PDB Chemical Component DUP

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 DUP

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
O4 C4 1.246 1.218
C4 C5 1.398 1.415
C4 N3 1.345 1.347
C5 C6 1.379 1.350
C5 H5 1.102 1.080
C6 N1 1.358 1.368
C6 H6 1.102 1.081
N3 C2 1.342 1.346
N3 HN3 1.020 0.970
C2 O2 1.248 1.217
C2 N1 1.393 1.344
N1 C1' 1.469 1.465
C1' C2' 1.517 1.544
C1' O4' 1.417 1.444
C1' H1' 1.115 1.090
C2' C3' 1.512 1.545
C2' H2'1 1.115 1.090
C2' H2'2 1.115 1.091
C3' O3' 1.436 1.428
C3' C4' 1.529 1.545
C3' H1 1.115 1.090
O3' H3' 0.949 0.966
O4' C4' 1.442 1.447
C4' C5' 1.528 1.530
C4' H4' 1.115 1.090
C5' O5' 1.431 1.428
C5' H5'1 1.115 1.089
C5' H5'2 1.114 1.090
O5' PA 1.620 1.609
PA O1A 1.503 1.480
PA O2A 1.509 1.610
PA N3A 1.688 1.682
O2A H2A 0.949 0.967
N3A PB 1.671 1.683
N3A H3A 1.021 1.009
PB O1B 1.524 1.479
PB O2B 1.484 1.609
PB O3B 1.616 1.609
O2B H2B 0.949 0.967
O3B PG 1.625 1.611
PG O2G 1.511 1.479
PG O1G 1.521 1.610
PG O3G 1.511 1.609
O1G H1G 0.949 0.967
O3G H3G 0.949 0.966

Bond Angles for DUP

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
O4 C4 C5 122.1 120.3
O4 C4 N3 118.8 120.4
C5 C4 N3 119.1 119.4
C4 C5 C6 118.2 119.1
C4 C5 H5 121.5 120.5
C4 N3 C2 122.9 120.3
C4 N3 HN3 118.6 119.9
C6 C5 H5 120.3 120.5
C5 C6 N1 121.7 119.7
C5 C6 H6 120.0 120.1
N1 C6 H6 118.4 120.2
C6 N1 C2 118.9 120.6
C6 N1 C1' 121.8 119.7
C2 N3 HN3 118.4 119.8
N3 C2 O2 119.7 119.5
N3 C2 N1 119.2 120.9
O2 C2 N1 121.1 119.6
C2 N1 C1' 119.3 119.7
N1 C1' C2' 110.6 110.4
N1 C1' O4' 108.8 110.4
N1 C1' H1' 108.2 110.4
C2' C1' O4' 106.6 104.8
C2' C1' H1' 110.4 110.4
C1' C2' C3' 105.0 104.1
C1' C2' H2'1 113.8 110.5
C1' C2' H2'2 113.8 110.5
O4' C1' H1' 112.2 110.3
C1' O4' C4' 111.1 105.4
C3' C2' H2'1 113.9 110.5
C3' C2' H2'2 113.9 110.5
C2' C3' O3' 112.0 110.5
C2' C3' C4' 102.6 104.2
C2' C3' H1 114.3 110.5
H2'1 C2' H2'2 96.6 110.6
O3' C3' C4' 114.9 110.5
O3' C3' H1 102.0 110.5
C3' O3' H3' 112.0 106.8
C4' C3' H1 111.5 110.5
C3' C4' O4' 104.7 104.7
C3' C4' C5' 115.3 110.7
C3' C4' H4' 109.8 110.3
O4' C4' C5' 112.2 110.4
O4' C4' H4' 113.0 110.4
C5' C4' H4' 102.0 110.3
C4' C5' O5' 111.6 109.5
C4' C5' H5'1 111.4 109.4
C4' C5' H5'2 111.4 109.5
O5' C5' H5'1 111.4 109.5
O5' C5' H5'2 111.4 109.5
C5' O5' PA 121.3 106.8
H5'1 C5' H5'2 99.0 109.5
O5' PA O1A 107.0 109.5
O5' PA O2A 105.1 109.5
O5' PA N3A 103.8 109.5
O1A PA O2A 119.8 109.4
O1A PA N3A 111.5 109.5
O2A PA N3A 108.2 109.5
PA O2A H2A 105.1 106.8
PA N3A PB 125.3 106.7
PA N3A H3A 106.6 106.7
PB N3A H3A 106.6 106.7
N3A PB O1B 109.1 109.4
