PDB Chemical Component TSP

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 TSP

Atom I Atom J Distance (Experimental Model) Distance (Ideal Model)
P OP1 1.458 1.480
P OP2 1.471 1.610
P OP3 1.589 1.611
P O5' 1.597 1.610
OP2 HOP2 0.950 0.967
OP3 HOP3 0.950 0.967
O5' C5' 1.453 1.429
C5' C4' 1.516 1.530
C5' H5' 1.100 1.090
C5' H5'' 1.100 1.089
C4' O4' 1.450 1.445
C4' C3' 1.514 1.550
C4' H4' 1.100 1.090
O4' C1' 1.426 1.437
C3' S3' 1.718 1.815
C3' C2' 1.514 1.548
C3' H3' 1.100 1.090
S3' HS3' 1.300 1.345
C2' C1' 1.502 1.541
C2' H2' 1.100 1.090
C2' H2'' 1.100 1.090
C1' N1 1.485 1.466
C1' H1' 1.101 1.090
N1 C2 1.376 1.345
N1 C6 1.379 1.368
C2 O2 1.224 1.216
C2 N3 1.367 1.346
N3 C4 1.376 1.349
N3 HN3 1.000 0.970
C4 O4 1.215 1.217
C4 C5 1.449 1.415
C5 C5M 1.495 1.507
C5 C6 1.337 1.351
C5M H71 1.100 1.090
C5M H72 1.100 1.090
C5M H73 1.100 1.090
C6 H6 1.080 1.080

Bond Angles for TSP

Atom I Atom J Atom K Angle (Experimental Model) Angle (Ideal Model)
OP1 P OP2 120.0 109.5
OP1 P OP3 109.1 109.5
OP1 P O5' 108.8 109.5
OP2 P OP3 109.5 109.4
OP2 P O5' 106.0 109.5
P OP2 HOP2 109.5 114.0
OP3 P O5' 101.9 109.5
P OP3 HOP3 109.5 114.0
P O5' C5' 121.0 123.0
O5' C5' C4' 110.8 109.5
O5' C5' H5' 109.1 109.4
O5' C5' H5'' 109.1 109.5
C4' C5' H5' 109.1 109.4
C4' C5' H5'' 109.1 109.5
C5' C4' O4' 109.0 110.6
C5' C4' C3' 112.3 110.6
C5' C4' H4' 110.1 110.6
H5' C5' H5'' 109.5 109.5
O4' C4' C3' 104.3 103.5
O4' C4' H4' 111.0 110.6
C4' O4' C1' 112.1 106.9
C3' C4' H4' 110.1 110.8
C4' C3' S3' 120.1 110.9
C4' C3' C2' 106.4 102.1
C4' C3' H3' 106.9 110.9
O4' C1' C2' 107.1 107.3
O4' C1' N1 108.8 109.8
O4' C1' H1' 112.7 109.9
S3' C3' C2' 110.9 110.9
S3' C3' H3' 104.9 110.8
C3' S3' HS3' 102.0 103.0
C2' C3' H3' 106.9 111.0
C3' C2' C1' 105.9 104.2
C3' C2' H2' 110.4 110.5
C3' C2' H2'' 110.3 110.5
C1' C2' H2' 110.4 110.5
C1' C2' H2'' 110.4 110.5
C2' C1' N1 104.3 109.9
C2' C1' H1' 111.6 109.9
H2' C2' H2'' 109.5 110.5
N1 C1' H1' 111.8 110.0
C1' N1 C2 117.9 119.7
C1' N1 C6 120.9 119.6
C2 N1 C6 121.1 120.7
N1 C2 O2 123.1 119.6
N1 C2 N3 114.8 120.9
N1 C6 C5 123.6 119.6
N1 C6 H6 118.2 120.2
O2 C2 N3 122.1 119.5
C2 N3 C4 127.1 120.2
C2 N3 HN3 116.5 119.9
C4 N3 HN3 116.5 119.9
