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jimboid merged 24 commits into from
Oct 14, 2025
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Add files via upload #12

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89 changes: 89 additions & 0 deletions compounds/MCL1_ligands/lig_27.mol2
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@<TRIPOS>MOLECULE
lig_27.pdbqt
38 40 1 0 0
SMALL
AMBER ff14SB


@<TRIPOS>ATOM
1 CA 4.9403 2.2329 1.0039 C.ar 1 UNL1 0.0413
2 N 4.0972 2.8649 1.9162 N.ar 1 UNL1 -0.2154
3 C 3.5010 3.8738 1.1872 C.ar 1 UNL1 -0.0403
4 C 2.5716 4.8239 1.6268 C.2 1 UNL1 -0.1500
5 C 2.1093 5.7703 0.6898 C.2 1 UNL1 -0.1430
6 C 2.5806 5.7478 -0.6429 C.2 1 UNL1 -0.1780
7 C 3.5190 4.7792 -1.0582 C.2 1 UNL1 -0.0960
8 C 3.9658 3.8424 -0.1151 C.ar 1 UNL1 -0.0710
9 C 4.8736 2.8070 -0.2477 C.ar 1 UNL1 -0.1802
10 C 5.6331 2.4022 -1.4956 C.3 1 UNL1 -0.0042
11 C 7.0990 2.8957 -1.4481 C.3 1 UNL1 -0.0944
12 C 8.1106 1.8901 -2.0416 C.3 1 UNL1 0.1114
13 O 8.0778 1.9234 -3.4868 O.2 1 UNL1 -0.3519
14 C 7.0824 1.3420 -4.2400 C.2 1 UNL1 0.1341
15 C 6.4818 0.1224 -3.8774 C.2 1 UNL1 -0.1815
16 C 5.4809 -0.4381 -4.6893 C.2 1 UNL1 -0.1105
17 C 5.0896 0.2121 -5.8716 C.2 1 UNL1 -0.1850
18 C 5.6996 1.4213 -6.2439 C.2 1 UNL1 -0.1105
19 C 6.6977 1.9803 -5.4277 C.2 1 UNL1 -0.1815
20 C 5.7947 1.0765 1.4177 C.2 1 UNL1 0.8433
21 O 5.7001 0.7272 2.5865 O.co2 1 UNL1 -0.8208
22 OXT 6.5521 0.5300 0.6283 O.co2 1 UNL1 -0.8208
23 H 3.9983 2.6102 2.8870 H 1 UNL1 0.3097
24 HC 2.2216 4.8307 2.6539 H 1 UNL1 0.1170
25 HC1 1.3884 6.5226 0.9949 H 1 UNL1 0.1070
26 HC2 2.2196 6.4839 -1.3545 H 1 UNL1 0.1070
27 HC3 3.8879 4.7605 -2.0782 H 1 UNL1 0.1210
28 HC4 5.1431 2.7796 -2.4009 H 1 UNL1 0.0542
29 HC5 5.6007 1.3098 -1.5747 H 1 UNL1 0.0542
30 HC6 7.1858 3.8692 -1.9464 H 1 UNL1 0.0342
31 HC7 7.3846 3.0601 -0.4011 H 1 UNL1 0.0342
32 HC8 7.9289 0.8847 -1.6396 H 1 UNL1 0.0852
33 HC9 9.1126 2.1887 -1.7117 H 1 UNL1 0.0852
34 HC10 6.7776 -0.3858 -2.9647 H 1 UNL1 0.1695
35 HC11 5.0081 -1.3723 -4.3979 H 1 UNL1 0.1210
36 HC12 4.3133 -0.2204 -6.4962 H 1 UNL1 0.1140
37 HC13 5.3982 1.9246 -7.1580 H 1 UNL1 0.1210
38 HC14 7.1744 2.9149 -5.7012 H 1 UNL1 0.1695
@<TRIPOS>BOND
1 18 17 2
2 18 19 1
3 17 16 1
4 19 14 2
5 16 15 2
6 14 15 1
7 14 13 1
8 7 6 2
9 7 8 1
10 6 5 1
11 10 11 1
12 10 9 1
13 13 12 1
14 11 12 1
15 8 9 ar
16 8 3 ar
17 5 4 2
18 9 1 ar
19 3 4 1
20 3 2 ar
21 1 20 1
22 1 2 ar
23 21 20 ar
