PDB Chemical Component C5L
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 C5L
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| OP2 |
P |
1.481 |
1.480 |
| O5' |
P |
1.603 |
1.609 |
| P |
OP3 |
1.598 |
1.610 |
| P |
OP1 |
1.485 |
1.610 |
| C2 |
N1 |
1.399 |
1.346 |
| C6 |
N1 |
1.373 |
1.363 |
| N1 |
C1' |
1.483 |
1.465 |
| N3 |
C2 |
1.346 |
1.331 |
| C2 |
O2 |
1.228 |
1.220 |
| C4 |
N3 |
1.313 |
1.327 |
| N4 |
C4 |
1.298 |
1.375 |
| C4 |
C5 |
1.441 |
1.410 |
| H41 |
N4 |
1.000 |
0.970 |
| H42 |
N4 |
1.000 |
0.970 |
| C7 |
C5 |
1.521 |
1.508 |
| C5 |
C6 |
1.352 |
1.354 |
| C6 |
H6 |
1.080 |
1.080 |
| H72 |
C7 |
1.100 |
1.089 |
| H73 |
C7 |
1.100 |
1.090 |
| C7 |
H71 |
1.100 |
1.089 |
| H1' |
C1' |
1.100 |
1.089 |
| C1' |
C2' |
1.522 |
1.550 |
| C1' |
O4' |
1.425 |
1.444 |
| H2' |
C2' |
1.100 |
1.090 |
| C2' |
O2' |
1.432 |
1.429 |
| C2' |
C3' |
1.529 |
1.547 |
| CA' |
O2' |
1.421 |
1.430 |
| H3' |
C3' |
1.101 |
1.090 |
| C3' |
C4' |
1.532 |
1.541 |
| C3' |
O3' |
1.422 |
1.429 |
| O3' |
HO3' |
0.950 |
0.968 |
| O4' |
C4' |
1.428 |
1.437 |
| C4' |
C5' |
1.536 |
1.531 |
| C4' |
H4' |
1.100 |
1.090 |
| O5' |
C5' |
1.420 |
1.429 |
| C5' |
H5' |
1.100 |
1.089 |
| C5' |
H5'' |
1.100 |
1.090 |
| HCA1 |
CA' |
1.100 |
1.089 |
| HCA2 |
CA' |
1.100 |
1.090 |
| CA' |
CB' |
1.533 |
1.530 |
| OC' |
CB' |
1.427 |
1.429 |
| CB' |
HCB2 |
1.100 |
1.090 |
| CB' |
HCB1 |
1.100 |
1.090 |
| CD' |
OC' |
1.424 |
1.429 |
| HCD1 |
CD' |
1.100 |
1.089 |
| HCD2 |
CD' |
1.100 |
1.090 |
| CD' |
HCD3 |
1.100 |
1.090 |
| OP1 |
HOP1 |
0.950 |
0.967 |
| OP3 |
HOP3 |
0.950 |
0.967 |
Bond Angles for C5L
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| OP2 |
P |
OP3 |
107.8 |
109.5 |
| O5' |
P |
OP3 |
105.2 |
109.5 |
| O5' |
P |
OP1 |
108.6 |
109.5 |
| OP1 |
P |
OP3 |
107.8 |
109.5 |
| P |
OP3 |
HOP3 |
109.5 |
114.0 |
| P |
OP1 |
HOP1 |
109.5 |
114.0 |
| C2 |
N1 |
C1' |
117.4 |
119.9 |
| C6 |
N1 |
C1' |
122.3 |
119.8 |
| N1 |
C1' |
C2' |
114.0 |
110.6 |
| N1 |
C1' |
O4' |
111.8 |
110.6 |
| N4 |
C4 |
C5 |
123.6 |
120.2 |
| C4 |
C5 |
C6 |
116.4 |
119.0 |
| C5 |
C6 |
H6 |
120.0 |
120.4 |
| C2' |
C1' |
O4' |
106.9 |
103.5 |
| C1' |
C2' |
O2' |
109.6 |
110.9 |
| C1' |
C2' |
C3' |
102.0 |
102.1 |
| C1' |
O4' |
C4' |
109.0 |
107.0 |
| O2' |
C2' |
C3' |
111.4 |
110.9 |
| C2' |
C3' |
C4' |
99.9 |
104.2 |
| C2' |
C3' |
O3' |
112.8 |
110.5 |
| O3' |
C3' |
C4' |
113.8 |
110.5 |
| C3' |
C4' |
C5' |
114.0 |
109.9 |
| C3' |
C4' |
H4' |
107.5 |
109.9 |
| C3' |
O3' |
HO3' |
109.5 |
114.0 |
| O4' |
C4' |
C5' |
112.4 |
109.9 |
| O4' |
C4' |
