Table 4.
Hydrogen-Bond Distances and Angles from Simulations
| Restrained
|
Unrestrained
|
|||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| W73
|
WH+73
|
NH4+ |
W73
|
WH+73
|
NH4+ |
|||||||
| D-H···A | RHD | θDHA | RHD | θDHA | RHD | θDHA | RHD | θDHA | RHD | θDHA | RHD | θDHA |
| W(H+)73···A9:O2P | 4.10 (38) | 77.3 (101) | 2.67 (20) | 110.8 (104) | 2.04 (12) | 149.8 (110) | 3.86 (27) | 74.2 (9.7) | 2.78 (13) | 112.9 (55) | 1.99 (12) | 152.5 (109) |
| W(H+)73···C17:O2′ | 4.41 (39) | 148.3 (104) | 3.10 (12) | 120.2 (57) | 3.12 (16) | 118.9 (74) | 4.67 (26) | 134.4 (10.5) | 3.91 (12) | 134.6 (48) | 3.24 (16) | 125.5 (75) |
| W(H+)73···G8:O2′ | 3.77 (41) | 119.1 (85) | 2.32 (13) | 108.7 (69) | 2.21 (12) | 137.1 (104) | 3.52 (30) | 120.1 (6.4) | 2.32 (11) | 106.9 (55) | 2.19 (11) | 144.5 (99) |
| W(H+)73···C1.1:O2P | 2.16 (26) | 154.8 (124) | 1.53 (04) | 169.5 (48) | 1.80 (13) | 155.4 (65) | 2.37 (18) | 148.0 (8.9) | 1.56 (04) | 166.3 (51) | 1.85 (16) | 154.5 (63) |
| W(H+)73···C1.1:O5′ | 2.69 (30) | 127.0 (97) | 3.29 (09) | 131.0 (59) | 3.35 (20) | 128.1 (95) | 2.45 (17) | 150.2 (9.0) | 3.49 (07) | 143.3 (49) | 3.37 (24) | 123.7 (95) |
| G12:HN2···W(H+)73:O | 2.07 (25) | 115.1 (69) | 3.53 (17) | 139.1 (122) | - | - | 2.78 (34) | 101.3 (119) | 3.68 (37) | 141.3 (114) | - | - |
| G12:H1···C17:O2′ | 2.20 (11) | 155.6 (56) | 2.24 (10) | 155.2 (53) | 2.17 (11) | 154.6 (58) | 2.03 (12) | 156.8 (7.0) | 1.90 (06) | 164.8 (57) | 2.11 (11) | 153.1 (60) |
| C17:H2′···G12:O6 | 4.08 (10) | 26.0 (48) | 3.59 (14) | 57.9 (64) | 3.95 (11) | 29.3 (51) | 4.07 (12) | 26.3 (5.4) | 4.02 (12) | 53.1 (48) | 3.85 (11) | 32.7 (52) |
| G8:H2′···C1.1:O5′ | 2.94 (16) | 105.6 (94) | 1.88 (11) | 153.1 (92) | 2.02 (13) | 145.3 (99) | 1.97 (18) | 152.3 (14.9) | 1.84 (08) | 156.5 (75) | 2.12 (16) | 138.1 (109) |
| G12:HN2···A9:N7 | 2.02 (07) | 152.5 (50) | 2.01 (07) | 149.8 (54) | 2.08 (11) | 143.8 (73) | 2.06 (11) | 142.1 (60) | 2.04 (08) | 153.0 (54) | 2.63 (18) | 125.9 (89) |
| A9:HN6···G12:N3 | 2.15 (09) | 160.6 (49) | 2.11 (08) | 160.0 (49) | 2.18 (10) | 161.3 (50) | 2.16 (11) | 156.6 (48) | 2.07 (09) | 154.6 (48) | 2.27 (11) | 151.6 (65) |
| A9:HN6···G12:O2′ | 2.21 (12) | 142.2 (63) | 2.29 (12) | 142.4 (65) | 2.38 (13) | 138.4 (63) | 2.21 (13) | 134.4 (70) | 2.14 (12) | 139.3 (63) | 2.60 (16) | 139.3 (62) |
Average hydrogen bond (D-H···A) distances (RHD in Å) and angles (θDHA in °) from restrained and unrestrained crystal simulations of the full-length hammerhead. Standard deviations are shown in parentheses divided by the decimal precision of the average quantity, e.g., 4.10(38) means 4.10 ± 0.38. Statistics were obtained from data taken for all four monomers in the crystal unit cell over 10 ns simulation, with data sampled every 1 ps. We designate “strong” and “weak” hydrogen bonds as having average lengths less than 2.2 and 2.5 Å, respectively, and average angles as having greater than 135° and 90°, respectively.