17 17 0.0000 #X94 +0 17 20 0.1720 E94 +0 17 22 0.0960 E94 +0 17 37 0.0640 E94 +0 17 43 -0.1350 E94 +0 18 18 0.0000 #X94 +0 18 20 0.0990 E94 +0 18 22 0.0230 E94 +0 18 32 -0.6500 #X94 +0 18 37 -0.0090 E94 +0 18 39 0.0140 E94 +0 18 43 -0.1380 X94 +0 18 48 -0.5895 X94 +0 18 55 -0.3580 E94 +0 18 58 -0.3700 E94 +0 18 62 0.2099 X94 +0 18 63 -0.0620 E94 +0 18 64 -0.0630 E94 +0 18 80 -0.0260 E94 +0 19 19 0.0000 #X94 +0 19 20 -0.1130 E94 +0 19 37 -0.2210 E94 +0 19 40 -0.3580 E94 +0 19 63 -0.2740 E94 +0 19 75 -0.3490 E94 +0 20 20 0.0000 #C94 +0 20 22 -0.0760 E94 +0 20 25 0.0310 E94 +0 20 26 -0.1230 E94 +0 20 30 -0.1380 #C94 +0 20 34 -0.4720 E94 +0 20 37 -0.1080 E94 +0 20 40 -0.2450 E94 +0 20 41 0.0710 E94 +0 20 43 -0.3070 E94 +0 20 45 -0.2410 E94 +0 22 22 0.0000 #C94 +0 22 30 -0.0710 E94 +0 22 34 -0.3960 E94 +0 22 37 -0.0320 E94 +0 22 40 -0.1690 E94 +0 22 41 0.1470 E94 +0 22 43 -0.2310 E94 +0 22 45 -0.1650 E94 +0 23 39 -0.2700 #C94 +0 23 62 -0.4000 #X94 +0 23 67 -0.2920 E94 +0 23 68 -0.3600 #C94 +0 25 25 0.0000 #X94 +0 25 32 -0.7000 #X94 +0 25 37 -0.1390 E94 +0 25 39 -0.1160 E94 +0 25 40 -0.2760 E94 +0 25 43 -0.3380 E94 +0 25 57 -0.1170 E94 +0 25 63 -0.1920 E94 +0 25 71 -0.0362 X94 +0 25 72 -0.6773 X94 +0 26 26 0.0000 #X94 +0 26 34 -0.3490 E94 +0 26 37 0.0150 E94 +0 26 40 -0.1220 E94 +0 26 71 0.0960 X94 +0 28 40 -0.4000 #C94 +0 28 43 -0.4200 #X94 +0 28 48 -0.4000 #X94 +0 30 30 0.0000 #C94 +0 30 40 -0.0980 E94 +1 30 67 0.0670 E94 +0 31 70 -0.4300 #C94 +0 32 41 0.6500 #C94 +0 32 45 0.5200 #X94 +0 32 67 0.6330 E94 +0 32 68 0.7500 #C94 +0 32 69 0.7500 #C94 +0 32 73 0.3500 #X94 +0 32 77 0.4500 #X94 +0 32 82 0.6330 E94 +0 34 36 0.4500 #C94 +0 34 37 0.3640 E94 +0 34 43 0.1650 E94 +0 35 37 0.3290 E94 +0 35 63 0.2760 E94 +0 36 54 -0.4000 #C94 +0 36 55 -0.4500 #C94 +0 36 56 -0.4500 #C94 +0 36 58 -0.4570 E94 +4 36 58 -0.4500 #C94 +0 36 81 -0.4500 #C94 +0 37 37 0.0000 #C94 +1 37 37 0.0000 #C94 +0 37 38 -0.3100 #C94 +0 37 39 0.0230 E94 +1 37 39 0.0230 E94 +0 37 40 -0.1000 #C94 +0 37 41 0.1790 E94 +0 37 43 -0.1990 E94 +0 37 45 -0.1330 E94 +0 37 46 -0.3020 E94 +0 37 55 -0.3490 E94 +0 37 56 -0.3110 E94 +1 37 57 0.0220 E94 +0 37 58 -0.3610 E94 +1 37 58 -0.3610 E94 +4 37 58 -0.3500 #C94 +0 37 61 -0.1380 E94 +0 37 62 0.0020 E94 +0 37 63 0.0000 #C94 +1 37 63 -0.0530 E94 +0 37 64 0.0000 #C94 +1 37 64 -0.0540 E94 +1 37 67 0.0280 E94 +0 37 69 -0.0895 C94 +0 37 78 -0.0410 E94 +0 37 81 -0.3870 E94 +1 37 81 -0.3870 E94 +0 38 38 0.0000 #C94 +0 38 63 0.2570 E94 +0 38 64 0.2560 E94 +0 38 69 0.3380 E94 +0 38 78 0.2690 E94 +1 39 39 0.0000 #C94 +0 39 40 -0.1600 E94 +0 39 45 -0.1560 E94 +0 39 63 -0.1516 C94 +1 39 63 -0.0760 E94 +0 39 64 -0.0770 E94 +1 39 64 -0.0770 E94 +0 39 65 -0.4180 C94 +0 39 78 -0.0640 E94 +0 40 40 0.0000 #C94 +0 40 45 0.0040 E94 +0 40 46 -0.1650 E94 +0 40 54 -0.1600 E94 +0 40 63 0.0840 E94 +0 40 64 0.0830 E94 +0 40 78 0.0960 E94 +0 41 41 0.0000 #C94 +0 41 55 -0.5280 E94 +0 41 62 -0.1770 E94 +0 41 72 -0.5000 #X94 +0 41 80 -0.1960 E94 +0 42 61 0.4920 E94 +0 43 43 0.0000 #X94 +0 43 45 0.0660 E94 +0 43 64 0.1450 E94 +0 44 63 0.0400 #C94 +0 44 65 -0.2207 C94 +0 44 78 0.0690 E94 +0 44 80 0.0930 E94 +0 45 63 0.0800 E94 +0 45 64 0.0790 E94 +0 45 78 0.0920 E94 +0 47 53 0.3700 #X94 +0 49 50 0.5673 C94 +0 51 52 0.5000 #X94 +0 55 57 0.3544 C94 +0 55 62 0.3510 E94 +0 55 64 0.2950 E94 +0 55 80 0.3320 E94 +0 56 57 0.4000 #C94 +0 56 63 0.2580 E94 +0 56 80 0.2700 E94 +4 57 58 -0.4000 #C94 +1 57 63 -0.0750 E94 +1 57 64 -0.0760 E94 +0 58 63 0.3080 E94 +0 58 64 0.3070 E94 +0 59 63 0.1400 #C94 +0 59 65 -0.1209 C94 +0 59 78 0.1690 E94 +0 59 80 0.1930 E94 +0 59 82 0.2380 E94 +0 60 61 0.3700 #X94 +0 62 63 -0.0550 E94 +0 62 64 -0.0560 E94 +0 63 63 0.0000 #C94 +1 63 63 0.0000 #C94 +0 63 64 0.0000 #C94 +0 63 66 -0.3381 C94 +0 63 72 -0.4000 E94 +0 63 78 0.0120 E94 +0 63 81 -0.3340 E94 +0 64 64 0.0000 #C94 +0 64 65 -0.2888 C94 +0 64 66 -0.2272 C94 +0 64 78 0.0130 E94 +0 64 81 -0.3330 E94 +0 64 82 0.0820 E94 +0 65 66 0.0000 #C94 +0 65 78 0.3070 E94 +0 65 81 -0.0390 E94 +0 65 82 0.3760 E94 +0 66 66 0.0000 #C94 +0 66 78 0.2990 E94 +0 66 81 -0.0470 E94 +0 71 75 -0.0958 X94 +0 72 73 0.4500 #X94 +0 76 76 0.0000 #X94 +0 76 78 0.4000 #X94 +0 78 78 0.0000 #C94 +1 78 78 0.0000 #C94 +0 78 79 -0.3030 E94 +0 78 81 -0.3500 #C94 +0 79 81 -0.0430 E94 +0 80 81 -0.4000 #C94 +$
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/mmffdef.par Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,192 @@ +* +* Copyright (c) Merck and Co., Inc., 1994 +* All Rights Reserved +* +* PRIMARY +* MMFF MMFF +*SYMBOL TYPE DEFAULT TYPES DEFINITION +* + CR 1 1 1 1 0 ALKYL CARBON + C=C 2 2 2 1 0 VINYLIC +* CSP2 2 2 2 1 0 GENERIC CSP2 +* CGD 2 2 2 1 0 GUANIDINE CARBON + C=O 3 3 3 1 0 GENERAL CARBONYL C +* C=N 3 3 3 1 0 C=N +* C=OR 3 3 3 1 0 KETONE OR ALDEHYDE CO +* C=ON 3 3 3 1 0 AMIDE CARBONYL +* COO 3 3 3 1 0 CARBOXYLIC ACID OF EST +* COON 3 3 3 1 0 CARBAMATE CARBONYL +* COOO 3 3 3 1 0 CARBONIC ACID OR ESTER +* C=OS 3 3 3 1 0 THIOESTER, C=O +* C=S 3 3 3 1 0 THIOESTER, C=S +* C=SN 3 3 3 1 0 THIOAMIDE +* CSO2 3 3 3 1 0 CARBON IN >C=SO2 + CSP 4 4 4 1 0 ACETYLENIC C +* =C= 4 4 4 1 0 ALLENIC C + HC 5 5 5 5 0 H-C +* HSI 5 5 5 5 0 H-SI +* HP 5 5 5 5 0 H-P + OR 6 6 6 6 0 O-CSP3 +* OH2 6 6 6 6 0 OXYGEN IN H2O +* OC=O 6 6 6 6 0 ESTER OR ACID -O- +* OC=C 6 6 6 6 0 ENOL OR PHEMOLIC O +* OC=N 6 6 6 6 0 OXYGEN IN -O-C=N MOIETY +* OSO3 6 6 6 6 0 DIVALENT O IN SULFATE +* OSO2 6 6 6 6 0 DIVALENT O IN SULFITE +* OSO 6 6 6 6 0 PAIR OF DIVALENT O ON S +* -OS 6 6 6 6 0 OTHER DIVALENT O ON S +* OPO3 6 6 6 6 0 DIVALENT O IN PHOSPHATE +* OPO2 6 6 6 6 0 DIVALENT O IN PHOSPHITE +* OPO 6 6 6 6 0 PAIR OF DIVALENT O ON P +* -OP 6 6 6 6 0 OTHER DIVALENT O ON P +* -O- 6 6 6 6 0 GENERAL DIVALENT OX + O=C 7 7 7 6 0 O=C, GENERIC +* O=CN 7 7 7 6 0 O=C IN AMIDES +* O=CR 7 7 7 6 0 O=C IN KET, ALD +* O=CO 7 7 7 6 0 O=C IN ACIDS, ESTERS +* O=S 7 7 7 6 0 TERMINAL O SULFOXIDES +* O=N 7 7 7 6 0 NITROSO-GROUP OXYGEN + NR 8 8 8 8 0 AMINE N + N=C 9 9 9 8 0 N=C, IMINES +* N=N 9 9 9 8 0 N=N, AZO COMPOUNDS + NC=O 10 10 10 8 0 N-C=O, AMIDES +* NC=S 10 10 10 8 0 N-C=S (DELOC LP) +* NN=C 10 10 10 8 0 N-N=C (DELOC LP) +* NN=N 10 10 10 8 0 N-N=N (DELOC LP) + F 11 11 11 11 0 FLUORINE + CL 12 12 12 12 0 CHLORINE + BR 13 13 13 13 0 BROMINE + I 14 14 14 14 0 IODINE + S 15 15 15 15 0 THIOL, SULFIDE + S=C 16 16 16 15 0 S DOUBLY BONDED TO C + S=O 17 17 17 15 0 SULFOXIDE S + SO2 18 18 18 15 0 SULFONE S +* SO2N 18 18 18 15 0 SULFONAMIDE S +* SO3 18 18 18 15 0 SULFONATE S +* =SO2 18 18 18 15 0 OXYGENATED SULFONE S +* SNO 18 18 18 15 0 NITROGEN ANALOG OF SO2 + SI 19 19 19 19 0 SILICON + CR4R 20 20 1 1 0 C IN CYCLOBUTYL + HOR 21 21 21 5 0 H-O, ALCOHOLS +* HO 21 21 21 5 0 GENERAL H ON O + CR3R 22 22 22 1 0 C IN CYCLOPROPLY + HNR 23 23 23 5 0 H-N, AMINES +* H3N 23 23 23 5 0 H, AMMONIA +* HPYL 23 23 23 5 0 H-N IN PYRROLE +* HN 23 23 23 5 0 GENERAL H-N + HOCO 24 24 24 5 0 H-O, ACIDS +* HOP 24 21 21 5 0 H-O-P, PHOS ACIDS + PO4 25 25 25 25 0 PHOSPHODIESTER +* PO3 25 25 25 25 0 TETRACRD P, 3 OXYGENS +* PO2 25 25 25 25 0 TETRACRD P, 2 OXYGENS +* PO 25 25 25 25 0 TETRACRD P, 2 OXYGENS +* PTET 25 25 25 25 0 GENERAL TETRACRD P + P 26 26 26 25 0 TRICOORDINATE P + HN=C 27 27 28 5 0 IMINE N-H +* HN=N 27 27 28 5 0 AZO N-H + HNCO 28 28 28 5 0 H-N, AMIDES +* HNCC 28 28 28 5 0 H-N, ENAMINES +* HNCS 28 28 28 5 0 H-N, THIOAMIDES +* HNCN 28 28 28 5 0 H-N, HN-C=N +* HNNC 28 28 28 5 0 H-N, HN-N=C +* HNNN 28 28 28 5 0 H-N, HN-N=N +* HSP2 28 28 28 5 0 GENERAL H ON SP2 N + HOCC 29 29 29 5 0 H-O, ENOLS, PHENOLS +* HOCN 29 29 29 5 0 H-O IN HO-C=N + CE4R 30 30 2 1 0 C=C IN 4-RING + HOH 31 31 31 31 0 H-OH + O2CM 32 32 7 6 0 O, CARBOXYLATE ANION +* OXN 32 32 7 6 0 OXIDE ON NITROHGEN +* O2N 32 32 7 6 0 NITRO-GROUP OXYGEN +* O2NO 32 32 7 6 0 NITRO-GROUP IN NITRATE +* O3N 32 32 7 6 0 NITRATE ANION OXYGEN +* O-S 32 32 7 6 0 SINGLE TERM O ON TET S +* O2S 32 32 7 6 0 SULFONES, SULFONAMIDES +* O3S 32 32 7 6 0 SULFONATES, TERM OX +* O4S 32 32 7 6 0 SO4(3-) +* OSMS 32 32 7 6 0 THIOSULFINATE O (-1/2) +* OP 32 32 7 6 0 TERMINAL O, O-P +* O2P 32 32 7 6 0 TERMINAL O, O2P GROUP +* O3P 32 32 7 6 0 TERMINAL O, O3P GROUP +* O4P 32 32 7 6 0 TERMINAL O, PO4(-3) +* O4CL 32 32 7 6 0 TERMINAL O IN CLO4(-) + HOS 33 33 21 5 0 H-O-S, SULF ACIDS + NR+ 34 34 8 8 0 N+, QUATERNARY N + OM 35 35 6 6 0 OXIDE OXYGEN ON SP3 C +* OM2 35 35 6 6 0 OXIDE OXYGEN ON SP2 C + HNR+ 36 36 36 5 0 H-N+ +* HNN+ 36 36 36 5 0 H ON IMIDAZOLIUM N +* HNC+ 36 36 36 5 0 H ON PROTONATED N+=C-N +* HGD+ 36 36 36 5 0 H ON GUANIDINIUM N + CB 37 37 2 1 0 AROMATIC C + NPYD 38 38 9 8 0 AROMATIC N, PYRIDINE + NPYL 39 39 10 8 0 AROMATIC N, PYRROLE + NC=C 40 40 10 8 0 N-C=C (DELOC LP) +* NC=N 40 40 10 8 0 N-C=N (DELOC LP) + CO2M 41 41 3 1 0 C IN CO2- ANION +* CS2M 41 41 3 1 0 THIOCARBOXYLATE C + NSP 42 42 42 8 0 N TRIPLE BONDED + NSO2 43 43 10 8 0 N, SULFONAMIDES + STHI 44 44 16 15 0 S IN THIOPHENE + NO2 45 45 10 8 0 NITRO GROUP N +* NO3 45 45 10 8 0 NITRATE GROUP N + N=O 46 46 9 8 0 NITROSO GROUP N + NAZT 47 47 42 8 0 TERMINAL N, AZIDE + NSO 48 48 9 8 0 DIVAL. N IN S(N)(O) GP + O+ 49 49 6 6 0 OXONIUM (TRICOORD) O + HO+ 50 50 21 5 0 H ON OXONIUM OXYGEN + O=+ 51 51 7 6 0 OXENIUM OXYGEN+ + HO=+ 52 52 21 5 0 H ON OXENIUM O+ + =N= 53 53 42 8 0 N TWICE DOUBLE BONDED + N+=C 54 54 9 8 0 IMINIUM NITROGEN +* N+=N 54 54 9 8 0 AZONIUM NITROGEN + NCN+ 55 55 10 8 0 N IN +N=C-N: ; Q=1/2 + NGD+ 56 56 10 8 0 GUANIDINIUM N; Q=1/3 + CGD+ 57 57 2 1 0 GUANIDINIUM CARBON +* CNN+ 57 57 2 1 0 C IN +N=C-N RESONANCE + NPD+ 58 58 10 8 0 N PYRIDINIUM ION + OFUR 59 59 6 6 0 AROMATIC O, FURAN + C% 60 60 4 1 0 ISONITRILE CARBON + NR% 61 61 42 8 0 ISONITRILE N + NM 62 62 10 8 0 SULFONAMIDE N- + C5A 63 63 2 1 0 ALPHA AROM 5-RING C + C5B 64 64 2 1 0 BETA AROM 5-RING C + N5A 65 65 9 8 0 ALPHA AROM 5-RING N + N5B 66 66 9 8 0 ALPHA AROM 5-RING N + N2OX 67 67 9 8 0 NITROGEN IN N-OXIDE + N3OX 68 68 8 8 0 NITROGEN IN N-OXIDE + NPOX 69 69 9 8 0 NITROGEN IN N-OXIDE + OH2 70 70 70 70 70 OXYGEN IN WATER + HS 71 71 5 5 0 H-S + S2CM 72 72 16 15 0 THIOCARBOXYLATE S +* S-P 72 72 16 15 0 TERMINAL SULFUR ON P +* SM 72 72 16 15 0 TERMINAL SULFUR ON C +* SSMO 72 72 16 15 0 TERM S, THIOSULFINATE + SO2M 73 73 18 15 0 SULFUR IN SULFINATE +* SSOM 73 73 18 15 0 SULFUR, THIOSULFINATE + =S=O 74 74 17 15 0 SULFINYL SULFUR, C=S=O + -P=C 75 75 26 25 0 P DOUBLY BONDED TO C + N5M 76 76 9 8 0 NEG N IN TETRAZOLE AN + CLO4 77 77 12 12 0 CHLORINE IN CLO4(-) + C5 78 78 2 1 0 GENERAL AROM 5-RING C + N5 79 79 9 8 0 GENERAL AROM 5-RING N + CIM+ 80 80 2 1 0 C IN N-C-N, IM+ ION + NIM+ 81 81 10 8 0 N IN N-C-N, IM+ ION + N5AX 82 82 9 8 0 5R NITROGEN IN N-OXIDE +* N5BX 82 82 9 8 0 5R NITROGEN IN N-OXIDE +* N5OX 82 82 9 8 0 5R NITROGEN IN N-OXIDE + FE+2 87 87 87 87 87 IRON +2 CATION + FE+3 88 88 88 88 88 IRON +3 CATION + F- 89 89 89 89 89 FLUORIDE ANION + CL- 90 90 90 90 90 CHLORIDE ANION + BR- 91 91 91 91 91 BROMIDE ANION + LI+ 92 92 92 92 92 LITHIUM CATION + NA+ 93 93 93 93 93 SODIUM CATION + K+ 94 94 94 94 94 POTASSIUM CATION + ZN+2 95 95 95 95 95 DIPOSITIVE ZINC CATION +* ZINC 95 95 95 95 95 DIPOSITIVE ZINC CATION + CA+2 96 96 96 96 96 DIPOSITIVE CALCIUM CATION + CU+1 97 97 97 97 97 MONOPOSITIVE COPPER CATION + CU+2 98 98 98 98 98 DIPOSITIVE COPPER CATION + MG+2 99 99 99 99 99 DIPOSITIVE MAGNESIUM CATION +$
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/mmffdfsb.par Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,39 @@ +* +* Copyright (c) Merck and Co., Inc., 1994 +* All Rights Reserved +* +* MMFF Default Stretch-Bend Parameters +* Row in +* Periodic Table +* IR JR KR F(I_J,K) F(K_J,I) + 0 1 0 0.15 0.15 + 0 1 1 0.10 0.30 + 0 1 2 0.05 0.35 + 0 1 3 0.05 0.35 + 0 1 4 0.05 0.35 + 0 2 0 0.00 0.00 + 0 2 1 0.00 0.15 + 0 2 2 0.00 0.15 + 0 2 3 0.00 0.15 + 0 2 4 0.00 0.15 + 1 1 1 0.30 0.30 + 1 1 2 0.30 0.50 + 1 1 3 0.30 0.50 + 1 1 4 0.30 0.50 + 2 1 2 0.50 0.50 + 2 1 3 0.50 0.50 + 2 1 4 0.50 0.50 + 3 1 3 0.50 0.50 + 3 1 4 0.50 0.50 + 4 1 4 0.50 0.50 + 1 2 1 0.30 0.30 + 1 2 2 0.25 0.25 + 1 2 3 0.25 0.25 + 1 2 4 0.25 0.25 + 2 2 2 0.25 0.25 + 2 2 3 0.25 0.25 + 2 2 4 0.25 0.25 + 3 2 3 0.25 0.25 + 3 2 4 0.25 0.25 + 4 2 4 0.25 0.25 +$
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/mmffoop.par Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,127 @@ +* +* Copyright (c) Merck and Co., Inc., 1994 +* All Rights Reserved +* +* MMFF OUT-OF-PLANE PARAMETERS- Rev: 15-OCT-93 Source: MMFF94 +* C94 - CORE MMFF94 parameter, from fits to HF/6-31G* 2nd D's +* #C94 - Value adjusted from CORE MMFF93 value +* +* MMFF atom types koop Source + 1 2 1 2 0.030 C94 + 1 2 2 2 0.027 C94 + 1 2 2 3 0.026 C94 + 1 2 2 5 0.013 C94 + 1 2 2 37 0.032 C94 + 2 2 2 5 0.013 C94 + 2 2 3 5 0.012 C94 + 2 2 5 5 0.006 C94 + 2 2 5 6 0.027 C94 + 2 2 5 37 0.017 C94 + 2 2 5 40 0.012 C94 + 2 2 5 41 0.008 C94 + 0 2 0 0 0.020 *-2-*-* C94 DEF + 1 3 1 7 0.146 C94 + 1 3 2 7 0.138 C94 + 1 3 3 7 0.134 C94 + 1 3 5 7 0.122 C94 + 1 3 6 7 0.141 C94 + 1 3 7 10 0.129 C94 + 1 3 7 37 0.138 C94 + 2 3 5 7 0.113 C94 + 2 3 5 9 0.081 C94 + 2 3 6 7 0.127 C94 + 2 3 7 10 0.116 C94 + 3 3 5 7 0.113 C94 + 3 3 6 7 0.127 C94 + 5 3 5 7 0.103 C94 + 5 3 5 9 0.074 C94 + 5 3 5 54 0.078 C94 + 5 3 6 7 0.119 C94 + 5 3 7 10 0.102 C94 + 5 3 9 40 0.067 C94 + 6 3 7 37 0.127 C94 + 7 3 10 10 0.113 C94 + 7 3 20 20 0.151 C94 + 9 3 40 40 0.057 C94 + 0 3 0 0 0.130 *-3-*-* C94 DEF + 0 8 0 0 0.000 *-8-*-* C94 DEF + 1 10 1 3 -0.02 #C94 (C93=-0.034) + 1 10 3 6 -0.033 C94 + 1 10 3 28 -0.02 #C94 (C93=-0.030) + 3 10 3 28 -0.030 C94 + 3 10 28 28 -0.019 C94 + 0 10 0 0 -0.020 *-10-*-* C94 DEF + 0 17 0 0 0.000 *-17-*-* E94 DEF + 0 26 0 0 0.000 *-26-*-* CE4 DEF + 5 30 20 30 0.008 C94 + 0 30 0 0 0.010 *-30-*-* C94 DEF + 1 37 37 37 0.040 C94 + 2 37 37 37 0.031 C94 + 3 37 37 37 0.027 C94 + 5 37 37 37 0.015 C94 + 5 37 37 38 0.046 C94 + 5 37 37 63 0.008 C94 + 5 37 37 64 0.012 C94 + 5 37 37 69 0.016 C94 + 5 37 38 38 0.084 C94 + 6 37 37 37 0.048 C94 + 15 37 37 37 0.025 C94 + 37 37 37 40 0.046 C94 + 0 37 0 0 0.035 *-37-*-* C94 DEF + 1 39 63 63 0.012 C94 + 23 39 63 63 -0.014 C94 + 23 39 63 65 0.021 C94 + 23 39 65 65 0.062 C94 + 0 39 0 0 0.020 *-39-*-* C94 DEF + 1 40 28 37 -0.006 C94 + 2 40 28 28 -0.007 C94 + 3 40 28 28 -0.007 C94 + 28 40 28 37 0.004 C94 + 0 40 0 0 -0.005 *-40-*-* C94 DEF + 1 41 32 32 0.178 C94 + 2 41 32 32 0.161 C94 + 5 41 32 32 0.158 C94 + 0 41 0 0 0.180 *-41-*-* C94 DEF + 0 43 0 0 0.000 *-43-*-* E94 DEF + 0 45 0 0 0.150 *-45-*-* E94 DEF + 50 49 50 50 0.000 #C94 + 0 49 0 0 0.000 *-49-*-* E94 DEF + 1 54 3 36 0.016 C94 + 3 54 36 36 0.018 C94 + 0 54 0 0 0.020 *-54-*-* C94 DEF + 1 55 36 57 0.020 #C94 + 36 55 36 57 0.020 #C94 + 0 55 0 0 0.020 *-55-*-* C94 DEF + 1 56 36 57 0.020 #C94 + 36 56 36 57 0.020 #C94 + 0 56 0 0 0.020 *-56-*-* C94 DEF + 5 57 55 55 0.038 C94 + 56 57 56 56 0.158 C94 + 0 57 0 0 0.080 *-57-*-* C94 DEF + 0 58 0 0 0.025 *-58-*-* E94 DEF + 5 63 39 64 0.019 C94 + 5 63 39 66 0.068 C94 + 5 63 44 64 0.014 C94 + 5 63 44 66 0.055 C94 + 5 63 59 64 0.033 C94 + 5 63 59 66 0.085 C94 + 37 63 39 64 0.010 C94 + 0 63 0 0 0.050 *-63-*-* C94 DEF + 5 64 63 64 0.006 C94 + 5 64 63 66 0.043 C94 + 5 64 64 65 0.052 C94 + 5 64 65 66 0.094 C94 + 37 64 63 64 -0.011 C94 + 0 64 0 0 0.040 *-64-*-* C94 DEF + 0 67 0 0 0.070 *-67-*-* E94 DEF + 32 69 37 37 0.067 C94 + 0 69 0 0 0.070 *-69-*-* C94 DEF + 0 73 0 0 0.000 *-73-*-* E94 DEF + 5 78 78 81 0.046 C94 + 0 78 0 0 0.045 *-78-*-* C94 DEF + 5 80 81 81 0.057 C94 + 0 80 0 0 0.080 *-80-*-* C94 DEF + 36 81 78 80 0.016 C94 + 0 81 0 0 0.025 *-81-*-* C94 DEF + 0 82 0 0 0.000 *-82-*-* E94 DEF +$
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/mmffpbci.par Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,106 @@ +* +* Copyright (c) Merck and Co., Inc., 1994 +* All Rights Reserved +* +* MMFF Partial Bond Charge Incs and Formal-Charge Adj. Factors: 19-MAY-1994 +* +* type pbci fcadj Origin/Comment +0 1 0.000 0.000 Fitted default +0 2 -0.135 0.000 Fitted default +0 3 -0.095 0.000 Fitted default +0 4 -0.200 0.000 Fitted default +0 5 -0.023 0.000 Fitted default +0 6 -0.243 0.000 Fitted default +0 7 -0.687 0.000 Fitted default +0 8 -0.253 0.000 Fitted default +0 9 -0.306 0.000 Fitted default +0 10 -0.244 0.000 Fitted default +0 11 -0.317 0.000 Fitted default +0 12 -0.304 0.000 Fitted default +0 13 -0.238 0.000 Fitted default +0 14 -0.208 0.000 Fitted default +0 15 -0.236 0.000 Fitted default +0 16 -0.475 0.000 Fitted default +0 17 -0.191 0.000 Fitted default +0 18 -0.118 0.000 Fitted default +0 19 0.094 0.000 Fitted default +0 20 -0.019 0.000 Fitted default +0 21 0.157 0.000 Fitted default +0 22 -0.095 0.000 Fitted default +0 23 0.193 0.000 Fitted default +0 24 0.257 0.000 Fitted default +0 25 0.012 0.000 Fitted default +0 26 -0.142 0.000 Fitted default +0 27 0.094 0.000 Fitted default +0 28 0.058 0.000 Fitted default +0 29 0.207 0.000 Fitted default +0 30 -0.166 0.000 Fitted default +0 31 0.161 0.000 Fitted default +0 32 -0.732 0.500 Fitted default +0 33 0.257 0.000 Fitted default +0 34 -0.491 0.000 Fitted default +0 35 -0.456 0.500 Fitted default +0 36 -0.031 0.000 Fitted default +0 37 -0.127 0.000 Fitted default +0 38 -0.437 0.000 Fitted default +0 39 -0.104 0.000 Fitted default +0 40 -0.264 0.000 Fitted default +0 41 0.052 0.000 Fitted default +0 42 -0.757 0.000 Fitted default +0 43 -0.326 0.000 Fitted default +0 44 -0.237 0.000 Fitted default +0 45 -0.260 0.000 Fitted default +0 46 -0.429 0.000 Fitted default +0 47 -0.418 0.000 Fitted default +0 48 -0.525 0.000 Fitted default +0 49 -0.283 0.000 Fitted default +0 50 0.284 0.000 Fitted default +0 51 -1.046 0.000 Fitted default +0 52 -0.546 0.000 Fitted default +0 53 -0.048 0.000 Fitted default +0 54 -0.424 0.000 Fitted default +0 55 -0.476 0.000 Fitted default +0 56 -0.438 0.000 Fitted default +0 57 -0.105 0.000 Fitted default +0 58 -0.488 0.000 Fitted default +0 59 -0.337 0.000 Fitted default +0 60 -0.635 0.000 Fitted default +0 61 -0.265 0.000 Fitted default +0 62 -0.125 0.250 Fitted default +0 63 -0.180 0.000 Fitted default +0 64 -0.181 0.000 Fitted default +0 65 -0.475 0.000 Fitted default +0 66 -0.467 0.000 Fitted default +0 67 -0.099 0.000 == 69 +0 68 -0.135 0.000 Fitted default +0 69 -0.099 0.000 Fitted default +0 70 -0.269 0.000 Fitted default +0 71 -0.071 0.000 Fitted default +0 72 -0.580 0.500 Fitted default +0 73 -0.200 0.000 Fitted default +0 74 -0.301 0.000 Fitted default +0 75 -0.255 0.000 Fitted default +0 76 -0.568 0.250 Fitted default +0 77 -0.282 0.000 Fitted default +0 78 -0.168 0.000 Fitted default +0 79 -0.471 0.000 == (65+66)/2 +0 80 -0.144 0.000 Fitted default +0 81 -0.514 0.000 Fitted default +0 82 -0.099 0.000 == 69 +0 83 0.000 0.000 Unused +0 84 0.000 0.000 Unused +0 85 0.000 0.000 Unused +0 86 0.000 0.000 Unused +0 87 0.000 0.000 Unused +0 88 0.000 0.000 Unused +0 89 0.000 0.000 Unused +0 90 0.000 0.000 Unused +0 91 0.000 0.000 Unused +0 92 1.000 0.000 Ionic charge +0 93 1.000 0.000 Ionic charge +0 94 1.000 0.000 Ionic charge +0 95 2.000 0.000 Ionic charge +0 96 2.000 0.000 Ionic charge +0 97 1.000 0.000 Ionic charge +0 98 2.000 0.000 Ionic charge +$
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/mmffprop.par Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,103 @@ +* +* Copyright (c) Merck and Co., Inc., 1993 +* All Rights Reserved +* +* MMFFPROP - MMFF atom-type properties +* +* atype aspec crd val pilp mltb arom lin sbmb + 1 6 4 4 0 0 0 0 0 + 2 6 3 4 0 2 0 0 1 + 3 6 3 4 0 2 0 0 1 + 4 6 2 4 0 3 0 1 1 + 5 1 1 1 0 0 0 0 0 + 6 8 2 2 1 0 0 0 0 + 7 8 1 2 0 2 0 0 0 + 8 7 3 3 1 0 0 0 0 + 9 7 2 3 0 2 0 0 1 + 10 7 3 3 1 1 0 0 0 + 11 9 1 1 1 0 0 0 0 + 12 17 1 1 1 0 0 0 0 + 13 35 1 1 1 0 0 0 0 + 14 53 1 1 1 0 0 0 0 + 15 16 2 2 1 0 0 0 0 + 16 16 1 2 0 2 0 0 0 + 17 16 3 4 0 2 0 0 0 + 18 16 4 4 0 0 0 0 0 + 19 14 4 4 0 0 0 0 0 + 20 6 4 4 0 0 0 0 0 + 21 1 1 1 0 0 0 0 0 + 22 6 4 4 0 0 0 0 0 + 23 1 1 1 0 0 0 0 0 + 24 1 1 1 0 0 0 0 0 + 25 15 4 4 0 0 0 0 0 + 26 15 3 3 1 0 0 0 0 + 27 1 1 1 0 0 0 0 0 + 28 1 1 1 0 0 0 0 0 + 29 1 1 1 0 0 0 0 0 + 30 6 3 4 0 2 0 0 1 + 31 1 1 1 0 0 0 0 0 + 32 8 1 12 1 1 0 0 0 + 33 1 1 1 0 0 0 0 0 + 34 7 4 4 0 0 0 0 0 + 35 8 1 1 1 1 0 0 0 + 36 1 1 1 0 0 0 0 0 + 37 6 3 4 0 2 1 0 1 + 38 7 2 3 0 2 1 0 0 + 39 7 3 3 1 1 1 0 1 + 40 7 3 3 1 0 0 0 0 + 41 6 3 4 0 1 0 0 0 + 42 7 1 3 0 3 0 0 0 + 43 7 3 3 1 0 0 0 0 + 44 16 2 2 1 1 1 0 0 + 45 7 3 4 0 2 0 0 0 + 46 7 2 3 0 2 0 0 0 + 47 7 1 2 0 2 0 0 0 + 48 7 2 2 0 0 0 0 0 + 49 8 3 3 0 0 0 0 0 + 50 1 1 1 0 0 0 0 0 + 51 8 2 3 0 2 0 0 0 + 52 1 1 1 0 0 0 0 0 + 53 7 2 4 0 2 0 1 0 + 54 7 3 4 0 2 0 0 1 + 55 7 3 34 0 1 0 0 0 + 56 7 3 34 0 1 0 0 0 + 57 6 3 4 0 2 0 0 1 + 58 7 3 4 0 1 1 0 1 + 59 8 2 2 1 1 1 0 0 + 60 6 1 3 0 3 0 0 0 + 61 7 2 4 0 3 0 1 0 + 62 7 2 2 1 0 0 0 0 + 63 6 3 4 0 2 1 0 1 + 64 6 3 4 0 2 1 0 1 + 65 7 2 3 0 2 1 0 0 + 66 7 2 3 0 2 1 0 0 + 67 7 3 4 0 2 0 0 1 + 68 7 4 4 0 0 0 0 0 + 69 7 3 4 0 1 1 0 0 + 70 8 2 2 1 0 0 0 0 + 71 1 1 1 0 0 0 0 0 + 72 16 1 1 1 1 0 0 0 + 73 16 3 3 0 0 0 0 0 + 74 16 2 4 0 2 0 0 0 + 75 15 2 3 0 2 0 0 1 + 76 7 2 2 1 0 0 0 0 + 77 17 4 4 0 0 0 0 0 + 78 6 3 4 0 2 1 0 1 + 79 7 2 3 0 2 1 0 0 + 80 6 3 4 0 2 0 0 1 + 81 7 3 4 0 1 1 0 1 + 82 7 3 4 0 1 1 0 0 + 87 26 0 0 0 0 0 0 0 + 88 26 0 0 0 0 0 0 0 + 89 9 0 0 0 0 0 0 0 + 90 17 0 0 0 0 0 0 0 + 91 35 0 0 0 0 0 0 0 + 92 3 0 0 0 0 0 0 0 + 93 11 0 0 0 0 0 0 0 + 94 19 0 0 0 0 0 0 0 + 95 30 0 0 0 0 0 0 0 + 96 20 0 0 0 0 0 0 0 + 97 29 0 0 0 0 0 0 0 + 98 29 0 0 0 0 0 0 0 + 99 12 0 0 0 0 0 0 0 +$
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/mmffs_oop.par Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,128 @@ +* +* Copyright (c) Merck and Co., Inc., 1994,1995,1996,1997,1998,1999 +* All Rights Reserved +* +* MMFF94s OUT-OF-PLANE PARAMETERS +* C94 - CORE MMFF94 parameter, from fits to HF/6-31G* 2nd D's +* C94S - CORE MMFF94s parameter,adjusted to promote planarity +* #C94 - Value adjusted from CORE MMFF94 value +* +* MMFF atom types koop Source + 0 2 0 0 0.020 *-2-*-* C94 DEF + 1 2 1 2 0.030 C94 + 1 2 2 2 0.027 C94 + 1 2 2 3 0.026 C94 + 1 2 2 5 0.013 C94 + 1 2 2 37 0.032 C94 + 2 2 2 5 0.013 C94 + 2 2 3 5 0.012 C94 + 2 2 5 5 0.006 C94 + 2 2 5 6 0.027 C94 + 2 2 5 37 0.017 C94 + 2 2 5 40 0.012 C94 + 2 2 5 41 0.008 C94 + 0 3 0 0 0.130 *-3-*-* C94 DEF + 1 3 1 7 0.146 C94 + 1 3 2 7 0.138 C94 + 1 3 3 7 0.134 C94 + 1 3 5 7 0.122 C94 + 1 3 6 7 0.141 C94 + 1 3 7 10 0.129 C94 + 1 3 7 37 0.138 C94 + 2 3 5 7 0.113 C94 + 2 3 5 9 0.081 C94 + 2 3 6 7 0.127 C94 + 2 3 7 10 0.116 C94 + 3 3 5 7 0.113 C94 + 3 3 6 7 0.127 C94 + 5 3 5 7 0.103 C94 + 5 3 5 9 0.074 C94 + 5 3 5 54 0.078 C94 + 5 3 6 7 0.119 C94 + 5 3 7 10 0.102 C94 + 5 3 9 40 0.067 C94 + 6 3 7 37 0.127 C94 + 7 3 10 10 0.113 C94 + 7 3 20 20 0.151 C94 + 9 3 40 40 0.057 C94 + 0 8 0 0 0.000 *-8-*-* C94 DEF + 0 10 0 0 0.015 *-10-*-* C94S DEF + 1 10 1 3 0.015 C94S + 1 10 3 6 0.015 C94 + 1 10 3 28 0.015 C94S + 3 10 3 28 0.015 C94S + 3 10 28 28 0.015 C94S + 0 17 0 0 0.000 *-17-*-* E94 DEF + 0 26 0 0 0.000 *-26-*-* CE4 DEF + 0 30 0 0 0.010 *-30-*-* C94 DEF + 5 30 20 30 0.008 C94 + 0 37 0 0 0.035 *-37-*-* C94 DEF + 1 37 37 37 0.040 C94 + 2 37 37 37 0.031 C94 + 3 37 37 37 0.027 C94 + 5 37 37 37 0.015 C94 + 5 37 37 38 0.046 C94 + 5 37 37 63 0.008 C94 + 5 37 37 64 0.012 C94 + 5 37 37 69 0.016 C94 + 5 37 38 38 0.084 C94 + 6 37 37 37 0.048 C94 + 15 37 37 37 0.025 C94 + 37 37 37 40 0.046 C94 + 0 39 0 0 0.020 *-39-*-* C94 DEF + 1 39 63 63 0.012 C94 + 23 39 63 63 -0.014 C94 + 23 39 63 65 0.021 C94 + 23 39 65 65 0.062 C94 + 0 40 0 0 0.030 *-40-*-* C94S DEF + 1 40 28 37 0.030 C94S + 2 40 28 28 0.030 C94S + 3 40 28 28 0.030 C94S + 28 40 28 37 0.030 C94S + 0 41 0 0 0.180 *-41-*-* C94 DEF + 1 41 32 32 0.178 C94 + 2 41 32 32 0.161 C94 + 5 41 32 32 0.158 C94 + 0 43 0 0 0.000 *-43-*-* E94 DEF + 0 45 0 0 0.150 *-45-*-* E94 DEF + 0 49 0 0 0.000 *-49-*-* E94 DEF + 50 49 50 50 0.000 #C94 + 0 54 0 0 0.020 *-54-*-* C94 DEF + 1 54 3 36 0.016 C94 + 3 54 36 36 0.018 C94 + 0 55 0 0 0.020 *-55-*-* C94 DEF + 1 55 36 57 0.020 #C94 + 36 55 36 57 0.020 #C94 + 0 56 0 0 0.020 *-56-*-* C94 DEF + 1 56 36 57 0.020 #C94 + 36 56 36 57 0.020 #C94 + 0 57 0 0 0.080 *-57-*-* C94 DEF + 5 57 55 55 0.038 C94 + 56 57 56 56 0.158 C94 + 0 58 0 0 0.025 *-58-*-* E94 DEF + 0 63 0 0 0.050 *-63-*-* C94 DEF + 5 63 39 64 0.019 C94 + 5 63 39 66 0.068 C94 + 5 63 44 64 0.014 C94 + 5 63 44 66 0.055 C94 + 5 63 59 64 0.033 C94 + 5 63 59 66 0.085 C94 + 37 63 39 64 0.010 C94 + 0 64 0 0 0.040 *-64-*-* C94 DEF + 5 64 63 64 0.006 C94 + 5 64 63 66 0.043 C94 + 5 64 64 65 0.052 C94 + 5 64 65 66 0.094 C94 + 37 64 63 64 -0.011 C94 + 0 67 0 0 0.070 *-67-*-* E94 DEF + 0 69 0 0 0.070 *-69-*-* C94 DEF + 32 69 37 37 0.067 C94 + 0 73 0 0 0.000 *-73-*-* E94 DEF + 0 78 0 0 0.045 *-78-*-* C94 DEF + 5 78 78 81 0.046 C94 + 0 80 0 0 0.080 *-80-*-* C94 DEF + 5 80 81 81 0.057 C94 + 0 81 0 0 0.025 *-81-*-* C94 DEF + 36 81 78 80 0.016 C94 + 0 82 0 0 0.000 *-82-*-* E94 DEF +$
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/mmffs_tor.par Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,939 @@ +* +* Copyright (c) Merck and Co., Inc., 1994,1995,1996,1997,1998,1999 +* All Rights Reserved +* +* MMFF94s TORSION PARAMETERS +* C94 - CORE MMFF94 parameter - from fits to conformational energies +* C94S - CORE MMFF94s parameter - from fits to conformational energies +* X94 - EXTD MMFF94 parameter - also from fits to conformational E's +* E94 - EXTD MMFF94 parameter - from empirical rule +* #E94 - Adjusted from empirical rule value +* +* atom types V1 V2 V3 Source +0 0 1 1 0 0.000 0.000 0.300 C94 0:*-1-1-* Def +5 0 1 1 0 0.200 -0.800 1.500 C94 5:*-1-1-* Def +0 1 1 1 1 0.103 0.681 0.332 C94 +5 1 1 1 1 0.144 -0.547 1.126 C94 +0 1 1 1 2 -0.295 0.438 0.584 C94 +0 1 1 1 3 0.066 -0.156 0.143 C94 +0 1 1 1 5 0.639 -0.630 0.264 C94 +0 1 1 1 6 -0.688 1.757 0.477 C94 +5 1 1 1 6 0.000 0.000 0.054 C94 +0 1 1 1 8 -1.420 -0.092 1.101 C94 +5 1 1 1 8 0.000 -0.158 0.323 C94 +0 1 1 1 11 0.593 0.662 1.120 C94 +0 1 1 1 12 -0.678 0.417 0.624 C94 +0 1 1 1 15 -0.714 0.698 0.000 C94 +0 1 1 1 34 -0.647 0.550 0.590 C94 +0 2 1 1 5 0.321 -0.411 0.144 C94 +0 3 1 1 3 0.443 0.000 -1.140 C94 +0 3 1 1 5 -0.256 0.058 0.000 C94 +0 3 1 1 6 -0.679 -0.029 0.000 C94 +0 5 1 1 5 0.284 -1.386 0.314 C94 +0 5 1 1 6 -0.654 1.072 0.279 C94 +0 5 1 1 8 -0.744 -1.235 0.337 C94 +0 5 1 1 10 0.000 0.000 0.418 C94S +0 5 1 1 11 0.000 0.516 0.291 C94 +0 5 1 1 12 0.678 -0.602 0.398 C94 +0 5 1 1 15 1.142 -0.644 0.367 C94 +0 5 1 1 25 0.000 0.000 0.295 X94 +0 5 1 1 34 0.692 -0.530 0.278 C94 +0 5 1 1 37 0.000 0.000 0.389 C94 +0 5 1 1 39 0.000 0.000 0.278 C94 +0 5 1 1 41 0.000 0.000 -0.141 C94 +0 5 1 1 56 0.000 0.000 0.324 C94 +0 5 1 1 68 0.000 0.000 0.136 C94 +0 6 1 1 6 0.408 1.397 0.961 C94 +5 6 1 1 6 0.313 -1.035 1.631 C94 +0 8 1 1 8 1.055 0.834 0.000 C94 +0 11 1 1 11 -0.387 -0.543 1.405 C94 +0 12 1 1 12 0.000 0.000 0.893 C94 +0 15 1 1 15 -0.177 0.000 0.049 C94 +0 0 1 2 0 0.000 0.000 0.000 C94 0:*-1-2-* Def +2 0 1 2 0 0.000 0.000 0.000 E94 2:*1-2-* Def +5 0 1 2 0 0.000 0.000 0.000 C94 5:*-1-2-* Def +0 0 1 2 2 0.000 0.000 -0.650 C94 0:*-1-2=2 Def +5 0 1 2 2 0.000 0.000 -0.650 C94 5:*-1-2=2 Def +0 1 1 2 1 0.419 0.296 0.282 C94 +0 1 1 2 2 -0.494 0.274 -0.630 C94 +0 1 1 2 5 0.075 0.000 0.358 C94 +0 2 1 2 2 -0.293 0.115 -0.508 C94 +0 2 1 2 5 0.301 0.104 0.507 C94 +0 3 1 2 1 0.565 -0.554 0.234 C94 +0 3 1 2 2 -0.577 -0.482 -0.427 C94 +0 3 1 2 5 0.082 0.000 0.123 C94 +0 5 1 2 1 0.000 -0.184 0.220 C94 +0 5 1 2 2 0.501 -0.410 -0.535 C94 +2 5 1 2 2 0.000 0.000 0.055 C94 +2 5 1 2 3 0.000 0.000 -0.108 C94 +0 5 1 2 5 -0.523 -0.228 0.208 C94 +2 5 1 2 37 0.000 0.000 0.000 C94 +0 6 1 2 1 -0.467 0.000 0.490 C94 +0 6 1 2 2 0.425 0.168 -0.875 C94 +0 6 1 2 5 0.000 0.136 0.396 C94 +0 8 1 2 1 -0.504 0.371 0.557 C94 +0 8 1 2 2 0.541 0.539 -1.009 C94 +0 8 1 2 5 0.000 0.204 0.464 C94 +0 0 1 3 0 0.000 0.400 0.300 C94 0:*-1-3-* Def +2 0 1 3 0 0.000 0.500 0.350 C94 2:*-1-3-* Def +5 0 1 3 0 0.000 0.000 0.000 E94 5:*1-3-* Def +0 0 1 3 1 0.000 0.000 0.550 C94 0:*-1-3-1 Def +0 0 1 3 5 0.000 0.200 0.700 C94 0:*-1-3-5 Def +0 0 1 3 7 0.000 0.400 0.400 C94 0:*-1-3-7 Def +0 1 1 3 1 0.103 0.177 0.545 C94 +0 1 1 3 5 -0.072 0.316 0.674 C94 +0 1 1 3 6 -0.117 -0.333 0.202 C94 +0 1 1 3 7 0.825 0.139 0.325 C94 +0 1 1 3 10 -0.763 1.244 0.986 C94S +0 2 1 3 5 0.663 -0.167 0.426 C94 +0 2 1 3 7 -0.758 0.112 0.563 C94 +0 5 1 3 1 -0.073 0.085 0.531 C94 +2 5 1 3 2 0.000 0.000 0.115 C94 +2 5 1 3 3 0.000 0.000 0.446 C94 +0 5 1 3 5 -0.822 0.501 1.008 C94 +0 5 1 3 6 0.000 -0.624 0.330 C94 +0 5 1 3 7 0.659 -1.407 0.308 C94 +0 5 1 3 10 -0.687 1.244 0.136 C94S +2 5 1 3 37 0.000 0.000 0.056 C94 +0 5 1 3 43 0.000 1.027 0.360 X94 +0 5 1 3 51 0.000 1.543 0.350 X94 +0 5 1 3 53 0.000 0.501 0.000 X94 +0 5 1 3 74 0.000 0.513 -0.344 X94 +0 5 1 3 75 0.000 0.511 -0.186 X94 +0 6 1 3 6 0.447 0.652 0.318 C94 +0 6 1 3 7 -0.395 0.730 -0.139 C94 +0 10 1 3 7 0.530 2.905 2.756 C94S +0 10 1 3 10 0.465 -0.241 1.850 C94S +0 0 1 4 0 0.000 0.000 0.000 C94 0:*-1-4-* Def +0 0 1 6 0 0.000 0.000 0.200 C94 0:*-1-6-* Def +5 0 1 6 0 0.000 -0.200 0.400 C94 5:*-1-6-* Def +0 1 1 6 1 -0.681 0.755 0.755 C94 +5 1 1 6 1 0.000 0.243 -0.596 C94 +0 1 1 6 3 -0.547 0.000 0.320 C94 +0 1 1 6 21 0.000 0.270 0.237 C94 +0 2 1 6 21 0.102 0.460 -0.128 C94 +0 3 1 6 21 -1.652 -1.660 0.283 C94 +0 5 1 6 1 0.571 0.319 0.570 C94 +0 5 1 6 2 0.000 0.000 0.306 C94 +0 5 1 6 3 0.572 0.000 -0.304 C94 +0 5 1 6 21 0.596 -0.276 0.346 C94 +0 5 1 6 25 0.000 0.000 0.061 X94 +0 5 1 6 37 0.000 0.000 0.106 C94 +0 5 1 6 45 0.000 0.000 -0.174 X94 +0 6 1 6 1 0.229 -0.710 0.722 C94 +5 6 1 6 1 0.000 0.000 0.040 C94 +0 6 1 6 21 1.488 -3.401 -0.320 C94 +0 37 1 6 21 0.712 1.320 -0.507 C94 +0 0 1 8 0 0.000 -0.300 0.500 C94 0:*-1-8-* Def +5 0 1 8 0 0.000 0.000 0.297 E94 5:*1-8-* Def +0 1 1 8 1 -0.439 0.786 0.272 C94 +5 1 1 8 1 0.115 -0.390 0.658 C94 +0 1 1 8 6 -0.608 0.339 1.496 C94 +0 1 1 8 23 -0.428 0.323 0.280 C94 +0 2 1 8 23 0.594 -0.409 0.155 C94 +0 5 1 8 1 0.393 -0.385 0.562 C94 +0 5 1 8 6 0.598 -0.158 0.399 C94 +0 5 1 8 23 -0.152 -0.440 0.357 C94 +0 0 1 9 0 0.000 0.000 0.000 C94 0:*-1-9-* Def +5 0 1 9 0 0.000 0.000 0.000 E94 5:*1-9-* Def +0 5 1 9 3 0.204 -0.335 -0.352 C94 +0 5 1 9 53 0.000 0.000 0.097 X94 +0 0 1 10 0 0.000 0.000 0.300 C94 0:*-1-10-* Def +5 0 1 10 0 0.000 0.000 0.000 E94 5:*1-10-* Def +0 0 1 10 3 0.000 0.000 1.000 C94 0:*-1-10-3 Def +0 1 1 10 3 -0.884 0.578 0.818 C94S +0 1 1 10 6 0.000 -0.379 0.565 C94S +0 1 1 10 28 0.750 -0.404 0.369 C94S +0 3 1 10 3 3.219 -2.699 1.875 C94S +0 3 1 10 28 0.207 0.461 0.324 C94S +0 5 1 10 1 0.000 0.000 0.706 C94S +0 5 1 10 3 -2.334 1.517 -0.065 C94S +0 5 1 10 6 0.000 0.688 0.665 C94S +0 5 1 10 28 -0.982 -0.207 0.166 C94S +0 0 1 15 0 0.000 0.000 0.400 C94 0:*-1-15-* Def +5 0 1 15 0 0.000 0.000 0.336 E94 5:*1-15-* Def +0 1 1 15 1 -1.047 0.170 0.398 C94 +0 1 1 15 15 -1.438 0.263 0.501 C94 +0 1 1 15 71 -0.376 -0.133 0.288 C94 +0 5 1 15 1 1.143 -0.231 0.447 C94 +0 5 1 15 15 1.555 -0.323 0.456 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38 69 0 0.000 6.000 0.000 E94 0:*-38-69-* Def +0 0 38 78 0 0.000 6.000 0.000 E94 0:*-38-78-* Def +0 0 39 40 0 0.000 0.000 0.000 E94 0:*-39-40-* Def +0 0 39 45 0 0.000 6.000 0.000 E94 0:*-39-45-* Def +0 0 39 63 0 0.000 4.000 0.000 C94 0:*-39-63-* Def +1 0 39 63 0 0.000 6.000 0.000 E94 1:*-39-63-* Def +5 0 39 63 0 0.000 3.600 0.000 E94 5:*-39-63-* Def +0 1 39 63 5 0.000 4.000 0.000 C94 +0 1 39 63 64 0.000 4.000 0.000 C94 +0 18 39 63 5 0.000 4.000 0.000 X94 +0 18 39 63 64 0.000 4.000 0.000 X94 +0 63 39 63 5 0.000 4.000 0.000 C94 +0 63 39 63 64 0.000 4.000 0.000 C94 +0 0 39 64 0 0.000 3.600 0.000 E94 0:*-39-64-* Def +1 0 39 64 0 0.000 6.000 0.000 E94 1:*-39-64-* Def +0 0 39 65 0 0.000 4.000 0.000 C94 0:*-39-65-* Def +0 0 39 78 0 0.000 3.600 0.000 E94 0:*-39-78-* Def +0 0 40 40 0 0.000 0.000 0.375 E94 0:*-40-40-* Def +0 0 40 45 0 0.000 3.600 0.000 E94 0:*-40-45-* Def +0 0 40 46 0 0.000 3.600 0.000 E94 0:*-40-46-* Def +0 0 40 54 0 0.000 3.600 0.000 E94 0:*-40-54-* Def +2 0 40 54 0 0.000 3.600 0.000 E94 2:*-40-54-* Def +0 0 40 63 0 0.000 3.600 0.000 E94 0:*-40-63-* Def +0 0 40 64 0 0.000 3.600 0.000 E94 0:*-40-64-* Def +0 0 40 78 0 0.000 3.600 0.000 E94 0:*-40-78-* Def +0 0 41 41 0 0.000 1.800 0.000 E94 0:*-41-41-* Def +0 0 41 55 0 0.000 4.800 0.000 E94 0:*-41-55-* Def +0 0 41 62 0 0.000 3.600 0.000 E94 0:*-41-62-* Def +0 0 41 80 0 0.000 1.800 0.000 E94 0:*-41-80-* Def +0 0 43 43 0 0.000 0.000 0.375 E94 0:*-43-43-* Def +0 0 43 45 0 0.000 3.600 0.000 E94 0:*-43-45-* Def +0 0 43 64 0 0.000 3.600 0.000 E94 0:*-43-64-* Def +0 0 44 57 0 0.000 7.000 0.000 C94 0:*-44-57-* Def +0 0 44 63 0 0.000 7.000 0.000 C94 0:*-44-63-* Def +0 0 44 65 0 0.000 7.000 0.000 C94 0:*-44-65-* Def +0 0 44 78 0 0.000 2.846 0.000 E94 0:*-44-78-* Def +0 0 44 80 0 0.000 2.846 0.000 E94 0:*-44-80-* Def +0 0 45 63 0 0.000 1.800 0.000 E94 0:*-45-63-* Def +0 0 45 64 0 0.000 1.800 0.000 E94 0:*-45-64-* Def +0 0 45 78 0 0.000 1.800 0.000 E94 0:*-45-78-* Def +0 0 55 57 0 0.000 10.000 0.000 C94 0:*-55-57-* Def +2 0 55 57 0 0.000 4.800 0.000 E94 2:*-55-57-* Def +5 0 55 57 0 0.000 4.800 0.000 E94 5:*-55-57-* Def +0 1 55 57 5 0.423 12.064 0.090 C94 +0 1 55 57 55 -0.428 12.044 0.000 C94 +0 36 55 57 5 -0.268 8.077 -0.806 C94 +0 36 55 57 55 0.273 8.025 0.692 C94 +0 0 55 62 0 0.000 3.600 0.000 E94 0:*-55-62-* Def +0 0 55 64 0 0.000 4.800 0.000 E94 0:*-55-64-* Def +0 0 55 80 0 0.000 4.800 0.000 E94 0:*-55-80-* Def +0 0 56 57 0 0.000 6.000 0.000 C94 0:*-56-57-* Def +0 1 56 57 56 0.000 6.886 -0.161 C94 +0 36 56 57 56 0.000 4.688 0.107 C94 +0 0 56 63 0 0.000 4.800 0.000 E94 0:*-56-63-* Def +0 0 56 80 0 0.000 4.800 0.000 E94 0:*-56-80-* Def +1 0 57 63 0 0.000 1.800 0.000 E94 1:*-57-63-* Def +1 0 57 64 0 0.000 1.800 0.000 E94 1:*-57-64-* Def +0 0 58 63 0 0.000 6.000 0.000 E94 0:*-58-63-* Def +0 0 58 64 0 0.000 6.000 0.000 E94 0:*-58-64-* Def +0 0 59 63 0 0.000 7.000 0.000 C94 0:*-59-63-* Def +0 0 59 65 0 0.000 7.000 0.000 C94 0:*-59-65-* Def +0 0 59 78 0 0.000 3.600 0.000 E94 0:*-59-78-* Def +0 0 59 80 0 0.000 3.600 0.000 E94 0:*-59-80-* Def +0 0 59 82 0 0.000 3.600 0.000 E94 0:*-59-82-* Def +0 0 62 63 0 0.000 3.600 0.000 E94 0:*-62-63-* Def +0 0 62 64 0 0.000 3.600 0.000 E94 0:*-62-64-* Def +1 0 63 63 0 0.000 1.800 0.000 E94 1:*-63-63-* Def +0 0 63 64 0 0.000 7.000 0.000 C94 0:*-63-64-* Def +0 5 63 64 5 0.000 7.000 0.000 C94 +0 5 63 64 64 0.000 7.000 0.000 C94 +0 39 63 64 5 0.000 7.000 0.000 C94 +0 39 63 64 64 0.000 7.000 0.000 C94 +0 0 63 66 0 0.000 7.000 0.000 C94 0:*-63-66-* Def +0 0 63 78 0 0.000 6.000 0.000 E94 0:*-63-78-* Def +0 0 63 81 0 0.000 6.000 0.000 E94 0:*-63-81-* Def +0 0 64 64 0 0.000 7.000 0.000 C94 0:*-64-64-* Def +1 0 64 64 0 0.000 1.800 0.000 E94 1:*-64-64-* Def +0 5 64 64 5 0.000 7.000 0.000 C94 +0 5 64 64 63 0.000 7.000 0.000 C94 +0 63 64 64 63 0.000 7.000 0.000 C94 +0 0 64 65 0 0.000 7.000 0.000 C94 0:*-64-65-* Def +0 0 64 66 0 0.000 7.000 0.000 C94 0:*-64-66-* Def +0 0 64 78 0 0.000 6.000 0.000 E94 0:*-64-78-* Def +0 0 64 81 0 0.000 6.000 0.000 E94 0:*-64-81-* Def +5 0 64 81 0 0.000 6.000 0.000 E94 5:*-64-81-* Def +0 0 64 82 0 0.000 6.000 0.000 E94 0:*-64-82-* Def +0 0 65 66 0 0.000 7.000 0.000 C94 0:*-65-66-* Def +0 0 65 78 0 0.000 6.000 0.000 E94 0:*-65-78-* Def +0 0 65 81 0 0.000 6.000 0.000 E94 0:*-65-81-* Def +0 0 65 82 0 0.000 6.000 0.000 E94 0:*-65-82-* Def +0 0 66 66 0 0.000 7.000 0.000 C94 0:*-66-66-* Def +0 0 66 78 0 0.000 6.000 0.000 E94 0:*-66-78-* Def +0 0 66 81 0 0.000 6.000 0.000 E94 0:*-66-81-* Def +0 0 67 67 0 0.000 12.000 0.000 E94 0:*-67-67-* Def +5 0 67 67 0 0.000 12.000 0.000 E94 5:*-67-67-* Def +0 0 76 76 0 0.000 3.600 0.000 E94 0:*-76-76-* Def +0 0 76 78 0 0.000 3.600 0.000 E94 0:*-76-78-* Def +0 0 78 78 0 0.000 7.000 0.000 C94 0:*-78-78-* Def +0 0 78 79 0 0.000 6.000 0.000 E94 0:*-78-79-* Def +0 0 78 81 0 0.000 4.000 0.000 C94 0:*-78-81-* Def +0 0 79 79 0 0.000 6.000 0.000 E94 0:*-79-79-* Def +0 0 79 81 0 0.000 6.000 0.000 E94 0:*-79-81-* Def +0 0 80 81 0 0.000 4.000 0.000 C94 0:*-80-81-* Def +$
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/mmffstbn.par Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,292 @@ +* +* Copyright (c) Merck and Co., Inc., 1994 +* All Rights Reserved +* +* MMFF STRETCH-BEND PARAMETERS- Rev: 23-FEB-93 Source: MMFF94 +* C94 - CORE MMFF94 parameter, from fits to HF/6-31G* 2nd D's +* X94 - EXTD MMFF94 parameter, also from fits to HF/6-31G* 2nd D's +* +* types I, J, K kbaIJK kbaKJI Source +0 1 1 1 0.206 0.206 C94 +0 1 1 2 0.136 0.197 C94 +0 1 1 3 0.211 0.092 C94 +0 1 1 5 0.227 0.070 C94 +0 1 1 6 0.173 0.417 C94 +0 1 1 8 0.136 0.282 C94 +0 1 1 10 0.187 0.338 C94 +0 1 1 11 0.209 0.633 C94 +0 1 1 12 0.176 0.386 C94 +0 1 1 15 0.139 0.217 C94 +0 1 1 34 0.236 0.436 C94 +0 1 1 37 0.152 0.260 C94 +0 1 1 39 0.144 0.595 C94 +0 1 1 41 0.122 0.051 C94 +0 1 1 56 0.262 0.451 C94 +0 1 1 68 0.186 0.125 C94 +0 2 1 2 0.282 0.282 C94 +0 2 1 3 0.206 0.022 C94 +0 2 1 5 0.234 0.088 C94 +0 2 1 6 0.183 0.387 C94 +0 2 1 8 0.214 0.363 C94 +0 3 1 5 0.157 0.115 C94 +0 3 1 6 -0.036 0.456 C94 +0 3 1 10 0.038 0.195 C94 +0 5 1 5 0.115 0.115 C94 +0 5 1 6 0.013 0.436 C94 +0 5 1 8 0.027 0.358 C94 +0 5 1 9 0.040 0.418 C94 +0 5 1 10 0.043 0.261 C94 +0 5 1 11 0.003 0.452 C94 +0 5 1 12 -0.018 0.380 C94 +0 5 1 15 0.018 0.255 C94 +0 5 1 18 0.121 0.218 X94 +0 5 1 20 0.069 0.327 C94 +0 5 1 22 0.055 0.267 X94 +0 5 1 34 -0.003 0.342 C94 +0 5 1 37 0.074 0.287 C94 +0 5 1 39 0.092 0.607 C94 +0 5 1 40 0.023 0.335 C94 +0 5 1 41 0.093 0.118 C94 +0 5 1 54 0.016 0.343 C94 +0 5 1 55 0.030 0.397 C94 +0 5 1 56 0.031 0.384 C94 +0 5 1 68 0.041 0.216 C94 +0 6 1 6 0.320 0.320 C94 +0 6 1 37 0.310 0.160 C94 +0 11 1 11 0.586 0.586 C94 +0 12 1 12 0.508 0.508 C94 +0 1 2 1 0.250 0.250 C94 +0 1 2 2 0.203 0.207 C94 +2 1 2 2 0.222 0.269 C94 +2 1 2 3 0.244 0.292 C94 +0 1 2 5 0.215 0.128 C94 +2 1 2 37 0.246 0.260 C94 +1 2 2 2 0.250 0.219 C94 +2 2 2 3 0.155 0.112 C94 +0 2 2 5 0.207 0.157 C94 +1 2 2 5 0.267 0.159 C94 +0 2 2 6 0.118 0.576 C94 +2 2 2 37 0.143 0.172 C94 +0 2 2 40 0.289 0.390 C94 +0 2 2 41 0.191 -0.047 C94 +1 3 2 5 0.264 0.156 C94 +0 5 2 5 0.140 0.140 C94 +0 5 2 6 0.213 0.502 C94 +2 5 2 37 0.153 0.288 C94 +0 5 2 40 0.070 0.463 C94 +0 5 2 41 0.191 0.005 C94 +0 1 3 1 0.358 0.358 C94 +2 1 3 2 0.246 0.409 C94 +2 1 3 3 0.303 0.145 C94 +0 1 3 5 0.321 0.183 C94 +0 1 3 6 0.338 0.732 C94 +0 1 3 7 0.154 0.856 C94 +0 1 3 10 0.223 0.732 C94 +2 1 3 37 0.217 0.207 C94 +1 2 3 5 0.407 0.159 C94 +1 2 3 6 0.429 0.473 C94 +1 2 3 7 0.214 0.794 C94 +1 2 3 9 0.227 0.610 C94 +1 2 3 10 0.298 0.600 C94 +1 3 3 5 0.251 0.133 C94 +1 3 3 6 0.066 0.668 C94 +1 3 3 7 -0.093 0.866 C94 +0 5 3 5 0.126 0.126 C94 +0 5 3 6 0.174 0.734 C94 +0 5 3 7 0.032 0.805 C94 +0 5 3 9 0.037 0.669 C94 +0 5 3 10 0.169 0.619 C94 +0 5 3 40 0.087 0.685 C94 +0 5 3 54 0.098 0.210 C94 +0 6 3 7 0.494 0.578 C94 +4 6 3 20 1.179 0.752 X94 +2 6 3 37 0.350 0.175 C94 +0 7 3 10 0.771 0.353 C94 +0 7 3 20 0.865 -0.181 C94 +2 7 3 37 0.707 0.007 C94 +0 9 3 40 0.680 0.260 C94 +0 10 3 10 1.050 1.050 C94 +4 20 3 20 0.536 0.536 C94 +0 40 3 40 0.482 0.482 C94 +0 1 6 1 0.309 0.309 C94 +0 1 6 2 0.157 0.375 C94 +0 1 6 3 -0.153 0.252 C94 +0 1 6 21 0.256 0.143 C94 +0 1 6 37 0.163 0.375 C94 +0 2 6 3 -0.228 0.052 C94 +0 2 6 29 0.259 0.163 C94 +4 3 6 20 0.456 0.379 X94 +0 3 6 24 0.215 0.064 C94 +0 3 6 37 -0.225 -0.320 C94 +0 8 6 21 0.304 0.055 C94 +0 10 6 21 0.419 0.158 C94 +0 18 6 33 0.309 0.120 X94 +4 20 6 20 0.739 0.739 C94 +0 29 6 37 0.130 0.241 C94 +0 31 6 31 0.227 0.227 X94 +0 1 8 1 0.312 0.312 C94 +0 1 8 6 0.212 0.354 C94 +0 1 8 23 0.309 0.135 C94 +0 6 8 23 0.418 0.020 C94 +4 20 8 20 0.653 0.653 C94 +0 20 8 23 0.128 0.122 C94 +0 23 8 23 0.190 0.190 C94 +0 1 9 3 0.326 0.580 C94 +0 3 9 27 0.464 0.222 C94 +0 1 10 1 0.063 0.063 C94 +0 1 10 3 -0.021 0.340 C94 +0 1 10 6 -0.024 0.374 C94 +0 1 10 28 0.155 -0.051 C94 +0 3 10 3 -0.219 -0.219 C94 +0 3 10 6 0.497 0.513 C94 +0 3 10 28 0.137 0.066 C94 +0 28 10 28 0.081 0.081 C94 +0 1 15 1 0.125 0.125 C94 +0 1 15 15 0.012 0.238 C94 +0 1 15 37 0.048 0.229 C94 +0 1 15 71 0.080 -0.012 C94 +0 15 15 71 0.172 -0.068 C94 +0 37 15 71 0.187 -0.027 C94 +0 71 15 71 0.045 0.045 C94 +0 1 18 1 0.023 0.023 X94 +0 1 18 6 0.003 0.213 X94 +0 1 18 32 -0.091 0.390 X94 +0 1 18 43 -0.008 0.607 X94 +0 6 18 6 0.088 0.088 X94 +0 6 18 32 0.123 0.369 X94 +0 32 18 32 0.404 0.404 X94 +0 32 18 43 0.384 0.281 X94 +0 43 18 43 0.428 0.428 X94 +0 1 20 5 0.290 0.098 C94 +0 1 20 20 0.179 0.004 C94 +0 3 20 5 -0.049 0.171 C94 +4 3 20 20 0.607 0.437 C94 +0 5 20 5 0.182 0.182 C94 +0 5 20 6 0.051 0.312 C94 +0 5 20 8 0.072 0.226 C94 +0 5 20 12 0.014 0.597 C94 +0 5 20 20 0.101 0.079 C94 +0 5 20 30 0.108 0.123 C94 +4 6 20 20 0.823 0.396 C94 +4 8 20 20 0.701 0.369 C94 +0 12 20 20 0.310 0.000 C94 +4 20 20 20 0.283 0.283 C94 +4 20 20 30 0.340 0.529 C94 +0 1 22 5 0.067 0.174 X94 +0 1 22 22 0.199 0.039 X94 +0 5 22 5 0.254 0.254 C94 +0 5 22 22 0.181 0.108 C94 +5 22 22 22 0.000 0.000 C94 +0 5 26 5 -0.121 -0.121 X94 +0 5 30 20 0.251 0.007 C94 +0 5 30 30 0.267 0.054 C94 +4 20 30 30 0.413 0.705 C94 +0 1 34 1 0.202 0.202 C94 +0 1 34 36 0.160 -0.009 C94 +0 36 34 36 0.087 0.087 C94 +0 1 37 37 0.485 0.311 C94 +1 2 37 37 0.321 0.235 C94 +1 3 37 37 0.179 0.217 C94 +0 5 37 37 0.279 0.250 C94 +0 5 37 38 0.267 0.389 C94 +0 5 37 63 0.216 0.434 C94 +0 5 37 64 0.167 0.364 C94 +0 5 37 69 0.273 0.391 C94 +0 6 37 37 0.830 0.339 C94 +0 15 37 37 0.650 0.259 C94 +0 37 37 37 -0.411 -0.411 C94 +0 37 37 38 -0.424 -0.466 C94 +0 37 37 40 0.429 0.901 C94 +0 37 37 63 -0.173 -0.215 C94 +0 37 37 64 -0.229 -0.229 C94 +0 37 37 69 -0.244 -0.555 C94 +0 38 37 38 -0.516 -0.516 C94 +0 37 38 37 -0.342 -0.342 C94 +0 37 38 38 -0.164 -1.130 C94 +0 1 39 63 0.313 0.500 C94 +0 23 39 63 -0.131 0.422 C94 +0 23 39 65 -0.122 0.281 C94 +0 63 39 63 0.469 0.469 C94 +0 63 39 65 0.741 0.506 C94 +0 65 39 65 0.706 0.706 C94 +0 1 40 28 0.238 0.091 C94 +0 1 40 37 0.153 0.590 C94 +0 2 40 28 0.342 0.156 C94 +0 3 40 28 0.228 0.104 C94 +0 28 40 28 0.094 0.094 C94 +0 28 40 37 0.186 0.423 C94 +0 1 41 32 0.503 0.943 C94 +0 2 41 32 0.594 0.969 C94 +0 5 41 32 0.276 0.852 C94 +0 32 41 32 0.652 0.652 C94 +0 18 43 23 0.377 0.057 X94 +0 23 43 23 0.082 0.082 X94 +0 63 44 63 0.591 0.591 C94 +0 63 44 65 0.857 0.978 C94 +0 50 49 50 0.072 0.072 C94 +0 1 54 3 0.192 -0.051 C94 +0 1 54 36 0.240 0.079 C94 +0 3 54 36 0.005 0.127 C94 +0 36 54 36 0.148 0.148 C94 +0 1 55 36 0.189 0.033 C94 +0 1 55 57 0.166 0.211 C94 +0 36 55 36 0.106 0.106 C94 +0 36 55 57 0.093 0.080 C94 +0 1 56 36 0.211 -0.040 C94 +0 1 56 57 0.026 0.386 C94 +0 36 56 36 0.101 0.101 C94 +0 36 56 57 0.108 0.068 C94 +0 5 57 55 0.043 0.420 C94 +0 55 57 55 0.125 0.125 C94 +0 56 57 56 0.431 0.431 C94 +0 58 57 58 0.732 0.732 C94 +0 63 59 63 0.497 0.497 C94 +0 63 59 65 0.723 0.874 C94 +0 5 63 39 0.009 0.654 C94 +0 5 63 44 -0.015 0.446 C94 +0 5 63 59 0.067 0.588 C94 +0 5 63 64 0.055 0.370 C94 +0 5 63 66 0.110 0.464 C94 +0 37 63 39 0.178 0.523 C94 +0 37 63 64 -0.045 0.497 C94 +0 39 63 64 0.422 0.409 C94 +0 39 63 66 0.436 0.525 C94 +0 44 63 64 0.581 0.426 C94 +0 44 63 66 0.542 0.365 C94 +0 59 63 64 0.852 0.332 C94 +0 59 63 66 0.775 0.300 C94 +0 5 64 63 0.086 0.345 C94 +0 5 64 64 0.085 0.369 C94 +0 5 64 65 0.051 0.436 C94 +0 5 64 66 0.113 0.452 C94 +0 37 64 63 0.059 0.299 C94 +0 37 64 64 0.277 0.377 C94 +0 63 64 64 0.206 0.030 C94 +0 63 64 66 0.171 0.078 C94 +0 64 64 65 0.079 0.403 C94 +0 65 64 66 0.406 0.066 C94 +0 39 65 64 0.528 0.644 C94 +0 39 65 66 0.397 0.258 C94 +0 44 65 64 0.816 0.543 C94 +0 59 65 64 1.177 0.594 C94 +0 63 66 64 0.213 -0.173 C94 +0 63 66 66 0.234 0.077 C94 +0 64 66 65 -0.149 0.383 C94 +0 65 66 66 0.199 0.101 C94 +0 1 68 1 0.217 0.217 C94 +0 1 68 23 0.285 0.050 C94 +0 1 68 32 -0.047 0.503 C94 +0 23 68 23 0.145 0.145 C94 +0 23 68 32 -0.182 0.504 C94 +0 32 69 37 1.018 0.418 C94 +0 37 69 37 -0.169 -0.169 C94 +0 31 70 31 0.210 0.210 C94 +0 5 78 78 0.279 0.250 C94 +0 5 78 81 0.083 0.250 C94 +0 78 78 81 -0.398 0.314 C94 +0 5 80 81 -0.101 0.691 C94 +0 81 80 81 0.732 0.732 C94 +0 36 81 78 0.021 0.368 C94 +0 36 81 80 0.018 0.422 C94 +0 78 81 80 0.366 0.419 C94 +$
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/mmfftor.par Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,938 @@ +* +* Copyright (c) Merck and Co., Inc., 1994 +* All Rights Reserved +* +* MMFF TORSION PARAMETERS- Rev: 26-OCT-94 Source: MMFF94 +* C94 - CORE MMFF94 parameter - from fits to conformational energies +* X94 - EXTD MMFF94 parameter - also from fits to conformational E's +* E94 - EXTD MMFF94 parameter - from empirical rule +* #E94 - Adjusted from empirical rule value +* +* atom types V1 V2 V3 Source +0 0 1 1 0 0.000 0.000 0.300 C94 0:*-1-1-* Def +5 0 1 1 0 0.200 -0.800 1.500 C94 5:*-1-1-* Def +0 1 1 1 1 0.103 0.681 0.332 C94 +5 1 1 1 1 0.144 -0.547 1.126 C94 +0 1 1 1 2 -0.295 0.438 0.584 C94 +0 1 1 1 3 0.066 -0.156 0.143 C94 +0 1 1 1 5 0.639 -0.630 0.264 C94 +0 1 1 1 6 -0.688 1.757 0.477 C94 +5 1 1 1 6 0.000 0.000 0.054 C94 +0 1 1 1 8 -1.420 -0.092 1.101 C94 +5 1 1 1 8 0.000 -0.158 0.323 C94 +0 1 1 1 11 0.593 0.662 1.120 C94 +0 1 1 1 12 -0.678 0.417 0.624 C94 +0 1 1 1 15 -0.714 0.698 0.000 C94 +0 1 1 1 34 -0.647 0.550 0.590 C94 +0 2 1 1 5 0.321 -0.411 0.144 C94 +0 3 1 1 3 0.443 0.000 -1.140 C94 +0 3 1 1 5 -0.256 0.058 0.000 C94 +0 3 1 1 6 -0.679 -0.029 0.000 C94 +0 5 1 1 5 0.284 -1.386 0.314 C94 +0 5 1 1 6 -0.654 1.072 0.279 C94 +0 5 1 1 8 -0.744 -1.235 0.337 C94 +0 5 1 1 10 0.000 0.000 0.427 C94 +0 5 1 1 11 0.000 0.516 0.291 C94 +0 5 1 1 12 0.678 -0.602 0.398 C94 +0 5 1 1 15 1.142 -0.644 0.367 C94 +0 5 1 1 25 0.000 0.000 0.295 X94 +0 5 1 1 34 0.692 -0.530 0.278 C94 +0 5 1 1 37 0.000 0.000 0.389 C94 +0 5 1 1 39 0.000 0.000 0.278 C94 +0 5 1 1 41 0.000 0.000 -0.141 C94 +0 5 1 1 56 0.000 0.000 0.324 C94 +0 5 1 1 68 0.000 0.000 0.136 C94 +0 6 1 1 6 0.408 1.397 0.961 C94 +5 6 1 1 6 0.313 -1.035 1.631 C94 +0 8 1 1 8 1.055 0.834 0.000 C94 +0 11 1 1 11 -0.387 -0.543 1.405 C94 +0 12 1 1 12 0.000 0.000 0.893 C94 +0 15 1 1 15 -0.177 0.000 0.049 C94 +0 0 1 2 0 0.000 0.000 0.000 C94 0:*-1-2-* Def +2 0 1 2 0 0.000 0.000 0.000 E94 2:*-1-2-* Def +5 0 1 2 0 0.000 0.000 0.000 C94 5:*-1-2-* Def +0 0 1 2 2 0.000 0.000 -0.650 C94 0:*-1-2=2 Def +5 0 1 2 2 0.000 0.000 -0.650 C94 5:*-1-2=2 Def +0 1 1 2 1 0.419 0.296 0.282 C94 +0 1 1 2 2 -0.494 0.274 -0.630 C94 +0 1 1 2 5 0.075 0.000 0.358 C94 +0 2 1 2 2 -0.293 0.115 -0.508 C94 +0 2 1 2 5 0.301 0.104 0.507 C94 +0 3 1 2 1 0.565 -0.554 0.234 C94 +0 3 1 2 2 -0.577 -0.482 -0.427 C94 +0 3 1 2 5 0.082 0.000 0.123 C94 +0 5 1 2 1 0.000 -0.184 0.220 C94 +0 5 1 2 2 0.501 -0.410 -0.535 C94 +2 5 1 2 2 0.000 0.000 0.055 C94 +2 5 1 2 3 0.000 0.000 -0.108 C94 +0 5 1 2 5 -0.523 -0.228 0.208 C94 +2 5 1 2 37 0.000 0.000 0.000 C94 +0 6 1 2 1 -0.467 0.000 0.490 C94 +0 6 1 2 2 0.425 0.168 -0.875 C94 +0 6 1 2 5 0.000 0.136 0.396 C94 +0 8 1 2 1 -0.504 0.371 0.557 C94 +0 8 1 2 2 0.541 0.539 -1.009 C94 +0 8 1 2 5 0.000 0.204 0.464 C94 +0 0 1 3 0 0.000 0.400 0.300 C94 0:*-1-3-* Def +2 0 1 3 0 0.000 0.500 0.350 C94 2:*-1-3-* Def +5 0 1 3 0 0.000 0.000 0.000 E94 5:*-1-3-* Def +0 0 1 3 1 0.000 0.000 0.550 C94 0:*-1-3-1 Def +0 0 1 3 5 0.000 0.200 0.700 C94 0:*-1-3-5 Def +0 0 1 3 7 0.000 0.400 0.400 C94 0:*-1-3-7 Def +0 1 1 3 1 0.103 0.177 0.545 C94 +0 1 1 3 5 -0.072 0.316 0.674 C94 +0 1 1 3 6 -0.117 -0.333 0.202 C94 +0 1 1 3 7 0.825 0.139 0.325 C94 +0 1 1 3 10 -0.927 1.112 1.388 C94 +0 2 1 3 5 0.663 -0.167 0.426 C94 +0 2 1 3 7 -0.758 0.112 0.563 C94 +0 5 1 3 1 -0.073 0.085 0.531 C94 +2 5 1 3 2 0.000 0.000 0.115 C94 +2 5 1 3 3 0.000 0.000 0.446 C94 +0 5 1 3 5 -0.822 0.501 1.008 C94 +0 5 1 3 6 0.000 -0.624 0.330 C94 +0 5 1 3 7 0.659 -1.407 0.308 C94 +0 5 1 3 10 -0.412 0.693 0.087 C94 +2 5 1 3 37 0.000 0.000 0.056 C94 +0 5 1 3 43 0.000 1.027 0.360 X94 +0 5 1 3 51 0.000 1.543 0.350 X94 +0 5 1 3 53 0.000 0.501 0.000 X94 +0 5 1 3 74 0.000 0.513 -0.344 X94 +0 5 1 3 75 0.000 0.511 -0.186 X94 +0 6 1 3 6 0.447 0.652 0.318 C94 +0 6 1 3 7 -0.395 0.730 -0.139 C94 +0 10 1 3 7 0.338 2.772 2.145 C94 +0 10 1 3 10 0.548 0.000 1.795 C94 +0 0 1 4 0 0.000 0.000 0.000 C94 0:*-1-4-* Def +0 0 1 6 0 0.000 0.000 0.200 C94 0:*-1-6-* Def +5 0 1 6 0 0.000 -0.200 0.400 C94 5:*-1-6-* Def +0 1 1 6 1 -0.681 0.755 0.755 C94 +5 1 1 6 1 0.000 0.243 -0.596 C94 +0 1 1 6 3 -0.547 0.000 0.320 C94 +0 1 1 6 21 0.000 0.270 0.237 C94 +0 2 1 6 21 0.102 0.460 -0.128 C94 +0 3 1 6 21 -1.652 -1.660 0.283 C94 +0 5 1 6 1 0.571 0.319 0.570 C94 +0 5 1 6 2 0.000 0.000 0.306 C94 +0 5 1 6 3 0.572 0.000 -0.304 C94 +0 5 1 6 21 0.596 -0.276 0.346 C94 +0 5 1 6 25 0.000 0.000 0.061 X94 +0 5 1 6 37 0.000 0.000 0.106 C94 +0 5 1 6 45 0.000 0.000 -0.174 X94 +0 6 1 6 1 0.229 -0.710 0.722 C94 +5 6 1 6 1 0.000 0.000 0.040 C94 +0 6 1 6 21 1.488 -3.401 -0.320 C94 +0 37 1 6 21 0.712 1.320 -0.507 C94 +0 0 1 8 0 0.000 -0.300 0.500 C94 0:*-1-8-* Def +5 0 1 8 0 0.000 0.000 0.297 E94 5:*-1-8-* Def +0 1 1 8 1 -0.439 0.786 0.272 C94 +5 1 1 8 1 0.115 -0.390 0.658 C94 +0 1 1 8 6 -0.608 0.339 1.496 C94 +0 1 1 8 23 -0.428 0.323 0.280 C94 +0 2 1 8 23 0.594 -0.409 0.155 C94 +0 5 1 8 1 0.393 -0.385 0.562 C94 +0 5 1 8 6 0.598 -0.158 0.399 C94 +0 5 1 8 23 -0.152 -0.440 0.357 C94 +0 0 1 9 0 0.000 0.000 0.000 C94 0:*-1-9-* Def +5 0 1 9 0 0.000 0.000 0.000 E94 5:*-1-9-* Def +0 5 1 9 3 0.204 -0.335 -0.352 C94 +0 5 1 9 53 0.000 0.000 0.097 X94 +0 0 1 10 0 0.000 0.000 0.300 C94 0:*-1-10-* Def +5 0 1 10 0 0.000 0.000 0.000 E94 5:*-1-10-* Def +0 0 1 10 3 0.000 0.000 1.000 C94 0:*-1-10-3 Def +0 1 1 10 3 -1.027 0.694 0.948 C94 +0 1 1 10 6 0.159 -0.552 0.198 C94 +0 1 1 10 28 0.552 -0.380 0.326 C94 +0 3 1 10 3 3.100 -2.529 1.494 C94 +0 3 1 10 28 0.079 0.280 0.402 C94 +0 5 1 10 1 0.000 0.000 0.779 C94 +0 5 1 10 3 -2.099 1.363 0.021 C94 +0 5 1 10 6 -0.162 0.832 0.552 C94 +0 5 1 10 28 -0.616 0.000 0.274 C94 +0 0 1 15 0 0.000 0.000 0.400 C94 0:*-1-15-* Def +5 0 1 15 0 0.000 0.000 0.336 E94 5:*-1-15-* Def +0 1 1 15 1 -1.047 0.170 0.398 C94 +0 1 1 15 15 -1.438 0.263 0.501 C94 +0 1 1 15 71 -0.376 -0.133 0.288 C94 +0 5 1 15 1 1.143 -0.231 0.447 C94 +0 5 1 15 15 1.555 -0.323 0.456 C94 +0 5 1 15 37 0.000 0.000 0.459 C94 +0 5 1 15 71 0.229 0.203 0.440 C94 +0 0 1 17 0 0.000 0.000 0.350 C94 0:*-1-17-* Def +5 0 1 17 0 0.000 0.000 0.000 E94 5:*-1-17-* Def +0 5 1 17 1 0.000 0.000 0.536 X94 +0 5 1 17 7 0.000 0.000 0.212 X94 +0 0 1 18 0 0.000 0.000 0.100 C94 0:*-1-18-* Def +5 0 1 18 0 0.000 0.000 0.112 E94 5:*-1-18-* Def +0 5 1 18 1 0.000 0.000 0.000 X94 +0 5 1 18 6 0.000 0.000 0.099 X94 +0 5 1 18 32 0.000 0.585 0.388 X94 +0 5 1 18 43 0.000 -0.412 0.121 X94 +0 5 1 18 48 0.000 0.000 0.195 X94 +0 5 1 18 62 0.000 0.000 -0.088 X94 +0 0 1 19 0 0.000 0.000 0.150 C94 0:*-1-19-* Def +5 0 1 19 0 0.000 0.000 0.179 E94 5:*1-19-* Def +0 5 1 19 5 0.000 0.000 0.196 X94 +0 5 1 19 6 0.000 0.000 0.176 X94 +0 5 1 19 12 0.000 0.000 0.152 X94 +0 0 1 20 0 0.000 0.000 0.350 C94 0:*-1-20-* Def +5 0 1 20 0 0.000 0.000 0.350 C94 5:*-1-20-* Def +0 5 1 20 5 0.000 0.000 0.344 C94 +0 5 1 20 20 0.000 0.000 0.361 C94 +0 0 1 22 0 0.000 0.000 0.236 E94 0:*1-22-* Def +5 0 1 22 0 0.000 0.000 0.236 E94 5:*1-22-* Def +0 0 1 25 0 0.000 0.000 0.300 C94 0:*-1-25-* Def +5 0 1 25 0 0.000 0.000 0.251 E94 5:*1-25-* Def +0 1 1 25 1 0.000 -0.207 0.232 X94 +0 1 1 25 32 0.000 0.288 0.218 X94 +0 5 1 25 1 0.000 0.152 0.235 X94 +0 5 1 25 6 0.000 0.000 0.495 X94 +0 5 1 25 32 0.000 -0.130 0.214 X94 +0 5 1 25 43 0.000 0.000 0.466 X94 +0 5 1 25 72 0.000 0.000 0.243 X94 +0 0 1 26 0 0.000 0.000 0.450 C94 0:*-1-26-* Def +5 0 1 26 0 0.000 0.000 0.376 E94 5:*1-26-* Def +0 5 1 26 12 0.000 0.000 0.439 X94 +0 5 1 26 71 0.000 0.000 0.472 X94 +0 0 1 34 0 0.000 0.000 0.250 C94 0:*-1-34-* Def +5 0 1 34 0 0.000 0.000 0.198 E94 5:*1-34-* Def +0 1 1 34 36 0.000 0.000 0.187 C94 +0 5 1 34 1 0.000 0.000 0.247 C94 +0 5 1 34 36 0.000 0.000 0.259 C94 +0 0 1 37 0 0.000 0.000 0.200 C94 0:*-1-37-* Def +5 0 1 37 0 0.000 0.000 0.000 E94 5:*1-37-* Def +0 1 1 37 37 0.000 0.449 0.000 C94 +0 5 1 37 37 0.000 -0.420 0.391 C94 +0 6 1 37 37 0.000 0.000 0.150 C94 +0 0 1 39 0 0.000 0.000 0.000 C94 0:*-1-39-* Def +5 0 1 39 0 0.000 0.000 0.000 E94 5:*1-39-* Def +0 1 1 39 63 0.000 -0.080 -0.056 C94 +0 5 1 39 63 0.000 0.000 -0.113 C94 +0 0 1 40 0 0.000 0.000 0.250 C94 0:*-1-40-* Def +5 0 1 40 0 0.000 0.000 0.297 E94 5:*1-40-* Def +0 5 1 40 28 0.000 -0.097 0.203 C94 +0 5 1 40 37 0.000 0.000 0.329 C94 +0 0 1 41 0 0.000 0.600 0.000 C94 0:*-1-41-* Def +0 1 1 41 32 0.000 1.263 0.000 C94 +0 5 1 41 32 0.000 0.000 -0.106 C94 +0 5 1 41 72 0.000 0.632 0.000 X94 +0 0 1 43 0 0.000 0.000 0.150 C94 0:*-1-43-* Def +5 0 1 43 0 0.000 0.000 0.297 E94 5:*1-43-* Def +0 5 1 43 18 0.357 -0.918 0.000 X94 +0 5 1 43 25 0.000 0.000 0.061 X94 +0 5 1 43 28 -0.249 0.382 0.343 X94 +0 0 1 45 0 0.000 0.000 0.100 C94 0:*-1-45-* Def +0 5 1 45 32 0.000 0.000 0.125 X94 +0 0 1 46 0 0.000 0.000 -0.500 C94 0:*-1-46-* Def +0 5 1 46 7 0.000 0.000 -0.540 X94 +0 0 1 54 0 0.000 0.000 0.000 C94 0:*-1-54-* Def +2 0 1 54 0 0.000 0.000 0.000 E94 2:*1-54-* Def +5 0 1 54 0 0.000 0.000 0.000 E94 5:*1-54-* Def +0 5 1 54 3 0.000 0.000 -0.315 C94 +0 5 1 54 36 0.000 0.000 0.315 C94 +0 0 1 55 0 0.000 0.000 0.000 C94 0:*-1-55-* Def +5 0 1 55 0 0.000 0.000 0.000 E94 5:*1-55-* Def +0 5 1 55 36 0.000 -0.058 0.084 C94 +0 5 1 55 57 0.000 -0.058 -0.092 C94 +0 0 1 56 0 0.000 0.000 -0.300 C94 0:*-1-56-* Def +0 1 1 56 36 0.875 0.668 -0.015 C94 +0 1 1 56 57 -0.870 0.775 -0.406 C94 +0 5 1 56 36 -0.958 -0.629 -0.372 C94 +0 5 1 56 57 0.952 -0.715 -0.483 C94 +0 0 1 57 0 0.000 0.000 0.000 E94 0:*1-57-* Def +5 0 1 57 0 0.000 0.000 0.000 E94 5:*1-57-* Def +0 0 1 58 0 0.000 0.000 0.000 E94 0:*1-58-* Def +0 0 1 62 0 0.000 0.000 0.250 C94 0:*-1-62-* Def +0 5 1 62 18 0.000 0.000 0.270 X94 +0 0 1 63 0 0.000 0.000 0.000 E94 0:*1-63-* Def +5 0 1 63 0 0.000 0.000 0.000 E94 5:*1-63-* Def +0 0 1 64 0 0.000 0.000 0.000 E94 0:*1-64-* Def +5 0 1 64 0 0.000 0.000 0.000 E94 5:*1-64-* Def +0 0 1 67 0 0.000 0.000 0.000 E94 0:*1-67-* Def +5 0 1 67 0 0.000 0.000 0.000 E94 5:*1-67-* Def +0 0 1 68 0 0.000 0.000 0.400 C94 0:*-1-68-* Def +0 1 1 68 1 -0.117 0.090 0.751 C94 +0 1 1 68 23 0.373 0.153 0.635 C94 +0 1 1 68 32 -0.090 -0.169 0.075 C94 +0 5 1 68 1 0.134 -0.112 0.329 C94 +0 5 1 68 23 -0.361 -0.202 0.560 C94 +0 5 1 68 32 0.072 0.218 0.093 C94 +0 0 1 73 0 0.000 0.000 0.500 C94 0:*-1-73-* Def +0 5 1 73 32 0.000 0.000 0.509 X94 +0 5 1 73 72 0.000 0.000 0.443 X94 +0 0 1 75 0 0.000 0.000 0.000 E94 0:*1-75-* Def +0 0 1 78 0 0.000 0.000 0.000 E94 0:*1-78-* Def +0 0 1 80 0 0.000 0.000 0.000 E94 0:*1-80-* Def +0 0 1 81 0 0.000 0.000 0.000 E94 0:*1-81-* Def +0 0 2 2 0 0.000 12.000 0.000 C94 0:*-2=2-* Def +1 0 2 2 0 0.000 1.800 0.000 C94 1:*=2-2=* Def +5 0 2 2 0 0.000 12.000 0.000 C94 5:*-2=2-* Def +0 1 2 2 1 -0.403 12.000 0.000 C94 +0 1 2 2 2 0.000 12.000 0.000 C94 +1 1 2 2 2 -0.418 2.089 -0.310 C94 +0 1 2 2 5 0.000 12.000 0.000 C94 +1 1 2 2 5 0.412 2.120 0.269 C94 +1 2 2 2 2 0.094 1.621 0.877 C94 +0 2 2 2 5 0.000 12.000 0.000 C94 +1 2 2 2 5 0.317 1.421 -0.870 C94 +0 3 2 2 5 0.000 12.000 0.000 C94 +0 5 2 2 5 0.000 12.000 0.000 C94 +1 5 2 2 5 -0.406 1.767 0.000 C94 +0 5 2 2 6 0.000 12.000 0.000 C94 +0 5 2 2 37 0.000 12.000 0.000 C94 +0 5 2 2 40 0.000 12.000 0.000 C94 +0 5 2 2 41 0.000 12.000 0.000 C94 +0 5 2 2 45 0.000 12.000 0.000 X94 +0 5 2 2 62 0.000 12.000 0.000 X94 +1 0 2 3 0 0.000 2.500 0.000 #E94 0:*-2-3-* Def +1 1 2 3 1 0.136 1.798 0.630 C94 +1 1 2 3 5 0.497 2.405 0.357 C94 +1 1 2 3 6 -0.211 1.925 -0.131 C94 +1 1 2 3 7 -0.401 2.028 -0.318 C94 +1 1 2 3 10 -0.084 2.214 -0.610 C94 +1 2 2 3 1 -0.325 1.553 -0.487 C94 +1 2 2 3 5 -0.295 2.024 -0.590 C94 +1 2 2 3 6 -0.143 1.466 0.000 C94 +1 2 2 3 7 0.362 1.978 0.000 C94 +1 2 2 3 9 0.296 1.514 0.481 C94 +1 2 2 3 10 0.095 1.583 0.380 C94 +1 5 2 3 1 0.213 1.728 -0.042 C94 +1 5 2 3 5 -0.208 1.622 0.223 C94 +1 5 2 3 6 0.359 1.539 0.194 C94 +1 5 2 3 7 0.000 2.046 0.000 C94 +1 5 2 3 9 -0.290 1.519 -0.470 C94 +1 5 2 3 10 0.000 1.395 0.227 C94 +1 0 2 4 0 0.000 0.000 0.000 C94 0:*-2-4-* Def +0 0 2 6 0 0.000 3.100 0.000 C94 0:*-2-6-* Def +2 0 2 6 0 0.000 3.600 0.000 E94 2:*-2-6-* Def +5 0 2 6 0 0.000 3.600 0.000 E94 5:*-2-6-* Def +0 2 2 6 1 -1.953 3.953 -1.055 C94 +0 2 2 6 3 -1.712 2.596 -0.330 C94 +0 2 2 6 29 -0.215 2.810 -0.456 C94 +0 5 2 6 1 1.951 3.936 1.130 C94 +0 5 2 6 3 1.719 2.628 0.360 C94 +0 5 2 6 29 0.216 2.808 0.456 C94 +1 0 2 9 0 0.000 1.800 0.000 E94 1:*-2-9-* Def +0 0 2 10 0 0.000 6.000 0.000 E94 0:*-2-10-* Def +2 0 2 10 0 0.000 6.000 0.000 E94 2:*-2-10-* Def +5 0 2 10 0 0.000 6.000 0.000 E94 5:*-2-10-* Def +0 0 2 15 0 0.000 1.423 0.000 E94 0:*-2-15-* Def +2 0 2 15 0 0.000 1.423 0.000 E94 2:*-2-15-* Def +5 0 2 15 0 0.000 1.423 0.000 E94 5:*-2-15-* Def +0 0 2 17 0 0.000 1.423 0.000 E94 0:*-2-17-* Def +0 0 2 18 0 0.000 0.000 0.000 E94 0:*-2-18-* Def +2 0 2 18 0 0.000 0.000 0.000 E94 2:*-2-18-* Def +5 0 2 18 0 0.000 0.000 0.000 E94 5:*-2-18-* Def +0 0 2 19 0 0.000 0.000 0.000 E94 0:*-2-19-* Def +0 0 2 20 0 0.000 0.000 0.000 E94 0:*-2-20-* Def +2 0 2 20 0 0.000 0.000 0.000 E94 2:*-2-20-* Def +0 0 2 22 0 0.000 0.000 0.000 E94 0:*-2-22-* Def +2 0 2 22 0 0.000 0.000 0.000 E94 2:*-2-22-* Def +5 0 2 22 0 0.000 0.000 0.000 E94 5:*-2-22-* Def +0 0 2 25 0 0.000 0.000 0.000 E94 0:*-2-25-* Def +0 0 2 30 0 0.000 12.000 0.000 E94 0:*-2-30-* Def +0 0 2 34 0 0.000 0.000 0.000 E94 0:*-2-34-* Def +2 0 2 34 0 0.000 0.000 0.000 E94 2:*-2-34-* Def +1 0 2 37 0 0.000 2.000 0.000 C94 1:*-2-37-* Def +1 1 2 37 37 0.000 2.952 -0.079 C94 +1 2 2 37 37 0.000 1.542 0.434 C94 +1 5 2 37 37 0.000 1.308 -0.357 C94 +1 0 2 39 0 0.000 6.000 0.000 E94 1:*-2-39-* Def +0 0 2 40 0 0.000 3.700 0.000 C94 0:*-2-40-* Def +2 0 2 40 0 0.000 3.600 0.000 E94 2:*-2-40-* Def +5 0 2 40 0 0.000 3.600 0.000 E94 5:*-2-40-* Def +0 2 2 40 28 0.000 3.756 -0.530 C94 +0 5 2 40 28 0.073 3.698 0.291 C94 +0 0 2 41 0 0.000 1.200 0.000 C94 0:*-2-41-* Def +2 0 2 41 0 0.000 1.800 0.000 E94 2:*-2-41-* Def +0 2 2 41 32 0.000 1.235 0.000 C94 +0 5 2 41 32 0.000 1.231 0.000 C94 +0 0 2 43 0 0.000 3.600 0.000 E94 0:*-2-43-* Def +2 0 2 43 0 0.000 3.600 0.000 E94 2:*-2-43-* Def +0 0 2 45 0 0.000 2.200 0.000 C94 0:*-2-45-* Def +2 0 2 45 0 0.000 1.800 0.000 E94 2:*-2-45-* Def +0 2 2 45 32 0.000 2.212 0.000 X94 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/mmffvdw.par Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,105 @@ +* +* Copyright (c) Merck and Co., Inc., 1994 +* All Rights Reserved +* +* power B Beta DARAD DAEPS +* 0.25 0.2 12. 0.8 0.5 +* +* type alpha-i N-i A-i G-i DA Symb Origin +*------------------------------------------------------------ + 1 1.050 2.490 3.890 1.282 - CR E94 + 2 1.350 2.490 3.890 1.282 - C=C E94 + 3 1.100 2.490 3.890 1.282 - C=O E94 + 4 1.300 2.490 3.890 1.282 - CSP E94 + 5 0.250 0.800 4.200 1.209 - HC C94 + 6 0.70 3.150 3.890 1.282 A OR C94 + 7 0.65 3.150 3.890 1.282 A O=C C94 + 8 1.15 2.820 3.890 1.282 A NR C94 + 9 0.90 2.820 3.890 1.282 A N=C C94 + 10 1.000 2.820 3.890 1.282 A NC=O E94 + 11 0.35 3.480 3.890 1.282 A F C94 + 12 2.300 5.100 3.320 1.345 A CL E94 + 13 3.400 6.000 3.190 1.359 A BR E94 + 14 5.500 6.950 3.080 1.404 A I E94 + 15 3.00 4.800 3.320 1.345 A S C94 + 16 3.900 4.800 3.320 1.345 A S=C E94 + 17 2.700 4.800 3.320 1.345 - SO E94 + 18 2.100 4.800 3.320 1.345 - SO2 E94 + 19 4.500 4.200 3.320 1.345 - SI E94 + 20 1.050 2.490 3.890 1.282 - CR3R E94 + 21 0.150 0.800 4.200 1.209 D HOR C94 + 22 1.100 2.490 3.890 1.282 - CR3R E94 + 23 0.150 0.800 4.200 1.209 D HNR C94 + 24 0.150 0.800 4.200 1.209 D HOCO C94 + 25 1.600 4.500 3.320 1.345 - PO4 E94 + 26 3.600 4.500 3.320 1.345 A P E94 + 27 0.150 0.800 4.200 1.209 D HN=C C94 + 28 0.150 0.800 4.200 1.209 D HNCO C94 + 29 0.150 0.800 4.200 1.209 D HOCC C94 + 30 1.350 2.490 3.890 1.282 - CE4R E94 + 31 0.150 0.800 4.200 1.209 D HOH C94 + 32 0.75 3.150 3.890 1.282 A O2CM C94 + 33 0.150 0.800 4.200 1.209 D HOS C94 + 34 1.00 2.820 3.890 1.282 - NR+ C94 + 35 1.50 3.150 3.890 1.282 A OM X94 + 36 0.150 0.800 4.200 1.209 D HNR+ C94 + 37 1.350 2.490 3.890 1.282 - CB E94 + 38 0.85 2.820 3.890 1.282 A NPYD C94 + 39 1.10 2.820 3.890 1.282 - NPYL C94 + 40 1.00 2.820 3.890 1.282 A NC=C E94 + 41 1.100 2.490 3.890 1.282 - CO2M C94 + 42 1.000 2.820 3.890 1.282 A NSP E94 + 43 1.000 2.820 3.890 1.282 A NSO2 E94 + 44 3.00 4.800 3.320 1.345 A STHI C94 + 45 1.150 2.820 3.890 1.282 - NO2 E94 + 46 1.300 2.820 3.890 1.282 - N=O E94 + 47 1.000 2.820 3.890 1.282 A NAZT X94 + 48 1.200 2.820 3.890 1.282 A NSO X94 + 49 1.00 3.150 3.890 1.282 - O+ X94 + 50 0.150 0.800 4.200 1.209 D HO+ C94 + 51 0.400 3.150 3.890 1.282 - O=+ E94 + 52 0.150 0.800 4.200 1.209 D HO=+ C94 + 53 1.000 2.820 3.890 1.282 - =N= X94 + 54 1.30 2.820 3.890 1.282 - N+=C C94 + 55 0.80 2.820 3.890 1.282 - NCN+ E94 + 56 0.80 2.820 3.890 1.282 - NGD+ E94 + 57 1.000 2.490 3.890 1.282 - CNN+ E94 + 58 0.80 2.820 3.890 1.282 - NPD+ E94 + 59 0.65 3.150 3.890 1.282 A OFUR C94 + 60 1.800 2.490 3.890 1.282 A C%- E94 + 61 0.800 2.820 3.890 1.282 A NR% E94 + 62 1.300 2.820 3.890 1.282 A NM X94 + 63 1.350 2.490 3.890 1.282 - C5A E94 + 64 1.350 2.490 3.890 1.282 - C5B E94 + 65 1.000 2.820 3.890 1.282 A N5A E94 + 66 0.75 2.820 3.890 1.282 A N5B C94 + 67 0.950 2.82 3.890 1.282 A N2OX X94 + 68 0.90 2.82 3.890 1.282 A N3OX C94 + 69 0.950 2.82 3.890 1.282 A NPOX C94 + 70 0.87 3.150 3.890 1.282 A OH2 C94 + 71 0.150 0.800 4.200 1.209 D HS C94 + 72 4.000 4.800 3.320 1.345 A SM X94 + 73 3.000 4.800 3.320 1.345 - SMO2 X94 + 74 3.000 4.800 3.320 1.345 - =S=O X94 + 75 4.000 4.500 3.320 1.345 A -P=C X94 + 76 1.200 2.820 3.890 1.282 A N5M X94 + 77 1.500 5.100 3.320 1.345 A CLO4 X94 + 78 1.350 2.490 3.890 1.282 - C5 X94 + 79 1.000 2.820 3.890 1.282 A N5 X94 + 80 1.000 2.490 3.890 1.282 - CIM+ C94 + 81 0.80 2.820 3.890 1.282 - NIM+ C94 + 82 0.950 2.82 3.890 1.282 A N5OX X94 + 87 0.45 6. 4. 1.4 - FE+2 X94 + 88 0.55 6. 4. 1.4 - FE+3 X94 + 89 1.4 3.48 3.890 1.282 A F- X94 + 90 4.5 5.100 3.320 1.345 A CL- X94 + 91 6.0 6.000 3.190 1.359 A BR- X94 + 92 0.15 2. 4. 1.3 - LI+ X94 + 93 0.4 3.5 4. 1.3 - NA+ X94 + 94 1.0 5. 4. 1.3 - K+ X94 + 95 0.43 6. 4. 1.4 - ZN+2 X94 + 96 0.9 5. 4. 1.4 - CA+2 X94 + 97 0.35 6. 4. 1.4 - CU+1 X94 + 98 0.40 6. 4. 1.4 - CU+2 X94 + 99 0.35 3.5 4. 1.3 - MG+2 X94 +$
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/mr.txt Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,168 @@ +###################################################################### +# Copyright OELIB: OpenEye Scientific Software, Santa Fe, +# U.S.A., 1999,2000,2001 +# Copyright JOELIB/JOELib2: Dept. Computer Architecture, University of +# Tuebingen, Germany, 2001,2002,2003,2004,2005 +# Copyright JOELIB/JOELib2: ALTANA PHARMA AG, Konstanz, Germany, +# 2003,2004,2005 +# +# Authors: Stephen Jelfs +# Joerg Kurt Wegner, me@cheminformatics.eu +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation version 2 of the License. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +###################################################################### +# MR Atomic Contributions +# ref. Wildman, S.A. and Crippen, G.M., J. Chem. Inf. Comput. +# Sci., 1999, 39, 868-873. +# Table below is adapted from above ref. +###################################################################### +;hydrogen +[*] 1.112 +[#6] 1.057 +[#1] 1.057 +[O][CX4] 1.395 +[O]c 1.395 +[O][#5] 1.395 +[O][#14] 1.395 +[O][#15] 1.395 +[O][#33] 1.395 +[O][#50] 1.395 +[#5] 1.395 +[#14] 1.395 +[#15] 1.395 +[#16] 1.395 +[#50] 1.395 +[#7] 0.9627 +[O][#7] 0.9627 +[O]C=[#6] 1.805 +[O]C=[#7] 1.805 +[O]C=O 1.805 +[O]C=S 1.805 +[O]O 1.805 +[O]S 1.805 +;heavy +[*] 0 +[#6] 3.243 +[CH4] 2.503 +[CH3]C 2.503 +[CH2](C)C 2.503 +[CH](C)(C)C 2.433 +[C](C)(C)(C)C 2.433 +[CH3][O,N,F,Cl,Br,#15,#16,#53;!a] 2.753 +[CH2X4][O,N,F,Cl,Br,#15,#16,#53;!a] 2.753 +[CHX4][O,N,F,Cl,Br,#15,#16,#53;!a] 2.731 +[CH0X4][O,N,F,Cl,Br,#15,#16,#53;!a] 2.731 +[C]=[A!#6] 5.007 +[CH2]=C 3.513 +[CH1](=C)A 3.513 +[CH0](=C)(A)A 3.513 +[C](=C)=C 3.513 +[CX2]#A 3.888 +[CH3]c 2.464 +[CH3][a!#6] 2.412 +[CH2X4]a 2.488 +[CHX4]a 2.582 +[CH0X4]a 2.576 +[c][#5,#14,#15,#33,#34,#50,#80] 4.041 +[c][#9] 3.257 +[c][#17] 3.564 +[c][#35] 3.18 +[c][#53] 3.104 +[cH] 3.35 +[c](:a)(:a):a 4.346 +[c](:a)(:a)-a 3.904 +[c](:a)(:a)-C 3.509 +[c](:a)(:a)-N 4.067 +[c](:a)(:a)-O 3.853 +[c](:a)(:a)-S 2.673 +[c](:a)(:a)=C 3.135 +[c](:a)(:a)=N 3.135 +[c](:a)(:a)=O 3.135 +[C](=C)(a)A 4.305 +[C](=C)(c)a 4.305 +[CH](=C)a 4.305 +[C]=c 4.305 +[CX4][!#6;!#7;!#8;!#9;!#15;!#16;!#17;!#35;!#53] 2.693 +[#7] 2.134 +[NH2+0]A 2.262 +[NH+0](A)A 2.173 +[NH2+0]a 2.827 +[NH+0](A)a 3 +[NH+0](a)a 3 +[NH+0]=A 1.757 +[NH+0]=a 1.757 +[N+0](=A)A 2.428 +[N+0](=A)a 2.428 +[N+0](=a)A 2.428 +[N+0](=a)a 2.428 +[N+0](A)(A)A 1.839 +[N+0](a)(A)A 2.819 +[N+0](a)(a)A 2.819 +[N+0](a)(a)a 2.819 +[N+0]#A 1.725 +[NH3+*] 2.134 +[NH2+*] 2.134 +[NH+*] 2.134 +[n+0] 2.202 +[n+*] 2.134 +[NH0+*](A)(A)(A)A 0.2604 +[NH0+*](=A)(A)A 0.2604 +[NH0+*](=A)(A)a 0.2604 +[NH0+*](=[#6])=[#7] 0.2604 +[N+*]#A 3.359 +[N-*] 3.359 +[N+*](=[N-*])=N 3.359 +[#8] 0.6865 +[o] 1.08 +[OH] 0.8238 +[OH2] 0.8238 +[O](C)C 1.085 +[OH0](C)[A!#6] 1.085 +[OH0]([A!#6])[A!#6] 1.085 +[O](A)a 1.182 +[O](a)a 1.182 +[O]=[#8] 3.367 +[O]=[#7] 3.367 +[OX1-*][#7] 3.367 +[OX1-*][#16] 0.7774 +[OX1-*][#15;#33;#43;#53] 0 +[O]=c 3.135 +[O]=[CH]C 0 +[O]=C(C)C 0 +[O]=[CH0](C)[A;!6] 0 +[O]=[CH]N 0 +[O]=[CH]O 0 +[O]=[CH2] 0 +[O]=[CX2]=O 0 +[O]=[CH]c 0.2215 +[O]=C(C)c 0.2215 +[O]=C(c)c 0.2215 +[O]=[CH0](c)[a!#6] 0.2215 +[O]=[CH0](c)[A!#6] 0.2215 +[O]=[CH0](C)[a!#6] 0.2215 +[O]=C([A!#6])[A!#6] 0.389 +[O]=C([A!#6])[a!#6] 0.389 +[O]=C([a!#6])[a!#6] 0.389 +[O-1]C(=O) 0.6865 +[#9-0] 1.108 +[#17-0] 5.853 +[#35-0] 8.927 +[#53-0] 14.02 +[#9-*] 1.108 +[#17-*] 5.853 +[#35-*] 8.927 +[#53-*] 14.02 +[#53+*] 14.02 +[#15] 6.920 +[S-0] 7.591 +[S-*] 7.365 +[S+*] 7.365 +[s] 6.691 +[B,Si,Ga,Ge,As,Se,Sn,Te,Pb,Nc,Nr,Kr,Xe,Rn] 5.754
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/patterns.txt Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,76 @@ +#Comments after SMARTS +############################################################################## +# # +# Open Babel file: patterns.txt # +# # +# Copyright (c) 2005 Chris Morley # +# Part of the Open Babel package, under the GNU General Public License (GPL)# +# # +# Functional groups for molecular fingerprinting based on Checkmol: # +# http://merian.pch.univie.ac.at/~nhaider/cheminf/fgtable.pdf # +# (Numbers 200+ are from Chris Swain) # +# SMARTS Patterns are used by finger3.cpp:PatternFP # +# Format of each line is a SMARTS pattern, then optionally # +# followed by a tab character and a pattern number and/or description # +# (everything after the tab will be ignored by the code) # +# A file of this format needs the same first line as this one. # +# An alternative format, as in SMARTS_InteLigand.txt, can also be used # +# # +# INCOMPLETE!! Really only useful to test the fingerprint FP3 # +############################################################################## +[+] 1 cation +[-] 2 anion +[#6][CX3](=O) 3 aldehyde or ketone +[CX3H1](=O)[#6] 4 aldehyde +[#6][CX3](=O)[#6] 5 ketone +[#6][CX3](=S) 6 thioaldehyde or thioketone +[CX3H1](=S) 7 thioaldehyde +[#6]C(=[S])[#6] 8 thioketone +[CX3]=N([#6,#1])[#6,#1] 9 imine +[#6,#1]C([#6,#1])=[N][N]([#6,#1])[#6,#1] 10 hydrazone +[#6,#1]C([#6,#1])=[N][N]([#6,#1])C(=[O])[N]([#6,#1])[#6,#1] 11 semicarbazone +[#6,#1]C([#6,#1])=[N][N]([#6,#1])C(=[S])[N]([#6,#1])[#6,#1] 12 thiosemicarbazone +[#6,#1]C([#6,#1])=[N][OH] 13 oxime +[#6,#1]C([#6,#1])=[N][O][#6] 14 oxime ether +[CX3]=C=O 15 ketene +[CX3]=C=O 16 keten acetyl derivative*** +[#6,#1]C([#6,#1])([OH])([OH]) 17 carbonyl hydrate +[#6,#1]C([#6,#1])([OH])(O[#6]) 18 hemiacetal +[#6,#1]C([#6,#1])(O[#6])(O[#6]) 19 acetal +[#6,#1]C([#6,#1])(N([#6,#1])[#6,#1])(O[#6]) 20 hemiaminal +[#6,#1]C([#6,#1])(N([#6,#1])[#6,#1])(N([#6,#1])[#6,#1]) 21 aminal +[#6,#1]C([#6,#1])(N([#6,#1])[#6,#1])([S][#6]) 22 thiohemiaminal +[#6,#1]C([#6,#1])([S][#6])([S][#6]) 23 thioacetal +[#6,#1]C([#6,#1])=C([#6,#1])N([#6,#1])[#6,#1] 24 enamine +[#6,#1]C([#6,#1])=C([#6,#1])[OH] 25 enol +[#6,#1]C([#6,#1])=C([#6,#1])O[#6] 26 enol ether +[#6][OH] 27 hydroxy compound +C[OH] 28 alcohol +[#6][CH2][OH] 29 primary alcohol +[#6][CH]([#6])[OH] 30 secondary alcohol +[#6][C]([#6])([#6])[OH] 31 tertiary alcohol +[#6,#1]C([#6,#1])([OH])C([#6,#1])([#6,#1])[OH] 32 1,2-diol +[#6,#1]C([#6,#1])([OH])C([#6,#1])([#6,#1])[NH2] 33 1,2-aminoalcohol +c[OH] 34 phenol +[OH]cc[OH] 35 1,2-diphenol +[OH]C=C[OH] 36 enediol +[#6]O[#6] 37 ether +COC 38 dialkyl ether +cOC 39 alkylaryl ether +cOc 40 diaryl ether +[#6]S[#6] 41 thioether +[#6]SS[#6] 42 disulfide +[#6]OO[#6] 43 peroxide +[#6]O[OH] 44 hydroperoxide +[a] 200 aryl +[!#6;$([N,O,S,F,Cl,Br,I,P])] 201 heteroatom +[!#6;!$([+0]);!$([F,Cl,Br,I]);!$([o,s,nX3]);!$([Nv5,Pv5,Sv4,Sv6])] 202 HBA +[$([N,O;!H0]),$(N(C)(C)C)] 203 HBD +[R] 204 Ring +[$([$([C;$(C=[$([O;D1;$(O=C)])])]);$(C[$([O;$([H1&-0,H0&-1])])]);$(C[#6,#1])])] 205 carboxylic acid +[$([$([C;$(C=[$([O;D1;$(O=C)])])]);$(C(=O)O[#6]);$(C[#6,#1])])] 206 ester +[$([N;+0,+1;$(N(=O)~[O;H0;-0,-1])])] 207 nitro +[$([C;$(C#[N;D1])])] 208 nitrile +[$([N;!$(N*=[!#6])]);$(N[$([a])]);!$(N~[!#6])] 209 aniline +[$([N;$(N[$([$([C;$(C=[$([O;D1;$(O=C)])])]);$(C(=O)(N)N)])])])] 210 urea +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/phmodel.txt Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,169 @@ +############################################################################## +# # +# Open Babel file: phmodel.txt # +# # +# Copyright (c) 1998-2001 by OpenEye Scientific Software, Inc. # +# Some portions Copyright (c) 2001-2003 by Geoffrey R. Hutchison # +# Part of the Open Babel package, under the GNU General Public License (GPL)# +# # +# pH model data (used by phmodel.cpp:OBPhModel) # +# # +# TRANSFORM: chemical transforms can be used to modify formal charges, bond # +# orders, and to delete atoms (i.e hydrogens). Changes are applied# +# to vector bound atoms (use the [:#] SMARTS notation) and bonds # +# between vector bound atoms. # +# SEEDCHARGE: used to seed partial charges. Seed partial charges # +# are used as initial values in Gasteiger charge calculation # +# # +############################################################################## + +#carboxylic acid # pKa +#TRANSFORM O=CO[#1:1] >> O=CO 4.0 # pKa from acid (AH) +TRANSFORM O=C[OD1-0:1] >> O=C[O-:1] 4.0 # pKa from acid (AH) + +#uncomment for vinylogous carboxylic acids (e.g. ascorbic acid) +TRANSFORM [O:1]=[C:2][C:3]=[C:4][O:5] >> [O-:1][C:2]=[C:3][C:4]=[O:5] 4.0 # pKa from acid (AH) + +#charged amine +TRANSFORM [N^3;!$(N~[!#6;!#1]):1] >> [N+:1] 10.0 # pKa from conjugated acid (BH+) + +#imidazole: note pKa=7.0 +#if you uncomment this, also uncomment the seedcharge statement below +TRANSFORM [nD2:1]1c[nH]cc1 >> [n+:1]1c[nH]cc1 7.0 + +#imine +TRANSFORM [ND3+0:1]=[#6] >> [ND3+:1]=[#6] 4.0 # pKa from conjugated acid (BH+) + +#tetrazole +TRANSFORM [nD2:1]([#1:2])1[nD2-0][nD2-0][nD2-0]c1 >> [n-:1]1nnnc1 4.89 #pKa from acid (AH) +TRANSFORM [nD2-0]1[nD2:1]([#1:2])[nD2-0][nD2-0]c1 >> n1[n-:1]nnc1 4.89 #pKa from acid (AH) +TRANSFORM [nD2-0:1]1[nD2-0][nD2-0][nD2-0]c1 >> [n-:1]1nnnc1 4.89 #pKa from acid (AH) + +#azide +TRANSFORM [ND1:1]=[ND2:2]=A >> [N-:1]=[N+:2]=A 1E+10 # always apply transformation +TRANSFORM [ND2:1]=[ND2:2]=A >> N=[N+:2]=A 1E+10 # always apply this transformation + +#hydroxamic acid +#TRANSFORM O=CN[OD1-0:1][#1:2] >> O=CN[O-:1] 8.0 +TRANSFORM O=CN[OD1-0:1] >> O=CN[O-:1] 8.0 + +#sulfinic acid +TRANSFORM [SD3](=O)[OD1:1] >> [SD3](=O)[O-:1] 2.0 +TRANSFORM [SD3](=O)[O:1][#1:2] >> [SD3](=O)[O-:1] 2.0 + +#sulfonic acid +TRANSFORM [SD4]([!D1])(=O)(=O)[OD1:1] >> [SD4]([!D1])(=O)(=O)[O-:1] -2.6 +TRANSFORM [SD4]([!D1])(=O)(=O)[O:1][#1:2] >> [SD4]([!D1])(=O)(=O)[O-:1] -2.6 +#sulfuric acid (same as sulfonic acid...) +#TRANSFORM [SD4]([!D1])(=O)(=O)[OD1:1] >> [SD4]([!D1])(=O)(=O)[O-:1] +#TRANSFORM [SD4]([!D1])(=O)(=O)[O:1][#1:2] >> [SD4]([!D1])(=O)(=O)[O-:1] + +#guanidine or amidine +TRANSFORM [#6^2+0:1](~[N^2])(~[N^2])* >> [#6+:1](~N)(~N)* 12.5 + +#phosphate ester +TRANSFORM [PD4](=O)([OD2])([OD2])[OD1:1] >> [PD4](=O)([OD2])([OD2])[O-:1] 2.0 +#TRANSFORM [PD4](=O)([OD2])([OD2])[OD1:1][#1:2] >> [PD4](=O)([OD2])([OD2])[O-:1] 2.0 + +#phosphoric acid +#TRANSFORM O=P([!D1])([O:1][#1:2])[O:3][#1:4] >> O=P([*D2,*D3])([O:1])[O:3] 2.12 +TRANSFORM O=P([!D1])([O:1][#1:2])[OD1] >> O=P([!D1])([O:1])O 2.12 +TRANSFORM O=P([*D2,*D3])([OD1:1])[OD1:2] >> O=P([*D2,*D3])([O-:1])[O-:2] 2.12 +#phosphate + +# +# Amino acids +# pKa sidechain +# aspartic acid +#TRANSFORM O=CC(N)CC(=O)O[#1:1] >> O=CC(N)CC(=O)O 3.8 +TRANSFORM O=C(O)C(N)CC(=O)[OD1:1] >> O=C(O)C(N)CC(=O)[O-:1] 3.8 +TRANSFORM O=C(NCC=O)C(N)CC(=O)[OD1:1] >> O=C(NCC=O)C(N)CC(=O)[O-:1] 3.8 + +# glutamic acid +#TRANSFORM O=CC(N)CCC(=O)O[#1:1] >> O=CC(N)CCC(=O)O 4.3 +TRANSFORM O=C(O)C(N)CCC(=O)[OD1:1] >> O=C(O)C(N)CCC(=O)[O-:1] 5.0 +TRANSFORM O=C(NCC=O)C(N)CCC(=O)[OD1:1] >> O=C(NCC=O)C(N)CCC(=O)[O-:1] 5.0 + +# arginine +TRANSFORM O=C(O)C(N)CCCNC(N)=[N:1] >> O=C(O)C(N)CCCNC(N)=[N+:1] 12.0 +TRANSFORM O=C(NCC=O)C(N)CCCNC(N)=[N:1] >> O=C(NCC=O)C(N)CCCNC(N)=[N+:1] 12.0 + +# lysine +TRANSFORM O=C(O)C(N)CCCC[N:1] >> O=C(O)C(N)CCCC[N+:1] 10.5 +TRANSFORM O=C(NCC=O)C(N)CCCC[N:1] >> O=C(NCC=O)C(N)CCCC[N+:1] 10.5 + +# histidine +TRANSFORM O=C(O)C(N)Cc1nc[n:1]c1 >> O=C(O)C(N)Cc1nc[n+:1]c1 6.08 +TRANSFORM O=C(NCC=O)C(N)Cc1nc[n:1]c1 >> O=C(NCC=O)C(N)Cc1nc[n+:1]c1 6.08 + +# cysteine +TRANSFORM O=C(O)C(N)C[S:1] >> O=C(O)C(N)C[S-:1] 8.28 +TRANSFORM O=C(NCC=O)C(N)C[S:1] >> O=C(NCC=O)C(N)C[S-:1] 8.28 + +# tyrosine +TRANSFORM O=C(O)C(N)Cc1ccc([O:1])cc1 >> O=C(O)C(N)Cc1ccc([O-:1])cc1 10.1 +TRANSFORM O=C(NCC=O)C(N)Cc1ccc([O:1])cc1 >> O=C(NCC=O)C(N)Cc1ccc([O-:1])cc1 10.1 + +# old: +# histidine +#TRANSFORM [nD2:1]1c[nD2]cc1 >> [n+:1]1c[nD2]cc1 +# uncomment for tryptophan +# TRANSFORM [nD2:1]1cccc1 >> [n+:1]1cccc1 +#, histidine pKa=6.0 + + +# +# Seeding partial charges for gasteiger calculation +# +#default charges +SEEDCHARGE [#6+] 1.0 +SEEDCHARGE [#6-] -1.0 +SEEDCHARGE [#7+] 1.0 +SEEDCHARGE [#7-] -1.0 +SEEDCHARGE [#8+] 1.0 +SEEDCHARGE [#8-] -1.0 +SEEDCHARGE [#15+] 1.0 +SEEDCHARGE [#15-] -1.0 +SEEDCHARGE [#16+] 1.0 +SEEDCHARGE [#16-] -1.0 + +#charges spread over multiple atoms +#carboxylic acid +SEEDCHARGE C(=O)[O-] 0.0 -0.5 -0.5 + +#amines +SEEDCHARGE [N+] 1.0 +#tetrazole +SEEDCHARGE [nD2]1[nD2][nD2][nD2]c1 -0.2 -0.2 -0.2 -0.2 -0.2 + +#sulfinic +SEEDCHARGE [SD3](=O)[O-] 0.0 -0.5 -0.5 +#sulfuric acid +SEEDCHARGE [SD4](=O)(=O)([O-])[OH1] 0.0 -0.33 -0.33 -0.33 0.0 +#sulfonic acid +SEEDCHARGE [SD4]([D2])(~[OD1])(~[OD1])~[OD1] 0.0 0.0 -0.33 -0.33 -0.33 + +#guanidine +SEEDCHARGE [#7^2]~[C^2](~[N^2])~[N^2] 0.33 0.0 0.33 0.33 + +#amidine +SEEDCHARGE [#6]~[C^2](~[N^2])~[N^2] 0.0 0.0 0.5 0.5 + +#phosphoate ester +SEEDCHARGE [PD4](=O)([OD2])([OD2])[OD1] 0.0 -0.5 0.0 0.0 -0.5 +#phosphoric acid +SEEDCHARGE O=P([!D1])([O-])[O-] -0.66 0.0 0.0 -0.66 -0.66 + + +#phosphuric acid +SEEDCHARGE P(=O)(=O)([O-])[O-] 0.0 0.0 0.0 -0.5 -0.5 +#phosphonic acid +SEEDCHARGE [#6]P(~[OD1])(~[OD1])~[OD1] 0.0 0.0 -0.33 -0.33 -0.33 + +#hydroxamic acid +SEEDCHARGE O=C[N;!$(N(C=O)C=O)][OD1] -0.5 0.0 0.0 -0.5 +SEEDCHARGE O=CN([OD1])NC=O -0.33 0.0 0.0 -0.33 0.0 0.0 -0.33 + +#imidazole: note pKa=7.0, histidine pKa=6.0 +#if you uncomment this, also uncomment the transform statement above +SEEDCHARGE [n+H]1c[nH]cc1 0.5 0.0 0.5 0.0 0.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/phmodeldata.h Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,248 @@ +/*************************************************************** +This file is part of the Open Babel project. +This is copyright under the GNU General Public License (GPL) +For more information, see <http://openbabel.org/> + +This file contains a binary representation of data tables + used by Open Babel. It is used as a fallback if the textual + data table is not found at runtime. It is not a normal header. +***************************************************************/ + + +#ifndef OB_PHMODELDATA_H +#define OB_PHMODELDATA_H + +namespace OpenBabel +{ +static const char PhModelData[] = { + 0x54,0x52,0x41,0x4E,0x53,0x46,0x4F,0x52,0x4D,0x20,0x4F,0x3D,0x43,0x5B,0x4F, + 0x44,0x31,0x2D,0x30,0x3A,0x31,0x5D,0x20,0x3E,0x3E,0x20,0x4F,0x3D,0x43,0x5B, + 0x4F,0x2D,0x3A,0x31,0x5D,0x09,0x09,0x09,0x09,0x09,0x34,0x2E,0x30,0x20,0x23, + 0x20,0x70,0x4B,0x61,0x20,0x66,0x72,0x6F,0x6D,0x20,0x61,0x63,0x69,0x64,0x20, + 0x28,0x41,0x48,0x29,0x0A,0x54,0x52,0x41,0x4E,0x53,0x46,0x4F,0x52,0x4D,0x20, + 0x5B,0x4F,0x3A,0x31,0x5D,0x3D,0x5B,0x43,0x3A,0x32,0x5D,0x5B,0x43,0x3A,0x33, + 0x5D,0x3D,0x5B,0x43,0x3A,0x34,0x5D,0x5B,0x4F,0x3A,0x35,0x5D,0x20,0x3E,0x3E, + 0x20,0x5B,0x4F,0x2D,0x3A,0x31,0x5D,0x5B,0x43,0x3A,0x32,0x5D,0x3D,0x5B,0x43, + 0x3A,0x33,0x5D,0x5B,0x43,0x3A,0x34,0x5D,0x3D,0x5B,0x4F,0x3A,0x35,0x5D,0x09, + 0x34,0x2E,0x30,0x20,0x23,0x20,0x70,0x4B,0x61,0x20,0x66,0x72,0x6F,0x6D,0x20, + 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+} // namespace OpenBabel +#endif // OB_PHMODELDATA_H +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/plugindefines.txt Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,67 @@ +# Data file for OBDefinable class. +# A # in the first column or a # followed by whitespace introduces a comment and +# the rest of the characters on a line are ignored. +# White space is trimmed from the front and back of the line. +# +# There can be any number of lines containing only whitespace and +# comment between objects, but none within an object. +# Lines which have "\n" at the end have this replaced by a new line +# character and the next line is concatenated. + +#SmartsDescriptor +#nHal # name of descriptor. Use for example --filter "nHal<3" +#[F,Cl,Br,I,At] # SMARTS defining the descriptor +#Number of halogen atoms\n #This comment has two lines because of \n at the end. +#count fluorine, chlorine, etc. #When listing plugins, use verbose option to see lines after the first + +#OpTransform # Description() for the class includes a line "OpTransform is definable" +#tautomers # ID. Commandline option to invoke is --tautomers +#tautomers.txt # Datafile containing transforms. If filename is * the data follows later in the entry. +#Replace tautomers with their standard forms. Not reliable at present. # An explanatory description. + +#OpTransform +#nodative # ID. Commandline option to invoke is --nodative +#* # There is no datafile; the transforms are at the end of the entry +#Replace [N+]([O-])=O by N(=O)=O +#TRANSFORM [N+:1](=O)[O-:2] >> [N:1](=O)=[O:2] + +CompoundFilter +L5 # ID +HBD<5 HBA1<10 MW<500 logP<5 # definition in terms of other descriptors or properties +Lipinski Rule of Five # description + +PatternFP +MACCS # ID of this fingerprint type +MACCS.txt # File containing the SMARTS patterns + +SmartsDescriptor +sbonds +*-* +Number of single bonds + +SmartsDescriptor +dbonds +*=* +Number of double bonds + +SmartsDescriptor +tbonds +*#* +Number of triple bonds + +SmartsDescriptor +abonds +*:* +Number of aromatic bonds + +SmartsDescriptor +bonds +*~* +Number of bonds\n +Add or remove hydrogens to count total or bonds between heavy atoms + +SmartsDescriptor +atoms +* +Number of atoms\n +Add or remove hydrogens to count total or heavy atoms
