PDB Chemical Component C38
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 C38
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O3P |
P |
1.497 |
1.610 |
| O3P |
H3P |
0.951 |
0.967 |
| P |
O1P |
1.491 |
1.479 |
| P |
O2P |
1.598 |
1.610 |
| P |
O5' |
1.589 |
1.609 |
| O2P |
H2P |
0.950 |
0.967 |
| O5' |
C5' |
1.400 |
1.429 |
| C5' |
C4' |
1.507 |
1.529 |
| C5' |
H5'1 |
1.115 |
1.091 |
| C5' |
H5'2 |
1.116 |
1.089 |
| C4' |
O4' |
1.450 |
1.446 |
| C4' |
C3' |
1.518 |
1.549 |
| C4' |
H4' |
1.115 |
1.090 |
| O4' |
C1' |
1.403 |
1.437 |
| C3' |
O3' |
1.408 |
1.428 |
| C3' |
C2' |
1.516 |
1.547 |
| C3' |
H3' |
1.115 |
1.091 |
| O3' |
HA |
0.950 |
0.967 |
| C2' |
C1' |
1.514 |
1.541 |
| C2' |
H2'1 |
1.115 |
1.090 |
| C2' |
H2'2 |
1.115 |
1.089 |
| C1' |
N1 |
1.479 |
1.464 |
| C1' |
H1' |
1.115 |
1.091 |
| N1 |
C2 |
1.410 |
1.346 |
| N1 |
C6 |
1.378 |
1.362 |
| C2 |
O2 |
1.248 |
1.219 |
| C2 |
N3 |
1.343 |
1.331 |
| N3 |
C4 |
1.341 |
1.327 |
| C4 |
N4 |
1.352 |
1.376 |
| C4 |
C5 |
1.461 |
1.410 |
| N4 |
H4N1 |
1.020 |
0.970 |
| N4 |
H4N2 |
1.020 |
0.970 |
| C5 |
C6 |
1.349 |
1.354 |
| C5 |
I |
1.515 |
2.094 |
| C6 |
H6 |
1.102 |
1.080 |
Bond Angles for C38
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| P |
O3P |
H3P |
121.0 |
106.8 |
| O3P |
P |
O1P |
121.0 |
109.5 |
| O3P |
P |
O2P |
111.3 |
109.5 |
| O3P |
P |
O5' |
107.5 |
109.5 |
| O1P |
P |
O2P |
101.6 |
109.5 |
| O1P |
P |
O5' |
109.8 |
109.5 |
| O2P |
P |
O5' |
104.4 |
109.5 |
| P |
O2P |
H2P |
111.2 |
106.8 |
| P |
O5' |
C5' |
119.7 |
106.8 |
| O5' |
C5' |
C4' |
110.0 |
109.5 |
| O5' |
C5' |
H5'1 |
112.1 |
109.4 |
| O5' |
C5' |
H5'2 |
112.0 |
109.4 |
| C4' |
C5' |
H5'1 |
112.0 |
109.5 |
| C4' |
C5' |
H5'2 |
112.0 |
109.5 |
| C5' |
C4' |
O4' |
111.7 |
110.8 |
| C5' |
C4' |
C3' |
114.7 |
110.7 |
| C5' |
C4' |
H4' |
108.2 |
110.6 |
| H5'1 |
C5' |
H5'2 |
98.3 |
109.5 |
| O4' |
C4' |
C3' |
105.7 |
103.6 |
| O4' |
C4' |
H4' |
108.1 |
110.5 |
| C4' |
O4' |
C1' |
108.0 |
106.9 |
| C3' |
C4' |
