{"id":"https://openalex.org/W2069344005","doi":"https://doi.org/10.1021/ci200595n","title":"PDB Ligand Conformational Energies Calculated Quantum-Mechanically","display_name":"PDB Ligand Conformational Energies Calculated Quantum-Mechanically","publication_year":2012,"publication_date":"2012-02-06","ids":{"openalex":"https://openalex.org/W2069344005","doi":"https://doi.org/10.1021/ci200595n","mag":"2069344005","pmid":"https://pubmed.ncbi.nlm.nih.gov/22303903"},"language":"en","primary_location":{"id":"doi:10.1021/ci200595n","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci200595n","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7491702","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5048549754","display_name":"Markus Sitzmann","orcid":null},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Markus Sitzmann","raw_affiliation_strings":["Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health , DHHS, NCI-Frederick, 376 Boyles Street, Frederick, Maryland 21702, USA"],"affiliations":[{"raw_affiliation_string":"Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health , DHHS, NCI-Frederick, 376 Boyles Street, Frederick, Maryland 21702, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008453767","display_name":"Iwona E. Weidlich","orcid":"https://orcid.org/0009-0004-5361-9090"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Iwona E. Weidlich","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070477116","display_name":"Igor Filippov","orcid":"https://orcid.org/0000-0003-2282-7773"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Igor V. Filippov","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063235026","display_name":"Chenzhong Liao","orcid":"https://orcid.org/0000-0001-7080-1768"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Chenzhong Liao","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064073801","display_name":"Megan L. Peach","orcid":"https://orcid.org/0000-0002-4290-5268"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Megan L. Peach","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110246499","display_name":"Wolf\u2010Dietrich Ihlenfeldt","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Wolf-Dietrich Ihlenfeldt","raw_affiliation_strings":["Xemistry GmbH, Hainholzweg\r11, D-61462 K\u00f6nigstein, Germany"],"affiliations":[{"raw_affiliation_string":"Xemistry GmbH, Hainholzweg\r11, D-61462 K\u00f6nigstein, Germany","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085943341","display_name":"Rajeshri G. Karki","orcid":"https://orcid.org/0000-0003-2210-5789"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Rajeshri G. Karki","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071993987","display_name":"Yu. V. Borodina","orcid":"https://orcid.org/0000-0002-6990-8354"},"institutions":[{"id":"https://openalex.org/I4210109390","display_name":"National Center for Biotechnology Information","ror":"https://ror.org/02meqm098","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I2800548410","https://openalex.org/I4210109390"]},{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yulia V. Borodina","raw_affiliation_strings":["National Center for Biotechnology Information, U.S.\rNational Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda Maryland 20894,\rUnited States","National Center for Biotechnology Information, U.S.#R#National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda Maryland 20894,#R#United States"],"affiliations":[{"raw_affiliation_string":"National Center for Biotechnology Information, U.S.\rNational Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda Maryland 20894,\rUnited States","institution_ids":["https://openalex.org/I4210109390","https://openalex.org/I1299303238"]},{"raw_affiliation_string":"National Center for Biotechnology Information, U.S.#R#National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda Maryland 20894,#R#United States","institution_ids":["https://openalex.org/I4210109390","https://openalex.org/I1299303238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069426753","display_name":"Ra\u00fal E. Cachau","orcid":"https://orcid.org/0000-0001-9260-2102"},"institutions":[{"id":"https://openalex.org/I4210140884","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210140884"]},{"id":"https://openalex.org/I880747138","display_name":"Science Applications International Corporation (United States)","ror":"https://ror.org/00zv91802","country_code":"US","type":"company","lineage":["https://openalex.org/I880747138"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Raul