PDB Chemical Component CM0

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 CM0

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
P O5' 1.576 1.620
P O3P 1.613 1.616
O5' C5' 1.430 1.416
P O1P 1.491 1.500
P O2P 1.503 1.617
C3' C4' 1.511 1.523
C5' C4' 1.504 1.523
N1 C2 1.378 1.414
C4' O4' 1.447 1.444
C3' C2' 1.521 1.514
C2 O2 1.227 1.233
C2 N3 1.374 1.400
C5 C4 1.484 1.482
N3 C4 1.396 1.387
C4 O4 1.219 1.228
C5 C6 1.353 1.336
N1 C6 1.383 1.391
C7 C8 1.504 1.504
C5 O5 1.329 1.375
C7 O5 1.528 1.408
C8 O8 1.373 1.357
N1 C1' 1.478 1.435
C2' C1' 1.534 1.519
O4' C1' 1.418 1.437
C2' O2' 1.412 1.413
C8 O9 1.225 1.221
C3' O3' 1.397 1.427
O2P H2P 0.950 0.982
O3P H3P 0.950 0.981
C5' H5'1 1.100 1.092
C5' H5'2 1.100 1.091
C4' H4' 1.100 1.095
C3' H3' 1.100 1.093
C1' H1' 1.100 1.094
C2' H2' 1.100 1.097
C6 H6 1.080 1.086
N3 H3 1.000 1.016
C7 H7C1 1.100 1.094
C7 H7C2 1.100 1.093
O8 H8 0.950 0.980
O2' HA 0.950 0.973
O3' HB 0.950 0.969

Bond Angles for CM0

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
O5' P O3P 102.1 102.9
P O5' C5' 121.9 118.5
O5' P O1P 110.1 114.9
O5' P O2P 106.2 103.7
O3P P O1P 107.2 115.0
O3P P O2P 109.0 103.3
P O3P H3P 109.5 118.9
O5' C5' C4' 109.1 108.6
O5' C5' H5'1 109.6 109.2
O5' C5' H5'2 109.7 109.3
O1P P O2P 120.7 115.3
P O2P H2P 109.5 118.9
C3' C4' C5' 112.7 113.3
C3' C4' O4' 104.5 105.9
C4' C3' C2' 103.6 102.1
C4' C3' O3' 110.8 107.9
C3' C4' H4' 110.6 112.2
C4' C3' H3' 114.1 114.5
C5' C4' O4' 109.1 108.2
C4' C5' H5'1 109.6 110.1
C4' C5' H5'2 109.7 110.1
C5' C4' H4' 106.1 109.3
N1 C2 O2 123.4 123.7
N1 C2 N3 114.6 115.2
C2 N1 C6 120.1 120.1
C2 N1 C1' 118.5 119.9
C4' O4' C1' 110.3 109.2
O4' C4' H4' 114.1 107.7
C3' C2' C1' 101.8 102.0
C3' C2' O2' 112.0 112.3
C2' C3' O3' 113.8 110.3
C2' C3' H3' 111.1 114.0
C3' C2' H2' 113.3 110.1
O2 C2 N3 122.0 121.1
C2 N3 C4 128.6 126.9
C2 N3 H3 115.7 116.6
C5 C4 N3 114.7 114.6
C5 C4 O4 129.7 121.4
C4 C5 C6 115.3 119.1
C4 C5 O5 119.8 117.6
N3 C4 O4 115.6 124.1
C4 N3 H3 115.7 116.5
N1 C6 C5 126.7 124.1
C6 C5 O5 125.0 123.4
C5 C6 H6 116.6 120.9
C6 N1 C1' 121.4 119.9
N1 C6 H6 116.6 115.0
C8 C7 O5 121.6 109.8
C7 C8 O8 122.6 110.2
C7 C8 O9 118.3 125.8
C8 C7 H7C1 105.6 109.4
C8 C7 H7C2 102.8 110.1
C5 O5 C7 136.1 112.8
O5 C7 H7C1 105.6 108.3
O5 C7 H7C2 102.8 109.0
O8 C8 O9 119.1 124.0
C8 O8 H8 109.5 111.9
N1 C1' C2' 115.4 112.5
N1 C1' O4' 108.3 109.0
N1 C1' H1' 105.6 107.3
O4' C1' C2' 107.4 106.5
