I believe the reason for the discrepancy here is that MolProbity by default places the hydrogens according to the centroid of the electron cloud (most relevant to x-ray crystallographic data) rather than the nuclear position. In a polar bond like N-H the difference can be quite substantial.
Cheers, Tristan Tristan Croll Research Fellow Cambridge Institute for Medical Research University of Cambridge CB2 0XY > On 28 Apr 2017, at 18:33, Bernhard Rupp <hofkristall...@gmail.com> 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/ > b...@hofkristallamt.org > +1 925 209 7429 > +43 767 571 0536 > ------------------------------------------------------ > Many plausible ideas vanish > at the presence of thought > ------------------------------------------------------ >
