PDB Chemical Component UD2

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 UD2

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
O4 C4 1.219 1.218
C4 N3 1.417 1.349
C4 C5 1.446 1.416
N3 C2 1.404 1.346
C5 C6 1.341 1.350
C2 O2 1.229 1.216
C2 N1 1.412 1.345
C6 N1 1.422 1.369
N1 C1B 1.491 1.465
O2' C2B 1.416 1.429
C1B C2B 1.530 1.550
C1B O4B 1.446 1.444
C2B C3B 1.521 1.548
O2A PA 1.463 1.479
O4B C4B 1.466 1.436
O6' C6' 1.423 1.429
O5B PA 1.595 1.610
O5B C5B 1.417 1.429
C3B C4B 1.526 1.541
C3B O3B 1.443 1.429
PA O3A 1.579 1.610
PA O1A 1.491 1.610
C4B C5B 1.515 1.531
O3A PB 1.573 1.610
C6' C5' 1.528 1.530
O2B PB 1.498 1.479
C5' O5' 1.476 1.429
C5' C4' 1.559 1.531
PB O1B 1.465 1.611
PB O1' 1.619 1.610
O5' C1' 1.473 1.429
C4' O4' 1.437 1.429
C4' C3' 1.552 1.531
O1' C1' 1.438 1.429
C1' C2' 1.552 1.531
C3' C2' 1.547 1.532
C3' O3' 1.419 1.429
C2' N2' 1.478 1.465
N2' C7' 1.346 1.348
C7' O7' 1.245 1.213
C7' C8' 1.523 1.506
C1' H1' 1.100 1.090
C2' H2' 1.100 1.089
C3' H3' 1.099 1.090
C4' H4' 1.100 1.090
C5' H5' 1.100 1.090
C6' H6'1 1.100 1.090
C6' H6'2 1.100 1.090
C8' H8'1 1.100 1.090
C8' H8'2 1.100 1.090
C8' H8'3 1.100 1.091
N2' HN2' 1.000 0.970
O3' HO3' 0.950 0.967
O4' HO4' 0.950 0.967
O6' HO6' 0.950 0.967
N3 HN3 1.000 0.970
C5 H5 1.080 1.080
C6 H6 1.080 1.080
C1B H1B 1.100 1.090
C2B H2B 1.100 1.090
O2' HO2' 0.950 0.967
C3B H3B 1.100 1.090
C4B H4B 1.100 1.090
O3B HO3A 0.950 0.967
C5B H5'1 1.100 1.090
C5B H5'2 1.100 1.090
O1A HOA2 0.950 0.967
O1B HOB2 0.950 0.967

Bond Angles for UD2

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
C4 N3 HN3 116.5 119.9
C4 C5 C6 119.3 119.1
C4 C5 H5 120.3 120.4
N3 C2 O2 122.5 119.5
C6 C5 H5 120.3 120.5
C5 C6 H6 118.5 120.1
C2 N1 C1B 117.5 119.7
C6 N1 C1B 121.1 119.7
N1 C1B C2B 110.0 110.6
N1 C1B O4B 111.3 110.6
N1 C1B H1B 106.9 110.6
O2' C2B C3B 113.4 110.9
O2' C2B H2B 101.7 110.8
C2B C1B O4B 106.5 103.4
C1B C2B C3B 103.8 102.1
C2B C1B H1B 111.7 110.6
C1B C2B H2B 111.7 110.9
C1B O4B C4B 109.1 107.0
O4B C1B H1B 110.4 110.7
C2B C3B C4B 104.0 104.1
C2B C3B O3B 114.3 110.4
C3B C2B H2B 112.4 110.9
C2B C3B H3B 109.6 110.5
O2A PA O3A 105.0 109.5
