PDB Chemical Component AD9

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 AD9

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
VG O1G 1.602 1.602
VG O2G 1.673 1.673
VG O3G 1.784 1.784
VG O3B 1.772 1.772
PB O1B 1.679 1.679
PB O2B 1.579 1.579
PB O3B 1.521 1.521
PB O3A 1.634 1.634
PA O1A 1.537 1.537
PA O2A 1.707 1.707
PA O3A 1.638 1.638
PA O5' 1.612 1.612
O5' C5' 1.465 1.465
C5' C4' 1.502 1.502
C4' O4' 1.466 1.466
C4' C3' 1.538 1.538
O4' C1' 1.468 1.468
C3' O3' 1.456 1.456
C3' C2' 1.546 1.546
C2' O2' 1.457 1.457
C2' C1' 1.562 1.562
C1' N9 1.468 1.468
N9 C8 1.414 1.414
N9 C4 1.388 1.388
C8 N7 1.317 1.317
N7 C5 1.395 1.395
C5 C6 1.429 1.429
C5 C4 1.416 1.416
C6 N6 1.360 1.360
C6 N1 1.379 1.379
N1 C2 1.368 1.368
C2 N3 1.359 1.359
C4 N3 1.372 1.372
O2G H2G1 0.950 0.950
O3G H3G1 0.950 0.950
O2B H2B 0.950 0.950
O2A H2A 0.951 0.951
C5' H5'1 1.101 1.101
C5' H5'2 1.100 1.100
C4' H4' 1.100 1.100
C3' H3' 1.100 1.100
C1' H1' 1.100 1.100
O3' HA 0.950 0.950
C2' H2' 1.100 1.100
O2' HB 0.950 0.950
C8 H8 1.080 1.080
N6 H6N1 1.000 1.000
N6 H6N2 1.000 0.999
C2 H2 1.081 1.081

Bond Angles for AD9

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
O1G VG O2G 109.5 109.5
O1G VG O3G 114.5 114.5
O1G VG O3B 104.6 104.6
O2G VG O3G 114.1 114.1
O2G VG O3B 99.5 99.5
VG O2G H2G1 109.5 109.5
O3G VG O3B 113.3 113.3
VG O3G H3G1 109.5 109.5
VG O3B PB 164.4 164.4
O1B PB O2B 113.5 113.5
O1B PB O3B 98.3 98.3
O1B PB O3A 101.4 101.4
O2B PB O3B 118.2 118.2
O2B PB O3A 110.5 110.5
PB O2B H2B 109.5 109.5
O3B PB O3A 113.0 113.0
PB O3A PA 130.5 130.5
O1A PA O2A 115.9 115.9
O1A PA O3A 116.0 116.0
O1A PA O5' 118.2 118.2
O2A PA O3A 102.4 102.4
O2A PA O5' 102.5 102.5
PA O2A H2A 109.5 109.5
O3A PA O5' 99.2 99.2
PA O5' C5' 127.9 127.9
O5' C5' C4' 109.2 109.2
O5' C5' H5'1 109.6 109.6
O5' C5' H5'2 109.7 109.7
C5' C4' O4' 107.7 107.7
C5' C4' C3' 114.8 114.8
C4' C5' H5'1 109.6 109.6
C4' C5' H5'2 109.6 109.6
C5' C4' H4' 105.0 105.0
O4' C4' C3' 101.6 101.6
C4' O4' C1' 110.5 110.5
O4' C4' H4' 117.5 117.5
C4' C3' O3' 111.3 111.3
C4' C3' C2' 101.4 101.4
C3' C4' H4' 110.7 110.7
C4' C3' H3' 115.0 115.0
