PDB Chemical Component UDP

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 UDP

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
N1 C2 1.430 1.346
N1 C6 1.412 1.368
N1 C1' 1.482 1.465
C2 N3 1.386 1.346
C2 O2 1.215 1.217
N3 C4 1.421 1.348
N3 HN3 0.999 0.970
C4 C5 1.459 1.416
C4 O4 1.230 1.218
C5 C6 1.322 1.351
C5 H5 1.081 1.080
C6 H6 1.080 1.079
C1' C2' 1.526 1.550
C1' O4' 1.399 1.444
C1' H1' 1.101 1.090
C2' O2' 1.469 1.430
C2' C3' 1.571 1.548
C2' H2' 1.100 1.091
O2' HO2' 0.950 0.966
C3' C4' 1.495 1.541
C3' O3' 1.410 1.429
C3' H3' 1.100 1.090
C4' O4' 1.478 1.437
C4' C5' 1.476 1.530
C4' H4' 1.100 1.090
O3' HO3' 0.950 0.967
C5' O5' 1.441 1.429
C5' H5'1 1.100 1.090
C5' H5'2 1.100 1.090
O5' PA 1.612 1.610
PA O1A 1.513 1.480
PA O2A 1.496 1.611
PA O3A 1.644 1.609
O2A HOA2 0.950 0.967
O3A PB 1.571 1.611
PB O1B 1.587 1.480
PB O2B 1.509 1.610
PB O3B 1.509 1.610
O2B HOB2 0.950 0.967
O3B HOB3 0.950 0.967

Bond Angles for UDP

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
C2 N1 C6 121.7 120.6
C2 N1 C1' 118.2 119.7
N1 C2 N3 114.3 121.0
N1 C2 O2 124.2 119.5
C6 N1 C1' 120.0 119.7
N1 C6 C5 122.5 119.7
N1 C6 H6 118.7 120.2
N1 C1' C2' 114.8 110.6
N1 C1' O4' 109.2 110.6
N1 C1' H1' 104.2 110.6
N3 C2 O2 121.5 119.5
C2 N3 C4 125.7 120.2
C2 N3 HN3 117.2 119.9
C4 N3 HN3 117.1 119.8
N3 C4 C5 116.0 119.4
N3 C4 O4 117.3 120.4
C5 C4 O4 126.6 120.3
C4 C5 C6 119.8 119.1
C4 C5 H5 120.1 120.5
C6 C5 H5 120.1 120.4
C5 C6 H6 118.8 120.1
C2' C1' O4' 103.4 103.5
C2' C1' H1' 110.0 110.6
C1' C2' O2' 108.3 110.9
C1' C2' C3' 102.5 102.1
C1' C2' H2' 115.3 110.9
O4' C1' H1' 115.5 110.8
C1' O4' C4' 113.0 107.0
O2' C2' C3' 111.3 110.9
O2' C2' H2' 107.0 110.8
C2' O2' HO2' 109.5 114.0
C3' C2' H2' 112.4 110.9
C2' C3' C4' 102.2 104.1
C2' C3' O3' 112.9 110.5
C2' C3' H3' 111.4 110.5
C4' C3' O3' 107.4 110.5
C4' C3' H3' 116.5 110.5
C3' C4' O4' 104.8 107.3
C3' C4' C5' 116.7 109.9
C3' C4' H4' 107.7 109.8
O3' C3' H3' 106.5 110.5
C3' O3' HO3' 109.5 114.0
O4' C4' C5' 108.7 109.9
O4' C4' H4' 115.7 109.9
C5' C4' H4' 103.7 110.0
C4' C5' O5' 104.4 109.5
C4' C5' H5'1 111.2 109.4
C4' C5' H5'2 111.2 109.5
O5' C5' H5'1 111.2 109.5
O5' C5' H5'2 111.2 109.5
C5' O5' PA 118.2 123.0
H5'1 C5' H5'2 107.7 109.5
O5' PA O1A 107.4 109.5
O5' PA O2A 114.5 109.5
O5' PA O3A 111.9 109.5
