M5M
Bonds
First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
P | OP1 | doub | 1.50Å | 1.48Å | |
P | OP2 | sing | 1.62Å | 1.48Å | |
P | O5' | sing | 1.62Å | 1.60Å | |
P | OP3 | sing | 1.62Å | 67.28Å | |
N2' | C6' | sing | 1.38Å | 1.33Å | |
N2' | C2' | sing | 1.44Å | 1.45Å | |
N2' | HN'2 | sing | 1.02Å | 1.02Å | |
C6' | C7' | sing | 1.49Å | 1.50Å | |
C6' | O8' | doub | 1.23Å | 1.23Å | |
C7' | H7'1 | sing | 1.10Å | 1.12Å | |
C7' | H7'2 | sing | 1.10Å | 1.12Å | |
C7' | H7'3 | sing | 1.10Å | 1.11Å | |
OP2 | HOP2 | sing | 0.98Å | 0.95Å | |
O5' | C5' | sing | 1.42Å | 1.43Å | |
C5' | C4' | sing | 1.52Å | 1.52Å | |
C5' | H5' | sing | 1.09Å | 1.12Å | |
C5' | H5'' | sing | 1.09Å | 1.11Å | |
C4' | O4' | sing | 1.44Å | 1.45Å | |
C4' | C3' | sing | 1.52Å | 1.52Å | |
C4' | H4' | sing | 1.10Å | 1.11Å | |
O4' | C1' | sing | 1.44Å | 1.42Å | |
C1' | N1 | sing | 1.44Å | 1.47Å | |
C1' | C2' | sing | 1.52Å | 1.53Å | |
C1' | H1' | sing | 1.09Å | 1.11Å | |
N1 | C6 | sing | 1.38Å | 1.37Å | |
N1 | C2 | sing | 1.42Å | 1.39Å | |
C6 | C5 | doub | 1.33Å | 1.34Å | |
C6 | H6 | sing | 1.08Å | 1.10Å | |
C2 | O2 | doub | 1.23Å | 1.24Å | |
C2 | N3 | sing | 1.38Å | 1.35Å | |
N3 | C4 | doub | 1.31Å | 1.33Å | |
C4 | N4 | sing | 1.38Å | 1.33Å | |
C4 | C5 | sing | 1.49Å | 1.42Å | |
N4 | HN41 | sing | 0.99Å | 1.02Å | |
N4 | HN42 | sing | 0.99Å | 1.02Å | |
C5 | H5 | sing | 1.08Å | 1.10Å | |
C2' | C3' | sing | 1.52Å | 1.52Å | |
C2' | H2' | sing | 1.10Å | 1.12Å | |
C3' | O3' | sing | 1.43Å | 1.43Å | |
C3' | H3' | sing | 1.09Å | 1.12Å | |
O3' | HO3' | sing | 0.97Å | 0.95Å | |
OP3 | HOP3 | sing | 0.98Å | 0.95Å |
Angles
First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
OP1 | P | OP2 | 119.5° | 115.3° |
OP1 | P | O5' | 108.5° | 115.0° |
OP1 | P | OP3 | 74.1° | 115.0° |
OP2 | P | O5' | 110.5° | 103.8° |
OP2 | P | OP3 | 68.9° | 103.3° |
P | OP2 | HOP2 | 119.5° | 118.9° |
O5' | P | OP3 | 80.7° | 102.8° |
P | O5' | C5' | 120.0° | 118.5° |
P | OP3 | HOP3 | 74.2° | 118.9° |
C6' | N2' | C2' | 124.3° | 123.1° |
C6' | N2' | HN'2 | 113.1° | 118.5° |
N2' | C6' | C7' | 115.1° | 114.0° |
N2' | C6' | O8' | 123.0° | 126.5° |
C2' | N2' | HN'2 | 122.6° | 118.4° |
N2' | C2' | C1' | 108.5° | 113.3° |
N2' | C2' | C3' | 108.1° | 114.0° |
N2' | C2' | H2' | 108.6° | 107.0° |
C7' | C6' | O8' | 121.9° | 119.5° |
C6' | C7' | H7'1 | 115.1° | 112.4° |
C6' | C7' | H7'2 | 110.1° | 112.4° |
C6' | C7' | H7'3 | 110.2° | 115.3° |
H7'1 | C7' | H7'2 | 110.2° | 105.3° |
