PDB Chemical Component ATD

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 ATD

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
P OP1 1.480 1.479
P OP2 1.478 1.610
P OP3 1.608 1.610
P O3' 1.616 1.609
OP2 HOP2 0.951 0.967
OP3 HOP3 0.951 0.968
O5' C5' 1.406 1.429
O5' HO'5 0.950 0.966
C5' C4' 1.521 1.530
C5' H5' 1.093 1.091
C5' H5'' 1.063 1.089
C4' O4' 1.407 1.432
C4' C3' 1.512 1.543
C4' H4' 1.049 1.090
O4' C1' 1.417 1.436
C3' O3' 1.401 1.428
C3' C2' 1.523 1.553
C3' H3' 1.063 1.091
C2' C1' 1.521 1.549
C2' H2' 1.081 1.089
C2' H2'' 1.085 1.089
C1' N1 1.483 1.465
C1' H1' 1.092 1.090
N1 C2 1.397 1.345
N1 C6 1.368 1.368
C2 O2 1.225 1.216
C2 N3 1.378 1.346
N3 C4 1.382 1.349
N3 H3 1.017 0.969
C4 O4 1.226 1.217
C4 C5 1.464 1.415
C5 C5M 1.512 1.507
C5 C6 1.352 1.350
C5M H71 1.090 1.090
C5M H72 1.079 1.089
C5M H73 1.089 1.090
C6 H6 1.077 1.080

Bond Angles for ATD

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
OP1 P OP2 120.5 109.5
OP1 P OP3 108.8 109.5
OP1 P O3' 109.1 109.5
OP2 P OP3 109.6 109.4
OP2 P O3' 108.4 109.5
P OP2 HOP2 120.4 106.8
OP3 P O3' 98.3 109.4
P OP3 HOP3 108.8 106.9
P O3' C3' 123.0 106.9
C5' O5' HO'5 112.9 106.8
O5' C5' C4' 113.0 109.5
O5' C5' H5' 109.6 109.5
O5' C5' H5'' 108.2 109.5
C4' C5' H5' 111.3 109.5
C4' C5' H5'' 106.2 109.4
C5' C4' O4' 117.0 109.8
C5' C4' C3' 111.8 109.9
C5' C4' H4' 106.7 109.8
H5' C5' H5'' 108.3 109.5
O4' C4' C3' 105.7 107.7
O4' C4' H4' 106.2 109.9
C4' O4' C1' 111.0 109.9
C3' C4' H4' 109.1 109.8
C4' C3' O3' 109.6 111.1
C4' C3' C2' 103.8 102.2
C4' C3' H3' 111.6 110.8
O4' C1' C2' 107.6 105.2
O4' C1' N1 112.9 110.4
O4' C1' H1' 104.8 110.3
O3' C3' C2' 112.4 110.9
O3' C3' H3' 107.5 110.7
C2' C3' H3' 112.0 110.8
C3' C2' C1' 103.2 101.0
C3' C2' H2' 112.8 111.1
C3' C2' H2'' 110.3 111.2
C1' C2' H2' 108.5 111.1
C1' C2' H2'' 112.3 111.1
C2' C1' N1 106.7 110.3
C2' C1' H1' 114.6 110.3
H2' C2' H2'' 109.6 111.0
N1 C1' H1' 110.3 110.3
C1' N1 C2 119.3 119.7
C1' N1 C6 119.5 119.7
C2 N1 C6 121.1 120.6
N1 C2 O2 123.3 119.5
N1 C2 N3 116.3 120.9
N1 C6 C5 121.5 119.7
N1 C6 H6 117.9 120.1
O2 C2 N3 120.4 119.5
C2 N3 C4 125.9 120.3
C2 N3 H3 115.9 119.9
C4 N3 H3 118.0 119.9
N3 C4 O4 118.8 120.3
