HPD
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| P | O5' | sing | 1.61Å | 1.61Å | |
| P | O1P | doub | 1.48Å | 1.49Å | |
| P | O2P | sing | 1.61Å | 1.53Å | |
| P | O3P | sing | 1.61Å | 1.52Å | |
| O5' | C5' | sing | 1.43Å | 1.44Å | |
| O2P | HOP2 | sing | 0.97Å | 0.95Å | |
| O3P | HOP3 | sing | 0.97Å | 0.95Å | |
| C5' | C4' | sing | 1.53Å | 1.54Å | |
| C5' | H5'1 | sing | 1.09Å | 1.11Å | |
| C5' | H5'2 | sing | 1.09Å | 1.11Å | |
| O4' | C4' | sing | 1.43Å | 1.41Å | |
| O4' | HO'4 | sing | 0.97Å | 0.95Å | |
| O3' | C3' | sing | 1.43Å | 1.41Å | |
| O3' | HO'3 | sing | 0.97Å | 0.95Å | |
| C1' | O1' | sing | 1.43Å | 1.39Å | |
| C1' | C2' | sing | 1.53Å | 1.53Å | |
| C1' | H1'1 | sing | 1.09Å | 1.11Å | |
| C1' | H1'2 | sing | 1.09Å | 1.12Å | |
| O1' | HO'1 | sing | 0.97Å | 0.95Å | |
| C3' | C4' | sing | 1.53Å | 1.55Å | |
| C3' | C2' | sing | 1.53Å | 1.55Å | |
| C3' | H3' | sing | 1.09Å | 1.11Å | |
| C4' | H4' | sing | 1.09Å | 1.12Å | |
| C2' | H2'1 | sing | 1.09Å | 1.12Å | |
| C2' | H2'2 | sing | 1.09Å | 1.12Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| O5' | P | O1P | 109.6° | 109.5° |
| O5' | P | O2P | 103.7° | 109.5° |
| O5' | P | O3P | 106.8° | 109.5° |
| P | O5' | C5' | 118.6° | 106.9° |
| O1P | P | O2P | 111.4° | 109.4° |
| O1P | P | O3P | 110.8° | 109.4° |
| O2P | P | O3P | 114.3° | 109.5° |
| P | O2P | HOP2 | 103.7° | 106.8° |
| P | O3P | HOP3 | 106.7° | 106.8° |
| O5' | C5' | C4' | 108.2° | 109.6° |
| O5' | C5' | H5'1 | 112.7° | 109.5° |
| O5' | C5' | H5'2 | 112.7° | 109.5° |
| C4' | C5' | H5'1 | 112.7° | 109.5° |
| C4' | C5' | H5'2 | 112.7° | 109.4° |
| C5' | C4' | O4' | 107.4° | 109.5° |
| C5' | C4' | C3' | 116.6° | 109.5° |
| C5' | C4' | H4' | 106.3° | 109.5° |
| H5'1 | C5' | H5'2 | 97.8° | 109.4° |
| C4' | O4' | HO'4 | 107.4° | 106.8° |
| O4' | C4' | C3' | 110.5° | 109.4° |
| O4' | C4' | H4' | 112.9° | 109.5° |
| C3' | O3' | HO'3 | 107.9° | 106.8° |
| O3' | C3' | C4' | 107.9° | 109.4° |
| O3' | C3' | C2' | 108.8° | 109.5° |
| O3' | C3' | H3' | 111.5° | 109.4° |
| O1' | C1' | C2' | 112.5° | 109.5° |
| O1' | C1' | H1'1 | 111.2° | 109.4° |
| O1' | C1' | H1'2 | 111.1° | 109.4° |
| C1' | O1' | HO'1 | 112.4° | 106.9° |
| C2' | C1' | H1'1 | 111.1° | 109.5° |
| C2' | C1' | H1'2 | 111.1° | 109.5° |
| C1' | C2' | C3' | 115.6° | 109.5° |
| C1' | C2' | H2'1 | 110.0° | 109.5° |
| C1' | C2' | H2'2 | 110.0° | 109.5° |
| H1'1 | C1' | H1'2 | 99.2° | 109.5° |
| C4' | C3' | C2' | 111.2° | 109.5° |
| C4' | C3' | H3' | 109.1° | 109.5° |
| C3' | C4' | H4' | 103.0° | 109.5° |
| C2' | C3' | H3' | 108.2° | 109.5° |
| C3' | C2' | H2'1 | 110.0° | 109.5° |
| C3' | C2' | H2'2 | 110.0° | 109.4° |
| H2'1 | C2' | H2'2 | 100.2° | 109.5° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| O5' | P | O1P | O2P | 114.1° | 120.0° |
| O5' | P | O1P | O3P | 117.5° | 120.0° |
| O5' | P | O2P | O3P | 115.8° | 120.1° |
| O5' | P | O2P | HOP2 | 180.0° | 180.0° |
| O5' | P | O3P | HOP3 | 180.0° | 60.0° |
| P | O5' | C5' | C4' | 158.8° | 180.0° |
| P | O5' | C5' | H5'1 | 33.5° | 59.9° |
| P | O5' | C5' | H5'2 | 76.0° | 60.0° |
| O1P | P | O2P | O3P | 126.5° | 119.9° |
