PDB Chemical Component U36

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 U36

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
P OP1 1.473 1.480
P OP2 1.490 1.609
P OP3 1.595 1.611
P O5' 1.585 1.610
OP2 HOP2 0.949 0.967
OP3 HOP3 0.950 0.967
O5' C5' 1.424 1.428
C5' C4' 1.500 1.530
C5' H5'1 1.100 1.090
C5' H5'2 1.100 1.090
C4' O4' 1.443 1.437
C4' C3' 1.509 1.542
C4' H4' 1.100 1.090
O4' C1' 1.411 1.444
C3' O3' 1.418 1.429
C3' C2' 1.522 1.548
C3' H3' 1.100 1.090
O3' HA 0.949 0.967
C2' O2' 1.414 1.430
C2' C1' 1.519 1.550
C2' H2' 1.100 1.090
O2' CA' 1.442 1.429
C1' N1 1.461 1.465
C1' H1' 1.100 1.090
N1 C2 1.373 1.345
N1 C6 1.369 1.368
C2 O2 1.218 1.216
C2 N3 1.371 1.346
N3 C4 1.382 1.349
N3 H3 1.000 0.970
C4 O4 1.231 1.218
C4 C5 1.427 1.415
C5 C6 1.346 1.351
C5 H5 1.080 1.080
C6 H6 1.080 1.080
CA' CB' 1.531 1.530
CA' HA'1 1.100 1.091
CA' HA'2 1.100 1.090
CB' OC' 1.467 1.429
CB' HB'1 1.101 1.090
CB' HB'2 1.100 1.090
CD' OC' 1.454 1.428
CD' HD'1 1.100 1.090
CD' HD'2 1.100 1.089
CD' HD'3 1.100 1.089

Bond Angles for U36

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
OP1 P OP2 120.2 109.5
OP1 P OP3 106.4 109.4
OP1 P O5' 109.6 109.5
OP2 P OP3 109.4 109.5
OP2 P O5' 105.8 109.5
P OP2 HOP2 109.5 114.0
OP3 P O5' 104.3 109.5
P OP3 HOP3 109.5 113.9
P O5' C5' 121.1 123.0
O5' C5' C4' 109.6 109.5
O5' C5' H5'1 109.5 109.5
O5' C5' H5'2 109.4 109.5
C4' C5' H5'1 109.4 109.5
C4' C5' H5'2 109.4 109.5
C5' C4' O4' 109.6 109.9
C5' C4' C3' 115.9 109.9
C5' C4' H4' 109.4 109.9
H5'1 C5' H5'2 109.5 109.4
O4' C4' C3' 102.4 107.3
O4' C4' H4' 110.1 109.9
C4' O4' C1' 109.6 107.0
C3' C4' H4' 109.2 110.0
C4' C3' O3' 111.7 110.5
C4' C3' C2' 101.5 104.2
C4' C3' H3' 109.5 110.5
O4' C1' C2' 107.2 103.5
O4' C1' N1 108.7 110.6
O4' C1' H1' 110.7 110.6
O3' C3' C2' 113.4 110.5
O3' C3' H3' 110.9 110.5
C3' O3' HA 109.5 114.0
C2' C3' H3' 109.4 110.6
C3' C2' O2' 111.2 110.9
C3' C2' C1' 101.1 102.1
C3' C2' H2' 111.0 110.9
O2' C2' C1' 109.0 110.9
O2' C2' H2' 112.7 110.8
C2' O2' CA' 112.4 114.0
C1' C2' H2' 111.1 111.0
C2' C1' N1 111.0 110.6
C2' C1' H1' 109.2 110.6
O2' CA' CB' 115.7 109.5
