H5P
Bonds
First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
C2 | O2 | doub | 1.21Å | 1.23Å | |
C2 | N3 | sing | 1.35Å | 1.39Å | |
C2 | C1' | sing | 1.50Å | 1.54Å | |
N3 | C4 | sing | 1.34Å | 1.38Å | |
N3 | HN3 | sing | 0.97Å | 1.02Å | |
C4 | O4 | doub | 1.22Å | 1.23Å | |
C4 | N5 | sing | 1.35Å | 1.41Å | |
N5 | C1' | sing | 1.46Å | 1.40Å | |
N5 | HN5 | sing | 0.97Å | 1.02Å | |
C1' | C2' | sing | 1.53Å | 1.49Å | |
C1' | O4' | sing | 1.43Å | 1.44Å | |
C2' | O2' | sing | 1.43Å | 1.41Å | |
C2' | C3' | sing | 1.55Å | 1.52Å | |
C2' | H2' | sing | 1.09Å | 1.12Å | |
O2' | HO2' | sing | 0.97Å | 0.95Å | |
C3' | O3' | sing | 1.43Å | 1.45Å | |
C3' | C4' | sing | 1.54Å | 1.54Å | |
C3' | H3' | sing | 1.09Å | 1.12Å | |
O3' | HO3' | sing | 0.97Å | 0.95Å | |
C4' | O4' | sing | 1.45Å | 1.41Å | |
C4' | C5' | sing | 1.53Å | 1.52Å | |
C4' | H4' | sing | 1.09Å | 1.11Å | |
C5' | O5' | sing | 1.43Å | 1.49Å | |
C5' | H5'1 | sing | 1.09Å | 1.12Å | |
C5' | H5'2 | sing | 1.09Å | 1.12Å | |
O5' | P | sing | 1.61Å | 1.62Å | |
P | O1P | doub | 1.48Å | 1.46Å | |
P | O2P | sing | 1.61Å | 1.48Å | |
P | O3P | sing | 1.61Å | 1.49Å | |
O2P | HOP2 | sing | 0.97Å | 0.95Å | |
O3P | HOP3 | sing | 0.97Å | 0.95Å |
Angles
First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
O2 | C2 | N3 | 129.4° | 127.4° |
O2 | C2 | C1' | 123.0° | 127.4° |
N3 | C2 | C1' | 106.9° | 105.2° |
C2 | N3 | C4 | 111.4° | 111.6° |
C2 | N3 | HN3 | 124.4° | 124.2° |
C2 | C1' | N5 | 101.8° | 104.7° |
C2 | C1' | C2' | 110.6° | 111.3° |
C2 | C1' | O4' | 111.1° | 111.6° |
C4 | N3 | HN3 | 124.2° | 124.2° |
N3 | C4 | O4 | 125.7° | 123.9° |
N3 | C4 | N5 | 106.1° | 112.4° |
O4 | C4 | N5 | 128.2° | 123.8° |
C4 | N5 | C1' | 113.7° | 106.1° |
C4 | N5 | HN5 | 123.4° | 127.0° |
C1' | N5 | HN5 | 122.9° | 126.9° |
N5 | C1' | C2' | 114.3° | 111.5° |
N5 | C1' | O4' | 112.7° | 111.8° |
C2' | C1' | O4' | 106.4° | 106.2° |
C1' | C2' | O2' | 109.6° | 110.7° |
C1' | C2' | C3' | 106.1° | 103.8° |
C1' | C2' | H2' | 113.8° | 110.6° |
C1' | O4' | C4' | 109.9° | 105.3° |
O2' | C2' | C3' | 115.0° | 110.5° |
O2' | C2' | H2' | 104.6° | 110.5° |
C2' | O2' | HO2' | 109.5° | 106.8° |
C3' | C2' | H2' | 108.1° | 110.6° |
C2' | C3' | O3' | 113.5° | 110.6° |
C2' | C3' | C4' | 99.7° | 104.2° |
C2' | C3' | H3' | 115.1° | 110.5° |
O3' | C3' | C4' | 114.2° | 110.6° |
O3' | C3' | H3' | 100.8° | 110.4° |
C3' | O3' | HO3' | 113.5° | 106.9° |
C4' | C3' | H3' | 114.3° | 110.5° |
C3' | C4' | O4' | 106.0° | 105.0° |
C3' | C4' | C5' | 112.3° | 110.6° |
C3' | C4' | H4' | 111.5° | 110.2° |
O4' | C4' | C5' | 113.6° | 110.3° |
