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 | 1.61Å | |
OP2 | HO1P | sing | 0.98Å | 0.95Å | |
O5' | C5' | sing | 1.42Å | 1.42Å | |
C5' | C4' | sing | 1.52Å | 1.54Å | |
C5' | H5' | sing | 1.09Å | 1.09Å | |
C5' | H5'' | sing | 1.09Å | 1.09Å | |
C4' | C3' | sing | 1.53Å | 1.51Å | |
C4' | C' | sing | 1.54Å | 1.53Å | |
C4' | H4' | sing | 1.10Å | 1.07Å | |
C3' | O3' | sing | 1.41Å | 1.43Å | |
C3' | C2' | sing | 1.53Å | 1.51Å | |
C3' | H3' | sing | 1.10Å | 1.06Å | |
O3' | HO3' | sing | 0.97Å | 0.95Å | |
C2' | C1' | sing | 1.53Å | 1.50Å | |
C2' | H2' | sing | 1.10Å | 1.06Å | |
C2' | H2'' | sing | 1.10Å | 1.05Å | |
C1' | N1 | sing | 1.44Å | 1.50Å | |
C1' | C' | sing | 1.54Å | 1.53Å | |
C1' | H1' | sing | 1.10Å | 1.08Å | |
N1 | C2 | sing | 1.41Å | 1.40Å | |
N1 | C6 | sing | 1.39Å | 1.38Å | |
C2 | O2 | doub | 1.23Å | 1.23Å | |
C2 | N3 | sing | 1.40Å | 1.39Å | |
N3 | C4 | sing | 1.39Å | 1.39Å | |
N3 | HN3 | sing | 1.02Å | 1.01Å | |
C4 | O4 | doub | 1.23Å | 1.23Å | |
C4 | C5 | sing | 1.49Å | 1.45Å | |
C5 | C5M | sing | 1.49Å | 1.52Å | |
C5 | C6 | doub | 1.34Å | 1.36Å | |
C5M | H71 | sing | 1.09Å | 1.09Å | |
C5M | H72 | sing | 1.09Å | 1.09Å | |
C5M | H73 | sing | 1.09Å | 1.09Å | |
C6 | H6 | sing | 1.09Å | 1.08Å | |
C' | CM' | sing | 1.52Å | 1.52Å | |
C' | H' | sing | 1.10Å | 1.09Å | |
CM' | HM'1 | sing | 1.09Å | 1.09Å | |
CM' | HM'2 | sing | 1.09Å | 1.09Å | |
CM' | HM'3 | sing | 1.09Å | 1.09Å | |
OP3 | P | sing | 1.62Å | 10.97Å | |
OP3 | HOP3 | sing | 0.98Å | 0.00Å |
Angles
First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
OP1 | P | OP2 | 119.4° | 115.3° |
OP1 | P | O5' | 107.2° | 115.0° |
OP1 | P | OP3 | 78.9° | 115.0° |
OP2 | P | O5' | 107.8° | 103.7° |
P | OP2 | HO1P | 119.4° | 119.0° |
OP2 | P | OP3 | 150.3° | 103.3° |
P | O5' | C5' | 123.2° | 118.5° |
O5' | P | OP3 | 86.2° | 103.0° |
O5' | C5' | C4' | 110.6° | 108.6° |
O5' | C5' | H5' | 110.5° | 109.2° |
O5' | C5' | H5'' | 109.0° | 109.2° |
C4' | C5' | H5' | 108.5° | 110.1° |
C4' | C5' | H5'' | 109.7° | 110.1° |
C5' | C4' | C3' | 110.9° | 112.7° |
C5' | C4' | C' | 116.7° | 113.9° |
C5' | C4' | H4' | 110.0° | 108.0° |
H5' | C5' | H5'' | 108.5° | 109.6° |
C3' | C4' | C' | 107.7° | 101.9° |
C3' | C4' | H4' | 102.4° | 109.6° |
C4' | C3' | O3' | 110.2° | 111.3° |
C4' | C3' | C2' | 105.3° | 103.3° |
C4' | C3' | H3' | 108.3° | 111.2° |
C' | C4' | H4' | 108.1° | 110.7° |
C4' | C' | C1' | 104.6° | 104.2° |
C4' | C' | CM' | 112.5° | 113.3° |
C4' | C' | H' | 109.7° | 109.2° |
O3' | C3' | C2' | 113.9° | 111.4° |
O3' | C3' | H3' | 109.5° | 108.9° |
C3' | O3' | HO3' | 110.2° | 107.2° |
C2' | C3' | H3' | 109.5° | 110.6° |
