PDB Chemical Component CDP

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 CDP

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
O3B PB 1.601 1.610
PB O1B 1.448 1.480
PB O2B 1.592 1.610
PB O3A 1.616 1.610
O3A PA 1.584 1.610
PA O1A 1.486 1.480
PA O2A 1.530 1.610
PA O5' 1.589 1.610
O5' C5' 1.424 1.429
C5' C4' 1.533 1.529
C5' H5'1 1.100 1.090
C5' H5'2 1.100 1.090
C4' O4' 1.411 1.437
C4' C3' 1.536 1.541
C4' H4' 1.100 1.090
O4' C1' 1.435 1.445
C3' O3' 1.438 1.428
C3' C2' 1.517 1.548
C3' H3' 1.100 1.090
O3' HA 0.950 0.968
C2' O2' 1.422 1.429
C2' C1' 1.531 1.549
C2' H2' 1.100 1.090
O2' HB 0.950 0.967
C1' N1 1.484 1.464
C1' H1' 1.100 1.091
N1 C2 1.396 1.346
N1 C6 1.362 1.363
C2 O2 1.235 1.220
C2 N3 1.365 1.332
N3 C4 1.369 1.327
C4 N4 1.331 1.375
C4 C5 1.426 1.410
N4 H4N1 1.000 0.970
N4 H4N2 1.000 0.970
C5 C6 1.401 1.355
C5 H5 1.080 1.080
C6 H6 1.081 1.079
HO1 O2A 0.950 0.967
HO2 O2B 0.950 0.967
HO3 O3B 0.950 0.967

Bond Angles for CDP

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
O3B PB O1B 100.6 109.5
O3B PB O2B 106.8 109.4
O3B PB O3A 103.2 109.5
O1B PB O2B 119.1 109.5
O1B PB O3A 105.5 109.5
O2B PB O3A 119.0 109.5
PB O3A PA 136.1 134.0
O3A PA O1A 110.5 109.4
O3A PA O2A 118.6 109.5
O3A PA O5' 96.6 109.5
O1A PA O2A 114.3 109.5
O1A PA O5' 106.6 109.5
O2A PA O5' 108.0 109.5
PA O5' C5' 117.8 123.0
O5' C5' C4' 111.7 109.5
O5' C5' H5'1 108.7 109.4
O5' C5' H5'2 108.3 109.5
C4' C5' H5'1 108.7 109.4
C4' C5' H5'2 108.2 109.5
C5' C4' O4' 110.5 109.9
C5' C4' C3' 115.0 109.9
C5' C4' H4' 103.0 109.9
H5'1 C5' H5'2 111.2 109.5
O4' C4' C3' 102.6 107.3
O4' C4' H4' 115.3 109.9
C4' O4' C1' 112.1 107.0
C3' C4' H4' 110.8 110.0
C4' C3' O3' 113.9 110.5
C4' C3' C2' 103.9 104.2
C4' C3' H3' 111.5 110.5
O4' C1' C2' 106.4 103.5
O4' C1' N1 108.8 110.6
O4' C1' H1' 114.1 110.6
O3' C3' C2' 112.7 110.5
O3' C3' H3' 102.5 110.5
C3' O3' HA 109.5 114.0
C2' C3' H3' 112.7 110.6
C3' C2' O2' 106.3 110.9
C3' C2' C1' 101.6 102.1
C3' C2' H2' 116.5 110.9
O2' C2' C1' 110.0 110.9
O2' C2' H2' 108.9 110.8
C2' O2' HB 109.5 114.0
C1' C2' H2' 113.2 110.9
C2' C1' N1 115.3 110.7
C2' C1' H1' 107.4 110.6
N1 C1' H1' 105.0 110.7
