PRD_000333
Bonds
First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
C1 | O1 | doub | 1.21Å | 1.28Å | |
C1 | O2 | sing | 1.35Å | 1.40Å | |
C1 | N | sing | 1.35Å | 1.29Å | |
O2 | C2 | sing | 1.45Å | 1.42Å | |
C2 | C3 | sing | 1.51Å | 1.61Å | |
C2 | H21 | sing | 1.09Å | 1.10Å | |
C2 | H22 | sing | 1.09Å | 1.10Å | |
C3 | C4 | doub | 1.38Å | 1.39Å | Aromatic |
C3 | C8 | sing | 1.38Å | 1.39Å | Aromatic |
C4 | C5 | sing | 1.38Å | 1.40Å | Aromatic |
C4 | H41 | sing | 1.08Å | 1.08Å | |
C5 | C6 | doub | 1.38Å | 1.39Å | Aromatic |
C5 | H51 | sing | 1.08Å | 1.08Å | |
C6 | C7 | sing | 1.38Å | 1.34Å | Aromatic |
C6 | H61 | sing | 1.08Å | 1.08Å | |
C7 | C8 | doub | 1.38Å | 1.39Å | Aromatic |
C7 | H71 | sing | 1.08Å | 1.08Å | |
C8 | H81 | sing | 1.08Å | 1.08Å | |
N | CA | sing | 1.46Å | 1.39Å | |
N | H | sing | 0.97Å | 1.00Å | |
CA | C | sing | 1.51Å | 1.51Å | |
CA | CB | sing | 1.53Å | 1.61Å | |
CA | HA | sing | 1.09Å | 1.10Å | |
C | O | doub | 1.21Å | 1.25Å | |
C | N1 | sing | 1.35Å | 1.34Å | |
CB | CG | sing | 1.51Å | 1.56Å | |
CB | HB2 | sing | 1.09Å | 1.10Å | |
CB | HB3 | sing | 1.09Å | 1.10Å | |
CG | CD1 | doub | 1.38Å | 1.37Å | Aromatic |
CG | CD2 | sing | 1.38Å | 1.38Å | Aromatic |
CD1 | CE1 | sing | 1.38Å | 1.42Å | Aromatic |
CD1 | HD1 | sing | 1.08Å | 1.08Å | |
CD2 | CE2 | doub | 1.38Å | 1.40Å | Aromatic |
CD2 | HD2 | sing | 1.08Å | 1.08Å | |
CE1 | CZ | doub | 1.38Å | 1.41Å | Aromatic |
CE1 | HE1 | sing | 1.08Å | 1.08Å | |
CE2 | CZ | sing | 1.38Å | 1.41Å | Aromatic |
CE2 | HE2 | sing | 1.08Å | 1.08Å | |
CZ | HZ | sing | 1.08Å | 1.08Å | |
N1 | CA1 | sing | 1.46Å | 1.40Å | |
N1 | H1 | sing | 0.97Å | 1.00Å | |
CA1 | C9 | sing | 1.51Å | 1.54Å | |
CA1 | CB1 | sing | 1.53Å | 1.52Å | |
CA1 | HA1 | sing | 1.09Å | 1.10Å | |
C9 | O3 | doub | 1.21Å | 1.22Å | |
C9 | CM | sing | 1.51Å | 1.63Å | |
CB1 | HB1 | sing | 1.09Å | 1.10Å | |
CB1 | HB21 | sing | 1.09Å | 1.10Å | |
CB1 | HB31 | sing | 1.09Å | 1.10Å | |
CM | HM1 | sing | 1.09Å | 1.10Å | |
CM | CL1 | sing | 1.80Å | 1.77Å | |
CM | HM2 | sing | 1.09Å | 1.10Å |
Angles
First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
O1 | C1 | O2 | 121.8° | 120.1° |
O1 | C1 | N | 116.3° | 120.0° |
O2 | C1 | N | 121.9° | 120.0° |
C1 | O2 | C2 | 104.9° | 117.0° |
C1 | N | CA | 134.1° | 120.0° |
