Table 1 The relative binding free energy and energy components (kcal/mol) for the five HLA-DR/Top1 complexes predicted by the MM-PB(GB)SA and QM/MM-GBSA methods.

∆E_vdW

−143.5 ± 2.3

−134.2 ± 1.6

−139.2 ± 3.0

−137.4 ± 1.1

−132.4 ± 2.0

∆E_ele

−584.7 ± 25.4

−599.1 ± 9.0

−576.4 ± 25.9

−769.5 ± 14.3

−498.3 ± 22.9

∆E_MM

−728.2 ± 25.5

−733.4 ± 8.1

−715.6 ± 27.3

−906.9 ± 15.2

−630.7 ± 23.6

∆E _QM

−22.5 ± 2.5

−33.9 ± 1.0

−36.7 ± 0.8

−47.4 ± 4.0

−24.6 ± 1.7

−T∆S

65.8 ± 1.7

66.2 ± 1.2

67.9 ± 1.2

69.3 ± 1.8

73.6 ± 2.3

∆G_sol(PBSA)

609.7 ± 25.0

620.1 ± 7.1

600.0 ± 24.6

786.3 ± 13.1

516.2 ± 22.6

∆G_sol(GBSA)

608.8 ± 23.8

613.3 ± 7.3

596.6 ± 25.4

780.0 ± 13.1

517.0 ± 21.5

∆G_sol(QM-GBSA)

629.2 ± 23.7

652.3 ± 8.1

623.8 ± 24.7

819.2 ± 12.2

575.8 ± 23.0

∆G_{bind(MM/PBSA)}

−52.7 ± 3.3

−47.0 ± 1.2

−47.8 ± 3.5

−51.2 ± 2.7

−40.9 ± 2.1

∆G_{bind(MM/GBSA)}

−53.6 ± 1.4

−53.4 ± 0.6

−51.1 ± 1.7

−57.6 ± 2.7

−40.1 ± 1.2

∆G_{bind(QM/MM-GBSA)}

−33.4 ± 1.4

−36.5 ± 0.6

−33.2 ± 1.8

−37.5 ± 2.3

−21.2 ± 1.7

∆∆G_{bind(MM/PBSA)}

−11.8

−6.1

−6.9

−10.3

0

∆∆G_{bind(MM/GBSA)}

−13.5

−13.3

−11.0

−17.5

0

∆∆G_{bind(QM/MM-GBSA)}

−12.2

−15.3

−12.0

−16.3

0