MDJ
Bonds
First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
P | O1P | sing | 1.61Å | 1.51Å | |
P | O2P | doub | 1.48Å | 1.48Å | |
P | O5' | sing | 1.61Å | 1.52Å | |
N1 | C2 | sing | 1.35Å | 1.38Å | |
N1 | C6 | sing | 1.36Å | 1.37Å | |
N1 | C1' | sing | 1.47Å | 1.46Å | |
C2 | O2 | doub | 1.22Å | 1.26Å | |
C2 | C3 | sing | 1.40Å | 1.42Å | |
C3 | C4 | doub | 1.39Å | 1.42Å | |
C3 | C20 | sing | 1.51Å | 1.49Å | |
C4 | N4 | sing | 1.38Å | 1.40Å | |
C4 | C5 | sing | 1.41Å | 1.40Å | |
N4 | HN4 | sing | 0.97Å | 1.00Å | |
N4 | HN4A | sing | 0.97Å | 1.00Å | |
C5 | C6 | doub | 1.35Å | 1.40Å | |
C5 | H5 | sing | 1.08Å | 1.08Å | |
C6 | H6 | sing | 1.08Å | 1.08Å | |
C1' | C2' | sing | 1.54Å | 1.55Å | |
C1' | O4' | sing | 1.44Å | 1.44Å | |
C1' | H1' | sing | 1.09Å | 1.10Å | |
C2' | C3' | sing | 1.55Å | 1.53Å | |
C2' | H2' | sing | 1.09Å | 1.10Å | |
C2' | H2'A | sing | 1.09Å | 1.10Å | |
C20 | O21 | sing | 1.43Å | 1.42Å | |
C20 | H20 | sing | 1.09Å | 1.10Å | |
C20 | H20A | sing | 1.09Å | 1.10Å | |
O21 | HO21 | sing | 0.97Å | 0.95Å | |
C3' | O3' | sing | 1.43Å | 1.43Å | |
C3' | C4' | sing | 1.55Å | 1.54Å | |
C3' | H3' | sing | 1.09Å | 1.10Å | |
O3' | HO3' | sing | 0.97Å | 0.95Å | |
C4' | O4' | sing | 1.44Å | 1.43Å | |
C4' | C5' | sing | 1.53Å | 1.55Å | |
C4' | H4' | sing | 1.09Å | 1.10Å | |
C5' | O5' | sing | 1.43Å | 1.34Å | |
C5' | H5' | sing | 1.09Å | 1.10Å | |
C5' | H5'A | sing | 1.09Å | 1.10Å | |
O8 | P | sing | 1.61Å | 1.51Å | |
O1P | H16 | sing | 0.97Å | 0.95Å | |
O8 | H17 | sing | 0.97Å | 0.95Å |
Angles
First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
O1P | P | O2P | 109.6° | 109.5° |
O1P | P | O5' | 108.3° | 109.5° |
O1P | P | O8 | 108.9° | 109.5° |
P | O1P | H16 | 109.5° | 114.0° |
O2P | P | O5' | 109.7° | 109.5° |
O2P | P | O8 | 109.6° | 109.4° |
P | O5' | C5' | 128.2° | 123.0° |
O5' | P | O8 | 110.7° | 109.5° |
C2 | N1 | C6 | 119.2° | 121.1° |
C2 | N1 | C1' | 120.6° | 119.4° |
N1 | C2 | O2 | 119.8° | 119.9° |
N1 | C2 | C3 | 121.7° | 120.2° |
C6 | N1 | C1' | 120.3° | 119.4° |
N1 | C6 | C5 | 121.8° | 120.9° |
N1 | C6 | H6 | 119.1° | 119.6° |
N1 | C1' | C2' | 112.0° | 109.9° |
N1 | C1' | O4' | 115.8° | 109.9° |
N1 | C1' | H1' | 102.2° | 109.9° |
O2 | C2 | C3 | 118.5° | 119.9° |
C2 | C3 | C4 | 117.8° | 119.1° |
C2 | C3 | C20 | 122.6° | 120.4° |
C4 | C3 | C20 | 119.6° | 120.4° |
C3 | C4 | N4 | 121.7° | 120.5° |
