RY
Bonds
First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
OP1 | P | doub | 1.48Å | 1.48Å | |
O2 | C2 | doub | 1.22Å | 1.22Å | |
O3' | C3' | sing | 1.43Å | 1.43Å | |
O2' | C2' | sing | 1.43Å | 1.42Å | |
P | OP2 | sing | 1.61Å | 1.49Å | |
P | O5' | sing | 1.61Å | 1.63Å | |
C2 | N3 | sing | 1.34Å | 1.33Å | |
C2 | N1 | sing | 1.35Å | 1.40Å | |
C3' | C4' | sing | 1.54Å | 1.55Å | |
C3' | C2' | sing | 1.55Å | 1.55Å | |
C4' | O4' | sing | 1.44Å | 1.43Å | |
C4' | C5' | sing | 1.53Å | 1.54Å | |
C1' | C2' | sing | 1.55Å | 1.52Å | |
C1' | O4' | sing | 1.44Å | 1.41Å | |
C1' | N1 | sing | 1.47Å | 1.49Å | |
N3 | C4 | sing | 1.39Å | 1.30Å | |
N1 | C6 | sing | 1.47Å | 1.37Å | |
C5' | O5' | sing | 1.43Å | 1.43Å | |
C4 | N4 | sing | 1.39Å | 1.31Å | |
C4 | C5 | doub | 1.33Å | 1.42Å | |
C6 | C5 | sing | 1.51Å | 1.36Å | |
P | OP3 | sing | 1.61Å | 1.61Å | |
C5' | H5'' | sing | 1.09Å | 1.10Å | |
C5' | H5' | sing | 1.09Å | 1.10Å | |
C4' | H4' | sing | 1.09Å | 1.10Å | |
C3' | H3' | sing | 1.09Å | 1.10Å | |
O3' | H1 | sing | 0.97Å | 0.95Å | |
C2' | H2' | sing | 1.09Å | 1.10Å | |
O2' | HO2' | sing | 0.97Å | 0.95Å | |
C1' | H1' | sing | 1.09Å | 1.10Å | |
N3 | H3 | sing | 0.97Å | 1.00Å | |
N4 | H41 | sing | 0.97Å | 1.00Å | |
N4 | H42 | sing | 0.97Å | 1.00Å | |
C5 | H5 | sing | 1.08Å | 1.08Å | |
C6 | H6 | sing | 1.09Å | 1.10Å | |
C6 | H2 | sing | 1.09Å | 1.10Å | |
OP2 | H4 | sing | 0.97Å | 0.95Å | |
OP3 | H7 | sing | 0.97Å | 0.95Å |
Angles
First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
OP1 | P | OP2 | 116.5° | 109.5° |
OP1 | P | O5' | 109.0° | 109.4° |
OP1 | P | OP3 | 107.2° | 109.5° |
O2 | C2 | N3 | 116.5° | 119.0° |
O2 | C2 | N1 | 124.0° | 119.0° |
O3' | C3' | C4' | 113.9° | 110.5° |
O3' | C3' | C2' | 110.1° | 110.5° |
O3' | C3' | H3' | 111.0° | 110.5° |
C3' | O3' | H1 | 109.5° | 114.0° |
O2' | C2' | C3' | 115.3° | 110.9° |
O2' | C2' | C1' | 110.8° | 111.0° |
O2' | C2' | H2' | 110.5° | 110.8° |
C2' | O2' | HO2' | 109.5° | 114.0° |
OP2 | P | O5' | 108.4° | 109.5° |
OP2 | P | OP3 | 108.2° | 109.5° |
P | OP2 | H4 | 109.5° | 114.0° |
P | O5' | C5' | 124.4° | 123.0° |
O5' | P | OP3 | 107.3° | 109.4° |
N3 | C2 | N1 | 119.4° | 121.9° |
C2 | N3 | C4 | 122.3° | 123.4° |
C2 | N3 | H3 | 118.8° | 118.3° |
C2 | N1 | C1' | 119.5° | 120.8° |
