{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,31]],"date-time":"2026-08-31T08:20:09Z","timestamp":1788164409324,"version":"build-2803163510"},"reference-count":31,"publisher":"American Chemical Society (ACS)","issue":"16","license":[{"start":{"date-parts":[[2027,8,12]],"date-time":"2027-08-12T00:00:00Z","timestamp":1818028800000},"content-version":"vor","delay-in-days":365,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"},{"start":{"date-parts":[[2026,8,12]],"date-time":"2026-08-12T00:00:00Z","timestamp":1786492800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2026,8,12]],"date-time":"2026-08-12T00:00:00Z","timestamp":1786492800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2026,8,12]],"date-time":"2026-08-12T00:00:00Z","timestamp":1786492800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-045"}],"funder":[{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["528562393 - FIP 26"],"award-info":[{"award-number":["528562393 - FIP 26"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100014690","name":"Ministerium f?r Kultur und Wissenschaft des Landes Nordrhein-Westfalen","doi-asserted-by":"publisher","award":["FKZ 005-2302-0023"],"award-info":[{"award-number":["FKZ 005-2302-0023"]}],"id":[{"id":"10.13039\/501100014690","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,8,24]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The Restrained Electrostatic Potential (RESP) method is widely used to derive electrostatic parameters for molecular mechanics-based models. However, conventional nuclei-centered charge models can struggle to reproduce anisotropic features such as halogen \u03c3-holes and electron lone-pair regions. Herein, an extension of the Psi4-compatible Python resp implementation of Alenaizen et al. is presented that enables partial atomic charge fitting to user-defined extra point sites represented as massless dummy particles. This reengineering introduces an INI-based configuration layer, a revised driver.py that propagates extra point sites through grid\/ESP handling, an updated espfit.py engine that continues to support multiconformer fitting, and an updated extras.py that includes functions for adding extra point centers to the fitting. Also introduced are functions for computing RMSE and RRMSE metrics, along with support for the recently developed van der Waals radii by Charry and Tkatchenko. Several examples are provided that demonstrate Stage 1 and Stage 2 fitting involving a single conformation, multiple conformations, as well as the generation and use of multiple spatial orientations. The resulting workflow is transparent, reproducible, and enables the development of both nuclei- and off-centered electrostatic models for molecular mechanics-based simulations.<\/jats:p>","DOI":"10.1021\/acs.jcim.6c02302","type":"journal-article","created":{"date-parts":[[2026,8,12]],"date-time":"2026-08-12T16:04:31Z","timestamp":1786550671000},"page":"9735-9742","source":"Crossref","is-referenced-by-count":0,"title":["Extending the Python RESP Framework for Extra Point\nCharge Fitting"],"prefix":"10.1021","volume":"66","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4581-920X","authenticated-orcid":true,"given":"Karl N.","family":"Kirschner","sequence":"first","affiliation":[{"name":"Bonn-Rhein-Sieg University of Applied Sciences , , ,","place":["Sankt Augustin, Germany, 53757"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,8,12]]},"reference":[{"key":"2026083104120900800_cit1","doi-asserted-by":"publisher","first-page":"10269","DOI":"10.1021\/j100142a004","article-title":"A Well-behaved Electrostatic\nPotential Based Method Using Charge Restraints for Deriving Atomic\nCharges: The RESP Model","volume":"97","author":"Bayly","year":"1993","journal-title":"J. Phys. Chem. A"},{"key":"2026083104120900800_cit2","doi-asserted-by":"publisher","DOI":"10.1002\/qua.26035","article-title":"Python\nImplementation of the Restrained\nElectrostatic Potential Charge Model","volume":"120","author":"Alenaizan","year":"2020","journal-title":"Int. J.