 |
W3M : Summary
Code 
|
W3M
|
One-letter code
|
X
|
Molecule name
|
1H-imidazole-5-carbonitrile
|
Systematic names
|
|
Formula
|
C4 H3 N3
|
Formal charge
|
0
|
Molecular weight
|
93.087 Da
|
SMILES
|
| Type | Program | Version | Descriptor |
|---|
|
SMILES
|
ACDLabs |
12.01 |
n1cncc1C#N |
|
SMILES
|
CACTVS |
3.385 |
N#Cc1[nH]cnc1 |
|
SMILES
|
OpenEye OEToolkits |
2.0.7 |
c1c([nH]cn1)C#N |
|
Canonical SMILES
|
CACTVS |
3.385 |
N#Cc1[nH]cnc1 |
|
Canonical SMILES
|
OpenEye OEToolkits |
2.0.7 |
c1c([nH]cn1)C#N |
|
IUPAC InChI | InChI=1S/C4H3N3/c5-1-4-2-6-3-7-4/h2-3H,(H,6,7) |
IUPAC InChI key | NWVGXXPWOYZODV-UHFFFAOYSA-N |
|
wwPDB Information |
Atom count
|
10 (7 without Hydrogen)
|
Polymer type
|
Bound ligand
|
Type description
|
non-polymer
|
Type code
|
HETAIN
|
Is modified
|
No
|
Standard parent
|
Not Assigned
|
Defined at
|
2020-09-24
|
Last modified at
|
2021-01-08
|
Status
|
Released
|
Obsoleted
|
Not Assigned
|
|
|
W3M : Atoms of Molecule
Total Number of Atoms: 10
| Record |
Atom Name |
Symbol |
PDB Name |
Stereochemistry |
Is Aromatic |
Is Leaving Atom |
Charge |
X-Coordinate |
Y-Coordinate |
Z-Coordinate |
| 1 |
N1 |
N |
N1 |
N |
Y |
N |
0 |
-0.555 |
1.076 |
0.0 |
| 2 |
N |
N |
N2 |
N |
N |
N |
0 |
2.854 |
0.013 |
0.0 |
| 3 |
C |
C |
C1 |
N |
N |
N |
0 |
1.718 |
-0.001 |
0.0 |
| 4 |
C1 |
C |
C2 |
N |
Y |
N |
0 |
0.286 |
-0.019 |
0.0 |
| 5 |
C3 |
C |
C3 |
N |
Y |
N |
0 |
-0.519 |
-1.123 |
0.0 |
| 6 |
N2 |
N |
N3 |
N |
Y |
N |
0 |
-1.786 |
-0.703 |
0.0 |
| 7 |
C2 |
C |
C4 |
N |
Y |
N |
0 |
-1.816 |
0.604 |
0.0 |
| 8 |
H1 |
H |
H1 |
N |
N |
N |
0 |
-0.288 |
2.008 |
0.003 |
| 9 |
H2 |
H |
H2 |
N |
N |
N |
0 |
-0.19 |
-2.151 |
0.0 |
| 10 |
H4 |
H |
H4 |
N |
N |
N |
0 |
-2.711 |
1.209 |
0.003 |
W3M : Chemical Bonds
Total Number of Bonds: 10
| Record |
First Atom |
Second Atom |
First Element |
Second Element |
Bond Order Type |
Bond Length |
Bond Stereochemistry |
Is Aromatic |
| 1 |
N |
C |
N |
C |
trip |
1.14 |
N |
N |
| 2 |
C |
C1 |
C |
C |
sing |
1.43 |
N |
N |
| 3 |
C3 |
C1 |
C |
C |
doub |
1.37 |
N |
Y |
| 4 |
C3 |
N2 |
C |
N |
sing |
1.33 |
N |
Y |
| 5 |
C1 |
N1 |
C |
N |
sing |
1.38 |
N |
Y |
| 6 |
N2 |
C2 |
N |
C |
doub |
1.31 |
N |
Y |
| 7 |
N1 |
C2 |
N |
C |
sing |
1.35 |
N |
Y |
| 8 |
N1 |
H1 |
N |
H |
sing |
0.97 |
N |
N |
| 9 |
C3 |
H2 |
C |
H |
sing |
1.08 |
N |
N |
| 10 |
C2 |
H4 |
C |
H |
sing |
1.08 |
N |
N |
W3M : Used in PDB Entries
Total Number of PDB Entries: 3
| Ligand Code |
PDB Entry ID |
Type |
Total |
Distinct |
| W3M |
5s4e  |
Bound ligand
|
3 |
1 |
| W3M |
7gq5 |
Bound ligand
|
2 |
1 |
| W3M |
7gqp |
Bound ligand
|
1 |
1 |
|
Protein Data Bank 
