PD5
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| NBF | C4 | sing | 1.36Å | 1.33Å | Aromatic |
| N3 | C4 | doub | 1.33Å | 1.34Å | Aromatic |
| C4 | C5 | sing | 1.41Å | 1.39Å | Aromatic |
| CBB | C5 | sing | 1.46Å | 1.39Å | Aromatic |
| C5 | C6 | doub | 1.41Å | 1.39Å | Aromatic |
| N1 | C6 | sing | 1.33Å | 1.34Å | Aromatic |
| C6 | NAC | sing | 1.38Å | 1.33Å | |
| C2 | N1 | doub | 1.32Å | 1.32Å | Aromatic |
| N3 | C2 | sing | 1.32Å | 1.32Å | Aromatic |
| CBE | CAA | sing | 1.53Å | 1.53Å | |
| CAA | HAA | sing | 1.09Å | 1.10Å | |
| CAA | HAAA | sing | 1.09Å | 1.10Å | |
| CAA | HAAB | sing | 1.09Å | 1.10Å | |
| CAB | CBE | sing | 1.53Å | 1.53Å | |
| CBE | NBF | sing | 1.46Å | 1.47Å | |
| CBE | HBE | sing | 1.09Å | 1.10Å | |
| CAB | HAB | sing | 1.09Å | 1.10Å | |
| CAB | HABA | sing | 1.09Å | 1.10Å | |
| CAB | HABB | sing | 1.09Å | 1.10Å | |
| NBF | NAS | sing | 1.40Å | 1.23Å | Aromatic |
| NAS | CBB | doub | 1.31Å | 1.33Å | Aromatic |
| C2 | H2 | sing | 1.08Å | 1.08Å | |
| NAC | HNAC | sing | 0.97Å | 1.00Å | |
| NAC | HNAA | sing | 0.97Å | 1.00Å | |
| CBB | CAZ | sing | 1.48Å | 1.39Å | Aromatic |
| CAN | CAZ | doub | 1.39Å | 1.39Å | Aromatic |
| CAZ | CAO | sing | 1.39Å | 1.39Å | Aromatic |
| CAO | CAM | doub | 1.38Å | 1.39Å | Aromatic |
| CAO | HAO | sing | 1.08Å | 1.08Å | |
| CAX | CAM | sing | 1.39Å | 1.39Å | Aromatic |
| CAM | HAM | sing | 1.08Å | 1.08Å | |
| CAN | CAL | sing | 1.38Å | 1.39Å | Aromatic |
| CAN | HAN | sing | 1.08Å | 1.08Å | |
| CAL | CAX | doub | 1.39Å | 1.39Å | Aromatic |
| CAL | HAL | sing | 1.08Å | 1.08Å | |
| CAX | NAT | sing | 1.40Å | 1.33Å | |
| CAV | NAT | sing | 1.35Å | 1.33Å | |
| NAT | HNAT | sing | 0.97Å | 1.00Å | |
| OAD | CAV | doub | 1.22Å | 1.23Å | |
| CAV | NAU | sing | 1.35Å | 1.33Å | |
| CAY | NAU | sing | 1.40Å | 1.33Å | |
| NAU | HNAU | sing | 0.97Å | 1.00Å | |
| CAP | CAY | doub | 1.39Å | 1.39Å | Aromatic |
| CAY | CAJ | sing | 1.39Å | 1.39Å | Aromatic |
| CBA | CAP | sing | 1.38Å | 1.39Å | Aromatic |
| CAP | HAP | sing | 1.08Å | 1.08Å | |
| CAH | CAJ | doub | 1.38Å | 1.39Å | Aromatic |
| CAJ | HAJ | sing | 1.08Å | 1.08Å | |
| CAK | CAH | sing | 1.38Å | 1.39Å | Aromatic |
| CAH | HAH | sing | 1.08Å | 1.08Å | |
