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add example of protein-ligand binding
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913 changes: 913 additions & 0 deletions
913
docs/source/examples/cbayesmbar_for_protein_ligand/main.ipynb
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docs/source/examples/cbayesmbar_for_protein_ligand/output/.gitignore
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|---|---|---|
| @@ -0,0 +1,2 @@ | ||
| * | ||
| !.gitignore |
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docs/source/examples/cbayesmbar_for_protein_ligand/structure/protein_phase/ejm_31.inpcrd
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,19 @@ | ||
| MOL | ||
| 32 | ||
| 6.2864062 1.7611250 7.0860312 6.9534063 2.6231250 6.2200312 | ||
| 6.2924062 3.1631250 5.1220312 4.9474063 2.8331250 4.8730312 | ||
| 4.2784062 1.9701250 5.7630312 4.9554063 1.4401250 6.8540312 | ||
| 2.6074063 1.5641250 5.4970312 4.2074063 3.3631250 3.7050312 | ||
| 4.0214063 2.6311250 2.7470312 3.7344063 4.6231250 3.7680312 | ||
| 2.9604063 5.3221250 2.8360312 2.2854063 4.7591250 1.7350312 | ||
| 1.4664063 5.5721250 0.9570312 1.3244063 6.8651250 1.2330312 | ||
| 1.9494063 7.4431250 2.2580312 2.7404063 6.6681250 3.1090312 | ||
| 1.7084063 8.7941250 2.5320312 2.5344062 9.6561250 3.1830312 | ||
| 3.6314063 9.3331250 3.6060312 2.0154062 11.0581250 3.3850312 | ||
| 7.1354062 4.2621250 4.0840312 0.9424063 11.1521250 3.2540312 | ||
| 6.8034063 1.3431250 7.9370312 7.9884062 2.8741250 6.4000312 | ||
| 4.4364063 0.7721250 7.5250312 3.9304062 5.1961250 4.5770312 | ||
| 2.4074063 3.7101250 1.5070312 0.9354062 5.1551250 0.1140312 | ||
| 3.1834062 7.1201250 3.9850312 0.8434063 9.2241250 2.2360312 | ||
| 2.5244063 11.7341250 2.6980312 2.2894062 11.4051250 4.3810312 | ||
| 7.1450000 10.9620000 7.8230000 90.0000000 90.0000000 90.0000000 |
35 changes: 35 additions & 0 deletions
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docs/source/examples/cbayesmbar_for_protein_ligand/structure/protein_phase/ejm_31.pdb
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,35 @@ | ||
| CRYST1 7.145 10.962 7.823 90.00 90.00 90.00 P 1 1 | ||
| ATOM 1 C1 MOL 1 2.714 -3.720 3.175 1.00 0.00 | ||
| ATOM 2 C2 MOL 1 3.381 -2.858 2.309 1.00 0.00 | ||
| ATOM 3 C3 MOL 1 2.720 -2.318 1.211 1.00 0.00 | ||
| ATOM 4 C4 MOL 1 1.375 -2.648 0.962 1.00 0.00 | ||
| ATOM 5 C5 MOL 1 0.706 -3.511 1.852 1.00 0.00 | ||
| ATOM 6 C6 MOL 1 1.383 -4.041 2.943 1.00 0.00 | ||
| ATOM 7 Cl1 MOL 1 -0.965 -3.917 1.586 1.00 0.00 | ||
| ATOM 8 C7 MOL 1 0.635 -2.118 -0.206 1.00 0.00 | ||
| ATOM 9 O1 MOL 1 0.449 -2.850 -1.164 1.00 0.00 | ||
| ATOM 10 N1 MOL 1 0.162 -0.858 -0.143 1.00 0.00 | ||
| ATOM 11 C8 MOL 1 -0.612 -0.159 -1.075 1.00 0.00 | ||
| ATOM 12 C9 MOL 1 -1.287 -0.722 -2.176 1.00 0.00 | ||
| ATOM 13 C10 MOL 1 -2.106 0.091 -2.954 1.00 0.00 | ||
| ATOM 14 N2 MOL 1 -2.248 1.384 -2.678 1.00 0.00 | ||
| ATOM 15 C11 MOL 1 -1.623 1.962 -1.653 1.00 0.00 | ||
| ATOM 16 C12 MOL 1 -0.832 1.187 -0.802 1.00 0.00 | ||
