PDB Chemical Component PPS

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 PPS

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
S2 OS1   1.630
S2 OS2   1.451
S2 OS3   1.451
S2 O6P   1.634
OS1 HO1   0.986
O6P P2 1.496 1.620
P2 O4P 1.494 1.502
P2 O5P 1.631 1.620
P2 O5' 1.626 1.618
O5P HO5P 0.950 0.980
O5' C5' 1.400 1.417
C5' C4' 1.520 1.517
C5' H5'1 1.115 1.091
C5' H5'2 1.115 1.091
C4' O4' 1.411 1.437
C4' C3' 1.503 1.519
C4' H4' 1.115 1.097
O4' C1' 1.426 1.444
C1' N9 1.463 1.464
C1' C2' 1.520 1.529
C1' H1' 1.115 1.095
N9 C4 1.399 1.367
N9 C8 1.424 1.371
C4 N3 1.314 1.342
C4 C5 1.373 1.385
N3 C2 1.333 1.350
C2 N1 1.319 1.355
C2 H2 1.103 1.085
N1 C6 1.335 1.355
C6 N6 1.341 1.405
C6 C5 1.449 1.392
N6 HN61 1.020 1.002
N6 HN62 1.020 1.003
C5 N7 1.446 1.372
N7 C8 1.349 1.316
C8 H8 1.103 1.082
C2' O2' 1.423 1.426
C2' C3' 1.465 1.517
C2' H2' 1.116 1.095
O2' HO2' 0.951 0.973
C3' O3' 1.419 1.412
C3' H3' 1.115 1.097
O3' P1 1.591 1.614
P1 O1P 1.493 1.617
P1 O2P 1.489 1.617
P1 O3P 1.464 1.500
O1P HO1P 0.950 0.981
O2P HO2P 0.950 0.981

Bond Angles for PPS

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
OS1 S2 OS2   107.5
OS1 S2 OS3   107.4
OS1 S2 O6P   102.6
S2 OS1 HO1   115.3
OS2 S2 OS3   120.6
OS2 S2 O6P   108.9
OS3 S2 O6P   108.4
S2 O6P P2   114.7
O6P P2 O4P 118.8 116.2
O6P P2 O5P 109.2 102.8
O6P P2 O5' 107.8 101.7
O4P P2 O5P 109.1 114.1
O4P P2 O5' 109.5 116.4
O5P P2 O5' 100.9 103.7
P2 O5P HO5P 109.2 119.0
P2 O5' C5' 121.5 118.6
O5' C5' C4' 112.8 108.7
O5' C5' H5'1 111.0 109.1
O5' C5' H5'2 111.0 109.2
C4' C5' H5'1 111.0 110.1
C4' C5' H5'2 111.0 110.1
C5' C4' O4' 114.5 109.8
C5' C4' C3' 111.3 113.5
C5' C4' H4' 103.3 108.7
H5'1 C5' H5'2 99.4 109.6
O4' C4' C3' 104.8 105.2
O4' C4' H4' 110.0 108.3
C4' O4' C1' 107.8 108.3
C3' C4' H4' 113.2 111.2
C4' C3' C2' 100.9 102.2
C4' C3' O3' 102.7 112.2
C4' C3' H3' 120.1 110.2
O4' C1' N9 110.4 109.4
O4' C1' C2' 104.7 107.6
O4' C1' H1' 113.0 108.2
N9 C1' C2' 112.1 113.7
N9 C1' H1' 105.6 105.2
C1' N9 C4 123.5 126.9
C1' N9 C8 130.4 126.1
C2' C1' H1' 111.2 112.6