| CBA | CAK | doub | 1.38Å | 1.39Å | Aromatic |
| CAK | HAK | sing | 1.08Å | 1.08Å | |
| CBG | CBA | sing | 1.51Å | 1.53Å | |
| FAG | CBG | sing | 1.40Å | 1.33Å | |
| FAE | CBG | sing | 1.40Å | 1.33Å | |
| CBG | FAF | sing | 1.40Å | 1.33Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| NBF | C4 | N3 | 134.4° | 134.5° |
| NBF | C4 | C5 | 105.9° | 106.9° |
| C4 | NBF | CBE | 123.3° | 125.3° |
| C4 | NBF | NAS | 112.4° | 109.4° |
| N3 | C4 | C5 | 119.7° | 118.7° |
| C4 | N3 | C2 | 120.1° | 120.7° |
| C4 | C5 | CBB | 104.6° | 106.5° |
| C4 | C5 | C6 | 118.5° | 118.5° |
| CBB | C5 | C6 | 136.9° | 135.1° |
| C5 | CBB | NAS | 107.0° | 107.4° |
| C5 | CBB | CAZ | 125.6° | 126.3° |
| C5 | C6 | N1 | 118.6° | 118.3° |
| C5 | C6 | NAC | 121.0° | 120.8° |
| N1 | C6 | NAC | 120.4° | 120.9° |
| C6 | N1 | C2 | 121.2° | 121.1° |
| C6 | NAC | HNAC | 109.5° | 120.0° |
| C6 | NAC | HNAA | 109.5° | 120.0° |
| N1 | C2 | N3 | 121.9° | 122.7° |
| N1 | C2 | H2 | 119.1° | 118.7° |
| N3 | C2 | H2 | 119.0° | 118.7° |
| CBE | CAA | HAA | 109.5° | 109.5° |
| CBE | CAA | HAAA | 109.5° | 109.5° |
| CBE | CAA | HAAB | 109.5° | 109.5° |
| CAA | CBE | CAB | 110.9° | 109.5° |
| CAA | CBE | NBF | 109.7° | 109.5° |
| CAA | CBE | HBE | 108.3° | 109.5° |
| HAA | CAA | HAAA | 109.5° | 109.5° |
| HAA | CAA | HAAB | 109.5° | 109.4° |
| HAAA | CAA | HAAB | 109.5° | 109.5° |
| CAB | CBE | NBF | 109.3° | 109.5° |
| CAB | CBE | HBE | 108.7° | 109.5° |
| CBE | CAB | HAB | 109.5° | 109.5° |
| CBE | CAB | HABA | 109.4° | 109.5° |
| CBE | CAB | HABB | 109.5° | 109.4° |
| NBF | CBE | HBE | 109.9° | 109.4° |
| CBE | NBF | NAS | 124.4° | 125.3° |
| HAB | CAB | HABA | 109.5° | 109.5° |
| HAB | CAB | HABB | 109.4° | 109.4° |
| HABA | CAB | HABB | 109.5° | 109.4° |
| NBF | NAS | CBB | 110.1° | 109.9° |
| NAS | CBB | CAZ | 127.4° | 126.3° |
| HNAC | NAC | HNAA | 109.4° | 120.0° |
| CBB | CAZ | CAN | 120.9° | 120.1° |
| CBB | CAZ | CAO | 119.4° | 120.1° |
| CAN | CAZ | CAO | 119.4° | 119.9° |
| CAZ | CAN | CAL | 120.5° | 120.0° |
| CAZ | CAN | HAN | 119.7° | 120.0° |
| CAZ | CAO | CAM | 120.0° | 120.0° |
| CAZ | CAO | HAO | 120.0° | 120.1° |
| CAM | CAO | HAO | 120.0° | 120.0° |
| CAO | CAM | CAX | 120.7° | 120.0° |
