Mercurial > repos > chemteam > biopdb_align_and_rmsd
changeset 0:6352d6dd74e2 draft default tip
planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit b90c5ab8f15397299e8baf2e903a9911c44d7668
| author | chemteam |
|---|---|
| date | Thu, 06 Jun 2024 07:09:14 +0000 |
| parents | |
| children | |
| files | BioPDB_align_and_rmsd.py BioPDB_align_and_rmsd.xml test-data/aligned_structure.pdb test-data/model.pdb test-data/reference_structure.pdb test-data/rmsd.tabular |
| diffstat | 6 files changed, 1070 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BioPDB_align_and_rmsd.py Thu Jun 06 07:09:14 2024 +0000 @@ -0,0 +1,107 @@ +#!/usr/bin/env python3 + +# The MIT License +# +# Copyright (c) 2010-2016 Anders S. Christensen +# +# Permission is hereby granted, free of charge, to any person obtaining a copy +# of this software and associated documentation files (the "Software"), to deal +# in the Software without restriction, including without limitation the rights +# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +# copies of the Software, and to permit persons to whom the Software is +# furnished to do so, subject to the following conditions: +# +# The above copyright notice and this permission notice shall be included in +# all copies or substantial portions of the Software. +# +# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +# # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +# THE SOFTWARE. + +import argparse + +import Bio.PDB + + +def __main__(): + parser = argparse.ArgumentParser( + description='Residues to be aligned') + parser.add_argument( + '--start_residue', default=None, + help='start residue') + parser.add_argument( + '--end_residue', default=None, + help='end residue') + parser.add_argument( + '--ref_structure', default=None, + help='reference structure') + parser.add_argument( + '--model', default=None, + help='model structure') + parser.add_argument( + '--aligned_structure', default=None, + help='aligned structure') + parser.add_argument( + '--rmsd', default=None, + help='rmsd') + args = parser.parse_args() + + # Select what residues numbers you wish to align + # and put them in a list + start_id = int(args.start_residue) + end_id = int(args.end_residue) + atoms_to_be_aligned = range(start_id, end_id + 1) + + # Start the parser + pdb_parser = Bio.PDB.PDBParser(QUIET=True) + + # Get the structures + ref_structure = pdb_parser.get_structure("reference", args.ref_structure) + sample_structure = pdb_parser.get_structure("sample", args.model) + + # Use the first model in the pdb-files for alignment + # Change the number 0 if you want to align to another structure + ref_model = ref_structure[0] + sample_model = sample_structure[0] + + # Make a list of the atoms (in the structures) you wish to align. + # In this case we use CA atoms whose index is in the specified range + ref_atoms = [] + sample_atoms = [] + + # Iterate of all chains in the model in order to find all residues + for ref_chain in ref_model: + # Iterate of all residues in each model in order to find proper atoms + for ref_res in ref_chain: + # Check if residue number ( .get_id() ) is in the list + if ref_res.get_id()[1] in atoms_to_be_aligned: + # Append CA atom to list + ref_atoms.append(ref_res['CA']) + + # Do the same for the sample structure + for sample_chain in sample_model: + for sample_res in sample_chain: + if sample_res.get_id()[1] in atoms_to_be_aligned: + sample_atoms.append(sample_res['CA']) + + # Now we initiate the superimposer: + super_imposer = Bio.PDB.Superimposer() + super_imposer.set_atoms(ref_atoms, sample_atoms) + super_imposer.apply(sample_model.get_atoms()) + + # Save RMSD into an output file: + with open(args.rmsd, 'w') as rmsd_out: + rmsd_out.write(str(super_imposer.rms)) + + # Save aligned coordinates of the model: + io = Bio.PDB.PDBIO() + io.set_structure(sample_structure) + io.save(args.aligned_structure) + + +if __name__ == "__main__": + __main__()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/BioPDB_align_and_rmsd.xml Thu Jun 06 07:09:14 2024 +0000 @@ -0,0 +1,69 @@ +<tool id="biopdb_align_and_rmsd" name="Align structures and compute relative RMSDs" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@"> + <description>using Biopython</description> + <macros> + <token name="@TOOL_VERSION@">1.79</token> + <token name="@GALAXY_VERSION@">0</token> + </macros> + <requirements> + <requirement type="package" version="1.79">biopython</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + + python3 '$__tool_directory__/BioPDB_align_and_rmsd.py' --start_residue '$start_residue' --end_residue '$end_residue' --ref_structure '$ref_structure' --model '$model' --aligned_structure '$aligned_structure' --rmsd '$rmsd_out' >> verbose.txt 2>&1 + + ]]></command> + <inputs> + <param name="start_residue" type="integer" label="Starting residue to align" help="This should be the same starting residue for the model and reference structure." value="0" /> + <param name="end_residue" type="integer" label="Ending residue to align" help="This should be the same ending residue for the model and reference structure." value="0"/> + <param name="ref_structure" type="data" format="pdb" label="Reference structure" help="This can be an experimental structure or another model you wish to compare against."/> + <param name="model" type="data" format="pdb" label="Sample structure" help="This is the structure you wish to align and compute a relative RMSD for. This can also be an experimental structure or another model."/> + </inputs> + + <outputs> + <data name="aligned_structure" format="pdb" label="PDB file of the aligned structure ${on_string}"></data> + <data name="rmsd_out" format="tabular" label="RMSD of the aligned structure ${on_string}"></data> + </outputs> + + <tests> + <test> + <param name="start_residue" value="1" /> + <param name="end_residue" value="15"/> + <param name="ref_structure" value="reference_structure.pdb" /> + <param name="model" value="model.pdb" /> + <output name="aligned_structure" ftype="pdb"> + <assert_contents> + <has_text text="ATOM 5 CA ARG 1 6.016 6.125 -0.066 1.00 0.00 C"/> + <has_text text="ATOM 29 CA HIS 2 4.909 5.168 3.434 1.00 0.00 C"/> + <has_text text="ATOM 46 CA TYR 3 7.956 4.326 5.551 1.00 0.00 C"/> + </assert_contents> + </output> + <output name="rmsd_out" ftype="tabular"> + <assert_contents> + <has_text text="5.492787964992471"/> + </assert_contents> + </output> + </test> + </tests> + + <help><![CDATA[ +Tool to align protein structures and compute relative RMSDs, using the alpha carbon