PDB Chemical Component E3C
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 E3C
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| OP2 |
P |
1.509 |
1.610 |
| C5' |
C4' |
1.508 |
1.530 |
| C5' |
O5' |
1.415 |
1.429 |
| P |
O5' |
1.592 |
1.610 |
| P |
OP1 |
1.508 |
1.480 |
| C4' |
O4' |
1.449 |
1.438 |
| C4' |
C3' |
1.515 |
1.540 |
| O3' |
C3' |
1.415 |
1.429 |
| O2' |
C2' |
1.419 |
1.429 |
| O4' |
C1' |
1.415 |
1.444 |
| C3' |
C2' |
1.521 |
1.548 |
| C2' |
C1' |
1.530 |
1.550 |
| C1' |
N1 |
1.479 |
1.465 |
| O2 |
C2 |
1.247 |
1.216 |
| N1 |
C2 |
1.414 |
1.340 |
| N1 |
C6 |
1.329 |
1.385 |
| C2 |
N3 |
1.407 |
1.348 |
| C6 |
C5 |
1.378 |
1.321 |
| N3 |
C31 |
1.479 |
1.465 |
| N3 |
C4 |
1.416 |
1.473 |
| C5 |
C4 |
1.378 |
1.514 |
| C31 |
C32 |
1.515 |
1.530 |
| C4 |
N4 |
1.343 |
1.469 |
| C1' |
H1 |
1.100 |
1.090 |
| C2' |
H2 |
1.100 |
1.091 |
| C3' |
H3 |
1.100 |
1.090 |
| C4 |
H4 |
1.100 |
1.090 |
| C4' |
H5 |
1.100 |
1.090 |
| C5 |
H6 |
1.080 |
1.080 |
| C5' |
H7 |
1.099 |
1.091 |
| C5' |
H8 |
1.100 |
1.091 |
| C6 |
H9 |
1.080 |
1.080 |
| N4 |
H10 |
1.000 |
1.009 |
| N4 |
H11 |
1.000 |
1.009 |
| O2' |
H13 |
0.950 |
0.967 |
| O3' |
H14 |
0.950 |
0.966 |
| OP2 |
H16 |
0.951 |
0.967 |
| C31 |
H17 |
1.100 |
1.090 |
| C31 |
H18 |
1.100 |
1.089 |
| C32 |
H19 |
1.100 |
1.090 |
| C32 |
H20 |
1.100 |
1.090 |
| C32 |
H21 |
1.100 |
1.090 |
| P |
OP3 |
1.606 |
1.610 |
| OP3 |
H12 |
0.950 |
0.967 |
Bond Angles for E3C
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| P |
OP2 |
H16 |
109.5 |
114.0 |
| OP2 |
P |
OP3 |
107.8 |
109.5 |
| C5' |
C4' |
O4' |
111.3 |
109.9 |
| C5' |
C4' |
H5 |
108.0 |
110.0 |
| O5' |
C5' |
H7 |
108.5 |
109.5 |
| O5' |
C5' |
H8 |
108.5 |
109.5 |
| O4' |
C4' |
H5 |
108.8 |
109.9 |
| C4' |
C3' |
H3 |
108.7 |
110.5 |
| O3' |
C3' |
H3 |
110.0 |
110.4 |
| O2' |
C2' |
H2 |
113.1 |
110.8 |
| O4' |
C1' |
H1 |
109.6 |
110.5 |
| C3' |
C2' |
H2 |
111.5 |
110.9 |
| C2' |
C1' |
N1 |
111.0 |
110.7 |
| C2' |
C1' |
H1 |
108.1 |
110.6 |
| C1' |
N1 |
C2 |
127.3 |
118.3 |
| C1' |
N1 |
C6 |
112.7 |
118.3 |
| N1 |
C1' |
H1 |
108.8 |
110.6 |
| N1 |
C2 |
