PDB Chemical Component 5NC
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 5NC
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| P |
OP1 |
1.459 |
1.479 |
| P |
OP2 |
1.426 |
1.610 |
| P |
OP3 |
1.636 |
1.609 |
| P |
O5' |
1.542 |
1.609 |
| OP2 |
HOP2 |
0.950 |
0.967 |
| OP3 |
HOP3 |
0.950 |
0.965 |
| O5' |
C5' |
1.456 |
1.428 |
| C5' |
C4' |
1.510 |
1.530 |
| C5' |
H5' |
1.115 |
1.090 |
| C5' |
H5'' |
1.114 |
1.089 |
| C4' |
O4' |
1.410 |
1.444 |
| C4' |
C3' |
1.471 |
1.549 |
| C4' |
H4' |
1.114 |
1.090 |
| O4' |
C1' |
1.378 |
1.438 |
| C3' |
O3' |
1.473 |
1.429 |
| C3' |
C2' |
1.555 |
1.547 |
| C3' |
H3' |
1.115 |
1.091 |
| O3' |
HO'3 |
0.950 |
0.966 |
| C2' |
C1' |
1.586 |
1.541 |
| C2' |
H2' |
1.116 |
1.089 |
| C2' |
H2'' |
1.115 |
1.090 |
| C1' |
N1 |
1.570 |
1.464 |
| C1' |
H1'1 |
1.114 |
1.091 |
| N1 |
C2 |
1.426 |
1.349 |
| N1 |
C6 |
1.462 |
1.350 |
| C2 |
O2 |
1.245 |
1.219 |
| C2 |
N3 |
1.389 |
1.336 |
| N3 |
C4 |
1.391 |
1.325 |
| C4 |
N4 |
1.343 |
1.373 |
| C4 |
N5 |
1.332 |
1.340 |
| N4 |
HN41 |
1.020 |
0.969 |
| N4 |
HN42 |
1.021 |
0.970 |
| N5 |
C6 |
1.521 |
1.309 |
| C6 |
H6 |
1.103 |
1.080 |
Bond Angles for 5NC
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| OP1 |
P |
OP2 |
118.7 |
109.4 |
| OP1 |
P |
OP3 |
105.7 |
109.5 |
| OP1 |
P |
O5' |
104.7 |
109.5 |
| OP2 |
P |
OP3 |
111.7 |
109.4 |
| OP2 |
P |
O5' |
106.1 |
109.5 |
| P |
OP2 |
HOP2 |
118.7 |
106.8 |
| OP3 |
P |
O5' |
109.5 |
109.5 |
| P |
OP3 |
HOP3 |
105.7 |
106.9 |
| P |
O5' |
C5' |
120.8 |
106.8 |
| O5' |
C5' |
C4' |
116.4 |
109.5 |
| O5' |
C5' |
H5' |
109.7 |
109.4 |
| O5' |
C5' |
H5'' |
109.7 |
109.5 |
| C4' |
C5' |
H5' |
109.7 |
109.5 |
| C4' |
C5' |
H5'' |
109.7 |
109.4 |
| C5' |
C4' |
O4' |
110.1 |
110.8 |
| C5' |
C4' |
C3' |
110.6 |
110.7 |
| C5' |
C4' |
H4' |
106.7 |
110.5 |
| H5' |
C5' |
H5'' |
100.5 |
109.5 |
| O4' |
C4' |
C3' |
103.9 |
103.6 |
| O4' |
C4' |
H4' |
113.1 |
110.5 |
| C4' |
O4' |
C1' |
114.0 |
106.9 |
| C3' |
C4' |
H4' |
112.5 |
110.6 |
| C4' |
C3' |
O3' |
113.9 |
111.0 |
| C4' |
C3' |
C2' |
100.2 |
102.1 |
| C4' |
C3' |
H3' |
112.0 |
110.9 |
| O4' |
C1' |
C2' |
100.6 |
107.4 |
| O4' |
C1' |
N1 |
108.0 |
109.9 |
| O4' |
C1' |
H1'1 |
120.5 |
109.9 |
| O3' |
C3' |
C2' |
107.2 |
110.9 |
| O3' |
C3' |
H3' |
105.6 |
110.8 |
| C3' |
O3' |
HO'3 |
113.8 |
