PY5
Bonds
First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
N1 | C2 | doub | 1.32Å | 1.37Å | Aromatic |
N1 | C6 | sing | 1.32Å | 1.36Å | Aromatic |
C2 | C2A | sing | 1.51Å | 1.51Å | |
C2 | C3 | sing | 1.39Å | 1.45Å | Aromatic |
C2A | H2A1 | sing | 1.09Å | 1.11Å | |
C2A | H2A2 | sing | 1.09Å | 1.11Å | |
C2A | H2A3 | sing | 1.09Å | 1.11Å | |
C3 | O3 | sing | 1.36Å | 1.36Å | |
C3 | C4 | doub | 1.39Å | 1.40Å | Aromatic |
O3 | HO3 | sing | 0.97Å | 0.95Å | |
C4 | C4A | sing | 1.51Å | 1.54Å | |
C4 | C5 | sing | 1.38Å | 1.45Å | Aromatic |
C4A | N | sing | 1.47Å | 1.54Å | |
C4A | H4A1 | sing | 1.09Å | 1.12Å | |
C4A | H4A2 | sing | 1.09Å | 1.12Å | |
C5 | C6 | doub | 1.38Å | 1.39Å | Aromatic |
C5 | C5A | sing | 1.51Å | 1.53Å | |
C6 | H6 | sing | 1.08Å | 1.10Å | |
C5A | O4P | sing | 1.43Å | 1.37Å | |
C5A | H5A1 | sing | 1.09Å | 1.12Å | |
C5A | H5A2 | sing | 1.09Å | 1.11Å | |
O4P | P | sing | 1.61Å | 1.57Å | |
P | O1P | doub | 1.48Å | 1.42Å | |
P | O2P | sing | 1.61Å | 1.51Å | |
P | O3P | sing | 1.61Å | 1.50Å | |
O2P | HOP2 | sing | 0.97Å | 0.95Å | |
O3P | HOP3 | sing | 0.97Å | 0.95Å | |
N | CA | sing | 1.47Å | 1.52Å | |
N | HN2 | sing | 1.01Å | 1.02Å | |
CA | C | sing | 1.51Å | 1.53Å | |
CA | CB | sing | 1.53Å | 1.52Å | |
CA | HA | sing | 1.09Å | 1.12Å | |
C | O | doub | 1.21Å | 1.35Å | |
C | OXT | sing | 1.34Å | 1.30Å | |
CB | CG | sing | 1.53Å | 1.52Å | |
CB | HB1 | sing | 1.09Å | 1.11Å | |
CB | HB2 | sing | 1.09Å | 1.12Å | |
CG | CD | sing | 1.53Å | 1.52Å | |
CG | HG1 | sing | 1.09Å | 1.11Å | |
CG | HG2 | sing | 1.09Å | 1.11Å | |
CD | HD1 | sing | 1.09Å | 1.12Å | |
CD | HD2 | sing | 1.09Å | 1.12Å | |
CD | HD3 | sing | 1.09Å | 1.12Å | |
OXT | HXT | sing | 0.97Å | 0.95Å |
Angles
First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
C2 | N1 | C6 | 121.9° | 121.8° |
N1 | C2 | C2A | 109.4° | 119.6° |
N1 | C2 | C3 | 118.6° | 120.7° |
N1 | C6 | C5 | 118.1° | 120.9° |
N1 | C6 | H6 | 119.9° | 119.6° |
C2A | C2 | C3 | 132.0° | 119.7° |
C2 | C2A | H2A1 | 109.4° | 109.5° |
C2 | C2A | H2A2 | 112.2° | 109.5° |
C2 | C2A | H2A3 | 112.2° | 109.4° |
C2 | C3 | O3 | 111.1° | 120.5° |
C2 | C3 | C4 | 123.7° | 119.0° |
H2A1 | C2A | H2A2 | 112.3° | 109.5° |
H2A1 | C2A | H2A3 | 112.2° | 109.5° |
H2A2 | C2A | H2A3 | 98.2° | 109.5° |
O3 | C3 | C4 | 125.2° | 120.5° |
C3 | O3 | HO3 | 111.0° | 106.8° |
C3 | C4 | C4A | 122.2° | 120.8° |
C3 | C4 | C5 | 111.6° | 118.4° |
C4A | C4 | C5 | 126.2° | 120.8° |