O4' C1' C2' 104.9 104.9
O4' C1' N9 109.8 109.8
O4' C1' H1' 114.3 114.3
O3' C3' C2' 113.4 113.4
O3' C3' H3' 103.3 103.3
C3' O3' HA 109.5 109.5
C3' C2' O2' 112.0 112.0
C3' C2' C1' 100.2 100.2
C2' C3' H3' 112.9 112.9
C3' C2' H2' 113.0 113.0
O2' C2' C1' 106.8 106.8
O2' C2' H2' 107.0 107.0
C2' O2' HB 109.5 109.5
C2' C1' N9 114.7 114.7
C2' C1' H1' 109.2 109.2
C1' C2' H2' 117.8 117.8
C1' N9 C8 128.8 128.8
C1' N9 C4 125.4 125.4
N9 C1' H1' 104.3 104.3
C8 N9 C4 105.8 105.8
N9 C8 N7 113.2 113.2
N9 C8 H8 123.4 123.4
N9 C4 C5 105.4 105.4
N9 C4 N3 128.6 128.6
C8 N7 C5 104.8 104.8
N7 C8 H8 123.4 123.4
N7 C5 C6 133.1 133.1
N7 C5 C4 110.8 110.8
C6 C5 C4 116.1 116.1
C5 C6 N6 122.9 122.9
C5 C6 N1 118.7 118.7
C5 C4 N3 126.0 126.0
N6 C6 N1 118.4 118.4
C6 N6 H6N1 109.5 109.5
C6 N6 H6N2 109.5 109.5
C6 N1 C2 119.7 119.7
N1 C2 N3 126.3 126.3
N1 C2 H2 116.9 116.9
C2 N3 C4 113.2 113.2
N3 C2 H2 116.8 116.8
H5'1 C5' H5'2 109.2 109.2
H6N1 N6 H6N2 109.4 109.5

Torsion Angles for AD9

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
O2G VG O1G O3G 230.4 230.4
O2G VG O1G O3B 105.9 105.9
O1G VG O2G H2G1 74.0 74.0
O3G VG O1G O3B 235.4 235.4
O1G VG O3G H3G1 114.0 114.0
O1G VG O3B PB 343.1 343.1
O1G VG O2G O3G 129.8 129.8
O1G VG O2G O3B 250.7 250.7
O3G VG O2G O3B 120.9 120.9
O2G VG O3G H3G1 241.3 241.3
O2G VG O3B PB 229.9 229.9
O1G VG O3G O2G 232.7 232.7
O1G VG O3G O3B 119.8 119.8
O2G VG O3G O3B 247.1 247.1
O3G VG O2G H2G1 304.2 304.2
O3G VG O3B PB 108.5 108.5
O1G VG O3B O2G 113.2 113.2
O1G VG O3B O3G 234.7 234.7
O2G VG O3B O3G 121.5 121.5
O3B VG O2G H2G1 183.2 183.2
O3B VG O3G H3G1 354.2 354.2
O1B PB O3B VG 121.3 121.3
O2B PB O3B VG 358.8 358.8
VG O3B PB O3A 227.5 227.5
VG O3B PB O1B 121.3 121.3
O2B PB O1B O3B 125.8 125.8
O2B PB O1B O3A 241.5 241.5
O1B PB O2B H2B 273.7 273.7
O3B PB O1B O3A 115.7 115.7
O1B PB O3A PA 357.6 357.6
VG O3B PB O2B 358.8 358.8
O1B PB O2B O3B 245.6 245.6
O1B PB O2B O3A 113.1 113.1
O3B PB O2B O3A 227.5 227.5
O2B PB O3A PA 118.3 118.3
O1B PB O3B O2B 122.5 122.5
O1B PB O3B O3A 253.8 253.8
O2B PB O3B O3A 131.3 131.3
O3B PB O2B H2B 28.2 28.2
O3B PB O3A PA 253.3 253.3
O1B PB O3A O2B 239.3 239.3
