PDB Chemical Component AP7

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 AP7

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
C1' N9 1.478 1.465
C1' C2' 1.525 1.549
C1' O4' 1.410 1.444
C1' H1' 1.100 1.090
N1 C2 1.352 1.321
N1 C6 1.360 1.329
N1 H1 1.000 0.970
C2 N3 1.346 1.316
C2 H2 1.080 1.080
N3 C4 1.361 1.330
C4 C5 1.359 1.404
C4 N9 1.371 1.372
C5 C6 1.410 1.405
C5 N7 1.369 1.355
C6 N6 1.358 1.383
N6 H61 1.000 0.970
N6 H62 1.000 0.970
N7 C8 1.329 1.302
C8 N9 1.349 1.363
C8 H8 1.080 1.080
C2' O2' 1.410 1.428
C2' C3' 1.504 1.548
C2' H2' 1.100 1.090
O2' HO2' 0.950 0.967
C3' O3' 1.426 1.429
C3' C4' 1.525 1.541
C3' H3' 1.100 1.090
O3' HO3' 0.950 0.967
C4' O4' 1.438 1.438
C4' C5' 1.512 1.530
C4' H4' 1.100 1.090
C5' O5' 1.426 1.429
C5' H5'' 1.100 1.091
C5' H5' 1.100 1.089
O5' P 1.600 1.609
OP1 P 1.480 1.481
OP2 P 1.480 1.610
OP2 HOP2 0.950 0.967
P OP3   1.611
OP3 HOP3   0.967

Bond Angles for AP7

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
N9 C1' C2' 113.5 110.6
N9 C1' O4' 111.2 110.6
N9 C1' H1' 103.6 110.5
C1' N9 C4 126.3 126.3
C1' N9 C8 127.4 126.3
C2' C1' O4' 102.5 103.5
C2' C1' H1' 112.0 110.6
C1' C2' O2' 115.4 110.9
C1' C2' C3' 100.7 102.1
C1' C2' H2' 109.5 110.9
O4' C1' H1' 114.3 110.8
C1' O4' C4' 116.5 106.9
C2 N1 C6 118.5 121.2
C2 N1 H1 120.7 119.4
N1 C2 N3 129.1 122.5
N1 C2 H2 115.4 118.8
C6 N1 H1 120.8 119.4
N1 C6 C5 117.4 118.5
N1 C6 N6 118.1 120.8
N3 C2 H2 115.5 118.7
C2 N3 C4 109.5 120.6
N3 C4 C5 128.0 119.1
N3 C4 N9 125.9 134.9
C5 C4 N9 106.1 106.0
C4 C5 C6 117.4 118.2
C4 C5 N7 111.0 107.1
C4 N9 C8 106.3 107.5
C6 C5 N7 131.5 134.7
C5 C6 N6 124.5 120.8
C5 N7 C8 103.9 109.5
C6 N6 H61 120.0 120.0
C6 N6 H62 120.0 120.0
H61 N6 H62 120.0 120.0
N7 C8 N9 112.7 109.9
N7 C8 H8 123.6 125.0
N9 C8 H8 123.6 125.1
O2' C2' C3' 102.6 110.9
O2' C2' H2' 107.7 110.8
C2' O2' HO2' 109.5 114.1
C3' C2' H2' 121.1 110.9
C2' C3' O3' 111.5 110.5
C2' C3' C4' 105.3 104.2
C2' C3' H3' 110.8 110.5
O3' C3' C4' 109.4 110.5
O3' C3' H3' 106.8 110.4
C3' O3' HO3' 109.5 114.0
C4' C3' H3' 112.9 110.6
C3' C4' O4' 93.5 107.3
C3' C4' C5' 114.4 109.9
C3' C4' H4' 116.4 109.9
O4' C4' C5' 109.2 109.9
O4' C4' H4' 121.1 109.8
C5' C4' H4' 102.6 110.0
C4' C5' O5' 110.1 109.5
C4' C5' H5'' 109.2 109.5
