PDB Chemical Component CMP
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 CMP
Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
P |
O1P |
1.474 |
1.479 |
P |
O2P |
1.486 |
1.610 |
P |
O5' |
1.598 |
1.606 |
P |
O3' |
1.598 |
1.615 |
O2P |
HOP2 |
0.951 |
0.967 |
O5' |
C5' |
1.437 |
1.435 |
C5' |
C4' |
1.505 |
1.518 |
C5' |
H5'1 |
1.115 |
1.090 |
C5' |
H5'2 |
1.115 |
1.090 |
C4' |
O4' |
1.454 |
1.427 |
C4' |
C3' |
1.510 |
1.551 |
C4' |
H4' |
1.115 |
1.089 |
O4' |
C1' |
1.422 |
1.446 |
C3' |
O3' |
1.409 |
1.414 |
C3' |
C2' |
1.519 |
1.538 |
C3' |
H3' |
1.115 |
1.089 |
C2' |
O2' |
1.419 |
1.429 |
C2' |
C1' |
1.531 |
1.547 |
C2' |
H2' |
1.115 |
1.090 |
O2' |
HO2' |
0.951 |
0.966 |
C1' |
N9 |
1.464 |
1.465 |
C1' |
H1' |
1.116 |
1.090 |
N9 |
C8 |
1.386 |
1.362 |
N9 |
C4 |
1.378 |
1.372 |
C8 |
N7 |
1.320 |
1.302 |
C8 |
H8 |
1.102 |
1.080 |
N7 |
C5 |
1.394 |
1.355 |
C5 |
C6 |
1.386 |
1.405 |
C5 |
C4 |
1.387 |
1.403 |
C6 |
N6 |
1.333 |
1.385 |
C6 |
N1 |
1.345 |
1.328 |
N6 |
HN61 |
1.020 |
0.970 |
N6 |
HN62 |
1.020 |
0.970 |
N1 |
C2 |
1.314 |
1.319 |
C2 |
N3 |
1.330 |
1.317 |
C2 |
H2 |
1.103 |
1.080 |
N3 |
C4 |
1.349 |
1.329 |
Bond Angles for CMP
Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
O1P |
P |
O2P |
120.3 |
109.2 |
O1P |
P |
O5' |
104.0 |
109.2 |
O1P |
P |
O3' |
108.1 |
109.1 |
O2P |
P |
O5' |
111.6 |
109.2 |
O2P |
P |
O3' |
107.7 |
109.2 |
P |
O2P |
HOP2 |
120.3 |
106.8 |
O5' |
P |
O3' |
104.0 |
110.9 |
P |
O5' |
C5' |
122.5 |
108.6 |
P |
O3' |
C3' |
117.8 |
105.4 |
O5' |
C5' |
C4' |
110.4 |
107.7 |
O5' |
C5' |
H5'1 |
111.9 |
109.8 |
O5' |
C5' |
H5'2 |
111.9 |
109.8 |
C4' |
C5' |
H5'1 |
111.8 |
109.8 |
C4' |
C5' |
H5'2 |
111.8 |
109.9 |
C5' |
C4' |
O4' |
111.7 |
115.7 |
C5' |
C4' |
C3' |
112.3 |
108.2 |
C5' |
C4' |
H4' |
103.8 |
109.8 |
H5'1 |
C5' |
H5'2 |
98.6 |
109.9 |
O4' |
C4' |
C3' |
101.4 |
102.9 |
O4' |
C4' |
H4' |
114.3 |
109.9 |
C4' |
O4' |
C1' |
109.0 |
105.6 |
C3' |
C4' |
H4' |
113.7 |
110.0 |
C4' |
C3' |
O3' |
104.4 |
107.3 |
C4' |
C3' |
C2' |
101.0 |
101.1 |
C4' |
C3' |
