TD9
Bonds
First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
S1 | C2 | sing | 1.71Å | 1.68Å | Aromatic |
S1 | C5 | sing | 1.76Å | 1.66Å | Aromatic |
C2 | N3 | doub | 1.29Å | 1.46Å | Aromatic |
C2 | C8 | sing | 1.51Å | 1.57Å | |
N3 | C4 | sing | 1.32Å | 1.41Å | Aromatic |
N3 | C35 | sing | 1.47Å | 1.47Å | |
C4 | C5 | doub | 1.34Å | 1.42Å | Aromatic |
C4 | C4A | sing | 1.51Å | 1.49Å | |
C5 | C5A | sing | 1.51Å | 1.51Å | |
C8 | C9 | sing | 1.53Å | 1.53Å | |
C8 | O9 | sing | 1.43Å | 1.43Å | |
C9 | C10 | sing | 1.53Å | 1.52Å | |
PA | O1A | doub | 1.48Å | 1.47Å | |
PA | O2A | sing | 1.61Å | 1.54Å | |
PA | O3A | sing | 1.61Å | 1.55Å | |
PA | O5G | sing | 1.61Å | 1.60Å | |
PB | O1B | sing | 1.61Å | 1.52Å | |
PB | O2B | sing | 1.61Å | 1.52Å | |
PB | O3A | sing | 1.61Å | 1.55Å | |
PB | O3B | doub | 1.48Å | 1.49Å | |
N1' | C2' | doub | 1.32Å | 1.34Å | Aromatic |
N1' | C6' | sing | 1.33Å | 1.34Å | Aromatic |
C10 | C12 | sing | 1.53Å | 1.53Å | |
O11 | C14 | sing | 1.34Å | 1.32Å | |
C12 | C14 | sing | 1.51Å | 1.50Å | |
O12 | C14 | doub | 1.21Å | 1.22Å | |
C2' | C2A | sing | 1.51Å | 1.50Å | |
C2' | N3' | sing | 1.32Å | 1.34Å | Aromatic |
N3' | C4' | doub | 1.33Å | 1.34Å | Aromatic |
C35 | C5' | sing | 1.51Å | 1.51Å | |
C4' | N4' | sing | 1.38Å | 1.34Å | |
C4' | C5' | sing | 1.40Å | 1.43Å | Aromatic |
C5' | C6' | doub | 1.38Å | 1.38Å | Aromatic |
C5A | C5B | sing | 1.53Å | 1.51Å | |
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 | H11 | sing | 0.97Å | 0.95Å | |
O1B | HO1B | sing | 0.97Å | 0.95Å | |
O2A | HO2A | sing | 0.97Å | 0.95Å | |
O2B | HO2B | sing | 0.97Å | 0.95Å |
Angles
First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
C2 | S1 | C5 | 94.7° | 90.3° |
S1 | C2 | N3 | 110.3° | 110.1° |
S1 | C2 | C8 | 126.4° | 125.0° |
S1 | C5 | C4 | 112.0° | 107.9° |
S1 | C5 | C5A | 120.9° | 126.0° |
N3 | C2 | C8 | 122.4° | 124.9° |
C2 | N3 | C4 | 110.8° | 117.1° |
C2 | N3 | C35 | 125.0° | 121.4° |
C2 | C8 | C9 | 112.9° | 109.5° |
C2 | C8 | O9 | 119.0° | 109.5° |
C2 | C8 | H8 | 105.7° | 109.5° |
C4 | N3 | C35 | 124.2° | 121.5° |
N3 | C4 | C5 | 112.1° | 114.5° |
N3 | C4 | C4A | 122.4° | 122.7° |
N3 | C35 | C5' | 114.0° | 109.5° |
N3 | C35 | H35 | 108.3° | 109.4° |