106.8 |
| C2' |
C3' |
H3' |
118.2 |
110.9 |
| C3' |
C2' |
C1' |
105.9 |
104.2 |
| C3' |
C2' |
H2' |
113.6 |
110.5 |
| C3' |
C2' |
H2'' |
113.6 |
110.5 |
| C1' |
C2' |
H2' |
113.5 |
110.6 |
| C1' |
C2' |
H2'' |
113.5 |
110.4 |
| C2' |
C1' |
N1 |
120.4 |
109.9 |
| C2' |
C1' |
H1'1 |
108.1 |
109.8 |
| H2' |
C2' |
H2'' |
96.9 |
110.5 |
| N1 |
C1' |
H1'1 |
100.6 |
109.9 |
| C1' |
N1 |
C2 |
120.6 |
120.2 |
| C1' |
N1 |
C6 |
124.4 |
120.2 |
| C2 |
N1 |
C6 |
114.9 |
119.6 |
| N1 |
C2 |
O2 |
114.4 |
120.3 |
| N1 |
C2 |
N3 |
122.3 |
119.5 |
| N1 |
C6 |
N5 |
120.6 |
120.0 |
| N1 |
C6 |
H6 |
117.8 |
120.0 |
| O2 |
C2 |
N3 |
123.3 |
120.2 |
| C2 |
N3 |
C4 |
122.1 |
120.0 |
| N3 |
C4 |
N4 |
121.1 |
119.8 |
| N3 |
C4 |
N5 |
122.0 |
120.3 |
| N4 |
C4 |
N5 |
116.9 |
119.8 |
| C4 |
N4 |
HN41 |
121.1 |
120.0 |
| C4 |
N4 |
HN42 |
108.1 |
120.0 |
| C4 |
N5 |
C6 |
117.9 |
120.5 |
| HN41 |
N4 |
HN42 |
108.0 |
120.0 |
| N5 |
C6 |
H6 |
121.7 |
120.0 |
Torsion Angles for 5NC
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| OP2 |
P |
OP1 |
OP3 |
233.7 |
119.9 |
| OP2 |
P |
OP1 |
O5' |
118.1 |
240.0 |
| OP1 |
P |
OP2 |
HOP2 |
180.0 |
300.0 |
| OP3 |
P |
OP1 |
O5' |
244.4 |
120.0 |
| OP1 |
P |
OP3 |
HOP3 |
180.0 |
179.9 |
| OP1 |
P |
O5' |
C5' |
151.8 |
60.0 |
| OP1 |
P |
OP2 |
OP3 |
123.3 |
240.0 |
| OP1 |
P |
OP2 |
O5' |
242.6 |
120.0 |
| OP3 |
P |
OP2 |
O5' |
119.3 |
240.0 |
| OP2 |
P |
OP3 |
HOP3 |
310.4 |
60.0 |
| OP2 |
P |
O5' |
C5' |
25.4 |
180.0 |
| OP1 |
P |
OP3 |
OP2 |
229.6 |
119.9 |
| OP1 |
P |
OP3 |
O5' |
112.3 |
240.0 |
| OP2 |
P |
OP3 |
O5' |
242.7 |
120.0 |
| OP3 |
P |
OP2 |
HOP2 |
56.7 |
60.0 |
| OP3 |
P |
O5' |
C5' |
264.7 |
299.9 |
| OP1 |
P |
O5' |
OP2 |
126.3 |
240.0 |
| OP1 |
P |
O5' |
OP3 |
247.1 |
120.0 |
| OP2 |
P |
O5' |
OP3 |
120.7 |
240.0 |
| O5' |
P |
OP2 |
HOP2 |
297.4 |
180.0 |
| O5' |
P |
OP3 |
HOP3 |
67.7 |
300.0 |
| P |
O5' |
C5' |
C4' |
194.8 |
180.0 |
| P |
O5' |
C5' |
H5' |
320.1 |
60.0 |
| P |
O5' |
C5' |
H5'' |
69.6 |
300.0 |
| HOP2 |
OP2 |
P |
OP3 |
56.7 |
60.0 |
| HOP2 |
OP2 |
P |
O5' |
297.4 |
180.0 |
| HOP3 |
OP3 |
P |
O5' |
67.7 |
300.0 |
| C4' |
C5' |
O5' |
H5' |
234.8 |
120.0 |
| C4' |
C5' |
O5' |
H5'' |
125.3 |
240.0 |
| O5' |
C5' |
C4' |
O4' |
79.4 |
65.7 |
| O5' |
C5' |
C4' |
C3' |
193.6 |
180.1 |
| O5' |
C5' |
C4' |
H4' |
316.3 |
302.9 |
