PDB Chemical Component PPW

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 PPW

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
P OP1 1.480 1.501
P OP2 1.483 1.617
P O5' 1.590 1.619
P OP3   1.617
OP2 HOP2 0.950 0.981
O5' C5' 1.421 1.417
N9 C4 1.372 1.364
N9 N8 1.380 1.351
N9 C1' 1.456 1.459
C4 N3 1.349 1.352
C4 C5 1.381 1.374
N3 C2 1.319 1.315
C2 N2 1.336 1.370
C2 N1 1.380 1.414
N2 HN21 1.020 0.993
N2 HN22 1.020 0.994
N1 C6 1.392 1.401
N1 HN1 1.020 1.016
C6 O6 1.238 1.225
C6 C5 1.420 1.437
C5 C7 1.411 1.401
N8 C7 1.307 1.339
C7 H7 1.103 1.081
C2' C1' 1.515 1.522
C2' C3' 1.517 1.512
C2' H2' 1.115 1.097
C2' H2'' 1.115 1.094
C5' C4' 1.510 1.523
C5' H5' 1.115 1.090
C5' H5'' 1.115 1.091
C4' O4' 1.446 1.443
C4' C3' 1.523 1.525
C4' H4' 1.115 1.095
O4' C1' 1.419 1.439
C1' H1' 1.115 1.095
C3' O3' 1.429 1.425
C3' H3' 1.115 1.093
O3' HO3' 0.950 0.969
OP3 HOP3   0.981

Bond Angles for PPW

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
OP1 P OP2 119.6 115.3
OP1 P O5' 107.9 115.0
OP1 P OP3   115.0
OP2 P O5' 108.6 103.7
OP2 P OP3   103.3
P OP2 HOP2 119.6 118.9
O5' P OP3   102.9
P O5' C5' 121.0 118.5
P OP3 HOP3   118.9
O5' C5' C4' 109.9 108.7
O5' C5' H5' 112.1 109.2
O5' C5' H5'' 112.0 109.2
C4 N9 N8 106.8 113.1
C4 N9 C1' 125.6 127.3
N9 C4 N3 125.6 125.1
N9 C4 C5 105.5 106.0
N8 N9 C1' 127.6 119.7
N9 N8 C7 113.3 103.7
N9 C1' C2' 114.8 114.3
N9 C1' O4' 107.2 110.0
N9 C1' H1' 106.4 105.9
N3 C4 C5 128.8 128.9
C4 N3 C2 111.9 113.3
C4 C5 C6 118.8 119.0
C4 C5 C7 110.6 105.1
N3 C2 N2 119.6 122.1
N3 C2 N1 124.0 122.5
N2 C2 N1 116.4 115.4
C2 N2 HN21 108.6 118.3
C2 N2 HN22 119.6 118.3
C2 N1 C6 125.2 125.2
C2 N1 HN1 116.9 117.5
HN21 N2 HN22 108.6 123.4
C6 N1 HN1 117.9 117.4
N1 C6 O6 119.9 125.2
N1 C6 C5 111.3 111.1
O6 C6 C5 128.8 123.8
C6 C5 C7 130.6 135.9
C5 C7 N8 103.8 112.1
C5 C7 H7 130.9 129.0
N8 C7 H7 125.3 118.9
C1' C2' C3' 101.8 101.6
C1' C2' H2' 115.2 110.5
C1' C2' H2'' 115.1 111.7
C2' C1' O4' 106.0 106.7
C2' C1' H1' 107.6 111.7
C3' C2' H2' 115.1 110.0
C3' C2' H2'' 115.1 114.2
C2' C3' C4' 102.7 103.2
C2' C3' O3' 110.4 108.4
C2' C3' H3' 112.9 113.7
H2' C2' H2'' 95.3 108.7
C4' C5' H5' 112.1 110.1
C4' C5' H5'' 112.0 110.1
C5' C4' O4' 109.6 108.0
