{ "antechamber": { "command_template": [ "antechamber", "-i", "input.sdf", "-fi", "sdf", "-o", "output.mol2", "-fo", "mol2", "-c", "bcc", "-nc", "0", "-at", "gaff2", "-pl", "20", "-ek", "maxcyc=0", "-rn", "B1P", "-s", "1" ], "log": { "path": "data/nnc2215-b1-gaff2-boundary-pilot/antechamber.log", "sha256": "56949f24b65dc41e5694029dc3c5f4966349740de17845099ace53169a9bdf22" }, "returncode": 0, "timed_out": false }, "fragment": { "atom_count_with_hydrogens": 74, "boundary_hydrogen_counts": { "AsnB3_NH2_cap_graph_hydrogens": 2, "PheB1_N_graph_hydrogens": 1 }, "cap_interpretation": "The AsnB3 N is retained at its model coordinate after downstream atoms are removed; its valence is saturated as neutral NH2. This is an explicit truncation cap, not the full Asn residue environment.", "connected_component_count": 1, "coordinate_mapping": { "exact_mapping_count": 1, "heavy_atom_coordinate_count": 37, "heavy_atoms": [ { "atom_index_zero_based": 0, "coordinates_angstrom": [ -0.152, 11.315, -10.184 ], "element": "N", "pdb_identity": { "altloc": "", "atom_name": "N", "chain": "B", "residue_name": "PHE", "residue_number": 1 }, "pdb_serial": 37, "source_map_id": null }, { "atom_index_zero_based": 1, "coordinates_angstrom": [ -0.328, 12.205, -9.041 ], "element": "C", "pdb_identity": { "altloc": "", "atom_name": "CA", "chain": "B", "residue_name": "PHE", "residue_number": 1 }, "pdb_serial": 38, "source_map_id": null }, { "atom_index_zero_based": 2, "coordinates_angstrom": [ -1.741, 12.814, -9.132 ], "element": "C", "pdb_identity": { "altloc": "", "atom_name": "C", "chain": "B", "residue_name": "PHE", "residue_number": 1 }, "pdb_serial": 39, "source_map_id": null }, { "atom_index_zero_based": 3, "coordinates_angstrom": [ -2.591, 12.274, -9.84 ], "element": "O", "pdb_identity": { "altloc": "", "atom_name": "O", "chain": "B", "residue_name": "PHE", "residue_number": 1 }, "pdb_serial": 40, "source_map_id": null }, { "atom_index_zero_based": 4, "coordinates_angstrom": [ 0.839, 13.226, -8.91 ], "element": "C", "pdb_identity": { "altloc": "", "atom_name": "CB", "chain": "B", "residue_name": "PHE", "residue_number": 1 }, "pdb_serial": 41, "source_map_id": null }, { "atom_index_zero_based": 5, "coordinates_angstrom": [ 1.271, 13.527, -7.48 ], "element": "C", "pdb_identity": { "altloc": "", "atom_name": "CG", "chain": "B", "residue_name": "PHE", "residue_number": 1 }, "pdb_serial": 42, "source_map_id": null }, { "atom_index_zero_based": 6, "coordinates_angstrom": [ 1.694, 12.479, -6.634 ], "element": "C", "pdb_identity": { "altloc": "", "atom_name": "CD1", "chain": "B", "residue_name": "PHE", "residue_number": 1 }, "pdb_serial": 44, "source_map_id": null }, { "atom_index_zero_based": 7, "coordinates_angstrom": [ 1.191, 14.843, -6.972 ], "element": "C", "pdb_identity": { "altloc": "", "atom_name": "CD2", "chain": "B", "residue_name": "PHE", "residue_number": 1 }, "pdb_serial": 43, "source_map_id": null }, { "atom_index_zero_based": 8, "coordinates_angstrom": [ 2.009, 12.739, -5.287 ], "element": "C", "pdb_identity": { "altloc": "", "atom_name": "CE1", "chain": "B", "residue_name": "PHE", "residue_number": 1 }, "pdb_serial": 46, "source_map_id": null }, { "atom_index_zero_based": 9, "coordinates_angstrom": [ 1.507, 15.101, -5.625 ], "element": "C", "pdb_identity": { "altloc": "", "atom_name": "CE2", "chain": "B", "residue_name": "PHE", "residue_number": 1 }, "pdb_serial": 45, "source_map_id": null }, { "atom_index_zero_based": 10, "coordinates_angstrom": [ 1.91, 14.048, -4.781 ], "element": "C", "pdb_identity": { "altloc": "", "atom_name": "CZ", "chain": "B", "residue_name": "PHE", "residue_number": 1 }, "pdb_serial": 47, "source_map_id": null }, { "atom_index_zero_based": 11, "coordinates_angstrom": [ -1.988, 13.909, -8.398 ], "element": "N", "pdb_identity": { "altloc": "", "atom_name": "N", "chain": "B", "residue_name": "VAL", "residue_number": 2 }, "pdb_serial": 57, "source_map_id": null }, { "atom_index_zero_based": 12, "coordinates_angstrom": [ -3.268, 14.581, -8.146 ], "element": "C", "pdb_identity": { "altloc": "", "atom_name": "CA", "chain": "B", "residue_name": "VAL", "residue_number": 2 }, "pdb_serial": 58, "source_map_id": null }, { "atom_index_zero_based": 13, "coordinates_angstrom": [ -4.002, 13.797, -7.037 ], "element": "C", "pdb_identity": { "altloc": "", "atom_name": "C", "chain": "B", "residue_name": "VAL", "residue_number": 2 }, "pdb_serial": 59, "source_map_id": null }, { "atom_index_zero_based": 14, "coordinates_angstrom": [ -5.192, 13.498, -7.121 ], "element": "O", "pdb_identity": { "altloc": "", "atom_name": "O", "chain": "B", "residue_name": "VAL", "residue_number": 2 }, "pdb_serial": 60, "source_map_id": null }, { "atom_index_zero_based": 15, "coordinates_angstrom": [ -4.062, 14.957, -9.439 ], "element": "C", "pdb_identity": { "altloc": "", "atom_name": "CB", "chain": "B", "residue_name": "VAL", "residue_number": 2 }, "pdb_serial": 61, "source_map_id": null }, { "atom_index_zero_based": 16, "coordinates_angstrom": [ -5.27, 15.873, -9.157 ], "element": "C", "pdb_identity": { "altloc": "", "atom_name": "CG1", "chain": "B", "residue_name": "VAL", "residue_number": 2 }, "pdb_serial": 62, "source_map_id": null }, { "atom_index_zero_based": 17, "coordinates_angstrom": [ -3.169, 15.647, -10.493 ], "element": "C", "pdb_identity": { "altloc": "", "atom_name": "CG2", "chain": "B", "residue_name": "VAL", "residue_number": 2 }, "pdb_serial": 63, "source_map_id": null }, { "atom_index_zero_based": 18, "coordinates_angstrom": [ -3.241, 13.404, -6.006 ], "element": "N", "pdb_identity": { "altloc": "", "atom_name": "N", "chain": "B", "residue_name": "ASN", "residue_number": 3 }, "pdb_serial": 73, "source_map_id": null }, { "atom_index_zero_based": 19, "coordinates_angstrom": [ 0.775, 10.36, -10.298 ], "element": "C", "pdb_identity": { "altloc": "", "atom_name": "C2", "chain": "B", "residue_name": "PHX", "residue_number": 0 }, "pdb_serial": 3, "source_map_id": 2 }, { "atom_index_zero_based": 20, "coordinates_angstrom": [ 1.686, 10.223, -9.485 ], "element": "O", "pdb_identity": { "altloc": "", "atom_name": "O1", "chain": "B", "residue_name": "PHX", "residue_number": 0 }, "pdb_serial": 6, "source_map_id": 3 }, { "atom_index_zero_based": 21, "coordinates_angstrom": [ 0.682, 9.42, -11.51 ], "element": "C", "pdb_identity": { "altloc": "", "atom_name": "C22", "chain": "B", "residue_name": "PHX", "residue_number": 0 }, "pdb_serial": 4, "source_map_id": 4 }, { "atom_index_zero_based": 22, "coordinates_angstrom": [ 0.021, 8.186, -11.201 ], "element": "O", "pdb_identity": { "altloc": "", "atom_name": "O223", "chain": "B", "residue_name": "PHX", "residue_number": 0 }, "pdb_serial": 5, "source_map_id": 5 }, { "atom_index_zero_based": 23, "coordinates_angstrom": [ 0.584, 7.37, -10.168 ], "element": "C", "pdb_identity": { "altloc": "", "atom_name": "C3", "chain": "B", "residue_name": "PHX", "residue_number": 0 }, "pdb_serial": 18, "source_map_id": 6 }, { "atom_index_zero_based": 24, "coordinates_angstrom": [ 2.054, 6.99, -10.413 ], "element": "C", "pdb_identity": { "altloc": "", "atom_name": "C", "chain": "B", "residue_name": "PHX", "residue_number": 0 }, "pdb_serial": 1, "source_map_id": 7 }, { "atom_index_zero_based": 25, "coordinates_angstrom": [ 2.391, 5.883, -9.57 ], "element": "O", "pdb_identity": { "altloc": "", "atom_name": "O", "chain": "B", "residue_name": "PHX", "residue_number": 0 }, "pdb_serial": 2, "source_map_id": 8 }, { "atom_index_zero_based": 26, "coordinates_angstrom": [ 3.775, 5.635, -9.501 ], "element": "C", "pdb_identity": { "altloc": "", "atom_name": "C232", "chain": "B", "residue_name": "PHX", "residue_number": 0 }, "pdb_serial": 7, "source_map_id": 9 }, { "atom_index_zero_based": 27, "coordinates_angstrom": [ 4.013, 4.389, -8.636 ], "element": "C", "pdb_identity": { "altloc": "", "atom_name": "C233", "chain": "B", "residue_name": "PHX", "residue_number": 0 }, "pdb_serial": 8, "source_map_id": 11 }, { "atom_index_zero_based": 28, "coordinates_angstrom": [ 3.445, 4.597, -7.348 ], "element": "O", "pdb_identity": { "altloc": "", "atom_name": "O238", "chain": "B", "residue_name": "PHX", "residue_number": 0 }, "pdb_serial": 13, "source_map_id": 12 }, { "atom_index_zero_based": 29, "coordinates_angstrom": [ 5.52, 4.132, -8.526 ], "element": "C", "pdb_identity": { "altloc": "", "atom_name": "C234", "chain": "B", "residue_name": "PHX", "residue_number": 0 }, "pdb_serial": 9, "source_map_id": 13 }, { "atom_index_zero_based": 30, "coordinates_angstrom": [ 5.761, 2.939, -7.786 ], "element": "O", "pdb_identity": { "altloc": "", "atom_name": "O239", "chain": "B", "residue_name": "PHX", "residue_number": 0 }, "pdb_serial": 14, "source_map_id": 14 }, { "atom_index_zero_based": 31, "coordinates_angstrom": [ 6.128, 4.025, -9.928 ], "element": "C", "pdb_identity": { "altloc": "", "atom_name": "C235", "chain": "B", "residue_name": "PHX", "residue_number": 0 }, "pdb_serial": 10, "source_map_id": 15 }, { "atom_index_zero_based": 32, "coordinates_angstrom": [ 7.525, 3.797, -9.803 ], "element": "O", "pdb_identity": { "altloc": "", "atom_name": "O240", "chain": "B", "residue_name": "PHX", "residue_number": 0 }, "pdb_serial": 15, "source_map_id": 16 }, { "atom_index_zero_based": 33, "coordinates_angstrom": [ 5.801, 5.307, -10.728 ], "element": "C", "pdb_identity": { "altloc": "", "atom_name": "C236", "chain": "B", "residue_name": "PHX", "residue_number": 0 }, "pdb_serial": 11, "source_map_id": 17 }, { "atom_index_zero_based": 34, "coordinates_angstrom": [ 6.289, 5.282, -12.183 ], "element": "C", "pdb_identity": { "altloc": "", "atom_name": "C241", "chain": "B", "residue_name": "PHX", "residue_number": 