PDB Chemical Component GPX

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 GPX

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
P1 O11 1.480 1.611
P1 O21 1.483 1.479
P1 O3' 1.622 1.632
P1 O2' 1.611 1.631
N9 C8 1.361 1.365
N9 C4 1.393 1.368
N9 C1' 1.381 1.464
C8 N7 1.302 1.301
C8 H8 1.104 1.080
N7 C5 1.402 1.356
C5 C6 1.375 1.415
C5 C4 1.363 1.399
C6 O6 1.233 1.219
C6 N1 1.381 1.351
N1 C2 1.372 1.363
N1 HN1 1.020 0.970
C2 N2 1.330 1.372
C2 N3 1.310 1.314
N2 HN21 1.019 0.970
N2 HN22 1.020 0.970
N3 C4 1.326 1.338
O11 HO1 0.951 0.967
O3' C3' 1.417 1.439
PA O1A 1.481 1.479
PA O2A 1.476 1.610
PA O3A 1.617 1.610
PA O5' 1.618 1.610
O2A HOA2 0.950 0.967
O3A PB 1.603 1.610
O5' C5' 1.479 1.428
PB O1B 1.490 1.479
PB O2B 1.478 1.610
PB O3B 1.479 1.609
O2B HOB2 0.950 0.967
O3B HOB3 0.950 0.966
C5' C4' 1.571 1.529
C5' H5'1 1.115 1.090
C5' H5'2 1.116 1.090
C4' O4' 1.411 1.444
C4' C3' 1.488 1.544
C4' H4' 1.115 1.090
O4' C1' 1.415 1.444
C1' C2' 1.516 1.544
C1' H1' 1.114 1.090
C2' O2' 1.437 1.449
C2' C3' 1.527 1.545
C2' H2' 1.116 1.090
C3' H3' 1.116 1.090

Bond Angles for GPX

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
O11 P1 O21 109.2 112.3
O11 P1 O3' 112.6 110.8
O11 P1 O2' 107.3 110.9
P1 O11 HO1 109.2 106.8
O21 P1 O3' 110.6 110.9
O21 P1 O2' 111.0 110.9
O3' P1 O2' 106.1 100.5
P1 O3' C3' 102.2 103.3
P1 O2' C2' 104.5 103.4
C8 N9 C4 103.5 107.5
C8 N9 C1' 128.6 126.2
N9 C8 N7 116.2 109.8
N9 C8 H8 124.0 125.1
C4 N9 C1' 127.4 126.3
N9 C4 C5 107.2 106.1
N9 C4 N3 125.0 134.2
N9 C1' O4' 104.9 110.4
N9 C1' C2' 116.2 110.4
N9 C1' H1' 106.5 110.3
N7 C8 H8 119.9 125.1
C8 N7 C5 102.9 109.3
N7 C5 C6 129.7 134.1
N7 C5 C4 110.2 107.3
C6 C5 C4 120.0 118.6
C5 C6 O6 128.6 120.9
C5 C6 N1 112.5 118.4
C5 C4 N3 127.8 119.6
O6 C6 N1 118.9 120.7
C6 N1 C2 123.2 120.3
C6 N1 HN1 118.7 119.9
C2 N1 HN1 118.1 119.8
N1 C2 N2 118.3 119.0
N1 C2 N3 124.2 121.9
N2 C2 N3 117.5 119.1
C2 N2 HN21 118.2 120.0
C2 N2 HN22 109.0 120.0
C2 N3 C4 112.3 121.2
HN21 N2 HN22 109.1 120.0
O3' C3' C4' 117.5 108.8
O3' C3' C2' 112.4 110.0
O3' C3' H3' 99.3 111.2
O1A PA O2A 109.4 109.4
O1A PA O3A 113.8 109.4
O1A PA O5' 115.6 109.5
O2A PA O3A 108.4 109.5
