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bound_molecules_bound_molecules_id_433acab7

Read-only

Get all bound molecules for a PDB entry, including carbohydrate polymers, Bound Molecule IDs, covalently bound ligands, CCD IDs, and connectivity.

Instructions

Returns information for all bound molecules for a given PDB entry ID, including carbohydrate polymers. Details include each Bound Molecule IDs (e.g: “bm1”, “bm2”), composition (covalently bound ligands with unique CCD IDs) and internal connectivity, or which bound are covalently bound together (e.g: [“F1”, “F6”] means bound ligands identified by author_residue_number “1” and “6” in chain_id “F” are covalently bound).

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
pdb_idYes4-character PDB id code. title: Pdb Id description: 4-character PDB id code.

Schema Changelog

Changes observed during successful MCP inspections.

  1. Addedv1.1.10

TDQS

A3.5/5.0
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already declare readOnlyHint=true and destructiveHint=false, so safety is covered, but the description goes further by describing the payload itself: Bound Molecule IDs (bm1, bm2), composition via unique CCD IDs, and a worked example of the connectivity notation. With no output schema present, this return-shape detail is genuinely additive.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

A single front-loaded sentence leads with the core purpose, then appends clarifying examples for the connectivity notation. It is dense but every clause (carbohydrate polymers, CCD composition, F1/F6 example) earns its place by decoding an otherwise opaque return field.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

For a one-parameter read-only lookup with no output schema, the description supplies enough about the returned content (IDs, composition, connectivity) that an agent can interpret results. It is nearly complete, lacking only sibling disambiguation against bound_mibmiib_id.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 100% and the single pdb_id parameter is fully documented in the schema as a 4-character PDB id code. The description adds no format, validation, or alternate-input meaning beyond 'for a given PDB entry ID', so the baseline 3 applies.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

States a specific verb and resource: returns all bound molecules for a given PDB entry ID, with an explicit scope note ('including carbohydrate polymers'). An agent knows exactly what data it gets. It stops short of naming or contrasting with the near-duplicate sibling bound_mibmiib_id, so it does not fully differentiate at selection time.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines2/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

There is no explicit when-to-use statement, no prerequisites, and no mention of alternatives such as the closely named bound_mibmiib_id sibling. The only implied context is that you must supply a PDB entry ID, which is already enforced by the required parameter.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.