O4B C4B C5B 109.4 109.9
O4B C4B H4B 111.6 110.0
O6' C6' H6'1 108.8 109.4
O6' C6' H6'2 108.3 109.5
O5B PA O3A 105.6 109.4
O5B PA O1A 112.9 109.5
O5B C5B H5'1 109.0 109.5
O5B C5B H5'2 108.7 109.5
C4B C3B O3B 108.4 110.5
C3B C4B C5B 111.7 109.9
C4B C3B H3B 115.4 110.6
C3B C4B H4B 109.2 109.8
O3B C3B H3B 105.3 110.5
C3B O3B HO3A 109.5 114.1
O1A PA O3A 106.2 109.5
PA O3A PB 137.2 134.0
PA O1A HOA2 109.5 114.0
C5B C4B H4B 107.3 109.8
C4B C5B H5'1 109.0 109.5
C4B C5B H5'2 108.7 109.4
O3A PB O1B 108.2 109.4
C6' C5' O5' 108.0 109.5
C6' C5' H5' 108.1 109.5
O5' C5' H5' 111.0 109.5
C5' C4' O4' 109.9 109.6
C5' C4' H4' 109.9 109.6
PB O1B HOB2 109.5 113.9
O5' C1' H1' 103.3 109.5
O4' C4' H4' 108.5 109.5
C4' O4' HO4' 109.5 114.0
C4' C3' O3' 109.8 109.5
C4' C3' H3' 109.6 109.7
O1' C1' H1' 104.9 109.5
C1' C2' N2' 109.7 109.5
C2' C1' H1' 110.6 109.5
C1' C2' H2' 109.9 109.5
C3' C2' N2' 111.4 109.5
C3' C2' H2' 108.1 109.6
O3' C3' H3' 108.9 109.5
C3' O3' HO3' 109.5 114.0
C2' N2' C7' 123.0 120.0
N2' C2' H2' 108.1 109.5
C2' N2' HN2' 118.5 120.0
N2' C7' O7' 124.0 120.0
C8' C7' O7' 119.5 120.0
C7' C8' H8'1 109.5 109.5
C7' C8' H8'2 109.4 109.5
C7' C8' H8'3 109.4 109.5
H6'1 C6' H6'2 111.1 109.5
H8'1 C8' H8'2 109.5 109.5
H8'1 C8' H8'3 109.5 109.4
H8'2 C8' H8'3 109.5 109.4
H5'1 C5B H5'2 110.6 109.5

Torsion Angles for UD2

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
O4 C4 N3 HN3 359.9 0.0
O4 C4 C5 H5 0.2 360.0
C4 N3 C2 O2 179.9 180.0
C5 C4 N3 HN3 179.9 180.0
C6 C5 C4 H5 180.0 179.8
C4 C5 C6 H6 179.9 180.1
N3 C2 N1 C1B 180.0 180.0
C4 C5 C6 H5 180.0 180.2
C5 C6 N1 C1B 180.0 179.8
O2 C2 N1 C1B 0.1 359.9
C6 N1 C2 C1B 180.0 180.3
C2 N1 C1B C2B 121.4 115.1
C2 N1 C1B O4B 239.2 229.1
C2 N1 C1B H1B 359.9 352.1
C2 N1 C6 C1B 180.0 179.7
C6 N1 C1B C2B 301.4 294.7
C6 N1 C1B O4B 59.2 48.7
C6 N1 C1B H1B 179.9 171.8
C2B C1B N1 O4B 242.2 246.0
N1 C1B C2B C3B 149.6 155.5
C2B C1B N1 H1B 121.5 122.9
N1 C1B C2B H2B 28.3 37.3
N1 C1B O4B C4B 222.6 201.5
O4B C1B N1 H1B 239.3 236.9
O2' C2B C1B O4B 152.8 155.2
C1B C2B O2' C3B 241.4 247.3
O2' C2B C1B H1B 32.2 36.6
C1B C2B O2' H2B 120.5 123.7
O2' C2B C3B C4B 207.0 220.9
O2' C2B C3B O3B 325.1 339.6