N3A PB O2B 106.8 109.5
N3A PB O3B 104.3 109.5
O1B PB O2B 115.5 109.5
O1B PB O3B 112.0 109.5
O2B PB O3B 108.4 109.4
PB O2B H2B 106.8 106.8
PB O3B PG 125.7 106.8
O3B PG O2G 112.9 109.5
O3B PG O1G 107.1 109.5
O3B PG O3G 104.3 109.5
O2G PG O1G 109.6 109.5
O2G PG O3G 109.8 109.5
O1G PG O3G 113.1 109.5
PG O1G H1G 107.1 106.7
PG O3G H3G 104.3 106.9

Torsion Angles for DUP

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
C5 C4 O4 N3 179.3 180.1
O4 C4 C5 C6 180.0 180.0
O4 C4 C5 H5 0.0 360.0
O4 C4 N3 C2 179.6 179.7
O4 C4 N3 HN3 359.6 0.0
O4 C4 C5 N3 180.7 179.9
C5 C4 N3 C2 0.2 359.7
C5 C4 N3 HN3 180.2 180.0
C6 C5 C4 H5 180.0 180.1
C4 C5 C6 N1 0.2 359.9
C4 C5 C6 H6 180.3 180.0
O4 C4 N3 C5 179.3 180.1
N3 C4 C5 C6 359.3 0.1
N3 C4 C5 H5 179.3 180.0
C2 N3 C4 HN3 180.0 179.7
C4 N3 C2 O2 181.5 180.0
C4 N3 C2 N1 0.7 0.5
C6 C5 C4 N3 359.3 0.1
C4 C5 C6 H5 180.0 179.9
N1 C6 C5 H6 180.0 179.9
C5 C6 N1 C2 0.7 0.2
C5 C6 N1 C1' 179.0 180.0
H5 C5 C4 N3 179.3 180.0
C4 C5 H5 C6 180.0 180.1
H5 C5 C6 N1 180.2 180.0
H5 C5 C6 H6 0.2 0.1
N1 C6 C5 H5 180.2 180.0
C5 C6 N1 H6 180.0 180.1
N3 C2 N1 C6 358.8 359.5
O2 C2 N1 C6 178.0 180.0
C2 N1 C6 C1' 181.7 180.2
C6 N1 C1' C2' 286.2 120.0
C6 N1 C1' O4' 43.0 235.4
C6 N1 C1' H1' 165.1 357.7
H6 C6 C5 H5 0.2 0.1
C5 C6 H6 N1 180.0 179.9
H6 C6 N1 C2 180.7 180.2
H6 C6 N1 C1' 359.0 360.0
C4 N3 C2 HN3 180.0 180.3
C6 N1 C2 N3 358.8 359.5
O2 C2 N3 N1 180.8 179.5
N3 C2 N1 C1' 180.5 179.7
C4 N3 HN3 C2 180.0 179.7
HN3 N3 C2 O2 1.5 359.7
HN3 N3 C2 N1 180.7 180.2
C6 N1 C2 O2 178.0 180.0
O2 C2 N3 HN3 1.5 359.7
N3 C2 O2 N1 179.2 180.5
O2 C2 N1 C1' 359.6 0.2
C2 N1 C6 H6 180.7 180.2
C6 N1 C2 C1' 178.4 179.8
N1 C2 N3 HN3 180.7 180.2
N3 C2 N1 O2 180.8 179.5
C2 N1 C1' C2' 104.5 299.8
C2 N1 C1' O4' 221.3 55.2
C2 N1 C1' H1' 343.4 177.5
C1' N1 C6 H6 359.0 360.0
C6 N1 C1' C2 181.7 180.2
C2' C1' N1 O4' 243.3 244.6
C2' C1' N1 H1' 121.1 122.3
N1 C1' C2' C3' 100.9 142.9
N1 C1' C2' H2'1 226.2 24.3
N1 C1' C2' H2'2 335.6 261.5
O4' C1' N1 H1' 237.9 237.8
N1 C1' O4' C4' 238.0 200.7
N1 C1' C2' O4' 118.1 118.9
N1 C1' C2' H1' 240.2 237.7
O4' C1' C2' H1' 122.1 118.8
C2' C1' O4' C4' 357.3 319.6
C3' C2' C1' H2'1 234.7 118.6
C3' C2' C1' H2'2 125.3 241.4
C1' C2' C3' O3' 152.7 118.6
C1' C2' C3' C4' 29.0 359.9
C1' C2' C3' H1 268.1 241.3
H2'1 C2' C1' H2'2 250.6 122.8
N1 C1' O4' C2' 240.7 241.1
N1 C1' O4' H1' 119.7 122.3
C2' C1' O4' H1' 239.0 241.2
O4' C1' C2' C3' 342.8 24.0
O4' C1' C2' H2'1 108.1 265.4
O4' C1' C2' H2'2 217.5 142.6
C3' C4' O4' C1' 21.3 40.3
C1' O4' C4' C5' 147.0 159.4
C1' O4' C4' H4' 261.7 281.7
