PDB Chemical Component DU

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 DU

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
OP3 P   1.618
OP3 HOP3   0.981
P OP1 1.490 1.501
P OP2 1.487 1.616
P O5' 1.597 1.619
OP2 HOP2 0.951 0.981
O5' C5' 1.441 1.418
C5' C4' 1.511 1.523
C5' H5' 1.100 1.092
C5' H5'' 1.100 1.093
C4' O4' 1.450 1.441
C4' C3' 1.529 1.522
C4' H4' 1.100 1.094
O4' C1' 1.425 1.434
C3' O3' 1.424 1.426
C3' C2' 1.523 1.511
C3' H3' 1.100 1.094
O3' HO3' 0.950 0.973
C2' C1' 1.523 1.520
C2' H2' 1.100 1.097
C2' H2'' 1.100 1.095
C1' N1 1.467 1.434
C1' H1' 1.100 1.095
N1 C2 1.382 1.412
N1 C6 1.372 1.389
C2 O2 1.220 1.233
C2 N3 1.379 1.402
N3 C4 1.376 1.386
N3 H3 0.999 1.016
C4 O4 1.229 1.227
C4 C5 1.426 1.477
C5 C6 1.333 1.336
C5 H5 1.080 1.083
C6 H6 1.080 1.085

Bond Angles for DU

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
P OP3 HOP3   118.9
OP3 P OP1   115.3
OP3 P OP2   103.3
OP3 P O5'   103.7
OP1 P OP2 119.4 115.0
OP1 P O5' 107.7 115.0
OP2 P O5' 108.8 102.9
P OP2 HOP2 109.5 118.9
P O5' C5' 120.5 118.5
O5' C5' C4' 110.6 108.9
O5' C5' H5' 108.8 109.0
O5' C5' H5'' 109.1 108.9
C4' C5' H5' 108.9 110.3
C4' C5' H5'' 109.1 110.3
C5' C4' O4' 110.4 107.9
C5' C4' C3' 116.7 112.9
C5' C4' H4' 102.6 109.5
H5' C5' H5'' 110.4 109.3
O4' C4' C3' 106.0 106.2
O4' C4' H4' 114.1 107.9
C4' O4' C1' 110.2 109.3
C3' C4' H4' 107.3 112.2
C4' C3' O3' 107.4 109.9
C4' C3' C2' 103.1 103.1
C4' C3' H3' 114.9 113.5
O4' C1' C2' 105.6 107.4
O4' C1' N1 107.5 109.3
O4' C1' H1' 115.1 108.0
O3' C3' C2' 109.9 109.7
O3' C3' H3' 108.7 107.4
C3' O3' HO3' 109.5 107.3
C2' C3' H3' 112.7 113.2
C3' C2' C1' 102.0 102.5
C3' C2' H2' 113.6 109.7
C3' C2' H2'' 112.0 114.1
C1' C2' H2' 113.6 110.6
C1' C2' H2'' 112.1 111.7
C2' C1' N1 114.6 112.8
C2' C1' H1' 108.1 111.5
H2' C2' H2'' 103.9 108.3
N1 C1' H1' 106.2 107.8
C1' N1 C2 118.2 121.3
C1' N1 C6 120.8 118.4
C2 N1 C6 121.0 120.3
N1 C2 O2 122.8 123.8
N1 C2 N3 114.8 115.1
N1 C6 C5 122.8 123.9
N1 C6 H6 118.6 115.6
O2 C2 N3 122.4 121.1
C2 N3 C4 126.8 126.8
C2 N3 H3 116.6 116.6
C4 N3 H3 116.6 116.6
N3 C4 O4 119.5 124.5
N3 C4 C5 114.8 114.6
O4 C4 C5 125.7 120.9
C4 C5 C6 119.8 119.3
C4 C5 H5 120.1 118.8
C6 C5 H5 120.1 121.9
C5 C6 H6 118.6 120.5

