jmolApplet0 - Jmol 14.4.3

Computationally docked structures of congeneric ligands similar to BDBM14677. This Compound is an exact match to PDB HET ID 256 in crystal structure 1O4Q, and this crystal structure was used to guide the docking calculations.

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JSmol exec jmolApplet0 start applet null

Jmol JavaScript applet jmolApplet0__6673950544502834__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript true

AppletRegistry.checkIn(jmolApplet0__6673950544502834__)

vwrOptions:

{ "name":"jmolApplet0","allowJavaScript":true,"applet":true,"documentBase":"https://bindingdb.org/rwd/bind/surflex.jsp?HET=256&PDB=1O4Q","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__6673950544502834__","codePath":"https://bindingdb.org/rwd/bind/jmol-14.4.3_2016.03.02/j2s/","display":"jmolApplet0_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"6673950544502834","bgcolor":"#FFFFFF" }

setting document base to "https://bindingdb.org/rwd/bind/surflex.jsp?HET=256&PDB=1O4Q"

Jmol Version: 14.4.3_2016.03.02 2016-03-02 09:52

java.vendor: Java2Script (HTML5)

java.version: 2016-03-02 13:00:37 (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)

loadScript jmol-14.4.3_2016.03.02/j2s/core/corescript.z.js

Jmol getValue emulate null

defaults = "Jmol"

Jmol getValue boxbgcolor null

Jmol getValue bgcolor #FFFFFF

backgroundColor = "#FFFFFF"

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

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Jmol getValue script null

Jmol getValue loadInline null

Jmol getValue load null

Jmol applet jmolApplet0__6673950544502834__ ready

script 1 started

FileManager.getAtomSetCollectionFromFile(../../data/surflex/1O4Q_256/1O4Q.pdb)

FileManager opening url https://bindingdb.org/data/surflex/1O4Q_256/1O4Q.pdb

The Resolver thinks Pdb

loadScript jmol-14.4.3_2016.03.02/j2s/core/corebio.z.js

SIGNALING PROTEIN 15-JUN-03 XXXX

CRYSTAL STRUCTURE OF SH2 IN COMPLEX WITH RU79256.

Setting space group name to P 21 21 21

XXXX

Time for openFile(../../data/surflex/1O4Q_256/1O4Q.pdb): 393 ms

reading 1020 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 Jmol

1020 atoms created

ModelSet: autobonding; use autobond=false to not generate bonds automatically

SIGNALING PROTEIN 15-JUN-03 XXXX

CRYSTAL STRUCTURE OF SH2 IN COMPLEX WITH RU79256.

XXXX

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appendNew = true

FileManager.getAtomSetCollectionFromFile(../../data/surflex/1O4Q_256/1O4Q_ligand0.mol2)

FileManager opening url https://bindingdb.org/data/surflex/1O4Q_256/1O4Q_ligand0.mol2

The Resolver thinks Mol2

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loadScript jmol-14.4.3_2016.03.02/j2s/J/adapter/readers/more/ForceFieldReader.js

1O4Q_ligand0

Time for openFile(../../data/surflex/1O4Q_256/1O4Q_ligand0.mol2): 423 ms

reading 20 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

1 models in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

Default Van der Waals type for model set to Jmol

Default Van der Waals type for model set to Babel

20 atoms created

ModelSet: not autobonding; use forceAutobond=true to force automatic bond creation

2 models

FileManager.getAtomSetCollectionFromFile(../../data/surflex/1O4Q_256/1O4Q-results.mol2)

FileManager opening url https://bindingdb.org/data/surflex/1O4Q_256/1O4Q-results.mol2

The Resolver thinks Mol2

BindingDB_14677

Time for openFile(../../data/surflex/1O4Q_256/1O4Q-results.mol2): 132 ms

reading 20 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

1 models in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.

Default Van der Waals type for model set to Jmol

Default Van der Waals type for model set to Babel

20 atoms created

ModelSet: not autobonding; use forceAutobond=true to force automatic bond creation

3 models

1020 atoms selected

20 atoms selected

0 atoms selected

Script completed

Jmol script terminated

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Compound	Structure File	Surflex Score*	IC50(nM)
Protein 1O4Q
Reference 256, BDBM14677
BDBM14677	1O4Q-results_14677.mol2	4.3632	3200000

*Higher Surflex scores correspond to higher quality docked structures.
Crystal structure of 256 from the 1O4Q is used as reference for docking the others.
CSV file for this table; mol2 file for the ligands.
Docked with Surflex v2710. Full input and output files are here.
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