diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index f73c256a..b2a67b5a 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -125,7 +125,7 @@ jobs:
         python devtools/scripts/molecule-regressions.py
 
     - name: Run mypy
-      if: ${{ matrix.python-version == '3.10' }}
+      if: ${{ matrix.python-version == '3.11' }}
       run: |
         # As of 01/23, JAX with mypy is too slow to use without a pre-built cache
         # https://github.com/openforcefield/openff-interchange/pull/578#issuecomment-1369979875
diff --git a/docs/releasehistory.md b/docs/releasehistory.md
index e41babb1..0291d588 100644
--- a/docs/releasehistory.md
+++ b/docs/releasehistory.md
@@ -23,6 +23,8 @@ Please note that all releases prior to a version 1.0.0 are considered pre-releas
 * Previously-deprecated examples are removed.
 * `ProperTorsionKey` no longer accepts an empty tuple as atom indices.
 * Fixes a regression in which some `ElectrostaticsCollection.charges` properties did not return cached values.
+* The `charge_from_molecules` argument must include only molecules that contain partial charges and are non-isomorphic with each other.
+* The `charge_from_molecules` argument as used by the OpenFF Toolkit is handled internally as `molecules_with_preset_charges`.
 
 ## 0.3.30 - 2024-08
 
diff --git a/docs/using/edges.md b/docs/using/edges.md
index 06211d4a..b7795b9b 100644
--- a/docs/using/edges.md
+++ b/docs/using/edges.md
@@ -1,5 +1,34 @@
 # Sharp edges
 
+## Quirks of charge assignment
+
+### Charge assignment hierarchy
+
+Interchange, following the [SMIRNOFF specification](https://openforcefield.github.io/standards/standards/smirnoff/#partial-charge-and-electrostatics-models), assigns charges to (heavy) atoms with the following priority:
+
+1. **Preset charges**: Look for molecule matches in the `charge_from_molecules` argument
+2. **Library charges**: Look for chemical environment matches in library charges
+3. **Charge increments**: Look for chemical environment matches in charge increments
+4. **AM1-BCC**: Try to run some variant of AM1-BCC (presumably this is were graph charges go)
+
+If charges are successfully assigned using a method, no lower-priority methods in this list are attempted. For example:
+
+* A force field with library charge parameters for peptides (i.e. a biopolymer force field, covering all appropriate residues) will NOT try to call AM1-BCC on a biopolymers.
+* If a ligand is successfully assigned preset charges, chemical environment matching of library charges and charge increments will be skipped, as will AM1-BCC.
+* If a variant of AM1-BCC (i.e. using something other than AM1 and/or using custom BCCs) is encoded in a `<ChargeIncrementModel>` section, other AM1-BCC implementations will not be called.
+* If preset charges are not provided, a force field like OpenFF's Parsley or Sage lines without (many) library charges or charge increments will attempt AM1-BCC on all molecules (except water and monoatomic ions).
+
+After all of these steps are complete and all heavy atoms given partial charges, virtual sites are assigned charges using the values of `charge_increment`s in the virtual site parameters. Because virtual site charge are only described by the force field, using preset charges with virtual sites is discouraged.
+
+### Preset charges
+
+The following restrictions are in place when using preset charges:
+
+* All molecules in the the `charge_from_molecules` list must be non-isomorphic with each other.
+* All molecules in the the `charge_from_molecules` list must have partial charges.
+
+Using preset charges with virtual sites is discouraged as it can provide surprising results.
+
 ## Quirks of `from_openmm`
 
