PDB Chemical Component 2OM
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 2OM
Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
P |
O5' |
1.614 |
1.610 |
O5' |
C5' |
1.428 |
1.429 |
C5' |
C4' |
1.527 |
1.530 |
C5' |
H5' |
1.101 |
1.090 |
C5' |
H5'A |
1.100 |
1.090 |
C3' |
C4' |
1.532 |
1.541 |
C4' |
O4' |
1.475 |
1.438 |
C4' |
H4' |
1.100 |
1.090 |
O4' |
C1' |
1.467 |
1.443 |
O3' |
C3' |
1.436 |
1.428 |
C3' |
C2' |
1.521 |
1.548 |
C3' |
H3' |
1.100 |
1.090 |
O3' |
HO3' |
0.950 |
0.967 |
C2' |
O2' |
1.424 |
1.429 |
C2' |
C1' |
1.531 |
1.550 |
C2' |
H2' |
1.100 |
1.089 |
O2' |
HO2' |
0.950 |
0.967 |
C1' |
N1 |
1.501 |
1.465 |
C1' |
H1' |
1.100 |
1.090 |
N1 |
C2 |
1.387 |
1.343 |
N1 |
C6 |
1.497 |
1.464 |
O2 |
C2 |
1.224 |
1.215 |
C2 |
N3 |
1.354 |
1.344 |
N3 |
C4 |
1.351 |
1.345 |
N3 |
HN3 |
1.000 |
0.970 |
C5 |
C4 |
1.513 |
1.508 |
C4 |
O4 |
1.208 |
1.213 |
C6 |
C5 |
1.553 |
1.527 |
C5 |
H5 |
1.100 |
1.091 |
C5 |
H5A |
1.100 |
1.089 |
C6 |
C7 |
1.502 |
1.508 |
C6 |
H6 |
1.100 |
1.090 |
OP1 |
P |
1.488 |
1.480 |
OP3 |
P |
1.614 |
1.611 |
P |
OP2 |
1.621 |
1.610 |
OP2 |
HOP2 |
0.950 |
0.967 |
OP3 |
HOP3 |
0.950 |
0.968 |
O71 |
C7 |
1.208 |
1.207 |
C7 |
O72 |
1.342 |
1.342 |
O72 |
HO72 |
0.950 |
0.966 |
Bond Angles for 2OM
Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
O5' |
C5' |
C4' |
110.5 |
109.5 |
O5' |
C5' |
H5' |
109.1 |
109.5 |
O5' |
C5' |
H5'A |
108.9 |
109.5 |
C4' |
C5' |
H5' |
109.1 |
109.5 |
C4' |
C5' |
H5'A |
108.9 |
109.5 |
C5' |
C4' |
O4' |
110.8 |
109.9 |
C5' |
C4' |
H4' |
106.7 |
109.9 |
H5' |
C5' |
H5'A |
110.3 |
109.5 |
C3' |
C4' |
H4' |
110.8 |
110.0 |
O4' |
C4' |
H4' |
111.0 |
109.9 |
C4' |
O4' |
C1' |
108.2 |
107.0 |
O4' |
C1' |
C2' |
104.7 |
103.5 |
O4' |
C1' |
N1 |
111.3 |
110.6 |
O4' |
C1' |
H1' |
112.3 |
110.6 |
O3' |
C3' |
C2' |
113.1 |
110.5 |
O3' |
C3' |
H3' |
104.7 |
110.6 |
C2' |
C3' |
H3' |
111.7 |
110.5 |
C3' |
C2' |
O2' |
111.2 |
110.9 |
C3' |
C2' |
C1' |
102.1 |
102.1 |
C3' |
C2' |
H2' |
114.8 |
110.9 |
O2' |
C2' |
C1' |
114.0 |
110.9 |
O2' |
C2' |
H2' |
103.1 |
110.8 |
C2' |
O2' |
HO2' |
109.5 |
114.0 |
C1' |
C2' |
H2' |
112.1 |
110.9 |
C2' |
C1' |
N1 |
112.1 |
110.6 |
C2' |
C1' |
H1' |
111.5 |
110.6 |
N1 |
C1' |
H1' |
105.0 |
110.7 |
C1' |
N1 |
C2 |
121.5 |
119.6 |
C1' |
N1 |
C6 |
117.3 |
119.5 |
