PDB Chemical Component APC

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 APC

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
PG O1G 1.479 1.479
PG O2G 1.511 1.610
PG O3G 1.524 1.610
PG O3B 1.612 1.610
O2G HOG2 0.949 0.967
O3G HOG3 0.949 0.967
PB O1B 1.528 1.479
PB O2B 1.497 1.609
PB O3B 1.605 1.610
PB C3A 1.794 1.822
O2B HOB2 0.951 0.967
PA O1A 1.529 1.480
PA O2A 1.498 1.610
PA C3A 1.770 1.821
PA O5' 1.596 1.610
O2A HOA2 0.950 0.966
C3A H3A1 1.115 1.090
C3A H3A2 1.115 1.090
O5' C5' 1.492 1.428
C5' C4' 1.504 1.530
C5' H5'1 1.114 1.090
C5' H5'2 1.116 1.090
C4' O4' 1.425 1.444
C4' C3' 1.484 1.544
C4' H4' 1.115 1.090
O4' C1' 1.468 1.445
C3' O3' 1.369 1.429
C3' C2' 1.486 1.547
C3' H3' 1.114 1.090
O3' HO3' 0.949 0.967
C2' O2' 1.447 1.429
C2' C1' 1.530 1.544
C2' H2' 1.114 1.090
O2' HO2' 0.949 0.966
C1' N9 1.453 1.464
C1' H1' 1.115 1.090
N9 C8 1.432 1.364
N9 C4 1.332 1.372
C8 N7 1.330 1.301
C8 H8 1.103 1.080
N7 C5 1.414 1.354
C5 C6 1.375 1.405
C5 C4 1.366 1.405
C6 N6 1.301 1.384
C6 N1 1.392 1.329
N6 HN61 1.020 0.970
N6 HN62 1.020 0.970
N1 C2 1.286 1.321
C2 N3 1.415 1.316
C2 H2 1.103 1.080
N3 C4 1.384 1.329

Bond Angles for APC

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
O1G PG O2G 113.2 109.5
O1G PG O3G 112.9 109.5
O1G PG O3B 109.1 109.5
O2G PG O3G 111.0 109.4
O2G PG O3B 103.3 109.5
PG O2G HOG2 113.2 106.8
O3G PG O3B 106.7 109.4
PG O3G HOG3 112.9 106.8
PG O3B PB 126.9 106.8
O1B PB O2B 119.5 109.5
O1B PB O3B 105.2 109.4
O1B PB C3A 108.0 109.5
O2B PB O3B 109.3 109.4
O2B PB C3A 109.0 109.5
PB O2B HOB2 119.4 106.7
O3B PB C3A 104.9 109.5
PB C3A PA 113.1 109.5
PB C3A H3A1 110.9 109.5
PB C3A H3A2 110.9 109.5
O1A PA O2A 115.6 109.5
O1A PA C3A 109.3 109.5
O1A PA O5' 104.8 109.4
O2A PA C3A 111.4 109.5
O2A PA O5' 109.0 109.5
PA O2A HOA2 115.5 106.8
C3A PA O5' 106.2 109.6
PA C3A H3A1 110.9 109.4
PA C3A H3A2 110.9 109.5
PA O5' C5' 119.3 106.9
H3A1 C3A H3A2 99.4 109.4
O5' C5' C4' 105.7 109.5
O5' C5' H5'1 113.7 109.5
O5' C5' H5'2 113.6 109.5
C4' C5' H5'1 113.6 109.4
C4' C5' H5'2 113.6 109.5
C5' C4' O4' 110.1 110.3
C5' C4' C3' 118.4 110.5
C5' C4' H4' 101.8 110.3
H5'1 C5' H5'2 96.8 109.5
O4' C4' C3' 107.1 104.8
O4' C4' H4' 114.3 110.4
C4' O4' C1' 101.3 105.2
C3' C4' H4' 105.2 110.4
C4' C3' O3' 115.7 110.5
C4' C3' C2' 103.1 104.1
C4' C3' H3' 111.9 110.5