O4' | C4' | H4' | 110.1° | 110.3° |
C5' | C4' | H4' | 103.5° | 110.3° |
C4' | C5' | O5' | 114.9° | 109.5° |
C4' | C5' | H5'1 | 110.2° | 109.5° |
C4' | C5' | H5'2 | 110.2° | 109.5° |
O5' | C5' | H5'1 | 110.3° | 109.4° |
O5' | C5' | H5'2 | 110.3° | 109.5° |
C5' | O5' | P | 122.7° | 106.8° |
H5'1 | C5' | H5'2 | 100.0° | 109.5° |
O5' | P | O1P | 99.4° | 109.5° |
O5' | P | O2P | 104.9° | 109.5° |
O5' | P | O3P | 104.0° | 109.5° |
O1P | P | O2P | 111.5° | 109.5° |
O1P | P | O3P | 110.0° | 109.5° |
O2P | P | O3P | 123.7° | 109.5° |
P | O2P | HOP2 | 104.8° | 106.8° |
P | O3P | HOP3 | 104.1° | 106.8° |
Dihedrals
First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
O2 | C2 | N3 | C1' | 171.2° | 180.0° |
O2 | C2 | N3 | C4 | 169.7° | 180.0° |
O2 | C2 | N3 | HN3 | 10.3° | 0.1° |
O2 | C2 | C1' | N5 | 170.7° | 180.0° |
O2 | C2 | C1' | C2' | 67.5° | 59.4° |
O2 | C2 | C1' | O4' | 50.5° | 59.0° |
C2 | N3 | C4 | HN3 | 180.0° | 179.9° |
C2 | N3 | C4 | O4 | 177.7° | 179.9° |
C2 | N3 | C4 | N5 | 1.2° | 0.1° |
N3 | C2 | C1' | N5 | 1.2° | 0.0° |
N3 | C2 | C1' | C2' | 120.6° | 120.6° |
N3 | C2 | C1' | O4' | 121.5° | 121.0° |
C1' | C2 | N3 | C4 | 1.5° | 0.0° |
C1' | C2 | N3 | HN3 | 178.5° | 179.9° |
C2 | C1' | N5 | C4 | 0.5° | 0.1° |
C2 | C1' | N5 | C2' | 119.3° | 120.5° |
C2 | C1' | N5 | O4' | 119.1° | 120.9° |
C2 | C1' | N5 | HN5 | 179.5° | 180.0° |
C2 | C1' | C2' | O4' | 120.8° | 121.6° |
C2 | C1' | C2' | O2' | 20.2° | 19.8° |
C2 | C1' | C2' | C3' | 104.4° | 98.8° |
C2 | C1' | C2' | H2' | 136.9° | 142.7° |
C2 | C1' | O4' | C4' | 126.7° | 82.5° |
N3 | C4 | O4 | N5 | 178.7° | 179.8° |
N3 | C4 | N5 | C1' | 0.4° | 0.1° |
N3 | C4 | N5 | HN5 | 179.6° | 180.0° |
HN3 | N3 | C4 | O4 | 2.3° | 0.1° |
HN3 | N3 | C4 | N5 | 178.8° | 180.0° |
O4 | C4 | N5 | C1' | 178.5° | 180.0° |
O4 | C4 | N5 | HN5 | 1.5° | 0.2° |
C4 | N5 | C1' | HN5 | 180.0° | 179.9° |
C4 | N5 | C1' | C2' | 118.7° | 120.5° |
C4 | N5 | C1' | O4' | 119.6° | 120.8° |
N5 | C1' | C2' | O4' | 125.1° | 121.9° |
N5 | C1' | C2' | O2' | 93.9° | 96.7° |
N5 | C1' | C2' | C3' | 141.4° | 144.8° |
N5 | C1' | C2' | H2' | 22.7° | 26.2° |
N5 | C1' | O4' | C4' | 119.7° | 160.7° |
HN5 | N5 | C1' | C2' | 61.3° | 59.6° |
HN5 | N5 | C1' | O4' | 60.4° | 59.0° |
C1' | C2' | O2' | C3' | 119.3° | 114.4° |
C1' | C2' | O2' | H2' | 122.3° | 122.9° |
C1' | C2' | C3' | H2' | 122.4° | 118.6° |
C1' | C2' | O2' | HO2' | 180.0° | 175.9° |
C1' | C2' | C3' | O3' | 91.8° | 119.4° |
C1' | C2' | C3' | C4' | 30.0° | 0.5° |
C1' | C2' | C3' | H3' | 152.8° | 118.1° |
C2' | C1' | O4' | C4' | 6.3° | 38.9° |
O4' | C1' | C2' | O2' | 141.0° | 141.4° |