H3' |
121.1 |
110.3 |
O4' |
C1' |
C2' |
106.7 |
107.3 |
O4' |
C1' |
N9 |
108.5 |
109.9 |
O4' |
C1' |
H1' |
114.3 |
109.9 |
O3' |
C3' |
C2' |
118.1 |
115.5 |
O3' |
C3' |
H3' |
105.0 |
110.7 |
C2' |
C3' |
H3' |
108.1 |
111.3 |
C3' |
C2' |
O2' |
111.1 |
110.6 |
C3' |
C2' |
C1' |
100.0 |
103.1 |
C3' |
C2' |
H2' |
114.4 |
110.6 |
O2' |
C2' |
C1' |
109.2 |
111.3 |
O2' |
C2' |
H2' |
106.0 |
110.6 |
C2' |
O2' |
HO2' |
111.1 |
106.8 |
C1' |
C2' |
H2' |
116.1 |
110.4 |
C2' |
C1' |
N9 |
115.7 |
109.9 |
C2' |
C1' |
H1' |
106.9 |
109.9 |
N9 |
C1' |
H1' |
105.0 |
109.9 |
C1' |
N9 |
C8 |
130.6 |
126.3 |
C1' |
N9 |
C4 |
123.7 |
126.3 |
C8 |
N9 |
C4 |
105.7 |
107.4 |
N9 |
C8 |
N7 |
113.7 |
110.0 |
N9 |
C8 |
H8 |
125.3 |
125.1 |
N9 |
C4 |
C5 |
105.9 |
106.1 |
N9 |
C4 |
N3 |
127.6 |
134.8 |
N7 |
C8 |
H8 |
121.0 |
125.0 |
C8 |
N7 |
C5 |
103.6 |
109.4 |
N7 |
C5 |
C6 |
132.4 |
134.6 |
N7 |
C5 |
C4 |
111.1 |
107.1 |
C6 |
C5 |
C4 |
116.6 |
118.2 |
C5 |
C6 |
N6 |
123.0 |
120.8 |
C5 |
C6 |
N1 |
118.1 |
118.4 |
C5 |
C4 |
N3 |
126.5 |
119.1 |
N6 |
C6 |
N1 |
118.9 |
120.8 |
C6 |
N6 |
HN61 |
123.0 |
120.0 |
C6 |
N6 |
HN62 |
107.4 |
120.0 |
C6 |
N1 |
C2 |
119.2 |
121.2 |
HN61 |
N6 |
HN62 |
107.4 |
120.0 |
N1 |
C2 |
N3 |
129.1 |
122.5 |
N1 |
C2 |
H2 |
114.7 |
118.8 |
N3 |
C2 |
H2 |
116.1 |
118.7 |
C2 |
N3 |
C4 |
110.5 |
120.6 |
Torsion Angles for CMP
Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
O2P |
P |
O1P |
O5' |
234.2 |
240.7 |
O2P |
P |
O1P |
O3' |
124.1 |
119.3 |
O1P |
P |
O2P |
HOP2 |
180.0 |
59.3 |
O5' |
P |
O1P |
O3' |
249.9 |
238.6 |
O1P |
P |
O5' |
C5' |
152.3 |
65.2 |
O1P |
P |
O3' |
C3' |
258.8 |
297.4 |
O1P |
P |
O2P |
O5' |
122.2 |
119.3 |
O1P |
P |
O2P |
O3' |
235.7 |
240.8 |
O5' |
P |
O2P |
O3' |
113.6 |
121.5 |
O2P |
P |
O5' |
C5' |
283.4 |
184.5 |
O2P |
P |
O3' |
C3' |
127.4 |
178.1 |
O1P |
P |
O5' |
O2P |
228.9 |
240.7 |
O1P |
P |
O5' |
O3' |
113.1 |
120.3 |
O2P |
P |
O5' |
O3' |
244.2 |
239.6 |
O5' |
P |
O2P |
HOP2 |
57.9 |
300.0 |
O5' |
P |
O3' |
C3' |
8.9 |
57.7 |
P |
O5' |
C5' |
C4' |
331.6 |
59.1 |
