PDB Chemical Component U2L

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 U2L

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
OP3 P   1.617
OP3 HOP3   0.980
P OP1 1.479 1.501
P OP2 1.480 1.618
P O5' 1.612 1.619
OP2 HOP2 0.950 0.980
O5' C5' 1.423 1.416
C5' C4' 1.532 1.523
C5' H5' 1.089 1.092
C5' H5'' 1.091 1.091
C4' O4' 1.410 1.444
C4' C3' 1.508 1.523
C4' H4' 1.075 1.095
O4' C1' 1.413 1.437
C3' O3' 1.433 1.427
C3' C2' 1.545 1.514
C3' H3' 1.091 1.093
O3' CA' 1.426 1.418
C2' O2' 1.434 1.413
C2' C1' 1.529 1.519
C2' H2' 1.096 1.097
O2' HO2' 0.950 0.973
C1' N1 1.496 1.435
C1' H1' 1.053 1.094
N1 C2 1.404 1.413
N1 C6 1.373 1.390
C2 O2 1.229 1.232
C2 N3 1.394 1.400
N3 C4 1.388 1.386
N3 H3 1.007 1.017
C4 O4 1.229 1.229
C4 C5 1.451 1.487
C5 C6 1.348 1.339
C5 C7 1.502 1.495
C6 H6 1.067 1.086
CA' CB' 1.537 1.517
CA' HA'1 1.089 1.095
CA' HA'2 1.090 1.094
CB' OC' 1.424 1.422
CB' HB'1 1.090 1.094
CB' HB'2 1.088 1.094
OC' CD' 1.419 1.420
CD' HD'1 1.091 1.093
CD' HD'2 1.090 1.093
CD' HD'3 1.089 1.093
C7 H71 1.086 1.089
C7 H72 1.090 1.089
C7 H73 1.106 1.090

Bond Angles for U2L

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
P OP3 HOP3   119.0
OP3 P OP1   115.3
OP3 P OP2   103.3
OP3 P O5'   103.8
OP1 P OP2 119.6 114.9
OP1 P O5' 108.1 115.0
OP2 P O5' 107.7 102.9
P OP2 HOP2 44.6 119.0
P O5' C5' 122.0 118.5
O5' C5' C4' 109.2 108.6
O5' C5' H5' 110.8 109.2
O5' C5' H5'' 109.5 109.3
C4' C5' H5' 108.9 110.1
C4' C5' H5'' 109.5 110.1
C5' C4' O4' 108.2 108.2
C5' C4' C3' 115.7 113.3
C5' C4' H4' 112.1 109.3
H5' C5' H5'' 108.9 109.6
O4' C4' C3' 106.8 105.9
O4' C4' H4' 112.1 107.7
C4' O4' C1' 106.6 109.2
C3' C4' H4' 101.9 112.2
C4' C3' O3' 110.9 107.9
C4' C3' C2' 103.2 102.1
C4' C3' H3' 101.2 114.5
O4' C1' C2' 109.3 106.5
O4' C1' N1 116.3 109.0
O4' C1' H1' 107.3 108.9
O3' C3' C2' 119.0 110.3
O3' C3' H3' 111.2 107.8
C3' O3' CA' 120.1 111.3
C2' C3' H3' 109.6 114.0
C3' C2' O2' 116.2 112.3
C3' C2' C1' 94.4 102.0
C3' C2' H2' 117.8 110.1
O3' CA' CB' 111.7 109.1
O3' CA' HA'1 111.4 108.1
O3' CA' HA'2 108.7 108.3
O2' C2' C1' 107.3 112.6
O2' C2' H2' 104.5 108.6
C2' O2' HO2' 116.2 107.1
C1' C2' H2' 116.4 111.1
C2' C1' N1 122.0 112.5
C2' C1' H1' 95.9 112.6
N1 C1' H1' 102.6 107.3
C1' N1 C2 116.9 121.3
