I would like to run an MD simulation at pH 7.4 for a protein-ligand system where the ligand is coenzyme A. How can I decide the protonation state of coenzyme A? I've seen in some sources that H's attached to phosphate groups break off (form O- there) and thus coenzyme A is deprotonated, but I'm not sure if this happens at pH 7.4.
I would appreciate your help. Thank you!