PDB Chemical Component AP2

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 AP2

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
PB O1B 1.504 1.480
PB O2B 1.460 1.610
PB O3B 1.508 1.609
PB C3A 1.751 1.823
O2B HOB2 0.949 0.967
O3B HOB3 0.949 0.967
C3A PA 1.627 1.822
C3A H3A1 1.116 1.089
C3A H3A2 1.115 1.090
PA O1A 1.474 1.480
PA O2A 1.481 1.610
PA O5' 1.603 1.609
O2A HOA2 0.950 0.966
O5' C5' 1.457 1.429
C5' C4' 1.563 1.529
C5' H5'1 1.115 1.090
C5' H5'2 1.114 1.089
C4' O4' 1.464 1.444
C4' C3' 1.534 1.544
C4' H4' 1.115 1.090
O4' C1' 1.488 1.444
C3' O3' 1.430 1.428
C3' C2' 1.618 1.547
C3' H3' 1.115 1.091
O3' HO3' 0.950 0.967
C2' O2' 1.452 1.429
C2' C1' 1.510 1.544
C2' H2' 1.115 1.091
O2' HO2' 0.950 0.968
C1' N9 1.504 1.464
C1' H1' 1.114 1.090
N9 C8 1.383 1.363
N9 C4 1.404 1.372
C8 N7 1.321 1.301
C8 H8 1.104 1.080
N7 C5 1.416 1.355
C5 C6 1.484 1.405
C5 C4 1.382 1.405
C6 N6 1.354 1.384
C6 N1 1.358 1.328
N6 HN61 1.019 0.970
N6 HN62 1.020 0.970
N1 C2 1.354 1.320
C2 N3 1.351 1.317
C2 H2 1.102 1.080
N3 C4 1.393 1.328

Bond Angles for AP2

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
O1B PB O2B 111.0 109.4
O1B PB O3B 117.7 109.5
O1B PB C3A 102.1 109.5
O2B PB O3B 110.5 109.5
O2B PB C3A 107.9 109.5
PB O2B HOB2 111.0 106.8
O3B PB C3A 106.7 109.5
PB O3B HOB3 117.7 106.8
PB C3A PA 132.0 109.5
PB C3A H3A1 104.4 109.5
PB C3A H3A2 104.4 109.5
PA C3A H3A1 104.4 109.5
PA C3A H3A2 104.4 109.5
C3A PA O1A 116.1 109.5
C3A PA O2A 114.7 109.5
C3A PA O5' 107.0 109.5
H3A1 C3A H3A2 104.4 109.5
O1A PA O2A 102.8 109.4
O1A PA O5' 106.5 109.4
O2A PA O5' 109.3 109.5
PA O2A HOA2 114.7 106.8
PA O5' C5' 116.6 106.8
O5' C5' C4' 114.8 109.5
O5' C5' H5'1 110.2 109.5
O5' C5' H5'2 110.2 109.5
C4' C5' H5'1 110.3 109.4
C4' C5' H5'2 110.3 109.4
C5' C4' O4' 115.6 110.4
C5' C4' C3' 101.1 110.5
C5' C4' H4' 109.6 110.3
H5'1 C5' H5'2 100.0 109.5
O4' C4' C3' 104.6 104.8
O4' C4' H4' 106.4 110.4
C4' O4' C1' 103.4 105.3
C3' C4' H4' 119.9 110.3
C4' C3' O3' 110.6 110.6
C4' C3' C2' 105.4 104.1
C4' C3' H3' 112.2 110.5
O4' C1' C2' 102.7 104.9
O4' C1' N9 108.0 110.4
O4' C1' H1' 118.5 110.4
O3' C3' C2' 111.8 110.6
