PDB Chemical Component DCM
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 DCM
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| N1 |
C2 |
1.410 |
1.344 |
| N1 |
C6 |
1.372 |
1.362 |
| N1 |
C1' |
1.476 |
1.465 |
| C2 |
N3 |
1.342 |
1.332 |
| C2 |
O2 |
1.241 |
1.220 |
| N3 |
C4 |
1.341 |
1.326 |
| C4 |
C5 |
1.430 |
1.410 |
| C4 |
N4 |
1.335 |
1.376 |
| C5 |
C6 |
1.342 |
1.353 |
| C5 |
H5 |
1.103 |
1.081 |
| C6 |
H6 |
1.103 |
1.080 |
| N4 |
HN41 |
1.019 |
0.970 |
| N4 |
HN42 |
1.020 |
0.970 |
| C1' |
C2' |
1.527 |
1.541 |
| C1' |
O4' |
1.418 |
1.437 |
| C1' |
H1' |
1.115 |
1.090 |
| C2' |
C3' |
1.523 |
1.547 |
| C2' |
H2'1 |
1.115 |
1.089 |
| C2' |
H2'2 |
1.115 |
1.091 |
| C3' |
C4' |
1.525 |
1.549 |
| C3' |
O3' |
1.421 |
1.429 |
| C3' |
H3' |
1.115 |
1.090 |
| C4' |
O4' |
1.458 |
1.445 |
| C4' |
C5' |
1.516 |
1.530 |
| C4' |
H4' |
1.115 |
1.090 |
| O3' |
HO3' |
0.950 |
0.968 |
| C5' |
O5' |
1.453 |
1.428 |
| C5' |
H5'1 |
1.116 |
1.090 |
| C5' |
H5'2 |
1.115 |
1.089 |
| O5' |
P |
1.599 |
1.611 |
| P |
O1P |
1.489 |
1.480 |
| P |
O2P |
1.494 |
1.610 |
| P |
O3P |
1.489 |
1.609 |
| O2P |
HOP2 |
0.950 |
0.967 |
| O3P |
HOP3 |
0.950 |
0.967 |
Bond Angles for DCM
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C2 |
N1 |
C6 |
120.0 |
120.3 |
| C2 |
N1 |
C1' |
118.5 |
119.8 |
| N1 |
C2 |
N3 |
119.3 |
121.1 |
| N1 |
C2 |
O2 |
118.9 |
119.5 |
| C6 |
N1 |
C1' |
120.8 |
119.8 |
| N1 |
C6 |
C5 |
121.2 |
119.3 |
| N1 |
C6 |
H6 |
120.5 |
120.4 |
| N1 |
C1' |
C2' |
114.4 |
109.9 |
| N1 |
C1' |
O4' |
109.0 |
109.9 |
| N1 |
C1' |
H1' |
105.4 |
109.9 |
| N3 |
C2 |
O2 |
121.9 |
119.5 |
| C2 |
N3 |
C4 |
120.3 |
120.7 |
| N3 |
C4 |
C5 |
121.8 |
119.6 |
| N3 |
C4 |
N4 |
118.2 |
120.2 |
| C5 |
C4 |
N4 |
120.0 |
120.2 |
| C4 |
C5 |
C6 |
117.3 |
119.0 |
| C4 |
C5 |
H5 |
124.4 |
120.5 |
| C4 |
N4 |
HN41 |
118.1 |
120.0 |
| C4 |
N4 |
HN42 |
109.1 |
120.0 |
| C6 |
C5 |
H5 |
118.3 |
120.5 |
| C5 |
C6 |
H6 |
118.3 |
120.4 |
| HN41 |
N4 |
HN42 |
109.1 |
120.0 |
| C2' |
C1' |
O4' |
105.8 |
107.4 |
| C2' |
C1' |
