############################################################################## # # # CIF PRIVATE CCDC DEFINITIONS # # ---------------------------- # # # # This dictionary contains the names and definitions of "private" data items # # recognised by the Cambridge Crystallographic Data Centre for the # # processing of CIFs. # # # # Copyright 2014 Cambridge Crystallographic Data Centre # ############################################################################## data_on_this_dictionary _dictionary_name cif_ccdc.dic _dictionary_version 1.3 _dictionary_update 2014-05-12 _dictionary_history ; 2003-11-21 Initial version GPS 2003-12-02 Add Russian and Archive numbers GPS 2004-01-23 Add _ccdc_publ_extra_info GPS 2014-05-12 Add _ccdc_geom[] data items ; ############# ## JOURNAL ## ############# data_ccdc_journal_manuscript_code _name '_ccdc_journal_manuscript_code' _category journal _type char _definition ; The manuscript code assigned by the journal publisher on submission of the manuscript for publication. ; ########## ## PUBL ## ########## data_ccdc_publ_extra_info _name '_ccdc_publ_extra_info' _category publ _type char _definition ; Extra information available in a publication, either in the manuscript or as supplementary data, which is not included in the cif. ; ############## ## DATABASE ## ############## data_ccdc_depnum_russian _name '_ccdc_depnum_russian' _category database _type char _definition ; Internal deposition number used by Russian abstractors to identify files containing structural information archived by the Cambridge Crystallographic Data Centre (CCDC). ; data_ccdc_depnum_archive _name '_ccdc_depnum_archive' _category database _type char _definition ; Internal archive number used by the Cambridge Crystallographic Data Centre (CCDC) to files containing structural information archived by the CCDC. ; ########################## ## GEOMETRIC PARAMETERS ## ########################## # The following data items can be included in a CIF exported from CCDC # software and are primarily used to facilitate transfer of data to # Accelrys software. #-- Distance -- data_ccdc_geom_distance_atom_site_label_ loop_ _name '_ccdc_geom_distance_atom_site_label_1' '_ccdc_geom_distance_atom_site_label_2' _category ccdc_geom_distance _type char _list yes _list_mandatory yes _list_link_parent '_atom_site_label' _definition ; The labels of two atom sites that define labels specified as _atom_site_label in the atom list. ; data_ccdc_geom_distance_site_symmetry_ loop_ _name '_ccdc_geom_distance_site_symmetry_1' '_ccdc_geom_distance_site_symmetry_2' _category ccdc_geom_distance _type char _list yes _list_reference '_ccdc_geom_distance_atom_site_label_' loop_ _example _example_detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' _definition ; The symmetry code of each atom site as the symmetry-equivalent position number 'n' and the cell translation number 'klm'. These numbers are combined to form the code 'n klm' or n_klm. The character string n_klm is composed as follows: n refers to the symmetry operation that is applied to the coordinates stored in _atom_site_fract_x, _atom_site_fract_y and _atom_site_fract_z. It must match a number given in _symmetry_equiv_pos_site_id. k, l and m refer to the translations that are subsequently applied to the symmetry transformed coordinates to generate the atom used in calculating the bond. These translations (x,y,z) are related to (k,l,m) by the relations k = 5 + x l = 5 + y m = 5 + z By adding 5 to the translations, the use of negative numbers is avoided. ; data_ccdc_geom_distance _name '_ccdc_geom_distance' _category ccdc_geom_distance _type numb _type_conditions esd _list yes _enumeration_range 0.0: _definition ; The value of a distance-based parameter resulting from a search of the CSD. Typically this will be the distance in Angstroms between two atoms identified by _ccdc_geom_distance_atom_site_label_[] but may also involve centroids or dummy points or may be the distance between a point and a plane. Alterntively, it may be the result of combining distance parameters or of applying a function to a distance as indicated by _ccdc_geom_distance_transformation. ; data_ccdc_geom_distance_query_id _name '_ccdc_geom_distance_query_id' _category ccdc_geom_distance _type numb _list yes _enumeration_range 0: _definition ; The identifier of a query that gives