Skip to main content
Glama
PDBeurope

PDBe MCP Servers

Official
by PDBeurope

get_bound_molecule_interactions_api_pdb_bound_molecule_inter

Read-only

Retrieve the full composition, internal connectivity, and detected interactions (covalent, hydrogen-bond, polar, van der Waals, hydrophobic, atom-plane) for a specific bound molecule in a PDB entry.

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.
Behavior4/5

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

Annotations declare readOnlyHint=true; the description adds details on the returned composition, connectivity, and interaction types, and mentions calculation for the preferred assembly, providing behavioral context beyond annotations.

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?

The description is a single paragraph that front-loads the purpose and provides sufficient detail without excessive verbosity. It is slightly long but well-structured.

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?

Given the complexity of the output and no output schema, the description adequately explains what the tool returns, including examples of connectivity and interaction types. It covers essential context.

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%; both parameters are described in the schema. The tool description repeats some of that information but does not add new semantic detail beyond 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?

The description clearly states the tool returns composition and high-level interactions for a specific bound molecule ID of a PDB entry, distinguishing it from sibling tools like get_bound_molecules that list bound molecules.

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?

The description implies usage after obtaining bm_id from the bound_molecules call, but does not explicitly state when to use vs alternatives or when not to use.

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

Install Server

Other Tools

Latest Blog Posts

MCP directory API

We provide all the information about MCP servers via our MCP API.

curl -X GET 'https://glama.ai/api/mcp/v1/servers/PDBeurope/PDBe-MCP-Servers'

If you have feedback or need assistance with the MCP directory API, please join our Discord server