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Commit message:
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/openduck commit a10eecd64de8f147547c4e3929497f87773c43f9" |
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added:
macros.xml openduck_chunk.xml test-data/1n2v_apo.pdb test-data/complex_system.pickle test-data/equil.chk test-data/ligand.mol test-data/ligand.pdb test-data/ligand_wqb.mol test-data/protein_out_prot.pdb |
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| diff -r 000000000000 -r 89c3bd4f50a3 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Apr 16 08:25:04 2020 -0400 |
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| @@ -0,0 +1,53 @@ +<macros> + <token name="@VERSION@">0.1.1</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="3.7">python</requirement> + <requirement type="package" version="0.25.2">yank</requirement> + <requirement type="package" version="1.6">pdbfixer</requirement> + <requirement type="package" version="0.6.0">openforcefield</requirement> + <requirement type="package" version="3.2.0">parmed</requirement> + <requirement type="package" version="@VERSION@">openduck</requirement> + </requirements> + </xml> + <xml name="interaction_params"> + <section name="ia" title="Parameters for the protein-ligand interaction" expanded="true"> + <param argument="chain_sel" type="text" label="Chain ID for selection" help="E.g. 'A', 'B', etc."> + <validator type="regex" message="Invalid chain ID">^[A-Z]$</validator> + </param> + <param argument="res_sel" type="text" label="Three letter residue code for selection" help="E.g. 'ASP', 'TYR', etc."> + <validator type="regex" message="Invalid chain ID">^[A-Z]{3}$</validator> + </param> + <param argument="resid_sel" type="text" label="Residue ID for selection" help="Position of residue in sequence, e.g. 163"> + <validator type="regex" message="Invalid chain ID">^[0-9]+$</validator> + </param> + <param argument="atom_sel" type="text" label="Atom to select within the chosen residue" help="E.g. 'OD2'"> + <validator type="regex" message="Invalid chain ID">^[A-Z0-9]+$</validator> + </param> + </section> + </xml> + <xml name="tar_param"> + <param argument="return_tar" type="boolean" checked="true" label="Return a tar file?" help="Return a tar file containing all files produced during the simulations."/> + </xml> + <xml name="tar_output"> + <data name="tar" format="tar" from_work_dir="allfiles.tar.gz" label="${tool.name} tarball"> + <filter>return_tar</filter> + </data> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1038/nchem.2660</citation> + <citation type="bibtex"> +@misc{Bradley2019, + author = {Bradley, Anthony}, + title = {OpenDUck source code}, + year = {2019}, + publisher = {GitHub}, + journal = {GitHub repository}, + howpublished = {URL: https://github.com/xchem/duck}, + commit = {b98bb78284e9c92837ac1e69fc2f06306ab1e28c} +} + </citation> + </citations> + </xml> +</macros> |
