PDB Chemical Component UPP

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 UPP

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
N1 C2 1.369 1.345
N1 C6 1.383 1.368
N1 C1B 1.461 1.465
C2 N3 1.368 1.346
C2 O2 1.225 1.216
N3 C4 1.390 1.348
N3 HN3 1.019 0.970
C4 C5 1.423 1.416
C4 O4 1.218 1.217
C5 C6 1.311 1.351
C5 H5 1.104 1.080
C6 H6 1.104 1.080
C1B C2B 1.511 1.544
C1B O4' 1.393 1.445
C1B H1' 1.114 1.090
C2B O2' 1.437 1.429
C2B C3B 1.539 1.545
C2B H2B 1.115 1.090
O2' HO2' 0.950 0.967
C3B C4B 1.529 1.545
C3B O3' 1.442 1.429
C3B H3B 1.115 1.090
C4B O4' 1.437 1.446
C4B C5B 1.523 1.530
C4B H4B 1.115 1.090
O3' HO3' 0.950 0.968
C5B O5' 1.436 1.429
C5B H5'1 1.115 1.090
C5B H5'2 1.115 1.090
O5' PA 1.591 1.609
PA O1A 1.492 1.480
PA O2A 1.487 1.609
PA O3A 1.641 1.610
O2A HOA2 0.951 0.967
O3A PB 1.559 1.611
PB O1B 1.575 1.479
PB O2B 1.461 1.609
PB O3B 1.476 1.610
O2B HOB2 0.949 0.968
O3B C1' 1.482 1.359
C1' C2' 1.419 1.387
C1' C6' 1.419 1.387
C2' C3' 1.418 1.382
C2' H2' 1.103 1.080
C3' C4' 1.417 1.382
C3' H3' 1.103 1.080
C4' C5' 1.420 1.382
C4' H4' 1.104 1.080
C5' C6' 1.417 1.381
C5' H5' 1.103 1.080
C6' H6' 1.102 1.080

Bond Angles for UPP

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
C2 N1 C6 122.9 120.6
C2 N1 C1B 114.5 119.7
N1 C2 N3 112.9 120.9
N1 C2 O2 124.4 119.5
C6 N1 C1B 122.2 119.7
N1 C6 C5 122.4 119.7
N1 C6 H6 121.6 120.2
N1 C1B C2B 117.4 110.4
N1 C1B O4' 107.6 110.5
N1 C1B H1' 104.9 110.3
N3 C2 O2 122.7 119.6
C2 N3 C4 127.2 120.3
C2 N3 HN3 115.5 119.8
C4 N3 HN3 117.3 119.9
N3 C4 C5 115.3 119.4
N3 C4 O4 116.6 120.4
C5 C4 O4 128.0 120.3
C4 C5 C6 118.8 119.1
C4 C5 H5 124.6 120.5
C6 C5 H5 116.6 120.4
C5 C6 H6 116.0 120.1
C2B C1B O4' 108.2 104.8
C2B C1B H1' 104.3 110.4
C1B C2B O2' 110.9 110.6
C1B C2B C3B 100.2 104.0
C1B C2B H2B 114.3 110.5
O4' C1B H1' 114.7 110.4
C1B O4' C4B 109.8 105.3
O2' C2B C3B 108.8 110.5
O2' C2B H2B 106.4 110.5
C2B O2' HO2' 110.8 106.8
C3B C2B H2B 116.2 110.5
C2B C3B C4B 101.7 104.2
C2B C3B O3' 114.5 110.5
C2B C3B H3B 112.7 110.5
C4B C3B O3' 113.1 110.5
C4B C3B H3B 114.1 110.5
C3B C4B O4' 105.6 104.7
C3B C4B C5B 118.8 110.7
C3B C4B H4B 105.5 110.2
O3' C3B H3B 101.3 110.5
C3B O3' HO3' 114.4 106.8
O4' C4B C5B 108.0 110.4
O4' C4B H4B 116.8 110.4
C5B C4B H4B 102.8 110.3
