HQ5
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| CD1 | CG | sing | 1.53Å | 1.53Å | |
| O3' | C3' | sing | 1.43Å | 1.43Å | |
| CG | CB | sing | 1.53Å | 1.53Å | |
| CG | CD2 | sing | 1.53Å | 1.52Å | |
| C4' | C3' | sing | 1.54Å | 1.53Å | |
| C4' | O4' | sing | 1.44Å | 1.45Å | |
| C4' | C5' | sing | 1.53Å | 1.52Å | |
| C3' | C2' | sing | 1.55Å | 1.53Å | |
| CB | CA | sing | 1.53Å | 1.53Å | |
| O4' | C1' | sing | 1.44Å | 1.42Å | |
| C5' | O5' | sing | 1.43Å | 1.47Å | |
| C1' | C2' | sing | 1.55Å | 1.53Å | |
| C1' | N1 | sing | 1.46Å | 1.47Å | |
| C2' | O2' | sing | 1.43Å | 1.42Å | |
| O2 | C2 | doub | 1.22Å | 1.23Å | |
| CA | N | sing | 1.47Å | 1.47Å | |
| CA | C | sing | 1.51Å | 1.52Å | |
| O5' | S | sing | 1.52Å | 1.60Å | |
| N1 | C2 | sing | 1.35Å | 1.40Å | |
| N1 | C6 | sing | 1.36Å | 1.37Å | |
| C | N3S | sing | 1.35Å | 1.41Å | |
| C | O | doub | 1.21Å | 1.23Å | |
| C2 | N3 | sing | 1.33Å | 1.36Å | |
| N3S | S | sing | 1.66Å | 1.60Å | |
| C6 | C5 | doub | 1.35Å | 1.34Å | |
| S | O1S | doub | 1.42Å | 1.42Å | |
| S | O2S | doub | 1.42Å | 1.42Å | |
| N3 | C4 | doub | 1.33Å | 1.34Å | |
| C5 | C4 | sing | 1.41Å | 1.43Å | |
| C4 | N4 | sing | 1.38Å | 1.33Å | |
| C5 | H1 | sing | 1.08Å | 1.08Å | |
| C6 | H2 | sing | 1.08Å | 1.08Å | |
| N | H3 | sing | 1.01Å | 1.00Å | |
| N | H4 | sing | 1.01Å | 1.00Å | |
| CA | H6 | sing | 1.09Å | 1.10Å | |
| CB | H7 | sing | 1.09Å | 1.10Å | |
| CB | H8 | sing | 1.09Å | 1.10Å | |
| CG | H9 | sing | 1.09Å | 1.10Å | |
| CD1 | H10 | sing | 1.09Å | 1.10Å | |
| CD1 | H11 | sing | 1.09Å | 1.10Å | |
| CD1 | H12 | sing | 1.09Å | 1.10Å | |
| CD2 | H13 | sing | 1.09Å | 1.10Å | |
| CD2 | H14 | sing | 1.09Å | 1.10Å | |
| CD2 | H15 | sing | 1.09Å | 1.10Å | |
| C1' | H16 | sing | 1.09Å | 1.10Å | |
| C2' | H17 | sing | 1.09Å | 1.10Å | |
| C3' | H18 | sing | 1.09Å | 1.10Å | |
| C4' | H19 | sing | 1.09Å | 1.10Å | |
| C5' | H20 | sing | 1.09Å | 1.10Å | |
| C5' | H21 | sing | 1.09Å | 1.10Å | |
| N3S | H22 | sing | 0.97Å | 1.00Å | |
| N4 | H23 | sing | 0.97Å | 1.00Å | |
| N4 | H24 | sing | 0.97Å | 1.00Å | |
| O2' | H25 | sing | 0.97Å | 0.95Å | |
| O3' | H26 | sing | 0.97Å | 0.95Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| CD1 | CG | CB | 109.6° | 109.5° |
| CD1 | CG | CD2 | 110.1° | 109.5° |
| CD1 | CG | H9 | 108.6° | 109.5° |
