PDB Chemical Component 3DR
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 3DR
Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
O5' |
P |
1.606 |
1.610 |
O5' |
C5' |
1.446 |
1.428 |
P |
OP1 |
1.499 |
1.480 |
P |
OP2 |
1.517 |
1.610 |
P |
OP3 |
1.528 |
1.609 |
OP2 |
HOP2 |
0.951 |
0.968 |
OP3 |
HOP3 |
0.951 |
0.967 |
C2' |
C1' |
1.530 |
1.544 |
C2' |
C3' |
1.508 |
1.545 |
C2' |
H2' |
1.114 |
1.090 |
C2' |
H2'' |
1.115 |
1.089 |
C5' |
C4' |
1.502 |
1.530 |
C5' |
H5' |
1.115 |
1.090 |
C5' |
H5'' |
1.115 |
1.090 |
C4' |
O4' |
1.449 |
1.447 |
C4' |
C3' |
1.523 |
1.544 |
C4' |
H4'1 |
1.115 |
1.089 |
O4' |
C1' |
1.415 |
1.445 |
C1' |
H1'1 |
1.115 |
1.090 |
C1' |
H1'2 |
1.115 |
1.089 |
C3' |
O3' |
1.415 |
1.429 |
C3' |
H3' |
1.115 |
1.090 |
O3' |
HO3' |
0.950 |
0.966 |
Bond Angles for 3DR
Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
P |
O5' |
C5' |
118.0 |
106.8 |
O5' |
P |
OP1 |
107.6 |
109.5 |
O5' |
P |
OP2 |
105.0 |
109.5 |
O5' |
P |
OP3 |
104.0 |
109.5 |
O5' |
C5' |
C4' |
109.3 |
109.5 |
O5' |
C5' |
H5' |
112.2 |
109.5 |
O5' |
C5' |
H5'' |
112.2 |
109.5 |
OP1 |
P |
OP2 |
114.2 |
109.4 |
OP1 |
P |
OP3 |
113.1 |
109.5 |
OP2 |
P |
OP3 |
111.9 |
109.5 |
P |
OP2 |
HOP2 |
105.0 |
106.8 |
P |
OP3 |
HOP3 |
104.1 |
106.8 |
C1' |
C2' |
C3' |
101.5 |
104.1 |
C1' |
C2' |
H2' |
115.2 |
110.5 |
C1' |
C2' |
H2'' |
115.2 |
110.5 |
C2' |
C1' |
O4' |
107.4 |
104.8 |
C2' |
C1' |
H1'1 |
113.0 |
110.4 |
C2' |
C1' |
H1'2 |
113.0 |
110.4 |
C3' |
C2' |
H2' |
115.3 |
110.4 |
C3' |
C2' |
H2'' |
115.2 |
110.6 |
C2' |
C3' |
C4' |
102.7 |
104.2 |
C2' |
C3' |
O3' |
111.6 |
110.5 |
C2' |
C3' |
H3' |
113.2 |
110.5 |
H2' |
C2' |
H2'' |
95.2 |
110.5 |
C4' |
C5' |
H5' |
112.3 |
109.4 |
C4' |
C5' |
H5'' |
112.3 |
109.5 |
C5' |
C4' |
O4' |
109.6 |
110.3 |
C5' |
C4' |
C3' |
117.6 |
110.7 |
C5' |
C4' |
H4'1 |
101.6 |
110.4 |
H5' |
C5' |
H5'' |
98.2 |
109.5 |
O4' |
C4' |
C3' |
102.0 |
104.7 |
O4' |
C4' |
H4'1 |
117.4 |
110.3 |
C4' |
O4' |
C1' |
109.7 |
105.3 |
C3' |
C4' |
H4'1 |
109.4 |
110.3 |
C4' |
C3' |
O3' |
111.5 |
110.5 |
C4' |
C3' |
H3' |
113.3 |
110.5 |
O4' |
C1' |
H1'1 |
113.0 |
110.3 |
O4' |
C1' |
H1'2 |
113.0 |
110.4 |
H1'1 |
C1' |
H1'2 |
97.4 |
110.4 |
O3' |
C3' |
H3' |