C5' C4' C3' 114.8 112.7
C5' C4' H4' 104.5 109.4
H5' C5' H5'' 98.4 109.6
O4' C4' C3' 105.5 106.8
O4' C4' H4' 113.9 107.7
C4' O4' C1' 110.2 108.7
C3' C4' H4' 108.7 112.0
C4' C3' O3' 108.5 109.6
C4' C3' H3' 114.7 114.0
O4' C1' H1' 115.1 108.1
O3' C3' H3' 107.6 107.8
C3' O3' HO3' 110.4 106.6

Torsion Angles for PPW

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
OP2 P OP1 O5' 124.6 120.6
OP2 P OP1 OP3   239.9
OP1 P OP2 HOP2 180.0 48.8
O5' P OP1 OP3   119.3
OP1 P O5' C5' 203.6 180.0
OP1 P OP3 HOP3   312.0
OP1 P OP2 O5' 235.7 233.4
OP1 P OP2 OP3   126.3
O5' P OP2 OP3   252.9
OP2 P O5' C5' 72.6 53.2
OP2 P OP3 HOP3   78.5
OP1 P O5' OP2 131.0 126.8
OP1 P O5' OP3   234.2
OP2 P O5' OP3   107.4
O5' P OP2 HOP2 304.4 175.4
O5' P OP3 HOP3   186.1
P O5' C5' C4' 152.9 180.0
P O5' C5' H5' 27.6 300.1
P O5' C5' H5'' 278.1 59.9
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' 304.4 175.4
HOP2 OP2 P OP3   282.5
C5' O5' P OP3   305.8
C4' C5' O5' H5' 125.3 239.9
C4' C5' O5' H5'' 234.8 120.1
O5' C5' C4' O4' 60.1 61.8
O5' C5' C4' C3' 178.6 179.5
O5' C5' C4' H4' 297.6 304.8
H5' C5' O5' H5'' 109.5 240.2
N8 N9 C4 C1' 180.9 180.0
C4 N9 N8 C7 0.5 0.0
C4 N9 C1' C2' 149.6 93.4
C4 N9 C1' O4' 267.1 213.5
C4 N9 C1' H1' 30.7 330.0
N3 C4 N9 C5 180.5 180.0
N9 C4 N3 C2 179.4 180.0
N9 C4 C5 C6 180.4 180.0
N9 C4 C5 C7 0.2 360.0
C4 N9 N8 C1' 179.1 180.0
N8 N9 C4 N3 180.1 180.0
N8 N9 C4 C5 359.6 360.0
N8 N9 C1' C2' 328.5 273.5
N8 N9 C1' O4' 86.0 33.5
N8 N9 C1' H1' 209.7 150.0
C5 C7 N8 N9 359.6 360.0
N9 N8 C7 H7 179.6 180.0
C4 N9 C1' N8 181.1 180.0
C1' N9 C4 N3 359.2 0.0
C1' N9 C4 C5 178.7 180.0
C1' N9 N8 C7 181.5 180.0
N9 C1' C2' C3' 151.3 154.5
N9 C1' C2' H2' 26.1 37.8
N9 C1' C2' H2'' 276.6 276.7
C2' C1' N9 O4' 242.5 240.0
C2' C1' N9 H1' 118.9 123.5
C4' O4' C1' N9 220.1 218.2
O4' C1' N9 H1' 236.4 243.5
N3 C4 N9 N8 180.1 180.0
N3 C4 N9 C1' 359.2 0.0
N9 C4 N3 C5 179.3 180.0
N3 C4 C5 C6 359.9 0.0
N3 C4 C5 C7 179.6 180.0
C4 N3 C2 N2 180.0 180.0
C4 N3 C2 N1 0.0 0.0
C5 C4 N9 N8 359.6 360.0
C5 C4 N9 C1' 178.7 180.0
N9 C4 C5 N3 180.6 180.0
C5 C4 N3 C2 0.1 360.0
N1 C6 C5 C4 0.1 360.0
O6 C6 C5 C4 180.2 180.0
C6 C5 C4 C7 180.3 180.0
C4 C5 C7 N8 0.1 0.0
C4 C5 C7 H7 180.1 180.0
