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[WIP] Molecule.from_pdb #1105

Merged
merged 29 commits into from
Oct 27, 2021
Merged

[WIP] Molecule.from_pdb #1105

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2867d96
Ability to get a networkx graph from an rdmol.
ijpulidos Sep 14, 2021
ce79263
Substructure file path as a keyword argument for perceiving residues.
ijpulidos Sep 14, 2021
4940b8d
Clarifying default behavior in docstring.
ijpulidos Sep 14, 2021
6552d16
Adding failing prototype to build networkx from openmm topology.
ijpulidos Sep 16, 2021
7f8b3b9
Changes and comments on getting networkx graph from molecule.
ijpulidos Sep 16, 2021
36e5552
monkey-patching problems with Proline (PRO). Sane indent defaults.
ijpulidos Oct 7, 2021
0645650
Make substructures scripts.
ijpulidos Oct 7, 2021
187063d
merge with topology-biopolyer-refactor and resolve conflicts
ijpulidos Oct 7, 2021
b17ede8
Prototype of from_pdb and substructure dict methods
ijpulidos Oct 7, 2021
5e5f42a
Making improved substructure libraries. Unspecified bond order instea…
ijpulidos Oct 13, 2021
930d909
add tests for nterm/cterm/mainchain ala, small fixes to molecule from…
j-wags Oct 18, 2021
767c092
Creating test class for PDB reading. Adding simple tests.
ijpulidos Oct 18, 2021
dc493ec
Using openff Molecule instead of RDkit's
ijpulidos Oct 18, 2021
bbb1e5d
Restructuring changes to use a separate class for from_pdb functional…
ijpulidos Oct 18, 2021
ef1807f
recursively remove leaving atoms one at a time, add peptide bond smarts
j-wags Oct 19, 2021
7554a15
update metadata assignment dict
j-wags Oct 19, 2021
17a8ef7
update substructure dicts to filter out N-, add tests and test files
j-wags Oct 19, 2021
7436972
lots of new monkey patches for weird HIS and TRP formal charges, test…
j-wags Oct 21, 2021
5fd1a6f
update tests now that caps are correctly identified
j-wags Oct 25, 2021
354cc76
Cleaning up Molecule.from_pdb, improving performance, extending tests.
j-wags Oct 26, 2021
f425351
Adding metadata to offmol before sanitization. TODO, after sanitization.
ijpulidos Oct 26, 2021
e463d27
solving merge conflicts
ijpulidos Oct 26, 2021
3f63b18
code cleanup and polishing
j-wags Oct 27, 2021
6f6de48
code cleanup and polishing
j-wags Oct 27, 2021
4e6af52
Recover metadata after rdkit sanitization roundtrip.
ijpulidos Oct 27, 2021
fdec5a9
solving merge conflicts
ijpulidos Oct 27, 2021
1fa8079
Fix for tests
j-wags Oct 27, 2021
c713129
Merge branch 'topology-biopolymer-refactor' into molecule-from-pdb-proto
j-wags Oct 27, 2021
1e2ff46