coordinates. + +.. class:: infomark + +**Inputs** + +PDB files for the reference structure, a model, as well as the starting and ending residues for the alignment. + +.. class:: infomark + +**Outputs** + +1) Tabular file containing the RMSD. +2) PDB file of the model with the aligned coordinates. + + + ]]></help> + <citations> + <citation type="doi">https://doi.org/10.1093/bioinformatics/btp163</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/aligned_structure.pdb Thu Jun 06 07:09:14 2024 +0000 @@ -0,0 +1,297 @@ +ATOM 1 N ARG 1 6.163 6.849 -0.948 1.00 0.00 N +ATOM 2 H1 ARG 1 5.435 6.700 -1.619 1.00 0.00 H +ATOM 3 H2 ARG 1 6.120 7.789 -0.616 1.00 0.00 H +ATOM 4 H3 ARG 1 7.049 6.675 -1.372 1.00 0.00 H +ATOM 5 CA ARG 1 6.016 6.125 -0.066 1.00 0.00 C +ATOM 6 HA ARG 1 5.815 5.356 -0.665 1.00 0.00 H +ATOM 7 CB ARG 1 7.270 6.726 0.577 1.00 0.00 C +ATOM 8 HB1 ARG 1 8.029 6.625 -0.062 1.00 0.00 H +ATOM 9 HB2 ARG 1 7.462 6.219 1.419 1.00 0.00 H +ATOM 10 CG ARG 1 7.154 8.197 0.955 1.00 0.00 C +ATOM 11 HG1 ARG 1 6.549 8.297 1.736 1.00 0.00 H +ATOM 12 HG2 ARG 1 6.783 8.712 0.177 1.00 0.00 H +ATOM 13 CD ARG 1 8.524 8.756 1.310 1.00 0.00 C +ATOM 14 HD1 ARG 1 9.137 8.652 0.517 1.00 0.00 H +ATOM 15 HD2 ARG 1 8.895 8.263 2.087 1.00 0.00 H +ATOM 16 NE ARG 1 8.483 10.179 1.655 1.00 0.00 N +ATOM 17 HE ARG 1 8.722 10.838 0.946 1.00 0.00 H +ATOM 18 CZ ARG 1 8.165 10.646 2.852 1.00 0.00 C +ATOM 19 NH1 ARG 1 7.833 9.810 3.832 1.00 0.00 N +ATOM 20 HH11 ARG 1 7.838 8.823 3.670 1.00 0.00 H +ATOM 21 HH12 ARG 1 7.597 10.167 4.731 1.00 0.00 H +ATOM 22 NH2 ARG 1 8.173 11.953 3.080 1.00 0.00 N +ATOM 23 HH21 ARG 1 8.424 12.588 2.345 1.00 0.00 H +ATOM 24 HH22 ARG 1 7.928 12.309 3.982 1.00 0.00 H +ATOM 25 C ARG 1 5.043 6.431 1.431 1.00 0.00 C +ATOM 26 O ARG 1 3.837 6.551 1.464 1.00 0.00 O +ATOM 27 N HIS 2 5.684 5.685 2.300 1.00 0.00 N +ATOM 28 H HIS 2 6.658 5.485 2.196 1.00 0.00 H +ATOM 29 CA HIS 2 4.909 5.168 3.434 1.00 0.00 C +ATOM 30 HA HIS 2 4.450 5.995 3.771 1.00 0.00 H +ATOM 31 CB HIS 2 3.866 4.060 3.283 1.00 0.00 C +ATOM 32 HB1 HIS 2 3.272 4.272 2.508 1.00 0.00 H +ATOM 33 HB2 HIS 2 3.313 4.002 4.112 1.00 0.00 H +ATOM 34 CG HIS 2 4.458 2.707 3.044 1.00 0.00 C +ATOM 35 ND1 HIS 2 4.929 2.263 1.832 1.00 0.00 N +ATOM 36 CE1 HIS 2 5.451 1.040 1.995 1.00 0.00 C +ATOM 37 HE1 HIS 2 5.867 0.500 1.271 1.00 0.00 H +ATOM 38 NE2 HIS 2 5.337 0.646 3.252 1.00 0.00 N +ATOM 39 HE2 HIS 2 5.631 -0.223 3.646 1.00 0.00 H +ATOM 40 CD2 HIS 2 4.697 1.692 3.918 1.00 0.00 C +ATOM 41 HD2 HIS 2 4.464 1.701 4.892 1.00 0.00 H +ATOM 42 C HIS 2 5.934 4.385 4.189 1.00 0.00 C +ATOM 43 O HIS 2 5.915 3.182 4.060 1.00 0.00 O +ATOM 44 N TYR 3 6.889 5.029 4.855 1.00 0.00 N +ATOM 45 H TYR 3 6.870 6.027 4.884 1.00 0.00 H +ATOM 46 CA TYR 3 7.956 4.326 5.551 1.00 0.00 C +ATOM 47 HA TYR 3 8.065 5.293 5.330 1.00 0.00 H +ATOM 48 CB TYR 3 8.817 4.757 6.736 1.00 0.00 C +ATOM 49 HB1 TYR 3 8.884 5.758 6.736 1.00 0.00 H +ATOM 50 HB2 TYR 3 9.727 4.358 6.645 1.00 0.00 H +ATOM 51 CG TYR 3 8.239 4.327 8.056 1.00 0.00 C +ATOM 52 CD1 TYR 3 7.364 5.158 8.726 1.00 0.00 C +ATOM 53 HD1 TYR 3 7.152 6.058 8.361 1.00 0.00 H +ATOM 54 CE1 TYR 3 6.772 4.760 9.913 1.00 0.00 C +ATOM 55 HE1 TYR 3 6.142 5.382 10.385 1.00 0.00 H +ATOM 56 CZ TYR 3 7.060 3.526 10.443 1.00 0.00 C +ATOM 57 OH TYR 3 6.390 3.139 11.589 1.00 0.00 O +ATOM 58 HH TYR 3 6.687 2.232 11.861 1.00 0.00 H +ATOM 59 CE2 TYR 3 7.944 2.664 9.798 1.00 0.00 C +ATOM 60 HE2 TYR 3 8.154 1.765 10.188 1.00 0.00 H +ATOM 61 CD2 TYR 3 8.533 3.080 8.602 1.00 0.00 C +ATOM 62 HD2 TYR 3 9.173 2.472 8.132 1.00 0.00 H +ATOM 63 C TYR 3 8.111 2.740 5.153 1.00 0.00 C +ATOM 64 O TYR 3 7.249 1.880 5.246 1.00 0.00 O +ATOM 65 N TYR 4 9.310 2.513 4.588 1.00 0.00 N +ATOM 66 H TYR 4 9.937 3.296 4.638 1.00 0.00 H +ATOM 67 CA TYR 4 9.819 1.418 3.968 1.00 0.00 C +ATOM 68 HA TYR 4 9.058 0.893 4.328 1.00 0.00 H +ATOM 69 CB TYR 4 9.798 1.029 2.490 1.00 0.00 C +ATOM 70 HB1 TYR 4 10.333 1.705 1.975 1.00 0.00 H +ATOM 71 HB2 TYR 4 8.857 1.049 2.173 1.00 0.00 H +ATOM 72 CG TYR 4 10.376 -0.348 2.209 1.00 0.00 C +ATOM 73 CD1 TYR 4 9.715 -1.458 2.723 1.00 0.00 C +ATOM 74 HD1 TYR 4 8.885 -1.320 3.280 1.00 0.00 H +ATOM 75 CE1 TYR 4 10.180 -2.731 2.491 1.00 0.00 C +ATOM 76 HE1 TYR 4 9.684 -3.515 2.864 1.00 0.00 H +ATOM 77 CZ TYR 4 11.327 -2.923 1.743 1.00 0.00 C +ATOM 78 OH TYR 4 11.772 -4.218 1.542 1.00 0.00 O +ATOM 79 HH TYR 4 12.610 -4.203 0.992 1.00 0.00 H +ATOM 80 CE2 TYR 4 12.014 -1.853 1.208 1.00 0.00 C +ATOM 81 HE2 TYR 4 12.839 -1.981 0.671 1.00 0.00 H +ATOM 82 CD2 TYR 4 11.514 -0.577 1.461 1.00 0.00 C +ATOM 83 HD2 TYR 4 12.003 0.213 1.100 1.00 0.00 H +ATOM 84 C TYR 4 11.243 1.315 4.427 1.00 0.00 C +ATOM 85 O TYR 4 12.070 1.936 3.802 1.00 0.00 O +ATOM 86 N LYS 5 11.521 0.655 5.543 1.00 0.00 N +ATOM 87 H LYS 5 10.781 0.199 6.035 1.00 0.00 H +ATOM 88 CA LYS 5 12.876 0.577 6.081 1.00 0.00 C +ATOM 89 HA LYS 5 12.281 0.494 6.878 1.00 0.00 H +ATOM 90 CB LYS 5 13.785 -0.276 5.197 1.00 0.00 C +ATOM 91 HB1 LYS 5 14.721 -0.237 5.566 1.00 0.00 H +ATOM 92 HB2 LYS 5 13.789 0.102 4.269 1.00 0.00 H +ATOM 93 CG LYS 5 13.332 -1.733 5.137 1.00 0.00 C +ATOM 94 HG1 LYS 5 12.361 -1.762 4.916 1.00 0.00 H +ATOM 95 HG2 LYS 5 13.488 -2.151 6.036 1.00 0.00 H +ATOM 96 CD LYS 5 14.083 -2.545 4.102 1.00 0.00 C +ATOM 97 HD1 LYS 5 15.065 -2.494 4.295 1.00 0.00 H +ATOM 98 HD2 LYS 5 13.904 -2.160 3.193 1.00 0.00 H +ATOM 99 CE LYS 5 13.630 -4.001 4.136 1.00 0.00 C +ATOM 100 HE1 LYS 5 12.631 -4.032 4.080 1.00 0.00 H +ATOM 101 HE2 LYS 5 13.938 -4.414 4.984 1.00 0.00 H +ATOM 102 NZ LYS 5 14.180 -4.798 3.003 1.00 0.00 N +ATOM 103 HZ1 LYS 5 13.857 -5.739 3.063 1.00 0.00 H +ATOM 104 HZ2 LYS 5 13.886 -4.394 2.132 1.00 0.00 H +ATOM 105 HZ3 LYS 5 15.182 -4.790 3.034 1.00 0.00 H +ATOM 106 C LYS 5 14.056 1.466 6.466 1.00 0.00 C +ATOM 107 O LYS 5 14.975 1.104 7.221 1.00 0.00 O +ATOM 108 N PHE 6 14.044 2.687 5.939 1.00 0.00 N +ATOM 109 H PHE 6 13.294 2.963 5.333 1.00 0.00 H +ATOM 110 CA PHE 6 15.159 3.608 6.256 1.00 0.00 C +ATOM 111 HA PHE 6 15.644 3.196 7.035 1.00 0.00 H +ATOM 112 CB PHE 6 16.298 3.863 5.272 1.00 0.00 C +ATOM 113 HB1 PHE 6 15.905 4.040 4.370 1.00 0.00 H +ATOM 114 HB2 PHE 6 16.875 3.045 5.224 1.00 0.00 H +ATOM 115 CG PHE 6 17.186 5.032 5.628 1.00 0.00 C +ATOM 116 CD1 PHE 6 18.040 4.960 6.717 1.00 0.00 C +ATOM 117 HD1 PHE 6 18.046 4.147 7.291 1.00 0.00 H +ATOM 118 CE1 PHE 6 18.902 6.016 7.016 1.00 0.00 C +ATOM 119 HE1 PHE 6 19.515 5.948 7.798 1.00 0.00 H +ATOM 120 CZ PHE 6 18.908 7.152 6.221 1.00 0.00 C +ATOM 121 HZ PHE 6 19.526 7.911 6.430 1.00 0.00 H +ATOM 122 CE2 PHE 6 18.046 7.238 5.139 1.00 0.00 C +ATOM 123 HE2 PHE 6 18.039 8.060 