\nQuantum Chem."},{"key":"2026083104120900800_cit3","doi-asserted-by":"publisher","DOI":"10.1063\/5.0006002","article-title":"PSI4 1.4: Open-source\nSoftware for High-throughput Quantum Chemistry","volume":"152","author":"Smith","year":"2020","journal-title":"J. Chem. Phys."},{"key":"2026083104120900800_cit4","doi-asserted-by":"publisher","DOI":"10.21105\/joss.04100","article-title":"PsiRESP:\nCalculating RESP Charges with Psi4","volume":"7","author":"Wang","year":"2022","journal-title":"J. Open\nSource Software"},{"key":"2026083104120900800_cit5","doi-asserted-by":"publisher","first-page":"3654","DOI":"10.1021\/acs.jctc.2c00230","article-title":"PyRESP: A Program for\nElectrostatic Parameterizations of Additive and Induced Dipole Polarizable\nForce Fields","volume":"18","author":"Zhao","year":"2022","journal-title":"J. Chem. Theory Comput."},{"key":"2026083104120900800_cit6","doi-asserted-by":"publisher","first-page":"4251","DOI":"10.1021\/acs.jcim.5c00041","article-title":"PyPE_RESP:\nA Tool to Facilitate and Standardize Derivation of RESP Charges","volume":"65","author":"Lapsien","year":"2025","journal-title":"J. Chem. Inf. Model."},{"key":"2026083104120900800_cit7","unstructured":"Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Petersson, G. A.; Nakatsuji, H.; Li, X.; Caricato, M.; Marenich, A. V.; Bloino, J.; Janesko, B. G.; Gomperts, R.; Mennucci, B.; Hratchian, H. P.; Ortiz, J. V.; Izmaylov, A. F.; Sonnenberg, J. L.; Williams-Young, D.; Ding, F.; Lipparini, F.; Egidi, F.; Goings, J.; Peng, B.; Petrone, A.; Henderson, T.; Ranasinghe, D.; Zakrzewski, V. G.; Gao, J.; Rega, N.; Zheng, G.; Liang, W.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Vreven, T.; Throssell, K.; Montgomery, J. A., Jr.; Peralta, J. E.; Ogliaro, F.; Bearpark, M. J.; Heyd, J. J.; Brothers, E. N.; Kudin, K. N.; Staroverov, V. N.; Keith, T. A.; Kobayashi, R.; Normand, J.; Raghavachari, K.; Rendell, A. P.; Burant, J. C.; Iyengar, S. S.; Tomasi, J.; Cossi, M.; Millam, J. M.; Klene, M.; Adamo, C.; Cammi, R.; Ochterski, J. W.; Martin, R. L.; Morokuma, K.; Farkas, O.; Foresman, J. B.; Fox, D. J.\n          Gaussian 16 Revision\nC.01; Gaussian Inc.: Wallingford CT, 2016."},{"key":"2026083104120900800_cit8","doi-asserted-by":"publisher","first-page":"6183","DOI":"10.1021\/acs.jcim.3c01153","article-title":"AmberTools","volume":"63","author":"Case","year":"2023","journal-title":"J. Chem. Inf. Model."},{"key":"2026083104120900800_cit9","doi-asserted-by":"publisher","first-page":"3173","DOI":"10.1021\/acs.jcim.5c03200","article-title":"QUICK and Robust ESP and RESP Charges\nfor Computational\nBiochemistry: Open-Source GPU Implementation","volume":"66","author":"Tripathy","year":"2026","journal-title":"J. Chem. Inf. Model."},{"key":"2026083104120900800_cit10","volume-title":"QUICK-25.03","author":"Manathunga","year":"2025"},{"key":"2026083104120900800_cit11","doi-asserted-by":"publisher","first-page":"W511","DOI":"10.1093\/nar\/gkr288","article-title":"R.E.D.\nServer: A Web Service for Deriving RESP and ESP Charges and Building\nForce Field Libraries for New Molecules and Molecular Fragments","volume":"39","author":"Vanquelef","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2026083104120900800_cit12","doi-asserted-by":"publisher","first-page":"1325","DOI":"10.1021\/ct2008389","article-title":"On Extension of the Current Biomolecular Empirical Force Field for\nthe Description of Halogen Bonds","volume":"8","author":"Kola\u0301r\u030c","year":"2012","journal-title":"J. Chem. Theory\nComput."