Remove unused tests, remove topology._to_networkx_from_openmm, fix te…
j-wags Oct 27, 2021
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20 changes: 20 additions & 0 deletions openff/toolkit/data/proteins/CTerminal_ALA.pdb
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CRYST1 48.000 48.000 48.000 90.00 90.00 90.00 P 1 1
ATOM 1 H1 ACE 1 25.899 25.081 24.293 1.00 0.00 H
ATOM 2 CH3 ACE 1 25.959 26.144 24.068 1.00 0.00 C
ATOM 3 H2 ACE 1 25.400 26.714 24.808 1.00 0.00 H
ATOM 4 H3 ACE 1 25.562 26.339 23.074 1.00 0.00 H
ATOM 5 C ACE 1 27.407 26.576 24.111 1.00 0.00 C
ATOM 6 O ACE 1 28.276 25.747 24.363 1.00 0.00 O
ATOM 7 N ALA 2 27.635 27.864 23.859 1.00 0.00 N
ATOM 8 H ALA 2 26.848 28.480 23.702 1.00 0.00 H
ATOM 9 CA ALA 2 28.912 28.579 23.914 1.00 0.00 C
ATOM 10 HA ALA 2 29.492 28.233 24.769 1.00 0.00 H
ATOM 11 CB ALA 2 29.700 28.309 22.623 1.00 0.00 C
ATOM 12 HB1 ALA 2 29.128 28.663 21.764 1.00 0.00 H
ATOM 13 HB2 ALA 2 30.648 28.848 22.665 1.00 0.00 H
ATOM 14 HB3 ALA 2 29.896 27.242 22.523 1.00 0.00 H
ATOM 15 C ALA 2 28.655 30.084 24.123 1.00 0.00 C
ATOM 16 O ALA 2 27.512 30.510 23.830 1.00 0.00 O
ATOM 17 OXT ALA 2 29.596 30.766 24.578 1.00 0.00 O
TER 18 ALA 2
END
30 changes: 30 additions & 0 deletions openff/toolkit/data/proteins/CTerminal_ALA_ALA.pdb
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CRYST1 48.000 48.000 48.000 90.00 90.00 90.00 P 1 1
ATOM 1 H1 ACE 1 25.966 25.121 24.502 1.00 0.00 H
ATOM 2 CH3 ACE 1 25.997 26.139 24.116 1.00 0.00 C
ATOM 3 H2 ACE 1 25.359 26.781 24.719 1.00 0.00 H
ATOM 4 H3 ACE 1 25.664 26.150 23.080 1.00 0.00 H
ATOM 5 C ACE 1 27.419 26.645 24.185 1.00 0.00 C
ATOM 6 O ACE 1 28.303 25.921 24.624 1.00 0.00 O
ATOM 7 N ALA 2 27.622 27.886 23.752 1.00 0.00 N
ATOM 8 H ALA 2 26.829 28.428 23.444 1.00 0.00 H
ATOM 9 CA ALA 2 28.899 28.601 23.773 1.00 0.00 C
ATOM 10 HA ALA 2 29.453 28.323 24.671 1.00 0.00 H
ATOM 11 CB ALA 2 29.721 28.191 22.541 1.00 0.00 C
ATOM 12 HB1 ALA 2 29.188 28.466 21.630 1.00 0.00 H
ATOM 13 HB2 ALA 2 30.686 28.700 22.556 1.00 0.00 H
ATOM 14 HB3 ALA 2 29.893 27.114 22.552 1.00 0.00 H
ATOM 15 C ALA 2 28.661 30.124 23.811 1.00 0.00 C
ATOM 16 O ALA 2 27.545 30.578 23.537 1.00 0.00 O
ATOM 17 N ALA 3 29.708 30.883 24.139 1.00 0.00 N
ATOM 18 H ALA 3 30.608 30.446 24.295 1.00 0.00 H
ATOM 19 CA ALA 3 29.780 32.346 24.156 1.00 0.00 C
ATOM 20 HA ALA 3 29.219 32.755 23.317 1.00 0.00 H
ATOM 21 CB ALA 3 29.180 32.867 25.471 1.00 0.00 C
ATOM 22 HB1 ALA 3 29.746 32.471 26.315 1.00 0.00 H
ATOM 23 HB2 ALA 3 29.241 33.956 25.483 1.00 0.00 H
ATOM 24 HB3 ALA 3 28.136 32.565 25.550 1.00 0.00 H
