I am not asking about ionic bonds. I am in this case asking about covalent bonds.
I have read this question:
Why do atoms repel when closer but attract when farther apart?
Where Swike says:
So, from where is this repulsive force coming? Well, it turns out that if you play enough with the mathematical foundations of quantum mechanics you arrive to the idea of Pauli exclusion. Therefore what exactly means that two electrons can't occupy the same place? Well, as it turns out it means that there is a repulsion between them that is proportional to the overlapping of the spreads of their existence. The repulsive force due to Pauli exclusion is what emerges when you try to get two electron clouds (the regions where the electrons are primarily existing) closer together.
I do understand that the PEP plays a role in the atoms' repulsion (so they cannot get too close) inside the molecule.
But this view is assuming that the original atoms before they entered the covalent bond (that were EM neutral) are the same atoms, with the same electron configuration inside the molecule.
Now the molecules share the valence electron shell's atoms when they enter the covalent bond and form a molecule.
But when they do that, they do something else too, they change their own electron configuration, to make the bond more stable, and the total energy of the molecule becomes smaller, the total electron configuration becomes more effective.
Now by doing that, the individual atoms' valence electron shells will become common, existing around the whole molecule as per QM.
Now this way, the individual atoms' electron configuration has changed. This will mean too, that (assuming they were EM neutral before the bond), they cannot be EM neutral as individual atoms when looking at them from inside the molecule.
If you look at each individual atom inside the molecule, these atoms' inner shells (specifically the most outer remaining inner shell) will be the one electron shells that will create the PEP repulsion.
Now but since these individual atoms (when looking at them inside the molecule), are not EM neutral anymore (since they now share some valence electrons, and they partially lost those negative charges), they must act like individual negative charges on their own inside the molecule (surrounded by a common valence shell).
So as I understand it, the repulsive force that counterbalances the attractive force of the bond itself (which comes from the QM phenomenon of van der waals and London forces) created by the sharing of some valence electrons, must be some part PEP and some part EM repulsion.
So the forces that act and create the bond:
attractive force, QM phenomenon, sharing of valence electrons, van der waals and London forces
EM repulsion between the individual (now not anymore EM neutral) inner atoms inside the molecule
Is this correct, does the repulsion inside the molecule between the individual atoms come from part PEP and part EM repulsion or just PEP?
Are the individual atoms inside the molecule still really EM neutral (after sharing valence electrons and changing their own electron configuration)?