| O1P | P | O5' | C5' | 51.1° | 60.0° |
| O1P | P | O2P | HOP2 | 62.3° | 60.0° |
| O1P | P | O3P | HOP3 | 60.8° | 180.0° |
| O2P | P | O5' | C5' | 170.1° | 180.0° |
| O2P | P | O3P | HOP3 | 66.0° | 60.1° |
| O3P | P | O5' | C5' | 68.9° | 60.0° |
| O3P | P | O2P | HOP2 | 64.2° | 60.0° |
| O5' | C5' | C4' | H5'1 | 125.3° | 120.1° |
| O5' | C5' | C4' | H5'2 | 125.2° | 120.0° |
| O5' | C5' | H5'1 | H5'2 | 118.6° | 120.0° |
| O5' | C5' | C4' | O4' | 69.8° | 60.0° |
| O5' | C5' | C4' | C3' | 165.5° | 180.0° |
| O5' | C5' | C4' | H4' | 51.4° | 60.0° |
| C4' | C5' | H5'1 | H5'2 | 118.6° | 119.9° |
| C5' | C4' | O4' | C3' | 128.2° | 120.0° |
| C5' | C4' | O4' | H4' | 117.0° | 120.0° |
| C5' | C4' | O4' | HO'4 | 180.0° | 60.0° |
| C5' | C4' | C3' | O3' | 54.6° | 60.0° |
| C5' | C4' | C3' | H4' | 116.0° | 120.0° |
| C5' | C4' | C3' | C2' | 173.9° | 180.0° |
| C5' | C4' | C3' | H3' | 66.7° | 60.0° |
| H5'1 | C5' | C4' | O4' | 55.5° | 179.9° |
| H5'1 | C5' | C4' | C3' | 69.2° | 60.0° |
| H5'1 | C5' | C4' | H4' | 176.6° | 60.1° |
| H5'2 | C5' | C4' | O4' | 164.9° | 60.0° |
| H5'2 | C5' | C4' | C3' | 40.3° | 59.9° |
| H5'2 | C5' | C4' | H4' | 73.9° | 180.0° |
| O4' | C4' | C3' | O3' | 177.7° | 180.0° |
| O4' | C4' | C3' | H4' | 120.9° | 120.0° |
| O4' | C4' | C3' | C2' | 63.0° | 60.0° |
| O4' | C4' | C3' | H3' | 56.3° | 60.0° |
| HO'4 | O4' | C4' | C3' | 51.8° | 60.0° |
| HO'4 | O4' | C4' | H4' | 63.0° | 180.0° |
| O3' | C3' | C2' | C1' | 63.0° | 60.0° |
| O3' | C3' | C4' | C2' | 119.3° | 120.0° |
| O3' | C3' | C4' | H3' | 121.4° | 119.9° |
| O3' | C3' | C2' | H3' | 121.4° | 120.0° |
| O3' | C3' | C4' | H4' | 61.4° | 60.1° |
| O3' | C3' | C2' | H2'1 | 171.7° | 180.0° |
| O3' | C3' | C2' | H2'2 | 62.3° | 60.0° |
| HO'3 | O3' | C3' | C4' | 179.9° | 60.1° |
| HO'3 | O3' | C3' | C2' | 59.1° | 60.0° |
| HO'3 | O3' | C3' | H3' | 60.2° | 180.0° |
| O1' | C1' | C2' | H1'1 | 125.3° | 120.0° |
| O1' | C1' | C2' | H1'2 | 125.3° | 120.0° |
| O1' | C1' | H1'1 | H1'2 | 117.0° | 119.9° |
| O1' | C1' | C2' | C3' | 45.0° | 180.0° |
| O1' | C1' | C2' | H2'1 | 80.3° | 60.0° |
| O1' | C1' | C2' | H2'2 | 170.3° | 60.1° |
| C2' | C1' | H1'1 | H1'2 | 116.9° | 120.0° |
| C2' | C1' | O1' | HO'1 | 180.0° | 180.0° |
| C1' | C2' | C3' | C4' | 178.3° | 180.0° |
| C1' | C2' | C3' | H2'1 | 125.3° | 120.1° |
| C1' | C2' | C3' | H2'2 | 125.3° | 120.0° |
| C1' | C2' | C3' | H3' | 58.4° | 60.0° |
| C1' | C2' | H2'1 | H2'2 | 115.8° | 120.0° |
| H1'1 | C1' | O1' | HO'1 | 54.7° | 60.0° |
| H1'1 | C1' | C2' | C3' | 170.3° | 60.0° |
| H1'1 | C1' | C2' | H2'1 | 45.0° | 180.0° |
| H1'1 | C1' | C2' | H2'2 | 64.4° | 59.9° |
| H1'2 | C1' | O1' | HO'1 | 54.8° | 59.9° |
| H1'2 | C1' | C2' | C3' | 80.3° | 60.0° |
| H1'2 | C1' | C2' | H2'1 | 154.4° | 60.0° |
| H1'2 | C1' | C2' | H2'2 | 45.0° | 180.0° |
| C4' | C3' | C2' | H3' | 119.9° | 120.0° |
| C4' | C3' | C2' | H2'1 | 53.0° | 59.9° |
| C4' | C3' | C2' | H2'2 | 56.4° | 60.0° |
| C2' | C3' | C4' | H4' | 57.9° | 60.0° |
| C3' | C2' | H2'1 | H2'2 | 115.8° | 119.9° |
| H3' | C3' | C4' | H4' | 177.2° | 180.0° |
| H3' | C3' | C2' | H2'1 | 66.9° | 60.1° |
| H3' | C3' | C2' | H2'2 | 176.3° | 180.0° |
