PDB Chemical Component XC5
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 XC5
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O2 |
C2 |
1.221 |
1.219 |
| C2 |
N3 |
1.351 |
1.331 |
| C2 |
N1 |
1.350 |
1.346 |
| N3 |
C4 |
1.331 |
1.327 |
| C2' |
C1' |
1.532 |
1.545 |
| C2' |
C3' |
1.547 |
1.545 |
| C1' |
N1 |
1.479 |
1.465 |
| C1' |
O4' |
1.427 |
1.444 |
| N1 |
C6 |
1.357 |
1.362 |
| O3' |
C3' |
1.443 |
1.429 |
| C4 |
N4 |
1.372 |
1.376 |
| C4 |
C5 |
1.405 |
1.410 |
| C3' |
C4' |
1.554 |
1.544 |
| O4' |
C4' |
1.449 |
1.444 |
| C4' |
C5' |
1.534 |
1.530 |
| C6 |
C5 |
1.366 |
1.354 |
| O1B |
PB |
1.493 |
1.480 |
| C5' |
O5' |
1.428 |
1.429 |
| O5' |
PA |
1.558 |
1.609 |
| PB |
O2B |
1.586 |
1.611 |
| PB |
C3A |
1.818 |
1.823 |
| PB |
O3B |
1.591 |
1.610 |
| C3A |
PA |
1.813 |
1.823 |
| O3B |
PG |
1.592 |
1.610 |
| PA |
O2A |
1.474 |
1.480 |
| PA |
O1A |
1.603 |
1.611 |
| PG |
O2G |
1.598 |
1.480 |
| PG |
O1G |
1.483 |
1.610 |
| PG |
O3G |
1.595 |
1.611 |
| O1A |
H1 |
0.950 |
0.966 |
| C3A |
H2 |
1.100 |
1.090 |
| C3A |
H3 |
1.100 |
1.089 |
| O2B |
H4 |
0.950 |
0.967 |
| O1G |
H5 |
0.950 |
0.967 |
| O3G |
H6 |
0.950 |
0.967 |
| C5 |
H7 |
1.080 |
1.080 |
| C6 |
H8 |
1.080 |
1.080 |
| N4 |
H9 |
1.000 |
0.970 |
| N4 |
H10 |
1.000 |
0.970 |
| C1' |
H11 |
1.100 |
1.090 |
| C2' |
H12 |
1.100 |
1.090 |
| C2' |
H13 |
1.100 |
1.091 |
| C3' |
H14 |
1.100 |
1.090 |
| C4' |
H15 |
1.100 |
1.090 |
| C5' |
H16 |
1.100 |
1.090 |
| C5' |
H17 |
1.100 |
1.090 |
| O3' |
H18 |
0.950 |
0.968 |
Bond Angles for XC5
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C2 |
N3 |
C4 |
120.4 |
120.7 |
| C2 |
N1 |
C6 |
119.6 |
120.4 |
| N3 |
C4 |
N4 |
120.8 |
120.2 |
| N3 |
C4 |
C5 |
119.4 |
119.6 |
| C2' |
C1' |
O4' |
106.1 |
104.8 |
| C2' |
C1' |
H11 |
109.7 |
110.4 |
| C2' |
C3' |
C4' |
99.1 |
104.1 |
| C3' |
C2' |
H12 |
111.3 |
110.5 |
| C3' |
C2' |
H13 |
111.3 |
110.5 |
| C2' |
C3' |
H14 |
110.5 |
110.6 |
| C1' |
O4' |
C4' |
110.4 |
105.3 |
| O4' |
C1' |
H11 |
111.3 |
110.4 |
| N1 |
C6 |
C5 |
119.9 |
119.3 |
| N1 |
C6 |
H8 |
120.1 |
120.4 |
| O3' |
C3' |
H14 |
112.0 |
110.5 |
| C5 |
C4 |
N4 |
119.8 |
120.2 |
| C4 |
N4 |
H9 |
120.0 |
120.0 |
| C4 |
N4 |
H10 |
120.0 |
120.0 |
| C4 |
C5 |
H7 |
120.4 |
120.5 |
| C3' |
C4' |
C5' |
111.0 |
110.4 |
| C4' |
C3' |
H14 |
110.4 |
110.5 |