N3 C4 C5 114.3 119.4
O4 C4 C5 126.9 120.3
C4 C5 C5M 122.5 120.5
C4 C5 C6 120.4 119.2
C5M C5 C6 117.2 120.4
C5 C5M H71 110.1 109.4
C5 C5M H72 109.1 109.5
C5 C5M H73 110.5 109.5
C5 C6 H6 120.6 120.2
H71 C5M H72 111.1 109.5
H71 C5M H73 108.8 109.4
H72 C5M H73 107.1 109.5

Torsion Angles for ATD

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
OP2 P OP1 OP3 127.6 120.0
OP2 P OP1 O3' 233.8 239.9
OP1 P OP2 HOP2 180.0 300.0
OP3 P OP1 O3' 106.2 120.0
OP1 P OP3 HOP3 180.1 180.0
OP1 P O3' C3' 350.5 60.0
OP1 P OP2 OP3 232.7 240.0
OP1 P OP2 O3' 126.6 120.1
OP3 P OP2 O3' 253.8 240.0
OP2 P OP3 HOP3 46.5 60.0
OP2 P O3' C3' 123.4 180.0
OP1 P OP3 OP2 133.6 120.0
OP1 P OP3 O3' 246.5 240.0
OP2 P OP3 O3' 112.9 120.0
OP3 P OP2 HOP2 307.2 60.0
OP3 P O3' C3' 237.3 300.0
OP1 P O3' OP2 227.1 240.0
OP1 P O3' OP3 113.2 120.0
OP2 P O3' OP3 246.1 240.0
O3' P OP2 HOP2 53.4 180.0
O3' P OP3 HOP3 293.6 300.0
C4' C3' O3' P 286.5 234.4
P O3' C3' C2' 171.7 121.5
P O3' C3' H3' 48.0 358.0
HOP2 OP2 P OP3 307.2 60.0
HOP2 OP2 P O3' 53.4 180.0
HOP3 OP3 P O3' 293.6 300.0
C4' C5' O5' H5' 124.8 120.0
C4' C5' O5' H5'' 242.8 240.0
O5' C5' C4' O4' 53.8 61.8
O5' C5' C4' C3' 175.9 180.0
O5' C5' C4' H4' 295.0 300.9
H5' C5' O5' H5'' 117.9 120.0
HO'5 O5' C5' C4' 180.0 180.0
HO'5 O5' C5' H5' 55.2 60.0
HO'5 O5' C5' H5'' 297.3 300.0
C4' C5' O5' HO'5 180.0 180.0
O5' C5' C4' H5' 236.1 240.0
O5' C5' C4' H5'' 118.4 120.0
H5' C5' C4' H5'' 242.3 240.0
O4' C4' C5' C3' 237.9 241.8
O4' C4' C5' H4' 118.7 120.9
C5' C4' O4' C1' 103.3 118.1
C3' C4' C5' H4' 240.8 239.2
C5' C4' C3' O3' 141.0 100.7
C5' C4' C3' C2' 261.2 219.0
C5' C4' C3' H3' 22.0 337.2
H5' C5' O5' HO'5 55.2 60.0
O5' C5' H5' C4' 125.7 120.0
O5' C5' H5' H5'' 242.1 240.0
C4' C5' H5' H5'' 116.4 119.9
H5' C5' C4' O4' 177.6 181.8
H5' C5' C4' C3' 299.7 300.1
H5' C5' C4' H4' 58.9 60.9
H5'' C5' O5' HO'5 297.3 300.0
O5' C5' H5'' C4' 238.5 240.0
O5' C5' H5'' H5' 118.8 120.0
C4' C5' H5'' H5' 240.3 240.0
H5'' C5' C4' O4' 295.3 301.8
H5'' C5' C4' C3' 57.4 60.0
H5'' C5' C4' H4' 176.6 180.9
O4' C4' C5' H5' 177.6 181.8
O4' C4' C5' H5'' 295.3 301.8
C5' C4' O4' C3' 125.2 119.6
C5' C4' O4' H4' 241.0 239.1
C3' C4' O4' H4' 115.8 119.5
O4' C4' C3' O3' 269.4 220.2
