PDB to MOL2 Converter
Convert PDB structures to MOL2 with SYBYL atom typing, bond perception, and chain selection.
Input
Output
Configure input settings on the left, then click "Convert"
Convert PDB structures to MOL2 with SYBYL atom typing, bond perception, and chain selection.
Convert Protein Data Bank files to Crystallographic Information File format
Convert Protein Data Bank files to FASTA sequence format
Convert CSV and TSV files containing sequence data to FASTA format with flexible column mapping and automatic delimiter detection
Translate DNA sequences to protein sequences using genetic code
Convert single-letter amino acid codes to three-letter codes
Reverse translate protein sequences to possible DNA sequences
Convert three-letter amino acid codes to single-letter codes
Convert TXT or plain text sequences into FASTA format files for DNA, RNA, and protein workflows with cleanup, validation, and downloads
Extract sequence features (CDS, mRNA, gene, etc.) from GenBank files in FASTA format with support for spliced features
Convert MOL2 ligand files into SMILES strings for registration, filtering, and downstream analysis.
Paste or upload a PDB file, or fetch one from the RCSB by ID, and the converter rewrites it into a Tripos MOL2 file in the browser. Atoms are assigned SYBYL atom types, bonds are perceived from the coordinates, and each residue becomes an entry in the @<TRIPOS>SUBSTRUCTURE section. The result downloads as a .mol2 file. Nothing is uploaded to a server.
A small ligand converts as follows. Input:
HETATM 1 C1 UNL A 1 -0.748 0.015 0.024 1.00 0.00 C
HETATM 2 O1 UNL A 1 0.667 0.015 0.024 1.00 0.00 O
HETATM 3 H1 UNL A 1 -1.142 -0.505 -0.861 1.00 0.00 H
HETATM 4 H2 UNL A 1 -1.142 -0.505 0.909 1.00 0.00 H
HETATM 5 H3 UNL A 1 -1.142 1.035 0.024 1.00 0.00 H
HETATM 6 H4 UNL A 1 0.962 0.535 0.789 1.00 0.00 H
ENDOutput with default settings:
@<TRIPOS>MOLECULE
Converted from PDB
6 5 1 0 0
SMALL
NO_CHARGES
@<TRIPOS>ATOM
1 C1 -0.7480 0.0150 0.0240 C.3 1 UNL 0.0000
2 O1 0.6670 0.0150 0.0240 O.3 1 UNL 0.0000
3 H1 -1.1420 -0.5050 -0.8610 H 1 UNL 0.0000
4 H2 -1.1420 -0.5050 0.9090 H 1 UNL 0.0000
5 H3 -1.1420 1.0350 0.0240 H 1 UNL 0.0000
6 H4 0.9620 0.5350 0.7890 H 1 UNL 0.0000
@<TRIPOS>BOND
1 1 3 1
2 1 4 1
3 1 5 1
4 1 2 1
5 2 6 1
@<TRIPOS>SUBSTRUCTURE
1 UNL1 1 RESIDUE 1 A UNL 0The element comes from columns 77 to 78 when present and is otherwise read from the atom name. Bonds are perceived from interatomic distances using element covalent radii, so the carbon, oxygen, and hydrogens are connected without any CONECT records in the input. Every bond is written as a single bond, which is why the C and O appear as 1 2 1 rather than a double bond. The molecule type is SMALL because no standard amino acids are present, and the charge type is NO_CHARGES because charges are off by default.
For a standard residue the converter assigns context-aware SYBYL atom types. An alanine fragment shows the backbone amide nitrogen as N.am, the carbonyl carbon as C.2, and the carbonyl oxygen as O.2:
@<TRIPOS>MOLECULE
Converted from PDB
5 4 1 0 0
PROTEIN
NO_CHARGES
@<TRIPOS>ATOM
1 N 11.1040 6.1340 6.6120 N.am 1 ALA 0.0000
2 CA 11.6390 6.0710 7.9670 C.3 1 ALA 0.0000
3 C 11.0240 7.1300 8.8750 C.2 1 ALA 0.0000
4 O 9.8520 7.0140 9.2500 O.2 1 ALA 0.0000
5 CB 11.4500 4.6730 8.5410 C.3 1 ALA 0.0000
@<TRIPOS>BOND
1 1 2 1
2 2 5 1
3 2 3 1
4 3 4 1
@<TRIPOS>SUBSTRUCTURE
1 ALA1 1 RESIDUE 1 A ALA 0Aromatic ring atoms in Phe, Tyr, Trp, and His become C.ar and N.ar, carboxylate oxygens in Asp and Glu become O.co2, and the molecule type is reported as PROTEIN when any standard residue is present.
| Format | Description |
|---|---|
.pdb, .ent | Protein Data Bank coordinate file with ATOM and HETATM records. |
Paste content directly, upload a file up to 50 MB, or fetch a structure from the RCSB by its four-character PDB ID. Multi-model files such as NMR ensembles are converted using the first model, with a notice when extra models are dropped.