C1' C2' O2' 110.8 112.6
C2' C1' H1' 106.4 112.6
C1' C2' H2' 114.5 111.1
O4' C1' H1' 113.9 108.9
O2' C2' H2' 104.6 108.6
C2' O2' HA 109.5 107.2
O3' C3' H3' 103.9 107.8
C3' O3' HB 109.5 106.4
H5'1 C5' H5'2 109.2 109.6
H7C1 C7 H7C2 119.5 110.2

Torsion Angles for CM0

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
O3P P O5' O1P 246.4 125.8
O3P P O5' O2P 114.1 252.6
O5' P O3P H3P 120.1 186.2
P O5' C5' C4' 174.5 150.0
P O5' C5' H5'1 294.5 270.0
P O5' C5' H5'2 54.4 29.9
O1P P O5' O2P 227.8 126.8
O5' P O2P H2P 155.1 175.4
O3P P O5' C5' 176.5 305.8
O5' P O3P O1P 115.7 234.2
O5' P O3P O2P 247.9 107.7
O1P P O3P O2P 132.2 233.5
O3P P O2P H2P 45.8 282.5
C5' O5' P O3P 176.5 305.8
C5' O5' P O1P 290.1 180.0
C5' O5' P O2P 62.4 53.2
C3' C4' C5' O5' 49.2 179.5
O5' C5' C4' O4' 293.6 62.4
C4' C5' O5' H5'1 240.0 239.9
C4' C5' O5' H5'2 120.1 120.1
O5' C5' C4' H4' 170.3 305.4
H5'1 C5' O5' H5'2 240.1 240.2
O5' P O1P O3P 249.7 119.3
O1P P O5' C5' 290.1 180.0
O5' P O1P O2P 124.2 239.4
O3P P O1P O2P 234.5 120.1
O1P P O3P H3P 4.4 311.9
O1P P O2P H2P 281.2 48.8
O5' P O2P O3P 109.3 252.9
O2P P O5' C5' 62.4 53.2
O5' P O2P O1P 234.0 126.5
O3P P O2P O1P 124.6 233.7
O2P P O3P H3P 232.2 78.5
O5' C5' C4' C3' 49.2 179.5
C5' C4' C3' O4' 241.7 241.6
C3' C4' C5' H5'1 289.2 60.0
C3' C4' C5' H5'2 169.3 299.1
C5' C4' C3' H4' 118.5 124.4
C3' C4' O4' C1' 20.0 347.2
O4' C4' C3' H4' 236.8 242.8
C4' C3' C2' C1' 33.5 322.9
C4' C3' C2' O2' 275.1 202.0
C2' C3' C4' O3' 122.4 116.3
C2' C3' C4' H3' 239.1 236.3
C4' C3' C2' H2' 157.0 80.9
O3' C3' C4' H3' 116.8 120.1
C4' C3' O3' HB 192.7 15.1
O5' C5' C4' H5'1 120.0 119.5
O5' C5' C4' H5'2 239.9 240.4
C3' C4' C5' O4' 115.6 117.1
C5' C4' C3' C2' 208.2 273.1
C5' C4' C3' O3' 85.8 156.8
C3' C4' C5' H4' 238.9 234.1
C5' C4' C3' H3' 329.0 36.8
C5' C4' O4' C1' 140.7 109.0
O4' C4' C5' H4' 123.3 117.0
H5'1 C5' C4' H5'2 119.9 120.9
O2 C2 N1 N3 180.0 179.9
N1 C2 N3 C4 359.8 360.0
N1 C2 N3 H3 179.8 180.0
C2 N1 C6 C5 358.3 360.0
C6 N1 C2 C1' 179.5 180.0
C2 N1 C6 H6 178.3 179.9
C2 N1 C1' C2' 68.5 94.4
C2 N1 C1' O4' 189.0 212.3
C2 N1 C1' H1' 311.3 330.0
C3' C4' O4' C5' 239.3 238.3
O4' C4' C3' C2' 326.5 31.5
O4' C4' C3' O3' 204.2 275.3
C3' C4' O4' H4' 120.9 120.2
O4' C4' C3' H3' 87.4 155.2
O4' C4' C5' H5'1 173.6 302.9
O4' C4' C5' H5'2 53.7 182.0
C5' C4' O4' H4' 241.6 241.9
N1 C1' O4' C4' 236.4 227.1
C4' O4' C1' C2' 1.7 348.7
C4' O4' C1' H1' 119.3 110.3
C2' C3' C4' C5' 208.2 273.1
