Firstly the two points are completely disconnected: A 'thing' and a 'human' are two different topics. It is a comparison as if you wrote a piece of code on a web application and someone comes and asks why is this optical drive not working when I hit print on the web page.
Only humans and no other species (living) have the ability to choose between right and wrong. One might argue that an animal say dog can choose, indeed a dog might love it's owner but when the owner holds a gun to shoot someone, a dog cannot decide if it is right or wrong, or when the owner wrestles with other person, the dog will inherently try to help the owner regardless of who is right or wrong.
Coming to the point of even an atom does not move without the permission of Allah, yes, it is like a program that Allah swt wrote with hardcoded values. From a thing to all living things except humans are pre-programmed with hardcoded values. The functions are different for each but every single one of them has fixed attributes.
Humans are dynamic. They have the ability to choose between right and wrong. There are morals, ethics and rules that govern the human society.
This is what Prophet Mohammed sws has to say about it and there cannot be a better explanation:
All reported: We were in a funeral in the graveyard of Gharqad that
Allah's Messenger (may peace be upon him) came to us and we sat around
him. He had a stick with him. He lowered his head and began to scratch
the earth with his stick, and then raid: There is not one amongst you
whom a scat in Paradise or Hell has not been allotted and about whom
it has not been written down whether he would be an evil person or a
blessed person. A person said: Allah's Messenger, should we not then
depend npon our destiny and abandon our deeds? Thereupon he said: Acts
of everyone will be facilitated in, that which has been created for
him so that whoever belongs to the com. pany of the blessed will have
good works made easier for himand whoever belongs to the unfortunate
ones will have evil acts made easier for him. He then recited this
verse (from the Qur'an):" Then, who gives to the needy and
guardsagainst evil and accepts the excellent (the truth of Islam and
the path of righteousness it prescribes), We shall make easy for him
the easy end and who is miserly and considers himself above need, We
shall make easy for him the dificult end". (XCii. 5-10).
-Sahih Muslim Book 033, Number 6398:
Another good read: Is man’s fate pre-destined or does he have freedom of will?
And Allah knows best.