InvestigationCIF Dictionary Documentation

Interactive documentation for the InvestigationCIF dictionary structure.

pdbx_investigation

The PDBX_INVESTIGATION category provides a information of an investigation associated with this file.
_pdbx_investigation.id Required
code
Description:
Uniquely identifies an investigation.
Examples:
1
_pdbx_investigation.type Required Enum
line
Description:
Describes the type of investigation.
Examples:
Ligand Screening
Enumeration:
Value Description
Ligand Screening .
Crystallization Screening .
Time-resolved .
Other .
(No description)
_pdbx_investigation.db Required Enum
text
Description:
Database for investigation. Defined categories. Other types to be determined at later date.
Enumeration:
Value Description
ligscreen Ligand screening investigation
other Customized investigation
(No description)
_pdbx_investigation.project_id Optional
text
Description:
Another id; however not mandatory and with no child categories. From an external source.
Examples:
fh123456
_pdbx_investigation.title Optional
text
Description:
A title for the data block. The author should attempt to convey the essence of the investigation archived in the CIF in the title, and to distinguish this investigation result from others.
_pdbx_investigation.details Optional
text
Description:
Additional details relevant to the investigation.
_pdbx_investigation.external_url Optional
line
Description:
A URL link to investigation-level data at an external resource.
Examples +

Example 1 ;

_pdbx_investigation.id            FH123
_pdbx_investigation.type          "Ligand Screening"
_pdbx_investigation.db            ligscreen
_pdbx_investigation.project_id    fh123456
_pdbx_investigation.title         "Frag Screen Investigation XYZ"
_pdbx_investigation.details       "Fragment screening project for Hemoglobin"
_pdbx_investigation.external_url  https://www.fragscreen-facility.org/123456789
;

   #

pdbx_investigation_archived_data

The PDBX_INVESTIGATION_ARCHIVED_DATA category contains the entries (PDB / EMDB / BMRB / etc) that are contained in the investigation.
_pdbx_investigation_archived_data.id Required
int
Description:
The value of _pdbx_investigation_archived_data.archived_data_id must uniquely identify a record in the PDBX_INVESTIGATION_ARCHIVED_DATA list.
_pdbx_investigation_archived_data.investigation_id Required
code
Description:
This data item is a pointer to _pdbx_investigation.id in the PDBX_INVESTIGATION category.
_pdbx_investigation_archived_data.archive_db_name Required Enum
code
Description:
The primary external resource where relevant experimental or processed data is archived.
Enumeration:
Value Description
AlphaFoldDB AlphaFoldDB
BMRB Biological Magnetic Resonance Bank
EMDB Electron Microscopy Data Bank
EMPIAR Electron Microscopy Public Image Archive
IRRMC Integrated Resource for Reproducibility in Macromolecular Crystallography
MA Model Archive
Other Other
PCDDB Protein Circular Dichroism Data Bank
PDB Protein Data Bank
PDB-IHM PDB-IHM
PubChem PubChem
SASBDB Small Angle Scattering Biological Data Bank
SBGRID SBGrid Consortium, Harvard Medical School
SWISS-MODEL SWISS-MODEL, SIB
Zenodo Zenodo, CERN
(No description)
_pdbx_investigation_archived_data.archive_db_acc Optional
code
Description:
The specific cc code for the data, e.g. pdb ID 1ABC.
_pdbx_investigation_archived_data.archived_data_details Optional
text
Description:
A description of any experiment/arcived data specific aspects. This can potential be the data archive entry title. Potentially this entry title can be pulled into the system if the section is blank.
_pdbx_investigation_archived_data.archived_data_url Optional
line
Description:
A URL link to experiment-level data at an external resource.
_pdbx_investigation_archived_data.archived_data_doi Optional
line
Description:
A doi to experiment-level data at an external resource.
Examples +

Theoretical example. ;

_pdbx_investgation_archived_data.investigation_id 
_pdbx_investgation_archived_data.id 
_pdbx_investgation_archived_data.archive_db_name 
_pdbx_investgation_archived_data.archive_db_acc 
_pdbx_investgation_archived_data.archived_data_details 
_pdbx_investgation_archived_data.archived_url 
_pdbx_investgation_archived_data.archived_doi
FH123   1  'X-ray Diffraction'  PDB   1A3N 'DEOXY HUMAN HEMOGLOBIN'  https://www.wwpdb.org/pdb?id=pdb_00001a3n   10.2210/pdb1a3n/pdb
FH123   2  'X-ray Diffraction'  PDB   4NI0 'Quaternary R3 CO-liganded hemoglobin structure in complex with a thiol containing compound'  https://www.wwpdb.org/pdb?id=pdb_00004ni0   10.2210/pdb4ni0/pdb
;

   #

pdbx_investigation_descript

The PDBX_INVESTIGATION_DESCRIPT category provides a mechanism to assign distinct combinations of sample source organism(s) (n=>1) a unique singular identifier. The source organism(s) will be referred to via their entity_id as defined in the PDBX_INVESTIGATION_DESCRIPT category.
_pdbx_investigation_descript.id Required
int
Description:
The value of _pdbx_investigation_descript.id must identify a distinct combination of sample source organism(s) used in one or more experiments.
_pdbx_investigation_descript.entity_id Required
int
Description:
This data item is a pointer to _pdbx_investigation_entity.entity_id in the PDBX_INVESTIGATION_ENTITY category. This identifer will therefore provide reference to a singular sample source organism.
Examples +

Theoretical example. ;

loop_
_pdbx_investigation_descript.id
_pdbx_investigation_descript.entity_id
1 1
1 2
#
;

   #

pdbx_investigation_entity

The PDBX_INVESTIGATION_ENTITY category records information about the sample used in the investigation such as the source organism of the gene, or if isolated from natural source, the source organism for the organelle, complex or polymer, decsribed in terms of scientific name and taxonomy id.
_pdbx_investigation_entity.entity_id Required
int
Description:
The value of _pdbx_investigation_entity.entity_id must uniquely identify a record in the PDBX_INVESTIGATION_ENTITY list.
_pdbx_investigation_entity.poly_entity_id Optional
int
Description:
This data item is a pointer to _pdbx_investigation_entity_poly.poly_entity_id in the PDBX_INVESTIGATION_ENTITY_POLY category. This identifer will therefore provide reference to a singular polymer entity.
_pdbx_investigation_entity.src_method Required Enum
ucode
Description:
Defines the production method for the entity.
Enumeration:
Value Description
man Entity isolated from a genetically manipulated source
nat Entity isolated from a natural source
syn Entity obtained synthetically
(No description)
_pdbx_investigation_entity.src_organism_scientific Required
text
Description:
The scientific name of the organism from which an entity within the sample was derived. The organism name is for the source of the gene for samples that are isolated from a genetically manipulated source (e.g. recombinant expression), or which are chemically synthesized. The organism name is for both the source of the gene and/or the entity if sample is isolated from a natural source.
Examples:
Mus musculus
_pdbx_investigation_entity.src_ncbi_taxonomy_id Required
line
Description:
NCBI Taxonomy identifier for the source organism. In this context, the source organism is the source of the gene for samples that are isolated from a genetically manipulated source (e.g. recombinant expression), or which are chemically synthesized. The organism name is for both the source of the gene and/or the entity if sample is isolated from a natural source. Reference: Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD, Tatusova TA, Rapp BA (2000). Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2000 Jan 1
Examples +

Theoretical example. ;

loop_
_pdbx_investigation_entity.entity_id 
_pdbx_investigation_entity.poly_entity_id 
_pdbx_investigation_entity.src_method
_pdbx_investigation_entity.src_organism_scientific 
_pdbx_investigation_entity.src_ncbi_taxonomy_id 
1  1   man  'Homo sapiens' 9606
2  2   man  'Homo sapiens' 9606
;