H7'1 | C7' | H7'3 | 110.2° | 105.3° |
H7'2 | C7' | H7'3 | 100.1° | 105.2° |
O5' | C5' | C4' | 111.4° | 108.9° |
O5' | C5' | H5' | 111.4° | 109.0° |
O5' | C5' | H5'' | 111.5° | 109.0° |
C4' | C5' | H5' | 111.5° | 110.3° |
C4' | C5' | H5'' | 111.5° | 110.4° |
C5' | C4' | O4' | 109.3° | 108.2° |
C5' | C4' | C3' | 118.5° | 113.3° |
C5' | C4' | H4' | 101.6° | 109.3° |
H5' | C5' | H5'' | 98.9° | 109.3° |
O4' | C4' | C3' | 103.8° | 105.8° |
O4' | C4' | H4' | 116.9° | 107.7° |
C4' | O4' | C1' | 109.5° | 109.4° |
C3' | C4' | H4' | 107.3° | 112.2° |
C4' | C3' | C2' | 101.6° | 102.4° |
C4' | C3' | O3' | 112.0° | 108.7° |
C4' | C3' | H3' | 113.2° | 113.6° |
O4' | C1' | N1 | 108.2° | 108.9° |
O4' | C1' | C2' | 107.3° | 107.0° |
O4' | C1' | H1' | 112.9° | 107.9° |
N1 | C1' | C2' | 112.6° | 112.7° |
N1 | C1' | H1' | 107.6° | 107.5° |
C1' | N1 | C6 | 121.1° | 118.6° |
C1' | N1 | C2 | 118.6° | 121.8° |
C2' | C1' | H1' | 108.5° | 112.6° |
C1' | C2' | C3' | 101.0° | 102.4° |
C1' | C2' | H2' | 114.9° | 110.6° |
C6 | N1 | C2 | 120.4° | 119.6° |
N1 | C6 | C5 | 120.9° | 122.6° |
N1 | C6 | H6 | 120.7° | 116.2° |
N1 | C2 | O2 | 118.7° | 121.1° |
N1 | C2 | N3 | 119.5° | 118.7° |
C5 | C6 | H6 | 118.4° | 121.2° |
C6 | C5 | C4 | 117.5° | 116.3° |
C6 | C5 | H5 | 118.3° | 123.1° |
O2 | C2 | N3 | 121.8° | 120.2° |
C2 | N3 | C4 | 119.8° | 121.1° |
N3 | C4 | N4 | 118.0° | 120.2° |
N3 | C4 | C5 | 122.0° | 121.6° |
N4 | C4 | C5 | 120.1° | 118.2° |
C4 | N4 | HN41 | 118.0° | 118.0° |
C4 | N4 | HN42 | 109.2° | 118.1° |
C4 | C5 | H5 | 124.2° | 120.6° |
HN41 | N4 | HN42 | 109.2° | 123.9° |
C3' | C2' | H2' | 115.2° | 109.5° |
C2' | C3' | O3' | 110.0° | 111.1° |
C2' | C3' | H3' | 115.1° | 113.4° |
O3' | C3' | H3' | 105.2° | 107.4° |
C3' | O3' | HO3' | 112.0° | 107.3° |
Dihedrals
First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
OP1 | P | OP2 | O5' | 127.0° | 126.7° |
OP1 | P | OP2 | OP3 | 56.3° | 126.3° |
OP1 | P | O5' | OP3 | 69.7° | 125.7° |
OP1 | P | OP2 | HOP2 | 180.0° | 48.8° |
OP1 | P | O5' | C5' | 46.6° | 179.9° |
OP1 | P | OP3 | HOP3 | 180.0° | 48.1° |
OP2 | P | O5' | OP3 | 63.2° | 107.4° |
OP2 | P | O5' | C5' | 179.5° | 53.2° |
OP2 | P | OP3 | HOP3 | 48.8° | 78.4° |
O5' | P | OP2 | HOP2 | 53.0° | 175.5° |
P | O5' | C5' | C4' | 161.2° | 180.0° |
P | O5' | C5' | H5' | 73.6° | 59.7° |
P | O5' | C5' | H5'' | 35.9° | 59.6° |
O5' | P | OP3 | HOP3 | 67.6° | 173.8° |
OP3 | P | OP2 | HOP2 | 123.7° | 77.5° |
OP3 | P | O5' | C5' | 116.3° | 54.2° |
