How are the 3D coordinates generated, and how accurate are they?

The SMILES is parsed and hydrogens are added. Each atom's hybridisation (sp, sp², sp³) follows from its σ bonds plus lone pairs, which sets standard bond lengths and ideal angles. A simplified force field — bond stretch, angles, planarity, staggered torsions, non-bonded repulsion, plus chirality and cis/trans restraints — is then minimised from several random starting points and the lowest-energy result is kept. Bond lengths are usually within about 0.02 Å of experiment and angles within about 2°, which is fine for teaching and for seeing the shape. It is not a quantum-chemistry optimisation and does not guarantee the global-minimum conformer; use Gaussian, ORCA or xtb for accurate work.

Does it show chirality and cis/trans isomers correctly?

Yes. In SMILES, @ and @@ on a bracket atom encode tetrahedral chirality, and the generated structure is made to match — L-alanine N[C@@H](C)C(=O)O gives the S configuration. The / and \ symbols around a double bond encode geometry: C/C=C/C is trans-2-butene (dihedral 180°) and C/C=C\C is cis-2-butene (dihedral 0°). If a SMILES has no such marks, the configuration of that centre or double bond is arbitrary.

Why is cyclohexane a chair and not a flat hexagon?

Saturated carbons are sp³ with ideal angles of about 109.5–111°, while a flat regular hexagon has 120° angles, which costs angle strain, and in a flat ring every neighbouring C–H bond is eclipsed, which costs torsional strain. The chair keeps every angle near tetrahedral and every bond staggered, so it is the lowest-energy conformation, with ring C–C–C–C dihedrals of about ±55°. Click four ring carbons in the viewer to check.

What can I do with the exported XYZ and MOL files?

XYZ is the simplest coordinate format — one line per atom with the element and x, y, z in ångströms — and works as a starting geometry for Gaussian, ORCA, xtb and similar programs. A MOL (V2000) file also stores bonds and charges and opens in Avogadro, PyMOL, ChemDraw and Jmol. Because the geometry here is approximate, re-optimise it in one of those programs before doing precise calculations.

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🧊3D Molecule Viewer from SMILES - Rotate, Measure Bond Lengths and Angles

Structural formulas on paper are flat, but molecules are three-dimensional: the four hydrogens of methane point to the corners of a tetrahedron with H–C–H angles of 109.5°, water is bent to about 104.5° because oxygen carries two lone pairs, all six carbons of benzene lie in one plane with C–C bonds of 1.39 Å, and cyclohexane is not a flat hexagon but a chair with ring dihedrals of about ±55°. Type a SMILES string (ethanol CCO, benzene c1ccccc1, trans-2-butene C/C=C/C) and this tool builds a 3D model in your browser: it adds hydrogens, assigns sp, sp² or sp³ hybridisation from the number of σ bonds plus lone pairs, takes standard bond lengths (C–C 1.54, C=C 1.34, C≡C 1.20, C–H 1.09, C=O 1.21 Å …) and ideal angles, and then minimises a small self-written force field (bond stretch, angles, planarity, staggered torsions, non-bonded repulsion) from several random starts. Stereo marks are respected: @/@@ chirality and / \ double-bond geometry, so L-alanine N[C@@H](C)C(=O)O comes out as the S enantiomer and β-D-glucopyranose as the all-equatorial chair. Drag to rotate, scroll or pinch to zoom, or let it spin; switch between ball-and-stick, space-filling (van der Waals radii), sticks and wireframe with depth cueing. Click 2, 3 or 4 atoms to read a distance, bond angle or dihedral — ethane's H–C–C–H dihedral is 60° (staggered), cis-2-butene's C–C=C–C is 0° and trans is 180°. Export the picture as PNG or SVG and the coordinates as XYZ or MOL for Avogadro, PyMOL or a quantum-chemistry package. The geometry is an approximate force-field estimate, not a quantum-chemistry optimised structure.

Free · No sign-up · Runs in your browserLast updated: 2026-10-29

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How to use 3D Molecule Viewer

1Enter a SMILES string or pick an example (water, methane, benzene, cyclohexane, glucose, caffeine, aspirin and more)
2Drag to rotate and scroll to zoom; choose ball-and-stick, space-filling, sticks or wireframe, and toggle hydrogens and atom labels
3Click 2–4 atoms to measure a distance, angle or dihedral, and export PNG, SVG, XYZ or MOL if you need it

FAQ

How are the 3D coordinates generated, and how accurate are they?: The SMILES is parsed and hydrogens are added. Each atom's hybridisation (sp, sp², sp³) follows from its σ bonds plus lone pairs, which sets standard bond lengths and ideal angles. A simplified force field — bond stretch, angles, planarity, staggered torsions, non-bonded repulsion, plus chirality and cis/trans restraints — is then minimised from several random starting points and the lowest-energy result is kept. Bond lengths are usually within about 0.02 Å of experiment and angles within about 2°, which is fine for teaching and for seeing the shape. It is not a quantum-chemistry optimisation and does not guarantee the global-minimum conformer; use Gaussian, ORCA or xtb for accurate work.
Does it show chirality and cis/trans isomers correctly?: Yes. In SMILES, @ and @@ on a bracket atom encode tetrahedral chirality, and the generated structure is made to match — L-alanine N[C@@H](C)C(=O)O gives the S configuration. The / and \ symbols around a double bond encode geometry: C/C=C/C is trans-2-butene (dihedral 180°) and C/C=C\C is cis-2-butene (dihedral 0°). If a SMILES has no such marks, the configuration of that centre or double bond is arbitrary.
Why is cyclohexane a chair and not a flat hexagon?: Saturated carbons are sp³ with ideal angles of about 109.5–111°, while a flat regular hexagon has 120° angles, which costs angle strain, and in a flat ring every neighbouring C–H bond is eclipsed, which costs torsional strain. The chair keeps every angle near tetrahedral and every bond staggered, so it is the lowest-energy conformation, with ring C–C–C–C dihedrals of about ±55°. Click four ring carbons in the viewer to check.
What can I do with the exported XYZ and MOL files?: XYZ is the simplest coordinate format — one line per atom with the element and x, y, z in ångströms — and works as a starting geometry for Gaussian, ORCA, xtb and similar programs. A MOL (V2000) file also stores bonds and charges and opens in Avogadro, PyMOL, ChemDraw and Jmol. Because the geometry here is approximate, re-optimise it in one of those programs before doing precise calculations.

Features

Builds 3D coordinates straight from SMILES, adds hydrogens, runs entirely in your browser
Standard bond lengths and hybridisation-based angles: methane 109.5°, water 104.5°, ammonia 106.7°, planar benzene with 1.39 Å bonds
Respects @/@@ chirality and / \ cis/trans marks; saturated six-membered rings form chairs
Ball-and-stick, space-filling (Bondi van der Waals radii), sticks and wireframe with CPK colours and depth cueing
Drag to rotate, wheel or pinch to zoom, auto-rotate, hide hydrogens, element or numbered labels
Click atoms to measure bond lengths, angles and dihedrals, with one-click copy
Table of bond length and angle statistics against reference values
Export PNG and SVG images, XYZ and MOL (V2000) coordinate files

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