104.7 |
110.5 |
C3' |
O3' |
HO3' |
111.6 |
106.8 |
Torsion Angles for 3DR
Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
P |
O5' |
C5' |
C4' |
168.6 |
180.0 |
P |
O5' |
C5' |
H5' |
293.8 |
60.0 |
P |
O5' |
C5' |
H5'' |
43.3 |
300.0 |
OP1 |
P |
O5' |
OP2 |
237.9 |
240.0 |
OP1 |
P |
O5' |
OP3 |
120.2 |
120.0 |
OP2 |
P |
O5' |
OP3 |
242.3 |
239.9 |
O5' |
P |
OP2 |
HOP2 |
179.9 |
180.0 |
O5' |
P |
OP3 |
HOP3 |
180.0 |
299.9 |
C5' |
O5' |
P |
OP1 |
307.3 |
60.0 |
C5' |
O5' |
P |
OP2 |
69.3 |
180.0 |
C5' |
O5' |
P |
OP3 |
187.0 |
300.0 |
C4' |
C5' |
O5' |
H5' |
234.7 |
120.0 |
C4' |
C5' |
O5' |
H5'' |
125.3 |
240.0 |
O5' |
C5' |
C4' |
O4' |
60.2 |
61.5 |
O5' |
C5' |
C4' |
C3' |
176.0 |
176.8 |
O5' |
C5' |
C4' |
H4'1 |
295.3 |
299.3 |
H5' |
C5' |
O5' |
H5'' |
250.6 |
120.0 |
OP1 |
P |
O5' |
C5' |
307.3 |
60.0 |
O5' |
P |
OP1 |
OP2 |
116.2 |
120.0 |
O5' |
P |
OP1 |
OP3 |
245.7 |
240.0 |
OP2 |
P |
OP1 |
OP3 |
129.5 |
120.0 |
OP1 |
P |
OP2 |
HOP2 |
297.6 |
299.9 |
OP1 |
P |
OP3 |
HOP3 |
63.5 |
180.0 |
OP2 |
P |
O5' |
C5' |
69.3 |
180.0 |
O5' |
P |
OP2 |
OP1 |
242.3 |
240.0 |
O5' |
P |
OP2 |
OP3 |
112.2 |
120.0 |
OP1 |
P |
OP2 |
OP3 |
229.9 |
240.0 |
OP2 |
P |
OP3 |
HOP3 |
292.9 |
60.0 |
OP3 |
P |
O5' |
C5' |
187.0 |
300.0 |
O5' |
P |
OP3 |
OP1 |
116.5 |
120.0 |
O5' |
P |
OP3 |
OP2 |
247.1 |
240.0 |
OP1 |
P |
OP3 |
OP2 |
130.6 |
120.0 |
OP3 |
P |
OP2 |
HOP2 |
67.7 |
59.9 |
HOP2 |
OP2 |
P |
OP3 |
67.7 |
59.9 |
C3' |
C2' |
C1' |
H2' |
234.7 |
118.6 |
C3' |
C2' |
C1' |
H2'' |
125.2 |
241.3 |
C1' |
C2' |
C3' |
C4' |
323.6 |
360.0 |
C1' |
C2' |
C3' |
O3' |
83.2 |
118.7 |
C1' |
C2' |
C3' |
H3' |
201.1 |
241.3 |
H2' |
C2' |
C1' |
H2'' |
250.5 |
122.7 |
C4' |
O4' |
C1' |
C2' |
5.9 |
319.6 |
O4' |
C1' |
C2' |
H1'1 |
234.7 |
241.2 |
O4' |
C1' |
C2' |
H1'2 |
125.3 |
118.9 |
H1'1 |
C1' |
C2' |
H1'2 |
250.5 |
237.7 |
C1' |
C2' |
C3' |
H2' |
125.3 |
241.4 |
C1' |
C2' |
C3' |
H2'' |
234.8 |
118.7 |
C3' |
C2' |
C1' |
O4' |
19.7 |
24.0 |
C3' |
C2' |
C1' |
H1'1 |
145.0 |
142.8 |
C3' |
C2' |
C1' |
H1'2 |
254.5 |
265.1 |
H2' |
C2' |
C3' |
H2'' |
109.5 |
237.3 |
C5' |
C4' |
C3' |
C2' |
280.5 |
217.3 |
O4' |
C4' |
C3' |
C2' |
40.4 |
336.1 |
C2' |
C3' |
C4' |
H4'1 |
165.4 |
94.8 |
C4' |