N3 | C35 | H35A | 108.3° | 109.4° |
C5 | C4 | C4A | 125.2° | 122.7° |
C4 | C5 | C5A | 127.0° | 126.1° |
C4 | C4A | H4A | 109.5° | 109.4° |
C4 | C4A | H4AA | 109.4° | 109.5° |
C4 | C4A | H4AB | 109.5° | 109.5° |
C5 | C5A | C5B | 109.1° | 109.5° |
C5 | C5A | H5A | 109.6° | 109.5° |
C5 | C5A | H5AA | 109.6° | 109.5° |
C9 | C8 | O9 | 105.1° | 109.5° |
C8 | C9 | C10 | 116.3° | 109.5° |
C9 | C8 | H8 | 106.1° | 109.5° |
C8 | C9 | H9 | 107.7° | 109.5° |
C8 | C9 | H9A | 107.7° | 109.5° |
O9 | C8 | H8 | 107.3° | 109.4° |
C8 | O9 | HO9 | 109.5° | 114.0° |
C9 | C10 | C12 | 112.8° | 109.5° |
C10 | C9 | H9 | 107.7° | 109.4° |
C10 | C9 | H9A | 107.7° | 109.5° |
C9 | C10 | H10 | 108.6° | 109.4° |
C9 | C10 | H10A | 108.6° | 109.5° |
O1A | PA | O2A | 120.8° | 109.5° |
O1A | PA | O3A | 118.5° | 109.5° |
O1A | PA | O5G | 116.3° | 109.5° |
O2A | PA | O3A | 98.4° | 109.5° |
O2A | PA | O5G | 101.0° | 109.4° |
PA | O2A | HO2A | 109.5° | 114.0° |
O3A | PA | O5G | 97.8° | 109.5° |
PA | O3A | PB | 152.7° | 134.0° |
PA | O5G | C5B | 120.7° | 123.0° |
O1B | PB | O2B | 105.8° | 109.5° |
O1B | PB | O3A | 97.6° | 109.5° |
O1B | PB | O3B | 111.9° | 109.5° |
PB | O1B | HO1B | 109.5° | 114.0° |
O2B | PB | O3A | 106.8° | 109.5° |
O2B | PB | O3B | 119.5° | 109.5° |
PB | O2B | HO2B | 109.5° | 114.0° |
O3A | PB | O3B | 112.8° | 109.5° |
C2' | N1' | C6' | 115.9° | 121.0° |
N1' | C2' | C2A | 117.3° | 119.1° |
N1' | C2' | N3' | 125.8° | 121.9° |
N1' | C6' | C5' | 124.4° | 119.2° |
N1' | C6' | H6' | 117.8° | 120.4° |
C10 | C12 | C14 | 114.9° | 109.5° |
C12 | C10 | H10 | 108.6° | 109.5° |
C12 | C10 | H10A | 108.6° | 109.5° |
C10 | C12 | H12 | 108.1° | 109.4° |
C10 | C12 | H12A | 108.1° | 109.5° |
O11 | C14 | C12 | 113.0° | 120.0° |
O11 | C14 | O12 | 123.5° | 120.0° |
C14 | O11 | H11 | 109.5° | 117.0° |
C12 | C14 | O12 | 123.5° | 120.0° |
C14 | C12 | H12 | 108.1° | 109.5° |
C14 | C12 | H12A | 108.1° | 109.5° |
C2A | C2' | N3' | 116.9° | 119.1° |
C2' | C2A | H2A | 109.5° | 109.5° |
C2' | C2A | H2AA | 109.5° | 109.5° |
C2' | C2A | H2AB | 109.4° | 109.5° |
C2' | N3' | C4' | 117.8° | 120.7° |
N3' | C4' | N4' | 116.4° | 120.6° |
N3' | C4' | C5' | 120.9° | 118.9° |
C35 | C5' | C4' | 126.9° | 120.8° |
