TD8
Bonds
First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
S1 | C2 | sing | 1.71Å | 1.74Å | Aromatic |
S1 | C5 | sing | 1.76Å | 1.72Å | Aromatic |
C2 | N3 | doub | 1.29Å | 1.37Å | Aromatic |
C2 | C8 | sing | 1.51Å | 1.50Å | |
N3 | C4 | sing | 1.32Å | 1.38Å | Aromatic |
N3 | C35 | sing | 1.46Å | 1.49Å | |
C4 | C5 | doub | 1.34Å | 1.49Å | Aromatic |
C4 | C4A | sing | 1.51Å | 1.51Å | |
C5 | C5A | sing | 1.51Å | 1.52Å | |
C8 | C9 | sing | 1.53Å | 1.51Å | |
C8 | O9 | sing | 1.43Å | 1.34Å | |
C9 | C10 | sing | 1.53Å | 1.51Å | |
PA | O1A | doub | 1.48Å | 1.52Å | |
PA | O2A | sing | 1.61Å | 1.54Å | |
PA | O3A | sing | 1.61Å | 1.63Å | |
PA | O5G | sing | 1.61Å | 1.62Å | |
PB | O1B | sing | 1.61Å | 1.50Å | |
PB | O2B | doub | 1.48Å | 1.50Å | |
PB | O3A | sing | 1.61Å | 1.65Å | |
PB | O3B | sing | 1.61Å | 1.53Å | |
N1' | C2' | doub | 1.32Å | 1.35Å | Aromatic |
N1' | C6' | sing | 1.33Å | 1.34Å | Aromatic |
C10 | C12 | sing | 1.53Å | 1.52Å | |
O11 | C14 | sing | 1.34Å | 1.26Å | |
C12 | C14 | sing | 1.51Å | 1.52Å | |
O12 | C14 | doub | 1.21Å | 1.26Å | |
C2' | C2A | sing | 1.51Å | 1.49Å | |
C2' | N3' | sing | 1.32Å | 1.35Å | Aromatic |
N3' | C4' | doub | 1.33Å | 1.36Å | Aromatic |
C35 | C5' | sing | 1.51Å | 1.54Å | |
C4' | N4' | sing | 1.39Å | 1.34Å | |
C4' | C5' | sing | 1.40Å | 1.40Å | Aromatic |
C5' | C6' | doub | 1.38Å | 1.39Å | Aromatic |
C5A | C5B | sing | 1.53Å | 1.53Å | |
C5B | O5G | sing | 1.43Å | 1.44Å | |
C8 | H8 | sing | 1.09Å | 1.10Å | |
C9 | H9 | sing | 1.09Å | 1.10Å | |
C9 | H9A | sing | 1.09Å | 1.10Å | |
O9 | HO9 | sing | 0.97Å | 0.95Å | |
C10 | H10 | sing | 1.09Å | 1.10Å | |
C10 | H10A | sing | 1.09Å | 1.10Å | |
C12 | H12 | sing | 1.09Å | 1.10Å | |
C12 | H12A | sing | 1.09Å | 1.10Å | |
C2A | H2A | sing | 1.09Å | 1.10Å | |
C2A | H2AA | sing | 1.09Å | 1.10Å | |
C2A | H2AB | sing | 1.09Å | 1.10Å | |
C35 | H35 | sing | 1.09Å | 1.10Å | |
C35 | H35A | sing | 1.09Å | 1.10Å | |
N4' | HN4' | sing | 0.97Å | 1.00Å | |
N4' | HN4A | sing | 0.97Å | 1.00Å | |
C4A | H4A | sing | 1.09Å | 1.10Å | |
C4A | H4AA | sing | 1.09Å | 1.10Å | |
C4A | H4AB | sing | 1.09Å | 1.10Å | |
C5A | H5A | sing | 1.09Å | 1.10Å | |
C5A | H5AA | sing | 1.09Å | 1.10Å | |
C5B | H5B | sing | 1.09Å | 1.10Å | |
C5B | H5BA | sing | 1.09Å | 1.10Å | |
C6' | H6' | sing | 1.08Å | 1.08Å | |
O11 | HO11 | sing | 0.97Å | 0.95Å | |