C3B C2B O2' H2B 239.0 236.4
O2' C2B C3B H3B 83.1 102.2
N1 C1B C2B O4B 120.7 118.5
N1 C1B C2B H1B 241.4 237.1
O2' C2B C1B C3B 123.9 118.2
O2' C2B C1B H2B 245.3 236.4
C2B C1B O4B C4B 342.5 319.9
O4B C1B C2B H1B 120.7 118.6
C1B C2B C3B C4B 331.4 339.1
C1B C2B C3B O3B 89.5 97.8
C3B C2B C1B H2B 121.4 118.2
C1B C2B C3B H3B 207.5 220.4
N1 C1B O4B C2B 240.1 241.5
N1 C1B O4B H1B 118.6 123.0
O4B C1B C2B C3B 28.9 37.0
C2B C1B O4B H1B 238.5 241.5
O4B C1B C2B H2B 267.5 278.8
C1B O4B C4B C5B 120.6 146.0
C1B O4B C4B H4B 239.3 267.0
O2' C2B C3B H2B 114.7 123.6
C3B C2B C1B O4B 28.9 37.0
C3B C2B C1B H1B 268.2 278.4
C1B C2B C3B H2B 239.1 241.8
C4B C3B C2B O3B 241.9 241.3
C2B C3B C4B C5B 258.8 238.5
C4B C3B C2B H3B 123.9 118.7
C2B C3B C4B H4B 140.2 117.6
O3B C3B C2B H3B 242.0 237.4
C2B C3B O3B HO3A 19.0 61.5
O5B PA O2A O3A 113.0 120.0
O1A PA O2A O3A 242.8 240.0
O2A PA O3A PB 233.0 320.0
O2A PA O1A HOA2 308.6 179.9
C4B O4B C1B H1B 104.0 78.5
O4B C4B C3B O3B 256.9 239.3
C3B C4B O4B C5B 238.4 240.6
O4B C4B C3B H3B 139.0 116.6
C3B C4B O4B H4B 119.8 119.5
C5B C4B O4B H4B 241.4 238.9
O4B C4B C5B H5'1 178.7 187.2
O4B C4B C5B H5'2 58.1 307.2
O6' C6' C5' H5' 329.2 305.0
H6'1 C6' O6' H6'2 239.1 120.0
O2A PA O5B O3A 247.4 240.0
PA O5B C5B H5'1 334.2 60.0
PA O5B C5B H5'2 94.8 300.0
O1A PA O5B O3A 115.7 120.0
O5B PA O3A PB 117.1 200.0
O5B PA O1A HOA2 76.8 300.0
O5B C5B C4B H4B 177.5 306.0
C4B C5B O5B H5'1 240.0 120.0
C4B C5B O5B H5'2 119.4 240.0
H5'1 C5B O5B H5'2 239.4 120.1
C1B O4B C4B C3B 359.1 26.5
C2B C3B C4B O3B 122.0 118.6
C4B C3B C2B H2B 92.3 97.3
C2B C3B C4B H3B 239.9 241.3
O4B C4B C3B C5B 120.1 119.5
O4B C4B C3B H4B 238.8 240.4
O3B C3B C4B H3B 117.8 122.7
C4B C3B O3B HO3A 134.5 176.2
C5B C4B C3B H4B 118.6 120.9
C3B C4B C5B H5'1 297.7 305.0
C3B C4B C5B H5'2 177.2 65.0
C2B C3B O3B C4B 244.5 245.3
O3B C3B C2B H2B 210.4 216.0
C2B C3B O3B H3B 120.4 122.6
O3B C3B C4B C5B 136.7 119.9
C4B C3B O3B H3B 236.0 237.3
O3B C3B C4B H4B 18.1 358.9
O5B PA O3A O1A 120.1 120.0
O3A PA O1A HOA2 192.1 59.9
PA O3A PB O1B 40.8 285.0
O2A PA O1A O3A 116.5 120.0
O5B PA O1A O3A 244.7 240.0
O1A PA O3A PB 357.0 80.1
O4B C4B C5B H4B 121.2 121.2