4.561 1.00 0.00 H +ATOM 124 CD2 PHE 6 17.195 6.174 4.842 1.00 0.00 C +ATOM 125 HD2 PHE 6 16.572 6.241 4.063 1.00 0.00 H +ATOM 126 C PHE 6 14.425 4.892 6.413 1.00 0.00 C +ATOM 127 O PHE 6 14.077 5.462 5.394 1.00 0.00 O +ATOM 128 N ASN 7 14.073 5.304 7.628 1.00 0.00 N +ATOM 129 H ASN 7 14.355 4.769 8.422 1.00 0.00 H +ATOM 130 CA ASN 7 13.296 6.516 7.839 1.00 0.00 C +ATOM 131 HA ASN 7 12.557 5.965 8.230 1.00 0.00 H +ATOM 132 CB ASN 7 14.130 7.557 8.619 1.00 0.00 C +ATOM 133 HB1 ASN 7 14.702 8.076 7.978 1.00 0.00 H +ATOM 134 HB2 ASN 7 14.705 7.083 9.284 1.00 0.00 H +ATOM 135 CG ASN 7 13.244 8.537 9.364 1.00 0.00 C +ATOM 136 OD1 ASN 7 12.067 8.728 9.050 1.00 0.00 O +ATOM 137 ND2 ASN 7 13.824 9.162 10.387 1.00 0.00 N +ATOM 138 HD21 ASN 7 14.783 8.966 10.619 1.00 0.00 H +ATOM 139 HD22 ASN 7 13.298 9.824 10.922 1.00 0.00 H +ATOM 140 C ASN 7 12.385 7.211 6.883 1.00 0.00 C +ATOM 141 O ASN 7 12.857 8.124 6.231 1.00 0.00 O +ATOM 142 N SER 8 11.154 6.753 6.700 1.00 0.00 N +ATOM 143 H SER 8 10.841 5.973 7.239 1.00 0.00 H +ATOM 144 CA SER 8 10.239 7.358 5.725 1.00 0.00 C +ATOM 145 HA SER 8 9.961 6.400 5.757 1.00 0.00 H +ATOM 146 CB SER 8 9.462 8.659 5.910 1.00 0.00 C +ATOM 147 HB1 SER 8 8.648 8.670 5.343 1.00 0.00 H +ATOM 148 HB2 SER 8 10.040 9.445 5.688 1.00 0.00 H +ATOM 149 OG SER 8 9.047 8.798 7.263 1.00 0.00 O +ATOM 150 HG SER 8 8.539 9.655 7.361 1.00 0.00 H +ATOM 151 C SER 8 10.570 8.172 4.519 1.00 0.00 C +ATOM 152 O SER 8 10.573 9.378 4.662 1.00 0.00 O +ATOM 153 N THR 9 10.951 7.566 3.404 1.00 0.00 N +ATOM 154 H THR 9 10.970 6.568 3.375 1.00 0.00 H +ATOM 155 CA THR 9 11.356 8.315 2.222 1.00 0.00 C +ATOM 156 HA THR 9 12.105 8.326 2.882 1.00 0.00 H +ATOM 157 CB THR 9 10.366 7.934 1.098 1.00 0.00 C +ATOM 158 HB THR 9 10.756 8.120 0.202 1.00 0.00 H +ATOM 159 CG2 THR 9 9.971 6.473 1.212 1.00 0.00 C +ATOM 160 HG21 THR 9 9.334 6.237 0.489 1.00 0.00 H +ATOM 161 HG22 THR 9 10.797 5.896 1.140 1.00 0.00 H +ATOM 162 HG23 THR 9 9.538 6.312 2.107 1.00 0.00 H +ATOM 163 OG1 THR 9 9.185 8.741 1.202 1.00 0.00 O +ATOM 164 HG1 THR 9 8.546 8.492 0.475 1.00 0.00 H +ATOM 165 C THR 9 12.291 9.432 1.772 1.00 0.00 C +ATOM 166 O THR 9 12.638 9.616 0.593 1.00 0.00 O +ATOM 167 N GLY 10 12.733 10.221 2.747 1.00 0.00 N +ATOM 168 H GLY 10 12.447 10.062 3.702 1.00 0.00 H +ATOM 169 CA GLY 10 13.640 11.338 2.401 1.00 0.00 C +ATOM 170 HA1 GLY 10 13.124 12.182 2.569 1.00 0.00 H +ATOM 171 HA2 GLY 10 13.817 11.255 1.415 1.00 0.00 H +ATOM 172 C GLY 10 14.998 11.496 3.093 1.00 0.00 C +ATOM 173 O GLY 10 15.687 12.521 3.034 1.00 0.00 O +ATOM 174 N ARG 11 15.389 10.434 3.790 1.00 0.00 N +ATOM 175 H ARG 11 14.825 9.618 3.833 1.00 0.00 H +ATOM 176 CA ARG 11 16.695 10.505 4.510 1.00 0.00 C +ATOM 177 HA ARG 11 17.274 11.259 4.224 1.00 0.00 H +ATOM 178 CB ARG 11 16.377 10.534 6.013 1.00 0.00 C +ATOM 179 HB1 ARG 11 17.239 10.541 6.507 1.00 0.00 H +ATOM 180 HB2 ARG 11 15.864 9.706 6.238 1.00 0.00 H +ATOM 181 CG ARG 11 15.547 11.735 6.474 1.00 0.00 C +ATOM 182 HG1 ARG 11 14.684 11.750 5.979 1.00 0.00 H +ATOM 183 HG2 ARG 11 16.052 12.582 6.289 1.00 0.00 H +ATOM 184 CD ARG 11 15.272 11.644 7.970 1.00 0.00 C +ATOM 185 HD1 ARG 11 16.137 11.620 8.469 1.00 0.00 H +ATOM 186 HD2 ARG 11 14.756 10.806 8.153 1.00 0.00 H +ATOM 187 NE ARG 11 14.493 12.759 8.510 1.00 0.00 N +ATOM 188 HE ARG 11 13.511 12.607 8.684 1.00 0.00 H +ATOM 189 CZ ARG 11 14.987 13.963 8.795 1.00 0.00 C +ATOM 190 NH1 ARG 11 16.270 14.223 8.584 1.00 0.00 N +ATOM 191 HH11 ARG 11 16.873 13.521 8.214 1.00 0.00 H +ATOM 192 HH12 ARG 11 16.632 15.139 8.799 1.00 0.00 H +ATOM 193 NH2 ARG 11 14.195 14.893 9.312 1.00 0.00 N +ATOM 194 HH21 ARG 11 13.237 14.693 9.493 1.00 0.00 H +ATOM 195 HH22 ARG 11 14.568 15.801 9.529 1.00 0.00 H +ATOM 196 C ARG 11 17.219 9.131 4.257 1.00 0.00 C +ATOM 197 O ARG 11 16.743 8.227 4.929 1.00 0.00 O +ATOM 198 N HIS 12 18.073 8.929 3.264 1.00 0.00 N +ATOM 199 H HIS 12 18.387 9.709 2.725 1.00 0.00 H +ATOM 200 CA HIS 12 18.558 7.597 2.928 1.00 0.00 C +ATOM 201 HA HIS 12 18.650 8.113 2.084 1.00 0.00 H +ATOM 202 CB HIS 12 19.417 6.997 4.049 1.00 0.00 C +ATOM 203 HB1 HIS 12 19.765 6.100 3.751 1.00 0.00 H +ATOM 204 HB2 HIS 12 18.849 6.871 4.861 1.00 0.00 H +ATOM 205 CG HIS 12 20.590 7.850 4.409 1.00 0.00 C +ATOM 206 ND1 HIS 12 21.124 7.900 5.687 1.00 0.00 N +ATOM 207 CE1 HIS 12 22.121 8.767 5.714 1.00 0.00 C +ATOM 208 HE1 HIS 12 22.668 8.988 6.510 1.00 0.00 H +ATOM 209 NE2 HIS 12 22.258 9.279 4.502 1.00 0.00 N +ATOM 210 HE2 HIS 12 22.931 9.960 4.237 1.00 0.00 H +ATOM 211 CD2 HIS 12 21.310 8.726 3.675 1.00 0.00 C +ATOM 212 HD2 HIS 12 21.188 8.919 2.700 1.00 0.00 H +ATOM 213 C HIS 12 18.072 6.178 2.618 1.00 0.00 C +ATOM 214 O HIS 12 18.745 5.328 2.034 1.00 0.00 O +ATOM 215 N TYR 13 16.827 5.923 3.005 1.00 0.00 N +ATOM 216 H TYR 13 16.281 6.619 3.479 1.00 0.00 H +ATOM 217 CA TYR 13 16.275 4.565 2.753 1.00 0.00 C +ATOM 218 HA TYR 13 16.816 3.757 2.534 1.00 0.00 H +ATOM 219 CB TYR 13 16.701 3.111 2.922 1.00 0.00 C +ATOM 220 HB1 TYR 13 15.894 2.526 2.794 1.00 0.00 H +ATOM 221 HB2 TYR 13 17.057 2.983 3.844 1.00 0.00 H +ATOM 222 CG TYR 13 17.749 2.651 1.951 1.00 0.00 C +ATOM 223 CD1 TYR 13 17.412 2.339 0.639 1.00 0.00 C +ATOM 224 HD1 TYR 13 16.464 2.435 0.340 1.00 0.00 H +ATOM 225 CE1 TYR 13 18.371 1.891 -0.250 1.00 0.00 C +ATOM 226 HE1 TYR 13 18.111 1.673 -1.199 1.00 0.00 H +ATOM 227 CZ TYR 13 19.674 1.751 0.161 1.00 0.00 C +ATOM 228 OH TYR 13 20.608 1.280 -0.742 1.00 0.00 O +ATOM 229 HH TYR 13 21.498 1.233 -0.298 1.00 0.00 H +ATOM 230 CE2 TYR 13 20.050 2.064 1.461 1.00 0.00 C +ATOM 231 HE2 TYR 13 20.994 1.963 1.751 1.00 0.00 H +ATOM 232 CD2 TYR 13 19.081 2.512 2.353 1.00 0.00 C +ATOM 233 HD2 TYR 13 19.337 2.734 3.290 1.00 0.00 H +ATOM 234 C TYR 13 14.837 5.335 2.496 1.00 0.00 C +ATOM 235 O TYR 13 14.360 6.226 3.196 1.00 0.00 O +ATOM 236 N HIS 14 14.291 4.946 1.341 1.00 0.00 N +ATOM 237 H HIS 14 14.760 4.167 0.913 1.00 0.00 H +ATOM 238 CA HIS 14 13.218 5.407 0.640 1.00 0.00 C +ATOM 239 HA HIS 14 12.542 5.939 1.153 1.00 0.00 H +ATOM 240 CB HIS 14 13.410 6.688 -0.189 1.00 0.00 C +ATOM 241 HB1 HIS 14 13.690 7.425 0.427 1.00 0.00 H +ATOM 242 HB2 HIS 14 12.540 6.914 -0.621 1.00 0.00 H +ATOM 243 CG HIS 14 14.442 6.566 -1.272 1.00 0.00 C +ATOM 244 ND1 HIS 14 15.780 6.840 -1.068 1.00 0.00 N +ATOM 245 CE1 HIS 14 16.441 6.646 -2.195 1.00 0.00 C +ATOM 246 HE1 HIS 14 17.430 6.768 -2.318 1.00 0.00 H +ATOM 247 NE2 HIS 14 15.580 6.264 -3.122 1.00 0.00 N +ATOM 248 HE2 HIS 14 15.816 6.041 -4.073 1.00 0.00 H +ATOM 249 CD2 HIS 14 14.319 6.208 -2.580 1.00 0.00 C +ATOM 250 HD2 HIS 14 13.483 5.947 -3.047 1.00 0.00 H +ATOM 251 C HIS 14 12.844 3.895 