PDB Chemical Component TPC

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 TPC

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
S5' C5' 1.831 1.813
S5' P   2.094
N1 C6 1.371 1.385
N1 C2 1.400 1.416
N1 C1' 1.475 1.434
C6 C5 1.336 1.331
C6 H6 1.081 1.085
C2 O2 1.236 1.232
C2 N3 1.353 1.384
N3 C4 1.336 1.307
C4 N4 1.336 1.376
C4 C5 1.425 1.486
N4 HN41 1.000 0.992
N4 HN42 1.000 0.991
C5 H5 1.081 1.081
C2' C1' 1.526 1.520
C2' C3' 1.524 1.511
C2' H2'1 1.100 1.097
C2' H2'2 1.100 1.095
C5' C4' 1.520 1.523
C5' H5'1 1.100 1.093
C5' H5'2 1.100 1.094
C4' O4' 1.445 1.441
C4' C3' 1.535 1.522
C4' H4' 1.100 1.094
O4' C1' 1.425 1.434
C1' H1' 1.100 1.095
C3' O3' 1.453 1.426
C3' H1 1.100 1.094
O3' H3' 0.950 0.973
P OP1   1.505
P OP2   1.622
P OP3   1.623
OP2 HO2P   0.981
OP3 HO3P   0.981

Bond Angles for TPC

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
C5' S5' P   105.1
S5' C5' C4' 112.1 110.5
S5' C5' H5'1 108.6 108.9
S5' C5' H5'2 108.0 108.8
S5' P OP1   111.4
S5' P OP2   109.3
S5' P OP3   108.8
C6 N1 C2 120.0 119.4
C6 N1 C1' 120.5 118.6
N1 C6 C5 121.2 122.7
N1 C6 H6 119.4 116.2
C2 N1 C1' 119.5 122.0
N1 C2 O2 119.2 121.0
N1 C2 N3 119.2 118.8
N1 C1' C2' 114.4 112.8
N1 C1' O4' 106.8 109.3
N1 C1' H1' 107.2 107.8
C5 C6 H6 119.4 121.1
C6 C5 C4 117.5 116.3
C6 C5 H5 121.3 123.1
O2 C2 N3 121.6 120.2
C2 N3 C4 119.9 121.1
N3 C4 N4 118.4 120.2
N3 C4 C5 121.9 121.7
N4 C4 C5 119.7 118.2
C4 N4 HN41 110.2 118.0
C4 N4 HN42 124.9 118.0
C4 C5 H5 121.2 120.6
HN41 N4 HN42 124.9 123.9
C1' C2' C3' 103.8 102.5
C1' C2' H2'1 111.4 110.6
C1' C2' H2'2 112.6 111.7
C2' C1' O4' 106.7 107.4
C2' C1' H1' 107.2 111.5
C3' C2' H2'1 111.4 109.7
C3' C2' H2'2 112.6 114.1
C2' C3' C4' 102.7 103.1
C2' C3' O3' 110.4 109.7
C2' C3' H1 112.6 113.2
H2'1 C2' H2'2 105.2 108.3
C4' C5' H5'1 108.6 110.2
C4' C5' H5'2 108.0 110.1
C5' C4' O4' 107.9 107.9
C5' C4' C3' 121.4 112.9
C5' C4' H4' 100.8 109.5
H5'1 C5' H5'2 111.6 108.1
O4' C4' C3' 104.9 106.2
O4' C4' H4' 118.6 107.9
C4' O4' C1' 111.2 109.3
C3' C4' H4' 104.1 112.2
C4' C3' O3' 107.6 109.9
C4' C3' H1 115.2 113.5
O4' C1' H1' 114.8 108.0
O3' C3' H1 108.1 107.4
C3' O3' H3' 109.5 107.3
OP1 P OP2   112.7
OP1 P OP3   112.7
OP2 P OP3   101.5
P OP2 HO2P   118.7
P OP3 HO3P   118.7

