Table 2.
Average Watson–Crick hydrogen bonding distances (and standard deviations) calculated over the last 800 ps of the MD trajectories
| Base pairs | S0:S | S1:S | S2:S | S3:S | S4:S |
|---|---|---|---|---|---|
| N1(1)…H3(36) | 2.01 (0.14) | 2.01(0.14) | 2.03 (0.15) | 4.56 (0.61) | 2.01 (0.18) |
| H61(1)…O4(36) | 2.06 (0.25) | 2.03(0.21) | 2.01 (0.20) | 5.12 (1.05) | 2.22 (0.39) |
| N1(2)…H3(35) | 1.97 (0.12) | 1.98(0.12) | 1.96 (0.11) | 1.98 (0.15) | 2.01 (0.13) |
| H61(2)…O4(35) | 2.04 (0.24) | 1.99(0.18) | 2.01 (0.20) | 2.02 (0.20) | 1.99 (0.18) |
| H41(3)…O6(34) | 2.01 (0.18) | 2.01(0.18) | 2.08 (0.38) | 1.98 (0.18) | 2.01 (0.19) |
| N3(3)…H1(34) | 1.96 (0.10) | 1.95(0.09) | 1.98 (0.17) | 1.96 (0.09) | 1.95 (0.10) |
| O2(3)…H21(34) | 1.88 (0.12) | 1.87(0.11) | 1.88 (0.12) | 1.91 (0.13) | 1.88 (0.11) |
| N1(4)…H3(33) | 1.96 (0.12) | 1.95(0.10) | 1.96 (0.11) | 1.98 (0.12) | 1.97 (0.12) |
| H61(4)…O4(33) | 2.02 (0.19) | 2.04(0.21) | 2.02 (0.20) | 1.99 (0.17) | 2.02 (0.20) |
| H3(5)…N1(32) | 1.96 (0.11) | 1.96(0.10) | 2.01 (0.13) | 1.96 (0.11) | 1.98 (0.11) |
| O4(5)…H61(32) | 2.05 (0.22) | 2.01(0.18) | 2.00 (0.18) | 2.10 (0.24) | 1.98 (0.15) |
| H41(6)…O6(31) | 1.97 (0.16) | 1.98(0.16) | 1.98 (0.16) | 2.00 (0.19) | 2.00 (0.17) |
| N3(6)…H1(31) | 1.95 (0.09) | 1.95(0.08) | 1.93 (0.08) | 1.94 (0.09) | 1.97 (0.10) |
| O2(6)…H21(31) | 1.91 (0.14) | 1.90(0.12) | 1.89 (0.12) | 1.89 (0.11) | 1.90 (0.14) |
| H3(7)…N1(30) | 1.95 (0.11) | 1.95(0.11) | 1.95 (0.11) | 1.94 (0.11) | 2.01 (0.14) |
| O4(7)…H61(30) | 2.04 (0.22) | 2.01(0.19) | 2.09 (0.26) | 2.09 (0.23) | 1.97 (0.16) |
| H41(8)…O6(29) | 1.98 (0.16) | 1.97(0.15) | 1.99 (0.18) | 1.98 (0.15) | 1.98 (0.15) |
| N3(8)…H1(29) | 1.93 (0.09) | 1.95(0.08) | 1.95 (0.09) | 1.95 (0.09) | 1.95 (0.10) |
| O2(8)…H21(29) | 1.91 (0.13) | 1.90(0.12) | 1.92 (0.13) | 1.90 (0.13) | 1.92 (0.13) |
| H41(9)…O6(28) | 2.06 (0.23) | 1.97(0.17) | 2.00 (0.20) | 1.96 (0.16) | 2.02 (0.20) |
| N3(9)…H1(28) | 1.95 (0.10) | 1.95(0.08) | 1.95 (0.10) | 1.94 (0.09) | 1.95 (0.09) |