| ATOM 17 N3 MOL 1 -1.864 3.313 -1.379 1.00 0.00 | ||
| ATOM 18 C13 MOL 1 -1.038 4.175 -0.728 1.00 0.00 | ||
| ATOM 19 O2 MOL 1 0.059 3.852 -0.305 1.00 0.00 | ||
| ATOM 20 C14 MOL 1 -1.557 5.577 -0.526 1.00 0.00 | ||
| ATOM 21 Cl2 MOL 1 3.563 -1.219 0.173 1.00 0.00 | ||
| ATOM 22 H1 MOL 1 -2.630 5.671 -0.657 1.00 0.00 | ||
| ATOM 23 H2 MOL 1 3.231 -4.138 4.026 1.00 0.00 | ||
| ATOM 24 H3 MOL 1 4.416 -2.607 2.489 1.00 0.00 | ||
| ATOM 25 H4 MOL 1 0.864 -4.709 3.614 1.00 0.00 | ||
| ATOM 26 H5 MOL 1 0.358 -0.285 0.666 1.00 0.00 | ||
| ATOM 27 H6 MOL 1 -1.165 -1.771 -2.404 1.00 0.00 | ||
| ATOM 28 H7 MOL 1 -2.637 -0.326 -3.797 1.00 0.00 | ||
| ATOM 29 H8 MOL 1 -0.389 1.639 0.074 1.00 0.00 | ||
| ATOM 30 H9 MOL 1 -2.729 3.743 -1.675 1.00 0.00 | ||
| ATOM 31 H10 MOL 1 -1.048 6.253 -1.213 1.00 0.00 | ||
| ATOM 32 H11 MOL 1 -1.283 5.924 0.470 1.00 0.00 | ||
| TER | ||
| END |
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312
docs/source/examples/cbayesmbar_for_protein_ligand/structure/protein_phase/ejm_31.prmtop
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.../source/examples/cbayesmbar_for_protein_ligand/structure/protein_phase/ejm_31_aligned.xyz
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,34 @@ | ||
| 32 | ||
| ejm_31 | ||
| C 6.79000 5.69400 -0.18000 | ||
| C 7.45700 6.55600 -1.04600 | ||
| C 6.79600 7.09600 -2.14400 | ||
| C 5.45100 6.76600 -2.39300 | ||
| C 4.78200 5.90300 -1.50300 | ||
| C 5.45900 5.37300 -0.41200 | ||
| Cl 3.11100 5.49700 -1.76900 | ||
| C 4.71100 7.29600 -3.56100 | ||
| O 4.52500 6.56400 -4.51900 | ||
| N 4.23800 8.55600 -3.49800 | ||
| C 3.46400 9.25500 -4.43000 | ||
| C 2.78900 8.69200 -5.53100 | ||
| C 1.97000 9.50500 -6.30900 | ||
| N 1.82800 10.79800 -6.03300 | ||
| C 2.45300 11.37600 -5.00800 | ||
| C 3.24400 10.60100 -4.15700 | ||
| N 2.21200 12.72700 -4.73400 | ||
| C 3.03800 13.58900 -4.08300 | ||
| O 4.13500 13.26600 -3.66000 | ||
| C 2.51900 14.99100 -3.88100 | ||
| Cl 7.63900 8.19500 -3.18200 | ||
| H 1.44600 15.08500 -4.01200 | ||
| H 7.30700 5.27600 0.67100 | ||
| H 8.49200 6.80700 -0.86600 | ||
| H 4.94000 4.70500 0.25900 | ||
| H 4.43400 9.12900 -2.68900 | ||
| H 2.91100 7.64300 -5.75900 | ||
| H 1.43900 9.08800 -7.15200 | ||
| H 3.68700 11.05300 -3.28100 | ||
| H 1.34700 13.15700 -5.03000 | ||
| H 3.02800 15.66700 -4.56800 | ||
| H 2.79300 15.33800 -2.88500 |
21 changes: 21 additions & 0 deletions
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docs/source/examples/cbayesmbar_for_protein_ligand/structure/protein_phase/ejm_42.inpcrd
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,21 @@ | ||
| MOL | ||
| 35 | ||
| 6.2911000 1.8033429 7.0889286 6.9581000 2.6653429 6.2229286 | ||
| 6.2971000 3.2053429 5.1249286 4.9521000 2.8753429 4.8759286 | ||
| 4.2831000 2.0123429 5.7659286 4.9601000 1.4823429 6.8569286 | ||
| 2.6121000 1.6063429 5.4999286 4.2121000 3.4053429 3.7079286 | ||
| 4.0261000 2.6733429 2.7499286 3.7391000 4.6653429 3.7709286 | ||
| 2.9651000 5.3643429 2.8389286 2.2901000 4.8013429 1.7379286 | ||
