PDB Chemical Component DA
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 DA
Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
OP3 |
P |
1.633 |
1.610 |
OP3 |
HOP3 |
0.951 |
0.967 |
P |
OP1 |
1.491 |
1.480 |
P |
OP2 |
1.440 |
1.610 |
P |
O5' |
1.582 |
1.609 |
OP2 |
HOP2 |
0.951 |
0.966 |
O5' |
C5' |
1.445 |
1.428 |
C5' |
C4' |
1.503 |
1.530 |
C5' |
H5' |
1.115 |
1.090 |
C5' |
H5'' |
1.115 |
1.089 |
C4' |
O4' |
1.438 |
1.446 |
C4' |
C3' |
1.527 |
1.549 |
C4' |
H4' |
1.115 |
1.089 |
O4' |
C1' |
1.444 |
1.436 |
C3' |
O3' |
1.450 |
1.429 |
C3' |
C2' |
1.521 |
1.547 |
C3' |
H3' |
1.115 |
1.090 |
O3' |
HO3' |
0.950 |
0.966 |
C2' |
C1' |
1.519 |
1.541 |
C2' |
H2' |
1.114 |
1.089 |
C2' |
H2'' |
1.116 |
1.091 |
C1' |
N9 |
1.450 |
1.466 |
C1' |
H1' |
1.116 |
1.090 |
N9 |
C8 |
1.368 |
1.362 |
N9 |
C4 |
1.375 |
1.372 |
C8 |
N7 |
1.294 |
1.301 |
C8 |
H8 |
1.103 |
1.080 |
N7 |
C5 |
1.387 |
1.355 |
C5 |
C6 |
1.409 |
1.405 |
C5 |
C4 |
1.389 |
1.405 |
C6 |
N6 |
1.333 |
1.384 |
C6 |
N1 |
1.351 |
1.329 |
N6 |
H61 |
1.021 |
0.970 |
N6 |
H62 |
1.020 |
0.971 |
N1 |
C2 |
1.344 |
1.319 |
C2 |
N3 |
1.326 |
1.316 |
C2 |
H2 |
1.104 |
1.080 |
N3 |
C4 |
1.340 |
1.329 |
Bond Angles for DA
Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
P |
OP3 |
HOP3 |
106.6 |
106.8 |
OP3 |
P |
OP1 |
106.6 |
109.5 |
OP3 |
P |
OP2 |
107.2 |
109.4 |
OP3 |
P |
O5' |
99.1 |
109.5 |
OP1 |
P |
OP2 |
121.5 |
109.5 |
OP1 |
P |
O5' |
110.7 |
109.5 |
OP2 |
P |
O5' |
109.3 |
109.5 |
P |
OP2 |
HOP2 |
121.4 |
106.8 |
P |
O5' |
C5' |
118.9 |
106.8 |
O5' |
C5' |
C4' |
107.6 |
109.5 |
O5' |
C5' |
H5' |
112.9 |
109.4 |
O5' |
C5' |
H5'' |
112.9 |
109.5 |
C4' |
C5' |
H5' |
112.9 |
109.5 |
C4' |
C5' |
H5'' |
112.8 |
109.5 |
C5' |
C4' |
O4' |
110.9 |
110.8 |
C5' |
C4' |
C3' |
115.8 |
110.6 |
C5' |
C4' |
H4' |
102.7 |
110.5 |
H5' |
C5' |
H5'' |
97.6 |
109.4 |
O4' |
C4' |
C3' |
105.0 |
103.6 |
O4' |
C4' |
H4' |
113.9 |
110.5 |
C4' |
O4' |
C1' |
112.1 |
106.8 |
C3' |
C4' |
H4' |
108.8 |
110.6 |
C4' |
C3' |
O3' |
106.3 |
111.0 |
C4' |
C3' |
C2' |