C2 N3 C4 C5 0.1 360.0
N2 C2 N3 N1 180.0 179.9
N3 C2 N2 HN21 54.7 232.7
N3 C2 N2 HN22 180.0 52.8
N3 C2 N1 C6 360.0 360.0
N3 C2 N1 HN1 180.0 179.9
N3 C2 N2 N1 180.0 180.1
N2 C2 N1 C6 180.0 180.0
N2 C2 N1 HN1 0.0 360.0
HN21 N2 C2 HN22 234.8 180.0
N3 C2 N1 N2 180.0 179.9
N1 C2 N2 HN21 234.7 52.7
N1 C2 N2 HN22 360.0 232.7
C6 N1 C2 HN1 180.0 180.0
C2 N1 C6 O6 179.9 180.0
C2 N1 C6 C5 360.0 0.0
HN21 N2 C2 N1 234.7 52.7
C2 N2 HN21 HN22 131.5 180.0
HN22 N2 C2 N1 360.0 232.7
C2 N2 HN22 HN21 234.7 180.0
C4 C5 C6 N1 0.1 360.0
C2 N1 C6 HN1 180.0 180.0
O6 C6 N1 C5 179.9 179.9
N1 C6 C5 C7 180.4 180.0
C2 N1 HN1 C6 180.0 180.0
HN1 N1 C6 O6 359.9 0.0
HN1 N1 C6 C5 180.0 180.1
C4 C5 C6 O6 180.2 180.0
O6 C6 N1 HN1 359.9 0.0
N1 C6 O6 C5 180.1 180.1
O6 C6 C5 C7 0.5 0.0
C4 C5 C6 C7 179.7 180.0
C5 C6 N1 HN1 180.0 180.1
N1 C6 C5 O6 179.9 179.9
C6 C5 C7 N8 179.8 180.0
C6 C5 C7 H7 359.8 360.0
N9 N8 C7 C5 359.6 360.0
C4 C5 C7 C6 180.3 180.0
N8 C7 C5 H7 180.0 180.0
C7 N8 N9 C1' 181.5 180.0
C5 C7 N8 H7 180.0 180.0
C5 C7 H7 N8 180.0 180.0
N9 C1' C2' O4' 118.2 121.8
N9 C1' C2' H1' 241.8 239.7
C3' C2' C1' H2' 125.3 116.7
C3' C2' C1' H2'' 234.8 237.8
C1' C2' C3' C4' 323.8 325.2
C1' C2' C3' O3' 79.3 81.3
C1' C2' C3' H3' 199.8 201.2
H2' C2' C1' H2'' 109.5 121.1
C4' O4' C1' C2' 343.2 342.7
O4' C1' C2' H1' 123.6 117.9
C1' C2' C3' H2' 234.7 243.0
C1' C2' C3' H2'' 125.2 120.4
C3' C2' C1' O4' 33.2 32.7
C3' C2' C1' H1' 269.5 274.8
H2' C2' C3' H2'' 250.5 237.5
C5' C4' C3' C2' 266.4 267.4
O4' C4' C3' C2' 27.2 25.9
C2' C3' C4' H4' 149.8 143.6
C4' C3' C2' O3' 244.5 243.8
C4' C3' C2' H3' 124.1 123.9
O3' C3' C2' H3' 239.6 240.1
C2' C3' O3' HO3' 180.0 294.7
C1' C2' H2' C3' 118.0 111.4
C1' C2' H2' H2'' 239.0 237.1
H2' C2' C1' O4' 267.9 276.0
H2' C2' C1' H1' 144.3 158.1
C3' C2' H2' H2'' 121.0 125.7
H2' C2' C3' C4' 89.1 82.2
H2' C2' C3' O3' 204.6 198.4
H2' C2' C3' H3' 325.1 318.3
C1' C2' H2'' C3' 242.0 245.4
C1' C2' H2'' H2' 121.0 122.1
H2'' C2' C1' O4' 158.4 154.9
H2'' C2' C1' H1' 34.8 37.0
C3' C2' H2'' H2' 239.0 236.7
H2'' C2' C3' C4' 198.6 204.8
H2'' C2' C3' O3' 314.1 320.9
H2'' C2' C3' H3' 74.5 80.8
O5' C5' C4' H5' 234.7 119.6
O5' C5' C4' H5'' 125.2 240.5
C2' C3' C4' C5' 266.4 267.4
