PDB Chemical Component D5M

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 D5M

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
O5' C5' 1.429 1.417
O5' P   1.619
C5' C4' 1.511 1.523
C5' H5'1 1.100 1.090
C5' H5'2 1.100 1.091
C4' O4' 1.451 1.443
C4' C3' 1.531 1.525
C4' H4' 1.100 1.095
O4' C1' 1.429 1.439
C3' O3' 1.444 1.425
C3' C2' 1.521 1.512
C3' H1 1.100 1.093
O3' H3' 0.950 0.969
C2' C1' 1.526 1.522
C2' H2'1 1.100 1.097
C2' H2'2 1.100 1.094
C1' N9 1.467 1.459
C1' H1' 1.100 1.095
N9 C8 1.382 1.371
N9 C4 1.379 1.368
C8 N7 1.315 1.317
C8 H8 1.080 1.082
N7 C5 1.393 1.373
C5 C6 1.413 1.390
C5 C4 1.391 1.386
C6 N6 1.336 1.405
C6 N1 1.356 1.355
N6 HN61 1.000 1.002
N6 HN62 1.000 1.002
N1 C2 1.346 1.355
C2 N3 1.335 1.351
C2 H2 1.080 1.084
N3 C4 1.352 1.342
P O1P   1.501
P O3P   1.617
P O2P   1.617
O3P H3P   0.981
O2P H2P   0.981

Bond Angles for D5M

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
C5' O5' P   118.5
O5' C5' C4' 111.4 108.7
O5' C5' H5'1 108.8 109.2
O5' C5' H5'2 108.4 109.2
O5' P O1P   115.0
O5' P O3P   103.7
O5' P O2P   102.9
C4' C5' H5'1 108.8 110.1
C4' C5' H5'2 108.4 110.1
C5' C4' O4' 109.0 108.0
C5' C4' C3' 114.9 112.7
C5' C4' H4' 105.0 109.4
H5'1 C5' H5'2 111.0 109.6
O4' C4' C3' 105.7 106.8
O4' C4' H4' 114.3 107.7
C4' O4' C1' 109.9 108.7
C3' C4' H4' 108.3 112.0
C4' C3' O3' 110.2 109.6
C4' C3' C2' 102.6 103.2
C4' C3' H1 112.7 114.0
O4' C1' C2' 106.0 106.7
O4' C1' N9 107.9 110.0
O4' C1' H1' 115.1 108.1
O3' C3' C2' 107.3 108.4
O3' C3' H1 108.4 107.8
C3' O3' H3' 109.5 106.6
C2' C3' H1 115.4 113.7
C3' C2' C1' 101.7 101.6
C3' C2' H2'1 112.2 110.0
C3' C2' H2'2 113.8 114.2
C1' C2' H2'1 112.2 110.5
C1' C2' H2'2 113.8 111.7
C2' C1' N9 115.8 114.3
C2' C1' H1' 107.1 111.7
H2'1 C2' H2'2 103.6 108.7
N9 C1' H1' 105.2 105.9
C1' N9 C8 128.5 126.2
C1' N9 C4 125.8 126.9
C8 N9 C4 105.7 106.9
N9 C8 N7 113.8 112.3
N9 C8 H8 123.1 122.2
N9 C4 C5 105.9 105.3
N9 C4 N3 127.3 127.5
N7 C8 H8 123.1 125.6
C8 N7 C5 103.9 104.9
N7 C5 C6 132.3 132.4
N7 C5 C4 110.7 110.7
C6 C5 C4 117.0 116.9
C5 C6 N6 123.6 120.7
C5 C6 N1 117.6 119.1
C5 C4 N3 126.8 127.2
