SPT
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| S5' | C5' | sing | 1.81Å | 1.79Å | |
| S5' | P | sing | 2.09Å | 83.66Å | |
| N1 | C6 | sing | 1.39Å | 1.38Å | |
| N1 | C2 | sing | 1.41Å | 1.38Å | |
| N1 | C1' | sing | 1.43Å | 1.47Å | |
| C6 | C5 | doub | 1.34Å | 1.33Å | |
| C6 | H6 | sing | 1.09Å | 1.08Å | |
| C2 | O2 | doub | 1.23Å | 1.22Å | |
| C2 | N3 | sing | 1.40Å | 1.37Å | |
| N3 | C4 | sing | 1.39Å | 1.38Å | |
| N3 | H3 | sing | 1.02Å | 1.00Å | |
| C4 | O4 | doub | 1.23Å | 1.22Å | |
| C4 | C5 | sing | 1.49Å | 1.44Å | |
| C5 | C5M | sing | 1.49Å | 1.50Å | |
| C5M | H71 | sing | 1.09Å | 1.10Å | |
| C5M | H72 | sing | 1.09Å | 1.10Å | |
| C5M | H73 | sing | 1.09Å | 1.10Å | |
| C2' | C1' | sing | 1.52Å | 1.52Å | |
| C2' | C3' | sing | 1.51Å | 1.52Å | |
| C2' | H2' | sing | 1.10Å | 1.10Å | |
| C2' | H2'' | sing | 1.09Å | 1.10Å | |
| C5' | C4' | sing | 1.52Å | 1.51Å | |
| C5' | H5' | sing | 1.09Å | 1.10Å | |
| C5' | H5'' | sing | 1.09Å | 1.10Å | |
| C4' | O4' | sing | 1.44Å | 1.45Å | |
| C4' | C3' | sing | 1.52Å | 1.53Å | |
| C4' | H4' | sing | 1.09Å | 1.10Å | |
| O4' | C1' | sing | 1.43Å | 1.43Å | |
| C1' | H1' | sing | 1.10Å | 1.10Å | |
| C3' | O3' | sing | 1.43Å | 1.43Å | |
| C3' | H3' | sing | 1.09Å | 1.10Å | |
| O3' | HO3' | sing | 0.97Å | 0.95Å | |
| OP3 | P | sing | 1.62Å | 0.00Å | |
| OP3 | HOP3 | sing | 0.98Å | 0.00Å | |
| P | OP1 | doub | 1.50Å | 0.00Å | |
| P | OP2 | sing | 1.62Å | 0.00Å | |
| OP2 | HOP2 | sing | 0.98Å | 0.00Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| C5' | S5' | P | 52.3° | 105.1° |
| S5' | C5' | C4' | 110.1° | 110.5° |
| S5' | C5' | H5' | 109.2° | 108.9° |
| S5' | C5' | H5'' | 109.1° | 108.8° |
| S5' | P | OP3 | 90.0° | 109.3° |
| S5' | P | OP1 | 90.0° | 111.4° |
| S5' | P | OP2 | 90.0° | 108.8° |
| C6 | N1 | C2 | 121.4° | 120.4° |
| C6 | N1 | C1' | 120.0° | 118.4° |
| N1 | C6 | C5 | 123.7° | 124.5° |
| N1 | C6 | H6 | 118.1° | 114.9° |
| C2 | N1 | C1' | 118.6° | 121.2° |
| N1 | C2 | O2 | 123.3° | 123.8° |
| N1 | C2 | N3 | 114.3° | 115.1° |
| N1 | C1' | C2' | 112.0° | 112.8° |
| N1 | C1' | O4' | 107.6° | 109.3° |
| N1 | C1' | H1' | 108.1° | 107.8° |
| C5 | C6 | H6 | 118.2° | 120.7° |
| C6 | C5 | C4 | 118.0° | 118.3° |
| C6 | C5 | C5M | 123.0° | 123.6° |
| O2 | C2 | N3 | 122.4° | 121.1° |
| C2 | N3 | C4 | 127.1° | 127.0° |