| H5' |
C5' |
O5' |
H5'' |
250.5 |
120.0 |
| O5' |
C5' |
C4' |
H5' |
125.2 |
240.0 |
| O5' |
C5' |
C4' |
H5'' |
234.7 |
120.1 |
| H5' |
C5' |
C4' |
H5'' |
109.5 |
240.0 |
| O4' |
C4' |
C5' |
C3' |
245.7 |
245.7 |
| O4' |
C4' |
C5' |
H4' |
123.0 |
122.8 |
| C5' |
C4' |
O4' |
C1' |
158.8 |
158.5 |
| C3' |
C4' |
C5' |
H4' |
237.3 |
237.1 |
| C5' |
C4' |
C3' |
O3' |
91.0 |
86.1 |
| C5' |
C4' |
C3' |
C2' |
205.2 |
204.3 |
| C5' |
C4' |
C3' |
H3' |
331.3 |
322.5 |
| O5' |
C5' |
H5' |
C4' |
231.0 |
120.0 |
| O5' |
C5' |
H5' |
H5'' |
115.5 |
240.0 |
| C4' |
C5' |
H5' |
H5'' |
244.5 |
120.0 |
| H5' |
C5' |
C4' |
O4' |
314.1 |
185.7 |
| H5' |
C5' |
C4' |
C3' |
68.4 |
300.0 |
| H5' |
C5' |
C4' |
H4' |
191.1 |
62.9 |
| O5' |
C5' |
H5'' |
C4' |
129.1 |
239.9 |
| O5' |
C5' |
H5'' |
H5' |
244.5 |
120.0 |
| C4' |
C5' |
H5'' |
H5' |
115.5 |
240.0 |
| H5'' |
C5' |
C4' |
O4' |
204.7 |
305.6 |
| H5'' |
C5' |
C4' |
C3' |
318.9 |
60.0 |
| H5'' |
C5' |
C4' |
H4' |
81.6 |
182.8 |
| O4' |
C4' |
C5' |
H5' |
314.1 |
185.7 |
| O4' |
C4' |
C5' |
H5'' |
204.7 |
305.6 |
| C5' |
C4' |
O4' |
C3' |
118.5 |
118.7 |
| C5' |
C4' |
O4' |
H4' |
240.8 |
237.2 |
| C3' |
C4' |
O4' |
H4' |
122.3 |
118.5 |
| O4' |
C4' |
C3' |
O3' |
209.1 |
204.8 |
| O4' |
C4' |
C3' |
C2' |
323.3 |
323.1 |
| O4' |
C4' |
C3' |
H3' |
89.4 |
81.2 |
| C4' |
O4' |
C1' |
C2' |
337.8 |
333.7 |
| C4' |
O4' |
C1' |
N1 |
210.8 |
214.2 |
| C4' |
O4' |
C1' |
H1'1 |
96.3 |
93.2 |
| C3' |
C4' |
C5' |
H5' |
68.4 |
300.0 |
| C3' |
C4' |
C5' |
H5'' |
318.9 |
60.0 |
| C5' |
C4' |
C3' |
O4' |
241.9 |
241.2 |
| C5' |
C4' |
C3' |
H4' |
119.2 |
122.8 |
| O4' |
C4' |
C3' |
H4' |
237.3 |
241.6 |
| C3' |
C4' |
O4' |
C1' |
40.3 |
39.8 |
| O3' |
C3' |
C4' |
C2' |
245.9 |
241.8 |
| O3' |
C3' |
C4' |
H3' |
119.7 |
123.6 |
| C4' |
C3' |
O3' |
HO'3 |
180.0 |
174.2 |
| C2' |
C3' |
C4' |
H3' |
233.9 |
241.8 |
| C4' |
C3' |
C2' |
C1' |
24.4 |
20.9 |
| C4' |
C3' |
C2' |
H2' |
149.6 |
262.1 |
| C4' |
C3' |
C2' |
H2'' |
259.1 |
139.5 |
| H4' |
C4' |
C5' |
H5' |
191.1 |
62.9 |
| H4' |
C4' |
C5' |
H5'' |
81.6 |
182.8 |
| C5' |
C4' |
H4' |
O4' |
121.1 |
123.0 |
| C5' |
C4' |
H4' |
C3' |
238.5 |
237.1 |
| O4' |
C4' |
H4' |
C3' |
117.4 |
114.1 |
| H4' |
C4' |
O4' |
C1' |
278.0 |
281.3 |
| H4' |
C4' |
C3' |
O3' |
331.8 |
323.3 |
| H4' |
C4' |
C3' |
C2' |
85.9 |
81.5 |