| 1.4711000 5.6143429 0.9599286 1.3291000 6.9073429 1.2359286 | ||
| 1.9541000 7.4853429 2.2609286 2.7451000 6.7103429 3.1119286 | ||
| 1.7131000 8.8363429 2.5349286 2.5391000 9.6983429 3.1859286 | ||
| 3.6361000 9.3753429 3.6089286 2.0201000 11.1003429 3.3879286 | ||
| 7.1401000 4.3043429 4.0869286 1.4911000 11.5003429 2.5289286 | ||
| 6.8081000 1.3853429 7.9399286 7.9931000 2.9163429 6.4029286 | ||
| 4.4411000 0.8143429 7.5279286 3.9351000 5.2383429 4.5799286 | ||
| 2.4121000 3.7523429 1.5099286 0.9401000 5.1973429 0.1169286 | ||
| 3.1881000 7.1623429 3.9879286 0.8481000 9.2663429 2.2389286 | ||
| 3.1631000 12.0083429 3.7359286 1.3641000 11.1213429 4.2589286 | ||
| 2.7901000 13.0223429 3.8819286 3.6381000 11.6603429 4.6529286 | ||
| 3.8911000 12.0023429 2.9249286 | ||
| 7.1450000 12.2080000 7.8230000 90.0000000 90.0000000 90.0000000 |
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docs/source/examples/cbayesmbar_for_protein_ligand/structure/protein_phase/ejm_42.pdb
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,38 @@ | ||
| CRYST1 7.145 12.208 7.823 90.00 90.00 90.00 P 1 1 | ||
| ATOM 1 C1 MOL 1 2.719 -4.301 3.177 1.00 0.00 | ||
| ATOM 2 C2 MOL 1 3.386 -3.439 2.311 1.00 0.00 | ||
| ATOM 3 C3 MOL 1 2.725 -2.899 1.213 1.00 0.00 | ||
| ATOM 4 C4 MOL 1 1.380 -3.229 0.964 1.00 0.00 | ||
| ATOM 5 C5 MOL 1 0.711 -4.092 1.854 1.00 0.00 | ||
| ATOM 6 C6 MOL 1 1.388 -4.622 2.945 1.00 0.00 | ||
| ATOM 7 Cl1 MOL 1 -0.960 -4.498 1.588 1.00 0.00 | ||
| ATOM 8 C7 MOL 1 0.640 -2.699 -0.204 1.00 0.00 | ||
| ATOM 9 O1 MOL 1 0.454 -3.431 -1.162 1.00 0.00 | ||
| ATOM 10 N1 MOL 1 0.167 -1.439 -0.141 1.00 0.00 | ||
| ATOM 11 C8 MOL 1 -0.607 -0.740 -1.073 1.00 0.00 | ||
| ATOM 12 C9 MOL 1 -1.282 -1.303 -2.174 1.00 0.00 | ||
| ATOM 13 C10 MOL 1 -2.101 -0.490 -2.952 1.00 0.00 | ||
| ATOM 14 N2 MOL 1 -2.243 0.803 -2.676 1.00 0.00 | ||
| ATOM 15 C11 MOL 1 -1.618 1.381 -1.651 1.00 0.00 | ||
| ATOM 16 C12 MOL 1 -0.827 0.606 -0.800 1.00 0.00 | ||
| ATOM 17 N3 MOL 1 -1.859 2.732 -1.377 1.00 0.00 | ||
| ATOM 18 C13 MOL 1 -1.033 3.594 -0.726 1.00 0.00 | ||
| ATOM 19 O2 MOL 1 0.064 3.271 -0.303 1.00 0.00 | ||
| ATOM 20 C14 MOL 1 -1.552 4.996 -0.524 1.00 0.00 | ||
| ATOM 21 Cl2 MOL 1 3.568 -1.800 0.175 1.00 0.00 | ||
| ATOM 22 H1 MOL 1 -2.081 5.396 -1.383 1.00 0.00 | ||
| ATOM 23 H2 MOL 1 3.236 -4.719 4.028 1.00 0.00 | ||
| ATOM 24 H3 MOL 1 4.421 -3.188 2.491 1.00 0.00 | ||
| ATOM 25 H4 MOL 1 0.869 -5.290 3.616 1.00 0.00 | ||
| ATOM 26 H5 MOL 1 0.363 -0.866 0.668 1.00 0.00 | ||
| ATOM 27 H6 MOL 1 -1.160 -2.352 -2.402 1.00 0.00 | ||
| ATOM 28 H7 MOL 1 -2.632 -0.907 -3.795 1.00 0.00 | ||
| ATOM 29 H8 MOL 1 -0.384 1.058 0.076 1.00 0.00 | ||
| ATOM 30 H9 MOL 1 -2.724 3.162 -1.673 1.00 0.00 | ||
| ATOM 31 C15 MOL 1 -0.409 5.904 -0.176 1.00 0.00 | ||
| ATOM 32 H10 MOL 1 -2.208 5.017 0.347 1.00 0.00 | ||
| ATOM 33 H11 MOL 1 -0.782 6.918 -0.030 1.00 0.00 | ||
| ATOM 34 H12 MOL 1 0.066 5.556 0.741 1.00 0.00 | ||
| ATOM 35 H13 MOL 1 0.319 5.898 -0.987 1.00 0.00 | ||
| TER | ||
| END |
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