PDB Chemical Component 4PD

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 4PD

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
P OP1 1.509 1.501
P OP2 1.509 1.618
P O5' 1.627 1.619
P OP3   1.616
OP2 HOP2 0.950 0.981
O5' C5' 1.421 1.418
C5' C4' 1.541 1.523
C5' H5' 1.101 1.092
C5' H5'' 1.100 1.093
C4' O4' 1.443 1.441
C4' C3' 1.534 1.522
C4' H4' 1.100 1.094
O4' C1' 1.435 1.434
C3' O3' 1.424 1.426
C3' C2' 1.516 1.511
C3' H3' 1.101 1.094
O3' HO3' 0.950 0.973
C2' C1' 1.525 1.520
C2' H2' 1.100 1.097
C2' H2'' 1.100 1.095
C1' N1 1.468 1.434
C1' H1' 1.100 1.095
N1 C2 1.407 1.416
N1 C6 1.390 1.388
C2 O2 1.233 1.234
C2 N3 1.383 1.405
N3 C4 1.348 1.362
N3 H19 1.000 1.015
C4 C5 1.455 1.460
C4 N17 1.305 1.304
C5 C6 1.326 1.328
C5 C14 1.421 1.423
C6 H6 1.080 1.084
C14 C15 1.348 1.349
C14 H14 1.080 1.076
C15 C16 1.488 1.488
C15 N17 1.400 1.398
C16 H161 1.100 1.092
C16 H162 1.100 1.092
C16 H163 1.100 1.092
OP3 HOP3   0.981

Bond Angles for 4PD

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
OP1 P OP2 121.3 115.3
OP1 P O5' 107.5 115.0
OP1 P OP3   115.0
OP2 P O5' 108.8 103.7
OP2 P OP3   103.3
P OP2 HOP2 109.5 118.9
O5' P OP3   102.9
P O5' C5' 118.4 118.5
P OP3 HOP3   118.9
O5' C5' C4' 111.9 108.9
O5' C5' H5' 108.1 109.0
O5' C5' H5'' 108.6 108.9
C4' C5' H5' 108.1 110.3
C4' C5' H5'' 108.7 110.3
C5' C4' O4' 110.0 107.9
C5' C4' C3' 115.6 112.9
C5' C4' H4' 104.4 109.5
H5' C5' H5'' 111.4 109.3
O4' C4' C3' 108.1 106.2
O4' C4' H4' 112.4 107.9
C4' O4' C1' 108.8 109.3
C3' C4' H4' 106.5 112.2
C4' C3' O3' 109.8 109.9
C4' C3' C2' 102.6 103.1
C4' C3' H3' 114.1 113.5
O4' C1' C2' 108.3 107.4
O4' C1' N1 109.3 109.3
O4' C1' H1' 112.4 108.0
O3' C3' C2' 110.8 109.7
O3' C3' H3' 106.4 107.4
C3' O3' HO3' 109.5 107.3
C2' C3' H3' 113.2 113.2
C3' C2' C1' 105.1 102.5
C3' C2' H2' 111.9 109.7
C3' C2' H2'' 111.0 114.1
C1' C2' H2' 111.9 110.6
C1' C2' H2'' 110.9 111.7
C2' C1' N1 114.9 112.8
C2' C1' H1' 106.5 111.5
H2' C2' H2'' 106.1 108.3
N1 C1' H1' 105.5 107.8
C1' N1 C2 118.8 118.8
C1' N1 C6 119.4 118.7
C2 N1 C6 121.7 122.5
N1 C2 O2 124.6 124.2
N1 C2 N3 116.2 115.0
N1 C6 C5 120.6 121.0
N1 C6 H6 119.7 116.9
O2 C2 N3 119.2 120.8
C2 N3 C4 123.1 123.8
C2 N3 H19 118.4 118.1
C4 N3 H19 118.5 118.1
N3 C4 C5 118.7 118.1
N3 C4 N17 128.6 129.1
C5 C4 N17 112.7 112.9
C4 C5 C6 119.2 119.6
C4 C5 C14 104.3 103.9
C4 N17 C15 103.5 103.5
C6 C5 C14 136.4 136.5
C5 C6 H6 119.7 122.1
