PDB Chemical Component PGN

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 PGN

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
P1 O4P 1.482 1.501
P1 O5P 1.480 1.617
P1 O6P   1.616
P1 O3' 1.612 1.615
O5P HOP5 0.950 0.981
O6P HOP6   0.981
P OP1 1.480 1.501
P OP2 1.481 1.617
P OP3   1.617
P O5' 1.622 1.620
OP2 HOP2 0.950 0.981
OP3 HOP3   0.981
O5' C5' 1.423 1.416
C5' C4' 1.539 1.517
C5' H5' 1.100 1.091
C5' H5'' 1.100 1.091
C4' O4' 1.415 1.436
C4' C3' 1.529 1.519
C4' H4' 1.100 1.097
O4' C1' 1.405 1.439
C3' O3' 1.420 1.413
C3' C2' 1.524 1.513
C3' H3' 1.100 1.097
C2' C1' 1.512 1.524
C2' H2' 1.100 1.095
C2' H2'' 1.100 1.099
C1' N9 1.476 1.464
C1' H1' 1.100 1.094
N9 C8 1.357 1.375
N9 C4 1.378 1.366
C8 N7 1.299 1.319
C8 H8 1.080 1.082
N7 C5 1.392 1.364
C5 C6 1.431 1.437
C5 C4 1.380 1.373
C6 O6 1.229 1.224
C6 N1 1.391 1.402
N1 C2 1.379 1.415
N1 HN1 1.000 1.017
C2 N2 1.333 1.371
C2 N3 1.347 1.315
N2 HN21 1.000 0.993
N2 HN22 1.000 0.994
N3 C4 1.365 1.352

Bond Angles for PGN

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
O4P P1 O5P 118.8 115.2
O4P P1 O6P   115.0
O4P P1 O3' 107.7 115.1
O5P P1 O6P   103.3
O5P P1 O3' 107.8 103.8
P1 O5P HOP5 109.5 118.9
O6P P1 O3'   102.6
P1 O6P HOP6   118.9
P1 O3' C3' 122.1 118.2
OP1 P OP2 119.3 115.3
OP1 P OP3   115.0
OP1 P O5' 108.1 115.0
OP2 P OP3   103.3
OP2 P O5' 109.3 103.7
P OP2 HOP2 109.5 118.9
OP3 P O5'   102.9
P OP3 HOP3   118.9
P O5' C5' 123.8 118.5
O5' C5' C4' 111.8 108.7
O5' C5' H5' 108.2 109.2
O5' C5' H5'' 108.7 109.2
C4' C5' H5' 108.2 110.1
C4' C5' H5'' 108.7 110.1
C5' C4' O4' 111.0 109.7
C5' C4' C3' 113.4 113.6
C5' C4' H4' 105.6 108.6
H5' C5' H5'' 111.3 109.6
O4' C4' C3' 109.5 105.5
O4' C4' H4' 109.8 108.2
C4' O4' C1' 106.5 108.1
C3' C4' H4' 107.2 111.1
C4' C3' O3' 109.7 112.4
C4' C3' C2' 99.7 101.8
C4' C3' H3' 115.7 111.5
O4' C1' C2' 104.5 107.7
O4' C1' N9 112.2 109.4
O4' C1' H1' 113.1 109.1
O3' C3' C2' 110.0 111.3
O3' C3' H3' 106.3 109.4
C2' C3' H3' 115.4 110.2
C3' C2' C1' 100.7 103.2
C3' C2' H2' 114.3 112.8
C3' C2' H2'' 112.5 109.9
C1' C2' H2' 114.3 114.1
C1' C2' H2'' 112.5 110.0
C2' C1' N9 115.0 113.8
C2' C1' H1' 110.1 111.7
H2' C2' H2'' 103.0 106.8
N9 C1' H1' 102.2 105.1
C1' N9 C8 126.2 126.1
C1' N9 C4 128.0 127.3
C8 N9 C4 104.9 106.6
N9 C8 N7 115.5 112.5
N9 C8 H8 122.2 122.0
N9 C4 C5 105.7 104.9
N9 C4 N3 127.5 126.0
N7 C8 H8 122.2 125.5
