Hi all,
I'm struggling to understand aromatic bond assignment. Are the rings of flavin aromatic? I think that the answer to that is probably yes, but what does that mean? I thought that a 6-membered ring was considered aromatic if all of the bonds of the ring were aromatic. Is this correct? Should I instead check for aromatic systems by looking at the atoms of rings (instead of the bonds of rings)? The RDKit-generated SMILES string seems to suggest aromatic rings. I am confused.
If I take either flavin.mol or the bond orders from the chemical component dictionary and make an RDKit molecule and ask RDKit to assign aromaticity (as happens by default, I understand when using Chem.MolFromMolFile()) then the C4X-C10 bond is assigned as single - not aromatic, like its neighbours. I thought that it should be aromatic. Is that a mistake?
Thanks,
Paul.
from rdkit import Chem
m = Chem.MolFromMolFile('flavin.mol')
for bond in m.GetBonds():
print bond.GetBeginAtomIdx(), bond.GetEndAtomIdx(), bond.GetBondType()
flavin.mol
Description: MOL mdl chemical test
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