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 |