O3' C3' H3' 106.0 110.4
C3' O3' HO3' 110.5 106.8
C2' C3' H3' 111.1 110.6
C3' C2' O2' 124.0 110.5
C3' C2' C1' 97.6 104.0
C3' C2' H2' 108.7 110.5
O2' C2' C1' 110.2 110.8
O2' C2' H2' 95.7 110.4
C2' O2' HO2' 123.9 106.8
C1' C2' H2' 122.9 110.4
C2' C1' N9 118.9 110.4
C2' C1' H1' 107.5 110.3
N9 C1' H1' 102.2 110.3
C1' N9 C8 126.6 126.2
C1' N9 C4 126.0 126.3
C8 N9 C4 104.8 107.5
N9 C8 N7 115.6 109.9
N9 C8 H8 124.3 125.0
N9 C4 C5 105.7 106.0
N9 C4 N3 127.1 135.0
N7 C8 H8 120.1 125.0
C8 N7 C5 102.2 109.5
N7 C5 C6 132.1 134.7
N7 C5 C4 111.8 107.1
C6 C5 C4 116.1 118.2
C5 C6 N6 121.0 120.8
C5 C6 N1 114.7 118.5
C5 C4 N3 127.2 119.0
N6 C6 N1 124.3 120.8
C6 N6 HN61 121.0 120.0
C6 N6 HN62 108.1 120.0
C6 N1 C2 124.7 121.2
HN61 N6 HN62 108.1 120.0
N1 C2 N3 124.2 122.4
N1 C2 H2 118.0 118.8
N3 C2 H2 117.8 118.8
C2 N3 C4 113.0 120.7

Torsion Angles for AP2

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
O2B PB O1B O3B 128.7 120.0
O2B PB O1B C3A 245.2 240.0
O1B PB O2B HOB2 180.0 300.0
O3B PB O1B C3A 116.4 120.1
O1B PB O3B HOB3 180.0 180.0
O1B PB C3A PA 181.1 60.0
O1B PB C3A H3A1 306.4 300.0
O1B PB C3A H3A2 55.8 180.0
O1B PB O2B O3B 227.5 240.0
O1B PB O2B C3A 111.2 120.0
O3B PB O2B C3A 243.7 239.9
O2B PB O3B HOB3 51.0 60.0
O2B PB C3A PA 298.2 180.0
O2B PB C3A H3A1 63.5 59.9
O2B PB C3A H3A2 172.9 299.9
O1B PB O3B O2B 129.0 119.9
O1B PB O3B C3A 246.1 240.0
O2B PB O3B C3A 117.1 120.0
O3B PB O2B HOB2 312.5 59.9
O3B PB C3A PA 56.9 300.0
O3B PB C3A H3A1 182.2 180.0
O3B PB C3A H3A2 291.6 60.0
O1B PB C3A O2B 242.9 240.1
O1B PB C3A O3B 124.2 120.0
O2B PB C3A O3B 241.3 240.0
C3A PB O2B HOB2 68.8 180.0
C3A PB O3B HOB3 293.9 300.0
PA C3A PB H3A1 234.7 120.0
PA C3A PB H3A2 125.3 240.0
PB C3A PA O1A 41.3 300.0
PB C3A PA O2A 161.1 60.0
PB C3A PA O5' 282.6 180.0
H3A1 C3A PB H3A2 250.6 120.0
HOB2 O2B PB O3B 312.5 59.9
HOB2 O2B PB C3A 68.8 180.0
HOB3 O3B PB C3A 293.9 300.0
PB C3A PA H3A1 125.3 240.0
PB C3A PA H3A2 234.7 120.0
H3A1 C3A PA H3A2 109.4 240.0
O1A PA C3A O2A 240.2 240.0
O1A PA C3A O5' 118.8 120.0
O2A PA C3A O5' 238.5 240.0
C3A PA O2A HOA2 180.0 60.0
C3A PA O5' C5' 54.3 180.0
