PDB Chemical Component C5X

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 C5X

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
C1 C2 1.533 1.530
C1 O1 1.415 1.428
C1 O5 1.422 1.425
C1 H1 1.115 1.090
C2 C3 1.531 1.533
C2 O2 1.416 1.429
C2 H2 1.116 1.090
C3 C4 1.536 1.532
C3 O3 1.404 1.429
C3 H3 1.114 1.090
C4 C5 1.536 1.530
C4 O4 1.423 1.428
C4 H4 1.115 1.090
C5 O5 1.430 1.425
C5 H51 1.115 1.090
C5 H52 1.115 1.090
O1 C1' 1.449 1.428
O2 HO2 0.950 0.967
O3 HO3 0.949 0.967
O4 HO4 0.951 0.967
C1' C2' 1.547 1.529
C1' H1'1 1.115 1.089
C1' H1'2 1.115 1.090
C2' C3' 1.539 1.529
C2' H2'1 1.115 1.090
C2' H2'2 1.116 1.089
C3' C4' 1.541 1.529
C3' H3'1 1.116 1.090
C3' H3'2 1.115 1.090
C4' C5' 1.505 1.529
C4' O' 1.420 1.429
C4' H4' 1.114 1.089
C5' O' 2.381 1.429
C5' H5'1 1.116 1.090
C5' H5'2 1.115 1.090

Bond Angles for C5X

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
C2 C1 O1 111.7 109.4
C2 C1 O5 108.8 109.8
C2 C1 H1 108.9 109.4
C1 C2 C3 106.5 109.1
C1 C2 O2 112.5 109.6
C1 C2 H2 109.5 109.5
O1 C1 O5 110.6 109.5
O1 C1 H1 106.9 109.4
C1 O1 C1' 116.7 106.9
O5 C1 H1 110.0 109.4
C1 O5 C5 114.1 107.6
C3 C2 O2 109.7 109.6
C3 C2 H2 112.4 109.4
C2 C3 C4 110.7 108.7
C2 C3 O3 111.3 109.6
C2 C3 H3 107.1 109.6
O2 C2 H2 106.3 109.5
C2 O2 HO2 112.6 106.8
C4 C3 O3 108.7 109.9
C4 C3 H3 109.8 109.4
C3 C4 C5 111.0 109.1
C3 C4 O4 108.9 109.6
C3 C4 H4 108.7 109.5
O3 C3 H3 109.2 109.6
C3 O3 HO3 111.3 106.8
C5 C4 O4 109.0 109.6
C5 C4 H4 108.5 109.5
C4 C5 O5 110.2 109.9
C4 C5 H51 112.0 109.4
C4 C5 H52 112.0 109.5
O4 C4 H4 110.7 109.5
C4 O4 HO4 108.9 106.8
O5 C5 H51 111.9 109.4
O5 C5 H52 111.9 109.4
H51 C5 H52 98.5 109.3
O1 C1' C2' 110.8 109.6
O1 C1' H1'1 111.7 109.4
O1 C1' H1'2 111.7 109.4
C2' C1' H1'1 111.7 109.5
C2' C1' H1'2 111.7 109.5
C1' C2' C3' 113.0 109.5
C1' C2' H2'1 111.0 109.5
C1' C2' H2'2 111.0 109.5
H1'1 C1' H1'2 98.7 109.4
C3' C2' H2'1 110.9 109.4
C3' C2' H2'2 110.9 109.5
C2' C3' C4' 112.4 109.5
C2' C3' H3'1 111.1 109.4
C2' C3' H3'2 111.1 109.5
H2'1 C2' H2'2 99.4 109.4
C4' C3' H3'1 111.1 109.5
C4' C3' H3'2 111.1 109.5
C3' C4' C5' 115.0 117.8
C3' C4' O' 108.0 117.8
C3' C4' H4' 106.6 115.7
H3'1 C3' H3'2 99.2 109.4
C5' C4' O' 109.0 57.7
C5' C4' H4' 105.6 117.7
C4' C5' O' 34.3 57.6
C4' C5' H5'1 151.8 117.8
C4' C5' H5'2 151.9 117.8
O' C4' H4' 112.9 117.8
C4' O' C5' 36.7 64.7
O' C5' H5'1 151.9 117.8
O' C5' H5'2 151.9 117.8
H5'1 C5' H5'2 45.3 115.7

Torsion Angles for C5X

