(Modeling proteins) (Chymotrypsin Mechanism: Step 1, Step 2, Step 3, Step 4, Step 5, Step 6)

Transition state between Steps 3 and 5 of Chymotrypsin Mechanism

  (PDB file) (ARC file)

The stationary point given here is not a transition state - it's a ground state geometry, but for a nonsense chemical system. The heat of formation is so high that it's obvious that this system is unrealistic. Toggle display all Toggle center picture Fit to screen Interesting parts: His57 Gly193 Asp194 Ser195 Trp252 Thr253 H2O Toggle spin Toggle stereo Console   Step 1 Step 2 Step 3 Step 4 Step 5 Step 6 Step 1           Step 2         Step 3       Step 4     Step 5   Step 6

Jmol._Canvas2D (Jmol) "jmolApplet0"[x] loadClass core.package loadClass java.lang.String loadClass core.package JSmol exec jmolApplet0 start applet null Jmol JavaScript applet jmolApplet0__166883757720289__ initializing Jmol getValue debug null Jmol getValue logLevel null Jmol getValue allowjavascript null AppletRegistry.checkIn(jmolApplet0__166883757720289__) nographics false nographics false headless false vwrOptions: { "name":"jmolApplet0","applet":true,"documentBase":"http://openmopac.net/manual/Step_3_5_Transition_state.html","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__166883757720289__","codePath":"http://openmopac.net/manual/../jsmol/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"166883757720289","bgcolor":"#C0C0C0" } setting document base to "http://openmopac.net/manual/Step_3_5_Transition_state.html" (C) 2015 Jmol Development Jmol Version: 14.4.0_2015.10.14 2015-10-14 19:01 java.vendor: Java2Script (HTML5) java.version: 2015-09-19 23:29:54 (JSmol/j2s) os.name: Mozilla/5.0 AppleWebKit/537.36 (KHTML, like Gecko; compatible; ClaudeBot/1.0; +claudebot@anthropic.com) Access: ALL memory: 0.0/0.0 processors available: 1 useCommandThread: false appletId:jmolApplet0 (signed) loadClass JS.ScriptManager Jmol getValue emulate null defaults = "Jmol" Jmol getValue boxbgcolor null Jmol getValue bgcolor #C0C0C0 backgroundColor = "#C0C0C0" Jmol getValue ANIMFRAMECallback null Jmol getValue APPLETREADYCallback Jmol._readyCallback APPLETREADYCallback = "Jmol._readyCallback" callback set for APPLETREADYCallback Jmol._readyCallback APPLETREADY Jmol getValue ATOMMOVEDCallback null Jmol getValue CLICKCallback null Jmol getValue DRAGDROPCallback null Jmol getValue ECHOCallback null Jmol getValue ERRORCallback null Jmol getValue EVALCallback null Jmol getValue HOVERCallback null Jmol getValue IMAGECallback null Jmol getValue LOADSTRUCTCallback null Jmol getValue MEASURECallback null Jmol getValue MESSAGECallback null Jmol getValue MINIMIZATIONCallback null Jmol getValue SERVICECallback null Jmol getValue PICKCallback null Jmol getValue RESIZECallback null Jmol getValue SCRIPTCallback null Jmol getValue SYNCCallback null Jmol getValue STRUCTUREMODIFIEDCallback null Jmol getValue doTranslate null language=en_US Jmol getValue popupMenu null Jmol getValue script null Jmol getValue loadInline null Jmol getValue load null Jmol applet jmolApplet0__166883757720289__ ready script 1 started      FileManager.getAtomSetCollectionFromFile(Step_3_5_Transition_state.pdb) FileManager opening url http://openmopac.net/manual/Step_3_5_Transition_state.pdb The Resolver thinks Pdb loadClass J.adapter.readers.pdb.PdbReader data-set: Step_3_5_transition_state_30p0_first Time for openFile(Step_3_5_Transition_state.pdb): 332 ms reading 4588 atoms ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false 1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them. Default Van der Waals type for model set to Babel 4588 atoms created ModelSet: autobonding; use autobond=false to not generate bonds automatically Jmol 14.4.0_2015.10.14 2015-10-14 19:01 DSSP analysis for model 1.1 - null      W. Kabsch and C. Sander, Biopolymers, vol 22, 1983, pp 2577-2637      We thank Wolfgang Kabsch and Chris Sander for writing the DSSP software, and we thank the CMBI for maintaining it to the extent that it was easy to re-engineer for our purposes. At this point in time, we make no guarantee that this code gives precisely the same analysis as the code available via license from CMBI at http://swift.cmbi.ru.nl/gv/dssp      All bioshapes have been deleted and must be regenerated. NOTE: Backbone amide hydrogen positions are present and will be ignored. Their positions will be approximated, as in standard DSSP analysis. Use SET dsspCalculateHydrogenAlways FALSE to not use this approximation.           data-set: Step_3_5_transition_state_30p0_first      measurementUnits = "angstroms" Standard Hbond calculation 897 hydrogen bonds loadClass JS.CmdExt 0 new bonds; 0 modified zoomLarge = false 4588 atoms hidden 4498 atoms hidden Script completed Jmol script terminated