P |
O5' |
C5' |
H5'1 |
96.8 |
299.6 |
P |
O5' |
C5' |
H5'2 |
206.3 |
178.7 |
O1P |
P |
O3' |
O2P |
131.3 |
119.3 |
O1P |
P |
O3' |
O5' |
249.9 |
239.6 |
O2P |
P |
O3' |
O5' |
118.5 |
120.4 |
O3' |
P |
O2P |
HOP2 |
304.3 |
178.5 |
O3' |
P |
O5' |
C5' |
39.2 |
304.9 |
C4' |
C3' |
O3' |
P |
300.7 |
295.4 |
P |
O3' |
C3' |
C2' |
189.6 |
183.5 |
P |
O3' |
C3' |
H3' |
69.1 |
55.9 |
HOP2 |
O2P |
P |
O5' |
57.9 |
300.0 |
HOP2 |
O2P |
P |
O3' |
304.3 |
178.5 |
C5' |
O5' |
P |
O3' |
39.2 |
304.9 |
C4' |
C5' |
O5' |
H5'1 |
234.8 |
119.5 |
C4' |
C5' |
O5' |
H5'2 |
125.3 |
240.4 |
O5' |
C5' |
C4' |
O4' |
218.2 |
176.9 |
O5' |
C5' |
C4' |
C3' |
331.4 |
291.8 |
O5' |
C5' |
C4' |
H4' |
94.6 |
51.8 |
H5'1 |
C5' |
O5' |
H5'2 |
250.5 |
120.9 |
O5' |
C5' |
C4' |
H5'1 |
125.3 |
240.5 |
O5' |
C5' |
C4' |
H5'2 |
234.7 |
119.5 |
H5'1 |
C5' |
C4' |
H5'2 |
109.5 |
239.0 |
O4' |
C4' |
C5' |
C3' |
246.8 |
245.1 |
O4' |
C4' |
C5' |
H4' |
123.6 |
125.1 |
C5' |
C4' |
O4' |
C1' |
149.8 |
161.2 |
C3' |
C4' |
C5' |
H4' |
236.7 |
239.9 |
C5' |
C4' |
C3' |
O3' |
72.4 |
72.9 |
C5' |
C4' |
C3' |
C2' |
195.5 |
194.3 |
C5' |
C4' |
C3' |
H3' |
314.6 |
312.3 |
O5' |
C5' |
H5'1 |
C4' |
235.5 |
118.2 |
O5' |
C5' |
H5'1 |
H5'2 |
117.8 |
239.2 |
C4' |
C5' |
H5'1 |
H5'2 |
242.3 |
120.9 |
H5'1 |
C5' |
C4' |
O4' |
92.9 |
296.4 |
H5'1 |
C5' |
C4' |
C3' |
206.1 |
51.3 |
H5'1 |
C5' |
C4' |
H4' |
329.4 |
171.3 |
O5' |
C5' |
H5'2 |
C4' |
124.5 |
241.7 |
O5' |
C5' |
H5'2 |
H5'1 |
242.2 |
120.8 |
C4' |
C5' |
H5'2 |
H5'1 |
117.7 |
239.1 |
H5'2 |
C5' |
C4' |
O4' |
343.5 |
57.4 |
H5'2 |
C5' |
C4' |
C3' |
96.7 |
172.2 |
H5'2 |
C5' |
C4' |
H4' |
219.9 |
292.3 |
O4' |
C4' |
C5' |
H5'1 |
92.9 |
296.4 |
O4' |
C4' |
C5' |
H5'2 |
343.5 |
57.4 |
C5' |
C4' |
O4' |
C3' |
119.8 |
117.9 |
C5' |
C4' |
O4' |
H4' |
242.5 |
235.0 |
C3' |
C4' |
O4' |
H4' |
122.7 |
117.1 |
O4' |
C4' |
C3' |
O3' |
191.8 |
195.9 |
O4' |
C4' |
C3' |
C2' |
314.8 |
317.4 |
O4' |
C4' |
C3' |
H3' |
73.9 |
75.3 |
C4' |
O4' |
C1' |
C2' |
357.2 |
333.3 |
C4' |
O4' |
C1' |
N9 |
232.0 |
213.8 |
C4' |
