XSX
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| N4 | C7 | sing | 1.47Å | 1.49Å | |
| C7 | C3 | sing | 1.53Å | 1.53Å | |
| C7 | C9 | sing | 1.51Å | 1.53Å | |
| C3 | C1 | sing | 1.53Å | 1.52Å | |
| C9 | O11 | doub | 1.21Å | 1.25Å | |
| C9 | O10 | sing | 1.34Å | 1.25Å | |
| C1 | N3 | sing | 1.47Å | 1.47Å | |
| O4 | C4 | doub | 1.22Å | 1.25Å | |
| N3 | C4 | sing | 1.35Å | 1.41Å | |
| N3 | C2 | sing | 1.35Å | 1.41Å | |
| C4 | C5 | sing | 1.42Å | 1.39Å | |
| O2 | C2 | doub | 1.22Å | 1.25Å | |
| C2 | N1 | sing | 1.35Å | 1.41Å | |
| C5 | C6 | doub | 1.35Å | 1.39Å | |
| N1 | C6 | sing | 1.37Å | 1.34Å | |
| N1 | C1' | sing | 1.47Å | 1.48Å | |
| C1' | O4' | sing | 1.44Å | 1.41Å | |
| C1' | C2' | sing | 1.55Å | 1.53Å | |
| O4' | C4' | sing | 1.44Å | 1.44Å | |
| OP2 | P | sing | 1.61Å | 1.51Å | |
| C2' | O2' | sing | 1.43Å | 1.42Å | |
| C2' | C3' | sing | 1.55Å | 1.53Å | |
| C4' | C3' | sing | 1.54Å | 1.52Å | |
| C4' | C5' | sing | 1.53Å | 1.51Å | |
| P | O5' | sing | 1.61Å | 1.59Å | |
| P | OP1 | doub | 1.48Å | 1.51Å | |
| O5' | C5' | sing | 1.43Å | 1.42Å | |
| C3' | O3' | sing | 1.43Å | 1.42Å | |
| C5' | H1 | sing | 1.09Å | 1.10Å | |
| C5' | H2 | sing | 1.09Å | 1.10Å | |
| C4' | H3 | sing | 1.09Å | 1.10Å | |
| C3' | H4 | sing | 1.09Å | 1.10Å | |
| O3' | H5 | sing | 0.97Å | 0.95Å | |
| C2' | H6 | sing | 1.09Å | 1.10Å | |
| O2' | H7 | sing | 0.97Å | 0.95Å | |
| C1' | H8 | sing | 1.09Å | 1.10Å | |
| C5 | H9 | sing | 1.08Å | 1.08Å | |
| C6 | H10 | sing | 1.08Å | 1.08Å | |
| C1 | H11 | sing | 1.09Å | 1.10Å | |
| C1 | H12 | sing | 1.09Å | 1.10Å | |
| C3 | H13 | sing | 1.09Å | 1.10Å | |
| C3 | H14 | sing | 1.09Å | 1.10Å | |
| C7 | H15 | sing | 1.09Å | 1.10Å | |
| N4 | H16 | sing | 1.01Å | 1.00Å | |
| N4 | H17 | sing | 1.01Å | 1.00Å | |
| O10 | H19 | sing | 0.97Å | 0.95Å | |
| OP2 | H21 | sing | 0.97Å | 0.95Å | |
| P | OP3 | sing | 1.61Å | 1.61Å | |
| OP3 | HO3' | sing | 0.97Å | 0.95Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| N4 | C7 | C3 | 110.2° | 109.5° |
| N4 | C7 | C9 | 109.1° | 109.5° |
| N4 | C7 | H15 | 109.4° | 109.4° |
| C7 | N4 | H16 | 109.5° | 111.0° |
| C7 | N4 | H17 | 109.5° | 111.0° |
| C3 | C7 | C9 | 110.5° | 109.5° |
| C7 | C3 | C1 | 113.6° | 109.4° |
| C7 | C3 | H13 | 108.4° | 109.5° |
| C7 | C3 | H14 | 108.4° | 109.5° |
| C3 | C7 | H15 | 108.8° | 109.5° |
| C7 | C9 | O11 | 117.0° | 120.0° |
| C7 | C9 | O10 | 117.0° | 120.0° |
| C9 | C7 | H15 | 108.8° | 109.5° |
