PDB Chemical Component CDW
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 CDW
Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
P |
OP1 |
1.476 |
1.480 |
P |
OP2 |
1.506 |
1.609 |
P |
O5' |
1.592 |
1.610 |
P |
OP3 |
1.574 |
1.611 |
O5' |
C5' |
1.420 |
1.429 |
C5' |
C4' |
1.536 |
1.530 |
C4' |
O4' |
1.448 |
1.445 |
C4' |
C3' |
1.525 |
1.549 |
O4' |
C1' |
1.410 |
1.438 |
C3' |
O3' |
1.402 |
1.429 |
C3' |
C2' |
1.501 |
1.548 |
C2' |
C1' |
1.520 |
1.542 |
C1' |
N1 |
1.439 |
1.465 |
N1 |
C2 |
1.382 |
1.342 |
N1 |
C6 |
1.421 |
1.461 |
C2 |
O2 |
1.219 |
1.216 |
C2 |
N3 |
1.419 |
1.343 |
N3 |
C4 |
1.324 |
1.388 |
N3 |
C6 |
1.501 |
1.457 |
C4 |
C5 |
1.411 |
1.314 |
OP2 |
HP2 |
0.950 |
0.967 |
OP3 |
HP3 |
0.950 |
0.967 |
C5' |
H51 |
1.100 |
1.090 |
C5' |
H52 |
1.100 |
1.090 |
C4' |
H4' |
1.099 |
1.089 |
C3' |
H3' |
1.100 |
1.090 |
C1' |
H1' |
1.100 |
1.090 |
O3' |
HA |
0.950 |
0.967 |
C2' |
H21 |
1.100 |
1.090 |
C2' |
H22 |
1.100 |
1.089 |
C6 |
C5 |
1.436 |
1.496 |
C6 |
H6 |
1.100 |
1.090 |
C4 |
H41C |
1.080 |
1.080 |
C5 |
H51C |
1.080 |
1.081 |
Bond Angles for CDW
Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
OP1 |
P |
OP2 |
121.4 |
109.5 |
OP1 |
P |
O5' |
105.0 |
109.5 |
OP1 |
P |
OP3 |
108.5 |
109.4 |
OP2 |
P |
O5' |
110.1 |
109.5 |
OP2 |
P |
OP3 |
106.3 |
109.5 |
P |
OP2 |
HP2 |
109.5 |
114.0 |
O5' |
P |
OP3 |
104.4 |
109.4 |
P |
O5' |
C5' |
121.8 |
123.0 |
P |
OP3 |
HP3 |
109.5 |
114.0 |
O5' |
C5' |
C4' |
109.6 |
109.5 |
O5' |
C5' |
H51 |
109.4 |
109.4 |
O5' |
C5' |
H52 |
109.4 |
109.4 |
C5' |
C4' |
O4' |
112.0 |
110.6 |
C5' |
C4' |
C3' |
113.1 |
110.6 |
C4' |
C5' |
H51 |
109.4 |
109.5 |
C4' |
C5' |
H52 |
109.4 |
109.5 |
C5' |
C4' |
H4' |
104.1 |
110.6 |
O4' |
C4' |
C3' |
105.9 |
103.5 |
C4' |
O4' |
C1' |
109.5 |
107.0 |
O4' |
C4' |
H4' |
111.5 |
110.6 |
C4' |
C3' |
O3' |
111.3 |
110.9 |
C4' |
C3' |
C2' |
106.3 |
102.1 |
C3' |
C4' |
H4' |
110.4 |
110.8 |
C4' |
C3' |
H3' |
109.5 |
110.9 |
O4' |
C1' |
C2' |
108.4 |
107.3 |
O4' |
C1' |
N1 |
108.7 |
109.9 |
O4' |
C1' |
H1' |
