On Thu, Nov 17, 2011, Crystal.CHIA-YU Ku wrote:
>
> I already did the literature, even if PubChem, checked FORMUL of the
> original pdb file, they all pointed out my ligand, thiamine monophosphate,
> carries one positive charge. But Junmei's and your point of view is that
> this ligand should carry one negative charge because two oxygen atoms of
> phosphate have no hydrogen. I am getting unclear and confused with the
> judgement criteria of ligand charge before running antechamber...
Antechamber can't tell you the answer. If you are near neutral pH, a
phosphate group will certainly not be neutral. If there is a metal ion near to
the phosphate in the structure, (not sure if this is true in your case), there
is even more reason to believe that the phosphate will be charged. Near
neutral pH, you might have either the -1 or the -2 charge, depending on the
environment in the protein. [I'm basically arguing by analogy to alkyl
phosphates here.]
....dac
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Received on Thu Nov 17 2011 - 20:00:03 PST
