Repository: openforcefield/openff-toolkit

Issue:
Molecule.atoms[index].partial_charge does not support setting
**Is your feature request related to a problem? Please describe.**
Currently, setting partial charges on an atom via the obvious route does not work:
```python
>>> molecule.atoms[0].partial_charge *= 2
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
AttributeError: can't set attribute
```
Instead, the only way to modify the partial charges in a `Molecule` object is via the less obvious
```python
>>> molecule.partial_charges[0] = 1.0 * unit.elementary_charge
```

**Describe the solution you'd like**
It would be useful for the obvious route to work as well.


Discussion:
codecov[bot]: # [Codecov](https://codecov.io/gh/openforcefield/openff-toolkit/pull/1537?src=pr&el=h1&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=openforcefield) Report
> Merging [#1537](https://codecov.io/gh/openforcefield/openff-toolkit/pull/1537?src=pr&el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=openforcefield) (dca7bb2) into [main](https://codecov.io/gh/openforcefield/openff-toolkit/commit/5a7bafb85d37cc23c0cbc553737b25896f6722ef?el=desc&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=openforcefield) (5a7bafb) will **decrease** coverage by `12.06%`.
> The diff coverage is `92.30%`.

<details><summary>Additional details and impacted files</summary>


</details>

Patch:
diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 8725c890..a5ad74d3 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -38,10 +38,6 @@ jobs:
             python-version: "3.9"
           - openeye: true
             python-version: "3.10"
-          # As of 7/6/22, this cannot solve due to a missing OpenMM build.
-          # Revisit when OpenMM 7.8+ is released and new builds are up.
-          - python-version: "3.10"
-            os: macos-latest
 
     env:
       OE_LICENSE: ${{ github.workspace }}/oe_license.txt
diff --git a/docs/releasehistory.md b/docs/releasehistory.md
index f5cfc15b..3b6092bd 100644
--- a/docs/releasehistory.md
+++ b/docs/releasehistory.md
@@ -11,6 +11,7 @@ Releases follow the `major.minor.micro` scheme recommended by [PEP440](https://w
 ### New features
 - [PR #1502](https://github.com/openforcefield/openff-toolkit/pull/1502): Adds Gasteiger charge computation using the RDKit backend.
 - [PR #1498](https://github.com/openforcefield/openff-toolkit/pull/1498): `Molecule.remap()` now supports partial mappings with the `partial` argument.
+- [PR #1528](https://github.com/openforcefield/openff-toolkit/pull/1528): `Topology.box_vectors` are can now be set with `openmm.unit.Quantity`s, which are internally converted.
 
 ### Behavior changes
 - [PR #1498](https://github.com/openforcefield/openff-toolkit/pull/1498): New, more complete, and more descriptive errors for `Molecule.remap()`.
diff --git a/examples/forcefield_modification/forcefield_modification.ipynb b/examples/forcefield_modification/forcefield_modification.ipynb
index d2af17c5..99997623 100644
--- a/examples/forcefield_modification/forcefield_modification.ipynb
+++ b/examples/forcefield_modification/forcefield_modification.ipynb
@@ -27,20 +27,7 @@
    "cell_type": "code",
    "execution_count": 1,
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "712a5350c9cf47c6938b14ac7ba53a13",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": []
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
+   "outputs": [],
    "source": [
     "from copy import deepcopy\n",
     "\n",
@@ -162,17 +149,29 @@
    "execution_count": 5,
    "metadata": {},
    "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "28c8d89a98754218aa207a85aa52b68d",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": []
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Initial energy is 271.2 kJ/mol; Minimized energy is 82.7 kJ/mol\n"
+      "Initial energy is 270.8 kJ/mol; Minimized energy is 82.3 kJ/mol\n"
      ]
     },
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "052210d0126c4e6a9d53cab24e501934",
+       "model_id": "cc9a8b5599c34204a90f0fb6170b4a63",
        "version_major": 2,
        "version_minor": 0
       },
@@ -207,15 +206,15 @@
     {
      "data": {
       "text/plain": [
-       "[{'Constraints': <openff.toolkit.topology.topology.ValenceDict at 0x7f9956739c40>,\n",
-       "  'Bonds': <openff.toolkit.topology.topology.ValenceDict at 0x7f9956769940>,\n",
-       "  'Angles': <openff.toolkit.topology.topology.ValenceDict at 0x7f9956718eb0>,\n",
-       "  'ProperTorsions': <openff.toolkit.topology.topology.ValenceDict at 0x7f994d84b430>,\n",
-       "  'ImproperTorsions': <openff.toolkit.topology.topology.ImproperDict at 0x7f995679fb20>,\n",
-       "  'vdW': <openff.toolkit.topology.topology.ValenceDict at 0x7f99565b7ca0>,\n",
-       "  'Electrostatics': <openff.toolkit.topology.topology.ValenceDict at 0x7f99564784f0>,\n",
+       "[{'Constraints': <openff.toolkit.topology.topology.ValenceDict at 0x17e4bbee0>,\n",
+       "  'Bonds': <openff.toolkit.topology.topology.ValenceDict at 0x17e4bbf70>,\n",
+       "  'Angles': <openff.toolkit.topology.topology.ValenceDict at 0x17dbe5760>,\n",
+       "  'ProperTorsions': <openff.toolkit.topology.topology.ValenceDict at 0x10f8decd0>,\n",
+       "  'ImproperTorsions': <openff.toolkit.topology.topology.ImproperDict at 0x17e4d6eb0>,\n",
+       "  'vdW': <openff.toolkit.topology.topology.ValenceDict at 0x17e470be0>,\n",
+       "  'Electrostatics': <openff.toolkit.topology.topology.ValenceDict at 0x17dc0b520>,\n",
        "  'LibraryCharges': {},\n",
-       "  'ToolkitAM1BCC': <openff.toolkit.topology.topology.ValenceDict at 0x7f99565b7c40>}]"
+       "  'ToolkitAM1BCC': <openff.toolkit.topology.topology.ValenceDict at 0x17e4b1d30>}]"
       ]
      },
      "execution_count": 6,
@@ -244,123 +243,123 @@
      "data": {
       "text/plain": [
        "{(0,\n",
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        " (0,\n",
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        " (0,\n",
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+       "  40): <BondType with smirks: [#6X4:1]-[#1:2]  id: b84  length: 1.093899492634 angstrom  k: 740.0934137725 kilocalorie / angstrom ** 2 / mole  >,\n",
        " (3,\n",
-       "  41): <BondType with smirks: [#6X4:1]-[#1:2]  id: b84  length: 1.093899492634 Å  k: 740.0934137725 kcal / mol / Å ** 2  >,\n",
+       "  41): <BondType with smirks: [#6X4:1]-[#1:2]  id: b84  length: 1.093899492634 angstrom  k: 740.0934137725 kilocalorie / angstrom ** 2 / mole  >,\n",
        " (4,\n",
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        " (4,\n",
-       "  11): <BondType with smirks: [#6X3:1]:[#6X3:2]  id: b5  length: 1.387193227181 Å  k: 721.5704889544 kcal / mol / Å ** 2  >,\n",
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        " (12,\n",
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        " (13,\n",
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        " (13,\n",
-       "  15): <BondType with smirks: [#6X4:1]-[#8X2H0:2]  id: b16  length: 1.425895053732 Å  k: 733.4817683494 kcal / mol / Å ** 2  >,\n",
+       "  15): <BondType with smirks: [#6X4:1]-[#8X2H0:2]  id: b16  length: 1.425895053732 angstrom  k: 733.4817683494 kilocalorie / angstrom ** 2 / mole  >,\n",
        " (13,\n",
-       "  19): <BondType with smirks: [#6X4:1]-[#6X4:2]  id: b1  length: 1.52190126495 Å  k: 529.2429715351 kcal / mol / Å ** 2  >,\n",
+       "  19): <BondType with smirks: [#6X4:1]-[#6X4:2]  id: b1  length: 1.52190126495 angstrom  k: 529.2429715351 kilocalorie / angstrom ** 2 / mole  >,\n",
        " (15,\n",
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+       "  16): <BondType with smirks: [#6X4:1]-[#8X2H0:2]  id: b16  length: 1.425895053732 angstrom  k: 733.4817683494 kilocalorie / angstrom ** 2 / mole  >,\n",
        " (16,\n",
-       "  17): <BondType with smirks: [#6X4:1]-[#6X4:2]  id: b1  length: 1.52190126495 Å  k: 529.2429715351 kcal / mol / Å ** 2  >,\n",
+       "  17): <BondType with smirks: [#6X4:1]-[#6X4:2]  id: b1  length: 1.52190126495 angstrom  k: 529.2429715351 kilocalorie / angstrom ** 2 / mole  >,\n",
        " (16,\n",
-       "  45): <BondType with smirks: [#6X4:1]-[#1:2]  id: b84  length: 1.093899492634 Å  k: 740.0934137725 kcal / mol / Å ** 2  >,\n",
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        " (16,\n",
-       "  46): <BondType with smirks: [#6X4:1]-[#1:2]  id: b84  length: 1.093899492634 Å  k: 740.0934137725 kcal / mol / Å ** 2  >,\n",
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        " (17,\n",
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+       "  18): <BondType with smirks: [#6X4:1]-[#6X4:2]  id: b1  length: 1.52190126495 angstrom  k: 529.2429715351 kilocalorie / angstrom ** 2 / mole  >,\n",
        " (17,\n",
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        " (17,\n",
-       "  48): <BondType with smirks: [#6X4:1]-[#1:2]  id: b84  length: 1.093899492634 Å  k: 740.0934137725 kcal / mol / Å ** 2  >,\n",
+       "  48): <BondType with smirks: [#6X4:1]-[#1:2]  id: b84  length: 1.093899492634 angstrom  k: 740.0934137725 kilocalorie / angstrom ** 2 / mole  >,\n",
        " (18,\n",
-       "  19): <BondType with smirks: [#6X4:1]-[#6X4:2]  id: b1  length: 1.52190126495 Å  k: 529.2429715351 kcal / mol / Å ** 2  >,\n",
+       "  19): <BondType with smirks: [#6X4:1]-[#6X4:2]  id: b1  length: 1.52190126495 angstrom  k: 529.2429715351 kilocalorie / angstrom ** 2 / mole  >,\n",
        " (18,\n",
-       "  49): <BondType with smirks: [#6X4:1]-[#1:2]  id: b84  length: 1.093899492634 Å  k: 740.0934137725 kcal / mol / Å ** 2  >,\n",
+       "  49): <BondType with smirks: [#6X4:1]-[#1:2]  id: b84  length: 1.093899492634 angstrom  k: 740.0934137725 kilocalorie / angstrom ** 2 / mole  >,\n",
        " (18,\n",
-       "  50): <BondType with smirks: [#6X4:1]-[#1:2]  id: b84  length: 1.093899492634 Å  k: 740.0934137725 kcal / mol / Å ** 2  >,\n",
+       "  50): <BondType with smirks: [#6X4:1]-[#1:2]  id: b84  length: 1.093899492634 angstrom  k: 740.0934137725 kilocalorie / angstrom ** 2 / mole  >,\n",
        " (19,\n",
-       "  20): <BondType with smirks: [#6X4:1]-[#1:2]  id: b84  length: 1.093899492634 Å  k: 740.0934137725 kcal / mol / Å ** 2  >,\n",
+       "  20): <BondType with smirks: [#6X4:1]-[#1:2]  id: b84  length: 1.093899492634 angstrom  k: 740.0934137725 kilocalorie / angstrom ** 2 / mole  >,\n",
        " (19,\n",
-       "  21): <BondType with smirks: [#6X4:1]-[#6X4:2]  id: b1  length: 1.52190126495 Å  k: 529.2429715351 kcal / mol / Å ** 2  >,\n",
+       "  21): <BondType with smirks: [#6X4:1]-[#6X4:2]  id: b1  length: 1.52190126495 angstrom  k: 529.2429715351 kilocalorie / angstrom ** 2 / mole  >,\n",
        " (21,\n",
-       "  22): <BondType with smirks: [#6X4:1]-[#1:2]  id: b84  length: 1.093899492634 Å  k: 740.0934137725 kcal / mol / Å ** 2  >,\n",
+       "  22): <BondType with smirks: [#6X4:1]-[#1:2]  id: b84  length: 1.093899492634 angstrom  k: 740.0934137725 kilocalorie / angstrom ** 2 / mole  >,\n",
        " (21,\n",
-       "  23): <BondType with smirks: [#6X4:1]-[#6X3:2]  id: b2  length: 1.498646816465 Å  k: 579.4762652679 kcal / mol / Å ** 2  >,\n",
+       "  23): <BondType with smirks: [#6X4:1]-[#6X3:2]  id: b2  length: 1.498646816465 angstrom  k: 579.4762652679 kilocalorie / angstrom ** 2 / mole  >,\n",
        " (21,\n",
-       "  32): <BondType with smirks: [#6:1]-[#7:2]  id: b7  length: 1.464762957261 Å  k: 732.6809445917 kcal / mol / Å ** 2  >,\n",
+       "  32): <BondType with smirks: [#6:1]-[#7:2]  id: b7  length: 1.464762957261 angstrom  k: 732.6809445917 kilocalorie / angstrom ** 2 / mole  >,\n",
        " (23,\n",
-       "  24): <BondType with smirks: [#6X3:1]:[#6X3:2]  id: b5  length: 1.387193227181 Å  k: 721.5704889544 kcal / mol / Å ** 2  >,\n",
+       "  24): <BondType with smirks: [#6X3:1]:[#6X3:2]  id: b5  length: 1.387193227181 angstrom  k: 721.5704889544 kilocalorie / angstrom ** 2 / mole  >,\n",
        " (23,\n",
-       "  31): <BondType with smirks: [#6X3:1]:[#6X3:2]  id: b5  length: 1.387193227181 Å  k: 721.5704889544 kcal / mol / Å ** 2  >,\n",
+       "  31): <BondType with smirks: [#6X3:1]:[#6X3:2]  id: b5  length: 1.387193227181 angstrom  k: 721.5704889544 kilocalorie / angstrom ** 2 / mole  >,\n",
        " (24,\n",
-       "  25): <BondType with smirks: [#6X3:1]:[#6X3:2]  id: b5  length: 1.387193227181 Å  k: 721.5704889544 kcal / mol / Å ** 2  >,\n",
+       "  25): <BondType with smirks: [#6X3:1]:[#6X3:2]  id: b5  length: 1.387193227181 angstrom  k: 721.5704889544 kilocalorie / angstrom ** 2 / mole  >,\n",
        " (24,\n",
-       "  51): <BondType with smirks: [#6X3:1]-[#1:2]  id: b85  length: 1.085358495916 Å  k: 794.5091579238 kcal / mol / Å ** 2  >,\n",
+       "  51): <BondType with smirks: [#6X3:1]-[#1:2]  id: b85  length: 1.085358495916 angstrom  k: 794.5091579238 kilocalorie / angstrom ** 2 / mole  >,\n",
        " (25,\n",
-       "  26): <BondType with smirks: [#6X3:1]-[#8X2H1:2]  id: b18  length: 1.369745182308 Å  k: 771.5209191174 kcal / mol / Å ** 2  >,\n",
+       "  26): <BondType with smirks: [#6X3:1]-[#8X2H1:2]  id: b18  length: 1.369745182308 angstrom  k: 771.5209191174 kilocalorie / angstrom ** 2 / mole  >,\n",
        " (25,\n",
-       "  27): <BondType with smirks: [#6X3:1]:[#6X3:2]  id: b5  length: 1.387193227181 Å  k: 721.5704889544 kcal / mol / Å ** 2  >,\n",
+       "  27): <BondType with smirks: [#6X3:1]:[#6X3:2]  id: b5  length: 1.387193227181 angstrom  k: 721.5704889544 kilocalorie / angstrom ** 2 / mole  >,\n",
        " (26,\n",
-       "  52): <BondType with smirks: [#8:1]-[#1:2]  id: b88  length: 0.9716763312559 Å  k: 1087.053566377 kcal / mol / Å ** 2  >,\n",
+       "  52): <BondType with smirks: [#8:1]-[#1:2]  id: b88  length: 0.9716763312559 angstrom  k: 1087.053566377 kilocalorie / angstrom ** 2 / mole  >,\n",
        " (27,\n",
-       "  28): <BondType with smirks: [#6X3:1]-[#8X2H1:2]  id: b18  length: 1.369745182308 Å  k: 771.5209191174 kcal / mol / Å ** 2  >,\n",
+       "  28): <BondType with smirks: [#6X3:1]-[#8X2H1:2]  id: b18  length: 1.369745182308 angstrom  k: 771.5209191174 kilocalorie / angstrom ** 2 / mole  >,\n",
        " (27,\n",
-       "  29): <BondType with smirks: [#6X3:1]:[#6X3:2]  id: b5  length: 1.387193227181 Å  k: 721.5704889544 kcal / mol / Å ** 2  >,\n",
+       "  29): <BondType with smirks: [#6X3:1]:[#6X3:2]  id: b5  length: 1.387193227181 angstrom  k: 721.5704889544 kilocalorie / angstrom ** 2 / mole  >,\n",
        " (28,\n",
-       "  53): <BondType with smirks: [#8:1]-[#1:2]  id: b88  length: 0.9716763312559 Å  k: 1087.053566377 kcal / mol / Å ** 2  >,\n",
+       "  53): <BondType with smirks: [#8:1]-[#1:2]  id: b88  length: 0.9716763312559 angstrom  k: 1087.053566377 kilocalorie / angstrom ** 2 / mole  >,\n",
        " (29,\n",
-       "  30): <BondType with smirks: [#6:1]-[#9:2]  id: b68  length: 1.352926211207 Å  k: 808.7710029616 kcal / mol / Å ** 2  >,\n",
+       "  30): <BondType with smirks: [#6:1]-[#9:2]  id: b68  length: 1.352926211207 angstrom  k: 808.7710029616 kilocalorie / angstrom ** 2 / mole  >,\n",
        " (29,\n",
-       "  31): <BondType with smirks: [#6X3:1]:[#6X3:2]  id: b5  length: 1.387193227181 Å  k: 721.5704889544 kcal / mol / Å ** 2  >,\n",
+       "  31): <BondType with smirks: [#6X3:1]:[#6X3:2]  id: b5  length: 1.387193227181 angstrom  k: 721.5704889544 kilocalorie / angstrom ** 2 / mole  >,\n",
        " (31,\n",
-       "  54): <BondType with smirks: [#6X3:1]-[#1:2]  id: b85  length: 1.085358495916 Å  k: 794.5091579238 kcal / mol / Å ** 2  >,\n",
+       "  54): <BondType with smirks: [#6X3:1]-[#1:2]  id: b85  length: 1.085358495916 angstrom  k: 794.5091579238 kilocalorie / angstrom ** 2 / mole  >,\n",
        " (32,\n",
-       "  55): <BondType with smirks: [#7:1]-[#1:2]  id: b87  length: 1.019481865027 Å  k: 1010.288992386 kcal / mol / Å ** 2  >}"
+       "  55): <BondType with smirks: [#7:1]-[#1:2]  id: b87  length: 1.019481865027 angstrom  k: 1010.288992386 kilocalorie / angstrom ** 2 / mole  >}"
       ]
      },
      "execution_count": 7,
@@ -408,7 +407,7 @@
     {
      "data": {
       "text/plain": [
-       "<BondType with smirks: [#6:1]-[#9:2]  id: b68  length: 1.352926211207 Å  k: 808.7710029616 kcal / mol / Å ** 2  >"
+       "<BondType with smirks: [#6:1]-[#9:2]  id: b68  length: 1.352926211207 angstrom  k: 808.7710029616 kilocalorie / angstrom ** 2 / mole  >"
       ]
      },
      "execution_count": 8,
@@ -497,13 +496,13 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Initial energy is 127154.3 kJ/mol; Minimized energy is 100.2 kJ/mol\n"
+      "Initial energy is 127153.9 kJ/mol; Minimized energy is 99.8 kJ/mol\n"
      ]
     },
     {
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@@ -541,18 +540,18 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "(33, 0, 34) <AngleType with smirks: [#1:1]-[#6X4:2]-[#1:3]  angle: 115.6030999533 deg  k: 97.55298529519 kcal / mol / rad ** 2  id: a2  >\n",
-      "(33, 0, 35) <AngleType with smirks: [#1:1]-[#6X4:2]-[#1:3]  angle: 115.6030999533 deg  k: 97.55298529519 kcal / mol / rad ** 2  id: a2  >\n",
-      "(34, 0, 35) <AngleType with smirks: [#1:1]-[#6X4:2]-[#1:3]  angle: 115.6030999533 deg  k: 97.55298529519 kcal / mol / rad ** 2  id: a2  >\n",
-      "(36, 2, 37) <AngleType with smirks: [#1:1]-[#6X4:2]-[#1:3]  angle: 115.6030999533 deg  k: 97.55298529519 kcal / mol / rad ** 2  id: a2  >\n",
-      "(36, 2, 38) <AngleType with smirks: [#1:1]-[#6X4:2]-[#1:3]  angle: 115.6030999533 deg  k: 97.55298529519 kcal / mol / rad ** 2  id: a2  >\n",
-      "(37, 2, 38) <AngleType with smirks: [#1:1]-[#6X4:2]-[#1:3]  angle: 115.6030999533 deg  k: 97.55298529519 kcal / mol / rad ** 2  id: a2  >\n",
-      "(39, 3, 40) <AngleType with smirks: [#1:1]-[#6X4:2]-[#1:3]  angle: 115.6030999533 deg  k: 97.55298529519 kcal / mol / rad ** 2  id: a2  >\n",
-      "(39, 3, 41) <AngleType with smirks: [#1:1]-[#6X4:2]-[#1:3]  angle: 115.6030999533 deg  k: 97.55298529519 kcal / mol / rad ** 2  id: a2  >\n",
-      "(40, 3, 41) <AngleType with smirks: [#1:1]-[#6X4:2]-[#1:3]  angle: 115.6030999533 deg  k: 97.55298529519 kcal / mol / rad ** 2  id: a2  >\n",
-      "(45, 16, 46) <AngleType with smirks: [#1:1]-[#6X4:2]-[#1:3]  angle: 115.6030999533 deg  k: 97.55298529519 kcal / mol / rad ** 2  id: a2  >\n",
-      "(47, 17, 48) <AngleType with smirks: [#1:1]-[#6X4:2]-[#1:3]  angle: 115.6030999533 deg  k: 97.55298529519 kcal / mol / rad ** 2  id: a2  >\n",
-      "(49, 18, 50) <AngleType with smirks: [#1:1]-[#6X4:2]-[#1:3]  angle: 115.6030999533 deg  k: 97.55298529519 kcal / mol / rad ** 2  id: a2  >\n"
+      "(33, 0, 34) <AngleType with smirks: [#1:1]-[#6X4:2]-[#1:3]  angle: 115.6030999533 degree  k: 97.55298529519 kilocalorie / mole / radian ** 2  id: a2  >\n",
+      "(33, 0, 35) <AngleType with smirks: [#1:1]-[#6X4:2]-[#1:3]  angle: 115.6030999533 degree  k: 97.55298529519 kilocalorie / mole / radian ** 2  id: a2  >\n",
+      "(34, 0, 35) <AngleType with smirks: [#1:1]-[#6X4:2]-[#1:3]  angle: 115.6030999533 degree  k: 97.55298529519 kilocalorie / mole / radian ** 2  id: a2  >\n",
+      "(36, 2, 37) <AngleType with smirks: [#1:1]-[#6X4:2]-[#1:3]  angle: 115.6030999533 degree  k: 97.55298529519 kilocalorie / mole / radian ** 2  id: a2  >\n",
+      "(36, 2, 38) <AngleType with smirks: [#1:1]-[#6X4:2]-[#1:3]  angle: 115.6030999533 degree  k: 97.55298529519 kilocalorie / mole / radian ** 2  id: a2  >\n",
+      "(37, 2, 38) <AngleType with smirks: [#1:1]-[#6X4:2]-[#1:3]  angle: 115.6030999533 degree  k: 97.55298529519 kilocalorie / mole / radian ** 2  id: a2  >\n",
+      "(39, 3, 40) <AngleType with smirks: [#1:1]-[#6X4:2]-[#1:3]  angle: 115.6030999533 degree  k: 97.55298529519 kilocalorie / mole / radian ** 2  id: a2  >\n",
+      "(39, 3, 41) <AngleType with smirks: [#1:1]-[#6X4:2]-[#1:3]  angle: 115.6030999533 degree  k: 97.55298529519 kilocalorie / mole / radian ** 2  id: a2  >\n",
+      "(40, 3, 41) <AngleType with smirks: [#1:1]-[#6X4:2]-[#1:3]  angle: 115.6030999533 degree  k: 97.55298529519 kilocalorie / mole / radian ** 2  id: a2  >\n",
+      "(45, 16, 46) <AngleType with smirks: [#1:1]-[#6X4:2]-[#1:3]  angle: 115.6030999533 degree  k: 97.55298529519 kilocalorie / mole / radian ** 2  id: a2  >\n",
+      "(47, 17, 48) <AngleType with smirks: [#1:1]-[#6X4:2]-[#1:3]  angle: 115.6030999533 degree  k: 97.55298529519 kilocalorie / mole / radian ** 2  id: a2  >\n",
+      "(49, 18, 50) <AngleType with smirks: [#1:1]-[#6X4:2]-[#1:3]  angle: 115.6030999533 degree  k: 97.55298529519 kilocalorie / mole / radian ** 2  id: a2  >\n"
      ]
     }
    ],
@@ -590,13 +589,13 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Initial energy is 129550.7 kJ/mol; Minimized energy is 114.2 kJ/mol\n"
+      "Initial energy is 129550.3 kJ/mol; Minimized energy is 113.7 kJ/mol\n"
      ]
     },
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "d3b48ee35c754cb6b7dea82e22c63c01",
