PDB Chemical Component APN
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 APN
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| C8' |
C7' |
1.543 |
1.507 |
| C8' |
N9 |
1.485 |
1.464 |
| C8' |
H8'1 |
1.100 |
1.090 |
| C8' |
H8'2 |
1.100 |
1.090 |
| C7' |
O7' |
1.232 |
1.213 |
| C7' |
N4' |
1.360 |
1.347 |
| C5' |
C |
1.532 |
1.506 |
| C5' |
N4' |
1.484 |
1.466 |
| C5' |
H5'1 |
1.100 |
1.090 |
| C5' |
H5'2 |
1.100 |
1.090 |
| C |
O |
1.228 |
1.209 |
| C |
OXT |
1.337 |
1.343 |
| OXT |
HXT |
0.951 |
0.967 |
| N4' |
C3' |
1.481 |
1.465 |
| C3' |
C2' |
1.540 |
1.529 |
| C3' |
H3'1 |
1.100 |
1.090 |
| C3' |
H3'2 |
1.100 |
1.091 |
| C2' |
N |
1.452 |
1.469 |
| C2' |
H2'1 |
1.100 |
1.090 |
| C2' |
H2'2 |
1.100 |
1.090 |
| N |
H |
1.000 |
1.009 |
| N |
H2 |
1.000 |
1.009 |
| N |
H3 |
1.000 |
1.009 |
| N9 |
C8 |
1.374 |
1.364 |
| N9 |
C4 |
1.383 |
1.372 |
| C8 |
N7 |
1.301 |
1.302 |
| C8 |
H8 |
1.080 |
1.080 |
| N7 |
C5 |
1.396 |
1.355 |
| C5 |
C6 |
1.427 |
1.406 |
| C5 |
C4 |
1.383 |
1.404 |
| C6 |
N6 |
1.336 |
1.384 |
| C6 |
N1 |
1.354 |
1.328 |
| N6 |
HN61 |
1.000 |
0.970 |
| N6 |
HN62 |
1.000 |
0.970 |
| N1 |
C2 |
1.338 |
1.322 |
| C2 |
N3 |
1.343 |
1.316 |
| C2 |
H21 |
1.080 |
1.080 |
| N3 |
C4 |
1.378 |
1.329 |
Bond Angles for APN
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C7' |
C8' |
N9 |
115.2 |
109.5 |
| C7' |
C8' |
H8'1 |
107.6 |
109.5 |
| C7' |
C8' |
H8'2 |
107.6 |
109.4 |
| C8' |
C7' |
O7' |
117.3 |
120.0 |
| C8' |
C7' |
N4' |
121.0 |
120.0 |
| N9 |
C8' |
H8'1 |
107.6 |
109.4 |
| N9 |
C8' |
H8'2 |
107.6 |
109.5 |
| C8' |
N9 |
C8 |
126.4 |
126.3 |
| C8' |
N9 |
C4 |
128.3 |
126.3 |
| H8'1 |
C8' |
H8'2 |
111.3 |
109.5 |
| O7' |
C7' |
N4' |
121.6 |
120.0 |
| C7' |
N4' |
C5' |
120.2 |
120.0 |
| C7' |
N4' |
C3' |
123.0 |
120.0 |
| C |
C5' |
N4' |
113.8 |
109.5 |
| C |
C5' |
H5'1 |
108.1 |
109.5 |
| C |
C5' |
H5'2 |
108.1 |
109.5 |
| C5' |
C |
O |
120.7 |
120.0 |
| C5' |
C |
OXT |
116.1 |
120.0 |
| N4' |
C5' |
H5'1 |
108.1 |
109.4 |
| N4' |
C5' |
H5'2 |
108.1 |
109.4 |
| C5' |
N4' |
C3' |
116.8 |
120.0 |
