PDB Chemical Component PAP

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 PAP

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
PB O1B 1.483 1.479
PB O2B 1.507 1.610
PB O3B 1.494 1.610
PB O3A 1.692 1.610
O2B HOB2 0.950 0.967
O3B HOB3 0.950 0.967
PA O1A 1.502 1.479
PA O2A 1.510 1.609
PA O3A 1.722 1.610
PA O5' 1.659 1.609
O2A HOA2 0.950 0.967
O5' C5' 1.441 1.428
C5' C4' 1.464 1.529
C5' H5'1 1.116 1.090
C5' H5'2 1.116 1.089
C4' O4' 1.434 1.443
C4' C3' 1.407 1.544
C4' H4' 1.115 1.090
O4' C1' 1.406 1.444
C3' O3' 1.503 1.428
C3' C2' 1.566 1.547
C3' H3' 1.114 1.090
O3' P 1.730 1.610
P O1 1.519 1.480
P O2 1.522 1.609
P O3 1.506 1.610
O2 HO2 0.949 0.967
O3 HO3 0.949 0.966
C2' O2' 1.454 1.428
C2' C1' 1.596 1.543
C2' H2' 1.116 1.090
O2' HO2' 0.950 0.966
C1' N9 1.538 1.466
C1' H1' 1.114 1.090
N9 C8 1.461 1.362
N9 C4 1.391 1.371
C8 N7 1.346 1.301
C8 H8 1.103 1.081
N7 C5 1.445 1.355
C5 C6 1.414 1.406
C5 C4 1.424 1.404
C6 N6 1.273 1.384
C6 N1 1.360 1.329
N6 HN61 1.020 0.970
N6 HN62 1.020 0.970
N1 C2 1.322 1.321
C2 N3 1.353 1.317
C2 H2 1.104 1.081
N3 C4 1.385 1.329

Bond Angles for PAP

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
O1B PB O2B 113.5 109.5
O1B PB O3B 115.1 109.5
O1B PB O3A 114.7 109.4
O2B PB O3B 114.6 109.5
O2B PB O3A 112.4 109.5
PB O2B HOB2 113.5 106.8
O3B PB O3A 83.0 109.5
PB O3B HOB3 115.2 106.8
PB O3A PA 137.8 106.8
O1A PA O2A 115.1 109.5
O1A PA O3A 113.1 109.5
O1A PA O5' 116.4 109.5
O2A PA O3A 112.2 109.4
O2A PA O5' 109.4 109.4
PA O2A HOA2 115.0 106.8
O3A PA O5' 87.6 109.5
PA O5' C5' 114.6 106.8
O5' C5' C4' 109.5 109.5
O5' C5' H5'1 112.3 109.4
O5' C5' H5'2 112.2 109.5
C4' C5' H5'1 112.2 109.5
C4' C5' H5'2 112.2 109.5
C5' C4' O4' 116.3 110.4
C5' C4' C3' 105.6 110.5
C5' C4' H4' 107.1 110.3
H5'1 C5' H5'2 98.2 109.5
O4' C4' C3' 107.8 104.8
O4' C4' H4' 104.7 110.4
C4' O4' C1' 104.8 105.3
C3' C4' H4' 115.7 110.3
C4' C3' O3' 99.8 110.6
C4' C3' C2' 93.4 104.1
C4' C3' H3' 128.7 110.5
O4' C1' C2' 91.7 104.9
O4' C1' N9 98.9 110.3
O4' C1' H1' 135.7 110.3
O3' C3' C2' 120.8 110.5
O3' C3' H3' 105.0 110.5
C3' O3' P 135.8 106.8