C4' C5' H5' 109.3 109.5
O5' C5' H5'' 109.3 109.4
O5' C5' H5' 109.3 109.5
C5' O5' P 120.0 123.0
H5'' C5' H5' 109.7 109.5
O5' P OP1 108.0 109.5
O5' P OP2 108.0 109.5
O5' P OP3   109.5
OP1 P OP2 117.4 109.4
OP1 P OP3   109.5
P OP2 HOP2 109.5 114.0
OP2 P OP3   109.5
P OP3 HOP3   114.0

Torsion Angles for AP7

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
C2' C1' N9 O4' 245.0 245.9
C2' C1' N9 H1' 121.8 122.9
N9 C1' C2' O2' 211.7 273.7
N9 C1' C2' C3' 102.0 155.5
N9 C1' C2' H2' 333.4 37.3
O4' C1' N9 H1' 236.7 237.0
N9 C1' O4' C4' 226.4 201.4
N3 C4 N9 C1' 360.0 0.1
C5 C4 N9 C1' 180.0 180.0
C4 N9 C1' C8 180.0 180.0
N7 C8 N9 C1' 180.0 180.0
C1' N9 C8 H8 360.0 360.0
N9 C1' C2' O4' 120.0 118.5
N9 C1' C2' H1' 243.1 237.2
C2' C1' N9 C4 92.5 85.0
C2' C1' N9 C8 272.5 265.0
O4' C1' C2' H1' 123.1 118.7
C2' C1' O4' C4' 348.0 320.0
O2' C2' C1' C3' 109.7 118.2
O2' C2' C1' H2' 238.3 236.5
C1' C2' O2' HO2' 180.0 180.0
C3' C2' C1' H2' 128.6 118.2
C1' C2' C3' O3' 159.3 97.8
C1' C2' C3' C4' 40.7 339.1
C1' C2' C3' H3' 278.2 220.3
N9 C1' O4' C2' 238.4 241.5
N9 C1' O4' H1' 116.9 122.9
O4' C1' N9 C4 207.5 199.1
O4' C1' N9 C8 27.5 19.1
C2' C1' O4' H1' 238.5 241.4
O4' C1' C2' O2' 91.7 155.2
O4' C1' C2' C3' 342.0 37.0
O4' C1' C2' H2' 213.4 278.8
C3' C4' O4' C1' 35.2 26.5
C1' O4' C4' C5' 152.6 145.9
C1' O4' C4' H4' 271.3 267.1
N9 C1' H1' C2' 122.7 122.9
N9 C1' H1' O4' 238.8 237.1
H1' C1' N9 C4 330.7 322.1
H1' C1' N9 C8 150.7 142.1
C2' C1' H1' O4' 116.1 114.2
H1' C1' C2' O2' 328.6 36.6
H1' C1' C2' C3' 218.9 278.3
H1' C1' C2' H2' 90.3 160.1
H1' C1' O4' C4' 109.5 78.5
C6 N1 C2 H1 180.0 180.2
C2 N1 C6 C5 359.9 0.1
C2 N1 C6 N6 180.0 179.9
N3 C2 N1 H2 180.0 180.0
N1 C2 N3 C4 359.9 359.9
C2 N1 C6 H1 180.0 179.8
C6 N1 C2 N3 0.1 0.0
C6 N1 C2 H2 180.1 180.0
C4 C5 C6 N1 0.0 359.9
N1 C6 C5 N7 180.0 180.0
C5 C6 N1 N6 180.0 180.1
N1 C6 N6 H61 180.0 0.1
N1 C6 N6 H62 360.0 180.0
C2 N1 H1 C6 180.0 180.2
H1 N1 C2 N3 180.1 179.8
H1 N1 C2 H2 0.1 359.8
H1 N1 C6 C5 179.9 180.2
H1 N1 C6 N6 360.0 0.1
N3 C2 N1 C6 0.1 0.0
N3 C2 N1 H1 180.1 179.8
N1 C2 N3 H2 180.0 180.0
C2 N3 C4 C5 0.0 0.0
C2 N3 C4 N9 180.1 180.0
H2 C2 N1 C6 180.1 180.0
H2 C2 N1 H1 0.1 359.8
N1 C2 H2 N3 180.0 180.0
H2 C2 N3 C4 179.9 180.0
C1' N9 C4 N3 360.0 0.1