O2A PA O5' 107.2 109.5
PA O2A HOA2 109.4 106.8
O3A PA O5' 101.9 109.5
PA O3A PB 126.8 106.8
PA O5' C5' 107.4 106.8
O3A PB O1B 115.8 109.4
O3A PB O2B 107.2 109.5
O3A PB O3B 105.5 109.5
O5' C5' C4' 115.2 109.5
O5' C5' H5'1 110.1 109.4
O5' C5' H5'2 110.1 109.5
O1B PB O2B 109.6 109.5
O1B PB O3B 108.7 109.5
O2B PB O3B 109.9 109.4
PB O2B HOB2 107.1 106.8
PB O3B HOB3 105.5 106.8
C4' C5' H5'1 110.1 109.5
C4' C5' H5'2 110.1 109.5
C5' C4' O4' 112.6 110.4
C5' C4' C3' 109.8 110.5
C5' C4' H4' 105.8 110.3
H5'1 C5' H5'2 100.1 109.4
O4' C4' C3' 105.2 104.8
O4' C4' H4' 110.4 110.4
C4' O4' C1' 111.7 105.3
C3' C4' H4' 113.2 110.4
C4' C3' C2' 100.5 104.1
C4' C3' H3' 111.4 111.2
O4' C1' C2' 104.0 104.8
O4' C1' H1' 118.3 110.4
C2' C1' H1' 107.4 110.3
C1' C2' O2' 112.2 109.0
C1' C2' C3' 102.1 104.1
C1' C2' H2' 111.6 111.0
O2' C2' C3' 106.6 109.0
O2' C2' H2' 107.5 111.1
C3' C2' H2' 116.8 112.3
C2' C3' H3' 116.6 111.3

Torsion Angles for GPX

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
O21 P1 O11 O3' 236.8 235.3
O21 P1 O11 O2' 120.4 124.7
O3' P1 O11 O2' 243.6 249.4
O11 P1 O3' C3' 111.4 82.5
O11 P1 O2' C2' 227.2 277.9
O11 P1 O21 O3' 124.4 124.6
O11 P1 O21 O2' 241.9 235.4
O21 P1 O11 HO1 180.0 55.4
O3' P1 O21 O2' 117.5 110.8
O21 P1 O3' C3' 233.8 207.9
O21 P1 O2' C2' 107.9 152.4
O11 P1 O3' O21 237.6 234.6
O11 P1 O3' O2' 117.1 117.2
O3' P1 O11 HO1 303.2 180.0
O21 P1 O3' O2' 239.5 242.6
O3' P1 O2' C2' 347.7 35.0
P1 O3' C3' C4' 137.5 136.0
P1 O3' C3' C2' 21.6 22.5
P1 O3' C3' H3' 257.6 258.8
O11 P1 O2' O21 119.2 125.4
O11 P1 O2' O3' 239.4 242.8
O2' P1 O11 HO1 59.5 290.7
O21 P1 O2' O3' 120.2 117.4
O2' P1 O3' C3' 354.3 325.3
C1' C2' O2' P1 273.6 223.9
P1 O2' C2' C3' 24.6 336.9
P1 O2' C2' H2' 150.5 101.2
C4 N9 C8 C1' 172.3 180.0
C8 N9 C4 C5 0.2 360.0
C8 N9 C4 N3 180.4 180.0
C8 N9 C1' O4' 55.3 27.0
C8 N9 C1' C2' 301.1 271.5
C8 N9 C1' H1' 181.5 149.3
N7 C8 N9 H8 180.0 179.9
N9 C8 N7 C5 0.2 0.0
C8 N9 C4 C1' 187.6 180.0
C4 N9 C8 N7 359.8 360.0
C4 N9 C8 H8 179.8 180.1
C4 N9 C1' O4' 244.7 207.0
C4 N9 C1' C2' 130.5 91.5
C4 N9 C1' H1' 10.9 329.3
N7 C5 C4 N9 359.9 0.0
C6 C5 C4 N9 179.9 180.0
C5 C4 N9 N3 179.8 180.0
C2 N3 C4 N9 180.4 180.0