| CAO | CAM | HAM | 119.6° | 120.0° |
| CAX | CAM | HAM | 119.6° | 120.0° |
| CAM | CAX | CAL | 119.2° | 120.1° |
| CAM | CAX | NAT | 118.0° | 119.9° |
| CAL | CAN | HAN | 119.7° | 120.0° |
| CAN | CAL | CAX | 120.2° | 120.0° |
| CAN | CAL | HAL | 119.9° | 120.0° |
| CAX | CAL | HAL | 119.9° | 120.0° |
| CAL | CAX | NAT | 122.5° | 119.9° |
| CAX | NAT | CAV | 126.8° | 120.0° |
| CAX | NAT | HNAT | 116.6° | 120.0° |
| CAV | NAT | HNAT | 116.6° | 120.0° |
| NAT | CAV | OAD | 122.9° | 120.0° |
| NAT | CAV | NAU | 114.2° | 120.0° |
| OAD | CAV | NAU | 122.9° | 120.0° |
| CAV | NAU | CAY | 127.3° | 120.0° |
| CAV | NAU | HNAU | 116.3° | 120.0° |
| CAY | NAU | HNAU | 116.3° | 119.9° |
| NAU | CAY | CAP | 123.5° | 120.1° |
| NAU | CAY | CAJ | 117.3° | 120.0° |
| CAP | CAY | CAJ | 119.2° | 119.9° |
| CAY | CAP | CBA | 120.3° | 119.9° |
| CAY | CAP | HAP | 119.9° | 120.0° |
| CAY | CAJ | CAH | 120.9° | 119.9° |
| CAY | CAJ | HAJ | 119.6° | 120.0° |
| CBA | CAP | HAP | 119.8° | 120.0° |
| CAP | CBA | CAK | 119.9° | 120.1° |
| CAP | CBA | CBG | 121.5° | 120.0° |
| CAH | CAJ | HAJ | 119.5° | 120.1° |
| CAJ | CAH | CAK | 119.5° | 120.1° |
| CAJ | CAH | HAH | 120.3° | 120.0° |
| CAK | CAH | HAH | 120.3° | 119.9° |
| CAH | CAK | CBA | 120.2° | 120.1° |
| CAH | CAK | HAK | 119.9° | 119.9° |
| CBA | CAK | HAK | 119.9° | 119.9° |
| CAK | CBA | CBG | 118.6° | 120.0° |
| CBA | CBG | FAG | 109.3° | 109.4° |
| CBA | CBG | FAE | 111.1° | 109.5° |
| CBA | CBG | FAF | 109.1° | 109.5° |
| FAG | CBG | FAE | 109.1° | 109.5° |
| FAG | CBG | FAF | 109.2° | 109.5° |
| FAE | CBG | FAF | 109.1° | 109.5° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| NBF | C4 | N3 | C5 | 179.5° | 179.7° |
| NBF | C4 | C5 | CBB | 0.1° | 0.2° |
| NBF | C4 | C5 | C6 | 179.6° | 179.8° |
| NBF | C4 | N3 | C2 | 179.5° | 179.7° |
| C4 | NBF | CBE | CAA | 150.0° | 120.0° |
| C4 | NBF | CBE | CAB | 88.2° | 120.0° |
| C4 | NBF | CBE | NAS | 178.7° | 179.9° |
| C4 | NBF | CBE | HBE | 31.0° | 0.0° |
| C4 | NBF | NAS | CBB | 0.3° | 0.3° |
| N3 | C4 | C5 | CBB | 179.7° | 180.0° |
| N3 | C4 | C5 | C6 | 0.0° | 0.0° |
| C4 | N3 | C2 | N1 | 0.0° | 0.1° |
| N3 | C4 | NBF | CBE | 1.7° | 0.3° |