C1' N1 C6 123.7 118.5
C2 N1 C6 119.4 120.2
N1 C2 O2 123.4 123.8
N1 C2 N3 117.1 115.1
N1 C6 C5 122.5 124.5
N1 C6 H6 124.4 114.7
O2 C2 N3 119.5 121.1
C2 N3 C4 125.9 127.0
C2 N3 H3 117.1 116.4
C4 N3 H3 117.1 116.6
N3 C4 O4 120.1 123.6
N3 C4 C5 113.3 114.8
O4 C4 C5 126.5 121.6
C4 C5 C6 121.8 118.4
C4 C5 C7 123.1 118.0
C6 C5 C7 115.2 123.6
C5 C6 H6 113.1 120.7
C5 C7 H71 111.6 109.7
C5 C7 H72 109.8 109.8
C5 C7 H73 103.2 109.7
CB' CA' HA'1 108.9 111.1
CB' CA' HA'2 107.0 110.5
CA' CB' OC' 114.3 109.0
CA' CB' HB'1 107.5 111.1
CA' CB' HB'2 110.0 110.5
HA'1 CA' HA'2 109.1 109.6
OC' CB' HB'1 107.2 108.1
OC' CB' HB'2 110.1 108.3
CB' OC' CD' 114.8 111.5
HB'1 CB' HB'2 107.4 109.7
OC' CD' HD'1 110.4 109.5
OC' CD' HD'2 109.0 109.5
OC' CD' HD'3 110.4 109.0
HD'1 CD' HD'2 108.9 110.1
HD'1 CD' HD'3 109.8 109.3
HD'2 CD' HD'3 108.3 109.4
H71 C7 H72 111.5 109.4
H71 C7 H73 113.1 109.4
H72 C7 H73 107.2 108.9

Torsion Angles for U2L

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
OP1 P OP3 OP2   126.2
OP1 P OP3 O5'   233.4
OP2 P OP3 O5'   107.1
OP3 P OP2 HOP2   78.5
OP3 P O5' C5'   53.2
HOP3 OP3 P OP1   48.7
HOP3 OP3 P OP2   282.5
HOP3 OP3 P O5'   175.4
OP1 P OP3 HOP3   48.7
OP3 P OP1 OP2   240.0
OP3 P OP1 O5'   120.7
OP2 P OP1 O5' 236.5 240.7
OP1 P OP2 HOP2 66.0 312.0
OP1 P O5' C5' 275.4 180.1
OP2 P OP3 HOP3   282.5
OP3 P OP2 OP1   126.5
OP3 P OP2 O5'   252.3
OP1 P OP2 O5' 123.7 125.8
OP2 P O5' C5' 45.9 305.8
O5' P OP3 HOP3   175.4
OP3 P O5' OP1   233.1
OP3 P O5' OP2   107.4
OP1 P O5' OP2 229.5 234.2
O5' P OP2 HOP2 302.3 186.2
P O5' C5' C4' 220.3 180.0
P O5' C5' H5' 340.3 300.1
P O5' C5' H5'' 100.4 59.9
HOP2 OP2 P O5' 302.3 186.2
C4' C5' O5' H5' 240.1 239.9
C4' C5' O5' H5'' 119.9 120.1
O5' C5' C4' O4' 296.8 62.4
O5' C5' C4' C3' 56.5 179.5
O5' C5' C4' H4' 172.7 305.4
H5' C5' O5' H5'' 239.8 240.2
O5' C5' C4' H5' 121.1 119.5
O5' C5' C4' H5'' 240.1 240.4
H5' C5' C4' H5'' 119.0 120.9
O4' C4' C5' C3' 240.3 242.9
O4' C4' C5' H4' 124.1 117.0
C5' C4' O4' C1' 130.6 109.0
C3' C4' C5' H4' 243.7 234.1
C5' C4' C3' O3' 79.6 156.8
C5' C4' C3' C2' 208.1 273.1
C5' C4' C3' H3' 321.6 36.8
O5' C5' H5' C4' 239.9 240.8
O5' C5' H5' H5'' 120.5 119.6
C4' C5' H5' H5'' 240.6 238.8
H5' C5' C4' O4' 175.7 302.9