| C3' |
C4' |
H15 |
110.6 |
110.4 |
| O4' |
C4' |
C5' |
109.9 |
110.4 |
| O4' |
C4' |
H15 |
112.2 |
110.4 |
| C4' |
C5' |
O5' |
108.2 |
109.5 |
| C5' |
C4' |
H15 |
110.9 |
110.3 |
| C4' |
C5' |
H16 |
109.8 |
109.5 |
| C4' |
C5' |
H17 |
109.8 |
109.5 |
| C6 |
C5 |
H7 |
120.3 |
120.5 |
| O1B |
PB |
O2B |
111.0 |
109.5 |
| O1B |
PB |
O3B |
107.7 |
109.5 |
| O2B |
PB |
O3B |
108.5 |
109.5 |
| PB |
O2B |
H4 |
109.5 |
114.0 |
| PB |
C3A |
H2 |
107.7 |
109.4 |
| PB |
C3A |
H3 |
107.8 |
109.5 |
| PB |
O3B |
PG |
125.8 |
134.0 |
| O3B |
PG |
O2G |
108.9 |
109.5 |
| O3B |
PG |
O1G |
105.0 |
109.5 |
| O3B |
PG |
O3G |
109.8 |
109.5 |
| O1A |
PA |
O2A |
108.6 |
109.5 |
| PA |
O1A |
H1 |
109.5 |
114.0 |
| O1G |
PG |
O2G |
113.2 |
109.4 |
| O2G |
PG |
O3G |
109.9 |
109.5 |
| O1G |
PG |
O3G |
109.9 |
109.5 |
| PG |
O1G |
H5 |
109.5 |
114.0 |
| PG |
O3G |
H6 |
109.5 |
113.9 |
| H2 |
C3A |
H3 |
109.4 |
109.5 |
| H9 |
N4 |
H10 |
120.0 |
120.0 |
| H12 |
C2' |
H13 |
109.4 |
110.5 |
| H16 |
C5' |
H17 |
109.5 |
109.5 |
Torsion Angles for XC5
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| N3 |
C2 |
N1 |
C6 |
0.4 |
0.0 |
| C2 |
N3 |
C4 |
N4 |
179.7 |
180.0 |
| C2 |
N3 |
C4 |
C5 |
359.5 |
360.0 |
| C2 |
N1 |
C6 |
C5 |
360.0 |
0.0 |
| C2 |
N1 |
C6 |
H8 |
180.0 |
180.0 |
| C5 |
C4 |
N3 |
N4 |
179.8 |
179.9 |
| N3 |
C4 |
N4 |
H9 |
0.0 |
359.9 |
| N3 |
C4 |
N4 |
H10 |
180.0 |
180.0 |
| N3 |
C4 |
C5 |
H7 |
180.9 |
180.0 |
| C2' |
C1' |
O4' |
C4' |
356.2 |
319.5 |
| O4' |
C1' |
C2' |
H11 |
120.3 |
118.9 |
| C3' |
C2' |
C1' |
O4' |
335.7 |
23.9 |
| C3' |
C2' |
C1' |
H11 |
215.4 |
265.1 |
| O3' |
C3' |
C2' |
H14 |
235.7 |
237.3 |
| C2' |
C3' |
C4' |
C5' |
199.8 |
217.2 |
| C4' |
C3' |
C2' |
H14 |
115.9 |
118.6 |
| C2' |
C3' |
C4' |
H15 |
76.3 |
94.9 |
| H12 |
C2' |
C3' |
H13 |
122.4 |
122.7 |
| C1' |
N1 |
C6 |
H8 |
0.0 |
0.2 |
| C2' |
C1' |
O4' |
H11 |
240.7 |
241.1 |
| C1' |
O4' |
C4' |
C5' |
148.0 |
159.3 |
| C1' |
O4' |
C4' |
H15 |
271.9 |
281.6 |
| N1 |
C6 |
C5 |
H7 |
179.4 |
179.9 |
| O3' |
C3' |
C2' |
H12 |
41.7 |
360.0 |
| O3' |
C3' |
C2' |
H13 |
279.3 |
237.3 |
| C2' |
C3' |
O3' |
H14 |
123.4 |
122.7 |
| C4' |
C3' |
O3' |
H14 |
233.8 |
237.4 |
| O3' |
C3' |
C4' |
H15 |
319.3 |
336.3 |
| N3 |
C4 |
N4 |
C5 |
179.8 |
179.9 |
| N4 |
C4 |
C5 |
H7 |
0.7 |
360.0 |
| H9 |
N4 |
