PDB Chemical Component CDF

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 CDF

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
O3B PB 1.514 1.480
PB O1B 1.516 1.609
PB O2B 1.516 1.610
PB O3A 1.626 1.610
O3A PA 1.621 1.610
PA O1A 1.514 1.610
PA O2A 1.510 1.480
PA O5' 1.619 1.610
O5' C5' 1.428 1.429
C5' C4' 1.526 1.530
C4' O4' 1.434 1.433
C4' C3' 1.522 1.543
O4' C1' 1.426 1.437
C3' O3' 1.430 1.429
C3' C2' 1.517 1.553
C2' O2' 1.428 1.429
C2' C1' 1.530 1.550
C1' N1 1.483 1.464
N1 C2 1.423 1.346
N1 C6 1.344 1.363
C2 O2 1.244 1.220
C2 N3 1.352 1.332
N3 C4 1.352 1.327
C4 N4 1.348 1.376
C4 C5 1.388 1.410
O1B H1B 0.950 0.968
O2B H2B 0.950 0.968
O1A H1A 0.950 0.968
C5' H5'1 1.100 1.090
C5' H5'2 1.100 1.091
C4' H4' 1.100 1.090
C3' H3' 1.100 1.091
C1' H1' 1.100 1.090
O3' HA 0.950 0.968
C2' H2' 1.100 1.089
O2' HB 0.950 0.968
N4 H41N 1.000 0.970
N4 H42N 1.000 0.970
C6 C5 1.391 1.354
C5 H5 1.079 1.080
C6 H6 1.079 1.080

Bond Angles for CDF

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
O3B PB O1B 113.9 109.5
O3B PB O2B 113.9 109.5
O3B PB O3A 104.5 109.5
O1B PB O2B 113.3 109.5
O1B PB O3A 103.1 109.5
PB O1B H1B 109.5 114.0
O2B PB O3A 106.8 109.4
PB O2B H2B 109.5 114.0
PB O3A PA 124.8 134.0
O3A PA O1A 108.7 109.5
O3A PA O2A 107.7 109.5
O3A PA O5' 101.8 109.5
O1A PA O2A 118.3 109.5
O1A PA O5' 108.8 109.5
PA O1A H1A 109.5 114.0
O2A PA O5' 110.3 109.5
PA O5' C5' 122.8 123.0
O5' C5' C4' 112.9 109.5
O5' C5' H5'1 108.3 109.5
O5' C5' H5'2 107.6 109.5
C5' C4' O4' 112.0 109.8
C5' C4' C3' 107.5 109.8
C4' C5' H5'1 108.3 109.5
C4' C5' H5'2 107.5 109.4
C5' C4' H4' 108.3 109.8
O4' C4' C3' 106.9 107.6
C4' O4' C1' 106.3 110.0
O4' C4' H4' 108.9 109.8
C4' C3' O3' 111.0 110.8
C4' C3' C2' 105.5 102.3
C3' C4' H4' 113.4 110.0
C4' C3' H3' 112.4 110.9
O4' C1' C2' 104.9 105.1
O4' C1' N1 116.6 110.3
O4' C1' H1' 111.8 110.2
O3' C3' C2' 113.0 110.8
O3' C3' H3' 104.8 110.7
C3' O3' HA 109.5 114.0
C3' C2' O2' 108.6 111.1
C3' C2' C1' 101.6 101.0
C2' C3' H3' 110.4 111.0
C3' C2' H2' 116.2 111.2
O2' C2' C1' 113.0 111.1
O2' C2' H2' 105.5 111.0
C2' O2' HB 109.5 114.0
C2' C1' N1 118.7 110.3
C2' C1' H1' 109.3 110.3
C1' C2' H2' 112.1 111.1
C1' N1 C2 126.4 119.8
C1' N1 C6 115.1 119.9
N1 C1' H1' 95.2 110.4
C2 N1 C6 118.5 120.3
N1 C2 O2 122.8 119.4