N3 |
120.1 |
121.8 |
| N1 |
C6 |
H9 |
119.1 |
119.4 |
| C2 |
N3 |
C31 |
116.5 |
120.9 |
| C2 |
N3 |
C4 |
117.7 |
118.3 |
| C6 |
C5 |
H6 |
119.8 |
120.9 |
| N3 |
C31 |
C32 |
120.5 |
109.4 |
| N3 |
C31 |
H17 |
106.7 |
109.5 |
| N3 |
C31 |
H18 |
106.7 |
109.5 |
| N3 |
C4 |
N4 |
124.8 |
107.9 |
| N3 |
C4 |
H4 |
90.1 |
107.9 |
| C5 |
C4 |
N4 |
115.1 |
107.9 |
| C5 |
C4 |
H4 |
90.0 |
107.9 |
| C32 |
C31 |
H17 |
106.6 |
109.4 |
| C32 |
C31 |
H18 |
106.7 |
109.4 |
| C31 |
C32 |
H19 |
109.5 |
109.5 |
| C31 |
C32 |
H20 |
109.5 |
109.5 |
| C31 |
C32 |
H21 |
109.5 |
109.4 |
| N4 |
C4 |
H4 |
90.0 |
107.7 |
| C4 |
N4 |
H10 |
109.5 |
111.0 |
| C4 |
N4 |
H11 |
109.5 |
111.0 |
| H7 |
C5' |
H8 |
109.5 |
109.4 |
| H10 |
N4 |
H11 |
109.5 |
111.0 |
| H17 |
C31 |
H18 |
109.5 |
109.5 |
| H19 |
C32 |
H20 |
109.5 |
109.5 |
| H19 |
C32 |
H21 |
109.5 |
109.5 |
| H20 |
C32 |
H21 |
109.4 |
109.4 |
| P |
OP3 |
H12 |
109.5 |
114.0 |
Torsion Angles for E3C
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| OP2 |
P |
OP3 |
H12 |
129.9 |
300.0 |
| O4' |
C4' |
C5' |
H5 |
119.3 |
121.1 |
| C5' |
C4' |
C3' |
H3 |
308.7 |
357.2 |
| O5' |
C5' |
C4' |
O4' |
284.8 |
66.4 |
| O5' |
C5' |
C4' |
H5 |
165.5 |
305.3 |
| H7 |
C5' |
O5' |
H8 |
118.9 |
119.9 |
| P |
O5' |
C5' |
H7 |
63.5 |
60.0 |
| P |
O5' |
C5' |
H8 |
304.7 |
300.0 |
| C5' |
C4' |
O4' |
H5 |
241.1 |
238.9 |
| O4' |
C4' |
C3' |
H3 |
71.4 |
116.8 |
| C4' |
O4' |
C1' |
H1 |
112.2 |
78.8 |
| O3' |
C3' |
C4' |
H3 |
123.1 |
122.6 |
| C4' |
C3' |
C2' |
H2 |
157.1 |
97.3 |
| C4' |
C3' |
O3' |
H3 |
237.6 |
237.4 |
| O3' |
C3' |
C2' |
H2 |
279.8 |
216.1 |
| C3' |
C2' |
O2' |
H2 |
234.0 |
236.3 |
| O2' |
C2' |
C1' |
H1 |
336.4 |
36.7 |
| C2' |
C1' |
O4' |
H1 |
242.6 |
241.5 |
| N1 |
C1' |
O4' |
H1 |
120.6 |
122.8 |
| O2' |
C2' |
C3' |
H2 |
126.9 |
123.6 |
| C3' |
C2' |
C1' |
N1 |
100.8 |
155.5 |
| C3' |
C2' |
C1' |
H1 |
220.0 |
278.4 |
| O4' |
C1' |
C2' |
H1 |
118.3 |
118.5 |
| C2' |
C1' |
N1 |
C2 |
274.0 |
117.2 |
| C2' |
C1' |
N1 |
C6 |
89.9 |
297.2 |
| N1 |
C1' |
C2' |
H1 |
240.8 |
237.1 |
| O4' |
C1' |
N1 |
H1 |
238.9 |
237.2 |
| C2' |
