# Distorted thiazole ring after docking **URL:** \ **Category:** HADDOCK\ **Created:** [May 27, 2022, 3:01am UTC](https://ask.bioexcel.eu/t/distorted-thiazole-ring-after-docking/3736 "2022-05-27T03:01:07Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![halniss](https://avatars.discourse-cdn.com/v4/letter/h/e5b9ba/32.png) [@halniss](https://ask.bioexcel.eu/u/halniss)\ **Post date:** [May 27, 2022, 3:01am UTC](https://ask.bioexcel.eu/t/distorted-thiazole-ring-after-docking/3736/1 "2022-05-27T03:01:07Z")
![IMG_20220527_062712](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/1X/ded189f0feb869da3965be32ff03ebf47b2195f7.jpeg) 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 ---
**Author:** ![honoratorv](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/honoratorv/32/672_2.png) [@honoratorv](https://ask.bioexcel.eu/u/honoratorv)\ **Post date:** [May 31, 2022, 10:34am UTC](https://ask.bioexcel.eu/t/distorted-thiazole-ring-after-docking/3736/2 "2022-05-31T10:34:31Z")
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. ---
**Author:** ![halniss](https://avatars.discourse-cdn.com/v4/letter/h/e5b9ba/32.png) [@halniss](https://ask.bioexcel.eu/u/halniss)\ **Post date:** [May 31, 2022, 10:59am UTC](https://ask.bioexcel.eu/t/distorted-thiazole-ring-after-docking/3736/3 "2022-05-31T10:59:36Z")
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 ![](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/1X/040d15d60ced9ab4f54e0f2a7ed7384a11fe599f.png) Hasan Yaser Hasan Al Niss​ Associate professor College of Pharmacy Medicinal Chemistry T: +97165057427 | E: [**halniss@sharjah.ac.ae**](mailto:halniss@sharjah.ac.ae) [![UoS Channel @ LinkedIn](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/1X/300bc7c85aa94b7d0aa9682d9592dac3ee63f68f.png "UoS Channel @ LinkedIn")](https://www.linkedin.com/school/university-of-sharjah) [![UoS Channel @ Twitter](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/1X/2307192752dfed8dfbf5c7d798be092c32600445.png "UoS Channel @ Twitter")](http://www.twitter.com/usharjah) [![UoS Channel @ Facebook](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/1X/0e041183eaa8fdfa06f23dbebfd5943b5120dfdf.png "UoS Channel @ Facebook")](http://www.facebook.com/usharjah) [![UoS Channel @ Instagram](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/1X/f9ed535a230b47d2b923c0bd951420f61af2d2bc.png "UoS Channel @ Instagram")](https://www.instagram.com/usharjah) [![UoS Channel @ YouTube](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/1X/529d4d1a432bd9ecb55b10581bec9d8387b4c048.png "UoS Channel @ YouTube")](http://www.youtube.com/usharjah) > [**www.sharjah.ac.ae**](https://www.sharjah.ac.ae/) [cluster1\_1.pdb](https://ask.bioexcel.eu/uploads/short-url/nR4Ha4NLQxiHNoWtj6MKUfsRmRc.pdb) (59.8 KB) ---
**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:** [May 31, 2022, 11:14am UTC](https://ask.bioexcel.eu/t/distorted-thiazole-ring-after-docking/3736/4 "2022-05-31T11:14:30Z")
Looks like only one of the two groups is giving problems. What was the starting model? ---
**Author:** ![halniss](https://avatars.discourse-cdn.com/v4/letter/h/e5b9ba/32.png) [@halniss](https://ask.bioexcel.eu/u/halniss)\ **Post date:** [May 31, 2022, 11:39am UTC](https://ask.bioexcel.eu/t/distorted-thiazole-ring-after-docking/3736/5 "2022-05-31T11:39:16Z")
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. ![](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/1X/040d15d60ced9ab4f54e0f2a7ed7384a11fe599f.png) Hasan Yaser Hasan Al Niss​ Associate professor College of Pharmacy Medicinal Chemistry T: +97165057427 | E: [**halniss@sharjah.ac.ae**](mailto:halniss@sharjah.ac.ae) [![UoS Channel @ LinkedIn](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/1X/300bc7c85aa94b7d0aa9682d9592dac3ee63f68f.png "UoS Channel @ LinkedIn")](https://www.linkedin.com/school/university-of-sharjah) [![UoS Channel @ Twitter](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/1X/2307192752dfed8dfbf5c7d798be092c32600445.png "UoS Channel @ Twitter")](http://www.twitter.com/usharjah) [![UoS Channel @ Facebook](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/1X/0e041183eaa8fdfa06f23dbebfd5943b5120dfdf.png "UoS Channel @ Facebook")](http://www.facebook.com/usharjah) [![UoS Channel @ Instagram](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/1X/f9ed535a230b47d2b923c0bd951420f61af2d2bc.png "UoS Channel @ Instagram")](https://www.instagram.com/usharjah) [![UoS Channel @ YouTube](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/1X/529d4d1a432bd9ecb55b10581bec9d8387b4c048.png "UoS Channel @ YouTube")](http://www.youtube.com/usharjah) > [**www.sharjah.ac.ae**](https://www.sharjah.ac.ae/) [MGB4\_ACTAGT.pdb](https://ask.bioexcel.eu/uploads/short-url/zsdrTWlo3YqKA8mXfdkeKKseL5j.pdb) (67.1 KB) ---
**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:** [July 15, 2022, 2:41pm UTC](https://ask.bioexcel.eu/t/distorted-thiazole-ring-after-docking/3736/6 "2022-07-15T14:41:56Z")
There is indeed something fishy with the second thiazole ring of each ligand. Must come from the way PRODRG defines the topology - we do not have control on that. However looking at your input model after deleting the connect statements, I do see before running HADDOCK already something strange in the second thiazole. The geometry must not be good from the start for that one. Any optimisation you can do before docking? ![Screenshot 2022-07-15 at 16.40.26](https://europe1.discourse-cdn.com/flex013/uploads/bioexcel/original/1X/a625321786190269d80583fda5a48e6e62325d98.png)