2YR
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| S | C8 | sing | 1.81Å | 1.81Å | |
| C8 | C9 | sing | 1.53Å | 1.52Å | |
| N4 | C9 | sing | 1.46Å | 1.49Å | |
| N4 | C4 | sing | 1.38Å | 1.33Å | |
| C4 | N3 | doub | 1.33Å | 1.34Å | |
| C4 | C5 | sing | 1.41Å | 1.43Å | |
| N3 | C2 | sing | 1.33Å | 1.35Å | |
| C5 | C6 | doub | 1.35Å | 1.34Å | |
| C2 | O2 | doub | 1.22Å | 1.24Å | |
| C2 | N1 | sing | 1.35Å | 1.40Å | |
| C6 | N1 | sing | 1.36Å | 1.37Å | |
| N1 | C1' | sing | 1.46Å | 1.48Å | |
| C2' | C3' | sing | 1.55Å | 1.52Å | |
| C2' | C1' | sing | 1.54Å | 1.53Å | |
| C3' | O3' | sing | 1.43Å | 1.43Å | |
| C3' | C4' | sing | 1.55Å | 1.52Å | |
| C1' | O4' | sing | 1.44Å | 1.43Å | |
| O4' | C4' | sing | 1.44Å | 1.45Å | |
| C4' | C5' | sing | 1.53Å | 1.51Å | |
| C5' | O5' | sing | 1.43Å | 1.44Å | |
| O5' | P | sing | 1.61Å | 1.59Å | |
| OP2 | P | sing | 1.61Å | 1.48Å | |
| P | OP1 | doub | 1.48Å | 1.48Å | |
| OP2 | 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 | |
| C2' | H9 | sing | 1.09Å | 1.10Å | |
| C1' | H10 | sing | 1.09Å | 1.10Å | |
| N4 | H11 | sing | 0.97Å | 1.00Å | |
| C5 | H12 | sing | 1.08Å | 1.08Å | |
| C6 | H13 | sing | 1.08Å | 1.08Å | |
| S | H14 | sing | 1.34Å | 1.30Å | |
| C8 | H15 | sing | 1.09Å | 1.10Å | |
| C8 | H16 | sing | 1.09Å | 1.10Å | |
| C9 | H17 | sing | 1.09Å | 1.10Å | |
| C9 | H18 | sing | 1.09Å | 1.10Å | |
| P | OP3 | sing | 1.61Å | 46.00Å | |
| OP3 | H20 | sing | 0.97Å | 0.00Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| S | C8 | C9 | 108.9° | 109.5° |
| C8 | S | H14 | 102.0° | 103.0° |
| S | C8 | H15 | 109.6° | 109.5° |
| S | C8 | H16 | 109.6° | 109.5° |
| C8 | C9 | N4 | 166.8° | 109.5° |
| C9 | C8 | H15 | 109.6° | 109.5° |
| C9 | C8 | H16 | 109.6° | 109.5° |
| C8 | C9 | H17 | 93.8° | 109.5° |
| C8 | C9 | H18 | 93.8° | 109.4° |
| C9 | N4 | C4 | 125.8° | 120.0° |
| C9 | N4 | H11 | 117.1° | 120.0° |
| N4 | C9 | H17 | 93.8° | 109.5° |
| N4 | C9 | H18 | 93.8° | 109.4° |
| N4 | C4 | N3 | 117.9° | 120.2° |
| N4 | C4 | C5 | 120.2° | 120.2° |
| C4 | N4 | H11 | 117.1° | 120.0° |
| N3 | C4 | C5 | 121.9° | 119.6° |
| C4 | N3 | C2 | 119.9° | 120.7° |
| C4 | C5 | C6 | 117.5° | 119.0° |
| C4 | C5 | H12 | 121.2° | 120.5° |
| N3 | C2 | O2 | 121.7° | 119.4° |
| N3 | C2 | N1 | 119.4° | 121.1° |
| C5 | C6 | N1 | 121.0° | 119.3° |
| C6 | C5 | H12 | 121.2° | 120.5° |
| C5 | C6 | H13 | 119.5° | 120.4° |
| O2 | C2 | N1 | 119.0° | 119.5° |
| C2 | N1 | C6 | 120.2° | 120.3° |
| C2 | N1 | C1' | 118.8° | 119.8° |
| C6 | N1 | C1' | 121.0° | 119.8° |
