The current hydrogen bond specifications are given in the list box - edit the variables for the selected specification in the edit boxes on the right.
If the Hydrogen bonds box in the Generate Bonds dialog is checked these specification will be used to set up bonds for atoms involved in hydrogen bonding. As ATOMS considers each possible pair of atoms in the input list, it will test the type numbers against those in this list
If one member of the pair has type number 1 (hydrogen), 99 (deuterium) or 98 (tritium), and the other member of the pair has one of the type numbers in this list, hydrogen bonds will be set up. If both members of the pair have type numbers indicating hydrogen, no bonds at all will be set up. Note that atomic numbers in this list (non-hydrogen) do not need to be atomic numbers, but hydrogen itself (and deuterium and tritium) must have the default atomic numbers.
Two separate input bonds will be set up for each hydrogen-other pair: a short or strong bond in which the other (the atom in this list) is the hydrogen donor in a hydrogen bond; and a long bond or hydrogen bond itself in which the other atom is the acceptor. For normal, strong (non hydrogen) bonds between H and the other atom, the minimum distance is 0.2 Angstroms and the maximum bond distance is the minimum distance (Min) in this table. For hydrogen bonds between H and the other atom, the minimum bond distance is the minimum distance in this table and the maximum bond distance is the maximum distance (Max) in this table. That is, the Min value is the boundary between donor bonds and acceptor bonds, and the Max distance is the longest possible acceptor bond.
The Intermol (Intermolecular) flag determines whether bonds will be considered to be intermolecular (see Bond Data dialog) for purposes of locating molecules.
Any input bond specifications set up with this option can always be edited through the Input Bonds dialog.