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Thanks Ian.
Is it possible to force Jligand to keep only two hydrogens in this case? I tried setting the N's charge to 0, but it reverts back to 1 after regularization.

Thanks,
Abhinav
______________________________________
Abhinav Kumar, Ph.D.
The Joint Center for Structural Genomics
MS99, SLAC National Accelerator Laboratory
2575 Sand Hill Rd, Menlo Park, CA 94025
(650) 926-2992


On 08/07/2014 10:02 AM, Ian Tickle wrote:
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Hi, I would say three: aliphatic amines such as the one you show are weak bases so at neutral pH the protonated form predominates.  Aromatic amines are obviously trickier.

Cheers

-- Ian


On 7 August 2014 17:37, Abhinav Kumar <[log in to unmask]> wrote:
Hi,

I am making a ligand in Jligand (figure attached) and have a question about valency of nitrogen.
Jligand puts three hydrogens on nitrogen N1 when the ligand is regularized.

Should there be two hydrogens or three?

--
Thanks,
Abhinav
______________________________________
Abhinav Kumar, Ph.D.
The Joint Center for Structural Genomics
MS99, SLAC National Accelerator Laboratory
2575 Sand Hill Rd, Menlo Park, CA 94025
(650) 926-2992