O2' CA' HA'1 107.9 109.4
O2' CA' HA'2 107.9 109.5
N1 C1' H1' 110.0 110.7
C1' N1 C2 117.5 119.7
C1' N1 C6 121.3 119.7
C2 N1 C6 121.2 120.6
N1 C2 O2 122.8 119.5
N1 C2 N3 115.0 120.9
N1 C6 C5 122.7 119.7
N1 C6 H6 118.6 120.2
O2 C2 N3 122.1 119.6
C2 N3 C4 127.1 120.3
C2 N3 H3 116.5 119.9
C4 N3 H3 116.5 119.9
N3 C4 O4 119.1 120.3
N3 C4 C5 114.5 119.4
O4 C4 C5 126.3 120.3
C4 C5 C6 119.4 119.1
C4 C5 H5 120.3 120.4
C6 C5 H5 120.3 120.5
C5 C6 H6 118.6 120.1
CB' CA' HA'1 107.9 109.4
CB' CA' HA'2 107.9 109.5
CA' CB' OC' 117.3 109.5
CA' CB' HB'1 107.5 109.5
CA' CB' HB'2 107.5 109.5
HA'1 CA' HA'2 109.5 109.5
OC' CB' HB'1 107.5 109.4
OC' CB' HB'2 107.5 109.5
CB' OC' CD' 110.6 114.0
HB'1 CB' HB'2 109.4 109.5
OC' CD' HD'1 109.5 109.5
OC' CD' HD'2 109.4 109.5
OC' CD' HD'3 109.5 109.5
HD'1 CD' HD'2 109.5 109.5
HD'1 CD' HD'3 109.4 109.4
HD'2 CD' HD'3 109.5 109.5

Torsion Angles for U36

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
OP2 P OP1 OP3 124.9 240.0
OP2 P OP1 O5' 237.1 120.1
OP1 P OP2 HOP2 0.0 59.9
OP3 P OP1 O5' 112.2 240.0
OP1 P OP3 HOP3 0.0 180.0
OP1 P O5' C5' 58.5 305.0
OP1 P OP2 OP3 236.5 119.9
OP1 P OP2 O5' 124.7 240.0
OP3 P OP2 O5' 248.2 120.0
OP2 P OP3 HOP3 228.7 299.9
OP2 P O5' C5' 189.6 185.0
OP1 P OP3 OP2 131.3 240.0
OP1 P OP3 O5' 244.2 120.0
OP2 P OP3 O5' 112.9 239.9
OP3 P OP2 HOP2 123.5 300.0
OP3 P O5' C5' 304.9 65.0
OP1 P O5' OP2 229.0 120.0
OP1 P O5' OP3 113.6 240.1
OP2 P O5' OP3 244.6 120.0
O5' P OP2 HOP2 235.4 179.9
O5' P OP3 HOP3 115.8 60.0
P O5' C5' C4' 163.1 180.0
P O5' C5' H5'1 283.1 300.0
P O5' C5' H5'2 43.1 60.0
HOP2 OP2 P OP3 123.5 300.0
HOP2 OP2 P O5' 235.4 179.9
HOP3 OP3 P O5' 115.8 60.0
C4' C5' O5' H5'1 240.0 240.0
C4' C5' O5' H5'2 120.0 120.0
O5' C5' C4' O4' 296.0 66.5
O5' C5' C4' C3' 51.2 184.3
O5' C5' C4' H4' 175.2 305.5
H5'1 C5' O5' H5'2 240.0 240.0
O5' C5' C4' H5'1 120.0 120.0
O5' C5' C4' H5'2 240.0 240.0
H5'1 C5' C4' H5'2 120.0 119.9
O4' C4' C5' C3' 244.8 242.2
O4' C4' C5' H4' 120.8 121.0
C5' C4' O4' C1' 152.4 145.9
C3' C4' C5' H4' 236.0 238.8
C5' C4' C3' O3' 78.0 119.9
C5' C4' C3' C2' 199.2 238.6
C5' C4' C3' H3' 314.8 357.4
