[Chimera-users] H-Bond Parameters

Elaine Meng meng at cgl.ucsf.edu
Thu Jul 16 14:16:24 PDT 2020

Hi Luke,
It is a little more complicated  than that.  Chimera uses the detailed parameters in tables 5-8 of 

Three-dimensional hydrogen-bond geometry and probability information from a crystal survey. Mills JE, Dean PM. J Comput Aided Mol Des. 1996 Dec;10(6):607-22.

... and there are several different angles that need to be satisfied.

Looks like these H2SO4 molecules are the donor type with distance and angle values in Table 8, and acceptor type with distance and angle values in Table 5.  All criteria (within the tolerances) must be satisfied. The definitions of the different angles are given in figures in the paper.  If you do not have fulltext access to this paper, let me know.

Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jul 16, 2020, at 10:05 AM, Luke Kurfman-Student <luke.kurfman at furman.edu> wrote:
> Hello Sr./Ms.,
> I'm using UCSF Chimera to analyze the hydrogen bonding of some structures of mine, in this case a system of three sulfuric acids. When I attempt to analyze this structure by changing the "Relax constraints by:" :<image.png>
> The bond on the left gets eliminated before the bond on the right, even though by calculating the angle with the Angles/Torsion tool, between the O--H-------O of each hydrogen bond, I get an angle of 146.337 for the bond on the left, whereas for the angle on the right I get an angle of 144.189. It should not logically cut off the hydrogen bond on the left before the one on the right since the left hydrogen bond is shorter and straighter. Thus, I'm wondering why is chimera cutting the left angle off, and also is there a way for it to automatically display what chimera finds is the bond angle without using the angle/torsion tool? I've also tried different combinations of 3-4 atoms to get different bond angles, but no success in determining this difference. By adjusting the H-bond constraints by trial and error, the bond angle difference appears to be about 1.603 degrees according to what chimera automatically finds:
> <image.png>
> Any help is appreciated,
> Luke
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