 ### Modified masses are ignored
diff --git a/openff/interchange/_tests/conftest.py b/openff/interchange/_tests/conftest.py
index e9fa9cbe..25a2ff70 100644
--- a/openff/interchange/_tests/conftest.py
+++ b/openff/interchange/_tests/conftest.py
@@ -84,7 +84,7 @@ def sage_with_sigma_hole(sage):
             smirks="[#6:1]-[#17:2]",
             distance=1.4 * unit.angstrom,
             type="BondCharge",
-            match="once",
+            match="all_permutations",
             charge_increment1=0.1 * unit.elementary_charge,
             charge_increment2=0.2 * unit.elementary_charge,
         ),
diff --git a/openff/interchange/_tests/unit_tests/smirnoff/test_create.py b/openff/interchange/_tests/unit_tests/smirnoff/test_create.py
index 58e70516..84959447 100644
--- a/openff/interchange/_tests/unit_tests/smirnoff/test_create.py
+++ b/openff/interchange/_tests/unit_tests/smirnoff/test_create.py
@@ -7,6 +7,7 @@
 from openff.interchange._tests import get_test_file_path
 from openff.interchange.constants import kcal_mol, kcal_mol_a2
 from openff.interchange.exceptions import (
+    PresetChargesError,
     UnassignedAngleError,
     UnassignedBondError,
     UnassignedTorsionError,
@@ -21,6 +22,7 @@
     _upconvert_vdw_handler,
     library_charge_from_molecule,
 )
+from openff.interchange.warnings import PresetChargesAndVirtualSitesWarning
 
 
 def _get_interpolated_bond_k(bond_handler) -> float:
@@ -160,7 +162,8 @@ def test_library_charges_from_molecule():
     assert library_charges.charge == [*mol.partial_charges]
 
 
-class TestChargeFromMolecules:
+class TestPresetCharges:
+    @pytest.mark.slow
     def test_charge_from_molecules_basic(self, sage):
         molecule = Molecule.from_smiles("CCO")
         molecule.assign_partial_charges(partial_charge_method="am1bcc")
@@ -231,6 +234,98 @@ def test_charges_from_molecule_reordered(
 
         assert numpy.allclose(expected_charges, found_charges)
 
+    def test_error_when_any_missing_partial_charges(self, sage):
+        topology = Topology.from_molecules(
+            [
+                Molecule.from_smiles("C"),
+                Molecule.from_smiles("CCO"),
+            ],
+        )
+
+        with pytest.raises(
+            PresetChargesError,
+            match="All.*must have partial charges",
+        ):
+            sage.create_interchange(
+                topology,
+                charge_from_molecules=[Molecule.from_smiles("C")],
+            )
+
+    def test_error_multiple_isomorphic_molecules(self, sage, ethanol, reversed_ethanol):
+        # these ethanol fixtures *do* have charges, if they didn't have charges it would be
+        # ambiguous which error should be raised
+        topology = Topology.from_molecules([ethanol, reversed_ethanol, ethanol])
+
+        with pytest.raises(
+            PresetChargesError,
+            match="All molecules.*isomorphic.*unique",
+        ):
+            sage.create_interchange(
+                topology,
+                charge_from_molecules=[ethanol, reversed_ethanol],
+            )
+
+    def test_virtual_site_charge_increments_applied_after_preset_charges_water(
+        self,
+        tip4p,
+        water,
+    ):
+        """
+        Test that charge increments to/from virtual sites are still applied after preset charges are set.
+
+        This is funky user input, since preset charges override library charges, which are important for water.
+        """
+        water.partial_charges = Quantity(
+            [-2.0, 1.0, 1.0],
+            "elementary_charge",
+        )
+
+        with pytest.warns(PresetChargesAndVirtualSitesWarning):
+            # This dict is probably ordered O H H VS
+            charges = tip4p.create_interchange(
+                water.to_topology(),
+                charge_from_molecules=[water],
+            )["Electrostatics"].charges
+
+        # tip4p_fb.offxml is meant to result in charges of -1.0517362213526 (VS) 0 (O) and 0.5258681106763 (H)
+        # the force field has 0.0 for all library charges (skipping AM1-BCC), so preset charges screw this up.
+        # the resulting charges, if using preset charges of [-2, 1, 1], should be the result of adding together
+        # [-2, 1, 1, 0] (preset charges) and
+        # [0, 1.5258681106763001, 1.5258681106763001, -1.0517362213526] (charge increments)
+
+        numpy.testing.assert_allclose(
+            [charge.m for charge in charges.values()],
+            [-2.0, 1.5258681106763001, 1.5258681106763001, -1.0517362213526],
+        )
+
+    def test_virtual_site_charge_increments_applied_after_preset_charges_ligand(
+        self,
+        sage_with_sigma_hole,
+    ):
+        ligand = Molecule.from_mapped_smiles("[C:1]([Cl:2])([Cl:3])([Cl:4])[Cl:5]")
+
+        ligand.partial_charges = Quantity(
+            [1.2, -0.3, -0.3, -0.3, -0.3],
+            "elementary_charge",
+        )
+
+        with pytest.warns(PresetChargesAndVirtualSitesWarning):
+            # This dict is probably ordered C Cl Cl Cl Cl VS VS VS VS
+            charges = sage_with_sigma_hole.create_interchange(
+                ligand.to_topology(),
+                charge_from_molecules=[ligand],
+            )["Electrostatics"].charges
+
+        # this fake sigma hole parameter shifts 0.1 e from the carbon and 0.2 e from the chlorine, so the
+        # resulting charges should be like
+        # [1.2, -0.3, -0.3, -0.3, -0.3] +
+        # [0.4, 0.2, 0.2, 0.2, 0.2, -0.3, -0.3, -0.3, -0.3]
+
+        numpy.testing.assert_allclose(
+            [charge.m for charge in charges.values()],
+            [1.6, -0.1, -0.1, -0.1, -0.1, -0.3, -0.3, -0.3, -0.3],
+        )
+
 
