jmolApplet0 - Jmol 14.4.3

Computationally docked structures of congeneric ligands similar to BDBM50009672. This Compound is an exact match to PDB HET ID SAH in crystal structure 1JQD, 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__059813107906378__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript true

AppletRegistry.checkIn(jmolApplet0__059813107906378__)

vwrOptions:

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

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)

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processors available: 1

useCommandThread: false

appletId:jmolApplet0 (signed)

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Jmol getValue bgcolor #FFFFFF

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Jmol getValue ANIMFRAMECallback null

Jmol getValue APPLETREADYCallback Jmol._readyCallback

APPLETREADYCallback = "Jmol._readyCallback"

callback set for APPLETREADYCallback Jmol._readyCallback APPLETREADY

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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

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Jmol applet jmolApplet0__059813107906378__ ready

script 1 started

FileManager.getAtomSetCollectionFromFile(../../data/surflex/1JQD_SAH/1JQD.pdb)

FileManager opening url https://bindingdb.org/data/surflex/1JQD_SAH/1JQD.pdb

The Resolver thinks Pdb

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TRANSFERASE 06-AUG-01 XXXX

CRYSTAL STRUCTURE ANALYSIS OF HUMAN HISTAMINE

METHYLTRANSFERASE (THR105 POLYMORPHIC VARIANT) COMPLEXED

WITH ADOHCY AND HISTAMINE

Setting space group name to P 6

XXXX

Time for openFile(../../data/surflex/1JQD_SAH/1JQD.pdb): 782 ms

reading 2407 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

2407 atoms created

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

TRANSFERASE 06-AUG-01 XXXX

CRYSTAL STRUCTURE ANALYSIS OF HUMAN HISTAMINE

METHYLTRANSFERASE (THR105 POLYMORPHIC VARIANT) COMPLEXED

WITH ADOHCY AND HISTAMINE

XXXX

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appendNew = true

FileManager.getAtomSetCollectionFromFile(../../data/surflex/1JQD_SAH/1JQD_ligand0.mol2)

FileManager opening url https://bindingdb.org/data/surflex/1JQD_SAH/1JQD_ligand0.mol2

The Resolver thinks Mol2

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1JQD_ligand0

Time for openFile(../../data/surflex/1JQD_SAH/1JQD_ligand0.mol2): 500 ms

reading 46 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

46 atoms created

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

2 models

FileManager.getAtomSetCollectionFromFile(../../data/surflex/1JQD_SAH/1JQD-results.mol2)

FileManager opening url https://bindingdb.org/data/surflex/1JQD_SAH/1JQD-results.mol2

The Resolver thinks Mol2

BindingDB_50009672

Time for openFile(../../data/surflex/1JQD_SAH/1JQD-results.mol2): 202 ms

reading 94 atoms

ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false

2 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

94 atoms created

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

4 models

2407 atoms selected

46 atoms selected

0 atoms selected

Script completed

Jmol script terminated

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Compound	Structure File	Surflex Score*	Ki(nM)
Protein 1JQD
Reference SAH, BDBM50009672
BDBM50009672	1JQD-results_50009672.mol2	11.7461	18100
BDBM50026331	1JQD-results_50026331.mol2	11.2711	10400

*Higher Surflex scores correspond to higher quality docked structures.
Crystal structure of SAH from the 1JQD 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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