C2' C3' H3' 110.3 110.5
C3' C2' O2' 96.6 110.5
C3' C2' C1' 89.7 104.0
C3' C2' H2' 134.0 110.5
O3' P O1 104.0 109.4
O3' P O2 107.3 109.5
O3' P O3 97.2 109.5
O1 P O2 115.0 109.5
O1 P O3 115.7 109.5
O2 P O3 114.9 109.4
P O2 HO2 107.3 106.8
P O3 HO3 97.2 106.8
O2' C2' C1' 124.7 110.8
O2' C2' H2' 104.3 110.4
C2' O2' HO2' 96.6 106.9
C1' C2' H2' 110.0 110.5
C2' C1' N9 131.7 110.4
C2' C1' H1' 105.5 110.5
N9 C1' H1' 99.0 110.3
C1' N9 C8 127.3 126.3
C1' N9 C4 130.1 126.3
C8 N9 C4 102.6 107.4
N9 C8 N7 118.1 110.0
N9 C8 H8 124.9 125.0
N9 C4 C5 106.8 106.0
N9 C4 N3 126.5 134.9
N7 C8 H8 117.0 125.0
C8 N7 C5 98.8 109.4
N7 C5 C6 131.7 134.7
N7 C5 C4 113.8 107.1
C6 C5 C4 114.5 118.2
C5 C6 N6 118.1 120.8
C5 C6 N1 120.9 118.5
C5 C4 N3 126.7 119.1
N6 C6 N1 120.8 120.8
C6 N6 HN61 118.1 119.9
C6 N6 HN62 109.1 120.0
C6 N1 C2 117.0 121.2
HN61 N6 HN62 109.1 120.0
N1 C2 N3 131.7 122.5
N1 C2 H2 112.7 118.7
N3 C2 H2 115.6 118.8
C2 N3 C4 109.2 120.6

Torsion Angles for PAP

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
O2B PB O1B O3B 135.0 120.0
O2B PB O1B O3A 228.9 240.1
O1B PB O2B HOB2 180.1 300.0
O3B PB O1B O3A 93.9 120.0
O1B PB O3B HOB3 180.0 180.0
O1B PB O3A PA 298.0 60.0
O1B PB O2B O3B 224.8 240.0
O1B PB O2B O3A 132.2 119.9
O3B PB O2B O3A 267.4 240.0
O2B PB O3B HOB3 45.5 60.0
O2B PB O3A PA 69.6 180.0
O1B PB O3B O2B 134.5 120.0
O1B PB O3B O3A 246.0 240.0
O2B PB O3B O3A 111.5 120.0
O3B PB O2B HOB2 315.3 60.0
O3B PB O3A PA 183.4 300.0
O1B PB O3A O2B 228.4 240.0
O1B PB O3A O3B 114.5 120.0
O2B PB O3A O3B 246.2 240.0
O3A PB O2B HOB2 47.8 180.0
O3A PB O3B HOB3 294.0 300.0
O1A PA O3A PB 308.2 60.0
O2A PA O3A PB 176.0 300.0
PB O3A PA O5' 66.0 180.0
HOB2 O2B PB O3B 315.3 60.0
HOB2 O2B PB O3A 47.8 180.0
HOB3 O3B PB O3A 294.0 300.0
PB O3A PA O1A 308.2 60.0
O2A PA O1A O3A 130.7 120.0
O2A PA O1A O5' 230.0 240.0
O1A PA O2A HOA2 180.0 180.0
O3A PA O1A O5' 99.3 120.0
O1A PA O5' C5' 162.2 300.0
PB O3A PA O2A 176.0 300.0
O1A PA O2A O3A 228.8 240.0
O1A PA O2A O5' 133.3 120.0
O3A PA O2A O5' 264.5 240.0
O2A PA O5' C5' 294.8 60.0
O1A PA O3A O2A 132.2 120.0
O1A PA O3A O5' 242.2 240.0
