PDB Chemical Component D3T

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 D3T

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
PA O1A 1.487 1.501
PA O2A 1.487 1.618
PA O5' 1.596 1.619
PA O3A 1.595 1.615
O2A HOA2 0.950 0.980
O5' C5' 1.424 1.417
C5' C4' 1.515 1.522
C5' H5'1 1.114 1.095
C5' H5'2 1.115 1.095
C4' O4' 1.453 1.438
C4' C3' 1.519 1.521
C4' H4' 1.115 1.094
O4' C1' 1.420 1.434
C1' N1 1.483 1.433
C1' C2' 1.528 1.517
C1' H1' 1.115 1.095
N1 C6 1.382 1.389
N1 C2 1.380 1.411
C6 C5 1.344 1.338
C6 H6 1.103 1.085
C2 O2 1.218 1.232
C2 N3 1.369 1.399
N3 C4 1.379 1.387
N3 HN3 1.020 1.017
C4 O4 1.232 1.227
C4 C5 1.448 1.487
C5 C5M 1.498 1.496
C5M H5M1 1.114 1.089
C5M H5M2 1.115 1.090
C5M H5M3 1.115 1.090
C2' C3' 1.526 1.509
C2' H2'1 1.115 1.098
C2' H2'2 1.115 1.094
C3' H3'1 1.115 1.097
C3' H3'2 1.115 1.094
O3A PB 1.591 1.615
PB O1B 1.481 1.500
PB O2B 1.484 1.617
PB O3B 1.597 1.615
O2B HOB2 0.950 0.981
O3B PG 1.595 1.596
PG O1G 1.490 1.447
PG O2G 1.480 1.601
PG O3G 1.519 1.600
O3G HOG3 0.950 0.981
HO1 O2G 0.950 0.981

Bond Angles for D3T

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
O1A PA O2A 120.0 114.2
O1A PA O5' 106.5 114.1
O1A PA O3A 109.4 115.1
O2A PA O5' 110.9 104.0
O2A PA O3A 109.5 103.5
PA O2A HOA2 120.0 118.9
O5' PA O3A 98.4 104.7
PA O5' C5' 121.4 120.0
PA O3A PB 126.9 131.9
O5' C5' C4' 110.2 109.0
O5' C5' H5'1 112.0 108.8
O5' C5' H5'2 111.9 108.8
C4' C5' H5'1 111.9 110.5
C4' C5' H5'2 111.9 110.6
C5' C4' O4' 109.8 108.4
C5' C4' C3' 115.5 113.1
C5' C4' H4' 103.4 108.9
H5'1 C5' H5'2 98.5 109.1
O4' C4' C3' 103.9 106.5
O4' C4' H4' 115.2 108.7
C4' O4' C1' 109.6 108.9
C3' C4' H4' 109.4 111.2
C4' C3' C2' 102.1 102.7
C4' C3' H3'1 115.0 109.5
C4' C3' H3'2 115.0 113.7
O4' C1' N1 109.2 109.4
O4' C1' C2' 107.4 106.9
O4' C1' H1' 112.2 108.1
N1 C1' C2' 112.9 112.9
N1 C1' H1' 106.7 108.0
C1' N1 C6 121.5 118.4
C1' N1 C2 117.5 121.2
C2' C1' H1' 108.5 111.4
C1' C2' C3' 101.7 101.9
C1' C2' H2'1 115.2 111.0
C1' C2' H2'2 115.2 112.8
C6 N1 C2 121.0 120.4
N1 C6 C5 123.6 124.4
N1 C6 H6 119.7 114.8