N1 C1' H1' C2' 121.2 122.3
N1 C1' H1' O4' 240.0 237.7
C2' C1' H1' O4' 118.8 115.4
H1' C1' C2' C3' 220.7 265.2
H1' C1' C2' H2'1 346.0 146.6
H1' C1' C2' H2'2 95.4 23.8
H1' C1' O4' C4' 118.3 78.4
C3' C2' C1' O4' 342.8 24.0
C3' C2' C1' H1' 220.7 265.2
C1' C2' C3' H2'1 125.2 241.3
C1' C2' C3' H2'2 234.8 118.7
H2'1 C2' C3' H2'2 109.5 237.4
O3' C3' C2' C4' 123.7 118.7
O3' C3' C2' H1 244.6 237.4
C2' C3' O3' H3' 180.0 63.3
C4' C3' C2' H1 120.9 118.6
C2' C3' C4' O4' 329.4 336.2
C2' C3' C4' C5' 205.6 217.3
C2' C3' C4' H4' 91.0 94.9
H2'1 C2' C1' O4' 108.1 265.4
H2'1 C2' C1' H1' 346.0 146.6
C1' C2' H2'1 C3' 239.6 114.7
C1' C2' H2'1 H2'2 119.7 237.3
C3' C2' H2'1 H2'2 240.1 122.6
H2'1 C2' C3' O3' 27.5 237.3
H2'1 C2' C3' C4' 263.7 118.6
H2'1 C2' C3' H1 142.8 360.0
H2'2 C2' C1' O4' 217.5 142.6
H2'2 C2' C1' H1' 95.4 23.8
C1' C2' H2'2 C3' 120.4 245.3
C1' C2' H2'2 H2'1 240.3 122.7
C3' C2' H2'2 H2'1 119.9 237.4
H2'2 C2' C3' O3' 277.9 360.0
H2'2 C2' C3' C4' 154.2 241.2
H2'2 C2' C3' H1 33.3 122.6
O3' C3' C2' H2'1 27.5 237.3
O3' C3' C2' H2'2 277.9 360.0
C2' C3' O3' C4' 243.4 245.2
C2' C3' O3' H1 122.7 122.7
C4' C3' O3' H1 239.3 237.4
O3' C3' C4' O4' 207.5 217.5
O3' C3' C4' C5' 83.7 98.6
O3' C3' C4' H4' 329.2 336.2
C1' O4' C4' C3' 21.3 40.3
C4' C3' C2' H2'1 263.7 118.6
C4' C3' C2' H2'2 154.2 241.2
C2' C3' C4' O3' 121.8 118.7
C2' C3' C4' H1 237.2 241.3
O3' C3' C4' H1 115.4 122.6
C4' C3' O3' H3' 296.6 178.1
O4' C4' C3' C5' 123.8 118.9
O4' C4' C3' H4' 238.3 241.3
C5' C4' C3' H4' 114.5 122.4
C3' C4' C5' O5' 55.2 176.9
C3' C4' C5' H5'1 180.4 296.9
C3' C4' C5' H5'2 289.9 56.9
H1 C3' C2' H2'1 142.8 360.0
H1 C3' C2' H2'2 33.3 122.6
C2' C3' H1 O3' 238.9 237.3
C2' C3' H1 C4' 115.8 114.7
O3' C3' H1 C4' 236.9 237.4
H1 C3' O3' H3' 57.3 300.7
H1 C3' C4' O4' 92.2 94.9
H1 C3' C4' C5' 328.4 336.0
H1 C3' C4' H4' 213.8 213.6
H3' O3' C3' C4' 296.6 178.1
H3' O3' C3' H1 57.3 300.7
C4' O4' C1' H1' 118.3 78.4
O4' C4' C3' H1 92.2 94.9
C3' C4' O4' C5' 234.2 240.9
C3' C4' O4' H4' 119.5 118.7
C5' C4' O4' H4' 245.3 237.8
O4' C4' C5' O5' 295.4 61.5
O4' C4' C5' H5'1 60.6 181.5
O4' C4' C5' H5'2 170.1 301.5
C5' C4' C3' H1 328.4 336.0
C3' C4' C5' O4' 119.8 115.4
C3' C4' C5' H4' 241.0 237.6
O4' C4' C5' H4' 121.3 122.2
O5' C5' C4' H5'1 234.8 240.0
O5' C5' C4' H5'2 125.3 120.0
C4' C5' O5' PA 168.2 180.0
H5'1 C5' C4' H5'2 250.5 240.0
H4' C4' C3' H1 213.8 213.6
C3' C4' H4' O4' 243.4 244.8
C3' C4' H4' C5' 122.8 122.6
O4' C4' H4' C5' 239.3 237.7
H4' C4' C5' O5' 174.1 299.3
H4' C4' C5' H5'1 299.4 59.3
H4' C4' C5' H5'2 48.9 179.2