O2A PA O3A O5' 110.0 120.0
O3A PA O2A HOA2 311.2 300.0
O3A PA O5' C5' 47.5 180.0
O1A PA O5' O2A 227.4 240.0
O1A PA O5' O3A 114.7 120.0
O2A PA O5' O3A 247.3 240.0
O5' PA O2A HOA2 46.7 60.0
PA O5' C5' C4' 124.7 180.0
PA O5' C5' H5'1 249.9 60.0
PA O5' C5' H5'2 359.4 300.0
HOA2 O2A PA O3A 311.2 300.0
HOA2 O2A PA O5' 46.7 60.0
C4' C5' O5' H5'1 234.7 120.0
C4' C5' O5' H5'2 125.3 240.0
O5' C5' C4' O4' 173.9 61.5
O5' C5' C4' C3' 293.4 177.0
O5' C5' C4' H4' 57.3 299.2
H5'1 C5' O5' H5'2 250.6 120.0
O5' C5' C4' H5'1 125.3 240.1
O5' C5' C4' H5'2 234.7 120.0
H5'1 C5' C4' H5'2 109.4 239.9
O4' C4' C5' C3' 240.5 244.5
O4' C4' C5' H4' 116.7 122.3
C5' C4' O4' C1' 124.8 159.4
C3' C4' C5' H4' 236.2 237.8
C5' C4' C3' O3' 150.0 98.3
C5' C4' C3' C2' 272.1 217.0
C5' C4' C3' H3' 31.7 335.7
O5' C5' H5'1 C4' 236.2 120.0
O5' C5' H5'1 H5'2 118.2 240.0
C4' C5' H5'1 H5'2 241.9 120.0
H5'1 C5' C4' O4' 48.6 181.4
H5'1 C5' C4' C3' 168.1 296.9
H5'1 C5' C4' H4' 292.0 59.2
O5' C5' H5'2 C4' 123.8 240.0
O5' C5' H5'2 H5'1 241.8 119.9
C4' C5' H5'2 H5'1 118.1 239.9
H5'2 C5' C4' O4' 299.2 301.5
H5'2 C5' C4' C3' 58.7 57.0
H5'2 C5' C4' H4' 182.6 179.2
O4' C4' C5' H5'1 48.6 181.4
O4' C4' C5' H5'2 299.2 301.5
C5' C4' O4' C3' 118.3 119.0
C5' C4' O4' H4' 242.0 237.7
C3' C4' O4' H4' 123.8 118.8
O4' C4' C3' O3' 275.0 217.3
O4' C4' C3' C2' 37.1 336.0
O4' C4' C3' H3' 156.6 94.7
C4' O4' C1' C2' 314.3 319.6
C4' O4' C1' N9 181.5 200.7
C4' O4' C1' H1' 68.7 78.5
C3' C4' C5' H5'1 168.1 296.9
C3' C4' C5' H5'2 58.7 57.0
C5' C4' C3' O4' 235.0 241.0
C5' C4' C3' H4' 118.2 122.2
O4' C4' C3' H4' 243.2 241.2
C3' C4' O4' C1' 6.5 40.5
O3' C3' C4' C2' 237.9 241.3
O3' C3' C4' H3' 118.4 122.6
C4' C3' O3' P 226.2 240.0
C2' C3' C4' H3' 240.4 241.4
C4' C3' C2' O2' 173.7 241.1
C4' C3' C2' C1' 298.6 0.1
C4' C3' C2' H2' 56.5 118.6
H4' C4' C5' H5'1 292.0 59.2
H4' C4' C5' H5'2 182.6 179.2
C5' C4' H4' O4' 124.1 122.3
C5' C4' H4' C3' 242.6 237.7
O4' C4' H4' C3' 118.5 115.4
H4' C4' O4' C1' 242.8 281.7
H4' C4' C3' O3' 31.8 336.1
H4' C4' C3' C2' 153.9 94.8
H4' C4' C3' H3' 273.5 213.5
C1' O4' C4' C3' 6.5 40.5