PB C3A H3A1 PA 218.8 120.0
PB C3A H3A1 H3A2 109.4 240.0
PA C3A H3A1 H3A2 250.6 120.0
H3A1 C3A PA O1A 276.0 60.0
H3A1 C3A PA O2A 35.8 180.0
H3A1 C3A PA O5' 157.3 300.0
PB C3A H3A2 PA 141.2 240.0
PB C3A H3A2 H3A1 250.6 120.0
PA C3A H3A2 H3A1 109.4 240.0
H3A2 C3A PA O1A 166.6 180.0
H3A2 C3A PA O2A 286.4 300.0
H3A2 C3A PA O5' 47.9 60.0
O1A PA C3A H3A1 276.0 60.0
O1A PA C3A H3A2 166.6 180.0
C3A PA O1A O2A 126.0 120.0
C3A PA O1A O5' 241.0 240.0
O2A PA O1A O5' 114.9 120.0
O1A PA O2A HOA2 306.9 180.0
O1A PA O5' C5' 289.6 60.0
O2A PA C3A H3A1 35.8 180.0
O2A PA C3A H3A2 286.4 300.0
C3A PA O2A O1A 233.1 240.0
C3A PA O2A O5' 120.2 120.0
O1A PA O2A O5' 247.1 240.0
O2A PA O5' C5' 179.1 300.0
O5' PA C3A H3A1 157.3 300.0
O5' PA C3A H3A2 47.9 60.0
C3A PA O5' O1A 124.8 120.0
C3A PA O5' O2A 235.2 240.0
O1A PA O5' O2A 110.4 120.0
O5' PA O2A HOA2 59.8 300.0
PA O5' C5' C4' 154.1 180.0
PA O5' C5' H5'1 279.4 60.0
PA O5' C5' H5'2 28.8 300.0
HOA2 O2A PA O5' 59.8 300.0
C4' C5' O5' H5'1 234.7 120.0
C4' C5' O5' H5'2 125.3 240.0
O5' C5' C4' O4' 68.8 61.4
O5' C5' C4' C3' 181.1 176.9
O5' C5' C4' H4' 308.6 299.2
H5'1 C5' O5' H5'2 250.6 120.0
O5' C5' C4' H5'1 125.3 240.0
O5' C5' C4' H5'2 234.8 120.0
H5'1 C5' C4' H5'2 109.5 240.0
O4' C4' C5' C3' 247.7 244.5
O4' C4' C5' H4' 120.2 122.2
C5' C4' O4' C1' 143.8 159.5
C3' C4' C5' H4' 232.5 237.7
C5' C4' C3' O3' 114.1 98.3
C5' C4' C3' C2' 235.1 217.0
C5' C4' C3' H3' 356.1 335.8
O5' C5' H5'1 C4' 232.2 120.0
O5' C5' H5'1 H5'2 116.0 240.0
C4' C5' H5'1 H5'2 243.8 119.9
H5'1 C5' C4' O4' 303.5 181.5
H5'1 C5' C4' C3' 55.8 297.0
H5'1 C5' C4' H4' 183.3 59.2
O5' C5' H5'2 C4' 127.8 240.0
O5' C5' H5'2 H5'1 244.0 120.0
C4' C5' H5'2 H5'1 116.1 240.1
H5'2 C5' C4' O4' 194.0 301.4
H5'2 C5' C4' C3' 306.3 56.9
H5'2 C5' C4' H4' 73.8 179.2
O4' C4' C5' H5'1 303.5 181.5
O4' C4' C5' H5'2 194.0 301.4
C5' C4' O4' C3' 110.2 119.0
C5' C4' O4' H4' 238.0 237.8
C3' C4' O4' H4' 127.8 118.8
O4' C4' C3' O3' 234.6 217.2
O4' C4' C3' C2' 355.5 336.0
O4' C4' C3' H3' 116.5 94.7
C4' O4' C1' C2' 307.8 319.6
C4' O4' C1' N9 181.4 200.7
C4' O4' C1' H1' 66.0 78.4
C3' C4' C5' H5'1 55.8 297.0
C3' C4' C5' H5'2 306.3 56.9
