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41 4 1 0 0 0 0 0 0 0 0 0 0 1.972885 0.38063 0.679077 0
41 4 1 0 0 0 0 0 0 0 0 0 0 1.960663 -0.413223 -0.928909 0
41 5 1 0 0 0 0 0 0 0 0 0 0 0.981857 1.921463 -0.992111 0
41 6 1 0 0 0 0 0 0 0 0 0 0 -1.309372 2.283279 0.037933 0
41 6 1 0 0 0 0 0 0 0 0 0 0 -0.033539 2.031708 1.272888 0
41 1 1 0 0 0 0 0 0 0 0 0 0 -2.052933 0.717285 1.881104 0
42 15 1 0 0 0 0 0 0 0 0 0 0 0.275696 0.374954 -2.411163 0
Each line represents a data record containing one or
more fields of information about the model. Each
field is delimited by space(s) or a tab.
The fields in the MacroModel format file used by
Chem3D are:
1. Line 1 contains 2 fields: the first field is the
number of atoms and the second field is the
name of the molecule. The molecule name is
the file name when the file is created using
Chem3D.
2. Lines 2-19 each contain 17 fields describing
information about one atom and its attached
bond. The first field contains the atom type.
The second through thirteenth fields represent
6 pairs of numbers describing the bonds that
this atom makes to other atoms. The first
number of each pair is the serial number of the
other atom, and the second number is the bond
type. The fourteenth field is the X coordinate,
the fifteenth field is the Y coordinate, the
sixteenth field is the Z coordinate and finally,
and the seventeenth field is the color of the
atom.
Atom colors are ignored by Chem3D. This
field will contain a zero if the file was created
using Chem3D.
NOTE: Atom types are user-definable. See “Editing File
Format Atom Types” on page 241 for instructions on
modifying or creating an atom type.
For example, the following illustrates the atom and
bond components for C6 and bond 3 of
cyclohexanol:
311
511611710000-0.606857 1.525177 0.459900 0
FORTRAN Formats
The FORTRAN format for each record of the
MacroModel format is as follows:
Line
Number
Each pair of numbers represents an
atom to which this atom is bonded Atom Color
Atom Type Serial Number Bond Type X Y Z
Coordinates
Description
1 number of
atoms and
molecule name
(file name
MDL MolFile
FORTRAN
Format
1X,I5,2X,A
The MDL MolFile 1 format is defined in the article
“Description of Several Chemical Structure File
Formats Used by Computer Programs Developed
at Molecular Design Limited” found in the Journal
1. MDL MACCS-II is a product of MDL
Information Systems, Inc. (previously called
Molecular Design, Limited).
250• File Formats CambridgeSoft
File Format Examples