O1B PB O3A O3B 104.3 104.3
O2B PB O3A O3B 225.0 225.0
O3A PB O2B H2B 160.6 160.6
O1A PA O3A PB 311.2 311.2
O2A PA O3A PB 78.5 78.5
PB O3A PA O5' 183.5 183.5
PB O3A PA O1A 311.2 311.2
O2A PA O1A O3A 239.8 239.8
O2A PA O1A O5' 122.2 122.2
O1A PA O2A H2A 277.6 277.6
O3A PA O1A O5' 242.4 242.4
O1A PA O5' C5' 153.5 153.5
PB O3A PA O2A 78.5 78.5
O1A PA O2A O3A 127.3 127.3
O1A PA O2A O5' 229.7 229.7
O3A PA O2A O5' 102.4 102.4
O2A PA O5' C5' 24.6 24.6
O1A PA O3A O2A 232.7 232.7
O1A PA O3A O5' 127.7 127.7
O2A PA O3A O5' 255.0 255.0
O3A PA O2A H2A 150.3 150.3
O3A PA O5' C5' 279.7 279.7
O1A PA O5' O2A 128.8 128.8
O1A PA O5' O3A 233.8 233.8
O2A PA O5' O3A 105.0 105.0
O5' PA O2A H2A 47.9 47.9
PA O5' C5' C4' 221.5 221.5
PA O5' C5' H5'1 341.5 341.5
PA O5' C5' H5'2 101.3 101.3
O5' C5' C4' O4' 306.1 306.1
O5' C5' C4' C3' 58.3 58.3
C4' C5' O5' H5'1 240.0 240.0
C4' C5' O5' H5'2 120.1 120.1
O5' C5' C4' H4' 180.1 180.1
H5'1 C5' O5' H5'2 240.1 240.1
O5' C5' C4' H5'1 120.0 120.0
O5' C5' C4' H5'2 239.9 239.9
O4' C4' C5' C3' 247.8 247.8
C5' C4' O4' C1' 147.2 147.2
O4' C4' C5' H4' 126.0 126.0
C5' C4' C3' O3' 79.8 79.8
C5' C4' C3' C2' 200.7 200.7
C3' C4' C5' H4' 238.2 238.2
C5' C4' C3' H3' 322.8 322.8
H5'1 C5' C4' H5'2 119.9 119.9
C5' C4' O4' C3' 120.9 120.9
O4' C4' C5' H5'1 186.1 186.1
O4' C4' C5' H5'2 66.2 66.2
C5' C4' O4' H4' 241.9 241.8
O4' C4' C3' O3' 195.6 195.6
O4' C4' C3' C2' 316.5 316.5
C3' C4' O4' H4' 120.9 120.9
O4' C4' C3' H3' 78.6 78.6
C4' O4' C1' C2' 1.5 1.5
C4' O4' C1' N9 237.7 237.7
C4' O4' C1' H1' 121.0 121.0
C5' C4' C3' O4' 244.2 244.2
C3' C4' C5' H5'1 298.3 298.3
C3' C4' C5' H5'2 178.5 178.5
C5' C4' C3' H4' 118.6 118.6
C3' C4' O4' C1' 26.2 26.2
O4' C4' C3' H4' 234.4 234.5
O3' C3' C4' C2' 239.1 239.1
O3' C3' C4' H3' 117.0 117.0
C4' C3' O3' HA 124.2 124.2
C4' C3' C2' O2' 291.0 291.0
C4' C3' C2' C1' 43.8 43.8
C2' C3' C4' H3' 237.9 237.9
C4' C3' C2' H2' 170.0 170.0
C1' O4' C4' C3' 26.2 26.2
C1' O4' C4' H4' 265.3 265.3
C3' C2' C1' O4' 331.7 331.7
O2' C2' C1' O4' 88.5 88.5
C2' C1' O4' N9 123.8 123.8
C2' C1' O4' H1' 240.5 240.5
O4' C1' C2' H2' 208.8 208.8
O4' C1' N9 C8 1.6 1.6