C1 | N | H | 113.0° | 119.9° |
O2 | C2 | C3 | 111.7° | 109.5° |
O2 | C2 | H21 | 108.7° | 109.5° |
O2 | C2 | H22 | 108.7° | 109.5° |
C3 | C2 | H21 | 108.7° | 109.5° |
C3 | C2 | H22 | 108.7° | 109.4° |
C2 | C3 | C4 | 120.2° | 120.0° |
C2 | C3 | C8 | 119.7° | 120.0° |
H21 | C2 | H22 | 110.2° | 109.4° |
C4 | C3 | C8 | 120.1° | 120.0° |
C3 | C4 | C5 | 118.9° | 120.1° |
C3 | C4 | H41 | 120.5° | 120.0° |
C3 | C8 | C7 | 120.1° | 120.0° |
C3 | C8 | H81 | 120.0° | 120.0° |
C5 | C4 | H41 | 120.6° | 119.9° |
C4 | C5 | C6 | 118.8° | 120.0° |
C4 | C5 | H51 | 120.6° | 120.1° |
C6 | C5 | H51 | 120.6° | 120.0° |
C5 | C6 | C7 | 122.5° | 120.0° |
C5 | C6 | H61 | 118.7° | 120.0° |
C7 | C6 | H61 | 118.8° | 120.0° |
C6 | C7 | C8 | 119.3° | 120.0° |
C6 | C7 | H71 | 120.3° | 120.0° |
C8 | C7 | H71 | 120.3° | 120.0° |
C7 | C8 | H81 | 119.9° | 120.0° |
CA | N | H | 112.9° | 120.1° |
N | CA | C | 106.1° | 109.4° |
N | CA | CB | 111.6° | 109.5° |
N | CA | HA | 111.8° | 109.5° |
C | CA | CB | 113.5° | 109.5° |
C | CA | HA | 109.8° | 109.5° |
CA | C | O | 110.1° | 120.0° |
CA | C | N1 | 125.8° | 120.0° |
CB | CA | HA | 104.1° | 109.5° |
CA | CB | CG | 113.5° | 109.4° |
CA | CB | HB2 | 108.1° | 109.5° |
CA | CB | HB3 | 108.2° | 109.5° |
O | C | N1 | 123.7° | 120.0° |
C | N1 | CA1 | 121.5° | 120.0° |
C | N1 | H1 | 119.3° | 120.0° |
CG | CB | HB2 | 108.2° | 109.5° |
CG | CB | HB3 | 108.2° | 109.5° |
CB | CG | CD1 | 118.5° | 119.9° |
CB | CG | CD2 | 119.8° | 120.0° |
HB2 | CB | HB3 | 110.8° | 109.5° |
CD1 | CG | CD2 | 121.4° | 120.1° |
CG | CD1 | CE1 | 120.0° | 120.0° |
CG | CD1 | HD1 | 120.0° | 120.0° |
CG | CD2 | CE2 | 120.4° | 120.0° |
CG | CD2 | HD2 | 119.8° | 120.1° |
CE1 | CD1 | HD1 | 120.0° | 120.0° |
CD1 | CE1 | CZ | 118.2° | 120.0° |
CD1 | CE1 | HE1 | 120.9° | 120.0° |
CE2 | CD2 | HD2 | 119.8° | 120.0° |
CD2 | CE2 | CZ | 119.1° | 120.0° |
CD2 | CE2 | HE2 | 120.5° | 120.0° |
CZ | CE1 | HE1 | 120.9° | 120.0° |
CE1 | CZ | CE2 | 120.2° | 120.0° |
CE1 | CZ | HZ | 119.9° | 120.0° |
CZ | CE2 | HE2 | 120.5° | 120.0° |
CE2 | CZ | HZ | 119.9° | 120.0° |
CA1 | N1 | H1 | 119.3° | 120.0° |
N1 | CA1 | C9 | 112.1° | 109.5° |
N1 | CA1 | CB1 | 107.9° | 109.5° |
N1 | CA1 | HA1 | 107.0° | 109.5° |
C9 | CA1 | CB1 | 103.5° | 109.4° |
C9 | CA1 | HA1 | 111.2° | 109.5° |
