JMH
Bonds
First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
OP1 | P | doub | 1.48Å | 1.51Å | |
N4 | C4 | doub | 1.31Å | 1.35Å | |
P | OP2 | sing | 1.61Å | 1.51Å | |
P | O5' | sing | 1.61Å | 1.59Å | |
C5 | C4 | sing | 1.47Å | 1.39Å | |
C5 | C6 | doub | 1.35Å | 1.39Å | |
C4 | N3 | sing | 1.39Å | 1.40Å | |
C6 | N1 | sing | 1.37Å | 1.34Å | |
O4' | C1' | sing | 1.44Å | 1.41Å | |
O4' | C4' | sing | 1.44Å | 1.45Å | |
N3 | C31 | sing | 1.46Å | 1.46Å | |
N3 | C2 | sing | 1.35Å | 1.41Å | |
O5' | C5' | sing | 1.43Å | 1.42Å | |
C5' | C4' | sing | 1.53Å | 1.50Å | |
N1 | C2 | sing | 1.34Å | 1.41Å | |
N1 | C1' | sing | 1.47Å | 1.48Å | |
C2 | O2 | doub | 1.22Å | 1.25Å | |
C1' | C2' | sing | 1.55Å | 1.53Å | |
C4' | C3' | sing | 1.54Å | 1.51Å | |
C3' | C2' | sing | 1.55Å | 1.52Å | |
C3' | O3' | sing | 1.43Å | 1.41Å | |
C2' | O2' | sing | 1.43Å | 1.42Å | |
P | OP3 | sing | 1.61Å | 1.60Å | |
C5 | H1 | sing | 1.08Å | 1.08Å | |
C1' | H2 | sing | 1.09Å | 1.10Å | |
C2' | H3 | sing | 1.09Å | 1.10Å | |
C3' | H4 | sing | 1.09Å | 1.10Å | |
C4' | H6 | sing | 1.09Å | 1.10Å | |
C5' | H7 | sing | 1.09Å | 1.10Å | |
C5' | H8 | sing | 1.09Å | 1.10Å | |
C6 | H9 | sing | 1.08Å | 1.08Å | |
C31 | H10 | sing | 1.09Å | 1.10Å | |
C31 | H11 | sing | 1.09Å | 1.10Å | |
C31 | H12 | sing | 1.09Å | 1.10Å | |
N4 | H13 | sing | 0.97Å | 1.00Å | |
O2' | H16 | sing | 0.97Å | 0.95Å | |
O3' | H17 | sing | 0.97Å | 0.95Å | |
OP2 | H18 | sing | 0.97Å | 0.95Å | |
OP3 | H19 | sing | 0.97Å | 0.95Å |
Angles
First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
OP1 | P | OP2 | 119.8° | 109.5° |
OP1 | P | O5' | 107.9° | 109.5° |
OP1 | P | OP3 | 108.1° | 109.4° |
N4 | C4 | C5 | 120.4° | 120.8° |
N4 | C4 | N3 | 120.4° | 120.8° |
C4 | N4 | H13 | 112.0° | 120.0° |
OP2 | P | O5' | 108.5° | 109.5° |
OP2 | P | OP3 | 108.0° | 109.5° |
P | OP2 | H18 | 109.5° | 113.9° |
P | O5' | C5' | 120.6° | 123.0° |
O5' | P | OP3 | 103.3° | 109.5° |
C4 | C5 | C6 | 120.4° | 118.5° |
C5 | C4 | N3 | 119.3° | 118.4° |
C4 | C5 | H1 | 119.8° | 120.7° |
C5 | C6 | N1 | 121.7° | 120.1° |
C6 | C5 | H1 | 119.8° | 120.8° |
C5 | C6 | H9 | 119.2° | 119.9° |
C4 | N3 | C31 | 120.4° | 120.2° |
C4 | N3 | C2 | 119.2° | 119.6° |
C6 | N1 | C2 | 119.5° | 121.8° |
C6 | N1 | C1' | 121.2° | 119.1° |