O5' C5' H5'1 C4' 239.9 240.0
O5' C5' H5'1 H5'2 119.9 120.1
C4' C5' H5'1 H5'2 240.1 240.0
H5'1 C5' C4' O4' 176.0 306.4
H5'1 C5' C4' C3' 291.2 64.3
H5'1 C5' C4' H4' 55.2 185.4
O5' C5' H5'2 C4' 120.1 120.0
O5' C5' H5'2 H5'1 240.0 240.0
C4' C5' H5'2 H5'1 119.9 120.0
H5'2 C5' C4' O4' 56.0 186.5
H5'2 C5' C4' C3' 171.2 304.3
H5'2 C5' C4' H4' 295.2 65.5
O4' C4' C5' H5'1 176.0 306.4
O4' C4' C5' H5'2 56.0 186.5
C5' C4' O4' C3' 123.5 119.4
C5' C4' O4' H4' 239.6 239.0
C3' C4' O4' H4' 116.1 119.6
O4' C4' C3' O3' 197.3 239.3
O4' C4' C3' C2' 318.4 358.0
O4' C4' C3' H3' 74.0 116.8
C4' O4' C1' C2' 355.9 319.9
C4' O4' C1' N1 235.8 201.4
C4' O4' C1' H1' 114.9 78.4
C3' C4' C5' H5'1 291.2 64.3
C3' C4' C5' H5'2 171.2 304.3
C5' C4' C3' O4' 240.8 240.6
C5' C4' C3' H4' 124.1 121.1
O4' C4' C3' H4' 243.3 240.5
C3' C4' O4' C1' 28.8 26.5
O3' C3' C4' C2' 238.8 241.3
O3' C3' C4' H3' 123.2 122.5
C4' C3' O3' HA 180.0 298.6
C2' C3' C4' H3' 244.4 241.2
C4' C3' C2' O2' 282.8 220.9
C4' C3' C2' C1' 38.4 339.1
C4' C3' C2' H2' 156.4 97.4
H4' C4' C5' H5'1 55.2 185.4
H4' C4' C5' H5'2 295.2 65.5
C5' C4' H4' O4' 120.5 121.0
C5' C4' H4' C3' 232.2 238.9
O4' C4' H4' C3' 111.7 117.9
H4' C4' O4' C1' 272.8 266.9
H4' C4' C3' O3' 314.0 358.8
H4' C4' C3' C2' 75.2 117.5
H4' C4' C3' H3' 190.7 236.3
C1' O4' C4' C3' 28.8 26.5
C1' O4' C4' H4' 272.8 266.9
C3' C2' C1' O4' 337.9 37.1
O2' C2' C1' O4' 95.2 155.2
O4' C1' C2' H2' 220.0 278.8
C2' C1' O4' N1 120.1 118.5
C2' C1' O4' H1' 241.0 241.5
N1 C1' O4' H1' 120.9 123.0
O4' C1' N1 C2 199.5 233.6
O4' C1' N1 C6 20.4 53.3
O3' C3' C4' H4' 314.0 358.8
C4' C3' O3' C2' 114.0 114.7
C4' C3' O3' H3' 237.5 237.5
C2' C3' O3' H3' 123.6 122.7
O3' C3' C2' O2' 42.8 339.6
O3' C3' C2' C1' 158.4 97.8
O3' C3' C2' H2' 276.4 216.1
C2' C3' C4' H4' 75.2 117.5
C4' C3' C2' O3' 240.1 241.3
C4' C3' C2' H3' 115.7 118.7
O4' C1' C2' C3' 337.9 37.1
O3' C3' C2' H3' 235.6 237.3
C2' C3' O3' HA 66.0 183.8
O2' C2' C3' C1' 244.4 241.8
O2' C2' C3' H2' 126.4 123.5
C3' C2' O2' CA' 172.4 268.6
C1' C2' C3' H2' 242.0 241.7
C3' C2' C1' N1 96.6 155.6
C3' C2' C1' H1' 218.0 278.6
H3' C3' C4' H4' 190.7 236.3
C4' C3' H3' O3' 123.7 122.5
