PDB Chemical Component 2ND
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 2ND
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| O6 |
C6 |
1.230 |
1.220 |
| C6 |
N1 |
1.401 |
1.352 |
| C6 |
C5 |
1.390 |
1.417 |
| N1 |
C2 |
1.400 |
1.357 |
| N1 |
HN1 |
1.020 |
0.970 |
| C2 |
N3 |
1.322 |
1.304 |
| C2 |
H2 |
1.103 |
1.080 |
| N3 |
C4 |
1.342 |
1.341 |
| C4 |
C5 |
1.390 |
1.398 |
| C4 |
N9 |
1.332 |
1.368 |
| C5 |
N7 |
1.329 |
1.353 |
| N7 |
C8 |
1.330 |
1.302 |
| C8 |
N9 |
1.330 |
1.363 |
| C8 |
H8 |
1.103 |
1.080 |
| N9 |
C1' |
1.483 |
1.465 |
| C1' |
O4' |
1.439 |
1.437 |
| C1' |
C2' |
1.533 |
1.541 |
| C1' |
H1' |
1.115 |
1.089 |
| O4' |
C4' |
1.438 |
1.444 |
| C2' |
C3' |
1.529 |
1.549 |
| C2' |
H2'1 |
1.115 |
1.091 |
| C2' |
H2'2 |
1.115 |
1.090 |
| C3' |
O3' |
1.430 |
1.430 |
| C3' |
C4' |
1.528 |
1.550 |
| C3' |
H3' |
1.115 |
1.090 |
| O3' |
H1 |
0.950 |
0.967 |
| C4' |
C5' |
1.531 |
1.530 |
| C4' |
H4' |
1.115 |
1.090 |
| C5' |
O5' |
1.430 |
1.429 |
| C5' |
H5'1 |
1.115 |
1.089 |
| C5' |
H5'2 |
1.115 |
1.091 |
| O5' |
H5' |
0.950 |
0.967 |
Bond Angles for 2ND
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O6 |
C6 |
N1 |
120.4 |
120.9 |
| O6 |
C6 |
C5 |
120.8 |
120.9 |
| N1 |
C6 |
C5 |
118.8 |
118.2 |
| C6 |
N1 |
C2 |
119.3 |
120.4 |
| C6 |
N1 |
HN1 |
120.4 |
119.9 |
| C6 |
C5 |
C4 |
119.0 |
118.4 |
| C6 |
C5 |
N7 |
133.6 |
134.3 |
| C2 |
N1 |
HN1 |
120.3 |
119.7 |
| N1 |
C2 |
N3 |
120.1 |
122.1 |
| N1 |
C2 |
H2 |
122.8 |
118.9 |
| N3 |
C2 |
H2 |
117.1 |
118.9 |
| C2 |
N3 |
C4 |
122.2 |
121.3 |
| N3 |
C4 |
C5 |
120.6 |
119.6 |
| N3 |
C4 |
N9 |
132.3 |
134.3 |
| C5 |
C4 |
N9 |
107.0 |
106.2 |
| C4 |
C5 |
N7 |
107.4 |
107.3 |
| C4 |
N9 |
C8 |
107.9 |
107.4 |
| C4 |
N9 |
C1' |
127.3 |
126.3 |
| C5 |
N7 |
C8 |
107.9 |
109.3 |
| N7 |
C8 |
N9 |
109.8 |
109.8 |
| N7 |
C8 |
H8 |
125.1 |
125.1 |
| N9 |
C8 |
H8 |
125.1 |
125.1 |
| C8 |
N9 |
C1' |
124.8 |
126.3 |
| N9 |
C1' |
O4' |
110.5 |
109.9 |
| N9 |
C1' |
C2' |
113.3 |
110.0 |
| N9 |
C1' |
H1' |
105.3 |
109.9 |
| O4' |
C1' |
C2' |
107.1 |
107.3 |
| O4' |
C1' |
H1' |
111.8 |
109.9 |
| C1' |
O4' |
C4' |
108.1 |
107.0 |
| C2' |
C1' |
H1' |
108.9 |
109.9 |
| C1' |
C2' |
C3' |
102.2 |
104.3 |
| C1' |
C2' |
H2'1 |
115.0 |
110.4 |
| C1' |
C2' |
