If you choose to store the bond angles for later use (not absolutely necessary, as we'll see), you need a three-dimensional array:
double ***phi = new double** [mol.natom];
for(int i=0; i < mol.natom; i++) {
phi[i] = new double* [mol.natom];
for(int j=0; j < mol.natom; j++) {
phi[i][j] = new double[mol.natom];
}
}