 @skip_if_missing("openmm")
 class TestPartialBondOrdersFromMolecules:
diff --git a/openff/interchange/common/_nonbonded.py b/openff/interchange/common/_nonbonded.py
index d55b0de6..be2b5202 100644
--- a/openff/interchange/common/_nonbonded.py
+++ b/openff/interchange/common/_nonbonded.py
@@ -101,7 +101,7 @@ class ElectrostaticsCollection(_NonbondedCollection):
     nonperiodic_potential: Literal["Coulomb", "cutoff", "no-cutoff"] = Field("Coulomb")
     exception_potential: Literal["Coulomb"] = Field("Coulomb")
 
-    _charges: dict[Any, _ElementaryChargeQuantity] = PrivateAttr(default_factory=dict)
+    _charges: dict[Any, _ElementaryChargeQuantity] = PrivateAttr()
     _charges_cached: bool = PrivateAttr(default=False)
 
     @computed_field  # type: ignore[misc]
@@ -110,7 +110,7 @@ def charges(
         self,
     ) -> dict[TopologyKey | LibraryChargeTopologyKey | VirtualSiteKey, _ElementaryChargeQuantity]:
         """Get the total partial charge on each atom, including virtual sites."""
-        if len(self._charges) == 0 or self._charges_cached is False:  # type: ignore[has-type]
+        if len(self._charges) == 0 or self._charges_cached is False:
             self._charges.update(self._get_charges(include_virtual_sites=False))
             self._charges_cached = True
 
diff --git a/openff/interchange/components/interchange.py b/openff/interchange/components/interchange.py
index 4b3fd94e..f7261d4e 100644
--- a/openff/interchange/components/interchange.py
+++ b/openff/interchange/components/interchange.py
@@ -109,7 +109,9 @@ def from_smirnoff(
             positions are taken from the molecules in topology, if present on all molecules.
         charge_from_molecules : `List[openff.toolkit.molecule.Molecule]`, optional
             If specified, partial charges will be taken from the given molecules
-            instead of being determined by the force field.
+            instead of being determined by the force field. All molecules in this list
+            must have partial charges assigned and must not be isomorphic with any other
+            molecules in the list.
         partial_bond_orders_from_molecules : List[openff.toolkit.molecule.Molecule], optional
             If specified, partial bond orders will be taken from the given molecules
             instead of being determined by the force field.
@@ -144,7 +146,7 @@ def from_smirnoff(
             topology=topology,
             box=box,
             positions=positions,
-            charge_from_molecules=charge_from_molecules,
+            molecules_with_preset_charges=charge_from_molecules,
             partial_bond_orders_from_molecules=partial_bond_orders_from_molecules,
             allow_nonintegral_charges=allow_nonintegral_charges,
         )
diff --git a/openff/interchange/exceptions.py b/openff/interchange/exceptions.py
index be0967d9..6cf325d8 100644
--- a/openff/interchange/exceptions.py
+++ b/openff/interchange/exceptions.py
@@ -314,6 +314,12 @@ class MissingPartialChargesError(InterchangeException):
     """
 
