Ligand Chemistry

Molecule:

Distinct chemical molecule that is composed by atoms and bonds

Attributes:

• Code:
  The code of the molecule
• 3 letter code:
  The short 3 letter code of the molecule as referenced in PDB
  Search operators:
  • like: case insensitive matching. % or * will match for any zero or more characters and ? or . will match for any single character
• Extended Code:
  The extended code of the molecule uniquely identifying the variant. It includes the short code
• Molecule name:
  The standard molecule name
  Search operators:
  • like: This performs search using molecule names, systematic names or synonyms, case insensitive matching. % or * will match for any zero or more characters and ? or . will match for any single character
• All atoms:
  The total number of atoms
• All atoms except hydrogen:
  The total number of non-hydrogen atoms
• Formal charge
• Stereo smile:
  Representation of the molecule using the smile string notation that includes stereochemistry information
  Search operators:
  • exact stereo structure: the graph represented by the smile will be examined as a complete graph for an exact structure match, taking into consideration any stereo descriptors.Instead of a smile string you may also give the code of an existing small molecule
• Non stereo smile:
  Representation of the molecule using the smile string notation that does not include stereochemistry information
  Search operators:
  • has substructure: the molecules that contain the graph represented by the smile as a substructure, without taking into consideration any stereo descriptors.
  • is substructure of: the molecules that are contained as substructures in the graph represented by the smile, without taking into consideration any stereo descriptors.
  • exact structure: the graph represented by the smile will be examined as a complete graph for an exact structure match, without taking into consideration any stereo descriptors. Instead of a smile string you may also give the code of an existing small molecule
• Systematic name:
  The generated IUPAC systematic name
• IUPAC Inchi:
  The IUPAC Inchi string for the molecule (http://www.iupac.org/inchi/)
• Molecule details
• Formula:
  Chemical formula of the molecule listing the number of atoms from each chemical element
  Search operators:
  • formula range: formula range matching, example: N0 O5 C1-8 will return all molecules that have exactly 5 oxygens, 1 up to 8 carbons do not have nitrogens while they may have any number of other types of atoms
• Defined at:
  The initial date that the molecule was first defined
• Last modified at:
  The date that the molecule was last modified
• EBI name:
  The EBI defined name
• EBI Id:
  The EBI internal identifier
• Additional name:
  Externally defined name (defined by RCSB)
• Classification:
  Classification of molecules (defined by RCSB)
• Cas reg number:
  CAS Registry number
• Therapeutic category:
  Categorisation of molecules based on therapeutic category
• Merck Id:
  Merck Index Identifier
• Polymer topology:
  Topological classification of molecule based on its possible status in the polymer (i.e. free, start, linking, substructure)
• Polymer code:
  The types of polymers that the molecule is used for
• Polymer sub type:
  The sub types of the molecule in the polymer
• Hetgroup type:
  Hetgroup type (defined by RCSB)
• Superceded by:
  The current molecule is identical and has been superceded by that molecule
• Parent:
  The current molecule has as non-standard parent that molecule
• Topological variant:
  The current molecule is a topological variant of that molecule

Relations:

• Atoms:
  The atoms that compose the molecule
• Bonds:
  The bonds between atoms of the molecule
• Coordinates:
  All available sets of coordinates of atoms of the molecule
• References in macromolecules:
  The macromolecules where this molecule is referenced
• Energy types:
  All available sets of energy types of atoms of the molecule
• Synonyms:
  Synonyms of the molecule
• Images of molecule:
  Additional images of the molecule
• Web links:
  Additional web references of the molecule
• CSSR References:
  References in the CSSR database
• Chemical groups:
  Chemical groups that the molecules belong
• From depositions:
  Depositions that were used to define the molecule
• Rings:
  Rings of atoms in molecule
• Planes:
  Planes of atoms in molecule
• Classification

Atom of molecule:

Atom of a chemical element, that composes a molecule

Attributes:

