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2024-11-25 09:59:13 -08:00
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37
example/Eg5/3zcw_frag.sdf Normal file
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@@ -0,0 +1,37 @@
RDKit 3D
10 6 0 0 0 0 0 0 0 0999 V2000
-6.6990 12.5560 26.2140 O 0 0 0 0 0 0 0 0 0 0 0 0
-7.8020 11.6690 26.5150 C 0 0 0 0 0 0 0 0 0 0 0 0
-6.0470 12.5610 28.9520 F 0 0 0 0 0 0 0 0 0 0 0 0
1.9720 15.3280 31.9080 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2140 16.3220 31.9250 O 0 0 0 0 0 0 0 0 0 0 0 0
3.1030 15.4050 32.4260 O 0 0 0 0 0 0 0 0 0 0 0 0
1.9860 6.9200 29.4810 F 0 0 0 0 0 0 0 0 0 0 0 0
2.1020 7.0750 30.8070 C 0 0 0 0 0 0 0 0 0 0 0 0
2.6090 6.0020 31.4070 F 0 0 0 0 0 0 0 0 0 0 0 0
2.8920 8.0970 31.0400 F 0 0 0 0 0 0 0 0 0 0 0 0
2 1 1 0
5 4 1 0
6 4 1 0
8 7 1 6
9 8 1 0
10 8 1 0
M END
> <core> (1)
0
> <idx> (1)
0
> <frag_idx> (1)
3
> <internalRgroupSmiles> (1)
*OC([H])([H])[H]
> <RLABEL_PROCESSED> (1)
1
$$$$

75
example/Eg5/3zcw_ligand.sdf Normal file
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@@ -0,0 +1,75 @@
RDKit 3D
33 36 0 0 0 0 0 0 0 0999 V2000
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2.6090 6.0020 31.4070 F 0 0 0 0 0 0 0 0 0 0 0 0
2.8920 8.0970 31.0400 F 0 0 0 0 0 0 0 0 0 0 0 0
0.7020 7.4200 31.3110 C 0 0 0 0 0 0 0 0 0 0 0 0
0.2000 6.7210 32.4080 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.0690 7.0120 32.8720 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.8170 8.0010 32.2420 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.3190 8.7010 31.1530 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.0450 8.4120 30.6790 C 0 0 0 0 0 0 0 0 0 0 0 0
0.4590 9.1940 29.4640 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0320 10.6050 29.4640 N 0 0 0 0 0 0 0 0 0 0 0 0
0.6560 11.5940 30.1310 C 0 0 0 0 0 0 0 0 0 0 0 0
1.7710 11.6090 30.9700 C 0 0 0 0 0 0 0 0 0 0 0 0
2.1990 12.8200 31.5460 C 0 0 0 0 0 0 0 0 0 0 0 0
1.5070 14.0030 31.2710 C 0 0 0 0 0 0 0 0 0 0 0 0
1.9720 15.3280 31.9080 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2140 16.3220 31.9250 O 0 0 0 0 0 0 0 0 0 0 0 0
3.1030 15.4050 32.4260 O 0 0 0 0 0 0 0 0 0 0 0 0
0.3840 13.9760 30.4340 C 0 0 0 0 0 0 0 0 0 0 0 0
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2 1 1 6
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M END
$$$$

2699
example/Eg5/3zcw_protein.pdb Normal file
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File diff suppressed because it is too large Load Diff

