PDB Chemical Component EMA
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 EMA
Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
PG |
O1G |
1.463 |
1.609 |
PG |
O2G |
1.447 |
1.479 |
PG |
O3G |
1.486 |
1.610 |
PG |
O3B |
1.611 |
1.610 |
O1G |
H1G |
0.950 |
0.967 |
O3G |
H3G |
0.950 |
0.967 |
PB |
O1B |
1.499 |
1.479 |
PB |
O2B |
1.466 |
1.609 |
PB |
O3B |
1.639 |
1.610 |
PB |
O3A |
1.576 |
1.611 |
O2B |
H2B |
0.950 |
0.967 |
PA |
O1A |
1.473 |
1.480 |
PA |
O2A |
1.486 |
1.610 |
PA |
O3A |
1.598 |
1.609 |
PA |
C5' |
1.604 |
1.823 |
O2A |
H2A |
0.949 |
0.966 |
C5' |
O5' |
1.493 |
1.428 |
C5' |
H5'1 |
1.115 |
1.090 |
C5' |
H5'2 |
1.116 |
1.090 |
O5' |
C4' |
1.532 |
1.429 |
C4' |
C1' |
1.606 |
1.530 |
C4' |
H4'1 |
1.116 |
1.090 |
C4' |
H4'2 |
1.115 |
1.090 |
C1' |
N9 |
1.570 |
1.465 |
C1' |
H1'1 |
1.115 |
1.090 |
C1' |
H1'2 |
1.115 |
1.090 |
N9 |
C8 |
1.437 |
1.363 |
N9 |
C4 |
1.343 |
1.371 |
C8 |
N7 |
1.372 |
1.302 |
C8 |
H8 |
1.103 |
1.080 |
N7 |
C5 |
1.362 |
1.354 |
C5 |
C6 |
1.439 |
1.405 |
C5 |
C4 |
1.351 |
1.404 |
C6 |
N6 |
1.319 |
1.384 |
C6 |
N1 |
1.355 |
1.328 |
N6 |
HN61 |
1.020 |
0.970 |
N6 |
HN62 |
1.020 |
0.970 |
N1 |
C2 |
1.339 |
1.320 |
C2 |
N3 |
1.354 |
1.316 |
C2 |
H2 |
1.104 |
1.079 |
N3 |
C4 |
1.417 |
1.329 |
Bond Angles for EMA
Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
O1G |
PG |
O2G |
115.0 |
109.5 |
O1G |
PG |
O3G |
113.8 |
109.5 |
O1G |
PG |
O3B |
104.1 |
109.5 |
PG |
O1G |
H1G |
115.1 |
106.8 |
O2G |
PG |
O3G |
114.4 |
109.5 |
O2G |
PG |
O3B |
99.2 |
109.5 |
O3G |
PG |
O3B |
108.4 |
109.4 |
PG |
O3G |
H3G |
113.8 |
106.8 |
PG |
O3B |
PB |
133.4 |
106.8 |
O1B |
PB |
O2B |
118.3 |
109.5 |
O1B |
PB |
O3B |
108.6 |
109.5 |
O1B |
PB |
O3A |
107.6 |
109.5 |
O2B |
PB |
O3B |
108.8 |
109.5 |
O2B |
PB |
O3A |
113.1 |
109.4 |
PB |
O2B |
H2B |
118.2 |
106.8 |
O3B |
PB |
O3A |
98.6 |
109.4 |
PB |
O3A |
PA |
135.9 |
106.8 |
O1A |
PA |
O2A |
119.0 |
109.5 |
O1A |
PA |
O3A |
104.5 |
109.5 |
O1A |
PA |
C5' |
104.7 |