C4B C5B O5' 108.4 109.5
C4B C5B H5'1 112.6 109.5
C4B C5B H5'2 112.7 109.4
O5' C5B H5'1 112.6 109.5
O5' C5B H5'2 112.6 109.4
C5B O5' PA 121.5 106.8
H5'1 C5B H5'2 97.8 109.5
O5' PA O1A 110.7 109.5
O5' PA O2A 111.5 109.5
O5' PA O3A 103.3 109.5
O1A PA O2A 113.5 109.4
O1A PA O3A 110.4 109.5
O2A PA O3A 107.0 109.5
PA O2A HOA2 111.5 106.7
PA O3A PB 132.4 106.8
O3A PB O1B 102.8 109.5
O3A PB O2B 117.8 109.4
O3A PB O3B 107.5 109.4
O1B PB O2B 108.2 109.5
O1B PB O3B 113.6 109.5
O2B PB O3B 107.2 109.5
PB O2B HOB2 117.7 106.8
PB O3B C1' 128.1 106.8
O3B C1' C2' 122.1 120.1
O3B C1' C6' 117.2 120.1
C2' C1' C6' 120.3 119.9
C1' C2' C3' 119.6 119.9
C1' C2' H2' 120.2 120.1
C1' C6' C5' 120.0 120.0
C1' C6' H6' 120.1 120.0
C3' C2' H2' 120.2 120.0
C2' C3' C4' 120.1 120.1
C2' C3' H3' 120.0 120.0
C4' C3' H3' 119.9 120.0
C3' C4' C5' 120.2 120.1
C3' C4' H4' 119.8 120.0
C5' C4' H4' 120.0 119.9
C4' C5' C6' 119.7 120.1
C4' C5' H5' 120.2 120.0
C6' C5' H5' 120.1 120.0
C5' C6' H6' 119.9 120.0

Torsion Angles for UPP

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
C6 N1 C2 C1B 187.1 179.7
C2 N1 C6 C5 6.5 0.3
C2 N1 C6 H6 186.4 180.2
C2 N1 C1B C2B 125.6 299.7
C2 N1 C1B O4' 247.8 55.2
C2 N1 C1B H1' 10.4 177.4
N3 C2 N1 O2 178.2 179.5
N1 C2 N3 C4 359.0 0.5
N1 C2 N3 HN3 179.1 180.2
C2 N1 C6 C1B 172.4 180.3
C6 N1 C2 N3 358.6 359.5
C6 N1 C2 O2 180.4 180.0
C6 N1 C1B C2B 298.5 120.0
C6 N1 C1B O4' 60.8 235.5
C6 N1 C1B H1' 183.4 357.7
C4 C5 C6 N1 351.3 360.0
N1 C6 C5 H5 171.3 180.0
C5 C6 N1 H6 180.1 180.0
C2 N1 C1B C6 187.0 179.7
C1B N1 C2 N3 171.6 179.8
C1B N1 C2 O2 353.4 0.3
C1B N1 C6 C5 194.1 180.0
C1B N1 C6 H6 14.0 359.9
C2B C1B N1 O4' 237.7 244.5
C2B C1B N1 H1' 115.2 122.2
N1 C1B C2B O2' 269.2 261.7
N1 C1B C2B C3B 154.5 143.0
N1 C1B C2B H2B 29.5 24.4
O4' C1B N1 H1' 237.4 237.7
N1 C1B O4' C4B 217.8 200.6
N3 C2 N1 C6 358.6 359.5
N3 C2 N1 C1B 171.6 179.8
N1 C2 N3 O2 181.7 180.5
C4 N3 C2 HN3 180.0 180.3
C2 N3 C4 C5 358.7 359.7
C2 N3 C4 O4 175.2 179.7
O2 C2 N1 C6 180.4 180.0
O2 C2 N1 C1B 353.4 0.3
N1 C2 O2 N3 178.1 179.5
O2 C2 N3 C4 177.3 180.0
O2 C2 N3 HN3 357.3 359.7
C4 N3 C2 O2 177.3 180.0
C2 N3 C4 HN3 180.0 179.7
C5 C4 N3 O4 183.5 180.0
N3 C4 C5 C6 6.1 0.0
N3 C4 C5 H5 186.1 180.0
HN3 N3 C2 O2 357.3 359.7
C2 N3 HN3 C4 180.0 180.3