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| diff -r 000000000000 -r 89c3bd4f50a3 openduck_chunk.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/openduck_chunk.xml Thu Apr 16 08:25:04 2020 -0400 |
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| @@ -0,0 +1,85 @@ +<tool id="openduck_chunk" name="OpenDUck chunk" version="@VERSION@"> + <description>for dynamic undocking</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ + cp '$ligand' ./ligand.sdf && + duck_chunk + -p '$protein' + -l ./ligand.sdf + -c '$cutoff' + $ignore_buffers + ## -i is interaction, e.g. A_ASP_156_OD2 + -i '${ia.chain_sel}'_'${ia.res_sel}'_'${ia.resid_sel}'_'${ia.atom_sel}' + + #if $return_tar: + && tar -czf allfiles.tar.gz --exclude=allfiles.tar.gz * + #end if + + ]]></command> + <inputs> + <param argument="protein" type="data" format='pdb' label="PDB file for apoprotein"/> + <param argument="ligand" type="data" format='sdf,mol' label="SDF/MOL file containing a single ligand"/> + <param argument="cutoff" type="float" min="0" value="5" label="Cutoff" help="Cutoff for chunk generation (in angstroms)" /> + <param argument="ignore_buffers" type="select" label="Ignore buffers (solvent, ions etc.)?"> + <option value="">Remove buffers</option> + <option value="-b">Leave buffers</option> + </param> + <expand macro="interaction_params" /> + <expand macro="tar_param" /> + + </inputs> + <outputs> + <data name="chunk" format="pdb" from_work_dir="protein_out_prot.pdb" label="${tool.name} PDB file"/> + <expand macro="tar_output" /> + </outputs> + <tests> + <test expect_num_outputs="1"> + <param name="protein" value="1n2v_apo.pdb" /> + <param name="ligand" value="ligand.mol" /> + <param name="cutoff" value="5" /> + <param name="ignore_buffers" value="" /> + <param name="chain_sel" value="A" /> + <param name="res_sel" value="ASP" /> + <param name="resid_sel" value="156" /> + <param name="atom_sel" value="OD2" /> + <param name="return_tar" value="false" /> + <output name="chunk" file="protein_out_prot.pdb" /> + </test> + </tests> + <help><![CDATA[ + +.. class:: infomark + +**What it does** + +Produce chunk automatically for dynamic undocking (DUck). Chunking entails selecting a region of the protein which is used for a DUck simulation. + +This Galaxy tool uses OpenDUck, an open-source implementation of the original DUck method, using OpenMM