C1' O4' C4' H4' 242.8 281.7
C3' C2' C1' O4' 65.7 23.9
O2' C2' C1' O4' 163.6 142.6
O4' C1' C2' H2' 288.3 265.3
C2' C1' O4' N9 132.8 118.9
C2' C1' O4' H1' 245.6 241.0
N9 C1' O4' H1' 112.8 122.2
O4' C1' N9 C8 264.0 27.0
O4' C1' N9 C4 79.8 207.1
O3' C3' C4' H4' 31.8 336.1
C4' C3' O3' C2' 100.0 114.7
C4' C3' O3' H3' 225.3 237.3
C2' C3' O3' H3' 125.3 122.6
O3' C3' C2' O2' 277.2 359.9
O3' C3' C2' C1' 42.1 118.8
O3' C3' C2' H2' 160.0 237.4
C3' O3' P O1 191.4 60.0
C3' O3' P O2 313.7 180.0
C3' O3' P O3 72.6 300.0
C2' C3' C4' H4' 153.9 94.8
C4' C3' C2' O3' 256.5 241.2
C4' C3' C2' H3' 133.7 118.6
O4' C1' C2' C3' 65.7 23.9
O3' C3' C2' H3' 237.2 237.4
C2' C3' O3' P 126.2 125.3
O2' C2' C3' C1' 235.1 241.1
O2' C2' C3' H2' 117.2 122.5
C3' C2' O2' HO2' 180.1 180.0
C1' C2' C3' H2' 242.1 241.4
C3' C2' C1' N9 169.3 142.7
C3' C2' C1' H1' 287.1 265.0
H3' C3' C4' H4' 273.5 213.5
C4' C3' H3' O3' 116.2 122.7
C4' C3' H3' C2' 247.8 245.4
O3' C3' H3' C2' 131.6 122.6
H3' C3' O3' P 0.9 2.7
H3' C3' C2' O2' 40.0 122.5
H3' C3' C2' C1' 164.9 241.4
H3' C3' C2' H2' 282.9 360.0
P O3' C3' C2' 126.2 125.3
P O3' C3' H3' 0.9 2.7
O1 P O3' O2 237.7 240.0
O1 P O3' O3 118.8 120.0
O2 P O3' O3 241.1 240.0
O3' P O2 HO2 180.0 180.1
O3' P O3 HO3 180.0 300.0
O3' P O1 O2 117.1 120.0
O3' P O1 O3 254.8 240.0
O2 P O1 O3 137.7 120.0
O1 P O2 HO2 295.2 300.0
O1 P O3 HO3 70.7 180.0
O3' P O2 O1 244.8 240.0
O3' P O2 O3 106.8 120.0
O1 P O2 O3 221.9 240.0
O2 P O3 HO3 292.9 60.0
O3' P O3 O1 109.3 119.9
O3' P O3 O2 247.1 240.0
O1 P O3 O2 137.8 120.0
O3 P O2 HO2 73.2 60.1
HO2 O2 P O3 73.2 60.1
O4' C1' C2' O2' 163.6 142.6
O2' C2' C3' H3' 40.0 122.5
C3' C2' O2' C1' 94.2 114.7
C3' C2' O2' H2' 221.4 237.4
C1' C2' O2' H2' 127.2 122.7
O2' C2' C1' N9 267.1 261.5
O2' C2' C1' H1' 24.9 23.7
O4' C1' C2' N9 256.4 241.1
O4' C1' C2' H1' 138.7 118.9
C1' C2' C3' H3' 164.9 241.4
C3' C2' C1' O2' 262.2 241.2
C3' C2' C1' H2' 137.4 118.6
O2' C2' C1' H2' 235.3 237.3
C1' C2' O2' HO2' 85.9 65.3
N9 C1' C2' H1' 242.2 237.8
C2' C1' N9 C8 163.6 271.5
C2' C1' N9 C4 339.4 91.6
H2' C2' C3' H3' 282.9 360.0
C3' C2' H2' O2' 114.2 122.6
