PDU
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| C5M | C5B | sing | 1.47Å | 1.46Å | |
| OP1 | P | doub | 1.48Å | 1.48Å | |
| C5B | C5A | trip | 1.17Å | 1.19Å | |
| C5A | C5 | sing | 1.43Å | 1.43Å | |
| C2' | C3' | sing | 1.55Å | 1.49Å | |
| C2' | C1' | sing | 1.54Å | 1.51Å | |
| C3' | O3' | sing | 1.43Å | 1.44Å | |
| C3' | C4' | sing | 1.55Å | 1.51Å | |
| C5 | C6 | doub | 1.36Å | 1.35Å | |
| C5 | C4 | sing | 1.47Å | 1.45Å | |
| P | O5' | sing | 1.61Å | 1.65Å | |
| P | OP2 | sing | 1.61Å | 1.48Å | |
| O5' | C5' | sing | 1.43Å | 1.43Å | |
| O4 | C4 | doub | 1.22Å | 1.23Å | |
| C6 | N1 | sing | 1.37Å | 1.37Å | |
| C4 | N3 | sing | 1.35Å | 1.38Å | |
| C5' | C4' | sing | 1.53Å | 1.52Å | |
| N1 | C1' | sing | 1.46Å | 1.50Å | |
| N1 | C2 | sing | 1.34Å | 1.41Å | |
| C4' | O4' | sing | 1.44Å | 1.46Å | |
| N3 | C2 | sing | 1.34Å | 1.41Å | |
| C1' | O4' | sing | 1.44Å | 1.44Å | |
| C2 | O2 | doub | 1.22Å | 1.23Å | |
| P | OP3 | sing | 1.61Å | 1.65Å | |
| OP2 | HOP2 | sing | 0.97Å | 0.95Å | |
| C5' | H5' | sing | 1.09Å | 1.10Å | |
| C5' | H5'' | sing | 1.09Å | 1.10Å | |
| C4' | H4' | sing | 1.09Å | 1.10Å | |
| C3' | H3' | sing | 1.09Å | 1.10Å | |
| O3' | H2 | sing | 0.97Å | 0.95Å | |
| C2' | H2'' | sing | 1.09Å | 1.10Å | |
| C2' | H2' | sing | 1.09Å | 1.10Å | |
| C1' | H1' | sing | 1.09Å | 1.10Å | |
| N3 | H3 | sing | 0.97Å | 1.00Å | |
| C5M | H71 | sing | 1.09Å | 1.10Å | |
| C5M | H72 | sing | 1.09Å | 1.10Å | |
| C5M | H73 | sing | 1.09Å | 1.10Å | |
| C6 | H6 | sing | 1.08Å | 1.08Å | |
| OP3 | HOP3 | sing | 0.97Å | 0.95Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| C5M | C5B | C5A | 176.9° | 180.0° |
| C5B | C5M | H71 | 109.5° | 109.5° |
| C5B | C5M | H72 | 109.5° | 109.5° |
| C5B | C5M | H73 | 109.5° | 109.5° |
| OP1 | P | O5' | 107.5° | 109.5° |
| OP1 | P | OP2 | 118.4° | 109.5° |
| OP1 | P | OP3 | 107.3° | 109.5° |
| C5B | C5A | C5 | 176.4° | 179.9° |
| C5A | C5 | C6 | 120.4° | 120.9° |
| C5A | C5 | C4 | 117.6° | 120.8° |
| C3' | C2' | C1' | 108.8° | 104.2° |
| C2' | C3' | O3' | 110.3° | 110.9° |
| C2' | C3' | C4' | 99.1° | 102.1° |
| C2' | C3' | H3' | 111.4° | 111.0° |
| C3' | C2' | H2'' | 109.6° | 110.5° |
| C3' | C2' | H2' | 109.6° | 110.5° |
| C2' | C1' | N1 | 105.8° | 109.9° |
| C2' | C1' | O4' | 98.9° | 107.3° |
| C1' | C2' | H2'' | 109.7° | 110.5° |
| C1' | C2' | H2' | 109.6° | 110.5° |
