PDB Chemical Component DOC
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 DOC
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| N1 |
C2 |
1.422 |
1.344 |
| N1 |
C6 |
1.362 |
1.363 |
| N1 |
C1' |
1.478 |
1.465 |
| C2 |
N3 |
1.338 |
1.332 |
| C2 |
O2 |
1.256 |
1.220 |
| N3 |
C4 |
1.315 |
1.326 |
| C4 |
C5 |
1.448 |
1.409 |
| C4 |
N4 |
1.329 |
1.376 |
| C5 |
C6 |
1.352 |
1.354 |
| C5 |
H5 |
1.103 |
1.080 |
| C6 |
H6 |
1.103 |
1.080 |
| N4 |
HN41 |
1.019 |
0.969 |
| N4 |
HN42 |
1.019 |
0.970 |
| C1' |
C2' |
1.519 |
1.540 |
| C1' |
O4' |
1.408 |
1.437 |
| C1' |
H1' |
1.115 |
1.090 |
| C2' |
C3' |
1.530 |
1.548 |
| C2' |
H2' |
1.116 |
1.090 |
| C2' |
H2'' |
1.116 |
1.090 |
| C3' |
C4' |
1.537 |
1.549 |
| C3' |
H3'1 |
1.115 |
1.090 |
| C3' |
H3'2 |
1.116 |
1.090 |
| C4' |
O4' |
1.437 |
1.445 |
| C4' |
C5' |
1.508 |
1.529 |
| C4' |
H4' |
1.115 |
1.090 |
| C5' |
O5' |
1.409 |
1.428 |
| C5' |
H5' |
1.114 |
1.090 |
| C5' |
H5'' |
1.115 |
1.090 |
| O5' |
P |
1.603 |
1.610 |
| P |
OP1 |
1.479 |
1.479 |
| P |
OP2 |
1.471 |
1.610 |
| P |
OP3 |
1.569 |
1.609 |
| OP2 |
HOP2 |
0.950 |
0.967 |
| OP3 |
HOP3 |
0.950 |
0.966 |
Bond Angles for DOC
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C2 |
N1 |
C6 |
120.7 |
120.3 |
| C2 |
N1 |
C1' |
118.5 |
119.8 |
| N1 |
C2 |
N3 |
119.1 |
121.1 |
| N1 |
C2 |
O2 |
119.9 |
119.5 |
| C6 |
N1 |
C1' |
120.8 |
119.8 |
| N1 |
C6 |
C5 |
120.1 |
119.3 |
| N1 |
C6 |
H6 |
120.3 |
120.3 |
| N1 |
C1' |
C2' |
120.7 |
109.9 |
| N1 |
C1' |
O4' |
109.3 |
109.9 |
| N1 |
C1' |
H1' |
101.8 |
109.9 |
| N3 |
C2 |
O2 |
120.9 |
119.4 |
| C2 |
N3 |
C4 |
120.7 |
120.7 |
| N3 |
C4 |
C5 |
121.9 |
119.6 |
| N3 |
C4 |
N4 |
116.4 |
120.2 |
| C5 |
C4 |
N4 |
121.6 |
120.2 |
| C4 |
C5 |
C6 |
117.4 |
119.0 |
| C4 |
C5 |
H5 |
124.5 |
120.5 |
| C4 |
N4 |
HN41 |
116.4 |
120.0 |
| C4 |
N4 |
HN42 |
109.7 |
119.9 |
| C6 |
C5 |
H5 |
118.1 |
120.5 |
| C5 |
C6 |
H6 |
119.6 |
120.4 |
| HN41 |
N4 |
HN42 |
109.7 |
120.0 |
| C2' |
C1' |
O4' |
111.1 |
107.5 |
