Table 5. Summary of NOE distance violations from unrestrained MD simulations of the three duplexes using the NMR data obtained in-house (see Materials and Methods’ section) and 1NAJ (only for DDD)^a.

Force-field	N° of violations	Largest violation (Å)	Average violation (Å)
DDD
BSC1	40 | 2b	0.94 | 0.76	0.51 | 0.76
BSC0	37 | 6	2.11 | 1.35	0.66 | 0.83
BSC0OL15	46 | 4	0.94 | 0.79	0.48 | 0.77
BSC0OL1	32 | 4	1.98 | 1.17	0.65 | 1.00
BSC0OL1+OL4	35 | 5	1.27 | 0.87	0.54 | 0.63
CG	50 | 42	1.50 | 1.40	0.65 | 0.60
C36	124 | 93	6.86 | 6.44	2.63 | 2.57
SEQ2
BSC1	45	1.25	0.54
BSC0	53	4.15	0.83
BSC0OL15	46	1.37	0.54
BSC0OL1	42	1.53	0.64
BSC0OL1+OL4	46	1.56	0.61
CG	61	1.92	0.78
C36	66	2.42	0.87
SEQ3
BSC1	51	1.19	0.59
BSC0	51	2.18	0.78
BSC0OL15	56	1.30	0.55
BSC0OL1	81	4.73	1.89
BSC0OL1+OL4	84	5.52	1.84
CG	78	5.37	1.86
C36	86	3.37	0.94

^aWe considered an experimental restraint violated when its average penalty energy was above 3·kT. See the footnote comment to Table 2 and the ‘Materials and Methods’ section for additional details.

^bNumber reported in italic were computed using the NMR restraints from PDB code 1NAJ.