PDB Chemical Component H2U

The following tables include covalent bond distance, bond angle and torsion angle values for the experimental model and ideal geometries stored in the definition for this chemical component.

Bond Distances for H2U

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
P OP1 1.487 1.479
P OP2 1.488 1.611
P OP3 1.612 1.610
P O5' 1.603 1.609
OP2 HOP2 0.950 0.968
OP3 HOP3 0.950 0.966
O5' C5' 1.439 1.428
C5' C4' 1.516 1.529
C5' H5' 1.115 1.090
C5' H5'' 1.115 1.090
C4' O4' 1.445 1.446
C4' C3' 1.517 1.544
C4' H4' 1.115 1.090
O4' C1' 1.416 1.445
C3' O3' 1.451 1.429
C3' C2' 1.530 1.544
C3' H3' 1.116 1.090
O3' HO3' 0.950 0.967
C1' C2' 1.536 1.544
C1' N1 1.471 1.465
C1' H1' 1.115 1.089
C2' O2' 1.411 1.428
C2' H2' 1.116 1.090
O2' HO2' 0.950 0.966
N1 C2 1.389 1.341
N1 C6 1.476 1.464
C2 O2 1.219 1.216
C2 N3 1.373 1.343
N3 C4 1.380 1.346
N3 HN3 1.020 0.970
C4 O4 1.234 1.212
C4 C5 1.506 1.507
C5 C6 1.504 1.530
C5 H51 1.115 1.089
C5 H52 1.116 1.090
C6 H61 1.116 1.090
C6 H62 1.115 1.090

Bond Angles for H2U

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
OP1 P OP2 119.0 109.4
OP1 P OP3 105.9 109.5
OP1 P O5' 106.5 109.5
OP2 P OP3 111.2 109.4
OP2 P O5' 110.4 109.4
P OP2 HOP2 119.0 106.7
OP3 P O5' 102.5 109.5
P OP3 HOP3 105.9 106.8
P O5' C5' 119.3 106.8
O5' C5' C4' 111.2 109.6
O5' C5' H5' 111.5 109.5
O5' C5' H5'' 111.5 109.5
C4' C5' H5' 111.6 109.5
C4' C5' H5'' 111.6 109.4
C5' C4' O4' 108.7 110.4
C5' C4' C3' 115.5 110.7
C5' C4' H4' 104.1 110.3
H5' C5' H5'' 98.8 109.5
O4' C4' C3' 103.0 104.7
O4' C4' H4' 116.4 110.3
C4' O4' C1' 109.3 105.4
C3' C4' H4' 109.6 110.2
C4' C3' O3' 111.4 110.5
C4' C3' C2' 101.6 104.2
C4' C3' H3' 117.5 110.5
O4' C1' C2' 107.2 104.8
O4' C1' N1 107.4 110.5
O4' C1' H1' 114.1 110.4
O3' C3' C2' 119.5 110.5
O3' C3' H3' 98.8 110.5
C3' O3' HO3' 111.3 106.9
C2' C3' H3' 109.0 110.5
C3' C2' C1' 102.3 104.1
C3' C2' O2' 115.9 110.5
C3' C2' H2' 111.8 110.5
C2' C1' N1 114.3 110.4
C2' C1' H1' 107.1 110.3
C1' C2' O2' 113.9 110.7
C1' C2' H2' 113.9 110.5
N1 C1' H1' 106.9 110.4
C1' N1 C2 116.8 119.6
C1' N1 C6 121.2 119.5
O2' C2' H2' 99.7 110.4
C2' O2' HO2' 115.8 106.9
C2 N1 C6 121.9 120.9
N1 C2 O2 122.4 119.2
N1 C2 N3 116.1 121.7
N1 C6 C5 112.2 109.5
N1 C6 H61 111.2 109.5
N1 C6 H62 111.2 109.5
O2 C2 N3 121.5 119.2
C2 N3 C4 128.2 120.9
C2 N3 HN3 115.6 119.6
C4 N3 HN3 116.2 119.5
N3 C4 O4 119.1 120.1
N3 C4 C5 114.8 120.0
O4 C4 C5 125.6 120.0
C4 C5 C6 113.7 109.2
C4 C5 H51 110.7 109.6
C4 C5 H52 110.7 109.5
C6 C5 H51 110.7 109.5
C6 C5 H52 110.6 109.5
C5 C6 H61 111.2 109.4
C5 C6 H62 111.2 109.5
H51 C5 H52 99.6 109.5
H61 C6 H62 99.1 109.4