O1A PA O2A 112.1 109.5
O1A PA O3A 107.1 109.5
O2A PA O3A 103.6 109.5
PA O2A HOA2 109.5 114.0
PA O3A PB 131.1 134.0
O3A PB O1B 102.3 109.4
O3A PB O2B 108.1 109.5
O3A PB O3B 109.8 109.5
O1B PB O2B 114.6 109.5
O1B PB O3B 108.5 109.5
O2B PB O3B 112.9 109.5
PB O2B HOB2 109.5 113.9
PB O3B HOB3 109.5 114.0

Torsion Angles for UDP

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
C6 N1 C2 C1' 184.0 180.3
C2 N1 C6 C5 358.9 0.0
C2 N1 C6 H6 178.9 180.0
C2 N1 C1' C2' 119.6 115.0
C2 N1 C1' O4' 235.1 229.1
C2 N1 C1' H1' 359.1 352.2
N3 C2 N1 O2 182.0 180.1
N1 C2 N3 C4 358.9 359.9
N1 C2 N3 HN3 178.9 179.9
C2 N1 C6 C1' 175.9 179.7
C6 N1 C2 N3 1.6 0.1
C6 N1 C2 O2 179.6 179.9
C6 N1 C1' C2' 295.6 294.7
C6 N1 C1' O4' 51.1 48.8
C6 N1 C1' H1' 175.2 171.9
C4 C5 C6 N1 360.0 359.9
N1 C6 C5 H5 180.0 180.0
C5 C6 N1 H6 180.0 180.0
C2 N1 C1' C6 184.0 180.3
C1' N1 C2 N3 177.5 179.8
C1' N1 C2 O2 355.5 359.7
C1' N1 C6 C5 183.0 180.3
C1' N1 C6 H6 3.0 0.3
C2' C1' N1 O4' 244.5 246.0
C2' C1' N1 H1' 120.4 122.9
N1 C1' C2' O2' 271.0 273.7
N1 C1' C2' C3' 153.2 155.5
N1 C1' C2' H2' 30.8 37.3
O4' C1' N1 H1' 236.0 236.9
N1 C1' O4' C4' 217.3 201.5
N3 C2 N1 C6 1.6 0.1
N3 C2 N1 C1' 177.5 179.8
N1 C2 N3 O2 178.1 179.9
C4 N3 C2 HN3 180.0 180.0
C2 N3 C4 C5 0.2 360.0
C2 N3 C4 O4 178.2 180.0
O2 C2 N1 C6 179.6 179.9
O2 C2 N1 C1' 355.5 359.7
N1 C2 O2 N3 182.1 180.1
O2 C2 N3 C4 180.8 180.1
O2 C2 N3 HN3 0.8 0.1
C4 N3 C2 O2 180.8 180.1
C2 N3 C4 HN3 180.0 180.0
C5 C4 N3 O4 182.0 180.0
N3 C4 C5 C6 0.4 0.1
N3 C4 C5 H5 180.5 180.0
HN3 N3 C2 O2 0.8 0.1
C2 N3 HN3 C4 180.0 180.0
HN3 N3 C4 C5 180.2 180.0
HN3 N3 C4 O4 358.2 0.0
N1 C6 C5 C4 360.0 359.9
C5 C4 N3 HN3 180.2 180.0
N3 C4 C5 O4 177.8 180.0
C6 C5 C4 H5 180.0 180.1
C4 C5 C6 H6 180.0 179.9
O4 C4 N3 HN3 358.2 0.0
N3 C4 O4 C5 182.2 180.0
O4 C4 C5 C6 182.6 180.0
O4 C4 C5 H5 2.7 359.9
C5 C6 N1 C1' 183.0 180.3
N1 C6 C5 H6 180.0 180.0
C6 C5 C4 O4 182.6 180.0
C4 C5 C6 H5 180.0 179.9
H5 C5 C4 O4 2.7 359.9
C4 C5 H5 C6 180.0 180.1
H5 C5 C6 H6 360.0 0.0
H6 C6 N1 C1' 3.0 0.3
N1 C6 H6 C5 180.0 180.0
H6 C6 C5 H5 360.0 0.0
N1 C1' C2' O4' 118.9 118.5
N1 C1' C2' H1' 242.8 237.2
O4' C1' C2' H1' 123.9 118.7
C2' C1' O4' C4' 340.0 319.9
O2' C2' C1' C3' 117.7 118.2
O2' C2' C1' H2' 240.2 236.4
C1' C2' O2' HO2' 180.0 180.0
C3' C2' C1' H2' 122.5 118.2