and AmberTools. + +_____ + +.. class:: infomark + +**Input** + + - PDB file for protein + - SDF/MOL file for ligand + - Parameters defining the protein-ligand interaction + +_____ + + +.. class:: infomark + +**Output** + + - PDB file containing the chunked protein ready for system preparation. + +A tar file is also produced as a optional output, containing all files produced by the tool. + + ]]></help> + <expand macro="citations" /> +</tool> \ No newline at end of file |
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| diff -r 000000000000 -r 89c3bd4f50a3 test-data/1n2v_apo.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/1n2v_apo.pdb Thu Apr 16 08:25:04 2020 -0400 |
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| b'@@ -0,0 +1,3648 @@\n+HEADER TRANSFERASE 24-OCT-02 1N2V \n+TITLE CRYSTAL STRUCTURE OF TGT IN COMPLEX WITH 2-BUTYL-5,6-DIHYDRO-1H- \n+TITLE 2 IMIDAZO[4,5-D]PYRIDAZINE-4,7-DIONE \n+COMPND MOL_ID: 1; \n+COMPND 2 MOLECULE: QUEUINE TRNA-RIBOSYLTRANSFERASE; \n+COMPND 3 CHAIN: A; \n+COMPND 4 SYNONYM: TRNA-GUANINE TRANSGLYCOSYLASE, GUANINE INSERTION ENZYME, \n+COMPND 5 TGT; \n+COMPND 6 EC: 2.4.2.29; \n+COMPND 7 ENGINEERED: YES \n+SOURCE MOL_ID: 1; \n+SOURCE 2 ORGANISM_SCIENTIFIC: ZYMOMONAS MOBILIS; \n+SOURCE 3 ORGANISM_TAXID: 542; \n+SOURCE 4 GENE: TGT; \n+SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); \n+SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; \n+SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); \n+SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; \n+SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET9D \n+KEYWDS PROTEIN-LIGAND COMPLEX, TRANSFERASE \n+EXPDTA X-RAY DIFFRACTION \n+AUTHOR R.BRENK,L.NAERUM,U.GRAEDLER,H.-D.GERBER,G.A.GARCIA,K.REUTER, \n+AUTHOR 2 M.T.STUBBS,G.KLEBE \n+REVDAT 4 31-JAN-18 1N2V 1 REMARK \n+REVDAT 3 13-JUL-11 1N2V 1 VERSN \n+REVDAT 2 24-FEB-09 1N2V 1 VERSN \n+REVDAT 1 08-APR-03 1N2V 0 \n+JRNL AUTH R.BRENK,L.NAERUM,U.GRAEDLER,H.-D.GERBER,G.A.GARCIA,K.REUTER, \n+JRNL AUTH 2 M.T.STUBBS,G.KLEBE \n+JRNL TITL VIRTUAL SCREENING FOR SUBMICROMOLAR LEADS OF TRNA-GUANINE \n+JRNL TITL 2 TRANSGLYCOSYLASE BASED ON A NEW UNEXPECTED BINDING MODE \n+JRNL TITL 3 DETECTED BY CRYSTAL STRUCTURE ANALYSIS \n+JRNL REF J.MED.CHEM. V. 46 1133 2003 \n+JRNL REFN ISSN 0022-2623 \n+JRNL PMID 12646024 \n+JRNL DOI 10.1021/JM0209937 \n+REMARK 2 \n+REMARK 2 RESOLUTION. 