M1Y
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| OP1 | P | doub | 1.48Å | 1.50Å | |
| P | OP2 | sing | 1.61Å | 1.50Å | |
| P | O5' | sing | 1.61Å | 1.59Å | |
| O5' | C5' | sing | 1.43Å | 1.42Å | |
| C5' | C4' | sing | 1.53Å | 1.51Å | |
| O4' | C4' | sing | 1.44Å | 1.44Å | |
| O4' | C1' | sing | 1.44Å | 1.39Å | |
| C4' | C3' | sing | 1.55Å | 1.53Å | |
| C1 | N1 | sing | 1.47Å | 1.51Å | |
| C1' | C5 | sing | 1.51Å | 1.48Å | |
| C1' | C2' | sing | 1.54Å | 1.51Å | |
| C6 | N1 | sing | 1.37Å | 1.37Å | |
| C6 | C5 | doub | 1.35Å | 1.34Å | |
| C3' | O3' | sing | 1.43Å | 1.43Å | |
| C3' | C2' | sing | 1.55Å | 1.52Å | |
| N1 | C2 | sing | 1.35Å | 1.39Å | |
| C5 | C4 | sing | 1.42Å | 1.45Å | |
| C2' | O2' | sing | 1.43Å | 1.42Å | |
| C2 | O2 | doub | 1.22Å | 1.23Å | |
| C2 | N3 | sing | 1.35Å | 1.38Å | |
| C4 | N3 | sing | 1.35Å | 1.42Å | |
| C4 | O4 | doub | 1.22Å | 1.21Å | |
| C1 | H1 | sing | 1.09Å | 1.10Å | |
| C1 | H2 | sing | 1.09Å | 1.10Å | |
| C1 | H3 | sing | 1.09Å | 1.10Å | |
| C1' | H4 | sing | 1.09Å | 1.10Å | |
| C2' | H5 | sing | 1.09Å | 1.10Å | |
| C3' | H6 | sing | 1.09Å | 1.10Å | |
| C4' | H7 | sing | 1.09Å | 1.10Å | |
| C5' | H8 | sing | 1.09Å | 1.10Å | |
| C5' | H9 | sing | 1.09Å | 1.10Å | |
| C6 | H10 | sing | 1.08Å | 1.08Å | |
| N3 | H11 | sing | 0.97Å | 1.00Å | |
| O2' | H12 | sing | 0.97Å | 0.95Å | |
| O3' | H13 | sing | 0.97Å | 0.95Å | |
| OP2 | H15 | sing | 0.97Å | 0.95Å | |
| P | OP3 | sing | 1.61Å | 1.60Å | |
| OP3 | H17 | sing | 0.97Å | 0.95Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| OP1 | P | OP2 | 120.9° | 109.5° |
| OP1 | P | O5' | 107.2° | 109.4° |
| OP1 | P | OP3 | 108.9° | 109.5° |
| OP2 | P | O5' | 107.2° | 109.4° |
| P | OP2 | H15 | 109.5° | 114.0° |
| OP2 | P | OP3 | 106.9° | 109.5° |
| P | O5' | C5' | 121.8° | 123.0° |
| O5' | P | OP3 | 104.7° | 109.5° |
| O5' | C5' | C4' | 110.7° | 109.5° |
| O5' | C5' | H8 | 109.2° | 109.5° |
| O5' | C5' | H9 | 109.2° | 109.4° |
| C5' | C4' | O4' | 109.1° | 110.8° |
| C5' | C4' | C3' | 117.8° | 110.6° |
| C5' | C4' | H7 | 107.8° | 110.5° |
| C4' | C5' | H8 | 109.1° | 109.5° |
| C4' | C5' | H9 | 109.1° | 109.5° |
| C4' | O4' | C1' | 110.7° | 107.0° |
| O4' | C4' | C3' | 105.7° | 103.5° |
| O4' | C4' | H7 | 108.7° | 110.6° |
| O4' | C1' | C5 | 104.6° | 109.9° |
| O4' | C1' | C2' | 107.4° | 107.3° |