C2 |
N1 |
C6 |
121.2 |
120.9 |
N1 |
C2 |
N3 |
121.6 |
121.6 |
N1 |
C6 |
C5 |
114.0 |
109.7 |
N1 |
C6 |
C7 |
111.6 |
109.5 |
N1 |
C6 |
H6 |
104.5 |
109.5 |
C2 |
N3 |
C4 |
122.3 |
121.0 |
C2 |
N3 |
HN3 |
118.9 |
119.5 |
C4 |
N3 |
HN3 |
118.8 |
119.6 |
N3 |
C4 |
O4 |
119.7 |
120.0 |
C5 |
C4 |
O4 |
119.4 |
120.0 |
C6 |
C5 |
H5 |
108.7 |
109.6 |
C6 |
C5 |
H5A |
108.1 |
109.4 |
H5 |
C5 |
H5A |
111.4 |
109.5 |
C7 |
C6 |
H6 |
110.4 |
109.4 |
C6 |
C7 |
O72 |
119.6 |
120.0 |
P |
OP2 |
HOP2 |
109.5 |
114.0 |
O71 |
C7 |
O72 |
119.4 |
120.0 |
C7 |
O72 |
HO72 |
109.5 |
117.0 |
Torsion Angles for 2OM
Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
P |
O5' |
C5' |
H5' |
278.4 |
300.1 |
P |
O5' |
C5' |
H5'A |
38.8 |
60.0 |
C4' |
C5' |
O5' |
H5' |
240.0 |
239.9 |
C4' |
C5' |
O5' |
H5'A |
119.6 |
120.0 |
O5' |
C5' |
C4' |
O4' |
81.8 |
66.5 |
O5' |
C5' |
C4' |
H4' |
320.9 |
305.4 |
H5' |
C5' |
O5' |
H5'A |
239.6 |
240.0 |
O5' |
C5' |
C4' |
H5' |
120.0 |
120.0 |
O5' |
C5' |
C4' |
H5'A |
240.4 |
240.0 |
H5' |
C5' |
C4' |
H5'A |
120.4 |
120.0 |
C3' |
C4' |
C5' |
H4' |
239.2 |
238.8 |
O4' |
C4' |
C5' |
H4' |
121.0 |
121.0 |
C5' |
C4' |
O4' |
C1' |
119.7 |
145.9 |
O5' |
C5' |
H5' |
C4' |
239.2 |
240.0 |
O5' |
C5' |
H5' |
H5'A |
119.6 |
120.0 |
C4' |
C5' |
H5' |
H5'A |
240.4 |
240.0 |
H5' |
C5' |
C4' |
O4' |
321.8 |
306.5 |
H5' |
C5' |
C4' |
H4' |
200.9 |
185.4 |
O5' |
C5' |
H5'A |
C4' |
120.6 |
120.0 |
O5' |
C5' |
H5'A |
H5' |
240.3 |
240.0 |
C4' |
C5' |
H5'A |
H5' |
119.7 |
120.1 |
H5'A |
C5' |
C4' |
O4' |
201.4 |
186.5 |
H5'A |
C5' |
C4' |
H4' |
80.5 |
65.4 |
C3' |
C4' |
C5' |
H5' |
80.0 |
64.3 |
C3' |
C4' |
C5' |
H5'A |
319.6 |
304.3 |
C5' |
C4' |
C3' |
H4' |
118.4 |
121.1 |
O4' |
C4' |
C3' |
H4' |
239.1 |
240.5 |
C3' |
C4' |
O4' |
C1' |
358.9 |
26.5 |
O4' |
C4' |
C5' |
H5' |
321.8 |
306.5 |
O4' |
C4' |
C5' |
H5'A |
201.4 |
186.5 |
C5' |
C4' |
O4' |
H4' |
241.6 |
239.0 |
C3' |
C4' |
O4' |
H4' |
120.8 |
119.6 |
C4' |
O4' |
C1' |
C2' |
337.3 |
319.9 |
C4' |
O4' |
C1' |
N1 |
215.9 |
201.4 |
C4' |
O4' |
C1' |
H1' |
98.5 |
78.4 |
H4' |
C4' |
C5' |
H5' |
200.9 |
185.4 |
H4' |
C4' |
C5' |
H5'A |
80.5 |
65.4 |
C5' |
C4' |
H4' |
O4' |
120.8 |
121.0 |
H4' |
C4' |
O4' |
C1' |
238.1 |
267.0 |
C1' |
O4' |
C4' |
H4' |
238.1 |
267.0 |
C3' |
C2' |
C1' |
O4' |
37.5 |
37.1 |