0.120 1.00 0.00 C +ATOM 252 O HIS 14 13.593 3.109 -0.452 1.00 0.00 O +ATOM 253 N TYR 15 11.605 3.554 0.517 1.00 0.00 N +ATOM 254 H TYR 15 11.088 4.305 0.928 1.00 0.00 H +ATOM 255 CA TYR 15 10.935 2.376 0.465 1.00 0.00 C +ATOM 256 HA TYR 15 11.554 1.894 -0.153 1.00 0.00 H +ATOM 257 CB TYR 15 10.849 1.249 1.494 1.00 0.00 C +ATOM 258 HB1 TYR 15 10.387 1.601 2.314 1.00 0.00 H +ATOM 259 HB2 TYR 15 11.774 0.964 1.740 1.00 0.00 H +ATOM 260 CG TYR 15 10.097 0.029 1.004 1.00 0.00 C +ATOM 261 CD1 TYR 15 10.630 -0.696 -0.046 1.00 0.00 C +ATOM 262 HD1 TYR 15 11.481 -0.401 -0.472 1.00 0.00 H +ATOM 263 CE1 TYR 15 9.996 -1.819 -0.522 1.00 0.00 C +ATOM 264 HE1 TYR 15 10.390 -2.333 -1.277 1.00 0.00 H +ATOM 265 CZ TYR 15 8.804 -2.248 0.041 1.00 0.00 C +ATOM 266 OH TYR 15 8.177 -3.367 -0.476 1.00 0.00 O +ATOM 267 HH TYR 15 7.340 -3.539 0.032 1.00 0.00 H +ATOM 268 CE2 TYR 15 8.240 -1.551 1.092 1.00 0.00 C +ATOM 269 HE2 TYR 15 7.376 -1.842 1.509 1.00 0.00 H +ATOM 270 CD2 TYR 15 8.911 -0.419 1.551 1.00 0.00 C +ATOM 271 HD2 TYR 15 8.507 0.095 2.309 1.00 0.00 H +ATOM 272 C TYR 15 9.664 2.861 0.052 1.00 0.00 C +ATOM 273 O TYR 15 8.971 3.443 0.899 1.00 0.00 O +ATOM 274 N TYR 16 9.271 2.638 -1.197 1.00 0.00 N +ATOM 275 H TYR 16 9.843 2.127 -1.832 1.00 0.00 H +ATOM 276 CA TYR 16 7.881 3.222 -1.640 1.00 0.00 C +ATOM 277 HA TYR 16 7.323 3.698 -0.967 1.00 0.00 H +ATOM 278 CB TYR 16 7.902 4.327 -2.708 1.00 0.00 C +ATOM 279 HB1 TYR 16 6.968 4.509 -3.023 1.00 0.00 H +ATOM 280 HB2 TYR 16 8.461 4.038 -3.486 1.00 0.00 H +ATOM 281 CG TYR 16 8.497 5.589 -2.119 1.00 0.00 C +ATOM 282 CD1 TYR 16 7.681 6.521 -1.452 1.00 0.00 C +ATOM 283 HD1 TYR 16 6.705 6.363 -1.385 1.00 0.00 H +ATOM 284 CE1 TYR 16 8.251 7.665 -0.884 1.00 0.00 C +ATOM 285 HE1 TYR 16 7.681 8.343 -0.415 1.00 0.00 H +ATOM 286 CZ TYR 16 9.613 7.845 -0.992 1.00 0.00 C +ATOM 287 OH TYR 16 10.280 8.925 -0.455 1.00 0.00 O +ATOM 288 HH TYR 16 11.259 8.834 -0.658 1.00 0.00 H +ATOM 289 CE2 TYR 16 10.405 6.921 -1.632 1.00 0.00 C +ATOM 290 HE2 TYR 16 11.390 7.079 -1.703 1.00 0.00 H +ATOM 291 CD2 TYR 16 9.859 5.774 -2.194 1.00 0.00 C +ATOM 292 HD2 TYR 16 10.443 5.106 -2.649 1.00 0.00 H +ATOM 293 C TYR 16 7.301 1.973 -2.027 1.00 0.00 C +ATOM 294 OC1 TYR 16 6.199 1.574 -1.415 1.00 0.00 O +ATOM 295 OC2 TYR 16 7.872 1.342 -2.927 1.00 0.00 O +TER 296 TYR 16 +END
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/model.pdb Thu Jun 06 07:09:14 2024 +0000 @@ -0,0 +1,301 @@ +TITLE Georgetown Riga Oslo Madrid Amsterdam Chisinau Stockholm +REMARK THIS IS A SIMULATION BOX +CRYST1 17.408 18.717 19.156 90.00 90.00 90.00 P 1 1 +MODEL 1 +ATOM 1 N ARG 1 -1.000 -0.440 0.360 1.00 0.00 +ATOM 2 H1 ARG 1 -1.290 0.040 1.190 1.00 0.00 +ATOM 3 H2 ARG 1 -1.690 -0.320 -0.350 1.00 0.00 +ATOM 4 H3 ARG 1 -0.880 -1.410 0.560 1.00 0.00 +ATOM 5 CA ARG 1 0.000 0.000 0.000 1.00 0.00 +ATOM 6 HA ARG 1 0.380 0.020 0.920 1.00 0.00 +ATOM 7 CB ARG 1 -0.030 -1.000 -1.160 1.00 0.00 +ATOM 8 HB1 ARG 1 -0.090 -1.920 -0.780 1.00 0.00 +ATOM 9 HB2 ARG 1 0.820 -0.900 -1.680 1.00 0.00 +ATOM 10 CG ARG 1 -1.180 -0.810 -2.140 1.00 0.00 +ATOM 11 HG1 ARG 1 -1.030 0.010 -2.680 1.00 0.00 +ATOM 12 HG2 ARG 1 -2.040 -0.720 -1.630 1.00 0.00 +ATOM 13 CD ARG 1 -1.280 -2.010 -3.070 1.00 0.00 +ATOM 14 HD1 ARG 1 -1.430 -2.840 -2.520 1.00 0.00 +ATOM 15 HD2 ARG 1 -0.440 -2.100 -3.590 1.00 0.00 +ATOM 16 NE ARG 1 -2.390 -1.900 -4.020 1.00 0.00 +ATOM 17 HE ARG 1 -3.240 -2.370 -3.800 1.00 0.00 +ATOM 18 CZ ARG 1 -2.330 -1.230 -5.160 1.00 0.00 +ATOM 19 NH1 ARG 1 -1.220 -0.580 -5.500 1.00 0.00 +ATOM 20 HH11 ARG 1 -0.420 -0.610 -4.900 1.00 0.00 +ATOM 21 HH12 ARG 1 -1.180 -0.080 -6.360 1.00 0.00 +ATOM 22 NH2 ARG 1 -3.380 -1.200 -5.970 1.00 0.00 +ATOM 23 HH21 ARG 1 -4.220 -1.690 -5.720 1.00 0.00 +ATOM 24 HH22 ARG 1 -3.340 -0.690 -6.830 1.00 0.00 +ATOM 25 C ARG 1 0.220 1.390 -1.140 1.00 0.00 +ATOM 26 O ARG 1 -0.080 2.540 -0.900 1.00 0.00 +ATOM 27 N HIS 2 1.370 1.080 -1.690 1.00 0.00 +ATOM 28 H HIS 2 1.670 0.130 -1.770 1.00 0.00 +ATOM 29 CA HIS 2 2.190 2.190 -2.190 1.00 0.00 +ATOM 30 HA HIS 2 1.530 2.710 -2.740 1.00 0.00 +ATOM 31 CB HIS 2 2.920 3.160 -1.260 1.00 0.00 +ATOM 32 HB1 HIS 2 2.290 3.470 -0.550 1.00 0.00 +ATOM 33 HB2 HIS 2 3.240 3.950 -1.780 1.00 0.00 +ATOM 34 CG HIS 2 4.110 2.560 -0.580 1.00 0.00 +ATOM 35 ND1 HIS 2 4.050 1.740 0.520 1.00 0.00 +ATOM 36 CE1 HIS 2 5.290 1.330 0.820 1.00 0.00 +ATOM 37 HE1 HIS 2 5.520 0.720 1.570 1.00 0.00 +ATOM 38 NE2 HIS 2 6.170 1.850 -0.020 1.00 0.00 +ATOM 39 HE2 HIS 2 7.160 1.720 -0.020 1.00 0.00 +ATOM 40 CD2 HIS 2 5.430 2.640 -0.900 1.00 0.00 +ATOM 41 HD2 HIS 2 5.810 3.170 -1.660 1.00 0.00 +ATOM 42 C HIS 2 3.390 1.480 -2.730 1.00 0.00 +ATOM 43 O HIS 2 4.390 1.490 -2.050 1.00 0.00 +ATOM 44 N TYR 3 3.280 0.770 -3.850 1.00 0.00 +ATOM 45 H TYR 3 2.410 0.770 -4.340 1.00 0.00 +ATOM 46 CA TYR 3 4.390 0.000 -4.390 1.00 0.00 +ATOM 47 HA TYR 3 3.460 -0.200 -4.690 1.00 0.00 +ATOM 48 CB TYR 3 4.680 -0.450 -5.820 1.00 0.00 +ATOM 49 HB1 TYR 3 3.810 -0.540 -6.310 1.00 0.00 +ATOM 50 HB2 TYR 3 5.150 -1.330 -5.800 1.00 0.00 +ATOM 51 CG TYR 3 5.540 0.530 -6.570 1.00 0.00 +ATOM 52 CD1 TYR 3 4.950 1.550 -7.290 1.00 0.00 +ATOM 53 HD1 TYR 3 3.960 1.610 -7.350 1.00 0.00 +ATOM 54 CE1 TYR 3 5.720 2.500 -7.940 1.00 0.00 +ATOM 55 HE1 TYR 3 5.270 3.230 -8.460 1.00 0.00 +ATOM 56 CZ TYR 3 7.090 2.430 -7.880 1.00 0.00 +ATOM 57 OH TYR 3 7.820 3.440 -8.480 1.00 0.00 +ATOM 58 HH TYR 3 8.790 3.270 -8.360 1.00 0.00 +ATOM 59 CE2 TYR 3 7.720 1.410 -7.170 1.00 0.00 +ATOM 60 HE2 TYR 3 8.720 1.360 -7.130 1.00 0.00 +ATOM 61 CD2 TYR 3 6.930 0.460 -6.520 1.00 0.00 +ATOM 62 HD2 TYR 3 7.370 -0.280 -6.010 1.00 0.00 +ATOM 63 C TYR 3 5.640 -0.230 -3.350 1.00 0.00 +ATOM 64 O TYR 3 6.290 0.640 -2.790 1.00 0.00 +ATOM 65 N TYR 4 5.800 -1.540 -3.090 1.00 0.00 +ATOM 66 H TYR 4 5.240 -2.140 -3.670 1.00 0.00 +ATOM 67 CA TYR 4 6.580 -2.190 -2.190 1.00 0.00 +ATOM 68 HA TYR 4 7.070 -1.340 -2.040 1.00 0.00 +ATOM 69 CB TYR 4 6.270 -2.630 -0.760 1.00 0.00 +ATOM 70 HB1 TYR 4 5.540 -3.320 -0.790 1.00 0.00 +ATOM 71 HB2 TYR 4 5.950 -1.840 -0.250 1.00 0.00 +ATOM 72 CG TYR 4 7.460 -3.230 -0.030 1.00 0.00 +ATOM 73 CD1 TYR 4 8.550 -2.410 0.240 1.00 0.00 +ATOM 74 HD1 TYR 4 8.530 -1.450 -0.070 1.00 0.00 +ATOM 75 CE1 TYR 4 9.650 -2.890 0.910 1.00 0.00 +ATOM 76 HE1 TYR 4 10.420 -2.280 1.100 1.00 0.00 +ATOM 77 CZ TYR 4 9.690 -4.210 1.320 1.00 0.00 +ATOM 78 OH TYR 4 10.820 -4.660 1.980 1.00 0.00 +ATOM 79 HH TYR 4 10.710 -5.630 2.210 1.00 0.00 +ATOM 80 CE2 TYR 4 8.630 -5.060 1.080 1.00 0.00 +ATOM 81 HE2 TYR 4 8.650 -6.010 1.370 1.00 0.00 +ATOM 82 CD2 TYR 4 7.530 -4.540 0.400 1.00 0.00 +ATOM 83 HD2 TYR 4 6.760 -5.140 0.200 