| C2 | N3 | H3 | 116.5° | 116.4° |
| C4 | N3 | H3 | 116.5° | 116.6° |
| N3 | C4 | O4 | 120.0° | 123.6° |
| N3 | C4 | C5 | 115.4° | 114.8° |
| O4 | C4 | C5 | 124.5° | 121.6° |
| C4 | C5 | C5M | 118.9° | 118.1° |
| C5 | C5M | H71 | 109.5° | 109.7° |
| C5 | C5M | H72 | 109.5° | 109.8° |
| C5 | C5M | H73 | 109.5° | 109.7° |
| H71 | C5M | H72 | 109.5° | 109.4° |
| H71 | C5M | H73 | 109.4° | 109.4° |
| H72 | C5M | H73 | 109.5° | 108.9° |
| C1' | C2' | C3' | 103.0° | 102.5° |
| C1' | C2' | H2' | 111.7° | 110.6° |
| C1' | C2' | H2'' | 113.0° | 111.7° |
| C2' | C1' | O4' | 106.4° | 107.4° |
| C2' | C1' | H1' | 109.2° | 111.5° |
| C3' | C2' | H2' | 111.7° | 109.7° |
| C3' | C2' | H2'' | 113.1° | 114.1° |
| C2' | C3' | C4' | 103.4° | 103.1° |
| C2' | C3' | O3' | 109.5° | 109.7° |
| C2' | C3' | H3' | 114.0° | 113.2° |
| H2' | C2' | H2'' | 104.6° | 108.3° |
| C4' | C5' | H5' | 109.3° | 110.2° |
| C4' | C5' | H5'' | 109.1° | 110.1° |
| C5' | C4' | O4' | 109.3° | 107.9° |
| C5' | C4' | C3' | 113.2° | 112.9° |
| C5' | C4' | H4' | 105.9° | 109.5° |
| H5' | C5' | H5'' | 110.0° | 108.1° |
| O4' | C4' | C3' | 105.7° | 106.2° |
| O4' | C4' | H4' | 113.4° | 107.9° |
| C4' | O4' | C1' | 110.6° | 109.3° |
| C3' | C4' | H4' | 109.5° | 112.2° |
| C4' | C3' | O3' | 111.2° | 109.9° |
| C4' | C3' | H3' | 112.3° | 113.5° |
| O4' | C1' | H1' | 113.5° | 108.0° |
| O3' | C3' | H3' | 106.5° | 107.4° |
| C3' | O3' | HO3' | 109.5° | 107.3° |
| P | OP3 | HOP3 | 90.0° | 118.7° |
| OP3 | P | OP1 | 90.0° | 112.7° |
| OP3 | P | OP2 | 90.0° | 101.5° |
| OP1 | P | OP2 | 90.0° | 112.7° |
| P | OP2 | HOP2 | 90.0° | 118.7° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| S5' | C5' | C4' | H5' | 120.0° | 120.4° |
| S5' | C5' | C4' | H5'' | 119.7° | 120.3° |
| S5' | C5' | H5' | H5'' | 119.7° | 118.1° |
| S5' | C5' | C4' | O4' | 127.9° | 63.3° |
| S5' | C5' | C4' | C3' | 114.6° | 179.6° |
| S5' | C5' | C4' | H4' | 5.4° | 53.9° |
| C5' | S5' | P | OP3 | 90.0° | 54.8° |
| C5' | S5' | P | OP1 | 90.0° | 180.0° |
| C5' | S5' | P | OP2 | 90.0° | 55.2° |
| P | S5' | C5' | C4' | 40.9° | 180.0° |
| P | S5' | C5' | H5' | 79.1° | 58.8° |
| P | S5' | C5' | H5'' | 160.6° | 58.9° |
| S5' | P | OP3 | OP1 | 90.0° | 124.4° |
| S5' | P | OP3 | OP2 | 90.0° | 114.8° |
| S5' | P | OP3 | HOP3 | 90.0° | 172.4° |
| S5' | P | OP1 | OP2 | 90.0° | 122.6° |