| C2' | C1' | H1' | 111.3° | 109.8° |
| O3' | C3' | C4' | 111.8° | 110.9° |
| O3' | C3' | H3' | 112.3° | 110.8° |
| C3' | O3' | H2 | 109.5° | 114.0° |
| C3' | C4' | C5' | 114.4° | 110.6° |
| C3' | C4' | O4' | 108.1° | 103.4° |
| C3' | C4' | H4' | 109.1° | 110.8° |
| C4' | C3' | H3' | 111.1° | 110.9° |
| C6 | C5 | C4 | 122.0° | 118.3° |
| C5 | C6 | N1 | 121.3° | 119.4° |
| C5 | C6 | H6 | 119.3° | 120.3° |
| C5 | C4 | O4 | 124.9° | 120.7° |
| C5 | C4 | N3 | 114.5° | 118.6° |
| O5' | P | OP2 | 106.6° | 109.4° |
| P | O5' | C5' | 119.7° | 123.0° |
| O5' | P | OP3 | 109.9° | 109.5° |
| OP2 | P | OP3 | 106.9° | 109.5° |
| P | OP2 | HOP2 | 109.5° | 113.9° |
| O5' | C5' | C4' | 122.9° | 109.4° |
| O5' | C5' | H5' | 106.0° | 109.4° |
| O5' | C5' | H5'' | 106.0° | 109.5° |
| O4 | C4 | N3 | 120.6° | 120.7° |
| C6 | N1 | C1' | 117.6° | 119.3° |
| C6 | N1 | C2 | 120.8° | 121.4° |
| N1 | C6 | H6 | 119.4° | 120.3° |
| C4 | N3 | C2 | 125.1° | 120.3° |
| C4 | N3 | H3 | 117.5° | 119.8° |
| C5' | C4' | O4' | 106.4° | 110.7° |
| C4' | C5' | H5' | 106.0° | 109.5° |
| C4' | C5' | H5'' | 106.0° | 109.5° |
| C5' | C4' | H4' | 108.9° | 110.6° |
| C1' | N1 | C2 | 121.5° | 119.3° |
| N1 | C1' | O4' | 115.8° | 109.9° |
| N1 | C1' | H1' | 111.5° | 110.0° |
| N1 | C2 | N3 | 116.3° | 121.9° |
| N1 | C2 | O2 | 122.7° | 119.1° |
| C4' | O4' | C1' | 110.8° | 107.0° |
| O4' | C4' | H4' | 109.8° | 110.7° |
| N3 | C2 | O2 | 121.0° | 119.0° |
| C2 | N3 | H3 | 117.4° | 119.8° |
| O4' | C1' | H1' | 112.5° | 109.9° |
| P | OP3 | HOP3 | 109.5° | 113.9° |
| H5' | C5' | H5'' | 109.5° | 109.5° |
| H2'' | C2' | H2' | 109.5° | 110.6° |
| H71 | C5M | H72 | 109.5° | 109.4° |
| H71 | C5M | H73 | 109.5° | 109.5° |
| H72 | C5M | H73 | 109.4° | 109.5° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| C5M | C5B | C5A | C5 | 8.4° | 160.3° |
| C5B | C5M | H71 | H72 | 120.0° | 120.0° |
| C5B | C5M | H71 | H73 | 120.0° | 120.0° |
| C5B | C5M | H72 | H73 | 120.0° | 120.0° |
| OP1 | P | O5' | OP2 | 128.0° | 120.0° |
| OP1 | P | O5' | OP3 | 116.5° | 120.0° |
| OP1 | P | OP2 | OP3 | 121.2° | 120.0° |
| OP1 | P | O5' | C5' | 103.7° | 55.0° |
| OP1 | P | OP2 | HOP2 | 0.0° | 180.0° |
| OP1 | P | OP3 | HOP3 | 0.0° | 60.0° |
| C5B | C5A | C5 | C6 | 146.8° | 37.2° |
| C5B | C5A | C5 | C4 | 34.4° | 143.4° |
| C5A | C5B | C5M | H71 | 180.0° | 17.4° |
| C5A | C5B | C5M | H72 | 60.0° | 102.5° |