1.00 0.00 +ATOM 84 C TYR 4 7.120 -3.390 -2.910 1.00 0.00 +ATOM 85 O TYR 4 6.440 -4.390 -2.900 1.00 0.00 +ATOM 86 N LYS 5 8.240 -3.280 -3.610 1.00 0.00 +ATOM 87 H LYS 5 8.730 -2.410 -3.610 1.00 0.00 +ATOM 88 CA LYS 5 8.780 -4.390 -4.390 1.00 0.00 +ATOM 89 HA LYS 5 9.100 -3.570 -4.860 1.00 0.00 +ATOM 90 CB LYS 5 9.300 -5.510 -3.490 1.00 0.00 +ATOM 91 HB1 LYS 5 9.590 -6.280 -4.070 1.00 0.00 +ATOM 92 HB2 LYS 5 8.560 -5.820 -2.890 1.00 0.00 +ATOM 93 CG LYS 5 10.480 -5.060 -2.630 1.00 0.00 +ATOM 94 HG1 LYS 5 10.240 -4.210 -2.170 1.00 0.00 +ATOM 95 HG2 LYS 5 11.270 -4.910 -3.230 1.00 0.00 +ATOM 96 CD LYS 5 10.870 -6.080 -1.580 1.00 0.00 +ATOM 97 HD1 LYS 5 11.080 -6.950 -2.030 1.00 0.00 +ATOM 98 HD2 LYS 5 10.100 -6.210 -0.950 1.00 0.00 +ATOM 99 CE LYS 5 12.090 -5.600 -0.800 1.00 0.00 +ATOM 100 HE1 LYS 5 11.920 -4.670 -0.470 1.00 0.00 +ATOM 101 HE2 LYS 5 12.880 -5.610 -1.400 1.00 0.00 +ATOM 102 NZ LYS 5 12.390 -6.460 0.380 1.00 0.00 +ATOM 103 HZ1 LYS 5 13.190 -6.110 0.860 1.00 0.00 +ATOM 104 HZ2 LYS 5 11.600 -6.470 1.000 1.00 0.00 +ATOM 105 HZ3 LYS 5 12.570 -7.400 0.080 1.00 0.00 +ATOM 106 C LYS 5 8.370 -5.410 -5.450 1.00 0.00 +ATOM 107 O LYS 5 9.180 -6.030 -6.160 1.00 0.00 +ATOM 108 N PHE 6 7.060 -5.600 -5.580 1.00 0.00 +ATOM 109 H PHE 6 6.420 -5.090 -5.000 1.00 0.00 +ATOM 110 CA PHE 6 6.580 -6.580 -6.580 1.00 0.00 +ATOM 111 HA PHE 6 7.370 -6.780 -7.170 1.00 0.00 +ATOM 112 CB PHE 6 6.120 -7.980 -6.180 1.00 0.00 +ATOM 113 HB1 PHE 6 5.500 -7.900 -5.400 1.00 0.00 +ATOM 114 HB2 PHE 6 6.920 -8.520 -5.910 1.00 0.00 +ATOM 115 CG PHE 6 5.400 -8.740 -7.270 1.00 0.00 +ATOM 116 CD1 PHE 6 6.090 -9.200 -8.380 1.00 0.00 +ATOM 117 HD1 PHE 6 7.060 -9.000 -8.480 1.00 0.00 +ATOM 118 CE1 PHE 6 5.440 -9.950 -9.360 1.00 0.00 +ATOM 119 HE1 PHE 6 5.950 -10.280 -10.150 1.00 0.00 +ATOM 120 CZ PHE 6 4.090 -10.240 -9.230 1.00 0.00 +ATOM 121 HZ PHE 6 3.620 -10.780 -9.930 1.00 0.00 +ATOM 122 CE2 PHE 6 3.390 -9.770 -8.130 1.00 0.00 +ATOM 123 HE2 PHE 6 2.410 -9.970 -8.030 1.00 0.00 +ATOM 124 CD2 PHE 6 4.050 -9.030 -7.150 1.00 0.00 +ATOM 125 HD2 PHE 6 3.540 -8.690 -6.360 1.00 0.00 +ATOM 126 C PHE 6 5.390 -5.870 -7.120 1.00 0.00 +ATOM 127 O PHE 6 4.380 -5.880 -6.440 1.00 0.00 +ATOM 128 N ASN 7 5.500 -5.160 -8.240 1.00 0.00 +ATOM 129 H ASN 7 6.370 -5.160 -8.730 1.00 0.00 +ATOM 130 CA ASN 7 4.390 -4.390 -8.780 1.00 0.00 +ATOM 131 HA ASN 7 4.920 -3.550 -8.650 1.00 0.00 +ATOM 132 CB ASN 7 3.960 -4.960 -10.150 1.00 0.00 +ATOM 133 HB1 ASN 7 3.320 -5.720 -10.010 1.00 0.00 +ATOM 134 HB2 ASN 7 4.770 -5.280 -10.640 1.00 0.00 +ATOM 135 CG ASN 7 3.270 -3.910 -11.000 1.00 0.00 +ATOM 136 OD1 ASN 7 2.760 -2.900 -10.510 1.00 0.00 +ATOM 137 ND2 ASN 7 3.270 -4.150 -12.310 1.00 0.00 +ATOM 138 HD21 ASN 7 3.710 -4.980 -12.670 1.00 0.00 +ATOM 139 HD22 ASN 7 2.830 -3.500 -12.930 1.00 0.00 +ATOM 140 C ASN 7 3.200 -3.850 -8.060 1.00 0.00 +ATOM 141 O ASN 7 2.190 -4.530 -8.070 1.00 0.00 +ATOM 142 N SER 8 3.310 -2.730 -7.360 1.00 0.00 +ATOM 143 H SER 8 4.180 -2.240 -7.360 1.00 0.00 +ATOM 144 CA SER 8 2.190 -2.190 -6.580 1.00 0.00 +ATOM 145 HA SER 8 3.000 -1.890 -6.080 1.00 0.00 +ATOM 146 CB SER 8 0.990 -1.430 -7.140 1.00 0.00 +ATOM 147 HB1 SER 8 0.590 -0.840 -6.450 1.00 0.00 +ATOM 148 HB2 SER 8 0.300 -2.070 -7.480 1.00 0.00 +ATOM 149 OG SER 8 1.390 -0.610 -8.230 1.00 0.00 +ATOM 150 HG SER 8 0.590 -0.120 -8.580 1.00 0.00 +ATOM 151 C SER 8 1.000 -2.910 -6.040 1.00 0.00 +ATOM 152 O SER 8 -0.000 -2.900 -6.730 1.00 0.00 +ATOM 153 N THR 9 1.110 -3.610 -4.920 1.00 0.00 +ATOM 154 H THR 9 1.980 -3.610 -4.430 1.00 0.00 +ATOM 155 CA THR 9 0.000 -4.390 -4.390 1.00 0.00 +ATOM 156 HA THR 9 0.410 -4.890 -5.150 1.00 0.00 +ATOM 157 CB THR 9 -0.330 -3.800 -3.000 1.00 0.00 +ATOM 158 HB THR 9 -0.820 -4.460 -2.440 1.00 0.00 +ATOM 159 CG2 THR 9 0.940 -3.350 -2.300 1.00 0.00 +ATOM 160 HG21 THR 9 0.720 -2.970 -1.410 1.00 0.00 +ATOM 161 HG22 THR 9 1.560 -4.140 -2.190 1.00 0.00 +ATOM 162 HG23 THR 9 1.400 -2.650 -2.860 1.00 0.00 +ATOM 163 OG1 THR 9 -1.200 -2.670 -3.150 1.00 0.00 +ATOM 164 HG1 THR 9 -1.410 -2.290 -2.250 1.00 0.00 +ATOM 165 C THR 9 -1.020 -5.450 -4.790 1.00 0.00 +ATOM 166 O THR 9 -1.640 -6.160 -3.980 1.00 0.00 +ATOM 167 N GLY 10 -1.210 -5.580 -6.100 1.00 0.00 +ATOM 168 H GLY 10 -0.700 -5.000 -6.750 1.00 0.00 +ATOM 169 CA GLY 10 -2.190 -6.580 -6.580 1.00 0.00 +ATOM 170 HA1 GLY 10 -2.950 -6.060 -6.980 1.00 0.00 +ATOM 171 HA2 GLY 10 -2.520 -7.060 -5.760 1.00 0.00 +ATOM 172 C GLY 10 -1.790 -7.650 -7.600 1.00 0.00 +ATOM 173 O GLY 10 -2.600 -8.350 -8.220 1.00 0.00 +ATOM 174 N ARG 11 -0.480 -7.770 -7.790 1.00 0.00 +ATOM 175 H ARG 11 0.160 -7.200 -7.290 1.00 0.00 +ATOM 176 CA ARG 11 0.000 -8.780 -8.780 1.00 0.00 +ATOM 177 HA ARG 11 -0.690 -9.440 -9.050 1.00 0.00 +ATOM 178 CB ARG 11 0.580 -8.000 -9.970 1.00 0.00 +ATOM 179 HB1 ARG 11 0.940 -8.660 -10.620 1.00 0.00 +ATOM 180 HB2 ARG 11 1.320 -7.420 -9.630 1.00 0.00 +ATOM 181 CG ARG 11 -0.420 -7.100 -10.700 1.00 0.00 +ATOM 182 HG1 ARG 11 -0.800 -6.440 -10.060 1.00 0.00 +ATOM 183 HG2 ARG 11 -1.160 -7.660 -11.080 1.00 0.00 +ATOM 184 CD ARG 11 0.270 -6.360 -11.840 1.00 0.00 +ATOM 185 HD1 ARG 11 0.660 -7.020 -12.480 1.00 0.00 +ATOM 186 HD2 ARG 11 1.000 -5.790 -11.460 1.00 0.00 +ATOM 187 NE ARG 11 -0.610 -5.480 -12.610 1.00 0.00 +ATOM 188 HE ARG 11 -0.570 -4.490 -12.420 1.00 0.00 +ATOM 189 CZ ARG 11 -1.460 -5.890 -13.550 1.00 0.00 +ATOM 190 NH1 ARG 11 -1.560 -7.180 -13.840 1.00 0.00 +ATOM 191 HH11 ARG 11 -1.000 -7.850 -13.360 1.00 0.00 +ATOM 192 HH12 ARG 11 -2.210 -7.480 -14.550 1.00 0.00 +ATOM 193 NH2 ARG 11 -2.190 -5.000 -14.210 1.00 0.00 +ATOM 194 HH21 ARG 11 -2.100 -4.030 -14.010 1.00 0.00 +ATOM 195 HH22 ARG 11 -2.830 -5.310 -14.920 1.00 0.00 +ATOM 196 C ARG 11 1.190 -9.320 -8.060 1.00 0.00 +ATOM 197 O ARG 11 2.200 -8.630 -8.070 1.00 0.00 +ATOM 198 N HIS 12 1.080 -10.440 -7.360 1.00 0.00 +ATOM 199 H HIS 12 0.210 -10.930 -7.360 1.00 0.00 +ATOM 200 CA HIS 12 2.190 -10.970 -6.580 1.00 0.00 +ATOM 201 HA HIS 12 1.380 -11.340 -6.140 1.00 0.00 +ATOM 202 CB HIS 12 3.360 -11.410 -7.470 1.00 0.00 +ATOM 203 HB1 HIS 12 4.080 -11.810 -6.890 1.00 0.00 +ATOM 204 HB2 HIS 12 3.730 -10.610 -7.940 1.00 0.00 +ATOM 205 CG HIS 12 2.970 -12.430 -8.490 1.00 0.00 +ATOM 206 ND1 HIS 12 3.580 -12.530 -9.730 1.00 0.00 +ATOM 207 CE1 HIS 12 3.000 -13.490 -10.430 1.00 0.00 +ATOM 208 HE1 HIS 12 3.250 -13.760 -11.350 1.00 0.00 +ATOM 209 NE2 HIS 12 2.040 -14.020 -9.690 1.00 0.00 +ATOM 210 HE2 HIS 12 1.440 -14.760 -9.970 1.00 0.00 +ATOM 211 CD2 HIS 12 2.000 -13.370 -8.480 1.00 0.00 +ATOM 212 HD2 HIS 12 1.380 -13.570 -7.720 1.00 0.00 +ATOM 213 C HIS 12 3.220 -10.570 -5.520 1.00 0.00 +ATOM 214 O HIS 12 