C5 C14 C15 104.7 104.9
C5 C14 H14 127.6 127.1
C15 C14 H14 127.7 128.0
C14 C15 C16 125.8 126.0
C14 C15 N17 114.8 114.9
C16 C15 N17 119.3 119.1
C15 C16 H161 109.5 110.1
C15 C16 H162 109.5 110.1
C15 C16 H163 109.5 110.1
H161 C16 H162 109.5 109.0
H161 C16 H163 109.4 109.0
H162 C16 H163 109.5 108.5

Torsion Angles for 4PD

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
OP2 P OP1 O5' 126.0 120.6
OP2 P OP1 OP3   239.9
OP1 P OP2 HOP2 263.5 48.8
O5' P OP1 OP3   119.3
OP1 P O5' C5' 170.0 179.9
OP1 P OP3 HOP3   312.0
OP1 P OP2 O5' 234.5 233.4
OP1 P OP2 OP3   126.3
O5' P OP2 OP3   252.9
OP2 P O5' C5' 36.9 53.2
OP2 P OP3 HOP3   78.5
OP1 P O5' OP2 133.1 126.8
OP1 P O5' OP3   234.2
OP2 P O5' OP3   107.4
O5' P OP2 HOP2 29.0 175.4
O5' P OP3 HOP3   186.2
P O5' C5' C4' 171.8 180.0
P O5' C5' H5' 52.9 300.4
P O5' C5' H5'' 291.9 59.6
OP1 P OP3 OP2   233.5
OP1 P OP3 O5'   125.8
OP2 P OP3 O5'   252.3
OP3 P OP2 HOP2   282.5
OP3 P O5' C5'   305.8
HOP2 OP2 P O5' 29.0 175.4
HOP2 OP2 P OP3   282.5
C5' O5' P OP3   305.8
C4' C5' O5' H5' 119.0 239.6
C4' C5' O5' H5'' 240.0 120.4
O5' C5' C4' O4' 307.3 62.4
O5' C5' C4' C3' 69.9 179.5
O5' C5' C4' H4' 186.5 305.3
H5' C5' O5' H5'' 121.0 240.8
O5' C5' C4' H5' 241.0 119.6
O5' C5' C4' H5'' 120.0 240.5
H5' C5' C4' H5'' 239.0 120.9
O4' C4' C5' C3' 237.3 242.9
O4' C4' C5' H4' 120.8 117.1
C5' C4' O4' C1' 142.6 108.6
C3' C4' C5' H4' 243.5 234.2
C5' C4' C3' O3' 92.7 154.2
C5' C4' C3' C2' 210.6 271.2
C5' C4' C3' H3' 333.4 34.0
O5' C5' H5' C4' 121.3 240.5
O5' C5' H5' H5'' 240.7 119.0
C4' C5' H5' H5'' 119.3 238.5
H5' C5' C4' O4' 66.2 302.9
H5' C5' C4' C3' 188.9 60.0
H5' C5' C4' H4' 305.4 185.7
O5' C5' H5'' C4' 238.0 119.4
O5' C5' H5'' H5' 119.0 241.0
C4' C5' H5'' H5' 241.0 121.5
H5'' C5' C4' O4' 187.3 181.9
H5'' C5' C4' C3' 310.0 299.0
H5'' C5' C4' H4' 66.5 64.8
O4' C4' C5' H5' 66.2 302.9
O4' C4' C5' H5'' 187.3 181.9
C5' C4' O4' C3' 127.0 121.4
C5' C4' O4' H4' 244.2 241.8
C3' C4' O4' H4' 117.2 120.5
O4' C4' C3' O3' 216.4 272.3
O4' C4' C3' C2' 334.3 29.2
O4' C4' C3' H3' 97.1 152.1
C4' O4' C1' C2' 1.2 351.0
C4' O4' C1' N1 235.3 228.3
C4' O4' C1' H1' 118.6 111.3
C3' C4' C5' H5' 188.9 60.0
C3' C4' C5' H5'' 310.0 299.0
C5' C4' C3' O4' 236.3 241.9
C5' C4' C3' H4' 115.3 124.3
O4' C4' C3' H4' 239.1 242.4
C3' C4' O4' C1' 15.6 347.3
O3' C3' C4' C2' 242.1 243.1
O3' C3' C4' H3' 119.3 120.2
C4' C3' O3' HO3' 10.1 255.2
C2' C3' C4' H3' 237.2 237.2
C4' C3' C2' C1' 25.4 326.6
C4' C3' C2' H2' 263.8 84.1
C4' C3' C2' H2'' 145.4 205.7
H4' C4' C5' H5' 305.4 185.7
H4' C4' C5' H5'' 66.5 64.8
C5' C4' H4' O4' 119.2 117.1
C5' C4' H4' C3' 237.3 233.8
O4' C4' H4' C3' 118.1 116.7
H4' C4' O4' C1' 258.4 226.8
H4' C4' C3' O3' 337.4 29.9
H4' C4' C3' C2' 95.2 146.9
H4' C4' C3' H3' 218.0 269.7
C1' O4' C4' C3' 15.6 347.3
C1' O4' C4' H4' 258.4 226.8
C3' C2' C1' O4' 342.5 26.9
O4' C1' C2' H2' 104.2 270.0
O4' C1' C2' H2'' 222.5 149.4
C2' C1' O4' N1 125.9 122.7
C2' C1' O4' H1' 242.6 239.7
N1 C1' O4' H1' 116.7 117.0
O4' C1' N1 C2 236.8 212.9
O4' C1' N1 C6 55.6 32.9
O3' C3' C4' H4' 337.4 29.9
C4' C3' O3' C2' 112.7 112.7
C4' C3' O3' H3' 236.1 236.1
C2' C3' O3' H3' 123.4 123.4
O3' C3' C2' C1' 142.6 83.6
O3' C3' C2' H2' 21.0 201.1
O3' C3' C2' H2'' 262.6 322.8
C2' C3' C4' H4' 95.2 146.9
C4' C3' C2' O3' 242.8 242.9
C4' C3' C2' H3' 123.4 123.0
O4' C1' C2' C3' 342.5 26.9
O3' C3' C2' H3' 240.6 240.1
C2' C3' O3' HO3' 257.4 142.5
C1' C2' C3' H2' 121.7 242.5
C1' C2' C3' H2'' 240.0 120.8
C3' C2' C1' N1 105.0 147.4
C3' C2' C1' H1' 221.4 268.8
H2' C2' C3' H2'' 118.4 238.3
H3' C3' C4' H4' 218.0 269.7
C4' C3' H3' O3' 121.2 121.7
C4' C3' H3' C2' 243.2 242.9
O3' C3' H3' C2' 121.9 121.3
H3' C3' O3' HO3' 134.0 19.0
H3' C3' C2' C1' 262.0 203.6
H3' C3' C2' H2' 140.3 321.1
H3' C3' C2' H2'' 22.0 82.7
HO3' O3' C3' C2' 257.4 142.5
HO3' O3' C3' H3' 134.0 19.0
O4' C1' C2' N1 237.5 239.5
O4' C1' C2' H1' 121.1 118.1
C1' C2' C3' H3' 262.0 203.6
C3' C2' C1' H2' 238.3 116.9
C3' C2' C1' H2'' 120.0 237.5
H2' C2' C1' H2'' 241.7 120.7
N1 C1' C2' H1' 243.6 238.6
C2' C1' N1 C2 114.8 93.5
C2' C1' N1 C6 293.6 273.5
H2' C2' C3' H3' 140.3 321.1
C3' C2' H2' C1' 117.6 247.7
C3' C2' H2' H2'' 238.8 125.1
C1' C2' H2' H2'' 121.2 237.3
H2' C2' C1' N1 226.7 30.6
H2' C2' C1' H1' 343.0 151.9
H2'' C2' C3' H3' 22.0 82.7
C3' C2' H2'' C1' 243.6 115.6
C3' C2' H2'' H2' 121.8 237.5
C1' C2' H2'' H2' 238.2 122.0
H2'' C2' C1' N1 345.0 269.9
H2'' C2' C1' H1' 101.4 31.3
O4' C1' N1 C2' 122.0 119.4
O4' C1' N1 H1' 238.9 242.9
N1 C1' C2' H2' 226.7 30.6
N1 C1' C2' H2'' 345.0 269.9
C2' C1' N1 H1' 116.9 123.5
C2 N1 C1' C6 181.2 180.0
C1' N1 C2 O2 5.6 360.0
C1' N1 C2 N3 183.9 180.0
C1' N1 C6 C5 180.6 180.0
C1' N1 C6 H6 0.6 0.1
O4' C1' H1' C2' 241.5 242.3
O4' C1' H1' N1 119.0 118.0
H1' C1' C2' H2' 343.0 151.9
H1' C1' C2' H2'' 101.4 31.3
C2' C1' H1' N1 237.5 235.7
