Y3U
Bonds
First atom | Second atom | Bond order type | Distance (experimental model) | Distance (ideal model) | Properties |
C3U | N3 | sing | 1.47Å | 1.47Å | |
O2 | C2 | doub | 1.22Å | 1.22Å | |
N3 | C2 | sing | 1.35Å | 1.39Å | |
N3 | C4 | sing | 1.35Å | 1.40Å | |
C2 | N1 | sing | 1.35Å | 1.39Å | |
O4 | C4 | doub | 1.22Å | 1.23Å | |
C4 | C5 | sing | 1.42Å | 1.45Å | |
N1 | C1' | sing | 1.46Å | 1.49Å | |
N1 | C6 | sing | 1.37Å | 1.38Å | |
C1' | O4' | sing | 1.44Å | 1.41Å | |
C1' | C2' | sing | 1.54Å | 1.52Å | |
O4' | C4' | sing | 1.44Å | 1.45Å | |
C5 | C6 | doub | 1.35Å | 1.35Å | |
O3' | C3' | sing | 1.43Å | 1.43Å | |
C4' | C3' | sing | 1.55Å | 1.54Å | |
C4' | C5' | sing | 1.53Å | 1.51Å | |
O2' | C2' | sing | 1.43Å | 1.41Å | |
C2' | C3' | sing | 1.55Å | 1.53Å | |
C5' | O5' | sing | 1.43Å | 1.47Å | |
O5' | SBI | sing | 1.52Å | 1.59Å | |
CE1 | CD1 | doub | 1.38Å | 1.39Å | Aromatic |
CE1 | CZ | sing | 1.39Å | 1.39Å | Aromatic |
CD1 | CG | sing | 1.38Å | 1.39Å | Aromatic |
SBI | NAT | sing | 1.66Å | 1.59Å | |
SBI | OAE | doub | 1.42Å | 1.42Å | |
SBI | OAD | doub | 1.42Å | 1.42Å | |
NAT | C | sing | 1.35Å | 1.37Å | |
OH | CZ | sing | 1.36Å | 1.36Å | |
CZ | CE2 | doub | 1.39Å | 1.39Å | Aromatic |
CG | CB | sing | 1.51Å | 1.51Å | |
CG | CD2 | doub | 1.38Å | 1.39Å | Aromatic |
CB | CA | sing | 1.53Å | 1.54Å | |
CA | C | sing | 1.51Å | 1.50Å | |
CA | N | sing | 1.47Å | 1.46Å | |
C | O | doub | 1.21Å | 1.23Å | |
CE2 | CD2 | sing | 1.38Å | 1.39Å | Aromatic |
C3U | H1 | sing | 1.09Å | 1.10Å | |
C3U | H2 | sing | 1.09Å | 1.10Å | |
C3U | H3 | sing | 1.09Å | 1.10Å | |
C5 | H4 | sing | 1.08Å | 1.08Å | |
C6 | H5 | sing | 1.08Å | 1.08Å | |
C1' | H6 | sing | 1.09Å | 1.10Å | |
C4' | H7 | sing | 1.09Å | 1.10Å | |
C5' | H8 | sing | 1.09Å | 1.10Å | |
C5' | H9 | sing | 1.09Å | 1.10Å | |
NAT | H10 | sing | 0.97Å | 1.00Å | |
CA | H11 | sing | 1.09Å | 1.10Å | |
N | H12 | sing | 1.01Å | 1.00Å | |
N | H13 | sing | 1.01Å | 1.00Å | |
CB | H15 | sing | 1.09Å | 1.10Å | |
CB | H16 | sing | 1.09Å | 1.10Å | |
CD1 | H17 | sing | 1.08Å | 1.08Å | |
CE1 | H18 | sing | 1.08Å | 1.08Å | |
OH | H19 | sing | 0.97Å | 0.95Å | |
CE2 | H20 | sing | 1.08Å | 1.08Å | |
CD2 | H21 | sing | 1.08Å | 1.08Å | |
C3' | H22 | sing | 1.09Å | 1.10Å | |
O3' | H23 | sing | 0.97Å | 0.95Å | |
C2' | H24 | sing | 1.09Å | 1.10Å | |
O2' | H25 | sing | 0.97Å | 0.95Å |
Angles
