Table 3.

Populations of the U13/U18 and U10/U21 H-bonding arrangements and the median distances between the A16(OP2) and U18(O4′) atoms and planes of bases 14 and 16, respectively, in MD simulations of the NSR

	U13/U18		U10/U21a
Base pair variant/simulationb	2a	1a	2a	1a	2b	1b	A16(OP2)/Base14 anion-π	U18(O4′)/A16 lone pair-π
NMRc	100%	0%	100%	0%	0%	0%	2.93 ± 0.07 Å	3.01 ± 0.04 Å
2n0j_wt	87%	13%	46%	11%	38%	5%	3.22 ± 0.25 Å	3.10 ± 0.13 Å
2n0j_RIO_wt	96%	4%	60%	40%	0%	0%	3.22 ± 0.22 Å	3.00 ± 0.09 Å
2n0j_RIO_wt_CaseP_OPC	97%	3%	66%	34%	0%	0%	3.22 ± 0.16 Å	3.06 ± 0.09 Å
2n0j_RIO_wt_HBfix_A	99%	1%	79%	21%	0%	0%	3.14 ± 0.17 Å	3.02 ± 0.09 Å
2n0j_RIO_wt_HBfix_B	98%	2%	62%	38%	0%	0%	3.10 ± 0.14 Å	3.00 ± 0.09 Å
2n0j_RIO_wt_HBfix_C	99%	1%	69%	31%	0%	0%	3.10 ± 0.14 Å	3.01 ± 0.09 Å
2n0j_RIO_wt_Na	96%	4%	60%	40%	0%	0%	3.29 ± 0.26 Å	3.00 ± 0.09 Å
2n0j_C14+	27%	73%	43%	10%	38%	9%	2.95 ± 0.11 Å	3.29 ± 0.19 Å
2n0j_RIO_C14+	84%	16%	60%	40%	0%	0%	2.96 ± 0.11 Å	3.00 ± 0.09 Å

^aThere are two possible cWW base pair arrangements for base pair U10/U21 (see Figure 3 and Ref. (6)). In arrangement ‘2a’, there are U21(N3)/U10(O2) and U10(N3)/U21(O4) H-bonds while in arrangement ‘2b’, there are U10(N3)/U21(O2) and U21(N3)/U10(O4) H-bonds. In case of the single H-bond variants (indicated as arrangements ‘1a/1b’), the H-bond involving the O2 atom is water-mediated (Figure 3). Note that due to steric hindrance, only one cWW base pair arrangement and one water-mediated variant was observed for the U13/U18 base pair (Figure 3).

^bFor systems where multiple parallel simulations were conducted (see Table 1), the analyses were computed for the combined one-microsecond simulation ensembles.

^cThe ‘NMR’ dataset refers to the experimental NMR ensemble of the wild-type NSR in complex with RIO (PDB: 2n0j) (32).