N which
signifies that the database is in version 3.0 format; the next line contains
the reference code, the number of heavy (nonhydrogen) atoms, the number of
hydrogens, the number of charges (currently assumed to equal the total number
of atoms), and the number of flagged atoms (format A9,4I3); next are the vdw
types of the atoms (reusable format 40I2); next are the integerized charges
(reusable format 16I5); next are the flagged atom listings, if any (reusable
format 20I4); finally, the integerized coordinates of the atoms are given
(reusable format 16I5). The coordinates are generated by translation to the
positive quadrant, multiplication by 1000, and rounding to the nearest integer.
The first three numbers are the coordinates for the first heavy atom, the next
three are for the second heavy atom, and so on. The hydrogen coordinates are
listed after the heavy atom coordinates.
For an example molecule, see here.