| { |
| "n_total": 31572, |
| "sample_size": 8000, |
| "atoms_per_structure": { |
| "min": 709, |
| "max": 50092, |
| "mean": 6829.78375 |
| }, |
| "bounding_box_extent_angstrom": { |
| "side_min": 21.65899658203125, |
| "side_max": 221.00599670410156, |
| "diagonal_min": 45.237691696034425, |
| "diagonal_max": 274.62297143473495 |
| }, |
| "elements": { |
| "count": 14, |
| "atomic_numbers": [ |
| 1, |
| 4, |
| 6, |
| 7, |
| 8, |
| 9, |
| 15, |
| 16, |
| 17, |
| 33, |
| 34, |
| 35, |
| 53, |
| 80 |
| ], |
| "symbols": [ |
| "H", |
| "Be", |
| "C", |
| "N", |
| "O", |
| "F", |
| "P", |
| "S", |
| "Cl", |
| "As", |
| "Se", |
| "Br", |
| "I", |
| "Hg" |
| ], |
| "counts": { |
| "1": 27169131, |
| "4": 1, |
| "6": 17498478, |
| "7": 4701257, |
| "8": 5119687, |
| "9": 2694, |
| "15": 2375, |
| "16": 142235, |
| "17": 1496, |
| "33": 121, |
| "34": 431, |
| "35": 276, |
| "53": 84, |
| "80": 4 |
| } |
| }, |
| "label_y": { |
| "min": -2.966576337814331, |
| "max": 14.0, |
| "mean": 6.467261703925151 |
| }, |
| "exact": { |
| "num_complexes": 32275, |
| "num_sm": 31572, |
| "num_poly": 703, |
| "num_unique_pdb_ids": 18160, |
| "components": { |
| "protein": { |
| "total_atoms": 217467858, |
| "min": 683, |
| "mean": 6738.0, |
| "max": 50050, |
| "zero_length": 0 |
| }, |
| "ligand": { |
| "total_atoms": 1528172, |
| "min": 4, |
| "mean": 47.3, |
| "max": 233, |
| "zero_length": 0 |
| }, |
| "water": { |
| "total_atoms": 7276591, |
| "min": 0, |
| "mean": 225.5, |
| "max": 2232, |
| "zero_length": 1392 |
| }, |
| "additives": { |
| "total_atoms": 1024858, |
| "min": 0, |
| "mean": 31.8, |
| "max": 912, |
| "zero_length": 9256 |
| } |
| }, |
| "pocket": "NOT shipped \u2014 HiQBind provides none; use HiQBind(pocket_cutoff=<A>) at load", |
| "elements_z": [ |
| 1, |
| 3, |
| 4, |
| 5, |
| 6, |
| 7, |
| 8, |
| 9, |
| 11, |
| 12, |
| 13, |
| 15, |
| 16, |
| 17, |
| 19, |
| 20, |
| 23, |
| 25, |
| 26, |
| 27, |
| 28, |
| 29, |
| 30, |
| 31, |
| 33, |
| 34, |
| 35, |
| 36, |
| 37, |
| 38, |
| 39, |
| 42, |
| 44, |
| 48, |
| 49, |
| 52, |
| 53, |
| 54, |
| 55, |
| 56, |
| 59, |
| 62, |
| 63, |
| 64, |
| 65, |
| 70, |
| 74, |
| 76, |
| 77, |
| 78, |
| 79, |
| 80, |
| 81, |
| 82, |
| 92, |
| 95, |
| 96 |
| ], |
| "elements_symbols": [ |
| "H", |
| "Li", |
| "Be", |
| "B", |
| "C", |
| "N", |
| "O", |
| "F", |
| "Na", |
| "Mg", |
| "Al", |
| "P", |
| "S", |
| "Cl", |
| "K", |
| "Ca", |
| "V", |
| "Mn", |
| "Fe", |
| "Co", |
| "Ni", |
| "Cu", |
| "Zn", |
| "Ga", |
| "As", |
| "Se", |
| "Br", |
| "Kr", |
| "Rb", |
| "Sr", |
| "Y", |
| "Mo", |
| "Ru", |
| "Cd", |
| "In", |
| "Te", |
| "I", |
| "Xe", |
| "Cs", |
| "Ba", |
| "Pr", |
| "Sm", |
| "Eu", |
| "Gd", |
| "Tb", |
| "Yb", |
| "W", |
| "Os", |
| "Ir", |
| "Pt", |
| "Au", |
| "Hg", |
| "Tl", |
| "Pb", |
| "U", |
| "Am", |
| "Cm" |
| ], |
| "n_elements": 57, |
| "res_name_vocab_size": 1043, |
| "chain_vocab_size": 56, |
| "residues_per_complex": { |
| "min": 61, |
| "mean": 655.8, |
| "max": 4735 |
| }, |
| "insertion_code_vocab_size": 25, |
| "ligand_bond_orders": [ |
| 1.0, |
| 2.0, |
| 3.0 |
| ], |
| "ligand_edges_total": 1592129, |