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
O1 C1 C2 O5 122.4 120.1
O1 C1 C2 H1 242.2 240.2
C2 C1 O1 C1' 179.8 179.7
O5 C1 C2 H1 119.8 120.1
C2 C1 O5 C5 294.2 292.5
C3 C2 C1 O2 239.8 239.9
C3 C2 C1 H2 121.8 119.7
C1 C2 C3 C4 302.4 306.5
C1 C2 C3 O3 181.4 186.4
C1 C2 C3 H3 62.1 66.0
O2 C2 C1 H2 242.0 239.8
C1 C2 O2 HO2 180.0 59.9
C2 C1 O1 O5 238.7 239.7
C2 C1 O1 H1 119.0 119.8
O1 C1 C2 C3 185.3 181.3
O1 C1 C2 O2 305.5 301.4
O1 C1 C2 H2 63.5 61.5
O5 C1 O1 H1 240.3 240.2
O1 C1 O5 C5 171.2 172.4
C1 O1 C1' C2' 199.7 180.0
C1 O1 C1' H1'1 324.9 300.0
C1 O1 C1' H1'2 74.5 59.9
C2 C1 O5 O1 123.0 120.1
C2 C1 O5 H1 240.9 239.9
O5 C1 C2 C3 62.9 61.1
O5 C1 C2 O2 183.1 181.2
O5 C1 C2 H2 301.1 301.4
O1 C1 O5 H1 117.9 119.9
O5 C1 O1 C1' 301.1 300.0
C4 C5 O5 C1 58.3 67.6
C1 O5 C5 H51 293.0 307.5
C1 O5 C5 H52 183.6 187.8
C2 C1 H1 O1 239.2 240.2
C2 C1 H1 O5 119.1 120.3
H1 C1 C2 C3 303.1 301.1
H1 C1 C2 O2 63.3 61.2
H1 C1 C2 H2 181.3 181.4
O1 C1 H1 O5 239.9 240.1
H1 C1 O1 C1' 60.8 59.9
H1 C1 O5 C5 53.4 52.5
C3 C2 C1 O1 185.3 181.3
C3 C2 C1 O5 62.9 61.1
C3 C2 C1 H1 303.1 301.1
C1 C2 C3 O2 122.1 120.1
C1 C2 C3 H2 240.1 240.2
O2 C2 C3 H2 118.0 120.1
C3 C2 O2 HO2 298.3 179.6
C4 C3 C2 O3 121.0 120.1
C4 C3 C2 H3 240.3 240.5
C2 C3 C4 C5 52.3 53.5
C2 C3 C4 O4 172.3 173.5
C2 C3 C4 H4 293.0 293.6
O3 C3 C2 H3 119.3 120.4
C2 C3 O3 HO3 180.0 180.0
O2 C2 C1 O1 305.5 301.4
O2 C2 C1 O5 183.1 181.2
O2 C2 C1 H1 63.3 61.2
C1 C2 O2 C3 241.6 240.2
C1 C2 O2 H2 119.9 120.2
C3 C2 O2 H2 238.2 240.0
O2 C2 C3 C4 180.4 186.4
O2 C2 C3 O3 59.4 66.3
O2 C2 C3 H3 300.1 306.0
H2 C2 C1 O1 63.5 61.5
H2 C2 C1 O5 301.1 301.4
H2 C2 C1 H1 181.3 181.4
C1 C2 H2 C3 118.2 119.6
C1 C2 H2 O2 238.2 239.8
C3 C2 H2 O2 120.0 120.2
H2 C2 C3 C4 62.4 66.3
H2 C2 C3 O3 301.4 306.2
H2 C2 C3 H3 182.1 185.8
H2 C2 O2 HO2 60.1 299.7
C4 C3 C2 O2 180.4 186.4
C4 C3 C2 H2 62.4 66.3
C2 C3 C4 O3 237.5 240.1
C2 C3 C4 H3 118.0 119.6
O3 C3 C4 H3 240.6 239.6
C4 C3 O3 HO3 57.8 60.6
C5 C4 C3 O4 240.0 240.0
C5 C4 C3 H4 119.3 119.8
C3 C4 C5 O5 310.0 298.9
C3 C4 C5 H51 75.2 59.0
C3 C4 C5 H52 184.8 178.7
O4 C4 C3 H4 239.3 239.8
C3 C4 O4 HO4 180.0 180.2
O3 C3 C2 O2 59.4 66.3
O3 C3 C2 H2 301.4 306.2
C2 C3 O3 C4 122.1 119.4
C2 C3 O3 H3 242.0 239.7
C4 C3 O3 H3 119.8 120.3
O3 C3 C4 C5 174.8 173.4
O3 C3 C4 O4 294.8 293.4
O3 C3 C4 H4 55.5 53.6
H3 C3 C2 O2 300.1 306.0
H3 C3 C2 H2 182.1 185.8
C2 C3 H3 C4 239.8 241.0
C2 C3 H3 O3 120.7 120.4