C1' |
N1 |
H1 |
118.8 |
122.9 |
| C1' |
N1 |
C2 |
N3 |
178.8 |
180.0 |
| C1' |
N1 |
C6 |
H9 |
1.8 |
360.0 |
| O2 |
C2 |
N3 |
C31 |
1.9 |
0.3 |
| C1' |
N1 |
C2 |
C6 |
175.6 |
179.9 |
| C2 |
N1 |
C1' |
H1 |
155.2 |
354.3 |
| N1 |
C2 |
N3 |
C31 |
179.9 |
179.9 |
| N1 |
C2 |
N3 |
C4 |
357.3 |
359.9 |
| C1' |
N1 |
C6 |
C2 |
183.8 |
180.1 |
| C6 |
N1 |
C1' |
H1 |
331.1 |
174.2 |
| C6 |
N1 |
C2 |
N3 |
3.2 |
0.1 |
| N1 |
C6 |
C5 |
H6 |
180.4 |
180.0 |
| C2 |
N3 |
C31 |
C32 |
231.5 |
90.0 |
| C2 |
N3 |
C31 |
H17 |
353.1 |
209.9 |
| C2 |
N3 |
C31 |
H18 |
110.0 |
330.0 |
| C2 |
N3 |
C4 |
N4 |
181.0 |
122.0 |
| C2 |
N3 |
C4 |
H4 |
271.1 |
238.1 |
| C1' |
N1 |
C6 |
C5 |
181.8 |
180.0 |
| C6 |
C5 |
C4 |
N4 |
180.2 |
238.0 |
| C6 |
C5 |
C4 |
H4 |
90.1 |
121.9 |
| C2 |
N3 |
C31 |
C4 |
177.1 |
180.0 |
| C31 |
N3 |
C4 |
N4 |
358.1 |
302.0 |
| C31 |
N3 |
C4 |
H4 |
88.2 |
58.1 |
| C32 |
C31 |
N3 |
H17 |
238.5 |
240.0 |
| C32 |
C31 |
N3 |
H18 |
121.5 |
120.0 |
| N3 |
C31 |
C32 |
H19 |
180.0 |
300.0 |
| N3 |
C31 |
C32 |
H20 |
300.0 |
60.1 |
| N3 |
C31 |
C32 |
H21 |
60.0 |
180.0 |
| H17 |
C31 |
N3 |
H18 |
243.1 |
239.9 |
| C2 |
N3 |
C4 |
C31 |
182.9 |
180.0 |
| C5 |
C4 |
N3 |
N4 |
180.1 |
238.1 |
| C5 |
C4 |
N3 |
H4 |
90.1 |
121.9 |
| N4 |
C4 |
N3 |
H4 |
269.9 |
243.9 |
| N3 |
C4 |
N4 |
H10 |
180.0 |
176.3 |
| N3 |
C4 |
N4 |
H11 |
300.0 |
300.2 |
| C2 |
N3 |
C4 |
C5 |
1.1 |
0.0 |
| N3 |
C4 |
C5 |
N4 |
179.9 |
122.0 |
| N3 |
C4 |
C5 |
H4 |
269.9 |
238.1 |
| N4 |
C4 |
C5 |
H4 |
90.0 |
116.1 |
| C5 |
C4 |
N4 |
H10 |
359.9 |
303.8 |
| C5 |
C4 |
N4 |
H11 |
119.9 |
67.7 |
| N3 |
C31 |
C32 |
H17 |
121.5 |
120.0 |
| N3 |
C31 |
C32 |
H18 |
238.5 |
240.0 |
| H17 |
C31 |
C32 |
H18 |
116.9 |
120.0 |
| H19 |
C32 |
C31 |
H20 |
240.0 |
240.0 |
| H19 |
C32 |
C31 |
H21 |
120.0 |
120.0 |
| H20 |
C32 |
C31 |
H21 |
240.0 |
240.1 |
| N3 |
C4 |
N4 |
H4 |
90.1 |
116.3 |
| C5 |
C4 |
N4 |
H4 |
270.0 |
243.8 |
| H10 |
N4 |
C4 |
H11 |
240.0 |
236.0 |
| C2' |
C1' |
H1 |
N1 |
239.4 |
237.0 |
| H1 |
C1' |
N1 |
C2 |
155.2 |
354.3 |
| H1 |
C1' |
N1 |
C6 |
331.1 |
174.2 |
| H2 |
C2' |
C1' |
N1 |
342.2 |
37.3 |
