mol and mol2

The keyword mol provides the initial molecular coordinates.
For certain tasks, such as transition state searches, a second structure must be specified using the mol2 option.

Explicit XYZ Coordinates

You can simply provide XYZ coordinates in Ångström:

mol
    O   0.00000000000000      0.05011194954430      0.05011194954224
    H   0.00000000000000     -0.06080277603381      1.01069082652926
    H   0.00000000000000      1.01069082648951     -0.06080277607149
end

XYZ File Name

You can provide the name of the XYZ file (including the path, if necessary):

mol
  ../mols/water.xyz
end

PDB File Name

You can provide the name of the PDB file (including the path, if necessary):

mol
  proteins/ala3.pdb
end

Theoretical Background

XYZ File Format

An XYZ file is a text format used to describe the geometry of a molecule. Its structure is as follows:
1. Number of atoms: The first line contains an integer representing the total number of atoms in the molecule.
2. Comment line: The second line is typically a comment, which may provide additional information about the molecule.
3. Atomic coordinates: Each subsequent line includes the element symbol of an atom followed by its Cartesian coordinates (x, y, z), typically expressed in Ångströms.

3
water molecule
O    0.000000    0.000000    0.116863
H    0.000000    0.764949   -0.467453
H    0.000000   -0.764949   -0.467453

PDB File Format

The Protein Data Bank (PDB) file format is a comprehensive text format widely used to store three-dimensional structural information of biological macromolecules, such as proteins and nucleic acids.
Each PDB file contains detailed information, including the molecule's name, source species, sequence, secondary structure, and crystallographic parameters.
In Qbics, only atomic records are used—specifically, lines beginning with ATOM and HETATM.

Each atomic record in a PDB file provides detailed information about an atom:
1. Record Type: Indicates the type of record, such as ATOM or HETATM.
2. Atom Serial Number: A unique identifier for each atom.
3. Atom Name: The element symbol, possibly with additional characters to distinguish atoms within the same residue.
4. Residue Name: The name of the residue (e.g., ALA for alanine).
5. Residue Sequence Number: The position of the residue in the sequence.
6. X, Y, Z Coordinates: The atom’s Cartesian coordinates in Ångströms.
7. Occupancy: The fraction of the molecule present at this position (a crystallographic parameter not used by Qbics).
8. Temperature Factor (B-factor): Indicates atomic displacement or mobility (also not used by Qbics).
9. Element Symbol: The chemical element symbol.

ATOM      1  N   SER    10       9.630  40.740  60.970  0.00  0.00           N  
ATOM      2  HT1 SER    10       9.940  40.000  61.630  0.00  0.00           H  
ATOM      3  HT2 SER    10       8.910  41.340  61.420  0.00  0.00           H  
ATOM      4  HT3 SER    10      10.450  41.360  60.880  0.00  0.00           H  
ATOM      5  CA  SER    10       9.180  40.240  59.600  0.00  0.00           C  
ATOM      6  HA  SER    10       9.510  39.210  59.580  0.00  0.00           H  

Input Examples

Example: Transition State Search Using mol and mol2 to Specify Reactant and Product

Perform a transition state search using the NEB method at the xTB level of theory, with the reactant and product structures specified in mol and mol2, respectively:

opt
    type       neb
    num_images 10
    neb_k      0.01
end

mol # N-C-H
    C 0. 0.  0.289
    N 0. 0. -1.128
    H 0. 0.  1.099
end

mol2 # H-N-C
   C  0.403 -0.780 -0.690
   N -0.021  0.041  0.036
   H -0.382  0.739  0.654
end

xtb
    chrg 0
end

task
    opt xtb
end

In this file, the structures defined by mol and mol2 are shown below: