diff --git a/Code/GraphMol/ChemReactions/ReactionWriter.cpp b/Code/GraphMol/ChemReactions/ReactionWriter.cpp
index 8a75a9d73..c881fed41 100644
--- a/Code/GraphMol/ChemReactions/ReactionWriter.cpp
+++ b/Code/GraphMol/ChemReactions/ReactionWriter.cpp
@@ -119,18 +119,17 @@ std::string ChemicalReactionToRxnSmiles(const ChemicalReaction &rxn,
 //! returns an RXN block for a reaction
 std::string ChemicalReactionToV3KRxnBlock(const ChemicalReaction &rxn,
                                           bool separateAgents) {
-  if (separateAgents) {
-    // V3000 doesn't seem to support agent blocks
-    BOOST_LOG(rdWarningLog)
-        << "V3000 RXN blocks do not support separating agents. Agents will be "
-           "written to the reactants block"
-        << std::endl;
-  }
   std::ostringstream res;
   res << "$RXN V3000\n\n      RDKit\n\n";
-  res << "M  V30 COUNTS "
-      << rxn.getNumReactantTemplates() + rxn.getNumAgentTemplates() << " "
-      << rxn.getNumProductTemplates();
+
+  if (separateAgents) {
+    res << "M  V30 COUNTS " << rxn.getNumReactantTemplates() << " "
+        << rxn.getNumProductTemplates() << " " << rxn.getNumAgentTemplates();
+  } else {
+    res << "M  V30 COUNTS "
+        << rxn.getNumReactantTemplates() + rxn.getNumAgentTemplates() << " "
+        << rxn.getNumProductTemplates();
+  }
   res << "\n";
 
   res << "M  V30 BEGIN REACTANT\n";
@@ -140,11 +139,13 @@ std::string ChemicalReactionToV3KRxnBlock(const ChemicalReaction &rxn,
     MolOps::findSSSR(*rt);
     res << FileParserUtils::getV3000CTAB(*rt, -1);
   }
-  for (const auto &rt : boost::make_iterator_range(rxn.beginAgentTemplates(),
-                                                   rxn.endAgentTemplates())) {
-    // to write the mol block, we need ring information:
-    MolOps::findSSSR(*rt);
-    res << FileParserUtils::getV3000CTAB(*rt, -1);
+  if (!separateAgents) {
+    for (const auto &rt : boost::make_iterator_range(rxn.beginAgentTemplates(),
+                                                     rxn.endAgentTemplates())) {
+      // to write the mol block, we need ring information:
+      MolOps::findSSSR(*rt);
+      res << FileParserUtils::getV3000CTAB(*rt, -1);
+    }
   }
   res << "M  V30 END REACTANT\n";
   res << "M  V30 BEGIN PRODUCT\n";
@@ -155,6 +156,17 @@ std::string ChemicalReactionToV3KRxnBlock(const ChemicalReaction &rxn,
     res << FileParserUtils::getV3000CTAB(*rt, -1);
   }
   res << "M  V30 END PRODUCT\n";
+  if (separateAgents) {
+    res << "M  V30 BEGIN AGENT\n";
+    for (const auto &rt : boost::make_iterator_range(rxn.beginAgentTemplates(),
+                                                     rxn.endAgentTemplates())) {
+      // to write the mol block, we need ring information:
+      MolOps::findSSSR(*rt);
+      res << FileParserUtils::getV3000CTAB(*rt, -1);
+    }
+    res << "M  V30 END AGENT\n";
+  }
+
   res << "M  END\n";
   return res.str();
 }
diff --git a/Code/GraphMol/ChemReactions/catch_tests.cpp b/Code/GraphMol/ChemReactions/catch_tests.cpp
index 26ed329ba..3668a2c58 100644
--- a/Code/GraphMol/ChemReactions/catch_tests.cpp
+++ b/Code/GraphMol/ChemReactions/catch_tests.cpp
@@ -1269,3 +1269,107 @@ TEST_CASE("CDXML Parser") {
