{ "site": "MolDraw Docs", "publisher": "LabCanvas", "updated": "2026-10-11", "pages": [ { "title": "Introduction to MolDraw", "url": "https://www.moldraw.com/docs/get-started/what-is-moldraw-free-online-chemical-structure-editor/", "md": "https://www.moldraw.com/docs/get-started/what-is-moldraw-free-online-chemical-structure-editor.md", "section": "Get started", "summary": "MolDraw is a free chemical structure editor that runs in your browser. You can draw molecules and reactions, view them in 3D, and export figures for papers and slides.", "updated": "2026-10-11", "headings": [ "What you can do with MolDraw", "Do you need an account", "Where to start", "Questions and answers" ], "text": " What you can do with MolDraw # Draw molecules, rings and reactions on an open canvas. Turn a name, SMILES or CAS number into a structure. See the formula, weight and name of what you draw. Rotate your molecule in 3D. Export PNG, SVG, PDF, MOL, CDXML and more. Add plugins for NMR, ChEMBL data and more. Do you need an account # You do not need an account to draw. Your work saves in your browser. Sign in when you want plugins, Community posts or cloud features. Where to start # Open the MolDraw editor . Follow Draw your first structure . Learn the keyboard shortcuts to work faster. Tip Every page has a short answer at the top. Read that first if you are in a hurry. " }, { "title": "Draw your first structure", "url": "https://www.moldraw.com/docs/get-started/how-to-draw-your-first-chemical-structure-in-moldraw/", "md": "https://www.moldraw.com/docs/get-started/how-to-draw-your-first-chemical-structure-in-moldraw.md", "section": "Get started", "summary": "Click the benzene ring, click the canvas, add a bond, then place an oxygen. Click Clean up and open Info to see the name, formula and weight. This guide draws phenol in six steps.", "updated": "2026-10-11", "headings": [ "Before you start", "Animated steps", "The parts of the screen", "Step by step", "Save or share your structure", "Faster ways to do the same thing", "Questions and answers" ], "text": " Before you start # Open the MolDraw editor . You do not need to sign in. If the canvas has a drawing, click Clear canvas (the red bin) first. ▶ Animated Text and images Download the animation (MP4) ▶ Play The full walkthrough in 19 seconds. Orange rings show each click. Step by step, animated Download the animation (MP4) ▶ Play Click the benzene button. Step 1. Pick the benzene ring. In the ring bar at the bottom left, click the benzene button. Download the animation (MP4) ▶ Play One click places the ring. Step 2. Place the ring. Click once on an empty part of the canvas. A benzene ring appears where you click. Download the animation (MP4) ▶ Play Pick the bond tool, then click the top atom. Step 3. Add a bond. Click the single bond tool in the left rail. Then click the top atom of the ring. A new bond grows from that atom. Download the animation (MP4) ▶ Play Pick O, then click the end of the bond. Step 4. Make it an oxygen. Click O in the atom palette. Then click the free end of the new bond. The end turns into OH. Download the animation (MP4) ▶ Play Click Clean up. Step 5. Tidy the drawing. Click Clean up in the tools row. MolDraw fixes bond lengths and angles. Download the animation (MP4) ▶ Play Select all, then click Info. Step 6. Check what you drew. Press Ctrl + A to select all. Click Info at the top. The panel shows the name, formula and weight. The parts of the screen # The main parts of the screen. 1 Ring bar. 2 Left tool rail. 3 Atom palette. 4 Canvas. Step by step " }, { "title": "The MolDraw screen", "url": "https://www.moldraw.com/docs/get-started/moldraw-editor-interface-toolbar-and-panels-explained/", "md": "https://www.moldraw.com/docs/get-started/moldraw-editor-interface-toolbar-and-panels-explained.md", "section": "Get started", "summary": "The screen has a top bar, a tools row, a left tool rail, an atom palette, a ring bar and the canvas. A 3D panel sits on the right.", "updated": "2026-10-11", "headings": [ "Top bar", "Editor row", "Ribbons", "Left tool rail", "Atom palette and ring bar", "Canvas and 3D panel", "Questions and answers" ], "text": " 1 Ring bar. 2 Left tool rail. 3 Atom palette. 4 Canvas. Top bar # The top bar has My designs , the search box, and the Home , Draw and Info tabs. It also has the language menu, Updates and your account. Editor row # This row holds File , Select , Community , Copy SMILES , Paste SMILES , Copy SVG , Paste and Download . Ribbons # Home, Draw and Style are ribbons. Only one is open at a time. Home has Clean up, hydrogens, 3D Clean Up, aromatize and zoom. Draw has the pencil, shapes, images and glassware. Style sets font, bond width and the structure look. Left tool rail # The rail holds the tools you use most. You get select, erase, charges, lone pairs, bonds, chains, atom labels, arrows, brackets and orbitals. A small arrow under a button opens more choices. Atom palette and ring bar # The atom palette next to the canvas has H, C, N, O, S, P, F, Cl, Br and I. The grid button opens the full periodic table. The ring bar at the bottom has