C35 | C5' | C6' | 117.9° | 120.9° |
C5' | C35 | H35 | 108.3° | 109.5° |
C5' | C35 | H35A | 108.3° | 109.5° |
N4' | C4' | C5' | 122.3° | 120.5° |
C4' | N4' | HN4' | 109.5° | 120.0° |
C4' | N4' | HN4A | 109.5° | 120.0° |
C4' | C5' | C6' | 115.2° | 118.4° |
C5' | C6' | H6' | 117.8° | 120.4° |
C5A | C5B | O5G | 113.9° | 109.5° |
C5B | C5A | H5A | 109.6° | 109.5° |
C5B | C5A | H5AA | 109.6° | 109.5° |
C5A | C5B | H5B | 108.4° | 109.4° |
C5A | C5B | H5BA | 108.3° | 109.5° |
O5G | C5B | H5B | 108.3° | 109.5° |
O5G | C5B | H5BA | 108.4° | 109.5° |
H9 | C9 | H9A | 109.5° | 109.5° |
H10 | C10 | H10A | 109.5° | 109.5° |
H12 | C12 | H12A | 109.5° | 109.5° |
H2A | C2A | H2AA | 109.5° | 109.5° |
H2A | C2A | H2AB | 109.5° | 109.5° |
H2AA | C2A | H2AB | 109.4° | 109.4° |
H35 | C35 | H35A | 109.5° | 109.5° |
HN4' | N4' | HN4A | 109.5° | 119.9° |
H4A | C4A | H4AA | 109.4° | 109.5° |
H4A | C4A | H4AB | 109.4° | 109.5° |
H4AA | C4A | H4AB | 109.5° | 109.5° |
H5A | C5A | H5AA | 109.5° | 109.4° |
H5B | C5B | H5BA | 109.4° | 109.5° |
Dihedrals
First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
S1 | C2 | N3 | C8 | 169.3° | 179.9° |
S1 | C2 | N3 | C4 | 4.2° | 0.1° |
S1 | C2 | N3 | C35 | 173.7° | 180.0° |
C2 | S1 | C5 | C4 | 1.6° | 0.0° |
C2 | S1 | C5 | C5A | 175.7° | 180.0° |
S1 | C2 | C8 | C9 | 99.3° | 75.0° |
S1 | C2 | C8 | O9 | 136.8° | 45.0° |
S1 | C2 | C8 | H8 | 16.2° | 165.0° |
C5 | S1 | C2 | N3 | 3.3° | 0.0° |
C5 | S1 | C2 | C8 | 165.4° | 180.0° |
S1 | C5 | C4 | N3 | 0.6° | 0.0° |
S1 | C5 | C4 | C5A | 177.1° | 180.0° |
S1 | C5 | C4 | C4A | 173.3° | 180.0° |
S1 | C5 | C5A | C5B | 70.5° | 90.0° |
S1 | C5 | C5A | H5A | 49.4° | 30.1° |
S1 | C5 | C5A | H5AA | 169.5° | 150.0° |
C2 | N3 | C4 | C35 | 177.9° | 179.9° |
C2 | N3 | C4 | C5 | 3.0° | 0.0° |
C2 | N3 | C4 | C4A | 171.1° | 179.9° |
N3 | C2 | C8 | C9 | 68.1° | 104.9° |
N3 | C2 | C8 | O9 | 55.7° | 135.1° |
C2 | N3 | C35 | C5' | 104.7° | 92.3° |
N3 | C2 | C8 | H8 | 176.3° | 15.1° |
C2 | N3 | C35 | H35 | 134.6° | 27.8° |
C2 | N3 | C35 | H35A | 16.0° | 147.7° |
C8 | C2 | N3 | C4 | 165.1° | 180.0° |
C8 | C2 | N3 | C35 | 17.0° | 0.1° |
C2 | C8 | C9 | O9 | 131.2° | 120.0° |
C2 | C8 | C9 | H8 | 115.3° | 120.0° |