C4 N3 C2 H2 179.9 180.0
C5 C4 N3 N9 180.0 180.1
N3 C4 C5 C6 360.0 0.0
N3 C4 C5 N7 180.0 180.0
N3 C4 N9 C8 180.0 180.0
C1' N9 C4 C5 180.0 180.0
N1 C6 C5 C4 0.0 359.9
N3 C4 C5 N9 180.0 180.0
C5 C4 N9 C8 0.0 360.0
C6 C5 C4 N7 180.0 180.1
C4 C5 C6 N6 180.0 180.0
C4 C5 N7 C8 360.0 0.0
C4 N9 C1' C2' 92.5 85.0
C4 N9 C1' O4' 207.5 199.1
C4 N9 C1' H1' 330.7 322.1
C1' N9 C4 C8 180.0 180.0
N3 C4 N9 C5 180.0 180.0
N9 C4 C5 C6 180.0 180.1
N9 C4 C5 N7 360.0 360.0
N7 C8 N9 C4 360.0 0.0
C4 N9 C8 H8 180.0 180.0
C5 C6 N1 H1 179.9 180.2
N1 C6 C5 N6 180.0 179.9
C6 C5 C4 N9 180.0 180.1
C4 C5 C6 N7 180.0 179.9
C6 C5 N7 C8 180.0 179.9
C5 C6 N6 H61 0.0 180.0
C5 C6 N6 H62 180.0 359.9
N7 C5 C4 N9 360.0 360.0
C4 C5 N7 C6 180.0 180.1
N7 C5 C6 N6 360.0 0.1
C5 N7 C8 N9 0.0 360.0
C5 N7 C8 H8 180.0 180.0
N6 C6 N1 H1 360.0 0.1
N1 C6 N6 C5 180.0 180.1
N6 C6 C5 N7 360.0 0.1
H61 N6 C6 H62 180.0 180.1
C6 N6 H61 H62 180.0 179.9
C6 N6 H62 H61 180.0 180.1
C1' N9 C8 N7 180.0 180.0
C4 N9 C8 N7 360.0 0.0
N9 C8 N7 H8 180.0 180.0
C8 N9 C1' C2' 272.5 265.0
C8 N9 C1' O4' 27.5 19.1
C8 N9 C1' H1' 150.7 142.1
C1' N9 C8 C4 180.0 180.0
N7 C8 N9 H8 180.0 180.0
N7 C8 H8 N9 180.0 180.0
O2' C2' C1' O4' 91.7 155.2
O2' C2' C1' H1' 328.6 36.6
C1' C2' O2' C3' 251.5 247.2
C1' C2' O2' H2' 122.7 123.6
C3' C2' O2' H2' 231.2 236.4
O2' C2' C3' O3' 40.0 339.5
O2' C2' C3' C4' 281.3 220.9
O2' C2' C3' H3' 158.9 102.1
C3' C2' C1' O4' 342.0 37.0
C3' C2' C1' H1' 218.9 278.3
C1' C2' C3' O2' 119.4 118.3
C1' C2' C3' H2' 239.3 241.8
O2' C2' C3' H2' 120.0 123.5
C3' C2' O2' HO2' 288.5 292.8
O3' C3' C2' C4' 118.6 118.7
O3' C3' C2' H3' 241.1 237.5
C2' C3' O3' HO3' 180.0 61.5
C4' C3' C2' H3' 122.4 118.8
C2' C3' C4' O4' 315.4 358.0
C2' C3' C4' C5' 202.4 238.5
C2' C3' C4' H4' 82.8 117.3
H2' C2' C1' O4' 213.4 278.8
H2' C2' C1' H1' 90.3 160.1
C1' C2' H2' O2' 233.7 236.3
C1' C2' H2' C3' 116.3 112.7
O2' C2' H2' C3' 242.6 236.4
H2' C2' O2' HO2' 57.3 56.4
H2' C2' C3' O3' 280.0 216.0
H2' C2' C3' C4' 161.3 97.4
H2' C2' C3' H3' 38.9 338.5
HO2' O2' C2' C3' 288.5 292.8
HO2' O2' C2' H2' 57.3 56.4
O3' C3' C2' H2' 280.0 216.0
C2' C3' O3' C4' 243.8 245.2
C2' C3' O3' H3' 121.3 122.6
C4' C3' O3' H3' 237.4 237.4
O3' C3' C4' O4' 195.3 239.3
O3' C3' C4' C5' 82.4 119.9
O3' C3' C4' H4' 322.8 358.7
