Chemical Components in the PDB

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TRM : Summary

Code

TRM

One-letter code

X

Molecule name

1H-BENOXIMIDAZOLE-2-CARBOXYLIC ACID

Systematic names

ProgramVersionName
ACDLabs 10.04 1H-benzimidazole-2-carboxylic acid
OpenEye OEToolkits 1.5.0 1H-benzimidazole-2-carboxylic acid

Formula

C8 H6 N2 O2

Formal charge

0

Molecular weight

162.145 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(O)c2nc1ccccc1n2
SMILES CACTVS 3.341 OC(=O)c1[nH]c2ccccc2n1
SMILES OpenEye OEToolkits 1.5.0 c1ccc2c(c1)[nH]c(n2)C(=O)O
Canonical SMILES CACTVS 3.341 OC(=O)c1[nH]c2ccccc2n1
Canonical SMILES OpenEye OEToolkits 1.5.0 c1ccc2c(c1)[nH]c(n2)C(=O)O

IUPAC InChI

InChI=1S/C8H6N2O2/c11-8(12)7-9-5-3-1-2-4-6(5)10-7/h1-4H,(H,9,10)(H,11,12)

IUPAC InChI key

RHXSYTACTOMVLJ-UHFFFAOYSA-N
TRM

wwPDB Information

Atom count

18 (12 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2000-09-12

Last modified at

2023-11-03

Status

Released

Obsoleted

Not Assigned



TRM : Atoms of Molecule

Total Number of Atoms: 18
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 NG N NG N Y N 0 1.043 0.003 0.403
2 CD1 C CD1 N Y N 0 -0.029 0.0 1.152
3 NE1 N NE1 N Y N 0 -1.147 0.0 0.359
4 CE2 C CE2 N Y N 0 -0.716 0.0 -0.946
5 CZ2 C CZ2 N Y N 0 -1.361 0.0 -2.176
6 CH2 C CH2 N Y N 0 -0.619 0.0 -3.337
7 CZ3 C CZ3 N Y N 0 0.768 0.0 -3.287
8 CE3 C CE3 N Y N 0 1.423 -0.001 -2.09
9 CD2 C CD2 N Y N 0 0.692 0.0 -0.894
10 C C C N N N 0 -0.034 0.0 2.631
11 O O O N N N 0 -1.088 0.0 3.234
12 OXT O OXT N N Y 0 1.129 -0.001 3.308
13 HE11 H 1HE1 N N N 0 -2.069 0.0 0.662
14 HZ21 H 1HZ2 N N N 0 -2.44 0.0 -2.222
15 HH21 H 1HH2 N N N 0 -1.121 0.0 -4.293
16 HZ31 H 1HZ3 N N N 0 1.336 -0.001 -4.206
17 HE31 H 1HE3 N N N 0 2.503 -0.001 -2.064
18 HXT H HXT N N Y 0 1.125 0.0 4.275



TRM : Chemical Bonds

Total Number of Bonds: 19
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 NG CD1 N C doub 1.31 N Y
2 NG CD2 N C sing 1.34 N Y
3 CD1 NE1 C N sing 1.37 N Y
4 CD1 C C C sing 1.48 N N
5 NE1 CE2 N C sing 1.37 N Y
6 NE1 HE11 N H sing 0.97 N N
7 CE2 CZ2 C C doub 1.39 N Y
8 CE2 CD2 C C sing 1.41 N Y
9 CZ2 CH2 C C sing 1.38 N Y
10 CZ2 HZ21 C H sing 1.08 N N
11 CH2 CZ3 C C doub 1.39 N Y
12 CH2 HH21 C H sing 1.08 N N
13 CZ3 CE3 C C sing 1.36 N Y
14 CZ3 HZ31 C H sing 1.08 N N
15 CE3 CD2 C C doub 1.4 N Y
16 CE3 HE31 C H sing 1.08 N N
17 C O C O doub 1.21 N N
18 C OXT C O sing 1.35 N N
19 OXT HXT O H sing 0.97 N N



TRM : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
TRM 5mho Open in New Window Polymer component 2 1