O4' |
C1' |
H1' |
115.2 |
92.8 |
P |
O3' |
C3' |
C4' |
300.7 |
295.4 |
C3' |
C4' |
C5' |
H5'1 |
206.1 |
51.3 |
C3' |
C4' |
C5' |
H5'2 |
96.7 |
172.2 |
C5' |
C4' |
C3' |
O4' |
240.6 |
237.0 |
C5' |
C4' |
C3' |
H4' |
117.5 |
119.9 |
O4' |
C4' |
C3' |
H4' |
236.9 |
243.0 |
C3' |
C4' |
O4' |
C1' |
30.0 |
43.4 |
O3' |
C3' |
C4' |
C2' |
236.9 |
238.6 |
O3' |
C3' |
C4' |
H3' |
117.8 |
120.7 |
C2' |
C3' |
C4' |
H3' |
240.9 |
242.1 |
C4' |
C3' |
C2' |
O2' |
287.5 |
266.4 |
C4' |
C3' |
C2' |
C1' |
42.7 |
25.5 |
C4' |
C3' |
C2' |
H2' |
167.5 |
143.5 |
H4' |
C4' |
C5' |
H5'1 |
329.4 |
171.3 |
H4' |
C4' |
C5' |
H5'2 |
219.9 |
292.3 |
C5' |
C4' |
H4' |
O4' |
121.9 |
128.4 |
C5' |
C4' |
H4' |
C3' |
237.7 |
241.0 |
O4' |
C4' |
H4' |
C3' |
115.8 |
112.6 |
H4' |
C4' |
O4' |
C1' |
267.3 |
286.3 |
H4' |
C4' |
C3' |
O3' |
314.9 |
313.0 |
H4' |
C4' |
C3' |
C2' |
78.0 |
74.4 |
H4' |
C4' |
C3' |
H3' |
197.1 |
192.3 |
C1' |
O4' |
C4' |
C3' |
30.0 |
43.4 |
C1' |
O4' |
C4' |
H4' |
267.3 |
286.3 |
C3' |
C2' |
C1' |
O4' |
334.7 |
359.0 |
O2' |
C2' |
C1' |
O4' |
91.4 |
117.6 |
O4' |
C1' |
C2' |
H2' |
211.1 |
240.8 |
C2' |
C1' |
O4' |
N9 |
125.2 |
119.5 |
C2' |
C1' |
O4' |
H1' |
242.0 |
240.6 |
N9 |
C1' |
O4' |
H1' |
116.8 |
121.1 |
O4' |
C1' |
N9 |
C8 |
42.2 |
28.2 |
O4' |
C1' |
N9 |
C4 |
223.7 |
208.3 |
O3' |
C3' |
C4' |
H4' |
314.9 |
313.0 |
C4' |
C3' |
O3' |
C2' |
111.1 |
111.9 |
C4' |
C3' |
O3' |
H3' |
231.6 |
239.5 |
C2' |
C3' |
O3' |
H3' |
120.5 |
127.6 |
O3' |
C3' |
C2' |
O2' |
40.4 |
21.9 |
O3' |
C3' |
C2' |
C1' |
155.6 |
141.0 |
O3' |
C3' |
C2' |
H2' |
280.5 |
259.1 |
C2' |
C3' |
C4' |
H4' |
78.0 |
74.4 |
C4' |
C3' |
C2' |
O3' |
247.0 |
244.5 |
C4' |
C3' |
C2' |
H3' |
128.1 |
117.2 |
O4' |
C1' |
C2' |
C3' |
334.7 |
359.0 |
O3' |
C3' |
C2' |
H3' |
241.1 |
232.7 |
O2' |
C2' |
C3' |
C1' |
244.8 |
240.9 |
O2' |
C2' |
C3' |
H2' |
120.0 |
122.9 |
C3' |
C2' |
O2' |
HO2' |
180.0 |
180.0 |
C1' |
C2' |
C3' |
H2' |
235.2 |
242.0 |
C3' |
C2' |
C1' |
N9 |
95.5 |
118.5 |
C3' |
C2' |
C1' |
H1' |
212.0 |
239.5 |
H3' |
C3' |
C4' |
H4' |
