JD5
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| OAJ | PAI | doub | 1.48Å | 1.63Å | |
| OAL | PAI | sing | 1.61Å | 1.58Å | |
| PAI | OAK | sing | 1.61Å | 1.55Å | |
| PAI | CAH | sing | 1.82Å | 1.79Å | |
| NAB | CAC | doub | 1.32Å | 1.40Å | Aromatic |
| NAB | CAA | sing | 1.32Å | 1.42Å | Aromatic |
| CAC | CAD | sing | 1.39Å | 1.40Å | Aromatic |
| CAA | CAF | doub | 1.39Å | 1.37Å | Aromatic |
| CAH | NAG | sing | 1.47Å | 1.47Å | |
| CAH | PAM | sing | 1.82Å | 1.87Å | |
| OAO | PAM | doub | 1.48Å | 1.58Å | |
| CAD | NAG | sing | 1.40Å | 1.37Å | |
| CAD | CAE | doub | 1.39Å | 1.38Å | Aromatic |
| CAF | CAE | sing | 1.40Å | 1.40Å | Aromatic |
| CAF | CAQ | sing | 1.48Å | 1.45Å | |
| PAM | OAP | sing | 1.61Å | 1.52Å | |
| PAM | OAN | sing | 1.61Å | 1.49Å | |
| CAQ | CAV | doub | 1.39Å | 1.37Å | Aromatic |
| CAQ | CAR | sing | 1.39Å | 1.38Å | Aromatic |
| CAV | CAU | sing | 1.38Å | 1.39Å | Aromatic |
| CAR | CAS | doub | 1.38Å | 1.44Å | Aromatic |
| CAU | CAT | doub | 1.39Å | 1.39Å | Aromatic |
| CAS | CAT | sing | 1.39Å | 1.38Å | Aromatic |
| CAT | OAW | sing | 1.36Å | 1.42Å | |
| OAW | CAX | sing | 1.43Å | 1.39Å | |
| CAY | CAX | sing | 1.53Å | 1.39Å | |
| CAY | CAZ | sing | 1.53Å | 1.40Å | |
| CAX | CAZ | sing | 1.53Å | 1.45Å | |
| OAK | H1 | sing | 0.97Å | 0.95Å | |
| OAL | H2 | sing | 0.97Å | 0.95Å | |
| CAH | H3 | sing | 1.09Å | 1.10Å | |
| OAP | H4 | sing | 0.97Å | 0.95Å | |
| OAN | H5 | sing | 0.97Å | 0.95Å | |
| NAG | H6 | sing | 0.97Å | 1.00Å | |
| CAE | H7 | sing | 1.08Å | 1.08Å | |
| CAC | H8 | sing | 1.08Å | 1.08Å | |
| CAA | H9 | sing | 1.08Å | 1.08Å | |
| CAV | H10 | sing | 1.08Å | 1.08Å | |
| CAU | H11 | sing | 1.08Å | 1.08Å | |
| CAR | H12 | sing | 1.08Å | 1.08Å | |
| CAS | H13 | sing | 1.08Å | 1.08Å | |
| CAX | H14 | sing | 1.09Å | 1.10Å | |
| CAY | H15 | sing | 1.09Å | 1.10Å | |
| CAY | H16 | sing | 1.09Å | 1.10Å | |
| CAZ | H17 | sing | 1.09Å | 1.10Å | |
| CAZ | H18 | sing | 1.09Å | 1.10Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| OAJ | PAI | OAL | 108.2° | 109.4° |
| OAJ | PAI | OAK | 106.6° | 109.5° |
| OAJ | PAI | CAH | 112.2° | 109.5° |
| OAL | PAI | OAK | 108.5° | 109.5° |
| OAL | PAI | CAH | 108.2° | 109.5° |