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/psa.txt Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,68 @@ +###################################################################### +# Copyright OELIB: OpenEye Scientific Software, Santa Fe, +# U.S.A., 1999,2000,2001 +# Copyright JOELIB/JOELib2: Dept. Computer Architecture, University of +# Tuebingen, Germany, 2001,2002,2003,2004,2005 +# Copyright JOELIB/JOELib2: ALTANA PHARMA AG, Konstanz, Germany, +# 2003,2004,2005 +# +# Authors: Stephen Jelfs +# Joerg Kurt Wegner, me@cheminformatics.eu +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation version 2 of the License. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +###################################################################### +# Atomic Contributions to Polar Surface Area PSA +# ref. Ertl P., Rohde R., Selzer P., J. Med. Chem. 2000, 43, 3714-3717 +###################################################################### +;heavy +[*] 0.00 +[N](-*)(-*)-* 3.24 +[N](-*)=* 12.36 +[N]#* 23.79 +[N](-*)(=*)=* 11.68 +[N](=*)#* 13.60 +[N]1(-*)-*-*1 3.01 +[NH](-*)-* 12.03 +[NH]1-*-*1 21.94 +[NH]=* 23.85 +[NH2]-* 26.02 +[N+](-*)(-*)(-*)-* 0.00 +[N+](-*)(-*)=* 3.01 +[N+](-*)#* 4.36 +[NH+](-*)(-*)-* 4.44 +[NH+](-*)=* 13.97 +[NH2+](-*)-* 16.61 +[NH2+]=* 25.59 +[NH3+]-* 27.64 +[n](:*):* 12.89 +[n](:*)(:*):* 4.41 +[n](-*)(:*):* 4.93 +[n](=*)(:*):* 8.39 +[nH](:*):* 15.79 +[n+](:*)(:*):* 4.10 +[n+](-*)(:*):* 3.88 +[nH+](:*):* 14.14 +[O](-*)-* 9.23 +[O]1-*-*1 12.53 +[O]=* 17.07 +[OH]-* 20.23 +[O-]-* 23.06 +[o](:*):* 13.14 +[S](-*)-* 25.30 +[S]=* 32.09 +[S](-*)(-*)=* 19.21 +[S](-*)(-*)(=*)=* 8.38 +[SH]-* 38.80 +[s](:*):* 28.24 +[s](=*)(:*):* 21.70 +[P](-*)(-*)-* 13.59 +[P](-*)=* 34.14 +[P](-*)(-*)(-*)=* 9.81 +[PH](-*)(-*)=* 23.47
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/qeq.txt Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,116 @@ +# +# Open Babel file: qeq.txt +# +# Charge parameters for the QEq and QTPIE methods +# Used by QEqCharges and QTPIECharges, which are daughters of OBChargeModel +# +# Parameters: +# +# Elt: Element symbol +# Eneg: Atomic electronegativity (Volts) +# Hard: Atomic (chemical) hardness (Volts/e) +# Radius: screening radius (Angstrom) +# Elt Eneg Hard Radius +H 4.528 13.8904 0.8271 +He 9.66 29.8400 1.7640 +Li 3.006 4.7720 2.4076 +Be 4.877 8.8860 1.2930 +B 5.11 9.5000 1.2094 +C 5.343 10.1260 1.1346 +N 6.899 11.7600 0.9770 +O 8.741 13.3640 0.8597 +F 10.874 14.9480 0.7686 +Ne 11.04 21.1000 1.4394 +Na 2.843 4.5920 2.5020 +Mg 3.951 7.3860 1.5555 +Al 4.06 7.1800 1.6002 +Si 4.168 6.9740 1.6474 +P 5.463 8.0000 1.4362 +S 6.928 8.9720 1.2806 +Cl 8.564 9.8920 1.1615 +Ar 9.465 12.7100 1.2259 +K 2.421 3.8400 2.9920 +Ca 3.231 5.7600 1.9947 +Sc 3.395 6.1600 1.8651 +Ti 3.47 6.7600 1.6996 +V 3.65 6.8200 1.6846 +Cr 3.415 7.7300 1.4863 +Mn 3.325 8.2100 1.3994 +Fe 3.76 8.2800 1.3876 +Co 4.105 8.3500 1.3760 +Ni 4.465 8.4100 1.3661 +Cu 4.2 8.4400 1.3613 +Zn 5.106 8.5700 1.3406 +Ga 3.641 6.3200 1.8179 +Ge 4.051 6.8760 1.6709 +As 5.188 7.6180 1.5082 +Se 6.428 8.2620 1.3906 +Br 7.79 8.8500 1.2982 +Kr 8.505 11.4300 1.0268 +Rb 2.331 3.6920 3.1119 +Sr 3.024 4.8800 2.3544 +Y 3.83 5.6200 2.0444 +Zr 3.4 7.1000 1.6182 +Nb 3.55 6.7600 1.6996 +Mo 3.465 7.5100 1.5299 +Tc 3.29 7.9800 1.4398 +Ru 3.575 8.0300 1.4308 +Rh 3.975 8.0100 1.4344 +Pd 4.32 8.0000 1.4362 +Ag 4.436 6.2680 1.8330 +Cd 5.034 7.9140 1.4518 +In 3.506 5.7920 1.9836 +Sn 3.987 6.2480 1.8389 +Sb 4.899 6.6840 1.7189 +Te 5.816 7.0520 1.6292 +I 6.822 7.5240 1.5270 +Xe 7.595 9.9500 1.1547 +Cs 2.183 3.4220 3.3575 +Ba 2.814 4.7920 2.3976 +La 2.8355 5.4830 2.0954 +Ce 2.774 5.3840 2.1340 +Pr 2.858 5.1280 2.2405 +Nd 2.8685 5.2410 2.1922 +Pm 2.881 5.3460 2.1491 +Sm 2.9115 5.4390 2.1124 +Eu 2.8785 5.5750 2.0609 +Gd 3.1665 5.9490 1.9313 +Tb 3.018 5.6680 2.0270 +Dy 3.0555 5.7430 2.0006 +Ho 3.127 5.7820 1.9871 +Er 3.1865 5.8290 1.9711 +Tm 3.2514 5.8658 1.9587 +Yb 3.2889 5.9300 1.9375 +Lu 2.9629 4.9258 2.3325 +Hf 3.7 6.8000 1.6896 +Ta 5.1 5.7000 2.0157 +W 4.63 6.6200 1.7355 +Re 3.96 7.8400 1.4655 +Os 5.14 7.2600 1.5825 +Ir 5 8.0000 1.4362 +Pt 4.79 8.8600 1.2968 +Au 4.894 5.1720 2.2214 +Hg 6.27 8.3200 1.3809 +Tl 3.2 5.8000 1.9809 +Pb3 3.9 7.0600 1.6274 +Bi 4.69 7.4800 1.5360 +Po 4.21 8.4200 1.3645 +At 4.75 9.5000 1.2094 +Rn 5.37 10.7400 1.0698 +Fr 2 4.0000 2.8723 +Ra 2.843 4.8680 2.3602 +Ac 2.835 5.6700 2.0263 +Th 3.175 5.8100 1.9775 +Pa 2.985 5.8100 1.9775 +U 3.341 5.7060 2.0135 +Np 3.549 5.4340 2.1143 +Pu 3.243 5.6380 2.0378 +Am 2.9895 6.0070 1.9126 +Cm 2.8315 6.3790 1.8011 +Bk 3.1935 6.0710 1.8925 +Cf 3.197 6.2020 1.8525 +Es 3.333 6.1780 1.8597 +Fm 3.4 6.2000 1.8531 +Md 3.47 6.2200 1.8471 +No 3.475 6.3500 1.8093 +Lr 3.5 6.4000 1.7952
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/resdata.h Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,920 @@ +/*************************************************************** +This file is part of the Open Babel project. +This is copyright under the GNU General Public License (GPL) +For more information, see <http://openbabel.org/> + +This file contains a binary representation of data tables + used by Open Babel. It is used as a fallback if the textual + data table is not found at runtime. It is not a normal header. +***************************************************************/ + + +#ifndef OB_RESDATA_H +#define OB_RESDATA_H + +namespace OpenBabel +{ +static const char ResidueData[] = { + 0x52,0x45,0x53,0x20,0x41,0x4C,0x41,0x0A,0x41,0x54,0x4F,0x4D,0x20,0x43,0x41, + 0x20,0x43,0x33,0x20,0x33,0x0A,0x41,0x54,0x4F,0x4D,0x20,0x4E,0x20,0x4E,0x61, + 0x6D,0x20,0x32,0x0A,0x41,0x54,0x4F,0x4D,0x20,0x43,0x42,0x20,0x43,0x33,0x20, + 0x33,0x0A,0x41,0x54,0x4F,0x4D,0x20,0x43,0x20,0x43,0x61,0x63,0x20,0x32,0x0A, + 0x41,0x54,0x4F,0x4D,0x20,0x4F,0x20,0x4F,0x32,0x20,0x32,0x0A,0x42,0x4F,0x4E, + 0x44,0x20,0x43,0x41,0x20,0x4E,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43, + 0x41,0x20,0x43,0x42,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x41,0x20, + 0x43,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x43,0x20,0x4F,0x20,0x32,0x0A, + 0x42,0x4F,0x4E,0x44,0x20,0x4E,0x20,0x48,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44, + 0x20,0x4E,0x20,0x48,0x4E,0x20,0x31,0x0A,0x42,0x4F,0x4E,0x44,0x20,0x48,0x41, + 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0x42,0x4F,0x4E,0x44,0x20,0x43,0x41,0x43,0x20,0x43,0x42,0x43,0x20,0x31,0x0A, + 0x42,0x4F,0x4E,0x44,0x20,0x4E,0x44,0x20,0x43,0x31,0x44,0x20,0x31,0x0A,0x42, + 0x4F,0x4E,0x44,0x20,0x4E,0x44,0x20,0x43,0x34,0x44,0x20,0x31,0x0A,0x42,0x4F, + 0x4E,0x44,0x20,0x43,0x31,0x44,0x20,0x43,0x32,0x44,0x20,0x31,0x0A,0x42,0x4F, + 0x4E,0x44,0x20,0x43,0x32,0x44,0x20,0x43,0x33,0x44,0x20,0x31,0x0A,0x42,0x4F, + 0x4E,0x44,0x20,0x43,0x32,0x44,0x20,0x43,0x4D,0x44,0x20,0x31,0x0A,0x42,0x4F, + 0x4E,0x44,0x20,0x43,0x33,0x44,0x20,0x43,0x34,0x44,0x20,0x31,0x0A,0x42,0x4F, + 0x4E,0x44,0x20,0x43,0x33,0x44,0x20,0x43,0x41,0x44,0x20,0x31,0x0A,0x42,0x4F, + 0x4E,0x44,0x20,0x43,0x41,0x44,0x20,0x43,0x42,0x44,0x20,0x31,0x0A,0x42,0x4F, + 0x4E,0x44,0x20,0x43,0x42,0x44,0x20,0x43,0x47,0x44,0x20,0x31,0x0A,0x42,0x4F, + 0x4E,0x44,0x20,0x43,0x47,0x44,0x20,0x4F,0x31,0x44,0x20,0x32,0x0A,0x42,0x4F, + 0x4E,0x44,0x20,0x43,0x47,0x44,0x20,0x4F,0x32,0x44,0x20,0x31,0x0A,0x45,0x4E, + 0x44,0x0A,0x00}; + +} // namespace OpenBabel +#endif // OB_RESDATA_H +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/resdata.txt Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,1139 @@ +############################################################################## +# # +# Open Babel file: resdata.txt # +# # +# Copyright (c) 1998-2001 by OpenEye Scientific Software, Inc. # +# Some portions Copyright (c) 2001-2003 by Geoffrey R. Hutchison # +# Part of the Open Babel package, under the GNU General Public License (GPL)# +# # +# Residue records are specified as follows: (used by data.cpp:OBResidueData)# +# RES <name> # +# ATOM Name Type Hybridization (hydrogens are implicit) # +# BOND Name1 Name2 BondOrder (where Name1, Name2 are ATOM records) # +# END # +# # +############################################################################## + +RES ALA +ATOM CA C3 3 +ATOM N Nam 2 +ATOM CB C3 3 +ATOM C Cac 2 +ATOM O O2 2 +BOND CA N 1 +BOND CA CB 1 +BOND CA C 1 +BOND C O 2 +BOND N H 1 +BOND N HN 1 +BOND HA CA 1 +BOND 1HB CB 1 +BOND 2HB CB 1 +BOND 3HB CB 1 +END + +RES ARG +ATOM CA C3 3 +ATOM N Nam 2 +ATOM CB C3 3 +ATOM C Cac 2 +ATOM O O2 2 +ATOM CG C3 3 +ATOM CD C3 3 +ATOM NE Ng+ 2 +ATOM CZ C+ 2 +ATOM NH2 Ng+ 2 +ATOM NH1 Ng+ 2 +BOND CA N 1 +BOND CA CB 1 +BOND CA C 1 +BOND C O 2 +BOND CB CG 1 +BOND CG CD 1 +BOND CD NE 1 +BOND NE CZ 1 +BOND CZ NH2 2 +BOND CZ NH1 1 +BOND N H 1 +BOND HN N 1 +BOND NH1 1HH1 1 +BOND NH1 2HH1 1 +BOND NE HE 1 +BOND NH2 1HH2 1 +BOND NH2 2HH2 1 +BOND NH1 HH1 1 +BOND NH2 HH2 1 +BOND HA CA 1 +BOND 1HB CB 1 +BOND 2HB CB 1 +BOND 1HD CD 1 +BOND 2HD CD 1 +BOND 1HG CG 1 +BOND 2HG CG 1 +END + +RES ARZ +ATOM CA C3 3 +ATOM N Nam 2 +ATOM CB C3 3 +ATOM C Cac 2 +ATOM O O2 2 +ATOM CG C3 3 +ATOM CD C3 3 +ATOM NE Ng+ 2 +ATOM CZ C+ 2 +ATOM NH2 Ng+ 2 +ATOM NH1 Ng+ 2 +BOND CA N 1 +BOND CA CB 1 +BOND CA C 1 +BOND C O 2 +BOND CB CG 1 +BOND CG CD 1 +BOND CD NE 1 +BOND NE CZ 1 +BOND CZ NH2 1 +BOND CZ NH1 2 +BOND N H 1 +BOND N HN 1 +BOND NH1 HH1 1 +BOND NE HE 1 +BOND NH2 1HH2 1 +BOND NH2 2HH2 1 +END + +RES ASN +ATOM CA C3 3 +ATOM N Nam 2 +ATOM CB C3 3 +ATOM C Cac 2 +ATOM O O2 2 +ATOM CG C3 3 +ATOM ND2 Nam 2 +ATOM OD1 O2 2 +BOND CA N 1 +BOND CA CB 1 +BOND CA C 1 +BOND C O 2 +BOND CB CG 1 +BOND CG ND2 1 +BOND CG OD1 2 +BOND N H 1 +BOND N HN 1 +BOND HA CA 1 +BOND 1HB CB 1 +BOND 2HB CB 1 +BOND ND2 1HD2 1 +BOND ND2 2HD2 1 +BOND ND2 HD2 1 +END + +RES ASP +ATOM CA C3 3 +ATOM N Nam 2 +ATOM CB C3 3 +ATOM C Cac 2 +ATOM O O2 2 +ATOM CG C2 2 +ATOM OD2 O2 2 +ATOM OD1 O3 3 +BOND CA N 1 +BOND CA CB 1 +BOND CA C 1 +BOND C O 2 +BOND CB CG 1 +BOND CG OD2 2 +BOND CG OD1 1 +BOND N H 1 +BOND N HN 1 +BOND HA CA 1 +BOND 1HB CB 1 +BOND 2HB CB 1 +END + +RES ASH +ATOM CA C3 3 +ATOM N Nam 2 +ATOM CB C3 3 +ATOM C Cac 2 +ATOM O O2 2 +ATOM CG C2 2 +ATOM OD2 O3 3 +ATOM OD1 O2 2 +BOND CA N 1 +BOND CA CB 1 +BOND CA C 1 +BOND C O 2 +BOND CB CG 1 +BOND CG OD2 1 +BOND CG OD1 2 +BOND N H 1 +BOND N HN 1 +BOND OD2 HD2 1 +END + +RES CYS +ATOM CA C3 3 +ATOM N Nam 2 +ATOM CB C3 3 +ATOM C Cac 2 +ATOM O O2 2 +ATOM SG S3 3 +BOND SG CB 1 +BOND CA N 1 +BOND CA CB 1 +BOND CA C 1 +BOND C O 2 +BOND CB SG 1 +BOND N H 1 +BOND N HN 1 +BOND CA HA 1 +BOND 1HB CB 1 +BOND 2HB CB 1 +BOND SG HG 1 +END + +RES CYX +ATOM CA C3 3 +ATOM N Nam 2 +ATOM CB C3 3 +ATOM C Cac 2 +ATOM O O2 2 +ATOM SG S3 3 +BOND CA N 1 +BOND CA CB 1 +BOND CA C 1 +BOND C O 2 +BOND CB SG 1 +BOND N H 1 +END + +RES GLN +ATOM CA C3 3 +ATOM N Nam 2 +ATOM CB C3 3 +ATOM C Cac 2 +ATOM O O2 2 +ATOM CG C3 3 +ATOM CD C2 2 +ATOM NE2 Nam 2 +ATOM OE1 O2 2 +BOND CA N 1 +BOND CA CB 1 +BOND CA C 1 +BOND C O 2 +BOND CB CG 1 +BOND CG CD 1 +BOND CD NE2 1 +BOND CD OE1 2 +BOND N H 1 +BOND N HN 1 +BOND CA HA 1 +BOND 1HB CB 1 +BOND 2HB CB 1 +BOND 1HG CG 1 +BOND 2HG CG 1 +BOND NE2 1HE2 1 +BOND NE2 2HE2 1 +BOND NE2 HE2 1 +END + +RES GLU +ATOM CA C3 3 +ATOM N Nam 2 +ATOM CB C3 3 +ATOM C Cac 2 +ATOM O O2 2 +ATOM CG C3 3 +ATOM CD C2 2 +ATOM OE2 O3 3 +ATOM OE1 O2 2 +BOND CA N 1 +BOND CA CB 1 +BOND CA C 1 +BOND C O 2 +BOND CB CG 1 +BOND CG CD 1 +BOND CD OE2 1 +BOND CD OE1 2 +BOND N H 1 +BOND N 1H 1 +BOND N 2H 1 +BOND N 3H 1 +BOND HA CA 1 +BOND 1HB CB 1 +BOND 2HB CB 1 +BOND 1HG CG 1 +BOND 2HG CG 1 +END + +RES GLY +ATOM CA C3 3 +ATOM N Nam 2 +ATOM C Cac 2 +ATOM O O2 2 +BOND CA N 1 +BOND CA C 1 +BOND C O 2 +BOND N H 1 +BOND N HN 1 +BOND 1HA CA 1 +BOND 2HA CA 1 +END + +RES GLZ +ATOM CA C3 3 +ATOM N Nam 2 +ATOM CB C3 3 +ATOM C Cac 2 +ATOM O O2 2 +ATOM CG C3 3 +ATOM CD C2 2 +ATOM OE2 O3 3 +ATOM OE1 O2 2 +BOND CA N 1 +BOND CA CB 1 +BOND CA C 1 +BOND C O 2 +BOND CB CG 1 +BOND CG CD 1 +BOND CD OE2 1 +BOND CD OE1 2 +BOND N H 1 +BOND OE2 HE2 1 +END + +RES HID +ATOM CA C3 3 +ATOM N Nam 2 +ATOM CB C3 3 +ATOM C C3 3 +ATOM O O2 2 +ATOM CG C2 2 +ATOM ND1 Npl 2 +ATOM CD2 C2 2 +ATOM NE2 N2 2 +ATOM CE1 C2 2 +BOND CA N 1 +BOND CA CB 1 +BOND CA C 1 +BOND C O 2 +BOND CB CG 1 +BOND CG ND1 1 +BOND CG CD2 2 +BOND CD2 NE2 1 +BOND NE2 CE1 2 +BOND CE1 ND1 1 +BOND N H 1 +BOND ND1 HD1 1 +END + +RES HIE +ATOM CA C3 3 +ATOM N Nam 2 +ATOM CB C3 3 +ATOM C Cac 2 +ATOM O O2 2 +ATOM CG C2 2 +ATOM ND1 Npl 2 +ATOM CD2 C2 2 +ATOM NE2 Npl 2 +ATOM CE1 C3 3 +BOND CA N 1 +BOND CA CB 1 +BOND CA C 1 +BOND C O 2 +BOND CB CG 1 +BOND CG ND1 1 +BOND CG CD2 2 +BOND CD2 NE2 1 +BOND NE2 CE1 1 +BOND CE1 ND1 1 +BOND N H 1 +BOND NE2 HE2 1 +END + +RES HIP +ATOM CA C3 3 +ATOM N Nam 2 +ATOM CB C3 3 +ATOM C Cac 2 +ATOM O O2 2 +ATOM CG C2 2 +ATOM ND1 Npl 2 +ATOM CD2 C2 2 +ATOM NE2 Npl 2 +ATOM CE1 C3 3 +BOND CA N 1 +BOND CA CB 1 +BOND CA C 1 +BOND C O 2 +BOND CB CG 1 +BOND CG ND1 1 +BOND CG CD2 2 +BOND CD2 NE2 1 +BOND NE2 CE1 1 +BOND CE1 ND1 1 +BOND N H 1 +BOND ND1 HD1 1 +BOND NE2 HE2 1 +END + +RES HIS +ATOM CA C3 3 +ATOM N Nam 2 +ATOM CB C3 3 +ATOM C Cac 2 +ATOM O O2 2 +ATOM CG C2 2 +ATOM ND1 Npl 2 +ATOM CD2 C2 2 +ATOM NE2 Npl 2 +ATOM CE1 C2 2 +BOND CA N 1 +BOND CA CB 1 +BOND CA C 1 +BOND C O 2 +BOND CB CG 1 +BOND CG ND1 1 +BOND CG CD2 2 +BOND CD2 NE2 1 +BOND NE2 CE1 2 +BOND CE1 ND1 1 +BOND N H 1 +BOND N HN 1 +BOND HA CA 1 +BOND 1HB CB 1 +BOND 2HB CB 1 +BOND 1HD ND1 1 +BOND 2HD CD2 1 +BOND 1HE CE1 1 +BOND ND1 HD1 1 +BOND NE2 HE2 1 +END + +RES ILE +ATOM CA C3 3 +ATOM N Nam 2 +ATOM CB C3 3 +ATOM C Cac 2 +ATOM O O2 2 +ATOM CG2 C3 3 +ATOM CG1 C3 3 +ATOM CD1 C3 3 +BOND CA N 1 +BOND CA CB 1 +BOND CA C 1 +BOND C O 2 +BOND CB CG2 1 +BOND CB CG1 1 +BOND CG1 CD1 1 +BOND N H 1 +BOND N HN 1 +BOND CA HA 1 +BOND HB CB 1 +BOND 1HG1 CG1 1 +BOND 2HG1 CG1 1 +BOND 1HG2 CG2 1 +BOND 2HG2 CG2 1 +BOND 3HG2 CG2 1 +BOND 1HD1 CD1 1 +BOND 2HD1 CD1 1 +BOND 3HD1 CD1 1 +END + +RES LEU +ATOM CA C3 3 +ATOM N Nam 2 +ATOM CB C3 3 +ATOM C Cac 2 +ATOM O O2 2 +ATOM CG C3 3 +ATOM CD1 C3 3 +ATOM CD2 C3 3 +BOND CA N 1 +BOND CA CB 1 +BOND CA C 1 +BOND C O 2 +BOND CB CG 1 +BOND CG CD1 1 +BOND CG CD2 1 +BOND N H 1 +BOND N HN 1 +BOND HA CA 1 +BOND 1HB CB 1 +BOND 2HB CB 1 +BOND 1HD1 CD1 1 +BOND 2HD1 CD1 1 +BOND 3HD1 CD1 1 +BOND 1HD2 CD2 1 +BOND 2HD2 CD2 1 +BOND 3HD2 CD2 1 +BOND HG CG 1 +END + +RES LYS +ATOM CA C3 3 +ATOM N Nam 2 +ATOM CB C3 3 +ATOM C Cac 2 +ATOM O O2 2 +ATOM CG C3 3 +ATOM CD C3 3 +ATOM CE C3 3 +ATOM NZ N3+ 3 +BOND CA N 1 +BOND CA CB 1 +BOND CA C 1 +BOND C O 2 +BOND CB CG 1 +BOND CG CD 1 +BOND CD CE 1 +BOND CE NZ 1 +BOND N H 1 +BOND N HN 1 +BOND HA CA 1 +BOND 1HB CB 1 +BOND 2HB CB 1 +BOND 1HD CD 1 +BOND 2HD CD 1 +BOND 1HG CG 1 +BOND 2HG CG 1 +BOND 1HE CE 1 +BOND 2HE CE 1 +BOND NZ 3HZ 1 +BOND NZ HZ3 1 +BOND NZ 2HZ 1 +BOND NZ HZ2 1 +BOND NZ 1HZ 1 +BOND NZ HZ1 1 +END + +RES LYZ +ATOM CA C3 3 +ATOM N Nam 2 +ATOM CB C3 3 +ATOM C Cac 2 +ATOM O O2 2 +ATOM CG C3 3 +ATOM CD C3 3 +ATOM CE C3 3 +ATOM NZ N3+ 3 +BOND CA N 1 +BOND CA CB 1 +BOND CA C 1 +BOND C O 2 +BOND CB CG 1 +BOND CG CD 1 +BOND CD CE 1 +BOND CE NZ 1 +BOND N H 1 +BOND NZ HZ2 1 +BOND NZ HZ1 1 +END + +RES MET +ATOM CA C3 3 +ATOM N Nam 2 +ATOM CB C3 3 +ATOM C Cac 2 +ATOM O O2 2 +ATOM CG C3 3 +ATOM SD S3 3 +ATOM CE C3 3 +BOND CA N 1 +BOND CA CB 1 +BOND CA C 1 +BOND C O 2 +BOND CB CG 1 +BOND CG SD 1 +BOND SD CE 1 +BOND N H 1 +BOND N HN 1 +BOND HA CA 1 +BOND 1HB CB 1 +BOND 2HB CB 1 +BOND 1HG CG 1 +BOND 2HG CG 1 +BOND 1HE CE 1 +BOND 2HE CE 1 +BOND 3HE CE 1 +END + +RES PHE +ATOM CA C3 3 +ATOM N Nam 2 +ATOM CB C3 3 +ATOM C Cac 2 +ATOM O O2 2 +ATOM CG Car 2 +ATOM CD1 Car 2 +ATOM CD2 Car 2 +ATOM CE2 Car 2 +ATOM CZ Car 2 +ATOM CE1 Car 2 +BOND CA N 1 +BOND CA CB 1 +BOND CA C 1 +BOND C O 2 +BOND CB CG 1 +BOND CG CD1 1 +BOND CG CD2 2 +BOND CD2 CE2 1 +BOND CE2 CZ 2 +BOND CZ CE1 1 +BOND CE1 CD1 2 +BOND N H 1 +BOND N HN 1 +BOND HA CA 1 +BOND 1HB CB 1 +BOND 2HB CB 1 +BOND 1HD CD1 1 +BOND 2HD CD2 1 +BOND 1HE CE1 1 +BOND 2HE CE2 1 +BOND HZ CZ 1 +END + +RES PRO +ATOM CA C3 3 +ATOM C Cac 2 +ATOM CB C3 3 +ATOM N Nam 2 +ATOM CD C3 3 +ATOM CG C3 3 +ATOM O O2 2 +BOND CA C 1 +BOND CA CB 1 +BOND CA N 1 +BOND N CD 1 +BOND CD CG 1 +BOND CG CB 1 +BOND C O 2 +BOND 1HB CB 1 +BOND 2HB CB 1 +BOND 1HG CG 1 +BOND 2HG CG 1 +BOND 1HD CD 1 +BOND 2HD CD 1 +BOND HA CA 1 +BOND HN N 1 +END + +RES PSE +ATOM CA C3 3 +ATOM N Nam 2 +ATOM CB C3 3 +ATOM C Cac 2 +ATOM O O2 2 +ATOM OG O3 3 +ATOM PD P3 3 +ATOM OE2 O- 3 +ATOM OE3 O- 3 +ATOM OE1 O- 3 +BOND CA N 1 +BOND CA CB 1 +BOND CA C 1 +BOND C O 2 +BOND CB OG 1 +BOND OG PD 1 +BOND PD OE2 1 +BOND PD OE3 1 +BOND PD OE1 1 +BOND N H 1 +END + +RES PSM +ATOM CA C3 3 +ATOM N Nam 2 +ATOM CB C3 3 +ATOM C Cac 2 +ATOM O O2 2 +ATOM OG O3 3 +ATOM PD P3 3 +ATOM OE2 O- 3 +ATOM OE3 O- 3 +ATOM OE1 O- 3 +BOND CA N 1 +BOND CA CB 1 +BOND CA C 1 +BOND C O 2 +BOND CB OG 1 +BOND OG PD 1 +BOND PD OE2 1 +BOND PD OE3 1 +BOND PD OE1 1 +BOND N H 1 +BOND OE3 HE3 1 +END + +RES PTM +ATOM CA C3 3 +ATOM N Nam 2 +ATOM CB C3 3 +ATOM C Cac 2 +ATOM O O2 2 +ATOM CG Car 2 +ATOM CD1 Car 2 +ATOM CD2 Car 2 +ATOM CE2 Car 2 +ATOM CZ Car 2 +ATOM OH O3 3 +ATOM CE1 Car 2 +ATOM PQ P3 3 +ATOM OI3 O- 3 +ATOM OI2 O- 3 +ATOM OI1 O- 3 +BOND CA N 1 +BOND CA CB 1 +BOND CA C 1 +BOND C O 2 +BOND CB CG 1 +BOND CG CD1 2 +BOND CG CD2 1 +BOND CD2 CE2 2 +BOND CE2 CZ 1 +BOND CZ OH 1 +BOND CZ CE1 2 +BOND CE1 CD1 1 +BOND OH PQ 1 +BOND PQ OI3 1 +BOND PQ OI2 1 +BOND PQ OI1 1 +BOND N H 1 +BOND OI2 HI2 1 +END + +RES PTY +ATOM CA C3 3 +ATOM N Nam 2 +ATOM CB C3 3 +ATOM C Cac 2 +ATOM O O2 2 +ATOM CG Car 2 +ATOM CD1 Car 2 +ATOM CD2 Car 2 +ATOM CE2 Car 2 +ATOM CZ Car 2 +ATOM OH O3 3 +ATOM CE1 Car 2 +ATOM PQ P3 3 +ATOM OI3 O- 3 +ATOM OI2 O- 3 +ATOM OI1 O- 3 +BOND CA N 1 +BOND CA CB 1 +BOND CA C 1 +BOND C O 2 +BOND CB CG 1 +BOND CG CD1 2 +BOND CG CD2 1 +BOND CD2 CE2 2 +BOND CE2 CZ 1 +BOND CZ OH 1 +BOND CZ CE1 2 +BOND CE1 CD1 1 +BOND OH PQ 1 +BOND PQ OI3 1 +BOND PQ OI2 1 +BOND PQ OI1 1 +BOND N H 1 +END + +RES SER +ATOM CA C3 3 +ATOM N Nam 2 +ATOM CB C3 3 +ATOM C Cac 2 +ATOM O O2 2 +ATOM OG O3 3 +BOND CA N 1 +BOND CA CB 1 +BOND CA C 1 +BOND C O 2 +BOND CB OG 1 +BOND N H 1 +BOND N HN 1 +BOND HA CA 1 +BOND 1HB CB 1 +BOND 2HB CB 1 +BOND OG HG 1 +END + +RES THR +ATOM CA C3 3 +ATOM N Nam 2 +ATOM CB C3 3 +ATOM C Cac 2 +ATOM O O2 2 +ATOM CG2 C3 3 +ATOM OG1 O3 3 +BOND CA N 1 +BOND CA CB 1 +BOND CA C 1 +BOND C O 2 +BOND CB CG2 1 +BOND CB OG1 1 +BOND N H 1 +BOND HN N 1 +BOND N 1H 1 +BOND N 2H 1 +BOND N 3H 1 +BOND OG1 HG1 1 +BOND OG1 1HG 1 +BOND HB CB 1 +BOND HA CA 1 +BOND 1HG2 CG2 1 +BOND 2HG2 CG2 1 +BOND 3HG2 CG2 1 +END + +RES TRP +ATOM CA C3 3 +ATOM N Nam 2 +ATOM CB C3 3 +ATOM C Cac 2 +ATOM O O2 2 +ATOM CG Car 2 +ATOM CD1 Car 2 +ATOM CD2 Car 2 +ATOM CE3 Car 2 +ATOM CE2 Car 2 +ATOM CZ2 Car 2 +ATOM NE1 Nar 2 +ATOM CH2 Car 2 +ATOM CZ3 Car 2 +BOND CA N 1 +BOND CA CB 1 +BOND CA C 1 +BOND C O 2 +BOND CB CG 1 +BOND CG CD1 2 +BOND CG CD2 1 +BOND CD2 CE3 2 +BOND CD2 CE2 1 +BOND CE2 CZ2 2 +BOND CE2 NE1 1 +BOND NE1 CD1 1 +BOND CZ2 CH2 1 +BOND CH2 CZ3 2 +BOND CZ3 CE3 1 +BOND N H 1 +BOND N HN 1 +BOND HA CA 1 +BOND 1HB CB 1 +BOND 2HB CB 1 +BOND 1HD CD1 1 +BOND 1HE CE1 1 +BOND 2HZ CZ2 1 +BOND 3HZ CZ3 1 +BOND 3HE CE3 1 +BOND 2HH CH2 1 +BOND NE1 HE1 1 +BOND NE1 1HE 1 +END + +RES TYR +ATOM CA C3 3 +ATOM N Nam 2 +ATOM CB C3 3 +ATOM C Cac 2 +ATOM O O2 2 +ATOM CG Car 2 +ATOM CD1 Car 2 +ATOM CD2 Car 2 +ATOM CE2 Car 2 +ATOM CZ Car 2 +ATOM OH O3 3 +ATOM CE1 Car 2 +BOND CA N 1 +BOND CA CB 1 +BOND CA C 1 +BOND C O 2 +BOND CB CG 1 +BOND CG CD1 2 +BOND CG CD2 1 +BOND CD2 CE2 2 +BOND CE2 CZ 1 +BOND CZ OH 1 +BOND CZ CE1 2 +BOND CE1 CD1 1 +BOND N H 1 +BOND OH HH 1 +BOND N HN 1 +BOND HA CA 1 +BOND 1HB CB 1 +BOND 2HB CB 1 +BOND 1HD CD1 1 +BOND 2HD CD2 1 +BOND 1HE CE1 1 +BOND 2HE CE2 1 +BOND HZ CZ 1 +END + +RES VAL +ATOM CA C3 3 +ATOM N Nam 2 +ATOM CB C3 3 +ATOM C Cac 2 +ATOM O O2 2 +ATOM CG2 C3 3 +ATOM CG1 C3 3 +BOND CA N 1 +BOND CA CB 1 +BOND CA C 1 +BOND C O 2 +BOND CB CG2 1 +BOND CB CG1 1 +BOND N H 1 +BOND N HN 1 +BOND HA CA 1 +BOND HB CB 1 +BOND 1HG1 CG1 1 +BOND 2HG1 CG1 1 +BOND 3HG1 CG1 1 +BOND 1HG2 CG2 1 +BOND 2HG2 CG2 1 +BOND 3HG2 CG2 1 +END + +RES TIP +ATOM OH2 O3 3 +BOND OH2 H1 1 +BOND OH2 H2 1 +END + +RES HOH +ATOM O O3 3 +ATOM 1H +ATOM 2H +BOND O 1H 1 +BOND O 2H 1 +END + +RES WAT +ATOM O O3 3 +ATOM H1 +ATOM H2 +BOND O H1 1 +BOND O H2 1 +END + +RES INH +ATOM P +ATOM O1P +ATOM O2P +ATOM O3P +ATOM O5 +ATOM C5 +ATOM C4 +ATOM O4 +ATOM C3 +ATOM C1 +ATOM O3 +ATOM C2 +ATOM O2 +ATOM N9 +ATOM C8 +ATOM N7 +ATOM C6 +ATOM O6 +ATOM N1 +ATOM N3 +BOND P O1P 2 +BOND P O2P 1 +BOND P O3P 1 +BOND P O5 1 +BOND O5 C5 1 +BOND C5 C4 1 +BOND C4 O4 1 +BOND C4 C3 1 +BOND O4 C1 1 +BOND C3 O3 1 +BOND C3 C2 1 +BOND O3 H1 1 +BOND C2 O2 1 +BOND C2 C1 1 +BOND O2 H2 1 +BOND C1 N9 1 +BOND N9 C8 1 +BOND N9 C4 1 +BOND C8 N7 2 +BOND N7 C5 1 +BOND C5 C6 1 +BOND C6 O6 2 +BOND C6 N1 1 +BOND N1 C2 1 +BOND N1 H3 1 +BOND C2 N3 2 +BOND N3 C4 1 +END + +RES UMP +ATOM N1 +ATOM C2 +ATOM C6 +ATOM C1 +ATOM N3 +ATOM O2 +ATOM C4 +ATOM C5 +ATOM O4 +ATOM C3 +ATOM O3 +ATOM O5 +ATOM P +ATOM O1P +ATOM O2P +ATOM O3P +BOND N1 C2 1 +BOND N1 C6 1 +BOND N1 C1 1 +BOND C2 N3 1 +BOND C2 O2 1 +BOND C2 H5 1 +BOND N3 C4 1 +BOND N3 H1 1 +BOND C4 C5 1 +BOND C4 O4 1 +BOND C4 H6 1 +BOND C5 C6 1 +BOND C5 H7 1 +BOND C5 H8 1 +BOND C6 H9 1 +BOND C6 H10 1 +BOND O2 H2 1 +BOND O4 H3 1 +BOND C1 C2 1 +BOND C1 O4 1 +BOND C1 H11 1 +BOND C2 C3 1 +BOND C2 H12 1 +BOND C2 H13 1 +BOND C3 C4 1 +BOND C3 O3 1 +BOND C3 H14 1 +BOND C4 H15 1 +BOND O3 H4 1 +BOND C5 O5 1 +BOND C5 H16 1 +BOND C5 H17 1 +BOND O5 P 1 +BOND P O1P 2 +BOND P O2P 2 +BOND P O3P 2 +END + +RES HED +ATOM C1 +ATOM O1 +ATOM C2 +ATOM S3 +ATOM S4 +ATOM C5 +ATOM C6 +ATOM O6 +BOND C1 O1 2 +BOND C1 C2 1 +BOND C2 S3 1 +BOND S3 S4 1 +BOND S4 C5 1 +BOND C5 C6 1 +BOND C6 O6 2 +END + +RES HEM +ATOM FE +ATOM NA +ATOM NB +ATOM NC +ATOM ND +ATOM CHA +ATOM C1A +ATOM C4D +ATOM CHB +ATOM C4A +ATOM C1B +ATOM CHC +ATOM C4B +ATOM C1C +ATOM CHD +ATOM C4C +ATOM C1D +ATOM C2A +ATOM C3A +ATOM CAA +ATOM CMA +ATOM CBA +ATOM CGA +ATOM O1A +ATOM O2A +ATOM C2B +ATOM C3B +ATOM CMB +ATOM CAB +ATOM CBB +ATOM C2C +ATOM C3C +ATOM CMC +ATOM CAC C3 3 +ATOM CBC +ATOM C2D +ATOM C3D +ATOM CMD +ATOM CAD +ATOM CBD +ATOM CGD +ATOM O1D +ATOM O2D +BOND FE NA 1 +BOND FE NB 1 +BOND FE NC 1 +BOND FE ND 1 +BOND CHA C1A 1 +BOND CHA C4D 1 +BOND CHB C4A 1 +BOND CHB C1B 1 +BOND CHC C4B 1 +BOND CHC C1C 1 +BOND CHD C4C 1 +BOND CHD C1D 1 +BOND NA C1A 1 +BOND NA C4A 1 +BOND C1A C2A 1 +BOND C2A C3A 1 +BOND C2A CAA 1 +BOND C3A C4A 1 +BOND C3A CMA 1 +BOND CAA CBA 1 +BOND CBA CGA 1 +BOND CGA O1A 2 +BOND CGA O2A 1 +BOND NB C1B 1 +BOND NB C4B 1 +BOND C1B C2B 1 +BOND C2B C3B 1 +BOND C2B CMB 1 +BOND C3B C4B 1 +BOND C3B CAB 1 +BOND CAB CBB 1 +BOND NC C1C 1 +BOND NC C4C 1 +BOND C1C C2C 1 +BOND C2C C3C 1 +BOND C2C CMC 1 +BOND C3C C4C 1 +BOND C3C CAC 1 +BOND CAC CBC 1 +BOND ND C1D 1 +BOND ND C4D 1 +BOND C1D C2D 1 +BOND C2D C3D 1 +BOND C2D CMD 1 +BOND C3D C4D 1 +BOND C3D CAD 1 +BOND CAD CBD 1 +BOND CBD CGD 1 +BOND CGD O1D 2 +BOND CGD O2D 1 +END
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/ringtyp.txt Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,71 @@ +############################################################################## +# # +# Open Babel file: ringtyp.txt # +# # +# Copyright (c) 2007 Tim Vandermeersch # +# Part of the Open Babel package, under the GNU General Public License (GPL)# +# # +# SMARTS patterns for ring typing (used by typer.cpp:OBRingTyper) # +# (involved in MMFF94 atom typing, among other things) # +# # +# RINGTYP: used to assign the ring types # +# # +############################################################################## + +# +# 5 membered rings +# +# ring name smarts pattern +RINGTYP thiophene s1cccc1 +RINGTYP furan o1cccc1 +RINGTYP pyrrole n1cccc1 + +RINGTYP thiazole s1c[nD2]cc1 +RINGTYP thiazole_cation s1c[nD3]cc1 # needed by MMFF +RINGTYP oxazole o1c[nD2]cc1 +RINGTYP oxazole_cation o1c[nD3]cc1 # needed by MMFF +RINGTYP imidazole [nD3]1c[nD2]cc1 +RINGTYP imidazole_cation [nD3]1c[nD3]cc1 # needed by MMFF + +RINGTYP isothiazole s1[nD2]ccc1 +RINGTYP isothiazole_cation s1[nD3]ccc1 # needed by MMFF +RINGTYP isoxazole o1[nD2]ccc1 +RINGTYP isoxazole_cation o1[nD3]ccc1 # needed by MMFF +RINGTYP pyrazole [nD3]1[nD2]ccc1 +RINGTYP pyrazole_anion [nD2]1[nD2]ccc1 # needed by MMFF + + +RINGTYP 1,2,3-thiadiazole s1[nD2][nD2]cc1 +RINGTYP 1,2,3-thiadiazole_cation s1[nD2][nD3]cc1 # needed by MMFF +RINGTYP 1,2,4-thiadiazole s1[nD2]c[nD2]c1 +RINGTYP 1,2,4-thiadiazole_cation s1[nD2]c[nD3]c1 # needed by MMFF +RINGTYP 1,3,4-thiadiazole s1c[nD2][nD2]c1 +RINGTYP 1,3,4-thiadiazole_cation s1c[nD2][nD3]c1 # needed by MMFF + +RINGTYP 1,2,3-oxadiazole o1[nD2][nD2]cc1 +RINGTYP 1,2,3-oxadiazole_cation o1[nD2][nD3]cc1 # needed by MMFF +RINGTYP 1,2,4-oxadiazole o1[nD2]c[nD2]c1 +RINGTYP 1,2,4-oxadiazole_cation o1[nD2]c[nD3]c1 # needed by MMFF + +RINGTYP 1,2,3-triazole [nD3]1[nD2][nD2]cc1 +RINGTYP 1,2,3-triazole_anion [nD2]1[nD2][nD2]cc1 # needed by MMFF +RINGTYP 1,2,4-triazole [nD3]1[nD2]c[nD2]c1 +RINGTYP 1,2,4-triazole_anion [nD2]1[nD2]c[nD2]c1 # needed by MMFF +RINGTYP 1,3,4-triazole [nD3]1c[nD2][nD2]c1 +RINGTYP 1,3,4-triazole_cation [nD3]1c[nD3][nD2]c1 # needed by MMFF + +RINGTYP 1,2,3,4-tetrazole [nD3]1[nD2][nD2][nD2]c1 +RINGTYP 1,2,3,4-tetrazole_cation [nD3]1[nD2][nD2][nD3]c1 # needed by MMFF +RINGTYP 1,2,3,5-tetrazole [nD3]1[nD2][nD2]c[nD2]1 +RINGTYP 1,2,3,5-tetrazole_anion [nD2]1[nD2][nD2]c[nD2]1 # needed by MMFF + +# +# 6 membered rings +# +# ring name smarts pattern +RINGTYP benzene c1ccccc1 +RINGTYP pyridine n1ccccc1 +RINGTYP pyridazine n1ncccc1 +RINGTYP pyrimidine n1cnccc1 +RINGTYP pyrazine n1ccncc1 +#
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/space-groups.txt Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,9508 @@ +1 +P 1 +P 1 +x,y,z + +2 +-P 1 +P -1 +x,y,z +-x,-y,-z + +3 +P 2y +P 2,P 1 2 1 +x,y,z +-x,y,-z + +3 +P 2x +P 2 1 1 +x,y,z +x,-y,-z + +3 +P 2 +P 1 1 2 +x,y,z +-x,-y,z + +4 +P 2yb +P 21,P 1 21 1 +x,y,z +-x,1/2+y,-z + +4 +P 2xa +P 21 1 1 +x,y,z +1/2+x,-y,-z + +4 +P 2c +P 1 1 21 +x,y,z +-x,-y,1/2+z + +5 +C 2y +C 2,C 1 2 1 +x,y,z +-x,y,-z +1/2+x,1/2+y,z +1/2-x,1/2+y,-z + +5 +A 2y +A 1 2 1 +x,y,z +-x,y,-z +x,1/2+y,1/2+z +-x,1/2+y,1/2-z + +5 +I 2y +I 1 2 1 +x,y,z +-x,y,-z +1/2+x,1/2+y,1/2+z +1/2-x,1/2+y,1/2-z + +5 +A 2 +A 1 1 2 +x,y,z +-x,-y,z +x,1/2+y,1/2+z +-x,1/2-y,1/2+z + +5 +B 2 +B 1 1 2 +x,y,z +-x,-y,z +1/2+x,y,1/2+z +1/2-x,-y,1/2+z + +5 +I 2 +I 1 1 2 +x,y,z +-x,-y,z +1/2+x,1/2+y,1/2+z +1/2-x,1/2-y,1/2+z + +5 +B 2x +B 2 1 1 +x,y,z +x,-y,-z +1/2+x,y,1/2+z +1/2+x,-y,1/2-z + +5 +C 2x +C 2 1 1 +x,y,z +x,-y,-z +1/2+x,1/2+y,z +1/2+x,1/2-y,-z + +5 +I 2x 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+1/2+y,1/2+z,1/2+x +-x,-y,-z +1/2-x,1/2-y,1/2-z +z,x,y +1/2+z,1/2+x,1/2+y +-y,-z,-x +1/2-y,1/2-z,1/2-x +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/space-groups.xsl Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,29 @@ +<xsl:stylesheet version = '1.0' + xmlns:xsl='http://www.w3.org/1999/XSL/Transform'> +<xsl:output method="text"/> + +<xsl:template match="/"> + <xsl:apply-templates select="//group"/> +</xsl:template> + +<xsl:template match="group"> + <xsl:value-of select="@id"/> + <xsl:text> </xsl:text> + <xsl:value-of select="@Hall"/> + <xsl:text> </xsl:text> + <xsl:if test="@HMs"> + <xsl:value-of select="@HMs"/> + <xsl:text>,</xsl:text> + </xsl:if> + <xsl:value-of select="@HM"/> + <xsl:text> </xsl:text> + <xsl:apply-templates select="transform"/> + <xsl:text> </xsl:text> +</xsl:template> + +<xsl:template match="transform"> + <xsl:value-of select="."/> + <xsl:text> </xsl:text> +</xsl:template> + +</xsl:stylesheet>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/superatom.txt Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,113 @@ +# Translations of superatom labels to SMILES. +# First atom of SMILES string should be the one connected to the rest of +# the molecule. +# Empty lines and lines starting with # are ignored. +# Originally from http://cactus.nci.nih.gov/osra/ +# The left-aligned form is the one recognized in MDL alias lines; +# the right-aligned form may be used in 2D depiction. +# The whole list is used to look up alias names; +# only the part up to a line starting with ## is used to generate aliases. +# and here the largest fragments should be first; +#left right SMILES color +CO2Et EtO2C C(=O)OCC +COOEt EtOOC C(=O)OCC +OiBu iBuO OCC(C)C +tBu tBu C(C)(C)C +nBu nBu CCCC +iPr iPr C(C)C +nPr nPr CCC +Et Et CC +NCF3 F3CN NC(F)(F)F +CF3 F3C C(F)(F)F +CCl3 Cl3C C(Cl)(Cl)Cl +CN NC C#N +NC CN [N+]#[C-] +N(OH)CH3 CH3(OH)N N(O)C +NO2 O2N N(=O)=O +NO ON N=O +SO3H HO3S S(=O)(=O)O +COOH HOOC C(=O)O blue +OEt EtO OCC +OAc AcO OC(=O)C +NHAc AcNH NC(=O)C +Ac Ac C(=O)C +CHO OHC C=O +NMe MeN NC +SMe MeS SC +OMe MeO OC +COO- -OOC C(=O)[O-] +## Only entries above this line are used to *generate* aliases. +Ph Ph c1ccccc1 +OR RO O* +R R * +OBz BzO OCc1ccccc1 +THPO THPO O[C@@H]1OCCCC1 +NOH HON NO +CO2Me MeO2C C(=O)OC +COOMe MeOOC C(=O)OC +SO2Me MeO2S S(=O)(=O)C +NMe2 Me2N N(C)C +CO2R RO2C C(=O)O* +COOR ROOC C(=O)O* +NHZ ZNH NC(=O)OCC1=CC=CC=C1 +CH2OH HOCH2 CO +CH2NH2 H2NCH2 CN +Me Me C +OBn BnO OCC1=CC=CC=C1 +NHAm AmNH NCCCCC +OAm AmO OCCCCC +CO2Am AmO2C C(=O)OCCCCC +COOAm AmOOC C(=O)OCCCCC +SAm AmS SCCCCC +NHBn BnNH NCC1=CC=CC=C1 +CO2Bn BnO2C C(=O)OCC1=CC=CC=C1 +SnBu3 Bu3Sn [Sn](CCCC)(CCCC)CCCC +NHBu BuNH NCCCC +OBu BuO OCCCC +CO2Bu BuO2C C(=O)OCCCC +COOBu BuOOC C(=O)OCCCC +SBu BuS SCCCC +CBr3 Br3C C(Br)(Br)Br +NHCbz CbzNH NC(=O)OCC1=CC=CC=C1 +SO2Cl ClSO2 S(Cl)(=O)=O +COBr BrCO C(=O)Br +COBu BuCO C(=O)CCCC +COCF3 F3CCO C(=O)C(F)(F)F +COCl ClCO C(=O)Cl +COCO COCO C(=O)C=O +COEt EtCO C(=O)CC +COF FCO C(=O)F +COMe MeCO C(=O)C +CONEt2 Et2NCO C(=O)(CC)NCC +CONH2 H2NCO C(=O)N +CONHEt EtHNCO C(=O)NCC +CONHMe MeHNCO C(=O)NC +CONMe2 Me2NCO C(=O)(C)NC +COSH HSOC C(=O)S +NEt2 Et2N N(CC)CC +NEt3 Et3N N(CC)(CC)CC +NHEt EtNH NCC +SO2NH2 H2NSO2 S(=O)(N)=O +NHOH HONH ON +NMe2 Me2N N(C)C +OMs MsO CS(O)(=O)=O +OCN NCO N=C=O +SCN NCS N=C=S +NHAm AmHN NCCCCC +NHBn BuHN NCC1=CC=CC=C1 +NHBu BuHN NCCCC +NHEt EtHB NCC +NHOH HOHN NO +NHPr PrHN NCCC +NO ON N=O +POEt2 EtO2P P(OCC)OCC +POEt3 EtO3P P(OCC)(OCC)OCC +POOEt2 Et2OOP P(=O)(OCC)OCC +PrNH HNPr CCCN +SEt CCS SCC +#Aliases from samples provided with InChI +CH HC [CH] +CH- HC- [CH-] +D D [2H] +ND2 D2N [N]([2H])[2H] +DS SD [S][2H]
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/svgformat.script Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,45 @@ +<script type="text/ecmascript"> + <![CDATA[ + addEventListener('DOMMouseScroll', wheel, false); + onmousewheel = wheel; + var svgEl = document.getElementById("topsvg"); + var startx=0; + var starty=0; + function wheel(evt){ + evt = evt ? evt : window.event; + var normal = evt.detail ? evt.detail * -1 : evt.wheelDelta / 40; + var vb = new Array(4); + var vbtext = svgEl.getAttributeNS(null,"viewBox"); + vb = vbtext.split(" "); + var zoom = (normal<0)? 1.41 : 0.71; + //var dwidth = parseFloat(Math.max(vb[2],vb[3])) * (1-zoom); + vb[0] = parseFloat(vb[0]) + parseFloat(vb[2])*(1-zoom) * evt.clientX/innerWidth; + vb[1] = parseFloat(vb[1]) + parseFloat(vb[3])*(1-zoom) * evt.clientY/innerHeight; + vb[2] = parseFloat(vb[2]) * zoom; + vb[3] = parseFloat(vb[3]) * zoom; + svgEl.setAttributeNS(null, "viewBox", vb.join(" ")); + } + onmousedown = function(evt) { + startx = evt.clientX; + starty = evt.clientY; + } + onmousemove=function(evt) { + if(startx!=0 && starty!=0 + && ((evt.clientX - startx)*(evt.clientX - startx)+(evt.clientY - starty)*(evt.clientY - starty)>100)) + { + var vbtext = svgEl.getAttributeNS(null,"viewBox"); + vb = vbtext.split(" "); + var maxwh = Math.max(parseFloat(vb[2]),parseFloat(vb[3])); + vb[0] = parseFloat(vb[0]) - (evt.clientX - startx)*maxwh/innerWidth; + vb[1] = parseFloat(vb[1]) - (evt.clientY - starty)*maxwh/innerHeight; + svgEl.setAttributeNS(null, "viewBox", vb.join(" ")); + startx = evt.clientX; + starty = evt.clientY; + } + } + onmouseup=function() { + startx=0; + starty=0; + } + ]]> +</script>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/templates.sdf Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,27 @@ + + ACD/Labs10200816283D + + 10 12 0 0 0 0 0 0 0 0 1 V2000 + 11.7466 -9.2167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 11.0827 -10.5962 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 11.4479 -11.8018 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 12.8589 -12.6696 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 14.3767 -11.8246 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 14.5800 -10.5556 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 13.9565 -9.1175 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 12.8891 -8.7118 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 12.5532 -9.6158 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 12.4814 -11.1730 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 8 1 0 0 0 0 + 1 2 2 0 0 0 0 + 2 3 1 0 0 0 0 + 3 5 1 0 0 0 0 + 3 4 1 0 0 0 0 + 4 10 1 0 0 0 0 + 4 5 1 0 0 0 0 + 5 6 1 0 0 0 0 + 6 7 2 0 0 0 0 + 7 8 1 0 0 0 0 + 8 9 1 0 0 0 0 + 9 10 2 0 0 0 0 +M END
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/torlib.h Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,479 @@ +/*************************************************************** +This file is part of the Open Babel project. +This is copyright under the GNU General Public License (GPL) +For more information, see <http://openbabel.org/> + +This file contains a binary representation of data tables + used by Open Babel. It is used as a fallback if the textual + data table is not found at runtime. It is not a normal header. +***************************************************************/ + + +#ifndef OB_TORLIB_H +#define OB_TORLIB_H + +namespace OpenBabel +{ +static const char TorsionDefaults[] = { + 0x53,0x50,0x33,0x2D,0x53,0x50,0x33,0x20,0x36,0x30,0x2E,0x30,0x20,0x2D,0x36, + 0x30,0x2E,0x30,0x20,0x31,0x38,0x30,0x2E,0x30,0x20,0x0A,0x53,0x50,0x32,0x2D, + 0x53,0x50,0x32,0x20,0x30,0x2E,0x30,0x20,0x31,0x38,0x30,0x2E,0x30,0x20,0x2D, + 0x33,0x30,0x2E,0x30,0x20,0x33,0x30,0x2E,0x30,0x20,0x31,0x35,0x30,0x2E,0x30, + 0x20,0x2D,0x31,0x35,0x30,0x2E,0x30,0x20,0x0A,0x53,0x50,0x33,0x2D,0x53,0x50, + 0x32,0x20,0x30,0x2E,0x30,0x20,0x33,0x30,0x2E,0x30,0x20,0x2D,0x33,0x30,0x2E, + 0x30,0x20,0x36,0x30,0x2E,0x30,0x20,0x2D,0x36,0x30,0x2E,0x30,0x20,0x31,0x32, + 0x30,0x2E,0x30,0x20,0x2D,0x31,0x32,0x30,0x2E,0x30,0x20,0x2D,0x31,0x35,0x30, + 0x2E,0x30,0x20,0x31,0x35,0x30,0x2E,0x30,0x20,0x31,0x38,0x30,0x2E,0x30,0x20, + 0x2D,0x39,0x30,0x2E,0x30,0x20,0x39,0x30,0x2E,0x30,0x0A,0x4F,0x40,0x5B,0x43, + 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0x2E,0x30,0x20,0x2D,0x33,0x30,0x2E,0x30,0x0A,0x5B,0x43,0x44,0x33,0x5D,0x5B, + 0x4F,0x44,0x32,0x5D,0x5B,0x43,0x44,0x32,0x5D,0x5B,0x4F,0x44,0x32,0x5D,0x20, + 0x31,0x20,0x32,0x20,0x33,0x20,0x34,0x20,0x36,0x30,0x2E,0x30,0x20,0x2D,0x36, + 0x30,0x2E,0x30,0x20,0x31,0x38,0x30,0x2E,0x30,0x20,0x31,0x30,0x30,0x2E,0x30, + 0x20,0x2D,0x31,0x30,0x30,0x2E,0x30,0x0A,0x5B,0x43,0x44,0x31,0x5D,0x5B,0x43, + 0x44,0x32,0x5D,0x5B,0x43,0x44,0x32,0x5D,0x5B,0x2A,0x44,0x32,0x5D,0x5B,0x2A, + 0x44,0x32,0x5D,0x5B,0x2A,0x44,0x32,0x5D,0x20,0x32,0x20,0x33,0x20,0x34,0x20, + 0x35,0x20,0x31,0x38,0x30,0x2E,0x30,0x0A,0x5B,0x43,0x44,0x31,0x5D,0x5B,0x43, + 0x44,0x32,0x5D,0x5B,0x43,0x44,0x32,0x5D,0x5B,0x2A,0x44,0x32,0x5D,0x5B,0x2A, + 0x44,0x32,0x5D,0x5B,0x2A,0x44,0x32,0x5D,0x20,0x31,0x20,0x32,0x20,0x33,0x20, + 0x34,0x20,0x31,0x38,0x30,0x2E,0x30,0x0A,0x5B,0x2A,0x44,0x32,0x5E,0x33,0x5D, + 0x5B,0x2A,0x44,0x32,0x5E,0x33,0x5D,0x5B,0x2A,0x44,0x32,0x5E,0x33,0x5D,0x5B, + 0x2A,0x44,0x32,0x5E,0x33,0x5D,0x5B,0x2A,0x44,0x32,0x5E,0x33,0x5D,0x5B,0x2A, + 0x44,0x32,0x5E,0x33,0x5D,0x20,0x32,0x20,0x33,0x20,0x34,0x20,0x35,0x20,0x31, + 0x38,0x30,0x2E,0x30,0x0A,0x5B,0x61,0x44,0x33,0x5D,0x63,0x4E,0x28,0x7E,0x5B, + 0x4F,0x44,0x31,0x5D,0x29,0x7E,0x5B,0x4F,0x44,0x31,0x5D,0x20,0x31,0x20,0x32, + 0x20,0x33,0x20,0x34,0x20,0x30,0x2E,0x30,0x20,0x36,0x30,0x2E,0x30,0x20,0x2D, + 0x36,0x30,0x2E,0x30,0x0A,0x5B,0x61,0x5D,0x63,0x4E,0x28,0x7E,0x5B,0x4F,0x44, + 0x31,0x5D,0x29,0x7E,0x5B,0x4F,0x44,0x31,0x5D,0x20,0x31,0x20,0x32,0x20,0x33, + 0x20,0x34,0x20,0x30,0x2E,0x30,0x0A,0x2A,0x2A,0x43,0x28,0x46,0x29,0x28,0x46, + 0x29,0x46,0x20,0x31,0x20,0x32,0x20,0x33,0x20,0x34,0x20,0x30,0x2E,0x30,0x0A, + 0x5B,0x61,0x5D,0x63,0x43,0x28,0x43,0x6C,0x29,0x28,0x43,0x6C,0x29,0x43,0x6C, + 0x20,0x31,0x20,0x32,0x20,0x33,0x20,0x34,0x20,0x30,0x2E,0x30,0x0A,0x61,0x5B, + 0x50,0x44,0x33,0x5D,0x28,0x61,0x29,0x2D,0x5B,0x50,0x44,0x33,0x5D,0x28,0x61, + 0x29,0x61,0x20,0x31,0x20,0x32,0x20,0x34,0x20,0x35,0x20,0x31,0x38,0x30,0x2E, + 0x30,0x20,0x36,0x30,0x2E,0x30,0x20,0x2D,0x36,0x30,0x2E,0x30,0x0A,0x50,0x50, + 0x63,0x63,0x20,0x31,0x20,0x32,0x20,0x33,0x20,0x34,0x20,0x36,0x30,0x2E,0x30, + 0x20,0x2D,0x36,0x30,0x2E,0x30,0x0A,0x00}; + +} // namespace OpenBabel +#endif // OB_TORLIB_H +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/torlib.txt Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,224 @@ +############################################################################## +# # +# Open Babel file: torlib.txt # +# # +# Copyright (c) 1998-2001 by OpenEye Scientific Software, Inc. # +# Some portions Copyright (c) 2001-2005 by Geoffrey R. Hutchison # +# Part of the Open Babel package, under the GNU General Public License (GPL)# +# # +# First three lines represent: (used by rotor.cpp::OBRotorRules # +# Hybridization pair (atom types around a rotatable bond) # +# followed by a list of default bond rotation angles (in degrees) # +# # +# Later lines should specify: # +# * A SMARTS pattern for the rotor rule # +# * A set of 4 "reference atoms" (as integers, numbered from 1 # +# in the specified SMARTS pattern # +# * At least one torsion value (in degrees) # +# * Optionally ending with "Delta" and a delta value # +# (i.e., the resolution of a dihedral step # +# # +# SMARTS rules will be attempted first, then hybridization # +# # +############################################################################## + +SP3-SP3 60.0 -60.0 180.0 +SP2-SP2 0.0 180.0 -30.0 30.0 150.0 -150.0 +SP3-SP2 0.0 30.0 -30.0 60.0 -60.0 120.0 -120.0 -150.0 150.0 180.0 -90.0 90.0 + +# Many of these rules came from the Supporting Information +# from Irwin, et. al., J. Med. Chem. (2006) 49(23) 6789-6801 + +#polysaccaride bridges +O@[CD3]O[CD3]([#1])@C 2 3 4 5 0.0 30.0 -30.0 180.0 +O@[CD3]([#1])O[CD3]([#1])@C 3 2 4 5 0.0 30.0 -30.0 180.0 + +#acids +[OD1]~C(~[OD1])[CX4](*)* 1 2 4 5 30.0 -30.0 -60.0 60.0 90.0 -90.0 0.0 180.0 +[a]cC([OD1])=O 1 2 3 4 0.0 20.0 -20.0 +[OD1]C(=O)[CD2]C 1 2 4 5 0.0 45.0 90.0 + +#sulfonamides +NS(=O)(=O)c1[cD2][cD2]a[cD2][cD2]1 1 2 5 6 90.0 +c([aD2])S(=O)(=O)[ND2][CD2] 1 3 6 7 60.0 -60.0 +O=S(=O)N[CX4D3]* 2 4 5 6 -90.0 90.0 120.0 -120.0 +O=S(=O)N[CX4D2]* 2 4 5 6 -90.0 90.0 120.0 -120.0 +[c]S(=O)(=O)NC 1 2 5 6 -70.0 70.0 90.0 -90.0 50.0 -50.0 +*=*-S(=O)(=O)C 1 2 3 6 90.0 -90.0 60.0 -60.0 +O=S(=O)N[CH2] 1 2 4 5 -60.0 60.0 180.0 0.0 30.0 -30.0 +[aD2]c([aD2])S(=O)(=O)[ND2^3] 1 2 4 7 90.0 -90.0 120.0 -120.0 60.0 -60.0 +[aD2]c([aD3])S(=O)(=O)[ND2^3] 1 2 4 7 80.0 -80.0 110.0 -110.0 +[aD3]c([aD3])S(=O)(=O)[ND2^3] 1 2 4 7 70.0 -70.0 110.0 -110.0 +[aD2]c([aD2])S(=O)(=O)[CD2^3] 1 2 4 7 90.0 -90.0 110.0 -110.0 70.0 -70.0 +[a]cS(=O)(=O)[C,N] 1 2 3 6 60.0 -60.0 90.0 -90.0 120.0 -120.0 0.0 180.0 +aS(=O)(=O)[ND2]a 1 2 5 6 90.0 -90.0 +aaNS(=O)(=O) 1 2 3 4 90.0 -90.0 + +#sulfone +O=S(=O)[CD2][CD3][#1] 2 4 5 6 30.0 -30.0 + +#hydrazides +[O,S]=C[ND2][ND2] 1 2 3 4 0.0 180.0 +[O,S]=C[ND2][ND2]-,=* 2 3 4 5 180.0 90.0 -90.0 + +#cyclopropyl-ketones +O=CC1([#1])[CD2][CD2]1 1 2 3 4 180.0 +O=CC1([#1])CC1 1 2 3 4 180.0 160.0 -160.0 0.0 20.0 -20.0 +O=CC1([*])CC1 1 2 3 4 180.0 160.0 -160.0 0.0 120.0 -120.0 90.0 -90.0 30.0 -30.0 + +#epoxy-ketone +O=C([*D2])C1([#1])O[CD2,CD3]1 1 2 4 5 0.0 180.0 + +#opposite end of tert amide +O=C([ND3])[CD2]* 1 2 4 5 0.0 30.0 -30.0 100.0 -100.0 80.0 -80.0 +O=C([CD3^3])[CD2]* 1 2 4 5 0.0 30.0 -30.0 +O=C([ND3])[CD3][#1] 1 2 4 5 180.0 150.0 -150.0 120.0 -120.0 + +#misc +[CD2]C(=O)[ND2]-!@[CD3][#1] 2 4 5 6 0.0 30.0 -30.0 60.0 -60.0 180.0 +[cD2]c([cD2])-!@[CD2^3][CD3^3] 1 2 4 5 90.0 -90.0 70.0 -70.0 110.0 -110.0 +c[CD2][ND3](C)c 1 2 3 4 90.0 -90.0 60.0 -60.0 120.0 -120.0 + +#carbonyls +O=CC=O 1 2 3 4 180.0 0.0 120.0 -120.0 90.0 -90.0 +C=CC=O 1 2 3 4 0.0 180.0 20.0 -20.0 160.0 -160.0 +O=C[CD2][ND2] 1 2 3 4 0.0 -30.0 30.0 150.0 -150.0 180.0 +O=C[CD2]C=O 1 2 3 4 0.0 -30.0 30.0 60.0 -60.0 130.0 -130.0 +O=C(c)[ND2][CD3][#1] 2 4 5 6 0.0 -30.0 30.0 +O=C[ND2][CD3]* 2 3 4 5 20.0 -20.0 120 -120.0 60.0 -60.0 0.0 +O=CN[CD2]* 2 3 4 5 180.0 150.0 -150.0 -120.0 120.0 0.0 30.0 -30.0 +O=Ccc[OD1] 1 2 3 4 0.0 180.0 90.0 -90.0 30.0 -30.0 +O=C[CD4][CD1] 1 2 3 4 0.0 30.0 -30.0 60.0 -60.0 120.0 -120.0 +O=C[CD3][OD1] 1 2 3 4 0.0 30.0 -30.0 60.0 -60.0 120.0 -120.0 +O=C[CD2][CD1] 1 2 3 4 0.0 30.0 -30.0 60.0 -60.0 90.0 -90.0 120.0 -120.0 +O=C[CD3][#1] 1 2 3 4 0.0 30.0 -30.0 180.0 +#O=C[CD3]* 1 2 3 4 0.0 90.0 -90.0 30.0 -30.0 -120.0 120.0 60.0 -60.0 + +#amidene and guanidine +[aD3]cC(~[ND1])~[ND1] 1 2 3 4 0.0 30.0 +[a]cC(~[ND1])~[ND1] 1 2 3 4 0.0 30.0 +*[ND2]~C(~[ND1])~[ND1] 1 2 3 4 0.0 30.0 +[CD2][CD2][ND2]~C(~[ND1])~[ND1] 1 2 3 4 -70.0 70.0 90.0 -90.0 110.0 -110.0 + +#ether +aCO[CD2] 1 2 3 4 180.0 100.0 -100.0 + +#isoprene +C=C[CX4D2]* 1 2 3 4 0.0 180.0 90.0 -90.0 60.0 -60.0 30.0 -30.0 +C=Cc[a] 1 2 3 4 0.0 90.0 -90.0 180.0 30.0 -30.0 150.0 -150.0 + +#aryl secondary amines +[aD2]c([aD2])[ND2][CD2] 1 2 4 5 0.0 180.0 +[aD2]c([aD3])[ND2][CD2] 1 2 4 5 0.0 +[aD2]c([aD2])[ND2][CD1] 1 2 4 5 0.0 90.0 -90.0 180.0 +ac[ND2][CD2] 1 2 3 4 90.0 -90.0 160.0 -160.0 20.0 -20.0 + +#aromatic subtituents +[aD3]c([aD3])[CD2]C 1 2 4 5 90.0 -90.0 60.0 -60.0 120.0 -120.0 +[aD2]c([aD2])[ND3]([CD1])[CD2] 1 2 4 5 0.0 180.0 +[aD3][c,n]([aD2])[C^3D3][#1] 1 2 4 5 0.0 -30.0 30.0 60.0 -60.0 160.0 -160.0 +a[CD2X4][ND3^3]* 1 2 3 4 60.0 -60.0 180.0 160.0 -160.0 90.0 -90.0 120.0 -120.0 +an[CD2X4][CD1] 1 2 3 4 90.0 -90.0 +[aD3]c([aD2])C(=O)[C^3] 1 2 4 5 0.0 20.0 -20.0 150.0 -150.0 180.0 +[aD3]c([aD2])O[CD2] 1 2 3 4 180.0 +a[ND2][CD2X4][CD2X4] 1 2 3 4 180.0 160.0 -160.0 80.0 -80.0 60.0 -60.0 +[ND1]C(=O)c([aD3]) 1 2 4 5 0.0 180.0 30.0 -30.0 150.0 -150.0 +[aD2]c([aD2])c([aD2])[aD2] 1 2 4 5 -150.0 -30.0 30.0 150.0 +[a]c[CD2][*D2] 1 2 3 4 -90.0 90.0 180.0 0.0 30.0 -30.0 150.0 -150.0 +[a]cC(=O)c[a] 1 2 3 4 -150.0 -30.0 0.0 30.0 150.0 180.0 +[a]cC(=O)[*D2] 1 2 3 4 0.0 180.0 30.0 -30.0 150.0 -150.0 +[a]cOC 1 2 3 4 0.0 180.0 30.0 -30.0 150.0 -150.0 + +#borderline low-res +[CD2]C(=O)[ND2][CD3][#1] 2 4 5 6 90.0 -90.0 60.0 -60.0 120.0 -120.0 + +#conjugated substituents +a[CD2]C=* 1 2 3 4 150.0 -150.0 180.0 30.0 -30.0 0.0 +C=CC=C 1 2 3 4 0.0 180.0 30.0 -30.0 150.0 -150.0 60.0 -60.0 120.0 -120.0 +cO[CD2]* 1 2 3 4 0.0 30.0 -30.0 60.0 -60.0 90.0 -90.0 180.0 +C=N[ND2]*=,:* 2 3 4 5 0.0 30.0 -30.0 150.0 -150.0 180.0 +c[CD2][ND2]c 1 2 3 4 60.0 -60.0 80.0 -80.0 180.0 +C=[CD3][ND3]* 1 2 3 4 30.0 -30.0 60.0 -60.0 90.0 -90.0 0.0 180.0 + +#ureas +[ND2]C(=O)Nc[nD2] 2 4 5 6 0.0 180.0 +[ND2]C(=O)[ND2]* 1 2 4 5 0.0 180.0 + +#carbamates +C[ND2]C(=O)O 1 2 3 4 0.0 180.0 +[ND2]C(=O)OC 3 2 4 5 0.0 +OC(=O)N* 3 2 4 5 0.0 20.0 -20.0 120.0 -120.0 160.0 -160.0 180.0 + +#piperidine amide +O=CN1[CD2][CD2][CD2][CD2][CD2]1 1 2 3 4 0.0 + +#amides and esters +[*D2]C(=O)O[CD3][#1] 2 4 5 6 0.0 30.0 -30.0 +[OD2]C(=O)[CD2][CD2^3] 3 2 4 5 0.0 30.0 -30.0 120.0 -120.0 180.0 +[O,SD1]=C(C)[ND2]C=[O,S] 1 2 4 5 0.0 180.0 +[O,SD1]=C(C)[ND2][#7,#8]=* 1 2 4 5 0.0 180.0 +[O,SD1]=C(C)[ND2]N 1 2 4 5 0.0 180.0 +[O,SD1]=C(C)cn 1 2 4 5 0.0 180.0 +[O,SD1]=C([#6])[ND2]* 1 2 4 5 0.0 20.0 -20.0 +[O,SD1]=C[ND2]* 1 2 3 4 0.0 20.0 -20.0 180 +O=C[ND3][CD3X4][#1] 2 3 4 5 0.0 180.0 20.0 -20.0 +O=CNc([aD2,aD3])[aD3] 2 3 4 5 20.0 -20.0 -90.0 90.0 60.0 -60.0 120.0 -120.0 0.0 +O=CNc[a] 2 3 4 5 -20.0 20.0 90.0 -90.0 -160.0 160.0 +O=C([CD2,CD3])O[CD2] 1 2 4 5 0.0 +O=C([CD1])O[CD1] 1 2 4 5 0.0 +[O,S]=CO[CD1] 1 2 3 4 0.0 20.0 -20.0 180.0 +O=CO[CD2][CD1] 2 3 4 5 180.0 +O=CO[CD2]* 2 3 4 5 180.0 60.0 -60.0 90.0 -90.0 +O=CO[CD3]* 2 3 4 5 120.0 -120.0 180.0 0.0 60.0 -60.0 +O=CO[CD4]* 2 3 4 5 -60.0 60.0 120.0 80.0 -80.0 +O=CO[CD3,CD4] 1 2 3 4 0.0 30.0 -30.0 60.0 -60.0 +O=CO* 1 2 3 4 0.0 30.0 -30.0 60.0 -60.0 +O=C[ND3]([*D3])[*D3] 1 2 3 4 20.0 -20.0 0.0 180 150.0 -150.0 +O=C[ND3]* 1 2 3 4 0.0 180.0 +CC[ND3](CC)[CD2,CD3]* 2 3 6 7 180.0 60.0 -60.0 120.0 -120.0 0.0 180.0 30.0 -30.0 +[a][CD2][CD2][ND3] 1 2 3 4 90.0 -90.0 180.0 60.0 -60.0 +[ND3]C(=O)[nD3]* 1 2 4 5 90.0 -90.0 60.0 -60.0 120.0 -120.0 +[CD2]OC(=O)[CD2][CD3] 4 3 5 6 0.0 150.0 -150.0 + +#t-butyl +C([CD1])([CD1])([CD1])c[a] 2 1 5 6 90.0 30.0 +**C([CD1])([CD1])[CD1] 1 2 3 4 180.0 150.0 + +#propyl +[CD1]C([CD1])([#1])[CD2]* 4 2 5 6 60.0 -60.0 + +#highly substituted alkane +#[CD2]C(=O)[ND2]-!@[CD3][#1] 2 4 5 6 +*[CD2X4][CD3X4]([#1])[CD3] 1 2 3 4 180.0 60.0 -60.0 40.0 -40.0 +c[CD2^3][CD3^3][#1] 1 2 3 4 180.0 60.0 -60.0 +[CD2^3][CD2^3][CD3^3][#1] 1 2 3 4 60.0 -60.0 180.0 30.0 -30.0 0.0 160.0 -160.0 120.0 -120.0 +[*D2][CD2][CRH]([*R])[*R] 1 2 3 4 30.0 -30.0 120.0 -120.0 150.0 -150.0 60.0 -60.0 180.0 0.0 +[*D2][CD2][CX4D3][*D2] 1 2 3 4 30.0 -30.0 120.0 -120.0 150.0 -150.0 60.0 -60.0 180.0 +*[CHD3][CH2D2]* 1 2 3 4 150.0 -150.0 60.0 -60.0 180.0 -90.0 90.0 0.0 30.0 -30.0 +[CD1]C([CD1])[CD2]* 1 2 4 5 60.0 -60.0 180.0 80.0 -80.0 30.0 -30.0 + +#long unsubstituted alkanes +[CD3][OD2][CD2][OD2] 1 2 3 4 60.0 -60.0 180.0 100.0 -100.0 +[CD1][CD2][CD2][*D2][*D2][*D2] 2 3 4 5 180.0 +[CD1][CD2][CD2][*D2][*D2][*D2] 1 2 3 4 180.0 +[*D2^3][*D2^3][*D2^3][*D2^3][*D2^3][*D2^3] 2 3 4 5 180.0 + +#nitro +[aD3]cN(~[OD1])~[OD1] 1 2 3 4 0.0 60.0 -60.0 +[a]cN(~[OD1])~[OD1] 1 2 3 4 0.0 + +#trifluoromethyl +**C(F)(F)F 1 2 3 4 0.0 + +#trichloromethyl +[a]cC(Cl)(Cl)Cl 1 2 3 4 0.0 + +#CSD SPECIFIC RULES +a[PD3](a)-[PD3](a)a 1 2 4 5 180.0 60.0 -60.0 +PPcc 1 2 3 4 60.0 -60.0 + +#phosphorus containing groups +#[OD1]~PO* 1 2 3 4 0.0 -30.0 30.0 -60.0 60.0 120.0 -120.0 +#[OD1]~P(~[OD1])(~[OD1])[OD2][CD2]* 2 5 6 7 0.0 60.0 120.0 180.0 -120.0 -60.0 +#S=POc 1 2 3 4 0.0 -60.0 60.0 90.0 -90.0 +#[a]cCP(c)(c)c 1 2 3 4 90.0 -90.0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/types.h Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,709 @@ +/*************************************************************** +This file is part of the Open Babel project. +This is copyright under the GNU General Public License (GPL) +For more information, see <http://openbabel.org/> + +This file contains a binary representation of data tables + used by Open Babel. It is used as a fallback if the textual + data table is not found at runtime. It is not a normal header. +***************************************************************/ + + +#ifndef OB_TYPES_H +#define OB_TYPES_H + +namespace OpenBabel +{ +static const char TypesData[] = { + 0x31,0x39,0x34,0x09,0x32,0x30,0x0A,0x49,0x4E,0x54,0x09,0x41,0x54,0x4E,0x09, + 0x48,0x59,0x42,0x09,0x4D,0x4D,0x44,0x09,0x4D,0x4D,0x32,0x09,0x58,0x59,0x5A, + 0x09,0x41,0x4C,0x43,0x09,0x48,0x41,0x44,0x09,0x4D,0x43,0x4D,0x4C,0x09,0x43, + 0x33,0x44,0x09,0x53,0x59,0x42,0x09,0x4D,0x4F,0x4C,0x09,0x4D,0x41,0x50,0x09, + 0x44,0x52,0x45,0x09,0x58,0x45,0x44,0x09,0x44,0x4F,0x4B,0x09,0x4D,0x33,0x44, + 0x09,0x49,0x44,0x58,0x09,0x53,0x42,0x4E,0x20,0x50,0x43,0x4D,0x0A,0x58,0x09, + 0x30,0x09,0x30,0x09,0x36,0x32,0x09,0x30,0x09,0x58,0x09,0x44,0x75,0x09,0x30, + 0x09,0x58,0x09,0x30,0x09,0x44,0x75,0x09,0x32,0x36,0x09,0x58,0x09,0x58,0x09, + 0x32,0x31,0x09,0x32,0x35,0x09,0x75,0x6E,0x2E,0x30,0x09,0x30,0x09,0x32,0x36, + 0x20,0x30,0x0A,0x4D,0x6E,0x09,0x32,0x35,0x09,0x30,0x09,0x36,0x32,0x09,0x30, + 0x09,0x4D,0x6E,0x09,0x44,0x75,0x09,0x30,0x09,0x4D,0x09,0x32,0x35,0x38,0x09, + 0x4D,0x6E,0x09,0x32,0x36,0x09,0x4D,0x6E,0x09,0x4D,0x6E,0x09,0x32,0x30,0x09, + 0x32,0x35,0x09,0x4D,0x6E,0x2E,0x30,0x09,0x31,0x09,0x32,0x36,0x20,0x4D,0x6E, + 0x0A,0x46,0x65,0x09,0x32,0x36,0x09,0x30,0x09,0x36,0x32,0x09,0x30,0x09,0x46, + 0x65,0x09,0x44,0x75,0x09,0x30,0x09,0x4D,0x09,0x32,0x36,0x36,0x09,0x46,0x65, + 0x09,0x32,0x36,0x09,0x46,0x65,0x09,0x46,0x65,0x09,0x32,0x30,0x09,0x32,0x35, + 0x09,0x46,0x65,0x2E,0x36,0x09,0x32,0x09,0x32,0x36,0x20,0x46,0x65,0x0A,0x44, + 0x75,0x09,0x30,0x09,0x30,0x09,0x36,0x31,0x09,0x30,0x09,0x44,0x75,0x09,0x44, + 0x75,0x09,0x30,0x09,0x5A,0x09,0x30,0x09,0x44,0x75,0x09,0x32,0x36,0x09,0x44, + 0x75,0x09,0x44,0x75,0x09,0x32,0x30,0x09,0x32,0x35,0x09,0x75,0x6E,0x2E,0x30, + 0x09,0x33,0x09,0x32,0x36,0x20,0x30,0x0A,0x43,0x33,0x09,0x36,0x09,0x33,0x09, + 0x33,0x09,0x31,0x09,0x43,0x09,0x43,0x33,0x09,0x34,0x09,0x43,0x09,0x36,0x34, + 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0x09,0x31,0x09,0x30,0x09,0x34,0x32,0x09,0x32,0x34,0x09,0x48,0x09,0x48,0x09, + 0x30,0x09,0x48,0x09,0x31,0x31,0x09,0x48,0x09,0x31,0x33,0x09,0x48,0x09,0x48, + 0x5F,0x48,0x42,0x09,0x31,0x35,0x09,0x36,0x09,0x48,0x2E,0x31,0x09,0x31,0x39, + 0x30,0x09,0x32,0x36,0x20,0x32,0x38,0x0A,0x4F,0x09,0x38,0x09,0x32,0x09,0x32, + 0x30,0x09,0x37,0x09,0x4F,0x09,0x4F,0x33,0x09,0x30,0x09,0x4F,0x09,0x38,0x36, + 0x09,0x4F,0x2E,0x09,0x39,0x09,0x4F,0x33,0x09,0x4F,0x5F,0x33,0x09,0x32,0x36, + 0x09,0x31,0x32,0x09,0x4F,0x2E,0x33,0x09,0x31,0x39,0x31,0x09,0x32,0x36,0x20, + 0x34,0x36,0x0A,0x43,0x33,0x09,0x36,0x09,0x33,0x09,0x33,0x09,0x31,0x09,0x43, + 0x09,0x43,0x33,0x09,0x34,0x09,0x43,0x09,0x36,0x34,0x09,0x43,0x2E,0x33,0x09, + 0x31,0x09,0x43,0x33,0x09,0x43,0x5F,0x33,0x09,0x31,0x09,0x35,0x09,0x43,0x2E, + 0x34,0x09,0x31,0x39,0x32,0x09,0x31,0x20,0x32,0x32,0x0A,0x43,0x72,0x09,0x32, + 0x34,0x09,0x30,0x09,0x30,0x09,0x30,0x09,0x43,0x72,0x09,0x30,0x09,0x30,0x09, + 0x30,0x09,0x30,0x09,0x43,0x72,0x2E,0x74,0x68,0x09,0x30,0x09,0x30,0x09,0x30, + 0x09,0x30,0x09,0x30,0x09,0x30,0x09,0x31,0x39,0x33,0x09,0x32,0x36,0x20,0x43, + 0x72,0x0A,0x44,0x75,0x09,0x30,0x09,0x30,0x09,0x36,0x31,0x09,0x30,0x09,0x44, + 0x75,0x09,0x44,0x75,0x09,0x30,0x09,0x5A,0x09,0x30,0x09,0x4C,0x70,0x09,0x32, + 0x36,0x09,0x44,0x75,0x09,0x44,0x75,0x09,0x32,0x30,0x09,0x32,0x35,0x09,0x75, + 0x6E,0x2E,0x30,0x09,0x31,0x39,0x34,0x09,0x32,0x36,0x20,0x30,0x0A,0x00}; + +} // namespace OpenBabel +#endif // OB_TYPES_H +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/OpenBabel/types.txt Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,213 @@ +############################################################################## +# # +# Open Babel file: types.txt # +# # +# Copyright (c) 1998-2001 by OpenEye Scientific Software, Inc. # +# Some portions Copyright (c) 2001-2005 Geoffrey R. Hutchison # +# Part of the Open Babel package, under the GNU General Public License (GPL)# +# # +# Conversion between different external atom types # +# (used by data.cpp:OBTypeTable) # +# # +# First line specifies size of the table: # rows # columns # +# Second line specifies type names used in the code # +# Remaining lines specify equivalent atomic type names in each column # +# # +############################################################################## +194 20 +INT ATN HYB MMD MM2 XYZ ALC HAD MCML C3D SYB MOL MAP DRE XED DOK M3D IDX SBN PCM +X 0 0 62 0 X Du 0 X 0 Du 26 X X 21 25 un.0 0 26 0 +Mn 25 0 62 0 Mn Du 0 M 258 Mn 26 Mn Mn 20 25 Mn.0 1 26 Mn +Fe 26 0 62 0 Fe Du 0 M 266 Fe 26 Fe Fe 20 25 Fe.6 2 26 Fe +Du 0 0 61 0 Du Du 0 Z 0 Du 26 Du Du 20 25 un.0 3 26 0 +C3 6 3 3 1 C C3 4 C 64 C.3 1 C3 C_3 1 5 C.4 4 1 1 +C2 6 2 2 2 C C2 3 C 63 C.2 2 C2 C_2 2 1 C.3 5 2 2 +C2 6 2 2 38 C C2 3 C 63 C.2 2 C2 C_2 2 1 C.3 6 2 2 +C1 6 1 1 4 C C1 2 C 62 C.1 4 C1 C_1 4 1 C.2 7 4 4 +Cac 6 2 2 3 C C2 0 C 63 C.2 2 C2 C_2 2 1 C.3 8 2 3 +Cbl 6 2 2 3 C C2 3 C 63 C.2 2 C2 C_2 2 1 C.3 9 2 2 +C- 6 2 10 27 C C3 4 C 64 C.3 1 C3 C_3 1 1 C.4 10 1 48 +N3+ 7 3 32 39 N N3+ 4 N 79 N.4 31 N3 N_3 5 9 N.4 11 31 41 +N3 7 3 26 8 N N3 3 N 73 N.3 5 N3 N_3 6 10 N.4 12 5 8 +N2 7 2 25 9 N NPL3 2 N 72 N.2 19 N2 N_2 8 8 N.3 13 6 9 +Npl 7 2 25 9 N NPL3 3 N 72 N.pl3 19 N2 N_2 9 8 N.3 14 19 9 +Naz 7 2 25 37 N N2 0 N 72 N.2 6 N2 N_2 7 8 N.2 15 6 9 +N1 7 1 24 10 N N1 0 N 71 N.1 7 N1 N_1 23 8 N.2 16 7 10 +Nox 7 2 26 8 N N2 0 N 72 N.4 6 N2 N_2 6 8 N.3 17 31 9 +Ntr 7 2 25 9 N N2 0 N 72 N.pl3 6 N2 N_2 8 8 N.3 18 19 9 +Ng+ 7 2 35 8 N NPL3 3 N 79 N.pl3 31 N2 N_2 5 9 N.3 19 19 37 +O3 8 3 16 6 O O3 2 O 82 O.3 8 O3 O_3 10 12 O.4 20 8 6 +Oes 8 3 16 6 O O3 2 O 82 O.3 8 O3 O_2 11 12 O.4 21 8 6 +O2 8 2 15 7 O O2 0 O 81 O.2 9 O2 O_2 11 11 O.3 22 9 7 +O- 8 2 20 7 O O2 0 O 86 O.co2 9 O2 O_3 26 12 O.R 23 32 42 +S3 16 3 49 15 S S3 0 S 164 S.3 10 S3 S_3 12 14 S.4 24 10 15 +S 16 3 52 16 S S3 0 S 164 S.3 10 S3 S_3 12 14 S.2 25 10 15 +S3+ 16 3 49 16 S S3 0 S 164 S.3 10 S3 S_3 12 14 S.4 26 10 16 +S2 16 2 49 17 S S2 0 S 161 S.2 18 S2 S_3 13 14 S.3 27 18 15 +Sac 16 2 49 17 S SO 0 S 161 S.3 29 S3 S_3 12 14 S.4 28 10 15 +So2 16 3 49 18 S SO2 0 S 161 S.O2 30 S3 S_3 12 14 S.4 29 30 17 +Sox 16 2 49 18 S SO2 0 S 161 S.O 30 S3 S_3 12 14 S.4 30 29 17 +S 16 3 49 15 S S3 0 S 164 S.3 10 S3 S_3 12 14 S.2 31 10 15 +Bac 5 0 54 27 B B 0 B 53 B 26 B2 B_2 20 20 B.0 32 26 26 +Box 5 0 54 26 B B 0 B 53 B 26 B2 B_2 20 20 B.0 33 26 26 +B 5 0 55 27 B B 0 B 53 B 26 B3 B_3 20 20 B.0 34 26 26 +P3 15 3 53 25 P P3 0 P 159 P.3 12 P3 P_3 14 13 P.4 35 12 25 +Pac 15 2 53 25 P P3 0 P 159 P.3 12 P3 P_3 14 13 P.4 36 12 25 +Pox 15 3 53 25 P P3 0 P 159 P.3 12 P3 P_3 14 13 P.4 37 12 25 +P3+ 15 3 53 25 P P3 0 P 154 P.3 12 P3 P_3 14 13 P.4 38 12 25 +P 15 3 53 25 P P3 0 P 159 P.3 12 P3 P_3 14 13 P.4 39 12 25 +HC 1 0 41 5 H H 0 H 11 H 13 H H_ 15 7 H.1 40 13 5 +H- 1 0 45 5 H H 0 H 11 H 13 H H_ 15 6 H.1 41 13 5 +H 1 0 48 5 H H 0 H 11 H 13 H H_ 15 6 H.1 42 13 5 +H 1 0 48 5 D H 0 H 12 H 13 H H_ 15 6 H.1 43 13 5 +DC 1 0 48 36 D H 0 D 19 H 13 D H_ 15 6 H.1 44 13 36 +D 1 0 48 36 D H 0 D 19 H 13 D H_ 15 6 H.1 45 13 36 +F 9 0 56 11 F F 0 F 91 F 16 F F_ 16 15 F.1 46 16 11 +Cl 17 0 57 12 Cl CL 0 L 171 Cl 15 Cl Cl 17 16 Cl.1 47 15 12 +Br 35 0 58 13 Br BR 0 R 351 Br 14 Br Br 18 17 Br.1 48 14 13 +I 53 0 59 14 I I 0 I 531 I 17 I I_ 19 18 I.1 49 17 14 +Ge 32 0 62 31 Ge GE 0 E 324 Ge 26 Ge Ge3 20 25 Ge.4 50 26 Ge +Sn 50 0 62 32 Sn SN 0 X 504 Sn 26 Sn Xx 20 25 Sn.0 51 26 Sn +Pb 82 0 62 33 Pb PB 0 Z 824 Pb 26 Pb Xx 20 25 Pb.0 52 26 Pb +Se 34 0 62 34 Se SE 0 Z 342 Se 26 Se Se3 20 25 Se.4 53 26 34 +Te 52 0 62 35 Te TE 0 Z 0 Te 26 Te Te3 20 25 Te.4 54 26 35 +O 8 0 23 6 O O 0 Z 82 O.3 8 O O_3 10 12 O.4 55 8 6 +Lp 0 0 63 20 Lp Lp 0 Z 10 LP 20 Lp Xx 30 25 ep.1 56 20 20 +C- 6 0 10 0 C C2 0 C 61 C.2 2 C-3 Xx 2 5 C.4 57 2 48 +C. 6 0 12 0 C C2 0 C 0 C.2 2 C.3 Xx 2 5 C.3 58 2 29 +NC 7 0 29 9 N N2 0 N 72 N.2 6 N2 N_2 8 8 N.3 59 6 8 +N2+ 7 0 36 9 N N2 0 N 78 N.2 6 N2 N_2 7 8 N.3 60 6 9 +Z0 0 0 62 0 Du Du 0 Z 0 Du 26 Xx Xx 20 25 un.0 61 26 0 +HO 1 0 42 21 H H 0 H 11 H 13 H H_HB 15 25 H.1 62 13 21 +H+ 1 0 44 5 H H 0 H 11 H 13 H H_ 15 6 H.0 63 13 5 +HN 1 0 43 23 H H 0 H 11 H 13 H H_HB 15 6 H.1 64 13 23 +C3 6 0 3 22 H H 0 C 64 H 13 C3 C_3 1 5 C.4 65 13 1 +H 1 0 43 28 H H 0 H 11 H 13 H H_ 15 6 H.1 66 13 5 +Cx 6 0 62 29 C C 0 C 64 C 1 Xx Xx 20 5 un.0 67 26 1 +N2 7 0 25 40 N N2 0 N 72 N 6 N2 N_2 8 8 N.3 68 26 9 +HO 1 0 42 24 H H 0 H 11 H 13 H H_HB 15 6 H.1 69 26 21 +W 74 0 62 0 W W 0 W 744 W 26 W Xx 20 25 W.0 70 26 W +Car 6 2 2 2 C C2 3 C 2 C.ar 3 C2 C_R 3 1 C.R 71 3 40 +Nar 7 2 25 9 N NPL3 2 N 37 N.ar 11 N2 N_R 8 8 N.R 72 11 9 +Nam 7 2 25 9 N NPL3 3 N 9 N.am 28 N2 N_2 8 8 N.3 73 28 9 +Na 11 0 25 9 Na Na 0 Z 9 Na 21 NA Na 20 19 Na.6 74 21 Na +K 19 0 0 0 K K 0 Z 190 K 22 K Xx 20 19 K.0 75 22 K +Ca 20 0 0 0 Ca Ca 0 Z 200 Ca 23 CA Ca 20 21 Ca.6 76 23 Ca +Li 3 0 62 0 Li LI 0 M 258 Li 26 Li Li 20 25 Li.0 77 24 Li +Al 13 0 0 0 Al Al 0 Z 133 Al 25 AL Al3 20 20 Al.6 78 25 Al +Si 14 0 60 0 Si Si 4 Z 19 Si 27 SI Si3 20 24 Si.4 79 27 Si +OCO2 8 0 18 47 O O 1 O 47 O.co2 32 O2 O_2 11 1 O.3 80 32 7 +C+ 6 2 11 30 C C2 3 C 2 C.cat 33 C2 C_2 2 1 C.3 81 33 30 +O2 8 0 15 41 O O2 0 O 81 O.2 9 O2 O_2 11 11 O.R 82 9 7 +Pd 46 0 62 464 Pd Du 0 Z 464 Pd 26 Du Du 20 25 Pd.0 83 26 Pd +Pt 78 0 62 464 Pt Du 0 Z 464 Pt 26 Pt Du 20 25 Pt.0 84 26 Pt +Ni 28 0 62 0 Ni Du 0 M 284 Ni 26 Ni Ni 20 25 Ni.0 85 26 Ni +Cu 29 0 62 0 Cu Du 0 M 000 Cu 26 Cu Cu 20 25 Cu.0 86 26 Cu +N4 7 0 32 39 N N3+ 4 N 79 N.4 31 N3 N_3 5 9 N.4 87 31 41 +Npl 7 2 25 9 N NPL3 3 N 72 N.pl3N 19 N2 N_2 9 8 N.3 88 19 9 +O- 8 2 20 7 O O2 0 O 86 O.co2O 9 O2 O_3 26 12 O.R 89 32 41 +C+ 6 2 11 30 C C2 3 C 2 C.catC 33 C2 C_2 2 1 C.3 90 33 30 +O 8 2 20 7 O O3 0 O 86 O. 9 O3 O_3 26 12 O.3 91 26 6 +C 6 3 3 1 C C3 4 C 64 C. 1 C3 C_3 1 5 C.4 92 26 1 +V 23 0 62 0 V Du 0 Z 234 V 0 V Du 20 25 V.0 93 26 V +Zn 30 0 62 0 Zn Zn 0 Z 234 Zn 0 V Zn 20 25 Zn.0 94 26 Zn +Cany 6 0 62 30 C C 3 C 2 C. 33 C C 2 1 C.0 95 26 1 +Nany 7 0 62 30 N N 3 N 2 N. 33 N N 2 1 N.0 96 26 8 +Oany 8 0 62 30 O O 3 O 2 O. 33 O O 2 1 O.0 97 26 6 +Sany 16 0 62 30 S S 3 S 2 S. 33 S S 2 1 S.0 98 26 15 +Rar 6 0 62 30 C C 3 C 2 R.ar 33 C C 2 1 C.0 99 26 1 +R 6 0 62 30 C C 3 C 2 R. 33 C C 2 1 C.0 100 26 1 +Nr 6 0 62 30 C C 3 C 2 Nr. 33 C C 2 1 C.0 101 26 8 +O.co2 8 2 20 7 O O2 0 O 86 O.co2 9 O2 O_3 26 12 O.R 102 32 7 +So 16 2 49 18 S SO2 0 S 161 S.O2 30 S3 S_3 12 14 S.4 103 30 17 +He 2 0 0 0 He 0 0 0 0 He 0 0 0 0 0 0 104 26 He +Be 4 0 0 0 Be 0 0 0 0 Be 0 0 0 0 0 0 105 26 Be +Ne 10 0 0 0 Ne 0 0 0 0 Ne 0 0 0 0 0 0 106 26 Ne +Mg 12 0 0 0 Mg 0 0 0 0 Mg 0 0 0 0 0 0 107 26 Mg +Sc 21 0 0 0 Sc 0 0 0 0 Sc 0 0 0 0 0 0 108 26 Sc +Ti 22 0 0 0 Ti 0 0 0 0 Ti 0 0 0 0 0 0 109 26 Ti +Cr 24 0 0 0 Cr 0 0 0 0 Cr.oh 0 0 0 0 0 0 110 26 Cr +Co 27 0 0 0 Co 0 0 0 0 Co.oh 0 0 0 0 0 0 111 26 Co +Ga 31 0 0 0 Ga 0 0 0 0 Ga 0 0 0 0 0 0 112 26 Ga +As 33 0 0 0 As 0 0 0 0 As 0 0 0 0 0 0 113 26 As +Kr 36 0 0 0 Kr 0 0 0 0 Kr 0 0 0 0 0 0 114 26 Kr +Rb 37 0 0 0 Rb 0 0 0 0 Rb 0 0 0 0 0 0 115 26 Rb +Sr 38 0 0 0 Sr 0 0 0 0 Sr 0 0 0 0 0 0 116 26 Sr +Y 39 0 0 0 Y 0 0 0 0 Y 0 0 0 0 0 0 117 26 Y +Zr 40 0 0 0 Zr 0 0 0 0 Zr 0 0 0 0 0 0 118 26 Zr +Nb 41 0 0 0 Nb 0 0 0 0 Nb 0 0 0 0 0 0 119 26 Nb +Mo 42 0 0 0 Mo 0 0 0 0 Mo 0 0 0 0 0 0 120 26 Mo +Tc 43 0 0 0 Tc 0 0 0 0 Tc 0 0 0 0 0 0 121 26 Tc +Ru 44 0 0 0 Ru 0 0 0 0 Ru 0 0 0 0 0 0 122 26 Ru +Rh 45 0 0 0 Rh 0 0 0 0 Rh 0 0 0 0 0 0 123 26 Rh +Ag 47 0 0 0 Ag 0 0 0 0 Ag 0 0 0 0 0 0 124 26 Ag +Cd 48 0 0 0 Cd 0 0 0 0 Cd 0 0 0 0 0 0 125 26 Cd +In 49 0 0 0 In 0 0 0 0 In 0 0 0 0 0 0 126 26 In +Sb 51 0 0 0 Sb 0 0 0 0 Sb 0 0 0 0 0 0 127 26 Sb +Xe 54 0 0 0 Xe 0 0 0 0 Xe 0 0 0 0 0 0 128 26 Xe +Cs 55 0 0 0 Cs 0 0 0 0 Cs 0 0 0 0 0 0 129 26 Cs +Ba 56 0 0 0 Ba 0 0 0 0 Ba 0 0 0 0 0 0 130 26 Ba +La 57 0 0 0 La 0 0 0 0 La 0 0 0 0 0 0 131 26 La +Ce 58 0 0 0 Ce 0 0 0 0 Ce 0 0 0 0 0 0 132 26 Ce +Pr 59 0 0 0 Pr 0 0 0 0 Pr 0 0 0 0 0 0 133 26 Pr +Nd 60 0 0 0 Nd 0 0 0 0 Nd 0 0 0 0 0 0 134 26 Nd +Pm 61 0 0 0 Pm 0 0 0 0 Pm 0 0 0 0 0 0 135 26 Pm +Sm 62 0 0 0 Sm 0 0 0 0 Sm 0 0 0 0 0 0 136 26 Sm +Eu 63 0 0 0 Eu 0 0 0 0 Eu 0 0 0 0 0 0 137 26 Eu +Gd 64 0 0 0 Gd 0 0 0 0 Gd 0 0 0 0 0 0 138 26 Gd +Tb 65 0 0 0 Tb 0 0 0 0 Tb 0 0 0 0 0 0 139 26 Tb +Dy 66 0 0 0 Dy 0 0 0 0 Dy 0 0 0 0 0 0 140 26 Dy +Ho 67 0 0 0 Ho 0 0 0 0 Ho 0 0 0 0 0 0 141 26 Ho +Er 68 0 0 0 Er 0 0 0 0 Er 0 0 0 0 0 0 142 26 Er +Tm 69 0 0 0 Tm 0 0 0 0 Tm 0 0 0 0 0 0 143 26 Tm +Yb 70 0 0 0 Yb 0 0 0 0 Yb 0 0 0 0 0 0 144 26 Yb +Lu 71 0 0 0 Lu 0 0 0 0 Lu 0 0 0 0 0 0 145 26 Lu +Hf 72 0 0 0 Hf 0 0 0 0 Hf 0 0 0 0 0 0 146 26 Hf +Ta 73 0 0 0 Ta 0 0 0 0 Ta 0 0 0 0 0 0 147 26 Ta +Re 75 0 0 0 Re 0 0 0 0 Re 0 0 0 0 0 0 148 26 Re +Os 76 0 0 0 Os 0 0 0 0 Os 0 0 0 0 0 0 149 26 Os +Ir 77 0 0 0 Ir 0 0 0 0 Ir 0 0 0 0 0 0 150 26 Ir +Au 79 0 0 0 Au 0 0 0 0 Au 0 0 0 0 0 0 151 26 Au +Hg 80 0 0 0 Hg 0 0 0 0 Hg 0 0 0 0 0 0 152 26 Hg +Tl 81 0 0 0 Tl 0 0 0 0 Tl 0 0 0 0 0 0 153 26 Tl +Bi 83 0 0 0 Bi 0 0 0 0 Bi 0 0 0 0 0 0 154 26 Bi +Po 84 0 0 0 Po 0 0 0 0 Po 0 0 0 0 0 0 155 26 Po +At 85 0 0 0 At 0 0 0 0 At 0 0 0 0 0 0 156 26 At +Rn 86 0 0 0 Rn 0 0 0 0 Rn 0 0 0 0 0 0 157 26 Rn +Fr 87 0 0 0 Fr 0 0 0 0 Fr 0 0 0 0 0 0 158 26 Fr +Ra 88 0 0 0 Ra 0 0 0 0 Ra 0 0 0 0 0 0 159 26 Ra +Ac 89 0 0 0 Ac 0 0 0 0 Ac 0 0 0 0 0 0 160 26 Ac +Th 90 0 0 0 Th 0 0 0 0 Th 0 0 0 0 0 0 161 26 Th +Pa 91 0 0 0 Pa 0 0 0 0 Pa 0 0 0 0 0 0 162 26 Pa +U 92 0 0 0 U 0 0 0 0 U 0 0 0 0 0 0 163 26 U +Np 93 0 0 0 Np 0 0 0 0 Np 0 0 0 0 0 0 164 26 Np +Pu 94 0 0 0 Pu 0 0 0 0 Pu 0 0 0 0 0 0 165 26 Pu +Am 95 0 0 0 Am 0 0 0 0 Am 0 0 0 0 0 0 166 26 Am +Cm 96 0 0 0 Cm 0 0 0 0 Cm 0 0 0 0 0 0 167 26 Cm +Bk 97 0 0 0 Bk 0 0 0 0 Bk 0 0 0 0 0 0 168 26 Bk +Cf 98 0 0 0 Cf 0 0 0 0 Cf 0 0 0 0 0 0 169 26 Cf +Es 99 0 0 0 Es 0 0 0 0 Es 0 0 0 0 0 0 170 26 Es +Fm 100 0 0 0 Fm 0 0 0 0 Fm 0 0 0 0 0 0 171 26 Fm +Md 101 0 0 0 Md 0 0 0 0 Md 0 0 0 0 0 0 172 26 Md +No 102 0 0 0 No 0 0 0 0 No 0 0 0 0 0 0 173 26 No +Lr 103 0 0 0 Lr 0 0 0 0 Lr 0 0 0 0 0 0 174 26 Lr +Rf 104 0 0 0 Rf 0 0 0 0 Rf 0 0 0 0 0 0 175 26 Rf +Db 105 0 0 0 Db 0 0 0 0 Db 0 0 0 0 0 0 176 26 Db +Sg 106 0 0 0 Sg 0 0 0 0 Sg 0 0 0 0 0 0 177 26 Sg +Bh 107 0 0 0 Bh 0 0 0 0 Bh 0 0 0 0 0 0 178 26 Bh +Hs 108 0 0 0 Hs 0 0 0 0 Hs 0 0 0 0 0 0 179 26 Hs +Mt 109 0 0 0 Mt 0 0 0 0 Mt 0 0 0 0 0 0 180 26 Mt +Ar 18 0 0 0 Ar 0 0 0 0 Ar 0 0 0 0 0 0 181 26 Ar +B2 5 0 54 26 B B 0 B 53 B 26 B2 B_2 20 20 B.0 182 26 26 +B3 5 0 55 27 B B 0 B 53 B 26 B3 B_3 20 20 B.0 183 26 27 +N 7 0 62 30 N N 3 N 2 N. 33 N N 2 1 N.0 184 26 8 +HS 1 0 42 21 H H 0 H 11 H 13 H H_HB 15 25 H.1 185 26 5 +HB 1 0 42 21 H H 0 H 11 H 13 H H_b 15 25 H.1 186 26 5 +Oar 8 2 15 7 O O2 0 O 81 O.2 9 O2 O_R 11 11 O.3 187 26 7 +O1 8 0 62 30 O O 3 O 2 O. 33 O O_1 2 1 O.0 188 26 7 +HO 1 0 42 24 H H 0 H 11 H 13 H H_HB 15 6 H.1 189 26 24 +HO 1 0 42 24 H H 0 H 11 H 13 H H_HB 15 6 H.1 190 26 28 +O 8 2 20 7 O O3 0 O 86 O. 9 O3 O_3 26 12 O.3 191 26 46 +C3 6 3 3 1 C C3 4 C 64 C.3 1 C3 C_3 1 5 C.4 192 1 22 +Cr 24 0 0 0 Cr 0 0 0 0 Cr.th 0 0 0 0 0 0 193 26 Cr +Du 0 0 61 0 Du Du 0 Z 0 Lp 26 Du Du 20 25 un.0 194 26 0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/QSAR/atomic_electron_affinities.data Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,88 @@ +# atomic electron affinities, taken from CRC Handbook of Chemistry and Physics, 79th edition, 1998; non-excistant values like unstable ions have 0.0 +0.754593 +0.0 +0.6180 +0.0 +0.277 +1.2629 +0.0 +1.4611103 +3.401190 +0.0 +0.547926 +0.0 +0.441 +1.385 +0.7465 +2.077104 +3.61269 +0.0 +0.50147 +0.02455 +0.188 +0.079 +0.525 +0.666 +0.0 +0.151 +0.662 +1.156 +1.235 +0.0 +0.3 +1.233 +0.81 +2.020670 +3.363590 +0.0 +0.48592 +0.048 +0.307 +0.426 +0.893 +0.748 +0.55 +1.05 +1.137 +0.562 +1.302 +0.0 +0.3 +1.112 +1.046 +1.9708 +3.059038 +0.0 +0.471626 +0.15 +0.5 +0.0 +0.0 +0.0 +0.0 +0.0 +0.0 +0.0 +0.0 +0.0 +0.0 +0.0 +0.0 +0.0 +0.0 +0.0 +0.322 +0.815 +0.15 +1.1 +1.5638 +2.128 +2.30863 +0.0 +0.2 +0.364 +0.946 +1.9 +2.8 +0.0 +0.46
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/QSAR/atomic_ionization_potentials.data Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,73 @@ +# atomic ionization potentials (neutral atom and +1 ion), CRC Handbook of Chemistry and Physics, 79th edition, 1998 +13.59844 20.02 +24.58741 54.41778 +5.39172 75.64018 +9.3227 18.21116 +8.29803 25.15484 +11.26030 24.38332 +14.53414 29.6013 +13.61806 35.11730 +17.42282 34.97082 +21.5646 40.96328 +5.13908 47.2864 +7.64624 15.03528 +5.98577 18.82856 +8.15169 16.34585 +10.48669 19.7694 +10.36001 23.3379 +12.96764 23.814 +15.75962 27.62967 +4.34066 31.63 +6.11316 11.87172 +6.5615 12.79967 +6.8281 13.5755 +6.7463 14.66 +6.7665 16.4857 +7.43402 15.63999 +7.9024 16.1878 +7.8810 17.083 +7.6398 18.16884 +7.72638 20.29240 +9.3942 17.96440 +5.99930 20.5142 +7.8994 15.93462 +9.7886 18.633 +9.75238 21.19 +11.81381 21.8 +13.99961 24.35985 +4.17713 27.285 +5.6949 11.03013 +6.2171 12.24 +6.63390 13.13 +6.75885 14.32 +7.09243 16.16 +7.28 15.26 +7.36050 16.76 +7.45890 18.08 +8.3369 19.43 +7.5763 21.49 +8.9938 16.90832 +5.78636 18.8698 +7.3439 14.63225 +8.6084 16.53051 +9.0096 18.6 +10.45126 19.1313 +12.1298 21.20979 +3.89390 23.15745 +5.21170 10.00390 +5.770 11.060 +5.5387 10.85 +5.464 10.55 +5.5250 10.73 +5.58 10.9 +5.6436 11.07 +5.6704 11.241 +6.1501 12.09 +5.8638 11.52 +5.9389 11.67 +6.0215 11.80 +6.1077 11.93 +6.18431 12.05 +6.25416 12.1761 +5.4259 13.9 +6.82507 14.9
