GDN
Bonds
| First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
| N1 | CA1 | sing | 1.44Å | 1.46Å | |
| N1 | HN1 | sing | 1.01Å | 1.00Å | |
| N1 | HN2A | sing | 1.01Å | 1.00Å | |
| CA1 | C1 | sing | 1.52Å | 1.52Å | |
| CA1 | CB1 | sing | 1.53Å | 1.52Å | |
| CA1 | HA1 | sing | 1.09Å | 1.10Å | |
| C1 | O11 | doub | 1.22Å | 1.24Å | |
| C1 | O12 | sing | 1.36Å | 1.24Å | |
| O12 | H12 | sing | 0.98Å | 0.95Å | |
| CB1 | CG1 | sing | 1.53Å | 1.51Å | |
| CB1 | HB11 | sing | 1.10Å | 1.10Å | |
| CB1 | HB12 | sing | 1.10Å | 1.10Å | |
| CG1 | CD1 | sing | 1.52Å | 1.51Å | |
| CG1 | HG11 | sing | 1.10Å | 1.10Å | |
| CG1 | HG12 | sing | 1.10Å | 1.10Å | |
| CD1 | OE1 | doub | 1.23Å | 1.23Å | |
| CD1 | N2 | sing | 1.39Å | 1.32Å | |
| N2 | CA2 | sing | 1.44Å | 1.45Å | |
| N2 | HN2 | sing | 1.02Å | 1.00Å | |
| CA2 | C2 | sing | 1.53Å | 1.53Å | |
| CA2 | CB2 | sing | 1.53Å | 1.54Å | |
| CA2 | HA2 | sing | 1.10Å | 1.10Å | |
| C2 | O2 | doub | 1.23Å | 1.22Å | |
| C2 | N3 | sing | 1.39Å | 1.32Å | |
| CB2 | SG2 | sing | 1.82Å | 1.83Å | |
| CB2 | HB21 | sing | 1.10Å | 1.10Å | |
| CB2 | HB22 | sing | 1.09Å | 1.10Å | |
| SG2 | C1' | sing | 1.76Å | 37.46Å | |
| N3 | CA3 | sing | 1.44Å | 1.46Å | |
| N3 | HN3 | sing | 1.02Å | 1.00Å | |
| CA3 | C3 | sing | 1.50Å | 1.51Å | |
| CA3 | HA31 | sing | 1.09Å | 1.10Å | |
| CA3 | HA32 | sing | 1.09Å | 1.10Å | |
| C3 | O31 | doub | 1.22Å | 1.24Å | |
| C3 | O32 | sing | 1.36Å | 1.24Å | |
| O32 | H32 | sing | 0.98Å | 0.95Å | |
| C1' | C2' | doub | 1.41Å | 0.00Å | Aromatic |
| C1' | C6' | sing | 1.41Å | 0.00Å | Aromatic |
| C2' | C3' | sing | 1.39Å | 0.00Å | Aromatic |
| C2' | N2' | sing | 1.42Å | 0.00Å | |
| C3' | C4' | doub | 1.39Å | 0.00Å | Aromatic |
| C3' | H3' | sing | 1.09Å | 0.00Å | |
| C4' | C5' | sing | 1.40Å | 0.00Å | Aromatic |
| C4' | N4' | sing | 1.42Å | 0.00Å | |
| C5' | C6' | doub | 1.39Å | 0.00Å | Aromatic |
| C5' | H5' | sing | 1.09Å | 0.00Å | |
| C6' | H6' | sing | 1.09Å | 0.00Å | |
| N2' | O2A | sing | 1.25Å | 0.00Å | |
| N2' | O2B | doub | 1.25Å | 0.00Å | |
| N4' | O4A | sing | 1.26Å | 0.00Å | |
| N4' | O4B | doub | 1.26Å | 0.00Å |
Angles
| First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
| CA1 | N1 | HN1 | 109.5° | 119.0° |
| CA1 | N1 | HN2A | 109.5° | 119.1° |
| N1 | CA1 | C1 | 111.2° | 106.5° |
| N1 | CA1 | CB1 | 109.7° | 112.4° |
| N1 | CA1 | HA1 | 108.4° | 106.0° |
| HN1 | N1 | HN2A | 109.4° | 120.5° |