C1' C2' O2' 120.6 109.3
C1' C2' C3' 97.9 102.9
C1' C2' H2' 111.5 114.0
C4 N9 C8 106.0 107.0
N9 C4 N3 126.4 127.5
N9 C4 C5 108.1 105.2
N9 C8 N7 111.0 112.2
N9 C8 H8 126.8 122.2
N3 C4 C5 125.5 127.2
C4 N3 C2 111.7 110.5
C4 C5 C6 116.5 116.9
C4 C5 N7 109.2 110.8
N3 C2 N1 131.3 128.9
N3 C2 H2 115.0 115.6
N1 C2 H2 113.7 115.5
C2 N1 C6 116.1 117.5
N1 C6 N6 116.3 120.2
N1 C6 C5 118.5 119.1
N6 C6 C5 125.1 120.7
C6 N6 HN61 109.7 119.5
C6 N6 HN62 116.3 119.4
C6 C5 N7 134.2 132.4
HN61 N6 HN62 109.7 120.8
C5 N7 C8 105.2 104.8
N7 C8 H8 122.3 125.6
O2' C2' C3' 112.9 111.2
O2' C2' H2' 96.1 106.9
C2' O2' HO2' 120.6 107.3
C3' C2' H2' 119.4 112.6
C2' C3' O3' 113.3 113.5
C2' C3' H3' 110.6 109.5
O3' C3' H3' 109.1 109.0
C3' O3' P1 119.0 118.1
O3' P1 O1P 103.5 103.8
O3' P1 O2P 106.0 102.6
O3' P1 O3P 100.4 115.2
O1P P1 O2P 115.8 103.3
O1P P1 O3P 114.1 115.3
P1 O1P HO1P 103.5 118.9
O2P P1 O3P 114.8 115.0
P1 O2P HO2P 105.9 118.9

Torsion Angles for PPS

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
OS2 S2 OS1 OS3   228.8
OS2 S2 OS1 O6P   114.7
OS3 S2 OS1 O6P   245.9
OS1 S2 O6P P2   173.7
OS1 S2 OS2 OS3   123.4
OS1 S2 OS2 O6P   249.6
OS2 S2 OS1 HO1   161.5
OS3 S2 OS2 O6P   126.2
OS2 S2 O6P P2   60.0
OS1 S2 OS3 OS2   236.5
OS1 S2 OS3 O6P   110.2
OS3 S2 OS1 HO1   292.7
OS2 S2 OS3 O6P   233.6
OS3 S2 O6P P2   287.1
OS1 S2 O6P OS2   113.7
OS1 S2 O6P OS3   246.6
O6P S2 OS1 HO1   46.9
OS2 S2 O6P OS3   132.9
S2 O6P P2 O4P   300.0
S2 O6P P2 O5P   174.7
S2 O6P P2 O5'   67.4
HO1 OS1 S2 OS2   161.5
HO1 OS1 S2 OS3   292.7
HO1 OS1 S2 O6P   46.9
O4P P2 O6P O5P 125.9 125.3
O4P P2 O6P O5' 234.7 232.5
O5P P2 O6P O5' 108.8 107.2
O6P P2 O5P HO5P 180.0 79.5
O6P P2 O5' C5' 305.1 172.7
O6P P2 O4P O5P 234.0 240.7
O6P P2 O4P O5' 124.4 119.8
O5P P2 O4P O5' 250.4 239.2
O4P P2 O5P HO5P 48.7 312.9
O4P P2 O5' C5' 75.8 300.0
O6P P2 O5P O4P 131.3 126.7
O6P P2 O5P O5' 246.6 254.3
O4P P2 O5P O5' 115.3 127.7
O5P P2 O5' C5' 190.7 66.2
O6P P2 O5' O4P 229.4 232.7
O6P P2 O5' O5P 114.4 106.5
O4P P2 O5' O5P 245.1 233.8
O5' P2 O5P HO5P 293.4 185.2