H4' |
108.2 |
110.6 |
| C4' |
C3' |
O3' |
107.9 |
111.0 |
| C4' |
C3' |
C2' |
104.2 |
102.1 |
| C4' |
C3' |
H3' |
112.1 |
110.9 |
| O4' |
C1' |
C2' |
103.2 |
107.4 |
| O4' |
C1' |
N1 |
108.6 |
109.9 |
| O4' |
C1' |
H1' |
110.2 |
109.9 |
| O3' |
C3' |
C2' |
108.0 |
110.9 |
| O3' |
C3' |
H3' |
112.1 |
110.7 |
| C3' |
O3' |
HA |
108.0 |
106.9 |
| C2' |
C3' |
H3' |
112.1 |
110.9 |
| C3' |
C2' |
C1' |
101.9 |
104.2 |
| C3' |
C2' |
H2'1 |
115.1 |
110.5 |
| C3' |
C2' |
H2'2 |
115.1 |
110.6 |
| C1' |
C2' |
H2'1 |
115.1 |
110.5 |
| C1' |
C2' |
H2'2 |
115.1 |
110.4 |
| C2' |
C1' |
N1 |
114.2 |
109.9 |
| C2' |
C1' |
H1' |
110.2 |
109.8 |
| H2'1 |
C2' |
H2'2 |
95.4 |
110.5 |
| N1 |
C1' |
H1' |
110.2 |
109.8 |
| C1' |
N1 |
C2 |
118.1 |
119.8 |
| C1' |
N1 |
C6 |
121.5 |
119.9 |
| C2 |
N1 |
C6 |
120.3 |
120.3 |
| N1 |
C2 |
O2 |
119.5 |
119.4 |
| N1 |
C2 |
N3 |
119.5 |
121.1 |
| N1 |
C6 |
C5 |
121.4 |
119.3 |
| N1 |
C6 |
H6 |
120.3 |
120.3 |
| O2 |
C2 |
N3 |
121.1 |
119.4 |
| C2 |
N3 |
C4 |
120.6 |
120.7 |
| N3 |
C4 |
N4 |
115.6 |
120.2 |
| N3 |
C4 |
C5 |
121.8 |
119.6 |
| N4 |
C4 |
C5 |
122.6 |
120.2 |
| C4 |
N4 |
H4N1 |
115.6 |
120.0 |
| C4 |
N4 |
H4N2 |
122.6 |
120.0 |
| C4 |
C5 |
C6 |
116.3 |
118.9 |
| C4 |
C5 |
I |
121.1 |
120.5 |
| H4N1 |
N4 |
H4N2 |
121.8 |
120.0 |
| C6 |
C5 |
I |
122.6 |
120.6 |
| C5 |
C6 |
H6 |
118.2 |
120.3 |
Torsion Angles for C38
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O1P |
P |
O3P |
O2P |
240.9 |
240.0 |
| O1P |
P |
O3P |
O5' |
127.1 |
120.0 |
| O2P |
P |
O3P |
O5' |
246.3 |
240.0 |
| O3P |
P |
O2P |
H2P |
179.9 |
60.0 |
| O3P |
P |
O5' |
C5' |
195.4 |
180.0 |
| H3P |
O3P |
P |
O1P |
180.0 |
300.0 |
| H3P |
O3P |
P |
O2P |
299.2 |
60.0 |
| H3P |
O3P |
P |
O5' |
52.9 |
180.0 |
| O1P |
P |
O3P |
H3P |
180.0 |
300.0 |
| O3P |
P |
O1P |
O2P |
123.8 |
120.0 |
| O3P |
P |
O1P |
O5' |
233.9 |
240.0 |
| O2P |
P |
O1P |
O5' |
110.1 |
120.0 |
| O1P |
P |
O2P |
H2P |
310.1 |
180.0 |
| O1P |
P |
O5' |
C5' |
61.9 |
60.0 |
| O2P |
P |