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        "version_minor": 0
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@@ -642,15 +641,15 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "(9, 32, 21) <AngleType with smirks: [*:1]~[#7X3$(*~[#6X3,#6X2,#7X2+0]):2]~[*:3]  angle: 117.3465570514 deg  k: 110.8436430155 kcal / mol / rad ** 2  id: a20  >\n",
-      "(13, 15, 16) <AngleType with smirks: [*:1]-[#8:2]-[*:3]  angle: 110.3538806181 deg  k: 130.181232192 kcal / mol / rad ** 2  id: a28  >\n",
-      "Initial energy is 132120.2 kJ/mol; Minimized energy is 401.0 kJ/mol\n"
+      "(9, 32, 21) <AngleType with smirks: [*:1]~[#7X3$(*~[#6X3,#6X2,#7X2+0]):2]~[*:3]  angle: 117.3465570514 degree  k: 110.8436430155 kilocalorie / mole / radian ** 2  id: a20  >\n",
+      "(13, 15, 16) <AngleType with smirks: [*:1]-[#8:2]-[*:3]  angle: 110.3538806181 degree  k: 130.181232192 kilocalorie / mole / radian ** 2  id: a28  >\n",
+      "Initial energy is 132119.8 kJ/mol; Minimized energy is 400.5 kJ/mol\n"
      ]
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     {
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@@ -734,35 +733,35 @@
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-       "<path class=\"bond-13 atom-4 atom-13\" d=\"M 190.7,184.6 L 166.3,231.4\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
-       "<path class=\"bond-14 atom-5 atom-14\" d=\"M 249.7,218.5 L 217.1,258.3\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
-       "<path class=\"bond-15 atom-5 atom-15\" d=\"M 249.7,218.5 L 279.4,261.0\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
-       "<path class=\"atom-3\" d=\"M 180.8 116.8 Q 180.8 111.6, 183.3 108.7 Q 185.9 105.8, 190.7 105.8 Q 195.5 105.8, 198.1 108.7 Q 200.7 111.6, 200.7 116.8 Q 200.7 122.1, 198.1 125.1 Q 195.5 128.0, 190.7 128.0 Q 185.9 128.0, 183.3 125.1 Q 180.8 122.1, 180.8 116.8 M 190.7 125.6 Q 194.0 125.6, 195.8 123.4 Q 197.6 121.1, 197.6 116.8 Q 197.6 112.5, 195.8 110.4 Q 194.0 108.2, 190.7 108.2 Q 187.4 108.2, 185.6 110.4 Q 183.8 112.5, 183.8 116.8 Q 183.8 121.2, 185.6 123.4 Q 187.4 125.6, 190.7 125.6 \" fill=\"#FF0000\"/>\n",
-       "<path class=\"atom-6\" d=\"M 326.6 235.5 L 329.5 235.5 L 329.5 244.7 L 340.6 244.7 L 340.6 235.5 L 343.6 235.5 L 343.6 257.1 L 340.6 257.1 L 340.6 247.1 L 329.5 247.1 L 329.5 257.1 L 326.6 257.1 L 326.6 235.5 \" fill=\"#000000\"/>\n",
-       "<path class=\"atom-7\" d=\"M 366.8 164.1 L 369.7 164.1 L 369.7 173.3 L 380.8 173.3 L 380.8 164.1 L 383.7 164.1 L 383.7 185.8 L 380.8 185.8 L 380.8 175.8 L 369.7 175.8 L 369.7 185.8 L 366.8 185.8 L 366.8 164.1 \" fill=\"#000000\"/>\n",
-       "<path class=\"atom-8\" d=\"M 366.4 109.6 L 369.3 109.6 L 369.3 118.8 L 380.4 118.8 L 380.4 109.6 L 383.3 109.6 L 383.3 131.2 L 380.4 131.2 L 380.4 121.2 L 369.3 121.2 L 369.3 131.2 L 366.4 131.2 L 366.4 109.6 \" fill=\"#000000\"/>\n",
-       "<path class=\"atom-9\" d=\"M 324.4 43.2 L 327.3 43.2 L 327.3 52.4 L 338.4 52.4 L 338.4 43.2 L 341.3 43.2 L 341.3 64.8 L 338.4 64.8 L 338.4 54.8 L 327.3 54.8 L 327.3 64.8 L 324.4 64.8 L 324.4 43.2 \" fill=\"#000000\"/>\n",
-       "<path class=\"atom-10\" d=\"M 277.5 15.7 L 280.5 15.7 L 280.5 24.9 L 291.6 24.9 L 291.6 15.7 L 294.5 15.7 L 294.5 37.3 L 291.6 37.3 L 291.6 27.3 L 280.5 27.3 L 280.5 37.3 L 277.5 37.3 L 277.5 15.7 \" fill=\"#000000\"/>\n",
-       "<path class=\"atom-11\" d=\"M 194.0 22.5 L 196.9 22.5 L 196.9 31.7 L 208.0 31.7 L 208.0 22.5 L 210.9 22.5 L 210.9 44.1 L 208.0 44.1 L 208.0 34.1 L 196.9 34.1 L 196.9 44.1 L 194.0 44.1 L 194.0 22.5 \" fill=\"#000000\"/>\n",
-       "<path class=\"atom-12\" d=\"M 116.3 157.5 L 119.2 157.5 L 119.2 166.8 L 130.3 166.8 L 130.3 157.5 L 133.2 157.5 L 133.2 179.2 L 130.3 179.2 L 130.3 169.2 L 119.2 169.2 L 119.2 179.2 L 116.3 179.2 L 116.3 157.5 \" fill=\"#000000\"/>\n",
-       "<path class=\"atom-13\" d=\"M 151.3 233.1 L 154.2 233.1 L 154.2 242.3 L 165.3 242.3 L 165.3 233.1 L 168.2 233.1 L 168.2 254.7 L 165.3 254.7 L 165.3 244.7 L 154.2 244.7 L 154.2 254.7 L 151.3 254.7 L 151.3 233.1 \" fill=\"#000000\"/>\n",
-       "<path class=\"atom-14\" d=\"M 198.5 259.9 L 201.4 259.9 L 201.4 269.1 L 212.5 269.1 L 212.5 259.9 L 215.5 259.9 L 215.5 281.5 L 212.5 281.5 L 212.5 271.5 L 201.4 271.5 L 201.4 281.5 L 198.5 281.5 L 198.5 259.9 \" fill=\"#000000\"/>\n",
-       "<path class=\"atom-15\" d=\"M 279.7 262.7 L 282.6 262.7 L 282.6 271.9 L 293.7 271.9 L 293.7 262.7 L 296.6 262.7 L 296.6 284.3 L 293.7 284.3 L 293.7 274.3 L 282.6 274.3 L 282.6 284.3 L 279.7 284.3 L 279.7 262.7 \" fill=\"#000000\"/>\n",
+       "<path class=\"bond-0 atom-0 atom-5\" d=\"M 308.9,182.2 L 249.5,216.5\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-1 atom-0 atom-1\" d=\"M 308.9,182.2 L 309.0,113.6\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-2 atom-1 atom-2\" d=\"M 309.0,113.6 L 249.5,79.4\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-3 atom-2 atom-3\" d=\"M 249.5,79.4 L 227.4,92.1\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-3 atom-2 atom-3\" d=\"M 227.4,92.1 L 205.4,104.7\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-4 atom-3 atom-4\" d=\"M 190.2,130.4 L 190.3,156.2\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-4 atom-3 atom-4\" d=\"M 190.3,156.2 L 190.3,181.9\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-5 atom-4 atom-5\" d=\"M 190.3,181.9 L 249.5,216.5\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-6 atom-0 atom-6\" d=\"M 308.9,182.2 L 328.9,228.1\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-7 atom-0 atom-7\" d=\"M 308.9,182.2 L 363.6,174.2\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-8 atom-1 atom-8\" d=\"M 309.0,113.6 L 350.7,117.6\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-9 atom-1 atom-9\" d=\"M 309.0,113.6 L 327.6,66.2\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-10 atom-2 atom-10\" d=\"M 249.5,79.4 L 269.9,50.3\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-11 atom-2 atom-11\" d=\"M 249.5,79.4 L 217.1,43.1\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-12 atom-4 atom-12\" d=\"M 190.3,181.9 L 136.4,170.1\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-13 atom-4 atom-13\" d=\"M 190.3,181.9 L 175.1,213.7\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-14 atom-5 atom-14\" d=\"M 249.5,216.5 L 219.1,253.3\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"bond-15 atom-5 atom-15\" d=\"M 249.5,216.5 L 276.9,255.5\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
+       "<path class=\"atom-3\" d=\"M 177.2 113.6 Q 177.2 106.8, 180.6 103.0 Q 184.0 99.2, 190.2 99.2 Q 196.5 99.2, 199.9 103.0 Q 203.2 106.8, 203.2 113.6 Q 203.2 120.4, 199.8 124.4 Q 196.4 128.2, 190.2 128.2 Q 184.0 128.2, 180.6 124.4 Q 177.2 120.5, 177.2 113.6 M 190.2 125.0 Q 194.6 125.0, 196.9 122.2 Q 199.2 119.2, 199.2 113.6 Q 199.2 108.0, 196.9 105.2 Q 194.6 102.4, 190.2 102.4 Q 185.9 102.4, 183.6 105.2 Q 181.2 108.0, 181.2 113.6 Q 181.2 119.3, 183.6 122.2 Q 185.9 125.0, 190.2 125.0 \" fill=\"#FF0000\"/>\n",
+       "<path class=\"atom-6\" d=\"M 324.9 230.2 L 328.8 230.2 L 328.8 242.3 L 343.3 242.3 L 343.3 230.2 L 347.1 230.2 L 347.1 258.6 L 343.3 258.6 L 343.3 245.5 L 328.8 245.5 L 328.8 258.6 L 324.9 258.6 L 324.9 230.2 \" fill=\"#000000\"/>\n",
+       "<path class=\"atom-7\" d=\"M 365.7 158.1 L 369.6 158.1 L 369.6 170.2 L 384.1 170.2 L 384.1 158.1 L 387.9 158.1 L 387.9 186.4 L 384.1 186.4 L 384.1 173.4 L 369.6 173.4 L 369.6 186.4 L 365.7 186.4 L 365.7 158.1 \" fill=\"#000000\"/>\n",
+       "<path class=\"atom-8\" d=\"M 352.8 104.8 L 356.7 104.8 L 356.7 116.8 L 371.2 116.8 L 371.2 104.8 L 375.0 104.8 L 375.0 133.1 L 371.2 133.1 L 371.2 120.0 L 356.7 120.0 L 356.7 133.1 L 352.8 133.1 L 352.8 104.8 \" fill=\"#000000\"/>\n",
+       "<path class=\"atom-9\" d=\"M 323.0 35.7 L 326.8 35.7 L 326.8 47.7 L 341.3 47.7 L 341.3 35.7 L 345.2 35.7 L 345.2 64.0 L 341.3 64.0 L 341.3 50.9 L 326.8 50.9 L 326.8 64.0 L 323.0 64.0 L 323.0 35.7 \" fill=\"#000000\"/>\n",
+       "<path class=\"atom-10\" d=\"M 270.3 19.8 L 274.2 19.8 L 274.2 31.8 L 288.6 31.8 L 288.6 19.8 L 292.5 19.8 L 292.5 48.1 L 288.6 48.1 L 288.6 35.0 L 274.2 35.0 L 274.2 48.1 L 270.3 48.1 L 270.3 19.8 \" fill=\"#000000\"/>\n",
+       "<path class=\"atom-11\" d=\"M 192.7 14.0 L 196.6 14.0 L 196.6 26.1 L 211.0 26.1 L 211.0 14.0 L 214.9 14.0 L 214.9 42.4 L 211.0 42.4 L 211.0 29.3 L 196.6 29.3 L 196.6 42.4 L 192.7 42.4 L 192.7 14.0 \" fill=\"#000000\"/>\n",
+       "<path class=\"atom-12\" d=\"M 112.1 153.1 L 115.9 153.1 L 115.9 165.1 L 130.4 165.1 L 130.4 153.1 L 134.3 153.1 L 134.3 181.4 L 130.4 181.4 L 130.4 168.3 L 115.9 168.3 L 115.9 181.4 L 112.1 181.4 L 112.1 153.1 \" fill=\"#000000\"/>\n",
+       "<path class=\"atom-13\" d=\"M 156.2 215.8 L 160.0 215.8 L 160.0 227.9 L 174.5 227.9 L 174.5 215.8 L 178.3 215.8 L 178.3 244.2 L 174.5 244.2 L 174.5 231.1 L 160.0 231.1 L 160.0 244.2 L 156.2 244.2 L 156.2 215.8 \" fill=\"#000000\"/>\n",
+       "<path class=\"atom-14\" d=\"M 194.8 255.2 L 198.6 255.2 L 198.6 267.2 L 213.1 267.2 L 213.1 255.2 L 216.9 255.2 L 216.9 283.5 L 213.1 283.5 L 213.1 270.4 L 198.6 270.4 L 198.6 283.5 L 194.8 283.5 L 194.8 255.2 \" fill=\"#000000\"/>\n",
+       "<path class=\"atom-15\" d=\"M 277.3 257.6 L 281.1 257.6 L 281.1 269.7 L 295.6 269.7 L 295.6 257.6 L 299.4 257.6 L 299.4 286.0 L 295.6 286.0 L 295.6 272.9 L 281.1 272.9 L 281.1 286.0 L 277.3 286.0 L 277.3 257.6 \" fill=\"#000000\"/>\n",
        "</svg>"
       ],
       "text/plain": [
@@ -791,7 +790,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "smirks = \"C1C[C:1]-[O:2]-[C:3]C1\""
+    "cyclic_oxygen_smirks = \"C1C[C:1]-[O:2]-[C:3]C1\""
    ]
   },
   {
@@ -816,19 +815,21 @@
   {
    "cell_type": "code",
    "execution_count": 17,
-   "metadata": {},
+   "metadata": {
+    "scrolled": true
+   },
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Initial energy is 883.6 kJ/mol; Minimized energy is 301.0 kJ/mol\n"
+      "Initial energy is 883.2 kJ/mol; Minimized energy is 300.5 kJ/mol\n"
      ]
     },
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "58be1b42169742b7b11499211259b427",
+       "model_id": "90c1351993a643af9ce00af518e9a9c5",
        "version_major": 2,
        "version_minor": 0
       },
@@ -843,7 +844,7 @@
    "source": [
     "# Define the new angle parameter\n",
     "angle_parameter = offtk_parameters.AngleHandler.AngleType(\n",
-    "    smirks=smirks,\n",
+    "    smirks=cyclic_oxygen_smirks,\n",
     "    angle=179 * unit.degree,\n",
     "    k=134.5019777341 * unit.kilocalorie / (unit.mole * unit.radians**2),\n",
     ")\n",
@@ -863,6 +864,115 @@
     "Perfect! The two cyclic heteroatoms are nearly linear while the hydroxyl group retains its characteristic angle."
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Bonus: Adding a cosmetic attribute to the new parameter\n",
+    "\n",
+    "In some cases, you might want to tag a particular attribute with extra data. This might be useful, for example, in communicating to a fitting tool which parameters should be fitted, or simply to add extra metadata.. The toolkit allows for _cosmetic attributes_, which can be stored to individual parameters, will be included out when the `ForceField` object is written to disk, but will not otherwise affect the parameterization machinery. The API point for this is [`ParameterType.add_cosmetic_attribute`](https://docs.openforcefield.org/projects/toolkit/en/stable/api/generated/openff.toolkit.typing.engines.smirnoff.ParameterType.html#openff.toolkit.typing.engines.smirnoff.ParameterType.add_cosmetic_attribute).\n",
+    "\n",
+    "Let's use this to tag our modified and new parameters with a note about why we introduced it."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 18,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "angles_handler.parameters[cyclic_nitrogen_smirks].add_cosmetic_attribute(\n",
+    "    attr_name=\"note\",\n",
+    "    attr_value=\"funky pseudo-linear cyclic nitrogen\",\n",
+    ")\n",
+    "\n",
+    "angles_handler.parameters[cyclic_oxygen_smirks].add_cosmetic_attribute(\n",
+    "    attr_name=\"note\",\n",
+    "    attr_value=\"funky pseudo-linear cyclic oxygen\",\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "We we look at these parameter now, they include this attribute tacked on at the end:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 19,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "<AngleType with smirks: [*:1]~[#7X3$(*~[#6X3,#6X2,#7X2+0]):2]~[*:3]  angle: 179 degree  k: 110.8436430155 kilocalorie / mole / radian ** 2  id: a20  note: funky pseudo-linear cyclic nitrogen  >"
+      ]
+     },
+     "execution_count": 19,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "angles_handler.parameters[cyclic_nitrogen_smirks]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 20,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "<AngleType with smirks: C1C[C:1]-[O:2]-[C:3]C1  angle: 179 degree  k: 134.5019777341 kilocalorie / mole / radian ** 2  note: funky pseudo-linear cyclic oxygen  >"
+      ]
+     },
+     "execution_count": 20,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "angles_handler.parameters[cyclic_oxygen_smirks]"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Cometic attributes are included by default when [writing to disk](https://docs.openforcefield.org/projects/toolkit/en/stable/api/generated/openff.toolkit.typing.engines.smirnoff.ForceField.html#openff.toolkit.typing.engines.smirnoff.ForceField.to_file). (This can be turned off by flipping the argument `discard_cosmetic_attributes` to `True`.) Let's write out our modified force field and search through the file for the note we added."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 21,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "force_field.to_file(\"modified.offxml\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 22,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "        <Angle smirks=\"[*:1]~[#7X3$(*~[#6X3,#6X2,#7X2+0]):2]~[*:3]\" angle=\"179 * degree ** 1\" k=\"110.8436430155 * mole ** -1 * radian ** -2 * kilocalorie ** 1\" id=\"a20\" note=\"funky pseudo-linear cyclic nitrogen\"></Angle>\r\n",
+      "        <Angle smirks=\"C1C[C:1]-[O:2]-[C:3]C1\" angle=\"179 * degree ** 1\" k=\"134.5019777341 * kilocalorie ** 1 * mole ** -1 * radian ** -2\" note=\"funky pseudo-linear cyclic oxygen\"></Angle>\r\n"
+     ]
+    }
+   ],
+   "source": [
+    "!grep funky modified.offxml"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -887,7 +997,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.12"
+   "version": "3.9.15"
   },
   "widgets": {
    "application/vnd.jupyter.widget-state+json": {
diff --git a/openff/toolkit/data/systems/monomers/butanol.frcmod b/openff/toolkit/data/systems/monomers/butanol.frcmod
deleted file mode 100644
index c60366e5..00000000
--- a/openff/toolkit/data/systems/monomers/butanol.frcmod
+++ /dev/null
@@ -1,15 +0,0 @@
-Remark line goes here
-MASS
-
-BOND
-
-ANGLE
-
-DIHE
-
-IMPROPER
-
-NONBON
-
-
-
diff --git a/openff/toolkit/data/systems/monomers/butanol.inpcrd b/openff/toolkit/data/systems/monomers/butanol.inpcrd
deleted file mode 100644
index 59e5564a..00000000
--- a/openff/toolkit/data/systems/monomers/butanol.inpcrd
+++ /dev/null
@@ -1,10 +0,0 @@
-MOL
-    15
-   0.3900000  -1.0210000  -0.0850000  -0.5800000  -2.0240000   0.5200000
-  -1.9310000  -1.9920000  -0.1890000  -2.9050000  -2.9950000   0.4140000
-  -4.1380000  -2.9160000  -0.2880000   1.3560000  -1.0500000   0.4290000
-   0.5590000  -1.2300000  -1.1460000  -0.0100000  -0.0060000   0.0030000
-  -0.1470000  -3.0290000   0.4520000  -0.7120000  -1.7990000   1.5850000
-  -2.3650000  -0.9870000  -0.1340000  -1.8040000  -2.2070000  -1.2570000
-  -2.5190000  -4.0160000   0.3260000  -3.0900000  -2.7740000   1.4700000
-  -4.7340000  -3.5650000   0.1190000
diff --git a/openff/toolkit/data/systems/monomers/butanol.prmtop b/openff/toolkit/data/systems/monomers/butanol.prmtop
deleted file mode 100644
index 8c21d99c..00000000
--- a/openff/toolkit/data/systems/monomers/butanol.prmtop
+++ /dev/null
@@ -1,187 +0,0 @@
-%VERSION  VERSION_STAMP = V0001.000  DATE = 06/27/16  12:06:11                  
-%FLAG TITLE                                                                     
-%FORMAT(20a4)                                                                   
-MOL                                                                             
-%FLAG POINTERS                                                                  
-%FORMAT(10I8)                                                                   
-      15       5      10       4      22       3      31       4       0       0
-      70       1       4       3       4       5       8       9       5       0
-       0       0       0       0       0       0       0       0      15       0
-       0
-%FLAG ATOM_NAME                                                                 
-%FORMAT(20a4)                                                                   
-C1  C2  C3  C4  O1  H1  H2  H3  H4  H5  H6  H7  H8  H9  H10 
-%FLAG CHARGE                                                                    
-%FORMAT(5E16.8)                                                                 
- -1.67280714E+00 -1.44685062E+00 -1.55618442E+00  2.41445475E+00 -1.09844024E+01
-  6.30491580E-01  6.30491580E-01  6.30491580E-01  6.88802940E-01  6.88802940E-01
-  9.98582040E-01  9.98582040E-01  3.62623770E-01  3.62623770E-01  7.25429763E+00
-%FLAG ATOMIC_NUMBER                                                             
-%FORMAT(10I8)                                                                   
-       6       6       6       6       8       1       1       1       1       1
-       1       1       1       1       1
-%FLAG MASS                                                                      
-%FORMAT(5E16.8)                                                                 
-  1.20100000E+01  1.20100000E+01  1.20100000E+01  1.20100000E+01  1.60000000E+01
-  1.00800000E+00  1.00800000E+00  1.00800000E+00  1.00800000E+00  1.00800000E+00
-  1.00800000E+00  1.00800000E+00  1.00800000E+00  1.00800000E+00  1.00800000E+00
-%FLAG ATOM_TYPE_INDEX                                                           
-%FORMAT(10I8)                                                                   
