[Zinc-fans] help

[John J. Irwin]

Hi Filippo

Thanks for your email.

Filippo Marchioni wrote:
> Dear ZINC users,
> I am new on this mailing list and I hope my question will be
> appropriate. 
>
> I notice that in compounds like ZINC01607240 
> (3-[4-[(4-amino-1,2-dimethyl-6-quinolyl)amino]-1,6-dimethyl-pyrimidin-2-yl]-1-(4-methoxyphenyl)-guanidine)
>
> the pyrimidin and the quinolin group are positively charged but the
> charge assigned in the mol2 file for these two nitrogen still negative.
> Am I completely missing the point or there is a problem?
>   
There may well be a problem with this molecule. However, the one you
describe is not it, I would say. The "charges" on the pyridine and the
quinoline are formally +1, but the partial atomic charge as calculated
at the semi-empirical level by AMSOL is delta negative. This is not
inconsistent, and should not be surprising. For example, many atoms will
have significant partial atomic charges (both + and -) and yet be
formally uncharged in a lewis structure.

Good luck!

John

> Thanks for your help
>
> best
> Filippo
>
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