109.4 |
O2A |
PA |
O3A |
112.2 |
109.5 |
O2A |
PA |
C5' |
110.0 |
109.5 |
PA |
O2A |
H2A |
119.0 |
106.7 |
O3A |
PA |
C5' |
105.5 |
109.5 |
PA |
C5' |
O5' |
133.2 |
109.5 |
PA |
C5' |
H5'1 |
104.0 |
109.5 |
PA |
C5' |
H5'2 |
104.0 |
109.5 |
O5' |
C5' |
H5'1 |
104.1 |
109.4 |
O5' |
C5' |
H5'2 |
104.1 |
109.4 |
C5' |
O5' |
C4' |
116.1 |
106.8 |
H5'1 |
C5' |
H5'2 |
104.7 |
109.5 |
O5' |
C4' |
C1' |
115.6 |
109.5 |
O5' |
C4' |
H4'1 |
110.0 |
109.5 |
O5' |
C4' |
H4'2 |
110.0 |
109.4 |
C1' |
C4' |
H4'1 |
110.0 |
109.5 |
C1' |
C4' |
H4'2 |
110.0 |
109.4 |
C4' |
C1' |
N9 |
128.3 |
109.5 |
C4' |
C1' |
H1'1 |
105.6 |
109.5 |
C4' |
C1' |
H1'2 |
105.6 |
109.4 |
H4'1 |
C4' |
H4'2 |
100.2 |
109.5 |
N9 |
C1' |
H1'1 |
105.7 |
109.5 |
N9 |
C1' |
H1'2 |
105.7 |
109.4 |
C1' |
N9 |
C8 |
138.7 |
126.3 |
C1' |
N9 |
C4 |
117.9 |
126.3 |
H1'1 |
C1' |
H1'2 |
103.7 |
109.5 |
C8 |
N9 |
C4 |
103.4 |
107.4 |
N9 |
C8 |
N7 |
110.6 |
110.0 |
N9 |
C8 |
H8 |
126.6 |
125.0 |
N9 |
C4 |
C5 |
110.8 |
106.0 |
N9 |
C4 |
N3 |
123.1 |
134.9 |
N7 |
C8 |
H8 |
122.8 |
125.0 |
C8 |
N7 |
C5 |
104.4 |
109.4 |
N7 |
C5 |
C6 |
133.1 |
134.7 |
N7 |
C5 |
C4 |
110.7 |
107.1 |
C6 |
C5 |
C4 |
116.1 |
118.2 |
C5 |
C6 |
N6 |
120.5 |
120.8 |
C5 |
C6 |
N1 |
119.4 |
118.4 |
C5 |
C4 |
N3 |
126.0 |
119.1 |
N6 |
C6 |
N1 |
120.0 |
120.8 |
C6 |
N6 |
HN61 |
120.5 |
120.0 |
C6 |
N6 |
HN62 |
108.2 |
120.0 |
C6 |
N1 |
C2 |
119.4 |
121.2 |
HN61 |
N6 |
HN62 |
108.2 |
120.0 |
N1 |
C2 |
N3 |
127.0 |
122.4 |
N1 |
C2 |
H2 |
115.9 |
118.8 |
N3 |
C2 |
H2 |
117.1 |
118.8 |
C2 |
N3 |
C4 |
111.9 |
120.7 |
Torsion Angles for EMA
Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
O2G |
PG |
O1G |
O3G |
134.8 |
240.0 |
O2G |
PG |
O1G |
O3B |
252.6 |
120.0 |
O3G |
PG |
O1G |
O3B |
117.9 |
240.0 |
O1G |
PG |
O3G |
H3G |
180.0 |
60.1 |
O1G |
PG |
O3B |
PB |
62.5 |
180.0 |
O1G |
PG |
O2G |
O3G |
225.5 |
120.0 |
O1G |
PG |
O2G |
O3B |
110.4 |
239.9 |
O2G |
PG |
O1G |
H1G |
180.0 |
300.0 |
O3G |
PG |
O2G |
O3B |
244.9 |
