JKM
Bonds
First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
O20 | P | sing | 1.65Å | 1.70Å | |
O3P | P | doub | 1.48Å | 1.50Å | |
P | O2P | sing | 1.61Å | 1.61Å | |
P | O2' | sing | 1.64Å | 1.74Å | |
C1' | N1 | sing | 1.47Å | 1.52Å | |
C2 | N1 | sing | 1.35Å | 1.50Å | |
N1 | C6 | sing | 1.37Å | 1.42Å | |
O2 | C2 | doub | 1.22Å | 1.20Å | |
C2 | N3 | sing | 1.35Å | 1.42Å | |
N3 | C4 | sing | 1.35Å | 1.35Å | |
C4 | C5 | sing | 1.42Å | 1.44Å | |
C4 | O4 | doub | 1.22Å | 1.34Å | |
C6 | C5 | doub | 1.35Å | 1.36Å | |
C5 | H5 | sing | 1.08Å | 1.08Å | |
C6 | H6 | sing | 1.08Å | 1.08Å | |
O4' | C1' | sing | 1.46Å | 1.45Å | |
C2' | C1' | sing | 1.52Å | 1.53Å | |
C1' | H1' | sing | 1.09Å | 1.10Å | |
C3' | C2' | sing | 1.57Å | 1.58Å | |
C2' | O2' | sing | 1.41Å | 1.38Å | |
C2' | H2' | sing | 1.09Å | 1.10Å | |
O20 | C3' | sing | 1.41Å | 1.40Å | |
O2P | HO2P | sing | 0.97Å | 0.95Å | |
C4' | C3' | sing | 1.51Å | 1.54Å | |
C3' | H3' | sing | 1.09Å | 1.10Å | |
C4' | C5' | sing | 1.53Å | 1.55Å | |
C4' | O4' | sing | 1.45Å | 1.43Å | |
C4' | H4' | sing | 1.09Å | 1.10Å | |
O5' | C5' | sing | 1.43Å | 1.41Å | |
C5' | H5' | sing | 1.09Å | 1.10Å | |
C5' | H5'A | sing | 1.09Å | 1.10Å | |
O5' | HO5' | sing | 0.97Å | 0.95Å | |
N3 | HN3 | sing | 0.97Å | 1.00Å |
Angles
First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
O20 | P | O3P | 120.6° | 110.7° |
O20 | P | O2P | 104.1° | 110.7° |
O20 | P | O2' | 90.9° | 103.1° |
P | O20 | C3' | 110.2° | 99.4° |
O3P | P | O2P | 113.8° | 110.6° |
O3P | P | O2' | 117.9° | 110.7° |
O2P | P | O2' | 106.4° | 110.7° |
P | O2P | HO2P | 109.5° | 113.9° |
P | O2' | C2' | 105.5° | 101.8° |
C1' | N1 | C2 | 131.0° | 119.7° |
C1' | N1 | C6 | 111.0° | 119.7° |
N1 | C1' | O4' | 115.5° | 110.6° |
N1 | C1' | C2' | 121.8° | 110.6° |
N1 | C1' | H1' | 104.8° | 110.6° |
C2 | N1 | C6 | 118.0° | 120.6° |
N1 | C2 | O2 | 122.0° | 119.6° |
N1 | C2 | N3 | 117.6° | 120.9° |
N1 | C6 | C5 | 123.5° | 119.7° |
N1 | C6 | H6 | 118.3° | 120.2° |
O2 | C2 | N3 | 120.3° | 119.5° |
C2 | N3 | C4 | 119.2° | 120.2° |
C2 | N3 | HN3 | 120.4° | 119.9° |
N3 | C4 | C5 | 125.4° | 119.4° |
N3 | C4 | O4 | 121.7° | 120.3° |
C4 | N3 | HN3 | 120.4° | 119.9° |
C5 | C4 | O4 | 112.9° | 120.3° |
C4 | C5 | C6 | 116.3° | 119.1° |
C4 | C5 | H5 | 121.8° | 120.4° |
C6 | C5 | H5 | 121.9° | 120.5° |
C5 | C6 | H6 | 118.3° | 120.1° |
O4' | C1' | C2' | 103.1° | 103.2° |
O4' | C1' | H1' | 105.5° | 110.9° |
C1' | O4' | C4' | 110.6° | 109.3° |
C2' | C1' | H1' | 104.7° | 110.7° |
C1' | C2' | C3' | 96.2° | 99.0° |
C1' | C2' | O2' | 127.3° | 124.4° |
C1' | C2' | H2' | 109.8° | 109.6° |
C3' | C2' | O2' | 98.7° | 104.0° |
C3' | C2' | H2' | 109.2° | 108.6° |
C2' | C3' | O20 | 102.9° | 102.4° |
C2' | C3' | C4' | 103.4° | 100.1° |
