Hello, Recently, I countered such a question.
I can not get the good conformation for a small molecule with tri-phosphate, like below: https://www.rcsb.org/ligand/ET9 NC1=NC(=O)c2ncn([C@H]3C[C@H](O)[C@ @H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)C3=C)c2N1 The most difficult part I think is that it includes the tri-phosphate (too flexible). Can RDKit handle small molecules with tri-phosphate and get reasonable conformations? Thanks, Ming
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