N1 | C6 | H9 | 119.1° | 120.0° |
C1' | O4' | C4' | 109.4° | 107.0° |
O4' | C1' | N1 | 109.4° | 110.6° |
O4' | C1' | C2' | 107.4° | 103.5° |
O4' | C1' | H2 | 110.0° | 110.8° |
O4' | C4' | C5' | 110.2° | 110.0° |
O4' | C4' | C3' | 103.1° | 107.3° |
O4' | C4' | H6 | 109.8° | 109.8° |
C31 | N3 | C2 | 120.4° | 120.2° |
N3 | C31 | H10 | 109.5° | 109.5° |
N3 | C31 | H11 | 109.5° | 109.5° |
N3 | C31 | H12 | 109.4° | 109.5° |
N3 | C2 | N1 | 120.0° | 121.6° |
N3 | C2 | O2 | 119.1° | 119.2° |
O5' | C5' | C4' | 111.2° | 109.5° |
O5' | C5' | H7 | 109.0° | 109.4° |
O5' | C5' | H8 | 109.1° | 109.5° |
C5' | C4' | C3' | 115.6° | 109.9° |
C5' | C4' | H6 | 109.0° | 109.9° |
C4' | C5' | H7 | 109.0° | 109.5° |
C4' | C5' | H8 | 109.0° | 109.5° |
C2 | N1 | C1' | 119.3° | 119.1° |
N1 | C2 | O2 | 120.9° | 119.2° |
N1 | C1' | C2' | 112.6° | 110.6° |
N1 | C1' | H2 | 109.0° | 110.5° |
C1' | C2' | C3' | 101.0° | 102.1° |
C1' | C2' | O2' | 108.1° | 110.9° |
C2' | C1' | H2 | 108.4° | 110.6° |
C1' | C2' | H3 | 111.5° | 111.0° |
C4' | C3' | C2' | 102.0° | 104.2° |
C4' | C3' | O3' | 113.7° | 110.5° |
C4' | C3' | H4 | 108.2° | 110.6° |
C3' | C4' | H6 | 108.9° | 109.9° |
C2' | C3' | O3' | 114.7° | 110.4° |
C3' | C2' | O2' | 110.7° | 110.9° |
C3' | C2' | H3 | 111.6° | 110.9° |
C2' | C3' | H4 | 108.2° | 110.5° |
O3' | C3' | H4 | 109.6° | 110.4° |
C3' | O3' | H17 | 109.5° | 114.0° |
O2' | C2' | H3 | 113.3° | 110.8° |
C2' | O2' | H16 | 109.5° | 114.0° |
P | OP3 | H19 | 109.5° | 114.0° |
H7 | C5' | H8 | 109.5° | 109.5° |
H10 | C31 | H11 | 109.4° | 109.5° |
H10 | C31 | H12 | 109.5° | 109.5° |
H11 | C31 | H12 | 109.5° | 109.5° |
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 | OP3 | 124.3° | 120.0° |
OP1 | P | O5' | OP3 | 114.3° | 120.0° |
OP1 | P | O5' | C5' | 157.7° | 55.1° |
OP1 | P | OP2 | H18 | 0.0° | 180.0° |
OP1 | P | OP3 | H19 | 0.0° | 60.0° |
N4 | C4 | C5 | N3 | 179.9° | 179.4° |
N4 | C4 | C5 | C6 | 179.9° | 180.0° |
N4 | C4 | N3 | C31 | 0.3° | 0.6° |
N4 | C4 | N3 | C2 | 180.0° | 179.8° |
N4 | C4 | C5 | H1 | 0.1° | 0.5° |
OP2 | P | O5' | OP3 | 114.4° | 120.0° |
OP2 | P | O5' | C5' | 71.1° | 64.9° |
OP2 | P | OP3 | H19 | 131.0° | 60.0° |
P | O5' | C5' | C4' | 157.5° | 180.0° |
P | O5' | C5' | H7 | 82.3° | 60.1° |
P | O5' | C5' | H8 | 37.2° | 59.9° |
