Good afternoon,
I am generating 3D structures in .pdb format starting from smiles
notation. I am working with chiral molecules, and noted that the 3D
structure obtained when generating the molecule explicitly indicating
the configuration of the stereocenter is sligthly different from that
obtained when the configuration of the stereocenter is not explicitly
indicated. A pair of examples are as follows:
#No explicit stereochemistry in the 1st chiral center
m =
Chem.MolFromSmiles('CCCCC(C(=O)COc1c(F)c(F)cc(F)c1F)n1cc([C@@](C)(NCc2ccn3nccc3n2)C2CCCC2)nn1´)
m3d = Chem.AddHs(m)
AllChem.EmbedMolecule(m3d, AllChem.ETKDG())
print(Chem.MolToPDBBlock(m3d, flavor=2),file = open(' molecule1.pdb', 'w+'))
#Explicit stereochemistry in the 1st chiral center
m =
Chem.MolFromSmiles('CCCC[C@@H](C(=O)COc1c(F)c(F)cc(F)c1F)n1cc([C@@](C)(NCc2ccn3nccc3n2)C2CCCC2)nn1´)
m3d = Chem.AddHs(m)
AllChem.EmbedMolecule(m3d, AllChem.ETKDG())
print(Chem.MolToPDBBlock(m3d, flavor=2),file = open(' molecule2.pdb', 'w+'))
So in both cases I get the S,S enantiomers, but molecule1 is not
perfectly superimposable on molecule2, which leads to further resp
fitted charges differences.
Any idea why expicitly indicating the configuration of the first
stereocenter is giving slighlty different results regarding the 3D
conformation compared to not indicating it?
Thanks in advance for the help,
best regards
Alfredo
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