PDB Chemical Component XYA
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 XYA
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O5' |
C5' |
1.423 |
1.429 |
| O5' |
H5' |
0.950 |
0.967 |
| C5' |
C4' |
1.537 |
1.531 |
| C5' |
H5'1 |
1.114 |
1.090 |
| C5' |
H5'2 |
1.115 |
1.089 |
| C4' |
O4' |
1.430 |
1.444 |
| C4' |
C3' |
1.497 |
1.544 |
| C4' |
H4' |
1.115 |
1.090 |
| O4' |
C1' |
1.458 |
1.444 |
| C1' |
N9 |
1.502 |
1.465 |
| C1' |
C2' |
1.547 |
1.545 |
| C1' |
H1' |
1.114 |
1.090 |
| N9 |
C8 |
1.362 |
1.363 |
| N9 |
C4 |
1.406 |
1.373 |
| C8 |
N7 |
1.292 |
1.301 |
| C8 |
H8 |
1.103 |
1.080 |
| N7 |
C5 |
1.393 |
1.355 |
| C5 |
C6 |
1.411 |
1.405 |
| C5 |
C4 |
1.386 |
1.405 |
| C6 |
N1 |
1.370 |
1.329 |
| C6 |
N6 |
1.325 |
1.384 |
| N1 |
C2 |
1.339 |
1.320 |
| C2 |
N3 |
1.357 |
1.316 |
| C2 |
H2 |
1.103 |
1.080 |
| N3 |
C4 |
1.376 |
1.329 |
| N6 |
HN61 |
1.020 |
0.970 |
| N6 |
HN62 |
1.020 |
0.970 |
| C2' |
O2' |
1.420 |
1.430 |
| C2' |
C3' |
1.518 |
1.548 |
| C2' |
H2' |
1.114 |
1.089 |
| O2' |
H1 |
0.950 |
0.967 |
| C3' |
O3' |
1.401 |
1.429 |
| C3' |
H3' |
1.115 |
1.090 |
| O3' |
H3 |
0.950 |
0.967 |
Bond Angles for XYA
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C5' |
O5' |
H5' |
110.6 |
106.8 |
| O5' |
C5' |
C4' |
110.6 |
109.4 |
| O5' |
C5' |
H5'1 |
111.8 |
109.5 |
| O5' |
C5' |
H5'2 |
111.8 |
109.5 |
| C4' |
C5' |
H5'1 |
111.8 |
109.5 |
| C4' |
C5' |
H5'2 |
111.8 |
109.5 |
| C5' |
C4' |
O4' |
111.6 |
110.3 |
| C5' |
C4' |
C3' |
114.3 |
110.5 |
| C5' |
C4' |
H4' |
102.8 |
110.3 |
| H5'1 |
C5' |
H5'2 |
98.6 |
109.5 |
| O4' |
C4' |
C3' |
102.8 |
104.8 |
| O4' |
C4' |
H4' |
114.2 |
110.4 |
| C4' |
O4' |
C1' |
110.5 |
105.2 |
| C3' |
C4' |
H4' |
111.6 |
110.4 |
| C4' |
C3' |
C2' |
102.2 |
104.1 |
| C4' |
C3' |
O3' |
110.9 |
110.5 |
| C4' |
C3' |
H3' |
115.9 |
110.6 |
| O4' |
C1' |
N9 |
101.9 |
110.4 |
| O4' |
C1' |
C2' |
104.3 |
104.9 |
| O4' |
C1' |
H1' |
121.4 |
110.4 |
| N9 |
C1' |
C2' |
119.8 |
110.3 |