| H5'1 |
C5' |
H5'2 |
110.8 |
109.5 |
| O |
C |
OXT |
123.2 |
119.9 |
| C |
OXT |
HXT |
109.5 |
117.0 |
| N4' |
C3' |
C2' |
114.5 |
109.5 |
| N4' |
C3' |
H3'1 |
107.8 |
109.5 |
| N4' |
C3' |
H3'2 |
107.8 |
109.4 |
| C2' |
C3' |
H3'1 |
107.8 |
109.5 |
| C2' |
C3' |
H3'2 |
107.9 |
109.5 |
| C3' |
C2' |
N |
110.3 |
109.5 |
| C3' |
C2' |
H2'1 |
109.2 |
109.4 |
| C3' |
C2' |
H2'2 |
109.2 |
109.5 |
| H3'1 |
C3' |
H3'2 |
111.1 |
109.4 |
| N |
C2' |
H2'1 |
109.2 |
109.4 |
| N |
C2' |
H2'2 |
109.2 |
109.5 |
| C2' |
N |
H |
109.5 |
109.4 |
| C2' |
N |
H2 |
109.4 |
109.5 |
| C2' |
N |
H3 |
109.5 |
109.4 |
| H2'1 |
C2' |
H2'2 |
109.8 |
109.5 |
| H |
N |
H2 |
109.5 |
109.6 |
| H |
N |
H3 |
109.5 |
109.4 |
| H2 |
N |
H3 |
109.5 |
109.5 |
| C8 |
N9 |
C4 |
105.1 |
107.4 |
| N9 |
C8 |
N7 |
114.5 |
110.0 |
| N9 |
C8 |
H8 |
122.7 |
125.0 |
| N9 |
C4 |
C5 |
106.1 |
106.1 |
| N9 |
C4 |
N3 |
128.3 |
134.9 |
| N7 |
C8 |
H8 |
122.7 |
125.0 |
| C8 |
N7 |
C5 |
104.0 |
109.4 |
| N7 |
C5 |
C6 |
133.5 |
134.7 |
| N7 |
C5 |
C4 |
110.3 |
107.2 |
| C6 |
C5 |
C4 |
116.2 |
118.2 |
| C5 |
C6 |
N6 |
123.9 |
120.8 |
| C5 |
C6 |
N1 |
119.1 |
118.5 |
| C5 |
C4 |
N3 |
125.6 |
119.1 |
| N6 |
C6 |
N1 |
116.9 |
120.8 |
| C6 |
N6 |
HN61 |
109.5 |
120.0 |
| C6 |
N6 |
HN62 |
109.5 |
120.0 |
| C6 |
N1 |
C2 |
118.7 |
121.1 |
| HN61 |
N6 |
HN62 |
109.5 |
120.0 |
| N1 |
C2 |
N3 |
128.0 |
122.5 |
| N1 |
C2 |
H21 |
116.0 |
118.7 |
| N3 |
C2 |
H21 |
116.0 |
118.8 |
| C2 |
N3 |
C4 |
112.3 |
120.7 |
Torsion Angles for APN
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| N9 |
C8' |
C7' |
H8'1 |
240.0 |
240.0 |
| N9 |
C8' |
C7' |
H8'2 |
120.0 |
120.0 |
| C7' |
C8' |
N9 |
C8 |
230.0 |
265.0 |
| C7' |
C8' |
N9 |
C4 |
56.2 |
84.7 |
| H8'1 |
C8' |
C7' |
H8'2 |
240.0 |
240.0 |
| O7' |
C7' |
C8' |
N4' |
182.5 |
180.0 |
| C8' |
C7' |
N4' |
C5' |
195.0 |
0.0 |
| C8' |
C7' |
N4' |
C3' |
16.4 |
180.0 |
| C7' |
C8' |
N9 |
H8'1 |
120.0 |
120.0 |
| C7' |
C8' |
N9 |
H8'2 |
240.0 |
240.0 |
| N9 |
C8' |
C7' |
O7' |
64.9 |
0.0 |
| N9 |
C8' |
C7' |
N4' |
242.4 |
180.0 |
| H8'1 |
C8' |
N9 |
H8'2 |