H2'2 |
115.0 |
110.5 |
| O4' |
C4' |
C3' |
102.4 |
103.6 |
| O4' |
C4' |
C5' |
109.6 |
110.6 |
| O4' |
C4' |
H4' |
115.2 |
110.6 |
| C3' |
C2' |
H2'1 |
115.0 |
110.4 |
| C3' |
C2' |
H2'2 |
115.0 |
110.6 |
| C2' |
C3' |
O3' |
110.6 |
110.9 |
| C2' |
C3' |
C4' |
101.0 |
102.0 |
| C2' |
C3' |
H3' |
114.8 |
110.9 |
| H2'1 |
C2' |
H2'2 |
95.4 |
110.5 |
| O3' |
C3' |
C4' |
111.4 |
111.1 |
| O3' |
C3' |
H3' |
105.1 |
110.8 |
| C3' |
O3' |
H1 |
110.6 |
106.7 |
| C4' |
C3' |
H3' |
114.1 |
110.8 |
| C3' |
C4' |
C5' |
113.1 |
110.6 |
| C3' |
C4' |
H4' |
111.9 |
110.7 |
| C5' |
C4' |
H4' |
104.9 |
110.6 |
| C4' |
C5' |
O5' |
109.2 |
109.5 |
| C4' |
C5' |
H5'1 |
112.3 |
109.5 |
| C4' |
C5' |
H5'2 |
112.3 |
109.4 |
| O5' |
C5' |
H5'1 |
112.3 |
109.5 |
| O5' |
C5' |
H5'2 |
112.3 |
109.4 |
| C5' |
O5' |
H5' |
109.2 |
106.8 |
| H5'1 |
C5' |
H5'2 |
98.1 |
109.5 |
Torsion Angles for 2ND
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| N1 |
C6 |
O6 |
C5 |
179.5 |
180.0 |
| O6 |
C6 |
N1 |
C2 |
180.7 |
180.0 |
| O6 |
C6 |
N1 |
HN1 |
0.7 |
359.9 |
| O6 |
C6 |
C5 |
C4 |
179.4 |
180.3 |
| O6 |
C6 |
C5 |
N7 |
358.5 |
0.0 |
| O6 |
C6 |
N1 |
C5 |
180.5 |
180.0 |
| N1 |
C6 |
C5 |
C4 |
359.9 |
0.3 |
| N1 |
C6 |
C5 |
N7 |
178.9 |
180.0 |
| C2 |
N1 |
C6 |
HN1 |
180.0 |
180.1 |
| C6 |
N1 |
C2 |
N3 |
359.9 |
359.9 |
| C6 |
N1 |
C2 |
H2 |
179.9 |
180.0 |
| O6 |
C6 |
C5 |
N1 |
179.5 |
180.0 |
| C5 |
C6 |
N1 |
C2 |
0.2 |
0.0 |
| C5 |
C6 |
N1 |
HN1 |
180.2 |
180.0 |
| N3 |
C4 |
C5 |
C6 |
359.9 |
359.4 |
| C6 |
C5 |
C4 |
N9 |
179.1 |
180.2 |
| C4 |
C5 |
C6 |
N7 |
180.9 |
180.3 |
| C6 |
C5 |
N7 |
C8 |
181.0 |
180.0 |
| C2 |
N1 |
C6 |
C5 |
0.2 |
0.0 |
| C6 |
N1 |
C2 |
HN1 |
180.0 |
179.9 |
| N3 |
C2 |
N1 |
H2 |
180.0 |
180.0 |
| N1 |
C2 |
N3 |
C4 |
359.9 |
359.7 |
| HN1 |
N1 |
C6 |
C5 |
180.2 |
180.0 |
| C6 |
N1 |
HN1 |
C2 |
180.0 |
180.1 |
| HN1 |
N1 |
C2 |
N3 |
179.9 |
180.0 |
| HN1 |
N1 |
C2 |
H2 |
359.9 |
0.0 |
| N3 |
C2 |
N1 |
HN1 |
179.9 |
180.0 |
| N1 |
C2 |
N3 |
H2 |
180.0 |
180.0 |
| C2 |
N3 |
C4 |
C5 |
0.2 |
0.7 |
| C2 |
N3 |
C4 |
N9 |
181.3 |
179.5 |
| H2 |
C2 |
N1 |
HN1 |
359.9 |
0.0 |
| N1 |
C2 |
H2 |
N3 |
180.0 |
180.0 |
| H2 |
C2 |
N3 |
C4 |
179.9 |
179.7 |
| C6 |
C5 |
C4 |
N3 |
359.9 |
359.4 |
| C4 |
N3 |
C2 |
H2 |
