LigandBox

2020/03/26

Web Site: http://www.mypresto5.com/ligandbox/cgi-bin/index.cgi?LANG=en
FTP Site: ftp://ftp.biosciencedbc.jp/archive/ligandbox/

The 'ready-to-dock' database of small chemical compounds, for virtual drug screening on computer docking studies.

README Content

  1. Database Component
  2. Data Description
  3. License
  4. Update History
  5. Literature
  6. Contact address

1. Database Component

  1. README
  2. Compounds of Namiki (Single Conformer)
  3. Compounds of Namiki
  4. Compounds of PDB (Single Conformer)
  5. Compounds of PDB
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2. Data Description

2.1 README

Data name README
Description of data contents HTML file to describe "LigandBox" data.
File README_e.html (English)
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2.2 Compounds of Namiki (Single Conformer)

Data name Compounds of Namiki (Single Conformer)
Description of data contents

Extracted single conformer data from each compound provided by Namiki Shoji Co.,Ltd. (Oct. 2017). They are assembled on a file in Mol2 format. Comments in Mol2 format are extracted to another CSV file. They can be searched in simple search.
File ligandbox_namiki_single.zip (CSV format) (174MB)
Namiki_Single.mol2.gz (Mol2 format) (6GB)

Data items are the following:
Data itemDescription
LIGANDBOX_ID ID in LigandBox
SINGLE "ture" if the entry is extacted as single conformer, else "false".
SOURCE Source of this compound
SOURCE_ID ID in the source
MOLECULAR_FORMULA Molecular formula
MOLECULAR_WEIGHT Molecular weight
MOLECULAR_CHARGE Molecular charge
NUM_OF_DONOR Number of hydrogen bond donors
NUM_OF_ACCEPTOR Number of hydrogen bond acceptors
NUM_OF_CHIRAL_ATOMS Number of chiral atoms
TPSA Topological Polar Surface Area
HOMO Highest Occupied Molecular Orbital energy
LUMO Lowest Unoccupied Molecular Orbital energy
LOGP Partition coefficient
LOGS Solubility
MOL2_FILE URL of mol2 file for the entry
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2.3 Compounds of Namiki

Data name Compounds of Namiki
Description of data contents

Compounds provided by Namiki Shoji Co.,Ltd. (Oct. 2017). All conformers are included in it. They are assembled on a file in Mol2 format. Comments in Mol2 format are extracted to another CSV file. They can be searched in simple search.
File ligandbox_namiki_multiple.zip (CSV format) (199MB)
Namiki_Multiple.mol2.gz (Mol2 format) (8.8GB)

Data items are the following:
Data itemDescription
LIGANDBOX_ID ID in LigandBox
SINGLE "TRUE" if the entry is extacted as single conformer, else "FALSE".
SOURCE Source of this compound
SOURCE_ID ID in the source
MOLECULAR_FORMULA Molecular formula
MOLECULAR_WEIGHT Molecular weight
MOLECULAR_CHARGE Molecular charge
NUM_OF_DONOR Number of hydrogen bond donors
NUM_OF_ACCEPTOR Number of hydrogen bond acceptors
NUM_OF_CHIRAL_ATOMS Number of chiral atoms
TPSA Topological Polar Surface Area
HOMO Highest Occupied Molecular Orbital energy
LUMO Lowest Unoccupied Molecular Orbital energy
LOGP Partition coefficient
LOGS Solubility
MOL2_FILE URL of mol2 file for the entry
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2.4 Compounds of PDB (Single Conformer)

Data name Compounds of PDB (Single Conformer)
Description of data contents

Extracted single conformer data from each compound in PDB. They are assembled on a file in Mol2 format. Comments in Mol2 format are extracted to another CSV file. They can be searched in simple search.
File ligandbox_pdb_single.zip (CSV format) (888KB)
PDB_Single.mol2.gz (Mol2 format) (31MB)

