5PY
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| P | O5' | sing | 1.62Å | 1.59Å | |
| P | OP2 | sing | 1.62Å | 1.46Å | |
| P | OP3 | sing | 1.62Å | 57.50Å | |
| P | OP1 | doub | 1.50Å | 1.46Å | |
| OP2 | HOP2 | sing | 0.98Å | 0.95Å | |
| O5' | C5' | sing | 1.42Å | 1.34Å | |
| C5' | C4' | sing | 1.52Å | 1.52Å | |
| C5' | H5' | sing | 1.09Å | 1.10Å | |
| C5' | H5'' | sing | 1.09Å | 1.10Å | |
| C4' | C3' | sing | 1.52Å | 1.53Å | |
| C4' | O4' | sing | 1.44Å | 1.43Å | |
| C4' | H4' | sing | 1.09Å | 1.10Å | |
| O4' | C1' | sing | 1.43Å | 1.42Å | |
| C1' | N1 | sing | 1.43Å | 1.48Å | |
| C1' | C2' | sing | 1.52Å | 1.53Å | |
| C1' | H1' | sing | 1.10Å | 1.10Å | |
| N1 | C2 | sing | 1.42Å | 1.39Å | |
| N1 | C6 | sing | 1.39Å | 1.39Å | |
| C2 | N3 | sing | 1.39Å | 1.38Å | |
| C2 | O2 | doub | 1.23Å | 1.22Å | |
| N3 | C4 | doub | 1.29Å | 1.37Å | |
| C4 | C5 | sing | 1.47Å | 1.45Å | |
| C4 | H4 | sing | 1.10Å | 1.08Å | |
| C5 | C5M | sing | 1.49Å | 1.50Å | |
| C5 | C6 | doub | 1.34Å | 1.35Å | |
| C5M | H71 | sing | 1.09Å | 1.10Å | |
| C5M | H72 | sing | 1.09Å | 1.10Å | |
| C5M | H73 | sing | 1.09Å | 1.10Å | |
| C6 | H6 | sing | 1.09Å | 1.08Å | |
| C2' | C3' | sing | 1.51Å | 1.53Å | |
| C2' | H2' | sing | 1.10Å | 1.10Å | |
| C2' | H2'' | sing | 1.09Å | 1.10Å | |
| C3' | O3' | sing | 1.43Å | 1.45Å | |
| C3' | H3' | sing | 1.09Å | 1.10Å | |
| O3' | HO3' | sing | 0.97Å | 0.95Å | |
| OP3 | HOP3 | sing | 0.98Å | 0.00Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| O5' | P | OP2 | 95.2° | 103.7° |
| O5' | P | OP3 | 108.7° | 102.9° |
| O5' | P | OP1 | 115.8° | 115.0° |
| P | O5' | C5' | 127.8° | 118.5° |
| OP2 | P | OP3 | 13.7° | 103.3° |
| OP2 | P | OP1 | 118.1° | 115.3° |
| P | OP2 | HOP2 | 109.5° | 118.9° |
| OP3 | P | OP1 | 112.4° | 115.0° |
| P | OP3 | HOP3 | 90.0° | 118.9° |
| O5' | C5' | C4' | 109.7° | 108.9° |
| O5' | C5' | H5' | 109.4° | 109.0° |
| O5' | C5' | H5'' | 109.3° | 108.9° |
| C4' | C5' | H5' | 109.4° | 110.3° |
| C4' | C5' | H5'' | 109.4° | 110.3° |
| C5' | C4' | C3' | 120.1° | 112.9° |
| C5' | C4' | O4' | 100.0° | 107.9° |
| C5' | C4' | H4' | 108.0° | 109.5° |
| H5' | C5' | H5'' | 109.7° | 109.3° |
| C3' | C4' | O4' | 106.0° | 106.2° |
| C3' | C4' | H4' | 102.2° | 112.2° |
