GMX
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| C6' | C5' | sing | 1.53Å | 1.53Å | |
| OP1 | P | sing | 1.61Å | 1.60Å | |
| O3' | C3' | sing | 1.43Å | 1.46Å | |
| C5' | O5' | sing | 1.43Å | 1.42Å | |
| C5' | C4' | sing | 1.53Å | 1.50Å | |
| P | O5' | sing | 1.61Å | 1.60Å | |
| P | OP2 | sing | 1.61Å | 1.57Å | |
| C4' | C3' | sing | 1.55Å | 1.53Å | |
| C4' | O4' | sing | 1.44Å | 1.44Å | |
| C3' | C2' | sing | 1.54Å | 1.52Å | |
| O2' | C2' | sing | 1.43Å | 1.44Å | |
| O4' | C1' | sing | 1.44Å | 1.44Å | |
| C2' | C1' | sing | 1.54Å | 1.52Å | |
| C1' | N9 | sing | 1.46Å | 1.50Å | |
| C8 | N9 | sing | 1.36Å | 1.36Å | Aromatic |
| C8 | N7 | doub | 1.30Å | 1.35Å | Aromatic |
| N9 | C4 | sing | 1.36Å | 1.35Å | Aromatic |
| N7 | C5 | sing | 1.35Å | 1.39Å | Aromatic |
| C4 | N3 | sing | 1.37Å | 1.36Å | |
| C4 | C5 | doub | 1.39Å | 1.39Å | Aromatic |
| N3 | C2 | sing | 1.36Å | 1.36Å | |
| C5 | C6 | sing | 1.47Å | 1.40Å | |
| C2 | N2 | sing | 1.37Å | 1.36Å | |
| C2 | N1 | doub | 1.32Å | 1.35Å | |
| C6 | N1 | sing | 1.34Å | 1.36Å | |
| C6 | O6 | doub | 1.22Å | 1.24Å | |
| OP2 | H1 | sing | 0.97Å | 0.95Å | |
| OP1 | H2 | sing | 0.97Å | 0.95Å | |
| C5' | H3 | sing | 1.09Å | 1.10Å | |
| C6' | H4 | sing | 1.09Å | 1.10Å | |
| C6' | H5 | sing | 1.09Å | 1.10Å | |
| C6' | H6 | sing | 1.09Å | 1.10Å | |
| C4' | H7 | sing | 1.09Å | 1.10Å | |
| C1' | H8 | sing | 1.09Å | 1.10Å | |
| C2' | H9 | sing | 1.09Å | 1.10Å | |
| O2' | H10 | sing | 0.97Å | 0.95Å | |
| C3' | H11 | sing | 1.09Å | 1.10Å | |
| O3' | H12 | sing | 0.97Å | 0.95Å | |
| C8 | H13 | sing | 1.08Å | 1.08Å | |
| N2 | H14 | sing | 0.97Å | 1.00Å | |
| N2 | H15 | sing | 0.97Å | 1.00Å | |
| N3 | H16 | sing | 0.97Å | 1.00Å | |
| P | OP3 | doub | 1.48Å | 1.58Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| C6' | C5' | O5' | 111.9° | 109.5° |
| C6' | C5' | C4' | 111.0° | 109.5° |
| C6' | C5' | H3 | 107.6° | 109.4° |
| C5' | C6' | H4 | 109.5° | 109.5° |
| C5' | C6' | H5 | 109.5° | 109.5° |
| C5' | C6' | H6 | 109.4° | 109.4° |
| OP1 | P | O5' | 106.2° | 109.5° |
| OP1 | P | OP2 | 120.5° | 109.5° |
| P | OP1 | H2 | 109.5° | 114.0° |
| OP1 | P | OP3 | 107.4° | 109.5° |
| O3' | C3' | C4' | 112.0° | 110.5° |
| O3' | C3' | C2' | 113.8° | 110.6° |
| O3' | C3' | H11 | 110.9° | 110.5° |
| C3' | O3' | H12 | 109.5° | 114.0° |
| O5' | C5' | C4' | 109.2° | 109.5° |
| C5' | O5' | P | 123.3° | 123.0° |
| O5' | C5' | H3 | 109.0° | 109.5° |
| C5' | C4' | C3' | 114.0° | 110.4° |
| C5' | C4' | O4' | 110.6° | 110.4° |
| C4' | C5' | H3 | 107.9° | 109.4° |
| C5' | C4' | H7 | 108.8° | 110.3° |
| O5' | P | OP2 | 109.8° | 109.4° |
| O5' | P | OP3 | 103.6° | 109.4° |
