PDB Chemical Component AD2

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 AD2

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
P1 OP1 1.486 1.501
P1 OP2 1.487 1.617
P1 O5' 1.592 1.620
P1 OP3   1.617
OP2 HOP2 0.951 0.981
O5' C5' 1.427 1.416
P2 O5P 1.486 1.617
P2 O4P 1.482 1.501
P2 O6P 1.519 1.616
P2 O3' 1.607 1.615
O5P HOP5 0.950 0.981
O6P HOP6 0.950 0.981
N9 C4 1.375 1.368
N9 C8 1.373 1.371
N9 C1' 1.464 1.464
C4 N3 1.343 1.342
C4 C5 1.383 1.385
N3 C2 1.329 1.351
C2 N1 1.337 1.355
C2 H2 1.103 1.085
N1 C6 1.351 1.354
C6 N6 1.334 1.405
C6 C5 1.399 1.392
N6 H61 1.020 1.003
N6 H62 1.020 1.002
C5 N7 1.386 1.373
N7 C8 1.310 1.316
C8 H8 1.103 1.082
C2' C1' 1.520 1.524
C2' C3' 1.516 1.513
C2' H2'1 1.115 1.095
C2' H2'2 1.115 1.099
C5' C4' 1.509 1.517
C5' H5'1 1.115 1.091
C5' H5'2 1.115 1.091
C4' O4' 1.447 1.436
C4' C3' 1.527 1.519
C4' H4' 1.115 1.097
O4' C1' 1.419 1.439
C1' H1' 1.115 1.094
C3' O3' 1.427 1.413
C3' H3' 1.115 1.097
OP3 HOP3   0.981

Bond Angles for AD2

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
OP1 P1 OP2 119.6 115.3
OP1 P1 O5' 108.3 115.0
OP1 P1 OP3   115.0
OP2 P1 O5' 108.5 103.7
OP2 P1 OP3   103.3
P1 OP2 HOP2 119.7 118.9
O5' P1 OP3   102.9
P1 O5' C5' 120.7 118.5
P1 OP3 HOP3   118.9
O5' C5' C4' 109.8 108.7
O5' C5' H5'1 112.1 109.2
O5' C5' H5'2 112.1 109.2
O5P P2 O4P 119.5 115.2
O5P P2 O6P 108.7 103.3
O5P P2 O3' 107.2 103.8
P2 O5P HOP5 119.5 118.9
O4P P2 O6P 108.4 115.0
O4P P2 O3' 107.8 115.1
O6P P2 O3' 104.2 102.6
P2 O6P HOP6 108.7 118.9
P2 O3' C3' 119.1 118.2
C4 N9 C8 105.8 106.8
C4 N9 C1' 127.2 127.0
N9 C4 N3 127.6 127.5
N9 C4 C5 105.7 105.3
C8 N9 C1' 127.0 126.2
N9 C8 N7 113.8 112.3
N9 C8 H8 125.2 122.1
N9 C1' C2' 112.9 113.8
N9 C1' O4' 107.8 109.4
N9 C1' H1' 107.4 105.1
N3 C4 C5 126.7 127.2
C4 N3 C2 110.6 110.4
C4 C5 C6 117.1 116.9
C4 C5 N7 110.8 110.7
N3 C2 N1 129.3 128.8
N3 C2 H2 115.0 115.6
N1 C2 H2 115.7 115.6
C2 N1 C6 118.5 117.5
N1 C6 N6 118.8 120.2
N1 C6 C5 117.7 119.1
N6 C6 C5 123.5 120.7
C6 N6 H61 108.9 119.4
C6 N6 H62 118.8 119.4
C6 C5 N7 132.1 132.4
H61 N6 H62 108.9 120.9
C5 N7 C8 103.9 104.8
N7 C8 H8 121.0 125.5
C1' C2' C3' 103.7 103.2
C1' C2' H2'1 114.4 114.1
C1' C2' H2'2 114.4 110.0
C2' C1' O4' 106.6 107.7
C2' C1' H1' 108.6 111.7
C3' C2' H2'1 114.4 112.8
C3' C2' H2'2 114.4 109.9
C2' C3' C4' 104.0 101.8
C2' C3' O3' 111.7 111.3
C2' C3' H3' 112.5 110.2
H2'1 C2' H2'2 96.1 106.8
C4' C5' H5'1 112.1 110.1
