PDBe database documentation

Entities of Ligands

The entities that belong to a specific mart
Entity Details: A=Number of attributes of the Entity
R=Number of relations of the Entity
T=Name of the database table
I=Approximation of the number of instances of the entity

Ligands Consistent and enriched library of ligands, small molecules and monomers that are referred as residues and hetgroups in any PDB entry
Ligand A:62, R:31, T:CHEM_COMP, I:0	Distinct chemical molecule that is composed by atoms and bonds
Atom of ligand A:27, R:15, T:CHEM_ATOM, I:0	Atom of a chemical element, that composes a molecule
Ligand bond A:14, R:3, T:CHEM_BOND, I:0	A bond between two atoms of the molecule
Coordinates of molecule atoms A:15, R:4, T:CHEM_MODEL_COORD, I:0	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)
Chirality A:16, R:5, T:CHEM_CHIRALITY, I:0	The Chirality ordering of the substituents of a stereocenter
Molecule synonym A:6, R:1, T:COMP_SYNONYM, I:0	Molecule synonyms
Molecule images A:6, R:1, T:COMP_IMG_FILE, I:0	Additional molecule images
Molecule web links A:7, R:1, T:COMP_URL, I:0	Web links with information about the molecule
CSSR References A:6, R:1, T:CSSR_REF_COMP, I:0	References in CSSR Chemical Database Service at Daresbury. The databank is compiled by the Cambridge Crystallographic Data Centre (CCDC) (http://cds.dl.ac.uk/cds/manuals/cssr.html)
Atom energy types A:18, R:6, T:ATOM_ENERGY_TYPE, I:0	Energy type classification of the atom for a specific library. There are many classifications of atoms based on different energy type sets (libraries)
Defining depositions A:7, R:1, T:HETGROUP, I:0	Depositions that were used as a source for defining the molecule. It does not contain all references of molecules in depositions
Chemical Groups A:4, R:1, T:CHEM_GROUP_MEMBERSHIP, I:0	Chemical groups that a molecule belongs in
References in macromolecules A:5, R:0, T:COMP_OCCURENCES, I:0	The macromolecules that reference each ligand
Rings of molecule A:5, R:2, T:CHEM_RING, I:0	The rings that the molecule contains
Atoms of the ring A:8, R:3, T:CHEM_RING_ATOM, I:0	The atoms of the molecule that this ring contains
Plane of molecule A:10, R:2, T:CHEM_PLANE, I:0	The planes that the molecule contains
Atoms of the plane A:9, R:3, T:CHEM_PLANE_ATOM, I:0	The atoms of the molecule that this plane contains
Atom Nomenclature A:8, R:2, T:ATOM_NOMENCLATURE, I:0	Different naming schemes for ligand atoms based on different standards and conventions, i.e. ANSIG (http://www-ccmr-nmr.bioc.cam.ac.uk/public/ANSIG/ansig.html)
Polymer Topology A:3, R:1, T:POLYMER_TOPOLOGY, I:0	Topology of a small molecule (ligand). Describes the position of the small molecule in a polymer chain. For bound molecules and ligands, only the free topology is available, but for aminoacids, nucleic-acids and other polymer components, all topological variants (like start, linking, free) are separately modeled.
Polymer Type A:4, R:1, T:POLYMER_TYPE, I:0	Type of the polymer that this small molecule forms (polyribonucleotide, polypeptide(D), polysaccharide(D) etc)
Formula A:4, R:1, T:FORMULA, I:0	A molecular formula is identical for all structular isomers of a ligand and is closely related with its weight, number of atoms etc
EBI Classification A:2, R:0, T:COMP_EBI_CLASS1, I:0	Primary classification of ligands and small molecules as defined at EBI
RCSB Classification A:2, R:0, T:COMP_RCSB_CLASS1, I:0	Primary classification of ligands and small molecules as defined at RCSB
Element A:8, R:3, T:ELEMENT, I:0	The periodic table of the chemical elements with usefull details about mass, atomic number, radius etc
EBI 2nd Classification A:2, R:0, T:COMP_EBI_CLASS2, I:0	Secondary classification of ligands and small molecules as defined at EBI

Attributes/Relations of Ligands Entities

The attributes and relations that belong to a specific entity
Attribute Details: Type of the attribute String

:String,

:Integer,

:Number,

:Date,

:Unknown
C=Name of the database column
S=Maximum size of the attribute
=Actual average size used for the attribute
Naming

The attribute is a part of the name of an instance

The attribute is a part of the reference key of an instance
Hidden

The attribute is not supposed to be visible and used for queries
Summery

The attribute is supposed to be used in summary reports (lists) for the entity

Relation Details: Cardinality of the relation

:Optional, Many

:Many

=Reverse relation of the entity that the relation refers to

=Entity that this relation establishes an association (reverse entity)