HN3 N3 C4 C5 178.7 180.0
HN3 N3 C4 O4 355.1 0.0
N1 C6 C5 C4 351.3 360.0
C5 C4 N3 HN3 178.7 180.0
N3 C4 C5 O4 176.0 180.0
C6 C5 C4 H5 180.0 180.0
C4 C5 C6 H6 171.3 180.0
O4 C4 N3 HN3 355.1 0.0
N3 C4 O4 C5 184.0 180.0
O4 C4 C5 C6 190.1 180.1
O4 C4 C5 H5 10.1 0.0
C5 C6 N1 C1B 194.1 180.0
N1 C6 C5 H6 180.0 180.0
C6 C5 C4 O4 190.1 180.1
C4 C5 C6 H5 180.0 180.0
H5 C5 C4 O4 10.1 0.0
C4 C5 H5 C6 180.0 180.0
H5 C5 C6 H6 351.3 0.0
H6 C6 N1 C1B 14.0 359.9
N1 C6 H6 C5 180.0 180.0
H6 C6 C5 H5 351.3 0.0
N1 C1B C2B O4' 121.9 119.0
N1 C1B C2B H1' 244.5 237.8
O4' C1B C2B H1' 122.6 118.9
C2B C1B O4' C4B 345.6 319.5
O2' C2B C1B C3B 114.7 118.7
O2' C2B C1B H2B 239.7 237.3
C1B C2B O2' HO2' 180.0 183.9
C3B C2B C1B H2B 125.0 118.6
C1B C2B C3B C4B 323.2 359.9
C1B C2B C3B O3' 85.4 118.6
C1B C2B C3B H3B 200.6 241.3
N1 C1B O4' C2B 232.2 241.1
N1 C1B O4' H1' 116.3 122.2
C2B C1B O4' H1' 244.1 241.1
O4' C1B C2B O2' 147.3 142.7
O4' C1B C2B C3B 32.5 24.0
O4' C1B C2B H2B 267.6 265.4
C3B C4B O4' C1B 349.5 40.3
C1B O4' C4B C5B 117.5 159.5
C1B O4' C4B H4B 232.7 281.7
N1 C1B H1' C2B 124.0 122.2
N1 C1B H1' O4' 242.2 237.7
C2B C1B H1' O4' 118.2 115.5
H1' C1B C2B O2' 24.7 23.8
H1' C1B C2B C3B 270.0 265.1
H1' C1B C2B H2B 145.0 146.5
H1' C1B O4' C4B 101.5 78.4
O2' C2B C1B O4' 147.3 142.7
O2' C2B C1B H1' 24.7 23.8
C1B C2B O2' C3B 250.8 245.3
C1B C2B O2' H2B 124.9 122.7
C3B C2B O2' H2B 234.1 237.4
O2' C2B C3B C4B 206.9 241.1
O2' C2B C3B O3' 329.1 359.9
O2' C2B C3B H3B 84.2 122.5
C3B C2B C1B O4' 32.5 24.0
C3B C2B C1B H1' 270.0 265.1
C1B C2B C3B O2' 116.3 118.8
C1B C2B C3B H2B 236.4 241.4
O2' C2B C3B H2B 120.0 122.6
C3B C2B O2' HO2' 289.2 298.6
C4B C3B C2B O3' 237.8 241.3
C4B C3B C2B H3B 122.6 118.7
C2B C3B C4B O4' 30.2 336.2
C2B C3B C4B C5B 268.9 217.3
C2B C3B C4B H4B 154.4 94.9
O3' C3B C2B H3B 244.9 237.4
C2B C3B O3' HO3' 180.0 63.3
H2B C2B C1B O4' 267.6 265.4
H2B C2B C1B H1' 145.0 146.5
C1B C2B H2B O2' 237.3 237.2
C1B C2B H2B C3B 116.0 114.6
O2' C2B H2B C3B 238.7 237.4
H2B C2B O2' HO2' 55.1 61.2
H2B C2B C3B C4B 86.8 118.5
H2B C2B C3B O3' 209.1 237.3
H2B C2B C3B H3B 324.2 359.9
HO2' O2' C2B C3B 289.2 298.6
HO2' O2' C2B H2B 55.1 61.2
C1B O4' C4B C3B 349.5 40.3
C4B C3B C2B H2B 86.8 118.5
C2B C3B C4B O3' 123.2 118.8
C2B C3B C4B H3B 238.3 241.3
O3' C3B C4B H3B 115.1 122.6