Torsion Angles for H2U

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
OP2 P OP1 OP3 234.0 120.0
OP2 P OP1 O5' 125.5 240.1
OP1 P OP2 HOP2 180.0 300.0
OP3 P OP1 O5' 251.4 120.1
OP1 P OP3 HOP3 180.0 180.0
OP1 P O5' C5' 309.8 60.0
OP1 P OP2 OP3 123.4 240.0
OP1 P OP2 O5' 236.4 120.0
OP3 P OP2 O5' 113.0 240.0
OP2 P OP3 HOP3 310.6 60.0
OP2 P O5' C5' 179.3 180.0
OP1 P OP3 OP2 229.4 120.0
OP1 P OP3 O5' 111.4 239.9
OP2 P OP3 O5' 242.1 119.9
OP3 P OP2 HOP2 56.6 60.0
OP3 P O5' C5' 60.8 299.9
OP1 P O5' OP2 130.5 240.1
OP1 P O5' OP3 249.0 120.1
OP2 P O5' OP3 118.5 240.1
O5' P OP2 HOP2 303.5 180.0
O5' P OP3 HOP3 68.6 300.1
P O5' C5' C4' 206.2 180.0
P O5' C5' H5' 331.5 60.0
P O5' C5' H5'' 80.9 300.0
HOP2 OP2 P OP3 56.6 60.0
HOP2 OP2 P O5' 303.5 180.0
HOP3 OP3 P O5' 68.6 300.1
C4' C5' O5' H5' 234.7 120.0
C4' C5' O5' H5'' 125.3 240.0
O5' C5' C4' O4' 297.9 61.4
O5' C5' C4' C3' 53.0 176.9
O5' C5' C4' H4' 173.2 299.2
H5' C5' O5' H5'' 250.6 120.0
O5' C5' C4' H5' 125.3 240.0
O5' C5' C4' H5'' 234.7 120.0
H5' C5' C4' H5'' 109.5 240.1
O4' C4' C5' C3' 244.9 244.5
O4' C4' C5' H4' 124.6 122.2
C5' C4' O4' C1' 91.1 159.5
C3' C4' C5' H4' 239.8 237.7
C5' C4' C3' O3' 153.8 98.6
C5' C4' C3' C2' 282.2 217.2
C5' C4' C3' H3' 41.0 336.0
O5' C5' H5' C4' 234.9 120.1
O5' C5' H5' H5'' 117.4 240.0
C4' C5' H5' H5'' 242.5 119.9
H5' C5' C4' O4' 172.6 181.5
H5' C5' C4' C3' 287.8 296.9
H5' C5' C4' H4' 48.0 59.3
O5' C5' H5'' C4' 125.1 239.9
O5' C5' H5'' H5' 242.6 120.0
C4' C5' H5'' H5' 117.5 240.1
H5'' C5' C4' O4' 63.1 301.4
H5'' C5' C4' C3' 178.3 56.9
H5'' C5' C4' H4' 298.5 179.2
O4' C4' C5' H5' 172.6 181.5
O4' C4' C5' H5'' 63.1 301.4
C5' C4' O4' C3' 123.0 119.2
C5' C4' O4' H4' 243.0 237.8
C3' C4' O4' H4' 120.0 118.6
O4' C4' C3' O3' 272.1 217.5
O4' C4' C3' C2' 40.5 336.2
O4' C4' C3' H3' 159.3 94.9
C4' O4' C1' C2' 9.7 319.6
C4' O4' C1' N1 246.5 200.7
C4' O4' C1' H1' 128.1 78.3
C3' C4' C5' H5' 287.8 296.9
C3' C4' C5' H5'' 178.3 56.9
C5' C4' C3' O4' 241.7 241.1
C5' C4' C3' H4' 117.2 122.4
O4' C4' C3' H4' 235.5 241.3
C3' C4' O4' C1' 328.1 40.3
O3' C3' C4' C2' 231.6 241.3
O3' C3' C4' H3' 112.9 122.6
C4' C3' O3' HO3' 180.1 178.1
C2' C3' C4' H3' 241.2 241.3
C4' C3' C2' C1' 325.9 359.9