| C3 | C1 | N3 | 145.6° | 109.4° |
| C3 | C1 | H11 | 99.8° | 109.5° |
| C3 | C1 | H12 | 99.8° | 109.5° |
| C1 | C3 | H13 | 108.4° | 109.5° |
| C1 | C3 | H14 | 108.4° | 109.5° |
| O11 | C9 | O10 | 125.5° | 120.0° |
| C9 | O10 | H19 | 109.5° | 117.0° |
| C1 | N3 | C4 | 120.5° | 119.9° |
| C1 | N3 | C2 | 120.5° | 119.9° |
| N3 | C1 | H11 | 99.8° | 109.4° |
| N3 | C1 | H12 | 99.8° | 109.5° |
| O4 | C4 | N3 | 120.6° | 120.3° |
| O4 | C4 | C5 | 119.8° | 120.3° |
| C4 | N3 | C2 | 119.0° | 120.3° |
| N3 | C4 | C5 | 119.6° | 119.4° |
| N3 | C2 | O2 | 120.2° | 119.5° |
| N3 | C2 | N1 | 119.5° | 120.9° |
| C4 | C5 | C6 | 120.1° | 119.1° |
| C4 | C5 | H9 | 119.9° | 120.4° |
| O2 | C2 | N1 | 120.3° | 119.6° |
| C2 | N1 | C6 | 120.1° | 120.7° |
| C2 | N1 | C1' | 120.6° | 119.7° |
| C5 | C6 | N1 | 121.6° | 119.6° |
| C6 | C5 | H9 | 119.9° | 120.4° |
| C5 | C6 | H10 | 119.2° | 120.1° |
| C6 | N1 | C1' | 119.2° | 119.7° |
| N1 | C6 | H10 | 119.2° | 120.2° |
| N1 | C1' | O4' | 107.7° | 110.4° |
| N1 | C1' | C2' | 114.7° | 110.4° |
| N1 | C1' | H8 | 108.5° | 110.4° |
| O4' | C1' | C2' | 108.5° | 104.8° |
| C1' | O4' | C4' | 110.6° | 105.3° |
| O4' | C1' | H8 | 109.5° | 110.4° |
| C1' | C2' | O2' | 108.3° | 110.5° |
| C1' | C2' | C3' | 102.6° | 104.0° |
| C1' | C2' | H6 | 111.0° | 110.6° |
| C2' | C1' | H8 | 107.9° | 110.4° |
| O4' | C4' | C3' | 104.8° | 104.8° |
| O4' | C4' | C5' | 108.3° | 110.4° |
| O4' | C4' | H3 | 110.2° | 110.5° |
| OP2 | P | O5' | 107.0° | 109.5° |
| OP2 | P | OP1 | 119.9° | 109.5° |
| P | OP2 | H21 | 109.5° | 114.0° |
| OP2 | P | OP3 | 105.4° | 109.5° |
| O2' | C2' | C3' | 110.6° | 110.5° |
| O2' | C2' | H6 | 112.8° | 110.5° |
| C2' | O2' | H7 | 109.5° | 114.0° |
| C2' | C3' | C4' | 104.0° | 104.1° |
| C2' | C3' | O3' | 113.0° | 110.6° |
| C2' | C3' | H4 | 108.7° | 110.6° |
| C3' | C2' | H6 | 111.0° | 110.5° |
| C3' | C4' | C5' | 114.9° | 110.4° |
| C4' | C3' | O3' | 111.8° | 110.5° |
| C3' | C4' | H3 | 109.2° | 110.3° |
| C4' | C3' | H4 | 108.8° | 110.5° |
| C4' | C5' | O5' | 110.2° | 109.5° |
| C4' | C5' | H1 | 109.3° | 109.5° |
| C4' | C5' | H2 | 109.3° | 109.5° |
| C5' | C4' | H3 | 109.3° | 110.3° |
| O5' | P | OP1 | 108.8° | 109.4° |
| P | O5' | C5' | 121.8° | 123.0° |
| O5' | P | OP3 | 104.6° | 109.5° |
| OP1 | P | OP3 | 110.1° | 109.5° |
| O5' | C5' | H1 | 109.3° | 109.5° |
| O5' | C5' | H2 | 109.3° | 109.4° |
| O3' | C3' | H4 | 110.3° | 110.5° |
| C3' | O3' | H5 | 109.5° | 114.0° |
| H1 | C5' | H2 | 109.4° | 109.5° |
| H11 | C1 | H12 | 109.5° | 109.5° |
| H13 | C3 | H14 | 109.5° | 109.5° |
| H16 | N4 | H17 | 109.5° | 111.1° |
| P | OP3 | HO3' | 109.5° | 114.0° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| N4 | C7 | C3 | C9 | 120.7° | 120.0° |
| N4 | C7 | C3 | H15 | 119.9° | 120.0° |
| N4 | C7 | C9 | H15 | 119.3° | 120.0° |
| N4 | C7 | C3 | C1 | 176.4° | 65.0° |
| N4 | C7 | C9 | O11 | 63.3° | 20.0° |
| N4 | C7 | C9 | O10 | 124.2° | 160.0° |
| N4 | C7 | C3 | H13 | 55.8° | 55.0° |
| N4 | C7 | C3 | H14 | 63.0° | 175.0° |
| C7 | N4 | H16 | H17 | 120.0° | 124.0° |
| C3 | C7 | C9 | H15 | 119.4° | 120.0° |
| C7 | C3 | C1 | H13 | 120.6° | 120.0° |
| C7 | C3 | C1 | H14 | 120.6° | 120.0° |
| C3 | C7 | C9 | O11 | 58.0° | 100.0° |
| C3 | C7 | C9 | O10 | 114.5° | 80.0° |
| C7 | C3 | C1 | N3 | 122.2° | 180.0° |
| C7 | C3 | C1 | H11 | 113.8° | 60.1° |
| C7 | C3 | C1 | H12 | 1.9° | 60.0° |
| C7 | C3 | H13 | H14 | 118.1° | 120.0° |
| C3 | C7 | N4 | H16 | 180.0° | 59.9° |
| C3 | C7 | N4 | H17 | 60.0° | 176.0° |
| C9 | C7 | C3 | C1 | 55.7° | 175.0° |
| C7 | C9 | O11 | O10 | 171.8° | 180.0° |
| C9 | C7 | C3 | H13 | 64.9° | 65.0° |
| C9 | C7 | C3 | H14 | 176.4° | 55.0° |
| C9 | C7 | N4 | H16 | 58.5° | 60.1° |
| C9 | C7 | N4 | H17 | 178.5° | 64.0° |
| C7 | C9 | O10 | H19 | 171.8° | 180.0° |
| C3 | C1 | N3 | H11 | 124.0° | 120.0° |
| C3 | C1 | N3 | H12 | 124.0° | 120.0° |
| C3 | C1 | N3 | C4 | 26.2° | 90.1° |
| C3 | C1 | N3 | C2 | 154.0° | 90.5° |
| C3 | C1 | H11 | H12 | 104.2° | 120.0° |
| C1 | C3 | H13 | H14 | 118.1° | 120.0° |
| C1 | C3 | C7 | H15 | 63.7° | 55.0° |
| O11 | C9 | C7 | H15 | 177.4° | 140.0° |
| O11 | C9 | O10 | H19 | 0.0° | 0.0° |
| O10 | C9 | C7 | H15 | 4.9° | 40.0° |
| C1 | N3 | C4 | O4 | 0.1° | 0.6° |
| C1 | N3 | C4 | C2 | 179.8° | 179.4° |
| C1 | N3 | C4 | C5 | 179.9° | 180.0° |
| C1 | N3 | C2 | O2 | 0.2° | 0.3° |
| C1 | N3 | C2 | N1 | 178.9° | 179.8° |
| N3 | C1 | H11 | H12 | 104.2° | 120.0° |
| N3 | C1 | C3 | H13 | 1.5° | 60.0° |
| N3 | C1 | C3 | H14 | 117.2° | 60.0° |
| O4 | C4 | N3 | C5 | 180.0° | 179.4° |
| O4 | C4 | N3 | C2 | 179.9° | 180.0° |
| O4 | C4 | C5 | C6 | 180.0° | 180.0° |
| O4 | C4 | C5 | H9 | 0.0° | 0.3° |
| C4 | N3 | C2 | O2 | 180.0° | 179.7° |
| C4 | N3 | C2 | N1 | 0.9° | 0.4° |
| N3 | C4 | C5 | C6 | 0.0° | 0.5° |
| N3 | C4 | C5 | H9 | 180.0° | 179.7° |
| C4 | N3 | C1 | H11 | 150.3° | 150.0° |
| C4 | N3 | C1 | H12 | 97.8° | 29.9° |