24 20 22 ar
25 2 23 1
26 24 4 1
27 25 5 1
28 26 6 1
29 27 7 1
30 28 10 1
31 29 10 1
32 30 11 1
33 31 11 1
34 32 12 1
35 33 12 1
36 34 15 1
37 35 16 1
38 36 17 1
39 37 18 1
40 38 19 1
@<TRIPOS>SUBSTRUCTURE
1 UNL1 1 RESIDUE 4 A UNL1 0 ROOT
49 changes: 49 additions & 0 deletions compounds/MCL1_ligands/lig_27.pdbqt
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REMARK Name = lig_27.pdbqt
REMARK 6 active torsions:
REMARK status: ('A' for Active; 'I' for Inactive)
REMARK 1 A between atoms: CA_1 and C_20
REMARK 2 A between atoms: C_9 and C_10
REMARK 3 A between atoms: C_10 and C_11
REMARK 4 A between atoms: C_11 and C_12
REMARK 5 A between atoms: C_12 and O_13
REMARK 6 A between atoms: O_13 and C_14
REMARK x y z vdW Elec q Type
REMARK _______ _______ _______ _____ _____ ______ ____
ROOT
ATOM 1 CA UNL A 1 4.940 2.233 1.004 0.00 0.00 +0.041 A
ATOM 2 N UNL A 1 4.097 2.865 1.916 0.00 0.00 -0.215 N
ATOM 3 C UNL A 1 3.501 3.874 1.187 0.00 0.00 -0.040 A
ATOM 4 C UNL A 1 2.572 4.824 1.627 0.00 0.00 -0.033 C
ATOM 5 C UNL A 1 2.109 5.770 0.690 0.00 0.00 -0.036 C
ATOM 6 C UNL A 1 2.581 5.748 -0.643 0.00 0.00 -0.071 C
ATOM 7 C UNL A 1 3.519 4.779 -1.058 0.00 0.00 +0.025 C
ATOM 8 C UNL A 1 3.966 3.842 -0.115 0.00 0.00 -0.071 A
ATOM 9 C UNL A 1 4.874 2.807 -0.248 0.00 0.00 -0.180 A
ATOM 10 H UNL A 1 3.998 2.610 2.887 0.00 0.00 +0.310 HD
ENDROOT
BRANCH 1 11
ATOM 11 C UNL A 1 5.795 1.077 1.418 0.00 0.00 +0.843 C
ATOM 12 O UNL A 1 5.700 0.727 2.587 0.00 0.00 -0.821 OA
ATOM 13 OXT UNL A 1 6.552 0.530 0.628 0.00 0.00 -0.821 OA
ENDBRANCH 1 11
BRANCH 9 14
ATOM 14 C UNL A 1 5.633 2.402 -1.496 0.00 0.00 +0.104 C
BRANCH 14 15
ATOM 15 C UNL A 1 7.099 2.896 -1.448 0.00 0.00 -0.026 C
BRANCH 15 16
ATOM 16 C UNL A 1 8.111 1.890 -2.042 0.00 0.00 +0.282 C
BRANCH 16 17
ATOM 17 O UNL A 1 8.078 1.923 -3.487 0.00 0.00 -0.352 OA
BRANCH 17 18
ATOM 18 C UNL A 1 7.082 1.342 -4.240 0.00 0.00 +0.134 C
ATOM 19 C UNL A 1 6.482 0.122 -3.877 0.00 0.00 -0.012 C
ATOM 20 C UNL A 1 5.481 -0.438 -4.689 0.00 0.00 +0.010 C
ATOM 21 C UNL A 1 5.090 0.212 -5.872 0.00 0.00 -0.071 C
ATOM 22 C UNL A 1 5.700 1.421 -6.244 0.00 0.00 +0.010 C
ATOM 23 C UNL A 1 6.698 1.980 -5.428 0.00 0.00 -0.012 C
ENDBRANCH 17 18
ENDBRANCH 16 17
ENDBRANCH 15 16
ENDBRANCH 14 15
ENDBRANCH 9 14
TORSDOF 6
95 changes: 95 additions & 0 deletions compounds/MCL1_ligands/lig_28.mol2
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@<TRIPOS>MOLECULE
lig_28.pdbqt