C8 N9 C1' C4 170.6 180.0
C1' N9 C8 N7 187.4 180.0
C1' N9 C8 H8 7.5 0.1
C1' N9 C4 C5 172.6 180.0
C1' N9 C4 N3 352.8 0.0
C4' O4' C1' N9 229.4 200.7
O4' C1' N9 C2' 114.2 115.5
O4' C1' N9 H1' 233.8 237.7
C2' C1' N9 H1' 119.6 122.2
N9 C1' C2' O2' 258.3 258.9
N9 C1' C2' C3' 144.6 142.7
N9 C1' C2' H2' 19.1 21.7
N7 C8 N9 C4 359.8 360.0
N7 C8 N9 C1' 187.4 180.0
N9 C8 N7 H8 180.0 180.1
C8 N7 C5 C6 180.0 180.0
C8 N7 C5 C4 359.9 359.9
H8 C8 N9 C4 179.8 180.1
H8 C8 N9 C1' 7.5 0.1
N9 C8 H8 N7 180.0 179.9
H8 C8 N7 C5 180.2 180.0
N9 C4 C5 N7 359.9 0.0
C5 N7 C8 H8 180.2 180.0
C6 C5 N7 C4 180.0 180.1
N7 C5 C6 O6 0.8 360.0
N7 C5 C6 N1 179.8 179.7
N7 C5 C4 N3 179.7 180.0
N9 C4 C5 C6 179.9 180.0
N7 C5 C6 C4 180.0 179.9
C6 C5 C4 N3 359.7 360.0
O6 C6 C5 N1 181.0 180.3
C5 C6 N1 C2 0.3 0.6
C5 C6 N1 HN1 180.3 179.9
C5 C4 N9 C1' 172.6 180.0
N9 C4 C5 N3 180.2 180.0
N7 C5 C4 C6 180.0 180.1
C4 C5 C6 O6 180.8 180.0
C4 C5 C6 N1 359.8 359.7
C2 N3 C4 C5 0.7 0.0
O6 C6 C5 C4 180.8 180.0
C5 C6 O6 N1 179.0 179.7
O6 C6 N1 C2 179.4 180.3
O6 C6 N1 HN1 359.4 359.6
N1 C6 C5 C4 359.8 359.7
C5 C6 N1 O6 180.9 180.3
C2 N1 C6 HN1 180.0 180.6
C6 N1 C2 N2 180.7 179.7
C6 N1 C2 N3 0.1 359.4
C6 N1 C2 HN1 180.0 179.4
N2 C2 N1 N3 180.6 180.2
N1 C2 N2 HN21 180.0 179.8
N1 C2 N2 HN22 54.7 359.4
N1 C2 N3 C4 359.4 0.3
C6 N1 HN1 C2 180.0 180.6
HN1 N1 C2 N2 0.7 0.3
HN1 N1 C2 N3 180.1 180.0
N2 C2 N1 HN1 0.7 0.3
N1 C2 N2 N3 179.5 179.8
N2 C2 N3 C4 178.9 180.0
HN21 N2 C2 HN22 125.2 180.4
N9 C4 N3 C2 180.4 180.0
C5 C4 N3 C2 0.7 0.0
N3 C2 N1 HN1 180.1 180.0
N1 C2 N3 N2 180.6 180.2
N3 C2 N2 HN21 0.5 0.0
N3 C2 N2 HN22 235.3 179.7
HN21 N2 C2 N3 0.5 0.0
C2 N2 HN21 HN22 234.8 179.6
HN22 N2 C2 N3 235.3 179.7
C2 N2 HN22 HN21 130.4 180.4
N3 C4 N9 C1' 352.8 0.0
N9 C4 N3 C5 179.7 179.9
HO1 O11 P1 O21 180.0 55.4
HO1 O11 P1 O3' 303.2 180.0
HO1 O11 P1 O2' 59.5 290.7
C3' O3' P1 O2' 354.3 325.3
C5' C4' C3' O3' 151.8 99.8
O4' C4' C3' O3' 273.2 218.7
O3' C3' C4' H4' 33.8 337.5
C4' C3' O3' C2' 115.9 113.4
C4' C3' O3' H3' 239.8 237.2
C1' C2' C3' O3' 86.2 116.6
O2' C2' C3' O3' 328.4 0.4
O3' C3' C2' H2' 208.3 236.8
C2' C3' O3' H3' 124.0 123.7
O2A PA O1A O3A 238.6 240.0
O2A PA O1A O5' 121.2 120.0
