PDB Chemical Component DZM

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 DZM

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
P OP2 1.510 1.610
P OP1 1.510 1.480
P O5' 1.609 1.610
N1 C2 1.301 1.324
N1 C6 1.358 1.323
C2 C3 1.289 1.366
C3 C4 1.490 1.393
C3 C3M 1.507 1.507
C4 C5 1.369 1.406
C4 N9 1.339 1.374
C5 C6 1.385 1.404
C5 N7 1.346 1.355
C6 N6 1.354 1.388
N7 C8 1.357 1.302
C8 N9 1.342 1.362
N9 C1' 1.483 1.465
C1' C2' 1.523 1.541
C1' O4' 1.428 1.437
C2' C3' 1.521 1.549
C3' O3' 1.431 1.429
C3' C4' 1.522 1.550
C4' O4' 1.424 1.443
C4' C5' 1.519 1.530
C5' O5' 1.424 1.429
P OP3 1.720 1.610
C2 H2 1.080 1.079
N6 HN6 1.000 0.970
N6 HN6A 0.999 0.970
C8 H8 1.080 1.080
C1' H1' 1.100 1.090
OP2 HOP2 0.950 0.966
C2' H2' 1.100 1.090
C2' H2'A 1.101 1.090
C3' H3' 1.100 1.090
O3' HO3' 0.950 0.967
C3M H3M 1.100 1.090
C3M H3MA 1.100 1.089
C3M H3MB 1.100 1.090
C4' H4' 1.100 1.090
C5' H5' 1.100 1.090
C5' H5'A 1.100 1.091
OP3 HOP3 0.950 0.967

Bond Angles for DZM

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
OP2 P OP1 120.8 109.5
OP2 P O5' 107.9 109.5
OP2 P OP3 102.0 109.5
P OP2 HOP2 109.5 114.0
OP1 P O5' 107.6 109.5
OP1 P OP3 104.5 109.5
P O5' C5' 120.4 123.0
O5' P OP3 114.3 109.5
C2 N1 C6 123.2 122.3
N1 C2 C3 122.7 121.5
N1 C2 H2 118.6 119.2
N1 C6 C5 119.6 120.0
N1 C6 N6 120.7 120.0
C2 C3 C4 117.5 119.1
C2 C3 C3M 119.5 120.5
C3 C2 H2 118.7 119.3
C4 C3 C3M 123.0 120.4
C3 C4 C5 119.4 118.7
C3 C4 N9 131.1 135.2
C3 C3M H3M 109.5 109.4
C3 C3M H3MA 109.4 109.5
C3 C3M H3MB 109.5 109.5
C5 C4 N9 109.5 106.1
C4 C5 C6 117.6 118.5
C4 C5 N7 107.0 106.9
C4 N9 C8 106.5 107.4
C4 N9 C1' 127.9 126.3
C6 C5 N7 135.5 134.6
C5 C6 N6 119.7 120.0
C5 N7 C8 107.3 109.6
C6 N6 HN6 109.5 120.0
C6 N6 HN6A 109.5 120.0
N7 C8 N9 109.8 110.0
N7 C8 H8 125.1 125.0
C8 N9 C1' 125.6 126.3
N9 C8 H8 125.1 125.0
N9 C1' C2' 111.7 109.9
N9 C1' O4' 108.8 109.9
N9 C1' H1' 107.6 109.9
C2' C1' O4' 106.7 107.3
C1' C2' C3' 104.8 104.2
C2' C1' H1' 109.6 109.9
C1' C2' H2' 111.1 110.5
C1' C2' H2'A 111.1 110.5
C1' O4' C4' 110.6 107.0
O4' C1' H1' 112.5 110.0
C2' C3' O3' 111.0 110.9
C2' C3' C4' 106.2 102.1
C3' C2' H2' 111.1 110.4
C3' C2' H2'A 111.1 110.5
C2' C3' H3' 110.6 110.9
O3' C3' C4' 109.6 110.9
O3' C3' H3' 107.4 110.8
C3' O3' HO3' 109.5 114.0
C3' C4' O4' 107.0 103.5
C3' C4' C5' 111.5 110.6
C4' C3' H3' 112.1 110.9
C3' C4' H4' 109.6 110.6
O4' C4' C5' 109.1 110.6