58
example/IMDPH/5OU3_fragment.sdf Normal file
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@@ -0,0 +1,58 @@
linker_ligand_vina_14.mol2
PyMOL2.4 3D 0
25 27 0 0 0 0 0 0 0 0999 V2000
132.8550 -16.1870 -4.4690 O 0 0 0 0 0 0 0 0 0 0 0 0
131.7040 -16.4450 -3.6260 C 0 0 0 0 0 0 0 0 0 0 0 0
131.8170 -17.2990 -2.5230 C 0 0 0 0 0 0 0 0 0 0 0 0
130.6800 -17.5850 -1.7050 C 0 0 0 0 0 0 0 0 0 0 0 0
129.4670 -17.0260 -2.0200 C 0 0 0 0 0 0 0 0 0 0 0 0
129.3460 -16.1820 -3.1360 C 0 0 0 0 0 0 0 0 0 0 0 0
130.4640 -15.9110 -3.9350 C 0 0 0 0 0 0 0 0 0 0 0 0
128.1880 -17.2590 -1.1870 C 0 0 0 0 0 0 0 0 0 0 0 0
127.0230 -16.4970 -1.1610 C 0 0 0 0 0 0 0 0 0 0 0 0
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124.8900 -16.6300 0.0310 C 0 0 0 0 0 0 0 0 0 0 0 0
126.8160 -18.2000 0.2050 C 0 0 0 0 0 0 0 0 0 0 0 0
128.0390 -18.2950 -0.3470 N 0 0 0 0 0 0 0 0 0 0 0 0
132.2920 -12.1440 -2.9340 C 0 0 0 0 0 0 0 0 0 0 0 0
132.3400 -12.1360 -1.5780 N 0 0 0 0 0 0 0 0 0 0 0 0
131.8610 -10.9840 -1.1620 C 0 0 0 0 0 0 0 0 0 0 0 0
131.5060 -10.2130 -2.2680 C 0 0 0 0 0 0 0 0 0 0 0 0
131.7770 -10.9470 -3.3530 N 0 0 0 0 0 0 0 0 0 0 0 0
131.7570 -10.6110 0.3310 C 0 0 0 0 0 0 0 0 0 0 0 0
131.6810 -11.6310 1.2810 C 0 0 0 0 0 0 0 0 0 0 0 0
131.5940 -11.3010 2.6490 C 0 0 0 0 0 0 0 0 0 0 0 0
131.5750 -9.9720 3.0300 C 0 0 0 0 0 0 0 0 0 0 0 0
131.6410 -8.9560 2.0800 C 0 0 0 0 0 0 0 0 0 0 0 0
131.7340 -9.2830 0.6980 C 0 0 0 0 0 0 0 0 0 0 0 0
131.4500 -9.5090 4.8560 Br 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
2 7 2 0 0 0 0
3 4 2 0 0 0 0
4 5 1 0 0 0 0
5 6 2 0 0 0 0
5 8 1 0 0 0 0
6 7 1 0 0 0 0
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9 10 1 0 0 0 0
10 11 1 0 0 0 0
10 12 1 0 0 0 0
12 13 2 0 0 0 0
14 15 1 0 0 0 0
14 18 2 0 0 0 0
15 16 1 0 0 0 0
16 17 2 0 0 0 0
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19 20 1 0 0 0 0
19 24 2 0 0 0 0
20 21 2 0 0 0 0
21 22 1 0 0 0 0
22 23 2 0 0 0 0
22 25 1 0 0 0 0
23 24 1 0 0 0 0
M END
$$$$

