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

[Kenji MATSUI]

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.

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<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: image.png]
you can show this figure when you open the attached file

Wheat: Ligand  the other color:protein

[image: image.png]

H-bond parameter
[image: image.png]

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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
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