mol and mol2

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:

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):

mol
  ../mols/water.xyz
end

PDB File Name

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

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:

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

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:

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 and possibly 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 coordinates in Angstrom.
7. Occupancy: The fraction of the molecule present at this position. This is a crystallographic parameter NOT used by Qbics.
8. Temperature Factor (B-factor): Indicates the atomic displacement or mobility. This is a crystallographic parameter 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 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:

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: