# Do I need to fill in missing side chains and loops before protein-ligand docking for VLS?

I am going to screen a set of small molecules against a CYP450 2C9 protein target. The structure I am using exactly is 5A5I. Do I need to fill in missing side chains and loops before performing VLS? I assume while preparing the protein I should leave water molecules in the structure as there is a bond between $$Fe^{2+}$$ and water that is involved in the binding of a ligand.