> I use babel to remove salts from smiles and I have encountered that babel
> changes heterocyclic compounds with nitrogens, see example below.
This will trigger aromaticity perception, but the structure is unchanged.
> input:
> C[C@H](CN1CCC(CC1)N2C(=O)Nc3cc(Cl)ccc23)NC(=O)c4cc5ccccc5[nH]4.OC(=O)C(F)(F)F
vs.
> output: C[C@H](CN1CCC(CC1)n1c(=O)[nH]c2cc(Cl)ccc12)NC(=O)c1cc2ccccc2[nH]1
If I depict these, e.g.
https://cactus.nci.nih.gov/chemical/structure/C%5BC@H%5D(CN1CCC(CC1)N2C(=O)Nc3cc(Cl)ccc23)NC(=O)c4cc5ccccc5%5BnH%5D4.OC(=O)C(F)(F)F/image
<https://cactus.nci.nih.gov/chemical/structure/C[C@H](CN1CCC(CC1)N2C(=O)Nc3cc(Cl)ccc23)NC(=O)c4cc5ccccc5[nH]4.OC(=O)C(F)(F)F/image>
https://cactus.nci.nih.gov/chemical/structure/C%5BC@H%5D(CN1CCC(CC1)n1c(=O)%5BnH%5Dc2cc(Cl)ccc12)NC(=O)c1cc2ccccc2%5BnH%5D1/image
<https://cactus.nci.nih.gov/chemical/structure/C[C@H](CN1CCC(CC1)n1c(=O)[nH]c2cc(Cl)ccc12)NC(=O)c1cc2ccccc2[nH]1/image>
There is no difference. What's happened is that in the Open Babel aromaticity
model, the [nH]c(=O)n motif is aromatic. In your input, it's marked as
aliphatic.
The bond orders are otherwise identical. What bonds are added?
-Geoff
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