I have a set of ligands that I want to calculate the binding energy for. If one was to calculate binding energy based on this equation :

EnergyBinding = EnergyComplex - (EnergyLigand + EnergyReceptor)

to compare various ligands in terms of tighter binding(IC50) shall I choose the one with the most negative binding energy or the one with lowest free energy of the complex. Lets say I have 3 ligands : Ligand 1 , Ligand 2, and Ligand 3, where ligand 1 had the most negative EnergyBinding followed by Ligand 2 and finally Ligand 3. However when complexed with ligand 3, the whole complex yields lower energyComplex than either ligand 1 or ligand 2. Which one shall i count on ? Energy of binding or total complex energy ? 

Appreciated