CA1 | C9 | O3 | 114.2° | 120.0° |
CA1 | C9 | CM | 128.0° | 120.0° |
CB1 | CA1 | HA1 | 115.2° | 109.5° |
CA1 | CB1 | HB1 | 109.5° | 109.5° |
CA1 | CB1 | HB21 | 109.5° | 109.4° |
CA1 | CB1 | HB31 | 109.4° | 109.5° |
O3 | C9 | CM | 117.2° | 120.0° |
C9 | CM | HM1 | 109.5° | 109.5° |
C9 | CM | CL1 | 109.4° | 109.5° |
C9 | CM | HM2 | 109.5° | 109.5° |
HB1 | CB1 | HB21 | 109.5° | 109.5° |
HB1 | CB1 | HB31 | 109.5° | 109.4° |
HB21 | CB1 | HB31 | 109.5° | 109.5° |
HM1 | CM | CL1 | 109.5° | 109.5° |
HM1 | CM | HM2 | 109.5° | 109.5° |
CL1 | CM | HM2 | 109.5° | 109.5° |
Dihedrals
First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
O1 | C1 | O2 | N | 177.2° | 179.8° |
O1 | C1 | O2 | C2 | 52.4° | 0.0° |
O1 | C1 | N | CA | 12.6° | 0.0° |
O1 | C1 | N | H | 167.4° | 180.0° |
C1 | O2 | C2 | C3 | 117.3° | 180.0° |
C1 | O2 | C2 | H21 | 122.7° | 60.0° |
C1 | O2 | C2 | H22 | 2.7° | 60.0° |
O2 | C1 | N | CA | 170.0° | 179.7° |
O2 | C1 | N | H | 10.0° | 0.3° |
N | C1 | O2 | C2 | 124.8° | 179.8° |
C1 | N | CA | H | 180.0° | 180.0° |
C1 | N | CA | C | 88.5° | 155.0° |
C1 | N | CA | CB | 147.3° | 85.1° |
C1 | N | CA | HA | 31.2° | 35.0° |
O2 | C2 | C3 | H21 | 120.0° | 120.1° |
O2 | C2 | C3 | H22 | 120.0° | 120.0° |
O2 | C2 | H21 | H22 | 119.1° | 120.0° |
O2 | C2 | C3 | C4 | 160.4° | 90.0° |
O2 | C2 | C3 | C8 | 19.6° | 90.2° |
C3 | C2 | H21 | H22 | 119.1° | 119.9° |
C2 | C3 | C4 | C8 | 180.0° | 179.9° |
C2 | C3 | C4 | C5 | 177.9° | 180.0° |
C2 | C3 | C4 | H41 | 2.1° | 0.1° |
C2 | C3 | C8 | C7 | 180.0° | 179.7° |
C2 | C3 | C8 | H81 | 0.0° | 0.1° |
H21 | C2 | C3 | C4 | 40.4° | 30.1° |
H21 | C2 | C3 | C8 | 139.6° | 149.8° |
H22 | C2 | C3 | C4 | 79.7° | 150.1° |
H22 | C2 | C3 | C8 | 100.4° | 29.8° |
C3 | C4 | C5 | H41 | 180.0° | 179.9° |
C3 | C4 | C5 | C6 | 4.4° | 0.0° |
C3 | C4 | C5 | H51 | 175.6° | 180.0° |
C4 | C3 | C8 | C7 | 0.0° | 0.4° |
C4 | C3 | C8 | H81 | 180.0° | 179.8° |
C8 | C3 | C4 | C5 | 2.0° | 0.2° |
C8 | C3 | C4 | H41 | 177.9° | 179.8° |
C3 | C8 | C7 | C6 | 0.3° | 0.4° |
C3 | C8 | C7 | H81 | 180.0° | 179.8° |
C3 | C8 | C7 | H71 | 179.7° | 179.8° |
C4 | C5 | C6 | H51 | 180.0° | 180.0° |
C4 | C5 | C6 | C7 | 4.9° | 0.1° |
C4 | C5 | C6 | H61 | 175.1° | 179.9° |
H41 | C4 | C5 | C6 | 175.6° | 179.9° |
H41 | C4 | C5 | H51 | 4.4° | 0.0° |