104.3 |
102.1 |
C4' |
C3' |
H3' |
115.7 |
110.9 |
O4' |
C1' |
C2' |
105.2 |
107.5 |
O4' |
C1' |
N9 |
107.6 |
109.8 |
O4' |
C1' |
H1' |
115.8 |
109.9 |
O3' |
C3' |
C2' |
112.3 |
110.9 |
O3' |
C3' |
H3' |
108.1 |
110.8 |
C3' |
O3' |
HO3' |
106.3 |
106.9 |
C2' |
C3' |
H3' |
110.1 |
111.0 |
C3' |
C2' |
C1' |
103.6 |
104.2 |
C3' |
C2' |
H2' |
114.5 |
110.5 |
C3' |
C2' |
H2'' |
114.4 |
110.4 |
C1' |
C2' |
H2' |
114.4 |
110.6 |
C1' |
C2' |
H2'' |
114.4 |
110.5 |
C2' |
C1' |
N9 |
115.7 |
109.9 |
C2' |
C1' |
H1' |
107.7 |
109.9 |
H2' |
C2' |
H2'' |
96.0 |
110.5 |
N9 |
C1' |
H1' |
105.3 |
109.8 |
C1' |
N9 |
C8 |
128.2 |
126.3 |
C1' |
N9 |
C4 |
124.6 |
126.3 |
C8 |
N9 |
C4 |
106.1 |
107.5 |
N9 |
C8 |
N7 |
113.5 |
110.0 |
N9 |
C8 |
H8 |
125.7 |
125.0 |
N9 |
C4 |
C5 |
105.6 |
106.0 |
N9 |
C4 |
N3 |
128.1 |
135.0 |
N7 |
C8 |
H8 |
120.8 |
125.0 |
C8 |
N7 |
C5 |
105.1 |
109.5 |
N7 |
C5 |
C6 |
133.1 |
134.7 |
N7 |
C5 |
C4 |
109.7 |
107.1 |
C6 |
C5 |
C4 |
117.3 |
118.2 |
C5 |
C6 |
N6 |
123.2 |
120.8 |
C5 |
C6 |
N1 |
117.3 |
118.5 |
C5 |
C4 |
N3 |
126.2 |
119.0 |
N6 |
C6 |
N1 |
119.5 |
120.8 |
C6 |
N6 |
H61 |
123.2 |
120.0 |
C6 |
N6 |
H62 |
107.3 |
120.0 |
C6 |
N1 |
C2 |
119.0 |
121.2 |
H61 |
N6 |
H62 |
107.3 |
120.0 |
N1 |
C2 |
N3 |
128.7 |
122.5 |
N1 |
C2 |
H2 |
116.5 |
118.7 |
N3 |
C2 |
H2 |
114.8 |
118.7 |
C2 |
N3 |
C4 |
111.5 |
120.6 |
Torsion Angles for DA
Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
OP1 |
P |
OP3 |
OP2 |
131.5 |
240.0 |
OP1 |
P |
OP3 |
O5' |
245.1 |
120.0 |
OP2 |
P |
OP3 |
O5' |
113.5 |
240.0 |
OP3 |
P |
OP2 |
HOP2 |
302.7 |
60.1 |
OP3 |
P |
O5' |
C5' |
288.5 |
180.0 |
HOP3 |
OP3 |
P |
OP1 |
180.0 |
300.0 |
HOP3 |
OP3 |
P |
OP2 |
48.5 |
60.0 |
HOP3 |
OP3 |
P |
O5' |
295.0 |
180.0 |
OP1 |
P |
OP3 |
HOP3 |
180.0 |
300.0 |
OP3 |
P |
OP1 |
OP2 |
237.0 |
119.9 |
OP3 |
P |
OP1 |
O5' |
106.8 |
240.0 |
OP2 |
P |
OP1 |
O5' |
229.8 |
120.1 |
OP1 |
P |
OP2 |
HOP2 |
180.0 |
180.0 |
OP1 |
P |
O5' |
C5' |
40.2 |
60.0 |
OP2 |
P |
OP3 |
HOP3 |
48.5 |
60.0 |
OP3 |
P |
OP2 |
OP1 |
122.7 |