C6' | N2' | C2' | HN'2 | 180.0° | 179.9° |
N2' | C6' | C7' | O8' | 178.4° | 180.0° |
N2' | C6' | C7' | H7'1 | 180.0° | 120.7° |
N2' | C6' | C7' | H7'2 | 54.7° | 120.6° |
N2' | C6' | C7' | H7'3 | 54.7° | 0.0° |
C6' | N2' | C2' | C1' | 115.3° | 92.2° |
C6' | N2' | C2' | C3' | 135.9° | 151.2° |
C6' | N2' | C2' | H2' | 10.2° | 29.9° |
C2' | N2' | C6' | C7' | 144.9° | 179.9° |
C2' | N2' | C6' | O8' | 36.8° | 0.1° |
N2' | C2' | C3' | C4' | 74.9° | 157.6° |
N2' | C2' | C1' | O4' | 86.5° | 149.6° |
N2' | C2' | C1' | N1 | 154.6° | 90.7° |
N2' | C2' | C1' | C3' | 113.5° | 123.2° |
N2' | C2' | C1' | H2' | 121.8° | 120.1° |
N2' | C2' | C1' | H1' | 35.7° | 31.2° |
N2' | C2' | C3' | H2' | 121.7° | 119.9° |
N2' | C2' | C3' | O3' | 43.8° | 41.7° |
N2' | C2' | C3' | H3' | 162.4° | 79.5° |
HN'2 | N2' | C6' | C7' | 35.1° | 0.0° |
HN'2 | N2' | C6' | O8' | 143.2° | 180.0° |
HN'2 | N2' | C2' | C1' | 64.7° | 87.9° |
HN'2 | N2' | C2' | C3' | 44.1° | 28.7° |
HN'2 | N2' | C2' | H2' | 169.8° | 149.9° |
C6' | C7' | H7'1 | H7'2 | 125.2° | 122.7° |
C6' | C7' | H7'1 | H7'3 | 125.3° | 126.3° |
C6' | C7' | H7'2 | H7'3 | 116.0° | 126.3° |
O8' | C6' | C7' | H7'1 | 1.7° | 59.2° |
O8' | C6' | C7' | H7'2 | 126.9° | 59.4° |
O8' | C6' | C7' | H7'3 | 123.7° | 179.9° |
H7'1 | C7' | H7'2 | H7'3 | 116.1° | 111.0° |
O5' | C5' | C4' | H5' | 125.2° | 119.5° |
O5' | C5' | C4' | H5'' | 125.3° | 119.6° |
O5' | C5' | H5' | H5'' | 117.4° | 119.1° |
O5' | C5' | C4' | O4' | 55.1° | 62.4° |
O5' | C5' | C4' | C3' | 63.5° | 179.5° |
O5' | C5' | C4' | H4' | 179.3° | 54.6° |
C4' | C5' | H5' | H5'' | 117.4° | 121.5° |
C5' | C4' | O4' | C3' | 127.4° | 121.7° |
C5' | C4' | O4' | H4' | 114.6° | 118.1° |
C5' | C4' | C3' | H4' | 114.2° | 124.3° |
C5' | C4' | O4' | C1' | 149.3° | 105.5° |
C5' | C4' | C3' | C2' | 159.5° | 86.3° |
C5' | C4' | C3' | O3' | 83.2° | 156.1° |
C5' | C4' | C3' | H3' | 35.5° | 36.5° |
H5' | C5' | C4' | O4' | 179.7° | 57.1° |
H5' | C5' | C4' | C3' | 61.7° | 60.0° |
H5' | C5' | C4' | H4' | 55.5° | 174.1° |
H5'' | C5' | C4' | O4' | 70.1° | 177.9° |
H5'' | C5' | C4' | C3' | 171.2° | 60.9° |
H5'' | C5' | C4' | H4' | 54.0° | 65.0° |
O4' | C4' | C3' | H4' | 124.4° | 117.3° |
C4' | O4' | C1' | N1 | 118.3° | 128.6° |
C4' | O4' | C1' | C2' | 3.4° | 6.5° |
C4' | O4' | C1' | H1' | 122.8° | 115.0° |
O4' | C4' | C3' | C2' | 38.0° | 32.1° |
O4' | C4' | C3' | O3' | 155.4° | 85.5° |
O4' | C4' | C3' | H3' | 85.9° | 154.9° |
C3' | C4' | O4' | C1' | 21.9° | 16.2° |
C4' | C3' | C2' | C1' | 38.9° | 34.9° |