C5' C4' C3' O4' 239.6 241.1
C5' C4' C3' H4' 120.5 122.3
O4' C4' C3' H4' 240.9 241.2
C3' C4' O4' C1' 33.5 40.5
O3' C3' C4' C2' 239.1 241.3
O3' C3' C4' H3' 118.1 122.6
C4' C3' O3' HO3' 180.0 180.0
C2' C3' C4' H3' 239.0 241.3
C4' C3' C2' O2' 214.3 241.2
C4' C3' C2' C1' 334.9 0.1
C4' C3' C2' H2' 103.4 118.6
H4' C4' C5' H5'1 183.3 59.2
H4' C4' C5' H5'2 73.8 179.2
C5' C4' H4' O4' 125.7 122.2
C5' C4' H4' C3' 243.9 237.6
O4' C4' H4' C3' 118.2 115.4
H4' C4' O4' C1' 265.7 281.7
H4' C4' C3' O3' 353.6 336.1
H4' C4' C3' C2' 114.6 94.8
H4' C4' C3' H3' 235.6 213.5
C1' O4' C4' C3' 33.5 40.5
C1' O4' C4' H4' 265.7 281.7
C3' C2' C1' O4' 45.7 23.8
O2' C2' C1' O4' 176.2 142.6
O4' C1' C2' H2' 287.6 265.3
C2' C1' O4' N9 126.4 118.9
C2' C1' O4' H1' 241.7 241.2
N9 C1' O4' H1' 115.4 122.3
O4' C1' N9 C8 64.7 27.0
O4' C1' N9 C4 223.5 207.0
O3' C3' C4' H4' 353.6 336.1
C4' C3' O3' C2' 117.1 114.7
C4' C3' O3' H3' 238.2 237.4
C2' C3' O3' H3' 121.1 122.7
O3' C3' C2' O2' 334.5 359.9
O3' C3' C2' C1' 95.1 118.8
O3' C3' C2' H2' 223.6 237.3
C2' C3' C4' H4' 114.6 94.8
C4' C3' C2' O3' 239.8 241.3
C4' C3' C2' H3' 121.7 118.7
O4' C1' C2' C3' 45.7 23.8
O3' C3' C2' H3' 241.9 237.4
C2' C3' O3' HO3' 62.9 65.3
O2' C2' C3' C1' 239.4 241.0
O2' C2' C3' H2' 110.8 122.6
C3' C2' O2' HO2' 180.1 298.5
C1' C2' C3' H2' 231.4 241.5
C3' C2' C1' N9 164.7 142.8
C3' C2' C1' H1' 280.0 265.0
H3' C3' C4' H4' 235.6 213.5
C4' C3' H3' O3' 120.8 122.6
C4' C3' H3' C2' 242.3 245.3
O3' C3' H3' C2' 121.6 122.7
H3' C3' O3' HO3' 301.8 302.6
H3' C3' C2' O2' 92.6 122.5
H3' C3' C2' C1' 213.2 241.5
H3' C3' C2' H2' 341.7 360.0
HO3' O3' C3' C2' 62.9 65.3
HO3' O3' C3' H3' 301.8 302.6
O4' C1' C2' O2' 176.2 142.6
O2' C2' C3' H3' 92.6 122.5
C3' C2' O2' C1' 114.6 114.7
C3' C2' O2' H2' 242.8 237.4
C1' C2' O2' H2' 128.2 122.7
O2' C2' C1' N9 295.2 261.5
O2' C2' C1' H1' 50.5 23.7
O4' C1' C2' N9 241.0 241.1
O4' C1' C2' H1' 125.7 118.9
C1' C2' C3' H3' 213.2 241.5
C3' C2' C1' O2' 229.5 241.3
C3' C2' C1' H2' 118.1 118.6
O2' C2' C1' H2' 248.6 237.3
C1' C2' O2' HO2' 65.4 183.8
N9 C1' C2' H1' 244.7 237.8
C2' C1' N9 C8 308.5 271.5
C2' C1' N9 C4 107.3 91.5
