# FFCharge Data
This directory contains the charge data used by FFCharge.
## File Format
The `charges.csv` file uses CSV format with the following columns:
| `scheme` | Force field scheme identifier |
| `position` | Residue position in chain |
| `residue` | Residue name (3-letter code) |
| `atom` | Atom name |
| `charge` | Partial charge value (elementary charge units) |
## Data Coverage
| Protein | 8,169 | 29 | 3 |
| Nucleic Acid | 1,321 | 10 | 2 |
| Water | 15 | 1 | 5 |
| Ion | 66 | 66 | 1 |
---
## Protein Residues
### Standard Amino Acids
| ALA | Alanine | 0 |
| ARG | Arginine (protonated) | +1 |
| ASN | Asparagine | 0 |
| ASP | Aspartate (deprotonated) | −1 |
| CYS | Cysteine | 0 |
| CYX | Cystine (disulfide-bonded) | 0 |
| GLN | Glutamine | 0 |
| GLU | Glutamate (deprotonated) | −1 |
| GLY | Glycine | 0 |
| HID | Histidine (δ-protonated) | 0 |
| HIE | Histidine (ε-protonated) | 0 |
| HIP | Histidine (doubly protonated) | +1 |
| ILE | Isoleucine | 0 |
| LEU | Leucine | 0 |
| LYS | Lysine (protonated) | +1 |
| MET | Methionine | 0 |
| PHE | Phenylalanine | 0 |
| PRO | Proline | 0 |
| SER | Serine | 0 |
| THR | Threonine | 0 |
| TRP | Tryptophan | 0 |
| TYR | Tyrosine | 0 |
| VAL | Valine | 0 |
### Non-Standard/Protonation Variants
| ARN | Arginine (neutral) | 0 |
| ASH | Aspartate (protonated) | 0 |
| CYM | Cysteine (deprotonated) | −1 |
| GLH | Glutamate (protonated) | 0 |
| LYN | Lysine (neutral) | 0 |
| TYM | Tyrosinate (deprotonated) | −1 |
### Protein Atom Names by Residue and Position
> **Position Key**: `n` = N-terminal, `n-` = N-terminal deprotonated, `m` = Middle, `c` = C-terminal, `c+` = C-terminal protonated
| ALA | n | N, H1, H2, H3, CA, HA, C, O, CB, HB1, HB2, HB3 |
| ALA | n- | N, H1, H2, CA, HA, C, O, CB, HB1, HB2, HB3 |
| ALA | m | N, H, CA, HA, C, O, CB, HB1, HB2, HB3 |
| ALA | c | N, H, CA, HA, C, O, OXT, CB, HB1, HB2, HB3 |
| ALA | c+ | N, H, CA, HA, C, O, OXT, HOXT, CB, HB1, HB2, HB3 |
| ARG | n | N, H1, H2, H3, CA, HA, C, O, CB, CD, CG, CZ, NE, NH1, NH2, HB2, HB3, HD2, HD3, HE, HG2, HG3, HH11, HH12, HH21, HH22 |
| ARG | n- | N, H1, H2, CA, HA, C, O, CB, CD, CG, CZ, NE, NH1, NH2, HB2, HB3, HD2, HD3, HE, HG2, HG3, HH11, HH12, HH21, HH22 |
| ARG | m | N, H, CA, HA, C, O, CB, CD, CG, CZ, NE, NH1, NH2, HB2, HB3, HD2, HD3, HE, HG2, HG3, HH11, HH12, HH21, HH22 |
| ARG | c | N, H, CA, HA, C, O, OXT, CB, CD, CG, CZ, NE, NH1, NH2, HB2, HB3, HD2, HD3, HE, HG2, HG3, HH11, HH12, HH21, HH22 |
| ARG | c+ | N, H, CA, HA, C, O, OXT, HOXT, CB, CD, CG, CZ, NE, NH1, NH2, HB2, HB3, HD2, HD3, HE, HG2, HG3, HH11, HH12, HH21, HH22 |