O4' C4' H4' 112.0 110.6
C4' C5' O5' 108.2 109.5
C5' C4' H4' 107.6 110.7
C4' C5' H5' 109.9 109.5
C4' C5' H5'A 109.9 109.5
O5' C5' H5' 109.9 109.5
O5' C5' H5'A 109.9 109.5
P OP3 HOP3 109.5 114.0
HN6 N6 HN6A 109.5 120.0
H2' C2' H2'A 107.9 110.6
H3M C3M H3MA 109.5 109.5
H3M C3M H3MB 109.4 109.4
H3MA C3M H3MB 109.5 109.5
H5' C5' H5'A 109.1 109.5

Torsion Angles for DZM

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
OP1 P OP2 O5' 235.8 240.0
OP1 P OP2 OP3 115.1 120.0
OP2 P O5' C5' 30.3 295.0
O5' P OP2 OP3 239.3 240.0
OP2 P OP3 HOP3 126.5 60.1
OP2 P OP1 O5' 124.3 120.0
OP2 P OP1 OP3 246.2 240.0
OP1 P OP2 HOP2 360.0 180.0
OP1 P O5' C5' 162.1 55.0
O5' P OP1 OP3 121.9 120.0
OP1 P OP3 HOP3 0.0 300.0
OP2 P O5' OP1 228.2 240.0
OP2 P O5' OP3 112.7 120.0
O5' P OP2 HOP2 124.2 300.0
OP1 P O5' OP3 244.5 240.0
C4' C5' O5' P 176.5 180.0
P O5' C5' H5' 56.5 60.0
P O5' C5' H5'A 296.5 300.0
O5' P OP3 HOP3 242.7 180.1
C2 N1 C6 C5 360.0 0.1
C2 N1 C6 N6 179.9 180.0
N1 C2 C3 C4 359.9 0.0
N1 C2 C3 C3M 179.9 179.9
C3 C2 N1 H2 180.0 180.0
C6 N1 C2 C3 0.1 360.0
C6 N1 C2 H2 180.2 179.9
C4 C5 C6 N1 359.9 359.9
N1 C6 C5 N7 180.0 180.0
C5 C6 N1 N6 180.1 180.1
N1 C6 N6 HN6 360.0 0.0
N1 C6 N6 HN6A 120.0 180.0
C3 C2 N1 C6 0.1 360.0
N1 C2 C3 H2 180.0 180.0
C4 C3 C2 C3M 180.0 180.1
C2 C3 C4 C5 360.0 360.0
C2 C3 C4 N9 180.2 180.0
C2 C3 C3M H3M 90.0 96.0
C2 C3 C3M H3MA 210.0 216.1
C2 C3 C3M H3MB 330.0 336.1
C2 C3 C4 C3M 180.0 179.9
C4 C3 C2 H2 179.9 180.1
C4 C3 C3M H3M 270.0 275.9
C4 C3 C3M H3MA 30.0 36.0
C4 C3 C3M H3MB 150.0 156.1
C5 C4 C3 N9 179.8 180.0
C3 C4 C5 C6 0.1 0.0
C3 C4 C5 N7 180.0 180.0
C3 C4 N9 C8 180.0 180.0
C3 C4 N9 C1' 359.6 359.9
C2 C3 C3M C4 180.0 180.1
C3M C3 C2 H2 359.9 360.0
C3M C3 C4 C5 180.0 180.1
C3M C3 C4 N9 0.2 0.1
H3M C3M C3 H3MA 240.0 240.0
H3M C3M C3 H3MB 120.0 119.9
H3MA C3M C3 H3MB 240.0 239.9
N1 C6 C5 C4 359.9 359.9
C5 C4 C3 C3M 180.0 180.1
C3 C4 C5 N9 180.1 180.0
C5 C4 N9 C8 0.1 0.0
C5 C4 N9 C1' 179.7 180.0
C6 C5 C4 N7 180.1 180.0
C4 C5 C6 N6 180.0 180.0
C4 C5 N7 C8 0.1 360.0
N9 C4 C3 C3M 0.2 0.1
C3 C4 N9 C5 179.8 180.0
N9 C4 C5 C6 180.0 180.0
N9 C4 C5 N7 359.9 0.0
N7 C8 N9 C4 359.9 359.9
C8 N9 C4 C1' 180.4 180.1
C4 N9 C8 H8 179.9 180.1
C4 N9 C1' C2' 140.5 83.0
C4 N9 C1' O4' 258.0 200.8
C4 N9 C1' H1' 20.2 322.0
N1 C6 C5 N6 179.9 179.9
C6 C5 C4 N9 180.0 180.0
C4 C5 C6 N7 179.8 180.0
C6 C5 N7 C8 179.9 179.9
C5 C6 N6 HN6 179.9 179.9