C2 | C8 | O9 | H8 | 119.7° | 120.0° |
C2 | C8 | C9 | C10 | 88.2° | 175.0° |
C2 | C8 | C9 | H9 | 150.8° | 65.0° |
C2 | C8 | C9 | H9A | 32.8° | 55.0° |
C2 | C8 | O9 | HO9 | 180.0° | 60.0° |
N3 | C4 | C5 | C4A | 174.0° | 180.0° |
N3 | C4 | C5 | C5A | 177.8° | 180.0° |
C4 | N3 | C35 | C5' | 72.9° | 87.6° |
C4 | N3 | C35 | H35 | 47.8° | 152.3° |
C4 | N3 | C35 | H35A | 166.4° | 32.4° |
N3 | C4 | C4A | H4A | 93.1° | 94.7° |
N3 | C4 | C4A | H4AA | 146.9° | 145.3° |
N3 | C4 | C4A | H4AB | 26.8° | 25.3° |
C35 | N3 | C4 | C5 | 174.9° | 179.9° |
C35 | N3 | C4 | C4A | 11.0° | 0.0° |
N3 | C35 | C5' | H35 | 120.7° | 120.0° |
N3 | C35 | C5' | H35A | 120.7° | 120.0° |
N3 | C35 | C5' | C4' | 62.4° | 174.1° |
N3 | C35 | C5' | C6' | 116.8° | 5.9° |
N3 | C35 | H35 | H35A | 117.9° | 119.9° |
C4 | C5 | C5A | C5B | 112.6° | 90.0° |
C5 | C4 | C4A | H4A | 93.5° | 85.3° |
C5 | C4 | C4A | H4AA | 26.5° | 34.7° |
C5 | C4 | C4A | H4AB | 146.5° | 154.7° |
C4 | C5 | C5A | H5A | 127.5° | 150.0° |
C4 | C5 | C5A | H5AA | 7.4° | 30.0° |
C4A | C4 | C5 | C5A | 3.8° | 0.1° |
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 | 120.0° | 120.0° |
C5 | C5A | C5B | H5AA | 119.9° | 120.0° |
C5 | C5A | C5B | O5G | 167.3° | 180.0° |
C5 | C5A | H5A | H5AA | 120.2° | 120.0° |
C5 | C5A | C5B | H5B | 46.6° | 60.0° |
C5 | C5A | C5B | H5BA | 72.0° | 60.0° |
C9 | C8 | O9 | H8 | 112.7° | 120.0° |
C8 | C9 | C10 | H9 | 121.0° | 120.0° |
C8 | C9 | C10 | H9A | 121.0° | 120.0° |
C8 | C9 | C10 | C12 | 83.7° | 180.0° |
C8 | C9 | H9 | H9A | 116.9° | 120.0° |
C9 | C8 | O9 | HO9 | 52.4° | 60.0° |
C8 | C9 | C10 | H10 | 155.8° | 60.0° |
C8 | C9 | C10 | H10A | 36.7° | 60.0° |
O9 | C8 | C9 | C10 | 140.6° | 65.0° |
O9 | C8 | C9 | H9 | 19.6° | 55.0° |
O9 | C8 | C9 | H9A | 98.4° | 175.0° |
C9 | C10 | C12 | H10 | 120.5° | 119.9° |
C9 | C10 | C12 | H10A | 120.5° | 120.0° |
C9 | C10 | C12 | C14 | 176.2° | 180.0° |
C10 | C9 | C8 | H8 | 27.1° | 55.0° |
C10 | C9 | H9 | H9A | 116.9° | 120.0° |
C9 | C10 | H10 | H10A | 118.5° | 120.0° |
C9 | C10 | C12 | H12 | 63.0° | 60.0° |
C9 | C10 | C12 | H12A | 55.5° | 60.0° |
O1A | PA | O2A | O3A | 130.5° | 120.0° |
O1A | PA | O2A | O5G | 129.8° | 120.0° |
O1A | PA | O3A | O5G | 125.7° | 120.0° |
