overlay = new ol.Overlay({
  element: container,
  stopEvent: false,
  autoPan: true,
  autoPanMargin: 20,
  autoPanAnimation: {
    duration: 50
  }
});

var mouseOver = false;
function createOverlay(width) {
  container = document.getElementById('popup');
  container.style.width = width;
  container.onmouseover = function() {
    mouseOver = true;   // when cursor is targeting overlay we enable this boolean
  };
  container.onmouseout = function() {
    mouseOver = false;  // and disable when out
  };
  ...
}

map.on("pointerdrag", function(e) {
  if (mouseOver) {
    e.stopPropagation();
    return;
  }
});

map.on("click", function(e) {
  if (mouseOver) {
    return;
  }
  // rest of chart creation logic here
}