C8 N7 C5 102.9 103.9
N7 C5 C6 129.8 128.6
N7 C5 C4 110.7 112.1
C6 C5 C4 119.6 119.3
C5 C6 O6 128.3 123.8
C5 C6 N1 112.5 110.7
C5 C4 N3 126.7 129.1
O6 C6 N1 119.2 125.4
C6 N1 C2 124.4 125.3
C6 N1 HN1 117.8 117.4
C2 N1 HN1 117.8 117.4
N1 C2 N2 115.8 115.3
N1 C2 N3 123.5 122.7
N2 C2 N3 120.7 122.0
C2 N2 HN21 125.4 118.3
C2 N2 HN22 109.2 118.3
C2 N3 C4 113.2 113.0
HN21 N2 HN22 125.3 123.4

Torsion Angles for PGN

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
O5P P1 O4P O6P   239.9
O5P P1 O4P O3' 122.8 120.9
O4P P1 O5P HOP5 283.6 48.8
O6P P1 O4P O3'   241.0
O4P P1 O6P HOP6   312.0
O4P P1 O3' C3' 184.1 300.0
O4P P1 O5P O6P   126.3
O4P P1 O5P O3' 237.2 233.2
O6P P1 O5P O3'   106.9
O5P P1 O6P HOP6   78.5
O5P P1 O3' C3' 54.8 173.1
O4P P1 O6P O5P   233.6
O4P P1 O6P O3'   125.8
O5P P1 O6P O3'   252.2
O6P P1 O5P HOP5   282.6
O6P P1 O3' C3'   65.7
O4P P1 O3' O5P 129.3 126.9
O4P P1 O3' O6P   234.3
O5P P1 O3' O6P   107.4
O3' P1 O5P HOP5 46.4 175.7
O3' P1 O6P HOP6   186.2
C4' C3' O3' P1 202.4 173.4
P1 O3' C3' C2' 93.7 60.0
P1 O3' C3' H3' 328.2 297.9
HOP5 O5P P1 O6P   282.6
HOP5 O5P P1 O3' 46.4 175.7
HOP6 O6P P1 O3'   186.2
OP2 P OP1 OP3   239.9
OP2 P OP1 O5' 234.3 120.6
OP1 P OP2 HOP2 335.4 48.8
OP3 P OP1 O5'   240.7
OP1 P OP3 HOP3   311.9
OP1 P O5' C5' 311.7 180.0
OP1 P OP2 OP3   126.3
OP1 P OP2 O5' 125.1 233.4
OP3 P OP2 O5'   107.1
OP2 P OP3 HOP3   78.4
OP2 P O5' C5' 83.1 53.2
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
OP1 P O5' OP2 228.6 126.8
OP1 P O5' OP3   234.2
OP2 P O5' OP3   107.4
O5' P OP2 HOP2 210.3 175.4
O5' P OP3 HOP3   186.1
P O5' C5' C4' 245.5 180.0
P O5' C5' H5' 126.5 300.1
P O5' C5' H5'' 5.5 59.9
HOP2 OP2 P OP3   282.5
HOP2 OP2 P O5' 210.3 175.4
HOP3 OP3 P O5'   186.1
C4' C5' O5' H5' 119.0 239.9
C4' C5' O5' H5'' 240.0 120.1
O5' C5' C4' O4' 300.7 61.8
O5' C5' C4' C3' 64.5 179.5
O5' C5' C4' H4' 181.7 303.7
H5' C5' O5' H5'' 121.0 240.2
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' 236.2 242.2
O4' C4' C5' H4' 119.0 118.0
C5' C4' O4' C1' 135.1 148.9
C3' C4' C5' H4' 242.8 235.8
C5' C4' C3' O3' 138.0 83.6
C5' C4' C3' C2' 253.5 202.8
C5' C4' C3' H3' 17.8 320.3
O5' C5' H5' C4' 121.3 240.7
O5' C5' H5' H5'' 240.6 119.5
C4' C5' H5' H5'' 119.4 238.8
H5' C5' C4' O4' 59.7 302.2
H5' C5' C4' C3' 183.5 60.0
H5' C5' C4' H4' 300.7 184.1
O5' C5' H5'' C4' 238.1 119.2
O5' C5' H5'' H5' 119.0 240.4
