PDB Chemical Component 2DA
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 2DA
Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
P |
OP1 |
1.484 |
1.479 |
P |
OP2 |
1.484 |
1.610 |
P |
OP3 |
1.611 |
1.609 |
P |
O5' |
1.594 |
1.609 |
OP2 |
HOP2 |
0.950 |
0.967 |
OP3 |
HOP3 |
0.950 |
0.967 |
O5' |
C5' |
1.420 |
1.428 |
C5' |
C4' |
1.507 |
1.531 |
C5' |
H5' |
1.116 |
1.089 |
C5' |
H5'' |
1.115 |
1.090 |
C4' |
O4' |
1.451 |
1.446 |
C4' |
C3' |
1.518 |
1.549 |
C4' |
H4' |
1.115 |
1.089 |
O4' |
C1' |
1.414 |
1.437 |
C3' |
C2' |
1.524 |
1.548 |
C3' |
H3'1 |
1.115 |
1.089 |
C3' |
H3'2 |
1.116 |
1.091 |
C2' |
C1' |
1.529 |
1.540 |
C2' |
H2' |
1.115 |
1.090 |
C2' |
H2'' |
1.115 |
1.090 |
C1' |
N9 |
1.463 |
1.464 |
C1' |
H1' |
1.114 |
1.090 |
N9 |
C8 |
1.375 |
1.362 |
N9 |
C4 |
1.375 |
1.373 |
C8 |
N7 |
1.311 |
1.301 |
C8 |
H8 |
1.103 |
1.080 |
N7 |
C5 |
1.390 |
1.354 |
C5 |
C6 |
1.412 |
1.406 |
C5 |
C4 |
1.384 |
1.404 |
C6 |
N6 |
1.332 |
1.383 |
C6 |
N1 |
1.351 |
1.329 |
N6 |
HN61 |
1.019 |
0.971 |
N6 |
HN62 |
1.021 |
0.970 |
N1 |
C2 |
1.344 |
1.320 |
C2 |
N3 |
1.331 |
1.316 |
C2 |
H2 |
1.103 |
1.080 |
N3 |
C4 |
1.345 |
1.329 |
Bond Angles for 2DA
Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
OP1 |
P |
OP2 |
119.5 |
109.5 |
OP1 |
P |
OP3 |
110.0 |
109.5 |
OP1 |
P |
O5' |
107.3 |
109.4 |
OP2 |
P |
OP3 |
106.1 |
109.5 |
OP2 |
P |
O5' |
108.7 |
109.5 |
P |
OP2 |
HOP2 |
119.5 |
106.8 |
OP3 |
P |
O5' |
104.4 |
109.5 |
P |
OP3 |
HOP3 |
109.9 |
106.9 |
P |
O5' |
C5' |
121.9 |
106.8 |
O5' |
C5' |
C4' |
110.0 |
109.5 |
O5' |
C5' |
H5' |
112.0 |
109.5 |
O5' |
C5' |
H5'' |
112.0 |
109.5 |
C4' |
C5' |
H5' |
112.0 |
109.4 |
C4' |
C5' |
H5'' |
112.0 |
109.4 |
C5' |
C4' |
O4' |
109.4 |
110.7 |
C5' |
C4' |
C3' |
115.5 |
110.6 |
C5' |
C4' |
H4' |
104.0 |
110.5 |
H5' |
C5' |
H5'' |
98.4 |
109.5 |
O4' |
C4' |
C3' |
104.7 |
103.6 |
O4' |
C4' |
H4' |
114.9 |
110.6 |
C4' |
O4' |
C1' |
109.7 |
106.8 |
C3' |
C4' |
H4' |
108.7 |
110.6 |
C4' |
C3' |
C2' |
101.9 |
102.1 |
C4' |
C3' |