O4' C1' C2' 105.1 104.9
O4' C1' N9 108.3 110.4
O4' C1' H1' 116.1 110.3
O3' C3' C2' 115.1 110.5
O3' C3' H3' 99.0 110.4
C3' O3' HO3' 115.7 106.8
C2' C3' H3' 112.5 110.6
C3' C2' O2' 112.1 110.5
C3' C2' C1' 105.3 104.0
C3' C2' H2' 110.9 110.5
O2' C2' C1' 110.5 110.8
O2' C2' H2' 105.8 110.5
C2' O2' HO2' 112.1 106.8
C1' C2' H2' 112.5 110.4
C2' C1' N9 117.4 110.4
C2' C1' H1' 106.8 110.4
N9 C1' H1' 103.5 110.3
C1' N9 C8 119.8 126.3
C1' N9 C4 131.2 126.3
C8 N9 C4 108.9 107.4
N9 C8 N7 108.3 110.0
N9 C8 H8 128.7 125.0
N9 C4 C5 106.7 106.0
N9 C4 N3 129.1 134.9
N7 C8 H8 122.9 125.0
C8 N7 C5 105.8 109.5
N7 C5 C6 127.9 134.7
N7 C5 C4 110.3 107.1
C6 C5 C4 121.8 118.2
C5 C6 N6 129.0 120.8
C5 C6 N1 116.3 118.5
C5 C4 N3 124.2 119.1
N6 C6 N1 114.7 120.8
C6 N6 HN61 129.0 120.0
C6 N6 HN62 105.4 120.0
C6 N1 C2 118.6 121.2
HN61 N6 HN62 105.4 120.0
N1 C2 N3 130.2 122.5
N1 C2 H2 109.0 118.8
N3 C2 H2 120.8 118.8
C2 N3 C4 108.9 120.6

Torsion Angles for APC

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
O2G PG O1G O3G 127.2 120.0
O2G PG O1G O3B 245.6 240.0
O1G PG O2G HOG2 180.0 300.0
O3G PG O1G O3B 118.5 120.0
O1G PG O3G HOG3 180.0 180.0
O1G PG O3B PB 56.0 60.0
O1G PG O2G O3G 231.9 240.0
O1G PG O2G O3B 117.8 120.0
O3G PG O2G O3B 246.0 240.0
O2G PG O3G HOG3 51.7 60.0
O2G PG O3B PB 176.7 180.0
O1G PG O3G O2G 128.3 120.0
O1G PG O3G O3B 240.2 240.0
O2G PG O3G O3B 111.9 120.0
O3G PG O2G HOG2 308.1 60.0
O3G PG O3B PB 293.8 300.0
O1G PG O3B O2G 239.4 240.0
O1G PG O3B O3G 122.2 120.0
O2G PG O3B O3G 242.9 240.0
O3B PG O2G HOG2 62.2 180.0
O3B PG O3G HOG3 299.8 300.0
O1B PB O3B PG 22.3 300.0
O2B PB O3B PG 151.8 60.0
PG O3B PB C3A 268.6 180.0
HOG2 O2G PG O3G 308.1 60.0
HOG2 O2G PG O3B 62.2 180.0
HOG3 O3G PG O3B 299.8 300.0
PG O3B PB O1B 22.3 300.0
O2B PB O1B O3B 236.8 240.0
O2B PB O1B C3A 125.2 120.1
O1B PB O2B HOB2 180.0 180.0
O3B PB O1B C3A 248.4 240.0
O1B PB C3A PA 70.4 60.0
O1B PB C3A H3A1 195.8 300.0
O1B PB C3A H3A2 305.2 180.1
PG O3B PB O2B 151.8 60.0
O1B PB O2B O3B 121.2 120.0
O1B PB O2B C3A 235.3 240.0
O3B PB O2B C3A 114.1 120.0
O2B PB C3A PA 299.2 300.0
O2B PB C3A H3A1 64.6 180.0
O2B PB C3A H3A2 173.9 60.0
O1B PB O3B O2B 230.5 240.0
O1B PB O3B C3A 113.8 120.0
O2B PB O3B C3A 243.3 240.0
O3B PB O2B HOB2 58.8 60.0
O3B PB C3A PA 182.3 180.0
O3B PB C3A H3A1 307.6 60.0
O3B PB C3A H3A2 57.0 300.0
O1B PB C3A O2B 131.2 120.0
O1B PB C3A O3B 248.2 240.0
O2B PB C3A O3B 117.0 120.0
C3A PB O2B HOB2 304.7 300.0
O1A PA C3A PB 323.8 300.0
O2A PA C3A PB 92.7 60.0
PB C3A PA O5' 211.3 180.0
PA C3A PB H3A1 234.7 120.0
PA C3A PB H3A2 125.3 239.9
H3A1 C3A PB H3A2 250.6 120.0
HOB2 O2B PB O3B 58.8 60.0
HOB2 O2B PB C3A 304.7 300.0
PB C3A PA O1A 323.8 300.0
O2A PA O1A C3A 233.4 240.0
O2A PA O1A O5' 120.0 119.9
O1A PA O2A HOA2 180.0 180.0
C3A PA O1A O5' 246.6 239.9
O1A PA C3A H3A1 198.5 60.0
O1A PA C3A H3A2 89.1 180.0
O1A PA O5' C5' 172.8 60.0
PB C3A PA O2A 92.7 60.0
O1A PA O2A C3A 125.5 120.0
O1A PA O2A O5' 242.3 240.1
C3A PA O2A O5' 116.8 120.1
O2A PA C3A H3A1 327.4 180.0
O2A PA C3A H3A2 218.0 300.0
O2A PA O5' C5' 48.5 300.0
PB C3A PA H3A1 125.3 240.0
PB C3A PA H3A2 234.7 120.0
O1A PA C3A O2A 231.1 240.0
O1A PA C3A O5' 112.6 120.0
O2A PA C3A O5' 241.4 240.0
C3A PA O2A HOA2 54.5 60.1
C3A PA O5' C5' 288.4 180.0
H3A1 C3A PA H3A2 109.4 240.0
O1A PA O5' O2A 124.3 119.9
O1A PA O5' C3A 244.4 240.0
O2A PA O5' C3A 120.1 120.0
O5' PA O2A HOA2 297.7 300.0
O5' PA C3A H3A1 85.9 300.0
O5' PA C3A H3A2 336.5 60.0
PA O5' C5' C4' 163.7 180.0
PA O5' C5' H5'1 289.0 60.0
PA O5' C5' H5'2 38.5 300.0
HOA2 O2A PA C3A 54.5 60.1
HOA2 O2A PA O5' 297.7 300.0
PB C3A H3A1 PA 233.4 120.0
PB C3A H3A1 H3A2 116.7 240.0
H3A1 C3A PA O5' 85.9 300.0
PA C3A H3A1 H3A2 243.3 120.0
PB C3A H3A2 PA 126.5 240.0
PB C3A H3A2 H3A1 243.3 120.0
H3A2 C3A PA O5' 336.5 60.0
PA C3A H3A2 H3A1 116.7 240.0
C4' C5' O5' H5'1 234.7 119.9
C4' C5' O5' H5'2 125.2 240.0
O5' C5' C4' O4' 295.5 61.4
O5' C5' C4' C3' 59.1 176.9
O5' C5' C4' H4' 173.8 299.3
H5'1 C5' O5' H5'2 250.5 120.0
O5' C5' C4' H5'1 125.3 240.0
O5' C5' C4' H5'2 234.7 120.0
H5'1 C5' C4' H5'2 109.4 240.1
O4' C4' C5' C3' 236.4 244.5
O4' C4' C5' H4' 121.6 122.2
C5' C4' O4' C1' 173.7 159.5
C3' C4' C5' H4' 245.3 237.6
C5' C4' C3' O3' 74.9 98.4
C5' C4' C3' C2' 201.4 217.0
C5' C4' C3' H3' 322.5 335.8
O5' C5' H5'1 C4' 239.1 120.0
O5' C5' H5'1 H5'2 119.6 239.9
C4' C5' H5'1 H5'2 240.5 119.9
H5'1 C5' C4' O4' 170.2 181.4
H5'1 C5' C4' C3' 293.8 296.9
H5'1 C5' C4' H4' 48.5 59.3
O5' C5' H5'2 C4' 120.9 240.0
O5' C5' H5'2 H5'1 240.4 120.1
C4' C5' H5'2 H5'1 119.5 240.1
H5'2 C5' C4' O4' 60.7 301.4
H5'2 C5' C4' C3' 184.4 56.8
H5'2 C5' C4' H4' 299.1 179.2
