The interaction energies calculated, by DFT functionals, ranged from −88.98 kcal/mol to −110.73 kcal/mol for 3FMH and −82.14 kcal/mol to −104.41 kcal/mol for 3FLZ. These results are consistent with those of MP2, indicating the importance of functional calculation with D3 dispersion correction. Among the DFT functionals, the results for higher rungs of Jacob’s ladder showed lower interaction energies than those for the lower rungs, such as TPSS versus B3LYP. The results using D3 correction showed improvements in describing weak interactions. MP2 is more computationally expensive than DFT; however, the energy calculated by MP2 was similar to that by DFT-D3 (such as M06-2x). Therefore, these results suggested that DFT with dispersion correction is the better choice for efficient calculation of interaction energy.