120.0 |
O2G |
PG |
O3G |
H3G |
45.0 |
180.0 |
O2G |
PG |
O3B |
PB |
181.3 |
60.0 |
O1G |
PG |
O3G |
O2G |
135.0 |
240.0 |
O1G |
PG |
O3G |
O3B |
244.6 |
120.0 |
O3G |
PG |
O1G |
H1G |
45.3 |
60.0 |
O2G |
PG |
O3G |
O3B |
109.6 |
240.0 |
O3G |
PG |
O3B |
PB |
301.0 |
300.0 |
O1G |
PG |
O3B |
O2G |
241.1 |
120.0 |
O1G |
PG |
O3B |
O3G |
121.5 |
240.0 |
O3B |
PG |
O1G |
H1G |
287.4 |
180.0 |
O2G |
PG |
O3B |
O3G |
240.3 |
120.0 |
O3B |
PG |
O3G |
H3G |
295.3 |
300.0 |
O1B |
PB |
O3B |
PG |
309.4 |
299.9 |
O2B |
PB |
O3B |
PG |
79.4 |
60.0 |
PG |
O3B |
PB |
O3A |
197.5 |
180.0 |
H1G |
O1G |
PG |
O2G |
180.0 |
300.0 |
H1G |
O1G |
PG |
O3G |
45.3 |
60.0 |
H1G |
O1G |
PG |
O3B |
287.4 |
180.0 |
H3G |
O3G |
PG |
O3B |
295.3 |
300.0 |
PG |
O3B |
PB |
O1B |
309.4 |
299.9 |
O2B |
PB |
O1B |
O3B |
235.5 |
239.9 |
O2B |
PB |
O1B |
O3A |
129.6 |
120.0 |
O1B |
PB |
O2B |
H2B |
180.0 |
180.0 |
O3B |
PB |
O1B |
O3A |
254.2 |
240.1 |
O1B |
PB |
O3A |
PA |
303.8 |
60.0 |
PG |
O3B |
PB |
O2B |
79.4 |
60.0 |
O1B |
PB |
O2B |
O3B |
124.4 |
120.0 |
O1B |
PB |
O2B |
O3A |
232.9 |
240.0 |
O3B |
PB |
O2B |
O3A |
108.5 |
120.0 |
O2B |
PB |
O3A |
PA |
171.3 |
300.0 |
O1B |
PB |
O3B |
O2B |
230.0 |
239.9 |
O1B |
PB |
O3B |
O3A |
112.0 |
120.0 |
O2B |
PB |
O3B |
O3A |
241.9 |
240.0 |
O3B |
PB |
O2B |
H2B |
55.6 |
60.0 |
O3B |
PB |
O3A |
PA |
56.5 |
180.0 |
O1B |
PB |
O3A |
O2B |
132.5 |
120.0 |
O1B |
PB |
O3A |
O3B |
247.3 |
240.1 |
O2B |
PB |
O3A |
O3B |
114.8 |
120.0 |
O3A |
PB |
O2B |
H2B |
307.1 |
300.0 |
O1A |
PA |
O3A |
PB |
292.0 |
300.0 |
O2A |
PA |
O3A |
PB |
62.3 |
60.0 |
PB |
O3A |
PA |
C5' |
182.0 |
180.0 |
H2B |
O2B |
PB |
O3B |
55.6 |
60.0 |
H2B |
O2B |
PB |
O3A |
307.1 |
300.0 |
PB |
O3A |
PA |
O1A |
292.0 |
300.0 |
O2A |
PA |
O1A |
O3A |
233.9 |
239.9 |
O2A |
PA |
O1A |
C5' |
123.3 |
120.0 |
O1A |
PA |
O2A |
H2A |
180.0 |
180.0 |
O3A |
PA |
O1A |
C5' |
249.4 |
240.0 |
O1A |
PA |
C5' |
O5' |
181.0 |
60.0 |
O1A |
PA |
C5' |
H5'1 |
306.3 |
180.0 |
O1A |
PA |