C5 C6 N6 HN6A 299.9 360.0
N7 C5 C4 N9 359.9 0.0
C4 C5 N7 C6 180.1 180.0
N7 C5 C6 N6 0.2 0.0
C5 N7 C8 N9 0.0 0.1
C5 N7 C8 H8 180.0 179.9
N1 C6 N6 C5 180.1 180.1
N6 C6 C5 N7 0.2 0.0
HN6 N6 C6 HN6A 240.0 180.0
C4 N9 C8 N7 359.9 359.9
N7 C8 N9 C1' 180.3 180.0
N9 C8 N7 H8 180.0 180.1
C4 N9 C8 C1' 179.6 179.9
N7 C8 N9 H8 180.0 179.9
C8 N9 C1' C2' 320.0 262.9
C8 N9 C1' O4' 77.5 20.7
C8 N9 C1' H1' 199.7 141.9
C4 N9 C1' C8 180.5 180.1
C1' N9 C8 H8 0.3 0.1
C2' C1' N9 O4' 242.5 242.2
N9 C1' C2' C3' 137.4 121.5
C2' C1' N9 H1' 120.3 121.0
N9 C1' C2' H2' 257.3 240.1
N9 C1' C2' H2'A 17.4 2.8
N9 C1' O4' C4' 216.4 214.1
O4' C1' N9 H1' 237.9 238.8
N9 C1' C2' O4' 118.8 119.4
N9 C1' C2' H1' 240.9 239.0
C2' C1' O4' C4' 337.1 333.5
O4' C1' C2' H1' 122.1 119.5
C1' C2' C3' O3' 110.9 139.1
C1' C2' C3' C4' 351.8 20.9
C3' C2' C1' H2' 240.0 241.4
C3' C2' C1' H2'A 120.0 118.7
C1' C2' C3' H3' 230.0 262.6
H2' C2' C1' H2'A 240.0 237.3
N9 C1' O4' C2' 239.4 240.6
N9 C1' O4' H1' 119.1 121.1
O4' C1' C2' C3' 18.6 2.0
C2' C1' O4' H1' 239.7 240.5
O4' C1' C2' H2' 138.6 120.7
O4' C1' C2' H2'A 258.6 243.4
C3' C4' O4' C1' 17.5 40.1
C1' O4' C4' C5' 138.3 158.6
C1' O4' C4' H4' 257.3 281.6
C3' C2' C1' O4' 18.6 2.0
C3' C2' C1' H1' 256.5 242.5
C1' C2' C3' H2' 120.0 118.7
C1' C2' C3' H2'A 240.0 241.3
O3' C3' C2' C4' 119.0 118.2
O3' C3' C2' H3' 240.9 236.4
C2' C3' O3' HO3' 180.0 61.4
C2' C3' C4' O4' 355.0 323.0
C2' C3' C4' C5' 235.8 204.5
C4' C3' C2' H3' 121.9 118.2
C2' C3' C4' H4' 116.7 81.5
H2' C2' C3' H2'A 120.0 122.6
C2' C3' O3' C4' 243.0 247.3
O3' C3' C2' H2' 350.9 20.4
O3' C3' C2' H2'A 230.8 257.8
C2' C3' O3' H3' 121.1 123.6
O3' C3' C4' O4' 235.1 204.8
O3' C3' C4' C5' 115.8 86.3
C4' C3' O3' H3' 238.1 236.3
O3' C3' C4' H4' 356.8 323.3
C1' O4' C4' C3' 17.5 40.1
C2' C3' C4' O3' 120.0 118.2
C4' C3' C2' H2' 231.8 262.2
C4' C3' C2' H2'A 111.8 139.5
C2' C3' C4' H3' 239.1 241.8
O3' C3' C4' H3' 119.1 123.6
C4' C3' O3' HO3' 297.0 174.1
O4' C4' C3' C5' 119.2 118.5
O4' C4' C3' H4' 238.3 241.5
C3' C4' C5' O5' 53.4 185.0
C5' C4' C3' H4' 119.0 123.0
C3' C4' C5' H5' 173.4 305.0
C3' C4' C5' H5'A 293.4 65.0
C4' O4' C1' H1' 97.3 93.0
C3' C4' O4' C5' 239.2 241.5
O4' C4' C3' H3' 116.0 81.2
C3' C4' O4' H4' 120.2 118.5
O4' C4' C5' O5' 295.4 70.9
C5' C4' O4' H4' 241.0 237.0
O4' C4' C5' H5' 55.4 190.9
O4' C4' C5' H5'A 175.4 310.9
P O5' C5' C4' 176.5 180.0
C3' C4' C5' O4' 118.0 114.1