| PAI | OAL | H2 | 109.5° | 114.0° |
| OAK | PAI | CAH | 113.1° | 109.5° |
| PAI | OAK | H1 | 109.5° | 114.0° |
| PAI | CAH | NAG | 108.8° | 109.5° |
| PAI | CAH | PAM | 109.5° | 109.5° |
| PAI | CAH | H3 | 110.5° | 109.5° |
| CAC | NAB | CAA | 117.4° | 121.9° |
| NAB | CAC | CAD | 120.7° | 120.9° |
| NAB | CAC | H8 | 119.7° | 119.5° |
| NAB | CAA | CAF | 123.5° | 120.8° |
| NAB | CAA | H9 | 118.3° | 119.6° |
| CAC | CAD | NAG | 123.2° | 120.4° |
| CAC | CAD | CAE | 118.3° | 119.1° |
| CAD | CAC | H8 | 119.7° | 119.5° |
| CAA | CAF | CAE | 115.8° | 119.0° |
| CAA | CAF | CAQ | 124.2° | 120.5° |
| CAF | CAA | H9 | 118.2° | 119.6° |
| NAG | CAH | PAM | 102.9° | 109.5° |
| CAH | NAG | CAD | 120.7° | 120.0° |
| NAG | CAH | H3 | 115.2° | 109.4° |
| CAH | NAG | H6 | 106.6° | 119.9° |
| CAH | PAM | OAO | 104.3° | 109.4° |
| CAH | PAM | OAP | 112.7° | 109.5° |
| CAH | PAM | OAN | 108.9° | 109.4° |
| PAM | CAH | H3 | 109.6° | 109.5° |
| OAO | PAM | OAP | 108.2° | 109.5° |
| OAO | PAM | OAN | 111.7° | 109.5° |
| NAG | CAD | CAE | 118.4° | 120.4° |
| CAD | NAG | H6 | 106.6° | 120.0° |
| CAD | CAE | CAF | 124.1° | 118.2° |
| CAD | CAE | H7 | 118.0° | 120.9° |
| CAE | CAF | CAQ | 119.9° | 120.5° |
| CAF | CAE | H7 | 117.9° | 120.9° |
| CAF | CAQ | CAV | 117.3° | 120.1° |
| CAF | CAQ | CAR | 127.6° | 120.1° |
| OAP | PAM | OAN | 110.9° | 109.5° |
| PAM | OAP | H4 | 109.5° | 114.0° |
| PAM | OAN | H5 | 109.5° | 114.0° |
| CAV | CAQ | CAR | 115.0° | 119.9° |
| CAQ | CAV | CAU | 123.4° | 119.9° |
| CAQ | CAV | H10 | 118.3° | 120.0° |
| CAQ | CAR | CAS | 122.4° | 119.9° |
| CAQ | CAR | H12 | 118.8° | 120.1° |
| CAV | CAU | CAT | 122.6° | 120.1° |
| CAU | CAV | H10 | 118.3° | 120.1° |
| CAV | CAU | H11 | 118.7° | 120.0° |
| CAR | CAS | CAT | 121.2° | 120.1° |
| CAS | CAR | H12 | 118.8° | 120.0° |
| CAR | CAS | H13 | 119.4° | 120.0° |
| CAU | CAT | CAS | 115.3° | 120.1° |
| CAU | CAT | OAW | 117.0° | 120.0° |
| CAT | CAU | H11 | 118.7° | 119.9° |
| CAS | CAT | OAW | 127.6° | 119.9° |
| CAT | CAS | H13 | 119.4° | 119.9° |
| CAT | OAW | CAX | 116.3° | 117.0° |
| OAW | CAX | CAY | 107.8° | 117.5° |
| OAW | CAX | CAZ | 120.5° | 117.5° |
| OAW | CAX | H14 | 118.6° | 115.6° |
