{
  "assessment": {
    "all_eight_variants_completed": true,
    "bonded_parameter_gaps_inventoried": true,
    "clinical_use": false,
    "full_insulin_topology_or_openmm_system_created": false,
    "gaff2_partial_charges_assigned": true,
    "limits": [
      "The B29 source endpoint NH2 cap is not the attached LysB29 NZ-in-residue environment; atom charges at the protein junction are therefore not final.",
      "The chosen open coordinates are publisher-supplied model-built coordinates, and their source-to-coordinate map is one of 16 exact element-adjacency embeddings.",
      "AM1-BCC/GAFF2 plus parmchk2 output is a candidate fragment assignment, not a reviewed force field.",
      "The eight outputs test arbitrary carboxylate Lewis-label sensitivity; no charge averaging or atom-type normalization is performed.",
      "Custom LysB29 boundary-residue charges and cross-boundary bonded terms remain unassigned.",
      "PheB1/B1 fragment parameters, insulin termini, protein compatibility, full system assembly, and force-field validation remain open.",
      "No solvent, ions, target receptor complex, MD, affinity, pharmacology, or clinical conclusion is included."
    ],
    "md_run": false,
    "validated_conjugate_force_fields": 0
  },
  "carboxylate_resonance_charge_sensitivity": {
    "compared_variant_count": 8,
    "largest_per_atom_absolute_charge_range_e": 0.0,
    "per_source_atom": []
  },
  "component_graph": {
    "atom_count_with_hydrogens": 161,
    "formal_charge": -3,
    "formula": "C62H69N16O14-3",
    "heavy_atom_count": 92,
    "heavy_atom_input_mapping_is_authoritative": false,
    "resonance_variant_count_completed": 8
  },
  "inputs": {
    "ambertools_package": {
      "package_md5": "b1ece4272978a9c2e5e261fd57c36222",
      "version_build": "26.0-cuda_None_nompi_py312h52216ed_100"
    },
    "audit_script": {
      "path": "audit_nnc2215_ambertools_parameterization_pilot.py",
      "sha256": "358ee8115de0eed9e7c3010f770c07bcc73a30b17cf689472d4b3bfd8315d8a0"
    },
    "environment_lock": {
      "path": "pag-chemistry-environment-macos-arm64.lock.txt",
      "sha256": "608d83e646a04e939b5b6b38619337b2822966113beb60c8368f90ecba803d6d"
    },
    "open_model_coordinate_candidate": {
      "coordinates_are_model_built": true,
      "hash_unchanged_after_run": true,
      "map_id_to_pdb_serial": {
        "1": 896,
        "10": 905,
        "11": 904,
        "12": 903,
        "13": 847,
        "14": 849,
        "15": 839,
        "16": 841,
        "17": 843,
        "18": 845,
        "19": 856,
        "2": 895,
        "20": 857,
        "21": 852,
        "22": 853,
        "23": 854,
        "24": 855,
        "25": 846,
        "26": 848,
        "27": 838,
        "28": 840,
        "29": 842,
        "3": 900,
        "30": 844,
        "31": 865,
        "32": 866,
        "33": 867,
        "34": 868,
        "35": 863,
        "36": 864,
        "37": 874,
        "38": 891,
        "39": 888,
        "4": 899,
        "40": 894,
        "41": 837,
        "42": 832,
        "43": 890,
        "44": 887,
        "45": 893,
        "46": 851,
        "47": 873,
        "48": 889,
        "49": 886,
        "5": 898,
        "50": 892,
        "51": 836,
        "52": 870,
        "53": 872,
        "54": 908,
        "55": 835,
        "56": 879,
        "57": 885,
        "58": 882,
        "59": 876,
        "6": 897,
        "60": 869,
        "61": 871,
        "62": 907,
        "63": 850,
        "64": 878,
        "65": 884,
        "66": 881,
        "67": 833,
        "68": 909,
        "69": 910,
        "7": 902,
        "70": 911,
        "71": 834,
        "72": 877,
        "73": 883,
        "74": 880,
        "75": 875,
        "76": 861,
        "77": 859,
        "78": 862,
        "79": 502,
        "8": 901,
        "80": 501,
        "81": 496,
        "82": 495,
        "83": 494,
        "84": 497,
        "85": 498,
        "86": 505,
        "87": 506,
        "88": 499,
        "89": 500,
        "9": 906,
        "90": 503,
        "91": 504,
        "92": 480
      },
      "mapping_id": "exact_mapping_01",
      "mapping_index_zero_based": 0,
      "one_of_sixteen_graph_embeddings": true,
      "path": "structures/nnc2215-open-source-corrected-candidate.pdb",
      "sha256": "2ee2d8cb8479c1a881704725c13462a84134b6f47313fe2d78d5f8382decdccc",
      "sha256_expected_by_topology_audit": "2ee2d8cb8479c1a881704725c13462a84134b6f47313fe2d78d5f8382decdccc"
    },
    "product_graph": {
      "path": "structures/nnc2215-b29-linker-roof-product.smi",
      "sha256": "b677316c1fced61045d2eebab4de85cdb2f1ef956280d18ab9d610df1181bd40"