O1B | HO1B | sing | 0.97Å | 0.95Å | |
O2A | HO2A | sing | 0.97Å | 0.95Å | |
O3B | HO3B | sing | 0.97Å | 0.95Å |
Angles
First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
C2 | S1 | C5 | 93.8° | 90.3° |
S1 | C2 | N3 | 111.8° | 110.2° |
S1 | C2 | C8 | 111.2° | 124.9° |
S1 | C5 | C4 | 107.4° | 108.0° |
S1 | C5 | C5A | 117.2° | 126.0° |
N3 | C2 | C8 | 130.9° | 124.9° |
C2 | N3 | C4 | 113.8° | 117.1° |
C2 | N3 | C35 | 121.6° | 121.5° |
C2 | C8 | C9 | 113.1° | 109.5° |
C2 | C8 | O9 | 118.4° | 109.5° |
C2 | C8 | H8 | 101.6° | 109.5° |
C4 | N3 | C35 | 124.6° | 121.5° |
N3 | C4 | C5 | 113.2° | 114.5° |
N3 | C4 | C4A | 125.8° | 122.7° |
N3 | C35 | C5' | 112.1° | 109.5° |
N3 | C35 | H35 | 108.8° | 109.4° |
N3 | C35 | H35A | 108.8° | 109.4° |
C5 | C4 | C4A | 121.0° | 122.8° |
C4 | C5 | C5A | 135.4° | 126.0° |
C4 | C4A | H4A | 109.5° | 109.4° |
C4 | C4A | H4AA | 109.4° | 109.5° |
C4 | C4A | H4AB | 109.4° | 109.4° |
C5 | C5A | C5B | 107.2° | 109.4° |
C5 | C5A | H5A | 110.0° | 109.5° |
C5 | C5A | H5AA | 110.0° | 109.4° |
C9 | C8 | O9 | 115.8° | 109.5° |
C8 | C9 | C10 | 110.6° | 109.5° |
C9 | C8 | H8 | 101.5° | 109.5° |
C8 | C9 | H9 | 109.2° | 109.5° |
C8 | C9 | H9A | 109.2° | 109.5° |
O9 | C8 | H8 | 103.0° | 109.5° |
C8 | O9 | HO9 | 109.5° | 114.0° |
C9 | C10 | C12 | 113.2° | 109.5° |
C10 | C9 | H9 | 109.2° | 109.5° |
C10 | C9 | H9A | 109.2° | 109.5° |
C9 | C10 | H10 | 108.5° | 109.4° |
C9 | C10 | H10A | 108.5° | 109.5° |
O1A | PA | O2A | 118.5° | 109.5° |
O1A | PA | O3A | 109.5° | 109.5° |
O1A | PA | O5G | 104.3° | 109.5° |
O2A | PA | O3A | 110.4° | 109.5° |
O2A | PA | O5G | 107.4° | 109.5° |
PA | O2A | HO2A | 109.5° | 114.0° |
O3A | PA | O5G | 105.9° | 109.5° |
PA | O3A | PB | 128.9° | 134.0° |
PA | O5G | C5B | 116.5° | 123.0° |
O1B | PB | O2B | 113.6° | 109.5° |
O1B | PB | O3A | 108.3° | 109.5° |
O1B | PB | O3B | 110.3° | 109.5° |
PB | O1B | HO1B | 109.5° | 114.0° |
O2B | PB | O3A | 102.9° | 109.5° |
O2B | PB | O3B | 116.3° | 109.5° |
O3A | PB | O3B | 104.5° | 109.4° |
PB | O3B | HO3B | 109.5° | 114.0° |
C2' | N1' | C6' | 121.3° | 121.0° |
N1' | C2' | C2A | 121.2° | 119.0° |
N1' | C2' | N3' | 119.5° | 121.9° |
N1' | C6' | C5' | 121.2° | 119.2° |
N1' | C6' | H6' | 119.4° | 120.4° |
C10 | C12 | C14 | 117.2° | 109.5° |
C12 | C10 | H10 | 108.5° | 109.5° |
C12 | C10 | H10A | 108.5° | 109.5° |
C10 | C12 | H12 | 107.5° | 109.5° |
