Molecule Drawing Tool

With this free molecule builder, you can draw your structure, visualize in rotatable 3D, measure bond lengths and angles, and export as a PNG image or 3D object. The latter are how I create animations in my YouTube videos, so I wanted to make this more accessible.

Draw in 2D

Search / Import

Searches are sent to PubChem through this site. Import replaces your current drawing; save it first if needed. SMILES must resolve to a PubChem compound.

Import ChemDraw CDXML (.cdxml)

Choose CDXML file

For direct paste: in ChemDraw select your structure, then choose Edit → Copy As → CDXML Text. Click once inside the 2D editor and press Ctrl/Cmd+V. Ordinary Copy may paste incorrectly because browsers cannot read ChemDraw’s native clipboard format.

Paste CDXML text manually

Import project JSON (.json)

Open an editable Molecule Lab project previously saved with Download JSON. Kekule project JSON only (maximum 2 MB); importing replaces the current drawing.

Examples

File

View

Structure

Arrange

Templates

Structure templatesChoose a template, then click an atom to attach, a bond to fuse a ring, or empty canvas to place it.

Search structures

Rings join or fuse at clicked atoms or bonds. Other fragments attach to atoms through their defined connection site. Click blank canvas for a standalone structure. Esc cancels.

Shortcuts

Reaction schemes and mechanisms

Draw reactants and products as separate molecules in the editor. Use the built-in Arrows & lines tool for reaction arrows, equilibrium arrows, plus signs, and curved arrow symbols. Use Text for reaction conditions; numbers in recognized chemical formulae automatically become subscripts (H2O → H₂O, CH3OH → CH₃OH). These arrows are graphical annotations, not computed electron flow. Save the JSON project to preserve the complete scheme; the 3D viewer visualizes molecules separately, not a reaction.

Enable drawing shortcuts

Hover over an atom or bond (or select one) and press a key. Over atoms, 2 adds =O and 3 adds a complete tert-butyl group (a NEW central carbon with three methyls); over bonds, 1/2/3 still change bond order. Shift+letters attach groups instead of replacing atoms. Rings grow from atoms or fuse to bonds where valence allows.

Drawing tools & templates

Choose Structure → Templates, then choose a category or search for a structure. Click an atom to attach, a bond to fuse a ring, or blank canvas to insert it once. Native ring tools remain available.

X Bond toolSpace Select tool

Atoms & groups

O Replace with ON Replace with N S Replace with SF Replace with F B Replace with BrL Replace with Cl I Replace with IH Replace with H D Replace with DM Add methyl E Add ethylP Add phenyl Y Add Boc

Hover over an atom: functional groups

2 Add carbonyl (=O) on C3 Add complete tBu on C Shift+O Attach OHShift+N Attach NH₂ Shift+M Attach OMeShift+F Attach CF₃ 9 Attach C≡N0 Attach CO₂Me Shift+2 Add =CH₂Shift+3 Add ≡CH

Bonds & fused rings

1 Add C (atom) / single (bond)2 Double bond (bond hover) 3 Triple bond (bond hover)W Solid wedge H Hashed wedgeY Wavy wedge V 3-membered4 4-membered 5 5-membered6 6-membered 7 7-membered8 8-membered A BenzeneZ Cyclopentadiene

Canvas alignment grid

Alt+Shift+G Show / hide gridGrid is visual only; no snapping or exported lines

Chemical validation

Alt+Shift+V Check structureLive and markers toggles below 2D editor

Arrange selected objects

Select complete molecules or graphical objects. Open Arrange in the editor toolbar, or use these shortcuts. Alignment, distribution and nudging move whole objects, not individual bonds.

Ctrl+Shift+Alt+L Left edgesCtrl+Shift+Alt+R Right edges Ctrl+Shift+Alt+C Left/right centersCtrl+Shift+Alt+T Top edges Ctrl+Shift+Alt+B Bottom edgesCtrl+Shift+Alt+M Top/bottom centers Ctrl+Shift+Alt+H Distribute horizontallyCtrl+Shift+Alt+V Distribute vertically Ctrl+Shift+H Flip horizontallyCtrl+Shift+V Flip vertically Ctrl+G GroupCtrl+Shift+G Ungroup Ctrl+K Scale selection (percent) Ctrl+Shift+left-drag Duplicate moleculeDrag a bond or atom; release to place the copy (one Undo) Ctrl+Shift+Alt+S Preview reaction scheme cleanup T Text tool Ctrl+B/I/U Bold / italic / underline selected text Alt+Shift+↓ / Alt+Shift+↑ Subscript / superscript Ctrl+P Copy structure image to other apps Arrow keys Nudge selection 1 ptShift+Arrow Nudge selection 10 pt

Press X for the bond tool, Space for Select; hover carbon and press 1 for snapped 45-degree zig-zags. Hover a bond to change its order or fuse a ring. Press a wedge/hash key again to reverse its narrow end. Ctrl/Cmd/Alt, text inputs, and undo/redo remain unchanged.

Status:

Loading the chemistry editor…

Check structure Initializing chemical validation…

Live Atom markers

Validation details

Checking…

Explore in 3D

Style

Atom labels Show hydrogens

Live 3D preview Updates after you finish an edit

Your live 3D preview will appear here after drawing a valid molecule.

Waiting for a drawing

Geometry explorer

Measurement

2D ↔ 3D atom highlighting is available when the molecular graphs match.