O2' |
C2' |
C1' |
O4' |
157.6 |
155.2 |
O4' |
C1' |
C2' |
H2' |
274.2 |
278.9 |
C2' |
C1' |
O4' |
N1 |
121.3 |
118.5 |
C2' |
C1' |
O4' |
H1' |
238.8 |
241.5 |
N1 |
C1' |
O4' |
H1' |
117.5 |
123.0 |
O4' |
C1' |
N1 |
C2 |
43.5 |
53.5 |
O4' |
C1' |
N1 |
C6 |
224.1 |
233.3 |
O3' |
C3' |
C4' |
H4' |
24.6 |
358.8 |
C2' |
C3' |
O3' |
H3' |
121.8 |
122.6 |
O3' |
C3' |
C2' |
O2' |
319.4 |
339.6 |
O3' |
C3' |
C2' |
C1' |
81.4 |
97.8 |
O3' |
C3' |
C2' |
H2' |
202.9 |
216.0 |
C2' |
C3' |
C4' |
H4' |
145.4 |
117.5 |
O4' |
C1' |
C2' |
C3' |
37.5 |
37.1 |
O3' |
C3' |
C2' |
H3' |
242.2 |
237.3 |
O2' |
C2' |
C3' |
C1' |
238.0 |
241.8 |
O2' |
C2' |
C3' |
H2' |
116.5 |
123.6 |
C3' |
C2' |
O2' |
HO2' |
338.1 |
298.5 |
C1' |
C2' |
C3' |
H2' |
238.5 |
241.8 |
C3' |
C2' |
C1' |
N1 |
158.4 |
155.5 |
C3' |
C2' |
C1' |
H1' |
275.8 |
278.5 |
H3' |
C3' |
C4' |
H4' |
266.9 |
236.1 |
O3' |
C3' |
H3' |
C2' |
122.8 |
122.6 |
H3' |
C3' |
C2' |
O2' |
77.2 |
102.3 |
H3' |
C3' |
C2' |
C1' |
199.2 |
220.5 |
H3' |
C3' |
C2' |
H2' |
320.7 |
338.7 |
HO3' |
O3' |
C3' |
C2' |
162.8 |
65.2 |
HO3' |
O3' |
C3' |
H3' |
40.9 |
302.6 |
O4' |
C1' |
C2' |
O2' |
157.6 |
155.2 |
O2' |
C2' |
C3' |
H3' |
77.2 |
102.3 |
C3' |
C2' |
O2' |
C1' |
114.7 |
112.7 |
C3' |
C2' |
O2' |
H2' |
236.5 |
236.3 |
C1' |
C2' |
O2' |
H2' |
121.7 |
123.7 |
O2' |
C2' |
C1' |
N1 |
278.4 |
273.7 |
O2' |
C2' |
C1' |
H1' |
35.8 |
36.7 |
O4' |
C1' |
C2' |
N1 |
239.2 |
241.5 |
O4' |
C1' |
C2' |
H1' |
121.7 |
118.6 |
C1' |
C2' |
C3' |
H3' |
199.2 |
220.5 |
C3' |
C2' |
C1' |
O2' |
240.0 |
241.8 |
C3' |
C2' |
C1' |
H2' |
123.4 |
118.2 |
O2' |
C2' |
C1' |
H2' |
243.4 |
236.4 |
C1' |
C2' |
O2' |
HO2' |
223.3 |
185.8 |
N1 |
C1' |
C2' |
H1' |
242.6 |
237.0 |
C2' |
C1' |
N1 |
C2 |
286.6 |
299.4 |
C2' |
C1' |
N1 |
C6 |
107.1 |
119.2 |
H2' |
C2' |
C3' |
H3' |
320.7 |
338.7 |
C3' |
C2' |
H2' |
O2' |
121.1 |
123.6 |
C3' |
C2' |
H2' |
C1' |
244.2 |
247.3 |
O2' |
C2' |
H2' |
C1' |
123.0 |
123.7 |
H2' |
C2' |
O2' |
HO2' |
101.6 |
62.1 |
H2' |
C2' |
C1' |
N1 |
35.0 |
37.3 |
H2' |
C2' |
C1' |
H1' |
152.4 |
160.3 |
HO2' |
O2' |
C2' |
C1' |
223.3 |
185.8 |
HO2' |
O2' |
C2' |
H2' |
101.6 |
62.1 |
O4' |
C1' |
N1 |
C2' |
117.0 |
114.1 |
O4' |
C1' |
N1 |
H1' |
238.2 |
237.0 |
N1 |
C1' |
C2' |
H2' |
35.0 |
37.3 |
C2' |
C1' |
N1 |
H1' |
121.3 |