P2 O5' C5' C4' 204.6 180.0
P2 O5' C5' H5'1 79.3 300.1
P2 O5' C5' H5'2 329.8 59.9
HO5P O5P P2 O5' 293.4 185.2
C4' C5' O5' H5'1 125.3 239.9
C4' C5' O5' H5'2 234.8 120.2
O5' C5' C4' O4' 306.6 62.1
O5' C5' C4' C3' 65.3 179.5
O5' C5' C4' H4' 187.1 303.8
H5'1 C5' O5' H5'2 109.5 240.3
O5' C5' C4' H5'1 234.7 119.5
O5' C5' C4' H5'2 125.2 240.4
H5'1 C5' C4' H5'2 250.5 120.9
O4' C4' C5' C3' 241.3 242.6
O4' C4' C5' H4' 119.6 118.3
C5' C4' O4' C1' 110.2 148.9
C3' C4' C5' H4' 238.2 235.7
C5' C4' C3' C2' 274.2 202.9
C5' C4' C3' O3' 157.1 80.9
C5' C4' C3' H3' 36.0 319.3
O5' C5' H5'1 C4' 126.3 240.8
O5' C5' H5'1 H5'2 243.1 119.5
C4' C5' H5'1 H5'2 116.8 238.7
H5'1 C5' C4' O4' 71.9 302.6
H5'1 C5' C4' C3' 190.5 60.1
H5'1 C5' C4' H4' 312.3 184.3
O5' C5' H5'2 C4' 233.7 119.3
O5' C5' H5'2 H5'1 116.9 240.5
C4' C5' H5'2 H5'1 243.2 121.3
H5'2 C5' C4' O4' 181.4 181.7
H5'2 C5' C4' C3' 300.0 299.1
H5'2 C5' C4' H4' 61.8 63.4
O4' C4' C5' H5'1 71.9 302.6
O4' C4' C5' H5'2 181.4 181.7
C5' C4' O4' C3' 122.3 122.5
C5' C4' O4' H4' 244.3 241.5
C3' C4' O4' H4' 122.0 119.0
O4' C4' C3' C2' 38.5 323.0
O4' C4' C3' O3' 281.4 201.0
O4' C4' C3' H3' 160.3 79.3
C4' O4' C1' N9 221.1 231.0
C4' O4' C1' C2' 341.9 355.0
C4' O4' C1' H1' 103.1 116.9
C3' C4' C5' H5'1 190.5 60.1
C3' C4' C5' H5'2 300.0 299.1
C5' C4' C3' O4' 235.7 239.9
C5' C4' C3' H4' 115.8 122.9
O4' C4' C3' H4' 240.2 243.0
C3' C4' O4' C1' 347.9 26.4
C1' C2' C3' C4' 313.0 32.8
O2' C2' C3' C4' 184.9 275.9
C4' C3' C2' H2' 73.2 156.0
C2' C3' C4' O3' 117.1 121.9
C2' C3' C4' H3' 238.2 243.6
O3' C3' C4' H3' 121.1 121.7
C4' C3' O3' P1 233.7 175.2
H4' C4' C5' H5'1 312.3 184.3
H4' C4' C5' H5'2 61.8 63.4
C5' C4' H4' O4' 122.6 119.3
C5' C4' H4' C3' 239.5 234.4
O4' C4' H4' C3' 116.9 115.1
H4' C4' O4' C1' 225.9 267.4
H4' C4' C3' C2' 158.4 79.9
H4' C4' C3' O3' 41.3 318.0
H4' C4' C3' H3' 280.1 196.3
C1' O4' C4' C3' 347.9 26.4
C1' O4' C4' H4' 225.9 267.4
N9 C1' O4' C2' 239.1 236.0
N9 C1' O4' H1' 118.0 114.1
O4' C1' N9 C4 251.1 213.9
O4' C1' N9 C8 74.4 33.9
C2' C1' O4' H1' 238.8 238.0