197.1 |
192.3 |
C4' |
C3' |
H3' |
O3' |
117.5 |
118.7 |
C4' |
C3' |
H3' |
C2' |
244.4 |
248.6 |
O3' |
C3' |
H3' |
C2' |
126.9 |
129.9 |
H3' |
C3' |
C2' |
O2' |
159.3 |
149.2 |
H3' |
C3' |
C2' |
C1' |
274.5 |
268.3 |
H3' |
C3' |
C2' |
H2' |
39.3 |
26.4 |
O4' |
C1' |
C2' |
O2' |
91.4 |
117.6 |
O2' |
C2' |
C3' |
H3' |
159.3 |
149.2 |
C3' |
C2' |
O2' |
C1' |
109.4 |
114.0 |
C3' |
C2' |
O2' |
H2' |
235.1 |
237.1 |
C1' |
C2' |
O2' |
H2' |
125.8 |
123.1 |
O2' |
C2' |
C1' |
N9 |
212.2 |
237.1 |
O2' |
C2' |
C1' |
H1' |
328.7 |
358.2 |
O4' |
C1' |
C2' |
N9 |
239.2 |
240.5 |
O4' |
C1' |
C2' |
H1' |
122.7 |
119.4 |
C1' |
C2' |
C3' |
H3' |
274.5 |
268.3 |
C3' |
C2' |
C1' |
O2' |
243.3 |
241.4 |
C3' |
C2' |
C1' |
H2' |
123.6 |
118.2 |
O2' |
C2' |
C1' |
H2' |
240.3 |
236.8 |
C1' |
C2' |
O2' |
HO2' |
70.6 |
66.0 |
N9 |
C1' |
C2' |
H1' |
243.5 |
239.0 |
C2' |
C1' |
N9 |
C8 |
282.4 |
270.3 |
C2' |
C1' |
N9 |
C4 |
103.9 |
90.4 |
H2' |
C2' |
C3' |
H3' |
39.3 |
26.4 |
C3' |
C2' |
H2' |
O2' |
122.8 |
122.9 |
C3' |
C2' |
H2' |
C1' |
244.2 |
246.5 |
O2' |
C2' |
H2' |
C1' |
121.4 |
123.6 |
H2' |
C2' |
O2' |
HO2' |
304.9 |
302.9 |
H2' |
C2' |
C1' |
N9 |
331.9 |
0.3 |
H2' |
C2' |
C1' |
H1' |
88.4 |
121.4 |
HO2' |
O2' |
C2' |
C1' |
70.6 |
66.0 |
HO2' |
O2' |
C2' |
H2' |
304.9 |
302.9 |
O4' |
C1' |
N9 |
C2' |
119.8 |
117.9 |
O4' |
C1' |
N9 |
H1' |
237.4 |
238.9 |
N9 |
C1' |
C2' |
H2' |
331.9 |
0.3 |
C2' |
C1' |
N9 |
H1' |
117.6 |
121.0 |
C8 |
N9 |
C1' |
C4 |
178.4 |
179.9 |
C1' |
N9 |
C8 |
N7 |
182.8 |
180.0 |
C1' |
N9 |
C8 |
H8 |
2.8 |
0.0 |
C1' |
N9 |
C4 |
C5 |
177.7 |
180.2 |
C1' |
N9 |
C4 |
N3 |
358.2 |
360.0 |
O4' |
C1' |
H1' |
C2' |
242.2 |
242.1 |
O4' |
C1' |
H1' |
N9 |
118.8 |
121.1 |
H1' |
C1' |
C2' |
H2' |
88.4 |
121.4 |
C2' |
C1' |
H1' |
N9 |
236.6 |
239.0 |
H1' |
C1' |
N9 |
C8 |
164.8 |
149.2 |
H1' |
C1' |
N9 |
C4 |
346.3 |
329.3 |
C8 |
N9 |
C1' |
H1' |
164.8 |
149.2 |
C1' |
N9 |
C8 |
C4 |
181.4 |
180.1 |
C8 |
N9 |
C4 |
C5 |
358.9 |
0.3 |
C8 |
N9 |
C4 |
N3 |
179.5 |
180.0 |
N7 |
C8 |
N9 |
H8 |
180.0 |
180.0 |
N9 |
C8 |