C5' |
H5'2 |
55.8 |
300.0 |
PB |
O3A |
PA |
O2A |
62.3 |
60.0 |
O1A |
PA |
O2A |
O3A |
122.3 |
120.1 |
O1A |
PA |
O2A |
C5' |
239.4 |
240.0 |
O3A |
PA |
O2A |
C5' |
117.0 |
120.0 |
O2A |
PA |
C5' |
O5' |
52.1 |
300.0 |
O2A |
PA |
C5' |
H5'1 |
177.4 |
60.0 |
O2A |
PA |
C5' |
H5'2 |
286.8 |
180.1 |
O1A |
PA |
O3A |
O2A |
229.8 |
240.0 |
O1A |
PA |
O3A |
C5' |
110.0 |
120.0 |
O2A |
PA |
O3A |
C5' |
240.3 |
240.0 |
O3A |
PA |
O2A |
H2A |
57.7 |
60.0 |
O3A |
PA |
C5' |
O5' |
290.9 |
180.0 |
O3A |
PA |
C5' |
H5'1 |
56.2 |
300.0 |
O3A |
PA |
C5' |
H5'2 |
165.7 |
60.0 |
O1A |
PA |
C5' |
O2A |
128.9 |
120.0 |
O1A |
PA |
C5' |
O3A |
250.1 |
240.0 |
O2A |
PA |
C5' |
O3A |
121.1 |
120.0 |
C5' |
PA |
O2A |
H2A |
300.7 |
300.0 |
O5' |
C5' |
PA |
H5'1 |
234.7 |
240.0 |
O5' |
C5' |
PA |
H5'2 |
125.3 |
120.0 |
PA |
C5' |
O5' |
C4' |
290.9 |
89.9 |
H5'1 |
C5' |
PA |
H5'2 |
250.6 |
239.9 |
H2A |
O2A |
PA |
O3A |
57.7 |
60.0 |
H2A |
O2A |
PA |
C5' |
300.7 |
300.0 |
PA |
C5' |
O5' |
H5'1 |
125.3 |
120.0 |
PA |
C5' |
O5' |
H5'2 |
234.7 |
240.0 |
H5'1 |
C5' |
O5' |
H5'2 |
109.5 |
120.0 |
C5' |
O5' |
C4' |
C1' |
198.2 |
180.0 |
C5' |
O5' |
C4' |
H4'1 |
323.5 |
300.1 |
C5' |
O5' |
C4' |
H4'2 |
72.9 |
60.1 |
PA |
C5' |
H5'1 |
O5' |
217.9 |
240.0 |
PA |
C5' |
H5'1 |
H5'2 |
108.9 |
120.1 |
O5' |
C5' |
H5'1 |
H5'2 |
251.0 |
240.1 |
H5'1 |
C5' |
O5' |
C4' |
165.6 |
329.9 |
PA |
C5' |
H5'2 |
O5' |
142.1 |
120.0 |
PA |
C5' |
H5'2 |
H5'1 |
251.1 |
240.0 |
O5' |
C5' |
H5'2 |
H5'1 |
109.0 |
119.9 |
H5'2 |
C5' |
O5' |
C4' |
56.2 |
209.9 |
C4' |
O5' |
C5' |
H5'1 |
165.6 |
329.9 |
C4' |
O5' |
C5' |
H5'2 |
56.2 |
209.9 |
C1' |
C4' |
O5' |
H4'1 |
234.7 |
239.9 |
C1' |
C4' |
O5' |
H4'2 |
125.3 |
119.9 |
O5' |
C4' |
C1' |
N9 |
2.3 |
180.0 |
O5' |
C4' |
C1' |
H1'1 |
127.5 |
300.1 |
O5' |
C4' |
C1' |
H1'2 |
237.0 |
60.1 |
H4'1 |
C4' |
O5' |
H4'2 |
250.5 |
240.0 |
O5' |
C4' |
C1' |
H4'1 |
125.3 |
120.1 |
O5' |
C4' |
C1' |
H4'2 |
234.7 |
240.1 |
H4'1 |
C4' |
C1' |
H4'2 |
109.4 |