C3' C2' H2' C1' 250.0 245.5
O2' C2' H2' C1' 135.8 122.9
H2' C2' O2' HO2' 318.7 302.6
H2' C2' C1' N9 31.9 24.1
H2' C2' C1' H1' 149.6 146.4
HO2' O2' C2' C1' 85.9 65.3
HO2' O2' C2' H2' 318.7 302.6
O4' C1' N9 C2' 100.4 115.5
O4' C1' N9 H1' 220.7 237.8
N9 C1' C2' H2' 31.9 24.1
C2' C1' N9 H1' 120.3 122.3
C8 N9 C1' C4 184.2 180.0
C1' N9 C8 N7 176.3 180.0
C1' N9 C8 H8 356.3 0.0
C1' N9 C4 C5 183.9 180.2
C1' N9 C4 N3 2.6 360.0
O4' C1' H1' C2' 250.9 244.5
O4' C1' H1' N9 112.8 122.2
H1' C1' C2' H2' 149.6 146.4
C2' C1' H1' N9 221.9 237.7
H1' C1' N9 C8 43.2 149.2
H1' C1' N9 C4 219.1 329.2
C8 N9 C1' H1' 43.2 149.2
C1' N9 C8 C4 176.7 180.0
C8 N9 C4 C5 0.5 0.3
C8 N9 C4 N3 179.2 180.0
N7 C8 N9 H8 180.0 180.0
N9 C8 N7 C5 0.1 359.7
C4 N9 C1' H1' 219.1 329.2
C1' N9 C4 C8 183.4 180.0
C4 N9 C8 N7 359.6 360.0
C4 N9 C8 H8 179.6 180.0
N7 C5 C4 N9 359.6 359.6
C6 C5 C4 N9 178.1 180.4
C5 C4 N9 N3 181.2 180.3
C2 N3 C4 N9 182.6 180.0
N7 C8 N9 C4 359.6 360.0
N9 C8 N7 H8 180.0 180.0
C8 N7 C5 C6 181.9 179.5
C8 N7 C5 C4 0.2 0.4
H8 C8 N9 C4 179.6 180.0
N9 C8 H8 N7 180.0 180.0
H8 C8 N7 C5 180.1 179.7
N9 C4 C5 N7 359.6 359.6
C5 N7 C8 H8 180.1 179.7
C6 C5 N7 C4 181.7 179.0
N7 C5 C6 N6 352.7 0.8
N7 C5 C6 N1 177.6 180.4
N7 C5 C4 N3 180.8 179.8
N9 C4 C5 C6 178.1 180.4
N7 C5 C6 C4 178.3 181.1
C6 C5 C4 N3 359.4 0.6
N6 C6 C5 N1 175.1 180.3
C5 C6 N6 HN61 180.0 179.7
C5 C6 N6 HN62 54.8 359.4
C5 C6 N1 C2 1.3 0.4
N9 C4 C5 N3 178.8 179.8
N7 C5 C4 C6 181.4 179.2
C4 C5 C6 N6 174.4 179.7
C4 C5 C6 N1 359.3 359.4
C2 N3 C4 C5 1.1 359.7
N6 C6 C5 C4 174.4 179.7
C5 C6 N6 N1 184.9 179.6
N6 C6 N1 C2 186.4 180.0
HN61 N6 C6 HN62 125.2 180.3
N1 C6 C5 C4 359.3 359.4
C5 C6 N1 N6 174.9 180.3
N1 C6 N6 HN61 355.0 0.1
N1 C6 N6 HN62 229.9 179.8
C6 N1 C2 N3 359.2 359.9
C6 N1 C2 H2 179.2 179.9
HN61 N6 C6 N1 355.0 0.1
C6 N6 HN61 HN62 234.8 179.7
HN62 N6 C6 N1 229.9 179.8
C6 N6 HN62 HN61 130.3 180.3
N3 C2 N1 H2 180.0 180.0
N1 C2 N3 C4 359.6 0.0
N9 C4 N3 C2 182.6 180.0
C5 C4 N3 C2 1.1 359.7
N1 C2 N3 H2 180.0 180.0
N1 C2 H2 N3 180.0 180.0
H2 C2 N3 C4 179.6 180.0
N9 C4 N3 C5 181.5 180.3
C4 N3 C2 H2 179.6 180.0