Wrong Phosphate Bond order

[FinnOD]

Hi,

Excellent work, thank you.

In 5u8c_84J_B_301_ligand_refined.sdf the phosphorus has valence 6 instead of 5. This is due to two of the oxygens being double bonded to the phosphorus, and one single bonded, whereas it should be two single bonds (P-O(-)) and one double bond (P=O). The RDKit will error when sanitizing this.

I am referring to files found in the figshare archive, perhaps this issue has already been fixed?

Kind regards,

Finn

[KSUN63]

Hi Finn,

Thanks and nice catch! We will have to look a bit more closely with our algorithm but based on some initial quick checks, this issue shouldn't have happened in the first place. The SMILES string here looks correct: https://www.rcsb.org/ligand/84J

Best,
Oliver

[FinnOD]

Cool! It is interesting that its fine on the PDB, maybe dimorphite screwed it up? I was surprised you didn't find it with this check.

If I find more issues like this, should each type of case be its own GitHub issue, or would you prefer them in one agglomerated issue?

[KSUN63]

Yes, that's certainly bizarre since we have additional ligand SMILES check as well so in the end everything is supposed to be RDKit-parsable. I'd appreciate if you can have one file for all of the errors so we can deal with it when we have time.