109.9 |
109.9 |
O3' |
C3' |
C2' |
106.7 |
110.9 |
O3' |
C3' |
H3' |
109.1 |
110.8 |
C3' |
O3' |
HA |
109.5 |
114.0 |
C3' |
C2' |
C1' |
105.3 |
104.2 |
C2' |
C3' |
H3' |
113.9 |
110.9 |
C3' |
C2' |
H21 |
110.9 |
110.5 |
C3' |
C2' |
H22 |
111.8 |
110.5 |
C2' |
C1' |
N1 |
107.3 |
109.9 |
C2' |
C1' |
H1' |
111.3 |
109.9 |
C1' |
C2' |
H21 |
110.9 |
110.5 |
C1' |
C2' |
H22 |
111.8 |
110.5 |
C1' |
N1 |
C2 |
133.2 |
133.9 |
C1' |
N1 |
C6 |
129.6 |
133.9 |
N1 |
C1' |
H1' |
111.1 |
110.0 |
C2 |
N1 |
C6 |
90.2 |
92.2 |
N1 |
C2 |
O2 |
130.4 |
133.8 |
N1 |
C2 |
N3 |
94.6 |
92.3 |
N1 |
C6 |
N3 |
89.5 |
83.2 |
N1 |
C6 |
C5 |
134.0 |
118.7 |
N1 |
C6 |
H6 |
103.4 |
118.6 |
O2 |
C2 |
N3 |
135.0 |
133.9 |
C2 |
N3 |
C4 |
134.5 |
120.5 |
C2 |
N3 |
C6 |
85.7 |
92.3 |
C4 |
N3 |
C6 |
92.4 |
92.0 |
N3 |
C4 |
C5 |
91.9 |
92.2 |
N3 |
C4 |
H41C |
134.0 |
133.9 |
N3 |
C6 |
C5 |
84.1 |
82.5 |
N3 |
C6 |
H6 |
145.2 |
124.2 |
C4 |
C5 |
C6 |
91.6 |
93.3 |
C5 |
C4 |
H41C |
134.0 |
133.9 |
C4 |
C5 |
H51C |
134.2 |
133.3 |
H51 |
C5' |
H52 |
109.6 |
109.5 |
H21 |
C2' |
H22 |
106.3 |
110.5 |
C5 |
C6 |
H6 |
107.6 |
118.6 |
C6 |
C5 |
H51C |
134.2 |
133.4 |
Torsion Angles for CDW
Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
OP2 |
P |
OP1 |
O5' |
125.5 |
239.9 |
OP2 |
P |
OP1 |
OP3 |
236.6 |
120.0 |
OP1 |
P |
OP2 |
HP2 |
205.0 |
180.0 |
O5' |
P |
OP1 |
OP3 |
111.1 |
240.1 |
OP1 |
P |
O5' |
C5' |
178.1 |
305.0 |
OP1 |
P |
OP3 |
HP3 |
127.5 |
60.1 |
OP1 |
P |
OP2 |
O5' |
236.9 |
120.0 |
OP1 |
P |
OP2 |
OP3 |
124.4 |
240.0 |
O5' |
P |
OP2 |
OP3 |
247.5 |
120.0 |
OP2 |
P |
O5' |
C5' |
45.9 |
65.0 |
OP2 |
P |
OP3 |
HP3 |
259.6 |
300.1 |
OP1 |
P |
O5' |
OP2 |
132.2 |
239.9 |
OP1 |
P |
O5' |
OP3 |
246.0 |
119.9 |
OP2 |
P |
O5' |
OP3 |
113.8 |
240.0 |
O5' |
P |
OP2 |
HP2 |
328.1 |
59.9 |
O5' |
P |
OP3 |
HP3 |
16.0 |
180.0 |
P |
O5' |
C5' |
C4' |
173.3 |
180.0 |
P |
O5' |
C5' |
H51 |
293.2 |
300.0 |
P |
O5' |
C5' |
H52 |
53.3 |
60.0 |
OP1 |
P |
OP3 |
OP2 |
228.0 |
120.0 |
OP1 |
P |
OP3 |
O5' |
111.5 |
240.0 |
OP2 |
P |
OP3 |