O5B C5B C4B H5'1 120.0 240.0
O5B C5B C4B H5'2 240.6 120.0
C5B C4B C3B O3B 136.7 119.9
C5B C4B C3B H3B 18.9 357.2
C3B C4B C5B H4B 240.3 239.1
H5'1 C5B C4B H5'2 120.6 240.0
O3A PB O1B HOB2 54.6 300.0
O5' C5' C6' H5' 120.2 120.0
C6' C5' C4' O4' 302.3 302.3
C6' C5' C4' H4' 61.6 62.5
O2B PB O1B HOB2 287.6 180.0
C6' C5' O5' H5' 241.7 240.0
O5' C5' C4' O4' 64.5 62.3
O5' C5' C4' H4' 183.8 182.4
C5' O5' C1' H1' 187.5 178.8
O4' C4' C5' H4' 240.7 239.9
C5' C4' O4' HO4' 218.5 60.3
C5' C4' C3' O3' 179.8 176.8
C5' C4' C3' H3' 299.4 297.1
PB O1' C1' H1' 298.8 330.0
O1' C1' O5' H1' 245.7 240.0
C2' C1' O5' H1' 118.7 120.0
O5' C1' C2' H2' 296.4 297.6
C5' C4' O4' H4' 120.2 120.2
O4' C4' C3' O3' 59.3 56.9
O4' C4' C3' H3' 178.8 177.1
C4' C3' C2' N2' 179.5 183.1
C4' C3' C2' H2' 60.8 62.9
O3' C3' C4' H3' 240.4 239.8
C4' C3' O3' HO3' 219.6 60.5
O5' C1' O1' H1' 113.4 120.0
C2' C1' O1' H1' 241.1 240.0
O1' C1' C2' H2' 166.0 177.6
O5' C1' C2' H1' 245.7 240.0
O1' C1' C2' H1' 115.4 120.0
C3' C2' C1' N2' 237.4 240.1
C3' C2' C1' H2' 118.7 120.0
C1' C2' N2' C7' 75.9 85.0
N2' C2' C1' H2' 241.3 239.9
C1' C2' N2' HN2' 255.9 265.1
C1' C2' C3' N2' 121.6 119.9
C3' C2' C1' H1' 169.3 177.6
C1' C2' C3' H2' 240.2 240.1
C3' C2' N2' C7' 197.5 204.6
N2' C2' C3' H2' 118.6 120.2
C3' C2' N2' HN2' 17.5 24.7
C4' C3' O3' H3' 119.9 120.3
O3' C3' C2' N2' 59.0 63.3
O3' C3' C2' H2' 300.4 303.1
N2' C2' C1' H1' 291.9 297.5
C1' C2' N2' H2' 119.8 120.1
C3' C2' N2' H2' 241.4 239.7
C2' N2' C7' O7' 337.5 360.0
C7' N2' C2' H2' 316.1 324.9
C2' N2' C7' HN2' 180.0 180.1
C8' C7' N2' O7' 180.5 180.0
N2' C7' C8' H8'1 33.8 180.0
N2' C7' C8' H8'2 153.8 300.1
N2' C7' C8' H8'3 273.8 60.0
O7' C7' C8' H8'1 214.3 360.0
O7' C7' C8' H8'2 334.3 120.1
O7' C7' C8' H8'3 94.3 240.0
C2' N2' C7' C8' 158.0 180.0
N2' C7' C8' O7' 179.5 180.0
H8'1 C8' C7' H8'2 240.0 239.9
H8'1 C8' C7' H8'3 120.0 120.0
H8'2 C8' C7' H8'3 240.0 240.1
H1' C1' C2' N2' 291.9 297.5
H1' C1' C2' H2' 50.6 57.6
C1' C2' H2' N2' 240.3 239.9
H2' C2' C1' H1' 50.6 57.6
C3' C2' H2' N2' 120.7 120.2
H2' C2' N2' C7' 316.1 324.9
H2' C2' N2' HN2' 136.1 144.9
C4' C3' H3' O3' 239.9 239.8
H3' C3' C2' N2' 299.4 303.1