},{"key":"2026083104120900800_cit13","doi-asserted-by":"publisher","first-page":"4812","DOI":"10.1016\/j.bmc.2016.06.034","article-title":"Parametrization of Halogen Bonds\nin the CHARMM General Force Field: Improved Treatment of Ligand-protein\nInteractions","volume":"24","author":"Gutie\u0301rrez","year":"2016","journal-title":"Bioorg. Med. Chem."},{"key":"2026083104120900800_cit14","doi-asserted-by":"publisher","first-page":"89","DOI":"10.1016\/j.cplett.2018.09.052","article-title":"Halogen Bonding\nin the Framework of Classical Force Fields: The Case of Chlorine","volume":"712","author":"Franchini","year":"2018","journal-title":"Chem. Phys. Lett."},{"key":"2026083104120900800_cit15","doi-asserted-by":"publisher","first-page":"1083","DOI":"10.1021\/acs.jctc.7b01086","article-title":"Polarizable Empirical Force Field\nfor Halogen-Containing\nCompounds Based on the Classical Drude Oscillator","volume":"14","author":"Lin","year":"2018","journal-title":"J. Chem. Theory Comput."},{"key":"2026083104120900800_cit16","doi-asserted-by":"publisher","first-page":"5383","DOI":"10.1021\/acs.jctc.8b00278","article-title":"Biomolecular Simulations\nof Halogen Bonds with a GROMOS Force Field","volume":"14","author":"Nunes","year":"2018","journal-title":"J. Chem. Theory Comput."},{"key":"2026083104120900800_cit17","doi-asserted-by":"publisher","DOI":"10.1063\/5.0014280","article-title":"Automated\nParameterization of Quantum-mechanically\nDerived Force-fields Including Explicit Sigma Holes: A Pathway to\nEnergetic and Structural Features of Halogen Bonds in Gas and Condensed\nPhase","volume":"153","author":"Campetella","year":"2020","journal-title":"J. Chem. Phys."},{"key":"2026083104120900800_cit18","doi-asserted-by":"publisher","first-page":"573","DOI":"10.1016\/0301-0104(94)00310-6","article-title":"Multicentric Charges for the Accurate\nRepresentation of Electrostatic Interactions in Force-field Calculations\nfor Small Molecules","volume":"189","author":"Alema\u0301n","year":"1994","journal-title":"Chem. Phys."},{"key":"2026083104120900800_cit19","doi-asserted-by":"publisher","first-page":"1632","DOI":"10.1002\/(SICI)1096-987X(199710)18:133.0.CO;2-S","article-title":"Advancing beyond\nthe Atom-centered Model in Additive\nand Nonadditive Molecular Mechanics","volume":"18","author":"Dixon","year":"1997","journal-title":"J. Comput.\nChem."},{"key":"2026083104120900800_cit20","doi-asserted-by":"publisher","first-page":"1587","DOI":"10.1021\/ct600180x","article-title":"Atomic Level Anisotropy in the Electrostatic\nModeling of Lone Pairs for a Polarizable Force Field Based on the\nClassical Drude Oscillator","volume":"2","author":"Harder","year":"2006","journal-title":"J. Chem. Theory\nComput."},{"key":"2026083104120900800_cit21","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-017-16203-w","article-title":"Influences of Lone-pair\nElectrons on Directionality\nof Hydrogen Bonds Formed by Hydrophilic Amino Acid Side Chains in\nMolecular Dynamics Simulation","volume":"7","author":"Oroguchi","year":"2017","journal-title":"Sci. Rep."},{"key":"2026083104120900800_cit22","doi-asserted-by":"publisher","first-page":"3495","DOI":"10.1021\/acs.jctc.0c00976","article-title":"W-RESP: Well-Restrained\nElectrostatic Potential-Derived Charges. Revisiting the Charge Derivation\nModel","volume":"17","author":"Janec\u030cek","year":"2021","journal-title":"J. Chem. Theory Comput."},{"key":"2026083104120900800_cit23","doi-asserted-by":"publisher","first-page":"7464","DOI":"10.1021\/acs.jcim.3c01561","article-title":"Assessment of Halogen\nOff-Center Point-Charge Models\nUsing Explicit Solvent Simulations","volume":"63","author":"Fortuna","year":"2023","journal-title":"J. Chem.