| N9 |
C1' |
H1' |
106.4 |
110.3 |
| C1' |
N9 |
C8 |
123.5 |
126.3 |
| C1' |
N9 |
C4 |
132.5 |
126.3 |
| C2' |
C1' |
H1' |
104.1 |
110.4 |
| C1' |
C2' |
O2' |
112.6 |
110.8 |
| C1' |
C2' |
C3' |
101.2 |
103.9 |
| C1' |
C2' |
H2' |
112.7 |
110.5 |
| C8 |
N9 |
C4 |
103.8 |
107.4 |
| N9 |
C8 |
N7 |
117.0 |
110.0 |
| N9 |
C8 |
H8 |
124.0 |
124.9 |
| N9 |
C4 |
C5 |
105.3 |
106.0 |
| N9 |
C4 |
N3 |
129.1 |
134.9 |
| N7 |
C8 |
H8 |
119.1 |
125.1 |
| C8 |
N7 |
C5 |
102.6 |
109.5 |
| N7 |
C5 |
C6 |
132.2 |
134.7 |
| N7 |
C5 |
C4 |
111.3 |
107.1 |
| C6 |
C5 |
C4 |
116.6 |
118.2 |
| C5 |
C6 |
N1 |
119.1 |
118.4 |
| C5 |
C6 |
N6 |
121.0 |
120.8 |
| C5 |
C4 |
N3 |
125.7 |
119.1 |
| N1 |
C6 |
N6 |
119.9 |
120.8 |
| C6 |
N1 |
C2 |
119.2 |
121.2 |
| C6 |
N6 |
HN61 |
108.1 |
120.0 |
| C6 |
N6 |
HN62 |
121.0 |
120.0 |
| N1 |
C2 |
N3 |
126.8 |
122.5 |
| N1 |
C2 |
H2 |
115.9 |
118.8 |
| N3 |
C2 |
H2 |
117.3 |
118.7 |
| C2 |
N3 |
C4 |
112.7 |
120.6 |
| HN61 |
N6 |
HN62 |
108.1 |
120.0 |
| O2' |
C2' |
C3' |
108.9 |
110.5 |
| O2' |
C2' |
H2' |
105.5 |
110.5 |
| C2' |
O2' |
H1 |
112.6 |
106.8 |
| C3' |
C2' |
H2' |
116.1 |
110.5 |
| C2' |
C3' |
O3' |
116.2 |
110.6 |
| C2' |
C3' |
H3' |
110.5 |
110.4 |
| O3' |
C3' |
H3' |
101.8 |
110.4 |
| C3' |
O3' |
H3 |
110.9 |
106.8 |
Torsion Angles for XYA
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C4' |
C5' |
O5' |
H5'1 |
125.3 |
120.0 |
| C4' |
C5' |
O5' |
H5'2 |
234.8 |
240.0 |
| O5' |
C5' |
C4' |
O4' |
63.4 |
66.4 |
| O5' |
C5' |
C4' |
C3' |
179.4 |
181.9 |
| O5' |
C5' |
C4' |
H4' |
300.5 |
304.2 |
| H5'1 |
C5' |
O5' |
H5'2 |
109.5 |
120.0 |
| H5' |
O5' |
C5' |
C4' |
180.0 |
180.0 |
| H5' |
O5' |
C5' |
H5'1 |
54.7 |
60.0 |
| H5' |
O5' |
C5' |
H5'2 |
305.3 |
300.0 |
| C4' |
C5' |
O5' |
H5' |
180.0 |
180.0 |
| O5' |
C5' |
C4' |
H5'1 |
234.7 |
240.0 |
| O5' |
C5' |
C4' |
H5'2 |
125.3 |
120.0 |
| H5'1 |
C5' |
C4' |
H5'2 |
250.5 |
240.0 |
| O4' |
C4' |
C5' |
C3' |
243.9 |
244.5 |
| O4' |
C4' |
C5' |
