# Preliminary Extension Dictionary for A La Mode V 0.0.01 1998. # # A set of extensions to the mmCIF dictionary added for retrieval and # manipulation of ligand and monomer components of macro molecules. # # John Westbrook and Les Clowney # Nucleic Acid Database Project # Rutgers University data_cif_alamode.dic _dictionary.title cif_alamode.dic _dictionary.version 0.0.01 _dictionary.datablock_id cif_alamode.dic ################### ## NDB_COMPOSITE ## ################### save_NDB_COMPOSITE _category.description ; Data items in the NDB_COMPOSITE category give details about the subunits that were combined to generate a complex chemical component. ; _category.id ndb_composite _category.mandatory_code no _category_key.name '_ndb_composite.comp_id' loop_ _category_group.id 'inclusive_group' 'ndb_chem_comp_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example - from a mmCIF where ribose_C2endo was first modified by adding bonds, angles and torsions from the mmCIF with comp_id all_ribose_gamma_+scm. This produced a compound with the comp_id ribose_C2endo_O3H_O5H_gamma_+sc. The final structure (comp_id A_anti) combines CIFS for ade_neu and ribose_C2endo_O3H_O5H_gamma_+sc. Two processes are recorded in this category: a) copying a bond from one CIF to another, as in the row ribose_C2endo all_ribose_gamma_+sc sugar 'angle: copied C5*-C4*-C3*' and b) combining a CIF (one chem_comp.id) with others to generate a structure having a new value of the field, as in row: A_anti ade_neu base 'merge geometry' . ; ; loop_ _ndb_composite.comp_id _ndb_composite.sub_comp_id _ndb_composite.sub_type _ndb_composite.details A_anti ade_neu base 'merge geometry' A_anti ribose_C2endo_O3H_O5H_gamma_+sc sugar 'merge geometry' ribose_C2endo ribose_C2endo_O3H sugar 'bond: copied C3*-O3*' ribose_C2endo ribose_C2endo_O5H sugar 'bond: copied C5*-O5*' ribose_C2endo all_ribose_gamma_+sc sugar 'tor: copied gamma' ribose_C2endo all_ribose_gamma_+sc sugar 'tor: copied O4*-C4*-C5*-O5*' ribose_C2endo all_ribose_gamma_+sc sugar 'angle: copied C5*-C4*-C3*' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__ndb_composite.comp_id _item_description.description ; The target comp_id. ; _item.name '_ndb_composite.comp_id' _item.category_id ndb_composite _item.mandatory_code no _item_type.code code save_ save__ndb_composite.sub_comp_id _item_description.description ; The comp_id that was added. ; _item.name '_ndb_composite.sub_comp_id' _item.category_id ndb_composite _item.mandatory_code no _item_type.code code save_ save__ndb_composite.sub_type _item_description.description ; The type of the added comp_id. ; _item.name '_ndb_composite.sub_type' _item.category_id ndb_composite _item.mandatory_code no _item_type.code code save__ndb_composite.description _item_description.description ; The description of the operation. ; _item.name '_ndb_composite.description' _item.category_id ndb_composite _item.mandatory_code no _item_type.code text save_ ################## ## NDB_DBSEARCH ## ################## save_NDB_DBSEARCH _category.description ; Data items in the NDB_DBSEARCH category give details about the database searches used as the source of other data, including coordinates, geometries (CHEM_COMP_BOND, CHEM_COMP_ANGLE and CHEM_COMP_TOR) and NDB_DBITEM: in each of these other categories there is a descriptor *.dbsearch_id pointing to the data item ndb_dbsearch.id in this category. The related CHEM_COMP_ATOM, CHEM_COMP_BOND, CHEM_COMP_ANGLE, etc. categories describe the detailed geometry of these chemical components. ; _category.id ndb_dbsearch _category.mandatory_code no _category_key.name '_ndb_dbsearch.id' loop_ _category_group.id 'inclusive_group' 'ndb_chem_comp_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example - based on a search of the Cambridge Structural Database for cytosine-containing crystals ; ; _ndb_dbsearch.id cyt_neu _ndb_dbsearch.sample_size 45 _ndb_dbsearch.time 'Fri May 9 13:49:31 1997' _ndb_dbsearch.db csd _ndb_dbsearch.dbversion 512 _ndb_dbsearch.dbreleasedate 'Sep 15 19:34:11 BST 1996' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__ndb_dbsearch.id _item_description.description ; The identifier for a particular database search. ; _item.name '_ndb_dbsearch.id' _item.category_id ndb_dbsearch _item.mandatory_code no _item_type.code code save_ save__ndb_dbsearch.sample_size _item_description.description ; The number of dbitems used from the given database search. ; _item.name '_ndb_dbsearch.sample_size' _item.category_id ndb_dbsearch _item.mandatory_code no _item_type.code int save_ save__ndb_dbsearch.sample_time _item_description.description ; The time at which the given database search was performed. ; _item.name '_ndb_dbsearch.time' _item.category_id ndb_dbsearch _item.mandatory_code no _item_type.code date save_ save__ndb_dbsearch.db _item_description.description ; The database used for the given search. ; _item.name '_ndb_dbsearch.db' _item.category_id ndb_dbsearch _item.mandatory_code no _item_type.code code save_ save__ndb_dbsearch.db_version _item_description.description ; An identifier of the version of the database used for the search. ; _item.name '_ndb_dbsearch.db_version' _item.category_id ndb_dbsearch _item.mandatory_code no _item_type.code line save_ save__ndb_dbsearch.releasedate _item_description.description ; The date of release for the given database search: similar information as dbversion. ; _item.name '_ndb_dbsearch.releasedate' _item.category_id ndb_dbsearch _item.mandatory_code no _item_type.code date save_ ################ ## NDB_DBITEM ## ################ save_NDB_DBITEM _category.description ; Data items in the NDB_DBITEM category rerord the names of refcodes pointers to the searches used to obtain them, and some details about the quailty of the item (R factor and C-C esd). ; _category.id ndb_dbitem _category.mandatory_code