IsomericSMILES -> Chem.Mol -> CanonicalSMILES wrong result when `sanitize=True`

SMILES.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from rdkit import Chem"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "original: CN1CCN(C(=O)O[C@H]2c3nccnc3C(=O)N2c2ccc(Cl)cn2)CC1\n"
     ]
    }
   ],
   "source": [
    "smiles = 'CN1CCN(CC1)C(=O)O[C@H]2C3=NC=CN=C3C(=O)N2C4=NC=C(C=C4)Cl'\n",
    "smiles = Chem.MolToSmiles(Chem.MolFromSmiles(smiles))\n",
    "print('original:', smiles)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "can1: CN1CCN(CC1)C(=O)OC1c2nccnc2C(=O)N1c1ccc(Cl)cn1\n"
     ]
    }
   ],
   "source": [
    "mol1 = Chem.MolFromSmiles(smiles, sanitize=False)\n",
    "can1 = Chem.MolToSmiles(mol1, isomericSmiles=False, canonical=True)\n",
    "print('can1:', can1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "can2: CN1CCN(C(=O)OC2c3nccnc3C(=O)N2c2ccc(Cl)cn2)CC1\n"
     ]
    }
   ],
   "source": [
    "mol2 = Chem.MolFromSmiles(smiles, sanitize=True)\n",
    "can2 = Chem.MolToSmiles(mol2, isomericSmiles=False, canonical=True)\n",
    "print('can2:', can2)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "ename": "AssertionError",
     "evalue": "",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mAssertionError\u001b[0m                            Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-5-13a40edd7147>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0;32massert\u001b[0m \u001b[0mcan1\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0mcan2\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[0;31mAssertionError\u001b[0m: "
     ]
    }
   ],
   "source": [
    "assert can1 == can2"
   ]
  }
 ],
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