N3 C4 O4 119.6 120.3
N3 C4 C5 115.5 119.4
O4 C4 C5 124.9 120.3
C4 C5 C5M 118.7 120.5
C4 C5 C6 117.8 119.1
C5M C5 C6 123.5 120.4
C5 C5M H71 109.5 109.4
C5 C5M H72 109.5 109.5
C5 C5M H73 109.5 109.5
C5 C6 H6 118.2 120.1
H71 C5M H72 109.5 109.5
H71 C5M H73 109.4 109.4
H72 C5M H73 109.5 109.5

Torsion Angles for TSP

Atom I Atom J Atom K Atom L Angle (Experimental Model) Angle (Ideal Model)
OP2 P OP1 OP3 232.6 240.0
OP2 P OP1 O5' 122.2 120.0
OP1 P OP2 HOP2 0.0 60.0
OP3 P OP1 O5' 249.6 240.0
OP1 P OP3 HOP3 360.0 180.0
OP1 P O5' C5' 188.4 305.0
OP1 P OP2 OP3 127.3 120.0
OP1 P OP2 O5' 236.5 240.0
OP3 P OP2 O5' 109.2 120.0
OP2 P OP3 HOP3 133.1 300.0
OP2 P O5' C5' 58.1 185.0
OP1 P OP3 OP2 226.9 240.0
OP1 P OP3 O5' 115.0 120.0
OP2 P OP3 O5' 248.1 240.0
OP3 P OP2 HOP2 232.7 300.0
OP3 P O5' C5' 303.6 65.0
OP1 P O5' OP2 130.3 120.0
OP1 P O5' OP3 244.8 240.0
OP2 P O5' OP3 114.5 120.0
O5' P OP2 HOP2 123.6 180.0
O5' P OP3 HOP3 245.0 60.0
P O5' C5' C4' 189.5 180.0
P O5' C5' H5' 309.7 300.0
P O5' C5' H5'' 69.3 60.0
HOP2 OP2 P OP3 232.7 300.0
HOP2 OP2 P O5' 123.6 180.0
HOP3 OP3 P O5' 245.0 60.0
C4' C5' O5' H5' 239.8 240.0
C4' C5' O5' H5'' 120.2 120.0
O5' C5' C4' O4' 272.7 66.5
O5' C5' C4' C3' 27.8 180.5
O5' C5' C4' H4' 150.8 303.6
H5' C5' O5' H5'' 240.4 240.0
O5' C5' C4' H5' 120.2 119.9
O5' C5' C4' H5'' 239.8 240.0
H5' C5' C4' H5'' 119.6 120.1
O4' C4' C5' C3' 244.9 246.0
O4' C4' C5' H4' 121.9 122.9
C5' C4' O4' C1' 138.7 158.6
C3' C4' C5' H4' 237.0 236.9
C5' C4' C3' S3' 94.7 86.3
C5' C4' C3' C2' 221.7 204.5
C5' C4' C3' H3' 335.6 322.8
O5' C5' H5' C4' 238.8 240.0
O5' C5' H5' H5'' 119.4 120.0
C4' C5' H5' H5'' 240.6 240.0
H5' C5' C4' O4' 152.5 306.5
H5' C5' C4' C3' 267.6 60.5
H5' C5' C4' H4' 30.6 183.6
O5' C5' H5'' C4' 121.2 120.0
O5' C5' H5'' H5' 240.6 240.0
C4' C5' H5'' H5' 119.4 120.0
H5'' C5' C4' O4' 32.9 186.5
H5'' C5' C4' C3' 148.0 300.5
H5'' C5' C4' H4' 271.0 63.6
O4' C4' C5' H5' 152.5 306.5
O4' C4' C5' H5'' 32.9 186.5
C5' C4' O4' C3' 120.1 118.5
C5' C4' O4' H4' 238.6 237.2
C3' C4' O4' H4' 118.5 118.7
O4' C4' C3' S3' 212.6 204.8
O4' C4' C3' C2' 339.6 322.9
O4' C4' C3' H3' 93.5 81.3
C4' O4' C1' C2' 351.0 333.4
C4' O4' C1' N1 238.7 214.1