C4' C3' H3' C2' 249.5 245.2
O3' C3' H3' C2' 125.9 122.7
H3' C3' O3' HA 302.5 61.1
H3' C3' C2' O2' 167.1 102.2
H3' C3' C2' C1' 282.8 220.4
H3' C3' C2' H2' 40.7 338.7
HA O3' C3' C2' 66.0 183.8
HA O3' C3' H3' 302.5 61.1
O4' C1' C2' O2' 95.2 155.2
O2' C2' C3' H3' 167.1 102.2
C3' C2' O2' C1' 110.7 112.7
C3' C2' O2' H2' 234.5 236.4
C1' C2' O2' H2' 123.9 123.7
O2' C2' C1' N1 213.8 273.7
O2' C2' C1' H1' 335.2 36.7
C2' O2' CA' CB' 233.4 180.0
C2' O2' CA' HA'1 354.3 300.0
C2' O2' CA' HA'2 112.5 60.0
O4' C1' C2' N1 241.4 241.5
O4' C1' C2' H1' 119.9 118.5
C1' C2' C3' H3' 282.8 220.4
C3' C2' C1' O2' 242.8 241.8
C3' C2' C1' H2' 117.9 118.3
O2' C2' C1' H2' 235.2 236.4
C1' C2' O2' CA' 61.8 155.9
N1 C1' C2' H1' 238.6 237.0
C2' C1' N1 C2 81.7 119.5
C2' C1' N1 C6 262.6 299.2
H2' C2' C3' H3' 40.7 338.7
C3' C2' H2' O2' 125.6 123.6
C3' C2' H2' C1' 248.3 247.2
O2' C2' H2' C1' 122.7 123.6
H2' C2' O2' CA' 297.9 32.2
H2' C2' C1' N1 338.6 37.3
H2' C2' C1' H1' 100.1 160.3
CA' O2' C2' C1' 61.8 155.9
CA' O2' C2' H2' 297.9 32.2
CB' CA' O2' HA'1 239.1 240.0
CB' CA' O2' HA'2 120.9 120.0
O2' CA' CB' OC' 66.9 65.0
O2' CA' CB' HB'1 188.1 184.9
O2' CA' CB' HB'2 305.8 305.0
HA'1 CA' O2' HA'2 241.8 240.0
O4' C1' N1 C2' 117.7 114.1
O4' C1' N1 H1' 238.7 237.0
N1 C1' C2' H2' 338.6 37.3
C2' C1' N1 H1' 120.9 123.0
C2 N1 C1' C6 179.1 180.3
C1' N1 C2 O2 0.7 360.0
C1' N1 C2 N3 181.4 180.0
C1' N1 C6 C5 178.3 179.7
C1' N1 C6 H6 358.3 360.0
O4' C1' H1' C2' 242.2 245.9
O4' C1' H1' N1 120.2 123.0
H1' C1' C2' H2' 100.1 160.3
C2' C1' H1' N1 238.0 237.0
H1' C1' N1 C2 320.8 356.5
H1' C1' N1 C6 141.7 176.3
C2 N1 C1' H1' 320.8 356.5
C1' N1 C2 C6 180.9 179.7
C2 N1 C6 C5 359.2 359.4
C2 N1 C6 H6 179.2 179.7
O2 C2 N1 N3 179.3 180.0
N1 C2 N3 C4 359.9 359.9
N1 C2 N3 H3 179.9 180.0
C6 N1 C1' H1' 141.7 176.3
C1' N1 C6 C2 179.0 180.3
C6 N1 C2 O2 179.8 180.3
C6 N1 C2 N3 0.5 0.3
C4 C5 C6 N1 0.6 0.5
N1 C6 C5 H5 180.6 180.2
C5 C6 N1 H6 180.0 179.7
O2 C2 N1 C6 179.8 180.3
N1 C2 O2 N3 180.7 180.0
O2 C2 N3 C4 180.6 180.0
O2 C2 N3 H3 0.6 0.0
N3 C2 N1 C6 0.5 0.3
N1 C2 N3 O2 179.3 180.0
C4 N3 C2 H3 180.0 179.9
C2 N3 C4 O4 180.9 180.1