| C2' |
C1' |
H1' |
99.6 |
109.9 |
| C1' |
C2' |
C3' |
103.3 |
104.2 |
| C1' |
C2' |
H2' |
114.6 |
110.6 |
| C1' |
C2' |
H2'' |
114.6 |
110.6 |
| O4' |
C1' |
H1' |
113.6 |
109.9 |
| C1' |
O4' |
C4' |
110.6 |
106.8 |
| C3' |
C2' |
H2' |
114.6 |
110.4 |
| C3' |
C2' |
H2'' |
114.6 |
110.4 |
| C2' |
C3' |
C4' |
107.2 |
102.1 |
| C2' |
C3' |
H3'1 |
113.0 |
110.9 |
| C2' |
C3' |
H3'2 |
113.1 |
110.9 |
| H2' |
C2' |
H2'' |
95.8 |
110.5 |
| C4' |
C3' |
H3'1 |
113.1 |
110.9 |
| C4' |
C3' |
H3'2 |
113.1 |
110.9 |
| C3' |
C4' |
O4' |
107.1 |
103.6 |
| C3' |
C4' |
C5' |
114.6 |
110.7 |
| C3' |
C4' |
H4' |
107.0 |
110.6 |
| H3'1 |
C3' |
H3'2 |
97.4 |
110.9 |
| O4' |
C4' |
C5' |
107.6 |
110.8 |
| O4' |
C4' |
H4' |
114.2 |
110.5 |
| C5' |
C4' |
H4' |
106.6 |
110.5 |
| C4' |
C5' |
O5' |
110.7 |
109.6 |
| C4' |
C5' |
H5' |
111.7 |
109.5 |
| C4' |
C5' |
H5'' |
111.7 |
109.4 |
| O5' |
C5' |
H5' |
111.8 |
109.5 |
| O5' |
C5' |
H5'' |
111.7 |
109.5 |
| C5' |
O5' |
P |
114.5 |
106.8 |
| H5' |
C5' |
H5'' |
98.7 |
109.4 |
| O5' |
P |
OP1 |
112.3 |
109.5 |
| O5' |
P |
OP2 |
107.1 |
109.5 |
| O5' |
P |
OP3 |
101.6 |
109.5 |
| OP1 |
P |
OP2 |
122.3 |
109.5 |
| OP1 |
P |
OP3 |
103.2 |
109.5 |
| OP2 |
P |
OP3 |
108.3 |
109.4 |
| P |
OP2 |
HOP2 |
107.1 |
106.8 |
| P |
OP3 |
HOP3 |
101.6 |
106.9 |
Torsion Angles for DOC
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C6 |
N1 |
C2 |
C1' |
181.6 |
180.0 |
| C2 |
N1 |
C6 |
C5 |
359.4 |
359.7 |
| C2 |
N1 |
C6 |
H6 |
179.5 |
180.0 |
| C2 |
N1 |
C1' |
C2' |
94.8 |
300.3 |
| C2 |
N1 |
C1' |
O4' |
225.4 |
58.3 |
| C2 |
N1 |
C1' |
H1' |
345.9 |
179.3 |
| N3 |
C2 |
N1 |
O2 |
180.1 |
180.0 |
| N1 |
C2 |
N3 |
C4 |
0.1 |
0.0 |
| C2 |
N1 |
C6 |
C1' |
178.4 |
180.0 |
| C6 |
N1 |
C2 |
N3 |
0.3 |
0.0 |
| C6 |
N1 |
C2 |
O2 |
180.2 |
180.0 |
| C6 |
N1 |
C1' |
C2' |
273.2 |
120.3 |
| C6 |
N1 |
C1' |
O4' |
43.8 |
238.3 |
| C6 |
N1 |
C1' |
H1' |
164.3 |
359.3 |
| C4 |
C5 |
C6 |
N1 |
0.4 |
0.4 |
| N1 |
C6 |
C5 |
H5 |
180.4 |
180.0 |
| C5 |
C6 |
N1 |
H6 |