C4' C5' H5'' H5' 240.9 121.2
H5'' C5' C4' O4' 180.7 181.3
H5'' C5' C4' C3' 304.5 299.1
H5'' C5' C4' H4' 61.7 63.3
O4' C4' C5' H5' 59.7 302.2
O4' C4' C5' H5'' 180.7 181.3
C5' C4' O4' C3' 126.0 122.8
C5' C4' O4' H4' 243.5 241.7
C3' C4' O4' H4' 117.5 119.0
O4' C4' C3' O3' 262.6 203.8
O4' C4' C3' C2' 18.1 323.0
O4' C4' C3' H3' 142.5 80.5
C4' O4' C1' C2' 326.7 355.4
C4' O4' C1' N9 201.5 231.2
C4' O4' C1' H1' 86.5 116.8
P1 O3' C3' C4' 202.4 173.4
C3' C4' C5' H5' 183.5 60.0
C3' C4' C5' H5'' 304.5 299.1
C5' C4' C3' O4' 235.4 239.8
C5' C4' C3' H4' 116.2 122.8
O4' C4' C3' H4' 240.9 243.0
C3' C4' O4' C1' 9.1 26.2
O3' C3' C4' C2' 244.5 240.8
O3' C3' C4' H3' 120.2 123.3
C2' C3' C4' H3' 235.6 242.5
C4' C3' C2' C1' 324.0 33.0
C4' C3' C2' H2' 201.0 156.6
C4' C3' C2' H2'' 84.0 275.7
H4' C4' C5' H5' 300.7 184.1
H4' C4' C5' H5'' 61.7 63.3
C5' C4' H4' O4' 119.8 119.0
C5' C4' H4' C3' 238.7 234.3
O4' C4' H4' C3' 118.9 115.3
H4' C4' O4' C1' 251.6 267.2
H4' C4' C3' O3' 21.8 320.8
H4' C4' C3' C2' 137.2 80.0
H4' C4' C3' H3' 261.6 197.5
C1' O4' C4' C3' 9.1 26.2
C1' O4' C4' H4' 251.6 267.2
C3' C2' C1' O4' 44.2 341.4
O4' C1' C2' H2' 167.3 218.6
O4' C1' C2' H2'' 284.2 98.6
C2' C1' O4' N9 125.3 124.2
C2' C1' O4' H1' 240.2 238.6
N9 C1' O4' H1' 114.9 114.5
O4' C1' N9 C8 122.9 33.0
O4' C1' N9 C4 290.7 212.9
O3' C3' C4' H4' 21.8 320.8
C4' C3' O3' C2' 108.7 113.4
C4' C3' O3' H3' 234.3 235.5
C2' C3' O3' H3' 125.6 122.1
O3' C3' C2' C1' 79.3 152.9
O3' C3' C2' H2' 316.2 276.6
O3' C3' C2' H2'' 199.3 35.7
C2' C3' C4' H4' 137.2 80.0
C4' C3' C2' O3' 244.7 240.1
C4' C3' C2' H3' 124.6 118.4
O4' C1' C2' C3' 44.2 341.4
O3' C3' C2' H3' 239.8 238.4
C1' C2' C3' H2' 123.0 236.3
C1' C2' C3' H2'' 240.0 117.3
C3' C2' C1' N9 167.7 102.8
C3' C2' C1' H1' 282.4 221.6
H2' C2' C3' H2'' 117.0 240.9
H3' C3' C4' H4' 261.6 197.5
C4' C3' H3' O3' 122.0 125.0
C4' C3' H3' C2' 244.3 247.7
O3' C3' H3' C2' 122.2 122.7
H3' C3' C2' C1' 199.5 274.5
H3' C3' C2' H2' 76.4 38.2
H3' C3' C2' H2'' 319.5 157.3
O4' C1' C2' N9 236.6 238.6
O4' C1' C2' H1' 121.8 119.8
C1' C2' C3' H3' 199.5 274.5
C3' C2' C1' H2' 236.9 122.8
C3' C2' C1' H2'' 120.0 242.8
H2' C2' C1' H2'' 243.1 120.0
N9 C1' C2' H1' 245.3 241.2
C2' C1' N9 C8 3.6 272.5
C2' C1' N9 C4 171.4 92.5
H2' C2' C3' H3' 76.4 38.2
C3' C2' H2' C1' 115.4 242.6
C3' C2' H2' H2'' 237.6 120.9
C1' C2' H2' H2'' 122.3 238.2
