Answer for Since the protein is homo-dimer, should I get the same binding affinity values of ligand in two monomers?


No, it is not necessary that if a protein is homo-dimer, then it should have a same binding affinity for both chains because the binding residues might be different in both the chains so it depends on the amino acids to which the ligand is binding. The presence of different functional groups in amino acids effects the bond formation between the ligand and the residues, and thereby the binding affinity. Most of the time, binding affinity is same for both the chains.