Yes, I know HBDA is a distance-angle relation restraint rather than distance restraint. The problem is there's a pair with N-H...O angle 107 degree while H...O distance is 7.6A, which is obviously violated HBDA restraint, but not reported in violations. I think that term may be not used at all because they are too far away. By the way, that hydrogen bond is between protein and ligand, does it matter?
On Thu, Nov 3, 2016 at 3:12 PM, Charles Schwieters <[email protected]> wrote: > > Hello Qinhong-- > > > > > Does HBDA only work in a limited distance? I have this question because a > > hydrogen bond pair defined in my HBDA table is always far away (>6A) > from each > > other, while it is not reported in violations. Other hydrogen bond pairs > close > > from each other are normally reported if violated. So I think maybe the > software > > thinks there's no hydrogen bond at all when exceeding certain distance, > and thus > > not using that HBDA term? > > > > The HBDA term is not a distance restraint. Rather, it enforces a > geometrical > relationship between the HN-O distance and the O-HN-N angle. A > distance restraint is also required to keep the atoms close. Please > see J. Am. Chem. Soc. 124, 10621-10626 (2002). > > best regards-- > Charles > -- Qinhong Yu Ames' Lab Department of Chemistry UC Davis
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