C4' O4' C1' H1' 114.1 92.9
C3' C4' C5' H5' 267.6 60.5
C3' C4' C5' H5'' 148.0 300.5
C5' C4' C3' O4' 242.1 241.5
C5' C4' C3' H4' 123.0 123.0
O4' C4' C3' H4' 240.9 241.5
C3' C4' O4' C1' 18.5 40.1
S3' C3' C4' C2' 233.1 241.8
S3' C3' C4' H3' 119.1 123.5
C4' C3' S3' HS3' 180.0 180.1
C2' C3' C4' H3' 246.0 241.7
C4' C3' C2' C1' 15.5 20.9
C4' C3' C2' H2' 135.0 139.6
C4' C3' C2' H2'' 256.1 262.2
H4' C4' C5' H5' 30.6 183.6
H4' C4' C5' H5'' 271.0 63.6
C5' C4' H4' O4' 120.7 122.9
C5' C4' H4' C3' 235.7 237.0
O4' C4' H4' C3' 115.0 114.1
H4' C4' O4' C1' 260.0 281.4
H4' C4' C3' S3' 331.8 323.3
H4' C4' C3' C2' 98.7 81.5
H4' C4' C3' H3' 212.6 199.8
C1' O4' C4' C3' 18.5 40.1
C1' O4' C4' H4' 260.0 281.4
C3' C2' C1' O4' 355.5 2.1
O4' C1' C2' H2' 236.0 243.4
O4' C1' C2' H2'' 114.9 120.8
C2' C1' O4' N1 112.3 119.4
C2' C1' O4' H1' 236.9 240.5
N1 C1' O4' H1' 124.6 121.1
O4' C1' N1 C2 223.0 53.6
O4' C1' N1 C6 46.5 233.2
S3' C3' C4' H4' 331.8 323.3
C4' C3' S3' C2' 124.8 112.7
C4' C3' S3' H3' 239.9 236.4
C2' C3' S3' H3' 115.1 123.7
S3' C3' C2' C1' 147.8 139.1
S3' C3' C2' H2' 267.2 257.8
S3' C3' C2' H2'' 28.3 20.4
C2' C3' C4' H4' 98.7 81.5
C4' C3' C2' S3' 227.7 241.8
C4' C3' C2' H3' 114.0 118.3
O4' C1' C2' C3' 355.5 2.1
S3' C3' C2' H3' 246.2 236.4
C2' C3' S3' HS3' 55.2 67.4
C1' C2' C3' H2' 240.6 241.3
C1' C2' C3' H2'' 119.4 118.7
C3' C2' C1' N1 110.8 121.4
C3' C2' C1' H1' 231.6 242.6
H2' C2' C3' H2'' 238.9 237.4
H3' C3' C4' H4' 212.6 199.8
C4' C3' H3' S3' 128.6 123.6
C4' C3' H3' C2' 246.4 247.2
S3' C3' H3' C2' 117.8 123.6
H3' C3' S3' HS3' 300.1 303.7
H3' C3' C2' C1' 261.6 262.6
H3' C3' C2' H2' 21.0 21.3
H3' C3' C2' H2'' 142.1 143.9
HS3' S3' C3' C2' 55.2 67.4
HS3' S3' C3' H3' 300.1 303.7
O4' C1' C2' N1 244.7 240.6
O4' C1' C2' H1' 123.8 119.5
C1' C2' C3' H3' 261.6 262.6
C3' C2' C1' H2' 119.4 118.7
C3' C2' C1' H2'' 240.6 241.3
H2' C2' C1' H2'' 121.1 122.6
N1 C1' C2' H1' 239.1 238.9
C2' C1' N1 C2 108.9 295.7
C2' C1' N1 C6 292.4 115.4
H2' C2' C3' H3' 21.0 21.3
C3' C2' H2' C1' 243.3 245.2
C3' C2' H2' H2'' 121.6 122.6
C1' C2' H2' H2'' 238.3 237.4
H2' C2' C1' N1 351.3 2.7
H2' C2' C1' H1' 112.2 123.9
H2'' C2' C3' H3' 142.1 143.9
C3' C2' H2'' C1' 116.7 114.8
