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 |