configs/known_good_pdb_complexes.yaml

{
  "complexes": [
    {
      "pdb_id": "4HG7",
      "target_name": "MDM2",
      "receptor_chain": "A",
      "reference_ligand_resname": "NUT",
      "reference_ligand_chain": "A",
      "available_hetero_ligands": [
        {"resname": "NUT", "chain": "A", "residue_id": "201", "atom_count": 40, "candidate_ligand": true}
      ],
      "checked_download": true,
      "checked_parse": true,
      "checked_reference_ligand": true,
      "notes": "Local parser check confirmed NUT chain A as the reference ligand."
    },
    {
      "pdb_id": "4WKQ",
      "target_name": "EGFR",
      "receptor_chain": "A",
      "reference_ligand_resname": "IRE",
      "reference_ligand_chain": "A",
      "available_hetero_ligands": [
        {"resname": "IRE", "chain": "A", "residue_id": "1101", "atom_count": 31, "candidate_ligand": true}
      ],
      "checked_download": true,
      "checked_parse": true,
      "checked_reference_ligand": true,
      "notes": "Local parser check confirmed IRE chain A."
    },
    {
      "pdb_id": "1IEP",
      "target_name": "ABL1",
      "receptor_chain": "A",
      "reference_ligand_resname": "STI",
      "reference_ligand_chain": "A",
      "available_hetero_ligands": [
        {"resname": "STI", "chain": "A", "residue_id": "201", "atom_count": 37, "candidate_ligand": true},
        {"resname": "STI", "chain": "B", "residue_id": "202", "atom_count": 37, "candidate_ligand": true}
      ],
      "checked_download": true,
      "checked_parse": true,
      "checked_reference_ligand": true,
      "notes": "Use chain A unless the alternate biological assembly is explicitly desired."
    },
    {
      "pdb_id": "1A52",
      "target_name": "Estrogen receptor alpha",
      "receptor_chain": "A",
      "reference_ligand_resname": "EST",
      "reference_ligand_chain": "A",
      "available_hetero_ligands": [
        {"resname": "EST", "chain": "A", "residue_id": "1", "atom_count": 20, "candidate_ligand": true},
        {"resname": "EST", "chain": "B", "residue_id": "2", "atom_count": 20, "candidate_ligand": true},
        {"resname": "AU", "chain": "A", "residue_id": "265", "atom_count": 3, "candidate_ligand": false},
        {"resname": "AU", "chain": "B", "residue_id": "266", "atom_count": 3, "candidate_ligand": false}
      ],
      "checked_download": true,
      "checked_parse": true,
      "checked_reference_ligand": true,
      "notes": "Correct reference ligand is EST, not MK1. AU entries are ignored as ions/metals."
    },
    {
      "pdb_id": "1T46",
      "target_name": "ABL1 alternative complex",
      "receptor_chain": "A",
      "reference_ligand_resname": "STI",
      "reference_ligand_chain": "A",
      "available_hetero_ligands": [
        {"resname": "STI", "chain": "A", "residue_id": "3", "atom_count": 37, "candidate_ligand": true}
      ],
      "checked_download": true,
      "checked_parse": true,
      "checked_reference_ligand": true,
      "notes": "Single clear STI ligand in chain A."
    },
    {
      "pdb_id": "3PTB",
      "target_name": "Trypsin",
      "receptor_chain": "A",
      "reference_ligand_resname": "BEN",
      "reference_ligand_chain": "A",
      "available_hetero_ligands": [
        {"resname": "BEN", "chain": "A", "residue_id": "1", "atom_count": 9, "candidate_ligand": true}
      ],
      "checked_download": true,
      "checked_parse": true,
      "checked_reference_ligand": true,
      "notes": "Compact benchmark target with benzamidine."
    },
    {
      "pdb_id": "2HYY",
      "target_name": "ABL1 tetrameric assembly",
      "receptor_chain": "A",
      "reference_ligand_resname": "STI",
      "reference_ligand_chain": "A",
      "available_hetero_ligands": [
        {"resname": "STI", "chain": "A", "residue_id": "600", "atom_count": 37, "candidate_ligand": true},
        {"resname": "STI", "chain": "B", "residue_id": "600", "atom_count": 37, "candidate_ligand": true},
        {"resname": "STI", "chain": "C", "residue_id": "600", "atom_count": 37, "candidate_ligand": true},
        {"resname": "STI", "chain": "D", "residue_id": "600", "atom_count": 37, "candidate_ligand": true}
      ],
      "checked_download": true,
      "checked_parse": true,
      "checked_reference_ligand": true,
      "notes": "Tetrameric structure; chain A is the default receptor chain for the portable pipeline."
    },
    {
      "pdb_id": "1HSG",
      "target_name": "HIV protease",
      "receptor_chain": "A,B",
      "reference_ligand_resname": "MK1",
      "reference_ligand_chain": "B",
      "available_hetero_ligands": [
        {"resname": "MK1", "chain": "B", "residue_id": "902", "atom_count": 45, "candidate_ligand": true}
      ],
      "checked_download": true,
      "checked_parse": true,
      "checked_reference_ligand": true,
      "notes": "Validated locally as a multi-chain receptor target with one clear ligand."
    },
    {
      "pdb_id": "1HVR",
      "target_name": "HIV reverse transcriptase",
      "receptor_chain": "A",
      "reference_ligand_resname": "XK2",
      "reference_ligand_chain": "A",
      "available_hetero_ligands": [
        {"resname": "XK2", "chain": "A", "residue_id": "263", "atom_count": 46, "candidate_ligand": true}
      ],
      "checked_download": true,
      "checked_parse": true,
      "checked_reference_ligand": true,
      "notes": "Validated locally as a single-chain receptor with one clear organic ligand."
    }
  ]
}