N1 C2 O2 123.3 123.9
N1 C2 N3 114.8 115.0
C5 C6 H6 116.7 120.8
C6 C5 C4 118.0 118.4
C6 C5 C5M 123.0 123.6
O2 C2 N3 122.0 121.1
C2 N3 C4 127.5 127.0
C2 N3 HN3 115.8 116.5
C4 N3 HN3 116.6 116.5
N3 C4 O4 119.7 123.6
N3 C4 C5 115.1 114.8
O4 C4 C5 125.1 121.7
C4 C5 C5M 119.0 118.0
C5 C5M H5M1 107.4 109.7
C5 C5M H5M2 123.0 109.7
C5 C5M H5M3 107.4 109.7
H5M1 C5M H5M2 107.4 109.3
H5M1 C5M H5M3 102.4 109.4
H5M2 C5M H5M3 107.4 108.9
C3' C2' H2'1 115.2 109.7
C3' C2' H2'2 115.2 113.6
C2' C3' H3'1 115.0 109.2
C2' C3' H3'2 115.0 113.6
H2'1 C2' H2'2 95.3 107.7
H3'1 C3' H3'2 95.5 108.0
O3A PB O1B 107.8 115.0
O3A PB O2B 109.3 104.0
O3A PB O3B 99.2 101.8
O1B PB O2B 119.7 114.9
O1B PB O3B 108.4 115.6
O2B PB O3B 110.4 103.8
PB O2B HOB2 109.3 119.0
PB O3B PG 122.6 131.3
O3B PG O1G 108.9 108.3
O3B PG O2G 108.6 111.6
O3B PG O3G 98.4 112.0
O1G PG O2G 119.4 107.5
O1G PG O3G 106.5 107.7
O2G PG O3G 112.9 109.5
PG O3G HOG3 98.4 119.5

Torsion Angles for D3T

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
O2A PA O1A O5' 233.1 240.5
O2A PA O1A O3A 127.7 119.5
O1A PA O2A HOA2 180.0 314.2
O5' PA O1A O3A 254.6 239.0
O1A PA O5' C5' 193.6 180.0
O1A PA O3A PB 123.6 60.0
O1A PA O2A O5' 124.8 125.0
O1A PA O2A O3A 232.4 234.1
O5' PA O2A O3A 107.6 109.1
O2A PA O5' C5' 325.8 305.1
O2A PA O3A PB 350.2 294.6
O1A PA O5' O2A 227.9 234.9
O1A PA O5' O3A 113.2 126.6
O2A PA O5' O3A 245.3 251.7
O5' PA O2A HOA2 55.1 189.2
O5' PA O3A PB 234.4 186.0
PA O5' C5' C4' 224.8 180.0
PA O5' C5' H5'1 99.5 300.6
PA O5' C5' H5'2 350.1 59.4
O1A PA O3A O2A 133.4 125.3
O1A PA O3A O5' 249.1 234.0
O2A PA O3A O5' 115.8 108.7
O3A PA O2A HOA2 307.6 80.0
O3A PA O5' C5' 80.5 53.4
PA O3A PB O1B 166.7 60.1
PA O3A PB O2B 35.1 293.6
PA O3A PB O3B 279.5 185.9
HOA2 O2A PA O5' 55.1 189.2
HOA2 O2A PA O3A 307.6 80.0
C5' O5' PA O3A 80.5 53.4
C4' C5' O5' H5'1 125.3 239.4
C4' C5' O5' H5'2 234.7 120.7
O5' C5' C4' O4' 302.1 61.7
O5' C5' C4' C3' 59.1 179.6
O5' C5' C4' H4' 178.7 303.7
H5'1 C5' O5' H5'2 109.5 241.3
O5' C5' C4' H5'1 234.7 119.5
O5' C5' C4' H5'2 125.3 240.4
H5'1 C5' C4' H5'2 250.6 120.9