| N1 | C6 | H13 | 119.5° | 120.3° |
| N1 | C1' | C2' | 115.0° | 109.9° |
| N1 | C1' | O4' | 108.3° | 109.9° |
| N1 | C1' | H10 | 108.9° | 110.0° |
| C3' | C2' | C1' | 103.8° | 104.2° |
| C2' | C3' | O3' | 114.3° | 110.9° |
| C2' | C3' | C4' | 102.5° | 102.1° |
| C2' | C3' | H6 | 109.4° | 111.0° |
| C3' | C2' | H8 | 110.9° | 110.5° |
| C3' | C2' | H9 | 110.9° | 110.5° |
| C2' | C1' | O4' | 106.9° | 107.2° |
| C1' | C2' | H8 | 110.9° | 110.5° |
| C1' | C2' | H9 | 110.9° | 110.5° |
| C2' | C1' | H10 | 108.2° | 109.8° |
| O3' | C3' | C4' | 110.3° | 110.9° |
| O3' | C3' | H6 | 110.7° | 110.8° |
| C3' | O3' | H7 | 109.5° | 114.0° |
| C3' | C4' | O4' | 104.5° | 103.6° |
| C3' | C4' | C5' | 113.8° | 110.6° |
| C3' | C4' | H5 | 108.6° | 110.6° |
| C4' | C3' | H6 | 109.3° | 110.9° |
| C1' | O4' | C4' | 109.9° | 107.0° |
| O4' | C1' | H10 | 109.5° | 109.9° |
| O4' | C4' | C5' | 111.4° | 110.7° |
| O4' | C4' | H5 | 109.6° | 110.7° |
| C4' | C5' | O5' | 111.2° | 109.4° |
| C4' | C5' | H3 | 109.0° | 109.5° |
| C4' | C5' | H4 | 109.1° | 109.5° |
| C5' | C4' | H5 | 108.8° | 110.5° |
| C5' | O5' | P | 120.2° | 123.0° |
| O5' | C5' | H3 | 109.0° | 109.4° |
| O5' | C5' | H4 | 109.0° | 109.5° |
| O5' | P | OP2 | 109.8° | 109.5° |
| O5' | P | OP1 | 107.3° | 109.5° |
| O5' | P | OP3 | 70.2° | 109.5° |
| OP2 | P | OP1 | 119.4° | 109.5° |
| P | OP2 | H2 | 109.5° | 114.0° |
| OP2 | P | OP3 | 89.3° | 109.5° |
| OP1 | P | OP3 | 61.1° | 109.4° |
| H3 | C5' | H4 | 109.5° | 109.5° |
| H8 | C2' | H9 | 109.5° | 110.5° |
| H15 | C8 | H16 | 109.5° | 109.4° |
| H17 | C9 | H18 | 109.5° | 109.5° |
| P | OP3 | H20 | 90.0° | 113.9° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| S | C8 | C9 | H15 | 119.9° | 120.0° |
| S | C8 | C9 | H16 | 119.9° | 120.0° |
| S | C8 | C9 | N4 | 36.1° | 180.0° |
| S | C8 | H15 | H16 | 120.3° | 119.9° |
| S | C8 | C9 | H17 | 161.2° | 60.0° |
| S | C8 | C9 | H18 | 89.0° | 60.0° |
| C8 | C9 | N4 | H17 | 125.1° | 120.0° |
| C8 | C9 | N4 | H18 | 125.1° | 120.0° |
| C8 | C9 | N4 | C4 | 112.8° | 180.0° |
| C8 | C9 | N4 | H11 | 67.2° | 0.0° |
| C9 | C8 | S | H14 | 180.0° | 179.9° |
| C9 | C8 | H15 | H16 | 120.3° | 120.0° |
| C8 | C9 | H17 | H18 | 95.4° | 120.0° |
| C9 | N4 | C4 | H11 | 180.0° | 179.9° |
| C9 | N4 | C4 | N3 | 104.4° | 0.1° |
| C9 | N4 | C4 | C5 | 75.3° | 180.0° |
| N4 | C9 | C8 | H15 | 83.8° | 60.0° |
| N4 | C9 | C8 | H16 | 156.0° | 59.9° |
| N4 | C9 | H17 | H18 | 95.4° | 120.0° |
| N4 | C4 | N3 | C5 | 179.7° | 179.9° |
| N4 | C4 | N3 | C2 | 179.7° | 179.9° |