C4 | C4A | N | 104.8° | 109.5° |
C4 | C4A | H4A1 | 114.0° | 109.5° |
C4 | C4A | H4A2 | 114.0° | 109.5° |
C4 | C5 | C6 | 126.2° | 119.2° |
C4 | C5 | C5A | 123.0° | 120.4° |
N | C4A | H4A1 | 114.0° | 109.4° |
N | C4A | H4A2 | 114.0° | 109.5° |
C4A | N | CA | 111.1° | 106.7° |
C4A | N | HN2 | 111.6° | 106.7° |
H4A1 | C4A | H4A2 | 96.4° | 109.5° |
C6 | C5 | C5A | 110.8° | 120.4° |
C5 | C6 | H6 | 122.0° | 119.5° |
C5 | C5A | O4P | 117.6° | 109.4° |
C5 | C5A | H5A1 | 109.3° | 109.4° |
C5 | C5A | H5A2 | 109.3° | 109.5° |
O4P | C5A | H5A1 | 109.2° | 109.4° |
O4P | C5A | H5A2 | 109.3° | 109.5° |
C5A | O4P | P | 124.1° | 106.8° |
H5A1 | C5A | H5A2 | 100.8° | 109.5° |
O4P | P | O1P | 111.6° | 109.4° |
O4P | P | O2P | 104.5° | 109.5° |
O4P | P | O3P | 104.4° | 109.5° |
O1P | P | O2P | 122.2° | 109.4° |
O1P | P | O3P | 103.8° | 109.5° |
O2P | P | O3P | 109.1° | 109.5° |
P | O2P | HOP2 | 104.5° | 106.8° |
P | O3P | HOP3 | 104.4° | 106.8° |
CA | N | HN2 | 111.7° | 106.7° |
N | CA | C | 110.0° | 109.4° |
N | CA | CB | 110.6° | 109.5° |
N | CA | HA | 108.7° | 109.4° |
C | CA | CB | 110.6° | 109.5° |
C | CA | HA | 108.8° | 109.5° |
CA | C | O | 111.4° | 120.0° |
CA | C | OXT | 124.4° | 120.1° |
CB | CA | HA | 108.0° | 109.5° |
CA | CB | CG | 114.8° | 109.5° |
CA | CB | HB1 | 110.3° | 109.5° |
CA | CB | HB2 | 110.3° | 109.5° |
O | C | OXT | 124.2° | 120.0° |
C | OXT | HXT | 124.4° | 120.0° |
CG | CB | HB1 | 110.3° | 109.5° |
CG | CB | HB2 | 110.2° | 109.5° |
CB | CG | CD | 112.9° | 109.5° |
CB | CG | HG1 | 110.9° | 109.4° |
CB | CG | HG2 | 111.0° | 109.4° |
HB1 | CB | HB2 | 99.9° | 109.4° |
CD | CG | HG1 | 110.9° | 109.5° |
CD | CG | HG2 | 110.9° | 109.5° |
CG | CD | HD1 | 112.9° | 109.5° |
CG | CD | HD2 | 111.0° | 109.4° |
CG | CD | HD3 | 111.0° | 109.5° |
HG1 | CG | HG2 | 99.4° | 109.5° |
HD1 | CD | HD2 | 111.0° | 109.5° |
HD1 | CD | HD3 | 110.9° | 109.5° |
HD2 | CD | HD3 | 99.3° | 109.5° |
Dihedrals
First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
N1 | C2 | C2A | C3 | 179.5° | 180.0° |
N1 | C2 | C2A | H2A1 | 180.0° | 90.0° |
N1 | C2 | C2A | H2A2 | 54.7° | 30.1° |
N1 | C2 | C2A | H2A3 | 54.8° | 150.0° |
N1 | C2 | C3 | O3 | 179.8° | 179.9° |
N1 | C2 | C3 | C4 | 0.7° | 0.0° |
C2 | N1 | C6 | C5 | 1.1° | 0.3° |
C2 | N1 | C6 | H6 | 178.9° | 180.0° |
C6 | N1 | C2 | C2A | 179.6° | 180.0° |
C6 | N1 | C2 | C3 | 0.8° | 0.0° |
N1 | C6 | C5 | C4 | 1.3° | 0.5° |
N1 | C6 | C5 | H6 | 180.0° | 179.7° |