no _category_key.name '_ndb_dbitem.id' loop_ _category_group.id 'inclusive_group' 'ndb_chem_comp_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example - based on a search of the Cambridge Structural Database for cytosine-containing crystals ; ; loop_ _ndb_dbitem.id _ndb_dbitem.dbsearch_id _ndb_dbitem.molecule_id _ndb_dbitem.r_factor _ndb_dbitem.sigma _ndb_dbitem.compound _ndb_dbitem.citation acytid cyt_neu 1 3.30 0.001-0.005A 'ALPHA-CYTIDINE (FOR STEREOISOMER SEE CYTIDI10)' 'M.L.POST,G.I.BIRNBAUM,C.P.HUBER,D.SHUGAR 1977, BIOCHIM.BIOPHYS.ACTA, 479, 133' bagxiq01 cyt_neu 1 5.90 0.006-0.010A ; 3',5'-O-(1,1,3,3-TETRAISOPROPYLDISILOX-1,3-DIYL)-CYTIDINE ; 'M.J.ROBINS,J.S.WILSON,L.SAWYER,M.N.G.JAMES 1983, CAN.J.CHEM., 61, 1911' ...other items omitted ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__ndb_dbitem.id _item_description.description ; The identifier for a particular database item. ; _item.name '_ndb_dbitem.id' _item.category_id ndb_dbitem _item.mandatory_code no _item_type.code code save_ save__ndb_dbitem.molecule_id _item_description.description ; The identifier for a particular database item that may have more than one distinct molecule in a structure. ; _item.name '_ndb_dbitem.molecule_id' _item.category_id ndb_dbitem _item.mandatory_code no _item_type.code code save_ save__ndb_dbitem.r_factor _item_description.description ; The R factor contained in the database for the structure identified by the dbitem.id descriptor. ; _item.name '_ndb_dbitem.r_factor' _item.category_id ndb_dbitem _item.mandatory_code no _item_type.code float save_ save__ndb_dbitem.sigma _item_description.description ; The estimated standard deviation of the average C-C distances between carbons in the chemical component. ; _item.name '_ndb_dbitem.sigma' _item.category_id ndb_dbitem _item.mandatory_code no _item_type.code float save_ save__ndb_dbitem.compound _item_description.description ; The chemical name of the complete structure as stored in the database. ; _item.name '_ndb_dbitem.compound' _item.category_id ndb_dbitem _item.mandatory_code no _item_type.code text save_ save__ndb_dbitem.citation _item_description.description ; The bibliographic citation for the structure extracted from the database. ; _item.name '_ndb_dbitem.citation' _item.category_id ndb_dbitem _item.mandatory_code no _item_type.code text save_ ######################## ## NDB_DBITEM_EXCLUDE ## ######################## save_NDB_DBITEM_EXCLUDE _category.description ; Data items in the NDB_DBITEM_EXCLUDE category record the names of dbitems (pointers to the NDB_DBITEM category) that are to be excluded from the results of a database search. ; _category.id ndb_dbitem_exclude _category.mandatory_code no _category_key.name '_ndb_dbitem_exclude.name' loop_ _category_group.id 'inclusive_group' 'ndb_chem_comp_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example - based on a search of the Cambridge Structural Database for cytosine-containing crystals ; ; _ndb_dbitem_exclude.name zozvuf _ndb_dbitem_exclude.parameter N3-C4-C5 _ndb_dbitem_exclude.db csd _ndb_dbitem_exclude.dbsearch_id cyt_neu _ndb_dbitem_exclude.text 'value:118.8 4.5 sds from mean (mean:121.7 sd:0.6)' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__ndb_dbitem_exclude.name _item_description.description ; The identifier for a particular database item. ; _item.name '_ndb_dbitem_exclude.name' _item.category_id ndb_dbitem_exclude _item.mandatory_code no _item_type.code code save_ save__ndb_dbitem_exclude.db _item_description.description ; The the database from which the item is obtained. ; _item.name '_ndb_dbitem_exclude.db' _item.category_id ndb_dbitem_exclude _item.mandatory_code no _item_type.code line save_ save__ndb_dbitem_exclude.dbsearch_id _item_description.description ; The identifier for a particular database search. ; _item.name '_ndb_dbitem_exclude.name' _item.category_id ndb_dbitem_exclude _item.mandatory_code no _item_type.code code save_ save__ndb_dbitem_exclude.text _item_description.description ; The description of why an item is to be excluded, in the example given, this is due to the distance of the value from the population mean. ; _item.name '_ndb_dbitem_exclude.text' _item.category_id ndb_dbitem_exclude _item.mandatory_code no _item_type.code text save_ save__ndb_dbitem_exclude.parameter _item_description.description ; An optional parameter involved in rejecting an item. ; _item.name '_ndb_dbitem_exclude.parameter' _item.category_id ndb_dbitem_exclude _item.mandatory_code no _item_type.code text save_ #################### ## NDB_CONSTRAINT ## #################### save_NDB_CONSTRAINT _category.description ; Data items in the NDB_CONSTRAINT category give details about the constraints used in a particular database search, as well as those used in subsequent filtering operations. For example, when searching for ribose residues in a glycosidic linkage with one of the nitrogenous bases A, G, C, T, or U and initial search constraint constraint is that the glycosidic linkage be present, while the chirality is enforced as a second filter. Each of these is recorded in NDB_CONSTRAINT. ; _category.id ndb_constraint _category.mandatory_code no loop_ _category_key.name '_ndb_constraint.dsearch_id' '_ndb_constraint.label' loop_ _category_group.id 'inclusive_group' 'ndb_chem_comp_group' save_ save__ndb_constraint.name _item_description.description ; Optional name associated with the constraint. ; _item.name '_ndb_constraint.id' _item.category_id ndb_constraint _item.mandatory_code no _item_type.code line save_ save__ndb_constraint.label _item_description.description ; Internal label applied to a constraint. ; _item.name '_ndb_constraint.id' _item.category_id ndb_constraint _item.mandatory_code no _item_type.code line save_ save__ndb_constraint.db _item_description.description ; Internal name for target