H4' |
122.9 |
122.2 |
| C5' |
C4' |
O4' |
C1' |
95.5 |
159.5 |
| C3' |
C4' |
C5' |
H4' |
239.0 |
237.7 |
| C5' |
C4' |
C3' |
C2' |
281.1 |
217.1 |
| C5' |
C4' |
C3' |
O3' |
45.6 |
335.9 |
| C5' |
C4' |
C3' |
H3' |
160.9 |
98.5 |
| H5'1 |
C5' |
O5' |
H5' |
54.7 |
60.0 |
| O5' |
C5' |
H5'1 |
C4' |
124.6 |
120.0 |
| O5' |
C5' |
H5'1 |
H5'2 |
242.3 |
240.0 |
| C4' |
C5' |
H5'1 |
H5'2 |
117.7 |
120.0 |
| H5'1 |
C5' |
C4' |
O4' |
188.6 |
186.4 |
| H5'1 |
C5' |
C4' |
C3' |
304.7 |
301.9 |
| H5'1 |
C5' |
C4' |
H4' |
65.8 |
64.2 |
| H5'2 |
C5' |
O5' |
H5' |
305.3 |
300.0 |
| O5' |
C5' |
H5'2 |
C4' |
235.4 |
240.0 |
| O5' |
C5' |
H5'2 |
H5'1 |
117.7 |
120.0 |
| C4' |
C5' |
H5'2 |
H5'1 |
242.3 |
240.0 |
| H5'2 |
C5' |
C4' |
O4' |
298.1 |
306.5 |
| H5'2 |
C5' |
C4' |
C3' |
54.2 |
61.9 |
| H5'2 |
C5' |
C4' |
H4' |
175.2 |
184.3 |
| O4' |
C4' |
C5' |
H5'1 |
188.6 |
186.4 |
| O4' |
C4' |
C5' |
H5'2 |
298.1 |
306.5 |
| C5' |
C4' |
O4' |
C3' |
122.9 |
118.9 |
| C5' |
C4' |
O4' |
H4' |
243.9 |
237.8 |
| C3' |
C4' |
O4' |
H4' |
121.0 |
118.9 |
| O4' |
C4' |
C3' |
C2' |
42.2 |
335.9 |
| O4' |
C4' |
C3' |
O3' |
166.7 |
94.8 |
| O4' |
C4' |
C3' |
H3' |
282.0 |
217.4 |
| C4' |
O4' |
C1' |
N9 |
236.3 |
200.7 |
| C4' |
O4' |
C1' |
C2' |
1.7 |
319.5 |
| C4' |
O4' |
C1' |
H1' |
118.4 |
78.5 |
| C3' |
C4' |
C5' |
H5'1 |
304.7 |
301.9 |
| C3' |
C4' |
C5' |
H5'2 |
54.2 |
61.9 |
| C5' |
C4' |
C3' |
O4' |
238.9 |
241.1 |
| C5' |
C4' |
C3' |
H4' |
116.0 |
122.3 |
| O4' |
C4' |
C3' |
H4' |
237.1 |
241.1 |
| C3' |
C4' |
O4' |
C1' |
332.6 |
40.5 |
| C1' |
C2' |
C3' |
C4' |
319.5 |
0.1 |
| O2' |
C2' |
C3' |
C4' |
200.7 |
241.2 |
| C4' |
C3' |
C2' |
H2' |
81.8 |
118.7 |
| C2' |
C3' |
C4' |
O3' |
235.5 |
241.2 |
| C2' |
C3' |
C4' |
H3' |
120.2 |
118.6 |
| O3' |
C3' |
C4' |
H3' |
244.7 |
237.4 |
| C4' |
C3' |
O3' |
H3 |
180.0 |
61.5 |
| H4' |
C4' |
C5' |
H5'1 |
65.8 |
64.2 |
| H4' |
C4' |
C5' |
H5'2 |
175.2 |
184.3 |
| C5' |
C4' |
H4' |
O4' |
121.1 |
122.2 |
| C5' |
