MDL SD format files contain a structure and associated data. The information about a molecule is stored in the following format:

Header Block describes the molecule.
Connection table defines the molecular structure.
Data block (optional) contains Vamp results.
Terminator line a line containing four dollar signs ($$$$),
indicating the end of information on the molecule.

Header block

Line 1:

contains the molecule name: a description of the molecule in free format.

FORTRAN format: (A80)

Line 2:

molecule header: contains the users initials (IN), program name (PROG), date and time (DATETIME), dimension (DIM), scaling factors (SCAL1, SCAL2), energy (ENGY), and internal registry code (INTREG).

IN  PROG  DATETIME  DIM  SCAL1  SCAL2  ENGY  INTREG
FORTRAN format: (A2, A8, A10, A2, I2, F10.5, F12.5, I6)

Line 3:

comment line: comments may be added in free format (otherwise a blank line must be added).

FORTRAN format: (A80)

Connection table

Counts Line:

A header line with information about the molecule and the connection table.

FORTRAN format: (2I3)

Atom Block:

One line per atom, including the atomic co-ordinates (X, Y, Z), symbol (SYM), mass difference for the isotope (MASS), formal charge (CHARGE), and stereo parity indicator (STEREO).

X  Y  Z  SYM  MASS  CHARGE  STEREO
FORTRAN format: (3F10.4, 1X, A3, A2, A3, A3)

Bond Block:

One line per bond specifying the two atoms connected by the bond (ATOM1, ATOM2), the bond type (TYPE), stereochemistry (BONDST), and topology (TOPOL).

ATOM1   ATOM2   TYPE   BONDST   NX   TOPOL
FORTRAN format: (4I3

Data block

The data block contains a series of data items, each of which has the following format:

Data Header

a data header is indicated by the greater than symbol >. The header line may contain the Field Name (enclosed by angle brackets) and/or Field Number (DTn) for the data. The external registry number may also be included in any Data Header and should be enclosed by rounded brackets ( ).

Data

data may extend over multiple lines, up to a maximum of 200 characters in total (up to 80 characters per line).

Blank line

a blank line indicating the end of the data item.