diff --git a/abfe_tutorial/abfe_analysis.ipynb b/abfe_tutorial/abfe_analysis.ipynb
index 9d5738a..9ba2ee1 100644
--- a/abfe_tutorial/abfe_analysis.ipynb
+++ b/abfe_tutorial/abfe_analysis.ipynb
@@ -33,32 +33,24 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "--2025-10-21 11:53:17--  https://zenodo.org/records/17348229/files/abfe_results.zip\n",
-      "Resolving zenodo.org (zenodo.org)... 188.185.45.92, 188.185.43.25, 188.185.48.194, ...\n",
-      "Connecting to zenodo.org (zenodo.org)|188.185.45.92|:443... connected.\n",
-      "HTTP request sent, awaiting response... 200 OK\n",
-      "Length: 1005319 (982K) [application/octet-stream]\n",
-      "Saving to: ‘abfe_results.zip’\n",
-      "\n",
-      "abfe_results.zip    100%[===================>] 981.76K   718KB/s    in 1.4s    \n",
-      "\n",
-      "2025-10-21 11:53:20 (718 KB/s) - ‘abfe_results.zip’ saved [1005319/1005319]\n",
-      "\n",
+      "  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current\n",
+      "                                 Dload  Upload   Total   Spent    Left  Speed\n",
+      "100 3092k  100 3092k    0     0   897k      0  0:00:03  0:00:03 --:--:--  897k\n",
       "Archive:  abfe_results.zip\n",
-      "   creating: abfe_results/\n",
-      "   creating: abfe_results/results_2/\n",
-      "  inflating: abfe_results/toluene_results.json  \n",
-      "   creating: abfe_results/results_1/\n",
-      "   creating: abfe_results/results_0/\n",
-      "  inflating: abfe_results/results_2/1.json  \n",
-      "  inflating: abfe_results/results_1/1.json  \n",
-      "  inflating: abfe_results/results_0/1.json  \n"
+      "  inflating: abfe_results/README.md  \n",
+      "  inflating: abfe_results/abfe_results_single_unit/results_2/1.json  \n",
+      "  inflating: abfe_results/abfe_results_single_unit/toluene_results.json  \n",
+      "  inflating: abfe_results/abfe_results_single_unit/results_1/1.json  \n",
+      "  inflating: abfe_results/abfe_results_single_unit/results_0/1.json  \n",
+      "  inflating: abfe_results/abfe_results_multiple_units/results_2/ligand1_transformation.json  \n",
+      "  inflating: abfe_results/abfe_results_multiple_units/results_1/ligand1_transformation.json  \n",
+      "  inflating: abfe_results/abfe_results_multiple_units/results_0/ligand1_transformation.json  \n"
      ]
     }
    ],
    "source": [
-    "!wget https://zenodo.org/records/17348229/files/abfe_results.zip\n",
-    "!unzip abfe_results.zip"
+    "!curl -O https://zenodo.org/records/19498687/files/abfe_results.zip\n",
+    "!unzip -o abfe_results.zip"
    ]
   },
   {
@@ -108,6 +100,38 @@
   {
    "cell_type": "code",
    "execution_count": 3,
+   "id": "08afcbcf-34a8-4450-a967-eb4ed5800ee1",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def _get_name(result: dict) -> str:\n",
+    "    \"\"\"Get the ligand name from a unit's results data.\n",
+    "\n",
+    "    Parameters\n",
+    "    ----------\n",
+    "    result : dict\n",
+    "        A results dict.\n",
+    "\n",
+    "    Returns\n",
+    "    -------\n",
+    "    str\n",
+    "        Ligand name corresponding to the results.\n",
+    "    \"\"\"\n",
+    "\n",
+    "    solvent_data = list(result[\"protocol_result\"][\"data\"][\"solvent\"].values())[0][0]\n",
+    "    try:\n",
+    "        name = solvent_data[\"inputs\"][\"setup_results\"][\"inputs\"][\"alchemical_components\"][\"stateA\"][\n",
+    "            0\n",
+    "        ][\"molprops\"][\"ofe-name\"]\n",
+    "    except KeyError:\n",
+    "        name = solvent_data[\"inputs\"][\"alchemical_components\"][\"stateA\"][0][\"molprops\"][\"ofe-name\"]\n",
+    "\n",
+    "    return str(name)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
    "id": "04ccdedd-84e3-4ccc-ae42-4f3772acb115",
    "metadata": {},
    "outputs": [],
@@ -153,14 +177,16 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 5,
    "id": "3733c540-de62-45a0-ba66-268397a38b49",
    "metadata": {},
    "outputs": [],
    "source": [
+    "\n",
+    "\n",
     "def _get_legs_from_result_jsons(\n",
-    "    result_fns: list[pathlib.Path]\n",
-    ") -> dict[tuple[str, str], dict[str, list]]:\n",
+    "    result_fns: list[pathlib.Path],\n",
+    ") -> dict[str, dict[str, list]]:\n",
     "    \"\"\"\n",