C2 | N1 | C6 | 119.1° | 118.5° |
C4' | C3' | C2' | 103.0° | 104.2° |
C3' | C4' | O4' | 104.6° | 107.3° |
C3' | C4' | C5' | 113.8° | 109.9° |
C3' | C4' | H4' | 108.3° | 110.0° |
C4' | C3' | H3' | 109.2° | 110.5° |
C3' | C2' | C1' | 102.0° | 102.1° |
C2' | C3' | H3' | 109.3° | 110.5° |
C3' | C2' | H2' | 108.7° | 110.9° |
O4' | C4' | C5' | 111.7° | 109.9° |
C4' | O4' | C1' | 104.8° | 107.0° |
O4' | C4' | H4' | 109.9° | 109.9° |
C4' | C5' | O5' | 114.9° | 109.5° |
C4' | C5' | H5'' | 108.1° | 109.5° |
C4' | C5' | H5' | 108.1° | 109.4° |
C5' | C4' | H4' | 108.4° | 109.9° |
C2' | C1' | O4' | 102.0° | 103.5° |
C2' | C1' | N1 | 114.1° | 110.6° |
C1' | C2' | H2' | 109.1° | 110.9° |
C2' | C1' | H1' | 108.4° | 110.6° |
O4' | C1' | N1 | 113.4° | 110.6° |
O4' | C1' | H1' | 109.8° | 110.6° |
C1' | N1 | C6 | 121.4° | 120.8° |
N1 | C1' | H1' | 108.8° | 110.7° |
N3 | C4 | N4 | 119.2° | 119.5° |
N3 | C4 | C5 | 121.1° | 121.1° |
C4 | N3 | H3 | 118.9° | 118.3° |
N1 | C6 | C5 | 120.2° | 117.2° |
N1 | C6 | H6 | 106.7° | 107.9° |
N1 | C6 | H2 | 106.7° | 107.9° |
O5' | C5' | H5'' | 108.1° | 109.5° |
O5' | C5' | H5' | 108.1° | 109.5° |
N4 | C4 | C5 | 119.7° | 119.4° |
C4 | N4 | H41 | 109.5° | 119.9° |
C4 | N4 | H42 | 109.5° | 120.0° |
C4 | C5 | C6 | 117.7° | 118.0° |
C4 | C5 | H5 | 121.1° | 121.0° |
C6 | C5 | H5 | 121.2° | 121.0° |
C5 | C6 | H6 | 106.7° | 108.1° |
C5 | C6 | H2 | 106.7° | 107.7° |
P | OP3 | H7 | 109.5° | 114.0° |
H5'' | C5' | H5' | 109.5° | 109.5° |
H41 | N4 | H42 | 109.5° | 120.0° |
H6 | C6 | H2 | 109.5° | 107.7° |
Dihedrals
First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
OP1 | P | OP2 | O5' | 123.2° | 120.0° |
OP1 | P | OP2 | OP3 | 120.7° | 120.1° |
OP1 | P | O5' | OP3 | 115.7° | 120.0° |
OP1 | P | O5' | C5' | 5.3° | 55.0° |
OP1 | P | OP2 | H4 | 0.0° | 60.0° |
OP1 | P | OP3 | H7 | 0.0° | 180.0° |
O2 | C2 | N3 | N1 | 177.5° | 180.0° |
O2 | C2 | N1 | C1' | 4.3° | 0.1° |
O2 | C2 | N3 | C4 | 176.4° | 180.0° |
O2 | C2 | N1 | C6 | 174.2° | 179.7° |
O2 | C2 | N3 | H3 | 3.6° | 0.0° |
O3' | C3' | C2' | O2' | 14.4° | 20.5° |
O3' | C3' | C4' | C2' | 119.3° | 118.7° |
O3' | C3' | C4' | H3' | 124.7° | 122.6° |
O3' | C3' | C2' | H3' | 122.1° | 122.7° |
O3' | C3' | C4' | O4' | 131.7° | 120.7° |
O3' | C3' | C4' | C5' | 106.0° | 119.9° |