O3P |
H3P |
299.2 |
60.0 |
| O3P |
P |
O2P |
O1P |
229.8 |
240.0 |
| O3P |
P |
O2P |
O5' |
115.6 |
120.0 |
| O1P |
P |
O2P |
O5' |
245.8 |
240.0 |
| O2P |
P |
O5' |
C5' |
313.6 |
300.0 |
| O5' |
P |
O3P |
H3P |
52.9 |
180.0 |
| O3P |
P |
O5' |
O1P |
133.4 |
120.0 |
| O3P |
P |
O5' |
O2P |
241.7 |
240.0 |
| O1P |
P |
O5' |
O2P |
108.3 |
120.0 |
| O5' |
P |
O2P |
H2P |
64.3 |
300.0 |
| P |
O5' |
C5' |
C4' |
147.6 |
180.0 |
| P |
O5' |
C5' |
H5'1 |
22.4 |
60.0 |
| P |
O5' |
C5' |
H5'2 |
272.9 |
300.0 |
| H2P |
O2P |
P |
O5' |
64.3 |
300.0 |
| C4' |
C5' |
O5' |
H5'1 |
125.3 |
120.0 |
| C4' |
C5' |
O5' |
H5'2 |
234.7 |
239.9 |
| O5' |
C5' |
C4' |
O4' |
280.2 |
65.8 |
| O5' |
C5' |
C4' |
C3' |
40.5 |
180.0 |
| O5' |
C5' |
C4' |
H4' |
161.3 |
302.9 |
| H5'1 |
C5' |
O5' |
H5'2 |
109.5 |
119.9 |
| O5' |
C5' |
C4' |
H5'1 |
234.7 |
240.0 |
| O5' |
C5' |
C4' |
H5'2 |
125.3 |
120.0 |
| H5'1 |
C5' |
C4' |
H5'2 |
250.6 |
240.0 |
| O4' |
C4' |
C5' |
C3' |
239.7 |
245.7 |
| O4' |
C4' |
C5' |
H4' |
118.9 |
122.8 |
| C5' |
C4' |
O4' |
C1' |
146.0 |
158.5 |
| C3' |
C4' |
C5' |
H4' |
239.2 |
237.1 |
| C5' |
C4' |
C3' |
O3' |
127.7 |
86.1 |
| C5' |
C4' |
C3' |
C2' |
242.3 |
204.4 |
| C5' |
C4' |
C3' |
H3' |
3.7 |
322.6 |
| O5' |
C5' |
H5'1 |
C4' |
124.1 |
120.0 |
| O5' |
C5' |
H5'1 |
H5'2 |
242.1 |
240.1 |
| C4' |
C5' |
H5'1 |
H5'2 |
117.9 |
120.1 |
| H5'1 |
C5' |
C4' |
O4' |
45.6 |
185.7 |
| H5'1 |
C5' |
C4' |
C3' |
165.8 |
300.0 |
| H5'1 |
C5' |
C4' |
H4' |
286.6 |
62.9 |
| O5' |
C5' |
H5'2 |
C4' |
235.9 |
240.0 |
| O5' |
C5' |
H5'2 |
H5'1 |
118.0 |
119.9 |
| C4' |
C5' |
H5'2 |
H5'1 |
242.1 |
240.0 |
| H5'2 |
C5' |
C4' |
O4' |
155.0 |
305.8 |
| H5'2 |
C5' |
C4' |
C3' |
275.2 |
60.0 |
| H5'2 |
C5' |
C4' |
H4' |
36.1 |
182.9 |
| O4' |
C4' |
C5' |
H5'1 |
45.6 |
185.7 |
| O4' |
C4' |
C5' |
H5'2 |
155.0 |
305.8 |
| C5' |
C4' |
O4' |
C3' |
125.4 |
118.7 |
| C5' |
C4' |
O4' |
H4' |
241.1 |
237.1 |
| C3' |
C4' |
O4' |
H4' |
115.7 |
118.5 |
| O4' |
C4' |
C3' |
O3' |
251.2 |
204.8 |