O5' | P | OP2 | H18 | 124.3° | 60.0° |
O5' | P | OP3 | H19 | 114.2° | 180.0° |
C4 | C5 | C6 | H1 | 180.0° | 179.5° |
C4 | C5 | C6 | N1 | 0.4° | 0.4° |
C5 | C4 | N3 | C31 | 179.8° | 180.0° |
C5 | C4 | N3 | C2 | 0.1° | 0.4° |
C4 | C5 | C6 | H9 | 179.6° | 179.6° |
C5 | C4 | N4 | H13 | 179.9° | 174.8° |
C6 | C5 | C4 | N3 | 0.2° | 0.6° |
C5 | C6 | N1 | H9 | 180.0° | 179.9° |
C5 | C6 | N1 | C2 | 0.3° | 0.1° |
C5 | C6 | N1 | C1' | 179.7° | 179.8° |
C4 | N3 | C31 | C2 | 179.8° | 179.6° |
C4 | N3 | C2 | N1 | 0.0° | 0.0° |
C4 | N3 | C2 | O2 | 179.8° | 180.0° |
N3 | C4 | C5 | H1 | 179.8° | 179.9° |
C4 | N3 | C31 | H10 | 180.0° | 65.1° |
C4 | N3 | C31 | H11 | 60.0° | 174.9° |
C4 | N3 | C31 | H12 | 60.0° | 55.0° |
N3 | C4 | N4 | H13 | 0.0° | 4.6° |
C6 | N1 | C1' | O4' | 19.4° | 49.3° |
C6 | N1 | C2 | N3 | 0.1° | 0.3° |
C6 | N1 | C2 | C1' | 180.0° | 179.7° |
C6 | N1 | C2 | O2 | 179.7° | 179.7° |
C6 | N1 | C1' | C2' | 99.9° | 64.7° |
N1 | C6 | C5 | H1 | 179.7° | 179.8° |
C6 | N1 | C1' | H2 | 139.7° | 172.4° |
C1' | O4' | C4' | C5' | 150.1° | 146.0° |
O4' | C1' | N1 | C2 | 160.6° | 131.0° |
O4' | C1' | N1 | C2' | 119.4° | 114.1° |
O4' | C1' | N1 | H2 | 120.3° | 123.0° |
O4' | C1' | C2' | H2 | 118.8° | 118.7° |
C1' | O4' | C4' | C3' | 26.2° | 26.5° |
O4' | C1' | C2' | C3' | 23.3° | 37.0° |
O4' | C1' | C2' | O2' | 92.9° | 155.2° |
O4' | C1' | C2' | H3 | 141.9° | 81.2° |
C1' | O4' | C4' | H6 | 89.8° | 92.9° |
O4' | C4' | C5' | O5' | 72.6° | 67.1° |
O4' | C4' | C5' | C3' | 116.4° | 117.9° |
O4' | C4' | C5' | H6 | 120.6° | 121.1° |
C4' | O4' | C1' | N1 | 124.1° | 158.6° |
C4' | O4' | C1' | C2' | 1.6° | 40.1° |
O4' | C4' | C3' | H6 | 116.6° | 119.4° |
O4' | C4' | C3' | C2' | 40.0° | 2.1° |
O4' | C4' | C3' | O3' | 164.0° | 120.7° |
C4' | O4' | C1' | H2 | 116.1° | 78.5° |
O4' | C4' | C3' | H4 | 73.9° | 116.7° |
O4' | C4' | C5' | H7 | 167.1° | 172.9° |
O4' | C4' | C5' | H8 | 47.6° | 52.9° |
C31 | N3 | C2 | N1 | 179.8° | 179.6° |
C31 | N3 | C2 | O2 | 0.0° | 0.4° |
N3 | C31 | H10 | H11 | 120.0° | 120.0° |
N3 | C31 | H10 | H12 | 120.0° | 120.0° |
N3 | C31 | H11 | H12 | 120.0° | 120.0° |
N3 | C2 | N1 | O2 | 179.8° | 180.0° |
N3 | C2 | N1 | C1' | 179.9° | 180.0° |
C2 | N3 | C31 | H10 | 0.2° | 115.3° |
C2 | N3 | C31 | H11 | 119.7° | 4.7° |