-       1       1       1       1       2       3       3       3       3       3
-       3       3       4       4       5
-%FLAG NUMBER_EXCLUDED_ATOMS                                                     
-%FORMAT(10I8)                                                                   
-      10      12      12       8       5       4       3       2       3       2
-       3       2       2       1       1
-%FLAG NONBONDED_PARM_INDEX                                                      
-%FORMAT(10I8)                                                                   
-       1       2       4       7      11       2       3       5       8      12
-       4       5       6       9      13       7       8       9      10      14
-      11      12      13      14      15
-%FLAG RESIDUE_LABEL                                                             
-%FORMAT(20a4)                                                                   
-MOL 
-%FLAG RESIDUE_POINTER                                                           
-%FORMAT(10I8)                                                                   
-       1
-%FLAG BOND_FORCE_CONSTANT                                                       
-%FORMAT(5E16.8)                                                                 
-  3.03100000E+02  3.37300000E+02  3.14100000E+02  3.35900000E+02  3.69600000E+02
-%FLAG BOND_EQUIL_VALUE                                                          
-%FORMAT(5E16.8)                                                                 
-  1.53500000E+00  1.09200000E+00  1.42600000E+00  1.09300000E+00  9.74000000E-01
-%FLAG ANGLE_FORCE_CONSTANT                                                      
-%FORMAT(5E16.8)                                                                 
-  6.32100000E+01  4.63700000E+01  6.77200000E+01  4.63600000E+01  4.70900000E+01
-  5.09700000E+01  3.94300000E+01  3.91800000E+01
-%FLAG ANGLE_EQUIL_VALUE                                                         
-%FORMAT(5E16.8)                                                                 
-  1.93085858E+00  1.92073567E+00  1.90991462E+00  1.92108473E+00  1.88774893E+00
-  1.91776860E+00  1.89106506E+00  1.91200902E+00
-%FLAG DIHEDRAL_FORCE_CONSTANT                                                   
-%FORMAT(5E16.8)                                                                 
-  2.00000000E-01  2.50000000E-01  1.80000000E-01  1.60000000E-01  1.55555556E-01
-  2.50000000E-01  0.00000000E+00  1.50000000E-01  1.66666667E-01
-%FLAG DIHEDRAL_PERIODICITY                                                      
-%FORMAT(5E16.8)                                                                 
-  1.00000000E+00  2.00000000E+00  3.00000000E+00  3.00000000E+00  3.00000000E+00
-  1.00000000E+00  3.00000000E+00  3.00000000E+00  3.00000000E+00
-%FLAG DIHEDRAL_PHASE                                                            
-%FORMAT(5E16.8)                                                                 
-  3.14159400E+00  3.14159400E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
-  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
-%FLAG SCEE_SCALE_FACTOR                                                         
-%FORMAT(5E16.8)                                                                 
-  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00
-  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00
-%FLAG SCNB_SCALE_FACTOR                                                         
-%FORMAT(5E16.8)                                                                 
-  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
-  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
-%FLAG SOLTY                                                                     
-%FORMAT(5E16.8)                                                                 
-  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
-%FLAG LENNARD_JONES_ACOEF                                                       
-%FORMAT(5E16.8)                                                                 
-  1.04308023E+06  7.91544157E+05  5.81803229E+05  9.71708117E+04  6.82786631E+04
-  7.51607703E+03  6.78771368E+04  4.66922514E+04  4.98586848E+03  3.25969625E+03
-  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
-%FLAG LENNARD_JONES_BCOEF                                                       
-%FORMAT(5E16.8)                                                                 
-  6.75612247E+02  6.93079947E+02  6.99746810E+02  1.26919150E+02  1.25287818E+02
-  2.17257828E+01  1.06076943E+02  1.03606917E+02  1.76949863E+01  1.43076527E+01
-  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
-%FLAG BONDS_INC_HYDROGEN                                                        
-%FORMAT(10I8)                                                                   
-       0      15       2       0      18       2       0      21       2       3
-      24       2       3      27       2       6      30       2       6      33
-       2       9      36       4       9      39       4      12      42       5
-%FLAG BONDS_WITHOUT_HYDROGEN                                                    
-%FORMAT(10I8)                                                                   
-       0       3       1       3       6       1       6       9       1       9
-      12       3
-%FLAG ANGLES_INC_HYDROGEN                                                       
-%FORMAT(10I8)                                                                   
-       0       3      24       2       0       3      27       2       3       0
-      15       2       3       0      18       2       3       0      21       2
-       3       6      30       2       3       6      33       2       6       3
-      24       2       6       3      27       2       6       9      36       4
-       6       9      39       4       9       6      30       2       9       6
-      33       2       9      12      42       5      12       9      36       6
-      12       9      39       6      15       0      18       7      15       0
-      21       7      18       0      21       7      24       3      27       7
-      30       6      33       7      36       9      39       8
-%FLAG ANGLES_WITHOUT_HYDROGEN                                                   
-%FORMAT(10I8)                                                                   
-       0       3       6       1       3       6       9       1       6       9
-      12       3
-%FLAG DIHEDRALS_INC_HYDROGEN                                                    
-%FORMAT(10I8)                                                                   
-       0       3       6      30       4       0       3       6      33       4
-       3       6       9      36       5       3       6       9      39       5
-      15       0       3       6       4      18       0       3       6       4
-      21       0       3       6       4       6       9      12      42       6
-       6       9     -12      42       4       9       6       3      24       4
-       9       6       3      27       4      12       9       6      30       6
-      12       9      -6      30       7      12       9       6      33       6
-      12       9      -6      33       7      15       0       3      24       8
-      15       0       3      27       8      18       0       3      24       8
-      18       0       3      27       8      21       0       3      24       8
-      21       0       3      27       8      24       3       6      30       8
-      24       3       6      33       8      27       3       6      30       8
-      27       3       6      33       8      30       6       9      36       5
-      30       6       9      39       5      33       6       9      36       5
-      33       6       9      39       5      36       9      12      42       9
-      39       9      12      42       9
-%FLAG DIHEDRALS_WITHOUT_HYDROGEN                                                
-%FORMAT(10I8)                                                                   
-       0       3       6       9       1       0       3      -6       9       2
-       0       3      -6       9       3       3       6       9      12       5
-%FLAG EXCLUDED_ATOMS_LIST                                                       
-%FORMAT(10I8)                                                                   
-       2       3       4       6       7       8       9      10      11      12
-       3       4       5       6       7       8       9      10      11      12
-      13      14       4       5       6       7       8       9      10      11
-      12      13      14      15       5       9      10      11      12      13
-      14      15      11      12      13      14      15       7       8       9
-      10       8       9      10       9      10      10      11      12      11
-      12      12      13      14      13      14      14      15      15       0
-%FLAG HBOND_ACOEF                                                               
-%FORMAT(5E16.8)                                                                 
-
-%FLAG HBOND_BCOEF                                                               
-%FORMAT(5E16.8)                                                                 
-
-%FLAG HBCUT                                                                     
-%FORMAT(5E16.8)                                                                 
-
-%FLAG AMBER_ATOM_TYPE                                                           
-%FORMAT(20a4)                                                                   
-c3  c3  c3  c3  oh  hc  hc  hc  hc  hc  hc  hc  h1  h1  ho  
-%FLAG TREE_CHAIN_CLASSIFICATION                                                 
-%FORMAT(20a4)                                                                   
-BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
-%FLAG JOIN_ARRAY                                                                
-%FORMAT(10I8)                                                                   
-       0       0       0       0       0       0       0       0       0       0
-       0       0       0       0       0
-%FLAG IROTAT                                                                    
-%FORMAT(10I8)                                                                   
-       0       0       0       0       0       0       0       0       0       0
-       0       0       0       0       0
-%FLAG RADIUS_SET                                                                
-%FORMAT(1a80)                                                                   
-modified Bondi radii (mbondi)                                                   
-%FLAG RADII                                                                     
-%FORMAT(5E16.8)                                                                 
-  1.70000000E+00  1.70000000E+00  1.70000000E+00  1.70000000E+00  1.50000000E+00
-  1.30000000E+00  1.30000000E+00  1.30000000E+00  1.30000000E+00  1.30000000E+00
-  1.30000000E+00  1.30000000E+00  1.30000000E+00  1.30000000E+00  8.00000000E-01
-%FLAG SCREEN                                                                    
-%FORMAT(5E16.8)                                                                 
-  7.20000000E-01  7.20000000E-01  7.20000000E-01  7.20000000E-01  8.50000000E-01
-  8.50000000E-01  8.50000000E-01  8.50000000E-01  8.50000000E-01  8.50000000E-01
-  8.50000000E-01  8.50000000E-01  8.50000000E-01  8.50000000E-01  8.50000000E-01
-%FLAG IPOL                                                                      
-%FORMAT(1I8)                                                                    
-       0
diff --git a/openff/toolkit/data/systems/monomers/cyclohexane.frcmod b/openff/toolkit/data/systems/monomers/cyclohexane.frcmod
deleted file mode 100644
index c60366e5..00000000
--- a/openff/toolkit/data/systems/monomers/cyclohexane.frcmod
+++ /dev/null
@@ -1,15 +0,0 @@
-Remark line goes here
-MASS
-
-BOND
-
-ANGLE
-
-DIHE
-
-IMPROPER
-
-NONBON
-
-
-
diff --git a/openff/toolkit/data/systems/monomers/cyclohexane.inpcrd b/openff/toolkit/data/systems/monomers/cyclohexane.inpcrd
deleted file mode 100644
index cc894067..00000000
--- a/openff/toolkit/data/systems/monomers/cyclohexane.inpcrd
+++ /dev/null
@@ -1,11 +0,0 @@
-MOL
-    18
-   0.3260000   0.2270000  -1.4210000  -1.0120000  -0.3780000  -1.0040000
-  -1.4190000   0.0670000   0.3980000  -0.3260000  -0.2270000   1.4210000
-   1.0120000   0.3780000   1.0050000   1.4190000  -0.0670000  -0.3980000
-   0.2150000   1.3130000  -1.5340000   0.6200000  -0.1680000  -2.4000000
-  -1.7870000  -0.0890000  -1.7230000  -0.9420000  -1.4720000  -1.0330000
-  -1.6320000   1.1440000   0.3910000  -2.3450000  -0.4390000   0.6920000
-  -0.6210000   0.1680000   2.4000000  -0.2150000  -1.3130000   1.5340000
-   0.9420000   1.4720000   1.0330000   1.7880000   0.0880000   1.7230000
-   2.3460000   0.4400000  -0.6910000   1.6320000  -1.1430000  -0.3910000
diff --git a/openff/toolkit/data/systems/monomers/cyclohexane.prmtop b/openff/toolkit/data/systems/monomers/cyclohexane.prmtop
deleted file mode 100644
index dbba0fa9..00000000
--- a/openff/toolkit/data/systems/monomers/cyclohexane.prmtop
+++ /dev/null
@@ -1,202 +0,0 @@
-%VERSION  VERSION_STAMP = V0001.000  DATE = 06/27/16  12:04:22                  
-%FLAG TITLE                                                                     
-%FORMAT(20a4)                                                                   
-MOL                                                                             
-%FLAG POINTERS                                                                  
-%FORMAT(10I8)                                                                   
-      18       2      12       6      30       6      48      18       0       0
-     106       1       6       6      18       2       3       5       2       0
-       0       0       0       0       0       0       0       0      18       0
-       0
-%FLAG ATOM_NAME                                                                 
-%FORMAT(20a4)                                                                   
-C1  C2  C3  C4  C5  C6  H1  H2  H3  H4  H5  H6  H7  H8  H9  H10 H11 H12 
-%FLAG CHARGE                                                                    
-%FORMAT(5E16.8)                                                                 
- -1.38671703E+00 -1.37578365E+00 -1.37578365E+00 -1.37578365E+00 -1.37578365E+00
- -1.37578365E+00  6.88802940E-01  6.88802940E-01  6.88802940E-01  6.88802940E-01
-  6.88802940E-01  6.88802940E-01  6.88802940E-01  6.88802940E-01  6.88802940E-01
-  6.88802940E-01  6.88802940E-01  6.88802940E-01
-%FLAG ATOMIC_NUMBER                                                             
-%FORMAT(10I8)                                                                   
-       6       6       6       6       6       6       1       1       1       1
-       1       1       1       1       1       1       1       1
-%FLAG MASS                                                                      
-%FORMAT(5E16.8)                                                                 
-  1.20100000E+01  1.20100000E+01  1.20100000E+01  1.20100000E+01  1.20100000E+01
-  1.20100000E+01  1.00800000E+00  1.00800000E+00  1.00800000E+00  1.00800000E+00
-  1.00800000E+00  1.00800000E+00  1.00800000E+00  1.00800000E+00  1.00800000E+00
-  1.00800000E+00  1.00800000E+00  1.00800000E+00
-%FLAG ATOM_TYPE_INDEX                                                           
-%FORMAT(10I8)                                                                   
-       1       1       1       1       1       1       2       2       2       2
-       2       2       2       2       2       2       2       2
-%FLAG NUMBER_EXCLUDED_ATOMS                                                     
-%FORMAT(10I8)                                                                   
-      15      14      13      12      11      10       5       4       3       2
-       3       2       3       2       3       2       1       1
-%FLAG NONBONDED_PARM_INDEX                                                      
-%FORMAT(10I8)                                                                   
-       1       2       2       3
-%FLAG RESIDUE_LABEL                                                             
-%FORMAT(20a4)                                                                   
-MOL 
-%FLAG RESIDUE_POINTER                                                           
-%FORMAT(10I8)                                                                   
-       1
-%FLAG BOND_FORCE_CONSTANT                                                       
-%FORMAT(5E16.8)                                                                 
-  3.03100000E+02  3.37300000E+02
-%FLAG BOND_EQUIL_VALUE                                                          
-%FORMAT(5E16.8)                                                                 
-  1.53500000E+00  1.09200000E+00
-%FLAG ANGLE_FORCE_CONSTANT                                                      
-%FORMAT(5E16.8)                                                                 
-  6.32100000E+01  4.63700000E+01  3.94300000E+01
-%FLAG ANGLE_EQUIL_VALUE                                                         
-%FORMAT(5E16.8)                                                                 
-  1.93085858E+00  1.92073567E+00  1.89106506E+00
-%FLAG DIHEDRAL_FORCE_CONSTANT                                                   
-%FORMAT(5E16.8)                                                                 
-  2.00000000E-01  2.50000000E-01  1.80000000E-01  1.60000000E-01  1.50000000E-01
-%FLAG DIHEDRAL_PERIODICITY                                                      
-%FORMAT(5E16.8)                                                                 
-  1.00000000E+00  2.00000000E+00  3.00000000E+00  3.00000000E+00  3.00000000E+00
-%FLAG DIHEDRAL_PHASE                                                            
-%FORMAT(5E16.8)                                                                 
-  3.14159400E+00  3.14159400E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
-%FLAG SCEE_SCALE_FACTOR                                                         
-%FORMAT(5E16.8)                                                                 
-  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00
-%FLAG SCNB_SCALE_FACTOR                                                         
-%FORMAT(5E16.8)                                                                 
-  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
-%FLAG SOLTY                                                                     
-%FORMAT(5E16.8)                                                                 
-  0.00000000E+00  0.00000000E+00
-%FLAG LENNARD_JONES_ACOEF                                                       
-%FORMAT(5E16.8)                                                                 
-  1.04308023E+06  9.71708117E+04  7.51607703E+03
-%FLAG LENNARD_JONES_BCOEF                                                       
-%FORMAT(5E16.8)                                                                 
-  6.75612247E+02  1.26919150E+02  2.17257828E+01
-%FLAG BONDS_INC_HYDROGEN                                                        
-%FORMAT(10I8)                                                                   
-       0      18       2       0      21       2       3      24       2       3
-      27       2       6      30       2       6      33       2       9      36
-       2       9      39       2      12      42       2      12      45       2
-      15      48       2      15      51       2
-%FLAG BONDS_WITHOUT_HYDROGEN                                                    
-%FORMAT(10I8)                                                                   
-       0      15       1       0       3       1       3       6       1       6
-       9       1       9      12       1      12      15       1
-%FLAG ANGLES_INC_HYDROGEN                                                       
-%FORMAT(10I8)                                                                   
-       0      15      48       2       0      15      51       2       0       3
-      24       2       0       3      27       2       3       0      18       2
-       3       0      21       2       3       6      30       2       3       6
-      33       2       6       3      24       2       6       3      27       2
-       6       9      36       2       6       9      39       2       9       6
-      30       2       9       6      33       2       9      12      42       2
-       9      12      45       2      12       9      36       2      12       9
-      39       2      12      15      48       2      12      15      51       2
-      15       0      18       2      15       0      21       2      15      12
-      42       2      15      12      45       2      18       0      21       3
-      24       3      27       3      30       6      33       3      36       9
-      39       3      42      12      45       3      48      15      51       3
-%FLAG ANGLES_WITHOUT_HYDROGEN                                                   
-%FORMAT(10I8)                                                                   
-       0      15      12       1       0       3       6       1       3       0
-      15       1       3       6       9       1       6       9      12       1
-       9      12      15       1
-%FLAG DIHEDRALS_INC_HYDROGEN                                                    
-%FORMAT(10I8)                                                                   
-       0      15      12      42       4       0      15      12      45       4
-       0       3       6      30       4       0       3       6      33       4
-       3       0      15      48       4       3       0      15      51       4
-       3       6       9      36       4       3       6       9      39       4
-      18       0       3       6       4      21       0       3       6       4
-       6       9      12      42       4       6       9      12      45       4
-       9       6       3      24       4       9       6       3      27       4
-       9      12      15      48       4       9      12      15      51       4
-      12       9       6      30       4      12       9       6      33       4
-      18       0      15      12       4      21       0      15      12       4
-      15       0       3      24       4      15       0       3      27       4
-      15      12       9      36       4      15      12       9      39       4
-      18       0      15      48       5      18       0      15      51       5
-      18       0       3      24       5      18       0       3      27       5
-      21       0      15      48       5      21       0      15      51       5
-      21       0       3      24       5      21       0       3      27       5
-      24       3       6      30       5      24       3       6      33       5
-      27       3       6      30       5      27       3       6      33       5
-      30       6       9      36       5      30       6       9      39       5
-      33       6       9      36       5      33       6       9      39       5
-      36       9      12      42       5      36       9      12      45       5
-      39       9      12      42       5      39       9      12      45       5
-      42      12      15      48       5      42      12      15      51       5
-      45      12      15      48       5      45      12      15      51       5
-%FLAG DIHEDRALS_WITHOUT_HYDROGEN                                                
-%FORMAT(10I8)                                                                   
-       0      15      12       9       1       0      15     -12       9       2
-       0      15     -12       9       3       0       3      -6       9       1
-       0       3      -6       9       2       0       3      -6       9       3
-       3       0      15      12       1       3       0     -15      12       2
-       3       0     -15      12       3       3       6      -9      12       1
-       3       6      -9      12       2       3       6      -9      12       3
-      15       0       3       6       1      15       0      -3       6       2
-      15       0      -3       6       3       6       9     -12      15       1
-       6       9     -12      15       2       6       9     -12      15       3
-%FLAG EXCLUDED_ATOMS_LIST                                                       
-%FORMAT(10I8)                                                                   
-       2       3       4       5       6       7       8       9      10      11
-      12      15      16      17      18       3       4       5       6       7
-       8       9      10      11      12      13      14      17      18       4
-       5       6       7       8       9      10      11      12      13      14
-      15      16       5       6       9      10      11      12      13      14
-      15      16      17      18       6       7       8      11      12      13
-      14      15      16      17      18       7       8       9      10      13
-      14      15      16      17      18       8       9      10      17      18
-       9      10      17      18      10      11      12      11      12      12
-      13      14      13      14      14      15      16      15      16      16
-      17      18      17      18      18       0
-%FLAG HBOND_ACOEF                                                               
-%FORMAT(5E16.8)                                                                 
-
-%FLAG HBOND_BCOEF                                                               
-%FORMAT(5E16.8)                                                                 
-
-%FLAG HBCUT                                                                     
-%FORMAT(5E16.8)                                                                 
-
-%FLAG AMBER_ATOM_TYPE                                                           
-%FORMAT(20a4)                                                                   
-c3  c3  c3  c3  c3  c3  hc  hc  hc  hc  hc  hc  hc  hc  hc  hc  hc  hc  
-%FLAG TREE_CHAIN_CLASSIFICATION                                                 
-%FORMAT(20a4)                                                                   
-BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
-%FLAG JOIN_ARRAY                                                                
-%FORMAT(10I8)                                                                   
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-%FORMAT(1a80)                                                                   
-modified Bondi radii (mbondi)                                                   
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-%FORMAT(1I8)                                                                    
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diff --git a/openff/toolkit/data/systems/monomers/ethanol.frcmod b/openff/toolkit/data/systems/monomers/ethanol.frcmod
deleted file mode 100644
index c60366e5..00000000
--- a/openff/toolkit/data/systems/monomers/ethanol.frcmod
+++ /dev/null
@@ -1,15 +0,0 @@
-Remark line goes here
-MASS
-
-BOND
-
-ANGLE
-
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-
-IMPROPER
-
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-
-
-
diff --git a/openff/toolkit/data/systems/monomers/ethanol.inpcrd b/openff/toolkit/data/systems/monomers/ethanol.inpcrd
deleted file mode 100644
index 55daeed5..00000000
--- a/openff/toolkit/data/systems/monomers/ethanol.inpcrd
+++ /dev/null
@@ -1,7 +0,0 @@
-MOL
-     9
-   1.0620000  -0.2680000  -0.0010000   1.9100000   0.9130000  -0.4220000
-   1.5170000   1.3240000  -1.7230000   1.3390000  -0.6110000   1.0000000
-  -0.0000000  -0.0000000  -0.0010000   1.1800000  -1.0990000  -0.7040000
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-   2.0790000   2.0790000  -1.9610000
diff --git a/openff/toolkit/data/systems/monomers/ethanol.prmtop b/openff/toolkit/data/systems/monomers/ethanol.prmtop
deleted file mode 100644
index 338c546e..00000000
--- a/openff/toolkit/data/systems/monomers/ethanol.prmtop
+++ /dev/null
@@ -1,154 +0,0 @@
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-MOL                                                                             
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-  1.20100000E+01  1.20100000E+01  1.60000000E+01  1.00800000E+00  1.00800000E+00
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-       1       1       2       3       3       3       4       4       5
-%FLAG NUMBER_EXCLUDED_ATOMS                                                     
-%FORMAT(10I8)                                                                   
-       8       7       6       4       3       2       2       1       1
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-%FORMAT(10I8)                                                                   
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-%FLAG RESIDUE_LABEL                                                             
-%FORMAT(20a4)                                                                   
-MOL 
-%FLAG RESIDUE_POINTER                                                           
-%FORMAT(10I8)                                                                   
-       1
-%FLAG BOND_FORCE_CONSTANT                                                       
-%FORMAT(5E16.8)                                                                 
-  3.03100000E+02  3.37300000E+02  3.14100000E+02  3.35900000E+02  3.69600000E+02
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-%FORMAT(5E16.8)                                                                 
-  1.53500000E+00  1.09200000E+00  1.42600000E+00  1.09300000E+00  9.74000000E-01
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-%FORMAT(5E16.8)                                                                 
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-%FORMAT(5E16.8)                                                                 
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-%FORMAT(5E16.8)                                                                 
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-  1.00000000E+00  3.00000000E+00  3.00000000E+00  3.00000000E+00  3.00000000E+00
-%FLAG DIHEDRAL_PHASE                                                            
-%FORMAT(5E16.8)                                                                 
-  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00  0.00000000E+00
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-%FORMAT(5E16.8)                                                                 
-  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00  1.20000000E+00
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-%FORMAT(5E16.8)                                                                 
-  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00  2.00000000E+00
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-%FORMAT(5E16.8)                                                                 
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-%FORMAT(5E16.8)                                                                 
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-%FLAG DIHEDRALS_WITHOUT_HYDROGEN                                                
-%FORMAT(10I8)                                                                   
-
-%FLAG EXCLUDED_ATOMS_LIST                                                       
-%FORMAT(10I8)                                                                   
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-%FLAG HBOND_ACOEF                                                               
-%FORMAT(5E16.8)                                                                 
-
-%FLAG HBOND_BCOEF                                                               
-%FORMAT(5E16.8)                                                                 
-
-%FLAG HBCUT                                                                     
-%FORMAT(5E16.8)                                                                 
-
-%FLAG AMBER_ATOM_TYPE                                                           
-%FORMAT(20a4)                                                                   
-c3  c3  oh  hc  hc  hc  h1  h1  ho  
-%FLAG TREE_CHAIN_CLASSIFICATION                                                 
-%FORMAT(20a4)                                                                   
-BLA BLA BLA BLA BLA BLA BLA BLA BLA 
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-%FORMAT(10I8)                                                                   
-       0       0       0       0       0       0       0       0       0
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-%FORMAT(10I8)                                                                   
-       0       0       0       0       0       0       0       0       0
-%FLAG RADIUS_SET                                                                
-%FORMAT(1a80)                                                                   
-modified Bondi radii (mbondi)                                                   
-%FLAG RADII                                                                     
-%FORMAT(5E16.8)                                                                 
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-%FORMAT(5E16.8)                                                                 
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-%FLAG IPOL                                                                      
-%FORMAT(1I8)                                                                    
-       0
diff --git a/openff/toolkit/data/systems/monomers/methane.frcmod b/openff/toolkit/data/systems/monomers/methane.frcmod
deleted file mode 100644
index c60366e5..00000000
--- a/openff/toolkit/data/systems/monomers/methane.frcmod
+++ /dev/null
@@ -1,15 +0,0 @@
-Remark line goes here
-MASS
-
-BOND
-
-ANGLE
-
-DIHE
-
-IMPROPER
-
-NONBON
-
-
-
diff --git a/openff/toolkit/data/systems/monomers/methane.inpcrd b/openff/toolkit/data/systems/monomers/methane.inpcrd
deleted file mode 100644
index cbf0e00c..00000000
--- a/openff/toolkit/data/systems/monomers/methane.inpcrd
+++ /dev/null
@@ -1,5 +0,0 @@
-MOL
-     5
-  -0.0000000  -0.0000000   0.0000000   0.5540000   0.8000000   0.4960000
-   0.6830000  -0.8130000  -0.2540000  -0.7780000  -0.3730000   0.6690000
-  -0.4590000   0.3870000  -0.9120000
diff --git a/openff/toolkit/data/systems/monomers/methane.prmtop b/openff/toolkit/data/systems/monomers/methane.prmtop
deleted file mode 100644
index 23430c78..00000000
--- a/openff/toolkit/data/systems/monomers/methane.prmtop
+++ /dev/null
@@ -1,131 +0,0 @@
-%VERSION  VERSION_STAMP = V0001.000  DATE = 06/27/16  12:06:10                  
-%FLAG TITLE                                                                     
-%FORMAT(20a4)                                                                   
-MOL                                                                             
-%FLAG POINTERS                                                                  
-%FORMAT(10I8)                                                                   
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-%FORMAT(20a4)                                                                   
-C1  H1  H2  H3  H4  
-%FLAG CHARGE                                                                    
-%FORMAT(5E16.8)                                                                 
- -1.98258624E+00  4.95646560E-01  4.95646560E-01  4.95646560E-01  4.95646560E-01
-%FLAG ATOMIC_NUMBER                                                             
-%FORMAT(10I8)                                                                   
-       6       1       1       1       1
-%FLAG MASS                                                                      
-%FORMAT(5E16.8)                                                                 
-  1.20100000E+01  1.00800000E+00  1.00800000E+00  1.00800000E+00  1.00800000E+00
-%FLAG ATOM_TYPE_INDEX                                                           
-%FORMAT(10I8)                                                                   
-       1       2       2       2       2
-%FLAG NUMBER_EXCLUDED_ATOMS                                                     
-%FORMAT(10I8)                                                                   
-       4       3       2       1       1
-%FLAG NONBONDED_PARM_INDEX                                                      
-%FORMAT(10I8)                                                                   
-       1       2       2       3
-%FLAG RESIDUE_LABEL                                                             
-%FORMAT(20a4)                                                                   
-MOL 
-%FLAG RESIDUE_POINTER                                                           
-%FORMAT(10I8)                                                                   
-       1
-%FLAG BOND_FORCE_CONSTANT                                                       
-%FORMAT(5E16.8)                                                                 
-  3.37300000E+02
-%FLAG BOND_EQUIL_VALUE                                                          
-%FORMAT(5E16.8)                                                                 
-  1.09200000E+00
-%FLAG ANGLE_FORCE_CONSTANT                                                      
-%FORMAT(5E16.8)                                                                 
-  3.94300000E+01
-%FLAG ANGLE_EQUIL_VALUE                                                         
-%FORMAT(5E16.8)                                                                 
-  1.89106506E+00
-%FLAG DIHEDRAL_FORCE_CONSTANT                                                   
-%FORMAT(5E16.8)                                                                 
-
-%FLAG DIHEDRAL_PERIODICITY                                                      
-%FORMAT(5E16.8)                                                                 
-
-%FLAG DIHEDRAL_PHASE                                                            
-%FORMAT(5E16.8)                                                                 
-
-%FLAG SCEE_SCALE_FACTOR                                                         
-%FORMAT(5E16.8)                                                                 
-
-%FLAG SCNB_SCALE_FACTOR                                                         
-%FORMAT(5E16.8)                                                                 
-
-%FLAG SOLTY                                                                     
-%FORMAT(5E16.8)                                                                 
-  0.00000000E+00  0.00000000E+00
-%FLAG LENNARD_JONES_ACOEF                                                       
-%FORMAT(5E16.8)                                                                 
-  1.04308023E+06  9.71708117E+04  7.51607703E+03
-%FLAG LENNARD_JONES_BCOEF                                                       
-%FORMAT(5E16.8)                                                                 
-  6.75612247E+02  1.26919150E+02  2.17257828E+01
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-%FORMAT(10I8)                                                                   
-       0       3       1       0       6       1       0       9       1       0
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-%FLAG BONDS_WITHOUT_HYDROGEN                                                    
-%FORMAT(10I8)                                                                   
-
-%FLAG ANGLES_INC_HYDROGEN                                                       
-%FORMAT(10I8)                                                                   
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-%FORMAT(10I8)                                                                   
-
-%FLAG DIHEDRALS_INC_HYDROGEN                                                    
-%FORMAT(10I8)                                                                   
-
-%FLAG DIHEDRALS_WITHOUT_HYDROGEN                                                
-%FORMAT(10I8)                                                                   
-
-%FLAG EXCLUDED_ATOMS_LIST                                                       
-%FORMAT(10I8)                                                                   
-       2       3       4       5       3       4       5       4       5       5
-       0
-%FLAG HBOND_ACOEF                                                               
-%FORMAT(5E16.8)                                                                 
-
-%FLAG HBOND_BCOEF                                                               
-%FORMAT(5E16.8)                                                                 
-
-%FLAG HBCUT                                                                     
-%FORMAT(5E16.8)                                                                 
-
-%FLAG AMBER_ATOM_TYPE                                                           
-%FORMAT(20a4)                                                                   
-c3  hc  hc  hc  hc  
-%FLAG TREE_CHAIN_CLASSIFICATION                                                 
-%FORMAT(20a4)                                                                   
-BLA BLA BLA BLA BLA 
-%FLAG JOIN_ARRAY                                                                
-%FORMAT(10I8)                                                                   
-       0       0       0       0       0
-%FLAG IROTAT                                                                    
-%FORMAT(10I8)                                                                   
-       0       0       0       0       0
-%FLAG RADIUS_SET                                                                
-%FORMAT(1a80)                                                                   
-modified Bondi radii (mbondi)                                                   
-%FLAG RADII                                                                     
-%FORMAT(5E16.8)                                                                 
-  1.70000000E+00  1.30000000E+00  1.30000000E+00  1.30000000E+00  1.30000000E+00
-%FLAG SCREEN                                                                    
-%FORMAT(5E16.8)                                                                 
-  7.20000000E-01  8.50000000E-01  8.50000000E-01  8.50000000E-01  8.50000000E-01
-%FLAG IPOL                                                                      
-%FORMAT(1I8)                                                                    
-       0
diff --git a/openff/toolkit/data/systems/monomers/propane.frcmod b/openff/toolkit/data/systems/monomers/propane.frcmod
deleted file mode 100644
index c60366e5..00000000
--- a/openff/toolkit/data/systems/monomers/propane.frcmod
+++ /dev/null
@@ -1,15 +0,0 @@
-Remark line goes here
-MASS
-
-BOND
-
-ANGLE
-
-DIHE
-
-IMPROPER
-
-NONBON
-
-
-
diff --git a/openff/toolkit/data/systems/monomers/propane.inpcrd b/openff/toolkit/data/systems/monomers/propane.inpcrd
deleted file mode 100644
index 5ccfb035..00000000
--- a/openff/toolkit/data/systems/monomers/propane.inpcrd
+++ /dev/null
@@ -1,8 +0,0 @@
-MOL
-    11
-  -0.5530000  -0.2790000   0.9030000   0.3850000  -0.4430000   2.0870000
-   1.1310000   0.8190000   2.3890000  -1.0900000  -1.2100000   0.6960000
-  -1.2980000   0.5000000   1.0970000   0.0090000  -0.0000000   0.0060000
-  -0.1910000  -0.7420000   2.9700000   1.1010000  -1.2440000   1.8770000
-   1.7960000   0.6630000   3.2470000   0.4380000   1.6290000   2.6400000
-   1.7440000   1.1210000   1.5340000
diff --git a/openff/toolkit/data/systems/monomers/propane.prmtop b/openff/toolkit/data/systems/monomers/propane.prmtop
deleted file mode 100644
index e2fd83c5..00000000
--- a/openff/toolkit/data/systems/monomers/propane.prmtop
+++ /dev/null
@@ -1,160 +0,0 @@
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-%FORMAT(20a4)                                                                   
-MOL                                                                             
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-%FORMAT(20a4)                                                                   
-C1  C2  C3  H1  H2  H3  H4  H5  H6  H7  H8  
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-%FORMAT(5E16.8)                                                                 
- -1.68556275E+00 -1.48329522E+00 -1.68191829E+00  5.86758060E-01  5.86758060E-01
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-  5.86758060E-01
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-%FORMAT(10I8)                                                                   
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-%FORMAT(5E16.8)                                                                 
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-%FORMAT(10I8)                                                                   
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-%FORMAT(10I8)                                                                   
-      10       9       8       4       3       2       4       3       2       1
-       1
-%FLAG NONBONDED_PARM_INDEX                                                      
-%FORMAT(10I8)                                                                   
-       1       2       2       3
-%FLAG RESIDUE_LABEL                                                             
-%FORMAT(20a4)                                                                   
-MOL 
-%FLAG RESIDUE_POINTER                                                           
-%FORMAT(10I8)                                                                   
-       1
-%FLAG BOND_FORCE_CONSTANT                                                       
-%FORMAT(5E16.8)                                                                 
-  3.03100000E+02  3.37300000E+02
-%FLAG BOND_EQUIL_VALUE                                                          
-%FORMAT(5E16.8)                                                                 
-  1.53500000E+00  1.09200000E+00
-%FLAG ANGLE_FORCE_CONSTANT                                                      
-%FORMAT(5E16.8)                                                                 
-  6.32100000E+01  4.63700000E+01  3.94300000E+01
-%FLAG ANGLE_EQUIL_VALUE                                                         
-%FORMAT(5E16.8)                                                                 
-  1.93085858E+00  1.92073567E+00  1.89106506E+00
-%FLAG DIHEDRAL_FORCE_CONSTANT                                                   
-%FORMAT(5E16.8)                                                                 
-  1.60000000E-01  1.50000000E-01
-%FLAG DIHEDRAL_PERIODICITY                                                      
-%FORMAT(5E16.8)                                                                 
-  3.00000000E+00  3.00000000E+00
-%FLAG DIHEDRAL_PHASE                                                            
-%FORMAT(5E16.8)                                                                 
-  0.00000000E+00  0.00000000E+00
-%FLAG SCEE_SCALE_FACTOR                                                         
-%FORMAT(5E16.8)                                                                 
-  1.20000000E+00  1.20000000E+00
-%FLAG SCNB_SCALE_FACTOR                                                         
-%FORMAT(5E16.8)                                                                 
-  2.00000000E+00  2.00000000E+00
-%FLAG SOLTY                                                                     
-%FORMAT(5E16.8)                                                                 
-  0.00000000E+00  0.00000000E+00
-%FLAG LENNARD_JONES_ACOEF                                                       
-%FORMAT(5E16.8)                                                                 
-  1.04308023E+06  9.71708117E+04  7.51607703E+03
-%FLAG LENNARD_JONES_BCOEF                                                       
-%FORMAT(5E16.8)                                                                 
-  6.75612247E+02  1.26919150E+02  2.17257828E+01
-%FLAG BONDS_INC_HYDROGEN                                                        
-%FORMAT(10I8)                                                                   
-       0       9       2       0      12       2       0      15       2       3
-      18       2       3      21       2       6      24       2       6      27
-       2       6      30       2
-%FLAG BONDS_WITHOUT_HYDROGEN                                                    
-%FORMAT(10I8)                                                                   
-       0       3       1       3       6       1
-%FLAG ANGLES_INC_HYDROGEN                                                       
-%FORMAT(10I8)                                                                   
-       0       3      18       2       0       3      21       2       3       0
-       9       2       3       0      12       2       3       0      15       2
-       3       6      24       2       3       6      27       2       3       6
-      30       2       6       3      18       2       6       3      21       2
-       9       0      12       3       9       0      15       3      12       0
-      15       3      18       3      21       3      24       6      27       3
-      24       6      30       3      27       6      30       3
-%FLAG ANGLES_WITHOUT_HYDROGEN                                                   
-%FORMAT(10I8)                                                                   
-       0       3       6       1
-%FLAG DIHEDRALS_INC_HYDROGEN                                                    
-%FORMAT(10I8)                                                                   
-       0       3       6      24       1       0       3       6      27       1
-       0       3       6      30       1       9       0       3       6       1
-      12       0       3       6       1      15       0       3       6       1
-       9       0       3      18       2       9       0       3      21       2
-      12       0       3      18       2      12       0       3      21       2
-      15       0       3      18       2      15       0       3      21       2
-      18       3       6      24       2      18       3       6      27       2
-      18       3       6      30       2      21       3       6      24       2
-      21       3       6      27       2      21       3       6      30       2
-%FLAG DIHEDRALS_WITHOUT_HYDROGEN                                                
-%FORMAT(10I8)                                                                   
-
-%FLAG EXCLUDED_ATOMS_LIST                                                       
-%FORMAT(10I8)                                                                   
-       2       3       4       5       6       7       8       9      10      11
-       3       4       5       6       7       8       9      10      11       4
-       5       6       7       8       9      10      11       5       6       7
-       8       6       7       8       7       8       8       9      10      11
-       9      10      11      10      11      11       0
-%FLAG HBOND_ACOEF                                                               
-%FORMAT(5E16.8)                                                                 
-
-%FLAG HBOND_BCOEF                                                               
-%FORMAT(5E16.8)                                                                 
-
-%FLAG HBCUT                                                                     
-%FORMAT(5E16.8)                                                                 
-
-%FLAG AMBER_ATOM_TYPE                                                           
-%FORMAT(20a4)                                                                   
-c3  c3  c3  hc  hc  hc  hc  hc  hc  hc  hc  
-%FLAG TREE_CHAIN_CLASSIFICATION                                                 
-%FORMAT(20a4)                                                                   
-BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA BLA 
-%FLAG JOIN_ARRAY                                                                
-%FORMAT(10I8)                                                                   
-       0       0       0       0       0       0       0       0       0       0
-       0
-%FLAG IROTAT                                                                    
-%FORMAT(10I8)                                                                   
-       0       0       0       0       0       0       0       0       0       0
-       0
-%FLAG RADIUS_SET                                                                
-%FORMAT(1a80)                                                                   
-modified Bondi radii (mbondi)                                                   
-%FLAG RADII                                                                     
-%FORMAT(5E16.8)                                                                 
-  1.70000000E+00  1.70000000E+00  1.70000000E+00  1.30000000E+00  1.30000000E+00
-  1.30000000E+00  1.30000000E+00  1.30000000E+00  1.30000000E+00  1.30000000E+00
-  1.30000000E+00
-%FLAG SCREEN                                                                    
-%FORMAT(5E16.8)                                                                 
-  7.20000000E-01  7.20000000E-01  7.20000000E-01  8.50000000E-01  8.50000000E-01
-  8.50000000E-01  8.50000000E-01  8.50000000E-01  8.50000000E-01  8.50000000E-01
-  8.50000000E-01
-%FLAG IPOL                                                                      
-%FORMAT(1I8)                                                                    
-       0
diff --git a/openff/toolkit/topology/molecule.py b/openff/toolkit/topology/molecule.py
index 741545b7..2652f805 100644
--- a/openff/toolkit/topology/molecule.py
+++ b/openff/toolkit/topology/molecule.py
@@ -60,6 +60,7 @@ from openff.toolkit.utils.exceptions import (
     InvalidAtomMetadataError,
     InvalidBondOrderError,
     InvalidConformerError,
+    MissingPartialChargesError,
     MultipleMoleculesInPDBError,
     RemapIndexError,
     SmilesParsingError,
@@ -362,6 +363,35 @@ class Atom(Particle):
             index = self.molecule_atom_index
             return self._molecule._partial_charges[index]
 