    },
    "product_map_legend": {
      "path": "data/nnc2215-b29-linker-roof-product-map.json",
      "sha256": "eb028433748cf294744ac02f381e909f029f79916484a2e05dfbf966f7faa0c5"
    },
    "topology_audit": {
      "path": "data/nnc2215-b29-topology-audit.json",
      "sha256": "edd4d9911170e3688c80f6b8ca3f4339ebee7815c1bb596cfa2dfaca468d96c6"
    }
  },
  "method": {
    "atom_type_set": "GAFF2",
    "bonded_parameter_lookups": "GAFF2 with ff14SB available as a comparison set; parmchk2-generated terms are not validated",
    "carboxylate_map_groups": [
      [
        52,
        53,
        54
      ],
      [
        60,
        61,
        62
      ],
      [
        68,
        69,
        70
      ]
    ],
    "charge_method": "AM1-BCC (Antechamber bcc)",
    "declared_charge_state": "three B29 carboxylates deprotonated; neutral NH2 source endpoint cap; net formal charge -3",
    "input_geometry": "heavy-atom coordinates copied from the public active/open model-built candidate using selected topology-audit embedding exact_mapping_01 (zero-based index 0); explicit hydrogens added by RDKit",
    "pdb_or_source_coordinates_modified": false,
    "rdkit_version": "2026.03.1",
    "resonance_variants": 8,
    "sqm_geometry_optimization": "disabled with maxcyc=0 to avoid changing the selected model geometry in a vacuum; the resulting charges remain geometry- and model-dependent",
    "tools": "AmberTools 26 Antechamber and parmchk2"
  },
  "purpose": "Test AmberTools GAFF2/AM1-BCC feasibility on an isolated source-mapped B29 conjugate component under the conditional tri-carboxylate charge state.",
  "schema": "dia-health-one.nnc2215-b29-gaff2-parameterization-pilot.v1",
  "status": "PILOT_ONLY; COMPLETE_CONJUGATE_FORCE_FIELD_NOT_VALIDATED",
  "variants": [
    {
      "anionic_oxygen_map_ids": [
        53,
        61,
        69
      ],
      "antechamber": {
        "command_template": [
          "antechamber",
          "-i",
          "input.sdf",
          "-fi",
          "sdf",
          "-o",
          "output.mol2",
          "-fo",
          "mol2",
          "-c",
          "bcc",
          "-nc",
          "-3",
          "-at",
          "gaff2",
          "-pl",
          "20",
          "-ek",
          "maxcyc=0",
          "-rn",
          "B29",
          "-s",
          "1"
        ],
        "log_sha256": "56949f24b65dc41e5694029dc3c5f4966349740de17845099ace53169a9bdf22",
        "returncode": 0,
        "timed_out": false
      },
      "atom_count_with_hydrogens": 161,
      "bond_count_with_hydrogens": 168,
      "formal_charge": -3,
      "formula": "C62H69N16O14-3",
      "frcmod": {
        "generated_parameter_record_count": 26,
        "generated_records": [
          {
            "line": "ca-c3-ns-c    6    0.000         0.000           2.000      same as X -c3-n -X , penalty score=  0.0",
            "section": "DIHE"
          },
          {
            "line": "ca-c3-ns-hn   6    0.000         0.000           2.000      same as X -c3-n -X , penalty score=  0.0",
            "section": "DIHE"
          },
          {
            "line": "o -c -ns-c3   4   10.000       180.000           2.000      same as X -c -n -X , penalty score=  0.0",
            "section": "DIHE"
          },
          {
            "line": "ns-c -ns-c3   4   10.000       180.000           2.000      same as X -c -n -X , penalty score=  0.0",
            "section": "DIHE"
          },
          {
            "line": "ns-c -ns-ca   4   10.000       180.000           2.000      same as X -c -n -X , penalty score=  0.0",
            "section": "DIHE"
          },
          {
            "line": "ns-c -ns-hn   4   10.000       180.000           2.000      same as X -c -n -X , penalty score=  0.0",
            "section": "DIHE"
          },
          {
            "line": "o -c -ns-ca   4   10.000       180.000           2.000      same as X -c -n -X , penalty score=  0.0",
            "section": "DIHE"
          },
          {
            "line": "o -c -ns-hn   1    2.500       180.000          -2.000      same as o -c -n -hn",
            "section": "DIHE"
          },
          {
            "line": "o -c -ns-hn   1    2.000         0.000           1.000      same as o -c -n -hn, penalty score=  0.0",
            "section": "DIHE"
          },
          {
            "line": "ca-ca-ns-hn   4    1.800       180.000           2.000      same as X -ca-n -X , penalty score=  0.0",
            "section": "DIHE"
          },
          {
            "line": "os-c -nt-hn   4   10.000       180.000           2.000      same as X -c -n -X , penalty score=  0.0",