rise to a distance-based parameter reported by _ccdc_geom_distance. ; data_ccdc_geom_distance_fragment_id _name '_ccdc_geom_distance_fragment_id' _category ccdc_geom_distance _type numb _list yes _enumeration_range 0: _definition ; The identifier of a hit fragment containing a distance-based parameter reported by _ccdc_geom_distance. ; data_ccdc_geom_distance_parameter_label _name '_ccdc_geom_distance_parameter_label' _category ccdc_geom_distance _type char _list yes _definition ; The label associated with a particular value of _ccdc_geom_distance ; data_ccdc_geom_distance_transformation _name '_ccdc_geom_distance_transformation' _category ccdc_geom_distance _type char _list yes _definition ; Indicates that a value reported by _ccdc_geom_distance has been transformed by either a function or by combining more than one parameter. If more than one transformation has been applied then these are represented as a space separated list. Likely values are: nint : nearest integer sum : sum of more than one distance average : average of more than one distance min : minimum of more than one distance max : maximum of more than one distance ; #-- Angle -- data_ccdc_geom_angle_atom_site_label_ loop_ _name '_ccdc_geom_angle_atom_site_label_1' '_ccdc_geom_angle_atom_site_label_2' '_ccdc_geom_angle_atom_site_label_3' _category ccdc_geom_angle _type char _list yes _list_mandatory yes _list_link_parent '_atom_site_label' _definition ; The labels of three atom sites that define labels specified as _atom_site_label in the atom list. ; data_ccdc_geom_angle_site_symmetry_ loop_ _name '_ccdc_geom_angle_site_symmetry_1' '_ccdc_geom_angle_site_symmetry_2' '_ccdc_geom_angle_site_symmetry_3' _category ccdc_geom_angle _type char _list yes _list_reference '_ccdc_geom_angle_atom_site_label_' loop_ _example _example_detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' _definition ; The symmetry code of each atom site as the symmetry-equivalent position number 'n' and the cell translation number 'klm'. These numbers are combined to form the code 'n klm' or n_klm. The character string n_klm is composed as follows: n refers to the symmetry operation that is applied to the coordinates stored in _atom_site_fract_x, _atom_site_fract_y and _atom_site_fract_z. It must match a number given in _symmetry_equiv_pos_site_id. k, l and m refer to the translations that are subsequently applied to the symmetry transformed coordinates to generate the atom used in calculating the bond. These translations (x,y,z) are related to (k,l,m) by the relations k = 5 + x l = 5 + y m = 5 + z By adding 5 to the translations, the use of negative numbers is avoided. ; data_ccdc_geom_angle _name '_ccdc_geom_angle' _category ccdc_geom_angle _type numb _type_conditions esd _list yes _enumeration_range 0.0: _definition ; The value of a angle-based parameter resulting from a search of the CSD. Typically this will be the angle in degrees between atoms identified by _ccdc_geom_angle_atom_site_label_[] but may also involve centroids or dummy points or may be the angle between planes and vectors. Alterntively, it may be the result of combining angle parameters or of applying a function to an angle as indicated by _ccdc_geom_angle_transformation. ; data_ccdc_geom_angle_query_id _name '_ccdc_geom_angle_query_id' _category ccdc_geom_angle _type numb _list yes _enumeration_range 0: _definition ; The identifier of a query that gives rise to an angle-based parameter reported by _ccdc_geom_angle. ; data_ccdc_geom_angle_fragment_id _name '_ccdc_geom_angle_fragment_id' _category ccdc_geom_angle _type numb _list yes _enumeration_range 0: _definition ; The identifier of a hit fragment containing an angle-based parameter reported by _ccdc_geom_distance. ; data_ccdc_geom_angle_parameter_label _name '_ccdc_geom_angle_parameter_label' _category ccdc_geom_angle _type char _list yes _definition ; The label associated with a particular value of _ccdc_geom_angle. ; data_ccdc_geom_angle_transformation _name '_ccdc_geom_angle_transformation' _category ccdc_geom_angle _type char _list yes _definition ; Indicates that a value reported by _ccdc_geom_angle has been transformed by either a function or by combining more than one parameter. If more than one transformation has been applied then these are represented as a space separated list. Likely values are: nint : nearest