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/QSAR/atomic_polarizabilities.data Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,101 @@ +# atomic ground state polarizabilities, taken from CRC Handbook of Chemistry and Physics, 79th edition, 1998 +0.666793 +0.204956 +24.3 +5.6 +3.03 +1.76 +1.1 +0.802 +0.557 +0.3956 +24.08 +10.6 +6.8 +5.38 +3.63 +2.9 +2.18 +1.6411 +43.4 +22.8 +17.8 +14.6 +12.4 +11.6 +9.4 +8.4 +7.5 +6.8 +6.1 +7.1 +8.12 +6.07 +4.31 +3.77 +3.05 +2.4844 +47.3 +27.6 +22.7 +17.9 +15.7 +12.8 +11.4 +9.6 +8.6 +4.8 +7.2 +7.2 +10.2 +7.7 +6.6 +5.5 +5.35 +4.044 +59.6 +39.7 +31.1 +29.6 +28.2 +31.4 +30.1 +28.8 +27.7 +23.5 +25.5 +24.5 +23.6 +22.7 +21.8 +21.0 +21.9 +16.2 +13.1 +11.1 +9.7 +8.5 +7.6 +6.5 +5.8 +5.7 +7.6 +6.8 +7.4 +6.8 +6.0 +5.3 +48.7 +38.3 +32.1 +32.1 +25.4 +24.9 +24.8 +24.5 +23.3 +23.0 +22.7 +20.5 +19.7 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/QSAR/dragon_descriptors.txt Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,1665 @@ +MW molecular weight +AMW average molecular weight +Sv sum of atomic van der Waals volumes (scaled on Carbon atom) +Se sum of atomic Sanderson electronegativities (scaled on Carbon atom) +Sp sum of atomic polarizabilities (scaled on Carbon atom) +Ss sum of Kier-Hall electrotopological states +Mv mean atomic van der Waals volume (scaled on Carbon atom) +Me mean atomic Sanderson electronegativity (scaled on Carbon atom) +Mp mean atomic polarizability (scaled on Carbon atom) +Ms mean electrotopological state +nAT number of atoms +nSK number of non-H atoms +nBT number of bonds +nBO number of non-H bonds +nBM number of multiple bonds +SCBO sum of conventional bond orders (H-depleted) +ARR aromatic ratio +nCIC number of rings +nCIR number of circuits +RBN number of rotatable bonds +RBF rotatable bond fraction +nDB number of double bonds +nTB number of triple bonds +nAB number of aromatic bonds +nH number of Hydrogen atoms +nC number of Carbon atoms +nN number of Nitrogen atoms +nO number of Oxygen atoms +nP number of Phosphorous atoms +nS number of Sulfur atoms +nF number of Fluorine atoms +nCL number of Chlorine atoms +nBR number of Bromine atoms +nI number of Iodine atoms +nB number of Boron atoms +nHM number of heavy atoms +nX number of halogen atoms +nR03 number of 3-membered rings +nR04 number of 4-membered rings +nR05 number of 5-membered rings +nR06 number of 6-membered rings +nR07 number of 7-membered rings +nR08 number of 8-membered rings +nR09 number of 9-membered rings +nR10 number of 10-membered rings +nR11 number of 11-membered rings +nR12 number of 12-membered rings +nBnz number of benzene-like rings +ZM1 first Zagreb index M1 +ZM1V first Zagreb index by valence vertex degrees +ZM2 second Zagreb index M2 +ZM2V second Zagreb index by valence vertex degrees +Qindex Quadratic index +SNar Narumi simple topological index (log) +HNar Narumi harmonic topological index +GNar Narumi geometric topological index +Xt Total structure connectivity index +Dz Pogliani index +Ram ramification index +Pol polarity number +LPRS log of product of row sums (PRS) +VDA average vertex distance degree +MSD mean square distance index (Balaban) +SMTI Schultz Molecular Topological Index (MTI) +SMTIV Schultz MTI by valence vertex degrees +GMTI Gutman Molecular Topological Index +GMTIV Gutman MTI by valence vertex degrees +Xu Xu index +SPI superpendentic index +W Wiener W index +WA mean Wiener index +Har Harary H index +Har2 square reciprocal distance sum index +QW quasi-Wiener index (Kirchhoff number) +TI1 first Mohar index TI1 +TI2 second Mohar index TI2 +STN spanning tree number (log) +HyDp hyper-distance-path index +RHyDp reciprocal hyper-distance-path index +w detour index +ww hyper-detour index +Rww reciprocal hyper-detour index +D/D distance/detour index +Wap all-path Wiener index +WhetZ Wiener-type index from Z weighted distance matrix (Barysz matrix) +Whetm Wiener-type index from mass weighted distance matrix +Whetv Wiener-type index from van der Waals weighted distance matrix +Whete Wiener-type index from electronegativity weighted distance matrix +Whetp Wiener-type index from polarizability weighted distance matrix +J Balaban distance connectivity index +JhetZ Balaban-type index from Z weighted distance matrix (Barysz matrix) +Jhetm Balaban-type index from mass weighted distance matrix +Jhetv Balaban-type index from van der Waals weighted distance matrix +Jhete Balaban-type index from electronegativity weighted distance matrix +Jhetp Balaban-type index from polarizability weighted distance matrix +MAXDN maximal electrotopological negative variation +MAXDP maximal electrotopological positive variation +DELS molecular electrotopological variation +TIE E-state topological parameter +S0K Kier symmetry index +S1K 1-path Kier alpha-modified shape index +S2K 2-path Kier alpha-modified shape index +S3K 3-path Kier alpha-modified shape index +PHI Kier flexibility index +BLI Kier benzene-likeliness index +PW2 path/walk 2 - Randic shape index +PW3 path/walk 3 - Randic shape index +PW4 path/walk 4 - Randic shape index +PW5 path/walk 5 - Randic shape index +PJI2 2D Petitjean shape index +CSI eccentric connectivity index +ECC eccentricity +AECC average eccentricity +DECC eccentric +MDDD mean distance degree deviation +UNIP unipolarity +CENT centralization +VAR variation +BAC Balaban centric index +Lop Lopping centric index +ICR radial centric information index +D/Dr03 distance/detour ring index of order 3 +D/Dr04 distance/detour ring index of order 4 +D/Dr05 distance/detour ring index of order 5 +D/Dr06 distance/detour ring index of order 6 +D/Dr07 distance/detour ring index of order 7 +D/Dr08 distance/detour ring index of order 8 +D/Dr09 distance/detour ring index of order 9 +D/Dr10 distance/detour ring index of order 10 +D/Dr11 distance/detour ring index of order 11 +D/Dr12 distance/detour ring index of order 12 +T(N..N) sum of topological distances between N..N +T(N..O) sum of topological distances between N..O +T(N..S) sum of topological distances between N..S +T(N..P) sum of topological distances between N..P +T(N..F) sum of topological distances between N..F +T(N..Cl) sum of topological distances between N..Cl +T(N..Br) sum of topological distances between N..Br +T(N..I) sum of topological distances between N..I +T(O..O) sum of topological distances between O..O +T(O..S) sum of topological distances between O..S +T(O..P) sum of topological distances between O..P +T(O..F) sum of topological distances between O..F +T(O..Cl) sum of topological distances between O..Cl +T(O..Br) sum of topological distances between O..Br +T(O..I) sum of topological distances between O..I +T(S..S) sum of topological distances between S..S +T(S..P) sum of topological distances between S..P +T(S..F) sum of topological distances between S..F +T(S..Cl) sum of topological distances between S..Cl +T(S..Br) sum of topological distances between S..Br +T(S..I) sum of topological distances between S..I +T(P..P) sum of topological distances between P..P +T(P..F) sum of topological distances between P..F +T(P..Cl) sum of topological distances between P..Cl +T(P..Br) sum of topological distances between P..Br +T(P..I) sum of topological distances between P..I +T(F..F) sum of topological distances between F..F +T(F..Cl) sum of topological distances between F..Cl +T(F..Br) sum of topological distances between F..Br +T(F..I) sum of topological distances between F..I +T(Cl..Cl) sum of topological distances between Cl..Cl +T(Cl..Br) sum of topological distances between Cl..Br +T(Cl..I) sum of topological distances between Cl..I +T(Br..Br) sum of topological distances between Br..Br +T(Br..I) sum of topological distances between Br..I +T(I..I) sum of topological distances between I..I +MWC01 molecular walk count of order 01 (number of non-H bonds, nBO) +MWC02 molecular walk count of order 02 +MWC03 molecular walk count of order 03 +MWC04 molecular walk count of order 04 +MWC05 molecular walk count of order 05 +MWC06 molecular walk count of order 06 +MWC07 molecular walk count of order 07 +MWC08 molecular walk count of order 08 +MWC09 molecular walk count of order 09 +MWC10 molecular walk count of order 10 +TWC total walk count +SRW01 self-returning walk count of order 01 (number of non-H atoms, nSK) +SRW02 self-returning walk count of order 02 (twice the number of non-H bonds) +SRW03 self-returning walk count of order 03 +SRW04 self-returning walk count of order 04 +SRW05 self-returning walk count of order 05 +SRW06 self-returning walk count of order 06 +SRW07 self-returning walk count of order 07 +SRW08 self-returning walk count of order 08 +SRW09 self-returning walk count of order 09 +SRW10 self-returning walk count of order 10 +MPC01 molecular path count of order 01 (number of non-H bonds, nBO) +MPC02 molecular path count of order 02 (Gordon-Scantlebury index) +MPC03 molecular path count of order 03 +MPC04 molecular path count of order 04 +MPC05 molecular path count of order 05 +MPC06 molecular path count of order 06 +MPC07 molecular path count of order 07 +MPC08 molecular path count of order 08 +MPC09 molecular path count of order 09 +MPC10 molecular path count of order 10 +piPC01 molecular multiple path count of order 01 (sum of conventional bond orders, SCBO) +piPC02 molecular multiple path count of order 02 +piPC03 molecular multiple path count of order 03 +piPC04 molecular multiple path count of order 04 +piPC05 molecular multiple path count of order 05 +piPC06 molecular multiple path count of order 06 +piPC07 molecular multiple path count of order 07 +piPC08 molecular multiple path count of order 08 +piPC09 molecular multiple path count of order 09 +piPC10 molecular multiple path count of order 10 +TPC total path count +piID conventional bond-order ID number +PCR ratio of multiple path count over path count +PCD difference between multiple path count and path count +CID Randic ID number +BID Balaban ID number +ISIZ information index on molecular size +IAC total information index of atomic composition +AAC mean information index on atomic composition +IDE mean information content on the distance equality +IDM mean information content on the distance magnitude +IDDE mean information content on the distance degree equality +IDDM mean information content on the distance degree magnitude +IDET total information content on the distance equality +IDMT total information content on the distance magnitude +IVDE mean information content on the vertex degree equality +IVDM mean information content on the vertex degree magnitude +HVcpx graph vertex complexity index +HDcpx graph distance complexity index (log) +Uindex Balaban U index +Vindex Balaban V index +Xindex Balaban X index +Yindex Balaban Y index +IC0 information content index (neighborhood symmetry of 0-order) +TIC0 total information content index (neighborhood symmetry of 0-order) +SIC0 structural information content (neighborhood symmetry of 0-order) +CIC0 complementary information content (neighborhood symmetry of 0-order) +BIC0 bond information content (neighborhood symmetry of 0-order) +IC1 information content index (neighborhood symmetry of 1-order) +TIC1 total information content index (neighborhood symmetry of 1-order) +SIC1 structural information content (neighborhood symmetry of 1-order) +CIC1 complementary information content (neighborhood symmetry of 1-order) +BIC1 bond information content (neighborhood symmetry of 1-order) +IC2 information content index (neighborhood symmetry of 2-order) +TIC2 total information content index (neighborhood symmetry of 2-order) +SIC2 structural information content (neighborhood symmetry of 2-order) +CIC2 complementary information content (neighborhood symmetry of 2-order) +BIC2 bond information content (neighborhood symmetry of 2-order) +IC3 information content index (neighborhood symmetry of 3-order) +TIC3 total information content index (neighborhood symmetry of 3-order) +SIC3 structural information content (neighborhood symmetry of 3-order) +CIC3 complementary information content (neighborhood symmetry of 3-order) +BIC3 bond information content (neighborhood symmetry of 3-order) +IC4 information content index (neighborhood symmetry of 4-order) +TIC4 total information content index (neighborhood symmetry of 4-order) +SIC4 structural information content (neighborhood symmetry of 4-order) +CIC4 complementary information content (neighborhood symmetry of 4-order) +BIC4 bond information content (neighborhood symmetry of 4-order) +IC5 information content index (neighborhood symmetry of 5-order) +TIC5 total information content index (neighborhood symmetry of 5-order) +SIC5 structural information content (neighborhood symmetry of 5-order) +CIC5 complementary information content (neighborhood symmetry of 5-order) +BIC5 bond information content (neighborhood symmetry of 5-order) +ATS1m Broto-Moreau autocorrelation of a topological structure - lag 1 / weighted by atomic masses +ATS2m Broto-Moreau autocorrelation of a topological structure - lag 2 / weighted by atomic masses +ATS3m Broto-Moreau autocorrelation of a topological structure - lag 3 / weighted by atomic masses +ATS4m Broto-Moreau autocorrelation of a topological structure - lag 4 / weighted by atomic masses +ATS5m Broto-Moreau autocorrelation of a topological structure - lag 5 / weighted by atomic masses +ATS6m Broto-Moreau autocorrelation of a topological structure - lag 6 / weighted by atomic masses +ATS7m Broto-Moreau autocorrelation of a topological structure - lag 7 / weighted by atomic masses +ATS8m Broto-Moreau autocorrelation of a topological structure - lag 8 / weighted by atomic masses +ATS1v Broto-Moreau autocorrelation of a topological structure - lag 1 / weighted by atomic van der Waals volumes +ATS2v Broto-Moreau autocorrelation of a topological structure - lag 2 / weighted by atomic van der Waals volumes +ATS3v Broto-Moreau autocorrelation of a topological structure - lag 3 / weighted by atomic van der Waals volumes +ATS4v Broto-Moreau autocorrelation of a topological structure - lag 4 / weighted by atomic van der Waals volumes +ATS5v Broto-Moreau autocorrelation of a topological structure - lag 5 / weighted by atomic van der Waals volumes +ATS6v Broto-Moreau autocorrelation of a topological structure - lag 6 / weighted by atomic van der Waals volumes +ATS7v Broto-Moreau autocorrelation of a topological structure - lag 7 / weighted by atomic van der Waals volumes +ATS8v Broto-Moreau autocorrelation of a topological structure - lag 8 / weighted by atomic van der Waals volumes +ATS1e Broto-Moreau autocorrelation of a topological structure - lag 1 / weighted by atomic Sanderson electronegativities +ATS2e Broto-Moreau autocorrelation of a topological structure - lag 2 / weighted by atomic Sanderson electronegativities +ATS3e Broto-Moreau autocorrelation of a topological structure - lag 3 / weighted by atomic Sanderson electronegativities +ATS4e Broto-Moreau autocorrelation of a topological structure - lag 4 / weighted by atomic Sanderson electronegativities +ATS5e Broto-Moreau autocorrelation of a topological structure - lag 5 / weighted by atomic Sanderson electronegativities +ATS6e Broto-Moreau autocorrelation of a topological structure - lag 6 / weighted by atomic Sanderson electronegativities +ATS7e Broto-Moreau autocorrelation of a topological structure - lag 7 / weighted by atomic Sanderson electronegativities +ATS8e Broto-Moreau autocorrelation of a topological structure - lag 8 / weighted by atomic Sanderson electronegativities +ATS1p Broto-Moreau autocorrelation of a topological structure - lag 1 / weighted by atomic polarizabilities +ATS2p Broto-Moreau autocorrelation of a topological structure - lag 2 / weighted by atomic polarizabilities +ATS3p Broto-Moreau autocorrelation of a topological structure - lag 3 / weighted by atomic polarizabilities +ATS4p Broto-Moreau autocorrelation of a topological structure - lag 4 / weighted by atomic polarizabilities +ATS5p Broto-Moreau autocorrelation of a topological structure - lag 5 / weighted by atomic polarizabilities +ATS6p Broto-Moreau autocorrelation of a topological structure - lag 6 / weighted by atomic polarizabilities +ATS7p Broto-Moreau autocorrelation of a topological structure - lag 7 / weighted by atomic polarizabilities +ATS8p Broto-Moreau autocorrelation of a topological structure - lag 8 / weighted by atomic polarizabilities +MATS1m Moran autocorrelation - lag 1 / weighted by atomic masses +MATS2m Moran autocorrelation - lag 2 / weighted by atomic masses +MATS3m Moran autocorrelation - lag 3 / weighted by atomic masses +MATS4m Moran autocorrelation - lag 4 / weighted by atomic masses +MATS5m Moran autocorrelation - lag 5 / weighted by atomic masses +MATS6m Moran autocorrelation - lag 6 / weighted by atomic masses +MATS7m Moran autocorrelation - lag 7 / weighted by atomic masses +MATS8m Moran autocorrelation - lag 8 / weighted by atomic masses +MATS1v Moran autocorrelation - lag 1 / weighted by atomic van der Waals volumes +MATS2v Moran autocorrelation - lag 2 / weighted by atomic van der Waals volumes +MATS3v Moran autocorrelation - lag 3 / weighted by atomic van der Waals volumes +MATS4v Moran autocorrelation - lag 4 / weighted by atomic van der Waals volumes +MATS5v Moran autocorrelation - lag 5 / weighted by atomic van der Waals volumes +MATS6v Moran autocorrelation - lag 6 / weighted by atomic van der Waals volumes +MATS7v Moran autocorrelation - lag 7 / weighted by atomic van der Waals volumes +MATS8v Moran autocorrelation - lag 8 / weighted by atomic van der Waals volumes +MATS1e Moran autocorrelation - lag 1 / weighted by atomic Sanderson electronegativities +MATS2e Moran autocorrelation - lag 2 / weighted by atomic Sanderson electronegativities +MATS3e Moran autocorrelation - lag 3 / weighted by atomic Sanderson electronegativities +MATS4e Moran autocorrelation - lag 4 / weighted by atomic Sanderson electronegativities +MATS5e Moran autocorrelation - lag 5 / weighted by atomic Sanderson electronegativities +MATS6e Moran autocorrelation - lag 6 / weighted by atomic Sanderson electronegativities +MATS7e Moran autocorrelation - lag 7 / weighted by atomic Sanderson electronegativities +MATS8e Moran autocorrelation - lag 8 / weighted by atomic Sanderson electronegativities +MATS1p Moran autocorrelation - lag 1 / weighted by atomic polarizabilities +MATS2p Moran autocorrelation - lag 2 / weighted by atomic polarizabilities +MATS3p Moran autocorrelation - lag 3 / weighted by atomic polarizabilities +MATS4p Moran autocorrelation - lag 4 / weighted by atomic polarizabilities +MATS5p Moran autocorrelation - lag 5 / weighted by atomic polarizabilities +MATS6p Moran autocorrelation - lag 6 / weighted by atomic polarizabilities +MATS7p Moran autocorrelation - lag 7 / weighted by atomic polarizabilities +MATS8p Moran autocorrelation - lag 8 / weighted by atomic polarizabilities +GATS1m Geary autocorrelation - lag 1 / weighted by atomic masses +GATS2m Geary autocorrelation - lag 2 / weighted by atomic masses +GATS3m Geary autocorrelation - lag 3 / weighted by atomic masses +GATS4m Geary autocorrelation - lag 4 / weighted by atomic masses +GATS5m Geary autocorrelation - lag 5 / weighted by atomic masses +GATS6m Geary autocorrelation - lag 6 / weighted by atomic masses +GATS7m Geary autocorrelation - lag 7 / weighted by atomic masses +GATS8m Geary autocorrelation - lag 8 / weighted by atomic masses +GATS1v Geary autocorrelation - lag 1 / weighted by atomic van der Waals volumes +GATS2v Geary autocorrelation - lag 2 / weighted by atomic van der Waals volumes +GATS3v Geary autocorrelation - lag 3 / weighted by atomic van der Waals volumes +GATS4v Geary autocorrelation - lag 4 / weighted by atomic van der Waals volumes +GATS5v Geary autocorrelation - lag 5 / weighted by atomic van der Waals volumes +GATS6v Geary autocorrelation - lag 6 / weighted by atomic van der Waals volumes +GATS7v Geary autocorrelation - lag 7 / weighted by atomic van der Waals volumes +GATS8v Geary autocorrelation - lag 8 / weighted by atomic van der Waals volumes +GATS1e Geary autocorrelation - lag 1 / weighted by atomic Sanderson electronegativities +GATS2e Geary autocorrelation - lag 2 / weighted by atomic Sanderson electronegativities +GATS3e Geary autocorrelation - lag 3 / weighted by atomic Sanderson electronegativities +GATS4e Geary autocorrelation - lag 4 / weighted by atomic Sanderson electronegativities +GATS5e Geary autocorrelation - lag 5 / weighted by atomic Sanderson electronegativities +GATS6e Geary autocorrelation - lag 6 / weighted by atomic Sanderson electronegativities +GATS7e Geary autocorrelation - lag 7 / weighted by atomic Sanderson electronegativities +GATS8e Geary autocorrelation - lag 8 / weighted by atomic Sanderson electronegativities +GATS1p Geary autocorrelation - lag 1 / weighted by atomic polarizabilities +GATS2p Geary autocorrelation - lag 2 / weighted by atomic polarizabilities +GATS3p Geary autocorrelation - lag 3 / weighted by atomic polarizabilities +GATS4p Geary autocorrelation - lag 4 / weighted by atomic polarizabilities +GATS5p Geary autocorrelation - lag 5 / weighted by atomic polarizabilities +GATS6p Geary autocorrelation - lag 6 / weighted by atomic polarizabilities +GATS7p Geary autocorrelation - lag 7 / weighted by atomic polarizabilities +GATS8p Geary autocorrelation - lag 8 / weighted by atomic polarizabilities +EPS0 edge connectivity index of order 0 +EPS1 edge connectivity index of order 1 +EEig01x Eigenvalue 01from edge adj. matrix weighted by edge degrees +EEig02x Eigenvalue 02from edge adj. matrix weighted by edge degrees +EEig03x Eigenvalue 03from edge adj. matrix weighted by edge degrees +EEig04x Eigenvalue 04from edge adj. matrix weighted by edge degrees +EEig05x Eigenvalue 05from edge adj. matrix weighted by edge degrees +EEig06x Eigenvalue 06from edge adj. matrix weighted by edge degrees +EEig07x Eigenvalue 07from edge adj. matrix weighted by edge degrees +EEig08x Eigenvalue 08from edge adj. matrix weighted by edge degrees +EEig09x Eigenvalue 09from edge adj. matrix weighted by edge degrees +EEig10x Eigenvalue 10from edge adj. matrix weighted by edge degrees +EEig11x Eigenvalue 11from edge adj. matrix weighted by edge degrees +EEig12x Eigenvalue 12from edge adj. matrix weighted by edge degrees +EEig13x Eigenvalue 13from edge adj. matrix weighted by edge degrees +EEig14x Eigenvalue 14from edge adj. matrix weighted by edge degrees +EEig15x Eigenvalue 15from edge adj. matrix weighted by edge degrees +EEig01d Eigenvalue 01 from edge adj. matrix weighted by dipole moments +EEig02d Eigenvalue 02 from edge adj. matrix weighted by dipole moments +EEig03d Eigenvalue 03 from edge adj. matrix weighted by dipole moments +EEig04d Eigenvalue 04 from edge adj. matrix weighted by dipole moments +EEig05d Eigenvalue 05 from edge adj. matrix weighted by dipole moments +EEig06d Eigenvalue 06 from edge adj. matrix weighted by dipole moments +EEig07d Eigenvalue 07 from edge adj. matrix weighted by dipole moments +EEig08d Eigenvalue 08 from edge adj. matrix weighted by dipole moments +EEig09d Eigenvalue 09 from edge adj. matrix weighted by dipole moments +EEig10d Eigenvalue 10 from edge adj. matrix weighted by dipole moments +EEig11d Eigenvalue 11 from edge adj. matrix weighted by dipole moments +EEig12d Eigenvalue 12 from edge adj. matrix weighted by dipole moments +EEig13d Eigenvalue 13 from edge adj. matrix weighted by dipole moments +EEig14d Eigenvalue 14 from edge adj. matrix weighted by dipole moments +EEig15d Eigenvalue 15 from edge adj. matrix weighted by dipole moments +EEig01r Eigenvalue 01 from edge adj. matrix weighted by resonance integrals +EEig02r Eigenvalue 02 from edge adj. matrix weighted by resonance integrals +EEig03r Eigenvalue 03 from edge adj. matrix weighted by resonance integrals +EEig04r Eigenvalue 04 from edge adj. matrix weighted by resonance integrals +EEig05r Eigenvalue 05 from edge adj. matrix weighted by resonance integrals +EEig06r Eigenvalue 06 from edge adj. matrix weighted by resonance integrals +EEig07r Eigenvalue 07 from edge adj. matrix weighted by resonance integrals +EEig08r Eigenvalue 08 from edge adj. matrix weighted by resonance integrals +EEig09r Eigenvalue 09 from edge adj. matrix weighted by resonance integrals +EEig10r Eigenvalue 10 from edge adj. matrix weighted by resonance integrals +EEig11r Eigenvalue 11 from edge adj. matrix weighted by resonance integrals +EEig12r Eigenvalue 12 from edge adj. matrix weighted by resonance integrals +EEig13r Eigenvalue 13 from edge adj. matrix weighted by resonance integrals +EEig14r Eigenvalue 14 from edge adj. matrix weighted by resonance integrals +EEig15r Eigenvalue 15 from edge adj. matrix weighted by resonance integrals +ESpm01u Spectral moment 01 from edge adj. matrix +ESpm02u Spectral moment 02 from edge adj. matrix +ESpm03u Spectral moment 03 from edge adj. matrix +ESpm04u Spectral moment 04 from edge adj. matrix +ESpm05u Spectral moment 05 from edge adj. matrix +ESpm06u Spectral moment 06 from edge adj. matrix +ESpm07u Spectral moment 07 from edge adj. matrix +ESpm08u Spectral moment 08 from edge adj. matrix +ESpm09u Spectral moment 09 from edge adj. matrix +ESpm10u Spectral moment 10 from edge adj. matrix +ESpm11u Spectral moment 11 from edge adj. matrix +ESpm12u Spectral moment 12 from edge adj. matrix +ESpm13u Spectral moment 13 from edge adj. matrix +ESpm14u Spectral moment 14 from edge adj. matrix +ESpm15u Spectral moment 15 from edge adj. matrix +ESpm01x Spectral moment 01 from edge adj. matrix weighted by edge degrees +ESpm02x Spectral moment 02 from edge adj. matrix weighted by edge degrees +ESpm03x Spectral moment 03 from edge adj. matrix weighted by edge degrees +ESpm04x Spectral moment 04 from edge adj. matrix weighted by edge degrees +ESpm05x Spectral moment 05 from edge adj. matrix weighted by edge degrees +ESpm06x Spectral moment 06 from edge adj. matrix weighted by edge degrees +ESpm07x Spectral moment 07 from edge adj. matrix weighted by edge degrees +ESpm08x Spectral moment 08 from edge adj. matrix weighted by edge degrees +ESpm09x Spectral moment 09 from edge adj. matrix weighted by edge degrees +ESpm10x Spectral moment 10 from edge adj. matrix weighted by edge degrees +ESpm11x Spectral moment 11 from edge adj. matrix weighted by edge degrees +ESpm12x Spectral moment 12 from edge adj. matrix weighted by edge degrees +ESpm13x Spectral moment 13 from edge adj. matrix weighted by edge degrees +ESpm14x Spectral moment 14 from edge adj. matrix weighted by edge degrees +ESpm15x Spectral moment 15 from edge adj. matrix weighted by edge degrees +ESpm01d Spectral moment 01 from edge adj. matrix weighted by dipole moments +ESpm02d Spectral moment 02 from edge adj. matrix weighted by dipole moments +ESpm03d Spectral moment 03 from edge adj. matrix weighted by dipole moments +ESpm04d Spectral moment 04 from edge adj. matrix weighted by dipole moments +ESpm05d Spectral moment 05 from edge adj. matrix weighted by dipole moments +ESpm06d Spectral moment 06 from edge adj. matrix weighted by dipole moments +ESpm07d Spectral moment 07 from edge adj. matrix weighted by dipole moments +ESpm08d Spectral moment 08 from edge adj. matrix weighted by dipole moments +ESpm09d Spectral moment 09 from edge adj. matrix weighted by dipole moments +ESpm10d Spectral moment 10 from edge adj. matrix weighted by dipole moments +ESpm11d Spectral moment 11 from edge adj. matrix weighted by dipole moments +ESpm12d Spectral moment 12 from edge adj. matrix weighted by dipole moments +ESpm13d Spectral moment 13 from edge adj. matrix weighted by dipole moments +ESpm14d Spectral moment 14 from edge adj. matrix weighted by dipole moments +ESpm15d Spectral moment 15 from edge adj. matrix weighted by dipole moments +ESpm01r Spectral moment 01 from edge adj. matrix weighted by resonance integrals +ESpm02r Spectral moment 02 from edge adj. matrix weighted by resonance integrals +ESpm03r Spectral moment 03 from edge adj. matrix weighted by resonance integrals +ESpm04r Spectral moment 04 from edge adj. matrix weighted by resonance integrals +ESpm05r Spectral moment 05 from edge adj. matrix weighted by resonance integrals +ESpm06r Spectral moment 06 from edge adj. matrix weighted by resonance integrals +ESpm07r Spectral moment 07 from edge adj. matrix weighted by resonance integrals +ESpm08r Spectral moment 08 from edge adj. matrix weighted by resonance integrals +ESpm09r Spectral moment 09 from edge adj. matrix weighted by resonance integrals +ESpm10r Spectral moment 10 from edge adj. matrix weighted by resonance integrals +ESpm11r Spectral moment 11 from edge adj. matrix weighted by resonance integrals +ESpm12r Spectral moment 12 from edge adj. matrix weighted by resonance integrals +ESpm13r Spectral moment 13 from edge adj. matrix weighted by resonance integrals +ESpm14r Spectral moment 14 from edge adj. matrix weighted by resonance integrals +ESpm15r Spectral moment 15 from edge adj. matrix weighted by resonance integrals +BEHm1 highest eigenvalue n. 1 of Burden matrix / weighted by atomic masses +BEHm2 highest eigenvalue n. 2 of Burden matrix / weighted by atomic masses +BEHm3 highest eigenvalue n. 3 of Burden matrix / weighted by atomic masses +BEHm4 highest eigenvalue n. 4 of Burden matrix / weighted by atomic masses +BEHm5 highest eigenvalue n. 5 of Burden matrix / weighted by atomic masses +BEHm6 highest eigenvalue n. 6 of Burden matrix / weighted by atomic masses +BEHm7 highest eigenvalue n. 7 of Burden matrix / weighted by atomic masses +BEHm8 highest eigenvalue n. 8 of Burden matrix / weighted by atomic masses +BELm1 lowest eigenvalue n. 1 of Burden matrix / weighted by atomic masses +BELm2 lowest eigenvalue n. 2 of Burden matrix / weighted by atomic masses +BELm3 lowest eigenvalue n. 3 of Burden matrix / weighted by atomic masses +BELm4 lowest eigenvalue n. 4 of Burden matrix / weighted by atomic masses +BELm5 lowest eigenvalue n. 5 of Burden matrix / weighted by atomic masses +BELm6 lowest eigenvalue n. 6 of Burden matrix / weighted by atomic masses +BELm7 lowest eigenvalue n. 7 of Burden matrix / weighted by atomic masses +BELm8 lowest eigenvalue n. 8 of Burden matrix / weighted by atomic masses +BEHv1 highest eigenvalue n. 1 of Burden matrix / weighted by atomic van der Waals volumes +BEHv2 highest eigenvalue n. 2 of Burden matrix / weighted by atomic van der Waals volumes +BEHv3 highest eigenvalue n. 3 of Burden matrix / weighted by atomic van der Waals volumes +BEHv4 highest eigenvalue n. 4 of Burden matrix / weighted by atomic van der Waals volumes +BEHv5 highest eigenvalue n. 5 of Burden matrix / weighted by atomic van der Waals volumes +BEHv6 highest eigenvalue n. 6 of Burden matrix / weighted by atomic van der Waals volumes +BEHv7 highest eigenvalue n. 7 of Burden matrix / weighted by atomic van der Waals volumes +BEHv8 highest eigenvalue n. 8 of Burden matrix / weighted by atomic van der Waals volumes +BELv1 lowest eigenvalue n. 1 of Burden matrix / weighted by atomic van der Waals volumes +BELv2 lowest eigenvalue n. 2 of Burden matrix / weighted by atomic van der Waals volumes +BELv3 lowest eigenvalue n. 3 of Burden matrix / weighted by atomic van der Waals volumes +BELv4 lowest eigenvalue n. 4 of Burden matrix / weighted by atomic van der Waals volumes +BELv5 lowest eigenvalue n. 5 of Burden matrix / weighted by atomic van der Waals volumes +BELv6 lowest eigenvalue n. 6 of Burden matrix / weighted by atomic van der Waals volumes +BELv7 lowest eigenvalue n. 7 of Burden matrix / weighted by atomic van der Waals volumes +BELv8 lowest eigenvalue n. 8 of Burden matrix / weighted by atomic van der Waals volumes +BEHe1 highest eigenvalue n. 1 of Burden matrix / weighted by atomic Sanderson electronegativities +BEHe2 highest eigenvalue n. 2 of Burden matrix / weighted by atomic Sanderson electronegativities +BEHe3 highest eigenvalue n. 3 of Burden matrix / weighted by atomic Sanderson electronegativities +BEHe4 highest eigenvalue n. 4 of Burden matrix / weighted by atomic Sanderson electronegativities +BEHe5 highest eigenvalue n. 5 of Burden matrix / weighted by atomic Sanderson electronegativities +BEHe6 highest eigenvalue n. 6 of Burden matrix / weighted by atomic Sanderson electronegativities +BEHe7 highest eigenvalue n. 7 of Burden matrix / weighted by atomic Sanderson electronegativities +BEHe8 highest eigenvalue n. 8 of Burden matrix / weighted by atomic Sanderson electronegativities +BELe1 lowest eigenvalue n. 1 of Burden matrix / weighted by atomic Sanderson electronegativities +BELe2 lowest eigenvalue n. 2 of Burden matrix / weighted by atomic Sanderson electronegativities +BELe3 lowest eigenvalue n. 3 of Burden matrix / weighted by atomic Sanderson electronegativities +BELe4 lowest eigenvalue n. 4 of Burden matrix / weighted by atomic Sanderson electronegativities +BELe5 lowest eigenvalue n. 5 of Burden matrix / weighted by atomic Sanderson electronegativities +BELe6 lowest eigenvalue n. 6 of Burden matrix / weighted by atomic Sanderson electronegativities +BELe7 lowest eigenvalue n. 7 of Burden matrix / weighted by atomic Sanderson electronegativities +BELe8 lowest eigenvalue n. 8 of Burden matrix / weighted by atomic Sanderson electronegativities +BEHp1 highest eigenvalue n. 1 of Burden matrix / weighted by atomic polarizabilities +BEHp2 highest eigenvalue n. 2 of Burden matrix / weighted by atomic polarizabilities +BEHp3 highest eigenvalue n. 3 of Burden matrix / weighted by atomic polarizabilities +BEHp4 highest eigenvalue n. 4 of Burden matrix / weighted by atomic polarizabilities +BEHp5 highest eigenvalue n. 5 of Burden matrix / weighted by atomic polarizabilities +BEHp6 highest eigenvalue n. 6 of Burden matrix / weighted by atomic polarizabilities +BEHp7 highest eigenvalue n. 7 of Burden matrix / weighted by atomic polarizabilities +BEHp8 highest eigenvalue n. 8 of Burden matrix / weighted by atomic polarizabilities +BELp1 lowest eigenvalue n. 1 of Burden matrix / weighted by atomic polarizabilities +BELp2 lowest eigenvalue n. 2 of Burden matrix / weighted by atomic polarizabilities +BELp3 lowest eigenvalue n. 3 of Burden matrix / weighted by atomic polarizabilities +BELp4 lowest eigenvalue n. 4 of Burden matrix / weighted by atomic polarizabilities +BELp5 lowest eigenvalue n. 5 of Burden matrix / weighted by atomic polarizabilities +BELp6 lowest eigenvalue n. 6 of Burden matrix / weighted by atomic polarizabilities +BELp7 lowest eigenvalue n. 7 of Burden matrix / weighted by atomic polarizabilities +BELp8 lowest eigenvalue n. 8 of Burden matrix / weighted by atomic polarizabilities +GGI1 topological charge index of order 1 +GGI2 topological charge index of order 2 +GGI3 topological charge index of order 3 +GGI4 topological charge index of order 4 +GGI5 topological charge index of order 5 +GGI6 topological charge index of order 6 +GGI7 topological charge index of order 7 +GGI8 topological charge index of order 8 +GGI9 topological charge index of order 9 +GGI10 topological charge index of order 10 +JGI1 mean topological charge index of order1 +JGI2 mean topological charge index of order2 +JGI3 mean topological charge index of order3 +JGI4 mean topological charge index of order4 +JGI5 mean topological charge index of order5 +JGI6 mean topological charge index of order6 +JGI7 mean topological charge index of order7 +JGI8 mean topological charge index of order8 +JGI9 mean topological charge index of order9 +JGI10 mean topological charge index of order10 +JGT global topological charge index +LP1 Lovasz-Pelikan index (leading eigenvalue) +Eig1Z Leading eigenvalue from Z weighted distance matrix (Barysz matrix) +Eig1m Leading eigenvalue from mass weighted distance matrix +Eig1v Leading eigenvalue from van der Waals weighted distance matrix +Eig1e Leading eigenvalue from electronegativity weighted distance matrix +Eig1p Leading eigenvalue from polarizability weighted distance matrix +SEigZ Eigenvalue sum from Z weighted distance matrix (Barysz matrix) +SEigm Eigenvalue sum from mass weighted distance matrix +SEigv Eigenvalue sum from van der Waals weighted distance matrix +SEige Eigenvalue sum from electronegativity weighted distance matrix +SEigp Eigenvalue sum from polarizability weighted distance matrix +AEigZ Absolute eigenvalue sum from Z weighted distance matrix (Barysz matrix) +AEigm Absolute eigenvalue sum from mass weighted distance matrix +AEigv Absolute eigenvalue sum from van der Waals weighted distance matrix +AEige Absolute eigenvalue sum from electronegativity weighted distance matrix +AEigp Absolute eigenvalue sum from polarizability weighted distance matrix +VEA1 eigenvector coefficient sum from adjacency matrix +VEA2 average eigenvector coefficient sum from adjacency matrix +VRA1 Randic-type eigenvector-based index from adjacency matrix +VRA2 average Randic-type eigenvector-based index from adjacency matrix +VED1 eigenvector coefficient sum from distance matrix +VED2 average eigenvector coefficient sum from distance matrix +VRD1 Randic-type eigenvector-based index from distance matrix +VRD2 average Randic-type eigenvector-based index from distance matrix +VEZ1 eigenvector coefficient sum from Z weighted distance matrix (Barysz matrix) +VEZ2 average eigenvector coefficient sum from Z weighted distance matrix (Barysz matrix) +VRZ1 Randic-type eigenvector-based index from Z weighted distance matrix (Barysz matrix) +VRZ2 average Randic-type eigenvector-based index from Z weighted distance matrix (Barysz matrix) +VEm1 eigenvector coefficient sum from mass weighted distance matrix +VEm2 average eigenvector coefficient sum from mass weighted distance matrix +VRm1 Randic-type eigenvector-based index from mass weighted distance matrix +VRm2 average Randic-type eigenvector-based index from mass weighted distance matrix +VEv1 eigenvector coefficient sum from van der Waals weighted distance matrix +VEv2 average eigenvector coefficient sum from van der Waals weighted distance matrix +VRv1 Randic-type eigenvector-based index from van der Waals weighted distance matrix +VRv2 average Randic-type eigenvector-based index from van der Waals weighted distance matrix +VEe1 eigenvector coefficient sum from electronegativity weighted distance matrix +VEe2 average eigenvector coefficient sum from electronegativity weighted distance matrix +VRe1 Randic-type eigenvector-based index from electronegativity weighted distance matrix +VRe2 average Randic-type eigenvector-based index from electronegativity weighted distance matrix +VEp1 eigenvector coefficient sum from polarizability weighted distance matrix +VEp2 average eigenvector coefficient sum from polarizability weighted distance matrix +VRp1 Randic-type eigenvector-based index from polarizability weighted distance matrix +VRp2 average Randic-type eigenvector-based index from polarizability weighted distance matrix +DP01 molecular profile no. 01 +DP02 molecular profile no. 02 +DP03 molecular profile no. 03 +DP04 molecular profile no. 04 +DP05 molecular profile no. 05 +DP06 molecular profile no. 06 +DP07 molecular profile no. 07 +DP08 molecular profile no. 08 +DP09 molecular profile no. 09 +DP10 molecular profile no. 10 +DP11 molecular profile no. 11 +DP12 molecular profile no. 12 +DP13 molecular profile no. 13 +DP14 molecular profile no. 14 +DP15 molecular profile no. 15 +DP16 molecular profile no. 16 +DP17 molecular profile no. 17 +DP18 molecular profile no. 18 +DP19 molecular profile no. 19 +DP20 molecular profile no. 20 +SP01 shape profile no. 01 +SP02 shape profile no. 02 +SP03 shape profile no. 03 +SP04 shape profile no. 04 +SP05 shape profile no. 05 +SP06 shape profile no. 06 +SP07 shape profile no. 07 +SP08 shape profile no. 08 +SP09 shape profile no. 09 +SP10 shape profile no. 10 +SP11 shape profile no. 11 +SP12 shape profile no. 12 +SP13 shape profile no. 13 +SP14 shape profile no. 14 +SP15 shape profile no. 15 +SP16 shape profile no. 16 +SP17 shape profile no. 17 +SP18 shape profile no. 18 +SP19 shape profile no. 19 +SP20 shape profile no. 20 +SHP2 average shape profile index of order 2 +W3D 3D-Wiener index +J3D 3D-Balaban index +H3D 3D-Harary index +AGDD average geometric distance degree +DDI D/D index +ADDD average distance/distance degree +G1 gravitational index G1 +G2 gravitational index G2 (bond-restricted) +RGyr radius of gyration (mass weighted) +SPAN span R +SPAM average span R +MEcc molecular eccentricity +SPH spherosity +ASP asphericity +FDI folding degree index +PJI3 3D Petijean shape index +L/Bw length-to-breadth ratio by WHIM +SEig absolute eigenvalue sum on geometry matrix +HOMA Harmonic Oscillator Model of Aromaticity index +RCI Jug RC index +AROM aromaticity (trial) +HOMT HOMA total (trial) +DISPm d COMMA2 value / weighted by atomic masses +QXXm Qxx COMMA2 value / weighted by atomic masses +QYYm Qyy COMMA2 value / weighted by atomic masses +QZZm Qzz COMMA2 value / weighted by atomic masses +DISPv d COMMA2 value / weighted by atomic van der Waals volumes +QXXv Qxx COMMA2 value / weighted by atomic van der Waals volumes +QYYv Qyy COMMA2 value / weighted by atomic van der Waals volumes +QZZv Qzz COMMA2 value / weighted by atomic van der Waals volumes +DISPe d COMMA2 value / weighted by atomic Sanderson electronegativities +QXXe Qxx COMMA2 value / weighted by atomic Sanderson electronegativities +QYYe Qyy COMMA2 value / weighted by atomic Sanderson electronegativities +QZZe Qzz COMMA2 value / weighted by atomic Sanderson electronegativities +DISPp d COMMA2 value / weighted by atomic polarizabilities +QXXp Qxx COMMA2 value / weighted by atomic polarizabilities +QYYp Qyy COMMA2 value / weighted by atomic polarizabilities +QZZp Qzz COMMA2 value / weighted by atomic polarizabilities +G(N..N) sum of geometrical distances between N..N +G(N..O) sum of geometrical distances between N..O +G(N..S) sum of geometrical distances between N..S +G(N..P) sum of geometrical distances between N..P +G(N..F) sum of geometrical distances between N..F +G(N..Cl) sum of geometrical distances between N..Cl +G(N..Br) sum of geometrical distances between N..Br +G(N..I) sum of geometrical distances between N..I +G(O..O) sum of geometrical distances between O..O +G(O..S) sum of geometrical distances between O..S +G(O..P) sum of geometrical distances between O..P +G(O..F) sum of geometrical distances between O..F +G(O..Cl) sum of geometrical distances between O..Cl +G(O..Br) sum of geometrical distances between O..Br +G(O..I) sum of geometrical distances between O..I +G(S..S) sum of geometrical distances between S..S +G(S..P) sum of geometrical distances between S..P +G(S..F) sum of geometrical distances between S..F +G(S..Cl) sum of geometrical distances between S..Cl +G(S..Br) sum of geometrical distances between S..Br +G(S..I) sum of geometrical distances between S..I +G(P..P) sum of geometrical distances between P..P +G(P..F) sum of geometrical distances between P..F +G(P..Cl) sum of geometrical distances between P..Cl +G(P..Br) sum of geometrical distances between P..Br +G(P..I) sum of geometrical distances between P..I +G(F..F) sum of geometrical distances between F..F +G(F..Cl) sum of geometrical distances between F..Cl +G(F..Br) sum of geometrical distances between F..Br +G(F..I) sum of geometrical distances between F..I +G(Cl..Cl) sum of geometrical distances between Cl..Cl +G(Cl..Br) sum of geometrical distances between Cl..Br +G(Cl..I) sum of geometrical distances between Cl..I +G(Br..Br) sum of geometrical distances between Br..Br +G(Br..I) sum of geometrical distances between Br..I +G(I..I) sum of geometrical distances between I..I +RDF010u Radial Distribution Function - 1.0 / unweighted +RDF015u Radial Distribution Function - 1.5 / unweighted +RDF020u Radial Distribution Function - 2.0 / unweighted +RDF025u Radial Distribution Function - 2.5 / unweighted +RDF030u Radial Distribution Function - 3.0 / unweighted +RDF035u Radial Distribution Function - 3.5 / unweighted +RDF040u Radial Distribution Function - 4.0 / unweighted +RDF045u Radial Distribution Function - 4.5 / unweighted +RDF050u Radial Distribution Function - 5.0 / unweighted +RDF055u Radial Distribution Function - 5.5 / unweighted +RDF060u Radial Distribution Function - 6.0 / unweighted +RDF065u Radial Distribution Function - 6.5 / unweighted +RDF070u Radial Distribution Function - 7.0 / unweighted +RDF075u Radial Distribution Function - 7.5 / unweighted +RDF080u Radial Distribution Function - 8.0 / unweighted +RDF085u Radial Distribution Function - 8.5 / unweighted +RDF090u Radial Distribution Function - 9.0 / unweighted +RDF095u Radial Distribution Function - 9.5 / unweighted +RDF100u Radial Distribution Function - 10.0 / unweighted +RDF105u Radial Distribution Function - 10.5 / unweighted +RDF110u Radial Distribution Function - 11.0 / unweighted +RDF115u Radial Distribution Function - 11.5 / unweighted +RDF120u Radial Distribution Function - 12.0 / unweighted +RDF125u Radial Distribution Function - 12.5 / unweighted +RDF130u Radial Distribution Function - 13.0 / unweighted +RDF135u Radial Distribution Function - 13.5 / unweighted +RDF140u Radial Distribution Function - 14.0 / unweighted +RDF145u Radial Distribution Function - 14.5 / unweighted +RDF150u Radial Distribution Function - 15.0 / unweighted +RDF155u Radial Distribution Function - 15.5 / unweighted +RDF010m Radial Distribution Function - 1.0 / weighted by atomic masses +RDF015m Radial Distribution Function - 1.5 / weighted by atomic masses +RDF020m Radial Distribution Function - 2.0 / weighted by atomic masses +RDF025m Radial Distribution Function - 2.5 / weighted by atomic masses +RDF030m Radial Distribution Function - 3.0 / weighted by atomic masses +RDF035m Radial Distribution Function - 3.5 / weighted by atomic masses +RDF040m Radial Distribution Function - 4.0 / weighted by atomic masses +RDF045m Radial Distribution Function - 4.5 / weighted by atomic masses +RDF050m Radial Distribution Function - 5.0 / weighted by atomic masses +RDF055m Radial Distribution Function - 5.5 / weighted by atomic masses +RDF060m Radial Distribution Function - 6.0 / weighted by atomic masses +RDF065m Radial Distribution Function - 6.5 / weighted by atomic masses +RDF070m Radial Distribution Function - 7.0 / weighted by atomic masses +RDF075m Radial Distribution Function - 7.5 / weighted by atomic masses +RDF080m Radial Distribution Function - 8.0 / weighted by atomic masses +RDF085m Radial Distribution Function - 8.5 / weighted by atomic masses +RDF090m Radial Distribution Function - 9.0 / weighted by atomic masses +RDF095m Radial Distribution Function - 9.5 / weighted by atomic masses +RDF100m Radial Distribution Function - 10.0 / weighted by atomic masses +RDF105m Radial Distribution Function - 10.5 / weighted by atomic masses +RDF110m Radial Distribution Function - 11.0 / weighted by atomic masses +RDF115m Radial Distribution Function - 11.5 / weighted by atomic masses +RDF120m Radial Distribution Function - 12.0 / weighted by atomic masses +RDF125m Radial Distribution Function - 12.5 / weighted by atomic masses +RDF130m Radial Distribution Function - 13.0 / weighted by atomic masses +RDF135m Radial Distribution Function - 13.5 / weighted by atomic masses +RDF140m Radial Distribution Function - 14.0 / weighted by atomic masses +RDF145m Radial Distribution Function - 14.5 / weighted by atomic masses +RDF150m Radial Distribution Function - 15.0 / weighted by atomic masses +RDF155m Radial Distribution Function - 15.5 / weighted by atomic masses +RDF010v Radial Distribution Function - 1.0 / weighted by atomic van der Waals volumes +RDF015v Radial Distribution Function - 1.5 / weighted by atomic van der Waals volumes +RDF020v Radial Distribution Function - 2.0 / weighted by atomic van der Waals volumes +RDF025v Radial Distribution Function - 2.5 / weighted by atomic van der Waals volumes +RDF030v Radial Distribution Function - 3.0 / weighted by atomic van der Waals volumes +RDF035v Radial Distribution Function - 3.5 / weighted by atomic van der Waals volumes +RDF040v Radial Distribution Function - 4.0 / weighted by atomic van der Waals volumes +RDF045v Radial Distribution Function - 4.5 / weighted by atomic van der Waals volumes +RDF050v Radial Distribution Function - 5.0 / weighted by atomic van der Waals volumes +RDF055v Radial Distribution Function - 5.5 / weighted by atomic van der Waals volumes +RDF060v Radial Distribution Function - 6.0 / weighted by atomic van der Waals volumes +RDF065v Radial Distribution Function - 6.5 / weighted by atomic van der Waals volumes +RDF070v Radial Distribution Function - 7.0 / weighted by atomic van der Waals volumes +RDF075v Radial Distribution Function - 7.5 / weighted by atomic van der Waals volumes +RDF080v Radial Distribution Function - 8.0 / weighted by atomic van der Waals volumes +RDF085v Radial Distribution Function - 8.5 / weighted by atomic van der Waals volumes +RDF090v Radial Distribution Function - 9.0 / weighted by atomic van der Waals volumes +RDF095v Radial Distribution Function - 9.5 / weighted by atomic van der Waals volumes +RDF100v Radial Distribution Function - 10.0 / weighted by atomic van der Waals volumes +RDF105v Radial Distribution Function - 10.5 / weighted by atomic van der Waals volumes +RDF110v Radial Distribution Function - 11.0 / weighted by atomic van der Waals volumes +RDF115v Radial Distribution Function - 11.5 / weighted by atomic van der Waals volumes +RDF120v Radial Distribution Function - 12.0 / weighted by atomic van der Waals volumes +RDF125v Radial Distribution Function - 12.5 / weighted by atomic van der Waals volumes +RDF130v Radial Distribution Function - 13.0 / weighted by atomic van der Waals volumes +RDF135v Radial Distribution Function - 13.5 / weighted by atomic van der Waals volumes +RDF140v Radial Distribution Function - 14.0 / weighted by atomic van der Waals volumes +RDF145v Radial Distribution Function - 14.5 / weighted by atomic van der Waals volumes +RDF150v Radial Distribution Function - 15.0 / weighted by atomic van der Waals volumes +RDF155v Radial Distribution Function - 15.5 / weighted by atomic van der Waals volumes +RDF010e Radial Distribution Function - 1.0 / weighted by atomic Sanderson electronegativities +RDF015e Radial Distribution Function - 1.5 / weighted by atomic Sanderson electronegativities +RDF020e Radial Distribution Function - 2.0 / weighted by atomic Sanderson electronegativities +RDF025e Radial Distribution Function - 2.5 / weighted by atomic Sanderson electronegativities +RDF030e Radial Distribution Function - 3.0 / weighted by atomic Sanderson electronegativities +RDF035e Radial Distribution Function - 3.5 / weighted by atomic Sanderson electronegativities +RDF040e Radial Distribution Function - 4.0 / weighted by atomic Sanderson electronegativities +RDF045e Radial Distribution Function - 4.5 / weighted by atomic Sanderson electronegativities +RDF050e Radial Distribution Function - 5.0 / weighted by atomic Sanderson electronegativities +RDF055e Radial Distribution Function - 5.5 / weighted by atomic Sanderson electronegativities +RDF060e Radial Distribution Function - 6.0 / weighted by atomic Sanderson electronegativities +RDF065e Radial Distribution Function - 6.5 / weighted by atomic Sanderson electronegativities +RDF070e Radial Distribution Function - 7.0 / weighted by atomic Sanderson electronegativities +RDF075e Radial Distribution Function - 7.5 / weighted by atomic Sanderson electronegativities +RDF080e Radial Distribution Function - 8.0 / weighted by atomic Sanderson electronegativities +RDF085e Radial Distribution Function - 8.5 / weighted by atomic Sanderson electronegativities +RDF090e Radial Distribution Function - 9.0 / weighted by atomic Sanderson electronegativities +RDF095e Radial Distribution Function - 9.5 / weighted by atomic Sanderson electronegativities +RDF100e Radial Distribution Function - 10.0 / weighted by atomic Sanderson electronegativities +RDF105e Radial Distribution Function - 10.5 / weighted by atomic Sanderson electronegativities +RDF110e Radial Distribution Function - 11.0 / weighted by atomic Sanderson electronegativities +RDF115e Radial Distribution Function - 11.5 / weighted by atomic Sanderson electronegativities +RDF120e Radial Distribution Function - 12.0 / weighted by atomic Sanderson electronegativities +RDF125e Radial Distribution Function - 12.5 / weighted by atomic Sanderson electronegativities +RDF130e Radial Distribution Function - 13.0 / weighted by atomic Sanderson electronegativities +RDF135e Radial Distribution Function - 13.5 / weighted by atomic Sanderson electronegativities +RDF140e Radial Distribution Function - 14.0 / weighted by atomic Sanderson electronegativities +RDF145e Radial Distribution Function - 14.5 / weighted by atomic Sanderson electronegativities +RDF150e Radial Distribution Function - 15.0 / weighted by atomic Sanderson electronegativities +RDF155e Radial Distribution Function - 15.5 / weighted by atomic Sanderson electronegativities +RDF010p Radial Distribution Function - 1.0 / weighted by atomic polarizabilities +RDF015p Radial Distribution Function - 1.5 / weighted by atomic polarizabilities +RDF020p Radial Distribution Function - 2.0 / weighted by atomic polarizabilities +RDF025p Radial Distribution Function - 2.5 / weighted by atomic polarizabilities +RDF030p Radial Distribution Function - 3.0 / weighted by atomic polarizabilities +RDF035p Radial Distribution Function - 3.5 / weighted by atomic polarizabilities +RDF040p Radial Distribution Function - 4.0 / weighted by atomic polarizabilities +RDF045p Radial Distribution Function - 4.5 / weighted by atomic polarizabilities +RDF050p Radial Distribution Function - 5.0 / weighted by atomic polarizabilities +RDF055p Radial Distribution Function - 5.5 / weighted by atomic polarizabilities +RDF060p Radial Distribution Function - 6.0 / weighted by atomic polarizabilities +RDF065p Radial Distribution Function - 6.5 / weighted by atomic polarizabilities +RDF070p Radial Distribution Function - 7.0 / weighted by atomic polarizabilities +RDF075p Radial Distribution Function - 7.5 / weighted by atomic polarizabilities +RDF080p Radial Distribution Function - 8.0 / weighted by atomic polarizabilities +RDF085p Radial Distribution Function - 8.5 / weighted by atomic polarizabilities +RDF090p Radial Distribution Function - 9.0 / weighted by atomic polarizabilities +RDF095p Radial Distribution Function - 9.5 / weighted by atomic polarizabilities +RDF100p Radial Distribution Function - 10.0 / weighted by atomic polarizabilities +RDF105p Radial Distribution Function - 10.5 / weighted by atomic polarizabilities +RDF110p Radial Distribution Function - 11.0 / weighted by atomic polarizabilities +RDF115p Radial Distribution Function - 11.5 / weighted by atomic polarizabilities +RDF120p Radial Distribution Function - 12.0 / weighted by atomic polarizabilities +RDF125p Radial Distribution Function - 12.5 / weighted by atomic polarizabilities +RDF130p Radial Distribution Function - 13.0 / weighted by atomic polarizabilities +RDF135p Radial Distribution Function - 13.5 / weighted by atomic polarizabilities +RDF140p Radial Distribution Function - 14.0 / weighted by atomic polarizabilities +RDF145p Radial Distribution Function - 14.5 / weighted by atomic polarizabilities +RDF150p Radial Distribution Function - 15.0 / weighted by atomic polarizabilities +RDF155p Radial Distribution Function - 15.5 / weighted by atomic polarizabilities +Mor01u 3D-MoRSE - signal 01 / unweighted +Mor02u 3D-MoRSE - signal 02 / unweighted +Mor03u 3D-MoRSE - signal 03 / unweighted +Mor04u 3D-MoRSE - signal 04 / unweighted +Mor05u 3D-MoRSE - signal 05 / unweighted +Mor06u 3D-MoRSE - signal 06 / unweighted +Mor07u 3D-MoRSE - signal 07 / unweighted +Mor08u 3D-MoRSE - signal 08 / unweighted +Mor09u 3D-MoRSE - signal 09 / unweighted +Mor10u 3D-MoRSE - signal 10 / unweighted +Mor11u 3D-MoRSE - signal 11 / unweighted +Mor12u 3D-MoRSE - signal 12 / unweighted +Mor13u 3D-MoRSE - signal 13 / unweighted +Mor14u 3D-MoRSE - signal 14 / unweighted +Mor15u 3D-MoRSE - signal 15 / unweighted +Mor16u 3D-MoRSE - signal 16 / unweighted +Mor17u 3D-MoRSE - signal 17 / unweighted +Mor18u 3D-MoRSE - signal 18 / unweighted +Mor19u 3D-MoRSE - signal 19 / unweighted +Mor20u 3D-MoRSE - signal 20 / unweighted +Mor21u 3D-MoRSE - signal 21 / unweighted +Mor22u 3D-MoRSE - signal 22 / unweighted +Mor23u 3D-MoRSE - signal 23 / unweighted +Mor24u 3D-MoRSE - signal 24 / unweighted +Mor25u 3D-MoRSE - signal 25 / unweighted +Mor26u 3D-MoRSE - signal 26 / unweighted +Mor27u 3D-MoRSE - signal 27 / unweighted +Mor28u 3D-MoRSE - signal 28 / unweighted +Mor29u 3D-MoRSE - signal 29 / unweighted +Mor30u 3D-MoRSE - signal 30 / unweighted +Mor31u 3D-MoRSE - signal 31 / unweighted +Mor32u 3D-MoRSE - signal 32 / unweighted +Mor01m 3D-MoRSE - signal 01 / weighted by atomic masses +Mor02m 3D-MoRSE - signal 02 / weighted by atomic masses +Mor03m 3D-MoRSE - signal 03 / weighted by atomic masses +Mor04m 3D-MoRSE - signal 04 / weighted by atomic masses +Mor05m 3D-MoRSE - signal 05 / weighted by atomic masses +Mor06m 3D-MoRSE - signal 06 / weighted by atomic masses +Mor07m 3D-MoRSE - signal 07 / weighted by atomic masses +Mor08m 3D-MoRSE - signal 08 / weighted by atomic masses +Mor09m 3D-MoRSE - signal 09 / weighted by atomic masses +Mor10m 3D-MoRSE - signal 10 / weighted by atomic masses +Mor11m 3D-MoRSE - signal 11 / weighted by atomic masses +Mor12m 3D-MoRSE - signal 12 / weighted by atomic masses +Mor13m 3D-MoRSE - signal 13 / weighted by atomic masses +Mor14m 3D-MoRSE - signal 14 / weighted by atomic masses +Mor15m 3D-MoRSE - signal 15 / weighted by atomic masses +Mor16m 3D-MoRSE - signal 16 / weighted by atomic masses +Mor17m 3D-MoRSE - signal 17 / weighted by atomic masses +Mor18m 3D-MoRSE - signal 18 / weighted by atomic masses +Mor19m 3D-MoRSE - signal 19 / weighted by atomic masses +Mor20m 3D-MoRSE - signal 20 / weighted by atomic masses +Mor21m 3D-MoRSE - signal 21 / weighted by atomic masses +Mor22m 3D-MoRSE - signal 22 / weighted by atomic masses +Mor23m 3D-MoRSE - signal 23 / weighted by atomic masses +Mor24m 3D-MoRSE - signal 24 / weighted by atomic masses +Mor25m 3D-MoRSE - signal 25 / weighted by atomic masses +Mor26m 3D-MoRSE - signal 26 / weighted by atomic masses +Mor27m 3D-MoRSE - signal 27 / weighted by atomic masses +Mor28m 3D-MoRSE - signal 28 / weighted by atomic masses +Mor29m 3D-MoRSE - signal 29 / weighted by atomic masses +Mor30m 3D-MoRSE - signal 30 / weighted by atomic masses +Mor31m 3D-MoRSE - signal 31 / weighted by atomic masses +Mor32m 3D-MoRSE - signal 32 / weighted by atomic masses +Mor01v 3D-MoRSE - signal 01 / weighted by atomic van der Waals volumes +Mor02v 3D-MoRSE - signal 02 / weighted by atomic van der Waals volumes +Mor03v 3D-MoRSE - signal 03 / weighted by atomic van der Waals volumes +Mor04v 3D-MoRSE - signal 04 / weighted by atomic van der Waals volumes +Mor05v 3D-MoRSE - signal 05 / weighted by atomic van der Waals volumes +Mor06v 3D-MoRSE - signal 06 / weighted by atomic van der Waals volumes +Mor07v 3D-MoRSE - signal 07 / weighted by atomic van der Waals volumes +Mor08v 3D-MoRSE - signal 08 / weighted by atomic van der Waals volumes +Mor09v 3D-MoRSE - signal 09 / weighted by atomic van der Waals volumes +Mor10v 3D-MoRSE - signal 10 / weighted by atomic van der Waals volumes +Mor11v 3D-MoRSE - signal 11 / weighted by atomic van der Waals volumes +Mor12v 3D-MoRSE - signal 12 / weighted by atomic van der Waals volumes +Mor13v 3D-MoRSE - signal 13 / weighted by atomic van der Waals volumes +Mor14v 3D-MoRSE - signal 14 / weighted by atomic van der Waals volumes +Mor15v 3D-MoRSE - signal 15 / weighted by atomic van der Waals volumes +Mor16v 3D-MoRSE - signal 16 / weighted by atomic van der Waals volumes +Mor17v 3D-MoRSE - signal 17 / weighted by atomic van der Waals volumes +Mor18v 3D-MoRSE - signal 18 / weighted by atomic van der Waals volumes +Mor19v 3D-MoRSE - signal 19 / weighted by atomic van der Waals volumes +Mor20v 3D-MoRSE - signal 20 / weighted by atomic van der Waals volumes +Mor21v 3D-MoRSE - signal 21 / weighted by atomic van der Waals volumes +Mor22v 3D-MoRSE - signal 22 / weighted by atomic van der Waals volumes +Mor23v 3D-MoRSE - signal 23 / weighted by atomic van der Waals volumes +Mor24v 3D-MoRSE - signal 24 / weighted by atomic van der Waals volumes +Mor25v 3D-MoRSE - signal 25 / weighted by atomic van der Waals volumes +Mor26v 3D-MoRSE - signal 26 / weighted by atomic van der Waals volumes +Mor27v 3D-MoRSE - signal 27 / weighted by atomic van der Waals volumes +Mor28v 3D-MoRSE - signal 28 / weighted by atomic van der Waals volumes +Mor29v 3D-MoRSE - signal 29 / weighted by atomic van der Waals volumes +Mor30v 3D-MoRSE - signal 30 / weighted by atomic van der Waals volumes +Mor31v 3D-MoRSE - signal 31 / weighted by atomic van der Waals volumes +Mor32v 3D-MoRSE - signal 32 / weighted by atomic van der Waals volumes +Mor01e 3D-MoRSE - signal 01 / weighted by atomic Sanderson electronegativities +Mor02e 3D-MoRSE - signal 02 / weighted by atomic Sanderson electronegativities +Mor03e 3D-MoRSE - signal 03 / weighted by atomic Sanderson electronegativities +Mor04e 3D-MoRSE - signal 04 / weighted by atomic Sanderson electronegativities +Mor05e 3D-MoRSE - signal 05 / weighted by atomic Sanderson electronegativities +Mor06e 3D-MoRSE - signal 06 / weighted by atomic Sanderson electronegativities +Mor07e 3D-MoRSE - signal 07 / weighted by atomic Sanderson electronegativities +Mor08e 3D-MoRSE - signal 08 / weighted by atomic Sanderson electronegativities +Mor09e 3D-MoRSE - signal 09 / weighted by atomic Sanderson electronegativities +Mor10e 3D-MoRSE - signal 10 / weighted by atomic Sanderson electronegativities +Mor11e 3D-MoRSE - signal 11 / weighted by atomic Sanderson electronegativities +Mor12e 3D-MoRSE - signal 12 / weighted by atomic Sanderson electronegativities +Mor13e 3D-MoRSE - signal 13 / weighted by atomic Sanderson electronegativities +Mor14e 3D-MoRSE - signal 14 / weighted by atomic Sanderson electronegativities +Mor15e 3D-MoRSE - signal 15 / weighted by atomic Sanderson electronegativities +Mor16e 3D-MoRSE - signal 16 / weighted by atomic Sanderson electronegativities +Mor17e 3D-MoRSE - signal 17 / weighted by atomic Sanderson electronegativities +Mor18e 3D-MoRSE - signal 18 / weighted by atomic Sanderson electronegativities +Mor19e 3D-MoRSE - signal 19 / weighted by atomic Sanderson electronegativities +Mor20e 3D-MoRSE - signal 20 / weighted by atomic Sanderson electronegativities +Mor21e 3D-MoRSE - signal 21 / weighted by atomic Sanderson electronegativities +Mor22e 3D-MoRSE - signal 22 / weighted by atomic Sanderson electronegativities +Mor23e 3D-MoRSE - signal 23 / weighted by atomic Sanderson electronegativities +Mor24e 3D-MoRSE - signal 24 / weighted by atomic Sanderson electronegativities +Mor25e 3D-MoRSE - signal 25 / weighted by atomic Sanderson electronegativities +Mor26e 3D-MoRSE - signal 26 / weighted by atomic Sanderson electronegativities +Mor27e 3D-MoRSE - signal 27 / weighted by atomic Sanderson electronegativities +Mor28e 3D-MoRSE - signal 28 / weighted by atomic Sanderson electronegativities +Mor29e 3D-MoRSE - signal 29 / weighted by atomic Sanderson electronegativities +Mor30e 3D-MoRSE - signal 30 / weighted by atomic Sanderson electronegativities +Mor31e 3D-MoRSE - signal 31 / weighted by atomic Sanderson electronegativities +Mor32e 3D-MoRSE - signal 32 / weighted by atomic Sanderson electronegativities +Mor01p 3D-MoRSE - signal 01 / weighted by atomic polarizabilities +Mor02p 3D-MoRSE - signal 02 / weighted by atomic polarizabilities +Mor03p 3D-MoRSE - signal 03 / weighted by atomic polarizabilities +Mor04p 3D-MoRSE - signal 04 / weighted by atomic polarizabilities +Mor05p 3D-MoRSE - signal 05 / weighted by atomic polarizabilities +Mor06p 3D-MoRSE - signal 06 / weighted by atomic polarizabilities +Mor07p 3D-MoRSE - signal 07 / weighted by atomic polarizabilities +Mor08p 3D-MoRSE - signal 08 / weighted by atomic polarizabilities +Mor09p 3D-MoRSE - signal 09 / weighted by atomic polarizabilities +Mor10p 3D-MoRSE - signal 10 / weighted by atomic polarizabilities +Mor11p 3D-MoRSE - signal 11 / weighted by atomic polarizabilities +Mor12p 3D-MoRSE - signal 12 / weighted by atomic polarizabilities +Mor13p 3D-MoRSE - signal 13 / weighted by atomic polarizabilities +Mor14p 3D-MoRSE - signal 14 / weighted by atomic polarizabilities +Mor15p 3D-MoRSE - signal 15 / weighted by atomic polarizabilities +Mor16p 3D-MoRSE - signal 16 / weighted by atomic polarizabilities +Mor17p 3D-MoRSE - signal 17 / weighted by atomic polarizabilities +Mor18p 3D-MoRSE - signal 18 / weighted by atomic polarizabilities +Mor19p 3D-MoRSE - signal 19 / weighted by atomic polarizabilities +Mor20p 3D-MoRSE - signal 20 / weighted by atomic polarizabilities +Mor21p 3D-MoRSE - signal 21 / weighted by atomic polarizabilities +Mor22p 3D-MoRSE - signal 22 / weighted by atomic polarizabilities +Mor23p 3D-MoRSE - signal 23 / weighted by atomic polarizabilities +Mor24p 3D-MoRSE - signal 24 / weighted by atomic polarizabilities +Mor25p 3D-MoRSE - signal 25 / weighted by atomic polarizabilities +Mor26p 3D-MoRSE - signal 26 / weighted by atomic polarizabilities +Mor27p 3D-MoRSE - signal 27 / weighted by atomic polarizabilities +Mor28p 3D-MoRSE - signal 28 / weighted by atomic polarizabilities +Mor29p 3D-MoRSE - signal 29 / weighted by atomic polarizabilities +Mor30p 3D-MoRSE - signal 30 / weighted by atomic polarizabilities +Mor31p 3D-MoRSE - signal 31 / weighted by atomic polarizabilities +Mor32p 3D-MoRSE - signal 32 / weighted by atomic polarizabilities +L1u 1st component size directional WHIM index / unweighted +L2u 2nd component size directional WHIM index / unweighted +L3u 3rd component size directional WHIM index / unweighted +P1u 1st component shape directional WHIM index / unweighted +P2u 2nd component shape directional WHIM index / unweighted +G1u 1st component symmetry directional WHIM index / unweighted +G2u 2st component symmetry directional WHIM index / unweighted +G3u 3st component symmetry directional WHIM index / unweighted +E1u 1st component accessibility directional WHIM index / unweighted +E2u 2nd component accessibility directional WHIM index / unweighted +E3u 3rd component accessibility directional WHIM index / unweighted +L1m 1st component size directional WHIM index / weighted by atomic masses +L2m 2nd component size directional WHIM index / weighted by atomic masses +L3m 3rd component size directional WHIM index / weighted by atomic masses +P1m 1st component shape directional WHIM index / weighted by atomic masses +P2m 2nd component shape directional WHIM index / weighted by atomic masses +G1m 1st component symmetry directional WHIM index / weighted by atomic masses +G2m 2st component symmetry directional WHIM index / weighted by atomic masses +G3m 3st component symmetry directional WHIM index / weighted by atomic masses +E1m 1st component accessibility directional WHIM index / weighted by atomic masses +E2m 2nd component accessibility directional WHIM index / weighted by atomic masses +E3m 3rd component accessibility directional WHIM index / weighted by atomic masses +L1v 1st component size directional WHIM index / weighted by atomic van der Waals volumes +L2v 2nd component size directional WHIM index / weighted by atomic van der Waals volumes +L3v 3rd component size directional WHIM index / weighted by atomic van der Waals volumes +P1v 1st component shape directional WHIM index / weighted by atomic van der Waals volumes +P2v 2nd component shape directional WHIM index / weighted by atomic van der Waals volumes +G1v 1st component symmetry directional WHIM index / weighted by atomic van der Waals volumes +G2v 2st component symmetry directional WHIM index / weighted by atomic van der Waals volumes +G3v 3st component symmetry directional WHIM index / weighted by atomic van der Waals volumes +E1v 1st component accessibility directional WHIM index / weighted by atomic van der Waals volumes +E2v 2nd component accessibility directional WHIM index / weighted by atomic van der Waals volumes +E3v 3rd component accessibility directional WHIM index / weighted by atomic van der Waals volumes +L1e 1st component size directional WHIM index / weighted by atomic Sanderson electronegativities +L2e 2nd component size directional WHIM index / weighted by atomic Sanderson electronegativities +L3e 3rd component size directional WHIM index / weighted by atomic Sanderson electronegativities +P1e 1st component shape directional WHIM index / weighted by atomic Sanderson electronegativities +P2e 2nd component shape directional WHIM index / weighted by atomic Sanderson electronegativities +G1e 1st component symmetry directional WHIM index / weighted by atomic Sanderson electronegativities +G2e 2st component symmetry directional WHIM index / weighted by atomic Sanderson electronegativities +G3e 3st component symmetry directional WHIM index / weighted by atomic Sanderson electronegativities +E1e 1st component accessibility directional WHIM index / weighted by atomic Sanderson electronegativities +E2e 2nd component accessibility directional WHIM index / weighted by atomic Sanderson electronegativities +E3e 3rd component accessibility directional WHIM index / weighted by atomic Sanderson electronegativities +L1p 1st component size directional WHIM index / weighted by atomic polarizabilities +L2p 2nd component size directional WHIM index / weighted by atomic polarizabilities +L3p 3rd component size directional WHIM index / weighted by atomic polarizabilities +P1p 1st component shape directional WHIM index / weighted by atomic polarizabilities +P2p 2nd component shape directional WHIM index / weighted by atomic polarizabilities +G1p 1st component symmetry directional WHIM index / weighted by atomic polarizabilities +G2p 2st component symmetry directional WHIM index / weighted by atomic polarizabilities +G3p 3st component symmetry directional WHIM index / weighted by atomic polarizabilities +E1p 1st component accessibility directional WHIM index / weighted by atomic polarizabilities +E2p 2nd component accessibility directional WHIM index / weighted by atomic polarizabilities +E3p 3rd component accessibility directional WHIM index / weighted by atomic polarizabilities +L1s 1st component size directional WHIM index / weighted by atomic electrotopological states +L2s 2nd component size directional WHIM index / weighted by atomic electrotopological states +L3s 3rd component size directional WHIM index / weighted by atomic electrotopological states +P1s 1st component shape directional WHIM index / weighted by atomic electrotopological states +P2s 2nd component shape directional WHIM index / weighted by atomic electrotopological states +G1s 1st component symmetry directional WHIM index / weighted by atomic electrotopological states +G2s 2st component symmetry directional WHIM index / weighted by atomic electrotopological states +G3s 3st component symmetry directional WHIM index / weighted by atomic electrotopological states +E1s 1st component accessibility directional WHIM index / weighted by atomic electrotopological states +E2s 2nd component accessibility directional WHIM index / weighted by atomic electrotopological states +E3s 3rd component accessibility directional WHIM index / weighted by atomic electrotopological states +Tu T total size index / unweighted +Tm T total size index / weighted by atomic masses +Tv T total size index / weighted by atomic van der Waals volumes +Te T total size index / weighted by atomic Sanderson electronegativities +Tp T total size index / weighted by atomic polarizabilities +Ts T total size index / weighted by atomic electrotopological states +Au A total size index / unweighted +Am A total size index / weighted by atomic masses +Av A total size index / weighted by atomic van der Waals volumes +Ae A total size index / weighted by atomic Sanderson electronegativities +Ap A total size index / weighted by atomic polarizabilities +As A total size index / weighted by atomic electrotopological states +Gu G total symmetry index / unweighted +Gm G total symmetry index / weighted by atomic masses +Gs G total symmetry index / weighted by atomic electrotopological states +Ku K global shape index / unweighted +Km K global shape index / weighted by atomic masses +Kv K global shape index / weighted by atomic van der Waals volumes +Ke K global shape index / weighted by atomic Sanderson electronegativities +Kp K global shape index / weighted by atomic polarizabilities +Ks K global shape index / weighted by atomic electrotopological states +Du D total accessibility index / unweighted +Dm D total accessibility index / weighted by atomic masses +Dv D total accessibility index / weighted by atomic van der Waals volumes +De D total accessibility index / weighted by atomic Sanderson electronegativities +Dp D total accessibility index / weighted by atomic polarizabilities +Ds D total accessibility index / weighted by atomic electrotopological states +Vu V total size index / unweighted +Vm V total size index / weighted by atomic masses +Vv V total size index / weighted by atomic van der Waals volumes +Ve V total size index / weighted by atomic Sanderson electronegativities +Vp V total size index / weighted by atomic polarizabilities +Vs V total size index / weighted by atomic electrotopological states +ITH total information content on the leverage equality +ISH standardized information content on the leverage equality +HIC mean information content on the leverage magnitude +HGM geometric mean on the leverage magnitude +H0u H autocorrelation of lag 0 / unweighted +H1u H autocorrelation of lag 1 / unweighted +H2u H autocorrelation of lag 2 / unweighted +H3u H autocorrelation of lag 3 / unweighted +H4u H autocorrelation of lag 4 / unweighted +H5u H autocorrelation of lag 5 / unweighted +H6u H autocorrelation of lag 6 / unweighted +H7u H autocorrelation of lag 7 / unweighted +H8u H autocorrelation of lag 8 / unweighted +HTu H total index / unweighted +HATS0u leverage-weighted autocorrelation of lag 0 / unweighted +HATS1u leverage-weighted autocorrelation of lag 1 / unweighted +HATS2u leverage-weighted autocorrelation of lag 2 / unweighted +HATS3u leverage-weighted autocorrelation of lag 3 / unweighted +HATS4u leverage-weighted autocorrelation of lag 4 / unweighted +HATS5u leverage-weighted autocorrelation of lag 5 / unweighted +HATS6u leverage-weighted autocorrelation of lag 6 / unweighted +HATS7u leverage-weighted autocorrelation of lag 7 / unweighted +HATS8u leverage-weighted autocorrelation of lag 8 / unweighted +HATSu leverage-weighted total index / unweighted +H0m H autocorrelation of lag 0 / weighted by atomic masses +H1m H autocorrelation of lag 1 / weighted by atomic masses +H2m H autocorrelation of lag 2 / weighted by atomic masses +H3m H autocorrelation of lag 3 / weighted by atomic masses +H4m H autocorrelation of lag 4 / weighted by atomic masses +H5m H autocorrelation of lag 5 / weighted by atomic masses +H6m H autocorrelation of lag 6 / weighted by atomic masses +H7m H autocorrelation of lag 7 / weighted by atomic masses +H8m H autocorrelation of lag 8 / weighted by atomic masses +HTm H total index / weighted by atomic masses +HATS0m leverage-weighted autocorrelation of lag 0 / weighted by atomic masses +HATS1m leverage-weighted autocorrelation of lag 1 / weighted by atomic masses +HATS2m leverage-weighted autocorrelation of lag 2 / weighted by atomic masses +HATS3m leverage-weighted autocorrelation of lag 3 / weighted by atomic masses +HATS4m leverage-weighted autocorrelation of lag 4 / weighted by atomic masses +HATS5m leverage-weighted autocorrelation of lag 5 / weighted by atomic masses +HATS6m leverage-weighted autocorrelation of lag 6 / weighted by atomic masses +HATS7m leverage-weighted autocorrelation of lag 7 / weighted by atomic masses +HATS8m leverage-weighted autocorrelation of lag 8 / weighted by atomic masses +HATSm leverage-weighted total index / weighted by atomic masses +H0v H autocorrelation of lag 0 / weighted by atomic van der Waals volumes +H1v H autocorrelation of lag 1 / weighted by atomic van der Waals volumes +H2v H autocorrelation of lag 2 / weighted by atomic van der Waals volumes +H3v H autocorrelation of lag 3 / weighted by atomic van der Waals volumes +H4v H autocorrelation of lag 4 / weighted by atomic van der Waals volumes +H5v H autocorrelation of lag 5 / weighted by atomic van der Waals volumes +H6v H autocorrelation of lag 6 / weighted by atomic van der Waals volumes +H7v H autocorrelation of lag 7 / weighted by atomic van der Waals volumes +H8v H autocorrelation of lag 8 / weighted by atomic van der Waals volumes +HTv H total index / weighted by atomic van der Waals volumes +HATS0v leverage-weighted autocorrelation of lag 0 / weighted by atomic van der Waals volumes +HATS1v leverage-weighted autocorrelation of lag 1 / weighted by atomic van der Waals volumes +HATS2v leverage-weighted autocorrelation of lag 2 / weighted by atomic van der Waals volumes +HATS3v leverage-weighted autocorrelation of lag 3 / weighted by atomic van der Waals volumes +HATS4v leverage-weighted autocorrelation of lag 4 / weighted by atomic van der Waals volumes +HATS5v leverage-weighted autocorrelation of lag 5 / weighted by atomic van der Waals volumes +HATS6v leverage-weighted autocorrelation of lag 6 / weighted by atomic van der Waals volumes +HATS7v leverage-weighted autocorrelation of lag 7 / weighted by atomic van der Waals volumes +HATS8v leverage-weighted autocorrelation of lag 8 / weighted by atomic van der Waals volumes +HATSv leverage-weighted total index / weighted by atomic van der Waals volumes +H0e H autocorrelation of lag 0 / weighted by atomic Sanderson electronegativities +H1e H autocorrelation of lag 1 / weighted by atomic Sanderson electronegativities +H2e H autocorrelation of lag 2 / weighted by atomic Sanderson electronegativities +H3e H autocorrelation of lag 3 / weighted by atomic Sanderson electronegativities +H4e H autocorrelation of lag 4 / weighted by atomic Sanderson electronegativities +H5e H autocorrelation of lag 5 / weighted by atomic Sanderson electronegativities +H6e H autocorrelation of lag 6 / weighted by atomic Sanderson electronegativities +H7e H autocorrelation of lag 7 / weighted by atomic Sanderson electronegativities +H8e H autocorrelation of lag 8 / weighted by atomic Sanderson electronegativities +HTe H total index / weighted by atomic Sanderson electronegativities +HATS0e leverage-weighted autocorrelation of lag 0 / weighted by atomic Sanderson electronegativities +HATS1e leverage-weighted autocorrelation of lag 1 / weighted by atomic Sanderson electronegativities +HATS2e leverage-weighted autocorrelation of lag 2 / weighted by atomic Sanderson electronegativities +HATS3e leverage-weighted autocorrelation of lag 3 / weighted by atomic Sanderson electronegativities +HATS4e leverage-weighted autocorrelation of lag 4 / weighted by atomic Sanderson electronegativities +HATS5e leverage-weighted autocorrelation of lag 5 / weighted by atomic Sanderson electronegativities +HATS6e leverage-weighted autocorrelation of lag 6 / weighted by atomic Sanderson electronegativities +HATS7e leverage-weighted autocorrelation of lag 7 / weighted by atomic Sanderson electronegativities +HATS8e leverage-weighted autocorrelation of lag 8 / weighted by atomic Sanderson electronegativities +HATSe leverage-weighted total index / weighted by atomic Sanderson electronegativities +H0p H autocorrelation of lag 0 / weighted by atomic polarizabilities +H1p H autocorrelation of lag 1 / weighted by atomic polarizabilities +H2p H autocorrelation of lag 2 / weighted by atomic polarizabilities +H3p H autocorrelation of lag 3 / weighted by atomic polarizabilities +H4p H autocorrelation of lag 4 / weighted by atomic polarizabilities +H5p H autocorrelation of lag 5 / weighted by atomic polarizabilities +H6p H autocorrelation of lag 6 / weighted by atomic polarizabilities +H7p H autocorrelation of lag 7 / weighted by atomic polarizabilities +H8p H autocorrelation of lag 8 / weighted by atomic polarizabilities +HTp H total index / weighted by atomic polarizabilities +HATS0p leverage-weighted autocorrelation of lag 0 / weighted by atomic polarizabilities +HATS1p leverage-weighted autocorrelation of lag 1 / weighted by atomic polarizabilities +HATS2p