Chemical Components in the PDB

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DEN : Summary

Code

DEN

One-letter code

X

Molecule name

INDENE

Systematic names

ProgramVersionName
ACDLabs 10.04 1H-indene
OpenEye OEToolkits 1.5.0 1H-indene

Formula

C9 H8

Formal charge

0

Molecular weight

116.16 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 c1cccc2c1C=CC2
SMILES CACTVS 3.341 C1C=Cc2ccccc12
SMILES OpenEye OEToolkits 1.5.0 c1ccc2c(c1)CC=C2
Canonical SMILES CACTVS 3.341 C1C=Cc2ccccc12
Canonical SMILES OpenEye OEToolkits 1.5.0 c1ccc2c(c1)CC=C2

IUPAC InChI

InChI=1S/C9H8/c1-2-5-9-7-3-6-8(9)4-1/h1-6H,7H2

IUPAC InChI key

YBYIRNPNPLQARY-UHFFFAOYSA-N
DEN

wwPDB Information

Atom count

17 (9 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

1999-07-08

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



DEN : Atoms of Molecule

Total Number of Atoms: 17
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 N N N 0 1.167 0.0 -1.647
2 C2 C C2 N N N 0 -0.099 0.0 -2.471
3 C3 C C3 N N N 0 -1.131 0.0 -1.645
4 C4 C C4 N Y N 0 -1.394 0.0 0.963
5 C5 C C5 N Y N 0 -0.712 0.0 2.162
6 C6 C C6 N Y N 0 0.67 0.0 2.181
7 C7 C C7 N Y N 0 1.381 0.0 0.992
8 C8 C C8 N Y N 0 0.71 0.0 -0.208
9 C9 C C9 N Y N 0 -0.685 0.0 -0.24
10 H11 H 1H1 N N N 0 1.753 -0.894 -1.856
11 H12 H 2H1 N N N 0 1.753 0.894 -1.856
12 H2 H H2 N N N 0 -0.151 0.0 -3.55
13 H3 H H3 N N N 0 -2.164 0.0 -1.959
14 H4 H H4 N N N 0 -2.474 0.0 0.955
15 H5 H H5 N N N 0 -1.262 0.0 3.092
16 H6 H H6 N N N 0 1.197 0.0 3.123
17 H7 H H7 N N N 0 2.461 0.0 1.008



DEN : Chemical Bonds

Total Number of Bonds: 18
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1 C2 C C sing 1.51 N N
2 C1 C8 C C sing 1.51 N N
3 C1 H11 C H sing 1.09 N N
4 C1 H12 C H sing 1.09 N N
5 C2 C3 C C doub 1.32 N N
6 C2 H2 C H sing 1.08 N N
7 C3 C9 C C sing 1.47 N N
8 C3 H3 C H sing 1.08 N N
9 C4 C5 C C doub 1.38 N Y
10 C4 C9 C C sing 1.4 N Y
11 C4 H4 C H sing 1.08 N N
12 C5 C6 C C sing 1.38 N Y
13 C5 H5 C H sing 1.08 N N
14 C6 C7 C C doub 1.39 N Y
15 C6 H6 C H sing 1.08 N N
16 C7 C8 C C sing 1.37 N Y
17 C7 H7 C H sing 1.08 N N
18 C8 C9 C C doub 1.4 N Y



DEN : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
DEN 183l Open in New Window Bound ligand 1 1