C4' C5' H5'2 112.1 110.1
C5' C4' O4' 109.0 109.7
C5' C4' C3' 112.1 113.6
C5' C4' H4' 107.2 108.6
H5'1 C5' H5'2 98.3 109.6
O4' C4' C3' 106.5 105.5
O4' C4' H4' 112.6 108.2
C4' O4' C1' 110.7 108.1
C3' C4' H4' 109.6 111.1
C4' C3' O3' 112.1 112.4
C4' C3' H3' 112.1 111.5
O4' C1' H1' 113.7 109.1
O3' C3' H3' 104.6 109.4

Torsion Angles for AD2

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
OP2 P1 OP1 O5' 235.0 120.6
OP2 P1 OP1 OP3   239.9
OP1 P1 OP2 HOP2 180.0 48.8
O5' P1 OP1 OP3   119.3
OP1 P1 O5' C5' 40.8 180.0
OP1 P1 OP3 HOP3   311.9
OP1 P1 OP2 O5' 124.9 233.4
OP1 P1 OP2 OP3   126.3
O5' P1 OP2 OP3   252.9
OP2 P1 O5' C5' 172.1 53.2
OP2 P1 OP3 HOP3   78.4
OP1 P1 O5' OP2 228.7 126.8
OP1 P1 O5' OP3   234.2
OP2 P1 O5' OP3   107.4
O5' P1 OP2 HOP2 55.1 175.4
O5' P1 OP3 HOP3   186.1
P1 O5' C5' C4' 198.7 180.0
P1 O5' C5' H5'1 73.5 300.1
P1 O5' C5' H5'2 324.0 59.9
OP1 P1 OP3 OP2   233.5
OP1 P1 OP3 O5'   125.8
OP2 P1 OP3 O5'   252.3
OP3 P1 OP2 HOP2   282.5
OP3 P1 O5' C5'   305.8
HOP2 OP2 P1 O5' 55.1 175.4
HOP2 OP2 P1 OP3   282.5
C5' O5' P1 OP3   305.8
C4' C5' O5' H5'1 125.2 239.9
C4' C5' O5' H5'2 234.7 120.1
O5' C5' C4' O4' 284.9 61.8
O5' C5' C4' C3' 42.6 179.5
O5' C5' C4' H4' 162.8 303.7
H5'1 C5' O5' H5'2 109.5 240.2
O4P P2 O5P O6P 235.0 126.3
O4P P2 O5P O3' 122.9 233.2
O6P P2 O5P O3' 247.9 106.9
O5P P2 O6P HOP6 180.0 78.5
O5P P2 O3' C3' 27.6 173.1
O5P P2 O4P O6P 125.2 239.9
O5P P2 O4P O3' 237.4 120.9
O4P P2 O5P HOP5 180.0 48.8
O6P P2 O4P O3' 112.2 241.0
O4P P2 O6P HOP6 311.3 312.0
O4P P2 O3' C3' 257.7 300.0
O5P P2 O6P O4P 228.7 126.4
O5P P2 O6P O3' 114.1 252.2
O6P P2 O5P HOP5 305.0 282.6
O4P P2 O6P O3' 245.4 125.8
O6P P2 O3' C3' 142.8 65.7
O5P P2 O3' O4P 129.9 233.1
O5P P2 O3' O6P 244.9 107.4
O3' P2 O5P HOP5 57.1 175.7
O4P P2 O3' O6P 115.0 234.3
O3' P2 O6P HOP6 65.9 186.2
C2' C3' O3' P2 98.6 60.0
C4' C3' O3' P2 214.9 173.4
P2 O3' C3' H3' 336.6 297.9
HOP5 O5P P2 O4P 180.0 48.8
HOP5 O5P P2 O6P 305.0 282.6
HOP5 O5P P2 O3' 57.1 175.7
HOP6 O6P P2 O3' 65.9 186.2
C8 N9 C4 C1' 179.1 180.0
C4 N9 C8 N7 359.1 0.0
C4 N9 C8 H8 179.1 180.0
C4 N9 C1' C2' 179.2 92.5
C4 N9 C1' O4' 296.6 213.0
C4 N9 C1' H1' 59.5 330.1
N3 C4 N9 C5 179.5 179.9
N9 C4 N3 C2 180.8 180.0
N9 C4 C5 C6 179.1 180.0
N9 C4 C5 N7 359.2 360.0
C4 N9 C8 C1' 180.9 180.0
C8 N9 C4 N3 180.5 179.9
C8 N9 C4 C5 1.0 0.0
C8 N9 C1' C2' 0.3 272.5
C8 N9 C1' O4' 117.8 33.0
C8 N9 C1' H1' 240.6 150.0
C5 N7 C8 N9 0.4 360.0