N1 C2 N3 119.9 121.1
N1 C6 C5 121.6 119.3
N1 C6 H6 119.2 120.3
O2 C2 N3 117.4 119.4
C2 N3 C4 121.1 120.6
N3 C4 N4 119.7 120.2
N3 C4 C5 120.4 119.6
N4 C4 C5 119.9 120.2
C4 N4 H41N 110.1 120.0
C4 N4 H42N 125.0 120.0
C4 C5 C6 118.6 119.0
C4 C5 H5 120.7 120.5
H5'1 C5' H5'2 112.2 109.4
H41N N4 H42N 124.9 120.0
C6 C5 H5 120.7 120.5
C5 C6 H6 119.2 120.4

Torsion Angles for CDF

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
O1B PB O3B O2B 132.0 240.0
O1B PB O3B O3A 248.2 120.1
O3B PB O1B H1B 352.6 180.0
O2B PB O3B O3A 116.1 240.1
O3B PB O2B H2B 180.3 300.0
O3B PB O3A PA 70.8 45.1
O3B PB O1B O2B 227.7 120.0
O3B PB O1B O3A 112.7 240.0
O2B PB O1B O3A 245.0 120.0
O1B PB O2B H2B 48.0 60.0
O1B PB O3A PA 190.2 285.0
O3B PB O2B O1B 132.3 240.0
O3B PB O2B O3A 245.2 120.0
O1B PB O2B O3A 112.8 240.0
O2B PB O1B H1B 124.9 60.0
O2B PB O3A PA 309.8 165.0
O3B PB O3A O1B 240.6 120.0
O3B PB O3A O2B 121.0 240.0
O1B PB O3A O2B 240.4 120.0
O3A PB O1B H1B 239.9 300.0
O3A PB O2B H2B 295.2 180.0
PB O3A PA O1A 176.2 285.0
PB O3A PA O2A 305.5 45.0
PB O3A PA O5' 61.5 164.9
O1A PA O3A O2A 230.7 240.0
O1A PA O3A O5' 114.7 120.0
O3A PA O1A H1A 116.9 300.0
O2A PA O3A O5' 244.0 240.0
O3A PA O5' C5' 172.3 185.0
O3A PA O1A O2A 123.2 120.0
O3A PA O1A O5' 249.9 240.0
O2A PA O1A O5' 126.7 120.0
O1A PA O5' C5' 57.6 64.9
O3A PA O2A O1A 236.3 240.0
O3A PA O2A O5' 110.3 120.0
O1A PA O2A O5' 234.0 240.0
O2A PA O1A H1A 353.7 180.0
O2A PA O5' C5' 286.4 305.0
O3A PA O5' O1A 114.7 120.0
O3A PA O5' O2A 245.9 240.0
O1A PA O5' O2A 131.2 120.0
O5' PA O1A H1A 227.0 60.0
PA O5' C5' C4' 224.8 180.0
PA O5' C5' H5'1 344.8 300.1
PA O5' C5' H5'2 106.3 60.0
O5' C5' C4' O4' 24.7 66.5
O5' C5' C4' C3' 141.8 184.6
C4' C5' O5' H5'1 240.0 239.9
C4' C5' O5' H5'2 118.5 120.0
O5' C5' C4' H4' 264.6 305.7
H5'1 C5' O5' H5'2 238.5 240.0
O5' C5' C4' H5'1 120.0 120.1
O5' C5' C4' H5'2 241.5 240.0
O4' C4' C5' C3' 242.9 241.9
C5' C4' O4' C1' 92.0 117.8
O4' C4' C5' H4' 120.1 120.9
C5' C4' C3' O3' 119.0 101.0
C5' C4' C3' C2' 241.7 219.2
C3' C4' C5' H4' 237.2 238.9
C5' C4' C3' H3' 2.1 337.6
H5'1 C5' C4' H5'2 121.5 119.9
C5' C4' O4' C3' 117.4 119.5
O4' C4' C5' H5'1 264.7 306.4
O4' C4' C5' H5'2 143.2 186.5
C5' C4' O4' H4' 240.2 239.1
O4' C4' C3' O3' 239.4 220.4
