PDB Chemical Component NCU
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 NCU
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O3' |
C3' |
1.421 |
1.430 |
| OP2 |
P |
1.603 |
1.610 |
| C3' |
C2' |
1.513 |
1.557 |
| C3' |
C4' |
1.520 |
1.553 |
| OP1 |
P |
1.596 |
1.480 |
| P |
O5' |
1.639 |
1.611 |
| O5' |
C5' |
1.421 |
1.429 |
| C5' |
C4' |
1.511 |
1.530 |
| O2' |
C2' |
1.458 |
1.442 |
| O2' |
N6' |
1.422 |
1.465 |
| C2' |
C1' |
1.530 |
1.548 |
| C4' |
C6' |
1.574 |
1.580 |
| C4' |
O4' |
1.445 |
1.441 |
| C7' |
N6' |
1.454 |
1.470 |
| C6' |
N6' |
1.510 |
1.470 |
| C7 |
C5 |
1.487 |
1.507 |
| O4' |
C1' |
1.435 |
1.433 |
| C1' |
N1 |
1.471 |
1.465 |
| C6 |
C5 |
1.342 |
1.354 |
| C6 |
N1 |
1.369 |
1.363 |
| C5 |
C4 |
1.424 |
1.410 |
| N1 |
C2 |
1.391 |
1.345 |
| C4 |
N4 |
1.335 |
1.376 |
| C4 |
N3 |
1.334 |
1.326 |
| C2 |
N3 |
1.351 |
1.331 |
| C2 |
O2 |
1.242 |
1.220 |
| C7 |
H1 |
1.100 |
1.091 |
| C7 |
H2 |
1.100 |
1.090 |
| C7 |
H3 |
1.100 |
1.089 |
| C6 |
HOP2 |
1.080 |
1.080 |
| OP2 |
H4 |
0.950 |
0.966 |
| N4 |
H41 |
1.000 |
0.970 |
| N4 |
H42 |
1.000 |
0.970 |
| C2' |
H2' |
1.100 |
1.091 |
| C5' |
H5' |
1.100 |
1.089 |
| C5' |
H5'' |
1.100 |
1.090 |
| C1' |
H1' |
1.100 |
1.090 |
| C3' |
H3' |
1.100 |
1.090 |
| O3' |
HO3' |
0.950 |
0.967 |
| C6' |
H15 |
1.100 |
1.090 |
| C6' |
H16 |
1.100 |
1.090 |
| C7' |
H17 |
1.101 |
1.090 |
| C7' |
H18 |
1.100 |
1.089 |
| C7' |
H19 |
1.101 |
1.090 |
| P |
OP3 |
1.607 |
1.610 |
| OP3 |
HOP3 |
0.950 |
0.967 |
Bond Angles for NCU
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O3' |
C3' |
H3' |
107.4 |
111.2 |
| OP2 |
P |
O5' |
102.1 |
109.4 |
| OP2 |
P |
OP3 |
110.8 |
109.5 |
| C3' |
C2' |
H2' |
112.8 |
113.8 |
| C3' |
C4' |
C6' |
109.5 |
105.9 |
| OP1 |
P |
O5' |
104.1 |
109.5 |
| OP1 |
P |
OP3 |
112.5 |
109.5 |
| P |
O5' |
C5' |
120.9 |
123.0 |
| O5' |
P |
OP3 |
104.9 |
109.5 |
| O5' |
C5' |
C4' |
110.2 |
109.4 |
| O5' |
C5' |
H5' |
109.3 |
109.5 |
| O5' |
C5' |
H5'' |
109.3 |
109.5 |
| C5' |
C4' |
C6' |
110.2 |
112.6 |
| C5' |
C4' |
O4' |
111.5 |
113.7 |
| C4' |
C5' |
H5' |
109.3 |