rings from three to eight atoms and the Library. Canvas and 3D panel # The canvas has no edges. Pan with the hand tool or by holding Space and dragging. The 3D panel shows your molecule in 3D. Hide it with the 3D button. " }, { "title": "Save and open your work", "url": "https://www.moldraw.com/docs/get-started/how-to-save-and-open-chemical-drawings-in-moldraw/", "md": "https://www.moldraw.com/docs/get-started/how-to-save-and-open-chemical-drawings-in-moldraw.md", "section": "Get started", "summary": "MolDraw saves your drawing in your browser by itself. Open old drawings from My designs. Use File, Save to keep a .moldraw file on your computer.", "updated": "2026-10-11", "headings": [ "Autosave", "Open My designs", "Save a file to your computer", "Open a file", "Questions and answers" ], "text": " Autosave # Every change saves in this browser. You do not need to press save. Your drawings stay on this device. Open My designs # Click My designs at the top left. Click a card to open that drawing. Use folders to group your work. Save a file to your computer # Click File . Click Save , or press Ctrl + S . MolDraw downloads a .moldraw file with everything on the canvas. Open a file # Click File , then Open . You can open MolDraw, MOL, CDX and CDXML files. Warning Drawings live in this browser only. If you clear browser data, they are gone. Save a .moldraw file for anything important. " }, { "title": "Keyboard shortcuts", "url": "https://www.moldraw.com/docs/get-started/moldraw-keyboard-shortcuts-list/", "md": "https://www.moldraw.com/docs/get-started/moldraw-keyboard-shortcuts-list.md", "section": "Get started", "summary": "Press ? in the editor to see every shortcut. The most used are Ctrl+Z to undo, Ctrl+C to copy, 1, 2 and 3 for bond types, and letters like O or N to pick an element.", "updated": "2026-10-11", "headings": [ "Editing", "Selection (Select menu)", "Navigation", "Tools", "Atom labels (placement element when no atom selected)", "Type-to-rename (one atom selected)", "3D Structure Perspective", "Modifiers & canvas", "Questions and answers" ], "text": " On a Mac, use ⌘ where this page says Ctrl. Change any shortcut in Settings , Shortcuts . Editing # Action Keys Cancel edit / clear selection / close menus Esc Erase selected object Delete or Backspace Undo Ctrl Z Redo Ctrl Y or Ctrl Shift Z Select all Ctrl A Copy fragment Ctrl C Paste fragment Ctrl V Save entire canvas (.moldraw) Ctrl S Selection (Select menu) # Action Keys Deselect Ctrl Shift A Invert selection Ctrl Shift I Select connected Ctrl Shift C Grow selection Ctrl Shift G Same as selection Ctrl Shift S Select all rings Ctrl Shift R Select heteroatoms Ctrl Shift H Chain atoms Alt Shift C Longest path Alt Shift L Side chains Alt Shift S All 5-rings Alt Shift 5 All 6-rings Alt Shift 6 Aromatic atoms Alt Shift A Charged atoms Alt Shift Q Wedge / dash atoms Alt Shift W CIP R / S centers Alt Shift R Aliases / R-groups Alt Shift G Bonds in selection Alt Shift B All bonds Ctrl Alt B Select tool V Lasso select tool L Navigation # Action Keys Pan canvas (hand tool) Hand drag Temporary pan (hold, then drag) Space drag Pan Middle-click drag Pan vertically Scroll wheel Pan horizontally Shift Scroll Zoom toward pointer Ctrl Scroll or ⌘ Scroll Zoom in Ctrl = or Ctrl + Zoom out Ctrl - Reset zoom (100%) Ctrl 1 Fit all objects Ctrl 0 Pinch zoom Two-finger pinch Two-finger pan Two-finger drag Touch pan on empty canvas Touch drag Tools # Action Keys Single bond 1 Double bond 2 Triple bond 3 Benzene ring B Select tool V Lasso select tool L Open this shortcuts panel ? or Shift / Atom la" }, { "title": "Draw atoms", "url": "https://www.moldraw.com/docs/drawing/how-to-draw-atoms-and-change-elements/", "md": "https://www.moldraw.com/docs/drawing/how-to-draw-atoms-and-change-elements.md", "section": "Draw structures", "summary": "Pick an element in the atom palette, then click the canvas or the end of a bond. Click an atom to change it. Use the periodic table for other elements.", "updated": "2026-10-11", "headings": [ "Keyboard tricks", "Change an atom", "Questions and answers" ], "text": " Click an element in the atom palette, for example N . Click an empty spot to place it. Or click an atom to change it. For other elements, click the grid button and pick from the periodic table. Keyboard tricks # With nothing selected, press a letter like N or O to set the element. With one atom selected, type a symbol to rename it. Type Cl or Br for two letters. Type groups like Me , Ph or OMe too. Change an atom # Right click an atom. You can set the element, isotope, charge, explicit H, lone pairs and radicals. Tip The A button places an \"any atom\". It is the same as * in SMILES. " }, { "title": "Draw bonds", "url": "https://www.moldraw.com/docs/drawing/how-to-draw-single-double-triple-and-wedge-bonds/", "md": "https://www.moldraw.com/docs/drawing/how-to-draw-single-double-triple-and-wedge-bonds.md", "section": "Draw structures", "summary": "Pick a bond type in the left rail and drag from atom to atom. Click a bond to change its type. Press 1, 2 or 3 for single, double or triple