[Chimera-users] Question: Why hydrogen bonds are not displayed?

[Elaine Meng]

Hi Kenji,
There is no single agreed method for finding H-bonds.  Different people may use different methods and parameter values, so it is not surprising if your calculations give different results sometimes.  However, we allow people to adjust parameters with the "Relax H-bond constraints" section.  You just need to experiment with increasing the values if you want to find a specific result.

In this case, you can find this "H-bond" by increasing the relax values to 1.5 angstroms and 45 degrees.  It has both a long distance and a poor angle.

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


> On Oct 15, 2022, at 2:54 AM, Kenji MATSUI via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Dear Chimera 
> 
> I am sorry to interrupt your busy schedule.
> 
> My name is Matsui, and I am a second-year master's student at a Japanese university.
> Thank you for taking time out of your busy schedule to respond to my question the other day.
> 
> I am now looking at protein-ligand interactions.
> 
> We found in the paper that His 421 interacted with another ligand.
> 
> Therefore, the interaction between His-421 and the ligand.
> 
> Problem :However, no hydrogen bonds were displayed.(first figure)
> 
> I would like you to ask why this is caused.
> 
> ----------------------------------------------------------
> <detail>
> This is because the distance between the His-421 and OH oxygen atoms was 3.7 Å.
> A ligand with a structure similar to this one in the paper formed a hydrogen bond with His-421 at 3.8 Å.
> 
> The thing  I tried 
> The Relax H-bond constraints section was adjusted from 3.0 to 5.0.
> 
> 
> <image.png>
> you can show this figure when you open the attached file
> 
> Wheat: Ligand  the other color:protein 
> 
> <image.png>
> 
> H-bond parameter
> <image.png>
> 
> ---------------------------------------------------------------------------
> 
> Kenji Matsui
>  Graduate School of Tokyo University of Agriculture and Technology　M2
> 2-24-16, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan
>  Mail: s214903z at st.go.tuat.ac.jp
> <LXRα_25-HC(overlay_1P8D).py>_______________________________________________
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