C2' C3' C4' O4' 326.5 31.5
C4' C3' C2' O3' 239.7 245.5
C2' C3' C4' H4' 89.7 148.7
C4' C3' C2' H3' 122.9 124.0
N1 C1' C2' C3' 98.6 150.0
O4' C1' C2' C3' 337.7 30.7
C1' C2' C3' O2' 118.5 120.8
C3' C2' C1' H1' 215.4 271.5
C1' C2' C3' H2' 236.6 242.0
O2' C2' C3' H2' 118.1 121.1
C3' C2' O2' HA 354.8 167.7
O3' C3' C2' H3' 243.2 238.5
C2' C3' O3' HB 76.5 264.4
N1 C2 O2 N3 180.0 180.1
O2 C2 N1 C6 181.7 180.0
O2 C2 N1 C1' 2.2 360.0
O2 C2 N3 C4 179.8 180.0
O2 C2 N3 H3 359.8 0.1
N1 C2 N3 O2 180.0 179.9
N3 C2 N1 C6 1.7 0.0
N3 C2 N1 C1' 182.2 180.0
C5 C4 N3 C2 358.7 360.0
C2 N3 C4 O4 178.3 179.9
C4 N3 C2 H3 180.0 180.0
C2 N3 C4 C5 358.7 360.0
N3 C4 C5 O4 179.5 180.0
C5 C4 N3 H3 178.7 179.9
N1 C6 C5 C4 0.0 359.9
C6 C5 C4 O5 181.1 180.1
C4 C5 C6 H6 180.0 180.1
C4 C5 O5 C7 359.2 180.0
C2 N3 C4 H3 180.0 180.0
C5 C4 N3 O4 180.4 180.0
N3 C4 C5 C6 1.3 0.1
N3 C4 C5 O5 180.2 180.0
C5 C4 O4 N3 179.5 179.9
O4 C4 C5 C6 181.8 180.1
O4 C4 C5 O5 0.6 0.1
O4 C4 N3 H3 358.3 359.9
C6 C5 C4 N3 1.3 0.1
C6 C5 C4 O4 181.8 180.1
C4 C5 C6 O5 178.8 179.9
C5 C6 N1 C1' 177.8 180.0
N1 C6 C5 H6 180.0 179.9
C6 C5 O5 C7 177.9 359.9
C6 N1 C2 O2 181.7 180.0
C6 N1 C2 N3 1.7 0.0
C2 N1 C6 C1' 180.5 180.0
C4 C5 C6 N1 0.0 359.9
N1 C6 C5 O5 181.3 180.0
C5 C6 N1 H6 180.0 180.1
C6 N1 C1' C2' 249.0 274.4
C6 N1 C1' O4' 9.5 32.3
C6 N1 C1' H1' 131.8 150.0
C5 O5 C7 C8 0.6 180.7
O5 C7 C8 H7C1 240.0 118.7
O5 C7 C8 H7C2 114.0 239.9
O8 C8 C7 O9 179.5 180.0
C7 C8 O8 H8 180.5 180.0
H7C1 C7 C8 H7C2 234.0 121.2
O5 C5 C4 N3 180.2 180.0
O5 C5 C4 O4 0.6 0.1
C4 C5 O5 C6 181.3 180.1
O5 C5 C6 H6 1.2 0.1
C8 C7 O5 C5 0.6 180.7
C5 O5 C7 H7C1 240.6 300.0
C5 O5 C7 H7C2 114.6 59.9
O5 C7 C8 O8 90.7 178.6
O5 C7 C8 O9 271.2 358.7
C8 C7 O5 H7C1 120.0 240.7
C8 C7 O5 H7C2 246.0 120.8
H7C1 C7 O5 H7C2 126.0 240.1
O8 C8 C7 O5 90.7 178.6
C7 C8 O8 O9 180.5 180.0
O8 C8 C7 H7C1 210.7 59.9
O8 C8 C7 H7C2 336.7 298.7
C1' N1 C2 O2 2.2 360.0
C1' N1 C2 N3 182.2 180.0
C2 N1 C1' C6 179.5 180.0
C4' O4' C1' N1 236.4 227.1
C3' C2' C1' N1 98.6 150.0
C1' N1 C6 C5 177.8 180.0
C1' N1 C6 H6 357.8 359.9
O4' C1' N1 C2' 120.5 117.9
N1 C1' C2' O2' 218.0 270.6
C2' C1' N1 H1' 117.2 124.4
N1 C1' C2' H2' 336.0 32.7
O4' C1' N1 H1' 237.7 242.3
C3' C2' C1' O2' 240.7 239.4
C1' C2' C3' O3' 153.9 77.4
C1' C2' C3' H3' 270.7 198.9
C3' C2' C1' H2' 122.6 117.3
N1 C1' C2' O4' 120.9 119.3
N1 C1' C2' H1' 243.3 238.6
O4' C1' C2' H1' 122.3 119.3
O2' C2' C1' H2' 242.0 237.9