0 }, "pdb_serial": 16, "source_map_id": 18 }, { "atom_index_zero_based": 35, "coordinates_angstrom": [ 5.969, 6.5, -12.857 ], "element": "O", "pdb_identity": { "altloc": "", "atom_name": "O242", "chain": "B", "residue_name": "PHX", "residue_number": 0 }, "pdb_serial": 17, "source_map_id": 19 }, { "atom_index_zero_based": 36, "coordinates_angstrom": [ 4.369, 5.438, -10.763 ], "element": "O", "pdb_identity": { "altloc": "", "atom_name": "O237", "chain": "B", "residue_name": "PHX", "residue_number": 0 }, "pdb_serial": 12, "source_map_id": 10 } ], "mapping_id": "mapping_001", "mapping_index_chosen_by_geometry": false, "source_map_1_is_protein_phe_n": true, "state": "active_open" }, "element_counts_heavy": { "C": 24, "N": 3, "O": 10 }, "formal_charge": 0, "formula": "C24H37N3O10", "heavy_atom_count": 37, "stereochemistry_cip": { "B1_source_maps": { "11": "R", "13": "S", "15": "S", "17": "R", "9": "R" }, "PheB1_CA": "S", "ValB2_CA": "S" } }, "frcmod": { "candidate_accepted": true, "generated": true, "generated_parameter_record_count": 65, "generated_records": [ { "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": "c3-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-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": "nt-c -c3-ns 1 0.100 180.000 -1.000 same as n -c -c3-n", "section": "DIHE" }, { "line": "nt-c -c3-ns 1 2.120 180.000 2.000 same as n -c -c3-n , penalty score= 0.0", "section": "DIHE" }, { "line": "c3-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": "nt-c -c3-c3 1 0.000 180.000 -4.000 same as n -c -c3-c3", "section": "DIHE" }, { "line": "nt-c -c3-c3 1 0.710 180.000 2.000 same as n -c -c3-c3, penalty score= 0.0", "section": "DIHE" }, { "line": "c3-c3-os-c6 1 0.750 0.000 -3.000 same as c3-c3-os-c3", "section": "DIHE" }, { "line": "c3-c3-os-c6 1 0.080 0.000 -2.000 same as c3-c3-os-c3", "section": "DIHE" }, { "line": "c3-c3-os-c6 1 0.880 180.000 1.000 same as c3-c3-os-c3, penalty score= 0.0", "section": "DIHE" }, { "line": "c6-c6-os-c3 1 0.750 0.000 -3.000 same as c3-c3-os-c3", "section": "DIHE" }, { "line": "c6-c6-os-c3 1 0.080 0.000 -2.000 same as c3-c3-os-c3", "section": "DIHE" }, { "line": "c6-c6-os-c3 1 0.880 180.000 1.000 same as c3-c3-os-c3, penalty score= 0.0", "section": "DIHE" }, { "line": "os-c6-os-c3 1 0.850 0.000 -3.000 same as os-c3-os-c3", "section": "DIHE" }, { "line": "os-c6-os-c3 1 0.850 0.000 -2.000 same as os-c3-os-c3", "section": "DIHE" }, { "line": "os-c6-os-c3 1 0.460 180.000 1.000 same as os-c3-os-c3, penalty score= 0.0", "section": "DIHE" }, { "line": "h2-c6-os-c3 3 1.150 0.000 3.000 same as X -c3-os-X , penalty score= 0.0", "section": "DIHE" }, { "line": "oh-c6-c6-os 1 1.070 0.000 -3.000 same as oh-c3-c6-os", "section": "DIHE" }, { "line": "oh-c6-c6-os 1 0.730 180.000 -2.000 same as oh-c3-c6-os", "section": "DIHE" }, { "line": "oh-c6-c6-os 1 0.670 180.000 1.000 same as oh-c3-c6-os, penalty score= 0.0", "section": "DIHE" }, { "line": "c6-c6-c6-os 9 1.400 0.000 3.000 same as X -c3-c3-X , penalty score= 0.0", "section": "DIHE" }, { "line": "h1-c6-c6-os 1 0.000 0.000 -3.000 same as h1-c3-c3-os", "section": "DIHE" }, { "line": "h1-c6-c6-os 1 0.250 0.000 1.000 same as h1-c3-c3-os, penalty score= 0.0", "section": "DIHE" }, { "line": "c6-c6-oh-ho 1 0.060 0.000 3.000 same as c3-c3-oh-ho, penalty score= 0.0", "section": "DIHE" }, { "line": "c6-c6-c6-oh 1 0.180 0.000 3.000 same as c3-c3-c3-oh, penalty score= 0.0", "section": "DIHE" }, { "line": "c6-c6-c6-c6 1 0.520 0.000 3.000 same as c3-c3-c3-c3, penalty score= 0.0", "section": "DIHE" }, { "line": "c6-c6-c6-h1 9 1.400 0.000 3.000 same as X -c3-c3-X , penalty score= 0.0", "section": "DIHE" }, { "line": "oh-c6-c6-oh 1 1.440 0.000 -3.000 same as oh-c3-c3-oh", "section": "DIHE" }, { "line": "oh-c6-c6-oh 1 1.000 0.000 1.000 same as oh-c3-c3-oh, penalty score= 0.0", "section": "DIHE" }, { "line": "h1-c6-c6-oh 1 0.000 0.000 -3.000 same as h1-c3-c3-oh", "section": "DIHE" }, { "line": "h1-c6-c6-oh 1 0.250 0.000 1.000 same as h1-c3-c3-oh, penalty score= 0.0", "section": "DIHE" }, { "line": "c3-c6-c6-c6 1 0.520 0.000 3.000 same as c3-c3-c3-c3, penalty score= 0.0", "section": "DIHE" }, { "line": "oh-c3-c6-c6 1 0.180 0.000 3.000 same as c3-c3-c3-oh, penalty score= 0.0", "section": "DIHE" }, { "line": "h1-c3-c6-c6 9 1.400 0.000 3.000 same as X -c3-c3-X , penalty score= 0.0", "section": "DIHE" }, { "line": "c3-c6-c6-oh 1 0.180 0.000 3.000 same as c3-c3-c3-oh, penalty score= 0.0", "section": "DIHE" }, { "line": "c6-c3-oh-ho 1 0.060 0.000 3.000 same as c3-c3-oh-ho, penalty score= 0.0", "section": "DIHE" }, { "line": "c3-c6-os-c6 1 0.750 0.000 -3.000 same as c3-c3-os-c3", "section": "DIHE" }, { "line": "c3-c6-os-c6 1 0.080 0.000 -2.000 same as c3-c3-os-c3", "section": "DIHE" }, { "line": "c3-c6-os-c6 1 0.880 180.000 1.000 same as c3-c3-os-c3, penalty score= 0.0", "section": "DIHE" }, { "line": "h1-c3-c6-os 1 0.000 0.000 -3.000 same as h1-c3-c3-os", "section": "DIHE" }, { "line": "h1-c3-c6-os 1 0.250 0.000 1.000 same as h1-c3-c3-os, penalty score= 0.0", "section": "DIHE" }, { "line": "c -c3-ns-hn 6 0.000 0.000 2.000 same as X -c3-n -X , penalty score= 0.0", "section": "DIHE" }, { "line": "c3-c3-ns-hn 6 0.000 0.000 2.000 same as X -c3-n -X , 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": "h1-c3-os-c6 1 0.337 0.000 3.000 same as h1-c3-os-c3, penalty score= 0.0", "section": "DIHE" }, { "line": "h2-c6-c6-oh 9 1.400 0.000 3.000 same as X -c3-c3-X , penalty score= 0.0", "section": "DIHE" }, { "line": "c6-c6-c6-h2 9 1.400 0.000 3.000 same as X -c3-c3-X , penalty score= 0.0", "section": "DIHE" }, { "line": "h1-c6-c6-h2 9 1.400 0.000 3.000 same as X -c3-c3-X , penalty score= 0.0", "section": "DIHE" }, { "line": "h2-c6-os-c6 3 1.150 0.000 3.000 same as X -c3-os-X , penalty score= 0.0", "section": "DIHE" }, { "line": "h1-c6-oh-ho 1 0.123 0.000 3.000 same as h1-c3-oh-ho, penalty score= 0.0", "section": "DIHE" }, { "line": "h1-c6-c6-h1 9 1.400 0.000 3.000 same as X -c3-c3-X , penalty score= 0.0", "section": "DIHE" }, { "line": "c3-c6-c6-h1 9 1.400 0.000 3.000 same as X -c3-c3-X , penalty score= 0.0", "section": "DIHE" }, { "line": "oh-c3-c6-h1 1 0.000 0.000 -3.000 same as h1-c3-c3-oh", "section": "DIHE" }, { "line": "oh-c3-c6-h1 1 0.250 0.000 1.000 same as h1-c3-c3-oh, penalty score= 0.0", "section": "DIHE" }, { "line": "h1-c3-c6-h1 9 1.400 0.000 3.000 same as X -c3-c3-X , penalty score= 0.0", "section": "DIHE" }, { "line": "h1-c6-os-c6 1 0.337 0.000 3.000 same as h1-c3-os-c3, 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": "c3-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": "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": "c3-nt-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 -hn-nt-hn 1.1 180.0 2.0 Same as X -X -n -hn, penalty score= 6.0 (use general term))", "section": "IMPROPER" } ], "maximum_penalty_score": 6.0, "path": "data/nnc2215-b1-gaff2-boundary-pilot/b1_boundary_fragment.frcmod", "penalty_score_record_count": 46, "records_with_attention_marker": 0, "records_with_penalty_score_at_least_20": 0, "sha256": "622e2ebedd410b847f1ad89a83947c790442d65ae20c2e8c15fbd52afd02924a", "validation_status": "tool_and_MOL2_correspondence_checks_passed" }, "inputs": { "active_open_model_candidate": { "hash_unchanged_after_run": true, "path": "structures/nnc2215-open-source-corrected-candidate.pdb", "sha256": "2ee2d8cb8479c1a881704725c13462a84134b6f47313fe2d78d5f8382decdccc", "sha256_expected_by_b1_topology_audit": "2ee2d8cb8479c1a881704725c13462a84134b6f47313fe2d78d5f8382decdccc" }, "ambertools_lock": { "path": "pag-chemistry-environment-macos-arm64.lock.txt", "sha256": "608d83e646a04e939b5b6b38619337b2822966113beb60c8368f90ecba803d6d" }, "ambertools_package": { "package_md5": "b1ece4272978a9c2e5e261fd57c36222", "version_build": "26.0-cuda_None_nompi_py312h52216ed_100" }, "audit_script": { "path": "audit_nnc2215_b1_ambertools_parameterization_pilot.py", "sha256": "0971500b4c54e3c5a5c88e878c2e29b866070455bdabcba8be1244918bf353c4" }, "b1_topology_audit": { "path": "data/nnc2215-b1-topology-audit.json", "sha256": "4ee0feac680641f60b465f343837923488877bf04ea03e927f62efad707e79ce" }, "b29_graph_and_map": { "graph": { "path": "structures/nnc2215-b29-linker-roof-product.smi", "sha256": "b677316c1fced61045d2eebab4de85cdb2f1ef956280d18ab9d610df1181bd40" }, "map_legend": { "path": "data/nnc2215-b29-linker-roof-product-map.json", "sha256": "eb028433748cf294744ac02f381e909f029f79916484a2e05dfbf966f7faa0c5" }, "purpose": "Input required by the existing full-graph builder; the selected fragment contains no B29 atoms." }, "coordinate_reconciliation": { "path": "data/nnc2215-carbon-reconciliation-candidate.json", "sha256": "7aed13e3d8bcd13d9aa8b3e468f8831b5dec322caf3de454dd67f68087d4e133" }, "formula_audit": { "path": "data/nnc2215-model-formula-audit.json", "sha256": "ad5cf3035fa16330239f69ef7fee95e0a2c02b6944d309f20e56219799775260" }, "full_conjugate_graph": { "path": "data/nnc2215-full-conjugate-graph.json", "sha256": "fb9feaed3537196515c62656d890c0e92b42c9b7da15955dd516b1d82dd178dc" }, "full_graph_builder": { "path": "audit_nnc2215_full_conjugate_graph.py", "sha256": "c0fe69b50f4b3439b27863c8c54e7d9847fd0ac9ffc6c6966e14004ae022d85f" }, "parameterization_helper_script": { "path": "audit_nnc2215_ambertools_parameterization_pilot.py", "sha256": "358ee8115de0eed9e7c3010f770c07bcc73a30b17cf689472d4b3bfd8315d8a0" }, "source_graph": { "path": "structures/nnc2215-b1-glucoside-attachment.smi", "sha256": "94ef8ea011bc968beb3fb4a3e8846b64182c602faf7fe041461cd33c4e5a02b4" }, "source_map_legend": { "path": "data/nnc2215-b1-glucoside-atom-map.json", "sha256": "a45953599aa2eb490275da3cfe595a3b702148da690a6baf17c6751925878e81" } }, "limits": [ "The active/open coordinates are model-built, and the pilot does not establish that this conformation is experimentally resolved.", "The AsnB3 NH2 cap omits the remaining AsnB3 environment and makes the AM1-BCC charges cap-dependent.", "The PheB1 hydrogen-record discrepancy is not resolved; PDB hydrogens are not used for proton placement.", "Generated GAFF2 types, AM1-BCC charges, and parmchk2 terms are feasibility outputs only and are not validated for transferability or protein-bound cross-boundary use.", "B29 mapping/protonation, full insulin microstate and total charge, complete force-field construction, target pose, MD, affinity, and clinical outcome remain unresolved." ], "method": { "antechamber_charge_method": "AM1-BCC (Antechamber bcc)", "atom_type_set": "GAFF2", "bonded_parameter_lookup": "ff14SB available to parmchk2 as a comparison set; generated terms are not validated", "declared_formal_charge": 0, "fragment_definition": "B1 source maps 2\u201319 + PheB1 + ValB2 + AsnB3 N as a neutral NH2 cap", "geometry_optimization": "disabled with maxcyc=0", "input_geometry": "active/open publisher-supplied model-built heavy-atom coordinates; no geometry optimization; explicit hydrogens added by RDKit", "nvidia_gpu_used": false, "pdb_hydrogen_records_used": false }, "mol2": { "atom_count": 74, "atom_parameters": [ { "atom_index_zero_based": 0, "element": "N", "gaff2_type": "ns", "mol2_atom_name": "N1", "partial_charge_e": -0.1469, "pdb_identity": "B:1:PHE:N", "pdb_serial": 37 }, { "atom_index_zero_based": 1, "element": "C", "gaff2_type": "c3", "mol2_atom_name": "C1", "partial_charge_e": -0.0653, "pdb_identity": "B:1:PHE:CA", "pdb_serial": 38 }, { "atom_index_zero_based": 2, "element": "C", "gaff2_type": "c", "mol2_atom_name": "C2", "partial_charge_e": 0.5751, "pdb_identity": "B:1:PHE:C", "pdb_serial": 39 }, { "atom_index_zero_based": 3, "element": "O", "gaff2_type": "o", "mol2_atom_name": "O1", "partial_charge_e": -0.6281, "pdb_identity": "B:1:PHE:O", "pdb_serial": 40 }, { "atom_index_zero_based": 4, "element": "C", "gaff2_type": "c3", "mol2_atom_name": "C3", "partial_charge_e": 0.0139, "pdb_identity": "B:1:PHE:CB", "pdb_serial": 41 }, { "atom_index_zero_based": 5, "element": "C", "gaff2_type": "ca", "mol2_atom_name": "C4", "partial_charge_e": -0.1063, "pdb_identity": "B:1:PHE:CG", "pdb_serial": 42 }, { "atom_index_zero_based": 6, "element": "C", "gaff2_type": "ca", "mol2_atom_name": "C5", "partial_charge_e": -0.1065, "pdb_identity": "B:1:PHE:CD1", "pdb_serial": 44 }, { "atom_index_zero_based": 7, "element": "C", "gaff2_type": "ca", "mol2_atom_name": "C6", "partial_charge_e": -0.1065, "pdb_identity": "B:1:PHE:CD2", "pdb_serial": 43 }, { "atom_index_zero_based": 8, "element": "C", "gaff2_type": "ca", "mol2_atom_name": "C7", "partial_charge_e": -0.099, "pdb_identity": "B:1:PHE:CE1", "pdb_serial": 46 }, { "atom_index_zero_based": 9, "element": "C", "gaff2_type": "ca", "mol2_atom_name": "C8", "partial_charge_e": -0.099, "pdb_identity": "B:1:PHE:CE2", "pdb_serial": 45 }, { "atom_index_zero_based": 10, "element": "C", "gaff2_type": "ca", "mol2_atom_name": "C9", "partial_charge_e": -0.102, "pdb_identity": "B:1:PHE:CZ", "pdb_serial": 47 }, { "atom_index_zero_based": 11, "element": "N", "gaff2_type": "ns", "mol2_atom_name": "N2", "partial_charge_e": -0.1889, "pdb_identity": "B:2:VAL:N", "pdb_serial": 57 }, { "atom_index_zero_based": 12, "element": "C", "gaff2_type": "c3", "mol2_atom_name": "C10", "partial_charge_e": -0.0423, "pdb_identity": "B:2:VAL:CA", "pdb_serial": 58 }, { "atom_index_zero_based": 13, "element": "C", "gaff2_type": "c", "mol2_atom_name": "C11", "partial_charge_e": 0.5561, "pdb_identity": "B:2:VAL:C", "pdb_serial": 59 }, { "atom_index_zero_based": 14, "element": "O", "gaff2_type": "o", "mol2_atom_name": "O2", "partial_charge_e": -0.6211, "pdb_identity": "B:2:VAL:O", "pdb_serial": 60 }, { "atom_index_zero_based": 15, "element": "C", "gaff2_type": "c3", "mol2_atom_name": "C12", "partial_charge_e": -0.0517, "pdb_identity": "B:2:VAL:CB", "pdb_serial": 61 }, { "atom_index_zero_based": 16, "element": "C", "gaff2_type": "c3", "mol2_atom_name": "C13", "partial_charge_e": 0.0064, "pdb_identity": "B:2:VAL:CG1", "pdb_serial": 62 }, { "atom_index_zero_based": 17, "element": "C", "gaff2_type": "c3", "mol2_atom_name": "C14", "partial_charge_e": 0.0064, "pdb_identity": "B:2:VAL:CG2", "pdb_serial": 63 }, { "atom_index_zero_based": 18, "element": "N", "gaff2_type": "nt", "mol2_atom_name": "N3", "partial_charge_e": -0.227, "pdb_identity": "B:3:ASN:N", "pdb_serial": 73 }, { "atom_index_zero_based": 19, "component": "B1", "element": "C", "gaff2_type": "c", "mol2_atom_name": "C15", "partial_charge_e": 0.5351, "pdb_identity": "B:0:PHX:C2", "pdb_serial": 3, "source_map_id": 