H2' C2' C1' N9 290.7 340.0
H2' C2' C1' H1' 45.5 98.8
H2'' C2' C3' H3' 319.5 157.3
C3' C2' H2'' C1' 247.1 112.9
C3' C2' H2'' H2' 123.6 237.3
C1' C2' H2'' H2' 236.5 124.3
H2'' C2' C1' N9 47.7 220.0
H2'' C2' C1' H1' 162.4 338.8
O4' C1' N9 C2' 119.3 120.5
O4' C1' N9 H1' 238.5 242.9
N9 C1' C2' H2' 290.7 340.0
N9 C1' C2' H2'' 47.7 220.0
C2' C1' N9 H1' 119.3 122.5
C8 N9 C1' C4 192.2 180.0
C1' N9 C8 N7 164.9 180.0
C1' N9 C8 H8 344.9 359.9
C1' N9 C4 C5 195.4 180.0
C1' N9 C4 N3 13.5 0.0
O4' C1' H1' C2' 243.5 241.1
O4' C1' H1' N9 120.8 117.2
H1' C1' C2' H2' 45.5 98.8
H1' C1' C2' H2'' 162.4 338.8
C2' C1' H1' N9 237.3 236.1
H1' C1' N9 C8 244.4 150.0
H1' C1' N9 C4 52.1 330.0
C8 N9 C1' H1' 244.4 150.0
C1' N9 C8 C4 170.0 180.0
C8 N9 C4 C5 5.2 360.0
C8 N9 C4 N3 183.3 180.0
N7 C8 N9 H8 180.0 180.1
N9 C8 N7 C5 2.6 360.0
C4 N9 C1' H1' 52.1 330.0
C1' N9 C4 C8 190.2 180.0
C4 N9 C8 N7 354.8 0.0
C4 N9 C8 H8 174.9 180.0
N7 C5 C4 N9 356.0 0.0
C6 C5 C4 N9 175.8 180.0
C5 C4 N9 N3 181.9 180.0
C2 N3 C4 N9 181.6 180.0
N7 C8 N9 C4 354.8 0.0
N9 C8 N7 H8 180.0 179.9
C8 N7 C5 C6 181.2 180.0
C8 N7 C5 C4 1.0 360.0
H8 C8 N9 C4 174.9 180.0
N9 C8 H8 N7 180.0 180.1
H8 C8 N7 C5 182.6 180.1
N9 C4 C5 N7 356.0 0.0
C5 N7 C8 H8 182.6 180.1
C6 C5 N7 C4 180.2 180.0
N7 C5 C6 O6 3.2 360.0
N7 C5 C6 N1 182.6 180.0
N7 C5 C4 N3 177.9 180.0
N9 C4 C5 C6 175.8 180.0
N7 C5 C6 C4 179.8 180.0
C6 C5 C4 N3 357.7 0.0
O6 C6 C5 N1 180.6 180.0
C5 C6 N1 C2 359.1 0.0
C5 C6 N1 HN1 179.1 180.0
N9 C4 C5 N3 178.1 180.0
N7 C5 C4 C6 180.2 180.0
C4 C5 C6 O6 183.5 180.0
C4 C5 C6 N1 2.9 360.0
C2 N3 C4 C5 359.3 360.0
O6 C6 C5 C4 183.5 180.0
C5 C6 O6 N1 179.4 180.0
O6 C6 N1 C2 178.6 180.0
O6 C6 N1 HN1 358.6 360.0
N1 C6 C5 C4 2.9 360.0
C5 C6 N1 O6 180.5 180.0
C2 N1 C6 HN1 180.0 180.0
C6 N1 C2 N2 179.9 180.0
C6 N1 C2 N3 357.8 360.0
C6 N1 C2 HN1 180.0 180.0
N2 C2 N1 N3 182.1 180.0
N1 C2 N2 HN21 0.0 42.6
N1 C2 N2 HN22 180.0 222.6
N1 C2 N3 C4 2.9 0.0
C6 N1 HN1 C2 180.0 180.0
HN1 N1 C2 N2 359.9 0.1
HN1 N1 C2 N3 177.8 180.0
N2 C2 N1 HN1 359.9 0.1
N1 C2 N2 N3 178.0 180.0
N2 C2 N3 C4 180.7 180.0
HN21 N2 C2 HN22 180.0 180.0
N9 C4 N3 C2 181.6 180.0
C5 C4 N3 C2 359.3 360.0
N3 C2 N1 HN1 177.8 180.0
N1 C2 N3 N2 182.2 180.0
N3 C2 N2 HN21 182.1 222.6
N3 C2 N2 HN22 2.0 42.6
HN21 N2 C2 N3 182.1 222.6
C2 N2 HN21 HN22 180.0 180.0
HN22 N2 C2 N3 2.0 42.6
C2 N2 HN22 HN21 180.0 180.0
N9 C4 N3 C5 182.3 180.0