C1' C2' C3' C4' 323.5 339.1
C1' C2' C3' O3' 78.6 97.8
C1' C2' C3' H3' 198.4 220.4
N1 C1' O4' C2' 237.3 241.5
N1 C1' O4' H1' 117.1 123.0
C2' C1' O4' H1' 239.8 241.4
O4' C1' C2' O2' 152.1 155.2
O4' C1' C2' C3' 34.4 37.0
O4' C1' C2' H2' 271.9 278.8
C3' C4' O4' C1' 356.4 26.5
C1' O4' C4' C5' 121.8 146.0
C1' O4' C4' H4' 238.0 267.1
N1 C1' H1' C2' 123.6 122.9
N1 C1' H1' O4' 240.2 237.0
C2' C1' H1' O4' 116.5 114.1
H1' C1' C2' O2' 28.2 36.6
H1' C1' C2' C3' 270.4 278.3
H1' C1' C2' H2' 148.0 160.1
H1' C1' O4' C4' 100.2 78.5
O2' C2' C1' O4' 152.1 155.2
O2' C2' C1' H1' 28.2 36.6
C1' C2' O2' C3' 248.1 247.3
C1' C2' O2' H2' 124.8 123.6
C3' C2' O2' H2' 236.8 236.4
O2' C2' C3' C4' 208.0 220.9
O2' C2' C3' O3' 323.0 339.6
O2' C2' C3' H3' 82.8 102.2
C3' C2' C1' O4' 34.4 37.0
C3' C2' C1' H1' 270.4 278.3
C1' C2' C3' O2' 115.6 118.2
C1' C2' C3' H2' 235.6 241.8
O2' C2' C3' H2' 120.1 123.5
C3' C2' O2' HO2' 291.9 292.7
C4' C3' C2' O3' 244.9 241.3
C4' C3' C2' H3' 125.2 118.7
C2' C3' C4' O4' 24.8 358.0
C2' C3' C4' C5' 264.5 238.5
C2' C3' C4' H4' 148.5 117.4
O3' C3' C2' H3' 240.2 237.4
C2' C3' O3' HO3' 180.0 61.4
H2' C2' C1' O4' 271.9 278.8
H2' C2' C1' H1' 148.0 160.1
C1' C2' H2' O2' 239.5 236.4
C1' C2' H2' C3' 117.0 112.8
O2' C2' H2' C3' 237.5 236.4
H2' C2' O2' HO2' 55.2 56.3
H2' C2' C3' C4' 87.9 97.3
H2' C2' C3' O3' 203.0 216.0
H2' C2' C3' H3' 322.7 338.7
HO2' O2' C2' C3' 291.9 292.7
HO2' O2' C2' H2' 55.2 56.3
C1' O4' C4' C3' 356.4 26.5
C4' C3' C2' H2' 87.9 97.3
C2' C3' C4' O3' 119.0 118.7
C2' C3' C4' H3' 238.3 241.4
O3' C3' C4' H3' 119.3 122.7
C4' C3' O3' HO3' 291.8 176.2
O4' C4' C3' C5' 120.3 119.4
O4' C4' C3' H4' 236.3 240.6
C5' C4' C3' H4' 116.0 121.1
C3' C4' C5' O5' 58.0 185.0
C3' C4' C5' H5'1 178.0 305.0
C3' C4' C5' H5'2 298.0 65.0
O3' C3' C2' H2' 203.0 216.0
C2' C3' O3' C4' 248.2 245.3
C2' C3' O3' H3' 122.6 122.6
C4' C3' O3' H3' 234.4 237.3
O3' C3' C4' O4' 265.8 239.3
O3' C3' C4' C5' 145.5 119.9
O3' C3' C4' H4' 29.6 358.7
H3' C3' C2' H2' 322.7 338.7
C2' C3' H3' C4' 116.7 114.7
C2' C3' H3' O3' 236.5 237.4
C4' C3' H3' O3' 119.8 122.7
H3' C3' C4' O4' 146.5 116.6
H3' C3' C4' C5' 26.2 357.2
H3' C3' C4' H4' 270.2 236.1
H3' C3' O3' HO3' 57.4 298.8
C4' O4' C1' H1' 100.2 78.5
O4' C4' C3' O3' 265.8 239.3
O4' C4' C3' H3' 146.5 116.6
C3' C4' O4' C5' 234.5 240.6