| N3 | C4 | NBF | NAS | 179.5° | 179.7° |
| C4 | N3 | C2 | H2 | 180.0° | 180.0° |
| C4 | C5 | CBB | C6 | 179.6° | 180.0° |
| C4 | C5 | C6 | N1 | 0.1° | 0.0° |
| C4 | C5 | C6 | NAC | 179.4° | 180.0° |
| C5 | C4 | N3 | C2 | 0.0° | 0.0° |
| C5 | C4 | NBF | CBE | 178.7° | 180.0° |
| C5 | C4 | NBF | NAS | 0.1° | 0.0° |
| C4 | C5 | CBB | NAS | 0.3° | 0.4° |
| C4 | C5 | CBB | CAZ | 179.6° | 180.0° |
| CBB | C5 | C6 | N1 | 179.7° | 180.0° |
| CBB | C5 | C6 | NAC | 0.2° | 0.0° |
| C5 | CBB | NAS | NBF | 0.3° | 0.4° |
| C5 | CBB | NAS | CAZ | 179.9° | 179.6° |
| C5 | CBB | CAZ | CAN | 55.6° | 135.9° |
| C5 | CBB | CAZ | CAO | 131.0° | 44.4° |
| C5 | C6 | N1 | NAC | 179.5° | 180.0° |
| C5 | C6 | N1 | C2 | 0.1° | 0.0° |
| C6 | C5 | CBB | NAS | 179.4° | 179.6° |
| C5 | C6 | NAC | HNAC | 98.3° | 14.7° |
| C5 | C6 | NAC | HNAA | 141.7° | 165.3° |
| C6 | C5 | CBB | CAZ | 0.8° | 0.0° |
| C6 | N1 | C2 | N3 | 0.0° | 0.1° |
| C6 | N1 | C2 | H2 | 180.0° | 180.0° |
| N1 | C6 | NAC | HNAC | 82.2° | 165.3° |
| N1 | C6 | NAC | HNAA | 37.8° | 14.7° |
| NAC | C6 | N1 | C2 | 179.4° | 180.0° |
| C6 | NAC | HNAC | HNAA | 120.0° | 179.9° |
| N1 | C2 | N3 | H2 | 180.0° | 179.9° |
| CBE | CAA | HAA | HAAA | 120.0° | 120.0° |
| CBE | CAA | HAA | HAAB | 120.0° | 120.0° |
| CBE | CAA | HAAA | HAAB | 120.0° | 120.0° |
| CAA | CBE | CAB | NBF | 121.1° | 120.0° |
| CAA | CBE | CAB | HBE | 119.0° | 120.1° |
| CAA | CBE | NBF | HBE | 119.0° | 120.0° |
| CAA | CBE | CAB | HAB | 46.6° | 59.9° |
| CAA | CBE | CAB | HABA | 166.6° | 180.0° |
| CAA | CBE | CAB | HABB | 73.4° | 60.0° |
| CAA | CBE | NBF | NAS | 31.3° | 60.0° |
| HAA | CAA | HAAA | HAAB | 120.0° | 120.0° |
| HAA | CAA | CBE | CAB | 156.3° | 60.0° |
| HAA | CAA | CBE | NBF | 35.5° | 60.0° |
| HAA | CAA | CBE | HBE | 84.4° | 179.9° |
| HAAA | CAA | CBE | CAB | 83.7° | 60.0° |
| HAAA | CAA | CBE | NBF | 155.5° | 180.0° |
| HAAA | CAA | CBE | HBE | 35.6° | 60.1° |
| HAAB | CAA | CBE | CAB | 36.3° | 180.0° |
| HAAB | CAA | CBE | NBF | 84.5° | 60.0° |
| HAAB | CAA | CBE | HBE | 155.6° | 59.9° |
| CAB | CBE | NBF | HBE | 119.2° | 120.0° |
| CBE | CAB | HAB | HABA | 120.0° | 120.1° |
| CBE | CAB | HAB | HABB | 120.0° | 120.0° |