N1 | C6 | C5 | C5A | 179.8° | 180.0° |
C2 | C2A | H2A1 | H2A2 | 125.3° | 120.0° |
C2 | C2A | H2A1 | H2A3 | 125.2° | 119.9° |
C2 | C2A | H2A2 | H2A3 | 118.1° | 119.9° |
C2A | C2 | C3 | O3 | 0.7° | 0.1° |
C2A | C2 | C3 | C4 | 179.8° | 180.0° |
C3 | C2 | C2A | H2A1 | 0.5° | 90.0° |
C3 | C2 | C2A | H2A2 | 124.8° | 149.9° |
C3 | C2 | C2A | H2A3 | 125.7° | 30.0° |
C2 | C3 | O3 | C4 | 179.1° | 179.9° |
C2 | C3 | O3 | HO3 | 180.0° | 89.9° |
C2 | C3 | C4 | C4A | 179.9° | 180.0° |
C2 | C3 | C4 | C5 | 0.8° | 0.2° |
H2A1 | C2A | H2A2 | H2A3 | 118.2° | 120.1° |
O3 | C3 | C4 | C4A | 1.1° | 0.1° |
O3 | C3 | C4 | C5 | 179.8° | 179.7° |
C4 | C3 | O3 | HO3 | 0.9° | 89.9° |
C3 | C4 | C4A | C5 | 179.0° | 179.8° |
C3 | C4 | C4A | N | 27.7° | 89.9° |
C3 | C4 | C4A | H4A1 | 97.6° | 30.0° |
C3 | C4 | C4A | H4A2 | 153.0° | 150.0° |
C3 | C4 | C5 | C6 | 1.1° | 0.5° |
C3 | C4 | C5 | C5A | 179.5° | 179.9° |
C4 | C4A | N | H4A1 | 125.3° | 120.0° |
C4 | C4A | N | H4A2 | 125.3° | 120.0° |
C4 | C4A | H4A1 | H4A2 | 119.9° | 120.0° |
C4A | C4 | C5 | C6 | 179.8° | 179.8° |
C4A | C4 | C5 | C5A | 1.4° | 0.3° |
C4 | C4A | N | CA | 159.8° | 180.0° |
C4 | C4A | N | HN2 | 34.5° | 66.2° |
C5 | C4 | C4A | N | 151.3° | 90.3° |
C5 | C4 | C4A | H4A1 | 83.5° | 149.7° |
C5 | C4 | C4A | H4A2 | 25.9° | 29.7° |
C4 | C5 | C6 | C5A | 178.6° | 179.5° |
C4 | C5 | C6 | H6 | 178.7° | 179.8° |
C4 | C5 | C5A | O4P | 26.2° | 179.5° |
C4 | C5 | C5A | H5A1 | 151.5° | 60.6° |
C4 | C5 | C5A | H5A2 | 99.1° | 59.4° |
N | C4A | H4A1 | H4A2 | 119.9° | 120.0° |
C4A | N | CA | HN2 | 125.2° | 113.8° |
C4A | N | CA | C | 179.9° | 90.0° |
C4A | N | CA | CB | 57.7° | 150.0° |
C4A | N | CA | HA | 60.8° | 30.0° |
H4A1 | C4A | N | CA | 34.5° | 60.0° |
H4A1 | C4A | N | HN2 | 90.8° | 173.8° |
H4A2 | C4A | N | CA | 74.9° | 60.0° |
H4A2 | C4A | N | HN2 | 159.8° | 53.8° |
C6 | C5 | C5A | O4P | 152.4° | 0.1° |
C6 | C5 | C5A | H5A1 | 27.2° | 120.0° |
C6 | C5 | C5A | H5A2 | 82.3° | 120.0° |
C5A | C5 | C6 | H6 | 0.1° | 0.3° |
C5 | C5A | O4P | H5A1 | 125.3° | 119.9° |
C5 | C5A | O4P | H5A2 | 125.3° | 120.0° |
C5 | C5A | H5A1 | H5A2 | 115.1° | 120.0° |
C5 | C5A | O4P | P | 156.9° | 179.9° |
O4P | C5A | H5A1 | H5A2 | 115.0° | 120.1° |
C5A | O4P | P | O1P | 64.9° | 60.0° |
C5A | O4P | P | O2P | 161.1° | 179.9° |
C5A | O4P | P | O3P | 46.6° | 60.0° |
H5A1 | C5A | O4P | P | 31.6° | 60.1° |
H5A2 | C5A | O4P | P | 77.8° | 60.0° |
O4P | P | O1P | O2P | 124.6° | 120.0° |