C3' C4' O4' H4' 118.4 119.4
C5' C4' O4' H4' 243.9 238.9
O4' C4' C5' O5' 299.8 67.2
O4' C4' C5' H5'1 59.8 187.1
O4' C4' C5' H5'2 179.8 307.2
C5' C4' C3' O3' 145.5 119.9
C5' C4' C3' H3' 26.2 357.2
C3' C4' C5' O4' 118.2 117.9
C3' C4' C5' H4' 241.9 239.0
O4' C4' C5' H4' 123.7 121.1
O5' C5' C4' H5'1 240.0 240.0
O5' C5' C4' H5'2 120.0 120.0
C4' C5' O5' PA 176.5 180.0
H5'1 C5' C4' H5'2 240.0 240.0
H4' C4' C3' O3' 29.6 358.7
H4' C4' C3' H3' 270.2 236.1
C3' C4' H4' O4' 243.2 242.1
C3' C4' H4' C5' 124.2 121.1
O4' C4' H4' C5' 241.0 238.9
H4' C4' C5' O5' 176.2 306.1
H4' C4' C5' H5'1 296.2 66.1
H4' C4' C5' H5'2 56.2 186.1
HO3' O3' C3' H3' 57.4 298.8
O5' C5' C4' H4' 176.2 306.1
C4' C5' O5' H5'1 120.0 120.0
C4' C5' O5' H5'2 240.0 240.0
H5'1 C5' O5' H5'2 120.0 120.0
C5' O5' PA O1A 171.1 305.0
C5' O5' PA O2A 296.3 65.0
C5' O5' PA O3A 53.8 185.0
H5'1 C5' C4' H4' 296.2 66.1
C4' C5' H5'1 O5' 244.2 240.0
C4' C5' H5'1 H5'2 122.1 120.0
O5' C5' H5'1 H5'2 237.9 240.0
H5'1 C5' O5' PA 56.5 60.0
H5'2 C5' C4' H4' 56.2 186.1
C4' C5' H5'2 O5' 115.9 120.0
C4' C5' H5'2 H5'1 237.9 240.0
O5' C5' H5'2 H5'1 122.1 120.0
H5'2 C5' O5' PA 296.5 300.0
PA O5' C5' H5'1 56.5 60.0
PA O5' C5' H5'2 296.5 300.0
O1A PA O5' O2A 234.8 240.0
O1A PA O5' O3A 117.2 120.0
O2A PA O5' O3A 242.5 240.0
O5' PA O2A HOA2 237.3 59.9
O5' PA O3A PB 43.1 165.0
O5' PA O1A O2A 126.7 120.0
O5' PA O1A O3A 239.6 240.0
O2A PA O1A O3A 112.9 120.0
O1A PA O2A HOA2 360.0 179.9
O1A PA O3A PB 285.7 45.0
O5' PA O2A O1A 237.3 240.0
O5' PA O2A O3A 122.2 120.0
O1A PA O2A O3A 244.9 239.9
O2A PA O3A PB 167.0 285.0
O5' PA O3A O1A 117.4 120.0
O5' PA O3A O2A 236.1 240.0
O1A PA O3A O2A 118.7 120.0
O3A PA O2A HOA2 115.1 300.0
PA O3A PB O1B 160.8 320.0
PA O3A PB O2B 39.5 80.0
PA O3A PB O3B 275.9 200.0
HOA2 O2A PA O3A 115.1 300.0
O1B PB O3A O2B 121.4 240.0
O1B PB O3A O3B 244.9 120.0
O2B PB O3A O3B 123.5 240.0
O3A PB O2B HOB2 113.4 60.1
O3A PB O3B HOB3 248.9 180.0
O3A PB O1B O2B 243.3 120.0
O3A PB O1B O3B 116.0 240.0
O2B PB O1B O3B 232.8 120.0
O1B PB O2B HOB2 0.0 180.0
O1B PB O3B HOB3 360.0 60.0
O3A PB O2B O1B 113.4 240.1
O3A PB O2B O3B 238.4 120.0
O1B PB O2B O3B 125.0 240.0
O2B PB O3B HOB3 128.2 300.0
O3A PB O3B O1B 248.9 120.0
O3A PB O3B O2B 120.7 240.0
O1B PB O3B O2B 231.8 120.0
O3B PB O2B HOB2 235.0 300.0
HOB2 O2B PB O3B 235.0 300.0