H5' C5' C4' H5'' 250.5 120.9
O4' C4' C5' C3' 241.5 242.3
O4' C4' C5' H4' 122.5 117.0
C5' C4' O4' C1' 117.4 116.0
C3' C4' C5' H4' 241.0 234.7
C5' C4' C3' O3' 149.5 152.1
C5' C4' C3' H3' 29.3 31.2
O5' C5' H5' C4' 124.1 240.8
O5' C5' H5' H5'' 242.0 119.6
C4' C5' H5' H5'' 117.9 238.8
H5' C5' C4' O4' 185.4 302.2
H5' C5' C4' C3' 303.9 60.0
H5' C5' C4' H4' 62.9 185.3
O5' C5' H5'' C4' 235.9 119.2
O5' C5' H5'' H5' 118.0 240.4
C4' C5' H5'' H5' 242.0 121.2
H5'' C5' C4' O4' 294.8 181.3
H5'' C5' C4' C3' 53.4 299.1
H5'' C5' C4' H4' 172.4 64.3
N9 C1' O4' C4' 220.1 218.2
C2' C1' O4' C4' 343.2 342.7
C2' C3' C4' O4' 27.2 25.9
O4' C4' C5' H5' 185.4 302.2
O4' C4' C5' H5'' 294.8 181.3
C5' C4' O4' C3' 124.1 121.5
C5' C4' O4' H4' 243.3 242.0
C3' C4' O4' H4' 119.2 120.5
O4' C4' C3' O3' 270.4 270.6
O4' C4' C3' H3' 150.1 149.7
C4' O4' C1' H1' 102.0 103.1
C4' C3' C2' H2' 89.1 82.2
C4' C3' C2' H2'' 198.6 204.8
C2' C3' C4' O3' 116.9 115.3
C2' C3' C4' H3' 237.1 236.3
C3' C4' C5' H5' 303.9 60.0
C3' C4' C5' H5'' 53.4 299.1
C5' C4' C3' O4' 239.2 241.5
C5' C4' C3' H4' 116.6 123.8
O4' C4' C3' H4' 237.5 242.3
C3' C4' O4' C1' 353.3 354.5
O3' C3' C4' H3' 120.3 120.9
C4' C3' O3' HO3' 291.8 46.6
H4' C4' C5' H5' 62.9 185.3
H4' C4' C5' H5'' 172.4 64.3
C5' C4' H4' O4' 119.6 117.2
C5' C4' H4' C3' 237.0 234.3
O4' C4' H4' C3' 117.4 117.2
H4' C4' O4' C1' 234.1 234.0
H4' C4' C3' O3' 32.9 28.3
H4' C4' C3' H3' 272.6 267.4
N9 C1' O4' C2' 236.9 235.5
N9 C1' O4' H1' 118.1 115.2
O4' C1' C2' C3' 33.2 32.7
O4' C1' C2' H2' 267.9 276.0
O4' C1' C2' H2'' 158.4 154.9
C2' C1' O4' H1' 241.2 239.7
C1' O4' C4' C3' 353.3 354.5
C1' O4' C4' H4' 234.1 234.0
N9 C1' H1' C2' 123.5 125.1
N9 C1' H1' O4' 241.4 242.2
H1' C1' C2' C3' 269.5 274.8
H1' C1' C2' H2' 144.3 158.1
H1' C1' C2' H2'' 34.8 37.0
C2' C1' H1' O4' 117.9 117.1
O3' C3' C2' H2' 204.6 198.4
O3' C3' C2' H2'' 314.1 320.9
C2' C3' O3' C4' 248.2 248.1
C2' C3' O3' H3' 123.6 123.5
O3' C3' C4' H4' 32.9 28.3
C4' C3' O3' H3' 235.4 235.4
H3' C3' C2' H2' 325.1 318.3
H3' C3' C2' H2'' 74.5 80.8
C2' C3' H3' C4' 117.2 117.9
C2' C3' H3' O3' 238.0 239.8
H3' C3' C4' H4' 272.6 267.4
C4' C3' H3' O3' 120.8 121.9
H3' C3' O3' HO3' 56.4 171.2
HO3' O3' C3' H3' 56.4 171.2