+    @partial_charge.setter
+    def partial_charge(self, charge):
+        if self.molecule.partial_charges is None:
+            raise MissingPartialChargesError(
+                "Cannot set individual atom's partial charge if it is in a molecule with no partial charges. "
+                "Instead, use the `Molecule.partial_charges` setter. If this behavior is important to you, "
+                "please raise an issue describing your use case."
+            )
+
+        if not isinstance(charge, (unit.Quantity, float)):
+            raise ValueError(
+                "Cannot set partial charge with an object that is not a openff.unit.Quantity or float. "
+                f"Found object of type {type(charge)}."
+            )
+
+        if isinstance(charge, float):
+            charge = unit.Quantity(charge, unit.elementary_charge)
+
+        if not isinstance(charge.m, float):
+            raise ValueError(
+                "Cannot set partial charge with an object that is not a wrapped int or float. "
+                f"Found unit-wrapped {type(charge.m)}."
+            )
+
+        molecule_partial_charges = self.molecule.partial_charges
+        molecule_partial_charges[self.molecule_atom_index] = charge
+
+        self.molecule.partial_charges = molecule_partial_charges
+
     @property
     def is_aromatic(self):
         """
@@ -3642,9 +3672,11 @@ class FrozenMolecule(Serializable):
 
         Examples
         --------
-        >>> from openff.toolkit.tests.utils import get_monomer_mol2_file_path
-        >>> mol2_file_path = get_monomer_mol2_file_path('cyclohexane')
-        >>> molecule = Molecule.from_file(mol2_file_path)
+
+        >>> from openff.toolkit import Molecule
+        >>> from openff.toolkit.utils.utils import get_data_file_path
+        >>> sdf_file_path = get_data_file_path("molecules/toluene.sdf")
+        >>> molecule = Molecule.from_file(sdf_file_path)
 