O4' C4' C3' C2' 29.6 338.6
O4' C4' C3' H3' 150.4 96.7
C4' O4' C1' C2' 4.9 24.2
C4' O4' C1' N1 122.4 143.2
C4' O4' C1' H1' 242.5 265.3
P O3' C3' C4' 286.5 234.4
C3' C4' C5' H5' 299.7 300.1
C3' C4' C5' H5'' 57.4 60.0
C5' C4' C3' O4' 231.6 240.4
C5' C4' C3' H4' 117.7 120.8
O4' C4' C3' H4' 246.1 240.4
C3' C4' O4' C1' 338.1 358.5
O3' C3' C4' C2' 239.8 241.7
O3' C3' C4' H3' 119.0 123.5
C2' C3' C4' H3' 239.2 241.9
C4' C3' C2' C1' 334.1 34.1
C4' C3' C2' H2' 91.1 276.2
C4' C3' C2' H2'' 214.0 152.0
H4' C4' C5' H5' 58.9 60.9
H4' C4' C5' H5'' 176.6 180.9
C5' C4' H4' O4' 125.6 120.9
C5' C4' H4' C3' 239.1 239.1
O4' C4' H4' C3' 113.5 118.2
H4' C4' O4' C1' 222.3 238.9
H4' C4' C3' O3' 23.3 339.8
H4' C4' C3' C2' 143.5 98.2
H4' C4' C3' H3' 264.3 216.3
C1' O4' C4' C3' 338.1 358.5
C1' O4' C4' H4' 222.3 238.9
C3' C2' C1' O4' 13.8 323.7
O4' C1' C2' H2' 253.8 81.6
O4' C1' C2' H2'' 132.5 205.7
C2' C1' O4' N1 242.5 241.0
C2' C1' O4' H1' 122.4 118.9
N1 C1' O4' H1' 239.9 238.0
O4' C1' N1 C2 143.5 302.8
O4' C1' N1 C6 322.3 122.7
O3' C3' C4' H4' 23.3 339.8
C4' C3' O3' C2' 114.8 113.0
C4' C3' O3' H3' 238.5 236.4
C2' C3' O3' H3' 123.7 123.4
O3' C3' C2' C1' 92.5 152.6
O3' C3' C2' H2' 209.4 34.7
O3' C3' C2' H2'' 332.3 270.5
C2' C3' C4' H4' 143.5 98.2
C4' C3' C2' O3' 241.7 241.5
C4' C3' C2' H3' 120.5 118.2
O4' C1' C2' C3' 13.8 323.7
O3' C3' C2' H3' 238.9 236.7
C1' C2' C3' H2' 243.1 117.9
C1' C2' C3' H2'' 120.2 242.1
C3' C2' C1' N1 252.3 204.6
C3' C2' C1' H1' 130.0 82.6
H2' C2' C3' H2'' 237.1 124.2
H3' C3' C4' H4' 264.3 216.3
C4' C3' H3' O3' 120.2 123.8
C4' C3' H3' C2' 244.1 247.2
O3' C3' H3' C2' 123.9 123.5
H3' C3' C2' C1' 213.6 275.9
H3' C3' C2' H2' 330.6 158.0
H3' C3' C2' H2'' 93.4 33.8
O4' C1' C2' N1 121.4 119.0
O4' C1' C2' H1' 243.8 241.1
C1' C2' C3' H3' 213.6 275.9
C3' C2' C1' H2' 119.9 242.1
C3' C2' C1' H2'' 241.2 118.0
H2' C2' C1' H2'' 121.3 235.9
N1 C1' C2' H1' 122.4 122.1
C2' C1' N1 C2 261.5 58.7
C2' C1' N1 C6 80.3 238.6
H2' C2' C3' H3' 330.6 158.0
C3' C2' H2' C1' 246.2 111.6
C3' C2' H2' H2'' 123.3 235.7
C1' C2' H2' H2'' 237.0 124.2
H2' C2' C1' N1 132.4 322.5
H2' C2' C1' H1' 10.0 200.5
H2'' C2' C3' H3' 93.4 33.8
C3' C2' H2'' C1' 114.5 248.4