bonds.", "updated": "2026-10-11", "headings": [ "Bond types", "Shortcuts", "Questions and answers" ], "text": " Click the bond button in the left rail. Open the small arrow for more types. Drag from an atom to draw a bond. Or click an atom to grow a bond from it. Click an existing bond to switch it to the chosen type. Bond types # Single, double, triple, aromatic, wedge, hash, wavy, bold, dative, hydrogen bond (dotted), cis/trans, any and centroid bonds are all in the bond menu. Shortcuts # 1 single, 2 double, 3 triple. B benzene ring. Tip The Chain tool draws a zigzag chain in one drag. Watch the count as you drag. " }, { "title": "Rings and structures", "url": "https://www.moldraw.com/docs/drawing/how-to-draw-benzene-cyclohexane-and-fused-rings/", "md": "https://www.moldraw.com/docs/drawing/how-to-draw-benzene-cyclohexane-and-fused-rings.md", "section": "Draw structures", "summary": "Use the ring bar at the bottom to place rings from 3 to 8 atoms. Click a ring atom or bond to fuse a new ring. Clean up tidies the shape.", "updated": "2026-10-11", "headings": [ "Special rings", "Select and move", "Questions and answers" ], "text": " Click a ring in the ring bar, such as benzene or cyclohexane. Click empty canvas to place it. Click an atom or bond of a ring to fuse or attach another ring. Click Clean up to even out bonds and angles. Special rings # The small arrow under cyclohexane gives chair and boat shapes. The arrow under benzene gives a tilted arene for metal complexes. Cyclopentadiene has a Cp option. Select and move # Drag a box with the select tool. Hold Shift and drag for a lasso. Use the handles to rotate or resize. Note For ChemDraw style ring shapes, turn on Indigo layout in Settings . " }, { "title": "Atom labels and R-groups", "url": "https://www.moldraw.com/docs/drawing/how-to-add-atom-labels-and-r-groups/", "md": "https://www.moldraw.com/docs/drawing/how-to-add-atom-labels-and-r-groups.md", "section": "Draw structures", "summary": "Pick the atom label tool (A) and click an atom. Type a label like Ph, COOH or R1. MolDraw can expand known labels into full structures.", "updated": "2026-10-11", "headings": [ "Expand or collapse a label", "Questions and answers" ], "text": " Click the Atom label tool in the left rail. Click an atom. Type a label, such as Ph , COOH , Boc or R1 . Press Enter . Expand or collapse a label # Right click a label. Pick Expand to show every atom. Pick Collapse to go back to the short label. Tip Labels MolDraw does not know stay as text. They still show on your figure. " }, { "title": "Stereochemistry", "url": "https://www.moldraw.com/docs/drawing/how-to-draw-stereochemistry-wedge-hash-and-r-s-labels/", "md": "https://www.moldraw.com/docs/drawing/how-to-draw-stereochemistry-wedge-hash-and-r-s-labels.md", "section": "Draw structures", "summary": "Use wedge and hash bonds for 3D centers. Open Chemistry and pick Show CIP labels to see R and S. Right click to invert a center.", "updated": "2026-10-11", "headings": [ "More stereo tools", "Questions and answers" ], "text": " Pick Wedge up or Hash down in the bond menu. Drag from the stereo center to the outer atom. Open Chemistry and click Show CIP labels to see R, S, E and Z. More stereo tools # Right click a suitable atom, bond or ring. You can invert a center or make Newman, Fischer, chair and boat views. Warning Wedges point away from the stereo center. Draw from the center outward. " }, { "title": "Lone pairs, radicals and charges", "url": "https://www.moldraw.com/docs/drawing/how-to-add-lone-pairs-radicals-and-formal-charges/", "md": "https://www.moldraw.com/docs/drawing/how-to-add-lone-pairs-radicals-and-formal-charges.md", "section": "Draw structures", "summary": "Pick the lone pair tool and click an atom to add a pair of dots. Use the radical tool for one dot. Charge tools add plus and minus marks you can drag around the atom.", "updated": "2026-10-11", "headings": [ "Charges", "When to show lone pairs", "Questions and answers" ], "text": " Click the Lone pair tool in the left rail. Click an atom. A pair of dots appears. Drag the dots around the atom to a free side. For a radical, open the small arrow and pick the radical tool. Charges # Use + and − in the rail. Click again for +2 or −2. The rail also has circled charges and δ+ and δ−. When to show lone pairs # Show lone pairs when you draw mechanisms. A curved arrow should start at a lone pair or a bond. Oxygen in water has two pairs. Nitrogen in ammonia has one. Tip Check that charges match electrons. Oxygen with three bonds and one lone pair is +1. " }, { "title": "Polymer brackets", "url": "https://www.moldraw.com/docs/drawing/how-to-draw-polymer-repeat-unit-brackets/", "md": "https://www.moldraw.com/docs/drawing/how-to-draw-polymer-repeat-unit-brackets.md", "section": "Draw structures", "summary": "Select the repeat unit, then click the Brackets tool. Click the small n to change the number of units.", "updated": "2026-10-11", "headings": [ "Questions and answers" ], "text": " Select two or more atoms of the repeat unit. Click Brackets in the left rail. Click the subscript to type n, m or a