PDB Chemical Component JM5
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 JM5
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| C |
OA2 |
1.242 |
1.342 |
| N |
CA |
1.451 |
1.470 |
| N |
HN |
1.000 |
1.009 |
| N |
HNA |
1.000 |
1.010 |
| C1 |
C2 |
1.351 |
1.507 |
| C2 |
H2 |
1.100 |
1.090 |
| C2 |
H2A |
1.100 |
1.090 |
| S3 |
C2 |
1.771 |
1.814 |
| S3 |
C4 |
1.759 |
1.813 |
| C4 |
C5 |
1.522 |
1.530 |
| C4 |
H4 |
1.100 |
1.090 |
| C4 |
H4A |
1.100 |
1.090 |
| C5 |
C6 |
1.507 |
1.530 |
| C5 |
H5 |
1.100 |
1.090 |
| C5 |
H5A |
1.100 |
1.090 |
| C6 |
H6 |
1.100 |
1.090 |
| C6 |
H6A |
1.100 |
1.090 |
| C6 |
H6B |
1.100 |
1.089 |
| CA |
C |
1.519 |
1.507 |
| CA |
CB |
1.541 |
1.530 |
| CA |
HA |
1.100 |
1.090 |
| CB |
HB |
1.100 |
1.090 |
| CB |
HBA |
1.100 |
1.090 |
| CD |
HD |
1.100 |
1.090 |
| NE |
C1 |
1.348 |
1.370 |
| NE |
CD |
1.286 |
1.465 |
| CG |
CB |
1.525 |
1.530 |
| CG |
CD |
1.524 |
1.531 |
| CG |
HG |
1.100 |
1.090 |
| CG |
HGA |
1.099 |
1.090 |
| NH |
C1 |
1.263 |
1.293 |
| NH |
HNH |
1.000 |
0.971 |
| OA1 |
C |
1.243 |
1.209 |
| OA2 |
HOA2 |
0.950 |
0.967 |
| CD |
H20 |
1.100 |
1.090 |
| NE |
H21 |
1.000 |
0.969 |
Bond Angles for JM5
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| CA |
C |
OA2 |
120.1 |
120.0 |
| OA1 |
C |
OA2 |
118.8 |
120.0 |
| C |
OA2 |
HOA2 |
109.5 |
117.0 |
| CA |
N |
HN |
109.5 |
111.0 |
| CA |
N |
HNA |
109.4 |
111.0 |
| N |
CA |
CB |
110.2 |
109.5 |
| N |
CA |
HA |
107.6 |
109.4 |
| HN |
N |
HNA |
109.5 |
110.9 |
| C1 |
C2 |
H2 |
106.0 |
109.5 |
| C1 |
C2 |
H2A |
106.0 |
109.5 |
| H2 |
C2 |
H2A |
112.7 |
109.5 |
| S3 |
C2 |
H2 |
106.0 |
109.5 |
| S3 |
C2 |
H2A |
106.0 |
109.4 |
| S3 |
C4 |
C5 |
108.8 |
109.5 |
| S3 |
C4 |
H4 |
109.7 |
109.5 |
| S3 |
C4 |
H4A |
109.7 |
109.5 |
| C5 |
C4 |
H4 |
109.7 |
109.4 |
| C5 |
C4 |
H4A |
109.7 |
109.5 |
| C4 |
C5 |
C6 |
109.7 |
109.5 |
| C4 |
C5 |
H5 |
109.4 |
109.5 |
| C4 |
C5 |
H5A |
109.4 |
109.5 |
| H4 |
C4 |
H4A |
109.2 |
109.4 |
| C6 |
C5 |
H5 |
109.4 |
109.4 |
| C6 |
C5 |
H5A |
109.4 |
109.4 |
| C5 |
C6 |
H6 |
109.5 |
