PDB Chemical Component D4T

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 D4T

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
PC O1C 1.486 1.610
PC O2C 1.487 1.610
PC O3C 1.486 1.481
PC O7' 1.605 1.609
O1C H1CO 0.950 0.966
O2C H2CO 0.949 0.967
O7' PB 1.602 1.610
PB O1B 1.487 1.480
PB O2B 1.484 1.611
PB O6' 1.594 1.611
O2B H2BO 0.950 0.967
O6' PA 1.596 1.610
PA O1A 1.494 1.480
PA O2A 1.495 1.610
PA O5' 1.593 1.610
O2A H2AO 0.950 0.967
O5' C5' 1.433 1.429
C5' C4' 1.521 1.530
C5' H5'1 1.115 1.090
C5' H5'2 1.115 1.091
C4' O4' 1.449 1.440
C4' C3' 1.512 1.512
C4' H4'C 1.115 1.089
O4' C1' 1.406 1.440
C1' N1 1.472 1.465
C1' C2' 1.515 1.512
C1' H1'C 1.114 1.090
N1 C6 1.378 1.368
N1 C2 1.376 1.346
C6 C5 1.336 1.350
C6 H66 1.103 1.081
C2 O2 1.218 1.216
C2 N3 1.366 1.345
N3 C4 1.378 1.348
N3 HN3 1.019 0.970
C4 O4 1.230 1.218
C4 C5 1.453 1.417
C5 C5A 1.494 1.507
C5A HCA1 1.115 1.090
C5A HCA2 1.115 1.090
C5A HCA3 1.116 1.090
C2' C3' 1.346 1.314
C2' H2'C 1.103 1.079
C3' H3'C 1.104 1.080

Bond Angles for D4T

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
O1C PC O2C 118.0 109.4
O1C PC O3C 105.3 109.5
O1C PC O7' 105.0 109.5
PC O1C H1CO 118.0 106.8
O2C PC O3C 118.1 109.4
O2C PC O7' 105.8 109.5
PC O2C H2CO 117.9 106.9
O3C PC O7' 102.9 109.5
PC O7' PB 135.1 106.8
O7' PB O1B 109.9 109.5
O7' PB O2B 110.0 109.5
O7' PB O6' 102.5 109.5
O1B PB O2B 119.1 109.5
O1B PB O6' 107.7 109.5
O2B PB O6' 106.2 109.4
PB O2B H2BO 110.0 106.8
PB O6' PA 131.7 106.8
O6' PA O1A 108.6 109.5
O6' PA O2A 107.4 109.4
O6' PA O5' 101.0 109.4
O1A PA O2A 119.2 109.5
O1A PA O5' 108.6 109.5
O2A PA O5' 110.6 109.5
PA O2A H2AO 107.4 106.9
PA O5' C5' 120.5 106.8
O5' C5' C4' 111.0 109.5
O5' C5' H5'1 111.6 109.5
O5' C5' H5'2 111.6 109.4
C4' C5' H5'1 111.7 109.5
C4' C5' H5'2 111.7 109.5
C5' C4' O4' 109.9 110.2
C5' C4' C3' 117.4 110.2
C5' C4' H4'C 102.4 110.2
H5'1 C5' H5'2 98.7 109.4
O4' C4' C3' 105.7 105.7
O4' C4' H4'C 114.9 110.2
C4' O4' C1' 109.5 103.7
C3' C4' H4'C 106.9 110.2
C4' C3' C2' 108.8 108.4
C4' C3' H3'C 130.3 125.8
O4' C1' N1 107.6 110.2
O4' C1' C2' 106.6 105.8
O4' C1' H1'C 113.5 110.2
N1 C1' C2' 112.4 110.2
N1 C1' H1'C 107.9 110.1
C1' N1 C6 120.5 119.7
C1' N1 C2 118.0 119.7
C2' C1' H1'C 108.9 110.2
C1' C2' C3' 109.2 108.3
C1' C2' H2'C 130.2 125.9
C6 N1 C2 121.5 120.6
N1 C6 C5 123.4 119.7
N1 C6 H66 119.9 120.1
