PDB Chemical Component AZT

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 AZT

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
PA O1A 1.483 1.501
PA O2A 1.478 1.617
PA O3A 1.594 1.615
PA O5' 1.583 1.618
O2A HOA2 0.950 0.980
O3A PB 1.635 1.615
PB O1B 1.474 1.500
PB O2B 1.494 1.617
PB O3B 1.575 1.615
O2B HOB2 0.950 0.981
O3B PG 1.610 1.616
PG O1G 1.485 1.501
PG O2G 1.497 1.616
PG O3G 1.596 1.617
O2G HOG2 0.950 0.981
O3G HOG3 0.950 0.981
O5' C5' 1.402 1.417
C5' C4' 1.504 1.524
C5' H5'1 1.115 1.094
C5' H5'2 1.115 1.094
C4' O4' 1.443 1.440
C4' C3' 1.533 1.523
C4' H4' 1.115 1.095
O4' C1' 1.417 1.433
C3' N3' 1.385 1.469
C3' C2' 1.536 1.511
C3' H3' 1.114 1.094
N3' N4' 1.290 1.242
N4' N5'   1.141
C2' C1' 1.512 1.518
C2' H2'1 1.114 1.098
C2' H2'2 1.115 1.094
C1' N1 1.514 1.433
C1' H1' 1.115 1.096
N1 C2 1.409 1.414
N1 C6 1.398 1.391
C2 O2 1.276 1.233
C2 N3 1.379 1.399
N3 C4 1.362 1.386
N3 HN3 1.020 1.017
C4 O4 1.358 1.229
C4 C5 1.413 1.487
C5 C5A 1.517 1.496
C5 C6 1.382 1.339
C5A H51 1.114 1.089
C5A H52 1.115 1.090
C5A H53 1.115 1.089
C6 H6 1.102 1.087

Bond Angles for AZT

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
O1A PA O2A 118.8 114.4
O1A PA O3A 109.3 114.2
O1A PA O5' 108.2 114.8
O2A PA O3A 110.4 103.2
O2A PA O5' 108.4 104.4
PA O2A HOA2 118.8 118.9
O3A PA O5' 100.0 104.5
PA O3A PB 135.5 131.4
PA O5' C5' 117.0 120.0
O3A PB O1B 108.0 115.6
O3A PB O2B 113.6 104.2
O3A PB O3B 99.1 101.6
O1B PB O2B 118.8 114.8
O1B PB O3B 107.5 115.0
O2B PB O3B 107.8 103.9
PB O2B HOB2 113.6 118.9
PB O3B PG 131.7 131.8
O3B PG O1G 107.7 114.6
O3B PG O2G 107.6 103.6
O3B PG O3G 97.3 103.1
O1G PG O2G 118.9 115.4
O1G PG O3G 110.4 115.1
O2G PG O3G 112.6 103.5
PG O2G HOG2 107.5 118.9
PG O3G HOG3 97.3 118.9
O5' C5' C4' 109.7 109.0
O5' C5' H5'1 112.1 108.8
O5' C5' H5'2 112.1 108.8
C4' C5' H5'1 112.1 110.6
C4' C5' H5'2 112.1 110.5
C5' C4' O4' 108.8 107.9
C5' C4' C3' 113.6 112.6
C5' C4' H4' 106.6 108.7
H5'1 C5' H5'2 98.3 109.1
O4' C4' C3' 107.6 106.8
O4' C4' H4' 112.6 108.2
C4' O4' C1' 109.4 109.1
C3' C4' H4' 107.8 112.4
C4' C3' N3' 119.0 109.0
C4' C3' C2' 103.7 103.0