| C1 | CA1 | CB1 | 110.3° | 110.2° |
| C1 | CA1 | HA1 | 107.9° | 109.2° |
| CA1 | C1 | O11 | 117.4° | 125.3° |
| CA1 | C1 | O12 | 119.4° | 111.9° |
| CB1 | CA1 | HA1 | 109.3° | 112.2° |
| CA1 | CB1 | CG1 | 114.8° | 113.4° |
| CA1 | CB1 | HB11 | 107.7° | 109.3° |
| CA1 | CB1 | HB12 | 106.5° | 109.8° |
| O11 | C1 | O12 | 123.1° | 122.8° |
| C1 | O12 | H12 | 109.5° | 115.3° |
| CG1 | CB1 | HB11 | 107.7° | 108.4° |
| CG1 | CB1 | HB12 | 106.6° | 109.6° |
| CB1 | CG1 | CD1 | 111.7° | 113.6° |
| CB1 | CG1 | HG11 | 108.7° | 110.7° |
| CB1 | CG1 | HG12 | 108.2° | 108.7° |
| HB11 | CB1 | HB12 | 113.7° | 106.1° |
| CD1 | CG1 | HG11 | 108.7° | 109.4° |
| CD1 | CG1 | HG12 | 108.2° | 106.9° |
| CG1 | CD1 | OE1 | 121.1° | 123.3° |
| CG1 | CD1 | N2 | 115.8° | 111.7° |
| HG11 | CG1 | HG12 | 111.2° | 107.3° |
| OE1 | CD1 | N2 | 122.9° | 125.1° |
| CD1 | N2 | CA2 | 121.2° | 122.7° |
| CD1 | N2 | HN2 | 119.4° | 118.7° |
| CA2 | N2 | HN2 | 119.4° | 118.6° |
| N2 | CA2 | C2 | 111.0° | 108.9° |
| N2 | CA2 | CB2 | 109.7° | 112.3° |
| N2 | CA2 | HA2 | 108.7° | 105.6° |
| C2 | CA2 | CB2 | 110.5° | 113.4° |
| C2 | CA2 | HA2 | 107.8° | 107.6° |
| CA2 | C2 | O2 | 120.7° | 123.0° |
| CA2 | C2 | N3 | 117.2° | 112.2° |
| CB2 | CA2 | HA2 | 109.1° | 108.7° |
| CA2 | CB2 | SG2 | 115.5° | 113.8° |
| CA2 | CB2 | HB21 | 107.5° | 110.5° |
| CA2 | CB2 | HB22 | 106.1° | 110.0° |
| O2 | C2 | N3 | 122.0° | 124.8° |
| C2 | N3 | CA3 | 123.3° | 122.7° |
| C2 | N3 | HN3 | 118.3° | 119.5° |
| SG2 | CB2 | HB21 | 107.5° | 107.3° |
| SG2 | CB2 | HB22 | 106.2° | 107.4° |
| CB2 | SG2 | C1' | 122.4° | 99.6° |
| HB21 | CB2 | HB22 | 114.3° | 107.6° |
| SG2 | C1' | C2' | 90.0° | 123.1° |
| SG2 | C1' | C6' | 90.0° | 118.7° |
| CA3 | N3 | HN3 | 118.4° | 117.8° |
| N3 | CA3 | C3 | 110.5° | 108.6° |
| N3 | CA3 | HA31 | 109.1° | 109.0° |
| N3 | CA3 | HA32 | 108.9° | 109.1° |
| C3 | CA3 | HA31 | 109.1° | 109.6° |
| C3 | CA3 | HA32 | 108.9° | 109.9° |
| CA3 | C3 | O31 | 118.9° | 126.5° |
| CA3 | C3 | O32 | 118.4° | 109.9° |
| HA31 | CA3 | HA32 | 110.3° | 110.6° |
| O31 | C3 | O32 | 122.7° | 123.6° |
| C3 | O32 | H32 | 109.5° | 111.9° |
| C2' | C1' | C6' | 90.0° | 118.1° |
| C1' | C2' | C3' | 90.0° | 120.9° |
| C1' | C2' | N2' | 90.0° | 121.0° |
| C1' | C6' | C5' | 90.0° | 120.9° |
| C1' | C6' | H6' | 90.0° | 120.3° |
| C3' | C2' | N2' | 90.0° | 118.1° |
| C2' | C3' | C4' | 90.0° | 120.0° |
| C2' | C3' | H3' | 90.0° | 120.1° |
| C2' | N2' | O2A | 90.0° | 118.8° |