 
+class PresetChargesError(InterchangeException):
+    """
+    The `charge_from_molecules` is structured in an undefined way.
+    """
+
+
 class UnassignedValenceError(InterchangeException):
     """Exception raised when there are valence terms for which a ParameterHandler did not find matches."""
 
diff --git a/openff/interchange/foyer/_nonbonded.py b/openff/interchange/foyer/_nonbonded.py
index bfc94310..e3f180a4 100644
--- a/openff/interchange/foyer/_nonbonded.py
+++ b/openff/interchange/foyer/_nonbonded.py
@@ -60,7 +60,7 @@ class FoyerElectrostaticsHandler(ElectrostaticsCollection):
     force_field_key: str = "atoms"
     cutoff: _DistanceQuantity = 9.0 * unit.angstrom
 
-    _charges: dict[TopologyKey, Quantity] = PrivateAttr(default_factory=dict)  # type: ignore[assignment]
+    _charges: dict[TopologyKey, Quantity] = PrivateAttr(dict())
 
     def store_charges(
         self,
diff --git a/openff/interchange/smirnoff/_create.py b/openff/interchange/smirnoff/_create.py
index 56dfab7d..6411eac9 100644
--- a/openff/interchange/smirnoff/_create.py
+++ b/openff/interchange/smirnoff/_create.py
@@ -1,3 +1,5 @@
+import warnings
+
 from openff.toolkit import ForceField, Molecule, Quantity, Topology
 from openff.toolkit.typing.engines.smirnoff import ParameterHandler
 from openff.toolkit.typing.engines.smirnoff.plugins import load_handler_plugins
@@ -8,6 +10,7 @@
 from openff.interchange.components.toolkit import _check_electrostatics_handlers
 from openff.interchange.exceptions import (
     MissingParameterHandlerError,
+    PresetChargesError,
     SMIRNOFFHandlersNotImplementedError,
 )
 from openff.interchange.plugins import load_smirnoff_plugins
@@ -25,6 +28,7 @@
     SMIRNOFFProperTorsionCollection,
 )
 from openff.interchange.smirnoff._virtual_sites import SMIRNOFFVirtualSiteCollection
+from openff.interchange.warnings import PresetChargesAndVirtualSitesWarning
 
 _SUPPORTED_PARAMETER_HANDLERS: set[str] = {
     "Constraints",
@@ -93,17 +97,61 @@ def validate_topology(value):
         )
 
