Hi, I've got two questions: 1) am trying to convert smiles to 3D structures, using gen3D, but babel appears to have issues with the stereochemistry: example: MDL mol file with desired stereo-chemistry, including 3D-coords and protons: mol-beclomethasone_dipropionate.mol (included below)
prompt> /usr/local/babel3/bin/obabel -imol mol-beclomethasone_dipropionate.mol -ocan -O canfrommolob3.canprompt> /usr/local/babel3/bin/obabel --gen3D -ican canfrommolob3.can -omol -O molfromcanob3.mol==============================*** Open Babel Warning in CorrectStereoAtoms Could not correct 4 stereocenter(s) in this molecule (SW03057) with Atom Ids as follows: 9 10 15 16 Warning: Stereochemistry is wrong, using the distance geometry method instead 1 molecule converted prompt>cat canfrommolob3.can OCC(=O)[C@@]1(O)[C@@H](C)C[C@@H]2[C@]1(C)C[C@H](O)[C@]1([C@H]2CCC2=CC(=O)C=C[C@]12C)Cl SW03057 original mol file included below. if i view the original input mol (mol-beclomethasone_dipropionate.mol) and the output molfromcanob3.mol they have different stereo chemistry which is obviously unexpected/wrong- is there a way to get what I want?(I work on debian/buster, the example above was babel 3.0.0a2, but with 2.4.1 I see the same problem) 2) I have a bunch of sdf files, including 3D coords and protons, some of the molecules are charged (e.g. protonated amines, etc) is there a way to automatically neutralize them (convert them to to the same molecules but with net charge zero)? thanks for any help!regardsMichael the original mol file: SW03057 -OEChem-08191318353D 57 60 0 1 0 0 0 0 0999 V2000 2.7904 3.1944 -1.2372 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9065 1.2037 -0.1442 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7440 2.4222 -1.5463 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8560 0.4283 -0.4566 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9498 2.6329 -0.5186 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7054 -1.4928 0.7641 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8229 -1.0183 -0.0282 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5744 -1.3353 0.7919 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1941 -2.5950 1.4462 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2856 0.6538 -0.1370 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2829 -0.8792 0.0856 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.9646 -1.1753 0.9356 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.6530 -2.5542 1.9723 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.0401 1.0985 -0.9481 C 0 0 2 0 0 0 0 0 0 0 0 0 1.6235 0.9382 -1.2204 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.3116 -1.3107 1.2916 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.2890 -0.8538 0.2047 C 0 0 2 0 0 0 0 0 0 0 0 0 0.3301 0.6457 -0.3294 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.3392 -3.9024 1.7819 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6246 0.2259 -2.5976 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4992 -1.6908 -1.0890 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5876 -0.2625 0.7623 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9180 3.3313 -0.2373 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.0973 -2.5859 0.3583 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.1805 0.6410 -2.2876 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.5148 -0.2934 2.2788 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.5313 -0.3272 -0.2860 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5008 1.6620 1.2207 Cl 0 0 0 0 0 0 0 0 0 0 0 0 2.8164 4.2435 -1.5079 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7594 0.8162 0.4029 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9225 2.8850 -2.0890 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8546 -1.6610 -0.9161 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7081 -1.2789 0.5649 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5427 -2.4183 0.9613 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6567 -0.8743 1.7837 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0640 -3.3335 0.6474 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5002 -2.8567 2.2521 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3226 1.2482 0.7830 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1979 0.8981 -0.6959 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2147 -1.4824 -0.8253 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8898 -0.5529 1.8379 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6038 -2.3774 3.0558 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0645 2.1937 -1.0083 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4170 -4.1332 0.7199 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3396 -3.8743 2.2129 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7629 -4.6855 2.2738 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5409 -0.8397 -2.4359 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5509 0.4560 -3.1052 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7827 0.5848 -3.1732 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4975 -2.7371 -0.8227 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6912 -1.4732 -1.7712 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4472 -1.4132 -1.5248 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9730 0.6332 0.6370 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1277 -0.2099 1.7113 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9899 1.0465 -2.6375 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1426 -0.6597 2.9178 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.0693 0.4831 -0.2416 H 0 0 0 0 0 0 0 0 0 0 0 0 1 3 2 0 0 0 0 1 5 1 0 0 0 0 2 4 2 0 0 0 0 2 5 1 0 0 0 0 3 15 1 0 0 0 0 4 7 1 0 0 0 0 4 15 1 0 0 0 0 5 23 2 0 0 0 0 6 16 1 0 0 0 0 6 22 1 0 0 0 0 6 24 2 0 0 0 0 7 8 1 0 0 0 0 8 11 1 0 0 0 0 9 12 1 0 0 0 0 9 13 1 0 0 0 0 10 14 1 0 0 0 0 10 17 1 0 0 0 0 11 12 1 0 0 0 0 11 18 1 0 0 0 0 12 17 1 0 0 0 0 13 16 1 0 0 0 0 13 19 1 0 0 0 0 14 18 1 0 0 0 0 14 25 1 0 0 0 0 15 18 1 0 0 0 0 15 20 1 6 0 0 0 16 17 1 0 0 0 0 16 26 1 1 0 0 0 17 21 1 6 0 0 0 18 28 1 1 0 0 0 22 27 1 0 0 0 0 1 29 1 0 0 0 0 2 30 1 0 0 0 0 3 31 1 0 0 0 0 7 32 1 0 0 0 0 7 33 1 0 0 0 0 8 34 1 0 0 0 0 8 35 1 0 0 0 0 9 36 1 0 0 0 0 9 37 1 0 0 0 0 10 38 1 0 0 0 0 10 39 1 0 0 0 0 11 40 1 6 0 0 0 12 41 1 1 0 0 0 13 42 1 1 0 0 0 14 43 1 1 0 0 0 19 44 1 0 0 0 0 19 45 1 0 0 0 0 19 46 1 0 0 0 0 20 47 1 0 0 0 0 20 48 1 0 0 0 0 20 49 1 0 0 0 0 21 50 1 0 0 0 0 21 51 1 0 0 0 0 21 52 1 0 0 0 0 22 53 1 0 0 0 0 22 54 1 0 0 0 0 25 55 1 0 0 0 0 26 56 1 0 0 0 0 27 57 1 0 0 0 0 M END $$$$
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