C4' C3' H3' 107.2 113.6
O4' C1' C2' 106.9 107.1
O4' C1' N1 107.7 109.4
O4' C1' H1' 113.6 108.1
N3' C3' C2' 109.8 109.2
N3' C3' H3' 100.9 108.6
C3' N3' N4' 174.2 115.6
C2' C3' H3' 116.9 113.2
C3' C2' C1' 103.1 102.5
C3' C2' H2'1 114.6 109.3
C3' C2' H2'2 114.6 114.5
N3' N4' N5'   179.4
C1' C2' H2'1 114.6 110.4
C1' C2' H2'2 114.6 112.3
C2' C1' N1 113.1 112.7
C2' C1' H1' 108.3 111.6
H2'1 C2' H2'2 95.9 107.7
N1 C1' H1' 107.4 107.8
C1' N1 C2 131.7 121.4
C1' N1 C6 101.8 118.6
C2 N1 C6 121.1 120.0
N1 C2 O2 118.9 123.7
N1 C2 N3 118.3 115.2
N1 C6 C5 119.4 124.6
N1 C6 H6 120.8 114.6
O2 C2 N3 122.7 121.1
C2 N3 C4 121.1 127.0
C2 N3 HN3 120.1 116.4
C4 N3 HN3 118.9 116.6
N3 C4 O4 120.2 123.6
N3 C4 C5 121.2 114.8
O4 C4 C5 118.6 121.6
C4 C5 C5A 117.0 118.0
C4 C5 C6 118.9 118.4
C5A C5 C6 123.7 123.6
C5 C5A H51 117.0 109.8
C5 C5A H52 109.4 109.7
C5 C5A H53 109.4 109.7
C5 C6 H6 119.7 120.7
H51 C5A H52 109.5 109.3
H51 C5A H53 109.5 109.4
H52 C5A H53 100.7 108.9

Torsion Angles for AZT

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
O2A PA O1A O3A 232.0 241.4
O2A PA O1A O5' 124.0 120.7
O1A PA O2A HOA2 180.0 313.7
O3A PA O1A O5' 252.0 239.3
O1A PA O3A PB 53.3 60.0
O1A PA O5' C5' 9.5 180.0
O1A PA O2A O3A 127.4 124.6
O1A PA O2A O5' 236.1 233.7
O3A PA O2A O5' 108.6 109.1
O2A PA O3A PB 185.8 184.7
O2A PA O5' C5' 239.4 54.0
O1A PA O3A O2A 227.5 235.3
O1A PA O3A O5' 113.4 126.3
O2A PA O3A O5' 245.9 251.0
O3A PA O2A HOA2 52.6 189.1
O3A PA O5' C5' 123.8 305.9
PA O3A PB O1B 115.9 60.0
PA O3A PB O2B 341.8 293.0
PA O3A PB O3B 227.8 185.3
O1A PA O5' O2A 130.0 126.0
O1A PA O5' O3A 245.7 234.1
O2A PA O5' O3A 115.6 108.1
O5' PA O2A HOA2 303.9 80.0
O5' PA O3A PB 299.9 293.7
PA O5' C5' C4' 179.3 180.0
PA O5' C5' H5'1 304.5 300.6
PA O5' C5' H5'2 54.0 59.4
HOA2 O2A PA O3A 52.6 189.1
HOA2 O2A PA O5' 303.9 80.0
PB O3A PA O5' 299.9 293.7
O1B PB O3A O2B 134.0 127.0
O1B PB O3A O3B 248.1 234.7
O2B PB O3A O3B 114.1 107.7
O3A PB O2B HOB2 180.0 176.2
O3A PB O3B PG 70.4 294.3
O3A PB O1B O2B 228.7 238.6
O3A PB O1B O3B 106.0 118.1
O2B PB O1B O3B 237.3 239.5
O1B PB O2B HOB2 51.2 48.8
O1B PB O3B PG 182.7 60.0
