[Chimera-users] Criteras about hydrogen bonds in chimera

Elaine Meng meng at cgl.ucsf.edu
Mon Mar 31 16:00:53 PDT 2008

Hi Junwei,
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  
those amounts).
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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