H2' C2' C3' H3' 341.7 360.0
C3' C2' H2' O2' 128.8 122.6
C3' C2' H2' C1' 247.4 245.5
O2' C2' H2' C1' 118.5 122.9
H2' C2' O2' HO2' 297.2 61.1
H2' C2' C1' N9 46.6 24.2
H2' C2' C1' H1' 161.8 146.4
HO2' O2' C2' C1' 65.4 183.8
HO2' O2' C2' H2' 297.2 61.1
O4' C1' N9 C2' 116.2 115.5
O4' C1' N9 H1' 234.3 237.7
N9 C1' C2' H2' 46.6 24.2
C2' C1' N9 H1' 118.1 122.2
C8 N9 C1' C4 201.2 180.1
C1' N9 C8 N7 162.5 180.0
C1' N9 C8 H8 342.5 0.0
C1' N9 C4 C5 197.4 180.2
C1' N9 C4 N3 17.5 0.1
O4' C1' H1' C2' 244.3 244.6
O4' C1' H1' N9 118.4 122.3
H1' C1' C2' H2' 161.8 146.4
C2' C1' H1' N9 234.1 237.8
H1' C1' N9 C8 190.4 149.3
H1' C1' N9 C4 349.2 329.3
C8 N9 C1' H1' 190.4 149.3
C1' N9 C8 C4 162.4 179.9
C8 N9 C4 C5 359.9 0.2
C8 N9 C4 N3 180.1 180.1
N7 C8 N9 H8 180.0 180.0
N9 C8 N7 C5 359.9 359.7
C4 N9 C1' H1' 349.2 329.3
C1' N9 C4 C8 197.5 180.1
C4 N9 C8 N7 0.1 0.0
C4 N9 C8 H8 180.1 180.1
N7 C5 C4 N9 0.1 359.7
C6 C5 C4 N9 180.3 180.4
C5 C4 N9 N3 179.8 180.1
C2 N3 C4 N9 179.7 180.0
N7 C8 N9 C4 0.1 0.0
N9 C8 N7 H8 180.0 180.0
C8 N7 C5 C6 179.7 179.5
C8 N7 C5 C4 360.0 0.4
H8 C8 N9 C4 180.1 180.1
N9 C8 H8 N7 180.0 180.0
H8 C8 N7 C5 180.0 179.7
N9 C4 C5 N7 0.1 359.7
C5 N7 C8 H8 180.0 179.7
C6 C5 N7 C4 179.8 179.1
N7 C5 C6 N6 0.3 0.7
N7 C5 C6 N1 180.1 180.5
N7 C5 C4 N3 179.9 179.8
N9 C4 C5 C6 180.3 180.4
N7 C5 C6 C4 180.3 181.0
C6 C5 C4 N3 0.1 0.5
N6 C6 C5 N1 180.2 180.2
C5 C6 N6 HN61 180.0 179.7
C5 C6 N6 HN62 54.7 359.5
C5 C6 N1 C2 0.2 0.2
N9 C4 C5 N3 180.2 179.9
N7 C5 C4 C6 179.8 179.3
C4 C5 C6 N6 180.1 179.7
C4 C5 C6 N1 359.8 359.5
C2 N3 C4 C5 359.9 359.8
N6 C6 C5 C4 180.1 179.7
C5 C6 N6 N1 179.7 179.8
N6 C6 N1 C2 180.0 180.0
HN61 N6 C6 HN62 125.3 180.2
N1 C6 C5 C4 359.8 359.5
C5 C6 N1 N6 180.2 180.2
N1 C6 N6 HN61 0.3 360.0
N1 C6 N6 HN62 234.9 179.7
C6 N1 C2 N3 359.8 0.1
C6 N1 C2 H2 179.8 180.0
HN61 N6 C6 N1 0.3 360.0
C6 N6 HN61 HN62 234.7 179.8
HN62 N6 C6 N1 234.9 179.7
C6 N6 HN62 HN61 132.6 180.2
N3 C2 N1 H2 180.0 180.1
N1 C2 N3 C4 0.1 359.9
N9 C4 N3 C2 179.7 180.0
C5 C4 N3 C2 359.9 359.8
N1 C2 N3 H2 180.0 179.9
N1 C2 H2 N3 180.0 180.1
H2 C2 N3 C4 180.1 180.0
N9 C4 N3 C5 179.8 180.1
C4 N3 C2 H2 180.1 180.0