First atom | Second atom | Third atom | Angle (experimental model) | Angle (ideal model) |
C3U | N3 | C2 | 117.2° | 119.9° |
C3U | N3 | C4 | 118.4° | 119.9° |
N3 | C3U | H1 | 109.5° | 109.5° |
N3 | C3U | H2 | 109.5° | 109.5° |
N3 | C3U | H3 | 109.5° | 109.4° |
O2 | C2 | N3 | 121.0° | 119.5° |
O2 | C2 | N1 | 123.2° | 119.5° |
C2 | N3 | C4 | 124.5° | 120.2° |
N3 | C2 | N1 | 115.8° | 121.0° |
N3 | C4 | O4 | 119.4° | 120.3° |
N3 | C4 | C5 | 115.7° | 119.4° |
C2 | N1 | C1' | 115.5° | 119.7° |
C2 | N1 | C6 | 122.7° | 120.6° |
O4 | C4 | C5 | 124.9° | 120.3° |
C4 | C5 | C6 | 120.5° | 119.1° |
C4 | C5 | H4 | 119.8° | 120.5° |
C1' | N1 | C6 | 121.7° | 119.7° |
N1 | C1' | O4' | 110.4° | 110.4° |
N1 | C1' | C2' | 117.1° | 110.4° |
N1 | C1' | H6 | 108.1° | 110.3° |
N1 | C6 | C5 | 120.8° | 119.7° |
N1 | C6 | H5 | 119.6° | 120.2° |
O4' | C1' | C2' | 104.2° | 104.8° |
C1' | O4' | C4' | 107.2° | 105.3° |
O4' | C1' | H6 | 109.1° | 110.3° |
C1' | C2' | O2' | 111.3° | 110.6° |
C1' | C2' | C3' | 98.9° | 104.1° |
C2' | C1' | H6 | 107.7° | 110.4° |
C1' | C2' | H24 | 110.8° | 110.5° |
O4' | C4' | C3' | 106.0° | 104.8° |
O4' | C4' | C5' | 110.0° | 110.4° |
O4' | C4' | H7 | 109.5° | 110.4° |
C6 | C5 | H4 | 119.8° | 120.4° |
C5 | C6 | H5 | 119.6° | 120.1° |
O3' | C3' | C4' | 111.0° | 110.5° |
O3' | C3' | C2' | 110.5° | 110.6° |
O3' | C3' | H22 | 111.9° | 110.5° |
C3' | O3' | H23 | 109.5° | 114.0° |
C3' | C4' | C5' | 114.3° | 110.3° |
C4' | C3' | C2' | 102.4° | 104.0° |
C3' | C4' | H7 | 108.3° | 110.4° |
C4' | C3' | H22 | 110.3° | 110.5° |
C4' | C5' | O5' | 107.0° | 109.5° |
C5' | C4' | H7 | 108.7° | 110.4° |
C4' | C5' | H8 | 110.1° | 109.5° |
C4' | C5' | H9 | 110.1° | 109.5° |
O2' | C2' | C3' | 112.2° | 110.5° |
O2' | C2' | H24 | 112.4° | 110.5° |
C2' | O2' | H25 | 109.5° | 114.0° |
C2' | C3' | H22 | 110.4° | 110.5° |
C3' | C2' | H24 | 110.6° | 110.5° |
C5' | O5' | SBI | 119.1° | 114.0° |
O5' | C5' | H8 | 110.1° | 109.4° |
O5' | C5' | H9 | 110.1° | 109.4° |
O5' | SBI | NAT | 103.3° | 107.2° |
O5' | SBI | OAE | 105.4° | 106.4° |
O5' | SBI | OAD | 107.1° | 106.4° |
CD1 | CE1 | CZ | 119.8° | 119.9° |
CE1 | CD1 | CG | 120.9° | 120.0° |
CE1 | CD1 | H17 | 119.5° | 120.0° |
CD1 | CE1 | H18 | 120.1° | 120.0° |
CE1 | CZ | OH | 119.6° | 120.0° |
CE1 | CZ | CE2 | 119.8° | 119.9° |
CZ | CE1 | H18 | 120.1° | 120.0° |
CD1 | CG | CB | 120.7° | 119.9° |
