Table 4.

Revisit binding free energy differences (kcal mol⁻¹) of FEP+ calculations in literature

	|ΔΔG exp| < 1.37	1.37 ≤ |ΔΔG exp| < 2.73	|ΔΔG exp| ≥ 2.73	Total
Wang et al.,12 OPLS2.1, Figure 3a
No. of transformations	257	66	7	330
Underestimations [%]	51	71	86	55
(ΔΔG cal–ΔΔG exp)/N	−0.04	−0.59	−1.56	−0.18
Roos et al.,19 OPLS3, Figure 3c
No. of transformations	348	98	23	469
Underestimations [%]	55	71	74	59
(ΔΔG cal–ΔΔG exp)/N	−0.12	−0.71	−0.82	−0.28
Roos et al.,19 OPLS3e, Figure 3d
No. of transformations	348	98	23	469
Underestimations [%]	52	71	65	57
(ΔΔG cal–ΔΔG exp)/N	−0.03	−0.53	−0.51	−0.16
Pérez‐Benito et al.,20 all ligand pairs with 5 ns simulations from LO datasets, Figure 3b
No. of transformations	10	79	92	181
Underestimations [%]	70	65	83	74
(ΔΔG cal–ΔΔG exp)/N	−0.13	−0.43	−1.14	−0.78

“Underestimations” is the percentage of pairs of which ΔΔG _cal < ΔΔG _exp when the ligand pairs are rearranged so that ΔΔG _exp ≥ 0 kcal mol⁻¹. The average underestimation (ΔΔG _cal – ΔΔG _exp)/N is also calculated after making the ΔΔG _exp ≥ 0 rearrangement.