Table 2.

Average RMSD of the simulations for RNA duplex, RNA hairpin, B-DNA duplex in water, and Z-DNA crystal lattice. For RNA molecules, the average RMSD values for each of the two trajectories were calculated. Loop RMSD for RNA hairpins was calculated by superposing the loop and the nearest two base-pair stems and calculating the RMSD of the loop only. The maximum RMSD between NMR structures of the same PDB entry was also calculated, except for 1MIS, 1SZY, and 1D20, each of which has only one NMR structure.

Type	PDB	Average heavy-atom RMSD without terminal base pair (Å)		Average heavy-atom RMSD with all residues (Å)		Loop RMSD (Å)		Maximum all-atom RMSD between NMR structures (Å)
RNA Duplex	2JXQ	1.25	1.41	1.98	2.38	—		0.44
	1MIS	1.51	1.54	1.77	1.74	—		—
	1F5G	1.97	1.98	2.53	2.53	—		1.20
	2L8F	1.50	1.47	2.42	2.14	—		1.09
RNA Hairpin	2KOC	1.72	1.90	1.78	1.95	1.71	2.14	0.97
	1ZIH	2.13	1.83	2.22	1.91	1.95	1.61	1.41
	1SZY	1.66	1.94	1.79	2.00	1.53	2.05	—
B-DNA Duplex	1NAJ	1.29		2.54		—		0.25
	1D42	1.63		1.87		—		1.78
	2HKB	1.55		2.01		—		0.47
	1D20	2.18		3.27		—		—
Z-DNA Crystal	1LJX	1.16		1.45		—		—
	292D	1.32		1.89		—		—
B-DNA Crystal	1D23 unit	0.90		0.93		—		—
	1D23 super	0.88		0.89		—		—
RNA Crystal	1RNA unit	1.22		1.34		—		—
	1RNA super	1.32		1.47		—		—