O3A PB O2B O1B 128.7 127.5
O3A PB O2B O3B 251.3 253.9
O1B PB O2B O3B 122.6 126.5
O2B PB O3B PG 311.9 186.3
O3A PB O3B O1B 247.8 234.3
O3A PB O3B O2B 118.5 108.0
O1B PB O3B O2B 230.8 233.7
O3B PB O2B HOB2 288.7 282.3
PB O3B PG O1G 358.4 300.1
PB O3B PG O2G 127.7 173.5
PB O3B PG O3G 244.2 65.9
HOB2 O2B PB O3B 288.7 282.3
O1G PG O3B O2G 230.7 126.5
O1G PG O3B O3G 114.2 234.2
O2G PG O3B O3G 243.5 107.6
O3B PG O2G HOG2 180.0 174.5
O3B PG O3G HOG3 180.0 186.1
O3B PG O1G O2G 122.6 239.8
O3B PG O1G O3G 254.9 119.3
O2G PG O1G O3G 132.3 239.5
O1G PG O2G HOG2 302.7 48.4
O1G PG O3G HOG3 67.9 311.7
O3B PG O2G O1G 237.3 126.1
O3B PG O2G O3G 106.0 252.7
O1G PG O2G O3G 228.6 126.6
O2G PG O3G HOG3 292.5 78.4
O3B PG O3G O1G 112.0 234.5
O3B PG O3G O2G 247.5 107.7
O1G PG O3G O2G 135.5 233.2
O3G PG O2G HOG2 74.0 281.8
HOG2 O2G PG O3G 74.0 281.8
C4' C5' O5' H5'1 234.7 239.4
C4' C5' O5' H5'2 125.3 120.6
O5' C5' C4' O4' 257.8 181.9
O5' C5' C4' C3' 17.5 299.5
O5' C5' C4' H4' 136.1 64.8
H5'1 C5' O5' H5'2 250.5 241.2
O5' C5' C4' H5'1 125.3 119.5
O5' C5' C4' H5'2 234.7 240.5
H5'1 C5' C4' H5'2 109.5 120.9
O4' C4' C5' C3' 240.2 242.3
O4' C4' C5' H4' 121.7 117.1
C5' C4' O4' C1' 131.4 112.4
C3' C4' C5' H4' 241.4 234.7
C5' C4' C3' N3' 128.8 152.6
C5' C4' C3' C2' 251.0 268.5
C5' C4' C3' H3' 15.3 31.4
O5' C5' H5'1 C4' 236.1 240.4
O5' C5' H5'1 H5'2 118.0 118.6
C4' C5' H5'1 H5'2 242.0 238.2
H5'1 C5' C4' O4' 132.5 62.4
H5'1 C5' C4' C3' 252.3 180.0
H5'1 C5' C4' H4' 10.9 305.3
O5' C5' H5'2 C4' 123.9 119.6
O5' C5' H5'2 H5'1 241.9 241.4
C4' C5' H5'2 H5'1 118.0 121.8
H5'2 C5' C4' O4' 23.1 301.4
H5'2 C5' C4' C3' 142.8 59.1
H5'2 C5' C4' H4' 261.4 184.3
O4' C4' C5' H5'1 132.5 62.4
O4' C4' C5' H5'2 23.1 301.4
C5' C4' O4' C3' 123.4 121.3
C5' C4' O4' H4' 242.1 242.6
C3' C4' O4' H4' 118.7 121.2
O4' C4' C3' N3' 249.2 270.9
O4' C4' C3' C2' 11.5 26.8
O4' C4' C3' H3' 135.8 149.7
C4' O4' C1' C2' 335.2 347.3
C4' O4' C1' N1 213.4 224.8
C4' O4' C1' H1' 94.6 107.6
C3' C4' C5' H5'1 252.3 180.0
C3' C4' C5' H5'2 142.8 59.1
C5' C4' C3' O4' 239.6 241.7
C5' C4' C3' H4' 117.9 123.2
O4' C4' C3' H4' 238.3 241.5
C3' C4' O4' C1' 8.0 351.1