integer sin : sine cos : cosine tan : tangent sum : sum of more than one angle average : average of more than one angle min : minimum of more than one angle max : maximum of more than one angle ; #-- Torsion -- data_ccdc_geom_torsion_atom_site_label_ loop_ _name '_ccdc_geom_torsion_atom_site_label_1' '_ccdc_geom_torsion_atom_site_label_2' '_ccdc_geom_torsion_atom_site_label_3' '_ccdc_geom_torsion_atom_site_label_4' _category ccdc_geom_torsion _type char _list yes _list_mandatory yes _list_link_parent '_atom_site_label' _definition ; The labels of four atom sites that define labels specified as _atom_site_label in the atom list. ; data_ccdc_geom_torsion_site_symmetry_ loop_ _name '_ccdc_geom_torsion_site_symmetry_1' '_ccdc_geom_torsion_site_symmetry_2' '_ccdc_geom_torsion_site_symmetry_3' '_ccdc_geom_torsion_site_symmetry_4' _category ccdc_geom_torsion _type char _list yes _list_reference '_ccdc_geom_torsion_atom_site_label_' loop_ _example _example_detail . 'no symmetry or translation to site' 4 '4th symmetry operation applied' 7_645 '7th symm. posn.; +a on x; -b on y' _definition ; The symmetry code of each atom site as the symmetry-equivalent position number 'n' and the cell translation number 'klm'. These numbers are combined to form the code 'n klm' or n_klm. The character string n_klm is composed as follows: n refers to the symmetry operation that is applied to the coordinates stored in _atom_site_fract_x, _atom_site_fract_y and _atom_site_fract_z. It must match a number given in _symmetry_equiv_pos_site_id. k, l and m refer to the translations that are subsequently applied to the symmetry transformed coordinates to generate the atom used in calculating the bond. These translations (x,y,z) are related to (k,l,m) by the relations k = 5 + x l = 5 + y m = 5 + z By adding 5 to the translations, the use of negative numbers is avoided. ; data_ccdc_geom_torsion _name '_ccdc_geom_torsion' _category ccdc_geom_torsion _type numb _type_conditions esd _list yes _definition ; The value of a torsion-based parameter resulting from a search of the CSD. Typically this will be the torsion in degrees involving atoms identified by _ccdc_geom_torsion_atom_site_label_[] but may also involve centroids or dummy points. Alterntively, it may be the result of combining torsion parameters or of applying a function to a torsion as indicated by _ccdc_geom_torsion_transformation. ; data_ccdc_geom_torsion_query_id _name '_ccdc_geom_torsion_query_id' _category ccdc_geom_torsion _type numb _list yes _enumeration_range 0: _definition ; The identifier of a query that gives rise to a torsion-based parameter reported by _ccdc_geom_torsion. ; data_ccdc_geom_torsion_fragment_id _name '_ccdc_geom_torsion_fragment_id' _category ccdc_geom_torsion _type numb _list yes _enumeration_range 0: _definition ; The identifier of a hit fragment containing a torsion-based parameter reported by _ccdc_geom_distance. ; data_ccdc_geom_torsion_parameter_label _name '_ccdc_geom_torsion_parameter_label' _category ccdc_geom_torsion _type char _list yes _definition ; The label associated with a particular value of _ccdc_geom_torsion. ; data_ccdc_geom_torsion_transformation _name '_ccdc_geom_torsion_transformation' _category ccdc_geom_torsion _type char _list yes _definition ; Indicates that a value reported by _ccdc_geom_torsion has been transformed by either a function or by combining more than one parameter. If more than one transformation has been applied then these are represented as a space separated list. Likely values are: nint : nearest integer sin : sine cos : cosine tan : tangent abs : absolute sum : sum of more than one torsion min : minimum of more than one torsion max : maximum of more than one torsion ; #################### ## GEOM_BOND_TYPE ## #################### data_ccdc_geom_bond_type _name '_ccdc_geom_bond_type' _category geom_bond _type char _list yes _list_reference '_geom_bond_atom_site_label_' loop_ _enumeration _enumeration_detail S 'single bond' D 'double bond' T 'triple bond' Q 'quadruple bond' A 'aromatic bond' C 'polymeric bond' E 'delocalized double bond' P 'pi bond' . 'unknown bond type' _enumeration_default . _definition ; The chemical bond type associated with the connection between the two sites _geom_bond_atom_site_label_1 and *_2. Primarily used for transfer of data between CCDC and Accelrys software. ;