E. Cachau","raw_affiliation_strings":["Advanced\rStructure Analysis Collaboratory, Information Systems Program, SAIC-Frederick,\rInc., National Cancer Institute at Frederick, Frederick, Maryland 21702, United States","Advanced#R#Structure Analysis Collaboratory, Information Systems Program, SAIC-Frederick,#R#Inc., National Cancer Institute at Frederick, Frederick, Maryland 21702, United States"],"affiliations":[{"raw_affiliation_string":"Advanced\rStructure Analysis Collaboratory, Information Systems Program, SAIC-Frederick,\rInc., National Cancer Institute at Frederick, Frederick, Maryland 21702, United States","institution_ids":["https://openalex.org/I880747138","https://openalex.org/I4210140884"]},{"raw_affiliation_string":"Advanced#R#Structure Analysis Collaboratory, Information Systems Program, SAIC-Frederick,#R#Inc., National Cancer Institute at Frederick, Frederick, Maryland 21702, United States","institution_ids":["https://openalex.org/I880747138","https://openalex.org/I4210140884"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5078864876","display_name":"Marc C. Nicklaus","orcid":"https://orcid.org/0000-0002-4775-7030"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Marc C. Nicklaus","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5048549754"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":2.2716,"has_fulltext":false,"cited_by_count":64,"citation_normalized_percentile":{"value":0.88684266,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"52","issue":"3","first_page":"739","last_page":"756"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10163","display_name":"Metal complexes synthesis and properties","score":0.9995999932289124,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T10163","display_name":"Metal complexes synthesis and properties","score":0.9995999932289124,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T11747","display_name":"Metal-Catalyzed Oxygenation Mechanisms","score":0.9983000159263611,"subfield":{"id":"https://openalex.org/subfields/1604","display_name":"Inorganic Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9977999925613403,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/protein-data-bank","display_name":"Protein Data Bank (RCSB PDB)","score":0.7303914427757263},{"id":"https://openalex.org/keywords/quantum-chemical","display_name":"Quantum chemical","score":0.6301642656326294},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.6016657948493958},{"id":"https://openalex.org/keywords/quantum","display_name":"Quantum","score":0.5433801412582397},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.4189107120037079},{"id":"https://openalex.org/keywords/crystallography","display_name":"Crystallography","score":0.3918006122112274},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.34181010723114014},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.31916967034339905},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.2688741087913513},{"id":"https://openalex.org/keywords/quantum-mechanics","display_name":"Quantum mechanics","score":0.16035035252571106},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.11329269409179688},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.10203090310096741},{"id":"https://openalex.org/keywords/organic-chemistry","display_name":"Organic chemistry","score":0.06104514002799988}],"concepts":[{"id":"https://openalex.org/C65556437","wikidata":"https://www.wikidata.org/wiki/Q766195","display_name":"Protein Data Bank (RCSB PDB)","level":2,"score":0.7303914427757263},{"id":"https://openalex.org/C2991951333","wikidata":"https://www.wikidata.org/wiki/Q188403","display_name":"Quantum chemical","level":3,"score":0.6301642656326294},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.6016657948493958},{"id":"https://openalex.org/C84114770","wikidata":"https://www.wikidata.org/wiki/Q46344","display_name":"Quantum","level":2,"score":0.5433801412582397},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.4189107120037079},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.3918006122112274},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.34181010723114014},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.31916967034339905},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.2688741087913513},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.16035035252571106},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.11329269409179688},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.10203090310096741},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.