Table 2. Summary of 41 Functional Groups Used in the JR method and Their Corresponding SMARTS Codes Used in JRgui Program9,15,22a.
| nonring increments | ring increments | halogen increments | |||
|---|---|---|---|---|---|
| –CH3 | [CX4H3] | –CH2– | [R;CX4H2] | –F | [F] |
| –CH2– | [!R;CX4H2] | >CH– | [R;CX4H] | –Cl | [Cl] |
| >CH– | [!R;CX4H] | >C< | [R;CX4H0] | –Br | [Br] |
| >C< | [!R;CX4H0] | =CH– | [R;CX3H1,cX3H1] | –I | [I] |
| =CH2 | [CX3H2] | =C< | [$([R;#6X3H0]);!$([R;#6X3H0]=[#8])] | ||
| =CH– | [!R;CX3H1;!$([CX3H1](=O))] | ||||
| =C< | [$([!R;#6X3H0]);!$([!R;#6X3H0]=[#8])] | ||||
| =C= | [$([CX2H0](=*)=*)] | ||||
| #CH | [$([CX2H1]#[!#7])] | ||||
| #C– | [$([CX2H0]#[!#7])] | ||||
| oxygen increments | nitrogen increments | sulfur increments | |||
|---|---|---|---|---|---|
| –OH (alcohol) | [OX2H;!$([OX2H]-[#6]=[O]);!$([OX2H]-a)] | –NH2 | [NX3H2] | –SH | [SX2H] |
| –OH (phenol) | [O;H1;$(O-!@c)] | >NH (nonring) | [NX3H1;!R] | –S– (nonring) | [#16X2H0;!R] |
| –O– (nonring) | [OX2H0;!R;!$([OX2H0]-[#6]=[#8])] | >NH (ring) | [#7X3H1;R] | –S– (ring) | [#16X2H0;R] |
| –O– (ring) | [#8X2H0;R;!$([#8X2H0]∼[#6]=[#8])] | >N– (nonring) | [#7X3H0;!$([#7](∼O)∼O)] | ||
| >C=O (nonring) | [$([CX3H0](=[OX1]));!$([CX3](=[OX1])-[OX2]);!R]=O | –N= (nonring) | [#7X2H0;!R] | ||
| >C=O (ring) | [$([#6X3H0](=[OX1]));!$([#6X3](=[#8X1])∼[#8X2]);R]=O | –N= (ring) | [#7X2H0;R] | ||
| O#CH– (aldehyde) | [CH;D2;$(C-!@C)](=O) | =NH | [#7X2H1] | ||
| –COOH (acid) | [OX2H]-[C]=O | –CN | [#6X2]#[#7X1H0] | ||
| –COO– (ester) | [#6X3H0;!$([#6X3H0](∼O)(∼O)(∼O))](=[#8X1])[#8X2H0] | –NO2 | [$([#7X3,#7X3+][!#8])](=[O])∼[O-] | ||
| =O (except as above) | [OX1H0;!$([OX1H0]∼[#6X3]);!$([OX1H0]∼[#7X3]∼[#8])] | ||||
a
The codes are double-checked by visualizing them via online tool SMARTSviewer at Center for Bioinformatics at University of Hamburg.23