| CG | CD1 | H10 | 109.5° | 109.5° |
| CG | CD1 | H11 | 109.4° | 109.5° |
| CG | CD1 | H12 | 109.5° | 109.5° |
| O3' | C3' | C4' | 112.2° | 110.6° |
| O3' | C3' | C2' | 110.3° | 110.5° |
| O3' | C3' | H18 | 111.5° | 110.4° |
| C3' | O3' | H26 | 109.5° | 114.0° |
| CB | CG | CD2 | 111.1° | 109.4° |
| CG | CB | CA | 114.5° | 109.5° |
| CG | CB | H7 | 108.2° | 109.5° |
| CG | CB | H8 | 108.2° | 109.5° |
| CB | CG | H9 | 108.6° | 109.5° |
| CD2 | CG | H9 | 108.7° | 109.5° |
| CG | CD2 | H13 | 109.5° | 109.5° |
| CG | CD2 | H14 | 109.5° | 109.4° |
| CG | CD2 | H15 | 109.5° | 109.5° |
| C3' | C4' | O4' | 105.5° | 107.3° |
| C3' | C4' | C5' | 116.4° | 109.9° |
| C4' | C3' | C2' | 102.4° | 104.2° |
| C4' | C3' | H18 | 110.0° | 110.5° |
| C3' | C4' | H19 | 107.6° | 109.9° |
| O4' | C4' | C5' | 110.7° | 109.9° |
| C4' | O4' | C1' | 110.1° | 107.0° |
| O4' | C4' | H19 | 108.6° | 109.9° |
| C4' | C5' | O5' | 108.5° | 109.5° |
| C5' | C4' | H19 | 107.7° | 110.0° |
| C4' | C5' | H20 | 109.7° | 109.5° |
| C4' | C5' | H21 | 109.7° | 109.5° |
| C3' | C2' | C1' | 100.8° | 102.1° |
| C3' | C2' | O2' | 111.7° | 110.9° |
| C3' | C2' | H17 | 110.5° | 110.9° |
| C2' | C3' | H18 | 110.0° | 110.5° |
| CB | CA | N | 115.8° | 109.4° |
| CB | CA | C | 111.3° | 109.5° |
| CB | CA | H6 | 109.0° | 109.5° |
| CA | CB | H7 | 108.2° | 109.5° |
| CA | CB | H8 | 108.2° | 109.4° |
| O4' | C1' | C2' | 106.4° | 103.5° |
| O4' | C1' | N1 | 108.8° | 110.6° |
| O4' | C1' | H16 | 110.3° | 110.7° |
| C5' | O5' | S | 120.8° | 114.0° |
| O5' | C5' | H20 | 109.7° | 109.5° |
| O5' | C5' | H21 | 109.7° | 109.5° |
| C2' | C1' | N1 | 113.2° | 110.6° |
| C1' | C2' | O2' | 110.5° | 110.9° |
| C2' | C1' | H16 | 108.7° | 110.7° |
| C1' | C2' | H17 | 110.6° | 110.9° |
| C1' | N1 | C2 | 118.6° | 119.9° |
| C1' | N1 | C6 | 121.0° | 119.8° |
| N1 | C1' | H16 | 109.4° | 110.5° |
| O2' | C2' | H17 | 112.2° | 110.8° |
| C2' | O2' | H25 | 109.5° | 114.0° |
| O2 | C2 | N1 | 119.0° | 119.4° |
| O2 | C2 | N3 | 122.1° | 119.4° |
| N | CA | C | 101.3° | 109.5° |
| CA | N | H3 | 109.5° | 111.0° |
| CA | N | H4 | 109.4° | 111.0° |
| N | CA | H6 | 109.8° | 109.5° |
| CA | C | N3S | 114.7° | 120.0° |
| CA | C | O | 126.3° | 120.0° |
| C | CA | H6 | 109.2° | 109.5° |
| O5' | S | N3S | 108.0° | 107.2° |
| O5' | S | O1S | 107.8° | 106.4° |