| O2(9)…H21(28) | 1.88 (0.12) | 1.92(0.14) | 1.88 (0.11) | 1.87 (0.11) | 1.90 (0.12) |
| H3(10)…N1(27) | 1.96 (0.11) | 1.94(0.10) | 1.96 (0.11) | 1.99 (0.13) | 1.94 (0.11) |
| O4(10)…H61(27) | 1.98 (0.16) | 2.01(0.20) | 1.97 (0.16) | 1.97 (0.17) | 2.04 (0.21) |
| O6(11)…H41(26) | 1.99 (0.17) | 1.97(0.15) | 1.97 (0.16) | 1.98 (0.15) | 1.98 (0.15) |
| H1(11)…N3(26) | 1.97 (0.10) | 1.96(0.09) | 1.96 (0.09) | 1.96 (0.09) | 1.97 (0.09) |
| H21(11)…O2(26) | 1.89 (0.12) | 1.92(0.13) | 1.90 (0.13) | 1.90 (0.12) | 1.89 (0.12) |
| N1(12)…H3(25) | 1.99 (0.12) | 1.97(0.11) | 1.97 (0.12) | 1.99 (0.11) | 2.08 (0.14) |
| H61(12)…O4(25) | 1.96 (0.16) | 1.99(0.17) | 1.97 (0.17) | 2.05 (0.19) | 1.92 (0.14) |
| O6(13)…H41(24) | 1.96 (0.15) | 1.99(0.18) | 2.01 (0.19) | 1.96 (0.15) | 2.09 (0.35) |
| H1(13)…N3(24) | 1.94 (0.09) | 1.95(0.09) | 1.95 (0.10) | 1.94 (0.09) | 1.98 (0.16) |
| H21(13)…O2(24) | 1.88 (0.11) | 1.89(0.12) | 1.91 (0.14) | 1.87 (0.12) | 1.84 (0.11) |
| O6(14)…H41(23) | 1.96 (0.16) | 1.98(0.17) | 2.00 (0.21) | 2.03 (0.22) | 1.99 (0.16) |
| H1(14)…N3(23) | 1.95 (0.09) | 1.94(0.08) | 1.96 (0.10) | 1.97 (0.10) | 1.98 (0.10) |
| H21(14)…O2(23) | 1.88 (0.12) | 1.90(0.13) | 1.90 (0.13) | 1.93 (0.13) | 1.90 (0.12) |
| O6(15)…H41(22) | 1.96 (0.14) | 1.98(0.19) | 1.99 (0.17) | 1.96 (0.18) | 2.01 (0.18) |
| H1(15)…N3(22) | 1.96 (0.08) | 1.94(0.09) | 1.97 (0.10) | 1.97 (0.10) | 1.97 (0.10) |
| H21(15)…O2(22) | 1.90 (0.12) | 1.92(0.14) | 1.94 (0.15) | 1.97 (0.16) | 1.90 (0.14) |
| N1(16)…H3(21) | 1.98 (0.12) | 1.94(0.11) | 1.95 (0.12) | 1.98 (0.12) | 1.99 (0.12) |
| H61(16)…O4(21) | 2.01 (0.20) | 2.05(0.20) | 2.14 (0.26) | 1.98 (0.18) | 2.00 (0.18) |
| N1(17)…H3(20) | 1.98 (0.12) | 2.01(0.13) | 2.09 (0.17) | 1.95 (0.11) | 1.95 (0.10) |
| H61(17)…O4(20) | 2.01 (0.20) | 2.01(0.17) | 1.98 (0.17) | 3.62 (0.24) | 2.04 (0.19) |
| H41(18)…O6(19) | 2.11 (0.49) | 6.72(2.33) | 2.01 (0.20) | 2.14 (0.53) | 2.03 (0.23) |
| N3(18)…H1(19) | 2.03 (0.23) | 4.86(1.95) | 1.97 (0.10) | 2.02 (0.23) | 1.97 (0.11) |
| O2(18)…H21(19) | 1.92 (0.15) | 3.88(1.47) | 1.89 (0.13) | 1.90 (0.14) | 1.92 (0.15) |