AMO
Bonds
First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
P | O1P | doub | 1.48Å | 1.50Å | |
P | O2P | sing | 1.61Å | 1.49Å | |
P | O3P | sing | 1.61Å | 1.65Å | |
P | O5' | sing | 1.61Å | 1.60Å | |
O2P | HOP2 | sing | 0.97Å | 0.95Å | |
O3P | C | sing | 1.34Å | 1.20Å | |
O5' | C5' | sing | 1.43Å | 1.44Å | |
C5' | C4' | sing | 1.53Å | 1.51Å | |
C5' | H5'1 | sing | 1.09Å | 1.12Å | |
C5' | H5'2 | sing | 1.09Å | 1.12Å | |
C4' | O4' | sing | 1.44Å | 1.45Å | |
C4' | C3' | sing | 1.54Å | 1.52Å | |
C4' | H4' | sing | 1.09Å | 1.11Å | |
O4' | C1' | sing | 1.44Å | 1.41Å | |
C1' | N9 | sing | 1.46Å | 1.46Å | |
C1' | C2' | sing | 1.55Å | 1.53Å | |
C1' | H1' | sing | 1.09Å | 1.12Å | |
N9 | C4 | sing | 1.37Å | 1.37Å | Aromatic |
N9 | C8 | sing | 1.36Å | 1.37Å | Aromatic |
C4 | N3 | sing | 1.33Å | 1.34Å | Aromatic |
C4 | C5 | doub | 1.40Å | 1.38Å | Aromatic |
N3 | C2 | doub | 1.32Å | 1.32Å | Aromatic |
C2 | N1 | sing | 1.32Å | 1.33Å | Aromatic |
C2 | H2 | sing | 1.08Å | 1.10Å | |
N1 | C6 | doub | 1.33Å | 1.35Å | Aromatic |
C6 | N6 | sing | 1.38Å | 1.33Å | |
C6 | C5 | sing | 1.40Å | 1.40Å | Aromatic |
N6 | H61 | sing | 0.97Å | 1.02Å | |
N6 | H62 | sing | 0.97Å | 1.02Å | |
C5 | N7 | sing | 1.36Å | 1.39Å | Aromatic |
N7 | C8 | doub | 1.30Å | 1.31Å | Aromatic |
C8 | H8 | sing | 1.08Å | 1.10Å | |
C2' | C3' | sing | 1.55Å | 1.53Å | |
C2' | O2' | sing | 1.43Å | 1.41Å | |
C2' | H2'2 | sing | 1.09Å | 1.11Å | |
C3' | O3' | sing | 1.43Å | 1.42Å | |
C3' | H3' | sing | 1.09Å | 1.11Å | |
O3' | HO'3 | sing | 0.97Å | 0.95Å | |
N | CA | sing | 1.47Å | 1.49Å | |
N | H | sing | 1.01Å | 1.02Å | |
N | HN2 | sing | 1.01Å | 1.02Å | |
CA | CB | sing | 1.53Å | 1.53Å | |
CA | C | sing | 1.51Å | 1.52Å | |
CA | HA | sing | 1.09Å | 1.11Å | |
CB | CG | sing | 1.51Å | 1.52Å | |
CB | HB1 | sing | 1.09Å | 1.12Å | |
CB | HB2 | sing | 1.09Å | 1.11Å | |
CG | OD1 | doub | 1.21Å | 1.25Å | |
CG | OD2 | sing | 1.34Å | 1.24Å | |
OD2 | HD2 | sing | 0.97Å | 0.95Å | |
C | O | doub | 1.21Å | 1.23Å | |
O2' | H2'1 | sing | 0.97Å | 0.95Å |
Angles
First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
O1P | P | O2P | 119.4° | 109.5° |
O1P | P | O3P | 104.4° | 109.4° |
O1P | P | O5' | 107.3° | 109.4° |
O2P | P | O3P | 97.0° | 109.5° |
O2P | P | O5' | 106.0° | 109.5° |
P | O2P | HOP2 | 119.3° | 106.8° |
O3P | P | O5' | 123.7° | 109.5° |
P | O3P | C | 126.6° | 120.0° |