     "    Iterate over a list of result JSONs and populate a dict of dicts with all data needed\n",
     "    for results processing.\n",
@@ -175,8 +201,8 @@
     "\n",
     "    Returns\n",
     "    -------\n",
-    "    legs: dict[str,,dict[str, list]]\n",
-    "        Data extracted from the given result JSONs, organized by the ligand name and simulation type.\n",
+    "    legs: dict[str, dict[str, list]]\n",
+    "        Data extracted from the given result JSONs, organized by the leg's ligand name and simulation type.\n",
     "    \"\"\"\n",
     "    from collections import defaultdict\n",
     "\n",
@@ -187,66 +213,42 @@
     "        if name is None:  # this means it couldn't find name and/or simtype\n",
     "            continue\n",
     "\n",
-    "        dgs[name]['overall'].append([result[\"estimate\"], result[\"uncertainty\"]])\n",
-    "        proto_key = [\n",
-    "                k\n",
-    "                for k in result[\"unit_results\"].keys()\n",
-    "                if k.startswith(\"ProtocolUnitResult\") \n",
-    "            ]\n",
+    "        dgs[name][\"overall\"].append([result[\"estimate\"], result[\"uncertainty\"]])\n",
+    "        proto_key = [k for k in result[\"unit_results\"].keys() if k.startswith(\"ProtocolUnitResult\")]\n",
     "        for p in proto_key:\n",
+    "            # In openfe v1.9+, we only want to pick up results from\n",
+    "            # the Analysis Unit. To ensure backwards compatibility with\n",
+    "            # prior releases of openfe v1.x, we exclude Setup and Simulation\n",
+    "            if (\n",
+    "                \"Setup\" in result[\"unit_results\"][p][\"source_key\"]\n",
+    "                or \"Simulation\" in result[\"unit_results\"][p][\"source_key\"]\n",
+    "            ):\n",
+    "                continue\n",
     "            if \"unit_estimate\" in result[\"unit_results\"][p][\"outputs\"]:\n",
     "                simtype = result[\"unit_results\"][p][\"outputs\"][\"simtype\"]\n",
     "                dg = result[\"unit_results\"][p][\"outputs\"][\"unit_estimate\"]\n",
     "                dg_error = result[\"unit_results\"][p][\"outputs\"][\"unit_estimate_error\"]\n",
-    "                \n",
+    "\n",
     "                dgs[name][simtype].append([dg, dg_error])\n",
     "            if \"standard_state_correction\" in result[\"unit_results\"][p][\"outputs\"]:\n",
     "                corr = result[\"unit_results\"][p][\"outputs\"][\"standard_state_correction\"]\n",
-    "                dgs[name][\"standard_state_correction\"].append([corr, 0*unit.kilocalorie_per_mole])\n",
+    "                # In openfe v1.9+, standard state corrections are set to 0 kcal/mol\n",
+    "                # when no correction is being applied (e.g. no restraints).\n",
+    "                # To make raw outputs similar to pre-v1.9, we exclude corrections\n",
+    "                # if they are close to 0.\n",
+    "                if not np.isclose(corr.m, 0):\n",
+    "                    dgs[name][\"standard_state_correction\"].append(\n",
+    "                        [corr, 0 * unit.kilocalorie_per_mole]\n",
+    "                    )\n",
     "            else:\n",
     "                continue\n",
-    "\n",
-    "    return dgs"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 5,
-   "id": "08afcbcf-34a8-4450-a967-eb4ed5800ee1",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "def _get_name(result:dict) -> str:\n",
-    "    \"\"\"Get the ligand name from a unit's results data.\n",
-    "\n",
-    "    Parameters\n",
-    "    ----------\n",
-    "    result : dict\n",
-    "        A results dict.\n",
-    "\n",
-    "    Returns\n",
-    "    -------\n",
-    "    str\n",
-    "        Ligand name corresponding to the results.\n",
-    "    \"\"\"\n",
-    "    try:\n",
-    "        nm = list(result['unit_results'].values())[0]['name']\n",
-    "\n",
-    "    except KeyError:\n",
-    "        raise ValueError(\"Failed to guess name\")\n",
-    "\n",
-    "    toks = nm.split('Binding, ')\n",
-    "    if 'solvent' in toks[1]:\n",
-    "        name = toks[1].split(' solvent')[0]\n",
-    "    if 'complex' in toks[1]:\n",
-    "        name = toks[1].split(' complex')[0]\n",
-    "    return name"
