PDB Chemical Component Dictionary Format Description: mmCIF Format

mmCIF format combines collections of related data items (tokens) into categories. A category is essentially a table in which each token represents a row in the table. The question mark (?) is used to mark an item value as missing. A period (.) may be used to identify that there is no appropriate value for the item or that a value has been intentionally omitted.

Vectors and tables of data may be encoded in mmCIF using a loop_ directive. To build a table, the data item names corresponding to the table columns are preceded by the loop_ directive, and followed by the corresponding rows of data.

Note: Further description of mmCIF syntax and structure can be found here.

In an mmCIF format coordinate file the chem_comp category is used to describe the chemical components in an entry. The chemical name for the chemical component is given by chem_comp.name, the chemical formula by chem_comp.formula, and the molecular weight by chem_comp.forumla_weight.

For example entry 1a7p contains the non-standard residue acetic acid (ID code: ACY):

loop_

_chem_comp.id

_chem_comp.type

_chem_comp.mon_nstd_flag

_chem_comp.name

_chem_comp.pdbx_synonyms

_chem_comp.formula

_chem_comp.formula_weight

ACY non-polymer . 'ACETIC ACID' ? 'C2 H4 O2' 60.052

Further information describing each non-standard residue is then provided in the Chemical Component Dictionary.Dictionary Record Format.

Note: Please see the mmCIF format dictionary for more information about the chem_comp category. Further description of mmCIF syntax can be found here.

Dictionary Record Format

In the mmCIF format Chemical Component Dictionary, each chemical component is defined by sets of tokens in the three categories: chem_comp (Table 1), chem_comp_atom (Table 2), chem_comp_bond (Table 3).

Table 1: chem_comp category
Token	Definition	Example
_chem_comp.id	The alphanumeric code for the chemical component.	HYP
_chem_comp.name	The name of the chemical component.	4-HYDROXYPROLINE
_chem_comp.type	The type of monomer.	L-peptide linking
_chem_comp.pdbx_type	A preliminary internal classification used by PDB.	ATOMP
_chem_comp.formula	The chemical formula of the chemical component.	C5 H9 N1 O3'
_chem_comp.pdbx_synonyms	Synonym list for the non-standard residue.	HYDROXYPROLINE
_chem_comp.mon_nstd_parent	A name of the parent monomer of the chemical component if the entry results from a modification of a standard monomer.	PRO
_chem_comp.pdbx_formal_charge	The formal charge on the chemical component.	+1
_chem_comp.mon_nstd_flag	Flag indicating whether or not the chemical component is a "standard" monomer.	n
_chem_comp.formula_weight	Formula mass in daltons of the chemical component.	131.131

Table 2: chem_comp_atom category: tokens in this section are looped through for each atom in the chemical component
Token	Definition	Example
_chem_comp_atom.comp_id	Same as _chem_comp.id	HYP
_chem_comp_atom.atom_id	Identifier for each atom in the chemical component.	CA
_chem_comp_atom.type_symbol	The atom type for each atom in the chemical component.	C
_chem_comp_atom.charge	The formal charge assigned to each atom in the chemical component.	0
_chem_comp_atom.model_Cartn_x	The x component of the coordinates for each atom in the chemical component specified as orthogonal angstroms.	26.052
_chem_comp_atom.model_Cartn_y	The y component of the coordinates for each atom in the chemical component specified as orthogonal angstroms.	5.609
_chem_comp_atom.model_Cartn_z	The z component of the coordinates for each atom in the chemical component specified as orthogonal angstroms.	5.594
_chem_comp_atom.pdbx_align	Determines which column the atom name appears in PDB coordinate files. The possible values are 0 or 1.	1

Table 3: chem_comp_bond category: tokens in this section are looped through for each bond in the chemical component
Token	Definition	Example
_chem_comp_bond.comp_id	Same as _chem_comp.id	HYP
_chem_comp_bond.atom_id_1	The id of the first of the two atoms that define the bond.	N
_chem_comp_bond.atom_id_2	The id of the second of the two atoms that define the bond.	CA
_chem_comp_bond.value_order	The bond order of the chemical bond associated with the specified atoms.	SING