O5' |
243.5 |
120.0 |
OP3 |
P |
OP2 |
HP2 |
80.6 |
299.9 |
OP3 |
P |
O5' |
C5' |
292.1 |
185.0 |
C5' |
O5' |
P |
OP3 |
292.1 |
185.0 |
O5' |
C5' |
C4' |
O4' |
278.2 |
66.5 |
O5' |
C5' |
C4' |
C3' |
37.7 |
180.5 |
C4' |
C5' |
O5' |
H51 |
240.0 |
240.0 |
C4' |
C5' |
O5' |
H52 |
119.9 |
120.0 |
O5' |
C5' |
C4' |
H4' |
157.5 |
303.6 |
H51 |
C5' |
O5' |
H52 |
239.9 |
240.0 |
O5' |
C5' |
C4' |
H51 |
120.0 |
120.0 |
O5' |
C5' |
C4' |
H52 |
240.1 |
240.0 |
O4' |
C4' |
C5' |
C3' |
240.5 |
245.9 |
C5' |
C4' |
O4' |
C1' |
146.1 |
158.6 |
O4' |
C4' |
C5' |
H4' |
120.6 |
122.8 |
C5' |
C4' |
C3' |
O3' |
104.6 |
86.3 |
C5' |
C4' |
C3' |
C2' |
220.4 |
204.5 |
C3' |
C4' |
C5' |
H4' |
240.2 |
236.9 |
C5' |
C4' |
C3' |
H3' |
343.9 |
322.7 |
H51 |
C5' |
C4' |
H52 |
120.1 |
120.0 |
C5' |
C4' |
O4' |
C3' |
123.7 |
118.5 |
O4' |
C4' |
C5' |
H51 |
158.2 |
306.5 |
O4' |
C4' |
C5' |
H52 |
38.1 |
186.5 |
C5' |
C4' |
O4' |
H4' |
243.8 |
237.2 |
O4' |
C4' |
C3' |
O3' |
227.6 |
204.7 |
O4' |
C4' |
C3' |
C2' |
343.4 |
322.9 |
C3' |
C4' |
O4' |
H4' |
120.1 |
118.7 |
O4' |
C4' |
C3' |
H3' |
106.9 |
81.2 |
C4' |
O4' |
C1' |
C2' |
340.6 |
333.5 |
C4' |
O4' |
C1' |
N1 |
224.3 |
214.1 |
C4' |
O4' |
C1' |
H1' |
102.5 |
92.9 |
C5' |
C4' |
C3' |
O4' |
237.0 |
241.5 |
C3' |
C4' |
C5' |
H51 |
277.7 |
60.5 |
C3' |
C4' |
C5' |
H52 |
157.6 |
300.5 |
C5' |
C4' |
C3' |
H4' |
116.2 |
123.0 |
C3' |
C4' |
O4' |
C1' |
22.4 |
40.1 |
O4' |
C4' |
C3' |
H4' |
239.1 |
241.4 |
O3' |
C3' |
C4' |
C2' |
244.2 |
241.8 |
O3' |
C3' |
C4' |
H3' |
120.7 |
123.6 |
C4' |
C3' |
O3' |
HA |
232.5 |
180.0 |
C4' |
C3' |
C2' |
C1' |
5.3 |
20.9 |
C2' |
C3' |
C4' |
H3' |
236.5 |
241.8 |
C4' |
C3' |
C2' |
H21 |
125.3 |
139.5 |
C4' |
C3' |
C2' |
H22 |
243.8 |
262.2 |
C1' |
O4' |
C4' |
C3' |
22.4 |
40.1 |
C1' |
O4' |
C4' |
H4' |
262.3 |
281.4 |
C3' |
C2' |
C1' |
O4' |
8.1 |
2.0 |
C2' |
C1' |
O4' |
N1 |
116.3 |
119.4 |
C2' |
C1' |
O4' |
H1' |
238.1 |
240.6 |
O4' |
C1' |
C2' |
H21 |
248.1 |
243.4 |
O4' |
C1' |
C2' |
H22 |
129.7 |
120.8 |
O4' |
C1' |
N1 |
C2 |