2, "source_map_role": "B1 linker carbonyl carbon; amide carbonyl attached to PheB1 N." }, { "atom_index_zero_based": 20, "component": "B1", "element": "O", "gaff2_type": "o", "mol2_atom_name": "O3", "partial_charge_e": -0.6711, "pdb_identity": "B:0:PHX:O1", "pdb_serial": 6, "source_map_id": 3, "source_map_role": "B1 amide carbonyl oxygen." }, { "atom_index_zero_based": 21, "component": "B1", "element": "C", "gaff2_type": "c3", "mol2_atom_name": "C16", "partial_charge_e": 0.1414, "pdb_identity": "B:0:PHX:C22", "pdb_serial": 4, "source_map_id": 4, "source_map_role": "Methylene alpha to the carbonyl; source NMR group OCH2C=O." }, { "atom_index_zero_based": 22, "component": "B1", "element": "O", "gaff2_type": "os", "mol2_atom_name": "O4", "partial_charge_e": -0.3936, "pdb_identity": "B:0:PHX:O223", "pdb_serial": 5, "source_map_id": 5, "source_map_role": "Ether oxygen between the carbonyl-alpha methylene and the ethylene linker." }, { "atom_index_zero_based": 23, "component": "B1", "element": "C", "gaff2_type": "c3", "mol2_atom_name": "C17", "partial_charge_e": 0.1994, "pdb_identity": "B:0:PHX:C3", "pdb_serial": 18, "source_map_id": 6, "source_map_role": "First ethylene-linker methylene, adjacent to map 5." }, { "atom_index_zero_based": 24, "component": "B1", "element": "C", "gaff2_type": "c3", "mol2_atom_name": "C18", "partial_charge_e": 0.1534, "pdb_identity": "B:0:PHX:C", "pdb_serial": 1, "source_map_id": 7, "source_map_role": "Second ethylene-linker methylene, adjacent to the glycosidic-side ether oxygen map 8." }, { "atom_index_zero_based": 25, "component": "B1", "element": "O", "gaff2_type": "os", "mol2_atom_name": "O5", "partial_charge_e": -0.3726, "pdb_identity": "B:0:PHX:O", "pdb_serial": 2, "source_map_id": 8, "source_map_role": "Glycosidic-side ether oxygen linking the ethylene linker to glucose C1." }, { "atom_index_zero_based": 26, "component": "B1", "element": "C", "gaff2_type": "c6", "mol2_atom_name": "C19", "partial_charge_e": 0.3899, "pdb_identity": "B:0:PHX:C232", "pdb_serial": 7, "source_map_id": 9, "source_map_role": "Anomeric glucose carbon; beta-D glycosidic attachment site." }, { "atom_index_zero_based": 27, "component": "B1", "element": "C", "gaff2_type": "c6", "mol2_atom_name": "C20", "partial_charge_e": 0.1281, "pdb_identity": "B:0:PHX:C233", "pdb_serial": 8, "source_map_id": 11, "source_map_role": "Glucose C2 stereocenter bearing a free hydroxyl at map 12." }, { "atom_index_zero_based": 28, "component": "B1", "element": "O", "gaff2_type": "oh", "mol2_atom_name": "O6", "partial_charge_e": -0.5608, "pdb_identity": "B:0:PHX:O238", "pdb_serial": 13, "source_map_id": 12, "source_map_role": "Free hydroxyl oxygen at glucose C2." }, { "atom_index_zero_based": 29, "component": "B1", "element": "C", "gaff2_type": "c6", "mol2_atom_name": "C21", "partial_charge_e": 0.1091, "pdb_identity": "B:0:PHX:C234", "pdb_serial": 9, "source_map_id": 13, "source_map_role": "Glucose C3 stereocenter bearing a free hydroxyl at map 14." }, { "atom_index_zero_based": 30, "component": "B1", "element": "O", "gaff2_type": "oh", "mol2_atom_name": "O7", "partial_charge_e": -0.5698, "pdb_identity": "B:0:PHX:O239", "pdb_serial": 14, "source_map_id": 14, "source_map_role": "Free hydroxyl oxygen at glucose C3." }, { "atom_index_zero_based": 31, "component": "B1", "element": "C", "gaff2_type": "c6", "mol2_atom_name": "C22", "partial_charge_e": 0.1641, "pdb_identity": "B:0:PHX:C235", "pdb_serial": 10, "source_map_id": 15, "source_map_role": "Glucose C4 stereocenter bearing a free hydroxyl at map 16." }, { "atom_index_zero_based": 32, "component": "B1", "element": "O", "gaff2_type": "oh", "mol2_atom_name": "O8", "partial_charge_e": -0.5828, "pdb_identity": "B:0:PHX:O240", "pdb_serial": 15, "source_map_id": 16, "source_map_role": "Free hydroxyl oxygen at glucose C4." }, { "atom_index_zero_based": 33, "component": "B1", "element": "C", "gaff2_type": "c6", "mol2_atom_name": "C23", "partial_charge_e": 0.1271, "pdb_identity": "B:0:PHX:C236", "pdb_serial": 11, "source_map_id": 17, "source_map_role": "Glucose C5 stereocenter; bears the C6 hydroxymethyl substituent and ring oxygen map 10." }, { "atom_index_zero_based": 34, "component": "B1", "element": "C", "gaff2_type": "c3", "mol2_atom_name": "C24", "partial_charge_e": 0.2264, "pdb_identity": "B:0:PHX:C241", "pdb_serial": 16, "source_map_id": 18, "source_map_role": "Glucose C6 hydroxymethyl carbon." }, { "atom_index_zero_based": 35, "component": "B1", "element": "O", "gaff2_type": "oh", "mol2_atom_name": "O9", "partial_charge_e": -0.5878, "pdb_identity": "B:0:PHX:O242", "pdb_serial": 17, "source_map_id": 19, "source_map_role": "Free hydroxyl oxygen at glucose C6." }, { "atom_index_zero_based": 36, "component": "B1", "element": "O", "gaff2_type": "os", "mol2_atom_name": "O10", "partial_charge_e": -0.4186, "pdb_identity": "B:0:PHX:O237", "pdb_serial": 