{
  "species": "chignolin",
  "pdb_id": "1UAO",
  "common_name": "chignolin",
  "sequence": "GYDPETGTWG",
  "n_residues": 10,
  "n_atoms_heavy": 75,
  "energy_Ha": null,
  "_energy_note": "Energy from a converged RealQM run will be filled in by the next pipeline pass; this initial entry uses sequence-derived parameters only.",
  "net_charge_e": -2,
  "mass_Da": 1100,
  "end_to_end_au": 18.0,
  "end_to_end_AA": 9.5,
  "bounding_box_au": {
    "x": [-9.0, 9.0],
    "y": [-7.0, 7.0],
    "z": [-5.0, 5.0]
  },
  "hydrodynamic_radius_au": 9.0,
  "hydrophobicity_avg_kd": -1.34,
  "diffusion_translational_au_per_step": "~3e-6 cm^2/s @300K (Stokes-Einstein, eta_water)",
  "residues": [
    { "chain": "A", "num": 1,  "name": "GLY", "aa": "G", "hydrophobicity_kd": -0.4, "sidechain_charge":  0 },
    { "chain": "A", "num": 2,  "name": "TYR", "aa": "Y", "hydrophobicity_kd": -1.3, "sidechain_charge":  0 },
    { "chain": "A", "num": 3,  "name": "ASP", "aa": "D", "hydrophobicity_kd": -3.5, "sidechain_charge": -1 },
    { "chain": "A", "num": 4,  "name": "PRO", "aa": "P", "hydrophobicity_kd": -1.6, "sidechain_charge":  0 },
    { "chain": "A", "num": 5,  "name": "GLU", "aa": "E", "hydrophobicity_kd": -3.5, "sidechain_charge": -1 },
    { "chain": "A", "num": 6,  "name": "THR", "aa": "T", "hydrophobicity_kd": -0.7, "sidechain_charge":  0 },
    { "chain": "A", "num": 7,  "name": "GLY", "aa": "G", "hydrophobicity_kd": -0.4, "sidechain_charge":  0 },
    { "chain": "A", "num": 8,  "name": "THR", "aa": "T", "hydrophobicity_kd": -0.7, "sidechain_charge":  0 },
    { "chain": "A", "num": 9,  "name": "TRP", "aa": "W", "hydrophobicity_kd": -0.9, "sidechain_charge":  0 },
    { "chain": "A", "num": 10, "name": "GLY", "aa": "G", "hydrophobicity_kd": -0.4, "sidechain_charge":  0 }
  ],
  "modes": "TODO - C-alpha Hessian via displacement runs",
  "surface_electrostatic": "TODO - marching-cubes on density grid",
  "provenance": {
    "method": "RealQM via molecule.js (real-space multiphase non-overlap)",
    "structure_source": "PDB 1UAO (Honda et al., Structure 2004)",
    "extraction_tool": "protein_reduce.html",
    "structure_url": "https://files.rcsb.org/download/1UAO.pdb",
    "notes": "Sequence-derived parameters are exact; spatial and energetic parameters are placeholders pending a full RealQM run with the loaded PDB structure."
  }
}