H5' C5' C4' C3' 295.3 60.0
H5' C5' C4' H4' 51.6 185.9
O5' C5' H5'' C4' 119.7 119.2
O5' C5' H5'' H5' 238.7 240.4
C4' C5' H5'' H5' 119.0 121.2
H5'' C5' C4' O4' 56.7 182.0
H5'' C5' C4' C3' 176.3 299.1
H5'' C5' C4' H4' 292.6 65.0
O4' C4' C5' H5' 175.7 302.9
O4' C4' C5' H5'' 56.7 182.0
C5' C4' O4' C3' 125.2 121.7
C5' C4' O4' H4' 235.9 241.9
C3' C4' O4' H4' 110.8 120.2
O4' C4' C3' O3' 200.1 275.3
O4' C4' C3' C2' 328.5 31.5
O4' C4' C3' H3' 82.0 155.2
C4' O4' C1' C2' 23.7 348.7
C4' O4' C1' N1 240.8 227.1
C4' O4' C1' H1' 126.6 110.3
C3' C4' C5' H5' 295.3 60.0
C3' C4' C5' H5'' 176.3 299.1
C5' C4' C3' O4' 239.6 241.6
C5' C4' C3' H4' 121.9 124.4
O4' C4' C3' H4' 242.3 242.8
C3' C4' O4' C1' 5.4 347.2
O3' C3' C4' C2' 231.5 243.7
O3' C3' C4' H3' 118.1 120.1
C4' C3' O3' CA' 78.2 290.8
C2' C3' C4' H3' 246.6 236.3
C4' C3' C2' O2' 289.3 202.0
C4' C3' C2' C1' 41.0 322.9
C4' C3' C2' H2' 164.1 80.9
H4' C4' C5' H5' 51.6 185.9
H4' C4' C5' H5'' 292.6 65.0
C5' C4' H4' O4' 121.8 117.3
C5' C4' H4' C3' 235.6 233.5
O4' C4' H4' C3' 113.8 116.2
H4' C4' O4' C1' 254.6 227.0
H4' C4' C3' O3' 317.8 32.5
H4' C4' C3' C2' 86.3 148.7
H4' C4' C3' H3' 199.7 272.4
C1' O4' C4' C3' 5.4 347.2
C1' O4' C4' H4' 254.6 227.0
C3' C2' C1' O4' 319.6 30.7
O2' C2' C1' O4' 78.8 151.3
O4' C1' C2' H2' 195.4 273.4
C2' C1' O4' N1 142.9 121.6
C2' C1' O4' H1' 257.1 238.4
N1 C1' O4' H1' 114.1 116.8
O4' C1' N1 C2 288.2 212.2
O4' C1' N1 C6 108.2 32.3
O3' C3' C4' H4' 317.8 32.5
C4' C3' O3' C2' 119.4 110.7
C4' C3' O3' H3' 248.1 235.8
C2' C3' O3' H3' 128.8 125.1
O3' C3' C2' O2' 52.6 316.5
O3' C3' C2' C1' 164.3 77.4
O3' C3' C2' H2' 287.4 195.4
C3' O3' CA' CB' 185.1 179.0
C3' O3' CA' HA'1 307.1 300.0
C3' O3' CA' HA'2 67.3 58.8
C2' C3' C4' H4' 86.3 148.7
C4' C3' C2' O3' 236.7 245.5
C4' C3' C2' H3' 107.2 124.0
O4' C1' C2' C3' 319.6 30.7
O3' C3' C2' H3' 230.5 238.5
C2' C3' O3' CA' 318.8 180.0
O2' C2' C3' C1' 248.2 239.2
O2' C2' C3' H2' 125.2 121.1
C3' C2' O2' HO2' 180.0 168.8
C1' C2' C3' H2' 237.0 242.0
C3' C2' C1' N1 100.0 150.0
C3' C2' C1' H1' 208.8 271.5
H3' C3' C4' H4' 199.7 272.4
C4' C3' H3' O3' 117.9 120.1
C4' C3' H3' C2' 251.5 243.0
O3' C3' H3' C2' 133.6 122.8
H3' C3' O3' CA' 190.0 54.9
H3' C3' C2' O2' 182.1 78.0
H3' C3' C2' C1' 293.8 198.9
