PDB Chemical Component UR3

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 UR3

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
P OP1 1.476 1.480
P OP2 1.485 1.610
P O5' 1.596 1.610
P OP3   1.610
OP2 HOP2 0.950 0.967
O5' C5' 1.451 1.429
C5' C4' 1.525 1.530
C5' H5' 1.100 1.090
C5' H5'' 1.100 1.089
C4' O4' 1.453 1.438
C4' C3' 1.517 1.541
C4' H4' 1.100 1.090
O4' C1' 1.422 1.443
C1' N1 1.470 1.464
C1' C2' 1.527 1.550
C1' H1' 1.100 1.090
N1 C6 1.373 1.369
N1 C2 1.384 1.345
C6 C5 1.334 1.350
C6 H6 1.080 1.079
C2 O2 1.227 1.216
C2 N3 1.378 1.346
N3 C3U 1.487 1.464
N3 C4 1.386 1.348
C3U H3U1 1.100 1.090
C3U H3U2 1.100 1.090
C3U H3U3 1.100 1.090
C4 O4 1.235 1.218
C4 C5 1.427 1.416
C5 H5 1.080 1.081
C2' O2' 1.412 1.429
C2' C3' 1.520 1.548
C2' H2' 1.100 1.090
O2' HO2' 0.950 0.968
C3' O3' 1.405 1.429
C3' H3' 1.099 1.089
O3' HO3' 0.950 0.967
OP3 HOP3   0.967

Bond Angles for UR3

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
OP1 P OP2 119.6 109.5
OP1 P O5' 108.1 109.5
OP1 P OP3   109.5
OP2 P O5' 109.5 109.4
OP2 P OP3   109.4
P OP2 HOP2 109.5 114.0
O5' P OP3   109.5
P O5' C5' 120.7 123.0
P OP3 HOP3   114.0
O5' C5' C4' 111.3 109.5
O5' C5' H5' 109.0 109.4
O5' C5' H5'' 109.0 109.5
C4' C5' H5' 109.0 109.5
C4' C5' H5'' 109.0 109.5
C5' C4' O4' 111.1 109.9
C5' C4' C3' 117.3 109.9
C5' C4' H4' 108.1 109.8
H5' C5' H5'' 109.5 109.5
O4' C4' C3' 102.9 107.3
O4' C4' H4' 109.0 109.9
C4' O4' C1' 109.3 107.0
C3' C4' H4' 108.1 110.0
C4' C3' C2' 102.2 104.1
C4' C3' O3' 111.4 110.5
C4' C3' H3' 110.2 110.5
O4' C1' N1 109.2 110.6
O4' C1' C2' 107.5 103.5
O4' C1' H1' 109.7 110.6
N1 C1' C2' 113.0 110.6
N1 C1' H1' 109.1 110.5
C1' N1 C6 121.5 119.7
C1' N1 C2 117.6 119.7
C2' C1' H1' 108.3 110.7
C1' C2' O2' 109.2 110.9
C1' C2' C3' 101.1 102.1
C1' C2' H2' 110.6 110.9
C6 N1 C2 120.9 120.6
N1 C6 C5 122.9 119.7
N1 C6 H6 118.5 120.1
N1 C2 O2 122.7 119.5
N1 C2 N3 114.9 121.0
C5 C6 H6 118.6 120.2
C6 C5 C4 120.0 119.1
C6 C5 H5 120.0 120.4
O2 C2 N3 122.4 119.5
C2 N3 C3U 116.5 119.9
C2 N3 C4 126.7 120.2
C3U N3 C4 116.8 119.9
N3 C3U H3U1 109.5 109.5
N3 C3U H3U2 109.5 109.5
N3 C3U H3U3 109.5 109.5
N3 C4 O4 120.0 120.3
N3 C4 C5 114.5 119.4
H3U1 C3U H3U2 109.5 109.4
H3U1 C3U H3U3 109.4 109.5