number. Click Brackets again for more types. You get polymer n, copolymer m and parenthesis (CH₂)n. Brackets move with the structure. " }, { "title": "Text, shapes and images", "url": "https://www.moldraw.com/docs/drawing/how-to-add-text-shapes-images-and-lab-glassware/", "md": "https://www.moldraw.com/docs/drawing/how-to-add-text-shapes-images-and-lab-glassware.md", "section": "Draw structures", "summary": "Open the Draw ribbon to add text, shapes, images and glassware. Click the canvas to place them and drag to move.", "updated": "2026-10-11", "headings": [ "Add text", "Shapes, images and glassware", "Questions and answers" ], "text": " Add text # Click the Text button (T) in the tools row. Click empty canvas and type. Press Esc when you are done. Shapes, images and glassware # Shapes gives arrows, boxes and outlines. Image adds PNG, JPEG, WebP, GIF or SVG files. Glassware adds lab apparatus. You can set a liquid level. " }, { "title": "Style and display", "url": "https://www.moldraw.com/docs/drawing/how-to-change-structure-style-colors-and-display/", "md": "https://www.moldraw.com/docs/drawing/how-to-change-structure-style-colors-and-display.md", "section": "Draw structures", "summary": "Open Color and style to change colors, font, bond width and the structure look. Settings control hydrogens, labels, grid and snap.", "updated": "2026-10-11", "headings": [ "Settings", "Questions and answers" ], "text": " Select what you want to change, or nothing for the whole drawing. Click Color and style in the tools row. Pick colors, label style or the Look , such as Ball and stick. Settings # Click Settings (gear). You can change implicit hydrogens, colored atom labels, grid and snap. You can also save style presets. Tip For ACS style in a paper, pick a style preset in Settings, then export SVG. " }, { "title": "Reaction arrows", "url": "https://www.moldraw.com/docs/reactions/how-to-draw-reaction-arrows-with-reagents/", "md": "https://www.moldraw.com/docs/reactions/how-to-draw-reaction-arrows-with-reagents.md", "section": "Reactions and schemes", "summary": "Pick the Reaction arrow tool and drag between molecules. Choose the arrow kind in the top bar. Type reagents above or below the arrow.", "updated": "2026-10-11", "headings": [ "Questions and answers" ], "text": " Click Reaction arrow in the left rail. Drag from the starting material to the product. In the top bar, pick the kind: straight, equilibrium, retrosynthetic and more. Click above or below the arrow to type reagents and conditions. Tip Open Chemistry and click Automap to match atoms across the arrow. " }, { "title": "Build a reaction scheme", "url": "https://www.moldraw.com/docs/reactions/how-to-make-a-chemical-reaction-scheme/", "md": "https://www.moldraw.com/docs/reactions/how-to-make-a-chemical-reaction-scheme.md", "section": "Reactions and schemes", "summary": "Draw the reactants and products, add an arrow, then add reagents. Export as RXN, SVG or PNG. Start from a named reaction in the Library to save time.", "updated": "2026-10-11", "headings": [ "Start from a template", "Questions and answers" ], "text": " Draw the starting material. Draw the product to the right. Add a reaction arrow between them. Type reagents on the arrow. Download the scheme as SVG, PNG or RXN. Start from a template # Open Library and pick a named reaction. Edit it to match your work. Note You can paste a reaction SMILES like CCO>>CC=O . MolDraw draws both sides and the arrow. " }, { "title": "Library and templates", "url": "https://www.moldraw.com/docs/library/how-to-use-the-structure-library-and-templates/", "md": "https://www.moldraw.com/docs/library/how-to-use-the-structure-library-and-templates.md", "section": "Library and templates", "summary": "Open Library in the ring bar to place ready-made structures. It has functional groups, ligands, amino acids, polymers, COFs, MOFs and named reactions.", "updated": "2026-10-11", "headings": [ "Questions and answers" ], "text": " Click Library at the end of the ring bar. Search or pick a category. Click an item, then click the canvas to place it. Library is not the same as My designs . My designs holds your own saved drawings. " }, { "title": "Copy and paste SMILES", "url": "https://www.moldraw.com/docs/import-export/how-to-copy-and-paste-smiles-inchi-and-mol/", "md": "https://www.moldraw.com/docs/import-export/how-to-copy-and-paste-smiles-inchi-and-mol.md", "section": "Import, export and sharing", "summary": "Click Copy SMILES to copy your structure as text. Click Paste SMILES to draw from a SMILES string. Right click for more formats like InChI and MOL.", "updated": "2026-10-11", "headings": [ "More copy formats", "Questions and answers" ], "text": " Select a molecule, or nothing for the whole canvas. Click Copy SMILES in the editor row. To draw from text, click Paste SMILES and paste the string. More copy formats # Right click and open Copy as . You get SMILES, InChI, InChIKey, MOL V2000, MOL V3000, CDXML, SVG, PNG, SLN, HELM, FASTA and BILN. Tip Ctrl + C copies an SVG picture. Paste it straight into Word or PowerPoint. To learn SMILES, read the SMILES