179.9 |
179.7 |
| C5 |
C4 |
N3 |
N9 |
178.9 |
181.1 |
| N3 |
C4 |
C5 |
N7 |
180.6 |
179.6 |
| N3 |
C4 |
N9 |
C8 |
179.2 |
180.6 |
| N3 |
C4 |
N9 |
C1' |
1.5 |
0.9 |
| C6 |
C5 |
C4 |
N7 |
179.3 |
179.7 |
| N3 |
C4 |
C5 |
N9 |
180.8 |
179.2 |
| C5 |
C4 |
N9 |
C8 |
0.2 |
359.6 |
| C5 |
C4 |
N9 |
C1' |
182.4 |
179.9 |
| C4 |
C5 |
N7 |
C8 |
0.1 |
359.7 |
| N3 |
C4 |
N9 |
C5 |
179.1 |
181.0 |
| N9 |
C4 |
C5 |
N7 |
359.8 |
0.4 |
| N7 |
C8 |
N9 |
C4 |
359.9 |
0.3 |
| C4 |
N9 |
C8 |
H8 |
179.9 |
180.3 |
| C8 |
N9 |
C4 |
C1' |
177.8 |
179.7 |
| C4 |
N9 |
C1' |
O4' |
111.3 |
203.2 |
| C4 |
N9 |
C1' |
C2' |
351.1 |
85.4 |
| C4 |
N9 |
C1' |
H1' |
232.2 |
324.2 |
| C6 |
C5 |
N7 |
C4 |
180.9 |
180.3 |
| N7 |
C5 |
C4 |
N9 |
359.8 |
0.4 |
| C5 |
N7 |
C8 |
N9 |
360.0 |
0.0 |
| C5 |
N7 |
C8 |
H8 |
180.0 |
180.0 |
| C4 |
N9 |
C8 |
N7 |
359.9 |
0.3 |
| N9 |
C8 |
N7 |
H8 |
180.0 |
180.0 |
| N7 |
C8 |
N9 |
C1' |
177.7 |
180.0 |
| C4 |
N9 |
C8 |
C1' |
182.2 |
180.3 |
| N7 |
C8 |
N9 |
H8 |
180.0 |
180.0 |
| C8 |
N9 |
C1' |
O4' |
293.9 |
23.6 |
| C8 |
N9 |
C1' |
C2' |
173.7 |
265.7 |
| C8 |
N9 |
C1' |
H1' |
54.8 |
144.6 |
| N7 |
C8 |
H8 |
N9 |
180.0 |
180.0 |
| H8 |
C8 |
N9 |
C1' |
357.7 |
360.0 |
| C4 |
N9 |
C1' |
C8 |
177.4 |
179.7 |
| C1' |
N9 |
C8 |
H8 |
357.7 |
360.0 |
| O4' |
C1' |
N9 |
C2' |
120.1 |
117.9 |
| O4' |
C1' |
N9 |
H1' |
239.1 |
239.0 |
| N9 |
C1' |
O4' |
C4' |
248.8 |
213.9 |
| C2' |
C1' |
N9 |
H1' |
119.0 |
121.2 |
| N9 |
C1' |
C2' |
C3' |
137.4 |
121.6 |
| N9 |
C1' |
C2' |
H2'1 |
12.2 |
240.2 |
| N9 |
C1' |
C2' |
H2'2 |
262.7 |
2.8 |
| N9 |
C1' |
O4' |
C2' |
236.2 |
240.4 |
| N9 |
C1' |
O4' |
H1' |
117.0 |
121.0 |
| C2' |
C1' |
O4' |
H1' |
240.8 |
240.5 |
| O4' |
C1' |
C2' |
C3' |
15.3 |
2.2 |
| O4' |
C1' |
C2' |
H2'1 |
250.1 |
120.8 |
| O4' |
C1' |
C2' |
H2'2 |
140.6 |
243.3 |
| C1' |
O4' |
C4' |
C3' |
324.5 |
40.0 |
| C1' |
O4' |
C4' |
C5' |
84.8 |
158.5 |
| C1' |
O4' |
C4' |
H4' |
202.8 |
281.4 |
| N9 |
C1' |
C2' |
O4' |
122.1 |
119.5 |
| N9 |
C1' |
C2' |
H1' |
243.1 |
238.9 |
| O4' |
C1' |
C2' |
H1' |
121.0 |
119.4 |
| C2' |
C1' |
O4' |
C4' |
12.7 |
333.5 |
| C3' |
C2' |
C1' |
H2'1 |
125.3 |
241.4 |
| C3' |
C2' |
C1' |
H2'2 |
234.7 |
118.9 |
| C1' |
C2' |
C3' |
O3' |
82.6 |
139.1 |
| C1' |
C2' |
C3' |
C4' |