O4' | C1' | C2' | C3' | 16.4° | 22.8° |
O4' | C1' | C2' | H2' | 102.4° | 95.7° |
C1' | O4' | C4' | C3' | 26.2° | 38.9° |
C1' | O4' | C4' | C5' | 97.6° | 158.1° |
C1' | O4' | C4' | H4' | 146.9° | 79.8° |
O2' | C2' | C3' | H2' | 116.4° | 122.7° |
O2' | C2' | C3' | O3' | 29.4° | 0.7° |
O2' | C2' | C3' | C4' | 151.2° | 118.1° |
O2' | C2' | C3' | H3' | 86.0° | 123.2° |
C3' | C2' | O2' | HO2' | 60.7° | 61.5° |
C2' | C3' | O3' | C4' | 113.3° | 114.8° |
C2' | C3' | O3' | H3' | 123.6° | 122.6° |
C2' | C3' | C4' | H3' | 123.3° | 118.7° |
C2' | C3' | O3' | HO3' | 180.0° | 178.1° |
C2' | C3' | C4' | O4' | 34.2° | 23.4° |
C2' | C3' | C4' | C5' | 90.4° | 142.4° |
C2' | C3' | C4' | H4' | 154.0° | 95.3° |
H2' | C2' | O2' | HO2' | 57.7° | 61.2° |
H2' | C2' | C3' | O3' | 145.8° | 122.0° |
H2' | C2' | C3' | C4' | 92.4° | 119.1° |
H2' | C2' | C3' | H3' | 30.4° | 0.5° |
O3' | C3' | C4' | H3' | 115.4° | 122.5° |
O3' | C3' | C4' | O4' | 87.1° | 142.2° |
O3' | C3' | C4' | C5' | 148.3° | 98.8° |
O3' | C3' | C4' | H4' | 32.7° | 23.5° |
C4' | C3' | O3' | HO3' | 66.7° | 63.2° |
C3' | C4' | O4' | C5' | 123.7° | 119.2° |
C3' | C4' | O4' | H4' | 120.7° | 118.7° |
C3' | C4' | C5' | H4' | 120.4° | 122.2° |
C3' | C4' | C5' | O5' | 46.3° | 177.1° |
C3' | C4' | C5' | H5'1 | 79.0° | 62.9° |
C3' | C4' | C5' | H5'2 | 171.5° | 57.1° |
H3' | C3' | O3' | HO3' | 56.4° | 59.3° |
H3' | C3' | C4' | O4' | 157.5° | 95.3° |
H3' | C3' | C4' | C5' | 32.9° | 23.7° |
H3' | C3' | C4' | H4' | 82.7° | 146.0° |
O4' | C4' | C5' | H4' | 119.4° | 122.1° |
O4' | C4' | C5' | O5' | 73.9° | 61.4° |
O4' | C4' | C5' | H5'1 | 160.8° | 178.6° |
O4' | C4' | C5' | H5'2 | 51.3° | 58.6° |
C4' | C5' | O5' | H5'1 | 125.3° | 120.0° |
C4' | C5' | O5' | H5'2 | 125.3° | 120.0° |
C4' | C5' | H5'1 | H5'2 | 116.0° | 120.0° |
C4' | C5' | O5' | P | 123.4° | 180.0° |
H4' | C4' | C5' | O5' | 166.7° | 60.7° |
H4' | C4' | C5' | H5'1 | 41.4° | 59.3° |
H4' | C4' | C5' | H5'2 | 68.1° | 179.3° |
O5' | C5' | H5'1 | H5'2 | 116.1° | 119.9° |
C5' | O5' | P | O1P | 166.1° | 60.0° |
C5' | O5' | P | O2P | 78.6° | 180.0° |
C5' | O5' | P | O3P | 52.6° | 60.0° |
H5'1 | C5' | O5' | P | 111.3° | 60.0° |
H5'2 | C5' | O5' | P | 1.8° | 59.9° |
O5' | P | O1P | O2P | 110.2° | 120.0° |
O5' | P | O1P | O3P | 108.8° | 120.0° |
O5' | P | O2P | O3P | 118.6° | 120.0° |
O5' | P | O2P | HOP2 | 180.0° | 180.0° |
O5' | P | O3P | HOP3 | 180.0° | 60.0° |
O1P | P | O2P | O3P | 134.7° | 120.0° |
O1P | P | O2P | HOP2 | 73.4° | 60.0° |
O1P | P | O3P | HOP3 | 74.3° | 180.0° |
O2P | P | O3P | HOP3 | 61.0° | 60.0° |
O3P | P | O2P | HOP2 | 61.4° | 60.0° |