O1A | PA | O3A | PB | 179.4° | 40.0° |
O1A | PA | O5G | C5B | 64.6° | 55.0° |
O1A | PA | O2A | HO2A | 0.0° | 180.0° |
O2A | PA | O3A | O5G | 102.4° | 120.0° |
O2A | PA | O3A | PB | 48.6° | 80.0° |
O2A | PA | O5G | C5B | 162.8° | 65.0° |
PA | O3A | PB | O1B | 31.6° | 165.0° |
PA | O3A | PB | O2B | 140.8° | 75.0° |
PA | O3A | PB | O3B | 86.0° | 45.0° |
O3A | PA | O5G | C5B | 62.6° | 175.0° |
O3A | PA | O2A | HO2A | 130.5° | 60.0° |
O5G | PA | O3A | PB | 53.8° | 160.0° |
PA | O5G | C5B | C5A | 175.2° | 180.0° |
PA | O5G | C5B | H5B | 64.1° | 60.0° |
PA | O5G | C5B | H5BA | 54.5° | 60.0° |
O5G | PA | O2A | HO2A | 129.9° | 60.0° |
O1B | PB | O2B | O3A | 103.3° | 120.0° |
O1B | PB | O2B | O3B | 127.3° | 120.0° |
O1B | PB | O3A | O3B | 117.6° | 120.0° |
O1B | PB | O2B | HO2B | 127.3° | 60.0° |
O2B | PB | O3A | O3B | 133.2° | 120.0° |
O2B | PB | O1B | HO1B | 131.7° | 60.0° |
O3A | PB | O1B | HO1B | 118.3° | 180.0° |
O3A | PB | O2B | HO2B | 129.4° | 60.0° |
O3B | PB | O1B | HO1B | 0.0° | 60.0° |
O3B | PB | O2B | HO2B | 0.0° | 180.0° |
N1' | C2' | C2A | N3' | 178.6° | 180.0° |
N1' | C2' | N3' | C4' | 1.7° | 0.0° |
C2' | N1' | C6' | C5' | 1.3° | 0.1° |
N1' | C2' | C2A | H2A | 0.0° | 90.0° |
N1' | C2' | C2A | H2AA | 120.0° | 149.9° |
N1' | C2' | C2A | H2AB | 120.0° | 30.0° |
C2' | N1' | C6' | H6' | 178.7° | 180.0° |
C6' | N1' | C2' | C2A | 179.3° | 180.0° |
C6' | N1' | C2' | N3' | 0.8° | 0.1° |
N1' | C6' | C5' | C35 | 178.7° | 180.0° |
N1' | C6' | C5' | C4' | 0.7° | 0.1° |
N1' | C6' | C5' | H6' | 180.0° | 179.9° |
C10 | C12 | C14 | O11 | 131.9° | 180.0° |
C10 | C12 | C14 | H12 | 120.8° | 120.0° |
C10 | C12 | C14 | H12A | 120.8° | 120.0° |
C10 | C12 | C14 | O12 | 48.8° | 0.0° |
C12 | C10 | C9 | H9 | 37.2° | 60.0° |
C12 | C10 | C9 | H9A | 155.2° | 60.0° |
C12 | C10 | H10 | H10A | 118.4° | 120.0° |
C10 | C12 | H12 | H12A | 117.5° | 120.0° |
O11 | C14 | C12 | O12 | 179.3° | 179.9° |
O11 | C14 | C12 | H12 | 107.3° | 60.0° |
O11 | C14 | C12 | H12A | 11.1° | 60.0° |
C14 | C12 | C10 | H10 | 55.7° | 60.0° |
C14 | C12 | C10 | H10A | 63.3° | 60.0° |
C14 | C12 | H12 | H12A | 117.5° | 120.0° |
C12 | C14 | O11 | H11 | 179.4° | 180.0° |
O12 | C14 | C12 | H12 | 72.0° | 119.9° |