N6 C6 N1 118.8 120.2
C6 N6 HN61 109.5 119.5
C6 N6 HN62 109.5 119.4
C6 N1 C2 118.7 117.5
HN61 N6 HN62 109.5 120.8
N1 C2 N3 129.3 128.8
N1 C2 H2 115.4 115.5
N3 C2 H2 115.3 115.7
C2 N3 C4 110.6 110.5
O1P P O3P   115.3
O1P P O2P   115.0
O3P P O2P   103.3
P O3P H3P   118.9
P O2P H2P   118.9

Torsion Angles for D5M

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
C5' O5' P O1P   180.0
C5' O5' P O3P   53.2
C5' O5' P O2P   305.8
C4' C5' O5' H5'1 240.0 239.9
C4' C5' O5' H5'2 119.2 120.1
O5' C5' C4' O4' 57.8 61.8
O5' C5' C4' C3' 176.2 179.5
O5' C5' C4' H4' 295.0 304.8
H5'1 C5' O5' H5'2 239.2 240.2
P O5' C5' C4'   180.0
P O5' C5' H5'1   300.1
P O5' C5' H5'2   59.9
O1P P O5' O3P   126.8
O1P P O5' O2P   234.2
O3P P O5' O2P   107.4
O5' P O3P H3P   175.4
O5' P O2P H2P   186.1
C4' C5' O5' P   180.0
O5' C5' C4' H5'1 120.0 119.6
O5' C5' C4' H5'2 240.8 240.5
H5'1 C5' C4' H5'2 120.8 120.9
O4' C4' C5' C3' 241.7 242.3
O4' C4' C5' H4' 122.8 117.0
C5' C4' O4' C1' 116.5 116.0
C3' C4' C5' H4' 241.1 234.7
C5' C4' C3' O3' 153.8 152.1
C5' C4' C3' C2' 267.9 267.4
C5' C4' C3' H1 32.6 31.2
H5'1 C5' O5' P   300.1
O5' C5' H5'1 C4' 238.4 240.8
O5' C5' H5'1 H5'2 119.2 119.6
C4' C5' H5'1 H5'2 240.8 238.8
H5'1 C5' C4' O4' 297.8 302.2
H5'1 C5' C4' C3' 56.1 60.0
H5'1 C5' C4' H4' 175.0 185.3
H5'2 C5' O5' P   59.9
O5' C5' H5'2 C4' 121.1 119.2
O5' C5' H5'2 H5'1 240.5 240.4
C4' C5' H5'2 H5'1 119.5 121.2
H5'2 C5' C4' O4' 177.0 181.3
H5'2 C5' C4' C3' 295.3 299.1
H5'2 C5' C4' H4' 54.2 64.3
O4' C4' C5' H5'1 297.8 302.2
O4' C4' C5' H5'2 177.0 181.3
C5' C4' O4' C3' 123.9 121.5
C5' C4' O4' H4' 242.9 242.0
C3' C4' O4' H4' 119.0 120.5
O4' C4' C3' O3' 274.0 270.6
O4' C4' C3' C2' 28.0 25.9
O4' C4' C3' H1 152.7 149.7
C4' O4' C1' C2' 343.6 342.7
C4' O4' C1' N9 218.9 218.2
C4' O4' C1' H1' 101.8 103.1
C3' C4' C5' H5'1 56.1 60.0
C3' C4' C5' H5'2 295.3 299.1
C5' C4' C3' O4' 239.8 241.5
C5' C4' C3' H4' 117.0 123.8
O4' C4' C3' H4' 237.1 242.3
C3' C4' O4' C1' 352.6 354.5
O3' C3' C4' C2' 246.0 244.7
O3' C3' C4' H1 121.2 120.9
C4' C3' O3' H3' 159.3 46.6
C2' C3' C4' H1 235.3 236.3
C4' C3' C2' C1' 323.3 325.2