109.5 |
| C4' |
C5' |
H5'' |
109.3 |
109.5 |
| O2' |
C2' |
H2' |
113.7 |
113.6 |
| O2' |
N6' |
C6' |
113.7 |
111.9 |
| C2' |
C1' |
O4' |
107.0 |
107.1 |
| C1' |
C2' |
H2' |
112.6 |
113.8 |
| C2' |
C1' |
H1' |
109.3 |
110.0 |
| O4' |
C4' |
C6' |
105.0 |
106.2 |
| C4' |
C6' |
N6' |
113.2 |
109.1 |
| C4' |
C6' |
H15 |
108.5 |
109.6 |
| C4' |
C6' |
H16 |
108.5 |
109.6 |
| C4' |
O4' |
C1' |
108.0 |
109.4 |
| N6' |
C6' |
H15 |
108.5 |
109.5 |
| N6' |
C6' |
H16 |
108.5 |
109.4 |
| C7 |
C5 |
C6 |
118.1 |
120.5 |
| C7 |
C5 |
C4 |
124.5 |
120.5 |
| C5 |
C7 |
H1 |
109.5 |
109.4 |
| C5 |
C7 |
H2 |
109.5 |
109.5 |
| C5 |
C7 |
H3 |
109.5 |
109.5 |
| O4' |
C1' |
H1' |
110.6 |
109.9 |
| C6 |
C5 |
C4 |
117.4 |
119.0 |
| C5 |
C6 |
HOP2 |
119.5 |
120.4 |
| C6 |
N1 |
C2 |
120.4 |
120.3 |
| C5 |
C4 |
N4 |
120.4 |
120.2 |
| C5 |
C4 |
N3 |
121.9 |
119.6 |
| N1 |
C2 |
N3 |
119.4 |
121.1 |
| N1 |
C2 |
O2 |
118.7 |
119.4 |
| N3 |
C4 |
N4 |
117.8 |
120.2 |
| C4 |
N4 |
H41 |
120.0 |
120.0 |
| C4 |
N4 |
H42 |
120.0 |
120.0 |
| C4 |
N3 |
C2 |
120.0 |
120.7 |
| O2 |
C2 |
N3 |
121.9 |
119.5 |
| H1 |
C7 |
H2 |
109.5 |
109.4 |
| H1 |
C7 |
H3 |
109.4 |
109.5 |
| H2 |
C7 |
H3 |
109.5 |
109.5 |
| H41 |
N4 |
H42 |
120.0 |
120.0 |
| H5' |
C5' |
H5'' |
109.5 |
109.4 |
| H15 |
C6' |
H16 |
109.5 |
109.7 |
| H17 |
C7' |
H18 |
109.5 |
109.5 |
| H17 |
C7' |
H19 |
109.4 |
109.5 |
| H18 |
C7' |
H19 |
109.5 |
109.5 |
| P |
OP3 |
HOP3 |
109.5 |
114.0 |
Torsion Angles for NCU
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O3' |
C3' |
C2' |
H2' |
290.9 |
278.7 |
| O3' |
C3' |
C4' |
C6' |
299.1 |
313.2 |
| OP1 |
P |
OP2 |
O5' |
245.5 |
120.0 |
| OP1 |
P |
OP2 |
OP3 |
134.2 |
240.0 |
| OP2 |
P |
O5' |
C5' |
56.5 |
65.0 |
| O5' |
P |
OP2 |
OP3 |
248.7 |
120.0 |
| OP2 |
P |
OP3 |
HOP3 |
138.1 |
299.9 |
| O2' |
C2' |
C3' |
H2' |
126.2 |
126.0 |
| C1' |
C2' |
C3' |
H2' |
239.6 |
237.3 |
| C3' |
C2' |
C1' |
H1' |
215.7 |
216.5 |
| C4' |
C3' |
C2' |
H2' |
161.2 |
161.2 |
| C5' |
C4' |
C3' |
C6' |
126.0 |
123.9 |
| C3' |
C4' |
C5' |
H5' |
296.0 |
65.4 |
| C3' |
C4' |
C5' |
H5'' |
176.2 |
