PDB Chemical Component HDF

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 HDF

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
N1 C2 1.371 1.329
N1 C10 1.382 1.326
C2 O2 1.224 1.218
C2 N3 1.362 1.341
N3 C4 1.381 1.353
N3 HN3 1.020 0.970
C4 O4 1.224 1.216
C4 C4A 1.432 1.471
C4A C5 1.356 1.381
C4A C10 1.390 1.465
C5 C5A 1.349 1.412
C5 H5 1.103 1.080
C5A C6 1.335 1.406
C5A C9A 1.368 1.411
C6 C7 1.346 1.361
C6 H6 1.103 1.080
C7 C8 1.365 1.397
C7 H7 1.103 1.080
C8 O8 1.366 1.356
C8 C9 1.347 1.384
O8 HO8 0.950 0.967
C9 C9A 1.340 1.390
C9 H9 1.103 1.079
C9A N10 1.369 1.380
N10 C10 1.356 1.362
N10 C1' 1.341 1.465
C1' C2' 1.533 1.529
C1' H1'1 1.115 1.090
C1' H1'2 1.115 1.090
C2' O2' 1.416 1.428
C2' C3' 1.557 1.530
C2' H2' 1.115 1.091
O2' HO2' 0.951 0.967
C3' O3' 1.409 1.428
C3' C4' 1.519 1.530
C3' H3' 1.116 1.089
O3' HO3' 0.951 0.967
C4' O4' 1.417 1.428
C4' C5' 1.494 1.530
C4' H4' 1.115 1.090
O4' HO4' 0.950 0.967
C5' O5' 1.430 1.429
C5' H5'1 1.114 1.090
C5' H5'2 1.115 1.088
O5' HO5' 0.949 0.967

Bond Angles for HDF

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
C2 N1 C10 127.7 121.5
N1 C2 O2 123.4 118.0
N1 C2 N3 115.0 124.0
N1 C10 C4A 112.5 118.4
N1 C10 N10 124.7 121.9
O2 C2 N3 121.6 118.0
C2 N3 C4 125.6 121.1
C2 N3 HN3 116.4 119.4
C4 N3 HN3 118.0 119.4
N3 C4 O4 118.4 121.4
N3 C4 C4A 113.9 117.2
O4 C4 C4A 127.7 121.4
C4 C4A C5 115.5 122.3
C4 C4A C10 125.2 117.8
C5 C4A C10 119.2 119.9
C4A C5 C5A 119.7 118.8
C4A C5 H5 120.4 120.6
C4A C10 N10 122.8 119.7
C5A C5 H5 119.9 120.6
C5 C5A C6 118.8 120.0
C5 C5A C9A 119.6 120.2
C6 C5A C9A 121.6 119.8
C5A C6 C7 119.8 120.0
C5A C6 H6 119.6 120.1
C5A C9A C9 118.8 119.3
C5A C9A N10 123.2 120.8
C7 C6 H6 120.5 120.0
C6 C7 C8 118.8 120.5
C6 C7 H7 120.0 119.8
C8 C7 H7 121.3 119.7
C7 C8 O8 119.2 119.7
C7 C8 C9 121.4 120.5
O8 C8 C9 119.0 119.8
C8 O8 HO8 119.2 106.8
C8 C9 C9A 119.6 119.9
C8 C9 H9 120.5 120.0
C9A C9 H9 119.9 120.0
C9 C9A N10 117.9 119.8
C9A N10 C10 115.4 120.4
C9A N10 C1' 122.2 119.7
C10 N10 C1' 117.8 119.8
N10 C1' C2' 120.8 109.5
N10 C1' H1'1 108.2 109.4
N10 C1' H1'2 108.2 109.4
C2' C1' H1'1 108.1 109.5
C2' C1' H1'2 108.1 109.5
C1' C2' O2' 110.9 109.5
C1' C2' C3' 123.6 109.5
C1' C2' H2' 99.4 109.4
H1'1 C1' H1'2 101.8 109.5
O2' C2' C3' 115.9 109.5
O2' C2' H2' 111.9 109.4
C2' O2' HO2' 110.9 106.7
C3' C2' H2' 91.1 109.5
C2' C3' O3' 116.3 109.4
C2' C3' C4' 125.8 109.5
C2' C3' H3' 87.5 109.5
O3' C3' C4' 105.2 109.5
O3' C3' H3' 117.1 109.5
C3' O3' HO3' 116.3 106.8
