PDB Chemical Component DA

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 DA

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
OP3 P 1.633 1.610
OP3 HOP3 0.951 0.967
P OP1 1.491 1.480
P OP2 1.440 1.610
P O5' 1.582 1.609
OP2 HOP2 0.951 0.966
O5' C5' 1.445 1.428
C5' C4' 1.503 1.530
C5' H5' 1.115 1.090
C5' H5'' 1.115 1.089
C4' O4' 1.438 1.446
C4' C3' 1.527 1.549
C4' H4' 1.115 1.089
O4' C1' 1.444 1.436
C3' O3' 1.450 1.429
C3' C2' 1.521 1.547
C3' H3' 1.115 1.090
O3' HO3' 0.950 0.966
C2' C1' 1.519 1.541
C2' H2' 1.114 1.089
C2' H2'' 1.116 1.091
C1' N9 1.450 1.466
C1' H1' 1.116 1.090
N9 C8 1.368 1.362
N9 C4 1.375 1.372
C8 N7 1.294 1.301
C8 H8 1.103 1.080
N7 C5 1.387 1.355
C5 C6 1.409 1.405
C5 C4 1.389 1.405
C6 N6 1.333 1.384
C6 N1 1.351 1.329
N6 H61 1.021 0.970
N6 H62 1.020 0.971
N1 C2 1.344 1.319
C2 N3 1.326 1.316
C2 H2 1.104 1.080
N3 C4 1.340 1.329

Bond Angles for DA

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
P OP3 HOP3 106.6 106.8
OP3 P OP1 106.6 109.5
OP3 P OP2 107.2 109.4
OP3 P O5' 99.1 109.5
OP1 P OP2 121.5 109.5
OP1 P O5' 110.7 109.5
OP2 P O5' 109.3 109.5
P OP2 HOP2 121.4 106.8
P O5' C5' 118.9 106.8
O5' C5' C4' 107.6 109.5
O5' C5' H5' 112.9 109.4
O5' C5' H5'' 112.9 109.5
C4' C5' H5' 112.9 109.5
C4' C5' H5'' 112.8 109.5
C5' C4' O4' 110.9 110.8
C5' C4' C3' 115.8 110.6
C5' C4' H4' 102.7 110.5
H5' C5' H5'' 97.6 109.4
O4' C4' C3' 105.0 103.6
O4' C4' H4' 113.9 110.5
C4' O4' C1' 112.1 106.8
C3' C4' H4' 108.8 110.6
C4' C3' O3' 106.3 111.0
C4' C3' C2' 104.3 102.1
C4' C3' H3' 115.7 110.9
O4' C1' C2' 105.2 107.5
O4' C1' N9 107.6 109.8
O4' C1' H1' 115.8 109.9
O3' C3' C2' 112.3 110.9
O3' C3' H3' 108.1 110.8
C3' O3' HO3' 106.3 106.9
C2' C3' H3' 110.1 111.0
C3' C2' C1' 103.6 104.2
C3' C2' H2' 114.5 110.5
C3' C2' H2'' 114.4 110.4
C1' C2' H2' 114.4 110.6
C1' C2' H2'' 114.4 110.5
C2' C1' N9 115.7 109.9
C2' C1' H1' 107.7 109.9
H2' C2' H2'' 96.0 110.5
N9 C1' H1' 105.3 109.8
C1' N9 C8 128.2 126.3
C1' N9 C4 124.6 126.3
C8 N9 C4 106.1 107.5
N9 C8 N7 113.5 110.0
N9 C8 H8 125.7 125.0
N9 C4 C5 105.6 106.0
N9 C4 N3 128.1 135.0
N7 C8 H8 120.8 125.0
C8 N7 C5 105.1 109.5
N7 C5 C6 133.1 134.7
