PYO
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| OP3 | P | sing | 1.61Å | 1.60Å | |
| OP3 | HOP3 | sing | 0.97Å | 0.95Å | |
| P | OP1 | sing | 1.61Å | 1.49Å | |
| P | OP2 | doub | 1.48Å | 1.49Å | |
| P | O5' | sing | 1.61Å | 1.59Å | |
| OP1 | HOP1 | sing | 0.97Å | 0.95Å | |
| O5' | C5' | sing | 1.43Å | 1.41Å | |
| C5' | C4' | sing | 1.53Å | 1.50Å | |
| C5' | H5'' | sing | 1.09Å | 1.11Å | |
| C5' | H5' | sing | 1.09Å | 1.11Å | |
| C4' | O4' | sing | 1.45Å | 1.46Å | |
| C4' | C3' | sing | 1.54Å | 1.52Å | |
| C4' | H4' | sing | 1.09Å | 1.11Å | |
| O4' | C1' | sing | 1.44Å | 1.42Å | |
| C3' | O3' | sing | 1.43Å | 1.41Å | |
| C3' | C2' | sing | 1.55Å | 1.53Å | |
| C3' | H3' | sing | 1.09Å | 1.11Å | |
| C1' | C2' | sing | 1.54Å | 1.53Å | |
| C1' | N1 | sing | 1.46Å | 1.48Å | |
| C1' | H1' | sing | 1.09Å | 1.12Å | |
| O3' | HO3 | sing | 0.97Å | 0.95Å | |
| C2' | O2' | sing | 1.43Å | 1.41Å | |
| C2' | H2' | sing | 1.09Å | 1.12Å | |
| O2' | HO2 | sing | 0.97Å | 0.95Å | |
| N1 | C6 | sing | 1.36Å | 1.33Å | |
| N1 | C2 | sing | 1.35Å | 1.40Å | |
| C6 | C5 | doub | 1.36Å | 1.34Å | |
| C6 | HC6 | sing | 1.08Å | 1.10Å | |
| C2 | O2 | doub | 1.22Å | 1.27Å | |
| C2 | N3 | sing | 1.33Å | 1.37Å | |
| C5 | C4 | sing | 1.40Å | 1.37Å | |
| C5 | HC5 | sing | 1.08Å | 1.10Å | |
| N3 | C4 | doub | 1.32Å | 1.32Å | |
| C4 | HC4 | sing | 1.08Å | 1.10Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| P | OP3 | HOP3 | 107.5° | 106.8° |
| OP3 | P | OP1 | 107.5° | 109.4° |
| OP3 | P | OP2 | 109.0° | 109.4° |
| OP3 | P | O5' | 105.1° | 109.4° |
| OP1 | P | OP2 | 119.4° | 109.5° |
| OP1 | P | O5' | 107.3° | 109.5° |
| P | OP1 | HOP1 | 107.4° | 106.9° |
| OP2 | P | O5' | 107.6° | 109.5° |
| P | O5' | C5' | 118.7° | 106.8° |
| O5' | C5' | C4' | 111.6° | 109.5° |
| O5' | C5' | H5'' | 111.4° | 109.5° |
| O5' | C5' | H5' | 111.4° | 109.4° |
| C4' | C5' | H5'' | 111.4° | 109.5° |
| C4' | C5' | H5' | 111.4° | 109.5° |
| C5' | C4' | O4' | 111.5° | 110.4° |
| C5' | C4' | C3' | 110.5° | 110.7° |
| C5' | C4' | H4' | 106.4° | 110.3° |
| H5'' | C5' | H5' | 99.0° | 109.5° |
| O4' | C4' | C3' | 106.0° | 104.7° |
| O4' | C4' | H4' | 110.8° | 110.4° |
| C4' | O4' | C1' | 109.6° | 105.4° |
| C3' | C4' | H4' | 111.8° | 110.3° |
| C4' | C3' | O3' | 109.1° | 110.6° |
| C4' | C3' | C2' | 102.2° | 104.2° |
| C4' | C3' | H3' | 115.1° | 110.5° |
| O4' | C1' | C2' | 105.2° | 104.8° |
| O4' | C1' | N1 | 108.8° | 110.5° |
| O4' | C1' | H1' | 115.1° | 110.3° |
| O3' | C3' | C2' | 111.7° | 110.5° |
| O3' | C3' | H3' | 106.2° | 110.5° |
| C3' | O3' | HO3 | 109.2° | 106.8° |
| C2' | C3' | H3' | 112.6° | 110.5° |
| C3' | C2' | C1' | 100.9° | 104.1° |
| C3' | C2' | O2' | 113.0° | 110.5° |
| C3' | C2' | H2' | 114.1° | 110.5° |
| C2' | C1' | N1 | 115.8° | 110.3° |
| C2' | C1' | H1' | 108.0° | 110.3° |