C10 | C12 | H12A | 107.5° | 109.5° |
O11 | C14 | C12 | 120.4° | 120.0° |
O11 | C14 | O12 | 123.4° | 120.0° |
C14 | O11 | HO11 | 109.5° | 117.0° |
C12 | C14 | O12 | 116.1° | 120.0° |
C14 | C12 | H12 | 107.5° | 109.5° |
C14 | C12 | H12A | 107.5° | 109.5° |
C2A | C2' | N3' | 119.3° | 119.1° |
C2' | C2A | H2A | 109.5° | 109.5° |
C2' | C2A | H2AA | 109.5° | 109.4° |
C2' | C2A | H2AB | 109.5° | 109.5° |
C2' | N3' | C4' | 121.0° | 120.6° |
N3' | C4' | N4' | 115.6° | 120.5° |
N3' | C4' | C5' | 120.7° | 119.0° |
C35 | C5' | C4' | 124.9° | 120.9° |
C35 | C5' | C6' | 118.9° | 120.8° |
C5' | C35 | H35 | 108.8° | 109.5° |
C5' | C35 | H35A | 108.8° | 109.5° |
N4' | C4' | C5' | 123.7° | 120.5° |
C4' | N4' | HN4' | 109.5° | 120.0° |
C4' | N4' | HN4A | 109.5° | 120.0° |
C4' | C5' | C6' | 116.2° | 118.3° |
C5' | C6' | H6' | 119.4° | 120.4° |
C5A | C5B | O5G | 115.6° | 109.5° |
C5B | C5A | H5A | 110.1° | 109.5° |
C5B | C5A | H5AA | 110.1° | 109.5° |
C5A | C5B | H5B | 107.9° | 109.5° |
C5A | C5B | H5BA | 107.9° | 109.5° |
O5G | C5B | H5B | 107.9° | 109.4° |
O5G | C5B | H5BA | 107.9° | 109.4° |
H9 | C9 | H9A | 109.5° | 109.5° |
H10 | C10 | H10A | 109.4° | 109.5° |
H12 | C12 | H12A | 109.5° | 109.5° |
H2A | C2A | H2AA | 109.4° | 109.5° |
H2A | C2A | H2AB | 109.5° | 109.5° |
H2AA | C2A | H2AB | 109.5° | 109.5° |
H35 | C35 | H35A | 109.5° | 109.5° |
HN4' | N4' | HN4A | 109.5° | 119.9° |
H4A | C4A | H4AA | 109.5° | 109.5° |
H4A | C4A | H4AB | 109.5° | 109.5° |
H4AA | C4A | H4AB | 109.5° | 109.5° |
H5A | C5A | H5AA | 109.5° | 109.5° |
H5B | C5B | H5BA | 109.5° | 109.5° |
Dihedrals
First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
S1 | C2 | N3 | C8 | 149.5° | 180.0° |
S1 | C2 | N3 | C4 | 0.5° | 0.0° |
S1 | C2 | N3 | C35 | 177.0° | 180.0° |
C2 | S1 | C5 | C4 | 2.1° | 0.0° |
C2 | S1 | C5 | C5A | 179.4° | 180.0° |
S1 | C2 | C8 | C9 | 69.6° | 75.0° |
S1 | C2 | C8 | O9 | 150.2° | 45.0° |
S1 | C2 | C8 | H8 | 38.4° | 165.0° |
C5 | S1 | C2 | N3 | 1.0° | 0.0° |
C5 | S1 | C2 | C8 | 154.7° | 180.0° |
S1 | C5 | C4 | N3 | 2.8° | 0.0° |
S1 | C5 | C4 | C5A | 176.7° | 180.0° |
S1 | C5 | C4 | C4A | 179.8° | 180.0° |
S1 | C5 | C5A | C5B | 59.8° | 90.0° |
S1 | C5 | C5A | H5A | 59.9° | 30.0° |
S1 | C5 | C5A | H5AA | 179.4° | 150.0° |
C2 | N3 | C4 | C35 | 176.3° | 180.0° |
C2 | N3 | C4 | C5 | 2.1° | 0.0° |
C2 | N3 | C4 | C4A | 179.1° | 180.0° |
