Water molecules + Prosthetic group in Docking

[pier.dileonardo]

Dear all,

I'm performing a docking experiment in which I use as receptor a flavoprotein (structure predicted by using I-TASSER) and as ligand NAD and NADP, in order to get which one has the highest binding energy.

Should the receptor include other molecules, such as Water Molecules and/or his Prosthetic Group (e.g. FMN), or should I clean every other molecule and use only the protein part of the enzyme as a receptor?

Moreover, if the catalysis of the enzyme is reversible, do you think I should analyze the binding energies using both the oxidized and reduced version of NAD / NADP as ligand, or is this irrelevant?

Thank you all