| C2' | N2' | O2B | 90.0° | 118.8° |
| C4' | C3' | H3' | 90.0° | 119.9° |
| C3' | C4' | C5' | 90.0° | 120.0° |
| C3' | C4' | N4' | 90.0° | 120.1° |
| C5' | C4' | N4' | 90.0° | 120.0° |
| C4' | C5' | C6' | 90.0° | 120.0° |
| C4' | C5' | H5' | 90.0° | 120.7° |
| C4' | N4' | O4A | 90.0° | 119.0° |
| C4' | N4' | O4B | 90.0° | 119.0° |
| C6' | C5' | H5' | 90.0° | 119.2° |
| C5' | C6' | H6' | 90.0° | 118.8° |
| O2A | N2' | O2B | 90.0° | 122.4° |
| O4A | N4' | O4B | 90.0° | 122.0° |
Dihedrals
| First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
| CA1 | N1 | HN1 | HN2A | 120.0° | 166.4° |
| N1 | CA1 | C1 | CB1 | 121.9° | 122.2° |
| N1 | CA1 | C1 | HA1 | 118.8° | 114.1° |
| N1 | CA1 | CB1 | HA1 | 118.8° | 119.4° |
| N1 | CA1 | C1 | O11 | 17.3° | 35.9° |
| N1 | CA1 | C1 | O12 | 160.7° | 146.4° |
| N1 | CA1 | CB1 | CG1 | 160.9° | 62.3° |
| N1 | CA1 | CB1 | HB11 | 40.9° | 58.7° |
| N1 | CA1 | CB1 | HB12 | 81.4° | 174.7° |
| HN1 | N1 | CA1 | C1 | 131.8° | 133.9° |
| HN1 | N1 | CA1 | CB1 | 9.6° | 105.2° |
| HN1 | N1 | CA1 | HA1 | 109.8° | 17.7° |
| HN2A | N1 | CA1 | C1 | 108.2° | 59.4° |
| HN2A | N1 | CA1 | CB1 | 129.6° | 61.4° |
| HN2A | N1 | CA1 | HA1 | 10.2° | 175.7° |
| C1 | CA1 | CB1 | HA1 | 118.4° | 121.9° |
| CA1 | C1 | O11 | O12 | 178.0° | 177.5° |
| CA1 | C1 | O12 | H12 | 177.9° | 177.8° |
| C1 | CA1 | CB1 | CG1 | 76.3° | 179.0° |
| C1 | CA1 | CB1 | HB11 | 163.7° | 60.0° |
| C1 | CA1 | CB1 | HB12 | 41.3° | 56.0° |
| CB1 | CA1 | C1 | O11 | 104.6° | 86.4° |
| CB1 | CA1 | C1 | O12 | 77.4° | 91.3° |
| CA1 | CB1 | CG1 | HB11 | 120.0° | 121.6° |
| CA1 | CB1 | CG1 | HB12 | 117.6° | 123.1° |
| CA1 | CB1 | HB11 | HB12 | 117.8° | 118.3° |
| CA1 | CB1 | CG1 | CD1 | 173.1° | 58.4° |
| CA1 | CB1 | CG1 | HG11 | 66.9° | 65.1° |
| CA1 | CB1 | CG1 | HG12 | 54.1° | 177.3° |
| HA1 | CA1 | C1 | O11 | 136.1° | 150.0° |
| HA1 | CA1 | C1 | O12 | 42.0° | 32.3° |
| HA1 | CA1 | CB1 | CG1 | 42.1° | 57.1° |
| HA1 | CA1 | CB1 | HB11 | 77.9° | 178.1° |
| HA1 | CA1 | CB1 | HB12 | 159.8° | 65.9° |
| O11 | C1 | O12 | H12 | 0.0° | 0.0° |
| CG1 | CB1 | HB11 | HB12 | 117.9° | 117.6° |
| CB1 | CG1 | CD1 | HG11 | 120.0° | 124.2° |
| CB1 | CG1 | CD1 | HG12 | 119.0° | 119.9° |
| CB1 | CG1 | HG11 | HG12 | 119.1° | 118.5° |
| CB1 | CG1 | CD1 | OE1 | 22.3° | 31.3° |
| CB1 | CG1 | CD1 | N2 | 152.8° | 150.0° |
| HB11 | CB1 | CG1 | CD1 | 53.1° | 180.0° |
| HB11 | CB1 | CG1 | HG11 | 173.1° | 56.5° |