179.9 |
179.7 |
| C2 |
N1 |
C1' |
C6 |
181.6 |
180.0 |
| C1' |
N1 |
C2 |
N3 |
178.7 |
180.0 |
| C1' |
N1 |
C2 |
O2 |
358.6 |
0.0 |
| C1' |
N1 |
C6 |
C5 |
181.1 |
179.8 |
| C1' |
N1 |
C6 |
H6 |
1.1 |
0.0 |
| C2' |
C1' |
N1 |
O4' |
229.4 |
242.0 |
| C2' |
C1' |
N1 |
H1' |
108.9 |
121.0 |
| N1 |
C1' |
C2' |
C3' |
138.7 |
121.4 |
| N1 |
C1' |
C2' |
H2' |
264.0 |
240.1 |
| N1 |
C1' |
C2' |
H2'' |
13.4 |
2.8 |
| O4' |
C1' |
N1 |
H1' |
239.5 |
239.0 |
| N1 |
C1' |
O4' |
C4' |
215.9 |
214.2 |
| N3 |
C2 |
N1 |
C6 |
0.3 |
0.0 |
| N3 |
C2 |
N1 |
C1' |
178.7 |
180.0 |
| N1 |
C2 |
N3 |
O2 |
179.9 |
180.0 |
| C2 |
N3 |
C4 |
C5 |
359.8 |
0.1 |
| C2 |
N3 |
C4 |
N4 |
180.2 |
180.0 |
| O2 |
C2 |
N1 |
C6 |
180.2 |
180.0 |
| O2 |
C2 |
N1 |
C1' |
358.6 |
0.0 |
| N1 |
C2 |
O2 |
N3 |
180.1 |
180.0 |
| O2 |
C2 |
N3 |
C4 |
180.1 |
180.0 |
| C4 |
N3 |
C2 |
O2 |
180.1 |
180.0 |
| C5 |
C4 |
N3 |
N4 |
179.5 |
180.2 |
| N3 |
C4 |
C5 |
C6 |
0.0 |
359.6 |
| N3 |
C4 |
C5 |
H5 |
179.9 |
180.1 |
| N3 |
C4 |
N4 |
HN41 |
180.0 |
359.9 |
| N3 |
C4 |
N4 |
HN42 |
54.7 |
179.7 |
| N1 |
C6 |
C5 |
C4 |
0.4 |
0.4 |
| N3 |
C4 |
C5 |
N4 |
180.5 |
179.8 |
| C5 |
C4 |
N4 |
HN41 |
0.5 |
179.8 |
| C5 |
C4 |
N4 |
HN42 |
235.2 |
359.5 |
| C6 |
C5 |
C4 |
H5 |
180.1 |
179.5 |
| C4 |
C5 |
C6 |
H6 |
180.3 |
180.2 |
| N3 |
C4 |
N4 |
C5 |
179.5 |
180.2 |
| N4 |
C4 |
C5 |
C6 |
179.5 |
179.8 |
| N4 |
C4 |
C5 |
H5 |
359.5 |
0.2 |
| HN41 |
N4 |
C4 |
HN42 |
125.3 |
180.3 |
| C5 |
C6 |
N1 |
C1' |
181.1 |
179.8 |
| N1 |
C6 |
C5 |
H6 |
180.1 |
180.3 |
| C6 |
C5 |
C4 |
N4 |
179.5 |
179.8 |
| C4 |
C5 |
C6 |
H5 |
179.9 |
180.5 |
| H5 |
C5 |
C4 |
N4 |
359.5 |
0.2 |
| C4 |
C5 |
H5 |
C6 |
180.1 |
179.5 |
| H5 |
C5 |
C6 |
H6 |
0.4 |
359.7 |
| H6 |
C6 |
N1 |
C1' |
1.1 |
0.0 |
| N1 |
C6 |
H6 |
C5 |
179.9 |
179.7 |
| H6 |
C6 |
C5 |
H5 |
0.4 |
359.7 |
| C4 |
N4 |
HN41 |
HN42 |
234.7 |
179.7 |
| C4 |
N4 |
HN42 |
HN41 |
129.1 |
180.3 |
| N1 |
C1' |
C2' |
O4' |
129.9 |
119.5 |
| N1 |
C1' |
C2' |
H1' |
250.0 |
239.0 |
| O4' |
C1' |