120.0 |
120.0 |
| C8 |
N9 |
C8' |
C4 |
173.8 |
180.3 |
| C8' |
N9 |
C8 |
N7 |
184.4 |
180.0 |
| C8' |
N9 |
C8 |
H8 |
4.4 |
360.0 |
| C8' |
N9 |
C4 |
C5 |
176.0 |
179.9 |
| C8' |
N9 |
C4 |
N3 |
355.9 |
0.8 |
| C7' |
C8' |
H8'1 |
N9 |
235.2 |
240.0 |
| C7' |
C8' |
H8'1 |
H8'2 |
117.6 |
120.0 |
| H8'1 |
C8' |
C7' |
O7' |
184.9 |
120.0 |
| H8'1 |
C8' |
C7' |
N4' |
2.5 |
300.0 |
| N9 |
C8' |
H8'1 |
H8'2 |
242.4 |
240.0 |
| H8'1 |
C8' |
N9 |
C8 |
109.9 |
145.0 |
| H8'1 |
C8' |
N9 |
C4 |
296.2 |
324.7 |
| C7' |
C8' |
H8'2 |
N9 |
124.7 |
120.0 |
| C7' |
C8' |
H8'2 |
H8'1 |
242.4 |
240.0 |
| H8'2 |
C8' |
C7' |
O7' |
304.9 |
240.0 |
| H8'2 |
C8' |
C7' |
N4' |
122.5 |
60.0 |
| N9 |
C8' |
H8'2 |
H8'1 |
117.6 |
120.0 |
| H8'2 |
C8' |
N9 |
C8 |
349.9 |
25.0 |
| H8'2 |
C8' |
N9 |
C4 |
176.2 |
204.7 |
| O7' |
C7' |
C8' |
N9 |
64.9 |
0.0 |
| O7' |
C7' |
C8' |
H8'1 |
184.9 |
120.0 |
| O7' |
C7' |
C8' |
H8'2 |
304.9 |
240.0 |
| C8' |
C7' |
O7' |
N4' |
177.5 |
180.0 |
| O7' |
C7' |
N4' |
C5' |
12.4 |
180.0 |
| O7' |
C7' |
N4' |
C3' |
193.8 |
0.0 |
| N4' |
C7' |
C8' |
N9 |
242.4 |
180.0 |
| N4' |
C7' |
C8' |
H8'1 |
2.5 |
300.0 |
| N4' |
C7' |
C8' |
H8'2 |
122.5 |
60.0 |
| C8' |
C7' |
N4' |
O7' |
182.6 |
180.0 |
| C |
C5' |
N4' |
C7' |
223.8 |
90.0 |
| C7' |
N4' |
C5' |
H5'1 |
103.8 |
330.0 |
| C7' |
N4' |
C5' |
H5'2 |
343.8 |
210.0 |
| C5' |
N4' |
C7' |
C3' |
178.6 |
180.0 |
| C7' |
N4' |
C3' |
C2' |
254.2 |
90.0 |
| C7' |
N4' |
C3' |
H3'1 |
14.2 |
210.0 |
| C7' |
N4' |
C3' |
H3'2 |
134.2 |
330.0 |
| C7' |
N4' |
C5' |
C |
223.8 |
90.0 |
| N4' |
C5' |
C |
H5'1 |
240.0 |
240.0 |
| N4' |
C5' |
C |
H5'2 |
120.0 |
120.0 |
| C |
C5' |
N4' |
C3' |
42.5 |
270.0 |
| H5'1 |
C5' |
C |
H5'2 |
240.0 |
239.9 |
| O |
C |
C5' |
OXT |
182.0 |
180.0 |
| C5' |
C |
OXT |
HXT |
182.1 |
180.0 |
| C7' |
N4' |
C5' |
C3' |
181.3 |
180.0 |
| C |
C5' |
N4' |
H5'1 |
120.0 |
120.0 |
| C |
C5' |
N4' |
H5'2 |
240.0 |
240.0 |
| N4' |
C5' |
C |
O |
254.8 |
360.0 |
| N4' |
C5' |
C |
OXT |
72.8 |
180.0 |
| H5'1 |
C5' |
N4' |
H5'2 |
120.0 |
120.0 |
| C5' |
N4' |
C3' |
C2' |
75.5 |