H1' |
108.5 |
109.8 |
| C1' |
C2' |
C3' |
100.7 |
104.2 |
| C1' |
C2' |
H2'1 |
115.6 |
110.5 |
| C1' |
C2' |
H2'2 |
115.7 |
110.4 |
| O4' |
C1' |
H1' |
114.0 |
109.9 |
| C1' |
O4' |
C4' |
109.7 |
106.9 |
| C3' |
C2' |
H2'1 |
115.6 |
110.5 |
| C3' |
C2' |
H2'2 |
115.6 |
110.5 |
| C2' |
C3' |
C4' |
102.3 |
102.1 |
| C2' |
C3' |
O3' |
111.1 |
110.9 |
| C2' |
C3' |
H3' |
113.1 |
110.9 |
| H2'1 |
C2' |
H2'2 |
94.8 |
110.5 |
| C4' |
C3' |
O3' |
109.6 |
110.9 |
| C4' |
C3' |
H3' |
114.5 |
110.9 |
| C3' |
C4' |
O4' |
105.3 |
103.6 |
| C3' |
C4' |
C5' |
115.2 |
110.7 |
| C3' |
C4' |
H4' |
108.5 |
110.6 |
| O3' |
C3' |
H3' |
106.3 |
110.8 |
| C3' |
O3' |
HO3' |
111.1 |
106.7 |
| O4' |
C4' |
C5' |
109.6 |
110.8 |
| O4' |
C4' |
H4' |
114.3 |
110.5 |
| C5' |
C4' |
H4' |
104.2 |
110.5 |
| C4' |
C5' |
O5' |
110.2 |
109.5 |
| C4' |
C5' |
H5'1 |
112.0 |
109.4 |
| C4' |
C5' |
H5'2 |
112.0 |
109.4 |
| O5' |
C5' |
H5'1 |
111.9 |
109.5 |
| O5' |
C5' |
H5'2 |
111.9 |
109.6 |
| C5' |
O5' |
P |
121.6 |
106.8 |
| H5'1 |
C5' |
H5'2 |
98.5 |
109.4 |
| O5' |
P |
O1P |
100.7 |
109.5 |
| O5' |
P |
O2P |
100.8 |
109.5 |
| O5' |
P |
O3P |
98.1 |
109.5 |
| O1P |
P |
O2P |
116.9 |
109.4 |
| O1P |
P |
O3P |
117.4 |
109.5 |
| O2P |
P |
O3P |
117.1 |
109.5 |
| P |
O2P |
HOP2 |
100.7 |
106.8 |
| P |
O3P |
HOP3 |
98.1 |
106.8 |
Torsion Angles for DCM
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C6 |
N1 |
C2 |
C1' |
189.8 |
180.0 |
| C2 |
N1 |
C6 |
C5 |
358.8 |
359.7 |
| C2 |
N1 |
C6 |
H6 |
178.8 |
179.9 |
| C2 |
N1 |
C1' |
C2' |
68.7 |
300.3 |
| C2 |
N1 |
C1' |
O4' |
187.0 |
58.3 |
| C2 |
N1 |
C1' |
H1' |
309.7 |
179.3 |
| N3 |
C2 |
N1 |
O2 |
179.0 |
180.0 |
| N1 |
C2 |
N3 |
C4 |
355.2 |
360.0 |
| C2 |
N1 |
C6 |
C1' |
170.0 |
180.0 |
| C6 |
N1 |
C2 |
N3 |
3.9 |
0.0 |
| C6 |
N1 |
C2 |
O2 |
184.8 |
180.0 |
| C6 |
N1 |
C1' |
C2' |
238.9 |
120.3 |
| C6 |
N1 |
C1' |
O4' |
357.1 |
238.3 |
| C6 |
N1 |
C1' |
H1' |
119.8 |
359.3 |
| C4 |
C5 |
C6 |
N1 |
359.6 |
0.4 |
| N1 |
C6 |
C5 |
H5 |
179.6 |
180.0 |
| C5 |
C6 |
N1 |
H6 |
180.0 |