109.5 |
| C5 |
C6 |
H6A |
109.4 |
109.4 |
| C5 |
C6 |
H6B |
109.5 |
109.5 |
| H5 |
C5 |
H5A |
109.5 |
109.5 |
| H6 |
C6 |
H6A |
109.5 |
109.4 |
| H6 |
C6 |
H6B |
109.4 |
109.5 |
| H6A |
C6 |
H6B |
109.5 |
109.5 |
| CB |
CA |
HA |
110.0 |
109.5 |
| CA |
CB |
HB |
107.5 |
109.5 |
| CA |
CB |
HBA |
107.4 |
109.5 |
| HB |
CB |
HBA |
111.4 |
109.5 |
| CG |
CB |
HB |
107.5 |
109.4 |
| CG |
CB |
HBA |
107.5 |
109.5 |
| NE |
CD |
HD |
105.4 |
109.5 |
| CG |
CD |
HD |
105.4 |
109.5 |
| HD |
CD |
H20 |
113.2 |
109.5 |
| NE |
CD |
H20 |
105.4 |
109.5 |
| CG |
CD |
H20 |
105.4 |
109.4 |
| HG |
CG |
HGA |
109.4 |
109.5 |
Torsion Angles for JM5
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| N |
CA |
C |
OA2 |
184.1 |
160.0 |
| HN |
N |
CA |
HNA |
240.0 |
236.1 |
| CB |
CA |
N |
HA |
119.9 |
120.0 |
| N |
CA |
CB |
HB |
59.0 |
55.0 |
| N |
CA |
CB |
HBA |
179.0 |
175.0 |
| CA |
N |
HN |
HNA |
120.0 |
123.9 |
| HN |
N |
CA |
CB |
59.2 |
176.1 |
| HN |
N |
CA |
HA |
299.2 |
56.1 |
| CA |
N |
HNA |
HN |
240.0 |
236.1 |
| HNA |
N |
CA |
CB |
179.1 |
300.0 |
| HNA |
N |
CA |
HA |
59.2 |
180.0 |
| H2 |
C2 |
C1 |
H2A |
240.0 |
240.0 |
| S3 |
C2 |
C1 |
H2 |
240.0 |
240.0 |
| S3 |
C2 |
C1 |
H2A |
120.0 |
120.0 |
| C1 |
C2 |
H2 |
H2A |
115.5 |
120.0 |
| S3 |
C2 |
H2 |
H2A |
244.5 |
240.0 |
| C1 |
C2 |
H2A |
H2 |
244.5 |
240.0 |
| S3 |
C2 |
H2A |
H2 |
115.5 |
120.0 |
| C1 |
C2 |
S3 |
H2 |
120.0 |
120.0 |
| C1 |
C2 |
S3 |
H2A |
240.0 |
240.0 |
| H2 |
C2 |
S3 |
H2A |
120.0 |
120.0 |
| C4 |
S3 |
C2 |
H2 |
108.0 |
60.0 |
| C4 |
S3 |
C2 |
H2A |
348.1 |
300.0 |
| C5 |
C4 |
S3 |
H4 |
240.0 |
240.0 |
| C5 |
C4 |
S3 |
H4A |
120.0 |
120.0 |
| S3 |
C4 |
C5 |
C6 |
96.1 |
180.0 |
| S3 |
C4 |
C5 |
H5 |
216.1 |
300.0 |
| S3 |
C4 |
C5 |
H5A |
336.1 |
60.0 |
| H4 |
C4 |
S3 |
H4A |
240.0 |
240.0 |
| S3 |
C4 |
C5 |
H4 |
120.0 |
120.0 |
| S3 |
C4 |
C5 |
H4A |
240.0 |
240.0 |
| H4 |
C4 |
C5 |
H4A |
120.0 |
119.9 |
| C6 |
C5 |
C4 |
H5 |
240.0 |
240.0 |
| C6 |
C5 |
C4 |
H5A |
120.0 |
120.0 |
| C4 |
C5 |
C6 |
H6 |
180.0 |
300.0 |
| C4 |
C5 |
C6 |
H6A |