N7 C5 C4 109.7 107.1
C6 C5 C4 117.3 118.2
C5 C6 N6 123.2 120.8
C5 C6 N1 117.3 118.5
C5 C4 N3 126.2 119.0
N6 C6 N1 119.5 120.8
C6 N6 H61 123.2 120.0
C6 N6 H62 107.3 120.0
C6 N1 C2 119.0 121.2
H61 N6 H62 107.3 120.0
N1 C2 N3 128.7 122.5
N1 C2 H2 116.5 118.7
N3 C2 H2 114.8 118.7
C2 N3 C4 111.5 120.6

Torsion Angles for DA

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
OP1 P OP3 OP2 131.5 240.0
OP1 P OP3 O5' 245.1 120.0
OP2 P OP3 O5' 113.5 240.0
OP3 P OP2 HOP2 302.7 60.1
OP3 P O5' C5' 288.5 180.0
HOP3 OP3 P OP1 180.0 300.0
HOP3 OP3 P OP2 48.5 60.0
HOP3 OP3 P O5' 295.0 180.0
OP1 P OP3 HOP3 180.0 300.0
OP3 P OP1 OP2 237.0 119.9
OP3 P OP1 O5' 106.8 240.0
OP2 P OP1 O5' 229.8 120.1
OP1 P OP2 HOP2 180.0 180.0
OP1 P O5' C5' 40.2 60.0
OP2 P OP3 HOP3 48.5 60.0
OP3 P OP2 OP1 122.7 240.0
OP3 P OP2 O5' 253.5 120.0
OP1 P OP2 O5' 130.8 240.0
OP2 P O5' C5' 176.6 299.9
O5' P OP3 HOP3 295.0 180.0
OP3 P O5' OP1 248.3 120.0
OP3 P O5' OP2 111.9 240.0
OP1 P O5' OP2 223.6 120.1
O5' P OP2 HOP2 49.2 300.1
P O5' C5' C4' 147.4 180.0
P O5' C5' H5' 272.6 60.0
P O5' C5' H5'' 22.2 300.0
HOP2 OP2 P O5' 49.2 300.1
C4' C5' O5' H5' 234.8 120.0
C4' C5' O5' H5'' 125.2 240.0
O5' C5' C4' O4' 290.4 65.7
O5' C5' C4' C3' 50.0 180.0
O5' C5' C4' H4' 168.4 302.9
H5' C5' O5' H5'' 250.4 119.9
O5' C5' C4' H5' 125.3 240.0
O5' C5' C4' H5'' 234.8 120.0
H5' C5' C4' H5'' 109.5 240.0
O4' C4' C5' C3' 240.5 245.7
O4' C4' C5' H4' 122.0 122.8
C5' C4' O4' C1' 118.1 158.5
C3' C4' C5' H4' 241.6 237.1
C5' C4' C3' O3' 142.7 86.1
C5' C4' C3' C2' 261.6 204.3
C5' C4' C3' H3' 22.6 322.5
O5' C5' H5' C4' 237.6 120.0
O5' C5' H5' H5'' 118.9 240.0
C4' C5' H5' H5'' 241.2 120.0
H5' C5' C4' O4' 165.2 185.7
H5' C5' C4' C3' 284.7 300.0
H5' C5' C4' H4' 43.1 62.9
O5' C5' H5'' C4' 122.3 239.9
O5' C5' H5'' H5' 241.1 119.9
C4' C5' H5'' H5' 118.8 240.0
H5'' C5' C4' O4' 55.7 305.7
H5'' C5' C4' C3' 175.2 60.0
H5'' C5' C4' H4' 293.6 182.9
O4' C4' C5' H5' 165.2 185.7
O4' C4' C5' H5'' 55.7 305.7
C5' C4' O4' C3' 125.9 118.7
C5' C4' O4' H4' 244.8 237.2
C3' C4' O4' H4' 118.9 118.5
O4' C4' C3' O3' 265.4 204.8
O4' C4' C3' C2' 24.3 323.0
O4' C4' C3' H3' 145.4 81.3