324.6 |
20.7 |
| C1' |
C2' |
C3' |
H3' |
201.3 |
262.7 |
| H2'1 |
C2' |
C1' |
H2'2 |
109.5 |
237.5 |
| N9 |
C1' |
H1' |
O4' |
239.9 |
239.0 |
| N9 |
C1' |
H1' |
C2' |
121.9 |
121.2 |
| O4' |
C1' |
H1' |
C2' |
241.9 |
242.2 |
| H1' |
C1' |
O4' |
C4' |
131.9 |
92.9 |
| H1' |
C1' |
C2' |
C3' |
254.3 |
242.8 |
| H1' |
C1' |
C2' |
H2'1 |
129.0 |
1.4 |
| H1' |
C1' |
C2' |
H2'2 |
19.6 |
123.9 |
| C4' |
O4' |
C1' |
C2' |
12.7 |
333.5 |
| C4' |
O4' |
C1' |
H1' |
131.9 |
92.9 |
| C2' |
C3' |
C4' |
O4' |
43.8 |
323.2 |
| O3' |
C3' |
C4' |
O4' |
286.3 |
204.9 |
| O4' |
C4' |
C3' |
H3' |
167.6 |
81.3 |
| C3' |
C4' |
O4' |
C5' |
239.7 |
241.5 |
| C3' |
C4' |
O4' |
H4' |
121.7 |
118.6 |
| C5' |
C4' |
O4' |
H4' |
242.0 |
237.2 |
| O4' |
C4' |
C5' |
O5' |
56.9 |
68.6 |
| O4' |
C4' |
C5' |
H5'1 |
291.6 |
308.6 |
| O4' |
C4' |
C5' |
H5'2 |
182.2 |
188.5 |
| C3' |
C2' |
C1' |
H1' |
254.3 |
242.8 |
| C1' |
C2' |
C3' |
H2'1 |
234.7 |
118.6 |
| C1' |
C2' |
C3' |
H2'2 |
125.3 |
241.2 |
| O4' |
C4' |
C3' |
C2' |
43.8 |
323.2 |
| H2'1 |
C2' |
C3' |
H2'2 |
250.6 |
122.6 |
| O3' |
C3' |
C2' |
C4' |
118.1 |
118.4 |
| O3' |
C3' |
C2' |
H3' |
241.3 |
236.4 |
| C2' |
C3' |
O3' |
H1 |
180.0 |
61.5 |
| C4' |
C3' |
C2' |
H3' |
123.2 |
118.0 |
| C2' |
C3' |
C4' |
C5' |
286.0 |
204.6 |
| C2' |
C3' |
C4' |
H4' |
167.8 |
81.8 |
| H2'1 |
C2' |
C1' |
H1' |
129.0 |
1.4 |
| C1' |
C2' |
H2'1 |
C3' |
118.3 |
245.2 |
| C1' |
C2' |
H2'1 |
H2'2 |
239.1 |
122.5 |
| C3' |
C2' |
H2'1 |
H2'2 |
120.8 |
237.4 |
| H2'1 |
C2' |
C3' |
O3' |
207.9 |
20.4 |
| H2'1 |
C2' |
C3' |
C4' |
89.9 |
262.0 |
| H2'1 |
C2' |
C3' |
H3' |
326.6 |
144.0 |
| H2'2 |
C2' |
C1' |
H1' |
19.6 |
123.9 |
| C1' |
C2' |
H2'2 |
C3' |
241.7 |
115.0 |
| C1' |
C2' |
H2'2 |
H2'1 |
120.9 |
237.5 |
| C3' |
C2' |
H2'2 |
H2'1 |
239.2 |
122.5 |
| H2'2 |
C2' |
C3' |
O3' |
317.3 |
257.9 |
| H2'2 |
C2' |
C3' |
C4' |
199.3 |
139.5 |
| H2'2 |
C2' |
C3' |
H3' |
76.0 |
21.5 |
| O4' |
C4' |
C3' |
O3' |
286.3 |
204.9 |
| O3' |
C3' |
C2' |
H2'1 |
207.9 |
20.4 |
| O3' |
C3' |
C2' |
H2'2 |
317.3 |
257.9 |
| C2' |
C3' |
O3' |
C4' |
248.5 |
247.3 |
| C2' |
C3' |
O3' |
H3' |
124.4 |
123.6 |
| C4' |
C3' |
O3' |
H3' |
236.0 |
236.4 |
| O3' |
C3' |
C4' |
C5' |
168.5 |
86.4 |
| O3' |
C3' |
C4' |
H4' |
50.3 |