O12 | C14 | C12 | H12A | 169.6° | 120.1° |
O12 | C14 | O11 | H11 | 0.0° | 0.0° |
C2A | C2' | N3' | C4' | 176.8° | 180.0° |
C2' | C2A | H2A | H2AA | 120.0° | 120.1° |
C2' | C2A | H2A | H2AB | 120.0° | 120.0° |
C2' | C2A | H2AA | H2AB | 119.9° | 120.0° |
C2' | N3' | C4' | N4' | 169.0° | 180.0° |
C2' | N3' | C4' | C5' | 3.8° | 0.0° |
N3' | C2' | C2A | H2A | 178.6° | 90.0° |
N3' | C2' | C2A | H2AA | 58.6° | 30.0° |
N3' | C2' | C2A | H2AB | 61.4° | 150.0° |
N3' | C4' | C5' | C35 | 176.0° | 180.0° |
N3' | C4' | N4' | C5' | 172.7° | 180.0° |
N3' | C4' | C5' | C6' | 3.3° | 0.0° |
N3' | C4' | N4' | HN4' | 0.0° | 5.2° |
N3' | C4' | N4' | HN4A | 120.0° | 174.8° |
C35 | C5' | C4' | N4' | 11.6° | 0.0° |
C35 | C5' | C4' | C6' | 179.3° | 180.0° |
C5' | C35 | H35 | H35A | 118.0° | 120.1° |
C35 | C5' | C6' | H6' | 1.3° | 0.1° |
N4' | C4' | C5' | C6' | 169.1° | 179.9° |
C4' | N4' | HN4' | HN4A | 120.0° | 180.0° |
C4' | C5' | C35 | H35 | 176.9° | 65.9° |
C4' | C5' | C35 | H35A | 58.2° | 54.1° |
C5' | C4' | N4' | HN4' | 172.7° | 174.8° |
C5' | C4' | N4' | HN4A | 52.6° | 5.1° |
C4' | C5' | C6' | H6' | 179.3° | 180.0° |
C6' | C5' | C35 | H35 | 3.8° | 114.1° |
C6' | C5' | C35 | H35A | 122.5° | 125.9° |
C5A | C5B | O5G | H5B | 120.7° | 119.9° |
C5A | C5B | O5G | H5BA | 120.7° | 120.0° |
C5B | C5A | H5A | H5AA | 120.2° | 120.0° |
C5A | C5B | H5B | H5BA | 118.0° | 120.0° |
O5G | C5B | C5A | H5A | 72.8° | 60.0° |
O5G | C5B | C5A | H5AA | 47.4° | 60.0° |
O5G | C5B | H5B | H5BA | 118.0° | 120.0° |
H8 | C8 | C9 | H9 | 93.9° | 175.0° |
H8 | C8 | C9 | H9A | 148.1° | 65.0° |
H8 | C8 | O9 | HO9 | 60.3° | 180.0° |
H9 | C9 | C10 | H10 | 83.3° | 180.0° |
H9 | C9 | C10 | H10A | 157.7° | 60.0° |
H9A | C9 | C10 | H10 | 34.7° | 60.0° |
H9A | C9 | C10 | H10A | 84.3° | 180.0° |
H10 | C10 | C12 | H12 | 176.5° | 179.9° |
H10 | C10 | C12 | H12A | 65.1° | 60.0° |
H10A | C10 | C12 | H12 | 57.5° | 60.0° |
H10A | C10 | C12 | H12A | 176.0° | 180.0° |
H2A | C2A | H2AA | H2AB | 120.0° | 120.0° |
H4A | C4A | H4AA | H4AB | 120.0° | 120.0° |
H5A | C5A | C5B | H5B | 166.6° | 180.0° |
H5A | C5A | C5B | H5BA | 47.9° | 60.0° |
H5AA | C5A | C5B | H5B | 73.3° | 60.0° |
H5AA | C5A | C5B | H5BA | 168.0° | 180.0° |