C2 N3 C4 C5 360.0 0.0
C2 N3 C4 H3 180.0 180.1
O4 C4 N3 C5 180.9 180.0
N3 C4 C5 C6 359.8 359.7
N3 C4 C5 H5 179.8 180.0
C2 N3 H3 C4 180.0 179.9
H3 N3 C4 O4 0.9 0.0
H3 N3 C4 C5 179.9 180.0
O4 C4 N3 H3 0.9 0.0
N3 C4 O4 C5 179.0 180.0
O4 C4 C5 C6 178.8 179.7
O4 C4 C5 H5 358.8 360.0
N1 C6 C5 C4 0.6 0.5
C5 C4 N3 H3 179.9 180.0
N3 C4 C5 O4 181.0 180.0
C6 C5 C4 H5 180.0 179.7
C4 C5 C6 H6 180.6 180.3
N1 C6 C5 H6 180.0 180.3
C4 C5 C6 H5 180.0 180.3
C4 C5 H5 C6 180.0 179.7
H5 C5 C6 H6 0.6 360.0
N1 C6 H6 C5 180.0 179.7
H6 C6 C5 H5 0.6 360.0
O2' CA' CB' HA'1 120.9 120.0
O2' CA' CB' HA'2 239.1 239.9
HA'1 CA' CB' HA'2 118.2 120.0
OC' CB' CA' HB'1 238.9 240.0
OC' CB' CA' HB'2 121.2 120.0
CA' CB' OC' CD' 121.2 180.0
HB'1 CB' CA' HB'2 242.3 240.0
O2' CA' HA'1 CB' 234.3 240.0
O2' CA' HA'1 HA'2 117.2 120.1
CB' CA' HA'1 HA'2 242.9 240.0
HA'1 CA' CB' OC' 306.0 305.0
HA'1 CA' CB' HB'1 67.2 65.0
HA'1 CA' CB' HB'2 184.9 185.0
O2' CA' HA'2 CB' 125.7 120.0
O2' CA' HA'2 HA'1 242.8 240.0
CB' CA' HA'2 HA'1 117.1 120.0
HA'2 CA' CB' OC' 187.8 185.1
HA'2 CA' CB' HB'1 309.0 305.0
HA'2 CA' CB' HB'2 66.7 65.0
OC' CB' CA' HA'1 306.0 305.0
OC' CB' CA' HA'2 187.8 185.1
CA' CB' OC' HB'1 121.1 120.0
CA' CB' OC' HB'2 238.8 240.0
HB'1 CB' OC' HB'2 117.7 120.0
CB' OC' CD' HD'1 180.0 180.0
CB' OC' CD' HD'2 300.0 299.9
CB' OC' CD' HD'3 60.0 60.0
HB'1 CB' CA' HA'1 67.2 65.0
HB'1 CB' CA' HA'2 309.0 305.0
CA' CB' HB'1 OC' 232.9 240.0
CA' CB' HB'1 HB'2 116.4 120.0
OC' CB' HB'1 HB'2 243.6 240.0
HB'1 CB' OC' CD' 0.1 60.1
HB'2 CB' CA' HA'1 184.9 185.0
HB'2 CB' CA' HA'2 66.7 65.0
CA' CB' HB'2 OC' 127.2 120.0
CA' CB' HB'2 HB'1 243.6 240.0
OC' CB' HB'2 HB'1 116.4 120.0
HB'2 CB' OC' CD' 242.4 300.0
CD' OC' CB' HB'1 0.1 60.1
CD' OC' CB' HB'2 242.4 300.0
HD'1 CD' OC' HD'2 240.0 240.0
HD'1 CD' OC' HD'3 120.0 119.9
HD'2 CD' OC' HD'3 240.0 239.9
OC' CD' HD'1 HD'2 120.0 120.0
OC' CD' HD'1 HD'3 240.0 240.0
HD'2 CD' HD'1 HD'3 120.0 120.0
OC' CD' HD'2 HD'1 240.0 240.0
OC' CD' HD'2 HD'3 120.0 120.0
HD'1 CD' HD'2 HD'3 240.0 240.0
OC' CD' HD'3 HD'1 120.0 120.0
OC' CD' HD'3 HD'2 240.0 240.0
HD'1 CD' HD'3 HD'2 120.0 120.0