   #

pdbx_investigation_entity_nonpoly

The PDBX_INVESTIGATION_ENTITY_NONPOLY category records information about the small molecules / non-polymers present in the sample and includes information such as name, molecular weight, an InChI and InChIkey descriptor. This can include sample buffer components, protein crystallization conditions, additatives, ligands that co-exist with protein (e.g. heme for hemoglobin), cryoprotectant agents, etc, etc.
_pdbx_investigation_entity_nonpoly.nonpoly_entity_id Required
int
Description:
The value of _pdbx_investigation_entity_nonpoly.entity_id must uniquely identify a record in the PDBX_INVESTIGATION_ENTITY_NONPOLY list.
_pdbx_investigation_entity_nonpoly.name Optional
text
Description:
The full name of the small molecule component.
Examples:
alanine
_pdbx_investigation_entity_nonpoly.chem_comp_id Optional
text
Description:
The Chemical Component Dictionary (CCD) code for the small molecule. In instances where codes are unknown or yet-to-be processed "?" can be used as a placeholder.
_pdbx_investigation_entity_nonpoly.formula Optional
text
Description:
The formula for the chemical component. Formulae are written according to the following rules: (1) Only recognized element symbols may be used. (2) Each element symbol is followed by a 'count' number. A count of '1' may be omitted. (3) A space or parenthesis must separate each cluster of (element symbol + count), but in general parentheses are not used. (4) The order of elements depends on whether carbon is present or not. If carbon is present, the order should be: C, then H, then the other elements in alphabetical order of their symbol. If carbon is not present, the elements are listed purely in alphabetic order of their symbol. This is the 'Hill' system used by Chemical Abstracts.
Examples:
C18 H19 N7 O8 S
_pdbx_investigation_entity_nonpoly.formula_weight Optional
float
Description:
Formula mass in daltons of the small molecule component.
_pdbx_investigation_entity_nonpoly.inchi_descriptor Optional
text
Description:
This InChI descriptor value for the small molecule component.
_pdbx_investigation_entity_nonpoly.inchi_descriptor_software Optional
line
Description:
This data item contains the name of the program or software library used to compute the InChI descriptor for the small molecule component.
_pdbx_investigation_entity_nonpoly.inchi_descriptor_software_version Optional
text
Description:
This data item contains the version of the program or software library used to compute the InChI descriptor for the small molecule component.
_pdbx_investigation_entity_nonpoly.inchikey Required
text
Description:
This InChIKey descriptor descriptor value for the small molecule component.
_pdbx_investigation_entity_nonpoly.inchikey_software Optional
line
Description:
This data item contains the name of the program or software library used to compute the InChIKey descriptor for the small molecule component.
_pdbx_investigation_entity_nonpoly.inchikey_software_version Optional
text
Description:
This data item contains the version of the program or software library used to compute the InChIKey descriptor for the small molecule component.
_pdbx_investigation_entity_nonpoly.isomeric_smiles Optional
text
Description:
This SMILES descriptor for the small molecule component including information about configuration around double bonds and chirality. An isomeric SMILES is also known as an CANONICALIZED SMILES.
_pdbx_investigation_entity_nonpoly.isomeric_smiles_software Optional
line
Description:
This data item contains the name of the program or software library used to compute the SMILES descriptor for the small molecule component.
_pdbx_investigation_entity_nonpoly.isomeric_smiles_software_version Optional
text
Description:
This data item contains the version of the program or software library used to compute the SMILES descriptor for the small molecule component.
_pdbx_investigation_entity_nonpoly.cas_identifier Optional
text
Description:
This Chemical Abstracts Service (CAS) identifier for the small molecule component.
Examples +

Theoretical example. ;

loop_
_pdbx_investigation_entity_nonpoly.nonpoly_entity_id 
_pdbx_investigation_entity_nonpoly.name                
_pdbx_investigation_entity_nonpoly.chem_comp_id
_pdbx_investigation_entity_nonpoly.formula 
_pdbx_investigation_entity_nonpoly.formula_weight 
_pdbx_investigation_entity_nonpoly.inchi_descriptor
_pdbx_investigation_entity_nonpoly.inchi_descriptor_software
_pdbx_investigation_entity_nonpoly.inchi_descriptor_software_version
_pdbx_investigation_entity_nonpoly.inchikey
_pdbx_investigation_entity_nonpoly.inchikey_software
_pdbx_investigation_entity_nonpoly.inchikey_software_version
_pdbx_investigation_entity_nonpoly.isomeric_smiles
_pdbx_investigation_entity_nonpoly.isomeric_smiles_software
_pdbx_investigation_entity_nonpoly.isomeric_smiles_software_version
_pdbx_investigation_entity_nonpoly.cas_identifier
1 'Tris Buffer'        TRS 'C4 H12 N O3'   122.143 'InChI=1S/C4H11NO3/c5-4(1-6,2-7)3-8/h6-8H,1-3,5H2/p+1'                   INCHI  1.03  LENZDBCJOHFCAS-UHFFFAOYSA-O  INCHI  1.03  '[NH3+]C(CO)(CO)CO'         CACTVS  3.341   77-86-1
2 'MOPS Buffer'        MPO 'C7 H15 N O4 S' 209.263 'InChI=1S/C7H15NO4S/c9-13(10,11)7-1-2-8-3-5-12-6-4-8/h1-7H2,(H,9,10,11)' INCHI  1.03  DVLFYONBTKHTER-UHFFFAOYSA-N  INCHI  1.03  'O[S](=O)(=O)CCCN1CCOCC1'   CACTVS  3.341   1132-61-2
3 'DTT'                DTT 'C4 H10 O2 S2'  154.251 'InChI=1S/C4H10O2S2/c5-3(1-7)4(6)2-8/h3-8H,1-2H2/t3-,4-/m0/s1'           INCHI  1.03  VHJLVAABSRFDPM-IMJSIDKUSA-N  INCHI  1.03  'O[C@@H](CS)[C@@H](O)CS'    CACTVS  3.341   3483-12-3
4 'CALCIUM ION'        CA   Ca              40.078 'InChI=1S/Ca/q+2'                                                        INCHI  1.03  BHPQYMZQTOCNFJ-UHFFFAOYSA-N  INCHI  1.03  '[Ca++]'                    CACTVS  3.341   ?
5 'MAGNESIUM ION'      MG   Mg              24.305 'InChI=1S/Mg/q+2'                                                        INCHI  1.03  JLVVSXFLKOJNIY-UHFFFAOYSA-N  INCHI  1.03  '[Mg++]'                    CACTVS  3.341   ?
6 'TRIETHYLENE GLYCOL' PGE 'C6 H14 O4'     150.173 'InChI=1S/C6H14O4/c7-1-3-9-5-6-10-4-2-8/h7-8H,1-6H2'                     INCHI  1.03  ZIBGPFATKBEMQZ-UHFFFAOYSA-N  INCHI  1.03  CCOCCOCCO                   CACTVS  3.341   ?
7  water               HOH 'H2 O'           18.015 'InChI=1S/H2O/h1H2'                                                      INCHI  1.03  XLYOFNOQVPJJNP-UHFFFAOYSA-N  INCHI  1.03  O                           CACTVS  3.341   ?
#
;