300.1 |
53.5 |
O4' |
C1' |
N1 |
C6 |
81.6 |
233.2 |
N1 |
C1' |
O4' |
H1' |
121.8 |
121.2 |
C4' |
C3' |
O3' |
C2' |
115.6 |
112.7 |
O3' |
C3' |
C4' |
H4' |
348.4 |
323.3 |
C4' |
C3' |
O3' |
H3' |
239.0 |
236.4 |
O3' |
C3' |
C2' |
C1' |
124.3 |
139.1 |
C2' |
C3' |
O3' |
H3' |
123.5 |
123.6 |
O3' |
C3' |
C2' |
H21 |
244.3 |
257.7 |
O3' |
C3' |
C2' |
H22 |
2.7 |
20.5 |
C4' |
C3' |
C2' |
O3' |
241.1 |
241.8 |
C2' |
C3' |
C4' |
H4' |
104.3 |
81.5 |
C4' |
C3' |
C2' |
H3' |
120.7 |
118.3 |
O4' |
C1' |
C2' |
C3' |
8.1 |
2.0 |
O3' |
C3' |
C2' |
H3' |
239.6 |
236.5 |
C2' |
C3' |
O3' |
HA |
116.9 |
67.2 |
C3' |
C2' |
C1' |
N1 |
125.4 |
121.4 |
C3' |
C2' |
C1' |
H1' |
247.1 |
242.6 |
C1' |
C2' |
C3' |
H21 |
240.0 |
241.4 |
C1' |
C2' |
C3' |
H22 |
121.6 |
118.7 |
H21 |
C2' |
C3' |
H22 |
241.6 |
237.3 |
O4' |
C1' |
C2' |
N1 |
242.7 |
240.6 |
O4' |
C1' |
C2' |
H1' |
121.0 |
119.4 |
C1' |
C2' |
C3' |
H3' |
244.7 |
262.6 |
C3' |
C2' |
C1' |
H21 |
120.0 |
118.7 |
C3' |
C2' |
C1' |
H22 |
238.4 |
241.3 |
C2' |
C1' |
N1 |
C2 |
183.0 |
295.7 |
C2' |
C1' |
N1 |
C6 |
324.5 |
115.4 |
N1 |
C1' |
C2' |
H1' |
238.3 |
238.8 |
H21 |
C2' |
C1' |
H22 |
118.4 |
122.6 |
O4' |
C1' |
N1 |
C2' |
117.1 |
117.8 |
O4' |
C1' |
N1 |
H1' |
238.9 |
238.9 |
C2' |
C1' |
N1 |
H1' |
121.8 |
121.1 |
N1 |
C1' |
C2' |
H21 |
5.4 |
2.8 |
N1 |
C1' |
C2' |
H22 |
247.0 |
240.1 |
C2 |
N1 |
C1' |
C6 |
218.4 |
180.3 |
C1' |
N1 |
C2 |
O2 |
330.8 |
359.3 |
C1' |
N1 |
C2 |
N3 |
151.8 |
179.3 |
C1' |
N1 |
C6 |
N3 |
206.5 |
180.7 |
C1' |
N1 |
C6 |
C5 |
287.8 |
258.3 |
C1' |
N1 |
C6 |
H6 |
59.2 |
55.3 |
C1' |
N1 |
C2 |
C6 |
151.4 |
179.8 |
C2 |
N1 |
C1' |
H1' |
61.1 |
174.6 |
C2 |
N1 |
C6 |
N3 |
359.6 |
0.5 |
C2 |
N1 |
C6 |
C5 |
80.9 |
78.1 |
C2 |
N1 |
C6 |
H6 |
212.2 |
235.1 |
O2 |
C2 |
N1 |
N3 |
179.0 |
180.1 |
N1 |
C2 |
N3 |
C4 |
270.5 |
266.9 |
N1 |
C2 |
N3 |
C6 |
359.6 |
0.5 |
C1' |
N1 |
C6 |
C2 |
207.0 |
180.2 |
C6 |
N1 |
C1' |
H1' |
202.7 |
354.3 |
C6 |
N1 |
C2 |
O2 |
179.4 |
179.6 |
C6 |
N1 |
C2 |
N3 |
0.4 |
359.5 |
C2 |
N3 |
C6 |
N1 |
0.4 |