| CAX | CAY | CAZ | 62.6° | 60.0° |
| CAY | CAX | CAZ | 59.2° | 60.0° |
| CAY | CAX | H14 | 118.5° | 117.5° |
| CAX | CAY | H15 | 119.6° | 117.5° |
| CAX | CAY | H16 | 119.6° | 117.6° |
| CAY | CAZ | CAX | 58.2° | 60.0° |
| CAZ | CAY | H15 | 119.6° | 117.5° |
| CAZ | CAY | H16 | 119.6° | 117.6° |
| CAY | CAZ | H17 | 120.3° | 117.4° |
| CAY | CAZ | H18 | 120.3° | 117.5° |
| CAZ | CAX | H14 | 117.2° | 117.5° |
| CAX | CAZ | H17 | 120.3° | 117.5° |
| CAX | CAZ | H18 | 120.3° | 117.5° |
| H15 | CAY | H16 | 109.4° | 115.5° |
| H17 | CAZ | H18 | 109.5° | 115.6° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| OAJ | PAI | OAL | OAK | 115.2° | 120.0° |
| OAJ | PAI | OAL | CAH | 121.7° | 120.0° |
| OAJ | PAI | OAK | CAH | 123.7° | 120.0° |
| OAJ | PAI | CAH | NAG | 71.3° | 60.0° |
| OAJ | PAI | CAH | PAM | 177.0° | 180.0° |
| OAJ | PAI | OAK | H1 | 0.0° | 180.0° |
| OAJ | PAI | OAL | H2 | 0.0° | 60.0° |
| OAJ | PAI | CAH | H3 | 56.1° | 60.0° |
| OAL | PAI | OAK | CAH | 120.0° | 120.0° |
| OAL | PAI | CAH | NAG | 169.5° | 60.0° |
| OAL | PAI | CAH | PAM | 57.8° | 60.0° |
| OAL | PAI | OAK | H1 | 116.3° | 60.1° |
| OAL | PAI | CAH | H3 | 63.1° | 179.9° |
| OAK | PAI | CAH | NAG | 49.3° | 180.0° |
| OAK | PAI | CAH | PAM | 62.4° | 60.0° |
| OAK | PAI | OAL | H2 | 115.2° | 59.9° |
| OAK | PAI | CAH | H3 | 176.7° | 60.0° |
| PAI | CAH | NAG | PAM | 116.1° | 120.0° |
| PAI | CAH | NAG | H3 | 124.7° | 120.0° |
| PAI | CAH | PAM | H3 | 121.4° | 120.0° |
| PAI | CAH | PAM | OAO | 61.4° | 60.0° |
| PAI | CAH | NAG | CAD | 72.9° | 75.0° |
| PAI | CAH | PAM | OAP | 55.7° | 180.0° |
| PAI | CAH | PAM | OAN | 179.2° | 60.0° |
| CAH | PAI | OAK | H1 | 123.7° | 60.0° |
| CAH | PAI | OAL | H2 | 121.7° | 180.0° |
| PAI | CAH | NAG | H6 | 48.6° | 105.0° |
| NAB | CAC | CAD | H8 | 180.0° | 179.9° |
| CAC | NAB | CAA | CAF | 0.1° | 0.3° |
| NAB | CAC | CAD | NAG | 178.6° | 180.0° |
| NAB | CAC | CAD | CAE | 0.7° | 0.3° |
| CAC | NAB | CAA | H9 | 179.8° | 179.9° |
| CAA | NAB | CAC | CAD | 1.0° | 0.0° |
| NAB | CAA | CAF | H9 | 180.0° | 179.6° |
| NAB | CAA | CAF | CAE | 2.4° | 0.3° |
| NAB | CAA | CAF | CAQ | 180.0° | 180.0° |
| CAA | NAB | CAC | H8 | 179.0° | 180.0° |
| CAC | CAD | NAG | CAH | 29.7° | 0.3° |
