PDB Chemical Component EDC
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 EDC
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| P |
OP3 |
1.590 |
1.610 |
| OP3 |
HOP3 |
0.950 |
0.966 |
| OP1 |
P |
1.515 |
1.479 |
| O5' |
P |
1.624 |
1.610 |
| P |
OP2 |
1.508 |
1.610 |
| C2 |
N1 |
1.414 |
1.344 |
| N1 |
C1' |
1.477 |
1.466 |
| N1 |
C6 |
1.348 |
1.374 |
| O2 |
C2 |
1.254 |
1.215 |
| N3 |
C2 |
1.348 |
1.343 |
| C8 |
N3 |
1.341 |
1.374 |
| N3 |
C4 |
1.347 |
1.374 |
| N4 |
C4 |
1.342 |
1.316 |
| C4 |
C5 |
1.395 |
1.465 |
| C7 |
N4 |
1.348 |
1.341 |
| C5 |
C6 |
1.393 |
1.347 |
| C5 |
H5 |
1.080 |
1.080 |
| C6 |
H6 |
1.080 |
1.080 |
| C8 |
C7 |
1.380 |
1.347 |
| C7 |
H7 |
1.080 |
1.080 |
| C8 |
H8 |
1.080 |
1.080 |
| C1' |
C2' |
1.527 |
1.541 |
| C1' |
O4' |
1.437 |
1.437 |
| C1' |
H1' |
1.100 |
1.090 |
| C2' |
C3' |
1.517 |
1.549 |
| C2' |
H2' |
1.100 |
1.090 |
| C2' |
H2'' |
1.100 |
1.090 |
| O3' |
C3' |
1.433 |
1.429 |
| C3' |
C4' |
1.522 |
1.550 |
| C3' |
H3' |
1.099 |
1.089 |
| O3' |
HO3' |
0.950 |
0.968 |
| O4' |
C4' |
1.428 |
1.444 |
| C4' |
C5' |
1.537 |
1.530 |
| C4' |
H4' |
1.100 |
1.090 |
| O5' |
C5' |
1.429 |
1.429 |
| C5' |
H5' |
1.100 |
1.090 |
| C5' |
H5'' |
1.100 |
1.090 |
| OP2 |
HOP2 |
0.950 |
0.967 |
Bond Angles for EDC
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| P |
OP3 |
HOP3 |
109.5 |
114.0 |
| OP1 |
P |
OP2 |
121.1 |
109.5 |
| O5' |
P |
OP2 |
107.9 |
109.5 |
| P |
OP2 |
HOP2 |
109.5 |
114.0 |
| C2 |
N1 |
C1' |
120.1 |
119.2 |
| C2 |
N1 |
C6 |
118.8 |
121.6 |
| C6 |
N1 |
C1' |
121.1 |
119.2 |
| N1 |
C1' |
C2' |
114.5 |
109.9 |
| N1 |
C1' |
O4' |
110.5 |
109.8 |
| N1 |
C1' |
H1' |
108.2 |
109.9 |
| N1 |
C6 |
C5 |
120.7 |
120.0 |
| N1 |
C6 |
H6 |
119.7 |
120.0 |
| N3 |
C4 |
C5 |
120.1 |
118.7 |
| N4 |
C4 |
C5 |
131.2 |
133.1 |
| C4 |
C5 |
C6 |
119.1 |
118.3 |
| C4 |
C5 |
H5 |
120.5 |
120.8 |
| C6 |
C5 |
H5 |
120.5 |
120.8 |
| C5 |
C6 |
H6 |
119.7 |
120.0 |
| C8 |
C7 |
H7 |
126.6 |
125.7 |
| C2' |
C1' |
O4' |
107.3 |
107.3 |
| C2' |
C1' |
H1' |
107.5 |
109.9 |
| C1' |
C2' |
C3' |
103.9 |
104.1 |
| C1' |
C2' |
H2' |
110.8 |
110.5 |
| C1' |
C2' |
H2'' |
110.8 |
110.5 |
| O4' |
C1' |
H1' |
108.6 |
110.0 |
| C1' |
O4' |
C4' |
111.1 |
107.0 |
| C3' |
C2' |
H2' |
110.8 |
110.5 |
| C3' |
C2' |
H2'' |
110.8 |
110.5 |
| C2' |
C3' |
C4' |