The relation is the containment relation of the entity

The relation is associated with an external entity from a different mart
Hidden

The relation is not supposed to be visible and used for queries

Ligand Distinct chemical molecule that is composed by atoms and bonds Reference attributes:Chem Comp Id - Naming attributes:Ligand code
Chem Comp Id C:CHEM_COMP_ID, S:10, A:0.0	The database identifier of the Chem Comp
Ligand code C:CHEM_COMP_CODE, S:12, A:0.0	The standard extended molecule code of the aminoacid or ligand. It is composed by the PDB 3 letter code with an optional topological indicator appended after an underscore
Beilstein Code C:BEILSTEIN_CODE, S:20, A:0.0	The Id of the Beilstein database whenever available (http://www.mdl.com/products/pdfs/cfb_brochure.pdf)
Cas Base C:CAS_BASE, S:20, A:0.0
Cas reg number C:CAS_REG_CODE, S:20, A:0.0	CAS Registry number (http://www.cas.org/EO/regsys.html)
Cas Ribonucleoside C:CAS_RIBONUCLEOSIDE, S:20, A:0.0
Exchange cif code C:CIF_CODE, S:3, A:0.0	The short 3 letter code of the molecule as referenced in PDB and exchanged in the wwPDB
1 Letter Code C:CODE_1_LETTER, S:5, A:0.0	One code letter for the ligand (aminoacid, nucleic acid) in order to construct sequences.
3 Letter Code C:CODE_3_LETTER, S:3, A:0.0	This attribute provides a code from the chem comp dictionary for standard residues. This attribute must be the same for small molecules that represent our variations on topology/chemistry for a polymer component e.g. All ALA's should have a code_3_letter of ALA. All adenosine nucleotides should have a 3 letter code of A, except for those that have a topology of 'free'. This code is now obsolete and the Comp Code should be used instead in most cases
Details C:DETAILS, S:4000, A:0.0
Primary EBI Classification C:EBI_CLASS1, S:255, A:0.0	The primary EBI classification
Ebi Class1Id C:EBI_CLASS1_ID, S:10, A:0.0	The database identifier of the Ebi Class1
Secondary EBI Classification C:EBI_CLASS2, S:255, A:0.0	The secondary EBI classification
Ebi Class2Id C:EBI_CLASS2_ID, S:10, A:0.0	The database identifier of the Ebi Class2
EBI Id C:EBI_NO, S:10, A:0.0	The EBI internal identifier
EBI name C:EBI_RESERVED_NAME, S:700, A:0.0	The EBI defined name
Extended Code C:EXTENDED_CODE, S:12, A:0.0	The extended code of the molecule uniquely identifying the variant. It includes the short code
Fingerprint C:FINGERPRINT, S:1000, A:0.0	Fingerprint, a bitstring in hexadecimal format giving which segments from a predefined set of 500 the molecule contains
Formal Charge C:FORMAL_CHARGE, S:0, A:0.0
Formula C:FORMULA, S:700, A:0.0	Chemical formula of the molecule listing the number of atoms from each chemical element
Formula Id C:FORMULA_ID, S:10, A:0.0	The database identifier of the Formula
Defined at C:INITIAL_DATE, S:0, A:0.0	The initial date that the molecule was first defined
Merck Id C:MERCK_CODE, S:20, A:0.0	Merck Index Identifier (http://www.merck.com/pubs/mmanual/)
Model Details C:MODEL_DETAILS, S:4000, A:0.0
Model Method C:MODEL_METHOD, S:4000, A:0.0
Modification Details C:MODIFICATION_DETAILS, S:255, A:0.0
Last modified at C:MODIFIED_DATE, S:0, A:0.0	The date that the molecule was last modified
Molecule name C:NAME, S:700, A:0.0	The standard molecule name
NCI Equivalent code C:NCI_EQUIV_CHEM_COMP_CODE, S:12, A:0.0	NCI equivalent ligand (for future use)
Nci Equiv Chem Comp Id C:NCI_EQUIV_CHEM_COMP_ID, S:0, A:0.0	The database identifier of the Nci Equiv Chem Comp
Ndb Connect Modification C:NDB_CONNECT_MODIFICATION, S:255, A:0.0	Local data items describing ligand and monomer modifications (obsolete)
Ndb Type C:NDB_TYPE, S:6, A:0.0	Old NDB classification scheme for this chemical component. NDB internal type code.
Nonstereo Hash C:NONSTEREO_HASH, S:256, A:0.0	The CACTVS (http://www2.chemie.uni-erlangen.de/software/cactvs/index.html) hashcode the uniquely identifies the structure of a small molecule without taking into account its stereo-congiguration. Two ligands with the same non stereo hashcode are stereo-isomers
Non stereo smile C:NONSTEREO_SMILES, S:500, A:0.0	Representation of the molecule using the smile string notation (http://www.daylight.com/dayhtml/smiles/) that does not include stereochemistry information
Parent ligand code C:NSTD_PARENT_CHEM_COMP_CODE, S:12, A:0.0	The current molecule has as non-standard parent that molecule
Non-standard Parent Comp Id C:NSTD_PARENT_CHEM_COMP_ID, S:0, A:0.0	The database identifier of the Non-standard Parent Chem Comp
All atoms C:NUM_ATOMS_ALL, S:10, A:0.0	The total number of atoms
All atoms except hydrogen C:NUM_ATOMS_NON_H, S:10, A:0.0	The total number of non-hydrogen atoms
Topological variant code C:PDB_TOPOL_VAR_CHEM_COMP_CODE, S:12, A:0.0	The current molecule is a topological variant of that molecule
PDB Topol Var Chem Comp Id C:PDB_TOPOL_VAR_CHEM_COMP_ID, S:0, A:0.0	The database identifier of the Pdb Topol Var Chem Comp
Polymer code C:POLYMER_CODE, S:255, A:0.0	The types of polymers that the molecule is used for
Polymer sub type C:POLYMER_SUBTYPE, S:10, A:0.0	The sub types of the molecule in the polymer
Polymer topology C:POLYMER_TOPOLOGY, S:255, A:0.0	Topological classification of molecule based on its possible status in the polymer (i.e. free, start, linking, substructure)
Polymer Topology Id C:POLYMER_TOPOLOGY_ID, S:10, A:0.0	The database identifier of the Polymer Topology
Polymer Type Id C:POLYMER_TYPE_ID, S:10, A:0.0	The database identifier of the Polymer Type
Processed By C:PROCESSED_BY, S:5, A:0.0	The site where the ligand was processed (i.e EBI, RCSB)
Classification C:RCSB_CLASS1, S:255, A:0.0	Classification of molecules (defined by RCSB)
Rcsb Class1Id C:RCSB_CLASS1_ID, S:10, A:0.0	The database identifier of the Rcsb Class1
Hetgroup type C:RCSB_HETTYPE, S:30, A:0.0	Hetgroup type (defined by RCSB)
Additional name C:RCSB_RESERVED_NAME, S:255, A:0.0	Externally defined name (defined by RCSB)
Rna Abbrev C:RNA_ABBREV, S:255, A:0.0	This is the abbreviation used for a modified rna species taken from the modified rna database at (http://www-medlib.med.utah.edu/RNAmods/) (for future use)
Sigma Aldrich Code C:SIGMA_ALDRICH_CODE, S:20, A:0.0	The code of the Sigma Aldrich database whenever available (http://www.sigmaaldrich.com)
Stereo Hash C:STEREO_HASH, S:256, A:0.0	The CACTVS (http://www2.chemie.uni-erlangen.de/software/cactvs/index.html) hashcode the uniquely identifies the structure of a small molecule taking into account its stereo-congiguration. When 2 ligands have the same stereo-hash then either they are the same ligand (one is obsolete and marked as superceded by the other), or their stereo-configuration can not be determined yet, because there are not complete observed coordinates.
Stereo smile C:STEREO_SMILES, S:500, A:0.0	Representation of the molecule using the smile string notation (http://www.daylight.com/dayhtml/smiles/) that includes stereochemistry information
Superceded by C:SUPERCEDED_BY_CHEM_COMP_CODE, S:12, A:0.0	The current molecule is identical and has been superceded by that molecule
Superceded By Chem Comp Id C:SUPERCEDED_BY_CHEM_COMP_ID, S:0, A:0.0	The database identifier of the Superceded By Chem Comp
Systematic name C:SYSTEMATIC_NAME, S:2000, A:0.0	The generated IUPAC systematic name
Therapeutic category C:THERAPUTIC_CAT, S:255, A:0.0	Categorisation of molecules based on therapeutic category
Superceded By 1 Letter C:SUPERCEDED_BY_CODE_1_LETTER, S:0, A:0.0	The 1 letter code of the ligand that has superceded (made obsolete) this ligand
Weight C:WEIGHT, S:0, A:0.0	The molecular weight of the ligand
Superceded By 3 Letter C:SUPERCEDED_BY_CODE_3_LETTER, S:0, A:0.0	The 3 letter code of the ligand that has superceded (made obsolete) this ligand
NCI number C:NCI_NUMBER, S:0, A:0.0	NCI number (for future use)
of related	The formula of the ligand Reverse relation:has of Reverse entity:Formula - Relation attributes:Formula Id
NCI equivalent related	Reverse relation:NCI equivalent of of Reverse entity:Ligand - Relation attributes:Nci Equiv Chem Comp Id
topological variant related	Reverse relation:topological variant of of Reverse entity:Ligand - Relation attributes:PDB Topol Var Chem Comp Id
has related	The energy types of the ligand atoms Reverse relation:in of Reverse entity:Atom energy types - Relation attributes:Chem Comp Id
has related	The atoms of the molecule Reverse relation:of of Reverse entity:Atom of ligand - Relation attributes:Chem Comp Id
has related	The bonds of the molecule Reverse relation:in of Reverse entity:Ligand bond - Relation attributes:Chem Comp Id
has related	The chiral stereocenters of the molecule Reverse relation:in of Reverse entity:Chirality - Relation attributes:Chem Comp Id
NCI equivalent of related	Reverse relation:NCI equivalent of Reverse entity:Ligand - Relation attributes:Chem Comp Id
non-standard parent of related	Reverse relation:non-standard parent of Reverse entity:Ligand - Relation attributes:Chem Comp Id
has related	Reverse relation:has of Reverse entity:Chemical Groups - Relation attributes:Chem Comp Id
has related	The model-reference coordinates of the atoms of the molecule Reverse relation:in of Reverse entity:Coordinates of molecule atoms - Relation attributes:Chem Comp Id
of related	The polymer type of the ligand Reverse relation:of of Reverse entity:Polymer Type - Relation attributes:Polymer Type Id
of related	The polymer topology of the ligand Reverse relation:of of Reverse entity:Polymer Topology - Relation attributes:Polymer Topology Id
is superceded by related	This is an obsolete ligand which is identical and has been supereced by the related ligand Reverse relation:supercedes of Reverse entity:Ligand - Relation attributes:Superceded By Chem Comp Id
has related	The alternative images (image file names) of the molecule Reverse relation:of of Reverse entity:Molecule images - Relation attributes:Chem Comp Id
referred related	The residues that refer to this reference ligand Reverse relation:refers of Reverse entity:Residue - Relation attributes:Chem Comp Id
corresponds related	The bound molecules (sequences) that correspond to this ligand Reverse relation:corresponds of Reverse entity:Molecule - Relation attributes:Chem Comp Id
corresponds related	The bound molecule chains that correspond to this ligand Reverse relation:refers of Reverse entity:Chain - Relation attributes:Chem Comp Id
referred related	The macromolecule atoms that refer to this reference ligand Reverse relation:reference of Reverse entity:Atom - Relation attributes:Chem Comp Id
has related	Reverse relation:of of Reverse entity:CSSR References - Relation attributes:Chem Comp Id
has related	The ring atoms of the molecule Reverse relation:in of Reverse entity:Atoms of the ring - Relation attributes:Chem Comp Id
has related	The planes of the molecule Reverse relation:of of Reverse entity:Plane of molecule - Relation attributes:Chem Comp Id
topological variant of related	Reverse relation:topological variant of Reverse entity:Ligand - Relation attributes:Chem Comp Id
supercedes related	The obsolete ligands that are identical and have been supereced by this ligand Reverse relation:is superceded by of Reverse entity:Ligand - Relation attributes:Chem Comp Id
has related	The nomenclatures of the ligand atoms Reverse relation:of of Reverse entity:Atom Nomenclature - Relation attributes:Chem Comp Id
non-standard parent related	Reverse relation:non-standard parent of of Reverse entity:Ligand - Relation attributes:Non-standard Parent Comp Id
has related	The planar atoms of the molecule Reverse relation:in of Reverse entity:Atoms of the plane - Relation attributes:Chem Comp Id
has related	The rings of the molecule Reverse relation:in of Reverse entity:Rings of molecule - Relation attributes:Chem Comp Id
has related	The synonyms of the molecule Reverse relation:of of Reverse entity:Molecule synonym - Relation attributes:Chem Comp Id
has related	The URL's with information about the molecule Reverse relation:of of Reverse entity:Molecule web links - Relation attributes:Chem Comp Id
has related	The hetgroups in PDB files that where used as a source to model the ligand Reverse relation:of of Reverse entity:Defining depositions - Relation attributes:Chem Comp Id

