.. tip::
    All input files can be downloaded: :download:`Files <https://zhjun-sci.com/qbics/input_library/keywords-mol.tar.gz>`.

mol and mol2
=================

.. contents::
   :local:

The keyword ``mol`` gives the initial molecular coordinates. For some tasks like transition state search, another structure has to be given in option ``mol2``.

Explicit XYZ Coordinates
-------------------------

You can simply give XYZ coordinates in Angstrom:

.. code-block:: bash
     :linenos:

     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 give the XYZ file name (path can be included if necessary):

.. code-block:: bash
      :linenos:

      mol
        ../mols/water.xyz
      end
     
     
PDB File Name
-------------------------

You can give the PDB file name (path can be included if necessary):

.. code-block:: bash
      :linenos:

      mol
        proteins/ala3.pdb
      end

Theoretical Background
-------------------------

XYZ File Format
^^^^^^^^^^^^^^^^^^^^^^

An XYZ file is a text format employed to depict the geometry of a molecule. Its structure is delineated as such:

#. Number of atoms: The initial line consists of an integer representing the total number of atoms in the molecule.
#. Comment line: The second line typically comprises a comment that can be utilized to provide information regarding the molecule.
#. Each subsequent line contains the elemental symbol of an atom and its corresponding Cartesian coordinates (x, y, z), typically expressed in Angstroms.

.. code-block:: bash
   :linenos:

   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 textual format widely used to store three-dimensional structural information of biological macromolecules, such as proteins and nucleic acids. Each PDB file contains detailed data, including the molecule's name, source species, sequence, secondary structure, and crystallographic parameters. In Qbics, only **atomic records** is used, i.e., lines starting with ``ATOM`` and ``HETATM``.

Each atomic record in a PDB file provides specific information about an atom:

#. **Record Type**: Indicates the type of record, such as ``ATOM`` or ``HETATM``.
#. **Atom Serial Number**: A unique identifier for each atom.
#. **Atom Name**: The element symbol and possibly additional characters to distinguish atoms within the same residue.
#. **Residue Name**: The name of the residue (e.g., ``ALA`` for alanine).
#. **Residue Sequence Number**: The position of the residue in the sequence.
#. **X, Y, Z Coordinates**: The atom's coordinates in Angstrom.
#. **Occupancy**: The fraction of the molecule present at this position. This is a crystallographic parameter NOT used by Qbics.
#. **Temperature Factor (B-factor)**: Indicates the atomic displacement or mobility. This is a crystallographic parameter NOT used by Qbics.
#. **Element Symbol**: The chemical element symbol.

.. code-block:: bash
   :linenos:
   
   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  

.. warning::

    Some software generates a PDB file format **without** "Element Symbol" column. In this case, Qbics will guess the element symbol based on the "Atom Name" column. However, this is dangerous and should be avoided since "Atom Name" is in principle arbitrary and can be misleading. For example, ``CLA`` can mean either chlorine or carbon atom in different PDB files. Therefore, **it is recommended to always include the "Element Symbol" column in the PDB file for Qbics calculations.**

Input Examples
-------------------------

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

Search the transition state using NEB at xTB level of theory, with reactant and product structure giving in ``mol`` and ``mol2``, respectively:

.. code-block:: bash
    :linenos:
    :caption: mol-1.inp
    
    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, strucutures defined in ``mol`` and ``mol2`` are shown below:

.. figure:: figs/mol-1.jpg