| Atom | Functional group | Atom type | Description | Frequency |
| C | Alkane | C1a | R-CH3 | 16473 |
| C1b | R-CH2-R | 20193 | ||
| C1c | R-CH(-R)-R | 4964 | ||
| C1d | R-C(-R)2-R | 698 | ||
| Cyclic alkane | C1x | ring-CH2-ring | 14010 | |
| C1y | ring-CH(-R)-ring | 27376 | ||
| C1z | ring-C(-R)2-ring | 4463 | ||
| Alkene | C2a | R=CH2 | 634 | |
| C2b | R=CH-R | 3965 | ||
| C2c | R=C(-R)2 | 1914 | ||
| Cyclic alkene | C2x | ring-CH=ring | 2964 | |
| C2y | ring-C(-R)=ring or ring-C(=R)-ring | 3722 | ||
| Alkyne | C3a | R≡CH | 43 | |
| C3b | R≡C-R | 282 | ||
| Aldehyde | C4a | R-CH=O | 350 | |
| Ketone | C5a | R-C(=O)-R | 3595 | |
| Cyclic ketone | C5x | ring-C(=O)-ring | 2257 | |
| Carboxylic acid | C6a | R-C(=O)-OH | 3190 | |
| Carboxylic ester | C7a | R-C(=O)-O-R | 1691 | |
| C7x | ring-C(=O)-O-ring | 869 | ||
| Aromatic ring | C8x | ring-CH=ring | 19905 | |
| C8y | ring-C(-R)=ring | 20511 | ||
| Undefined C | C0 | 8 | ||
| N | Amine | N1a | R-NH2 | 2440 |
| N1b | R-NH-R | 3003 | ||
| N1c | R-N(-R)2 | 374 | ||
| N1d | R-N(-R)3+ | 105 | ||
| Cyclic amine | N1x | ring-NH-ring | 806 | |
| N1y | ring-N(-R)-ring | 1464 | ||
| Imine | N2a | R=N-H | 230 | |
| N2b | R=N-R | 163 | ||
| Cyclic imine | N2x | ring-N=ring | 357 | |
| N2y | ring-N(-R)+=ring | 14 | ||
| Cyan | N3a | R≡N | 119 | |
| Aromatic ring | N4x | ring-NH-ring | 785 | |
| N4y | ring-N(-R)-ring | 840 | ||
| N5x | ring-N=ring | 2131 | ||
| N5y | ring-N(-R)+=ring | 59 | ||
| Undefined N | N0 | 194 | ||
| O | Hydroxy | O1a | R-OH | 18369 |
| O1b | N-OH | 198 | ||
| O1c | P-OH | 3111 | ||
| O1d | S-OH | 332 | ||
| Ether | O2a | R-O-R | 4199 | |
| O2b | P-O-R | 2481 | ||
| O2c | P-O-P | 502 | ||
| O2x | ring-O-ring | 5853 | ||
| Oxo | O3a | N=O | 134 | |
| O3b | P=O | 2248 | ||
| O3c | S=O | 941 | ||
| Aldehyde | O4a | R-CH=O | 350 | |
| Ketone | O5a | R-C(=O)-R | 3595 | |
| O5x | ring-C(=O)-ring | 2862 | ||
| Carboxylic acid | O6a | R-C(=0)-OH | 6384 | |
| Ester | O7a | R-C(=O)-O-R | 3382 | |
| O7x | ring-C(=O)-O-ring | 1738 | ||
| Undefined O | O0 | 127 | ||
| S | Thiol | S1a | R-SH | 100 |
| Thioether | S2a | R-S-R | 420 | |
| S2x | ring-S-ring | 261 | ||
| Disulfide | S3a | R-S-S-R | 45 | |
| S3x | ring-S-S-ring | 48 | ||
| Sulfate | S4a | R-SO3 | 267 | |
| Undefined S | S0 | 223 | ||
| P | Attatched to other elements | P1a | P-R | 112 |
| Attatched to oxygen | P1b | P-O | 2158 | |
| Other | Halogens | X | F, Cl, Br, I | 1419 |
| Others | Z | 261 | ||