Bonds
First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
P | OP1 | doub | 1.48Å | 1.48Å | |
P | OP2 | sing | 1.61Å | 1.49Å | |
P | O5' | sing | 1.61Å | 1.59Å | |
P | OXT | sing | 1.61Å | 1.61Å | |
O5' | C5' | sing | 1.43Å | 1.41Å | |
C5' | C4' | sing | 1.53Å | 1.51Å | |
C5' | H5'1 | sing | 1.09Å | 1.10Å | |
C5' | H5'2 | sing | 1.09Å | 1.10Å | |
C4' | O4' | sing | 1.44Å | 1.45Å | |
C4' | C3' | sing | 1.54Å | 1.52Å | |
C4' | H4' | sing | 1.09Å | 1.10Å | |
O4' | C1' | sing | 1.44Å | 1.42Å | |
C3' | O3' | sing | 1.43Å | 1.42Å | |
C3' | C2' | sing | 1.55Å | 1.52Å | |
C3' | H3' | sing | 1.09Å | 1.10Å | |
O3' | HA | sing | 0.97Å | 0.95Å | |
C2' | O2' | sing | 1.43Å | 1.41Å | |
C2' | C1' | sing | 1.55Å | 1.53Å | |
C2' | H2' | sing | 1.09Å | 1.10Å | |
O2' | HB | sing | 0.97Å | 0.95Å | |
C1' | N1 | sing | 1.46Å | 1.47Å | |
C1' | H1' | sing | 1.09Å | 1.10Å | |
N1 | C2 | sing | 1.35Å | 1.39Å | |
N1 | C6 | sing | 1.37Å | 1.39Å | |
C2 | O2 | doub | 1.22Å | 1.22Å | |
C2 | N3 | sing | 1.35Å | 1.37Å | |
N3 | C4 | sing | 1.35Å | 1.38Å | |
N3 | H3 | sing | 0.97Å | 1.00Å | |
C4 | O4 | doub | 1.22Å | 1.23Å | |
C4 | C5 | sing | 1.42Å | 1.44Å | |
C5 | C6 | doub | 1.35Å | 1.34Å | |
C5 | I | sing | 2.10Å | 1.63Å | |
C6 | H6 | sing | 1.08Å | 1.08Å | |
OP2 | H11 | sing | 0.97Å | 0.95Å | |
OXT | H12 | sing | 0.97Å | 0.95Å |
Angles
First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
OP1 | P | OP2 | 119.5° | 109.5° |
OP1 | P | O5' | 108.9° | 109.5° |
OP1 | P | OXT | 106.5° | 109.5° |
OP2 | P | O5' | 107.2° | 109.4° |
OP2 | P | OXT | 110.4° | 109.5° |
P | OP2 | H11 | 109.5° | 114.0° |
O5' | P | OXT | 103.1° | 109.5° |
P | O5' | C5' | 120.3° | 123.0° |
P | OXT | H12 | 109.5° | 114.0° |
O5' | C5' | C4' | 110.6° | 109.5° |
O5' | C5' | H5'1 | 109.1° | 109.5° |
O5' | C5' | H5'2 | 108.9° | 109.5° |
C4' | C5' | H5'1 | 109.1° | 109.5° |
C4' | C5' | H5'2 | 108.8° | 109.5° |
C5' | C4' | O4' | 110.3° | 109.8° |
C5' | C4' | C3' | 112.2° | 109.9° |
C5' | C4' | H4' | 105.7° | 109.9° |
H5'1 | C5' | H5'2 | 110.3° | 109.4° |
O4' | C4' | C3' | 104.9° | 107.3° |
O4' | C4' | H4' | 112.9° | 109.8° |
C4' | O4' | C1' | 109.6° | 106.9° |
C3' | C4' | H4' | 111.0° | 110.1° |
C4' | C3' | O3' | 109.5° | 110.5° |
C4' | C3' | C2' | 102.4° | 104.2° |
C4' | C3' | H3' | 115.4° | 110.4° |
O4' | C1' | C2' | 106.9° | 103.5° |
O4' | C1' | N1 | 107.9° | 110.6° |
O4' | C1' | H1' | 113.9° | 110.5° |
O3' | C3' | C2' | 113.3° | 110.6° |
O3' | C3' | H3' | 104.8° | 110.4° |
C3' | O3' | HA | 109.5° | 114.0° |
C2' | C3' | H3' | 111.7° | 110.6° |
C3' | C2' | O2' | 111.4° | 110.9° |
C3' | C2' | C1' | 101.1° | 102.1° |
C3' | C2' | H2' | 113.9° | 111.0° |
O2' | C2' | C1' | 110.4° | 110.9° |
O2' | C2' | H2' | 105.2° | 110.8° |
C2' | O2' | HB | 109.5° | 114.0° |
C1' | C2' | H2' | 114.9° | 110.9° |