| HB11 | CB1 | CG1 | HG12 | 65.9° | 61.1° |
| HB12 | CB1 | CG1 | CD1 | 69.3° | 64.6° |
| HB12 | CB1 | CG1 | HG11 | 50.7° | 171.9° |
| HB12 | CB1 | CG1 | HG12 | 171.7° | 54.2° |
| CD1 | CG1 | HG11 | HG12 | 119.1° | 115.6° |
| CG1 | CD1 | OE1 | N2 | 174.8° | 178.5° |
| CG1 | CD1 | N2 | CA2 | 179.6° | 178.7° |
| CG1 | CD1 | N2 | HN2 | 0.3° | 1.3° |
| HG11 | CG1 | CD1 | OE1 | 142.3° | 155.5° |
| HG11 | CG1 | CD1 | N2 | 32.8° | 25.8° |
| HG12 | CG1 | CD1 | OE1 | 96.7° | 88.7° |
| HG12 | CG1 | CD1 | N2 | 88.1° | 90.1° |
| OE1 | CD1 | N2 | CA2 | 4.6° | 0.1° |
| OE1 | CD1 | N2 | HN2 | 175.4° | 180.0° |
| CD1 | N2 | CA2 | HN2 | 180.0° | 180.0° |
| CD1 | N2 | CA2 | C2 | 124.3° | 145.3° |
| CD1 | N2 | CA2 | CB2 | 113.3° | 88.3° |
| CD1 | N2 | CA2 | HA2 | 5.9° | 30.0° |
| N2 | CA2 | C2 | CB2 | 121.9° | 125.9° |
| N2 | CA2 | C2 | HA2 | 118.9° | 114.0° |
| N2 | CA2 | CB2 | HA2 | 118.9° | 116.4° |
| N2 | CA2 | C2 | O2 | 154.4° | 6.0° |
| N2 | CA2 | C2 | N3 | 27.8° | 175.1° |
| N2 | CA2 | CB2 | SG2 | 64.5° | 63.1° |
| N2 | CA2 | CB2 | HB21 | 55.5° | 176.0° |
| N2 | CA2 | CB2 | HB22 | 178.2° | 57.4° |
| HN2 | N2 | CA2 | C2 | 55.7° | 34.8° |
| HN2 | N2 | CA2 | CB2 | 66.7° | 91.7° |
| HN2 | N2 | CA2 | HA2 | 174.1° | 150.0° |
| C2 | CA2 | CB2 | HA2 | 118.4° | 119.6° |
| CA2 | C2 | O2 | N3 | 177.7° | 178.7° |
| C2 | CA2 | CB2 | SG2 | 172.9° | 60.9° |
| C2 | CA2 | CB2 | HB21 | 67.1° | 60.0° |
| C2 | CA2 | CB2 | HB22 | 55.6° | 178.6° |
| CA2 | C2 | N3 | CA3 | 179.9° | 178.9° |
| CA2 | C2 | N3 | HN3 | 0.1° | 4.0° |
| CB2 | CA2 | C2 | O2 | 32.5° | 119.8° |
| CB2 | CA2 | C2 | N3 | 149.7° | 59.0° |
| CA2 | CB2 | SG2 | HB21 | 120.0° | 122.6° |
| CA2 | CB2 | SG2 | HB22 | 117.3° | 122.0° |
| CA2 | CB2 | HB21 | HB22 | 117.5° | 120.1° |
| CA2 | CB2 | SG2 | C1' | 38.6° | 180.0° |
| HA2 | CA2 | C2 | O2 | 86.7° | 120.0° |
| HA2 | CA2 | C2 | N3 | 91.1° | 61.1° |
| HA2 | CA2 | CB2 | SG2 | 54.5° | 179.6° |
| HA2 | CA2 | CB2 | HB21 | 174.5° | 59.6° |
| HA2 | CA2 | CB2 | HB22 | 62.8° | 59.0° |
| O2 | C2 | N3 | CA3 | 2.3° | 0.0° |
| O2 | C2 | N3 | HN3 | 177.7° | 177.1° |
| C2 | N3 | CA3 | HN3 | 180.0° | 177.1° |
| C2 | N3 | CA3 | C3 | 107.8° | 90.0° |
| C2 | N3 | CA3 | HA31 | 12.2° | 150.6° |
| C2 | N3 | CA3 | HA32 | 132.7° | 29.7° |
| SG2 | CB2 | HB21 | HB22 | 117.6° | 115.3° |
| CB2 | SG2 | C1' | C2' | 90.0° | 120.0° |
| CB2 | SG2 | C1' | C6' | 90.0° | 60.0° |
| HB21 | CB2 | SG2 | C1' | 81.4° | 57.3° |