O4' C4' C5' C3' 242.9 242.2
O4' C4' C5' H4' 123.4 118.0
C5' C4' O4' C1' 147.5 111.7
C3' C4' C5' H4' 240.5 235.9
C5' C4' C3' C2' 202.4 270.2
C5' C4' C3' H3'1 77.1 154.3
C5' C4' C3' H3'2 327.6 33.3
O5' C5' H5'1 C4' 124.3 240.3
O5' C5' H5'1 H5'2 242.1 118.5
C4' C5' H5'1 H5'2 117.8 238.2
H5'1 C5' C4' O4' 67.4 302.2
H5'1 C5' C4' C3' 184.4 60.0
H5'1 C5' C4' H4' 304.0 184.2
O5' C5' H5'2 C4' 235.7 119.7
O5' C5' H5'2 H5'1 117.9 241.5
C4' C5' H5'2 H5'1 242.2 121.7
H5'2 C5' C4' O4' 176.8 181.3
H5'2 C5' C4' C3' 293.9 299.1
H5'2 C5' C4' H4' 53.4 63.3
O4' C4' C5' H5'1 67.4 302.2
O4' C4' C5' H5'2 176.8 181.3
C5' C4' O4' C3' 124.1 121.9
C5' C4' O4' H4' 243.7 241.8
C3' C4' O4' H4' 119.6 119.9
O4' C4' C3' C2' 322.7 29.1
O4' C4' C3' H3'1 197.5 273.2
O4' C4' C3' H3'2 88.0 152.3
C4' O4' C1' N1 237.5 224.5
C4' O4' C1' C2' 0.3 347.1
C4' O4' C1' H1' 119.5 107.2
C3' C4' C5' H5'1 184.4 60.0
C3' C4' C5' H5'2 293.9 299.1
C5' C4' C3' O4' 239.6 241.1
C5' C4' C3' H4' 116.2 122.9
O4' C4' C3' H4' 236.5 241.8
C3' C4' O4' C1' 23.4 349.7
C1' C2' C3' C4' 36.5 324.6
C4' C3' C2' H2'1 161.8 82.3
C4' C3' C2' H2'2 271.3 202.9
C2' C3' C4' H3'1 125.2 115.9
C2' C3' C4' H3'2 234.8 236.8
H3'1 C3' C4' H3'2 109.5 120.9
H4' C4' C5' H5'1 304.0 184.2
H4' C4' C5' H5'2 53.4 63.3
C5' C4' H4' O4' 119.9 117.9
C5' C4' H4' C3' 236.4 234.8
O4' C4' H4' C3' 116.5 116.9
H4' C4' O4' C1' 263.7 229.9
H4' C4' C3' C2' 86.2 147.3
H4' C4' C3' H3'1 321.0 31.4
H4' C4' C3' H3'2 211.4 270.5
C1' O4' C4' C3' 23.4 349.7
C1' O4' C4' H4' 263.7 229.9
N1 C1' O4' C2' 237.2 237.4
N1 C1' O4' H1' 118.1 117.3
O4' C1' N1 C6 26.5 32.7
O4' C1' N1 C2 206.1 212.6
C2' C1' O4' H1' 240.8 239.9
O4' C1' C2' C3' 336.5 30.6
O4' C1' C2' H2'1 211.2 273.8
O4' C1' C2' H2'2 101.7 152.7
O4' C1' N1 C2' 119.5 119.0
O4' C1' N1 H1' 238.5 242.6
C2' C1' N1 H1' 119.1 123.6
N1 C1' C2' C3' 97.0 151.0
N1 C1' C2' H2'1 331.7 34.2
N1 C1' C2' H2'2 222.2 273.2
C6 N1 C1' C2 180.4 180.1
C1' N1 C6 C5 179.4 180.0
C1' N1 C6 H6 359.4 360.0
C1' N1 C2 O2 0.1 0.1
C1' N1 C2 N3 180.2 180.0
C4' C3' C2' C1' 36.5 324.6
O4' C1' C2' N1 239.5 239.6