C1' N1 C2 115.5 119.9
C1' N1 C6 123.3 119.8
C2 N1 C6 119.5 120.3
N1 C2 O2 120.2 119.4
N1 C2 N3 121.7 121.1
N1 C6 C5 119.2 119.3
N1 C6 H6 120.4 120.4
O2 C2 N3 118.0 119.5
C2 N3 C4 120.5 120.7
N3 C4 N4 117.7 120.2
N3 C4 C5 118.0 119.7
N4 C4 C5 124.3 120.2
C4 N4 H4N1 109.7 120.0
C4 N4 H4N2 125.2 120.0
C4 C5 C6 120.6 119.0
C4 C5 H5 119.7 120.6
H4N1 N4 H4N2 125.2 120.0
C6 C5 H5 119.7 120.5
C5 C6 H6 120.4 120.3

Torsion Angles for CDP

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
O1B PB O3B O2B 235.1 240.0
O1B PB O3B O3A 108.8 120.0
O2B PB O3B O3A 233.7 240.0
O3B PB O3A PA 122.5 80.0
O3B PB O1B O2B 116.1 120.0
O3B PB O1B O3A 253.0 240.0
O2B PB O1B O3A 136.8 120.0
O1B PB O3A PA 17.4 320.0
O3B PB O2B O1B 247.2 240.0
O3B PB O2B O3A 116.2 120.0
O1B PB O2B O3A 228.9 240.0
O2B PB O3A PA 240.5 200.0
O3B PB O3A O1B 105.1 120.0
O3B PB O3A O2B 241.9 240.0
O1B PB O3A O2B 136.9 120.0
PB O3A PA O1A 93.6 45.0
PB O3A PA O2A 318.8 285.0
PB O3A PA O5' 204.1 165.0
O1A PA O3A O2A 134.8 120.0
O1A PA O3A O5' 249.5 240.0
O2A PA O3A O5' 114.7 120.0
O3A PA O5' C5' 60.9 185.0
O3A PA O1A O2A 223.1 240.0
O3A PA O1A O5' 103.8 120.0
O2A PA O1A O5' 240.7 240.0
O1A PA O5' C5' 174.6 305.0
O3A PA O2A O1A 133.2 120.0
O3A PA O2A O5' 251.7 240.0
O1A PA O2A O5' 118.5 120.0
O2A PA O5' C5' 297.9 65.0
O3A PA O5' O1A 246.3 240.1
O3A PA O5' O2A 123.0 120.0
O1A PA O5' O2A 236.7 240.0
PA O5' C5' C4' 187.2 180.0
PA O5' C5' H5'1 307.2 300.0
PA O5' C5' H5'2 68.2 60.0
C4' C5' O5' H5'1 240.0 240.0
C4' C5' O5' H5'2 119.0 120.1
O5' C5' C4' O4' 295.6 66.4
O5' C5' C4' C3' 51.2 184.3
O5' C5' C4' H4' 171.9 305.4
H5'1 C5' O5' H5'2 239.0 240.0
O5' C5' C4' H5'1 120.0 119.9
O5' C5' C4' H5'2 240.9 240.0
H5'1 C5' C4' H5'2 120.9 120.0
O4' C4' C5' C3' 244.5 242.1
O4' C4' C5' H4' 123.7 121.0
C5' C4' O4' C1' 146.4 145.9
C3' C4' C5' H4' 239.3 238.9
C5' C4' C3' O3' 81.4 119.9
C5' C4' C3' C2' 204.4 238.5
C5' C4' C3' H3' 326.0 357.3
O5' C5' H5'1 C4' 238.2 240.0
O5' C5' H5'1 H5'2 119.1 120.0
C4' C5' H5'1 H5'2 240.9 239.9
H5'1 C5' C4' O4' 175.6 306.5
H5'1 C5' C4' C3' 291.2 64.3
H5'1 C5' C4' H4' 51.9 185.5
O5' C5' H5'2 C4' 121.2 120.0
O5' C5' H5'2 H5'1 240.6 240.0