120.0 |
N9 |
C1' |
C4' |
H1'1 |
234.7 |
240.0 |
N9 |
C1' |
C4' |
H1'2 |
125.3 |
119.9 |
C4' |
C1' |
N9 |
C8 |
323.9 |
90.0 |
C4' |
C1' |
N9 |
C4 |
146.5 |
270.1 |
H1'1 |
C1' |
C4' |
H1'2 |
250.6 |
239.9 |
O5' |
C4' |
H4'1 |
C1' |
231.6 |
239.9 |
O5' |
C4' |
H4'1 |
H4'2 |
115.8 |
119.9 |
C1' |
C4' |
H4'1 |
H4'2 |
244.2 |
240.0 |
H4'1 |
C4' |
C1' |
N9 |
237.0 |
59.9 |
H4'1 |
C4' |
C1' |
H1'1 |
2.3 |
180.0 |
H4'1 |
C4' |
C1' |
H1'2 |
111.7 |
300.0 |
O5' |
C4' |
H4'2 |
C1' |
128.4 |
120.0 |
O5' |
C4' |
H4'2 |
H4'1 |
244.2 |
240.0 |
C1' |
C4' |
H4'2 |
H4'1 |
115.8 |
120.0 |
H4'2 |
C4' |
C1' |
N9 |
127.6 |
299.9 |
H4'2 |
C4' |
C1' |
H1'1 |
252.8 |
60.0 |
H4'2 |
C4' |
C1' |
H1'2 |
2.2 |
180.0 |
N9 |
C1' |
C4' |
H4'1 |
237.0 |
59.9 |
N9 |
C1' |
C4' |
H4'2 |
127.6 |
299.9 |
C4' |
C1' |
N9 |
H1'1 |
125.2 |
120.0 |
C4' |
C1' |
N9 |
H1'2 |
234.7 |
240.1 |
H1'1 |
C1' |
N9 |
H1'2 |
109.5 |
120.1 |
C8 |
N9 |
C1' |
C4 |
177.4 |
180.0 |
C1' |
N9 |
C8 |
N7 |
178.7 |
180.0 |
C1' |
N9 |
C8 |
H8 |
358.7 |
359.9 |
C1' |
N9 |
C4 |
C5 |
181.8 |
180.3 |
C1' |
N9 |
C4 |
N3 |
358.5 |
359.9 |
H1'1 |
C1' |
C4' |
H4'1 |
2.3 |
180.0 |
H1'1 |
C1' |
C4' |
H4'2 |
252.8 |
60.0 |
C4' |
C1' |
H1'1 |
N9 |
221.7 |
240.0 |
C4' |
C1' |
H1'1 |
H1'2 |
110.8 |
120.0 |
N9 |
C1' |
H1'1 |
H1'2 |
249.1 |
240.0 |
H1'1 |
C1' |
N9 |
C8 |
198.7 |
330.0 |
H1'1 |
C1' |
N9 |
C4 |
21.3 |
150.1 |
H1'2 |
C1' |
C4' |
H4'1 |
111.7 |
300.0 |
H1'2 |
C1' |
C4' |
H4'2 |
2.2 |
180.0 |
C4' |
C1' |
H1'2 |
N9 |
138.3 |
120.0 |
C4' |
C1' |
H1'2 |
H1'1 |
249.2 |
240.0 |
N9 |
C1' |
H1'2 |
H1'1 |
110.9 |
120.0 |
H1'2 |
C1' |
N9 |
C8 |
89.2 |
210.0 |
H1'2 |
C1' |
N9 |
C4 |
271.8 |
30.0 |
C8 |
N9 |
C1' |
H1'1 |
198.7 |
330.0 |
C8 |
N9 |
C1' |
H1'2 |
89.2 |
210.0 |
C1' |
N9 |
C8 |
C4 |
182.4 |
180.0 |
C8 |
N9 |
C4 |
C5 |
3.5 |
0.3 |
C8 |
N9 |
C4 |
N3 |
180.3 |
180.0 |
N7 |
C8 |
N9 |
H8 |
179.9 |
180.1 |
N9 |
C8 |
N7 |
C5 |
2.4 |
359.7 |
C4 |
N9 |
C1' |
H1'1 |
21.3 |
150.1 |
C4 |
N9 |
C1' |
H1'2 |
271.8 |
30.0 |
C1' |
