vmd

 set t1 [atomselect top {
    
    type 1}]
 set t2 [atomselect top {
    
    type 2}]
 set t3 [atomselect top {
    
    type 3}]
 set t4 [atomselect top {
    
    type 4}]
 set t5 [atomselect top {
    
    type 5}]

$t1 set name si 
$t2 set name o 
$t3 set name h
$t4 set name h
$t5 set name o

set silica [atomselect top {
    
    type 1 and type 2}]
set water [atomselect top {
    
    type 3 and type 4 and type 5}]

within 5 of {
    
    type 1 or type 2}

type 3 or type 4 or type 5