O4' C1' C2' H1' 121.5 117.9
N1 C1' C2' H1' 242.0 238.3
C2' C1' N1 C6 267.0 273.7
C2' C1' N1 C2 86.6 93.6
C3' C2' C1' H2'1 125.3 116.8
C3' C2' C1' H2'2 234.7 237.8
C1' C2' C3' H3'1 161.8 80.7
C1' C2' C3' H3'2 271.3 201.3
H2'1 C2' C1' H2'2 109.5 121.0
O4' C1' H1' N1 119.6 118.3
O4' C1' H1' C2' 241.5 242.8
N1 C1' H1' C2' 121.9 124.5
H1' C1' N1 C6 147.9 150.1
H1' C1' N1 C2 327.5 330.0
H1' C1' C2' C3' 215.0 272.7
H1' C1' C2' H2'1 89.7 155.9
H1' C1' C2' H2'2 340.2 34.8
C6 N1 C1' C2' 267.0 273.7
C6 N1 C1' H1' 147.9 150.1
C1' N1 C6 C2 179.6 179.9
C6 N1 C2 O2 179.7 180.0
C6 N1 C2 N3 359.8 360.0
C5 C6 N1 H6 180.0 180.0
N1 C6 C5 C4 0.6 360.0
N1 C6 C5 C5M 180.9 180.0
C2 N1 C1' C2' 86.6 93.6
C2 N1 C1' H1' 327.5 330.0
C1' N1 C2 C6 180.4 180.1
C2 N1 C6 C5 359.8 0.0
C2 N1 C6 H6 179.8 180.1
O2 C2 N1 N3 179.9 180.0
N1 C2 N3 C4 0.2 360.0
N1 C2 N3 HN3 180.2 180.0
C5 C6 N1 C2 359.8 0.0
N1 C6 C5 H6 180.0 180.0
N3 C4 C5 C6 359.5 360.0
O4 C4 C5 C6 179.3 180.0
C4 C5 C6 C5M 179.7 180.0
C6 C5 C5M H5M1 54.7 120.4
C6 C5 C5M H5M2 180.0 0.3
C6 C5 C5M H5M3 305.2 240.6
H6 C6 N1 C2 179.8 180.1
N1 C6 H6 C5 180.0 180.0
H6 C6 C5 C4 180.6 180.0
H6 C6 C5 C5M 0.9 0.0
N1 C2 O2 N3 180.1 180.0
O2 C2 N3 C4 180.3 179.9
O2 C2 N3 HN3 0.4 360.0
N1 C2 N3 O2 179.9 180.0
C4 N3 C2 HN3 180.0 179.9
C2 N3 C4 O4 180.3 180.0
C2 N3 C4 C5 0.2 0.1
C6 C5 C4 N3 359.5 360.0
C2 N3 C4 HN3 180.0 180.1
O4 C4 N3 C5 180.1 180.0
N3 C4 C5 C5M 179.2 179.9
C2 N3 HN3 C4 180.0 180.0
HN3 N3 C4 O4 0.3 360.0
HN3 N3 C4 C5 180.2 180.0
C6 C5 C4 O4 179.3 180.0
O4 C4 N3 HN3 0.3 360.0
N3 C4 O4 C5 179.9 180.0
O4 C4 C5 C5M 359.0 359.9
C4 C5 C6 H6 180.6 180.0
C6 C5 C4 C5M 180.3 180.0
C5 C4 N3 HN3 180.2 180.0
N3 C4 C5 O4 180.1 180.0
C4 C5 C5M H5M1 235.0 300.4
C4 C5 C5M H5M2 0.3 180.3
C4 C5 C5M H5M3 125.6 60.7
C5M C5 C6 H6 0.9 0.0
C6 C5 C5M C4 179.7 180.0
H5M1 C5M C5 H5M2 234.8 120.1
H5M1 C5M C5 H5M3 109.5 239.7
H5M2 C5M C5 H5M3 234.7 119.6
C5 C5M H5M1 H5M2 134.1 239.6
C5 C5M H5M1 H5M3 247.1 120.4
H5M2 C5M H5M1 H5M3 113.0 240.8
C5 C5M H5M2 H5M1 234.8 120.4
C5 C5M H5M2 H5M3 125.3 239.9