notation guide . " }, { "title": "Download and file formats", "url": "https://www.moldraw.com/docs/import-export/how-to-export-png-svg-pdf-mol-and-cdxml-files/", "md": "https://www.moldraw.com/docs/import-export/how-to-export-png-svg-pdf-mol-and-cdxml-files.md", "section": "Import, export and sharing", "summary": "Click Download and pick a format. Use SVG or PDF for papers, PNG for slides, and MOL, SDF or CDXML to move to other chemistry software.", "updated": "2026-10-11", "headings": [ "Which format to pick", "Save the whole canvas", "Questions and answers" ], "text": " Click Download in the editor row. Pick a format. For PNG and JPEG, set size and background in the dialog. Which format to pick # Format Use it for SVG Papers and posters. Sharp at any size. PDF Journals and printing. PNG / PNG (white) Slides, Word and the web. JPEG Small photos. SMILES (.smi) Text, databases, code. MOL / SDF Other chemistry software. SDF keeps 3D coordinates. CDXML / CDX ChemDraw. RXN Reactions. InChI Database lookup. SMARTS Substructure search. CML, XYZ Other tools and 3D programs. GLB, OBJ, X3D 3D models from the 3D panel. Save the whole canvas # Click File , then Save . You get a .moldraw file with structures, arrows, text and images. " }, { "title": "Search PubChem", "url": "https://www.moldraw.com/docs/import-export/how-to-search-pubchem-by-name-or-cas-number/", "md": "https://www.moldraw.com/docs/import-export/how-to-search-pubchem-by-name-or-cas-number.md", "section": "Import, export and sharing", "summary": "Type a name or CAS number in the search box at the top. MolDraw draws the structure from PubChem.", "updated": "2026-10-11", "headings": [ "Questions and answers" ], "text": " Click the search box at the top left. Type a name like caffeine or a CAS number. Pick a result. MolDraw places the structure on the canvas. The PubChem panel also does advanced search and batch SMILES import. Batch import lays molecules out on a grid. " }, { "title": "Names, formula and properties", "url": "https://www.moldraw.com/docs/analyze/how-to-find-iupac-name-molecular-formula-and-weight/", "md": "https://www.moldraw.com/docs/analyze/how-to-find-iupac-name-molecular-formula-and-weight.md", "section": "Analyze and 3D", "summary": "Select a molecule and click Info. You see the name, formula, weight, SMILES, InChI, exact mass, logP and more.", "updated": "2026-10-11", "headings": [ "Questions and answers" ], "text": " Select the molecule. Press Ctrl + A for everything. Click Info at the top. Click the copy icon next to any value. The details panel lists name, formula, weight and more. For spectra, see NMR Analyser and the mass spectrum predictor . " }, { "title": "3D viewer", "url": "https://www.moldraw.com/docs/analyze/how-to-view-molecules-in-3d/", "md": "https://www.moldraw.com/docs/analyze/how-to-view-molecules-in-3d.md", "section": "Analyze and 3D", "summary": "The 3D panel builds a 3D model from your drawing. Drag to rotate it. Use 3D Clean Up to show your 2D drawing in perspective.", "updated": "2026-10-11", "headings": [ "Questions and answers" ], "text": " Make sure the 3D panel is open. Click 3D in the tools row if not. Drag in the panel to rotate. Scroll to zoom. Press Ctrl + Shift + D for 3D Clean Up on the canvas. Use the Protein tab to load a PDB entry. See Protein viewer . " }, { "title": "AI assistant", "url": "https://www.moldraw.com/docs/ai/how-to-use-the-ai-chemistry-assistant/", "md": "https://www.moldraw.com/docs/ai/how-to-use-the-ai-chemistry-assistant.md", "section": "AI", "summary": "Click AI in the tools row to open the chat. Add your Gemini API key once. Ask it to draw, name or edit structures.", "updated": "2026-10-11", "headings": [ "Questions and answers" ], "text": " Click AI in the tools row. Paste your Gemini API key in the panel or in Settings , AI . Type a request, such as \"Draw aspirin\". The assistant can place structures on the canvas. Note Your key stays in your browser. Google's free tier is enough to try it. For spectra, see AI Spectroscopy . " }, { "title": "Plugins overview", "url": "https://www.moldraw.com/docs/plugins/moldraw-plugins-overview-and-how-to-install/", "md": "https://www.moldraw.com/docs/plugins/moldraw-plugins-overview-and-how-to-install.md", "section": "Plugins", "summary": "Plugins add extra features to MolDraw. Open Settings, then Plugins, and click Install. Most need a free account.", "updated": "2026-10-11", "headings": [ "All plugins", "Questions and answers" ], "text": " 1 Plugins section. 