+    "    return dgs\n"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 6,
-   "id": "a5d4aef3-1fab-40b4-848c-d59df8ee1441",
+   "id": "0621e3a2-7906-4661-a640-c414456f8869",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -254,16 +256,8 @@
     "    \"\"\"\n",
     "    Calculate the error of the estimate as the std of the repeats\n",
     "    \"\"\"\n",
-    "    return np.std([v[0].m for v in r[\"overall\"]])"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 7,
-   "id": "0621e3a2-7906-4661-a640-c414456f8869",
-   "metadata": {},
-   "outputs": [],
-   "source": [
+    "    return np.std([v[0].m for v in r[\"overall\"]])\n",
+    "    \n",
     "def _error_mbar(r):\n",
     "    \"\"\"\n",
     "    Calculate the error of the estimate using the reported MBAR errors.\n",
@@ -291,7 +285,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 7,
    "id": "5821b7f7-6aed-4138-9502-44df3af52647",
    "metadata": {},
    "outputs": [],
@@ -304,7 +298,7 @@
     "\n",
     "    Parameters\n",
     "    ----------\n",
-    "    results_files : list[ps.PathLike | str]\n",
+    "    results_files : list[os.PathLike]\n",
     "        A list of directors with ABFE result files to process.\n",
     "\n",
     "    Returns\n",
@@ -314,6 +308,7 @@
     "    \"\"\"\n",
     "    # find and filter result jsons\n",
     "    result_fns = _collect_result_jsons(results_files)\n",
+    "\n",
     "    # pair legs of simulations together into dict of dicts\n",
     "    sim_results = _get_legs_from_result_jsons(result_fns)\n",
     "\n",
@@ -322,7 +317,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 8,
    "id": "e021b2ea-db13-4e47-a6d1-cf5229b5b494",
    "metadata": {},
    "outputs": [],
@@ -363,7 +358,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 9,
    "id": "b077c4e2-373a-4314-a527-186bb4683262",
    "metadata": {},
    "outputs": [],
@@ -418,35 +413,13 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 10,
    "id": "7bc49c0e-6fec-409c-a01c-42c35f57dcc6",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/home/ialibay/software/mambaforge/install/envs/openfe/lib/python3.12/site-packages/openmoltools/utils.py:9: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.\n",
-      "  from pkg_resources import resource_filename\n",
-      "/home/ialibay/software/mambaforge/install/envs/openfe/lib/python3.12/site-packages/Bio/Application/__init__.py:39: BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated.\n",
-      "\n",
-      "Due to the on going maintenance burden of keeping command line application\n",
-      "wrappers up to date, we have decided to deprecate and eventually remove these\n",
-      "modules.\n",
-      "\n",
-      "We instead now recommend building your command line and invoking it directly\n",
-      "with the subprocess module.\n",
-      "  warnings.warn(\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "# Specify paths to result directories\n",
-    "results_dir = [\n",
-    "    pathlib.Path(\"abfe_results/results_0\"),\n",
-    "    pathlib.Path(\"abfe_results/results_1\"),\n",
-    "    pathlib.Path(\"abfe_results/results_2\"),\n",
-    "]\n",
+    "results_dir = [pathlib.Path(\"abfe_results/abfe_results_multiple_units\")]\n",
     "dgs = extract_results_dict(results_dir)"
    ]
   },
@@ -463,7 +436,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 11,
    "id": "46996a74-709c-41f2-ac39-0f77fb33371e",
    "metadata": {},
    "outputs": [],
@@ -474,7 +447,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
+   "execution_count": 12,
    "id": "d1a6ad61-1e5a-4d8a-9067-9ed428ef145c",
    "metadata": {},
    "outputs": [
@@ -508,8 +481,8 @@
        "    <tr>\n",
        "      <th>0</th>\n",
        "      <td>1</td>\n",
-       "      <td>-18.36</td>\n",
-       "      <td>0.98</td>\n",
+       "      <td>-20.87</td>\n",
+       "      <td>0.47</td>\n",
        "    </tr>\n",
        "  </tbody>\n",
        "</table>\n",
@@ -517,10 +490,10 @@
       ],
       "text/plain": [
        "  ligand DG (kcal/mol) uncertainty (kcal/mol)\n",
-       "0      1        -18.36                   0.98"
+       "0      1        -20.87                   0.47"
       ]
      },
-     "execution_count": 13,