| C1' | C2' | O2' | 112.9° | 110.7° |
| C1' | C2' | H2' | 114.1° | 110.5° |
| N1 | C1' | H1' | 104.4° | 110.3° |
| C1' | N1 | C6 | 120.5° | 120.0° |
| C1' | N1 | C2 | 117.8° | 119.9° |
| O2' | C2' | H2' | 102.3° | 110.4° |
| C2' | O2' | HO2 | 113.1° | 106.9° |
| C6 | N1 | C2 | 121.7° | 120.1° |
| N1 | C6 | C5 | 119.3° | 119.2° |
| N1 | C6 | HC6 | 119.9° | 120.4° |
| N1 | C2 | O2 | 121.8° | 119.5° |
| N1 | C2 | N3 | 118.1° | 121.0° |
| C5 | C6 | HC6 | 120.8° | 120.4° |
| C6 | C5 | C4 | 119.1° | 119.1° |
| C6 | C5 | HC5 | 119.4° | 120.5° |
| O2 | C2 | N3 | 120.1° | 119.5° |
| C2 | N3 | C4 | 118.7° | 120.8° |
| C4 | C5 | HC5 | 121.5° | 120.4° |
| C5 | C4 | N3 | 123.0° | 119.8° |
| C5 | C4 | HC4 | 120.6° | 120.2° |
| N3 | C4 | HC4 | 116.4° | 120.0° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| OP3 | P | OP1 | OP2 | 124.7° | 120.0° |
| OP3 | P | OP1 | O5' | 112.6° | 120.0° |
| OP3 | P | OP2 | O5' | 113.5° | 119.9° |
| OP3 | P | OP1 | HOP1 | 180.0° | 60.0° |
| OP3 | P | O5' | C5' | 170.3° | 180.0° |
| HOP3 | OP3 | P | OP1 | 180.0° | 60.0° |
| HOP3 | OP3 | P | OP2 | 49.3° | 60.1° |
| HOP3 | OP3 | P | O5' | 65.9° | 180.0° |
| OP1 | P | OP2 | O5' | 122.6° | 120.1° |
| OP1 | P | O5' | C5' | 75.5° | 60.1° |
| OP2 | P | OP1 | HOP1 | 55.3° | 180.0° |
| OP2 | P | O5' | C5' | 54.2° | 60.0° |
| O5' | P | OP1 | HOP1 | 67.4° | 59.9° |
| P | O5' | C5' | C4' | 172.7° | 180.0° |
| P | O5' | C5' | H5'' | 47.5° | 60.0° |
| P | O5' | C5' | H5' | 62.1° | 60.0° |
| O5' | C5' | C4' | H5'' | 125.3° | 120.0° |
| O5' | C5' | C4' | H5' | 125.3° | 119.9° |
| O5' | C5' | H5'' | H5' | 117.4° | 120.0° |
| O5' | C5' | C4' | O4' | 45.3° | 61.4° |
| O5' | C5' | C4' | C3' | 163.0° | 176.9° |
| O5' | C5' | C4' | H4' | 75.5° | 60.8° |
| C4' | C5' | H5'' | H5' | 117.3° | 120.0° |
| C5' | C4' | O4' | C3' | 120.3° | 119.1° |
| C5' | C4' | O4' | H4' | 118.2° | 122.2° |
| C5' | C4' | C3' | H4' | 118.3° | 122.3° |
| C5' | C4' | O4' | C1' | 116.3° | 159.5° |
| C5' | C4' | C3' | O3' | 147.7° | 98.5° |
| C5' | C4' | C3' | C2' | 93.9° | 142.8° |
| C5' | C4' | C3' | H3' | 28.5° | 24.1° |
| H5'' | C5' | C4' | O4' | 80.0° | 58.5° |
| H5'' | C5' | C4' | C3' | 37.7° | 56.9° |
| H5'' | C5' | C4' | H4' | 159.2° | 179.2° |
| H5' | C5' | C4' | O4' | 170.6° | 178.6° |
| H5' | C5' | C4' | C3' | 71.8° | 63.1° |
| H5' | C5' | C4' | H4' | 49.7° | 59.2° |
| O4' | C4' | C3' | H4' | 120.8° | 118.7° |
| O4' | C4' | C3' | O3' | 91.3° | 142.5° |
| O4' | C4' | C3' | C2' | 27.0° | 23.8° |
| O4' | C4' | C3' | H3' | 149.5° | 94.9° |
| C4' | O4' | C1' | C2' | 20.9° | 40.4° |
| C4' | O4' | C1' | N1 | 145.5° | 159.3° |
| C4' | O4' | C1' | H1' | 97.8° | 78.4° |
| C3' | C4' | O4' | C1' | 4.0° | 40.3° |
| C4' | C3' | O3' | C2' | 112.3° | 114.8° |
| C4' | C3' | O3' | H3' | 124.6° | 122.6° |
| C4' | C3' | C2' | H3' | 124.1° | 118.7° |