| HB22 | CB2 | SG2 | C1' | 155.8° | 58.1° |
| SG2 | C1' | C2' | C6' | 90.0° | 180.0° |
| SG2 | C1' | C2' | C3' | 90.0° | 180.0° |
| SG2 | C1' | C2' | N2' | 90.0° | 0.0° |
| SG2 | C1' | C6' | C5' | 90.0° | 180.0° |
| SG2 | C1' | C6' | H6' | 90.0° | 0.0° |
| N3 | CA3 | C3 | HA31 | 120.0° | 119.0° |
| N3 | CA3 | C3 | HA32 | 119.6° | 119.3° |
| N3 | CA3 | HA31 | HA32 | 119.6° | 119.9° |
| N3 | CA3 | C3 | O31 | 16.2° | 29.0° |
| N3 | CA3 | C3 | O32 | 164.4° | 151.0° |
| HN3 | N3 | CA3 | C3 | 72.2° | 92.8° |
| HN3 | N3 | CA3 | HA31 | 167.8° | 26.5° |
| HN3 | N3 | CA3 | HA32 | 47.3° | 147.4° |
| C3 | CA3 | HA31 | HA32 | 119.6° | 121.3° |
| CA3 | C3 | O31 | O32 | 179.4° | 179.9° |
| CA3 | C3 | O32 | H32 | 179.4° | 179.9° |
| HA31 | CA3 | C3 | O31 | 103.8° | 90.0° |
| HA31 | CA3 | C3 | O32 | 75.6° | 90.0° |
| HA32 | CA3 | C3 | O31 | 135.7° | 148.2° |
| HA32 | CA3 | C3 | O32 | 44.8° | 31.7° |
| O31 | C3 | O32 | H32 | 0.0° | 0.0° |
| C1' | C2' | C3' | N2' | 90.0° | 180.0° |
| C1' | C2' | C3' | C4' | 90.0° | 0.1° |
| C1' | C2' | C3' | H3' | 90.0° | 180.0° |
| C2' | C1' | C6' | C5' | 90.0° | 0.0° |
| C2' | C1' | C6' | H6' | 90.0° | 180.0° |
| C1' | C2' | N2' | O2A | 90.0° | 180.0° |
| C1' | C2' | N2' | O2B | 90.0° | 0.0° |
| C6' | C1' | C2' | C3' | 90.0° | 0.0° |
| C6' | C1' | C2' | N2' | 90.0° | 180.0° |
| C1' | C6' | C5' | C4' | 90.0° | 0.0° |
| C1' | C6' | C5' | H6' | 90.0° | 180.0° |
| C1' | C6' | C5' | H5' | 90.0° | 180.0° |
| C2' | C3' | C4' | H3' | 90.0° | 179.9° |
| C2' | C3' | C4' | C5' | 90.0° | 0.1° |
| C2' | C3' | C4' | N4' | 90.0° | 180.0° |
| C3' | C2' | N2' | O2A | 90.0° | 0.1° |
| C3' | C2' | N2' | O2B | 90.0° | 180.0° |
| N2' | C2' | C3' | C4' | 90.0° | 180.0° |
| N2' | C2' | C3' | H3' | 90.0° | 0.1° |
| C2' | N2' | O2A | O2B | 90.0° | 180.0° |
| C3' | C4' | C5' | N4' | 90.0° | 179.9° |
| C3' | C4' | C5' | C6' | 90.0° | 0.0° |
| C3' | C4' | C5' | H5' | 90.0° | 180.0° |
| C3' | C4' | N4' | O4A | 90.0° | 180.0° |
| C3' | C4' | N4' | O4B | 90.0° | 0.0° |
| H3' | C3' | C4' | C5' | 90.0° | 180.0° |
| H3' | C3' | C4' | N4' | 90.0° | 0.1° |
| C4' | C5' | C6' | H5' | 90.0° | 179.9° |
| C4' | C5' | C6' | H6' | 90.0° | 180.0° |
| C5' | C4' | N4' | O4A | 90.0° | 0.1° |
| C5' | C4' | N4' | O4B | 90.0° | 180.0° |
| N4' | C4' | C5' | C6' | 90.0° | 180.0° |
| N4' | C4' | C5' | H5' | 90.0° | 0.1° |
| C4' | N4' | O4A | O4B | 90.0° | 180.0° |
| H5' | C5' | C6' | H6' | 90.0° | 0.0° |
