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: Indicate which atoms are connected in non-carcinogenic type molecules.
Evidence: label = '-' means molecules are non-carcinogenic

SQL:
SELECT DISTINCT T1.atom_id FROM atom AS T1 INNER JOIN molecule AS T2 ON T1.molecule_id = T2.molecule_id INNER JOIN connected AS T3 ON T1.atom_id = T3.atom_id WHERE T2.label = '-'