Ligand adding H issue and new unsupported ion record

[KleinesMesser]

Bad ligand protonation:

• SO4^2- is added with two H atoms, making it a neutral molecule when pH=7.
• EPE in 3WIW
• U12 in 2GG2. This time it is not only protonation status problem. N2 in U12 has 5 covalent bonds ...
• GLV in 4PXE. Oxoacetic acid becomes hydroxyacetic acid. This could be a tricky one because if there are no H atoms, it is hard for the algorithm to distinguish if C-O is a double bond or a single bond.
• SAM in 1rjd. S+ atom is added to 4 valance.
• FAD in 2YG4
• TPO in 5TJ3

New ion:

• MN (Mn+2) in 1K20.

Name of co-crystal molecules:

• GOL in 1K20
• EDO in 2VC7

[shaoqx]

Softwares to try: Standalone ligand protonation:

• RDkit (https://www.rdkit.org/)
• reduce (http://kinemage.biochem.duke.edu/software/README.reduce.html)
• Dimorphite (from https://durrantlab.pitt.edu/dimorphite-dl/) - requires SMILES?
• Protons from OpenMM (https://protons.readthedocs.io/en/latest/) - Constant pH MD
• Protonate3D (http://www.ccl.net/cca/documents/proton/proton.htm)
• LigPrep using Epik v7 (https://www.schrodinger.com/products/ligprep, https://pubs.acs.org/doi/10.1021/acs.jctc.3c00044)

Coupled with polypeptide protonation

• Protoss (https://doi.org/10.1186/1758-2946-6-12; https://proteins.plus/)
• MCCE2 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2735604/) - looks too many manual steps

(current: PyBel)

[shaoqx]

Another option will be just use the ligand database from PDB as initial input and see how it can advance