| ARN | n | N, H1, H2, H3, CA, HA, C, O, CB, CD, CG, CZ, NE, NH1, NH2, HB2, HB3, HD2, HD3, HE, HG2, HG3, HH11, HH12, HH21 |
| ARN | n- | N, H1, H2, CA, HA, C, O, CB, CD, CG, CZ, NE, NH1, NH2, HB2, HB3, HD2, HD3, HE, HG2, HG3, HH11, HH12, HH21 |
| ARN | m | N, H, CA, HA, C, O, CB, CD, CG, CZ, NE, NH1, NH2, HB2, HB3, HD2, HD3, HE, HG2, HG3, HH11, HH12, HH21 |
| ARN | c | N, H, CA, HA, C, O, OXT, CB, CD, CG, CZ, NE, NH1, NH2, HB2, HB3, HD2, HD3, HE, HG2, HG3, HH11, HH12, HH21 |
| ARN | c+ | N, H, CA, HA, C, O, OXT, HOXT, CB, CD, CG, CZ, NE, NH1, NH2, HB2, HB3, HD2, HD3, HE, HG2, HG3, HH11, HH12, HH21 |
| ASH | n | N, H1, H2, H3, CA, HA, C, O, CB, CG, OD1, OD2, HB2, HB3, HD2 |
| ASH | n- | N, H1, H2, CA, HA, C, O, CB, CG, OD1, OD2, HB2, HB3, HD2 |
| ASH | m | N, H, CA, HA, C, O, CB, CG, OD1, OD2, HB2, HB3, HD2 |
| ASH | c | N, H, CA, HA, C, O, OXT, CB, CG, OD1, OD2, HB2, HB3, HD2 |
| ASH | c+ | N, H, CA, HA, C, O, OXT, HOXT, CB, CG, OD1, OD2, HB2, HB3, HD2 |
| ASN | n | N, H1, H2, H3, CA, HA, C, O, CB, CG, ND2, OD1, HB2, HB3, HD21, HD22 |
| ASN | n- | N, H1, H2, CA, HA, C, O, CB, CG, ND2, OD1, HB2, HB3, HD21, HD22 |
| ASN | m | N, H, CA, HA, C, O, CB, CG, ND2, OD1, HB2, HB3, HD21, HD22 |
| ASN | c | N, H, CA, HA, C, O, OXT, CB, CG, ND2, OD1, HB2, HB3, HD21, HD22 |
| ASN | c+ | N, H, CA, HA, C, O, OXT, HOXT, CB, CG, ND2, OD1, HB2, HB3, HD21, HD22 |
| ASP | n | N, H1, H2, H3, CA, HA, C, O, CB, CG, OD1, OD2, HB2, HB3 |
| ASP | n- | N, H1, H2, CA, HA, C, O, CB, CG, OD1, OD2, HB2, HB3 |
| ASP | m | N, H, CA, HA, C, O, CB, CG, OD1, OD2, HB2, HB3 |
| ASP | c | N, H, CA, HA, C, O, OXT, CB, CG, OD1, OD2, HB2, HB3 |
| ASP | c+ | N, H, CA, HA, C, O, OXT, HOXT, CB, CG, OD1, OD2, HB2, HB3 |
| CYM | n | N, H1, H2, H3, CA, HA, C, O, CB, SG, HB2, HB3 |
| CYM | n- | N, H1, H2, CA, HA, C, O, CB, SG, HB2, HB3 |
| CYM | m | N, H, CA, HA, C, O, CB, SG, HB2, HB3 |
| CYM | c | N, H, CA, HA, C, O, OXT, CB, SG, HB2, HB3 |
| CYM | c+ | N, H, CA, HA, C, O, OXT, HOXT, CB, SG, HB2, HB3 |
| CYS | n | N, H1, H2, H3, CA, HA, C, O, CB, SG, HB2, HB3, HG |
| CYS | n- | N, H1, H2, CA, HA, C, O, CB, SG, HB2, HB3, HG |
| CYS | m | N, H, CA, HA, C, O, CB, SG, HB2, HB3, HG |
| CYS | c | N, H, CA, HA, C, O, OXT, CB, SG, HB2, HB3, HG |
| CYS | c+ | N, H, CA, HA, C, O, OXT, HOXT, CB, SG, HB2, HB3, HG |
| CYX | n | N, H1, H2, H3, CA, HA, C, O, CB, SG, HB2, HB3 |
| CYX | n- | N, H1, H2, CA, HA, C, O, CB, SG, HB2, HB3 |
| CYX | m | N, H, CA, HA, C, O, CB, SG, HB2, HB3 |
| CYX | c | N, H, CA, HA, C, O, OXT, CB, SG, HB2, HB3 |
