{
  "n_total": 4463,
  "sample_size": 4463,
  "atoms_per_structure": {
    "min": 115,
    "max": 1085,
    "mean": 397.0734931660318
  },
  "bounding_box_extent_angstrom": {
    "side_min": 10.526999950408936,
    "side_max": 47.270999908447266,
    "diagonal_min": 25.27603114136397,
    "diagonal_max": 59.69870791297603
  },
  "elements": {
    "count": 23,
    "atomic_numbers": [
      1,
      6,
      7,
      8,
      9,
      11,
      12,
      15,
      16,
      17,
      19,
      20,
      25,
      26,
      27,
      28,
      29,
      30,
      35,
      38,
      48,
      53,
      55
    ],
    "symbols": [
      "H",
      "C",
      "N",
      "O",
      "F",
      "Na",
      "Mg",
      "P",
      "S",
      "Cl",
      "K",
      "Ca",
      "Mn",
      "Fe",
      "Co",
      "Ni",
      "Cu",
      "Zn",
      "Br",
      "Sr",
      "Cd",
      "I",
      "Cs"
    ],
    "counts": {
      "1": 682255,
      "6": 702697,
      "7": 178352,
      "8": 197780,
      "9": 995,
      "11": 26,
      "12": 177,
      "15": 824,
      "16": 7325,
      "17": 659,
      "19": 3,
      "20": 61,
      "25": 59,
      "26": 27,
      "27": 26,
      "28": 8,
      "29": 4,
      "30": 686,
      "35": 130,
      "38": 1,
      "48": 1,
      "53": 42,
      "55": 1
    }
  },
  "label_y": {
    "min": 2.0,
    "max": 11.920000076293945,
    "mean": 6.453963702605921
  },
  "exact": {
    "num_complexes": 4463,
    "unique_pdb_ids": 4463,
    "components": {
      "protein": {
        "total_atoms": 27769649,
        "min": 566,
        "mean": 6222.1934,
        "max": 74903,
        "zero_length": 0
      },
      "pocket": {
        "total_atoms": 1658646,
        "min": 100,
        "mean": 371.6437,
        "max": 1021,
        "zero_length": 0
      },
      "ligand": {
        "total_atoms": 113493,
        "min": 6,
        "mean": 25.4298,
        "max": 71,
        "zero_length": 0
      }
    },
    "pocket_provenance": "ATOM3D's OWN published selection (protein atoms within 6.0 A of any ligand atom); STORED because it is the source convention the seq-id benchmarks are defined on, not a crop we invented. It is a RESIDUE shell (0 of 122,736 pocket residues truncated) and it EXCLUDES water entirely.",
    "elements_z": [
      1,
      3,
      6,
      7,
      8,
      9,
      11,
      12,
      15,
      16,
      17,
      19,
      20,
      25,
      26,
      27,
      28,
      29,
      30,
      34,
      35,
      38,
      48,
      53,
      55,
      80
    ],
    "elements_symbols": [
      "H",
      "Li",
      "C",
      "N",
      "O",
      "F",
      "Na",
      "Mg",
      "P",
      "S",
      "Cl",
      "K",
      "Ca",
      "Mn",
      "Fe",
      "Co",
      "Ni",
      "Cu",
      "Zn",
      "Se",
      "Br",
      "Sr",
      "Cd",
      "I",
      "Cs",
      "Hg"
    ],
    "n_elements": 26,
    "elements_per_component": {
      "protein": {
        "n": 22,
        "symbols": [
          "H",
          "Li",
          "C",
          "N",
          "O",
          "Na",
          "Mg",
          "P",
          "S",
          "K",
          "Ca",
          "Mn",
          "Fe",
          "Co",
          "Ni",
          "Cu",
          "Zn",
          "Se",
          "Sr",
          "Cd",
          "Cs",
          "Hg"
        ]
      },
      "pocket": {
        "n": 18,
        "symbols": [
          "H",
          "C",
          "N",
          "O",
          "Na",
          "Mg",
          "S",
          "K",
          "Ca",
          "Mn",
          "Fe",
          "Co",
          "Ni",
          "Cu",
          "Zn",
          "Sr",
          "Cd",
          "Cs"
        ]
      },
      "ligand": {
        "n": 9,
        "symbols": [
          "C",
          "N",
          "O",
          "F",
          "P",
          "S",
          "Cl",
          "Br",
          "I"
        ]
      }
    },
    "vocab_sizes": {
      "res_name": 50,
      "chain": 33,
      "insertion_code": 21,
      "hetero": 30
    },
    "residue_identity": {
      "res_idx": "derived key, contiguous 0..R-1 over protein+ligand per complex; the pocket INHERITS the protein numbering, so pocket res_idx is a subset, neither contiguous nor disjoint",
      "merged_residue_complexes": {
        "protein": 0,
        "pocket": 0
      },
      "total_residues": 3311198,
      "residues_per_complex": {
        "min": 89,
        "mean": 741.922,
        "max": 9102