H4' |
108.9 |
110.0 |
| C5' |
C4' |
H4' |
107.4 |
109.9 |
| C4' |
C5' |
H5' |
109.0 |
109.4 |
| C4' |
C5' |
H5'' |
109.0 |
109.5 |
| O5' |
C5' |
H5' |
109.0 |
109.5 |
| O5' |
C5' |
H5'' |
109.0 |
109.5 |
| H5' |
C5' |
H5'' |
109.5 |
109.5 |
| CA' |
CB' |
HCB2 |
108.5 |
109.5 |
| CA' |
CB' |
HCB1 |
108.5 |
109.5 |
| OC' |
CB' |
HCB2 |
108.5 |
109.5 |
| OC' |
CB' |
HCB1 |
108.5 |
109.5 |
| HCB1 |
CB' |
HCB2 |
109.5 |
109.4 |
| HCD1 |
CD' |
HCD3 |
109.4 |
109.5 |
| HCD2 |
CD' |
HCD3 |
109.5 |
109.4 |
Torsion Angles for C5L
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| O5' |
P |
OP2 |
OP3 |
113.2 |
120.0 |
| OP1 |
P |
OP2 |
OP3 |
237.2 |
240.0 |
| OP2 |
P |
OP3 |
HOP3 |
360.0 |
300.0 |
| OP2 |
P |
OP1 |
HOP1 |
360.0 |
180.0 |
| OP2 |
P |
O5' |
OP3 |
245.1 |
240.0 |
| OP1 |
P |
O5' |
OP3 |
115.2 |
120.0 |
| O5' |
P |
OP3 |
HOP3 |
245.0 |
180.0 |
| O5' |
P |
OP1 |
HOP1 |
123.7 |
300.0 |
| O5' |
P |
OP3 |
OP1 |
115.8 |
120.0 |
| OP3 |
P |
OP1 |
HOP1 |
237.2 |
60.0 |
| OP2 |
P |
OP1 |
OP3 |
122.8 |
120.0 |
| O5' |
P |
OP1 |
OP3 |
246.5 |
240.0 |
| OP1 |
P |
OP3 |
HOP3 |
129.2 |
60.0 |
| C6 |
N1 |
C2 |
C1' |
180.4 |
180.2 |
| C2 |
N1 |
C1' |
C2' |
86.1 |
295.0 |
| C2 |
N1 |
C1' |
O4' |
207.4 |
49.0 |
| C2 |
N1 |
C6 |
C1' |
179.6 |
179.8 |
| C6 |
N1 |
C1' |
C2' |
265.7 |
114.8 |
| C6 |
N1 |
C1' |
O4' |
27.0 |
228.8 |
| C2' |
C1' |
N1 |
O4' |
238.6 |
246.0 |
| N1 |
C1' |
C2' |
O2' |
212.6 |
273.7 |
| N1 |
C1' |
C2' |
C3' |
94.4 |
155.5 |
| N1 |
C1' |
O4' |
C4' |
242.4 |
201.5 |
| N3 |
C2 |
N1 |
C1' |
175.1 |
180.0 |
| O2 |
C2 |
N1 |
C1' |
355.0 |
0.1 |
| N4 |
C4 |
C5 |
C6 |
176.9 |
179.7 |
| C4 |
C5 |
C6 |
H6 |
181.0 |
180.0 |
| C7 |
C5 |
C6 |
H6 |
357.3 |
359.7 |
| C5 |
C6 |
N1 |
C1' |
183.0 |
179.7 |
| H6 |
C6 |
N1 |
C1' |
3.0 |
0.2 |
| N1 |
C1' |
C2' |
O4' |
124.1 |
118.4 |
| C2' |
C1' |
O4' |
C4' |
7.8 |
319.9 |
| O2' |
C2' |
C1' |
C3' |
118.2 |
118.2 |
| C1' |
C2' |
C3' |
C4' |
37.9 |
339.1 |
| C1' |
C2' |
C3' |
O3' |
159.2 |
97.8 |
| N1 |
C1' |
O4' |
C2' |
234.6 |
241.5 |
| O4' |
C1' |
C2' |
O2' |
88.5 |
155.2 |
| O4' |
C1' |
C2' |
C3' |
330.4 |
37.1 |
| C1' |
O4' |
C4' |
C5' |
143.0 |
146.0 |
| C1' |
O4' |
C4' |
H4' |
261.9 |
267.1 |
| O2' |
C2' |
C1' |
O4' |
88.5 |
155.2 |
| C1' |
C2' |
O2' |
C3' |
247.9 |
247.3 |
| O2' |
C2' |
C3' |
C4' |
281.1 |
220.9 |
| O2' |
C2' |
C3' |
O3' |
42.3 |
339.7 |
| C3' |
C2' |
C1' |
O4' |
330.4 |
37.1 |
| C1' |
C2' |
C3' |
O2' |
116.8 |
118.1 |
| O3' |
C3' |
C2' |
C4' |
121.2 |
118.7 |
| C2' |
C3' |
C4' |
C5' |
200.6 |
238.6 |
| C2' |
C3' |
C4' |
H4' |
81.6 |
117.6 |
