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ebi-pdbe-bound_mibmiib_id_9eb5b2d0

Read-only

Retrieve composition and high-level interactions for a specific bound molecule ID in a PDB entry, including linked ligands and contacts with surrounding residues or ligands.

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

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. Addedv2.0.1

TDQS

A3.9/5.0
Behavior4/5

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

Annotations already cover the safety profile (readOnlyHint=true, destructiveHint=false, idempotentHint=false), and the description adds genuine context beyond them: results are computed for the preferred assembly, the interaction categories enumerated (covalent, hydrogen-bond, polar, van der Waals, hydrophobic, atom-plane), and the exact meaning of the internal connectivity notation. It does not discuss pagination or response size, but for a read-only lookup that is a minor omission.

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 that leads with the return content and then qualifies it; every clause carries information. It is dense with parenthetical examples, which slightly hurts scannability but nothing is redundant.

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?

With no output schema, the description must carry the return-value burden, and it does so thoroughly by naming the three content blocks and giving a concrete notation example. It stops short of describing the actual response shape or field names, which leaves a small gap for a two-parameter data-returning tool.

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%, so both parameters are already documented, and the description only adds a bm_id example ('bm1') and the 4-character PDB id format implicitly. The residue-number/chain-id example illustrates output content rather than parameter semantics, so no real lift over the schema.

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

Purpose5/5

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

States a specific verb ('Returns') and precisely enumerates the resource content: composition, internal connectivity between covalently linked ligands, and detected interactions for one Bound Molecule ID of a PDB entry. The detail about CCD IDs and the ["F1","F6"] connectivity format clearly separates it from the sibling bound_molecules listing tool and from the hetcode-based interaction tools.

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

Usage Guidelines3/5

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

Usage is only implied: the reader must infer that this is the drill-down after obtaining a bm_id, and that hint lives in the input schema rather than the description. No alternatives (e.g., bound_molecules, comp_intx_comp_intx_hetcode) are named and there are no when-not conditions.

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

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