Atom of ligand Atom of a chemical element, that composes a molecule Reference attributes:Chem Atom Id - Naming attributes:Ligand code,PDB name
Chem Atom Id C:CHEM_ATOM_ID, S:10, A:0.0	The database identifier of the Chem Atom
Ligand code C:CHEM_COMP_CODE, S:12, A:0.0	The standard extended molecule code of the aminoacid or ligand. It is composed by the PDB 3 letter code with an optional topological indicator appended after an underscore
PDB name C:NAME, S:8, A:0.0	The atom name as it is defined in PDB. References of the atom in PDB format will use this name
Charge C:CHARGE, S:0, A:0.0	The formal charge of the atom as specified in the chem comp dictionary
Chem Comp Id C:CHEM_COMP_ID, S:10, A:0.0	The database identifier of the Chem Comp
PDB Atom Format Prefix C:CHEM_ATOM_NAME_PDB_LS, S:1, A:0.0	This column includes the space(s) that have to be prefixed to the atom names in order to export them in PDB format. Spaces is atom names are not significant (ie it is not allowed to have 'CA ' and ' CA' in the same ligand or residue) but have to be preserved since many programs (like rasmol) use these spaces in order to determine the element of the atom.
Chirality C:CHIRALITY, S:1, A:0.0	The stereocenter indicator denoting the chirality of the atom as specified by the molecule dictionary. R means that substituents circulate clockwise (order by lowest priority) and S counter clockwise
Default Model X C:DEFAULT_MODEL_X, S:0, A:0.0	The standard idealised X coordinate of the atom.
Default Model Y C:DEFAULT_MODEL_Y, S:0, A:0.0	The standard idealised Y coordinate of the atom.
Default Model Z C:DEFAULT_MODEL_Z, S:0, A:0.0	The standard idealised Z coordinate of the atom.
Element Id C:ELEMENT_ID, S:10, A:0.0	The database identifier of the Element
Element Symbol C:ELEMENT_SYMBOL, S:15, A:0.0	The standard one or two character symbol of the chemical element of the atom
Incomplete valence C:INCOMPLETE_VALENCE, S:10, A:0.0	The incomplete valence of the atom (number of missing hydrogens). This is only used for non-free molecules.
Leaving Flag C:LEAVING_FLAG, S:1, A:0.0	Defined in the chem comp dictionary, this flag is 'Y' if this atom is lost from the compound on formation of a common/standard link (e.g. the linking oxygen of sugars).
Hydrogen Donor-Acceptor C:N_H_DONOR_ACCEPTOR, S:1, A:0.0	Defined in the chem comp dictionary this denotes the hydrogen bonding potential of the atom and takes values (D-Donor,A-Acceptor,B-Both)
Number of Neighbours C:NUM_OF_NEIGHBOURS, S:0, A:0.0	The number of neighbours of the atom (other atoms that are covalently bonded)
Number of Non-H Neighbours C:NUM_OF_NON_H_NEIGHBOURS, S:0, A:0.0	The number of neighbours of the atom that are not hydrogens
PDB Ordering C:ORDERING, S:4, A:0.0	The ordering of the atom as was defined in the PDB file that it was used for its definition
Ring Flag C:RING_FLAG, S:1, A:0.0	Flag denoting that this atom belongs at least in one ring
Standard Name C:STANDARD_NAME, S:12, A:0.0	The EBI standard atom name that attempts to solve all the PDB name problems (i.e. always start with element name)
Standard Ordering C:STANDARD_ORDERING, S:0, A:0.0	The EBI standard ordering of the atom. Atoms should be listed in this order in any reference of the molecule, when the standard name is used
Substruct Code C:SUBSTRUCT_CODE, S:5, A:0.0	The chemical nature of an atom within a chemical component that assigns the atom to a substructure of the component, if appropriate. 'main' 'main chain of an amino acid' 'side' 'side chain of an amino acid' 'base' 'base of a nucleic acid' 'phos' 'phosphate of a nucleic acid' 'suga' 'sugar of a nucleic acid' 'none' 'not appropriate for this monomer'
Superceded By Chem Atom Id C:SUPERCEDED_BY_CHEM_ATOM_ID, S:10, A:0.0
Superceded By Atom Name C:SUPERCEDED_BY_CHEM_ATOM_NAME, S:24, A:0.0	The standard PDB name of the atom that supercedes this atom
Superceded By Ordering C:SUPERCEDED_BY_ORDERING, S:4, A:0.0	The PDB standard ordering of the atom that supercedes this
Superceded By Standard Name C:SUPERCEDED_BY_STANDARD_NAME, S:36, A:0.0	The EBI standard atom name that supercedes this
Superceded By Standard Ordering C:SUPERCEDED_BY_STD_ORDERING, S:0, A:0.0	The EBI standard ordering of the atom that supercedes this
of related	The ligand that the atom belongs in Reverse relation:has of Reverse entity:Ligand - Relation attributes:Chem Comp Id
has type related	The energy type that this atom has (based on library atom types) Reverse relation:of of Reverse entity:Atom energy types - Relation attributes:Chem Atom Id
has related	The alternative nomenclatures that this atom has Reverse relation:of of Reverse entity:Atom Nomenclature - Relation attributes:Chem Atom Id
is first related	The bonds where the atom is the first atom of the bond Reverse relation:first of Reverse entity:Ligand bond - Relation attributes:Chem Atom Id
is second related	The bonds where the atom is the second atom of the bond Reverse relation:second of Reverse entity:Ligand bond - Relation attributes:Chem Atom Id
is related	The element of the atom Reverse relation:are of Reverse entity:Element - Relation attributes:Element Id
referred related	The macromolecule atom coordinates that refer to this reference atom Reverse relation:reference of Reverse entity:Atom Data - Relation attributes:Chem Atom Id
referred related	The macromolecule atoms that refer to this reference atom Reverse relation:reference of Reverse entity:Atom - Relation attributes:Chem Atom Id
is chiral related	The stereocenters where this is the chiral atom Reverse relation:chiral atom of Reverse entity:Chirality - Relation attributes:Chem Atom Id
is 1st related	The stereocenter where this is the 1st neighbour atom Reverse relation:1st atom of Reverse entity:Chirality - Relation attributes:Chem Atom Id
is 2nd related	The stereocenter where this is the 2nd neighbour atom Reverse relation:2nd atom of Reverse entity:Chirality - Relation attributes:Chem Atom Id
is 3rd related	The stereocenter where this is the 3rd neighbour atom Reverse relation:3rd atom of Reverse entity:Chirality - Relation attributes:Chem Atom Id
has related	The model-reference coordinates (from different data sources ie. PDB-Idealised) for this atom Reverse relation:of of Reverse entity:Coordinates of molecule atoms - Relation attributes:Chem Atom Id
in related	The planes where this atom is in Reverse relation:of of Reverse entity:Atoms of the plane - Relation attributes:Chem Atom Id
in related	The rings where this atom is in Reverse relation:for of Reverse entity:Atoms of the ring - Relation attributes:Chem Atom Id

Ligand bond A bond between two atoms of the molecule Reference attributes:Chem Bond Id - Naming attributes:Ligand code,First atom,Second atom
Chem Bond Id C:CHEM_BOND_ID, S:10, A:0.0	The database identifier of the Chem Bond
Ligand code C:CHEM_COMP_CODE, S:12, A:0.0	The standard extended molecule code of the aminoacid or ligand. It is composed by the PDB 3 letter code with an optional topological indicator appended after an underscore
First atom C:CHEM_ATOM_1_NAME, S:8, A:0.0	The standard name of the first atom
Second atom C:CHEM_ATOM_2_NAME, S:8, A:0.0	The standard name of the second atom
Chem Atom 1Id C:CHEM_ATOM_1_ID, S:10, A:0.0	The database identifier of the Chem Atom 1
1st atom ordering C:CHEM_ATOM_1_ORDERING, S:4, A:0.0	The standard ordering of the first atom of the bond. Bond default ordering is by using the order of the 1st and then the 2nd atom
Chem Atom 2Id C:CHEM_ATOM_2_ID, S:10, A:0.0	The database identifier of the Chem Atom 2
2nd atom ordering C:CHEM_ATOM_2_ORDERING, S:4, A:0.0	The standard ordering of the second atom of the bond
Bond order C:CHEM_BOND_ORDER, S:0, A:0.0	The numerical bond order.
Bond order type C:CHEM_BOND_TYPE, S:4, A:0.0	The enumerated bond order (i.e. single, double).
Chem Comp Id C:CHEM_COMP_ID, S:10, A:0.0	The database identifier of the Chem Comp
Bond aromaticity C:EXTENDED_TYPE, S:5, A:0.0	The bond type for aromaticity. Aromatic bonds are modeled as single or double having aromatic bond type
Bond stereochemistry C:STEREOCHEM, S:1, A:0.0	The stereoisomer indicator for the bond. E means that biggest priority substituents are on the same side and Z that are not
Bond length C:VALUE_DISTANCE, S:40, A:0.0	The length of the bond determined by the distance of the 2 atoms is space based on the default atom coordinates
first related	The first atom of the bond Reverse relation:is first of Reverse entity:Atom of ligand - Relation attributes:Chem Atom 1Id
second related	The second atom of the bond Reverse relation:is second of Reverse entity:Atom of ligand - Relation attributes:Chem Atom 2Id
in related	The ligand where the bond belongs Reverse relation:has of Reverse entity:Ligand - Relation attributes:Chem Comp Id

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) Reference attributes:Chem Model Coord Id - Naming attributes:Ligand code,Atom name,Data Source Name,Data Source Version
Chem Model Coord Id C:CHEM_MODEL_COORD_ID, S:10, A:0.0	The database identifier of the Chem Model Coord
Ligand code C:CHEM_COMP_CODE, S:12, A:0.0	The standard extended molecule code of the aminoacid or ligand. It is composed by the PDB 3 letter code with an optional topological indicator appended after an underscore
Atom name C:CHEM_ATOM_NAME, S:8, A:0.0	The standard PDB name of the atom in the molecule
Data Source Name C:DATA_SOURCE_NAME, S:20, A:0.0	The data source that provided these coordinates for the atom (program,service etc.)
Data Source Version C:DATA_SOURCE_VERSION, S:8, A:0.0	The version of the data source
Chem Atom Id C:CHEM_ATOM_ID, S:10, A:0.0	The database identifier of the Chem Atom
Atom ordering C:CHEM_ATOM_ORDERING, S:4, A:0.0	The standard ordering of the atom in the molecule as defined in the ligand dictionary. Atoms should always be presented based on their ordering
PDB Atom Format Prefix C:CHEM_ATOM_NAME_PDB_LS, S:1, A:0.0	This column includes the space(s) that have to be prefixed to the atom names in order to export them in PDB format. Spaces is atom names are not significant (ie it is not allowed to have 'CA ' and ' CA' in the same ligand or residue) but have to be preserved since many programs (like rasmol) use these spaces in order to determine the element of the atom.
Chem Comp Id C:CHEM_COMP_ID, S:10, A:0.0	The database identifier of the Chem Comp
Data Source Id C:DATA_SOURCE_ID, S:10, A:0.0	The database identifier of the Data Source
Element Id C:ELEMENT_ID, S:10, A:0.0	The database identifier of the Element
Element Symbol C:ELEMENT_SYMBOL, S:15, A:0.0	The standard one or two character symbol of the chemical element of the atom
X coordinate C:MODEL_X, S:0, A:0.0	The X coordinate in 3D space
Y coordinate C:MODEL_Y, S:0, A:0.0	The Y coordinate in 3D space
Z coordinate C:MODEL_Z, S:0, A:0.0	The Z coordinate in 3D space
in related	The ligand of the atom that this coordinates correspond Reverse relation:has of Reverse entity:Ligand - Relation attributes:Chem Comp Id
of related	The data source where these model coordinates came from (ie. PDB, Corina) Reverse relation:has of Reverse entity:Reference libraries - Relation attributes:Data Source Id
is related	The element that the ligand atom has Reverse relation:has of Reverse entity:Element - Relation attributes:Element Id
of related	The ligand atom that this coordinates correspond Reverse relation:has of Reverse entity:Atom of ligand - Relation attributes:Chem Atom Id

Chirality The Chirality ordering of the substituents of a stereocenter Reference attributes:Chem Chirality Id - Naming attributes:Ligand code,Chiral atom
Chem Chirality Id C:CHEM_CHIRALITY_ID, S:10, A:0.0	The database identifier of the Chem Chirality
Chem Atom 1Id C:CHEM_ATOM_1_ID, S:10, A:0.0	The database identifier of the Chem Atom 1
First atom C:CHEM_ATOM_1_NAME, S:8, A:0.0	The first in priority atom name
1st atom ordering C:CHEM_ATOM_1_ORDER, S:4, A:0.0
Chem Atom 2Id C:CHEM_ATOM_2_ID, S:10, A:0.0	The database identifier of the Chem Atom 2
Second atom C:CHEM_ATOM_2_NAME, S:8, A:0.0	The second in priority atom name
2nd atom ordering C:CHEM_ATOM_2_ORDER, S:4, A:0.0
Chem Atom 3Id C:CHEM_ATOM_3_ID, S:10, A:0.0	The database identifier of the Chem Atom 3
Third atom C:CHEM_ATOM_3_NAME, S:8, A:0.0	The third in priority atom name
3rd atom ordering C:CHEM_ATOM_3_ORDER, S:4, A:0.0
Ligand code C:CHEM_COMP_CODE, S:12, A:0.0	The standard extended molecule code of the aminoacid or ligand. It is composed by the PDB 3 letter code with an optional topological indicator appended after an underscore
Chem Comp Id C:CHEM_COMP_ID, S:10, A:0.0	The database identifier of the Chem Comp
Chiral Chem Atom Id C:CHIRAL_CHEM_ATOM_ID, S:10, A:0.0	The database identifier of the Chiral Chem Atom
Chiral atom C:CHIRAL_CHEM_ATOM_NAME, S:8, A:0.0	The chiral atom standard PDB name
Chiral atom ordering C:CHIRAL_CHEM_ATOM_ORDER, S:4, A:0.0
Volume sign C:VOLUME_SIGN, S:1, A:0.0	The sign of the chirality (+ clockwise, - anticlockwise)
in related	The ligand where the chiral stereocenter belongs Reverse relation:has of Reverse entity:Ligand - Relation attributes:Chem Comp Id
1st atom related	The 1st atom in the chiral environment Reverse relation:is 1st of Reverse entity:Atom of ligand - Relation attributes:Chem Atom 1Id
chiral atom related	The chiral atom Reverse relation:is chiral of Reverse entity:Atom of ligand - Relation attributes:Chiral Chem Atom Id
3rd atom related	The 3rd atom in the chiral environment Reverse relation:is 3rd of Reverse entity:Atom of ligand - Relation attributes:Chem Atom 3Id
2nd atom related	The 2nd atom in the chiral environment Reverse relation:is 2nd of Reverse entity:Atom of ligand - Relation attributes:Chem Atom 2Id

Molecule synonym Molecule synonyms Reference attributes:Comp Synonym Id - Naming attributes:Ligand code,Synonym
Comp Synonym Id C:COMP_SYNONYM_ID, S:10, A:0.0	The database identifier of the Comp Synonym
Ligand code C:CHEM_COMP_CODE, S:12, A:0.0	The standard extended molecule code of the aminoacid or ligand. It is composed by the PDB 3 letter code with an optional topological indicator appended after an underscore
Chem Comp Id C:CHEM_COMP_ID, S:10, A:0.0	The database identifier of the Chem Comp
Synonym C:NAME_SYNONYM, S:700, A:0.0	The synonym of the molecule
Serial C:SERIAL, S:10, A:0.0	Prioritises the synonyms of a molecule
Alternative Synonym C:UNAME_SYNONYM, S:700, A:0.0
of related	Reverse relation:has of Reverse entity:Ligand - Relation attributes:Chem Comp Id

