you can use fractions like this

.container {
    border: 1px solid black;
    padding-bottom: 25%;
    height: 100%;
    width: auto;
    display: grid;
    grid-gap: 5px;
  grid-template-columns: 1fr 1fr 1fr;
  grid-template-rows: auto;
    /* justify-content: center; */
    justify-items: center;
    align-items: center;

}

.container div {
    width: 100px;
    height: 100px;
}

And the result will be like in the picture.

If you want a more grouped solution, you have to district container to fixe width and Positionate the container to center, or use flex.

OR formate DIV

<div>
    <div class="container">
    <div style="background-color: rgb(87, 217, 93);">1</div>
    <div style="background-color: rgb(227, 84, 18);">2</div>
    <div style="background-color: rgb(230, 73, 115);">3</div>
    <div style="background-color: rgb(0, 255, 255);">4</div>
    <div style="background-color: rgb(221, 245, 7);">5</div>
    <div style="background-color: rgb(227, 84, 18);">6</div>
</div>
</div>

Here:

div{
    margin: 0 auto;
    padding: 0;
    width: 100%;
}

.container {
    border: 1px solid black;
    padding-bottom: 25%;
    width: fit-content;
    display: grid;
    grid-gap: 5px;
  grid-template-columns: 1fr 1fr 1fr;
  grid-template-rows: auto;
    /* justify-content: center; */
    justify-items: center;
    align-items: center;
}

.container div {
    width: 100px;
    height: 100px;
}

I think you want to use justify-content instead of align-content Here’s an example with justify-content:space-between;

EDIT: I figured out what you wanted, its bacuse you were giving your border space with padding only at the bottom and it wasn’t adjusting to it. Change padding-bottom to just padding You’re align-content: center is indeed working. Here look what I did.

.container {
	border: 1px solid black;
	height: 100%;
  padding: 25%;
	display: grid;
	grid-gap: 5px;
	grid-template-columns:repeat(3, 100px);
	grid-template-rows: repeat(2,100px);
	/*justify-content: center;*/
  justify-content: center;
  align-content: center;
}

<div class="container">
	<div style="background-color: rgb(87, 217, 93);">1</div>
	<div style="background-color: rgb(227, 84, 18);">2</div>
	<div style="background-color: rgb(230, 73, 115);">3</div>
	<div style="background-color: rgb(0, 255, 255);">4</div>
	<div style="background-color: rgb(221, 245, 7);">5</div>
	<div style="background-color: rgb(227, 84, 18);">6</div>
  </div>

Now i solved them. Giving padding size isnot working with align-content.
i deleted padding size and gave the div heigh and width.

.container {
	border: 1px solid black;
	height: 100%;
  	/*padding-bottom: 25%;*/
	display: grid;
	grid-gap: 5px;
	grid-template-columns:repeat(3, 100px);
	grid-template-rows: repeat(2,100px);
	/*justify-content: center;*/
  	align-content: end;
  	height: 500px;
  	width: 500px;
}

<div class="container">
	<div style="background-color: rgb(87, 217, 93);">1</div>
	<div style="background-color: rgb(227, 84, 18);">2</div>
	<div style="background-color: rgb(230, 73, 115);">3</div>
	<div style="background-color: rgb(0, 255, 255);">4</div>
	<div style="background-color: rgb(221, 245, 7);">5</div>
	<div style="background-color: rgb(227, 84, 18);">6</div>
  
 </div>

When i used these codes they dont work especially align-content doesnt work for chrome .

.container {
  border: 1px solid black;
  padding-bottom: 25%;
  height: 100%;
  display: grid;
  grid-gap: 5px;
  grid-template-columns:repeat(3, 100px);
  grid-template-rows: repeat(2,100px);
  /* justify-content: center; */
  align-content:center;
}

<div class="container">
  <div style="background-color: rgb(87, 217, 93);">1</div>
  <div style="background-color: rgb(227, 84, 18);">2</div>
  <div style="background-color: rgb(230, 73, 115);">3</div>
  <div style="background-color: rgb(0, 255, 255);">4</div>
  <div style="background-color: rgb(221, 245, 7);">5</div>
  <div style="background-color: rgb(227, 84, 18);">6</div>
</div>