179.8 |
| C2 |
N1 |
C1' |
C6 |
189.8 |
180.0 |
| C1' |
N1 |
C2 |
N3 |
174.1 |
180.0 |
| C1' |
N1 |
C2 |
O2 |
355.1 |
360.0 |
| C1' |
N1 |
C6 |
C5 |
188.8 |
179.8 |
| C1' |
N1 |
C6 |
H6 |
8.8 |
359.9 |
| C2' |
C1' |
N1 |
O4' |
241.8 |
242.0 |
| C2' |
C1' |
N1 |
H1' |
119.1 |
121.0 |
| N1 |
C1' |
C2' |
C3' |
156.4 |
121.5 |
| N1 |
C1' |
C2' |
H2'1 |
281.6 |
240.2 |
| N1 |
C1' |
C2' |
H2'2 |
31.1 |
2.8 |
| O4' |
C1' |
N1 |
H1' |
237.3 |
238.9 |
| N1 |
C1' |
O4' |
C4' |
217.2 |
214.2 |
| N3 |
C2 |
N1 |
C6 |
3.9 |
0.0 |
| N3 |
C2 |
N1 |
C1' |
174.1 |
180.0 |
| N1 |
C2 |
N3 |
O2 |
181.0 |
180.0 |
| C2 |
N3 |
C4 |
C5 |
3.2 |
0.2 |
| C2 |
N3 |
C4 |
N4 |
184.6 |
180.0 |
| O2 |
C2 |
N1 |
C6 |
184.8 |
180.0 |
| O2 |
C2 |
N1 |
C1' |
355.1 |
360.0 |
| N1 |
C2 |
O2 |
N3 |
179.0 |
180.0 |
| O2 |
C2 |
N3 |
C4 |
174.2 |
180.0 |
| C4 |
N3 |
C2 |
O2 |
174.2 |
180.0 |
| C5 |
C4 |
N3 |
N4 |
178.6 |
180.2 |
| N3 |
C4 |
C5 |
C6 |
359.5 |
359.6 |
| N3 |
C4 |
C5 |
H5 |
179.5 |
180.0 |
| N3 |
C4 |
N4 |
HN41 |
180.0 |
360.0 |
| N3 |
C4 |
N4 |
HN42 |
54.7 |
179.7 |
| N1 |
C6 |
C5 |
C4 |
359.6 |
0.4 |
| N3 |
C4 |
C5 |
N4 |
181.4 |
179.8 |
| C5 |
C4 |
N4 |
HN41 |
1.4 |
179.8 |
| C5 |
C4 |
N4 |
HN42 |
236.1 |
359.5 |
| C6 |
C5 |
C4 |
H5 |
180.0 |
179.6 |
| C4 |
C5 |
C6 |
H6 |
179.6 |
180.3 |
| N3 |
C4 |
N4 |
C5 |
178.6 |
180.2 |
| N4 |
C4 |
C5 |
C6 |
178.1 |
179.8 |
| N4 |
C4 |
C5 |
H5 |
358.0 |
0.2 |
| HN41 |
N4 |
C4 |
HN42 |
125.3 |
180.3 |
| C5 |
C6 |
N1 |
C1' |
188.8 |
179.8 |
| N1 |
C6 |
C5 |
H6 |
180.0 |
180.2 |
| C6 |
C5 |
C4 |
N4 |
178.1 |
179.8 |
| C4 |
C5 |
C6 |
H5 |
180.0 |
180.4 |
| H5 |
C5 |
C4 |
N4 |
358.0 |
0.2 |
| C4 |
C5 |
H5 |
C6 |
180.0 |
179.6 |
| H5 |
C5 |
C6 |
H6 |
359.6 |
359.8 |
| H6 |
C6 |
N1 |
C1' |
8.8 |
359.9 |
| N1 |
C6 |
H6 |
C5 |
180.0 |
179.8 |
| H6 |
C6 |
C5 |
H5 |
359.6 |
359.8 |
| C4 |
N4 |
HN41 |
HN42 |
234.7 |
179.7 |
| C4 |
N4 |
HN42 |
HN41 |
130.4 |
180.3 |
| N1 |
C1' |
C2' |
O4' |
120.0 |
119.5 |
| N1 |
C1' |
C2' |
H1' |
242.7 |
239.0 |
| O4' |
C1' |
C2' |
H1' |
122.7 |
119.5 |
| C2' |
