PDB Chemical Component 5PC

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 5PC

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
OP3 P   1.618
OP3 HOP3   0.981
P OP1 1.476 1.501
P OP2 1.482 1.616
P O5' 1.628 1.619
OP2 HOP2 0.949 0.981
C5' O5' 1.432 1.418
C5' C4' 1.538 1.523
C5' H5' 1.090 1.092
C5' H5'' 1.090 1.093
C4' O4' 1.415 1.441
C4' C3' 1.531 1.522
C4' H4' 1.091 1.094
O4' C1' 1.403 1.434
C3' O3' 1.411 1.426
C3' C2' 1.530 1.511
C3' H3' 1.090 1.094
O3' HO3' 0.949 0.973
C2' C1' 1.514 1.520
C2' H2' 1.090 1.097
C2' H2'' 1.089 1.095
C1' N1 1.437 1.434
C1' H1' 1.091 1.095
N1 C2 1.310 1.414
N1 C6 1.296 1.386
C2 O2 1.218 1.232
C2 N3 1.298 1.383
N3 C4 1.271 1.309
C4 N4 1.270 1.378
C4 C5 1.357 1.496
N4 H41 1.011 0.990
N4 H42 1.010 0.990
C5 C6 1.327 1.336
C5 C7 1.461 1.420
C6 H6 1.080 1.086
C7 C8 1.203 1.200
C8 C9 1.455 1.462
C9 H91 1.089 1.094
C9 H92 1.090 1.094
C9 H93 1.090 1.095

Bond Angles for 5PC

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
P OP3 HOP3   118.9
OP3 P OP1   115.3
OP3 P OP2   103.3
OP3 P O5'   103.7
OP1 P OP2 119.5 115.0
OP1 P O5' 109.2 115.0
OP2 P O5' 108.4 102.9
P OP2 HOP2 149.7 118.9
P O5' C5' 122.6 118.5
O5' C5' C4' 112.5 108.9
O5' C5' H5' 108.5 109.0
O5' C5' H5'' 108.9 108.9
C4' C5' H5' 109.4 110.3
C4' C5' H5'' 108.7 110.3
C5' C4' O4' 114.4 107.9
C5' C4' C3' 116.0 112.9
C5' C4' H4' 105.9 109.5
H5' C5' H5'' 108.8 109.3
O4' C4' C3' 107.4 106.2
O4' C4' H4' 106.0 107.9
C4' O4' C1' 105.1 109.3
C3' C4' H4' 106.4 112.2
C4' C3' O3' 110.4 109.9
C4' C3' C2' 102.6 103.1
C4' C3' H3' 107.8 113.5
O4' C1' C2' 106.7 107.4
O4' C1' N1 106.6 109.3
O4' C1' H1' 109.9 108.0
O3' C3' C2' 114.9 109.7
O3' C3' H3' 110.8 107.4
C3' O3' HO3' 110.4 107.3
C2' C3' H3' 109.8 113.2
C3' C2' C1' 104.2 102.5
C3' C2' H2' 112.3 109.7
C3' C2' H2'' 108.6 114.1
C1' C2' H2' 108.9 110.6
C1' C2' H2'' 112.3 111.7
C2' C1' N1 110.6 112.8
C2' C1' H1' 110.4 111.5
H2' C2' H2'' 110.5 108.3
N1 C1' H1' 112.4 107.8
C1' N1 C2 121.3 121.9
C1' N1 C6 120.6 118.5
C2 N1 C6 118.0 119.6
N1 C2 O2 120.8 121.1
N1 C2 N3 121.0 118.7
N1 C6 C5 124.9 123.0
N1 C6 H6 118.6 115.3
O2 C2 N3 118.1 120.2
C2 N3 C4 118.2 121.4
N3 C4 N4 119.9 118.8