C4 |
H10 |
180.0 |
179.9 |
| N3 |
C4 |
C5 |
N4 |
180.2 |
180.1 |
| N1 |
C6 |
C5 |
C4 |
359.4 |
359.9 |
| C5 |
C4 |
N4 |
H9 |
180.2 |
180.0 |
| C5 |
C4 |
N4 |
H10 |
0.2 |
0.1 |
| C6 |
C5 |
C4 |
H7 |
180.0 |
180.1 |
| C4' |
C3' |
C2' |
H12 |
281.8 |
241.3 |
| C4' |
C3' |
C2' |
H13 |
159.5 |
118.7 |
| C2' |
C3' |
C4' |
H14 |
244.1 |
241.3 |
| C1' |
O4' |
C4' |
C3' |
30.2 |
40.5 |
| O3' |
C3' |
C4' |
H14 |
127.1 |
122.6 |
| O4' |
C4' |
C3' |
C5' |
117.1 |
118.9 |
| O4' |
C4' |
C3' |
H15 |
240.6 |
241.1 |
| C3' |
C4' |
C5' |
O5' |
51.8 |
185.0 |
| C5' |
C4' |
C3' |
H15 |
123.5 |
122.3 |
| C3' |
C4' |
C5' |
H16 |
171.6 |
305.0 |
| C3' |
C4' |
C5' |
H17 |
292.0 |
65.0 |
| C4' |
O4' |
C1' |
H11 |
115.5 |
78.4 |
| C3' |
C4' |
O4' |
C5' |
242.2 |
241.1 |
| O4' |
C4' |
C3' |
H14 |
72.8 |
94.7 |
| C3' |
C4' |
O4' |
H15 |
118.3 |
118.9 |
| O4' |
C4' |
C5' |
O5' |
299.7 |
69.6 |
| C5' |
C4' |
O4' |
H15 |
236.1 |
237.7 |
| O4' |
C4' |
C5' |
H16 |
59.6 |
189.6 |
| O4' |
C4' |
C5' |
H17 |
179.9 |
309.6 |
| C5' |
C4' |
C3' |
H14 |
315.7 |
335.9 |
| C3' |
C4' |
C5' |
H15 |
236.7 |
237.7 |
| O4' |
C4' |
C5' |
H15 |
124.6 |
122.3 |
| H16 |
C5' |
C4' |
H17 |
239.6 |
240.0 |
| N1 |
C6 |
C5 |
H8 |
180.0 |
179.9 |
| C6 |
C5 |
C4 |
N4 |
180.7 |
180.0 |
| C4 |
C5 |
C6 |
H7 |
180.0 |
179.9 |
| O2B |
PB |
O1B |
O3B |
241.3 |
240.0 |
| O1B |
PB |
O2B |
H4 |
0.0 |
180.0 |
| O1B |
PB |
C3A |
H2 |
235.0 |
300.0 |
| O1B |
PB |
C3A |
H3 |
353.0 |
180.0 |
| O1B |
PB |
O3B |
PG |
181.8 |
300.0 |
| O5' |
C5' |
C4' |
H15 |
175.1 |
307.3 |
| C4' |
C5' |
O5' |
H16 |
119.8 |
120.0 |
| C4' |
C5' |
O5' |
H17 |
240.2 |
240.0 |
| O5' |
PA |
O1A |
H1 |
237.2 |
60.0 |
| O1B |
PB |
O2B |
O3B |
118.2 |
120.0 |
| O2B |
PB |
C3A |
H2 |
110.1 |
180.0 |
| O2B |
PB |
C3A |
H3 |
228.1 |
60.1 |
| O2B |
PB |
O3B |
PG |
302.1 |
60.1 |
| H2 |
C3A |
PB |
H3 |
242.0 |
120.0 |
| O1B |
PB |
O3B |
O2B |
239.8 |
240.0 |
| O3B |
PB |
O2B |
H4 |
241.8 |
59.9 |
| O3B |
PB |
C3A |
H2 |
351.3 |
60.1 |
| O3B |
PB |
C3A |
H3 |
109.3 |
300.1 |
| PB |
O3B |
PG |
O2G |
131.3 |
319.9 |
| PB |
O3B |
PG |
O1G |
9.8 |
200.0 |
| PB |
O3B |
PG |
O3G |
251.7 |
80.0 |
| C3A |
PA |
O1A |
H1 |
116.9 |
300.0 |
| O1G |
PG |
O3B |
O2G |
238.5 |
240.0 |
| O2G |
PG |
O3B |
O3G |
239.6 |
240.0 |
| O1G |
PG |
O3B |
O3G |
118.1 |
120.0 |
| O3B |
PG |