C1' |
O4' |
C4' |
340.8 |
333.7 |
| C3' |
C2' |
C1' |
H2'1 |
234.7 |
241.3 |
| C3' |
C2' |
C1' |
H2'2 |
125.3 |
118.7 |
| C1' |
C2' |
C3' |
C4' |
321.2 |
20.9 |
| C1' |
C2' |
C3' |
O3' |
78.1 |
139.1 |
| C1' |
C2' |
C3' |
H3' |
197.5 |
262.7 |
| H2'1 |
C2' |
C1' |
H2'2 |
250.5 |
237.4 |
| N1 |
C1' |
O4' |
C2' |
236.5 |
240.5 |
| N1 |
C1' |
O4' |
H1' |
117.4 |
121.1 |
| C2' |
C1' |
O4' |
H1' |
240.9 |
240.6 |
| O4' |
C1' |
C2' |
C3' |
36.3 |
1.9 |
| O4' |
C1' |
C2' |
H2'1 |
161.6 |
120.6 |
| O4' |
C1' |
C2' |
H2'2 |
271.1 |
243.3 |
| C3' |
C4' |
O4' |
C1' |
353.9 |
39.9 |
| C1' |
O4' |
C4' |
C5' |
118.4 |
158.6 |
| C1' |
O4' |
C4' |
H4' |
234.9 |
281.4 |
| N1 |
C1' |
H1' |
C2' |
122.9 |
121.0 |
| N1 |
C1' |
H1' |
O4' |
240.5 |
238.9 |
| C2' |
C1' |
H1' |
O4' |
117.6 |
117.9 |
| H1' |
C1' |
C2' |
C3' |
273.6 |
242.5 |
| H1' |
C1' |
C2' |
H2'1 |
38.9 |
1.2 |
| H1' |
C1' |
C2' |
H2'2 |
148.4 |
123.8 |
| H1' |
C1' |
O4' |
C4' |
99.9 |
93.1 |
| C3' |
C2' |
C1' |
O4' |
36.3 |
1.9 |
| C3' |
C2' |
C1' |
H1' |
273.6 |
242.5 |
| C1' |
C2' |
C3' |
H2'1 |
125.3 |
118.7 |
| C1' |
C2' |
C3' |
H2'2 |
234.7 |
241.4 |
| H2'1 |
C2' |
C3' |
H2'2 |
109.4 |
122.7 |
| C4' |
C3' |
C2' |
O3' |
243.1 |
241.8 |
| C4' |
C3' |
C2' |
H3' |
123.7 |
118.2 |
| C2' |
C3' |
C4' |
O4' |
28.7 |
323.0 |
| C2' |
C3' |
C4' |
C5' |
267.8 |
204.3 |
| C2' |
C3' |
C4' |
H4' |
151.4 |
81.4 |
| O3' |
C3' |
C2' |
H3' |
240.6 |
236.5 |
| C2' |
C3' |
O3' |
HO3' |
179.9 |
61.5 |
| H2'1 |
C2' |
C1' |
O4' |
161.6 |
120.6 |
| H2'1 |
C2' |
C1' |
H1' |
38.9 |
1.2 |
| C1' |
C2' |
H2'1 |
C3' |
242.8 |
245.2 |
| C1' |
C2' |
H2'1 |
H2'2 |
121.5 |
122.6 |
| C3' |
C2' |
H2'1 |
H2'2 |
238.6 |
237.3 |
| H2'1 |
C2' |
C3' |
C4' |
196.0 |
262.2 |
| H2'1 |
C2' |
C3' |
O3' |
312.8 |
20.4 |
| H2'1 |
C2' |
C3' |
H3' |
72.2 |
143.9 |
| H2'2 |
C2' |
C1' |
O4' |
271.1 |
243.3 |
| H2'2 |
C2' |
C1' |
H1' |
148.4 |
123.8 |
| C1' |
C2' |
H2'2 |
C3' |
117.2 |
114.7 |
| C1' |
C2' |
H2'2 |
H2'1 |
238.6 |
237.4 |
| C3' |
C2' |
H2'2 |
H2'1 |
121.4 |
122.6 |
| H2'2 |
C2' |