| CYX | c+ | N, H, CA, HA, C, O, OXT, HOXT, CB, SG, HB2, HB3 |
| GLH | n | N, H1, H2, H3, CA, HA, C, O, CB, CD, CG, OE1, OE2, HB2, HB3, HE2, HG2, HG3 |
| GLH | n- | N, H1, H2, CA, HA, C, O, CB, CD, CG, OE1, OE2, HB2, HB3, HE2, HG2, HG3 |
| GLH | m | N, H, CA, HA, C, O, CB, CD, CG, OE1, OE2, HB2, HB3, HE2, HG2, HG3 |
| GLH | c | N, H, CA, HA, C, O, OXT, CB, CD, CG, OE1, OE2, HB2, HB3, HE2, HG2, HG3 |
| GLH | c+ | N, H, CA, HA, C, O, OXT, HOXT, CB, CD, CG, OE1, OE2, HB2, HB3, HE2, HG2, HG3 |
| GLN | n | N, H1, H2, H3, CA, HA, C, O, CB, CD, CG, NE2, OE1, HB2, HB3, HE21, HE22, HG2, HG3 |
| GLN | n- | N, H1, H2, CA, HA, C, O, CB, CD, CG, NE2, OE1, HB2, HB3, HE21, HE22, HG2, HG3 |
| GLN | m | N, H, CA, HA, C, O, CB, CD, CG, NE2, OE1, HB2, HB3, HE21, HE22, HG2, HG3 |
| GLN | c | N, H, CA, HA, C, O, OXT, CB, CD, CG, NE2, OE1, HB2, HB3, HE21, HE22, HG2, HG3 |
| GLN | c+ | N, H, CA, HA, C, O, OXT, HOXT, CB, CD, CG, NE2, OE1, HB2, HB3, HE21, HE22, HG2, HG3 |
| GLU | n | N, H1, H2, H3, CA, HA, C, O, CB, CD, CG, OE1, OE2, HB2, HB3, HG2, HG3 |
| GLU | n- | N, H1, H2, CA, HA, C, O, CB, CD, CG, OE1, OE2, HB2, HB3, HG2, HG3 |
| GLU | m | N, H, CA, HA, C, O, CB, CD, CG, OE1, OE2, HB2, HB3, HG2, HG3 |
| GLU | c | N, H, CA, HA, C, O, OXT, CB, CD, CG, OE1, OE2, HB2, HB3, HG2, HG3 |
| GLU | c+ | N, H, CA, HA, C, O, OXT, HOXT, CB, CD, CG, OE1, OE2, HB2, HB3, HG2, HG3 |
| GLY | n | N, H1, H2, H3, CA, HA2, HA3, C, O |
| GLY | n- | N, H1, H2, CA, HA2, HA3, C, O |
| GLY | m | N, H, CA, HA2, HA3, C, O |
| GLY | c | N, H, CA, HA2, HA3, C, O, OXT |
| GLY | c+ | N, H, CA, HA2, HA3, C, O, OXT, HOXT |
| HID | n | N, H1, H2, H3, CA, HA, C, O, CB, CD2, CE1, CG, ND1, NE2, HB2, HB3, HD1, HD2, HE1 |
| HID | n- | N, H1, H2, CA, HA, C, O, CB, CD2, CE1, CG, ND1, NE2, HB2, HB3, HD1, HD2, HE1 |
| HID | m | N, H, CA, HA, C, O, CB, CD2, CE1, CG, ND1, NE2, HB2, HB3, HD1, HD2, HE1 |
| HID | c | N, H, CA, HA, C, O, OXT, CB, CD2, CE1, CG, ND1, NE2, HB2, HB3, HD1, HD2, HE1 |
| HID | c+ | N, H, CA, HA, C, O, OXT, HOXT, CB, CD2, CE1, CG, ND1, NE2, HB2, HB3, HD1, HD2, HE1 |
| HIE | n | N, H1, H2, H3, CA, HA, C, O, CB, CD2, CE1, CG, ND1, NE2, HB2, HB3, HD2, HE1, HE2 |
| HIE | n- | N, H1, H2, CA, HA, C, O, CB, CD2, CE1, CG, ND1, NE2, HB2, HB3, HD2, HE1, HE2 |
| HIE | m | N, H, CA, HA, C, O, CB, CD2, CE1, CG, ND1, NE2, HB2, HB3, HD2, HE1, HE2 |
| HIE | c | N, H, CA, HA, C, O, OXT, CB, CD2, CE1, CG, ND1, NE2, HB2, HB3, HD2, HE1, HE2 |
| HIE | c+ | N, H, CA, HA, C, O, OXT, HOXT, CB, CD2, CE1, CG, ND1, NE2, HB2, HB3, HD2, HE1, HE2 |
