basics of thermodinamics say that a reaction with negative free energy is spontaneous. negative binding free energy values  during Molecular Docking mean that guest is bound tu host

Roughly speaking, positive Gibbs free energy means that no binding is detected between host molecule and its guest.

Reaction spontaneity tells that reactant will react at their own or any external energy source will be required to let them react. Simply negative sign signifies that reaction is going to occur at its own under NTP.  In a docking experiment one usually look for a ligand which can bind easily with desired protein to get post binding effect and that must not involve any third entity (ideally) thats why negative Gibbs Free Energy is preferable for better binding.   

how higher the value of free binding energy, the higher the requested energy to break that binding between two molecules. So, the negative values show a related binding between ligand and protein.

If one was to calculate binding energy based on this equation :

EnergyBinding = EnergyComplex - EnergyLigand - EnergyReceptor

to compare various ligands in terms of tighter binding shall I choose the one with the most negative binding energy or the one with lowest free energy of the complex. Lets say I have 3 ligands : Ligand 1 , Ligand 2, and Ligand 3, where ligand 1 had the most negative EnergyBinding followed by Ligand 2 and finally Ligand 3. However when complexed with ligand 3, the whole complex yields lower energyComplex than either ligand 1 or ligand 2. Which one shall i count on ? Energy of binding or total complex energy ? 

Entropy: A concept that is not a physical quantity

https://www.researchgate.net/publication/230554936_Entropy_A_concept_that_is_not_a_physical_quantity

Se relaciona con el grado de favorabilidad que tiene el ligando de relacionarse con el receptor y esta de ser espontanea. puede ser debil intermedia o fuerte, generalmente mayor a -18 es fuerte y entre 0y -4 es debil.

Why is the binding of DNA and protein sometimes observed to be positive? Is it because the binding is temporary?

In analogy with any spontaneous process, protein–ligand binding occurs only when the change in Gibbs free energy (ΔG) of the system is negative when the system reaches an equilibrium state at constant pressure and temperature. Because the protein–ligand association extent is determined by the magnitude of the negative ΔG, it can be considered that ΔG determines the stability of any given protein–ligand complex, or, alternatively, the binding affinity of a ligand to a given acceptor. It should be noted that the free energy is a function of the states of a system and, as thus, ΔG are defined merely by the initial and final thermodynamic states, regardless of the pathway connecting these two states.