| C4' | C3' | C2' | 103.5° | 103.1° |
| C4' | C3' | O3' | 110.5° | 109.9° |
| C4' | C3' | H3' | 112.5° | 113.5° |
| O4' | C4' | H4' | 121.7° | 107.9° |
| C4' | O4' | C1' | 108.6° | 109.3° |
| O4' | C1' | N1 | 108.4° | 109.3° |
| O4' | C1' | C2' | 106.8° | 107.4° |
| O4' | C1' | H1' | 114.0° | 108.0° |
| N1 | C1' | C2' | 115.1° | 112.8° |
| N1 | C1' | H1' | 105.5° | 107.8° |
| C1' | N1 | C2 | 116.8° | 121.8° |
| C1' | N1 | C6 | 120.8° | 118.4° |
| C2' | C1' | H1' | 107.2° | 111.5° |
| C1' | C2' | C3' | 98.1° | 102.5° |
| C1' | C2' | H2' | 113.4° | 110.6° |
| C1' | C2' | H2'' | 115.7° | 111.7° |
| C2 | N1 | C6 | 122.2° | 119.8° |
| N1 | C2 | N3 | 114.0° | 118.6° |
| N1 | C2 | O2 | 122.5° | 121.1° |
| N1 | C6 | C5 | 122.6° | 123.0° |
| N1 | C6 | H6 | 118.7° | 115.6° |
| N3 | C2 | O2 | 123.5° | 120.3° |
| C2 | N3 | C4 | 126.6° | 119.0° |
| N3 | C4 | C5 | 117.0° | 125.8° |
| N3 | C4 | H4 | 121.5° | 118.5° |
| C5 | C4 | H4 | 121.5° | 115.7° |
| C4 | C5 | C5M | 119.8° | 119.7° |
| C4 | C5 | C6 | 117.6° | 113.9° |
| C5M | C5 | C6 | 122.4° | 126.4° |
| C5 | C5M | H71 | 109.5° | 110.1° |
| C5 | C5M | H72 | 109.5° | 110.2° |
| C5 | C5M | H73 | 109.5° | 110.1° |
| C5 | C6 | H6 | 118.7° | 121.5° |
| H71 | C5M | H72 | 109.5° | 109.0° |
| H71 | C5M | H73 | 109.4° | 108.9° |
| H72 | C5M | H73 | 109.5° | 108.5° |
| C3' | C2' | H2' | 113.5° | 109.7° |
| C3' | C2' | H2'' | 115.7° | 114.1° |
| C2' | C3' | O3' | 108.9° | 109.7° |
| C2' | C3' | H3' | 114.0° | 113.2° |
| H2' | C2' | H2'' | 101.1° | 108.3° |
| O3' | C3' | H3' | 107.5° | 107.4° |
| C3' | O3' | HO3' | 109.5° | 107.3° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| O5' | P | OP2 | OP3 | 168.6° | 107.1° |
| O5' | P | OP2 | OP1 | 123.0° | 126.6° |
| O5' | P | OP3 | OP1 | 129.5° | 125.8° |
| O5' | P | OP2 | HOP2 | 119.7° | 175.4° |
| P | O5' | C5' | C4' | 98.8° | 180.0° |
| P | O5' | C5' | H5' | 21.2° | 59.6° |
| P | O5' | C5' | H5'' | 141.3° | 59.6° |
| O5' | P | OP3 | HOP3 | 90.0° | 173.8° |
| OP2 | P | OP3 | OP1 | 117.5° | 126.5° |
| OP2 | P | O5' | C5' | 162.2° | 53.2° |
| OP2 | P | OP3 | HOP3 | 90.0° | 78.5° |
| OP3 | P | OP2 | HOP2 | 49.0° | 77.5° |
| OP3 | P | O5' | C5' | 159.4° | 54.2° |
| OP1 | P | OP2 | HOP2 | 117.4° | 48.8° |
| OP1 | P | O5' | C5' | 73.0° | 179.9° |