H3' C3' C2' H2' 56.9 316.9
CA' O3' C3' C2' 318.8 180.0
CA' O3' C3' H3' 190.0 54.9
CB' CA' O3' HA'1 238.0 239.0
CB' CA' O3' HA'2 117.8 120.3
O3' CA' CB' OC' 77.3 299.1
O3' CA' CB' HB'1 196.1 180.0
O3' CA' CB' HB'2 312.8 58.0
HA'1 CA' O3' HA'2 239.8 241.3
O4' C1' C2' O2' 78.8 151.3
O2' C2' C3' H3' 182.1 78.0
C3' C2' O2' C1' 104.1 114.5
C3' C2' O2' H2' 228.3 238.0
C1' C2' O2' H2' 124.2 123.5
O2' C2' C1' N1 219.2 270.6
O2' C2' C1' H1' 328.0 32.1
O4' C1' C2' N1 219.6 240.7
O4' C1' C2' H1' 110.7 119.3
C1' C2' C3' H3' 293.8 198.9
C3' C2' C1' O2' 240.8 239.4
C3' C2' C1' H2' 124.1 117.3
O2' C2' C1' H2' 243.3 237.9
C1' C2' O2' HO2' 75.9 54.3
N1 C1' C2' H1' 251.1 238.6
C2' C1' N1 C2 150.4 94.3
C2' C1' N1 C6 330.4 274.4
H2' C2' C3' H3' 56.9 316.9
C3' C2' H2' O2' 130.8 123.3
C3' C2' H2' C1' 249.0 247.7
O2' C2' H2' C1' 118.2 124.4
H2' C2' O2' HO2' 311.7 290.8
H2' C2' C1' N1 335.8 32.7
H2' C2' C1' H1' 84.7 154.2
HO2' O2' C2' C1' 75.9 54.3
HO2' O2' C2' H2' 311.7 290.8
O4' C1' N1 C2' 137.8 117.9
O4' C1' N1 H1' 243.2 242.3
N1 C1' C2' H2' 335.8 32.7
C2' C1' N1 H1' 105.3 124.4
C2 N1 C1' C6 180.0 179.9
C1' N1 C2 O2 0.1 0.1
C1' N1 C2 N3 180.2 180.0
C1' N1 C6 C5 179.6 180.0
C1' N1 C6 H6 359.3 360.0
O4' C1' H1' C2' 247.7 242.1
O4' C1' H1' N1 123.0 117.8
H1' C1' C2' H2' 84.7 154.2
C2' C1' H1' N1 235.3 235.7
H1' C1' N1 C2 45.1 329.9
H1' C1' N1 C6 225.0 150.0
C2 N1 C1' H1' 45.1 329.9
C1' N1 C2 C6 180.0 180.1
C2 N1 C6 C5 359.6 0.0
C2 N1 C6 H6 179.3 180.0
O2 C2 N1 N3 179.9 180.1
N1 C2 N3 C4 360.0 360.0
N1 C2 N3 H3 180.0 180.1
C6 N1 C1' H1' 225.0 150.0
C1' N1 C6 C2 180.0 179.9
C6 N1 C2 O2 180.1 180.0
C6 N1 C2 N3 0.2 360.0
C4 C5 C6 N1 0.3 0.0
N1 C6 C5 C7 180.4 180.0
C5 C6 N1 H6 180.3 180.0
O2 C2 N1 C6 180.1 180.0
N1 C2 O2 N3 180.1 179.9
O2 C2 N3 C4 180.1 179.9
O2 C2 N3 H3 0.1 0.0
N3 C2 N1 C6 0.2 360.0
N1 C2 N3 O2 179.9 180.1
C4 N3 C2 H3 180.0 179.9
C2 N3 C4 O4 179.9 180.1
C2 N3 C4 C5 360.0 0.1
C2 N3 C4 H3 180.0 180.1
O4 C4 N3 C5 179.9 180.0
N3 C4 C5 C6 359.9 360.0
N3 C4 C5 C7 179.8 180.0
C2 N3 H3 C4 180.0 179.9
H3 N3 C4 O4 359.9 360.0
H3 N3 C4 C5 179.9 180.0
O4 C4 N3 H3 359.9 360.0
N3 C4 O4 C5 180.1 180.0
O4 C4 C5 C6 180.0 180.0
O4 C4 C5 C7 359.9 360.0
N1 C6 C5 C4 0.3 0.0
C5 C4 N3 H3 179.9 180.0
N3 C4 C5 O4 179.9 180.0