ATOM 25 C ALA 3 31.243 32.793 23.975 1.00 0.00 C
ATOM 26 O ALA 3 32.128 31.938 24.215 1.00 0.00 O
ATOM 27 OXT ALA 3 31.438 33.965 23.590 1.00 0.00 O
TER 28 ALA 3
END
34 changes: 34 additions & 0 deletions openff/toolkit/data/proteins/CTerminal_ARG.pdb
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CRYST1 48.000 48.000 48.000 90.00 90.00 90.00 P 1 1
ATOM 1 H1 ACE 1 25.680 25.183 24.302 1.00 0.00 H
ATOM 2 CH3 ACE 1 25.793 26.253 24.135 1.00 0.00 C
ATOM 3 H2 ACE 1 25.303 26.805 24.935 1.00 0.00 H
ATOM 4 H3 ACE 1 25.358 26.528 23.176 1.00 0.00 H
ATOM 5 C ACE 1 27.265 26.598 24.129 1.00 0.00 C
ATOM 6 O ACE 1 28.098 25.710 24.289 1.00 0.00 O
ATOM 7 N ARG 2 27.568 27.881 23.930 1.00 0.00 N
ATOM 8 H ARG 2 26.816 28.550 23.813 1.00 0.00 H
ATOM 9 CA ARG 2 28.903 28.493 23.972 1.00 0.00 C
ATOM 10 HA ARG 2 29.455 28.107 24.827 1.00 0.00 H
ATOM 11 CB ARG 2 29.661 28.168 22.672 1.00 0.00 C
ATOM 12 HB2 ARG 2 29.792 27.087 22.598 1.00 0.00 H
ATOM 13 HB3 ARG 2 29.079 28.515 21.816 1.00 0.00 H
ATOM 14 CG ARG 2 31.035 28.846 22.657 1.00 0.00 C
ATOM 15 HG2 ARG 2 30.903 29.927 22.595 1.00 0.00 H
ATOM 16 HG3 ARG 2 31.569 28.604 23.578 1.00 0.00 H
ATOM 17 CD ARG 2 31.884 28.419 21.464 1.00 0.00 C
ATOM 18 HD2 ARG 2 32.107 27.354 21.548 1.00 0.00 H
ATOM 19 HD3 ARG 2 31.321 28.601 20.546 1.00 0.00 H
ATOM 20 NE ARG 2 33.131 29.201 21.444 1.00 0.00 N
ATOM 21 HE ARG 2 33.209 29.897 22.169 1.00 0.00 H
ATOM 22 CZ ARG 2 34.112 29.107 20.575 1.00 0.00 C
ATOM 23 NH1 ARG 2 34.087 28.245 19.599 1.00 0.00 N
ATOM 24 HH11 ARG 2 33.285 27.645 19.524 1.00 0.00 H
ATOM 25 HH12 ARG 2 34.839 28.184 18.941 1.00 0.00 H
ATOM 26 NH2 ARG 2 35.148 29.889 20.673 1.00 0.00 N
ATOM 27 HH21 ARG 2 35.182 30.566 21.415 1.00 0.00 H
ATOM 28 HH22 ARG 2 35.897 29.824 20.012 1.00 0.00 H
ATOM 29 C ARG 2 28.778 30.003 24.189 1.00 0.00 C
ATOM 30 O ARG 2 27.747 30.547 23.740 1.00 0.00 O
ATOM 31 OXT ARG 2 29.739 30.566 24.753 1.00 0.00 O
TER 32 ARG 2
END
34 changes: 34 additions & 0 deletions openff/toolkit/data/proteins/CTerminal_TRP.pdb
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CRYST1 48.000 48.000 48.000 90.00 90.00 90.00 P 1 1
ATOM 1 H1 ACE 1 25.876 25.449 25.239 1.00 0.00 H
ATOM 2 CH3 ACE 1 25.947 26.112 24.379 1.00 0.00 C
ATOM 3 H2 ACE 1 25.049 26.722 24.303 1.00 0.00 H
ATOM 4 H3 ACE 1 26.077 25.530 23.469 1.00 0.00 H
ATOM 5 C ACE 1 27.141 27.023 24.558 1.00 0.00 C
ATOM 6 O ACE 1 27.774 26.988 25.608 1.00 0.00 O
ATOM 7 N TRP 2 27.426 27.813 23.523 1.00 0.00 N
ATOM 8 H TRP 2 26.840 27.770 22.701 1.00 0.00 H
ATOM 9 CA TRP 2 28.490 28.817 23.425 1.00 0.00 C