105.3 |
102.1 |
| C2' |
C3' |
H3' |
111.0 |
110.9 |
| H2' |
C2' |
H2'' |
109.5 |
110.6 |
| O3' |
C3' |
C4' |
109.3 |
110.9 |
| O3' |
C3' |
H3' |
112.3 |
110.9 |
| C4' |
C3' |
H3' |
111.0 |
110.9 |
| C3' |
C4' |
C5' |
113.4 |
110.6 |
| C3' |
C4' |
H4' |
108.9 |
110.6 |
| O4' |
C4' |
C5' |
110.9 |
110.6 |
| O4' |
C4' |
H4' |
110.2 |
110.7 |
| C5' |
C4' |
H4' |
108.7 |
110.6 |
| C4' |
C5' |
H5' |
108.9 |
109.4 |
| C4' |
C5' |
H5'' |
108.9 |
109.4 |
| O5' |
C5' |
H5' |
108.9 |
109.5 |
| O5' |
C5' |
H5'' |
108.9 |
109.5 |
| H5' |
C5' |
H5'' |
109.5 |
109.5 |
Torsion Angles for EDC
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| OP1 |
P |
OP3 |
HOP3 |
0.0 |
300.0 |
| O5' |
P |
OP1 |
OP2 |
122.7 |
240.0 |
| OP1 |
P |
OP2 |
HOP2 |
360.0 |
180.0 |
| O5' |
P |
OP3 |
HOP3 |
110.7 |
180.0 |
| OP1 |
P |
O5' |
OP2 |
229.2 |
120.0 |
| O5' |
P |
OP2 |
HOP2 |
238.3 |
300.0 |
| OP2 |
P |
OP3 |
HOP3 |
226.1 |
60.0 |
| C6 |
N1 |
C2 |
C1' |
181.4 |
180.2 |
| C2 |
N1 |
C1' |
C2' |
71.4 |
115.3 |
| C2 |
N1 |
C1' |
O4' |
192.7 |
233.1 |
| C2 |
N1 |
C1' |
H1' |
311.6 |
354.2 |
| C2 |
N1 |
C6 |
C5 |
359.2 |
359.4 |
| C2 |
N1 |
C6 |
H6 |
179.2 |
179.7 |
| C2 |
N1 |
C1' |
C6 |
181.4 |
180.2 |
| C1' |
N1 |
C6 |
C5 |
180.6 |
179.7 |
| C1' |
N1 |
C6 |
H6 |
0.6 |
359.9 |
| C2' |
C1' |
N1 |
O4' |
238.7 |
242.1 |
| C2' |
C1' |
N1 |
H1' |
119.8 |
121.0 |
| N1 |
C1' |
C2' |
C3' |
133.5 |
121.4 |
| N1 |
C1' |
C2' |
H2' |
252.6 |
240.1 |
| N1 |
C1' |
C2' |
H2'' |
14.4 |
2.8 |
| O4' |
C1' |
N1 |
H1' |
241.2 |
238.9 |
| N1 |
C1' |
O4' |
C4' |
242.0 |
214.1 |
| C2 |
N1 |
C6 |
C1' |
178.6 |
179.8 |
| C6 |
N1 |
C1' |
C2' |
250.0 |
295.0 |
| C6 |
N1 |
C1' |
O4' |
11.3 |
52.9 |
| C6 |
N1 |
C1' |
H1' |
130.2 |
174.0 |
| C4 |
C5 |
C6 |
N1 |
0.5 |
0.6 |
| N1 |
C6 |
C5 |
H5 |
180.5 |
180.2 |
| C5 |
C6 |
N1 |
H6 |
180.0 |
179.7 |
| O2 |
C2 |
N1 |
C1' |
358.7 |
360.0 |
| O2 |
C2 |
N1 |
C6 |
180.1 |
180.2 |
| N3 |
C2 |
N1 |
C1' |
179.4 |
180.0 |
| N3 |
C2 |
N1 |
C6 |
0.8 |
0.3 |
| N4 |
C4 |
N3 |
C5 |
180.1 |
179.9 |
| N3 |
C4 |
C5 |
C6 |
359.9 |
359.6 |
| N3 |
C4 |
C5 |
H5 |
179.9 |
180.0 |
| N3 |
C4 |
N4 |
C5 |
179.9 |
180.1 |
| N4 |
C4 |
C5 |
C6 |
179.7 |
179.7 |
| N4 |
C4 |
C5 |
H5 |
359.7 |
0.1 |
| N1 |
C6 |
C5 |
C4 |
0.5 |
0.6 |
| C6 |
C5 |
C4 |
H5 |
180.0 |
179.6 |
| C4 |
C5 |
C6 |
H6 |
180.5 |
180.4 |