N3 | C2 | C8 | C9 | 140.8° | 105.1° |
N3 | C2 | C8 | O9 | 0.6° | 135.0° |
C2 | N3 | C35 | C5' | 91.5° | 92.1° |
N3 | C2 | C8 | H8 | 111.2° | 14.9° |
C2 | N3 | C35 | H35 | 148.1° | 147.9° |
C2 | N3 | C35 | H35A | 28.9° | 28.0° |
C8 | C2 | N3 | C4 | 150.0° | 180.0° |
C8 | C2 | N3 | C35 | 33.6° | 0.0° |
C2 | C8 | C9 | O9 | 141.3° | 120.0° |
C2 | C8 | C9 | H8 | 108.0° | 120.0° |
C2 | C8 | O9 | H8 | 111.1° | 120.0° |
C2 | C8 | C9 | C10 | 117.9° | 175.0° |
C2 | C8 | C9 | H9 | 2.2° | 55.0° |
C2 | C8 | C9 | H9A | 121.9° | 65.0° |
C2 | C8 | O9 | HO9 | 180.0° | 60.0° |
N3 | C4 | C5 | C4A | 177.1° | 180.0° |
N3 | C4 | C5 | C5A | 179.4° | 180.0° |
C4 | N3 | C35 | C5' | 84.6° | 87.9° |
C4 | N3 | C35 | H35 | 35.8° | 32.0° |
C4 | N3 | C35 | H35A | 155.0° | 152.0° |
N3 | C4 | C4A | H4A | 91.8° | 89.7° |
N3 | C4 | C4A | H4AA | 148.2° | 150.3° |
N3 | C4 | C4A | H4AB | 28.2° | 30.3° |
C35 | N3 | C4 | C5 | 178.5° | 180.0° |
C35 | N3 | C4 | C4A | 4.6° | 0.0° |
N3 | C35 | C5' | H35 | 120.4° | 120.0° |
N3 | C35 | C5' | H35A | 120.4° | 120.0° |
N3 | C35 | C5' | C4' | 68.9° | 175.7° |
N3 | C35 | C5' | C6' | 111.0° | 4.4° |
N3 | C35 | H35 | H35A | 118.8° | 120.0° |
C4 | C5 | C5A | C5B | 116.7° | 90.0° |
C5 | C4 | C4A | H4A | 91.5° | 90.3° |
C5 | C4 | C4A | H4AA | 28.5° | 29.7° |
C5 | C4 | C4A | H4AB | 148.5° | 149.7° |
C4 | C5 | C5A | H5A | 123.7° | 150.0° |
C4 | C5 | C5A | H5AA | 3.0° | 29.9° |
C4A | C4 | C5 | C5A | 3.5° | 0.0° |
C4 | C4A | H4A | H4AA | 120.0° | 120.0° |
C4 | C4A | H4A | H4AB | 120.0° | 120.0° |
C4 | C4A | H4AA | H4AB | 120.0° | 120.0° |
C5 | C5A | C5B | H5A | 119.6° | 120.0° |
C5 | C5A | C5B | H5AA | 119.6° | 119.9° |
C5 | C5A | C5B | O5G | 151.0° | 180.0° |
C5 | C5A | H5A | H5AA | 121.0° | 120.0° |
C5 | C5A | C5B | H5B | 30.1° | 60.0° |
C5 | C5A | C5B | H5BA | 88.2° | 60.0° |
C9 | C8 | O9 | H8 | 109.8° | 120.0° |
C8 | C9 | C10 | H9 | 120.2° | 120.0° |
C8 | C9 | C10 | H9A | 120.2° | 120.0° |
C8 | C9 | C10 | C12 | 95.8° | 180.0° |
C8 | C9 | H9 | H9A | 119.5° | 120.0° |
C9 | C8 | O9 | HO9 | 40.8° | 60.0° |
C8 | C9 | C10 | H10 | 24.8° | 60.0° |
C8 | C9 | C10 | H10A | 143.6° | 60.0° |
O9 | C8 | C9 | C10 | 100.7° | 65.0° |
O9 | C8 | C9 | H9 | 139.1° | 175.0° |
O9 | C8 | C9 | H9A | 19.4° | 55.0° |
C9 | C10 | C12 | H10 | 120.6° | 119.9° |
C9 | C10 | C12 | H10A | 120.6° | 120.0° |
C9 | C10 | C12 | C14 | 54.2° | 180.0° |