C4' O4' C1' C2' 347.9 333.7
C4' O4' C1' N9 224.0 214.2
C4' O4' C1' H1' 106.6 93.2
C3' C4' C5' H5' 284.7 300.0
C3' C4' C5' H5'' 175.2 60.0
C5' C4' C3' O4' 237.3 241.2
C5' C4' C3' H4' 115.0 122.8
O4' C4' C3' H4' 237.7 241.6
C3' C4' O4' C1' 352.3 39.9
O3' C3' C4' C2' 241.1 241.8
O3' C3' C4' H3' 120.1 123.6
C4' C3' O3' HO3' 179.9 174.2
C2' C3' C4' H3' 239.0 241.8
C4' C3' C2' C1' 328.8 20.9
C4' C3' C2' H2' 94.0 262.1
C4' C3' C2' H2'' 203.5 139.5
H4' C4' C5' H5' 43.1 62.9
H4' C4' C5' H5'' 293.6 182.9
C5' C4' H4' O4' 120.0 123.0
C5' C4' H4' C3' 236.7 237.1
O4' C4' H4' C3' 116.7 114.1
H4' C4' O4' C1' 233.4 281.4
H4' C4' C3' O3' 27.7 323.3
H4' C4' C3' C2' 146.6 81.4
H4' C4' C3' H3' 267.6 199.7
C1' O4' C4' C3' 352.3 39.9
C1' O4' C4' H4' 233.4 281.4
C3' C2' C1' O4' 26.8 1.9
O4' C1' C2' H2' 261.5 120.7
O4' C1' C2' H2'' 152.0 243.3
C2' C1' O4' N9 123.9 119.5
C2' C1' O4' H1' 241.3 240.5
N9 C1' O4' H1' 117.4 121.0
O4' C1' N9 C8 84.0 28.2
O4' C1' N9 C4 278.3 208.4
O3' C3' C4' H4' 27.7 323.3
C4' C3' O3' C2' 113.5 112.7
C4' C3' O3' H3' 235.1 236.4
C2' C3' O3' H3' 121.6 123.7
O3' C3' C2' C1' 83.5 139.2
O3' C3' C2' H2' 208.8 20.3
O3' C3' C2' H2'' 318.2 257.8
C2' C3' C4' H4' 146.6 81.4
C4' C3' C2' O3' 245.3 241.8
C4' C3' C2' H3' 124.7 118.2
O4' C1' C2' C3' 26.8 1.9
O3' C3' C2' H3' 239.5 236.4
C2' C3' O3' HO3' 66.5 61.5
C1' C2' C3' H2' 234.7 118.8
C1' C2' C3' H2'' 125.2 241.4
C3' C2' C1' N9 145.3 121.4
C3' C2' C1' H1' 262.8 242.4
H2' C2' C3' H2'' 250.5 122.6
H3' C3' C4' H4' 267.6 199.7
C4' C3' H3' O3' 119.1 123.7
C4' C3' H3' C2' 242.1 247.3
O3' C3' H3' C2' 123.0 123.6
H3' C3' O3' HO3' 304.8 297.8
H3' C3' C2' C1' 204.0 262.7
H3' C3' C2' H2' 329.3 143.9
H3' C3' C2' H2'' 78.8 21.4
HO3' O3' C3' C2' 66.5 61.5
HO3' O3' C3' H3' 304.8 297.8
O4' C1' C2' N9 241.4 240.5
O4' C1' C2' H1' 124.0 119.6
C1' C2' C3' H3' 204.0 262.7
C3' C2' C1' H2' 125.3 241.2
C3' C2' C1' H2'' 234.8 118.6
H2' C2' C1' H2'' 109.5 237.4
N9 C1' C2' H1' 242.6 239.0
C2' C1' N9 C8 326.8 270.2
C2' C1' N9 C4 161.0 90.3
H2' C2' C3' H3' 329.3 143.9
C3' C2' H2' C1' 240.7 114.9
C3' C2' H2' H2'' 120.3 237.5
C1' C2' H2' H2'' 239.7 122.6
H2' C2' C1' N9 20.0 240.2