113
example/IMDPH/5OU3_ligand.mol2 Normal file
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@@ -0,0 +1,113 @@
# created with PyMOL 2.4.1
@<TRIPOS>MOLECULE
linker_ligand_vina_14.mol2
50 53 1
SMALL
USER_CHARGES
@<TRIPOS>ATOM
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2 C02 134.027 -15.428 -4.022 C.3 1 AUN1 0.217
3 O03 132.855 -16.187 -4.469 O.3 1 AUN1 -0.337
4 C04 131.704 -16.445 -3.626 C.2 1 AUN1 0.070
5 C05 131.817 -17.299 -2.523 C.2 1 AUN1 0.037
6 C06 130.680 -17.585 -1.705 C.2 1 AUN1 0.016
7 C07 129.467 -17.026 -2.020 C.2 1 AUN1 -0.006
8 C08 129.346 -16.182 -3.136 C.2 1 AUN1 0.016
9 C09 130.464 -15.911 -3.935 C.2 1 AUN1 0.037
10 C10 128.188 -17.259 -1.187 C.2 1 AUN1 0.084
11 C11 127.023 -16.497 -1.161 C.2 1 AUN1 0.123
12 N12 126.207 -17.073 -0.315 N.pl3 1 AUN1 -0.354
13 C13 124.890 -16.630 0.031 C.3 1 AUN1 0.156
14 C14 126.816 -18.200 0.205 C.2 1 AUN1 0.209
15 N15 128.039 -18.295 -0.347 N.2 1 AUN1 -0.242
16 C16 133.543 -14.231 -3.145 C.2 1 AUN1 0.265
17 O17 133.873 -14.170 -1.972 O.2 1 AUN1 -0.270
18 N18 132.725 -13.210 -3.716 N.pl3 1 AUN1 -0.155
19 C19 132.292 -12.144 -2.934 C.2 1 AUN1 0.707
20 N20 132.340 -12.136 -1.578 N.pl3 1 AUN1 -0.188
21 C21 131.861 -10.984 -1.162 C.2 1 AUN1 0.077
22 C22 131.506 -10.213 -2.268 C.2 1 AUN1 0.167
23 N23 131.777 -10.947 -3.353 N.2 1 AUN1 -0.074
24 C24 131.757 -10.611 0.331 C.2 1 AUN1 -0.007
25 C25 131.681 -11.631 1.281 C.2 1 AUN1 0.015
26 C26 131.594 -11.301 2.649 C.2 1 AUN1 0.020
27 C27 131.575 -9.972 3.030 C.2 1 AUN1 0.011
28 C29 131.641 -8.956 2.080 C.2 1 AUN1 0.020
29 C30 131.734 -9.283 0.698 C.2 1 AUN1 0.015
30 BR1 131.450 -9.509 4.856 Br 1 AUN1 -0.051
31 H01 135.919 -15.508 -5.031 H 1 AUN1 0.000
32 H02 134.518 -15.302 -6.108 H 1 AUN1 0.000
33 H03 135.098 -13.933 -5.130 H 1 AUN1 0.000
34 H04 134.652 -16.082 -3.413 H 1 AUN1 0.000
35 H05 132.780 -17.750 -2.286 H 1 AUN1 0.000
36 H06 130.776 -18.241 -0.840 H 1 AUN1 0.000
37 H07 128.381 -15.737 -3.381 H 1 AUN1 0.000
38 H08 130.357 -15.272 -4.811 H 1 AUN1 0.000
39 H09 126.827 -15.592 -1.736 H 1 AUN1 0.000
40 H10 124.189 -17.458 -0.074 H 1 AUN1 0.000
41 H11 124.884 -16.278 1.063 H 1 AUN1 0.000
42 H12 124.593 -15.818 -0.632 H 1 AUN1 0.000
43 H13 126.383 -18.888 0.931 H 1 AUN1 0.000
44 H14 131.088 -9.206 -2.252 H 1 AUN1 0.000
45 H15 131.689 -12.675 0.968 H 1 AUN1 0.000
46 H16 131.542 -12.088 3.401 H 1 AUN1 0.000
47 H17 131.622 -7.912 2.394 H 1 AUN1 0.000
48 H18 131.786 -8.498 -0.056 H 1 AUN1 0.000
49 8HN1 132.460 -13.259 -4.688 H 1 AUN1 0.187
50 0HN2 132.660 -12.821 -0.908 H 1 AUN1 0.184
@<TRIPOS>BOND
1 1 2 1
2 1 31 1
3 1 32 1
4 1 33 1
5 2 16 1
6 2 34 1
7 2 3 1
8 3 4 1
9 4 5 1
10 5 6 2
11 5 35 1
12 6 36 1
13 6 7 1
14 7 10 1
15 7 8 2
16 8 37 1
17 4 9 2
18 8 9 1
19 9 38 1
20 10 11 2
21 10 15 1
22 11 12 1
23 11 39 1
24 12 13 1
25 12 14 1
26 13 40 1
27 13 41 1
28 13 42 1
29 14 43 1
30 14 15 2
31 16 17 2
32 16 18 1
33 18 19 1
34 19 20 1
35 20 21 1
36 20 50 1
37 21 24 1
38 21 22 2
39 22 44 1
40 19 23 2
41 22 23 1
42 24 25 1
43 24 29 2
44 25 26 2
45 25 45 1
46 26 27 1
47 26 46 1
48 27 30 1
49 27 28 2
50 28 47 1
51 28 29 1
52 29 48 1
53 18 49 1
@<TRIPOS>SUBSTRUCTURE
1 AUN1 1 GROUP 1 **** AUN