| "edge_convention": "one entry per bond (not both directions), as in LBA", |
| "affinity_type_counts": { |
| "ec50": 436, |
| "ic50": 11686, |
| "kd": 10169, |
| "ki": 9984 |
| }, |
| "affinity_sign_counts": { |
| "<": 168, |
| "<=": 137, |
| "=": 31342, |
| ">": 88, |
| ">=": 192, |
| "~": 348 |
| }, |
| "affinity_unit_counts": { |
| "M": 540, |
| "fM": 4, |
| "mM": 1476, |
| "nM": 17105, |
| "pM": 281, |
| "uM": 12865, |
| "unknown": 4 |
| }, |
| "affinity_source_counts": { |
| "BindingDB": 8645, |
| "BioLiP": 37, |
| "MOAD": 23593 |
| }, |
| "neglog_aff": { |
| "min": -2.96658, |
| "max": 14.0, |
| "mean": 6.43053, |
| "n_nan": 4 |
| }, |
| "log_affinity": { |
| "min": -14.0, |
| "max": 2.96658, |
| "mean": -6.43053, |
| "n_nan": 4 |
| }, |
| "affinity_value": { |
| "min": 1e-14, |
| "max": 500000000.0, |
| "mean": 141926.0, |
| "n_nan": 0 |
| }, |
| "resolution": { |
| "min": 0.66, |
| "max": 7.88, |
| "mean": 2.05335, |
| "n_nan": 461 |
| }, |
| "year": { |
| "min": 1982.0, |
| "max": 2022.0, |
| "mean": 2012.38, |
| "n_nan": 0 |
| }, |
| "mw": { |
| "min": 44.037, |
| "max": 1820.15, |
| "mean": 381.428, |
| "n_nan": 0 |
| }, |
| "logp": { |
| "min": -23.011, |
| "max": 13.6536, |
| "mean": 1.04652, |
| "n_nan": 0 |
| }, |
| "tpsa": { |
| "min": 0.0, |
| "max": 786.07, |
| "mean": 112.206, |
| "n_nan": 0 |
| }, |
| "qed": { |
| "min": 0.0117604, |
| "max": 0.947347, |
| "mean": 0.502505, |
| "n_nan": 0 |
| }, |
| "additives_composition": { |
| "total_atoms": 1024858, |
| "distinct_residue_names": 966, |
| "note": "classes are indicative, from a curated residue list used ONLY for this summary \u2014 the shipped data classifies nothing beyond entity_type (water / metal_ion / other_hetero). Cofactors are the largest class but a minority, which is why the component is called \"additives\" and not \"cofactors\".", |
| "by_class": { |
| "cofactor_nucleotide": { |
| "atoms": 375002, |
| "percent": 36.6 |
| }, |
| "cryoprotectant_buffer_detergent": { |
| "atoms": 220225, |
| "percent": 21.5 |
| }, |
| "other_incl_lipid": { |
| "atoms": 147312, |
| "percent": 14.4 |
| }, |
| "ion_salt_small_anion": { |
| "atoms": 145998, |
| "percent": 14.2 |
| }, |
| "sugar": { |
| "atoms": 136321, |
| "percent": 13.3 |
| } |
| }, |
| "top20_residues": { |
| "NAG": 104832, |
| "HEM": 103103, |
| "NAP": 76604, |
| "SO4": 69000, |
| "GOL": 60238, |
| "EDO": 56687, |
| "FAD": 38961, |
| "NAD": 36195, |
| "H4B": 29818, |
| "NDP": 27909, |
| "DMS": 26721, |
| "ACT": 14920, |
| "PO4": 12905, |
| "1PE": 10885, |
| "BTB": 10808, |
| "PEG": 9888, |
| "ZN": 9331, |
| "CLR": 9156, |
| "ADP": 7886, |
| "GTP": 6408 |
| } |
| }, |
| "water": { |
| "total_atoms": 7276591, |
| "note": "HOH only, split into its own file so it can be excluded from the download" |
| }, |
| "units": { |
| "pos": "angstrom", |
| "neglog_aff": "unitless (-log10 of affinity in M; pKd-like)", |
| "log_affinity": "unitless (log10 of affinity in M)", |
| "affinity_value": "in affinity_unit (fM..M), per-complex", |
| "resolution": "angstrom (NaN for 461 NMR structures)", |
| "mw": "g/mol", |
| "tpsa": "angstrom^2", |
| "logp": "unitless", |
| "qed": "unitless [0,1]" |
| } |
| } |
| } |