H3'1 |
115.1 |
110.9 |
C4' |
C3' |
H3'2 |
115.1 |
110.9 |
O4' |
C1' |
C2' |
107.4 |
107.4 |
O4' |
C1' |
N9 |
107.8 |
109.8 |
O4' |
C1' |
H1' |
113.5 |
109.9 |
C2' |
C3' |
H3'1 |
115.1 |
110.9 |
C2' |
C3' |
H3'2 |
115.1 |
110.9 |
C3' |
C2' |
C1' |
101.6 |
104.2 |
C3' |
C2' |
H2' |
115.2 |
110.5 |
C3' |
C2' |
H2'' |
115.2 |
110.5 |
H3'1 |
C3' |
H3'2 |
95.3 |
110.8 |
C1' |
C2' |
H2' |
115.2 |
110.5 |
C1' |
C2' |
H2'' |
115.2 |
110.5 |
C2' |
C1' |
N9 |
113.8 |
109.9 |
C2' |
C1' |
H1' |
107.4 |
109.9 |
H2' |
C2' |
H2'' |
95.2 |
110.6 |
N9 |
C1' |
H1' |
107.1 |
109.9 |
C1' |
N9 |
C8 |
128.0 |
126.3 |
C1' |
N9 |
C4 |
126.2 |
126.3 |
C8 |
N9 |
C4 |
105.9 |
107.4 |
N9 |
C8 |
N7 |
113.8 |
110.0 |
N9 |
C8 |
H8 |
125.2 |
125.0 |
N9 |
C4 |
C5 |
105.7 |
106.0 |
N9 |
C4 |
N3 |
127.3 |
134.9 |
N7 |
C8 |
H8 |
121.0 |
125.0 |
C8 |
N7 |
C5 |
103.8 |
109.4 |
N7 |
C5 |
C6 |
132.4 |
134.7 |
N7 |
C5 |
C4 |
110.8 |
107.1 |
C6 |
C5 |
C4 |
116.9 |
118.2 |
C5 |
C6 |
N6 |
123.8 |
120.8 |
C5 |
C6 |
N1 |
117.7 |
118.4 |
C5 |
C4 |
N3 |
127.0 |
119.1 |
N6 |
C6 |
N1 |
118.5 |
120.8 |
C6 |
N6 |
HN61 |
123.8 |
120.0 |
C6 |
N6 |
HN62 |
107.1 |
120.0 |
C6 |
N1 |
C2 |
118.6 |
121.2 |
HN61 |
N6 |
HN62 |
107.1 |
120.0 |
N1 |
C2 |
N3 |
129.3 |
122.5 |
N1 |
C2 |
H2 |
115.9 |
118.7 |
N3 |
C2 |
H2 |
114.8 |
118.7 |
C2 |
N3 |
C4 |
110.6 |
120.6 |
Torsion Angles for 2DA
Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
OP2 |
P |
OP1 |
OP3 |
237.0 |
120.0 |
OP2 |
P |
OP1 |
O5' |
124.1 |
240.0 |
OP1 |
P |
OP2 |
HOP2 |
180.0 |
300.0 |
OP3 |
P |
OP1 |
O5' |
247.1 |
120.0 |
OP1 |
P |
OP3 |
HOP3 |
180.0 |
180.0 |
OP1 |
P |
O5' |
C5' |
172.2 |
60.0 |
OP1 |
P |
OP2 |
OP3 |
124.8 |
240.0 |
OP1 |
P |
OP2 |
O5' |
236.5 |
120.0 |
OP3 |
P |
OP2 |
O5' |
111.7 |
240.0 |
OP2 |
P |
OP3 |
HOP3 |
310.5 |
60.0 |
OP2 |
P |
O5' |
C5' |
41.7 |
180.0 |
OP1 |
P |
OP3 |
OP2 |
229.5 |
120.0 |
OP1 |
P |
OP3 |
O5' |
114.8 |
240.0 |
OP2 |
P |
OP3 |
O5' |
245.3 |
120.0 |
OP3 |
P |
OP2 |
HOP2 |
55.2 |
60.1 |
OP3 |
P |
O5' |
C5' |
288.8 |
300.0 |