C4' | C3' | C2' | O3' | 118.8° | 116.0° |
C4' | C3' | C2' | H3' | 122.6° | 122.9° |
C4' | C3' | C2' | H2' | 163.4° | 82.5° |
C4' | C3' | O3' | H3' | 123.3° | 123.4° |
C4' | C3' | O3' | HO3' | 180.0° | 144.4° |
H4' | C4' | O4' | C1' | 96.1° | 136.4° |
H4' | C4' | C3' | C2' | 86.4° | 149.4° |
H4' | C4' | C3' | O3' | 31.0° | 31.7° |
H4' | C4' | C3' | H3' | 149.7° | 87.9° |
O4' | C1' | N1 | C2' | 118.3° | 118.6° |
O4' | C1' | N1 | H1' | 122.2° | 116.7° |
O4' | C1' | C2' | H1' | 122.2° | 118.4° |
O4' | C1' | N1 | C6 | 12.3° | 33.3° |
O4' | C1' | N1 | C2 | 168.2° | 146.7° |
O4' | C1' | C2' | C3' | 27.0° | 26.3° |
O4' | C1' | C2' | H2' | 151.7° | 90.3° |
N1 | C1' | C2' | H1' | 118.9° | 121.9° |
C1' | N1 | C6 | C2 | 179.4° | 180.0° |
C1' | N1 | C6 | C5 | 178.4° | 180.0° |
C1' | N1 | C6 | H6 | 1.6° | 0.1° |
C1' | N1 | C2 | O2 | 1.9° | 0.0° |
C1' | N1 | C2 | N3 | 178.2° | 180.0° |
N1 | C1' | C2' | C3' | 91.8° | 146.0° |
N1 | C1' | C2' | H2' | 32.8° | 29.4° |
C2' | C1' | N1 | C6 | 106.0° | 85.3° |
C2' | C1' | N1 | C2 | 73.4° | 94.7° |
C1' | C2' | C3' | H2' | 124.5° | 117.4° |
C1' | C2' | C3' | O3' | 157.7° | 81.1° |
C1' | C2' | C3' | H3' | 83.7° | 157.8° |
H1' | C1' | N1 | C6 | 134.5° | 150.0° |
H1' | C1' | N1 | C2 | 46.0° | 30.1° |
H1' | C1' | C2' | C3' | 149.2° | 92.1° |
H1' | C1' | C2' | H2' | 86.1° | 151.3° |
N1 | C6 | C5 | H6 | 180.0° | 179.9° |
C6 | N1 | C2 | O2 | 178.7° | 180.0° |
C6 | N1 | C2 | N3 | 1.2° | 0.0° |
N1 | C6 | C5 | C4 | 0.1° | 0.0° |
N1 | C6 | C5 | H5 | 180.0° | 179.9° |
C2 | N1 | C6 | C5 | 1.0° | 0.0° |
C2 | N1 | C6 | H6 | 179.0° | 180.0° |
N1 | C2 | O2 | N3 | 179.9° | 180.0° |
N1 | C2 | N3 | C4 | 0.2° | 0.0° |
C6 | C5 | C4 | N3 | 1.1° | 0.0° |
C6 | C5 | C4 | N4 | 178.5° | 180.0° |
C6 | C5 | C4 | H5 | 180.0° | 180.0° |
H6 | C6 | C5 | C4 | 179.9° | 179.9° |
H6 | C6 | C5 | H5 | 0.1° | 0.0° |
O2 | C2 | N3 | C4 | 179.6° | 180.0° |
C2 | N3 | C4 | N4 | 178.7° | 180.0° |
C2 | N3 | C4 | C5 | 0.9° | 0.0° |
N3 | C4 | N4 | C5 | 179.6° | 180.0° |
N3 | C4 | N4 | HN41 | 180.0° | 124.9° |
N3 | C4 | N4 | HN42 | 54.7° | 55.0° |
N3 | C4 | C5 | H5 | 179.0° | 180.0° |
C4 | N4 | HN41 | HN42 | 125.3° | 179.9° |
N4 | C4 | C5 | H5 | 1.4° | 0.0° |
C5 | C4 | N4 | HN41 | 0.4° | 55.1° |
C5 | C4 | N4 | HN42 | 125.7° | 125.0° |
C2' | C3' | O3' | H3' | 124.5° | 124.6° |
C2' | C3' | O3' | HO3' | 67.9° | 103.5° |
H2' | C2' | C3' | O3' | 77.8° | 161.5° |
H2' | C2' | C3' | H3' | 40.8° | 40.4° |
H3' | C3' | O3' | HO3' | 56.7° | 21.1° |