   #

pdbx_investigation_entity_poly

The PDBX_INVESTIGATION_ENTITY_POLY category records information about the polymers used in the investigation such as polymer-type, one-letter sequence code, and any external DB accession.
_pdbx_investigation_entity_poly.poly_entity_id Required
int
Description:
The value of _pdbx_investigation_entity_poly.poly_entity_id must uniquely identify a record in the PDBX_INVESTIGATION_ENTITY_POLY list.
_pdbx_investigation_entity_poly.type Required Enum
ucode
Description:
Defines the type of the entity.
Enumeration:
Value Description
polypeptide(D) .
polypeptide(L) .
polydeoxyribonucleotide .
polyribonucleotide .
polydeoxyribonucleotide/polyribonucleotide hybrid .
cyclic-pseudo-peptide .
peptide nucleic acid .
other .
(No description)
_pdbx_investigation_entity_poly.seq_one_letter_code_sample Optional
text
Description:
Canonical sequence of protein or nucleic acid polymer in standard one-letter codes of amino acids or nucleotides, corresponding to the sequence in _pdbx_investigation_entity_poly.seq_one_letter_code_with_ntsd. Non-standard amino acids/nucleotides are represented by letter 'X', or the parent amino acid/nucleotide if the Chemical Component Dictionary (CCD) code has _chem_comp.mon_nstd_parent_comp_id record. For modifications with several parent amino acids, all corresponding parent amino acid codes will be listed (ex. chromophores). Deoxynucleotides are represented by their canonical one-letter codes of A, C, G, or T. A for alanine or adenine B for ambiguous asparagine/aspartic-acid R for arginine N for asparagine D for aspartic-acid C for cysteine or cystine or cytosine Q for glutamine E for glutamic-acid Z for ambiguous glutamine/glutamic acid G for glycine or guanine H for histidine I for isoleucine L for leucine K for lysine M for methionine F for phenylalanine P for proline S for serine T for threonine or thymine W for tryptophan Y for tyrosine V for valine U for uracil O for water X for other
_pdbx_investigation_entity_poly.seq_one_letter_code_with_ntsd Required
text
Description:
Sequence of protein or nucleic acid polymer in standard one-letter codes of amino acids or nucleotides. Non-standard amino acids/nucleotides are represented by their Chemical Component Dictionary (CCD) codes in parenthesis. Deoxynucleotides are represented by the specially-assigned 2-letter CCD codes in parenthesis, with 'D' prefix added to their ribonucleotide counterparts. A for Alanine or Adenosine-5'-monophosphate C for Cysteine or Cytidine-5'-monophosphate D for Aspartic acid E for Glutamic acid F for Phenylalanine G for Glycine or Guanosine-5'-monophosphate H for Histidine I for Isoleucine or Inosinic Acid L for Leucine K for Lysine M for Methionine N for Asparagine or Unknown ribonucleotide O for Pyrrolysine P for Proline Q for Glutamine R for Arginine S for Serine T for Threonine U for Selenocysteine or Uridine-5'-monophosphate V for Valine W for Tryptophan Y for Tyrosine (DA) for 2'-deoxyadenosine-5'-monophosphate (DC) for 2'-deoxycytidine-5'-monophosphate (DG) for 2'-deoxyguanosine-5'-monophosphate (DT) for Thymidine-5'-monophosphate (MSE) for Selenomethionine (SEP) for Phosphoserine (PTO) for Phosphothreonine (PTR) for Phosphotyrosine (PCA) for Pyroglutamic acid (UNK) for Unknown amino acid (ACE) for Acetylation cap (NH2) for Amidation cap
Examples:
(MSE)SHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGAAFNVEFD
_pdbx_investigation_entity_poly.ref_db_name Optional Enum
code
Description:
The external resource where reference sequence information is stored.
Enumeration:
Value Description
GB Genbank
UNP UniProt
(No description)
_pdbx_investigation_entity_poly.ref_db_acc Optional
code
Description:
The accession code for the related reference information at the relevant external sequence resource.
_pdbx_investigation_entity_poly.ref_db_code Optional
code
Description:
More related reference information, for example an additional identifier for ref_db_name and ref_db_acc. However, this additional identifier may not be unchanged between database releases (aka it is not a stable_identifier and thus it is not enough to be the only identifier).
Examples +

Theoretical example. ;

loop_
_pdbx_investigation_entity_poly.poly_entity_id 
_pdbx_investigation_entity_poly.type 
_pdbx_investigation_entity_poly.seq_one_letter_code_sample 
_pdbx_investigation_entity_poly.seq_one_letter_code_with_ntsd 
_pdbx_investigation_entity_poly.ref_db_name 
_pdbx_investigation_entity_poly.ref_db_acc 
_pdbx_investigation_entity_poly.ref_db_code 
1  polypeptide(L)   MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH (MSE)VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAV(MSE)GNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH    UNP  P68871   HBB_HUMAN
2  polypeptide(L)   MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR      (MSE)VLSPADKTNVKAAWGKVGAHAGEYGAEALER(MSE)FLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDD(MSE)PNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR     UNP  P69905   HBA_HUMAN
;

   #

pdbx_investigation_focus

The PDBX_INVESTIGATION_FOCUS category contains top level data for the investigation. This catogory is designed to capture the focus / commonality between the set of experiments.
_pdbx_investigation_focus.investigation_id Required
code
Description:
This data item is a pointer to _pdbx_investigation.id in the PDBX_INVESTIGATION category.
_pdbx_investigation_focus.key_component_id Required
code
Description:
The value of _pdbx_investigation_focus.key_component_id must uniquely identify a record in the PDBX_INVESTIGATION_FOCUS list.
_pdbx_investigation_focus.key_component_name Optional
text
Description:
A textual description of the macromolecular target.
_pdbx_investigation_focus.comp_ref_db_acc Optional
code
Description:
The accession code for the related reference information at the relevant external sequence resource.
_pdbx_investigation_focus.comp_ref_db_name Optional Enum
code
Description:
The external resource where reference sequence information is stored.
Enumeration:
Value Description
GB Genbank
UNP UniProt
(No description)
_pdbx_investigation_focus.comp_ref_db_code Optional
code
Description:
More related reference information, for example an additional identifier for db and db_acc. However, this additional identifier may not be unchanged between database releases (aka it is not a stable_identifier and thus it is not enough to be the only identifier).
Examples +

Theoretical example. ;

_pdbx_investigation_focus.investigation_id 
_pdbx_investigation_focus.key_component_name
_pdbx_investigation_focus.key_component_id  
_pdbx_investigation_focus.comp_ref_db_acc 
_pdbx_investigation_focus.comp_ref_db_name 
_pdbx_investigation_focus.comp_ref_db_code
FH123   Hemoglobin1    1  P68871  UNP  HBB_HUMAN
FH123   Hemoglobin2    2  P69905  UNP  HBA_HUMAN
;

   #

pdbx_investigation_nonpoly_descript

The PDBX_INVESTIGATION_NONPOLY_DESCRIPT category describes the chemical components in the protein sample or crystallization conditions. It provides a mechanism to assign distinct combinations of small molecules (n=>1) a unique singular identifier. For example if there are two crystal condition, id 1 corresponse to one buffer, precipitant, additive combination, whereas id 2 is a different combination. The small molecules in the comnbination will be referred to via their entity_id as defined in the PDBX_INVESTIGATION_ENTITY_NONPOLY category.
_pdbx_investigation_nonpoly_descript.id Required
int
Description:
The value of _pdbx_investigation_nonpoly_descript.id must identify a distinct combination of small molecule components used in one or more experiments.
_pdbx_investigation_nonpoly_descript.nonpoly_entity_id Required
int
Description:
This data item is a pointer to _pdbx_investigation_entity_nonpoly.nonpoly_entity_id in the PDBX_INVESTIGATION_ENTITY_NONPOLY category. This identifer will therefore provide reference to a singular small molecule.
Examples +