| O4' |
C4' |
C3' |
C2' |
5.9 |
323.1 |
| O4' |
C4' |
C3' |
H3' |
127.3 |
81.3 |
| C4' |
O4' |
C1' |
C2' |
321.4 |
333.7 |
| C4' |
O4' |
C1' |
N1 |
199.9 |
214.1 |
| C4' |
O4' |
C1' |
H1' |
79.1 |
93.1 |
| C3' |
C4' |
C5' |
H5'1 |
165.8 |
300.0 |
| C3' |
C4' |
C5' |
H5'2 |
275.2 |
60.0 |
| C5' |
C4' |
C3' |
O4' |
236.5 |
241.3 |
| C5' |
C4' |
C3' |
H4' |
120.8 |
122.9 |
| O4' |
C4' |
C3' |
H4' |
244.4 |
241.6 |
| C3' |
C4' |
O4' |
C1' |
20.6 |
39.8 |
| O3' |
C3' |
C4' |
C2' |
245.4 |
241.7 |
| O3' |
C3' |
C4' |
H3' |
123.9 |
123.5 |
| C4' |
C3' |
O3' |
HA |
180.0 |
174.2 |
| C2' |
C3' |
C4' |
H3' |
238.6 |
241.8 |
| C4' |
C3' |
C2' |
C1' |
332.4 |
20.9 |
| C4' |
C3' |
C2' |
H2'1 |
207.1 |
262.1 |
| C4' |
C3' |
C2' |
H2'2 |
97.6 |
139.5 |
| H4' |
C4' |
C5' |
H5'1 |
286.6 |
62.9 |
| H4' |
C4' |
C5' |
H5'2 |
36.1 |
182.9 |
| C5' |
C4' |
H4' |
O4' |
121.2 |
123.0 |
| C5' |
C4' |
H4' |
C3' |
235.2 |
237.1 |
| O4' |
C4' |
H4' |
C3' |
114.1 |
114.1 |
| H4' |
C4' |
O4' |
C1' |
265.0 |
281.4 |
| H4' |
C4' |
C3' |
O3' |
6.9 |
323.2 |
| H4' |
C4' |
C3' |
C2' |
121.5 |
81.5 |
| H4' |
C4' |
C3' |
H3' |
242.9 |
199.7 |
| C1' |
O4' |
C4' |
C3' |
20.6 |
39.8 |
| C1' |
O4' |
C4' |
H4' |
265.0 |
281.4 |
| C3' |
C2' |
C1' |
O4' |
40.7 |
2.0 |
| O4' |
C1' |
C2' |
H2'1 |
165.9 |
120.6 |
| O4' |
C1' |
C2' |
H2'2 |
275.4 |
243.2 |
| C2' |
C1' |
O4' |
N1 |
121.5 |
119.6 |
| C2' |
C1' |
O4' |
H1' |
242.3 |
240.6 |
| N1 |
C1' |
O4' |
H1' |
120.8 |
121.0 |
| O4' |
C1' |
N1 |
C2 |
248.3 |
58.3 |
| O4' |
C1' |
N1 |
C6 |
70.5 |
238.2 |
| O3' |
C3' |
C4' |
H4' |
6.9 |
323.2 |
| C4' |
C3' |
O3' |
C2' |
112.1 |
112.8 |
| C4' |
C3' |
O3' |
H3' |
236.1 |
236.4 |
| C2' |
C3' |
O3' |
H3' |
124.0 |
123.6 |
| O3' |
C3' |
C2' |
C1' |
87.0 |
139.2 |
| O3' |
C3' |
C2' |
H2'1 |
321.7 |
20.5 |
| O3' |
C3' |
C2' |
H2'2 |
212.2 |
257.9 |
| C2' |
C3' |
C4' |
H4' |
121.5 |
81.5 |
| C4' |
C3' |
C2' |
O3' |
245.4 |
241.7 |
| C4' |
C3' |
C2' |
H3' |
121.4 |
118.2 |
| O4' |
C1' |
C2' |
C3' |
40.7 |
2.0 |
