Dear colleagues,
I got two conformers of a molecule. It looks like they have the same chirality
(S, I believe). But RDKit perceives them as different. Is it a bug, or did I
miss anything?
Thank you.
Ling
> mol = Chem.MolFromMolFile("input.sdf", removeHs=False)
> AllChem.AssignAtomChiralTagsFromStructure(mol)
> print Chem.FindMolChiralCenters(mol, includeUnassigned=True)
2tmn
981 3D
22 21 0 0 1 0 0 0 0 0999 V2000
35.3767 41.8461 -4.6496 N 0 3 0 0 0 0 0 0 0 0 0 0
36.3367 42.1451 -3.5550 C 0 0 0 0 0 0 0 0 0 0 0 0
35.5737 42.6599 -2.3579 C 0 0 0 0 0 0 0 0 0 0 0 0
34.7339 43.5557 -2.4146 O 0 0 0 0 0 0 0 0 0 0 0 0
37.3722 43.1800 -4.0056 C 0 0 0 0 0 0 0 0 0 0 0 0
38.2341 42.7854 -5.2225 C 0 0 0 0 0 0 0 0 0 0 0 0
39.2692 43.8812 -5.4952 C 0 0 0 0 0 0 0 0 0 0 0 0
38.9414 41.4435 -5.0422 C 0 0 0 0 0 0 0 0 0 0 0 0
34.8243 42.6729 -4.9120 H 0 0 0 0 0 0 0 0 0 0 0 0
38.0385 43.3928 -3.1576 H 0 0 0 0 0 0 0 0 0 0 0 0
36.8582 44.1246 -4.2354 H 0 0 0 0 0 0 0 0 0 0 0 0
34.7137 41.1107 -4.3682 H 0 0 0 0 0 0 0 0 0 0 0 0
36.8017 41.1954 -3.2735 H 0 0 0 0 0 0 0 0 0 0 0 0
35.8217 42.1824 -1.3952 H 0 0 0 0 0 0 0 0 0 0 0 0
37.5905 42.7227 -6.1080 H 0 0 0 0 0 0 0 0 0 0 0 0
38.7874 44.8596 -5.5986 H 0 0 0 0 0 0 0 0 0 0 0 0
39.8084 43.6821 -6.4271 H 0 0 0 0 0 0 0 0 0 0 0 0
40.0044 43.9489 -4.6849 H 0 0 0 0 0 0 0 0 0 0 0 0
39.5361 41.4235 -4.1223 H 0 0 0 0 0 0 0 0 0 0 0 0
38.2231 40.6192 -5.0070 H 0 0 0 0 0 0 0 0 0 0 0 0
39.6118 41.2416 -5.8851 H 0 0 0 0 0 0 0 0 0 0 0 0
35.8513 41.5073 -5.4975 H 0 0 0 0 0 0 0 0 0 0 0 0
1 9 1 0 0 0 0
2 1 1 1 0 0 0
1 12 1 0 0 0 0
1 22 1 0 0 0 0
2 3 1 0 0 0 0
2 5 1 0 0 0 0
2 13 1 0 0 0 0
3 4 2 0 0 0 0
3 14 1 0 0 0 0
5 6 1 0 0 0 0
5 10 1 0 0 0 0
5 11 1 0 0 0 0
6 7 1 0 0 0 0
6 8 1 0 0 0 0
6 15 1 0 0 0 0
7 16 1 0 0 0 0
7 17 1 0 0 0 0
7 18 1 0 0 0 0
8 19 1 0 0 0 0
8 20 1 0 0 0 0
8 21 1 0 0 0 0
M CHG 1 1 1
M END
$$$$
2tmn
3D
Structure written by MMmdl.
22 21 0 0 1 0 999 V2000
35.4170 41.5840 -4.5590 N 0 3 0 0 0 0
36.4970 42.1070 -3.7400 C 0 0 2 0 0 0
37.8260 41.4200 -4.0320 C 0 0 0 0 0 0
38.8450 42.1020 -3.8700 O 0 0 0 0 0 0
36.2170 41.9220 -2.2430 C 0 0 0 0 0 0
37.2180 42.4800 -1.2800 C 0 0 0 0 0 0
37.4030 43.9860 -1.5290 C 0 0 0 0 0 0
36.5540 42.0260 0.0330 C 0 0 0 0 0 0
34.7201 42.3022 -4.6959 H 0 0 0 0 0 0
36.1182 40.8543 -2.0470 H 0 0 0 0 0 0
35.2586 42.3951 -2.0289 H 0 0 0 0 0 0
34.9967 40.7910 -4.0956 H 0 0 0 0 0 0
36.6040 43.1723 -3.9446 H 0 0 0 0 0 0
37.8752 40.3930 -4.3626 H 0 0 0 0 0 0
38.1720 41.9677 -1.4048 H 0 0 0 0 0 0
37.8230 44.4527 -0.6380 H 0 0 0 0 0 0
36.4373 44.4382 -1.7551 H 0 0 0 0 0 0
38.0798 44.1347 -2.3704 H 0 0 0 0 0 0
37.3222 41.7052 0.7366 H 0 0 0 0 0 0
35.9921 42.8557 0.4619 H 0 0 0 0 0 0
35.8777 41.1957 -0.1700 H 0 0 0 0 0 0
35.7836 41.2949 -5.4546 H 0 0 0 0 0 0
1 9 1 0 0 0
1 2 1 0 0 0
1 12 1 0 0 0
1 22 1 0 0 0
2 3 1 0 0 0
2 5 1 0 0 0
2 13 1 0 0 0
3 4 2 0 0 0
3 14 1 0 0 0
5 6 1 0 0 0
5 10 1 0 0 0
5 11 1 0 0 0
6 7 1 0 0 0
6 8 1 0 0 0
6 15 1 0 0 0
7 16 1 0 0 0
7 17 1 0 0 0
7 18 1 0 0 0
8 19 1 0 0 0
8 20 1 0 0 0
8 21 1 0 0 0
M CHG 1 1 1
M END
$$$$
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