Theoretical example. ;

loop_
_pdbx_investigation_nonpoly_descript.id
_pdbx_investigation_nonpoly_descript.nonpoly_entity_id
1 1
1 4
1 5
1 6 
1 7
2 2
2 4
2 5
2 6
2 7
3 2
3 3
3 4
3 5
3 6
3 7
4 1
4 3
4 4
4 5
4 6
4 7
#
;

   #

pdbx_investigation_poly_descript

The PDBX_INVESTIGATION_POLY_DESCRIPT category provides a mechanism to assign distinct combinations of polymers (n=>1) a unique singular identifier. Polymers will be referred to via their entity_id as defined in the PDBX_INVESTIGATION_POLY_DESCRIPT category.
_pdbx_investigation_poly_descript.id Required
int
Description:
The value of _pdbx_investigation_poly_descript.id must identify a distinct combination of polymer components used in one or more experiments.
_pdbx_investigation_poly_descript.poly_entity_id Required
int
Description:
This data item is a pointer to _pdbx_investigation_poly_entity.poly_entity_id in the PDBX_INVESTIGATION_ENTITY_POLY category. This identifer will therefore provide reference to a singular polymer entity.
Examples +

Theoretical example. ;

loop_
_pdbx_investigation_poly_descript.id
_pdbx_investigation_poly_descript.poly_entity_id
1 1
1 2
#
;

   #

pdbx_investigation_sample

The PDBX_INVESTIGATION_SAMPLE category contains the description of sample that was common for a series of experiments. Each record is an aggregation of polymers and non-polymers.
_pdbx_investigation_sample.sample_id Required
code
Description:
The value of _pdbx_investigation_sample.sample_id must uniquely identify a record in the PDBX_INVESTIGATION_SAMPLE list.
_pdbx_investigation_sample.investigation_id Required
code
Description:
This data item is a pointer to _pdbx_investigation.id in the PDBX_INVESTIGATION category.
_pdbx_investigation_sample.poly_descript_id Optional
int
Description:
This data item is a pointer to _pdbx_investigation_poly_descript.id in the PDBX_INVESTIGATION_POLY_DESCRIPT category. This identifer will form a reference to an aggregated list (n=>1) of macromolecular sample components.
_pdbx_investigation_sample.nonpoly_descript_id Optional
int
Description:
This data item is a pointer to _pdbx_investigation_nonpoly_descript.id in the PDBX_INVESTIGATION_NONPOLY_DESCRIPT category. This identifer will form a reference to an aggregated list (n=>1) of small molecule sample components. These "small molecules" are those which are not classes as polymers or compounds (or those directly derived from) the fragment library. If an experiment has an associated PDB entry - these non-polymers do not have to be modelled. However they should be described as a sample component.
_pdbx_investigation_sample.descript_id Optional
int
Description:
This data item is a pointer to _pdbx_investigation_entity.descript_id in the PDBX_INVESTIGATION_ENTITY category. This identifer will form a reference to an aggregated list (n=>1) of describing the source organism(s).
Examples +

Theoretical example 1. ;

loop_
_pdbx_investigation_sample.sample_id
_pdbx_investigation_sample.investigation_id
_pdbx_investigation_sample.poly_descript_id
_pdbx_investigation_sample.nonpoly_descript_id
_pdbx_investigation_sample.descript_id
1  1     1   1   1   
2  1     1   2   1   
3  1     2   3   2   
4  1     3   4   3
;

   #

pdbx_ligscreen_investigation_author

Data items in the PDBX_LIGSCREEN_INVESTIGATION_AUTHOR category record details about the authors associated with an investigation campaign generating data for a small molecule library or series screened against a target.
_pdbx_ligscreen_investigation_author.campaign_id Required
Description:
This data item is a pointer to _pdbx_ligscreen_investigation_campaign.campaign_id in the PDBX_LIGSCREEN_INVESTIGATION_CAMPAIGN category.
_pdbx_ligscreen_investigation_author.investigation_id Required
Description:
This data item is a pointer to _pdbx_investigation.id in the PDBX_INVESTIGATION category.
_pdbx_ligscreen_investigation_author.ordinal Required
int
Description:
This data item defines the order of the author's name in the list of authors associated with a campaign.
Examples:
1
_pdbx_ligscreen_investigation_author.name Required
line
Description:
List people responsible for the contents of this entry. Hyphens, apostrophes and blank spaces are allowed in the last names. Special characters and character modifiers should NOT be used.
Examples:
Bleary, Percival R.
_pdbx_ligscreen_investigation_author.identifier_ORCID Optional
orcid_id
Description:
The Open Researcher and Contributor ID (ORCID).
Examples:
0000-0002-6681-547X
Examples +

Sample data. ;

loop_
    _pdbx_ligscreen_investigation_author.campaign_id"  
    _pdbx_ligscreen_investigation_author.investigation_id"  
    _pdbx_ligscreen_investigation_author.ordinal"  
    _pdbx_ligscreen_investigation_author.name"  
      1   FH123     1  'Navia, M.A.'
      1   FH123     2  'Fitzgerald, P.M.D.'
      1   FH123     3  'McKeever, B.M.'
      1   FH123     4  'Leu, C.-T.'
      1   FH123     5  'Heimbach, J.C.'
      1   FH123     6  'Herber, W.K.'
      1   FH123     7  'Sigal, I.S.'
      1   FH123     8  'Darke, P.L.'
      1   FH123     9  'Springer, J.P.'
      2   FH123     1  'Navia, M.A.'
      2   FH123     2  'Fitzgerald, P.M.D.'
      2   FH123     3  'McKeever, B.M.'
      2   FH123     4  'Leu, C.-T.'
      2   FH123     5  'Heimbach, J.C.'
      2   FH123     6  'Herber, W.K.'
      2   FH123     7  'Sigal, I.S.'
      2   FH123     8  'Diehl, R.E.'
      2   FH123     9  'Hill, W.S.'
;

