PDB Chemical Component 5SE
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 5SE
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| P |
O5' |
1.573 |
1.610 |
| N1 |
C1' |
1.429 |
1.465 |
| N1 |
C2 |
1.387 |
1.346 |
| C2 |
O2 |
1.222 |
1.220 |
| N3 |
C2 |
1.350 |
1.331 |
| C4 |
N3 |
1.304 |
1.327 |
| N4 |
C4 |
1.323 |
1.375 |
| N4 |
HN4 |
1.000 |
0.969 |
| N4 |
HN4A |
1.000 |
0.971 |
| C5 |
C4 |
1.423 |
1.409 |
| C5 |
C6 |
1.332 |
1.354 |
| C6 |
N1 |
1.339 |
1.362 |
| C6 |
H6 |
1.081 |
1.080 |
| C1' |
H1' |
1.100 |
1.090 |
| OP3 |
P |
1.468 |
1.611 |
| OP3 |
HOP3 |
0.950 |
0.967 |
| C2' |
C1' |
1.502 |
1.541 |
| C2' |
H2' |
1.100 |
1.090 |
| C2' |
H2'A |
1.100 |
1.090 |
| OP2 |
P |
1.452 |
1.609 |
| OP2 |
HOP2 |
0.950 |
0.968 |
| C3' |
C2' |
1.503 |
1.548 |
| C3' |
C4' |
1.511 |
1.550 |
| C3' |
H3' |
1.100 |
1.090 |
| O3' |
C3' |
1.417 |
1.429 |
| O3' |
HO3' |
0.950 |
0.967 |
| C4' |
O4' |
1.438 |
1.446 |
| C4' |
H4' |
1.100 |
1.089 |
| O4' |
C1' |
1.411 |
1.437 |
| C5' |
C4' |
1.519 |
1.531 |
| C5' |
H5' |
1.100 |
1.089 |
| C5' |
H5'A |
1.100 |
1.090 |
| O5' |
C5' |
1.385 |
1.429 |
| CA5 |
SE5 |
1.973 |
1.960 |
| CA5 |
HA5 |
1.100 |
1.090 |
| CA5 |
HA5A |
1.100 |
1.089 |
| CA5 |
HA5B |
1.100 |
1.090 |
| SE5 |
C5 |
1.919 |
1.960 |
| P |
OP1 |
1.720 |
1.480 |
Bond Angles for 5SE
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| OP3 |
P |
O5' |
105.6 |
109.5 |
| OP2 |
P |
O5' |
109.7 |
109.5 |
| P |
O5' |
C5' |
121.4 |
123.0 |
| O5' |
P |
OP1 |
159.7 |
109.5 |
| C2 |
N1 |
C1' |
118.3 |
119.8 |
| C6 |
N1 |
C1' |
121.2 |
119.9 |
| N1 |
C1' |
H1' |
107.4 |
109.8 |
| N1 |
C2 |
O2 |
117.9 |
119.4 |
| HN4 |
N4 |
HN4A |
120.0 |
120.0 |
| C5 |
C6 |
H6 |
120.9 |
120.4 |
| C2' |
C1' |
H1' |
103.0 |
109.8 |
| O4' |
C1' |
H1' |
115.8 |
109.9 |
| OP3 |
P |
OP1 |
85.9 |
109.4 |
| H2' |
C2' |
H2'A |
104.0 |
110.4 |
| C3' |
C2' |
H2' |
114.5 |
110.5 |
| C3' |
C2' |
H2'A |
114.5 |
110.6 |
| OP2 |
P |
OP1 |
76.2 |
109.5 |
| C4' |
C3' |
H3' |
112.1 |
110.9 |
| O3' |
C3' |
C4' |
112.9 |
110.9 |
| C3' |
C4' |
O4' |
97.0 |
103.6 |
| C3' |