O4' C1' C2' O2' 163.7 100.1
O4' C1' C2' C3' 41.1 341.9
O4' C1' C2' H2' 275.1 219.6
O4' C1' N9 C2' 116.3 120.3
O4' C1' N9 H1' 237.6 244.0
C2' C1' N9 H1' 121.3 123.6
N9 C1' C2' O2' 283.4 221.5
N9 C1' C2' C3' 160.8 103.2
N9 C1' C2' H2' 34.8 341.0
C4 N9 C1' C8 176.7 180.0
C1' N9 C4 N3 7.0 360.0
C1' N9 C4 C5 185.4 180.0
C1' N9 C8 N7 170.6 180.0
C1' N9 C8 H8 350.6 360.0
C4' C3' C2' C1' 313.0 32.8
O4' C1' C2' N9 240.3 238.7
O4' C1' C2' H1' 122.3 119.2
N9 C1' C2' H1' 242.0 240.5
C2' C1' N9 C4 134.9 93.6
C2' C1' N9 C8 318.1 273.6
O2' C2' C1' C3' 122.6 118.2
O2' C2' C1' H2' 248.6 240.5
C1' C2' O2' HO2' 180.0 128.0
C3' C2' C1' H2' 126.0 122.2
C1' C2' C3' O3' 62.0 153.8
C1' C2' C3' H3' 184.8 275.9
O4' C1' H1' N9 120.7 116.8
O4' C1' H1' C2' 242.6 241.2
N9 C1' H1' C2' 121.9 124.3
H1' C1' N9 C4 13.5 330.0
H1' C1' N9 C8 196.8 150.0
H1' C1' C2' O2' 41.4 340.9
H1' C1' C2' C3' 278.8 222.7
H1' C1' C2' H2' 152.8 100.5
C4 N9 C1' C2' 134.9 93.6
C4 N9 C1' H1' 13.5 330.0
C1' N9 C4 C8 182.6 180.0
C4 N9 C8 N7 353.4 0.0
C4 N9 C8 H8 173.4 180.0
N3 C4 N9 C5 181.6 180.0
N9 C4 N3 C2 184.0 180.0
N9 C4 C5 C6 180.5 180.0
N9 C4 C5 N7 1.6 0.0
C8 N9 C1' C2' 318.1 273.6
C8 N9 C1' H1' 196.8 150.0
C1' N9 C8 C4 177.2 180.0
C8 N9 C4 N3 184.4 180.0
C8 N9 C4 C5 2.8 360.0
C5 N7 C8 N9 7.3 0.0
N7 C8 N9 H8 180.0 180.0
N3 C4 N9 C8 184.4 180.0
N9 C4 N3 C5 178.2 180.0
N3 C4 C5 C6 359.0 0.0
N3 C4 C5 N7 180.0 180.0
C4 N3 C2 N1 354.0 0.0
C4 N3 C2 H2 174.0 180.1
C5 C4 N9 C8 2.8 360.0
N9 C4 C5 N3 181.5 180.0
C5 C4 N3 C2 5.8 360.0
N1 C6 C5 C4 355.2 360.0
N6 C6 C5 C4 170.8 180.0
C6 C5 C4 N7 179.0 180.0
C4 C5 N7 C8 354.5 360.0
C2 N3 C4 C5 5.8 360.0
N1 C2 N3 H2 180.0 180.0
N3 C2 N1 C6 0.6 360.0
N3 C2 N1 H2 180.0 180.0
C2 N1 C6 N6 189.0 180.0
C2 N1 C6 C5 4.9 0.0
N3 C2 H2 N1 180.0 180.0
H2 C2 N1 C6 180.6 179.9
C4 C5 C6 N1 355.2 360.0
C6 N1 C2 H2 180.6 179.9
N6 C6 N1 C5 184.0 180.0
N1 C6 N6 HN61 54.7 177.9
N1 C6 N6 HN62 180.0 4.2
N1 C6 C5 N7 173.9 179.9
C4 C5 C6 N6 170.8 180.0
N1 C6 N6 C5 175.7 180.0
N6 C6 C5 N7 349.4 359.9
HN61 N6 C6 HN62 234.7 173.8