| O5' | S | O2S | 103.5° | 106.4° |
| C2 | N1 | C6 | 120.4° | 120.3° |
| N1 | C2 | N3 | 118.9° | 121.1° |
| N1 | C6 | C5 | 121.3° | 119.2° |
| N1 | C6 | H2 | 119.4° | 120.4° |
| N3S | C | O | 119.0° | 120.0° |
| C | N3S | S | 125.4° | 120.0° |
| C | N3S | H22 | 117.3° | 120.0° |
| C2 | N3 | C4 | 120.4° | 120.6° |
| N3S | S | O1S | 108.7° | 106.4° |
| N3S | S | O2S | 107.3° | 106.4° |
| S | N3S | H22 | 117.3° | 120.0° |
| C6 | C5 | C4 | 117.5° | 119.0° |
| C6 | C5 | H1 | 121.2° | 120.5° |
| C5 | C6 | H2 | 119.4° | 120.4° |
| O1S | S | O2S | 120.9° | 123.1° |
| N3 | C4 | C5 | 121.6° | 119.7° |
| N3 | C4 | N4 | 117.9° | 120.2° |
| C5 | C4 | N4 | 120.5° | 120.2° |
| C4 | C5 | H1 | 121.3° | 120.6° |
| C4 | N4 | H23 | 120.0° | 120.1° |
| C4 | N4 | H24 | 120.0° | 120.0° |
| H3 | N | H4 | 109.5° | 111.1° |
| H7 | CB | H8 | 109.5° | 109.5° |
| H10 | CD1 | H11 | 109.5° | 109.5° |
| H10 | CD1 | H12 | 109.5° | 109.5° |
| H11 | CD1 | H12 | 109.5° | 109.5° |
| H13 | CD2 | H14 | 109.5° | 109.4° |
| H13 | CD2 | H15 | 109.5° | 109.5° |
| H14 | CD2 | H15 | 109.5° | 109.4° |
| H20 | C5' | H21 | 109.5° | 109.4° |
| H23 | N4 | H24 | 120.0° | 119.9° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| CD1 | CG | CB | CD2 | 121.9° | 120.0° |
| CD1 | CG | CB | H9 | 118.6° | 120.0° |
| CD1 | CG | CD2 | H9 | 118.9° | 120.0° |
| CD1 | CG | CB | CA | 174.0° | 174.2° |
| CD1 | CG | CB | H7 | 65.2° | 54.2° |
| CD1 | CG | CB | H8 | 53.3° | 65.9° |
| CG | CD1 | H10 | H11 | 120.0° | 120.0° |
| CG | CD1 | H10 | H12 | 120.0° | 120.0° |
| CG | CD1 | H11 | H12 | 120.0° | 120.0° |
| CD1 | CG | CD2 | H13 | 180.0° | 180.0° |
| CD1 | CG | CD2 | H14 | 60.0° | 60.0° |
| CD1 | CG | CD2 | H15 | 60.0° | 60.0° |
| O3' | C3' | C4' | C2' | 118.3° | 118.8° |
| O3' | C3' | C4' | H18 | 124.8° | 122.5° |
| O3' | C3' | C4' | O4' | 89.5° | 120.8° |
| O3' | C3' | C4' | C5' | 147.3° | 119.8° |
| O3' | C3' | C2' | H18 | 123.5° | 122.5° |
| O3' | C3' | C2' | C1' | 82.4° | 97.9° |
| O3' | C3' | C2' | O2' | 35.0° | 20.2° |
| O3' | C3' | C2' | H17 | 160.6° | 143.9° |
| O3' | C3' | C4' | H19 | 26.3° | 1.4° |
| CB | CG | CD2 | H9 | 119.5° | 120.0° |
| CG | CB | CA | H7 | 120.7° | 120.0° |
| CG | CB | CA | H8 | 120.7° | 120.0° |
| CG | CB | CA | N | 81.2° | 65.3° |
| CG | CB | CA | C | 163.8° | 174.7° |