C5' C4' C3' H3' 356.7 322.7
C3' C4' C5' H4' 239.7 237.0
O4' C4' C5' H4' 121.8 123.0
O5' C5' C4' H5' 240.0 240.0
O5' C5' C4' H5'A 120.0 120.0
H5' C5' C4' H5'A 240.0 240.0
C5' O5' P OP3 277.6 175.0
O5' C5' C4' H4' 173.7 308.0
C4' C5' O5' H5' 120.0 120.0
C4' C5' O5' H5'A 240.0 240.0
H5' C5' O5' H5'A 120.0 120.0
OP2 P OP3 OP1 126.5 120.0
OP2 P OP3 O5' 243.8 240.0
OP3 P OP2 HOP2 244.9 60.0
OP1 P OP3 O5' 117.3 120.0
OP3 P O5' C5' 277.6 175.0
H2 C2 N1 C6 180.2 179.9
N1 C2 H2 C3 180.0 180.0
H2 C2 C3 C4 179.9 180.1
H2 C2 C3 C3M 359.9 360.0
C6 N6 HN6 HN6A 120.0 180.0
C6 N6 HN6A HN6 240.0 180.0
N7 C8 H8 N9 180.0 180.2
H8 C8 N9 C1' 0.3 0.1
N9 C1' H1' C2' 121.6 121.0
N9 C1' H1' O4' 240.2 238.9
C2' C1' H1' O4' 118.6 117.9
H1' C1' C2' C3' 256.5 242.5
H1' C1' C2' H2' 16.5 1.1
H1' C1' C2' H2'A 136.5 123.8
H1' C1' O4' C4' 97.3 93.0
HOP2 OP2 P OP1 360.0 180.0
HOP2 OP2 P O5' 124.2 300.0
HOP2 OP2 P OP3 244.9 60.0
H2' C2' C1' O4' 138.6 120.7
C1' C2' H2' C3' 243.8 245.2
H2' C2' C1' H1' 16.5 1.1
C1' C2' H2' H2'A 121.9 122.7
H2' C2' C3' O3' 350.9 20.4
H2' C2' C3' C4' 231.8 262.2
C3' C2' H2' H2'A 238.1 237.4
H2' C2' C3' H3' 110.0 144.0
H2'A C2' C1' O4' 258.6 243.4
C1' C2' H2'A C3' 116.2 114.8
H2'A C2' C1' H1' 136.5 123.8
C1' C2' H2'A H2' 238.1 237.4
H2'A C2' C3' O3' 230.8 257.8
H2'A C2' C3' C4' 111.8 139.5
C3' C2' H2'A H2' 121.9 122.6
H2'A C2' C3' H3' 350.0 21.3
C2' C3' H3' O3' 238.7 236.4
C2' C3' H3' C4' 118.4 112.7
H3' C3' C2' H2' 110.0 144.0
H3' C3' C2' H2'A 350.0 21.3
O3' C3' H3' C4' 239.6 236.3
H3' C3' O3' HO3' 58.9 297.8
H3' C3' C4' O4' 116.0 81.2
H3' C3' C4' C5' 356.7 322.7
H3' C3' C4' H4' 237.7 199.6
HO3' O3' C3' C4' 297.0 174.1
HO3' O3' C3' H3' 58.9 297.8
C3 C3M H3M H3MA 120.0 120.0
C3 C3M H3M H3MB 240.0 240.1
H3MA C3M H3M H3MB 120.0 120.0
C3 C3M H3MA H3M 240.0 240.0
C3 C3M H3MA H3MB 120.0 120.1
H3M C3M H3MA H3MB 240.0 240.0
C3 C3M H3MB H3M 120.0 119.9
C3 C3M H3MB H3MA 240.0 239.9
H3M C3M H3MB H3MA 120.0 120.0
C3' C4' H4' O4' 241.4 246.0
C3' C4' H4' C5' 121.4 123.0
H4' C4' C3' H3' 237.7 199.6
O4' C4' H4' C5' 240.1 237.0
H4' C4' C5' O5' 173.7 308.0
H4' C4' C5' H5' 293.7 68.0
H4' C4' C5' H5'A 53.7 187.9
C4' C5' H5' O5' 241.1 240.0
H5' C5' C4' H4' 293.7 68.0
C4' C5' H5' H5'A 120.5 120.0
O5' C5' H5' H5'A 239.5 240.0
C4' C5' H5'A O5' 118.9 120.0
H5'A C5' C4' H4' 53.7 187.9
C4' C5' H5'A H5' 239.5 240.0
O5' C5' H5'A H5' 120.5 120.0