| H2 |
C2' |
C1' |
H1 |
101.5 |
160.2 |
| H3 |
C3' |
C2' |
H2 |
42.8 |
338.6 |
| N3 |
C4 |
H4 |
N4 |
235.2 |
243.7 |
| C5 |
C4 |
H4 |
N4 |
115.1 |
116.2 |
| H4 |
C4 |
N4 |
H10 |
89.9 |
60.0 |
| H4 |
C4 |
N4 |
H11 |
209.9 |
184.0 |
| C5' |
C4' |
H5 |
O4' |
120.9 |
121.1 |
| H5 |
C4' |
C3' |
H3 |
186.2 |
236.1 |
| H6 |
C5 |
C4 |
N4 |
0.2 |
58.1 |
| H6 |
C5 |
C4 |
H4 |
270.2 |
301.9 |
| H7 |
C5' |
C4' |
O4' |
45.4 |
186.4 |
| H7 |
C5' |
C4' |
H5 |
286.1 |
65.4 |
| O5' |
C5' |
H7 |
H8 |
241.8 |
240.0 |
| H8 |
C5' |
C4' |
O4' |
164.3 |
306.4 |
| H8 |
C5' |
C4' |
H5 |
44.9 |
185.3 |
| O5' |
C5' |
H8 |
H7 |
118.3 |
120.0 |
| H9 |
C6 |
C5 |
H6 |
0.4 |
0.0 |
| H10 |
N4 |
C4 |
H4 |
89.9 |
60.0 |
| C4 |
N4 |
H10 |
H11 |
120.0 |
123.9 |
| H11 |
N4 |
C4 |
H4 |
209.9 |
184.0 |
| C4 |
N4 |
H11 |
H10 |
240.0 |
236.0 |
| H13 |
O2' |
C2' |
H2 |
306.0 |
56.4 |
| H14 |
O3' |
C3' |
H3 |
302.4 |
298.9 |
| H16 |
OP2 |
P |
OP3 |
236.9 |
300.0 |
| N3 |
C31 |
H17 |
C32 |
230.1 |
240.0 |
| N3 |
C31 |
H17 |
H18 |
115.0 |
120.1 |
| C32 |
C31 |
H17 |
H18 |
245.0 |
240.0 |
| H17 |
C31 |
C32 |
H19 |
58.5 |
180.0 |
| H17 |
C31 |
C32 |
H20 |
178.5 |
300.1 |
| H17 |
C31 |
C32 |
H21 |
298.4 |
60.0 |
| N3 |
C31 |
H18 |
C32 |
129.9 |
120.0 |
| N3 |
C31 |
H18 |
H17 |
245.0 |
239.9 |
| C32 |
C31 |
H18 |
H17 |
115.0 |
120.0 |
| H18 |
C31 |
C32 |
H19 |
301.5 |
60.0 |
| H18 |
C31 |
C32 |
H20 |
61.5 |
180.1 |
| H18 |
C31 |
C32 |
H21 |
181.5 |
300.0 |
| H19 |
C32 |
C31 |
H17 |
58.5 |
180.0 |
| H19 |
C32 |
C31 |
H18 |
301.5 |
60.0 |
| C31 |
C32 |
H19 |
H20 |
120.0 |
120.0 |
| C31 |
C32 |
H19 |
H21 |
240.0 |
240.0 |
| H20 |
C32 |
H19 |
H21 |
120.0 |
120.0 |
| H20 |
C32 |
C31 |
H17 |
178.5 |
300.1 |
| H20 |
C32 |
C31 |
H18 |
61.5 |
180.1 |
| C31 |
C32 |
H20 |
H19 |
240.0 |
240.0 |
| C31 |
C32 |
H20 |
H21 |
120.0 |
119.9 |
| H19 |
C32 |
H20 |
H21 |
240.0 |
240.0 |
| H21 |
C32 |
C31 |
H17 |
298.4 |
60.0 |
| H21 |
C32 |
C31 |
H18 |
181.5 |
300.0 |
| C31 |
C32 |
H21 |
H19 |
120.0 |
120.0 |
| C31 |
C32 |
H21 |
H20 |
240.0 |
240.0 |
| H19 |
C32 |
H21 |
H20 |
120.0 |
120.0 |
| OP3 |
P |
OP2 |
H16 |
236.9 |
300.0 |