C4' C3' H3' 103.6 109.5
C3' C4' O4' 111.8 109.5
C3' C4' C5' 122.9 109.5
C3' C4' H4' 97.6 109.5
O4' C4' C5' 111.9 109.4
O4' C4' H4' 113.0 109.5
C4' O4' HO4' 111.8 106.8
C5' C4' H4' 97.4 109.4
C4' C5' O5' 110.0 109.5
C4' C5' H5'1 112.0 109.4
C4' C5' H5'2 112.0 109.5
O5' C5' H5'1 112.0 109.4
O5' C5' H5'2 112.0 109.5
C5' O5' HO5' 110.0 106.8
H5'1 C5' H5'2 98.4 109.5

Torsion Angles for HDF

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
C2 N1 C10 C4A 355.9 0.6
C2 N1 C10 N10 173.5 179.7
O2 C2 N1 N3 176.8 180.0
N1 C2 N3 C4 359.2 360.0
N1 C2 N3 HN3 179.2 180.0
C10 N1 C2 O2 180.5 179.6
C10 N1 C2 N3 3.7 359.7
C4 C4A C10 N1 1.8 359.4
C5 C4A C10 N1 177.8 179.7
C4A C10 N1 N10 182.4 180.9
C9A N10 C10 N1 184.2 180.4
N1 C10 N10 C1' 27.8 0.7
O2 C2 N1 C10 180.5 179.6
N1 C2 O2 N3 183.4 180.0
O2 C2 N3 C4 182.3 180.0
O2 C2 N3 HN3 2.3 0.1
N3 C2 N1 C10 3.7 359.7
N1 C2 N3 O2 176.9 180.0
C4 N3 C2 HN3 180.0 180.0
C2 N3 C4 O4 180.5 180.0
C2 N3 C4 C4A 359.0 0.0
C2 N3 C4 HN3 180.0 180.0
O4 C4 N3 C4A 181.5 180.0
N3 C4 C4A C5 184.3 180.0
N3 C4 C4A C10 0.5 0.3
C2 N3 HN3 C4 180.0 180.0
HN3 N3 C4 O4 0.5 360.0
HN3 N3 C4 C4A 178.9 180.0
O4 C4 N3 HN3 0.5 360.0
N3 C4 O4 C4A 178.2 180.0
O4 C4 C4A C5 2.6 360.0
O4 C4 C4A C10 178.8 180.3
N1 C10 C4A C4 1.8 359.4
C4A C4 N3 HN3 178.9 180.0
N3 C4 C4A O4 181.7 180.0
C5 C4A C4 C10 183.8 179.7
C4 C4A C5 C5A 175.8 180.0
C4 C4A C5 H5 355.8 0.1
C4 C4A C10 N10 184.1 180.3
N1 C10 C4A C5 177.8 179.7
C4 C4A C5 C10 176.4 180.3
C5 C4A C10 N10 0.2 0.6
C5A C5 C4A H5 180.0 179.9
C4A C5 C5A C6 180.4 180.0
C4A C5 C5A C9A 359.2 360.0
N1 C10 C4A N10 177.6 179.1
C4 C4A C10 C5 183.9 179.7
C10 C4A C5 C5A 359.4 359.7
C10 C4A C5 H5 179.4 179.8
C9A N10 C10 C4A 1.5 359.4
C4A C10 N10 C1' 205.1 179.7
C5A C5 C4A C10 359.4 359.7
C4A C5 C5A H5 180.0 180.1
C6 C5A C5 C9A 181.1 180.0
C5 C5A C6 C7 178.0 180.0
C5 C5A C6 H6 358.0 360.0
C5 C5A C9A C9 182.7 180.0
C5 C5A C9A N10 2.7 0.0
H5 C5 C4A C10 179.4 179.8
C4A C5 H5 C5A 180.0 179.9
H5 C5 C5A C6 0.4 359.9
H5 C5 C5A C9A 179.2 179.9
C6 C5A C5 H5 0.4 359.9
C5 C5A C6 C9A 178.8 180.0
C6 C5A C9A C9 1.5 360.0
C6 C5A C9A N10 181.5 180.0
C7 C6 C5A H6 180.0 180.0
C5A C6 C7 C8 359.8 360.0
C5A C6 C7 H7 179.7 180.0
C9A C5A C5 H5 179.2 179.9
C5 C5A C9A C6 181.2 180.0
C9A C5A C6 C7 359.2 360.0
C9A C5A C6 H6 179.2 180.0
C8 C9 C9A C5A 359.0 0.0
C5A C9A C9 H9 179.0 180.0
C9 C9A C5A N10 179.9 180.0
C5A C9A N10 C10 357.0 0.3
C5A C9A N10 C1' 152.3 180.0
C7 C6 C5A C9A 359.2 360.0
C5A C6 C7 H6 180.0 180.0