N7 C8 N9 H8 180.0 180.0
C4 N9 C1' C8 178.9 180.1
C1' N9 C4 N3 1.4 359.9
C1' N9 C4 C5 181.9 180.0
C1' N9 C8 N7 178.2 180.0
C1' N9 C8 H8 358.2 0.0
N9 C1' C2' C3' 145.7 102.8
N9 C1' C2' H2'1 20.5 340.0
N9 C1' C2' H2'2 271.0 220.0
C2' C1' N9 O4' 242.6 239.5
C2' C1' N9 H1' 119.7 122.5
C4' O4' C1' N9 222.4 231.2
O4' C1' N9 H1' 237.1 242.9
N3 C4 N9 C8 180.5 179.9
N3 C4 N9 C1' 1.4 359.9
N9 C4 N3 C5 180.6 180.1
N3 C4 C5 C6 359.6 0.1
N3 C4 C5 N7 179.7 180.0
C4 N3 C2 N1 0.1 0.0
C4 N3 C2 H2 180.1 180.0
C5 C4 N9 C8 1.0 0.0
C5 C4 N9 C1' 181.9 180.0
N9 C4 C5 N3 179.5 179.9
C5 C4 N3 C2 0.2 359.9
N1 C6 C5 C4 0.3 359.9
N6 C6 C5 C4 180.3 180.0
C6 C5 C4 N7 179.9 180.0
C4 C5 N7 C8 0.2 0.0
C2 N3 C4 C5 0.2 359.9
N1 C2 N3 H2 180.0 180.0
N3 C2 N1 C6 359.9 359.9
N3 C2 N1 H2 180.0 180.0
C2 N1 C6 N6 179.9 180.0
C2 N1 C6 C5 360.0 0.1
N3 C2 H2 N1 180.0 180.0
H2 C2 N1 C6 179.9 180.0
C4 C5 C6 N1 0.3 359.9
C6 N1 C2 H2 179.9 180.0
N6 C6 N1 C5 179.9 179.9
N1 C6 N6 H61 54.8 265.4
N1 C6 N6 H62 180.0 91.6
N1 C6 C5 N7 180.2 180.0
C4 C5 C6 N6 180.3 180.0
N1 C6 N6 C5 180.1 180.1
N6 C6 C5 N7 0.2 0.0
H61 N6 C6 H62 234.7 173.8
C4 C5 C6 N7 180.1 180.0
N1 C6 C5 N6 179.9 179.9
C5 C6 N6 H61 234.7 85.4
C5 C6 N6 H62 359.9 271.6
C6 C5 N7 C8 180.3 180.0
H61 N6 C6 C5 234.7 85.4
C6 N6 H61 H62 130.8 186.3
H62 N6 C6 C5 359.9 271.6
C6 N6 H62 H61 234.7 173.7
N9 C8 N7 C5 0.4 360.0
C4 C5 N7 C6 179.9 180.0
C5 N7 C8 H8 180.4 180.0
N7 C8 N9 C1' 178.2 180.0
N9 C8 N7 H8 180.0 180.0
H8 C8 N9 C1' 358.2 0.0
N9 C8 H8 N7 180.0 180.0
N9 C1' C2' O4' 118.1 121.4
N9 C1' C2' H1' 241.0 241.2
C3' C2' C1' H2'1 125.2 122.8
C3' C2' C1' H2'2 234.7 242.8
C1' C2' C3' C4' 332.0 33.0
C1' C2' C3' O3' 93.1 152.9
C1' C2' C3' H3' 210.4 274.5
H2'1 C2' C1' H2'2 109.5 120.0
C4' O4' C1' C2' 343.8 355.4
O4' C1' C2' H1' 122.8 119.8
P2 O3' C3' C2' 98.6 60.0
C1' C2' C3' H2'1 234.7 236.3
C1' C2' C3' H2'2 125.3 117.3
C3' C2' C1' O4' 27.6 341.4
C3' C2' C1' H1' 264.8 221.6
H2'1 C2' C3' H2'2 250.5 240.9
C5' C4' C3' C2' 260.1 202.8
O4' C4' C3' C2' 19.2 323.0
C2' C3' C4' H4' 141.3 80.0
C4' C3' C2' O3' 238.9 240.1
C4' C3' C2' H3' 121.6 118.4
O3' C3' C2' H3' 242.7 238.4
C1' C2' H2'1 C3' 119.4 117.4
C1' C2' H2'1 H2'2 239.7 238.2
H2'1 C2' C1' O4' 262.4 218.6
H2'1 C2' C1' H1' 139.5 98.8
C3' C2' H2'1 H2'2 120.3 120.9
H2'1 C2' C3' C4' 97.2 156.6
H2'1 C2' C3' O3' 218.3 276.6
H2'1 C2' C3' H3' 335.6 38.2
C1' C2' H2'2 C3' 240.6 247.1
C1' C2' H2'2 H2'1 120.3 124.3