      },
      "pocket_residues_total": 122736,
      "pocket_res_idx_subset_of_protein": true,
      "author_key_3part_collisions": {
        "protein": {
          "colliding_keys": 5,
          "complexes": 5,
          "pdb_ids": [
            "3mi2",
            "3upk",
            "3v4t",
            "4w9f",
            "4w9h"
          ]
        },
        "pocket": {
          "colliding_keys": 0,
          "complexes": 0,
          "pdb_ids": []
        }
      },
      "author_key_4part_collisions": {
        "protein": {
          "colliding_keys": 0,
          "complexes": 0,
          "pdb_ids": []
        },
        "pocket": {
          "colliding_keys": 0,
          "complexes": 0,
          "pdb_ids": []
        }
      },
      "res_seq": {
        "protein": {
          "min": -20,
          "max": 5069,
          "atoms_le_0": 18665,
          "complexes_with_le_0": 313
        },
        "pocket": {
          "min": -4,
          "max": 4027,
          "atoms_le_0": 197,
          "complexes_with_le_0": 8
        },
        "ligand": {
          "min": 0,
          "max": 0,
          "atoms_le_0": 113493,
          "complexes_with_le_0": 4463
        }
      },
      "insertion_code": {
        "vocab_size": 21,
        "vocab": [
          " ",
          "C",
          "B",
          "A",
          "D",
          "E",
          "F",
          "G",
          "H",
          "I",
          "J",
          "K",
          "L",
          "M",
          "P",
          "W",
          "N",
          "Q",
          "R",
          "S",
          "T"
        ],
        "protein_complexes_using_one": 372,
        "pocket_complexes_using_one": 212,
        "protein_atoms_with_one": 86164,
        "pocket_atoms_with_one": 9701,
        "distinct_non_blank": 20,
        "water_artefact": {
          "atoms": 7866,
          "complexes": 5,
          "note": "NOT author insertion codes: in 5 complexes (2qwb..2qwf) ATOM3D spilled the water's chain id into this column; those waters read chain == '.'. Shipped verbatim. 15 letters are involved (E F G H J K L M N P Q R S T W); the genuine author insertion codes are the non-water rows."
        },
        "protein_atoms_non_water_with_one": 78298
      },
      "invariants_over_all_complexes": {
        "protein_plus_ligand_is_0..R-1_per_complex": true,
        "ligand_is_one_pseudo_residue_at_R-1": true,
        "pocket_res_idx_subset_of_protein": true,
        "pocket_residues": 122736,
        "pocket_residues_truncated": 0
      }
    },
    "hetero_counts": {
      "protein": {
        " ": 26375178,
        "W": 1384783,
        "H_MSE": 1729,
        "H_ZN": 1360,
        "H_PTR": 1250,
        "H_CA": 974,
        "H_MG": 770,
        "H_TPO": 765,
        "H_SEP": 644,
        "H_CSO": 513,
        "H_NA": 433,
        "H_CD": 202,
        "H_LLP": 176,
        "H_MN": 156,
        "H_PCA": 156,
        "H_K": 96,
        "H_NI": 78,
        "H_FE": 67,
        "H_KCX": 65,
        "H_CAS": 61,
        "H_HG": 48,
        "H_CO": 48,
        "H_ACE": 45,
        "H_FE2": 22,
        "H_CSD": 8,
        "H_LI": 6,
        "H_CU": 6,
        "H_CS": 6,
        "H_SR": 2,
        "H_IAS": 2
      },
      "pocket": {
        " ": 1657566,
        "H_ZN": 686,
        "H_MG": 177,
        "H_CA": 61,
        "H_MN": 59,
        "H_NA": 26,
        "H_CO": 26,
        "H_FE": 21,
        "H_NI": 8,
        "H_FE2": 6,
        "H_CU": 4,
        "H_K": 3,
        "H_CD": 1,
        "H_SR": 1,
        "H_CS": 1
      },
      "ligand": {
        " ": 113493
      }
    },
    "water": {
      "hetero_W_atoms": 1384783,
      "res_name_HOH_atoms": 1384783,
      "identical": true,
      "note": "waters live in the protein component; the pocket has none"
    },
    "entity_type_counts": {
      "protein": {
        "protein": 26375178,
        "water": 1384783,
        "metal_ion": 4333,
        "other_hetero": 5355
      },
      "pocket": {
        "protein": 1657566,
        "metal_ion": 1080
      },
      "ligand": {
        "ligand": 113493
      }
    },
    "hydrogens": {
      "protein": {
        "n_hydrogen": 11328810,
        "fraction": 0.408,
        "complexes_with_zero_H": 0
      },
      "pocket": {
        "n_hydrogen": 682255,
        "fraction": 0.4113,
        "complexes_with_zero_H": 0
      },
      "ligand": {
        "n_hydrogen": 0,
        "fraction": 0.0,
        "complexes_with_zero_H": 4463
      }