C5 | C6 | C7 | H61 | 180.0° | 179.8° |
C5 | C6 | C7 | C8 | 2.8° | 0.3° |
C5 | C6 | C7 | H71 | 177.1° | 179.9° |
H51 | C5 | C6 | C7 | 175.1° | 180.0° |
H51 | C5 | C6 | H61 | 4.9° | 0.1° |
C6 | C7 | C8 | H71 | 180.0° | 179.8° |
C6 | C7 | C8 | H81 | 179.7° | 179.7° |
H61 | C6 | C7 | C8 | 177.1° | 179.9° |
H61 | C6 | C7 | H71 | 2.9° | 0.1° |
H71 | C7 | C8 | H81 | 0.4° | 0.1° |
N | CA | C | CB | 123.0° | 119.9° |
N | CA | C | HA | 121.0° | 120.0° |
N | CA | CB | HA | 120.7° | 120.0° |
N | CA | C | O | 62.5° | 0.0° |
N | CA | C | N1 | 110.1° | 180.0° |
N | CA | CB | CG | 85.6° | 65.1° |
N | CA | CB | HB2 | 34.4° | 54.9° |
N | CA | CB | HB3 | 154.4° | 175.0° |
H | N | CA | C | 91.5° | 25.0° |
H | N | CA | CB | 32.7° | 94.9° |
H | N | CA | HA | 148.8° | 145.0° |
C | CA | CB | HA | 119.4° | 120.0° |
CA | C | O | N1 | 172.8° | 180.0° |
C | CA | CB | CG | 154.5° | 175.0° |
C | CA | CB | HB2 | 85.5° | 65.0° |
C | CA | CB | HB3 | 34.5° | 55.1° |
CA | C | N1 | CA1 | 175.0° | 180.0° |
CA | C | N1 | H1 | 5.1° | 0.0° |
CB | CA | C | O | 60.5° | 119.9° |
CB | CA | C | N1 | 126.9° | 60.1° |
CA | CB | CG | HB2 | 120.0° | 120.0° |
CA | CB | CG | HB3 | 120.0° | 120.0° |
CA | CB | HB2 | HB3 | 118.3° | 120.0° |
CA | CB | CG | CD1 | 68.4° | 90.1° |
CA | CB | CG | CD2 | 105.9° | 90.3° |
HA | CA | C | O | 176.5° | 120.0° |
HA | CA | C | N1 | 10.9° | 60.0° |
HA | CA | CB | CG | 35.1° | 55.0° |
HA | CA | CB | HB2 | 155.1° | 175.0° |
HA | CA | CB | HB3 | 84.9° | 65.0° |
O | C | N1 | CA1 | 3.3° | 0.0° |
O | C | N1 | H1 | 176.7° | 180.0° |
C | N1 | CA1 | H1 | 180.0° | 180.0° |
C | N1 | CA1 | C9 | 87.7° | 155.0° |
C | N1 | CA1 | CB1 | 158.9° | 85.0° |
C | N1 | CA1 | HA1 | 34.5° | 35.0° |
CG | CB | HB2 | HB3 | 118.4° | 120.0° |
CB | CG | CD1 | CD2 | 174.3° | 179.7° |
CB | CG | CD1 | CE1 | 178.4° | 180.0° |
CB | CG | CD1 | HD1 | 1.6° | 0.1° |
CB | CG | CD2 | CE2 | 179.6° | 180.0° |
CB | CG | CD2 | HD2 | 0.5° | 0.1° |
HB2 | CB | CG | CD1 | 171.6° | 30.0° |
HB2 | CB | CG | CD2 | 14.0° | 149.7° |
HB3 | CB | CG | CD1 | 51.6° | 150.0° |
HB3 | CB | CG | CD2 | 134.1° | 29.7° |
CG | CD1 | CE1 | HD1 | 180.0° | 179.9° |
CD1 | CG | CD2 | CE2 | 5.4° | 0.4° |
CD1 | CG | CD2 | HD2 | 174.7° | 179.7° |
CG | CD1 | CE1 | CZ | 8.7° | 0.1° |
CG | CD1 | CE1 | HE1 | 171.2° | 180.0° |