305.5 |
| O4' |
C4' |
C3' |
C6' |
248.6 |
248.1 |
| C3' |
C4' |
C6' |
N6' |
310.3 |
297.1 |
| C3' |
C4' |
C6' |
H15 |
70.8 |
56.9 |
| C3' |
C4' |
C6' |
H16 |
189.8 |
177.3 |
| OP2 |
P |
OP1 |
O5' |
113.5 |
240.0 |
| OP2 |
P |
OP1 |
OP3 |
226.5 |
120.0 |
| OP1 |
P |
O5' |
C5' |
182.5 |
305.0 |
| O5' |
P |
OP1 |
OP3 |
113.0 |
240.0 |
| OP1 |
P |
OP3 |
HOP3 |
0.0 |
59.9 |
| OP2 |
P |
O5' |
OP3 |
115.6 |
240.0 |
| OP1 |
P |
O5' |
OP3 |
241.7 |
120.0 |
| P |
O5' |
C5' |
C4' |
166.9 |
180.0 |
| P |
O5' |
C5' |
H5' |
287.0 |
300.0 |
| P |
O5' |
C5' |
H5'' |
46.8 |
60.0 |
| O5' |
P |
OP3 |
HOP3 |
247.5 |
180.0 |
| C5' |
O5' |
P |
OP3 |
300.9 |
185.0 |
| O5' |
C5' |
C4' |
C6' |
181.8 |
305.7 |
| O5' |
C5' |
C4' |
O4' |
298.0 |
66.6 |
| C4' |
C5' |
O5' |
H5' |
239.9 |
240.0 |
| C4' |
C5' |
O5' |
H5'' |
120.1 |
120.0 |
| H5' |
C5' |
O5' |
H5'' |
240.2 |
240.0 |
| C3' |
C4' |
C5' |
C6' |
234.3 |
239.8 |
| O5' |
C5' |
C4' |
H5' |
120.1 |
120.1 |
| O5' |
C5' |
C4' |
H5'' |
239.9 |
240.0 |
| O4' |
C4' |
C5' |
C6' |
116.2 |
120.9 |
| C5' |
C4' |
C6' |
N6' |
180.6 |
172.7 |
| C5' |
C4' |
C6' |
H15 |
301.1 |
292.5 |
| C5' |
C4' |
C6' |
H16 |
60.1 |
52.9 |
| C5' |
C4' |
O4' |
C1' |
155.2 |
151.7 |
| H5' |
C5' |
C4' |
H5'' |
119.8 |
120.0 |
| C3' |
C2' |
O2' |
H2' |
234.3 |
233.9 |
| C1' |
C2' |
O2' |
H2' |
125.9 |
126.0 |
| O2' |
C2' |
C1' |
H1' |
328.5 |
327.9 |
| N6' |
O2' |
C2' |
H2' |
187.6 |
192.2 |
| C4' |
C6' |
N6' |
O2' |
32.3 |
51.2 |
| O2' |
N6' |
C6' |
H15 |
271.8 |
291.3 |
| O2' |
N6' |
C6' |
H16 |
152.8 |
171.1 |
| C3' |
C2' |
C1' |
H2' |
120.6 |
122.7 |
| O2' |
C2' |
C1' |
H2' |
233.4 |
234.1 |
| C4' |
O4' |
C1' |
C2' |
357.1 |
358.0 |
| O4' |
C1' |
C2' |
H1' |
119.8 |
119.4 |
| C5' |
C4' |
C6' |
O4' |
120.2 |
125.0 |
| C6' |
C4' |
C5' |
H5' |
61.7 |
185.7 |
| C6' |
C4' |
C5' |
H5'' |
301.9 |
65.7 |
| O2' |
N6' |
C6' |
C4' |
32.3 |
51.2 |
| C6' |
C4' |
O4' |
C1' |
274.5 |
276.1 |
| N6' |
C6' |
C4' |
H15 |
239.5 |
240.2 |
| N6' |
C6' |
C4' |
H16 |
120.5 |
119.8 |
| H15 |
C6' |
C4' |
H16 |
241.1 |
239.6 |
| C3' |
C4' |
O4' |
C6' |
114.7 |
111.6 |