| CBE | CAB | HABA | HABB | 120.0° | 120.0° |
| CAB | CBE | NBF | NAS | 90.5° | 60.1° |
| NBF | CBE | CAB | HAB | 167.7° | 60.1° |
| NBF | CBE | CAB | HABA | 72.3° | 60.0° |
| NBF | CBE | CAB | HABB | 47.7° | 180.0° |
| CBE | NBF | NAS | CBB | 178.5° | 179.8° |
| HBE | CBE | CAB | HAB | 72.4° | NaN° |
| HBE | CBE | CAB | HABA | 47.7° | 59.9° |
| HBE | CBE | CAB | HABB | 167.7° | 60.0° |
| HBE | CBE | NBF | NAS | 150.3° | 179.9° |
| HAB | CAB | HABA | HABB | 120.0° | 119.9° |
| NBF | NAS | CBB | CAZ | 179.5° | 180.0° |
| NAS | CBB | CAZ | CAN | 124.3° | 43.6° |
| NAS | CBB | CAZ | CAO | 49.1° | 136.1° |
| CBB | CAZ | CAN | CAO | 173.5° | 179.7° |
| CBB | CAZ | CAO | CAM | 172.0° | 180.0° |
| CBB | CAZ | CAO | HAO | 8.0° | 0.1° |
| CBB | CAZ | CAN | CAL | 171.8° | 180.0° |
| CBB | CAZ | CAN | HAN | 8.2° | 0.0° |
| CAN | CAZ | CAO | CAM | 1.6° | 0.3° |
| CAN | CAZ | CAO | HAO | 178.4° | 179.8° |
| CAZ | CAN | CAL | HAN | 180.0° | 180.0° |
| CAZ | CAN | CAL | CAX | 0.1° | 0.0° |
| CAZ | CAN | CAL | HAL | 179.9° | 180.0° |
| CAZ | CAO | CAM | HAO | 180.0° | 179.9° |
| CAZ | CAO | CAM | CAX | 0.0° | 0.1° |
| CAZ | CAO | CAM | HAM | 180.0° | 180.0° |
| CAO | CAZ | CAN | CAL | 1.6° | 0.3° |
| CAO | CAZ | CAN | HAN | 178.4° | 179.7° |
| CAO | CAM | CAX | HAM | 180.0° | 179.9° |
| CAO | CAM | CAX | CAL | 1.6° | 0.2° |
| CAO | CAM | CAX | NAT | 171.5° | 179.9° |
| HAO | CAO | CAM | CAX | 180.0° | 180.0° |
| HAO | CAO | CAM | HAM | 0.0° | 0.1° |
| CAM | CAX | CAL | CAN | 1.5° | 0.2° |
| CAM | CAX | CAL | NAT | 172.8° | 179.9° |
| CAM | CAX | CAL | HAL | 178.5° | 179.8° |
| CAM | CAX | NAT | CAV | 179.8° | 36.1° |
| CAM | CAX | NAT | HNAT | 0.2° | 143.9° |
| HAM | CAM | CAX | CAL | 178.5° | 179.7° |
| HAM | CAM | CAX | NAT | 8.5° | 0.1° |
| CAN | CAL | CAX | HAL | 180.0° | 180.0° |
| CAN | CAL | CAX | NAT | 171.2° | 179.9° |
| HAN | CAN | CAL | CAX | 179.9° | 180.0° |
| HAN | CAN | CAL | HAL | 0.1° | 0.0° |
| CAL | CAX | NAT | CAV | 7.0° | 144.0° |
| CAL | CAX | NAT | HNAT | 173.0° | 36.0° |
| HAL | CAL | CAX | NAT | 8.7° | 0.1° |
| CAX | NAT | CAV | HNAT | 180.0° | 180.0° |
| CAX | NAT | CAV | OAD | 1.6° | 5.1° |
| CAX | NAT | CAV | NAU | 178.7° | 174.9° |
| NAT | CAV | OAD | NAU | 179.6° | 180.0° |