| Setting | Description |
|---|---|
Atom typing scheme | SYBYL atom types assigns context-aware Tripos types such as C.ar, N.am, and O.co2 for standard residues, falling back to sp3 element types for ligands. Simple element types writes the bare element symbol instead. Default: SYBYL atom types. |
Generate bonds | Perceive bonds from interatomic distances using element covalent radii with a 0.45 Å tolerance. Turn off for an atoms-only file with no @<TRIPOS>BOND section. Default: on. |
Assign formal charges | Place approximate formal charges on ionizable groups (Asp, Glu, and the C-terminus negative; Lys and Arg positive) and set the charge type to USER_CHARGES. These are not Gasteiger charges. Default: off. |
Include hydrogens | Keep hydrogen atoms. Turn off for a heavy-atom-only file. Default: on. |
Include water | Keep water molecules such as HOH and WAT. Default: off. |
Chain selection | Which chains to export. All chains keeps every chain, First chain only keeps the first chain in the file, and Specific chains keeps only the IDs you list. Default: All chains. |
Chain IDs | Comma-separated chain IDs (for example A,B,C), used when chain selection is Specific chains. Default: A,B. |
| File | Contents |
|---|---|
name.mol2 | The converted structure with @<TRIPOS>MOLECULE, @<TRIPOS>ATOM, an optional @<TRIPOS>BOND block, and an @<TRIPOS>SUBSTRUCTURE block, one entry per residue. |
conversion-summary.txt | Molecule type, the chains found and exported, residue, atom, and bond counts, the atom typing scheme, charge handling, hydrogens and waters removed, and a note on how bonds were perceived. |
Both files are named after the input file (an uploaded 1abc.pdb produces 1abc.mol2 and conversion-summary.txt) and appear in the Files tab to copy or download. Warnings, such as the multi-model notice, the formal-charge caveat, or a request for chains that were not found, also show above the output.
PDB (Protein Data Bank) is a fixed-width coordinate format built for macromolecules. It records atom positions along with biological context such as chains, residues, and CONECT connectivity, but it carries no atom typing and no bond order beyond CONECT.
MOL2 (Tripos MOL2), developed for the SYBYL modeling suite, stores atoms with SYBYL atom types, explicit bonds, partial charges, and substructure definitions in tagged sections. The SYBYL atom type encodes both the element and its chemical environment, for example C.3 for an sp3 carbon, C.ar for an aromatic carbon, and O.co2 for a carboxylate oxygen, which force fields and docking tools use to look up parameters.
Converting PDB to MOL2 is common when preparing a structure for docking with tools such as GOLD or DOCK, for QSAR modeling, or for loading into SYBYL and similar packages. The atom types in this converter cover the standard amino acids and fall back to element sp3 types for other groups. Bonds are perceived from geometry and written as single bonds, so keep an explicit chemistry source if a downstream tool needs aromatic or double bond orders.
| Goal | Tool |
|---|---|
| Convert a PDB to a small-molecule SDF | PDB to SDF |
| Turn an SDF back into a PDB structure | SDF to PDB |
| Keep full macromolecular metadata as mmCIF | PDB to CIF |
| Extract the protein sequence from a structure | PDB to FASTA |
For standard amino acids it assigns context-aware SYBYL types: N.am for backbone amide nitrogen, C.2 and O.2 for the carbonyl, C.ar and N.ar for aromatic rings in Phe, Tyr, Trp, and His, O.co2 for Asp and Glu carboxylates, C.cat and N.pl3 for the Arg guanidinium, and N.4 for the Lys amine. Ligands and other groups fall back to sp3 element types such as C.3, N.3, and O.3. Choose Simple element types to write bare element symbols instead.
No. Bonds are perceived from interatomic distances and are all written as single bonds. The geometry and which atoms are connected are preserved, but double, triple, and aromatic bond orders are not assigned. Atom types still distinguish aromatic atoms (C.ar, N.ar), even though the bonds between them are written as single bonds.
No. Charges are off by default, and the file is written as NO_CHARGES. Turning on Assign formal charges places approximate formal charges on ionizable groups (Asp, Glu, and the C-terminus negative; Lys and Arg positive) and marks the file USER_CHARGES. For Gasteiger or other computed partial charges, use software such as OpenBabel or antechamber.
No. Connectivity comes entirely from the coordinates. Bonds are perceived with element covalent radii and a 0.45 Å tolerance, which detects disulfides and other longer bonds that a fixed cutoff would miss.
Hydrogens are kept by default and can be removed with Include hydrogens. Water molecules such as HOH and WAT are removed by default and can be kept with Include water. Use Chain selection to export all chains, the first chain only, or a specific list of chain IDs. The summary file reports how many hydrogens and waters were dropped and which chains were exported.