Solved: The script we used (from deepchem) converts the ligand into PDB format, and I assume that based on spatial proximity, a covalent bond between an oxygen and a fluorine was formed erroneously.
From: Greg Landrum <greg.land...@gmail.com> Sent: Thursday, June 6, 2019 8:25 PM To: Mateo Vacacela <mvacac...@cdrd.ca> Cc: rdkit-discuss@lists.sourceforge.net Subject: Re: [Rdkit-discuss] Sanitization Error: Explicit valence greater than permitted for normal protein On Thu, Jun 6, 2019 at 8:00 PM Mateo Vacacela <mvacac...@cdrd.ca<mailto:mvacac...@cdrd.ca>> wrote: Just as a follow up, I’m getting a similar error with the following ligand molecule: ValueError: Sanitization error: Explicit valence for atom # 21 F, 2, is greater than permitted Again, the error message is telling you what the problem is: there's an F atom in the structure (#21) that has a valence of 2. That's illegal for F. Two notes about the SDF that you included in your message: 1) the SDF format is an old one and is sensitive to the amount of whitespace. When you copied the text into your email some spaces got lost, which makes the file unuseable. 2) The structure in that file does not produce the error message you report. After editng the file by hand to add the spaces back in (I've attached the editing file to the message), I was able to read it without problems: In [16]: m = Chem.MolFromMolFile('/tmp/ligand.mol') In [17]: Best, -greg
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