• Atom name in the molecule:
  The EBI standard atom name that solves all the PDB name problems (i.e. always start with element name)
• EBI Ordering:
  The EBI standard ordering of the atom. Atoms should be listed in this order in any reference of the molecule
• PDB name:
  The atom name as it is defined in PDB. References of the atom in PDB format will use this name
• PDB Ordering:
  The ordering of the atom as was defined in the PDB file that it was used for its definition
• Atom stereochemistry:
  The stereocenter indicator denoting the chirality of the atom. R means that substituents circulate clockwise (order by lowest priority) and S counter clockwise
• Element symbol:
  The standard one or two character symbol of the element of the atom
• Is leaving atom:
  Flag denoting that this is a possible leaving atom
• Is ring atom:
  Flag denoting that this atom belongs at least in one ring
• Charge:
  Charge of the atom
• Incomplete valence:
  The incomplete valence of the atom (number of missing hydrogens). This is only used for non-free molecules.
• X coordinate:
  The standard idealised X coordinate of the atom.
• Y coordinate:
  The standard idealised Y coordinate of the atom.
• Z coordinate:
  The standard idealised Z coordinate of the atom.

Relations:

• Has bonds in molecule:
  Bonds of the atom.
• Chirality order:
  Order of substituents of a chiral atom.
• Energy types:
  Energy types of the atom for different libraries
• Of molecule

Chemical bond:

A bond between two atoms of the molecule

Attributes:

• First atom:
  The standard name of the first atom
• Second atom:
  The standard name of the second atom
• Bond order:
  The numerical bond order.
• Bond order type:
  The enumerated bond order (i.e. single, double).
• Bond aromaticity:
  The bond type for aromaticity. Aromatic bonds are modeled as single or double having aromatic bond type
• Bond length:
  The length of the bond determined by the distance of the 2 atoms is space based on the default atom coordinates
• Bond stereochemistry:
  The stereoisomer indicator for the bond. E means that biggest priority substituents are on the same side and Z that are not

Relations:

Coordinates of molecule atoms:

The coordinates of the atom. This is a different entity because atoms may have more than one set of coordinates for different libraries (i.e. PDB, idealised etc)

Attributes:

• Library:
  The library that defines these coordinates for the atom
• Atom name:
  The standard atom name
• Element symbol:
  The standard one or two character symbol of the element of the atom
• X coordinate:
  The X coordinate in 3D space
• Y coordinate:
  The Y coordinate in 3D space
• Z coordinate:
  The Z coordinate in 3D space

Relations:

Chirality:

The Chirality ordering of the substituents of a stereocenter

Attributes:

• Chiral atom:
  The chiral atom name
• First atom:
  The first in priority atom name
• Second atom:
  The second in priority atom name
• Third atom:
  The third in priority atom name
• Volume sign:
  The sign of the chirality (+ clockwise, - anticlockwise)

Relations:

Molecule synonym:

Molecule synonyms

Attributes:

• Serial number:
  Prioritises the synonyms of a molecule
• Code:
  The standard code of the molecule
• Synonym:
  The synonym of the molecule

Relations:

Molecule images:

Additional molecule images

Attributes:

• File name
• Details:
  Details of this image

Relations:

Molecule web links:

Web links with information about the molecule

Attributes:

• URL
• Details:
  Details about the link
• Serial number:
  Prioritisation of the links
• Image file name:
  Image of the molecule on the link

Relations:

CSSR References:

References in CSSR Chemical Database Service at Daresbury. The databank is compiled by the Cambridge Crystallographic Data Centre (CCDC)

Attributes:

• CCDC Id:
  Cambridge Crystallographic Data Centre identifier
• CSSR Id:
  CSSR identifier
• Reference:
  The actual reference

Relations:

Atom energy types:

Energy type classification of the atom for a specific library. There are many classifications of atoms based on different energy type sets (libraries)

Attributes:

