'Most distances between bonded atoms were settled long ago
to high accuracy, but, in the case of
hydrogens, the values in common use often differ by
as much as 20%.'
Phenix / MolProbity Hydrogen Parameter Update
Deis, L. N., Verma, V., Videau, L. L., Prisant, M. G., Moriarty, N. W.,
Headd, J. J., Chen, V. B., Adams, P. D., Snoeyink, J., Richardson, J. S. &
Richardson, D. C. (2013). Comput. Crystallogr. Newsl. 4, 9–10.
On 28 Apr 2017, at 18:33, Bernhard Rupp <[email protected]> wrote:
Dear Fellows of the Bond,
when validating a QM refined homology model with Molprobity, I noticed various
8 sigma deviations in the carbon-hydrogen bond distances.
Out of curiosity, I then used refmac to calculate riding Hs for the same model,
and at least in one instance (N-H backbone) there are
significant differences between Molprobity and Refmac H bond distances
(differences to the QM distances in other
instances I find interesting, but less relevant for us).
The riding H vs Molprobity presumably should be consistent, because if we use
them in VDW restraints but
they differ from the validation target, systematic bias will occur. I have no
feel how significant that effect
might be – maybe someone more erudite can comment.
Examples
distance MP REF QM
backbone N-H 0.86 1.01 1.00
phenyl C-H 0.93 0.93 1.09
Best, BR
PS: If someone has accurate experimental values for CH distances I’d appreciate
a link.
No access to CSD.
------------------------------------------------------
Bernhard Rupp
Crystallographiae Vindicis Militum Ordo
http://www.hofkristallamt.org/ <http://www.hofkristallamt.org/>
[email protected] <mailto:[email protected]>
+1 925 209 7429
+43 767 571 0536
------------------------------------------------------
Many plausible ideas vanish
at the presence of thought
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Dr Ben Bax
York Structural Biology Laboratory,
Department of Chemistry,
University of York,
York YO10 5DD
[email protected]
