PDB Chemical Component PGP

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 PGP

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
P1 O4P 1.491 1.480
P1 O5P 1.495 1.610
P1 O6P 1.593 1.610
P1 O3' 1.613 1.610
O5P HOP5 0.951 0.966
O6P HOP6 0.951 0.966
P OP1 1.489 1.479
P OP2 1.488 1.610
P OP3 1.607 1.611
P O5' 1.595 1.610
OP2 HOP2 0.950 0.967
OP3 HOP3 0.950 0.967
O5' C5' 1.429 1.430
C5' C4' 1.512 1.530
C5' H5' 1.114 1.090
C5' H5'' 1.115 1.089
C4' O4' 1.451 1.444
C4' C3' 1.519 1.544
C4' H4' 1.116 1.090
O4' C1' 1.417 1.443
C3' O3' 1.431 1.428
C3' C2' 1.531 1.546
C3' H3' 1.115 1.089
C2' O2' 1.420 1.428
C2' C1' 1.533 1.544
C2' H2' 1.114 1.090
O2' HO2' 0.950 0.966
C1' N9 1.461 1.464
C1' H1' 1.114 1.090
N9 C8 1.375 1.365
N9 C4 1.379 1.368
C8 N7 1.305 1.300
C8 H8 1.103 1.080
N7 C5 1.389 1.356
C5 C6 1.422 1.414
C5 C4 1.377 1.399
C6 O6 1.232 1.219
C6 N1 1.393 1.351
N1 C2 1.371 1.363
N1 HN1 1.019 0.970
C2 N2 1.349 1.373
C2 N3 1.334 1.314
N2 HN21 1.020 0.970
N2 HN22 1.019 0.970
N3 C4 1.353 1.337

Bond Angles for PGP

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
O4P P1 O5P 119.8 109.5
O4P P1 O6P 108.0 109.5
O4P P1 O3' 106.9 109.5
O5P P1 O6P 107.1 109.5
O5P P1 O3' 110.2 109.5
P1 O5P HOP5 119.8 106.8
O6P P1 O3' 103.6 109.5
P1 O6P HOP6 108.0 106.8
P1 O3' C3' 120.0 106.8
OP1 P OP2 119.9 109.5
OP1 P OP3 110.6 109.4
OP1 P O5' 107.6 109.5
OP2 P OP3 104.5 109.5
OP2 P O5' 108.8 109.5
P OP2 HOP2 119.8 106.8
OP3 P O5' 104.4 109.4
P OP3 HOP3 110.6 106.8
P O5' C5' 120.8 106.8
O5' C5' C4' 110.3 109.5
O5' C5' H5' 111.9 109.4
O5' C5' H5'' 111.9 109.4
C4' C5' H5' 111.9 109.5
C4' C5' H5'' 111.9 109.5
C5' C4' O4' 110.6 110.4
C5' C4' C3' 114.9 110.5
C5' C4' H4' 103.5 110.3
H5' C5' H5'' 98.6 109.5
O4' C4' C3' 105.0 104.8
O4' C4' H4' 113.7 110.4
C4' O4' C1' 109.7 105.3
C3' C4' H4' 109.4 110.4
C4' C3' O3' 109.3 110.5
C4' C3' C2' 102.2 104.1
C4' C3' H3' 115.6 110.5
O4' C1' C2' 107.7 104.9
O4' C1' N9 107.7 110.4
O4' C1' H1' 114.2 110.4
O3' C3' C2' 113.3 110.5
O3' C3' H3' 105.0 110.4
C2' C3' H3' 111.7 110.6
C3' C2' O2' 113.3 110.6
C3' C2' C1' 101.7 104.0
C3' C2' H2' 112.0 110.5
O2' C2' C1' 109.2 110.8
O2' C2' H2' 105.0 110.4
C2' O2' HO2' 113.3 106.8
C1' C2' H2' 115.9 110.4
C2' C1' N9 115.7 110.4
C2' C1' H1' 105.9 110.4
N9 C1' H1' 105.9 110.3
C1' N9 C8 126.8 126.3
C1' N9 C4 126.9 126.3
C8 N9 C4 106.3 107.4
N9 C8 N7 113.1 109.9
N9 C8 H8 125.7 125.1
N9 C4 C5 105.3 106.1
N9 C4 N3 126.2 134.2
N7 C8 H8 121.2 125.1