| S5' | P | OP2 | HOP2 | 90.0° | 172.2° |
| C6 | N1 | C2 | C1' | 179.9° | 180.0° |
| N1 | C6 | C5 | H6 | 180.0° | 180.0° |
| C6 | N1 | C2 | O2 | 179.7° | 180.0° |
| C6 | N1 | C2 | N3 | 0.1° | 0.0° |
| N1 | C6 | C5 | C4 | 0.1° | 0.0° |
| N1 | C6 | C5 | C5M | 179.8° | 180.0° |
| C6 | N1 | C1' | C2' | 75.8° | 86.5° |
| C6 | N1 | C1' | O4' | 40.8° | 32.9° |
| C6 | N1 | C1' | H1' | 163.8° | 150.0° |
| C2 | N1 | C6 | C5 | 0.3° | 0.0° |
| C2 | N1 | C6 | H6 | 179.7° | 180.0° |
| N1 | C2 | O2 | N3 | 179.8° | 180.0° |
| N1 | C2 | N3 | C4 | 0.2° | 0.0° |
| N1 | C2 | N3 | H3 | 179.8° | 180.0° |
| C2 | N1 | C1' | C2' | 104.0° | 93.5° |
| C2 | N1 | C1' | O4' | 139.3° | 147.2° |
| C2 | N1 | C1' | H1' | 16.3° | 30.0° |
| C1' | N1 | C6 | C5 | 179.8° | 180.0° |
| C1' | N1 | C6 | H6 | 0.2° | 0.0° |
| C1' | N1 | C2 | O2 | 0.2° | 0.0° |
| C1' | N1 | C2 | N3 | 180.0° | 180.0° |
| N1 | C1' | C2' | O4' | 117.4° | 120.5° |
| N1 | C1' | C2' | H1' | 119.7° | 121.4° |
| N1 | C1' | C2' | C3' | 145.7° | 147.4° |
| N1 | C1' | C2' | H2' | 94.3° | 30.6° |
| N1 | C1' | C2' | H2'' | 23.4° | 90.1° |
| N1 | C1' | O4' | C4' | 132.6° | 131.7° |
| N1 | C1' | O4' | H1' | 119.5° | 117.0° |
| C6 | C5 | C4 | N3 | 0.2° | 0.1° |
| C6 | C5 | C4 | O4 | 179.7° | 179.9° |
| C6 | C5 | C4 | C5M | 179.9° | 180.0° |
| C6 | C5 | C5M | H71 | 165.6° | 119.7° |
| C6 | C5 | C5M | H72 | 45.5° | 0.5° |
| C6 | C5 | C5M | H73 | 74.5° | 120.2° |
| H6 | C6 | C5 | C4 | 179.9° | 180.0° |
| H6 | C6 | C5 | C5M | 0.2° | 0.0° |
| O2 | C2 | N3 | C4 | 180.0° | 179.9° |
| O2 | C2 | N3 | H3 | 0.0° | 0.0° |
| C2 | N3 | C4 | H3 | 180.0° | 179.9° |
| C2 | N3 | C4 | O4 | 179.5° | 179.9° |
| C2 | N3 | C4 | C5 | 0.4° | 0.1° |
| N3 | C4 | O4 | C5 | 179.9° | 180.0° |
| N3 | C4 | C5 | C5M | 179.9° | 180.0° |
| H3 | N3 | C4 | O4 | 0.5° | 0.0° |
| H3 | N3 | C4 | C5 | 179.6° | 180.0° |
| O4 | C4 | C5 | C5M | 0.2° | 0.0° |
| C4 | C5 | C5M | H71 | 14.3° | 60.4° |
| C4 | C5 | C5M | H72 | 134.3° | 179.4° |
| C4 | C5 | C5M | H73 | 105.7° | 59.8° |
| C5 | C5M | H71 | H72 | 120.0° | 120.4° |
| C5 | C5M | H71 | H73 | 120.0° | 120.4° |
| C5 | C5M | H72 | H73 | 120.0° | 120.1° |
| H71 | C5M | H72 | H73 | 119.9° | 119.5° |
| C1' | C2' | C3' | H2' | 120.0° | 117.5° |
| C1' | C2' | C3' | H2'' | 122.4° | 120.8° |
| C1' | C2' | H2' | H2'' | 122.6° | 122.7° |