C3' |
C4' |
86.6 |
139.5 |
| H2'2 |
C2' |
C3' |
O3' |
203.4 |
257.7 |
| H2'2 |
C2' |
C3' |
H3' |
322.8 |
21.3 |
| C1' |
O4' |
C4' |
C3' |
353.9 |
39.9 |
| C4' |
C3' |
C2' |
H2'1 |
196.0 |
262.2 |
| C4' |
C3' |
C2' |
H2'2 |
86.6 |
139.5 |
| C2' |
C3' |
C4' |
O3' |
117.9 |
118.2 |
| C2' |
C3' |
C4' |
H3' |
237.2 |
241.7 |
| O3' |
C3' |
C4' |
H3' |
119.3 |
123.5 |
| C4' |
C3' |
O3' |
HO3' |
292.3 |
174.2 |
| O4' |
C4' |
C3' |
C5' |
120.9 |
118.7 |
| O4' |
C4' |
C3' |
H4' |
237.2 |
241.6 |
| C5' |
C4' |
C3' |
H4' |
116.3 |
122.9 |
| C3' |
C4' |
C5' |
O5' |
280.0 |
180.0 |
| C3' |
C4' |
C5' |
H5'1 |
45.2 |
300.0 |
| C3' |
C4' |
C5' |
H5'2 |
154.7 |
59.9 |
| O3' |
C3' |
C2' |
H2'1 |
312.8 |
20.4 |
| O3' |
C3' |
C2' |
H2'2 |
203.4 |
257.7 |
| C2' |
C3' |
O3' |
C4' |
247.7 |
247.3 |
| C2' |
C3' |
O3' |
H3' |
123.4 |
123.6 |
| C4' |
C3' |
O3' |
H3' |
235.7 |
236.4 |
| O3' |
C3' |
C4' |
O4' |
270.7 |
204.8 |
| O3' |
C3' |
C4' |
C5' |
149.8 |
86.1 |
| O3' |
C3' |
C4' |
H4' |
33.5 |
323.2 |
| H3' |
C3' |
C2' |
H2'1 |
72.2 |
143.9 |
| H3' |
C3' |
C2' |
H2'2 |
322.8 |
21.3 |
| C2' |
C3' |
H3' |
C4' |
116.7 |
112.8 |
| C2' |
C3' |
H3' |
O3' |
237.9 |
236.4 |
| C4' |
C3' |
H3' |
O3' |
121.1 |
123.6 |
| H3' |
C3' |
C4' |
O4' |
151.4 |
81.3 |
| H3' |
C3' |
C4' |
C5' |
30.5 |
322.6 |
| H3' |
C3' |
C4' |
H4' |
274.2 |
199.7 |
| H3' |
C3' |
O3' |
HO3' |
56.6 |
297.8 |
| C4' |
O4' |
C1' |
H1' |
99.9 |
93.1 |
| O4' |
C4' |
C3' |
O3' |
270.7 |
204.8 |
| O4' |
C4' |
C3' |
H3' |
151.4 |
81.3 |
| C3' |
C4' |
O4' |
C5' |
235.5 |
241.3 |
| C3' |
C4' |
O4' |
H4' |
119.0 |
118.5 |
| C5' |
C4' |
O4' |
H4' |
243.5 |
237.1 |
| O4' |
C4' |
C5' |
O5' |
161.4 |
65.7 |
| O4' |
C4' |
C5' |
H5'1 |
286.7 |
185.7 |
| O4' |
C4' |
C5' |
H5'2 |
36.2 |
305.6 |
| C5' |
C4' |
C3' |
O3' |
149.8 |
86.1 |
| C5' |
C4' |
C3' |
H3' |
30.5 |
322.6 |
| C3' |
C4' |
C5' |
O4' |
118.6 |
114.3 |
| C3' |
C4' |
C5' |
H4' |
241.2 |
237.1 |
| O4' |
C4' |
C5' |
H4' |
122.7 |
122.8 |
| O5' |
C5' |
C4' |
H5'1 |
234.8 |
240.0 |
| O5' |
C5' |
C4' |
H5'2 |
125.3 |