736
example/IMDPH/5OU3_pocket_8.0.ply Normal file
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@@ -0,0 +1,736 @@
ply
format ascii 1.0
comment Generated by PyMesh
element vertex 264
property float x
property float y
property float z
property float charge
property float hbond
property float hphob
property float nx
property float ny
property float nz
property float si
element face 455
property list uchar int vertex_indices
end_header
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133.08 -5.39488 9.46975 0.396282 0.148885 -3.9 0.939411 0.142253 0.311884 0.41963
132.744 -20.562 2.47025 0.124531 0 1.30829 0.326202 0.944589 -0.0366633 0.353013
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130.547 -6.44075 2.43175 0.366508 0 4.2 0.76055 -0.395513 -0.51491 -0.735026
130.576 -7.406 4.1065 0.291506 0 4.2 0.837384 -0.498725 -0.223745 -0.709929
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4879
example/IMDPH/5OU3_protein.pdb Normal file
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25
example/adrb1/2VT4_frag.sdf Normal file
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@@ -0,0 +1,25 @@
*****
PyMOL2.5 3D 0
10 9 0 0 1 0 0 0 0 0999 V2000
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25.5660 3.0570 -0.0240 C 0 0 1 0 0 0 0 0 0 0 0 0
26.2630 4.2520 -0.6910 C 0 0 0 0 0 0 0 0 0 0 0 0
26.9110 3.8510 -1.9410 N 0 3 0 0 0 0 0 0 0 0 0 0
27.7870 4.9400 -2.4080 C 0 0 0 0 0 0 0 0 0 0 0 0
29.0440 4.9700 -1.5050 C 0 0 0 0 0 0 0 0 0 0 0 0
27.0620 6.3200 -2.3240 C 0 0 0 0 0 0 0 0 0 0 0 0
24.6660 3.6160 1.0780 C 0 0 0 0 0 0 0 0 0 0 0 0
25.5330 3.9350 2.1590 O 0 0 0 0 0 0 0 0 0 0 0 0
28.1550 4.6290 -3.8810 C 0 0 0 0 0 0 0 0 0 0 0 0
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8 9 1 0 0 0 0
M END
$$$$

94
example/adrb1/2VT4_ligand.sdf Normal file
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@@ -0,0 +1,94 @@
*****
OpenBabel12082211133D
43 44 0 0 1 0 0 0 0 0999 V2000
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25.0780 4.6550 3.2030 C 0 0 0 0 0 0 0 0 0 0 0 0
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23.2840 5.2990 4.6530 C 0 0 0 0 0 0 0 0 0 0 0 0
24.1640 6.0620 5.4170 C 0 0 0 0 0 0 0 0 0 0 0 0
25.5130 6.1200 5.0640 C 0 0 0 0 0 0 0 0 0 0 0 0
25.9620 5.4170 3.9460 C 0 0 0 0 0 0 0 0 0 0 0 0
26.5750 6.7510 5.5740 N 0 0 0 0 0 0 0 0 0 0 0 0
27.6180 6.4450 4.8040 C 0 0 0 0 0 0 0 0 0 0 0 0
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28.9670 6.9090 5.0460 C 0 0 0 0 0 0 0 0 0 0 0 0
28.1550 4.6290 -3.8810 C 0 0 0 0 0 0 0 0 0 0 0 0
24.3455 1.6277 -0.5038 H 0 0 0 0 0 0 0 0 0 0 0 0
26.3234 2.3630 0.3693 H 0 0 0 0 0 0 0 0 0 0 0 0
27.0252 4.6497 -0.0049 H 0 0 0 0 0 0 0 0 0 0 0 0
25.5132 5.0266 -0.9096 H 0 0 0 0 0 0 0 0 0 0 0 0
26.2141 3.6628 -2.6331 H 0 0 0 0 0 0 0 0 0 0 0 0
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29.7344 5.7476 -1.8636 H 0 0 0 0 0 0 0 0 0 0 0 0
26.8032 6.5357 -1.2769 H 0 0 0 0 0 0 0 0 0 0 0 0
27.7277 7.1076 -2.7067 H 0 0 0 0 0 0 0 0 0 0 0 0
26.1442 6.2893 -2.9295 H 0 0 0 0 0 0 0 0 0 0 0 0
24.1332 4.5126 0.7284 H 0 0 0 0 0 0 0 0 0 0 0 0
23.9180 2.8705 1.3856 H 0 0 0 0 0 0 0 0 0 0 0 0
23.0513 3.9981 2.9579 H 0 0 0 0 0 0 0 0 0 0 0 0
22.2394 5.2568 4.9238 H 0 0 0 0 0 0 0 0 0 0 0 0
23.8043 6.6058 6.2780 H 0 0 0 0 0 0 0 0 0 0 0 0
26.5848 7.3413 6.3811 H 0 0 0 0 0 0 0 0 0 0 0 0
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M CHG 1 5 1
M END
$$$$