N1 C2 O2 123.0 119.5
N1 C2 N3 114.7 120.9
C5 C6 H66 116.7 120.1
C6 C5 C4 117.9 119.1
C6 C5 C5A 122.9 120.5
O2 C2 N3 122.2 119.5
C2 N3 C4 127.1 120.3
C2 N3 HN3 116.0 119.9
C4 N3 HN3 116.9 119.8
N3 C4 O4 119.5 120.4
N3 C4 C5 115.3 119.4
O4 C4 C5 125.2 120.3
C4 C5 C5A 119.2 120.4
C5 C5A HCA1 123.0 109.5
C5 C5A HCA2 107.5 109.5
C5 C5A HCA3 107.5 109.4
HCA1 C5A HCA2 107.4 109.5
HCA1 C5A HCA3 107.4 109.5
HCA2 C5A HCA3 102.3 109.5
C3' C2' H2'C 120.6 125.8
C2' C3' H3'C 120.9 125.8

Torsion Angles for D4T

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
O2C PC O1C O3C 134.3 119.9
O2C PC O1C O7' 242.6 240.0
O1C PC O2C H2CO 180.0 300.0
O3C PC O1C O7' 108.3 120.0
O1C PC O7' PB 44.7 80.0
O1C PC O2C O3C 231.4 240.0
O1C PC O2C O7' 117.0 120.0
O2C PC O1C H1CO 180.0 300.0
O3C PC O2C O7' 245.6 240.0
O2C PC O7' PB 170.2 200.0
O1C PC O3C O2C 134.3 119.9
O1C PC O3C O7' 250.3 240.0
O3C PC O1C H1CO 45.7 180.0
O2C PC O3C O7' 116.0 120.0
O3C PC O2C H2CO 308.5 59.9
O3C PC O7' PB 294.7 320.0
O1C PC O7' O2C 234.5 240.0
O1C PC O7' O3C 110.0 120.0
O7' PC O1C H1CO 297.4 60.0
O2C PC O7' O3C 235.5 240.0
O7' PC O2C H2CO 63.0 180.0
PC O7' PB O1B 351.9 320.0
PC O7' PB O2B 124.9 80.0
PC O7' PB O6' 237.6 200.0
H1CO O1C PC O2C 180.0 300.0
H1CO O1C PC O3C 45.7 180.0
H1CO O1C PC O7' 297.4 60.0
H2CO O2C PC O3C 308.5 59.9
H2CO O2C PC O7' 63.0 180.0
O1B PB O7' O2B 227.0 240.0
O1B PB O7' O6' 114.4 120.0
O2B PB O7' O6' 247.4 240.0
O7' PB O2B H2BO 180.0 60.0
O7' PB O6' PA 74.3 165.0
O7' PB O1B O2B 128.2 120.0
O7' PB O1B O6' 249.0 240.0
O2B PB O1B O6' 120.9 120.0
O1B PB O2B H2BO 308.1 180.0
O1B PB O6' PA 318.4 45.0
O7' PB O2B O1B 231.9 240.0
O7' PB O2B O6' 110.2 120.0
O1B PB O2B O6' 238.4 240.0
O2B PB O6' PA 189.8 285.0
O7' PB O6' O1B 115.9 120.0
O7' PB O6' O2B 244.6 240.0
O1B PB O6' O2B 128.6 120.0
O6' PB O2B H2BO 69.8 300.0
PB O6' PA O1A 6.4 320.0
PB O6' PA O2A 136.6 80.0
PB O6' PA O5' 252.4 200.0
H2BO O2B PB O6' 69.8 300.0
O1A PA O6' O2A 229.9 240.0
O1A PA O6' O5' 114.1 120.0
O2A PA O6' O5' 244.2 240.0
O6' PA O2A H2AO 180.0 59.9
O6' PA O5' C5' 91.4 175.1
O6' PA O1A O2A 123.3 120.0
O6' PA O1A O5' 251.1 240.0
O2A PA O1A O5' 127.7 120.0
O1A PA O2A H2AO 303.9 180.0
O1A PA O5' C5' 337.4 55.0
O6' PA O2A O1A 236.1 240.0
O6' PA O2A O5' 109.3 119.9
O1A PA O2A O5' 233.2 240.0
O2A PA O5' C5' 204.9 295.0
O6' PA O5' O1A 114.0 120.0
