I am generating 3D structures from canonical SMILES and I am facing several
issues.
The first is that OpenBabel does not seem to be able to produce structures
with the right sterochemistry in certain cases (even if it is explicitly
indicated in the SMILES). As far as I can tell, this happens with fused
rings where both (contiguous) shared atoms are sterocenters.
The workaround I found is converting the SMILES to mol2 with Balloon
(because Omega2 fails with a few of them) and then:
obabel ${ligandid}.mol2 -O ${ligandid}.sdf --conformer --nconf 200 --score
energy --writeconformers
The problem is that obabel seems to reprotonate certain functional groups
(such as carboxylic acids which are deprotonated on purpose). Is there a way
to prevent such behaviour?
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