Distorted thiazole ring after docking

Hi,
I used Haddock web sever for the docking of a small molecule with DNA duplex. Everything went fine, but when I inspected the generated pdb files, I found one of the thiazole rings of the ligand completely distorted. The sulfur atom formed 4 bonds with all atoms in the ring, which looked as a sphere. Has anyone encountered such a problem?.
Thank you in advance

Best regards
Hasan

This is usually simply a visualization issue - pymol might try to connect atoms that are within a certain distance. Try opening it in a different visualizer.

Thank you for your reply. I used the Discovery Studio , Pymol and Chimera visualizer, however, I faced the same problem. I attached the pdb file for your reference.

Regards,
Hasan

Hasan Yaser Hasan Al Niss​

Associate professor

College of Pharmacy
Medicinal Chemistry

T: +97165057427 |
E:
halniss@sharjah.ac.ae

UoS Channel @ LinkedIn UoS Channel @ Twitter UoS Channel @ Facebook UoS Channel @ Instagram UoS Channel @ YouTube

www.sharjah.ac.ae

cluster1_1.pdb (59.8 KB)

Looks like only one of the two groups is giving problems.

What was the starting model?

The starting structure is 2MNE. I modified 2mne structure by replacing the pyridine ring of the ligand with a thiazole ring. The modified pdb file is attached.

Hasan Yaser Hasan Al Niss​

Associate professor

College of Pharmacy
Medicinal Chemistry

T: +97165057427 |
E:
halniss@sharjah.ac.ae

UoS Channel @ LinkedIn UoS Channel @ Twitter UoS Channel @ Facebook UoS Channel @ Instagram UoS Channel @ YouTube

www.sharjah.ac.ae

MGB4_ACTAGT.pdb (67.1 KB)