C4' |
H4' |
C3' |
237.1 |
237.6 |
| O4' |
C4' |
H4' |
C3' |
116.0 |
115.4 |
| H4' |
C4' |
O4' |
C1' |
211.5 |
281.6 |
| H4' |
C4' |
C3' |
C2' |
165.1 |
94.8 |
| H4' |
C4' |
C3' |
O3' |
289.5 |
213.6 |
| H4' |
C4' |
C3' |
H3' |
44.8 |
336.2 |
| C1' |
O4' |
C4' |
C3' |
332.6 |
40.5 |
| C1' |
O4' |
C4' |
H4' |
211.5 |
281.6 |
| N9 |
C1' |
O4' |
C2' |
234.6 |
241.1 |
| N9 |
C1' |
O4' |
H1' |
117.9 |
122.2 |
| O4' |
C1' |
N9 |
C8 |
293.5 |
22.0 |
| O4' |
C1' |
N9 |
C4 |
106.9 |
202.0 |
| C2' |
C1' |
O4' |
H1' |
243.2 |
241.0 |
| O4' |
C1' |
C2' |
O2' |
140.4 |
142.6 |
| O4' |
C1' |
C2' |
C3' |
24.2 |
23.9 |
| O4' |
C1' |
C2' |
H2' |
259.5 |
265.3 |
| O4' |
C1' |
N9 |
C2' |
114.4 |
115.5 |
| O4' |
C1' |
N9 |
H1' |
231.9 |
237.7 |
| C2' |
C1' |
N9 |
H1' |
117.5 |
122.2 |
| N9 |
C1' |
C2' |
O2' |
253.5 |
261.4 |
| N9 |
C1' |
C2' |
C3' |
137.3 |
142.8 |
| N9 |
C1' |
C2' |
H2' |
12.6 |
24.2 |
| C8 |
N9 |
C1' |
C4 |
186.6 |
180.0 |
| C1' |
N9 |
C8 |
N7 |
174.5 |
180.0 |
| C1' |
N9 |
C8 |
H8 |
354.5 |
360.0 |
| C1' |
N9 |
C4 |
C5 |
186.3 |
180.2 |
| C1' |
N9 |
C4 |
N3 |
5.8 |
0.0 |
| C4' |
C3' |
C2' |
C1' |
319.5 |
0.1 |
| O4' |
C1' |
C2' |
N9 |
246.9 |
241.1 |
| O4' |
C1' |
C2' |
H1' |
128.2 |
118.9 |
| N9 |
C1' |
C2' |
H1' |
241.3 |
237.8 |
| C2' |
C1' |
N9 |
C8 |
179.1 |
266.5 |
| C2' |
C1' |
N9 |
C4 |
352.5 |
86.5 |
| O2' |
C2' |
C1' |
C3' |
116.1 |
118.7 |
| O2' |
C2' |
C1' |
H2' |
240.8 |
237.3 |
| C1' |
C2' |
O2' |
H1 |
180.0 |
183.9 |
| C3' |
C2' |
C1' |
H2' |
124.7 |
118.6 |
| C1' |
C2' |
C3' |
O3' |
198.7 |
241.4 |
| C1' |
C2' |
C3' |
H3' |
83.4 |
118.8 |
| O4' |
C1' |
H1' |
N9 |
115.6 |
122.2 |
| O4' |
C1' |
H1' |
C2' |
243.1 |
244.4 |
| N9 |
C1' |
H1' |
C2' |
127.5 |
122.2 |
| H1' |
C1' |
N9 |
C8 |
61.6 |
144.3 |
| H1' |
C1' |
N9 |
C4 |
235.0 |
324.3 |
| H1' |
C1' |
C2' |
O2' |
12.2 |
23.6 |
| H1' |
C1' |
C2' |
C3' |
256.0 |
264.9 |
| H1' |
C1' |
C2' |
H2' |
131.3 |
146.4 |
| C8 |
N9 |
C1' |
C2' |
179.1 |
266.5 |
| C8 |
N9 |