H3U2 C3U H3U3 109.5 109.5
O4 C4 C5 125.4 120.3
C4 C5 H5 120.0 120.5
O2' C2' C3' 112.2 110.9
O2' C2' H2' 112.4 110.7
C2' O2' HO2' 109.5 114.0
C3' C2' H2' 110.8 110.9
C2' C3' O3' 110.4 110.5
C2' C3' H3' 110.2 110.5
O3' C3' H3' 112.0 110.6
C3' O3' HO3' 109.5 114.0

Torsion Angles for UR3

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
OP2 P OP1 O5' 233.9 240.0
OP2 P OP1 OP3   120.0
OP1 P OP2 HOP2 0.0 180.0
O5' P OP1 OP3   239.9
OP1 P O5' C5' 45.3 305.1
OP1 P OP3 HOP3   60.0
OP1 P OP2 O5' 125.5 120.0
OP1 P OP2 OP3   240.0
O5' P OP2 OP3   120.0
OP2 P O5' C5' 177.2 65.1
OP2 P OP3 HOP3   300.0
OP1 P O5' OP2 228.1 240.0
OP1 P O5' OP3   120.0
OP2 P O5' OP3   240.0
O5' P OP2 HOP2 234.5 60.0
O5' P OP3 HOP3   180.0
P O5' C5' C4' 179.5 180.0
P O5' C5' H5' 299.7 299.9
P O5' C5' H5'' 59.2 60.0
OP1 P OP3 OP2   120.0
OP1 P OP3 O5'   240.0
OP2 P OP3 O5'   120.0
OP3 P OP2 HOP2   300.0
OP3 P O5' C5'   185.0
HOP2 OP2 P O5' 234.5 60.0
HOP2 OP2 P OP3   300.0
C5' O5' P OP3   185.0
C4' C5' O5' H5' 239.7 240.0
C4' C5' O5' H5'' 120.3 120.0
O5' C5' C4' O4' 295.3 66.4
O5' C5' C4' C3' 53.3 184.3
O5' C5' C4' H4' 175.8 305.4
H5' C5' O5' H5'' 240.5 240.0
O5' C5' C4' H5' 120.3 119.9
O5' C5' C4' H5'' 239.7 240.0
H5' C5' C4' H5'' 119.5 120.0
O4' C4' C5' C3' 242.0 242.1
O4' C4' C5' H4' 119.5 121.0
C5' C4' O4' C1' 152.1 146.0
C3' C4' C5' H4' 237.5 238.8
C5' C4' C3' C2' 197.9 238.5
C5' C4' C3' O3' 80.0 119.9
C5' C4' C3' H3' 315.1 357.2
O5' C5' H5' C4' 238.3 240.0
O5' C5' H5' H5'' 119.2 120.0
C4' C5' H5' H5'' 240.8 240.0
H5' C5' C4' O4' 175.0 306.5
H5' C5' C4' C3' 293.1 64.3
H5' C5' C4' H4' 55.6 185.5
O5' C5' H5'' C4' 121.7 120.0
O5' C5' H5'' H5' 240.8 240.0
C4' C5' H5'' H5' 119.2 120.0
H5'' C5' C4' O4' 55.6 186.4
H5'' C5' C4' C3' 173.6 304.3
H5'' C5' C4' H4' 296.1 65.5
O4' C4' C5' H5' 175.0 306.5
O4' C4' C5' H5'' 55.6 186.4
C5' C4' O4' C3' 126.4 119.4
C5' C4' O4' H4' 241.1 239.0
C3' C4' O4' H4' 114.6 119.6
O4' C4' C3' C2' 320.2 357.9
O4' C4' C3' O3' 202.3 239.3
O4' C4' C3' H3' 77.4 116.6
C4' O4' C1' N1 235.8 201.4
C4' O4' C1' C2' 358.7 320.0
C4' O4' C1' H1' 116.3 78.6
C3' C4' C5' H5' 293.1 64.3
C3' C4' C5' H5'' 173.6 304.3
C5' C4' C3' O4' 237.7 240.6
C5' C4' C3' H4' 122.5 121.0