C10 | C9 | C8 | H8 | 9.9° | 55.0° |
C10 | C9 | H9 | H9A | 119.5° | 120.0° |
C9 | C10 | H10 | H10A | 118.2° | 120.0° |
C9 | C10 | C12 | H12 | 66.9° | 60.0° |
C9 | C10 | C12 | H12A | 175.3° | 60.0° |
O1A | PA | O2A | O3A | 127.3° | 120.0° |
O1A | PA | O2A | O5G | 117.7° | 120.0° |
O1A | PA | O3A | O5G | 111.9° | 120.0° |
O1A | PA | O3A | PB | 23.0° | 45.0° |
O1A | PA | O5G | C5B | 146.2° | 55.0° |
O1A | PA | O2A | HO2A | 0.0° | 180.0° |
O2A | PA | O3A | O5G | 116.0° | 120.0° |
O2A | PA | O3A | PB | 155.2° | 75.0° |
O2A | PA | O5G | C5B | 87.2° | 65.0° |
PA | O3A | PB | O1B | 11.6° | 75.0° |
PA | O3A | PB | O2B | 109.0° | 45.0° |
PA | O3A | PB | O3B | 129.2° | 165.0° |
O3A | PA | O5G | C5B | 30.7° | 175.0° |
O3A | PA | O2A | HO2A | 127.3° | 60.0° |
O5G | PA | O3A | PB | 88.9° | 165.0° |
PA | O5G | C5B | C5A | 160.1° | 180.0° |
PA | O5G | C5B | H5B | 79.0° | 60.0° |
PA | O5G | C5B | H5BA | 39.2° | 60.0° |
O5G | PA | O2A | HO2A | 117.8° | 60.0° |
O1B | PB | O2B | O3A | 116.9° | 120.0° |
O1B | PB | O2B | O3B | 129.6° | 120.0° |
O1B | PB | O3A | O3B | 117.6° | 120.0° |
O1B | PB | O3B | HO3B | 131.3° | 60.0° |
O2B | PB | O3A | O3B | 121.8° | 120.0° |
O2B | PB | O1B | HO1B | 0.0° | 180.0° |
O2B | PB | O3B | HO3B | 0.0° | 60.0° |
O3A | PB | O1B | HO1B | 113.7° | 60.0° |
O3A | PB | O3B | HO3B | 112.5° | 180.0° |
O3B | PB | O1B | HO1B | 132.6° | 60.0° |
N1' | C2' | C2A | N3' | 180.0° | 180.0° |
N1' | C2' | N3' | C4' | 0.1° | 0.1° |
C2' | N1' | C6' | C5' | 1.9° | 0.1° |
N1' | C2' | C2A | H2A | 0.0° | 90.0° |
N1' | C2' | C2A | H2AA | 120.0° | 150.0° |
N1' | C2' | C2A | H2AB | 120.0° | 30.0° |
C2' | N1' | C6' | H6' | 178.1° | 180.0° |
C6' | N1' | C2' | C2A | 177.8° | 179.9° |
C6' | N1' | C2' | N3' | 2.1° | 0.1° |
N1' | C6' | C5' | C35 | 179.5° | 180.0° |
N1' | C6' | C5' | C4' | 0.4° | 0.1° |
N1' | C6' | C5' | H6' | 180.0° | 179.9° |
C10 | C12 | C14 | O11 | 46.0° | 180.0° |
C10 | C12 | C14 | H12 | 121.1° | 120.0° |
C10 | C12 | C14 | H12A | 121.1° | 120.0° |
C10 | C12 | C14 | O12 | 136.1° | 0.0° |
C12 | C10 | C9 | H9 | 144.0° | 60.0° |
C12 | C10 | C9 | H9A | 24.3° | 60.0° |
C12 | C10 | H10 | H10A | 118.3° | 120.0° |
C10 | C12 | H12 | H12A | 116.5° | 120.0° |
O11 | C14 | C12 | O12 | 178.0° | 179.9° |
O11 | C14 | C12 | H12 | 167.1° | 60.0° |
O11 | C14 | C12 | H12A | 75.1° | 60.0° |
C14 | C12 | C10 | H10 | 174.8° | 60.0° |