| C2' | C1' | O4' | C4' | 12.3° | 9.0° |
| C1' | C2' | C3' | C4' | 32.8° | 33.4° |
| C2' | C1' | O4' | H1' | 120.2° | 120.3° |
| C1' | C2' | C3' | O3' | 85.9° | 83.6° |
| C1' | C2' | C3' | H3' | 155.0° | 156.4° |
| C3' | C2' | H2' | H2'' | 122.6° | 125.1° |
| C2' | C3' | C4' | C5' | 93.4° | 88.8° |
| C2' | C3' | C4' | O4' | 26.1° | 29.2° |
| C2' | C3' | C4' | O3' | 117.5° | 116.9° |
| C2' | C3' | C4' | H3' | 123.3° | 122.8° |
| C2' | C3' | C4' | H4' | 148.6° | 146.9° |
| C3' | C2' | C1' | O4' | 28.3° | 26.9° |
| C3' | C2' | C1' | H1' | 94.6° | 91.2° |
| C2' | C3' | O3' | H3' | 123.7° | 123.4° |
| C2' | C3' | O3' | HO3' | 148.5° | 119.3° |
| H2' | C2' | C3' | C4' | 152.8° | 84.1° |
| H2' | C2' | C1' | O4' | 148.3° | 90.0° |
| H2' | C2' | C1' | H1' | 25.4° | 151.9° |
| H2' | C2' | C3' | O3' | 34.1° | 158.9° |
| H2' | C2' | C3' | H3' | 85.0° | 38.9° |
| H2'' | C2' | C3' | C4' | 89.6° | 154.3° |
| H2'' | C2' | C1' | O4' | 94.0° | 149.4° |
| H2'' | C2' | C1' | H1' | 143.1° | 31.3° |
| H2'' | C2' | C3' | O3' | 151.8° | 37.2° |
| H2'' | C2' | C3' | H3' | 32.6° | 82.7° |
| C4' | C5' | H5' | H5'' | 119.7° | 120.5° |
| C5' | C4' | O4' | C3' | 122.1° | 121.4° |
| C5' | C4' | O4' | H4' | 117.9° | 118.2° |
| C5' | C4' | C3' | H4' | 118.0° | 124.3° |
| C5' | C4' | O4' | C1' | 113.3° | 108.6° |
| C5' | C4' | C3' | O3' | 149.1° | 154.2° |
| C5' | C4' | C3' | H3' | 29.9° | 34.0° |
| H5' | C5' | C4' | O4' | 7.9° | 57.2° |
| H5' | C5' | C4' | C3' | 125.4° | 60.0° |
| H5' | C5' | C4' | H4' | 114.6° | 174.3° |
| H5'' | C5' | C4' | O4' | 112.3° | 176.4° |
| H5'' | C5' | C4' | C3' | 5.1° | 59.3° |
| H5'' | C5' | C4' | H4' | 125.2° | 66.5° |
| O4' | C4' | C3' | H4' | 122.5° | 117.6° |
| C4' | O4' | C1' | H1' | 107.8° | 111.3° |
| O4' | C4' | C3' | O3' | 91.3° | 87.7° |
| O4' | C4' | C3' | H3' | 149.4° | 152.1° |
| C3' | C4' | O4' | C1' | 8.8° | 12.7° |
| C4' | C3' | O3' | H3' | 122.7° | 123.9° |
| C4' | C3' | O3' | HO3' | 97.9° | 128.0° |
| H4' | C4' | O4' | C1' | 128.8° | 133.2° |
| H4' | C4' | C3' | O3' | 31.2° | 29.9° |
| H4' | C4' | C3' | H3' | 88.1° | 90.3° |
| H3' | C3' | O3' | HO3' | 24.8° | 4.1° |
| OP3 | P | OP1 | OP2 | 90.0° | 114.2° |
| OP3 | P | OP2 | HOP2 | 90.0° | 72.7° |
| HOP3 | OP3 | P | OP1 | 90.0° | 48.0° |
| HOP3 | OP3 | P | OP2 | 90.0° | 72.8° |
| OP1 | P | OP2 | HOP2 | 90.0° | 48.2° |