| P | OP2 | H1 | 109.5° | 114.0° |
| OP2 | P | OP3 | 108.1° | 109.5° |
| C3' | C4' | O4' | 105.2° | 104.8° |
| C4' | C3' | C2' | 99.6° | 104.1° |
| C3' | C4' | H7 | 108.5° | 110.4° |
| C4' | C3' | H11 | 110.0° | 110.5° |
| C4' | O4' | C1' | 108.0° | 105.2° |
| O4' | C4' | H7 | 109.7° | 110.4° |
| C3' | C2' | O2' | 108.0° | 110.6° |
| C3' | C2' | C1' | 101.0° | 104.1° |
| C3' | C2' | H9 | 112.6° | 110.6° |
| C2' | C3' | H11 | 110.0° | 110.5° |
| O2' | C2' | C1' | 107.7° | 110.5° |
| O2' | C2' | H9 | 114.0° | 110.4° |
| C2' | O2' | H10 | 109.5° | 114.1° |
| O4' | C1' | C2' | 107.0° | 104.8° |
| O4' | C1' | N9 | 108.3° | 110.3° |
| O4' | C1' | H8 | 111.2° | 110.4° |
| C2' | C1' | N9 | 110.0° | 110.4° |
| C2' | C1' | H8 | 109.9° | 110.5° |
| C1' | C2' | H9 | 112.6° | 110.5° |
| C1' | N9 | C8 | 128.2° | 126.3° |
| C1' | N9 | C4 | 123.1° | 126.2° |
| N9 | C1' | H8 | 110.3° | 110.3° |
| N9 | C8 | N7 | 110.0° | 109.6° |
| C8 | N9 | C4 | 108.7° | 107.5° |
| N9 | C8 | H13 | 125.0° | 125.2° |
| C8 | N7 | C5 | 106.1° | 109.2° |
| N7 | C8 | H13 | 125.0° | 125.2° |
| N9 | C4 | N3 | 131.3° | 134.7° |
| N9 | C4 | C5 | 107.1° | 106.4° |
| N7 | C5 | C4 | 108.1° | 107.4° |
| N7 | C5 | C6 | 134.9° | 134.5° |
| N3 | C4 | C5 | 121.6° | 118.9° |
| C4 | N3 | C2 | 119.3° | 120.5° |
| C4 | N3 | H16 | 120.4° | 119.7° |
| C4 | C5 | C6 | 117.0° | 118.1° |
| N3 | C2 | N2 | 119.0° | 118.7° |
| N3 | C2 | N1 | 121.0° | 122.5° |
| C2 | N3 | H16 | 120.3° | 119.8° |
| C5 | C6 | N1 | 120.6° | 118.6° |
| C5 | C6 | O6 | 121.4° | 120.7° |
| N2 | C2 | N1 | 120.0° | 118.8° |
| C2 | N2 | H14 | 120.0° | 120.0° |
| C2 | N2 | H15 | 120.0° | 120.0° |
| C2 | N1 | C6 | 120.4° | 121.4° |
| N1 | C6 | O6 | 118.0° | 120.7° |
| H4 | C6' | H5 | 109.5° | 109.5° |
| H4 | C6' | H6 | 109.5° | 109.5° |
| H5 | C6' | H6 | 109.5° | 109.4° |
| H14 | N2 | H15 | 120.0° | 120.0° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| C6' | C5' | O5' | C4' | 123.4° | 120.1° |
| C6' | C5' | O5' | H3 | 118.9° | 120.0° |
| C6' | C5' | C4' | H3 | 117.7° | 120.0° |
| C6' | C5' | O5' | P | 73.7° | 120.0° |
| C6' | C5' | C4' | C3' | 73.6° | 180.0° |
| C6' | C5' | C4' | O4' | 168.2° | 64.6° |
| C5' | C6' | H4 | H5 | 120.0° | 120.0° |
| C5' | C6' | H4 | H6 | 120.0° | 120.0° |
| C5' | C6' | H5 | H6 | 120.0° | 119.9° |
| C6' | C5' | C4' | H7 | 47.6° | 57.7° |
| OP1 | P | O5' | C5' | 59.0° | 65.0° |
| OP1 | P | O5' | OP2 | 131.7° | 120.0° |
| OP1 | P | O5' | OP3 | 113.0° | 120.0° |
| OP1 | P | OP2 | OP3 | 123.9° | 120.0° |
| OP1 | P | OP2 | H1 | 123.9° | 60.1° |
| O3' | C3' | C4' | C5' | 77.8° | 98.5° |
| O3' | C3' | C4' | C2' | 120.7° | 118.7° |
| O3' | C3' | C4' | H11 | 123.8° | 122.7° |