359.5 |
C4 |
N3 |
C6 |
N1 |
134.8 |
120.2 |
N3 |
C6 |
N1 |
C5 |
278.7 |
282.4 |
N3 |
C6 |
N1 |
H6 |
147.4 |
125.4 |
C4 |
C5 |
C6 |
N1 |
276.0 |
282.0 |
C5 |
C6 |
N1 |
H6 |
228.6 |
203.0 |
N1 |
C6 |
C5 |
H51C |
96.0 |
101.9 |
O2 |
C2 |
N1 |
C6 |
179.4 |
179.6 |
N1 |
C2 |
O2 |
N3 |
181.4 |
179.9 |
O2 |
C2 |
N3 |
C4 |
91.6 |
86.8 |
O2 |
C2 |
N3 |
C6 |
180.7 |
180.4 |
N3 |
C2 |
N1 |
C6 |
0.4 |
359.5 |
N1 |
C2 |
N3 |
O2 |
178.9 |
180.1 |
N1 |
C6 |
N3 |
C2 |
0.4 |
359.5 |
C4 |
N3 |
C2 |
C6 |
270.9 |
266.3 |
C2 |
N3 |
C4 |
C5 |
85.8 |
93.8 |
C2 |
N3 |
C4 |
H41C |
265.8 |
273.9 |
C2 |
N3 |
C6 |
C5 |
226.0 |
239.3 |
C2 |
N3 |
C6 |
H6 |
113.6 |
119.6 |
N1 |
C6 |
N3 |
C4 |
134.8 |
120.2 |
C2 |
N3 |
C4 |
C6 |
86.3 |
93.8 |
C4 |
N3 |
C6 |
C5 |
0.5 |
0.0 |
C4 |
N3 |
C6 |
H6 |
248.0 |
240.3 |
N3 |
C4 |
C5 |
C6 |
0.5 |
0.0 |
C5 |
C4 |
N3 |
H41C |
180.0 |
179.9 |
N3 |
C4 |
C5 |
H51C |
180.5 |
180.1 |
N1 |
C6 |
N3 |
C5 |
134.4 |
120.2 |
N1 |
C6 |
N3 |
H6 |
246.9 |
239.9 |
C2 |
N3 |
C6 |
C4 |
225.6 |
239.3 |
C6 |
N3 |
C4 |
C5 |
359.5 |
360.0 |
C6 |
N3 |
C4 |
H41C |
179.5 |
180.1 |
C4 |
C5 |
C6 |
N3 |
359.6 |
360.0 |
C5 |
C6 |
N3 |
H6 |
112.5 |
119.7 |
N3 |
C6 |
C5 |
H51C |
179.6 |
179.9 |
N1 |
C6 |
C5 |
C4 |
276.0 |
282.0 |
C5 |
C4 |
N3 |
C6 |
359.5 |
360.0 |
N3 |
C4 |
C5 |
H41C |
180.0 |
180.1 |
N3 |
C6 |
C5 |
C4 |
359.6 |
360.0 |
C4 |
C5 |
C6 |
H6 |
146.0 |
125.0 |
C6 |
C5 |
C4 |
H51C |
180.0 |
179.9 |
HP2 |
OP2 |
P |
O5' |
328.1 |
59.9 |
HP2 |
OP2 |
P |
OP3 |
80.6 |
299.9 |
O5' |
C5' |
H51 |
C4' |
239.9 |
240.0 |
O5' |
C5' |
H51 |
H52 |
119.9 |
119.9 |
H51 |
C5' |
C4' |
O4' |
158.2 |
306.5 |
H51 |
C5' |
C4' |
C3' |
277.7 |
60.5 |
C4' |
C5' |
H51 |
H52 |
240.1 |
240.0 |
H51 |
C5' |
C4' |
H4' |
37.6 |
183.6 |
O5' |
C5' |
H52 |
C4' |
120.1 |
120.0 |
O5' |
C5' |
H52 |
H51 |
240.0 |
240.1 |
H52 |
C5' |
C4' |
O4' |
38.1 |
186.5 |
H52 |
C5' |
C4' |
C3' |
157.6 |
300.5 |
C4' |
C5' |
H52 |
H51 |
120.0 |
120.0 |
H52 |
C5' |
C4' |
H4' |
277.5 |
63.6 |
C5' |
C4' |
H4' |
O4' |
120.9 |
122.8 |
C5' |
C4' |
H4' |