C8 N7 C5 104.4 109.3
N7 C5 C6 130.2 134.1
N7 C5 C4 110.9 107.2
C6 C5 C4 118.9 118.6
C5 C6 O6 128.4 120.9
C5 C6 N1 111.9 118.4
C5 C4 N3 128.5 119.6
O6 C6 N1 119.8 120.8
C6 N1 C2 124.9 120.3
C6 N1 HN1 118.3 119.9
C2 N1 HN1 116.7 119.8
N1 C2 N2 116.1 119.0
N1 C2 N3 123.8 121.9
N2 C2 N3 120.1 119.0
C2 N2 HN21 116.0 120.0
C2 N2 HN22 109.8 120.0
C2 N3 C4 112.0 121.2
HN21 N2 HN22 109.9 120.0

Torsion Angles for PGP

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
O5P P1 O4P O6P 237.1 120.0
O5P P1 O4P O3' 126.2 240.0
O4P P1 O5P HOP5 180.0 300.0
O6P P1 O4P O3' 249.1 120.0
O4P P1 O6P HOP6 180.0 180.0
O4P P1 O3' C3' 159.6 60.0
O4P P1 O5P O6P 123.3 240.0
O4P P1 O5P O3' 235.3 120.0
O6P P1 O5P O3' 112.1 240.0
O5P P1 O6P HOP6 310.3 60.0
O5P P1 O3' C3' 27.8 180.0
O4P P1 O6P O5P 229.7 120.0
O4P P1 O6P O3' 113.1 240.0
O5P P1 O6P O3' 243.5 120.0
O6P P1 O5P HOP5 56.7 60.0
O6P P1 O3' C3' 273.5 300.0
O4P P1 O3' O5P 131.8 240.0
O4P P1 O3' O6P 246.1 120.0
O5P P1 O3' O6P 114.3 240.0
O3' P1 O5P HOP5 304.7 180.0
O3' P1 O6P HOP6 66.8 300.0
C4' C3' O3' P1 215.1 240.0
P1 O3' C3' C2' 101.8 125.3
P1 O3' C3' H3' 339.6 2.6
HOP5 O5P P1 O6P 56.7 60.0
HOP5 O5P P1 O3' 304.7 180.0
HOP6 O6P P1 O3' 66.8 300.0
OP2 P OP1 OP3 238.3 120.0
OP2 P OP1 O5' 124.9 240.0
OP1 P OP2 HOP2 180.0 300.0
OP3 P OP1 O5' 246.6 119.9
OP1 P OP3 HOP3 180.0 180.0
OP1 P O5' C5' 165.7 60.0
OP1 P OP2 OP3 124.6 240.0
OP1 P OP2 O5' 235.7 120.0
OP3 P OP2 O5' 111.1 240.0
OP2 P OP3 HOP3 310.3 60.0
OP2 P O5' C5' 34.4 180.0
OP1 P OP3 OP2 229.7 120.0
OP1 P OP3 O5' 115.4 240.0
OP2 P OP3 O5' 245.7 120.0
OP3 P OP2 HOP2 55.4 60.0
OP3 P O5' C5' 283.2 300.0
OP1 P O5' OP2 131.3 240.0
OP1 P O5' OP3 242.5 119.9
OP2 P O5' OP3 111.2 240.0
O5' P OP2 HOP2 304.3 180.0
O5' P OP3 HOP3 64.6 300.0
P O5' C5' C4' 201.1 180.0
P O5' C5' H5' 326.4 60.0
P O5' C5' H5'' 75.9 300.0
HOP2 OP2 P OP3 55.4 60.0
HOP2 OP2 P O5' 304.3 180.0
HOP3 OP3 P O5' 64.6 300.0
C4' C5' O5' H5' 234.7 120.0
C4' C5' O5' H5'' 125.2 240.0
O5' C5' C4' O4' 288.4 61.5
O5' C5' C4' C3' 47.0 176.9
O5' C5' C4' H4' 166.2 299.3
H5' C5' O5' H5'' 250.5 119.9
O5' C5' C4' H5' 125.3 240.0
O5' C5' C4' H5'' 234.8 120.0
H5' C5' C4' H5'' 109.5 240.0
O4' C4' C5' C3' 241.4 244.6
O4' C4' C5' H4' 122.2 122.2
C5' C4' O4' C1' 145.2 159.5
C3' C4' C5' H4' 240.8 237.6
C5' C4' C3' O3' 83.0 98.4
C5' C4' C3' C2' 203.4 217.0
C5' C4' C3' H3' 324.9 335.8
O5' C5' H5' C4' 235.6 120.0
O5' C5' H5' H5'' 117.8 240.1
C4' C5' H5' H5'' 242.2 120.1
H5' C5' C4' O4' 163.1 181.5
