Alchemy 2000 Molecule format


An AL2 file begins in the very first line of the file. Every line (except comments) begins with a keyword in brackets. Comments (if any ) usually begin in the second line right after [CHEMFILE] keyword and are preceded by a semi-colon. The following is a short description of the items that can be found in an AL2 file.

General Features

Field description:

[CHEMFILE] V100 { n }:

                [CHEMFILE]      - denotes the beginning of AL2 file;
                V100            - version number;
                { n }           - number of molecules in a file


[MOLECULE] { n } { m }  { MolType }  { nAA } {MolName}:

                [MOLECULE]      - beginning of the molecule;
                { n }           - molecule ordinal number in a file;
                { m }           - number of atoms in a current molecule;
                { MolType }     - molecule type. 
                                  It can be one of :
                                  UNKNOWN, 
                                  SMALL,
                                  FRAGMENT,
                                  PROTEIN,
                                  PEPTIDE,
                                  HETGROUP,
                                  WATER
                { nAA }         - number of AminoAcids if MolType = PROTEIN
                {MolName}       - Molecule name (NOT the file name).


[A] {n} {m} {S} {AT} {AC} {X} {Y} {Z} {nb} {nob bt} {nob bt} ... 
                [A]             - This keyword begins atom description;
                {n}             - Atom ordinal number in a molecule;
                {m}             - Atom number;
                {S}             - Atom symbol;
                {AT}            - Atom type;
                {AC}            - Atom charge;
                {X}             - Atom X-coordinate;
                {Y}             - Atom Y-coordinate;
                {Z}             - Atom Z-coordinate;
                {nb}>           - number of "neighbors" of the atom;
                {nob bt}        - The neighbor's ordinal number (nob) and the bond type.
                                  Bond types can be ;
                                  "s"  - simple;       
                                  "d"  - double; 
                                  "t"  - triple;        					
                                  "a"  - aromatic;

[ENDM] 
                [ENDM]          - This keyword ends molecule description;
                {n}             - Ordinal number of the molecule that has been described;

Properties fields

In addition to all above-mentioned required fields, a molecule MAY contain various kinds of properties, that are contained in the [MOLECULE] - [ENDM] block;

Properties

[BF]    -       brutto formula;
[P]     -       contains (if any) 4 values: 
                Surface, 
                Ovality, 
                Volume, 
                Molecular Weight;
[EV]    -       Lumo, Homo
[EV1]   -       Eigenvalues (and one of them is Homo. 
                It is usually the last one)
[EV2]   -       Eigenvalues (and one of them is Lumo. 
                It is usually the first one)
[%]     -       Displays percentage of all the elements in a molecule;
[D]     -       Displays dipole
[EN1]   -       Displays: 
                Final Heat, 
                Total Energy, 
                Electric Energy, 
                CoreCore, 
                Ioniz.Potential
[EN2]   -       Displays: 
                Total Steric Energy, 
                Compression, 
                Bending, 
                Bend-Bend, 
                Stretch-Bend, 
                Vanderwaals 1,4 Energy
[EN3]   -       Displays: 
                Vanderwaals Other, 
                Totsional,
                Torsion-Stretch, 
                Dipole-Dipole, 
                Charge-Charge, 
                Charge-Dipole
[EN4]   -       Displays: 
                Energy, 
                Enthalpy, 
                Entropy, 
                Free Energy, 
                Heat of Capacity,
                Heat Of Formation;

View (rendering, labeling, etc.) FIELDS:

A molecule block may also contain labeling and rendering information. Here is a brief description. There may be some additional items in the [I] - string that are used internally by the program;

