TR5
Bonds
First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
O2' | C2' | sing | 1.43Å | 1.44Å | |
C2 | N3 | doub | 1.32Å | 1.49Å | Aromatic |
C2 | N1 | sing | 1.33Å | 1.50Å | Aromatic |
O3' | C3' | sing | 1.43Å | 1.44Å | |
N3 | C4 | sing | 1.34Å | 1.35Å | Aromatic |
N1 | C6 | doub | 1.33Å | 1.35Å | Aromatic |
C2' | C3' | sing | 1.55Å | 1.54Å | |
C2' | C1' | sing | 1.55Å | 1.56Å | |
C3' | C4' | sing | 1.54Å | 1.52Å | |
C4 | C5 | doub | 1.38Å | 1.33Å | Aromatic |
C4 | N9 | sing | 1.36Å | 1.34Å | Aromatic |
C6 | C5 | sing | 1.38Å | 1.33Å | Aromatic |
C6 | N61 | sing | 1.37Å | 1.36Å | |
C62 | N61 | sing | 1.46Å | 1.49Å | |
C1' | N9 | sing | 1.46Å | 1.50Å | |
C1' | O4' | sing | 1.44Å | 1.45Å | |
C5 | C7 | sing | 1.46Å | 1.32Å | Aromatic |
N9 | C8 | sing | 1.39Å | 1.34Å | Aromatic |
N61 | N71 | sing | 1.40Å | 1.31Å | |
C4' | C5' | sing | 1.53Å | 1.53Å | |
C4' | O4' | sing | 1.44Å | 1.43Å | |
C5' | O5' | sing | 1.43Å | 1.43Å | |
C7 | C8 | doub | 1.35Å | 1.34Å | Aromatic |
C7 | C72 | sing | 1.47Å | 1.35Å | |
N71 | C72 | doub | 1.31Å | 1.35Å | |
C72 | N73 | sing | 1.39Å | 1.34Å | |
O5' | PB | sing | 1.61Å | 1.61Å | |
O2 | PB | doub | 1.48Å | 1.60Å | |
O1 | PB | sing | 1.61Å | 1.48Å | |
PB | O3 | sing | 1.61Å | 1.47Å | |
O3 | H1 | sing | 0.97Å | 0.95Å | |
O1 | H2 | sing | 0.97Å | 0.95Å | |
C5' | H3 | sing | 1.09Å | 1.10Å | |
C5' | H4 | sing | 1.09Å | 1.10Å | |
C4' | H5 | sing | 1.09Å | 1.10Å | |
C3' | H6 | sing | 1.09Å | 1.10Å | |
O3' | H7 | sing | 0.97Å | 0.95Å | |
C2' | H8 | sing | 1.09Å | 1.10Å | |
O2' | H9 | sing | 0.97Å | 0.95Å | |
C1' | H10 | sing | 1.09Å | 1.10Å | |
C8 | H11 | sing | 1.08Å | 1.08Å | |
C2 | H12 | sing | 1.08Å | 1.08Å | |
C62 | H13 | sing | 1.09Å | 1.10Å | |
C62 | H14 | sing | 1.09Å | 1.10Å | |
C62 | H15 | sing | 1.09Å | 1.10Å | |
N73 | H16 | sing | 0.97Å | 1.00Å | |
N73 | H17 | sing | 0.97Å | 1.00Å |
Angles
First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
O2' | C2' | C3' | 111.5° | 110.9° |
O2' | C2' | C1' | 112.5° | 110.9° |
O2' | C2' | H8 | 110.0° | 110.9° |
C2' | O2' | H9 | 109.5° | 114.0° |
N3 | C2 | N1 | 112.6° | 125.6° |
C2 | N3 | C4 | 120.6° | 119.9° |
N3 | C2 | H12 | 123.7° | 117.2° |
C2 | N1 | C6 | 121.9° | 119.0° |
N1 | C2 | H12 | 123.7° | 117.2° |
O3' | C3' | C2' | 113.1° | 110.6° |
O3' | C3' | C4' | 109.7° | 110.5° |
O3' | C3' | H6 | 110.1° | 110.4° |
C3' | O3' | H7 | 109.5° | 114.0° |
N3 | C4 | C5 | 120.4° | 114.3° |
N3 | C4 | N9 | 133.4° | 140.6° |
N1 | C6 | C5 | 118.7° | 115.3° |
N1 | C6 | N61 | 122.9° | 127.8° |
C3' | C2' | C1' | 105.7° | 102.1° |
C2' | C3' | C4' | 106.2° | 104.2° |
C2' | C3' | H6 | 108.7° | 110.4° |
C3' | C2' | H8 | 108.6° | 110.9° |
C2' | C1' | N9 | 110.4° | 110.6° |
C2' | C1' | O4' | 105.5° | 103.5° |
C1' | C2' | H8 | 108.4° | 110.8° |
C2' | C1' | H10 | 110.0° | 110.6° |
C3' | C4' | C5' | 109.5° | 109.9° |
C3' | C4' | O4' | 108.0° | 107.3° |
C3' | C4' | H5 | 110.2° | 110.0° |
C4' | C3' | H6 | 109.0° | 110.5° |
C5 | C4 | N9 | 106.2° | 105.1° |
C4 | C5 | C6 | 125.8° | 125.9° |
C4 | C5 | C7 | 111.1° | 110.0° |
C4 | N9 | C1' | 124.6° | 124.6° |
C4 | N9 | C8 | 108.1° | 110.9° |
C5 | C6 | N61 | 118.3° | 116.9° |
C6 | C5 | C7 | 123.1° | 124.1° |
C6 | N61 | C62 | 121.0° | 119.7° |
C6 | N61 | N71 | 119.8° | 120.7° |
C62 | N61 | N71 | 119.2° | 119.7° |
N61 | C62 | H13 | 109.5° | 109.5° |
N61 | C62 | H14 | 109.4° | 109.5° |
N61 | C62 | H15 | 109.5° | 109.5° |
N9 | C1' | O4' | 108.6° | 110.7° |
C1' | N9 | C8 | 127.3° | 124.5° |
N9 | C1' | H10 | 110.8° | 110.5° |
C1' | O4' | C4' | 112.0° | 107.0° |
O4' | C1' | H10 | 111.5° | 110.8° |
C5 | C7 | C8 | 106.1° | 104.2° |
C5 | C7 | C72 | 117.8° | 114.6° |
N9 | C8 | C7 | 108.6° | 109.9° |
N9 | C8 | H11 | 125.7° | 125.1° |
N61 | N71 | C72 | 120.9° | 125.2° |
C5' | C4' | O4' | 107.5° | 109.9° |
C4' | C5' | O5' | 108.6° | 109.5° |
C4' | C5' | H3 | 109.7° | 109.5° |
C4' | C5' | H4 | 109.7° | 109.5° |
C5' | C4' | H5 | 110.1° | 109.9° |
O4' | C4' | H5 | 111.5° | 109.9° |
C5' | O5' | PB | 120.4° | 123.0° |
O5' | C5' | H3 | 109.7° | 109.4° |
O5' | C5' | H4 | 109.7° | 109.5° |
C8 | C7 | C72 | 136.2° | 141.2° |
C7 | C8 | H11 | 125.7° | 125.0° |
C7 | C72 | N71 | 120.0° | 118.5° |
C7 | C72 | N73 | 117.5° | 120.8° |
N71 | C72 | N73 | 122.5° | 120.7° |
C72 | N73 | H16 | 120.0° | 119.9° |
C72 | N73 | H17 | 120.0° | 120.0° |
O5' | PB | O2 | 102.4° | 109.5° |
O5' | PB | O1 | 107.8° | 109.5° |
O5' | PB | O3 | 108.3° | 109.5° |