12, "source_map_id": 10, "source_map_role": "Glucopyranose ring oxygen between glucose C5 and C1." }, { "atom_index_zero_based": 37, "element": "H", "gaff2_type": "hn", "mol2_atom_name": "H1", "parent_atom_index_zero_based": 0, "parent_pdb_serial": 37, "partial_charge_e": 0.2015 }, { "atom_index_zero_based": 38, "element": "H", "gaff2_type": "h1", "mol2_atom_name": "H2", "parent_atom_index_zero_based": 1, "parent_pdb_serial": 38, "partial_charge_e": 0.0597 }, { "atom_index_zero_based": 39, "element": "H", "gaff2_type": "hc", "mol2_atom_name": "H3", "parent_atom_index_zero_based": 4, "parent_pdb_serial": 41, "partial_charge_e": 0.0372 }, { "atom_index_zero_based": 40, "element": "H", "gaff2_type": "hc", "mol2_atom_name": "H4", "parent_atom_index_zero_based": 4, "parent_pdb_serial": 41, "partial_charge_e": 0.0372 }, { "atom_index_zero_based": 41, "element": "H", "gaff2_type": "ha", "mol2_atom_name": "H5", "parent_atom_index_zero_based": 6, "parent_pdb_serial": 44, "partial_charge_e": 0.1195 }, { "atom_index_zero_based": 42, "element": "H", "gaff2_type": "ha", "mol2_atom_name": "H6", "parent_atom_index_zero_based": 7, "parent_pdb_serial": 43, "partial_charge_e": 0.1195 }, { "atom_index_zero_based": 43, "element": "H", "gaff2_type": "ha", "mol2_atom_name": "H7", "parent_atom_index_zero_based": 8, "parent_pdb_serial": 46, "partial_charge_e": 0.108 }, { "atom_index_zero_based": 44, "element": "H", "gaff2_type": "ha", "mol2_atom_name": "H8", "parent_atom_index_zero_based": 9, "parent_pdb_serial": 45, "partial_charge_e": 0.108 }, { "atom_index_zero_based": 45, "element": "H", "gaff2_type": "ha", "mol2_atom_name": "H9", "parent_atom_index_zero_based": 10, "parent_pdb_serial": 47, "partial_charge_e": 0.107 }, { "atom_index_zero_based": 46, "element": "H", "gaff2_type": "hn", "mol2_atom_name": "H10", "parent_atom_index_zero_based": 11, "parent_pdb_serial": 57, "partial_charge_e": 0.1825 }, { "atom_index_zero_based": 47, "element": "H", "gaff2_type": "h1", "mol2_atom_name": "H11", "parent_atom_index_zero_based": 12, "parent_pdb_serial": 58, "partial_charge_e": 0.0357 }, { "atom_index_zero_based": 48, "element": "H", "gaff2_type": "hc", "mol2_atom_name": "H12", "parent_atom_index_zero_based": 15, "parent_pdb_serial": 61, "partial_charge_e": 0.0617 }, { "atom_index_zero_based": 49, "element": "H", "gaff2_type": "hc", "mol2_atom_name": "H13", "parent_atom_index_zero_based": 16, "parent_pdb_serial": 62, "partial_charge_e": 0.007367 }, { "atom_index_zero_based": 50, "element": "H", "gaff2_type": "hc", "mol2_atom_name": "H14", "parent_atom_index_zero_based": 16, "parent_pdb_serial": 62, "partial_charge_e": 0.007367 }, { "atom_index_zero_based": 51, "element": "H", "gaff2_type": "hc", "mol2_atom_name": "H15", "parent_atom_index_zero_based": 16, "parent_pdb_serial": 62, "partial_charge_e": 0.007367 }, { "atom_index_zero_based": 52, "element": "H", "gaff2_type": "hc", "mol2_atom_name": "H16", "parent_atom_index_zero_based": 17, "parent_pdb_serial": 63, "partial_charge_e": 0.007367 }, { "atom_index_zero_based": 53, "element": "H", "gaff2_type": "hc", "mol2_atom_name": "H17", "parent_atom_index_zero_based": 17, "parent_pdb_serial": 63, "partial_charge_e": 0.007367 }, { "atom_index_zero_based": 54, "element": "H", "gaff2_type": "hc", "mol2_atom_name": "H18", "parent_atom_index_zero_based": 17, "parent_pdb_serial": 63, "partial_charge_e": 0.007367 }, { "atom_index_zero_based": 55, "element": "H", "gaff2_type": "hn", "mol2_atom_name": "H19", "parent_atom_index_zero_based": 18, "parent_pdb_serial": 73, "partial_charge_e": 0.1645 }, { "atom_index_zero_based": 56, "element": "H", "gaff2_type": "hn", "mol2_atom_name": "H20", "parent_atom_index_zero_based": 18, "parent_pdb_serial": 73, "partial_charge_e": 0.1645 }, { "atom_index_zero_based": 57, "element": "H", "gaff2_type": "h1", "mol2_atom_name": "H21", "parent_atom_index_zero_based": 21, "parent_pdb_serial": 4, "parent_source_map_id": 4, "partial_charge_e": 0.0262 }, { "atom_index_zero_based": 58, "element": "H", "gaff2_type": "h1", "mol2_atom_name": "H22", "parent_atom_index_zero_based": 21, "parent_pdb_serial": 4, "parent_source_map_id": 4, "partial_charge_e": 0.0262 }, { "atom_index_zero_based": 59, "element": "H", "gaff2_type": "h1", "mol2_atom_name": "H23", "parent_atom_index_zero_based": 23, "parent_pdb_serial": 18, "parent_source_map_id": 6, "partial_charge_e": 0.0267 }, { "atom_index_zero_based": 60, "element": "H", "gaff2_type": "h1", "mol2_atom_name": "H24", "parent_atom_index_zero_based": 23, "parent_pdb_serial": 18, "parent_source_map_id": 6, "partial_charge_e": 0.0267 }, { "atom_index_zero_based": 61, "element": "H", "gaff2_type": "h1", "mol2_atom_name": "H25", "parent_atom_index_zero_based": 24, "parent_pdb_serial": 1, "parent_source_map_id": 