O4' C4' C3' C2' 2.1 338.6
C3' C4' O4' H4' 122.8 119.7
O4' C4' C3' H3' 122.5 97.0
C4' O4' C1' C2' 38.8 24.4
C4' O4' C1' N1 172.4 143.3
C4' O4' C1' H1' 280.5 265.5
C5' C4' C3' O4' 239.6 240.6
C3' C4' C5' H5'1 21.8 64.5
C3' C4' C5' H5'2 260.3 304.6
C5' C4' C3' H4' 119.7 121.0
C3' C4' O4' C1' 334.5 358.3
O4' C4' C3' H4' 240.1 240.4
O3' C3' C4' C2' 237.3 241.8
O3' C3' C4' H3' 117.0 123.4
C4' C3' O3' HA 108.0 180.0
C4' C3' C2' O2' 139.2 152.0
C4' C3' C2' C1' 19.9 34.2
C2' C3' C4' H3' 239.7 241.6
C4' C3' C2' H2' 257.9 276.2
C1' O4' C4' C3' 334.5 358.3
C1' O4' C4' H4' 211.7 238.7
C3' C2' C1' O4' 324.1 323.6
O2' C2' C1' O4' 207.9 205.7
C2' C1' O4' N1 226.4 241.1
C2' C1' O4' H1' 118.4 118.9
O4' C1' C2' H2' 88.9 81.5
O4' C1' N1 C2 273.1 181.4
O4' C1' N1 C6 94.8 1.2
N1 C1' O4' H1' 251.9 237.8
C4' C3' O3' C2' 118.3 112.8
O3' C3' C4' H4' 359.4 340.0
C4' C3' O3' H3' 238.5 236.5
O3' C3' C2' O2' 260.7 270.2
O3' C3' C2' C1' 141.3 152.3
C2' C3' O3' H3' 120.2 123.7
O3' C3' C2' H2' 19.4 34.4
C4' C3' C2' O3' 238.6 241.8
C2' C3' C4' H4' 122.1 98.2
C4' C3' C2' H3' 121.6 118.3
O4' C1' C2' C3' 324.1 323.6
O3' C3' C2' H3' 243.1 236.5
C2' C3' O3' HA 349.8 67.1
O2' C2' C3' C1' 119.3 117.9
O2' C2' C3' H2' 241.3 235.8
C3' C2' O2' HB 334.8 61.5
C3' C2' C1' N1 191.7 204.7
C3' C2' C1' H1' 84.1 82.4
C1' C2' C3' H2' 122.0 118.0
O4' C1' C2' O2' 207.9 205.7
C3' C2' O2' C1' 248.1 248.4
O2' C2' C3' H3' 17.6 33.7
C3' C2' O2' H2' 125.3 124.2
O2' C2' C1' N1 75.5 86.7
O2' C2' C1' H1' 328.0 324.5
C1' C2' O2' H2' 237.2 235.8
O4' C1' C2' N1 132.4 118.9
O4' C1' C2' H1' 240.0 241.2
C3' C2' C1' O2' 116.2 117.9
C1' C2' C3' H3' 258.2 275.9
C3' C2' C1' H2' 235.3 242.0
O2' C2' C1' H2' 119.1 124.1
C1' C2' O2' HB 86.7 173.0
C2' C1' N1 C2 40.2 297.1
C2' C1' N1 C6 221.9 116.9
N1 C1' C2' H1' 107.5 122.3
O4' C1' N1 C2' 232.9 244.3
O4' C1' N1 H1' 117.6 122.1
C2' C1' N1 H1' 244.6 237.8
N1 C1' C2' H2' 316.4 322.6
C2 N1 C1' C6 178.3 180.2
C1' N1 C2 O2 1.5 360.0
C1' N1 C2 N3 181.4 180.0
C1' N1 C6 C5 178.6 179.7
C1' N1 C6 H6 358.6 360.0
C1' N1 C2 C6 181.7 179.8
C2 N1 C1' H1' 155.6 59.3
C2 N1 C6 C5 0.1 359.5
C2 N1 C6 H6 180.1 179.7
O2 C2 N1 N3 180.2 180.0
N1 C2 N3 C4 0.3 0.0
C1' N1 C6 C2 178.5 180.2
C6 N1 C1' H1' 337.3 239.1
C6 N1 C2 O2 179.8 180.2
C6 N1 C2 N3 359.6 0.2