3.830 -11.370 -4.810 1.00 0.00 +ATOM 215 N TYR 13 3.400 -9.260 -5.390 1.00 0.00 +ATOM 216 H TYR 13 2.900 -8.610 -5.970 1.00 0.00 +ATOM 217 CA TYR 13 4.390 -8.780 -4.390 1.00 0.00 +ATOM 218 HA TYR 13 5.100 -9.340 -3.970 1.00 0.00 +ATOM 219 CB TYR 13 5.820 -9.090 -3.960 1.00 0.00 +ATOM 220 HB1 TYR 13 6.140 -8.350 -3.360 1.00 0.00 +ATOM 221 HB2 TYR 13 6.400 -9.130 -4.770 1.00 0.00 +ATOM 222 CG TYR 13 5.980 -10.380 -3.210 1.00 0.00 +ATOM 223 CD1 TYR 13 5.620 -10.470 -1.870 1.00 0.00 +ATOM 224 HD1 TYR 13 5.240 -9.670 -1.410 1.00 0.00 +ATOM 225 CE1 TYR 13 5.790 -11.650 -1.170 1.00 0.00 +ATOM 226 HE1 TYR 13 5.520 -11.700 -0.200 1.00 0.00 +ATOM 227 CZ TYR 13 6.320 -12.750 -1.800 1.00 0.00 +ATOM 228 OH TYR 13 6.500 -13.910 -1.070 1.00 0.00 +ATOM 229 HH TYR 13 6.890 -14.610 -1.660 1.00 0.00 +ATOM 230 CE2 TYR 13 6.680 -12.700 -3.140 1.00 0.00 +ATOM 231 HE2 TYR 13 7.060 -13.500 -3.590 1.00 0.00 +ATOM 232 CD2 TYR 13 6.510 -11.510 -3.840 1.00 0.00 +ATOM 233 HD2 TYR 13 6.770 -11.460 -4.800 1.00 0.00 +ATOM 234 C TYR 13 3.350 -7.520 -4.150 1.00 0.00 +ATOM 235 O TYR 13 2.790 -6.870 -5.030 1.00 0.00 +ATOM 236 N HIS 14 3.090 -7.360 -2.850 1.00 0.00 +ATOM 237 H HIS 14 3.670 -7.920 -2.250 1.00 0.00 +ATOM 238 CA HIS 14 2.190 -6.580 -2.190 1.00 0.00 +ATOM 239 HA HIS 14 1.830 -5.790 -2.690 1.00 0.00 +ATOM 240 CB HIS 14 0.730 -7.060 -2.150 1.00 0.00 +ATOM 241 HB1 HIS 14 0.400 -7.150 -3.090 1.00 0.00 +ATOM 242 HB2 HIS 14 0.190 -6.380 -1.660 1.00 0.00 +ATOM 243 CG HIS 14 0.540 -8.380 -1.460 1.00 0.00 +ATOM 244 ND1 HIS 14 0.620 -9.590 -2.120 1.00 0.00 +ATOM 245 CE1 HIS 14 0.410 -10.570 -1.260 1.00 0.00 +ATOM 246 HE1 HIS 14 0.420 -11.550 -1.480 1.00 0.00 +ATOM 247 NE2 HIS 14 0.190 -10.040 -0.070 1.00 0.00 +ATOM 248 HE2 HIS 14 0.010 -10.560 0.770 1.00 0.00 +ATOM 249 CD2 HIS 14 0.260 -8.670 -0.160 1.00 0.00 +ATOM 250 HD2 HIS 14 0.140 -8.020 0.580 1.00 0.00 +ATOM 251 C HIS 14 3.230 -6.350 -0.940 1.00 0.00 +ATOM 252 O HIS 14 3.800 -7.220 -0.290 1.00 0.00 +ATOM 253 N TYR 15 3.490 -5.040 -0.780 1.00 0.00 +ATOM 254 H TYR 15 2.920 -4.440 -1.340 1.00 0.00 +ATOM 255 CA TYR 15 4.390 -4.390 -0.000 1.00 0.00 +ATOM 256 HA TYR 15 4.650 -5.160 0.580 1.00 0.00 +ATOM 257 CB TYR 15 5.820 -3.950 -0.310 1.00 0.00 +ATOM 258 HB1 TYR 15 5.790 -3.260 -1.040 1.00 0.00 +ATOM 259 HB2 TYR 15 6.340 -4.740 -0.630 1.00 0.00 +ATOM 260 CG TYR 15 6.550 -3.360 0.880 1.00 0.00 +ATOM 261 CD1 TYR 15 6.820 -4.180 1.960 1.00 0.00 +ATOM 262 HD1 TYR 15 6.520 -5.130 1.950 1.00 0.00 +ATOM 263 CE1 TYR 15 7.490 -3.700 3.060 1.00 0.00 +ATOM 264 HE1 TYR 15 7.680 -4.300 3.830 1.00 0.00 +ATOM 265 CZ TYR 15 7.910 -2.380 3.110 1.00 0.00 +ATOM 266 OH TYR 15 8.560 -1.920 4.240 1.00 0.00 +ATOM 267 HH TYR 15 8.790 -0.960 4.120 1.00 0.00 +ATOM 268 CE2 TYR 15 7.660 -1.530 2.050 1.00 0.00 +ATOM 269 HE2 TYR 15 7.950 -0.570 2.070 1.00 0.00 +ATOM 270 CD2 TYR 15 6.980 -2.050 0.950 1.00 0.00 +ATOM 271 HD2 TYR 15 6.790 -1.440 0.180 1.00 0.00 +ATOM 272 C TYR 15 3.560 -3.330 0.460 1.00 0.00 +ATOM 273 O TYR 15 3.300 -2.420 -0.340 1.00 0.00 +ATOM 274 N TYR 16 3.140 -3.350 1.720 1.00 0.00 +ATOM 275 H TYR 16 3.410 -4.080 2.340 1.00 0.00 +ATOM 276 CA TYR 16 2.190 -2.190 2.190 1.00 0.00 +ATOM 277 HA TYR 16 1.970 -1.460 1.550 1.00 0.00 +ATOM 278 CB TYR 16 0.750 -2.580 2.560 1.00 0.00 +ATOM 279 HB1 TYR 16 0.290 -1.800 2.990 1.00 0.00 +ATOM 280 HB2 TYR 16 0.760 -3.350 3.200 1.00 0.00 +ATOM 281 CG TYR 16 0.000 -2.990 1.310 1.00 0.00 +ATOM 282 CD1 TYR 16 -0.670 -2.030 0.530 1.00 0.00 +ATOM 283 HD1 TYR 16 -0.670 -1.080 0.810 1.00 0.00 +ATOM 284 CE1 TYR 16 -1.330 -2.420 -0.640 1.00 0.00 +ATOM 285 HE1 TYR 16 -1.820 -1.750 -1.200 1.00 0.00 +ATOM 286 CZ TYR 16 -1.300 -3.750 -1.000 1.00 0.00 +ATOM 287 OH TYR 16 -1.900 -4.240 -2.140 1.00 0.00 +ATOM 288 HH TYR 16 -1.740 -5.230 -2.190 1.00 0.00 +ATOM 289 CE2 TYR 16 -0.630 -4.680 -0.240 1.00 0.00 +ATOM 290 HE2 TYR 16 -0.630 -5.640 -0.520 1.00 0.00 +ATOM 291 CD2 TYR 16 0.040 -4.310 0.920 1.00 0.00 +ATOM 292 HD2 TYR 16 0.530 -4.990 1.460 1.00 0.00 +ATOM 293 C TYR 16 3.020 -1.730 3.260 1.00 0.00 +ATOM 294 OC1 TYR 16 3.450 -0.480 3.230 1.00 0.00 +ATOM 295 OC2 TYR 16 3.280 -2.540 4.160 1.00 0.00 +TER +ENDMDL
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reference_structure.pdb Thu Jun 06 07:09:14 2024 +0000 @@ -0,0 +1,295 @@ +ATOM 1 N ARG A 1 4.345 0.094 -2.471 1.00 0.00 N +ATOM 2 CA ARG A 1 4.715 1.455 -2.099 1.00 0.00 C +ATOM 3 C ARG A 1 3.639 2.103 -1.238 1.00 0.00 C +ATOM 4 O ARG A 1 2.990 3.062 -1.655 1.00 0.00 O +ATOM 5 CB ARG A 1 4.948 2.305 -3.340 1.00 0.00 C +ATOM 6 CG ARG A 1 6.134 1.882 -4.191 1.00 0.00 C +ATOM 7 CD ARG A 1 6.340 2.800 -5.341 1.00 0.00 C +ATOM 8 NE ARG A 1 7.480 2.406 -6.153 1.00 0.00 N +ATOM 9 CZ ARG A 1 7.941 3.099 -7.212 1.00 0.00 C +ATOM 10 NH1 ARG A 1 7.349 4.215 -7.575 1.00 0.00 N1+ +ATOM 11 NH2 ARG A 1 8.987 2.656 -7.887 1.00 0.00 N +ATOM 12 H1 ARG A 1 5.067 -0.306 -3.035 1.00 0.00 H +ATOM 13 H2 ARG A 1 4.223 -0.456 -1.646 1.00 0.00 H +ATOM 14 H3 ARG A 1 3.489 0.111 -2.989 1.00 0.00 H +ATOM 15 HA ARG A 1 5.642 1.416 -1.526 1.00 0.00 H +ATOM 16 HB2 ARG A 1 4.061 2.275 -3.972 1.00 0.00 H +ATOM 17 HB3 ARG A 1 5.106 3.342 -3.045 1.00 0.00 H +ATOM 18 HG2 ARG A 1 7.039 1.887 -3.583 1.00 0.00 H +ATOM 19 HG3 ARG A 1 5.964 0.878 -4.581 1.00 0.00 H +ATOM 20 HD2 ARG A 1 5.453 2.794 -5.974 1.00 0.00 H +ATOM 21 HD3 ARG A 1 6.516 3.810 -4.973 1.00 0.00 H +ATOM 22 HE ARG A 1 7.961 1.552 -5.904 1.00 0.00 H +ATOM 23 HH11 ARG A 1 6.549 4.554 -7.059 1.00 0.00 H +ATOM 24 HH12 ARG A 1 7.694 4.735 -8.369 1.00 0.00 H +ATOM 25 HH21 ARG A 1 9.442 1.797 -7.608 1.00 0.00 H +ATOM 26 HH22 ARG A 1 9.332 3.175 -8.681 1.00 0.00 H +ATOM 27 N HIS A 2 3.454 1.573 -0.033 1.00 0.00 N +ATOM 28 CA HIS A 2 2.481 2.121 0.904 1.00 0.00 C +ATOM 29 C HIS A 2 3.154 2.584 2.190 1.00 0.00 C +ATOM 30 O HIS A 2 2.600 3.391 2.936 1.00 0.00 O +ATOM 31 CB HIS A 2 1.401 1.085 1.230 1.00 0.00 C +ATOM 32 CG HIS A 2 0.648 0.602 0.029 1.00 0.00 C +ATOM 33 ND1 HIS A 2 -0.190 1.418 -0.701 1.00 0.00 N +ATOM 34 CD2 HIS A 2 0.606 -0.612 -0.568 1.00 0.00 C +ATOM 35 CE1 HIS A 2 -0.715 0.726 -1.697 1.00 0.00 C +ATOM 36 NE2 HIS A 2 -0.248 -0.508 -1.638 1.00 0.00 N +ATOM 37 H HIS A 2 4.002 0.770 0.241 1.00 0.00 H +ATOM 38 HA HIS A 2 1.994 2.987 0.457 1.00 0.00 H +ATOM 39 HB2 HIS A 2 1.859 0.223 1.716 1.00 0.00 H +ATOM 40 HB3 HIS A 2 0.685 1.514 1.931 1.00 0.00 H +ATOM 41 HD1 HIS A 2 -0.325 2.400 -0.565 1.00 0.00 H +ATOM 42 HD2 HIS A 2 1.096 -1.562 -0.350 1.00 0.00 H +ATOM 43 HE1 HIS A 2 -1.408 1.195 -2.395 1.00 0.00 H +ATOM 44 N TYR A 3 4.352 2.068 2.443 1.00 0.00 N +ATOM 45 CA TYR A 3 5.068 2.364 3.679 1.00 0.00 C +ATOM 46 C TYR A 3 6.428 2.985 3.391 1.00 0.00 C +ATOM 47 O TYR A 3 7.018 2.751 2.336 1.00 0.00 O +ATOM 48 CB TYR A 3 5.230 1.096 4.520 1.00 0.00 C +ATOM 49 CG TYR A 3 3.919 0.453 4.915 1.00 0.00 C +ATOM 50 CD1 TYR A 3 3.318 -0.470 4.071 1.00 0.00 C +ATOM 51 CD2 TYR A 3 3.319 0.786 6.120 1.00 0.00 C +ATOM 52 CE1 TYR A 3 2.121 -1.057 4.432 1.00 0.00 C +ATOM 53 CE2 TYR A 3 2.121 0.198 6.480 1.00 0.00 C +ATOM 54 CZ TYR A 3 1.523 -0.720 5.641 1.00 0.00 C +ATOM 55 OH TYR A 3 0.331 -1.305 6.000 1.00 0.00 O +ATOM 56 H TYR A 3 4.777 1.454 1.763 1.00 0.00 H +ATOM 57 HA TYR A 3 4.487 3.089 4.249 1.00 0.00 H +ATOM 58 HB2 TYR A 3 5.816 0.363 3.964 1.00 0.00 H +ATOM 59 HB3 TYR A 3 5.781 1.332 5.430 1.00 0.00 H +ATOM 60 HD1 TYR A 3 3.790 -0.731 3.124 1.00 0.00 H +ATOM 61 HD2 TYR A 3 3.791 1.511 6.782 1.00 0.00 H +ATOM 62 HE1 TYR A 3 1.648 -1.782 3.769 1.00 0.00 H +ATOM 63 HE2 TYR A 3 1.649 0.460 7.427 1.00 0.00 H +ATOM 64 HH TYR A 3 0.053 -0.965 6.854 1.00 0.00 H +ATOM 65 N TYR A 4 6.922 3.778 4.335 1.00 0.00 N +ATOM 66 CA TYR A 4 8.238 4.393 4.209 1.00 0.00 C +ATOM 67 C TYR A 4 9.228 3.784 5.193 1.00 0.00 C +ATOM 68 O TYR A 4 8.845 3.321 6.268 1.00 0.00 O +ATOM 69 CB TYR A 4 8.145 5.906 4.418 1.00 0.00 C +ATOM 70 CG TYR A 4 7.441 6.635 3.296 1.00 0.00 C +ATOM 71 CD1 TYR A 4 6.067 6.822 3.344 1.00 0.00 C +ATOM 72 CD2 TYR A 4 8.168 7.117 2.218 1.00 0.00 C +ATOM 73 CE1 TYR A 4 5.424 7.488 2.319 1.00 0.00 C +ATOM 74 CE2 TYR A 4 7.525 7.783 1.193 1.00 0.00 C +ATOM 75 CZ TYR A 4 6.159 7.969 1.241 1.00 0.00 C +ATOM 76 OH TYR A 4 5.518 8.633 0.220 1.00 0.00 O +ATOM 77 H TYR A 4 6.372 3.960 5.163 1.00 0.00 H +ATOM 78 HA TYR A 4 8.614 4.203 3.203 1.00 0.00 H +ATOM 79 HB2 TYR A 4 7.611 6.113 5.347 1.00 0.00 H +ATOM 80 HB3 TYR A 4 9.147 6.322 4.518 1.00 0.00 H +ATOM 81 HD1 TYR A 4 5.495 6.443 4.192 1.00 0.00 H +ATOM 82 HD2 TYR A 4 9.248 6.969 2.179 1.00 0.00 H +ATOM 83 HE1 TYR A 4 4.345 7.635 2.357 1.00 0.00 H +ATOM 84 HE2 TYR A 4 8.097 8.161 0.345 1.00 0.00 H +ATOM 85 HH TYR A 4 6.073 8.625 -0.563 1.00 0.00 H +ATOM 86 N LYS A 5 10.503 3.786 4.821 1.00 0.00 N +ATOM 87 CA LYS A 5 11.578 3.499 5.763 1.00 0.00 C +ATOM 88 C LYS A 5 12.476 4.713 5.961 1.00 0.00 C +ATOM 89 O LYS A 5 12.580 5.570 5.083 1.00 0.00 O +ATOM 90 CB LYS A 5 12.405 2.304 5.285 1.00 0.00 C +ATOM 91 CG LYS A 5 11.626 1.000 5.184 1.00 0.00 C +ATOM 92 CD LYS A 5 11.188 0.510 6.556 1.00 0.00 C +ATOM 93 CE LYS A 5 10.523 -0.857 6.470 1.00 0.00 C +ATOM 94 NZ LYS A 5 10.057 -1.333 7.801 1.00 0.00 N1+ +ATOM 95 H LYS A 5 10.735 3.992 3.859 1.00 0.00 H +ATOM 96 HA LYS A 5 11.134 3.252 6.729 1.00 0.00 H +ATOM 97 HB2 LYS A 5 12.823 2.522 4.302 1.00 0.00 H +ATOM 98 HB3 LYS A 5 13.240 2.143 5.968 1.00 0.00 H +ATOM 99 HG2 LYS A 5 10.743 1.151 4.562 1.00 0.00 H +ATOM 100 HG3 LYS A 5 12.251 0.238 4.718 1.00 0.00 H +ATOM 101 HD2 LYS A 5 12.056 0.442 7.213 1.00 0.00 H +ATOM 102 HD3 LYS A 5 10.482 1.219 6.987 1.00 0.00 H +ATOM 103 HE2 LYS A 5 9.669 -0.804 5.797 1.00 0.00 H +ATOM 104 HE3 LYS A 5 11.231 -1.581 6.067 1.00 0.00 H +ATOM 105 HZ1 LYS A 5 9.624 -2.240 7.701 1.00 0.00 H +ATOM 106 HZ2 LYS A 5 10.846 -1.404 8.429 1.00 0.00 H +ATOM 107 HZ3 LYS A 5 9.386 -0.679 8.177 1.00 0.00 H +ATOM 108 N PHE A 6 13.124 4.781 7.119 1.00 0.00 N +ATOM 109 CA PHE A 6 14.005 5.897 7.440 1.00 0.00 C +ATOM 110 C PHE A 6 15.391 5.696 6.839 1.00 0.00 C +ATOM 111 O PHE A 6 16.023 4.660 7.047 1.00 0.00 O +ATOM 112 CB PHE A 6 14.121 6.068 8.955 1.00 0.00 C +ATOM 113 CG PHE A 6 14.990 7.221 9.370 1.00 0.00 C +ATOM 114 CD1 PHE A 6 14.558 8.529 9.206 1.00 0.00 C +ATOM 115 CD2 PHE A 6 16.242 7.001 9.925 1.00 0.00 C +ATOM 116 CE1 PHE A 6 15.357 9.590 9.587 1.00 0.00 C +ATOM 117 CE2 PHE A 6 17.042 8.060 10.308 1.00 0.00 C +ATOM 118 CZ PHE A 6 16.599 9.356 10.139 1.00 0.00 C +ATOM 119 H PHE A 6 13.004 4.040 7.795 1.00 0.00 H +ATOM 120 HA PHE A 6 13.578 6.808 7.017 1.00 0.00 H +ATOM 121 HB2 PHE A 6 13.130 6.219 9.381 1.00 0.00 H +ATOM 122 HB3 PHE A 6 14.530 5.159 9.394 1.00 0.00 H +ATOM 123 HD1 PHE A 6 13.575 8.714 8.771 1.00 0.00 H +ATOM 124 HD2 PHE A 6 16.592 5.977 10.059 1.00 0.00 H +ATOM 125 HE1 PHE A 6 15.005 10.613 9.452 1.00 0.00 H +ATOM 126 HE2 PHE A 6 18.023 7.873 10.744 1.00 0.00 H +ATOM 127 HZ PHE A 6 17.229 10.192 10.438 1.00 0.00 H +ATOM 128 N ASN A 7 15.857 6.692 6.094 1.00 0.00 N +ATOM 129 CA ASN A 7 17.195 6.654 5.515 1.00 0.00 C +ATOM 130 C ASN A 7 18.218 7.288 6.449 1.00 0.00 C +ATOM 131 O ASN A 7 17.883 8.159 7.252 1.00 0.00 O +ATOM 132 CB ASN A 7 17.211 7.340 4.161 1.00 0.00 C +ATOM 133 CG ASN A 7 18.447 7.022 3.366 1.00 0.00 C +ATOM 134 OD1 ASN A 7 19.466 7.713 3.477 1.00 0.00 O +ATOM 135 ND2 ASN A 7 18.377 5.988 2.567 1.00 0.00 N +ATOM 136 H ASN A 7 15.270 7.496 5.923 1.00 0.00 H +ATOM 137 HA ASN A 7 17.484 5.611 5.379 1.00 0.00 H +ATOM 138 HB2 ASN A 7 16.335 7.034 3.587 1.00 0.00 H +ATOM 139 HB3 ASN A 7 17.150 8.420 4.300 1.00 0.00 H +ATOM 140 HD21 ASN A 7 19.169 5.729 2.013 1.00 0.00 H +ATOM 141 HD22 ASN A 7 17.532 5.457 2.509 1.00 0.00 H +ATOM 142 N SER A 8 19.466 6.846 6.339 1.00 0.00 N +ATOM 143 CA SER A 8 20.537 7.356 7.187 1.00 0.00 C +ATOM 144 C SER A 8 20.785 8.837 6.930 1.00 0.00 C +ATOM 145 O SER A 8 21.376 9.530 7.759 1.00 0.00 O +ATOM 146 CB SER A 8 21.811 6.571 6.947 1.00 0.00 C +ATOM 147 OG SER A 8 22.312 6.808 5.660 1.00 0.00 O +ATOM 148 H SER A 8 19.679 6.139 5.650 1.00 0.00 H +ATOM 149 HA SER A 8 20.240 7.235 8.230 1.00 0.00 H +ATOM 150 HB2 SER A 8 22.558 6.854 7.689 1.00 0.00 H +ATOM 151 HB3 SER A 8 21.613 5.508 7.073 1.00 0.00 H +ATOM 152 HG SER A 8 22.103 7.723 5.459 1.00 0.00 H +ATOM 153 N THR A 9 20.331 9.317 5.778 1.00 0.00 N +ATOM 154 CA THR A 9 20.520 10.712 5.401 1.00 0.00 C +ATOM 155 C THR A 9 19.485 11.608 6.070 1.00 0.00 C +ATOM 156 O THR A 9 19.589 12.834 6.024 1.00 0.00 O +ATOM 157 CB THR A 9 20.446 10.889 3.873 1.00 0.00 C +ATOM 158 OG1 THR A 9 19.184 10.407 3.394 1.00 0.00 O +ATOM 159 CG2 THR A 9 21.570 10.122 3.193 1.00 0.00 C +ATOM 160 H THR A 9 19.842 8.698 5.146 1.00 0.00 H +ATOM 161 HA THR A 9 21.507 11.031 5.736 1.00 0.00 H +ATOM 162 HB THR A 9 20.534 11.947 3.624 1.00 0.00 H +ATOM 163 HG1 THR A 9 19.188 9.447 3.394 1.00 0.00 H +ATOM 164 HG21 THR A 9 21.502 10.258 2.114 1.00 0.00 H +ATOM 165 HG22 THR A 9 22.531 10.494 3.547 1.00 0.00 H +ATOM 166 HG23 THR A 9 21.481 9.062 3.430 1.00 0.00 H +ATOM 167 N GLY A 10 18.487 10.989 6.691 1.00 0.00 N +ATOM 168 CA GLY A 10 17.366 11.725 7.262 1.00 0.00 C +ATOM 169 C GLY A 10 16.170 11.726 6.319 1.00 0.00 C +ATOM 170 O GLY A 10 15.068 12.122 6.698 1.00 0.00 O +ATOM 171 H GLY A 10 18.506 9.982 6.770 1.00 0.00 H +ATOM 172 HA2 GLY A 10 17.082 