CD1 | CG | CD2 | 118.6° | 120.1° |
CG | CD1 | H17 | 119.5° | 120.0° |
NAT | SBI | OAE | 105.9° | 106.4° |
NAT | SBI | OAD | 112.6° | 106.4° |
SBI | NAT | C | 128.2° | 120.0° |
SBI | NAT | H10 | 115.9° | 120.0° |
OAE | SBI | OAD | 121.0° | 123.1° |
NAT | C | CA | 114.3° | 120.0° |
NAT | C | O | 121.6° | 120.0° |
C | NAT | H10 | 115.9° | 120.0° |
OH | CZ | CE2 | 120.6° | 120.1° |
CZ | OH | H19 | 109.5° | 114.0° |
CZ | CE2 | CD2 | 119.8° | 120.0° |
CZ | CE2 | H20 | 120.1° | 120.0° |
CB | CG | CD2 | 120.8° | 119.9° |
CG | CB | CA | 113.2° | 109.5° |
CG | CB | H15 | 108.5° | 109.5° |
CG | CB | H16 | 108.5° | 109.5° |
CG | CD2 | CE2 | 121.0° | 120.1° |
CG | CD2 | H21 | 119.5° | 120.0° |
CB | CA | C | 100.0° | 109.5° |
CB | CA | N | 110.7° | 109.4° |
CB | CA | H11 | 111.0° | 109.5° |
CA | CB | H15 | 108.5° | 109.5° |
CA | CB | H16 | 108.5° | 109.5° |
C | CA | N | 110.9° | 109.5° |
CA | C | O | 124.0° | 120.0° |
C | CA | H11 | 111.5° | 109.5° |
N | CA | H11 | 112.1° | 109.5° |
CA | N | H12 | 109.5° | 111.0° |
CA | N | H13 | 109.5° | 111.0° |
CD2 | CE2 | H20 | 120.1° | 120.0° |
CE2 | CD2 | H21 | 119.5° | 119.9° |
H1 | C3U | H2 | 109.5° | 109.6° |
H1 | C3U | H3 | 109.5° | 109.5° |
H2 | C3U | H3 | 109.5° | 109.4° |
H8 | C5' | H9 | 109.5° | 109.5° |
H12 | N | H13 | 109.5° | 111.0° |
H15 | CB | H16 | 109.5° | 109.4° |
Dihedrals
First atom | Second atom | Third atom | Fourth atom | Torsion (experimental model) | Torsion (ideal model) |
C3U | N3 | C2 | O2 | 0.2° | 0.0° |
C3U | N3 | C2 | C4 | 179.7° | 179.7° |
C3U | N3 | C2 | N1 | 179.6° | 179.8° |
C3U | N3 | C4 | O4 | 0.6° | 0.0° |
C3U | N3 | C4 | C5 | 179.1° | 179.9° |
N3 | C3U | H1 | H2 | 120.0° | 120.0° |
N3 | C3U | H1 | H3 | 120.0° | 119.9° |
N3 | C3U | H2 | H3 | 120.0° | 119.9° |
O2 | C2 | N3 | N1 | 179.4° | 179.8° |
O2 | C2 | N3 | C4 | 179.4° | 179.8° |
O2 | C2 | N1 | C1' | 3.0° | 0.0° |
O2 | C2 | N1 | C6 | 178.5° | 179.8° |
C2 | N3 | C4 | O4 | 179.7° | 179.8° |
C2 | N3 | C4 | C5 | 0.6° | 0.2° |
N3 | C2 | N1 | C1' | 177.7° | 179.8° |
N3 | C2 | N1 | C6 | 0.9° | 0.5° |
C2 | N3 | C3U | H1 | 180.0° | 90.0° |
C2 | N3 | C3U | H2 | 60.0° | 149.9° |
C2 | N3 | C3U | H3 | 60.0° | 30.0° |
C4 | N3 | C2 | N1 | 0.1° | 0.5° |
N3 | C4 | O4 | C5 | 179.7° | 180.0° |
N3 | C4 | C5 | C6 | 0.2° | 0.0° |
C4 | N3 | C3U | H1 | 0.3° | 89.7° |
C4 | N3 | C3U | H2 | 120.3° | 30.3° |