C8 C7 C6 H7 180.0 180.0
C6 C7 C8 O8 187.5 180.0
C6 C7 C8 C9 0.7 0.0
H6 C6 C5A C9A 179.2 180.0
C5A C6 H6 C7 180.0 180.0
H6 C6 C7 C8 179.8 180.0
H6 C6 C7 H7 359.8 360.0
C8 C7 C6 H6 179.8 180.0
C6 C7 C8 H7 180.0 180.0
O8 C8 C7 C9 186.9 179.9
C7 C8 O8 HO8 180.0 270.0
C7 C8 C9 C9A 0.0 359.9
C7 C8 C9 H9 180.0 180.0
H7 C7 C6 H6 359.8 360.0
C6 C7 H7 C8 180.0 180.0
H7 C7 C8 O8 7.5 360.0
H7 C7 C8 C9 180.7 180.0
O8 C8 C7 H7 7.5 360.0
C7 C8 O8 C9 173.3 180.0
O8 C8 C9 C9A 173.1 180.0
O8 C8 C9 H9 353.1 0.0
C5A C9A C9 C8 359.0 0.0
C9 C8 C7 H7 180.7 180.0
C7 C8 C9 O8 186.9 179.9
C9 C8 O8 HO8 6.7 89.9
C9A C9 C8 H9 180.0 180.0
C8 C9 C9A N10 178.9 180.1
HO8 O8 C8 C9 6.7 89.9
C5A C9A C9 N10 180.1 180.0
C8 C9 C9A H9 180.0 180.0
C9 C9A N10 C10 177.1 180.3
C9 C9A N10 C1' 332.3 360.0
C8 C9 H9 C9A 180.0 180.0
H9 C9 C9A N10 358.9 0.0
N1 C10 N10 C9A 184.2 180.4
C4A C10 N10 C9A 1.5 359.4
C5A C9A N10 C9 179.9 180.0
N10 C9A C9 H9 358.9 0.0
C10 N10 C9A C1' 204.7 180.3
C9A N10 C1' C2' 105.0 90.0
C9A N10 C1' H1'1 230.2 330.0
C9A N10 C1' H1'2 339.7 210.1
N1 C10 N10 C4A 182.7 180.9
C9A N10 C10 C1' 156.4 179.7
C10 N10 C1' C2' 259.7 269.7
C10 N10 C1' H1'1 24.9 149.7
C10 N10 C1' H1'2 134.4 29.8
C9A N10 C1' C10 205.3 180.3
C2' C1' N10 H1'1 234.8 120.0
C2' C1' N10 H1'2 125.3 240.0
N10 C1' C2' O2' 280.8 59.9
N10 C1' C2' C3' 65.2 180.0
N10 C1' C2' H2' 162.9 300.0
H1'1 C1' N10 H1'2 250.5 120.0
N10 C1' C2' H1'1 125.3 240.0
N10 C1' C2' H1'2 234.7 120.0
H1'1 C1' C2' H1'2 109.4 240.0
O2' C2' C1' C3' 215.6 239.9
O2' C2' C1' H2' 117.9 119.9
C1' C2' O2' HO2' 180.0 60.1
C3' C2' C1' H2' 262.3 240.0
C1' C2' C3' O3' 345.2 300.0
C1' C2' C3' C4' 209.4 180.0
C1' C2' C3' H3' 104.3 60.0
N10 C1' H1'1 C2' 227.6 120.0
N10 C1' H1'1 H1'2 113.8 240.1
C2' C1' H1'1 H1'2 246.3 120.0
H1'1 C1' C2' O2' 155.6 179.9
H1'1 C1' C2' C3' 300.0 300.0
H1'1 C1' C2' H2' 37.7 60.0
N10 C1' H1'2 C2' 132.5 240.0
N10 C1' H1'2 H1'1 246.2 119.9
C2' C1' H1'2 H1'1 113.7 240.0
H1'2 C1' C2' O2' 46.2 300.0
H1'2 C1' C2' C3' 190.5 60.0
H1'2 C1' C2' H2' 288.2 180.0
O2' C2' C1' H1'1 155.6 179.9
O2' C2' C1' H1'2 46.2 300.0
C1' C2' O2' C3' 147.4 120.0
C1' C2' O2' H2' 250.0 240.1
C3' C2' O2' H2' 102.6 120.0
O2' C2' C3' O3' 128.0 60.0
O2' C2' C3' C4' 352.2 300.0
O2' C2' C3' H3' 247.1 180.0
C3' C2' C1' H1'1 300.0 300.0
C3' C2' C1' H1'2 190.5 60.0
C1' C2' C3' O2' 217.2 240.0
C1' C2' C3' H2' 102.1 120.0
O2' C2' C3' H2' 244.9 240.0
C3' C2' O2' HO2' 32.7 300.0
O3' C3' C2' C4' 135.8 120.0
O3' C3' C2' H3' 240.9 240.0