N3' C3' C4' C2' 237.7 244.1
N3' C3' C4' H3' 113.4 121.2
C4' C3' N3' N4' 170.3 265.8
C2' C3' C4' H3' 235.7 237.1
C4' C3' C2' C1' 334.9 326.8
C4' C3' C2' H2'1 100.2 84.0
C4' C3' C2' H2'2 209.7 204.9
H4' C4' C5' H5'1 10.9 305.3
H4' C4' C5' H5'2 261.4 184.3
C5' C4' H4' O4' 119.2 116.9
C5' C4' H4' C3' 237.7 234.6
O4' C4' H4' C3' 118.5 117.7
H4' C4' O4' C1' 249.3 229.8
H4' C4' C3' N3' 10.9 29.4
H4' C4' C3' C2' 133.2 145.3
H4' C4' C3' H3' 257.5 268.2
C1' O4' C4' C3' 8.0 351.1
C1' O4' C4' H4' 249.3 229.8
C3' C2' C1' O4' 31.0 29.1
O4' C1' C2' H2'1 265.7 272.7
O4' C1' C2' H2'2 156.3 152.5
C2' C1' O4' N1 121.8 122.5
C2' C1' O4' H1' 240.7 239.7
N1 C1' O4' H1' 118.8 117.2
O4' C1' N1 C2 234.0 212.6
O4' C1' N1 C6 80.8 32.7
N3' C3' C4' H4' 10.9 29.4
C4' C3' N3' C2' 119.2 111.8
C4' C3' N3' H3' 243.2 235.8
C2' C3' N3' H3' 124.0 123.9
N3' C3' C2' C1' 103.1 82.6
N3' C3' C2' H2'1 228.4 199.7
N3' C3' C2' H2'2 337.9 320.6
C3' N3' N4' N5'   184.1
C2' C3' C4' H4' 133.2 145.3
C4' C3' C2' N3' 231.8 244.2
C4' C3' C2' H3' 117.7 123.1
O4' C1' C2' C3' 31.0 29.1
N3' C3' C2' H3' 246.0 238.9
C2' C3' N3' N4' 51.1 154.0
C1' C2' C3' H2'1 234.7 242.9
C1' C2' C3' H2'2 125.2 121.9
C3' C2' C1' N1 149.4 149.5
C3' C2' C1' H1' 268.3 271.0
H2'1 C2' C3' H2'2 250.5 239.1
H3' C3' C4' H4' 257.5 268.2
C4' C3' H3' N3' 125.2 121.5
C4' C3' H3' C2' 244.2 243.0
N3' C3' H3' C2' 118.9 121.5
H3' C3' N3' N4' 287.1 30.1
H3' C3' C2' C1' 217.2 203.7
H3' C3' C2' H2'1 342.4 320.8
H3' C3' C2' H2'2 92.0 81.8
N4' N3' C3' C2' 51.1 154.0
N4' N3' C3' H3' 287.1 30.1
O4' C1' C2' N1 241.6 239.6
O4' C1' C2' H1' 122.7 118.1
C1' C2' C3' H3' 217.2 203.7
C3' C2' C1' H2'1 125.3 116.4
C3' C2' C1' H2'2 234.7 236.6
H2'1 C2' C1' H2'2 109.5 120.2
N1 C1' C2' H1' 241.1 238.5
C2' C1' N1 C2 116.0 93.6
C2' C1' N1 C6 322.9 273.6
H2'1 C2' C3' H3' 342.4 320.8
C3' C2' H2'1 C1' 241.0 247.9
C3' C2' H2'1 H2'2 120.5 125.0
C1' C2' H2'1 H2'2 239.6 237.0
H2'1 C2' C1' N1 24.2 33.1
H2'1 C2' C1' H1' 143.0 154.6
H2'2 C2' C3' H3' 92.0 81.8
C3' C2' H2'2 C1' 119.0 116.4
C3' C2' H2'2 H2'1 239.4 238.2
C1' C2' H2'2 H2'1 120.5 121.7
H2'2 C2' C1' N1 274.7 272.9
