M ALS- atom list and exclusive list
M APO- Rgroup attachment point
M CHG- charge
M RAD- radical
M ISO- isotope mass numbers
M RGP- Rgroup labels on root structure
M LOG- Rgroup logic
M LIN- link nodes
M SUB- substitution count query property (s)
M UNS- unsaturated atom query property (u)
M RBC- ring bond count query property (rb)
M STY- Sgroup type
M SST- Sgroup subtype
M SCN- Sgroup connectivity (head-to-head, head-to-tail or either/unknown)
M SAL- atoms that define the Sgroup
M SPA- multiple group parent atom list (paradigmatic repeating unit atoms)
M SBL- Sgroup's crossing bonds
M SMT- Sgroup label
M SPL- Sgroup parent list
M SDS EXP- Sgroup expansion
M SDT- Data sgroup field description
M SDD- Data sgroup display information
M SCD- Data sgroup data
M SED- Data sgroup data end of line
M SNC- Sgroup component numbers
M CRS- Sgroup correspondence
M SDI- display coordinates in each S-group bracket
M SBT- the displayed S-group bracket style
M SAP- the S-group attachment point information
M MRV SMA- SMARTS H, X, R, r, a, A properties (Marvin extension)
A- Atom alias
V- Atom value
If the number of atoms or bonds exceeds 999, in case of reactions with Rgroups or when there is enhanced stereo in the molecule the extended format is used. In an extended MOLfile, the following properties and features are supported:
MASS- isotope mass number
HCOUNT- number of implicit hydrogens
STBOX- stereo care box
INVRET- inversion/retention flag
ATTCHPT- R-group attachment point
RGROUPS- R-groups that comprise this R# atom
SUBST- Substitution count query property (s)
UNSAT- Unsaturated atom query property (u)
RBCNT- Ring bond count query property
CFG- bond stereo configuration: up or down
TOPO- bond topology: ring or chain
STBOX- stereo care box
LINKNODE- Link nodes.
A reaction file consists of a REACTANT block, a PRODUCT block, and (optionally) an AGENT block. Reaction files containing reaction agents are non-standard.
Each block starts with 'Molecule or Reaction Identifier'. The form of a molecule identifier must be one of the following:
$MFMT $MIREG N $MFMT $MEREG N $MIREG N $MEREG N.
$MFMT means that a molecule is given in a molfile format,
is the internal and
is the external registry number of the molecule. Similarly, the identifier has the following form,
$RFMT $RIREG N $RFMT $REREG N $RIREG N $REREG N.
$RFMT means that a reaction is given in a rxnfile format,
is internal and
is the external registry number of the reaction.
A reaction agent is a molecule structure that does not take part in the chemical reaction, but is added to the reaction equation for informative purpose only. Agents are normally displayed graphically above the reaction arrow, added to the reaction file after the reactants and the products. The number of agents is displayed in the file header (after the number of reactants and the number of products) if it is non-zero. Reaction files containing agents are non-standard.
In SDfiles read by marvin, the name field is special, it overrides the molecule name specified in the molfile part.
Incompatibility note: The MDL definition declares the maximal line length for molecule properties in 200 characters. We ignore this limit.
A special feature of Marvin RGfiles is that they can contain a reaction as the root structure. This feature is non-standard, such mixed RG/Rxnfiles can only be imported by Marvin.