ATOM 10 HA TRP 2 28.580 29.369 24.359 1.00 0.00 H
ATOM 11 CB TRP 2 29.819 28.113 23.111 1.00 0.00 C
ATOM 12 HB2 TRP 2 30.048 27.421 23.923 1.00 0.00 H
ATOM 13 HB3 TRP 2 29.692 27.527 22.200 1.00 0.00 H
ATOM 14 CG TRP 2 30.998 29.018 22.926 1.00 0.00 C
ATOM 15 CD1 TRP 2 31.383 29.550 21.746 1.00 0.00 C
ATOM 16 HD1 TRP 2 30.856 29.386 20.814 1.00 0.00 H
ATOM 17 NE1 TRP 2 32.473 30.377 21.937 1.00 0.00 N
ATOM 18 HE1 TRP 2 32.872 30.935 21.199 1.00 0.00 H
ATOM 19 CE2 TRP 2 32.831 30.439 23.267 1.00 0.00 C
ATOM 20 CZ2 TRP 2 33.827 31.146 23.959 1.00 0.00 C
ATOM 21 HZ2 TRP 2 34.506 31.790 23.423 1.00 0.00 H
ATOM 22 CH2 TRP 2 33.912 31.018 25.356 1.00 0.00 C
ATOM 23 HH2 TRP 2 34.665 31.564 25.906 1.00 0.00 H
ATOM 24 CZ3 TRP 2 33.000 30.194 26.041 1.00 0.00 C
ATOM 25 HZ3 TRP 2 33.052 30.111 27.116 1.00 0.00 H
ATOM 26 CE3 TRP 2 32.002 29.491 25.335 1.00 0.00 C
ATOM 27 HE3 TRP 2 31.287 28.879 25.866 1.00 0.00 H
ATOM 28 CD2 TRP 2 31.896 29.587 23.930 1.00 0.00 C
ATOM 29 C TRP 2 28.117 29.831 22.334 1.00 0.00 C
ATOM 30 O TRP 2 27.672 29.360 21.261 1.00 0.00 O
ATOM 31 OXT TRP 2 28.233 31.045 22.604 1.00 0.00 O
TER 32 TRP 2
END
25 changes: 25 additions & 0 deletions openff/toolkit/data/proteins/MainChain_ALA.pdb
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CRYST1 48.000 48.000 48.000 90.00 90.00 90.00 P 1 1
ATOM 1 H1 ACE 1 25.950 25.179 24.582 1.00 0.00 H
ATOM 2 CH3 ACE 1 25.986 26.176 24.145 1.00 0.00 C
ATOM 3 H2 ACE 1 25.332 26.843 24.703 1.00 0.00 H
ATOM 4 H3 ACE 1 25.673 26.131 23.104 1.00 0.00 H
ATOM 5 C ACE 1 27.405 26.691 24.218 1.00 0.00 C
ATOM 6 O ACE 1 28.285 25.999 24.713 1.00 0.00 O
ATOM 7 N ALA 2 27.621 27.909 23.728 1.00 0.00 N
ATOM 8 H ALA 2 26.838 28.435 23.370 1.00 0.00 H
ATOM 9 CA ALA 2 28.916 28.589 23.730 1.00 0.00 C
ATOM 10 HA ALA 2 29.471 28.288 24.620 1.00 0.00 H
ATOM 11 CB ALA 2 29.710 28.153 22.489 1.00 0.00 C
ATOM 12 HB1 ALA 2 29.172 28.440 21.584 1.00 0.00 H
ATOM 13 HB2 ALA 2 30.691 28.627 22.488 1.00 0.00 H
ATOM 14 HB3 ALA 2 29.844 27.070 22.499 1.00 0.00 H
ATOM 15 C ALA 2 28.737 30.119 23.778 1.00 0.00 C
ATOM 16 O ALA 2 27.675 30.634 23.429 1.00 0.00 O
ATOM 17 N NME 3 29.784 30.841 24.197 1.00 0.00 N
ATOM 18 H NME 3 30.622 30.348 24.461 1.00 0.00 H
ATOM 19 CH3 NME 3 29.784 32.300 24.293 1.00 0.00 C
ATOM 20 HH31 NME 3 28.951 32.628 24.918 1.00 0.00 H
ATOM 21 HH32 NME 3 30.720 32.652 24.729 1.00 0.00 H
ATOM 22 HH33 NME 3 29.663 32.734 23.299 1.00 0.00 H
TER 23 NME 3
END
35 changes: 35 additions & 0 deletions openff/toolkit/data/proteins/MainChain_ALA_ALA.pdb
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CRYST1 48.000 48.000 48.000 90.00 90.00 90.00 P 1 1
ATOM 1 H1 ACE 1 25.898 25.204 24.465 1.00 0.00 H
ATOM 2 CH3 ACE 1 25.965 26.197 24.023 1.00 0.00 C
ATOM 3 H2 ACE 1 25.276 26.871 24.530 1.00 0.00 H
ATOM 4 H3 ACE 1 25.721 26.143 22.963 1.00 0.00 H
ATOM 5 C ACE 1 27.376 26.711 24.184 1.00 0.00 C
ATOM 6 O ACE 1 28.219 26.023 24.745 1.00 0.00 O
ATOM 7 N ALA 2 27.627 27.923 23.696 1.00 0.00 N
ATOM 8 H ALA 2 26.870 28.444 23.279 1.00 0.00 H
ATOM 9 CA ALA 2 28.919 28.605 23.776 1.00 0.00 C
ATOM 10 HA ALA 2 29.414 28.316 24.706 1.00 0.00 H
ATOM 11 CB ALA 2 29.795 28.154 22.598 1.00 0.00 C
ATOM 12 HB1 ALA 2 29.321 28.429 21.654 1.00 0.00 H
ATOM 13 HB2 ALA 2 30.774 28.629 22.659 1.00 0.00 H
ATOM 14 HB3 ALA 2 29.928 27.071 22.630 1.00 0.00 H
ATOM 15 C ALA 2 28.737 30.134 23.791 1.00 0.00 C
ATOM 16 O ALA 2 27.696 30.645 23.377 1.00 0.00 O
ATOM 17 N ALA 3 29.757 30.863 24.249 1.00 0.00 N
ATOM 18 H ALA 3 30.604 30.392 24.534 1.00 0.00 H
ATOM 19 CA ALA 3 29.782 32.325 24.309 1.00 0.00 C
ATOM 20 HA ALA 3 29.214 32.723 23.466 1.00 0.00 H
ATOM 21 CB ALA 3 29.108 32.780 25.612 1.00 0.00 C
ATOM 22 HB1 ALA 3 29.658 32.391 26.470 1.00 0.00 H
ATOM 23 HB2 ALA 3 29.091 33.869 25.662 1.00 0.00 H
ATOM 24 HB3 ALA 3 28.082 32.412 25.646 1.00 0.00 H
ATOM 25 C ALA 3 31.224 32.854 24.202 1.00 0.00 C
ATOM 26 O ALA 3 32.178 32.113 24.438 1.00 0.00 O
ATOM 27 N NME 4 31.379 34.139 23.857 1.00 0.00 N
ATOM 28 H NME 4 30.550 34.685 23.686 1.00 0.00 H
ATOM 29 CH3 NME 4 32.677 34.798 23.722 1.00 0.00 C
ATOM 30 HH31 NME 4 33.332 34.199 23.086 1.00 0.00 H
ATOM 31 HH32 NME 4 32.556 35.788 23.280 1.00 0.00 H
ATOM 32 HH33 NME 4 33.144 34.897 24.704 1.00 0.00 H
TER 33 NME 4
END
39 changes: 39 additions & 0 deletions openff/toolkit/data/proteins/MainChain_ARG.pdb
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CRYST1 48.000 48.000 48.000 90.00 90.00 90.00 P 1 1
ATOM 1 H1 ACE 1 26.138 25.214 24.583 1.00 0.00 H
ATOM 2 CH3 ACE 1 26.124 26.209 24.139 1.00 0.00 C
ATOM 3 H2 ACE 1 25.413 26.835 24.676 1.00 0.00 H
ATOM 4 H3 ACE 1 25.837 26.135 23.092 1.00 0.00 H
ATOM 5 C ACE 1 27.506 26.811 24.243 1.00 0.00 C
ATOM 6 O ACE 1 28.418 26.182 24.765 1.00 0.00 O
ATOM 7 N ARG 2 27.671 28.039 23.742 1.00 0.00 N
ATOM 8 H ARG 2 26.871 28.490 23.320 1.00 0.00 H
ATOM 9 CA ARG 2 28.942 28.780 23.768 1.00 0.00 C
ATOM 10 HA ARG 2 29.476 28.515 24.682 1.00 0.00 H
ATOM 11 CB ARG 2 29.787 28.342 22.555 1.00 0.00 C
ATOM 12 HB2 ARG 2 29.888 27.255 22.575 1.00 0.00 H
ATOM 13 HB3 ARG 2 29.263 28.617 21.637 1.00 0.00 H
ATOM 14 CG ARG 2 31.194 28.957 22.536 1.00 0.00 C