2.10 ANGSTROMS. \n+REMARK 3 \n+REMARK 3 REFINEMENT. \n+REMARK 3 PROGRAM : CNS \n+REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- \n+REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, \n+REMARK 3 : READ,RICE,SIMONSON,WARREN \n+REMARK 3 \n+REMARK 3 REFINEMENT TARGET : NULL \n+REMARK 3 \n+REMARK 3 DATA USED IN REFINEMENT. \n+REMARK 3 RESOLUTION RANGE HIGH (ANGSTRO'..b'OH A1402 14.839 14.036 18.435 1.00 31.20 O \n+HETATM 3176 O HOH A1403 12.834 14.653 24.686 1.00 38.35 O \n+HETATM 3177 O HOH A1404 11.155 17.746 22.938 1.00 24.69 O \n+HETATM 3178 O HOH A1405 12.127 16.079 16.701 1.00 41.76 O \n+HETATM 3179 O HOH A1500 9.930 20.957 -4.818 1.00 39.17 O \n+HETATM 3180 O HOH A1501 -8.281 4.491 18.296 1.00 32.01 O \n+HETATM 3181 O HOH A1502 20.194 21.390 29.658 1.00 38.20 O \n+HETATM 3182 O HOH A1503 34.681 8.351 29.478 1.00 38.84 O \n+HETATM 3183 O HOH A1504 17.854 -9.630 8.443 1.00 46.93 O \n+HETATM 3184 O HOH A1505 14.372 0.727 35.945 1.00 33.80 O \n+HETATM 3185 O HOH A1506 30.211 -8.708 22.010 1.00 35.78 O \n+HETATM 3186 O HOH A1507 -3.191 24.726 28.755 1.00 51.56 O \n+HETATM 3187 O HOH A1508 23.436 -12.641 20.878 1.00 46.25 O \n+HETATM 3188 O HOH A1509 23.191 3.590 36.316 1.00 36.10 O \n+HETATM 3189 O HOH A1511 8.692 8.107 42.504 1.00 33.50 O \n+HETATM 3190 O HOH A1512 2.017 21.499 34.078 1.00 49.77 O \n+HETATM 3191 O HOH A1513 27.178 -4.258 5.223 1.00 32.32 O \n+HETATM 3192 O HOH A1514 6.064 28.184 15.338 1.00 42.88 O \n+HETATM 3193 O HOH A1516 33.757 3.553 -4.967 1.00 47.63 O \n+HETATM 3194 O HOH A1517 24.915 4.564 -9.803 1.00 41.80 O \n+HETATM 3195 O HOH A1518 16.421 -1.663 34.927 1.00 42.84 O \n+HETATM 3196 O HOH A1519 -12.120 1.460 19.135 1.00 44.79 O \n+HETATM 3197 O HOH A1520 35.720 -3.354 0.524 1.00 47.21 O \n+HETATM 3198 O HOH A1521 1.657 -7.407 17.749 1.00 47.33 O \n+HETATM 3199 O HOH A1522 30.429 14.120 38.314 1.00 42.34 O \n+HETATM 3200 O HOH A1525 30.246 14.537 5.225 1.00 42.14 O \n+HETATM 3201 O HOH A1526 14.377 24.575 -2.027 1.00 36.91 O \n+CONECT 2367 2904 \n+CONECT 2383 2904 \n+CONECT 2401 2904 \n+CONECT 2612 2904 \n+CONECT 2904 2367 2383 2401 2612 \n+CONECT 2905 2906 2918 \n+CONECT 2906 2905 2907 2911 \n+CONECT 2907 2906 2908 \n+CONECT 2908 2907 2909 \n+CONECT 2909 2908 2910 \n+CONECT 2910 2909 \n+CONECT 2911 2906 2912 \n+CONECT 2912 2911 2913 2918 \n+CONECT 2913 2912 2914 2919 \n+CONECT 2914 2913 2915 \n+CONECT 2915 2914 2916 \n+CONECT 2916 2915 2917 2918 \n+CONECT 2917 2916 \n+CONECT 2918 2905 2912 2916 \n+CONECT 2919 2913 \n+MASTER 318 0 2 18 17 0 5 6 3200 1 20 30 \n+END \n' |
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| diff -r 000000000000 -r 89c3bd4f50a3 test-data/complex_system.pickle |
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| Binary file test-data/complex_system.pickle has changed |
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| diff -r 000000000000 -r 89c3bd4f50a3 test-data/equil.chk |