2 Install, Disable or Uninstall. Sign in to MolDraw. Click Settings (gear icon). Click Plugins . Click Install next to the plugin you want. All plugins # NMR Analyser : Predict 1H, 13C, COSY, HSQC and HMBC spectra. You get peak tables and atom labels. ChEMBL : Look up bioactivity, targets and similar compounds in ChEMBL for any molecule. Electrostatic Potential (MEP) : Color a 3D surface by electrostatic potential from Gasteiger charges. Compare Molecules : Compare structures side by side. See Tanimoto similarity, group changes and export CSV. Protein Viewer : Load a PDB entry by ID or file. Show cartoon or surface and export images. Smart Draw : Sketch with a pen, mouse or finger. Strokes turn into bonds, rings and labels. AI Spectroscopy : Ask the AI chat for NMR, mass and UV-Vis predictions of your molecule. Themes (Ball-and-Stick) : Switch the 2D canvas to a colored ball and stick look for slides and posters. Note Protein viewer and Themes are on by default. They work without an account. " }, { "title": "NMR Analyser plugin", "url": "https://www.moldraw.com/docs/plugins/nmr-analyser-plugin-predict-1h-13c-and-2d-nmr-spectra/", "md": "https://www.moldraw.com/docs/plugins/nmr-analyser-plugin-predict-1h-13c-and-2d-nmr-spectra.md", "section": "Plugins", "summary": "Install NMR Analyser from Settings, Plugins, draw a molecule, open the NMR tab, pick an experiment and press Predict.", "updated": "2026-10-11", "headings": [ "What it does", "Who it is for", "How to use it", "Tips", "Questions and answers" ], "text": " Predicted 1H spectrum of chloramphenicol. Each signal has a letter. The table lists shift, integral, splitting and J. NMR tab in the right-hand analysis panel. Experiment buttons: 1H, 13C, COSY, HSQC, HMBC. Predict runs the prediction for the current canvas structure. Labels / Signals toggle peak letters and the signal list. What it does # The plugin predicts NMR spectra for the structure on your canvas. 1D 1H and 13C spectra show peaks with letters. The table gives shift, integral, splitting and coupling constant for each letter. 2D COSY, HSQC and HMBC show as contour plots. You can see which atoms are linked. Each run goes into History . Switch between molecules or experiments there. To learn the basics, read How to read an NMR spectrum . Who it is for # Students who check a structure against a lab spectrum. Teachers who make worked examples. Chemists who want a quick sanity check. How to use it # Open the MolDraw editor and sign in. Click Settings , then Plugins , then Install next to NMR Analyser. Draw or paste your structure (e.g. paste a SMILES with Paste SMILES ). Open the NMR tab in the right panel (callout 1). Choose the experiment, 1H or 13C for 1D, or COSY/HSQC/HMBC for 2D (callout 2). Press Predict (callout 3). The spectrum appears in a few seconds. Drag a box to zoom into a ppm range, scroll to scale intensity, double-click to reset. Turn on Labels (callout 4) to match peak letters with the table and hover a row to highlight the atoms. Export the plot (PNG/SVG) " }, { "title": "ChEMBL plugin", "url": "https://www.moldraw.com/docs/plugins/chembl-plugin-bioactivity-and-drug-target-lookup/", "md": "https://www.moldraw.com/docs/plugins/chembl-plugin-bioactivity-and-drug-target-lookup.md", "section": "Plugins", "summary": "Install ChEMBL from Settings, Plugins, open the ChEMBL tab, click Use canvas or type a name/ID, then press Lookup.", "updated": "2026-10-11", "headings": [ "What it does", "Who it is for", "How to use it", "Tips", "Questions and answers" ], "text": " Searching "aspirin" finds CHEMBL25. You can load it, add it to the canvas or send it to Compare. ChEMBL tab in the analysis panel. Query box: a name, ChEMBL ID (e.g. CHEMBL25) or the canvas structure. Lookup runs the search. Result tabs: Overview, Targets, Activity and Similar. What it does # ChEMBL is a free database of drug-like molecules. EMBL-EBI runs it. It holds millions of activity data points. Search finds a compound by name, ChEMBL ID or your drawing. Targets lists proteins the compound was tested on. Activity lists values like IC50 and Ki. Similar finds look-alike compounds. Load any of them to the canvas. Who it is for # Medicinal chemistry students. Researchers who check known activity. Teachers who show real drug data. How to use it # Open the MolDraw editor and sign in. Click Settings , then Plugins , then Install next to ChEMBL. Draw a molecule or leave the canvas empty if you will search by name. Open the ChEMBL tab (callout 1). Type a name or ChEMBL ID in the query box (callout 2) or press Use canvas . Press Lookup (callout 3). Browse the Overview, Targets, Activity, Similar tabs (callout 4). Use Load to canvas , Append or Send to Compare to keep working with a hit. Tips # If a drawn structure is not found, check stereochemistry and charges; InChIKey matching is exact. Activity values from different assays are not directly comparable; open the assay link for conditions. Pair with Lipinski's rule of five and drug-likeness to screen hits. " }, { "title": "Electrostatic Potential (MEP) plugin", "url": "https://www.moldraw.com/docs/plugins/mep-plugin-molecular-electrostatic-potential-surface/", "md": "https://www.moldraw.com/docs/plugins/mep-plugin-molecular-electrostatic-potential-surface.md", "section": "Plugins", "summary": "Install MEP from Settings, Plugins, draw a molecule, open the MEP tab and press Show in 3D.", "updated": "2026-10-11", "headings": [ "What it does", "Who it is for", "How to use it", "Tips", "Questions and answers" ], "text": " MEP for chloramphenicol. Oxygen atoms are most negative (red). Carbons with H are a bit positive (blue). MEP tab in the analysis panel. Colour scale from most electron-rich (red) to