database. ; _item.name '_ndb_constraint.id' _item.category_id ndb_constraint _item.mandatory_code no _item_type.code line save_ save__ndb_constraint.dbsearch_id _item_description.description ; Database search indentifier. ; _item.name '_ndb_constraint.id' _item.category_id ndb_constraint _item.mandatory_code no _item_type.code code save_ save__ndb_constraint.text _item_description.description ; Internal value of text associated with the constraint. ; _item.name '_ndb_constraint.id' _item.category_id ndb_constraint _item.mandatory_code no _item_type.code text save_ save__ndb_constraint.test_number _item_description.description ; Internal ordering number applied to a constraint. ; _item.name '_ndb_constraint.number' _item.category_id ndb_constraint _item.mandatory_code no _item_type.code int save_ save__ndb_constraint.description _item_description.description ; Text description the constraint ; _item.name '_ndb_constraint.description' _item.category_id ndb_constraint _item.mandatory_code no _item_type.code text save_ save_NDB_DBSEARCH _category.description ; This category records the details of each database search. ; _category.id ndb_dbsearch _category.mandatory_code no _category_key.name '_ndb_dbsearch.dsearch_id' loop_ _category_group.id 'inclusive_group' 'ndb_chem_comp_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example - based on a search of the Cambridge Structural Database for cytosine-containing crystals ; ; _ndb_dbsearch.id cyt_neu _ndb_dbsearch.sample_size 45 _ndb_dbsearch.time 'Fri May 9 13:49:31 1997' _ndb_dbsearch.db csd _ndb_dbsearch.dbversion 512 _ndb_dbsearch.dbreleasedate 'Sep 15 19:34:11 BST 1996' ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__ndb_dbsearch.id _item_description.description ; The identifier for a particular database search. ; _item.name '_ndb_dbsearch.id' _item.category_id ndb_dbsearch _item.mandatory_code no _item_type.code code save_ save__ndb_dbsearch.sample_size _item_description.description ; The number of dbitems used from the given database search. ; _item.name '_ndb_dbsearch.sample_size' _item.category_id ndb_dbsearch _item.mandatory_code no _item_type.code int save_ save__ndb_dbsearch.sample_time _item_description.description ; The time at which the given database search was performed. ; _item.name '_ndb_dbsearch.time' _item.category_id ndb_dbsearch _item.mandatory_code no _item_type.code date save_ save__ndb_dbsearch.db _item_description.description ; The database used for the given search. ; _item.name '_ndb_dbsearch.db' _item.category_id ndb_dbsearch _item.mandatory_code no _item_type.code code save_ save__ndb_dbsearch.db_version _item_description.description ; An identifier of the version of the database used for the search. ; _item.name '_ndb_dbsearch.db_version' _item.category_id ndb_dbsearch _item.mandatory_code no _item_type.code line save_ save__ndb_dbsearch.releasedate _item_description.description ; The date of release for the given database search: similar information as dbversion. ; _item.name '_ndb_dbsearch.releasedate' _item.category_id ndb_dbsearch _item.mandatory_code no _item_type.code date save_ ######################## ## NDB_CHEM_COMP_BOND ## ######################## save_NDB_CHEM_COMP_BOND ; Data items in the NDB_CHEM_COMP_BOND category record details about the sources of values for bonds in a chemical component, and their deviation from values in model structures: A model structure in the set of coordinates which minimizes the difference between the average internal geometries and the corresponding internal geometries of the model. Data items in the NDB_CHEM_COMP_BOND parallel the CHEM_COMP_BOND category and share a common comp_id descriptor. This category contains a pointer for each geometry to the database search that was used to obtain it. ; _category.id ndb_chem_comp_bond _category.mandatory_code no loop_ _category_key.name '_ndb_chem_comp_bond.comp_id' '_ndb_chem_comp_bond.atom_id_1' '_ndb_chem_comp_bond.atom_id_2' '_ndb_chem_comp_bond.dbsearch_id' loop_ _category_group.id 'inclusive_group' 'ndb_chem_comp_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example - based on model for neutral cytosine ; ; loop_ _ndb_chem_comp_bond.comp_id _ndb_chem_comp_bond.atom_id_1 _ndb_chem_comp_bond.atom_id_2 _ndb_chem_comp_bond.csd_bond_order _ndb_chem_comp_bond.dbsearch_id _ndb_chem_comp_bond.value_dist_calc _ndb_chem_comp_bond.value_dist _ndb_chem_comp_bond.value_dist_delta cyt_neu N1 C2 '1,2,5 ' cyt_neu 1.3966 1.3965 -0.0001 cyt_neu C2 N3 '1,2,5 ' cyt_neu 1.3532 1.3530 -0.0002 cyt_neu N3 C4 '1,2,5 ' cyt_neu 1.3379 1.3379 0.0000 cyt_neu C4 C5 '1,2,5 ' cyt_neu 1.4260 1.4261 0.0001 cyt_neu C5 C6 '1,2,5 ' cyt_neu 1.3397 1.3398 0.0001 cyt_neu C6 N1 '1,2,5 ' cyt_neu 1.3652 1.3652 0.0000 cyt_neu C2 O2 '1,2,5 ' cyt_neu 1.2398 1.2398 0.0000 cyt_neu C4 N4 '1,2,5 ' cyt_neu 1.3316 1.3316 0.0000 cyt_neu N1 C1* '1,2,5 ' cyt_neu 1.4722 1.4722 0.0000 cyt_neu N4 H4A 1 cyt_neu . . . cyt_neu N4 H4B 1 cyt_neu . . . cyt_neu C5 H5 1 cyt_neu . . . cyt_neu C6 H6 1 cyt_neu . . . ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__ndb_chem_comp_bond.atom_id_1 _item_description.description ; The id of the first of the two atoms that define the bond. ; _item.name '_ndb_chem_comp_bond.atom_id_1' _item.category_id ndb_chem_comp_bond _item.mandatory_code yes _item_dependent.dependent_name '_ndb_chem_comp_bond.atom_id_2' _item_type.code code save_ save__ndb_chem_comp_bond.atom_id_2 _item_description.description ; The id of the second of the two atoms that define the bond. ; _item.name '_ndb_chem_comp_bond.atom_id_2' _item.category_id ndb_chem_comp_bond _item.mandatory_code yes _item_dependent.dependent_name '_ndb_chem_comp_bond.atom_id_1' _item_type.code code save_ save__ndb_chem_comp_bond.comp_id _item_description.description ; This data item is a pointer to _chem_comp.id in the CHEM_COMP category. ; _item.name '_ndb_chem_comp_bond.comp_id' _item.category_id ndb_chem_comp_bond _item.mandatory_code yes _item_type.code code save_ save__ndb_chem_comp_bond.dbsearch_id _item_description.description ; This data item is a pointer to _ndb_dbsearch_id in the NDB_DBSEARCH category. ; _item.name '_ndb_chem_comp_bond.dbsearch_id' _item.category_id ndb_chem_comp_bond _item.mandatory_code yes _item_type.code code save_ save__ndb_chem_comp_bond.value_dist _item_description.description ; This data item is the average distance between atoms _ndb_chem_comp_bond.atom_id_1 and _ndb_chem_comp_bond.atom_id_2. ; _item.name '_ndb_chem_comp_bond.value_dist' _item.category_id ndb_chem_comp_bond _item.mandatory_code no _item_type.code float save_ save__ndb_chem_comp_bond.value_dist_esd _item_description.description ; This data item is the esd of the bond. ; _item.name '_ndb_chem_comp_bond.value_dist_esd' _item.category_id ndb_chem_comp_bond _item.mandatory_code no _item_type.code float save_ save__ndb_chem_comp_bond.value_dist_calc _item_description.description ; This data item is the calculated distance between atoms ndb_chem_comp_bond.atom_id_1 and ndb_chem_comp_bond.atom_id_2 in the model structure. ; _item.name '_ndb_chem_comp_bond.value_dist_calc' _item.category_id ndb_chem_comp_bond _item.mandatory_code no _item_type.code float save_ save__ndb_chem_comp_bond.value_dist_delta _item_description.description ; This data item is the difference betweeen the _ndb_chem_comp.value_dist and the _ndb_chem_comp.value_dist_calc data_items. ; _item.name '_ndb_chem_comp_bond.value_dist_delta' _item.category_id ndb_chem_comp_bond _item.mandatory_code no _item_type.code float save_ ######################### ## NDB_CHEM_COMP_ANGLE ## ######################### save_NDB_CHEM_COMP_ANGLE _category.description ; Data items in the NDB_CHEM_COMP_ANGLE category record details about the source of the values for angles in a chemical component, and also compare these average internal geometries with that calculated for the model structures: A model structure is the set of coordinates which minimizes the difference between the average internal geometries and the corresponding internal geometries of the model. Angles are designated by three atoms, with the second atom forming the vertex of the angle. Target values may be specified as angles in degrees, as a distance between the first and third atoms, or both. ; _category.id ndb_chem_comp_angle _category.mandatory_code no loop_ _category_key.name '_ndb_chem_comp_angle.comp_id' '_ndb_chem_comp_angle.atom_id_1' '_ndb_chem_comp_angle.atom_id_2' '_ndb_chem_comp_angle.atom_id_3' '_ndb_chem_comp_angle.dbsearch_id' loop_ _category_group.id 'inclusive_group' 'ndb_chem_comp_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ ; Example - based on model for neutral cytosine ; ; loop_ _ndb_chem_comp_angle.comp_id _ndb_chem_comp_angle.atom_id_1 _ndb_chem_comp_angle.atom_id_2 _ndb_chem_comp_angle.atom_id_3 _ndb_chem_comp_angle.dbsearch_id _ndb_chem_comp_angle.value_angle_calc _ndb_chem_comp_angle.value_angle _ndb_chem_comp_angle.value_angle_delta cyt_neu C6 N1 C2 cyt_neu 120.35 120.31 -0.04 cyt_neu N1 C2 N3 cyt_neu 119.24 119.19 -0.05 cyt_neu C2 N3 C4 cyt_neu 120.06 120.03 -0.03 cyt_neu N3 C4 C5 cyt_neu 121.67 121.63 -0.04 # ... other rows deleted ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__ndb_chem_comp_angle.atom_id_1 _item_description.description ; The id of the first of the three atoms that define the angle. This data item is a pointer to _chem_comp_atom.atom_id in the chem_comp_atom category. ; _item.name '_ndb_chem_comp_angle.atom_id_1' _item.mandatory_code yes loop_ _item_dependent.dependent_name '_ndb_chem_comp_angle.atom_id_2' '_ndb_chem_comp_angle.atom_id_3' save_ save__chem_comp_angle.atom_id_2 _item_description.description ; The id of the second of the three atoms that define the angle. The second atom is taken to be the apex of the angle. This data item is a pointer to _chem_comp_atom.atom_id in the chem_comp_atom category. ; _item.name '_ndb_chem_comp_angle.atom_id_2' _item.mandatory_code yes loop_ _item_dependent.dependent_name '_ndb_chem_comp_angle.atom_id_1' '_ndb_chem_comp_angle.atom_id_3' save_ save__ndb_chem_comp_angle.atom_id_3 _item_description.description ; The id of the third of the three atoms that define the angle. This data item is a pointer to _chem_comp_atom.atom_id in the chem_comp_atom category. ; _item.name '_ndb_chem_comp_angle.atom_id_3' _item.mandatory_code yes loop_ _item_dependent.dependent_name '_ndb_chem_comp_angle.atom_id_1' '_ndb_chem_comp_angle.atom_id_2' save_ save__ndb_chem_comp_angle.comp_id _item_description.description ; This data item is a pointer to _chem_comp.id in the CHEM_COMP category. ; _item.name '_ndb_chem_comp_angle.comp_id' _item.mandatory_code yes save_ save__ndb_chem_comp_angle.value_angle _item_description.description ; The value that should be taken as the target value for the angle associated with the specified atoms, expressed in degrees. ; _item.name '_ndb_chem_comp_angle.value_angle' _item.category_id ndb_chem_comp_angle _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum 180.0 -180.0 180.0 0.0 0.0 0.0 _item_related.related_name '_ndb_chem_comp_angle.value_angle_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code degrees save_ save__ndb_chem_comp_angle.value_angle_esd _item_description.description ; The estimated standard deviation of _ndb_chem_comp_angle.value_angle. ; _item.name '_ndb_chem_comp_angle.value_angle_esd' _item.category_id ndb_chem_comp_angle _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum 180.0 -180.0 180.0 0.0 0.0 0.0 _item_related.related_name '_ndb_chem_comp_angle.value_angle' _item_related.function_code associated_value _item_type.code float _item_units.code degrees save_ save__ndb_chem_comp_angle.value_dist _item_description.description ; This data item is the average distance between atoms _chem_comp_angle.atom_id_1 and _chem_comp_angle.atom_id_3. ; _item.name '_ndb_chem_comp_angle.value_dist' _item.category_id ndb_chem_comp_angle _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_ndb_chem_comp_angle.value_dist_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__ndb_chem_comp_angle.value_dist_esd _item_description.description ; The estimated standard deviation of _ndb_chem_comp_angle.value_dist. ; _item.name '_ndb_chem_comp_angle.value_dist_esd' _item.category_id ndb_chem_comp_angle _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_ndb_chem_comp_angle.value_dist' _item_related.function_code associated_value _item_type.code float _item_units.code angstroms save_ save__ndb_chem_comp_angle.value_angle_calc _item_description.description ; The value calculated for the specified angle in the model structure. ; _item.name '_ndb_chem_comp_angle.value_angle_calc' _item.category_id ndb_chem_comp_angle _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum 180.0 0.0 0.0 0.0 _item_related.related_name '_ndb_chem_comp_angle.value_angle_delta' _item_related.function_code associated_calc _item_type.code float _item_type_conditions.code calc _item_units.code degrees save_ save__ndb_chem_comp_angle.value_angle_delta _item_description.description ; This data item is the difference betweeen the _ndb_chem_comp_angle.value_angle and the _ndb_chem_comp_angle.value_angle_calc data items. ; _item.name '_ndb_chem_comp_angle.value_delta' _item.category_id ndb_chem_comp_angle _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum 180.0 0.0 0.0 0.0 _item_related.related_name '_ndb_chem_comp_angle.value_delta' _item_related.function_code associated_calc _item_type.code float _item_type_conditions.code calc _item_units.code degrees save_ save__ndb_chem_comp_angle.value_dist_calc _item_description.description ; The value calculated for the angle (using the idealized coordinates) between the atoms specified by _ndb_chem_comp_angle.atom_id_1 and _ndb_chem_comp_angle.atom_id_3. ; _item.name '_ndb_chem_comp_angle.value_dist_calc' _item.category_id ndb_chem_comp_angle _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_ndb_chem_comp_angle.value_dist_delta' _item_related.function_code associated_delta _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__ndb_chem_comp_angle.value_dist_delta _item_description.description _item.name '_ndb_chem_comp_angle.value_dist_delta' _item.category_id ndb_chem_comp_angle _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_ndb_chem_comp_angle.value_dist_calc' _item_related.function_code associated_calc _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__ndb_chem_comp_angle.dbsearch_id _item_description.description ; This data item is a pointer to _ndb_dbsearch_id in the NDB_DBSEARCH category. ; _item.name '_ndb_chem_comp_angle.dbsearch_id' _item.category_id ndb_chem_comp_angle _item.mandatory_code yes _item_type.code code save_ ####################### ## NDB_CHEM_COMP_TOR ## ####################### save_NDB_CHEM_COMP_TOR _category.description ; Data items in the NDB_CHEM_COMP_TOR category record details about the sources of torsion angles in a chemical component and the deviation of the torsion values from ones calculated for a model structure: A model structure is the set of coordinates which minimizes the difference between the average internal geometries and the corresponding internal geometries of the model. ; _category.id ndb_chem_comp_tor _category.mandatory_code no loop_ _category_key.name '_ndb_chem_comp_tor.comp_id' '_ndb_chem_comp_tor.id' '_ndb_chem_comp_tor.db_searchid' loop_ _category_group.id 'inclusive_group' 'ndb_chem_comp_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example - based on model for adenine ; ; loop_ _ndb_chem_comp_tor.comp_id _ndb_chem_comp_tor.id _ndb_chem_comp_tor.dbsearch_id A_anti N1-C2-N3-C4 ade_neu A_anti C2-N3-C4-C5 ade_neu A_anti N3-C4-C5-C6 ade_neu A_anti C4-C5-C6-N1 ade_neu A_anti C5-C6-N1-C2 ade_neu A_anti C6-N1-C2-N3 ade_neu A_anti N9-C4-C5-N7 ade_neu A_anti C4-C5-N7-C8 ade_neu A_anti C5-N7-C8-N9 ade_neu A_anti N7-C8-N9-C4 ade_neu A_anti C8-N9-C4-C5 ade_neu A_anti C2-N1-C6-N6 ade_neu A_anti C4*-O4*-C1*-C2* ribose A_anti O4*-C1*-C2*-C3* ribose A_anti C1*-C2*-C3*-C4* ribose A_anti C2*-C3*-C4*-O4* ribose A_anti C3*-C4*-O4*-C1* ribose A_anti C2*-C3*-C4*-C5* ribose A_anti gamma all_ribose_gamma A_anti delta ribose A_anti O4*-C4*-C3*-O3* ribose A_anti C4*-O4*-C1*-N ribose A_anti O4*-C4*-C5*-O5* all_ribose_gamma A_anti C5*-C4*-O4*-C1* ribose A_anti C1*-C2*-C3*-O3* ribose A_anti C3*-C2*-C1*-N ribose A_anti O3*-C3*-C2*-O2* ribose ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__ndb_chem_comp_tor.id _item_description.description ; The value of _ndb_chem_comp_tor.id must uniquely identify a record in the CHEM_COMP_TOR list. ; loop_ _item.name _item.category_id _item.mandatory_code '_ndb_chem_comp_tor.id' ndb_chem_comp_tor yes '_ndb_chem_comp_tor_value.tor_id' ndb_chem_comp_tor_value yes loop_ _item_linked.child_name _item_linked.parent_name '_ndb_chem_comp_tor_value.tor_id' '_ndb_chem_comp_tor.id' _item_type.code code save_ save__ndb_chem_comp_tor.comp_id _item_description.description ; This data item is a pointer to _chem_comp.id in the CHEM_COMP category. ; _item.name '_ndb_chem_comp_tor.comp_id' _item.mandatory_code yes save_ save__ndb_chem_comp_tor.dbsearch_id _item_description.description ; This data item is a pointer to _ndb_chem_comp_dbsearch.id in the NDB_CHEM_COMP_DBSEARCH category. ; _item.name '_ndb_chem_comp_tor.dbsearch_id' _item.mandatory_code yes _item_linked.child_name '_ndb_chem_comp_tor_value.dbsearch_id' _item_linked.parent_name '_ndb_dbsearch.id' save_ save__ndb_chem_comp_tor.value_angle_calc _item_description.description ; The value calculated for the