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Datasets:
LiteFold
/
PDB-CCD

Modalities:
Tabular
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parquet
Size:
10K - 100K
Tags:
biology
chemistry
structural-biology
pdb
chemical-components
mmcif
Libraries:
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License:
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xet
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PDB-CCD
File size: 4,550 Bytes
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{
  "source": "LiteFold/PDB-CCD",
  "component_rows": 50054,
  "splits": {
    "train": 45045,
    "test": 5009
  },
  "split_strategy": "deterministic sha256(component_id) % 10; bucket 0 is test, buckets 1-9 are train",
  "release_status_counts": {
    "REL": 49292,
    "OBS": 762
  },
  "component_type_counts": {
    "NON-POLYMER": 26117,
    "non-polymer": 19493,
    "L-PEPTIDE LINKING": 923,
    "L-peptide linking": 580,
    "peptide-like": 556,
    "D-saccharide": 405,
    "DNA LINKING": 325,
    "RNA LINKING": 223,
    "D-saccharide, alpha linking": 203,
    "D-saccharide, beta linking": 173,
    "saccharide": 137,
    "DNA linking": 134,
    "RNA linking": 129,
    "D-PEPTIDE LINKING": 96,
    "D-peptide linking": 68,
    "L-saccharide, alpha linking": 63,
    "peptide linking": 62,
    "L-saccharide": 60,
    "SACCHARIDE": 51,
    "PEPTIDE-LIKE": 48,
    "PEPTIDE LINKING": 44,
    "D-SACCHARIDE": 43,
    "L-saccharide, beta linking": 35,
    "L-peptide NH3 amino terminus": 25,
    "L-peptide COOH carboxy terminus": 13,
    "L-SACCHARIDE": 8,
    "RNA OH 3 prime terminus": 5,
    "L-RNA LINKING": 5,
    "L-DNA LINKING": 4,
    "D-beta-peptide, C-gamma linking": 3,
    "DNA OH 3 prime terminus": 3,
    "L-beta-peptide, C-gamma linking": 3,
    "RNA OH 5 prime terminus": 2,
    "L-gamma-peptide, C-delta linking": 2,
    "L-RNA linking": 2,
    "L-PEPTIDE COOH CARBOXY TERMINUS": 2,
    "DNA OH 5 prime terminus": 2,
    "D-gamma-peptide, C-delta linking": 1,
    "D-PEPTIDE NH3 AMINO TERMINUS": 1,
    "Peptide-like": 1,
    "L-DNA linking": 1,
    "D-peptide COOH carboxy terminus": 1,
    "DNA OH 3 PRIME TERMINUS": 1,
    "D-peptide NH3 amino terminus": 1
  },
  "pdbx_type_counts": {
    "HETAIN": 45506,
    "ATOMP": 1831,
    "ATOMS": 1182,
    "ATOMN": 820,
    "missing": 256,
    "HETAD": 247,
    "HETAI": 135,
    "HETIC": 38,
    "HETAC": 32,
    "HETAS": 5,
    "hetain": 2
  },
  "max_modified_date": "2026-04-24",
  "components_with_atoms": 49947,
  "components_with_bonds": 49921,
  "components_with_descriptors": 50052,
  "components_with_identifiers": 37058,
  "components_with_pcm": 613,
  "top_elements": {
    "H": 1082721,
    "C": 898683,
    "O": 199913,
    "N": 152744,
    "F": 17030,
    "S": 15656,
    "CL": 8840,
    "P": 7757,
    "BR": 1827,
    "B": 983,
    "FE": 445,
    "I": 427,
    "W": 426,
    "MO": 205,
    "V": 195,
    "RU": 156,
    "SE": 154,
    "CO": 78,
    "SI": 63,
    "CU": 63,
    "PT": 58,
    "MG": 41,
    "NI": 40,
    "RH": 38,
    "MN": 36,
    "AS": 32,
    "IR": 28,
    "D": 23,
    "HG": 22,
    "ZN": 20
  },
  "descriptor_type_counts": {
    "SMILES": 134251,
    "SMILES_CANONICAL": 100067,
    "InChI": 50046,
    "InChIKey": 50045,
    "INCHI": 4
  },
  "identifier_type_counts": {
    "SYSTEMATIC NAME": 70318,
    "IUPAC CARBOHYDRATE SYMBOL": 301,
    "CONDENSED IUPAC CARBOHYDRATE SYMBOL": 173,
    "COMMON NAME": 169,
    "SNFG CARBOHYDRATE SYMBOL": 122
  },
  "columns": [
    "component_id",
    "name",
    "component_type",
    "pdbx_type",
    "formula",
    "formula_weight",
    "formal_charge",
    "mon_nstd_parent_comp_id",
    "one_letter_code",
    "three_letter_code",
    "pdbx_synonyms",
    "synonym_names",
    "synonym_provenances",
    "synonym_types",
    "initial_date",
    "modified_date",
    "release_status",
    "ambiguous_flag",
    "replaced_by",
    "replaces",
    "model_coordinates_missing_flag",
    "ideal_coordinates_missing_flag",
    "model_coordinates_db_code",
    "processing_site",
    "atom_ids",
    "atom_alt_ids",
    "atom_elements",
    "atom_charges",
    "atom_aromatic_flags",
    "atom_leaving_flags",
    "atom_stereo_configs",
    "atom_count",
    "heavy_atom_count",
    "hydrogen_atom_count",
    "bond_atom_id_1",
    "bond_atom_id_2",
    "bond_orders",
    "bond_aromatic_flags",
    "bond_stereo_configs",
    "bond_count",
    "descriptor_types",
    "descriptor_programs",
    "descriptor_program_versions",
    "descriptors",
    "canonical_smiles",
    "smiles",
    "inchi",
    "inchikey",
    "identifier_types",
    "identifier_programs",
    "identifier_program_versions",
    "identifiers",
    "systematic_names",
    "audit_actions",
    "audit_dates",
    "audit_processing_sites",
    "related_component_ids",
    "related_relationship_types",
    "pcm_ids",
    "pcm_modified_residue_ids",
    "pcm_types",
    "pcm_categories",
    "pcm_positions",
    "feature_types",
    "feature_values",
    "split_bucket"
  ],
  "source_files_used": [
    "components.cif.gz"
  ]
}