| O4' | C1' | H4 | 112.9° | 110.0° |
| C4' | C3' | O3' | 114.4° | 110.9° |
| C4' | C3' | C2' | 105.0° | 102.1° |
| C4' | C3' | H6 | 106.5° | 111.0° |
| C3' | C4' | H7 | 107.5° | 110.6° |
| C1 | N1 | C6 | 118.9° | 119.7° |
| C1 | N1 | C2 | 121.1° | 119.7° |
| N1 | C1 | H1 | 109.5° | 109.5° |
| N1 | C1 | H2 | 109.5° | 109.4° |
| N1 | C1 | H3 | 109.5° | 109.5° |
| C5 | C1' | C2' | 108.8° | 109.9° |
| C1' | C5 | C6 | 118.7° | 120.5° |
| C1' | C5 | C4 | 123.0° | 120.5° |
| C5 | C1' | H4 | 111.6° | 109.9° |
| C1' | C2' | C3' | 102.3° | 104.2° |
| C1' | C2' | O2' | 107.3° | 110.5° |
| C2' | C1' | H4 | 111.2° | 109.8° |
| C1' | C2' | H5 | 111.9° | 110.5° |
| N1 | C6 | C5 | 122.9° | 119.7° |
| C6 | N1 | C2 | 120.0° | 120.6° |
| N1 | C6 | H10 | 118.5° | 120.2° |
| C6 | C5 | C4 | 118.4° | 119.1° |
| C5 | C6 | H10 | 118.5° | 120.1° |
| O3' | C3' | C2' | 116.2° | 110.9° |
| O3' | C3' | H6 | 107.6° | 110.7° |
| C3' | O3' | H13 | 109.5° | 114.0° |
| C3' | C2' | O2' | 109.7° | 110.5° |
| C3' | C2' | H5 | 111.7° | 110.6° |
| C2' | C3' | H6 | 106.5° | 110.9° |
| N1 | C2 | O2 | 120.7° | 119.5° |
| N1 | C2 | N3 | 120.1° | 120.9° |
| C5 | C4 | N3 | 118.7° | 119.4° |
| C5 | C4 | O4 | 122.7° | 120.3° |
| O2' | C2' | H5 | 113.3° | 110.4° |
| C2' | O2' | H12 | 109.5° | 114.0° |
| O2 | C2 | N3 | 119.2° | 119.6° |
| C2 | N3 | C4 | 119.8° | 120.3° |
| C2 | N3 | H11 | 120.1° | 119.9° |
| N3 | C4 | O4 | 118.6° | 120.3° |
| C4 | N3 | H11 | 120.1° | 119.8° |
| H1 | C1 | H2 | 109.5° | 109.5° |
| H1 | C1 | H3 | 109.5° | 109.6° |
| H2 | C1 | H3 | 109.5° | 109.4° |
| H8 | C5' | H9 | 109.5° | 109.5° |
| P | OP3 | H17 | 109.5° | 114.0° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| OP1 | P | OP2 | O5' | 123.0° | 120.0° |
| OP1 | P | OP2 | OP3 | 125.2° | 120.0° |
| OP1 | P | O5' | OP3 | 115.6° | 120.0° |
| OP1 | P | O5' | C5' | 14.5° | 55.0° |
| OP1 | P | OP2 | H15 | 0.0° | 180.0° |
| OP1 | P | OP3 | H17 | 0.0° | 60.1° |
| OP2 | P | O5' | OP3 | 113.3° | 120.0° |
| OP2 | P | O5' | C5' | 145.7° | 65.0° |
| OP2 | P | OP3 | H17 | 132.2° | 60.0° |
| P | O5' | C5' | C4' | 148.9° | 180.0° |
| P | O5' | C5' | H8 | 90.9° | 60.0° |
| P | O5' | C5' | H9 | 28.8° | 60.0° |
| O5' | P | OP2 | H15 | 123.0° | 60.0° |
| O5' | P | OP3 | H17 | 114.3° | 180.0° |
| O5' | C5' | C4' | H8 | 120.2° | 120.0° |
| O5' | C5' | C4' | H9 | 120.2° | 120.0° |