C1' |
H1' |
61.6 |
144.3 |
| C1' |
N9 |
C8 |
C4 |
175.0 |
180.0 |
| C8 |
N9 |
C4 |
C5 |
0.6 |
0.2 |
| C8 |
N9 |
C4 |
N3 |
180.2 |
180.0 |
| N7 |
C8 |
N9 |
H8 |
180.0 |
180.0 |
| N9 |
C8 |
N7 |
C5 |
0.2 |
359.8 |
| C4 |
N9 |
C1' |
C2' |
352.5 |
86.5 |
| C4 |
N9 |
C1' |
H1' |
235.0 |
324.3 |
| C1' |
N9 |
C4 |
C8 |
185.7 |
180.0 |
| C4 |
N9 |
C8 |
N7 |
359.5 |
360.0 |
| C4 |
N9 |
C8 |
H8 |
179.5 |
180.0 |
| N7 |
C5 |
C4 |
N9 |
359.5 |
359.6 |
| C6 |
C5 |
C4 |
N9 |
179.4 |
180.3 |
| C5 |
C4 |
N9 |
N3 |
180.4 |
180.2 |
| C2 |
N3 |
C4 |
N9 |
180.6 |
180.0 |
| N7 |
C8 |
N9 |
C4 |
359.5 |
360.0 |
| N9 |
C8 |
N7 |
H8 |
180.0 |
180.0 |
| C8 |
N7 |
C5 |
C6 |
180.4 |
179.5 |
| C8 |
N7 |
C5 |
C4 |
0.2 |
0.4 |
| H8 |
C8 |
N9 |
C4 |
179.5 |
180.0 |
| N9 |
C8 |
H8 |
N7 |
180.0 |
180.0 |
| H8 |
C8 |
N7 |
C5 |
180.2 |
179.8 |
| N9 |
C4 |
C5 |
N7 |
359.5 |
359.6 |
| C5 |
N7 |
C8 |
H8 |
180.2 |
179.8 |
| C6 |
C5 |
N7 |
C4 |
180.1 |
179.1 |
| N7 |
C5 |
C6 |
N1 |
180.1 |
180.5 |
| N7 |
C5 |
C6 |
N6 |
0.2 |
0.7 |
| N7 |
C5 |
C4 |
N3 |
179.9 |
179.8 |
| N9 |
C4 |
C5 |
C6 |
179.4 |
180.3 |
| N7 |
C5 |
C6 |
C4 |
179.9 |
180.9 |
| C6 |
C5 |
C4 |
N3 |
359.8 |
0.5 |
| N1 |
C6 |
C5 |
N6 |
179.9 |
179.8 |
| C5 |
C6 |
N1 |
C2 |
359.9 |
0.2 |
| C5 |
C6 |
N6 |
HN61 |
54.7 |
179.8 |
| C5 |
C6 |
N6 |
HN62 |
180.0 |
359.5 |
| N9 |
C4 |
C5 |
N3 |
179.6 |
179.8 |
| N7 |
C5 |
C4 |
C6 |
180.1 |
179.3 |
| C4 |
C5 |
C6 |
N1 |
0.2 |
359.5 |
| C4 |
C5 |
C6 |
N6 |
180.3 |
179.7 |
| C2 |
N3 |
C4 |
C5 |
0.1 |
359.8 |
| N1 |
C6 |
C5 |
C4 |
0.2 |
359.5 |
| C5 |
C6 |
N1 |
N6 |
180.1 |
180.2 |
| N1 |
C6 |
N6 |
HN61 |
234.8 |
359.9 |
| N1 |
C6 |
N6 |
HN62 |
0.1 |
179.6 |
| C6 |
N1 |
C2 |
N3 |
359.9 |
0.1 |
| C6 |
N1 |
C2 |
H2 |
179.9 |
180.0 |
| N6 |
C6 |
C5 |
C4 |
180.3 |
179.7 |
| C5 |
C6 |
N6 |
N1 |
179.9 |
179.8 |
| N6 |
C6 |
N1 |
C2 |
179.9 |
180.0 |
| HN61 |
N6 |
C6 |
HN62 |
234.7 |
180.3 |
| C2 |
N1 |
C6 |
N6 |
179.9 |
180.0 |
| N3 |
C2 |
N1 |
H2 |
180.0 |
180.1 |