C4' |
H4' |
113.1 |
110.7 |
| O3' |
C3' |
H3' |
105.0 |
110.8 |
| O4' |
C4' |
H4' |
120.1 |
110.5 |
| C5' |
C4' |
H4' |
102.1 |
110.7 |
| H5' |
C5' |
H5'A |
107.6 |
109.5 |
| O5' |
C5' |
H5' |
111.3 |
109.5 |
| O5' |
C5' |
H5'A |
111.3 |
109.5 |
| SE5 |
CA5 |
HA5 |
109.5 |
109.5 |
| SE5 |
CA5 |
HA5A |
109.5 |
109.5 |
| SE5 |
CA5 |
HA5B |
109.4 |
109.5 |
| HA5 |
CA5 |
HA5A |
109.4 |
109.5 |
| HA5 |
CA5 |
HA5B |
109.5 |
109.5 |
| HA5A |
CA5 |
HA5B |
109.5 |
109.5 |
Torsion Angles for 5SE
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| OP3 |
P |
O5' |
OP1 |
122.7 |
120.0 |
| OP2 |
P |
O5' |
OP1 |
256.2 |
240.0 |
| P |
O5' |
C5' |
H5' |
60.6 |
60.0 |
| P |
O5' |
C5' |
H5'A |
300.6 |
300.0 |
| C1' |
N1 |
C2 |
O2 |
355.7 |
360.0 |
| C2' |
C1' |
N1 |
H1' |
115.2 |
120.9 |
| O4' |
C1' |
N1 |
H1' |
236.3 |
239.0 |
| C6 |
N1 |
C2 |
C1' |
184.4 |
180.3 |
| C2 |
N1 |
C1' |
H1' |
322.3 |
174.4 |
| O2 |
C2 |
N1 |
C1' |
355.7 |
360.0 |
| N3 |
C2 |
N1 |
C1' |
176.5 |
180.0 |
| C5 |
C6 |
N1 |
C1' |
183.9 |
179.7 |
| C2 |
N1 |
C6 |
C1' |
175.4 |
179.7 |
| C6 |
N1 |
C1' |
H1' |
137.8 |
354.0 |
| H6 |
C6 |
N1 |
C1' |
3.9 |
0.3 |
| OP2 |
P |
OP3 |
O5' |
233.9 |
240.0 |
| OP3 |
P |
O5' |
C5' |
36.4 |
65.0 |
| O5' |
P |
OP3 |
OP1 |
197.0 |
240.0 |
| OP2 |
P |
OP3 |
OP1 |
70.9 |
120.0 |
| HOP3 |
OP3 |
P |
O5' |
197.0 |
60.0 |
| HOP3 |
OP3 |
P |
OP1 |
0.0 |
180.0 |
| N1 |
C1' |
C2' |
H1' |
242.4 |
239.1 |
| O4' |
C1' |
C2' |
H1' |
123.5 |
119.5 |
| H2' |
C2' |
C1' |
H1' |
329.5 |
1.1 |
| C3' |
C2' |
H2' |
H2'A |
234.3 |
237.3 |
| H2'A |
C2' |
C1' |
H1' |
89.5 |
123.6 |
| C3' |
C2' |
H2'A |
H2' |
125.7 |
122.6 |
| OP3 |
P |
OP2 |
O5' |
124.3 |
120.0 |
| OP2 |
P |
O5' |
C5' |
169.9 |
185.0 |
| O5' |
P |
OP2 |
OP1 |
159.7 |
120.0 |
| OP3 |
P |
OP2 |
OP1 |
284.0 |
240.0 |
| HOP2 |
OP2 |
P |
O5' |
159.7 |
180.0 |
| HOP2 |
OP2 |
P |
OP1 |
360.0 |
59.9 |
| C3' |
C2' |
C1' |
H1' |
209.4 |
242.4 |
| H2' |
C2' |
C3' |
H2'A |
119.9 |
122.6 |
| C4' |
C3' |
C2' |
H2' |
288.0 |
262.2 |
| C4' |
C3' |
C2' |
H2'A |
168.1 |
139.6 |
| O3' |
C3' |
C4' |
H3' |
118.4 |