C4' C3' C2' O2' 201.4 241.1
C4' C3' C2' H2' 88.1 118.6
H4' C4' C5' H5' 48.0 59.3
H4' C4' C5' H5'' 298.5 179.2
C5' C4' H4' O4' 119.5 122.2
C5' C4' H4' C3' 235.9 237.4
O4' C4' H4' C3' 116.4 115.2
H4' C4' O4' C1' 208.1 281.7
H4' C4' C3' O3' 36.7 336.2
H4' C4' C3' C2' 165.0 94.9
H4' C4' C3' H3' 283.8 213.6
C1' O4' C4' C3' 328.1 40.3
C1' O4' C4' H4' 208.1 281.7
C3' C2' C1' O4' 16.1 24.0
C2' C1' O4' N1 123.2 118.9
C2' C1' O4' H1' 241.6 241.3
O4' C1' C2' O2' 141.9 142.7
O4' C1' C2' H2' 255.3 265.3
N1 C1' O4' H1' 118.3 122.4
O4' C1' N1 C2 319.2 55.1
O4' C1' N1 C6 138.3 235.4
O3' C3' C4' H4' 36.7 336.2
C4' C3' O3' C2' 118.0 114.8
C4' C3' O3' H3' 235.8 237.4
C2' C3' O3' H3' 117.8 122.6
O3' C3' C2' C1' 88.9 118.7
O3' C3' C2' O2' 324.4 359.8
O3' C3' C2' H2' 211.1 237.3
C2' C3' C4' H4' 165.0 94.9
C4' C3' C2' O3' 237.1 241.3
C4' C3' C2' H3' 124.7 118.7
O4' C1' C2' C3' 16.1 24.0
O3' C3' C2' H3' 247.6 237.4
C2' C3' O3' HO3' 62.0 63.3
C3' C2' C1' N1 134.9 142.9
C3' C2' C1' H1' 253.2 265.2
C1' C2' C3' O2' 124.5 118.9
C1' C2' C3' H2' 237.8 241.3
O2' C2' C3' H2' 113.3 122.5
C3' C2' O2' HO2' 180.0 298.6
H3' C3' C4' H4' 283.8 213.6
C4' C3' H3' O3' 119.7 122.6
C4' C3' H3' C2' 245.2 245.2
O3' C3' H3' C2' 125.5 122.6
H3' C3' O3' HO3' 304.3 300.7
H3' C3' C2' C1' 201.2 241.3
H3' C3' C2' O2' 76.7 122.4
H3' C3' C2' H2' 323.4 359.9
HO3' O3' C3' C2' 62.0 63.3
HO3' O3' C3' H3' 304.3 300.7
O4' C1' C2' N1 241.1 241.1
O4' C1' C2' H1' 122.9 118.8
C1' C2' C3' H3' 201.2 241.3
C3' C2' C1' O2' 234.2 241.2
C3' C2' C1' H2' 120.8 118.6
N1 C1' C2' H1' 241.7 237.7
C2' C1' N1 C2 200.5 299.8
C2' C1' N1 C6 19.6 120.0
O2' C2' C1' H2' 246.6 237.4
C1' C2' O2' HO2' 61.7 183.8
O4' C1' N1 C2' 118.7 115.4
O4' C1' N1 H1' 237.1 237.6
C2' C1' N1 H1' 118.4 122.2
N1 C1' C2' O2' 260.8 261.6
N1 C1' C2' H2' 14.2 24.2
C2 N1 C1' C6 180.9 179.7
C1' N1 C2 O2 9.4 6.0
C1' N1 C2 N3 189.6 185.5
C1' N1 C6 C5 148.1 144.2
C1' N1 C6 H61 273.4 264.1
C1' N1 C6 H62 22.8 24.1
O4' C1' H1' C2' 241.5 244.7
O4' C1' H1' N1 118.6 122.4
C2' C1' H1' N1 237.0 237.7
H1' C1' C2' O2' 19.0 23.9
H1' C1' C2' H2' 132.4 146.5
H1' C1' N1 C2 82.1 177.5
H1' C1' N1 C6 261.2 357.8
O2' C2' C3' H3' 76.7 122.4