N9 |
C4 |
C8 |
178.2 |
180.0 |
C4 |
N9 |
C8 |
N7 |
356.3 |
0.0 |
C4 |
N9 |
C8 |
H8 |
176.4 |
179.9 |
N7 |
C5 |
C4 |
N9 |
357.7 |
359.5 |
C6 |
C5 |
C4 |
N9 |
175.1 |
180.3 |
C5 |
C4 |
N9 |
N3 |
183.2 |
180.3 |
C2 |
N3 |
C4 |
N9 |
183.0 |
180.0 |
N7 |
C8 |
N9 |
C4 |
356.3 |
0.0 |
N9 |
C8 |
N7 |
H8 |
180.1 |
179.9 |
C8 |
N7 |
C5 |
C6 |
183.1 |
179.5 |
C8 |
N7 |
C5 |
C4 |
359.8 |
0.5 |
H8 |
C8 |
N9 |
C4 |
176.4 |
179.9 |
N9 |
C8 |
H8 |
N7 |
179.9 |
180.1 |
H8 |
C8 |
N7 |
C5 |
182.3 |
179.8 |
N9 |
C4 |
C5 |
N7 |
357.7 |
359.5 |
C5 |
N7 |
C8 |
H8 |
182.3 |
179.8 |
C6 |
C5 |
N7 |
C4 |
183.3 |
179.0 |
N7 |
C5 |
C6 |
N6 |
357.1 |
0.8 |
N7 |
C5 |
C6 |
N1 |
180.1 |
180.5 |
N7 |
C5 |
C4 |
N3 |
181.1 |
179.8 |
N9 |
C4 |
C5 |
C6 |
175.1 |
180.3 |
N7 |
C5 |
C6 |
C4 |
176.6 |
181.1 |
C6 |
C5 |
C4 |
N3 |
358.4 |
0.6 |
N6 |
C6 |
C5 |
N1 |
177.0 |
180.2 |
C5 |
C6 |
N6 |
HN61 |
180.0 |
179.8 |
C5 |
C6 |
N6 |
HN62 |
54.8 |
359.5 |
C5 |
C6 |
N1 |
C2 |
356.8 |
0.3 |
N9 |
C4 |
C5 |
N3 |
176.7 |
179.7 |
N7 |
C5 |
C4 |
C6 |
182.7 |
179.2 |
C4 |
C5 |
C6 |
N6 |
180.5 |
179.7 |
C4 |
C5 |
C6 |
N1 |
3.6 |
359.4 |
C2 |
N3 |
C4 |
C5 |
359.3 |
359.7 |
N6 |
C6 |
C5 |
C4 |
180.5 |
179.7 |
C5 |
C6 |
N6 |
N1 |
183.1 |
179.7 |
N6 |
C6 |
N1 |
C2 |
179.8 |
180.0 |
HN61 |
N6 |
C6 |
HN62 |
125.2 |
180.3 |
N1 |
C6 |
C5 |
C4 |
3.6 |
359.4 |
C5 |
C6 |
N1 |
N6 |
177.0 |
180.2 |
N1 |
C6 |
N6 |
HN61 |
356.9 |
0.0 |
N1 |
C6 |
N6 |
HN62 |
231.7 |
179.7 |
C6 |
N1 |
C2 |
N3 |
0.7 |
360.0 |
C6 |
N1 |
C2 |
H2 |
180.7 |
180.0 |
HN61 |
N6 |
C6 |
N1 |
356.9 |
0.0 |
C6 |
N6 |
HN61 |
HN62 |
234.8 |
179.7 |
HN62 |
N6 |
C6 |
N1 |
231.7 |
179.7 |
C6 |
N6 |
HN62 |
HN61 |
132.1 |
180.3 |
N3 |
C2 |
N1 |
H2 |
179.9 |
179.9 |
N1 |
C2 |
N3 |
C4 |
1.3 |
0.0 |
N9 |
C4 |
N3 |
C2 |
183.0 |
180.0 |
C5 |
C4 |
N3 |
C2 |
359.3 |
359.7 |
N1 |
C2 |
N3 |
H2 |
180.1 |
180.1 |
N1 |
C2 |
H2 |
N3 |
180.0 |
179.9 |
H2 |
C2 |
N3 |
C4 |
181.2 |
180.0 |
N9 |
C4 |
N3 |
C5 |
183.7 |
180.4 |
C4 |
N3 |
C2 |
H2 |
181.2 |
180.0 |