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Ligand Database in MDWeb (Amber Parameters)
- MoDEL Ligand Library
- AMBER parameter database (Richard Bryce - Manchester)
- Modified Nucleic Acid Parameters Database (John SantaLucia - Wayne)
| 1DA | 1MA | 1MG | 2MG | 2PH | 2PR | 4HA | 5GP |
| 5MC | 5MU | 7MG | 8OG | 998 | A80 | ABC | ACM |
| ACN | ACT | ACY | ADE | ADN | ADP | AHA | APF |
| ARN | ATP | AZI | B18 | BDN | BGL | BHP | BMA |
| BME | BML | BNZ | BOG | BU1 | Br- | CA2 | CBI |
| CHX | CIT | CMO | CO3 | COT | CYH | CYN | Ca2 |
| Cd2 | Co2 | Cs+ | Cu2 | DCM | DDQ | DGG | DIO |
| DM | DMF | DMS | DNC | DOX | DTT | EDO | EHN |
| EOH | EPE | F10 | FMN | Fe2 | GDP | GLA | GLB |
| GOL | H2U | HEM | IDA | IMD | IND | INT | IOL |
| IPA | IPH | K+ | KDG | LDA | LYN | LYS | Li+ |
| M2G | MAN | MEE | MES | MG2 | MOH | MPD | MR9 |
| MSM | MTX | Mg2 | Mn2 | NAD | NEO | NH3 | NH4 |
| NO3 | Na+ | Ni2 | OAA | OMC | OMG | OXL | OXY |
| PBP | PEG | PGA | PLM | PO2 | POP | PP7 | PPI |
| PPV | PSU | PYD | RGUA | RIP | RRT | RTL | S6G |
| S6G3 | S6G5 | SAM | SB2 | SBI | SDG | SIN | SKD |
| SO4 | SOA | SPM | SUL | TAR | TCD | THM | TNL |
| TRS | TTD | TYM | URA | URE | V25 | WAT | YG |
| Zn2 | apf | arg | gly | lys | sHBO | tRNA | thioG_TG |