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| Binary file test-data/equil.chk has changed |
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| diff -r 000000000000 -r 89c3bd4f50a3 test-data/ligand.mol --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ligand.mol Thu Apr 16 08:25:04 2020 -0400 |
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| @@ -0,0 +1,37 @@ +ligand.pdb + OpenBabel03242012003D + + 15 16 0 0 1 0 0 0 0 0999 V2000 + 15.4350 16.8530 20.4090 N 0 0 0 0 0 0 0 0 0 0 0 0 + 16.5900 17.0760 19.8060 C 0 0 0 0 0 0 0 0 0 0 0 0 + 16.7440 17.0260 18.2840 C 0 0 0 0 0 0 0 0 0 0 0 0 + 15.6650 17.7690 17.4320 C 0 0 0 0 0 0 0 0 0 0 0 0 + 16.3420 18.3730 16.1580 C 0 0 0 0 0 0 0 0 0 0 0 0 + 15.3430 19.1170 15.2380 C 0 0 0 0 0 0 0 0 0 0 0 0 + 17.4900 17.3220 20.6050 N 0 0 0 0 0 0 0 0 0 0 0 0 + 17.0380 17.3010 21.9580 C 0 0 0 0 0 0 0 0 0 0 0 0 + 17.7020 17.5270 23.2770 C 0 0 0 0 0 0 0 0 0 0 0 0 + 16.8750 17.4100 24.4010 N 0 0 0 0 0 0 0 0 0 0 0 0 + 15.4120 17.0790 24.3150 N 0 0 0 0 0 0 0 0 0 0 0 0 + 14.7400 16.8560 23.0980 C 0 0 0 0 0 0 0 0 0 0 0 0 + 13.5080 16.5760 23.0100 O 0 0 0 0 0 0 0 0 0 0 0 0 + 15.6460 16.9830 21.8390 C 0 0 1 0 0 0 0 0 0 0 0 0 + 18.9000 17.7960 23.3310 O 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 2 0 0 0 0 + 2 7 1 0 0 0 0 + 3 2 1 0 0 0 0 + 4 3 1 0 0 0 0 + 5 4 1 0 0 0 0 + 6 5 1 0 0 0 0 + 7 8 2 0 0 0 0 + 8 9 1 0 0 0 0 + 9 15 2 0 0 0 0 + 9 10 1 0 0 0 0 + 11 10 2 0 0 0 0 + 12 11 1 0 0 0 0 + 13 12 2 0 0 0 0 + 14 1 1 6 0 0 0 + 14 8 1 0 0 0 0 + 14 12 1 0 0 0 0 +M END +$$$$ |
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| diff -r 000000000000 -r 89c3bd4f50a3 test-data/ligand.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ligand.pdb Thu Apr 16 08:25:04 2020 -0400 |
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| @@ -0,0 +1,28 @@ +COMPND ligand.pdb +HETATM 1 N1 UNL 1 15.435 16.853 20.409 1.00 0.00 N +HETATM 2 C1 UNL 1 16.590 17.076 19.806 1.00 0.00 C +HETATM 3 C2 UNL 1 16.744 17.026 18.284 1.00 0.00 C +HETATM 4 C3 UNL 1 15.665 17.769 17.432 1.00 0.00 C +HETATM 5 C4 UNL 1 16.342 18.373 16.158 1.00 0.00 C +HETATM 6 C5 UNL 1 15.343 19.117 15.238 1.00 0.00 C +HETATM 7 N2 UNL 1 17.490 17.322 20.605 1.00 0.00 N +HETATM 8 C6 UNL 1 17.038 17.301 21.958 1.00 0.00 C +HETATM 9 C7 UNL 1 17.702 17.527 23.277 1.00 0.00 C +HETATM 10 N3 UNL 1 16.875 17.410 24.401 1.00 0.00 N +HETATM 11 N4 UNL 1 15.412 17.079 24.315 1.00 0.00 N +HETATM 12 C8 UNL 1 14.740 16.856 23.098 1.00 0.00 C +HETATM 13 O1 UNL 1 13.508 16.576 23.010 1.00 0.00 O +HETATM 14 C9 UNL 1 15.646 16.983 21.839 1.00 0.00 C +HETATM 15 O2 UNL 1 18.900 17.796 23.331 1.00 0.00 O +CONECT 1 2 2 14 +CONECT 2 3 7 +CONECT 3 4 +CONECT 4 5 +CONECT 5 6 +CONECT 7 8 8 +CONECT 8 9 14 +CONECT 9 10 15 15 +CONECT 10 11 11 +CONECT 11 12 +CONECT 12 13 13 14 +END |