| C2 | N3 | C4 | C5 | 0.0° | 0.6° |
| N3 | C2 | O2 | N1 | 179.1° | 180.0° |
| N3 | C2 | N1 | C6 | 1.9° | 0.1° |
| N3 | C2 | N1 | C1' | 177.7° | 179.9° |
| C2 | N3 | C1 | H11 | 29.9° | 29.4° |
| C2 | N3 | C1 | H12 | 82.0° | 149.5° |
| C4 | C5 | C6 | H9 | 180.0° | 179.7° |
| C4 | C5 | C6 | N1 | 1.1° | 0.2° |
| C4 | C5 | C6 | H10 | 178.9° | 179.8° |
| O2 | C2 | N1 | C6 | 178.9° | 180.0° |
| O2 | C2 | N1 | C1' | 3.1° | 0.0° |
| C2 | N1 | C6 | C5 | 2.0° | 0.0° |
| C2 | N1 | C6 | C1' | 175.9° | 180.0° |
| C2 | N1 | C1' | O4' | 142.2° | 126.5° |
| C2 | N1 | C1' | C2' | 96.9° | 118.1° |
| C2 | N1 | C1' | H8 | 23.8° | 4.1° |
| C2 | N1 | C6 | H10 | 178.0° | 180.0° |
| C5 | C6 | N1 | H10 | 180.0° | 180.0° |
| C5 | C6 | N1 | C1' | 177.9° | 180.0° |
| C6 | N1 | C1' | O4' | 33.6° | 53.5° |
| C6 | N1 | C1' | C2' | 87.3° | 61.8° |
| C6 | N1 | C1' | H8 | 152.1° | 175.9° |
| N1 | C6 | C5 | H9 | 178.9° | 180.0° |
| N1 | C1' | O4' | C2' | 124.7° | 118.8° |
| N1 | C1' | O4' | H8 | 117.8° | 122.4° |
| N1 | C1' | C2' | H8 | 121.0° | 122.3° |
| N1 | C1' | O4' | C4' | 127.1° | 159.3° |
| N1 | C1' | C2' | O2' | 139.1° | 98.5° |
| N1 | C1' | C2' | C3' | 103.8° | 142.8° |
| N1 | C1' | C2' | H6 | 14.8° | 24.1° |
| C1' | N1 | C6 | H10 | 2.1° | 0.0° |
| O4' | C1' | C2' | H8 | 118.6° | 118.8° |
| O4' | C1' | C2' | O2' | 100.4° | 142.6° |
| O4' | C1' | C2' | C3' | 16.6° | 24.0° |
| C1' | O4' | C4' | C3' | 20.7° | 40.4° |
| C1' | O4' | C4' | C5' | 143.8° | 159.3° |
| C1' | O4' | C4' | H3 | 96.6° | 78.4° |
| O4' | C1' | C2' | H6 | 135.3° | 94.7° |
| C2' | C1' | O4' | C4' | 2.4° | 40.5° |
| C1' | C2' | O2' | C3' | 111.7° | 114.6° |
| C1' | C2' | O2' | H6 | 123.3° | 122.8° |
| C1' | C2' | C3' | H6 | 118.7° | 118.8° |
| C1' | C2' | C3' | C4' | 28.2° | 0.0° |
| C1' | C2' | C3' | O3' | 149.6° | 118.7° |
| C1' | C2' | C3' | H4 | 87.6° | 118.7° |
| C1' | C2' | O2' | H7 | 180.0° | 176.1° |
| O4' | C4' | C3' | C2' | 30.3° | 23.9° |
| O4' | C4' | C3' | C5' | 118.7° | 118.9° |
| O4' | C4' | C3' | H3 | 118.0° | 118.9° |
| O4' | C4' | C5' | H3 | 120.1° | 122.4° |
| O4' | C4' | C5' | O5' | 68.0° | 69.6° |
| O4' | C4' | C3' | O3' | 152.6° | 142.6° |
| O4' | C4' | C5' | H1 | 52.1° | 50.4° |
| O4' | C4' | C5' | H2 | 171.8° | 170.4° |
| O4' | C4' | C3' | H4 | 85.4° | 94.8° |
| C4' | O4' | C1' | H8 | 115.1° | 78.3° |
| OP2 | P | O5' | OP1 | 130.8° | 120.0° |
| OP2 | P | O5' | OP3 | 111.5° | 120.0° |
| OP2 | P | OP1 | OP3 | 122.5° | 120.0° |