C3' | C2' | C1' | 106.5° | 105.4° |
C3' | C2' | H2' | 114.9° | 109.9° |
C3' | C2' | H2'' | 106.3° | 111.3° |
C1' | C2' | H2' | 107.4° | 109.8° |
C1' | C2' | H2'' | 114.1° | 113.8° |
C2' | C1' | N1 | 113.1° | 111.9° |
C2' | C1' | C' | 103.4° | 106.2° |
C2' | C1' | H1' | 103.8° | 109.4° |
H2' | C2' | H2'' | 107.9° | 106.6° |
N1 | C1' | C' | 112.9° | 111.2° |
N1 | C1' | H1' | 113.7° | 106.4° |
C1' | N1 | C2 | 120.3° | 121.1° |
C1' | N1 | C6 | 119.3° | 118.4° |
C' | C1' | H1' | 109.0° | 111.8° |
C1' | C' | CM' | 108.2° | 112.5° |
C1' | C' | H' | 112.1° | 109.7° |
C2 | N1 | C6 | 120.5° | 120.5° |
N1 | C2 | O2 | 123.4° | 123.9° |
N1 | C2 | N3 | 116.2° | 114.9° |
N1 | C6 | C5 | 122.4° | 124.4° |
N1 | C6 | H6 | 117.5° | 114.9° |
O2 | C2 | N3 | 120.4° | 121.1° |
C2 | N3 | C4 | 126.1° | 127.0° |
C2 | N3 | HN3 | 117.9° | 116.4° |
C4 | N3 | HN3 | 116.0° | 116.6° |
N3 | C4 | O4 | 120.2° | 123.6° |
N3 | C4 | C5 | 114.3° | 114.8° |
O4 | C4 | C5 | 125.5° | 121.5° |
C4 | C5 | C5M | 120.2° | 118.1° |
C4 | C5 | C6 | 120.4° | 118.3° |
C5M | C5 | C6 | 119.5° | 123.6° |
C5 | C5M | H71 | 109.9° | 109.8° |
C5 | C5M | H72 | 109.5° | 109.7° |
C5 | C5M | H73 | 110.5° | 109.7° |
C5 | C6 | H6 | 120.1° | 120.8° |
H71 | C5M | H72 | 109.1° | 109.3° |
H71 | C5M | H73 | 108.9° | 109.4° |
H72 | C5M | H73 | 109.0° | 108.9° |
CM' | C' | H' | 109.7° | 108.0° |
C' | CM' | HM'1 | 109.0° | 110.6° |
C' | CM' | HM'2 | 109.4° | 110.6° |
C' | CM' | HM'3 | 108.8° | 110.6° |
HM'1 | CM' | HM'2 | 110.5° | 108.3° |
HM'1 | CM' | HM'3 | 108.2° | 108.3° |
HM'2 | CM' | HM'3 | 110.9° | 108.3° |
P | OP3 | HOP3 | 90.0° | 119.0° |
Dihedrals
First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
OP1 | P | OP2 | O5' | 122.5° | 126.6° |
OP1 | P | OP2 | OP3 | 122.8° | 126.2° |
OP1 | P | O5' | OP3 | 77.1° | 125.8° |
OP1 | P | OP2 | HO1P | 180.0° | 48.8° |
OP1 | P | O5' | C5' | 163.6° | 180.0° |
OP1 | P | OP3 | HOP3 | 90.0° | 48.0° |
OP2 | P | O5' | OP3 | 153.2° | 107.4° |
OP2 | P | O5' | C5' | 66.7° | 53.2° |
OP2 | P | OP3 | HOP3 | 90.0° | 78.5° |
O5' | P | OP2 | HO1P | 57.6° | 175.4° |
P | O5' | C5' | C4' | 136.2° | 180.0° |
P | O5' | C5' | H5' | 16.1° | 60.0° |
P | O5' | C5' | H5'' | 103.1° | 59.9° |
O5' | P | OP3 | HOP3 | 90.0° | 173.8° |
HO1P | OP2 | P | OP3 | 57.2° | 77.5° |
O5' | C5' | C4' | H5' | 121.4° | 119.5° |
O5' | C5' | C4' | H5'' | 120.3° | 119.5° |
O5' | C5' | H5' | H5'' | 119.5° | 119.6° |
O5' | C5' | C4' | C3' | 59.1° | 54.9° |
O5' | C5' | C4' | C' | 64.6° | 60.5° |
O5' | C5' | C4' | H4' | 171.7° | 176.1° |
C5' | O5' | P | OP3 | 86.5° | 54.2° |
C4' | C5' | H5' | H5'' | 119.1° | 121.2° |
C5' | C4' | C3' | C' | 128.8° | 122.4° |