            "section": "DIHE"
          },
          {
            "line": "o -c -nt-hn   1    2.500       180.000          -2.000      same as o -c -n -hn",
            "section": "DIHE"
          },
          {
            "line": "o -c -nt-hn   1    2.000         0.000           1.000      same as o -c -n -hn, penalty score=  0.0",
            "section": "DIHE"
          },
          {
            "line": "h1-c3-ns-hn   6    0.000         0.000           2.000      same as X -c3-n -X , penalty score=  0.0",
            "section": "DIHE"
          },
          {
            "line": "c -c3-ns-hn         1.1          180.0         2.0          Same as X -X -n -hn, penalty score=  6.0 (use general term))",
            "section": "IMPROPER"
          },
          {
            "line": "ns-ns-c -o         10.5          180.0         2.0          Using general improper torsional angle  X- X- c- o, penalty score=  6.0)",
            "section": "IMPROPER"
          },
          {
            "line": "c -ca-ns-hn         1.1          180.0         2.0          Same as X -X -n -hn, penalty score=  6.0 (use general term))",
            "section": "IMPROPER"
          },
          {
            "line": "ca-ca-ca-ns        10.5          180.0         2.0          Same as X -X -cc-X , penalty score= 41.9 (use general term))",
            "section": "IMPROPER"
          },
          {
            "line": "ca-ca-ca-ha         1.1          180.0         2.0          Using general improper torsional angle  X- X-ca-ha, penalty score=  6.0)",
            "section": "IMPROPER"
          },
          {
            "line": "c -ca-ca-ca        10.5          180.0         2.0          Same as X -X -cc-X , penalty score= 41.9 (use general term))",
            "section": "IMPROPER"
          },
          {
            "line": "ca-o -c -o          1.1          180.0         2.0          Using general improper torsional angle  X- o- c- o, penalty score=  3.0)",
            "section": "IMPROPER"
          },
          {
            "line": "c3-cc-na-nc         1.1          180.0         2.0          Using the default value",
            "section": "IMPROPER"
          },
          {
            "line": "c3-cc-cd-nd        10.5          180.0         2.0          Using general improper torsional angle  X- X-cd- X, penalty score=  9.0)",
            "section": "IMPROPER"
          },
          {
            "line": "nt-o -c -os         1.1          180.0         2.0          Using the default value",
            "section": "IMPROPER"
          },
          {
            "line": "c -hn-nt-hn         1.1          180.0         2.0          Same as X -X -n -hn, penalty score=  6.0 (use general term))",
            "section": "IMPROPER"
          },
          {
            "line": "cd-h4-cc-na        10.5          180.0         2.0          Using general improper torsional angle  X- X-cc- X, penalty score=  9.0)",
            "section": "IMPROPER"
          }
        ],
        "maximum_penalty_score": 41.9,
        "path": "data/nnc2215-b29-gaff2-pilot/resonance_01.frcmod",
        "penalty_score_record_count": 22,
        "records_with_attention_marker": 0,
        "records_with_penalty_score_at_least_20": 2,
        "sha256": "a1d1250a4dd58612c18fadcdb01fa25d53351051c2046a6bad81507c8920fa33"
      },
      "input_sdf": {
        "path": "data/nnc2215-b29-gaff2-pilot/resonance_01.sdf",
        "sha256": "9f1a44f68ff0fdfd11e364d95803a4b59883558e00af75a0eec6a6ee6d4eadae"
      },
      "mol2": {
        "atom_count": 161,
        "atom_type_counts": {
          "c": 10,
          "c3": 20,
          "ca": 30,
          "cc": 1,
          "cd": 1,
          "h1": 16,
          "h4": 1,
          "ha": 9,
          "hc": 29,
          "hn": 14,
          "na": 1,
          "nc": 1,
          "nd": 1,
          "ns": 12,
          "nt": 1,
          "o": 13,
          "os": 1
        },
        "bond_count": 168,
        "charge_sum_within_0_01e_tolerance": true,
        "charged_atoms_by_source_map": [
          {
            "atom_type": "ca",
            "element": "C",
            "partial_charge_e": -0.0223,
            "source_map_id": 1
          },
          {
            "atom_type": "c3",
            "element": "C",
            "partial_charge_e": -0.0151,
            "source_map_id": 31
          },
          {
            "atom_type": "c3",
            "element": "C",
            "partial_charge_e": 0.0099,
            "source_map_id": 32
          },
          {
            "atom_type": "ca",
            "element": "C",
            "partial_charge_e": -0.1323,
            "source_map_id": 2
          },