H5' C5' C4' C3' 281.8 296.9
H5' C5' C4' H4' 41.0 59.3
O5' C5' H5'' C4' 124.3 240.0
O5' C5' H5'' H5' 242.2 119.9
C4' C5' H5'' H5' 117.8 239.9
H5'' C5' C4' O4' 53.6 301.5
H5'' C5' C4' C3' 172.3 56.9
H5'' C5' C4' H4' 291.4 179.3
O4' C4' C5' H5' 163.1 181.5
O4' C4' C5' H5'' 53.6 301.5
C5' C4' O4' C3' 124.5 118.9
C5' C4' O4' H4' 244.0 237.8
C3' C4' O4' H4' 119.5 118.9
O4' C4' C3' O3' 204.8 217.2
O4' C4' C3' C2' 325.1 335.9
O4' C4' C3' H3' 86.7 94.7
C4' O4' C1' C2' 2.4 319.5
C4' O4' C1' N9 236.9 200.6
C4' O4' C1' H1' 119.6 78.4
P1 O3' C3' C4' 215.1 240.0
C3' C4' C5' H5' 281.8 296.9
C3' C4' C5' H5'' 172.3 56.9
C5' C4' C3' O4' 238.2 241.1
C5' C4' C3' H4' 115.9 122.3
O4' C4' C3' H4' 237.6 241.2
C3' C4' O4' C1' 20.7 40.6
O3' C3' C4' C2' 239.7 241.3
O3' C3' C4' H3' 118.1 122.6
C2' C3' C4' H3' 238.5 241.2
C4' C3' C2' O2' 278.0 241.2
C4' C3' C2' C1' 35.1 0.2
C4' C3' C2' H2' 159.5 118.6
H4' C4' C5' H5' 41.0 59.3
H4' C4' C5' H5'' 291.4 179.3
C5' C4' H4' O4' 120.1 122.2
C5' C4' H4' C3' 237.0 237.6
O4' C4' H4' C3' 117.0 115.4
H4' C4' O4' C1' 261.2 281.7
H4' C4' C3' O3' 327.2 336.1
H4' C4' C3' C2' 87.5 94.7
H4' C4' C3' H3' 209.0 213.5
C1' O4' C4' C3' 20.7 40.6
C1' O4' C4' H4' 261.2 281.7
C3' C2' C1' O4' 336.1 23.9
O2' C2' C1' O4' 96.0 142.6
O4' C1' C2' H2' 214.3 265.3
C2' C1' O4' N9 125.5 118.9
C2' C1' O4' H1' 242.8 241.1
N9 C1' O4' H1' 117.3 122.2
O4' C1' N9 C8 30.2 27.0
O4' C1' N9 C4 211.9 206.9
O3' C3' C4' H4' 327.2 336.1
C4' C3' O3' C2' 113.3 114.7
C4' C3' O3' H3' 235.4 237.4
C2' C3' O3' H3' 122.2 122.7
O3' C3' C2' O2' 35.5 359.9
O3' C3' C2' C1' 152.6 118.8
O3' C3' C2' H2' 277.0 237.3
C2' C3' C4' H4' 87.5 94.7
C4' C3' C2' O3' 242.5 241.3
C4' C3' C2' H3' 124.1 118.7
O4' C1' C2' C3' 336.1 23.9
O3' C3' C2' H3' 241.6 237.4
O2' C2' C3' C1' 242.9 241.0
O2' C2' C3' H2' 118.5 122.6
C3' C2' O2' HO2' 180.0 180.1
C1' C2' C3' H2' 235.6 241.5
C3' C2' C1' N9 96.6 142.7
C3' C2' C1' H1' 213.6 264.9
H3' C3' C4' H4' 209.0 213.5
C4' C3' H3' O3' 120.5 122.6
C4' C3' H3' C2' 243.7 245.3
O3' C3' H3' C2' 123.2 122.7
H3' C3' C2' O2' 153.9 122.5
H3' C3' C2' C1' 270.9 241.4
H3' C3' C2' H2' 35.3 359.9
O4' C1' C2' O2' 96.0 142.6
O2' C2' C3' H3' 153.9 122.5
C3' C2' O2' C1' 112.6 114.7
C3' C2' O2' H2' 237.5 237.4
C1' C2' O2' H2' 124.9 122.7
O2' C2' C1' N9 216.5 261.5
O2' C2' C1' H1' 333.5 23.7
O4' C1' C2' N9 239.5 241.1
O4' C1' C2' H1' 122.5 118.9
C1' C2' C3' H3' 270.9 241.4
C3' C2' C1' O2' 240.0 241.2
C3' C2' C1' H2' 121.8 118.5