Data items are the following:
Data itemDescription
LIGANDBOX_ID ID in LigandBox
SINGLE "true" if the entry is extacted as single conformer, else "false".
SOURCE Source of this compound
SOURCE_ID ID in the source
MOLECULAR_FORMULA Molecular formula
MOLECULAR_WEIGHT Molecular weight
MOLECULAR_CHARGE Molecular charge
NUM_OF_DONOR Number of hydrogen bond donors
NUM_OF_ACCEPTOR Number of hydrogen bond acceptors
NUM_OF_CHIRAL_ATOMS Number of chiral atoms
TPSA Topological Polar Surface Area
HOMO Highest Occupied Molecular Orbital energy
LUMO Lowest Unoccupied Molecular Orbital energy
LOGP Partition coefficient
LOGS Solubility
MOL2_FILE URL of mol2 file for the entry
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2.5 Compounds of PDB

Data name Compounds of PDB
Description of data contents

Compounds in PDB. All conformers are included in it. They are assembled on a file in Mol2 format. Comments in Mol2 format are extracted to another CSV file. They can be searched in simple search.
File ligandbox_pdb_multiple.zip (CSV format) (1.5MB)
PDB_Multiple.mol2.gz (Mol2 format) (102MB)

Data items are the following:
Data itemDescription
LIGANDBOX_ID ID in LigandBox
SINGLE "TRUE" if the entry is extacted as single conformer, else "FALSE".
SOURCE Source of this compound
SOURCE_ID ID in the source
MOLECULAR_FORMULA Molecular formula
MOLECULAR_WEIGHT Molecular weight
MOLECULAR_CHARGE Molecular charge
NUM_OF_DONOR Number of hydrogen bond donors
NUM_OF_ACCEPTOR Number of hydrogen bond acceptors
NUM_OF_CHIRAL_ATOMS Number of chiral atoms
TPSA Topological Polar Surface Area
HOMO Highest Occupied Molecular Orbital energy
LUMO Lowest Unoccupied Molecular Orbital energy
LOGP Partition coefficient
LOGS Solubility
MOL2_FILE URL of mol2 file for the entry
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3. License

Last updated : 2020/03/16

You may use this database in compliance with the terms and conditions of the license described below. The license specifies the license terms regarding the use of this database and the requirements you must follow in using this database.

Creative Commons License

The license for this database is specified in the Creative Commons Attribution-Share Alike 4.0 International.
If you use data from this database, please be sure attribute this database as follows: "LigandBox © Technology Research Association for Next generation natural products chemistry licensed under CC Attribution-Share Alike 4.0 International".

The summary of the Creative Commons Attribution-Share Alike 4.0 International is found here.

With regard to this database, you are licensed to:

  1. freely access part or whole of this database, and acquire data;
  2. freely redistribute part or whole of the data from this database; and
  3. freely create and distribute database and other adapted materials based on part or whole of the data from this database,

under the license, as long as you comply with the following conditions:

  1. You must attribute this database in the manner specified by the author or licensor when distributing part or whole of this database or any adapted material.
  2. You must distribute any adapted material based on part or whole of the data from this database under CC Attribution-Share Alike 4.0 (or later), or CC Attribution-Share Alike Compatible License (the list is here).
  3. You need to contact the Licensor shown below to request a license for use of this database or any part thereof not licensed under the license.

https://www.mypresto5.jp/en/contact/

About Providing Links to This Database

You can freely provide links to all contents in this database. But, contents might be changed without notice.

 

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4. Update History

DateUpdate contents
2020/03/26 Simple search tables of single and multiple conformer are integrated. URL of mol2 files are changed.
2020/03/16 LigandBox English archive site is opened.
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5. Literature

Kawabata,T., Sugihara, Y., Fukunishi, Y., Nakamura, H.
LigandBox : a database for 3D structures of chemical compounds.
BIOPHYSICS,9,113-121.
PMID: 27493549

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6. Contact address

When you have any question about "LigandBox", contact the following:

https://www.mypresto5.jp/contact/

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