I’d like to change the substituent group of the molecule to other one and reorder the index because I want to connect the index continuously after changing of the substituent group. But I cannot find the option that can rearrange the index. I used ‘Edit - Reindex Atoms’ in IQmol but it was not effective. Are there any tools to make it more convenient? Should I draw the whole structure of the molecule again?
You may need to redraw the whole structure. I sometimes use MolDen to do similar things, as it has the option to point and click and define the order of the atoms (and also has a Z-matrix editor, which is helpful for small molecules). You can get XYZ coordinates into a MolDen-formatted output file by running some trivial (low-cost) job and setting MOLDEN_FORMAT=TRUE in $rem. MolDen-formatted input file appears at the end of the Q-Chem output file, needs to be extracted and saved to separate file (i.e., don’t try to get MolDen to read the Q-Chem output file).