123.0 |
C2 |
N1 |
C1' |
C6 |
179.5 |
180.2 |
C1' |
N1 |
C2 |
N3 |
171.5 |
174.3 |
C1' |
N1 |
C6 |
C5 |
198.9 |
215.7 |
C1' |
N1 |
C6 |
C7 |
75.6 |
95.8 |
C1' |
N1 |
C6 |
H6 |
316.3 |
335.9 |
O4' |
C1' |
H1' |
C2' |
242.8 |
245.9 |
O4' |
C1' |
H1' |
N1 |
121.2 |
122.9 |
H1' |
C1' |
C2' |
H2' |
152.4 |
160.3 |
C2' |
C1' |
H1' |
N1 |
238.4 |
237.1 |
H1' |
C1' |
N1 |
C2 |
165.3 |
176.5 |
H1' |
C1' |
N1 |
C6 |
345.8 |
356.2 |
C2 |
N1 |
C1' |
H1' |
165.3 |
176.5 |
C1' |
N1 |
C2 |
C6 |
180.5 |
179.7 |
C2 |
N1 |
C6 |
C5 |
19.4 |
35.5 |
C2 |
N1 |
C6 |
C7 |
256.1 |
275.6 |
C2 |
N1 |
C6 |
H6 |
136.8 |
155.6 |
N1 |
C2 |
N3 |
C4 |
9.5 |
348.0 |
N1 |
C2 |
N3 |
HN3 |
189.4 |
168.0 |
C6 |
N1 |
C1' |
H1' |
345.8 |
356.2 |
C1' |
N1 |
C6 |
C2 |
179.5 |
180.3 |
C6 |
N1 |
C2 |
N3 |
350.9 |
354.5 |
N1 |
C6 |
C5 |
H5 |
211.8 |
193.6 |
N1 |
C6 |
C5 |
H5A |
90.8 |
73.6 |
C7 |
C6 |
N1 |
H6 |
119.3 |
120.0 |
N1 |
C6 |
C7 |
O72 |
203.5 |
180.0 |
O2 |
C2 |
N3 |
HN3 |
9.6 |
347.9 |
N3 |
C2 |
N1 |
C6 |
350.9 |
354.5 |
C4 |
N3 |
C2 |
HN3 |
180.0 |
180.0 |
C2 |
N3 |
C4 |
O4 |
158.9 |
175.5 |
C2 |
N3 |
C4 |
HN3 |
180.0 |
180.0 |
C5 |
C4 |
N3 |
O4 |
179.6 |
180.1 |
C2 |
N3 |
HN3 |
C4 |
180.0 |
180.0 |
HN3 |
N3 |
C4 |
O4 |
338.9 |
355.5 |
N1 |
C6 |
C5 |
C4 |
331.8 |
313.6 |
C5 |
C4 |
N3 |
HN3 |
158.5 |
175.6 |
N3 |
C4 |
C5 |
O4 |
180.4 |
179.9 |
O4 |
C4 |
N3 |
HN3 |
338.9 |
355.5 |
N1 |
C6 |
C5 |
C7 |
235.0 |
240.0 |
N1 |
C6 |
C5 |
H6 |
115.5 |
120.2 |
C6 |
C5 |
C4 |
O4 |
210.2 |
214.1 |
H5 |
C5 |
C6 |
H5A |
121.0 |
120.1 |
H5 |
C5 |
C4 |
O4 |
330.2 |
334.2 |
C6 |
C5 |
H5 |
H5A |
241.0 |
240.0 |
H5A |
C5 |
C4 |
O4 |
91.2 |
94.3 |
C6 |
C5 |
H5A |
H5 |
119.3 |
120.1 |
N1 |
C6 |
C7 |
C5 |
126.4 |
120.1 |
N1 |
C6 |
C7 |
H6 |
244.3 |
240.0 |
C7 |
C6 |
C5 |
H5 |
336.8 |
313.6 |
C7 |
C6 |
C5 |
H5A |
215.7 |
193.6 |
O71 |
C7 |
C6 |
O72 |
179.8 |
180.0 |
C6 |
C7 |
O72 |
HO72 |
179.8 |
180.0 |
N1 |
C6 |
H6 |
C5 |
238.4 |
239.7 |
N1 |
C6 |
H6 |
C7 |
120.1 |
120.0 |
H6 |
C6 |
C5 |
H5 |
96.3 |
73.5 |
H6 |
C6 |
C5 |
H5A |
335.3 |
313.4 |
H6 |
C6 |
C7 |
O72 |
319.2 |
300.0 |
OP1 |
P |
OP2 |
HOP2 |
160.9 |
180.0 |
OP3 |
P |
OP2 |
HOP2 |
280.2 |
300.0 |
O71 |
C7 |
C6 |
H6 |
138.9 |
120.0 |
C6 |
C7 |
O71 |
O72 |
180.2 |
180.0 |
O71 |
C7 |
O72 |
HO72 |
0.0 |
0.0 |
O72 |
C7 |
C6 |
H6 |
319.2 |
300.0 |