| HIP | n | N, H1, H2, H3, CA, HA, C, O, CB, CD2, CE1, CG, ND1, NE2, HB2, HB3, HD1, HD2, HE1, HE2 |
| HIP | n- | N, H1, H2, CA, HA, C, O, CB, CD2, CE1, CG, ND1, NE2, HB2, HB3, HD1, HD2, HE1, HE2 |
| HIP | m | N, H, CA, HA, C, O, CB, CD2, CE1, CG, ND1, NE2, HB2, HB3, HD1, HD2, HE1, HE2 |
| HIP | c | N, H, CA, HA, C, O, OXT, CB, CD2, CE1, CG, ND1, NE2, HB2, HB3, HD1, HD2, HE1, HE2 |
| HIP | c+ | N, H, CA, HA, C, O, OXT, HOXT, CB, CD2, CE1, CG, ND1, NE2, HB2, HB3, HD1, HD2, HE1, HE2 |
| ILE | n | N, H1, H2, H3, CA, HA, C, O, CB, CD1, CG1, CG2, HB, HD11, HD12, HD13, HG12, HG13, HG21, HG22, HG23 |
| ILE | n- | N, H1, H2, CA, HA, C, O, CB, CD1, CG1, CG2, HB, HD11, HD12, HD13, HG12, HG13, HG21, HG22, HG23 |
| ILE | m | N, H, CA, HA, C, O, CB, CD1, CG1, CG2, HB, HD11, HD12, HD13, HG12, HG13, HG21, HG22, HG23 |
| ILE | c | N, H, CA, HA, C, O, OXT, CB, CD1, CG1, CG2, HB, HD11, HD12, HD13, HG12, HG13, HG21, HG22, HG23 |
| ILE | c+ | N, H, CA, HA, C, O, OXT, HOXT, CB, CD1, CG1, CG2, HB, HD11, HD12, HD13, HG12, HG13, HG21, HG22, HG23 |
| LEU | n | N, H1, H2, H3, CA, HA, C, O, CB, CD1, CD2, CG, HB2, HB3, HD11, HD12, HD13, HD21, HD22, HD23, HG |
| LEU | n- | N, H1, H2, CA, HA, C, O, CB, CD1, CD2, CG, HB2, HB3, HD11, HD12, HD13, HD21, HD22, HD23, HG |
| LEU | m | N, H, CA, HA, C, O, CB, CD1, CD2, CG, HB2, HB3, HD11, HD12, HD13, HD21, HD22, HD23, HG |
| LEU | c | N, H, CA, HA, C, O, OXT, CB, CD1, CD2, CG, HB2, HB3, HD11, HD12, HD13, HD21, HD22, HD23, HG |
| LEU | c+ | N, H, CA, HA, C, O, OXT, HOXT, CB, CD1, CD2, CG, HB2, HB3, HD11, HD12, HD13, HD21, HD22, HD23, HG |
| LYN | n | N, H1, H2, H3, CA, HA, C, O, CB, CD, CE, CG, NZ, HB2, HB3, HD2, HD3, HE2, HE3, HG2, HG3, HZ1, HZ2 |
| LYN | n- | N, H1, H2, CA, HA, C, O, CB, CD, CE, CG, NZ, HB2, HB3, HD2, HD3, HE2, HE3, HG2, HG3, HZ1, HZ2 |
| LYN | m | N, H, CA, HA, C, O, CB, CD, CE, CG, NZ, HB2, HB3, HD2, HD3, HE2, HE3, HG2, HG3, HZ1, HZ2 |
| LYN | c | N, H, CA, HA, C, O, OXT, CB, CD, CE, CG, NZ, HB2, HB3, HD2, HD3, HE2, HE3, HG2, HG3, HZ1, HZ2 |
| LYN | c+ | N, H, CA, HA, C, O, OXT, HOXT, CB, CD, CE, CG, NZ, HB2, HB3, HD2, HD3, HE2, HE3, HG2, HG3, HZ1, HZ2 |
| LYS | n | N, H1, H2, H3, CA, HA, C, O, CB, CD, CE, CG, NZ, HB2, HB3, HD2, HD3, HE2, HE3, HG2, HG3, HZ1, HZ2, HZ3 |
| LYS | n- | N, H1, H2, CA, HA, C, O, CB, CD, CE, CG, NZ, HB2, HB3, HD2, HD3, HE2, HE3, HG2, HG3, HZ1, HZ2, HZ3 |
| LYS | m | N, H, CA, HA, C, O, CB, CD, CE, CG, NZ, HB2, HB3, HD2, HD3, HE2, HE3, HG2, HG3, HZ1, HZ2, HZ3 |
| LYS | c | N, H, CA, HA, C, O, OXT, CB, CD, CE, CG, NZ, HB2, HB3, HD2, HD3, HE2, HE3, HG2, HG3, HZ1, HZ2, HZ3 |