C2' C3' O3' HO3' 180.0 300.0
C4' C3' C2' H3' 105.1 120.0
C2' C3' C4' O4' 259.2 60.0
C2' C3' C4' C5' 36.7 180.0
C2' C3' C4' H4' 140.6 299.9
H2' C2' C1' H1'1 37.7 60.0
H2' C2' C1' H1'2 288.2 180.0
C1' C2' H2' O2' 117.1 119.9
C1' C2' H2' C3' 235.7 240.0
O2' C2' H2' C3' 118.6 120.0
H2' C2' O2' HO2' 290.0 180.0
H2' C2' C3' O3' 243.1 180.0
H2' C2' C3' C4' 107.3 60.0
H2' C2' C3' H3' 2.2 300.0
HO2' O2' C2' C3' 32.7 300.0
HO2' O2' C2' H2' 290.0 180.0
O3' C3' C2' H2' 243.1 180.0
C2' C3' O3' C4' 215.9 240.0
C2' C3' O3' H3' 101.5 120.0
C4' C3' O3' H3' 245.6 240.0
O3' C3' C4' O4' 119.6 300.0
O3' C3' C4' C5' 257.0 60.0
O3' C3' C4' H4' 1.0 179.9
C4' C3' C2' H2' 107.3 60.0
C2' C3' C4' O3' 139.6 120.0
C2' C3' C4' H3' 263.1 240.0
O3' C3' C4' H3' 123.5 120.0
C4' C3' O3' HO3' 324.1 60.0
O4' C4' C3' C5' 222.6 240.0
O4' C4' C3' H4' 118.6 120.1
C3' C4' O4' HO4' 180.0 60.0
C5' C4' C3' H4' 256.0 240.0
C3' C4' C5' O5' 172.9 180.0
C3' C4' C5' H5'1 298.1 60.0
C3' C4' C5' H5'2 47.6 300.0
H3' C3' C2' H2' 2.2 300.0
C2' C3' H3' O3' 241.6 240.0
C2' C3' H3' C4' 126.3 120.0
O3' C3' H3' C4' 244.7 240.0
H3' C3' O3' HO3' 78.5 180.0
H3' C3' C4' O4' 356.1 180.0
H3' C3' C4' C5' 133.6 300.0
H3' C3' C4' H4' 237.5 60.0
HO3' O3' C3' C4' 324.1 60.0
HO3' O3' C3' H3' 78.5 180.0
O4' C4' C3' H3' 356.1 180.0
C3' C4' O4' C5' 142.2 120.0
C3' C4' O4' H4' 251.0 240.0
C5' C4' O4' H4' 108.8 120.0
O4' C4' C5' O5' 310.3 300.0
O4' C4' C5' H5'1 75.5 180.0
O4' C4' C5' H5'2 185.0 60.0
C5' C4' C3' H3' 133.6 300.0
C3' C4' C5' O4' 222.6 240.0
C3' C4' C5' H4' 104.1 120.0
O4' C4' C5' H4' 241.5 240.0
C5' C4' O4' HO4' 37.8 300.0
O5' C5' C4' H5'1 234.8 119.9
O5' C5' C4' H5'2 125.3 239.9
C4' C5' O5' HO5' 180.0 180.0
H5'1 C5' C4' H5'2 250.5 120.0
H4' C4' C3' H3' 237.5 60.0
C3' C4' H4' O4' 117.6 120.0
C3' C4' H4' C5' 235.3 240.0
O4' C4' H4' C5' 117.7 120.0
H4' C4' O4' HO4' 289.0 180.0
H4' C4' C5' O5' 68.8 60.0
H4' C4' C5' H5'1 194.1 300.0
H4' C4' C5' H5'2 303.5 180.0
HO4' O4' C4' C5' 37.8 300.0
HO4' O4' C4' H4' 289.0 180.0
O5' C5' C4' H4' 68.8 60.0
C4' C5' O5' H5'1 125.2 240.0
C4' C5' O5' H5'2 234.7 120.1
H5'1 C5' O5' H5'2 109.5 240.0
H5'1 C5' C4' H4' 194.1 300.0
C4' C5' H5'1 O5' 235.8 120.0
C4' C5' H5'1 H5'2 117.9 240.0
O5' C5' H5'1 H5'2 242.1 120.0
H5'1 C5' O5' HO5' 54.7 300.0
H5'2 C5' C4' H4' 303.5 180.0
C4' C5' H5'2 O5' 124.2 239.9
C4' C5' H5'2 H5'1 242.1 120.0
O5' C5' H5'2 H5'1 117.9 240.1
H5'2 C5' O5' HO5' 305.3 59.9
HO5' O5' C5' H5'1 54.7 300.0
HO5' O5' C5' H5'2 305.3 59.9