H3' C3' C2' H2' 180.8 182.9
H3' C3' O3' HO3' 99.7 300.2
C5' C4' H4' O4' 239.8 239.8
H4' C4' O4' HO4' 98.3 300.1
H4' C4' C3' O3' 300.0 296.8
H4' C4' C3' H3' 59.6 57.0
C6' C5' H5' O5' 118.3 120.0
H5' C5' C4' O4' 184.4 182.3
H5' C5' C4' H4' 303.7 302.4
O6' C6' H6'1 H6'2 119.1 240.0
H6'1 C6' C5' O5' 329.3 185.0
H6'1 C6' C5' H5' 209.2 65.0
O6' C6' H6'2 H6'1 240.6 120.0
H6'2 C6' C5' O5' 208.4 305.0
H6'2 C6' C5' H5' 88.3 185.0
H8'1 C8' C7' O7' 214.3 360.0
C7' C8' H8'1 H8'2 120.0 120.1
C7' C8' H8'1 H8'3 240.0 240.0
H8'2 C8' H8'1 H8'3 120.0 119.9
H8'2 C8' C7' O7' 334.3 120.1
C7' C8' H8'2 H8'1 240.0 239.9
C7' C8' H8'2 H8'3 120.0 120.0
H8'1 C8' H8'2 H8'3 240.0 240.0
H8'3 C8' C7' O7' 94.3 240.0
C7' C8' H8'3 H8'1 120.0 120.0
C7' C8' H8'3 H8'2 240.0 240.1
H8'1 C8' H8'3 H8'2 120.0 120.0
C2' N2' HN2' C7' 180.0 179.9
HN2' N2' C2' H2' 136.1 144.9
HN2' N2' C7' O7' 157.5 179.9
HO3' O3' C3' H3' 99.7 300.2
HO4' O4' C4' H4' 98.3 300.1
HO6' O6' C6' H6'1 250.5 60.0
HO6' O6' C6' H6'2 11.4 300.0
HN3 N3 C2 O2 359.9 360.0
C4 C5 H5 C6 180.0 179.8
H5 C5 C6 H6 359.9 359.8
H6 C6 C5 H5 359.9 359.8
H6 C6 N1 C1B 0.0 0.2
N1 C1B H1B C2B 120.4 122.9
N1 C1B H1B O4B 238.8 237.0
C2B C1B H1B O4B 118.3 114.1
H1B C1B C2B C3B 268.2 278.4
H1B C1B C2B H2B 146.9 160.2
H1B C1B O4B C4B 104.0 78.5
O2' C2B H2B C3B 238.3 236.4
H2B C2B C1B O4B 267.5 278.8
C1B C2B H2B C3B 116.2 112.7
H2B C2B C1B H1B 146.9 160.2
H2B C2B C3B C4B 92.3 97.3
H2B C2B C3B O3B 210.4 216.0
H2B C2B C3B H3B 328.4 338.6
HO2' O2' C2B C3B 177.6 292.7
HO2' O2' C2B H2B 298.5 56.3
C2B C3B H3B C4B 117.0 114.8
C2B C3B H3B O3B 236.6 237.4
H3B C3B C2B H2B 328.4 338.6
C4B C3B H3B O3B 119.6 122.7
H3B C3B C4B C5B 18.9 357.2
H3B C3B C4B H4B 260.3 236.2
H3B C3B O3B HO3A 258.6 298.9
O4B C4B H4B C5B 240.1 238.9
H4B C4B C3B O3B 18.1 358.9
C3B C4B H4B C5B 121.3 121.0
H4B C4B C3B H3B 260.3 236.2
H4B C4B C5B H5'1 57.5 66.0
H4B C4B C5B H5'2 296.9 186.0
HO3A O3B C3B H3B 258.6 298.9
O5B C5B H5'1 H5'2 119.4 239.9
H5'1 C5B C4B H4B 57.5 66.0
C4B C5B H5'1 H5'2 240.6 119.9
O5B C5B H5'2 H5'1 240.4 120.1
H5'2 C5B C4B H4B 296.9 186.0
C4B C5B H5'2 H5'1 119.6 240.0
HOA2 O1A PA O3A 192.1 59.9