P | O5' | C5' | 121.2° | 106.8° |
O3P | C | CA | 112.6° | 120.0° |
O3P | C | O | 126.7° | 120.0° |
O5' | C5' | C4' | 110.4° | 109.5° |
O5' | C5' | H5'1 | 111.9° | 109.5° |
O5' | C5' | H5'2 | 111.9° | 109.5° |
C4' | C5' | H5'1 | 111.9° | 109.4° |
C4' | C5' | H5'2 | 111.9° | 109.5° |
C5' | C4' | O4' | 109.3° | 109.9° |
C5' | C4' | C3' | 116.2° | 109.9° |
C5' | C4' | H4' | 103.5° | 109.8° |
H5'1 | C5' | H5'2 | 98.5° | 109.5° |
O4' | C4' | C3' | 104.3° | 107.4° |
O4' | C4' | H4' | 115.5° | 109.9° |
C4' | O4' | C1' | 109.4° | 107.0° |
C3' | C4' | H4' | 108.6° | 109.9° |
C4' | C3' | C2' | 102.7° | 104.0° |
C4' | C3' | O3' | 110.8° | 110.8° |
C4' | C3' | H3' | 113.7° | 110.4° |
O4' | C1' | N9 | 109.0° | 110.7° |
O4' | C1' | C2' | 108.3° | 103.5° |
O4' | C1' | H1' | 112.0° | 110.6° |
N9 | C1' | C2' | 113.5° | 110.8° |
N9 | C1' | H1' | 106.7° | 110.5° |
C1' | N9 | C4 | 125.0° | 126.3° |
C1' | N9 | C8 | 128.9° | 126.2° |
C2' | C1' | H1' | 107.4° | 110.6° |
C1' | C2' | C3' | 101.4° | 102.1° |
C1' | C2' | O2' | 108.7° | 110.9° |
C1' | C2' | H2'2 | 116.9° | 110.9° |
C4 | N9 | C8 | 106.0° | 107.4° |
N9 | C4 | N3 | 127.3° | 134.9° |
N9 | C4 | C5 | 105.7° | 106.0° |
N9 | C8 | N7 | 113.7° | 110.0° |
N9 | C8 | H8 | 124.9° | 125.0° |
N3 | C4 | C5 | 127.0° | 119.1° |
C4 | N3 | C2 | 110.7° | 120.6° |
C4 | C5 | C6 | 117.0° | 118.2° |
C4 | C5 | N7 | 110.9° | 107.1° |
N3 | C2 | N1 | 129.0° | 122.5° |
N3 | C2 | H2 | 114.9° | 118.8° |
N1 | C2 | H2 | 116.1° | 118.8° |
C2 | N1 | C6 | 118.9° | 121.2° |
N1 | C6 | N6 | 118.6° | 120.8° |
N1 | C6 | C5 | 117.4° | 118.5° |
N6 | C6 | C5 | 124.0° | 120.8° |
C6 | N6 | H61 | 118.5° | 120.0° |
C6 | N6 | H62 | 108.9° | 120.0° |
C6 | C5 | N7 | 132.1° | 134.7° |
H61 | N6 | H62 | 108.9° | 120.0° |
C5 | N7 | C8 | 103.6° | 109.4° |
N7 | C8 | H8 | 121.3° | 125.0° |
C3' | C2' | O2' | 114.7° | 110.9° |
C3' | C2' | H2'2 | 111.2° | 111.0° |
C2' | C3' | O3' | 111.5° | 110.5° |
C2' | C3' | H3' | 113.1° | 110.5° |
O2' | C2' | H2'2 | 104.2° | 110.8° |
C2' | O2' | H2'1 | 108.7° | 106.8° |
O3' | C3' | H3' | 105.3° | 110.4° |
C3' | O3' | HO'3 | 110.8° | 106.8° |
CA | N | H | 110.9° | 106.7° |
CA | N | HN2 | 111.7° | 106.7° |
N | CA | CB | 110.9° | 109.4° |
N | CA | C | 109.5° | 109.6° |
N | CA | HA | 108.5° | 109.5° |
H | N | HN2 | 111.7° | 106.7° |
CB | CA | C | 109.7° | 109.5° |
CB | CA | HA | 108.4° | 109.4° |
CA | CB | CG | 112.7° | 109.5° |