| C5A | C5B | C5M | H73 | 60.0° | 137.4° |
| C5A | C5 | C6 | C4 | 178.8° | 179.5° |
| C5A | C5 | C4 | O4 | 0.7° | 0.2° |
| C5A | C5 | C6 | N1 | 179.2° | 180.0° |
| C5A | C5 | C4 | N3 | 179.2° | 179.7° |
| C5A | C5 | C6 | H6 | 0.8° | 0.5° |
| C3' | C2' | C1' | H2'' | 119.9° | 118.7° |
| C3' | C2' | C1' | H2' | 119.9° | 118.6° |
| C2' | C3' | O3' | C4' | 109.3° | 112.7° |
| C2' | C3' | O3' | H3' | 125.0° | 123.7° |
| C2' | C3' | C4' | H3' | 117.3° | 118.3° |
| C2' | C3' | C4' | C5' | 101.0° | 155.5° |
| C3' | C2' | C1' | N1 | 158.3° | 121.5° |
| C2' | C3' | C4' | O4' | 17.4° | 37.0° |
| C3' | C2' | C1' | O4' | 38.1° | 2.0° |
| C2' | C3' | C4' | H4' | 136.7° | 81.6° |
| C2' | C3' | O3' | H2 | 180.0° | 67.3° |
| C3' | C2' | H2'' | H2' | 120.3° | 122.6° |
| C3' | C2' | C1' | H1' | 80.4° | 117.4° |
| C1' | C2' | C3' | O3' | 83.0° | 139.0° |
| C1' | C2' | C3' | C4' | 34.5° | 20.9° |
| C2' | C1' | N1 | C6 | 58.0° | 114.7° |
| C2' | C1' | N1 | O4' | 108.4° | 117.8° |
| C2' | C1' | N1 | H1' | 121.2° | 121.1° |
| C2' | C1' | N1 | C2 | 121.5° | 65.0° |
| C2' | C1' | O4' | C4' | 25.7° | 26.5° |
| C2' | C1' | O4' | H1' | 117.6° | 119.4° |
| C1' | C2' | C3' | H3' | 151.6° | 97.4° |
| C1' | C2' | H2'' | H2' | 120.3° | 122.6° |
| O3' | C3' | C4' | H3' | 126.4° | 123.5° |
| O3' | C3' | C4' | C5' | 142.6° | 86.3° |
| O3' | C3' | C4' | O4' | 99.0° | 155.2° |
| O3' | C3' | C4' | H4' | 20.4° | 36.7° |
| O3' | C3' | C2' | H2'' | 157.1° | 102.3° |
| O3' | C3' | C2' | H2' | 36.9° | 20.4° |
| C3' | C4' | C5' | O5' | 66.9° | 179.5° |
| C3' | C4' | C5' | O4' | 119.4° | 114.0° |
| C3' | C4' | C5' | H4' | 122.3° | 123.0° |
| C3' | C4' | O4' | H4' | 118.9° | 118.6° |
| C3' | C4' | O4' | C1' | 5.8° | 40.1° |
| C3' | C4' | C5' | H5' | 171.2° | 60.6° |
| C3' | C4' | C5' | H5'' | 54.9° | 59.5° |
| C4' | C3' | O3' | H2 | 70.7° | 180.0° |
| C4' | C3' | C2' | H2'' | 85.4° | 139.6° |
| C4' | C3' | C2' | H2' | 154.4° | 97.7° |
| C6 | C5 | C4 | O4 | 179.5° | 179.7° |
| C5 | C6 | N1 | H6 | 180.0° | 179.4° |
| C6 | C5 | C4 | N3 | 0.3° | 0.3° |
| C5 | C6 | N1 | C1' | 179.7° | 179.7° |
| C5 | C6 | N1 | C2 | 0.1° | 0.6° |
| C5 | C4 | O4 | N3 | 179.8° | 179.9° |
| C4 | C5 | C6 | N1 | 0.4° | 0.6° |
| C5 | C4 | N3 | C2 | 0.1° | 0.0° |
| C5 | C4 | N3 | H3 | 179.9° | 180.0° |
| C4 | C5 | C6 | H6 | 179.6° | 180.0° |
| O5' | P | OP2 | OP3 | 117.5° | 120.0° |