   #

pdbx_ligscreen_investigation_campaign

The PDBX_LIGSCREEN_INVESTIGATION_CAMPAIGN category is another top level category. This category 'campaign' can cluster information in child catergories per year or facility or processing pipeline software used. Key aspect: there can be more than one campaign per investigation. Also, an investigation might take more than one year and pipeline software may change.
_pdbx_ligscreen_investigation_campaign.campaign_id Required
code
Description:
The value of _pdbx_ligscreen_investigation_campaign.campaign_id enables there to be different campaigns associated for one investigation. Details shared between campaigns can be found in PDBX_LIGSCREEN_INVESTIGATION_SCREENING_EXP category.
_pdbx_ligscreen_investigation_campaign.investigation_id Required
code
Description:
This data item is a pointer to _pdbx_investigation.id in the PDBX_INVESTIGATION category.
_pdbx_ligscreen_investigation_campaign.proc_pipeline Optional Enum
code
Description:
The computational pipeline used for data analysis.
Enumeration:
Value Description
CRIMS Crystallographic Information Management System
XCE XChem Explorer
FMA FragMaxApp
OTHER Other
(No description)
_pdbx_ligscreen_investigation_campaign.pipeline_version Optional
text
Description:
The verison of the computational pipeline version used for data analysis.
Examples:
v4
_pdbx_ligscreen_investigation_campaign.year Optional
int
Description:
The year that the ligand or fragment screening campaign started.
Examples:
2022
_pdbx_ligscreen_investigation_campaign.facility Optional Enum
line
Description:
The facility where the ligand or fragment screening was carried out.
Enumeration:
Value Description
AichiSR Aichi Synchrotron Radiation Center, Seto (Japan)
ALBA ALBA Synchrotron, Barcelona (Spain)
ALS Advanced Light Source, Berkeley (USA)
APS Advanced Photon Source, Argonne (USA)
Australian Synchrotron Australian Synchrotron, Melbourne (Australia)
BESSY Berlin Electron Storage ring company for SYnchrotron radiation, Berlin (Germany)
BSRF Beijing Synchrotron Radiation Facility, Beijing (China)
CAMD Center for Advanced Microstructures and Devices, Baton Rouge (USA)
CHESS Cornell High Energy Synchrotron Source, Ithaca (USA)
CLSI Canadian Light Source (Canada)
Diamond Diamond Light source, South Oxfordshire (UK)
ELETTRA Elettra Sincrotrone, Trieste (Italy)
EMBL/DESY, HAMBURG DESY NanoLab / EMBL, Hamburg (Germany)
ESRF ESRF and EMBL, Grenoble (France)
European XFEL European X-Ray Free-Electron Laser Facility, Schenefeld (Germany)
FRM II The Research Neutron Source Heinz Maier-Leibnitz, Garching (Germany)
KURCHATOV SNC Kurchatov Center for Synchrotron Radiation and Nanotechnology, Moscow (Russia)
JPARC MLF Japan Proton Accelerator Research Complex, Tokai (Japan)
JRR-3M JRR-3M Neutron Source, Japan Research Reactor No.3 Modified, Tokai (Japan)
KCSRNT Kurchatov Center for Synchrotron Radiation and Nanotechnology, Moscow (Russia)
ILL Institut Laue-Langevin neutron scattering facilities, Grenoble (France)
ISIS ISIS Neutron and Muon Source, Rutherford Appleton Laboratory of the Science and Technology Facilities Council, South Oxfordshire (UK)
LANSCE Los Alamos Neutron Science Center, Los Alamos (USA)
LNLS Laboratorio Nacional de Luz Sincrotron, Campinas (Brazil)
LNLS SIRIUS Laboratorio Nacional de Luz Sincrotron - SIRIUS, Campinas (Brazil)
LURE LURE synchrotron radiation Laboratory, Orsay (France)
MAX II MAX II, Lund (Sweden)
MAX IV MAX IV, Lund (Sweden)
MPG/DESY, HAMBURG MPG/DESY at DORIS III, Hamburg (Germany)
NFPSS National Facility for Protein Science, Shanghai (China)
NSLS National Synchrotron Light Source, Upton (USA)
NSLS-II National Synchrotron Light Source II, Upton (USA)
NSRL National Synchrotron Radiation Laboratory, Hefei (China)
NSRRC National Synchroton Radiation Research Center, Taipei (Taiwan)
ORNL High Flux Isotope Reactor Oak Ridge National Laboratory - High Flux Isotope Reactor (USA)
ORNL Spallation Neutron Source Oak Ridge National Laboratory - Spallation Neutron Source (USA)
PAL/PLS Pohang Accelerator Laboratory - Synchrotron, Pohang (Korea)
PAL-XFEL Pohang Accelerator Laboratory - X-ray free-electron laser, Pohang (Korea)
PETRA II, DESY Positron–Electron Tandem Ring Accelerator (PETRA) II and DESY NanoLab, Hamburg-Bahrenfeld (Germany)
PETRA III, EMBL c/o DESY Positron–Electron Tandem Ring Accelerator (PETRA) III, EMBL and DESY NanoLab, Hamburg-Bahrenfeld (Germany)
PETRA III, DESY Positron–Electron Tandem Ring Accelerator (PETRA) III and DESY NanoLab, Hamburg-Bahrenfeld (Germany)
Photon Factory Photon Factory, Tsukuba (Japan)
RRCAT INDUS-2 Raja Ramanna Centre for Advanced Technology, Indus-2, Indore City (India)
SACLA SACLA, Japan's First X-ray Free Electron Laser (XFEL) facility, Aioi (Japan)
SAGA-LS Saga Light Source, Tosu, Saga (Japan)
SLAC LCLS Stanford Linear Accelerator Center - Linac Coherent Light Source, Menlo Park (USA)
SLRI Synchrotron Light Research Institute, Nakhon Ratchasima (Thailand)
SLS Swiss Light Source, Villigen (Switzerland)
SOLEIL SOLEIL, The French National Synchrotron Facility, Saint-Aubin (France)
SPring-8 Super Photon ring 8 GeV, Aioi (Japan)
SRS Synchrotron Radiation Source, Daresbury (UK)
SSRF Shanghai Synchrotron Radiation Facility, Shanghai (China)
SSRL Stanford Synchrotron Radiation Lightsource, Menlo Park (USA)
SwissFEL ARAMIS SwissFEL, X-ray free-electron laser, Canton of Aargau (Switzerland)
(No description)
_pdbx_ligscreen_investigation_campaign.internal_id Optional
code
Description:
The internal investigation ID used at the fragment screening facility.
Examples + 
Theoretical example 1.
;
  
;

pdbx_ligscreen_investigation_lib_component

The PDBX_LIGSCREEN_INVESTIGATION_LIB_COMPONENT category records information about the chemical compounds in the Chemical Library (e.g. fragment), or Chemical Series used in the investigation such as name, molecular weight, an InChI and InChIkey descriptor.
_pdbx_ligscreen_investigation_lib_component.id Required
int
Description:
The value of pdbx_ligscreen_investigation_lib_component.id must uniquely identify a record in the PDBX_LIGSCREEN_INVESTIGATION_LIB_COMPONENT list.
_pdbx_ligscreen_investigation_lib_component.parent_id Optional
int
Description:
This data item is enables there to be a precursor decsribed as well as the reacted chemical entity once it is covalently bound to the protein. This data item has been designed to capture before and after chemical structures of fragments in fragment-based covalent ligand discovery investigation
_pdbx_ligscreen_investigation_lib_component.name Optional
text
Description:
The full name or alphanumeric identifier for the Chemical Library or Series compound.
_pdbx_ligscreen_investigation_lib_component.details Optional
text
Description:
A description of any specific aspects relating to the Chemical Library or Series compound.
_pdbx_ligscreen_investigation_lib_component.chem_comp_id Optional
text
Description:
The wwPDB Chemical Component Dictionary (CCD) code for the Chemical Library or Series compound. In instances where codes are unknown or yet-to-be processed, '?' can be used as placeholders.
_pdbx_ligscreen_investigation_lib_component.formula Optional
text
Description:
The formula for the Chemical Library or Series component. Formulae are written according to the following rules: (1) Only recognized element symbols may be used. (2) Each element symbol is followed by a 'count' number. A count of '1' may be omitted. (3) A space or parenthesis must separate each cluster of (element symbol + count), but in general parentheses are not used. (4) The order of elements depends on whether carbon is present or not. If carbon is present, the order should be: C, then H, then the other elements in alphabetical order of their symbol. If carbon is not present, the elements are listed purely in alphabetic order of their symbol. This is the 'Hill' system used by Chemical Abstracts.
Examples:
C29 H40 N2 O7 S
_pdbx_ligscreen_investigation_lib_component.formula_weight Optional
float
Description:
Formula mass in daltons of the Chemical Library or Chemical Series compound.
_pdbx_ligscreen_investigation_lib_component.inchi_descriptor Optional
text
Description:
This InChI descriptor value for the Chemical Library or Chemical Series compound.
_pdbx_ligscreen_investigation_lib_component.inchi_descriptor_software Optional
line
Description:
This data item contains the name of the program or software library used to compute the InChI descriptor for the Chemical Library or Chemical Series compound.
_pdbx_ligscreen_investigation_lib_component.inchi_descriptor_software_version Optional
text
Description:
This data item contains the version of the program or software library used to compute the InChI descriptor for the Chemical Library or Chemical Series compound.
_pdbx_ligscreen_investigation_lib_component.inchikey Required
text
Description:
This InChIKey descriptor value for the Chemical Library or Chemical Series compound.
_pdbx_ligscreen_investigation_lib_component.inchi_software Optional
line
Description:
This data item contains the name of the program or software library used to compute the InChIKey descriptor for the Chemical Library or Chemical Series compound.
_pdbx_ligscreen_investigation_lib_component.inchi_software_version Optional
text
Description:
This data item contains the version of the program or software library used to compute the InChI descriptor for the Chemical Library or Chemical Series compound.
_pdbx_ligscreen_investigation_lib_component.isomeric_smiles Optional
text
Description:
This SMILES descriptor for Chemical Library or Chemical Series compound including information about configuration around double bonds and chirality. An isomeric SMILES is also known as an CANONICALIZED SMILES.
_pdbx_ligscreen_investigation_lib_component.isomeric_smiles_software Optional
line
Description:
This data item contains the name of the program or library used to compute the SMILES descriptor for the Chemical Library or Chemical Series compound.
_pdbx_ligscreen_investigation_lib_component.isomeric_smiles_software_version Optional
text
Description:
This data item contains the version of the program or library used to compute the SMILES descriptor for the Chemical Library or Chemical Series compound.
_pdbx_ligscreen_investigation_lib_component.cas_identifier Optional
text
Description:
This Chemical Abstracts Service (CAS) identifier for the Chemical Library or Chemical Series compound.
Examples +