O2' C2' C1' H2' 241.8 237.3
C1' C2' O2' HO2' 67.4 65.3
N9 C1' C2' H1' 243.0 237.8
C2' C1' N9 C8 269.6 271.5
C2' C1' N9 C4 91.3 91.5
H2' C2' C3' H3' 35.3 359.9
C3' C2' H2' O2' 123.3 122.6
C3' C2' H2' C1' 243.9 245.5
O2' C2' H2' C1' 120.5 122.9
H2' C2' O2' HO2' 302.5 302.6
H2' C2' C1' N9 334.8 24.2
H2' C2' C1' H1' 91.8 146.4
HO2' O2' C2' C1' 67.4 65.3
HO2' O2' C2' H2' 302.5 302.6
O4' C1' N9 C2' 120.5 115.5
O4' C1' N9 H1' 237.5 237.7
N9 C1' C2' H2' 334.8 24.2
C2' C1' N9 H1' 116.9 122.2
C8 N9 C1' C4 178.3 180.1
C1' N9 C8 N7 182.4 180.0
C1' N9 C8 H8 2.3 0.0
C1' N9 C4 C5 177.6 180.0
C1' N9 C4 N3 358.9 0.1
O4' C1' H1' C2' 241.7 244.5
O4' C1' H1' N9 118.3 122.2
H1' C1' C2' H2' 91.8 146.4
C2' C1' H1' N9 236.6 237.8
H1' C1' N9 C8 152.7 149.3
H1' C1' N9 C4 334.4 329.2
C8 N9 C1' H1' 152.7 149.3
C1' N9 C8 C4 181.4 179.9
C8 N9 C4 C5 359.0 360.0
C8 N9 C4 N3 180.3 180.1
N7 C8 N9 H8 180.1 180.0
N9 C8 N7 C5 359.5 360.0
C4 N9 C1' H1' 334.4 329.2
C1' N9 C4 C8 178.6 180.1
C4 N9 C8 N7 1.0 0.0
C4 N9 C8 H8 180.9 180.1
N7 C5 C4 N9 0.7 0.0
C6 C5 C4 N9 181.4 180.1
C5 C4 N9 N3 178.7 179.9
C2 N3 C4 N9 177.8 179.9
N7 C8 N9 C4 1.0 0.0
N9 C8 N7 H8 179.9 180.0
C8 N7 C5 C6 179.1 179.9
C8 N7 C5 C4 359.8 360.0
H8 C8 N9 C4 180.9 180.1
N9 C8 H8 N7 180.1 180.0
H8 C8 N7 C5 179.6 180.0
N9 C4 C5 N7 0.7 0.0
C5 N7 C8 H8 179.6 180.0
C6 C5 N7 C4 179.3 180.0
N7 C5 C6 O6 1.2 0.1
N7 C5 C6 N1 181.2 179.7
N7 C5 C4 N3 179.4 180.0
N9 C4 C5 C6 181.4 180.1
N7 C5 C6 C4 180.8 180.0
C6 C5 C4 N3 0.1 360.0
O6 C6 C5 N1 180.0 180.3
C5 C6 N1 C2 359.7 0.6
C5 C6 N1 HN1 179.7 180.0
N9 C4 C5 N3 181.3 180.1
N7 C5 C4 C6 179.4 180.0
C4 C5 C6 O6 180.4 180.0
C4 C5 C6 N1 0.4 359.7
C2 N3 C4 C5 359.3 0.0
O6 C6 C5 C4 180.4 180.0
C5 C6 O6 N1 180.0 179.7
O6 C6 N1 C2 179.7 180.3
O6 C6 N1 HN1 359.7 359.7
N1 C6 C5 C4 0.4 359.7
C5 C6 N1 O6 180.0 180.3
C2 N1 C6 HN1 180.1 180.6
C6 N1 C2 N2 179.4 179.7
C6 N1 C2 N3 359.6 359.3
C6 N1 C2 HN1 179.9 179.4
N2 C2 N1 N3 179.7 180.4
N1 C2 N2 HN21 180.1 179.6
N1 C2 N2 HN22 54.7 359.4
N1 C2 N3 C4 0.8 0.3
C6 N1 HN1 C2 180.1 180.6
HN1 N1 C2 N2 359.4 0.3
HN1 N1 C2 N3 179.7 179.9
N2 C2 N1 HN1 359.4 0.3
N1 C2 N2 N3 180.3 179.6
N2 C2 N3 C4 181.1 180.0
HN21 N2 C2 HN22 125.3 180.2
N9 C4 N3 C2 177.8 179.9
C5 C4 N3 C2 359.3 0.0
N3 C2 N1 HN1 179.7 179.9
N1 C2 N3 N2 179.7 180.4
N3 C2 N2 HN21 359.8 360.0
N3 C2 N2 HN22 234.4 179.8
HN21 N2 C2 N3 359.8 360.0
C2 N2 HN21 HN22 234.7 179.8
HN22 N2 C2 N3 234.4 179.8
C2 N2 HN22 HN21 128.8 180.2
N9 C4 N3 C5 178.4 179.9