| OP1 | P | OP3 | HOP3 | 90.0° | 48.0° |
| O5' | C5' | C4' | H5' | 120.0° | 119.6° |
| O5' | C5' | C4' | H5'' | 119.9° | 119.5° |
| O5' | C5' | H5' | H5'' | 119.9° | 119.0° |
| O5' | C5' | C4' | C3' | 91.7° | 179.5° |
| O5' | C5' | C4' | O4' | 153.1° | 62.4° |
| O5' | C5' | C4' | H4' | 24.9° | 54.7° |
| C4' | C5' | H5' | H5'' | 119.9° | 121.5° |
| C5' | C4' | C3' | O4' | 112.1° | 118.1° |
| C5' | C4' | C3' | H4' | 119.5° | 124.3° |
| C5' | C4' | O4' | H4' | 118.6° | 118.2° |
| C5' | C4' | O4' | C1' | 126.2° | 108.6° |
| C5' | C4' | C3' | C2' | 87.5° | 88.8° |
| C5' | C4' | C3' | O3' | 156.1° | 154.2° |
| C5' | C4' | C3' | H3' | 36.0° | 34.0° |
| H5' | C5' | C4' | C3' | 148.4° | 60.0° |
| H5' | C5' | C4' | O4' | 33.1° | 57.1° |
| H5' | C5' | C4' | H4' | 95.1° | 174.3° |
| H5'' | C5' | C4' | C3' | 28.2° | 61.0° |
| H5'' | C5' | C4' | O4' | 87.0° | 178.1° |
| H5'' | C5' | C4' | H4' | 144.8° | 64.8° |
| C3' | C4' | O4' | H4' | 115.9° | 120.5° |
| C3' | C4' | O4' | C1' | 0.7° | 12.7° |
| C4' | C3' | C2' | C1' | 37.4° | 33.4° |
| C4' | C3' | C2' | O3' | 117.5° | 117.1° |
| C4' | C3' | C2' | H3' | 122.5° | 123.0° |
| C4' | C3' | C2' | H2' | 157.4° | 84.1° |
| C4' | C3' | C2' | H2'' | 86.3° | 154.3° |
| C4' | C3' | O3' | H3' | 123.1° | 123.9° |
| C4' | C3' | O3' | HO3' | 47.9° | 128.0° |
| C4' | O4' | C1' | N1 | 150.7° | 131.7° |
| C4' | O4' | C1' | C2' | 26.0° | 9.0° |
| C4' | O4' | C1' | H1' | 92.1° | 111.3° |
| O4' | C4' | C3' | C2' | 24.6° | 29.2° |
| O4' | C4' | C3' | O3' | 91.8° | 87.7° |
| O4' | C4' | C3' | H3' | 148.1° | 152.1° |
| H4' | C4' | O4' | C1' | 115.2° | 133.2° |
| H4' | C4' | C3' | C2' | 153.0° | 146.9° |
| H4' | C4' | C3' | O3' | 36.6° | 29.9° |
| H4' | C4' | C3' | H3' | 83.5° | 90.3° |
| O4' | C1' | N1 | C2' | 119.6° | 119.4° |
| O4' | C1' | N1 | H1' | 122.5° | 117.1° |
| O4' | C1' | C2' | H1' | 122.5° | 118.1° |
| O4' | C1' | N1 | C2 | 176.1° | 147.2° |
| O4' | C1' | N1 | C6 | 0.6° | 32.9° |
| O4' | C1' | C2' | C3' | 39.6° | 26.9° |
| O4' | C1' | C2' | H2' | 159.6° | 90.0° |
| O4' | C1' | C2' | H2'' | 84.2° | 149.4° |
| N1 | C1' | C2' | H1' | 117.0° | 121.4° |
| C1' | N1 | C2 | C6 | 175.4° | 179.9° |
| C1' | N1 | C2 | N3 | 179.1° | 179.9° |
| C1' | N1 | C2 | O2 | 2.8° | 0.0° |
