Current ligands
May 18, 2026 ยท View on GitHub
A list of the ligands currently natively available for conversion within CCD2MD. For addition of other molecules, the use of pos2cif is recommended if AF3 can be used. Otherwise, additional mappings can be created, as documented in the CCD2MD paper.
| Name | CCDName | CHARMMName | CGName | Note |
|---|---|---|---|---|
| Cardiolipin | CARD | CARD | Palmitoyl-oleoyl cardiolipin (POCL2), new lipidome mapping available | |
| Cholesterol | CLR | CHL1 | CHL1 | New lipidome mapping available |
| DGPC | DGPC | DGPC | New lipidome mapping available | |
| DGPE | DGPE | DGPE | New lipidome mapping available | |
| DLPC | DLPC | DLPC | New lipidome mapping available | |
| DLPE | WNZ | DLPE | DLPE | New lipidome mapping available |
| DMPC | MC3 | DMPC | DMPC | New lipidome mapping available |
| DMPE | 46E | DMPE | DMPE | New lipidome mapping available |
| DMPI | DMPI | DMPI | New lipidome mapping available | |
| DMPS | DMPS | DMPS | New lipidome mapping available | |
| DNPC | DNPC | DNPC | New lipidome mapping available | |
| DNPE | DNPE | DNPE | New lipidome mapping available | |
| dodecylBDmaltoside | LMT | BDDM | ||
| DOPC | DOPC | DOPC | New lipidome mapping available | |
| DOPE | DOPE | DOPE | New lipidome mapping available | |
| DOPS | 17F | DOPS | DOPS | New lipidome mapping available |
| DPG3 | DPG3 | DPG3 | Non-native in CHARMM36 | |
| DPPC | PCF | DPPC | DPPC | New lipidome mapping available |
| DPPE | DPPE | DPPE | New lipidome mapping available | |
| DYPC | DYPC | DYPC | New lipidome mapping available | |
| DYPE | DYPE | DYPE | New lipidome mapping available | |
| laurylBMNglycol | LMN | BLMN | BLMNG in CHARMM | |
| LIP1 | LIP1 | LIP1 | Non-native in CHARMM36 | |
| LIP2 | LIP2 | LIP2 | Non-native in CHARMM36 | |
| LIP3 | LIP3 | LIP3 | Non-native in CHARMM36 | |
| LIPA | LIPA | LIPA | Non-native in CHARMM36 | |
| OBDglucopyranoside | BOG | BOG1 | BOG in CHARMM36 | |
| POPI 3 phosphate | POP1 | POP1 | POPI13 in CHARMM36, new lipidome mapping available | |
| POPI 3,4 bisphosphate | POP2 | POP2 | POPI2D in CHARMM36, new lipidome mapping available | |
| POPI 3,4,5 trisphosphate | POP3 | POP3 | POPI34 in CHARMM36, new lipidome mapping available | |
| POPI 4 phosphate | POP4 | POP4 | POPI14 in CHARMM36, new lipidome mapping available | |
| POPI 5 phosphate | POP5 | POP5 | POPI15 in CHARMM36, new lipidome mapping available | |
| POPI 4,5 bisphosphate | POP6 | POP6 | POPI24 in CHARMM36, new lipidome mapping available | |
| POPI 3,5 bisphosphate | POP7 | POP7 | POPI2A in CHARMM36, new lipidome mapping available | |
| POPA | D21 | POPA | POPA | New lipidome mappi, new lipidome mapping available |
| POPC | POV | POPC | POPC | New lipidome mappi, new lipidome mapping available |
| POPE | 6OU | POPE | POPE | New lipidome mappi, new lipidome mapping available |
| POPE_SMILES | POES | POPE | POPE | From SMILES string, new lipidome mapping available |
| POPG | PGW | POPG | POPG | New lipidome mapping available |
| POPI | POPI | POPI | New lipidome mapping available | |
| POPS | D39 | POPS | POPS | New lipidome mapping available |
| RAMP | RAMP | RAMP | Non-native in CHARMM36 | |
| REMP | KDL | REMP | REMP | |
| SSM1 | SSM1 | SSM1 | SSM in CHARMM36, new lipidome mapping available | |
| TMM | TMM1 | TMM1 | Non-native in CHARMM36 | |
| TMMA | TMMA | TMMA | Non-native in CHARMM36 | |
| undecaprenyl phosphate | 5TR | UNP1 | UDP1 | |
| undecaprenyl pyrophosphate | UDP2 | UDP2 | UNDPP in CHARMM36 |
Post-translational Modifications
| Name | CCDName | CHARMMName | CGName |
|---|---|---|---|
| CYSD | CYSD | CYSD | |
| CYSF | CYSF | CYSF | |
| CYSG | CYSG | CYSG | |
| CYSP | CYSP | CYSP | |
| CYST | CYST | CYST | |
| GLYM | GLYM | GLYM |
SMILES strings
Note any modification which does not affect the order of atoms can be made (e.g. changes to chiral centres/charges/double bonds). The name of the SMILES string must differ from the CHARMM name if wishing to utilise userCCD codes, and should not be more than 4 charaters if wishing to convert to CG. Ideally, it should also differ from utilised CCD codes.
| POPE_SMILES | POES | POPE |CCCCCCCC\C=C/CCCCCCCC(=O)O[C@H](COC(=O)CCCCCCCCCCCCCCC)COP(O)(=O)OCCN |
For issues and suggestions, please feel free to add these via GitHub or contact Kat Blow at katarina.blow[at]warwick.ac.uk