Torsion Angles for DU

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
OP1 P OP3 OP2   126.3
OP1 P OP3 O5'   233.4
OP2 P OP3 O5'   107.1
OP3 P OP2 HOP2   78.5
OP3 P O5' C5'   53.2
HOP3 OP3 P OP1   48.8
HOP3 OP3 P OP2   282.5
HOP3 OP3 P O5'   175.4
OP1 P OP3 HOP3   48.8
OP3 P OP1 OP2   239.9
OP3 P OP1 O5'   120.6
OP2 P OP1 O5' 124.6 240.7
OP1 P OP2 HOP2 159.6 312.0
OP1 P O5' C5' 170.6 179.9
OP2 P OP3 HOP3   282.5
OP3 P OP2 OP1   126.5
OP3 P OP2 O5'   252.3
OP1 P OP2 O5' 236.0 125.8
OP2 P O5' C5' 39.9 305.8
O5' P OP3 HOP3   175.4
OP3 P O5' OP1   233.2
OP3 P O5' OP2   107.4
OP1 P O5' OP2 130.8 234.2
O5' P OP2 HOP2 283.6 186.2
P O5' C5' C4' 208.5 180.0
P O5' C5' H5' 89.0 300.4
P O5' C5' H5'' 328.5 59.6
HOP2 OP2 P O5' 283.6 186.2
C4' C5' O5' H5' 119.5 239.6
C4' C5' O5' H5'' 240.0 120.4
O5' C5' C4' O4' 287.2 62.4
O5' C5' C4' C3' 48.3 179.5
O5' C5' C4' H4' 165.3 305.3
H5' C5' O5' H5'' 120.5 240.8
O5' C5' C4' H5' 240.5 119.6
O5' C5' C4' H5'' 120.0 240.5
H5' C5' C4' H5'' 239.5 120.9
O4' C4' C5' C3' 239.0 242.9
O4' C4' C5' H4' 121.9 117.1
C5' C4' O4' C1' 124.5 108.6
C3' C4' C5' H4' 243.0 234.2
C5' C4' C3' O3' 144.5 154.2
C5' C4' C3' C2' 260.5 271.2
C5' C4' C3' H3' 23.5 34.0
O5' C5' H5' C4' 120.6 240.5
O5' C5' H5' H5'' 240.3 119.0
C4' C5' H5' H5'' 119.7 238.5
H5' C5' C4' O4' 46.8 302.9
H5' C5' C4' C3' 167.8 60.0
H5' C5' C4' H4' 284.8 185.7
O5' C5' H5'' C4' 239.1 119.4
O5' C5' H5'' H5' 119.5 241.0
C4' C5' H5'' H5' 240.4 121.5
H5'' C5' C4' O4' 167.3 181.9
H5'' C5' C4' C3' 288.3 299.0
H5'' C5' C4' H4' 45.3 64.8
O4' C4' C5' H5' 46.8 302.9
O4' C4' C5' H5'' 167.3 181.9
C5' C4' O4' C3' 127.2 121.4
C5' C4' O4' H4' 245.1 241.8
C3' C4' O4' H4' 117.8 120.5
O4' C4' C3' O3' 267.9 272.3
O4' C4' C3' C2' 23.9 29.2
O4' C4' C3' H3' 146.8 152.1
C4' O4' C1' C2' 340.2 351.0
C4' O4' C1' N1 217.4 228.3
C4' O4' C1' H1' 99.3 111.3
C3' C4' C5' H5' 167.8 60.0
C3' C4' C5' H5'' 288.3 299.0
C5' C4' C3' O4' 236.7 241.9
C5' C4' C3' H4' 114.4 124.3
O4' C4' C3' H4' 237.8 242.4
C3' C4' O4' C1' 357.3 347.3
O3' C3' C4' C2' 244.0 243.1
O3' C3' C4' H3' 121.1 120.2
C4' C3' O3' HO3' 231.2 232.0
C2' C3' C4' H3' 237.1 237.2
C4' C3' C2' C1' 325.3 326.6
C4' C3' C2' H2' 202.7 84.1
C4' C3' C2' H2'' 85.3 205.7
H4' C4' C5' H5' 284.8 185.7
H4' C4' C5' H5'' 45.3 64.8
C5' C4' H4' O4' 119.4 117.1
C5' C4' H4' C3' 236.5 233.8
O4' C4' H4' C3' 117.0 116.7
H4' C4' O4' C1' 239.5 226.8
H4' C4' C3' O3' 30.1 29.9
H4' C4' C3' C2' 146.1 146.9
H4' C4' C3' H3' 269.0 269.7
C1' O4' C4' C3' 357.3 347.3
C1' O4' C4' H4' 239.5 226.8
C3' C2' C1' O4' 34.0 26.9
O4' C1' C2' H2' 156.7 270.0
O4' C1' C2' H2'' 274.0 149.4
C2' C1' O4' N1 122.8 122.7
C2' C1' O4' H1' 240.9 239.7
N1 C1' O4' H1' 118.1 117.0
O4' C1' N1 C2 241.6 212.9
O4' C1' N1 C6 61.1 32.9
O3' C3' C4' H4' 30.1 29.9
C4' C3' O3' C2' 111.4 112.7
C4' C3' O3' H3' 235.1 236.1