         """
 
@@ -4129,9 +4161,9 @@ class FrozenMolecule(Serializable):
 
         Create a molecule from an RDKit molecule
 
+        >>> from openff.toolkit import Molecule
         >>> from rdkit import Chem
-        >>> from openff.toolkit.tests.utils import get_data_file_path
-        >>> rdmol = Chem.MolFromMolFile(get_data_file_path('systems/monomers/ethanol.sdf'))
+        >>> rdmol = Chem.MolFromSmiles("CCO")
         >>> molecule = Molecule.from_rdkit(rdmol)
 
         """
@@ -4208,11 +4240,12 @@ class FrozenMolecule(Serializable):
 
         Create a ``Molecule`` from an OpenEye OEMol
 
+        >>> from openff.toolkit import Molecule
         >>> from openeye import oechem
-        >>> from openff.toolkit.tests.utils import get_data_file_path
-        >>> ifs = oechem.oemolistream(get_data_file_path('systems/monomers/ethanol.mol2'))
-        >>> oemols = list(ifs.GetOEGraphMols())
-        >>> molecule = Molecule.from_openeye(oemols[0])
+        >>> oemol = oechem.OEMol()
+        >>> oechem.OESmilesToMol(oemol, '[H]C([H])([H])C([H])([H])O[H]')
+        True
+        >>> molecule = Molecule.from_openeye(oemol)
 
         """
         toolkit = OpenEyeToolkitWrapper()
diff --git a/openff/toolkit/topology/topology.py b/openff/toolkit/topology/topology.py
index 0694e5f2..f0f24fde 100644
--- a/openff/toolkit/topology/topology.py
+++ b/openff/toolkit/topology/topology.py
@@ -601,7 +601,14 @@ class Topology(Serializable):
             self._box_vectors = None
             return
         if not hasattr(box_vectors, "units"):
-            raise InvalidBoxVectorsError("Given unitless box vectors")
+            if hasattr(box_vectors, "unit"):
+                # this is probably an openmm.unit.Quantity; we should gracefully import OpenMM but
+                # the chances of this being an object with the two previous conditions met is low
+                box_vectors = ensure_quantity(box_vectors, "openff")
+
+            else:
+                raise InvalidBoxVectorsError("Given unitless box vectors")
+
         # Unit.compatible_units() returns False with itself, for some reason
         if (box_vectors.units != unit.nm) and (
             box_vectors.units not in unit.nm.compatible_units()


Test patch:
diff --git a/openff/toolkit/tests/test_molecule.py b/openff/toolkit/tests/test_molecule.py
index 320b554a..ad5f2cef 100644
--- a/openff/toolkit/tests/test_molecule.py
+++ b/openff/toolkit/tests/test_molecule.py
@@ -56,6 +56,7 @@ from openff.toolkit.utils.exceptions import (
     IncompatibleUnitError,
     InvalidBondOrderError,
     InvalidConformerError,
+    MissingPartialChargesError,
     MultipleMoleculesInPDBError,
     NotBondedError,
     RemapIndexError,
@@ -370,6 +371,57 @@ class TestAtom:
         with pytest.raises(AssertionError, match="already has an associated molecule"):
             atom.molecule = mol
 
+    @pytest.fixture()
+    def water_without_charges(self):
+        return Molecule.from_mapped_smiles("[H:2][O:1][H:3]")
+
+    @pytest.fixture()
+    def water(self, water_without_charges):
+        water_without_charges.assign_partial_charges("formal_charge")
+        water = water_without_charges
+        return water
+
+    def test_set_partial_charge(self, water):
+        water.atoms[0].partial_charge = 12.0 * unit.elementary_charge
+        water.atoms[1].partial_charge = -4.0
+        water.atoms[2].partial_charge = -8.0
+
+        assert np.allclose(
+            water.partial_charges,
+            unit.Quantity([12, -4, -8], unit.elementary_charge),
+        )
+
+        assert np.allclose(
+            [atom.partial_charge.m for atom in water.atoms],
+            [12, -4, -8],
+        )
+
+    def test_set_partial_charges_no_charges(self, water_without_charges):
+        with pytest.raises(
+            MissingPartialChargesError, match="in a molecule with no partial charges."
+        ):
+            water_without_charges.atoms[2].partial_charge = 0.0 * unit.elementary_charge
+
+    def test_set_partial_charges_int(self, water):
+        with pytest.raises(ValueError, match="Cannot set.*'int'"):
+            water.atoms[2].partial_charge = 4
+
+    def test_set_partial_charges_openmm_quantity(self, water):
+        import openmm.unit
+
+        with pytest.raises(ValueError, match="Cannot set.*openmm.unit"):
+            water.atoms[2].partial_charge = 0.0 * openmm.unit.elementary_charge
+
+    def test_set_partial_charges_array(self, water):
+        with pytest.raises(ValueError, match="unit-wrapped.*numpy.ndarray"):
+            water.atoms[2].partial_charge = unit.Quantity(
+                [0.0, 0.0], unit.elementary_charge
+            )
+
+    def test_set_partial_charges_bogus(self, water):
+        with pytest.raises(ValueError, match="Cannot set.*class 'str'"):
+            water.atoms[2].partial_charge = "the right charge"
+
 
 class TestBond:
     def test_float_bond_order(self):
@@ -945,7 +997,27 @@ class TestMolecule:
     @pytest.mark.parametrize("molecule", mini_drug_bank())
     def test_to_networkx(self, molecule):
         """Test conversion to NetworkX graph."""
-        molecule.to_networkx()
+        graph = molecule.to_networkx()
+
+        assert graph.number_of_nodes() == molecule.n_atoms
+        assert graph.number_of_edges() == molecule.n_bonds
+
+        for bond in molecule.bonds:
+            edge = graph.get_edge_data(bond.atom1_index, bond.atom2_index)
+
+            for attr in ["stereochemistry", "bond_order", "is_aromatic"]:
+                assert edge[attr] == getattr(bond, attr)
+
+        for node_index, node in graph.nodes(data=True):
+            atom = molecule.atom(node_index)
+
+            for attr in [
+                "atomic_number",
+                "is_aromatic",
+                "stereochemistry",
+                "formal_charge",
+            ]:
+                assert node[attr] == getattr(atom, attr)
 
     @requires_rdkit
     @pytest.mark.parametrize("molecule", mini_drug_bank())
diff --git a/openff/toolkit/tests/test_topology.py b/openff/toolkit/tests/test_topology.py
index c9ba9d23..d5f4eecb 100644
--- a/openff/toolkit/tests/test_topology.py
+++ b/openff/toolkit/tests/test_topology.py
@@ -204,6 +204,16 @@ class TestTopology:
             topology.box_vectors = good_vectors
             assert (topology.box_vectors == good_vectors * np.eye(3)).all()
 
+    def test_issue_1527(self):
+        """Test the error handling of setting box vectors with an OpenMM quantity."""
+        import numpy
+        import openmm.unit
+
+        topology = Topology()
+        topology.box_vectors = numpy.ones(3) * openmm.unit.nanometer
+
+        assert isinstance(topology.box_vectors, unit.Quantity)
+
     def test_is_periodic(self):
         """Test the getter and setter for is_periodic"""
         vacuum_top = Topology()