DOI: 10.5281/zenodo.17993963
title: GALP Binding-Site Outputs and Folded Adsorbate Probability Distributions

description: This dataset contains the binding-site outputs generated using the in-house GALP code, together with the corresponding folded adsorption density profiles, for each experimental MOF and for each force-field/charge-method combination:UFF/REPEAT, UFF/DDEC6, UFF/MEPO-ML, DREIDING/REPEAT, DREIDING/DDEC6, and DREIDING/MEPO-ML.These datasets provide the final processed outputs used for the comparison between experimental and simulated binding sites in the paper “How well do conventional atomistic simulations predict adsorption binding sites in MOFs compared to experiment?”

The compressed archive titled "MOF-74_absorption_phases.tar.gz" contains the different phases for each of the MOF-74 MOFs (Co, Fe, Zn) presented in the study Queen et al. 2014, which compares the primary, secondary and tertiary sites discussed in our paper. For MOF-74 (Co, Fe, Zn), the RMSD values reported in Table 1 were computed using the Stage-2 adsorption phase for each metal, as provided in this archive.

Each compressed archive (UFF_REPEAT.tar.gz, UFF_DDEC6.tar.gz, UFF_MEPO-ML.tar.gz, DREIDING_REPEAT.tar.gz, DREIDING_DDEC6.tar.gz, DREIDING_MEPO-ML.tar.gz) contains one directory per MOF, with the following contents.



Note: The pseudoatom label “O” refers to the adsorbate CH4, which is modelled as a single-site molecule in GALP. This is a temporary internal naming convention and does not represent an oxygen atom.The pseudoatom “CM” corresponds to the center-of-mass of the guest “O”.The pseudoatom “Xex” represents the xenon guest atom (Xe).


Files



FIELD -- A file in DLPOLY FIELD format defining the force field and interaction parameters used for guest–host binding energy calculations.

GALA.inp -- Input file specifying the parameters used by the GALA code for binding-site extraction.

gala.log -- Log file recording all operations and diagnostics from the GALA run.

gala.err -- Error file recording any warning or errors that would be printed to the command line.

Prob_Guest_<guest>_Site_<site>_folded.cube -- Raw folded adsorbate probability distributions for each site in guest molecule.

GALA.cif -- CIF file containing only the extracted binding sites (the MOF framework is removed for RMSD calculations).

LIT.cif -- CIF file containing the experimentally determined binding sites (MOF structure removed for RMSD comparison).

STRUC.cif -- CIF file of the simulation-ready MOF structure, excluding any adsorbates.

*.vesta -- Visualization file combining LIT.cif, STRUC.cif, and GALA.cif, used for direct structural comparison of experimental and simulated binding sites. PNG files resulting from these visualizations may also be present.

rmsd_results.txt -- Output from the RMSD calculation between GALA.cif and LIT.cif.

s2_reordered.cif -- Reordered version of LIT.cif, matching the atom order of GALA.cif for 1:1 RMSD comparison.


Subdirectories



DL_poly_BS/ -- Directory generated by GALA to compute guest–host interaction energies for each binding site. Each subdirectory within DL_poly_BS contains DLPOLY input/output files for the framework and for each binding-site configuration.



The <framework>_<guest> subdirectory contains the framework with a randomly placed guest configuration, used to calculate the framework’s electrostatic reference energy. This energy is subtracted from each binding-site configuration energy in GALA. In this configuration, any guest charges are zeroed out. (See the GALP documentation for more details on the energy decomposition and binding energy calculation procedure.)



GALA_Output/ -- Directory generated by GALA containing the processed binding-site information



<guest>_binding_sites.cif -- Binding sites in CIF format, listed in order of decreasing occupancy

<guest>_binding_sites_fractional.xyz -- Fractional coordinates of all binding sites within the MOF unit cell

<guest>_gala_binding_sites.xyz -- Cartesian coordinates of each binding site, ordered by decreasing occupancy. This file also reports:



Total binding energy (Ebind)

Electrostatic contribution percentage (esp%)

van der Waals energy (Evdw)

Electrostatic energy (Eesp)

Relative occupancy (%) (occ)



<guest>_guest_information.xyz -- Contains guest information and binding sites listed in order of increasing occupancy, including absolute occupancy values and both fractional and Cartesian coordinates

<guest>_gala_local_maxima.cif -- Raw local maxima extracted from the probability map prior to any pruning or molecular fitting.




Directory Naming Convention

Each directory label encodes the key details of the corresponding simulation. The label is composed of sections separated by a double underscore (__). The directory labels closely match the MOF names reported in Table 1 of the main text, using filesystem-compatible formatting, following the convention:



<Structure_Name>__<Guest_Molecule>__<Temperature>__<Pressure>


Reference CSV File

The dataset also includes a reference index file, "Experimental_MOF_Dataset.csv", that provides a clear mapping between each directory and its corresponding reference DOI. The CSV additionally includes Boolean fields indicating which MOFs were used in different parts of the study:



In_Table1_Set: Systems included in the main binding-site comparison (Table 1).

In_RMSE_RMSD_Set: Systems used for RMSE and RMSD comparisons across force-field and charge-method combinations.

Has_Isotherms: Systems for which adsorption isotherms were computed and analyzed.