          {
            "atom_type": "ca",
            "element": "C",
            "partial_charge_e": -0.0538,
            "source_map_id": 3
          },
          {
            "atom_type": "c3",
            "element": "C",
            "partial_charge_e": 0.0109,
            "source_map_id": 33
          },
          {
            "atom_type": "c3",
            "element": "C",
            "partial_charge_e": 0.0019,
            "source_map_id": 34
          },
          {
            "atom_type": "ca",
            "element": "C",
            "partial_charge_e": -0.1333,
            "source_map_id": 4
          },
          {
            "atom_type": "ca",
            "element": "C",
            "partial_charge_e": -0.0538,
            "source_map_id": 5
          },
          {
            "atom_type": "c3",
            "element": "C",
            "partial_charge_e": 0.0109,
            "source_map_id": 35
          },
          {
            "atom_type": "c3",
            "element": "C",
            "partial_charge_e": 0.0019,
            "source_map_id": 36
          },
          {
            "atom_type": "ca",
            "element": "C",
            "partial_charge_e": -0.1323,
            "source_map_id": 6
          },
          {
            "atom_type": "c3",
            "element": "C",
            "partial_charge_e": 0.1108,
            "source_map_id": 47
          },
          {
            "atom_type": "ns",
            "element": "N",
            "partial_charge_e": -0.2659,
            "source_map_id": 48
          },
          {
            "atom_type": "c",
            "element": "C",
            "partial_charge_e": 0.5926,
            "source_map_id": 49
          },
          {
            "atom_type": "o",
            "element": "O",
            "partial_charge_e": -0.6766,
            "source_map_id": 50
          },
          {
            "atom_type": "ns",
            "element": "N",
            "partial_charge_e": -0.0721,
            "source_map_id": 51
          },
          {
            "atom_type": "ca",
            "element": "C",
            "partial_charge_e": -0.1229,
            "source_map_id": 25
          },
          {
            "atom_type": "ca",
            "element": "C",
            "partial_charge_e": -0.125,
            "source_map_id": 26
          },
          {
            "atom_type": "ca",
            "element": "C",
            "partial_charge_e": -0.082,
            "source_map_id": 27
          },
          {
            "atom_type": "ca",
            "element": "C",
            "partial_charge_e": -0.0691,
            "source_map_id": 28
          },
          {
            "atom_type": "c",
            "element": "C",
            "partial_charge_e": 0.9567,
            "source_map_id": 68
          },
          {
            "atom_type": "o",
            "element": "O",
            "partial_charge_e": -0.8853,
            "source_map_id": 69
          },
          {
            "atom_type": "o",
            "element": "O",
            "partial_charge_e": -0.8853,
            "source_map_id": 70
          },
          {
            "atom_type": "ca",
            "element": "C",
            "partial_charge_e": -0.0445,
            "source_map_id": 29
          },
          {
            "atom_type": "ca",
            "element": "C",
            "partial_charge_e": -0.1359,
            "source_map_id": 30
          },
          {
            "atom_type": "ns",
            "element": "N",
            "partial_charge_e": -0.0861,
            "source_map_id": 71
          },
          {
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            "element": "C",
            "partial_charge_e": 0.5916,
            "source_map_id": 72
          },
          {
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            "element": "O",
            "partial_charge_e": -0.6546,
            "source_map_id": 73
          },
          {
            "atom_type": "ns",
            "element": "N",
            "partial_charge_e": -0.2644,
            "source_map_id": 74
          },
          {
            "atom_type": "c3",
            "element": "C",
            "partial_charge_e": 0.1048,
            "source_map_id": 75
          },
          {
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            "element": "C",
            "partial_charge_e": -0.1333,
            "source_map_id": 12
          },
          {
            "atom_type": "ca",
            "element": "C",
            "partial_charge_e": -0.0273,
            "source_map_id": 7
          },
          {
            "atom_type": "c3",
            "element": "C",
