PDB to MOL2 Converter

How to convert PDB to MOL2

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
END

Output 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 0

The 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 0

Aromatic 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.

Input

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.

Settings

Results

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.

What are PDB and MOL2

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.

Which converter should I use

FAQ

What atom types does the converter assign?

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.

Does PDB to MOL2 assign bond orders?

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.

Are the charges real Gasteiger charges?

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.

Are PDB CONECT records used?

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.

How are hydrogens, water, and chains handled?

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.