| C4' | C3' | C2' | C1' | 38.1° | 0.1° |
| C4' | C3' | O3' | HO3 | 180.0° | 178.1° |
| C4' | C3' | C2' | O2' | 159.0° | 118.9° |
| C4' | C3' | C2' | H2' | 84.7° | 118.5° |
| H4' | C4' | O4' | C1' | 125.4° | 78.3° |
| H4' | C4' | C3' | O3' | 29.5° | 23.8° |
| H4' | C4' | C3' | C2' | 147.8° | 94.9° |
| H4' | C4' | C3' | H3' | 89.8° | 146.4° |
| O4' | C1' | C2' | C3' | 36.9° | 23.9° |
| O4' | C1' | C2' | N1 | 120.1° | 119.0° |
| O4' | C1' | C2' | H1' | 123.4° | 118.8° |
| O4' | C1' | N1 | H1' | 123.3° | 122.3° |
| O4' | C1' | C2' | O2' | 157.9° | 142.7° |
| O4' | C1' | C2' | H2' | 85.9° | 94.6° |
| O4' | C1' | N1 | C6 | 6.7° | 124.5° |
| O4' | C1' | N1 | C2 | 172.8° | 55.1° |
| O3' | C3' | C2' | H3' | 119.4° | 122.6° |
| O3' | C3' | C2' | C1' | 78.4° | 118.7° |
| O3' | C3' | C2' | O2' | 42.5° | 0.2° |
| O3' | C3' | C2' | H2' | 158.8° | 122.7° |
| C3' | C2' | C1' | O2' | 121.0° | 118.7° |
| C3' | C2' | C1' | H2' | 122.8° | 118.6° |
| C3' | C2' | C1' | N1 | 157.0° | 143.0° |
| C3' | C2' | C1' | H1' | 86.5° | 94.8° |
| C2' | C3' | O3' | HO3 | 67.7° | 63.3° |
| C3' | C2' | O2' | H2' | 123.1° | 122.5° |
| C3' | C2' | O2' | HO2 | 180.0° | 61.4° |
| H3' | C3' | C2' | C1' | 162.2° | 118.7° |
| H3' | C3' | O3' | HO3 | 55.4° | 59.3° |
| H3' | C3' | C2' | O2' | 76.9° | 122.4° |
| H3' | C3' | C2' | H2' | 39.4° | 0.1° |
| C2' | C1' | N1 | H1' | 118.5° | 122.2° |
| C1' | C2' | O2' | H2' | 123.1° | 122.7° |
| C1' | C2' | O2' | HO2 | 66.2° | 176.1° |
| C2' | C1' | N1 | C6 | 111.5° | 120.0° |
| C2' | C1' | N1 | C2 | 69.0° | 60.4° |
| N1 | C1' | C2' | O2' | 82.0° | 98.3° |
| N1 | C1' | C2' | H2' | 34.2° | 24.4° |
| C1' | N1 | C6 | C2 | 179.4° | 179.6° |
| C1' | N1 | C6 | C5 | 178.8° | 180.0° |
| C1' | N1 | C6 | HC6 | 1.1° | 0.1° |
| C1' | N1 | C2 | O2 | 1.3° | 0.4° |
| C1' | N1 | C2 | N3 | 178.7° | 179.8° |
| H1' | C1' | C2' | O2' | 34.5° | 23.9° |
| H1' | C1' | C2' | H2' | 150.7° | 146.6° |
| H1' | C1' | N1 | C6 | 130.0° | 2.2° |
| H1' | C1' | N1 | C2 | 49.5° | 177.4° |
| H2' | C2' | O2' | HO2 | 56.9° | 61.1° |
| N1 | C6 | C5 | HC6 | 180.0° | 179.9° |
| C6 | N1 | C2 | O2 | 179.2° | 180.0° |
| C6 | N1 | C2 | N3 | 0.7° | 0.6° |
| N1 | C6 | C5 | C4 | 0.1° | 0.1° |
| N1 | C6 | C5 | HC5 | 179.9° | 180.0° |
| C2 | N1 | C6 | C5 | 0.6° | 0.4° |
| C2 | N1 | C6 | HC6 | 179.4° | 179.7° |
| N1 | C2 | O2 | N3 | 180.0° | 179.4° |
| N1 | C2 | N3 | C4 | 0.3° | 0.6° |
| C6 | C5 | C4 | HC5 | 179.9° | 179.9° |
| C6 | C5 | C4 | N3 | 0.4° | 0.0° |
| C6 | C5 | C4 | HC4 | 179.6° | 180.0° |
| HC6 | C6 | C5 | C4 | 180.0° | 180.0° |
| HC6 | C6 | C5 | HC5 | 0.1° | 0.1° |
| O2 | C2 | N3 | C4 | 179.7° | 180.0° |
| C2 | N3 | C4 | C5 | 0.3° | 0.3° |
| C2 | N3 | C4 | HC4 | 179.7° | 179.7° |
| C5 | C4 | N3 | HC4 | 180.0° | 180.0° |
| HC5 | C5 | C4 | N3 | 179.7° | 180.0° |
| HC5 | C5 | C4 | HC4 | 0.3° | 0.0° |