11.276 8.214 1.00 0.00 H +ATOM 173 HA3 GLY A 10 17.671 12.750 7.469 1.00 0.00 H +ATOM 174 N ARG A 11 16.394 11.279 5.087 1.00 0.00 N +ATOM 175 CA ARG A 11 15.324 11.181 4.102 1.00 0.00 C +ATOM 176 C ARG A 11 14.483 9.930 4.324 1.00 0.00 C +ATOM 177 O ARG A 11 14.830 9.074 5.138 1.00 0.00 O +ATOM 178 CB ARG A 11 15.895 11.161 2.692 1.00 0.00 C +ATOM 179 CG ARG A 11 16.617 12.433 2.275 1.00 0.00 C +ATOM 180 CD ARG A 11 17.151 12.334 0.893 1.00 0.00 C +ATOM 181 NE ARG A 11 18.229 11.363 0.796 1.00 0.00 N +ATOM 182 CZ ARG A 11 18.770 10.933 -0.360 1.00 0.00 C +ATOM 183 NH1 ARG A 11 18.324 11.397 -1.507 1.00 0.00 N1+ +ATOM 184 NH2 ARG A 11 19.750 10.046 -0.342 1.00 0.00 N +ATOM 185 H ARG A 11 17.329 11.001 4.828 1.00 0.00 H +ATOM 186 HA ARG A 11 14.679 12.055 4.203 1.00 0.00 H +ATOM 187 HB2 ARG A 11 16.600 10.336 2.597 1.00 0.00 H +ATOM 188 HB3 ARG A 11 15.091 10.988 1.976 1.00 0.00 H +ATOM 189 HG2 ARG A 11 15.924 13.274 2.316 1.00 0.00 H +ATOM 190 HG3 ARG A 11 17.451 12.616 2.953 1.00 0.00 H +ATOM 191 HD2 ARG A 11 16.354 12.026 0.216 1.00 0.00 H +ATOM 192 HD3 ARG A 11 17.537 13.304 0.582 1.00 0.00 H +ATOM 193 HE ARG A 11 18.599 10.983 1.658 1.00 0.00 H +ATOM 194 HH11 ARG A 11 17.576 12.075 -1.521 1.00 0.00 H +ATOM 195 HH12 ARG A 11 18.730 11.075 -2.374 1.00 0.00 H +ATOM 196 HH21 ARG A 11 20.093 9.690 0.540 1.00 0.00 H +ATOM 197 HH22 ARG A 11 20.155 9.724 -1.208 1.00 0.00 H +ATOM 198 N HIS A 12 13.377 9.830 3.595 1.00 0.00 N +ATOM 199 CA HIS A 12 12.542 8.635 3.630 1.00 0.00 C +ATOM 200 C HIS A 12 12.375 8.039 2.238 1.00 0.00 C +ATOM 201 O HIS A 12 12.457 8.749 1.235 1.00 0.00 O +ATOM 202 CB HIS A 12 11.166 8.952 4.224 1.00 0.00 C +ATOM 203 CG HIS A 12 11.203 9.277 5.685 1.00 0.00 C +ATOM 204 ND1 HIS A 12 11.572 10.517 6.162 1.00 0.00 N +ATOM 205 CD2 HIS A 12 10.917 8.524 6.774 1.00 0.00 C +ATOM 206 CE1 HIS A 12 11.511 10.513 7.483 1.00 0.00 C +ATOM 207 NE2 HIS A 12 11.117 9.316 7.878 1.00 0.00 N +ATOM 208 H HIS A 12 13.106 10.602 3.002 1.00 0.00 H +ATOM 209 HA HIS A 12 13.015 7.879 4.257 1.00 0.00 H +ATOM 210 HB2 HIS A 12 10.729 9.800 3.697 1.00 0.00 H +ATOM 211 HB3 HIS A 12 10.503 8.100 4.081 1.00 0.00 H +ATOM 212 HD2 HIS A 12 10.591 7.484 6.774 1.00 0.00 H +ATOM 213 HE1 HIS A 12 11.745 11.354 8.134 1.00 0.00 H +ATOM 214 N TYR A 13 12.141 6.733 2.183 1.00 0.00 N +ATOM 215 CA TYR A 13 11.932 6.044 0.915 1.00 0.00 C +ATOM 216 C TYR A 13 10.941 4.897 1.067 1.00 0.00 C +ATOM 217 O TYR A 13 10.763 4.360 2.160 1.00 0.00 O +ATOM 218 CB TYR A 13 13.261 5.527 0.361 1.00 0.00 C +ATOM 219 CG TYR A 13 13.936 4.505 1.249 1.00 0.00 C +ATOM 220 CD1 TYR A 13 13.804 3.152 0.973 1.00 0.00 C +ATOM 221 CD2 TYR A 13 14.687 4.921 2.338 1.00 0.00 C +ATOM 222 CE1 TYR A 13 14.420 2.219 1.784 1.00 0.00 C +ATOM 223 CE2 TYR A 13 15.303 3.988 3.149 1.00 0.00 C +ATOM 224 CZ TYR A 13 15.172 2.642 2.875 1.00 0.00 C +ATOM 225 OH TYR A 13 15.786 1.712 3.682 1.00 0.00 O +ATOM 226 H TYR A 13 12.106 6.203 3.042 1.00 0.00 H +ATOM 227 HA TYR A 13 11.509 6.753 0.202 1.00 0.00 H +ATOM 228 HB2 TYR A 13 13.096 5.073 -0.617 1.00 0.00 H +ATOM 229 HB3 TYR A 13 13.947 6.363 0.222 1.00 0.00 H +ATOM 230 HD1 TYR A 13 13.214 2.825 0.117 1.00 0.00 H +ATOM 231 HD2 TYR A 13 14.790 5.984 2.555 1.00 0.00 H +ATOM 232 HE1 TYR A 13 14.317 1.156 1.567 1.00 0.00 H +ATOM 233 HE2 TYR A 13 15.893 4.314 4.006 1.00 0.00 H +ATOM 234 HH TYR A 13 16.252 2.163 4.390 1.00 0.00 H +ATOM 235 N HIS A 14 10.299 4.526 -0.035 1.00 0.00 N +ATOM 236 CA HIS A 14 9.377 3.397 -0.041 1.00 0.00 C +ATOM 237 C HIS A 14 10.125 2.074 0.062 1.00 0.00 C +ATOM 238 O HIS A 14 11.204 1.914 -0.509 1.00 0.00 O +ATOM 239 CB HIS A 14 8.517 3.407 -1.310 1.00 0.00 C +ATOM 240 CG HIS A 14 7.361 4.356 -1.246 1.00 0.00 C +ATOM 241 ND1 HIS A 14 6.396 4.286 -0.263 1.00 0.00 N +ATOM 242 CD2 HIS A 14 7.015 5.395 -2.041 1.00 0.00 C +ATOM 243 CE1 HIS A 14 5.505 5.243 -0.458 1.00 0.00 C +ATOM 244 NE2 HIS A 14 5.858 5.929 -1.530 1.00 0.00 N +ATOM 245 H HIS A 14 10.454 5.039 -0.891 1.00 0.00 H +ATOM 246 HA HIS A 14 8.711 3.467 0.818 1.00 0.00 H +ATOM 247 HB2 HIS A 14 9.135 3.679 -2.166 1.00 0.00 H +ATOM 248 HB3 HIS A 14 8.128 2.406 -1.493 1.00 0.00 H +ATOM 249 HD2 HIS A 14 7.467 5.827 -2.934 1.00 0.00 H +ATOM 250 HE1 HIS A 14 4.657 5.358 0.217 1.00 0.00 H +ATOM 251 N TYR A 15 9.545 1.128 0.792 1.00 0.00 N +ATOM 252 CA TYR A 15 10.069 -0.232 0.840 1.00 0.00 C +ATOM 253 C TYR A 15 8.971 -1.255 0.581 1.00 0.00 C +ATOM 254 O TYR A 15 9.074 -2.073 -0.333 1.00 0.00 O +ATOM 255 CB TYR A 15 10.737 -0.501 2.191 1.00 0.00 C +ATOM 256 CG TYR A 15 11.506 -1.803 2.243 1.00 0.00 C +ATOM 257 CD1 TYR A 15 12.641 -1.969 1.464 1.00 0.00 C +ATOM 258 CD2 TYR A 15 11.075 -2.830 3.070 1.00 0.00 C +ATOM 259 CE1 TYR A 15 13.344 -3.158 1.512 1.00 0.00 C +ATOM 260 CE2 TYR A 15 11.777 -4.018 3.117 1.00 0.00 C +ATOM 261 CZ TYR A 15 12.907 -4.184 2.343 1.00 0.00 C +ATOM 262 OH TYR A 15 13.607 -5.368 2.390 1.00 0.00 O +ATOM 263 H TYR A 15 8.720 1.356 1.328 1.00 0.00 H +ATOM 264 HA TYR A 15 10.816 -0.343 0.054 1.00 0.00 H +ATOM 265 HB2 TYR A 15 11.426 0.311 2.424 1.00 0.00 H +ATOM 266 HB3 TYR A 15 9.979 -0.522 2.973 1.00 0.00 H +ATOM 267 HD1 TYR A 15 12.980 -1.162 0.814 1.00 0.00 H +ATOM 268 HD2 TYR A 15 10.182 -2.699 3.681 1.00 0.00 H +ATOM 269 HE1 TYR A 15 14.236 -3.289 0.900 1.00 0.00 H +ATOM 270 HE2 TYR A 15 11.438 -4.826 3.767 1.00 0.00 H +ATOM 271 HH TYR A 15 14.359 -5.318 1.796 1.00 0.00 H +ATOM 272 N TYR A 16 7.918 -1.204 1.391 1.00 0.00 N +ATOM 273 CA TYR A 16 6.737 -2.027 1.164 1.00 0.00 C +ATOM 274 C TYR A 16 5.672 -1.262 0.389 1.00 0.00 C +ATOM 275 O TYR A 16 5.762 -1.149 -0.802 1.00 0.00 O +ATOM 276 CB TYR A 16 6.168 -2.526 2.495 1.00 0.00 C +ATOM 277 CG TYR A 16 7.070 -3.502 3.217 1.00 0.00 C +ATOM 278 CD1 TYR A 16 7.534 -3.207 4.491 1.00 0.00 C +ATOM 279 CD2 TYR A 16 7.434 -4.692 2.605 1.00 0.00 C +ATOM 280 CE1 TYR A 16 8.358 -4.099 5.150 1.00 0.00 C +ATOM 281 CE2 TYR A 16 8.258 -5.584 3.264 1.00 0.00 C +ATOM 282 CZ TYR A 16 8.719 -5.291 4.531 1.00 0.00 C +ATOM 283 OH TYR A 16 9.539 -6.179 5.187 1.00 0.00 O +ATOM 284 OXT TYR A 16 4.744 -0.771 0.970 1.00 0.00 O1- +ATOM 285 H TYR A 16 7.938 -0.579 2.184 1.00 0.00 H +ATOM 286 HA TYR A 16 7.026 -2.890 0.564 1.00 0.00 H +ATOM 287 HB2 TYR A 16 5.989 -1.676 3.155 1.00 0.00 H +ATOM 288 HB3 TYR A 16 5.209 -3.013 2.321 1.00 0.00 H +ATOM 289 HD1 TYR A 16 7.248 -2.272 4.972 1.00 0.00 H +ATOM 290 HD2 TYR A 16 7.071 -4.924 1.603 1.00 0.00 H +ATOM 291 HE1 TYR A 16 8.722 -3.868 6.150 1.00 0.00 H +ATOM 292 HE2 TYR A 16 8.544 -6.520 2.782 1.00 0.00 H +ATOM 293 HH TYR A 16 9.705 -6.938 4.622 1.00 0.00 H +TER 294 TYR A 16 +END