O5' C5' C4' H4' 174.1 299.3
C4' C5' O5' H5'1 125.2 119.9
C4' C5' O5' H5'2 234.7 240.0
H5'1 C5' O5' H5'2 109.5 120.0
C5' O5' PA O1A 52.3 60.0
C5' O5' PA O2A 180.7 179.9
C5' O5' PA N3A 294.3 300.0
H5'1 C5' C4' H4' 299.4 59.3
C4' C5' H5'1 O5' 234.7 240.0
C4' C5' H5'1 H5'2 117.3 120.0
O5' C5' H5'1 H5'2 242.6 239.9
H5'1 C5' O5' PA 43.0 60.1
H5'2 C5' C4' H4' 48.9 179.2
C4' C5' H5'2 O5' 125.3 120.0
C4' C5' H5'2 H5'1 242.7 240.1
O5' C5' H5'2 H5'1 117.4 120.0
H5'2 C5' O5' PA 293.5 300.0
PA O5' C5' H5'1 43.0 60.1
PA O5' C5' H5'2 293.5 300.0
O1A PA O5' O2A 231.6 240.0
O1A PA O5' N3A 118.0 120.0
O2A PA O5' N3A 246.4 240.0
O5' PA O2A H2A 180.0 60.0
O5' PA N3A PB 125.2 180.0
O5' PA N3A H3A 359.9 293.8
O5' PA O1A O2A 119.3 120.0
O5' PA O1A N3A 247.1 240.0
O2A PA O1A N3A 127.8 120.0
O1A PA O2A H2A 300.2 179.9
O1A PA N3A PB 10.3 60.0
O1A PA N3A H3A 245.1 173.8
O5' PA O2A O1A 239.7 240.0
O5' PA O2A N3A 110.5 120.0
O1A PA O2A N3A 230.8 240.0
O2A PA N3A PB 236.5 300.0
O2A PA N3A H3A 111.3 53.8
O5' PA N3A O1A 114.9 120.0
O5' PA N3A O2A 248.6 240.0
O1A PA N3A O2A 133.8 120.0
N3A PA O2A H2A 69.5 300.0
PB N3A PA H3A 125.3 246.2
PA N3A PB O1B 26.0 300.0
PA N3A PB O2B 151.5 60.0
PA N3A PB O3B 266.2 179.9
H2A O2A PA N3A 69.5 300.0
PA N3A PB H3A 234.7 113.8
O1B PB N3A O2B 234.5 240.0
O1B PB N3A O3B 119.8 120.0
O2B PB N3A O3B 245.3 240.0
N3A PB O2B H2B 180.0 60.0
N3A PB O3B PG 111.3 180.0
PA N3A H3A PB 135.9 246.2
H3A N3A PB O1B 151.3 186.2
H3A N3A PB O2B 276.8 306.2
H3A N3A PB O3B 31.5 66.2
O1B PB N3A H3A 151.3 186.2
N3A PB O1B O2B 120.3 120.0
N3A PB O1B O3B 245.1 240.0
O2B PB O1B O3B 124.8 120.0
O1B PB O2B H2B 301.6 180.0
O1B PB O3B PG 353.5 60.0
O2B PB N3A H3A 276.8 306.2
N3A PB O2B O1B 238.4 240.0
N3A PB O2B O3B 111.8 120.0
O1B PB O2B O3B 233.4 240.0
O2B PB O3B PG 224.8 300.0
O3B PB N3A H3A 31.5 66.2
N3A PB O3B O1B 117.9 120.0
N3A PB O3B O2B 246.5 240.0
O1B PB O3B O2B 128.7 120.0
O3B PB O2B H2B 68.2 300.0
PB O3B PG O2G 326.5 60.0
PB O3B PG O1G 87.2 180.0
PB O3B PG O3G 207.4 300.0
H2B O2B PB O3B 68.2 300.0
O2G PG O3B O1G 239.3 240.0
O2G PG O3B O3G 119.2 120.0
O1G PG O3B O3G 239.9 240.0
O3B PG O1G H1G 179.9 180.0
O3B PG O3G H3G 180.0 300.0
O3B PG O2G O1G 119.3 120.0
O3B PG O2G O3G 244.1 240.0
O1G PG O2G O3G 124.8 120.0
O2G PG O1G H1G 302.8 300.0
O2G PG O3G H3G 58.8 180.0
O3B PG O1G O2G 237.2 240.0
O3B PG O1G O3G 114.3 120.0
O2G PG O1G O3G 237.1 240.0
O1G PG O3G H3G 296.0 60.0
O3B PG O3G O2G 121.3 120.0
O3B PG O3G O1G 244.0 240.0
O2G PG O3G O1G 122.7 120.0
O3G PG O1G H1G 65.7 60.0
H1G O1G PG O3G 65.7 60.0