Table 2.

Calculated binding free energies (ΔG) and hydrogen bond occupancies of selected intercalation binding models

Complex	H-bond occupancy (%)		ΔG (kcal/mol)		Coralyne angle (°)
	Res 6–19	Res 7–18	Avg	Dev	Avg	Dev
cisWH(a)-c1-270d	42.3	63.8	− 25.33	3.42	216.78	6.73
cisWH(b)-alt-c1-45d	75.5	82.0	− 28.01	2.75	10.03	5.05
transHH-c1-0d	56.8	58.9	− 26.15	3.47	22.25	7.03
transHH-c1-225d	58.3	59.6	− 25.46	3.66	219.93	15.55
transWH-c1-45d	59.0	66.8	− 26.53	3.72	29.78	17.06
transWH-c1-180d	61.2	59.8	− 32.48	3.12	193.57	5.81
transWH-c1-270d-f	53.9	59.7	− 27.39	3.77	184.24	13.07
transWS-c1-45d-f	45.4	57.9	− 25.02	4.28	336.51	7.25
transWW-c1-0d	63.8	62.9	− 28.73	2.95	344.21	3.85
transWW-c1-135d-f	57.3	64.3	− 31.06	2.73	148.89	4.93
transWW-c1-315d-f	61.1	64.4	− 29.68	2.74	325.29	4.09

Only the polar and non-polar contributions of the free energies were calculated. The free energies of the complex [homo-(dA) duplex and coralyne], receptor [homo-(dA) duplex] and ligand (coralyne) were calculated using the partial structures extracted from the same snapshots. ΔG was averaged over the final 1 ns period. The naming convention of the complexes is explained in the text. The occupancies of the H-bonds were calculated separately for the two base pairs (between residue 6 and 19 and between residue 7 and 18).