Torsion Angles for TPC

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
C5' S5' P OP1   300.0
C5' S5' P OP2   174.8
C5' S5' P OP3   64.8
C4' C5' S5' H5'1 240.0 238.8
C4' C5' S5' H5'2 118.9 121.1
S5' C5' C4' O4' 203.8 63.3
S5' C5' C4' C3' 324.6 180.4
S5' C5' C4' H4' 78.7 306.1
H5'1 C5' S5' H5'2 238.8 242.3
P S5' C5' C4'   180.0
P S5' C5' H5'1   301.2
P S5' C5' H5'2   58.9
OP1 P S5' OP2   125.2
OP1 P S5' OP3   235.2
OP2 P S5' OP3   110.0
S5' P OP2 HO2P   172.5
S5' P OP3 HO3P   187.9
C2 N1 C6 C1' 179.0 180.0
C6 N1 C2 O2 172.5 180.0
C6 N1 C2 N3 353.2 360.0
C6 N1 C1' C2' 261.6 273.5
C6 N1 C1' O4' 19.4 32.9
C6 N1 C1' H1' 142.9 150.0
C5 C6 N1 H6 180.0 180.0
N1 C6 C5 C4 0.5 0.0
N1 C6 C5 H5 180.5 179.9
C6 N1 C2 C1' 181.0 180.0
C2 N1 C6 C5 4.2 0.0
C2 N1 C6 H6 184.2 180.0
C2 N1 C1' C2' 82.6 93.5
C2 N1 C1' O4' 200.4 212.9
C2 N1 C1' H1' 323.8 330.0
O2 C2 N1 N3 179.3 180.0
N1 C2 N3 C4 4.5 0.0
C6 N1 C1' C2 179.0 180.0
C1' N1 C6 C5 185.2 180.0
C1' N1 C6 H6 5.2 360.0
C1' N1 C2 O2 351.5 0.0
C1' N1 C2 N3 172.3 180.0
N1 C1' C2' C3' 139.3 147.4
N1 C1' C2' H2'1 259.3 30.6
N1 C1' C2' H2'2 17.3 269.9
C2' C1' N1 O4' 242.2 240.6
C2' C1' N1 H1' 118.7 123.5
C4' O4' C1' N1 235.2 228.3
O4' C1' N1 H1' 236.5 242.9
C5 C6 N1 C2 4.2 0.0
C5 C6 N1 C1' 185.2 180.0
N1 C6 C5 H6 180.0 180.0
N3 C4 C5 C6 357.2 360.0
N4 C4 C5 C6 177.0 180.0
C4 C5 C6 H5 180.0 180.1
H6 C6 N1 C2 184.2 180.0
H6 C6 N1 C1' 5.2 360.0
N1 C6 H6 C5 180.0 180.0
H6 C6 C5 C4 180.5 180.0
H6 C6 C5 H5 0.5 360.0
O2 C2 N1 C1' 351.5 0.0
N1 C2 O2 N3 180.8 180.0
O2 C2 N3 C4 185.3 180.0
N3 C2 N1 C1' 172.3 180.0
N1 C2 N3 O2 179.2 180.0
C2 N3 C4 N4 180.5 180.0
C2 N3 C4 C5 0.2 360.0
C6 C5 C4 N3 357.2 360.0
N4 C4 N3 C5 180.2 180.0
N3 C4 N4 HN41 180.0 162.3
N3 C4 N4 HN42 360.0 342.4
N3 C4 C5 H5 177.2 180.1
C6 C5 C4 N4 177.0 180.0
N3 C4 N4 C5 179.8 180.0
N4 C4 C5 H5 357.0 0.1
HN41 N4 C4 HN42 180.0 179.9
C4 C5 C6 H6 180.5 180.0
C6 C5 C4 H5 180.0 179.9
N3 C4 C5 N4 180.2 180.0
C5 C4 N4 HN41 0.2 342.3
C5 C4 N4 HN42 180.2 162.4
HN41 N4 C4 C5 0.2 342.3
C4 N4 HN41 HN42 180.0 180.1
HN42 N4 C4 C5 180.2 162.4
C4 N4 HN42 HN41 180.0 179.9
H5 C5 C6 H6 0.5 360.0
C6 C5 H5 C4 180.0 180.1
N1 C1' C2' O4' 117.8 120.5
N1 C1' C2' H1' 241.3 238.6
C3' C2' C1' H2'1 240.0 116.9
C3' C2' C1' H2'2 122.1 237.5
C1' C2' C3' C4' 328.6 326.6
C1' C2' C3' O3' 83.1 83.6
C1' C2' C3' H1 204.1 203.6
H2'1 C2' C1' H2'2 242.1 120.7
C4' O4' C1' C2' 357.9 351.0
O4' C1' C2' H1' 123.5 118.1
C1' C2' C3' H2'1 120.0 242.5
C1' C2' C3' H2'2 237.9 120.8
C3' C2' C1' O4' 21.5 26.9
C3' C2' C1' H1' 258.0 268.8
H2'1 C2' C3' H2'2 117.9 238.3
C5' C4' C3' C2' 268.2 271.2
O4' C4' C3' C2' 30.6 29.2
C2' C3' C4' H4' 155.9 146.9
C4' C3' C2' O3' 245.5 242.9
C4' C3' C2' H1 124.5 123.0
O3' C3' C2' H1 239.0 240.1
C2' C3' O3' H3' 128.5 119.3
C1' C2' H2'1 C3' 244.6 112.3
C1' C2' H2'1 H2'2 122.3 237.3
H2'1 C2' C1' O4' 141.5 270.0
H2'1 C2' C1' H1' 18.0 151.9
C3' C2' H2'1 H2'2 237.8 125.1
H2'1 C2' C3' C4' 208.6 84.1