| C5' |
C4' |
O4' |
C6' |
240.7 |
235.6 |
| O4' |
C4' |
C5' |
H5' |
177.9 |
306.5 |
| O4' |
C4' |
C5' |
H5'' |
58.1 |
186.6 |
| C2' |
C1' |
O4' |
C4' |
357.1 |
358.0 |
| O4' |
C4' |
C6' |
N6' |
60.4 |
47.6 |
| O4' |
C4' |
C6' |
H15 |
181.0 |
167.4 |
| O4' |
C4' |
C6' |
H16 |
299.9 |
287.8 |
| C4' |
O4' |
C1' |
H1' |
116.1 |
117.4 |
| C7' |
N6' |
C6' |
H15 |
33.3 |
55.9 |
| C7' |
N6' |
C6' |
H16 |
274.4 |
295.7 |
| C4' |
C6' |
N6' |
H15 |
120.5 |
119.9 |
| C4' |
C6' |
N6' |
H16 |
239.5 |
240.1 |
| H15 |
C6' |
N6' |
H16 |
119.0 |
120.2 |
| C6 |
C5 |
C7 |
C4 |
177.9 |
180.1 |
| C7 |
C5 |
C6 |
HOP2 |
2.5 |
360.0 |
| C7 |
C5 |
C4 |
N4 |
359.8 |
0.1 |
| C7 |
C5 |
C4 |
N3 |
179.2 |
180.0 |
| H1 |
C7 |
C5 |
H2 |
240.0 |
240.1 |
| H1 |
C7 |
C5 |
H3 |
120.0 |
120.0 |
| H2 |
C7 |
C5 |
H3 |
240.0 |
239.9 |
| O4' |
C1' |
C2' |
H2' |
214.9 |
213.2 |
| C2' |
C1' |
O4' |
H1' |
241.0 |
240.6 |
| C1' |
O4' |
C4' |
C6' |
274.5 |
276.1 |
| C7 |
C5 |
C6 |
C4 |
181.9 |
179.9 |
| C6 |
C5 |
C7 |
H1 |
180.0 |
90.1 |
| C6 |
C5 |
C7 |
H2 |
300.0 |
210.0 |
| C6 |
C5 |
C7 |
H3 |
60.0 |
330.0 |
| C5 |
C6 |
N1 |
C2 |
358.0 |
360.0 |
| C6 |
C5 |
C4 |
N4 |
181.9 |
180.0 |
| C6 |
C5 |
C4 |
N3 |
1.3 |
360.0 |
| C6 |
N1 |
C2 |
N3 |
1.7 |
0.0 |
| C6 |
N1 |
C2 |
O2 |
181.4 |
180.0 |
| C7 |
C5 |
C4 |
C6 |
177.9 |
180.1 |
| C4 |
C5 |
C7 |
H1 |
2.1 |
270.0 |
| C4 |
C5 |
C7 |
H2 |
122.1 |
29.9 |
| C4 |
C5 |
C7 |
H3 |
242.1 |
150.0 |
| C4 |
C5 |
C6 |
HOP2 |
180.6 |
180.1 |
| N3 |
C4 |
C5 |
N4 |
179.4 |
180.0 |
| C5 |
C4 |
N4 |
H41 |
179.4 |
360.0 |
| C5 |
C4 |
N4 |
H42 |
359.4 |
179.9 |
| C5 |
C4 |
N3 |
C2 |
358.4 |
0.0 |
| C4 |
N3 |
C2 |
N1 |
0.1 |
360.0 |
| O2 |
C2 |
N1 |
N3 |
179.7 |
180.0 |
| C5 |
C4 |
N4 |
N3 |
179.4 |
180.0 |
| N4 |
C4 |
N3 |
C2 |
177.8 |
180.0 |
| H41 |
N4 |
C4 |
H42 |
180.0 |
180.0 |
| C5 |
C4 |
N3 |
N4 |
180.6 |
180.0 |
| N1 |
C2 |
N3 |
C4 |
0.1 |
360.0 |
| N3 |
C4 |
N4 |
H41 |
360.0 |
180.0 |
| N3 |
C4 |
N4 |
H42 |
180.0 |
359.9 |
| O2 |
C2 |
N3 |
C4 |
180.4 |
180.0 |
| N1 |
C2 |
N3 |
O2 |
179.7 |
180.0 |
| C2 |
N3 |
C4 |
N4 |
177.8 |
180.0 |
| N1 |
C2 |