Theoretical example. ;

loop_
_pdbx_ligscreen_investigation_lib_component.id
_pdbx_ligscreen_investigation_lib_component.parent_id
_pdbx_ligscreen_investigation_lib_component.name
_pdbx_ligscreen_investigation_lib_component.details
_pdbx_ligscreen_investigation_lib_component.chem_comp_id
_pdbx_ligscreen_investigation_lib_component.formula
_pdbx_ligscreen_investigation_lib_component.formula_weight
_pdbx_ligscreen_investigation_lib_component.inchi_descriptor
_pdbx_ligscreen_investigation_lib_component.inchi_descriptor_software
_pdbx_ligscreen_investigation_lib_component.inchi_descriptor_software_version
_pdbx_ligscreen_investigation_lib_component.inchikey
_pdbx_ligscreen_investigation_lib_component.inchikey_software
_pdbx_ligscreen_investigation_lib_component.inchikey_software_version
_pdbx_ligscreen_investigation_lib_component.isomeric_smiles
_pdbx_ligscreen_investigation_lib_component.isomeric_smiles_software
_pdbx_ligscreen_investigation_lib_component.isomeric_smiles_software_version
_pdbx_ligscreen_investigation_lib_component.cas_identifier
1  1   VT00249  "unbound form"  ?   C9H9NO2      163.2  'InChI=1S/C9H9NO2/c11-9-10-8(6-12-9)7-4-2-1-3-5-7/h1-5,8H,6H2,(H,10,11)/t8-/m0/s1'                                    INCHI  1.03  QDMNNMIOWVJVLY-QMMMGPOBSA-N   INCHI  1.03   ?   ?   ?   ? 
2  1   VT00245  ?               ?   C9H8N2O2S    208.2  'InChI=1S/C9H8N2O2S/c1-5-2-3-8(14-5)6-4-7(9(12)13)11-10-6/h2-4H,1H3,(H,10,11)(H,12,13)'                               INCHI  1.03  JIJVBLCUMDFCFW-UHFFFAOYSA-N   INCHI  1.03   ?   ?   ?   ? 
3  1   VT00220  ?               ?   C6H6F3N3O    193.1  'InChI=1S/C6H6F3N3O/c1-12-3(5(10)13)2-4(11-12)6(7,8)9/h2H,1H3,(H2,10,13)'                                             INCHI  1.03  RGXJDXSOGHNPHB-UHFFFAOYSA-N   INCHI  1.03   ?   ?   ?   ? 
4  1   VT00087  ?               ?   C8H12N4      164.2  'InChI=1S/C8H12N4/c9-7-5-10-6-8(11-7)12-3-1-2-4-12/h5-6H,1-4H2,(H2,9,11)'                                             INCHI  1.03  DRGYQBNAVLYUSQ-UHFFFAOYSA-N   INCHI  1.03   ?   ?   ?   ? 
5  1   VT00225  ?               ?   C5H5F3N2     150.1  'InChI=1S/C5H5F3N2/c1-3-2-4(10-9-3)5(6,7)8/h2H,1H3,(H,9,10)'                                                          INCHI  1.03  DLCHCAYDSKIFIN-UHFFFAOYSA-N   INCHI  1.03   ?   ?   ?   ? 
6  1   VT00162  ?               ?   C12H9N3      195.2  'InChI=1S/C12H9N3/c1-2-6-11-10(5-1)14-12(15-11)9-4-3-7-13-8-9/h1-8H,(H,14,15)'                                        INCHI  1.03  BOUOQESVDURNSB-UHFFFAOYSA-N   INCHI  1.03   ?   ?   ?   ? 
7  1   VT00257  ?               ?   C6H10N2O3S   190.2  'InChI=1S/C6H10N2O3S/c1-4-6(5(2)11-8-4)12(9,10)7-3/h7H,1-3H3'                                                         INCHI  1.03  PBAHROBCZQANJL-UHFFFAOYSA-N   INCHI  1.03   ?   ?   ?   ? 
8  1   VT00084  ?               ?   C12H15NO4S   269.3  'InChI=1S/C12H15NO4S/c1-9-4-6-10(7-5-9)18(16,17)13-8-2-3-11(13)12(14)15/h4-7,11H,2-3,8H2,1H3,(H,14,15)/t11-/m0/s1'    INCHI  1.03  CGPHGPCHVUSFFA-NSHDSACASA-N   INCHI  1.03   ?   ?   ?   ? 
9  1   VT00190  ?               ?   C10H12N2O    176.2  'InChI=1S/C10H12N2O/c1-8-11-9-4-2-3-5-10(9)12(8)6-7-13/h2-5,13H,6-7H2,1H3'                                            INCHI  1.03  CURPBJGJXFWNMF-UHFFFAOYSA-N   INCHI  1.03   ?   ?   ?   ?
;

   #

pdbx_ligscreen_investigation_lib_component_mix

The PDBX_LIGSCREEN_INVESTIGATION_LIB_COMPONENT_MIX category provides a mechanism to assign distinct combinations from the screened Chemical Library or Series compounds (n=>1) a unique singular identifier. This is particularly useful when each experiment involves the target being exposed to a mixture of compounds, as occurs on occasion with fragment screening libraries. Individual ligands or fragments in this category are referred to via their id as defined in the PDBX_LIGSCREEN_INVESTIGATION_LIB_COMPONENT category.
_pdbx_ligscreen_investigation_lib_component_mix.id Required
int
Description:
The value of _pdbx_ligscreen_investigation_lib_component_mix.id must identify a distinct combination of one or more Chemical Library, Chemical Series or Fragment compound(s) used in one or more experiments.
_pdbx_ligscreen_investigation_lib_component_mix.lib_component_id Required
int
Description:
This data item is a pointer to _pdbx_ligscreen_investigation_lib_component.id in the PDBX_LIGSCREEN_INVESTIGATION_LIB_COMPONENT category. This identifer will therefore provide reference to a singular Chemical Library, Chemical Series or Fragment compound.
_pdbx_ligscreen_investigation_lib_component_mix.internal_id Optional
code
Description:
The internal ID for screening solution for the Chemical library, Chemical Series or Fragment screening facility. For example the ID could refered to the well in the plate, in combination of the screening plate number. This informationis from the author of investigation and provided as-is.
Examples +