| O3' |
C3' |
C2' |
H3' |
236.0 |
236.5 |
| C2' |
C3' |
O3' |
HA |
67.9 |
61.4 |
| C1' |
C2' |
C3' |
H2'1 |
125.2 |
118.7 |
| C1' |
C2' |
C3' |
H2'2 |
234.7 |
241.3 |
| C3' |
C2' |
C1' |
N1 |
158.3 |
121.5 |
| C3' |
C2' |
C1' |
H1' |
283.0 |
242.4 |
| H2'1 |
C2' |
C3' |
H2'2 |
109.5 |
122.6 |
| H3' |
C3' |
C4' |
H4' |
242.9 |
199.7 |
| C4' |
C3' |
H3' |
O3' |
121.6 |
123.7 |
| C4' |
C3' |
H3' |
C2' |
243.3 |
247.3 |
| O3' |
C3' |
H3' |
C2' |
121.7 |
123.6 |
| H3' |
C3' |
O3' |
HA |
303.9 |
297.8 |
| H3' |
C3' |
C2' |
C1' |
211.0 |
262.7 |
| H3' |
C3' |
C2' |
H2'1 |
85.7 |
144.0 |
| H3' |
C3' |
C2' |
H2'2 |
336.2 |
21.3 |
| HA |
O3' |
C3' |
C2' |
67.9 |
61.4 |
| HA |
O3' |
C3' |
H3' |
303.9 |
297.8 |
| O4' |
C1' |
C2' |
N1 |
242.3 |
240.4 |
| O4' |
C1' |
C2' |
H1' |
117.7 |
119.5 |
| C1' |
C2' |
C3' |
H3' |
211.0 |
262.7 |
| C3' |
C2' |
C1' |
H2'1 |
234.7 |
241.3 |
| C3' |
C2' |
C1' |
H2'2 |
125.3 |
118.8 |
| H2'1 |
C2' |
C1' |
H2'2 |
250.5 |
237.4 |
| N1 |
C1' |
C2' |
H1' |
235.3 |
239.1 |
| C2' |
C1' |
N1 |
C2 |
133.8 |
300.3 |
| C2' |
C1' |
N1 |
C6 |
316.0 |
120.2 |
| H2'1 |
C2' |
C3' |
H3' |
85.7 |
144.0 |
| C3' |
C2' |
H2'1 |
C1' |
118.1 |
114.8 |
| C3' |
C2' |
H2'1 |
H2'2 |
239.0 |
237.3 |
| C1' |
C2' |
H2'1 |
H2'2 |
121.0 |
122.5 |
| H2'1 |
C2' |
C1' |
N1 |
283.6 |
240.2 |
| H2'1 |
C2' |
C1' |
H1' |
48.2 |
1.1 |
| H2'2 |
C2' |
C3' |
H3' |
336.2 |
21.3 |
| C3' |
C2' |
H2'2 |
C1' |
241.9 |
245.2 |
| C3' |
C2' |
H2'2 |
H2'1 |
121.0 |
122.6 |
| C1' |
C2' |
H2'2 |
H2'1 |
239.1 |
237.4 |
| H2'2 |
C2' |
C1' |
N1 |
33.1 |
2.8 |
| H2'2 |
C2' |
C1' |
H1' |
157.7 |
123.7 |
| O4' |
C1' |
N1 |
C2' |
114.5 |
118.0 |
| O4' |
C1' |
N1 |
H1' |
239.2 |
238.9 |
| N1 |
C1' |
C2' |
H2'1 |
283.6 |
240.2 |
| N1 |
C1' |
C2' |
H2'2 |
33.1 |
2.8 |
| C2' |
C1' |
N1 |
H1' |
124.7 |
120.9 |
| C2 |
N1 |
C1' |
C6 |
177.8 |
180.1 |
| C1' |
N1 |
C2 |
O2 |
3.7 |
359.9 |
| C1' |
N1 |
C2 |
N3 |
184.0 |
180.0 |
| C1' |
N1 |
C6 |
C5 |
175.1 |
179.8 |
| C1' |
N1 |
C6 |
H6 |
355.1 |