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| diff -r 000000000000 -r 89c3bd4f50a3 test-data/ligand_wqb.mol --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ligand_wqb.mol Thu Apr 16 08:25:04 2020 -0400 |
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| @@ -0,0 +1,39 @@ +ligand.pdb + OpenBabel03242012003D + + 15 16 0 0 1 0 0 0 0 0999 V2000 + 15.4350 16.8530 20.4090 N 0 0 0 0 0 0 0 0 0 0 0 0 + 16.5900 17.0760 19.8060 C 0 0 0 0 0 0 0 0 0 0 0 0 + 16.7440 17.0260 18.2840 C 0 0 0 0 0 0 0 0 0 0 0 0 + 15.6650 17.7690 17.4320 C 0 0 0 0 0 0 0 0 0 0 0 0 + 16.3420 18.3730 16.1580 C 0 0 0 0 0 0 0 0 0 0 0 0 + 15.3430 19.1170 15.2380 C 0 0 0 0 0 0 0 0 0 0 0 0 + 17.4900 17.3220 20.6050 N 0 0 0 0 0 0 0 0 0 0 0 0 + 17.0380 17.3010 21.9580 C 0 0 0 0 0 0 0 0 0 0 0 0 + 17.7020 17.5270 23.2770 C 0 0 0 0 0 0 0 0 0 0 0 0 + 16.8750 17.4100 24.4010 N 0 0 0 0 0 0 0 0 0 0 0 0 + 15.4120 17.0790 24.3150 N 0 0 0 0 0 0 0 0 0 0 0 0 + 14.7400 16.8560 23.0980 C 0 0 0 0 0 0 0 0 0 0 0 0 + 13.5080 16.5760 23.0100 O 0 0 0 0 0 0 0 0 0 0 0 0 + 15.6460 16.9830 21.8390 C 0 0 1 0 0 0 0 0 0 0 0 0 + 18.9000 17.7960 23.3310 O 0 0 0 0 0 0 0 0 0 0 0 0 + 2 1 2 0 0 0 0 + 2 7 1 0 0 0 0 + 3 2 1 0 0 0 0 + 4 3 1 0 0 0 0 + 5 4 1 0 0 0 0 + 6 5 1 0 0 0 0 + 7 8 2 0 0 0 0 + 8 9 1 0 0 0 0 + 9 15 2 0 0 0 0 + 9 10 1 0 0 0 0 + 11 10 2 0 0 0 0 + 12 11 1 0 0 0 0 + 13 12 2 0 0 0 0 + 14 1 1 6 0 0 0 + 14 8 1 0 0 0 0 + 14 12 1 0 0 0 0 +M END +> <SCORE.DUCK_WQB> +-0.015815293149895382 +$$$$ |
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| diff -r 000000000000 -r 89c3bd4f50a3 test-data/protein_out_prot.pdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/protein_out_prot.pdb Thu Apr 16 08:25:04 2020 -0400 |
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| b'@@ -0,0 +1,142 @@\n+ATOM 1 HH31 ACE 1 11.587 15.836 30.944 1.00 0.00\n+ATOM 2 CH3 ACE 1 11.982 16.349 30.067 1.00 0.00\n+ATOM 3 HH32 ACE 1 11.223 17.020 29.665 1.00 0.00\n+ATOM 4 HH33 ACE 1 12.255 15.615 29.309 1.00 0.00\n+ATOM 5 C ACE 1 13.223 17.171 30.422 1.00 0.00\n+ATOM 6 O ACE 1 13.659 17.198 31.578 1.00 0.00\n+ATOM 7 N ASP 2 13.794 17.834 29.424 1.00 0.00\n+ATOM 8 H ASP 2 13.416 17.784 28.489 1.00 0.00\n+ATOM 9 CA ASP 2 15.000 18.614 29.639 1.00 0.00\n+ATOM 10 HA ASP 2 15.137 18.814 30.702 1.00 0.00\n+ATOM 11 CB ASP 2 16.212 17.830 29.129 1.00 0.00\n+ATOM 12 HB2 ASP 2 17.106 18.364 29.452 1.00 0.00\n+ATOM 13 HB3 ASP 2 16.196 16.840 29.585 1.00 0.00\n+ATOM 14 CG ASP 2 16.225 17.690 27.612 1.00 0.00\n+ATOM 15 OD1 ASP 2 15.147 17.775 