@<TRIPOS>ATOM
Each data record associated with this RTI consists of a single data line. This data line contains all the information necessary to reconstruct one atom contained within the molecule. The atom ID numbers associated with the atoms in the molecule will be assigned sequentially when the .mol2 file is read into SYBYL.
Format:
atom_id atom_name x y z atom_type [subst_id [subst_name [charge [status_bit]]]]
- atom_id (integer) = the ID number of the atom at the time the file was created. This is provided for reference only and is not used when the .mol2 file is read into SYBYL.
- atom_name (string) = the name of the atom.
- x (real) = the x coordinate of the atom.
- y (real) = the y coordinate of the atom.
- z (real) = the z coordinate of the atom.
- atom_type (string) = the SYBYL atom type for the atom.
- subst_id (integer) = the ID number of the substructure containing the atom.
- subst_name (string) = the name of the substructure containing the atom.
- charge (real) = the charge associated with the atom.
- status_bit (string) = the internal SYBYL status bits associated with the atom. These should never be set by the user. Valid status bits are DSPMOD, TYPECOL, CAP, BACKBONE, DICT, ESSENTIAL, WATER and DIRECT.
Example:
1 CA -0.149 0.299 0.000 C.3 1 ALA1 0.000 BACKBONE|DICT|DIRECT
1 CA -0.149 0.299 0.000 C.3
In the first example the atom has ID number 1. It is named CA and is located at (-0.149, 0.299, 0.000). Its atom type is C.3. It belongs to the substructure with ID 1 which is named ALA1. The charge associated with the atom is 0.000 and the SYBYL status bits associated with the atom are BACKBONE, DICT, and DIRECT. Example two is the minimal information necessary for the MOL2 command to create an atom.