| LYS | c+ | N, H, CA, HA, C, O, OXT, HOXT, CB, CD, CE, CG, NZ, HB2, HB3, HD2, HD3, HE2, HE3, HG2, HG3, HZ1, HZ2, HZ3 |
| MET | n | N, H1, H2, H3, CA, HA, C, O, CB, CE, CG, SD, HB2, HB3, HE1, HE2, HE3, HG2, HG3 |
| MET | n- | N, H1, H2, CA, HA, C, O, CB, CE, CG, SD, HB2, HB3, HE1, HE2, HE3, HG2, HG3 |
| MET | m | N, H, CA, HA, C, O, CB, CE, CG, SD, HB2, HB3, HE1, HE2, HE3, HG2, HG3 |
| MET | c | N, H, CA, HA, C, O, OXT, CB, CE, CG, SD, HB2, HB3, HE1, HE2, HE3, HG2, HG3 |
| MET | c+ | N, H, CA, HA, C, O, OXT, HOXT, CB, CE, CG, SD, HB2, HB3, HE1, HE2, HE3, HG2, HG3 |
| PHE | n | N, H1, H2, H3, CA, HA, C, O, CB, CD1, CD2, CE1, CE2, CG, CZ, HB2, HB3, HD1, HD2, HE1, HE2, HZ |
| PHE | n- | N, H1, H2, CA, HA, C, O, CB, CD1, CD2, CE1, CE2, CG, CZ, HB2, HB3, HD1, HD2, HE1, HE2, HZ |
| PHE | m | N, H, CA, HA, C, O, CB, CD1, CD2, CE1, CE2, CG, CZ, HB2, HB3, HD1, HD2, HE1, HE2, HZ |
| PHE | c | N, H, CA, HA, C, O, OXT, CB, CD1, CD2, CE1, CE2, CG, CZ, HB2, HB3, HD1, HD2, HE1, HE2, HZ |
| PHE | c+ | N, H, CA, HA, C, O, OXT, HOXT, CB, CD1, CD2, CE1, CE2, CG, CZ, HB2, HB3, HD1, HD2, HE1, HE2, HZ |
| PRO | n | N, H2, H3, CA, HA, C, O, CB, CD, CG, HB2, HB3, HD2, HD3, HG2, HG3 |
| PRO | n- | N, H2, CA, HA, C, O, CB, CD, CG, HB2, HB3, HD2, HD3, HG2, HG3 |
| PRO | m | N, CA, HA, C, O, CB, CD, CG, HB2, HB3, HD2, HD3, HG2, HG3 |
| PRO | c | N, CA, HA, C, O, OXT, CB, CD, CG, HB2, HB3, HD2, HD3, HG2, HG3 |
| PRO | c+ | N, CA, HA, C, O, OXT, HOXT, CB, CD, CG, HB2, HB3, HD2, HD3, HG2, HG3 |
| SER | n | N, H1, H2, H3, CA, HA, C, O, CB, OG, HB2, HB3, HG |
| SER | n- | N, H1, H2, CA, HA, C, O, CB, OG, HB2, HB3, HG |
| SER | m | N, H, CA, HA, C, O, CB, OG, HB2, HB3, HG |
| SER | c | N, H, CA, HA, C, O, OXT, CB, OG, HB2, HB3, HG |
| SER | c+ | N, H, CA, HA, C, O, OXT, HOXT, CB, OG, HB2, HB3, HG |
| THR | n | N, H1, H2, H3, CA, HA, C, O, CB, CG2, OG1, HB, HG1, HG21, HG22, HG23 |
| THR | n- | N, H1, H2, CA, HA, C, O, CB, CG2, OG1, HB, HG1, HG21, HG22, HG23 |
| THR | m | N, H, CA, HA, C, O, CB, CG2, OG1, HB, HG1, HG21, HG22, HG23 |
| THR | c | N, H, CA, HA, C, O, OXT, CB, CG2, OG1, HB, HG1, HG21, HG22, HG23 |
| THR | c+ | N, H, CA, HA, C, O, OXT, HOXT, CB, CG2, OG1, HB, HG1, HG21, HG22, HG23 |
| TRP | n | N, H1, H2, H3, CA, HA, C, O, CB, CD1, CD2, CE2, CE3, CG, CH2, CZ2, CZ3, NE1, HB2, HB3, HD1, HE1, HE3, HH2, HZ2, HZ3 |
| TRP | n- | N, H1, H2, CA, HA, C, O, CB, CD1, CD2, CE2, CE3, CG, CH2, CZ2, CZ3, NE1, HB2, HB3, HD1, HE1, HE3, HH2, HZ2, HZ3 |
| TRP | m | N, H, CA, HA, C, O, CB, CD1, CD2, CE2, CE3, CG, CH2, CZ2, CZ3, NE1, HB2, HB3, HD1, HE1, HE3, HH2, HZ2, HZ3 |
