MOL V2000 files

• Bond block:
  • bond type: 1, 2, 3, aromatic, "any", "single or double", "single or aromatic", "double or aromatic" or "hydrogen"
  • bond stereo information: up or down
  • bond topology: ring or chain
• Properties block:
  • 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

Extended MOLfiles (V3000)

• Bond block:
  • bond type: 1, 2, 3, aromatic, "any", "single or double", "single or aromatic", "double or aromatic"
  • CFG - bond stereo configuration: up or down
  • TOPO - bond topology: ring or chain
  • STBOX - stereo care box
• LINKNODE - Link nodes.
• Sgroup block:
  • ATOMS - atoms that define the Sgroup
  • PATOMS - multiple group parent atom list (paradigmatic repeating unit atoms)
  • XBONDS - crossing bonds
  • MULT - multiple group multiplier
  • CONNECT - connectivity (head-to-head, head-to-tail or either/unknown)
  • LABEL - display label
  • PARENT - parent Sgroup
  • ESTATE - expanded state
  • FIELDNAME - data Sgroup field name
  • FIELDINFO - data Sgroup field information (type and units)
  • FIELDDISP - data Sgroup field display information
  • QUERYTYPE - data Sgroup program query code
  • QUERYOP - data Sgroup query operator
  • FIELDDATA - data Sgroup field value
  • BRKXYZ - display coordinates in each S-group bracket
  • BRKTYP - the displayed S-group bracket style
  • COMPNO - Sgroup component numbers
  • CBONDS - Sgroup's crossing bonds
  • XBHEAD, XBCORR - Sgroup correspondence
  • SUBTYPE - Sgroup subtype
  • CLASS - Sgroup class; AA: amino acid
  • CSTATE - Sgroup contracted state
  • ESTATE - Sgroup expanded state
  • SAP - the S-group attachment point information
  Collection block:
  Enhanced stereo features, see also the V3ec and  V3ea export options.
  • MDLV30/STEABS - ABSOLUTE stereochemical group
  • MDLV30/STEREL - OR stereochemical group
  • MDLV30/STERAC - AND stereochemical group
  Atom highlighting.
  • MDLV30/HILITE - Highlighted atoms and bonds, currently as represented as atom/bond set 1. (This feature is experimental and import only!)
• Rgroup blocks with RLOGIC entries
• Template block (import only)

Reaction files (V2000)

$MFMT $MIREG N
$MFMT $MEREG N
$MIREG N
$MEREG N.

Here $MFMT means that a molecule is given in a molfile format, $MIREG N is the internal and $MEREG N 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.

Here $RFMT means that a reaction is given in a rxnfile format, $RIREG N is internal and $REREG N 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.

Extended reaction files (V3000)

SD Files

RG Files