O2 | PB | O1 | 107.7° | 109.4° |
O2 | PB | O3 | 109.9° | 109.5° |
O1 | PB | O3 | 119.4° | 109.5° |
PB | O1 | H2 | 109.5° | 114.0° |
PB | O3 | H1 | 109.5° | 114.0° |
H3 | C5' | H4 | 109.5° | 109.5° |
H13 | C62 | H14 | 109.5° | 109.5° |
H13 | C62 | H15 | 109.5° | 109.4° |
H14 | C62 | H15 | 109.5° | 109.5° |
H16 | N73 | H17 | 120.0° | 120.0° |
Dihedrals
First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
O2' | C2' | C3' | O3' | 2.2° | 20.3° |
O2' | C2' | C3' | C1' | 122.5° | 118.2° |
O2' | C2' | C3' | H8 | 121.4° | 123.7° |
O2' | C2' | C1' | H8 | 121.8° | 123.6° |
O2' | C2' | C3' | C4' | 118.2° | 139.0° |
O2' | C2' | C1' | N9 | 133.5° | 86.2° |
O2' | C2' | C1' | O4' | 109.4° | 155.2° |
O2' | C2' | C3' | H6 | 124.7° | 102.3° |
O2' | C2' | C1' | H10 | 11.0° | 36.6° |
N3 | C2 | N1 | H12 | 180.0° | 180.0° |
N3 | C2 | N1 | C6 | 0.1° | 0.2° |
C2 | N3 | C4 | C5 | 0.1° | 0.0° |
C2 | N3 | C4 | N9 | 179.4° | 179.3° |
N1 | C2 | N3 | C4 | 0.1° | 0.0° |
C2 | N1 | C6 | C5 | 0.1° | 0.4° |
C2 | N1 | C6 | N61 | 179.7° | 180.0° |
O3' | C3' | C2' | C4' | 120.4° | 118.8° |
O3' | C3' | C2' | H6 | 122.5° | 122.6° |
O3' | C3' | C2' | C1' | 124.7° | 97.9° |
O3' | C3' | C4' | H6 | 120.6° | 122.5° |
O3' | C3' | C4' | C5' | 126.4° | 119.7° |
O3' | C3' | C4' | O4' | 116.9° | 120.8° |
O3' | C3' | C4' | H5 | 5.1° | 1.4° |
O3' | C3' | C2' | H8 | 119.2° | 144.0° |
N3 | C4 | C5 | N9 | 179.7° | 179.5° |
N3 | C4 | C5 | C6 | 0.1° | 0.3° |
N3 | C4 | N9 | C1' | 1.5° | 0.5° |
N3 | C4 | C5 | C7 | 180.0° | 180.0° |
N3 | C4 | N9 | C8 | 179.8° | 179.8° |
C4 | N3 | C2 | H12 | 179.9° | 180.0° |
N1 | C6 | C5 | C4 | 0.1° | 0.5° |
N1 | C6 | C5 | N61 | 179.7° | 179.7° |
N1 | C6 | N61 | C62 | 0.0° | 0.0° |
N1 | C6 | C5 | C7 | 179.9° | 179.8° |
N1 | C6 | N61 | N71 | 179.9° | 180.0° |
C6 | N1 | C2 | H12 | 180.0° | 179.8° |
C3' | C2' | C1' | H8 | 116.2° | 118.2° |
C2' | C3' | C4' | H6 | 116.9° | 118.7° |
C3' | C2' | C1' | N9 | 104.5° | 155.6° |
C3' | C2' | C1' | O4' | 12.6° | 37.0° |
C2' | C3' | C4' | C5' | 111.1° | 121.4° |
C2' | C3' | C4' | O4' | 5.6° | 2.0° |
C2' | C3' | C4' | H5 | 127.6° | 117.4° |
C2' | C3' | O3' | H7 | 180.0° | 65.1° |
C3' | C2' | O2' | H9 | 180.0° | 61.5° |
C3' | C2' | C1' | H10 | 132.9° | 81.6° |