C3' C2' H2'' H2' 235.2 124.2
C1' C2' H2'' H2' 120.7 235.8
H2'' C2' C1' N1 11.1 86.7
H2'' C2' C1' H1' 248.7 324.6
O4' C1' N1 C2' 242.0 244.1
O4' C1' N1 H1' 116.9 122.0
N1 C1' C2' H2' 132.4 322.5
N1 C1' C2' H2'' 11.1 86.7
C2' C1' N1 H1' 234.9 237.9
C2 N1 C1' C6 181.2 180.1
C1' N1 C2 O2 2.5 359.9
C1' N1 C2 N3 183.7 180.0
C1' N1 C6 C5 173.0 180.1
C1' N1 C6 H6 353.8 0.0
O4' C1' H1' C2' 117.8 115.8
O4' C1' H1' N1 238.2 237.9
H1' C1' C2' H2' 10.0 200.5
H1' C1' C2' H2'' 248.7 324.6
C2' C1' H1' N1 120.4 122.1
H1' C1' N1 C2 26.6 180.8
H1' C1' N1 C6 205.3 0.7
C2 N1 C1' H1' 26.6 180.8
C1' N1 C2 C6 178.8 179.9
C2 N1 C6 C5 351.8 360.0
C2 N1 C6 H6 172.5 180.0
O2 C2 N1 N3 178.8 179.9
N1 C2 N3 C4 0.9 359.7
N1 C2 N3 H3 175.3 180.0
C6 N1 C1' H1' 205.3 0.7
C1' N1 C6 C2 181.2 180.1
C6 N1 C2 O2 183.7 180.0
C6 N1 C2 N3 4.9 0.1
C4 C5 C6 N1 5.6 0.2
C5M C5 C6 N1 186.4 180.0
C5 C6 N1 H6 179.2 180.0
O2 C2 N1 C6 183.7 180.0
N1 C2 O2 N3 181.3 180.1
O2 C2 N3 C4 182.0 179.8
O2 C2 N3 H3 356.4 0.1
N3 C2 N1 C6 4.9 0.1
N1 C2 N3 O2 178.8 179.9
C4 N3 C2 H3 185.6 179.7
C2 N3 C4 O4 178.4 180.1
C2 N3 C4 C5 356.8 0.4
C2 N3 C4 H3 174.3 180.3
O4 C4 N3 C5 181.6 179.6
N3 C4 C5 C5M 179.1 179.8
N3 C4 C5 C6 360.0 359.6
C2 N3 H3 C4 185.1 179.7
H3 N3 C4 O4 4.1 359.8
H3 N3 C4 C5 182.5 180.1
O4 C4 N3 H3 4.1 359.8
N3 C4 O4 C5 178.1 180.4
O4 C4 C5 C5M 357.3 0.1
O4 C4 C5 C6 178.2 180.0
N1 C6 C5 C4 5.6 0.2
C5 C4 N3 H3 182.5 180.1
N3 C4 C5 O4 181.8 179.6
C5M C5 C4 C6 179.1 180.1
C4 C5 C5M H71 323.4 359.8
C4 C5 C5M H72 85.6 119.7
C4 C5 C5M H73 203.2 239.8
C4 C5 C6 H6 184.8 180.2
N1 C6 C5 C5M 186.4 180.0
C4 C5 C5M C6 180.8 179.9
C5M C5 C6 H6 5.6 0.0
H71 C5M C5 H72 237.8 240.0
H71 C5M C5 H73 120.2 120.0
H72 C5M C5 H73 242.4 240.0
N1 C6 C5 H6 180.8 180.0
C4 C5 C6 C5M 179.2 180.1
C6 C5 C5M H71 142.6 179.9
C6 C5 C5M H72 264.8 299.9
C6 C5 C5M H73 22.3 59.9
H71 C5M C5 C6 142.6 179.9
C5 C5M H71 H72 121.0 120.0
C5 C5M H71 H73 238.8 239.9
H72 C5M H71 H73 117.8 120.0
H72 C5M C5 C6 264.8 299.9
C5 C5M H72 H71 238.4 240.1
C5 C5M H72 H73 119.6 120.1
H71 C5M H72 H73 241.2 240.0
H73 C5M C5 C6 22.3 59.9
C5 C5M H73 H71 121.0 120.0
C5 C5M H73 H72 241.2 240.0
H71 C5M H73 H72 120.3 120.0
N1 C6 H6 C5 179.2 180.0