240.0 |
OP3 |
P |
OP2 |
O5' |
253.5 |
120.0 |
OP1 |
P |
OP2 |
O5' |
130.8 |
240.0 |
OP2 |
P |
O5' |
C5' |
176.6 |
299.9 |
O5' |
P |
OP3 |
HOP3 |
295.0 |
180.0 |
OP3 |
P |
O5' |
OP1 |
248.3 |
120.0 |
OP3 |
P |
O5' |
OP2 |
111.9 |
240.0 |
OP1 |
P |
O5' |
OP2 |
223.6 |
120.1 |
O5' |
P |
OP2 |
HOP2 |
49.2 |
300.1 |
P |
O5' |
C5' |
C4' |
147.4 |
180.0 |
P |
O5' |
C5' |
H5' |
272.6 |
60.0 |
P |
O5' |
C5' |
H5'' |
22.2 |
300.0 |
HOP2 |
OP2 |
P |
O5' |
49.2 |
300.1 |
C4' |
C5' |
O5' |
H5' |
234.8 |
120.0 |
C4' |
C5' |
O5' |
H5'' |
125.2 |
240.0 |
O5' |
C5' |
C4' |
O4' |
290.4 |
65.7 |
O5' |
C5' |
C4' |
C3' |
50.0 |
180.0 |
O5' |
C5' |
C4' |
H4' |
168.4 |
302.9 |
H5' |
C5' |
O5' |
H5'' |
250.4 |
119.9 |
O5' |
C5' |
C4' |
H5' |
125.3 |
240.0 |
O5' |
C5' |
C4' |
H5'' |
234.8 |
120.0 |
H5' |
C5' |
C4' |
H5'' |
109.5 |
240.0 |
O4' |
C4' |
C5' |
C3' |
240.5 |
245.7 |
O4' |
C4' |
C5' |
H4' |
122.0 |
122.8 |
C5' |
C4' |
O4' |
C1' |
118.1 |
158.5 |
C3' |
C4' |
C5' |
H4' |
241.6 |
237.1 |
C5' |
C4' |
C3' |
O3' |
142.7 |
86.1 |
C5' |
C4' |
C3' |
C2' |
261.6 |
204.3 |
C5' |
C4' |
C3' |
H3' |
22.6 |
322.5 |
O5' |
C5' |
H5' |
C4' |
237.6 |
120.0 |
O5' |
C5' |
H5' |
H5'' |
118.9 |
240.0 |
C4' |
C5' |
H5' |
H5'' |
241.2 |
120.0 |
H5' |
C5' |
C4' |
O4' |
165.2 |
185.7 |
H5' |
C5' |
C4' |
C3' |
284.7 |
300.0 |
H5' |
C5' |
C4' |
H4' |
43.1 |
62.9 |
O5' |
C5' |
H5'' |
C4' |
122.3 |
239.9 |
O5' |
C5' |
H5'' |
H5' |
241.1 |
119.9 |
C4' |
C5' |
H5'' |
H5' |
118.8 |
240.0 |
H5'' |
C5' |
C4' |
O4' |
55.7 |
305.7 |
H5'' |
C5' |
C4' |
C3' |
175.2 |
60.0 |
H5'' |
C5' |
C4' |
H4' |
293.6 |
182.9 |
O4' |
C4' |
C5' |
H5' |
165.2 |
185.7 |
O4' |
C4' |
C5' |
H5'' |
55.7 |
305.7 |
C5' |
C4' |
O4' |
C3' |
125.9 |
118.7 |
C5' |
C4' |
O4' |
H4' |
244.8 |
237.2 |
C3' |
C4' |
O4' |
H4' |
118.9 |
118.5 |
O4' |
C4' |
C3' |
O3' |
265.4 |
204.8 |
O4' |
C4' |
C3' |
C2' |
24.3 |
323.0 |
O4' |
C4' |
C3' |
H3' |
145.4 |
81.3 |
C4' |
O4' |
C1' |
C2' |
347.9 |
333.7 |
C4' |
O4' |
C1' |
N9 |
224.0 |
214.2 |
C4' |
O4' |
C1' |
H1' |
106.6 |
93.2 |
C3' |