| C5 |
C6 |
N1 |
C1' |
180.6 |
179.7 |
| N1 |
C6 |
C5 |
H6 |
180.0 |
180.3 |
| C4 |
C5 |
C6 |
H5 |
180.0 |
180.4 |
| C4 |
C5 |
H5 |
C6 |
180.0 |
179.6 |
| H5 |
C5 |
C6 |
H6 |
0.5 |
360.0 |
| H6 |
C6 |
N1 |
C1' |
0.6 |
359.9 |
| N1 |
C6 |
H6 |
C5 |
180.0 |
179.7 |
| H6 |
C6 |
C5 |
H5 |
0.5 |
360.0 |
| H8 |
C8 |
C7 |
H7 |
359.8 |
0.1 |
| N1 |
C1' |
C2' |
O4' |
123.1 |
119.4 |
| N1 |
C1' |
C2' |
H1' |
239.8 |
239.0 |
| O4' |
C1' |
C2' |
H1' |
116.7 |
119.6 |
| C2' |
C1' |
O4' |
C4' |
7.5 |
333.5 |
| C3' |
C2' |
C1' |
H2' |
240.9 |
241.4 |
| C3' |
C2' |
C1' |
H2'' |
119.1 |
118.6 |
| C1' |
C2' |
C3' |
C4' |
336.8 |
20.9 |
| C1' |
C2' |
C3' |
H3' |
216.6 |
262.7 |
| H2' |
C2' |
C1' |
H2'' |
238.2 |
237.3 |
| N1 |
C1' |
O4' |
C2' |
234.5 |
240.6 |
| N1 |
C1' |
O4' |
H1' |
118.5 |
121.0 |
| C2' |
C1' |
O4' |
H1' |
244.0 |
240.5 |
| O4' |
C1' |
C2' |
C3' |
10.4 |
2.0 |
| O4' |
C1' |
C2' |
H2' |
129.5 |
120.7 |
| O4' |
C1' |
C2' |
H2'' |
251.3 |
243.4 |
| C1' |
O4' |
C4' |
C5' |
100.5 |
158.6 |
| C1' |
O4' |
C4' |
H4' |
220.9 |
281.5 |
| N1 |
C1' |
H1' |
C2' |
124.1 |
121.0 |
| N1 |
C1' |
H1' |
O4' |
240.0 |
239.0 |
| C2' |
C1' |
H1' |
O4' |
115.8 |
118.0 |
| H1' |
C1' |
C2' |
C3' |
253.7 |
242.4 |
| H1' |
C1' |
C2' |
H2' |
12.8 |
1.1 |
| H1' |
C1' |
C2' |
H2'' |
134.6 |
123.8 |
| H1' |
C1' |
O4' |
C4' |
123.5 |
93.0 |
| C3' |
C2' |
C1' |
O4' |
10.4 |
2.0 |
| C3' |
C2' |
C1' |
H1' |
253.7 |
242.4 |
| C1' |
C2' |
C3' |
H2' |
119.1 |
118.6 |
| C1' |
C2' |
C3' |
H2'' |
240.9 |
241.3 |
| H2' |
C2' |
C3' |
H2'' |
121.8 |
122.7 |
| O3' |
C3' |
C2' |
C4' |
116.5 |
118.2 |
| O3' |
C3' |
C2' |
H3' |
236.7 |
236.4 |
| C4' |
C3' |
C2' |
H3' |
120.2 |
118.2 |
| C2' |
C3' |
C4' |
C5' |
266.9 |
204.5 |
| C2' |
C3' |
C4' |
H4' |
145.8 |
81.6 |
| H2' |
C2' |
C1' |
O4' |
129.5 |
120.7 |
| H2' |
C2' |
C1' |
H1' |
12.8 |
1.1 |
| C1' |
C2' |
H2' |
C3' |
245.1 |
245.3 |
| C1' |
C2' |
H2' |
H2'' |
122.6 |
122.7 |
| C3' |
C2' |
H2' |
H2'' |
237.5 |
237.4 |
| H2' |
C2' |
C3' |
C4' |
217.7 |
262.3 |
| H2' |
C2' |
C3' |
H3' |
97.5 |
144.0 |
| H2'' |
C2' |
C1' |
O4' |
251.3 |
243.4 |
| H2'' |
C2' |
C1' |
H1' |
134.6 |
123.8 |
| C1' |
C2' |
H2'' |
C3' |
114.9 |
114.7 |
| C1' |
C2' |
H2'' |
H2' |
237.4 |
237.3 |
| C3' |
C2' |
H2'' |
H2' |
122.5 |
122.6 |
| H2'' |
C2' |
C3' |
C4' |
95.9 |
139.5 |