O4' C1' N9 C4 182.2 182.2
N9 C1' O4' H1' 116.7 116.7
C4' C3' O3' C2' 113.6 113.6
O3' C3' C4' H4' 321.2 321.2
C4' C3' O3' H3' 236.1 236.1
O3' C3' C2' O2' 50.4 50.4
O3' C3' C2' C1' 163.2 163.2
C2' C3' O3' H3' 122.6 122.6
O3' C3' C2' H2' 289.4 289.4
C4' C3' C2' O3' 240.6 240.6
C2' C3' C4' H4' 82.1 82.0
C4' C3' C2' H3' 123.5 123.5
O4' C1' C2' C3' 331.7 331.7
O3' C3' C2' H3' 242.9 242.9
C2' C3' O3' HA 10.6 10.6
O2' C2' C3' C1' 247.1 247.1
O2' C2' C3' H2' 121.0 121.0
C3' C2' O2' HB 188.0 188.0
C3' C2' C1' N9 92.2 92.2
C3' C2' C1' H1' 208.8 208.8
C1' C2' C3' H2' 233.8 233.8
O4' C1' C2' O2' 88.5 88.5
C3' C2' O2' C1' 108.7 108.7
O2' C2' C3' H3' 167.4 167.4
C3' C2' O2' H2' 235.6 235.6
O2' C2' C1' N9 209.0 209.0
O2' C2' C1' H1' 325.7 325.7
C1' C2' O2' H2' 127.0 127.0
O4' C1' C2' N9 239.5 239.5
O4' C1' C2' H1' 122.9 122.9
C3' C2' C1' O2' 243.2 243.2
C1' C2' C3' H3' 280.3 280.3
C3' C2' C1' H2' 122.9 122.9
O2' C2' C1' H2' 239.7 239.7
C1' C2' O2' HB 79.3 79.3
C2' C1' N9 C8 243.8 243.8
C2' C1' N9 C4 64.4 64.4
N9 C1' C2' H1' 243.4 243.4
O4' C1' N9 C2' 117.8 117.8
O4' C1' N9 H1' 237.2 237.2
C2' C1' N9 H1' 119.4 119.4
N9 C1' C2' H2' 329.3 329.3
C8 N9 C1' C4 179.4 179.4
C1' N9 C8 N7 180.7 180.7
C1' N9 C8 H8 0.7 0.7
C1' N9 C4 C5 179.2 179.2
C1' N9 C4 N3 359.6 359.6
C1' N9 C8 C4 180.5 180.5
C8 N9 C1' H1' 124.4 124.4
C8 N9 C4 C5 359.7 359.7
C8 N9 C4 N3 180.1 180.1
N9 C8 N7 C5 0.1 0.1
N7 C8 N9 H8 180.0 180.0
C1' N9 C4 C8 179.5 179.5
C4 N9 C1' H1' 305.0 305.0
C4 N9 C8 N7 0.1 0.1
C4 N9 C8 H8 180.1 180.1
N7 C5 C4 N9 0.4 0.4
C6 C5 C4 N9 180.5 180.5
C5 C4 N9 N3 179.6 179.6
C2 N3 C4 N9 179.6 179.6
N7 C8 N9 C4 0.1 0.1
N9 C8 N7 H8 180.0 180.0
C8 N7 C5 C6 179.5 179.5
C8 N7 C5 C4 359.6 359.6
N9 C4 C5 N7 0.4 0.4
C5 N7 C8 H8 180.1 180.1
C6 C5 N7 C4 179.9 179.9
N7 C5 C6 N6 359.7 359.7
N7 C5 C6 N1 180.0 180.0
N7 C5 C4 N3 180.0 180.0
N9 C4 C5 C6 180.5 180.5
N7 C5 C6 C4 180.1 180.1
C6 C5 C4 N3 0.1 0.1
N6 C6 C5 N1 179.7 179.7
C5 C6 N6 H6N1 37.5 37.5
C5 C6 N6 H6N2 157.5 157.5
C5 C6 N1 C2 360.0 360.0
N9 C4 C5 N3 180.4 180.4
N7 C5 C4 C6 179.9 179.9
C4 C5 C6 N6 179.6 179.6
C4 C5 C6 N1 359.9 359.9
C2 N3 C4 C5 0.1 0.1
