What Is RXN file format?

RXN, stands for Reaction, is a reaction file format extended from the MDL Molfile format for molecules. RXN is also called MDL Rxnfile or RDF (Reaction Data File).

There are 2 versions of RXN formats that are used by chemical software.

1. MDL RXN V2000 - Extended from the SDF/Molfile V2000 format use the following file structure:

$RXN
{RXN header lines}
$MOL
{Molfile V2000 of Reactant/Produdct/Agent molecule}
$MOL
{Molfile V2000 of Reactant/Produdct/Agent molecule}
...

Example of a MDL RXN V2000 file:

$RXN
FYI-2000001
FYIcenter.com

  1  2
$MOL
FYI-1000001
FYIcenter.com

  3  2  0  0  0  0  0  0  0  0999 V2000
    1.8841   -2.3250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.7501   -2.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.6161   -2.3250    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
M  END
$MOL
FYI-1000002
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  2  1  0  0  0  0  0  0  0  0999 V2000
    6.5161   -2.6250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.5161   -2.6250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
M  END
$MOL
FYI-1000003
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  1  0  0  0  0  0  0  0  0  0999 V2000
    9.7161   -2.6875    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
M  END

2. MDL RXN V2000 - Extended from the SDF/Molfile V2000 format use the following file structure:

$RXN
{RXN header lines}
M  V30 COUNTS ...
M  V30 BEGIN REACTANT
{CTAB V3000 of reactant molecule}
{CTAB V3000 of reactant molecule}
...
M  V30 END REACTANT
M  V30 BEGIN PRODUCT
{CTAB V3000 of product molecule}
{CTAB V3000 of product molecule}
...
M  V30 END PRODUCT
M  V30 BEGIN AGENT
{CTAB V3000 of agent molecule}
{CTAB V3000 of agent molecule}
...
M  V30 END AGENT
M  END

Example of a MDL RXN V3000 file:

$RXN V3000
FYI-2000001
FYIcenter.com

M  V30 COUNTS 1 2
M  V30 BEGIN REACTANT
M  V30 BEGIN CTAB
M  V30 COUNTS 3 2 0 0 0
M  V30 BEGIN ATOM
M  V30 1 N 1.88406 -2.32504 0.0 0
M  V30 2 N 2.75009 -2.82504 0.0 0
M  V30 3 Cl 3.61611 -2.32504 0.0 0
M  V30 END ATOM
M  V30 BEGIN BOND
M  V30 1 1 1 2
M  V30 2 1 2 3
M  V30 END BOND
M  V30 END CTAB
M  V30 END REACTANT
M  V30 BEGIN PRODUCT
M  V30 BEGIN CTAB
M  V30 COUNTS 2 1 0 0 0
M  V30 BEGIN ATOM
M  V30 1 N 6.51611 -2.62504 0.0 0
M  V30 2 N 7.51611 -2.62504 0.0 0
M  V30 END ATOM
M  V30 BEGIN BOND
M  V30 1 1 1 2
M  V30 END BOND
M  V30 END CTAB
M  V30 BEGIN CTAB
M  V30 COUNTS 1 0 0 0 0
M  V30 BEGIN ATOM
M  V30 1 Cl 9.71611 -2.68754 0.0 0
M  V30 END ATOM
M  V30 BEGIN BOND
M  V30 END BOND
M  V30 END CTAB
M  V30 END PRODUCT
M  END

MDL Molfile, also call Mol file, or SDF (Structural Data File), was developed and published by Molecular Design Limited (MDL).

For more information, see "SDF/Mol File FAQ" tutorials.

⇒ CML (Chemical Markup Language) for Reactions

⇐ SMIRKS for Generic Reactions

⇑ Reaction Presentations and File Formats

⇑⇑ Reaction FAQ