O4' C4' C3' H4' 244.8 240.5
C3' C4' O4' C1' 25.7 26.5
C1' C2' C3' C4' 38.1 339.2
O2' C2' C3' C4' 281.8 220.9
C4' C3' C2' H2' 155.4 97.4
C2' C3' C4' O3' 117.9 118.6
C2' C3' C4' H3' 242.9 241.3
O3' C3' C4' H3' 124.9 122.7
C4' C3' O3' HO3' 180.0 179.9
H4' C4' C5' H5' 55.6 185.5
H4' C4' C5' H5'' 296.1 65.5
C5' C4' H4' O4' 120.8 121.0
C5' C4' H4' C3' 232.0 238.9
O4' C4' H4' C3' 111.2 118.0
H4' C4' O4' C1' 271.1 266.9
H4' C4' C3' C2' 75.5 117.4
H4' C4' C3' O3' 317.5 358.8
H4' C4' C3' H3' 192.6 236.1
C1' O4' C4' C3' 25.7 26.5
C1' O4' C4' H4' 271.1 266.9
N1 C1' O4' C2' 237.1 241.5
N1 C1' O4' H1' 119.5 122.9
O4' C1' N1 C6 12.4 53.5
O4' C1' N1 C2 192.8 233.3
C2' C1' O4' H1' 242.4 241.4
O4' C1' C2' O2' 94.9 155.3
O4' C1' C2' C3' 336.5 37.0
O4' C1' C2' H2' 219.2 278.8
O4' C1' N1 C2' 119.6 114.1
O4' C1' N1 H1' 240.1 237.1
C2' C1' N1 H1' 120.6 123.0
N1 C1' C2' O2' 215.5 273.8
N1 C1' C2' C3' 97.0 155.5
N1 C1' C2' H2' 339.7 37.3
C6 N1 C1' C2 179.6 180.2
C1' N1 C6 C5 180.9 180.0
C1' N1 C6 H6 0.9 0.0
C1' N1 C2 O2 357.8 360.0
C1' N1 C2 N3 178.5 180.0
C4' C3' C2' C1' 38.1 339.2
O4' C1' C2' N1 239.5 241.5
O4' C1' C2' H1' 118.5 118.6
N1 C1' C2' H1' 239.0 237.1
C2' C1' N1 C6 252.9 299.4
C2' C1' N1 C2 73.3 119.2
O2' C2' C1' C3' 118.4 118.2
O2' C2' C1' H2' 235.8 236.5
C1' C2' O2' HO2' 180.0 180.0
C3' C2' C1' H2' 117.4 118.2
C1' C2' C3' O3' 156.7 97.8
C1' C2' C3' H3' 280.9 220.5
O4' C1' H1' N1 119.5 122.9
O4' C1' H1' C2' 243.0 245.9
N1 C1' H1' C2' 123.4 122.9
H1' C1' N1 C6 132.3 176.4
H1' C1' N1 C2 312.7 356.2
H1' C1' C2' O2' 336.5 36.7
H1' C1' C2' C3' 218.0 278.4
H1' C1' C2' H2' 100.7 160.2
C6 N1 C1' C2' 252.9 299.4
C6 N1 C1' H1' 132.3 176.4
C1' N1 C6 C2 180.4 179.8
C6 N1 C2 O2 178.2 179.8
C6 N1 C2 N3 358.9 359.7
C5 C6 N1 H6 180.0 180.0
N1 C6 C5 C4 0.1 360.0
N1 C6 C5 H5 180.1 180.0
C2 N1 C1' C2' 73.3 119.2
C2 N1 C1' H1' 312.7 356.2
C1' N1 C2 C6 179.6 180.2
C2 N1 C6 C5 0.5 0.3
C2 N1 C6 H6 180.5 180.3
O2 C2 N1 N3 179.3 180.0
N1 C2 N3 C3U 182.9 180.0
N1 C2 N3 C4 1.3 360.0
C5 C6 N1 C2 0.5 0.3
N1 C6 C5 H6 180.0 180.0
N3 C4 C5 C6 0.0 359.7
O4 C4 C5 C6 182.6 179.9
C4 C5 C6 H5 180.0 180.0
H6 C6 N1 C2 180.5 180.3
N1 C6 H6 C5 180.0 180.0
H6 C6 C5 C4 180.1 180.0