Molecule images Additional molecule images Reference attributes:Comp Img File Id - Naming attributes:Ligand code,Image File Name
Comp Img File Id C:COMP_IMG_FILE_ID, S:10, A:0.0	The database identifier of the Comp Img File
Ligand code C:CHEM_COMP_CODE, S:12, A:0.0	The standard extended molecule code of the aminoacid or ligand. It is composed by the PDB 3 letter code with an optional topological indicator appended after an underscore
Chem Comp Id C:CHEM_COMP_ID, S:10, A:0.0	The database identifier of the Chem Comp
Details C:DETAILS, S:4000, A:0.0	Details of this image
Image File Name C:IMG_FILE_NAME, S:30, A:0.0
Related Flag C:RELATED_FLAG, S:1, A:0.0
of related	Reverse relation:has of Reverse entity:Ligand - Relation attributes:Chem Comp Id

Molecule web links Web links with information about the molecule Reference attributes:Comp Url Id - Naming attributes:Ligand code,Serial
Comp Url Id C:COMP_URL_ID, S:10, A:0.0	The database identifier of the Comp Url
Ligand code C:CHEM_COMP_CODE, S:12, A:0.0	The standard extended molecule code of the aminoacid or ligand. It is composed by the PDB 3 letter code with an optional topological indicator appended after an underscore
Chem Comp Id C:CHEM_COMP_ID, S:10, A:0.0	The database identifier of the Chem Comp
Details C:DETAILS, S:4000, A:0.0	Details about the link
Image file name C:IMAGE_FILE_NAME, S:30, A:0.0	Image of the molecule on the link
Serial C:SERIAL, S:10, A:0.0	Prioritisation of the links
URL C:URL, S:255, A:0.0	The actual URL that has information about the ligand
of related	Reverse relation:has of Reverse entity:Ligand - Relation attributes:Chem Comp Id

CSSR References References in CSSR Chemical Database Service at Daresbury. The databank is compiled by the Cambridge Crystallographic Data Centre (CCDC) (http://cds.dl.ac.uk/cds/manuals/cssr.html) Reference attributes:Cssr Ref Comp Id - Naming attributes:Ligand code,CSSR Id
Cssr Ref Comp Id C:CSSR_REF_COMP_ID, S:10, A:0.0	The database identifier of the Cssr Ref Comp
CCDC Id C:CCDC_CODE, S:12, A:0.0	Cambridge Crystallographic Data Centre identifier
Ligand code C:CHEM_COMP_CODE, S:12, A:0.0	The standard extended molecule code of the aminoacid or ligand. It is composed by the PDB 3 letter code with an optional topological indicator appended after an underscore
Chem Comp Id C:CHEM_COMP_ID, S:10, A:0.0	The database identifier of the Chem Comp
CSSR Id C:CSSR_CODE, S:10, A:0.0	CSSR identifier
Reference C:REFERENCE, S:2000, A:0.0	The actual reference
of related	Reverse relation:has of Reverse entity:Ligand - Relation attributes:Chem Comp Id

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) Reference attributes:Atom Energy Type Id - Naming attributes:Ligand code,Atom name,Energy type
Atom Energy Type Id C:ATOM_ENERGY_TYPE_ID, S:10, A:0.0	The database identifier of the Atom Energy Type
Ligand code C:CHEM_COMP_CODE, S:12, A:0.0	The standard extended molecule code of the aminoacid or ligand. It is composed by the PDB 3 letter code with an optional topological indicator appended after an underscore
Atom name C:CHEM_ATOM_NAME, S:8, A:0.0	The standard PDB name of the atom in the molecule
Energy type C:LIB_ATOM_NAME, S:8, A:0.0	Energy type name
Ccp4Lib Atom Id C:CCP4_LIB_ATOM_ID, S:0, A:0.0	The database identifier of the Ccp4Lib Atom
CCP4 energy type C:CCP4_LIB_ATOM_NAME, S:4000, A:0.0	CCP4 Energy type name
Chem Atom Id C:CHEM_ATOM_ID, S:10, A:0.0	The database identifier of the Chem Atom
Atom ordering C:CHEM_ATOM_ORDERING, S:0, A:0.0	The standard ordering of the atom in the molecule as defined in the ligand dictionary. Atoms should always be presented based on their ordering
Chem Comp Id C:CHEM_COMP_ID, S:10, A:0.0	The database identifier of the Chem Comp
Cns Lib Atom Id C:CNS_LIB_ATOM_ID, S:0, A:0.0	The database identifier of the Cns Lib Atom
CNS energy type C:CNS_LIB_ATOM_NAME, S:4000, A:0.0	CNS Energy type name
Data Source Id C:DATA_SOURCE_ID, S:10, A:0.0	The database identifier of the Data Source
Data Source Name C:DATA_SOURCE_NAME, S:20, A:0.0	The data source (library) that defines the energy type information
Data Source Version C:DATA_SOURCE_VERSION, S:8, A:0.0	The version of the data source (library) that defines the energy type information
Element Symbol C:ELEMENT_SYMBOL, S:15, A:0.0	The standard one or two character symbol of the chemical element of the atom
Lib Atom Id C:LIB_ATOM_ID, S:10, A:0.0	The database identifier of the Lib Atom
Partial charge C:PARTIAL_CHARGE, S:0, A:0.0	The exact partial charge as was calculated for the specific instance of the energy type for this atom in this molecule
Template instance C:TEMPLATE_INSTANCE, S:255, A:0.0	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
of related	Atom of the ligand that has the energy type Reverse relation:has type of Reverse entity:Atom of ligand - Relation attributes:Chem Atom Id
in related	Ligand where the atom that has the energy type belongs Reverse relation:has of Reverse entity:Ligand - Relation attributes:Chem Comp Id
of related	Data source (library) of the atom type Reverse relation:has of Reverse entity:Reference libraries - Relation attributes:Data Source Id
cns related	CNS library atom type Reverse relation:cns of Reverse entity:Atom type - Relation attributes:Cns Lib Atom Id
ccp4 related	CCP4 library atom type Reverse relation:ccp4 of Reverse entity:Atom type - Relation attributes:Ccp4Lib Atom Id
of related	Library atom type (for EBI library) Reverse relation:has of Reverse entity:Atom type - Relation attributes:Lib Atom Id

Defining depositions Depositions that were used as a source for defining the molecule. It does not contain all references of molecules in depositions Reference attributes:Hetgroup Id - Naming attributes:Ligand code,Serial,Accession Code
Hetgroup Id C:HETGROUP_ID, S:10, A:0.0	The database identifier of the Hetgroup
Ligand code C:CHEM_COMP_CODE, S:12, A:0.0	The standard extended molecule code of the aminoacid or ligand. It is composed by the PDB 3 letter code with an optional topological indicator appended after an underscore
Serial C:SERIAL, S:10, A:0.0	Serial order or the accession code used to load a ligand
Accession Code C:ACCESSION_CODE, S:8, A:0.0	The PDB accession code of the entry
Chem Comp Id C:CHEM_COMP_ID, S:10, A:0.0	The database identifier of the Chem Comp
Coordinates released at C:COORD_RELEASE_DATE, S:0, A:0.0	The date that the coordinates were loaded
Coordinates loaded C:COORDS_LOADED_FLAG, S:1, A:0.0	Flag denoting if the deposition was used as source for coordinates for the molecule
of related	Reverse relation:has of Reverse entity:Ligand - Relation attributes:Chem Comp Id