| CG | CB | CA | H6 | 43.2° | 54.7° |
| CG | CB | H7 | H8 | 117.7° | 120.0° |
| CB | CG | CD1 | H10 | 180.0° | 179.9° |
| CB | CG | CD1 | H11 | 60.0° | 60.1° |
| CB | CG | CD1 | H12 | 60.0° | 59.8° |
| CB | CG | CD2 | H13 | 58.3° | 60.0° |
| CB | CG | CD2 | H14 | 178.3° | 180.0° |
| CB | CG | CD2 | H15 | 61.7° | 60.0° |
| CD2 | CG | CB | CA | 64.0° | 65.8° |
| CD2 | CG | CB | H7 | 56.7° | 174.2° |
| CD2 | CG | CB | H8 | 175.2° | 54.2° |
| CD2 | CG | CD1 | H10 | 57.4° | 59.9° |
| CD2 | CG | CD1 | H11 | 177.5° | 179.9° |
| CD2 | CG | CD1 | H12 | 62.6° | 60.1° |
| CG | CD2 | H13 | H14 | 120.0° | 120.0° |
| CG | CD2 | H13 | H15 | 120.0° | 120.1° |
| CG | CD2 | H14 | H15 | 120.0° | 120.0° |
| C3' | C4' | O4' | C5' | 126.8° | 119.4° |
| C3' | C4' | O4' | H19 | 115.1° | 119.4° |
| C3' | C4' | C5' | H19 | 120.9° | 121.1° |
| C4' | C3' | C2' | H18 | 116.9° | 118.7° |
| C3' | C4' | O4' | C1' | 7.9° | 26.5° |
| C3' | C4' | C5' | O5' | 61.5° | 175.0° |
| C4' | C3' | C2' | C1' | 37.2° | 20.9° |
| C4' | C3' | C2' | O2' | 154.6° | 139.1° |
| C4' | C3' | C2' | H17 | 79.8° | 97.3° |
| C3' | C4' | C5' | H20 | 178.7° | 55.0° |
| C3' | C4' | C5' | H21 | 58.3° | 65.0° |
| C4' | C3' | O3' | H26 | 180.0° | 176.3° |
| O4' | C4' | C5' | H19 | 118.6° | 121.1° |
| O4' | C4' | C3' | C2' | 28.8° | 2.0° |
| O4' | C4' | C5' | O5' | 59.0° | 67.2° |
| C4' | O4' | C1' | C2' | 16.6° | 40.1° |
| C4' | O4' | C1' | N1 | 138.9° | 158.5° |
| C4' | O4' | C1' | H16 | 101.1° | 78.6° |
| O4' | C4' | C3' | H18 | 145.7° | 116.7° |
| O4' | C4' | C5' | H20 | 60.9° | 172.8° |
| O4' | C4' | C5' | H21 | 178.8° | 52.8° |
| C5' | C4' | C3' | C2' | 94.4° | 121.4° |
| C5' | C4' | O4' | C1' | 118.9° | 145.9° |
| C4' | C5' | O5' | H20 | 119.8° | 120.0° |
| C4' | C5' | O5' | H21 | 119.8° | 120.1° |
| C4' | C5' | O5' | S | 170.9° | 180.0° |
| C5' | C4' | C3' | H18 | 22.5° | 2.7° |
| C4' | C5' | H20 | H21 | 120.4° | 120.0° |
| C3' | C2' | C1' | O4' | 33.8° | 37.0° |
| C3' | C2' | C1' | O2' | 118.3° | 118.2° |
| C3' | C2' | C1' | H17 | 117.0° | 118.2° |
| C3' | C2' | C1' | N1 | 153.3° | 155.5° |
| C3' | C2' | O2' | H17 | 124.8° | 123.7° |
| C3' | C2' | C1' | H16 | 84.9° | 81.6° |
| C2' | C3' | C4' | H19 | 144.6° | 117.4° |
| C3' | C2' | O2' | H25 | 180.0° | 67.4° |
| C2' | C3' | O3' | H26 | 66.6° | 61.4° |
