. 2005 Dec 30;90(6):1865–1877. doi: 10.1529/biophysj.105.074344

TABLE 6.

Binding free energies from single-trajectory analysis

System	ΔE_ele	ΔE_vdw	ΔE_MM	ΔG_np	ΔG_pb	ΔG_SOL	ΔH	−TΔS	ΔG	ΔΔG
Unmodified	−6721 ± 108	−199 ± 6	−6920 ± 107	−11 ± 0.4	6793 ± 98	6782 ± 98	−138 ± 11	67 ± 13	−71 ± 17	0
10S(+)-trans-(A₁): II	−6540 ± 79	−197 ± 6	−6737 ± 80	−11 ± 0.3	6609 ± 83	6598 ± 83	−139 ± 17	75 ± 6	−64 ± 18	7
III	−6472 ± 78	−201 ± 7	−6672 ± 81	−11 ± 0.3	6554 ± 74	6543 ± 74	−129 ± 10	77 ± 14	−52 ± 18	19
10R(−)-trans-(A₁): II	−6579 ± 62	−199 ± 5	−6777 ± 62	−11 ± 0.3	6656 ± 56	6645 ± 56	−132 ± 9	78 ± 9	−54 ± 13	17
III	−6508 ± 79	−205 ± 6	−6713 ± 82	−11 ± 0.3	6591 ± 76	6580 ± 76	−133 ± 8	69 ± 10	−64 ± 18	7
IV	−6599 ± 74	−198 ± 7	−6797 ± 74	−11 ± 0.3	6676 ± 68	6665 ± 68	−132 ± 9	70 ± 8	−62 ± 12	9
10S(+)-trans-(A₂): III	−6566 ± 128	−198 ± 7	−6764 ± 131	−11 ± 0.3	6642 ± 119	6631 ± 119	−133 ± 14	70 ± 6	−63 ± 15	8
III-2	−6471 ± 152	−202 ± 7	−6673 ± 154	−11 ± 0.4	6551 ± 138	6540 ± 138	−133 ± 17	67 ± 5	−66 ± 18	5
IV	−6589 ± 76	−201 ± 7	−6790 ± 78	−11 ± 0.4	6670 ± 71	6659 ± 71	−131 ± 10	76 ± 10	−55 ± 14	16
10R(−)-trans-(A₂): I	−6534 ± 90	−197 ± 5	−6731 ± 90	−11 ± 0.2	6607 ± 83	6596 ± 83	−135 ± 10	74 ± 7	−61 ± 12	10
III	−6656 ± 62	−194 ± 7	−6850 ± 61	−11 ± 0.4	6733 ± 57	6712 ± 57	−138 ± 8	83 ± 11	−55 ± 14	16
IV	−6588 ± 75	−209 ± 6	−6797 ± 77	−12 ± 0.4	6679 ± 70	6667 ± 70	−130 ± 10	75 ± 15	−55 ± 18	16

ΔE_ele, ΔE_vdw, and ΔE_int (zeros; not shown) are electrostatic energy, van der Waals energy, and internal energy changes. ΔE_MM is the molecular mechanics energy change and ΔE_MM = ΔE_ele + ΔE_vdw + ΔE_int. G_np and ΔG_pb are nonpolar and electrostatic solvation free energy changes. ΔG_SOL is solvation free energy change and ΔG_SOL = ΔG_np + ΔG_pb. ΔH is enthalpy change and ΔH =ΔE_MM + ΔG_SOL. T is the absolute temperature and ΔS is the entropy change. ΔG is the binding free energy and ΔG = ΔE_MM + ΔG_SOL − TΔS. ΔΔG is the relative binding free energy of a BP-modified system compared to the unmodified one. Underlined are the lowest energy in each of the four combinations of carcinogen location (A₁ or A₂) and stereochemistry (10S(+) or 10R(−)). All energies have the unit of kcal/mol and are shown in both average and standard deviation (except ΔΔG). Although ΔH =ΔE_MM + ΔG_SOL, the large standard deviations of ΔE_MM and ΔG_SOL do not lead to large standard deviations of ΔH, which means fluctuations of these two terms are mostly canceled out.