| H4' |
C4' |
C3' |
H3' |
212.1 |
199.7 |
| C1' |
O4' |
C4' |
C3' |
40.3 |
39.8 |
| C1' |
O4' |
C4' |
H4' |
278.0 |
281.3 |
| C3' |
C2' |
C1' |
O4' |
357.0 |
1.9 |
| O4' |
C1' |
C2' |
H2' |
231.7 |
120.6 |
| O4' |
C1' |
C2' |
H2'' |
122.3 |
243.3 |
| C2' |
C1' |
O4' |
N1 |
127.0 |
119.5 |
| C2' |
C1' |
O4' |
H1'1 |
241.5 |
240.6 |
| N1 |
C1' |
O4' |
H1'1 |
114.6 |
121.0 |
| O4' |
C1' |
N1 |
C2 |
277.3 |
238.3 |
| O4' |
C1' |
N1 |
C6 |
101.7 |
58.3 |
| O3' |
C3' |
C4' |
H4' |
331.8 |
323.3 |
| C4' |
C3' |
O3' |
C2' |
109.9 |
112.8 |
| C4' |
C3' |
O3' |
H3' |
236.7 |
236.4 |
| C2' |
C3' |
O3' |
H3' |
126.8 |
123.6 |
| O3' |
C3' |
C2' |
C1' |
143.5 |
139.2 |
| O3' |
C3' |
C2' |
H2' |
268.8 |
20.4 |
| O3' |
C3' |
C2' |
H2'' |
18.3 |
257.8 |
| C2' |
C3' |
C4' |
H4' |
85.9 |
81.5 |
| C4' |
C3' |
C2' |
O3' |
240.9 |
241.7 |
| C4' |
C3' |
C2' |
H3' |
121.8 |
118.2 |
| O4' |
C1' |
C2' |
C3' |
357.0 |
1.9 |
| O3' |
C3' |
C2' |
H3' |
241.0 |
236.5 |
| C2' |
C3' |
O3' |
HO'3 |
70.0 |
61.5 |
| C1' |
C2' |
C3' |
H2' |
234.8 |
118.8 |
| C1' |
C2' |
C3' |
H2'' |
125.3 |
241.4 |
| C3' |
C2' |
C1' |
N1 |
115.3 |
121.4 |
| C3' |
C2' |
C1' |
H1'1 |
229.8 |
242.5 |
| H2' |
C2' |
C3' |
H2'' |
250.5 |
122.6 |
| H3' |
C3' |
C4' |
H4' |
212.1 |
199.7 |
| C4' |
C3' |
H3' |
O3' |
124.5 |
123.7 |
| C4' |
C3' |
H3' |
C2' |
244.3 |
247.3 |
| O3' |
C3' |
H3' |
C2' |
119.9 |
123.6 |
| H3' |
C3' |
O3' |
HO'3 |
303.2 |
297.9 |
| H3' |
C3' |
C2' |
C1' |
262.6 |
262.7 |
| H3' |
C3' |
C2' |
H2' |
27.8 |
143.9 |
| H3' |
C3' |
C2' |
H2'' |
137.3 |
21.3 |
| HO'3 |
O3' |
C3' |
C2' |
70.0 |
61.5 |
| HO'3 |
O3' |
C3' |
H3' |
303.2 |
297.9 |
| O4' |
C1' |
C2' |
N1 |
241.7 |
240.5 |
| O4' |
C1' |
C2' |
H1'1 |
127.1 |
119.4 |
| C1' |
C2' |
C3' |
H3' |
262.6 |
262.7 |
| C3' |
C2' |
C1' |
H2' |
125.3 |
241.3 |
| C3' |
C2' |
C1' |
H2'' |
234.7 |
118.6 |
| H2' |
C2' |
C1' |
H2'' |
109.4 |
237.4 |
| N1 |
C1' |
C2' |
H1'1 |
245.4 |
239.0 |
| C2' |
C1' |
N1 |
C2 |
162.8 |
120.3 |
| C2' |
C1' |
N1 |
C6 |
347.2 |
300.3 |
| H2' |
C2' |
C3' |
H3' |
27.8 |
143.9 |
| C3' |
C2' |
H2' |
C1' |
239.0 |
114.8 |
| C3' |
C2' |
H2' |
H2'' |
119.5 |
237.4 |
| C1' |
C2' |
H2' |
H2'' |
240.6 |
122.6 |
| H2' |
C2' |
C1' |
N1 |
350.0 |
240.2 |
| H2' |
C2' |
C1' |
H1'1 |
104.6 |
1.2 |
| H2'' |
C2' |
C3' |
H3' |
137.3 |
21.3 |
| C3' |
