Introduction

CONFLEX is a program that performs conformation searches, host-ligand coordination searches, and crystal structure searches of organic molecules based on molecular mechanics simulations. Additionally, the program can predict normal vibrations, thermodynamic quantity, ultraviolet and visible light absorption spectrum, circular dichroic spectrum, and NMR coupling constant which are taking into conformational distribution.
This manual explains the various functions of CONFLEX through practical caluclations using existing organic molecules.

Table of Contents

1. How to execute CONFLEX
   • Input files
   • Execution from CONFLEX Interface (Windows/Mac/Linux)
   • Execution from command line (Windows)
   • Execution from command line (Linux)
   • Execution from command line (Mac)
2. Geometry optimization and vibrational analysis
   • Execution of geometry optimization and vibrational analysis
   • Output files
   • Visualization of calculation results
   • Calculation including solvent effects
   • Geometry optimization with constraints
3. AMBER force field calculation
4. Customize force field parameters
5. Conformation search
   • Execution of conformation search
   • Output files
   • Expansion of conformation search space
   • Visualization of calculation results
   • Conformation search with solvent effect
6. Conformer clustering
   • What is a conformer clustering ?
   • Clustering of all conformers of n-pentane
   • Clustering of all conformers of β-Glucose
7. Host-Ligand coordination search
   • Overview of search method
   • Stable coordinations of two acetic acid molecules
   • Coordination search of glucose and water molecules
8. In-Situ Orientation search
   • Orientation search of Phenol in α-Cyclodextrin
   • Orientation search of acetic acid between two other acetic acid molecules
9. Crystal structure optimization
   • Definition of energy
   • Types of crystal structure optimization
   • Execution of crystal structure optimization
     • In the case of using CMF file
     • In the case of using CIF file
     • In the case of using MOL file
   • Structure optimization with constrains
     • Constraint by harmonic potential
     • Constraints of structure and position of specified molecule
   • Output files
   • Visualization of calculation results
   • Available space groups
   • Available X-ray sources
10. Crystal structure search
    • Crystal structure search from a structural formula
    • Crystal structure search for a multi component system
    • Crystal structure search using PXRD data
    • Output files
    • Visualization of search results
    • Restart of crystal structure search
    • Unavailable space groups
11. Grouping of crystal structures
12. Crystal surface analysis
    • Calculation of specific surface energy
      • How to perform the calculation
      • Calculation results
    • Calculation of interaction energy of molecule on/in crystal plane
      • How to perform the calculation
      • Calculation results
      • Regarding the alphabetical notation next to the energy
      • Difference of “IN” and “ON” in “Molecular State:”
      • How to use “Crystal Plane Translation”
      • How to use “Set Base Molecule”
13. Solvation free energy calculation
    • Definition of solvation free energy
    • Neutral glycine trimer
    • Calculation results
14. Calculation of water/octanol partition coefficient
    • Calculation of log P value
    • Relationship of log P value and solvation free energy
    • Calculation of log P value
    • Calculation results
15. NMR coupling constant calculation
    • Vicinal proton-proton coupling constant (³J_HH) calculation using Karplus-Imai equation
      • NMR-³J_HH calculation of initial and optimized structures
      • NMR-³J_HH calculation of multiple conformational isomers
    • ³J coupling constant calculation using Karplus equation and customized parameters
      • Conformation search and ³J calculation of β-D-Glucose
16. CD/UV spectrum analysis
    • Conformation search
    • CD/UV spectrum calculation
17. Amino acid residue substitution function
18. Dynamics simulation using the dynamic reaction coordinate (DRC) method
    • Overview of DRC method
    • Example calculation: α-D-Glucose + H₂O
19. Optimization and conformation search using Gaussian program
    • Environment setting
    • Conformation search of propylene glycol using B3LYP/6-31G(d) calculation
    • Calculation setting of Gaussian program using a file
    • Execution of Gaussian using a job scheduler (Linux)
    • Temporarily enable Gaussian preferences