N3 C4 C5 125.5 121.4
N4 C4 C5 114.3 119.8
C4 N4 H41 115.5 117.9
C4 N4 H42 115.2 117.9
C4 C5 C6 111.5 115.9
C4 C5 C7 124.0 122.5
H41 N4 H42 129.3 124.2
C6 C5 C7 124.3 121.6
C5 C6 H6 116.6 121.7
C5 C7 C8 172.4 180.0
C7 C8 C9 176.9 179.9
C8 C9 H91 108.2 110.9
C8 C9 H92 109.1 110.9
C8 C9 H93 109.8 110.9
H91 C9 H92 107.8 108.0
H91 C9 H93 110.2 108.1
H92 C9 H93 111.6 108.0

Torsion Angles for 5PC

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
OP1 P OP3 OP2   126.3
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   48.8
HOP3 OP3 P OP2   282.5
HOP3 OP3 P O5'   175.4
OP1 P OP3 HOP3   48.8
OP3 P OP1 OP2   239.9
OP3 P OP1 O5'   120.6
OP2 P OP1 O5' 125.4 240.7
OP1 P OP2 HOP2 352.9 312.0
OP1 P O5' C5' 174.0 179.9
OP2 P OP3 HOP3   282.5
OP3 P OP2 OP1   126.5
OP3 P OP2 O5'   252.3
OP1 P OP2 O5' 234.2 125.8
OP2 P O5' C5' 42.4 305.8
O5' P OP3 HOP3   175.4
OP3 P O5' OP1   233.2
OP3 P O5' OP2   107.4
OP1 P O5' OP2 131.7 234.2
O5' P OP2 HOP2 118.7 186.2
P O5' C5' C4' 170.4 180.0
P O5' C5' H5' 291.5 300.4
P O5' C5' H5'' 49.8 59.6
HOP2 OP2 P O5' 118.7 186.2
C4' C5' O5' H5' 238.8 239.6
C4' C5' O5' H5'' 120.6 120.4
O5' C5' C4' O4' 294.9 62.4
O5' C5' C4' C3' 60.8 179.5
O5' C5' C4' H4' 178.6 305.3
H5' C5' O5' H5'' 241.7 240.8
O5' C5' C4' H5' 120.7 119.6
O5' C5' C4' H5'' 239.3 240.5
H5' C5' C4' H5'' 118.7 120.9
O4' C4' C5' C3' 234.1 242.9
O4' C4' C5' H4' 116.3 117.1
C5' C4' O4' C1' 166.2 108.6
C3' C4' C5' H4' 242.2 234.2
C5' C4' C3' O3' 88.3 154.2
C5' C4' C3' C2' 211.3 271.2
C5' C4' C3' H3' 327.2 34.0
O5' C5' H5' C4' 237.0 240.5
O5' C5' H5' H5'' 118.4 119.0
C4' C5' H5' H5'' 241.4 238.5
H5' C5' C4' O4' 174.3 302.9
H5' C5' C4' C3' 300.1 60.0
H5' C5' C4' H4' 58.0 185.7
O5' C5' H5'' C4' 122.9 119.4
O5' C5' H5'' H5' 241.9 241.0
C4' C5' H5'' H5' 119.0 121.5
H5'' C5' C4' O4' 55.6 181.9
H5'' C5' C4' C3' 181.5 299.0
H5'' C5' C4' H4' 299.3 64.8
O4' C4' C5' H5' 174.3 302.9
O4' C4' C5' H5'' 55.6 181.9
C5' C4' O4' C3' 130.3 121.4
C5' C4' O4' H4' 243.7 241.8
C3' C4' O4' H4' 113.4 120.5
O4' C4' C3' O3' 217.7 272.3
O4' C4' C3' C2' 340.6 29.2
O4' C4' C3' H3' 96.5 152.1
C4' O4' C1' C2' 322.2 351.0
C4' O4' C1' N1 204.0 228.3