ATOM 15 HG2 ARG 2 31.121 30.043 22.463 1.00 0.00 H
ATOM 16 HG3 ARG 2 31.716 28.692 23.456 1.00 0.00 H
ATOM 17 CD ARG 2 31.981 28.424 21.331 1.00 0.00 C
ATOM 18 HD2 ARG 2 32.042 27.336 21.408 1.00 0.00 H
ATOM 19 HD3 ARG 2 31.438 28.683 20.419 1.00 0.00 H
ATOM 20 NE ARG 2 33.344 28.991 21.272 1.00 0.00 N
ATOM 21 HE ARG 2 33.600 29.629 22.006 1.00 0.00 H
ATOM 22 CZ ARG 2 34.256 28.739 20.348 1.00 0.00 C
ATOM 23 NH1 ARG 2 34.029 27.928 19.353 1.00 0.00 N
ATOM 24 HH11 ARG 2 33.132 27.480 19.289 1.00 0.00 H
ATOM 25 HH12 ARG 2 34.732 27.748 18.660 1.00 0.00 H
ATOM 26 NH2 ARG 2 35.428 29.305 20.406 1.00 0.00 N
ATOM 27 HH21 ARG 2 35.650 29.938 21.155 1.00 0.00 H
ATOM 28 HH22 ARG 2 36.117 29.111 19.703 1.00 0.00 H
ATOM 29 C ARG 2 28.683 30.288 23.768 1.00 0.00 C
ATOM 30 O ARG 2 28.008 30.786 22.875 1.00 0.00 O
ATOM 31 N NME 3 29.250 31.004 24.744 1.00 0.00 N
ATOM 32 H NME 3 29.758 30.508 25.458 1.00 0.00 H
ATOM 33 CH3 NME 3 29.101 32.453 24.889 1.00 0.00 C
ATOM 34 HH31 NME 3 28.055 32.699 25.084 1.00 0.00 H
ATOM 35 HH32 NME 3 29.712 32.817 25.716 1.00 0.00 H
ATOM 36 HH33 NME 3 29.407 32.954 23.968 1.00 0.00 H
TER 37 NME 3
END
26 changes: 26 additions & 0 deletions openff/toolkit/data/proteins/MainChain_CYS.pdb
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CRYST1 48.000 48.000 48.000 90.00 90.00 90.00 P 1 1
ATOM 1 H1 ACE 1 25.973 25.174 24.544 1.00 0.00 H
ATOM 2 CH3 ACE 1 25.997 26.195 24.165 1.00 0.00 C
ATOM 3 H2 ACE 1 25.393 26.837 24.805 1.00 0.00 H
ATOM 4 H3 ACE 1 25.611 26.217 23.148 1.00 0.00 H
ATOM 5 C ACE 1 27.425 26.686 24.169 1.00 0.00 C
ATOM 6 O ACE 1 28.326 25.956 24.559 1.00 0.00 O
ATOM 7 N CYS 2 27.631 27.926 23.732 1.00 0.00 N
ATOM 8 H CYS 2 26.835 28.482 23.454 1.00 0.00 H
ATOM 9 CA CYS 2 28.930 28.601 23.716 1.00 0.00 C
ATOM 10 HA CYS 2 29.492 28.302 24.603 1.00 0.00 H
ATOM 11 CB CYS 2 29.705 28.139 22.471 1.00 0.00 C
ATOM 12 HB2 CYS 2 29.719 27.047 22.449 1.00 0.00 H
ATOM 13 HB3 CYS 2 29.201 28.502 21.573 1.00 0.00 H
ATOM 14 SG CYS 2 31.419 28.741 22.503 1.00 0.00 S
ATOM 15 HG CYS 2 31.840 28.100 21.406 1.00 0.00 H
ATOM 16 C CYS 2 28.734 30.130 23.768 1.00 0.00 C
ATOM 17 O CYS 2 27.658 30.623 23.428 1.00 0.00 O
ATOM 18 N NME 3 29.759 30.876 24.196 1.00 0.00 N
ATOM 19 H NME 3 30.627 30.400 24.395 1.00 0.00 H
ATOM 20 CH3 NME 3 29.728 32.333 24.310 1.00 0.00 C
ATOM 21 HH31 NME 3 28.835 32.642 24.858 1.00 0.00 H
ATOM 22 HH32 NME 3 30.614 32.689 24.837 1.00 0.00 H
ATOM 23 HH33 NME 3 29.697 32.778 23.314 1.00 0.00 H
TER 24 NME 3
END
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