leverage-weighted autocorrelation of lag 2 / weighted by atomic polarizabilities +HATS3p leverage-weighted autocorrelation of lag 3 / weighted by atomic polarizabilities +HATS4p leverage-weighted autocorrelation of lag 4 / weighted by atomic polarizabilities +HATS5p leverage-weighted autocorrelation of lag 5 / weighted by atomic polarizabilities +HATS6p leverage-weighted autocorrelation of lag 6 / weighted by atomic polarizabilities +HATS7p leverage-weighted autocorrelation of lag 7 / weighted by atomic polarizabilities +HATS8p leverage-weighted autocorrelation of lag 8 / weighted by atomic polarizabilities +HATSp leverage-weighted total index / weighted by atomic polarizabilities +RCON Randic-type R matrix connectivity +RARS R matrix average row sum +REIG first eigenvalue of the R matrix +R1u R autocorrelation of lag 1 / unweighted +R2u R autocorrelation of lag 2 / unweighted +R3u R autocorrelation of lag 3 / unweighted +R4u R autocorrelation of lag 4 / unweighted +R5u R autocorrelation of lag 5 / unweighted +R6u R autocorrelation of lag 6 / unweighted +R7u R autocorrelation of lag 7 / unweighted +R8u R autocorrelation of lag 8 / unweighted +RTu R total index / unweighted +R1u+ R maximal autocorrelation of lag 1 / unweighted +R2u+ R maximal autocorrelation of lag 2 / unweighted +R3u+ R maximal autocorrelation of lag 3 / unweighted +R4u+ R maximal autocorrelation of lag 4 / unweighted +R5u+ R maximal autocorrelation of lag 5 / unweighted +R6u+ R maximal autocorrelation of lag 6 / unweighted +R7u+ R maximal autocorrelation of lag 7 / unweighted +R8u+ R maximal autocorrelation of lag 8 / unweighted +RTu+ R maximal index / unweighted +R1m R autocorrelation of lag 1 / weighted by atomic masses +R2m R autocorrelation of lag 2 / weighted by atomic masses +R3m R autocorrelation of lag 3 / weighted by atomic masses +R4m R autocorrelation of lag 4 / weighted by atomic masses +R5m R autocorrelation of lag 5 / weighted by atomic masses +R6m R autocorrelation of lag 6 / weighted by atomic masses +R7m R autocorrelation of lag 7 / weighted by atomic masses +R8m R autocorrelation of lag 8 / weighted by atomic masses +RTm R total index / weighted by atomic masses +R1m+ R maximal autocorrelation of lag 1 / weighted by atomic masses +R2m+ R maximal autocorrelation of lag 2 / weighted by atomic masses +R3m+ R maximal autocorrelation of lag 3 / weighted by atomic masses +R4m+ R maximal autocorrelation of lag 4 / weighted by atomic masses +R5m+ R maximal autocorrelation of lag 5 / weighted by atomic masses +R6m+ R maximal autocorrelation of lag 6 / weighted by atomic masses +R7m+ R maximal autocorrelation of lag 7 / weighted by atomic masses +R8m+ R maximal autocorrelation of lag 8 / weighted by atomic masses +RTm+ R maximal index / weighted by atomic masses +R1v R autocorrelation of lag 1 / weighted by atomic van der Waals volumes +R2v R autocorrelation of lag 2 / weighted by atomic van der Waals volumes +R3v R autocorrelation of lag 3 / weighted by atomic van der Waals volumes +R4v R autocorrelation of lag 4 / weighted by atomic van der Waals volumes +R5v R autocorrelation of lag 5 / weighted by atomic van der Waals volumes +R6v R autocorrelation of lag 6 / weighted by atomic van der Waals volumes +R7v R autocorrelation of lag 7 / weighted by atomic van der Waals volumes +R8v R autocorrelation of lag 8 / weighted by atomic van der Waals volumes +RTv R total index / weighted by atomic van der Waals volumes +R1v+ R maximal autocorrelation of lag 1 / weighted by atomic van der Waals volumes +R2v+ R maximal autocorrelation of lag 2 / weighted by atomic van der Waals volumes +R3v+ R maximal autocorrelation of lag 3 / weighted by atomic van der Waals volumes +R4v+ R maximal autocorrelation of lag 4 / weighted by atomic van der Waals volumes +R5v+ R maximal autocorrelation of lag 5 / weighted by atomic van der Waals volumes +R6v+ R maximal autocorrelation of lag 6 / weighted by atomic van der Waals volumes +R7v+ R maximal autocorrelation of lag 7 / weighted by atomic van der Waals volumes +R8v+ R maximal autocorrelation of lag 8 / weighted by atomic van der Waals volumes +RTv+ R maximal index / weighted by atomic van der Waals volumes +R1e R autocorrelation of lag 1 / weighted by atomic Sanderson electronegativities +R2e R autocorrelation of lag 2 / weighted by atomic Sanderson electronegativities +R3e R autocorrelation of lag 3 / weighted by atomic Sanderson electronegativities +R4e R autocorrelation of lag 4 / weighted by atomic Sanderson electronegativities +R5e R autocorrelation of lag 5 / weighted by atomic Sanderson electronegativities +R6e R autocorrelation of lag 6 / weighted by atomic Sanderson electronegativities +R7e R autocorrelation of lag 7 / weighted by atomic Sanderson electronegativities +R8e R autocorrelation of lag 8 / weighted by atomic Sanderson electronegativities +RTe R total index / weighted by atomic Sanderson electronegativities +R1e+ R maximal autocorrelation of lag 1 / weighted by atomic Sanderson electronegativities +R2e+ R maximal autocorrelation of lag 2 / weighted by atomic Sanderson electronegativities +R3e+ R maximal autocorrelation of lag 3 / weighted by atomic Sanderson electronegativities +R4e+ R maximal autocorrelation of lag 4 / weighted by atomic Sanderson electronegativities +R5e+ R maximal autocorrelation of lag 5 / weighted by atomic Sanderson electronegativities +R6e+ R maximal autocorrelation of lag 6 / weighted by atomic Sanderson electronegativities +R7e+ R maximal autocorrelation of lag 7 / weighted by atomic Sanderson electronegativities +R8e+ R maximal autocorrelation of lag 8 / weighted by atomic Sanderson electronegativities +RTe+ R maximal index / weighted by atomic Sanderson electronegativities +R1p R autocorrelation of lag 1 / weighted by atomic polarizabilities +R2p R autocorrelation of lag 2 / weighted by atomic polarizabilities +R3p R autocorrelation of lag 3 / weighted by atomic polarizabilities +R4p R autocorrelation of lag 4 / weighted by atomic polarizabilities +R5p R autocorrelation of lag 5 / weighted by atomic polarizabilities +R6p R autocorrelation of lag 6 / weighted by atomic polarizabilities +R7p R autocorrelation of lag 7 / weighted by atomic polarizabilities +R8p R autocorrelation of lag 8 / weighted by atomic polarizabilities +RTp R total index / weighted by atomic polarizabilities +R1p+ R maximal autocorrelation of lag 1 / weighted by atomic polarizabilities +R2p+ R maximal autocorrelation of lag 2 / weighted by atomic polarizabilities +R3p+ R maximal autocorrelation of lag 3 / weighted by atomic polarizabilities +R4p+ R maximal autocorrelation of lag 4 / weighted by atomic polarizabilities +R5p+ R maximal autocorrelation of lag 5 / weighted by atomic polarizabilities +R6p+ R maximal autocorrelation of lag 6 / weighted by atomic polarizabilities +R7p+ R maximal autocorrelation of lag 7 / weighted by atomic polarizabilities +R8p+ R maximal autocorrelation of lag 8 / weighted by atomic polarizabilities +RTp+ R maximal index / weighted by atomic polarizabilities +nCp number of terminal primary C(sp3) Y = any terminal atom or heteroaromatic group (i.e. H, X, OH, NH2, etc.) +nCs number of total secondary C(sp3) Y = H or any heteroatom +nCt number of total tertiary C(sp3) Y = H or any heteroatom +nCq number of total quaternary C(sp3) +nCrs number of ring secondary C(sp3) Y = H or any heteroatom +nCrt number of ring tertiary C(sp3) Y = H or any heteroatom +nCrq number of ring quaternary C(sp3) +nCar number of aromatic C(sp2) +nCbH number of unsubstituted benzene C(sp2) +nCb– number of substituted benzene C(sp2) Y = carbon or any heteroatom +nCconj number of non-aromatic conjugated C(sp2) +nR=Cp number of terminal primary C(sp2) Y = any terminal atom or heteroaromatic group (i.e. H, X, OH, NH2, etc.) +nR=Cs number of aliphatic secondary C(sp2) Y = H or any heteroatom +nR=Ct number of aliphatic tertiary C(sp2) +n=C= number of allenes groups +nR#CH/X number of terminal C(sp) Y = any terminal atom or heteroaromatic group (i.e. H, X, OH, NH2, etc.) +nR#C– number of non-terminal C(sp) Y = C or any non-terminal heteroatom +nROCN number of cyanates (aliphatic) +nArOCN number of cyanates (aromatic) +nRNCO number of isocyanates (aliphatic) +nArNCO number of isocyanates (aromatic) +nRSCN number of thiocyanates (aliphatic) +nArSCN number of thiocyanates (aromatic) +nRNCS number of isothiocyanates (aliphatic) +nArNCS number of isothiocyanates (aromatic) +nRCOOH number of carboxylic acids (aliphatic) +nArCOOH number of carboxylic acids (aromatic) +nRCOOR number of esters (aliphatic) Y = Ar or Al (not H)                                Al = H or aliphatic group linked through C +nArCOOR number of esters (aromatic) Y = Al or Ar +nRCONH2 number of primary amides (aliphatic) Al = H or aliphatic group linked through C +nArCONH2 number of primary amides (aromatic) +nRCONHR number of secondary amides (aliphatic)  Y = Ar or Al (not H, not C = O) Al = H or aliphatic group linked through C +nArCONHR number of secondary amides (aromatic) Y = Ar or Al (not H, not C = O) +nRCONR2 number of tertiary amides (aliphatic) Y = Ar or Al (not H, not C = O) Al = H or aliphatic group linked through C +nArCONR2 number of tertiary amides (aromatic) Y = Ar or Al (not H, not C = O) +nROCON number of (thio-) carbamates (aliphatic) Y = O or S Al = H or aliphatic group linked through any atom +nArOCON number of (thio-) carbamates (aromatic) Y1 = O or S Y2 = H or aliphatic or aromatic group linked through any atom Ar = aromatic group linked through any atom +nRCOX number of acyl halogenides (aliphatic) +nArCOX number of acyl halogenides (aromatic) +nRCSOH number of thioacids (aliphatic) +nArCSOH number of thioacids (aromatic) +nRCSSH number of dithioacids (aliphatic) +nArCSSH number of dithioacids (aromatic) +nRCOSR number of thioesters (aliphatic) Y = Ar or Al (not H) Al = H or aliphatic group linked through C +nArCOSR number of thioesters (aromatic) +nRCSSR number of dithioesters (aliphatic) Y = Ar or Al (not H) Al = H or aliphatic group linked through C +nArCSSR number of dithioesters (aromatic) Y = Ar or Al (not H) +nRCHO number of aldehydes (aliphatic) +nArCHO number of aldehydes (aromatic) +nRCO number of ketones (aliphatic) +nArCO number of ketones (aromatic) Y = Al or Ar +nCONN number of urea (-thio) derivatives Y = O or S +nC=O(OR)2 number of carbonate (-thio) derivatives Y = O or S +nN=C-N< number of amidine derivatives Y = C or H +nC(=N)N2 number of guanidine derivatives +nRC=N number of imines (aliphatic) Y = H,C or N (two-connected) Al = H or aliphatic group linked through C +nArC=N number of imines (aromatic) Y = H,C or N (two-connected) +nRCNO number of oximes (aliphatic) Y = H, Ar or Al +nArCNO number of oximes (aromatic) Y = H, Ar or Al +nRNH2 number of primary amines (aliphatic) Al = aliphatic group linked through C (not C = O) +nArNH2 number of primary amines (aromatic) +nRNHR number of secondary amines (aliphatic) Al = aliphatic group linked through C (not C = O) +nArNHR number of secondary amines (aromatic) Y = Ar or Al (not C = O) +nRNR2 number of tertiary amines (aliphatic) Al = aliphatic group linked through C (not C = O) +nArNR2 number of tertiary amines (aromatic) Y = Ar or Al (not C = O) +nN-N number of N hydrazines Y = C or H +nN=N number of N azo-derivatives Y = C or H +nRCN number of nitriles (aliphatic) +nArCN number of nitriles (aromatic) +nN+ number of positive charged N +nNq number of quaternary N +nRNHO number of hydroxylamines (aliphatic) Y = H, Al or Ar +nArNHO number of hydroxylamines (aromatic) Y = H, Al or Ar +nRNNOx number of N-nitroso groups (aliphatic) Al = H or aliphatic group linked through C +nArNNOx number of N-nitroso groups (aromatic) Y = H, Al or Ar +nRNO number of nitroso groups (aliphatic) +nArNO number of nitroso groups (aromatic) +nRNO2 number of nitro groups (aliphatic) Al = H or aliphatic group linked through carbon +nArNO2 number of nitro groups (aromatic) Al = aromatic group linked through carbon +nN(CO)2 number of imides (thio-) Y = H or C                Y1 = O or S +nC=N-N< number of hydrazones Y = C or H +nROH number of hydroxyl groups Al = aliphatic group linked through any atom +nArOH number of aromatic hydroxyls Ar = aromatic group linked through any atom +nOHp number of primary alcohols +nOHs number of secondary alcohols +nOHt number of tertiary alcohols +nROR number of ethers (aliphatic) Al = aliphatic group linked through C (not C = O, not C # N) +nArOR number of ethers (aromatic) Y = Ar or Al (not C = O, not C # N) +nROX number of hypohalogenides (aliphatic) +nArOX number of hypohalogenides (aromatic) +nO(C=O)2 number of anhydrides (thio-) Y = O or S +nH2O number of water molecules +nSH number of thiols +nC=S number of thioketones +nRSR number of sulfides +nRSSR number of disulfides +nSO number of sulfoxides +nS(=O)2 number of sulfones +nSOH number of sulfenic (thio-) acids Y = O or S +nSOOH number of sulfinic (thio-/dithio-)acids Y = O or S +nSO2OH number of sulfonic (thio-/dithio-) acids Y = O or S +nSO3OH number of sulfuric (thio-/dithio-) acids Y = O or S +nSO2 number of sulfites (thio-/ dithio-) Y = O or S +nSO3 number of sulfonates (thio- / dithio-) Y = O or S +nSO4 number of sulfates (thio- / dithio-) Y = O or S +nSO2N number of sulfonamides / sulfinamides / sulfenamides (thio- / dithio-) +nPO3 number of phosphites / thiophosphites Y = O or S +nPO4 number of phosphates / thiophosphates Y = O or S +nPR3 number of phosphanes Y = H, C, halogens +nP(=O)O2R number of phosphonates / thiophosphonates Y = O or S Y1 = H, C, halogens +nP(=O)R3/nPR5 number of phosphoranes / thiophosphoranes Y = O or S +nCH2RX number of CH2RX +nCHR2X number of CHR2X +nCR3X number of CR3X +nR=CHX number of R=CHX +nR=CRX number of R=CRX +nR#CX number of R#CX +nCHRX2 number of CHRX2 +nCR2X2 number of CR2X2 +nR=CX2 number of R=CX2 +nCRX3 number of CRX3 +nArX number of X on aromatic ring +nCXr number of X on ring C(sp3) +nCXr= number of X on ring C(sp2) +nCconjX number of X on exo-conjugated C +nAziridines number of Aziridines +nOxiranes number of Oxiranes +nThiranes number of Thiranes +nAzetidines number of Azetidines +nOxetanes number of Oxetanes +nThioethanes number of Thioethanes +nBeta-Lactams number of Beta-Lactams +nPyrrolidines number of Pyrrolidines +nOxolanes number of Oxolanes +nth-Thiophenes number of tetrahydro-Thiophenes +nPyrroles number of Pyrroles +nPyrazoles number of Pyrazoles +nImidazoles number of Imidazoles +nFuranes number of Furanes +nThiophenes number of Thiophenes +nOxazoles number of Oxazoles +nIsoxazoles number of Isoxazoles +nThiazoles number of Thiazoles +nIsothiazoles number of Isothiazoles +nTriazoles number of Triazoles +nPyridines number of Pyridines +nPyridazines number of Pyridazines +nPyrimidines number of Pyrimidines +nPyrazines number of Pyrazines +n135-Triazines number of 135-Triazines +n124-Triazines number of 124-Triazines +nHDon number of donor atoms for H-bonds (N and O) +nHAcc number of acceptor atoms for H-bonds (N, O, F) +nHBonds number of intramolecular H-bonds Y1 = B, N, O, Al, P, S Y2 = N, O, F The geometric distance between H and Y2 must be in the range 1 - 2,7 A. +C-001 CH3R / CH4 +C-002 CH2R2 +C-003 CHR3 +C-004 CR4 +C-005 CH3X +C-006 CH2RX +C-007 CH2X2 +C-008 CHR2X +C-009 CHRX2 +C-010 CHX3 +C-011 CR3X +C-012 CR2X2 +C-013 CRX3 +C-014 CX4 +C-015 =CH2 +C-016 =CHR +C-017 =CR2 +C-018 =CHX +C-019 =CRX +C-020 =CX2 +C-021 #CH +C-022 #CR / R=C=R +C-023 #CX +C-024 R--CH--R +C-025 R--CR--R +C-026 R--CX--R +C-027 R--CH--X +C-028 R--CR--X +C-029 R--CX--X +C-030 X--CH--X +C-031 X--CR--X +C-032 X--CX--X +C-033 R--CH..X +C-034 R--CR..X +C-035 R--CX..X +C-036 Al-CH=X +C-037 Ar-CH=X +C-038 Al-C(=X)-Al +C-039 Ar-C(=X)-R +C-040 R-C(=X)-X / R-C#X / X=C=X +C-041 X-C(=X)-X +C-042 X--CH..X +C-043 X--CR..X +C-044 X--CX..X +U-045 undefined +H-046 Ha attached to C0(sp3) no X attached to next C +H-047 Ha attached to C1(sp3) / C0(sp2) +H-048 Ha attached to C2(sp3) / C1(sp2) / C0(sp) +H-049 Ha attached to C3(sp3) / C2(sp2) / C3(sp2) / C3(sp) +H-050 H attached to heteroatom +H-051 H attached to alpha-Cb +H-052 Ha attached to C0(sp3) with 1X attached to next C +H-053 Ha attached to C0(sp3) with 2X attached to next C +H-054 Ha attached to C0(sp3) with 3X attached to next C +H-055 Ha attached to C0(sp3) with 4X attached to next C +O-056 alcohol +O-057 phenol / enol / carboxyl OH +O-058 =O +O-059 Al-O-Al +O-060 Al-O-Ar / Ar-O-Ar / R..O..R / R-O-C=X +O-061 O-- c +O-062 O- (negatively charged) +O-063 R-O-O-R +Se-064 Any-Se-Any +Se-065 =Se +N-066 Al-NH2 +N-067 Al2-NH +N-068 Al3-N +N-069 Ar-NH2 / X-NH2 +N-070 Ar-NH-Al +N-071 Ar-NAl2 +N-072 RCO-N< / >N-X=X +N-073 Ar2NH / Ar3N / Ar2N-Al / R..N..Rd +N-074 R#N / R=N- +N-075 R--N--Re / R--N--X +N-076 Ar-NO2 / R--N(--R)--Of / RO-NO +N-077 Al-NO2 +N-078 Ar-N=X / X-N=X +N-079 N+ (positively charged) +U-080 undefined +F-081 Fa attached to C1(sp3) +F-082 Fa attached to C2(sp3) +F-083 Fa attached to C3(sp3) +F-084 Fa attached to C1(sp2) +F-085 Fa attached to C2(sp2)-C4(sp2) / C1(sp) / C4(sp3) / X +Cl-086 Cla attached to C1(sp3) +Cl-087 Cla attached to C2(sp3) +Cl-088 Cla attached to C3(sp3) +Cl-089 Cla attached to C1(sp2) +Cl-090 Cla attached to C2(sp2)-C4(sp2) / C1(sp) / C4(sp3) / X +Br-091 Bra attached to C1(sp3) +Br-092 Bra attached to C2(sp3) +Br-093 Bra attached to C3(sp3) +Br-094 Bra attached to C1(sp2) +Br-095 Bra attached to C2(sp2)-C4(sp2) / C1(sp) / C4(sp3) / X +I-096 Ia attached to C1(sp3) +I-097 Ia attached to C2(sp3) +I-098 Ia attached to C3(sp3) +I-099 Ia attached to C1(sp2) +I-100 Ia attached to C2(sp2)-C4(sp2) / C1(sp) / C4(sp3) / X +F-101 fluoride ion +Cl-102 chloride ion +Br-103 bromide ion +I-104 iodide ion +U-105 undefined +S-106 R-SH +S-107 R2S / RS-SR +S-108 R=S +S-109 R-SO-R +S-110 R-SO2-R +Si-111 >Si< +B-112 >B- as in boranes +U-113 undefined +U-114 undefined +P-115 P ylids +P-116 R3-P=X +P-117 X3-P=X (phosphate) +P-118 PX3 (phosphite) +P-119 PR3 (phosphine) +P-120 C-P(X)2=X (phosphonate) +qpmax maximum positive charge +qnmax maximum negative charge +Qpos total positive charge +Qneg total negative charge +Qtot total absolute charge (electronic charge index - ECI) +Qmean mean absolute charge (charge polarization) +Q2 total squared charge +RPCG relative positive charge +RNCG relative negative charge +SPP submolecular polarity parameter +TE1 topological electronic descriptor +TE2 topological electronic descriptor (bond resctricted) +PCWTe partial charge weighted topological electronic descriptor +LDI local dipole index +Ui unsaturation index +Hy hydrophilic factor +AMR molar refractivity +TPSA(NO) topological polar surface area using N, O polar contributions +TPSA(tot) topological polar surface area using N, O, S, P polar contributions +MLogP Moriguchi octanol-water partition coefficient +MLOGP2 Squared Moriguchi octanol-water partition coeff. (logP^2) +ALOGP Ghose-Crippen octanol-water partition coeff. (logP) +ALOGP2 Squared Ghose-Crippen octanol-water partition coeff. (logP^2) +LAI Lipinski alert index +GVWAI-80 Ghose-Viswanadhan-Wendoloski drug-like index at 80% +GVWAI-50 Ghose-Viswanadhan-Wendoloski drug-like index at 50% +Inflammat-80 Ghose-Viswanadhan-Wendoloski antiinflammatory-like index at 80% +Inflammat-50 Ghose-Viswanadhan-Wendoloski antiinflammatory-like index at 50% +Depressant-80 Ghose-Viswanadhan-Wendoloski antidepressant-like index at 80% +Depressant-50 Ghose-Viswanadhan-Wendoloski antidepressant-like index at 50% +Psychotic-80 Ghose-Viswanadhan-Wendoloski antipsychotic-like index at 80% +Psychotic-50 Ghose-Viswanadhan-Wendoloski antipsychotic-like index at 50% +Hypertens-80 Ghose-Viswanadhan-Wendoloski antihypertensive-like index at 80% +Hypertens-50 Ghose-Viswanadhan-Wendoloski antihypertensive-like index at 50% +Hypnotic-80 Ghose-Viswanadhan-Wendoloski hypnotic-like index at 80% +Hypnotic-50 Ghose-Viswanadhan-Wendoloski hypnotic-like index at 50% +Neoplastic-80 Ghose-Viswanadhan-Wendoloski antineoplastic-like index at 80% +Neoplastic-50 Ghose-Viswanadhan-Wendoloski antineoplastic-like index at 50% +Infective-80 Ghose-Viswanadhan-Wendoloski antiinfective-like index at 80% +Infective-50 Ghose-Viswanadhan-Wendoloski antiinfective-like index at 50% +BLTF96 Verhaar model of Fish base-line toxicity for Fish (96h) from MLOGP (mmol/l) +BLTD48 Verhaar model of Daphnia base-line toxicity for Daphnia (48h) from MLOGP (mmol/l) +BLTA96 Verhaar model of Algae base-line toxicity for Algae (96h) from MLOGP (mmol/l) +B01[C-C] presence/absence of C-C at topological distance 1 +B01[C-N] presence/absence of C-N at topological distance 1 +B01[C-O] presence/absence of C-O at topological distance 1 +B01[C-S] presence/absence of C-S at topological distance 1 +B01[C-P] presence/absence of C-P at topological distance 1 +B01[C-F] presence/absence of C-F at topological distance 1 +B01[C-Cl] presence/absence of C-Cl at topological distance 1 +B01[C-Br] presence/absence of C-Br at topological distance 1 +B01[C-I] presence/absence of C-I at topological distance 1 +B01[C-B] presence/absence of C-B at topological distance 1 +B01[C-Si] presence/absence of C-Si at topological distance 1 +B01[C-X] presence/absence of C-X at topological distance 1 +B01[N-N] presence/absence of N-N at topological distance 1 +B01[N-O] presence/absence of N-O at topological distance 1 +......... .......................................................... +B10[Si-X] presence/absence of Si-X at topological distance 10 +B10[X-X] presence/absence of X-X at topological distance 10 +F01[C-C] frequency of C-C at topological distance 1 +F01[C-N] frequency of C-N at topological distance 1 +F01[C-O] frequency of C-O at topological distance 1 +F01[C-S] frequency of C-S at topological distance 1 +F01[C-P] frequency of C-P at topological distance 1 +F01[C-F] frequency of C-F at topological distance 1 +F01[C-Cl] frequency of C-Cl at topological distance 1 +F01[C-Br] frequency of C-Br at topological distance 1 +F01[C-I] frequency of C-I at topological distance 1 +F01[C-B] frequency of C-B at topological distance 1 +F01[C-Si] frequency of C-Si at topological distance 1 +F01[C-X] frequency of C-X at topological distance 1 +F01[N-N] frequency of N-N at topological distance 1 +F01[N-O] frequency of N-O at topological distance 1 +......... .......................................................... +F10[Si-X] frequency of Si-X at topological distance 10 +F10[X-X] frequency of X-X at topological distance 10
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/XRAY/spacegroups.dat Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,4926 @@ +P 1 1 +(X,Y,Z) + +P 1- 2 +(X,Y,Z) +(-X,-Y,-Z) + +P -1 2 +(X,Y,Z) +(-X,-Y,-Z) + +P 2 2 +(X,Y,Z) +(-X,Y,-Z) + +P 1 21 1 2 +(X,Y,Z) +(-X,Y+1/2,-Z) + +P 21 2 +(X,Y,Z) +(-X,Y+1/2,-Z) + +C 1 2 1 4 +(X,Y,Z) +(-X,Y,-Z) +(1/2+X,1/2+Y,Z) +(1/2-X,1/2+Y,-Z) + +C 2 4 +(X,Y,Z) +(-X,Y,-Z) +(1/2+X,1/2+Y,Z) +(1/2-X,1/2+Y,-Z) + +P M 2 +(X,Y,Z) +(X,-Y,Z) + +P C 2 +(X,Y,Z) +(X,-Y,1/2+Z) + +C M 4 +(X,Y,Z) +(X,-Y,Z) +(1/2+X,1/2+Y,Z) +(1/2+X,1/2-Y,Z) + +C C 4 +(X,Y,Z) +(X,-Y,1/2+Z) +(1/2+X,1/2+Y,Z) +(1/2+X,1/2-Y,1/2+Z) + +P 2/M 4 +(X,Y,Z) +(X,-Y,Z) +(-X,Y,-Z) +(-X,-Y,-Z) + +P 21/M 4 +(X,Y,Z) +(-X,1/2+Y,-Z) +(-X,-Y,-Z) +(X,1/2-Y,Z) + +C 2/M 8 +(X,Y,Z) +(X,-Y,Z) +(-X,Y,-Z) +(-X,-Y,-Z) +(1/2+X,1/2+Y,Z) +(1/2+X,1/2-Y,Z) +(1/2-X,1/2+Y,-Z) +(1/2-X,1/2-Y,-Z) + +P 2/C 4 +(X,Y,Z) +(-X,Y,1/2-Z) +(-X,-Y,-Z) +(X,-Y,1/2+Z) + +P 21/C 4 +(X,Y,Z) +(-X,-Y,-Z) +(-X,1/2+Y,1/2-Z) +(X,1/2-Y,1/2+Z) + +C 2/C 8 +(X,Y,Z) +(-X,Y,1/2-Z) +(-X,-Y,-Z) +(X,-Y,1/2+Z) +(1/2+X,1/2+Y,Z) +(1/2-X,1/2+Y,1/2-Z) +(1/2-X,1/2-Y,-Z) +(1/2+X,1/2-Y,1/2+Z) + +P 2 2 2 4 +(X,Y,Z) +(-X,-Y,Z) +(-X,Y,-Z) +(X,-Y,-Z) + +P 2 2 21 4 +(X,Y,Z) +(-X,-Y,1/2+Z) +(-X,Y,1/2-Z) +(X,-Y,-Z) + +P 21 21 2 4 +(X,Y,Z) +(-X,-Y,Z) +(1/2-X,1/2+Y,-Z) +(1/2+X,1/2-Y,-Z) + +P 21 21 21 4 +(X,Y,Z) +(1/2-X,-Y,1/2+Z) +(-X,1/2+Y,1/2-Z) +(1/2+X,1/2-Y,-Z) + +C 2 2 21 8 +(X,Y,Z) +(-X,-Y,1/2+Z) +(-X,Y,1/2-Z) +(X,-Y,-Z) +(1/2+X,1/2+Y,Z) +(1/2-X,1/2-Y,1/2+Z) +(1/2-X,1/2+Y,1/2-Z) +(1/2+X,1/2-Y,-Z) + +C 2 2 2 8 +(X,Y,Z) +(-X,-Y,Z) +(-X,Y,-Z) +(X,-Y,-Z) +(1/2+X,1/2+Y,Z) +(1/2-X,1/2-Y,Z) +(1/2-X,1/2+Y,-Z) +(1/2+X,1/2-Y,-Z) + +F 2 2 2 16 +(X,Y,Z) +(-X,-Y,Z) +(-X,Y,-Z) +(X,-Y,-Z) +(X,1/2+Y,1/2+Z) +(-X,1/2-Y,1/2+Z) +(-X,1/2+Y,1/2-Z) +(X,1/2-Y,1/2-Z) +(1/2+X,Y,1/2+Z) +(1/2-X,-Y,1/2+Z) +(1/2-X,Y,1/2-Z) +(1/2+X,-Y,1/2-Z) +(1/2+X,1/2+Y,Z) +(1/2-X,1/2-Y,Z) +(1/2-X,1/2+Y,-Z) +(1/2+X,1/2-Y,-Z) + +I 2 2 2 8 +(X,Y,Z) +(-X,-Y,Z) +(X,-Y,-Z) +(-X,Y,-Z) +(X+1/2,Y+1/2,Z+1/2) +(-X+1/2,-Y+1/2,Z+1/2) +(X+1/2,-Y+1/2,-Z+1/2) +(-X+1/2,Y+1/2,-Z+1/2) + +I 21 21 21 8 +(X,Y,Z) +(1/2-X,-Y,1/2+Z) +(-X,1/2+Y,1/2-Z) +(1/2+X,1/2-Y,-Z) +(1/2+X,1/2+Y,1/2+Z) +(-X,1/2-Y,Z) +(1/2-X,Y,-Z) +(X,-Y,1/2-Z) + +P M M 2 4 +(X,Y,Z) +(-X,-Y,Z) +(X,-Y,Z) +(-X,Y,Z) + +P M C 21 4 +(X,Y,Z) +(-X,-Y,1/2+Z) +(X,-Y,1/2+Z) +(-X,Y,Z) + +P C C 2 4 +(X,Y,Z) +(-X,-Y,Z) +(X,-Y,1/2+Z) +(-X,Y,1/2+Z) + +P M A 2 4 +(X,Y,Z) +(-X,-Y,Z) +(1/2+X,-Y,Z) +(1/2-X,Y,Z) + +P C A 21 4 +(X,Y,Z) +(-X,-Y,1/2+Z) +(1/2+X,-Y,Z) +(1/2-X,Y,1/2+Z) + +P N C 2 4 +(X,Y,Z) +(-X,-Y,Z) +(X,1/2-Y,1/2+Z) +(-X,1/2+Y,1/2+Z) + +P M N 21 4 +(X,Y,Z) +(1/2-X,-Y,1/2+Z) +(1/2+X,-Y,1/2+Z) +(-X,Y,Z) + +P B A 2 4 +(X,Y,Z) +(-X,-Y,Z) +(1/2+X,1/2-Y,Z) +(1/2-X,1/2+Y,Z) + +P N A 21 4 +(X,Y,Z) +(-X,-Y,1/2+Z) +(1/2+X,1/2-Y,Z) +(1/2-X,1/2+Y,1/2+Z) + +P N N 2 4 +(X,Y,Z) +(-X,-Y,Z) +(1/2+X,1/2-Y,1/2+Z) +(1/2-X,1/2+Y,1/2+Z) + +C M M 2 8 +(X,Y,Z) +(-X,-Y,Z) +(X,-Y,Z) +(-X,Y,Z) +(1/2+X,1/2+Y,Z) +(1/2-X,1/2-Y,Z) +(1/2+X,1/2-Y,Z) +(1/2-X,1/2+Y,Z) + +C M C 21 8 +(X,Y,Z) +(-X,-Y,1/2+Z) +(X,-Y,1/2+Z) +(-X,Y,Z) +(1/2+X,1/2+Y,Z) +(1/2-X,1/2-Y,1/2+Z) +(1/2+X,1/2-Y,1/2+Z) +(1/2-X,1/2+Y,Z) + +C C C 2 8 +(X,Y,Z) +(-X,-Y,Z) +(X,-Y,1/2+Z) +(-X,Y,1/2+Z) +(1/2+X,1/2+Y,Z) +(1/2-X,1/2-Y,Z) +(1/2+X,1/2-Y,1/2+Z) +(1/2-X,1/2+Y,1/2+Z) + +A M M 2 8 +(X,Y,Z) +(-X,-Y,Z) +(X,-Y,Z) +(-X,Y,Z) +(X,1/2+Y,1/2+Z) +(-X,1/2-Y,1/2+Z) +(X,1/2-Y,1/2+Z) +(-X,1/2+Y,1/2+Z) + +A B M 2 8 +(X,Y,Z) +(-X,-Y,Z) +(X,1/2-Y,Z) +(-X,1/2+Y,Z) +(X,1/2+Y,1/2+Z) +(-X,1/2-Y,1/2+Z) +(X,-Y,1/2+Z) +(-X,Y,1/2+Z) + +A M A 2 8 +(X,Y,Z) +(-X,-Y,Z) +(1/2+X,-Y,Z) +(1/2-X,Y,Z) +(X,1/2+Y,1/2+Z) +(-X,1/2-Y,1/2+Z) +(1/2+X,1/2-Y,1/2+Z) +(1/2-X,1/2+Y,1/2+Z) + +A B A 2 8 +(X,Y,Z) +(-X,-Y,Z) +(1/2+X,1/2-Y,Z) +(1/2-X,1/2+Y,Z) +(X,1/2+Y,1/2+Z) +(-X,1/2-Y,1/2+Z) +(1/2+X,-Y,1/2+Z) +(1/2-X,Y,1/2+Z) + +F M M 2 16 +(X,Y,Z) +(-X,-Y,Z) +(X,-Y,Z) +(-X,Y,Z) +(X,1/2+Y,1/2+Z) +(-X,1/2-Y,1/2+Z) +(X,1/2-Y,1/2+Z) +(-X,1/2+Y,1/2+Z) +(1/2+X,Y,1/2+Z) +(1/2-X,-Y,1/2+Z) +(1/2+X,-Y,1/2+Z) +(1/2-X,Y,1/2+Z) +(1/2+X,1/2+Y,Z) +(1/2-X,1/2-Y,Z) +(1/2+X,1/2-Y,Z) +(1/2-X,1/2+Y,Z) + +F D D 2 16 +(X,Y,Z) +(-X,-Y,Z) +(1/4+X,1/4-Y,1/4+Z) +(1/4-X,1/4+Y,1/4+Z) +(X,1/2+Y,1/2+Z) +(-X,1/2-Y,1/2+Z) +(1/4+X,3/4-Y,3/4+Z) +(1/4-X,3/4+Y,3/4+Z) +(1/2+X,Y,1/2+Z) +(1/2-X,-Y,1/2+Z) +(3/4+X,1/4-Y,3/4+Z) +(3/4-X,1/4+Y,3/4+Z) +(1/2+X,1/2+Y,Z) +(1/2-X,1/2-Y,Z) +(3/4+X,3/4-Y,1/4+Z) +(3/4-X,3/4+Y,1/4+Z) + +I M M 2 8 +(X,Y,Z) +(-X,-Y,Z) +(X,-Y,Z) +(-X,Y,Z) +(1/2+X,1/2+Y,1/2+Z) +(1/2-X,1/2-Y,1/2+Z) +(1/2+X,1/2-Y,1/2+Z) +(1/2-X,1/2+Y,1/2+Z) + +I B A 2 8 +(X,Y,Z) +(-X,-Y,Z) +(1/2+X,1/2-Y,Z) +(1/2-X,1/2+Y,Z) +(1/2+X,1/2+Y,1/2+Z) +(1/2-X,1/2-Y,1/2+Z) +(X,-Y,1/2+Z) +(-X,Y,1/2+Z) + +I M A 2 8 +(X,Y,Z) +(-X,-Y,Z) +(1/2+X,-Y,Z) +(1/2-X,Y,Z) +(1/2+X,1/2+Y,1/2+Z) +(1/2-X,1/2-Y,1/2+Z) +(X,1/2-Y,1/2+Z) +(-X,1/2+Y,1/2+Z) + +P M M M 8 +(X,Y,Z) +(-X,-Y,Z) +(-X,Y,-Z) +(X,-Y,-Z) +(-X,-Y,-Z) +(X,Y,-Z) +(X,-Y,Z) +(-X,Y,Z) + +P N N N 8 +(X,Y,Z) +(-X,-Y,Z) +(-X,Y,-Z) +(X,-Y,-Z) +(1/2-X,1/2-Y,1/2-Z) +(1/2+X,1/2+Y,1/2-Z) +(1/2+X,1/2-Y,1/2+Z) +(1/2-X,1/2+Y,1/2+Z) + +P C C M 8 +(X,Y,Z) +(-X,-Y,Z) +(-X,Y,1/2-Z) +(X,-Y,1/2-Z) +(-X,-Y,-Z) +(X,Y,-Z) +(X,-Y,1/2+Z) +(-X,Y,1/2+Z) + +P B A N 8 +(X,Y,Z) +(-X,-Y,Z) +(-X,Y,-Z) +(X,-Y,-Z) +(1/2-X,1/2-Y,-Z) +(1/2+X,1/2+Y,-Z) +(1/2+X,1/2-Y,Z) +(1/2-X,1/2+Y,Z) + +P M M A 8 +(X,Y,Z) +(1/2-X,-Y,Z) +(-X,Y,-Z) +(1/2+X,-Y,-Z) +(-X,-Y,-Z) +(1/2+X,Y,-Z) +(X,-Y,Z) +(1/2-X,Y,Z) + +P N N A 8 +(X,Y,Z) +(1/2-X,-Y,Z) +(1/2-X,1/2+Y,1/2-Z) +(X,1/2-Y,1/2-Z) +(-X,-Y,-Z) +(1/2+X,Y,-Z) +(1/2+X,1/2-Y,1/2+Z) +(-X,1/2+Y,1/2+Z) + +P M N A 8 +(X,Y,Z) +(1/2-X,-Y,1/2+Z) +(1/2-X,Y,1/2-Z) +(X,-Y,-Z) +(-X,-Y,-Z) +(1/2+X,Y,1/2-Z) +(1/2+X,-Y,1/2+Z) +(-X,Y,Z) + +P C C A 8 +(X,Y,Z) +(1/2-X,-Y,Z) +(-X,Y,1/2-Z) +(1/2+X,-Y,1/2-Z) +(-X,-Y,-Z) +(1/2+X,Y,-Z) +(X,-Y,1/2+Z) +(1/2-X,Y,1/2+Z) + +P B A M 8 +(X,Y,Z) +(-X,-Y,Z) +(1/2-X,1/2+Y,-Z) +(1/2+X,1/2-Y,-Z) +(-X,-Y,-Z) +(X,Y,-Z) +(1/2+X,1/2-Y,Z) +(1/2-X,1/2+Y,Z) + +P C C N 8 +(X,Y,Z) +(1/2-X,1/2-Y,Z) +(-X,1/2+Y,1/2-Z) +(1/2+X,-Y,1/2-Z) 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+(1/2+Y,1/2-Z,-X) +(1/2-Y,-Z,1/2+X) +(3/4+Y,1/4+X,1/4-Z) +(3/4-Y,3/4-X,3/4-Z) +(1/4+Y,1/4-X,3/4+Z) +(1/4-Y,3/4+X,1/4+Z) +(3/4+X,1/4+Z,1/4-Y) +(1/4-X,3/4+Z,1/4+Y) +(3/4-X,3/4-Z,3/4-Y) +(1/4+X,1/4-Z,3/4+Y) +(3/4+Z,1/4+Y,1/4-X) +(1/4+Z,1/4-Y,3/4+X) +(1/4-Z,3/4+Y,1/4+X) +(3/4-Z,3/4-Y,3/4-X) +(-X,-Y,-Z) +(1/2+X,Y,1/2-Z) +(X,1/2-Y,1/2+Z) +(1/2-X,1/2+Y,Z) +(-Z,-X,-Y) +(1/2-Z,1/2+X,Y) +(1/2+Z,X,1/2-Y) +(Z,1/2-X,1/2+Y) +(-Y,-Z,-X) +(Y,1/2-Z,1/2+X) +(1/2-Y,1/2+Z,X) +(1/2+Y,Z,1/2-X) +(1/4-Y,3/4-X,3/4+Z) +(1/4+Y,1/4+X,1/4+Z) +(3/4-Y,3/4+X,1/4-Z) +(3/4+Y,1/4-X,3/4-Z) +(1/4-X,3/4-Z,3/4+Y) +(3/4+X,1/4-Z,3/4-Y) +(1/4+X,1/4+Z,1/4+Y) +(3/4-X,3/4+Z,1/4-Y) +(1/4-Z,3/4-Y,3/4+X) +(3/4-Z,3/4+Y,1/4-X) +(3/4+Z,1/4-Y,3/4-X) +(1/4+Z,1/4+Y,1/4+X) +(1/2+X,1/2+Y,1/2+Z) +(-X,1/2-Y,Z) +(1/2-X,Y,-Z) +(X,-Y,1/2-Z) +(1/2+Z,1/2+X,1/2+Y) +(Z,-X,1/2-Y) +(-Z,1/2-X,Y) +(1/2-Z,X,-Y) +(1/2+Y,1/2+Z,1/2+X) +(1/2-Y,Z,-X) +(Y,-Z,1/2-X) +(-Y,1/2-Z,X) +(1/4+Y,3/4+X,3/4-Z) +(1/4-Y,1/4-X,1/4-Z) +(3/4+Y,3/4-X,1/4+Z) +(3/4-Y,1/4+X,3/4+Z) +(1/4+X,3/4+Z,3/4-Y) +(3/4-X,1/4+Z,3/4+Y) +(1/4-X,1/4-Z,1/4-Y) +(3/4+X,3/4-Z,1/4+Y) +(1/4+Z,3/4+Y,3/4-X) +(3/4+Z,3/4-Y,1/4+X) +(3/4-Z,1/4+Y,3/4+X) +(1/4-Z,1/4-Y,1/4-X) +(1/2-X,1/2-Y,1/2-Z) +(X,1/2+Y,-Z) +(1/2+X,-Y,Z) +(-X,Y,1/2+Z) +(1/2-Z,1/2-X,1/2-Y) +(-Z,X,1/2+Y) +(Z,1/2+X,-Y) +(1/2+Z,-X,Y) +(1/2-Y,1/2-Z,1/2-X) +(1/2+Y,-Z,X) +(-Y,Z,1/2+X) +(Y,1/2+Z,-X) +(3/4-Y,1/4-X,1/4+Z) +(3/4+Y,3/4+X,3/4+Z) +(1/4-Y,1/4+X,3/4-Z) +(1/4+Y,3/4-X,1/4-Z) +(3/4-X,1/4-Z,1/4+Y) +(1/4+X,3/4-Z,1/4-Y) +(3/4+X,3/4+Z,3/4+Y) +(1/4-X,1/4+Z,3/4-Y) +(3/4-Z,1/4-Y,1/4+X) +(1/4-Z,1/4+Y,3/4-X) +(1/4+Z,3/4-Y,1/4-X) +(3/4+Z,3/4+Y,3/4+X) + +B 2 4 +(X,Y,Z) +(-X,-Y,Z) +(1/2+X,+Y,1/2+Z) +(1/2-X,-Y,1/2+Z) + +P 1 1 21 2 +(X,Y,Z) +(-X,-Y,1/2+Z) + +P 2 21 21 4 +(X,Y,Z) +(X,-Y,-Z) +(-X,1/2+Y,1/2-Z) +(-X,1/2-Y,1/2+Z) + +P 21 2 21 4 +(X,Y,Z) +(-X,Y,-Z) +(1/2+X,-Y,1/2-Z) +(1/2-X,-Y,1/2+Z) + +I 1 2 1 4 +(X,Y,Z) +(-X,Y,-Z) +(1/2+X,1/2+Y,1/2+Z) +(1/2-X,1/2+Y,1/2-Z)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/atomtyping/AMBERTypes.dat Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,61 @@ +CT 6 4 * * * * +C 6 3 * * * (XA1) +CN 6 3 * * [RG5,RG6,AR1.AR2.AR3] (C3,C3,N3(H)) +CB 6 3 * * [RG5,RG6,AR1.AR2.AR3] * +CR 6 3 * * [RG5,AR1.AR2.AR3] (N3,N3) +CR 6 3 * * [RG5,AR1.AR2.AR3] (N2,N3(H)) +CK 6 3 * * [RG5,AR1.AR2.AR3] (N2,N3) +CC 6 3 0 * [RG5,AR1.AR2.AR3] (C3,N3(C3,H)) +CC 6 3 0 * [RG5,AR1.AR2.AR3] (C3,N2(C3)) +CW 6 3 * * [RG5,AR1.AR2.AR3] (C3,N3(H)) +CV 6 3 * * [RG5,AR1.AR2.AR3] (C3,N2) +C* 6 3 * * [RG5,AR1.AR2.AR3] (C3,C3) +CQ 6 3 * * [RG6,AR1.AR2.AR3] (N2,N2) +CM 6 3 * * [RG6,AR1.AR2.AR3] (C3,C3(N2(C3(N3(C3))))) +CM 6 3 * * [RG6,AR1.AR2.AR3] (C3,C3(N3(C3(N3(C3))))) +CM 6 3 * * [RG6,AR1.AR2.AR3] (C3,N3(C3(N2(C3(C3))))) +CM 6 3 * * [RG6,AR1.AR2.AR3] (N3,C3(C3(N3(C3(N3))))) +CA 6 3 * * [AR1.AR2.AR3] * +CD 6 3 * * * (C3,C3) +CM 6 3 * * * * +CZ 6 2 * * * * +H 1 1 * * * (N) +HS 1 1 * * * (S) +HP 1 1 * * * (C(N4)) +HW 1 1 * * * (O(H1)) +HO 1 1 * * * (O) +H1 1 1 * 1 * (C4) +H2 1 1 * 2 * (C4) +H3 1 1 * 3 * (C4) +HC 1 1 * * * (C4) +H4 1 1 * 1 * (XX[AR1.AR2.AR3]) +H5 1 1 * 2 * (XX[AR1.AR2.AR3]) +HA 1 1 * * * (XX[AR1.AR2.AR3]) +F 9 1 * * * * +Cl 17 1 * * * * +Br 35 1 * * * * +I 53 1 * * * * +N1 7 1 * * * * +NB 7 2 * * [RG5,AR1.AR2.AR3] * +NC 7 2 * * [RG6,AR1.AR2.AR3] * +N2 7 -1 * * * (C3(N3,N3)) +NO 7 -1 * * * (O1,O1) +NA 7 3 1 * [RG5.RG6,AR1.AR2.AR3] * +N2 7 3 * * [NR] (XX[AR1.AR2.AR3]) +N* 7 3 * * [AR1.AR2.AR3] * +N 7 3 * * * (C3(XA1)) +NT 7 3 * * * * +N3 7 4 * * * * +O2 8 1 * * * (C(O1)) +O2 8 1 * * * (P) +O 8 1 * * * (C) +O 8 1 * * * (S) +OH 8 2 1 * * * +OW 8 2 2 * * * +OS 8 2 * * * * +SH 16 2 1 * * * +SH 16 2 2 * * * +S 16 2 * * * * +SO 16 4 * * * * +LP 0 -1 * * * * +DU -1 -1 * * * *
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/atomtyping/GAFFTypes.dat Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,208 @@ +cx 6 4 * * [RG3] * +cy 6 4 * * [RG4] * +c3 6 4 * * * * +c 6 3 * * [2DL] (XA1) +c 6 3 * * [1DB,0DL] (XA1) +c 6 3 * * [3sb] (XA1) +cz 6 3 * * * (N3,N3,N3) +cp 6 3 * * [AR1,1RG6] (XX[AR1],XX[AR1],XX[AR1]) +ca 6 3 * * [AR1] * +cc 6 3 * * [sb,db,AR2] (C3(C3)) +cc 6 3 * * [sb,db,AR2] (C3(C2)) +cc 6 3 * * [sb,db,AR2] (C3(XB2)) +cc 6 3 * * [sb,db,AR2] (XB2(XB2)) +cc 6 3 * * [sb,db,AR2] (XB2(C2)) +cc 6 3 * * [sb,db,AR2] (XB2(C3)) +cc 6 3 * * [sb,db,AR2] (C3[sb']) +cc 6 3 * * [sb,db,AR2] (XB2[sb']) +cc 6 3 * * [sb,db,AR2] (XD3[sb',db]) +cc 6 3 * * [sb,db,AR2] (XD4[sb',db]) +cc 6 3 * * [sb,db,AR3] (C3(C3)) +cc 6 3 * * [sb,db,AR3] (C3(C2)) +cc 6 3 * * [sb,db,AR3] (C3(XB2)) +cc 6 3 * * [sb,db,AR3] (XB2(XB2)) +cc 6 3 * * [sb,db,AR3] (XB2(C2)) +cc 6 3 * * [sb,db,AR3] (XB2(C3)) +cc 6 3 * * [sb,db,AR3] (C3[sb']) +cc 6 3 * * [sb,db,AR3] (XB2[sb']) +cc 6 3 * * [sb,db,AR3] (XD3[sb',db]) +cc 6 3 * * [sb,db,AR3] (XD4[sb',db]) +ce 6 3 * * [sb,db] (C3[SB']) +ce 6 3 * * [sb,db] (C2[SB']) +ce 6 3 * * [sb,db] (XB2[SB']) +ce 6 3 * * [sb,db] (XD3[SB',db]) +ce 6 3 * * [sb,db] (XD4[SB',db]) +cu 6 3 * * [RG3] * +cv 6 3 * * [RG4] * +c2 6 3 * * * * +cg 6 2 * * [sb,tb] (C2[SB']) +cg 6 2 * * [sb,tb] (C3[SB']) +cg 6 2 * * [sb,tb] (N1[SB']) +cg 6 2 * * [sb,tb] (XB2[SB']) +c1 6 2 * * * * +c1 6 1 * * * * +hn 1 1 * * * (N) +ho 1 1 * * * (O) +hs 1 1 * * * (S) +hp 1 1 * * * (P) +hx 1 1 * * * (C(N4)) +hw 1 1 * * * (O(H1)) +h3 1 1 * 3 * (C4) +h2 1 1 * 2 * (C4) +h1 1 1 * 1 * (C4) +hc 1 1 * * * (C4) +h5 1 1 * 2 * (C3) +h4 1 1 * 1 * (C3) +ha 1 1 * * * * +f 9 -1 * * * * +cl 17 -1 * * * * +br 35 -1 * * * * +i 53 -1 * * * * +pc 15 2 * * [sb,db,AR2] (C3(C3)) +pc 15 2 * * [sb,db,AR2] (C3(C2)) +pc 15 2 * * [sb,db,AR2] (C3(XB2)) +pc 15 2 * * [sb,db,AR2] (XB2(C3)) +pc 15 2 * * [sb,db,AR2] (XB2(C2)) +pc 15 2 * * [sb,db,AR2] (XB2(XB2)) +pc 15 2 * * [sb,db,AR2] (C3[sb']) +pc 15 2 * * [sb,db,AR2] (C2[sb']) +pc 15 2 * * [sb,db,AR2] (XB2[sb']) +pc 15 2 * * [sb,db,AR2] (XD3[sb',db]) +pc 15 2 * * [sb,db,AR2] (XD4[sb',db]) +pc 15 2 * * [sb,db,AR3] (C3(C3)) +pc 15 2 * * [sb,db,AR3] (C3(C2)) +pc 15 2 * * [sb,db,AR3] (C3(XB2)) +pc 15 2 * * [sb,db,AR3] (XB2(C3)) +pc 15 2 * * [sb,db,AR3] (XB2(C2)) +pc 15 2 * * [sb,db,AR3] (XB2(XB2)) +pc 15 2 * * [sb,db,AR3] (C3[sb']) +pc 15 2 * * [sb,db,AR3] (C2[sb']) +pc 15 2 * * [sb,db,AR3] (XB2[sb']) +pc 15 2 * * [sb,db,AR3] (XD3[sb',db]) +pc 15 2 * * [sb,db,AR3] (XD4[sb',db]) +pb 15 2 * * [AR1] * +pe 15 2 * * [sb,db] (C3[sb']) +pe 15 2 * * [sb,db] (C2[SB']) +pe 15 2 * * [sb,db] (XA1[SB']) +pe 15 2 * * [sb,db] (XB2[SB']) +pe 15 2 * * [sb,db] (XD3[SB',DB]) +pe 15 2 * * [sb,db] (XD4[SB',DB]) +p2 15 2 * * * * +p2 15 1 * * * * +px 15 3 * * [db] (XB2[sb']) +px 15 3 * * [db] (C3[sb']) +px 15 3 * * [db] (XD3[sb',db]) +px 15 3 * * [db] (XD4[sb',db]) +p4 15 3 * * [db] (XA1) +p3 15 3 * * * * +py 15 4 * * [db] (XB2[sb']) +py 15 4 * * [db] (C3[sb']) +py 15 4 * * [db] (XD3[sb',db]) +py 15 4 * * [db] (XD4[sb',db]) +p5 15 4 * * * * +p5 15 5 * * * * +p5 15 6 * * * * +n 7 3 * * * (C3(XA1)) +n4 7 4 * * * * +no 7 3 * * * (O1,O1) +na 7 3 * * [AR1.AR2.AR3] * +nh 7 3 * * * (XX[AR1.AR2.AR3]) +nh 7 3 * * * (C3[DB]) +nh 7 3 * * * (N2[DB]) +nh 7 3 * * * (P2[DB]) +n3 7 3 * * * * +nb 7 2 * * [AR1] * +nc 7 2 * * [sb,db,AR2] (C3(C3)) +nc 7 2 * * [sb,db,AR2] (C3(C2)) +nc 7 2 * * [sb,db,AR2] (C3(XB2)) +nc 7 2 * * [sb,db,AR2] (XB2(C3)) +nc 7 2 * * [sb,db,AR2] (XB2(C2)) +nc 7 2 * * [sb,db,AR2] (XB2(XB2)) +nc 7 2 * * [sb,db,AR2] (C3[sb']) +nc 7 2 * * [sb,db,AR2] (XB2[sb']) +nc 7 2 * * [sb,db,AR2] (XD3[sb',db]) +nc 7 2 * * [sb,db,AR2] (XD4[sb',db]) +nc 7 2 * * [sb,db,AR3] (C3(C3)) +nc 7 2 * * [sb,db,AR3] (C3(C2)) +nc 7 2 * * [sb,db,AR3] (C3(XB2)) +nc 7 2 * * [sb,db,AR3] (XB2(C3)) +nc 7 2 * * [sb,db,AR3] (XB2(C2)) +nc 7 2 * * [sb,db,AR3] (XB2(XB2)) +nc 7 2 * * [sb,db,AR3] (C3[sb']) +nc 7 2 * * [sb,db,AR3] (XB2[sb']) +nc 7 2 * * [sb,db,AR3] (XD3[sb',db]) +nc 7 2 * * [sb,db,AR3] (XD4[sb',db]) +ne 7 2 * * [sb,db] (C2[SB']) +ne 7 2 * * [sb,db] (C3[SB']) +ne 7 2 * * [sb,db] (XA1[SB']) +ne 7 2 * * [sb,db] (XB2[SB']) +ne 7 2 * * [sb,db] (XD3[SB',db]) +ne 7 2 * * [sb,db] (XD4[SB',db]) +n1 7 2 * * [2db] * +n1 7 2 * * [tb,sb] * +n2 7 2 * * * * +n1 7 1 * * * * +o 8 1 * * * * +oh 8 2 1 * * * +oh 8 2 2 * * * +oh 8 3 1 * * * +oh 8 3 2 * * * +oh 8 3 3 * * * +os 8 2 * * * * +os 8 3 * * * * +os 8 -1 * * * * +s 16 1 * * * * +s2 16 2 * * [DB] * +s2 16 2 * * [TB] * +sh 16 2 1 * * * +sh 16 2 2 * * * +ss 16 2 * * * * +sx 16 3 * * [db] (XB2[sb']) +sx 16 3 * * [db] (C3[sb']) +sx 16 3 * * [db] (XD3[sb',db]) +sx 16 3 * * [db] (XD4[sb',db]) +s4 16 3 * * * * +sy 16 4 * * [db] (XB2[sb']) +sy 16 4 * * [db] (C3[sb']) +sy 16 4 * * [db] (XD3[sb',db]) +sy 16 4 * * [db] (XD4[sb',db]) +s6 16 4 * * * * +s6 16 5 * * * * +s6 16 6 * * * * +Li 3 -1 * * * * +Be 4 -1 * * * * +B 5 -1 * * * * +Na 11 -1 * * * * +Mg 12 -1 * * * * +Al 13 -1 * * * * +Si 14 -1 * * * * +K 19 -1 * * * * +Ca 20 -1 * * * * +Sr 38 -1 * * * * +Ba 56 -1 * * * * +Sc 21 -1 * * * * +Ti 22 -1 * * * * +V 23 -1 * * * * +Cr 24 -1 * * * * +Mn 25 -1 * * * * +Fe 26 -1 * * * * +Co 27 -1 * * * * +Ni 28 -1 * * * * +Cu 29 -1 * * * * +Zn 30 -1 * * * * +Ga 31 -1 * * * * +Ge 32 -1 * * * * +As 33 -1 * * * * +Se 34 -1 * * * * +Ru 44 -1 * * * * +Rh 45 -1 * * * * +Pd 46 -1 * * * * +Ag 47 -1 * * * * +Cd 48 -1 * * * * +Pt 78 -1 * * * * +Au 79 -1 * * * * +Hg 80 -1 * * * * +Tl 81 -1 * * * * +Pb 82 -1 * * * * +lp 0 1 * * * * +DU -1 -1 * * * *
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/atomtyping/SYBYLTypes.dat Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,66 @@ +C.3 6 4 * * * * +C.cat 6 3 * * * (N3,N3,N3) +C.ar 6 3 * * [AR1] * +C.2 6 3 * * * * +C.1 6 2 * * * * +C.1 6 1 * * * * +H 1 -1 * * * * +F 9 -1 * * * * +Cl 17 -1 * * * * +Br 35 -1 * * * * +I 53 -1 * * * * +P.3 15 -1 * * * * +N.4 7 4 * * * * +N.am 7 3 * * * (C3(XA1)) +N.pl3 7 3 * * * (O1,O1) +N.pl3 7 3 * * [AR1.AR2.AR3] * +N.3 7 3 * * * * +N.ar 7 2 * * [AR1] * +N.2 7 2 * * * * +N.1 7 1 * * * * +O.co2 8 1 * * * (C3(O1)) +O.co2 8 1 * * * (P(O1)) +O.2 8 1 * * * * +O.3 8 2 * * * * +S.2 16 1 * * * * +S.3 16 2 * * * * +S.o 16 3 * * * (O1[DB']) +S.o2 16 4 * * * (O1[DB'],O1[DB']) +s.3 16 -1 * * * * +Li 3 -1 * * * * +Be 4 -1 * * * * +B 5 -1 * * * * +Na 11 -1 * * * * +Mg 12 -1 * * * * +Al 13 -1 * * * * +Si 14 -1 * * * * +K 19 -1 * * * * +Ca 20 -1 * * * * +Sr 38 -1 * * * * +Ba 56 -1 * * * * +Sc 21 -1 * * * * +Ti 22 -1 * * * * +V 23 -1 * * * * +Cr 24 -1 * * * * +Mn 25 -1 * * * * +Fe 26 -1 * * * * +Co 27 -1 * * * * +Ni 28 -1 * * * * +Cu 29 -1 * * * * +Zn 30 -1 * * * * +Ga 31 -1 * * * * +Ge 32 -1 * * * * +As 33 -1 * * * * +Se 34 -1 * * * * +Ru 44 -1 * * * * +Rh 45 -1 * * * * +Pd 46 -1 * * * * +Ag 47 -1 * * * * +Cd 48 -1 * * * * +Pt 78 -1 * * * * +Au 79 -1 * * * * +Hg 80 -1 * * * * +Tl 81 -1 * * * * +Pb 82 -1 * * * * +lp 0 1 * * * * +ANY -1 -1 * * * * *
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/bond_lengths/BondOrder.xml Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,366 @@ +<?xml version="1.0" encoding="ISO-8859-1"?> +<table> + <!-- This file supplies improved penalty scores for different + atom types in bond type perception based on the work of + + Wang, J., Wang, W., Kollman P. A.; Case, D. A. "Automatic atom type and + bond type perception in molecular mechanical calculations". Journal of + Molecular Graphics and Modelling , 25, 2006, 247260 + + A penalty score of 0 means that the corresponding valence is optimal. + Note that the first matching entry is taken as the final atom type. + + Note that in the SMARTS strings we use atomic numbers rather than symbols (e.g. #8 instead of O). + The reason is that wrongly assigned aromatic bonds in the input would lead to failure to identify the + right rule! + --> + <!-- for charged H --> + <entry id="0"> + <elementstring>H</elementstring> + <smartstring>SMARTS([#1+])</smartstring> + <penalty valence="0">0</penalty> + </entry> + <entry id="1"> + <elementstring>H</elementstring> + <smartstring>SMARTS([#1])</smartstring> + <penalty valence="1">0</penalty> + </entry> + <entry id="2"> + <elementstring>F</elementstring> + <smartstring>SMARTS(F)</smartstring> + <penalty valence="0">64</penalty> + <penalty valence="1">0</penalty> + <penalty valence="2">64</penalty> + </entry> + <entry id="4"> + <elementstring>Br</elementstring> + <smartstring>SMARTS(Br)</smartstring> + <penalty valence="0">64</penalty> + <penalty valence="1">0</penalty> + <penalty valence="2">64</penalty> + </entry> + <entry id="5"> + <elementstring>I</elementstring> + <smartstring>SMARTS(I)</smartstring> + <penalty valence="0">64</penalty> + <penalty valence="1">0</penalty> + <penalty valence="2">64</penalty> + </entry> + <entry id="6"> <!-- SMARTS([CD1]~[ND2]) AND element(C)</smartstring> --> + <elementstring>C</elementstring> + <smartstring>SMARTS([$([#6D1](~[#7D2]))])</smartstring> + <penalty valence="3">0</penalty> + <penalty valence="4">1</penalty> + <penalty valence="5">32</penalty> + </entry> + <entry id="7"> + <elementstring>C</elementstring> + <smartstring>SMARTS([#6D1])</smartstring> + <penalty valence="3">1</penalty> + <penalty valence="4">0</penalty> + <penalty valence="5">32</penalty> + </entry> + <entry id="9"> + <elementstring>C</elementstring> + <smartstring>SMARTS([#6])</smartstring> + <penalty valence="2">64</penalty> + <penalty valence="3">32</penalty> + <penalty valence="4">0</penalty> + <penalty valence="5">32</penalty> + <penalty valence="6">64</penalty> + </entry> + <entry id="10"> + <elementstring>Si</elementstring> + <smartstring>SMARTS(Si)</smartstring> + <penalty valence="4">0</penalty> + </entry> + <entry id="11"> + <elementstring>N</elementstring> + <smartstring>SMARTS([$([#7D1](~[#7D2]))])</smartstring> <!--SMARTS([ND1]~[ND2]) AND SMARTS([ND1])</smartstring> --> + <penalty valence="2">0</penalty> + <penalty valence="3">0</penalty> + </entry> + <entry id="12"> + <elementstring>N</elementstring> + <smartstring>SMARTS([#7D1])</smartstring> + <penalty valence="2">3</penalty> + <penalty valence="3">0</penalty> + <penalty valence="4">32</penalty> + </entry> + <entry id="13"> + <elementstring>N</elementstring> + <smartstring>SMARTS([$([#7D2](~[#7D1]))])</smartstring> <!--SMARTS([ND1]~[ND2]) AND SMARTS([ND2])</smartstring> --> + <penalty valence="3">1</penalty> + <penalty valence="4">0</penalty> + </entry> + <entry id="14"> + <elementstring>N</elementstring> + <smartstring>SMARTS([#7D2])</smartstring> + <penalty valence="2">4</penalty> + <penalty valence="3">0</penalty> + <penalty valence="4">2</penalty> + </entry> + <entry id="151"><!-- for charged N in O == N+ __ O- --> + <elementstring>N</elementstring> + <smartstring>SMARTS([$([#7D3](~[#8D1-,#16D1-])~[#8D1,#16D1])])</smartstring> + <penalty valence="3">32</penalty> + <penalty valence="4">0</penalty> + <penalty valence="5">32</penalty> + <penalty valence="6">64</penalty> + </entry> + <entry id="15"> + <elementstring>N</elementstring> + <smartstring>SMARTS([$([#7D3](~[#8D1,#16D1])~[#8D1,#16D1])])</smartstring> + <penalty valence="3">64</penalty> + <penalty valence="4">32</penalty> + <penalty valence="5">0</penalty> + <penalty valence="6">32</penalty> + </entry> + <entry id="16"> + <elementstring>N</elementstring> + <!-- <smartstring>SMARTS([$(*OD1)&$(*aR)&n]) OR SMARTS([$(*OD1);$(*R);N])</smartstring> --> + <smartstring>SMARTS([$([#7D3](~[#8D1,#16D1])(~[!#8&!#16,!D1])(~[!#8&!#16,!D1]))])</smartstring> + <penalty valence="3">1</penalty> + <penalty valence="4">0</penalty> + </entry> + <entry id="17"> + <elementstring>N</elementstring> + <smartstring>SMARTS([#7D3])</smartstring> + <penalty valence="2">32</penalty> + <penalty valence="3">0</penalty> + <penalty valence="4">1</penalty> + <penalty valence="5">2</penalty> + </entry> + <entry id="181"><!-- for charged N in N+ H_4 --> + <elementstring>N</elementstring> + <smartstring>SMARTS([#7D4+])</smartstring> + <penalty valence="3">32</penalty> + <penalty valence="4">0</penalty> + </entry> + <entry id="18"> + <elementstring>N</elementstring> + <smartstring>SMARTS([#7D4])</smartstring> + <penalty valence="2">64</penalty> + <penalty valence="3">0</penalty> + <penalty valence="4">64</penalty> + </entry> + <entry id="182"> + <elementstring>N</elementstring> + <smartstring>SMARTS([#7D5])</smartstring> + <penalty valence="5">0</penalty> + </entry> + <entry id="191"><!-- for charged O- --> + <elementstring>O</elementstring> + <smartstring>SMARTS([#8D1-])</smartstring> + <penalty valence="1">0</penalty> + <penalty valence="2">32</penalty> + </entry> + <entry id="192"> + <elementstring>O</elementstring> + <smartstring>SMARTS([$([#8D1](~[#6D3]~[#8D1,#16D1]))])</smartstring> + <penalty valence="1">0</penalty> + <penalty valence="2">0</penalty> + </entry> + <entry id="19"> + <elementstring>O</elementstring> + <smartstring>SMARTS([#7D3](~[#8D1,#16D1])(~[!#8&!#16,!D1])(~[!#8&!#16,!D1])) AND element(O)</smartstring> + <penalty valence="1">0</penalty> + <penalty valence="2">1</penalty> + </entry> + <entry id="20"> + <elementstring>O</elementstring> + <smartstring> SMARTS([#8D1])</smartstring> + <penalty valence="1">1</penalty> + <penalty valence="2">0</penalty> + <penalty valence="3">64</penalty> + </entry> + <entry id="21"> + <elementstring>O</elementstring> + <smartstring>SMARTS([#8D2])</smartstring> + <penalty valence="1">32</penalty> + <penalty valence="2">0</penalty> + <penalty valence="3">64</penalty> + </entry> + <entry id="211"> + <elementstring>O</elementstring> + <smartstring>SMARTS([#8D3])</smartstring> + <penalty valence="3">0</penalty> + </entry> + <entry id="22"> + <elementstring>P</elementstring> + <smartstring>SMARTS(#15D1)</smartstring> + <penalty valence="2">2</penalty> + <penalty valence="3">0</penalty> + <penalty valence="4">32</penalty> + </entry> + <entry id="23"> + <elementstring>P</elementstring> + <smartstring>SMARTS(#15D2)</smartstring> + <penalty valence="2">4</penalty> + <penalty valence="3">0</penalty> + <penalty valence="4">2</penalty> + </entry> + <entry id="24"> + <elementstring>P</elementstring> + <smartstring>SMARTS(#15D3)</smartstring> + <penalty valence="2">32</penalty> + <penalty valence="3">0</penalty> + <penalty valence="4">1</penalty> + <penalty valence="5">2</penalty> + </entry> + <entry id="251"> + <elementstring>P</elementstring> + <!-- Note: this is _SLOW_ --> + <smartstring>SMARTS([$([#15D4](~[#8D1,#16D1])(~[!#8&!#16,!D1])(~[!#8&!#16,!D1,#8D1-,#16D1-])(~[#8D1-,#16D1-]))])</smartstring> + <penalty valence="5">0</penalty> + <penalty valence="6">32</penalty> + </entry> + <entry id="25"> + <elementstring>P</elementstring> + <!-- Note: this is _SLOW_ --> + <smartstring>SMARTS([$([#15D4](~[#8D1,#16D1])(~[!#8&!#16,!D1])(~[!#8&!#16,!D1])(~[#8D1,#16D1]))])</smartstring> + <penalty valence="5">32</penalty> + <penalty valence="6">0</penalty> + <penalty valence="7">32</penalty> + </entry> + <entry id="26"> + <elementstring>P</elementstring> + <smartstring>SMARTS([$([#15D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1])(~[!#8&!#16,!D1]))])</smartstring> + <penalty valence="6">32</penalty> + <penalty valence="7">0</penalty> + </entry> + <entry id="27"> + <elementstring>P</elementstring> + <!-- This rule should be the last PD4 rule because it should only match when the other rules fail! --> + <smartstring>SMARTS(#15D4)</smartstring> + <penalty valence="3">64</penalty> + <penalty valence="4">1</penalty> + <penalty valence="5">0</penalty> + <penalty valence="6">32</penalty> + </entry> + <entry id="28"> + <elementstring>S</elementstring> + <smartstring>SMARTS([#7D3](~[#16D1])(~[!#8&!#16,!D1])(~[!#8&!#16,!D1])) AND element(S)</smartstring> + <penalty valence="1">0</penalty> + <penalty valence="2">1</penalty> + </entry> + <entry id="291"> + <elementstring>S</elementstring> + <smartstring>SMARTS([$([#16D1](~[#6D3]~[#8D1,#16D1]))])</smartstring> + <penalty valence="1">0</penalty> + <penalty valence="2">0</penalty> + </entry> + <entry id="29"> + <elementstring>S</elementstring> + <smartstring>SMARTS([#16D1])</smartstring> + <penalty valence="1">2</penalty> + <penalty valence="2">0</penalty> + <penalty valence="3">64</penalty> + </entry> + <entry id="30"> + <elementstring>S</elementstring> + <smartstring>SMARTS([#16D2])</smartstring> + <penalty valence="1">2</penalty> + <penalty valence="2">0</penalty> + <penalty valence="3">64</penalty> + </entry> + <entry id="31"> + <elementstring>S</elementstring> + <smartstring>SMARTS([#16D3])</smartstring> + <penalty valence="3">1</penalty> + <penalty valence="4">0</penalty> + <penalty valence="5">2</penalty> + <penalty valence="6">2</penalty> + </entry> + <entry id="32"> + <elementstring>S</elementstring> + <smartstring> SMARTS([$([#16D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[!#8&!#16,!D1])(~[!#8&!#16,!D1]))])</smartstring> + <penalty valence="6">0</penalty> + <penalty valence="7">32</penalty> + </entry> + <entry id="331"><!--for a charged O in SO_4 --> + <elementstring>S</elementstring> + <smartstring>SMARTS([$([#16D4](~[#8D1-,#16D1-])(~[#8D1,#16D1])(~[#8D1,#16D1])(~[!#8&!#16,!D1]))])</smartstring> + <penalty valence="6">0</penalty> + </entry> + <entry id="33"> + <elementstring>S</elementstring> + <smartstring>SMARTS([$([#16D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1])(~[!#8&!#16,!D1]))])</smartstring> + <penalty valence="6">32</penalty> + <penalty valence="7">0</penalty> + </entry> + <entry id="34"> + <elementstring>S</elementstring> + <smartstring>SMARTS([$([#16D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1]))])</smartstring> + <penalty valence="6">32</penalty> + <penalty valence="7">0</penalty> + </entry> + <entry id="35"> + <elementstring>S</elementstring> + <smartstring>SMARTS([#16D4])</smartstring> + <penalty valence="4">4</penalty> + <penalty valence="5">2</penalty> + <penalty valence="6">0</penalty> + </entry> + <entry id="36"> + <elementstring>S</elementstring> + <smartstring>SMARTS([#16D5])</smartstring> + <penalty valence="5">2</penalty> + <penalty valence="6">0</penalty> + </entry> +<!-- The following rules are added to cope with ions --> + <entry id="40"> + <elementstring>Li</elementstring> + <smartstring>SMARTS([#3])</smartstring> + <penalty valence="0">0</penalty> + </entry> + <entry id="41"> + <elementstring>Na</elementstring> + <smartstring>SMARTS([#11])</smartstring> + <penalty valence="0">0</penalty> + </entry> + <entry id="42"> + <elementstring>Mg</elementstring> + <smartstring>SMARTS([#12])</smartstring> + <penalty valence="0">0</penalty> + </entry> + <entry id="43"> + <elementstring>K</elementstring> + <smartstring>SMARTS([#19])</smartstring> + <penalty valence="0">0</penalty> + </entry> + <entry id="44"> + <elementstring>Ca</elementstring> + <smartstring>SMARTS([#20])</smartstring> + <penalty valence="0">0</penalty> + </entry> + <entry id="45"> + <elementstring>Cu</elementstring> + <smartstring>SMARTS([#29])</smartstring> + <penalty valence="0">0</penalty> + </entry> + <entry id="46"> + <elementstring>Zn</elementstring> + <smartstring>SMARTS([#30])</smartstring> + <penalty valence="0">0</penalty> + </entry> + <entry id="47"> + <elementstring>Fe</elementstring> + <smartstring>SMARTS([#26])</smartstring> + <penalty valence="0">0</penalty> + </entry> + <entry id="48"> + <elementstring>Cl</elementstring> + <smartstring>SMARTS([#17-])</smartstring> + <penalty valence="0">0</penalty> + </entry> + <entry id="49"> + <elementstring>Cl</elementstring> + <smartstring>SMARTS([#17])</smartstring> + <penalty valence="0">64</penalty> + <penalty valence="1">0</penalty> + <penalty valence="2">64</penalty> + <penalty valence="3">128</penalty> + <penalty valence="4">128</penalty> + </entry> +</table>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/bond_lengths/BondOrderGAFF.xml Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,306 @@ +<?xml version="1.0" encoding="ISO-8859-1"?> +<table> + <!-- This file supplies penalty scores for different + atom types in bond type perception accoring to + + Wang, J., Wang, W., Kollman P. A.; Case, D. A. "Automatic atom type and + bond type perception in molecular mechanical calculations". Journal of + Molecular Graphics and Modelling , 25, 2006, 247260 + + A penalty score of 0 means that the corresponding valence is optimal. + Note that the first matching entry is taken as the final atom type. + + Note that in the SMARTS strings we use atomic numbers rather than symbols (e.g. #8 instead of O). + The reason is that wrongly assigned aromatic bonds in the input would lead to failure to identify the + right rule! + + Rev 14.12.2007 Conversion was done by Anna Dehof + --> + <entry id="1"> + <elementstring>H</elementstring> + <smartstring>SMARTS([#1])</smartstring> + <penalty valence="0">64</penalty> + <penalty valence="1">0</penalty> + <penalty valence="2">64</penalty> + </entry> + <entry id="2"> + <elementstring>F</elementstring> + <smartstring>SMARTS(F)</smartstring> + <penalty valence="0">64</penalty> + <penalty valence="1">0</penalty> + <penalty valence="2">64</penalty> + </entry> + <entry id="3"> + <elementstring>Cl</elementstring> + <smartstring>SMARTS(Cl)</smartstring> + <penalty valence="0">64</penalty> + <penalty valence="1">0</penalty> + <penalty valence="2">64</penalty> + </entry> + <entry id="4"> + <elementstring>Br</elementstring> + <smartstring>SMARTS(Br)</smartstring> + <penalty valence="0">64</penalty> + <penalty valence="1">0</penalty> + <penalty valence="2">64</penalty> + </entry> + <entry id="5"> + <elementstring>I</elementstring> + <smartstring>SMARTS(I)</smartstring> + <penalty valence="0">64</penalty> + <penalty valence="1">0</penalty> + <penalty valence="2">64</penalty> + </entry> + <entry id="6"> + <elementstring>C</elementstring> + <smartstring>SMARTS([$([#6D1](~[#7D2]))])</smartstring> + <!--SMARTS([CD1]~[ND2]) AND element(C)</smartstring> --> + <penalty valence="3">0</penalty> + <penalty valence="4">1</penalty> + <penalty valence="5">32</penalty> + </entry> + <entry id="7"> + <elementstring>C</elementstring> + <smartstring>SMARTS([#6D1])</smartstring> + <penalty valence="3">1</penalty> + <penalty valence="4">0</penalty> + <penalty valence="5">32</penalty> + </entry> + <entry id="8"> + <elementstring>C</elementstring> + <smartstring>SMARTS([$([#6D3](~[#8D1,#16D1])(~[#8D1,#16D1]))])</smartstring> + <penalty valence="4">32</penalty> + <penalty valence="5">0</penalty> + <penalty valence="6">32</penalty> + </entry> + <entry id="9"> + <elementstring>C</elementstring> + <smartstring>SMARTS([#6])</smartstring> + <penalty valence="2">64</penalty> + <penalty valence="3">32</penalty> + <penalty valence="4">0</penalty> + <penalty valence="5">32</penalty> + <penalty valence="6">64</penalty> + </entry> + <entry id="10"> + <elementstring>Si</elementstring> + <smartstring>SMARTS([#14])</smartstring> + <penalty valence="4">0</penalty> + </entry> + <entry id="11"> + <elementstring>N</elementstring> + <smartstring>SMARTS([$([#7D1](~[#7D2]))])</smartstring> + <penalty valence="2">0</penalty> + <penalty valence="3">0</penalty> + </entry> + <entry id="12"> + <elementstring>N</elementstring> + <smartstring>SMARTS([#7D1])</smartstring> + <penalty valence="2">3</penalty> + <penalty valence="3">0</penalty> + <penalty valence="4">32</penalty> + </entry> + <entry id="13"> + <elementstring>N</elementstring> + <smartstring>SMARTS([$([#7D2](~[#7D1]))])</smartstring> + <penalty valence="3">1</penalty> + <penalty valence="4">0</penalty> + </entry> + <entry id="14"> + <elementstring>N</elementstring> + <smartstring>SMARTS([#7D2])</smartstring> + <penalty valence="2">4</penalty> + <penalty valence="3">0</penalty> + <penalty valence="4">2</penalty> + </entry> + <entry id="15"> + <elementstring>N</elementstring> + <smartstring>SMARTS([$([#7D3](~[#8D1,#16D1])~[#8D1,#16D1])])</smartstring> + <penalty valence="3">64</penalty> + <penalty valence="4">32</penalty> + <penalty valence="5">0</penalty> + <penalty valence="6">32</penalty> + </entry> + <entry id="16"> + <elementstring>N</elementstring> + <!-- <smartstring>SMARTS([$(*OD1)&$(*aR)&n]) OR SMARTS([$(*OD1);$(*R);N])</smartstring> --> + <smartstring>SMARTS([$([#7D3](~[#8D1,#16D1])(~[!#8&!#16,!D1])(~[!#8&!#16,!D1]))])</smartstring> + <penalty valence="3">1</penalty> + <penalty valence="4">0</penalty> + </entry> + <entry id="17"> + <elementstring>N</elementstring> + <smartstring>SMARTS([#7D3])</smartstring> + <penalty valence="2">32</penalty> + <penalty valence="3">0</penalty> + <penalty valence="4">1</penalty> + <penalty valence="5">2</penalty> + </entry> + <entry id="18"> + <elementstring>N</elementstring> + <smartstring>SMARTS([#7D4])</smartstring> + <penalty valence="2">64</penalty> + <penalty valence="3">0</penalty> + <penalty valence="4">64</penalty> + </entry> + <entry id="19"> + <elementstring>O</elementstring> + <smartstring>SMARTS([#7D3](~[#8D1,#16D1])(~[!#8&!#16,!D1])(~[!#8&!#16,!D1])) AND element(O)</smartstring> + <penalty valence="1">0</penalty> + <penalty valence="2">1</penalty> + </entry> + <entry id="20"> + <elementstring>O</elementstring> + <smartstring>SMARTS([#8D1])</smartstring> + <penalty valence="1">1</penalty> + <penalty valence="2">0</penalty> + <penalty valence="3">64</penalty> + </entry> + <entry id="21"> + <elementstring>O</elementstring> + <smartstring>SMARTS([#8D2])</smartstring> + <penalty valence="1">32</penalty> + <penalty valence="2">0</penalty> + <penalty valence="3">64</penalty> + </entry> + <entry id="22"> + <elementstring>P</elementstring> + <smartstring>SMARTS(#15D1)</smartstring> + <penalty valence="2">2</penalty> + <penalty valence="3">0</penalty> + <penalty valence="4">32</penalty> + </entry> + <entry id="23"> + <elementstring>P</elementstring> + <smartstring>SMARTS(#15D2)</smartstring> + <penalty valence="2">4</penalty> + <penalty valence="3">0</penalty> + <penalty valence="4">2</penalty> + </entry> + <entry id="24"> + <elementstring>P</elementstring> + <smartstring>SMARTS(#15D3)</smartstring> + <penalty valence="2">32</penalty> + <penalty valence="3">0</penalty> + <penalty valence="4">1</penalty> + <penalty valence="5">2</penalty> + </entry> + <entry id="25"> + <elementstring>P</elementstring> + <!-- Note: this is _SLOW_ --> + <smartstring>SMARTS([$([#15D4](~[#8D1,#16D1])(~[!#8&!#16,!D1])(~[!#8&!#16,!D1])(~[#8D1,#16D1]))])</smartstring> + <penalty valence="5">32</penalty> + <penalty valence="6">0</penalty> + <penalty valence="7">32</penalty> + </entry> + <entry id="26"> + <elementstring>P</elementstring> + <smartstring>SMARTS([$([#15D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1])(~[!#8&!#16,!D1]))])</smartstring> + <penalty valence="6">32</penalty> + <penalty valence="7">0</penalty> + </entry> + <entry id="27"> + <elementstring>P</elementstring> + <!-- This rule should be the last PD4 rule because it should only match when the other rules fail! --> + <smartstring>SMARTS(#15D4)</smartstring> + <penalty valence="3">64</penalty> + <penalty valence="4">1</penalty> + <penalty valence="5">0</penalty> + <penalty valence="6">32</penalty> + </entry> + <entry id="28"> + <elementstring>S</elementstring> + <smartstring>SMARTS([#7D3](~[#16D1])(~[!#8&!#16,!D1])(~[!#8&!#16,!D1])) AND element(S)</smartstring> + <penalty valence="1">0</penalty> + <penalty valence="2">1</penalty> + </entry> + <entry id="29"> + <elementstring>S</elementstring> + <smartstring>SMARTS([#16D1])</smartstring> + <penalty valence="1">2</penalty> + <penalty valence="2">0</penalty> + <penalty valence="3">64</penalty> + </entry> + <entry id="30"> + <elementstring>S</elementstring> + <smartstring>SMARTS([#16D2])</smartstring> + <!-- These are the penalties given in the GAFF - paper; unfortunately, the values implemented in antechamber are different! + <penalty valence="1">32</penalty> + <penalty valence="2">0</penalty> + <penalty valence="3">32</penalty> + <penalty valence="4">1</penalty> --> + <penalty valence="1">2</penalty> + <penalty valence="2">0</penalty> + <penalty valence="3">64</penalty> + </entry> + <entry id="31"> + <elementstring>S</elementstring> + <smartstring>SMARTS([#16D3])</smartstring> + <penalty valence="3">1</penalty> + <penalty valence="4">0</penalty> + <penalty valence="5">2</penalty> + <penalty valence="6">2</penalty> + </entry> + <entry id="32"> + <elementstring>S</elementstring> + <smartstring> SMARTS([$([#16D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[!#8&!#16,!D1])(~[!#8&!#16,!D1]))])</smartstring> + <penalty valence="6">0</penalty> + <penalty valence="7">32</penalty> + </entry> + <entry id="33"> + <elementstring>S</elementstring> + <smartstring>SMARTS([$([#16D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1])(~[!#8&!#16,!D1]))])</smartstring> + <penalty valence="6">32</penalty> + <penalty valence="7">0</penalty> + </entry> + <entry id="34"> + <elementstring>S</elementstring> + <smartstring>SMARTS([$([#16D4](~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1])(~[#8D1,#16D1]))])</smartstring> + <penalty valence="6">32</penalty> + <penalty valence="7">0</penalty> + </entry> + <entry id="35"> + <elementstring>S</elementstring> + <smartstring>SMARTS([#16D4])</smartstring> + <penalty valence="4">4</penalty> + <penalty valence="5">2</penalty> + <penalty valence="6">0</penalty> + </entry> + <!-- The following rules are added to cope with ions --> + <entry id="40"> + <elementstring>Li</elementstring> + <smartstring>SMARTS([#3])</smartstring> + <penalty valence="0">0</penalty> + </entry> + <entry id="41"> + <elementstring>Na</elementstring> + <smartstring>SMARTS([#11])</smartstring> + <penalty valence="0">0</penalty> + </entry> + <entry id="42"> + <elementstring>Mg</elementstring> + <smartstring>SMARTS([#12])</smartstring> + <penalty valence="0">0</penalty> + </entry> + <entry id="43"> + <elementstring>K</elementstring> + <smartstring>SMARTS([#19])</smartstring> + <penalty valence="0">0</penalty> + </entry> + <entry id="44"> + <elementstring>Ca</elementstring> + <smartstring>SMARTS([#20])</smartstring> + <penalty valence="0">0</penalty> + </entry> + <entry id="45"> + <elementstring>Cu</elementstring> + <smartstring>SMARTS([#29])</smartstring> + <penalty valence="0">0</penalty> + </entry> + <entry id="46"> + <elementstring>Zn</elementstring> + <smartstring>SMARTS([#30])</smartstring> + <penalty valence="0">0</penalty> + </entry> + +</table>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/bond_lengths/bond_lengths.db Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,257 @@ +<node>BondLengthsDB + <node>1 + <node>Names + <node>Hydrogen</node> + <node>H</node> + </node> + <node>Partners + <node>6 + <node>BondLengths + <node>max<value>1.15</value></node> + <node>single<value>1.09</value></node> + <node>min<value>0.95</value></node> + </node> + </node> + <node>7 + <node>BondLengths + <node>max<value>1.10</value></node> + <node>single<value>1.03</value></node> + <node>min<value>0.9</value></node> + </node> + </node> + <node>8 + <node>BondLengths + <node>max<value>1.1</value></node> + <node>single<value>0.96</value></node> + <node>min<value>0.9</value></node> + </node> + </node> + <node>15 + <node>BondLengths + <node>max<value>1.5</value></node> + <node>single<value>1.0</value></node> + <node>min<value>0.9</value></node> + </node> + </node> + <node>16 + <node>BondLengths + <node>max<value>1.5</value></node> + <node>single<value>1.34</value></node> + <node>min<value>1.1</value></node> + </node> + </node> + </node> + </node> + <node>6 + <node>Names + <node>Carbon</node> + <node>C</node> + </node> + <node>Partners + <node>6 + <node>BondLengths + <node>max<value>1.75</value></node> + <node>single<value>1.47</value></node> + <node>aromatic<value>1.39</value></node> + <node>double<value>1.34</value></node> + <node>triple<value>1.18</value></node> + <node>min<value>1.15</value></node> + </node> + </node> + <node>7 + <node>BondLengths + <node>max<value>1.65</value></node> + <node>single<value>1.38</value></node> + <node>aromatic<value>1.33</value></node> + <node>double<value>1.29</value></node> + <node>triple<value>1.15</value></node> + <node>min<value>1.1</value></node> + </node> + </node> + <node>8 + <node>BondLengths + <node>max<value>1.55</value></node> + <node>single<value>1.42</value></node> + <node>double<value>1.20</value></node> + <node>min<value>1.10</value></node> + </node> + </node> + <node>9 + <node>BondLengths + <node>max<value>1.45</value></node> + <node>single<value>1.38</value></node> + <node>min<value>1.0</value></node> + </node> + </node> + <node>15 + <node>BondLengths + <node>max<value>1.95</value></node> + <node>single<value>1.8</value></node> + <node>min<value>1.7</value></node> + </node> + </node> + <node>16 + <node>BondLengths + <node>max<value>1.95</value></node> + <node>single<value>1.70</value></node> + <node>double<value>1.63</value></node> + <node>min<value>1.5</value></node> + </node> + </node> + <node>17 + <node>BondLengths + <node>max<value>1.9</value></node> + <node>single<value>1.8</value></node> + <node>min<value>1.0</value></node> + </node> + </node> + <node>35 + <node>BondLengths + <node>max<value>2.05</value></node> + <node>single<value>1.96</value></node> + <node>min<value>1.0</value></node> + </node> + </node> + <node>53 + <node>BondLengths + <node>max<value>2.3</value></node> + <node>single<value>2.1</value></node> + <node>min<value>1.0</value></node> + </node> + </node> + </node> + </node> + <node>7 + <node>Names + <node>Nitrogen</node> + <node>N</node> + </node> + <node>Partners + <node>7 + <node>BondLengths + <node>max<value>1.55</value></node> + <node>single<value>1.40</value></node> + <node>aromatic<value>1.32</value></node> + <node>double<value>1.22</value></node> + <node>min<value>1.0</value></node> + </node> + </node> + <node>8 + <node>BondLengths + <node>max<value>1.5</value></node> + <node>single<value>1.4</value></node> + <node>double<value>1.21</value></node> + <node>min<value>1.15</value></node> + </node> + </node> + <node>9 + <node>BondLengths + <node>max<value>1.5</value></node> + <node>single<value>1.35</value></node> + <node>min<value>1.25</value></node> + </node> + </node> + <node>15 + <node>BondLengths + <node>max<value>1.8</value></node> + <node>single<value>1.68</value></node> + <node>aromatic<value>1.60</value></node> + <node>double<value>1.58</value></node> + <node>min<value>1.5</value></node> + </node> + </node> + <node>16 + <node>BondLengths + <node>max<value>1.80</value></node> + <node>single<value>1.65</value></node> + <node>aromatic<value>1.56</value></node> + <node>double<value>1.54</value></node> + <node>min<value>1.50</value></node> + </node> + </node> + <node>17 + <node>BondLengths + <node>max<value>1.85</value></node> + <node>single<value>1.74</value></node> + <node>min<value>1.65</value></node> + </node> + </node> + <node>35 + <node>BondLengths + <node>max<value>2.0</value></node> + <node>single<value>1.84</value></node> + <node>min<value>1.7</value></node> + </node> + </node> + </node> + </node> + <node>8 + <node>Names + <node>Oxygen</node> + <node>O</node> + </node> + <node>Partners + <node>8 + <node>BondLengths + <node>max<value>1.55</value></node> + <node>single<value>1.47</value></node> + <node>min<value>1.40</value></node> + </node> + </node> + <node>15 + <node>BondLengths + <node>max<value>1.75</value></node> + <node>single<value>1.59</value></node> + <node>double<value>1.49</value></node> + <node>min<value>1.40</value></node> + </node> + </node> + <node>16 + <node>BondLengths + <node>max<value>1.75</value></node> + <node>single<value>1.56</value></node> + <node>double<value>1.43</value></node> + <node>min<value>1.38</value></node> + </node> + </node> + </node> + </node> + <node>15 + <node>Names + <node>Phosphorus</node> + <node>P</node> + </node> + <node>Partners + <node>15 + <node>BondLengths + <node>max<value>2.3</value></node> + <node>single<value>2.2</value></node> + <node>double<value>2.0</value></node> + <node>min<value>1.9</value></node> + </node> + </node> + <node>16 + <node>BondLengths + <node>max<value>2.2</value></node> + <node>double<value>1.95</value></node> + <node>min<value>1.85</value></node> + </node> + </node> + </node> + </node> + <node>16 + <node>Names + <node>Sulfur</node> + <node>S</node> + </node> + <node>Partners + <node>16 + <node>BondLengths + <node>max<value>2.2</value></node> + <node>single<value>2.07</value></node> + <node>min<value>1.9</value></node> + </node> + </node> + </node> + </node> +</node>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/bond_lengths/bond_lengths_mmff94.ini Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,1505 @@ +[BondLengths] +key:I key:deg_I key:J key:deg_J key:order value:r0 +@unit_r0=Angstrom +; +; +; I deg_I J deg_J order r0 + --- ------- --- ------- ------- --------- + C 1 C 1 1 1.508 + C 1 C 2 1 1.508 + C 1 C 3 1 1.508 + C 1 C 4 1 1.5086 + C 2 C 1 1 1.508 + C 2 C 2 1 1.5086 + C 2 C 3 1 1.5072 + C 2 C 4 1 1.5093 + C 3 C 1 1 1.508 + C 3 C 2 1 1.5072 + C 3 C 3 1 1.5066 + C 3 C 4 1 1.51 + C 4 C 1 1 1.5086 + C 4 C 2 1 1.5093 + C 4 C 3 1 1.51 + C 4 C 4 1 1.5121 + C 1 C 1 2 1.333 + C 1 C 2 2 1.333 + C 1 C 3 2 1.3333 + C 1 C 4 2 1.344 + C 2 C 1 2 1.333 + C 2 C 2 2 1.3333 + C 2 C 3 2 1.3341 + C 2 C 4 2 1.3453 + C 3 C 1 2 1.3333 + C 3 C 2 2 1.3341 + C 3 C 3 2 1.3358 + C 3 C 4 2 1.3477 + C 4 C 1 2 1.344 + C 4 C 2 2 1.3453 + C 4 C 3 2 1.3477 + C 4 C 4 2 1.3624 + C 1 C 1 3 1.192 + C 1 C 2 3 1.4529 + C 1 C 3 3 1.192 + C 1 C 4 3 1.1917 + C 2 C 1 3 1.452 + C 2 C 2 3 1.211 + C 2 C 3 3 1.3034 + C 2 C 4 3 1.4768 + C 3 C 1 3 1.192 + C 3 C 2 3 1.299 + C 3 C 3 3 1.3358 + C 3 C 4 3 1.4835 + C 4 C 1 3 1.1917 + C 4 C 2 3 1.468 + C 4 C 3 3 1.4833 + C 4 C 4 3 1.5121 + C 1 N 1 1 1.4556 + C 1 N 2 1 1.4556 + C 1 N 3 1 1.451 + C 1 N 4 1 1.4801 + C 1 N 5 1 1.5343 + C 2 N 1 1 1.4556 + C 2 N 3 1 1.4508 + C 2 N 4 1 1.4808 + C 3 N 1 1 1.4556 + C 3 N 3 1 1.4507 + C 3 N 4 1 1.4814 + C 4 N 1 1 1.4545 + C 4 N 3 1 1.452 + C 4 N 4 1 1.4757 + C 1 N 1 2 1.29 + C 1 N 2 2 1.29 + C 1 N 3 2 1.28 + C 1 N 4 2 1.2913 + C 1 N 5 2 1.2904 + C 2 N 1 2 1.29 + C 2 N 2 2 1.289 + C 2 N 3 2 1.2811 + C 2 N 4 2 1.2904 + C 2 N 5 2 1.2901 + C 3 N 1 2 1.2866 + C 3 N 2 2 1.2868 + C 3 N 3 2 1.2798 + C 3 N 4 2 1.2881 + C 3 N 5 2 1.2904 + C 4 N 1 2 1.3265 + C 4 N 2 2 1.3277 + C 4 N 3 2 1.29 + C 4 N 4 2 1.3347 + C 4 N 5 2 1.3364 + C 1 N 1 3 1.3756 + C 1 N 2 3 1.2075 + C 1 N 3 3 1.3756 + C 1 N 4 3 1.4018 + C 1 N 5 3 1.4163 + C 2 N 1 3 1.1897 + C 3 N 1 3 1.1154 + C 4 N 1 3 1.3758 + C 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/fragments/A.db Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,107 @@ +<node>A + <node>Names + <node>Adenine</node> + <node>Adenin</node> + <node>A</node> + </node> + <node>Atoms + <node>P<value>P 23.872 39.165 31.119</value></node> + <node>O1P<value>O 25.231 39.217 30.523</value></node> + <node>O2P<value>O 22.847 40.110 30.636</value></node> + <node>O5*<value>O 24.015 39.407 32.681</value></node> + <node>C5*<value>C 23.898 38.444 33.717</value></node> + <node>1H5*<value>H 23.427 37.536 33.341</value></node> + <node>2H5*<value>H 23.266 38.889 34.485</value></node> + <node>C4*<value>C 25.259 38.091 34.326</value></node> + <node>H4*<value>H 25.156 37.622 35.304</value></node> + <node>O4*<value>O 25.979 37.144 33.552</value></node> + <node>C3*<value>C 26.180 39.302 34.326</value></node> + <node>H3*<value>H 26.158 39.977 33.470</value></node> + <node>O3*<value>O 25.805 40.074 35.470</value></node> + <node>C2*<value>C 27.544 38.641 34.414</value></node> + <node>1H2*<value>H 28.301 39.314 34.011</value></node> + <node>2H2*<value>H 27.774 38.419 35.456</value></node> + <node>C1*<value>C 27.277 37.165 34.164</value></node> + <node>H1*<value>H 27.382 36.562 35.066</value></node> + <node>N9<value>N 28.236 36.536 33.230</value></node> + <node>C8<value>C 28.440 36.783 31.901</value></node> + <node>H8<value>H 27.912 37.594 31.421</value></node> + <node>N7<value>N 29.329 36.020 31.347</value></node> + <node>C5<value>C 29.751 35.206 32.384</value></node> + <node>C6<value>C 30.698 34.181 32.452</value></node> + <node>N6<value>N 31.417 33.777 31.410</value></node> + <node>1H6<value>H 32.088 33.030 31.518</value></node> + <node>2H6<value>H 31.292 34.217 30.509</value></node> + <node>N1<value>N 30.867 33.595 33.636</value></node> + <node>C2<value>C 30.158 33.991 34.674</value></node> + <node>2H<value>H 30.296 33.518 35.635</value></node> + <node>N3<value>N 29.245 34.933 34.744</value></node> + <node>C4<value>C 29.090 35.512 33.538</value></node> + </node> + <node>Bonds + <node>1<value>P O1P s</value></node> + <node>2<value>P O2P d</value></node> + <node>3<value>P O5* s</value></node> + <node>4<value>O5* C5* s</value></node> + <node>5<value>C5* C4* s</value></node> + <node>6<value>C4* O4* s</value></node> + <node>7<value>C4* C3* s</value></node> + <node>8<value>C3* O3* s</value></node> + <node>9<value>C3* C2* s</value></node> + <node>10<value>C2* C1* s</value></node> + <node>11<value>C1* O4* s</value></node> + <node>12<value>C1* N9 s</value></node> + <node>13<value>N9 C8 s</value></node> + <node>14<value>C8 N7 d</value></node> + <node>15<value>N7 C5 s</value></node> + <node>16<value>C5 C6 s</value></node> + <node>17<value>C5 C4 d</value></node> + <node>18<value>C4 N9 s</value></node> + <node>19<value>C6 N6 s</value></node> + <node>20<value>C6 N1 d</value></node> + <node>21<value>N1 C2 s</value></node> + <node>22<value>C2 N3 d</value></node> + <node>23<value>N3 C4 s</value></node> + <node>24<value>C5* 1H5* s</value></node> + <node>25<value>C5* 2H5* s</value></node> + <node>26<value>C4* H4* s</value></node> + <node>27<value>C1* H1* s</value></node> + <node>28<value>C3* H3* s</value></node> + <node>29<value>C2* 1H2* s</value></node> + <node>30<value>C2* 2H2* s</value></node> + <node>31<value>C8 H8 s</value></node> + <node>32<value>N6 1H6 s</value></node> + <node>33<value>N6 2H6 s</value></node> + <node>34<value>C2 2H s</value></node> + </node> + <node>Connections + <node>5-term<value>P 3-term s 1.62 0.5</value></node> + <node>3-term<value>O3* 5-term s 1.62 0.5</value></node> + </node> + <node>Properties + <node>NUCLEOTIDE</node> + </node> + <node>Variants + <node>A-M + <node>Properties + <node>5_PRIME</node> + <node>3_PRIME</node> + </node> + </node> + <node>Default + <node>Properties + </node> + </node> + <node>A-3 + <node>Properties + <node>3_PRIME</node> + </node> + </node> + <node>A-5 + <node>Properties + <node>5_PRIME</node> + </node> + </node> + </node> +</node> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/fragments/ACE.db Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,47 @@ +<node>ACE + <node>Names + <node>ACE</node> + <node>acetic acid</node> + </node> + <node>Atoms + <node>C<value>C -0.710977 -1.12008 0.000774821</value></node> + <node>CH3<value>C 0.0997794 -2.40762 0.00202052</value></node> + <node>O<value>O -1.92224 -1.17518 0.00112378</value></node> + <node>1HH3<value>H -0.167239 -2.98461 0.880642</value></node> + <node>2HH3<value>H 1.1711 -2.24422 -0.00400307</value></node> + <node>3HH3<value>H -0.176322 -2.99236 -0.868617</value></node> + <node>OXT<value>O -0.0809243 0.0851695 -0.000720861</value></node> + </node> + <node>Bonds + <node>1<value>C CH3 s</value></node> + <node>2<value>C O d</value></node> + <node>3<value>C OXT s</value></node> + <node>4<value>CH3 1HH3 s</value></node> + <node>5<value>CH3 2HH3 s</value></node> + <node>6<value>CH3 3HH3 s</value></node> + </node> + <node>Connections + <node>C-term + <value>C N-term s 1.33 0.5 + </value> + </node> + </node> + <node>Properties + </node> + <node>Variants + <node>ACE-N + <node>Delete + <node>OXT</node> + </node> + <node>Properties + <node>N_TERMINAL</node> + </node> + </node> + <node>ACE-M + <node>Properties + <node>C_TERMINAL</node> + <node>N_TERMINAL</node> + </node> + </node> + </node> +</node>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/fragments/ALA.db Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,82 @@ +<node>ALA + <node>Names + <node>Alanine</node> + <node>Alanin</node> + <node>Ala</node> + <node>A</node> + </node> + <node>Atoms + <node>N<value>N 0.09952427 1.425946 -0.01392276</value></node> + <node>3H<value>H 0.9122966 2.021833 0.09543685</value></node> + <node>CA<value>C -0.6343572 1.904422 -1.199327</value></node> + <node>HA<value>H -0.06613517 1.608824 -2.082189</value></node> + <node>C<value>C -0.7061328 3.434369 -1.195026</value></node> + <node>O<value>O 0.2770563 4.020259 -0.6877273</value></node> + <node>CB<value>C -2.018631 1.250585 -1.273356</value></node> + <node>1HB<value>H -2.525042 1.535779 -2.196084</value></node> + <node>2HB<value>H -1.909473 0.1656088 -1.256012</value></node> + <node>3HB<value>H -2.621985 1.560564 -0.4192078</value></node> + <node>OXT<value>O -1.554726 3.968913 -1.942107</value></node> + <node>1H<value>H -0.4859746 1.514033 0.8043322</value></node> + <node>2H<value>H 0.3756785 0.4622824 -0.137128</value></node> + </node> + <node>Bonds + <node>5<value>3H N s</value></node> + <node>6<value>CA N s</value></node> + <node>10<value>HA CA s</value></node> + <node>11<value>C CA s</value></node> + <node>14<value>O C d</value></node> + <node>15<value>CB CA s</value></node> + <node>19<value>1HB CB s</value></node> + <node>20<value>2HB CB s</value></node> + <node>21<value>3HB CB s</value></node> + <node>22<value>OXT C s</value></node> + <node>23<value>1H N s</value></node> + <node>24<value>2H N s</value></node> + </node> + <node>Connections + <node>N-term<value>N C-term s 1.33 0.5</value></node> + <node>C-term<value>C N-term s 1.33 0.5</value></node> + </node> + <node>Properties + <node>AMINO_ACID</node> + </node> + <node>Variants + <node>Default + <node>Delete + <node>OXT<value></value></node> + <node>1H<value></value></node> + <node>2H<value></value></node> + </node> + <node>Rename + <node>3H<value>H</value></node> + </node> + </node> + <node>ALA-M + <node>Properties + <node>C_TERMINAL</node> + <node>N_TERMINAL</node> + </node> + </node> + <node>ALA-C + <node>Delete + <node>1H<value></value></node> + <node>2H<value></value></node> + </node> + <node>Rename + <node>3H<value>H</value></node> + </node> + <node>Properties + <node>C_TERMINAL</node> + </node> + </node> + <node>ALA-N + <node>Delete + <node>OXT<value></value></node> + </node> + <node>Properties + <node>N_TERMINAL</node> + </node> + </node> + </node> +</node>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/fragments/ARG.db Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,110 @@ +<node>ARG + <node>Names + <node>Arginine</node> + <node>Arginin</node> + <node>Arg</node> + <node>R</node> + </node> + <node>Atoms + <node>N<value>N 0.04658213 1.228698 -0.008203848</value></node> + <node>3H<value>H 1.029144 1.468065 -0.01885969</value></node> + <node>CA<value>C -0.651675 1.900984 -1.120636</value></node> + <node>HA<value>H -0.1560273 1.589999 -2.041618</value></node> + <node>C<value>C -0.5384113 3.425156 -1.007164</value></node> + <node>O<value>O -0.4560871 4.056512 -2.083366</value></node> + <node>CB<value>C -2.115081 1.438444 -1.186192</value></node> + <node>1HB<value>H -2.126043 0.3475202 -1.20068</value></node> + <node>2HB<value>H -2.643967 1.778842 -0.2945162</value></node> + <node>CG<value>C -2.829752 1.953359 -2.443151</value></node> + <node>1HG<value>H -2.889884 3.042607 -2.412891</value></node> + <node>2HG<value>H -2.25911 1.654155 -3.324525</value></node> + <node>CD<value>C -4.246704 1.376451 -2.533151</value></node> + <node>1HD<value>H -4.174877 0.2870844 -2.574071</value></node> + <node>2HD<value>H -4.797596 1.672022 -1.637285</value></node> + <node>NE<value>N -4.940577 1.875193 -3.731703</value></node> + <node>HE<value>H -4.414851 2.512341 -4.314554</value></node> + <node>CZ<value>C -6.193176 1.546153 -4.088384</value></node> + <node>NH1<value>N -6.900425 0.7030471 -3.327994</value></node> + <node>1HH1<value>H -6.480561 0.3232263 -2.492691</value></node> + <node>2HH1<value>H -7.843661 0.4323652 -3.563007</value></node> + <node>NH2<value>N -6.730267 2.060851 -5.200565</value></node> + <node>1HH2<value>H -6.201764 2.698435 -5.778988</value></node> + <node>2HH2<value>H -7.669785 1.826959 -5.486362</value></node> + <node>OXT<value>O -0.796168 3.930999 0.1074273</value></node> + <node>1H<value>H -0.3621705 1.521632 0.867786</value></node> + <node>2H<value>H -0.05222332 0.2284002 -0.1067282</value></node> + </node> + <node>Bonds + <node>5<value>3H N s</value></node> + <node>6<value>CA N s</value></node> + <node>10<value>HA CA s</value></node> + <node>11<value>C CA s</value></node> + <node>14<value>O C d</value></node> + <node>15<value>CB CA s</value></node> + <node>19<value>1HB CB s</value></node> + <node>20<value>2HB CB s</value></node> + <node>21<value>CG CB s</value></node> + <node>25<value>1HG CG s</value></node> + <node>26<value>2HG CG s</value></node> + <node>27<value>CD CG s</value></node> + <node>31<value>1HD CD s</value></node> + <node>32<value>2HD CD s</value></node> + <node>33<value>NE CD s</value></node> + <node>36<value>HE NE s</value></node> + <node>37<value>CZ NE s</value></node> + <node>40<value>NH1 CZ a</value></node> + <node>43<value>1HH1 NH1 s</value></node> + <node>44<value>2HH1 NH1 s</value></node> + <node>45<value>NH2 CZ a</value></node> + <node>48<value>1HH2 NH2 s</value></node> + <node>49<value>2HH2 NH2 s</value></node> + <node>50<value>OXT C s</value></node> + <node>51<value>1H N s</value></node> + <node>52<value>2H N s</value></node> + </node> + <node>Connections + <node>N-term<value>N C-term s 1.33 0.5</value></node> + <node>C-term<value>C N-term s 1.33 0.5</value></node> + </node> + <node>Properties + <node>AMINO_ACID</node> + </node> + <node>Variants + <node>Default + <node>Delete + <node>OXT</node> + <node>1H</node> + <node>2H</node> + </node> + <node>Rename + <node>3H<value>H</value></node> + </node> + </node> + <node>ARG-M + <node>Properties + <node>C_TERMINAL</node> + <node>N_TERMINAL</node> + </node> + </node> + <node>ARG-C + <node>Delete + <node>1H</node> + <node>2H</node> + </node> + <node>Rename + <node>3H<value>H</value></node> + </node> + <node>Properties + <node>C_TERMINAL</node> + </node> + </node> + <node>ARG-N + <node>Delete + <node>OXT</node> + </node> + <node>Properties + <node>N_TERMINAL</node> + </node> + </node> + </node> +</node>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/fragments/ASN.db Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,90 @@ +<node>ASN + <node>Names + <node>Asparagine</node> + <node>Asparagin</node> + <node>Asn</node> + <node>N</node> + </node> + <node>Atoms + <node>N<value>N -0.01239826 1.297873 -0.0455736</value></node> + <node>3H<value>H 0.8807231 1.768826 0.03701005</value></node> + <node>CA<value>C -0.7474616 1.91653 -1.164926</value></node> + <node>HA<value>H -0.1937652 1.691628 -2.077897</value></node> + <node>C<value>C -0.757567 3.441771 -1.010304</value></node> + <node>O<value>O 0.3769885 3.962902 -0.9276295</value></node> + <node>CB<value>C -2.149851 1.302218 -1.30196</value></node> + <node>1HB<value>H -2.042859 0.2235991 -1.423685</value></node> + <node>2HB<value>H -2.723301 1.490943 -0.3934487</value></node> + <node>CG<value>C -2.91901 1.84635 -2.50453</value></node> + <node>OD1<value>O -2.442698 2.721974 -3.218464</value></node> + <node>ND2<value>N -4.125435 1.339006 -2.736042</value></node> + <node>1HD2<value>H -4.50376 0.6180301 -2.140929</value></node> + <node>2HD2<value>H -4.647904 1.686222 -3.525954</value></node> + <node>1H<value>H -0.5352049 1.417775 0.8102037</value></node> + <node>2H<value>H 0.1272759 0.3139404 -0.2256562</value></node> + <node>OXT<value>O -1.806735 3.963976 -0.572751</value></node> + </node> + <node>Bonds + <node>5<value>3H N s</value></node> + <node>6<value>CA N s</value></node> + <node>10<value>HA CA s</value></node> + <node>11<value>C CA s</value></node> + <node>14<value>O C d</value></node> + <node>15<value>CB CA s</value></node> + <node>19<value>1HB CB s</value></node> + <node>20<value>2HB CB s</value></node> + <node>21<value>CG CB s</value></node> + <node>24<value>OD1 CG d</value></node> + <node>25<value>ND2 CG s</value></node> + <node>28<value>1HD2 ND2 s</value></node> + <node>29<value>2HD2 ND2 s</value></node> + <node>30<value>1H N s</value></node> + <node>31<value>2H N s</value></node> + <node>32<value>OXT C s</value></node> + </node> + <node>Connections + <node>N-term<value>N C-term s 1.33 0.5</value></node> + <node>C-term<value>C N-term s 1.33 0.5</value></node> + </node> + <node>Properties + <node>AMINO_ACID</node> + </node> + <node>Variants + <node>Default + <node>Delete + <node>OXT</node> + <node>1H</node> + <node>2H</node> + </node> + <node>Rename + <node>3H<value>H</value></node> + </node> + </node> + <node>ASN-M + <node>Properties + <node>C_TERMINAL</node> + <node>N_TERMINAL</node> + </node> + </node> + <node>ASN-C + <node>Delete + <node>1H</node> + <node>2H</node> + </node> + <node>Rename + <node>3H<value>H</value></node> + </node> + <node>Properties + <node>C_TERMINAL</node> + </node> + </node> + <node>ASN-N + <node>Delete + <node>OXT</node> + </node> + <node>Properties + <node>N_TERMINAL</node> + </node> + </node> + </node> +</node>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/fragments/ASP.db Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,86 @@ +<node>ASP + <node>Names + <node>Aspartate</node> + <node>Aspartat</node> + <node>Asp</node> + <node>D</node> + </node> + <node>Atoms + <node>N<value>N 0.1006113 1.231053 -0.1065504</value></node> + <node>3H<value>H 0.7826706 1.919109 0.1901606</value></node> + <node>CA<value>C -0.6776782 1.854581 -1.196471</value></node> + <node>HA<value>H -0.140641 1.67647 -2.129506</value></node> + <node>C<value>C -0.7684437 3.377808 -1.00658</value></node> + <node>O<value>O -0.1755398 3.814352 0.008837678</value></node> + <node>CB<value>C -2.059715 1.201639 -1.304611</value></node> + <node>1HB<value>H -1.947421 0.1437317 -1.541582</value></node> + <node>2HB<value>H -2.583309 1.296861 -0.3531539</value></node> + <node>CG<value>C -2.895658 1.868856 -2.384729</value></node> + <node>OD1<value>O -2.861295 1.365629 -3.526181</value></node> + <node>OD2<value>O -3.508188 2.905267 -2.052321</value></node> + <node>OXT<value>O -0.9198192 4.048685 -2.051676</value></node> + <node>1H<value>H -0.5109496 1.02733 0.6709606</value></node> + <node>2H<value>H 0.5472904 0.3836241 -0.4264945</value></node> + </node> + <node>Bonds + <node>5<value>3H N s</value></node> + <node>6<value>CA N s</value></node> + <node>10<value>HA CA s</value></node> + <node>11<value>C CA s</value></node> + <node>14<value>O C d</value></node> + <node>15<value>CB CA s</value></node> + <node>19<value>1HB CB s</value></node> + <node>20<value>2HB CB s</value></node> + <node>21<value>CG CB s</value></node> + <node>24<value>OD1 CG a</value></node> + <node>25<value>OD2 CG a</value></node> + <node>26<value>OXT C s</value></node> + <node>27<value>1H N s</value></node> + <node>28<value>2H N s</value></node> + </node> + <node>Connections + <node>N-term<value>N C-term s 1.33 0.5</value></node> + <node>C-term<value>C N-term s 1.33 0.5</value></node> + </node> + <node>Properties + <node>AMINO_ACID</node> + </node> + <node>Variants + <node>Default + <node>Delete + <node>OXT</node> + <node>1H</node> + <node>2H</node> + </node> + <node>Rename + <node>3H<value>H</value></node> + </node> + </node> + <node>ASP-M + <node>Properties + <node>N_TERMINAL</node> + <node>C_TERMINAL</node> + </node> + </node> + <node>ASP-N + <node>Delete + <node>OXT</node> + </node> + <node>Properties + <node>N_TERMINAL</node> + </node> + </node> + <node>ASP-C + <node>Delete + <node>1H</node> + <node>2H</node> + </node> + <node>Rename + <node>3H<value>H</value></node> + </node> + <node>Properties + <node>C_TERMINAL</node> + </node> + </node> + </node> +</node>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/fragments/Benzene-Skeleton.db Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,23 @@ +<node>Benzene-Skeleton + <node>Names + <node>Benzene-Skeleton</node> + </node> + <node>Atoms + <node>C1<value>C 0.066248 -1.287634 0.144514</value></node> + <node>C2<value>C 0.057081 -0.613884 1.337852</value></node> + <node>C3<value>C 0.045766 0.796088 1.307799</value></node> + <node>C4<value>C 0.054862 1.462219 0.071058</value></node> + <node>C5<value>C 0.073086 0.728404 -1.129738</value></node> + <node>C6<value>C 0.091744 -0.671622 -1.107443</value></node> + </node> + <node>Bonds + <node>1<value>C1 C2 s</value></node> + <node>2<value>C2 C3 d</value></node> + <node>3<value>C3 C4 s</value></node> + <node>4<value>C4 C5 d</value></node> + <node>5<value>C5 C6 s</value></node> + <node>6<value>C6 C1 d</value></node> + </node> + <node>Properties + </node> +</node>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/fragments/C.db Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,102 @@ +<node>C + <node>Names + <node>Cytosine</node> + <node>Cytosin</node> + <node>C</node> + </node> + <node>Atoms + <node>P<value>P 15.644 29.327 35.222</value></node> + <node>O1P<value>O 15.393 28.440 36.382</value></node> + <node>O2P<value>O 14.638 30.335 34.831</value></node> + <node>O5*<value>O 15.947 28.383 33.968</value></node> + <node>C5*<value>C 16.069 28.915 32.657</value></node> + <node>1H5*<value>H 16.821 29.704 32.690</value></node> + <node>2H5*<value>H 15.119 29.333 32.322</value></node> + <node>C4*<value>C 16.513 27.844 31.682</value></node> + <node>H4*<value>H 16.609 28.228 30.666</value></node> + <node>O4*<value>O 17.830 27.370 32.014</value></node> + <node>C3*<value>C 15.542 26.637 31.746</value></node> + <node>H3*<value>H 14.654 26.736 32.370</value></node> + <node>O3*<value>O 15.186 26.233 30.429</value></node> + <node>C2*<value>C 16.448 25.569 32.322</value></node> + <node>1H2*<value>H 16.102 25.297 33.319</value></node> + <node>2H2*<value>H 16.428 24.689 31.678</value></node> + <node>C1*<value>C 17.781 25.967 31.722</value></node> + <node>H1*<value>H 17.935 25.853 30.649</value></node> + <node>N1<value>N 18.940 25.252 32.322</value></node> + <node>C6<value>C 18.970 24.882 33.637</value></node> + <node>H6<value>H 18.141 25.127 34.285</value></node> + <node>C5<value>C 20.022 24.211 34.147</value></node> + <node>H5<value>H 20.029 23.926 35.199</value></node> + <node>C4<value>C 21.100 23.907 33.243</value></node> + <node>N4<value>N 22.167 23.241 33.694</value></node> + <node>1H4<value>H 22.908 23.042 33.037</value></node> + <node>2H4<value>H 22.216 22.954 34.661</value></node> + <node>N3<value>N 21.059 24.280 31.953</value></node> + <node>C2<value>C 19.992 24.955 31.461</value></node> + <node>O2<value>O 19.963 25.291 30.279</value></node> + </node> + <node>Bonds + <node>1<value>P O1P s</value></node> + <node>2<value>P O2P d</value></node> + <node>3<value>P O5* s</value></node> + <node>4<value>O5* C5* s</value></node> + <node>5<value>C5* C4* s</value></node> + <node>6<value>C4* O4* s</value></node> + <node>7<value>C4* C3* s</value></node> + <node>8<value>C3* O3* s</value></node> + <node>9<value>C3* C2* s</value></node> + <node>10<value>C2* C1* s</value></node> + <node>11<value>C1* O4* s</value></node> + <node>12<value>C1* N1 s</value></node> + <node>13<value>N1 C6 s</value></node> + <node>14<value>C6 C5 d</value></node> + <node>15<value>C5 C4 s</value></node> + <node>16<value>C4 N4 s</value></node> + <node>17<value>C4 N3 d</value></node> + <node>18<value>N3 C2 s</value></node> + <node>19<value>C2 O2 d</value></node> + <node>20<value>C2 N1 s</value></node> + <node>21<value>C5* 1H5* s</value></node> + <node>22<value>C5* 2H5* s</value></node> + <node>23<value>C4* H4* s</value></node> + <node>24<value>C1* H1* s</value></node> + <node>25<value>C3* H3* s</value></node> + <node>26<value>C2* 1H2* s</value></node> + <node>27<value>C2* 2H2* s</value></node> + <node>28<value>C6 H6 s</value></node> + <node>29<value>C5 H5 s</value></node> + <node>30<value>N4 1H4 s</value></node> + <node>31<value>N4 2H4 s</value></node> + </node> + <node>Connections + <node>5-term<value>P 3-term s 1.62 0.5</value></node> + <node>3-term<value>O3* 5-term s 1.62 0.5</value></node> + </node> + <node>Properties + <node>NUCLEOTIDE</node> + </node> + <node>Variants + <node>C-M + <node>Properties + <node>5_PRIME</node> + <node>3_PRIME</node> + </node> + </node> + <node>Default + <node>Properties + </node> + </node> + <node>C-3 + <node>Properties + <node>3_PRIME</node> + </node> + </node> + <node>C-5 + <node>Properties + <node>5_PRIME</node> + </node> + </node> + </node> +</node> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/fragments/CA.db Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,18 @@ +<node>CA + <node>Names + <node>Calcium ion</node> + <node>Ca2+</node> + </node> + <node>Atoms + <node>CA<value>Ca 0.0 0.0 0.0</value></node> + </node> + <node>Bonds + </node> + <node>Connections + </node> + <node>Properties + </node> + <node>Variants + <node>Default</node> + </node> +</node>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/fragments/CYS.db Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,123 @@ +<node>CYS + <node>Names + <node>Cysteine</node> + <node>Cystein</node> + <node>Cys</node> + <node>C</node> + </node> + <node>Atoms + <node>N<value>N 0.02405081 1.288152 -0.04523527</value></node> + <node>3H<value>H 0.9139157 1.764642 0.02587458</value></node> + <node>CA<value>C -0.7231978 1.84877 -1.18869</value></node> + <node>HA<value>H -0.1383485 1.663318 -2.090963</value></node> + <node>C<value>C -0.8891953 3.364114 -1.049031</value></node> + <node>O<value>O 0.1143772 4.039036 -1.368143</value></node> + <node>CB<value>C -2.074845 1.154028 -1.367605</value></node> + <node>1HB<value>H -1.930864 0.09969049 -1.603445</value></node> + <node>2HB<value>H -2.672614 1.244251 -0.4604313</value></node> + <node>SG<value>S -2.936402 1.968095 -2.733035</value></node> + <node>HG<value>H -4.084388 1.292503 -2.621688</value></node> + <node>1H<value>H -0.5030248 1.428972 0.8047693</value></node> + <node>2H<value>H 0.1769028 0.3003187 -0.1898637</value></node> + <node>OXT<value>O -1.790595 3.760744 -0.2774832</value></node> + </node> + <node>Bonds + <node>5<value>3H N s</value></node> + <node>6<value>CA N s</value></node> + <node>10<value>HA CA s</value></node> + <node>11<value>C CA s</value></node> + <node>14<value>O C d</value></node> + <node>15<value>CB CA s</value></node> + <node>19<value>1HB CB s</value></node> + <node>20<value>2HB CB s</value></node> + <node>21<value>SG CB s</value></node> + <node>25<value>HG SG s</value></node> + <node>28<value>1H N s</value></node> + <node>29<value>2H N s</value></node> + <node>30<value>OXT C s</value></node> + </node> + <node>Connections + <node>N-term<value>N C-term s 1.33 0.5</value></node> + <node>C-term<value>C N-term s 1.33 0.5</value></node> + <node>S-term<value>SG S-term s 2.05 0.5</value></node> + </node> + <node>Properties + <node>AMINO_ACID</node> + </node> + <node>Variants + <node>Default + <node>Delete + <node>OXT</node> + <node>1H</node> + <node>2H</node> + </node> + <node>Rename + <node>3H<value>H</value></node> + </node> + </node> + <node>CYS-M + <node>Properties + <node>C_TERMINAL</node> + <node>N_TERMINAL</node> + </node> + </node> + <node>CYS-N + <node>Delete + <node>OXT</node> + </node> + <node>Properties + <node>N_TERMINAL</node> + </node> + </node> + <node>CYS-S + <node>Delete + <node>OXT</node> + <node>1H</node> + <node>2H</node> + <node>HG</node> + </node> + <node>Rename + <node>3H<value>H</value></node> + </node> + <node>Properties + <node>HAS_SSBOND</node> + </node> + </node> + <node>CYS-CS + <node>Delete + <node>1H</node> + <node>2H</node> + <node>HG</node> + </node> + <node>Rename + <node>3H<value>H</value></node> + </node> + <node>Properties + <node>C_TERMINAL</node> + <node>HAS_SSBOND</node> + </node> + </node> + <node>CYS-NS + <node>Delete + <node>OXT</node> + <node>HG</node> + </node> + <node>Properties + <node>N_TERMINAL</node> + <node>HAS_SSBOND</node> + </node> + </node> + <node>CYS-C + <node>Delete + <node>1H</node> + <node>2H</node> + </node> + <node>Rename + <node>3H<value>H</value></node> + </node> + <node>Properties + <node>C_TERMINAL</node> + </node> + </node> + </node> +</node>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/fragments/Editing-Fragments.db Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,47 @@ +<node>Fragments + <node>#include:ALA<value>fragments/ALA.db:/ALA</value></node> + <node>#include:ARG<value>fragments/ARG.db:/ARG</value></node> + <node>#include:ASP<value>fragments/ASP.db:/ASP</value></node> + <node>#include:ASN<value>fragments/ASN.db:/ASN</value></node> + <node>#include:CYS<value>fragments/CYS.db:/CYS</value></node> + <node>#include:GLN<value>fragments/GLN.db:/GLN</value></node> + <node>#include:GLU<value>fragments/GLU.db:/GLU</value></node> + <node>#include:GLY<value>fragments/GLY.db:/GLY</value></node> + <node>#include:HIS<value>fragments/HIS.db:/HIS</value></node> + <node>#include:ILE<value>fragments/ILE.db:/ILE</value></node> + <node>#include:LEU<value>fragments/LEU.db:/LEU</value></node> + <node>#include:LYS<value>fragments/LYS.db:/LYS</value></node> + <node>#include:MET<value>fragments/MET.db:/MET</value></node> + <node>#include:PHE<value>fragments/PHE.db:/PHE</value></node> + <node>#include:PRO<value>fragments/PRO.db:/PRO</value></node> + <node>#include:SER<value>fragments/SER.db:/SER</value></node> + <node>#include:THR<value>fragments/THR.db:/THR</value></node> + <node>#include:TRP<value>fragments/TRP.db:/TRP</value></node> + <node>#include:TYR<value>fragments/TYR.db:/TYR</value></node> + <node>#include:VAL<value>fragments/VAL.db:/VAL</value></node> + <node>#include:PCA<value>fragments/PCA.db:/PCA</value></node> + <node>#include:ACE<value>fragments/ACE.db:/ACE</value></node> + <node>#include:NME<value>fragments/NME.db:/NME</value></node> + <node>#include:CA<value>fragments/CA.db:/CA</value></node> + <node>#include:MG<value>fragments/MG.db:/MG</value></node> + <node>#include:ZN<value>fragments/ZN.db:/ZN</value></node> + <node>#include:HOH<value>fragments/HOH.db:/HOH</value></node> + <node>#include:A<value>fragments/A.db:/A</value></node> + <node>#include:C<value>fragments/C.db:/C</value></node> + <node>#include:G<value>fragments/G.db:/G</value></node> + <node>#include:T<value>fragments/T.db:/T</value></node> + <node>#include:U<value>fragments/U.db:/U</value></node> + <node>#include:Pyrrole-Skeleton<value>fragments/Pyrrole-Skeleton.db:/Pyrrole-Skeleton</value></node> + <node>#include:Benzene-Skeleton<value>fragments/Benzene-Skeleton.db:/Benzene-Skeleton</value></node> + <node>#include:Indole-Skeleton<value>fragments/Indole-Skeleton.db:/Indole-Skeleton</value></node> +</node> +<node>Names + <node>#include:Discover<value>fragments/Names.Discover.db:/Discover</value></node> + <node>#include:Amber<value>fragments/Names.Amber.db:/Amber</value></node> + <node>#include:CHARMM<value>fragments/Names.CHARMM.db:/CHARMM</value></node> + <node>#include:XPLOR<value>fragments/Names.XPLOR.db:/XPLOR</value></node> + <node>#include:Star<value>fragments/Names.Star.db:/Star</value></node> +</node> +<node>Defaults + <node>Naming<value>PDB</value></node> +</node>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/fragments/Fragments.db Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,46 @@ +<node>Fragments + <node>#include:ALA<value>fragments/ALA.db:/ALA</value></node> + <node>#include:ARG<value>fragments/ARG.db:/ARG</value></node> + <node>#include:ASP<value>fragments/ASP.db:/ASP</value></node> + <node>#include:ASN<value>fragments/ASN.db:/ASN</value></node> + <node>#include:CYS<value>fragments/CYS.db:/CYS</value></node> + <node>#include:GLN<value>fragments/GLN.db:/GLN</value></node> + <node>#include:GLU<value>fragments/GLU.db:/GLU</value></node> + <node>#include:GLY<value>fragments/GLY.db:/GLY</value></node> + <node>#include:HIS<value>fragments/HIS.db:/HIS</value></node> + <node>#include:ILE<value>fragments/ILE.db:/ILE</value></node> + <node>#include:LEU<value>fragments/LEU.db:/LEU</value></node> + <node>#include:LYS<value>fragments/LYS.db:/LYS</value></node> + <node>#include:MET<value>fragments/MET.db:/MET</value></node> + <node>#include:MSE<value>fragments/MSE.db:/MSE</value></node> + <node>#include:PHE<value>fragments/PHE.db:/PHE</value></node> + <node>#include:PRO<value>fragments/PRO.db:/PRO</value></node> + <node>#include:SER<value>fragments/SER.db:/SER</value></node> + <node>#include:THR<value>fragments/THR.db:/THR</value></node> + <node>#include:TRP<value>fragments/TRP.db:/TRP</value></node> + <node>#include:TYR<value>fragments/TYR.db:/TYR</value></node> + <node>#include:VAL<value>fragments/VAL.db:/VAL</value></node> + <node>#include:PCA<value>fragments/PCA.db:/PCA</value></node> + <node>#include:ACE<value>fragments/ACE.db:/ACE</value></node> + <node>#include:NME<value>fragments/NME.db:/NME</value></node> + <node>#include:CA<value>fragments/CA.db:/CA</value></node> + <node>#include:MG<value>fragments/MG.db:/MG</value></node> + <node>#include:ZN<value>fragments/ZN.db:/ZN</value></node> + <node>#include:HOH<value>fragments/HOH.db:/HOH</value></node> + <node>#include:A<value>fragments/A.db:/A</value></node> + <node>#include:C<value>fragments/C.db:/C</value></node> + <node>#include:G<value>fragments/G.db:/G</value></node> + <node>#include:T<value>fragments/T.db:/T</value></node> + <node>#include:U<value>fragments/U.db:/U</value></node> +</node> +<node>Names + <node>#include:Discover<value>fragments/Names.Discover.db:/Discover</value></node> + <node>#include:Amber<value>fragments/Names.Amber.db:/Amber</value></node> + <node>#include:CHARMM<value>fragments/Names.CHARMM.db:/CHARMM</value></node> + <node>#include:XPLOR<value>fragments/Names.XPLOR.db:/XPLOR</value></node> + <node>#include:Star<value>fragments/Names.Star.db:/Star</value></node> + <node>#include:DNA<value>fragments/Names.DNA.db:/DNA</value></node> +</node> +<node>Defaults + <node>Naming<value>PDB</value></node> +</node>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/fragments/G.db Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,107 @@ +<node>G + <node>Names + <node>Guanine</node> + <node>Guanin</node> + <node>G</node> + </node> + <node>Atoms + <node>P<value>P 32.612 26.662 40.051</value></node> + <node>O1P<value>O 33.579 26.377 41.135</value></node> + <node>O2P<value>O 32.257 25.612 39.055</value></node> + <node>O5*<value>O 31.233 27.248 40.656</value></node> + <node>C5*<value>C 31.159 28.416 41.468</value></node> + <node>1H5*<value>H 32.062 29.003 41.301</value></node> + <node>2H5*<value>H 31.095 28.140 42.520</value></node> + <node>C4*<value>C 29.940 29.254 41.095</value></node> + <node>H4*<value>H 29.785 30.090 41.777</value></node> + <node>O4*<value>O 30.102 29.870 39.801</value></node> + <node>C3*<value>C 28.712 28.348 41.021</value></node> + <node>O3*<value>O 27.645 28.918 41.772</value></node> + <node>H3*<value>H 28.886 27.326 41.358</value></node> + <node>C2*<value>C 28.364 28.341 39.559</value></node> + <node>1H2*<value>H 28.348 27.314 39.193</value></node> + <node>2H2*<value>H 27.382 28.792 39.416</value></node> + <node>C1*<value>C 28.928 29.637 39.018</value></node> + <node>H1*<value>H 28.284 30.517 39.013</value></node> + <node>N9<value>N 29.311 29.477 37.601</value></node> + <node>C8<value>C 30.238 28.616 37.067</value></node> + <node>H8<value>H 30.771 27.925 37.703</value></node> + <node>N7<value>N 30.381 28.736 35.780</value></node> + <node>C5<value>C 29.485 29.746 35.436</value></node> + <node>C6<value>C 29.204 30.305 34.166</value></node> + <node>O6<value>O 29.745 30.037 33.101</value></node> + <node>N1<value>N 28.225 31.296 34.247</value></node> + <node>1H<value>H 27.948 31.750 33.400</value></node> + <node>C2<value>C 27.605 31.699 35.418</value></node> + <node>N2<value>N 26.693 32.662 35.319</value></node> + <node>1H2<value>H 26.407 33.145 34.479</value></node> + <node>2H2<value>H 26.252 32.956 36.179</value></node> + <node>N3<value>N 27.881 31.170 36.610</value></node> + <node>C4<value>C 28.823 30.204 36.543</value></node> + </node> + <node>Bonds + <node>1<value>P O1P s</value></node> + <node>2<value>P O2P d</value></node> + <node>3<value>P O5* s</value></node> + <node>4<value>O5* C5* s</value></node> + <node>5<value>C5* C4* s</value></node> + <node>6<value>C4* O4* s</value></node> + <node>7<value>C4* C3* s</value></node> + <node>8<value>C3* O3* s</value></node> + <node>9<value>C3* C2* s</value></node> + <node>10<value>C2* C1* s</value></node> + <node>11<value>C1* O4* s</value></node> + <node>12<value>C1* N9 s</value></node> + <node>13<value>N9 C8 s</value></node> + <node>14<value>C8 N7 d</value></node> + <node>15<value>N7 C5 s</value></node> + <node>16<value>C5 C4 d</value></node> + <node>17<value>C4 N9 s</value></node> + <node>18<value>C5 C6 s</value></node> + <node>19<value>C6 O6 d</value></node> + <node>20<value>C6 N1 s</value></node> + <node>21<value>N1 C2 s</value></node> + <node>22<value>C2 N2 s</value></node> + <node>23<value>C2 N3 d</value></node> + <node>24<value>N3 C4 s</value></node> + <node>25<value>C5* 1H5* s</value></node> + <node>26<value>C5* 2H5* s</value></node> + <node>27<value>C4* H4* s</value></node> + <node>28<value>C1* H1* s</value></node> + <node>29<value>C3* H3* s</value></node> + <node>30<value>C2* 1H2* s</value></node> + <node>31<value>C2* 2H2* s</value></node> + <node>32<value>C8 H8 s</value></node> + <node>33<value>N1 1H s</value></node> + <node>34<value>N2 1H2 s</value></node> + <node>35<value>N2 2H2 s</value></node> + </node> + <node>Connections + <node>5-term<value>P 3-term s 1.62 0.5</value></node> + <node>3-term<value>O3* 5-term s 1.62 0.5</value></node> + </node> + <node>Properties + <node>NUCLEOTIDE</node> + </node> + <node>Variants + <node>G-M + <node>Properties + <node>5_PRIME</node> + <node>3_PRIME</node> + </node> + </node> + <node>Default + <node>Properties + </node> + </node> + <node>G-5 + <node>Properties + <node>5_PRIME</node> + </node> + <node>G-3 + <node>Properties + <node>3_PRIME</node> + </node> + </node> + </node> +</node>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/fragments/GLN.db Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,96 @@ +<node>GLN + <node>Names + <node>Glutamine</node> + <node>Glutamin</node> + <node>Gln</node> + <node>Q</node> + </node> + <node>Atoms + <node>N<value>N -1.694353 -0.2940789 3.487573</value></node> + <node>3H<value>H -1.993324 -0.7771879 2.60663</value></node> + <node>CA<value>C -1.339968 1.106833 3.061471</value></node> + <node>HA<value>H -2.035373 1.840381 3.535663</value></node> + <node>C<value>C -1.613526 1.110178 1.459362</value></node> + <node>O<value>O -1.452083 2.138383 0.8146671</value></node> + <node>CB<value>C 0.1053884 1.466314 3.38408</value></node> + <node>2HB<value>H 0.4078564 1.068117 4.376333</value></node> + <node>1HB<value>H 0.7844938 0.9955081 2.644168</value></node> + <node>CG<value>C 0.2953307 2.976142 3.377398</value></node> + <node>2HG<value>H -0.08479181 3.405704 2.425381</value></node> + <node>1HG<value>H -0.3113416 3.443596 4.179154</value></node> + <node>CD<value>C 1.757013 3.318817 3.588054</value></node> + <node>OE1<value>O 2.263759 3.493683 4.689262</value></node> + <node>NE2<value>N 2.607646 3.349533 2.459146</value></node> + <node>2HE2<value>H 3.553186 3.659591 2.602335</value></node> + <node>1HE2<value>H 2.182977 3.3032491 1.543895</value></node> + <node>OXT<value>O -2.00241 -0.02523248 1.056456</value></node> + <node>2H<value>H -2.440811 -0.2844597 4.149324</value></node> + <node>1H<value>H -0.9086809 -0.7656706 3.887856</value></node> + </node> + <node>Bonds + <node>1<value>3H N s</value></node> + <node>2<value>CA N s</value></node> + <node>3<value>HA CA s</value></node> + <node>4<value>C CA s</value></node> + <node>5<value>O C d</value></node> + <node>6<value>CB CA s</value></node> + <node>7<value>2HB CB s</value></node> + <node>8<value>1HB CB s</value></node> + <node>9<value>CG CB s</value></node> + <node>10<value>2HG CG s</value></node> + <node>11<value>1HG CG s</value></node> + <node>12<value>CD CG s</value></node> + <node>13<value>OE1 CD d</value></node> + <node>14<value>NE2 CD s</value></node> + <node>15<value>2HE2 NE2 s</value></node> + <node>16<value>1HE2 NE2 s</value></node> + <node>17<value>OXT C s</value></node> + <node>18<value>2H N s</value></node> + <node>19<value>1H N s</value></node> + </node> + <node>Connections + <node>N-term<value>N C-term s 1.33 0.5</value></node> + <node>C-term<value>C N-term s 1.33 0.5</value></node> + </node> + <node>Properties + <node>AMINO_ACID</node> + </node> + <node>Variants + <node>Default + <node>Delete + <node>OXT</node> + <node>1H</node> + <node>2H</node> + </node> + <node>Rename + <node>3H<value>H</value></node> + </node> + </node> + <node>GLN-M + <node>Properties + <node>C_TERMINAL</node> + <node>N_TERMINAL</node> + </node> + </node> + <node>GLN-C + <node>Delete + <node>1H</node> + <node>2H</node> + </node> + <node>Rename + <node>3H<value>H</value></node> + </node> + <node>Properties + <node>C_TERMINAL</node> + </node> + </node> + <node>GLN-N + <node>Delete + <node>OXT</node> + </node> + <node>Properties + <node>N_TERMINAL</node> + </node> + </node> + </node> +</node>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/fragments/GLU.db Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,92 @@ +<node>GLU + <node>Names + <node>Glutamate</node> + <node>Glutamat</node> + <node>Glu</node> + <node>Q</node> + </node> + <node>Atoms + <node>N<value>N 0.09036078 1.20944 -0.09877955</value></node> + <node>3H<value>H 0.992178 1.663159 -0.02552702</value></node> + <node>CA<value>C -0.6644503 1.887128 -1.167784</value></node> + <node>HA<value>H -0.1401839 1.690991 -2.10393</value></node> + <node>C<value>C -0.6415405 3.403009 -0.9416856</value></node> + <node>O<value>O 0.5018099 3.910433 -0.8834405</value></node> + <node>CB<value>C -2.078524 1.299661 -1.288965</value></node> + <node>1HB<value>H -2.006071 0.2127525 -1.352877</value></node> + <node>2HB<value>H -2.670931 1.54428 -0.4052964</value></node> + <node>CG<value>C -2.807634 1.790975 -2.546677</value></node> + <node>1HG<value>H -2.881274 2.877187 -2.559357</value></node> + <node>2HG<value>H -2.268831 1.463546 -3.436255</value></node> + <node>CD<value>C -4.223983 1.236637 -2.597517</value></node> + <node>OE1<value>O -5.044554 1.733033 -1.797006</value></node> + <node>OE2<value>O -4.450723 0.3260741 -3.421581</value></node> + <node>1H<value>H -0.4043283 1.301303 0.7769806</value></node> + <node>2H<value>H 0.2085563 0.2320959 -0.3244812</value></node> + <node>OXT<value>O -1.674247 3.928742 -0.470977</value></node> + </node> + <node>Bonds + <node>5<value>3H N s</value></node> + <node>6<value>CA N s</value></node> + <node>10<value>HA CA s</value></node> + <node>11<value>C CA s</value></node> + <node>14<value>O C d</value></node> + <node>15<value>CB CA s</value></node> + <node>19<value>1HB CB s</value></node> + <node>20<value>2HB CB s</value></node> + <node>21<value>CG CB s</value></node> + <node>25<value>1HG CG s</value></node> + <node>26<value>2HG CG s</value></node> + <node>27<value>CD CG s</value></node> + <node>30<value>OE1 CD a</value></node> + <node>31<value>OE2 CD a</value></node> + <node>32<value>1H N s</value></node> + <node>33<value>2H N s</value></node> + <node>34<value>OXT C s</value></node> + </node> + <node>Connections + <node>N-term<value>N C-term s 1.33 0.5</value></node> + <node>C-term<value>C N-term s 1.33 0.5</value></node> + </node> + <node>Properties + <node>AMINO_ACID</node> + </node> + <node>Variants + <node>Default + <node>Delete + <node>OXT</node> + <node>1H</node> + <node>2H</node> + </node> + <node>Rename + <node>3H<value>H</value></node> + </node> + </node> + <node>GLU-M + <node>Properties + <node>C_TERMINAL</node> + <node>N_TERMINAL</node> + </node> + </node> + <node>GLU-C + <node>Delete + <node>1H</node> + <node>2H</node> + </node> + <node>Rename + <node>3H<value>H</value></node> + </node> + <node>Properties + <node>C_TERMINAL</node> + </node> + </node> + <node>GLU-N + <node>Delete + <node>OXT</node> + </node> + <node>Properties + <node>N_TERMINAL</node> + </node> + </node> + </node> +</node>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/fragments/GLY.db Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,76 @@ +<node>GLY + <node>Names + <node>Glycine</node> + <node>Glycin</node> + <node>Gly</node> + <node>G</node> + </node> + <node>Atoms + <node>N<value>N 0.09000722 1.216287 -0.1108443</value></node> + <node>3H<value>H 0.8807056 1.803007 0.1270226</value></node> + <node>CA<value>C -0.6332095 1.869306 -1.215941</value></node> + <node>1HA<value>H -0.02850649 1.801736 -2.120623</value></node> + <node>2HA<value>H -1.579168 1.352425 -1.380715</value></node> + <node>C<value>C -0.8818576 3.344497 -0.910938</value></node> + <node>O<value>O 0.06351577 3.962237 -0.3713815</value></node> + <node>1H<value>H -0.5183882 1.138782 0.691625</value></node> + <node>2H<value>H 0.4027565 0.2984461 -0.3934918</value></node> + <node>OXT<value>O -1.901015 3.866009 -1.413833</value></node> + </node> + <node>Bonds + <node>5<value>3H N s</value></node> + <node>6<value>CA N s</value></node> + <node>10<value>1HA CA s</value></node> + <node>11<value>2HA CA s</value></node> + <node>12<value>C CA s</value></node> + <node>15<value>O C d</value></node> + <node>16<value>1H N s</value></node> + <node>17<value>2H N s</value></node> + <node>18<value>OXT C s</value></node> + </node> + <node>Connections + <node>N-term<value>N C-term s 1.33 0.5</value></node> + <node>C-term<value>C N-term s 1.33 0.5</value></node> + </node> + <node>Properties + <node>AMINO_ACID</node> + </node> + <node>Variants + <node>Default + <node>Delete + <node>OXT</node> + <node>1H</node> + <node>2H</node> + </node> + <node>Rename + <node>3H<value>H</value></node> + </node> + </node> + <node>GLY-M + <node>Properties + <node>C_TERMINAL</node> + <node>N_TERMINAL</node> + </node> + </node> + <node>GLY-C + <node>Delete + <node>1H</node> + <node>2H</node> + </node> + <node>Rename + <node>3H<value>H</value></node> + </node> + <node>Properties + <node>C_TERMINAL</node> + </node> + </node> + <node>GLY-N + <node>Delete + <node>OXT</node> + </node> + <node>Properties + <node>N_TERMINAL</node> + </node> + </node> + </node> +</node>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/fragments/HIS.db Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,99 @@ +<node>HIS + <node>Names + <node>Histidine</node> + <node>Histidin</node> + <node>His</node> + <node>H</node> + </node> + <node>Atoms + <node>N<value>N 0.2528806 1.616447 -0.2212145</value></node> + <node>3H<value>H 0.7991534 2.328624 0.245802</value></node> + <node>CA<value>C -0.9251888 2.215651 -0.8776516</value></node> + <node>HA<value>H -0.5465931 2.966134 -1.573552</value></node> + <node>C<value>C -1.833067 2.919479 0.1419996</value></node> + <node>O<value>O -2.654072 3.735267 -0.3389743</value></node> + <node>CB<value>C -1.677425 1.144471 -1.688265</value></node> + <node>1HB<value>H -0.9314069 0.53022 -2.195623</value></node> + <node>2HB<value>H -2.228334 0.4977131 -1.00345</value></node> + <node>CG<value>C -2.625881 1.668474 -2.74672</value></node> + <node>ND1<value>N -3.385668 2.821612 -2.671887</value></node> + <node>HD1<value>H -3.38348 3.467654 -1.88095</value></node> + <node>CD2<value>C -2.893428 1.068907 -3.947961</value></node> + <node>HD2<value>H -2.46763 0.1453506 -4.317409</value></node> + <node>CE1<value>C -4.09971 2.924621 -3.807559</value></node> + <node>HE1<value>H -4.788648 3.724259 -4.045286</value></node> + <node>NE2<value>N -3.815619 1.869323 -4.597533</value></node> + <node>HE2<value>H -4.210977 1.69118 -5.511979</value></node> + <node>1H<value>H -0.05550323 0.9331897 0.4557269</value></node> + <node>2H<value>H 0.827899 1.162407 -0.9164186</value></node> + <node>OXT<value>O -1.921441 2.400639 1.276749</value></node> + </node> + <node>Bonds + <node>5<value>3H N s</value></node> + <node>6<value>CA N s</value></node> + <node>10<value>HA CA s</value></node> + <node>11<value>C CA s</value></node> + <node>14<value>O C d</value></node> + <node>15<value>CB CA s</value></node> + <node>19<value>1HB CB s</value></node> + <node>20<value>2HB CB s</value></node> + <node>21<value>CG CB s</value></node> + <node>24<value>ND1 CG a</value></node> + <node>27<value>HD1 ND1 s</value></node> + <node>28<value>CD2 CG a</value></node> + <node>31<value>HD2 CD2 s</value></node> + <node>32<value>CE1 ND1 a</value></node> + <node>35<value>HE1 CE1 s</value></node> + <node>36<value>NE2 CE1 a</value></node> + <node>37<value>NE2 CD2 a</value></node> + <node>39<value>HE2 NE2 s</value></node> + <node>40<value>1H N s</value></node> + <node>41<value>2H N s</value></node> + <node>42<value>OXT C s</value></node> + </node> + <node>Connections + <node>N-term<value>N C-term s 1.33 0.5</value></node> + <node>C-term<value>C N-term s 1.33 0.5</value></node> + </node> + <node>Properties + <node>AMINO_ACID</node> + </node> + <node>Variants + <node>Default + <node>Delete + <node>OXT</node> + <node>1H</node> + <node>2H</node> + </node> + <node>Rename + <node>3H<value>H</value></node> + </node> + </node> + <node>HIS-M + <node>Properties + <node>C_TERMINAL</node> + <node>N_TERMINAL</node> + </node> + </node> + <node>HIS-C + <node>Delete + <node>1H</node> + <node>2H</node> + </node> + <node>Rename + <node>3H<value>H</value></node> + </node> + <node>Properties + <node>C_TERMINAL</node> + </node> + </node> + <node>HIS-N + <node>Delete + <node>OXT</node> + </node> + <node>Properties + <node>N_TERMINAL</node> + </node> + </node> + </node> +</node>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/fragments/HOH.db Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,21 @@ +<node>HOH + <node>Names + <node>Water</node> + </node> + <node>Atoms + <node>O <value>O 15.118 9.944 8.582</value></node> + <node>1H<value>H 15.211 9.386 7.809</value></node> + <node>2H<value>H 14.173 9.992 8.730</value></node> + </node> + <node>Bonds + <node>1<value>1H O s</value></node> + <node>2<value>2H O s</value></node> + </node> + <node>Connections + </node> + <node>Properties + </node> + <node>Variants + <node>Default</node> + </node> +</node>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/fragments/ILE.db Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,100 @@ +<node>ILE + <node>Names + <node>Isoleucine</node> + <node>Isoleucin</node> + <node>Ile</node> + <node>I</node> + </node> + <node>Atoms + <node>N<value>N 0.1219419 1.159209 -0.1919851</value></node> + <node>3H<value>H 0.9740559 1.689959 -0.04711162</value></node> + <node>CA<value>C -0.7030041 1.935257 -1.138673</value></node> + <node>HA<value>H -0.2842833 1.745549 -2.127681</value></node> + <node>C<value>C -0.5392811 3.43721 -0.8683466</value></node> + <node>O<value>O 0.4636989 3.750649 -0.1867381</value></node> + <node>CB<value>C -2.165631 1.439687 -1.121375</value></node> + <node>HB<value>H -2.124804 0.349284 -1.14618</value></node> + <node>CG1<value>C -2.945574 1.890833 -2.370761</value></node> + <node>1HG1<value>H -3.189406 2.951118 -2.312008</value></node> + <node>2HG1<value>H -2.330654 1.72068 -3.255403</value></node> + <node>CG2<value>C -2.890608 1.852801 0.1693949</value></node> + <node>1HG2<value>H -3.851115 1.343782 0.2388784</value></node> + <node>2HG2<value>H -2.299751 1.573039 1.041283</value></node> + <node>3HG2<value>H -3.060911 2.929328 0.1868919</value></node> + <node>CD1<value>C -4.249351 1.108805 -2.558935</value></node> + <node>1HD1<value>H -4.709754 1.403511 -3.502415</value></node> + <node>2HD1<value>H -4.043807 0.03831363 -2.586494</value></node> + <node>3HD1<value>H -4.947758 1.324118 -1.751006</value></node> + <node>1H<value>H -0.3580201 1.071109 0.6916124</value></node> + <node>2H<value>H 0.3236403 0.2433889 -0.5670705</value></node> + <node>OXT<value>O -1.135264 4.21782 -1.641576</value></node> + </node> + <node>Bonds + <node>5<value>3H N s</value></node> + <node>6<value>CA N s</value></node> + <node>10<value>HA CA s</value></node> + <node>11<value>C CA s</value></node> + <node>14<value>O C d</value></node> + <node>15<value>CB CA s</value></node> + <node>19<value>HB CB s</value></node> + <node>20<value>CG1 CB s</value></node> + <node>24<value>1HG1 CG1 s</value></node> + <node>25<value>2HG1 CG1 s</value></node> + <node>26<value>CG2 CB s</value></node> + <node>30<value>1HG2 CG2 s</value></node> + <node>31<value>2HG2 CG2 s</value></node> + <node>32<value>3HG2 CG2 s</value></node> + <node>33<value>CD1 CG1 s</value></node> + <node>37<value>1HD1 CD1 s</value></node> + <node>38<value>2HD1 CD1 s</value></node> + <node>39<value>3HD1 CD1 s</value></node> + <node>40<value>1H N s</value></node> + <node>41<value>2H N s</value></node> + <node>42<value>OXT C s</value></node> + </node> + <node>Connections + <node>N-term<value>N C-term s 1.33 0.5</value></node> + <node>C-term<value>C N-term s 1.33 0.5</value></node> + </node> + <node>Properties + <node>AMINO_ACID</node> + </node> + <node>Variants + <node>Default + <node>Delete + <node>OXT</node> + <node>1H</node> + <node>2H</node> + </node> + <node>Rename + <node>3H<value>H</value></node> + </node> + </node> + <node>ILE-M + <node>Properties + <node>C_TERMINAL</node> + <node>N_TERMINAL</node> + </node> + </node> + <node>ILE-C + <node>Delete + <node>1H</node> + <node>2H</node> + </node> + <node>Rename + <node>3H<value>H</value></node> + </node> + <node>Properties + <node>C_TERMINAL</node> + </node> + </node> + <node>ILE-N + <node>Delete + <node>OXT</node> + </node> + <node>Properties + <node>N_TERMINAL</node> + </node> + </node> + </node> +</node>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/fragments/Indole-Skeleton.db Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,30 @@ +<node>Indole-Skeleton + <node>Names + <node>Indole-Skeleton</node> + </node> + <node>Atoms + <node>C1<value>C 0.098272 0.968184 -2.108448</value></node> + <node>N2<value>N 0.106846 2.054217 -1.259124</value></node> + <node>C3<value>C 0.08464 1.665738 0.063892</value></node> + <node>C4<value>C 0.060104 0.240281 0.014949</value></node> + <node>C5<value>C 0.062069 -0.174574 -1.386187</value></node> + <node>C6<value>C 0.084854 2.377612 1.27264</value></node> + <node>C7<value>C 0.060305 1.667968 2.483589</value></node> + <node>C8<value>C 0.039354 0.262233 2.470668</value></node> + <node>C9<value>C 0.039595 -0.441663 1.251419</value></node> + </node> + <node>Bonds + <node>1<value>C1 N2 s</value></node> + <node>2<value>N2 C3 s</value></node> + <node>3<value>C3 C4 d</value></node> + <node>4<value>C4 C5 s</value></node> + <node>5<value>C5 C1 d</value></node> + <node>6<value>C3 C6 s</value></node> + <node>7<value>C6 C7 d</value></node> + <node>8<value>C7 C8 s</value></node> + <node>9<value>C8 C9 d</value></node> + <node>10<value>C9 C4 s</value></node> + </node> + <node>Properties + </node> +</node>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/fragments/LEU.db Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,100 @@ +<node>LEU + <node>Names + <node>Leucine</node> + <node>Leucin</node> + <node>Leu</node> + <node>L</node> + </node> + <node>Atoms + <node>N<value>N -0.003476313 1.235853 0.02699674</value></node> + <node>3H<value>H 0.7720473 1.82942 0.3005252</value></node> + <node>CA<value>C -0.6514053 1.883178 -1.129898</value></node> + <node>HA<value>H -0.07017973 1.598957 -2.006831</value></node> + <node>C<value>C -0.5708863 3.410168 -0.9936234</value></node> + <node>O<value>O 0.1419036 3.827524 -0.05211589</value></node> + <node>CB<value>C -2.091007 1.359104 -1.274005</value></node> + <node>1HB<value>H -2.046227 0.2694775 -1.310338</value></node> + <node>2HB<value>H -2.646399 1.642544 -0.3785246</value></node> + <node>CG<value>C -2.872831 1.847369 -2.507179</value></node> + <node>HG<value>H -3.019899 2.926006 -2.455012</value></node> + <node>CD1<value>C -2.162796 1.498542 -3.821336</value></node> + <node>1HD1<value>H -2.800384 1.766798 -4.664294</value></node> + <node>2HD1<value>H -1.228827 2.051352 -3.913459</value></node> + <node>3HD1<value>H -1.954294 0.4288859 -3.861405</value></node> + <node>CD2<value>C -4.261661 1.198464 -2.502073</value></node> + <node>1HD2<value>H -4.845348 1.564912 -3.347144</value></node> + <node>2HD2<value>H -4.171115 0.1141629 -2.575422</value></node> + <node>3HD2<value>H -4.785489 1.451318 -1.579679</value></node> + <node>OXT<value>O -0.8228753 4.072413 -2.02374</value></node> + <node>1H<value>H -0.6580312 1.186075 0.7945588</value></node> + <node>2H<value>H 0.3136166 0.3082535 -0.2161924</value></node> + </node> + <node>Bonds + <node>5<value>3H N s</value></node> + <node>6<value>CA N s</value></node> + <node>10<value>HA CA s</value></node> + <node>11<value>C CA s</value></node> + <node>14<value>O C d</value></node> + <node>15<value>CB CA s</value></node> + <node>19<value>1HB CB s</value></node> + <node>20<value>2HB CB s</value></node> + <node>21<value>CG CB s</value></node> + <node>25<value>HG CG s</value></node> + <node>26<value>CD1 CG s</value></node> + <node>30<value>1HD1 CD1 s</value></node> + <node>31<value>2HD1 CD1 s</value></node> + <node>32<value>3HD1 CD1 s</value></node> + <node>33<value>CD2 CG s</value></node> + <node>37<value>1HD2 CD2 s</value></node> + <node>38<value>2HD2 CD2 s</value></node> + <node>39<value>3HD2 CD2 s</value></node> + <node>40<value>OXT C s</value></node> + <node>41<value>1H N s</value></node> + <node>42<value>2H N s</value></node> + </node> + <node>Connections + <node>N-term<value>N C-term s 1.33 0.5</value></node> + <node>C-term<value>C N-term s 1.33 0.5</value></node> + </node> + <node>Properties + <node>AMINO_ACID</node> + </node> + <node>Variants + <node>Default + <node>Delete + <node>OXT</node> + <node>1H</node> + <node>2H</node> + </node> + <node>Rename + <node>3H<value>H</value></node> + </node> + </node> + <node>LEU-M + <node>Properties + <node>C_TERMINAL</node> + <node>N_TERMINAL</node> + </node> + </node> + <node>LEU-C + <node>Delete + <node>1H</node> + <node>2H</node> + </node> + <node>Rename + <node>3H<value>H</value></node> + </node> + <node>Properties + <node>C_TERMINAL</node> + </node> + </node> + <node>LEU-N + <node>Delete + <node>OXT</node> + </node> + <node>Properties + <node>N_TERMINAL</node> + </node> + </node> + </node> +</node>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/fragments/LYS.db Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,106 @@ +<node>LYS + <node>Names + <node>Lysine</node> + <node>Lysin</node> + <node>Lys</node> + <node>K</node> + </node> + <node>Atoms + <node>N<value>N 0.03796386 1.172592 -0.009692425</value></node> + <node>3H<value>H 1.016744 1.426445 0.004398665</value></node> + <node>CA<value>C -0.6562778 1.887361 -1.097957</value></node> + <node>HA<value>H -0.1455905 1.623495 -2.025311</value></node> + <node>C<value>C -0.5601511 3.406333 -0.9147748</value></node> + <node>O<value>O -0.5440148 4.087965 -1.963232</value></node> + <node>CB<value>C -2.114089 1.411355 -1.200695</value></node> + <node>1HB<value>H -2.113627 0.3206328 -1.233166</value></node> + <node>2HB<value>H -2.662723 1.730462 -0.3130743</value></node> + <node>CG<value>C -2.816849 1.934443 -2.461919</value></node> + <node>1HG<value>H -2.878444 3.023734 -2.425601</value></node> + <node>2HG<value>H -2.232982 1.645706 -3.338356</value></node> + <node>CD<value>C -4.230651 1.346997 -2.563318</value></node> + <node>1HD<value>H -4.153291 0.2577495 -2.598617</value></node> + <node>2HD<value>H -4.790445 1.632903 -1.669734</value></node> + <node>CE<value>C -4.93697 1.869824 -3.82334</value></node> + <node>1HE<value>H -4.991973 2.959915 -3.77821</value></node> + <node>2HE<value>H -4.353527 1.590667 -4.70365</value></node> + <node>NZ<value>N -6.304516 1.325968 -3.962642</value></node> + <node>1HZ<value>H -6.733165 1.692468 -4.802127</value></node> + <node>2HZ<value>H -6.276195 0.31765 -4.027733</value></node> + <node>3HZ<value>H -6.870414 1.591293 -3.16824</value></node> + <node>1H<value>H -0.3857403 1.416816 0.8740513</value></node> + <node>2H<value>H -0.04427324 0.17682 -0.1571643</value></node> + <node>OXT<value>O -0.7869474 3.85405 0.2308864</value></node> + </node> + <node>Bonds + <node>5<value>3H N s</value></node> + <node>6<value>CA N s</value></node> + <node>10<value>HA CA s</value></node> + <node>11<value>C CA s</value></node> + <node>14<value>O C d</value></node> + <node>15<value>CB CA s</value></node> + <node>19<value>1HB CB s</value></node> + <node>20<value>2HB CB s</value></node> + <node>21<value>CG CB s</value></node> + <node>25<value>1HG CG s</value></node> + <node>26<value>2HG CG s</value></node> + <node>27<value>CD CG s</value></node> + <node>31<value>1HD CD s</value></node> + <node>32<value>2HD CD s</value></node> + <node>33<value>CE CD s</value></node> + <node>37<value>1HE CE s</value></node> + <node>38<value>2HE CE s</value></node> + <node>39<value>NZ CE s</value></node> + <node>43<value>1HZ NZ s</value></node> + <node>44<value>2HZ NZ s</value></node> + <node>45<value>3HZ NZ s</value></node> + <node>46<value>1H N s</value></node> + <node>47<value>2H N s</value></node> + <node>48<value>OXT C s</value></node> + </node> + <node>Connections + <node>N-term<value>N C-term s 1.33 0.5</value></node> + <node>C-term<value>C N-term s 1.33 0.5</value></node> + </node> + <node>Properties + <node>AMINO_ACID</node> + </node> + <node>Variants + <node>Default + <node>Delete + <node>OXT</node> + <node>1H</node> + <node>2H</node> + </node> + <node>Rename + <node>3H<value>H</value></node> + </node> + </node> + <node>LYS-M + <node>Properties + <node>C_TERMINAL</node> + <node>N_TERMINAL</node> + </node> + </node> + <node>LYS-C + <node>Delete + <node>1H</node> + <node>2H</node> + </node> + <node>Rename + <node>3H<value>H</value></node> + </node> + <node>Properties + <node>C_TERMINAL</node> + </node> + </node> + <node>LYS-N + <node>Delete + <node>OXT</node> + </node> + <node>Properties + <node>N_TERMINAL</node> + </node> + </node> + </node> +</node>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/fragments/MET.db Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,96 @@ +<node>MET + <node>Names + <node>Methionine</node> + <node>Methionin</node> + <node>Met</node> + <node>M</node> + </node> + <node>Atoms + <node>N<value>N 0.0654056 1.215812 -0.06949145</value></node> + <node>3H<value>H 0.9974914 1.608735 -0.04203663</value></node> + <node>CA<value>C -0.6988745 1.893029 -1.131979</value></node> + <node>HA<value>H -0.1911148 1.68141 -2.074138</value></node> + <node>C<value>C -0.6694928 3.410054 -0.9194202</value></node> + <node>O<value>O 0.4107355 3.973423 -1.201833</value></node> + <node>CB<value>C -2.121216 1.317703 -1.225039</value></node> + <node>1HB<value>H -2.050125 0.2325057 -1.312704</value></node> + <node>2HB<value>H -2.682049 1.549083 -0.318349</value></node> + <node>CG<value>C -2.887041 1.8377 -2.448318</value></node> + <node>1HG<value>H -2.99595 2.919347 -2.383954</value></node> + <node>2HG<value>H -2.322049 1.593525 -3.347709</value></node> + <node>SD<value>S -4.546617 1.137771 -2.634913</value></node> + <node>CE<value>C -5.081393 1.965263 -4.148402</value></node> + <node>1HE<value>H -6.08969 1.634787 -4.393987</value></node> + <node>2HE<value>H -5.078839 3.043304 -3.993342</value></node> + <node>3HE<value>H -4.404794 1.706412 -4.961773</value></node> + <node>OXT<value>O -1.565656 3.902471 -0.1992161</value></node> + <node>1H<value>H -0.3889995 1.363342 0.8203897</value></node> + <node>2H<value>H 0.1172404 0.226119 -0.264187</value></node> + </node> + <node>Bonds + <node>5<value>3H N s</value></node> + <node>6<value>CA N s</value></node> + <node>10<value>HA CA s</value></node> + <node>11<value>C CA s</value></node> + <node>14<value>O C d</value></node> + <node>15<value>CB CA s</value></node> + <node>19<value>1HB CB s</value></node> + <node>20<value>2HB CB s</value></node> + <node>21<value>CG CB s</value></node> + <node>25<value>1HG CG s</value></node> + <node>26<value>2HG CG s</value></node> + <node>27<value>SD CG s</value></node> + <node>33<value>CE SD s</value></node> + <node>37<value>1HE CE s</value></node> + <node>38<value>2HE CE s</value></node> + <node>39<value>3HE CE s</value></node> + <node>40<value>OXT C s</value></node> + <node>41<value>1H N s</value></node> + <node>42<value>2H N s</value></node> + </node> + <node>Connections + <node>N-term<value>N C-term s 1.33 0.5</value></node> + <node>C-term<value>C N-term s 1.33 0.5</value></node> + </node> + <node>Properties + <node>AMINO_ACID</node> + </node> + <node>Variants + <node>Default + <node>Delete + <node>OXT</node> + <node>1H</node> + <node>2H</node> + </node> + <node>Rename + <node>3H<value>H</value></node> + </node> + </node> + <node>MET-M + <node>Properties + <node>N_TERMINAL</node> + <node>C_TERMINAL</node> + </node> + </node> + <node>MET-C + <node>Delete + <node>1H</node> + <node>2H</node> + </node> + <node>Rename + <node>3H<value>H</value></node> + </node> + <node>Properties + <node>C_TERMINAL</node> + </node> + </node> + <node>MET-N + <node>Delete + <node>OXT</node> + </node> + <node>Properties + <node>N_TERMINAL</node> + </node> + </node> + </node> +</node>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/fragments/MG.db Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,18 @@ +<node>MG + <node>Names + <node>Magnesium ion</node> + <node>Mg2+</node> + </node> + <node>Atoms + <node>MG<value>Mg 0.0 0.0 0.0</value></node> + </node> + <node>Bonds + </node> + <node>Connections + </node> + <node>Properties + </node> + <node>Variants + <node>Default</node> + </node> +</node>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/fragments/MSE.db Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,95 @@ +<node>MSE + <node>Names + <node>Selenomethionine</node> + <node>Selenomethionin</node> + <node>Mse</node> + </node> + <node>Atoms + <node>N<value>N 0.0654056 1.215812 -0.06949145</value></node> + <node>3H<value>H 0.9974914 1.608735 -0.04203663</value></node> + <node>CA<value>C -0.6988745 1.893029 -1.131979</value></node> + <node>HA<value>H -0.1911148 1.68141 -2.074138</value></node> + <node>C<value>C -0.6694928 3.410054 -0.9194202</value></node> + <node>O<value>O 0.4107355 3.973423 -1.201833</value></node> + <node>CB<value>C -2.121216 1.317703 -1.225039</value></node> + <node>1HB<value>H -2.050125 0.2325057 -1.312704</value></node> + <node>2HB<value>H -2.682049 1.549083 -0.318349</value></node> + <node>CG<value>C -2.887041 1.8377 -2.448318</value></node> + <node>1HG<value>H -2.99595 2.919347 -2.383954</value></node> + <node>2HG<value>H -2.322049 1.593525 -3.347709</value></node> + <node>SE<value>Se -4.546617 1.137771 -2.634913</value></node> + <node>CE<value>C -5.081393 1.965263 -4.148402</value></node> + <node>1HE<value>H -6.08969 1.634787 -4.393987</value></node> + <node>2HE<value>H -5.078839 3.043304 -3.993342</value></node> + <node>3HE<value>H -4.404794 1.706412 -4.961773</value></node> + <node>OXT<value>O -1.565656 3.902471 -0.1992161</value></node> + <node>1H<value>H -0.3889995 1.363342 0.8203897</value></node> + <node>2H<value>H 0.1172404 0.226119 -0.264187</value></node> + </node> + <node>Bonds + <node>5<value>3H N s</value></node> + <node>6<value>CA N s</value></node> + <node>10<value>HA CA s</value></node> + <node>11<value>C CA s</value></node> + <node>14<value>O C d</value></node> + <node>15<value>CB CA s</value></node> + <node>19<value>1HB CB s</value></node> + <node>20<value>2HB CB s</value></node> + <node>21<value>CG CB s</value></node> + <node>25<value>1HG CG s</value></node> + <node>26<value>2HG CG s</value></node> + <node>27<value>SE CG s</value></node> + <node>33<value>CE SE s</value></node> + <node>37<value>1HE CE s</value></node> + <node>38<value>2HE CE s</value></node> + <node>39<value>3HE CE s</value></node> + <node>40<value>OXT C s</value></node> + <node>41<value>1H N s</value></node> + <node>42<value>2H N s</value></node> + </node> + <node>Connections + <node>N-term<value>N C-term s 1.33 0.5</value></node> + <node>C-term<value>C N-term s 1.33 0.5</value></node> + </node> + <node>Properties + <node>AMINO_ACID</node> + </node> + <node>Variants + <node>Default + <node>Delete + <node>OXT</node> + <node>1H</node> + <node>2H</node> + </node> + <node>Rename + <node>3H<value>H</value></node> + </node> + </node> + <node>MET-M + <node>Properties + <node>N_TERMINAL</node> + <node>C_TERMINAL</node> + </node> + </node> + <node>MET-C + <node>Delete + <node>1H</node> + <node>2H</node> + </node> + <node>Rename + <node>3H<value>H</value></node> + </node> + <node>Properties + <node>C_TERMINAL</node> + </node> + </node> + <node>MET-N + <node>Delete + <node>OXT</node> + </node> + <node>Properties + <node>N_TERMINAL</node> + </node> + </node> + </node> +</node>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/fragments/NME.db Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,46 @@ +<node>NME + <node>Names + <node>Methylamine</node> + </node> + <node>Atoms + <node>N<value>N 0.724 0.000 -0.079</value></node> + <node>CH3<value>C -0.742 0.000 0.011</value></node> + <node>1H<value>H 1.046 0.810 0.431</value></node> + <node>2H<value>H 1.046 -0.810 0.431</value></node> + <node>1HH3<value>H -1.139 -0.861 -0.527</value></node> + <node>2HH3<value>H -1.042 -0.056 1.057</value></node> + <node>3HH3<value>H -1.133 0.917 -0.431</value></node> + </node> + <node>Bonds + <node>1<value>N CH3 s</value></node> + <node>2<value>N 1H s</value></node> + <node>3<value>N 2H s</value></node> + <node>4<value>CH3 1HH3 s</value></node> + <node>5<value>CH3 2HH3 s</value></node> + <node>6<value>CH3 3HH3 s</value></node> + </node> + <node>Connections + <node>N-term<value>N C-term s 1.33 0.5</value></node> + </node> + <node>Properties + </node> + <node>Variants + <node>NME-C + <node>Delete + <node>2H</node> + </node> + <node>Rename + <node>1H<value>H</value></node> + </node> + <node>Properties + <node>C_TERMINAL</node> + </node> + </node> + <node>NME-M + <node>Properties + <node>C_TERMINAL</node> + <node>N_TERMINAL</node> + </node> + </node> + </node> +</node>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/fragments/Names.Amber.db Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,486 @@ +<node>Amber<value>PDB</value> + <node>*:H1<value>*:1H</value></node> + <node>*:H2<value>*:2H</value></node> + <node>*:H3<value>*:3H</value></node> + <node>*:N<value>*:N</value></node> + <node>*:C<value>*:C</value></node> + <node>*:O<value>*:O</value></node> + <node>*:H<value>*:H</value></node> + <node>ALA:CA<value>ALA:CA</value></node> + <node>ALA:HA<value>ALA:HA</value></node> + <node>ALA:CB<value>ALA:CB</value></node> + <node>ALA:HB1<value>ALA:1HB</value></node> + <node>ALA:HB2<value>ALA:2HB</value></node> + <node>ALA:HB3<value>ALA:3HB</value></node> + <node>ARG:CA<value>ARG:CA</value></node> + <node>ARG:HA<value>ARG:HA</value></node> + <node>ARG:CB<value>ARG:CB</value></node> + <node>ARG:HB2<value>ARG:1HB</value></node> + <node>ARG:HB3<value>ARG:2HB</value></node> + <node>ARG:CG<value>ARG:CG</value></node> + <node>ARG:HG2<value>ARG:1HG</value></node> + <node>ARG:HG3<value>ARG:2HG</value></node> + <node>ARG:CD<value>ARG:CD</value></node> + <node>ARG:HD2<value>ARG:1HD</value></node> + <node>ARG:HD3<value>ARG:2HD</value></node> + <node>ARG:NE<value>ARG:NE</value></node> + <node>ARG:HE<value>ARG:HE</value></node> + <node>ARG:CZ<value>ARG:CZ</value></node> + <node>ARG:NH1<value>ARG:NH1</value></node> + <node>ARG:HH11<value>ARG:1HH1</value></node> + <node>ARG:HH12<value>ARG:2HH1</value></node> + <node>ARG:NH2<value>ARG:NH2</value></node> + <node>ARG:HH21<value>ARG:1HH2</value></node> + <node>ARG:HH22<value>ARG:2HH2</value></node> + <node>ASN:CA<value>ASN:CA</value></node> + <node>ASN:HA<value>ASN:HA</value></node> + <node>ASN:CB<value>ASN:CB</value></node> + <node>ASN:HB2<value>ASN:1HB</value></node> + <node>ASN:HB3<value>ASN:2HB</value></node> + <node>ASN:CG<value>ASN:CG</value></node> + <node>ASN:OD1<value>ASN:OD1</value></node> + <node>ASN:ND2<value>ASN:ND2</value></node> + <node>ASN:HD21<value>ASN:1HD2</value></node> + <node>ASN:HD22<value>ASN:2HD2</value></node> + <node>ASP:CA<value>ASP:CA</value></node> + <node>ASP:HA<value>ASP:HA</value></node> + <node>ASP:CB<value>ASP:CB</value></node> + <node>ASP:HB2<value>ASP:1HB</value></node> + <node>ASP:HB3<value>ASP:2HB</value></node> + <node>ASP:CG<value>ASP:CG</value></node> + <node>ASP:OD1<value>ASP:OD1</value></node> + <node>ASP:OD2<value>ASP:OD2</value></node> + <node>CYS:CA<value>CYS:CA</value></node> + <node>CYS:HA<value>CYS:HA</value></node> + <node>CYS:CB<value>CYS:CB</value></node> + <node>CYS:HB2<value>CYS:1HB</value></node> + <node>CYS:HB3<value>CYS:2HB</value></node> + <node>CYS:SG<value>CYS:SG</value></node> + <node>CYS:HG<value>CYS:HG</value></node> + <node>CYS:HSG<value>CYS:HG</value></node> + <node>GLU:CA<value>GLU:CA</value></node> + <node>GLU:HA<value>GLU:HA</value></node> + <node>GLU:CB<value>GLU:CB</value></node> + <node>GLU:HB2<value>GLU:1HB</value></node> + <node>GLU:HB3<value>GLU:2HB</value></node> + <node>GLU:CG<value>GLU:CG</value></node> + <node>GLU:HG2<value>GLU:1HG</value></node> + <node>GLU:HG3<value>GLU:2HG</value></node> + <node>GLU:CD<value>GLU:CD</value></node> + <node>GLU:OE1<value>GLU:OE1</value></node> + <node>GLU:OE2<value>GLU:OE2</value></node> + <node>GLN:CA<value>GLN:CA</value></node> + <node>GLN:HA<value>GLN:HA</value></node> + <node>GLN:CB<value>GLN:CB</value></node> + <node>GLN:HB2<value>GLN:1HB</value></node> + <node>GLN:HB3<value>GLN:2HB</value></node> + <node>GLN:CG<value>GLN:CG</value></node> + <node>GLN:HG2<value>GLN:1HG</value></node> + <node>GLN:HG3<value>GLN:2HG</value></node> + <node>GLN:CD<value>GLN:CD</value></node> + <node>GLN:OE1<value>GLN:OE1</value></node> + <node>GLN:NE2<value>GLN:NE2</value></node> + <node>GLN:HE21<value>GLN:1HE2</value></node> + <node>GLN:HE22<value>GLN:2HE2</value></node> + <node>GLY:CA<value>GLY:CA</value></node> + <node>GLY:HA2<value>GLY:1HA</value></node> + <node>GLY:HA3<value>GLY:2HA</value></node> + <node>HIS:CA<value>HIS:CA</value></node> + <node>HIS:HA<value>HIS:HA</value></node> + <node>HIS:CB<value>HIS:CB</value></node> + <node>HIS:HB2<value>HIS:1HB</value></node> + <node>HIS:HB3<value>HIS:2HB</value></node> + <node>HIS:CG<value>HIS:CG</value></node> + <node>HIS:ND1<value>HIS:ND1</value></node> + <node>HIS:HD1<value>HIS:HD1</value></node> + <node>HIS:CE1<value>HIS:CE1</value></node> + <node>HIS:HE1<value>HIS:HE1</value></node> + <node>HIS:NE2<value>HIS:NE2</value></node> + <node>HIS:HE2<value>HIS:HE2</value></node> + <node>HIS:CD2<value>HIS:CD2</value></node> + <node>HIS:HD2<value>HIS:HD2</value></node> + <node>ILE:CA<value>ILE:CA</value></node> + <node>ILE:HA<value>ILE:HA</value></node> + <node>ILE:CB<value>ILE:CB</value></node> + <node>ILE:HB<value>ILE:HB</value></node> + <node>ILE:CG2<value>ILE:CG2</value></node> + <node>ILE:HG21<value>ILE:1HG2</value></node> + <node>ILE:HG22<value>ILE:2HG2</value></node> + <node>ILE:HG23<value>ILE:3HG2</value></node> + <node>ILE:CG1<value>ILE:CG1</value></node> + <node>ILE:HG12<value>ILE:1HG1</value></node> + <node>ILE:HG13<value>ILE:2HG1</value></node> + <node>ILE:CD1<value>ILE:CD1</value></node> + <node>ILE:HD11<value>ILE:1HD1</value></node> + <node>ILE:HD12<value>ILE:2HD1</value></node> + <node>ILE:HD13<value>ILE:3HD1</value></node> + <node>LEU:CA<value>LEU:CA</value></node> + <node>LEU:HA<value>LEU:HA</value></node> + <node>LEU:CB<value>LEU:CB</value></node> + <node>LEU:HB2<value>LEU:1HB</value></node> + <node>LEU:HB3<value>LEU:2HB</value></node> + <node>LEU:CG<value>LEU:CG</value></node> + <node>LEU:HG<value>LEU:HG</value></node> + <node>LEU:CD1<value>LEU:CD1</value></node> + <node>LEU:HD11<value>LEU:1HD1</value></node> + <node>LEU:HD12<value>LEU:2HD1</value></node> + <node>LEU:HD13<value>LEU:3HD1</value></node> + <node>LEU:CD2<value>LEU:CD2</value></node> + <node>LEU:HD21<value>LEU:1HD2</value></node> + <node>LEU:HD22<value>LEU:2HD2</value></node> + <node>LEU:HD23<value>LEU:3HD2</value></node> + <node>LYS:CA<value>LYS:CA</value></node> + <node>LYS:HA<value>LYS:HA</value></node> + <node>LYS:CB<value>LYS:CB</value></node> + <node>LYS:HB2<value>LYS:1HB</value></node> + <node>LYS:HB3<value>LYS:2HB</value></node> + <node>LYS:CG<value>LYS:CG</value></node> + <node>LYS:HG2<value>LYS:1HG</value></node> + <node>LYS:HG3<value>LYS:2HG</value></node> + <node>LYS:CD<value>LYS:CD</value></node> + <node>LYS:HD2<value>LYS:1HD</value></node> + <node>LYS:HD3<value>LYS:2HD</value></node> + <node>LYS:CE<value>LYS:CE</value></node> + <node>LYS:HE2<value>LYS:1HE</value></node> + <node>LYS:HE3<value>LYS:2HE</value></node> + <node>LYS:NZ<value>LYS:NZ</value></node> + <node>LYS:HZ1<value>LYS:1HZ</value></node> + <node>LYS:HZ2<value>LYS:2HZ</value></node> + <node>LYS:HZ3<value>LYS:3HZ</value></node> + <node>MET:CA<value>MET:CA</value></node> + <node>MET:HA<value>MET:HA</value></node> + <node>MET:CB<value>MET:CB</value></node> + <node>MET:HB2<value>MET:1HB</value></node> + <node>MET:HB3<value>MET:2HB</value></node> + <node>MET:CG<value>MET:CG</value></node> + <node>MET:HG2<value>MET:1HG</value></node> + <node>MET:HG3<value>MET:2HG</value></node> + <node>MET:SD<value>MET:SD</value></node> + <node>MET:CE<value>MET:CE</value></node> + <node>MET:HE1<value>MET:1HE</value></node> + <node>MET:HE2<value>MET:2HE</value></node> + <node>MET:HE3<value>MET:3HE</value></node> + <node>PHE:CA<value>PHE:CA</value></node> + <node>PHE:HA<value>PHE:HA</value></node> + <node>PHE:CB<value>PHE:CB</value></node> + <node>PHE:HB2<value>PHE:1HB</value></node> + <node>PHE:HB3<value>PHE:2HB</value></node> + <node>PHE:CG<value>PHE:CG</value></node> + <node>PHE:CD1<value>PHE:CD1</value></node> + <node>PHE:HD1<value>PHE:HD1</value></node> + <node>PHE:CE1<value>PHE:CE1</value></node> + <node>PHE:HE1<value>PHE:HE1</value></node> + <node>PHE:CZ<value>PHE:CZ</value></node> + <node>PHE:HZ<value>PHE:HZ</value></node> + <node>PHE:CE2<value>PHE:CE2</value></node> + <node>PHE:HE2<value>PHE:HE2</value></node> + <node>PHE:CD2<value>PHE:CD2</value></node> + <node>PHE:HD2<value>PHE:HD2</value></node> + <node>PRO:CA<value>PRO:CA</value></node> + <node>PRO:HA<value>PRO:HA</value></node> + <node>PRO:CD<value>PRO:CD</value></node> + <node>PRO:HD2<value>PRO:1HD</value></node> + <node>PRO:HD3<value>PRO:2HD</value></node> + <node>PRO:CG<value>PRO:CG</value></node> + <node>PRO:HG2<value>PRO:1HG</value></node> + <node>PRO:HG3<value>PRO:2HG</value></node> + <node>PRO:CB<value>PRO:CB</value></node> + <node>PRO:HB2<value>PRO:1HB</value></node> + <node>PRO:HB3<value>PRO:2HB</value></node> + <node>SER:CA<value>SER:CA</value></node> + <node>SER:HA<value>SER:HA</value></node> + <node>SER:CB<value>SER:CB</value></node> + <node>SER:HB2<value>SER:1HB</value></node> + <node>SER:HB3<value>SER:2HB</value></node> + <node>SER:OG<value>SER:OG</value></node> + <node>SER:HG<value>SER:HG</value></node> + <node>THR:CA<value>THR:CA</value></node> + <node>THR:HA<value>THR:HA</value></node> + <node>THR:CB<value>THR:CB</value></node> + <node>THR:HB<value>THR:HB</value></node> + <node>THR:CG2<value>THR:CG2</value></node> + <node>THR:HG21<value>THR:1HG2</value></node> + <node>THR:HG22<value>THR:2HG2</value></node> + <node>THR:HG23<value>THR:3HG2</value></node> + <node>THR:OG1<value>THR:OG1</value></node> + <node>THR:HG1<value>THR:HG1</value></node> + <node>TRP:CA<value>TRP:CA</value></node> + <node>TRP:HA<value>TRP:HA</value></node> + <node>TRP:CB<value>TRP:CB</value></node> + <node>TRP:HB2<value>TRP:1HB</value></node> + <node>TRP:HB3<value>TRP:2HB</value></node> + <node>TRP:CG<value>TRP:CG</value></node> + <node>TRP:CD1<value>TRP:CD1</value></node> + <node>TRP:HD1<value>TRP:HD1</value></node> + <node>TRP:NE1<value>TRP:NE1</value></node> + <node>TRP:HE1<value>TRP:HE1</value></node> + <node>TRP:CE2<value>TRP:CE2</value></node> + <node>TRP:CZ2<value>TRP:CZ2</value></node> + <node>TRP:HZ2<value>TRP:HZ2</value></node> + <node>TRP:CH2<value>TRP:CH2</value></node> + <node>TRP:HH2<value>TRP:HH2</value></node> + <node>TRP:CZ3<value>TRP:CZ3</value></node> + <node>TRP:HZ3<value>TRP:HZ3</value></node> + <node>TRP:CE3<value>TRP:CE3</value></node> + <node>TRP:HE3<value>TRP:HE3</value></node> + <node>TRP:CD2<value>TRP:CD2</value></node> + <node>TYR:CA<value>TYR:CA</value></node> + <node>TYR:HA<value>TYR:HA</value></node> + <node>TYR:CB<value>TYR:CB</value></node> + <node>TYR:HB2<value>TYR:1HB</value></node> + <node>TYR:HB3<value>TYR:2HB</value></node> + <node>TYR:CG<value>TYR:CG</value></node> + <node>TYR:CD1<value>TYR:CD1</value></node> + <node>TYR:HD1<value>TYR:HD1</value></node> + <node>TYR:CE1<value>TYR:CE1</value></node> + <node>TYR:HE1<value>TYR:HE1</value></node> + <node>TYR:CZ<value>TYR:CZ</value></node> + <node>TYR:OH<value>TYR:OH</value></node> + <node>TYR:HH<value>TYR:HH</value></node> + <node>TYR:CE2<value>TYR:CE2</value></node> + <node>TYR:HE2<value>TYR:HE2</value></node> + <node>TYR:CD2<value>TYR:CD2</value></node> + <node>TYR:HD2<value>TYR:HD2</value></node> + <node>VAL:CA<value>VAL:CA</value></node> + <node>VAL:HA<value>VAL:HA</value></node> + <node>VAL:CB<value>VAL:CB</value></node> + <node>VAL:HB<value>VAL:HB</value></node> + <node>VAL:CG1<value>VAL:CG1</value></node> + <node>VAL:HG11<value>VAL:1HG1</value></node> + <node>VAL:HG12<value>VAL:2HG1</value></node> + <node>VAL:HG13<value>VAL:3HG1</value></node> + <node>VAL:CG2<value>VAL:CG2</value></node> + <node>VAL:HG21<value>VAL:1HG2</value></node> + <node>VAL:HG22<value>VAL:2HG2</value></node> + <node>VAL:HG23<value>VAL:3HG2</value></node> + <node>DC:P<value>C:P</value></node> + <node>DC:O1P<value>C:O1P</value></node> + <node>DC:O2P<value>C:O2P</value></node> + <node>DC:O5'<value>C:O5*</value></node> + <node>DC:C5'<value>C:C5*</value></node> + <node>DC:H5'1<value>C:1H5*</value></node> + <node>DC:H5'2<value>C:2H5*</value></node> + <node>DC:C4'<value>C:C4*</value></node> + <node>DC:H4'<value>C:H4*</value></node> + <node>DC:O4'<value>C:O4*</value></node> + <node>DC:C1'<value>C:C1*</value></node> + <node>DC:H1'<value>C:H1*</value></node> + <node>DC:N1<value>C:N1</value></node> + <node>DC:C6<value>C:C6</value></node> + <node>DC:H6<value>C:H6</value></node> + <node>DC:C5<value>C:C5</value></node> + <node>DC:H5<value>C:H5</value></node> + <node>DC:C4<value>C:C4</value></node> + <node>DC:N4<value>C:N4</value></node> + <node>DC:H41<value>C:1H4</value></node> + <node>DC:H42<value>C:2H4</value></node> + <node>DC:N3<value>C:N3</value></node> + <node>DC:C2<value>C:C2</value></node> + <node>DC:O2<value>C:O2</value></node> + <node>DC:C3'<value>C:C3*</value></node> + <node>DC:H3'<value>C:H3*</value></node> + <node>DC:C2'<value>C:C2*</value></node> + <node>DC:H2'1<value>C:1H2*</value></node> + <node>DC:H2'2<value>C:2H2*</value></node> + <node>DC:O3'<value>C:O3*</value></node> + <node>DA:P<value>A:P</value></node> + <node>DA:O1P<value>A:O1P</value></node> + <node>DA:O2P<value>A:O2P</value></node> + <node>DA:O5'<value>A:O5*</value></node> + <node>DA:C5'<value>A:C5*</value></node> + <node>DA:H5'1<value>A:1H5*</value></node> + <node>DA:H5'2<value>A:2H5*</value></node> + <node>DA:C4'<value>A:C4*</value></node> + <node>DA:H4'<value>A:H4*</value></node> + <node>DA:O4'<value>A:O4*</value></node> + <node>DA:C1'<value>A:C1*</value></node> + <node>DA:H1'<value>A:H1*</value></node> + <node>DA:N9<value>A:N9</value></node> + <node>DA:C8<value>A:C8</value></node> + <node>DA:H8<value>A:H8</value></node> + <node>DA:N7<value>A:N7</value></node> + <node>DA:C5<value>A:C5</value></node> + <node>DA:C6<value>A:C6</value></node> + <node>DA:N6<value>A:N6</value></node> + <node>DA:H61<value>A:1H6</value></node> + <node>DA:H62<value>A:2H6</value></node> + <node>DA:N1<value>A:N1</value></node> + <node>DA:C2<value>A:C2</value></node> + <node>DA:H2<value>A:2H</value></node> + <node>DA:N3<value>A:N3</value></node> + <node>DA:C4<value>A:C4</value></node> + <node>DA:C3'<value>A:C3*</value></node> + <node>DA:H3'<value>A:H3*</value></node> + <node>DA:C2'<value>A:C2*</value></node> + <node>DA:H2'1<value>A:1H2*</value></node> + <node>DA:H2'2<value>A:2H2*</value></node> + <node>DA:O3'<value>A:O3*</value></node> + <node>DT:P<value>T:P</value></node> + <node>DT:O1P<value>T:O1P</value></node> + <node>DT:O2P<value>T:O2P</value></node> + <node>DT:O5'<value>T:O5*</value></node> + <node>DT:C5'<value>T:C5*</value></node> + <node>DT:H5'1<value>T:1H5*</value></node> + <node>DT:H5'2<value>T:2H5*</value></node> + <node>DT:C4'<value>T:C4*</value></node> + <node>DT:H4'<value>T:H4*</value></node> + <node>DT:O4'<value>T:O4*</value></node> + <node>DT:C1'<value>T:C1*</value></node> + <node>DT:H1'<value>T:H1*</value></node> + <node>DT:N1<value>T:N1</value></node> + <node>DT:C6<value>T:C6</value></node> + <node>DT:H6<value>T:H6</value></node> + <node>DT:C5<value>T:C5</value></node> + <node>DT:C7<value>T:C5M</value></node> + <node>DT:H71<value>T:1H5M</value></node> + <node>DT:H72<value>T:2H5M</value></node> + <node>DT:H73<value>T:3H5M</value></node> + <node>DT:C4<value>T:C4</value></node> + <node>DT:O4<value>T:O4</value></node> + <node>DT:N3<value>T:N3</value></node> + <node>DT:H3<value>T:3H</value></node> + <node>DT:C2<value>T:C2</value></node> + <node>DT:O2<value>T:O2</value></node> + <node>DT:C3'<value>T:C3*</value></node> + <node>DT:H3'<value>T:H3*</value></node> + <node>DT:C2'<value>T:C2*</value></node> + <node>DT:H2'1<value>T:1H2*</value></node> + <node>DT:H2'2<value>T:2H2*</value></node> + <node>DT:O3'<value>T:O3*</value></node> + <node>DG:P<value>G:P</value></node> + <node>DG:O1P<value>G:O1P</value></node> + <node>DG:O2P<value>G:O2P</value></node> + <node>DG:O5'<value>G:O5*</value></node> + <node>DG:C5'<value>G:C5*</value></node> + <node>DG:H5'1<value>G:1H5*</value></node> + <node>DG:H5'2<value>G:2H5*</value></node> + <node>DG:C4'<value>G:C4*</value></node> + <node>DG:H4'<value>G:H4*</value></node> + <node>DG:O4'<value>G:O4*</value></node> + <node>DG:C1'<value>G:C1*</value></node> + <node>DG:H1'<value>G:H1*</value></node> + <node>DG:N9<value>G:N9</value></node> + <node>DG:C8<value>G:C8</value></node> + <node>DG:H8<value>G:H8</value></node> + <node>DG:N7<value>G:N7</value></node> + <node>DG:C5<value>G:C5</value></node> + <node>DG:C6<value>G:C6</value></node> + <node>DG:O6<value>G:O6</value></node> + <node>DG:N1<value>G:N1</value></node> + <node>DG:H1<value>G:1H</value></node> + <node>DG:C2<value>G:C2</value></node> + <node>DG:N2<value>G:N2</value></node> + <node>DG:H21<value>G:1H2</value></node> + <node>DG:H22<value>G:2H2</value></node> + <node>DG:N3<value>G:N3</value></node> + <node>DG:C4<value>G:C4</value></node> + <node>DG:C3'<value>G:C3*</value></node> + <node>DG:H3'<value>G:H3*</value></node> + <node>DG:C2'<value>G:C2*</value></node> + <node>DG:H2'1<value>G:1H2*</value></node> + <node>DG:H2'2<value>G:2H2*</value></node> + <node>DG:O3'<value>G:O3*</value></node> + + <node>*:OXT<value>*:OXT</value></node> + + <node>GLH:CA<value>GLH:CA</value></node> + <node>GLH:HA<value>GLH:HA</value></node> + <node>GLH:CB<value>GLH:CB</value></node> + <node>GLH:HB2<value>GLH:1HB</value></node> + <node>GLH:HB3<value>GLH:2HB</value></node> + <node>GLH:CG<value>GLH:CG</value></node> + <node>GLH:HG2<value>GLH:1HG</value></node> + <node>GLH:HG3<value>GLH:2HG</value></node> + <node>GLH:CD<value>GLH:CD</value></node> + <node>GLH:OE1<value>GLH:OE1</value></node> + <node>GLH:OE2<value>GLH:OE2</value></node> + <node>GLH:HE2<value>GLH:2HE</value></node> + + <node>HID:CA<value>HID:CA</value></node> + <node>HID:HA<value>HID:HA</value></node> + <node>HID:CB<value>HID:CB</value></node> + <node>HID:HB2<value>HID:1HB</value></node> + <node>HID:HB3<value>HID:2HB</value></node> + <node>HID:CG<value>HID:CG</value></node> + <node>HID:ND1<value>HID:ND1</value></node> + <node>HID:HD1<value>HID:HD1</value></node> + <node>HID:CE1<value>HID:CE1</value></node> + <node>HID:HE1<value>HID:HE1</value></node> + <node>HID:NE2<value>HID:NE2</value></node> + <node>HID:HE2<value>HID:HE2</value></node> + <node>HID:CD2<value>HID:CD2</value></node> + <node>HID:HD2<value>HID:HD2</value></node> + + <node>HIE:CA<value>HIE:CA</value></node> + <node>HIE:HA<value>HIE:HA</value></node> + <node>HIE:CB<value>HIE:CB</value></node> + <node>HIE:HB2<value>HIE:1HB</value></node> + <node>HIE:HB3<value>HIE:2HB</value></node> + <node>HIE:CG<value>HIE:CG</value></node> + <node>HIE:ND1<value>HIE:ND1</value></node> + <node>HIE:HD1<value>HIE:HD1</value></node> + <node>HIE:CE1<value>HIE:CE1</value></node> + <node>HIE:HE1<value>HIE:HE1</value></node> + <node>HIE:NE2<value>HIE:NE2</value></node> + <node>HIE:HE2<value>HIE:HE2</value></node> + <node>HIE:CD2<value>HIE:CD2</value></node> + <node>HIE:HD2<value>HIE:HD2</value></node> + + <node>HIP:CA<value>HIP:CA</value></node> + <node>HIP:HA<value>HIP:HA</value></node> + <node>HIP:CB<value>HIP:CB</value></node> + <node>HIP:HB2<value>HIP:1HB</value></node> + <node>HIP:HB3<value>HIP:2HB</value></node> + <node>HIP:CG<value>HIP:CG</value></node> + <node>HIP:ND1<value>HIP:ND1</value></node> + <node>HIP:HD1<value>HIP:HD1</value></node> + <node>HIP:CE1<value>HIP:CE1</value></node> + <node>HIP:HE1<value>HIP:HE1</value></node> + <node>HIP:NE2<value>HIP:NE2</value></node> + <node>HIP:HE2<value>HIP:HE2</value></node> + <node>HIP:CD2<value>HIP:CD2</value></node> + <node>HIP:HD2<value>HIP:HD2</value></node> + + <node>CYM:CA<value>CYM:CA</value></node> + <node>CYM:CB<value>CYM:CB</value></node> + <node>CYM:HA<value>CYM:HA</value></node> + <node>CYM:HB2<value>CYM:1HB</value></node> + <node>CYM:HB3<value>CYM:2HB</value></node> + <node>CYM:SG<value>CYM:SG</value></node> + <node>CYM:HN<value>CYM:HN</value></node> + + <node>CYX:CA<value>CYX:CA</value></node> + <node>CYX:CB<value>CYX:CB</value></node> + <node>CYX:HA<value>CYX:HA</value></node> + <node>CYX:HB2<value>CYX:1HB</value></node> + <node>CYX:HB3<value>CYX:2HB</value></node> + <node>CYX:SG<value>CYX:SG</value></node> + + <node>ACE:CH3<value>ACE:CH3</value></node> + <node>ACE:HH31<value>ACE:1HH3</value></node> + <node>ACE:HH32<value>ACE:2HH3</value></node> + <node>ACE:HH33<value>ACE:3HH3</value></node> + <node>NME:CH3<value>NME:CH3</value></node> + <node>NME:HH31<value>NME:1HH3</value></node> + <node>NME:HH32<value>NME:2HH3</value></node> + <node>NME:HH33<value>NME:3HH3</value></node> + + <node>LYN:NZ<value>LYN:NZ</value></node> + <node>LYN:CA<value>LYN:CA</value></node> + <node>LYN:CB<value>LYN:CB</value></node> + <node>LYN:CG<value>LYN:CG</value></node> + <node>LYN:CD<value>LYN:CD</value></node> + <node>LYN:CE<value>LYN:CE</value></node> + <node>LYN:HA<value>LYN:HA</value></node> + <node>LYN:HB2<value>LYN:1HB</value></node> + <node>LYN:HB3<value>LYN:2HB</value></node> + <node>LYN:HD2<value>LYN:1HD</value></node> + <node>LYN:HD3<value>LYN:2HD</value></node> + <node>LYN:HE2<value>LYN:1HE</value></node> + <node>LYN:HE3<value>LYN:2HE</value></node> + <node>LYN:HG2<value>LYN:1HG</value></node> + <node>LYN:HG3<value>LYN:2HG</value></node> + <node>LYN:HZ2<value>LYN:2HZ</value></node> + <node>LYN:HZ3<value>LYN:3HZ</value></node> +</node> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/fragments/Names.CHARMM.db Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,279 @@ +<node>CHARMM<value>PDB</value> + <node>*:H1<value>*:1H</value></node> + <node>*:H2<value>*:2H</value></node> + <node>*:H3<value>*:3H</value></node> + <node>*:N<value>*:N</value></node> + <node>*:C<value>*:C</value></node> + <node>*:CA<value>*:CA</value></node> + <node>*:O<value>*:O</value></node> + <node>*:H<value>*:H</value></node> + <node>*:OT1<value>*:O</value></node> + <node>*:OT2<value>*:OXT</value></node> + <node>*:OCT1<value>*:O</value></node> + <node>*:OCT2<value>*:OXT</value></node> + <node>*:HT1<value>*:1H</value></node> + <node>*:HT2<value>*:2H</value></node> + <node>*:HT3<value>*:3H</value></node> + <node>ALA:HB1<value>ALA:1HB</value></node> + <node>ALA:HB2<value>ALA:2HB</value></node> + <node>ALA:HB3<value>ALA:3HB</value></node> + <node>ARG:HB2<value>ARG:1HB</value></node> + <node>ARG:HB3<value>ARG:2HB</value></node> + <node>ARG:HG2<value>ARG:1HG</value></node> + <node>ARG:HG3<value>ARG:2HG</value></node> + <node>ARG:HD2<value>ARG:1HD</value></node> + <node>ARG:HD3<value>ARG:2HD</value></node> + <node>ARG:HH1<value>ARG:1HH1</value></node> + <node>ARG:HH2<value>ARG:1HH2</value></node> + <node>ARG:HH11<value>ARG:1HH1</value></node> + <node>ARG:HH12<value>ARG:2HH1</value></node> + <node>ARG:HH21<value>ARG:1HH2</value></node> + <node>ARG:HH22<value>ARG:2HH2</value></node> + <node>ASN:HB2<value>ASN:1HB</value></node> + <node>ASN:HB3<value>ASN:2HB</value></node> + <node>ASN:HD1<value>ASN:1HD1</value></node> + <node>ASN:HD2<value>ASN:1HD2</value></node> + <node>ASN:HD21<value>ASN:1HD2</value></node> + <node>ASN:HD22<value>ASN:2HD2</value></node> + <node>ASP:HB2<value>ASP:1HB</value></node> + <node>ASP:HB3<value>ASP:2HB</value></node> + <node>CYS:HB2<value>CYS:1HB</value></node> + <node>CYS:HB3<value>CYS:2HB</value></node> + <node>GLU:HB2<value>GLU:1HB</value></node> + <node>GLU:HB3<value>GLU:2HB</value></node> + <node>GLU:HG2<value>GLU:1HG</value></node> + <node>GLU:HG3<value>GLU:2HG</value></node> + <node>GLN:HB2<value>GLN:1HB</value></node> + <node>GLN:HB3<value>GLN:2HB</value></node> + <node>GLN:HG2<value>GLN:1HG</value></node> + <node>GLN:HG3<value>GLN:2HG</value></node> + <node>GLN:HE21<value>GLN:1HE2</value></node> + <node>GLN:HE22<value>GLN:2HE2</value></node> + <node>GLN:HE1<value>GLN:1HE1</value></node> + <node>GLN:HE2<value>GLN:1HE2</value></node> + <node>GLY:HA2<value>GLY:1HA</value></node> + <node>GLY:HA3<value>GLY:2HA</value></node> + <node>HIS:HB2<value>HIS:1HB</value></node> + <node>HIS:HB3<value>HIS:2HB</value></node> + <node>HIE:*<value>HIS:*</value></node> + <node>HID:*<value>HIS:*</value></node> + <node>HIP:*<value>HIS:*</value></node> + <node>ILE:HG21<value>ILE:1HG2</value></node> + <node>ILE:HG22<value>ILE:2HG2</value></node> + <node>ILE:HG23<value>ILE:3HG2</value></node> + <node>ILE:HG12<value>ILE:1HG1</value></node> + <node>ILE:HG13<value>ILE:2HG1</value></node> + <node>ILE:HD11<value>ILE:1HD1</value></node> + <node>ILE:HD12<value>ILE:2HD1</value></node> + <node>ILE:HD13<value>ILE:3HD1</value></node> + <node>ILE:CD<value>ILE:CD1</value></node> + <node>LEU:HB2<value>LEU:1HB</value></node> + <node>LEU:HB3<value>LEU:2HB</value></node> + <node>LEU:HD11<value>LEU:1HD1</value></node> + <node>LEU:HD12<value>LEU:2HD1</value></node> + <node>LEU:HD13<value>LEU:3HD1</value></node> + <node>LEU:HD21<value>LEU:1HD2</value></node> + <node>LEU:HD22<value>LEU:2HD2</value></node> + <node>LEU:HD23<value>LEU:3HD2</value></node> + <node>LYS:HB2<value>LYS:1HB</value></node> + <node>LYS:HB3<value>LYS:2HB</value></node> + <node>LYS:HG2<value>LYS:1HG</value></node> + <node>LYS:HG3<value>LYS:2HG</value></node> + <node>LYS:HD2<value>LYS:1HD</value></node> + <node>LYS:HD3<value>LYS:2HD</value></node> + <node>LYS:HE2<value>LYS:1HE</value></node> + <node>LYS:HE3<value>LYS:2HE</value></node> + <node>LYS:HZ1<value>LYS:1HZ</value></node> + <node>LYS:HZ2<value>LYS:2HZ</value></node> + <node>LYS:HZ3<value>LYS:3HZ</value></node> + <node>MET:HB2<value>MET:1HB</value></node> + <node>MET:HB3<value>MET:2HB</value></node> + <node>MET:HG2<value>MET:1HG</value></node> + <node>MET:HG3<value>MET:2HG</value></node> + <node>MET:HE1<value>MET:1HE</value></node> + <node>MET:HE2<value>MET:2HE</value></node> + <node>MET:HE3<value>MET:3HE</value></node> + <node>PHE:HB2<value>PHE:1HB</value></node> + <node>PHE:HB3<value>PHE:2HB</value></node> + <node>PRO:HD2<value>PRO:1HD</value></node> + <node>PRO:HD3<value>PRO:2HD</value></node> + <node>PRO:HG2<value>PRO:1HG</value></node> + <node>PRO:HG3<value>PRO:2HG</value></node> + <node>PRO:HB2<value>PRO:1HB</value></node> + <node>PRO:HB3<value>PRO:2HB</value></node> + <node>SER:HB2<value>SER:1HB</value></node> + <node>SER:HB3<value>SER:2HB</value></node> + <node>THR:HG21<value>THR:1HG2</value></node> + <node>THR:HG22<value>THR:2HG2</value></node> + <node>THR:HG23<value>THR:3HG2</value></node> + <node>TRP:HB2<value>TRP:1HB</value></node> + <node>TRP:HB3<value>TRP:2HB</value></node> + <node>TYR:HB2<value>TYR:1HB</value></node> + <node>TYR:HB3<value>TYR:2HB</value></node> + <node>VAL:HG11<value>VAL:1HG1</value></node> + <node>VAL:HG12<value>VAL:2HG1</value></node> + <node>VAL:HG13<value>VAL:3HG1</value></node> + <node>VAL:HG21<value>VAL:1HG2</value></node> + <node>VAL:HG22<value>VAL:2HG2</value></node> + <node>VAL:HG23<value>VAL:3HG2</value></node> + <node>ACE:HH31<value>ACE:1HH3</value></node> + <node>ACE:HH32<value>ACE:2HH3</value></node> + <node>ACE:HH33<value>ACE:3HH3</value></node> + <node>NME:HH31<value>NME:1HH3</value></node> + <node>NME:HH32<value>NME:2HH3</value></node> + <node>NME:HH33<value>NME:3HH3</value></node> + <node>ALA:CA<value>ALA:CA</value></node> + <node>ALA:HA<value>ALA:HA</value></node> + <node>ALA:CB<value>ALA:CB</value></node> + <node>ARG:CA<value>ARG:CA</value></node> + <node>ARG:HA<value>ARG:HA</value></node> + <node>ARG:CB<value>ARG:CB</value></node> + <node>ARG:CG<value>ARG:CG</value></node> + <node>ARG:CD<value>ARG:CD</value></node> + <node>ARG:NE<value>ARG:NE</value></node> + <node>ARG:HE<value>ARG:HE</value></node> + <node>ARG:CZ<value>ARG:CZ</value></node> + <node>ARG:NH1<value>ARG:NH1</value></node> + <node>ARG:NH2<value>ARG:NH2</value></node> + <node>ASN:CA<value>ASN:CA</value></node> + <node>ASN:HA<value>ASN:HA</value></node> + <node>ASN:CB<value>ASN:CB</value></node> + <node>ASN:CG<value>ASN:CG</value></node> + <node>ASN:OD1<value>ASN:OD1</value></node> + <node>ASN:ND2<value>ASN:ND2</value></node> + <node>ASP:CA<value>ASP:CA</value></node> + <node>ASP:HA<value>ASP:HA</value></node> + <node>ASP:CB<value>ASP:CB</value></node> + <node>ASP:CG<value>ASP:CG</value></node> + <node>ASP:OD1<value>ASP:OD1</value></node> + <node>ASP:OD2<value>ASP:OD2</value></node> + <node>CYS:CA<value>CYS:CA</value></node> + <node>CYS:HA<value>CYS:HA</value></node> + <node>CYS:CB<value>CYS:CB</value></node> + <node>CYS:SG<value>CYS:SG</value></node> + <node>CYS:HG<value>CYS:HG</value></node> + <node>GLU:CA<value>GLU:CA</value></node> + <node>GLU:HA<value>GLU:HA</value></node> + <node>GLU:CB<value>GLU:CB</value></node> + <node>GLU:CG<value>GLU:CG</value></node> + <node>GLU:CD<value>GLU:CD</value></node> + <node>GLU:OE1<value>GLU:OE1</value></node> + <node>GLU:OE2<value>GLU:OE2</value></node> + <node>GLN:CA<value>GLN:CA</value></node> + <node>GLN:HA<value>GLN:HA</value></node> + <node>GLN:CB<value>GLN:CB</value></node> + <node>GLN:CG<value>GLN:CG</value></node> + <node>GLN:CD<value>GLN:CD</value></node> + <node>GLN:OE1<value>GLN:OE1</value></node> + <node>GLN:NE2<value>GLN:NE2</value></node> + <node>GLY:CA<value>GLY:CA</value></node> + <node>HIS:CA<value>HIS:CA</value></node> + <node>HIS:HA<value>HIS:HA</value></node> + <node>HIS:CB<value>HIS:CB</value></node> + <node>HIS:CG<value>HIS:CG</value></node> + <node>HIS:ND1<value>HIS:ND1</value></node> + <node>HIS:HD1<value>HIS:HD1</value></node> + <node>HIS:CE1<value>HIS:CE1</value></node> + <node>HIS:HE1<value>HIS:HE1</value></node> + <node>HIS:NE2<value>HIS:NE2</value></node> + <node>HIS:HE2<value>HIS:HE2</value></node> + <node>HIS:CD2<value>HIS:CD2</value></node> + <node>HIS:HD2<value>HIS:HD2</value></node> + <node>ILE:CA<value>ILE:CA</value></node> + <node>ILE:HA<value>ILE:HA</value></node> + <node>ILE:CB<value>ILE:CB</value></node> + <node>ILE:HB<value>ILE:HB</value></node> + <node>ILE:CG2<value>ILE:CG2</value></node> + <node>ILE:CG1<value>ILE:CG1</value></node> + <node>ILE:CD1<value>ILE:CD1</value></node> + <node>LEU:CA<value>LEU:CA</value></node> + <node>LEU:HA<value>LEU:HA</value></node> + <node>LEU:CB<value>LEU:CB</value></node> + <node>LEU:CG<value>LEU:CG</value></node> + <node>LEU:HG<value>LEU:HG</value></node> + <node>LEU:CD1<value>LEU:CD1</value></node> + <node>LEU:CD2<value>LEU:CD2</value></node> + <node>LYS:CA<value>LYS:CA</value></node> + <node>LYS:HA<value>LYS:HA</value></node> + <node>LYS:CB<value>LYS:CB</value></node> + <node>LYS:CG<value>LYS:CG</value></node> + <node>LYS:CD<value>LYS:CD</value></node> + <node>LYS:CE<value>LYS:CE</value></node> + <node>LYS:NZ<value>LYS:NZ</value></node> + <node>MET:CA<value>MET:CA</value></node> + <node>MET:HA<value>MET:HA</value></node> + <node>MET:CB<value>MET:CB</value></node> + <node>MET:CG<value>MET:CG</value></node> + <node>MET:SD<value>MET:SD</value></node> + <node>MET:CE<value>MET:CE</value></node> + <node>PHE:CA<value>PHE:CA</value></node> + <node>PHE:HA<value>PHE:HA</value></node> + <node>PHE:CB<value>PHE:CB</value></node> + <node>PHE:CG<value>PHE:CG</value></node> + <node>PHE:CD1<value>PHE:CD1</value></node> + <node>PHE:HD1<value>PHE:HD1</value></node> + <node>PHE:CE1<value>PHE:CE1</value></node> + <node>PHE:HE1<value>PHE:HE1</value></node> + <node>PHE:CZ<value>PHE:CZ</value></node> + <node>PHE:HZ<value>PHE:HZ</value></node> + <node>PHE:CE2<value>PHE:CE2</value></node> + <node>PHE:HE2<value>PHE:HE2</value></node> + <node>PHE:CD2<value>PHE:CD2</value></node> + <node>PHE:HD2<value>PHE:HD2</value></node> + <node>PRO:CA<value>PRO:CA</value></node> + <node>PRO:HA<value>PRO:HA</value></node> + <node>PRO:CD<value>PRO:CD</value></node> + <node>PRO:CG<value>PRO:CG</value></node> + <node>PRO:CB<value>PRO:CB</value></node> + <node>SER:CA<value>SER:CA</value></node> + <node>SER:HA<value>SER:HA</value></node> + <node>SER:CB<value>SER:CB</value></node> + <node>SER:OG<value>SER:OG</value></node> + <node>SER:HG<value>SER:HG</value></node> + <node>THR:CA<value>THR:CA</value></node> + <node>THR:HA<value>THR:HA</value></node> + <node>THR:CB<value>THR:CB</value></node> + <node>THR:HB<value>THR:HB</value></node> + <node>THR:CG2<value>THR:CG2</value></node> + <node>THR:OG1<value>THR:OG1</value></node> + <node>THR:HG1<value>THR:HG1</value></node> + <node>TRP:CA<value>TRP:CA</value></node> + <node>TRP:HA<value>TRP:HA</value></node> + <node>TRP:CB<value>TRP:CB</value></node> + <node>TRP:CG<value>TRP:CG</value></node> + <node>TRP:CD1<value>TRP:CD1</value></node> + <node>TRP:HD1<value>TRP:HD1</value></node> + <node>TRP:NE1<value>TRP:NE1</value></node> + <node>TRP:HE1<value>TRP:HE1</value></node> + <node>TRP:CE2<value>TRP:CE2</value></node> + <node>TRP:CZ2<value>TRP:CZ2</value></node> + <node>TRP:HZ2<value>TRP:HZ2</value></node> + <node>TRP:CH2<value>TRP:CH2</value></node> + <node>TRP:HH2<value>TRP:HH2</value></node> + <node>TRP:CZ3<value>TRP:CZ3</value></node> + <node>TRP:HZ3<value>TRP:HZ3</value></node> + <node>TRP:CE3<value>TRP:CE3</value></node> + <node>TRP:HE3<value>TRP:HE3</value></node> + <node>TRP:CD2<value>TRP:CD2</value></node> + <node>TYR:CA<value>TYR:CA</value></node> + <node>TYR:HA<value>TYR:HA</value></node> + <node>TYR:CB<value>TYR:CB</value></node> + <node>TYR:CG<value>TYR:CG</value></node> + <node>TYR:CD1<value>TYR:CD1</value></node> + <node>TYR:HD1<value>TYR:HD1</value></node> + <node>TYR:CE1<value>TYR:CE1</value></node> + <node>TYR:HE1<value>TYR:HE1</value></node> + <node>TYR:CZ<value>TYR:CZ</value></node> + <node>TYR:OH<value>TYR:OH</value></node> + <node>TYR:HH<value>TYR:HH</value></node> + <node>TYR:CE2<value>TYR:CE2</value></node> + <node>TYR:HE2<value>TYR:HE2</value></node> + <node>TYR:CD2<value>TYR:CD2</value></node> + <node>TYR:HD2<value>TYR:HD2</value></node> + <node>VAL:CA<value>VAL:CA</value></node> + <node>VAL:HA<value>VAL:HA</value></node> + <node>VAL:CB<value>VAL:CB</value></node> + <node>VAL:HB<value>VAL:HB</value></node> + <node>VAL:CG1<value>VAL:CG1</value></node> + <node>VAL:CG2<value>VAL:CG2</value></node> +</node>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/fragments/Names.DNA.db Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,174 @@ +<node>DNA<value>PDB</value> + <node>C:P<value>C:P</value></node> + <node>DC:OP1<value>C:O1P</value></node> + <node>DC:OP2<value>C:O2P</value></node> + <node>DC:*<value>C:*</value></node> + <node>C:OP1<value>C:O1P</value></node> + <node>C:OP2<value>C:O2P</value></node> + <node>C:O5'<value>C:O5*</value></node> + <node>C:C5'<value>C:C5*</value></node> + <node>C:H5'<value>C:1H5*</value></node> + <node>C:H5''<value>C:2H5*</value></node> + <node>C:C4'<value>C:C4*</value></node> + <node>C:H4'<value>C:H4*</value></node> + <node>C:O4'<value>C:O4*</value></node> + <node>C:C1'<value>C:C1*</value></node> + <node>C:H1'<value>C:H1*</value></node> + <node>C:N1<value>C:N1</value></node> + <node>C:C6<value>C:C6</value></node> + <node>C:H6<value>C:H6</value></node> + <node>C:C5<value>C:C5</value></node> + <node>C:H5<value>C:H5</value></node> + <node>C:C4<value>C:C4</value></node> + <node>C:N4<value>C:N4</value></node> + <node>C:H41<value>C:1H4</value></node> + <node>C:H42<value>C:2H4</value></node> + <node>C:N3<value>C:N3</value></node> + <node>C:C2<value>C:C2</value></node> + <node>C:O2<value>C:O2</value></node> + <node>C:O2'<value>C:O2*</value></node> + <node>C:HO2'<value>C:HO3*</value></node> + <node>C:C3'<value>C:C3*</value></node> + <node>C:H3'<value>C:H3*</value></node> + <node>C:C2'<value>C:C2*</value></node> + <node>C:H2'<value>C:1H2*</value></node> + <node>C:H2''<value>C:2H2*</value></node> + <node>C:O3'<value>C:O3*</value></node> + <node>A:P<value>A:P</value></node> + <node>DA:OP1<value>A:O1P</value></node> + <node>DA:OP2<value>A:O2P</value></node> + <node>DA:*<value>A:*</value></node> + <node>A:OP1<value>A:O1P</value></node> + <node>A:OP2<value>A:O2P</value></node> + <node>A:O5'<value>A:O5*</value></node> + <node>A:C5'<value>A:C5*</value></node> + <node>A:H5'<value>A:1H5*</value></node> + <node>A:H5''<value>A:2H5*</value></node> + <node>A:C4'<value>A:C4*</value></node> + <node>A:H4'<value>A:H4*</value></node> + <node>A:O4'<value>A:O4*</value></node> + <node>A:C1'<value>A:C1*</value></node> + <node>A:H1'<value>A:H1*</value></node> + <node>A:N9<value>A:N9</value></node> + <node>A:C8<value>A:C8</value></node> + <node>A:H8<value>A:H8</value></node> + <node>A:N7<value>A:N7</value></node> + <node>A:C5<value>A:C5</value></node> + <node>A:C6<value>A:C6</value></node> + <node>A:N6<value>A:N6</value></node> + <node>A:H61<value>A:1H6</value></node> + <node>A:H62<value>A:2H6</value></node> + <node>A:N1<value>A:N1</value></node> + <node>A:C2<value>A:C2</value></node> + <node>A:H2<value>A:2H</value></node> + <node>A:N3<value>A:N3</value></node> + <node>A:C4<value>A:C4</value></node> + <node>A:C3'<value>A:C3*</value></node> + <node>A:H3'<value>A:H3*</value></node> + <node>A:C2'<value>A:C2*</value></node> + <node>A:H2'<value>A:1H2*</value></node> + <node>A:H2''<value>A:2H2*</value></node> + <node>A:O3'<value>A:O3*</value></node> + <node>U:P<value>U:P</value></node> + <node>U:OP1<value>U:O1P</value></node> + <node>U:OP2<value>U:O2P</value></node> + <node>U:O5'<value>U:O5*</value></node> + <node>U:C5'<value>U:C5*</value></node> + <node>U:H5'<value>U:1H5*</value></node> + <node>U:H5''<value>U:2H5*</value></node> + <node>U:C4'<value>U:C4*</value></node> + <node>U:H4'<value>U:H4*</value></node> + <node>U:O4'<value>U:O4*</value></node> + <node>U:C1'<value>U:C1*</value></node> + <node>U:H1'<value>U:H1*</value></node> + <node>U:N1<value>U:N1</value></node> + <node>U:C6<value>U:C6</value></node> + <node>U:H6<value>U:H6</value></node> + <node>U:C5<value>U:C5</value></node> + <node>U:C4<value>U:C4</value></node> + <node>U:O4<value>U:O4</value></node> + <node>U:N3<value>U:N3</value></node> + <node>U:H3<value>U:H3</value></node> + <node>U:C2<value>U:C2</value></node> + <node>U:O2<value>U:O2</value></node> + <node>U:O2'<value>U:O2*</value></node> + <node>U:HO2'<value>U:HO2*</value></node> + <node>U:C3'<value>U:C3*</value></node> + <node>U:H3'<value>U:H3*</value></node> + <node>U:C2'<value>U:C2*</value></node> + <node>U:H2'<value>U:1H2*</value></node> + <node>U:H2''<value>U:2H2*</value></node> + <node>U:O3'<value>U:O3*</value></node> + + <node>T:P<value>T:P</value></node> + <node>DT:OP1<value>T:O1P</value></node> + <node>DT:OP2<value>T:O2P</value></node> + <node>DT:*<value>T:*</value></node> + <node>T:OP1<value>T:O1P</value></node> + <node>T:OP2<value>T:O2P</value></node> + <node>T:O5'<value>T:O5*</value></node> + <node>T:C5'<value>T:C5*</value></node> + <node>T:H5'<value>T:1H5*</value></node> + <node>T:H5''<value>T:2H5*</value></node> + <node>T:C4'<value>T:C4*</value></node> + <node>T:H4'<value>T:H4*</value></node> + <node>T:O4'<value>T:O4*</value></node> + <node>T:C1'<value>T:C1*</value></node> + <node>T:H1'<value>T:H1*</value></node> + <node>T:N1<value>T:N1</value></node> + <node>T:C6<value>T:C6</value></node> + <node>T:H6<value>T:H6</value></node> + <node>T:C5<value>T:C5</value></node> + <node>T:C7<value>T:C5M</value></node> + <node>T:H71<value>T:1H5M</value></node> + <node>T:H72<value>T:2H5M</value></node> + <node>T:H73<value>T:3H5M</value></node> + <node>T:C4<value>T:C4</value></node> + <node>T:O4<value>T:O4</value></node> + <node>T:N3<value>T:N3</value></node> + <node>T:C2<value>T:C2</value></node> + <node>T:O2<value>T:O2</value></node> + <node>T:C3'<value>T:C3*</value></node> + <node>T:H3'<value>T:H3*</value></node> + <node>T:C2'<value>T:C2*</value></node> + <node>T:H2'<value>T:1H2*</value></node> + <node>T:H2''<value>T:2H2*</value></node> + <node>T:O3'<value>T:O3*</value></node> + <node>T:H3<value>T:3H</value></node> + <node>G:P<value>G:P</value></node> + <node>DG:OP1<value>G:O1P</value></node> + <node>DG:OP2<value>G:O2P</value></node> + <node>DG:*<value>G:*</value></node> + <node>G:OP1<value>G:O1P</value></node> + <node>G:OP2<value>G:O2P</value></node> + <node>G:O5'<value>G:O5*</value></node> + <node>G:C5'<value>G:C5*</value></node> + <node>G:H5'<value>G:1H5*</value></node> + <node>G:H5''<value>G:2H5*</value></node> + <node>G:C4'<value>G:C4*</value></node> + <node>G:H4'<value>G:H4*</value></node> + <node>G:O4'<value>G:O4*</value></node> + <node>G:C1'<value>G:C1*</value></node> + <node>G:H1'<value>G:H1*</value></node> + <node>G:N9<value>G:N9</value></node> + <node>G:C8<value>G:C8</value></node> + <node>G:H8<value>G:H8</value></node> + <node>G:N7<value>G:N7</value></node> + <node>G:C5<value>G:C5</value></node> + <node>G:C6<value>G:C6</value></node> + <node>G:O6<value>G:O6</value></node> + <node>G:N1<value>G:N1</value></node> + <node>G:H1<value>G:1H</value></node> + <node>G:C2<value>G:C2</value></node> + <node>G:N2<value>G:N2</value></node> + <node>G:H21<value>G:1H2</value></node> + <node>G:H22<value>G:2H2</value></node> + <node>G:N3<value>G:N3</value></node> + <node>G:C4<value>G:C4</value></node> + <node>G:C3'<value>G:C3*</value></node> + <node>G:H3'<value>G:H3*</value></node> + <node>G:C2'<value>G:C2*</value></node> + <node>G:H2'<value>G:1H2*</value></node> + <node>G:H2''<value>G:2H2*</value></node> + <node>G:O3'<value>G:O3*</value></node> +</node>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/fragments/Names.Discover.db Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,255 @@ +<node>Discover<value>PDB</value> + <node>*:H1<value>*:1H</value></node> + <node>*:H2<value>*:2H</value></node> + <node>*:H3<value>*:3H</value></node> + <node>*:N<value>*:N</value></node> + <node>*:O<value>*:O</value></node> + <node>*:C<value>*:C</value></node> + <node>*:HN<value>*:H</value></node> + <node>ALA:CA<value>ALA:CA</value></node> + <node>ALA:HA<value>ALA:HA</value></node> + <node>ALA:CB<value>ALA:CB</value></node> + <node>ALA:HB1<value>ALA:1HB</value></node> + <node>ALA:HB2<value>ALA:2HB</value></node> + <node>ALA:HB3<value>ALA:3HB</value></node> + <node>ARG:CA<value>ARG:CA</value></node> + <node>ARG:HA<value>ARG:HA</value></node> + <node>ARG:CB<value>ARG:CB</value></node> + <node>ARG:HB1<value>ARG:1HB</value></node> + <node>ARG:HB2<value>ARG:2HB</value></node> + <node>ARG:CG<value>ARG:CG</value></node> + <node>ARG:HG1<value>ARG:1HG</value></node> + <node>ARG:HG2<value>ARG:2HG</value></node> + <node>ARG:CD<value>ARG:CD</value></node> + <node>ARG:HD1<value>ARG:1HD</value></node> + <node>ARG:HD2<value>ARG:2HD</value></node> + <node>ARG:NE<value>ARG:NE</value></node> + <node>ARG:HE<value>ARG:HE</value></node> + <node>ARG:CZ<value>ARG:CZ</value></node> + <node>ARG:NH1<value>ARG:NH1</value></node> + <node>ARG:HH11<value>ARG:1HH1</value></node> + <node>ARG:HH12<value>ARG:2HH1</value></node> + <node>ARG:NH2<value>ARG:NH2</value></node> + <node>ARG:HH21<value>ARG:1HH2</value></node> + <node>ARG:HH22<value>ARG:2HH2</value></node> + <node>ASN:CA<value>ASN:CA</value></node> + <node>ASN:HA<value>ASN:HA</value></node> + <node>ASN:CB<value>ASN:CB</value></node> + <node>ASN:HB1<value>ASN:1HB</value></node> + <node>ASN:HB2<value>ASN:2HB</value></node> + <node>ASN:CG<value>ASN:CG</value></node> + <node>ASN:OD1<value>ASN:OD1</value></node> + <node>ASN:ND2<value>ASN:ND2</value></node> + <node>ASN:HD21<value>ASN:1HD2</value></node> + <node>ASN:HD22<value>ASN:2HD2</value></node> + <node>ASP:CA<value>ASP:CA</value></node> + <node>ASP:HA<value>ASP:HA</value></node> + <node>ASP:CB<value>ASP:CB</value></node> + <node>ASP:HB1<value>ASP:1HB</value></node> + <node>ASP:HB2<value>ASP:2HB</value></node> + <node>ASP:CG<value>ASP:CG</value></node> + <node>ASP:OD1<value>ASP:OD1</value></node> + <node>ASP:OD2<value>ASP:OD2</value></node> + <node>CYS:CA<value>CYS:CA</value></node> + <node>CYS:HA<value>CYS:HA</value></node> + <node>CYS:CB<value>CYS:CB</value></node> + <node>CYS:HB1<value>CYS:1HB</value></node> + <node>CYS:HB2<value>CYS:2HB</value></node> + <node>CYS:SG<value>CYS:SG</value></node> + <node>CYS:HG<value>CYS:HG</value></node> + <node>GLU:CA<value>GLU:CA</value></node> + <node>GLU:HA<value>GLU:HA</value></node> + <node>GLU:CB<value>GLU:CB</value></node> + <node>GLU:HB1<value>GLU:1HB</value></node> + <node>GLU:HB2<value>GLU:2HB</value></node> + <node>GLU:CG<value>GLU:CG</value></node> + <node>GLU:HG1<value>GLU:1HG</value></node> + <node>GLU:HG2<value>GLU:2HG</value></node> + <node>GLU:CD<value>GLU:CD</value></node> + <node>GLU:OE1<value>GLU:OE1</value></node> + <node>GLU:OE2<value>GLU:OE2</value></node> + <node>GLN:CA<value>GLN:CA</value></node> + <node>GLN:HA<value>GLN:HA</value></node> + <node>GLN:CB<value>GLN:CB</value></node> + <node>GLN:HB1<value>GLN:1HB</value></node> + <node>GLN:HB2<value>GLN:2HB</value></node> + <node>GLN:CG<value>GLN:CG</value></node> + <node>GLN:HG1<value>GLN:1HG</value></node> + <node>GLN:HG2<value>GLN:2HG</value></node> + <node>GLN:CD<value>GLN:CD</value></node> + <node>GLN:OE1<value>GLN:OE1</value></node> + <node>GLN:NE2<value>GLN:NE2</value></node> + <node>GLN:HE21<value>GLN:1HE2</value></node> + <node>GLN:HE22<value>GLN:2HE2</value></node> + <node>GLY:CA<value>GLY:CA</value></node> + <node>GLY:HA1<value>GLY:1HA</value></node> + <node>GLY:HA2<value>GLY:2HA</value></node> + <node>HIS:CA<value>HIS:CA</value></node> + <node>HIS:HA<value>HIS:HA</value></node> + <node>HIS:CB<value>HIS:CB</value></node> + <node>HIS:HB1<value>HIS:1HB</value></node> + <node>HIS:HB2<value>HIS:2HB</value></node> + <node>HIS:CG<value>HIS:CG</value></node> + <node>HIS:ND1<value>HIS:ND1</value></node> + <node>HIS:HD1<value>HIS:HD1</value></node> + <node>HIS:CE1<value>HIS:CE1</value></node> + <node>HIS:HE1<value>HIS:HE1</value></node> + <node>HIS:NE2<value>HIS:NE2</value></node> + <node>HIS:HE2<value>HIS:HE2</value></node> + <node>HIS:CD2<value>HIS:CD2</value></node> + <node>HIS:HD2<value>HIS:HD2</value></node> + <node>ILE:CA<value>ILE:CA</value></node> + <node>ILE:HA<value>ILE:HA</value></node> + <node>ILE:CB<value>ILE:CB</value></node> + <node>ILE:HB<value>ILE:HB</value></node> + <node>ILE:CG2<value>ILE:CG2</value></node> + <node>ILE:HG21<value>ILE:1HG2</value></node> + <node>ILE:HG22<value>ILE:2HG2</value></node> + <node>ILE:HG23<value>ILE:3HG2</value></node> + <node>ILE:CG1<value>ILE:CG1</value></node> + <node>ILE:HG11<value>ILE:1HG1</value></node> + <node>ILE:HG12<value>ILE:2HG1</value></node> + <node>ILE:CD1<value>ILE:CD1</value></node> + <node>ILE:HD11<value>ILE:1HD1</value></node> + <node>ILE:HD12<value>ILE:2HD1</value></node> + <node>ILE:HD13<value>ILE:3HD1</value></node> + <node>LEU:CA<value>LEU:CA</value></node> + <node>LEU:HA<value>LEU:HA</value></node> + <node>LEU:CB<value>LEU:CB</value></node> + <node>LEU:HB1<value>LEU:1HB</value></node> + <node>LEU:HB2<value>LEU:2HB</value></node> + <node>LEU:CG<value>LEU:CG</value></node> + <node>LEU:HG<value>LEU:HG</value></node> + <node>LEU:CD1<value>LEU:CD1</value></node> + <node>LEU:HD11<value>LEU:1HD1</value></node> + <node>LEU:HD12<value>LEU:2HD1</value></node> + <node>LEU:HD13<value>LEU:3HD1</value></node> + <node>LEU:CD2<value>LEU:CD2</value></node> + <node>LEU:HD21<value>LEU:1HD2</value></node> + <node>LEU:HD22<value>LEU:2HD2</value></node> + <node>LEU:HD23<value>LEU:3HD2</value></node> + <node>LYS:CA<value>LYS:CA</value></node> + <node>LYS:HA<value>LYS:HA</value></node> + <node>LYS:CB<value>LYS:CB</value></node> + <node>LYS:HB1<value>LYS:1HB</value></node> + <node>LYS:HB2<value>LYS:2HB</value></node> + <node>LYS:CG<value>LYS:CG</value></node> + <node>LYS:HG1<value>LYS:1HG</value></node> + <node>LYS:HG2<value>LYS:2HG</value></node> + <node>LYS:CD<value>LYS:CD</value></node> + <node>LYS:HD1<value>LYS:1HD</value></node> + <node>LYS:HD2<value>LYS:2HD</value></node> + <node>LYS:CE<value>LYS:CE</value></node> + <node>LYS:HE1<value>LYS:1HE</value></node> + <node>LYS:HE2<value>LYS:2HE</value></node> + <node>LYS:NZ<value>LYS:NZ</value></node> + <node>LYS:HZ1<value>LYS:1HZ</value></node> + <node>LYS:HZ2<value>LYS:2HZ</value></node> + <node>LYS:HZ3<value>LYS:3HZ</value></node> + <node>MET:CA<value>MET:CA</value></node> + <node>MET:HA<value>MET:HA</value></node> + <node>MET:CB<value>MET:CB</value></node> + <node>MET:HB1<value>MET:1HB</value></node> + <node>MET:HB2<value>MET:2HB</value></node> + <node>MET:CG<value>MET:CG</value></node> + <node>MET:HG1<value>MET:1HG</value></node> + <node>MET:HG2<value>MET:2HG</value></node> + <node>MET:SD<value>MET:SD</value></node> + <node>MET:CE<value>MET:CE</value></node> + <node>MET:HE1<value>MET:1HE</value></node> + <node>MET:HE2<value>MET:2HE</value></node> + <node>MET:HE3<value>MET:3HE</value></node> + <node>PHE:CA<value>PHE:CA</value></node> + <node>PHE:HA<value>PHE:HA</value></node> + <node>PHE:CB<value>PHE:CB</value></node> + <node>PHE:HB1<value>PHE:1HB</value></node> + <node>PHE:HB2<value>PHE:2HB</value></node> + <node>PHE:CG<value>PHE:CG</value></node> + <node>PHE:CD1<value>PHE:CD1</value></node> + <node>PHE:HD1<value>PHE:HD1</value></node> + <node>PHE:CE1<value>PHE:CE1</value></node> + <node>PHE:HE1<value>PHE:HE1</value></node> + <node>PHE:CZ<value>PHE:CZ</value></node> + <node>PHE:HZ<value>PHE:HZ</value></node> + <node>PHE:CE2<value>PHE:CE2</value></node> + <node>PHE:HE2<value>PHE:HE2</value></node> + <node>PHE:CD2<value>PHE:CD2</value></node> + <node>PHE:HD2<value>PHE:HD2</value></node> + <node>PRO:CA<value>PRO:CA</value></node> + <node>PRO:HA<value>PRO:HA</value></node> + <node>PRO:CD<value>PRO:CD</value></node> + <node>PRO:HD1<value>PRO:1HD</value></node> + <node>PRO:HD2<value>PRO:2HD</value></node> + <node>PRO:CG<value>PRO:CG</value></node> + <node>PRO:HG1<value>PRO:1HG</value></node> + <node>PRO:HG2<value>PRO:2HG</value></node> + <node>PRO:CB<value>PRO:CB</value></node> + <node>PRO:HB1<value>PRO:1HB</value></node> + <node>PRO:HB2<value>PRO:2HB</value></node> + <node>SER:CA<value>SER:CA</value></node> + <node>SER:HA<value>SER:HA</value></node> + <node>SER:CB<value>SER:CB</value></node> + <node>SER:HB1<value>SER:1HB</value></node> + <node>SER:HB2<value>SER:2HB</value></node> + <node>SER:OG<value>SER:OG</value></node> + <node>SER:HG<value>SER:HG</value></node> + <node>THR:CA<value>THR:CA</value></node> + <node>THR:HA<value>THR:HA</value></node> + <node>THR:CB<value>THR:CB</value></node> + <node>THR:HB<value>THR:HB</value></node> + <node>THR:CG2<value>THR:CG2</value></node> + <node>THR:HG21<value>THR:1HG2</value></node> + <node>THR:HG22<value>THR:2HG2</value></node> + <node>THR:HG23<value>THR:3HG2</value></node> + <node>THR:OG1<value>THR:OG1</value></node> + <node>THR:HG1<value>THR:HG1</value></node> + <node>TRP:CA<value>TRP:CA</value></node> + <node>TRP:HA<value>TRP:HA</value></node> + <node>TRP:CB<value>TRP:CB</value></node> + <node>TRP:HB1<value>TRP:1HB</value></node> + <node>TRP:HB2<value>TRP:2HB</value></node> + <node>TRP:CG<value>TRP:CG</value></node> + <node>TRP:CD1<value>TRP:CD1</value></node> + <node>TRP:HD1<value>TRP:HD1</value></node> + <node>TRP:NE1<value>TRP:NE1</value></node> + <node>TRP:HE1<value>TRP:HE1</value></node> + <node>TRP:CE2<value>TRP:CE2</value></node> + <node>TRP:CZ2<value>TRP:CZ2</value></node> + <node>TRP:HZ2<value>TRP:HZ2</value></node> + <node>TRP:CH2<value>TRP:CH2</value></node> + <node>TRP:HH2<value>TRP:HH2</value></node> + <node>TRP:CZ3<value>TRP:CZ3</value></node> + <node>TRP:HZ3<value>TRP:HZ3</value></node> + <node>TRP:CE3<value>TRP:CE3</value></node> + <node>TRP:HE3<value>TRP:HE3</value></node> + <node>TRP:CD2<value>TRP:CD2</value></node> + <node>TYR:CA<value>TYR:CA</value></node> + <node>TYR:HA<value>TYR:HA</value></node> + <node>TYR:CB<value>TYR:CB</value></node> + <node>TYR:HB1<value>TYR:1HB</value></node> + <node>TYR:HB2<value>TYR:2HB</value></node> + <node>TYR:CG<value>TYR:CG</value></node> + <node>TYR:CD1<value>TYR:CD1</value></node> + <node>TYR:HD1<value>TYR:HD1</value></node> + <node>TYR:CE1<value>TYR:CE1</value></node> + <node>TYR:HE1<value>TYR:HE1</value></node> + <node>TYR:CZ<value>TYR:CZ</value></node> + <node>TYR:OH<value>TYR:OH</value></node> + <node>TYR:HH<value>TYR:HH</value></node> + <node>TYR:CE2<value>TYR:CE2</value></node> + <node>TYR:HE2<value>TYR:HE2</value></node> + <node>TYR:CD2<value>TYR:CD2</value></node> + <node>TYR:HD2<value>TYR:HD2</value></node> + <node>VAL:CA<value>VAL:CA</value></node> + <node>VAL:HA<value>VAL:HA</value></node> + <node>VAL:CB<value>VAL:CB</value></node> + <node>VAL:HB<value>VAL:HB</value></node> + <node>VAL:CG1<value>VAL:CG1</value></node> + <node>VAL:HG11<value>VAL:1HG1</value></node> + <node>VAL:HG12<value>VAL:2HG1</value></node> + <node>VAL:HG13<value>VAL:3HG1</value></node> + <node>VAL:CG2<value>VAL:CG2</value></node> + <node>VAL:HG21<value>VAL:1HG2</value></node> + <node>VAL:HG22<value>VAL:2HG2</value></node> + <node>VAL:HG23<value>VAL:3HG2</value></node> +</node>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/fragments/Names.Star.db Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,261 @@ +<node>Star<value>PDB</value> + <node>*:H1<value>*:1H</value></node> + <node>*:H2<value>*:2H</value></node> + <node>*:H3<value>*:3H</value></node> + <node>*:HT1<value>*:1H</value></node> + <node>*:HT2<value>*:2H</value></node> + <node>*:HT3<value>*:3H</value></node> + <node>*:OT1<value>*:O</value></node> + <node>*:OT2<value>*:OXT</value></node> + <node>*:N<value>*:N</value></node> + <node>*:O<value>*:O</value></node> + <node>*:C<value>*:C</value></node> + <node>*:HN<value>*:H</value></node> + <node>*:H<value>*:H</value></node> + <node>ALA:CA<value>ALA:CA</value></node> + <node>ALA:HA<value>ALA:HA</value></node> + <node>ALA:CB<value>ALA:CB</value></node> + <node>ALA:HB1<value>ALA:1HB</value></node> + <node>ALA:HB2<value>ALA:2HB</value></node> + <node>ALA:HB3<value>ALA:3HB</value></node> + <node>ARG:CA<value>ARG:CA</value></node> + <node>ARG:HA<value>ARG:HA</value></node> + <node>ARG:CB<value>ARG:CB</value></node> + <node>ARG:HB2<value>ARG:1HB</value></node> + <node>ARG:HB3<value>ARG:2HB</value></node> + <node>ARG:CG<value>ARG:CG</value></node> + <node>ARG:HG2<value>ARG:1HG</value></node> + <node>ARG:HG3<value>ARG:2HG</value></node> + <node>ARG:CD<value>ARG:CD</value></node> + <node>ARG:HD2<value>ARG:1HD</value></node> + <node>ARG:HD3<value>ARG:2HD</value></node> + <node>ARG:NE<value>ARG:NE</value></node> + <node>ARG:HE<value>ARG:HE</value></node> + <node>ARG:CZ<value>ARG:CZ</value></node> + <node>ARG:NH1<value>ARG:NH1</value></node> + <node>ARG:HH11<value>ARG:1HH1</value></node> + <node>ARG:HH12<value>ARG:2HH1</value></node> + <node>ARG:NH2<value>ARG:NH2</value></node> + <node>ARG:HH21<value>ARG:1HH2</value></node> + <node>ARG:HH22<value>ARG:2HH2</value></node> + <node>ASN:CA<value>ASN:CA</value></node> + <node>ASN:HA<value>ASN:HA</value></node> + <node>ASN:CB<value>ASN:CB</value></node> + <node>ASN:HB2<value>ASN:1HB</value></node> + <node>ASN:HB3<value>ASN:2HB</value></node> + <node>ASN:CG<value>ASN:CG</value></node> + <node>ASN:OD1<value>ASN:OD1</value></node> + <node>ASN:ND2<value>ASN:ND2</value></node> + <node>ASN:HD21<value>ASN:1HD2</value></node> + <node>ASN:HD22<value>ASN:2HD2</value></node> + <node>ASP:CA<value>ASP:CA</value></node> + <node>ASP:HA<value>ASP:HA</value></node> + <node>ASP:CB<value>ASP:CB</value></node> + <node>ASP:HB2<value>ASP:1HB</value></node> + <node>ASP:HB3<value>ASP:2HB</value></node> + <node>ASP:CG<value>ASP:CG</value></node> + <node>ASP:OD1<value>ASP:OD1</value></node> + <node>ASP:OD2<value>ASP:OD2</value></node> + <node>CYS:CA<value>CYS:CA</value></node> + <node>CYS:HA<value>CYS:HA</value></node> + <node>CYS:CB<value>CYS:CB</value></node> + <node>CYS:HB2<value>CYS:1HB</value></node> + <node>CYS:HB3<value>CYS:2HB</value></node> + <node>CYS:SG<value>CYS:SG</value></node> + <node>CYS:HG<value>CYS:HG</value></node> + <node>GLU:CA<value>GLU:CA</value></node> + <node>GLU:HA<value>GLU:HA</value></node> + <node>GLU:CB<value>GLU:CB</value></node> + <node>GLU:HB2<value>GLU:1HB</value></node> + <node>GLU:HB3<value>GLU:2HB</value></node> + <node>GLU:CG<value>GLU:CG</value></node> + <node>GLU:HG2<value>GLU:1HG</value></node> + <node>GLU:HG3<value>GLU:2HG</value></node> + <node>GLU:CD<value>GLU:CD</value></node> + <node>GLU:OE1<value>GLU:OE1</value></node> + <node>GLU:OE2<value>GLU:OE2</value></node> + <node>GLN:CA<value>GLN:CA</value></node> + <node>GLN:HA<value>GLN:HA</value></node> + <node>GLN:CB<value>GLN:CB</value></node> + <node>GLN:HB2<value>GLN:1HB</value></node> + <node>GLN:HB3<value>GLN:2HB</value></node> + <node>GLN:CG<value>GLN:CG</value></node> + <node>GLN:HG2<value>GLN:1HG</value></node> + <node>GLN:HG3<value>GLN:2HG</value></node> + <node>GLN:CD<value>GLN:CD</value></node> + <node>GLN:OE1<value>GLN:OE1</value></node> + <node>GLN:NE2<value>GLN:NE2</value></node> + <node>GLN:HE21<value>GLN:1HE2</value></node> + <node>GLN:HE22<value>GLN:2HE2</value></node> + <node>GLY:CA<value>GLY:CA</value></node> + <node>GLY:HA2<value>GLY:1HA</value></node> + <node>GLY:HA3<value>GLY:2HA</value></node> + <node>HIS:CA<value>HIS:CA</value></node> + <node>HIS:HA<value>HIS:HA</value></node> + <node>HIS:CB<value>HIS:CB</value></node> + <node>HIS:HB2<value>HIS:1HB</value></node> + <node>HIS:HB3<value>HIS:2HB</value></node> + <node>HIS:CG<value>HIS:CG</value></node> + <node>HIS:ND1<value>HIS:ND1</value></node> + <node>HIS:HD1<value>HIS:HD1</value></node> + <node>HIS:CE1<value>HIS:CE1</value></node> + <node>HIS:HE1<value>HIS:HE1</value></node> + <node>HIS:NE2<value>HIS:NE2</value></node> + <node>HIS:HE2<value>HIS:HE2</value></node> + <node>HIS:CD2<value>HIS:CD2</value></node> + <node>HIS:HD2<value>HIS:HD2</value></node> + <node>ILE:CA<value>ILE:CA</value></node> + <node>ILE:HA<value>ILE:HA</value></node> + <node>ILE:CB<value>ILE:CB</value></node> + <node>ILE:HB<value>ILE:HB</value></node> + <node>ILE:CG2<value>ILE:CG2</value></node> + <node>ILE:HG21<value>ILE:1HG2</value></node> + <node>ILE:HG22<value>ILE:2HG2</value></node> + <node>ILE:HG23<value>ILE:3HG2</value></node> + <node>ILE:CG1<value>ILE:CG1</value></node> + <node>ILE:HG12<value>ILE:1HG1</value></node> + <node>ILE:HG13<value>ILE:2HG1</value></node> + <node>ILE:CD1<value>ILE:CD1</value></node> + <node>ILE:HD11<value>ILE:1HD1</value></node> + <node>ILE:HD12<value>ILE:2HD1</value></node> + <node>ILE:HD13<value>ILE:3HD1</value></node> + <node>LEU:CA<value>LEU:CA</value></node> + <node>LEU:HA<value>LEU:HA</value></node> + <node>LEU:CB<value>LEU:CB</value></node> + <node>LEU:HB2<value>LEU:1HB</value></node> + <node>LEU:HB3<value>LEU:2HB</value></node> + <node>LEU:CG<value>LEU:CG</value></node> + <node>LEU:HG<value>LEU:HG</value></node> + <node>LEU:CD1<value>LEU:CD1</value></node> + <node>LEU:HD11<value>LEU:1HD1</value></node> + <node>LEU:HD12<value>LEU:2HD1</value></node> + <node>LEU:HD13<value>LEU:3HD1</value></node> + <node>LEU:CD2<value>LEU:CD2</value></node> + <node>LEU:HD21<value>LEU:1HD2</value></node> + <node>LEU:HD22<value>LEU:2HD2</value></node> + <node>LEU:HD23<value>LEU:3HD2</value></node> + <node>LYS:CA<value>LYS:CA</value></node> + <node>LYS:HA<value>LYS:HA</value></node> + <node>LYS:CB<value>LYS:CB</value></node> + <node>LYS:HB2<value>LYS:1HB</value></node> + <node>LYS:HB3<value>LYS:2HB</value></node> + <node>LYS:CG<value>LYS:CG</value></node> + <node>LYS:HG2<value>LYS:1HG</value></node> + <node>LYS:HG3<value>LYS:2HG</value></node> + <node>LYS:CD<value>LYS:CD</value></node> + <node>LYS:HD2<value>LYS:1HD</value></node> + <node>LYS:HD3<value>LYS:2HD</value></node> + <node>LYS:CE<value>LYS:CE</value></node> + <node>LYS:HE2<value>LYS:1HE</value></node> + <node>LYS:HE3<value>LYS:2HE</value></node> + <node>LYS:NZ<value>LYS:NZ</value></node> + <node>LYS:HZ1<value>LYS:1HZ</value></node> + <node>LYS:HZ2<value>LYS:2HZ</value></node> + <node>LYS:HZ3<value>LYS:3HZ</value></node> + <node>MET:CA<value>MET:CA</value></node> + <node>MET:HA<value>MET:HA</value></node> + <node>MET:CB<value>MET:CB</value></node> + <node>MET:HB2<value>MET:1HB</value></node> + <node>MET:HB3<value>MET:2HB</value></node> + <node>MET:CG<value>MET:CG</value></node> + <node>MET:HG2<value>MET:1HG</value></node> + <node>MET:HG3<value>MET:2HG</value></node> + <node>MET:SD<value>MET:SD</value></node> + <node>MET:CE<value>MET:CE</value></node> + <node>MET:HE1<value>MET:1HE</value></node> + <node>MET:HE2<value>MET:2HE</value></node> + <node>MET:HE3<value>MET:3HE</value></node> + <node>PHE:CA<value>PHE:CA</value></node> + <node>PHE:HA<value>PHE:HA</value></node> + <node>PHE:CB<value>PHE:CB</value></node> + <node>PHE:HB2<value>PHE:1HB</value></node> + <node>PHE:HB3<value>PHE:2HB</value></node> + <node>PHE:CG<value>PHE:CG</value></node> + <node>PHE:CD1<value>PHE:CD1</value></node> + <node>PHE:HD1<value>PHE:HD1</value></node> + <node>PHE:CE1<value>PHE:CE1</value></node> + <node>PHE:HE1<value>PHE:HE1</value></node> + <node>PHE:CZ<value>PHE:CZ</value></node> + <node>PHE:HZ<value>PHE:HZ</value></node> + <node>PHE:CE2<value>PHE:CE2</value></node> + <node>PHE:HE2<value>PHE:HE2</value></node> + <node>PHE:CD2<value>PHE:CD2</value></node> + <node>PHE:HD2<value>PHE:HD2</value></node> + <node>PRO:CA<value>PRO:CA</value></node> + <node>PRO:HA<value>PRO:HA</value></node> + <node>PRO:CD<value>PRO:CD</value></node> + <node>PRO:HD2<value>PRO:1HD</value></node> + <node>PRO:HD3<value>PRO:2HD</value></node> + <node>PRO:CG<value>PRO:CG</value></node> + <node>PRO:HG2<value>PRO:1HG</value></node> + <node>PRO:HG3<value>PRO:2HG</value></node> + <node>PRO:CB<value>PRO:CB</value></node> + <node>PRO:HB2<value>PRO:1HB</value></node> + <node>PRO:HB3<value>PRO:2HB</value></node> + <node>SER:CA<value>SER:CA</value></node> + <node>SER:HA<value>SER:HA</value></node> + <node>SER:CB<value>SER:CB</value></node> + <node>SER:HB2<value>SER:1HB</value></node> + <node>SER:HB3<value>SER:2HB</value></node> + <node>SER:OG<value>SER:OG</value></node> + <node>SER:HG<value>SER:HG</value></node> + <node>THR:CA<value>THR:CA</value></node> + <node>THR:HA<value>THR:HA</value></node> + <node>THR:CB<value>THR:CB</value></node> + <node>THR:HB<value>THR:HB</value></node> + <node>THR:CG2<value>THR:CG2</value></node> + <node>THR:HG21<value>THR:1HG2</value></node> + <node>THR:HG22<value>THR:2HG2</value></node> + <node>THR:HG23<value>THR:3HG2</value></node> + <node>THR:OG1<value>THR:OG1</value></node> + <node>THR:HG1<value>THR:HG1</value></node> + <node>TRP:CA<value>TRP:CA</value></node> + <node>TRP:HA<value>TRP:HA</value></node> + <node>TRP:CB<value>TRP:CB</value></node> + <node>TRP:HB2<value>TRP:1HB</value></node> + <node>TRP:HB3<value>TRP:2HB</value></node> + <node>TRP:CG<value>TRP:CG</value></node> + <node>TRP:CD1<value>TRP:CD1</value></node> + <node>TRP:HD1<value>TRP:HD1</value></node> + <node>TRP:NE1<value>TRP:NE1</value></node> + <node>TRP:HE1<value>TRP:HE1</value></node> + <node>TRP:CE2<value>TRP:CE2</value></node> + <node>TRP:CZ2<value>TRP:CZ2</value></node> + <node>TRP:HZ2<value>TRP:HZ2</value></node> + <node>TRP:CH2<value>TRP:CH2</value></node> + <node>TRP:HH2<value>TRP:HH2</value></node> + <node>TRP:CZ3<value>TRP:CZ3</value></node> + <node>TRP:HZ3<value>TRP:HZ3</value></node> + <node>TRP:CE3<value>TRP:CE3</value></node> + <node>TRP:HE3<value>TRP:HE3</value></node> + <node>TRP:CD2<value>TRP:CD2</value></node> + <node>TYR:CA<value>TYR:CA</value></node> + <node>TYR:HA<value>TYR:HA</value></node> + <node>TYR:CB<value>TYR:CB</value></node> + <node>TYR:HB2<value>TYR:1HB</value></node> + <node>TYR:HB3<value>TYR:2HB</value></node> + <node>TYR:CG<value>TYR:CG</value></node> + <node>TYR:CD1<value>TYR:CD1</value></node> + <node>TYR:HD1<value>TYR:HD1</value></node> + <node>TYR:CE1<value>TYR:CE1</value></node> + <node>TYR:HE1<value>TYR:HE1</value></node> + <node>TYR:CZ<value>TYR:CZ</value></node> + <node>TYR:OH<value>TYR:OH</value></node> + <node>TYR:HH<value>TYR:HH</value></node> + <node>TYR:CE2<value>TYR:CE2</value></node> + <node>TYR:HE2<value>TYR:HE2</value></node> + <node>TYR:CD2<value>TYR:CD2</value></node> + <node>TYR:HD2<value>TYR:HD2</value></node> + <node>VAL:CA<value>VAL:CA</value></node> + <node>VAL:HA<value>VAL:HA</value></node> + <node>VAL:CB<value>VAL:CB</value></node> + <node>VAL:HB<value>VAL:HB</value></node> + <node>VAL:CG1<value>VAL:CG1</value></node> + <node>VAL:HG11<value>VAL:1HG1</value></node> + <node>VAL:HG12<value>VAL:2HG1</value></node> + <node>VAL:HG13<value>VAL:3HG1</value></node> + <node>VAL:CG2<value>VAL:CG2</value></node> + <node>VAL:HG21<value>VAL:1HG2</value></node> + <node>VAL:HG22<value>VAL:2HG2</value></node> + <node>VAL:HG23<value>VAL:3HG2</value></node> +</node>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/fragments/Names.XPLOR.db Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,256 @@ +<node>XPLOR<value>PDB</value> + <node>*:H1<value>*:1H</value></node> + <node>*:H2<value>*:2H</value></node> + <node>*:H3<value>*:3H</value></node> + <node>*:N<value>*:N</value></node> + <node>*:O<value>*:O</value></node> + <node>*:C<value>*:C</value></node> + <node>*:HN<value>*:H</value></node> + <node>*:H<value>*:H</value></node> + <node>ALA:CA<value>ALA:CA</value></node> + <node>ALA:HA<value>ALA:HA</value></node> + <node>ALA:CB<value>ALA:CB</value></node> + <node>ALA:HB1<value>ALA:1HB</value></node> + <node>ALA:HB2<value>ALA:2HB</value></node> + <node>ALA:HB3<value>ALA:3HB</value></node> + <node>ARG:CA<value>ARG:CA</value></node> + <node>ARG:HA<value>ARG:HA</value></node> + <node>ARG:CB<value>ARG:CB</value></node> + <node>ARG:HB1<value>ARG:1HB</value></node> + <node>ARG:HB2<value>ARG:2HB</value></node> + <node>ARG:CG<value>ARG:CG</value></node> + <node>ARG:HG1<value>ARG:1HG</value></node> + <node>ARG:HG2<value>ARG:2HG</value></node> + <node>ARG:CD<value>ARG:CD</value></node> + <node>ARG:HD1<value>ARG:1HD</value></node> + <node>ARG:HD2<value>ARG:2HD</value></node> + <node>ARG:NE<value>ARG:NE</value></node> + <node>ARG:HE<value>ARG:HE</value></node> + <node>ARG:CZ<value>ARG:CZ</value></node> + <node>ARG:NH1<value>ARG:NH1</value></node> + <node>ARG:HH11<value>ARG:1HH1</value></node> + <node>ARG:HH12<value>ARG:2HH1</value></node> + <node>ARG:NH2<value>ARG:NH2</value></node> + <node>ARG:HH21<value>ARG:1HH2</value></node> + <node>ARG:HH22<value>ARG:2HH2</value></node> + <node>ASN:CA<value>ASN:CA</value></node> + <node>ASN:HA<value>ASN:HA</value></node> + <node>ASN:CB<value>ASN:CB</value></node> + <node>ASN:HB1<value>ASN:1HB</value></node> + <node>ASN:HB2<value>ASN:2HB</value></node> + <node>ASN:CG<value>ASN:CG</value></node> + <node>ASN:OD1<value>ASN:OD1</value></node> + <node>ASN:ND2<value>ASN:ND2</value></node> + <node>ASN:HD21<value>ASN:1HD2</value></node> + <node>ASN:HD22<value>ASN:2HD2</value></node> + <node>ASP:CA<value>ASP:CA</value></node> + <node>ASP:HA<value>ASP:HA</value></node> + <node>ASP:CB<value>ASP:CB</value></node> + <node>ASP:HB1<value>ASP:1HB</value></node> + <node>ASP:HB2<value>ASP:2HB</value></node> + <node>ASP:CG<value>ASP:CG</value></node> + <node>ASP:OD1<value>ASP:OD1</value></node> + <node>ASP:OD2<value>ASP:OD2</value></node> + <node>CYS:CA<value>CYS:CA</value></node> + <node>CYS:HA<value>CYS:HA</value></node> + <node>CYS:CB<value>CYS:CB</value></node> + <node>CYS:HB1<value>CYS:1HB</value></node> + <node>CYS:HB2<value>CYS:2HB</value></node> + <node>CYS:SG<value>CYS:SG</value></node> + <node>CYS:HG<value>CYS:HG</value></node> + <node>GLU:CA<value>GLU:CA</value></node> + <node>GLU:HA<value>GLU:HA</value></node> + <node>GLU:CB<value>GLU:CB</value></node> + <node>GLU:HB1<value>GLU:1HB</value></node> + <node>GLU:HB2<value>GLU:2HB</value></node> + <node>GLU:CG<value>GLU:CG</value></node> + <node>GLU:HG1<value>GLU:1HG</value></node> + <node>GLU:HG2<value>GLU:2HG</value></node> + <node>GLU:CD<value>GLU:CD</value></node> + <node>GLU:OE1<value>GLU:OE1</value></node> + <node>GLU:OE2<value>GLU:OE2</value></node> + <node>GLN:CA<value>GLN:CA</value></node> + <node>GLN:HA<value>GLN:HA</value></node> + <node>GLN:CB<value>GLN:CB</value></node> + <node>GLN:HB1<value>GLN:1HB</value></node> + <node>GLN:HB2<value>GLN:2HB</value></node> + <node>GLN:CG<value>GLN:CG</value></node> + <node>GLN:HG1<value>GLN:1HG</value></node> + <node>GLN:HG2<value>GLN:2HG</value></node> + <node>GLN:CD<value>GLN:CD</value></node> + <node>GLN:OE1<value>GLN:OE1</value></node> + <node>GLN:NE2<value>GLN:NE2</value></node> + <node>GLN:HE21<value>GLN:1HE2</value></node> + <node>GLN:HE22<value>GLN:2HE2</value></node> + <node>GLY:CA<value>GLY:CA</value></node> + <node>GLY:HA1<value>GLY:1HA</value></node> + <node>GLY:HA2<value>GLY:2HA</value></node> + <node>HIS:CA<value>HIS:CA</value></node> + <node>HIS:HA<value>HIS:HA</value></node> + <node>HIS:CB<value>HIS:CB</value></node> + <node>HIS:HB1<value>HIS:1HB</value></node> + <node>HIS:HB2<value>HIS:2HB</value></node> + <node>HIS:CG<value>HIS:CG</value></node> + <node>HIS:ND1<value>HIS:ND1</value></node> + <node>HIS:HD1<value>HIS:HD1</value></node> + <node>HIS:CE1<value>HIS:CE1</value></node> + <node>HIS:HE1<value>HIS:HE1</value></node> + <node>HIS:NE2<value>HIS:NE2</value></node> + <node>HIS:HE2<value>HIS:HE2</value></node> + <node>HIS:CD2<value>HIS:CD2</value></node> + <node>HIS:HD2<value>HIS:HD2</value></node> + <node>ILE:CA<value>ILE:CA</value></node> + <node>ILE:HA<value>ILE:HA</value></node> + <node>ILE:CB<value>ILE:CB</value></node> + <node>ILE:HB<value>ILE:HB</value></node> + <node>ILE:CG2<value>ILE:CG2</value></node> + <node>ILE:HG21<value>ILE:1HG2</value></node> + <node>ILE:HG22<value>ILE:2HG2</value></node> + <node>ILE:HG23<value>ILE:3HG2</value></node> + <node>ILE:CG1<value>ILE:CG1</value></node> + <node>ILE:HG11<value>ILE:1HG1</value></node> + <node>ILE:HG12<value>ILE:2HG1</value></node> + <node>ILE:CD1<value>ILE:CD1</value></node> + <node>ILE:HD11<value>ILE:1HD1</value></node> + <node>ILE:HD12<value>ILE:2HD1</value></node> + <node>ILE:HD13<value>ILE:3HD1</value></node> + <node>LEU:CA<value>LEU:CA</value></node> + <node>LEU:HA<value>LEU:HA</value></node> + <node>LEU:CB<value>LEU:CB</value></node> + <node>LEU:HB1<value>LEU:1HB</value></node> + <node>LEU:HB2<value>LEU:2HB</value></node> + <node>LEU:CG<value>LEU:CG</value></node> + <node>LEU:HG<value>LEU:HG</value></node> + <node>LEU:CD1<value>LEU:CD1</value></node> + <node>LEU:HD11<value>LEU:1HD1</value></node> + <node>LEU:HD12<value>LEU:2HD1</value></node> + <node>LEU:HD13<value>LEU:3HD1</value></node> + <node>LEU:CD2<value>LEU:CD2</value></node> + <node>LEU:HD21<value>LEU:1HD2</value></node> + <node>LEU:HD22<value>LEU:2HD2</value></node> + <node>LEU:HD23<value>LEU:3HD2</value></node> + <node>LYS:CA<value>LYS:CA</value></node> + <node>LYS:HA<value>LYS:HA</value></node> + <node>LYS:CB<value>LYS:CB</value></node> + <node>LYS:HB1<value>LYS:1HB</value></node> + <node>LYS:HB2<value>LYS:2HB</value></node> + <node>LYS:CG<value>LYS:CG</value></node> + <node>LYS:HG1<value>LYS:1HG</value></node> + <node>LYS:HG2<value>LYS:2HG</value></node> + <node>LYS:CD<value>LYS:CD</value></node> + <node>LYS:HD1<value>LYS:1HD</value></node> + <node>LYS:HD2<value>LYS:2HD</value></node> + <node>LYS:CE<value>LYS:CE</value></node> + <node>LYS:HE1<value>LYS:1HE</value></node> + <node>LYS:HE2<value>LYS:2HE</value></node> + <node>LYS:NZ<value>LYS:NZ</value></node> + <node>LYS:HZ1<value>LYS:1HZ</value></node> + <node>LYS:HZ2<value>LYS:2HZ</value></node> + <node>LYS:HZ3<value>LYS:3HZ</value></node> + <node>MET:CA<value>MET:CA</value></node> + <node>MET:HA<value>MET:HA</value></node> + <node>MET:CB<value>MET:CB</value></node> + <node>MET:HB1<value>MET:1HB</value></node> + <node>MET:HB2<value>MET:2HB</value></node> + <node>MET:CG<value>MET:CG</value></node> + <node>MET:HG1<value>MET:1HG</value></node> + <node>MET:HG2<value>MET:2HG</value></node> + <node>MET:SD<value>MET:SD</value></node> + <node>MET:CE<value>MET:CE</value></node> + <node>MET:HE1<value>MET:1HE</value></node> + <node>MET:HE2<value>MET:2HE</value></node> + <node>MET:HE3<value>MET:3HE</value></node> + <node>PHE:CA<value>PHE:CA</value></node> + <node>PHE:HA<value>PHE:HA</value></node> + <node>PHE:CB<value>PHE:CB</value></node> + <node>PHE:HB1<value>PHE:1HB</value></node> + <node>PHE:HB2<value>PHE:2HB</value></node> + <node>PHE:CG<value>PHE:CG</value></node> + <node>PHE:CD1<value>PHE:CD1</value></node> + <node>PHE:HD1<value>PHE:HD1</value></node> + <node>PHE:CE1<value>PHE:CE1</value></node> + <node>PHE:HE1<value>PHE:HE1</value></node> + <node>PHE:CZ<value>PHE:CZ</value></node> + <node>PHE:HZ<value>PHE:HZ</value></node> + <node>PHE:CE2<value>PHE:CE2</value></node> + <node>PHE:HE2<value>PHE:HE2</value></node> + <node>PHE:CD2<value>PHE:CD2</value></node> + <node>PHE:HD2<value>PHE:HD2</value></node> + <node>PRO:CA<value>PRO:CA</value></node> + <node>PRO:HA<value>PRO:HA</value></node> + <node>PRO:CD<value>PRO:CD</value></node> + <node>PRO:HD1<value>PRO:1HD</value></node> + <node>PRO:HD2<value>PRO:2HD</value></node> + <node>PRO:CG<value>PRO:CG</value></node> + <node>PRO:HG1<value>PRO:1HG</value></node> + <node>PRO:HG2<value>PRO:2HG</value></node> + <node>PRO:CB<value>PRO:CB</value></node> + <node>PRO:HB1<value>PRO:1HB</value></node> + <node>PRO:HB2<value>PRO:2HB</value></node> + <node>SER:CA<value>SER:CA</value></node> + <node>SER:HA<value>SER:HA</value></node> + <node>SER:CB<value>SER:CB</value></node> + <node>SER:HB1<value>SER:1HB</value></node> + <node>SER:HB2<value>SER:2HB</value></node> + <node>SER:OG<value>SER:OG</value></node> + <node>SER:HG<value>SER:HG</value></node> + <node>THR:CA<value>THR:CA</value></node> + <node>THR:HA<value>THR:HA</value></node> + <node>THR:CB<value>THR:CB</value></node> + <node>THR:HB<value>THR:HB</value></node> + <node>THR:CG2<value>THR:CG2</value></node> + <node>THR:HG21<value>THR:1HG2</value></node> + <node>THR:HG22<value>THR:2HG2</value></node> + <node>THR:HG23<value>THR:3HG2</value></node> + <node>THR:OG1<value>THR:OG1</value></node> + <node>THR:HG1<value>THR:HG1</value></node> + <node>TRP:CA<value>TRP:CA</value></node> + <node>TRP:HA<value>TRP:HA</value></node> + <node>TRP:CB<value>TRP:CB</value></node> + <node>TRP:HB1<value>TRP:1HB</value></node> + <node>TRP:HB2<value>TRP:2HB</value></node> + <node>TRP:CG<value>TRP:CG</value></node> + <node>TRP:CD1<value>TRP:CD1</value></node> + <node>TRP:HD1<value>TRP:HD1</value></node> + <node>TRP:NE1<value>TRP:NE1</value></node> + <node>TRP:HE1<value>TRP:HE1</value></node> + <node>TRP:CE2<value>TRP:CE2</value></node> + <node>TRP:CZ2<value>TRP:CZ2</value></node> + <node>TRP:HZ2<value>TRP:HZ2</value></node> + <node>TRP:CH2<value>TRP:CH2</value></node> + <node>TRP:HH2<value>TRP:HH2</value></node> + <node>TRP:CZ3<value>TRP:CZ3</value></node> + <node>TRP:HZ3<value>TRP:HZ3</value></node> + <node>TRP:CE3<value>TRP:CE3</value></node> + <node>TRP:HE3<value>TRP:HE3</value></node> + <node>TRP:CD2<value>TRP:CD2</value></node> + <node>TYR:CA<value>TYR:CA</value></node> + <node>TYR:HA<value>TYR:HA</value></node> + <node>TYR:CB<value>TYR:CB</value></node> + <node>TYR:HB1<value>TYR:1HB</value></node> + <node>TYR:HB2<value>TYR:2HB</value></node> + <node>TYR:CG<value>TYR:CG</value></node> + <node>TYR:CD1<value>TYR:CD1</value></node> + <node>TYR:HD1<value>TYR:HD1</value></node> + <node>TYR:CE1<value>TYR:CE1</value></node> + <node>TYR:HE1<value>TYR:HE1</value></node> + <node>TYR:CZ<value>TYR:CZ</value></node> + <node>TYR:OH<value>TYR:OH</value></node> + <node>TYR:HH<value>TYR:HH</value></node> + <node>TYR:CE2<value>TYR:CE2</value></node> + <node>TYR:HE2<value>TYR:HE2</value></node> + <node>TYR:CD2<value>TYR:CD2</value></node> + <node>TYR:HD2<value>TYR:HD2</value></node> + <node>VAL:CA<value>VAL:CA</value></node> + <node>VAL:HA<value>VAL:HA</value></node> + <node>VAL:CB<value>VAL:CB</value></node> + <node>VAL:HB<value>VAL:HB</value></node> + <node>VAL:CG1<value>VAL:CG1</value></node> + <node>VAL:HG11<value>VAL:1HG1</value></node> + <node>VAL:HG12<value>VAL:2HG1</value></node> + <node>VAL:HG13<value>VAL:3HG1</value></node> + <node>VAL:CG2<value>VAL:CG2</value></node> + <node>VAL:HG21<value>VAL:1HG2</value></node> + <node>VAL:HG22<value>VAL:2HG2</value></node> + <node>VAL:HG23<value>VAL:3HG2</value></node> +</node>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/fragments/PCA.db Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,58 @@ +<node>PCA + <node>Names + <node>Pyroglutamate</node> + <node>Pyroglutamat</node> + <node>PCA</node> + </node> + <node>Atoms + <node>N<value>N 0.633233 -0.738520 0.753950</value></node> + <node>H<value>H 0.354342 -1.687937 0.623119</value></node> + <node>CA<value>C -0.480480 0.254947 0.696080</value></node> + <node>C<value>C -1.757691 -0.270758 -0.060790</value></node> + <node>O<value>O -1.739275 -1.432777 -0.530185</value></node> + <node>CB<value>C 0.102054 1.514384 0.035819</value></node> + <node>CG<value>C 1.511340 1.164025 -0.440294</value></node> + <node>CD<value>C 1.725147 -0.277577 -0.025832</value></node> + <node>OE<value>O 2.716615 -0.966582 -0.238284</value></node> + <node>HA<value>H -0.765277 0.458788 1.753344</value></node> + <node>1HB<value>H -0.540287 1.847529 -0.801287</value></node> + <node>2HB<value>H 0.122684 2.361261 0.746090</value></node> + <node>1HG<value>H 1.616550 1.265144 -1.535904</value></node> + <node>2HG<value>H 2.282434 1.821242 0.000860</value></node> + <node>OXT<value>O -2.740502 0.498543 -0.143251</value></node> + </node> + <node>Bonds + <node>4<value>H N s</value></node> + <node>5<value>C CA s</value></node> + <node>8<value>O C d</value></node> + <node>11<value>CB CA s</value></node> + <node>13<value>CG CB s</value></node> + <node>17<value>CD CG s</value></node> + <node>19<value>CD N s</value></node> + <node>20<value>OE CD d</value></node> + <node>21<value>HA CA s</value></node> + <node>22<value>1HB CB s</value></node> + <node>23<value>2HB CB s</value></node> + <node>24<value>1HG CG s</value></node> + <node>25<value>2HG CG s</value></node> + <node>26<value>OXT C s</value></node> + <node>27<value>N CA s</value></node> + </node> + <node>Connections + <node>C-term<value>C N-term s 1.33 0.5</value></node> + </node> + <node>Properties + </node> + <node>Variants + <node>Default + </node> + <node>PCA-N + <node>Delete + <node>OXT</node> + </node> + <node>Properties + <node>N_TERMINAL</node> + </node> + </node> + </node> +</node>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/fragments/PHE.db Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,103 @@ +<node>PHE + <node>Names + <node>Phenylalanine</node> + <node>Phenylalanin</node> + <node>Phe</node> + <node>F</node> + </node> + <node>Atoms + <node>N<value>N 0.1341407 1.351202 -0.07911759</value></node> + <node>3H<value>H 0.803193 2.035005 0.2534044</value></node> + <node>CA<value>C -0.7211604 2.001838 -1.087341</value></node> + <node>HA<value>H -0.07892336 2.270821 -1.926756</value></node> + <node>C<value>C -1.300131 3.307535 -0.5325462</value></node> + <node>O<value>O -0.4477309 4.171679 -0.229457</value></node> + <node>CB<value>C -1.791856 1.027805 -1.599674</value></node> + <node>1HB<value>H -1.28636 0.160502 -2.026756</value></node> + <node>2HB<value>H -2.380364 0.6727667 -0.7525354</value></node> + <node>CG<value>C -2.70873 1.607533 -2.661208</value></node> + <node>CD1<value>C -4.074711 1.815559 -2.387768</value></node> + <node>HD1<value>H -4.496757 1.527902 -1.435336</value></node> + <node>CD2<value>C -2.185439 1.971959 -3.916095</value></node> + <node>HD2<value>H -1.142983 1.801105 -4.144545</value></node> + <node>CE1<value>C -4.90709 2.399215 -3.358655</value></node> + <node>HE1<value>H -5.955226 2.557371 -3.147432</value></node> + <node>CE2<value>C -3.019025 2.554821 -4.88633</value></node> + <node>HE2<value>H -2.61471 2.832835 -5.84938</value></node> + <node>CZ<value>C -4.379117 2.771946 -4.606688</value></node> + <node>HZ<value>H -5.020426 3.217529 -5.354036</value></node> + <node>1H<value>H -0.4341985 1.034029 0.6931909</value></node> + <node>2H<value>H 0.6169096 0.5661594 -0.4922875</value></node> + <node>OXT<value>O -2.460581 3.26509 -0.06804343</value></node> + </node> + <node>Bonds + <node>5<value>3H N s</value></node> + <node>6<value>CA N s</value></node> + <node>10<value>HA CA s</value></node> + <node>11<value>C CA s</value></node> + <node>14<value>O C d</value></node> + <node>15<value>CB CA s</value></node> + <node>19<value>1HB CB s</value></node> + <node>20<value>2HB CB s</value></node> + <node>21<value>CG CB s</value></node> + <node>24<value>CD1 CG a</value></node> + <node>27<value>HD1 CD1 s</value></node> + <node>28<value>CD2 CG a</value></node> + <node>31<value>HD2 CD2 s</value></node> + <node>32<value>CE1 CD1 a</value></node> + <node>35<value>HE1 CE1 s</value></node> + <node>36<value>CE2 CD2 a</value></node> + <node>39<value>HE2 CE2 s</value></node> + <node>40<value>CZ CE1 a</value></node> + <node>41<value>CZ CE2 a</value></node> + <node>43<value>HZ CZ s</value></node> + <node>44<value>1H N s</value></node> + <node>45<value>2H N s</value></node> + <node>46<value>OXT C s</value></node> + </node> + <node>Connections + <node>N-term<value>N C-term s 1.33 0.5</value></node> + <node>C-term<value>C N-term s 1.33 0.5</value></node> + </node> + <node>Properties + <node>AMINO_ACID</node> + </node> + <node>Variants + <node>Default + <node>Delete + <node>OXT</node> + <node>1H</node> + <node>2H</node> + </node> + <node>Rename + <node>3H<value>H</value></node> + </node> + </node> + <node>PHE-M + <node>Properties + <node>C_TERMINAL</node> + <node>N_TERMINAL</node> + </node> + </node> + <node>PHE-C + <node>Delete + <node>1H</node> + <node>2H</node> + </node> + <node>Rename + <node>3H<value>H</value></node> + </node> + <node>Properties + <node>C_TERMINAL</node> + </node> + </node> + <node>PHE-N + <node>Delete + <node>OXT</node> + </node> + <node>Properties + <node>N_TERMINAL</node> + </node> + </node> + </node> +</node>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/fragments/PRO.db Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,85 @@ +<node>PRO + <node>Names + <node>Proline</node> + <node>Prolin</node> + <node>Pro</node> + <node>P</node> + </node> + <node>Atoms + <node>N<value>N 0.03190848 1.374047 -0.2465853</value></node> + <node>CA<value>C 0.4437964 0.4522487 -1.313841</value></node> + <node>HA<value>H -0.4329885 0.1122399 -1.866649</value></node> + <node>C<value>C 1.153984 -0.7795747 -0.7384319</value></node> + <node>O<value>O 2.396496 -0.7261156 -0.5988901</value></node> + <node>CB<value>C 1.34565 1.283736 -2.23033</value></node> + <node>1HB<value>H 2.062533 0.6767905 -2.785621</value></node> + <node>2HB<value>H 0.7182986 1.840951 -2.927554</value></node> + <node>CG<value>C 2.02933 2.275858 -1.278275</value></node> + <node>1HG<value>H 3.057449 1.966999 -1.081919</value></node> + <node>2HG<value>H 2.018846 3.280874 -1.702292</value></node> + <node>CD<value>C 1.21179 2.210818 0.01815094</value></node> + <node>1HD<value>H 0.9135454 3.204023 0.3557259</value></node> + <node>2HD<value>H 1.815136 1.733186 0.791898</value></node> + <node>OXT<value>O 0.4228693 -1.712297 -0.3395816</value></node> + <node>1H<value>H -0.2823305 0.8858488 0.5799416</value></node> + <node>2H<value>H -0.7056003 1.96474 -0.6034356</value></node> + </node> + <node>Bonds + <node>5<value>CA N s</value></node> + <node>9<value>HA CA s</value></node> + <node>10<value>C CA s</value></node> + <node>13<value>O C d</value></node> + <node>14<value>CB CA s</value></node> + <node>18<value>1HB CB s</value></node> + <node>19<value>2HB CB s</value></node> + <node>20<value>CG CB s</value></node> + <node>24<value>1HG CG s</value></node> + <node>25<value>2HG CG s</value></node> + <node>26<value>CD N s</value></node> + <node>27<value>CD CG s</value></node> + <node>30<value>1HD CD s</value></node> + <node>31<value>2HD CD s</value></node> + <node>32<value>OXT C s</value></node> + <node>33<value>1H N s</value></node> + <node>34<value>2H N s</value></node> + </node> + <node>Connections + <node>N-term<value>N C-term s 1.33 0.5</value></node> + <node>C-term<value>C N-term s 1.33 0.5</value></node> + </node> + <node>Properties + <node>AMINO_ACID</node> + </node> + <node>Variants + <node>Default + <node>Delete + <node>OXT</node> + <node>1H</node> + <node>2H</node> + </node> + </node> + <node>PRO-M + <node>Properties + <node>C_TERMINAL</node> + <node>N_TERMINAL</node> + </node> + </node> + <node>PRO-C + <node>Delete + <node>1H</node> + <node>2H</node> + </node> + <node>Properties + <node>C_TERMINAL</node> + </node> + </node> + <node>PRO-N + <node>Delete + <node>OXT</node> + </node> + <node>Properties + <node>N_TERMINAL</node> + </node> + </node> + </node> +</node>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/fragments/Pyrrole-Skeleton.db Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,21 @@ +<node>Pyrrole-Skeleton + <node>Names + <node>Pyrrole-Skeleton</node> + </node> + <node>Atoms + <node>C1<value>C -0.028662 -0.037639 1.451927</value></node> + <node>N2<value>N -0.002221 -1.136686 0.619895</value></node> + <node>C3<value>C 0.0447 -0.76844 -0.708243</value></node> + <node>C4<value>C 0.046187 0.65781 -0.681334</value></node> + <node>C5<value>C -0.008647 1.094253 0.712146</value></node> + </node> + <node>Bonds + <node>1<value>C1 N2 s</value></node> + <node>2<value>N2 C3 d</value></node> + <node>3<value>C3 C4 s</value></node> + <node>4<value>C4 C5 d</value></node> + <node>5<value>C5 C1 s</value></node> + </node> + <node>Properties + </node> +</node>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/fragments/SER.db Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,84 @@ +<node>SER + <node>Names + <node>Serine</node> + <node>Serin</node> + <node>Ser</node> + <node>S</node> + </node> + <node>Atoms + <node>N<value>N 0.1130663 1.226434 -0.1468897</value></node> + <node>3H<value>H 0.8968111 1.837972 0.05464922</value></node> + <node>CA<value>C -0.7048293 1.905604 -1.168307</value></node> + <node>HA<value>H -0.2017423 1.780946 -2.128185</value></node> + <node>C<value>C -0.7701361 3.410257 -0.8778276</value></node> + <node>O<value>O 