angle given the coordinates that minimize the difference between the average internal geometry and and that calculated from the coordinates. ; _item.name '_ndb_chem_comp_tor.value_calc' _item.category_id ndb_chem_comp_tor _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum 360.0 0.0 _item_related.related_name '_ndb_chem_comp_tor.value_delta' _item_related.function_code associated_calc _item_type.code float _item_type_conditions.code calc _item_units.code degrees save_ save__ndb_chem_comp_tor.value_angle_delta _item_description.description ; The value calculated for the angle given the coordinates that minimize the difference between the average internal geometry and and that calculated from the coordinates. ; _item.name '_ndb_chem_comp_tor.value_delta' _item.category_id ndb_chem_comp_tor _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum 360.0 0.0 _item_related.related_name '_ndb_chem_comp_tor.value_delta' _item_related.function_code associated_calc _item_type.code float _item_type_conditions.code calc _item_units.code degrees save_ save__ndb_chem_comp_tor.value_dist_calc _item_description.description ; The value calculated for the angle using coordinates minimize the difference between the average internal geometry and and that calculated from the coordinates between the atoms specified by _ndb_chem_comp_tor.atom_id_1 and _ndb_chem_comp_tor.atom_id_4. ; _item.name '_ndb_chem_comp_tor.value_dist_calc' _item.category_id ndb_chem_comp_tor _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_ndb_chem_comp_tor.value_dist_delta' _item_related.function_code associated_delta _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__ndb_chem_comp_tor.value_dist_delta _item_description.description _item.name '_ndb_chem_comp_tor.value_dist_delta' _item.category_id ndb_chem_comp_tor _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_ndb_chem_comp_tor.value_dist_calc' _item_related.function_code associated_calc _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ ######################## ## NDB_CHEM_LINK_BOND ## ######################## save_NDB_CHEM_LINK_BOND _category.description ; Data items in the NDB_CHEM_LINK_BOND category record details about the source of the bonds in a linkage between components in the chemical structure, and the deviations between these average internal geometries and those calculated from the model coordinates. ; _category.id ndb_chem_link_bond _category.mandatory_code no loop_ _category_key.name '_ndb_chem_link_bond.link_id' '_ndb_chem_link_bond.atom_id_1' '_ndb_chem_link_bond.atom_id_2' loop_ _category_group.id 'inclusive_group' 'ndb_chem_link_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example - ; ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__ndb_chem_link_bond.atom_1_comp_id _item_description.description ; This data item indicates whether atom 1 is found in the first or the second of the two components connected by the linkage. ; _item.name '_ndb_chem_link_bond.atom_1_comp_id' _item.category_id ndb_chem_link_bond _item.mandatory_code no loop_ _item_dependent.dependent_name '_ndb_chem_link_bond.atom_2_comp_id' loop_ _item_enumeration.value _item_enumeration.detail 1 'the atom is in component 1' 2 'the atom is in component 2' _item_type.code ucode save_ save__ndb_chem_link_bond.atom_2_comp_id _item_description.description ; This data item indicates whether atom 2 is found in the first or the second of the two chemical components connected by the linkage. ; _item.name '_ndb_chem_link_bond.atom_2_comp_id' _item.category_id ndb_chem_link_bond _item.mandatory_code no _item_dependent.dependent_name '_ndb_chem_link_bond.atom_1_comp_id' loop_ _item_enumeration.value _item_enumeration.detail 1 'the atom is in component 1' 2 'the atom is in component 2' _item_type.code ucode save_ save__ndb_chem_link_bond.atom_id_1 _item_description.description ; The id of the first of the two atoms that define the bond. As this data item does not point to a specific atom in a specific chemical component, it is not a child in the linkage sense. ; _item.name '_ndb_chem_link_bond.atom_id_1' _item.category_id ndb_chem_link_bond _item.mandatory_code yes loop_ _item_dependent.dependent_name '_ndb_chem_link_bond.atom_id_2' _item_type.code code save_ save__ndb_chem_link_bond.atom_id_2 _item_description.description ; The id of the second of the two atoms that define the bond. As this data item does not point to a specific atom in a specific component, it is not a child in the linkage sense. ; _item.name '_ndb_chem_link_bond.atom_id_2' _item.category_id ndb_chem_link_bond _item.mandatory_code yes _item_dependent.dependent_name '_ndb_chem_link_bond.atom_id_1' _item_type.code code save_ save__ndb_chem_link_bond.link_id _item_description.description ; This data item is a pointer to _ndb_chem_link.id in the NDB_CHEM_LINK category. ; _item.name '_ndb_chem_link_bond.link_id' _item.mandatory_code yes save_ save__ndb_chem_link_bond.value_dist _item_description.description ; The value that should be taken as the target for the chemical bond associated with the specified atoms, expressed as a distance. ; _item.name '_ndb_chem_link_bond.value_dist' _item.category_id ndb_chem_link_bond _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_ndb_chem_link_bond.value_dist_delta' _item_related.function_code associated_delta _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__ndb_chem_link_bond.value_dist_calc _item_description.description ; The estimated standard deviation of _ndb_chem_link_bond.value_dist_esd. ; _item.name '_ndb_chem_link_bond.value_dist_calc' _item.category_id ndb_chem_link_bond _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_ndb_chem_link_bond.value_delta' _item_related.function_code associated_delta _item_type.code float _item_units.code angstroms save_ save__ndb_chem_link_bond.value_dist_delta _item_description.description ; The estimated standard deviation of _ndb_chem_link_bond.value_dist_esd. ; _item.name '_ndb_chem_link_bond.value_dist_delta' _item.category_id ndb_chem_link_bond _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 loop_ _item_related.related_name _item_related.function_code '_ndb_chem_link_bond.value_calc' associated_calc '_ndb_chem_link_bond.value_dist' associated_dist _item_type.code float _item_units.code angstroms save_ ######################### ## NDB_CHEM_LINK_ANGLE ## ######################### save_NDB_CHEM_LINK_ANGLE _category.description ; Data items in the NDB_CHEM_LINK_ANGLE category record details about the sources of angles in a linkage between chemical groups, and their deviations from the corresponding angles in model structures. ; _category.id ndb_chem_link_angle _category.mandatory_code no loop_ _category_key.name '_ndb_chem_link_angle.link_id' '_ndb_chem_link_angle.atom_id_1' '_ndb_chem_link_angle.atom_id_2' '_ndb_chem_link_angle.atom_id_3' '_ndb_chem_link_angle.dbsearch_id' loop_ _category_group.id 'inclusive_group' 'ndb_chem_link_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; ; ; ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__ndb_chem_link_angle.atom_1_comp_id _item_description.description ; This data item indicates whether atom 1 is found in the first or the second of the two component connected by the linkage. ; _item.name '_ndb_chem_link_angle.atom_1_comp_id' _item.category_id ndb_chem_link_angle _item.mandatory_code no loop_ _item_dependent.dependent_name '_ndb_chem_link_angle.atom_2_comp_id' '_ndb_chem_link_angle.atom_3_comp_id' loop_ _item_enumeration.value _item_enumeration.detail 1 'the atom is in component 1' 2 'the atom is in component 2' _item_type.code ucode save_ save__ndb_chem_link_angle.atom_2_comp_id _item_description.description ; This data item indicates whether atom 2 is found in the first or the second of the two components connected by the linkage. ; _item.name '_ndb_chem_link_angle.atom_2_comp_id' _item.category_id ndb_chem_link_angle _item.mandatory_code no loop_ _item_dependent.dependent_name '_ndb_chem_link_angle.atom_1_comp_id' '_ndb_chem_link_angle.atom_3_comp_id' loop_ _item_enumeration.value _item_enumeration.detail 1 'the atom is in component 1' 2 'the atom is in component 2' _item_type.code ucode save_ save__ndb_chem_link_angle.atom_3_comp_id _item_description.description ; This data item indicates whether atom 3 is found in the first or the second of the two components connected by the linkage. ; _item.name '_ndb_chem_link_angle.atom_3_comp_id' _item.category_id ndb_chem_link_angle _item.mandatory_code no loop_ _item_dependent.dependent_name '_ndb_chem_link_angle.atom_1_comp_id' '_ndb_chem_link_angle.atom_2_comp_id' loop_ _item_enumeration.value _item_enumeration.detail 1 'the atom is in component 1' 2 'the atom is in component 2' _item_type.code ucode save_ save__ndb_chem_link_angle.atom_id_1 _item_description.description ; The id of the first of the three atoms that define the angle. As this data item does not point to a specific atom in a specific component, it is not a child in the linkage sense. ; _item.name '_ndb_chem_link_angle.atom_id_1' _item.category_id ndb_chem_link_angle _item.mandatory_code yes loop_ _item_dependent.dependent_name '_ndb_chem_link_angle.atom_id_2' '_ndb_chem_link_angle.atom_id_3' _item_type.code code save_ save__ndb_chem_link_angle.atom_id_2 _item_description.description ; The id of the second of the three atoms that define the angle. The second atom is taken to be the apex of the angle. As this data item does not point to a specific atom in a specific component, it is not a child in the linkage sense. ; _item.name '_ndb_chem_link_angle.atom_id_2' _item.category_id ndb_chem_link_angle _item.mandatory_code yes loop_ _item_dependent.dependent_name '_ndb_chem_link_angle.atom_id_1' '_ndb_chem_link_angle.atom_id_3' _item_type.code code save_ save__ndb_chem_link_angle.atom_id_3 _item_description.description ; The id of the third of the three atoms that define the angle. As this data item does not point to a specific atom in a specific component, it is not a child in the linkage sense. ; _item.name '_ndb_chem_link_angle.atom_id_3' _item.category_id ndb_chem_link_angle _item.mandatory_code yes loop_ _item_dependent.dependent_name '_ndb_chem_link_angle.atom_id_1' '_ndb_chem_link_angle.atom_id_2' _item_type.code code save_ save__ndb_chem_link_angle.link_id _item_description.description ; This data item is a pointer to _ndb_chem_link.id in the CHEM_LINK category. ; _item.name '_ndb_chem_link_angle.link_id' _item.mandatory_code yes save_ save__ndb_chem_link_angle.value_angle _item_description.description ; The value that should be taken as the target value for the angle associated with the specified atoms, expressed in degrees. ; _item.name '_ndb_chem_link_angle.value_angle' _item.category_id ndb_chem_link_angle _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum 180.0 180.0 180.0 0.0 0.0 0.0 _item_related.related_name '_ndb_chem_link_angle.value_angle_delta' _item_related.function_code associated_delta _item_type.code float # ?? _item_type_conditions.code esd _item_units.code degrees save_ save__chem_link_angle.value_angle_calc _item_description.description ; lsc The estimated standard deviation of _chem_link_angle.value_angle. ; _item.name '_chem_link_angle.value_angle_esd' _item.category_id chem_link_angle _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum 180.0 180.0 180.0 0.0 0.0 0.0 _item_related.related_name '_chem_link_angle.value_angle' _item_related.function_code associated_value _item_type.code float _item_units.code degrees save_ save__chem_link_angle.value_dist _item_description.description ; The value that should be taken as the target value for the angle associated with the specified atoms, expressed as the distance between the atoms specified by _chem_comp_angle.atom_id_1 and _chem_comp_angle.atom_id_3. ; _item.name '_chem_link_angle.value_dist' _item.category_id chem_link_angle _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_chem_link_angle.value_dist_esd' _item_related.function_code associated_esd _item_type.code float _item_type_conditions.code esd _item_units.code angstroms save_ save__chem_link_angle.value_dist_esd _item_description.description ; The estimated standard deviation of _chem_comp_angle.value_dist_esd. ; _item.name '_chem_link_angle.value_dist_esd' _item.category_id chem_link_angle _item.mandatory_code no loop_ _item_range.maximum _item_range.minimum . 