| TRP | c | N, H, CA, HA, C, O, OXT, CB, CD1, CD2, CE2, CE3, CG, CH2, CZ2, CZ3, NE1, HB2, HB3, HD1, HE1, HE3, HH2, HZ2, HZ3 |
| TRP | c+ | N, H, CA, HA, C, O, OXT, HOXT, CB, CD1, CD2, CE2, CE3, CG, CH2, CZ2, CZ3, NE1, HB2, HB3, HD1, HE1, HE3, HH2, HZ2, HZ3 |
| TYM | n | N, H1, H2, H3, CA, HA, C, O, CB, CD1, CD2, CE1, CE2, CG, CZ, OH, HB2, HB3, HD1, HD2, HE1, HE2 |
| TYM | n- | N, H1, H2, CA, HA, C, O, CB, CD1, CD2, CE1, CE2, CG, CZ, OH, HB2, HB3, HD1, HD2, HE1, HE2 |
| TYM | m | N, H, CA, HA, C, O, CB, CD1, CD2, CE1, CE2, CG, CZ, OH, HB2, HB3, HD1, HD2, HE1, HE2 |
| TYM | c | N, H, CA, HA, C, O, OXT, CB, CD1, CD2, CE1, CE2, CG, CZ, OH, HB2, HB3, HD1, HD2, HE1, HE2 |
| TYM | c+ | N, H, CA, HA, C, O, OXT, HOXT, CB, CD1, CD2, CE1, CE2, CG, CZ, OH, HB2, HB3, HD1, HD2, HE1, HE2 |
| TYR | n | N, H1, H2, H3, CA, HA, C, O, CB, CD1, CD2, CE1, CE2, CG, CZ, OH, HB2, HB3, HD1, HD2, HE1, HE2, HH |
| TYR | n- | N, H1, H2, CA, HA, C, O, CB, CD1, CD2, CE1, CE2, CG, CZ, OH, HB2, HB3, HD1, HD2, HE1, HE2, HH |
| TYR | m | N, H, CA, HA, C, O, CB, CD1, CD2, CE1, CE2, CG, CZ, OH, HB2, HB3, HD1, HD2, HE1, HE2, HH |
| TYR | c | N, H, CA, HA, C, O, OXT, CB, CD1, CD2, CE1, CE2, CG, CZ, OH, HB2, HB3, HD1, HD2, HE1, HE2, HH |
| TYR | c+ | N, H, CA, HA, C, O, OXT, HOXT, CB, CD1, CD2, CE1, CE2, CG, CZ, OH, HB2, HB3, HD1, HD2, HE1, HE2, HH |
| VAL | n | N, H1, H2, H3, CA, HA, C, O, CB, CG1, CG2, HB, HG11, HG12, HG13, HG21, HG22, HG23 |
| VAL | n- | N, H1, H2, CA, HA, C, O, CB, CG1, CG2, HB, HG11, HG12, HG13, HG21, HG22, HG23 |
| VAL | m | N, H, CA, HA, C, O, CB, CG1, CG2, HB, HG11, HG12, HG13, HG21, HG22, HG23 |
| VAL | c | N, H, CA, HA, C, O, OXT, CB, CG1, CG2, HB, HG11, HG12, HG13, HG21, HG22, HG23 |
| VAL | c+ | N, H, CA, HA, C, O, OXT, HOXT, CB, CG1, CG2, HB, HG11, HG12, HG13, HG21, HG22, HG23 |
---
## Nucleic Acid Residues
### DNA Residues
| DA | Deoxyadenosine | −1 |
| DC | Deoxycytidine | −1 |
| DG | Deoxyguanosine | −1 |
| DT | Deoxythymidine | −1 |
| DI | Deoxyinosine | −1 |
### RNA Residues
| A | Adenosine | −1 |
| C | Cytidine | −1 |
| G | Guanosine | −1 |
| U | Uridine | −1 |
| I | Inosine | −1 |
### Nucleic Acid Atom Names by Residue and Position
> **Position Key**: `5` = 5'-terminal, `m` = Middle, `3` = 3'-terminal
| A | 5 | C1', C2, C2', C3', C4, C4', C5, C5', C6, C8, N1, N3, N6, N7, N9, O2', O3', O4', O5', H1', H2, H2', H3', H4', H5', H5'', H61, H62, H8, HO2', HO5' |
| A | m | C1', C2, C2', C3', C4, C4', C5, C5', C6, C8, N1, N3, N6, N7, N9, O2', O3', O4', O5', OP1, OP2, P, H1', H2, H2', H3', H4', H5', H5'', H61, H62, H8, HO2' |
