Table 1.

The experimental and the calculated binding free energies (kcal/mol) using MM/PBSA for the six protein-ligand systems.

No.	ΔEvdw	ΔEele	ΔGPB	ΔGSA	ΔEele+ΔGPB	ΔEvdw+ΔGSA	TΔS	ΔGcal.	ΔGexp.
α-thrombin (εin = 4)
a1	−58.86±1.09a	−4.37±0.24	13.66±0.29	−7.61±0.17	9.28±0.04	−66.47±1.27	−22.81±1.57	−34.38±0.35	−12.39
a2	−62.42±1.69	−3.64±2.36	14.29±1.72	−7.65±0.03	10.65±0.64	−70.06±1.72	−20.20±3.01	−39.22±4.09	−10.08
a3	−52.69±1.18	−2.15±0.27	11.32±0.43	−6.68±0.24	9.16±0.16	−59.37±1.42	−20.01±0.65	−30.19±1.92	−8.92
a4	−50.58±2.58	−0.46±0.07	8.58±0.19	−6.42±0.13	8.12±0.12	57.00±2.71	−17.97±1.06	−30.92±1.53	−7.68
a5	−18.73±0.24	−33.35±0.28	44.56±0.10	−2.79±0.00	11.21±0.38	−21.51±0.24	−15.50±0.82	5.20±0.20	−3.98
a6	−57.79±0.46	−18.08±0.11	28.14±0.09	−7.11±0.01	10.06±0.02	−64.89±0.45	−24.99±1.73	−29.84±2.20	−10.6
a7	−58.27±0.17	−40.62±0.06	57.20±0.21	−7.02±0.04	16.58±0.28	−65.29±0.13	−22.53±0.33	−26.18±0.08	−11.57
avidin (εin = 1)
b1	−30.31±0.30	−172.54±4.72	177.89±4.58	−4.21±0.01	5.35±0.14	−34.52±0.31	−18.69±0.22	−10.48±0.39	−20.4
b2	−30.10±0.83	−156.76±4.74	167.42±4.55	−4.27±0.04	10.66±0.19	−34.57±0.79	−20.44±0.65	−3.27±0.33	−14.3
b3	−28.80±0.19	−165.47±5.49	168.64±2.62	−4.21±0.01	3.17±2.86	−33.01±0.17	−21.33±0.43	−8.50±2.61	−14.0
b4	−40.31±0.14	−28.99±0.50	55.52±1.49	−5.55±0.06	26.53±1.99	−45.86±0.19	−17.64±1.61	−1.87±3.41	−8.8
b5	−28.52±1.39	−21.67±7.19	39.47±4.80	−4.09±0.04	17.80±2.39	−32.61±1.43	−15.19±1.03	0.37±1.98	−8.2
b6	−25.53±1.00	−21.97±0.20	36.26±1.36	−3.69±0.28	14.29±1.16	−29.22±1.28	−14.30±1.61	0.63±1.48	−5.0
b7	−11.99±0.16	−25.11±0.30	28.23±0.06	−2.12±0.01	3.12±0.09	−14.10±0.16	−13.57±1.08	2.59±0.83	−4.5
cytochrome C peroxidase (εin = 1)
c1	−25.60±0.02	−352.29±0.21	365.41±0.32	−2.81±0.01	13.12±0.11	−28.41±0.03	−15.50±0.09	−15.29±0.14	−3.85
c2	−25.84±0.06	−354.14±0.11	363.18±0.80	−2.79±0.02	9.03±0.69	−28.63±0.04	−16.87±1.10	−19.60±0.73	−4.78
c3	−17.90±0.91	−361.70±3.03	369.11±10.1	−1.93±0.43	7.41±7.09	−19.82±1.34	−14.53±0.06	−12.41±8.43	−4.81
c4	−22.28±0.15	−353.88±1.88	364.08±3.20	−2.62±0.00	10.20±1.32	−24.90±0.16	−15.05±1.02	−14.70±1.16	−5.86
c5	−18.07±0.07	−365.62±6.40	377.83±2.66	−2.47±0.02	12.21±3.74	−20.53±0.05	−13.19±1.28	−8.32±3.79	−3.96
c6	−17.74±0.48	−377.44±0.95	381.86±1.05	−2.86±0.44	4.42±0.09	−20.60±0.05	−15.63±0.03	−16.18±0.05	−6.00
c7	−17.94±0.12	−372.64±3.54	376.95±3.28	−2.40±0.01	4.31±0.26	−20.34±0.12	−15.73±0.04	−16.02±0.38	−5.99
c8	−21.33±0.03	−360.68±2.15	374.32±2.77	−2.49±0.00	13.64±0.62	−23.83±0.03	−15.50±0.40	−10.19±0.59	−4.96
c9	−17.09±0.41	−372.32±1.53	371.75±0.19	−2.44±0.00	−0.57±1.73	−19.52±0.41	−15.44±0.14	−20.09±1.31	−5.21
c10	−20.72±0.31	−372.36±0.79	376.73±2.16	−3.29±0.43	4.37±1.37	−24.01±0.74	−15.45±2.08	−19.64±2.11	−4.92
c11	−21.89±0.08	−363.77±3.15	370.83±3.33	−2.64±0.01	7.06±0.19	−24.53±0.06	−14.50±0.33	−17.47±0.25	−4.92
c12	−18.40±0.08	−379.84±2.79	380.67±2.49	−2.48±0.00	0.83±0.30	−20.88±0.08	−14.39±0.48	−20.05±0.38	−7.07
c13	−16.64±0.04	−381.35±2.81	382.24±3.07	−2.78±0.42	0.89±0.26	−19.42±0.46	−13.81±0.31	−18.54±0.72	−5.02