| CB | CA | N | C | 120.6° | 120.0° |
| CB | CA | N | H6 | 124.0° | 120.0° |
| CB | CA | C | H6 | 120.5° | 120.0° |
| CB | CA | C | N3S | 115.1° | 80.0° |
| CB | CA | C | O | 64.5° | 100.0° |
| CB | CA | N | H3 | 180.0° | 54.0° |
| CB | CA | N | H4 | 60.0° | 70.0° |
| CA | CB | H7 | H8 | 117.8° | 120.0° |
| CA | CB | CG | H9 | 55.5° | 54.2° |
| O4' | C1' | C2' | N1 | 119.5° | 118.5° |
| O4' | C1' | C2' | H16 | 118.7° | 118.7° |
| O4' | C1' | N1 | H16 | 120.5° | 123.0° |
| O4' | C1' | C2' | O2' | 152.1° | 155.2° |
| O4' | C1' | N1 | C2 | 137.5° | 49.1° |
| O4' | C1' | N1 | C6 | 44.9° | 130.9° |
| O4' | C1' | C2' | H17 | 83.1° | 81.2° |
| C1' | O4' | C4' | H19 | 123.0° | 92.9° |
| C5' | O5' | S | N3S | 44.6° | 74.9° |
| C5' | O5' | S | O1S | 72.6° | 38.6° |
| C5' | O5' | S | O2S | 158.1° | 171.5° |
| O5' | C5' | C4' | H19 | 177.6° | 53.9° |
| O5' | C5' | H20 | H21 | 120.5° | 120.0° |
| C2' | C1' | N1 | H16 | 121.4° | 122.9° |
| C1' | C2' | O2' | H17 | 123.9° | 123.7° |
| C2' | C1' | N1 | C2 | 104.4° | 65.0° |
| C2' | C1' | N1 | C6 | 73.2° | 115.0° |
| C1' | C2' | C3' | H18 | 154.2° | 139.6° |
| C1' | C2' | O2' | H25 | 68.6° | 180.0° |
| N1 | C1' | C2' | O2' | 88.5° | 86.3° |
| C1' | N1 | C2 | O2 | 2.6° | 0.3° |
| C1' | N1 | C2 | C6 | 177.7° | 180.0° |
| C1' | N1 | C2 | N3 | 177.0° | 180.0° |
| C1' | N1 | C6 | C5 | 176.9° | 180.0° |
| C1' | N1 | C6 | H2 | 3.0° | 0.0° |
| N1 | C1' | C2' | H17 | 36.3° | 37.3° |
| O2' | C2' | C1' | H16 | 33.3° | 36.5° |
| O2' | C2' | C3' | H18 | 88.5° | 102.2° |
| O2 | C2 | N1 | N3 | 179.6° | 179.8° |
| O2 | C2 | N1 | C6 | 179.7° | 179.7° |
| O2 | C2 | N3 | C4 | 179.8° | 179.7° |
| N | CA | C | H6 | 115.9° | 120.0° |
| N | CA | C | N3S | 8.5° | 160.0° |
| N | CA | C | O | 171.9° | 20.0° |
| CA | N | H3 | H4 | 120.0° | 124.0° |
| N | CA | CB | H7 | 158.1° | 54.7° |
| N | CA | CB | H8 | 39.5° | 174.7° |
| CA | C | N3S | O | 179.6° | 180.0° |
| CA | C | N3S | S | 179.3° | 180.0° |
| C | CA | N | H3 | 59.4° | 65.9° |
| C | CA | N | H4 | 60.6° | 170.0° |
| C | CA | CB | H7 | 43.1° | 65.3° |
| C | CA | CB | H8 | 75.5° | 54.8° |
| CA | C | N3S | H22 | 0.8° | 0.0° |
| O5' | S | N3S | C | 62.2° | 65.0° |
| O5' | S | N3S | O1S | 116.6° | 113.5° |
| O5' | S | N3S | O2S | 111.0° | 113.6° |
| O5' | S | O1S | O2S | 118.6° | 122.9° |