| OP2 | P | O5' | C5' | 75.6° | 64.9° |
| OP2 | P | OP3 | HO3' | 130.6° | 60.0° |
| O2' | C2' | C3' | H6 | 126.0° | 122.6° |
| O2' | C2' | C3' | C4' | 87.2° | 118.7° |
| O2' | C2' | C3' | O3' | 34.3° | 0.1° |
| O2' | C2' | C3' | H4 | 157.0° | 122.7° |
| O2' | C2' | C1' | H8 | 18.2° | 23.8° |
| C2' | C3' | C4' | O3' | 122.2° | 118.7° |
| C2' | C3' | C4' | H4 | 115.7° | 118.7° |
| C2' | C3' | C4' | C5' | 149.1° | 142.8° |
| C2' | C3' | O3' | H4 | 121.9° | 122.7° |
| C2' | C3' | C4' | H3 | 87.7° | 95.0° |
| C2' | C3' | O3' | H5 | 180.0° | 65.3° |
| C3' | C2' | O2' | H7 | 68.2° | 61.5° |
| C3' | C2' | C1' | H8 | 135.2° | 94.8° |
| C3' | C4' | C5' | H3 | 123.2° | 122.2° |
| C3' | C4' | C5' | O5' | 48.7° | 175.0° |
| C4' | C3' | O3' | H4 | 121.2° | 122.6° |
| C3' | C4' | C5' | H1 | 168.9° | 65.1° |
| C3' | C4' | C5' | H2 | 71.4° | 55.0° |
| C4' | C3' | O3' | H5 | 63.0° | 180.0° |
| C4' | C3' | C2' | H6 | 146.8° | 118.7° |
| C4' | C5' | O5' | P | 154.0° | 180.0° |
| C4' | C5' | O5' | H1 | 120.1° | 120.0° |
| C4' | C5' | O5' | H2 | 120.1° | 120.0° |
| C5' | C4' | C3' | O3' | 88.7° | 98.5° |
| C4' | C5' | H1 | H2 | 119.7° | 120.0° |
| C5' | C4' | C3' | H4 | 33.3° | 24.1° |
| O5' | P | OP1 | OP3 | 114.1° | 120.0° |
| P | O5' | C5' | H1 | 33.9° | 60.0° |
| P | O5' | C5' | H2 | 85.9° | 60.1° |
| O5' | P | OP2 | H21 | 124.3° | 60.0° |
| O5' | P | OP3 | HO3' | 116.8° | 180.0° |
| OP1 | P | O5' | C5' | 153.6° | 55.1° |
| OP1 | P | OP2 | H21 | 0.0° | 180.0° |
| OP1 | P | OP3 | HO3' | 0.0° | 60.0° |
| O5' | C5' | H1 | H2 | 119.7° | 120.0° |
| O5' | C5' | C4' | H3 | 171.9° | 52.7° |
| C5' | O5' | P | OP3 | 35.9° | 175.0° |
| O3' | C3' | C4' | H3 | 34.6° | 23.7° |
| O3' | C3' | C2' | H6 | 91.7° | 122.5° |
| H1 | C5' | C4' | H3 | 68.0° | 172.7° |
| H2 | C5' | C4' | H3 | 51.8° | 67.2° |
| H3 | C4' | C3' | H4 | 156.6° | 146.3° |
| H4 | C3' | O3' | H5 | 58.1° | 57.5° |
| H4 | C3' | C2' | H6 | 31.0° | 0.1° |
| H6 | C2' | O2' | H7 | 56.8° | 61.1° |
| H6 | C2' | C1' | H8 | 106.1° | 146.5° |
| H9 | C5 | C6 | H10 | 1.1° | 0.1° |
| H11 | C1 | C3 | H13 | 125.6° | 180.0° |
| H11 | C1 | C3 | H14 | 6.8° | 60.0° |
| H12 | C1 | C3 | H13 | 122.5° | 60.0° |
| H12 | C1 | C3 | H14 | 118.7° | 180.0° |
| H13 | C3 | C7 | H15 | 175.7° | 175.0° |
| H14 | C3 | C7 | H15 | 56.9° | 65.0° |
| H15 | C7 | N4 | H16 | 60.4° | 179.9° |
| H15 | C7 | N4 | H17 | 59.6° | 56.0° |
| H21 | OP2 | P | OP3 | 124.8° | 60.0° |