26.988 1.00 0.00\n+ATOM 16 OD2 ASP 2 17.317 17.483 27.041 1.00 0.00\n+ATOM 17 C ASP 2 14.957 19.967 28.957 1.00 0.00\n+ATOM 18 O ASP 2 13.940 20.366 28.393 1.00 0.00\n+ATOM 19 N GLU 3 16.091 20.657 29.008 1.00 0.00\n+ATOM 20 H GLU 3 16.880 20.249 29.489 1.00 0.00\n+ATOM 21 CA GLU 3 16.253 21.976 28.408 1.00 0.00\n+ATOM 22 HA GLU 3 15.350 22.269 27.872 1.00 0.00\n+ATOM 23 CB GLU 3 16.513 22.995 29.523 1.00 0.00\n+ATOM 24 HB2 GLU 3 15.593 23.045 30.105 1.00 0.00\n+ATOM 25 HB3 GLU 3 17.308 22.572 30.137 1.00 0.00\n+ATOM 26 CG GLU 3 16.905 24.389 29.079 1.00 0.00\n+ATOM 27 HG2 GLU 3 17.834 24.333 28.512 1.00 0.00\n+ATOM 28 HG3 GLU 3 16.110 24.767 28.436 1.00 0.00\n+ATOM 29 CD GLU 3 17.089 25.326 30.261 1.00 0.00\n+ATOM 30 OE1 GLU 3 16.075 25.734 30.868 1.00 0.00\n+ATOM 31 OE2 GLU 3 18.252 25.643 30.595 1.00 0.00\n+ATOM 32 C GLU 3 17.442 21.903 27.445 1.00 0.00\n+ATOM 33 O GLU 3 18.591 21.823 27.880 1.00 0.00\n+ATOM 34 N CYS 4 17.163 21.906 26.143 1.00 0.00\n+ATOM 35 H CYS 4 16.202 21.930 25.832 1.00 0.00\n+ATOM 36 CA CYS 4 18.219 21.828 25.130 1.00 0.00\n+ATOM 37 HA CYS 4 18.903 21.014 25.369 1.00 0.00\n+ATOM 38 CB CYS 4 17.611 21.567 23.745 1.00 0.00\n+ATOM 39 HB2 CYS 4 16.992 20.670 23.774 1.00 0.00\n+ATOM 40 HB3 CYS 4 17.003 22.418 23.440 1.00 0.00\n+ATOM 41 SG CYS 4 18.818 21.304 22.408 1.00 0.00\n+ATOM 42 HG CYS 4 17.920 21.125 21.443 1.00 0.00\n+ATOM 43 C CYS 4 19.046 23.114 25.104 1.00 0.00\n+ATOM 44 O CYS 4 18.541 24.186 24.766 1.00 0.00\n+ATOM 45 N NME 5 20.321 22.991 25.461 1.00 0.00\n+ATOM 46 H NME 5 20.676 22.079 25.708 1.00 0.00\n+ATOM 47 CH3 NME 5 21.237 24.128 25.511 1.00 0.00\n+ATOM 48 HH31 NME 5 20.708 25.035 25.219 1.00 0.00\n+ATOM 49 HH32 NME 5 21.620 24.242 26.525 1.00 0.00\n+ATOM 50 HH33 NME 5 22.068 23.956 24.827 1.00 0.00\n+TER \n+ATOM 51 HH31 ACE 6 18.315 22.273 36.560 1.00 0.00\n+ATOM 52 CH3 ACE 6 18.810 22.050 35.615 1.00 0.00\n+ATOM 53 HH32 ACE 6 19.868 21.859 35.795 1.00 0.00\n+ATOM 54 HH33 ACE 6 18.705 22.899 34.940 1.00 0.00\n+ATOM 55 C ACE 6 18.198 20.820 34.951 1.00 0.00\n+ATOM 56 O ACE 6 17.267 20.217 35.484 1.00 0.00\n+ATOM 57 N SER 7 18.724 20.448 33.789 1.00 0.00\n+ATOM 58 H SER 7 19.475 20.970 33.360 1.00 0.00\n+ATOM 59 CA SER 7 '..b' 18.672 12.189 29.259 1.00 0.00\n+ATOM 81 H ILE 10 18.286 12.738 30.014 1.00 0.00\n+ATOM 82 CA ILE 10 19.397 12.884 28.198 1.00 0.00\n+ATOM 83 HA ILE 10 19.802 12.158 27.493 1.00 0.00\n+ATOM 84 CB ILE 10 18.502 13.881 27.448 1.00 0.00\n+ATOM 85 HB ILE 10 18.234 14.703 28.112 1.00 0.00\n+ATOM 86 CG2 ILE 10 19.259 14.430 26.238 1.00 0.00\n+ATOM 87 HG21 ILE 10 19.527 13.609 25.573 1.00 0.00\n+ATOM 88 HG22 ILE 10 18.626 15.138 25.703 