270.0 |
| C5' |
N4' |
C3' |
H3'1 |
195.5 |
30.0 |
| C5' |
N4' |
C3' |
H3'2 |
315.5 |
150.0 |
| C |
C5' |
H5'1 |
N4' |
236.5 |
240.0 |
| C |
C5' |
H5'1 |
H5'2 |
118.2 |
120.1 |
| H5'1 |
C5' |
C |
O |
14.8 |
120.0 |
| H5'1 |
C5' |
C |
OXT |
192.8 |
300.0 |
| N4' |
C5' |
H5'1 |
H5'2 |
241.8 |
240.0 |
| H5'1 |
C5' |
N4' |
C3' |
282.5 |
150.0 |
| C |
C5' |
H5'2 |
N4' |
123.5 |
120.0 |
| C |
C5' |
H5'2 |
H5'1 |
241.8 |
239.9 |
| H5'2 |
C5' |
C |
O |
134.8 |
240.0 |
| H5'2 |
C5' |
C |
OXT |
312.8 |
60.1 |
| N4' |
C5' |
H5'2 |
H5'1 |
118.2 |
120.0 |
| H5'2 |
C5' |
N4' |
C3' |
162.5 |
30.0 |
| O |
C |
C5' |
N4' |
254.8 |
360.0 |
| O |
C |
C5' |
H5'1 |
14.8 |
120.0 |
| O |
C |
C5' |
H5'2 |
134.8 |
240.0 |
| C5' |
C |
O |
OXT |
177.8 |
180.0 |
| O |
C |
OXT |
HXT |
0.0 |
0.0 |
| OXT |
C |
C5' |
N4' |
72.8 |
180.0 |
| OXT |
C |
C5' |
H5'1 |
192.8 |
300.0 |
| OXT |
C |
C5' |
H5'2 |
312.8 |
60.1 |
| C5' |
C |
OXT |
O |
182.1 |
180.0 |
| C7' |
N4' |
C3' |
C5' |
178.7 |
180.0 |
| C3' |
N4' |
C5' |
H5'1 |
282.5 |
150.0 |
| C3' |
N4' |
C5' |
H5'2 |
162.5 |
30.0 |
| C2' |
C3' |
N4' |
H3'1 |
240.0 |
240.0 |
| C2' |
C3' |
N4' |
H3'2 |
120.0 |
120.0 |
| N4' |
C3' |
C2' |
N |
64.7 |
180.0 |
| N4' |
C3' |
C2' |
H2'1 |
184.7 |
300.0 |
| N4' |
C3' |
C2' |
H2'2 |
304.8 |
60.0 |
| H3'1 |
C3' |
N4' |
H3'2 |
240.0 |
240.1 |
| N4' |
C3' |
C2' |
H3'1 |
120.0 |
120.0 |
| N4' |
C3' |
C2' |
H3'2 |
240.0 |
240.0 |
| H3'1 |
C3' |
C2' |
H3'2 |
120.0 |
120.0 |
| N |
C2' |
C3' |
H2'1 |
240.0 |
240.0 |
| N |
C2' |
C3' |
H2'2 |
120.0 |
120.0 |
| C3' |
C2' |
N |
H |
180.0 |
59.9 |
| C3' |
C2' |
N |
H2 |
300.0 |
180.0 |
| C3' |
C2' |
N |
H3 |
60.0 |
300.0 |
| H2'1 |
C2' |
C3' |
H2'2 |
240.0 |
240.0 |
| N4' |
C3' |
H3'1 |
C2' |
235.9 |
240.0 |
| N4' |
C3' |
H3'1 |
H3'2 |
117.9 |
119.9 |
| C2' |
C3' |
H3'1 |
H3'2 |
242.0 |
240.0 |
| H3'1 |
C3' |
C2' |
N |
304.8 |
60.0 |
| H3'1 |
C3' |
C2' |
H2'1 |
64.7 |
180.0 |
| H3'1 |
C3' |
C2' |
H2'2 |
184.8 |
300.0 |
| N4' |
C3' |
H3'2 |
C2' |
124.1 |
120.0 |
| N4' |
C3' |
H3'2 |
H3'1 |
242.1 |
240.0 |
| C2' |
C3' |
H3'2 |
H3'1 |