0.1 |
| O4' |
C1' |
H1' |
C2' |
246.8 |
242.0 |
| O4' |
C1' |
H1' |
N1 |
119.8 |
121.0 |
| H1' |
C1' |
C2' |
H2'1 |
48.2 |
1.1 |
| H1' |
C1' |
C2' |
H2'2 |
157.7 |
123.7 |
| C2' |
C1' |
H1' |
N1 |
233.1 |
239.0 |
| H1' |
C1' |
N1 |
C2 |
9.1 |
179.4 |
| H1' |
C1' |
N1 |
C6 |
191.3 |
359.3 |
| C2 |
N1 |
C1' |
H1' |
9.1 |
179.4 |
| C1' |
N1 |
C2 |
C6 |
182.1 |
179.9 |
| C2 |
N1 |
C6 |
C5 |
357.3 |
359.7 |
| C2 |
N1 |
C6 |
H6 |
177.4 |
180.0 |
| O2 |
C2 |
N1 |
N3 |
179.7 |
179.9 |
| N1 |
C2 |
N3 |
C4 |
359.8 |
359.8 |
| C6 |
N1 |
C1' |
H1' |
191.3 |
359.3 |
| C1' |
N1 |
C6 |
C2 |
177.8 |
180.1 |
| C6 |
N1 |
C2 |
O2 |
181.5 |
180.0 |
| C6 |
N1 |
C2 |
N3 |
1.9 |
0.1 |
| C4 |
C5 |
C6 |
N1 |
1.8 |
0.6 |
| N1 |
C6 |
C5 |
I |
181.9 |
180.0 |
| C5 |
C6 |
N1 |
H6 |
179.9 |
179.7 |
| O2 |
C2 |
N1 |
C6 |
181.5 |
180.0 |
| N1 |
C2 |
O2 |
N3 |
180.3 |
180.1 |
| O2 |
C2 |
N3 |
C4 |
180.1 |
179.9 |
| N3 |
C2 |
N1 |
C6 |
1.9 |
0.1 |
| N1 |
C2 |
N3 |
O2 |
179.7 |
179.9 |
| C2 |
N3 |
C4 |
N4 |
179.7 |
180.1 |
| C2 |
N3 |
C4 |
C5 |
359.4 |
0.4 |
| N4 |
C4 |
N3 |
C5 |
180.3 |
179.7 |
| N3 |
C4 |
N4 |
H4N1 |
180.0 |
0.0 |
| N3 |
C4 |
N4 |
H4N2 |
359.7 |
179.8 |
| N3 |
C4 |
C5 |
C6 |
359.8 |
359.4 |
| N3 |
C4 |
C5 |
I |
179.7 |
179.9 |
| N3 |
C4 |
N4 |
C5 |
179.7 |
180.3 |
| N4 |
C4 |
C5 |
C6 |
179.5 |
179.7 |
| N4 |
C4 |
C5 |
I |
359.4 |
0.3 |
| H4N1 |
N4 |
C4 |
H4N2 |
180.3 |
180.2 |
| N1 |
C6 |
C5 |
C4 |
1.8 |
0.6 |
| N3 |
C4 |
C5 |
N4 |
180.3 |
179.7 |
| C5 |
C4 |
N4 |
H4N1 |
0.3 |
179.7 |
| C5 |
C4 |
N4 |
H4N2 |
180.0 |
359.5 |
| C6 |
C5 |
C4 |
I |
180.1 |
179.5 |
| C4 |
C5 |
C6 |
H6 |
181.8 |
180.3 |
| H4N1 |
N4 |
C4 |
C5 |
0.3 |
179.7 |
| C4 |
N4 |
H4N1 |
H4N2 |
179.7 |
179.8 |
| H4N2 |
N4 |
C4 |
C5 |
180.0 |
359.5 |
| C4 |
N4 |
H4N2 |
H4N1 |
180.3 |
180.2 |
| N1 |
C6 |
C5 |
H6 |
180.1 |
180.3 |
| C4 |
C5 |
C6 |
I |
179.9 |
180.5 |
| C4 |
C5 |
I |
C6 |
180.1 |
179.5 |
| I |
C5 |
C6 |
H6 |
1.8 |
359.7 |
| N1 |
C6 |
H6 |
C5 |
179.9 |
179.7 |
| H6 |
C6 |
C5 |
I |
1.8 |
359.7 |