# Unusual bonds in -OSO3 of ligand after docking

**URL:** <https://ask.bioexcel.eu/t/unusual-bonds-in-oso3-of-ligand-after-docking/5951>\
**Category:** Uncategorized\
**Created:** [November 14, 2025, 7:32am UTC](https://ask.bioexcel.eu/t/unusual-bonds-in-oso3-of-ligand-after-docking/5951 "2025-11-14T07:32:52Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![ef25](https://avatars.discourse-cdn.com/v4/letter/e/b38774/32.png) [@ef25](https://ask.bioexcel.eu/u/ef25)\
**Post date:** [November 14, 2025, 7:32am UTC](https://ask.bioexcel.eu/t/unusual-bonds-in-oso3-of-ligand-after-docking/5951/1 "2025-11-14T07:32:52Z")

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Hello! I made my ligand molecule using Chemdraw and Chem3D. Before docking, I made sure that the pdb file has the correct format for docking. However, after docking, all my ligands have this unusual bond formed which I am sure is not in the beginning pdb file of ligand. I only input within ring dihedral angle restraints at force constant = 400. Are these unusual bonds a cosnequence of high force constant?

 ![image](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/2X/a/a5321459157b20edd7137af05cce1617b72ffad6.png)

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**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\
**Post date:** [November 14, 2025, 7:51am UTC](https://ask.bioexcel.eu/t/unusual-bonds-in-oso3-of-ligand-after-docking/5951/2 "2025-11-14T07:51:40Z")

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It is most likely a visualization issue

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**Author:** ![ef25](https://avatars.discourse-cdn.com/v4/letter/e/b38774/32.png) [@ef25](https://ask.bioexcel.eu/u/ef25)\
**Post date:** [November 14, 2025, 8:11am UTC](https://ask.bioexcel.eu/t/unusual-bonds-in-oso3-of-ligand-after-docking/5951/3 "2025-11-14T08:11:10Z")

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I tried to submit it for Refinement and the bond is gone. So if it is only a visualization issue, is it okay to not do the refinement?

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**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\
**Post date:** [November 14, 2025, 8:26am UTC](https://ask.bioexcel.eu/t/unusual-bonds-in-oso3-of-ligand-after-docking/5951/4 "2025-11-14T08:26:25Z")

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Did you try visualising it in a different viewer?