H5M1 C5M H5M2 H5M3 250.5 119.5
C5 C5M H5M3 H5M1 112.9 239.5
C5 C5M H5M3 H5M2 225.9 120.1
H5M1 C5M H5M3 H5M2 112.9 240.6
C2' C3' C4' H4' 86.2 147.3
C4' C3' C2' H3'1 234.7 243.9
C4' C3' C2' H3'2 125.3 123.2
C3' C2' C1' H1' 215.0 272.7
C1' C2' C3' H2'1 234.8 242.2
C1' C2' C3' H2'2 125.3 121.7
H2'1 C2' C3' H2'2 250.5 239.4
H3'1 C3' C2' H3'2 250.5 239.4
H2'1 C2' C1' H1' 89.7 155.9
C1' C2' H2'1 C3' 117.9 111.9
C1' C2' H2'1 H2'2 239.0 236.0
C3' C2' H2'1 H2'2 121.1 124.1
H2'1 C2' C3' H3'1 287.0 198.5
H2'1 C2' C3' H3'2 36.5 319.1
H2'2 C2' C1' H1' 340.2 34.8
C1' C2' H2'2 C3' 242.1 244.6
C1' C2' H2'2 H2'1 121.0 122.9
C3' C2' H2'2 H2'1 239.0 238.3
H2'2 C2' C3' H3'1 36.5 319.0
H2'2 C2' C3' H3'2 146.0 79.6
H3'1 C3' C4' H4' 321.0 31.4
C4' C3' H3'1 C2' 118.3 111.7
C4' C3' H3'1 H3'2 239.1 235.7
H3'1 C3' C2' H2'1 287.0 198.5
H3'1 C3' C2' H2'2 36.5 319.0
C2' C3' H3'1 H3'2 120.8 124.0
H3'2 C3' C4' H4' 211.4 270.5
C4' C3' H3'2 C2' 241.7 243.0
C4' C3' H3'2 H3'1 120.9 121.8
H3'2 C3' C2' H2'1 36.5 319.1
H3'2 C3' C2' H2'2 146.0 79.6
C2' C3' H3'2 H3'1 239.2 238.7
O1B PB O3A O2B 131.6 126.5
O1B PB O3A O3B 247.2 234.2
O2B PB O3A O3B 115.6 107.7
O3A PB O2B HOB2 180.0 79.0
O3A PB O3B PG 117.2 294.6
O3A PB O1B O2B 234.3 239.3
O3A PB O1B O3B 106.6 118.3
O2B PB O1B O3B 232.2 239.0
O1B PB O2B HOB2 55.0 312.4
O1B PB O3B PG 229.6 60.0
O3A PB O2B O1B 125.0 126.6
O3A PB O2B O3B 251.8 253.8
O1B PB O2B O3B 126.8 127.2
O2B PB O3B PG 2.5 186.8
O3A PB O3B O1B 247.6 234.6
O3A PB O3B O2B 114.7 107.8
O1B PB O3B O2B 227.1 233.2
O3B PB O2B HOB2 288.1 185.2
PB O3B PG O1G 313.5 60.0
PB O3B PG O2G 85.1 301.8
PB O3B PG O3G 202.8 178.6
HOB2 O2B PB O3B 288.1 185.2
O1G PG O3B O2G 228.4 118.2
O1G PG O3B O3G 110.7 241.4
O2G PG O3B O3G 242.3 123.3
O3B PG O3G HOG3 180.0 61.8
O3B PG O1G O2G 125.5 239.2
O3B PG O1G O3G 254.7 121.3
O2G PG O1G O3G 129.2 242.1
O1G PG O3G HOG3 67.3 180.8
O3B PG O2G O1G 234.3 118.7
O3B PG O2G O3G 108.1 235.4
O1G PG O2G O3G 233.7 116.7
O2G PG O3G HOG3 294.4 297.4
O3B PG O3G O1G 112.7 241.0
O3B PG O3G O2G 245.6 124.4
O1G PG O3G O2G 132.9 243.4