120.1 |
| C4' |
C5' |
O5' |
P |
141.0 |
180.0 |
| H5'1 |
C5' |
C4' |
H5'2 |
250.5 |
240.1 |
| H4' |
C4' |
C3' |
O3' |
33.5 |
323.2 |
| H4' |
C4' |
C3' |
H3' |
274.2 |
199.7 |
| C3' |
C4' |
H4' |
O4' |
242.8 |
245.9 |
| C3' |
C4' |
H4' |
C5' |
123.2 |
122.9 |
| O4' |
C4' |
H4' |
C5' |
240.4 |
237.0 |
| H4' |
C4' |
C5' |
O5' |
38.8 |
302.9 |
| H4' |
C4' |
C5' |
H5'1 |
164.0 |
62.9 |
| H4' |
C4' |
C5' |
H5'2 |
273.5 |
182.8 |
| HO3' |
O3' |
C3' |
H3' |
56.6 |
297.8 |
| O5' |
C5' |
C4' |
H4' |
38.8 |
302.9 |
| C4' |
C5' |
O5' |
H5'1 |
125.2 |
120.0 |
| C4' |
C5' |
O5' |
H5'2 |
234.7 |
240.0 |
| H5'1 |
C5' |
O5' |
H5'2 |
109.5 |
120.0 |
| C5' |
O5' |
P |
O1P |
300.7 |
60.0 |
| C5' |
O5' |
P |
O2P |
61.0 |
180.0 |
| C5' |
O5' |
P |
O3P |
180.7 |
300.0 |
| H5'1 |
C5' |
C4' |
H4' |
164.0 |
62.9 |
| C4' |
C5' |
H5'1 |
O5' |
235.7 |
240.0 |
| C4' |
C5' |
H5'1 |
H5'2 |
117.9 |
119.9 |
| O5' |
C5' |
H5'1 |
H5'2 |
242.2 |
239.9 |
| H5'1 |
C5' |
O5' |
P |
15.8 |
60.0 |
| H5'2 |
C5' |
C4' |
H4' |
273.5 |
182.8 |
| C4' |
C5' |
H5'2 |
O5' |
124.3 |
120.0 |
| C4' |
C5' |
H5'2 |
H5'1 |
242.1 |
240.1 |
| O5' |
C5' |
H5'2 |
H5'1 |
117.8 |
120.1 |
| H5'2 |
C5' |
O5' |
P |
266.3 |
300.0 |
| P |
O5' |
C5' |
H5'1 |
15.8 |
60.0 |
| P |
O5' |
C5' |
H5'2 |
266.3 |
300.0 |
| O1P |
P |
O5' |
O2P |
239.7 |
240.1 |
| O1P |
P |
O5' |
O3P |
120.0 |
120.1 |
| O2P |
P |
O5' |
O3P |
240.3 |
240.0 |
| O5' |
P |
O2P |
HOP2 |
180.0 |
180.0 |
| O5' |
P |
O3P |
HOP3 |
180.0 |
300.0 |
| O5' |
P |
O1P |
O2P |
108.0 |
119.9 |
| O5' |
P |
O1P |
O3P |
254.9 |
239.9 |
| O2P |
P |
O1P |
O3P |
146.9 |
120.0 |
| O1P |
P |
O2P |
HOP2 |
288.0 |
300.0 |
| O1P |
P |
O3P |
HOP3 |
73.4 |
180.0 |
| O5' |
P |
O2P |
O1P |
252.1 |
240.1 |
| O5' |
P |
O2P |
O3P |
105.0 |
120.0 |
| O1P |
P |
O2P |
O3P |
213.0 |
240.0 |
| O2P |
P |
O3P |
HOP3 |
286.5 |
60.0 |
| O5' |
P |
O3P |
O1P |
106.6 |
120.0 |
| O5' |
P |
O3P |
O2P |
253.4 |
240.0 |
| O1P |
P |
O3P |
O2P |
146.9 |
120.0 |
| O3P |
P |
O2P |
HOP2 |
75.0 |
60.0 |
| HOP2 |
O2P |
P |
O3P |
75.0 |
60.0 |