O3' | C3' | C2' | C1' | 105.8° | 97.8° |
O3' | C3' | C4' | H4' | 14.6° | 1.2° |
O3' | C3' | C2' | H2' | 139.1° | 144.0° |
O2' | C2' | C3' | C4' | 136.2° | 139.1° |
O2' | C2' | C3' | C1' | 120.2° | 118.3° |
O2' | C2' | C3' | H2' | 124.7° | 123.6° |
O2' | C2' | C1' | H2' | 121.9° | 123.6° |
O2' | C2' | C1' | O4' | 163.0° | 155.3° |
O2' | C2' | C1' | N1 | 74.3° | 86.2° |
O2' | C2' | C3' | H3' | 107.8° | 102.2° |
O2' | C2' | C1' | H1' | 47.1° | 36.8° |
OP2 | P | O5' | OP3 | 116.6° | 120.0° |
OP2 | P | O5' | C5' | 132.9° | 175.0° |
OP2 | P | OP3 | H7 | 126.3° | 60.0° |
P | O5' | C5' | C4' | 77.0° | 180.0° |
P | O5' | C5' | H5'' | 43.8° | 60.0° |
P | O5' | C5' | H5' | 162.2° | 60.0° |
O5' | P | OP2 | H4 | 123.2° | 180.0° |
O5' | P | OP3 | H7 | 116.9° | 60.0° |
N3 | C2 | N1 | C1' | 178.4° | 180.0° |
C2 | N3 | C4 | H3 | 180.0° | 180.0° |
N3 | C2 | N1 | C6 | 3.1° | 0.3° |
C2 | N3 | C4 | N4 | 179.3° | 180.0° |
C2 | N3 | C4 | C5 | 2.0° | 0.0° |
C2 | N1 | C1' | C2' | 107.7° | 64.8° |
C2 | N1 | C1' | O4' | 136.1° | 49.3° |
C2 | N1 | C1' | C6 | 178.5° | 179.8° |
N1 | C2 | N3 | C4 | 1.1° | 0.0° |
C2 | N1 | C6 | C5 | 2.0° | 0.5° |
C2 | N1 | C1' | H1' | 13.6° | 172.3° |
N1 | C2 | N3 | H3 | 178.9° | 180.0° |
C2 | N1 | C6 | H6 | 123.6° | 121.7° |
C2 | N1 | C6 | H2 | 119.5° | 122.2° |
C4' | C3' | C2' | H3' | 116.0° | 118.7° |
C3' | C4' | O4' | C5' | 123.6° | 119.4° |
C3' | C4' | O4' | H4' | 116.0° | 119.6° |
C3' | C4' | C5' | H4' | 120.5° | 121.2° |
C4' | C3' | C2' | C1' | 16.0° | 20.8° |
C3' | C4' | O4' | C1' | 39.1° | 26.5° |
C3' | C4' | C5' | O5' | 179.0° | 175.7° |
C3' | C4' | C5' | H5'' | 60.2° | 64.3° |
C3' | C4' | C5' | H5' | 58.2° | 55.7° |
C4' | C3' | O3' | H1 | 180.0° | 180.0° |
C4' | C3' | C2' | H2' | 99.1° | 97.3° |
C2' | C3' | C4' | O4' | 12.5° | 2.1° |
C2' | C3' | C4' | C5' | 134.7° | 121.5° |
C3' | C2' | C1' | H2' | 114.9° | 118.2° |
C3' | C2' | C1' | O4' | 39.7° | 37.0° |
C3' | C2' | C1' | N1 | 162.4° | 155.5° |
C2' | C3' | C4' | H4' | 104.7° | 117.5° |
C2' | C3' | O3' | H1 | 64.9° | 65.3° |
C3' | C2' | O2' | HO2' | 180.0° | 61.4° |
C3' | C2' | C1' | H1' | 76.2° | 81.5° |
O4' | C4' | C5' | H4' | 121.3° | 121.0° |
C4' | O4' | C1' | C2' | 50.1° | 40.0° |
C4' | O4' | C1' | N1 | 173.3° | 158.5° |
O4' | C4' | C5' | O5' | 60.8° | 66.4° |