Chemical Groups Chemical groups that a molecule belongs in Reference attributes:Chem Group Membership Id - Naming attributes:Ligand code,Chemical group
Chem Group Membership Id C:CHEM_GROUP_MEMBERSHIP_ID, S:10, A:0.0	The database identifier of the Chem Group Membership
Ligand code C:CHEM_COMP_CODE, S:12, A:0.0	The standard extended molecule code of the aminoacid or ligand. It is composed by the PDB 3 letter code with an optional topological indicator appended after an underscore
Chem Comp Id C:CHEM_COMP_ID, S:10, A:0.0	The database identifier of the Chem Comp
Chemical group C:CHEM_GROUP, S:20, A:0.0	The chemical group name
has related	Reverse relation:has of Reverse entity:Ligand - Relation attributes:Chem Comp Id

References in macromolecules The macromolecules that reference each ligand Reference attributes:Chem Comp Id,Entry Id - Naming attributes:Ligand code
Accession Code C:ACCESSION_CODE, S:8, A:0.0	The PDB accession code of the entry
Entry Id C:ENTRY_ID, S:10, A:0.0
Chem Comp Id C:CHEM_COMP_ID, S:0, A:0.0
Ligand code C:CHEM_COMP_CODE, S:9, A:0.0	The standard extended molecule code of the aminoacid or ligand. It is composed by the PDB 3 letter code with an optional topological indicator appended after an underscore
Number of occurrences C:OCCURENCES, S:0, A:0.0	The number of occurrences of the molecule in the macromolecule

Rings of molecule The rings that the molecule contains Reference attributes:Chem Ring Id - Naming attributes:Ligand code,Serial
Chem Ring Id C:CHEM_RING_ID, S:10, A:0.0	The database identifier of the Chem Ring
Ligand code C:CHEM_COMP_CODE, S:12, A:0.0	The standard extended molecule code of the aminoacid or ligand. It is composed by the PDB 3 letter code with an optional topological indicator appended after an underscore
Chem Comp Id C:CHEM_COMP_ID, S:10, A:0.0	The database identifier of the Chem Comp
Ring type C:CHEM_RING_TYPE, S:30, A:0.0	The type of the ring (i.e. aromatic)
Serial C:SERIAL, S:0, A:0.0	Serial number of the ring
has related	Reverse relation:of of Reverse entity:Atoms of the ring - Relation attributes:Chem Ring Id
in related	Reverse relation:has of Reverse entity:Ligand - Relation attributes:Chem Comp Id

Atoms of the ring The atoms of the molecule that this ring contains Reference attributes:Chem Ring Atom Id - Naming attributes:Ligand code,Ring serial,Atom name
Chem Ring Atom Id C:CHEM_RING_ATOM_ID, S:10, A:0.0	The database identifier of the Chem Ring Atom
Chem Atom Id C:CHEM_ATOM_ID, S:10, A:0.0	The database identifier of the Chem Atom
Atom name C:CHEM_ATOM_NAME, S:8, A:0.0	The standard PDB name of the atom in the molecule
Atom ordering C:CHEM_ATOM_ORDERING, S:4, A:0.0	The standard ordering of the atom in the molecule as defined in the ligand dictionary. Atoms should always be presented based on their ordering
Ligand code C:CHEM_COMP_CODE, S:12, A:0.0	The standard extended molecule code of the aminoacid or ligand. It is composed by the PDB 3 letter code with an optional topological indicator appended after an underscore
Chem Comp Id C:CHEM_COMP_ID, S:10, A:0.0	The database identifier of the Chem Comp
Chem Ring Id C:CHEM_RING_ID, S:10, A:0.0	The database identifier of the Chem Ring
Ring serial C:CHEM_RING_SERIAL, S:0, A:0.0	Serial number of the ring
for related	Reverse relation:in of Reverse entity:Atom of ligand - Relation attributes:Chem Atom Id
of related	Reverse relation:has of Reverse entity:Rings of molecule - Relation attributes:Chem Ring Id
in related	Reverse relation:has of Reverse entity:Ligand - Relation attributes:Chem Comp Id

Plane of molecule The planes that the molecule contains Reference attributes:Chem Plane Id - Naming attributes:Ligand code,Serial
Chem Plane Id C:CHEM_PLANE_ID, S:10, A:0.0	The database identifier of the Chem Plane
A factor C:A, S:0, A:0.0	Factor a of the plane equation (ax+by+c=0)
B factor C:B, S:0, A:0.0	Factor b of the plane equation (ax+by+c=0)
C factor C:C, S:0, A:0.0	Factor c of the plane equation (ax+by+c=0)
Ligand code C:CHEM_COMP_CODE, S:12, A:0.0	The standard extended molecule code of the aminoacid or ligand. It is composed by the PDB 3 letter code with an optional topological indicator appended after an underscore
Chem Comp Id C:CHEM_COMP_ID, S:10, A:0.0	The database identifier of the Chem Comp
Plane type C:CHEM_PLANE_TYPE, S:240, A:0.0	The method used for identifying the plane (from structure or from actual coordinates)
Number of atoms C:NUM_ATOMS_ALL, S:8, A:0.0	The number of atoms the plane contains
Number of non-hydrogen atoms C:NUM_ATOMS_NON_H, S:8, A:0.0	The number of non-hydrogen atoms the plane contains
Serial C:SERIAL, S:0, A:0.0	Serial number of the plane in the molecule
of related	The ligand where the plane belongs Reverse relation:has of Reverse entity:Ligand - Relation attributes:Chem Comp Id
has related	The planar atoms Reverse relation:in of Reverse entity:Atoms of the plane - Relation attributes:Chem Plane Id

Atoms of the plane The atoms of the molecule that this plane contains Reference attributes:Chem Plane Atom Id - Naming attributes:Ligand code,Serial,Atom name
Chem Plane Atom Id C:CHEM_PLANE_ATOM_ID, S:10, A:0.0	The database identifier of the Chem Plane Atom
Chem Atom Id C:CHEM_ATOM_ID, S:10, A:0.0	The database identifier of the Chem Atom
Atom name C:CHEM_ATOM_NAME, S:8, A:0.0	The standard PDB name of the atom in the molecule
Atom ordering C:CHEM_ATOM_ORDERING, S:4, A:0.0	The standard ordering of the atom in the molecule as defined in the ligand dictionary. Atoms should always be presented based on their ordering
Ligand code C:CHEM_COMP_CODE, S:12, A:0.0	The standard extended molecule code of the aminoacid or ligand. It is composed by the PDB 3 letter code with an optional topological indicator appended after an underscore
Chem Comp Id C:CHEM_COMP_ID, S:10, A:0.0	The database identifier of the Chem Comp
Chem Plane Id C:CHEM_PLANE_ID, S:10, A:0.0	The database identifier of the Chem Plane
Serial C:CHEM_PLANE_SERIAL, S:0, A:0.0	Serial number of the plane in the molecule
Distance C:DIST, S:0, A:0.0	Distance of the atom from the plane
of related	The ligand atom that is in the plane Reverse relation:in of Reverse entity:Atom of ligand - Relation attributes:Chem Atom Id
in related	The ligand where the planar atom belongs Reverse relation:has of Reverse entity:Ligand - Relation attributes:Chem Comp Id
in related	The plane where the planar atom belongs Reverse relation:has of Reverse entity:Plane of molecule - Relation attributes:Chem Plane Id