C2' |
H1' |
120.1 |
119.5 |
| C2' |
C1' |
O4' |
C4' |
351.5 |
333.7 |
| C3' |
C2' |
C1' |
H2' |
234.7 |
241.3 |
| C3' |
C2' |
C1' |
H2'' |
125.3 |
118.6 |
| C1' |
C2' |
C3' |
C4' |
354.2 |
20.9 |
| C1' |
C2' |
C3' |
H3'1 |
119.5 |
139.0 |
| C1' |
C2' |
C3' |
H3'2 |
228.9 |
262.7 |
| H2' |
C2' |
C1' |
H2'' |
250.6 |
237.3 |
| N1 |
C1' |
O4' |
C2' |
224.4 |
240.5 |
| N1 |
C1' |
O4' |
H1' |
113.0 |
121.0 |
| C2' |
C1' |
O4' |
H1' |
248.6 |
240.5 |
| O4' |
C1' |
C2' |
C3' |
8.8 |
1.9 |
| O4' |
C1' |
C2' |
H2' |
134.1 |
120.6 |
| O4' |
C1' |
C2' |
H2'' |
243.5 |
243.3 |
| C3' |
C4' |
O4' |
C1' |
4.3 |
39.9 |
| C1' |
O4' |
C4' |
C5' |
128.0 |
158.6 |
| C1' |
O4' |
C4' |
H4' |
246.0 |
281.4 |
| N1 |
C1' |
H1' |
C2' |
124.4 |
121.0 |
| N1 |
C1' |
H1' |
O4' |
242.6 |
239.0 |
| C2' |
C1' |
H1' |
O4' |
118.2 |
118.0 |
| H1' |
C1' |
C2' |
C3' |
248.7 |
242.4 |
| H1' |
C1' |
C2' |
H2' |
14.0 |
1.1 |
| H1' |
C1' |
C2' |
H2'' |
123.4 |
123.8 |
| H1' |
C1' |
O4' |
C4' |
102.9 |
93.2 |
| C3' |
C2' |
C1' |
O4' |
8.8 |
1.9 |
| C3' |
C2' |
C1' |
H1' |
248.7 |
242.4 |
| C1' |
C2' |
C3' |
H2' |
125.3 |
118.8 |
| C1' |
C2' |
C3' |
H2'' |
234.7 |
241.3 |
| H2' |
C2' |
C3' |
H2'' |
109.4 |
122.5 |
| C4' |
C3' |
C2' |
H3'1 |
234.7 |
241.8 |
| C4' |
C3' |
C2' |
H3'2 |
125.3 |
118.2 |
| C2' |
C3' |
C4' |
O4' |
1.3 |
323.1 |
| C2' |
C3' |
C4' |
C5' |
242.0 |
204.3 |
| C2' |
C3' |
C4' |
H4' |
124.1 |
81.5 |
| H3'1 |
C3' |
C2' |
H3'2 |
250.6 |
236.3 |
| H2' |
C2' |
C1' |
O4' |
134.1 |
120.6 |
| H2' |
C2' |
C1' |
H1' |
14.0 |
1.1 |
| C1' |
C2' |
H2' |
C3' |
240.8 |
245.2 |
| C1' |
C2' |
H2' |
H2'' |
120.4 |
122.7 |
| C3' |
C2' |
H2' |
H2'' |
239.6 |
237.5 |
| H2' |
C2' |
C3' |
C4' |
228.9 |
262.1 |
| H2' |
C2' |
C3' |
H3'1 |
354.2 |
20.3 |
| H2' |
C2' |
C3' |
H3'2 |
103.6 |
144.0 |
| H2'' |
C2' |
C1' |
O4' |
243.5 |
243.3 |
| H2'' |
C2' |
C1' |
H1' |
123.4 |
123.8 |
| C1' |
C2' |
H2'' |
C3' |
119.2 |
114.8 |
| C1' |
C2' |
H2'' |
H2' |
239.6 |
237.2 |
| C3' |
C2' |
H2'' |
H2' |