O4' | C4' | C5' | H5'' | 178.4° | 53.6° |
O4' | C4' | C5' | H5' | 60.0° | 173.6° |
O4' | C4' | C3' | H3' | 103.6° | 116.7° |
C4' | O4' | C1' | H1' | 64.8° | 78.4° |
C5' | C4' | O4' | C1' | 162.7° | 145.9° |
C4' | C5' | O5' | H5'' | 120.8° | 120.0° |
C4' | C5' | O5' | H5' | 120.8° | 120.0° |
C4' | C5' | H5'' | H5' | 117.5° | 120.0° |
C5' | C4' | C3' | H3' | 18.6° | 2.8° |
C2' | C1' | O4' | N1 | 123.2° | 118.5° |
C2' | C1' | O4' | H1' | 114.9° | 118.5° |
C2' | C1' | N1 | H1' | 121.2° | 122.9° |
C2' | C1' | N1 | C6 | 70.8° | 115.0° |
C1' | C2' | C3' | H3' | 132.1° | 139.5° |
C1' | C2' | O2' | HO2' | 64.8° | 174.2° |
O4' | C1' | N1 | H1' | 122.5° | 123.0° |
O4' | C1' | N1 | C6 | 45.4° | 130.9° |
C1' | O4' | C4' | H4' | 76.9° | 93.1° |
O4' | C1' | C2' | H2' | 75.1° | 81.2° |
C1' | N1 | C6 | C5 | 179.5° | 179.7° |
N1 | C1' | C2' | H2' | 47.5° | 37.4° |
C1' | N1 | C6 | H6 | 57.9° | 58.1° |
C1' | N1 | C6 | H2 | 59.0° | 58.0° |
N3 | C4 | N4 | C5 | 178.7° | 180.0° |
N3 | C4 | C5 | C6 | 2.9° | 0.3° |
N3 | C4 | N4 | H41 | 180.0° | 0.1° |
N3 | C4 | N4 | H42 | 60.0° | 180.0° |
N3 | C4 | C5 | H5 | 177.0° | 180.0° |
N1 | C6 | C5 | C4 | 0.9° | 0.5° |
N1 | C6 | C5 | H6 | 121.5° | 122.1° |
N1 | C6 | C5 | H2 | 121.5° | 121.8° |
C6 | N1 | C1' | H1' | 167.9° | 7.9° |
N1 | C6 | C5 | H5 | 179.1° | 179.7° |
N1 | C6 | H6 | H2 | 115.1° | 116.2° |
C5' | O5' | P | OP3 | 110.5° | 65.0° |
O5' | C5' | H5'' | H5' | 117.5° | 120.0° |
O5' | C5' | C4' | H4' | 60.5° | 54.5° |
N4 | C4 | C5 | C6 | 178.3° | 179.7° |
N4 | C4 | N3 | H3 | 0.6° | 0.0° |
C4 | N4 | H41 | H42 | 120.0° | 180.0° |
N4 | C4 | C5 | H5 | 1.7° | 0.0° |
C4 | C5 | C6 | H5 | 180.0° | 179.7° |
C5 | C4 | N3 | H3 | 178.1° | 180.0° |
C5 | C4 | N4 | H41 | 1.3° | 180.0° |
C5 | C4 | N4 | H42 | 118.7° | 0.0° |
C4 | C5 | C6 | H6 | 120.6° | 121.6° |
C4 | C5 | C6 | H2 | 122.4° | 122.4° |
C5 | C6 | H6 | H2 | 115.1° | 116.1° |
OP3 | P | OP2 | H4 | 120.7° | 60.0° |
H5'' | C5' | C4' | H4' | 60.3° | 174.6° |
H5' | C5' | C4' | H4' | 178.8° | 65.5° |
H4' | C4' | C3' | H3' | 139.2° | 123.8° |
H3' | C3' | O3' | H1 | 56.2° | 57.4° |
H3' | C3' | C2' | H2' | 16.9° | 21.4° |
H2' | C2' | O2' | HO2' | 56.2° | 62.2° |
H2' | C2' | C1' | H1' | 169.0° | 160.3° |
H5 | C5 | C6 | H6 | 59.4° | 58.2° |
H5 | C5 | C6 | H2 | 57.6° | 57.9° |