| NAT | CAV | NAU | CAY | 179.8° | 175.6° |
| NAT | CAV | NAU | HNAU | 0.2° | 4.4° |
| HNAT | NAT | CAV | OAD | 178.4° | 174.9° |
| HNAT | NAT | CAV | NAU | 1.3° | 5.1° |
| OAD | CAV | NAU | CAY | 0.6° | 4.4° |
| OAD | CAV | NAU | HNAU | 179.4° | 175.6° |
| CAV | NAU | CAY | HNAU | 180.0° | 180.0° |
| CAV | NAU | CAY | CAP | 0.1° | 143.3° |
| CAV | NAU | CAY | CAJ | 179.3° | 36.9° |
| NAU | CAY | CAP | CAJ | 179.3° | 179.8° |
| NAU | CAY | CAP | CBA | 179.1° | 180.0° |
| NAU | CAY | CAP | HAP | 0.9° | 0.0° |
| NAU | CAY | CAJ | CAH | 179.1° | 180.0° |
| NAU | CAY | CAJ | HAJ | 0.9° | 0.1° |
| HNAU | NAU | CAY | CAP | 179.9° | 36.6° |
| HNAU | NAU | CAY | CAJ | 0.7° | 143.1° |
| CAY | CAP | CBA | HAP | 180.0° | 180.0° |
| CAP | CAY | CAJ | CAH | 0.3° | 0.2° |
| CAP | CAY | CAJ | HAJ | 179.7° | 179.7° |
| CAY | CAP | CBA | CAK | 0.0° | 0.0° |
| CAY | CAP | CBA | CBG | 179.2° | 180.0° |
| CAJ | CAY | CAP | CBA | 0.2° | 0.2° |
| CAJ | CAY | CAP | HAP | 179.8° | 179.8° |
| CAY | CAJ | CAH | HAJ | 180.0° | 179.9° |
| CAY | CAJ | CAH | CAK | 0.2° | 0.0° |
| CAY | CAJ | CAH | HAH | 179.9° | 180.0° |
| CAP | CBA | CAK | CAH | 0.2° | 0.2° |
| CAP | CBA | CAK | CBG | 179.3° | 180.0° |
| CAP | CBA | CAK | HAK | 179.8° | 180.0° |
| CAP | CBA | CBG | FAG | 125.2° | 150.0° |
| CAP | CBA | CBG | FAE | 4.7° | 30.0° |
| CAP | CBA | CBG | FAF | 115.5° | 90.0° |
| HAP | CAP | CBA | CAK | 180.0° | 180.0° |
| HAP | CAP | CBA | CBG | 0.8° | 0.0° |
| CAJ | CAH | CAK | HAH | 180.0° | 180.0° |
| CAJ | CAH | CAK | CBA | 0.1° | 0.3° |
| CAJ | CAH | CAK | HAK | 179.9° | 180.0° |
| HAJ | CAJ | CAH | CAK | 179.9° | 179.9° |
| HAJ | CAJ | CAH | HAH | 0.1° | 0.1° |
| CAH | CAK | CBA | HAK | 180.0° | 179.7° |
| CAH | CAK | CBA | CBG | 179.1° | 179.7° |
| HAH | CAH | CAK | CBA | 179.9° | 179.8° |
| HAH | CAH | CAK | HAK | 0.1° | 0.0° |
| CAK | CBA | CBG | FAG | 55.6° | 30.0° |
| CAK | CBA | CBG | FAE | 176.0° | 150.0° |
| CAK | CBA | CBG | FAF | 63.8° | 90.0° |
| HAK | CAK | CBA | CBG | 0.9° | 0.0° |
| CBA | CBG | FAG | FAE | 121.6° | 120.0° |
| CBA | CBG | FAG | FAF | 119.2° | 120.0° |
| CBA | CBG | FAE | FAF | 120.2° | 120.0° |
| FAG | CBG | FAE | FAF | 119.3° | 120.0° |