C3' |
C2' |
O3' |
240.4 |
241.3 |
C4' |
C3' |
C2' |
H3' |
122.5 |
118.7 |
O3' |
C3' |
C2' |
H3' |
242.1 |
237.4 |
C2' |
C3' |
O3' |
HO3' |
180.1 |
63.3 |
C1' |
C2' |
H2' |
C3' |
242.2 |
114.6 |
C1' |
C2' |
H2' |
H2'' |
121.1 |
237.3 |
H2' |
C2' |
C1' |
O4' |
145.0 |
265.4 |
H2' |
C2' |
C1' |
H1'1 |
270.3 |
24.2 |
H2' |
C2' |
C1' |
H1'2 |
19.7 |
146.5 |
C3' |
C2' |
H2' |
H2'' |
238.9 |
122.7 |
H2' |
C2' |
C3' |
C4' |
198.3 |
118.6 |
H2' |
C2' |
C3' |
O3' |
317.9 |
237.3 |
H2' |
C2' |
C3' |
H3' |
75.8 |
359.9 |
C1' |
C2' |
H2'' |
C3' |
117.8 |
245.3 |
C1' |
C2' |
H2'' |
H2' |
238.9 |
122.7 |
H2'' |
C2' |
C1' |
O4' |
254.5 |
142.7 |
H2'' |
C2' |
C1' |
H1'1 |
19.8 |
261.5 |
H2'' |
C2' |
C1' |
H1'2 |
129.2 |
23.8 |
C3' |
C2' |
H2'' |
H2' |
121.1 |
237.4 |
H2'' |
C2' |
C3' |
C4' |
88.8 |
241.3 |
H2'' |
C2' |
C3' |
O3' |
208.4 |
360.0 |
H2'' |
C2' |
C3' |
H3' |
326.3 |
122.5 |
O5' |
C5' |
C4' |
H5' |
125.2 |
239.9 |
O5' |
C5' |
C4' |
H5'' |
234.7 |
120.0 |
C2' |
C3' |
C4' |
C5' |
280.5 |
217.3 |
H5' |
C5' |
C4' |
H5'' |
109.5 |
240.1 |
O4' |
C4' |
C5' |
C3' |
244.2 |
244.6 |
O4' |
C4' |
C5' |
H4'1 |
124.9 |
122.2 |
C5' |
C4' |
O4' |
C1' |
96.6 |
159.5 |
C3' |
C4' |
C5' |
H4'1 |
240.7 |
237.5 |
C5' |
C4' |
C3' |
O3' |
160.8 |
98.6 |
C5' |
C4' |
C3' |
H3' |
43.0 |
336.0 |
O5' |
C5' |
H5' |
C4' |
236.4 |
120.0 |
O5' |
C5' |
H5' |
H5'' |
118.1 |
240.0 |
C4' |
C5' |
H5' |
H5'' |
241.8 |
119.9 |
H5' |
C5' |
C4' |
O4' |
295.0 |
181.5 |
H5' |
C5' |
C4' |
C3' |
50.8 |
296.9 |
H5' |
C5' |
C4' |
H4'1 |
170.1 |
59.4 |
O5' |
C5' |
H5'' |
C4' |
123.7 |
240.0 |
O5' |
C5' |
H5'' |
H5' |
241.9 |
120.1 |
C4' |
C5' |
H5'' |
H5' |
118.2 |
240.1 |
H5'' |
C5' |
C4' |
O4' |
185.5 |
301.5 |
H5'' |
C5' |
C4' |
C3' |
301.3 |
56.8 |
H5'' |
C5' |
C4' |
H4'1 |
60.6 |
179.3 |
C2' |
C1' |
O4' |
C4' |
5.9 |
319.6 |
C2' |
C3' |
C4' |
O4' |
40.4 |
336.1 |
O4' |
C4' |
C5' |
H5' |
295.0 |
181.5 |
O4' |
C4' |
C5' |
H5'' |
185.5 |
301.5 |
C5' |
C4' |
O4' |
C3' |
125.4 |
119.1 |
C5' |
C4' |
O4' |
H4'1 |
244.8 |
237.8 |
C3' |
C4' |
O4' |
H4'1 |
119.4 |
118.7 |
O4' |
C4' |
C3' |
O3' |
280.7 |
217.4 |
O4' |
C4' |
C3' |
H3' |
162.9 |
94.9 |
C4' |
O4' |
C1' |
H1'1 |
240.6 |
200.7 |
C4' |
O4' |
C1' |
H1'2 |