| A | 3 | C1', C2, C2', C3', C4, C4', C5, C5', C6, C8, N1, N3, N6, N7, N9, O2', O3', O4', O5', OP1, OP2, P, H1', H2, H2', H3', H4', H5', H5'', H61, H62, H8, HO2', HO3' |
| C | 5 | C1', C2, C2', C3', C4, C4', C5, C5', C6, N1, N3, N4, O2, O2', O3', O4', O5', H1', H2', H3', H4', H41, H42, H5, H5', H5'', H6, HO2', HO5' |
| C | m | C1', C2, C2', C3', C4, C4', C5, C5', C6, N1, N3, N4, O2, O2', O3', O4', O5', OP1, OP2, P, H1', H2', H3', H4', H41, H42, H5, H5', H5'', H6, HO2' |
| C | 3 | C1', C2, C2', C3', C4, C4', C5, C5', C6, N1, N3, N4, O2, O2', O3', O4', O5', OP1, OP2, P, H1', H2', H3', H4', H41, H42, H5, H5', H5'', H6, HO2', HO3' |
| DA | 5 | C1', C2, C2', C3', C4, C4', C5, C5', C6, C8, N1, N3, N6, N7, N9, O3', O4', O5', H1', H2, H2', H2'', H3', H4', H5', H5'', H61, H62, H8, HO5' |
| DA | m | C1', C2, C2', C3', C4, C4', C5, C5', C6, C8, N1, N3, N6, N7, N9, O3', O4', O5', OP1, OP2, P, H1', H2, H2', H2'', H3', H4', H5', H5'', H61, H62, H8 |
| DA | 3 | C1', C2, C2', C3', C4, C4', C5, C5', C6, C8, N1, N3, N6, N7, N9, O3', O4', O5', OP1, OP2, P, H1', H2, H2', H2'', H3', H4', H5', H5'', H61, H62, H8, HO3' |
| DC | 5 | C1', C2, C2', C3', C4, C4', C5, C5', C6, N1, N3, N4, O2, O3', O4', O5', H1', H2', H2'', H3', H4', H41, H42, H5, H5', H5'', H6, HO5' |
| DC | m | C1', C2, C2', C3', C4, C4', C5, C5', C6, N1, N3, N4, O2, O3', O4', O5', OP1, OP2, P, H1', H2', H2'', H3', H4', H41, H42, H5, H5', H5'', H6 |
| DC | 3 | C1', C2, C2', C3', C4, C4', C5, C5', C6, N1, N3, N4, O2, O3', O4', O5', OP1, OP2, P, H1', H2', H2'', H3', H4', H41, H42, H5, H5', H5'', H6, HO3' |
| DG | 5 | C1', C2, C2', C3', C4, C4', C5, C5', C6, C8, N1, N2, N3, N7, N9, O3', O4', O5', O6, H1, H1', H2', H2'', H21, H22, H3', H4', H5', H5'', H8, HO5' |
| DG | m | C1', C2, C2', C3', C4, C4', C5, C5', C6, C8, N1, N2, N3, N7, N9, O3', O4', O5', O6, OP1, OP2, P, H1, H1', H2', H2'', H21, H22, H3', H4', H5', H5'', H8 |
| DG | 3 | C1', C2, C2', C3', C4, C4', C5, C5', C6, C8, N1, N2, N3, N7, N9, O3', O4', O5', O6, OP1, OP2, P, H1, H1', H2', H2'', H21, H22, H3', H4', H5', H5'', H8, HO3' |
| DI | 5 | C1', C2, C2', C3', C4, C4', C5, C5', C6, C8, N1, N3, N7, N9, O3', O4', O5', O6, H1, H1', H2, H2', H2'', H3', H4', H5', H5'', H8, HO5' |
| DI | m | C1', C2, C2', C3', C4, C4', C5, C5', C6, C8, N1, N3, N7, N9, O3', O4', O5', O6, OP1, OP2, P, H1, H1', H2, H2', H2'', H3', H4', H5', H5'', H8 |
| DI | 3 | C1', C2, C2', C3', C4, C4', C5, C5', C6, C8, N1, N3, N7, N9, O3', O4', O5', O6, OP1, OP2, P, H1, H1', H2, H2', H2'', H3', H4', H5', H5'', H8, HO3' |
