A nitrogen atom being wrongly protonated

chanataon · **Joined:** Fri Apr 01, 2016 10:58 pm **Posts:** 1

Hi all,

After I draw a ligand, no matter which method I use for geometry optimization,
one of the nitrogen atoms in my aromatic ring is protonated incorrectly (picture attached),
making it have 4 bonds which I don't think I want it.

Could anyone please suggest how I could fix this problem?

Thanks,
Jay

bikadi · **Joined:** Wed Oct 29, 2008 2:24 pm **Posts:** 204

Hi, try changing pH, it should help.

jaruwanchat · **Joined:** Mon Apr 04, 2016 1:40 am **Posts:** 1

Hi,

Thanks for the response; it does help! But I wonder if I should input the pH under physiological condition or the lowest pH that my compound is not protonated for docking calculation. Btw, my compound has an iso-cytosine ring contained in it.

Thanks in advance.

Jay

bikadi · **Joined:** Wed Oct 29, 2008 2:24 pm **Posts:** 204

You should try docking with different pHs if protonation is crucial in your system (docking will use the ligand in the form you prepared; protonated at low pH). Since local pH in the protein binding site can be very different from physiological condition, there is no golden rule which is the appropriate choice but you should consider your protein and known ligands.