C1' | C2' | C3' | C4' | 4.4° | 20.9° |
C2' | C1' | N9 | C4 | 63.8° | 84.7° |
C2' | C1' | N9 | O4' | 115.1° | 114.1° |
C2' | C1' | N9 | H10 | 122.1° | 122.8° |
C2' | C1' | O4' | H10 | 119.4° | 118.5° |
C2' | C1' | N9 | C8 | 114.1° | 95.0° |
C2' | C1' | O4' | C4' | 17.1° | 40.1° |
C1' | C2' | C3' | H6 | 112.8° | 139.6° |
C1' | C2' | O2' | H9 | 61.5° | 174.2° |
C3' | C4' | O4' | C1' | 14.6° | 26.5° |
C3' | C4' | C5' | O4' | 117.1° | 117.8° |
C3' | C4' | C5' | H5 | 121.3° | 121.2° |
C3' | C4' | O4' | H5 | 121.2° | 119.6° |
C3' | C4' | C5' | O5' | 163.7° | 175.8° |
C3' | C4' | C5' | H3 | 76.5° | 64.3° |
C3' | C4' | C5' | H4 | 43.8° | 55.7° |
C4' | C3' | O3' | H7 | 61.6° | 180.0° |
C4' | C3' | C2' | H8 | 120.4° | 97.2° |
C4 | C5 | C6 | C7 | 179.8° | 179.7° |
C4 | C5 | C6 | N61 | 179.8° | 179.9° |
C5 | C4 | N9 | C1' | 178.1° | 179.9° |
C5 | C4 | N9 | C8 | 0.2° | 0.4° |
C4 | C5 | C7 | C8 | 0.3° | 0.3° |
C4 | C5 | C7 | C72 | 179.9° | 179.8° |
N9 | C4 | C5 | C6 | 179.5° | 179.8° |
C4 | N9 | C1' | C8 | 178.0° | 179.6° |
C4 | N9 | C1' | O4' | 179.0° | 161.2° |
N9 | C4 | C5 | C7 | 0.3° | 0.4° |
C4 | N9 | C8 | C7 | 0.0° | 0.3° |
C4 | N9 | C1' | H10 | 58.2° | 38.2° |
C4 | N9 | C8 | H11 | 180.0° | 179.8° |
C5 | C6 | N61 | C62 | 179.6° | 179.6° |
C5 | C6 | N61 | N71 | 0.4° | 0.3° |
C6 | C5 | C7 | C8 | 179.5° | 180.0° |
C6 | C5 | C7 | C72 | 0.1° | 0.0° |
C6 | N61 | C62 | N71 | 179.9° | 179.9° |
N61 | C6 | C5 | C7 | 0.4° | 0.1° |
C6 | N61 | N71 | C72 | 0.1° | 0.4° |
C6 | N61 | C62 | H13 | 179.9° | 89.9° |
C6 | N61 | C62 | H14 | 59.9° | 150.0° |
C6 | N61 | C62 | H15 | 60.1° | 30.0° |
C62 | N61 | N71 | C72 | 180.0° | 179.5° |
N61 | C62 | H13 | H14 | 120.0° | 120.0° |
N61 | C62 | H13 | H15 | 120.0° | 120.0° |
N61 | C62 | H14 | H15 | 120.0° | 120.0° |
N9 | C1' | O4' | H10 | 122.3° | 122.9° |
N9 | C1' | O4' | C4' | 101.2° | 158.6° |
C1' | N9 | C8 | C7 | 178.2° | 180.0° |
N9 | C1' | C2' | H8 | 11.7° | 37.3° |
C1' | N9 | C8 | H11 | 1.8° | 0.1° |
O4' | C1' | N9 | C8 | 1.0° | 19.1° |
C1' | O4' | C4' | C5' | 103.4° | 145.9° |
C1' | O4' | C4' | H5 | 135.8° | 93.1° |
O4' | C1' | C2' | H8 | 128.8° | 81.2° |
C5 | C7 | C8 | N9 | 0.2° | 0.0° |
C5 | C7 | C8 | C72 | 179.5° | 180.0° |