C2 | N3 | C31 | H12 | 120.3° | 124.7° |
O5' | C5' | C4' | H7 | 120.3° | 119.9° |
O5' | C5' | C4' | H8 | 120.3° | 120.1° |
O5' | C5' | C4' | C3' | 43.8° | 175.0° |
C5' | O5' | P | OP3 | 43.3° | 175.1° |
O5' | C5' | C4' | H6 | 166.8° | 53.9° |
O5' | C5' | H7 | H8 | 119.2° | 120.0° |
C5' | C4' | C3' | H6 | 123.1° | 121.1° |
C5' | C4' | C3' | C2' | 160.4° | 121.6° |
C5' | C4' | C3' | O3' | 75.6° | 119.8° |
C5' | C4' | C3' | H4 | 46.4° | 2.8° |
C4' | C5' | H7 | H8 | 119.2° | 120.0° |
C2 | N1 | C1' | C2' | 80.1° | 115.0° |
C2 | N1 | C1' | H2 | 40.2° | 7.9° |
C2 | N1 | C6 | H9 | 179.7° | 180.0° |
C1' | N1 | C2 | O2 | 0.3° | 0.1° |
N1 | C1' | C2' | H2 | 120.7° | 122.8° |
N1 | C1' | C2' | C3' | 97.3° | 155.5° |
N1 | C1' | C2' | O2' | 146.5° | 86.3° |
N1 | C1' | C2' | H3 | 21.4° | 37.3° |
C1' | N1 | C6 | H9 | 0.3° | 0.3° |
C1' | C2' | C3' | C4' | 38.0° | 20.9° |
C1' | C2' | C3' | O2' | 114.3° | 118.2° |
C1' | C2' | C3' | H3 | 118.5° | 118.3° |
C1' | C2' | C3' | O3' | 161.4° | 97.8° |
C1' | C2' | O2' | H3 | 124.1° | 123.7° |
C1' | C2' | C3' | H4 | 76.0° | 139.7° |
C1' | C2' | O2' | H16 | 180.0° | 180.0° |
C4' | C3' | C2' | O3' | 123.4° | 118.7° |
C4' | C3' | C2' | H4 | 114.0° | 118.8° |
C4' | C3' | O3' | H4 | 121.3° | 122.7° |
C4' | C3' | C2' | O2' | 76.3° | 139.1° |
C4' | C3' | C2' | H3 | 156.6° | 97.4° |
C3' | C4' | C5' | H7 | 76.5° | 55.1° |
C3' | C4' | C5' | H8 | 164.0° | 64.9° |
C4' | C3' | O3' | H17 | 180.0° | 176.2° |
C2' | C3' | O3' | H4 | 121.9° | 122.5° |
C3' | C2' | O2' | H3 | 126.2° | 123.6° |
C3' | C2' | C1' | H2 | 142.0° | 81.6° |
C2' | C3' | C4' | H6 | 76.5° | 117.3° |
C3' | C2' | O2' | H16 | 70.3° | 67.3° |
C2' | C3' | O3' | H17 | 63.2° | 61.5° |
O3' | C3' | C2' | O2' | 47.1° | 20.4° |
O3' | C3' | C2' | H3 | 80.0° | 143.9° |
O3' | C3' | C4' | H6 | 47.5° | 1.3° |
O2' | C2' | C1' | H2 | 25.8° | 36.6° |
O2' | C2' | C3' | H4 | 169.7° | 102.1° |
OP3 | P | OP2 | H18 | 124.3° | 60.0° |
H1 | C5 | C6 | H9 | 0.4° | 0.1° |
H2 | C1' | C2' | H3 | 99.3° | 160.1° |
H3 | C2' | C3' | H4 | 42.6° | 21.4° |
H3 | C2' | O2' | H16 | 55.9° | 56.3° |
H4 | C3' | C4' | H6 | 169.5° | 123.9° |
H4 | C3' | O3' | H17 | 58.7° | 61.1° |
H6 | C4' | C5' | H7 | 46.6° | 66.0° |
H6 | C4' | C5' | H8 | 72.9° | 174.0° |
H10 | C31 | H11 | H12 | 120.0° | 120.0° |