TABLE 5.

Binding free energies from triplet-trajectory analysis

System	G(TATA/TBP)	G(TATA)	ΔG	ΔΔG
Unmodified	−15176 ± 44	−7008 ± 23	−34 ± 58	0
10S(+)-trans-(A1): II	−15086 ± 41	−6942 ± 20	−10 ± 55	+24
III	−15108 ± 32	−6952 ± 21	−22 ± 49	+12
10R(−)-trans-(A1): II	−15087 ± 40	−6942 ± 20	−11 ± 54	+23
III	−15130 ± 40	−6957 ± 19	−39 ± 54	−5
IV	−15069 ± 41	−6929 ± 23	−6 ± 56	+28
10S(+)-trans-(A2): III	−15143 ± 34	−6971 ± 20	−38 ± 50	−4
III-2	−15123 ± 38	−6964 ± 22	−25 ± 53	+9
IV	−15103 ± 45	−6979 ± 21	10 ± 58	+44
10R(−)-trans-(A2): I	−15101 ± 40	−6930 ± 23	−37 ± 55	−3
III	−15131 ± 44	−6953 ± 22	−44 ± 58	−10
IV	−15110 ± 42	−6956 ± 19	−20 ± 55	14

G(TATA/TBP) is the free energy of a TATA/TBP complex, G(TATA) is the free energy of corresponding free TATA DNA, ΔG is the binding free energy between TBP and TATA DNA, and ΔΔG is the relative binding free energy of a BP-modified TATA/TBP complex compared to the unmodified one. The free energy of free TBP G(TBP) is −8134 ± 30 kcal/mol. 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).