1.00 0.00\n+ATOM 89 HG23 ILE 10 20.165 14.935 26.574 1.00 0.00\n+ATOM 90 CG1 ILE 10 17.202 13.204 27.007 1.00 0.00\n+ATOM 91 HG12 ILE 10 17.460 12.463 26.251 1.00 0.00\n+ATOM 92 HG13 ILE 10 16.783 12.702 27.879 1.00 0.00\n+ATOM 93 CD1 ILE 10 16.171 14.176 26.436 1.00 0.00\n+ATOM 94 HD11 ILE 10 16.589 14.678 25.564 1.00 0.00\n+ATOM 95 HD12 ILE 10 15.276 13.627 26.144 1.00 0.00\n+ATOM 96 HD13 ILE 10 15.912 14.917 27.192 1.00 0.00\n+ATOM 97 C ILE 10 20.594 13.670 28.712 1.00 0.00\n+ATOM 98 O ILE 10 20.457 14.541 29.570 1.00 0.00\n+ATOM 99 N GLN 11 21.766 13.368 28.167 1.00 0.00\n+ATOM 100 H GLN 11 21.824 12.637 27.472 1.00 0.00\n+ATOM 101 CA GLN 11 22.991 14.052 28.552 1.00 0.00\n+ATOM 102 HA GLN 11 23.008 14.204 29.631 1.00 0.00\n+ATOM 103 CB GLN 11 24.213 13.215 28.156 1.00 0.00\n+ATOM 104 HB2 GLN 11 24.076 12.227 28.595 1.00 0.00\n+ATOM 105 HB3 GLN 11 24.202 13.133 27.069 1.00 0.00\n+ATOM 106 CG GLN 11 25.553 13.793 28.610 1.00 0.00\n+ATOM 107 HG2 GLN 11 25.527 14.871 28.448 1.00 0.00\n+ATOM 108 HG3 GLN 11 25.700 13.589 29.671 1.00 0.00\n+ATOM 109 CD GLN 11 26.728 13.213 27.835 1.00 0.00\n+ATOM 110 OE1 GLN 11 27.828 13.057 28.372 1.00 0.00\n+ATOM 111 NE2 GLN 11 26.504 12.911 26.559 1.00 0.00\n+ATOM 112 HE21 GLN 11 27.248 12.523 25.997 1.00 0.00\n+ATOM 113 HE22 GLN 11 25.591 13.071 26.158 1.00 0.00\n+ATOM 114 C GLN 11 23.088 15.417 27.878 1.00 0.00\n+ATOM 115 O GLN 11 22.808 15.560 26.684 1.00 0.00\n+ATOM 116 N GLN 12 23.479 16.422 28.657 1.00 0.00\n+ATOM 117 H GLN 12 23.652 16.258 29.639 1.00 0.00\n+ATOM 118 CA GLN 12 23.661 17.774 28.139 1.00 0.00\n+ATOM 119 HA GLN 12 23.498 17.777 27.061 1.00 0.00\n+ATOM 120 CB GLN 12 22.670 18.747 28.787 1.00 0.00\n+ATOM 121 HB2 GLN 12 22.750 18.609 29.865 1.00 0.00\n+ATOM 122 HB3 GLN 12 22.997 19.753 28.525 1.00 0.00\n+ATOM 123 CG GLN 12 21.219 18.556 28.356 1.00 0.00\n+ATOM 124 HG2 GLN 12 20.902 17.561 28.669 1.00 0.00\n+ATOM 125 HG3 GLN 12 20.598 19.306 28.846 1.00 0.00\n+ATOM 126 CD GLN 12 21.030 18.675 26.854 1.00 0.00\n+ATOM 127 OE1 GLN 12 21.644 19.520 26.207 1.00 0.00\n+ATOM 128 NE2 GLN 12 20.164 17.835 26.295 1.00 0.00\n+ATOM 129 HE21 GLN 12 20.001 17.872 25.299 1.00 0.00\n+ATOM 130 HE22 GLN 12 19.674 17.164 26.869 1.00 0.00\n+ATOM 131 C GLN 12 25.094 18.187 28.458 1.00 0.00\n+ATOM 132 O GLN 12 25.929 17.340 28.772 1.00 0.00\n+ATOM 133 N NME 13 25.380 19.482 28.377 1.00 0.00\n+ATOM 134 H NME 13 24.681 20.161 28.114 1.00 0.00\n+ATOM 135 CH3 NME 13 26.721 19.953 28.669 1.00 0.00\n+ATOM 136 HH31 NME 13 27.354 19.107 28.935 1.00 0.00\n+ATOM 137 HH32 NME 13 27.131 20.451 27.790 1.00 0.00\n+ATOM 138 HH33 NME 13 26.687 20.656 29.501 1.00 0.00\n+TER \n+END \n' |