CA | CB | HB1 | 111.0° | 109.4° |
CA | CB | HB2 | 111.1° | 109.5° |
C | CA | HA | 109.8° | 109.4° |
CA | C | O | 120.7° | 120.0° |
CG | CB | HB1 | 111.0° | 109.4° |
CG | CB | HB2 | 111.0° | 109.5° |
CB | CG | OD1 | 118.6° | 120.0° |
CB | CG | OD2 | 118.5° | 120.0° |
HB1 | CB | HB2 | 99.2° | 109.4° |
OD1 | CG | OD2 | 122.4° | 120.0° |
CG | OD2 | HD2 | 118.4° | 119.9° |
Dihedrals
First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
O1P | P | O2P | O3P | 110.8° | 120.0° |
O1P | P | O2P | O5' | 121.1° | 120.0° |
O1P | P | O3P | O5' | 122.7° | 119.9° |
O1P | P | O2P | HOP2 | 180.0° | 180.0° |
O1P | P | O3P | C | 90.4° | 60.1° |
O1P | P | O5' | C5' | 162.0° | 60.0° |
O2P | P | O3P | O5' | 114.5° | 120.1° |
O2P | P | O3P | C | 146.8° | 59.9° |
O2P | P | O5' | C5' | 33.5° | 60.0° |
O3P | P | O2P | HOP2 | 69.1° | 60.1° |
O3P | P | O5' | C5' | 76.6° | 180.0° |
P | O3P | C | CA | 158.9° | 179.9° |
P | O3P | C | O | 19.0° | 0.1° |
O5' | P | O2P | HOP2 | 59.0° | 60.0° |
O5' | P | O3P | C | 32.3° | 180.0° |
P | O5' | C5' | C4' | 121.5° | 180.0° |
P | O5' | C5' | H5'1 | 3.7° | 60.1° |
P | O5' | C5' | H5'2 | 113.1° | 60.0° |
O3P | C | CA | N | 166.4° | 150.1° |
O3P | C | CA | CB | 71.6° | 90.0° |
O3P | C | CA | O | 178.0° | 180.0° |
O3P | C | CA | HA | 47.3° | 30.0° |
O5' | C5' | C4' | H5'1 | 125.3° | 120.0° |
O5' | C5' | C4' | H5'2 | 125.3° | 120.0° |
O5' | C5' | H5'1 | H5'2 | 117.8° | 120.0° |
O5' | C5' | C4' | O4' | 60.9° | 61.7° |
O5' | C5' | C4' | C3' | 56.7° | 179.7° |
O5' | C5' | C4' | H4' | 175.5° | 59.3° |
C4' | C5' | H5'1 | H5'2 | 117.8° | 120.0° |
C5' | C4' | O4' | C3' | 124.8° | 119.5° |
C5' | C4' | O4' | H4' | 116.1° | 120.9° |
C5' | C4' | C3' | H4' | 116.0° | 121.0° |
C5' | C4' | O4' | C1' | 147.9° | 145.9° |
C5' | C4' | C3' | C2' | 156.4° | 121.4° |
C5' | C4' | C3' | O3' | 84.5° | 119.8° |
C5' | C4' | C3' | H3' | 33.9° | 2.8° |
H5'1 | C5' | C4' | O4' | 173.8° | 58.3° |
H5'1 | C5' | C4' | C3' | 68.6° | 59.7° |
H5'1 | C5' | C4' | H4' | 50.2° | 179.3° |
H5'2 | C5' | C4' | O4' | 64.4° | 178.3° |
H5'2 | C5' | C4' | C3' | 178.0° | 60.3° |
H5'2 | C5' | C4' | H4' | 59.2° | 60.7° |
O4' | C4' | C3' | H4' | 123.7° | 119.5° |
C4' | O4' | C1' | N9 | 124.5° | 158.7° |
C4' | O4' | C1' | C2' | 0.6° | 40.0° |
C4' | O4' | C1' | H1' | 117.6° | 78.4° |
O4' | C4' | C3' | C2' | 36.1° | 1.9° |
O4' | C4' | C3' | O3' | 155.2° | 120.6° |