O1G |
H5 |
118.7 |
180.0 |
| O3B |
PG |
O3G |
H6 |
240.3 |
59.9 |
| O2A |
PA |
O1A |
H1 |
360.0 |
180.0 |
| O3B |
PG |
O2G |
O1G |
243.6 |
240.0 |
| O3B |
PG |
O2G |
O3G |
120.3 |
120.0 |
| O1G |
PG |
O2G |
O3G |
236.7 |
240.0 |
| O2G |
PG |
O1G |
H5 |
360.0 |
60.1 |
| O2G |
PG |
O3G |
H6 |
0.0 |
180.0 |
| O3B |
PG |
O1G |
O2G |
118.7 |
120.0 |
| O3B |
PG |
O1G |
O3G |
242.0 |
240.0 |
| O2G |
PG |
O1G |
O3G |
123.3 |
120.0 |
| O1G |
PG |
O3G |
H6 |
125.3 |
300.0 |
| O3B |
PG |
O3G |
O2G |
240.2 |
240.0 |
| O3B |
PG |
O3G |
O1G |
115.0 |
120.0 |
| O1G |
PG |
O3G |
O2G |
125.2 |
120.0 |
| O3G |
PG |
O1G |
H5 |
236.7 |
300.1 |
| H1 |
O1A |
PA |
O2A |
360.0 |
180.0 |
| PB |
C3A |
H2 |
H3 |
116.9 |
240.0 |
| PB |
C3A |
H3 |
H2 |
243.1 |
119.9 |
| H4 |
O2B |
PB |
O3B |
241.8 |
59.9 |
| H5 |
O1G |
PG |
O2G |
360.0 |
60.1 |
| H5 |
O1G |
PG |
O3G |
236.7 |
300.1 |
| H7 |
C5 |
C4 |
N4 |
0.7 |
360.0 |
| N1 |
C6 |
H8 |
C5 |
180.0 |
180.1 |
| H8 |
C6 |
C5 |
H7 |
359.4 |
0.0 |
| C4 |
N4 |
H9 |
H10 |
180.0 |
180.1 |
| C4 |
N4 |
H10 |
H9 |
180.0 |
179.9 |
| C2' |
C1' |
H11 |
O4' |
117.1 |
115.4 |
| H11 |
C1' |
O4' |
C4' |
115.5 |
78.4 |
| H12 |
C2' |
C1' |
O4' |
94.6 |
142.6 |
| H12 |
C2' |
C1' |
H11 |
334.3 |
23.8 |
| H12 |
C2' |
C3' |
C4' |
281.8 |
241.3 |
| C3' |
C2' |
H12 |
H13 |
236.5 |
237.4 |
| H12 |
C2' |
C3' |
H14 |
165.9 |
122.7 |
| H13 |
C2' |
C1' |
O4' |
216.9 |
265.3 |
| H13 |
C2' |
C1' |
H11 |
96.6 |
146.5 |
| H13 |
C2' |
C3' |
C4' |
159.5 |
118.7 |
| C3' |
C2' |
H13 |
H12 |
123.5 |
122.6 |
| H13 |
C2' |
C3' |
H14 |
43.6 |
0.0 |
| C2' |
C3' |
H14 |
C4' |
108.6 |
114.7 |
| H14 |
C3' |
C2' |
H12 |
165.9 |
122.7 |
| H14 |
C3' |
C2' |
H13 |
43.6 |
0.0 |
| H14 |
C3' |
C4' |
C5' |
315.7 |
335.9 |
| H14 |
C3' |
C4' |
H15 |
192.2 |
213.6 |
| C3' |
C4' |
H15 |
C5' |
123.6 |
122.3 |
| H15 |
C4' |
C3' |
H14 |
192.2 |
213.6 |
| O4' |
C4' |
H15 |
C5' |
236.6 |
237.7 |
| H15 |
C4' |
C5' |
O5' |
175.1 |
307.3 |
| H15 |
C4' |
C5' |
H16 |
294.9 |
67.3 |
| H15 |
C4' |
C5' |
H17 |
55.3 |
187.3 |
| C4' |
C5' |
H16 |
O5' |
241.1 |
240.0 |
| H16 |
C5' |
C4' |
H15 |
294.9 |
67.3 |
| C4' |
C5' |
H16 |
H17 |
120.6 |
120.0 |
| C4' |
C5' |
H17 |
O5' |
118.9 |
120.0 |
| H17 |
C5' |
C4' |
H15 |
55.3 |
187.3 |
| C4' |
C5' |
H17 |
H16 |
239.5 |
240.0 |
| H18 |
O3' |
C3' |
H14 |
19.6 |
298.7 |