Table 3. Atom Types (or, Equivalently, EE Types) of the Force Fielda.
| atom type (EE type) | LJ type | usage |
|---|---|---|
| Aliphatic Carbon (United) Atoms | ||
| CH0 | CH0 | CH0 carbon atom (methanetetryl group) |
| CH1 | CH1 | CH1 carbon united atom (methanetriyl group) |
| CH2 | CH2 | CH2 carbon united atom (methylene group) |
| CH3 | CH3 | CH3 carbon united atom (methyl group) |
| CH4 | CH4 | CH4 carbon united atom (methane group) |
| Halogen | ||
| F_hal | F | fluorine atom |
| Cl_hal | Cl | chlorine atom |
| Br_hal | Br | bromine atom |
| I_hal | I | iodine atom |
| CH0_hal | CH0 | halogenated CH0 atom |
| CH1_hal | CH1 | halogenated CH1 united atom |
| CH2_hal | CH2 | halogenated CH2 united atom |
| CH3_hal | CH3 | halogenated CH3 united atom |
| Ether | ||
| O_eth | OC | ether oxygen atom |
| CH0_O_eth | CH0 | alkoxylated CH0 atom |
| CH1_O_eth | CH1 | alkoxylated CH1 united atom |
| CH2_O_eth | CH2 | alkoxylated CH2 united atom |
| CH3_O_eth | CH3 | alkoxylated CH3 united atom |
| Aldehyde | ||
| H_CO_ald | HC | aldehyde hydrogen atom |
| C_ald | C=O | aldehyde carbonyl carbon atom |
| O_ald | O=C | aldehyde carbonyl oxygen atom |
| Ketone | ||
| C_ket | C=O | ketone carbonyl carbon atom |
| O_ket | O=C | ketone carbonyl oxygen atom |
| Ester | ||
| H_CO_est | HC | formate ester hydrogen atom |
| C_est | C=O | ester carbonyl carbon atom |
| O_est | O=C | ester carbonyl oxygen atom |
| O_C_est | OC | ester acylated oxygen atom |
| CH0_O_est | CH0 | ester oxygen-linked CH0 atom |
| CH1_O_est | CH1 | ester oxygen-linked CH1 united atom |
| CH2_O_est | CH2 | ester oxygen-linked CH2 united atom |
| CH3_O_est | CH3 | ester oxygen-linked CH3 united atom |
| Alcohol | ||
| H_ol | HB | hydroxyl hydrogen atom |
| O_ol | OH | hydoxyl oxygen atom |
| CH0_O_ol | CH0 | hydroxylated CH0 atom |
| CH1_O_ol | CH1 | hydroxylated CH1 united atom |
| CH2_O_ol | CH2 | hydroxylated CH2 united atom |
| CH3_O_ol | CH3 | hydroxylated CH3 united atom |
| Carboxylic Acid | ||
| H_CO_acd | HC | formic acid hydrogen atom |
| C_acd | C = O | carboxylic acid carbonyl carbon atom |
| O_acd | O = C | carboxylic acid carbonyl oxygen atom |
| H_O_acd | HB | carboxylic acid hydroxyl hydrogen atom |
| O_H_acd | OH | carboxylic acid hydroxyl oxygen atom |
| Amine | ||
| H_N_amn | HB | amine hydrogen atom |
| N_amn | N_amn | amine nitrogen atom |
| CH0_N_amn | CH0 | aminated CH0 atom |
| CH1_N_amn | CH1 | aminated CH1 united atom |
| CH2_N_amn | CH2 | aminated CH2 united atom |
| CH3_N_amn | CH3 | aminated CH3 united atom |
| Amide | ||
| H_N_amd | HB | amide nitrogen-linked hydrogen atom |
| C_amd | C = O | amide carbonyl carbon atom |
| O_amd | O = C | amide carbonyl oxygen atom |
| N_amd | N_amd | amide acylated nitrogen atom |
| CH0_N_amd | CH0 | amide nitrogen-linked CH0 atom (estimated) |
| CH1_N_amd | CH1 | amide nitrogen-linked CH1 united atom |
| CH2_N_amd | CH2 | amide nitrogen-linked CH2 united atom |
| CH3_N_amd | CH3 | amide nitrogen-linked CH3 united atom |
a
The Natt = 56 atom types (or, equivalently, NattEE = 56 EE types) are listed, along with their usage and the associated LJ type (referring to the entries of Table 4). Initial (optimization start) and final (after optimization) values for these parameters can be found in Tables S.9 and S.7, respectively, in the Supporting Information.