C6 C5 C4 C7 180.1 180.0
C4 C5 C6 H6 180.6 180.0
C4 C5 C7 H71 96.6 244.2
C4 C5 C7 H72 332.4 124.0
C4 C5 C7 H73 218.4 4.4
N1 C6 C5 H6 179.7 180.0
C4 C5 C6 C7 179.9 180.0
C6 C5 C7 H71 276.6 64.2
C6 C5 C7 H72 152.4 304.0
C6 C5 C7 H73 38.3 184.4
C4 C5 C7 C6 180.1 180.0
C7 C5 C6 H6 0.7 360.0
H71 C7 C5 H72 124.2 120.2
H71 C7 C5 H73 238.3 239.8
H72 C7 C5 H73 114.1 119.6
N1 C6 H6 C5 180.3 180.0
H6 C6 C5 C7 0.7 360.0
O3' CA' CB' HA'1 123.5 119.1
O3' CA' CB' HA'2 241.2 241.1
HA'1 CA' CB' HA'2 117.7 122.0
OC' CB' CA' HB'1 241.1 119.1
OC' CB' CA' HB'2 124.4 241.1
CA' CB' OC' CD' 290.9 179.0
HB'1 CB' CA' HB'2 243.3 122.0
O3' CA' HA'1 CB' 236.4 240.3
O3' CA' HA'1 HA'2 120.0 117.8
CB' CA' HA'1 HA'2 243.6 237.5
HA'1 CA' CB' OC' 313.8 180.0
HA'1 CA' CB' HB'1 72.7 60.9
HA'1 CA' CB' HB'2 189.3 298.8
O3' CA' HA'2 CB' 120.7 119.4
O3' CA' HA'2 HA'1 238.3 242.2
CB' CA' HA'2 HA'1 117.6 122.8
HA'2 CA' CB' OC' 196.1 58.0
HA'2 CA' CB' HB'1 314.9 298.9
HA'2 CA' CB' HB'2 71.6 176.9
OC' CB' CA' HA'1 313.8 180.0
OC' CB' CA' HA'2 196.1 58.0
CA' CB' OC' HB'1 119.0 239.0
CA' CB' OC' HB'2 235.6 120.2
HB'1 CB' OC' HB'2 116.6 241.2
CB' OC' CD' HD'1 308.5 267.0
CB' OC' CD' HD'2 188.9 146.2
CB' OC' CD' HD'3 70.0 26.6
HB'1 CB' CA' HA'1 72.7 60.9
HB'1 CB' CA' HA'2 314.9 298.9
CA' CB' HB'1 OC' 236.7 119.7
CA' CB' HB'1 HB'2 118.4 237.5
OC' CB' HB'1 HB'2 241.7 117.9
HB'1 CB' OC' CD' 171.9 300.0
HB'2 CB' CA' HA'1 189.3 298.8
HB'2 CB' CA' HA'2 71.6 176.9
CA' CB' HB'2 OC' 126.8 240.7
CA' CB' HB'2 HB'1 243.2 122.9
OC' CB' HB'2 HB'1 116.4 242.2
HB'2 CB' OC' CD' 55.3 58.8
CD' OC' CB' HB'1 171.9 300.0
CD' OC' CB' HB'2 55.3 58.8
HD'1 CD' OC' HD'2 119.6 120.8
HD'1 CD' OC' HD'3 238.4 240.5
HD'2 CD' OC' HD'3 118.8 119.7
OC' CD' HD'1 HD'2 240.4 239.6
OC' CD' HD'1 HD'3 121.9 119.3
HD'2 CD' HD'1 HD'3 241.6 239.8
OC' CD' HD'2 HD'1 120.5 120.4
OC' CD' HD'2 HD'3 239.9 240.6
HD'1 CD' HD'2 HD'3 119.4 120.2
OC' CD' HD'3 HD'1 238.1 240.4
OC' CD' HD'3 HD'2 119.3 119.7
HD'1 CD' HD'3 HD'2 241.2 239.4
C5 C7 H71 H72 236.8 239.5
C5 C7 H71 H73 115.9 120.4
H72 C7 H71 H73 239.0 240.8
C5 C7 H72 H71 124.2 120.4
C5 C7 H72 H73 248.5 239.9
H71 C7 H72 H73 124.3 119.5
C5 C7 H73 H71 239.2 239.6
C5 C7 H73 H72 115.9 120.2
H71 C7 H73 H72 236.6 240.5