O2 |
N3 |
180.3 |
180.0 |
| C4 |
N3 |
C2 |
O2 |
180.4 |
180.0 |
| H1 |
C7 |
C5 |
C6 |
180.0 |
90.1 |
| H1 |
C7 |
C5 |
C4 |
2.1 |
270.0 |
| C5 |
C7 |
H1 |
H2 |
120.0 |
119.9 |
| C5 |
C7 |
H1 |
H3 |
240.0 |
240.0 |
| H2 |
C7 |
H1 |
H3 |
120.0 |
120.1 |
| H2 |
C7 |
C5 |
C6 |
300.0 |
210.0 |
| H2 |
C7 |
C5 |
C4 |
122.1 |
29.9 |
| C5 |
C7 |
H2 |
H1 |
240.0 |
240.1 |
| C5 |
C7 |
H2 |
H3 |
120.0 |
120.0 |
| H1 |
C7 |
H2 |
H3 |
240.0 |
240.0 |
| H3 |
C7 |
C5 |
C6 |
60.0 |
330.0 |
| H3 |
C7 |
C5 |
C4 |
242.1 |
150.0 |
| C5 |
C7 |
H3 |
H1 |
120.0 |
120.0 |
| C5 |
C7 |
H3 |
H2 |
240.0 |
240.0 |
| H1 |
C7 |
H3 |
H2 |
120.0 |
120.0 |
| HOP2 |
C6 |
C5 |
C4 |
180.6 |
180.1 |
| HOP2 |
C6 |
N1 |
C2 |
177.9 |
180.0 |
| H4 |
OP2 |
P |
O5' |
114.5 |
60.0 |
| H4 |
OP2 |
P |
OP3 |
225.8 |
300.0 |
| C4 |
N4 |
H41 |
H42 |
180.0 |
180.0 |
| C4 |
N4 |
H42 |
H41 |
180.0 |
180.0 |
| H2' |
C2' |
C1' |
O4' |
214.9 |
213.2 |
| H2' |
C2' |
C1' |
H1' |
95.1 |
93.8 |
| O5' |
C5' |
H5' |
C4' |
239.4 |
240.0 |
| O5' |
C5' |
H5' |
H5'' |
119.7 |
120.0 |
| H5' |
C5' |
C4' |
C6' |
61.7 |
185.7 |
| H5' |
C5' |
C4' |
O4' |
177.9 |
306.5 |
| C4' |
C5' |
H5' |
H5'' |
240.4 |
240.0 |
| O5' |
C5' |
H5'' |
C4' |
120.6 |
120.0 |
| O5' |
C5' |
H5'' |
H5' |
240.3 |
239.9 |
| H5'' |
C5' |
C4' |
C6' |
301.9 |
65.7 |
| H5'' |
C5' |
C4' |
O4' |
58.1 |
186.6 |
| C4' |
C5' |
H5'' |
H5' |
119.7 |
120.0 |
| C2' |
C1' |
H1' |
O4' |
117.5 |
117.7 |
| H1' |
C1' |
C2' |
H2' |
95.1 |
93.8 |
| H3' |
C3' |
C2' |
H2' |
50.6 |
43.6 |
| H3' |
C3' |
C4' |
C6' |
178.3 |
188.3 |
| HO3' |
O3' |
C3' |
H3' |
60.8 |
296.5 |
| C4' |
C6' |
H15 |
N6' |
236.6 |
240.4 |
| C4' |
C6' |
H15 |
H16 |
118.3 |
120.4 |
| N6' |
C6' |
H15 |
H16 |
241.7 |
239.9 |
| C4' |
C6' |
H16 |
N6' |
123.3 |
119.6 |
| C4' |
C6' |
H16 |
H15 |
241.7 |
239.6 |
| N6' |
C6' |
H16 |
H15 |
118.3 |
120.1 |
| H18 |
C7' |
H17 |
H19 |
120.0 |
120.1 |
| H17 |
C7' |
H18 |
H19 |
240.0 |
240.0 |
| H17 |
C7' |
H19 |
H18 |
120.0 |
120.0 |
| OP2 |
P |
OP3 |
O5' |
250.5 |
120.0 |
| OP1 |
P |
OP3 |
O5' |
112.5 |
240.0 |
| OP3 |
P |
O5' |
C5' |
300.9 |
185.0 |