118.0 |
120.0 |
| H3'2 |
C3' |
C2' |
N |
184.7 |
300.0 |
| H3'2 |
C3' |
C2' |
H2'1 |
304.7 |
60.0 |
| H3'2 |
C3' |
C2' |
H2'2 |
64.7 |
180.0 |
| N |
C2' |
C3' |
H3'1 |
304.8 |
60.0 |
| N |
C2' |
C3' |
H3'2 |
184.7 |
300.0 |
| C3' |
C2' |
N |
H2'1 |
120.0 |
120.0 |
| C3' |
C2' |
N |
H2'2 |
240.0 |
240.0 |
| H2'1 |
C2' |
N |
H2'2 |
120.0 |
120.0 |
| H |
N |
C2' |
H2 |
240.0 |
239.9 |
| H |
N |
C2' |
H3 |
120.0 |
119.9 |
| H2 |
N |
C2' |
H3 |
240.0 |
240.0 |
| H2'1 |
C2' |
C3' |
H3'1 |
64.7 |
180.0 |
| H2'1 |
C2' |
C3' |
H3'2 |
304.7 |
60.0 |
| C3' |
C2' |
H2'1 |
N |
239.3 |
240.0 |
| C3' |
C2' |
H2'1 |
H2'2 |
119.7 |
120.0 |
| N |
C2' |
H2'1 |
H2'2 |
240.3 |
240.0 |
| H2'1 |
C2' |
N |
H |
60.0 |
300.0 |
| H2'1 |
C2' |
N |
H2 |
180.0 |
60.1 |
| H2'1 |
C2' |
N |
H3 |
300.0 |
180.1 |
| H2'2 |
C2' |
C3' |
H3'1 |
184.8 |
300.0 |
| H2'2 |
C2' |
C3' |
H3'2 |
64.7 |
180.0 |
| C3' |
C2' |
H2'2 |
N |
120.7 |
120.0 |
| C3' |
C2' |
H2'2 |
H2'1 |
240.3 |
240.0 |
| N |
C2' |
H2'2 |
H2'1 |
119.6 |
120.0 |
| H2'2 |
C2' |
N |
H |
300.0 |
180.0 |
| H2'2 |
C2' |
N |
H2 |
60.0 |
300.0 |
| H2'2 |
C2' |
N |
H3 |
180.0 |
60.1 |
| H |
N |
C2' |
H2'1 |
60.0 |
300.0 |
| H |
N |
C2' |
H2'2 |
300.0 |
180.0 |
| C2' |
N |
H |
H2 |
120.0 |
120.0 |
| C2' |
N |
H |
H3 |
240.0 |
240.1 |
| H2 |
N |
H |
H3 |
120.0 |
120.1 |
| H2 |
N |
C2' |
H2'1 |
180.0 |
60.1 |
| H2 |
N |
C2' |
H2'2 |
60.0 |
300.0 |
| C2' |
N |
H2 |
H |
240.0 |
240.0 |
| C2' |
N |
H2 |
H3 |
120.0 |
120.0 |
| H |
N |
H2 |
H3 |
240.0 |
239.9 |
| H3 |
N |
C2' |
H2'1 |
300.0 |
180.1 |
| H3 |
N |
C2' |
H2'2 |
180.0 |
60.1 |
| C2' |
N |
H3 |
H |
120.0 |
119.9 |
| C2' |
N |
H3 |
H2 |
240.0 |
240.0 |
| H |
N |
H3 |
H2 |
120.0 |
120.1 |
| C8 |
N9 |
C8' |
H8'1 |
109.9 |
145.0 |
| C8 |
N9 |
C8' |
H8'2 |
349.9 |
25.0 |
| C8' |
N9 |
C8 |
C4 |
185.1 |
179.8 |
| C8 |
N9 |
C4 |
C5 |
1.2 |
359.6 |
| C8 |
N9 |
C4 |
N3 |
181.1 |
180.5 |
| N7 |
C8 |
N9 |
H8 |
180.0 |
180.0 |
| N9 |
C8 |
N7 |
C5 |
359.8 |
360.0 |
| C4 |
N9 |
C8' |
H8'1 |
296.2 |
324.7 |
| C4 |
N9 |
C8' |
H8'2 |
176.2 |
204.7 |
| C8' |
N9 |
C4 |