300.0 |
60.0 |
| C4 |
C5 |
C6 |
H6B |
60.0 |
180.0 |
| H5 |
C5 |
C4 |
H5A |
240.0 |
239.9 |
| S3 |
C4 |
H4 |
C5 |
240.5 |
240.0 |
| S3 |
C4 |
H4 |
H4A |
120.2 |
120.0 |
| C5 |
C4 |
H4 |
H4A |
239.7 |
240.1 |
| H4 |
C4 |
C5 |
C6 |
336.1 |
60.0 |
| H4 |
C4 |
C5 |
H5 |
96.1 |
179.9 |
| H4 |
C4 |
C5 |
H5A |
216.1 |
300.0 |
| S3 |
C4 |
H4A |
C5 |
119.5 |
120.0 |
| S3 |
C4 |
H4A |
H4 |
239.8 |
240.0 |
| C5 |
C4 |
H4A |
H4 |
120.3 |
119.9 |
| H4A |
C4 |
C5 |
C6 |
216.1 |
300.0 |
| H4A |
C4 |
C5 |
H5 |
336.1 |
60.0 |
| H4A |
C4 |
C5 |
H5A |
96.1 |
180.1 |
| C6 |
C5 |
C4 |
H4 |
336.1 |
60.0 |
| C6 |
C5 |
C4 |
H4A |
216.1 |
300.0 |
| C4 |
C5 |
C6 |
H5 |
120.0 |
120.0 |
| C4 |
C5 |
C6 |
H5A |
240.0 |
240.0 |
| H5 |
C5 |
C6 |
H5A |
120.0 |
120.0 |
| H6 |
C6 |
C5 |
H6A |
240.0 |
240.1 |
| H6 |
C6 |
C5 |
H6B |
120.0 |
120.0 |
| H6A |
C6 |
C5 |
H6B |
240.0 |
239.9 |
| H5 |
C5 |
C4 |
H4 |
96.1 |
179.9 |
| H5 |
C5 |
C4 |
H4A |
336.1 |
60.0 |
| C4 |
C5 |
H5 |
C6 |
239.8 |
240.0 |
| C4 |
C5 |
H5 |
H5A |
119.9 |
120.0 |
| C6 |
C5 |
H5 |
H5A |
240.1 |
240.1 |
| H5 |
C5 |
C6 |
H6 |
60.0 |
180.0 |
| H5 |
C5 |
C6 |
H6A |
180.0 |
300.0 |
| H5 |
C5 |
C6 |
H6B |
300.0 |
60.0 |
| H5A |
C5 |
C4 |
H4 |
216.1 |
300.0 |
| H5A |
C5 |
C4 |
H4A |
96.1 |
180.1 |
| C4 |
C5 |
H5A |
C6 |
120.2 |
120.0 |
| C4 |
C5 |
H5A |
H5 |
240.1 |
240.0 |
| C6 |
C5 |
H5A |
H5 |
119.9 |
119.9 |
| H5A |
C5 |
C6 |
H6 |
300.0 |
60.1 |
| H5A |
C5 |
C6 |
H6A |
60.0 |
180.0 |
| H5A |
C5 |
C6 |
H6B |
180.0 |
300.0 |
| H6 |
C6 |
C5 |
H5 |
60.0 |
180.0 |
| H6 |
C6 |
C5 |
H5A |
300.0 |
60.1 |
| C5 |
C6 |
H6 |
H6A |
120.0 |
119.9 |
| C5 |
C6 |
H6 |
H6B |
240.0 |
239.9 |
| H6A |
C6 |
H6 |
H6B |
120.0 |
120.0 |
| H6A |
C6 |
C5 |
H5 |
180.0 |
300.0 |
| H6A |
C6 |
C5 |
H5A |
60.0 |
180.0 |
| C5 |
C6 |
H6A |
H6 |
240.0 |
240.1 |
| C5 |
C6 |
H6A |
H6B |
120.0 |
120.1 |
| H6 |
C6 |
H6A |
H6B |
240.0 |
240.0 |
| H6B |
C6 |
C5 |
H5 |
300.0 |
60.0 |
| H6B |
C6 |
C5 |
H5A |
180.0 |
300.0 |
| C5 |
C6 |
H6B |
H6 |
120.0 |
120.0 |
| C5 |
C6 |
H6B |
H6A |
240.0 |
240.0 |
| H6 |
C6 |
H6B |
H6A |