C3 | C4 | C5 | 120.1° | 118.9° |
C3 | C20 | O21 | 110.4° | 109.5° |
C3 | C20 | H20 | 109.2° | 109.5° |
C3 | C20 | H20A | 109.2° | 109.5° |
N4 | C4 | C5 | 118.2° | 120.5° |
C4 | N4 | HN4 | 109.5° | 120.0° |
C4 | N4 | HN4A | 109.4° | 120.0° |
C4 | C5 | C6 | 119.3° | 119.8° |
C4 | C5 | H5 | 120.3° | 120.1° |
HN4 | N4 | HN4A | 109.5° | 120.0° |
C6 | C5 | H5 | 120.4° | 120.2° |
C5 | C6 | H6 | 119.1° | 119.5° |
C2' | C1' | O4' | 107.0° | 107.3° |
C2' | C1' | H1' | 111.9° | 109.9° |
C1' | C2' | C3' | 104.5° | 104.2° |
C1' | C2' | H2' | 111.2° | 110.4° |
C1' | C2' | H2'A | 111.1° | 110.5° |
O4' | C1' | H1' | 107.8° | 110.0° |
C1' | O4' | C4' | 110.2° | 107.0° |
C3' | C2' | H2' | 111.2° | 110.5° |
C3' | C2' | H2'A | 111.2° | 110.5° |
C2' | C3' | O3' | 110.7° | 110.9° |
C2' | C3' | C4' | 102.8° | 102.1° |
C2' | C3' | H3' | 113.6° | 110.9° |
H2' | C2' | H2'A | 107.7° | 110.6° |
O21 | C20 | H20 | 109.2° | 109.5° |
O21 | C20 | H20A | 109.1° | 109.4° |
C20 | O21 | HO21 | 109.5° | 114.0° |
H20 | C20 | H20A | 109.8° | 109.5° |
O3' | C3' | C4' | 111.2° | 110.9° |
O3' | C3' | H3' | 105.5° | 110.8° |
C3' | O3' | HO3' | 109.5° | 114.1° |
C4' | C3' | H3' | 113.1° | 110.9° |
C3' | C4' | O4' | 106.0° | 103.5° |
C3' | C4' | C5' | 113.9° | 110.6° |
C3' | C4' | H4' | 109.2° | 110.6° |
O4' | C4' | C5' | 110.4° | 110.6° |
O4' | C4' | H4' | 112.8° | 110.6° |
C5' | C4' | H4' | 104.7° | 110.7° |
C4' | C5' | O5' | 109.5° | 109.5° |
C4' | C5' | H5' | 109.5° | 109.5° |
C4' | C5' | H5'A | 109.4° | 109.5° |
O5' | C5' | H5' | 109.4° | 109.5° |
O5' | C5' | H5'A | 109.5° | 109.5° |
H5' | C5' | H5'A | 109.5° | 109.4° |
P | O8 | H17 | 109.5° | 114.0° |
Dihedrals
First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
O1P | P | O2P | O5' | 118.8° | 120.0° |
O1P | P | O2P | O8 | 119.5° | 120.0° |
O1P | P | O5' | O8 | 119.3° | 120.0° |
O1P | P | O5' | C5' | 138.2° | 64.9° |
O1P | P | O8 | H17 | 119.8° | 60.0° |
O2P | P | O5' | O8 | 121.1° | 120.0° |
O2P | P | O5' | C5' | 102.2° | 55.1° |
O2P | P | O1P | H16 | 0.0° | 180.0° |
O2P | P | O8 | H17 | 0.0° | 60.0° |
P | O5' | C5' | C4' | 167.0° | 180.0° |
P | O5' | C5' | H5' | 73.0° | 60.0° |
P | O5' | C5' | H5'A | 47.0° | 60.0° |
O5' | P | O1P | H16 | 119.7° | 60.0° |
O5' | P | O8 | H17 | 121.2° | 180.0° |
C2 | N1 | C6 | C1' | 178.6° | 179.7° |
N1 | C2 | O2 | C3 | 179.7° | 179.9° |
N1 | C2 | C3 | C4 | 1.3° | 0.1° |