C4' C5' H5'2 H5'1 119.4 120.0
H5'2 C5' C4' O4' 54.7 186.5
H5'2 C5' C4' C3' 170.2 304.3
H5'2 C5' C4' H4' 291.0 65.4
O4' C4' C5' H5'1 175.6 306.5
O4' C4' C5' H5'2 54.7 186.5
C5' C4' O4' C3' 123.1 119.4
C5' C4' O4' H4' 243.7 239.0
C3' C4' O4' H4' 120.6 119.6
O4' C4' C3' O3' 201.4 239.3
O4' C4' C3' C2' 324.4 358.0
O4' C4' C3' H3' 86.0 116.8
C4' O4' C1' C2' 358.2 320.0
C4' O4' C1' N1 233.4 201.4
C4' O4' C1' H1' 116.5 78.5
C3' C4' C5' H5'1 291.2 64.3
C3' C4' C5' H5'2 170.2 304.3
C5' C4' C3' O4' 240.0 240.5
C5' C4' C3' H4' 116.3 121.1
O4' C4' C3' H4' 236.3 240.5
C3' C4' O4' C1' 23.3 26.5
O3' C3' C4' C2' 237.0 241.4
O3' C3' C4' H3' 115.4 122.5
C4' C3' O3' HA 38.7 180.0
C2' C3' C4' H3' 238.3 241.2
C4' C3' C2' O2' 278.9 220.9
C4' C3' C2' C1' 34.0 339.1
C4' C3' C2' H2' 157.4 97.4
H4' C4' C5' H5'1 51.9 185.5
H4' C4' C5' H5'2 291.0 65.4
C5' C4' H4' O4' 120.5 121.0
C5' C4' H4' C3' 236.5 239.0
O4' C4' H4' C3' 116.0 117.9
H4' C4' O4' C1' 262.7 266.9
H4' C4' C3' O3' 325.1 358.8
H4' C4' C3' C2' 88.0 117.5
H4' C4' C3' H3' 209.7 236.3
C1' O4' C4' C3' 23.3 26.5
C1' O4' C4' H4' 262.7 266.9
C3' C2' C1' O4' 339.4 37.0
O2' C2' C1' O4' 91.7 155.2
O4' C1' C2' H2' 213.8 278.8
C2' C1' O4' N1 124.8 118.5
C2' C1' O4' H1' 241.7 241.5
N1 C1' O4' H1' 116.9 122.9
O4' C1' N1 C2 233.2 53.6
O4' C1' N1 C6 38.4 233.3
O3' C3' C4' H4' 325.1 358.8
C4' C3' O3' C2' 118.0 114.7
C4' C3' O3' H3' 239.4 237.4
C2' C3' O3' H3' 121.4 122.7
O3' C3' C2' O2' 42.6 339.5
O3' C3' C2' C1' 157.7 97.8
O3' C3' C2' H2' 281.1 216.0
C2' C3' C4' H4' 88.0 117.5
C4' C3' C2' O3' 236.3 241.3
C4' C3' C2' H3' 120.9 118.7
O4' C1' C2' C3' 339.4 37.0
O3' C3' C2' H3' 244.6 237.4
C2' C3' O3' HA 280.7 65.3
O2' C2' C3' C1' 244.9 241.8
O2' C2' C3' H2' 121.5 123.5
C3' C2' O2' HB 89.3 298.6
C1' C2' C3' H2' 236.6 241.7
C3' C2' C1' N1 100.1 155.5
C3' C2' C1' H1' 216.8 278.6
H3' C3' C4' H4' 209.7 236.3
C4' C3' H3' O3' 122.2 122.6
C4' C3' H3' C2' 243.6 245.2
O3' C3' H3' C2' 121.4 122.6
H3' C3' O3' HA 159.3 302.6
H3' C3' C2' O2' 158.0 102.2
H3' C3' C2' C1' 273.1 220.4
H3' C3' C2' H2' 36.5 338.7
HA O3' C3' C2' 280.7 65.3
HA O3' C3' H3' 159.3 302.6
O4' C1' C2' O2' 91.7 155.2
O2' C2' C3' H3' 158.0 102.2