0.0 0.0 0.0 _item_related.related_name '_chem_link_angle.value_dist' _item_related.function_code associated_value _item_type.code float _item_units.code angstroms save_ ####################### # NDB_CHEM_LINK_TOR ### ####################### save_NDB_CHEM_LINK_TOR _category.description ; Data items in the NDB_CHEM_LINK_TOR link parallels the CHEM_LINK_TOR category and share a common comp_id descriptor. This category contains a pointer for each geometry to the database search that was used to obtain it. ; _category.id ndb_chem_link_tor _category.mandatory_code no loop_ _category_key.name '_ndb_chem_link_tor.comp_id' '_ndb_chem_link_tor.atom_id_1' '_ndb_chem_link_tor.atom_id_2' '_ndb_chem_link_tor.atom_id_3' '_ndb_chem_link_tor.atom_id_4' '_ndb_chem_link_tor.atom_1_comp_id' '_ndb_chem_link_tor.atom_2_comp_id' '_ndb_chem_link_tor.atom_3_comp_id' '_ndb_chem_link_tor.atom_4_comp_id' '_ndb_chem_link_tor.dbsearch_id' loop_ _category_group.id 'inclusive_group' 'ndb_chem_link_group' loop_ _category_examples.detail _category_examples.case # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ; Example 1 - based on model for adenine linked with ribose ; ; loop_ _ndb_chem_link_tor.link_id _ndb_chem_link_tor.atom_id_1 _ndb_chem_link_tor.atom_id_2 _ndb_chem_link_tor.atom_id_3 _ndb_chem_link_tor.atom_id_4 _ndb_chem_link_tor.atom_1_comp_id _ndb_chem_link_tor.atom_2_comp_id _ndb_chem_link_tor.atom_3_comp_id _ndb_chem_link_tor.atom_4_comp_id _ndb_chem_link_tor.dbsearch_id ribose_purine C8 N9 C1* C2* 1 1 2 2 ribose_link_purine_1 ; # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - save_ save__ndb_chem_link_tor.atom_id_1 _item_description.description ; The id of the first of the four atoms that define the tor. This data item is a pointer to _chem_link_atom.atom_id in the CHEM_LINK_ATOM category. ; _item.name '_ndb_chem_link_tor.atom_id_1' _item.mandatory_code yes _item_type.code code loop_ _item_dependent.dependent_name '_ndb_chem_link_tor.atom_id_2' '_ndb_chem_link_tor.atom_id_3' '_ndb_chem_link_tor.atom_id_4' save_ save__ndb_chem_link_tor.atom_id_2 _item_description.description ; The id of the second of the four atoms that define the tor. This data item is a pointer to _chem_link_atom.atom_id in the CHEM_LINK_ATOM category. ; _item.name '_ndb_chem_link_tor.atom_id_2' _item.mandatory_code yes _item_type.code code loop_ _item_dependent.dependent_name '_ndb_chem_link_tor.atom_id_1' '_ndb_chem_link_tor.atom_id_3' '_ndb_chem_link_tor.atom_id_4' save_ save__ndb_chem_link_tor.atom_id_3 _item_description.description ; The id of the third of the four atoms that define the tor. This data item is a pointer to _chem_link_atom.atom_id in the CHEM_LINK_ATOM category. ; _item.name '_ndb_chem_link_tor.atom_id_3' _item.mandatory_code yes _item_type.code code loop_ _item_dependent.dependent_name '_ndb_chem_link_tor.atom_id_1' '_ndb_chem_link_tor.atom_id_2' '_ndb_chem_link_tor.atom_id_4' save_ save__ndb_chem_link_tor.atom_id_4 _item_description.description ; The id of the last of the four atoms that define the tor. This data item is a pointer to _chem_link_atom.atom_id in the CHEM_LINK_ATOM category. ; _item.name '_ndb_chem_link_tor.atom_id_4' _item.mandatory_code yes _item_type.code code loop_ _item_dependent.dependent_name '_ndb_chem_link_tor.atom_id_1' '_ndb_chem_link_tor.atom_id_2' '_ndb_chem_link_tor.atom_id_3' save_ save__ndb_chem_link_tor.atom_1_comp_id _item_description.description ; This data item is a pointer to _chem_comp.id in the CHEM_COMP category. ; _item.name '_ndb_chem_link_tor.atom_1_comp_id' _item.mandatory_code yes _item_type.code code loop_ _item_dependent.dependent_name '_ndb_chem_link_tor.atom_2_comp_id' '_ndb_chem_link_tor.atom_3_comp_id' '_ndb_chem_link_tor.atom_4_comp_id' save_ save__ndb_chem_link_tor.atom_2_comp_id _item_description.description ; This data item is a pointer to _chem_comp.id in the CHEM_COMP category. ; _item.name '_ndb_chem_link_tor.atom_2_comp_id' _item.mandatory_code yes _item_type.code code loop_ _item_dependent.dependent_name '_ndb_chem_link_tor.atom_1_comp_id' '_ndb_chem_link_tor.atom_3_comp_id' '_ndb_chem_link_tor.atom_4_comp_id' save_ save__ndb_chem_link_tor.atom_3_comp_id _item_description.description ; This data item is a pointer to _chem_comp.id in the CHEM_COMP category. ; _item.name '_ndb_chem_link_tor.atom_3_comp_id' _item.mandatory_code yes _item_type.code code loop_ _item_dependent.dependent_name '_ndb_chem_link_tor.atom_1_comp_id' '_ndb_chem_link_tor.atom_2_comp_id' '_ndb_chem_link_tor.atom_4_comp_id' save_ save__ndb_chem_link_tor.atom_4_comp_id _item_description.description ; This data item is a pointer to _chem_comp.id in the CHEM_COMP category. ; _item.name '_ndb_chem_link_tor.atom_4_comp_id' _item.mandatory_code yes _item_type.code code loop_ _item_dependent.dependent_name '_ndb_chem_link_tor.atom_1_comp_id' '_ndb_chem_link_tor.atom_2_comp_id' '_ndb_chem_link_tor.atom_3_comp_id' save_ save__ndb_chem_link_tor.dbsearch_id _item_description.description ; This data item is a pointer to _ndb_dbsearch_id in the NDB_DBSEARCH category. ; _item.name '_ndb_chem_link_tor.dbsearch_id' _item.mandatory_code yes _item_type.code code save_