N1 | C2 | C3 | C20 | 177.6° | 180.0° |
C2 | N1 | C6 | C5 | 3.9° | 0.1° |
C2 | N1 | C6 | H6 | 176.1° | 180.0° |
C2 | N1 | C1' | C2' | 67.2° | 115.0° |
C2 | N1 | C1' | O4' | 169.7° | 127.1° |
C2 | N1 | C1' | H1' | 52.8° | 6.0° |
C6 | N1 | C2 | O2 | 176.4° | 180.0° |
C6 | N1 | C2 | C3 | 4.0° | 0.1° |
N1 | C6 | C5 | C4 | 1.2° | 0.1° |
N1 | C6 | C5 | H6 | 180.0° | 179.9° |
N1 | C6 | C5 | H5 | 178.8° | 180.0° |
C6 | N1 | C1' | C2' | 111.4° | 65.3° |
C6 | N1 | C1' | O4' | 11.7° | 52.5° |
C6 | N1 | C1' | H1' | 128.6° | 173.6° |
C1' | N1 | C2 | O2 | 5.0° | 0.4° |
C1' | N1 | C2 | C3 | 174.6° | 179.7° |
C1' | N1 | C6 | C5 | 174.7° | 179.8° |
C1' | N1 | C6 | H6 | 5.3° | 0.3° |
N1 | C1' | C2' | O4' | 128.0° | 119.4° |
N1 | C1' | C2' | H1' | 114.2° | 121.0° |
N1 | C1' | O4' | H1' | 113.7° | 121.1° |
N1 | C1' | C2' | C3' | 140.5° | 121.4° |
N1 | C1' | C2' | H2' | 99.5° | 119.9° |
N1 | C1' | C2' | H2'A | 20.5° | 2.8° |
N1 | C1' | O4' | C4' | 118.3° | 145.9° |
O2 | C2 | C3 | C4 | 179.1° | 180.0° |
O2 | C2 | C3 | C20 | 2.0° | 0.1° |
C2 | C3 | C4 | C20 | 179.0° | 180.0° |
C2 | C3 | C4 | N4 | 177.7° | 179.9° |
C2 | C3 | C4 | C5 | 1.5° | 0.1° |
C2 | C3 | C20 | O21 | 118.3° | 58.4° |
C2 | C3 | C20 | H20 | 121.8° | 178.4° |
C2 | C3 | C20 | H20A | 1.7° | 61.5° |
C3 | C4 | N4 | C5 | 179.2° | 180.0° |
C3 | C4 | N4 | HN4 | 180.0° | 6.6° |
C3 | C4 | N4 | HN4A | 60.0° | 173.3° |
C3 | C4 | C5 | C6 | 1.6° | 0.1° |
C3 | C4 | C5 | H5 | 178.4° | 180.0° |
C4 | C3 | C20 | O21 | 62.9° | 121.6° |
C4 | C3 | C20 | H20 | 57.1° | 1.6° |
C4 | C3 | C20 | H20A | 177.2° | 118.5° |
C20 | C3 | C4 | N4 | 1.2° | 0.0° |
C20 | C3 | C4 | C5 | 179.6° | 179.9° |
C3 | C20 | O21 | H20 | 120.0° | 120.0° |
C3 | C20 | O21 | H20A | 120.0° | 120.0° |
C3 | C20 | H20 | H20A | 119.6° | 120.0° |
C3 | C20 | O21 | HO21 | 180.0° | 180.0° |
C4 | N4 | HN4 | HN4A | 120.0° | 180.0° |
N4 | C4 | C5 | C6 | 177.7° | 179.9° |
N4 | C4 | C5 | H5 | 2.3° | 0.0° |
C5 | C4 | N4 | HN4 | 0.8° | 173.4° |
C5 | C4 | N4 | HN4A | 119.3° | 6.6° |
C4 | C5 | C6 | H5 | 180.0° | 179.9° |
C4 | C5 | C6 | H6 | 178.8° | 180.0° |
H5 | C5 | C6 | H6 | 1.2° | 0.1° |
C2' | C1' | O4' | H1' | 120.5° | 119.5° |
C1' | C2' | C3' | H2' | 120.0° | 118.6° |
C1' | C2' | C3' | H2'A | 120.0° | 118.7° |
C1' | C2' | H2' | H2'A | 122.0° | 122.6° |
C1' | C2' | C3' | O3' | 93.0° | 139.1° |
C1' | C2' | C3' | C4' | 25.9° | 20.9° |