 
+def _preprocess_preset_charges(
+    molecules_with_preset_charges: list[Molecule] | None,
+) -> list[Molecule] | None:
+    """
+    Pre-process the molecules_with_preset_charges argument.
+
+    If molecules_with_preset_charges is None, return None.
+
+    If molecules_with_preset_charges is list[Molecule], ensure that
+
+    1. The input is a list of Molecules
+    2. Each molecule has assign partial charges
+    3. Ensure no molecules are isomorphic with another in the list
+
+    """
+    if molecules_with_preset_charges is None:
+        return None
+
+    molecule_set = {molecule.to_smiles() for molecule in molecules_with_preset_charges}
+
+    if len(molecule_set) != len(molecules_with_preset_charges):
+        raise PresetChargesError(
+            "All molecules in the molecules_with_preset_charges list must be isomorphically unique from each other",
+        )
+
+    for molecule in molecules_with_preset_charges:
+        if molecule.partial_charges is None:
+            raise PresetChargesError(
+                "All molecules in the molecules_with_preset_charges list must have partial charges assigned.",
+            )
+
+    return molecules_with_preset_charges
+
+
 def _create_interchange(
     force_field: ForceField,
     topology: Topology | list[Molecule],
     box: Quantity | None = None,
     positions: Quantity | None = None,
-    charge_from_molecules: list[Molecule] | None = None,
+    molecules_with_preset_charges: list[Molecule] | None = None,
     partial_bond_orders_from_molecules: list[Molecule] | None = None,
     allow_nonintegral_charges: bool = False,
 ) -> Interchange:
+    molecules_with_preset_charges = _preprocess_preset_charges(molecules_with_preset_charges)
+
     _check_supported_handlers(force_field)
 
+    if molecules_with_preset_charges is not None and "VirtualSites" in force_field.registered_parameter_handlers:
+        warnings.warn(
+            "Preset charges were provided (via `charge_from_molecules`) alongside a force field that includes "
+            "virtual site parameters. Note that virtual sites will be applied charges from the force field and "
+            "cannot be given preset charges.",
+            PresetChargesAndVirtualSitesWarning,
+        )
+
     # interchange = Interchange(topology=topology)
     # or maybe
     interchange = Interchange(topology=validate_topology(topology))
@@ -138,7 +186,7 @@ def _create_interchange(
         interchange,
         force_field,
         interchange.topology,
-        charge_from_molecules,
+        molecules_with_preset_charges,
         allow_nonintegral_charges,
     )
     _plugins(interchange, force_field, interchange.topology)
@@ -274,7 +322,7 @@ def _electrostatics(
     interchange: Interchange,
     force_field: ForceField,
     topology: Topology,
-    charge_from_molecules: list[Molecule] | None = None,
+    molecules_with_preset_charges: list[Molecule] | None = None,
     allow_nonintegral_charges: bool = False,
 ):
     if "Electrostatics" not in force_field.registered_parameter_handlers:
@@ -304,7 +352,7 @@ def _electrostatics(
                     if handler is not None
                 ],
                 topology=topology,
-                charge_from_molecules=charge_from_molecules,
+                molecules_with_preset_charges=molecules_with_preset_charges,
                 allow_nonintegral_charges=allow_nonintegral_charges,
             ),
         },
diff --git a/openff/interchange/smirnoff/_nonbonded.py b/openff/interchange/smirnoff/_nonbonded.py
index bde6bc3d..f95e5ce2 100644
--- a/openff/interchange/smirnoff/_nonbonded.py
+++ b/openff/interchange/smirnoff/_nonbonded.py
@@ -273,7 +273,7 @@ class SMIRNOFFElectrostaticsCollection(ElectrostaticsCollection, SMIRNOFFCollect
     )  # type: ignore[assignment]
     exception_potential: Literal["Coulomb"] = Field("Coulomb")
 
-    _charges: dict[Any, _ElementaryChargeQuantity] = PrivateAttr(default_factory=dict)
+    _charges: dict[Any, _ElementaryChargeQuantity] = PrivateAttr(dict())
     _charges_cached: bool = PrivateAttr(default=False)
 
     @classmethod
@@ -304,6 +304,19 @@ def charges(
     ) -> dict[TopologyKey | LibraryChargeTopologyKey | VirtualSiteKey, _ElementaryChargeQuantity]:
         """Get the total partial charge on each atom, including virtual sites."""
         if len(self._charges) == 0 or self._charges_cached is False:
+            # TODO: Clearing this dict **should not be necessary** but in some cases in appears
+            #       that this class attribute persists in some cases, possibly only on a single
+            #       thread. Ideas to try include
+            #           * Drop @computed_field ?
+            #           * Don't handle caching ourselves and let Pydantic do it (i.e. have this
+            #               function simply retrun ._get_charges(...)
+            #
+            #       Hopefully this isn't a major issue - caches for large systems should still
+            #       only be build once
+            #
+            #       Some more context: https://github.com/openforcefield/openff-interchange/issues/842#issuecomment-2394211357
+            self._charges.clear()
+
             self._charges.update(self._get_charges(include_virtual_sites=True))
             self._charges_cached = True
 