| N1 |
C2 |
N3 |
C4 |
0.1 |
359.9 |
| N9 |
C4 |
N3 |
C2 |
180.6 |
180.0 |
| C5 |
C4 |
N3 |
C2 |
0.1 |
359.8 |
| N1 |
C2 |
N3 |
H2 |
180.0 |
179.9 |
| N1 |
C2 |
H2 |
N3 |
180.0 |
180.1 |
| H2 |
C2 |
N3 |
C4 |
180.1 |
180.0 |
| N9 |
C4 |
N3 |
C5 |
180.5 |
180.2 |
| C4 |
N3 |
C2 |
H2 |
180.1 |
180.0 |
| C6 |
N6 |
HN61 |
HN62 |
132.6 |
179.7 |
| C6 |
N6 |
HN62 |
HN61 |
234.7 |
180.3 |
| C4' |
C3' |
C2' |
O2' |
200.7 |
241.2 |
| O2' |
C2' |
C1' |
H1' |
12.2 |
23.6 |
| C1' |
C2' |
O2' |
C3' |
248.5 |
245.4 |
| C1' |
C2' |
O2' |
H2' |
123.2 |
122.8 |
| C3' |
C2' |
O2' |
H2' |
234.7 |
237.4 |
| O2' |
C2' |
C3' |
O3' |
79.8 |
122.5 |
| O2' |
C2' |
C3' |
H3' |
324.6 |
359.9 |
| C2' |
C3' |
C4' |
H4' |
165.1 |
94.8 |
| C4' |
C3' |
C2' |
O3' |
120.8 |
118.7 |
| C4' |
C3' |
C2' |
H3' |
236.1 |
241.3 |
| C3' |
C2' |
C1' |
H1' |
256.0 |
264.9 |
| C1' |
C2' |
C3' |
O2' |
118.8 |
118.9 |
| C1' |
C2' |
C3' |
H2' |
237.7 |
241.5 |
| O2' |
C2' |
C3' |
H2' |
118.8 |
122.6 |
| C3' |
C2' |
O2' |
H1 |
291.5 |
298.5 |
| O3' |
C3' |
C2' |
H3' |
115.3 |
122.6 |
| C2' |
C3' |
O3' |
H3 |
296.1 |
176.2 |
| H2' |
C2' |
C1' |
H1' |
131.3 |
146.4 |
| C1' |
C2' |
H2' |
O2' |
236.8 |
237.1 |
| C1' |
C2' |
H2' |
C3' |
116.1 |
114.5 |
| O2' |
C2' |
H2' |
C3' |
239.3 |
237.4 |
| H2' |
C2' |
O2' |
H1 |
56.8 |
61.1 |
| H2' |
C2' |
C3' |
O3' |
321.0 |
359.9 |
| H2' |
C2' |
C3' |
H3' |
205.7 |
237.3 |
| H1 |
O2' |
C2' |
C3' |
291.5 |
298.5 |
| H1 |
O2' |
C2' |
H2' |
56.8 |
61.1 |
| O3' |
C3' |
C4' |
H4' |
289.5 |
213.6 |
| C4' |
C3' |
O3' |
C2' |
243.9 |
245.3 |
| C4' |
C3' |
O3' |
H3' |
123.8 |
122.7 |
| O3' |
C3' |
C2' |
H2' |
321.0 |
359.9 |
| C2' |
C3' |
O3' |
H3' |
239.9 |
237.4 |
| H3' |
C3' |
C4' |
H4' |
44.8 |
336.2 |
| C4' |
C3' |
H3' |
C2' |
115.6 |
114.6 |
| C4' |
C3' |
H3' |
O3' |
239.6 |
237.3 |
| H3' |
C3' |
C2' |
H2' |
205.7 |
237.3 |
| C2' |
C3' |
H3' |
O3' |
124.0 |
122.7 |
| H3' |
C3' |
O3' |
H3 |
56.2 |
298.8 |
| H3 |
O3' |
C3' |
H3' |
56.2 |
298.8 |