| N4 | C4 | C5 | C6 | 179.0° | 179.6° |
| N4 | C4 | C5 | H12 | 0.9° | 0.1° |
| C4 | N4 | C9 | H17 | 12.2° | 59.9° |
| C4 | N4 | C9 | H18 | 122.1° | 60.1° |
| N3 | C4 | C5 | C6 | 0.7° | 0.3° |
| C4 | N3 | C2 | O2 | 179.7° | 180.0° |
| C4 | N3 | C2 | N1 | 0.5° | 0.1° |
| N3 | C4 | N4 | H11 | 75.6° | 180.0° |
| N3 | C4 | C5 | H12 | 179.4° | 180.0° |
| C5 | C4 | N3 | C2 | 0.0° | 0.0° |
| C4 | C5 | C6 | H12 | 180.0° | 179.8° |
| C4 | C5 | C6 | N1 | 0.9° | 0.5° |
| C5 | C4 | N4 | H11 | 104.7° | 0.1° |
| C4 | C5 | C6 | H13 | 179.1° | 180.0° |
| N3 | C2 | O2 | N1 | 179.2° | 179.9° |
| N3 | C2 | N1 | C6 | 0.2° | 0.2° |
| N3 | C2 | N1 | C1' | 179.5° | 180.0° |
| C5 | C6 | N1 | C2 | 0.5° | 0.5° |
| C5 | C6 | N1 | H13 | 180.0° | 179.5° |
| C5 | C6 | N1 | C1' | 179.8° | 179.7° |
| O2 | C2 | N1 | C6 | 179.5° | 179.7° |
| O2 | C2 | N1 | C1' | 0.3° | 0.1° |
| C2 | N1 | C6 | C1' | 179.7° | 179.8° |
| C2 | N1 | C1' | C2' | 66.9° | 65.0° |
| C2 | N1 | C1' | O4' | 173.7° | 52.7° |
| C2 | N1 | C1' | H10 | 54.7° | 173.9° |
| C2 | N1 | C6 | H13 | 179.5° | 180.0° |
| C6 | N1 | C1' | C2' | 113.4° | 114.8° |
| C6 | N1 | C1' | O4' | 6.0° | 127.5° |
| C6 | N1 | C1' | H10 | 125.1° | 6.3° |
| N1 | C6 | C5 | H12 | 179.1° | 179.7° |
| N1 | C1' | C2' | C3' | 102.7° | 121.4° |
| N1 | C1' | C2' | O4' | 120.2° | 119.4° |
| N1 | C1' | C2' | H10 | 121.9° | 121.1° |
| N1 | C1' | O4' | H10 | 118.6° | 121.2° |
| N1 | C1' | O4' | C4' | 129.2° | 145.8° |
| N1 | C1' | C2' | H8 | 16.4° | 2.8° |
| N1 | C1' | C2' | H9 | 138.2° | 119.9° |
| C1' | N1 | C6 | H13 | 0.2° | 0.2° |
| C3' | C2' | C1' | H8 | 119.1° | 118.7° |
| C3' | C2' | C1' | H9 | 119.1° | 118.7° |
| C2' | C3' | O3' | C4' | 114.8° | 112.7° |
| C2' | C3' | O3' | H6 | 124.1° | 123.7° |
| C2' | C3' | C4' | H6 | 116.0° | 118.3° |
| C3' | C2' | C1' | O4' | 17.4° | 2.0° |
| C2' | C3' | C4' | O4' | 35.0° | 36.9° |
| C2' | C3' | C4' | C5' | 156.7° | 155.6° |
| C2' | C3' | C4' | H5 | 82.0° | 81.6° |
| C2' | C3' | O3' | H7 | 180.0° | 67.3° |
| C3' | C2' | H8 | H9 | 122.7° | 122.6° |
| C3' | C2' | C1' | H10 | 135.3° | 117.4° |
| C1' | C2' | C3' | O3' | 150.9° | 139.0° |
| C1' | C2' | C3' | C4' | 31.6° | 20.8° |
| C2' | C1' | O4' | H10 | 117.0° | 119.4° |
| C2' | C1' | O4' | C4' | 4.9° | 26.4° |
| C1' | C2' | C3' | H6 | 84.4° | 97.4° |
| C1' | C2' | H8 | H9 | 122.6° | 122.6° |
| O3' | C3' | C4' | H6 | 121.9° | 123.5° |
| O3' | C3' | C4' | O4' | 157.1° | 155.2° |
| O3' | C3' | C4' | C5' | 81.2° | 86.2° |
| O3' | C3' | C4' | H5 | 40.1° | 36.6° |