OP1 |
P |
O5' |
OP2 |
130.5 |
240.0 |
OP1 |
P |
O5' |
OP3 |
243.3 |
120.0 |
OP2 |
P |
O5' |
OP3 |
112.9 |
240.0 |
O5' |
P |
OP2 |
HOP2 |
303.5 |
180.1 |
O5' |
P |
OP3 |
HOP3 |
65.2 |
300.0 |
P |
O5' |
C5' |
C4' |
189.1 |
180.0 |
P |
O5' |
C5' |
H5' |
314.3 |
60.0 |
P |
O5' |
C5' |
H5'' |
63.8 |
300.0 |
HOP2 |
OP2 |
P |
OP3 |
55.2 |
60.1 |
HOP2 |
OP2 |
P |
O5' |
303.5 |
180.1 |
HOP3 |
OP3 |
P |
O5' |
65.2 |
300.0 |
C4' |
C5' |
O5' |
H5' |
234.7 |
120.0 |
C4' |
C5' |
O5' |
H5'' |
125.3 |
240.0 |
O5' |
C5' |
C4' |
O4' |
291.9 |
65.7 |
O5' |
C5' |
C4' |
C3' |
49.7 |
180.0 |
O5' |
C5' |
C4' |
H4' |
168.6 |
302.9 |
H5' |
C5' |
O5' |
H5'' |
250.6 |
120.0 |
O5' |
C5' |
C4' |
H5' |
125.2 |
240.0 |
O5' |
C5' |
C4' |
H5'' |
234.7 |
120.0 |
H5' |
C5' |
C4' |
H5'' |
109.5 |
240.0 |
O4' |
C4' |
C5' |
C3' |
242.2 |
245.7 |
O4' |
C4' |
C5' |
H4' |
123.2 |
122.9 |
C5' |
C4' |
O4' |
C1' |
144.1 |
158.5 |
C3' |
C4' |
C5' |
H4' |
241.0 |
237.1 |
C5' |
C4' |
C3' |
C2' |
204.3 |
204.3 |
C5' |
C4' |
C3' |
H3'1 |
329.6 |
86.1 |
C5' |
C4' |
C3' |
H3'2 |
79.1 |
322.5 |
O5' |
C5' |
H5' |
C4' |
235.8 |
120.0 |
O5' |
C5' |
H5' |
H5'' |
117.9 |
239.9 |
C4' |
C5' |
H5' |
H5'' |
242.0 |
119.9 |
H5' |
C5' |
C4' |
O4' |
166.6 |
185.7 |
H5' |
C5' |
C4' |
C3' |
284.5 |
300.0 |
H5' |
C5' |
C4' |
H4' |
43.4 |
62.9 |
O5' |
C5' |
H5'' |
C4' |
124.2 |
240.0 |
O5' |
C5' |
H5'' |
H5' |
242.2 |
120.0 |
C4' |
C5' |
H5'' |
H5' |
118.0 |
240.1 |
H5'' |
C5' |
C4' |
O4' |
57.1 |
305.7 |
H5'' |
C5' |
C4' |
C3' |
175.0 |
60.0 |
H5'' |
C5' |
C4' |
H4' |
293.9 |
182.8 |
O4' |
C4' |
C5' |
H5' |
166.6 |
185.7 |
O4' |
C4' |
C5' |
H5'' |
57.1 |
305.7 |
C5' |
C4' |
O4' |
C3' |
124.4 |
118.6 |
C5' |
C4' |
O4' |
H4' |
243.5 |
237.2 |
C3' |
C4' |
O4' |
H4' |
119.1 |
118.5 |
O4' |
C4' |
C3' |
C2' |
324.7 |
323.0 |
O4' |
C4' |
C3' |
H3'1 |
90.0 |
204.8 |
O4' |
C4' |
C3' |
H3'2 |
199.5 |
81.2 |
C4' |
O4' |
C1' |
C2' |
4.2 |
333.6 |
C4' |
O4' |
C1' |
N9 |
241.3 |
214.1 |
C4' |
O4' |
C1' |
H1' |
122.8 |
93.1 |
C3' |
C4' |
C5' |