| O3' | C3' | C4' | O4' | 160.9° | 142.7° |
| O3' | C3' | C2' | H11 | 125.2° | 122.7° |
| O3' | C3' | C2' | O2' | 47.9° | 0.1° |
| O3' | C3' | C2' | C1' | 160.7° | 118.6° |
| O3' | C3' | C4' | H7 | 43.6° | 23.7° |
| O3' | C3' | C2' | H9 | 78.9° | 122.7° |
| O5' | C5' | C4' | H3 | 118.4° | 120.0° |
| C5' | O5' | P | OP2 | 169.3° | 175.0° |
| O5' | C5' | C4' | C3' | 50.2° | 60.0° |
| O5' | C5' | C4' | O4' | 68.0° | 175.4° |
| O5' | C5' | C6' | H4 | 180.0° | 59.9° |
| O5' | C5' | C6' | H5 | 60.0° | 180.0° |
| O5' | C5' | C6' | H6 | 60.0° | 60.1° |
| O5' | C5' | C4' | H7 | 171.4° | 62.3° |
| C5' | O5' | P | OP3 | 54.0° | 55.0° |
| C4' | C5' | O5' | P | 162.9° | 119.9° |
| C5' | C4' | C3' | O4' | 121.2° | 118.8° |
| C5' | C4' | C3' | H7 | 121.4° | 122.2° |
| C5' | C4' | O4' | H7 | 120.1° | 122.3° |
| C5' | C4' | C3' | C2' | 161.5° | 142.8° |
| C5' | C4' | O4' | C1' | 145.9° | 159.4° |
| C4' | C5' | C6' | H4 | 57.7° | 180.0° |
| C4' | C5' | C6' | H5 | 62.3° | 60.0° |
| C4' | C5' | C6' | H6 | 177.7° | 60.0° |
| C5' | C4' | C3' | H11 | 45.9° | 24.2° |
| O5' | P | OP2 | OP3 | 112.4° | 120.0° |
| O5' | P | OP2 | H1 | 112.4° | 179.9° |
| O5' | P | OP1 | H2 | 110.3° | 60.0° |
| P | O5' | C5' | H3 | 45.2° | 0.0° |
| OP2 | P | OP1 | H2 | 124.3° | 60.0° |
| C3' | C4' | O4' | H7 | 116.5° | 118.9° |
| C4' | C3' | C2' | H11 | 115.5° | 118.6° |
| C4' | C3' | C2' | O2' | 71.5° | 118.7° |
| C3' | C4' | O4' | C1' | 22.4° | 40.5° |
| C4' | C3' | C2' | C1' | 41.4° | 0.1° |
| C3' | C4' | C5' | H3 | 168.6° | 60.0° |
| C4' | C3' | C2' | H9 | 161.8° | 118.6° |
| C4' | C3' | O3' | H12 | 180.0° | 180.0° |
| O4' | C4' | C3' | C2' | 40.2° | 23.9° |
| C4' | O4' | C1' | C2' | 4.9° | 40.5° |
| C4' | O4' | C1' | N9 | 113.7° | 159.3° |
| O4' | C4' | C5' | H3 | 50.4° | 55.4° |
| C4' | O4' | C1' | H8 | 125.0° | 78.4° |
| O4' | C4' | C3' | H11 | 75.3° | 94.7° |
| C3' | C2' | O2' | C1' | 108.3° | 114.7° |
| C3' | C2' | O2' | H9 | 126.0° | 122.7° |
| C3' | C2' | C1' | O4' | 30.0° | 24.1° |
| C3' | C2' | C1' | H9 | 120.4° | 118.7° |
| C3' | C2' | C1' | N9 | 87.5° | 142.8° |
| C2' | C3' | C4' | H7 | 77.1° | 95.0° |
| C3' | C2' | C1' | H8 | 150.8° | 94.9° |
| C3' | C2' | O2' | H10 | 180.0° | 65.3° |
| C2' | C3' | O3' | H12 | 67.9° | 65.4° |
| O2' | C2' | C1' | O4' | 83.1° | 142.8° |
| O2' | C2' | C1' | H9 | 126.6° | 122.5° |
| O2' | C2' | C1' | N9 | 159.4° | 98.4° |
| O2' | C2' | C1' | H8 | 37.8° | 23.9° |
| O2' | C2' | C3' | H11 | 173.0° | 122.7° |
| O4' | C1' | C2' | N9 | 117.5° | 118.8° |
| O4' | C1' | C2' | H8 | 120.9° | 118.9° |
| O4' | C1' | N9 | H8 | 121.9° | 122.3° |
| O4' | C1' | N9 | C8 | 10.8° | 23.8° |