C1' O4' C4' C3' 35.2 26.5
C4' C3' C2' H2' 161.3 97.4
C2' C3' C4' O3' 120.0 118.7
C2' C3' C4' H3' 238.9 241.2
O3' C3' C4' H3' 118.9 122.5
C4' C3' O3' HO3' 296.2 176.3
O4' C4' C3' C5' 113.0 119.4
O4' C4' C3' H4' 232.5 240.6
C5' C4' C3' H4' 119.6 121.2
C3' C4' C5' O5' 65.9 185.0
C3' C4' C5' H5'' 185.9 304.9
C3' C4' C5' H5' 305.9 65.0
H3' C3' C2' H2' 38.9 338.5
C2' C3' H3' O3' 238.3 237.4
C2' C3' H3' C4' 117.9 114.9
O3' C3' H3' C4' 239.6 237.4
H3' C3' O3' HO3' 58.8 298.9
H3' C3' C4' O4' 76.5 116.8
H3' C3' C4' C5' 323.5 357.3
H3' C3' C4' H4' 203.9 236.1
HO3' O3' C3' C4' 296.2 176.3
HO3' O3' C3' H3' 58.8 298.9
C4' O4' C1' H1' 109.5 78.5
O4' C4' C3' H3' 76.5 116.8
C3' C4' O4' C5' 242.6 240.5
C3' C4' O4' H4' 123.9 119.4
C5' C4' O4' H4' 241.3 238.9
O4' C4' C5' O5' 322.6 67.2
O4' C4' C5' H5'' 82.6 187.1
O4' C4' C5' H5' 202.6 307.1
C5' C4' C3' H3' 323.5 357.3
C3' C4' C5' O4' 103.3 117.8
C3' C4' C5' H4' 233.0 238.8
O4' C4' C5' H4' 129.7 121.0
O5' C5' C4' H5'' 240.0 240.1
O5' C5' C4' H5' 120.0 120.0
C4' C5' O5' P 141.9 180.0
H5'' C5' C4' H5' 240.0 240.0
H4' C4' C3' H3' 203.9 236.1
C3' C4' H4' O4' 247.7 242.2
C3' C4' H4' C5' 125.8 121.2
O4' C4' H4' C5' 238.1 239.0
H4' C4' C5' O5' 192.9 306.2
H4' C4' C5' H5'' 312.9 66.1
H4' C4' C5' H5' 72.9 186.1
O5' C5' C4' H4' 192.9 306.2
C4' C5' O5' H5'' 120.0 120.0
C4' C5' O5' H5' 240.0 239.9
H5'' C5' O5' H5' 120.0 120.0
C5' O5' P OP1 49.9 55.0
C5' O5' P OP2 177.9 174.9
C5' O5' P OP3   295.0
H5'' C5' C4' H4' 312.9 66.1
C4' C5' H5'' O5' 239.5 240.0
C4' C5' H5'' H5' 119.7 120.0
O5' C5' H5'' H5' 240.2 240.0
H5'' C5' O5' P 21.9 60.0
H5' C5' C4' H4' 72.9 186.1
C4' C5' H5' O5' 120.5 120.1
C4' C5' H5' H5'' 240.3 240.0
O5' C5' H5' H5'' 119.8 119.9
H5' C5' O5' P 261.9 300.1
P O5' C5' H5'' 21.9 60.0
P O5' C5' H5' 261.9 300.1
OP1 P O5' OP2 232.0 240.0
OP1 P O5' OP3   120.0
O5' P OP2 HOP2 237.6 180.0
OP2 P O5' OP3   240.0
O5' P OP3 HOP3   300.0
O5' P OP1 OP2 122.4 120.0
O5' P OP1 OP3   240.0
OP1 P OP2 HOP2 360.0 300.0
OP2 P OP1 OP3   120.0
OP1 P OP3 HOP3   180.0
O5' P OP2 OP1 237.6 240.0
O5' P OP2 OP3   120.0
OP1 P OP2 OP3   240.0
OP2 P OP3 HOP3   60.0
HOP2 OP2 P OP3   59.9
O5' P OP3 OP1   120.0
O5' P OP3 OP2   240.0
OP1 P OP3 OP2   120.0
OP3 P OP2 HOP2   59.9