Hydrogens and valence

Molecular structures with unusual valences are allowed although some restrictions are applied:

molecule is rejected if the 'Reject molecules with unusual valence' option is enabled in the general settings.
missing hydrogens can be automatically added if the option 'Add 2D hydrogens' is enabled in the general settings. In this case, only descriptors not depending on the atomic spatial coordinates can be calculated. This is due to the fact that, if hydrogens are lacking, Dragon implements an automatic H-add procedure based on the usual valences of atoms, but the coordinates of the added hydrogens are not known. Note that when the 'Add 2D hydrogens' option is enabled, unusual valences of atoms will be corrected by hydrogen addition to make up the rest of common valence and this may affect the final descriptor values. Whenever molecules are entered as SMILES notations, hydrogens are automatically added where they are not explicitly specified regardless of the option 'Add 2D hydrogens' has been checked.


The lowest normal valences of common atoms are:

H (1), B (3), C (4), N-P-As (3, 5), O (2), aliphatic S-Se (2, 4, 6), halogens-Li (1).


Aromatic S donating a lone pair is assigned a formal valence of 3 or 5. A three-connected N (or P) with a valence of 4, i.e. pyridyl N, must be specified by a formal positive charge N+.