| P | O5' | C5' | C4' | 169.1° | 180.0° |
| O5' | P | OP2 | HOP2 | 121.2° | 60.0° |
| P | O5' | C5' | H5' | 47.2° | 60.0° |
| P | O5' | C5' | H5'' | 69.1° | 60.0° |
| O5' | P | OP3 | HOP3 | 116.7° | 180.0° |
| OP2 | P | O5' | C5' | 128.3° | 65.0° |
| OP2 | P | OP3 | HOP3 | 128.0° | 60.1° |
| O5' | C5' | C4' | H5' | 121.8° | 119.9° |
| O5' | C5' | C4' | H5'' | 121.8° | 120.0° |
| O5' | C5' | C4' | O4' | 173.7° | 66.5° |
| C5' | O5' | P | OP3 | 12.8° | 175.0° |
| O5' | C5' | H5' | H5'' | 113.9° | 120.0° |
| O5' | C5' | C4' | H4' | 55.4° | 56.5° |
| O4 | C4 | N3 | C2 | 179.8° | 180.0° |
| O4 | C4 | N3 | H3 | 0.2° | 0.0° |
| C6 | N1 | C1' | C2 | 179.5° | 179.7° |
| C6 | N1 | C2 | N3 | 0.1° | 0.3° |
| C6 | N1 | C1' | O4' | 50.4° | 127.5° |
| C6 | N1 | C2 | O2 | 179.8° | 179.7° |
| C6 | N1 | C1' | H1' | 179.2° | 6.4° |
| C4 | N3 | C2 | N1 | 0.1° | 0.0° |
| C4 | N3 | C2 | H3 | 180.0° | 180.0° |
| C4 | N3 | C2 | O2 | 179.8° | 180.0° |
| C5' | C4' | O4' | H4' | 117.8° | 122.9° |
| C5' | C4' | O4' | C1' | 129.1° | 158.5° |
| C4' | C5' | H5' | H5'' | 114.0° | 120.1° |
| C5' | C4' | C3' | H3' | 16.3° | 37.2° |
| N1 | C1' | O4' | C4' | 138.1° | 146.0° |
| C1' | N1 | C2 | N3 | 179.4° | 180.0° |
| N1 | C1' | O4' | H1' | 129.9° | 121.2° |
| C1' | N1 | C2 | O2 | 0.7° | 0.1° |
| N1 | C1' | C2' | H2'' | 38.4° | 2.8° |
| N1 | C1' | C2' | H2' | 81.8° | 119.9° |
| C1' | N1 | C6 | H6 | 0.3° | 0.3° |
| N1 | C2 | N3 | O2 | 179.9° | 180.0° |
| C2 | N1 | C1' | O4' | 130.1° | 52.8° |
| C2 | N1 | C1' | H1' | 0.3° | 174.0° |
| N1 | C2 | N3 | H3 | 179.9° | 180.0° |
| C2 | N1 | C6 | H6 | 179.9° | 180.0° |
| O4' | C4' | C5' | H5' | 51.9° | 53.5° |
| O4' | C4' | C5' | H5'' | 64.5° | 173.5° |
| O4' | C4' | C3' | H3' | 134.7° | 81.3° |
| C4' | O4' | C1' | H1' | 92.0° | 92.8° |
| C1' | O4' | C4' | H4' | 113.1° | 78.6° |
| O4' | C1' | C2' | H2'' | 81.8° | 116.6° |
| O4' | C1' | C2' | H2' | 158.0° | 120.7° |
| O2 | C2 | N3 | H3 | 0.3° | 0.0° |
| OP3 | P | OP2 | HOP2 | 121.3° | 60.0° |
| H5' | C5' | C4' | H4' | 66.5° | 176.4° |
| H5'' | C5' | C4' | H4' | 177.2° | 63.5° |
| H4' | C4' | C3' | H3' | 106.0° | 160.2° |
| H3' | C3' | O3' | H2 | 55.1° | 56.4° |
| H3' | C3' | C2' | H2'' | 31.6° | 21.3° |
| H3' | C3' | C2' | H2' | 88.5° | 144.0° |
| H2'' | C2' | C1' | H1' | 159.7° | 124.0° |
| H2' | C2' | C1' | H1' | 39.5° | 1.2° |
| H71 | C5M | H72 | H73 | 120.0° | 120.0° |
