Database schema:

CREATE TABLE atom (
	atom_id TEXT NOT NULL -- atom id, example: ['TR000_1', 'TR000_2'],
	molecule_id TEXT DEFAULT NULL -- molecule id, example: ['TR000', 'TR001'],
	element TEXT DEFAULT NULL -- example: ['c', 'cl'],
	PRIMARY KEY (atom_id), 
	CONSTRAINT fk_atom_molecule FOREIGN KEY(molecule_id) REFERENCES molecule (molecule_id)
)


CREATE TABLE bond (
	bond_id TEXT NOT NULL -- example: ['TR000_2_3', 'TR000_1_2'],
	molecule_id TEXT DEFAULT NULL -- example: ['TR000', 'TR001'],
	bond_type TEXT DEFAULT NULL -- example: ['=', '-'],
	PRIMARY KEY (bond_id), 
	CONSTRAINT fk_bond_molecule FOREIGN KEY(molecule_id) REFERENCES molecule (molecule_id)
)


CREATE TABLE connected (
	atom_id TEXT NOT NULL -- atom id, example: ['TR000_1', 'TR000_2'],
	atom_id2 TEXT NOT NULL -- atom id 2, example: ['TR000_1', 'TR000_2'],
	bond_id TEXT DEFAULT NULL -- bond id, example: ['TR000_2_3', 'TR000_1_2'],
	PRIMARY KEY (atom_id, atom_id2), 
	CONSTRAINT fk_connected_bond FOREIGN KEY(bond_id) REFERENCES bond (bond_id),
	CONSTRAINT fk_connected_atom FOREIGN KEY(atom_id2) REFERENCES atom (atom_id),
	CONSTRAINT fk_connected_atom FOREIGN KEY(atom_id) REFERENCES atom (atom_id)
)


CREATE TABLE molecule (
	molecule_id TEXT NOT NULL -- molecule id, example: ['TR000', 'TR001'],
	label TEXT DEFAULT NULL -- example: ['+', '-'],
	PRIMARY KEY (molecule_id)
)

Question: What are the atoms that are bonded in the molecule TR001 with the bond ID of TR001_2_6?
Evidence: TR001 is the molecule id; TR001_2_6 is the bond id

SQL:
SELECT SUBSTR(T.bond_id, 1, 7) AS atom_id1 , T.molecule_id || SUBSTR(T.bond_id, 8, 2) AS atom_id2 FROM bond AS T WHERE T.molecule_id = 'TR001' AND T.bond_id = 'TR001_2_6'