What about the conformation of the docked ligand ?? Should the docked ligand exactly fall on the ligand which we already have?
Most of the time, when we dock in a specific site, the ligand get attached to the protein in the same conformation as in the original complex, except a few cases where the structure of ligand differs slightly. But it does not matter once you successfully bind the ligand in the specific site. Additionally, it also depends upon the purpose of your docking, if you are looking for an exact substitute of the bound ligand, then it should bind in the specific conformation, otherwise, a slight variation is also acceptable.