C1' C2' O2' HA 241.8 53.2
C1' O4' C4' H4' 259.1 227.0
C3' C2' C1' O4' 337.7 30.7
N1 C1' O4' C2' 234.7 238.4
N1 C1' O4' H1' 117.1 116.8
O4' C1' C2' O2' 97.0 151.3
C2' C1' O4' H1' 242.4 238.4
O4' C1' C2' H2' 215.1 273.4
C3' C2' O2' C1' 113.0 114.5
O2' C2' C3' O3' 35.4 316.5
O2' C2' C3' H3' 152.2 78.0
C3' C2' O2' H2' 236.8 238.0
O2' C2' C1' H1' 334.7 32.1
C1' C2' O2' H2' 123.9 123.5
O9 C8 C7 O5 271.2 358.7
C7 C8 O9 O8 179.5 180.0
O9 C8 C7 H7C1 31.2 240.0
O9 C8 C7 H7C2 157.2 118.7
O9 C8 O8 H8 360.0 0.0
O3' C3' C4' C5' 85.8 156.8
O3' C3' C4' O4' 204.2 275.3
C4' C3' O3' C2' 116.2 110.7
O3' C3' C4' H4' 327.3 32.5
C4' C3' O3' H3' 237.1 235.8
O3' C3' C2' C1' 153.9 77.4
O3' C3' C2' O2' 35.4 316.5
C2' C3' O3' H3' 120.9 125.1
O3' C3' C2' H2' 277.3 195.4
H3P O3P P O1P 4.4 311.9
H3P O3P P O2P 232.2 78.5
O5' C5' H5'1 C4' 240.3 240.8
O5' C5' H5'1 H5'2 120.1 119.6
H5'1 C5' C4' O4' 173.6 302.9
C4' C5' H5'1 H5'2 239.8 238.8
H5'1 C5' C4' H4' 50.3 185.9
O5' C5' H5'2 C4' 119.8 119.2
O5' C5' H5'2 H5'1 239.9 240.4
H5'2 C5' C4' O4' 53.7 182.0
C4' C5' H5'2 H5'1 120.1 121.2
H5'2 C5' C4' H4' 290.4 65.0
C3' C4' H4' C5' 122.5 126.5
C3' C4' H4' O4' 242.6 243.8
H4' C4' C3' C2' 89.7 148.7
H4' C4' C3' O3' 327.3 32.5
H4' C4' C3' H3' 210.5 272.4
C5' C4' H4' O4' 120.1 117.3
H4' C4' C5' H5'1 50.3 185.9
H4' C4' C5' H5'2 290.4 65.0
H4' C4' O4' C1' 259.1 227.0
H3' C3' C4' C5' 329.0 36.8
H3' C3' C4' O4' 87.4 155.2
C4' C3' H3' C2' 243.4 243.0
C4' C3' H3' O3' 120.7 120.1
H3' C3' C4' H4' 210.5 272.4
H3' C3' C2' C1' 270.7 198.9
H3' C3' C2' O2' 152.2 78.0
C2' C3' H3' O3' 237.3 237.2
H3' C3' C2' H2' 34.1 316.9
H3' C3' O3' HB 315.6 139.3
N1 C1' H1' C2' 123.2 124.3
N1 C1' H1' O4' 241.3 242.2
O4' C1' H1' C2' 241.8 242.1
H1' C1' C2' O2' 334.7 32.1
H1' C1' C2' H2' 92.8 154.2
C3' C2' H2' C1' 243.9 247.7
C3' C2' H2' O2' 122.3 123.3
H2' C2' C3' O3' 277.3 195.4
H2' C2' C3' H3' 34.1 316.9
C1' C2' H2' O2' 238.5 235.6
H2' C2' C1' H1' 92.8 154.2
H2' C2' O2' HA 117.9 289.7
N1 C6 H6 C5 180.0 180.1
H6 C6 C5 O5 1.2 0.1
H6 C6 N1 C1' 357.8 359.9
C2 N3 H3 C4 180.0 180.0
H3 N3 C4 O4 358.3 359.9
C8 C7 H7C1 O5 230.0 119.6
H7C1 C7 C8 O8 210.7 59.9
H7C1 C7 C8 O9 31.2 240.0
C8 C7 H7C1 H7C2 115.0 238.8
O5 C7 H7C1 H7C2 245.0 119.2
C8 C7 H7C2 O5 127.0 239.4
H7C2 C7 C8 O8 336.7 298.7
H7C2 C7 C8 O9 157.2 118.7
C8 C7 H7C2 H7C1 243.5 120.7
O5 C7 H7C2 H7C1 116.5 241.3
H8 O8 C8 O9 360.0 0.0
HA O2' C2' H2' 117.9 289.7
HB O3' C3' H3' 315.6 139.3