| C2' |
C3' |
O3' |
HO3' |
180.0 |
180.0 |
| H3' |
C3' |
C4' |
H4' |
196.4 |
236.2 |
| H3' |
C3' |
O3' |
HO3' |
56.8 |
57.4 |
| C1' |
O4' |
C4' |
C3' |
17.5 |
26.5 |
| C2' |
C3' |
C4' |
O3' |
120.5 |
118.7 |
| C4' |
C3' |
O3' |
HO3' |
293.0 |
294.8 |
| O4' |
C4' |
C3' |
C5' |
124.5 |
119.4 |
| O4' |
C4' |
C3' |
H4' |
243.5 |
240.4 |
| C5' |
C4' |
C3' |
H4' |
119.0 |
121.0 |
| C3' |
C4' |
C5' |
H5' |
176.9 |
305.0 |
| C3' |
C4' |
C5' |
H5'' |
296.4 |
65.0 |
| C2' |
C3' |
O3' |
C4' |
247.0 |
245.2 |
| O3' |
C3' |
C4' |
C5' |
80.1 |
119.8 |
| O3' |
C3' |
C4' |
H4' |
321.1 |
358.8 |
| HO3' |
O3' |
C3' |
C4' |
293.0 |
294.8 |
| C3' |
C4' |
O4' |
C5' |
234.5 |
240.6 |
| C3' |
C4' |
O4' |
H4' |
115.6 |
119.5 |
| C5' |
C4' |
O4' |
H4' |
241.1 |
238.9 |
| O4' |
C4' |
C5' |
H5' |
55.6 |
187.2 |
| O4' |
C4' |
C5' |
H5'' |
175.1 |
307.2 |
| C3' |
C4' |
C5' |
H4' |
241.0 |
239.0 |
| O4' |
C4' |
C5' |
H4' |
119.7 |
121.2 |
| O5' |
C5' |
C4' |
H5' |
239.7 |
240.0 |
| O5' |
C5' |
C4' |
H5'' |
120.3 |
120.0 |
| H5' |
C5' |
C4' |
H5'' |
240.6 |
240.0 |
| C3' |
C4' |
H4' |
C5' |
123.1 |
121.0 |
| O4' |
C4' |
H4' |
C5' |
238.1 |
238.9 |
| H4' |
C4' |
C5' |
H5' |
295.9 |
66.0 |
| H4' |
C4' |
C5' |
H5'' |
55.3 |
186.0 |
| C5' |
O5' |
P |
OP3 |
288.7 |
175.0 |
| C5' |
O5' |
P |
OP1 |
43.9 |
295.1 |
| O5' |
C5' |
C4' |
H4' |
175.6 |
306.0 |
| C4' |
C5' |
O5' |
H5' |
120.3 |
120.0 |
| C4' |
C5' |
O5' |
H5'' |
239.8 |
240.0 |
| H5' |
C5' |
O5' |
H5'' |
119.5 |
120.0 |
| H5' |
C5' |
C4' |
H4' |
295.9 |
66.0 |
| C4' |
C5' |
H5' |
H5'' |
119.1 |
120.0 |
| O5' |
C5' |
H5' |
H5'' |
240.8 |
240.0 |
| H5'' |
C5' |
C4' |
H4' |
55.3 |
186.0 |
| C4' |
C5' |
H5'' |
H5' |
240.8 |
240.0 |
| O5' |
C5' |
H5'' |
H5' |
119.2 |
120.0 |
| HCA1 |
CA' |
CB' |
HCB2 |
180.6 |
185.0 |
| HCA1 |
CA' |
CB' |
HCB1 |
299.5 |
65.0 |
| HCA2 |
CA' |
CB' |
HCB2 |
60.6 |
65.0 |
| HCA2 |
CA' |
CB' |
HCB1 |
179.5 |
305.0 |
| OC' |
CB' |
CA' |
HCB2 |
239.5 |
120.0 |
| OC' |
CB' |
CA' |
HCB1 |
120.6 |
240.0 |
| HCB1 |
CB' |
CA' |
HCB2 |
118.9 |
240.0 |
| CA' |
CB' |
OC' |
HCB2 |
120.5 |
240.0 |
| CA' |
CB' |
OC' |
HCB1 |
239.4 |
120.0 |
| HCB1 |
CB' |
OC' |
HCB2 |
241.1 |
120.0 |
| CA' |
CB' |
HCB2 |
HCB1 |
118.3 |
240.0 |
| OC' |
CB' |
HCB2 |
HCB1 |
241.7 |
120.0 |
| CA' |
CB' |
HCB1 |
HCB2 |
241.7 |
120.0 |
| OC' |
CB' |
HCB1 |
HCB2 |
118.2 |
240.0 |
| CD' |
OC' |
CB' |
HCB2 |
304.8 |
300.0 |
| CD' |
OC' |
CB' |
HCB1 |
185.9 |
60.0 |
| HCD2 |
CD' |
HCD1 |
HCD3 |
120.0 |
120.0 |
| HCD1 |
CD' |
HCD2 |
HCD3 |
240.0 |
239.9 |
| HOP1 |
OP1 |
P |
OP3 |
237.2 |
60.0 |