C3' C2' O2' C1' 109.2 112.8
C3' C2' O2' H2' 233.8 236.4
C1' C2' O2' H2' 124.6 123.6
O2' C2' C1' N1 212.4 273.7
O2' C2' C1' H1' 329.1 36.8
O4' C1' C2' N1 239.3 241.5
O4' C1' C2' H1' 122.6 118.4
C1' C2' C3' H3' 273.1 220.4
C3' C2' C1' O2' 247.7 241.8
C3' C2' C1' H2' 125.6 118.2
O2' C2' C1' H2' 237.9 236.5
C1' C2' O2' HB 340.0 185.9
N1 C1' C2' H1' 243.3 236.9
C2' C1' N1 C2 113.8 299.5
C2' C1' N1 C6 279.0 119.2
H2' C2' C3' H3' 36.5 338.7
C3' C2' H2' O2' 120.1 123.6
C3' C2' H2' C1' 242.8 247.2
O2' C2' H2' C1' 122.7 123.6
H2' C2' O2' HB 215.5 62.2
H2' C2' C1' N1 334.4 37.3
H2' C2' C1' H1' 91.1 160.3
HB O2' C2' C1' 340.0 185.9
HB O2' C2' H2' 215.5 62.2
O4' C1' N1 C2' 119.4 114.1
O4' C1' N1 H1' 237.4 237.1
N1 C1' C2' H2' 334.4 37.3
C2' C1' N1 H1' 118.0 123.0
C2 N1 C1' C6 194.8 180.3
C1' N1 C2 O2 347.9 359.9
C1' N1 C2 N3 165.2 180.0
C1' N1 C6 C5 190.7 179.8
C1' N1 C6 H6 10.7 360.0
O4' C1' H1' C2' 242.3 245.9
O4' C1' H1' N1 119.1 122.9
H1' C1' C2' H2' 91.1 160.3
C2' C1' H1' N1 236.8 237.0
H1' C1' N1 C2 355.8 176.5
H1' C1' N1 C6 161.0 356.2
C2 N1 C1' H1' 355.8 176.5
C1' N1 C2 C6 165.8 179.7
C2 N1 C6 C5 355.4 359.5
C2 N1 C6 H6 175.4 179.7
O2 C2 N1 N3 182.7 180.0
N1 C2 N3 C4 6.4 360.0
C6 N1 C1' H1' 161.0 356.2
C1' N1 C6 C2 195.3 180.3
C6 N1 C2 O2 182.1 180.2
C6 N1 C2 N3 359.3 0.3
C4 C5 C6 N1 4.4 0.5
N1 C6 C5 H5 184.4 180.3
C5 C6 N1 H6 180.0 179.8
O2 C2 N1 C6 182.1 180.2
N1 C2 O2 N3 177.4 180.0
O2 C2 N3 C4 183.7 180.0
N3 C2 N1 C6 359.3 0.3
N1 C2 N3 O2 182.7 180.0
C2 N3 C4 N4 175.7 180.1
C2 N3 C4 C5 353.5 360.0
N4 C4 N3 C5 182.2 180.1
N3 C4 N4 H4N1 180.0 360.0
N3 C4 N4 H4N2 0.0 180.0
N3 C4 C5 C6 1.2 359.8
N3 C4 C5 H5 181.2 179.9
N3 C4 N4 C5 177.6 179.9
N4 C4 C5 C6 178.8 179.7
N4 C4 C5 H5 358.8 359.9
H4N1 N4 C4 H4N2 180.0 180.0
N1 C6 C5 C4 4.4 0.5
N3 C4 C5 N4 182.4 180.1
C5 C4 N4 H4N1 2.4 180.1
C5 C4 N4 H4N2 182.4 0.1
C6 C5 C4 H5 180.0 179.8
C4 C5 C6 H6 184.3 180.3
H4N1 N4 C4 C5 2.4 180.1
C4 N4 H4N1 H4N2 180.0 180.0
H4N2 N4 C4 C5 182.4 0.1
C4 N4 H4N2 H4N1 180.0 180.0
N1 C6 C5 H6 180.0 180.2
C4 C5 C6 H5 180.0 180.2
C4 C5 H5 C6 180.0 179.8
H5 C5 C6 H6 4.3 0.1
N1 C6 H6 C5 180.0 179.8
H6 C6 C5 H5 4.3 0.1