+     "execution_count": 12,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -540,7 +513,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 14,
+   "execution_count": 13,
    "id": "8b2c1dd8-ffa3-4585-94a7-4a1ed1454f30",
    "metadata": {},
    "outputs": [],
@@ -551,7 +524,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 15,
+   "execution_count": 14,
    "id": "08b72901-9c71-460b-b5da-9fb4a35e07f7",
    "metadata": {},
    "outputs": [
@@ -587,43 +560,43 @@
        "      <th>0</th>\n",
        "      <td>complex</td>\n",
        "      <td>1</td>\n",
-       "      <td>36.87</td>\n",
-       "      <td>0.36</td>\n",
+       "      <td>36.34</td>\n",
+       "      <td>0.91</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>1</th>\n",
        "      <td>complex</td>\n",
        "      <td>1</td>\n",
-       "      <td>39.24</td>\n",
-       "      <td>0.44</td>\n",
+       "      <td>36.17</td>\n",
+       "      <td>0.80</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>2</th>\n",
        "      <td>complex</td>\n",
        "      <td>1</td>\n",
-       "      <td>37.46</td>\n",
-       "      <td>0.48</td>\n",
+       "      <td>34.77</td>\n",
+       "      <td>0.81</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>3</th>\n",
        "      <td>solvent</td>\n",
        "      <td>1</td>\n",
-       "      <td>10.57</td>\n",
-       "      <td>0.66</td>\n",
+       "      <td>6.5</td>\n",
+       "      <td>1.4</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>4</th>\n",
        "      <td>solvent</td>\n",
        "      <td>1</td>\n",
-       "      <td>10.48</td>\n",
-       "      <td>0.65</td>\n",
+       "      <td>5.4</td>\n",
+       "      <td>1.4</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>5</th>\n",
        "      <td>solvent</td>\n",
        "      <td>1</td>\n",
-       "      <td>10.41</td>\n",
-       "      <td>0.66</td>\n",
+       "      <td>5.5</td>\n",
+       "      <td>1.4</td>\n",
        "    </tr>\n",
        "    <tr>\n",
        "      <th>6</th>\n",
@@ -636,7 +609,7 @@
        "      <th>7</th>\n",
        "      <td>standard_state_correction</td>\n",
        "      <td>1</td>\n",
-       "      <td>-9.1</td>\n",
+       "      <td>-9.3</td>\n",
        "      <td>0.0</td>\n",
        "    </tr>\n",
        "    <tr>\n",
@@ -652,18 +625,18 @@
       ],
       "text/plain": [
        "                         leg ligand DG (kcal/mol) uncertainty (kcal/mol)\n",
-       "0                    complex      1         36.87                   0.36\n",
-       "1                    complex      1         39.24                   0.44\n",
-       "2                    complex      1         37.46                   0.48\n",
-       "3                    solvent      1         10.57                   0.66\n",
-       "4                    solvent      1         10.48                   0.65\n",
-       "5                    solvent      1         10.41                   0.66\n",
+       "0                    complex      1         36.34                   0.91\n",
+       "1                    complex      1         36.17                   0.80\n",
+       "2                    complex      1         34.77                   0.81\n",
+       "3                    solvent      1           6.5                    1.4\n",
+       "4                    solvent      1           5.4                    1.4\n",
+       "5                    solvent      1           5.5                    1.4\n",
        "6  standard_state_correction      1          -8.9                    0.0\n",
-       "7  standard_state_correction      1          -9.1                    0.0\n",
+       "7  standard_state_correction      1          -9.3                    0.0\n",
        "8  standard_state_correction      1          -9.0                    0.0"
       ]
      },
-     "execution_count": 15,
+     "execution_count": 14,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -671,6 +644,14 @@
    "source": [
     "df_raw"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "bf160a28-3aa1-4661-8f06-3a4a71d34ff2",
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {
@@ -689,7 +670,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.11"
+   "version": "3.12.13"
   },
   "widgets": {
    "application/vnd.jupyter.widget-state+json": {