[Chimera-users] Criteras about hydrogen bonds in chimera
meng at cgl.ucsf.edu
Mon Mar 31 16:00:53 PDT 2008
FindHBond (and command "findhbond" or "hbonds") uses detailed
criteria that depend on the atom types. There isn't just one
distance or angle, but different ones for different combinations of
donor and acceptor types.
As mentioned here,
the cutoffs are from a paper based on very-high-resolution small
molecule crystal structures:
J.E.J. Mills and P.M. Dean, "Three-dimensional hydrogen-bond geometry
and probability information from a crystal survey" J Comput-Aided Mol
Des 10: 607 (1996).
The cutoffs are in Tables 5-8. Depending on the atom types, there
may be two or three angle criteria, and donor-acceptor distance
criteria are mostly near 3.0-3.4, although they range from 2.87
(protonated carboxylic acid donor) to 3.73 (thiocarbonyl acceptor).
In addition, because structures in the PDB are generally lower
resolution than those small molecules, the values from the paper are
relaxed by 0.4 angstroms and 20 degrees (by default; you can change
Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
On Mar 28, 2008, at 1:17 AM, zhaojunwei wrote:
> Hi, all
> I have a question about the hbond. What is the definition about
> hydrogen bond in chimera?
> As we know, there're different criterias among softwares, I'm
> wondering the distence between donor atom and acceptor atom, and
> the angle of donor-hydrogen-acceptor in chimera.
> Any reply will be deeply appreciated!
> It'll be kind if you can send the reply to my address, cause I'm
> not in the mailing list.
> Junwei Zhao
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