            "partial_charge_e": 0.0049,
            "source_map_id": 78
          },
          {
            "atom_type": "c3",
            "element": "C",
            "partial_charge_e": -0.0304,
            "source_map_id": 79
          },
          {
            "atom_type": "c3",
            "element": "C",
            "partial_charge_e": -0.0597,
            "source_map_id": 80
          },
          {
            "atom_type": "na",
            "element": "N",
            "partial_charge_e": 0.5134,
            "source_map_id": 81
          },
          {
            "atom_type": "nc",
            "element": "N",
            "partial_charge_e": -0.3358,
            "source_map_id": 82
          },
          {
            "atom_type": "nd",
            "element": "N",
            "partial_charge_e": -0.322,
            "source_map_id": 83
          },
          {
            "atom_type": "cd",
            "element": "C",
            "partial_charge_e": 0.2196,
            "source_map_id": 88
          },
          {
            "atom_type": "c3",
            "element": "C",
            "partial_charge_e": -0.0187,
            "source_map_id": 87
          },
          {
            "atom_type": "c3",
            "element": "C",
            "partial_charge_e": -0.0474,
            "source_map_id": 86
          },
          {
            "atom_type": "c3",
            "element": "C",
            "partial_charge_e": 0.2254,
            "source_map_id": 85
          },
          {
            "atom_type": "os",
            "element": "O",
            "partial_charge_e": -0.4249,
            "source_map_id": 91
          },
          {
            "atom_type": "c",
            "element": "C",
            "partial_charge_e": 0.6901,
            "source_map_id": 84
          },
          {
            "atom_type": "o",
            "element": "O",
            "partial_charge_e": -0.642,
            "source_map_id": 90
          },
          {
            "atom_type": "nt",
            "element": "N",
            "partial_charge_e": -0.247,
            "source_map_id": 92
          },
          {
            "atom_type": "cc",
            "element": "C",
            "partial_charge_e": -0.3516,
            "source_map_id": 89
          },
          {
            "atom_type": "ca",
            "element": "C",
            "partial_charge_e": -0.1333,
            "source_map_id": 8
          },
          {
            "atom_type": "ca",
            "element": "C",
            "partial_charge_e": -0.0513,
            "source_map_id": 9
          },
          {
            "atom_type": "c3",
            "element": "C",
            "partial_charge_e": 0.0282,
            "source_map_id": 76
          },
          {
            "atom_type": "ca",
            "element": "C",
            "partial_charge_e": -0.1423,
            "source_map_id": 10
          },
          {
            "atom_type": "ca",
            "element": "C",
            "partial_charge_e": -0.0513,
            "source_map_id": 11
          },
          {
            "atom_type": "c3",
            "element": "C",
            "partial_charge_e": 0.0282,
            "source_map_id": 77
          },
          {
            "atom_type": "c3",
            "element": "C",
            "partial_charge_e": 0.1253,
            "source_map_id": 67
          },
          {
            "atom_type": "ns",
            "element": "N",
            "partial_charge_e": -0.2649,
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            "atom_type": "ns",
            "element": "N",
            "partial_charge_e": -0.2659,
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          },
          {
            "atom_type": "c3",
            "element": "C",
            "partial_charge_e": 0.1108,
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          }
        ],
        "net_charge_residual_e": 0.003995000000000193,
        "partial_charge_sum_e": -2.996005,
        "path": "data/nnc2215-b29-gaff2-pilot/resonance_08.mol2",
        "sha256": "ea04ba1c153334c74756b6c1d9b343a3fe5761c5265c5a3eb16efac1c1b5d327"
      },
      "parmchk2": {
        "command_template": [
          "parmchk2",
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          "output.mol2",
          "-f",
          "mol2",
          "-o",
          "output.frcmod",
          "-s",
          "2",
          "-frc",
          "ff14SB"
        ],
        "log_sha256": "3cadabec897fd961a14ae0f164fbcc2d872da835fd7c259079ac6fab44594c72",
        "returncode": 0,
        "timed_out": false
      },
      "variant_id": "resonance_08"
    }
  ]
}