electron-poor (blue). Show in 3D draws the coloured surface on the 3D model; Refresh charges recalculates after edits. Opacity slider for the surface. Charge table: Gasteiger partial charge for every heavy atom, sorted most negative first. What it does # The plugin works out Gasteiger partial charges for each atom. Then it colors a surface around the 3D model. Red is negative. Blue is positive. It is fast, but it is not a quantum calculation. Use it to compare, not for exact energies. For example, see which end is more negative or where a nucleophile will attack. Who it is for # Students who learn polarity. Teachers who make slides about charge. Anyone who wants a quick picture of charge in a molecule. How to use it # Open the MolDraw editor and sign in. Click Settings , then Plugins , then Install next to Electrostatic Potential (MEP). Draw a molecule (or load one by name using the PubChem search box). Open the MEP tab (callout 1); charges are calculated immediately. Read the colour scale (callout 2) and the charge table (callout 5). Press Show in 3D (callout 3) to paint the surface on the 3D model. Adjust Opacity (callout 4) to see the ball-and-stick model through the surface. Use Turn surface off to return to the plain 3D view. Tips # Compare related molecules, e.g. phenol vs. aniline, to see " }, { "title": "Compare Molecules plugin", "url": "https://www.moldraw.com/docs/plugins/compare-molecules-plugin-tanimoto-similarity/", "md": "https://www.moldraw.com/docs/plugins/compare-molecules-plugin-tanimoto-similarity.md", "section": "Plugins", "summary": "Install Compare molecules, open the Compare tab, press Add canvas for the reference, paste other SMILES and press Add SMILES.", "updated": "2026-10-11", "headings": [ "What it does", "Who it is for", "How to use it", "Tips", "Questions and answers" ], "text": " Chloramphenicol as the reference, next to salicylic acid and paracetamol. You see two similarity scores and a list of changes. Compare tab. Add canvas adds the current drawing (the first molecule is the reference). SMILES box: one SMILES per line, optional name after a space. Add SMILES adds them all to the table. CSV exports the comparison table. What it does # Pick one molecule as the reference. Add others to compare. Structure similarity is a Tanimoto score from fingerprints. Functional similarity compares the groups each molecule has. Changes lists groups gained, lost or changed. Export the table as CSV. Who it is for # Medicinal chemists who look at analogues. Students who compare isomers or drug series. How to use it # Open the MolDraw editor and sign in. Click Settings , then Plugins , then Install next to Compare Molecules. Draw the reference molecule. Open the Compare tab (callout 1) and press Add canvas (callout 2). Paste more structures as SMILES, one per line (callout 3), then press Add SMILES (callout 4). Click a row to see reference and selected structures side by side with the shared core highlighted. Sort by similarity, and press CSV (callout 5) to export. Tips # Tanimoto 1.00 can still hide stereo differences; check the stereo flag column. Use the ChEMBL plugin's Send to Compare to add database hits directly. To get SMILES, convert names with name to SMILES . " }, { "title": "Protein Viewer plugin", "url": "https://www.moldraw.com/docs/plugins/protein-viewer-plugin-view-pdb-structures-in-3d/", "md": "https://www.moldraw.com/docs/plugins/protein-viewer-plugin-view-pdb-structures-in-3d.md", "section": "Plugins", "summary": "Open the Protein tab, type a PDB ID such as 1HHO and press Go. It is installed by default and works without signing in.", "updated": "2026-10-11", "headings": [ "What it does", "Who it is for", "How to use it", "Tips", "Questions and answers" ], "text": " Haemoglobin (PDB 1HHO) as a cartoon. Each chain has its own color. The sequence of chain A is below. Protein tab. PDB ID box: type an ID and press Go (or use Open for a file). Display menu: cartoon, sticks, lines, spheres and colouring. Surface: molecular surface with opacity and colour. Sequence strip: click residues to select and style them. What it does # Open the Protein tab next to Structure. Type a PDB ID like 1HHO, or load a file. Display sets the style: cartoon, stick or surface. Color by chain, secondary structure or element. Click the sequence strip to select residues. Export a PNG of the view. Who it is for # Biochemistry students. Teachers who need protein figures. Researchers who want a quick look at a structure. How to use it # Open the editor (no sign-in needed) and click the Protein tab (callout 1). Type a PDB ID, e.g. 1HHO , and press Go (callout 2), or press Open to load a local file. Use Display (callout 3) to switch cartoon/sticks and colour by chain. Add a Surface (callout 4) and lower its opacity to see the backbone. Click residues in the sequence strip (callout 5) to highlight them. Press Export to download an image. Tips # Try 1HHO (haemoglobin), 1BNA (B-DNA), 6LU7 (SARS-CoV-2 main protease) or 1GFL (GFP). Calculate a protein's mass from its sequence with the protein molecular weight calculator . For docking