C4' |
C5' |
H5' |
284.7 |
300.0 |
C3' |
C4' |
C5' |
H5'' |
175.2 |
60.0 |
C5' |
C4' |
C3' |
O4' |
237.3 |
241.2 |
C5' |
C4' |
C3' |
H4' |
115.0 |
122.8 |
O4' |
C4' |
C3' |
H4' |
237.7 |
241.6 |
C3' |
C4' |
O4' |
C1' |
352.3 |
39.9 |
O3' |
C3' |
C4' |
C2' |
241.1 |
241.8 |
O3' |
C3' |
C4' |
H3' |
120.1 |
123.6 |
C4' |
C3' |
O3' |
HO3' |
179.9 |
174.2 |
C2' |
C3' |
C4' |
H3' |
239.0 |
241.8 |
C4' |
C3' |
C2' |
C1' |
328.8 |
20.9 |
C4' |
C3' |
C2' |
H2' |
94.0 |
262.1 |
C4' |
C3' |
C2' |
H2'' |
203.5 |
139.5 |
H4' |
C4' |
C5' |
H5' |
43.1 |
62.9 |
H4' |
C4' |
C5' |
H5'' |
293.6 |
182.9 |
C5' |
C4' |
H4' |
O4' |
120.0 |
123.0 |
C5' |
C4' |
H4' |
C3' |
236.7 |
237.1 |
O4' |
C4' |
H4' |
C3' |
116.7 |
114.1 |
H4' |
C4' |
O4' |
C1' |
233.4 |
281.4 |
H4' |
C4' |
C3' |
O3' |
27.7 |
323.3 |
H4' |
C4' |
C3' |
C2' |
146.6 |
81.4 |
H4' |
C4' |
C3' |
H3' |
267.6 |
199.7 |
C1' |
O4' |
C4' |
C3' |
352.3 |
39.9 |
C1' |
O4' |
C4' |
H4' |
233.4 |
281.4 |
C3' |
C2' |
C1' |
O4' |
26.8 |
1.9 |
O4' |
C1' |
C2' |
H2' |
261.5 |
120.7 |
O4' |
C1' |
C2' |
H2'' |
152.0 |
243.3 |
C2' |
C1' |
O4' |
N9 |
123.9 |
119.5 |
C2' |
C1' |
O4' |
H1' |
241.3 |
240.5 |
N9 |
C1' |
O4' |
H1' |
117.4 |
121.0 |
O4' |
C1' |
N9 |
C8 |
84.0 |
28.2 |
O4' |
C1' |
N9 |
C4 |
278.3 |
208.4 |
O3' |
C3' |
C4' |
H4' |
27.7 |
323.3 |
C4' |
C3' |
O3' |
C2' |
113.5 |
112.7 |
C4' |
C3' |
O3' |
H3' |
235.1 |
236.4 |
C2' |
C3' |
O3' |
H3' |
121.6 |
123.7 |
O3' |
C3' |
C2' |
C1' |
83.5 |
139.2 |
O3' |
C3' |
C2' |
H2' |
208.8 |
20.3 |
O3' |
C3' |
C2' |
H2'' |
318.2 |
257.8 |
C2' |
C3' |
C4' |
H4' |
146.6 |
81.4 |
C4' |
C3' |
C2' |
O3' |
245.3 |
241.8 |
C4' |
C3' |
C2' |
H3' |
124.7 |
118.2 |
O4' |
C1' |
C2' |
C3' |
26.8 |
1.9 |
O3' |
C3' |
C2' |
H3' |
239.5 |
236.4 |
C2' |
C3' |
O3' |
HO3' |
66.5 |
61.5 |
C1' |
C2' |
C3' |
H2' |
234.7 |
118.8 |
C1' |
C2' |
C3' |
H2'' |
125.2 |
241.4 |
C3' |
C2' |
C1' |
N9 |
145.3 |
121.4 |
C3' |
C2' |
C1' |
H1' |
262.8 |
242.4 |
H2' |
C2' |
C3' |
H2'' |
250.5 |
122.6 |
H3' |
C3' |
C4' |
H4' |
267.6 |
199.7 |
C4' |
C3' |