[I] { n } {*L} {*R} {Sl} {Sh}:
                [I]    - rendering parameters,  
                         i.e. how to show specific atom, labeling, rendering, selection...
                { n }  - Atom ordinal number.
                {*L }  - Labeling. 
                         May be one of the following:
                         0 - none, 
                         1 - Symbol, 
                         2 - Number and Symbol, 
                         3 - Number,
                         4 - Atom type, 
                         5 - Charge, 
                         6 - Chirality, 
                         7 - Build order,
                         8 - Build order and Symbol;
                {Sl}   - Selection.
                         May be one of the following:
                         U  - unselected, 
                         S  - selected, 
                         SS - special selected;
                {*R}   - Rendering. 
                         1 - Sticks, 
                         2 - Spheres, 
                         3 - Spheres and Sticks
                         4 - Balls and Sticks, 
                         5 - Disks, 
                         6 - Ribbons, 
                         7 - Tubes,
                         8 = Spheres (points);
                {Sh}   - Determines if to display or not rendering/labeling for a given atom. 
                         May be: 
                         Y (yes) - show rendering / labeling
                         N (no)  - don't show rendering / labeling;
Example of SMALL Molecule:

[CHEMFILE] V100 2
;1,2,4-TETRAMETHYLBENZENE
;E= -2.16 KCAL; E'=.082
;OPTIM W/ AM1
;THIS IS COMMENT
[MOLECULE] 1 21 SMALL 0 0
[A] 1 1 C Car -0.05857 -4.69577 -0.76877 -0.00000 3 2 a 6 a 7 s
[A] ...........................................................
[A] 21 21 H H 0.02775 -6.08475 2.04000 -0.90395 1 12 s
[I] 1 *1 *2 U Y 3 *2 U Y *2 U Y *2 U Y
[I] ...........................................................
[I] 21 *1 *2 U Y 1 *2 U Y
[ENDM] 1
[MOLECULE] 2 12 SMALL 0
................................................................
[ENDM] 2
[ENDFILE]
Example of PROTEIN Molecule:
[CHEMFILE] V100 1
[MOLECULE] 1 68 PROTEIN 4 MolName
[A] 1 1 H H/H - -5.99580 -3.62738 -2.13094 1 3 s 1
.............................................................
[A] 68 68 O O2/O -0.10000 2.18647 4.26944 1.21781 1 51 d 4
[AA] 1 A T ALA 1 - -8799 -8331 9000 0
[AA] 2 N T ASN 13 - -6025 176 9000 0
[AA] 3 R T ARG 27 - 4461 -2817 9000 0
[AA] 4 L T LEU 49 - 4567 -8065 9000 0
[ENDM] 1
[ENDFILE]
Example of PEPTIDE Molecule:

[CHEMFILE] V100 1
[MOLECULE] 1 68 PEPTIDE 0 Protein
[A] 1 1 H H - -6.29394 -4.72055 -2.13094 1 3 s 1
........................................................
[A] 68 68 O O2 -0.10000 1.88834 3.17627 1.21781 1 51 d 4
[FRAGLIB] 1 Protein -1 0,#874436248
[F] 1 0 0 1
[F] 2 1 0 1
[F] 3 2 0 1
[F] 4 3 0 1
[ENDM] 1
[ENDFILE]

Advanced Features

Advanced features are given rather briefly because many items are used internally by the program and are not supposed to be edited be the inexperienced user.

Protein Molecule

In addition, it contains information about amino acids.

Example: [AA] 1 A T ALA 1 - -8799 -8331 9000 0
Peptide Molecule

This is molecule built from a prior Protein molecule. In this case amino acids become fragments. So there is a reference to the pseudo fragment library. The other information is mostly used internally by the Alchemy.

Example:
[FRAGLIB] 1 Protein -1 0,#874436248
[F] 1 0 0 1
[F] 2 1 0 1
[F] 3 2 0 1
[F] 4 3 0 1
FragLib Molecule

This is molecule built from Fragment Libraries Components. It mainly contains reference to the fragment library from where separate fragments were obtained. The other information is mostly used internally by the Alchemy.

Example:

[FRAGLIB] 1 fragment
[F] 1 10 0 1
[F] 2 4 0 1