C4B C3B O3' HO3' 295.8 178.1
O4' C4B C3B C5B 121.3 118.9
O4' C4B C3B H4B 235.8 241.3
C5B C4B C3B H4B 114.5 122.3
C3B C4B C5B O5' 46.8 176.9
C3B C4B C5B H5'1 172.1 296.9
C3B C4B C5B H5'2 281.6 56.9
O3' C3B C2B H2B 209.1 237.3
C2B C3B O3' C4B 244.2 245.2
C2B C3B O3' H3B 121.6 122.6
C4B C3B O3' H3B 237.4 237.4
O3' C3B C4B O4' 267.0 217.4
O3' C3B C4B C5B 145.7 98.5
O3' C3B C4B H4B 31.2 336.2
H3B C3B C2B H2B 324.2 359.9
C2B C3B H3B C4B 115.4 114.8
C2B C3B H3B O3' 237.2 237.3
C4B C3B H3B O3' 121.8 122.6
H3B C3B C4B O4' 151.9 94.9
H3B C3B C4B C5B 30.6 336.0
H3B C3B C4B H4B 276.0 213.6
H3B C3B O3' HO3' 58.4 300.6
C4B O4' C1B H1' 101.5 78.4
O4' C4B C3B O3' 267.0 217.4
O4' C4B C3B H3B 151.9 94.9
C3B C4B O4' C5B 232.0 240.9
C3B C4B O4' H4B 116.8 118.6
C5B C4B O4' H4B 244.8 237.7
O4' C4B C5B O5' 286.8 61.5
O4' C4B C5B H5'1 52.1 181.5
O4' C4B C5B H5'2 161.5 301.5
C5B C4B C3B O3' 145.7 98.5
C5B C4B C3B H3B 30.6 336.0
C3B C4B C5B O4' 120.0 115.4
C3B C4B C5B H4B 244.1 237.7
O4' C4B C5B H4B 124.0 122.3
O5' C5B C4B H5'1 234.7 240.0
O5' C5B C4B H5'2 125.3 120.0
C4B C5B O5' PA 160.9 180.0
H5'1 C5B C4B H5'2 250.5 240.0
H4B C4B C3B O3' 31.2 336.2
H4B C4B C3B H3B 276.0 213.6
C3B C4B H4B O4' 243.2 244.8
C3B C4B H4B C5B 125.2 122.6
O4' C4B H4B C5B 242.0 237.7
H4B C4B C5B O5' 162.8 299.1
H4B C4B C5B H5'1 288.0 59.2
H4B C4B C5B H5'2 37.5 179.2
HO3' O3' C3B H3B 58.4 300.6
O5' C5B C4B H4B 162.8 299.1
C4B C5B O5' H5'1 125.3 120.0
C4B C5B O5' H5'2 234.7 240.0
H5'1 C5B O5' H5'2 109.4 120.0
C5B O5' PA O1A 193.3 300.0
C5B O5' PA O2A 320.5 60.0
C5B O5' PA O3A 75.1 180.0
H5'1 C5B C4B H4B 288.0 59.2
C4B C5B H5'1 O5' 237.0 240.0
C4B C5B H5'1 H5'2 118.6 120.0
O5' C5B H5'1 H5'2 241.5 240.0
H5'1 C5B O5' PA 35.6 60.0
H5'2 C5B C4B H4B 37.5 179.2
C4B C5B H5'2 O5' 123.0 120.0
C4B C5B H5'2 H5'1 241.5 240.0
O5' C5B H5'2 H5'1 118.5 120.0
H5'2 C5B O5' PA 286.2 300.0
PA O5' C5B H5'1 35.6 60.0
PA O5' C5B H5'2 286.2 300.0
O1A PA O5' O2A 232.7 240.0
O1A PA O5' O3A 118.1 120.0
O2A PA O5' O3A 245.4 240.0
O5' PA O2A HOA2 180.0 60.0
O5' PA O3A PB 48.3 179.9
O5' PA O1A O2A 126.2 120.0
O5' PA O1A O3A 246.3 240.0
O2A PA O1A O3A 120.1 120.0
O1A PA O2A HOA2 305.7 180.0
O1A PA O3A PB 290.0 60.0
O5' PA O2A O1A 234.2 240.0
O5' PA O2A O3A 112.3 120.0
