{"id":"https://openalex.org/W2005514110","doi":"https://doi.org/10.1021/ci100466h","title":"Short Nonbonded Contact Distances in Organic Molecules and Their Use as Atom-Clash Criteria in Conformer Validation and Searching","display_name":"Short Nonbonded Contact Distances in Organic Molecules and Their Use as Atom-Clash Criteria in Conformer Validation and Searching","publication_year":2011,"publication_date":"2011-03-18","ids":{"openalex":"https://openalex.org/W2005514110","doi":"https://doi.org/10.1021/ci100466h","mag":"2005514110","pmid":"https://pubmed.ncbi.nlm.nih.gov/21417266"},"language":"en","primary_location":{"id":"doi:10.1021/ci100466h","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci100466h","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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102905535","display_name":"Robin Taylor","orcid":"https://orcid.org/0000-0002-0391-2609"},"institutions":[{"id":"https://openalex.org/I141584323","display_name":"University of Hertfordshire","ror":"https://ror.org/0267vjk41","country_code":"GB","type":"education","lineage":["https://openalex.org/I141584323"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Robin Taylor","raw_affiliation_strings":["Taylor Cheminformatics Software, 54 Sherfield Avenue, Rickmansworth, Hertfordshire WD3 1NL, U.K"],"affiliations":[{"raw_affiliation_string":"Taylor Cheminformatics Software, 54 Sherfield Avenue, Rickmansworth, Hertfordshire WD3 1NL, U.K","institution_ids":["https://openalex.org/I141584323"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5102905535"],"corresponding_institution_ids":["https://openalex.org/I141584323"],"apc_list":null,"apc_paid":null,"fwci":3.1384,"has_fulltext":false,"cited_by_count":15,"citation_normalized_percentile":{"value":0.91384132,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"51","issue":"4","first_page":"897","last_page":"908"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10798","display_name":"Crystallography and molecular interactions","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1606","display_name":"Physical and Theoretical 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/T12852","display_name":"Chemical Thermodynamics and Molecular Structure","score":0.9983000159263611,"subfield":{"id":"https://openalex.org/subfields/1605","display_name":"Organic Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/intramolecular-force","display_name":"Intramolecular force","score":0.7959039211273193},{"id":"https://openalex.org/keywords/conformational-isomerism","display_name":"Conformational isomerism","score":0.7827526330947876},{"id":"https://openalex.org/keywords/van-der-waals-force","display_name":"van der Waals force","score":0.6433509588241577},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.6380553245544434},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.637299120426178},{"id":"https://openalex.org/keywords/ring","display_name":"Ring (chemistry)","score":0.564142107963562},{"id":"https://openalex.org/keywords/molecular-geometry","display_name":"Molecular geometry","score":0.5096945762634277},{"id":"https://openalex.org/keywords/atom","display_name":"Atom (system on chip)","score":0.5012021064758301},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.4806981682777405},{"id":"https://openalex.org/keywords/crystallography","display_name":"Crystallography","score":0.42265334725379944},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.24670487642288208},{"id":"https://openalex.org/keywords/organic-chemistry","display_name":"Organic chemistry","score":0.08090826869010925}],"concepts":[{"id":"https://openalex.org/C75079739","wikidata":"https://www.wikidata.org/wiki/Q1571801","display_name":"Intramolecular force","level":2,"score":0.7959039211273193},{"id":"https://openalex.org/C18705241","wikidata":"https://www.wikidata.org/wiki/Q1128023","display_name":"Conformational isomerism","level":3,"score":0.7827526330947876},{"id":"https://openalex.org/C126061179","wikidata":"https://www.wikidata.org/wiki/Q189627","display_name":"van der Waals force","level":3,"score":0.6433509588241577},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.6380553245544434},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.637299120426178},{"id":"https://openalex.org/C2780378348","wikidata":"https://www.wikidata.org/wiki/Q25351438","display_name":"Ring (chemistry)","level":2,"score":0.564142107963562},{"id":"https://openalex.org/C193547582","wikidata":"https://www.wikidata.org/wiki/Q911331","display_name":"Molecular geometry","level":3,"score":0.5096945762634277},{"id":"https://openalex.org/C58312451","wikidata":"https://www.wikidata.org/wiki/Q4817200","display_name":"Atom (system on chip)","level":2,"score":0.5012021064758301},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.4806981682777405},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.42265334725379944},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.24670487642288208},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.08090826869010925},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.0},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D006841","descriptor_name":"Hydrocarbons, Aromatic","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D006841","descriptor_name":"Hydrocarbons, Aromatic","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D006841","descriptor_name":"Hydrocarbons, Aromatic","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006860","descriptor_name":"Hydrogen Bonding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","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":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/ci100466h","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci100466h","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:21417266","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21417266","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}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":32,"referenced_works":["https://openalex.org/W1480654101","https://openalex.org/W1969585025","https://openalex.org/W1982441109","https://openalex.org/W1984220076","https://openalex.org/W1987398924","https://openalex.org/W1995850373","https://openalex.org/W1998691716","https://openalex.org/W1999118725","https://openalex.org/W2002755329","https://openalex.org/W2004343588","https://openalex.org/W2007459830","https://openalex.org/W2017702218","https://openalex.org/W2020770089","https://openalex.org/W2030841140","https://openalex.org/W2032842297","https://openalex.org/W2033127742","https://openalex.org/W2039709045","https://openalex.org/W2044038786","https://openalex.org/W2050449953","https://openalex.org/W2059028093","https://openalex.org/W2061776255","https://openalex.org/W2072537419","https://openalex.org/W2077467665","https://openalex.org/W2078374001","https://openalex.org/W2095026430","https://openalex.org/W2105976401","https://openalex.org/W2109415161","https://openalex.org/W2130479394","https://openalex.org/W2161239029","https://openalex.org/W2180271118","https://openalex.org/W2204230050","https://openalex.org/W4233278700"],"related_works":["https://openalex.org/W2023036309","https://openalex.org/W1972863456","https://openalex.org/W2089371831","https://openalex.org/W2052399476","https://openalex.org/W2810163160","https://openalex.org/W3083970380","https://openalex.org/W2037964119","https://openalex.org/W4220905048","https://openalex.org/W4385077663","https://openalex.org/W838464343"],"abstract_inverted_index":{"Short,":[0],"intramolecular":[1,254],"nonbonded":[2,92,191],"contact":[3],"distances":[4],"from":[5,13,87],"a":[6,76,154,224,244,272],"large":[7],"sample":[8],"of":[9,25,37,64,83,117,131,214,223,284],"organic":[10,85],"molecules":[11,86,206,228],"retrieved":[12],"the":[14,23,26,34,62,65,88,96,107,115,129,136,161,181,220,250,263,285],"Cambridge":[15],"Structural":[16],"Database":[17],"(CSD)":[18],"have":[19,90],"been":[20],"analyzed.":[21],"With":[22],"exception":[24],"element":[27],"pairs":[28],"N\u00b7\u00b7\u00b7S,":[29],"O\u00b7\u00b7\u00b7P,":[30],"O\u00b7\u00b7\u00b7S,":[31],"and":[32,99,147,247],"S\u00b7\u00b7\u00b7S,":[33],"first":[35,108],"percentiles":[36,73],"X\u00b7\u00b7\u00b7Y":[38],"distance":[39],"distributions":[40],"(X,":[41],"Y":[42],"=":[43],"C,":[44],"Br,":[45],"Cl,":[46],"F,":[47],"N,":[48],"O,":[49],"P,":[50],"S)":[51],"are":[52,74,177,234,267],"well":[53],"estimated":[54],"by":[55,160,198,243,262],"\u2211vdw":[56,60],"-0.5":[57],"\u00c5,":[58],"where":[59],"is":[61,158,166,202,259],"sum":[63],"Bondi":[66],"van":[67],"der":[68],"Waals":[69],"radii.":[70],"The":[71,257],"0.1th":[72,97],"typically":[75],"further":[77],"0.1":[78],"\u00c5":[79],"shorter.":[80],"Some":[81],"99%":[82],"well-refined":[84],"CSD":[89],"no":[91,100],"contacts":[93,104],"shorter":[94,105],"than":[95,102,106],"percentile":[98],"more":[101],"two":[103],"percentile.":[109],"This":[110,157,201],"can":[111,139],"be":[112,140,196,232],"used":[113,141],"as":[114,128],"basis":[116],"an":[118,215,277],"atom-clash":[119,289],"test":[120,138],"for":[121,205],"validating":[122],"less":[123],"precise":[124],"crystal-structure":[125],"data,":[126],"such":[127],"geometries":[130],"protein":[132],"ligands.":[133],"In":[134,183],"principle,":[135],"same":[137,221],"in":[142,153],"molecular":[143,170],"modeling":[144],"to":[145,188,211,231,252,270,276],"identify":[146],"filter":[148],"out":[149],"unacceptable":[150],"conformations":[151,185],"generated":[152],"conformational":[155],"search.":[156,182],"complicated":[159],"fact":[162,264],"that":[163,176,265,280],"conformer":[164],"generation":[165],"usually":[167],"performed":[168],"on":[169,219],"models":[171],"with":[172,249],"standard":[173],"bond":[174],"angles":[175],"not":[178],"relaxed":[179],"during":[180],"consequence,":[184],"often":[186],"appear":[187],"contain":[189],"untenable":[190],"contacts,":[192],"which":[193],"would,":[194],"however,":[195],"removed":[197],"bond-angle":[199],"relaxation.":[200],"particularly":[203,229],"likely":[204,230],"containing":[207,236],"conjugating":[208],"substituents":[209],"bonded":[210],"adjacent":[212],"atoms":[213],"aromatic":[216],"ring,":[217],"or":[218,238],"side":[222],"double":[225],"bond.":[226],"Other":[227],"affected":[233],"those":[235,248],"rings":[237],"other":[239],"bulky":[240],"groups":[241],"separated":[242],"single-atom":[245],"linkage,":[246],"capacity":[251],"form":[253],"hydrogen":[255],"bonds.":[256],"problem":[258],"greatly":[260],"ameliorated":[261],"there":[266],"many":[268],"ways":[269],"approximate":[271],"true":[273],"conformation,":[274],"leading":[275],"increased":[278],"probability":[279],"at":[281],"least":[282],"one":[283],"approximations":[286],"will":[287],"satisfy":[288],"criteria.":[290]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":4}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}