C2' |
H2'' |
C1' |
121.1 |
245.3 |
| C3' |
C2' |
H2'' |
H2' |
240.5 |
122.6 |
| C1' |
C2' |
H2'' |
H2' |
119.4 |
237.3 |
| H2'' |
C2' |
C1' |
N1 |
240.6 |
2.8 |
| H2'' |
C2' |
C1' |
H1'1 |
355.2 |
123.8 |
| O4' |
C1' |
N1 |
C2' |
114.5 |
118.0 |
| O4' |
C1' |
N1 |
H1'1 |
232.9 |
239.0 |
| N1 |
C1' |
C2' |
H2' |
350.0 |
240.2 |
| N1 |
C1' |
C2' |
H2'' |
240.6 |
2.8 |
| C2' |
C1' |
N1 |
H1'1 |
118.4 |
121.0 |
| C2 |
N1 |
C1' |
C6 |
175.6 |
180.0 |
| C1' |
N1 |
C2 |
O2 |
7.6 |
0.0 |
| C1' |
N1 |
C2 |
N3 |
185.9 |
180.0 |
| C1' |
N1 |
C6 |
N5 |
174.3 |
179.8 |
| C1' |
N1 |
C6 |
H6 |
354.3 |
0.0 |
| O4' |
C1' |
H1'1 |
C2' |
245.4 |
242.1 |
| O4' |
C1' |
H1'1 |
N1 |
118.4 |
121.1 |
| H1'1 |
C1' |
C2' |
H2' |
104.6 |
1.2 |
| H1'1 |
C1' |
C2' |
H2'' |
355.2 |
123.8 |
| C2' |
C1' |
H1'1 |
N1 |
233.0 |
239.0 |
| H1'1 |
C1' |
N1 |
C2 |
44.4 |
359.3 |
| H1'1 |
C1' |
N1 |
C6 |
228.8 |
179.3 |
| C2 |
N1 |
C1' |
H1'1 |
44.4 |
359.3 |
| C1' |
N1 |
C2 |
C6 |
184.0 |
180.0 |
| C2 |
N1 |
C6 |
N5 |
358.4 |
359.8 |
| C2 |
N1 |
C6 |
H6 |
178.5 |
180.0 |
| O2 |
C2 |
N1 |
N3 |
181.7 |
180.1 |
| N1 |
C2 |
N3 |
C4 |
356.3 |
360.0 |
| C6 |
N1 |
C1' |
H1'1 |
228.8 |
179.3 |
| C1' |
N1 |
C6 |
C2 |
175.8 |
180.0 |
| C6 |
N1 |
C2 |
O2 |
183.6 |
180.0 |
| C6 |
N1 |
C2 |
N3 |
1.9 |
359.9 |
| C4 |
N5 |
C6 |
N1 |
3.1 |
0.6 |
| N5 |
C6 |
N1 |
H6 |
180.0 |
179.7 |
| O2 |
C2 |
N1 |
C6 |
183.6 |
180.0 |
| N1 |
C2 |
O2 |
N3 |
178.3 |
179.9 |
| O2 |
C2 |
N3 |
C4 |
174.4 |
179.9 |
| N3 |
C2 |
N1 |
C6 |
1.9 |
359.9 |
| N1 |
C2 |
N3 |
O2 |
181.9 |
180.1 |
| C2 |
N3 |
C4 |
N4 |
186.2 |
180.0 |
| C2 |
N3 |
C4 |
N5 |
5.3 |
0.3 |
| N4 |
C4 |
N3 |
N5 |
180.9 |
179.7 |
| N3 |
C4 |
N4 |
HN41 |
180.0 |
180.1 |
| N3 |
C4 |
N4 |
HN42 |
54.7 |
359.8 |
| N3 |
C4 |
N5 |
C6 |
355.2 |
359.4 |
| N3 |
C4 |
N4 |
N5 |
179.1 |
180.3 |
| N4 |
C4 |
N5 |
C6 |
174.3 |
179.7 |
| HN41 |
N4 |
C4 |
HN42 |
125.2 |
180.3 |
| N1 |
C6 |
N5 |
C4 |
3.1 |
0.6 |
| N3 |
C4 |
N5 |
N4 |
180.9 |
179.7 |
| N5 |
C4 |
N4 |
HN41 |
0.9 |
359.7 |
| N5 |
C4 |
N4 |
HN42 |
235.6 |
179.4 |
| C4 |
N5 |
C6 |
H6 |
183.1 |
180.3 |
| HN41 |
N4 |
C4 |
N5 |
0.9 |
359.7 |
| C4 |
N4 |
HN41 |
HN42 |
234.7 |
179.7 |
| HN42 |
N4 |
C4 |
N5 |
235.6 |
179.4 |
| C4 |
N4 |
HN42 |
HN41 |
132.7 |
180.3 |
| N1 |
C6 |
N5 |
H6 |
180.0 |
180.3 |
| N1 |
C6 |
H6 |
N5 |
180.0 |
179.7 |