{ "schema_version": "1.0.0", "trajectory_id": "cb1r_local_trajectory", "id_namespace": "local", "record_status": "partial", "evidence_status": "computational", "curation_date": "2026-08-03", "purpose": "Support an evidence-bounded explanation of molecular dynamics for CB1R.", "publication": { "metadata_scope": "public", "raw_artifact_scope": "internal-only", "policy_note": "This public record exposes provenance identifiers and fixity hashes for auditability, but it does not publish the raw PDB, PSF, XTC, or mmCIF artifacts." }, "identity": { "target": "Cannabinoid receptor type 1", "gene": "CNR1", "organism": "Homo sapiens", "tax_id": 9606, "starting_structure_id": "5U09", "experimental_method": "X-ray diffraction", "experimental_resolution_angstrom": 2.6, "receptor_state": "inactive", "receptor_state_evidence_status": "external structural interpretation", "construct_status": "engineered experimental construct", "construct_notes": "The 5U09 record contains a fusion partner and an engineered receptor construct. Exact mutation and residue-coverage mapping for the processed trajectory remains pending.", "trajectory_lineage": { "candidate_source_structure_id": "5U09", "status": "inferred-from-local-system-correspondence", "limitation": "No simulation manifest or derivation record was found that directly links the processed local trajectory to the deposited 5U09 coordinates." }, "structural_mapping": { "status": "pending", "chains": null, "observed_residues": null, "missing_residues": null, "variant_records": null, "fusion_partner_mapping": null } }, "system": { "atom_count": 69095, "ligand": { "pdb_component_id": "7DY", "name": "taranabant", "presence_evidence_status": "observed in the local processed coordinates and the 5U09 structural record", "pharmacological_role": "inverse agonist", "pharmacological_role_evidence_status": "external structural-record annotation" }, "signaling_partner": null, "membrane": { "type": "homogeneous", "composition": ["POPC"], "evidence_basis": "Local processed PDB and PSF" }, "solvent": { "model": "TIP3P", "evidence_basis": "TIP3 residues in the local processed PDB" }, "ions": ["sodium", "chloride"] }, "protocol": { "method": "classical molecular dynamics", "software": null, "software_version": null, "force_field": "CHARMM36 family", "force_field_version": null, "force_field_status": "inferred-from-topology-header", "force_field_evidence": "PSF remarks reference CHARMM36 protein, lipid, carbohydrate, water-ion, and CGenFF topology families plus a local 7DY topology.", "integrator": null, "time_step_fs": null, "ensemble": null, "temperature_k": null, "pressure_bar": null, "thermostat": null, "barostat": null, "equilibration_ns": null, "production_ns": null, "saved_frame_interval_ns": null, "replicates": null }, "files": [ { "role": "trajectory", "repository_relative_path": "docking_Kannabium/animalia_ecs/11524_trj_164.xtc", "format": "XTC", "bytes": 639543056, "sha256": "e3a2d85b340630ae48291c429904a0fe36e34309c073bb10006b8ad1bbf63c84", "artifact_availability": "internal-only" }, { "role": "topology", "repository_relative_path": "docking_Kannabium/animalia_ecs/11528_dyn_164.psf", "format": "PSF", "bytes": 13058650, "sha256": "32438f87a2893e3148a9db6b03348b9bb26fb297566199ae62d41f6744f25071", "artifact_availability": "internal-only" }, { "role": "starting_coordinates", "repository_relative_path": "docking_Kannabium/animalia_ecs/11529_dyn_164.pdb", "format": "PDB", "bytes": 5596781, "sha256": "b38abb94b241413566d3923b171082d7c9b1007563c161d17255ca7891b6b616", "artifact_availability": "internal-only" }, { "role": "experimental_source", "repository_relative_path": "docking_Kannabium/animalia_ecs/5U09.cif", "format": "mmCIF", "bytes": 479100, "sha256": "fcc98ae50eddde2677f780f5286ec31cf779c28d70d84805089897728e191ef8", "artifact_availability": "internal-only" } ], "provenance": { "candidate_external_repository": "GPCRmd", "candidate_external_accession": "164", "candidate_accession_status": "unverified", "repository_attribution_status": "inferred-not-independently-matched", "inference_basis": "Local