H2' C2' C1' H1' 137.5 1.2
H2'' C2' C3' H3' 78.8 21.4
C3' C2' H2'' C1' 119.3 245.3
C3' C2' H2'' H2' 239.6 122.6
C1' C2' H2'' H2' 120.3 237.3
H2'' C2' C1' N9 270.6 2.8
H2'' C2' C1' H1' 28.0 123.8
O4' C1' N9 C2' 117.3 118.0
O4' C1' N9 H1' 236.0 239.0
N9 C1' C2' H2' 20.0 240.2
N9 C1' C2' H2'' 270.6 2.8
C2' C1' N9 H1' 118.7 121.0
C8 N9 C1' C4 165.8 179.9
C1' N9 C8 N7 191.6 180.1
C1' N9 C8 H8 11.6 0.1
C1' N9 C4 C5 168.0 180.2
C1' N9 C4 N3 347.7 359.9
O4' C1' H1' C2' 242.6 241.9
O4' C1' H1' N9 118.7 121.0
H1' C1' C2' H2' 137.5 1.2
H1' C1' C2' H2'' 28.0 123.8
C2' C1' H1' N9 236.1 239.0
H1' C1' N9 C8 208.0 149.3
H1' C1' N9 C4 42.3 329.4
C8 N9 C1' H1' 208.0 149.3
C1' N9 C8 C4 192.2 180.1
C8 N9 C4 C5 359.6 0.3
C8 N9 C4 N3 179.3 180.0
N7 C8 N9 H8 180.0 180.0
N9 C8 N7 C5 1.3 359.7
C4 N9 C1' H1' 42.3 329.4
C1' N9 C4 C8 168.4 179.9
C4 N9 C8 N7 359.4 360.0
C4 N9 C8 H8 179.5 180.0
N7 C5 C4 N9 1.3 359.5
C6 C5 C4 N9 181.1 180.3
C5 C4 N9 N3 180.2 180.3
C2 N3 C4 N9 180.1 180.0
N7 C8 N9 C4 359.4 360.0
N9 C8 N7 H8 180.0 180.0
C8 N7 C5 C6 178.6 179.5
C8 N7 C5 C4 358.4 0.4
H8 C8 N9 C4 179.5 180.0
N9 C8 H8 N7 180.0 180.0
H8 C8 N7 C5 181.3 179.7
N9 C4 C5 N7 1.3 359.5
C5 N7 C8 H8 181.3 179.7
C6 C5 N7 C4 180.2 179.0
N7 C5 C6 N6 357.8 0.7
N7 C5 C6 N1 178.1 180.5
N7 C5 C4 N3 181.5 179.8
N9 C4 C5 C6 181.1 180.3
N7 C5 C6 C4 179.8 181.0
C6 C5 C4 N3 1.4 0.6
N6 C6 C5 N1 179.7 180.3
C5 C6 N6 H61 180.0 179.7
C5 C6 N6 H62 54.8 359.5
C5 C6 N1 C2 1.0 0.3
N9 C4 C5 N3 179.8 179.7
N7 C5 C4 C6 180.1 179.2
C4 C5 C6 N6 178.0 179.7
C4 C5 C6 N1 358.3 359.4
C2 N3 C4 C5 359.8 359.7
N6 C6 C5 C4 178.0 179.7
C5 C6 N6 N1 180.3 179.7
N6 C6 N1 C2 181.3 180.0
H61 N6 C6 H62 125.2 180.2
N1 C6 C5 C4 358.3 359.4
C5 C6 N1 N6 179.7 180.3
N1 C6 N6 H61 359.7 360.0
N1 C6 N6 H62 234.5 179.8
C6 N1 C2 N3 0.4 360.0
C6 N1 C2 H2 180.4 179.9
H61 N6 C6 N1 359.7 360.0
C6 N6 H61 H62 234.8 179.8
H62 N6 C6 N1 234.5 179.8
C6 N6 H62 H61 134.3 180.2
N3 C2 N1 H2 180.0 180.0
N1 C2 N3 C4 359.2 0.0
N9 C4 N3 C2 180.1 180.0
C5 C4 N3 C2 359.8 359.7
N1 C2 N3 H2 180.0 180.0
N1 C2 H2 N3 180.0 180.0
H2 C2 N3 C4 179.2 180.1
N9 C4 N3 C5 180.3 180.4
C4 N3 C2 H2 179.2 180.1