H2'2 C2' C1' O4' 152.9 98.6
H2'2 C2' C1' H1' 30.1 338.8
C3' C2' H2'2 H2'1 239.7 237.3
H2'2 C2' C3' C4' 206.7 275.7
H2'2 C2' C3' O3' 327.8 35.7
H2'2 C2' C3' H3' 85.1 157.3
O5' C5' C4' H5'1 234.7 119.6
O5' C5' C4' H5'2 125.3 240.5
C2' C3' C4' C5' 260.1 202.8
H5'1 C5' C4' H5'2 250.5 120.9
O4' C4' C5' C3' 242.4 242.2
O4' C4' C5' H4' 122.1 118.0
C5' C4' O4' C1' 119.1 148.9
C3' C4' C5' H4' 239.8 235.8
C5' C4' C3' O3' 139.3 83.6
C5' C4' C3' H3' 22.0 320.3
O5' C5' H5'1 C4' 124.0 240.7
O5' C5' H5'1 H5'2 242.0 119.5
C4' C5' H5'1 H5'2 118.0 238.8
H5'1 C5' C4' O4' 50.2 302.2
H5'1 C5' C4' C3' 167.8 60.0
H5'1 C5' C4' H4' 288.1 184.1
O5' C5' H5'2 C4' 236.0 119.2
O5' C5' H5'2 H5'1 118.0 240.4
C4' C5' H5'2 H5'1 242.0 121.2
H5'2 C5' C4' O4' 159.7 181.3
H5'2 C5' C4' C3' 277.3 299.1
H5'2 C5' C4' H4' 37.5 63.3
N9 C1' O4' C4' 222.4 231.2
C2' C1' O4' C4' 343.8 355.4
C2' C3' C4' O4' 19.2 323.0
O4' C4' C5' H5'1 50.2 302.2
O4' C4' C5' H5'2 159.7 181.3
C5' C4' O4' C3' 121.1 122.8
C5' C4' O4' H4' 241.2 241.7
C3' C4' O4' H4' 120.1 119.0
O4' C4' C3' O3' 258.4 203.8
O4' C4' C3' H3' 141.1 80.5
C4' O4' C1' H1' 103.4 116.8
P2 O3' C3' C4' 214.9 173.4
C4' C3' C2' H2'1 97.2 156.6
C4' C3' C2' H2'2 206.7 275.7
C2' C3' C4' O3' 120.8 119.2
C2' C3' C4' H3' 238.1 242.5
C3' C4' C5' H5'1 167.8 60.0
C3' C4' C5' H5'2 277.3 299.1
C5' C4' C3' O4' 240.9 239.8
C5' C4' C3' H4' 118.8 122.8
O4' C4' C3' H4' 237.9 243.0
C3' C4' O4' C1' 358.0 26.2
O3' C3' C4' H3' 117.3 123.3
H4' C4' C5' H5'1 288.1 184.1
H4' C4' C5' H5'2 37.5 63.3
C5' C4' H4' O4' 119.8 119.0
C5' C4' H4' C3' 238.2 234.3
O4' C4' H4' C3' 118.4 115.3
H4' C4' O4' C1' 237.9 267.2
H4' C4' C3' O3' 20.5 320.8
H4' C4' C3' H3' 263.2 197.5
N9 C1' O4' C2' 238.5 235.8
N9 C1' O4' H1' 118.9 114.5
O4' C1' C2' C3' 27.6 341.4
O4' C1' C2' H2'1 262.4 218.6
O4' C1' C2' H2'2 152.9 98.6
C2' C1' O4' H1' 240.4 238.6
C1' O4' C4' C3' 358.0 26.2
C1' O4' C4' H4' 237.9 267.2
N9 C1' H1' C2' 122.4 123.9
N9 C1' H1' O4' 240.9 242.8
H1' C1' C2' C3' 264.8 221.6
H1' C1' C2' H2'1 139.5 98.8
H1' C1' C2' H2'2 30.1 338.8
C2' C1' H1' O4' 118.4 118.9
O3' C3' C2' H2'1 218.3 276.6
O3' C3' C2' H2'2 327.8 35.7
C2' C3' O3' C4' 243.7 246.6
C2' C3' O3' H3' 122.0 122.1
O3' C3' C4' H4' 20.5 320.8
C4' C3' O3' H3' 238.3 235.5
H3' C3' C2' H2'1 335.6 38.2
H3' C3' C2' H2'2 85.1 157.3
C2' C3' H3' C4' 116.9 112.3
C2' C3' H3' O3' 238.6 237.3
H3' C3' C4' H4' 263.2 197.5
C4' C3' H3' O3' 121.7 125.0