O1A PA O2A HOA2 180.0 179.9
O3A PA O1A O5' 242.6 240.0
O1A PA O3A PB 30.8 300.0
O1A PA O5' C5' 155.9 60.0
O1A PA O2A O3A 124.6 119.9
O1A PA O2A O5' 233.9 240.0
O3A PA O2A O5' 109.3 120.0
O2A PA O3A PB 152.8 60.0
O2A PA O5' C5' 33.6 300.0
O1A PA O3A O2A 238.0 240.1
O1A PA O3A O5' 125.1 120.0
O2A PA O3A O5' 247.1 240.0
O3A PA O2A HOA2 55.4 60.0
O3A PA O5' C5' 279.8 180.0
PA O3A PB O1B 89.1 60.0
PA O3A PB O2B 326.4 180.0
PA O3A PB O3B 209.3 300.0
O1A PA O5' O2A 122.3 120.0
O1A PA O5' O3A 236.1 240.0
O2A PA O5' O3A 113.8 120.0
O5' PA O2A HOA2 306.1 299.9
O5' PA O3A PB 265.7 180.0
PA O5' C5' C4' 271.9 180.0
PA O5' C5' H5'1 37.2 60.0
PA O5' C5' H5'2 146.6 300.0
HOA2 O2A PA O3A 55.4 60.0
HOA2 O2A PA O5' 306.1 299.9
PB O3A PA O5' 265.7 180.0
O1B PB O3A O2B 122.7 240.0
O1B PB O3A O3B 239.8 120.0
O2B PB O3A O3B 117.1 240.0
O3A PB O2B HOB2 180.0 180.0
O3A PB O3B HOB3 180.1 300.1
C4' C5' O5' H5'1 234.7 120.0
C4' C5' O5' H5'2 125.3 240.0
O5' C5' C4' O4' 164.8 61.5
O5' C5' C4' C3' 281.6 176.9
O5' C5' C4' H4' 44.1 299.2
H5'1 C5' O5' H5'2 250.5 120.0
O3A PB O1B O2B 238.6 120.0
O3A PB O1B O3B 118.5 240.0
O2B PB O1B O3B 239.8 120.0
O1B PB O2B HOB2 53.5 300.0
O1B PB O3B HOB3 304.8 180.1
O3A PB O2B O1B 126.4 240.0
O3A PB O2B O3B 245.8 120.0
O1B PB O2B O3B 119.4 240.0
O2B PB O3B HOB3 64.8 60.1
O3A PB O3B O1B 235.2 120.0
O3A PB O3B O2B 115.2 240.0
O1B PB O3B O2B 240.0 120.0
O3B PB O2B HOB2 294.1 60.0
HOB2 O2B PB O3B 294.1 60.0
O3' C3' C4' C5' 151.8 99.8
O5' C5' C4' H5'1 125.3 240.0
O5' C5' C4' H5'2 234.7 120.1
H5'1 C5' C4' H5'2 109.4 240.0
O4' C4' C5' C3' 243.1 244.6
O4' C4' C5' H4' 120.7 122.3
C5' C4' O4' C1' 101.7 159.4
C3' C4' C5' H4' 237.6 237.7
C5' C4' C3' C2' 274.0 217.1
C5' C4' C3' H3' 38.2 337.0
O5' C5' H5'1 C4' 231.9 120.0
O5' C5' H5'1 H5'2 116.0 240.0
C4' C5' H5'1 H5'2 244.1 120.0
H5'1 C5' C4' O4' 39.5 181.5
H5'1 C5' C4' C3' 156.4 296.9
H5'1 C5' C4' H4' 278.8 59.2
O5' C5' H5'2 C4' 128.1 239.9
O5' C5' H5'2 H5'1 244.0 119.9
C4' C5' H5'2 H5'1 115.9 240.0
H5'2 C5' C4' O4' 290.0 301.4
H5'2 C5' C4' C3' 46.9 56.9
H5'2 C5' C4' H4' 169.4 179.2
N9 C1' O4' C4' 229.4 200.7
O3' C3' C4' O4' 273.2 218.7