O6' PA O5' O2A 246.5 240.0
O1A PA O5' O2A 132.5 120.0
O5' PA O2A H2AO 70.7 300.0
PA O5' C5' C4' 217.5 180.0
PA O5' C5' H5'1 342.8 60.0
PA O5' C5' H5'2 92.2 300.0
H2AO O2A PA O5' 70.7 300.0
C4' C5' O5' H5'1 234.7 120.0
C4' C5' O5' H5'2 125.3 240.0
O5' C5' C4' O4' 293.3 66.5
O5' C5' C4' C3' 54.2 182.8
O5' C5' C4' H4'C 170.8 304.6
H5'1 C5' O5' H5'2 250.6 119.9
O5' C5' C4' H5'1 125.3 240.0
O5' C5' C4' H5'2 234.7 120.0
H5'1 C5' C4' H5'2 109.5 240.0
O4' C4' C5' C3' 239.2 243.7
O4' C4' C5' H4'C 122.5 121.9
C5' C4' O4' C1' 131.5 146.4
C3' C4' C5' H4'C 243.3 238.2
C5' C4' C3' C2' 234.3 223.5
C5' C4' C3' H3'C 54.2 43.6
O5' C5' H5'1 C4' 235.0 120.0
O5' C5' H5'1 H5'2 117.5 240.1
C4' C5' H5'1 H5'2 242.4 120.1
H5'1 C5' C4' O4' 168.1 186.5
H5'1 C5' C4' C3' 288.9 302.8
H5'1 C5' C4' H4'C 45.5 64.6
O5' C5' H5'2 C4' 124.9 240.0
O5' C5' H5'2 H5'1 242.5 120.0
C4' C5' H5'2 H5'1 117.6 239.9
H5'2 C5' C4' O4' 58.6 306.5
H5'2 C5' C4' C3' 179.4 62.8
H5'2 C5' C4' H4'C 296.1 184.6
O4' C4' C5' H5'1 168.1 186.5
O4' C4' C5' H5'2 58.6 306.5
C5' C4' O4' C3' 127.6 119.1
C5' C4' O4' H4'C 245.2 238.1
C3' C4' O4' H4'C 117.6 119.0
O4' C4' C3' C2' 357.3 342.6
O4' C4' C3' H3'C 177.2 162.7
C4' O4' C1' N1 235.8 213.6
C4' O4' C1' C2' 356.6 332.7
C4' O4' C1' H1'C 116.5 91.9
C3' C4' C5' H5'1 288.9 302.8
C3' C4' C5' H5'2 179.4 62.8
C5' C4' C3' O4' 237.0 240.9
C5' C4' C3' H4'C 114.2 121.8
O4' C4' C3' H4'C 237.2 240.9
C3' C4' O4' C1' 3.8 27.3
C1' C2' C3' C4' 0.7 0.1
C4' C3' C2' H2'C 180.7 180.0
C2' C3' C4' H3'C 180.1 179.9
H4'C C4' C5' H5'1 45.5 64.6
H4'C C4' C5' H5'2 296.1 184.6
C5' C4' H4'C O4' 119.1 121.9
C5' C4' H4'C C3' 236.0 238.1
O4' C4' H4'C C3' 116.9 116.3
H4'C C4' O4' C1' 246.2 268.3
H4'C C4' C3' C2' 120.1 101.6
H4'C C4' C3' H3'C 300.0 281.8
C1' O4' C4' C3' 3.8 27.3
C1' O4' C4' H4'C 246.2 268.3
N1 C1' O4' C2' 239.2 240.9
N1 C1' O4' H1'C 119.3 121.7
O4' C1' N1 C6 56.3 232.5
O4' C1' N1 C2 235.5 52.5
C2' C1' O4' H1'C 240.1 240.9
O4' C1' C2' C3' 1.7 17.2
O4' C1' C2' H2'C 181.7 197.4
O4' C1' N1 C2' 117.1 116.4
O4' C1' N1 H1'C 237.1 238.2
C2' C1' N1 H1'C 120.1 121.8
N1 C1' C2' C3' 119.3 136.3
N1 C1' C2' H2'C 299.4 316.5
C6 N1 C1' C2 180.7 179.9
C1' N1 C6 C5 178.3 180.0
C1' N1 C6 H66 358.3 0.1
C1' N1 C2 O2 2.1 360.0
C1' N1 C2 N3 182.0 180.0
C4' C3' C2' C1' 0.7 0.1
O4' C1' C2' N1 242.4 240.9
O4' C1' C2' H1'C 122.8 119.1
