Table 2.

H-bond lengths of the optimized base pairs and triplets obtained at the B3LYP level and r.m.s.d. values for the heavy atoms superimposition on the corresponding 1ehz structures (see also Figures 2 and 3)

Interaction	Base pair	H-bond length	H-bond length	H-bond length	RMSD (Å)
8–14–21	U8…A14	O2(U)–N6(A) 3.04	N3(U)–N7(A) 2.86		1.38
	A14…A21	N6(A)–N3(A) 3.06			0.21
9–12–23	U12…A23	O2(U)–N6(A) 2.96	N3(U)–N1(A) 2.88		0.27
	A9…A23	N6(A)–N7(A) 3.08	N7(A)–N6(A) 3.00		0.19
10–25–45	m2G10…C25	N2(m2G)–O2(C) 2.91	N1(m2G)–N3(C) 2.96	O6(m2G)–N4(C) 2.82	2.11
	m2G10…G45	O6(m2G)–N2(G) 2.88			0.38
	C25…G45	N4(C)–N3(G) 3.23
	G10…C25	N2(G)–O2(C) 2.92	N1(G)–N3(C) 2.96	06(G)–N4(C) 2.82
	G10…G45	O6(G)–N2(G) 2.89
	C25…G45	N4(C)–N3(G) 3.29
13–22–46	C13…G22	O2(C)–N2(G) 2.83	N3(C)–N1(G) 2.95	N4(C)–06(G) 2.94	0.17
	G22…m7G46	O6(G)–N1(m7G) 2.84	N7(G)–N1(m7G) 2.78		0.12
	C13…G22	O2(C)–N2(G) 2.90	N3(C)–N1(G) 2.95	N4(C)–06(G) 2.85
	G22…G46	O6(G)–N1(G) 3.13	N7(G)–N1(G) 2.88
15–48	G15…C48	N1(G)–O2(C) 2.80	N6(G)–O2(C) 2.99		1.15
18–55	G18…Ψ55	N1(G)–O2(Ψ) 2.95	N2(G)–O2(Ψ) 3.13		0.30
	G18…U55a	N1(G)–O2(U) 2.95	N2(G)–O2(U) 3.19
19–56	G19…C56	N2(G)–O2(C) 2.94	N1(G)–N3(C) 2.95	06(G)–N4(C) 2.80	0.45
26–44	m22G26…A44	N1(m22G)–N1(A) 3.03	O6(m22G)–N6(A) 2.84		0.25
	G26…A44	N1(G)–N1(A) 2.97	O6(G)–N6(A) 2.86
54–58	T54…A58	O2(T)–N6(A) 2.97	N3(T)–N7(A) 2.86
	T54…m1A58	O2(T)–N6(m1A) 2.72	N3(T)–N7(m1A) 2.92		0.21
	U54…A58	O2(U)–N6(A) 2.99	N3(U)–N7(A) 2.85
	U54…m1A58	O2(U)–N6(m1A) 2.73	N3(U)–N7(m1A) 2.92

^aComputed starting from the 1j1u coordinates.