5296
example/adrb1/2VT4_protein.pdb Normal file
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599
example/adrb1/adrb_pocket_8.0.ply Normal file
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ply
format ascii 1.0
comment Generated by PyMesh
element vertex 211
property float x
property float y
property float z
property float charge
property float hbond
property float hphob
property float nx
property float ny
property float nz
property float si
element face 371
property list uchar int vertex_indices
end_header
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33.2424 3.3845 5.03175 -1.08818 -0.231419 -3.5 0.197926 0.974085 -0.10947 0.999814
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18
example/drd2/6CM4_frag.sdf Normal file
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6CM4-ligand
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9517
example/drd2/6CM4_protein.pdb Normal file
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551
example/drd2/drd2_pocket_8.0.ply Normal file
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ply
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8.926 -6.97625 -15.661 -0.183523 0 4.2 0.828255 0.534202 0.169177 0.999868
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2.339 0.159438 -12.9886 -1.06329 0.189768 2.85984 -0.718439 0.327414 0.613714 -0.652409
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13.5253 9.3375 -9.8375 -1.30225 0 -0.8 0.264119 0.962921 0.0549862 0.195494
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9.70063 -6.79375 -17.9625 0.120436 0 4.2 0.882858 0.278003 0.378519 0.999892
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6.6075 -5.91638 -13.3737 -0.840079 0 -0.887693 0.132458 0.853777 0.503506 0.999864
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12.7401 6.04472 -5.94131 -2.37158 0 2.8 0.735897 -0.668216 -0.109286 0.283355
10.0344 3.12644 -11.1978 -1.40734 0 -0.0837754 0.322751 -0.792131 0.518035 -0.0667969
18.0298 4.61613 -16.4741 0.61004 0.058389 -3.5 0.24344 -0.964946 -0.0980613 0.999881
6.28578 4.86522 -10.4675 0.743675 0.201119 -1.3 -0.701128 -0.20742 0.6822 0.174663
7.07544 3.64525 -17.6606 -0.636859 0 -0.9 -0.846308 0.530409 0.0492874 0.360658
8.59122 9.77563 -7.80975 -2.42071 0 4.2 -0.674322 0.732868 -0.0905184 -0.292343
12.7908 9.94056 -0.727719 -2.59509 0 1.46986 0.156445 0.627207 0.762979 -0.999859
6.7205 -3.8635 -16.2006 0.414035 0.176508 -0.8 0.702762 0.247778 0.666882 0.554538
4.1575 -3.68337 -15.7405 -1.84792 -0.597894 -2.96512 -0.586741 -0.529384 0.612771 0.292448
17.353 -0.48425 -19.4007 -0.149131 0.921589 4.5 0.457186 -0.28491 0.8425 -0.999843
2.23375 -2.02472 -16.319 -1.10502 -0.157474 -2.44975 -0.955596 -0.243798 0.165527 -0.0975358
6.65516 -2.26319 -12.6712 -1.23172 0 -0.863576 0.22784 -0.747305 0.624199 -0.671553
10.5632 -1.33263 -14.7622 -0.625925 0 -1.3 0.357634 -0.786916 0.502852 -0.692407
12.2659 10.958 -2.53012 -2.56685 0 -0.793564 0.14667 0.897955 0.414927 -0.553201
6.00809 7.82672 -14.0573 -1.57392 0 -0.9 -0.315225 0.369359 -0.87419 -0.693821
11.9952 9.41291 -14.7622 -0.970472 0 2.90312 -0.292218 0.949034 0.118083 -0.278087
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10.8013 10.0306 -10.7427 -1.7703 0 2.8 0.0614299 0.962488 -0.26428 -0.40699
12.0793 9.33122 -11.9143 -1.53842 0 2.8 -0.0249575 0.990081 -0.138266 0.0641926
14.2399 9.46037 -2.33941 -2.46402 -0.10845 1.01587 0.901576 0.407682 0.14476 -0.999825
9.06631 1.75969 -12.8309 -0.542456 0.270798 -0.7 0.378631 -0.386432 0.841017 0.628037
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11.9113 -1.4295 -16.9515 -0.259317 0 -1.3 0.531158 -0.640092 0.555115 0.157007
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6.60638 -0.566391 -11.2141 -0.907294 0 -0.9 0.226405 -0.348891 0.909404 -0.825332
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16.8821 7.2235 -15.5985 -0.18306 0 4.2 0.527986 0.846217 0.0717405 0.999851
4.59956 2.28081 -18.6023 -0.633266 0 -0.9 -0.459694 0.884368 0.0810834 0.0831986
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123
example/smarca2/6HAX_frag.sdf Normal file
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M END
$$$$

145
example/smarca2/6HAX_ligand.sdf Normal file
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6HAX_ligand
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M END
$$$$

22504
example/smarca2/6HAX_protein.pdb Normal file
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956
example/smarca2/smarca2_pocket_8.0.ply Normal file
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ply
format ascii 1.0
comment Generated by PyMesh
element vertex 341
property float x
property float y
property float z
property float charge
property float hbond
property float hphob
property float nx
property float ny
property float nz
property float si
element face 598
property list uchar int vertex_indices
end_header
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