Atom Nomenclature Different naming schemes for ligand atoms based on different standards and conventions, i.e. ANSIG (http://www-ccmr-nmr.bioc.cam.ac.uk/public/ANSIG/ansig.html) Reference attributes:Atom Nomenclature Id - Naming attributes:Ligand code,Atom Name,Nomenclature,Name
Atom Nomenclature Id C:ATOM_NOMENCLATURE_ID, S:10, A:0.0	The database identifier of the Atom Nomenclature
Ligand code C:CHEM_COMP_CODE, S:12, A:0.0	The standard extended molecule code of the aminoacid or ligand. It is composed by the PDB 3 letter code with an optional topological indicator appended after an underscore
Atom Name C:CHEM_ATOM_NAME, S:8, A:0.0	The standard PDB name of the atom in the molecule
Nomenclature C:NOMENCLATURE, S:30, A:0.0	The nomenclature name (ie PDB, ANSIG etc)
Name C:NAME, S:8, A:0.0	The name of an atom based on this nomenclature
Chem Atom Id C:CHEM_ATOM_ID, S:10, A:0.0	The database identifier of the Chem Atom
Chem Comp Id C:CHEM_COMP_ID, S:10, A:0.0	The database identifier of the Chem Comp
Ordering C:ORDERING, S:4, A:0.0	The ordering of an atom in the molecule based on this nomenclature
of related	The atom that the nomenclature name corresponds Reverse relation:has of Reverse entity:Atom of ligand - Relation attributes:Chem Atom Id
of related	The ligand that the nomenclature name corresponds Reverse relation:has of Reverse entity:Ligand - Relation attributes:Chem Comp Id

Polymer Topology Topology of a small molecule (ligand). Describes the position of the small molecule in a polymer chain. For bound molecules and ligands, only the free topology is available, but for aminoacids, nucleic-acids and other polymer components, all topological variants (like start, linking, free) are separately modeled. Reference attributes:Polymer Topology Id - Naming attributes:Name
Polymer Topology Id C:POLYMER_TOPOLOGY_ID, S:10, A:0.0	The database identifier of the Polymer Topology
Details C:DETAILS, S:255, A:0.0	Description of the meaning of the topology
Name C:NAME, S:255, A:0.0	Names of topologies (i.e. start, linking, free ...)
of related	The ligands of this topology Reverse relation:of of Reverse entity:Ligand - Relation attributes:Polymer Topology Id

Polymer Type Type of the polymer that this small molecule forms (polyribonucleotide, polypeptide(D), polysaccharide(D) etc) Reference attributes:Polymer Type Id - Naming attributes:Polymer name,Polymer Subtype
Polymer Type Id C:POLYMER_TYPE_ID, S:10, A:0.0	The database identifier of the Polymer Type
Polymer code C:CODE, S:255, A:0.0
Polymer name C:NAME, S:255, A:0.0	The name of the polymer type
Polymer Subtype C:POLYMER_SUBTYPE, S:10, A:0.0	Identifies different polymer subtypes (i.e. singly/double protonated etc)
of related	The ligands of this polymer type Reverse relation:of of Reverse entity:Ligand - Relation attributes:Polymer Type Id

Formula A molecular formula is identical for all structular isomers of a ligand and is closely related with its weight, number of atoms etc Reference attributes:Formula Id - Naming attributes:Formula
Formula Id C:FORMULA_ID, S:10, A:0.0	The database identifier of the Formula
Formula C:FORMULA, S:700, A:0.0	The chemical formula of a small molecule (i.e. C3 H6 N1 O2)
Element Number C:ELEMENT_NUMBER, S:0, A:0.0	The number of different elements in the formula
Weight C:WEIGHT, S:0, A:0.0	The weight of small molecules derived directly by chemical formula
has related	Reverse relation:of of Reverse entity:Ligand - Relation attributes:Formula Id

EBI Classification Primary classification of ligands and small molecules as defined at EBI Reference attributes:Comp Ebi Class1Id - Naming attributes:Name
Comp Ebi Class1Id C:COMP_EBI_CLASS1_ID, S:10, A:0.0	The database identifier of the Comp Ebi Class1
Name C:NAME, S:255, A:0.0	EBI main classification of ligands and small molecules

RCSB Classification Primary classification of ligands and small molecules as defined at RCSB Reference attributes:Comp Rcsb Class1Id - Naming attributes:Name
Comp Rcsb Class1Id C:COMP_RCSB_CLASS1_ID, S:10, A:0.0	The database identifier of the Comp Ebi Class1
Name C:NAME, S:255, A:0.0	RCSB main classification of ligands and small molecules

Element The periodic table of the chemical elements with usefull details about mass, atomic number, radius etc Reference attributes:Element Id - Naming attributes:Symbol
Element Id C:ELEMENT_ID, S:10, A:0.0	The database identifier of the Element
Symbol C:SYMBOL, S:15, A:0.0	The standard element symbol
Atomic Number C:ATOMIC_NUMBER, S:3, A:0.0
Atomic Radius C:ATOMIC_RADIUS, S:0, A:0.0
Covalent Radius C:COVALENT_RADIUS, S:0, A:0.0
Formula Seq C:FORMULA_SEQ, S:10, A:0.0	The convention about the order in which elements appear in chemical formulas
Mass C:MASS, S:0, A:0.0
Name C:NAME, S:255, A:0.0	The full name of the element
are related	The ligand atoms that are of this element Reverse relation:is of Reverse entity:Atom of ligand - Relation attributes:Element Id
has related	The energy atoms types that are of this element Reverse relation:is of Reverse entity:Atom type - Relation attributes:Element Id
has related	The ligand atoms coordinates that are of this element Reverse relation:is of Reverse entity:Coordinates of molecule atoms - Relation attributes:Element Id

EBI 2nd Classification Secondary classification of ligands and small molecules as defined at EBI Reference attributes:Comp Ebi Class2Id - Naming attributes:Name
Comp Ebi Class2Id C:COMP_EBI_CLASS2_ID, S:10, A:0.0	The database identifier of the Comp Ebi Class1
Name C:NAME, S:255, A:0.0	EBI secondary classification of ligands and small molecules