H1' C1' N1 C2 357.9 330.0
H1' C1' N1 C6 176.7 150.0
C2 N1 C1' H1' 357.9 330.0
C1' N1 C2 C6 178.7 180.0
C2 N1 C6 C5 359.3 360.0
C2 N1 C6 H6 179.3 180.0
O2 C2 N1 N3 181.7 180.0
N1 C2 N3 C4 353.5 360.0
N1 C2 N3 H19 173.5 180.0
C6 N1 C1' H1' 176.7 150.0
C1' N1 C6 C2 181.3 180.0
C6 N1 C2 O2 186.8 180.0
C6 N1 C2 N3 5.1 0.1
C4 C5 C6 N1 357.4 0.0
N1 C6 C5 C14 178.0 180.0
C5 C6 N1 H6 180.0 179.9
O2 C2 N1 C6 186.8 180.0
N1 C2 O2 N3 178.2 180.0
O2 C2 N3 C4 171.9 180.0
O2 C2 N3 H19 351.9 0.0
N3 C2 N1 C6 5.1 0.1
N1 C2 N3 O2 181.6 180.0
C4 N3 C2 H19 180.0 180.0
C2 N3 C4 C5 3.4 0.0
C2 N3 C4 N17 183.5 180.0
C2 N3 C4 H19 180.0 180.0
C5 C4 N3 N17 179.9 180.1
N3 C4 C5 C6 1.4 360.0
N3 C4 C5 C14 180.9 180.0
N3 C4 N17 C15 179.3 180.0
C2 N3 H19 C4 180.0 180.0
H19 N3 C4 C5 183.5 180.0
H19 N3 C4 N17 3.5 360.0
N1 C6 C5 C4 357.4 0.0
C5 C4 N3 H19 183.5 180.0
N3 C4 C5 N17 180.1 179.9
C5 C4 N17 C15 359.4 359.9
C6 C5 C4 C14 180.5 180.0
C4 C5 C6 H6 177.3 180.0
C4 C5 C14 C15 359.3 0.0
C4 C5 C14 H14 179.3 180.0
N17 C4 N3 H19 3.5 360.0
N3 C4 N17 C5 179.9 180.1
N17 C4 C5 C6 181.3 180.0
N17 C4 C5 C14 0.8 0.0
C14 C15 N17 C4 0.2 0.1
C16 C15 N17 C4 180.4 180.0
N1 C6 C5 H6 180.0 180.1
C6 C5 C4 N17 181.3 180.0
C4 C5 C6 C14 179.4 180.0
C6 C5 C14 C15 178.7 180.0
C6 C5 C14 H14 358.8 0.0
C14 C5 C4 N17 0.8 0.0
C4 C5 C14 C6 180.6 180.0
C14 C5 C6 H6 358.0 360.0
C15 C14 C5 H14 180.0 180.0
C5 C14 C15 C16 180.1 180.1
C5 C14 C15 N17 0.4 359.9
N1 C6 H6 C5 180.0 179.9
H6 C6 C5 C14 358.0 360.0
C4 N17 C15 C14 0.2 0.1
C5 C14 C15 H14 180.0 180.0
C16 C15 C14 N17 179.7 180.1
C14 C15 C16 H161 328.2 317.4
C14 C15 C16 H162 208.2 197.2
C14 C15 C16 H163 88.2 77.5
C5 C14 H14 C15 180.0 180.0
H14 C14 C15 C16 0.1 0.1
H14 C14 C15 N17 180.4 179.9
C4 N17 C15 C16 180.4 180.0
C16 C15 C14 H14 0.1 0.1
C14 C15 C16 N17 180.3 179.9
H161 C16 C15 H162 120.0 120.2
H161 C16 C15 H163 240.1 239.8
H162 C16 C15 H163 120.0 119.6
N17 C15 C14 H14 180.4 179.9
C14 C15 N17 C16 179.8 180.1
N17 C15 C16 H161 148.0 137.5
N17 C15 C16 H162 28.0 17.3
N17 C15 C16 H163 267.9 257.7
H161 C16 C15 N17 148.0 137.5
C15 C16 H161 H162 240.0 239.1
C15 C16 H161 H163 120.0 120.9
H162 C16 H161 H163 240.0 241.8
H162 C16 C15 N17 28.0 17.3
C15 C16 H162 H161 120.0 120.9
C15 C16 H162 H163 240.0 239.4
H161 C16 H162 H163 120.0 118.5
H163 C16 C15 N17 267.9 257.7
C15 C16 H163 H161 240.0 239.2
C15 C16 H163 H162 120.0 120.6
H161 C16 H163 H162 240.0 241.4