| DT | 5 | C1', C2, C2', C3', C4, C4', C5, C5', C6, C7, N1, N3, O2, O3', O4, O4', O5', H1', H2', H2'', H3, H3', H4', H5', H5'', H6, H71, H72, H73, HO5' |
| DT | m | C1', C2, C2', C3', C4, C4', C5, C5', C6, C7, N1, N3, O2, O3', O4, O4', O5', OP1, OP2, P, H1', H2', H2'', H3, H3', H4', H5', H5'', H6, H71, H72, H73 |
| DT | 3 | C1', C2, C2', C3', C4, C4', C5, C5', C6, C7, N1, N3, O2, O3', O4, O4', O5', OP1, OP2, P, H1', H2', H2'', H3, H3', H4', H5', H5'', H6, H71, H72, H73, HO3' |
| G | 5 | C1', C2, C2', C3', C4, C4', C5, C5', C6, C8, N1, N2, N3, N7, N9, O2', O3', O4', O5', O6, H1, H1', H2', H21, H22, H3', H4', H5', H5'', H8, HO2', HO5' |
| G | m | C1', C2, C2', C3', C4, C4', C5, C5', C6, C8, N1, N2, N3, N7, N9, O2', O3', O4', O5', O6, OP1, OP2, P, H1, H1', H2', H21, H22, H3', H4', H5', H5'', H8, HO2' |
| G | 3 | C1', C2, C2', C3', C4, C4', C5, C5', C6, C8, N1, N2, N3, N7, N9, O2', O3', O4', O5', O6, OP1, OP2, P, H1, H1', H2', H21, H22, H3', H4', H5', H5'', H8, HO2', HO3' |
| I | 5 | C1', C2, C2', C3', C4, C4', C5, C5', C6, C8, N1, N3, N7, N9, O2', O3', O4', O5', O6, H1, H1', H2, H2', H3', H4', H5', H5'', H8, HO2', HO5' |
| I | m | C1', C2, C2', C3', C4, C4', C5, C5', C6, C8, N1, N3, N7, N9, O2', O3', O4', O5', O6, OP1, OP2, P, H1, H1', H2, H2', H3', H4', H5', H5'', H8, HO2' |
| I | 3 | C1', C2, C2', C3', C4, C4', C5, C5', C6, C8, N1, N3, N7, N9, O2', O3', O4', O5', O6, OP1, OP2, P, H1, H1', H2, H2', H3', H4', H5', H5'', H8, HO2', HO3' |
| U | 5 | C1', C2, C2', C3', C4, C4', C5, C5', C6, N1, N3, O2, O2', O3', O4, O4', O5', H1', H2', H3, H3', H4', H5, H5', H5'', H6, HO2', HO5' |
| U | m | C1', C2, C2', C3', C4, C4', C5, C5', C6, N1, N3, O2, O2', O3', O4, O4', O5', OP1, OP2, P, H1', H2', H3, H3', H4', H5, H5', H5'', H6, HO2' |
| U | 3 | C1', C2, C2', C3', C4, C4', C5, C5', C6, N1, N3, O2, O2', O3', O4, O4', O5', OP1, OP2, P, H1', H2', H3, H3', H4', H5, H5', H5'', H6, HO2', HO3' |
---
## Water
Water uses the residue name `HOH` with atoms `O`, `H1`, and `H2`. Both hydrogen atoms have identical charges.
| TIP3P | −0.834 | +0.417 |
| TIP3P-FB | −0.8484 | +0.4242 |
| SPC | −0.82 | +0.41 |
| SPC/E | −0.8476 | +0.4238 |
| OPC3 | −0.8952 | +0.4476 |
---
## Ions
All ions use formal (integer) charges.
### Cations
| +1 | AG, AU, CS, CU1, K, LI, NA, RB, TL |
| +2 | BA, CA, CD, CO, CU, EU, FE2, HG, MG, MN, NI, PB, PD, PT, SR, ZN |
| +3 | 3CO, 3NI, AL, AU3, CE, CR, DY, ER3, EU3, FE, GA, GD3, HO3, IN, IR3, LA, LU, MN3, ND, OS, PR, RH3, RU, SB, SM, TB, V, YB, YT3 |
| +4 | 4MO, IR, OS4, PT4, TH, ZR |
| +6 | 6MO, W |
### Anions
| −1 | BR, CL, F, IOD |