H6 C6 C5 H5 0.1 360.0
N1 C2 O2 N3 180.7 180.0
O2 C2 N3 C3U 3.6 0.0
O2 C2 N3 C4 182.0 179.9
N1 C2 N3 O2 179.3 180.0
C3U N3 C2 C4 181.5 180.1
C2 N3 C3U H3U1 180.0 90.0
C2 N3 C3U H3U2 300.0 209.9
C2 N3 C3U H3U3 60.0 330.0
C2 N3 C4 O4 176.8 180.1
C2 N3 C4 C5 359.2 0.3
C2 N3 C3U C4 178.6 179.9
C3U N3 C4 O4 355.3 0.0
C3U N3 C4 C5 177.7 180.2
H3U1 C3U N3 H3U2 240.0 240.0
H3U1 C3U N3 H3U3 120.0 120.0
H3U2 C3U N3 H3U3 240.0 240.0
C6 C5 C4 N3 0.0 359.7
C2 N3 C4 C3U 181.5 180.1
C4 N3 C3U H3U1 1.4 270.1
C4 N3 C3U H3U2 121.4 30.0
C4 N3 C3U H3U3 241.4 150.0
O4 C4 N3 C5 177.6 179.8
N3 C4 C5 H5 180.0 179.7
H3U1 C3U N3 C4 1.4 270.1
N3 C3U H3U1 H3U2 120.0 120.0
N3 C3U H3U1 H3U3 240.0 240.0
H3U2 C3U H3U1 H3U3 120.0 119.9
H3U2 C3U N3 C4 121.4 30.0
N3 C3U H3U2 H3U1 240.0 240.0
N3 C3U H3U2 H3U3 120.0 120.0
H3U1 C3U H3U2 H3U3 240.0 240.1
H3U3 C3U N3 C4 241.4 150.0
N3 C3U H3U3 H3U1 120.0 120.1
N3 C3U H3U3 H3U2 240.0 240.0
H3U1 C3U H3U3 H3U2 120.0 119.9
C6 C5 C4 O4 182.6 179.9
N3 C4 O4 C5 182.7 180.2
O4 C4 C5 H5 2.5 359.9
C4 C5 C6 H6 180.1 180.0
C6 C5 C4 H5 180.0 180.0
N3 C4 C5 O4 177.5 179.8
H5 C5 C6 H6 0.1 360.0
C6 C5 H5 C4 180.0 180.0
C4' C3' C2' O2' 281.8 220.9
O2' C2' C1' H1' 336.5 36.7
C1' C2' O2' C3' 248.8 247.2
C1' C2' O2' H2' 123.2 123.6
C3' C2' O2' H2' 234.4 236.4
O2' C2' C3' O3' 40.5 339.5
O2' C2' C3' H3' 164.7 102.2
C2' C3' C4' H4' 75.5 117.4
C4' C3' C2' O3' 241.4 241.4
C4' C3' C2' H3' 117.2 118.7
C3' C2' C1' H1' 218.0 278.4
C1' C2' C3' O2' 116.3 118.2
C1' C2' C3' H2' 242.7 241.8
O2' C2' C3' H2' 126.5 123.5
C3' C2' O2' HO2' 291.2 292.8
O3' C3' C2' H3' 235.8 237.3
C2' C3' O3' HO3' 67.2 65.2
H2' C2' C1' H1' 100.7 160.2
C1' C2' H2' O2' 237.6 236.4
C1' C2' H2' C3' 111.2 112.8
O2' C2' H2' C3' 233.6 236.4
H2' C2' O2' HO2' 56.8 56.4
H2' C2' C3' O3' 274.0 216.0
H2' C2' C3' H3' 38.2 338.7
HO2' O2' C2' C3' 291.2 292.8
HO2' O2' C2' H2' 56.8 56.4
O3' C3' C4' H4' 317.5 358.8
C4' C3' O3' C2' 112.9 114.7
C4' C3' O3' H3' 236.0 237.4
O3' C3' C2' H2' 274.0 216.0
C2' C3' O3' H3' 123.2 122.7
H3' C3' C4' H4' 192.6 236.1
C4' C3' H3' C2' 247.9 245.3
C4' C3' H3' O3' 124.6 122.6
H3' C3' C2' H2' 38.2 338.7
C2' C3' H3' O3' 236.7 237.4
H3' C3' O3' HO3' 304.0 302.6
HO3' O3' C3' H3' 304.0 302.6