c14	−19.34±0.12	−366.62±1.23	367.85±0.56	−2.62±0.00	1.22±0.66	−21.96±0.12	−15.22±0.93	−20.74±0.55	−4.73
c15	−11.42±0.03	−372.89±0.16	365.15±0.18	−2.42±0.44	−7.73±0.01	−13.84±0.42	−12.09±0.29	−21.57±0.43	−4.33
c16	−15.83±0.06	−375.74±2.87	375.48±1.02	−2.26±0.00	−0.26±1.86	−18.09±0.06	−15.19±0.04	−18.35±1.91	−5.82
c17	−16.35±0.00	−370.52±1.42	367.86±0.32	−2.34±0.00	−2.66±1.10	−18.69±0.01	−14.95±0.68	−21.34±1.11	−5.94
c18	−15.64±0.13	−369.60±2.73	369.33±0.75	−2.35±0.01	−0.27±3.47	−17.980.14	−16.93±0.07	−18.25±1.32	−6.06
neuraminidase (εin = 4)
d1	−22.63±0.30	−29.30±0.41	29.57±0.89	−3.99±0.38	0.27±0.49	−26.61±0.08	−21.97±1.02	−4.37±1.59	−4.09
d2	−22.95±0.57	−33.69±1.21	32.14±0.84	−4.65±0.03	−1.55±0.36	−27.60±0.59	−15.78±2.65	−13.36±2.88	−7.23
d3	−21.19±0.17	−26.07±0.54	27.55±0.43	−4.45±0.00	1.48±0.97	−25.64±0.17	−21.54±0.07	−2.62±0.72	−3.74
d4	−21.84±0.52	−22.36±0.17	25.43±0.18	−4.64±0.01	3.06±0.01	−26.49±0.53	−20.75±2.30	−2.68±2.84	−4.84
d5	−20.12±0.64	−23.62±0.04	25.55±0.64	−4.58±0.04	1.92±0.60	−24.71±0.68	−19.03±0.08	−3.75±1.20	−6.61
d6	−28.40±0.03	−22.53±3.39	26.83±1.90	−4.99±0.03	4.30±1.49	−33.39±0.05	−19.29±1.83	−9.80±3.26	−10.2
d7	−27.83±0.38	−3.53±0.35	9.44±0.80	−4.98±1.16	6.11±0.45	−32.81±1.55	−22.86±2.01	−3.84±0.05	−7.73
d8	−29.43±0.01	−13.36±0.42	19.34±0.24	−4.49±0.47	5.98±0.18	−33.92±0.46	−17.72±2.16	−10.22±1.89	−11.45
P450cam (εin = 1)
e1	−27.57±0.61	−9.10±0.27	21.78±0.57	−2.78±0.58	12.68±0.83	−30.35±0.03	−15.25±0.85	−2.43±0.01	−7.90
e2	−26.94±0.28	−0.14±0.04	13.22±0.56	−3.33±0.03	13.09±0.52	−30.27±0.25	−16.63±0.62	−0.56±0.15	−5.91
e3	−29.03±0.24	−8.59±0.12	25.51±0.79	−3.38±0.00	16.92±0.90	−32.41±0.24	−14.45±1.76	−1.04±2.42	−6.54
e4	−20.35±0.05	−1.85±0.10	12.69±0.50	−2.79±0.02	10.84±0.40	−23.14±0.03	−15.04±0.27	2.74±0.63	−5.57
e5	−21.13±0.24	−0.23±0.08	13.92±0.50	−2.37±0.55	13.69±0.57	−23.50±0.78	−14.40±0.32	4.60±0.11	−5.52
e6	−27.68±0.36	−9.02±2.34	22.91±0.38	−3.56±0.01	13.89±1.96	−31.25±0.35	−15.31±0.54	−2.04±1.06	−5.93
e7	−29.42±0.10	−4.32±0.16	20.62±0.68	−3.48±0.01	16.29±0.51	−32.89±0.10	−13.24±0.42	−3.36±0.83	−7.53
e8	−26.36±0.04	−0.03±0.01	12.65±0.03	−2.60±0.55	12.62±0.04	−28.96±0.51	−13.99±0.56	−2.34±0.01	−5.90
e9	−28.09±0.11	−2.87±0.07	16.98±0.08	−3.15±0.01	14.11±0.01	−31.23±0.10	−15.10±0.60	−2.03±0.69	−7.40
penicillopepsin (εin = 2)
f1	−50.93±1.01	−32.01±2.12	59.90±1.36	−8.59±0.00	27.89±3.48	−59.52±1.02	−22.43±1.30	−9.20±3.20	−12.83
f2	−41.34±1.58	−17.23±3.30	35.94±0.53	−6.78±0.18	18.70±3.83	−48.12±1.76	−22.01±0.44	−7.41±1.62	−10.51
f3	−48.82±1.24	−33.58±0.82	48.29±1.66	−7.34±0.13	14.71±0.84	−55.16±1.37	−24.89±0.64	−15.57±1.16	−12.27
f4	−40.62±2.30	−25.06±3.58	51.78±1.11	−6.79±0.29	26.72±2.47	−47.41±2.59	−16.09±1.52	−14.60±2.45	−10.91
f5	−38.63±4.78	−7.32±0.62	23.49±4.96	−5.48±0.85	16.17±4.34	−44.10±5.63	−20.06±0.16	−7.87±1.45	−8.37
f6	−42.23±4.33	−8.76±0.99	26.45±3.94	−6.60±0.05	17.69±2.96	−48.83±4.28	−21.31±0.23	−9.83±1.09	−7.03
f7	−45.28±2.23	−15.07±2.75	34.59±5.31	−7.51±0.48	19.52±2.56	−52.79±2.72	−23.67±2.29	−9.60±2.13	−6.80

^aThe statistical error was estimated based on the deviation between block averages.