O1A PA O2A O3A 238.0 240.0
O2A PA O3A PB 166.1 300.0
O5' PA O3A O1A 118.3 120.0
O5' PA O3A O2A 242.2 240.0
O1A PA O3A O2A 123.9 120.0
O3A PA O2A HOA2 67.7 300.0
PA O3A PB O1B 278.9 300.0
PA O3A PB O2B 37.6 60.0
PA O3A PB O3B 158.8 180.0
HOA2 O2A PA O3A 67.7 300.0
O1B PB O3A O2B 241.3 240.0
O1B PB O3A O3B 120.1 120.0
O2B PB O3A O3B 238.9 240.0
O3A PB O2B HOB2 180.0 59.9
O3A PB O3B C1' 295.9 180.1
O3A PB O1B O2B 125.3 120.0
O3A PB O1B O3B 244.2 240.0
O2B PB O1B O3B 118.9 120.0
O1B PB O2B HOB2 295.8 180.0
O1B PB O3B C1' 182.9 60.0
O3A PB O2B O1B 244.2 240.0
O3A PB O2B O3B 121.3 119.9
O1B PB O2B O3B 237.1 240.0
O2B PB O3B C1' 63.5 300.0
O3A PB O3B O1B 113.0 120.0
O3A PB O3B O2B 232.5 240.1
O1B PB O3B O2B 119.4 120.1
O3B PB O2B HOB2 58.7 300.0
PB O3B C1' C2' 91.1 90.0
PB O3B C1' C6' 263.9 269.7
HOB2 O2B PB O3B 58.7 300.0
C2' C1' O3B C6' 187.2 180.2
O3B C1' C2' C3' 173.3 180.1
O3B C1' C2' H2' 353.3 0.0
O3B C1' C6' C5' 185.7 179.6
O3B C1' C6' H6' 5.7 0.3
O3B C1' C2' C6' 172.6 179.8
C2' C1' C6' C5' 358.7 359.4
C2' C1' C6' H6' 178.6 180.1
C3' C2' C1' H2' 180.0 180.0
C1' C2' C3' C4' 358.7 360.0
C1' C2' C3' H3' 178.6 180.0
O3B C1' C6' C2' 187.1 180.2
C6' C1' C2' C3' 0.8 0.3
C6' C1' C2' H2' 180.8 180.3
C4' C5' C6' C1' 2.5 0.7
C1' C6' C5' H5' 182.5 180.3
C5' C6' C1' H6' 180.0 179.3
C3' C2' C1' C6' 0.8 0.3
C1' C2' C3' H2' 180.0 180.0
C4' C3' C2' H3' 180.1 180.0
C2' C3' C4' C5' 2.5 0.1
C2' C3' C4' H4' 182.5 180.0
H2' C2' C1' C6' 180.8 180.3
C1' C2' H2' C3' 180.0 180.0
H2' C2' C3' C4' 178.7 180.0
H2' C2' C3' H3' 358.6 360.0
C4' C3' C2' H2' 178.7 180.0
C2' C3' C4' H3' 179.9 180.0
C5' C4' C3' H4' 180.0 180.1
C3' C4' C5' C6' 356.9 359.6
C3' C4' C5' H5' 177.0 179.9
H3' C3' C2' H2' 358.6 360.0
C2' C3' H3' C4' 180.1 180.0
H3' C3' C4' C5' 182.5 180.1
H3' C3' C4' H4' 2.5 360.0
C1' C6' C5' C4' 2.5 0.7
C5' C4' C3' H3' 182.5 180.1
C3' C4' C5' H4' 180.0 179.9
C6' C5' C4' H5' 180.0 179.6
C4' C5' C6' H6' 182.5 180.0
H4' C4' C3' H3' 2.5 360.0
C3' C4' H4' C5' 180.0 180.1
H4' C4' C5' C6' 177.0 179.7
H4' C4' C5' H5' 357.0 0.1
C1' C6' C5' H6' 180.0 180.7
C6' C5' C4' H4' 177.0 179.7
C4' C5' C6' H5' 180.0 180.4
H5' C5' C4' H4' 357.0 0.1
C4' C5' H5' C6' 180.0 179.6
H5' C5' C6' H6' 2.5 359.6
C1' C6' H6' C5' 180.0 179.3
H6' C6' C5' H5' 2.5 359.6