GPCRmd-style filenames share the suffix dyn_164 or trj_164 and form a loadable PDB-PSF-XTC set.", "structural_sources": [ { "source_name": "RCSB Protein Data Bank", "source_identifier": "PDB:5U09", "doi": "10.2210/pdb5u09/pdb", "source_url": "https://www.rcsb.org/structure/5U09", "accessed_at": "2026-08-03", "retrieval_method": "web record review", "license_or_terms_note": "Linked for provenance; reuse remains subject to the provider's current terms.", "claim_supported": "Experimental CB1R structure record, ligand identity, method, resolution, and engineered construct context.", "claim_type": "fact", "evidence_class": "primary structural archive", "limitations": "The deposition record does not establish the derivation lineage of the local processed trajectory." }, { "source_name": "GPCRdb", "source_identifier": "Structure:5U09", "source_url": "https://gpcrdb.org/structure/5U09", "accessed_at": "2026-08-03", "retrieval_method": "curated web record review", "license_or_terms_note": "Linked for provenance; reuse remains subject to the provider's current terms.", "claim_supported": "Curated receptor state, ligand, species, and structural context for 5U09.", "claim_type": "inference", "source_role": "curated interpretation", "evidence_class": "secondary curated database", "limitations": "This record does not independently match the local files to a GPCRmd dynamics accession." }, { "source_name": "GPCRmd documentation", "source_identifier": "data-download documentation", "source_url": "https://gpcrmd-docs.readthedocs.io/en/latest/data-download.html", "accessed_at": "2026-08-03", "retrieval_method": "documentation review", "license_or_terms_note": "Linked for methodological context; reuse remains subject to the provider's current terms.", "claim_supported": "Repository-level context for GPCR molecular-dynamics files and downloads.", "claim_type": "fact", "source_role": "methodological context", "evidence_class": "repository documentation", "limitations": "The documentation does not confirm that the local suffix 164 corresponds to a specific public GPCRmd record." }, { "source_name": "High-resolution crystal structure of the human CB1 cannabinoid receptor", "source_identifier": "DOI:10.1038/nature20613", "source_url": "https://www.nature.com/articles/nature20613", "accessed_at": "2026-08-03", "retrieval_method": "primary publication review", "license_or_terms_note": "Linked for provenance; reuse remains subject to the publisher's current terms.", "claim_supported": "The experimental study reports the taranabant-bound human CB1 structure and supplies the primary pharmacological and structural context used to classify this inactive complex.", "claim_type": "fact", "source_role": "primary research publication", "evidence_class": "peer-reviewed primary literature", "limitations": "The publication does not establish the derivation lineage or protocol of the local processed trajectory." } ], "method_repository": "https://www.gpcrmd.org/", "local_loader": "docking_Kannabium/animalia_ecs/load_cb1r.tcl" }, "evidence_boundaries": { "supported_claims": [ "The local files form a CB1R molecular-dynamics coordinate, topology, and trajectory set.", "The local system is consistent with a simulation prepared from inactive 5U09 and contains 7DY, POPC, TIP3P water, sodium, and chloride.", "PSF remarks document CHARMM36-family topology sources and a local 7DY topology." ], "unsupported_claims": [ "The trajectory represents THC bound to CB1R.", "The existing editorial video was rendered from this trajectory.", "The trajectory demonstrates binding affinity, receptor efficacy, signaling bias, or physiological relevance.", "The run duration, ensemble, temperature, pressure, time step, convergence, and replicate count are known." ], "missing_artifacts": [ "simulation protocol", "parameter or configuration file", "execution log", "replicate manifest", "trajectory-to-video derivation record" ] } }