| CAC | CAD | NAG | CAE | 177.8° | 179.7° |
| CAC | CAD | CAE | CAF | 3.6° | 0.3° |
| CAC | CAD | NAG | H6 | 151.3° | 179.7° |
| CAC | CAD | CAE | H7 | 176.4° | 179.7° |
| CAA | CAF | CAE | CAD | 4.3° | 0.0° |
| CAA | CAF | CAE | CAQ | 177.8° | 179.6° |
| CAA | CAF | CAQ | CAV | 142.2° | 0.1° |
| CAA | CAF | CAQ | CAR | 33.4° | 179.7° |
| CAA | CAF | CAE | H7 | 175.7° | 180.0° |
| NAG | CAH | PAM | H3 | 123.1° | 120.0° |
| NAG | CAH | PAM | OAO | 177.0° | 60.0° |
| CAH | NAG | CAD | H6 | 121.5° | 180.0° |
| CAH | NAG | CAD | CAE | 148.1° | 180.0° |
| NAG | CAH | PAM | OAP | 59.8° | 60.0° |
| NAG | CAH | PAM | OAN | 63.7° | 180.0° |
| CAH | PAM | OAO | OAP | 120.2° | 120.0° |
| CAH | PAM | OAO | OAN | 117.4° | 119.9° |
| PAM | CAH | NAG | CAD | 171.0° | 165.0° |
| CAH | PAM | OAP | OAN | 122.3° | 120.0° |
| CAH | PAM | OAP | H4 | 114.8° | 60.0° |
| CAH | PAM | OAN | H5 | 114.6° | 180.0° |
| PAM | CAH | NAG | H6 | 67.5° | 15.0° |
| OAO | PAM | OAP | OAN | 122.8° | 120.1° |
| OAO | PAM | CAH | H3 | 60.0° | 180.0° |
| OAO | PAM | OAP | H4 | 0.0° | 180.0° |
| OAO | PAM | OAN | H5 | 0.0° | 60.1° |
| NAG | CAD | CAE | CAF | 178.5° | 180.0° |
| CAD | NAG | CAH | H3 | 51.7° | 44.9° |
| NAG | CAD | CAE | H7 | 1.5° | 0.0° |
| NAG | CAD | CAC | H8 | 1.4° | 0.0° |
| CAD | CAE | CAF | H7 | 180.0° | 180.0° |
| CAD | CAE | CAF | CAQ | 177.9° | 179.7° |
| CAE | CAD | NAG | H6 | 26.6° | 0.0° |
| CAE | CAD | CAC | H8 | 179.3° | 179.7° |
| CAE | CAF | CAQ | CAV | 35.4° | 179.7° |
| CAE | CAF | CAQ | CAR | 149.0° | 0.1° |
| CAE | CAF | CAA | H9 | 177.6° | 180.0° |
| CAF | CAQ | CAV | CAR | 176.2° | 179.8° |
| CAF | CAQ | CAV | CAU | 178.1° | 180.0° |
| CAF | CAQ | CAR | CAS | 176.9° | 180.0° |
| CAQ | CAF | CAE | H7 | 2.1° | 0.3° |
| CAQ | CAF | CAA | H9 | 0.0° | 0.4° |
| CAF | CAQ | CAV | H10 | 2.0° | 0.1° |
| CAF | CAQ | CAR | H12 | 3.1° | 0.0° |
| OAP | PAM | CAH | H3 | 177.1° | 60.0° |
| OAP | PAM | OAN | H5 | 120.9° | 60.0° |
| OAN | PAM | CAH | H3 | 59.4° | 60.0° |
| OAN | PAM | OAP | H4 | 122.9° | 60.0° |
| CAQ | CAV | CAU | H10 | 180.0° | 180.0° |
| CAV | CAQ | CAR | CAS | 1.2° | 0.2° |
| CAQ | CAV | CAU | CAT | 1.0° | 0.1° |
| CAQ | CAV | CAU | H11 | 179.0° | 180.0° |
