. Author manuscript; available in PMC: 2016 Sep 30.

Published in final edited form as: J Comput Chem. 2015 Jul 27;36(25):1859–1873. doi: 10.1002/jcc.24011

Table 5.

The coefficient of determination of Experimental and Predicted Binding Free Energies of Different MD Trajectory Lengths and Radii Sets in QM-MM/GBSA Calculations using the PM6 Hamiltonian.^a

Radii Sets	GB	R²_0.25ns^a	R²_0.5ns	R²_0.75ns	R²_1ns	R²_2ns	R²_3ns	R²_4ns	R²_5ns	R²_6ns
bondi	GB^HCT	0.54	0.61	0.57	0.52	0.41	0.28	0.18	0.14	0.14
mbondi	GB^HCT	0.49	0.55	0.51	0.46	0.36	0.30	0.26	0.25	0.27
mbondi2	GB^HCT	0.56	0.63	0.59	0.54	0.43	0.30	0.20	0.16	0.17

bondi	GB^OBC	0.15	0.21	0.20	0.17	0.09	0.04	0.01	0.01	0.01
mbondi	GB^OBC	0.13	0.18	0.16	0.13	0.07	0.05	0.04	0.03	0.04
mbondi2	GB^OBC	0.17	0.24	0.22	0.19	0.11	0.06	0.02	0.01	0.02

bondi	GB^OBC2	0.16	0.23	0.22	0.19	0.11	0.05	0.02	0.01	0.01
mbondi	GB^OBC2	0.12	0.17	0.15	0.11	0.05	0.02	0.01	0.01	0.02
mbondi2	GB^OBC2	0.17	0.24	0.23	0.19	0.11	0.05	0.02	0.01	0.02

bondi	GB^Neck	0.24	0.26	0.23	0.20	0.13	0.07	0.03	0.02	0.03
mbondi2	GB^Neck	0.26	0.29	0.26	0.23	0.15	0.09	0.05	0.04	0.05

bondi	GB^Neck2	0.52	0.57	0.55	0.56	0.56	0.57	0.57	0.60	0.64
mbondi2	GB^Neck2	0.53	0.57	0.54	0.56	0.56	0.57	0.58	0.60	0.64

R²_n: “R²” stands for coefficient of determination in the QM-MM/GBSA calculation. Here 100, 400, 1200, 2400 MD simulation frames were evenly extracted from one 0.25, 1, 3, 6 ns MD simulation trajectories, respectively.