C4 C5 C6 N1 0.1 0.5
N1 C6 C5 H5 180.1 180.2
C5 C6 N1 H6 180.0 179.8
O2 C2 N1 C6 179.8 180.2
N1 C2 O2 N3 179.8 180.0
O2 C2 N3 C4 180.2 180.0
N3 C2 N1 C6 359.6 0.2
N1 C2 N3 O2 180.2 180.0
C2 N3 C4 N4 180.0 180.0
C2 N3 C4 C5 360.0 0.0
N4 C4 N3 C5 180.1 180.0
N3 C4 N4 H41N 180.0 0.0
N3 C4 N4 H42N 360.0 180.0
N3 C4 C5 C6 359.8 359.7
N3 C4 C5 H5 179.8 180.0
N3 C4 N4 C5 179.9 180.0
N4 C4 C5 C6 179.8 179.7
N4 C4 C5 H5 359.8 360.0
H41N N4 C4 H42N 180.0 180.0
N1 C6 C5 C4 0.1 0.5
N3 C4 C5 N4 180.1 180.0
C5 C4 N4 H41N 0.1 180.0
C5 C4 N4 H42N 180.1 0.0
C6 C5 C4 H5 180.0 179.7
C4 C5 C6 H6 180.1 180.3
H1B O1B PB O2B 124.9 60.0
H1B O1B PB O3A 239.9 300.0
H2B O2B PB O3A 295.2 180.0
H1A O1A PA O2A 353.7 180.0
H1A O1A PA O5' 227.0 60.0
O5' C5' H5'1 C4' 237.2 239.9
O5' C5' H5'1 H5'2 118.6 120.0
H5'1 C5' C4' O4' 264.7 306.4
H5'1 C5' C4' C3' 21.8 64.5
C4' C5' H5'1 H5'2 241.4 240.0
H5'1 C5' C4' H4' 144.6 185.6
O5' C5' H5'2 C4' 121.9 120.0
O5' C5' H5'2 H5'1 240.9 240.0
H5'2 C5' C4' O4' 143.2 186.5
H5'2 C5' C4' C3' 260.3 304.6
C4' C5' H5'2 H5'1 119.0 120.0
H5'2 C5' C4' H4' 23.1 65.6
C5' C4' H4' O4' 122.1 120.8
C5' C4' H4' C3' 240.8 239.0
H4' C4' C5' H5'1 144.6 185.6
H4' C4' C5' H5'2 23.1 65.6
O4' C4' H4' C3' 118.8 118.2
H4' C4' O4' C1' 211.7 238.7
H4' C4' C3' O3' 359.4 340.0
H4' C4' C3' C2' 122.1 98.2
H4' C4' C3' H3' 242.4 216.6
C4' C3' H3' O3' 120.6 123.4
C4' C3' H3' C2' 242.6 247.0
H3' C3' C4' H4' 242.4 216.6
O3' C3' H3' C2' 121.9 123.6
H3' C3' O3' HA 229.6 303.4
H3' C3' C2' O2' 17.6 33.7
H3' C3' C2' C1' 258.2 275.9
H3' C3' C2' H2' 136.3 157.9
O4' C1' H1' C2' 115.7 115.6
O4' C1' H1' N1 238.6 237.8
C2' C1' H1' N1 122.9 122.2
H1' C1' C2' H2' 208.9 200.4
H1' C1' N1 C2 155.6 59.3
H1' C1' N1 C6 337.3 239.1
HA O3' C3' C2' 349.8 67.1
HA O3' C3' H3' 229.6 303.4
C3' C2' H2' O2' 239.6 235.8
C3' C2' H2' C1' 116.2 111.6
H2' C2' C3' H3' 136.3 157.9
O2' C2' H2' C1' 236.6 235.8
H2' C2' O2' HB 209.5 297.2
H2' C2' C1' N1 316.4 322.6
H2' C2' C1' H1' 208.9 200.4
HB O2' C2' C1' 86.7 173.0
HB O2' C2' H2' 209.5 297.2
H41N N4 C4 C5 0.1 180.0
C4 N4 H41N H42N 180.0 180.0
H42N N4 C4 C5 180.1 0.0
C4 N4 H42N H41N 180.0 180.0
N1 C6 C5 H6 180.0 180.2
C4 C5 C6 H5 180.0 180.3
C4 C5 H5 C6 180.0 179.7
H5 C5 C6 H6 0.1 0.0
N1 C6 H6 C5 180.0 179.8
H6 C6 C5 H5 0.1 0.0