H3' |
O3' |
119.1 |
123.7 |
C4' |
C3' |
H3' |
C2' |
242.1 |
247.3 |
O3' |
C3' |
H3' |
C2' |
123.0 |
123.6 |
H3' |
C3' |
O3' |
HO3' |
304.8 |
297.8 |
H3' |
C3' |
C2' |
C1' |
204.0 |
262.7 |
H3' |
C3' |
C2' |
H2' |
329.3 |
143.9 |
H3' |
C3' |
C2' |
H2'' |
78.8 |
21.4 |
HO3' |
O3' |
C3' |
C2' |
66.5 |
61.5 |
HO3' |
O3' |
C3' |
H3' |
304.8 |
297.8 |
O4' |
C1' |
C2' |
N9 |
241.4 |
240.5 |
O4' |
C1' |
C2' |
H1' |
124.0 |
119.6 |
C1' |
C2' |
C3' |
H3' |
204.0 |
262.7 |
C3' |
C2' |
C1' |
H2' |
125.3 |
241.2 |
C3' |
C2' |
C1' |
H2'' |
234.8 |
118.6 |
H2' |
C2' |
C1' |
H2'' |
109.5 |
237.4 |
N9 |
C1' |
C2' |
H1' |
242.6 |
239.0 |
C2' |
C1' |
N9 |
C8 |
326.8 |
270.2 |
C2' |
C1' |
N9 |
C4 |
161.0 |
90.3 |
H2' |
C2' |
C3' |
H3' |
329.3 |
143.9 |
C3' |
C2' |
H2' |
C1' |
240.7 |
114.9 |
C3' |
C2' |
H2' |
H2'' |
120.3 |
237.5 |
C1' |
C2' |
H2' |
H2'' |
239.7 |
122.6 |
H2' |
C2' |
C1' |
N9 |
20.0 |
240.2 |
H2' |
C2' |
C1' |
H1' |
137.5 |
1.2 |
H2'' |
C2' |
C3' |
H3' |
78.8 |
21.4 |
C3' |
C2' |
H2'' |
C1' |
119.3 |
245.3 |
C3' |
C2' |
H2'' |
H2' |
239.6 |
122.6 |
C1' |
C2' |
H2'' |
H2' |
120.3 |
237.3 |
H2'' |
C2' |
C1' |
N9 |
270.6 |
2.8 |
H2'' |
C2' |
C1' |
H1' |
28.0 |
123.8 |
O4' |
C1' |
N9 |
C2' |
117.3 |
118.0 |
O4' |
C1' |
N9 |
H1' |
236.0 |
239.0 |
N9 |
C1' |
C2' |
H2' |
20.0 |
240.2 |
N9 |
C1' |
C2' |
H2'' |
270.6 |
2.8 |
C2' |
C1' |
N9 |
H1' |
118.7 |
121.0 |
C8 |
N9 |
C1' |
C4 |
165.8 |
179.9 |
C1' |
N9 |
C8 |
N7 |
191.6 |
180.1 |
C1' |
N9 |
C8 |
H8 |
11.6 |
0.1 |
C1' |
N9 |
C4 |
C5 |
168.0 |
180.2 |
C1' |
N9 |
C4 |
N3 |
347.7 |
359.9 |
O4' |
C1' |
H1' |
C2' |
242.6 |
241.9 |
O4' |
C1' |
H1' |
N9 |
118.7 |
121.0 |
H1' |
C1' |
C2' |
H2' |
137.5 |
1.2 |
H1' |
C1' |
C2' |
H2'' |
28.0 |
123.8 |
C2' |
C1' |
H1' |
N9 |
236.1 |
239.0 |
H1' |
C1' |
N9 |
C8 |
208.0 |
149.3 |
H1' |
C1' |
N9 |
C4 |
42.3 |
329.4 |
C8 |
N9 |
C1' |
H1' |
208.0 |
149.3 |
C1' |
N9 |
C8 |
C4 |
192.2 |
180.1 |
C8 |
N9 |
C4 |
C5 |
359.6 |
0.3 |
C8 |
N9 |
C4 |
N3 |
179.3 |
180.0 |
N7 |
C8 |
N9 |
H8 |
180.0 |
180.0 |
N9 |
C8 |
N7 |