06104514002799988},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008968","descriptor_name":"Molecular Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011789","descriptor_name":"Quantum Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011789","descriptor_name":"Quantum Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011789","descriptor_name":"Quantum Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011789","descriptor_name":"Quantum Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011789","descriptor_name":"Quantum Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012997","descriptor_name":"Solvents","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012997","descriptor_name":"Solvents","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012997","descriptor_name":"Solvents","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012997","descriptor_name":"Solvents","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012997","descriptor_name":"Solvents","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018360","descriptor_name":"Crystallography, X-Ray","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018360","descriptor_name":"Crystallography, X-Ray","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018360","descriptor_name":"Crystallography, X-Ray","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018360","descriptor_name":"Crystallography, X-Ray","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018360","descriptor_name":"Crystallography, X-Ray","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1021/ci200595n","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci200595n","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:22303903","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22303903","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of chemical information and modeling","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:7491702","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7491702","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:7491702","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7491702","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"},"sustainable_development_goals":[{"display_name":"Affordable and clean energy","score":0.7099999785423279,"id":"https://metadata.un.org/sdg/7"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":60,"referenced_works":["https://openalex.org/W75072218","https://openalex.org/W143162329","https://openalex.org/W197413318","https://openalex.org/W1532613204","https://openalex.org/W1532848864","https://openalex.org/W1972558086","https://openalex.org/W1976798012","https://openalex.org/W1979914800","https://openalex.org/W1993046136","https://openalex.org/W1994857170","https://openalex.org/W1996295408","https://openalex.org/W1997151511","https://openalex.org/W2013083986","https://openalex.org/W2014238068","https://openalex.org/W2016168739","https://openalex.org/W2016455326","https://openalex.org/W2020429677","https://openalex.org/W2020770089","https://openalex.org/W2020983121","https://openalex.org/W2022108141","https://openalex.org/W2022418973","https://openalex.org/W2022946510","https://openalex.org/W2023242541","https://openalex.org/W2024534366","https://openalex.org/W2032097283","https://openalex.org/W2033852744","https://openalex.org/W2037790004","https://openalex.org/W2038597284","https://openalex.org/W2038840577","https://openalex.org/W2040244904","https://openalex.org/W2042129725","https://openalex.org/W2044038786","https://openalex.org/W2045873232","https://openalex.org/W2047161516","https://openalex.org/W2047651561","https://openalex.org/W2051872583","https://openalex.org/W2056572719","https://openalex.org/W2062291001","https://openalex.org/W2077467665","https://openalex.org/W2078374001","https://openalex.org/W2083221543","https://openalex.org/W2087359404","https://openalex.org/W2087894985","https://openalex.org/W2090338420","https://openalex.org/W2090469584","https://openalex.org/W2097186436","https://openalex.org/W2109415161","https://openalex.org/W2116426967","https://openalex.org/W2117699404","https://openalex.org/W2124026197","https://openalex.org/W2131639373","https://openalex.org/W2141773967","https://openalex.org/W2145355174","https://openalex.org/W2146465875","https://openalex.org/W2148694319","https://openalex.org/W2151694463","https://openalex.org/W2168941972","https://openalex.org/W2209568211","https://openalex.org/W2210622668","https://openalex.org/W2949387234"],"related_works":["https://openalex.org/W1980758437","https://openalex.org/W1970435430","https://openalex.org/W4387064608","https://openalex.org/W1966980303","https://openalex.org/W2006933535","https://openalex.org/W2949251425","https://openalex.org/W4383219987","https://openalex.org/W2987260751","https://openalex.org/W4391841267","https://openalex.org/W3013403514"],"abstract_inverted_index":{"We":[0,121,289],"present":[1],"here":[2],"a":[3,87,113,123,143,316],"greatly":[4],"updated":[5],"version":[6,67],"of":[7,15,36,47,68,73,78,90,99,107,115,126,129,135,152,177,193,211,222,229,231],"an":[8,339],"earlier":[9],"study":[10],"on":[11,38],"the":[12,19,34,65,69,74,83,132,138,173,179,186,201,223,261,271,294,308,323,327,332],"conformational":[13,181],"energies":[14,234,244],"protein-ligand":[16],"complexes":[17],"in":[18,64,82,188,341],"Protein":[20],"Data":[21],"Bank":[22],"(PDB)":[23],"[Nicklaus":[24],"et":[25],"al.":[26],"Bioorg.":[27],"Med.":[28],"Chem.":[29],"1995,":[30],"3,":[31],"411-428],":[32],"with":[33,137,248,255,270,293],"goal":[35],"improving":[37],"all":[39,79,178,190],"possible":[40,180],"aspects":[41],"such":[42,259,275],"as":[43,260,276],"number":[44,228],"and":[45,53,103,142,200,220,251,267,284],"selection":[46],"ligand":[48,61,91,272],"instances,":[49],"energy":[50,145,157,183,205,300],"calculations":[51,292],"performed,":[52],"additional":[54],"analyses":[55],"conducted.":[56],"Starting":[57],"from":[58],"about":[59,116],"357,000":[60],"instances":[62,81,92],"deposited":[63],"2008":[66],"Ligand":[70],"Expo":[71],"database":[72],"experimental":[75],"3D":[76],"coordinates":[77],"small-molecule":[80],"PDB,":[84],"we":[85],"created":[86],"\"high-quality\"":[88],"subset":[89],"by":[93],"various":[94],"filtering":[95],"steps":[96],"including":[97],"application":[98],"crystallographic":[100,224,256],"quality":[101,257],"criteria":[102],"structural":[104],"unambiguousness.":[105],"Submission":[106],"640":[108],"Gaussian":[109],"03":[110],"jobs":[111],"yielded":[112,299],"set":[114,141],"415":[117],"successfully":[118],"concluded":[119],"runs.":[120],"used":[122],"stepwise":[124],"optimization":[125,154],"internal":[127,191],"degrees":[128,192],"freedom":[130,194],"at":[131,147,238,326],"DFT":[133],"level":[134,330],"theory":[136],"B3LYP/6-31G(d)":[139],"basis":[140],"single-point":[144],"calculation":[146],"B3LYP/6-311++G(3df,2p)":[148],"after":[149],"each":[150],"round":[151],"(partial)":[153],"to":[155,160,213,338],"separate":[156],"changes":[158,167],"due":[159],"bond":[161,165],"length":[162],"stretches":[163],"vs":[164,168],"angle":[166],"torsion":[169],"changes.":[170],"Even":[171],"for":[172],"most":[174],"\"conservative\"":[175],"choice":[176],"energies-the":[182],"difference":[184],"between":[185],"conformation":[187,325],"which":[189,298],"except":[195],"torsions":[196],"have":[197],"been":[198],"optimized":[199,203],"fully":[202],"conformer-significant":[204],"values":[206],"were":[207,235,303],"found.":[208],"The":[209,243],"range":[210],"0":[212],"~25":[214],"kcal/mol":[215],"was":[216],"populated":[217],"quite":[218],"evenly":[219],"independently":[221],"resolution.":[225],"A":[226],"smaller":[227],"\"outliers\"":[230],"yet":[232],"higher":[233],"seen":[236],"only":[237],"resolutions":[239],"above":[240],"1.3":[241],"\u00c5.":[242],"showed":[245],"some":[246],"correlation":[247,286],"molecular":[249,328],"size":[250],"flexibility":[252],"but":[253,312],"not":[254,314],"metrics":[258,274],"Cruickshank":[262],"diffraction-component":[263],"precision":[264],"index":[265],"(DPI)":[266],"R(free)-R,":[268],"or":[269],"instance-specific":[273],"occupancy-weighted":[277],"B-factor":[278],"(OWAB),":[279],"real-space":[280,285],"R":[281],"factor":[282],"(RSR),":[283],"coefficient":[287],"(RSCC).":[288],"repeated":[290],"these":[291],"solvent":[295],"model":[296],"IEFPCM,":[297],"differences":[301],"that":[302],"generally":[304],"somewhat":[305],"lower":[306],"than":[307],"corresponding":[309],"vacuum":[310],"results":[311],"did":[313],"produce":[315],"qualitatively":[317],"different":[318],"picture.":[319],"Torsional":[320],"sampling":[321],"around":[322],"crystal":[324],"mechanics":[329],"using":[331],"MMFF94s":[333],"force":[334],"field":[335],"typically":[336],"led":[337],"increase":[340],"energy.":[342]},"counts_by_year":[{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":9},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":8},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":6},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":4},{"year":2012,"cited_by_count":4}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}