Monday stereochemistry blues, Using RDKit 2011.09.01 on Ubuntu GNU Linux 10.10.
When generating smiles via the "AssignAtomChiralTagsFromStructure" method not all stereo centres are defined as highlighted in the following (and attached) example: Expected smiles (including stereo) O=C1N2[C@@H](C(=O)[O-])C(C)(C)[S@](=O)[C@@H]2[C@@H]1NC(=O)Cc1ccccc1 Actual smiles (including stereo) c1ccc(CC(N[C@@H]2C(=O)N3[C@@H](C([O-])=O)C(C)(C)S(=O)[C@@H]32)=O)cc1 The S atom is a chiral centre (it has lone pairs), but has no stereochemistry defined. Some code to make it easy to reproduce: #!/usr/bin/env python """ Try to show incomplete stereochem @author: JP """ from rdkit import Chem from rdkit.Chem import AllChem mol_block = """LIGAND Insight 3D 0 41 43 0 0 0 0 0 11.7930 -2.1560 2.0530 O 0 0 0 0 0 0 12.8370 -2.6800 2.3630 C 0 0 0 0 0 0 13.1500 -3.9790 2.7790 N 0 0 0 0 0 0 12.3530 -5.0080 3.3790 C 0 0 0 0 0 0 11.3694 -4.5981 3.6583 H 0 0 0 0 0 0 12.1060 -6.2040 2.4480 C 0 0 0 0 0 0 12.4880 -6.2830 1.3210 O 0 5 0 0 0 0 11.4180 -7.1670 3.1260 O 0 0 0 0 0 0 13.1470 -5.3640 4.6560 C 0 0 0 0 0 0 14.0770 -6.6000 4.5160 C 0 0 0 0 0 0 14.7870 -6.6663 5.3551 H 0 0 0 0 0 0 13.4778 -7.5255 4.5226 H 0 0 0 0 0 0 14.6587 -6.5895 3.5834 H 0 0 0 0 0 0 12.2410 -5.6410 5.8740 C 0 0 0 0 0 0 12.8362 -5.8400 6.7766 H 0 0 0 0 0 0 11.5663 -4.7993 6.0925 H 0 0 0 0 0 0 11.6123 -6.5243 5.6740 H 0 0 0 0 0 0 14.1410 -3.8690 5.0030 S 0 0 0 0 0 0 14.4550 -3.5580 3.2470 C 0 0 0 0 0 0 15.2531 -4.2250 2.8833 H 0 0 0 0 0 0 14.2560 -2.1940 2.5600 C 0 0 0 0 0 0 14.8058 -2.1200 1.6161 H 0 0 0 0 0 0 14.3180 -0.9860 3.3330 N 0 0 0 0 0 0 13.7535 -1.0201 4.1773 H 0 0 0 0 0 0 14.9890 0.1200 2.9310 C 0 0 0 0 0 0 15.6650 0.3130 1.9230 O 0 0 0 0 0 0 14.9000 1.2820 3.9200 C 0 0 0 0 0 0 14.3836 1.0079 4.8508 H 0 0 0 0 0 0 14.3046 2.0692 3.4318 H 0 0 0 0 0 0 16.3010 1.7990 4.2240 C 0 0 0 0 0 0 16.8270 2.9210 3.6010 C 0 0 0 0 0 0 16.2472 3.4402 2.8108 H 0 0 0 0 0 0 18.0650 3.4310 4.0050 C 0 0 0 0 0 0 18.4634 4.3517 3.5439 H 0 0 0 0 0 0 18.8150 2.7570 4.9800 C 0 0 0 0 0 0 19.7984 3.1790 5.2793 H 0 0 0 0 0 0 18.3160 1.6020 5.5910 C 0 0 0 0 0 0 18.8868 1.0485 6.3556 H 0 0 0 0 0 0 17.0490 1.1580 5.2140 C 0 0 0 0 0 0 16.6253 0.2330 5.6679 H 0 0 0 0 0 0 13.2820 -2.7090 5.3380 O 0 0 0 0 0 0 1 2 2 0 0 0 2 3 1 0 0 0 2 21 1 0 0 0 3 4 1 0 0 0 3 19 1 0 0 0 4 6 1 0 0 0 4 9 1 0 0 0 4 5 1 0 0 0 6 7 1 0 0 0 6 8 2 0 0 0 9 10 1 0 0 0 9 14 1 0 0 0 9 18 1 0 0 0 10 11 1 0 0 0 10 12 1 0 0 0 10 13 1 0 0 0 14 15 1 0 0 0 14 16 1 0 0 0 14 17 1 0 0 0 18 19 1 0 0 0 18 41 2 0 0 0 19 21 1 0 0 0 19 20 1 0 0 0 21 23 1 0 0 0 21 22 1 0 0 0 23 25 1 0 0 0 23 24 1 0 0 0 25 26 2 0 0 0 25 27 1 0 0 0 27 30 1 0 0 0 27 28 1 0 0 0 27 29 1 0 0 0 30 31 2 0 0 0 30 39 1 0 0 0 31 33 1 0 0 0 31 32 1 0 0 0 33 35 2 0 0 0 33 34 1 0 0 0 35 37 1 0 0 0 35 36 1 0 0 0 37 39 2 0 0 0 37 38 1 0 0 0 39 40 1 0 0 0 M END""" mol = Chem.MolFromMolBlock(mol_block) AllChem.AssignAtomChiralTagsFromStructure(mol) print Chem.MolToSmiles(mol, isomericSmiles=True) - Jean-Paul Ebejer Early Stage Researcher
<<attachment: no_chiral_centre_defined.png>>
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