C4 C3 H3 O3 240.9 239.4
H3 C3 C4 C5 294.2 293.9
H3 C3 C4 O4 54.3 53.9
H3 C3 C4 H4 174.9 174.0
H3 C3 O3 HO3 298.0 300.3
C1 O5 C5 C4 58.3 67.6
C5 C4 C3 O3 174.8 173.4
C5 C4 C3 H3 294.2 293.9
C3 C4 C5 O4 120.0 120.0
C3 C4 C5 H4 240.6 240.1
O4 C4 C5 H4 120.6 120.2
C5 C4 O4 HO4 301.3 299.8
O5 C5 C4 H51 234.8 239.9
O5 C5 C4 H52 125.2 120.2
H51 C5 C4 H52 250.5 240.3
O4 C4 C3 O3 294.8 293.4
O4 C4 C3 H3 54.3 53.9
C3 C4 O4 C5 238.7 240.3
C3 C4 O4 H4 119.4 120.2
C5 C4 O4 H4 240.7 239.8
O4 C4 C5 O5 190.0 178.9
O4 C4 C5 H51 315.2 299.0
O4 C4 C5 H52 64.7 58.7
H4 C4 C3 O3 55.5 53.6
H4 C4 C3 H3 174.9 174.0
C3 C4 H4 C5 120.8 119.6
C3 C4 H4 O4 240.4 239.8
C5 C4 H4 O4 119.6 120.2
H4 C4 C5 O5 69.4 58.7
H4 C4 C5 H51 194.6 178.8
H4 C4 C5 H52 304.1 298.5
H4 C4 O4 HO4 60.6 60.0
C5 O5 C1 H1 53.4 52.5
O5 C5 C4 O4 190.0 178.9
O5 C5 C4 H4 69.4 58.7
C4 C5 O5 H51 125.3 120.1
C4 C5 O5 H52 234.7 239.8
H51 C5 O5 H52 109.4 119.7
H51 C5 C4 O4 315.2 299.0
H51 C5 C4 H4 194.6 178.8
C4 C5 H51 O5 235.7 239.6
C4 C5 H51 H52 117.9 119.8
O5 C5 H51 H52 242.2 240.2
H52 C5 C4 O4 64.7 58.7
H52 C5 C4 H4 304.1 298.5
C4 C5 H52 O5 124.3 120.4
C4 C5 H52 H51 242.1 240.2
O5 C5 H52 H51 117.7 119.8
C1' O1 C1 O5 301.1 300.0
C1' O1 C1 H1 60.8 59.9
C2' C1' O1 H1'1 234.8 240.0
C2' C1' O1 H1'2 125.2 120.1
O1 C1' C2' C3' 279.3 180.0
O1 C1' C2' H2'1 44.6 300.0
O1 C1' C2' H2'2 154.1 59.9
H1'1 C1' O1 H1'2 250.5 240.1
HO2 O2 C2 H2 60.1 299.7
HO3 O3 C3 H3 298.0 300.3
HO4 O4 C4 H4 60.6 60.0
O1 C1' C2' H1'1 125.3 120.0
O1 C1' C2' H1'2 234.7 240.0
H1'1 C1' C2' H1'2 109.5 119.9
C3' C2' C1' H2'1 234.7 240.0
C3' C2' C1' H2'2 125.2 120.1
C1' C2' C3' C4' 55.8 180.0
C1' C2' C3' H3'1 181.1 300.0
C1' C2' C3' H3'2 290.5 59.9
H2'1 C2' C1' H2'2 250.5 240.1
O1 C1' H1'1 C2' 235.2 239.9
O1 C1' H1'1 H1'2 117.7 119.9
C2' C1' H1'1 H1'2 242.4 240.0
H1'1 C1' C2' C3' 154.0 60.0
H1'1 C1' C2' H2'1 279.3 180.0
H1'1 C1' C2' H2'2 28.8 299.9
O1 C1' H1'2 C2' 124.8 120.1
O1 C1' H1'2 H1'1 242.3 240.1
C2' C1' H1'2 H1'1 117.6 120.0
H1'2 C1' C2' C3' 44.6 300.1
H1'2 C1' C2' H2'1 169.9 60.0
H1'2 C1' C2' H2'2 279.4 180.0
C3' C2' C1' H1'1 154.0 60.0
C3' C2' C1' H1'2 44.6 300.1
C1' C2' C3' H2'1 125.3 120.0
C1' C2' C3' H2'2 234.7 239.9
H2'1 C2' C3' H2'2 109.4 119.9
C4' C3' C2' H3'1 234.7 240.0
C4' C3' C2' H3'2 125.3 120.1
C2' C3' C4' C5' 197.3 178.6
C2' C3' C4' O' 75.4 112.5
C2' C3' C4' H4' 313.9 325.5
H3'1 C3' C2' H3'2 250.6 240.1
H2'1 C2' C1' H1'1 279.3 180.0