C1' | C2' | C3' | H3' | 148.4° | 97.3° |
C2' | C1' | O4' | C4' | 7.4° | 26.5° |
O4' | C1' | C2' | C3' | 12.5° | 2.0° |
O4' | C1' | C2' | H2' | 132.5° | 120.7° |
O4' | C1' | C2' | H2'A | 107.5° | 116.6° |
C1' | O4' | C4' | C3' | 24.4° | 40.1° |
C1' | O4' | C4' | C5' | 99.5° | 158.5° |
C1' | O4' | C4' | H4' | 143.8° | 78.4° |
H1' | C1' | C2' | C3' | 105.4° | 117.5° |
H1' | C1' | C2' | H2' | 14.7° | 1.2° |
H1' | C1' | C2' | H2'A | 134.6° | 123.8° |
H1' | C1' | O4' | C4' | 127.9° | 93.0° |
C3' | C2' | H2' | H2'A | 122.0° | 122.6° |
C2' | C3' | O3' | C4' | 113.7° | 112.7° |
C2' | C3' | O3' | H3' | 123.3° | 123.6° |
C2' | C3' | C4' | H3' | 122.9° | 118.2° |
C2' | C3' | O3' | HO3' | 180.0° | 61.4° |
C2' | C3' | C4' | O4' | 31.0° | 37.0° |
C2' | C3' | C4' | C5' | 90.6° | 155.5° |
C2' | C3' | C4' | H4' | 152.8° | 81.5° |
H2' | C2' | C3' | O3' | 27.0° | 20.4° |
H2' | C2' | C3' | C4' | 145.9° | 97.8° |
H2' | C2' | C3' | H3' | 91.6° | 144.0° |
H2'A | C2' | C3' | O3' | 147.0° | 102.2° |
H2'A | C2' | C3' | C4' | 94.1° | 139.5° |
H2'A | C2' | C3' | H3' | 28.4° | 21.3° |
O21 | C20 | H20 | H20A | 119.6° | 120.0° |
H20 | C20 | O21 | HO21 | 60.0° | 60.0° |
H20A | C20 | O21 | HO21 | 60.0° | 60.0° |
O3' | C3' | C4' | H3' | 118.6° | 123.6° |
O3' | C3' | C4' | O4' | 87.5° | 155.2° |
O3' | C3' | C4' | C5' | 150.9° | 86.3° |
O3' | C3' | C4' | H4' | 34.3° | 36.7° |
C4' | C3' | O3' | HO3' | 66.3° | 174.1° |
C3' | C4' | O4' | C5' | 123.9° | 118.5° |
C3' | C4' | O4' | H4' | 119.4° | 118.5° |
C3' | C4' | C5' | H4' | 119.2° | 122.9° |
C3' | C4' | C5' | O5' | 179.1° | 175.0° |
C3' | C4' | C5' | H5' | 60.9° | 55.0° |
C3' | C4' | C5' | H5'A | 59.1° | 65.0° |
H3' | C3' | O3' | HO3' | 56.7° | 62.2° |
H3' | C3' | C4' | O4' | 154.0° | 81.2° |
H3' | C3' | C4' | C5' | 32.3° | 37.3° |
H3' | C3' | C4' | H4' | 84.3° | 160.3° |
O4' | C4' | C5' | H4' | 121.6° | 123.0° |
O4' | C4' | C5' | O5' | 59.9° | 70.9° |
O4' | C4' | C5' | H5' | 179.9° | 169.0° |
O4' | C4' | C5' | H5'A | 60.1° | 49.1° |
C4' | C5' | O5' | H5' | 120.0° | 120.0° |
C4' | C5' | O5' | H5'A | 120.0° | 120.0° |
C4' | C5' | H5' | H5'A | 120.0° | 120.0° |
H4' | C4' | C5' | O5' | 61.7° | 52.1° |
H4' | C4' | C5' | H5' | 58.3° | 68.0° |
H4' | C4' | C5' | H5'A | 178.3° | 172.1° |
O5' | C5' | H5' | H5'A | 120.0° | 120.0° |
C5' | O5' | P | O8 | 18.9° | 175.0° |
O8 | P | O1P | H16 | 119.9° | 60.0° |