C3' C2' H2'' H2' 238.4 237.4
C1' C2' H2'' H2' 121.6 122.6
H2'' C2' C1' N1 230.2 240.1
H2'' C2' C1' H1' 351.1 1.3
O4' C1' N1 C2' 114.1 117.8
O4' C1' N1 H1' 234.8 238.9
N1 C1' C2' H2' 351.3 2.7
N1 C1' C2' H2'' 230.2 240.1
C2' C1' N1 H1' 120.7 121.1
C2 N1 C1' C6 176.5 180.3
C1' N1 C2 O2 9.4 360.0
C1' N1 C2 N3 188.5 180.0
C1' N1 C6 C5 172.6 179.7
C1' N1 C6 H6 352.7 0.0
O4' C1' H1' C2' 239.4 242.1
O4' C1' H1' N1 123.0 121.0
H1' C1' C2' H2' 112.2 123.9
H1' C1' C2' H2'' 351.1 1.3
C2' C1' H1' N1 243.6 238.9
H1' C1' N1 C2 348.2 174.7
H1' C1' N1 C6 171.7 354.3
C2 N1 C1' H1' 348.2 174.7
C1' N1 C2 C6 183.5 179.7
C2 N1 C6 C5 356.2 359.4
C2 N1 C6 H6 176.3 179.7
O2 C2 N1 N3 181.0 180.0
N1 C2 N3 C4 356.9 360.0
N1 C2 N3 HN3 176.9 179.9
C6 N1 C1' H1' 171.7 354.3
C1' N1 C6 C2 176.4 180.3
C6 N1 C2 O2 186.0 180.3
C6 N1 C2 N3 5.0 0.3
C4 C5 C6 N1 0.1 0.6
C5M C5 C6 N1 180.1 180.3
C5 C6 N1 H6 180.0 179.7
O2 C2 N1 C6 186.0 180.3
N1 C2 O2 N3 179.0 180.0
O2 C2 N3 C4 175.9 180.0
O2 C2 N3 HN3 355.9 359.9
N3 C2 N1 C6 5.0 0.3
N1 C2 N3 O2 181.0 180.0
C4 N3 C2 HN3 180.0 180.1
C2 N3 C4 O4 180.5 180.0
C2 N3 C4 C5 359.8 0.0
C2 N3 C4 HN3 180.0 179.9
O4 C4 N3 C5 180.7 179.9
N3 C4 C5 C5M 181.8 180.0
N3 C4 C5 C6 1.8 359.7
C2 N3 HN3 C4 180.0 180.1
HN3 N3 C4 O4 0.5 0.0
HN3 N3 C4 C5 179.8 180.1
O4 C4 N3 HN3 0.5 0.0
N3 C4 O4 C5 179.2 180.1
O4 C4 C5 C5M 1.0 0.0
O4 C4 C5 C6 181.0 179.7
N1 C6 C5 C4 0.1 0.6
C5 C4 N3 HN3 179.8 180.1
N3 C4 C5 O4 180.8 179.9
C5M C5 C4 C6 180.0 180.3
C4 C5 C5M H71 180.0 360.0
C4 C5 C5M H72 300.0 120.0
C4 C5 C5M H73 60.0 240.0
C4 C5 C6 H6 180.1 180.3
N1 C6 C5 C5M 180.1 180.3
C4 C5 C5M C6 180.0 179.7
C5M C5 C6 H6 0.1 0.0
H71 C5M C5 H72 240.0 240.0
H71 C5M C5 H73 120.0 119.9
H72 C5M C5 H73 240.0 240.0
N1 C6 C5 H6 180.0 180.3
C4 C5 C6 C5M 180.0 180.3
C6 C5 C5M H71 0.1 180.3
C6 C5 C5M H72 120.1 300.3
C6 C5 C5M H73 240.1 60.3
H71 C5M C5 C6 0.1 180.3
C5 C5M H71 H72 120.0 120.0
C5 C5M H71 H73 240.0 240.0
H72 C5M H71 H73 120.0 120.0
H72 C5M C5 C6 120.1 300.3
C5 C5M H72 H71 240.0 240.0
C5 C5M H72 H73 120.0 120.1
H71 C5M H72 H73 240.0 240.0
H73 C5M C5 C6 240.1 60.3
C5 C5M H73 H71 120.0 119.9
C5 C5M H73 H72 240.0 239.9
H71 C5M H73 H72 120.0 120.0
N1 C6 H6 C5 180.0 179.7