H2'1 C2' C1' H1'2 169.9 60.0
C1' C2' H2'1 C3' 233.6 239.9
C1' C2' H2'1 H2'2 116.8 120.0
C3' C2' H2'1 H2'2 243.3 240.0
H2'1 C2' C3' C4' 290.5 60.0
H2'1 C2' C3' H3'1 55.8 180.0
H2'1 C2' C3' H3'2 165.2 299.9
H2'2 C2' C1' H1'1 28.8 299.9
H2'2 C2' C1' H1'2 279.4 180.0
C1' C2' H2'2 C3' 126.4 120.1
C1' C2' H2'2 H2'1 243.1 240.1
C3' C2' H2'2 H2'1 116.7 119.9
H2'2 C2' C3' C4' 181.1 300.1
H2'2 C2' C3' H3'1 306.4 60.1
H2'2 C2' C3' H3'2 55.8 180.0
C4' C3' C2' H2'1 290.5 60.0
C4' C3' C2' H2'2 181.1 300.1
C2' C3' C4' H3'1 125.3 120.0
C2' C3' C4' H3'2 234.7 239.9
H3'1 C3' C4' H3'2 109.4 120.0
C5' C4' C3' O' 121.9 66.1
C5' C4' C3' H4' 243.4 213.1
C3' C4' C5' O' 238.6 253.1
C3' C4' C5' H5'1 3.9 0.0
C3' C4' C5' H5'2 113.3 146.3
O' C4' C3' H4' 121.5 147.0
C3' C4' O' C5' 125.5 106.9
H3'1 C3' C2' H2'1 55.8 180.0
H3'1 C3' C2' H2'2 306.4 60.1
C2' C3' H3'1 C4' 234.0 239.9
C2' C3' H3'1 H3'2 117.0 119.9
C4' C3' H3'1 H3'2 243.0 240.0
H3'1 C3' C4' C5' 72.0 58.6
H3'1 C3' C4' O' 310.1 352.5
H3'1 C3' C4' H4' 188.6 205.6
H3'2 C3' C2' H2'1 165.2 299.9
H3'2 C3' C2' H2'2 55.8 180.0
C2' C3' H3'2 C4' 126.0 120.1
C2' C3' H3'2 H3'1 243.0 240.1
C4' C3' H3'2 H3'1 117.0 120.0
H3'2 C3' C4' C5' 322.6 298.7
H3'2 C3' C4' O' 200.7 232.6
H3'2 C3' C4' H4' 79.2 85.6
C5' C4' C3' H3'1 72.0 58.6
C5' C4' C3' H3'2 322.6 298.7
C3' C4' C5' H4' 117.1 146.3
O' C4' C5' H4' 238.5 253.1
C5' C4' O' C5' 360.0 -0.0
O' C5' C4' H5'1 234.7 253.1
O' C5' C4' H5'2 125.3 106.8
H5'1 C5' C4' H5'2 250.6 213.7
O' C4' C3' H3'1 310.1 352.5
O' C4' C3' H3'2 200.7 232.6
C3' C4' O' H4' 242.4 213.7
C5' C4' O' H4' 116.9 106.8
O' C4' C5' O' -0.0 360.0
O' C4' C5' H5'1 125.3 106.9
O' C4' C5' H5'2 234.7 253.2
C4' O' C5' H5'1 234.8 253.2
C4' O' C5' H5'2 125.3 106.9
H4' C4' C3' H3'1 188.6 205.6
H4' C4' C3' H3'2 79.2 85.6
C3' C4' H4' C5' 237.3 213.0
C3' C4' H4' O' 118.4 147.0
C5' C4' H4' O' 241.1 293.9
H4' C4' C5' O' 121.5 106.9
H4' C4' C5' H5'1 246.7 213.8
H4' C4' C5' H5'2 356.2 0.0
H4' C4' O' C5' 243.1 253.2
O' C5' C4' O' -0.0 360.0
O' C5' C4' H4' 121.5 106.9
C4' C5' O' H5'1 125.2 106.8
C4' C5' O' H5'2 234.7 253.1
C5' O' C4' H4' 243.1 253.2
H5'1 C5' O' H5'2 109.5 146.3
H5'1 C5' C4' O' 125.3 106.9
H5'1 C5' C4' H4' 246.7 213.8
C4' C5' H5'1 O' 282.6 294.0
C4' C5' H5'1 H5'2 141.3 147.0
O' C5' H5'1 H5'2 218.7 213.0
H5'2 C5' C4' O' 234.7 253.2
H5'2 C5' C4' H4' 356.2 0.0
C4' C5' H5'2 O' 77.5 66.0
C4' C5' H5'2 H5'1 218.8 213.0
O' C5' H5'2 H5'1 141.3 147.0