C2' | C3' | H3' | 106.4° | 109.9° |
O2' | C2' | H2' | 112.1° | 109.7° |
O20 | C3' | C4' | 127.0° | 123.9° |
O20 | C3' | H3' | 108.6° | 110.0° |
C4' | C3' | H3' | 106.9° | 109.2° |
C3' | C4' | C5' | 105.1° | 110.2° |
C3' | C4' | O4' | 104.0° | 105.7° |
C3' | C4' | H4' | 111.4° | 110.2° |
C5' | C4' | O4' | 111.6° | 110.2° |
C5' | C4' | H4' | 111.2° | 110.2° |
C4' | C5' | O5' | 109.1° | 109.5° |
C4' | C5' | H5' | 109.6° | 109.4° |
C4' | C5' | H5'A | 109.6° | 109.5° |
O4' | C4' | H4' | 113.1° | 110.2° |
O5' | C5' | H5' | 109.6° | 109.5° |
O5' | C5' | H5'A | 109.6° | 109.5° |
C5' | O5' | HO5' | 109.5° | 114.0° |
H5' | C5' | H5'A | 109.4° | 109.5° |
Dihedrals
First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
O20 | P | O3P | O2P | 124.8° | 123.1° |
O20 | P | O3P | O2' | 109.5° | 113.7° |
O20 | P | O2P | O2' | 95.2° | 113.7° |
P | O20 | C3' | C2' | 31.9° | 46.2° |
O20 | P | O2' | C2' | 33.6° | 9.1° |
O20 | P | O2P | HO2P | 133.2° | 66.3° |
P | O20 | C3' | C4' | 150.0° | 157.6° |
P | O20 | C3' | H3' | 80.5° | 70.6° |
O3P | P | O2P | O2' | 131.6° | 123.1° |
O3P | P | O2' | C2' | 92.2° | 109.3° |
O3P | P | O20 | C3' | 125.7° | 143.0° |
O3P | P | O2P | HO2P | 0.0° | 56.9° |
O2P | P | O2' | C2' | 138.6° | 127.6° |
O2P | P | O20 | C3' | 105.0° | 93.9° |
P | O2' | C2' | C1' | 158.4° | 148.0° |
P | O2' | C2' | C3' | 53.7° | 36.5° |
P | O2' | C2' | H2' | 61.2° | 79.5° |
O2' | P | O20 | C3' | 2.2° | 24.5° |
O2' | P | O2P | HO2P | 131.6° | 180.0° |
C1' | N1 | C2 | C6 | 179.1° | 179.8° |
C1' | N1 | C2 | O2 | 1.2° | 0.2° |
C1' | N1 | C2 | N3 | 178.3° | 179.7° |
C1' | N1 | C6 | C5 | 179.8° | 179.8° |
C1' | N1 | C6 | H6 | 0.2° | 0.2° |
N1 | C1' | O4' | C2' | 135.3° | 118.4° |
N1 | C1' | O4' | H1' | 115.2° | 123.1° |
N1 | C1' | C2' | H1' | 118.2° | 123.0° |
N1 | C1' | C2' | C3' | 176.8° | 161.3° |
N1 | C1' | C2' | O2' | 77.3° | 84.8° |
N1 | C1' | C2' | H2' | 63.8° | 47.8° |
N1 | C1' | O4' | C4' | 169.1° | 143.2° |
N1 | C2 | O2 | N3 | 179.5° | 179.9° |
N1 | C2 | N3 | C4 | 1.2° | 0.1° |
C2 | N1 | C6 | C5 | 0.9° | 0.0° |
C2 | N1 | C6 | H6 | 179.1° | 180.0° |
C2 | N1 | C1' | O4' | 81.2° | 175.8° |
C2 | N1 | C1' | C2' | 45.0° | 62.1° |
C2 | N1 | C1' | H1' | 163.2° | 60.9° |
N1 | C2 | N3 | HN3 | 178.8° | 180.0° |
C6 | N1 | C2 | O2 | 179.7° | 180.0° |
C6 | N1 | C2 | N3 | 0.8° | 0.1° |
N1 | C6 | C5 | C4 | 2.0° | 0.0° |
N1 | C6 | C5 | H6 | 180.0° | 180.0° |
N1 | C6 | C5 | H5 | 178.0° | 180.0° |
C6 | N1 | C1' | O4' | 98.0° | 4.0° |
C6 | N1 | C1' | C2' | 135.8° | 117.6° |
C6 | N1 | C1' | H1' | 17.6° | 119.3° |
O2 | C2 | N3 | C4 | 179.2° | 180.0° |
O2 | C2 | N3 | HN3 | 0.7° | 0.1° |
C2 | N3 | C4 | HN3 | 180.0° | 179.9° |
C2 | N3 | C4 | C5 | 0.0° | 0.1° |
C2 | N3 | C4 | O4 | 179.8° | 180.0° |
N3 | C4 | C5 | O4 | 179.8° | 179.9° |