C4 C5 C6 N7 181.4 180.0
N1 C6 C5 N6 184.4 180.0
C5 C6 N6 HN61 239.1 357.9
C5 C6 N6 HN62 4.3 184.2
C6 C5 N7 C8 175.8 180.0
HN61 N6 C6 C5 239.1 357.9
C6 N6 HN61 HN62 129.0 186.3
HN62 N6 C6 C5 4.3 184.2
C6 N6 HN62 HN61 234.7 173.7
N9 C8 N7 C5 7.3 0.0
C4 C5 N7 C6 178.7 180.0
C5 N7 C8 H8 187.3 180.0
N9 C8 N7 H8 180.0 180.0
N9 C8 H8 N7 180.0 180.0
C4' C3' C2' O2' 184.9 275.9
O2' C2' C1' H1' 41.4 340.9
C1' C2' O2' C3' 244.9 247.1
C1' C2' O2' H2' 119.4 123.8
C3' C2' O2' H2' 234.5 236.7
O2' C2' C3' O3' 294.0 36.9
O2' C2' C3' H3' 56.8 159.0
C2' C3' C4' H4' 158.4 79.9
C4' C3' C2' O3' 251.0 239.0
C4' C3' C2' H3' 128.2 116.9
C3' C2' C1' H1' 278.8 222.7
C1' C2' C3' O2' 128.1 116.8
C1' C2' C3' H2' 239.8 236.8
O2' C2' C3' H2' 111.7 120.0
C3' C2' O2' HO2' 295.1 240.8
O3' C3' C2' H3' 237.2 237.9
C2' C3' O3' P1 125.8 60.0
H2' C2' C1' H1' 152.8 100.5
C1' C2' H2' O2' 233.7 239.2
C1' C2' H2' C3' 113.1 116.7
O2' C2' H2' C3' 239.4 237.5
H2' C2' O2' HO2' 60.6 4.2
H2' C2' C3' O3' 182.2 276.9
H2' C2' C3' H3' 305.0 39.0
HO2' O2' C2' C3' 295.1 240.8
HO2' O2' C2' H2' 60.6 4.2
O3' C3' C4' H4' 41.3 318.0
C4' C3' O3' C2' 107.9 115.2
C4' C3' O3' H3' 231.6 237.6
O3' C3' C2' H2' 182.2 276.9
C2' C3' O3' H3' 123.7 122.4
C3' O3' P1 O1P 20.5 173.0
C3' O3' P1 O2P 142.7 65.7
C3' O3' P1 O3P 262.4 300.0
H3' C3' C4' H4' 280.1 196.3
C4' C3' H3' C2' 243.2 248.3
C4' C3' H3' O3' 117.9 123.5
H3' C3' C2' H2' 305.0 39.0
C2' C3' H3' O3' 234.8 235.3
H3' C3' O3' P1 2.2 297.6
P1 O3' C3' H3' 2.2 297.6
O1P P1 O3' O2P 237.7 107.3
O1P P1 O3' O3P 118.1 233.0
O3' P1 O1P HO1P 180.0 175.8
O2P P1 O3' O3P 240.3 125.7
O3' P1 O2P HO2P 180.0 186.2
O3' P1 O1P O2P 115.4 253.2
O3' P1 O1P O3P 252.0 126.9
O2P P1 O1P O3P 136.5 233.7
O1P P1 O2P HO2P 294.0 78.5
O3' P1 O2P O1P 246.0 107.7
O3' P1 O2P O3P 109.7 234.2
O1P P1 O2P O3P 223.8 126.5
O2P P1 O1P HO1P 64.6 282.5
O3' P1 O3P O1P 110.0 239.1
O3' P1 O3P O2P 246.9 119.0
O1P P1 O3P O2P 137.0 239.9
O3P P1 O1P HO1P 288.1 48.8
O3P P1 O2P HO2P 70.2 312.0
HO1P O1P P1 O2P 64.6 282.5
HO1P O1P P1 O3P 288.1 48.8
HO2P O2P P1 O3P 70.2 312.0