| O5' | C5' | C4' | O4' | 8.9° | 70.8° |
| O5' | C5' | C4' | C3' | 129.2° | 175.0° |
| O5' | C5' | C4' | H7 | 108.9° | 52.1° |
| O5' | C5' | H8 | H9 | 119.4° | 120.0° |
| C5' | O5' | P | OP3 | 101.0° | 175.0° |
| C5' | C4' | O4' | C3' | 127.5° | 118.6° |
| C5' | C4' | O4' | H7 | 117.3° | 122.9° |
| C5' | C4' | O4' | C1' | 132.6° | 158.6° |
| C5' | C4' | C3' | H7 | 122.0° | 122.8° |
| C5' | C4' | C3' | O3' | 20.5° | 37.5° |
| C5' | C4' | C3' | C2' | 108.1° | 155.7° |
| C5' | C4' | C3' | H6 | 139.2° | 86.0° |
| C4' | C5' | H8 | H9 | 119.4° | 120.0° |
| O4' | C4' | C3' | H7 | 115.9° | 118.5° |
| C4' | O4' | C1' | C5 | 138.0° | 145.9° |
| C4' | O4' | C1' | C2' | 22.5° | 26.5° |
| O4' | C4' | C3' | O3' | 142.6° | 81.2° |
| O4' | C4' | C3' | C2' | 14.0° | 37.0° |
| C4' | O4' | C1' | H4 | 100.4° | 93.0° |
| O4' | C4' | C3' | H6 | 98.7° | 155.3° |
| O4' | C4' | C5' | H8 | 111.3° | 169.2° |
| O4' | C4' | C5' | H9 | 129.1° | 49.1° |
| C1' | O4' | C4' | C3' | 5.0° | 40.0° |
| O4' | C1' | C5 | C2' | 114.6° | 117.8° |
| O4' | C1' | C5 | H4 | 122.4° | 121.2° |
| O4' | C1' | C2' | H4 | 124.0° | 119.5° |
| O4' | C1' | C5 | C6 | 7.8° | 127.5° |
| O4' | C1' | C2' | C3' | 30.0° | 2.0° |
| O4' | C1' | C5 | C4 | 172.4° | 52.8° |
| O4' | C1' | C2' | O2' | 145.4° | 120.7° |
| O4' | C1' | C2' | H5 | 89.6° | 116.8° |
| C1' | O4' | C4' | H7 | 110.1° | 78.5° |
| C4' | C3' | C2' | C1' | 26.1° | 20.9° |
| C4' | C3' | O3' | C2' | 122.7° | 112.7° |
| C4' | C3' | O3' | H6 | 118.0° | 123.7° |
| C4' | C3' | C2' | H6 | 112.7° | 118.3° |
| C4' | C3' | C2' | O2' | 139.8° | 97.8° |
| C4' | C3' | C2' | H5 | 93.8° | 139.6° |
| C3' | C4' | C5' | H8 | 9.0° | 55.0° |
| C3' | C4' | C5' | H9 | 110.6° | 65.0° |
| C4' | C3' | O3' | H13 | 180.0° | 174.1° |
| C1 | N1 | C6 | C2 | 179.5° | 179.9° |
| C1 | N1 | C6 | C5 | 179.6° | 180.0° |
| C1 | N1 | C2 | O2 | 0.2° | 0.0° |
| C1 | N1 | C2 | N3 | 179.6° | 179.7° |
| N1 | C1 | H1 | H2 | 120.0° | 119.9° |
| N1 | C1 | H1 | H3 | 120.0° | 120.1° |
| N1 | C1 | H2 | H3 | 120.0° | 119.9° |
| C1 | N1 | C6 | H10 | 0.3° | 0.1° |
| C5 | C1' | C2' | H4 | 123.3° | 121.0° |
| C1' | C5 | C6 | N1 | 179.4° | 180.0° |
| C1' | C5 | C6 | C4 | 179.8° | 179.7° |
| C5 | C1' | C2' | C3' | 142.7° | 121.4° |
| C5 | C1' | C2' | O2' | 101.9° | 119.9° |
| C1' | C5 | C4 | N3 | 179.9° | 180.0° |
| C1' | C5 | C4 | O4 | 0.4° | 0.1° |