41 43 1 0 0
SMALL
AMBER ff14SB


@<TRIPOS>ATOM
1 C 7.1234 1.9823 -0.3641 C.ar 1 UNL1 -0.1862
2 CA 7.4252 3.3754 -0.6455 C.ar 1 UNL1 0.0483
3 N 8.3000 3.4696 -1.7323 N.ar 1 UNL1 -0.2144
4 C 8.5715 2.1793 -2.1456 C.ar 1 UNL1 -0.0433
5 C 9.4022 1.7752 -3.1982 C.2 1 UNL1 -0.1490
6 C 9.5409 0.3918 -3.4334 C.2 1 UNL1 -0.1450
7 C 8.8633 -0.5442 -2.6192 C.2 1 UNL1 -0.1800
8 C 8.0360 -0.1081 -1.5637 C.2 1 UNL1 -0.1050
9 C 7.9008 1.2699 -1.3543 C.ar 1 UNL1 -0.0730
10 C 6.1607 1.5021 0.6935 C.3 1 UNL1 0.0138
11 C 4.6803 1.7195 0.2977 C.3 1 UNL1 -0.1134
12 C 4.2487 0.9938 -0.9981 C.3 1 UNL1 0.1314
13 O 3.6817 -0.2974 -0.6922 O.2 1 UNL1 -0.3679
14 C 4.4859 -1.3765 -0.4112 C.2 1 UNL1 0.1201
15 C 4.6344 -1.7717 0.9271 C.2 1 UNL1 -0.1380
16 C 5.4407 -2.8736 1.2548 C.2 1 UNL1 -0.1300
17 C 6.0881 -3.5907 0.2362 C.2 1 UNL1 -0.1500
18 C 5.9232 -3.2105 -1.1064 C.2 1 UNL1 -0.1270
19 C 5.1168 -2.1060 -1.4420 C.2 1 UNL1 -0.0963
20 C 4.9551 -1.7122 -2.9045 C.3 1 UNL1 -0.0598
21 C 6.9319 4.6012 0.0484 C.2 1 UNL1 0.8383
22 OXT 6.1801 4.5215 1.0064 O.co2 1 UNL1 -0.8153
23 O 7.3229 5.6700 -0.4009 O.co2 1 UNL1 -0.8153
24 H 8.6456 4.3435 -2.0989 H 1 UNL1 0.3097
25 HC 9.9227 2.5042 -3.8108 H 1 UNL1 0.1160
26 HC1 10.1774 0.0436 -4.2412 H 1 UNL1 0.1060
27 HC2 8.9818 -1.6075 -2.8031 H 1 UNL1 0.1070
28 HC3 7.5183 -0.8160 -0.9249 H 1 UNL1 0.1250
29 HC4 6.3609 2.0191 1.6404 H 1 UNL1 0.0422
30 HC5 6.3359 0.4392 0.8921 H 1 UNL1 0.0422
31 HC6 4.0284 1.4186 1.1261 H 1 UNL1 0.0692
32 HC7 4.5135 2.7942 0.1588 H 1 UNL1 0.0692
33 HC8 5.0851 0.9094 -1.7028 H 1 UNL1 0.0562
34 HC9 3.4724 1.5997 -1.4811 H 1 UNL1 0.0562
35 HC10 4.1337 -1.2061 1.7061 H 1 UNL1 0.1450
36 HC11 5.5671 -3.1654 2.2935 H 1 UNL1 0.1220
37 HC12 6.7184 -4.4393 0.4862 H 1 UNL1 0.1190
38 HC13 6.4296 -3.7693 -1.8881 H 1 UNL1 0.1230
39 HC14 3.9342 -1.3699 -3.1146 H 1 UNL1 0.0500
40 HC15 5.6443 -0.9003 -3.1680 H 1 UNL1 0.0500
41 HC16 5.1627 -2.5560 -3.5732 H 1 UNL1 0.0500
@<TRIPOS>BOND
1 23 21 ar
2 5 4 2
3 5 6 1
4 3 4 ar
5 3 2 ar
6 21 2 1
7 21 22 ar
8 4 9 ar
9 6 7 2
10 2 1 ar
11 20 19 1
12 19 18 1
13 19 14 2
14 18 17 2
15 17 16 1
16 9 1 ar
17 9 8 2
18 16 15 2
19 14 15 1
20 14 13 1
21 7 8 1
22 12 13 1
23 12 11 1
24 1 10 1
25 11 10 1
26 3 24 1
27 25 5 1
28 26 6 1
29 27 7 1
30 28 8 1
31 29 10 1
32 30 10 1
33 31 11 1
34 32 11 1
35 33 12 1
36 34 12 1
37 35 15 1
38 36 16 1
39 37 17 1
40 38 18 1
41 39 20 1
42 40 20 1
43 41 20 1
@<TRIPOS>SUBSTRUCTURE
1 UNL1 2 RESIDUE 4 A UNL1 0 ROOT
51 changes: 51 additions & 0 deletions compounds/MCL1_ligands/lig_28.pdbqt
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REMARK Name = lig_28.pdbqt
REMARK 7 active torsions:
REMARK status: ('A' for Active; 'I' for Inactive)
REMARK 1 A between atoms: C_1 and C_10
REMARK 2 A between atoms: CA_2 and C_21
REMARK 3 A between atoms: C_10 and C_11
REMARK 4 A between atoms: C_11 and C_12
REMARK 5 A between atoms: C_12 and O_13
REMARK 6 A between atoms: O_13 and C_14
REMARK 7 A between atoms: C_19 and C_20
REMARK x y z vdW Elec q Type
REMARK _______ _______ _______ _____ _____ ______ ____
ROOT
ATOM 1 C UNL A 1 7.123 1.982 -0.364 0.00 0.00 -0.186 A
ATOM 2 CA UNL A 1 7.425 3.375 -0.645 0.00 0.00 +0.048 A
ATOM 3 N UNL A 1 8.300 3.470 -1.732 0.00 0.00 -0.214 N
ATOM 4 C UNL A 1 8.572 2.179 -2.146 0.00 0.00 -0.043 A
ATOM 5 C UNL A 1 9.402 1.775 -3.198 0.00 0.00 -0.033 C
ATOM 6 C UNL A 1 9.541 0.392 -3.433 0.00 0.00 -0.039 C
ATOM 7 C UNL A 1 8.863 -0.544 -2.619 0.00 0.00 -0.073 C
ATOM 8 C UNL A 1 8.036 -0.108 -1.564 0.00 0.00 +0.020 C
ATOM 9 C UNL A 1 7.901 1.270 -1.354 0.00 0.00 -0.073 A
ATOM 10 H UNL A 1 8.646 4.343 -2.099 0.00 0.00 +0.310 HD
ENDROOT
BRANCH 2 11
ATOM 11 C UNL A 1 6.932 4.601 0.048 0.00 0.00 +0.838 C
ATOM 12 OXT UNL A 1 6.180 4.521 1.006 0.00 0.00 -0.815 OA
ATOM 13 O UNL A 1 7.323 5.670 -0.401 0.00 0.00 -0.815 OA
ENDBRANCH 2 11
BRANCH 1 14
ATOM 14 C UNL A 1 6.161 1.502 0.694 0.00 0.00 +0.098 C
BRANCH 14 15
ATOM 15 C UNL A 1 4.680 1.720 0.298 0.00 0.00 +0.025 C
BRANCH 15 16
ATOM 16 C UNL A 1 4.249 0.994 -0.998 0.00 0.00 +0.244 C
BRANCH 16 17
ATOM 17 O UNL A 1 3.682 -0.297 -0.692 0.00 0.00 -0.368 OA
BRANCH 17 18
ATOM 18 C UNL A 1 4.486 -1.377 -0.411 0.00 0.00 +0.120 C
ATOM 19 C UNL A 1 4.634 -1.772 0.927 0.00 0.00 +0.007 C
ATOM 20 C UNL A 1 5.441 -2.874 1.255 0.00 0.00 -0.008 C
ATOM 21 C UNL A 1 6.088 -3.591 0.236 0.00 0.00 -0.031 C
ATOM 22 C UNL A 1 5.923 -3.211 -1.106 0.00 0.00 -0.004 C
ATOM 23 C UNL A 1 5.117 -2.106 -1.442 0.00 0.00 -0.096 C
ATOM 24 C UNL A 1 4.955 -1.712 -2.905 0.00 0.00 +0.090 C
ENDBRANCH 17 18
ENDBRANCH 16 17
ENDBRANCH 15 16
ENDBRANCH 14 15
ENDBRANCH 1 14
TORSDOF 6
95 changes: 95 additions & 0 deletions compounds/MCL1_ligands/lig_30.mol2
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@@ -0,0 +1,95 @@
@<TRIPOS>MOLECULE
lig_30.pdbqt
41 43 1 0 0
SMALL
AMBER ff14SB


@<TRIPOS>ATOM
1 C 2.9853 2.3369 -0.2136 C.ar 1 UNL1 -0.1932