Selected atoms: none

Molecular information

About accuracy

Molecule Lab turns 2D drawings into approximate 3D models for viewing, measuring, exploring conformations, and exporting images or files. Its optional PubChem lookup identifies matching compounds and retrieves molecular information; the drawing is shared with PubChem only when you request a lookup.

The new structure validator provides live, advisory valence, charge, bond and stereochemistry review. RDKit.js sanitization checks connected molecules when its browser runtime loads; stereochemical review is not complete CIP verification and some query/polymer structures cannot be checked. Warnings never edit structures, and unflagged molecules are not guaranteed to be chemically correct.

Generated conformers are computational estimates, not experimental structures or energy-ranked predictions. GLB/OBJ files are visual models, not editable chemical structures. Avoid sending confidential molecules to PubChem. Independently verify structures, stereochemistry, measurements, and exports before scientific use.

How to draw molecules online with this tool

If you need this spelled out, you probably have bigger things to worry about than chemistry, but here you go:

Draw your structure of interest, including stereochemistry, just like you would in Chemdraw or any other tool
If live 2D to 3D visualization is not enabled, click Visualize in 3D
Rotate that boi around and switch ball-and-stick vs. space-filling
Explore the molecule’s geometry by measuring bond lengths & angles
Export the shot as a PNG image or the other formats

Note: This is not academic precision for novel molecules, but I hope it’s useful for students or educators who are looking for a free and simple tool.

Download 3D molecule models as OBJ, GLB or SDF

If you want to use your molecule drawing outside of this page, you can export the molecular model as a 3D object (.obj or .glb). Pro tip: You can import these into PowerPoint and get some nice animations and rotations / movements. I’m personally a sucker for the Morph transition – if you know, you know 😎. Here is an example of what this can look like.

You can also save export the molecule drawing as a SDF file, and use it for Chem3D or other applications.

If there are any bugs or you have suggestions, let me know in the form above.

Overview of Features and Shortcuts

Search, import and export

Action	Shortcut or menu
Find or import a molecule	Search / Import
Load examples	Examples → Cubane / Random
Import CDXML or SMILES	File → Import CDXML / SMILES
Open / Save editable project (JSON)	File menu
Export structure(s) as SVG / PNG / CDXML	File menu
Export 3D PNG / SDF / GLB / OBJ	File menu

File and editing

Action	Shortcut or menu
New / Open / Save project	File menu
Undo / Redo	`Ctrl + Z / Ctrl + Y`
Cut / Copy / Paste	`Ctrl + X / Ctrl + C / Ctrl + V`
Select all / Delete	`Ctrl + A / Delete`
Copy structure(s) – for use in other apps	`Ctrl + P`

View and 3D tools

Action	Shortcut or menu
Show / hide drawing grid	`Alt + Shift + G`
Lone pairs / Zoom / Validation markers	View menu
Live 3D preview	Explore in 3D → Live 3D preview
3D display style / Atom labels / Hydrogens	Explore in 3D controls
Measure distances / angles / dihedrals	3D Geometry explorer
Explore conformations / Manipulate fragments	3D tools

Structure tools and fast atom replacement

Action	Shortcut or menu
Clean structure	`Ctrl + Shift + K`
Check structure	`Alt + Shift + V`
Live validation / Atom markers	Check structure panel
Molecular information (PubChem)	Structure → Molecular information
Other ring templates	Structure → Ring templates
Oxygen	`O`
Nitrogen	`N`
Sulfur	`S`
Fluorine	`F`
Chlorine	`L`
Bromine	`B`
Iodine	`I`
Hydrogen	`H`
Deuterium	`D`
Methyl	`M`
Ethyl	`E`
Phenyl	`P`
Boc group	`Y`

Bonds, stereochemistry and ring shortcuts

Bond or ring	Shortcut or menu
Selection tool	`Space`
Bond tool	`X`
Single bond	`1`
Double bond	`2`
Triple bond	`3`
Solid wedge (hover bond)	`W`
Hashed wedge (hover bond)	`H`
Wavy bond (hover bond)	`Y`
Cyclopropane	`V`
Cyclobutane	`4`
Cyclopentane	`5`
Cyclohexane	`6`
Cycloheptane	`7`
Cyclooctane	`8`
Benzene	`A`
Cyclopentadiene	`Z`

Text tools

Action	Shortcut or menu
Text tool	`T`
Bold	`Ctrl + B`
Italic	`Ctrl + I`
Underline	`Ctrl + U`
Subscript	`F9`
Superscript	`F10`

Reaction tools

Action	Shortcut or menu
Reaction arrows and symbols	Reaction menu
Arrange reaction scheme	`Ctrl + Shift + Alt + S`

Arrange tools

Action	Shortcut or menu
Align left	`Ctrl + Shift + Alt + L`
Align horizontal centers	`Ctrl + Shift + Alt + C`
Align right	`Ctrl + Shift + Alt + R`
Align top	`Ctrl + Shift + Alt + T`
Align vertical centers	`Ctrl + Shift + Alt + M`
Align bottom	`Ctrl + Shift + Alt + B`
Distribute horizontally / vertically	`Ctrl + Shift + Alt + H / V`
Group / Ungroup	`Ctrl + G / Ctrl + Shift + G`
Flip horizontally / vertically	`Ctrl + Shift + H / V`
Scale selection	`Ctrl + K`
Nudge / Nudge faster	`Arrow keys / Shift + Arrow keys`
Rotate selected structure	`Drag rotation handle`