C2' | C1' | N1 | 114.4° | 110.7° |
C2' | C1' | H1' | 107.4° | 110.7° |
N1 | C1' | H1' | 106.5° | 110.7° |
C1' | N1 | C2 | 118.3° | 119.7° |
C1' | N1 | C6 | 120.9° | 119.7° |
C2 | N1 | C6 | 120.8° | 120.6° |
N1 | C2 | O2 | 123.1° | 119.5° |
N1 | C2 | N3 | 115.0° | 120.9° |
N1 | C6 | C5 | 122.9° | 119.7° |
N1 | C6 | H6 | 118.5° | 120.1° |
O2 | C2 | N3 | 121.9° | 119.6° |
C2 | N3 | C4 | 127.3° | 120.3° |
C2 | N3 | H3 | 116.4° | 119.9° |
C4 | N3 | H3 | 116.4° | 119.8° |
N3 | C4 | O4 | 119.1° | 120.3° |
N3 | C4 | C5 | 114.8° | 119.4° |
O4 | C4 | C5 | 126.2° | 120.4° |
C4 | C5 | C6 | 119.3° | 119.1° |
C4 | C5 | I | 120.5° | 120.4° |
C6 | C5 | I | 120.1° | 120.4° |
C5 | C6 | H6 | 118.6° | 120.2° |
Dihedrals
First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
OP1 | P | OP2 | O5' | 124.4° | 120.0° |
OP1 | P | OP2 | OXT | 123.9° | 120.0° |
OP1 | P | O5' | OXT | 112.8° | 120.0° |
OP1 | P | O5' | C5' | 88.8° | 55.0° |
OP1 | P | OP2 | H11 | 92.0° | 60.0° |
OP1 | P | OXT | H12 | 134.3° | 180.0° |
OP2 | P | O5' | OXT | 116.6° | 120.0° |
OP2 | P | O5' | C5' | 41.9° | 175.0° |
OP2 | P | OXT | H12 | 94.6° | 59.9° |
P | O5' | C5' | C4' | 160.9° | 180.0° |
P | O5' | C5' | H5'1 | 40.9° | 60.0° |
P | O5' | C5' | H5'2 | 79.6° | 59.9° |
O5' | P | OP2 | H11 | 32.4° | 180.0° |
O5' | P | OXT | H12 | 19.7° | 60.0° |
OXT | P | O5' | C5' | 158.4° | 65.0° |
OXT | P | OP2 | H11 | 144.1° | 60.0° |
O5' | C5' | C4' | H5'1 | 120.0° | 120.0° |
O5' | C5' | C4' | H5'2 | 119.5° | 120.0° |
O5' | C5' | H5'1 | H5'2 | 119.5° | 120.0° |
O5' | C5' | C4' | O4' | 52.3° | 66.4° |
O5' | C5' | C4' | C3' | 168.9° | 175.7° |
O5' | C5' | C4' | H4' | 70.0° | 54.5° |
C4' | C5' | H5'1 | H5'2 | 119.5° | 120.0° |
C5' | C4' | O4' | C3' | 121.0° | 119.4° |
C5' | C4' | O4' | H4' | 118.0° | 120.9° |
C5' | C4' | C3' | H4' | 118.0° | 121.1° |
C5' | C4' | O4' | C1' | 137.2° | 145.9° |
C5' | C4' | C3' | O3' | 85.6° | 119.8° |
C5' | C4' | C3' | C2' | 153.9° | 121.4° |
C5' | C4' | C3' | H3' | 32.3° | 2.6° |
H5'1 | C5' | C4' | O4' | 67.7° | 53.6° |
H5'1 | C5' | C4' | C3' | 48.9° | 64.3° |
H5'1 | C5' | C4' | H4' | 170.0° | 174.5° |
H5'2 | C5' | C4' | O4' | 171.9° | 173.6° |
H5'2 | C5' | C4' | C3' | 71.6° | 55.7° |
H5'2 | C5' | C4' | H4' | 49.6° | 65.5° |
O4' | C4' | C3' | H4' | 122.2° | 119.5° |
O4' | C4' | C3' | O3' | 154.6° | 120.8° |
O4' | C4' | C3' | C2' | 34.1° | 2.0° |
O4' | C4' | C3' | H3' | 87.4° | 116.8° |
C4' | O4' | C1' | C2' | 8.4° | 40.0° |
C4' | O4' | C1' | N1 | 115.1° | 158.6° |
C4' | O4' | C1' | H1' | 127.0° | 78.5° |
C3' | C4' | O4' | C1' | 16.2° | 26.5° |
C4' | C3' | O3' | C2' | 113.6° | 114.8° |
C4' | C3' | O3' | H3' | 124.3° | 122.5° |
C4' | C3' | C2' | H3' | 124.0° | 118.7° |
C4' | C3' | O3' | HA | 62.2° | 180.0° |
C4' | C3' | C2' | O2' | 79.5° | 139.1° |