C3' |
238.4 |
237.0 |
H4' |
C4' |
C5' |
H51 |
37.6 |
183.6 |
H4' |
C4' |
C5' |
H52 |
277.5 |
63.6 |
O4' |
C4' |
H4' |
C3' |
117.4 |
114.2 |
H4' |
C4' |
O4' |
C1' |
262.3 |
281.4 |
H4' |
C4' |
C3' |
O3' |
348.4 |
323.3 |
H4' |
C4' |
C3' |
C2' |
104.3 |
81.5 |
H4' |
C4' |
C3' |
H3' |
227.7 |
199.8 |
C4' |
C3' |
H3' |
O3' |
122.1 |
123.6 |
C4' |
C3' |
H3' |
C2' |
241.2 |
247.2 |
H3' |
C3' |
C4' |
H4' |
227.7 |
199.8 |
O3' |
C3' |
H3' |
C2' |
119.1 |
123.6 |
H3' |
C3' |
O3' |
HA |
353.5 |
303.6 |
H3' |
C3' |
C2' |
C1' |
244.7 |
262.6 |
H3' |
C3' |
C2' |
H21 |
4.7 |
21.3 |
H3' |
C3' |
C2' |
H22 |
123.1 |
144.0 |
O4' |
C1' |
H1' |
C2' |
239.8 |
242.2 |
O4' |
C1' |
H1' |
N1 |
120.4 |
121.1 |
C2' |
C1' |
H1' |
N1 |
240.5 |
238.9 |
H1' |
C1' |
C2' |
H21 |
127.1 |
123.9 |
H1' |
C1' |
C2' |
H22 |
8.7 |
1.3 |
H1' |
C1' |
N1 |
C2 |
61.1 |
174.6 |
H1' |
C1' |
N1 |
C6 |
202.7 |
354.3 |
HA |
O3' |
C3' |
C2' |
116.9 |
67.2 |
HA |
O3' |
C3' |
H3' |
353.5 |
303.6 |
C3' |
C2' |
H21 |
C1' |
243.4 |
245.3 |
H21 |
C2' |
C3' |
H3' |
4.7 |
21.3 |
C3' |
C2' |
H21 |
H22 |
121.7 |
122.7 |
H21 |
C2' |
C1' |
N1 |
5.4 |
2.8 |
H21 |
C2' |
C1' |
H1' |
127.1 |
123.9 |
C1' |
C2' |
H21 |
H22 |
238.3 |
237.4 |
C3' |
C2' |
H22 |
C1' |
117.8 |
114.8 |
H22 |
C2' |
C3' |
H3' |
123.1 |
144.0 |
C3' |
C2' |
H22 |
H21 |
238.9 |
237.3 |
H22 |
C2' |
C1' |
N1 |
247.0 |
240.1 |
H22 |
C2' |
C1' |
H1' |
8.7 |
1.3 |
C1' |
C2' |
H22 |
H21 |
121.1 |
122.6 |
N1 |
C6 |
C5 |
N3 |
276.4 |
282.0 |
N1 |
C6 |
C5 |
H6 |
130.0 |
157.0 |
N3 |
C6 |
C5 |
H6 |
213.6 |
235.0 |
C6 |
C5 |
C4 |
H41C |
180.5 |
179.9 |
C4 |
C5 |
C6 |
H51C |
180.0 |
180.1 |
N1 |
C6 |
H6 |
N3 |
109.1 |
101.9 |
N1 |
C6 |
H6 |
C5 |
214.5 |
203.0 |
N3 |
C6 |
H6 |
C5 |
105.4 |
101.0 |
H6 |
C6 |
C5 |
H51C |
326.0 |
304.9 |
H41C |
C4 |
N3 |
C6 |
179.5 |
180.1 |
N3 |
C4 |
H41C |
C5 |
180.0 |
179.9 |
H41C |
C4 |
C5 |
C6 |
180.5 |
179.9 |
H41C |
C4 |
C5 |
H51C |
0.5 |
0.1 |
C4 |
C5 |
H51C |
C6 |
180.0 |
179.8 |
H51C |
C5 |
C4 |
H41C |
0.5 |
0.1 |
H51C |
C5 |
C6 |
H6 |
326.0 |
304.9 |