C5 | C7 | C72 | N71 | 0.3° | 0.0° |
C5 | C7 | C72 | N73 | 179.7° | 180.0° |
C5 | C7 | C8 | H11 | 179.9° | 180.0° |
N9 | C8 | C7 | H11 | 180.0° | 179.9° |
N9 | C8 | C7 | C72 | 179.7° | 179.9° |
C8 | N9 | C1' | H10 | 123.8° | 142.2° |
N61 | N71 | C72 | C7 | 0.2° | 0.3° |
N61 | N71 | C72 | N73 | 179.6° | 179.8° |
N71 | N61 | C62 | H13 | 0.0° | 90.0° |
N71 | N61 | C62 | H14 | 120.0° | 30.0° |
N71 | N61 | C62 | H15 | 120.0° | 150.0° |
C5' | C4' | O4' | H5 | 120.8° | 121.0° |
C4' | C5' | O5' | H3 | 119.9° | 120.0° |
C4' | C5' | O5' | H4 | 119.9° | 120.0° |
C4' | C5' | O5' | PB | 178.3° | 180.0° |
C4' | C5' | H3 | H4 | 120.4° | 120.0° |
C5' | C4' | C3' | H6 | 5.8° | 2.8° |
O4' | C4' | C5' | O5' | 46.6° | 66.5° |
O4' | C4' | C5' | H3 | 166.4° | 53.5° |
O4' | C4' | C5' | H4 | 73.3° | 173.5° |
O4' | C4' | C3' | H6 | 122.5° | 116.6° |
C4' | O4' | C1' | H10 | 136.5° | 78.5° |
C5' | O5' | PB | O2 | 42.8° | 54.9° |
C5' | O5' | PB | O1 | 70.7° | 65.0° |
C5' | O5' | PB | O3 | 158.8° | 175.0° |
O5' | C5' | H3 | H4 | 120.4° | 120.0° |
O5' | C5' | C4' | H5 | 75.0° | 54.5° |
C8 | C7 | C72 | N71 | 179.7° | 180.0° |
C8 | C7 | C72 | N73 | 0.8° | 0.0° |
C7 | C72 | N71 | N73 | 179.4° | 180.0° |
C72 | C7 | C8 | H11 | 0.3° | 0.0° |
C7 | C72 | N73 | H16 | 179.4° | 0.1° |
C7 | C72 | N73 | H17 | 0.6° | 179.9° |
N71 | C72 | N73 | H16 | 0.0° | 179.9° |
N71 | C72 | N73 | H17 | 180.0° | 0.0° |
C72 | N73 | H16 | H17 | 180.0° | 179.9° |
O5' | PB | O2 | O1 | 113.6° | 120.0° |
O5' | PB | O2 | O3 | 114.9° | 120.1° |
O5' | PB | O1 | O3 | 124.0° | 120.0° |
O5' | PB | O3 | H1 | 111.1° | 180.0° |
O5' | PB | O1 | H2 | 109.9° | 60.0° |
PB | O5' | C5' | H3 | 58.4° | 60.1° |
PB | O5' | C5' | H4 | 61.8° | 59.9° |
O2 | PB | O1 | O3 | 126.1° | 120.0° |
O2 | PB | O3 | H1 | 0.0° | 59.9° |
O2 | PB | O1 | H2 | 0.0° | 180.0° |
O1 | PB | O3 | H1 | 125.1° | 60.0° |
O3 | PB | O1 | H2 | 126.1° | 60.0° |
H3 | C5' | C4' | H5 | 44.8° | 174.5° |
H4 | C5' | C4' | H5 | 165.1° | 65.5° |
H5 | C4' | C3' | H6 | 115.4° | 123.9° |
H6 | C3' | O3' | H7 | 58.3° | 57.4° |
H6 | C3' | C2' | H8 | 3.3° | 21.4° |
H8 | C2' | O2' | H9 | 59.4° | 62.3° |
H8 | C2' | C1' | H10 | 110.8° | 160.2° |
H13 | C62 | H14 | H15 | 120.0° | 120.0° |