H2'2 C2' C1' H1' 33.6 34.4
O4' C1' N1 C2' 117.9 119.0
O4' C1' N1 H1' 237.3 242.7
N1 C1' C2' H2'1 24.2 33.1
N1 C1' C2' H2'2 274.7 272.9
C2' C1' N1 H1' 119.4 123.6
C2 N1 C1' C6 153.2 180.0
C1' N1 C2 O2 30.9 0.0
C1' N1 C2 N3 208.8 180.0
C1' N1 C6 C5 158.8 180.0
C1' N1 C6 H6 338.8 360.0
O4' C1' H1' C2' 241.4 242.5
O4' C1' H1' N1 119.0 118.2
H1' C1' C2' H2'1 143.0 154.6
H1' C1' C2' H2'2 33.6 34.4
C2' C1' H1' N1 237.6 235.7
H1' C1' N1 C2 356.6 330.0
H1' C1' N1 C6 203.5 150.0
C2 N1 C1' H1' 356.6 330.0
C1' N1 C2 C6 211.1 180.0
C2 N1 C6 C5 2.0 0.0
C2 N1 C6 H6 182.0 180.0
O2 C2 N1 N3 182.1 180.0
N1 C2 N3 C4 1.5 360.0
N1 C2 N3 HN3 181.6 180.0
C6 N1 C1' H1' 203.5 150.0
C1' N1 C6 C2 156.8 180.0
C6 N1 C2 O2 179.8 180.0
C6 N1 C2 N3 357.7 360.0
C4 C5 C6 N1 359.0 0.1
C5A C5 C6 N1 171.1 180.0
C5 C6 N1 H6 180.0 180.0
O2 C2 N1 C6 179.8 180.0
N1 C2 O2 N3 177.8 180.0
O2 C2 N3 C4 179.3 180.0
O2 C2 N3 HN3 359.4 0.0
N3 C2 N1 C6 357.7 360.0
N1 C2 N3 O2 182.2 180.0
C4 N3 C2 HN3 179.9 179.9
C2 N3 C4 O4 179.9 180.0
C2 N3 C4 C5 359.5 0.1
C2 N3 C4 HN3 180.1 180.1
O4 C4 N3 C5 180.4 179.9
N3 C4 C5 C5A 187.7 180.0
N3 C4 C5 C6 0.2 359.9
C2 N3 HN3 C4 179.9 179.9
HN3 N3 C4 O4 359.8 360.0
HN3 N3 C4 C5 179.4 180.0
O4 C4 N3 HN3 359.8 360.0
N3 C4 O4 C5 179.6 180.1
O4 C4 C5 C5A 7.2 0.0
O4 C4 C5 C6 179.8 180.0
N1 C6 C5 C4 359.0 0.1
C5 C4 N3 HN3 179.4 180.0
N3 C4 C5 O4 180.4 179.9
C5A C5 C4 C6 187.4 180.1
C4 C5 C5A H51 180.0 324.2
C4 C5 C5A H52 305.3 204.0
C4 C5 C5A H53 54.7 84.5
C4 C5 C6 H6 179.1 180.0
N1 C6 C5 C5A 171.1 180.0
C4 C5 C5A C6 172.2 179.9
C5A C5 C6 H6 351.1 360.0
H51 C5A C5 H52 234.7 120.2
H51 C5A C5 H53 125.2 239.8
H52 C5A C5 H53 250.5 119.6
N1 C6 C5 H6 180.0 180.0
C4 C5 C6 C5A 187.9 180.1
C6 C5 C5A H51 7.8 144.3
C6 C5 C5A H52 133.1 24.1
C6 C5 C5A H53 242.5 264.5
H51 C5A C5 C6 7.8 144.3
C5 C5A H51 H52 125.3 239.6
C5 C5A H51 H53 234.8 120.4
H52 C5A H51 H53 109.6 240.9
H52 C5A C5 C6 133.1 24.1
C5 C5A H52 H51 230.5 120.4
C5 C5A H52 H53 115.2 239.9
H51 C5A H52 H53 244.7 119.4
H53 C5A C5 C6 242.5 264.5
C5 C5A H53 H51 129.5 239.5
C5 C5A H53 H52 244.8 120.1
H51 C5A H53 H52 115.3 240.6
N1 C6 H6 C5 180.0 180.0