C2' C3' O3' H3' 123.7 123.4
O3' C3' C2' C1' 79.5 83.6
O3' C3' C2' H2' 316.9 201.1
O3' C3' C2' H2'' 199.5 322.8
C2' C3' C4' H4' 146.1 146.9
C4' C3' C2' O3' 245.8 242.9
C4' C3' C2' H3' 124.5 123.0
O4' C1' C2' C3' 34.0 26.9
O3' C3' C2' H3' 238.6 240.1
C2' C3' O3' HO3' 119.8 119.3
C1' C2' C3' H2' 122.7 242.5
C1' C2' C3' H2'' 240.0 120.8
C3' C2' C1' N1 152.1 147.4
C3' C2' C1' H1' 270.3 268.8
H2' C2' C3' H2'' 117.3 238.3
H3' C3' C4' H4' 269.0 269.7
C4' C3' H3' O3' 120.3 121.7
C4' C3' H3' C2' 242.4 242.9
O3' C3' H3' C2' 122.0 121.3
H3' C3' O3' HO3' 356.1 355.9
H3' C3' C2' C1' 200.9 203.6
H3' C3' C2' H2' 78.2 321.1
H3' C3' C2' H2'' 320.9 82.7
HO3' O3' C3' C2' 119.8 119.3
HO3' O3' C3' H3' 356.1 355.9
O4' C1' C2' N1 241.9 239.5
O4' C1' C2' H1' 123.7 118.1
C1' C2' C3' H3' 200.9 203.6
C3' C2' C1' H2' 237.3 116.9
C3' C2' C1' H2'' 120.0 237.5
H2' C2' C1' H2'' 242.6 120.7
N1 C1' C2' H1' 241.8 238.6
C2' C1' N1 C2 124.5 93.5
C2' C1' N1 C6 304.0 273.5
H2' C2' C3' H3' 78.2 321.1
C3' C2' H2' C1' 116.0 247.7
C3' C2' H2' H2'' 238.0 125.1
C1' C2' H2' H2'' 122.0 237.3
H2' C2' C1' N1 274.8 30.6
H2' C2' C1' H1' 33.0 151.9
H2'' C2' C3' H3' 320.9 82.7
C3' C2' H2'' C1' 246.1 115.6
C3' C2' H2'' H2' 123.0 237.5
C1' C2' H2'' H2' 237.0 122.0
H2'' C2' C1' N1 32.2 269.9
H2'' C2' C1' H1' 150.4 31.3
O4' C1' N1 C2' 117.1 119.4
O4' C1' N1 H1' 236.3 242.9
N1 C1' C2' H2' 274.8 30.6
N1 C1' C2' H2'' 32.2 269.9
C2' C1' N1 H1' 119.2 123.5
C2 N1 C1' C6 180.5 180.0
C1' N1 C2 O2 359.0 0.0
C1' N1 C2 N3 179.2 180.0
C1' N1 C6 C5 180.7 180.0
C1' N1 C6 H6 0.6 360.0
O4' C1' H1' C2' 242.2 242.3
O4' C1' H1' N1 118.8 118.0
H1' C1' C2' H2' 33.0 151.9
H1' C1' C2' H2'' 150.4 31.3
C2' C1' H1' N1 236.6 235.7
H1' C1' N1 C2 5.2 330.0
H1' C1' N1 C6 184.8 150.0
C2 N1 C1' H1' 5.2 330.0
C1' N1 C2 C6 179.5 180.0
C2 N1 C6 C5 0.2 360.0
C2 N1 C6 H6 180.2 180.0
O2 C2 N1 N3 179.8 180.0
N1 C2 N3 C4 0.5 0.0
N1 C2 N3 H3 180.5 180.0
C6 N1 C1' H1' 184.8 150.0
C1' N1 C6 C2 180.5 180.0
C6 N1 C2 O2 179.5 180.0
C6 N1 C2 N3 359.6 360.0
C4 C5 C6 N1 359.9 0.0
N1 C6 C5 H5 179.9 180.0
C5 C6 N1 H6 180.0 180.0
O2 C2 N1 C6 179.5 180.0
N1 C2 O2 N3 180.2 180.0
O2 C2 N3 C4 180.7 180.0
O2 C2 N3 H3 0.7 360.0
N3 C2 N1 C6 359.6 360.0
N1 C2 N3 O2 179.8 180.0
C4 N3 C2 H3 180.0 180.0
C2 N3 C4 O4 178.5 179.9
C2 N3 C4 C5 359.6 360.0
C2 N3 C4 H3 180.0 180.0
O4 C4 N3 C5 178.9 180.0
N3 C4 C5 C6 0.2 360.0
N3 C4 C5 H5 180.2 180.0
C2 N3 H3 C4 180.0 180.0
H3 N3 C4 O4 358.5 360.0
H3 N3 C4 C5 179.6 180.0
O4 C4 N3 H3 358.5 360.0
N3 C4 O4 C5 181.2 180.0
O4 C4 C5 C6 181.3 180.0
O4 C4 C5 H5 1.4 0.0
N1 C6 C5 C4 359.9 0.0
C5 C4 N3 H3 179.6 180.0
N3 C4 C5 O4 178.9 180.0
C6 C5 C4 H5 180.0 180.0
C4 C5 C6 H6 179.9 180.0
N1 C6 C5 H6 180.0 180.0
C4 C5 C6 H5 180.0 180.0
C4 C5 H5 C6 180.0 180.0
H5 C5 C6 H6 359.9 0.0
N1 C6 H6 C5 180.0 180.0
H6 C6 C5 H5 359.9 0.0