C4 | N3 | C3U | H3 | 119.7° | 150.2° |
N3 | C4 | C5 | H4 | 179.8° | 180.0° |
C2 | N1 | C1' | C6 | 178.5° | 179.7° |
C2 | N1 | C1' | O4' | 117.5° | 126.2° |
C2 | N1 | C1' | C2' | 123.5° | 118.4° |
C2 | N1 | C6 | C5 | 1.3° | 0.2° |
C2 | N1 | C6 | H5 | 178.7° | 179.8° |
C2 | N1 | C1' | H6 | 1.7° | 3.9° |
O4 | C4 | C5 | C6 | 179.8° | 180.0° |
O4 | C4 | C5 | H4 | 0.2° | 0.0° |
C4 | C5 | C6 | N1 | 0.7° | 0.0° |
C4 | C5 | C6 | H4 | 180.0° | 180.0° |
C4 | C5 | C6 | H5 | 179.3° | 180.0° |
N1 | C1' | O4' | C2' | 126.5° | 118.9° |
N1 | C1' | O4' | H6 | 118.6° | 122.2° |
N1 | C1' | C2' | H6 | 122.0° | 122.3° |
N1 | C1' | O4' | C4' | 163.3° | 159.4° |
C1' | N1 | C6 | C5 | 177.2° | 180.0° |
N1 | C1' | C2' | O2' | 73.5° | 98.5° |
N1 | C1' | C2' | C3' | 168.4° | 142.8° |
C1' | N1 | C6 | H5 | 2.9° | 0.0° |
N1 | C1' | C2' | H24 | 52.3° | 24.2° |
C6 | N1 | C1' | O4' | 63.9° | 53.6° |
C6 | N1 | C1' | C2' | 55.0° | 61.9° |
N1 | C6 | C5 | H5 | 180.0° | 180.0° |
N1 | C6 | C5 | H4 | 179.3° | 180.0° |
C6 | N1 | C1' | H6 | 176.8° | 175.8° |
O4' | C1' | C2' | H6 | 115.8° | 118.8° |
C1' | O4' | C4' | C3' | 11.6° | 40.5° |
C1' | O4' | C4' | C5' | 135.6° | 159.3° |
O4' | C1' | C2' | O2' | 164.3° | 142.6° |
O4' | C1' | C2' | C3' | 46.2° | 23.9° |
C1' | O4' | C4' | H7 | 105.0° | 78.3° |
O4' | C1' | C2' | H24 | 69.9° | 94.7° |
C2' | C1' | O4' | C4' | 36.8° | 40.5° |
C1' | C2' | C3' | O3' | 80.9° | 118.7° |
C1' | C2' | C3' | C4' | 37.3° | 0.0° |
C1' | C2' | O2' | C3' | 109.8° | 114.7° |
C1' | C2' | O2' | H24 | 124.9° | 122.7° |
C1' | C2' | C3' | H24 | 116.3° | 118.7° |
C1' | C2' | C3' | H22 | 154.8° | 118.6° |
C1' | C2' | O2' | H25 | 180.0° | 179.9° |
O4' | C4' | C3' | O3' | 100.5° | 142.7° |
O4' | C4' | C3' | C5' | 121.3° | 118.8° |
O4' | C4' | C3' | H7 | 117.4° | 118.8° |
O4' | C4' | C5' | H7 | 119.9° | 122.3° |
O4' | C4' | C3' | C2' | 17.5° | 24.0° |
O4' | C4' | C5' | O5' | 64.8° | 66.5° |
C4' | O4' | C1' | H6 | 78.0° | 78.4° |
O4' | C4' | C5' | H8 | 54.8° | 173.6° |
O4' | C4' | C5' | H9 | 175.6° | 53.5° |
O4' | C4' | C3' | H22 | 134.9° | 94.6° |
O3' | C3' | C4' | C2' | 117.9° | 118.7° |
O3' | C3' | C4' | H22 | 124.6° | 122.7° |
O3' | C3' | C4' | C5' | 138.3° | 98.5° |
O3' | C3' | C2' | O2' | 36.5° | 0.0° |
O3' | C3' | C2' | H22 | 124.3° | 122.7° |
O3' | C3' | C4' | H7 | 17.0° | 23.9° |
O3' | C3' | C2' | H24 | 162.8° | 122.6° |
