[Chimera-users] FindHBond tool not finding H-bonds with sulfur?

Eric Pettersen pett at cgl.ucsf.edu
Tue Jun 12 14:49:55 PDT 2018

Hi Gustavo,
	When defining hydrogen bonds, there are atoms that are clearly good donors or acceptors, and then there are others that could be considered very weak donors or acceptors (e.g. some forms of carbon as a donor).  Neutral sp3 sulfur as an acceptor is also such as case.  As per Geometric characteristics of hydrogen bonds involving sulfur atoms in proteins (https://doi.org/10.1002/prot.22327 <https://doi.org/10.1002/prot.22327>):

	"It is revealed that sulfur atom is a very poor H‐bond acceptor, but a moderately good H‐bond donor.”

We have chosen not to include very weak donors and acceptors in Chimera’s detection of hydrogen bonds.  Nonetheless, if you wish to have Chimera treat neutral sp3 sulfur as an acceptor, this can be accomplished with a fairly simple edit of Chimera’s code.  Namely edit the file <your Chimera>/share/FindHBond/base.py and find the lines that look like this (should be lines 404 and 405):

        genericAccInfo['Sar'] = genericAccInfo['S3-'] = (accGeneric,
                        _processArgTuple([3.83, 85], distSlop, angleSlop))

Below them, add two more lines for the neutral sp3 sulfur acceptor:

        genericAccInfo['S3'] = (accGeneric,
                        _processArgTuple([3.83, 89], distSlop, angleSlop))

Maintain the indentation level; indentation is significant in the Python language. If you are using a Mac, then <your Chimera> is Chimera.app/Contents/Resources.  With those two lines added, Chimera finds two hydrogen bonds involving the sulfur.


	Eric Pettersen
	UCSF Computer Graphics Lab

> On Jun 11, 2018, at 2:30 PM, Gustavo Seabra <gustavo.seabra at ufpe.br> wrote:
> Hi there,
> I’m trying to use the findHBond tool to count Hbonds in a system. However, I noticed ti does not find any HB involving sulfur atoms in my system.
> I’ve put together a simple example system here to show what I mean. After opening the files, I do:
> 1. Select the ligand (Select > Residue > LIG)
> 2. Tools > Surface/Binding Analysis > FindHBonds
> 3. Find These Bonds: Both
> 4. Relax H-bond constraints: (I tried even relaxing to 1A and 30deg, with no change)
> 5. Select “Only find H-bonds with at least one end selected”
> 6. Hit Apply.
> Chimera does find some HBonds involving nitrogen and oxygen, but no HBond is found involving the sulfur atom on the ligand, even though there is a serine (Ser525) close enough to make a HBond to the ligand S atom.
> So, I wonder what I am doing wrong here? Am I skipping any steps? I have checked in a different program (PoseView) and it can find the bond with no problem.
> Thank you very much,
> --
> Gustavo Seabra
> <6MMPr_1.mol2><receptor.pdb>
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