| C5 | C1' | C2' | H5 | 23.1° | 2.7° |
| C1' | C5 | C6 | H10 | 0.6° | 0.0° |
| C2' | C1' | C5 | C6 | 106.7° | 114.7° |
| C1' | C2' | C3' | O3' | 153.6° | 97.3° |
| C1' | C2' | C3' | O2' | 113.7° | 118.7° |
| C1' | C2' | C3' | H5 | 119.8° | 118.7° |
| C2' | C1' | C5 | C4 | 73.1° | 65.0° |
| C1' | C2' | O2' | H5 | 124.1° | 122.6° |
| C1' | C2' | C3' | H6 | 86.6° | 139.2° |
| C1' | C2' | O2' | H12 | 50.6° | 180.0° |
| N1 | C6 | C5 | H10 | 180.0° | 180.0° |
| N1 | C6 | C5 | C4 | 0.8° | 0.3° |
| C6 | N1 | C2 | O2 | 179.3° | 179.9° |
| C6 | N1 | C2 | N3 | 0.1° | 0.3° |
| C6 | N1 | C1 | H1 | 180.0° | 90.0° |
| C6 | N1 | C1 | H2 | 60.0° | 150.0° |
| C6 | N1 | C1 | H3 | 60.0° | 30.1° |
| C5 | C6 | N1 | C2 | 0.8° | 0.0° |
| C6 | C5 | C4 | N3 | 0.1° | 0.3° |
| C6 | C5 | C4 | O4 | 179.4° | 179.8° |
| C6 | C5 | C1' | H4 | 130.3° | 6.3° |
| O3' | C3' | C2' | H6 | 119.8° | 123.5° |
| O3' | C3' | C2' | O2' | 92.7° | 144.0° |
| O3' | C3' | C2' | H5 | 33.8° | 21.4° |
| O3' | C3' | C4' | H7 | 101.4° | 160.3° |
| C3' | C2' | O2' | H5 | 125.5° | 122.7° |
| C3' | C2' | C1' | H4 | 94.0° | 117.6° |
| C2' | C3' | C4' | H7 | 129.9° | 81.5° |
| C3' | C2' | O2' | H12 | 161.0° | 65.3° |
| C2' | C3' | O3' | H13 | 57.3° | 61.4° |
| N1 | C2 | O2 | N3 | 179.4° | 179.7° |
| N1 | C2 | N3 | C4 | 0.6° | 0.3° |
| C2 | N1 | C1 | H1 | 0.5° | 89.9° |
| C2 | N1 | C1 | H2 | 120.5° | 30.1° |
| C2 | N1 | C1 | H3 | 119.5° | 150.0° |
| C2 | N1 | C6 | H10 | 179.2° | 180.0° |
| N1 | C2 | N3 | H11 | 179.4° | 179.7° |
| C5 | C4 | N3 | C2 | 0.6° | 0.0° |
| C5 | C4 | N3 | O4 | 179.5° | 179.9° |
| C4 | C5 | C1' | H4 | 49.9° | 174.0° |
| C4 | C5 | C6 | H10 | 179.2° | 179.7° |
| C5 | C4 | N3 | H11 | 179.4° | 180.0° |
| O2' | C2' | C1' | H4 | 21.4° | 1.2° |
| O2' | C2' | C3' | H6 | 27.1° | 20.5° |
| O2 | C2 | N3 | C4 | 180.0° | 180.0° |
| O2 | C2 | N3 | H11 | 0.0° | 0.0° |
| C2 | N3 | C4 | H11 | 180.0° | 179.9° |
| C2 | N3 | C4 | O4 | 179.9° | 179.9° |
| O4 | C4 | N3 | H11 | 0.1° | 0.0° |
| H1 | C1 | H2 | H3 | 120.0° | 120.1° |
| H4 | C1' | C2' | H5 | 146.3° | 123.7° |
| H5 | C2' | C3' | H6 | 153.6° | 102.1° |
| H5 | C2' | O2' | H12 | 73.4° | 57.4° |
| H6 | C3' | C4' | H7 | 17.2° | 36.8° |
| H6 | C3' | O3' | H13 | 62.0° | 62.2° |
| H7 | C4' | C5' | H8 | 130.9° | 67.9° |
| H7 | C4' | C5' | H9 | 11.3° | 172.1° |
| H15 | OP2 | P | OP3 | 125.2° | 60.0° |