C14 | C12 | C10 | H10A | 66.4° | 60.0° |
C14 | C12 | H12 | H12A | 116.5° | 120.0° |
C12 | C14 | O11 | HO11 | 177.8° | 180.0° |
O12 | C14 | C12 | H12 | 15.0° | 120.0° |
O12 | C14 | C12 | H12A | 102.8° | 120.0° |
O12 | C14 | O11 | HO11 | 0.0° | 0.1° |
C2A | C2' | N3' | C4' | 179.9° | 180.0° |
C2' | C2A | H2A | H2AA | 120.0° | 120.0° |
C2' | C2A | H2A | H2AB | 120.0° | 120.0° |
C2' | C2A | H2AA | H2AB | 120.0° | 120.0° |
C2' | N3' | C4' | N4' | 176.3° | 180.0° |
C2' | N3' | C4' | C5' | 2.2° | 0.1° |
N3' | C2' | C2A | H2A | 180.0° | 90.0° |
N3' | C2' | C2A | H2AA | 60.0° | 30.0° |
N3' | C2' | C2A | H2AB | 60.0° | 150.0° |
N3' | C4' | C5' | C35 | 177.5° | 180.0° |
N3' | C4' | N4' | C5' | 178.4° | 180.0° |
N3' | C4' | C5' | C6' | 2.4° | 0.1° |
N3' | C4' | N4' | HN4' | 0.0° | 5.3° |
N3' | C4' | N4' | HN4A | 120.0° | 174.6° |
C35 | C5' | C4' | N4' | 4.1° | 0.0° |
C35 | C5' | C4' | C6' | 179.9° | 179.9° |
C5' | C35 | H35 | H35A | 118.8° | 120.0° |
C35 | C5' | C6' | H6' | 0.5° | 0.1° |
N4' | C4' | C5' | C6' | 176.0° | 180.0° |
C4' | N4' | HN4' | HN4A | 120.0° | 179.9° |
C4' | C5' | C35 | H35 | 170.7° | 64.3° |
C4' | C5' | C35 | H35A | 51.5° | 55.7° |
C5' | C4' | N4' | HN4' | 178.5° | 174.6° |
C5' | C4' | N4' | HN4A | 58.4° | 5.5° |
C4' | C5' | C6' | H6' | 179.6° | 180.0° |
C6' | C5' | C35 | H35 | 9.4° | 115.6° |
C6' | C5' | C35 | H35A | 128.6° | 124.4° |
C5A | C5B | O5G | H5B | 120.9° | 120.0° |
C5A | C5B | O5G | H5BA | 120.9° | 120.0° |
C5B | C5A | H5A | H5AA | 121.1° | 120.0° |
C5A | C5B | H5B | H5BA | 117.2° | 120.1° |
O5G | C5B | C5A | H5A | 89.4° | 60.0° |
O5G | C5B | C5A | H5AA | 31.3° | 60.1° |
O5G | C5B | H5B | H5BA | 117.2° | 119.9° |
H8 | C8 | C9 | H9 | 110.2° | 65.0° |
H8 | C8 | C9 | H9A | 130.1° | 175.0° |
H8 | C8 | O9 | HO9 | 68.9° | 180.0° |
H9 | C9 | C10 | H10 | 95.4° | 180.0° |
H9 | C9 | C10 | H10A | 23.4° | 60.0° |
H9A | C9 | C10 | H10 | 144.9° | 60.0° |
H9A | C9 | C10 | H10A | 96.2° | 180.0° |
H10 | C10 | C12 | H12 | 53.6° | 180.0° |
H10 | C10 | C12 | H12A | 64.1° | 60.0° |
H10A | C10 | C12 | H12 | 172.5° | 60.0° |
H10A | C10 | C12 | H12A | 54.7° | 180.0° |
H2A | C2A | H2AA | H2AB | 120.0° | 120.0° |
H4A | C4A | H4AA | H4AB | 120.0° | 120.1° |
H5A | C5A | C5B | H5B | 149.7° | 180.0° |
H5A | C5A | C5B | H5BA | 31.5° | 60.0° |
H5AA | C5A | C5B | H5B | 89.6° | 59.9° |
H5AA | C5A | C5B | H5BA | 152.2° | 180.0° |