User d83ec9d6e4
29-10-2006 12:26:54
When trying to canonicalize the following steroid structure, I recieve a warning about one chiral center, and the chirality information for that center is removed.
CC(C)(C1CC[C@@]([C@@]2(CC[C@]3(CCC(C)(C[C@@]3(C2=C4)[H])C)C(O)=O)C)5C)[C@H](O)CC[C@]1(C)[C@@]5([H])C4=O 3alpha-hydroxy-11-oxoolean-12-en-28-oic acid
C:\>molconvert smiles test.smi
WARNING: Chiral center has wrong connectivity at atom 7 in smiles: CC(C)(C1CC[C@@]([C@@]2(CC[C@]3(CCC(C)(C[C@@]3(C2=C4)[H])C)C(O)=O)C)5C)[C@H](O)CC[C@]1(C)[C@@]5([H])C4=O 3alpha-hydroxy-11-oxoolean-12-en-28-oic acid
The chirality is ignored.
[H][C@]12CC(C)(C)CC[C@@]1(CC[C@]3(C)C2=CC(=O)[C@]4([H])[C@@]5(C)CC[C@@H](O)C(C)(C)C5CCC34C)C(O)=O
Note that the output structure is different from the input structure, so for my purposes it is not useable.
This problem appears whenever I use this molecule (and many other steroid structures) with molconvert, mview, etc. I've checked this smiles string with Daylight's depict, ChemDraw, and none of these applications complain about this smiles string - it appears to me to be a completely valid smiles string. I suspect that this might be an bug in the JChem package itself.
http://www.daylight.com/daycgi/depict?434328432928433143435b4340405d285b4340405d322843435b43405d332843434328432928435b4340405d332843323d4334295b485d29432943284f293d4f2943293543295b4340485d284f2943435b43405d312843295b4340405d35285b485d2943343d4f
Any help would be very appreciated.
Noel
CC(C)(C1CC[C@@]([C@@]2(CC[C@]3(CCC(C)(C[C@@]3(C2=C4)[H])C)C(O)=O)C)5C)[C@H](O)CC[C@]1(C)[C@@]5([H])C4=O 3alpha-hydroxy-11-oxoolean-12-en-28-oic acid
C:\>molconvert smiles test.smi
WARNING: Chiral center has wrong connectivity at atom 7 in smiles: CC(C)(C1CC[C@@]([C@@]2(CC[C@]3(CCC(C)(C[C@@]3(C2=C4)[H])C)C(O)=O)C)5C)[C@H](O)CC[C@]1(C)[C@@]5([H])C4=O 3alpha-hydroxy-11-oxoolean-12-en-28-oic acid
The chirality is ignored.
[H][C@]12CC(C)(C)CC[C@@]1(CC[C@]3(C)C2=CC(=O)[C@]4([H])[C@@]5(C)CC[C@@H](O)C(C)(C)C5CCC34C)C(O)=O
Note that the output structure is different from the input structure, so for my purposes it is not useable.
This problem appears whenever I use this molecule (and many other steroid structures) with molconvert, mview, etc. I've checked this smiles string with Daylight's depict, ChemDraw, and none of these applications complain about this smiles string - it appears to me to be a completely valid smiles string. I suspect that this might be an bug in the JChem package itself.
http://www.daylight.com/daycgi/depict?434328432928433143435b4340405d285b4340405d322843435b43405d332843434328432928435b4340405d332843323d4334295b485d29432943284f293d4f2943293543295b4340485d284f2943435b43405d312843295b4340405d35285b485d2943343d4f
Any help would be very appreciated.
Noel