O4' | C4' | C3' | H3' | 86.4° | 116.7° |
C3' | C4' | O4' | C1' | 23.1° | 26.4° |
C4' | C3' | C2' | C1' | 34.6° | 21.0° |
C4' | C3' | C2' | O3' | 118.6° | 119.0° |
C4' | C3' | C2' | H3' | 122.9° | 118.6° |
C4' | C3' | C2' | O2' | 82.4° | 139.2° |
C4' | C3' | C2' | H2'2 | 159.6° | 97.2° |
C4' | C3' | O3' | H3' | 123.3° | 122.7° |
C4' | C3' | O3' | HO'3 | 180.0° | 176.2° |
H4' | C4' | O4' | C1' | 96.0° | 93.1° |
H4' | C4' | C3' | C2' | 87.5° | 117.6° |
H4' | C4' | C3' | O3' | 31.5° | 1.1° |
H4' | C4' | C3' | H3' | 149.9° | 123.8° |
O4' | C1' | N9 | C2' | 120.8° | 114.2° |
O4' | C1' | N9 | H1' | 121.1° | 122.9° |
O4' | C1' | C2' | H1' | 121.1° | 118.5° |
O4' | C1' | N9 | C4 | 124.8° | 151.7° |
O4' | C1' | N9 | C8 | 54.7° | 28.5° |
O4' | C1' | C2' | C3' | 21.8° | 37.1° |
O4' | C1' | C2' | O2' | 99.4° | 155.2° |
O4' | C1' | C2' | H2'2 | 143.0° | 81.2° |
N9 | C1' | C2' | H1' | 117.7° | 122.9° |
C1' | N9 | C4 | C8 | 179.6° | 179.8° |
C1' | N9 | C4 | N3 | 1.1° | 0.8° |
C1' | N9 | C4 | C5 | 179.4° | 179.8° |
C1' | N9 | C8 | N7 | 179.3° | 180.0° |
C1' | N9 | C8 | H8 | 0.7° | 0.0° |
N9 | C1' | C2' | C3' | 99.3° | 155.7° |
N9 | C1' | C2' | O2' | 139.4° | 86.1° |
N9 | C1' | C2' | H2'2 | 21.8° | 37.5° |
C2' | C1' | N9 | C4 | 114.4° | 94.1° |
C2' | C1' | N9 | C8 | 66.1° | 85.7° |
C1' | C2' | C3' | O2' | 117.0° | 118.2° |
C1' | C2' | C3' | H2'2 | 125.1° | 118.2° |
C1' | C2' | O2' | H2'2 | 125.4° | 123.6° |
C1' | C2' | C3' | O3' | 153.2° | 98.0° |
C1' | C2' | C3' | H3' | 88.4° | 139.5° |
C1' | C2' | O2' | H2'1 | 180.0° | 180.0° |
H1' | C1' | N9 | C4 | 3.7° | 28.9° |
H1' | C1' | N9 | C8 | 175.8° | 151.4° |
H1' | C1' | C2' | C3' | 143.0° | 81.4° |
H1' | C1' | C2' | O2' | 21.7° | 36.8° |
H1' | C1' | C2' | H2'2 | 95.9° | 160.4° |
N9 | C4 | N3 | C5 | 179.3° | 178.9° |
N9 | C4 | N3 | C2 | 179.6° | 179.5° |
N9 | C4 | C5 | C6 | 178.9° | 179.8° |
N9 | C4 | C5 | N7 | 0.0° | 0.4° |
C4 | N9 | C8 | N7 | 0.2° | 0.2° |
C4 | N9 | C8 | H8 | 179.8° | 179.8° |
C8 | N9 | C4 | N3 | 179.3° | 179.4° |
C8 | N9 | C4 | C5 | 0.1° | 0.4° |
N9 | C8 | N7 | C5 | 0.2° | 0.0° |
N9 | C8 | N7 | H8 | 180.0° | 180.0° |
C4 | N3 | C2 | N1 | 0.6° | 0.2° |
C4 | N3 | C2 | H2 | 179.4° | 179.7° |
N3 | C4 | C5 | C6 | 1.7° | 0.6° |
N3 | C4 | C5 | N7 | 179.5° | 179.6° |
C5 | C4 | N3 | C2 | 1.1° | 0.6° |
C4 | C5 | C6 | N1 | 1.6° | 0.3° |
C4 | C5 | C6 | N6 | 179.5° | 179.6° |