C4' | C3' | C2' | C1' | 37.8° | 20.9° |
C4' | C3' | C2' | H2' | 161.6° | 97.3° |
H4' | C4' | O4' | C1' | 104.8° | 93.1° |
H4' | C4' | C3' | O3' | 32.4° | 1.3° |
H4' | C4' | C3' | C2' | 88.1° | 117.5° |
H4' | C4' | C3' | H3' | 150.4° | 123.7° |
O4' | C1' | C2' | C3' | 29.2° | 37.0° |
O4' | C1' | C2' | O2' | 88.8° | 155.2° |
O4' | C1' | C2' | N1 | 119.4° | 118.5° |
O4' | C1' | C2' | H1' | 122.7° | 118.4° |
O4' | C1' | C2' | H2' | 152.4° | 81.2° |
O4' | C1' | N1 | H1' | 122.7° | 122.9° |
O4' | C1' | N1 | C2 | 176.7° | 126.4° |
O4' | C1' | N1 | C6 | 3.0° | 53.3° |
O3' | C3' | C2' | H3' | 118.1° | 122.6° |
O3' | C3' | C2' | O2' | 38.4° | 20.4° |
O3' | C3' | C2' | C1' | 155.7° | 97.8° |
O3' | C3' | C2' | H2' | 80.5° | 143.9° |
C2' | C3' | O3' | HA | 175.8° | 65.1° |
C3' | C2' | O2' | C1' | 111.5° | 112.7° |
C3' | C2' | O2' | H2' | 123.9° | 123.7° |
C3' | C2' | C1' | H2' | 123.2° | 118.3° |
C3' | C2' | O2' | HB | 71.3° | 61.5° |
C3' | C2' | C1' | N1 | 90.2° | 155.6° |
C3' | C2' | C1' | H1' | 151.9° | 81.4° |
H3' | C3' | O3' | HA | 62.1° | 57.5° |
H3' | C3' | C2' | O2' | 156.5° | 102.2° |
H3' | C3' | C2' | C1' | 86.2° | 139.6° |
H3' | C3' | C2' | H2' | 37.6° | 21.3° |
O2' | C2' | C1' | H2' | 118.8° | 123.6° |
O2' | C2' | C1' | N1 | 151.8° | 86.3° |
O2' | C2' | C1' | H1' | 33.9° | 36.8° |
C1' | C2' | O2' | HB | 40.2° | 174.2° |
C2' | C1' | N1 | H1' | 118.5° | 123.1° |
C2' | C1' | N1 | C2 | 64.5° | 119.5° |
C2' | C1' | N1 | C6 | 115.8° | 60.8° |
H2' | C2' | O2' | HB | 164.7° | 62.2° |
H2' | C2' | C1' | N1 | 33.0° | 37.3° |
H2' | C2' | C1' | H1' | 84.9° | 160.3° |
C1' | N1 | C2 | C6 | 179.7° | 179.7° |
C1' | N1 | C2 | O2 | 0.5° | 0.0° |
C1' | N1 | C2 | N3 | 179.6° | 180.0° |
C1' | N1 | C6 | C5 | 179.6° | 179.7° |
C1' | N1 | C6 | H6 | 0.4° | 0.0° |
H1' | C1' | N1 | C2 | 54.0° | 3.6° |
H1' | C1' | N1 | C6 | 125.7° | 176.2° |
N1 | C2 | O2 | N3 | 179.9° | 180.0° |
N1 | C2 | N3 | C4 | 0.1° | 0.1° |
N1 | C2 | N3 | H3 | 179.9° | 180.0° |
C2 | N1 | C6 | C5 | 0.0° | 0.6° |
C2 | N1 | C6 | H6 | 180.0° | 179.7° |
C6 | N1 | C2 | O2 | 179.8° | 179.8° |
C6 | N1 | C2 | N3 | 0.1° | 0.2° |
N1 | C6 | C5 | C4 | 0.0° | 0.6° |
N1 | C6 | C5 | H6 | 180.0° | 179.7° |
N1 | C6 | C5 | I | 179.6° | 179.7° |
O2 | C2 | N3 | C4 | 179.8° | 179.9° |
O2 | C2 | N3 | H3 | 0.2° | 0.0° |
C2 | N3 | C4 | H3 | 180.0° | 179.9° |
C2 | N3 | C4 | O4 | 179.9° | 180.0° |
C2 | N3 | C4 | C5 | 0.1° | 0.0° |
N3 | C4 | O4 | C5 | 180.0° | 179.9° |
N3 | C4 | C5 | C6 | 0.0° | 0.3° |
N3 | C4 | C5 | I | 179.6° | 180.0° |
H3 | N3 | C4 | O4 | 0.1° | 0.1° |
H3 | N3 | C4 | C5 | 179.9° | 179.9° |
O4 | C4 | C5 | C6 | 180.0° | 179.6° |
O4 | C4 | C5 | I | 0.4° | 0.0° |
C4 | C5 | C6 | I | 179.6° | 179.7° |
C4 | C5 | C6 | H6 | 180.0° | 179.7° |
I | C5 | C6 | H6 | 0.4° | 0.1° |