0.1488766 3.858471 -0.1539113</value></node> + <node>CB<value>C -2.088618 1.24965 -1.250489</value></node> + <node>1HB<value>H -1.956628 0.1725609 -1.368818</value></node> + <node>2HB<value>H -2.637483 1.435655 -0.3253672</value></node> + <node>OG<value>O -2.817839 1.744102 -2.356831</value></node> + <node>HG<value>H -3.648096 1.264079 -2.429246</value></node> + <node>OXT<value>O -1.487331 4.10633 -1.629405</value></node> + <node>1H<value>H -0.4311985 1.10388 0.6950446</value></node> + <node>2H<value>H 0.4303224 0.3296314 -0.4862972</value></node> + </node> + <node>Bonds + <node>5<value>3H N s</value></node> + <node>6<value>CA N s</value></node> + <node>10<value>HA CA s</value></node> + <node>11<value>C CA s</value></node> + <node>14<value>O C d</value></node> + <node>15<value>CB CA s</value></node> + <node>19<value>1HB CB s</value></node> + <node>20<value>2HB CB s</value></node> + <node>21<value>OG CB s</value></node> + <node>23<value>HG OG s</value></node> + <node>24<value>OXT C s</value></node> + <node>25<value>1H N s</value></node> + <node>26<value>2H N s</value></node> + </node> + <node>Connections + <node>N-term<value>N C-term s 1.33 0.5</value></node> + <node>C-term<value>C N-term s 1.33 0.5</value></node> + </node> + <node>Properties + <node>AMINO_ACID</node> + </node> + <node>Variants + <node>Default + <node>Delete + <node>OXT</node> + <node>1H</node> + <node>2H</node> + </node> + <node>Rename + <node>3H<value>H</value></node> + </node> + </node> + <node>SER-M + <node>Properties + <node>N_TERMINAL</node> + <node>C_TERMINAL</node> + </node> + </node> + <node>SER-N + <node>Delete + <node>OXT</node> + </node> + <node>Properties + <node>N_TERMINAL</node> + </node> + </node> + <node>SER-C + <node>Delete + <node>1H</node> + <node>2H</node> + </node> + <node>Rename + <node>3H<value>H</value></node> + </node> + <node>Properties + <node>C_TERMINAL</node> + </node> + </node> + </node> +</node>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/fragments/T.db Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,106 @@ +<node>T + <node>Names + <node>Thymine</node> + <node>Thymin</node> + <node>T</node> + </node> + <node>Atoms + <node>P<value>P 38.566 27.407 37.821</value></node> + <node>O1P<value>O 38.595 26.254 36.889</value></node> + <node>O2P<value>O 39.157 27.302 39.179</value></node> + <node>O5*<value>O 37.072 27.912 37.957</value></node> + <node>C5*<value>C 36.632 28.815 38.965</value></node> + <node>1H5*<value>H 37.233 29.724 38.959</value></node> + <node>2H5*<value>H 36.702 28.339 39.943</value></node> + <node>C4*<value>C 35.191 29.171 38.689</value></node> + <node>H4*<value>H 34.765 29.830 39.445</value></node> + <node>O4*<value>O 35.114 29.926 37.469</value></node> + <node>C3*<value>C 34.331 27.906 38.457</value></node> + <node>H3*<value>H 34.825 26.944 38.594</value></node> + <node>O3*<value>O 33.163 27.975 39.270</value></node> + <node>C2*<value>C 33.920 28.064 36.992</value></node> + <node>1H2*<value>H 34.360 27.260 36.402</value></node> + <node>2H2*<value>H 32.834 28.020 36.912</value></node> + <node>C1*<value>C 33.860 29.573 36.906</value></node> + <node>H1*<value>H 33.070 30.098 37.443</value></node> + <node>N1<value>N 33.730 30.096 35.526</value></node> + <node>C6<value>C 34.405 29.543 34.472</value></node> + <node>H6<value>H 35.056 28.699 34.642</value></node> + <node>C5<value>C 34.237 29.984 33.219</value></node> + <node>C5M<value>C 35.018 29.323 32.073</value></node> + <node>1H5M<value>H 34.762 28.265 32.021</value></node> + <node>2H5M<value>H 34.759 29.806 31.130</value></node> + <node>3H5M<value>H 36.088 29.429 32.253</value></node> + <node>C4<value>C 33.326 31.071 32.932</value></node> + <node>O4<value>O 33.094 31.529 31.816</value></node> + <node>N3<value>N 32.681 31.586 34.053</value></node> + <node>3H<value>H 31.993 32.416 33.893</value></node> + <node>C2<value>C 32.839 31.151 35.352</value></node> + <node>O2<value>O 32.225 31.690 36.276</value></node> + </node> + <node>Bonds + <node>1<value>P O1P s</value></node> + <node>2<value>P O2P d</value></node> + <node>3<value>P O5* s</value></node> + <node>4<value>O5* C5* s</value></node> + <node>5<value>C5* C4* s</value></node> + <node>6<value>C4* O4* s</value></node> + <node>7<value>C4* C3* s</value></node> + <node>8<value>C3* O3* s</value></node> + <node>9<value>C3* C2* s</value></node> + <node>10<value>C2* C1* s</value></node> + <node>11<value>C1* O4* s</value></node> + <node>12<value>C1* N1 s</value></node> + <node>13<value>N1 C6 s</value></node> + <node>14<value>C6 C5 d</value></node> + <node>15<value>C5 C5M s</value></node> + <node>16<value>C5 C4 s</value></node> + <node>17<value>C4 O4 d</value></node> + <node>18<value>C4 N3 s</value></node> + <node>19<value>N3 C2 s</value></node> + <node>20<value>C2 O2 d</value></node> + <node>21<value>C2 N1 s</value></node> + <node>22<value>C5* 1H5* s</value></node> + <node>23<value>C5* 2H5* s</value></node> + <node>24<value>C4* H4* s</value></node> + <node>25<value>C1* H1* s</value></node> + <node>26<value>C3* H3* s</value></node> + <node>27<value>C2* 1H2* s</value></node> + <node>28<value>C2* 2H2* s</value></node> + <node>29<value>C6 H6 s</value></node> + <node>30<value>C5M 1H5M s</value></node> + <node>31<value>C5M 2H5M s</value></node> + <node>32<value>C5M 3H5M s</value></node> + <node>33<value>N3 3H s</value></node> + </node> + <node>Connections + <node>5-term<value>P 3-term s 1.62 0.5</value></node> + <node>3-term<value>O3* 5-term s 1.62 0.5</value></node> + </node> + <node>Properties + <node>NUCLEOTIDE</node> + </node> + <node>Variants + <node>T-M + <node>Properties + <node>5_PRIME</node> + <node>3_PRIME</node> + </node> + </node> + <node>Default + <node>Properties + </node> + </node> + <node>T-3 + <node>Properties + <node>3_PRIME</node> + </node> + </node> + <node>T-5 + <node>Properties + <node>5_PRIME</node> + </node> + </node> + </node> +</node> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/fragments/THR.db Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,90 @@ +<node>THR + <node>Names + <node>Threonine</node> + <node>Threonin</node> + <node>Thr</node> + <node>T</node> + </node> + <node>Atoms + <node>N<value>N 0.07944571 1.265783 -0.06982248</value></node> + <node>3H<value>H 0.9103429 1.833856 0.0462634</value></node> + <node>CA<value>C -0.730729 1.899472 -1.127707</value></node> + <node>HA<value>H -0.2399387 1.69489 -2.079941</value></node> + <node>C<value>C -0.7224239 3.419906 -0.9435946</value></node> + <node>O<value>O 0.3746189 3.909003 -0.5883108</value></node> + <node>CB<value>C -2.153607 1.314487 -1.182294</value></node> + <node>HB<value>H -2.679771 1.729994 -2.044027</value></node> + <node>OG1<value>O -2.862524 1.651035 -0.00717756</value></node> + <node>HG1<value>H -3.698466 1.178201 0.002366092</value></node> + <node>CG2<value>C -2.126356 -0.2100642 -1.334626</value></node> + <node>1HG2<value>H -3.140605 -0.5875605 -1.466431</value></node> + <node>2HG2<value>H -1.532317 -0.4833375 -2.207111</value></node> + <node>3HG2<value>H -1.690858 -0.6725402 -0.448057</value></node> + <node>1H<value>H -0.4419178 1.260401 0.7952214</value></node> + <node>2H<value>H 0.324596 0.3214647 -0.3308986</value></node> + <node>OXT<value>O -1.661421 4.065769 -1.458723</value></node> + </node> + <node>Bonds + <node>5<value>3H N s</value></node> + <node>6<value>CA N s</value></node> + <node>10<value>HA CA s</value></node> + <node>11<value>C CA s</value></node> + <node>14<value>O C d</value></node> + <node>15<value>CB CA s</value></node> + <node>19<value>HB CB s</value></node> + <node>20<value>OG1 CB s</value></node> + <node>22<value>HG1 OG1 s</value></node> + <node>23<value>CG2 CB s</value></node> + <node>27<value>1HG2 CG2 s</value></node> + <node>28<value>2HG2 CG2 s</value></node> + <node>29<value>3HG2 CG2 s</value></node> + <node>30<value>1H N s</value></node> + <node>31<value>2H N s</value></node> + <node>32<value>OXT C s</value></node> + </node> + <node>Connections + <node>N-term<value>N C-term s 1.33 0.5</value></node> + <node>C-term<value>C N-term s 1.33 0.5</value></node> + </node> + <node>Properties + <node>AMINO_ACID</node> + </node> + <node>Variants + <node>Default + <node>Delete + <node>OXT</node> + <node>1H</node> + <node>2H</node> + </node> + <node>Rename + <node>3H<value>H</value></node> + </node> + </node> + <node>THR-M + <node>Properties + <node>C_TERMINAL</node> + <node>N_TERMINAL</node> + </node> + </node> + <node>THR-C + <node>Delete + <node>1H</node> + <node>2H</node> + </node> + <node>Rename + <node>3H<value>H</value></node> + </node> + <node>Properties + <node>C_TERMINAL</node> + </node> + </node> + <node>THR-N + <node>Delete + <node>OXT</node> + </node> + <node>Properties + <node>N_TERMINAL</node> + </node> + </node> + </node> +</node>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/fragments/TRP.db Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,112 @@ +<node>TRP + <node>Names + <node>Tryptophane</node> + <node>Tryptophan</node> + <node>Trp</node> + <node>W</node> + </node> + <node>Atoms + <node>N<value>N 0.06601259 1.26337 0.1174229</value></node> + <node>3H<value>H 0.6980239 1.889212 0.6011554</value></node> + <node>CA<value>C -0.7641827 2.069947 -0.7944807</value></node> + <node>HA<value>H -0.09635611 2.49911 -1.541994</value></node> + <node>C<value>C -1.398304 3.240995 -0.03709874</value></node> + <node>O<value>O -0.5874859 4.036549 0.4871631</value></node> + <node>CB<value>C -1.786919 1.186925 -1.524096</value></node> + <node>1HB<value>H -1.239827 0.4012884 -2.046958</value></node> + <node>2HB<value>H -2.428179 0.7027346 -0.7858279</value></node> + <node>CG<value>C -2.643165 1.884437 -2.539373</value></node> + <node>CD1<value>C -3.982776 2.050424 -2.457166</value></node> + <node>HD1<value>H -4.607287 1.697167 -1.648804</value></node> + <node>CD2<value>C -2.239992 2.518021 -3.792893</value></node> + <node>NE1<value>N -4.432695 2.747722 -3.558181</value></node> + <node>HE1<value>H -5.40488 2.982779 -3.697329</value></node> + <node>CE2<value>C -3.401079 3.062783 -4.417417</value></node> + <node>CE3<value>C -1.011219 2.68937 -4.467488</value></node> + <node>HE3<value>H -0.1073443 2.284464 -4.037195</value></node> + <node>CZ2<value>C -3.347395 3.744152 -5.642442</value></node> + <node>HZ2<value>H -4.246768 4.143939 -6.087246</value></node> + <node>CZ3<value>C -0.945238 3.371593 -5.697227</value></node> + <node>HZ3<value>H 0.006688994 3.489207 -6.194728</value></node> + <node>CH2<value>C -2.108581 3.899702 -6.284111</value></node> + <node>HH2<value>H -2.049103 4.422244 -7.228023</value></node> + <node>OXT<value>O -2.601413 3.132993 0.2872543</value></node> + <node>1H<value>H 0.590273 0.5789365 -0.4086703</value></node> + <node>2H<value>H -0.5252197 0.7968075 0.7903904</value></node> + </node> + <node>Bonds + <node>5<value>3H N s</value></node> + <node>6<value>CA N s</value></node> + <node>10<value>HA CA s</value></node> + <node>11<value>C CA s</value></node> + <node>14<value>O C d</value></node> + <node>15<value>CB CA s</value></node> + <node>19<value>1HB CB s</value></node> + <node>20<value>2HB CB s</value></node> + <node>21<value>CG CB s</value></node> + <node>24<value>CD1 CG a</value></node> + <node>27<value>HD1 CD1 s</value></node> + <node>28<value>CD2 CG a</value></node> + <node>31<value>NE1 CD1 a</value></node> + <node>34<value>HE1 NE1 s</value></node> + <node>35<value>CE2 CD2 a</value></node> + <node>36<value>CE2 NE1 a</value></node> + <node>39<value>CE3 CD2 a</value></node> + <node>41<value>HE3 CE3 s</value></node> + <node>42<value>CZ2 CE2 a</value></node> + <node>45<value>HZ2 CZ2 s</value></node> + <node>47<value>CZ3 CE3 a</value></node> + <node>49<value>HZ3 CZ3 s</value></node> + <node>50<value>CH2 CZ2 a</value></node> + <node>51<value>CH2 CZ3 a</value></node> + <node>53<value>HH2 CH2 s</value></node> + <node>54<value>OXT C s</value></node> + <node>55<value>1H N s</value></node> + <node>56<value>2H N s</value></node> + </node> + <node>Connections + <node>N-term<value>N C-term s 1.33 0.5</value></node> + <node>C-term<value>C N-term s 1.33 0.5</value></node> + </node> + <node>Properties + <node>AMINO_ACID</node> + </node> + <node>Variants + <node>Default + <node>Delete + <node>OXT</node> + <node>1H</node> + <node>2H</node> + </node> + <node>Rename + <node>3H<value>H</value></node> + </node> + </node> + <node>TRP-M + <node>Properties + <node>C_TERMINAL</node> + <node>N_TERMINAL</node> + </node> + </node> + <node>TRP-C + <node>Delete + <node>1H</node> + <node>2H</node> + </node> + <node>Rename + <node>3H<value>H</value></node> + </node> + <node>Properties + <node>C_TERMINAL</node> + </node> + </node> + <node>TRP-N + <node>Delete + <node>OXT</node> + </node> + <node>Properties + <node>N_TERMINAL</node> + </node> + </node> + </node> +</node>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/fragments/TYR.db Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,105 @@ +<node>TYR + <node>Names + <node>Tyrosine</node> + <node>Tyrosin</node> + <node>Tyr</node> + <node>Y</node> + </node> + <node>Atoms + <node>N<value>N 0.0892698 1.397582 0.01951128</value></node> + <node>3H<value>H 0.7468582 2.066645 0.3997705</value></node> + <node>CA<value>C -0.7022205 2.069859 -1.026261</value></node> + <node>HA<value>H -0.008099081 2.359834 -1.816127</value></node> + <node>C<value>C -1.325588 3.357111 -0.4775957</value></node> + <node>O<value>O -0.5109698 4.260831 -0.1874116</value></node> + <node>CB<value>C -1.734457 1.10693 -1.63201</value></node> + <node>1HB<value>H -1.201299 0.2395796 -2.0242</value></node> + <node>2HB<value>H -2.395853 0.7504926 -0.8408001</value></node> + <node>CG<value>C -2.557806 1.696825 -2.76258</value></node> + <node>CD1<value>C -3.932589 1.947373 -2.588092</value></node> + <node>HD1<value>H -4.418424 1.704676 -1.654011</value></node> + <node>CD2<value>C -1.942974 2.007092 -3.98996</value></node> + <node>HD2<value>H -0.8916094 1.806731 -4.138027</value></node> + <node>CE1<value>C -4.68326 2.520281 -3.629397</value></node> + <node>HE1<value>H -5.736402 2.710342 -3.483602</value></node> + <node>CE2<value>C -2.6951 2.579179 -5.030118</value></node> + <node>HE2<value>H -2.222162 2.818849 -5.971263</value></node> + <node>CZ<value>C -4.063968 2.83503 -4.851168</value></node> + <node>OH<value>O -4.785331 3.388967 -5.865766</value></node> + <node>HH<value>H -5.709894 3.51796 -5.645833</value></node> + <node>OXT<value>O -2.492483 3.282188 -0.03387626</value></node> + <node>1H<value>H -0.5246789 1.074702 0.7536617</value></node> + <node>2H<value>H 0.5865244 0.613409 -0.3778604</value></node> + </node> + <node>Bonds + <node>5<value>3H N s</value></node> + <node>6<value>CA N s</value></node> + <node>10<value>HA CA s</value></node> + <node>11<value>C CA s</value></node> + <node>14<value>O C d</value></node> + <node>15<value>CB CA s</value></node> + <node>19<value>1HB CB s</value></node> + <node>20<value>2HB CB s</value></node> + <node>21<value>CG CB s</value></node> + <node>24<value>CD1 CG a</value></node> + <node>27<value>HD1 CD1 s</value></node> + <node>28<value>CD2 CG a</value></node> + <node>31<value>HD2 CD2 s</value></node> + <node>32<value>CE1 CD1 a</value></node> + <node>35<value>HE1 CE1 s</value></node> + <node>36<value>CE2 CD2 a</value></node> + <node>39<value>HE2 CE2 s</value></node> + <node>40<value>CZ CE1 a</value></node> + <node>41<value>CZ CE2 a</value></node> + <node>43<value>OH CZ s</value></node> + <node>45<value>HH OH s</value></node> + <node>46<value>OXT C s</value></node> + <node>47<value>1H N s</value></node> + <node>48<value>2H N s</value></node> + </node> + <node>Connections + <node>N-term<value>N C-term s 1.33 0.5</value></node> + <node>C-term<value>C N-term s 1.33 0.5</value></node> + </node> + <node>Properties + <node>AMINO_ACID</node> + </node> + <node>Variants + <node>Default + <node>Delete + <node>OXT</node> + <node>1H</node> + <node>2H</node> + </node> + <node>Rename + <node>3H<value>H</value></node> + </node> + </node> + <node>TYR-M + <node>Properties + <node>C_TERMINAL</node> + <node>N_TERMINAL</node> + </node> + </node> + <node>TYR-C + <node>Delete + <node>1H</node> + <node>2H</node> + </node> + <node>Rename + <node>3H<value>H</value></node> + </node> + <node>Properties + <node>C_TERMINAL</node> + </node> + </node> + <node>TYR-N + <node>Delete + <node>OXT</node> + </node> + <node>Properties + <node>N_TERMINAL</node> + </node> + </node> + </node> +</node>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/fragments/U.db Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,99 @@ +<node>U + <node>Names + <node>Uracil</node> + <node>U</node> + </node> + <node>Atoms + <node>P<value>P 38.566 27.407 37.821</value></node> + <node>O1P<value>O 38.595 26.254 36.889</value></node> + <node>O2P<value>O 39.157 27.302 39.179</value></node> + <node>O5*<value>O 37.072 27.912 37.957</value></node> + <node>C5*<value>C 36.632 28.815 38.965</value></node> + <node>1H5*<value>H 37.233 29.724 38.959</value></node> + <node>2H5*<value>H 36.702 28.339 39.943</value></node> + <node>C4*<value>C 35.191 29.171 38.689</value></node> + <node>H4*<value>H 34.765 29.830 39.445</value></node> + <node>O4*<value>O 35.114 29.926 37.469</value></node> + <node>C3*<value>C 34.331 27.906 38.457</value></node> + <node>H3*<value>H 34.825 26.944 38.594</value></node> + <node>O3*<value>O 33.163 27.975 39.270</value></node> + <node>C2*<value>C 33.920 28.064 36.992</value></node> + <node>1H2*<value>H 34.360 27.260 36.402</value></node> + <node>2H2*<value>H 32.834 28.020 36.912</value></node> + <node>C1*<value>C 33.860 29.573 36.906</value></node> + <node>H1*<value>H 33.070 30.098 37.443</value></node> + <node>N1<value>N 33.730 30.096 35.526</value></node> + <node>C6<value>C 34.405 29.543 34.472</value></node> + <node>H6<value>H 35.056 28.699 34.642</value></node> + <node>C5<value>C 34.237 29.984 33.219</value></node> + <node>H5<value>H 35.018 29.323 32.073</value></node> + <node>C4<value>C 33.326 31.071 32.932</value></node> + <node>O4<value>O 33.094 31.529 31.816</value></node> + <node>N3<value>N 32.681 31.586 34.053</value></node> + <node>H3<value>H 31.993 32.416 33.893</value></node> + <node>C2<value>C 32.839 31.151 35.352</value></node> + <node>O2<value>O 32.225 31.690 36.276</value></node> + </node> + <node>Bonds + <node>1<value>P O1P s</value></node> + <node>2<value>P O2P d</value></node> + <node>3<value>P O5* s</value></node> + <node>4<value>O5* C5* s</value></node> + <node>5<value>C5* C4* s</value></node> + <node>6<value>C4* O4* s</value></node> + <node>7<value>C4* C3* s</value></node> + <node>8<value>C3* O3* s</value></node> + <node>9<value>C3* C2* s</value></node> + <node>10<value>C2* C1* s</value></node> + <node>11<value>C1* O4* s</value></node> + <node>12<value>C1* N1 s</value></node> + <node>13<value>N1 C6 s</value></node> + <node>14<value>C6 C5 d</value></node> + <node>15<value>C5 H5 s</value></node> + <node>16<value>C5 C4 s</value></node> + <node>17<value>C4 O4 d</value></node> + <node>18<value>C4 N3 s</value></node> + <node>19<value>N3 C2 s</value></node> + <node>20<value>C2 O2 d</value></node> + <node>21<value>C2 N1 s</value></node> + <node>22<value>C5* 1H5* s</value></node> + <node>23<value>C5* 2H5* s</value></node> + <node>24<value>C4* H4* s</value></node> + <node>25<value>C1* H1* s</value></node> + <node>26<value>C3* H3* s</value></node> + <node>27<value>C2* 1H2* s</value></node> + <node>28<value>C2* 2H2* s</value></node> + <node>29<value>C6 H6 s</value></node> + <node>30<value>N3 H3 s</value></node> + </node> + <node>Connections + <node>5-term<value>P 3-term s 1.62 0.5</value></node> + <node>3-term<value>O3* 5-term s 1.62 0.5</value></node> + </node> + <node>Properties + <node>NUCLEOTIDE</node> + </node> + <node>Variants + <node>U-M + <node>Properties + <node>5_PRIME</node> + <node>3_PRIME</node> + </node> + </node> + <node>Default + <node>Properties + </node> + </node> + <node>U-3 + <node>Properties + <node>3_PRIME</node> + </node> + </node> + <node>U-5 + <node>Properties + <node>5_PRIME</node> + </node> + </node> + </node> +</node> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/fragments/VAL.db Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,94 @@ +<node>VAL + <node>Names + <node>Valine</node> + <node>Valin</node> + <node>Val</node> + <node>V</node> + </node> + <node>Atoms + <node>N<value>N 0.08111785 1.2013 -0.133711</value></node> + <node>3H<value>H 0.9032491 1.762717 0.06032801</value></node> + <node>CA<value>C -0.698245 1.931722 -1.152099</value></node> + <node>HA<value>H -0.2125321 1.7346 -2.108571</value></node> + <node>C<value>C -0.5967644 3.443358 -0.9052255</value></node> + <node>O<value>O 0.3370198 3.799585 -0.1501447</value></node> + <node>CB<value>C -2.141793 1.389981 -1.219405</value></node> + <node>HB<value>H -2.073082 0.3006792 -1.23859</value></node> + <node>CG1<value>C -2.976131 1.780723 0.008393872</value></node> + <node>1HG1<value>H -3.953726 1.301327 -0.05053521</value></node> + <node>2HG1<value>H -2.483032 1.448739 0.9220271</value></node> + <node>3HG1<value>H -3.118463 2.860577 0.05077193</value></node> + <node>CG2<value>C -2.878923 1.800528 -2.501579</value></node> + <node>1HG2<value>H -3.809818 1.237256 -2.575363</value></node> + <node>2HG2<value>H -3.122159 2.862025 -2.496346</value></node> + <node>3HG2<value>H -2.266089 1.572718 -3.374182</value></node> + <node>OXT<value>O -1.142181 4.189281 -1.746952</value></node> + <node>1H<value>H -0.4588342 1.115157 0.7148547</value></node> + <node>2H<value>H 0.3376986 0.2854735 -0.4735033</value></node> + </node> + <node>Bonds + <node>5<value>3H N s</value></node> + <node>6<value>CA N s</value></node> + <node>10<value>HA CA s</value></node> + <node>11<value>C CA s</value></node> + <node>14<value>O C d</value></node> + <node>15<value>CB CA s</value></node> + <node>19<value>HB CB s</value></node> + <node>20<value>CG1 CB s</value></node> + <node>24<value>1HG1 CG1 s</value></node> + <node>25<value>2HG1 CG1 s</value></node> + <node>26<value>3HG1 CG1 s</value></node> + <node>27<value>CG2 CB s</value></node> + <node>31<value>1HG2 CG2 s</value></node> + <node>32<value>2HG2 CG2 s</value></node> + <node>33<value>3HG2 CG2 s</value></node> + <node>34<value>OXT C s</value></node> + <node>35<value>1H N s</value></node> + <node>36<value>2H N s</value></node> + </node> + <node>Connections + <node>N-term<value>N C-term s 1.33 0.5</value></node> + <node>C-term<value>C N-term s 1.33 0.5</value></node> + </node> + <node>Properties + <node>AMINO_ACID</node> + </node> + <node>Variants + <node>Default + <node>Delete + <node>OXT</node> + <node>1H</node> + <node>2H</node> + </node> + <node>Rename + <node>3H<value>H</value></node> + </node> + </node> + <node>VAL-M + <node>Properties + <node>N_TERMINAL</node> + <node>C_TERMINAL</node> + </node> + </node> + <node>VAL-C + <node>Delete + <node>1H</node> + <node>2H</node> + </node> + <node>Rename + <node>3H<value>H</value></node> + </node> + <node>Properties + <node>C_TERMINAL</node> + </node> + </node> + <node>VAL-N + <node>Delete + <node>OXT</node> + </node> + <node>Properties + <node>N_TERMINAL</node> + </node> + </node> + </node> +</node>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/fragments/ZN.db Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,18 @@ +<node>ZN + <node>Names + <node>Zinc ion</node> + <node>Zn2+</node> + </node> + <node>Atoms + <node>ZN<value>Zn 0.0 0.0 0.0</value></node> + </node> + <node>Bonds + </node> + <node>Connections + </node> + <node>Properties + </node> + <node>Variants + <node>Default</node> + </node> +</node>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/data/fragments/functionalGroups.smarts Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,133 @@ +C[*X1](C)([*X1])[*X1] terminal primary C(sp3) +[C,c]([C,c])([C,c])(*)* total secondary C(sp3) +[C,c]([C,c])([C,c])([C,c])* total tertiary C(sp3) +[C,c]([C,c])([C,c])([C,c])[C,c] total quaternary C(sp3) +[$([Cr,cr]([Cr,cr])([Cr,cr])(*)*),$([Cr,cr]([Cr,cr])([C,c])([*r])*)] ring secondary C(sp3) +[$([Cr,cr]([Cr,cr])([Cr,cr])([C,c])*),$([Cr,cr]([Cr,cr])([C,c])([C,c])[*r])] ring tertiary C(sp3) +[Cr,cr]([Cr,cr])([Cr,cr])([C,c])[C,c] ring quaternary C(sp3) +[cX3] aromatic C(sp2) +[Ch1,ch1]1[C,c][C,c][C,c][C,c][C,c]1 unsubstituted benzene C(sp2) +[Ch0,ch0]1[C,c][C,c][C,c][C,c][C,c]1 substituted benzene C(sp2) +O=CC1=CCCC=C1 non-aromatic conjugated C(sp2) +[C,c]=[C,c](*)(*) terminal primary C(sp2) +C=C(C)(*) aliphatic secondary C(sp2) +C=C(C)(C) aliphatic tertiary C(sp2) +[C,c]=[C,c]=[C,c] allenes groups +[*X1][C,c]#C terminal C(sp) +**[C,c]#C non-terminal C(sp) +OC#N cyanates +O=C=N isocyanates +SC#N thiocyanates +N=C=S isothiocyanates +[OH,Oh]C=O carboxylic acids +[*;!H]OC=O esters +[NH2,Nh2]C=O primary amides +[*;!H][NH,Nh]C=O secondary amides +[*;!H]N([*;!H])C=O tertiary amides +*N(*)C([O,S]*)=[O,S] (thio-)carbamates +[F,Cl,Br,I,At]C(*)=O acyl halogenides +[$([OH,Oh]C(*)=S),$([SH,Sh]C(*)=O)] thioacids +[SH,Sh]C(*)=S dithioacids +[$([*;!H]OC(*)=S),$([*;!H]SC(*)=O)] thioesters +[*;!H]SC(*)=S dithioesters +[CH,Ch](*)=O aldehydes +*C(*)=O ketones +[NX3]C([NX3])=[O,S] urea (-thio) derivatives +[OX2,SX2]C([OX2,SX2])=[O,S] carbonate (-thio) derivatives +[NX2]C([C,H])[NX3] amidine derivatives +[NX3]C(=[NX2])[NX3] guanidine derivatives +*C(*)=N[N,C,H] imines +*C(*)=NO* oximes +[NH2X3,Nh2X3] primary amines +[NH1X3,Nh1X3] secondary amines +[NH0X3;Nh0X3] tertiary amines +[C,H][NX3][NX3][C,H] N hydrazines +[C,H][NX2]=[NX2][C,H] N azo-derivatives +N#C* nitriles +[N+n] positive charged N +[NX4] quaternary N +*N(*)O* hydroxylamines +*N(*)N=O nitrosamine +*N=O nitroso groups +*N(O)=O nitro groups +[CX3](=[O,S])[NX3]([H,C])[CX3]=[O,S] imides +[C,H]C([C,H])=NN([C,H])[C,H] hydrazones +A[OX2h1,OX2H1] hydroxyl groups +a[OX2h1,OX2H1] aromatic hydroxyls +C[CH2,Ch2][OH,Oh] primary alcohols +C[CH,Ch](C)[OH,Oh] secondary alcohols +CC(C)(C)[OH,Oh] tertiary alcohols +*O* ethers +*O[F,Cl,Br,I,At] hypohalogenides +[CX3](=[O,S])O[CX3][O,S] anhydrides +[OH2,Oh2] water +C[SH,Sh] thiols +S=C(C)C thioketones +C[SX2]C sulfides +C[SX2][SX2]C disulfides +[$(CS(C)=O),$(C=S=O),$(S=S=O)] sulfoxides +[$(O=[SX4]=O),$(O=S(=[C,S])=O)] sulfones +[SX2][Oh1,OH1,Sh1,SH1] sulfenic acids +[SX3](=[O,S])[Oh1,OH1,Sh1,SH1] sulfinic acids +[SX4](=[O,S])(=[O,S])[Oh1,OH1,Sh1,SH1] sulfonic acids +[OX2,SX2][SX4](=[O,S])(=[O,S])[Oh1,OH1,Sh1,SH1] sulfuric acids +[SX3](=[O,S])[OX2,SX2] sulfites +[SX4](=[O,S])(=[O,S])[OX2,SX2] sulfonates +[OX2,SX2][SX4](=[O,S])(=[O,S])[OX2,SX2] sulfates +[$(C[SX4](=O)(=O)[NX3]),$(C[SX4](=S)(=O)[NX3]),$(C[SX3](=O)[NX3]),$(C[SX3](=S)[NX3]),$(CS[NX3])] sulfonamides/sulfinamides/sulfenamides +[O,S]P([O,S])[O,S] phosphites/thiophosphites +[O,S]P(=[O,S])([O,S])[O,S] phosphates/thiophosphates +[O,S]P([O,S])[O,S] phosphanes +[H,S,F,Cl,Br,I,At][PX4](=[S,O])([SX2,OX2])[SX2,OX2] phosphonates/thiophosphonates +[$([H,S,F,Cl,Br,I,At][PX4](=[S,O])([H,S,F,Cl,Br,I,At])[H,S,F,Cl,Br,I,At]),$([H,S,F,Cl,Br,I,At][PX5]([H,S,F,Cl,Br,I,At])([H,S,F,Cl,Br,I,At])([H,S,F,Cl,Br,I,At])[H,S,F,Cl,Br,I,At])] phosphoranes/thiophosphoranes +[F,Cl,Br,I,At][CX4h2,CX4H2,cx4h2,cx4H2][C,c] CH2RX +[F,Cl,Br,I,At][CX4h1,CX4H1,cX4h1,cX4H1]([C,c])[C,c] CHR2X +[F,Cl,Br,I,At][C,c]([C,c])([C,c])[C,c] CR3X +[C,c]=[CX3h1,cX3h1,CX3H1,cX3H1][F,Cl,Br,I,At] R=CHX +[C,c]=[C,c]([C,c])[F,Cl,Br,I,At] R=CRX +[F,Cl,Br,I,At]C#C R#CX +[F,Cl,Br,I,At][CX4h1,CX4H1,cX4h1,cX4H1]([C,c])[F,Cl,Br,I,At] CHRX2 +[F,Cl,Br,I,At][C,c]([C,c])([C,c])[F,Cl,Br,I,At] CR2X2 +[C,c]=[C,c]([F,Cl,Br,I,At])[F,Cl,Br,I,At] R=CX2 +[F,Cl,Br,I,At][C,c]([C,c])([F,Cl,Br,I,At])[F,Cl,Br,I,At] CRX3 +[F,Cl,Br,I,At][ar] halogene on aromatic ring +[CrX4,crX4][F,Cl,Br,I,At] X on ring C(sp3) +[CrX3,crX3][F,Cl,Br,I,At] X on ring C(sp2) +[C,c]=[C,c]([F,Cl,Br,I,At])[C,c]=[C,c] halogene on exo-conjugated C +[N,n]1@[C,c]@[C,c]1 Aziridines +[O,o]1@[C,c]@[C,c]1 Oxiranes +[S,s]1@[C,c]@[C,c]1 Thiranes +[N,n]1@[C,c]@[C,c]@[C,c]1 Azetidines +[O,o]1@[C,c]@[C,c]@[C,c]1 Oxetanes +[S,s]1@[C,c]@[C,c]@[C,c]1 Thioethanes +[N,n]12@[C,c]@[C,c]@[C,c]@[C,c]@[C,c]1(@[C,c]@C2(=O)) Beta-Lactams +[N,n]1@[C,c]@[C,c]@[C,c]1 Pyrrolidines +[O,o]1[C,c][C,c][C,c][C,c]1 Oxolanes +[S,s]1[C,c][C,c][C,c][C,c]1 tetrahydro-Thiophenes +[N,n]1@[C,c]@[C,c]@[C,c]@[C,c]1 Pyrroles +[N,n]1@[N,n]@[C,c]@[C,c]@[C,c]1 Pyrazoles +[N,n]1@[C,c]@[N,n]@[C,c]@[C,c]1 Imidazoles +[O,o]1[C,c]=[C,c][C,c]=[C,c]1 Furanes +[S,s]1[C,c]=[C,c][C,c]=[C,c]1 Thiophenes +[O,o]1@[C,c]@[N,n]@[C,c]@[C,c]1 Oxazoles +[O,o]1@[N,n]@[C,c]@[C,c]@[C,c]1 Isoxazoles +[S,s]1@[C,c]@[N,n]@[C,c]@[C,c]1 Thiazoles +[S,s]1@[N,n]@[C,c]@[C,c]@[C,c]1 Isothiazoles +[$([N,n]1@[N,n]@[C,c]@[N,n]@C1),$([N,n]1@[N,n]@[N,n]@[C,c]@[C,c]1)] Triazoles +[N,n]1@[C,c]@[C,c]@[C,c]@[C,c]@[C,c]1 Pyridines +[N,n]1@[C,c]@[C,c]@[C,c]@[C,c]@[N,n]1 Pyridazines +[N,n]1@[C,c]@[C,c]@[C,c]@[N,n]@[C,c]1 Pyrimidines +[N,n]1@[C,c]@[C,c]@[N,n]@[C,c]@[C,c]1 Pyrazines +[N,n]1@[C,c]@[N,n]@[C,c]@[N,n]@[C,c]1 135-Triazines +[N,n]1@[C,c]@[N,n]@[N,n]@[C,c]@[C,c]1 124-Triazines +[C,c]1([Oh1,OH1])[C,c][C,c][C,c][C,c][C,c]1 Phenoles +[C,c]1([C])[C,c][C,c][C,c][C,c][C,c]1 Phenyles +[C,c]1([CH3,ch3])[C,c][C,c][C,c][C,c][C,c]1 Toluenes +OC[C,c]1@[C,c](O)@[C,c](O)@[C,c](O)@[C,c](O)@[O,o]1 Glucose +OC[C,c]1(O)@[C,c](O)@[C,c](O)@[C,c](CO)[O,o]1 Fructose +[CH3,Ch3] Methyl +[F,Cl,Br,I,At] Halogenides +[CH2,Ch2,Ch3,CH3][CH2,Ch2][CH2,Ch2,Ch3,CH3] Propyl +[CH2,Ch2,Ch3,CH3][CH2,Ch2][CH2,Ch2][CH2,Ch2,Ch3,CH3] Butyl +[CH2,Ch2,Ch3,CH3][CH2,Ch2][CH2,Ch2][CH2,Ch2][CH2,Ch2,Ch3,CH3] Pentyl +CC=C([CH3,Ch3])([CH3,Ch3]) Prenyl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/galaxyconfigs/confFiles.py Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,32 @@ +# -*- coding: utf-8 -*- +""" +XML format classes +""" +import data +import logging +from galaxy.datatypes.sniff import * +import commands + +log = logging.getLogger(__name__) + + +class ini( data.Text ): + file_ext = "ini" + def sniff( self, filename ): + self.no_sections = commands.getstatusoutput("grep -c \"\[Docking-Settings\]\" "+filename) + if (self.no_sections[0] == 0) & (self.no_sections[1] > 0): + return True + else: + self.no_sections = commands.getstatusoutput("grep -c \"\[ReferenceArea\" "+filename) + if (self.no_sections[0] == 0) & (self.no_sections[1] > 0): + return True + else: + self.no_sections = commands.getstatusoutput("grep -c \"\[PharmacophoreConstraint\" "+filename) + if (self.no_sections[0] == 0) & (self.no_sections[1] > 0): + return True + else: + return False + + + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/galaxyconfigs/countResidues.sh Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,64 @@ +#!/bin/bash + +IFS=$'\n'; +residue_list="" +hetsys_list="" +hoh_list="" + +for line in $(cat $1); do + if [ "${line:0:4}" = "ATOM" ];then + residue_list+="${line:23:6}\n" + else + if [ "${line:0:6}" = "HETATM" ];then + s2=`echo $line | grep HOH` + if [ "$s2" != "" ];then + hoh_list+="${line:21:8}\n" + else + s3=`echo $line | grep WAT` + if [ "$s3" != "" ];then + hoh_list+="${line:21:8}\n" + else + hetsys_list+="${line:21:8}\n" + fi + fi + fi + fi +done + +IFS=$' '; +let num_res=`echo -e "\n"$residue_list | uniq | wc -l` +let num_hoh=`echo -e "\n"$hoh_list | uniq | wc -l` +let num_hetsys=`echo -e "\n"$hetsys_list | uniq | wc -l` + +# empty line at begin and end of lists -> substract 2 +let num_res-=2 +let num_hoh-=2 +let num_hetsys-=2 +if [ $num_res -lt 0 ]; then + let num_res=0 +fi +if [ $num_hoh -lt 0 ]; then + let num_hoh=0 +fi +if [ $num_hetsys -lt 0 ]; then + let num_hetsys=0 +fi + +echo -n "$num_res " +if [ $num_res -eq 1 ]; then + echo "residue" +else + echo "residues" +fi +echo -n "$num_hoh water " +if [ $num_hoh -eq 1 ]; then + echo "molecule" +else + echo "molecules" +fi +echo -n "$num_hetsys " +if [ $num_hetsys -eq 1 ]; then + echo "heterosystem" +else + echo "heterosystems" +fi
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/galaxyconfigs/datatypes_conf.xml Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,33 @@ +<?xml version="1.0"?> +<datatypes> + <registration converters_path="lib/galaxy/datatypes/converters" display_path="display_applications"> + <datatype extension="pdf" type="galaxy.datatypes.images:Image" mimetype="application/pdf"/> + <datatype extension="png" type="galaxy.datatypes.images:Image" mimetype="image/png"/> + <datatype extension="jpg" type="galaxy.datatypes.images:Image" mimetype="image/jpeg"/> + <datatype extension="gif" type="galaxy.datatypes.images:Image" mimetype="image/gif"/> + <datatype extension="svg" type="galaxy.datatypes.images:Image" mimetype="image/svg+xml"/> + + <datatype extension="txt" type="galaxy.datatypes.data:Text" display_in_upload="true"/> + <datatype extension="grd.tgz" type="galaxy.datatypes.molFiles:grdtgz" display_in_upload="true"/> + <datatype extension="mol2" type="galaxy.datatypes.molFiles:MOL2" display_in_upload="true"/> + <datatype extension="sdf" type="galaxy.datatypes.molFiles:SDF" display_in_upload="true"/> + <datatype extension="pdb" type="galaxy.datatypes.molFiles:PDB" display_in_upload="true"/> + <datatype extension="drf" type="galaxy.datatypes.molFiles:DRF" display_in_upload="true"/> + <datatype extension="mol2/sdf/drf" type="galaxy.datatypes.molFiles:GenericMolFile" display_in_upload="true"/> + <datatype extension="bvp" type="galaxy.datatypes.data:Data" display_in_upload="true"/> + <datatype extension="ini" type="galaxy.datatypes.confFiles:ini" display_in_upload="true"/> + + <!-- Datatypes for QuEasy --> + <datatype extension="dat" type="galaxy.datatypes.data:Text" display_in_upload="false"/> + <datatype extension="csv" type="galaxy.datatypes.data:Text" display_in_upload="true"/> + <datatype extension="mod" type="galaxy.datatypes.data:Text" display_in_upload="true"/> + </registration> + + <sniffers> + <sniffer type="galaxy.datatypes.confFiles:ini"/> + <sniffer type="galaxy.datatypes.molFiles:SDF"/> + <sniffer type="galaxy.datatypes.molFiles:MOL2"/> + <sniffer type="galaxy.datatypes.molFiles:DRF"/> + <sniffer type="galaxy.datatypes.molFiles:PDB"/> + </sniffers> +</datatypes>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/galaxyconfigs/molFiles.py Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,128 @@ +# -*- coding: utf-8 -*- + +import data +import logging +from galaxy.datatypes.sniff import * +import commands + +log = logging.getLogger(__name__) + +class GenericMolFile( data.Text ): + file_ext = "mol2/sdf/drf" + def check_filetype( self,filename ): + self.no_mols = commands.getstatusoutput("grep -c \\$\\$\\$\\$ "+filename) + if (self.no_mols[0] == 0) & (self.no_mols[1] > 0): + self.file_ext="sdf" + return True + self.no_mols = commands.getstatusoutput("grep -c @\<TRIPOS\>MOLECULE "+filename) + if (self.no_mols[0] == 0) & (self.no_mols[1] > 0): + self.file_ext="mol2" + return True + self.no_mols = commands.getstatusoutput("grep -c \"ligand id\" "+filename) + if (self.no_mols[0] == 0) & (self.no_mols[1] > 0): + self.file_ext="drf" + return True + self.no_mols = commands.getstatusoutput("grep -c HEADER "+filename) + if (self.no_mols[0] == 0) & (self.no_mols[1] > 0): + self.file_ext="pdb" + return True + return False + + def set_peek( self, dataset, is_multi_byte=False ): + if not dataset.dataset.purged: + if(self.check_filetype(dataset.file_name)) : + if (self.no_mols[1] == '1'): + dataset.blurb = "1 molecule" + else: + dataset.blurb = "%s molecules"%self.no_mols[1] + dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte ) + else: + dataset.peek = 'file does not exist' + dataset.blurb = 'file purged from disk' + + def get_mime(self): + return 'text/plain' + + +class GenericMultiMolFile( GenericMolFile ): + def set_peek( self, dataset, is_multi_byte=False ): + if not dataset.dataset.purged: + self.sniff(dataset.file_name) + if (self.no_mols[1] == '1'): + dataset.blurb = "1 molecule" + else: + dataset.blurb = "%s molecules"%self.no_mols[1] + dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte ) + else: + dataset.peek = 'file does not exist' + dataset.blurb = 'file purged from disk' + +class SDF( GenericMultiMolFile ): + file_ext = "sdf" + def sniff( self, filename ): + self.no_mols = commands.getstatusoutput("grep -c \\$\\$\\$\\$ "+filename) + if (self.no_mols[0] == 0) & (self.no_mols[1] > 0): + return True + else: + return False + +class MOL2( GenericMultiMolFile ): + file_ext = "mol2" + def sniff( self, filename ): + self.no_mols = commands.getstatusoutput("grep -c @\<TRIPOS\>MOLECULE "+filename) + if (self.no_mols[0] == 0) & (self.no_mols[1] > 0): + return True + else: + return False + +class DRF( GenericMultiMolFile ): + file_ext = "drf" + def sniff( self, filename ): + self.no_mols = commands.getstatusoutput("grep -c \"ligand id\" "+filename) + if (self.no_mols[0] == 0) & (self.no_mols[1] > 0): + return True + else: + return False + +class PDB( GenericMolFile ): + file_ext = "pdb" + def sniff( self, filename ): + self.no_mols = commands.getstatusoutput("grep -c HEADER "+filename) + if (self.no_mols[0] == 0) & (self.no_mols[1] > 0): + return True + else: + return False + def set_peek( self, dataset, is_multi_byte=False ): + #def set_peek( self, dataset, line_count=None, is_multi_byte=False ): + if not dataset.dataset.purged: + res = commands.getstatusoutput("lib/galaxy/datatypes/countResidues.sh "+dataset.file_name) + dataset.peek = res[1] + self.sniff(dataset.file_name) + if (self.no_mols[1] == '1'): + dataset.blurb = "1 protein structure" + else: + dataset.blurb = "%s protein structures"%self.no_mols[1] + else: + dataset.peek = 'file does not exist' + dataset.blurb = 'file purged from disk' + +class grd ( data.Text ) : + file_ext = "grd" + def set_peek( self, dataset, is_multi_byte=False ): + if not dataset.dataset.purged: + #dataset.peek = "" + dataset.blurb = "score-grids for docking" + else: + dataset.peek = 'file does not exist' + dataset.blurb = 'file purged from disk' + +class grdtgz ( data.Text ) : + file_ext = "grd.tgz" + def set_peek( self, dataset, is_multi_byte=False ): + if not dataset.dataset.purged: + #dataset.peek = "" + dataset.blurb = "compressed score-grids for docking" + else: + dataset.peek = 'file does not exist' + dataset.blurb = 'file purged from disk' +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/galaxyconfigs/tool_conf.xml Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,71 @@ +<?xml version="1.0"?> +<toolbox> + <label text="CADDSuite" id="cadds" /> + + <section name="Get Data" id="getext"> + <tool file="data_source/upload.xml"/> + <tool file="CADDSuite/galaxyconfigs/tools/CombiLibGenerator.xml"/> + <tool file="CADDSuite/galaxyconfigs/tools/PDBDownload.xml"/> + <tool file="CADDSuite/galaxyconfigs/tools/DBExporter.xml"/> + </section> + + <section name="Data preparation" id="dataPrep"> + <tool file="CADDSuite/galaxyconfigs/tools/PDBCutter.xml" /> + <tool file="CADDSuite/galaxyconfigs/tools/ProteinProtonator.xml" /> + <tool file="CADDSuite/galaxyconfigs/tools/Ligand3DGenerator.xml" /> + <tool file="CADDSuite/galaxyconfigs/tools/LigandFileSplitter.xml" /> + <tool file="CADDSuite/galaxyconfigs/tools/BindingDBCleaner.xml"/> + <tool file="CADDSuite/galaxyconfigs/tools/EvenSplit.xml"/> + <tool file="CADDSuite/galaxyconfigs/tools/PropertyModifier.xml"/> + <tool file="CADDSuite/galaxyconfigs/tools/MolFilter.xml"/> + </section> + + <section name="Checks and evaluations" id="checks"> + <tool file="CADDSuite/galaxyconfigs/tools/ProteinCheck.xml" /> + <tool file="CADDSuite/galaxyconfigs/tools/LigCheck.xml" /> + </section> + + <section name="Docking" id="dockingTools"> + <tool file="CADDSuite/galaxyconfigs/tools/WaterFinder.xml" /> + <tool file="CADDSuite/galaxyconfigs/tools/SpatialConstraintDefiner.xml" /> + <tool file="CADDSuite/galaxyconfigs/tools/InteractionConstraintDefiner.xml" /> + <tool file="CADDSuite/galaxyconfigs/tools/ConstraintsFinder.xml"/> + <tool file="CADDSuite/galaxyconfigs/tools/PocketDetector.xml"/> + <tool file="CADDSuite/galaxyconfigs/tools/GridBuilder.xml" /> + <tool file="CADDSuite/galaxyconfigs/tools/IMeedyDock.xml" /> + </section> + + <section name="Rescoring" id="rescoringsection"> + <tool file="CADDSuite/galaxyconfigs/tools/SimpleRescorer.xml"/> + <tool file="CADDSuite/galaxyconfigs/tools/TaGRes-train.xml"/> + <tool file="CADDSuite/galaxyconfigs/tools/TaGRes.xml"/> + <tool file="CADDSuite/galaxyconfigs/tools/AntitargetRescorer.xml" /> + </section> + + <section name="QuEasy (QSAR)" id="queasy"> + <tool file="CADDSuite/galaxyconfigs/tools/InputReader.xml" /> + <tool file="CADDSuite/galaxyconfigs/tools/ModelCreator.xml" /> + <tool file="CADDSuite/galaxyconfigs/tools/FeatureSelector.xml" /> + <tool file="CADDSuite/galaxyconfigs/tools/Validator.xml" /> + <tool file="CADDSuite/galaxyconfigs/tools/MolPredictor.xml" /> + <tool file="CADDSuite/galaxyconfigs/tools/AutoModel.xml" /> + </section> + + <section name="Analysis" id="analysis"> + <tool file="CADDSuite/galaxyconfigs/tools/ScoreAnalyzer.xml"/> + <tool file="CADDSuite/galaxyconfigs/tools/SimilarityAnalyzer.xml"/> + <tool file="CADDSuite/galaxyconfigs/tools/PropertyPlotter.xml"/> + <tool file="CADDSuite/galaxyconfigs/tools/RMSDCalculator.xml"/> + </section> + + <section name="Convert, combine and store" id="storeData"> + <tool file="CADDSuite/galaxyconfigs/tools/Converter.xml" /> + <tool file="CADDSuite/galaxyconfigs/tools/MolCombine.xml" /> + <tool file="CADDSuite/galaxyconfigs/tools/DockResultMerger.xml"/> + <tool file="CADDSuite/galaxyconfigs/tools/Filter.xml"/> + <tool file="CADDSuite/galaxyconfigs/tools/MolDepict.xml" /> + <tool file="CADDSuite/galaxyconfigs/tools/DBImporter.xml" /> + <tool file="CADDSuite/galaxyconfigs/tools/VendorFinder.xml" /> + </section> + +</toolbox> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/galaxyconfigs/tools/AntitargetRescorer.xml Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,32 @@ + +<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> +<tool id="antitargetrescorer" name="AntitargetRescorer" version="0.94"> + <description>rescore w/ anti-target dock-results</description> + <command interpreter="bash"><![CDATA[../../AntitargetRescorer +#if str( $t ) != '' and str( $t ) != 'None' : + -t "$t" +#end if +#if str( $at ) != '' and str( $at ) != 'None' : + -at "$at" +#end if +#if str( $o ) != '' and str( $o ) != 'None' : + -o "$o" +#end if + | tail -n 5 +]]></command> + <inputs> + <param name="t" label="input file w/ target dock-results" optional="false" type="data" format="mol2/sdf/drf"/> + <param name="at" label="input file w/ anti-target dock-results" optional="false" type="data" format="mol2/sdf/drf"/> + </inputs> + <outputs> + <data name="o" format="mol2/sdf/drf" format_source="t"/> + </outputs> + <help>This tool rescores docking output poses. +AntitargetRescoring can be used to try to enhance target specificity. Therefore, dock your compounds into your target of interest and into a (very) different protein and supply the docking results here. All compounds that received a very good antitarget-score will thus be penalized, i.e. they will have a much worse score within the output file. + +As input we need: + * a file containing the compounds that are to be rescored. Supported formats are mol2, sdf or drf (DockResultFile, xml-based). Those compound should have been docket into the specified protein (i.e. the target). + * a file containing the same compounds docked into the antitarget. + +Output of this tool is a file in the same format as the input ligand file containing all compounds with scores obtained by rescoring in form of a property 'antitarget_rescore'.</help> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/galaxyconfigs/tools/AutoModel.xml Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,27 @@ + +<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> +<tool id="automodel" name="AutoModel" version="1.1"> + <description>automatically find best QSAR model</description> + <command interpreter="bash"><![CDATA[../../AutoModel +#if str( $i ) != '' and str( $i ) != 'None' : + -i "$i" +#end if +#if str( $o ) != '' and str( $o ) != 'None' : + -o "$o" +#end if +#if str( $min_quality ) != '' and str( $min_quality ) != 'None' : + -min_quality "$min_quality" +#end if + | tail -n 5 +]]></command> + <inputs> + <param name="i" label="input data-file" optional="false" type="data" format="dat"/> + <param name="min_quality" label="minimal desired quality (default: 0.3)" optional="true" type="text" min="0.000000" max="1.000000" area="true" size="1x5" value="0.3"/> + </inputs> + <outputs> + <data name="o" format="mod"/> + </outputs> + <help>This tool tries to automatically find the best QSAR model for a given data set. + +It therefore applies nested validation, including feature selection, for each available model-type. The model with the best nested prediction quality is saved to the specified output file. However, if the best obtained nested prediction quality is smaller than the value specified by '-min_quality', an error will be shown and no model will be saved.</help> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/galaxyconfigs/tools/BindingDBCleaner.xml Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,36 @@ + +<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> +<tool id="bindingdbcleaner" name="BindingDBCleaner" version="0.94"> + <description>fix bindingdb.org downloads</description> + <command interpreter="bash"><![CDATA[../../BindingDBCleaner +#if str( $i ) != '' and str( $i ) != 'None' : + -i "$i" +#end if +#if str( $type ) != '' and str( $type ) != 'None' : + -type "$type" +#end if +#if str( $o ) != '' and str( $o ) != 'None' : + -o "$o" +#end if +#if str( $target ) != '' and str( $target ) != 'None' : + -target "$target" +#end if + | tail -n 5 +]]></command> + <inputs> + <param name="i" label="input file" optional="false" type="data" format="mol2/sdf/drf"/> + <param name="type" label="type of contained activity values: 'Ki' or 'IC50'" optional="false" type="select"> + <option value="IC50">IC50</option> + <option value="Ki">Ki</option> + </param> + <param name="target" label="binding-DB target name" optional="false" area="true" type="text" size="1x15"/> + </inputs> + <outputs> + <data name="o" format="mol2/sdf/drf" format_source="i"/> + </outputs> + <help>This tool cleans up the sd-properties contained in sd-files downloaded from bindingdb.org. + +For all compounds in the input file, the affinity value for the specified target is searched and retained but all other properties are removed. Furthermore, the IC50 or Ki value of each compound is converted to a binding-free-energy value in units of [kJ/mol] that is added as a property-tag named 'binding_free_energy'. + +All compounds in the input file for which no IC50 resp. Ki value for the specified target can found, are ignored and not written to the output file.</help> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/galaxyconfigs/tools/CombiLibGenerator.xml Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,33 @@ + +<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> +<tool id="combilibgenerator" name="CombiLibGenerator" version="0.94"> + <description>generate combinatorial lib</description> + <command interpreter="bash"><![CDATA[../../CombiLibGenerator +#if str( $i ) != '' and str( $i ) != 'None' : + -i "$i" +#end if +#if str( $o ) != '' and str( $o ) != 'None' : + -o "$o" +#end if + | tail -n 5 +]]></command> + <inputs> + <param name="i" label="input combi-lib file" optional="false" type="data" format="data"/> + </inputs> + <outputs> + <data name="o" format="mol2/sdf/drf"/> + </outputs> + <help>This tool generates a combinatorial library by combining the given molecule scaffolds with possible combinations of moieties. + +As input we need a text file specifying SMARTS expressions for the desired scaffolds and R-groups. Its format should look like the following example, although you may specify as many scaffolds and as many SMARTS expressions per R-group as you need: + +<scaffold> + Fc1ccc(cc1)C2=C(C([R1])=NO2)c3ccnc([R2])c3 + Fc1ccc(cc1)C2=NOC([R1])=C2cccnc([R2])c3 +<moietyR1> + [R1]C(C)(C)C +<moietyR2> + [R2]OC(C)(C)C + +Output of CombiLibGenerator is a file containing created topologies. Note that this tool does *not* generate any conformations but only topologies, so that all coordinates in the output file will be zero. Thus, apply Ligand3DGenerator to the output generated by CombiLibGenerator if you need 3D conformations.</help> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/galaxyconfigs/tools/ConstraintsFinder.xml Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,38 @@ + +<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> +<tool id="constraintsfinder" name="ConstraintsFinder" version="0.94"> + <description>find strongly interacting residues</description> + <command interpreter="bash"><![CDATA[../../ConstraintsFinder +#if str( $rec ) != '' and str( $rec ) != 'None' : + -rec "$rec" +#end if +#if str( $rl ) != '' and str( $rl ) != 'None' : + -rl "$rl" +#end if +#if str( $ini ) != '' and str( $ini ) != 'None' : + -ini "$ini" +#end if +#if str( $o ) != '' and str( $o ) != 'None' : + -o "$o" +#end if + | tail -n 5 +]]></command> + <inputs> + <param name="rec" label="receptor pdb-file" optional="false" type="data" format="pdb"/> + <param name="rl" label="reference-ligand" optional="false" type="data" format="mol2/sdf/drf"/> + <param name="ini" label="configuration file" optional="true" type="data" format="ini"/> + </inputs> + <outputs> + <data name="o" format="ini"/> + </outputs> + <help>This tool searches protein residues with which the reference ligand interacts strongly. +Therefore the interaction of the reference ligand to each residue is evaluated. Residues with a score worse (i.e. larger) than -2 are ignored. A maximum of 3 constraints are created for the most strongly interacting residues that met the above criterion. + +As input we need: + * a file containing a protonated protein in pdb-format + * a file containing a reference ligand. + This reference ligand should be located in the binding pocket. + Supported formats are mol2, sdf or drf (DockResultFile, xml-based). + +Output of this tool is a docking configuration file containing the created constraints. This file should in following pipeline steps be specified for grid precalculation and docking.</help> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/galaxyconfigs/tools/Converter.xml Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,50 @@ + +<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> +<tool id="converter" name="Converter" version="0.94"> + <description>interconvert molecular file-formats</description> + <command interpreter="bash"><![CDATA[../../Converter +#if str( $i ) != '' and str( $i ) != 'None' : + -i "$i" +#end if +#if str( $o ) != '' and str( $o ) != 'None' : + -o "$o" +#end if +#if str( $f ) != '' and str( $f ) != 'None' : + -f "$f" +#end if + | tail -n 5 +]]></command> + <inputs> + <param name="i" label="input file" optional="false" type="data" format="mol2/sdf/drf"/> + <param name="f" label="output format" optional="true" type="select"> + <option value="mol2">mol2</option> + <option value="sdf">sdf</option> + <option value="drf">drf</option> + <option value="pdb">pdb</option> + <option value="ac">ac</option> + <option value="ent">ent</option> + <option value="brk">brk</option> + <option value="hin">hin</option> + <option value="mol">mol</option> + <option value="xyz">xyz</option> + </param> + </inputs> + <outputs> + <data name="o" format="mol2/sdf/drf"> + <change_format> + <when input="f" value="mol2" format="mol2"/> + <when input="f" value="sdf" format="sdf"/> + <when input="f" value="drf" format="drf"/> + <when input="f" value="pdb" format="pdb"/> + <when input="f" value="ac" format="ac"/> + <when input="f" value="ent" format="ent"/> + <when input="f" value="brk" format="brk"/> + <when input="f" value="hin" format="hin"/> + <when input="f" value="mol" format="mol"/> + <when input="f" value="xyz" format="xyz"/> + </change_format> + </data> + </outputs> + <help>This tool can be used to convert between different molecular file-formats. +Supported formats are mol2, sdf, drf, pdb, ac, ent, brk, hin, mol, xyz.</help> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/galaxyconfigs/tools/DBExporter.xml Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,97 @@ + +<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> +<tool id="dbexporter" name="DBExporter" version="0.94 (ob)"> + <description>export molecules from data base</description> + <command interpreter="bash"><![CDATA[../../DBExporter +#if str( $o ) != '' and str( $o ) != 'None' : + -o "$o" +#end if +#if str( $start_id ) != '' and str( $start_id ) != 'None' : + -start_id "$start_id" +#end if +#if str( $end_id ) != '' and str( $end_id ) != 'None' : + -end_id "$end_id" +#end if +#if str( $min_logP ) != '' and str( $min_logP ) != 'None' : + -min_logP "$min_logP" +#end if +#if str( $max_logP ) != '' and str( $max_logP ) != 'None' : + -max_logP "$max_logP" +#end if +#if str( $min_MW ) != '' and str( $min_MW ) != 'None' : + -min_MW "$min_MW" +#end if +#if str( $max_MW ) != '' and str( $max_MW ) != 'None' : + -max_MW "$max_MW" +#end if +#if str( $max_mols ) != '' and str( $max_mols ) != 'None' : + -max_mols "$max_mols" +#end if +#if str( $target ) != '' and str( $target ) != 'None' : + -target "$target" +#end if +#if str( $q ) != '' and str( $q ) != 'None' : + -q "$q" +#end if +#if str( $min_sim ) != '' and str( $min_sim ) != 'None' : + -min_sim "$min_sim" +#end if +#if str( $max_sim ) != '' and str( $max_sim ) != 'None' : + -max_sim "$max_sim" +#end if +#if str( $smarts ) != '' and str( $smarts ) != 'None' : + -smarts "$smarts" +#end if +#if str( $smarts_file ) != '' and str( $smarts_file ) != 'None' : + -smarts_file "$smarts_file" +#end if +#if str( $uck ) != '' and str( $uck ) != 'None' : + -uck "$uck" +#end if +#if str( $d ) != '' and str( $d ) != 'None' : + -d "$d" +#end if +#if str( $u ) != '' and str( $u ) != 'None' : + -u "$u" +#end if +#if str( $h ) != '' and str( $h ) != 'None' : + -h "$h" +#end if +#if str( $port ) != '' and str( $port ) != 'None' : + -port "$port" +#end if +#if str( $p ) != '' and str( $p ) != 'None' : + -p "$p" +#end if +#if str( $s ) != '' and str( $s ) != 'None' : + -s +#end if + | tail -n 5 +]]></command> + <inputs> + <param name="q" label="query molecules for similarity searching" optional="true" type="data" format="mol2/sdf/drf"/> + <param name="smarts_file" label="SMARTS pattern" optional="true" type="data" format="data"/> + <param name="start_id" label="ID of the first conformation to be exported" optional="true" type="text" area="true" size="1x5" value=""/> + <param name="end_id" label="ID of the last conformation to be exported" optional="true" type="text" area="true" size="1x5" value=""/> + <param name="min_logP" label="minimal logP value" optional="true" type="text" min="-10.000000" max="10.000000" area="true" size="1x5" value=""/> + <param name="max_logP" label="maximal logP value" optional="true" type="text" min="-10.000000" max="10.000000" area="true" size="1x5" value=""/> + <param name="min_MW" label="minimal molecular weight" optional="true" type="text" area="true" size="1x5" value=""/> + <param name="max_MW" label="maximal molecular weight" optional="true" type="text" area="true" size="1x5" value=""/> + <param name="max_mols" label="max. number of molecules to be exported" optional="true" type="text" area="true" size="1x5" value=""/> + <param name="target" label="target/dataset name whose molecules should be exported" optional="true" area="true" type="text" size="1x15"/> + <param name="min_sim" label="minimal average similarity" optional="true" type="text" min="0.000000" max="1.000000" area="true" size="1x5" value=""/> + <param name="max_sim" label="maximal similarity" optional="true" type="text" min="0.000000" max="1.000000" area="true" size="1x5" value=""/> + <param name="smarts" label="SMARTS pattern" optional="true" area="true" type="text" size="1x15"/> + <param name="uck" label="UCK key" optional="true" area="true" type="text" size="1x15"/> + <param name="d" label="database name" optional="false" area="true" type="text" size="1x15"/> + <param name="u" label="database username" optional="false" area="true" type="text" size="1x15"/> + <param name="h" label="database host" optional="false" area="true" type="text" size="1x15"/> + <param name="port" label="database port" optional="true" type="text" area="true" size="1x5" value="3306"/> + <param name="p" label="database password" optional="false" area="true" type="text" size="1x15"/> + <param name="s" label="show summary of datasets in database" optional="true" type="boolean" truevalue="true" falsevalue=""/> + </inputs> + <outputs> + <data name="o" format="mol2/sdf/drf"/> + </outputs> + <help>This tool exports compounds from a database to a molecular file. Compounds can be filtered according to (among others) SMARTS expressions, logP, molecular weight, or similarity to query molecule(s) and dataset name.</help> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/galaxyconfigs/tools/DBImporter.xml Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,57 @@ + +<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> +<tool id="dbimporter" name="DBImporter" version="0.94 (ob)"> + <description>import molecules into data base</description> + <command interpreter="bash"><![CDATA[../../DBImporter +#if str( $i ) != '' and str( $i ) != 'None' : + -i "$i" +#end if +#if str( $target ) != '' and str( $target ) != 'None' : + -target "$target" +#end if +#if str( $d ) != '' and str( $d ) != 'None' : + -d "$d" +#end if +#if str( $u ) != '' and str( $u ) != 'None' : + -u "$u" +#end if +#if str( $h ) != '' and str( $h ) != 'None' : + -h "$h" +#end if +#if str( $port ) != '' and str( $port ) != 'None' : + -port "$port" +#end if +#if str( $p ) != '' and str( $p ) != 'None' : + -p "$p" +#end if +#if str( $vn ) != '' and str( $vn ) != 'None' : + -vn "$vn" +#end if +#if str( $vid ) != '' and str( $vid ) != 'None' : + -vid "$vid" +#end if +#if str( $vd ) != '' and str( $vd ) != 'None' : + -vd "$vd" +#end if +#if str( $vu ) != '' and str( $vu ) != 'None' : + -vu "$vu" +#end if + | tail -n 5 +]]></command> + <inputs> + <param name="i" label="input file" optional="false" type="data" format="mol2/sdf/drf"/> + <param name="target" label="target/dataset name whose molecules should be exported" optional="true" area="true" type="text" size="1x15"/> + <param name="d" label="database name" optional="false" area="true" type="text" size="1x15"/> + <param name="u" label="database username" optional="false" area="true" type="text" size="1x15"/> + <param name="h" label="database host" optional="false" area="true" type="text" size="1x15"/> + <param name="port" label="database port" optional="true" type="text" area="true" size="1x5" value="3306"/> + <param name="p" label="database password" optional="false" area="true" type="text" size="1x15"/> + <param name="vn" label="name of compound vendor" optional="true" area="true" type="text" size="1x15"/> + <param name="vid" label="name of vendor's compound-ID tag in sd-file" optional="true" area="true" type="text" size="1x15"/> + <param name="vd" label="vendor library date or version" optional="true" area="true" type="text" size="1x15"/> + <param name="vu" label="url from wich vendor library was obtained" optional="true" area="true" type="text" size="1x15"/> + </inputs> + <outputs/> + <help>This tool imports molecules into a database. +As input we need the file containing the molecules to be imported in sd-, mol2- or drf-format.</help> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/galaxyconfigs/tools/DockResultMerger.xml Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,49 @@ + +<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> +<tool id="dockresultmerger" name="DockResultMerger" version="0.94"> + <description>merge docking output files</description> + <command interpreter="bash"><![CDATA[../../DockResultMerger +#for $s in $series_i + #if str( "${s.i.file_name}" ) != '' and str( "${s.i.file_name}" ) != 'None' : + -i "${s.i.file_name}" + #end if +#end for +#if str( $o ) != '' and str( $o ) != 'None' : + -o "$o" +#end if +#if str( $score ) != '' and str( $score ) != 'None' : + -score "$score" +#end if +#if str( $min ) != '' and str( $min ) != 'None' : + -min "$min" +#end if +#if str( $max ) != '' and str( $max ) != 'None' : + -max "$max" +#end if +#if str( $k ) != '' and str( $k ) != 'None' : + -k "$k" +#end if +#if str( $rm ) != '' and str( $rm ) != 'None' : + -rm +#end if + | tail -n 5 +]]></command> + <inputs> + <repeat name="series_i" title="input files" min="1"> + <param name="i" label="input files" optional="false" type="data" format="mol2/sdf/drf"/> + </repeat> + <param name="score" label="score property name" optional="true" area="true" type="text" size="1x15" value="score"/> + <param name="min" label="minimal score value" optional="true" type="text" area="true" size="1x5" value=""/> + <param name="max" label="maximal score value" optional="true" type="text" area="true" size="1x5" value=""/> + <param name="k" label="number of output molecules" optional="true" type="text" area="true" size="1x5" value=""/> + <param name="rm" label="remove input files after merging" optional="true" type="boolean" truevalue="true" falsevalue=""/> + </inputs> + <outputs> + <data name="o" format="mol2/sdf/drf" format_source="i"/> + </outputs> + <help>This tool merges and sorts molecule files as generated by docking or rescoring. + +You need to specify the property-tag name of the scores according to which the molecules should be sorted. Optionally you can filter those compounds that were assigned a score above and/or below specified thresholds. If desired, you can furthermore choose to have only the compounds with the k best scores written to the output file. + + Output of DockResultMerger is one molecule containing the molecules found in input-files (that matched all filter criteria, if any), sorted ascendingly according to their scores.</help> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/galaxyconfigs/tools/EvenSplit.xml Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,41 @@ + +<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> +<tool id="evensplit" name="EvenSplit" version="0.94"> + <description>generate splits w/ equal property range</description> + <command interpreter="bash"><![CDATA[../../EvenSplit +#if str( $i ) != '' and str( $i ) != 'None' : + -i "$i" +#end if +#if str( $o1 ) != '' and str( $o1 ) != 'None' : + -o1 "$o1" +#end if +#if str( $o2 ) != '' and str( $o2 ) != 'None' : + -o2 "$o2" +#end if +#if str( $n ) != '' and str( $n ) != 'None' : + -n "$n" +#end if +#if str( $offset ) != '' and str( $offset ) != 'None' : + -offset "$offset" +#end if +#if str( $k ) != '' and str( $k ) != 'None' : + -k "$k" +#end if +#if str( $prop ) != '' and str( $prop ) != 'None' : + -prop "$prop" +#end if + | tail -n 5 +]]></command> + <inputs> + <param name="i" label="input file" optional="false" type="data" format="mol2/sdf/drf"/> + <param name="n" label="number of compounds to use from input file" optional="true" type="text" area="true" size="1x5" value=""/> + <param name="offset" label="extract each (i+offset)%k == 0 for o2" optional="true" type="text" area="true" size="1x5" value="0"/> + <param name="k" label="extract each k'th compound for 2nd output file" optional="true" type="text" area="true" size="1x5" value="2"/> + <param name="prop" label="property name" optional="false" area="true" type="text" size="1x15" value="binding_free_energy"/> + </inputs> + <outputs> + <data name="o1" format="mol2/sdf/drf" format_source="i"/> + <data name="o2" format="mol2/sdf/drf" format_source="i"/> + </outputs> + <help>This tool splits a molecule file into two subsets in such a way that each of them convers an equal range of a property. The property with respect to which this is to be done should be specified with '-prop'.</help> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/galaxyconfigs/tools/FeatureSelector.xml Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,41 @@ + +<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> +<tool id="featureselector" name="FeatureSelector" version="1.1"> + <description>run feature-selection on a QSAR model</description> + <command interpreter="bash"><![CDATA[../../FeatureSelector +#if str( $i ) != '' and str( $i ) != 'None' : + -i "$i" +#end if +#if str( $dat ) != '' and str( $dat ) != 'None' : + -dat "$dat" +#end if +#if str( $o ) != '' and str( $o ) != 'None' : + -o "$o" +#end if +#if str( $type ) != '' and str( $type ) != 'None' : + -type "$type" +#end if + | tail -n 5 +]]></command> + <inputs> + <param name="i" label="input mod-file" optional="false" type="data" format="mod"/> + <param name="dat" label="data-file" optional="false" type="data" format="dat"/> + <param name="type" label="feature-selection type" optional="false" type="select"> + <option value="remove_correlated">remove_correlated</option> + <option value="forward_selection">forward_selection</option> + <option value="backward_selection">backward_selection</option> + <option value="stepwise_selection">stepwise_selection</option> + <option value="twinscan">twinscan</option> + <option value="removeLowResponseCorrelation">removeLowResponseCorrelation</option> + </param> + </inputs> + <outputs> + <data name="o" format="mod"/> + </outputs> + <help>FeatureSelector runs a feature-selection for a given QSAR model. + +The type of feature-selection to be done is specified by '-type'. Input of this tool is a data file as generated by InputReader containing the training data for feature-selection and a QSAR model file as generated by ModelCreator (or this tool itself). Note that you can apply several feature-selection methods in succession by using the output of one call of this tool as input for the next call. +Model- and kernel-parameters (if any) will be automatically optimized by cross-validation after applying the desired feature-selection. + +Output of this tool is a model-file that can be used by other QuEasy tools (e.g. Validator).</help> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/galaxyconfigs/tools/GalaxyConfigGenerator.xml Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,30 @@ + +<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> +<tool id="galaxyconfiggenerator" name="GalaxyConfigGenerator" version="0.94"> + <description>generate galaxy tool-config files</description> + <command interpreter="bash"><![CDATA[../../GalaxyConfigGenerator +#if str( $i ) != '' and str( $i ) != 'None' : + -i "$i" +#end if +#if str( $o ) != '' and str( $o ) != 'None' : + -o "$o" +#end if +#if str( $ignore ) != '' and str( $ignore ) != 'None' : + -ignore "$ignore" +#end if +#if str( $s ) != '' and str( $s ) != 'None' : + -s "$s" +#end if + | tail -n 5 +]]></command> + <inputs> + <param name="i" label="input par-file" optional="false" type="data" format="data"/> + <param name="ignore" label="tool-parameter to be ignored, i.e. those for which no galaxy config entry should be created" optional="true" area="true" size="1x5"/> + </inputs> + <outputs> + <data name="o" format="xml"/> + <data name="s" format="data"/> + </outputs> + <help>This tool can be used to create galaxy tool-configuration files. +As input, please supply a parameter-file as written by '-write_par' by all of our tools.</help> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/galaxyconfigs/tools/GridBuilder.xml Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,38 @@ + +<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> +<tool id="gridbuilder" name="GridBuilder" version="0.94"> + <description>create score-grids for docking</description> + <command interpreter="bash"><![CDATA[../../GridBuilder +#if str( $rec ) != '' and str( $rec ) != 'None' : + -rec "$rec" +#end if +#if str( $rl ) != '' and str( $rl ) != 'None' : + -rl "$rl" +#end if +#if str( $ini ) != '' and str( $ini ) != 'None' : + -ini "$ini" +#end if +#if str( $grd ) != '' and str( $grd ) != 'None' : + -grd "$grd" +#end if + | tail -n 5 +]]></command> + <inputs> + <param name="rec" label="receptor pdb-file" optional="false" type="data" format="pdb"/> + <param name="rl" label="reference-ligand" optional="false" type="data" format="mol2/sdf/drf"/> + <param name="ini" label="configuration file" optional="true" type="data" format="ini"/> + </inputs> + <outputs> + <data name="grd" format="grd.tgz"/> + </outputs> + <help>This tool precalculates a score-grid for a binding pocket of a given receptor. + +As input we need: + * a file containing a protonated protein in pdb-format + * a file containing a reference ligand. + This reference ligand should be located in the binding pocket, + so that a grid can be precalculated around it. + Supported formats are mol2, sdf or drf (DockResultFile, xml-based). + +Output of this tool is a file containing the score-grids that can be used by docking-/scoring-tools (e.g. IMeedyDock).</help> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/galaxyconfigs/tools/IMGDock.xml Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,47 @@ + +<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> +<tool id="imeedydock" name="IMGDock" version="0.94"> + <description>Iterative Multi-Greedy Docking</description> + <command interpreter="bash"><![CDATA[../../IMGDock +#if str( $rec ) != '' and str( $rec ) != 'None' : + -rec "$rec" +#end if +#if str( $rl ) != '' and str( $rl ) != 'None' : + -rl "$rl" +#end if +#if str( $ini ) != '' and str( $ini ) != 'None' : + -ini "$ini" +#end if +#if str( $i ) != '' and str( $i ) != 'None' : + -i "$i" +#end if +#if str( $o ) != '' and str( $o ) != 'None' : + -o "$o" +#end if +#if str( $grd ) != '' and str( $grd ) != 'None' : + -grd "$grd" +#end if + | tail -n 5 +]]></command> + <inputs> + <param name="rec" label="receptor pdb-file" optional="false" type="data" format="pdb"/> + <param name="rl" label="reference-ligand" optional="false" type="data" format="mol2/sdf/drf"/> + <param name="ini" label="configuration file" optional="true" type="data" format="ini"/> + <param name="i" label="compounds to be docked" optional="false" type="data" format="mol2/sdf/drf"/> + <param name="grd" label="ScoreGrid file" optional="false" type="data" format="grd.tgz"/> + </inputs> + <outputs> + <data name="o" format="mol2/sdf/drf" format_source="i"/> + </outputs> + <help>IMGDock docks compounds into the binding pocket of a receptor using an iterative multi-greedy approach. +As input we need: + + * a file containing a protonated protein in pdb-format + * a file containing a reference ligand. This reference ligand should be located in the binding pocket. Supported formats are mol2, sdf or drf (DockResultFile, xml-based). + * a score-grid file generated by GridBuilder. This grid must have been precalculated for the same receptor and reference ligand as those that are to be used here. + * a file containing the compounds that are to be docked. Supported formats are mol2, sdf or drf (DockResultFile, xml-based). These molecules must have been assigned 3D coordinates (e.g. by Ligand3DGenerator) and should have been checked for errors using LigCheck. + +Output of this tool is a file containing all compounds docked into the binding pocket, with a property-tag named 'score' indicating the score obtained for each compound. + +Tip: If you want to parallelize docking, use LigandFileSplitter to separate your input file containing the compounds to be docked into several batches, dock each batch with this tool and merge the output files with DockResultMerger.</help> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/galaxyconfigs/tools/InputPartitioner.xml Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,28 @@ + +<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> +<tool id="inputpartitioner" name="InputPartitioner" version="1.1"> + <description>split QSAR data set</description> + <command interpreter="bash"><![CDATA[../../InputPartitioner +#if str( $i ) != '' and str( $i ) != 'None' : + -i "$i" +#end if +#if str( $o ) != '' and str( $o ) != 'None' : + -o "$o" +#end if +#if str( $n ) != '' and str( $n ) != 'None' : + -n "$n" +#end if + | tail -n 5 +]]></command> + <inputs> + <param name="i" label="input data-file" optional="false" type="data" format="dat"/> + <param name="n" label="number of partitions" optional="false" type="text" area="true" size="1x5" value=""/> + </inputs> + <outputs> + <data name="o" format="dat"/> + </outputs> + <help>InputPartitioner partitions a given QSAR data set into n partitions with evenly distributed response values. +Thus, this tool can be useful as part of a nested validation pipeline. +Input is a data file as generated by InputReader. +Output will be written to n files postfixed '_TRAIN<i>.dat' and '_TEST<i>.dat', where <i> is the ID of the resp. partition. For each of these partitions, the training set contains only those compounds that were not selected for the resp. test set.