7, "partial_charge_e": 0.0147 }, { "atom_index_zero_based": 62, "element": "H", "gaff2_type": "h1", "mol2_atom_name": "H26", "parent_atom_index_zero_based": 24, "parent_pdb_serial": 1, "parent_source_map_id": 7, "partial_charge_e": 0.0147 }, { "atom_index_zero_based": 63, "element": "H", "gaff2_type": "h2", "mol2_atom_name": "H27", "parent_atom_index_zero_based": 26, "parent_pdb_serial": 7, "parent_source_map_id": 9, "partial_charge_e": -0.0093 }, { "atom_index_zero_based": 64, "element": "H", "gaff2_type": "h1", "mol2_atom_name": "H28", "parent_atom_index_zero_based": 27, "parent_pdb_serial": 8, "parent_source_map_id": 11, "partial_charge_e": 0.0567 }, { "atom_index_zero_based": 65, "element": "H", "gaff2_type": "ho", "mol2_atom_name": "H29", "parent_atom_index_zero_based": 28, "parent_pdb_serial": 13, "parent_source_map_id": 12, "partial_charge_e": 0.379 }, { "atom_index_zero_based": 66, "element": "H", "gaff2_type": "h1", "mol2_atom_name": "H30", "parent_atom_index_zero_based": 29, "parent_pdb_serial": 9, "parent_source_map_id": 13, "partial_charge_e": 0.0097 }, { "atom_index_zero_based": 67, "element": "H", "gaff2_type": "ho", "mol2_atom_name": "H31", "parent_atom_index_zero_based": 30, "parent_pdb_serial": 14, "parent_source_map_id": 14, "partial_charge_e": 0.395 }, { "atom_index_zero_based": 68, "element": "H", "gaff2_type": "h1", "mol2_atom_name": "H32", "parent_atom_index_zero_based": 31, "parent_pdb_serial": 10, "parent_source_map_id": 15, "partial_charge_e": 0.0497 }, { "atom_index_zero_based": 69, "element": "H", "gaff2_type": "ho", "mol2_atom_name": "H33", "parent_atom_index_zero_based": 32, "parent_pdb_serial": 15, "parent_source_map_id": 16, "partial_charge_e": 0.404 }, { "atom_index_zero_based": 70, "element": "H", "gaff2_type": "h1", "mol2_atom_name": "H34", "parent_atom_index_zero_based": 33, "parent_pdb_serial": 11, "parent_source_map_id": 17, "partial_charge_e": 0.0127 }, { "atom_index_zero_based": 71, "element": "H", "gaff2_type": "h1", "mol2_atom_name": "H35", "parent_atom_index_zero_based": 34, "parent_pdb_serial": 16, "parent_source_map_id": 18, "partial_charge_e": 0.0217 }, { "atom_index_zero_based": 72, "element": "H", "gaff2_type": "h1", "mol2_atom_name": "H36", "parent_atom_index_zero_based": 34, "parent_pdb_serial": 16, "parent_source_map_id": 18, "partial_charge_e": 0.0217 }, { "atom_index_zero_based": 73, "element": "H", "gaff2_type": "ho", "mol2_atom_name": "H37", "parent_atom_index_zero_based": 35, "parent_pdb_serial": 17, "parent_source_map_id": 19, "partial_charge_e": 0.392 } ], "bond_count": 75, "candidate_accepted": true, "charge_correction_applied": false, "charge_sum_within_0_01e_tolerance": true, "gaff2_atom_type_counts": { "c": 3, "c3": 10, "c6": 5, "ca": 6, "h1": 14, "h2": 1, "ha": 5, "hc": 9, "hn": 4, "ho": 4, "ns": 2, "nt": 1, "o": 3, "oh": 4, "os": 3 }, "generated": true, "heavy_atom_count": 37, "mapping_validation": { "atom_coordinates_match_prepared_sdf": true, "atom_ids_sequential_in_prepared_sdf_order": true, "bond_graph_and_orders_match_prepared_sdf": true, "coordinate_tolerance_angstrom": 0.002, "element_order_matches_prepared_sdf": true, "maximum_coordinate_delta_angstrom": 0.000733 }, "net_charge_residual_e": 0.003002, "partial_charge_sum_e": 0.003002, "path": "data/nnc2215-b1-gaff2-boundary-pilot/b1_boundary_fragment.mol2", "sha256": "cd6bb91f1da0545d5604a13915f98bf1b2af3528db620f07f2c136f29f8c415a", "validation_status": "passed" }, "output_validation_error": null, "parmchk2": { "command_template": [ "parmchk2", "-i", "output.mol2", "-f", "mol2", "-o", "output.frcmod", "-s", "2", "-frc", "ff14SB" ], "log": { "path": "data/nnc2215-b1-gaff2-boundary-pilot/parmchk2.log", "sha256": "3cadabec897fd961a14ae0f164fbcc2d872da835fd7c259079ac6fab44594c72" }, "returncode": 0, "timed_out": false }, "partial_charge_bookkeeping": { "charge_correction_applied": false, "formal_charge": 0, "interpretation": "AM1-BCC result for this fragment geometry and declared cap; not a validated final charge assignment.", "partial_charge_sum_e": 0.003002, "residual_e": 0.003002 }, "purpose": "Test pinned AmberTools GAFF2/AM1-BCC feasibility for a source-mapped B1 glucoside in a local PheB1/ValB2 peptide context.", "schema": "dia-health-one.nnc2215-b1-gaff2-boundary-pilot.v1", "sdf": { "path": "data/nnc2215-b1-gaff2-boundary-pilot/b1_boundary_fragment.sdf", "sha256": "9c72be390bf06337c5e6b1e4b68c0e84c5ad0f64b7da58fdc80998765746c189" }, "software": { "amberhome": "/private/tmp/dia-target-tools-pinned", "antechamber_path": "/private/tmp/dia-target-tools-pinned/bin/antechamber", "parmchk2_path": "/private/tmp/dia-target-tools-pinned/bin/parmchk2", "python_version": "3.12.15", "rdkit_version": "2026.03.1" }, "status": "PILOT_ONLY; COMPLETE_CONJUGATE_FORCE_FIELD_NOT_VALIDATED", "validated_conjugate_force_field_count": 0 }