C4 | C5 | C6 | N7 | 178.6° | 179.7° |
C4 | C5 | N7 | C8 | 0.1° | 0.3° |
N3 | C2 | N1 | H2 | 180.0° | 180.0° |
N3 | C2 | N1 | C6 | 0.7° | 0.1° |
C2 | N1 | C6 | N6 | 179.9° | 180.0° |
C2 | N1 | C6 | C5 | 1.2° | 0.1° |
H2 | C2 | N1 | C6 | 179.3° | 179.9° |
N1 | C6 | N6 | C5 | 178.9° | 179.9° |
N1 | C6 | N6 | H61 | 180.0° | 0.1° |
N1 | C6 | N6 | H62 | 54.8° | 180.0° |
N1 | C6 | C5 | N7 | 179.8° | 179.9° |
C6 | N6 | H61 | H62 | 125.2° | 179.9° |
N6 | C6 | C5 | N7 | 1.0° | 0.0° |
C5 | C6 | N6 | H61 | 1.2° | 180.0° |
C5 | C6 | N6 | H62 | 126.4° | 0.1° |
C6 | C5 | N7 | C8 | 178.8° | 180.0° |
C5 | N7 | C8 | H8 | 179.8° | 179.9° |
C3' | C2' | O2' | H2'2 | 121.9° | 123.7° |
C2' | C3' | O3' | H3' | 123.0° | 122.5° |
C2' | C3' | O3' | HO'3 | 66.4° | 61.5° |
C3' | C2' | O2' | H2'1 | 67.3° | 67.3° |
O2' | C2' | C3' | O3' | 36.2° | 20.2° |
O2' | C2' | C3' | H3' | 154.7° | 102.3° |
H2'2 | C2' | C3' | O3' | 81.8° | 143.8° |
H2'2 | C2' | C3' | H3' | 36.7° | 21.3° |
H2'2 | C2' | O2' | H2'1 | 54.6° | 56.3° |
H3' | C3' | O3' | HO'3 | 56.7° | 61.1° |
CA | N | H | HN2 | 125.3° | 113.9° |
N | CA | CB | C | 121.1° | 120.1° |
N | CA | CB | HA | 119.0° | 120.0° |
N | CA | C | HA | 119.1° | 120.1° |
N | CA | CB | CG | 72.5° | 60.0° |
N | CA | CB | HB1 | 52.8° | 60.0° |
N | CA | CB | HB2 | 162.2° | 179.9° |
N | CA | C | O | 15.5° | 29.9° |
H | N | CA | CB | 180.0° | 60.0° |
H | N | CA | C | 58.8° | 60.0° |
H | N | CA | HA | 61.1° | 180.0° |
HN2 | N | CA | CB | 54.7° | 53.8° |
HN2 | N | CA | C | 175.9° | 173.8° |
HN2 | N | CA | HA | 64.2° | 66.1° |
CB | CA | C | HA | 119.0° | 119.9° |
CA | CB | CG | HB1 | 125.3° | 120.0° |
CA | CB | CG | HB2 | 125.3° | 120.1° |
CA | CB | HB1 | HB2 | 116.9° | 120.0° |
CA | CB | CG | OD1 | 138.6° | 0.0° |
CA | CB | CG | OD2 | 33.4° | 180.0° |
CB | CA | C | O | 106.4° | 90.1° |
C | CA | CB | CG | 166.4° | 180.0° |
C | CA | CB | HB1 | 68.3° | 60.0° |
C | CA | CB | HB2 | 41.1° | 59.9° |
HA | CA | CB | CG | 46.6° | 60.0° |
HA | CA | CB | HB1 | 171.9° | 180.0° |
HA | CA | CB | HB2 | 78.7° | 60.1° |
HA | CA | C | O | 134.6° | 150.0° |
CG | CB | HB1 | HB2 | 116.9° | 120.0° |
CB | CG | OD1 | OD2 | 171.7° | 180.0° |
CB | CG | OD2 | HD2 | 180.0° | 180.0° |
HB1 | CB | CG | OD1 | 13.3° | 120.0° |
HB1 | CB | CG | OD2 | 158.7° | 60.0° |
HB2 | CB | CG | OD1 | 96.1° | 120.0° |
HB2 | CB | CG | OD2 | 91.9° | 60.0° |
OD1 | CG | OD2 | HD2 | 8.2° | 0.0° |