Theoretical example. ;

loop_
_pdbx_ligscreen_investigation_lib_component_mix.id
_pdbx_ligscreen_investigation_lib_component_mix.lib_component_id
_pdbx_ligscreen_investigation_lib_component_mix.internal_id
1 1  Plate1_A1
1 2  Plate1_A1
1 3  Plate1_A1
2 4  Plate1_B1
2 5  Plate1_B1
2 6  Plate1_B1
3 7  Plate1_C1
3 8  Plate1_C1
3 9  Plate1_C1
;

   #

pdbx_ligscreen_investigation_screening_exp

The PDBX_LIGSCREEN_INVESTIGATION_SCREENING_EXP category contains the data records for each experiment in a ligand screening series. This includes the experimental method used, a list of any fragment(s) or library chemicals present, the other contents in the sample, and whether any data generated from the experiment was deposited in an archive. An "instance" item also allows for the description of experiments with multiple fragment hits results. A URL link to experiment-level data files at an external resource may also be given.
_pdbx_ligscreen_investigation_screening_exp.screening_exp_id Required
code
Description:
The value of _pdbx_ligscreen_investigation_screening_exp.id must uniquely identify a record in the pdbx_ligscreen_investigation_screening_exp list.
_pdbx_ligscreen_investigation_screening_exp.instance_id Required
int
Description:
This value of _pdbx_ligscreen_investigation_screening_exp.instance_id identifiers a specific data record, for a given experiment, in the pdbx_ligscreen_investigation_screening_exp category. For example if a liagnd or fragment is characterized by "Electron diffraction microscopy" an experiment will have two data records to link to both PDB and EMDB. Another example, to have both a hit ("On-site binding") and partial-hit ("Off-site binding"), an experiment will have two data records.
_pdbx_ligscreen_investigation_screening_exp.series_id Required
code
Description:
This data item is a pointer to _pdbx_ligscreen_investigation_series.series_id in the PDBX_LIGSCREEN_INVESTIGATION_SERIES category.
_pdbx_ligscreen_investigation_screening_exp.campaign_id Required
code
Description:
This data item is a pointer to _pdbx_ligscreen_investigation_campaign.campaign_id in the PDBX_LIGSCREEN_INVESTIGATION_CAMPAIGN category.
_pdbx_ligscreen_investigation_screening_exp.investigation_id Required
code
Description:
This data item is a pointer to _pdbx_investigation.id in the PDBX_INVESTIGATION category.
_pdbx_ligscreen_investigation_screening_exp.sample_id Required
code
Description:
This data item is a pointer to _pdbx_investigation_sample.sample_id in the PDBX_INVESTIGATION_SAMPLE category. This identifer indicates the non-fragment screening components in the sample composition.
_pdbx_ligscreen_investigation_screening_exp.lib_component_mix_id Required
int
Description:
This data item is a pointer to _pdbx_ligscreen_investigation_lib_component_mix.id in the PDBX_LIGSCREEN_INVETSIGATION_LIB_COMPONENT_MIX category. This identifer will form a reference to an aggregated list (n=>1) of components derived from the Chemical Library or Series.
_pdbx_ligscreen_investigation_screening_exp.exp_acc Optional
code
Description:
An experiment-specific accession code.
_pdbx_ligscreen_investigation_screening_exp.exp_method Required Enum
line
Description:
The experimental method used for characterisation of the experimental record.
Enumeration:
Value Description
DLS Dynamic Light Scattering
ELECTRON MICROSCOPY Electron Microscopy
EM CRYST Electron Crystallography
EPR Electron Paramagnetic Resonance
Fiber diffraction Fiber Diffraction
FRET Fluorescence Transfer
IR Infrared Spectroscopy
ITC Isothermal Titration Calorimetry
NEUTRON DIFFRACTION Neutron Diffraction
PREDICTION - Homology model Homology or comparative model based on existing templates
PREDICTION - Ab initio model Ab initio or template-free models
POWDER DIFFRACTION Powder Diffraction
SOLUTION NMR Solution NMR
SOLID-STATE NMR Solid-state NMR
SOLUTION SCATTERING Solution Scattering
SPR Surface Plasmon Resonance
X-RAY DIFFRACTION X-ray Diffraction
(No description)
_pdbx_ligscreen_investigation_screening_exp.exp_details Optional
text
Description:
A description of any experiment specific aspects.
_pdbx_ligscreen_investigation_screening_exp.exp_external_url Optional
line
Description:
A URL link to investigation-level data at an external resource.
_pdbx_ligscreen_investigation_screening_exp.data_deposited Optional
line
Description:
Indicate whether data was deposited for this experiment or not.
_pdbx_ligscreen_investigation_screening_exp.archived_data_id Optional
int
Description:
This data item is a pointer to _pdbx_investigation_archived.data_id in the PDBX_INVESTIGATION_ARCHIVED_DATA category.
Examples +

Theoretical example. ;

loop_
_pdbx_ligscreen_investigation_screening_exp.screening_exp_id
_pdbx_ligscreen_investigation_screening_exp.series_id
_pdbx_ligscreen_investigation_screening_exp.campaign_id
_pdbx_ligscreen_investigation_screening_exp.investigation_id
_pdbx_ligscreen_investigation_screening_exp.sample_id
_pdbx_ligscreen_investigation_screening_exp.lib_component_mix_id
_pdbx_ligscreen_investigation_screening_exp.exp_acc
_pdbx_ligscreen_investigation_screening_exp.exp_method
_pdbx_ligscreen_investigation_screening_exp.exp_details
_pdbx_ligscreen_investigation_screening_exp.exp_external_url
_pdbx_ligscreen_investigation_screening_exp.data_deposited
_pdbx_ligscreen_investigation_screening_exp.instance_id
_pdbx_ligscreen_investigation_screening_exp.archived_data_id
exp1   1 1   FH123   1 1   FH123/exp1   'X-RAY DIFFRACTION'   ? http://www.fraghub.org/fh123456/1    n  1    ?   
exp2   1 1   FH123   1 2   FH123/exp2   'X-RAY DIFFRACTION'   ? http://www.fraghub.org/fh123456/2    y  1    1   
exp3   1 1   FH123   1 3   FH123/exp3   'ELECTRON MICROSCOPY' ? http://www.fraghub.org/fh123456/3    y  1    2   
exp3   1 1   FH123   1 3   FH123/exp3   'ELECTRON MICROSCOPY' ? http://www.fraghub.org/fh123456/3    y  2    3   
exp4   1 1   FH123   1 4   FH123/exp4   'X-RAY DIFFRACTION'   ? http://www.fraghub.org/fh123456/4    n  1    ?   
exp5   1 1   FH123   2 5   FH123/exp5   'X-RAY DIFFRACTION'   ? http://www.fraghub.org/fh123456/5    n  1    ?   
exp6   1 1   FH123   2 6   FH123/exp6   'X-RAY DIFFRACTION'   ? http://www.fraghub.org/fh123456/6    n  1    ?   
exp7   1 1   FH123   2 7   FH123/exp7   'X-RAY DIFFRACTION'   ? http://www.fraghub.org/fh123456/7    n  1    ?   
exp8   1 1   FH123   2 8   FH123/exp8   'X-RAY DIFFRACTION'   ? http://www.fraghub.org/fh123456/8    n  1    ?
;