| O3' | C3' | C2' | H8 | 90.1° | 102.2° |
| O3' | C3' | C2' | H9 | 31.8° | 20.3° |
| C3' | C4' | O4' | C1' | 25.2° | 40.0° |
| C3' | C4' | O4' | C5' | 123.3° | 118.6° |
| C3' | C4' | O4' | H5 | 116.3° | 118.5° |
| C3' | C4' | C5' | H5 | 121.2° | 122.8° |
| C3' | C4' | C5' | O5' | 137.7° | 177.2° |
| C3' | C4' | C5' | H3 | 102.1° | 62.9° |
| C3' | C4' | C5' | H4 | 17.4° | 57.2° |
| C4' | C3' | O3' | H7 | 65.2° | 180.0° |
| C4' | C3' | C2' | H8 | 150.7° | 139.5° |
| C4' | C3' | C2' | H9 | 87.5° | 97.9° |
| C1' | O4' | C4' | C5' | 148.5° | 158.6° |
| C1' | O4' | C4' | H5 | 91.0° | 78.6° |
| O4' | C1' | C2' | H8 | 136.5° | 116.7° |
| O4' | C1' | C2' | H9 | 101.7° | 120.7° |
| O4' | C4' | C5' | H5 | 120.9° | 122.9° |
| O4' | C4' | C5' | O5' | 19.9° | 68.5° |
| O4' | C4' | C5' | H3 | 140.1° | 51.3° |
| O4' | C4' | C5' | H4 | 100.4° | 171.4° |
| O4' | C4' | C3' | H6 | 81.0° | 81.3° |
| C4' | O4' | C1' | H10 | 112.1° | 92.9° |
| C4' | C5' | O5' | H3 | 120.2° | 119.9° |
| C4' | C5' | O5' | H4 | 120.3° | 120.1° |
| C4' | C5' | O5' | P | 96.6° | 180.0° |
| C4' | C5' | H3 | H4 | 119.2° | 120.1° |
| C5' | C4' | C3' | H6 | 40.7° | 37.3° |
| C5' | O5' | P | OP2 | 138.9° | 175.1° |
| C5' | O5' | P | OP1 | 7.7° | 55.0° |
| O5' | C5' | H3 | H4 | 119.2° | 120.0° |
| O5' | C5' | C4' | H5 | 101.1° | 54.4° |
| C5' | O5' | P | OP3 | 57.2° | 64.9° |
| O5' | P | OP2 | OP1 | 124.5° | 120.0° |
| O5' | P | OP2 | OP3 | 68.6° | 120.0° |
| O5' | P | OP1 | OP3 | 54.7° | 120.0° |
| O5' | P | OP2 | H2 | 124.4° | 180.0° |
| P | O5' | C5' | H3 | 23.7° | 60.1° |
| P | O5' | C5' | H4 | 143.2° | 60.0° |
| O5' | P | OP3 | H20 | 90.0° | 60.0° |
| OP2 | P | OP1 | OP3 | 70.9° | 120.0° |
| OP2 | P | OP3 | H20 | 90.0° | 60.0° |
| OP1 | P | OP2 | H2 | 0.0° | 60.0° |
| OP1 | P | OP3 | H20 | 90.0° | 180.0° |
| H2 | OP2 | P | OP3 | 55.9° | 60.0° |
| H3 | C5' | C4' | H5 | 19.2° | 174.3° |
| H4 | C5' | C4' | H5 | 138.7° | 65.6° |
| H5 | C4' | C3' | H6 | 162.0° | 160.1° |
| H6 | C3' | O3' | H7 | 55.9° | 56.5° |
| H6 | C3' | C2' | H8 | 34.7° | 21.4° |
| H6 | C3' | C2' | H9 | 156.5° | 143.9° |
| H8 | C2' | C1' | H10 | 105.6° | 123.9° |
| H9 | C2' | C1' | H10 | 16.2° | 1.3° |
| H11 | N4 | C9 | H17 | 167.7° | 120.0° |
| H11 | N4 | C9 | H18 | 57.9° | 120.0° |
| H12 | C5 | C6 | H13 | 0.9° | 0.2° |
| H14 | S | C8 | H15 | 60.1° | 59.9° |
| H14 | S | C8 | H16 | 60.1° | 60.0° |
| H15 | C8 | C9 | H17 | 41.3° | 60.0° |
| H15 | C8 | C9 | H18 | 151.1° | 180.0° |
| H16 | C8 | C9 | H17 | 78.9° | 180.0° |
| H16 | C8 | C9 | H18 | 30.9° | 60.0° |