H5' |
284.5 |
300.0 |
C3' |
C4' |
C5' |
H5'' |
175.0 |
60.0 |
C5' |
C4' |
C3' |
O4' |
239.6 |
241.3 |
C5' |
C4' |
C3' |
H4' |
116.3 |
122.8 |
O4' |
C4' |
C3' |
H4' |
236.7 |
241.5 |
C3' |
C4' |
O4' |
C1' |
19.7 |
39.9 |
C2' |
C3' |
C4' |
H3'1 |
234.7 |
118.2 |
C2' |
C3' |
C4' |
H3'2 |
125.3 |
241.9 |
C4' |
C3' |
C2' |
C1' |
36.6 |
20.9 |
C4' |
C3' |
C2' |
H2' |
161.9 |
262.2 |
C4' |
C3' |
C2' |
H2'' |
271.3 |
139.5 |
H3'1 |
C3' |
C4' |
H3'2 |
250.6 |
123.6 |
H4' |
C4' |
C5' |
H5' |
43.4 |
62.9 |
H4' |
C4' |
C5' |
H5'' |
293.9 |
182.8 |
C5' |
C4' |
H4' |
O4' |
119.5 |
123.0 |
C5' |
C4' |
H4' |
C3' |
236.4 |
237.1 |
O4' |
C4' |
H4' |
C3' |
116.9 |
114.1 |
H4' |
C4' |
O4' |
C1' |
260.6 |
281.4 |
H4' |
C4' |
C3' |
C2' |
88.0 |
81.5 |
H4' |
C4' |
C3' |
H3'1 |
213.3 |
323.3 |
H4' |
C4' |
C3' |
H3'2 |
322.7 |
199.7 |
C1' |
O4' |
C4' |
C3' |
19.7 |
39.9 |
C1' |
O4' |
C4' |
H4' |
260.6 |
281.4 |
C3' |
C2' |
C1' |
O4' |
333.9 |
2.0 |
O4' |
C1' |
C2' |
H2' |
208.7 |
120.6 |
O4' |
C1' |
C2' |
H2'' |
99.2 |
243.3 |
C2' |
C1' |
O4' |
N9 |
122.9 |
119.6 |
C2' |
C1' |
O4' |
H1' |
241.4 |
240.5 |
N9 |
C1' |
O4' |
H1' |
118.5 |
120.9 |
O4' |
C1' |
N9 |
C8 |
26.7 |
28.4 |
O4' |
C1' |
N9 |
C4 |
207.5 |
208.2 |
C2' |
C3' |
C4' |
H4' |
88.0 |
81.5 |
C4' |
C3' |
C2' |
H3'1 |
125.3 |
241.7 |
C4' |
C3' |
C2' |
H3'2 |
234.7 |
118.2 |
O4' |
C1' |
C2' |
C3' |
333.9 |
2.0 |
H3'1 |
C3' |
C2' |
H3'2 |
109.4 |
236.4 |
C1' |
C2' |
C3' |
H2' |
234.7 |
118.7 |
C1' |
C2' |
C3' |
H2'' |
125.3 |
241.3 |
C3' |
C2' |
C1' |
N9 |
93.1 |
121.5 |
C3' |
C2' |
C1' |
H1' |
211.5 |
242.5 |
H2' |
C2' |
C3' |
H2'' |
250.6 |
122.6 |
H3'1 |
C3' |
C4' |
H4' |
213.3 |
323.3 |
C4' |
C3' |
H3'1 |
C2' |
241.9 |
112.8 |
C4' |
C3' |
H3'1 |
H3'2 |
120.9 |
236.4 |
C2' |
C3' |
H3'1 |
H3'2 |
239.1 |
123.6 |
H3'1 |
C3' |
C2' |
C1' |
271.3 |
139.1 |
H3'1 |
C3' |
C2' |
H2' |
36.6 |
20.4 |
H3'1 |
C3' |
C2' |
H2'' |
146.0 |
257.8 |
H3'2 |
C3' |
C4' |
H4' |
322.7 |
199.7 |
C4' |
C3' |
H3'2 |
C2' |
118.1 |
247.3 |
C4' |
C3' |
H3'2 |
H3'1 |