C5' | C4' | C3' | H4' | 117.3° | 120.3° |
C5' | C4' | C' | H4' | 124.6° | 121.9° |
C5' | C4' | C3' | O3' | 113.7° | 74.4° |
C5' | C4' | C3' | C2' | 123.0° | 166.0° |
C5' | C4' | C3' | H3' | 6.0° | 47.2° |
C5' | C4' | C' | C1' | 141.3° | 159.7° |
C5' | C4' | C' | CM' | 101.5° | 77.8° |
C5' | C4' | C' | H' | 20.8° | 42.6° |
H5' | C5' | C4' | C3' | 179.5° | 64.5° |
H5' | C5' | C4' | C' | 56.7° | 179.9° |
H5' | C5' | C4' | H4' | 67.0° | 56.7° |
H5'' | C5' | C4' | C3' | 61.2° | 174.5° |
H5'' | C5' | C4' | C' | 175.1° | 59.1° |
H5'' | C5' | C4' | H4' | 51.4° | 64.3° |
C3' | C4' | C' | H4' | 110.0° | 116.5° |
C4' | C3' | O3' | C2' | 118.1° | 114.7° |
C4' | C3' | O3' | H3' | 119.0° | 123.0° |
C4' | C3' | C2' | H3' | 116.2° | 119.1° |
C4' | C3' | O3' | HO3' | 180.0° | 167.9° |
C4' | C3' | C2' | C1' | 25.9° | 32.2° |
C4' | C3' | C2' | H2' | 92.8° | 86.1° |
C4' | C3' | C2' | H2'' | 147.9° | 156.0° |
C3' | C4' | C' | C1' | 15.9° | 38.1° |
C3' | C4' | C' | CM' | 133.1° | 160.6° |
C3' | C4' | C' | H' | 104.5° | 79.0° |
C' | C4' | C3' | O3' | 117.5° | 163.2° |
C' | C4' | C3' | C2' | 5.7° | 43.6° |
C' | C4' | C3' | H3' | 122.8° | 75.2° |
C4' | C' | C1' | C2' | 31.3° | 18.5° |
C4' | C' | C1' | N1 | 153.9° | 140.5° |
C4' | C' | C1' | CM' | 120.1° | 123.1° |
C4' | C' | C1' | H' | 118.8° | 116.8° |
C4' | C' | C1' | H1' | 78.7° | 100.8° |
C4' | C' | CM' | H' | 122.3° | 121.1° |
C4' | C' | CM' | HM'1 | 49.3° | 40.8° |
C4' | C' | CM' | HM'2 | 71.6° | 160.8° |
C4' | C' | CM' | HM'3 | 167.1° | 79.2° |
H4' | C4' | C3' | O3' | 3.6° | 45.9° |
H4' | C4' | C3' | C2' | 119.6° | 73.7° |
H4' | C4' | C3' | H3' | 123.3° | 167.5° |
H4' | C4' | C' | C1' | 94.1° | 78.4° |
H4' | C4' | C' | CM' | 23.1° | 44.2° |
H4' | C4' | C' | H' | 145.5° | 164.5° |
O3' | C3' | C2' | H3' | 122.9° | 121.3° |
O3' | C3' | C2' | C1' | 94.9° | 151.8° |
O3' | C3' | C2' | H2' | 146.4° | 33.5° |
O3' | C3' | C2' | H2'' | 27.1° | 84.4° |
C2' | C3' | O3' | HO3' | 61.9° | 53.2° |
C3' | C2' | C1' | H2' | 123.6° | 118.4° |
C3' | C2' | C1' | H2'' | 117.0° | 122.2° |
C3' | C2' | H2' | H2'' | 118.4° | 120.8° |
C3' | C2' | C1' | N1 | 158.2° | 113.2° |
C3' | C2' | C1' | C' | 35.8° | 8.4° |
C3' | C2' | C1' | H1' | 78.0° | 129.3° |
H3' | C3' | O3' | HO3' | 61.0° | 69.2° |
H3' | C3' | C2' | C1' | 142.1° | 86.9° |
H3' | C3' | C2' | H2' | 23.4° | 154.8° |
H3' | C3' | C2' | H2'' | 95.8° | 36.9° |
C1' | C2' | H2' | H2'' | 123.3° | 123.7° |
C2' | C1' | N1 | C' | 117.0° | 118.6° |
C2' | C1' | N1 | H1' | 118.1° | 119.4° |
C2' | C1' | C' | H1' | 110.0° | 119.3° |
C2' | C1' | N1 | C2 | 116.3° | 119.3° |
C2' | C1' | N1 | C6 | 63.9° | 60.6° |