CD2 | CG | CD1 | CE1 | 7.3° | 0.4° |
CD2 | CG | CD1 | HD1 | 172.7° | 179.8° |
CG | CD2 | CE2 | HD2 | 180.0° | 179.9° |
CG | CD2 | CE2 | CZ | 4.9° | 0.1° |
CG | CD2 | CE2 | HE2 | 175.1° | 180.0° |
CD1 | CE1 | CZ | HE1 | 180.0° | 179.9° |
CD1 | CE1 | CZ | CE2 | 8.4° | 0.1° |
CD1 | CE1 | CZ | HZ | 171.6° | 180.0° |
HD1 | CD1 | CE1 | CZ | 171.3° | 180.0° |
HD1 | CD1 | CE1 | HE1 | 8.8° | 0.1° |
CD2 | CE2 | CZ | CE1 | 6.5° | 0.1° |
CD2 | CE2 | CZ | HE2 | 180.0° | 179.9° |
CD2 | CE2 | CZ | HZ | 173.4° | 180.0° |
HD2 | CD2 | CE2 | CZ | 175.2° | 180.0° |
HD2 | CD2 | CE2 | HE2 | 4.9° | 0.1° |
CE1 | CZ | CE2 | HZ | 180.0° | 179.9° |
CE1 | CZ | CE2 | HE2 | 173.4° | 179.8° |
HE1 | CE1 | CZ | CE2 | 171.6° | 179.8° |
HE1 | CE1 | CZ | HZ | 8.4° | 0.1° |
HE2 | CE2 | CZ | HZ | 6.6° | 0.1° |
N1 | CA1 | C9 | CB1 | 116.1° | 120.0° |
N1 | CA1 | C9 | HA1 | 119.7° | 120.1° |
N1 | CA1 | CB1 | HA1 | 119.4° | 120.1° |
N1 | CA1 | C9 | O3 | 165.1° | 14.9° |
N1 | CA1 | C9 | CM | 4.9° | 165.0° |
N1 | CA1 | CB1 | HB1 | 180.0° | 180.0° |
N1 | CA1 | CB1 | HB21 | 60.0° | 60.1° |
N1 | CA1 | CB1 | HB31 | 60.0° | 60.0° |
H1 | N1 | CA1 | C9 | 92.3° | 25.0° |
H1 | N1 | CA1 | CB1 | 21.1° | 95.0° |
H1 | N1 | CA1 | HA1 | 145.6° | 145.0° |
C9 | CA1 | CB1 | HA1 | 121.5° | 119.9° |
CA1 | C9 | O3 | CM | 171.2° | 179.9° |
C9 | CA1 | CB1 | HB1 | 61.0° | 60.0° |
C9 | CA1 | CB1 | HB21 | 179.0° | 179.9° |
C9 | CA1 | CB1 | HB31 | 59.0° | 60.0° |
CA1 | C9 | CM | HM1 | 23.8° | 60.0° |
CA1 | C9 | CM | CL1 | 143.8° | 180.0° |
CA1 | C9 | CM | HM2 | 96.2° | 60.0° |
CB1 | CA1 | C9 | O3 | 78.8° | 105.0° |
CB1 | CA1 | C9 | CM | 111.2° | 75.0° |
CA1 | CB1 | HB1 | HB21 | 120.0° | 119.9° |
CA1 | CB1 | HB1 | HB31 | 120.0° | 120.0° |
CA1 | CB1 | HB21 | HB31 | 120.0° | 120.0° |
HA1 | CA1 | C9 | O3 | 45.4° | 135.0° |
HA1 | CA1 | C9 | CM | 124.6° | 44.9° |
HA1 | CA1 | CB1 | HB1 | 60.6° | 60.0° |
HA1 | CA1 | CB1 | HB21 | 59.4° | 60.0° |
HA1 | CA1 | CB1 | HB31 | 179.4° | 179.9° |
O3 | C9 | CM | HM1 | 166.4° | 120.0° |
O3 | C9 | CM | CL1 | 46.5° | 0.0° |
O3 | C9 | CM | HM2 | 73.5° | 120.0° |
C9 | CM | HM1 | CL1 | 120.0° | 120.0° |
C9 | CM | HM1 | HM2 | 120.0° | 120.0° |
C9 | CM | CL1 | HM2 | 120.0° | 120.0° |
HB1 | CB1 | HB21 | HB31 | 120.0° | 120.0° |
HM1 | CM | CL1 | HM2 | 120.0° | 120.0° |