123.6 |
| O4' |
C4' |
C3' |
H4' |
233.0 |
241.6 |
| C5' |
C4' |
C3' |
H4' |
117.8 |
123.1 |
| H3' |
C3' |
C2' |
H2' |
166.1 |
144.0 |
| H3' |
C3' |
C2' |
H2'A |
46.2 |
21.4 |
| O3' |
C3' |
H3' |
C4' |
237.0 |
236.4 |
| H3' |
C3' |
C4' |
O4' |
71.7 |
81.2 |
| H3' |
C3' |
C4' |
H4' |
198.7 |
199.6 |
| O3' |
C3' |
C2' |
H2' |
47.9 |
20.4 |
| O3' |
C3' |
C2' |
H2'A |
288.0 |
257.8 |
| C4' |
C3' |
O3' |
H3' |
237.5 |
236.3 |
| O3' |
C3' |
C4' |
O4' |
190.1 |
204.8 |
| O3' |
C3' |
C4' |
H4' |
317.1 |
323.2 |
| HO3' |
O3' |
C3' |
C4' |
293.0 |
174.1 |
| HO3' |
O3' |
C3' |
H3' |
55.5 |
297.8 |
| C4' |
O4' |
C1' |
H1' |
110.8 |
93.2 |
| O4' |
C4' |
C3' |
H3' |
71.7 |
81.2 |
| C3' |
C4' |
O4' |
H4' |
121.9 |
118.5 |
| C5' |
C4' |
O4' |
H4' |
243.0 |
237.1 |
| H4' |
C4' |
C3' |
H3' |
198.7 |
199.6 |
| C3' |
C4' |
H4' |
O4' |
246.4 |
245.9 |
| N1 |
C1' |
O4' |
H1' |
118.1 |
121.0 |
| C2' |
C1' |
O4' |
H1' |
244.5 |
240.5 |
| P |
O5' |
C5' |
C4' |
180.6 |
180.0 |
| C5' |
C4' |
C3' |
H3' |
316.5 |
322.7 |
| C3' |
C4' |
C5' |
H4' |
236.3 |
237.0 |
| O4' |
C4' |
C5' |
H4' |
128.0 |
122.8 |
| H5' |
C5' |
C4' |
H4' |
296.5 |
68.0 |
| O5' |
C5' |
H5' |
H5'A |
237.8 |
239.9 |
| H5'A |
C5' |
C4' |
H4' |
56.5 |
188.0 |
| O5' |
C5' |
H5'A |
H5' |
122.2 |
120.1 |
| C5' |
O5' |
P |
OP1 |
273.6 |
305.0 |
| O5' |
C5' |
C4' |
H4' |
176.5 |
308.0 |
| H5' |
C5' |
O5' |
H5'A |
120.0 |
120.1 |
| HA5 |
CA5 |
SE5 |
HA5A |
240.0 |
240.0 |
| HA5 |
CA5 |
SE5 |
HA5B |
120.0 |
120.0 |
| HA5A |
CA5 |
SE5 |
HA5B |
240.0 |
240.0 |
| SE5 |
CA5 |
HA5 |
HA5A |
120.0 |
120.0 |
| SE5 |
CA5 |
HA5 |
HA5B |
240.0 |
240.0 |
| HA5A |
CA5 |
HA5 |
HA5B |
120.0 |
120.0 |
| SE5 |
CA5 |
HA5A |
HA5 |
240.0 |
240.0 |
| SE5 |
CA5 |
HA5A |
HA5B |
120.0 |
120.0 |
| HA5 |
CA5 |
HA5A |
HA5B |
240.0 |
240.0 |
| SE5 |
CA5 |
HA5B |
HA5 |
120.0 |
120.0 |
| SE5 |
CA5 |
HA5B |
HA5A |
240.0 |
240.0 |
| HA5 |
CA5 |
HA5B |
HA5A |
120.0 |
120.0 |
| SE5 |
C5 |
C6 |
H6 |
1.9 |
359.7 |
| OP3 |
P |
OP1 |
O5' |
234.3 |
240.0 |
| OP2 |
P |
OP1 |
O5' |
109.7 |
120.0 |
| OP1 |
P |
O5' |
C5' |
273.6 |
305.0 |