C3' C2' O2' C1' 118.3 114.8
C3' C2' O2' H2' 239.9 237.5
O2' C2' C1' N1 260.8 261.6
O2' C2' C1' H1' 19.0 23.9
C1' C2' O2' H2' 121.6 122.7
H2' C2' C3' H3' 323.4 359.9
C3' C2' H2' C1' 244.7 245.3
C3' C2' H2' O2' 123.0 122.5
H2' C2' C1' N1 14.2 24.2
H2' C2' C1' H1' 132.4 146.5
C1' C2' H2' O2' 238.4 237.2
H2' C2' O2' HO2' 300.1 61.2
HO2' O2' C2' H2' 300.1 61.2
C2 N1 C1' H1' 82.1 177.5
C1' N1 C2 C6 179.1 180.3
C2 N1 C6 C5 327.2 324.4
C2 N1 C6 H61 92.4 84.4
C2 N1 C6 H62 201.9 204.4
O2 C2 N1 N3 179.8 180.5
N1 C2 N3 C4 2.4 12.5
N1 C2 N3 HN3 182.4 192.3
C6 N1 C1' H1' 261.2 357.8
C1' N1 C6 C2 180.9 179.7
C6 N1 C2 O2 190.3 185.7
C6 N1 C2 N3 10.5 5.2
C4 C5 C6 N1 41.8 46.7
N1 C6 C5 H51 276.5 166.6
N1 C6 C5 H52 167.1 286.8
C5 C6 N1 H61 234.7 240.0
C5 C6 N1 H62 125.3 120.1
H61 C6 N1 H62 250.6 240.1
O2 C2 N1 C6 190.3 185.7
N1 C2 O2 N3 180.3 179.5
O2 C2 N3 C4 182.6 192.0
O2 C2 N3 HN3 2.7 11.8
N3 C2 N1 C6 10.5 5.2
N1 C2 N3 O2 179.8 180.5
C4 N3 C2 HN3 180.0 180.1
C2 N3 C4 O4 180.9 184.2
C2 N3 C4 C5 8.9 4.2
C2 N3 C4 HN3 180.0 179.9
O4 C4 N3 C5 172.1 180.0
N3 C4 C5 C6 328.8 325.8
N3 C4 C5 H51 94.1 205.8
N3 C4 C5 H52 203.5 85.7
C2 N3 HN3 C4 180.0 180.1
HN3 N3 C4 O4 0.9 4.4
HN3 N3 C4 C5 188.9 184.4
O4 C4 N3 HN3 0.9 4.4
N3 C4 O4 C5 188.9 180.0
O4 C4 C5 C6 157.3 145.8
O4 C4 C5 H51 282.6 25.9
O4 C4 C5 H52 32.1 265.7
N1 C6 C5 C4 41.8 46.7
C5 C4 N3 HN3 188.9 184.4
N3 C4 C5 O4 171.5 180.0
C6 C5 C4 H51 234.7 120.0
C6 C5 C4 H52 125.2 240.1
C4 C5 C6 H61 276.5 286.6
C4 C5 C6 H62 167.1 166.7
H51 C5 C4 H52 250.5 120.2
N1 C6 C5 H61 125.3 120.0
N1 C6 C5 H62 234.7 240.0
C4 C5 C6 H51 125.3 240.0
C4 C5 C6 H52 234.7 119.9
H51 C5 C6 H52 109.4 239.9
H61 C6 C5 H62 109.4 119.9
C4 C5 H51 C6 233.0 119.8
C4 C5 H51 H52 116.5 239.8
C6 C5 H51 H52 243.5 120.1
H51 C5 C6 H61 151.2 46.6
H51 C5 C6 H62 41.8 286.7
C4 C5 H52 C6 126.9 240.3
C4 C5 H52 H51 243.5 120.2
C6 C5 H52 H51 116.5 239.9
H52 C5 C6 H61 41.8 166.7
H52 C5 C6 H62 292.4 46.8
N1 C6 H61 C5 234.1 239.9
N1 C6 H61 H62 117.1 120.0
H61 C6 C5 H51 151.2 46.6
H61 C6 C5 H52 41.8 166.7
C5 C6 H61 H62 242.9 240.0
N1 C6 H62 C5 125.9 120.1
N1 C6 H62 H61 242.9 240.0
H62 C6 C5 H51 41.8 286.7
H62 C6 C5 H52 292.4 46.8
C5 C6 H62 H61 117.0 119.9