O4' C4' C5' H5'1 170.2 181.4
O4' C4' C5' H5'2 60.7 301.4
C5' C4' O4' C3' 130.0 119.0
C5' C4' O4' H4' 246.1 237.9
C3' C4' O4' H4' 116.1 118.9
O4' C4' C3' O3' 200.0 217.3
O4' C4' C3' C2' 326.5 335.9
O4' C4' C3' H3' 87.6 94.7
C4' O4' C1' C2' 324.0 319.6
C4' O4' C1' N9 197.7 200.6
C4' O4' C1' H1' 81.8 78.5
C3' C4' C5' H5'1 293.8 296.9
C3' C4' C5' H5'2 184.4 56.8
C5' C4' C3' O4' 234.9 241.1
C5' C4' C3' H4' 112.8 122.3
O4' C4' C3' H4' 238.0 241.2
C3' C4' O4' C1' 43.7 40.5
O3' C3' C4' C2' 233.5 241.3
O3' C3' C4' H3' 112.4 122.5
C4' C3' O3' HO3' 180.0 180.0
C2' C3' C4' H3' 238.8 241.2
C4' C3' C2' O2' 249.3 241.2
C4' C3' C2' C1' 9.5 0.2
C4' C3' C2' H2' 131.4 118.6
H4' C4' C5' H5'1 48.5 59.3
H4' C4' C5' H5'2 299.1 179.2
C5' C4' H4' O4' 118.7 122.2
C5' C4' H4' C3' 235.9 237.6
O4' C4' H4' C3' 117.2 115.4
H4' C4' O4' C1' 287.5 281.6
H4' C4' C3' O3' 322.1 336.1
H4' C4' C3' C2' 88.5 94.8
H4' C4' C3' H3' 209.7 213.5
C1' O4' C4' C3' 43.7 40.5
C1' O4' C4' H4' 287.5 281.6
C3' C2' C1' O4' 16.1 23.8
O2' C2' C1' O4' 137.3 142.6
O4' C1' C2' H2' 255.2 265.3
C2' C1' O4' N9 126.3 119.0
C2' C1' O4' H1' 242.2 241.1
N9 C1' O4' H1' 115.9 122.2
O4' C1' N9 C8 250.8 27.1
O4' C1' N9 C4 68.1 207.1
O3' C3' C4' H4' 322.1 336.1
C4' C3' O3' C2' 120.1 114.7
C4' C3' O3' H3' 240.3 237.4
C2' C3' O3' H3' 120.2 122.7
O3' C3' C2' O2' 16.2 359.8
O3' C3' C2' C1' 136.4 118.8
O3' C3' C2' H2' 258.2 237.3
C2' C3' C4' H4' 88.5 94.8
C4' C3' C2' O3' 233.2 241.3
C4' C3' C2' H3' 120.7 118.7
O4' C1' C2' C3' 16.1 23.8
O3' C3' C2' H3' 247.5 237.4
C2' C3' O3' HO3' 59.9 65.4
O2' C2' C3' C1' 239.8 241.0
O2' C2' C3' H2' 118.0 122.6
C3' C2' O2' HO2' 179.9 298.6
C1' C2' C3' H2' 238.1 241.5
C3' C2' C1' N9 136.6 142.7
C3' C2' C1' H1' 252.2 264.9
H3' C3' C4' H4' 209.7 213.5
C4' C3' H3' O3' 122.4 122.6
C4' C3' H3' C2' 244.5 245.3
O3' C3' H3' C2' 122.1 122.7
H3' C3' O3' HO3' 299.7 302.6
H3' C3' C2' O2' 128.6 122.5
H3' C3' C2' C1' 248.8 241.4
H3' C3' C2' H2' 10.7 359.9
HO3' O3' C3' C2' 59.9 65.4
HO3' O3' C3' H3' 299.7 302.6
O4' C1' C2' O2' 137.3 142.6
O2' C2' C3' H3' 128.6 122.5
C3' C2' O2' C1' 117.1 114.7
C3' C2' O2' H2' 239.0 237.4
C1' C2' O2' H2' 121.9 122.7
O2' C2' C1' N9 257.8 261.5
O2' C2' C1' H1' 13.4 23.7
O4' C1' C2' N9 239.5 241.1
O4' C1' C2' H1' 123.9 118.9
C1' C2' C3' H3' 248.8 241.4
C3' C2' C1' O2' 238.8 241.2