| CAV | CAQ | CAR | H12 | 178.8° | 179.8° |
| CAR | CAQ | CAV | CAU | 1.9° | 0.2° |
| CAQ | CAR | CAS | H12 | 180.0° | 180.0° |
| CAQ | CAR | CAS | CAT | 2.4° | 0.1° |
| CAR | CAQ | CAV | H10 | 178.1° | 179.8° |
| CAQ | CAR | CAS | H13 | 177.6° | 180.0° |
| CAV | CAU | CAT | H11 | 180.0° | 180.0° |
| CAV | CAU | CAT | CAS | 4.4° | 0.3° |
| CAV | CAU | CAT | OAW | 178.4° | 180.0° |
| CAR | CAS | CAT | CAU | 5.0° | 0.3° |
| CAR | CAS | CAT | H13 | 180.0° | 180.0° |
| CAR | CAS | CAT | OAW | 178.1° | 180.0° |
| CAU | CAT | CAS | OAW | 176.9° | 179.7° |
| CAU | CAT | OAW | CAX | 148.3° | 6.7° |
| CAT | CAU | CAV | H10 | 179.0° | 180.0° |
| CAU | CAT | CAS | H13 | 175.0° | 179.7° |
| CAS | CAT | OAW | CAX | 34.9° | 173.6° |
| CAS | CAT | CAU | H11 | 175.6° | 179.7° |
| CAT | CAS | CAR | H12 | 177.6° | 180.0° |
| CAT | OAW | CAX | CAY | 96.4° | 133.8° |
| CAT | OAW | CAX | CAZ | 160.6° | 157.6° |
| OAW | CAT | CAU | H11 | 1.6° | 0.0° |
| OAW | CAT | CAS | H13 | 1.9° | 0.0° |
| CAT | OAW | CAX | H14 | 41.9° | 11.9° |
| OAW | CAX | CAY | CAZ | 115.4° | 107.5° |
| OAW | CAX | CAY | H14 | 138.3° | 145.0° |
| OAW | CAX | CAZ | H14 | 157.8° | 145.1° |
| OAW | CAX | CAY | H15 | 134.5° | 145.0° |
| OAW | CAX | CAY | H16 | 5.2° | 0.0° |
| OAW | CAX | CAZ | H17 | 157.4° | 0.0° |
| OAW | CAX | CAZ | H18 | 15.4° | 145.0° |
| CAX | CAY | CAZ | H15 | 110.2° | 107.5° |
| CAX | CAY | CAZ | H16 | 110.2° | 107.5° |
| CAY | CAX | CAZ | H14 | 108.6° | 107.5° |
| CAX | CAY | H15 | H16 | 143.3° | 145.7° |
| CAX | CAY | CAZ | H17 | 109.0° | 107.5° |
| CAX | CAY | CAZ | H18 | 109.0° | 107.4° |
| CAZ | CAY | H15 | H16 | 143.3° | 145.7° |
| CAY | CAZ | H17 | H18 | 145.7° | 145.7° |
| CAX | CAZ | H17 | H18 | 145.7° | 145.7° |
| H3 | CAH | NAG | H6 | 173.3° | 135.0° |
| H10 | CAV | CAU | H11 | 1.0° | 0.0° |
| H12 | CAR | CAS | H13 | 2.4° | 0.0° |
| H14 | CAX | CAY | H15 | 3.8° | 0.0° |
| H14 | CAX | CAY | H16 | 143.5° | 145.0° |
| H14 | CAX | CAZ | H17 | 0.4° | 145.1° |
| H14 | CAX | CAZ | H18 | 142.4° | 0.0° |
| H15 | CAY | CAZ | H17 | 1.2° | 145.0° |
| H15 | CAY | CAZ | H18 | 140.8° | 0.1° |
| H16 | CAY | CAZ | H17 | 140.8° | 0.1° |
| H16 | CAY | CAZ | H18 | 1.2° | 145.0° |