C5 |
1.3 |
359.7 |
C4 |
N9 |
C1' |
H1' |
42.3 |
329.4 |
C1' |
N9 |
C4 |
C8 |
168.4 |
179.9 |
C4 |
N9 |
C8 |
N7 |
359.4 |
360.0 |
C4 |
N9 |
C8 |
H8 |
179.5 |
180.0 |
N7 |
C5 |
C4 |
N9 |
1.3 |
359.5 |
C6 |
C5 |
C4 |
N9 |
181.1 |
180.3 |
C5 |
C4 |
N9 |
N3 |
180.2 |
180.3 |
C2 |
N3 |
C4 |
N9 |
180.1 |
180.0 |
N7 |
C8 |
N9 |
C4 |
359.4 |
360.0 |
N9 |
C8 |
N7 |
H8 |
180.0 |
180.0 |
C8 |
N7 |
C5 |
C6 |
178.6 |
179.5 |
C8 |
N7 |
C5 |
C4 |
358.4 |
0.4 |
H8 |
C8 |
N9 |
C4 |
179.5 |
180.0 |
N9 |
C8 |
H8 |
N7 |
180.0 |
180.0 |
H8 |
C8 |
N7 |
C5 |
181.3 |
179.7 |
N9 |
C4 |
C5 |
N7 |
1.3 |
359.5 |
C5 |
N7 |
C8 |
H8 |
181.3 |
179.7 |
C6 |
C5 |
N7 |
C4 |
180.2 |
179.0 |
N7 |
C5 |
C6 |
N6 |
357.8 |
0.7 |
N7 |
C5 |
C6 |
N1 |
178.1 |
180.5 |
N7 |
C5 |
C4 |
N3 |
181.5 |
179.8 |
N9 |
C4 |
C5 |
C6 |
181.1 |
180.3 |
N7 |
C5 |
C6 |
C4 |
179.8 |
181.0 |
C6 |
C5 |
C4 |
N3 |
1.4 |
0.6 |
N6 |
C6 |
C5 |
N1 |
179.7 |
180.3 |
C5 |
C6 |
N6 |
H61 |
180.0 |
179.7 |
C5 |
C6 |
N6 |
H62 |
54.8 |
359.5 |
C5 |
C6 |
N1 |
C2 |
1.0 |
0.3 |
N9 |
C4 |
C5 |
N3 |
179.8 |
179.7 |
N7 |
C5 |
C4 |
C6 |
180.1 |
179.2 |
C4 |
C5 |
C6 |
N6 |
178.0 |
179.7 |
C4 |
C5 |
C6 |
N1 |
358.3 |
359.4 |
C2 |
N3 |
C4 |
C5 |
359.8 |
359.7 |
N6 |
C6 |
C5 |
C4 |
178.0 |
179.7 |
C5 |
C6 |
N6 |
N1 |
180.3 |
179.7 |
N6 |
C6 |
N1 |
C2 |
181.3 |
180.0 |
H61 |
N6 |
C6 |
H62 |
125.2 |
180.2 |
N1 |
C6 |
C5 |
C4 |
358.3 |
359.4 |
C5 |
C6 |
N1 |
N6 |
179.7 |
180.3 |
N1 |
C6 |
N6 |
H61 |
359.7 |
360.0 |
N1 |
C6 |
N6 |
H62 |
234.5 |
179.8 |
C6 |
N1 |
C2 |
N3 |
0.4 |
360.0 |
C6 |
N1 |
C2 |
H2 |
180.4 |
179.9 |
H61 |
N6 |
C6 |
N1 |
359.7 |
360.0 |
C6 |
N6 |
H61 |
H62 |
234.8 |
179.8 |
H62 |
N6 |
C6 |
N1 |
234.5 |
179.8 |
C6 |
N6 |
H62 |
H61 |
134.3 |
180.2 |
N3 |
C2 |
N1 |
H2 |
180.0 |
180.0 |
N1 |
C2 |
N3 |
C4 |
359.2 |
0.0 |
N9 |
C4 |
N3 |
C2 |
180.1 |
180.0 |
C5 |
C4 |
N3 |
C2 |
359.8 |
359.7 |
N1 |
C2 |
N3 |
H2 |
180.0 |
180.0 |
N1 |
C2 |
H2 |
N3 |
180.0 |
180.0 |
H2 |
C2 |
N3 |
C4 |
179.2 |
180.1 |
N9 |
C4 |
N3 |
C5 |
180.3 |
180.4 |
C4 |
N3 |
C2 |
H2 |
179.2 |
180.1 |