120.4 |
122.5 |
| H2'' |
C2' |
C3' |
C4' |
119.5 |
139.6 |
| H2'' |
C2' |
C3' |
H3'1 |
244.8 |
257.8 |
| H2'' |
C2' |
C3' |
H3'2 |
354.2 |
21.5 |
| C1' |
O4' |
C4' |
C3' |
4.3 |
39.9 |
| C4' |
C3' |
C2' |
H2' |
228.9 |
262.1 |
| C4' |
C3' |
C2' |
H2'' |
119.5 |
139.6 |
| C2' |
C3' |
C4' |
H3'1 |
125.2 |
118.2 |
| C2' |
C3' |
C4' |
H3'2 |
234.7 |
241.8 |
| H3'1 |
C3' |
C4' |
H3'2 |
109.5 |
123.7 |
| O4' |
C4' |
C3' |
C5' |
119.3 |
118.8 |
| O4' |
C4' |
C3' |
H4' |
237.2 |
241.6 |
| C5' |
C4' |
C3' |
H4' |
117.9 |
122.8 |
| C3' |
C4' |
C5' |
O5' |
69.1 |
180.0 |
| C3' |
C4' |
C5' |
H5' |
194.4 |
300.1 |
| C3' |
C4' |
C5' |
H5'' |
303.9 |
60.0 |
| H3'1 |
C3' |
C2' |
H2' |
354.2 |
20.3 |
| H3'1 |
C3' |
C2' |
H2'' |
244.8 |
257.8 |
| C2' |
C3' |
H3'1 |
C4' |
237.9 |
247.3 |
| C2' |
C3' |
H3'1 |
H3'2 |
118.9 |
123.7 |
| C4' |
C3' |
H3'1 |
H3'2 |
241.0 |
236.4 |
| H3'1 |
C3' |
C4' |
O4' |
236.1 |
204.9 |
| H3'1 |
C3' |
C4' |
C5' |
116.8 |
86.1 |
| H3'1 |
C3' |
C4' |
H4' |
358.9 |
323.3 |
| H3'2 |
C3' |
C2' |
H2' |
103.6 |
144.0 |
| H3'2 |
C3' |
C2' |
H2'' |
354.2 |
21.5 |
| C2' |
C3' |
H3'2 |
C4' |
122.1 |
112.7 |
| C2' |
C3' |
H3'2 |
H3'1 |
241.1 |
236.3 |
| C4' |
C3' |
H3'2 |
H3'1 |
119.0 |
123.6 |
| H3'2 |
C3' |
C4' |
O4' |
126.6 |
81.2 |
| H3'2 |
C3' |
C4' |
C5' |
7.3 |
322.5 |
| H3'2 |
C3' |
C4' |
H4' |
249.4 |
199.6 |
| C4' |
O4' |
C1' |
H1' |
102.9 |
93.2 |
| O4' |
C4' |
C3' |
H3'1 |
236.1 |
204.9 |
| O4' |
C4' |
C3' |
H3'2 |
126.6 |
81.2 |
| C3' |
C4' |
O4' |
C5' |
236.4 |
241.3 |
| C3' |
C4' |
O4' |
H4' |
118.3 |
118.5 |
| C5' |
C4' |
O4' |
H4' |
241.9 |
237.2 |
| O4' |
C4' |
C5' |
O5' |
310.2 |
65.7 |
| O4' |
C4' |
C5' |
H5' |
75.5 |
185.7 |
| O4' |
C4' |
C5' |
H5'' |
184.9 |
305.6 |
| C5' |
C4' |
C3' |
H3'1 |
116.8 |
86.1 |
| C5' |
C4' |
C3' |
H3'2 |
7.3 |
322.5 |
| C3' |
C4' |
C5' |
O4' |
119.0 |
114.3 |
| C3' |
C4' |
C5' |
H4' |
241.8 |
237.1 |
| O4' |
C4' |
C5' |
H4' |
122.9 |
122.8 |
| O5' |
C5' |
C4' |
H5' |
234.7 |
239.9 |
| O5' |
C5' |
C4' |