| C1' | N1 | C6 | C5 | 177.9° | 179.9° |
| C1' | N1 | C6 | H6 | 2.1° | 0.0° |
| N1 | C1' | C2' | C3' | 160.0° | 147.4° |
| N1 | C1' | C2' | H2' | 80.0° | 30.6° |
| N1 | C1' | C2' | H2'' | 36.3° | 90.1° |
| C2' | C1' | N1 | C2 | 64.4° | 93.4° |
| C2' | C1' | N1 | C6 | 120.1° | 86.5° |
| C1' | C2' | C3' | H2' | 120.0° | 117.5° |
| C1' | C2' | C3' | H2'' | 123.8° | 120.8° |
| C1' | C2' | H2' | H2'' | 124.6° | 122.7° |
| C1' | C2' | C3' | O3' | 80.1° | 83.6° |
| C1' | C2' | C3' | H3' | 159.9° | 156.4° |
| H1' | C1' | N1 | C2 | 53.6° | 30.1° |
| H1' | C1' | N1 | C6 | 122.0° | 150.0° |
| H1' | C1' | C2' | C3' | 83.0° | 91.2° |
| H1' | C1' | C2' | H2' | 37.0° | 151.9° |
| H1' | C1' | C2' | H2'' | 153.3° | 31.3° |
| N1 | C2 | N3 | O2 | 178.1° | 179.9° |
| N1 | C2 | N3 | C4 | 2.4° | 0.0° |
| C2 | N1 | C6 | C5 | 2.6° | 0.0° |
| C2 | N1 | C6 | H6 | 177.4° | 179.9° |
| C6 | N1 | C2 | N3 | 3.7° | 0.0° |
| C6 | N1 | C2 | O2 | 178.2° | 179.9° |
| N1 | C6 | C5 | C4 | 0.1° | 0.1° |
| N1 | C6 | C5 | C5M | 174.2° | 180.0° |
| N1 | C6 | C5 | H6 | 180.0° | 179.9° |
| C2 | N3 | C4 | C5 | 0.0° | 0.0° |
| C2 | N3 | C4 | H4 | 179.9° | 180.0° |
| O2 | C2 | N3 | C4 | 179.5° | 179.9° |
| N3 | C4 | C5 | H4 | 180.0° | 180.0° |
| N3 | C4 | C5 | C5M | 173.1° | 180.0° |
| N3 | C4 | C5 | C6 | 1.4° | 0.1° |
| C4 | C5 | C5M | C6 | 174.2° | 180.0° |
| C4 | C5 | C5M | H71 | 3.1° | 110.3° |
| C4 | C5 | C5M | H72 | 123.1° | 129.5° |
| C4 | C5 | C5M | H73 | 116.9° | 9.8° |
| C4 | C5 | C6 | H6 | 179.9° | 179.9° |
| H4 | C4 | C5 | C5M | 6.9° | 0.0° |
| H4 | C4 | C5 | C6 | 178.6° | 179.9° |
| C5 | C5M | H71 | H72 | 120.0° | 121.0° |
| C5 | C5M | H71 | H73 | 120.0° | 120.9° |
| C5 | C5M | H72 | H73 | 120.0° | 120.7° |
| C5M | C5 | C6 | H6 | 5.8° | 0.1° |
| C6 | C5 | C5M | H71 | 171.1° | 69.8° |
| C6 | C5 | C5M | H72 | 51.1° | 50.5° |
| C6 | C5 | C5M | H73 | 69.0° | 170.2° |
| H71 | C5M | H72 | H73 | 120.0° | 118.4° |
| C3' | C2' | H2' | H2'' | 124.6° | 125.1° |
| C2' | C3' | O3' | H3' | 123.9° | 123.4° |
| C2' | C3' | O3' | HO3' | 65.1° | 119.3° |
| H2' | C2' | C3' | O3' | 39.9° | 158.9° |
| H2' | C2' | C3' | H3' | 80.0° | 38.9° |
| H2'' | C2' | C3' | O3' | 156.1° | 37.2° |
| H2'' | C2' | C3' | H3' | 36.2° | 82.7° |
| H3' | C3' | O3' | HO3' | 171.0° | 4.1° |