C3' C2' C1' H2' 120.9 118.5
O2' C2' C1' H2' 242.1 237.3
C1' C2' O2' HO2' 62.9 183.8
N9 C1' C2' H1' 244.4 237.8
C2' C1' N9 C8 132.0 271.5
C2' C1' N9 C4 309.3 91.5
H2' C2' C3' H3' 10.7 359.9
C3' C2' H2' O2' 121.7 122.6
C3' C2' H2' C1' 242.4 245.5
O2' C2' H2' C1' 120.7 122.9
H2' C2' O2' HO2' 300.9 61.1
H2' C2' C1' N9 15.7 24.2
H2' C2' C1' H1' 131.3 146.4
HO2' O2' C2' C1' 62.9 183.8
HO2' O2' C2' H2' 300.9 61.1
O4' C1' N9 C2' 118.8 115.6
O4' C1' N9 H1' 236.2 237.8
N9 C1' C2' H2' 15.7 24.2
C2' C1' N9 H1' 117.4 122.2
C8 N9 C1' C4 182.8 180.0
C1' N9 C8 N7 177.8 179.9
C1' N9 C8 H8 357.9 360.0
C1' N9 C4 C5 182.5 180.3
C1' N9 C4 N3 2.5 360.0
O4' C1' H1' C2' 243.1 244.5
O4' C1' H1' N9 118.6 122.2
H1' C1' C2' H2' 131.3 146.4
C2' C1' H1' N9 235.4 237.7
H1' C1' N9 C8 14.6 149.3
H1' C1' N9 C4 191.9 329.3
C8 N9 C1' H1' 14.6 149.3
C1' N9 C8 C4 177.8 180.0
C8 N9 C4 C5 360.0 0.3
C8 N9 C4 N3 180.0 180.0
N7 C8 N9 H8 180.0 180.0
N9 C8 N7 C5 360.0 359.8
C4 N9 C1' H1' 191.9 329.3
C1' N9 C4 C8 182.5 180.0
C4 N9 C8 N7 0.0 360.0
C4 N9 C8 H8 180.1 180.0
N7 C5 C4 N9 0.0 359.6
C6 C5 C4 N9 180.0 180.4
C5 C4 N9 N3 180.0 180.3
C2 N3 C4 N9 180.0 180.0
N7 C8 N9 C4 0.0 360.0
N9 C8 N7 H8 180.0 180.0
C8 N7 C5 C6 180.0 179.5
C8 N7 C5 C4 360.0 0.4
H8 C8 N9 C4 180.1 180.0
N9 C8 H8 N7 180.0 180.0
H8 C8 N7 C5 180.0 179.8
N9 C4 C5 N7 0.0 359.6
C5 N7 C8 H8 180.0 179.8
C6 C5 N7 C4 180.0 179.1
N7 C5 C6 N6 360.0 0.7
N7 C5 C6 N1 180.0 180.4
N7 C5 C4 N3 180.0 179.9
N9 C4 C5 C6 180.0 180.4
N7 C5 C6 C4 180.0 181.0
C6 C5 C4 N3 360.0 0.6
N6 C6 C5 N1 180.0 180.3
C5 C6 N6 HN61 179.9 179.7
C5 C6 N6 HN62 54.7 359.5
C5 C6 N1 C2 360.0 0.3
N9 C4 C5 N3 180.0 179.8
N7 C5 C4 C6 180.0 179.3
C4 C5 C6 N6 180.0 179.7
C4 C5 C6 N1 0.0 359.4
C2 N3 C4 C5 0.0 359.7
N6 C6 C5 C4 180.0 179.7
C5 C6 N6 N1 180.0 179.7
N6 C6 N1 C2 180.0 180.0
HN61 N6 C6 HN62 125.2 180.3
N1 C6 C5 C4 0.0 359.4
C5 C6 N1 N6 180.0 180.3
N1 C6 N6 HN61 359.9 360.0
N1 C6 N6 HN62 234.7 179.7
C6 N1 C2 N3 0.0 0.0
C6 N1 C2 H2 180.1 179.9
HN61 N6 C6 N1 359.9 360.0
C6 N6 HN61 HN62 234.8 179.7
HN62 N6 C6 N1 234.7 179.7
C6 N6 HN62 HN61 138.8 180.3
N3 C2 N1 H2 180.0 180.1
N1 C2 N3 C4 360.0 0.0
N9 C4 N3 C2 180.0 180.0
C5 C4 N3 C2 0.0 359.7
N1 C2 N3 H2 180.0 179.9
N1 C2 H2 N3 180.0 180.1
H2 C2 N3 C4 179.9 180.1
N9 C4 N3 C5 180.0 180.3
C4 N3 C2 H2 179.9 180.1