@@ -349,7 +362,7 @@ def _get_charges(
                     if potential_key.associated_handler in (
                         "LibraryCharges",
                         "ToolkitAM1BCCHandler",
-                        "charge_from_molecules",
+                        "molecules_with_preset_charges",
                         "ExternalSource",
                     ):
                         charges[atom_index] = _add_charges(
@@ -416,7 +429,7 @@ def create(
         cls,
         parameter_handler: Any,
         topology: Topology,
-        charge_from_molecules=None,
+        molecules_with_preset_charges=None,
         allow_nonintegral_charges: bool = False,
     ) -> Self:
         """
@@ -455,7 +468,7 @@ def create(
         handler.store_matches(
             parameter_handlers,
             topology,
-            charge_from_molecules=charge_from_molecules,
+            molecules_with_preset_charges=molecules_with_preset_charges,
             allow_nonintegral_charges=allow_nonintegral_charges,
         )
         handler._charges = dict()
@@ -777,12 +790,12 @@ def _assign_charges_from_molecules(
         cls,
         topology: Topology,
         unique_molecule: Molecule,
-        charge_from_molecules=Optional[list[Molecule]],
+        molecules_with_preset_charges=Optional[list[Molecule]],
     ) -> tuple[bool, dict, dict]:
-        if charge_from_molecules is None:
+        if molecules_with_preset_charges is None:
             return False, dict(), dict()
 
-        for molecule_with_charges in charge_from_molecules:
+        for molecule_with_charges in molecules_with_preset_charges:
             if molecule_with_charges.is_isomorphic_with(unique_molecule):
                 break
         else:
@@ -810,7 +823,7 @@ def _assign_charges_from_molecules(
             potential_key = PotentialKey(
                 id=mapped_smiles,
                 mult=index_in_molecule_with_charges,  # Not sure this prevents clashes in some corner cases
-                associated_handler="charge_from_molecules",
+                associated_handler="molecules_with_preset_charges",
                 bond_order=None,
             )
             potential = Potential(parameters={"charge": partial_charge})
@@ -823,7 +836,7 @@ def store_matches(
         self,
         parameter_handler: ElectrostaticsHandlerType | list[ElectrostaticsHandlerType],
         topology: Topology,
-        charge_from_molecules=None,
+        molecules_with_preset_charges=None,
         allow_nonintegral_charges: bool = False,
     ) -> None:
         """
@@ -846,10 +859,10 @@ def store_matches(
             flag, matches, potentials = self._assign_charges_from_molecules(
                 topology,
                 unique_molecule,
-                charge_from_molecules,
+                molecules_with_preset_charges,
             )
             # TODO: Here is where the toolkit calls self.check_charges_assigned(). Do we skip this
-            #       entirely given that we are not accepting `charge_from_molecules`?
+            #       entirely given that we are not accepting `molecules_with_preset_charges`?
 
             if not flag:
                 # TODO: Rename this method to something like `_find_matches`
diff --git a/openff/interchange/warnings.py b/openff/interchange/warnings.py
index 67ca825b..3a3dc4aa 100644
--- a/openff/interchange/warnings.py
+++ b/openff/interchange/warnings.py
@@ -21,5 +21,9 @@ class ForceFieldModificationWarning(UserWarning):
     """Warning for when a ForceField is modified."""
 
 
+class PresetChargesAndVirtualSitesWarning(UserWarning):
+    """Warning when possibly using preset charges and virtual sites together."""
+
+
 class InterchangeCombinationWarning(UserWarning):
     """Warning for when combining Interchange objects."""