C2' | C1' | C' | CM' | 151.4° | 141.6° |
C2' | C1' | C' | H' | 87.5° | 98.3° |
H2' | C2' | C1' | N1 | 34.7° | 128.5° |
H2' | C2' | C1' | C' | 87.8° | 110.0° |
H2' | C2' | C1' | H1' | 158.4° | 10.9° |
H2'' | C2' | C1' | N1 | 84.8° | 9.1° |
H2'' | C2' | C1' | C' | 152.8° | 130.6° |
H2'' | C2' | C1' | H1' | 39.0° | 108.5° |
N1 | C1' | C' | H1' | 127.4° | 118.8° |
C1' | N1 | C2 | C6 | 179.8° | 179.9° |
C1' | N1 | C2 | O2 | 2.6° | 0.1° |
C1' | N1 | C2 | N3 | 178.3° | 180.0° |
C1' | N1 | C6 | C5 | 176.4° | 180.0° |
C1' | N1 | C6 | H6 | 3.4° | 0.0° |
N1 | C1' | C' | CM' | 86.0° | 96.5° |
N1 | C1' | C' | H' | 35.1° | 23.7° |
C' | C1' | N1 | C2 | 126.7° | 122.0° |
C' | C1' | N1 | C6 | 53.1° | 58.0° |
C1' | C' | CM' | H' | 122.6° | 121.1° |
C1' | C' | CM' | HM'1 | 65.7° | 158.6° |
C1' | C' | CM' | HM'2 | 173.3° | 81.4° |
C1' | C' | CM' | HM'3 | 52.1° | 38.6° |
H1' | C1' | N1 | C2 | 1.8° | 0.0° |
H1' | C1' | N1 | C6 | 178.0° | 180.0° |
H1' | C1' | C' | CM' | 41.4° | 22.3° |
H1' | C1' | C' | H' | 162.5° | 142.5° |
N1 | C2 | O2 | N3 | 179.1° | 180.0° |
N1 | C2 | N3 | C4 | 2.3° | 0.0° |
N1 | C2 | N3 | HN3 | 176.2° | 180.0° |
C2 | N1 | C6 | C5 | 3.4° | 0.1° |
C2 | N1 | C6 | H6 | 176.8° | 180.0° |
C6 | N1 | C2 | O2 | 177.6° | 180.0° |
C6 | N1 | C2 | N3 | 1.6° | 0.0° |
N1 | C6 | C5 | C4 | 1.6° | 0.1° |
N1 | C6 | C5 | C5M | 178.4° | 180.0° |
N1 | C6 | C5 | H6 | 179.8° | 180.0° |
O2 | C2 | N3 | C4 | 178.6° | 180.0° |
O2 | C2 | N3 | HN3 | 2.9° | 0.0° |
C2 | N3 | C4 | HN3 | 178.5° | 180.0° |
C2 | N3 | C4 | O4 | 177.0° | 179.9° |
C2 | N3 | C4 | C5 | 3.9° | 0.0° |
N3 | C4 | O4 | C5 | 179.0° | 180.0° |
N3 | C4 | C5 | C5M | 178.1° | 179.9° |
N3 | C4 | C5 | C6 | 1.9° | 0.0° |
HN3 | N3 | C4 | O4 | 4.5° | 0.0° |
HN3 | N3 | C4 | C5 | 174.6° | 180.0° |
O4 | C4 | C5 | C5M | 1.0° | 0.1° |
O4 | C4 | C5 | C6 | 179.1° | 180.0° |
C4 | C5 | C5M | C6 | 180.0° | 179.9° |
C4 | C5 | C5M | H71 | 39.9° | 105.4° |
C4 | C5 | C5M | H72 | 79.9° | 134.4° |
C4 | C5 | C5M | H73 | 160.0° | 14.8° |
C4 | C5 | C6 | H6 | 178.6° | 180.0° |
C5 | C5M | H71 | H72 | 120.0° | 120.4° |
C5 | C5M | H71 | H73 | 121.1° | 120.5° |
C5 | C5M | H72 | H73 | 121.0° | 120.1° |
C5M | C5 | C6 | H6 | 1.3° | 0.1° |
C6 | C5 | C5M | H71 | 140.1° | 74.5° |
C6 | C5 | C5M | H72 | 100.1° | 45.6° |
C6 | C5 | C5M | H73 | 20.0° | 165.3° |
H71 | C5M | H72 | H73 | 118.8° | 119.5° |
C' | CM' | HM'1 | HM'2 | 120.3° | 121.3° |
C' | CM' | HM'1 | HM'3 | 118.2° | 121.3° |
C' | CM' | HM'2 | HM'3 | 120.0° | 121.3° |
H' | C' | CM' | HM'1 | 171.7° | 80.3° |
H' | C' | CM' | HM'2 | 50.7° | 39.7° |
H' | C' | CM' | HM'3 | 70.5° | 159.7° |
HM'1 | CM' | HM'2 | HM'3 | 120.0° | 117.3° |