H2'1 C2' C3' O3' 323.1 201.1
H2'1 C2' C3' H1 84.1 321.1
C1' C2' H2'2 C3' 117.0 244.4
C1' C2' H2'2 H2'1 238.5 122.0
H2'2 C2' C1' O4' 259.4 149.4
H2'2 C2' C1' H1' 136.0 31.3
C3' C2' H2'2 H2'1 121.5 237.5
H2'2 C2' C3' C4' 90.7 205.7
H2'2 C2' C3' O3' 205.2 322.8
H2'2 C2' C3' H1 326.2 82.7
C4' C5' S5' P   180.0
S5' C5' C4' H5'1 120.0 120.4
S5' C5' C4' H5'2 241.2 239.7
C2' C3' C4' C5' 268.2 271.2
H5'1 C5' C4' H5'2 121.2 119.3
O4' C4' C5' C3' 239.1 242.9
O4' C4' C5' H4' 125.0 117.1
C5' C4' O4' C1' 112.6 108.6
C3' C4' C5' H4' 245.9 234.2
C5' C4' C3' O3' 151.7 154.2
C5' C4' C3' H1 31.0 34.0
H5'1 C5' S5' P   301.2
S5' C5' H5'1 C4' 237.8 238.6
S5' C5' H5'1 H5'2 118.9 118.1
C4' C5' H5'1 H5'2 241.1 239.5
H5'1 C5' C4' O4' 83.8 302.8
H5'1 C5' C4' C3' 204.6 60.0
H5'1 C5' C4' H4' 318.7 185.7
H5'2 C5' S5' P   58.9
S5' C5' H5'2 C4' 121.5 121.3
S5' C5' H5'2 H5'1 240.7 241.9
C4' C5' H5'2 H5'1 119.3 120.5
H5'2 C5' C4' O4' 322.6 183.6
H5'2 C5' C4' C3' 83.5 300.7
H5'2 C5' C4' H4' 197.6 66.5
N1 C1' O4' C4' 235.2 228.3
C2' C1' O4' C4' 357.9 351.0
C2' C3' C4' O4' 30.6 29.2
O4' C4' C5' H5'1 83.8 302.8
O4' C4' C5' H5'2 322.6 183.6
C5' C4' O4' C3' 130.7 121.4
C5' C4' O4' H4' 246.4 241.8
C3' C4' O4' H4' 115.6 120.5
O4' C4' C3' O3' 274.0 272.3
O4' C4' C3' H1 153.4 152.1
C4' O4' C1' H1' 116.6 111.3
C4' C3' C2' H2'1 208.6 84.1
C4' C3' C2' H2'2 90.7 205.7
C2' C3' C4' O3' 116.6 116.9
C2' C3' C4' H1 237.2 237.2
C3' C4' C5' H5'1 204.6 60.0
C3' C4' C5' H5'2 83.5 300.7
C5' C4' C3' O4' 237.6 241.9
C5' C4' C3' H4' 112.4 124.3
O4' C4' C3' H4' 234.7 242.4
C3' C4' O4' C1' 341.8 347.3
O3' C3' C4' H1 120.6 120.2
C4' C3' O3' H3' 239.9 232.0
H4' C4' C5' H5'1 318.7 185.7
H4' C4' C5' H5'2 197.6 66.5
C5' C4' H4' O4' 117.5 117.1
C5' C4' H4' C3' 233.5 233.8
O4' C4' H4' C3' 116.0 116.7
H4' C4' O4' C1' 226.2 226.8
H4' C4' C3' O3' 39.3 29.9
H4' C4' C3' H1 278.7 269.7
N1 C1' O4' C2' 237.3 237.3
N1 C1' O4' H1' 118.6 117.0
O4' C1' C2' C3' 21.5 26.9
O4' C1' C2' H2'1 141.5 270.0
O4' C1' C2' H2'2 259.4 149.4
C2' C1' O4' H1' 241.4 239.7
C1' O4' C4' C3' 341.8 347.3
C1' O4' C4' H4' 226.2 226.8
N1 C1' H1' C2' 123.3 124.3
N1 C1' H1' O4' 241.6 242.0
H1' C1' C2' C3' 258.0 268.8
H1' C1' C2' H2'1 18.0 151.9
H1' C1' C2' H2'2 136.0 31.3
C2' C1' H1' O4' 118.4 117.7
O3' C3' C2' H2'1 323.1 201.1
O3' C3' C2' H2'2 205.2 322.8
C2' C3' O3' C4' 248.6 247.3
C2' C3' O3' H1 123.6 123.4
O3' C3' C4' H4' 39.3 29.9
C4' C3' O3' H1 235.0 236.1
H1 C3' C2' H2'1 84.1 321.1
H1 C3' C2' H2'2 326.2 82.7
C2' C3' H1 C4' 117.4 117.1
C2' C3' H1 O3' 237.7 238.7
H1 C3' C4' H4' 278.7 269.7
C4' C3' H1 O3' 120.4 121.7
H1 C3' O3' H3' 4.9 355.9
H3' O3' C3' H1 4.9 355.9
S5' P OP1 OP2   236.8
S5' P OP1 OP3   122.6
OP2 P OP1 OP3   245.9
OP1 P OP2 HO2P   48.1
OP1 P OP3 HO3P   311.9
S5' P OP2 OP1   124.4
S5' P OP2 OP3   245.2
OP1 P OP2 OP3   120.8
OP2 P OP3 HO3P   72.7
S5' P OP3 OP1   235.9
S5' P OP3 OP2   115.1
OP1 P OP3 OP2   239.2
OP3 P OP2 HO2P   287.3
HO2P OP2 P OP3   287.3