2 CA 1.6653 2.8089 -0.2456 C.ar 1 UNL1 -0.0372
3 N 1.5043 3.5462 -1.4325 N.ar 1 UNL1 -0.2144
4 C 2.6930 3.5340 -2.1284 C.ar 1 UNL1 -0.0423
5 C 2.9885 4.1298 -3.3603 C.2 1 UNL1 -0.1470
6 C 4.2942 3.9672 -3.8679 C.2 1 UNL1 -0.1450
7 C 5.2563 3.2266 -3.1427 C.2 1 UNL1 -0.1750
8 C 4.9237 2.6398 -1.9037 C.2 1 UNL1 -0.1040
9 C 3.6188 2.8144 -1.4221 C.ar 1 UNL1 -0.0730
10 C 3.5719 1.4708 0.8736 C.3 1 UNL1 0.0148
11 C 3.1881 -0.0189 0.7248 C.3 1 UNL1 -0.1124
12 C 3.4618 -0.5637 -0.6968 C.3 1 UNL1 0.1284
13 O 3.5991 -2.0000 -0.6560 O.2 1 UNL1 -0.3399
14 C 4.6975 -2.6567 -0.1388 C.2 1 UNL1 0.1531
15 C 4.6036 -4.0454 0.0287 C.2 1 UNL1 -0.1770
16 C 5.6900 -4.7746 0.5387 C.2 1 UNL1 -0.1040
17 C 6.8792 -4.1108 0.8811 C.2 1 UNL1 -0.1850
18 C 6.9861 -2.7187 0.7159 C.2 1 UNL1 -0.0453
19 C 8.2714 -1.9958 1.0815 C.3 1 UNL1 -0.0528
20 C 5.8948 -1.9963 0.2018 C.2 1 UNL1 -0.2050
21 C 0.5617 2.6150 0.7403 C.2 1 UNL1 0.9268
22 OXT 0.7350 1.9674 1.7601 O.co2 1 UNL1 -0.8143
23 O -0.5067 3.1393 0.4579 O.co2 1 UNL1 -0.8143
24 H 0.6369 3.9921 -1.6926 H 1 UNL1 0.3097
25 HC 2.2384 4.6948 -3.9038 H 1 UNL1 0.1170
26 HC1 4.5616 4.4133 -4.8208 H 1 UNL1 0.1070
27 HC2 6.2590 3.1080 -3.5418 H 1 UNL1 0.1080
28 HC3 5.6542 2.0707 -1.3389 H 1 UNL1 0.1170
29 HC4 3.2666 1.8330 1.8633 H 1 UNL1 0.0422
30 HC5 4.6650 1.5566 0.8537 H 1 UNL1 0.0422
31 HC6 3.7369 -0.5995 1.4752 H 1 UNL1 0.0672
32 HC7 2.1221 -0.1452 0.9529 H 1 UNL1 0.0672
33 HC8 4.3635 -0.1088 -1.1237 H 1 UNL1 0.0627
34 HC9 2.6203 -0.2889 -1.3462 H 1 UNL1 0.0627
35 HC10 3.6802 -4.5494 -0.2375 H 1 UNL1 0.1400
36 HC11 5.6089 -5.8498 0.6685 H 1 UNL1 0.1180
37 HC12 7.7170 -4.6781 1.2758 H 1 UNL1 0.1190
38 HC13 5.9855 -0.9243 0.0742 H 1 UNL1 0.1550
39 HC14 8.8485 -2.5567 1.8269 H 1 UNL1 0.0407
40 HC15 8.0611 -1.0049 1.5033 H 1 UNL1 0.0407
41 HC16 8.9048 -1.8577 0.1971 H 1 UNL1 0.0407
@<TRIPOS>BOND
1 6 5 1
2 6 7 2
3 5 4 2
4 7 8 1
5 4 3 ar
6 4 9 ar
7 3 2 ar
8 8 9 2
9 23 21 ar
10 9 1 ar
11 2 21 1
12 2 1 ar
13 21 22 ar
14 1 10 1
15 13 12 1
16 13 14 1
17 15 14 2
18 15 16 1
19 12 11 1
20 14 20 1
21 20 18 2
22 16 17 2
23 17 18 1
24 18 19 1
25 10 11 1
26 3 24 1
27 25 5 1
28 26 6 1
29 27 7 1
30 28 8 1
31 29 10 1
32 30 10 1
33 31 11 1
34 32 11 1
35 33 12 1
36 34 12 1
37 35 15 1
38 36 16 1
39 37 17 1
40 38 20 1
41 39 19 1
42 40 19 1
43 41 19 1
@<TRIPOS>SUBSTRUCTURE
1 UNL1 2 RESIDUE 4 A UNL1 0 ROOT
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