| S | O5' | C5' | H20 | 69.3° | 60.1° |
| S | O5' | C5' | H21 | 51.0° | 59.9° |
| O5' | S | N3S | H22 | 117.8° | 115.0° |
| C2 | N1 | C6 | C5 | 0.7° | 0.0° |
| N1 | C2 | N3 | C4 | 0.3° | 0.1° |
| C2 | N1 | C6 | H2 | 179.4° | 180.0° |
| C2 | N1 | C1' | H16 | 17.0° | 172.1° |
| C6 | N1 | C2 | N3 | 0.7° | 0.0° |
| N1 | C6 | C5 | H2 | 180.0° | 180.0° |
| N1 | C6 | C5 | C4 | 0.2° | 0.0° |
| N1 | C6 | C5 | H1 | 179.8° | 179.9° |
| C6 | N1 | C1' | H16 | 165.4° | 7.9° |
| C | N3S | S | H22 | 180.0° | 180.0° |
| C | N3S | S | O1S | 178.8° | 178.5° |
| C | N3S | S | O2S | 48.9° | 48.5° |
| N3S | C | CA | H6 | 124.4° | 40.0° |
| O | C | N3S | S | 0.4° | 0.0° |
| O | C | CA | H6 | 56.0° | 140.0° |
| O | C | N3S | H22 | 179.6° | 180.0° |
| C2 | N3 | C4 | C5 | 0.1° | 0.1° |
| C2 | N3 | C4 | N4 | 179.6° | 180.0° |
| N3S | S | O1S | O2S | 124.7° | 123.0° |
| C6 | C5 | C4 | N3 | 0.2° | 0.0° |
| C6 | C5 | C4 | H1 | 180.0° | 179.9° |
| C6 | C5 | C4 | N4 | 179.6° | 180.0° |
| O1S | S | N3S | H22 | 1.2° | 1.5° |
| O2S | S | N3S | H22 | 131.1° | 131.4° |
| N3 | C4 | C5 | N4 | 179.4° | 179.9° |
| N3 | C4 | C5 | H1 | 179.8° | 180.0° |
| N3 | C4 | N4 | H23 | 0.0° | 180.0° |
| N3 | C4 | N4 | H24 | 180.0° | 0.0° |
| C4 | C5 | C6 | H2 | 179.8° | 180.0° |
| C5 | C4 | N4 | H23 | 179.4° | 0.0° |
| C5 | C4 | N4 | H24 | 0.6° | 180.0° |
| N4 | C4 | C5 | H1 | 0.4° | 0.1° |
| C4 | N4 | H23 | H24 | 180.0° | 180.0° |
| H1 | C5 | C6 | H2 | 0.2° | 0.0° |
| H3 | N | CA | H6 | 56.0° | 174.0° |
| H4 | N | CA | H6 | 176.0° | 49.9° |
| H6 | CA | CB | H7 | 77.5° | 174.7° |
| H6 | CA | CB | H8 | 163.9° | 65.3° |
| H7 | CB | CG | H9 | 176.2° | 65.8° |
| H8 | CB | CG | H9 | 65.3° | 174.1° |
| H9 | CG | CD1 | H10 | 61.5° | 60.1° |
| H9 | CG | CD1 | H11 | 58.6° | 59.9° |
| H9 | CG | CD1 | H12 | 178.5° | 179.8° |
| H9 | CG | CD2 | H13 | 61.2° | 59.9° |
| H9 | CG | CD2 | H14 | 58.8° | 60.0° |
| H9 | CG | CD2 | H15 | 178.9° | 180.0° |
| H10 | CD1 | H11 | H12 | 120.0° | 120.0° |
| H13 | CD2 | H14 | H15 | 120.0° | 120.0° |
| H16 | C1' | C2' | H17 | 158.1° | 160.1° |
| H17 | C2' | C3' | H18 | 37.2° | 21.4° |
| H17 | C2' | O2' | H25 | 55.3° | 56.3° |
| H18 | C3' | C4' | H19 | 98.5° | 123.9° |
| H18 | C3' | O3' | H26 | 56.0° | 61.1° |
| H19 | C4' | C5' | H20 | 57.7° | 66.1° |
| H19 | C4' | C5' | H21 | 62.6° | 173.9° |
