Optimize 3d pdb cannot run haddock

HADDOCK
1

Previously, I run haddock using ligand extract from bound crystal. However, the docked result is not the same as reference crystal.

So now I try to optimize geometric my 2D structure that I download from pubchem and convert to 3d using avagadro. However the pdb produce missing some column, and cannot submit to Haddock for docking.

There I would like to know is it correct for me to just extract the ligand from bound crystal? Do I need to do any refinement? And is there a way to convert 2D to 3D without the missing column in PDB? Would appreciate if anyone can kindly advice.

2

In terms of conversion from smile to 3D, we like the omega toolkit from OpenEye (free for academics). But there are indeed other solutions.