| O4' | C1' | N9 | C4 | 167.2° | 156.5° |
| C1' | O4' | C4' | H7 | 94.1° | 78.4° |
| O4' | C1' | C2' | H9 | 150.3° | 94.7° |
| C2' | C1' | N9 | H8 | 121.4° | 122.4° |
| C2' | C1' | N9 | C8 | 105.8° | 91.5° |
| C2' | C1' | N9 | C4 | 76.2° | 88.2° |
| C1' | C2' | O2' | H10 | 71.7° | 180.0° |
| C1' | C2' | C3' | H11 | 74.1° | 118.7° |
| C1' | N9 | C8 | C4 | 178.2° | 179.8° |
| C1' | N9 | C8 | N7 | 178.1° | 180.0° |
| C1' | N9 | C4 | N3 | 4.2° | 0.8° |
| C1' | N9 | C4 | C5 | 177.5° | 179.8° |
| N9 | C1' | C2' | H9 | 32.9° | 24.1° |
| C1' | N9 | C8 | H13 | 1.9° | 0.0° |
| N9 | C8 | N7 | H13 | 180.0° | 180.0° |
| N9 | C8 | N7 | C5 | 0.6° | 0.0° |
| C8 | N9 | C4 | N3 | 177.4° | 179.5° |
| C8 | N9 | C4 | C5 | 0.9° | 0.4° |
| C8 | N9 | C1' | H8 | 132.8° | 146.1° |
| N7 | C8 | N9 | C4 | 0.2° | 0.3° |
| C8 | N7 | C5 | C4 | 1.1° | 0.2° |
| C8 | N7 | C5 | C6 | 178.6° | 180.0° |
| N9 | C4 | C5 | N7 | 1.2° | 0.4° |
| N9 | C4 | N3 | C5 | 178.1° | 179.0° |
| N9 | C4 | N3 | C2 | 179.5° | 179.5° |
| N9 | C4 | C5 | C6 | 178.6° | 179.8° |
| C4 | N9 | C1' | H8 | 45.3° | 34.2° |
| C4 | N9 | C8 | H13 | 179.8° | 179.8° |
| N9 | C4 | N3 | H16 | 0.4° | 0.7° |
| N7 | C5 | C4 | N3 | 177.3° | 179.6° |
| N7 | C5 | C4 | C6 | 179.8° | 179.8° |
| N7 | C5 | C6 | N1 | 178.0° | 180.0° |
| N7 | C5 | C6 | O6 | 0.1° | 0.0° |
| C5 | N7 | C8 | H13 | 179.4° | 180.0° |
| C4 | N3 | C2 | H16 | 180.0° | 179.7° |
| N3 | C4 | C5 | C6 | 3.0° | 0.6° |
| C4 | N3 | C2 | N2 | 178.5° | 179.7° |
| C4 | N3 | C2 | N1 | 1.1° | 0.3° |
| C5 | C4 | N3 | C2 | 2.4° | 0.6° |
| C4 | C5 | C6 | N1 | 2.3° | 0.3° |
| C4 | C5 | C6 | O6 | 179.6° | 179.7° |
| C5 | C4 | N3 | H16 | 177.6° | 179.7° |
| N3 | C2 | N2 | N1 | 179.6° | 180.0° |
| N3 | C2 | N1 | C6 | 0.5° | 0.0° |
| N3 | C2 | N2 | H14 | 179.6° | 180.0° |
| N3 | C2 | N2 | H15 | 0.4° | 0.0° |
| C5 | C6 | N1 | C2 | 1.2° | 0.0° |
| C5 | C6 | N1 | O6 | 178.1° | 180.0° |
| N2 | C2 | N1 | C6 | 179.0° | 180.0° |
| C2 | N2 | H14 | H15 | 180.0° | 180.0° |
| N2 | C2 | N3 | H16 | 1.5° | 0.0° |
| C2 | N1 | C6 | O6 | 179.3° | 180.0° |
| N1 | C2 | N2 | H14 | 0.0° | 0.0° |
| N1 | C2 | N2 | H15 | 180.0° | 180.0° |
| N1 | C2 | N3 | H16 | 178.9° | 180.0° |
| H1 | OP2 | P | OP3 | 0.0° | 59.9° |
| H2 | OP1 | P | OP3 | 0.0° | 180.0° |
| H3 | C5' | C6' | H4 | 60.2° | 60.0° |
| H3 | C5' | C6' | H5 | 179.8° | 60.0° |
| H3 | C5' | C6' | H6 | 59.8° | 179.9° |
| H3 | C5' | C4' | H7 | 70.2° | 177.7° |
| H4 | C6' | H5 | H6 | 120.0° | 120.0° |
| H7 | C4' | C3' | H11 | 167.3° | 146.4° |
| H8 | C1' | C2' | H9 | 88.8° | 146.4° |
| H9 | C2' | O2' | H10 | 54.0° | 57.4° |
| H9 | C2' | C3' | H11 | 46.3° | 0.0° |
| H11 | C3' | O3' | H12 | 56.8° | 57.3° |
