The hydration structure in the active site of human coagulation factor Xa (fXa) was investigated from the viewpoint of excess free energy. Water distribution in the active site of fXa was calculated using partly constrained molecular dynamics (MD) simulation. Then the free energy of the distribution was evaluated using grid inhomogeneous solvation theory (GIST). The analyzed excess free energy shows excellent correlation to the experimental binding affinity of known ligands only if the side chain fluctuation of the active site of fXa was taken into account. This result indicates that the side chain fluctuation generated by partly constrained MD has an important role for identifying the appropriate hydration structure, and that GIST in combination with partly constrained MD provides useful information for assessing the protein-ligand binding affinity.