239.1 |
123.7 |
C2' |
C3' |
H3'2 |
H3'1 |
120.9 |
236.4 |
H3'2 |
C3' |
C2' |
C1' |
161.9 |
262.7 |
H3'2 |
C3' |
C2' |
H2' |
287.2 |
144.0 |
H3'2 |
C3' |
C2' |
H2'' |
36.6 |
21.4 |
O4' |
C1' |
C2' |
N9 |
240.9 |
240.5 |
O4' |
C1' |
C2' |
H1' |
122.5 |
119.5 |
C1' |
C2' |
C3' |
H3'1 |
271.3 |
139.1 |
C1' |
C2' |
C3' |
H3'2 |
161.9 |
262.7 |
C3' |
C2' |
C1' |
H2' |
125.3 |
241.4 |
C3' |
C2' |
C1' |
H2'' |
234.8 |
118.7 |
H2' |
C2' |
C1' |
H2'' |
109.5 |
237.3 |
N9 |
C1' |
C2' |
H1' |
241.6 |
239.0 |
C2' |
C1' |
N9 |
C8 |
267.7 |
270.4 |
C2' |
C1' |
N9 |
C4 |
88.6 |
90.2 |
H2' |
C2' |
C3' |
H3'1 |
36.6 |
20.4 |
H2' |
C2' |
C3' |
H3'2 |
287.2 |
144.0 |
C3' |
C2' |
H2' |
C1' |
242.1 |
114.8 |
C3' |
C2' |
H2' |
H2'' |
121.0 |
237.4 |
C1' |
C2' |
H2' |
H2'' |
238.9 |
122.7 |
H2' |
C2' |
C1' |
N9 |
327.8 |
240.1 |
H2' |
C2' |
C1' |
H1' |
86.2 |
1.1 |
H2'' |
C2' |
C3' |
H3'1 |
146.0 |
257.8 |
H2'' |
C2' |
C3' |
H3'2 |
36.6 |
21.4 |
C3' |
C2' |
H2'' |
C1' |
117.9 |
245.2 |
C3' |
C2' |
H2'' |
H2' |
239.0 |
122.6 |
C1' |
C2' |
H2'' |
H2' |
121.1 |
237.3 |
H2'' |
C2' |
C1' |
N9 |
218.3 |
2.8 |
H2'' |
C2' |
C1' |
H1' |
336.7 |
123.8 |
O4' |
C1' |
N9 |
C2' |
118.9 |
118.0 |
O4' |
C1' |
N9 |
H1' |
237.5 |
239.0 |
N9 |
C1' |
C2' |
H2' |
327.8 |
240.1 |
N9 |
C1' |
C2' |
H2'' |
218.3 |
2.8 |
C2' |
C1' |
N9 |
H1' |
118.6 |
121.0 |
C8 |
N9 |
C1' |
C4 |
179.1 |
180.1 |
C1' |
N9 |
C8 |
N7 |
181.4 |
179.9 |
C1' |
N9 |
C8 |
H8 |
1.4 |
359.9 |
C1' |
N9 |
C4 |
C5 |
178.4 |
180.3 |
C1' |
N9 |
C4 |
N3 |
359.1 |
0.1 |
O4' |
C1' |
H1' |
C2' |
241.5 |
242.0 |
O4' |
C1' |
H1' |
N9 |
118.8 |
120.9 |
H1' |
C1' |
C2' |
H2' |
86.2 |
1.1 |
H1' |
C1' |
C2' |
H2'' |
336.7 |
123.8 |
C2' |
C1' |
H1' |
N9 |
237.4 |
238.9 |
H1' |
C1' |
N9 |
C8 |
149.2 |
149.3 |
H1' |
C1' |
N9 |
C4 |
330.1 |
329.2 |
C8 |
N9 |
C1' |
H1' |
149.2 |
149.3 |
C1' |
N9 |
C8 |
C4 |
180.7 |
179.9 |
C8 |
N9 |
C4 |
C5 |
359.2 |
0.2 |
C8 |
N9 |
C4 |
N3 |
179.9 |
180.0 |
N7 |
C8 |
N9 |
H8 |
180.0 |
180.0 |
N9 |
C8 |
N7 |
C5 |
359.8 |
359.7 |