    },
    "bfactor": {
      "protein": {
        "min": -9.37,
        "mean": 16.987,
        "max": 500.54,
        "n_atoms": 27769649,
        "n_zero": 11329695,
        "n_negative": 201,
        "n_hydrogen": 11328810,
        "n_hydrogen_zero": 11328810,
        "n_heavy_zero": 885
      },
      "pocket": {
        "min": -0.01,
        "mean": 13.3213,
        "max": 500.0,
        "n_atoms": 1658646,
        "n_zero": 682380,
        "n_negative": 27,
        "n_hydrogen": 682255,
        "n_hydrogen_zero": 682255,
        "n_heavy_zero": 125
      },
      "ligand": {
        "min": 0.0,
        "mean": 0.0,
        "max": 0.0,
        "n_atoms": 113493,
        "n_zero": 113493,
        "n_negative": 0,
        "n_hydrogen": 0,
        "n_hydrogen_zero": 0,
        "n_heavy_zero": 113493
      }
    },
    "occupancy": {
      "protein": {
        "min": -0.49,
        "mean": 0.9959,
        "max": 1.99,
        "n_distinct": 117,
        "n_not_one": 238151,
        "n_zero": 9239,
        "n_below_0": 2,
        "n_above_1": 22
      },
      "pocket": {
        "min": 0.0,
        "mean": 0.9954,
        "max": 1.21,
        "n_distinct": 98,
        "n_not_one": 16451,
        "n_zero": 298,
        "n_below_0": 0,
        "n_above_1": 1
      },
      "ligand": {
        "min": 1.0,
        "mean": 1.0,
        "max": 1.0,
        "n_distinct": 1,
        "n_not_one": 0,
        "n_zero": 0,
        "n_below_0": 0,
        "n_above_1": 0
      }
    },
    "is_alpha_carbon": {
      "protein": {
        "n_true": 1917382,
        "z_values": [
          6
        ]
      },
      "pocket": {
        "n_true": 121656,
        "z_values": [
          6
        ]
      },
      "ligand": {
        "n_true": 0,
        "z_values": []
      }
    },
    "label_neglog_aff": {
      "min": 2.0,
      "mean": 6.454,
      "max": 11.92
    },
    "splits": {
      "seq-id-30": {
        "train": 3507,
        "val": 466,
        "test": 490,
        "total": 4463
      },
      "seq-id-60": {
        "train": 3563,
        "val": 448,
        "test": 452,
        "total": 4463
      }
    },
    "ligand_bonds": {
      "total": 121187,
      "dtype": "torch.float32",
      "order_counts": {
        "1.0": 89491,
        "2.0": 31543,
        "3.0": 153
      },
      "convention": "one entry per bond (not both directions), as in HiQBind"
    },
    "file_sizes_gib": {
      "complexes.pt": 0.079,
      "protein.pt": 1.19
    },
    "units": {
      "pos": "angstrom",
      "bfactor": "angstrom^2 (B-factor)",
      "occupancy": "fraction, nominally [0,1] but NOT clamped -- the source states -0.49 .. 1.99 and it is shipped verbatim",
      "neglog_aff": "unitless (-log10 of the dissociation constant in M; pKd-like)"
    },
    "sampled_fields": "none in this block -- everything here is exact over all 4,463 complexes. The TOP-LEVEL atoms_per_structure / bounding_box_extent_angstrom / elements keys describe the pocket+ligand view only (all 4,463 complexes, so exhaustive for that view but NOT for the dataset: the protein component adds 3 elements).",
    "v1_regression": {
      "bitwise_identical": [
        "ligand_edge_index",
        "ligand_edge_ptr",
        "ligand_pos",
        "ligand_ptr",
        "ligand_z",
        "neglog_aff",
        "pocket_pos",
        "pocket_ptr",
        "pocket_z",
        "protein_pos",
        "protein_ptr",
        "protein_z",
        "seqid30_split",
        "seqid60_split"
      ],
      "differs": [],
      "ligand_edge_attr": {
        "v1_dtype": "torch.int64",
        "v2_dtype": "torch.float32",
        "values_equal": true
      },
      "v1_merged_residue_complexes": {
        "protein": 376,
        "pocket": 208
      },
      "v2_merged_residue_complexes": {
        "protein": 0,
        "pocket": 0
      },
      "is_alpha_carbon": {
        "protein": {
          "v1_true": 1918415,
          "v2_true": 1917382,
          "lost": 1033,
          "gained": 0,
          "z_of_lost": [
            20
          ],
          "lost_residues": 1033
        },
        "pocket": {
          "v1_true": 121717,
          "v2_true": 121656,
          "lost": 61,
          "gained": 0,
          "z_of_lost": [
            20
          ],
          "lost_residues": 61
        }
      },
      "v1_missing_fields": [
        "hetero",
        "insertion_code",
        "n_residues",
        "occupancy",
        "res_seq"
      ]
    }
  }
}