N7 |
C5 |
358.9 |
359.8 |
C4 |
N9 |
C1' |
H1' |
346.3 |
329.3 |
C1' |
N9 |
C4 |
C8 |
178.8 |
179.9 |
C4 |
N9 |
C8 |
N7 |
1.4 |
360.0 |
C4 |
N9 |
C8 |
H8 |
181.4 |
179.9 |
N7 |
C5 |
C4 |
N9 |
0.5 |
359.6 |
C6 |
C5 |
C4 |
N9 |
180.4 |
180.4 |
C5 |
C4 |
N9 |
N3 |
179.4 |
180.2 |
C2 |
N3 |
C4 |
N9 |
179.2 |
180.0 |
N7 |
C8 |
N9 |
C4 |
1.4 |
360.0 |
N9 |
C8 |
N7 |
H8 |
180.0 |
180.0 |
C8 |
N7 |
C5 |
C6 |
180.4 |
179.4 |
C8 |
N7 |
C5 |
C4 |
0.3 |
0.4 |
H8 |
C8 |
N9 |
C4 |
181.4 |
179.9 |
N9 |
C8 |
H8 |
N7 |
180.0 |
180.0 |
H8 |
C8 |
N7 |
C5 |
178.9 |
179.8 |
N9 |
C4 |
C5 |
N7 |
0.5 |
359.6 |
C5 |
N7 |
C8 |
H8 |
178.9 |
179.8 |
C6 |
C5 |
N7 |
C4 |
180.1 |
179.0 |
N7 |
C5 |
C6 |
N6 |
0.1 |
0.8 |
N7 |
C5 |
C6 |
N1 |
180.3 |
180.5 |
N7 |
C5 |
C4 |
N3 |
180.0 |
179.8 |
N9 |
C4 |
C5 |
C6 |
180.4 |
180.4 |
N7 |
C5 |
C6 |
C4 |
179.9 |
181.0 |
C6 |
C5 |
C4 |
N3 |
359.9 |
0.6 |
N6 |
C6 |
C5 |
N1 |
179.8 |
180.3 |
C5 |
C6 |
N6 |
HN61 |
180.0 |
179.7 |
C5 |
C6 |
N6 |
HN62 |
54.8 |
359.4 |
C5 |
C6 |
N1 |
C2 |
359.6 |
0.2 |
N9 |
C4 |
C5 |
N3 |
180.5 |
179.8 |
N7 |
C5 |
C4 |
C6 |
180.1 |
179.2 |
C4 |
C5 |
C6 |
N6 |
180.2 |
179.8 |
C4 |
C5 |
C6 |
N1 |
0.4 |
359.5 |
C2 |
N3 |
C4 |
C5 |
359.9 |
359.7 |
N6 |
C6 |
C5 |
C4 |
180.2 |
179.8 |
C5 |
C6 |
N6 |
N1 |
180.2 |
179.7 |
N6 |
C6 |
N1 |
C2 |
179.8 |
179.9 |
HN61 |
N6 |
C6 |
HN62 |
125.2 |
180.3 |
N1 |
C6 |
C5 |
C4 |
0.4 |
359.5 |
C5 |
C6 |
N1 |
N6 |
179.8 |
180.3 |
N1 |
C6 |
N6 |
HN61 |
359.8 |
0.0 |
N1 |
C6 |
N6 |
HN62 |
234.6 |
179.7 |
C6 |
N1 |
C2 |
N3 |
0.1 |
0.1 |
C6 |
N1 |
C2 |
H2 |
180.1 |
180.0 |
HN61 |
N6 |
C6 |
N1 |
359.8 |
0.0 |
C6 |
N6 |
HN61 |
HN62 |
234.8 |
179.7 |
HN62 |
N6 |
C6 |
N1 |
234.6 |
179.7 |
C6 |
N6 |
HN62 |
HN61 |
134.1 |
180.3 |
N3 |
C2 |
N1 |
H2 |
180.0 |
180.1 |
N1 |
C2 |
N3 |
C4 |
0.2 |
359.9 |
N9 |
C4 |
N3 |
C2 |
179.2 |
180.0 |
C5 |
C4 |
N3 |
C2 |
359.9 |
359.7 |
N1 |
C2 |
N3 |
H2 |
180.0 |
179.9 |
N1 |
C2 |
H2 |
N3 |
180.0 |
180.1 |
H2 |
C2 |
N3 |
C4 |
180.2 |
180.0 |
N9 |
C4 |
N3 |
C5 |
179.3 |
180.3 |
C4 |
N3 |
C2 |
H2 |
180.2 |
180.0 |