N6 C6 C5 C4 179.6 179.6
C5 C6 N6 N1 180.3 180.3
N6 C6 N1 C2 180.2 180.2
H6N1 N6 C6 H6N2 240.0 240.0
N1 C6 C5 C4 359.9 359.9
C5 C6 N1 N6 179.7 179.7
N1 C6 N6 H6N1 217.2 217.2
N1 C6 N6 H6N2 337.2 337.2
C6 N1 C2 N3 0.2 0.2
C6 N1 C2 H2 180.2 180.2
N1 C2 N3 C4 359.7 359.7
N3 C2 N1 H2 180.0 180.0
N9 C4 N3 C2 179.6 179.6
C5 C4 N3 C2 0.1 0.1
N1 C2 N3 H2 180.0 180.0
N9 C4 N3 C5 179.5 179.5
C4 N3 C2 H2 179.7 179.7
H2G1 O2G VG O3G 304.2 304.2
H2G1 O2G VG O3B 183.2 183.2
H3G1 O3G VG O3B 354.2 354.2
H2B O2B PB O3B 28.2 28.2
H2B O2B PB O3A 160.6 160.6
H2A O2A PA O3A 150.3 150.3
H2A O2A PA O5' 47.9 47.9
O5' C5' H5'1 C4' 240.3 240.3
O5' C5' H5'1 H5'2 120.2 120.2
H5'1 C5' C4' O4' 186.1 186.1
H5'1 C5' C4' C3' 298.3 298.3
C4' C5' H5'1 H5'2 239.9 239.9
H5'1 C5' C4' H4' 60.1 60.1
O5' C5' H5'2 C4' 119.8 119.8
O5' C5' H5'2 H5'1 239.9 239.9
H5'2 C5' C4' O4' 66.2 66.2
H5'2 C5' C4' C3' 178.5 178.5
C4' C5' H5'2 H5'1 120.1 120.1
H5'2 C5' C4' H4' 300.2 300.3
C5' C4' H4' O4' 119.6 119.6
C5' C4' H4' C3' 235.6 235.6
H4' C4' C5' H5'1 60.1 60.1
H4' C4' C5' H5'2 300.2 300.3
O4' C4' H4' C3' 116.0 116.0
H4' C4' O4' C1' 265.3 265.3
H4' C4' C3' O3' 321.2 321.2
H4' C4' C3' C2' 82.1 82.0
H4' C4' C3' H3' 204.2 204.2
C4' C3' H3' O3' 121.4 121.4
C4' C3' H3' C2' 244.3 244.3
H3' C3' C4' H4' 204.2 204.2
O3' C3' H3' C2' 122.9 122.9
H3' C3' O3' HA 248.1 248.1
H3' C3' C2' O2' 167.4 167.4
H3' C3' C2' C1' 280.3 280.3
H3' C3' C2' H2' 46.4 46.4
O4' C1' H1' C2' 242.9 242.9
O4' C1' H1' N9 119.8 119.8
C2' C1' H1' N9 236.9 236.9
H1' C1' C2' H2' 86.0 86.0
H1' C1' N9 C8 124.4 124.4
H1' C1' N9 C4 305.0 305.0
HA O3' C3' C2' 10.6 10.6
HA O3' C3' H3' 248.1 248.1
C3' C2' H2' O2' 123.7 123.7
C3' C2' H2' C1' 243.9 243.9
H2' C2' C3' H3' 46.4 46.4
O2' C2' H2' C1' 120.2 120.2
H2' C2' O2' HB 312.3 312.3
H2' C2' C1' N9 329.3 329.3
H2' C2' C1' H1' 86.0 86.0
HB O2' C2' C1' 79.3 79.3
HB O2' C2' H2' 312.3 312.3
H8 C8 N9 C4 180.1 180.1
N9 C8 H8 N7 180.0 180.0
H8 C8 N7 C5 180.1 180.1
H6N1 N6 C6 N1 217.2 217.2
C6 N6 H6N1 H6N2 120.0 120.0
H6N2 N6 C6 N1 337.2 337.2
C6 N6 H6N2 H6N1 240.0 240.0
N1 C2 H2 N3 180.0 180.0
H2 C2 N3 C4 179.7 179.7