C8 |
174.8 |
180.2 |
| C4 |
N9 |
C8 |
N7 |
359.3 |
0.3 |
| C4 |
N9 |
C8 |
H8 |
179.3 |
180.2 |
| N7 |
C5 |
C4 |
N9 |
358.6 |
0.4 |
| C6 |
C5 |
C4 |
N9 |
178.2 |
180.2 |
| C5 |
C4 |
N9 |
N3 |
180.2 |
179.1 |
| C2 |
N3 |
C4 |
N9 |
181.0 |
179.6 |
| N7 |
C8 |
N9 |
C4 |
359.3 |
0.3 |
| N9 |
C8 |
N7 |
H8 |
180.0 |
180.0 |
| C8 |
N7 |
C5 |
C6 |
181.5 |
180.0 |
| C8 |
N7 |
C5 |
C4 |
1.0 |
359.8 |
| H8 |
C8 |
N9 |
C4 |
179.3 |
180.2 |
| N9 |
C8 |
H8 |
N7 |
180.0 |
180.0 |
| H8 |
C8 |
N7 |
C5 |
179.8 |
180.0 |
| N9 |
C4 |
C5 |
N7 |
358.6 |
0.4 |
| C5 |
N7 |
C8 |
H8 |
179.8 |
180.0 |
| C6 |
C5 |
N7 |
C4 |
180.5 |
180.2 |
| N7 |
C5 |
C6 |
N6 |
1.9 |
0.0 |
| N7 |
C5 |
C6 |
N1 |
180.5 |
180.0 |
| N7 |
C5 |
C4 |
N3 |
178.7 |
179.6 |
| N9 |
C4 |
C5 |
C6 |
178.2 |
180.2 |
| N7 |
C5 |
C6 |
C4 |
179.5 |
179.8 |
| C6 |
C5 |
C4 |
N3 |
358.3 |
359.4 |
| N6 |
C6 |
C5 |
N1 |
181.4 |
180.1 |
| C5 |
C6 |
N6 |
HN61 |
178.6 |
360.0 |
| C5 |
C6 |
N6 |
HN62 |
298.7 |
180.0 |
| C5 |
C6 |
N1 |
C2 |
0.3 |
0.1 |
| N9 |
C4 |
C5 |
N3 |
179.8 |
180.8 |
| N7 |
C5 |
C4 |
C6 |
180.4 |
180.2 |
| C4 |
C5 |
C6 |
N6 |
182.4 |
180.3 |
| C4 |
C5 |
C6 |
N1 |
1.1 |
0.2 |
| C2 |
N3 |
C4 |
C5 |
0.8 |
0.6 |
| N6 |
C6 |
C5 |
C4 |
182.4 |
180.3 |
| C5 |
C6 |
N6 |
N1 |
178.6 |
179.9 |
| N6 |
C6 |
N1 |
C2 |
179.0 |
180.0 |
| HN61 |
N6 |
C6 |
HN62 |
240.0 |
180.0 |
| N1 |
C6 |
C5 |
C4 |
1.1 |
0.2 |
| C5 |
C6 |
N1 |
N6 |
181.3 |
180.1 |
| N1 |
C6 |
N6 |
HN61 |
360.0 |
180.0 |
| N1 |
C6 |
N6 |
HN62 |
120.0 |
0.1 |
| C6 |
N1 |
C2 |
N3 |
358.7 |
360.0 |
| C6 |
N1 |
C2 |
H21 |
178.7 |
180.0 |
| HN61 |
N6 |
C6 |
N1 |
360.0 |
180.0 |
| C6 |
N6 |
HN61 |
HN62 |
120.0 |
180.0 |
| HN62 |
N6 |
C6 |
N1 |
120.0 |
0.1 |
| C6 |
N6 |
HN62 |
HN61 |
239.9 |
180.0 |
| N3 |
C2 |
N1 |
H21 |
180.0 |
180.0 |
| N1 |
C2 |
N3 |
C4 |
0.8 |
359.7 |
| N9 |
C4 |
N3 |
C2 |
181.0 |
179.6 |
| C5 |
C4 |
N3 |
C2 |
0.8 |
0.6 |
| N1 |
C2 |
N3 |
H21 |
180.0 |
180.0 |
| N1 |
C2 |
H21 |
N3 |
180.0 |
180.0 |
| H21 |
C2 |
N3 |
C4 |
180.7 |
179.7 |
| N9 |
C4 |
N3 |
C5 |
180.2 |
179.0 |
| C4 |
N3 |
C2 |
H21 |
180.7 |
179.7 |