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bound_mibmiib_id_9eb5b2d0

Read-only

Retrieve a bound molecule's composition and interactions with surrounding residues or ligands using a PDB ID and its bound molecule ID.

Instructions

Returns composition and high-level interactions for a specific Bound Molecule ID (e.g., “bm1”) of a PDB entry ID. This includes its full composition (all covalently linked ligands with their CCD IDs), internal connectivity between those ligands (e.g: [“F1”, “F6”] means bound ligands identified by author_residue_number “1” and “6” in chain_id “F” are covalently bound), and all detected interactions between the bound molecule and surrounding residues or ligands (e.g., covalent, hydrogen-bond, polar, van der Waals, hydrophobic, and atom-plane interactions) calculated for the preferred assembly of the PDB entry.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
bm_idYesBound molecule ID (can be obtained from the output of bound_molecules call) title: Bm Id description: Bound molecule ID (can be obtained from the output of bound_molecules call)
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

A3.6/5.0
Behavior4/5

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

Annotations already declare readOnlyHint=true and destructiveHint=false, so the safety profile is covered. The description goes beyond that by enumerating exactly what is returned — full composition with CCD IDs, internal connectivity format, and the specific interaction types computed for the preferred assembly — which is meaningful behavioral context.

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?

Content is front-loaded into a single sentence and every clause conveys return-scope information. It is dense and crowded with parenthetical examples, but not padded with filler.

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

Completeness5/5

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

With no output schema, the description carries the full burden of describing returns, and it does so thoroughly — composition, connectivity encoding, and interaction categories. An agent knows what it will get back and the two required inputs.

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% for both parameters, so the schema already documents pdb_id and bm_id. The description adds a concrete bm_id example ('bm1') but nothing about pdb_id format or constraints, making this a baseline case.

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?

The description states a specific verb (returns) and resource (composition and high-level interactions for a specific Bound Molecule ID of a PDB entry), with a concrete example id ('bm1'). It is clear what the tool produces, though it does not explicitly differentiate itself from the sibling bound_molecules tool that supplies the bm_id.

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?

The description gives no when-to-use or when-not-to-use guidance and names no alternative. The only routing hint ('can be obtained from the output of bound_molecules call') lives in the schema field description, not the tool description.

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