C4' C3' C2' H2'1 83.3 82.2
C4' C3' C2' H2'2 200.5 204.8
H4' C4' C5' H5'1 175.0 185.3
H4' C4' C5' H5'2 54.2 64.3
C5' C4' H4' O4' 119.3 117.2
C5' C4' H4' C3' 236.8 234.3
O4' C4' H4' C3' 117.5 117.2
H4' C4' O4' C1' 233.6 234.0
H4' C4' C3' O3' 36.8 28.3
H4' C4' C3' C2' 150.9 143.6
H4' C4' C3' H1 275.6 267.4
C1' O4' C4' C3' 352.6 354.5
C1' O4' C4' H4' 233.6 234.0
C3' C2' C1' O4' 33.4 32.7
O4' C1' C2' H2'1 273.3 276.0
O4' C1' C2' H2'2 156.1 154.9
C2' C1' O4' N9 124.7 124.5
C2' C1' O4' H1' 241.8 239.7
N9 C1' O4' H1' 117.1 115.2
O4' C1' N9 C8 85.9 33.5
O4' C1' N9 C4 267.4 213.5
O3' C3' C4' H4' 36.8 28.3
C4' C3' O3' C2' 111.0 111.9
C4' C3' O3' H1 236.2 235.4
C2' C3' O3' H1 125.2 123.5
O3' C3' C2' C1' 79.4 81.3
O3' C3' C2' H2'1 199.4 198.4
O3' C3' C2' H2'2 316.7 320.9
C2' C3' C4' H4' 150.9 143.6
C4' C3' C2' O3' 243.9 243.8
C4' C3' C2' H1 123.0 123.9
O4' C1' C2' C3' 33.4 32.7
O3' C3' C2' H1 239.1 240.1
C2' C3' O3' H3' 48.3 294.7
C1' C2' C3' H2'1 240.0 243.0
C1' C2' C3' H2'2 122.8 120.4
C3' C2' C1' N9 153.0 154.5
C3' C2' C1' H1' 269.9 274.8
H2'1 C2' C3' H2'2 242.8 237.5
H1 C3' C4' H4' 275.6 267.4
C4' C3' H1 O3' 122.3 121.9
C4' C3' H1 C2' 242.6 242.1
O3' C3' H1 C2' 120.3 120.2
H1 C3' O3' H3' 283.1 171.2
H1 C3' C2' C1' 200.4 201.2
H1 C3' C2' H2'1 320.4 318.3
H1 C3' C2' H2'2 77.6 80.8
H3' O3' C3' C2' 48.3 294.7
H3' O3' C3' H1 283.1 171.2
O4' C1' C2' N9 240.3 238.2
O4' C1' C2' H1' 123.4 117.9
C1' C2' C3' H1 200.4 201.2
C3' C2' C1' H2'1 120.0 116.7
C3' C2' C1' H2'2 237.2 237.8
H2'1 C2' C1' H2'2 117.2 121.1
N9 C1' C2' H1' 243.1 239.7
C2' C1' N9 C8 327.3 273.4
C2' C1' N9 C4 148.8 93.5
H2'1 C2' C3' H1 320.4 318.3
C3' C2' H2'1 C1' 246.3 248.6
C3' C2' H2'1 H2'2 123.2 125.7
C1' C2' H2'1 H2'2 236.9 237.1
H2'1 C2' C1' N9 33.0 37.8
H2'1 C2' C1' H1' 149.9 158.1
H2'2 C2' C3' H1 77.6 80.8
C3' C2' H2'2 C1' 115.9 114.6
C3' C2' H2'2 H2'1 237.9 236.7
C1' C2' H2'2 H2'1 122.1 122.1
H2'2 C2' C1' N9 275.8 276.7
H2'2 C2' C1' H1' 32.7 37.0
O4' C1' N9 C2' 118.6 120.0
O4' C1' N9 H1' 236.6 243.5
N9 C1' C2' H2'1 33.0 37.8
N9 C1' C2' H2'2 275.8 276.7
C2' C1' N9 H1' 118.0 123.5
C8 N9 C1' C4 178.5 179.9