prep, use PDB to PDBQT . " }, { "title": "Smart Draw plugin", "url": "https://www.moldraw.com/docs/plugins/smart-draw-plugin-hand-drawn-sketch-to-structure/", "md": "https://www.moldraw.com/docs/plugins/smart-draw-plugin-hand-drawn-sketch-to-structure.md", "section": "Plugins", "summary": "Install Smart Draw, pick the Smart Draw pencil in the left toolbar, sketch, then pause or press Enter to convert.", "updated": "2026-10-11", "headings": [ "What it does", "Who it is for", "How to use it", "Tips", "Questions and answers" ], "text": " A hand-drawn hexagon with one extra stroke. Smart Draw turns it into methylcyclohexane. Smart Draw tool in the left toolbar. Sketch area: freehand strokes are recognised as a ring plus a substituent bond. What it does # Draw with the Smart Draw pencil. MolDraw reads your strokes. Straight strokes become bonds. Closed shapes become rings of the same size. Written letters become atom labels. The result is a normal MolDraw structure. You can edit it, clean it up or export it. Who it is for # Tablet and stylus users. Teachers who draw on a whiteboard. Students who find clicking slow. How to use it # Open the MolDraw editor and sign in. Click Settings , then Plugins , then Install next to Smart Draw. Install Smart Draw from Settings , Plugins. Select the Smart Draw tool in the left toolbar (callout 1). Sketch bonds or a ring on the canvas (callout 2). Keep strokes reasonably straight. Pause for about 1.2 s, or press Enter , to convert the strokes. Write a letter at a bond end to place a heteroatom, or switch to the normal tools to refine. Use Cleanup to tidy bond lengths and angles. Tips # Draw rings in one continuous stroke for the best recognition. On iPad, use Apple Pencil and enable the touch-screen settings in Settings , Touch screen. After converting, copy the SMILES with Copy SMILES or check the formula with the SMILES to formula tool. " }, { "title": "AI Spectroscopy plugin", "url": "https://www.moldraw.com/docs/plugins/ai-spectroscopy-plugin-predict-nmr-ms-and-uv-vis/", "md": "https://www.moldraw.com/docs/plugins/ai-spectroscopy-plugin-predict-nmr-ms-and-uv-vis.md", "section": "Plugins", "summary": "Add a Gemini API key in Settings , AI, install Spectroscopy, open AI chat and ask e.g. \"Predict the EI mass spectrum of this molecule\".", "updated": "2026-10-11", "headings": [ "What it does", "Who it is for", "How to use it", "Tips", "Questions and answers" ], "text": " The AI chat predicts NMR, EI mass and UV-Vis data for the structure on the canvas. AI chat button in the toolbar. Prompt box: describe which spectrum you want. What it does # The plugin sends your structure to the AI model. The model returns peaks in a fixed format. MolDraw shows them as tables and charts. The values come from a language model. Use them to learn and explain. Do not use them as reference data. Check real spectra in SDBS or NIST. Who it is for # Students who want a quick guess at a spectrum. Teachers who make practice problems. How to use it # Open the MolDraw editor and sign in. Click Settings , then Plugins , then Install next to AI Spectroscopy. Open Settings , AI and paste your Gemini API key (stored only in your browser). Install Spectroscopy from Settings , Plugins. Draw the molecule. Click AI chat (callout 1). Type a request in the prompt box (callout 2), e.g. \"Predict the 1H NMR spectrum\". Open the result window to see the spectrum, peak table and notes. Tips # Ask follow-up questions such as \"Why is the base peak at m/z 43?\" Check the molecular ion with the exact mass calculator . Learn to read the plots with the mass spectrum , IR and NMR guides. " }, { "title": "Themes (Ball-and-Stick) plugin", "url": "https://www.moldraw.com/docs/plugins/themes-plugin-ball-and-stick-2d-style/", "md": "https://www.moldraw.com/docs/plugins/themes-plugin-ball-and-stick-2d-style.md", "section": "Plugins", "summary": "Click Color & style in the toolbar and set Look to Ball and stick. Themes is installed by default.", "updated": "2026-10-11", "headings": [ "What it does", "Who it is for", "How to use it", "Tips", "Questions and answers" ], "text": " Chloramphenicol in the Ball and stick theme. Cl is green, O red, N blue and C grey. Color & style button in the toolbar. Look menu: choose Default or Ball and stick. What it does # Themes change only how structures are drawn, not the chemistry. You can apply the look to the selection or, with Apply to all , to every design. Label and ring-fill colours, opacity and atom/bond overrides in the same panel still work, and exports (PNG/SVG) keep the theme. Who it is for # Teachers and students making visually clear figures, and anyone who wants a 3D-style image without opening the 3D viewer. How to use it # Draw or load a structure. Click Color & style (callout 1). Set Look to Ball and stick (callout 2). Toggle Apply to all to restyle all open designs. Export with Download , PNG or SVG. Tips # For a true rotatable 3D model use the 3D molecular model viewer . Explore ready-made 3D pages in the molecule library . Switch back to Default for journal-style skeletal structures. " } ] }