• Energy type:
  Energy type name
• CCP4 energy type:
  CCP4 Energy type name
• CNS energy type:
  CNS Energy type name
• Library:
  The library that the energy type belongs in
• Molecule:
  The code of the molecule
• Atom name:
  The standard name of the atom
• Template:
  The template that defines the energy type. It is an encoding of an atoms environment based on a molecule subgraph specification
  Search operators:
  • like: case insensitive matching. % or * will match for any zero or more characters and ? or . will match for any single character
• Template instance:
  The template is a specification that contains wildcards and catch-all elements. The template instance provides the actual environment of the atom as this was found in this specific molecule
  Search operators:
  • like: case insensitive matching. % or * will match for any zero or more characters and ? or . will match for any single character
• Examples:
  Textual description of examples of molecules where this energy type can be found
  Search operators:
  • like: case insensitive matching. % or * will match for any zero or more characters and ? or . will match for any single character
• Partial charge:
  The exact partial charge as was calculated for the specific instance of the energy type for this atom in this molecule
• Library Charge:
  The partial charge for atoms for this energy type as this is defined in the library
• Mass:
  The mass for atoms for this energy type as this is defined in the library
• DW Radius:
  The van der Waals radius for atoms of this energy type as this is defined in the library
• DWH Radius:
  The van der Waals radius for hydrogens atoms of this energy type as this is defined in the library

Relations:

• Of library
• Of atom
• Of energy type

Defining depositions:

Depositions that were used as a source for defining the molecule. It does not contain all references of molecules in depositions

Attributes:

• Accession code:
  Accession code of the defining deposition
• Code:
  Molecule code
• Coordinates loaded:
  Flag denoting if the deposition was used as source for coordinates for the molecule
• Coordinates released at:
  The date that the coordinates were loaded

Relations:

• of molecule

Chemical Groups:

Chemical groups that a molecule belongs in

Attributes:

• Code:
  Molecule code
• Chemical group:
  The chemical group name

Relations:

• of molecule

Molecule Classification:

Classification of molecules based on generic structural characteristics

Attributes:

• Class name
  Search operators:
  • like: case insensitive matching. % or * will match for any zero or more characters and ? or . will match for any single character

Relations:

• Found in molecules

References in macromolecules:

The macromolecules that reference each ligand

Attributes:

• Ligand code:
  The code of the referenced molecule
  Search operators:
  • like: case insensitive matching. % or * will match for any zero or more characters and ? or . will match for any single character
• PDB entry ID:
  The PDB id of the entry where the molecule is referenced
  Search operators:
  • like: case insensitive matching. % or * will match for any zero or more characters and ? or . will match for any single character
• Number of occurrences:
  The number of occurrences of the molecule in the macromolecule
  Search operators:
  • between: is in the range of the input. For example: between 2.4 3.1
• Type:
  The way the ligand was used in the macromolecule

Relations:

• of molecule
• of deposition

Rings of molecule:

The rings that the molecule contains

Attributes:

• Molecule code:
  Standard molecule code
• Ring serial:
  Serial number of the ring
• Ring type:
  The type of the ring (i.e. aromatic)

Relations:

• of molecule
• Atoms:
  Atoms of the ring

Atoms of the ring:

The atoms of the molecule that this ring contains

Attributes:

• Molecule code:
  Standard name of the molecule
• Ring serial:
  Serial number of the ring
• Atom name:
  Standard name of the atom in the molecule

Relations:

• of ring
• atom

Plane of molecule:

The planes that the molecule contains

Attributes:

• Molecule code:
  Standard molecule code
• Serial:
  Serial number of the plane in the molecule
• Plane type:
  The method used for identifying the plane (from structure or from actual coordinates)
• Number of atoms:
  The number of atoms the plane contains
• Number of non-hydrogen atoms:
  The number of non-hydrogen atoms the plane contains
• A factor:
  Factor a of the plane equation (a*x+b*y+c=0)
• B factor:
  Factor b of the plane equation (a*x+b*y+c=0)
• C factor:
  Factor c of the plane equation (a*x+b*y+c=0)

Relations:

• of molecule
• Atoms:
  Atoms of the plane

Atoms of the plane:

The atoms of the molecule that this plane contains

Attributes:

• Atom name:
  Standard name of the atom in the molecule
• Serial:
  Serial number of the plane in the molecule
• Distance:
  Distance of the atom from the plane

Relations:

• of plane
• atom