N3 | C4 | C5 | C6 | 1.6° | 0.0° |
N3 | C4 | C5 | H5 | 178.4° | 179.9° |
C4 | C5 | C6 | H5 | 180.0° | 179.9° |
C4 | C5 | C6 | H6 | 178.0° | 179.9° |
C5 | C4 | N3 | HN3 | 180.0° | 179.9° |
O4 | C4 | C5 | C6 | 178.6° | 179.9° |
O4 | C4 | C5 | H5 | 1.4° | 0.0° |
O4 | C4 | N3 | HN3 | 0.2° | 0.1° |
H5 | C5 | C6 | H6 | 2.0° | 0.0° |
O4' | C1' | C2' | H1' | 110.2° | 118.7° |
O4' | C1' | C2' | C3' | 45.2° | 43.0° |
O4' | C1' | C2' | O2' | 151.1° | 156.9° |
O4' | C1' | C2' | H2' | 67.9° | 70.5° |
C1' | O4' | C4' | C3' | 5.3° | 5.2° |
C1' | O4' | C4' | C5' | 107.4° | 124.3° |
C1' | O4' | C4' | H4' | 126.3° | 113.9° |
C1' | C2' | C3' | O2' | 129.3° | 128.9° |
C1' | C2' | C3' | H2' | 113.5° | 114.3° |
C1' | C2' | O2' | H2' | 140.3° | 132.6° |
C1' | C2' | C3' | O20 | 175.6° | 173.6° |
C1' | C2' | C3' | C4' | 42.1° | 45.3° |
C1' | C2' | C3' | H3' | 70.3° | 69.5° |
C2' | C1' | O4' | C4' | 33.8° | 24.8° |
H1' | C1' | C2' | C3' | 65.0° | 75.7° |
H1' | C1' | C2' | O2' | 40.9° | 38.2° |
H1' | C1' | C2' | H2' | 178.0° | 170.8° |
H1' | C1' | O4' | C4' | 75.7° | 93.7° |
C3' | C2' | O2' | H2' | 114.9° | 116.0° |
C2' | C3' | O20 | C4' | 118.1° | 111.4° |
C2' | C3' | O20 | H3' | 112.4° | 116.8° |
C2' | C3' | C4' | H3' | 112.0° | 115.4° |
C2' | C3' | C4' | C5' | 141.6° | 150.7° |
C2' | C3' | C4' | O4' | 24.2° | 31.6° |
C2' | C3' | C4' | H4' | 97.9° | 87.5° |
O2' | C2' | C3' | O20 | 55.1° | 57.4° |
O2' | C2' | C3' | C4' | 171.4° | 174.3° |
O2' | C2' | C3' | H3' | 59.0° | 59.4° |
H2' | C2' | C3' | O20 | 62.1° | 59.3° |
H2' | C2' | C3' | C4' | 71.4° | 69.0° |
H2' | C2' | C3' | H3' | 176.2° | 176.1° |
O20 | C3' | C4' | H3' | 130.2° | 132.1° |
O20 | C3' | C4' | C5' | 100.6° | 96.8° |
O20 | C3' | C4' | O4' | 142.0° | 144.2° |
O20 | C3' | C4' | H4' | 20.0° | 25.0° |
C3' | C4' | C5' | O4' | 112.1° | 116.3° |
C3' | C4' | C5' | H4' | 120.7° | 121.9° |
C3' | C4' | O4' | H4' | 121.0° | 119.1° |
C3' | C4' | C5' | O5' | 75.1° | 175.0° |
C3' | C4' | C5' | H5' | 44.8° | 55.0° |
C3' | C4' | C5' | H5'A | 164.9° | 65.0° |
H3' | C3' | C4' | C5' | 29.6° | 35.3° |
H3' | C3' | C4' | O4' | 87.8° | 83.7° |
H3' | C3' | C4' | H4' | 150.1° | 157.1° |
C5' | C4' | O4' | H4' | 126.3° | 121.8° |
C4' | C5' | O5' | H5' | 119.9° | 120.0° |
C4' | C5' | O5' | H5'A | 120.0° | 120.0° |
C4' | C5' | H5' | H5'A | 120.2° | 120.0° |
C4' | C5' | O5' | HO5' | 180.0° | 180.0° |
O4' | C4' | C5' | O5' | 172.8° | 68.7° |
O4' | C4' | C5' | H5' | 67.2° | 171.3° |
O4' | C4' | C5' | H5'A | 52.9° | 51.3° |
H4' | C4' | C5' | O5' | 45.5° | 53.2° |
H4' | C4' | C5' | H5' | 165.5° | 66.9° |
H4' | C4' | C5' | H5'A | 74.4° | 173.2° |
O5' | C5' | H5' | H5'A | 120.2° | 120.0° |
H5' | C5' | O5' | HO5' | 60.1° | 60.0° |
H5'A | C5' | O5' | HO5' | 60.0° | 60.0° |