C1' N9 C8 N7 182.5 180.0
C1' N9 C8 H8 2.5 0.0
C1' N9 C4 C5 177.4 180.0
C1' N9 C4 N3 358.2 359.9
O4' C1' H1' C2' 242.4 242.9
O4' C1' H1' N9 118.7 117.8
H1' C1' C2' H2'1 149.9 158.1
H1' C1' C2' H2'2 32.7 37.0
C2' C1' H1' N9 236.3 234.9
H1' C1' N9 C8 209.3 150.0
H1' C1' N9 C4 30.8 330.1
C8 N9 C1' H1' 209.3 150.0
C1' N9 C8 C4 181.3 180.1
C8 N9 C4 C5 358.6 0.0
C8 N9 C4 N3 179.4 180.0
N7 C8 N9 H8 180.0 180.0
N9 C8 N7 C5 359.5 0.0
C4 N9 C1' H1' 30.8 330.1
C1' N9 C4 C8 178.8 179.9
C4 N9 C8 N7 1.2 360.0
C4 N9 C8 H8 181.2 180.0
N7 C5 C4 N9 1.2 360.0
C6 C5 C4 N9 181.5 180.0
C5 C4 N9 N3 179.2 180.1
C2 N3 C4 N9 178.9 180.0
N7 C8 N9 C4 1.2 360.0
N9 C8 N7 H8 180.0 180.0
C8 N7 C5 C6 179.2 180.0
C8 N7 C5 C4 359.6 0.0
H8 C8 N9 C4 181.2 180.0
N9 C8 H8 N7 180.0 180.0
H8 C8 N7 C5 179.5 180.0
N9 C4 C5 N7 1.2 360.0
C5 N7 C8 H8 179.5 180.0
C6 C5 N7 C4 179.6 180.0
N7 C5 C6 N6 359.2 360.0
N7 C5 C6 N1 179.6 180.0
N7 C5 C4 N3 180.4 180.0
N9 C4 C5 C6 181.5 180.0
N7 C5 C6 C4 180.4 180.0
C6 C5 C4 N3 0.7 0.1
N6 C6 C5 N1 179.6 180.0
C5 C6 N6 HN61 62.6 85.4
C5 C6 N6 HN62 182.6 271.6
C5 C6 N1 C2 0.4 0.0
N9 C4 C5 N3 180.8 179.9
N7 C5 C4 C6 179.7 180.0
C4 C5 C6 N6 178.9 180.0
C4 C5 C6 N1 359.2 359.9
C2 N3 C4 C5 359.9 359.9
N6 C6 C5 C4 178.9 180.0
C5 C6 N6 N1 180.4 180.0
N6 C6 N1 C2 180.7 180.0
HN61 N6 C6 HN62 240.0 173.8
N1 C6 C5 C4 359.2 359.9
C5 C6 N1 N6 179.6 180.0
N1 C6 N6 HN61 242.2 265.4
N1 C6 N6 HN62 2.3 91.6
C6 N1 C2 N3 0.2 360.0
C6 N1 C2 H2 180.2 180.0
HN61 N6 C6 N1 242.2 265.4
C6 N6 HN61 HN62 120.0 186.3
HN62 N6 C6 N1 2.3 91.6
C6 N6 HN62 HN61 240.0 173.7
N3 C2 N1 H2 180.0 180.0
N1 C2 N3 C4 359.7 0.0
N9 C4 N3 C2 178.9 180.0
C5 C4 N3 C2 359.9 359.9
N1 C2 N3 H2 180.0 180.0
N1 C2 H2 N3 180.0 180.0
H2 C2 N3 C4 179.7 180.0
N9 C4 N3 C5 179.0 180.1
C4 N3 C2 H2 179.7 180.0
O5' P O1P O3P   239.4
O5' P O1P O2P   119.3
O3P P O1P O2P   239.9
O1P P O3P H3P   48.8
O1P P O2P H2P   312.0
O5' P O3P O1P   126.6
O5' P O3P O2P   252.9
O1P P O3P O2P   126.3
O3P P O2P H2P   78.5
O5' P O2P O1P   234.2
O5' P O2P O3P   107.7
O1P P O2P O3P   233.5
O2P P O3P H3P   282.5
H3P O3P P O2P   282.5