| H2'' |
C2' |
C3' |
H3' |
335.7 |
21.3 |
| O3' |
C3' |
C2' |
H2' |
334.2 |
20.4 |
| O3' |
C3' |
C2' |
H2'' |
212.4 |
257.7 |
| C2' |
C3' |
O3' |
C4' |
246.1 |
247.3 |
| C2' |
C3' |
O3' |
H3' |
122.5 |
123.7 |
| C4' |
C3' |
O3' |
H3' |
236.3 |
236.4 |
| O3' |
C3' |
C4' |
C5' |
151.6 |
86.3 |
| O3' |
C3' |
C4' |
H4' |
30.5 |
323.4 |
| C1' |
O4' |
C4' |
C3' |
337.8 |
40.0 |
| C4' |
C3' |
C2' |
H2' |
217.7 |
262.3 |
| C4' |
C3' |
C2' |
H2'' |
95.9 |
139.5 |
| C2' |
C3' |
C4' |
H3' |
239.8 |
241.8 |
| O3' |
C3' |
C4' |
H3' |
124.5 |
123.6 |
| O4' |
C4' |
C3' |
C5' |
121.1 |
118.5 |
| O4' |
C4' |
C3' |
H4' |
242.2 |
241.4 |
| C5' |
C4' |
C3' |
H4' |
121.1 |
122.9 |
| C3' |
C4' |
C5' |
H5' |
163.9 |
305.0 |
| C3' |
C4' |
C5' |
H5'' |
283.3 |
65.0 |
| H3' |
C3' |
C2' |
H2' |
97.5 |
144.0 |
| H3' |
C3' |
C2' |
H2'' |
335.7 |
21.3 |
| C2' |
C3' |
H3' |
C4' |
116.8 |
112.8 |
| O3' |
C3' |
H3' |
C4' |
237.3 |
236.4 |
| H3' |
C3' |
C4' |
C5' |
27.1 |
322.7 |
| H3' |
C3' |
C4' |
H4' |
266.0 |
199.8 |
| HO3' |
O3' |
C3' |
C4' |
293.9 |
174.2 |
| HO3' |
O3' |
C3' |
H3' |
57.5 |
297.8 |
| C4' |
O4' |
C1' |
H1' |
123.5 |
93.0 |
| O4' |
C4' |
C3' |
H3' |
148.2 |
81.2 |
| C3' |
C4' |
O4' |
C5' |
237.3 |
241.5 |
| C3' |
C4' |
O4' |
H4' |
116.9 |
118.5 |
| C5' |
C4' |
O4' |
H4' |
239.6 |
237.1 |
| O4' |
C4' |
C5' |
H5' |
46.4 |
190.9 |
| O4' |
C4' |
C5' |
H5'' |
165.8 |
310.9 |
| C5' |
C4' |
C3' |
H3' |
27.1 |
322.7 |
| C3' |
C4' |
C5' |
H4' |
238.8 |
237.1 |
| O4' |
C4' |
C5' |
H4' |
121.3 |
123.0 |
| O5' |
C5' |
C4' |
H5' |
239.7 |
240.0 |
| O5' |
C5' |
C4' |
H5'' |
120.3 |
120.0 |
| H5' |
C5' |
C4' |
H5'' |
240.6 |
240.0 |
| H4' |
C4' |
C3' |
H3' |
266.0 |
199.8 |
| C3' |
C4' |
H4' |
C5' |
123.9 |
122.9 |
| O4' |
C4' |
H4' |
C5' |
238.2 |
237.0 |
| H4' |
C4' |
C5' |
H5' |
285.1 |
67.9 |
| H4' |
C4' |
C5' |
H5'' |
44.5 |
187.9 |
| C5' |
O5' |
P |
OP2 |
309.9 |
295.0 |
| O5' |
C5' |
C4' |
H4' |
164.8 |
307.9 |
| C4' |
C5' |
O5' |
H5' |
120.3 |
120.0 |
| C4' |
C5' |
O5' |
H5'' |
239.7 |
240.0 |
| H5' |
C5' |
O5' |
H5'' |
119.4 |
120.1 |
| H5' |
C5' |
C4' |
H4' |
285.1 |
67.9 |
| C4' |
C5' |
H5' |
H5'' |
119.0 |
120.0 |
| O5' |
C5' |
H5' |
H5'' |
241.0 |
239.9 |
| H5'' |
C5' |
C4' |
H4' |
44.5 |
187.9 |
| C4' |
C5' |
H5'' |
H5' |
241.0 |
240.0 |
| O5' |
C5' |
H5'' |
H5' |
119.1 |
120.0 |