I have been looking at the pKa scan for a molecule, single_ligand.sdf, attached below. At pH 7.4 one species dominates over the other, with about 78% versus 22%. The 78% molecule has an imidazole ring where one nitrogen has no hydrogen atom attached and is negatively charged. The 22% molecule has a 'normal' imidazole ring where the nitrogen has a hydrogen atom attached and is neutral.
When I then look at the dominant tautomer distribution, taking into account pH effects at pH 7.4, regardless of which protonation state (the 88% or the 22% one) I choose as a starting point, I end up with the exact same tautomer distribution, where the most dominant tautomer (with 100% distribution) has the 'normal' imidazole ring.
My question is: can the tautomer plugin entirely add/remove a hydrogen atom from a structure, thus modifying the total formal charge of the molecule? If so, then would you recommend that I do not calculate the major microspecies prior to calculating the dominant tautomer distribution, as it is taken into account when selecting the option to consider pH effect?