H5'' |
125.2 |
120.0 |
| C4' |
C5' |
O5' |
P |
181.5 |
180.0 |
| H5' |
C5' |
C4' |
H5'' |
250.5 |
240.1 |
| H4' |
C4' |
C3' |
H3'1 |
358.9 |
323.3 |
| H4' |
C4' |
C3' |
H3'2 |
249.4 |
199.6 |
| C3' |
C4' |
H4' |
O4' |
241.7 |
245.9 |
| C3' |
C4' |
H4' |
C5' |
123.0 |
122.9 |
| O4' |
C4' |
H4' |
C5' |
241.3 |
237.1 |
| H4' |
C4' |
C5' |
O5' |
187.3 |
302.9 |
| H4' |
C4' |
C5' |
H5' |
312.6 |
62.9 |
| H4' |
C4' |
C5' |
H5'' |
62.1 |
182.9 |
| O5' |
C5' |
C4' |
H4' |
187.3 |
302.9 |
| C4' |
C5' |
O5' |
H5' |
125.3 |
120.1 |
| C4' |
C5' |
O5' |
H5'' |
234.8 |
240.0 |
| H5' |
C5' |
O5' |
H5'' |
109.5 |
119.9 |
| C5' |
O5' |
P |
OP1 |
184.9 |
60.0 |
| C5' |
O5' |
P |
OP2 |
48.0 |
180.0 |
| C5' |
O5' |
P |
OP3 |
294.5 |
300.0 |
| H5' |
C5' |
C4' |
H4' |
312.6 |
62.9 |
| C4' |
C5' |
H5' |
O5' |
235.3 |
239.9 |
| C4' |
C5' |
H5' |
H5'' |
117.6 |
119.9 |
| O5' |
C5' |
H5' |
H5'' |
242.3 |
240.0 |
| H5' |
C5' |
O5' |
P |
56.2 |
60.0 |
| H5'' |
C5' |
C4' |
H4' |
62.1 |
182.9 |
| C4' |
C5' |
H5'' |
O5' |
124.7 |
120.1 |
| C4' |
C5' |
H5'' |
H5' |
242.4 |
240.1 |
| O5' |
C5' |
H5'' |
H5' |
117.7 |
120.0 |
| H5'' |
C5' |
O5' |
P |
306.7 |
300.0 |
| P |
O5' |
C5' |
H5' |
56.2 |
60.0 |
| P |
O5' |
C5' |
H5'' |
306.7 |
300.0 |
| OP1 |
P |
O5' |
OP2 |
137.0 |
240.0 |
| OP1 |
P |
O5' |
OP3 |
250.4 |
120.1 |
| OP2 |
P |
O5' |
OP3 |
113.5 |
240.1 |
| O5' |
P |
OP2 |
HOP2 |
180.0 |
180.1 |
| O5' |
P |
OP3 |
HOP3 |
180.0 |
300.0 |
| O5' |
P |
OP1 |
OP2 |
230.5 |
120.0 |
| O5' |
P |
OP1 |
OP3 |
108.6 |
240.0 |
| OP2 |
P |
OP1 |
OP3 |
238.0 |
120.0 |
| OP1 |
P |
OP2 |
HOP2 |
48.4 |
300.1 |
| OP1 |
P |
OP3 |
HOP3 |
296.4 |
180.0 |
| O5' |
P |
OP2 |
OP1 |
131.6 |
240.0 |
| O5' |
P |
OP2 |
OP3 |
251.2 |
120.0 |
| OP1 |
P |
OP2 |
OP3 |
119.5 |
240.0 |
| OP2 |
P |
OP3 |
HOP3 |
67.4 |
60.0 |
| O5' |
P |
OP3 |
OP1 |
243.6 |
120.0 |
| O5' |
P |
OP3 |
OP2 |
112.6 |
240.0 |
| OP1 |
P |
OP3 |
OP2 |
229.0 |
120.0 |
| OP3 |
P |
OP2 |
HOP2 |
288.8 |
60.1 |
| HOP2 |
OP2 |
P |
OP3 |
288.8 |
60.1 |