C3' | C4' | C5' | H7 | 121.1° | 122.3° |
C4' | C3' | C2' | O2' | 154.8° | 118.7° |
C4' | C3' | C2' | H22 | 117.4° | 118.6° |
C3' | C4' | C5' | O5' | 54.2° | 178.2° |
C3' | C4' | C5' | H8 | 173.8° | 58.2° |
C3' | C4' | C5' | H9 | 65.4° | 61.9° |
C4' | C3' | O3' | H23 | 180.0° | 180.0° |
C4' | C3' | C2' | H24 | 78.9° | 118.7° |
C5' | C4' | C3' | C2' | 103.8° | 142.8° |
C4' | C5' | O5' | H8 | 119.6° | 120.0° |
C4' | C5' | O5' | H9 | 119.6° | 120.0° |
C4' | C5' | O5' | SBI | 135.7° | 180.0° |
C4' | C5' | H8 | H9 | 121.1° | 120.1° |
C5' | C4' | C3' | H22 | 13.7° | 24.2° |
O2' | C2' | C3' | H24 | 126.3° | 122.7° |
O2' | C2' | C1' | H6 | 48.5° | 23.8° |
O2' | C2' | C3' | H22 | 87.8° | 122.7° |
C3' | C2' | C1' | H6 | 69.6° | 94.9° |
C2' | C3' | C4' | H7 | 134.9° | 94.9° |
C2' | C3' | O3' | H23 | 67.1° | 65.3° |
C3' | C2' | O2' | H25 | 70.2° | 65.3° |
C5' | O5' | SBI | NAT | 54.0° | 75.0° |
C5' | O5' | SBI | OAE | 56.9° | 38.5° |
C5' | O5' | SBI | OAD | 173.0° | 171.5° |
O5' | C5' | C4' | H7 | 175.3° | 55.9° |
O5' | C5' | H8 | H9 | 121.1° | 120.0° |
O5' | SBI | NAT | OAE | 110.5° | 113.6° |
O5' | SBI | NAT | OAD | 115.1° | 113.5° |
O5' | SBI | OAE | OAD | 121.4° | 123.0° |
O5' | SBI | NAT | C | 163.3° | 65.0° |
SBI | O5' | C5' | H8 | 104.7° | 60.0° |
SBI | O5' | C5' | H9 | 16.1° | 60.0° |
O5' | SBI | NAT | H10 | 16.7° | 115.0° |
CD1 | CE1 | CZ | H18 | 180.0° | 180.0° |
CE1 | CD1 | CG | H17 | 180.0° | 180.0° |
CD1 | CE1 | CZ | OH | 178.9° | 180.0° |
CD1 | CE1 | CZ | CE2 | 0.9° | 0.0° |
CE1 | CD1 | CG | CB | 179.2° | 180.0° |
CE1 | CD1 | CG | CD2 | 1.3° | 0.3° |
CZ | CE1 | CD1 | CG | 1.0° | 0.0° |
CE1 | CZ | OH | CE2 | 179.8° | 180.0° |
CE1 | CZ | CE2 | CD2 | 1.2° | 0.3° |
CZ | CE1 | CD1 | H17 | 179.0° | 180.0° |
CE1 | CZ | OH | H19 | 180.0° | 90.0° |
CE1 | CZ | CE2 | H20 | 178.8° | 180.0° |
CD1 | CG | CB | CD2 | 179.5° | 179.7° |
CD1 | CG | CB | CA | 61.1° | 89.7° |
CD1 | CG | CD2 | CE2 | 1.6° | 0.5° |
CD1 | CG | CB | H15 | 59.4° | 150.3° |
CD1 | CG | CB | H16 | 178.3° | 30.3° |
CG | CD1 | CE1 | H18 | 179.1° | 179.9° |
CD1 | CG | CD2 | H21 | 178.4° | 179.7° |
NAT | SBI | OAE | OAD | 129.6° | 122.9° |
SBI | NAT | C | H10 | 180.0° | 180.0° |
SBI | NAT | C | CA | 174.1° | 180.0° |
SBI | NAT | C | O | 2.1° | 0.0° |
OAE | SBI | NAT | C | 86.1° | 178.6° |
OAE | SBI | NAT | H10 | 93.9° | 1.4° |
OAD | SBI | NAT | C | 48.2° | 48.5° |