N1 C1' C2' H1'C 240.5 238.2
C2' C1' N1 C6 299.2 116.1
C2' C1' N1 C2 118.5 296.1
C3' C2' C1' H2'C 180.0 179.9
C1' C2' C3' H3'C 180.8 180.0
O4' C1' H1'C N1 119.2 121.8
O4' C1' H1'C C2' 241.4 243.6
N1 C1' H1'C C2' 122.3 121.8
H1'C C1' N1 C6 179.1 354.3
H1'C C1' N1 C2 358.4 174.3
H1'C C1' C2' C3' 238.8 258.1
H1'C C1' C2' H2'C 58.9 78.2
C6 N1 C1' C2' 299.2 116.1
C6 N1 C1' H1'C 179.1 354.3
C1' N1 C6 C2 179.3 180.1
C6 N1 C2 O2 181.4 180.0
C6 N1 C2 N3 1.3 0.0
C5 C6 N1 H66 180.0 179.9
N1 C6 C5 C4 359.5 0.3
N1 C6 C5 C5A 179.4 180.0
C2 N1 C1' C2' 118.5 296.1
C2 N1 C1' H1'C 358.4 174.3
C1' N1 C2 C6 180.7 179.9
C2 N1 C6 C5 359.1 359.9
C2 N1 C6 H66 179.0 180.0
O2 C2 N1 N3 180.1 180.0
N1 C2 N3 C4 359.8 359.7
N1 C2 N3 HN3 179.8 180.0
C5 C6 N1 C2 359.1 359.9
N1 C6 C5 H66 180.0 180.1
N3 C4 C5 C6 1.4 359.5
O4 C4 C5 C6 181.7 180.0
C4 C5 C6 C5A 180.2 180.3
C6 C5 C5A HCA1 180.0 90.0
C6 C5 C5A HCA2 305.3 210.0
C6 C5 C5A HCA3 54.7 330.0
H66 C6 N1 C2 179.0 180.0
N1 C6 H66 C5 180.0 179.9
H66 C6 C5 C4 179.6 180.2
H66 C6 C5 C5A 359.4 360.0
N1 C2 O2 N3 179.9 180.0
O2 C2 N3 C4 179.6 179.8
O2 C2 N3 HN3 359.7 0.1
N1 C2 N3 O2 180.1 180.0
C4 N3 C2 HN3 180.0 179.7
C2 N3 C4 O4 178.7 180.0
C2 N3 C4 C5 358.9 0.5
C6 C5 C4 N3 1.4 359.5
C2 N3 C4 HN3 180.0 180.3
O4 C4 N3 C5 179.7 179.5
N3 C4 C5 C5A 181.5 179.8
C2 N3 HN3 C4 180.0 179.7
HN3 N3 C4 O4 358.6 359.7
HN3 N3 C4 C5 178.9 180.2
C6 C5 C4 O4 181.7 180.0
O4 C4 N3 HN3 358.6 359.7
N3 C4 O4 C5 180.3 180.5
O4 C4 C5 C5A 1.8 0.2
C4 C5 C6 H66 179.6 180.2
C6 C5 C4 C5A 179.8 179.7
C5 C4 N3 HN3 178.9 180.2
N3 C4 C5 O4 179.7 179.5
C4 C5 C5A HCA1 359.8 269.7
C4 C5 C5A HCA2 125.1 29.7
C4 C5 C5A HCA3 234.5 149.7
C5A C5 C6 H66 359.4 360.0
C6 C5 C5A C4 180.2 180.3
HCA1 C5A C5 HCA2 234.8 240.0
HCA1 C5A C5 HCA3 125.3 120.0
HCA2 C5A C5 HCA3 250.5 240.0
C5 C5A HCA1 HCA2 125.3 120.0
C5 C5A HCA1 HCA3 234.7 240.1
HCA2 C5A HCA1 HCA3 109.4 120.0
C5 C5A HCA2 HCA1 225.9 240.0
C5 C5A HCA2 HCA3 113.0 119.9
HCA1 C5A HCA2 HCA3 247.1 240.0
C5 C5A HCA3 HCA1 134.1 120.0
C5 C5A HCA3 HCA2 247.0 240.0
HCA1 C5A HCA3 HCA2 112.9 120.0
C2' C3' C4' H4'C 120.1 101.6
C4' C3' C2' H3'C 179.9 180.1
C3' C2' C1' H1'C 238.8 258.1
C1' C2' C3' H2'C 180.0 180.1
H2'C C2' C1' H1'C 58.9 78.2
C1' C2' H2'C C3' 179.9 179.8
H2'C C2' C3' H3'C 0.7 359.9
H3'C C3' C4' H4'C 300.0 281.8
C4' C3' H3'C C2' 180.1 179.9
H3'C C3' C2' H2'C 0.7 359.9