C4 |
N9 |
C1' |
H1' |
330.1 |
329.2 |
C1' |
N9 |
C4 |
C8 |
179.3 |
180.1 |
C4 |
N9 |
C8 |
N7 |
0.7 |
0.0 |
C4 |
N9 |
C8 |
H8 |
180.7 |
180.0 |
N7 |
C5 |
C4 |
N9 |
0.8 |
359.6 |
C6 |
C5 |
C4 |
N9 |
181.0 |
180.4 |
C5 |
C4 |
N9 |
N3 |
179.3 |
180.3 |
C2 |
N3 |
C4 |
N9 |
178.9 |
180.0 |
N7 |
C8 |
N9 |
C4 |
0.7 |
0.0 |
N9 |
C8 |
N7 |
H8 |
180.0 |
180.0 |
C8 |
N7 |
C5 |
C6 |
179.4 |
179.4 |
C8 |
N7 |
C5 |
C4 |
359.6 |
0.4 |
H8 |
C8 |
N9 |
C4 |
180.7 |
180.0 |
N9 |
C8 |
H8 |
N7 |
180.0 |
180.0 |
H8 |
C8 |
N7 |
C5 |
179.8 |
179.7 |
N9 |
C4 |
C5 |
N7 |
0.8 |
359.6 |
C5 |
N7 |
C8 |
H8 |
179.8 |
179.7 |
C6 |
C5 |
N7 |
C4 |
179.7 |
179.0 |
N7 |
C5 |
C6 |
N6 |
0.2 |
0.8 |
N7 |
C5 |
C6 |
N1 |
180.1 |
180.5 |
N7 |
C5 |
C4 |
N3 |
180.1 |
179.8 |
N9 |
C4 |
C5 |
C6 |
181.0 |
180.4 |
N7 |
C5 |
C6 |
C4 |
180.3 |
181.1 |
C6 |
C5 |
C4 |
N3 |
0.3 |
0.6 |
N6 |
C6 |
C5 |
N1 |
180.1 |
180.3 |
C5 |
C6 |
N6 |
HN61 |
180.0 |
179.7 |
C5 |
C6 |
N6 |
HN62 |
54.7 |
359.5 |
C5 |
C6 |
N1 |
C2 |
360.0 |
0.3 |
N9 |
C4 |
C5 |
N3 |
180.7 |
179.8 |
N7 |
C5 |
C4 |
C6 |
179.8 |
179.2 |
C4 |
C5 |
C6 |
N6 |
179.9 |
179.7 |
C4 |
C5 |
C6 |
N1 |
359.8 |
359.4 |
C2 |
N3 |
C4 |
C5 |
359.8 |
359.7 |
N6 |
C6 |
C5 |
C4 |
179.9 |
179.7 |
C5 |
C6 |
N6 |
N1 |
179.9 |
179.7 |
N6 |
C6 |
N1 |
C2 |
179.9 |
180.0 |
HN61 |
N6 |
C6 |
HN62 |
125.2 |
180.2 |
N1 |
C6 |
C5 |
C4 |
359.8 |
359.4 |
C5 |
C6 |
N1 |
N6 |
180.1 |
180.3 |
N1 |
C6 |
N6 |
HN61 |
0.1 |
0.0 |
N1 |
C6 |
N6 |
HN62 |
234.8 |
179.8 |
C6 |
N1 |
C2 |
N3 |
0.1 |
360.0 |
C6 |
N1 |
C2 |
H2 |
180.1 |
179.9 |
HN61 |
N6 |
C6 |
N1 |
0.1 |
0.0 |
C6 |
N6 |
HN61 |
HN62 |
234.8 |
179.8 |
HN62 |
N6 |
C6 |
N1 |
234.8 |
179.8 |
C6 |
N6 |
HN62 |
HN61 |
134.8 |
180.2 |
N3 |
C2 |
N1 |
H2 |
180.0 |
180.1 |
N1 |
C2 |
N3 |
C4 |
0.0 |
0.0 |
N9 |
C4 |
N3 |
C2 |
178.9 |
180.0 |
C5 |
C4 |
N3 |
C2 |
359.8 |
359.7 |
N1 |
C2 |
N3 |
H2 |
180.0 |
179.9 |
N1 |
C2 |
H2 |
N3 |
180.0 |
180.1 |
H2 |
C2 |
N3 |
C4 |
180.0 |
180.1 |
N9 |
C4 |
N3 |
C5 |
179.2 |
180.3 |
C4 |
N3 |
C2 |
H2 |
180.0 |
180.1 |