OAD | SBI | NAT | H10 | 131.8° | 131.4° |
NAT | C | CA | CB | 77.0° | 80.0° |
NAT | C | CA | O | 176.1° | 180.0° |
NAT | C | CA | N | 166.2° | 160.0° |
NAT | C | CA | H11 | 40.4° | 39.9° |
OH | CZ | CE2 | CD2 | 178.6° | 179.7° |
OH | CZ | CE1 | H18 | 1.1° | 0.0° |
OH | CZ | CE2 | H20 | 1.4° | 0.0° |
CZ | CE2 | CD2 | CG | 1.6° | 0.5° |
CZ | CE2 | CD2 | H20 | 180.0° | 179.7° |
CE2 | CZ | CE1 | H18 | 179.1° | 179.9° |
CE2 | CZ | OH | H19 | 0.2° | 90.0° |
CZ | CE2 | CD2 | H21 | 178.4° | 179.7° |
CG | CB | CA | H15 | 120.5° | 120.1° |
CG | CB | CA | H16 | 120.6° | 120.0° |
CG | CB | CA | C | 171.9° | 175.0° |
CG | CB | CA | N | 54.9° | 65.0° |
CB | CG | CD2 | CE2 | 178.9° | 179.8° |
CG | CB | CA | H11 | 70.2° | 55.0° |
CG | CB | H15 | H16 | 118.3° | 120.0° |
CB | CG | CD1 | H17 | 0.8° | 0.1° |
CB | CG | CD2 | H21 | 1.1° | 0.0° |
CD2 | CG | CB | CA | 118.3° | 90.0° |
CG | CD2 | CE2 | H21 | 180.0° | 179.7° |
CD2 | CG | CB | H15 | 121.1° | 30.0° |
CD2 | CG | CB | H16 | 2.2° | 150.0° |
CD2 | CG | CD1 | H17 | 178.7° | 179.7° |
CG | CD2 | CE2 | H20 | 178.4° | 179.7° |
CB | CA | C | N | 116.8° | 120.0° |
CB | CA | C | H11 | 117.4° | 120.0° |
CB | CA | N | H11 | 124.5° | 120.0° |
CB | CA | C | O | 99.1° | 100.0° |
CB | CA | N | H12 | 180.0° | 176.1° |
CB | CA | N | H13 | 60.0° | 60.0° |
CA | CB | H15 | H16 | 118.3° | 120.0° |
C | CA | N | H11 | 125.4° | 120.0° |
CA | C | NAT | H10 | 5.9° | 0.0° |
C | CA | N | H12 | 69.9° | 64.0° |
C | CA | N | H13 | 50.1° | 60.0° |
C | CA | CB | H15 | 67.5° | 64.9° |
C | CA | CB | H16 | 51.3° | 55.0° |
N | CA | C | O | 17.7° | 19.9° |
CA | N | H12 | H13 | 120.0° | 123.9° |
N | CA | CB | H15 | 175.4° | 55.0° |
N | CA | CB | H16 | 65.7° | 175.0° |
O | C | NAT | H10 | 177.9° | 180.0° |
O | C | CA | H11 | 143.5° | 140.0° |
H1 | C3U | H2 | H3 | 120.0° | 120.1° |
H4 | C5 | C6 | H5 | 0.7° | 0.0° |
H6 | C1' | C2' | H24 | 174.3° | 146.5° |
H7 | C4' | C5' | H8 | 65.1° | 64.1° |
H7 | C4' | C5' | H9 | 55.7° | 175.9° |
H7 | C4' | C3' | H22 | 107.6° | 146.5° |
H11 | CA | N | H12 | 55.5° | 56.1° |
H11 | CA | N | H13 | 175.5° | 180.0° |
H11 | CA | CB | H15 | 50.3° | 175.1° |
H11 | CA | CB | H16 | 169.2° | 65.0° |
H17 | CD1 | CE1 | H18 | 0.9° | 0.0° |
H20 | CE2 | CD2 | H21 | 1.6° | 0.0° |
H22 | C3' | O3' | H23 | 56.3° | 57.3° |
H22 | C3' | C2' | H24 | 38.5° | 0.0° |
H24 | C2' | O2' | H25 | 55.1° | 57.3° |