   #

pdbx_ligscreen_investigation_screening_result

The PDBX_LIGSCREEN_INVESTIGATION_SCREENING_RESULT category relates experiment records to the any chemical library compound-binding or fragment-binding specific information. This includes the list of any chemical library ligand(s) or fragment(s) present, the assessment of the result, how that assessment was made, and any depositor provided details. An 'result' item also allows for the description of experiments with multiple ligand or fragment results.
_pdbx_ligscreen_investigation_screening_result.screening_exp_id Required
code
Description:
This data item is a pointer to _pdbx_ligscreen_investigation_screening_exp.screening_exp_id in the PDBX_LIGSCREEN_INVESTIGATION_SCREENING_EXP category. Each result listed in this category is thus linked to the experiment that generated the result. This id combined witn "result_id" gives each reported result a unique identifier.
_pdbx_ligscreen_investigation_screening_result.result_id Required
int
Description:
This value of _pdbx_ligscreen_investigation_screening_exp.result_id identifiers a specific data result record, for a given experiment, in the pdbx_ligscreen_investigation_screening_exp category. For example if a fragment is observed in the same experiment / structure to have binding in different places ('On-site binding') and partial-hit ('Off-site binding') there would be a result_id = 1 and result_id = 2.
_pdbx_ligscreen_investigation_screening_result.lib_component_id Optional
int
Description:
This data item is a pointer to _pdbx_ligscreen_investigation_lib_component.id in the PDBX_LIGSCREEN_INVESTIGATION_LIB_COMPONENT category. This therefore identifies a specific ligand or fragment component within the Chemical Library / Libraries / Series screened.
_pdbx_ligscreen_investigation_screening_result.outcome Required Enum
code
Description:
The approximate assessment of the Chemical Library or Series ligand-binding event. This is to be provided at deposition.
Enumeration:
Value Description
hit .
miss .
partial-hit .
in-progress .
(No description)
_pdbx_ligscreen_investigation_screening_result.outcome_assessment Optional Enum
code
Description:
The method used for hit assessment of the chemical library or series ligand-binding event.
Enumeration:
Value Description
automatic Binding assessed as part of the screening-facility's automated pipeline
refined Binding assessed after atomistic refinement
manual Binding assessed by direct human evaluation
in-progress Binding is still undergoing assessment
(No description)
_pdbx_ligscreen_investigation_screening_result.outcome_description Optional Enum
text
Description:
Simplified description of any specific chemical library or series ligand-binding aspects.
Enumeration:
Value Description
Unknown detail decription to be added
Off-site binding detail decription to be added
On-site binding detail decription to be added
Fragment unobserved detail decription to be added
Library chemical unobserved detail decription to be added
Highest affinity hit detail decription to be added
No diffraction detail decription to be added
(No description)
_pdbx_ligscreen_investigation_screening_result.outcome_details Optional
text
Description:
Further details about the chemical library or series ligand-binding result.
Examples +

Theoretical example. ;

loop_
_pdbx_ligscreen_investigation_screening_result.screening_exp_id
_pdbx_ligscreen_investigation_screening_result.result_id
_pdbx_ligscreen_investigation_screening_result.outcome
_pdbx_ligscreen_investigation_screening_result.lib_component_id
_pdbx_ligscreen_investigation_screening_result.outcome_assessment
_pdbx_ligscreen_investigation_screening_result.outcome_description
_pdbx_ligscreen_investigation_screening_result.outcome_details
exp1  1        miss           ?   automatic   Unknown                     ? 
exp2  1        partial-hit    2   automatic   "Off-site binding"          ? 
exp3  1        hit            3   manual      "On-site binding"           ? 
exp3  2        partial-hit    3   manual      "Off-site binding"          ? 
exp4  1        partial-hit    4   refined     "On-site binding"           ? 
exp5  1        hit            5   refined     "Highest affinity hit"      ? 
exp6  1        miss           ?   manual      "No diffraction"            ? 
exp7  1        miss           ?   manual      "No diffraction"            ? 
exp8  1        miss           ?   manual      "Fragment unobserved"       ?
;

   #

pdbx_ligscreen_investigation_series

The PDBX_LIGSCREEN_INVESTIGATION_SERIES category contains data pertinent to common sets (series) of experiments within an investigation. If a named fragments screen was used, it is captured here. Multiple experimental series could exist for a fragment screening investigation campaign.
_pdbx_ligscreen_investigation_series.series_id Required
code
Description:
The value of _investigation_series.id must uniquely identify a record in the pdbx_ligscreen_investigation_series list.
_pdbx_ligscreen_investigation_series.campaign_id Required
code
Description:
This data item is a pointer to pdbx_ligscreen_investigation_campaign.campaign_id in the PDBX_LIGSCREEN_INVESTIGATION_CAMPAIGN category.
_pdbx_ligscreen_investigation_series.investigation_id Required
code
Description:
This data item is a pointer to _pdbx_investigation.id in the PDBX_INVESTIGATION category.
_pdbx_ligscreen_investigation_series.type_of_library Required Enum
code
Description:
The type of the library, screen or series of chemicals used.
Enumeration:
Value Description
COMBLIB Combinatorial library - systematic sets of building blocks
DOS Diversity-Oriented library - covers broad chemical space
FRAGLIB Fragment screening library - low molecular weight compounds (fragments)
FOCUSEDLIB Focused library - specific therapeutic target or area
HTS High-throughput screening library
NATPROD Natural product library - compounds observed in natural sources
SAR Structure-activity-relationship series
OTHER Customized / in-house library or chemical series
(No description)
_pdbx_ligscreen_investigation_series.library Required Enum
code
Description:
The name of the library used.
Enumeration:
Value Description
Astex_MiniFrags Reference: https://doi.org/10.1016/j.drudis.2019.03.009
Cambridge3D Reference: https://doi.org/10.1039/d0sc01232g
DLS-DSiPoised Reference: https://doi.org/10.1039/C5SC03115J
EmamineEF Reference: https://enamine.net/compound-libraries/fragment-libraries/essential-library
EUOPEN-EFSL Reference: https://doi.org/10.1039/D3MD00724C
EUOPEN-MiniFrags Reference: https://doi.org/10.1039/D3MD00724C
Fraglites Reference: https://doi.org/10.1021/acs.jmedchem.9b00304
FragMAXlib Reference: https://fragmax.github.io/loginsetup.html#library-view
F2X-Entry Reference: https://doi.org/10.1016/j.str.2020.04.019
F2X-Universal Reference: https://doi.org/10.1016/j.str.2020.04.019
Leeds-3D Reference: https://doi.org/10.1039/C8OB00688A
SpotXplorer Reference: https://doi.org/10.1038/s41467-021-23443-y
York-3D Reference: https://doi.org/10.1002/chem.202001123
Other-Fraglib .
Other .
Unknown .
(No description)
_pdbx_ligscreen_investigation_series.library_batch Optional
code
Description:
Any batch-specific identifier describing the exact version of the library used.
_pdbx_ligscreen_investigation_series.lib_identification_method Required Enum
code
Description:
The method used to identify the library used. The provenance for the library name (listed in _pdbx_ligscreen_investigation_series.library item).
Enumeration:
Value Description
author Researcher who provided data confirmed the fragment libary identity.
manual_curation Reviewed by human curator, including examining publication associated with the research.
facility_curation Information provided from the facility where the experiment was performed.
automated_curation Script comparing chemicals from a set of known fragment libraries assigned most likely fragment library utilized.
other Undefined method.
unknown Unknown. Fragment library name may or may not be listed.
(No description)
_pdbx_ligscreen_investigation_series.lib_details Optional
text
Description:
A description of any library or series-specific information.
Examples:
Chemical library was purchased and received in 2015.
Examples + 
Theoretical example 1.
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