jmolApplet0 - Jmol 14.4.3

Computationally docked structures of congeneric ligands similar to BDBM50263771. This Compound is an exact match to PDB HET ID BZD in crystal structure 2QNB, and this crystal structure was used to guide the docking calculations.

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

JSmol exec jmolApplet0 start applet null

Jmol JavaScript applet jmolApplet0__33321604536158__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript true

AppletRegistry.checkIn(jmolApplet0__33321604536158__)

vwrOptions:

{ "name":"jmolApplet0","allowJavaScript":true,"applet":true,"documentBase":"https://bindingdb.org/rwd/bind/surflex.jsp?HET=BZD&PDB=2QNB","platform":"J.awtjs2d.Platform","fullName":"jmolApplet0__33321604536158__","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":"33321604536158","bgcolor":"#FFFFFF" }

setting document base to "https://bindingdb.org/rwd/bind/surflex.jsp?HET=BZD&PDB=2QNB"

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

Jmol getValue popupMenu null

Jmol getValue script null

Jmol getValue loadInline null

Jmol getValue load null

Jmol applet jmolApplet0__33321604536158__ ready

script 1 started

FileManager.getAtomSetCollectionFromFile(../../data/surflex/2QNB_BZD/2QNB.pdb)

FileManager opening url https://bindingdb.org/data/surflex/2QNB_BZD/2QNB.pdb

The Resolver thinks Pdb

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

TRANSFERASE 18-JUL-07 XXXX

GLYCOGEN PHOSPHORYLASE B IN COMPLEX WITH N-BENZOYL-N'-BETA-

D-GLUCOPYRANOSYL UREA

Setting space group name to P 43 21 2

XXXX

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XXXX

Time for openFile(../../data/surflex/2QNB_BZD/2QNB.pdb): 2595 ms

reading 14008 atoms

ModelSet: haveSymmetry:false haveUnitcells:true haveFractionalCoord:false

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

model 1.1 alternative locations: AB

model 1.2 alternative locations: AB

Default Van der Waals type for model set to Jmol

14008 atoms created

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

TRANSFERASE 18-JUL-07 XXXX

GLYCOGEN PHOSPHORYLASE B IN COMPLEX WITH N-BENZOYL-N'-BETA-

D-GLUCOPYRANOSYL UREA

XXXX

2 models

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appendNew = true

FileManager.getAtomSetCollectionFromFile(../../data/surflex/2QNB_BZD/2QNB_ligand1.mol2)

FileManager opening url https://bindingdb.org/data/surflex/2QNB_BZD/2QNB_ligand1.mol2

The Resolver thinks Mol2

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

2QNB_ligand1

Time for openFile(../../data/surflex/2QNB_BZD/2QNB_ligand1.mol2): 1942 ms

reading 41 atoms

ModelSet: haveSymmetry:false haveUnitcells:true haveFractionalCoord:false

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

model 1.1 alternative locations: AB

model 1.2 alternative locations: AB

Default Van der Waals type for model set to Jmol

Default Van der Waals type for model set to Babel

41 atoms created

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

3 models

FileManager.getAtomSetCollectionFromFile(../../data/surflex/2QNB_BZD/2QNB-results.mol2)

FileManager opening url https://bindingdb.org/data/surflex/2QNB_BZD/2QNB-results.mol2

The Resolver thinks Mol2

BindingDB_50263770

Time for openFile(../../data/surflex/2QNB_BZD/2QNB-results.mol2): 464 ms

reading 207 atoms

ModelSet: haveSymmetry:false haveUnitcells:true haveFractionalCoord:false

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

model 1.1 alternative locations: AB

model 1.2 alternative locations: AB

Default Van der Waals type for model set to Jmol

Default Van der Waals type for model set to Babel

207 atoms created

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

8 models

7004 atoms selected

41 atoms selected

0 atoms selected

Script completed

Jmol script terminated

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Compound	Structure File	Surflex Score*	Ki(nM)
Protein 2QNB
Reference BZD, BDBM50263771
BDBM50263770	2QNB-results_50263770.mol2	7.5548	305000;370000
BDBM50263771	2QNB-results_50263771.mol2	3.4482	4600
BDBM50263773	2QNB-results_50263773.mol2	3.6193	350
BDBM50295845	2QNB-results_50295845.mol2	3.3698	6000
BDBM50295846	2QNB-results_50295846.mol2	4.0957	6300

*Higher Surflex scores correspond to higher quality docked structures.
Crystal structure of BZD from the 2QNB 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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