120.0 |
120.0 |
| OA1 |
C |
CA |
OA2 |
178.1 |
180.2 |
| CA |
C |
OA2 |
HOA2 |
178.1 |
179.9 |
| CB |
CA |
C |
OA2 |
305.7 |
280.0 |
| CB |
CA |
N |
HN |
59.2 |
176.1 |
| CB |
CA |
N |
HNA |
179.1 |
300.0 |
| N |
CA |
CB |
HA |
241.5 |
240.1 |
| HB |
CB |
CA |
HBA |
240.0 |
240.0 |
| CG |
CB |
CA |
HB |
240.0 |
240.0 |
| CG |
CB |
CA |
HBA |
120.0 |
120.0 |
| HA |
CA |
C |
OA2 |
65.7 |
40.0 |
| HA |
CA |
N |
HN |
299.2 |
56.1 |
| HA |
CA |
N |
HNA |
59.2 |
180.0 |
| N |
CA |
HA |
CB |
120.1 |
120.0 |
| HA |
CA |
CB |
HB |
177.5 |
175.0 |
| HA |
CA |
CB |
HBA |
297.5 |
295.0 |
| HB |
CB |
CA |
HA |
177.5 |
175.0 |
| CA |
CB |
HB |
HBA |
117.5 |
120.0 |
| CG |
CB |
HB |
HBA |
242.5 |
240.0 |
| HBA |
CB |
CA |
HA |
297.5 |
295.0 |
| CA |
CB |
HBA |
HB |
242.5 |
240.0 |
| CG |
CB |
HBA |
HB |
117.5 |
119.9 |
| NE |
CD |
HD |
H20 |
114.7 |
120.1 |
| CG |
CD |
HD |
H20 |
245.3 |
240.1 |
| NE |
C1 |
C2 |
H2 |
181.7 |
300.0 |
| NE |
C1 |
C2 |
H2A |
301.7 |
60.0 |
| CG |
CD |
NE |
HD |
240.0 |
240.0 |
| HD |
CD |
NE |
H20 |
240.0 |
240.0 |
| CG |
CD |
NE |
H20 |
120.0 |
119.9 |
| CG |
CB |
CA |
HA |
57.5 |
55.0 |
| CA |
CB |
CG |
HB |
120.0 |
120.0 |
| CA |
CB |
CG |
HBA |
240.0 |
240.0 |
| HB |
CB |
CG |
HBA |
120.0 |
120.0 |
| CD |
CG |
CB |
HB |
32.8 |
60.1 |
| CD |
CG |
CB |
HBA |
272.8 |
300.1 |
| NE |
CD |
CG |
HD |
120.0 |
120.1 |
| HD |
CD |
CG |
H20 |
120.0 |
120.0 |
| NE |
CD |
CG |
H20 |
240.0 |
240.0 |
| HG |
CG |
CB |
HB |
152.8 |
180.0 |
| HG |
CG |
CB |
HBA |
32.8 |
60.0 |
| HG |
CG |
CD |
HD |
70.2 |
300.0 |
| HG |
CG |
CD |
H20 |
310.2 |
180.0 |
| HGA |
CG |
CB |
HB |
272.9 |
300.0 |
| HGA |
CG |
CB |
HBA |
152.8 |
180.0 |
| HGA |
CG |
CD |
HD |
310.2 |
180.0 |
| HGA |
CG |
CD |
H20 |
190.2 |
60.0 |
| NH |
C1 |
C2 |
H2 |
1.6 |
120.0 |
| NH |
C1 |
C2 |
H2A |
121.6 |
240.0 |
| CA |
C |
OA1 |
OA2 |
181.9 |
179.8 |
| OA1 |
C |
OA2 |
HOA2 |
360.0 |
359.7 |
| NE |
CD |
H20 |
HD |
245.3 |
239.9 |
| CG |
CD |
H20 |
HD |
114.7 |
120.0 |
| H21 |
NE |
CD |
HD |
126.3 |
120.0 |
| H21 |
NE |
CD |
H20 |
246.3 |
240.0 |