</help> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/galaxyconfigs/tools/InputReader.xml Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,68 @@ + +<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> +<tool id="inputreader" name="InputReader" version="1.1"> + <description>generate QSAR data set</description> + <command interpreter="bash"><![CDATA[../../InputReader +#if str( $i ) != '' and str( $i ) != 'None' : + -i "$i" +#end if +#if str( $o ) != '' and str( $o ) != 'None' : + -o "$o" +#end if +#if str( $act ) != '' and str( $act ) != 'None' : + -act "$act" +#end if +#if str( $csv ) != '' and str( $csv ) != 'None' : + -csv "$csv" +#end if +#if str( $csv_nr ) != '' and str( $csv_nr ) != 'None' : + -csv_nr "$csv_nr" +#end if +#if str( $csv_sep ) != '' and str( $csv_sep ) != 'None' : + -csv_sep "$csv_sep" +#end if +#if str( $sdp ) != '' and str( $sdp ) != 'None' : + -sdp +#end if +#if str( $no_cd ) != '' and str( $no_cd ) != 'None' : + -no_cd +#end if +#if str( $no_cr ) != '' and str( $no_cr ) != 'None' : + -no_cr +#end if +#if str( $csv_cl ) != '' and str( $csv_cl ) != 'None' : + -csv_cl +#end if +#if str( $csv_dl ) != '' and str( $csv_dl ) != 'None' : + -csv_dl +#end if + | tail -n 5 +]]></command> + <inputs> + <param name="i" label="input sd-file" optional="false" type="data" format="sdf"/> + <param name="csv" label="input csv-file w/ additional descriptors" optional="true" type="data" format="csv"/> + <param name="act" label="sd-property containing response values" optional="true" area="true" type="text" size="1x15"/> + <param name="csv_nr" label="no. of response variables in csv-file" optional="true" type="text" area="true" size="1x5" value=""/> + <param name="csv_sep" label="separator symbol in csv-file" optional="true" type="text" area="true" size="1x5" value=""/> + <param name="sdp" label="use sd-properties as additional descriptors" optional="true" type="boolean" truevalue="true" falsevalue=""/> + <param name="no_cd" label="do not center descriptors" optional="true" type="boolean" truevalue="true" falsevalue=""/> + <param name="no_cr" label="do not center response values" optional="true" type="boolean" truevalue="true" falsevalue=""/> + <param name="csv_cl" label="csv-file has compound (row) labels" optional="true" type="boolean" truevalue="true" falsevalue=""/> + <param name="csv_dl" label="csv-file has descriptor (column) labels" optional="true" type="boolean" truevalue="true" falsevalue=""/> + </inputs> + <outputs> + <data name="o" format="dat"/> + </outputs> + <help>This tool reads input from sd-files and generate features for QSAR analysis. +Activity data (response values) for a training set are taken from sd-properties of the input file; the name of this property can be specified by option '-act'. +The following number of features will be automatically created for each molecule in your sd-file: + + * 40 atom and bond count descriptors + * 2 connectivity indices (Balaban and Zagreb index) + * 4 partial charge descriptors + * 14 surface descriptors + * 133 topological descriptors (functional group counts) + +If desired, you can also read additional descriptors from a csv-file; in this case you need to specify the file with the above options. +Output of this tool is a data file that can be used by other QuEasy tools (e.g. ModelCreator).</help> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/galaxyconfigs/tools/InteractionConstraintDefiner.xml Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,37 @@ + +<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> +<tool id="interactionconstraintdefiner" name="InteractionConstraintDefiner" version="0.94"> + <description>define interaction constraint</description> + <command interpreter="bash"><![CDATA[../../InteractionConstraintDefiner +#if str( $res ) != '' and str( $res ) != 'None' : + -res "$res" +#end if +#if str( $ini ) != '' and str( $ini ) != 'None' : + -ini "$ini" +#end if +#if str( $s ) != '' and str( $s ) != 'None' : + -s "$s" +#end if +#if str( $p ) != '' and str( $p ) != 'None' : + -p "$p" +#end if +#if str( $o ) != '' and str( $o ) != 'None' : + -o "$o" +#end if + | tail -n 5 +]]></command> + <inputs> + <param name="ini" label="input configuration file" optional="true" type="data" format="ini"/> + <param name="res" label="residue ID" optional="false" area="true" type="text" size="1x15"/> + <param name="s" label="desired minimal interation (score) between ligand and specified residue(s)" optional="false" type="text" area="true" size="1x5" value="-2.0"/> + <param name="p" label="penalty value" optional="false" type="text" area="true" size="1x5" value="10"/> + </inputs> + <outputs> + <data name="o" format="ini"/> + </outputs> + <help>This tool allows to define interaction constraints for docking or scoring. + +The constraint to be created will enforce a specified minimal interaction between ligands and the specified residue(s) of the receptor. Please specify residue IDs in the following manner: <chain-ID>:<residue-ID>, e.g. A:57. If you want to use more than one residue, separate their IDs by commas, e.g. A:57,B:17. + +Output of this tool is a ini-file that contains the desired interaction constraint.</help> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/galaxyconfigs/tools/LigCheck.xml Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,45 @@ + +<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> +<tool id="ligcheck" name="LigCheck" version="0.94"> + <description>check molecules for errors</description> + <command interpreter="bash"><![CDATA[../../LigCheck +#if str( $i ) != '' and str( $i ) != 'None' : + -i "$i" +#end if +#if str( $o ) != '' and str( $o ) != 'None' : + -o "$o" +#end if +#if str( $ef ) != '' and str( $ef ) != 'None' : + -ef "$ef" +#end if +#if str( $ri ) != '' and str( $ri ) != 'None' : + -ri +#end if +#if str( $ut ) != '' and str( $ut ) != 'None' : + -ut +#end if + | tail -n 5 +]]></command> + <inputs> + <param name="i" label="input molecule file" optional="false" type="data" format="mol2/sdf/drf"/> + <param name="ef" label="error fraction; print error if fraction of invalid mols is larger" optional="true" type="text" area="true" size="1x5" value="0.5"/> + <param name="ri" label="remove invalid molecules." optional="true" type="boolean" truevalue="true" falsevalue=""/> + <param name="ut" label="check for unique topologies (default: check only for unique conformation)" optional="true" type="boolean" truevalue="true" falsevalue=""/> + </inputs> + <outputs> + <data name="o" format="mol2/sdf/drf" format_source="i"/> + </outputs> + <help>This tool checks all molecules of the given input file for errors. Supported formats are mol2, sdf or drf (DockResultFile, xml-based). + +The following checks are done for each molecule: + + * bond-lengths may not be completely senseless (i.e. <0.7 or >2.5 Angstroem) + * each 'molecule' in the input file may only contain one actual molecule, i.e. there may be no unconnected atoms or fragments. + * each atom must have a valid assigned element + * the molecule must be protonated (since this is necessary for docking/(re-)scoring). + * 3D coordinates must be present (instead of 2D coordinates; also necessary for docking/(re-)scoring) + * partial charges may not contain completely senseless values (>5 or <-5). + * each conformation should appear only once within the given file, otherwise it is rejected and not written to the output file. However, if option '-ut' is used, molecules will instead be checked for unique topologies. + +If option '-ri' is used, only those molecules that pass all those tests are written to the output file. If this option is not used, all molecules are written to output containing a property 'score_ligcheck' with a value of 1 if the molecule passed all tests or with a value of 0 if it did not pass them.</help> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/galaxyconfigs/tools/Ligand3DGenerator.xml Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,30 @@ + +<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> +<tool id="ligand3dgenerator" name="Ligand3DGenerator" version="0.94"> + <description>generate 3D coordinates for small molecules</description> + <command interpreter="bash"><![CDATA[../../Ligand3DGenerator +#if str( $i ) != '' and str( $i ) != 'None' : + -i "$i" +#end if +#if str( $o ) != '' and str( $o ) != 'None' : + -o "$o" +#end if +#if str( $ph ) != '' and str( $ph ) != 'None' : + -ph "$ph" +#end if + | tail -n 5 +]]></command> + <inputs> + <param name="i" label="input file" optional="false" type="data" format="mol2/sdf/drf"/> + <param name="ph" label="pH-value for pH-dep. protonation" optional="true" type="text" area="true" size="1x5" value="7.0"/> + </inputs> + <outputs> + <data name="o" format="mol2/sdf/drf" format_source="i"/> + </outputs> + <help>This tool generates 3D conformations for small molecules and adds hydrogens to them. +As input we only a chemical file containing valid topologies. Any 2D or 3D conformations in the input file are ignored, but the existence of the correct bond-orders is necessary. + +Note however, that the main purpose of this tool is to generate feasible start-conformations for docking or other optimization procedures. Therefore, the generated 3D coordinates for each fragment should be all right, but in extreme cases (i.e. very large and/or complex molecules) different fragments might still overlap with each other. + +Supported formats are mol2, sdf, drf, pdb, ac, ent, brk, hin, mol, xyz.</help> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/galaxyconfigs/tools/LigandFileSplitter.xml Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,84 @@ + +<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> +<tool id="ligandfilesplitter" name="LigandFileSplitter" version="0.94"> + <description>split molecule files</description> + <command interpreter="bash"><![CDATA[../../LigandFileSplitter +#if str( $i ) != '' and str( $i ) != 'None' : + -i "$i" +#end if +#if str( $no ) != '' and str( $no ) != 'None' : + -no "$no" +#end if +#if str( $o ) != '' and str( $o ) != 'None' : + -o "$o" +#end if +#if str( $o2 ) != '' and str( $o2 ) != 'None' : + -o "$o2" +#end if +#if str( $o3 ) != '' and str( $o3 ) != 'None' : + -o "$o3" +#end if +#if str( $o4 ) != '' and str( $o4 ) != 'None' : + -o "$o4" +#end if +#if str( $o5 ) != '' and str( $o5 ) != 'None' : + -o "$o5" +#end if +#if str( $o6 ) != '' and str( $o6 ) != 'None' : + -o "$o6" +#end if +#if str( $o7 ) != '' and str( $o7 ) != 'None' : + -o "$o7" +#end if +#if str( $o8 ) != '' and str( $o8 ) != 'None' : + -o "$o8" +#end if +#if str( $o9 ) != '' and str( $o9 ) != 'None' : + -o "$o9" +#end if +#if str( $o10 ) != '' and str( $o10 ) != 'None' : + -o "$o10" +#end if +#if str( $o11 ) != '' and str( $o11 ) != 'None' : + -o "$o11" +#end if +#if str( $o12 ) != '' and str( $o12 ) != 'None' : + -o "$o12" +#end if +#if str( $o13 ) != '' and str( $o13 ) != 'None' : + -o "$o13" +#end if +#if str( $o14 ) != '' and str( $o14 ) != 'None' : + -o "$o14" +#end if +#if str( $o15 ) != '' and str( $o15 ) != 'None' : + -o "$o15" +#end if + | tail -n 5 +]]></command> + <inputs> + <param name="i" label="input molecule file" optional="false" type="data" format="mol2/sdf/drf"/> + <param name="no" label="no. of splits to be created" optional="false" type="hidden" area="true" size="1x5" value="15"/> + </inputs> + <outputs> + <data name="o" format="mol2/sdf/drf" format_source="i"/> + <data name="o2" format="mol2/sdf/drf" format_source="i"/> + <data name="o3" format="mol2/sdf/drf" format_source="i"/> + <data name="o4" format="mol2/sdf/drf" format_source="i"/> + <data name="o5" format="mol2/sdf/drf" format_source="i"/> + <data name="o6" format="mol2/sdf/drf" format_source="i"/> + <data name="o7" format="mol2/sdf/drf" format_source="i"/> + <data name="o8" format="mol2/sdf/drf" format_source="i"/> + <data name="o9" format="mol2/sdf/drf" format_source="i"/> + <data name="o10" format="mol2/sdf/drf" format_source="i"/> + <data name="o11" format="mol2/sdf/drf" format_source="i"/> + <data name="o12" format="mol2/sdf/drf" format_source="i"/> + <data name="o13" format="mol2/sdf/drf" format_source="i"/> + <data name="o14" format="mol2/sdf/drf" format_source="i"/> + <data name="o15" format="mol2/sdf/drf" format_source="i"/> + </outputs> + <help>LigandFileSplitter splits a molecule file into a given number of subsets. +Note that the molecules are not sorted in any way for this. + +Since Galaxy does not support a flexible number of output-files, we will create 15 output files when you use LigandFileSplitter in Galaxy.</help> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/galaxyconfigs/tools/ModelCreator.xml Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,52 @@ + +<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> +<tool id="modelcreator" name="ModelCreator" version="1.1"> + <description>create a QSAR model</description> + <command interpreter="bash"><![CDATA[../../ModelCreator +#if str( $i ) != '' and str( $i ) != 'None' : + -i "$i" +#end if +#if str( $o ) != '' and str( $o ) != 'None' : + -o "$o" +#end if +#if str( $type ) != '' and str( $type ) != 'None' : + -type "$type" +#end if +#if str( $kernel ) != '' and str( $kernel ) != 'None' : + -kernel "$kernel" +#end if + | tail -n 5 +]]></command> + <inputs> + <param name="i" label="input dat-file" optional="false" type="data" format="dat"/> + <param name="type" label="model type" optional="false" type="select"> + <option value="MLR">MLR</option> + <option value="RR">RR</option> + <option value="PCR">PCR</option> + <option value="PLS">PLS</option> + <option value="OPLS">OPLS</option> + <option value="ALL">ALL</option> + <option value="KNN">KNN</option> + <option value="KPLS">KPLS</option> + <option value="KPCR">KPCR</option> + <option value="GP">GP</option> + <option value="LDA">LDA</option> + <option value="snB">snB</option> + <option value="nB">nB</option> + </param> + <param name="kernel" label="kernel type (in case of kernel-model)" optional="true" type="select"> + <option value="none">none</option> + <option value="polynomial">polynomial</option> + <option value="rbf">rbf</option> + <option value="sigmoidal">sigmoidal</option> + </param> + </inputs> + <outputs> + <data name="o" format="mod"/> + </outputs> + <help>ModelCreator creates a QSAR model using an input data set as generated by InputReader. + +The type of QSAR model to be used can be specified by '-type', the type of kernel-function (if any) can be chosen by '-kernel'. Optimization of model- and kernel-parmeters will be done automatically using cross-validation. + +Output of this tool is a model-file that can be used by other QuEasy tools (e.g. FeatureSelector).</help> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/galaxyconfigs/tools/MolCombine.xml Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,45 @@ + +<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> +<tool id="molcombine" name="MolCombine" version="0.94"> + <description>combine molecular files</description> + <command interpreter="bash"><![CDATA[../../MolCombine +#if str( $i1 ) != '' and str( $i1 ) != 'None' : + -i1 "$i1" +#end if +#if str( $i2 ) != '' and str( $i2 ) != 'None' : + -i2 "$i2" +#end if +#if str( $mode ) != '' and str( $mode ) != 'None' : + -mode "$mode" +#end if +#if str( $o ) != '' and str( $o ) != 'None' : + -o "$o" +#end if +#if str( $ignH ) != '' and str( $ignH ) != 'None' : + -ignH +#end if +#if str( $replace_prop ) != '' and str( $replace_prop ) != 'None' : + -replace_prop +#end if + | tail -n 5 +]]></command> + <inputs> + <param name="i1" label="input molecule file A" optional="false" type="data" format="mol2/sdf/drf"/> + <param name="i2" label="input molecule file B" optional="false" type="data" format="mol2/sdf/drf"/> + <param name="mode" label="'intersection', 'union' or 'b_not_a'" optional="false" type="select"> + <option value="intersection">intersection</option> + <option value="union">union</option> + <option value="b_not_a">b_not_a</option> + </param> + <param name="ignH" label="ignore hydrogens, i.e. match molecules to any protonation state." optional="true" type="boolean" truevalue="true" falsevalue=""/> + <param name="replace_prop" label="replace properties from file 1 w/ those from file 2" optional="true" type="boolean" truevalue="true" falsevalue=""/> + </inputs> + <outputs> + <data name="o" format="mol2/sdf/drf" format_source="i1"/> + </outputs> + <help>This tool generates the intersection or union of two given chemical files. Property-tags of molecules that appear in both input files are automatically merged. + +If you want to match molecules regardless of their protonation state, use option '-ignH'. + +Output of this tool is a file containing the union resp. intersection of all molecules of input A and B.</help> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/galaxyconfigs/tools/MolDepict.xml Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,28 @@ + +<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> +<tool id="moldepict" name="MolDepict" version="0.94"> + <description>create structure diagrams</description> + <command interpreter="bash"><![CDATA[../../MolDepict +#if str( $i ) != '' and str( $i ) != 'None' : + -i "$i" +#end if +#if str( $o ) != '' and str( $o ) != 'None' : + -o "$o" +#end if +#if str( $max ) != '' and str( $max ) != 'None' : + -max "$max" +#end if + | tail -n 5 +]]></command> + <inputs> + <param name="i" label="input file" optional="false" type="data" format="mol2/sdf/drf"/> + <param name="max" label="maximal number of pictures (default=60, 0=unlimited)" optional="true" type="text" area="true" size="1x5" value="60"/> + </inputs> + <outputs> + <data name="o" format="pdf"/> + </outputs> + <help>This tool create structure diagrams for small molecules. +Supported input-formats are mol, mol2, sdf, drf. + +Output of this tool is one pdf-file containing the structure diagrams for all molecules in the input-file.</help> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/galaxyconfigs/tools/MolFilter.xml Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,60 @@ + +<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> +<tool id="molfilter" name="MolFilter" version="0.9"> + <description>filter molecule files</description> + <command interpreter="bash"><![CDATA[../../MolFilter +#if str( $i ) != '' and str( $i ) != 'None' : + -i "$i" +#end if +#if str( $min_logP ) != '' and str( $min_logP ) != 'None' : + -min_logP "$min_logP" +#end if +#if str( $max_logP ) != '' and str( $max_logP ) != 'None' : + -max_logP "$max_logP" +#end if +#if str( $min_MW ) != '' and str( $min_MW ) != 'None' : + -min_MW "$min_MW" +#end if +#if str( $max_MW ) != '' and str( $max_MW ) != 'None' : + -max_MW "$max_MW" +#end if +#if str( $q ) != '' and str( $q ) != 'None' : + -q "$q" +#end if +#if str( $min_sim ) != '' and str( $min_sim ) != 'None' : + -min_sim "$min_sim" +#end if +#if str( $max_sim ) != '' and str( $max_sim ) != 'None' : + -max_sim "$max_sim" +#end if +#if str( $smarts ) != '' and str( $smarts ) != 'None' : + -smarts "$smarts" +#end if +#if str( $smarts_file ) != '' and str( $smarts_file ) != 'None' : + -smarts_file "$smarts_file" +#end if +#if str( $o ) != '' and str( $o ) != 'None' : + -o "$o" +#end if +-quiet + | tail -n 5 +]]></command> + <inputs> + <param name="i" label="input molecule-file" optional="false" type="data" format="mol2/sdf/drf"/> + <param name="q" label="query molecules for similarity searching" optional="true" type="data" format="txt"/> + <param name="smarts_file" label="SMARTS pattern" optional="true" type="data" format="data"/> + <param name="min_logP" label="minimal logP value" optional="true" type="text" area="true" size="1x5" value=""/> + <param name="max_logP" label="maximal logP value" optional="true" type="text" area="true" size="1x5" value=""/> + <param name="min_MW" label="minimal molecular weight" optional="true" type="text" area="true" size="1x5" value=""/> + <param name="max_MW" label="maximal molecular weight" optional="true" type="text" area="true" size="1x5" value=""/> + <param name="min_sim" label="minimal average similarity" optional="true" type="text" area="true" size="1x5" value=""/> + <param name="max_sim" label="maximal similarity" optional="true" type="text" area="true" size="1x5" value=""/> + <param name="smarts" label="SMARTS pattern" optional="true" area="true" type="text" size="1x15"/> + </inputs> + <outputs> + <data name="o" format="mol2/sdf/drf" format_source="i"/> + </outputs> + <help>MolFilter can filter molecules from a molecule input file according to SMARTS expressions, logP, molecular weight, or similarity to query molecule(s). + +Output of this tool is a molecule file that contains all compounds that fulfilled the specified search criteria.</help> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/galaxyconfigs/tools/MolPredictor.xml Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,50 @@ + +<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> +<tool id="molpredictor" name="MolPredictor" version="1.1"> + <description>predict molecule activities with QSAR model</description> + <command interpreter="bash"><![CDATA[../../MolPredictor +#if str( $i ) != '' and str( $i ) != 'None' : + -i "$i" +#end if +#if str( $mod ) != '' and str( $mod ) != 'None' : + -mod "$mod" +#end if +#if str( $o ) != '' and str( $o ) != 'None' : + -o "$o" +#end if +#if str( $csv ) != '' and str( $csv ) != 'None' : + -csv "$csv" +#end if +#if str( $csv_nr ) != '' and str( $csv_nr ) != 'None' : + -csv_nr "$csv_nr" +#end if +#if str( $csv_sep ) != '' and str( $csv_sep ) != 'None' : + -csv_sep "$csv_sep" +#end if +#if str( $csv_cl ) != '' and str( $csv_cl ) != 'None' : + -csv_cl +#end if +#if str( $csv_dl ) != '' and str( $csv_dl ) != 'None' : + -csv_dl +#end if + | tail -n 5 +]]></command> + <inputs> + <param name="i" label="input sd-file" optional="false" type="data" format="sdf"/> + <param name="mod" label="file containing QSAR model" optional="false" type="data" format="mod"/> + <param name="csv" label="input csv-file w/ additional descriptors" optional="true" type="data" format="csv"/> + <param name="csv_nr" label="no. of response variables in csv-file" optional="true" type="text" area="true" size="1x5" value=""/> + <param name="csv_sep" label="separator symbol in csv-file" optional="true" type="text" area="true" size="1x5" value=""/> + <param name="csv_cl" label="csv-file has compound (row) labels" optional="true" type="boolean" truevalue="true" falsevalue=""/> + <param name="csv_dl" label="csv-file has descriptor (column) labels" optional="true" type="boolean" truevalue="true" falsevalue=""/> + </inputs> + <outputs> + <data name="o" format="sdf"/> + </outputs> + <help>This tool predictes the response values of compounds in the given molecule file using the specified QSAR model. + +Input of this tool is a molecule file (sdf,mol2,drf) and a model-file as generated by ModelCreator or FeatureSelector. +Features for all molecules in the input file are generated automatically. However, if you used an additional, externally generated feature-set to generate your QSAR model, make sure to generate features in the same manner (i.e. using the same external tool with the same settings) for the molecule file to be used here and specify the csv-file with the above options. + +Output of this tool (as specified by '-o') is a molecule file containing the predicted values as a property tag named 'predicted_activity'.</help> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/galaxyconfigs/tools/PDBCutter.xml Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,46 @@ + +<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> +<tool id="pdbcutter" name="PDBCutter" version="0.94"> + <description>separate ligand and receptor</description> + <command interpreter="bash"><![CDATA[../../PDBCutter +#if str( $i ) != '' and str( $i ) != 'None' : + -i "$i" +#end if +#if str( $rec ) != '' and str( $rec ) != 'None' : + -rec "$rec" +#end if +#if str( $lig ) != '' and str( $lig ) != 'None' : + -lig "$lig" +#end if +#if str( $lig_chain ) != '' and str( $lig_chain ) != 'None' : + -lig_chain "$lig_chain" +#end if +#if str( $lig_name ) != '' and str( $lig_name ) != 'None' : + -lig_name "$lig_name" +#end if +#if str( $rm_ch ) != '' and str( $rm_ch ) != 'None' : + -rm_ch "$rm_ch" +#end if +#if str( $rm_res ) != '' and str( $rm_res ) != 'None' : + -rm_res "$rm_res" +#end if + | tail -n 5 +]]></command> + <inputs> + <param name="i" label="input pdb-file" optional="false" type="data" format="pdb"/> + <param name="lig_chain" label="chain-name of ligand" optional="false" area="true" type="text" size="1x15"/> + <param name="lig_name" label="ligand name" optional="false" area="true" type="text" size="1x15"/> + <param name="rm_ch" label="protein chains that are to be deleted" optional="true" area="true" type="text" size="1x15"/> + <param name="rm_res" label="pdb-residues that are to be deleted (e.g. water or ions)" optional="true" area="true" type="text" size="1x15"/> + </inputs> + <outputs> + <data name="rec" format="pdb"/> + <data name="lig" format="pdb"/> + </outputs> + <help>This tool splits a given pdb-file into two files containing receptor and reference ligand, respectively. + +The name of the reference ligand (exactly as it appears in the pdb-file) and the name of its chain need to be specified by '-lig_name' and '-lig_chain'. +Optionally, chains (e.g. in case of multimers) or pdb-residues (e.g. water or ions) that you don't need can be deleted from the receptor. In this case, specify their names with '-rm_ch' or '-rm_res'. + +Output of this tool is one pdb-file containing the receptor-structure, i.e. the protein w/o reference ligand and w/o undesired chains/residues (if any were specified), and one pdb-file containing the reference ligand.</help> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/galaxyconfigs/tools/PDBDownload.xml Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,25 @@ + +<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> +<tool id="pdbdownload" name="PDBDownload" version="0.94"> + <description>retrieve pdb-file from pdb.org</description> + <command interpreter="bash"><![CDATA[../../PDBDownload +#if str( $id ) != '' and str( $id ) != 'None' : + -id "$id" +#end if +#if str( $o ) != '' and str( $o ) != 'None' : + -o "$o" +#end if +#if str( $p ) != '' and str( $p ) != 'None' : + -p "$p" +#end if + | tail -n 5 +]]></command> + <inputs> + <param name="id" label="PDB ID for desired structure" optional="false" area="true" type="text" size="1x15"/> + <param name="p" label="proxy" optional="true" area="true" type="text" size="1x15"/> + </inputs> + <outputs> + <data name="o" format="pdb"/> + </outputs> + <help>Download a pdb-file from the pdb data bank (http://www.pdb.org/) using the specified ID of the desired protein structure.</help> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/galaxyconfigs/tools/PartialChargesCopy.xml Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,26 @@ + +<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> +<tool id="partialchargescopy" name="PartialChargesCopy" version="0.94"> + <description>transfer part. charges between files</description> + <command interpreter="bash"><![CDATA[../../PartialChargesCopy +#if str( $i ) != '' and str( $i ) != 'None' : + -i "$i" +#end if +#if str( $chr ) != '' and str( $chr ) != 'None' : + -chr "$chr" +#end if +#if str( $o ) != '' and str( $o ) != 'None' : + -o "$o" +#end if + | tail -n 5 +]]></command> + <inputs> + <param name="i" label="input molecule file" optional="false" type="data" format="mol2/sdf/drf"/> + <param name="chr" label="file containing the same molecules as the input file, but with (different) partial charges" optional="false" type="data" format="mol2"/> + </inputs> + <outputs> + <data name="o" format="mol2" format_source="i"/> + </outputs> + <help>This tool copies partial charges from a given file to the conformations read from a different file. +This can be useful when computing partial charges with external tools, most of which write output as mol2-files *without* support for storing molecular properties. By use of this tool we can thus assign the computed partial charges to the original molecules, thus retaining all properties.</help> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/galaxyconfigs/tools/PocketDetector.xml Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,38 @@ + +<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> +<tool id="pocketdetector" name="PocketDetector" version="0.94"> + <description>detect binding pocket</description> + <command interpreter="bash"><![CDATA[../../PocketDetector +#if str( $rec ) != '' and str( $rec ) != 'None' : + -rec "$rec" +#end if +#if str( $rl ) != '' and str( $rl ) != 'None' : + -rl "$rl" +#end if +#if str( $o ) != '' and str( $o ) != 'None' : + -o "$o" +#end if +#if str( $ini ) != '' and str( $ini ) != 'None' : + -ini "$ini" +#end if + | tail -n 5 +]]></command> + <inputs> + <param name="rec" label="receptor pdb-file" optional="false" type="data" format="pdb"/> + <param name="rl" label="reference ligand" optional="false" type="data" format="mol2/sdf/drf"/> + <param name="ini" label="input ini file" optional="true" type="data" format="ini"/> + </inputs> + <outputs> + <data name="o" format="ini"/> + </outputs> + <help>This tool tries to detect the binding pocket in which the reference ligand is located. +Therefore, probe atoms are placed above the protein surface at positions of relative deep burial. The cluster of probe atoms around the geometric center of the reference ligand is used for the description of the binding pocket. + +As input we need: + * a file containing a protonated protein in pdb-format. Furthermore, it should contain only relevant (i.e. strongly bound) water molecules as detected by WaterFinder. + * a file containing a reference ligand. + This reference ligand should be located in the binding pocket. + Supported formats are mol2, sdf or drf (DockResultFile, xml-based). + +Output of this tool is a docking configuration file that contains the description of the detected binding pocket. This file should in following pipeline steps be specified for docking and rescoring.</help> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/galaxyconfigs/tools/Predictor.xml Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,30 @@ + +<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> +<tool id="predictor" name="Predictor" version="1.1"> + <description>predict activities with QSAR model</description> + <command interpreter="bash"><![CDATA[../../Predictor +#if str( $i ) != '' and str( $i ) != 'None' : + -i "$i" +#end if +#if str( $dat ) != '' and str( $dat ) != 'None' : + -dat "$dat" +#end if +#if str( $o ) != '' and str( $o ) != 'None' : + -o "$o" +#end if + | tail -n 5 +]]></command> + <inputs> + <param name="i" label="input mod-file" optional="false" type="data" format="mod"/> + <param name="dat" label="data-file containing prediction data set" optional="false" type="data" format="dat"/> + </inputs> + <outputs> + <data name="o" format="txt"/> + </outputs> + <help>This tool predictes the response values of compounds in the given data-file using the specified QSAR model. + +Input of this tool is a model-file as generated by ModelCreator or FeatureSelector and a data-file generated by InputReader. + +Output of this tool (as specified by '-o') is a text file containing the predicted and, if any, the expected response values in one column each. +If you would prefer to use molecule files (sdf,mol2,drf) for input and output, please use the tool MolPredictor instead of this one.</help> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/galaxyconfigs/tools/PropertyModifier.xml Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,43 @@ + +<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> +<tool id="propertymodifier" name="PropertyModifier" version="0.94"> + <description>modify molecule property tags</description> + <command interpreter="bash"><![CDATA[../../PropertyModifier +#if str( $i ) != '' and str( $i ) != 'None' : + -i "$i" +#end if +#if str( $o ) != '' and str( $o ) != 'None' : + -o "$o" +#end if +#if str( $mode ) != '' and str( $mode ) != 'None' : + -mode "$mode" +#end if +#if str( $name ) != '' and str( $name ) != 'None' : + -name "$name" +#end if +#if str( $value ) != '' and str( $value ) != 'None' : + -value "$value" +#end if +#if str( $new_name ) != '' and str( $new_name ) != 'None' : + -new_name "$new_name" +#end if + | tail -n 5 +]]></command> + <inputs> + <param name="i" label="input file" optional="false" type="data" format="mol2/sdf/drf"/> + <param name="mode" label="'delete', 'add' or 'rename' properties" optional="false" type="select"> + <option value="add">add</option> + <option value="rename">rename</option> + <option value="delete">delete</option> + </param> + <param name="name" label="property name ('all' will erase all properties if in delete-mode)" optional="false" area="true" type="text" size="1x15"/> + <param name="value" label="property value (in case of prop. adding only)" optional="true" area="true" type="text" size="1x15"/> + <param name="new_name" label="new property name (in case of renaming only)" optional="true" area="true" type="text" size="1x15"/> + </inputs> + <outputs> + <data name="o" format="mol2/sdf/drf" format_source="i"/> + </outputs> + <help>With this tools you can add, rename or delete molecule property tags. +These tags can for example contain information about scores, binding-free-energy, IDs or names for the resp. molecule. +The output of this tool is a molecule file in which the desired property tags have been added/renamed/deleted (as chosen).</help> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/galaxyconfigs/tools/PropertyPlotter.xml Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,35 @@ + +<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> +<tool id="propertyplotter" name="PropertyPlotter" version="0.94"> + <description>plot molecule properties</description> + <command interpreter="bash"><![CDATA[../../PropertyPlotter +#if str( $i ) != '' and str( $i ) != 'None' : + -i "$i" +#end if +#if str( $p1 ) != '' and str( $p1 ) != 'None' : + -p1 "$p1" +#end if +#if str( $p2 ) != '' and str( $p2 ) != 'None' : + -p2 "$p2" +#end if +#if str( $o ) != '' and str( $o ) != 'None' : + -o "$o" +#end if +-quiet + | tail -n 5 +]]></command> + <inputs> + <param name="i" label="input file" optional="false" type="data" format="mol2/sdf/drf"/> + <param name="p1" label="name of property 1" optional="false" area="true" type="text" size="1x15"/> + <param name="p2" label="name of property 2" optional="true" area="true" type="text" size="1x15"/> + </inputs> + <outputs> + <data name="o" format="png"/> + </outputs> + <help>PropertyPlotter can be used to generate distribution- or scatter-plots of data contained in molecule property-tags. + +In case you want to create a scatter-plot, specify the name of both property-tags to be used with '-p1' and '-p2'. If you want to generate a distribution plot, just specify '-p1'. +The output graphic will created by use of gnuplot, so make sure to have it installed and in your PATH environment variable. + +The output of this tool is a plot in form of an eps or png-file (as chosen).</help> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/galaxyconfigs/tools/ProteinCheck.xml Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,34 @@ + +<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> +<tool id="proteincheck" name="ProteinCheck" version="0.94"> + <description>quality check for proteins structures</description> + <command interpreter="bash"><![CDATA[../../ProteinCheck +#if str( $i ) != '' and str( $i ) != 'None' : + -i "$i" +#end if +#if str( $o ) != '' and str( $o ) != 'None' : + -o "$o" +#end if +#if str( $bc ) != '' and str( $bc ) != 'None' : + -bc +#end if + | tail -n 5 +]]></command> + <inputs> + <param name="i" label="input pdb-file" optional="false" type="data" format="pdb"/> + <param name="bc" label="ignore broken chains" optional="true" type="boolean" truevalue="true" falsevalue=""/> + </inputs> + <outputs> + <data name="o" format="pdf"/> + </outputs> + <help>Check a given protein structure for the following errors: + * bond-lengths may not be completely senseless (i.e. <0.7 or >2.5 Angstroem) + * each chain may only contain one actual molecule, i.e. there may be no unconnected atoms or fragments. This test is skipped if the above box is checked. + * each atom must have a valid assigned element + * the protein must be protonated (since this is necessary for docking/(re-)scoring). + * 3D coordinates must be present (instead of 2D coordinates; also necessary for docking/(re-)scoring) + * there may be no senseless temperature factors (<1 or >100) + * there may be no sterical clashes between atoms + +A protein structure quality report, containing the results of those tests and a secondary structure prediction, a Ramachandran plot and a temperature factor plot will be generated and saved as a pdf-file.</help> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/galaxyconfigs/tools/ProteinProtonator.xml Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,29 @@ + +<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> +<tool id="proteinprotonator" name="ProteinProtonator" version="0.94"> + <description>protonate protein structures</description> + <command interpreter="bash"><![CDATA[../../ProteinProtonator +#if str( $i ) != '' and str( $i ) != 'None' : + -i "$i" +#end if +#if str( $o ) != '' and str( $o ) != 'None' : + -o "$o" +#end if +#if str( $ph ) != '' and str( $ph ) != 'None' : + -ph "$ph" +#end if + | tail -n 5 +]]></command> + <inputs> + <param name="i" label="input file" optional="false" type="data" format="pdb"/> + <param name="ph" label="pH-value for pH-dep. protonation" optional="true" type="text" area="true" size="1x5" value="7.0"/> + </inputs> + <outputs> + <data name="o" format="pdb" format_source="i"/> + </outputs> + <help>ProteinProtonator allows you add hydrogens to a protein structure. + +Note that all hydrogen atoms already present in the input file will be ignored. If desired, you can specify a specific pH value, for which protonation is to be done; otherwise a neutral pH will be assumed. + +Output of this tool is one pdb-file containing the input protein structure with added hydrogens atoms.</help> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/galaxyconfigs/tools/RMSDCalculator.xml Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,31 @@ + +<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> +<tool id="rmsdcalculator" name="RMSDCalculator" version="0.94"> + <description>calculate RMSD between poses</description> + <command interpreter="bash"><![CDATA[../../RMSDCalculator +#if str( $i ) != '' and str( $i ) != 'None' : + -i "$i" +#end if +#if str( $org ) != '' and str( $org ) != 'None' : + -org "$org" +#end if +#if str( $o ) != '' and str( $o ) != 'None' : + -o "$o" +#end if +-quiet + | tail -n 5 +]]></command> + <inputs> + <param name="i" label="input molecule file" optional="false" type="data" format="mol2/sdf/drf"/> + <param name="org" label="molecule file containing the original ('true') poses" optional="false" type="data" format="mol2/sdf/drf"/> + </inputs> + <outputs> + <data name="o" format="mol2/sdf/drf" format_source="i"/> + </outputs> + <help>This tool calculates the RMSD between different conformations of the same molecule. + +Therefore this tool can for example be used to evaluate the different between ligands taken from co-crystal structures and their poses generated by a docking. +Molecules may be sorted differently in the two input files; a topology hashkey will be used to match molecules to each other. + +Output of this tool is a molecule file which will for each molecule contain a property-tag 'RMSD' holding the calculated RMSD value.</help> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/galaxyconfigs/tools/ScoreAnalyzer.xml Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,55 @@ + +<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> +<tool id="scoreanalyzer" name="ScoreAnalyzer" version="0.94"> + <description>generate ROC or enrichment plots</description> + <command interpreter="bash"><![CDATA[../../ScoreAnalyzer +#if str( $mode ) != '' and str( $mode ) != 'None' : + -mode "$mode" +#end if +#if str( $title ) != '' and str( $title ) != 'None' : + -title "$title" +#end if +#if str( $o ) != '' and str( $o ) != 'None' : + -o "$o" +#end if +#if str( $i ) != '' and str( $i ) != 'None' : + -i "$i" +#end if +#if str( $s ) != '' and str( $s ) != 'None' : + -s "$s" +#end if +#if str( $e ) != '' and str( $e ) != 'None' : + -e "$e" +#end if +#if str( $t ) != '' and str( $t ) != 'None' : + -t "$t" +#end if +#if str( $b ) != '' and str( $b ) != 'None' : + -b +#end if + | tail -n 5 +]]></command> + <inputs> + <param name="i" label="input file" optional="false" type="data" format="mol2/sdf/drf"/> + <param name="mode" label="'roc', 'top50', 'scatter' or 'enrichment'" optional="false" type="select"> + <option value="roc">roc</option> + <option value="top50">top50</option> + <option value="scatter">scatter</option> + <option value="enrichment">enrichment</option> + </param> + <param name="title" label="plot title" optional="true" area="true" type="text" size="1x15"/> + <param name="s" label="score label" optional="false" area="true" type="text" size="1x15" value="score"/> + <param name="e" label="binding-free-energy/class label name" optional="false" area="true" type="text" size="1x15" value="binding_free_energy"/> + <param name="t" label="only in case of non-binary act. data: binding-free-energy threshold; compound with values *below* this threshold will be defined as binder" optional="true" area="true" type="text" size="1x15"/> + <param name="b" label="binary experimental activity data" optional="true" type="boolean" truevalue="true" falsevalue=""/> + </inputs> + <outputs> + <data name="o" format="png"/> + </outputs> + <help>This tool can be used generate plots that allow to evaluate the quality of docking or (re-)scoring. + +The type of plot to be generated must be chosen by either '-roc', '-top50', '-scatter' or '-enrichment'. The name of the property-tag that contains the scores to be evaluated (e.g. obtained by docking) is to be specified by '-s'; the name of the property-tag containing experimental data (e.g. binding-free-energy measurements or binder/non-binder info) by use '-e'. If the experimental reference data is not binary, then a threshold below which compound will be considered binders must be given with '-t'. +The output graphic will created by use of gnuplot, so make sure to have it installed and in your PATH environment variable. + +The output of this tool is a plot in form of an eps or png-file (as chosen).</help> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/galaxyconfigs/tools/SimilarityAnalyzer.xml Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,35 @@ + +<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> +<tool id="similarityanalyzer" name="SimilarityAnalyzer" version="0.9"> + <description>analyze similarity between molecule files</description> + <command interpreter="bash"><![CDATA[../../SimilarityAnalyzer +#if str( $i1 ) != '' and str( $i1 ) != 'None' : + -i1 "$i1" +#end if +#if str( $i2 ) != '' and str( $i2 ) != 'None' : + -i2 "$i2" +#end if +#if str( $o ) != '' and str( $o ) != 'None' : + -o "$o" +#end if +#if str( $title ) != '' and str( $title ) != 'None' : + -title "$title" +#end if +-quiet + | tail -n 5 +]]></command> + <inputs> + <param name="i1" label="input molecule file 1" optional="false" type="data" format="mol2/sdf/drf"/> + <param name="i2" label="input molecule file 2" optional="false" type="data" format="mol2/sdf/drf"/> + <param name="title" label="plot title" optional="true" area="true" type="text" size="1x15"/> + </inputs> + <outputs> + <data name="o" format="png"/> + </outputs> + <help>This tool evaluates the similarity between molecules in two input files and creates a distribution plot to visualize the result. + +Therefore, for each molecule a pathway-based, hashed binary fingerprint is generated and compared to the fingerprint of other molecules by use of the Tanimoto similarity measure. +The output graphic will created by use of gnuplot, so make sure to have it installed and in your PATH environment variable. + +The resulting plot (in form of an eps-, png- or pdf-file; as chosen) shows the distribution of similarity values obtained by comparing each molecule in input file 1 against each molecule in input file 2.</help> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/galaxyconfigs/tools/SimpleRescorer.xml Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,49 @@ + +<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> +<tool id="simplerescorer" name="SimpleRescorer" version="0.94"> + <description>rescore docking results</description> + <command interpreter="bash"><![CDATA[../../SimpleRescorer +#if str( $rec ) != '' and str( $rec ) != 'None' : + -rec "$rec" +#end if +#if str( $rl ) != '' and str( $rl ) != 'None' : + -rl "$rl" +#end if +#if str( $ini ) != '' and str( $ini ) != 'None' : + -ini "$ini" +#end if +#if str( $i ) != '' and str( $i ) != 'None' : + -i "$i" +#end if +#if str( $o ) != '' and str( $o ) != 'None' : + -o "$o" +#end if +#if str( $function ) != '' and str( $function ) != 'None' : + -function "$function" +#end if + | tail -n 5 +]]></command> + <inputs> + <param name="rec" label="receptor pdb-file" optional="false" type="data" format="pdb"/> + <param name="rl" label="reference-ligand" optional="false" type="data" format="mol2/sdf/drf"/> + <param name="ini" label="configuration file" optional="true" type="data" format="ini"/> + <param name="i" label="compounds to be rescored" optional="false" type="data" format="mol2/sdf/drf"/> + <param name="function" label="scoring function: 'MM', 'PLP' or 'PB'" optional="true" type="select"> + <option value="MM">MM</option> + <option value="PLP">PLP</option> + <option value="PB">PB</option> + </param> + </inputs> + <outputs> + <data name="o" format="mol2/sdf/drf" format_source="i"/> + </outputs> + <help>This tool rescores docking output poses. +A scoring function is used to evaluate the binding-free-energy of each compound. This is similar to the scoring done during docking; details depend on the config-file (if one is specified). + +As input we need: + * a file containing a protonated protein in pdb-format + * a file containing a reference ligand. This reference ligand should be located in the binding pocket. Supported formats are mol2, sdf or drf (DockResultFile, xml-based). + * a file containing the compounds that are to be rescored. Supported formats are mol2, sdf or drf (DockResultFile, xml-based). Those compound should have been docked into the specified protein. + +Output of this tool is a file in the same format as the input ligand file containing all compounds with scores obtained by rescoring in form of a property 're-score'.</help> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/galaxyconfigs/tools/SpatialConstraintDefiner.xml Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,45 @@ + +<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> +<tool id="spatialconstraintdefiner" name="SpatialConstraintDefiner" version="0.94"> + <description>define spatial constraint</description> + <command interpreter="bash"><![CDATA[../../SpatialConstraintDefiner +#if str( $ini ) != '' and str( $ini ) != 'None' : + -ini "$ini" +#end if +#if str( $i ) != '' and str( $i ) != 'None' : + -i "$i" +#end if +#if str( $o ) != '' and str( $o ) != 'None' : + -o "$o" +#end if +#if str( $type ) != '' and str( $type ) != 'None' : + -type "$type" +#end if +#if str( $n ) != '' and str( $n ) != 'None' : + -n "$n" +#end if +#if str( $p ) != '' and str( $p ) != 'None' : + -p "$p" +#end if + | tail -n 5 +]]></command> + <inputs> + <param name="ini" label="input configuration file" optional="true" type="data" format="ini"/> + <param name="i" label="input molecule file" optional="false" type="data" format="mol2/sdf/drf"/> + <param name="type" label="'fraction' or 'number' of compound atoms" optional="false" type="select"> + <option value="fraction">fraction</option> + <option value="number">number</option> + </param> + <param name="n" label="desired number/fraction of atoms in spatial area" optional="false" type="text" area="true" size="1x5" value=""/> + <param name="p" label="penalty value" optional="false" type="text" area="true" size="1x5" value="1e11"/> + </inputs> + <outputs> + <data name="o" format="ini"/> + </outputs> + <help>This tool allows to define spatial constraints for docking or scoring. + +For convenience, we use a molecule file as input and generate a boundary box around the contained compound. This molecule can therefore for example contain the reference ligand (obtained from a co-crystal structure), or a docked compound, or just a set of dummy atoms used to manually define the boundaries of the desired spatial constraint. +Furthermore, you need to specify how many atoms of the compound to be docked (or scored) should be located inside the spatial area. You can either specify a number of atoms or a fraction of molecule atoms for this. + +Output of this tool is a ini-file that contains the desired spatial constraint.</help> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/galaxyconfigs/tools/TaGRes-train.xml Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,61 @@ + +<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> +<tool id="tagres-train" name="TaGRes-train" version="0.94"> + <description>Target-specific Grid-Rescoring, training</description> + <command interpreter="bash"><![CDATA[../../TaGRes-train +#if str( $rec ) != '' and str( $rec ) != 'None' : + -rec "$rec" +#end if +#if str( $rl ) != '' and str( $rl ) != 'None' : + -rl "$rl" +#end if +#if str( $ini ) != '' and str( $ini ) != 'None' : + -ini "$ini" +#end if +#if str( $i ) != '' and str( $i ) != 'None' : + -i "$i" +#end if +#if str( $o ) != '' and str( $o ) != 'None' : + -o "$o" +#end if +#if str( $method ) != '' and str( $method ) != 'None' : + -method "$method" +#end if +#if str( $function ) != '' and str( $function ) != 'None' : + -function "$function" +#end if +#if str( $exp ) != '' and str( $exp ) != 'None' : + -exp "$exp" +#end if + | tail -n 5 +]]></command> + <inputs> + <param name="rec" label="receptor pdb-file" optional="false" type="data" format="pdb"/> + <param name="rl" label="reference-ligand" optional="false" type="data" format="mol2/sdf/drf"/> + <param name="ini" label="configuration file" optional="true" type="data" format="ini"/> + <param name="i" label="training compound data set" optional="false" type="data" format="mol2/sdf/drf"/> + <param name="method" label="rescoring type: 'Rescoring3D' or 'Rescoring4D', or 'Rescoring1D'" optional="false" type="select"> + <option value="Rescoring3D">Rescoring3D</option> + <option value="Rescoring4D">Rescoring4D</option> + <option value="Rescoring1D">Rescoring1D</option> + </param> + <param name="function" label="scoring function: 'MM' or 'PLP'" optional="true" type="select"> + <option value="MM">MM</option> + <option value="PLP">PLP</option> + </param> + <param name="exp" label="property-tag name containing experimentally determined binding-free-energies" optional="false" area="true" type="text" size="1x15" value="binding_free_energy"/> + </inputs> + <outputs> + <data name="o" format="mod"/> + </outputs> + <help>This tool generates a model for Target-specific Grid-Rescoring (TaGRes). +As input we need: + + * a file containing a protonated protein in pdb-format + * a file containing a reference ligand. This reference ligand should be located in the binding pocket. Supported formats are mol2, sdf or drf (DockResultFile, xml-based). + * a file containing a training data set, i.e. compounds whose binding-free-energy to the specified target is known and annotated in this file. Those compounds should have been docked into the specified protein. + +A scoring function is applied and an interaction-grid thereby generated for each input compound. Together with the known binding-free-energy, those grids are used to automatically search for the best linear or non-linear regression model that can approximate the binding-free-energy. After this model has been generated, you can pass it to the tool TaGRes and rescore (different) compounds with it. + +The output of this TaGRes-train is a file that contains the generated regression model. However, if no model with suitable prediction quality was found, an error will be shown and no model-file will be written.</help> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/galaxyconfigs/tools/TaGRes.xml Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,63 @@ + +<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> +<tool id="tagres" name="TaGRes" version="0.94"> + <description>Target-specific Grid-Rescoring</description> + <command interpreter="bash"><![CDATA[../../TaGRes +#if str( $rec ) != '' and str( $rec ) != 'None' : + -rec "$rec" +#end if +#if str( $rl ) != '' and str( $rl ) != 'None' : + -rl "$rl" +#end if +#if str( $ini ) != '' and str( $ini ) != 'None' : + -ini "$ini" +#end if +#if str( $i ) != '' and str( $i ) != 'None' : + -i "$i" +#end if +#if str( $mod ) != '' and str( $mod ) != 'None' : + -mod "$mod" +#end if +#if str( $o ) != '' and str( $o ) != 'None' : + -o "$o" +#end if +#if str( $method ) != '' and str( $method ) != 'None' : + -method "$method" +#end if +#if str( $function ) != '' and str( $function ) != 'None' : + -function "$function" +#end if + | tail -n 5 +]]></command> + <inputs> + <param name="rec" label="receptor pdb-file" optional="false" type="data" format="pdb"/> + <param name="rl" label="reference-ligand" optional="false" type="data" format="mol2/sdf/drf"/> + <param name="ini" label="configuration file" optional="true" type="data" format="ini"/> + <param name="i" label="compounds to be rescored" optional="false" type="data" format="mol2/sdf/drf"/> + <param name="mod" label="model-file generated by TaGRes-train" optional="false" type="data" format="data"/> + <param name="method" label="rescoring type: 'Rescoring3D' or 'Rescoring4D', or 'Rescoring1D'" optional="false" type="select"> + <option value="Rescoring3D">Rescoring3D</option> + <option value="Rescoring4D">Rescoring4D</option> + <option value="Rescoring1D">Rescoring1D</option> + </param> + <param name="function" label="scoring function: 'MM' or 'PLP'" optional="true" type="select"> + <option value="MM">MM</option> + <option value="PLP">PLP</option> + </param> + </inputs> + <outputs> + <data name="o" format="mol2/sdf/drf" format_source="i"/> + </outputs> + <help>This tool rescores docking output poses using Target-specific Grid-Rescoring. +Please generate a regression model for binding-affinity approximation for your protein target by use of the tool TaGRes-train before using this tool. +As input TaGRes needs: + + * a file containing a protonated protein in pdb-format + * a file containing a reference ligand. This reference ligand should be located in the binding pocket. Supported formats are mol2, sdf or drf (DockResultFile, xml-based). + * a file containing the compounds that are to be rescored. Supported formats are mol2, sdf or drf (DockResultFile, xml-based). Those compound should have been docked into the specified protein. + * a regression model file as generated by TaGRes-train for same protein target than the one specified here. + +TaGRes will evaluate each given input pose with a scoring function and apply the specified regression model to the score contributions generated this way, resulting in a re-score value, i.e. a (probably) enhanced approximation of the compound's binding-free-energy. + +Output of this tool is a file in the same format as the input ligand file containing all compounds with scores obtained by rescoring in form of a property 're-score'.</help> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/galaxyconfigs/tools/Validator.xml Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,36 @@ + +<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> +<tool id="validator" name="Validator" version="1.1"> + <description>evaluate quality of a QSAR model</description> + <command interpreter="bash"><![CDATA[../../Validator +#if str( $i ) != '' and str( $i ) != 'None' : + -i "$i" +#end if +#if str( $dat ) != '' and str( $dat ) != 'None' : + -dat "$dat" +#end if +#if str( $o ) != '' and str( $o ) != 'None' : + -o "$o" +#end if +#if str( $type ) != '' and str( $type ) != 'None' : + -type "$type" +#end if + | tail -n 5 +]]></command> + <inputs> + <param name="i" label="input mod-file" optional="false" type="data" format="mod"/> + <param name="dat" label="data-file" optional="false" type="data" format="dat"/> + <param name="type" label="feature-selection type" optional="false" type="select"> + <option value="cross validation">cross validation</option> + <option value="bootstrapping">bootstrapping</option> + <option value="response permutation">response permutation</option> + <option value="evaluate fit to test data">evaluate fit to test data</option> + </param> + </inputs> + <outputs> + <data name="o" format="txt"/> + </outputs> + <help>Validator evaluates the quality of a QSAR model. + +The validation technique to be used for this can selected by '-type'. As input this tools need a model-file as generate by InputReader or FeatureSelector and a data-file generated by InputReader containing the prediction data set. Note that the latter must contain response values so that predictions done by the supplied model can be compared to those values by the validation method.</help> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/galaxyconfigs/tools/VendorFinder.xml Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,49 @@ + +<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> +<tool id="vendorfinder" name="VendorFinder" version="0.94"> + <description>search vendors for compounds</description> + <command interpreter="bash"><![CDATA[../../VendorFinder +#if str( $i ) != '' and str( $i ) != 'None' : + -i "$i" +#end if +#if str( $d ) != '' and str( $d ) != 'None' : + -d "$d" +#end if +#if str( $u ) != '' and str( $u ) != 'None' : + -u "$u" +#end if +#if str( $h ) != '' and str( $h ) != 'None' : + -h "$h" +#end if +#if str( $port ) != '' and str( $port ) != 'None' : + -port "$port" +#end if +#if str( $p ) != '' and str( $p ) != 'None' : + -p "$p" +#end if +#if str( $o ) != '' and str( $o ) != 'None' : + -o "$o" +#end if +#if str( $opt ) != '' and str( $opt ) != 'None' : + -opt +#end if + | tail -n 5 +]]></command> + <inputs> + <param name="i" label="input file containing compounds" optional="false" type="data" format="mol2/sdf/drf"/> + <param name="d" label="database name" optional="false" area="true" type="text" size="1x15"/> + <param name="u" label="database username" optional="false" area="true" type="text" size="1x15"/> + <param name="h" label="database host" optional="false" area="true" type="text" size="1x15"/> + <param name="port" label="database port" optional="true" type="text" area="true" size="1x5" value="3306"/> + <param name="p" label="database password" optional="false" area="true" type="text" size="1x15"/> + <param name="opt" label="optimize purchase, i.e. select cheapest sources and sort by vendor" optional="true" type="boolean" truevalue="true" falsevalue=""/> + </inputs> + <outputs> + <data name="o" format="txt"/> + </outputs> + <help>This tool can be used to fetch information about vendors for each compound in the given input file from a data base. + +Of course, vendors can only be found if they have been stored in the database that is to be used here. Use DBImporter with molecules files obtained from the compound vendors of your choice in order to create such a database. + +Output of this tool is a text-file containing a list of vendor-name and vendor's compound-ID for each compound in the input file for which vendor-information was found in the database.</help> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/galaxyconfigs/tools/WaterFinder.xml Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,55 @@ + +<!--This is a configuration file for the integration of a CADDSuite tool into Galaxy (http://usegalaxy.org). This file was automatically generated using GalaxyConfigGenerator, so do not bother to make too many manual modifications.--> +<tool id="waterfinder" name="WaterFinder" version="0.94"> + <description>find strongly bound waters</description> + <command interpreter="bash"><![CDATA[../../WaterFinder +#if str( $rec ) != '' and str( $rec ) != 'None' : + -rec "$rec" +#end if +#if str( $rl ) != '' and str( $rl ) != 'None' : + -rl "$rl" +#end if +#if str( $ini ) != '' and str( $ini ) != 'None' : + -ini "$ini" +#end if +#if str( $wat ) != '' and str( $wat ) != 'None' : + -wat "$wat" +#end if +#if str( $o ) != '' and str( $o ) != 'None' : + -o "$o" +#end if +#if str( $ai ) != '' and str( $ai ) != 'None' : + -ai +#end if + | tail -n 5 +]]></command> + <inputs> + <param name="rec" label="receptor pdb-file" optional="false" type="data" format="pdb"/> + <param name="rl" label="reference-ligand" optional="false" type="data" format="mol2/sdf/drf"/> + <param name="ini" label="configuration file" optional="true" type="data" format="ini"/> + <param name="wat" label="input pdb-file containing water molecules (if not part of rec.-file)" optional="true" type="data" format="pdb"/> + <param name="ai" label="use ab-initio water search (ignore water in pdb-file), experimental!" optional="true" type="boolean" truevalue="true" falsevalue=""/> + </inputs> + <outputs> + <data name="o" format="pdb"/> + </outputs> + <help>This tool searches for crystal waters that + * either interact very strongly with the receptor + * or that interact strongly with receptor and reference ligand, + thus functioning as a water bridge. + +Water molecules in the pdb-structure (i.e. single oxygens) are automatically protonated and rotationally optimized before the search is done. + +As input we need: + * a file containing a protonated protein in pdb-format. + This file should contain water molecules that are to be evaluated by this tool. + However, you can also use a separate pdb-file as input for the water molecules (see below). + * a file containing a reference ligand. + This reference ligand should be located in the binding pocket. + Supported formats are mol2, sdf or drf (DockResultFile, xml-based). + * optionally a file in pdb-format containing water molecules. + If you specify such a file , all water molecules appearing in the + protein input-file (if any) will be ignored. + +Output of this tool is a pdb-file containing the protein and all detected strongly bound water molecules.</help> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/galaxyconfigs/tools/upload.xml Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,46 @@ +<?xml version="1.0"?> + +<tool name="Upload File" id="cadds_upload" version="1.1.2"> + <description> + from your computer + </description> + <action module="galaxy.tools.actions.upload" class="UploadToolAction"/> + <command interpreter="python"> + ../../../data_source/upload.py $GALAXY_ROOT_DIR $GALAXY_DATATYPES_CONF_FILE $paramfile + #set $outnum = 0 + #while $varExists('output%i' % $outnum): + #set $output = $getVar('output%i' % $outnum) + #set $outnum += 1 + ${output.dataset.dataset.id}:${output.files_path}:${output} + #end while + </command> + <inputs nginx_upload="true"> + <param name="file_type" type="select" label="File Format" help="Which format? See help below"> + <options from_parameter="tool.app.datatypes_registry.upload_file_formats" transform_lines="[ "%s%s%s" % ( line, self.separator, line ) for line in obj ]"> + <column name="value" index="1"/> + <column name="name" index="0"/> + <filter type="sort_by" column="0"/> + <filter type="add_value" name="Auto-detect" value="auto" index="0"/> + </options> + </param> + <param name="async_datasets" type="hidden" value="None"/> + <upload_dataset name="files" title="Specify Files for Dataset" file_type_name="file_type" metadata_ref="files_metadata"> + <param name="file_data" type="file" size="30" label="File" ajax-upload="true" help="TIP: For NGS and other large files (>~2GB), uploading via HTTP/FTP URL (below) is the most reliable method."> + <validator type="expression" message="You will need to reselect the file you specified (%s)." substitute_value_in_message="True">not ( ( isinstance( value, unicode ) or isinstance( value, str ) ) and value != "" )</validator> <!-- use validator to post message to user about needing to reselect the file, since most browsers won't accept the value attribute for file inputs --> + </param> + <param name="url_paste" type="text" area="true" size="5x35" label="URL/Text" help="Here you may specify a list of URLs (one per line) or paste the contents of a file."/> + <param name="ftp_files" type="ftpfile" label="Files uploaded via FTP"/> + <!-- + <param name="space_to_tab" type="select" display="checkboxes" multiple="True" label="Convert spaces to tabs" help="Use this option if you are entering intervals by hand."> + <option value="Yes">Yes</option> + </param> + --> + </upload_dataset> + <!--<param name="dbkey" type="genomebuild" label="Genome" />--> + <conditional name="files_metadata" title="Specify metadata" value_from="self:app.datatypes_registry.get_upload_metadata_params" value_ref="file_type" value_ref_in_group="False" /> + <!-- <param name="other_dbkey" type="text" label="Or user-defined Genome" /> --> + </inputs> + <help> + + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/install.sh Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,84 @@ +#!/bin/bash + +QT_DIR="" +INSTALL_DIR="" +#OPT="Linux_x86_64" + + +checkDir() +{ + echo -n "checking for "$1" ... " + if [ -f $QT_DIR/$1 ]; then + echo $QT_DIR/$1 + return 1 + else + echo "not found!" + return 0 + fi +} + +echo +cat license.txt +echo +echo -n "Do you agree to this license?! (y/n) " +read license_accepted +echo + +if [ "$license_accepted" != "y" ] && [ "$license_accepted" != "yes" ]; then + echo "License was not accepted, aborting." + exit 1 +fi + +echo -n "Please enter *absolute* path to install target-directory: " + +read INSTALL_DIR +if [ ! -d $INSTALL_DIR ]; then + mkdir $INSTALL_DIR +fi + +if [ ! -d $INSTALL_DIR ]; then + echo + echo "[Error:] The desired install-directory does not exist and could also not be created!" + echo "Perhaps there was a typo or you do not have permission to create this folder." + echo "Aborting install." + echo + exit 1 +fi + +# if [ -f /usr/lib/libQtCore.so.4 ] && [ -f /usr/lib/libQtGui.so.4 ]; then +# QT_DIR=/usr/lib +# else +# echo "Please enter absolute path to the directory containing" +# echo -n "your Qt4 libraries (version>=4.3.5): " +# read QT_DIR +# fi + +# checkDir libQtCore.so.4; ok=$?; +# checkDir libQtGui.so.4; if [ $ok = 1 ]; then let ok $?; fi +# #checkDir libQtOpenGL.so; if [ $ok = 1 ]; then ok=$?; fi +# +# if [ $ok != 1 ]; then +# echo "Aborting installation due to missing Qt4!" +# exit 1 +# fi + +cd bin +programs=`ls *.bin` +cd .. +for i in $programs; do + chmod +x ${i:0:${#i}-4} +done + + +mv * $INSTALL_DIR/ + +if [ -f $INSTALL_DIR/CADDSuite-description.txt ]; then + echo + echo + cat $INSTALL_DIR/CADDSuite-description.txt +fi + +echo +echo "Installation finished." +echo "You can find all installed programs in $INSTALL_DIR." +echo
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/license.txt Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,20 @@ +------------------------------------------------------------------------------- + CADDSuite - A flexible and open framework and workflow system + for computer-aided drug design +------------------------------------------------------------------------------- + +Copyright (C) 2011 Marcel Schumann + +CADDSuite is free software; you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation; either version 3 of the License, or (at +your option) any later version. + +CADDSuite is distributed in the hope that it will be useful, but +WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +General Public License for more details. + +You should have received a copy of the GNU General Public License +along with this program; if not, see <http://www.gnu.org/licenses/>. +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/rescoring_common Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,4 @@ +#!/bin/bash + export BASE_DIR=`dirname "$0"` + . "$BASE_DIR"/setPathes.sh + "$BASE_DIR"/bin/rescoring_common.bin "$@"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/setPathes.sh Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,10 @@ +#!/bin/bash +export LD_LIBRARY_PATH="$BASE_DIR"/lib +export DYLD_LIBRARY_PATH="$BASE_DIR"/lib +export BALL_DATA_PATH="$BASE_DIR"/data +export BABEL_DATADIR="$BASE_DIR"/data/OpenBabel/ +export QT_PLUGIN_PATH="$BASE_DIR"/lib/plugins/ +export PATH="$BASE_DIR"/bin:$PATH +export GDFONTPATH="$BASE_DIR"/data/fonts +export GNUPLOT_DEFAULT_GDFONT=FreeSans +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite/suite_config.xml Sun Jun 26 13:53:57 2011 -0400 @@ -0,0 +1,140 @@ +<suite id="CADDSuite_toolsuite" name="CADDSuite" version="0.94"> + +<description> +CADDSuite: A flexible and open framework for Computer-Aided Drug Design +</description> +<tool id="cadds_upload" name="Upload File" version="1.1.2"> + <description>from your computer</description> +</tool> +<tool id="antitargetrescorer" name="AntitargetRescorer" version="0.94"> + <description>rescore w/ anti-target dock-results</description> +</tool> +<tool id="bindingdbcleaner" name="BindingDBCleaner" version="0.94"> + <description>fix bindingdb.org downloads</description> +</tool> +<tool id="combilibgenerator" name="CombiLibGenerator" version="0.94"> + <description>generate combinatorial lib</description> +</tool> +<tool id="constraintsfinder" name="ConstraintsFinder" version="0.94"> + <description>find strongly interacting residues</description> +</tool> +<tool id="converter" name="Converter" version="0.94"> + <description>interconvert molecular file-formats</description> +</tool> +<tool id="dbexporter" name="DBExporter" version="0.94 (ob)"> + <description>export molecules from data base</description> +</tool> +<tool id="dbimporter" name="DBImporter" version="0.94 (ob)"> + <description>import molecules into data base</description> +</tool> +<tool id="dockresultmerger" name="DockResultMerger" version="0.94"> + <description>merge docking output files</description> +</tool> +<tool id="evensplit" name="EvenSplit" version="0.94"> + <description>generate splits w/ equal property range</description> +</tool> +<tool id="galaxyconfiggenerator" name="GalaxyConfigGenerator" version="0.94"> + <description>generate galaxy tool-config files</description> +</tool> +<tool id="gridbuilder" name="GridBuilder" version="0.94"> + <description>create score-grids for docking</description> +</tool> +<tool id="imeedydock" name="IMGDock" version="0.94"> + <description>Iterative Multi-Greedy Docking</description> +</tool> +<tool id="interactionconstraintdefiner" name="InteractionConstraintDefiner" version="0.94"> + <description>define interaction constraint</description> +</tool> +<tool id="ligcheck" name="LigCheck" version="0.94"> + <description>check molecules for errors</description> +</tool> +<tool id="ligand3dgenerator" name="Ligand3DGenerator" version="0.94"> + <description>generate 3D coordinates for small molecules</description> +</tool> +<tool id="ligandfilesplitter" name="LigandFileSplitter" version="0.94"> + <description>split molecule files</description> +</tool> +<tool id="molcombine" name="MolCombine" version="0.94"> + <description>combine molecular files</description> +</tool> +<tool id="moldepict" name="MolDepict" version="0.94"> + <description>create structure diagrams</description> +</tool> +<tool id="molfilter" name="MolFilter" version="0.9"> + <description>filter molecule files</description> +</tool> +<tool id="pdbcutter" name="PDBCutter" version="0.94"> + <description>separate ligand and receptor</description> +</tool> +<tool id="pdbdownload" name="PDBDownload" version="0.94"> + <description>retrieve pdb-file from pdb.org</description> +</tool> +<tool id="partialchargescopy" name="PartialChargesCopy" version="0.94"> + <description>transfer part. charges between files</description> +</tool> +<tool id="pocketdetector" name="PocketDetector" version="0.94"> + <description>detect binding pocket</description> +</tool> +<tool id="propertymodifier" name="PropertyModifier" version="0.94"> + <description>modify molecule property tags</description> +</tool> +<tool id="propertyplotter" name="PropertyPlotter" version="0.94"> + <description>plot molecule properties</description> +</tool> +<tool id="proteincheck" name="ProteinCheck" version="0.94"> + <description>quality check for proteins structures</description> +</tool> +<tool id="proteinprotonator" name="ProteinProtonator" version="0.94"> + <description>protonate protein structures</description> +</tool> +<tool id="rmsdcalculator" name="RMSDCalculator" version="0.94"> + <description>calculate RMSD between poses</description> +</tool> +<tool id="scoreanalyzer" name="ScoreAnalyzer" version="0.94"> + <description>generate ROC or enrichment plots</description> +</tool> +<tool id="similarityanalyzer" name="SimilarityAnalyzer" version="0.9"> + <description>analyze similarity between molecule files</description> +</tool> +<tool id="simplerescorer" name="SimpleRescorer" version="0.94"> + <description>rescore docking results</description> +</tool> +<tool id="spatialconstraintdefiner" name="SpatialConstraintDefiner" version="0.94"> + <description>define spatial constraint</description> +</tool> +<tool id="tagres-train" name="TaGRes-train" version="0.94"> + <description>Target-specific Grid-Rescoring, training</description> +</tool> +<tool id="tagres" name="TaGRes" version="0.94"> + <description>Target-specific Grid-Rescoring</description> +</tool> +<tool id="vendorfinder" name="VendorFinder" version="0.94"> + <description>search vendors for compounds</description> +</tool> +<tool id="waterfinder" name="WaterFinder" version="0.94"> + <description>find strongly bound waters</description> +</tool> +<tool id="automodel" name="AutoModel" version="1.1"> + <description>automatically find best QSAR model</description> +</tool> +<tool id="featureselector" name="FeatureSelector" version="1.1"> + <description>run feature-selection on a QSAR model</description> +</tool> +<tool id="inputpartitioner" name="InputPartitioner" version="1.1"> + <description>split QSAR data set</description> +</tool> +<tool id="inputreader" name="InputReader" version="1.1"> + <description>generate QSAR data set</description> +</tool> +<tool id="modelcreator" name="ModelCreator" version="1.1"> + <description>create a QSAR model</description> +</tool> +<tool id="molpredictor" name="MolPredictor" version="1.1"> + <description>predict molecule activities with QSAR model</description> +</tool> +<tool id="predictor" name="Predictor" version="1.1"> + <description>predict activities with QSAR model</description> +</tool> +<tool id="validator" name="Validator" version="1.1"> + <description>evaluate quality of a QSAR model</description> +</tool></suite>