131.2 |
78.4 |
C4' |
C3' |
C2' |
H2' |
198.3 |
118.6 |
C4' |
C3' |
C2' |
H2'' |
88.8 |
241.3 |
C2' |
C3' |
C4' |
O3' |
119.7 |
118.7 |
C2' |
C3' |
C4' |
H3' |
237.5 |
241.3 |
C3' |
C4' |
C5' |
H5' |
50.8 |
296.9 |
C3' |
C4' |
C5' |
H5'' |
301.3 |
56.8 |
C5' |
C4' |
C3' |
O4' |
240.1 |
241.1 |
C5' |
C4' |
C3' |
H4'1 |
115.2 |
122.5 |
O4' |
C4' |
C3' |
H4'1 |
235.1 |
241.3 |
C3' |
C4' |
O4' |
C1' |
331.2 |
40.4 |
O3' |
C3' |
C4' |
H3' |
117.9 |
122.6 |
C4' |
C3' |
O3' |
HO3' |
294.3 |
178.1 |
H4'1 |
C4' |
C5' |
H5' |
170.1 |
59.4 |
H4'1 |
C4' |
C5' |
H5'' |
60.6 |
179.3 |
C5' |
C4' |
H4'1 |
O4' |
119.5 |
122.2 |
C5' |
C4' |
H4'1 |
C3' |
235.0 |
237.3 |
O4' |
C4' |
H4'1 |
C3' |
115.4 |
115.2 |
H4'1 |
C4' |
O4' |
C1' |
211.8 |
281.7 |
H4'1 |
C4' |
C3' |
O3' |
45.7 |
336.1 |
H4'1 |
C4' |
C3' |
H3' |
287.8 |
213.5 |
O4' |
C1' |
C2' |
C3' |
19.7 |
24.0 |
O4' |
C1' |
C2' |
H2' |
145.0 |
265.4 |
O4' |
C1' |
C2' |
H2'' |
254.5 |
142.7 |
C2' |
C1' |
O4' |
H1'1 |
125.3 |
118.9 |
C2' |
C1' |
O4' |
H1'2 |
234.7 |
241.2 |
C1' |
O4' |
C4' |
C3' |
331.2 |
40.4 |
C1' |
O4' |
C4' |
H4'1 |
211.8 |
281.7 |
H1'1 |
C1' |
O4' |
H1'2 |
109.4 |
122.3 |
H1'1 |
C1' |
C2' |
C3' |
145.0 |
142.8 |
H1'1 |
C1' |
C2' |
H2' |
270.3 |
24.2 |
H1'1 |
C1' |
C2' |
H2'' |
19.8 |
261.5 |
C2' |
C1' |
H1'1 |
O4' |
237.8 |
244.6 |
C2' |
C1' |
H1'1 |
H1'2 |
118.9 |
122.3 |
O4' |
C1' |
H1'1 |
H1'2 |
241.1 |
237.7 |
H1'2 |
C1' |
C2' |
C3' |
254.5 |
265.1 |
H1'2 |
C1' |
C2' |
H2' |
19.7 |
146.5 |
H1'2 |
C1' |
C2' |
H2'' |
129.2 |
23.8 |
C2' |
C1' |
H1'2 |
O4' |
122.2 |
115.4 |
C2' |
C1' |
H1'2 |
H1'1 |
241.1 |
237.6 |
O4' |
C1' |
H1'2 |
H1'1 |
118.9 |
122.2 |
O3' |
C3' |
C2' |
H2' |
317.9 |
237.3 |
O3' |
C3' |
C2' |
H2'' |
208.4 |
360.0 |
C2' |
C3' |
O3' |
C4' |
245.8 |
245.2 |
C2' |
C3' |
O3' |
H3' |
122.9 |
122.6 |
O3' |
C3' |
C4' |
H4'1 |
45.7 |
336.1 |
C4' |
C3' |
O3' |
H3' |
237.1 |
237.4 |
H3' |
C3' |
C2' |
H2' |
75.8 |
359.9 |
H3' |
C3' |
C2' |
H2'' |
326.3 |
122.5 |
C2' |
C3' |
H3' |
C4' |
116.4 |
114.8 |
C2' |
C3' |
H3' |
O3' |
238.2 |
237.4 |
H3' |
C3' |
C4' |
H4'1 |
287.8 |
213.5 |
C4' |
C3' |
H3' |
O3' |
121.7 |
122.6 |
H3' |
C3' |
O3' |
HO3' |
57.2 |
300.7 |
HO3' |
O3' |
C3' |
H3' |
57.2 |
300.7 |