C4' O4' C1' H1' 81.9 111.3
C3' C4' C5' H5' 300.1 60.0
C3' C4' C5' H5'' 181.5 299.0
C5' C4' C3' O4' 230.7 241.9
C5' C4' C3' H4' 117.5 124.3
O4' C4' C3' H4' 246.8 242.4
C3' C4' O4' C1' 35.9 347.3
O3' C3' C4' C2' 237.1 243.1
O3' C3' C4' H3' 121.2 120.2
C4' C3' O3' HO3' 180.0 232.0
C2' C3' C4' H3' 244.1 237.2
C4' C3' C2' C1' 357.0 326.6
C4' C3' C2' H2' 239.3 84.1
C4' C3' C2' H2'' 116.9 205.7
H4' C4' C5' H5' 58.0 185.7
H4' C4' C5' H5'' 299.3 64.8
C5' C4' H4' O4' 121.9 117.1
C5' C4' H4' C3' 235.9 233.8
O4' C4' H4' C3' 114.1 116.7
H4' C4' O4' C1' 282.5 226.8
H4' C4' C3' O3' 330.8 29.9
H4' C4' C3' C2' 93.8 146.9
H4' C4' C3' H3' 209.7 269.7
C1' O4' C4' C3' 35.9 347.3
C1' O4' C4' H4' 282.5 226.8
C3' C2' C1' O4' 24.7 26.9
O4' C1' C2' H2' 144.7 270.0
O4' C1' C2' H2'' 267.4 149.4
C2' C1' O4' N1 118.1 122.7
C2' C1' O4' H1' 240.3 239.7
N1 C1' O4' H1' 122.1 117.0
O4' C1' N1 C2 210.3 212.8
O4' C1' N1 C6 35.0 32.9
O3' C3' C4' H4' 330.8 29.9
C4' C3' O3' C2' 115.4 112.7
C4' C3' O3' H3' 240.6 236.1
C2' C3' O3' H3' 125.2 123.4
O3' C3' C2' C1' 116.8 83.6
O3' C3' C2' H2' 359.2 201.1
O3' C3' C2' H2'' 236.7 322.8
C2' C3' C4' H4' 93.8 146.9
C4' C3' C2' O3' 240.2 242.9
C4' C3' C2' H3' 114.5 123.0
O4' C1' C2' C3' 24.7 26.9
O3' C3' C2' H3' 234.3 240.1
C2' C3' O3' HO3' 64.6 119.3
C1' C2' C3' H2' 117.7 242.5
C1' C2' C3' H2'' 240.1 120.8
C3' C2' C1' N1 140.2 147.4
C3' C2' C1' H1' 265.3 268.8
H2' C2' C3' H2'' 122.4 238.3
H3' C3' C4' H4' 209.7 269.7
C4' C3' H3' O3' 120.9 121.7
C4' C3' H3' C2' 248.9 242.9
O3' C3' H3' C2' 128.0 121.3
H3' C3' O3' HO3' 299.4 355.9
H3' C3' C2' C1' 242.6 203.6
H3' C3' C2' H2' 124.9 321.1
H3' C3' C2' H2'' 2.4 82.7
HO3' O3' C3' C2' 64.6 119.3
HO3' O3' C3' H3' 299.4 355.9
O4' C1' C2' N1 244.5 239.5
O4' C1' C2' H1' 119.4 118.1
C1' C2' C3' H3' 242.6 203.6
C3' C2' C1' H2' 240.0 116.9
C3' C2' C1' H2'' 117.3 237.5
H2' C2' C1' H2'' 237.3 120.7
N1 C1' C2' H1' 234.9 238.6
C2' C1' N1 C2 94.8 93.5
C2' C1' N1 C6 279.4 273.5
H2' C2' C3' H3' 124.9 321.1
C3' C2' H2' C1' 114.9 247.7
C3' C2' H2' H2'' 238.6 125.1
C1' C2' H2' H2'' 123.8 237.3
H2' C2' C1' N1 260.2 30.6
H2' C2' C1' H1' 25.3 151.9
H2'' C2' C3' H3' 2.4 82.7