O4P | P | O1P | O3P | 111.8° | 120.0° |
O4P | P | O2P | O3P | 111.1° | 120.1° |
O4P | P | O2P | HOP2 | 180.0° | 179.9° |
O4P | P | O3P | HOP3 | 180.0° | 60.0° |
O1P | P | O2P | O3P | 121.1° | 120.0° |
O1P | P | O2P | HOP2 | 52.2° | 60.0° |
O1P | P | O3P | HOP3 | 63.0° | 180.0° |
O2P | P | O3P | HOP3 | 68.8° | 60.0° |
O3P | P | O2P | HOP2 | 68.8° | 60.0° |
N | CA | C | CB | 122.5° | 120.0° |
N | CA | C | HA | 119.0° | 119.9° |
N | CA | CB | HA | 118.9° | 119.9° |
N | CA | C | O | 42.7° | 149.9° |
N | CA | C | OXT | 137.3° | 30.0° |
N | CA | CB | CG | 59.9° | 60.0° |
N | CA | CB | HB1 | 174.8° | 180.0° |
N | CA | CB | HB2 | 65.4° | 60.0° |
HN2 | N | CA | C | 54.7° | 23.8° |
HN2 | N | CA | CB | 177.1° | 96.2° |
HN2 | N | CA | HA | 64.4° | 143.8° |
C | CA | CB | HA | 119.0° | 120.1° |
CA | C | O | OXT | 180.0° | 179.9° |
C | CA | CB | CG | 62.2° | 180.0° |
C | CA | CB | HB1 | 63.1° | 60.0° |
C | CA | CB | HB2 | 172.5° | 60.0° |
CA | C | OXT | HXT | 180.0° | 180.0° |
CB | CA | C | O | 165.2° | 90.0° |
CB | CA | C | OXT | 14.8° | 90.0° |
CA | CB | CG | HB1 | 125.3° | 120.1° |
CA | CB | CG | HB2 | 125.3° | 120.0° |
CA | CB | HB1 | HB2 | 116.1° | 120.0° |
CA | CB | CG | CD | 165.0° | 180.0° |
CA | CB | CG | HG1 | 39.8° | 60.0° |
CA | CB | CG | HG2 | 69.7° | 60.0° |
HA | CA | C | O | 76.3° | 30.0° |
HA | CA | C | OXT | 103.7° | 149.9° |
HA | CA | CB | CG | 178.8° | 60.0° |
HA | CA | CB | HB1 | 55.9° | 60.1° |
HA | CA | CB | HB2 | 53.5° | 180.0° |
O | C | OXT | HXT | 0.0° | 0.1° |
CG | CB | HB1 | HB2 | 116.0° | 119.9° |
CB | CG | CD | HG1 | 125.2° | 120.0° |
CB | CG | CD | HG2 | 125.3° | 120.0° |
CB | CG | HG1 | HG2 | 116.9° | 120.0° |
CB | CG | CD | HD1 | 180.0° | 180.0° |
CB | CG | CD | HD2 | 54.7° | 60.0° |
CB | CG | CD | HD3 | 54.7° | 60.0° |
HB1 | CB | CG | CD | 69.6° | 59.9° |
HB1 | CB | CG | HG1 | 165.1° | 179.9° |
HB1 | CB | CG | HG2 | 55.6° | 60.0° |
HB2 | CB | CG | CD | 39.7° | 60.0° |
HB2 | CB | CG | HG1 | 85.5° | 60.0° |
HB2 | CB | CG | HG2 | 164.9° | 180.0° |
CD | CG | HG1 | HG2 | 116.8° | 120.0° |
CG | CD | HD1 | HD2 | 125.3° | 120.0° |
CG | CD | HD1 | HD3 | 125.3° | 120.0° |
CG | CD | HD2 | HD3 | 116.8° | 120.0° |
HG1 | CG | CD | HD1 | 54.8° | 60.0° |
HG1 | CG | CD | HD2 | 179.9° | 60.0° |
HG1 | CG | CD | HD3 | 70.5° | 179.9° |
HG2 | CG | CD | HD1 | 54.8° | 60.1° |
HG2 | CG | CD | HD2 | 70.6° | 180.0° |
HG2 | CG | CD | HD3 | 180.0° | 60.0° |
HD1 | CD | HD2 | HD3 | 116.8° | 120.1° |