\nInf. Model."},{"key":"2026083104120900800_cit24","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1016\/j.fluid.2015.11.028","article-title":"Parametrization of Two-center Lennard-Jones Plus Point-quadrupole\nForce Field Models by Multicriteria Optimization","volume":"411","author":"Sto\u0308bener","year":"2016","journal-title":"Fluid Phase Equilib."},{"key":"2026083104120900800_cit25","doi-asserted-by":"publisher","first-page":"1159","DOI":"10.1021\/acs.jctc.8b00739","article-title":"Quadrupole Correction:\nFrom Molecular\nElectrostatic Potential to Free Energies of Halogen Bonding","volume":"15","author":"Titov","year":"2019","journal-title":"J. Chem. Theory Comput."},{"key":"2026083104120900800_cit26","doi-asserted-by":"publisher","first-page":"7469","DOI":"10.1021\/acs.jctc.4c00784","article-title":"van der Waals Radii of Free and Bonded\nAtoms from Hydrogen\n(z = 1) to Oganesson (z = 118)","volume":"20","author":"Charry","year":"2024","journal-title":"J. Chem. Theory\nComput."},{"key":"2026083104120900800_cit27","doi-asserted-by":"publisher","first-page":"304","DOI":"10.1002\/jcc.540020312","article-title":"Representation\nof the Molecular Electrostatic Potential\nby a Net Atomic Charge Model","volume":"2","author":"Cox","year":"1981","journal-title":"J. Comput. Chem."},{"key":"2026083104120900800_cit28","doi-asserted-by":"publisher","first-page":"431","DOI":"10.1002\/jcc.540110404","article-title":"Atomic Charges Derived\nfrom Semiempirical Methods","volume":"11","author":"Besler","year":"1990","journal-title":"J. Comput. Chem."},{"key":"2026083104120900800_cit29","doi-asserted-by":"publisher","first-page":"7821","DOI":"10.1039\/c0cp00111b","article-title":"The R.E.D.\nTools: Advances in RESP and ESP Charge Derivation and Force Field\nLibrary Building","volume":"12","author":"Dupradeau","year":"2010","journal-title":"Phys. Chem. Chem. Phys."},{"key":"2026083104120900800_cit30","doi-asserted-by":"publisher","first-page":"864","DOI":"10.1002\/jcc.26841","article-title":"The Effect\nof Off-center \u03c3-hole on the Atom-centered Partial\nCharges in Halogenated\nMolecules","volume":"43","author":"Leskourova\u0301","year":"2022","journal-title":"J. Comput. Chem."},{"key":"2026083104120900800_cit31","doi-asserted-by":"publisher","DOI":"10.1038\/s42004-020-0291-4","article-title":"Non-bonded Force Field Model with\nAdvanced Restrained Electrostatic Potential Charges (RESP2)","volume":"3","author":"Schauperl","year":"2020","journal-title":"Commun. Chem."}],"container-title":["Journal of Chemical Information and Modeling"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jcim.6c02302","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/jcisd8\/article-pdf\/66\/16\/9735\/66516126\/acs.jcim.6c02302.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pubs.acs.org\/jcisd8\/article-pdf\/66\/16\/9735\/66516126\/acs.jcim.6c02302.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,31]],"date-time":"2026-08-31T08:12:18Z","timestamp":1788163938000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/jcisd8\/article\/66\/16\/9735\/5253686\/Extending-the-Python-RESP-Framework-for-Extra"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,12]]},"references-count":31,"journal-issue":{"issue":"16","published-online":{"date-parts":[[2026,8,12]]},"published-print":{"date-parts":[[2026,8,24]]}},"URL":"https:\/\/doi.org\/10.1021\/acs.jcim.6c02302","relation":{"has-preprint":[{"id-type":"doi","id":"10.26434\/chemrxiv.15002675\/v2","asserted-by":"object"}]},"ISSN":["1549-9596","1549-960X"],"issn-type":[{"value":"1549-9596","type":"print"},{"value":"1549-960X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,12]]}}}