C3' C2' H2'' C1' 245.3 115.6
C3' C2' H2'' H2' 123.6 237.5
C1' C2' H2'' H2' 238.3 122.0
H2'' C2' C1' N1 22.9 269.9
H2'' C2' C1' H1' 148.0 31.3
O4' C1' N1 C2' 115.6 119.4
O4' C1' N1 H1' 239.5 242.9
N1 C1' C2' H2' 260.2 30.6
N1 C1' C2' H2'' 22.9 269.9
C2' C1' N1 H1' 123.9 123.5
C2 N1 C1' C6 175.4 180.0
C1' N1 C2 O2 356.9 359.9
C1' N1 C2 N3 179.7 180.0
C1' N1 C6 C5 185.6 180.0
C1' N1 C6 H6 6.3 360.0
O4' C1' H1' C2' 242.6 242.3
O4' C1' H1' N1 118.6 118.0
H1' C1' C2' H2' 25.3 151.9
H1' C1' C2' H2'' 148.0 31.3
C2' C1' H1' N1 236.0 235.7
H1' C1' N1 C2 330.9 330.0
H1' C1' N1 C6 155.5 150.0
C2 N1 C1' H1' 330.9 330.0
C1' N1 C2 C6 184.5 180.0
C2 N1 C6 C5 10.1 0.0
C2 N1 C6 H6 190.8 180.0
O2 C2 N1 N3 177.3 179.9
N1 C2 N3 C4 356.4 360.0
C6 N1 C1' H1' 155.5 150.0
C1' N1 C6 C2 175.5 180.0
C6 N1 C2 O2 172.4 179.9
C6 N1 C2 N3 355.2 0.0
C4 C5 C6 N1 354.0 360.0
N1 C6 C5 C7 180.1 180.0
C5 C6 N1 H6 179.3 180.0
O2 C2 N1 C6 172.4 179.9
N1 C2 O2 N3 182.6 180.1
O2 C2 N3 C4 179.0 180.1
N3 C2 N1 C6 355.2 0.0
N1 C2 N3 O2 177.4 179.9
C2 N3 C4 N4 181.1 180.1
C2 N3 C4 C5 8.0 0.0
N4 C4 N3 C5 173.1 180.1
N3 C4 N4 H41 2.0 304.3
N3 C4 N4 H42 183.2 124.3
N3 C4 C5 C6 356.7 360.0
N3 C4 C5 C7 170.6 180.0
N3 C4 N4 C5 186.1 179.9
N4 C4 C5 C6 183.2 179.9
N4 C4 C5 C7 357.1 360.0
H41 N4 C4 H42 178.8 179.9
N1 C6 C5 C4 354.0 360.0
N3 C4 C5 N4 173.5 180.1
C5 C4 N4 H41 175.9 124.3
C5 C4 N4 H42 357.1 304.4
C6 C5 C4 C7 186.1 180.0
C4 C5 C6 H6 173.3 180.0
C4 C5 C7 C8 269.3 126.7
H41 N4 C4 C5 175.9 124.3
C4 N4 H41 H42 181.4 180.1
H42 N4 C4 C5 357.1 304.4
C4 N4 H42 H41 178.6 179.9
N1 C6 C5 H6 180.7 180.0
C4 C5 C6 C7 173.9 180.0
C6 C5 C7 C8 82.5 306.7
C4 C5 C7 C6 186.8 180.0
C7 C5 C6 H6 359.4 360.0
C5 C7 C8 C9 335.0 190.7
N1 C6 H6 C5 179.3 180.0
H6 C6 C5 C7 359.4 360.0
C7 C8 C9 H91 228.3 218.5
C7 C8 C9 H92 345.4 338.4
C7 C8 C9 H93 108.0 98.4
H91 C9 C8 H92 242.9 240.0
H91 C9 C8 H93 120.3 120.0
H92 C9 C8 H93 237.4 240.0
C8 C9 H91 H92 117.9 121.7
C8 C9 H91 H93 239.9 238.3
H92 C9 H91 H93 122.0 116.7
C8 C9 H92 H91 242.7 238.4
C8 C9 H92 H93 121.5 121.7
H91 C9 H92 H93 238.9 243.3
C8 C9 H93 H91 119.1 121.7
C8 C9 H93 H92 238.9 238.3
H91 C9 H93 H92 119.7 116.6