O4' C4' C5' H5'1 39.5 181.5
O4' C4' C5' H5'2 290.0 301.4
C5' C4' O4' C3' 119.6 118.9
C5' C4' O4' H4' 242.0 237.8
C3' C4' O4' H4' 122.4 118.8
O4' C4' C3' C2' 35.4 335.9
O4' C4' C3' H3' 159.6 95.9
C4' O4' C1' C2' 351.9 319.6
C4' O4' C1' H1' 110.8 78.4
O3' C3' C4' C2' 237.8 242.7
O3' C3' C4' H3' 113.6 122.8
C3' C4' C5' H5'1 156.4 296.9
C3' C4' C5' H5'2 46.9 56.9
C5' C4' C3' O4' 238.6 241.1
C5' C4' C3' H4' 118.0 122.3
O4' C4' C3' H4' 239.4 241.2
C3' C4' O4' C1' 342.2 40.5
C1' C2' C3' C4' 320.5 0.2
O2' C2' C3' C4' 202.6 244.0
C4' C3' C2' H2' 82.5 120.4
C2' C3' C4' H3' 235.8 240.1
H4' C4' C5' H5'1 278.8 59.2
H4' C4' C5' H5'2 169.4 179.2
C5' C4' H4' O4' 122.1 122.2
C5' C4' H4' C3' 239.7 237.6
O4' C4' H4' C3' 117.6 115.4
H4' C4' O4' C1' 219.8 281.7
H4' C4' C3' C2' 156.0 94.8
H4' C4' C3' H3' 280.2 214.7
N9 C1' O4' C2' 237.5 241.1
N9 C1' O4' H1' 118.5 122.3
C1' O4' C4' C3' 342.2 40.5
C1' O4' C4' H4' 219.8 281.7
C2' C1' O4' H1' 241.1 241.2
O4' C1' C2' O2' 143.6 139.9
O4' C1' C2' C3' 29.8 23.8
O4' C1' C2' H2' 264.3 262.7
P1 O2' C2' C1' 273.6 223.9
N9 C1' C2' O4' 114.7 119.0
N9 C1' C2' H1' 240.9 237.8
O3' C3' C2' C1' 86.2 116.6
C4' C3' C2' C1' 320.5 0.2
O4' C1' C2' H1' 126.1 118.8
O2' C2' C1' C3' 113.8 116.2
O2' C2' C1' H2' 239.3 237.2
C3' C2' C1' H2' 125.5 121.1
C1' C2' C3' H3' 200.0 240.3
N9 C1' H1' O4' 242.3 237.7
N9 C1' H1' C2' 125.2 122.3
O4' C1' H1' C2' 242.8 244.6
H1' C1' C2' O2' 17.5 21.1
H1' C1' C2' C3' 263.7 265.0
H1' C1' C2' H2' 138.2 143.9
O3' C3' C2' O2' 328.4 0.4
C4' C3' C2' O2' 202.6 244.0
O2' C2' C1' H1' 17.5 21.1
C1' C2' O2' C3' 249.0 247.0
C1' C2' O2' H2' 123.1 122.7
C3' C2' O2' H2' 234.1 235.7
O2' C2' C3' H3' 82.1 124.0
O3' C3' C2' C4' 125.8 116.4
O3' C3' C2' H3' 246.3 236.4
C2' C3' C4' H4' 156.0 94.8
C4' C3' C2' H3' 120.5 119.9
C3' C2' C1' H1' 263.7 265.0
C1' C2' C3' O2' 117.8 116.2
C1' C2' C3' H2' 237.9 239.8
O2' C2' C3' H2' 120.1 123.6
H2' C2' C1' H1' 138.2 143.9
C1' C2' H2' O2' 236.6 238.4
C1' C2' H2' C3' 116.9 116.1
O2' C2' H2' C3' 240.4 237.6
H2' C2' C3' H3' 322.0 0.5
O3' C3' H3' C4' 235.4 238.6
O3' C3' H3' C2' 120.9 123.0
H3' C3' C4' H4' 280.2 214.7
C4' C3' H3' C2' 245.5 244.4
H3' C3' C2' H2' 322.0 0.5