323.5 |
| O4' |
C4' |
C3' |
C5' |
117.9 |
118.5 |
| O4' |
C4' |
C3' |
H4' |
236.1 |
241.4 |
| C4' |
C3' |
C2' |
H2'1 |
89.9 |
262.0 |
| C4' |
C3' |
C2' |
H2'2 |
199.3 |
139.5 |
| C2' |
C3' |
C4' |
O3' |
117.5 |
118.3 |
| C2' |
C3' |
C4' |
H3' |
236.3 |
241.9 |
| O3' |
C3' |
C4' |
H3' |
118.8 |
123.6 |
| C4' |
C3' |
O3' |
H1 |
291.5 |
174.2 |
| C5' |
C4' |
C3' |
H4' |
118.2 |
122.9 |
| C3' |
C4' |
C5' |
O5' |
170.4 |
182.8 |
| C3' |
C4' |
C5' |
H5'1 |
45.2 |
62.8 |
| C3' |
C4' |
C5' |
H5'2 |
295.7 |
302.7 |
| H3' |
C3' |
C2' |
H2'1 |
326.6 |
144.0 |
| H3' |
C3' |
C2' |
H2'2 |
76.0 |
21.5 |
| C2' |
C3' |
H3' |
O3' |
238.2 |
236.3 |
| C2' |
C3' |
H3' |
C4' |
115.9 |
112.5 |
| O3' |
C3' |
H3' |
C4' |
237.7 |
236.2 |
| H3' |
C3' |
O3' |
H1 |
55.5 |
297.8 |
| H3' |
C3' |
C4' |
C5' |
49.7 |
322.7 |
| H3' |
C3' |
C4' |
H4' |
291.5 |
199.9 |
| H1 |
O3' |
C3' |
C4' |
291.5 |
174.2 |
| H1 |
O3' |
C3' |
H3' |
55.5 |
297.8 |
| O4' |
C4' |
C5' |
C3' |
246.5 |
245.8 |
| O4' |
C4' |
C5' |
H4' |
124.3 |
122.9 |
| C5' |
C4' |
C3' |
H3' |
49.7 |
322.7 |
| C3' |
C4' |
C5' |
H4' |
237.8 |
237.1 |
| O5' |
C5' |
C4' |
H5'1 |
125.2 |
120.0 |
| O5' |
C5' |
C4' |
H5'2 |
234.7 |
240.1 |
| C4' |
C5' |
O5' |
H5' |
180.0 |
180.0 |
| H5'1 |
C5' |
C4' |
H5'2 |
109.5 |
120.1 |
| O4' |
C4' |
H4' |
C3' |
116.4 |
114.3 |
| O4' |
C4' |
H4' |
C5' |
239.4 |
237.1 |
| H4' |
C4' |
C3' |
H3' |
291.5 |
199.9 |
| C3' |
C4' |
H4' |
C5' |
123.0 |
122.9 |
| H4' |
C4' |
C5' |
O5' |
292.6 |
305.7 |
| H4' |
C4' |
C5' |
H5'1 |
167.4 |
185.7 |
| H4' |
C4' |
C5' |
H5'2 |
57.9 |
65.7 |
| O5' |
C5' |
C4' |
H4' |
292.6 |
305.7 |
| C4' |
C5' |
O5' |
H5'1 |
234.7 |
239.9 |
| C4' |
C5' |
O5' |
H5'2 |
125.3 |
119.9 |
| H5'1 |
C5' |
O5' |
H5'2 |
250.5 |
240.0 |
| H5'1 |
C5' |
C4' |
H4' |
167.4 |
185.7 |
| C4' |
C5' |
H5'1 |
O5' |
123.5 |
120.0 |
| C4' |
C5' |
H5'1 |
H5'2 |
241.7 |
240.0 |
| O5' |
C5' |
H5'1 |
H5'2 |
118.2 |
120.0 |
| H5'1 |
C5' |
O5' |
H5' |
305.3 |
300.0 |
| H5'2 |
C5' |
C4' |
H4' |
57.9 |
65.7 |
| C4' |
C5' |
H5'2 |
O5' |
236.5 |
240.1 |
| C4' |
C5' |
H5'2 |
H5'1 |
118.3 |
120.1 |
| O5' |
C5' |
H5'2 |
H5'1 |
241.8 |
240.0 |
| H5'2 |
C5' |
O5' |
H5' |
54.7 |
60.1 |
| H5' |
O5' |
C5' |
H5'1 |
305.3 |
300.0 |
| H5' |
O5' |
C5' |
H5'2 |
54.7 |
60.1 |