Chemical Components in the PDB

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VRC : Summary

Code

VRC

One-letter code

X

Molecule name

(4S)-2-(aminomethyl)-4-nitrocyclohexa-2,5-dien-1-one

Systematic names

ProgramVersionName
ACDLabs 12.01 (4S)-2-(aminomethyl)-4-nitrocyclohexa-2,5-dien-1-one
OpenEye OEToolkits 2.0.7 2-(aminomethyl)-4-nitro-cyclohexa-2,5-dien-1-one

Formula

C7 H8 N2 O3

Formal charge

0

Molecular weight

168.15 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=N(=O)C1C=CC(=O)C(CN)=C1
SMILES CACTVS 3.385 NCC1=C[CH](C=CC1=O)[N](=O)=O
SMILES OpenEye OEToolkits 2.0.7 C1=CC(=O)C(=CC1N(=O)=O)CN
Canonical SMILES CACTVS 3.385 NCC1=C[C@H](C=CC1=O)[N](=O)=O
Canonical SMILES OpenEye OEToolkits 2.0.7 C1=CC(=O)C(=CC1N(=O)=O)CN

IUPAC InChI

InChI=1S/C7H8N2O3/c8-4-5-3-6(9(11)12)1-2-7(5)10/h1-3,6H,4,8H2

IUPAC InChI key

RIRRHVGTJTXLLP-UHFFFAOYSA-N
VRC

wwPDB Information

Atom count

20 (12 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2022-09-02

Last modified at

2022-10-28

Status

Released

Obsoleted

Not Assigned



VRC : Atoms of Molecule

Total Number of Atoms: 20
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N1 N N1 N N N 0 -3.068 -1.687 0.512
2 O1 O O1 N N N 0 3.329 -0.797 0.625
3 C1 C C1 N N N 0 -0.264 1.995 0.025
4 C5 C C2 S N N 0 1.164 0.055 0.623
5 C6 C C3 N N N 0 -2.23 -1.306 -0.632
6 C4 C C4 N N N 0 0.051 -0.824 0.147
7 C3 C C5 N N N 0 -1.149 -0.362 -0.172
8 C2 C C6 N N N 0 -1.421 1.084 -0.067
9 O2 O O2 N N N 0 -2.56 1.51 -0.056
10 C C C7 N N N 0 0.928 1.504 0.337
11 N N N2 N N N 0 2.405 -0.36 -0.036
12 O O O3 N N N 0 2.511 -0.269 -1.246
13 H1 H H1 N N N 0 -3.801 -2.32 0.23
14 H2 H H2 N N N 0 -2.51 -2.086 1.252
15 H4 H H4 N N N 0 -0.387 3.051 -0.163
16 H5 H H5 N N N 0 1.279 -0.076 1.699
17 H6 H H6 N N N 0 -1.774 -2.199 -1.061
18 H7 H H7 N N N 0 -2.845 -0.815 -1.386
19 H8 H H8 N N N 0 0.236 -1.884 0.054
20 H9 H H9 N N N 0 1.767 2.182 0.386



VRC : Chemical Bonds

Total Number of Bonds: 20
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O N O N doub 1.22 N N
2 N O1 N O doub 1.22 N N
3 N C5 N C sing 1.47 N N
4 C4 C5 C C sing 1.5 N N
5 C4 C3 C C doub 1.32 N N
6 C5 C C C sing 1.5 N N
7 C6 C3 C C sing 1.51 N N
8 C6 N1 C N sing 1.47 N N
9 C3 C2 C C sing 1.48 N N
10 C C1 C C doub 1.33 N N
11 C2 C1 C C sing 1.48 N N
12 C2 O2 C O doub 1.22 N N
13 N1 H1 N H sing 1.01 N N
14 N1 H2 N H sing 1.01 N N
15 C1 H4 C H sing 1.08 N N
16 C5 H5 C H sing 1.09 N N
17 C6 H6 C H sing 1.09 N N
18 C6 H7 C H sing 1.09 N N
19 C4 H8 C H sing 1.08 N N
20 C H9 C H sing 1.08 N N



VRC : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
VRC 7fm0 Open in New Window Bound ligand 1 1