        CHECK(smarts == "[#6&D2:2]1:[#6&D2:3]:[#6&D2:4]:[#6&D3:1](:[#6&D2:5]:[#6&D2:6]:1)-[#17&D1].[#6&D3](-[#5&D2]-[#6&D3:7]1:[#6&D2:8]:[#6&D2:9]:[#6&D2:10]:[#6&D2:11]:[#6&D2:12]:1)(-[#8&D1])-[#8&D1]>>[#6:1]1=[#6:5]-[#6:6](=[#6:2]-[#6:3]=[#6:4]-1)-[#6:7]1-[#6:8]=[#6:9]-[#6:10]=[#6:11]-[#6:12]=1");
   }
 }
+
+TEST_CASE("Github #5785: separateAgents ignored for V3000 RXN files") {
+  SECTION("general separateAgents parse testing: V2000"){
+    std::string rxnb = R"RXN($RXN
+
+      RDKit
+
+  1  1  1
+$MOL
+
+     RDKit          2D
+
+  2  1  0  0  0  0  0  0  0  0999 V2000
+    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  1  0  0
+    1.2990    0.7500    0.0000 O   0  0  0  0  0  0  0  0  0  2  0  0
+  1  2  1  0
+M  END
+$MOL
+
+     RDKit          2D
+
+  2  1  0  0  0  0  0  0  0  0999 V2000
+    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  1  0  0
+    1.2990    0.7500    0.0000 O   0  0  0  0  0  0  0  0  0  2  0  0
+  1  2  2  0
+M  END
+$MOL
+
+     RDKit          2D
+
+  1  0  0  0  0  0  0  0  0  0999 V2000
+    0.0000    0.0000    0.0000 Pt  0  0  0  0  0  0  0  0  0  0  0  0
+M  END
+)RXN";
+    std::unique_ptr<ChemicalReaction> rxn(RxnBlockToChemicalReaction(rxnb));
+    REQUIRE(rxn);
+    CHECK(rxn->getNumReactantTemplates()==1);
+    CHECK(rxn->getNumProductTemplates()==1);
+    CHECK(rxn->getNumAgentTemplates()==1);
+
+    auto orxn = ChemicalReactionToRxnBlock(*rxn,true);
+    CHECK(orxn.find("  1  1  1") != std::string::npos);
+    
+  }
+  SECTION("general separateAgents parse testing: V3000"){
+    std::string rxnb = R"RXN($RXN V3000
+
+      Mrv2211  121520220816
+
+M  V30 COUNTS 1 1 1
+M  V30 BEGIN REACTANT
+M  V30 BEGIN CTAB
+M  V30 COUNTS 2 1 0 0 0
+M  V30 BEGIN ATOM
+M  V30 1 C -4.8977 -0.385 0 1
+M  V30 2 O -3.564 0.385 0 2
+M  V30 END ATOM
+M  V30 BEGIN BOND
+M  V30 1 1 1 2
+M  V30 END BOND
+M  V30 END CTAB
+M  V30 END REACTANT
+M  V30 BEGIN PRODUCT
+M  V30 BEGIN CTAB
+M  V30 COUNTS 2 1 0 0 0
+M  V30 BEGIN ATOM
+M  V30 1 C 4.444 -0.385 0 1
+M  V30 2 O 5.7777 0.385 0 2
+M  V30 END ATOM
+M  V30 BEGIN BOND
+M  V30 1 2 1 2
+M  V30 END BOND
+M  V30 END CTAB
+M  V30 END PRODUCT
+M  V30 BEGIN AGENT
+M  V30 BEGIN CTAB
+M  V30 COUNTS 1 0 0 0 0
+M  V30 BEGIN ATOM
+M  V30 1 Pt 0 1.54 0 0
+M  V30 END ATOM
+M  V30 END CTAB
+M  V30 END AGENT
+M  END
+)RXN";
+std::unique_ptr<ChemicalReaction> rxn(RxnBlockToChemicalReaction(rxnb));
+    REQUIRE(rxn);
+    CHECK(rxn->getNumReactantTemplates()==1);
+    CHECK(rxn->getNumProductTemplates()==1);
+    CHECK(rxn->getNumAgentTemplates()==1);
+   
+    {    // with separate agents
+      auto orxn = ChemicalReactionToV3KRxnBlock(*rxn,true);
+      CHECK(orxn.find("COUNTS 1 1 1") != std::string::npos);
+      CHECK(orxn.find("BEGIN AGENT") != std::string::npos);
+      CHECK(orxn.find("END AGENT") != std::string::npos);
+    }
+    {    // without separate agents
+      auto orxn = ChemicalReactionToV3KRxnBlock(*rxn,false);
+      CHECK(orxn.find("COUNTS 2 1") != std::string::npos);
+      CHECK(orxn.find("BEGIN AGENT") == std::string::npos);
+      CHECK(orxn.find("END AGENT") == std::string::npos);
+    }
+  }
+}
\ No newline at end of file
diff --git a/Code/GraphMol/FileParsers/MolFileWriter.cpp b/Code/GraphMol/FileParsers/MolFileWriter.cpp
index 75580f2c8..8d8507630 100644
--- a/Code/GraphMol/FileParsers/MolFileWriter.cpp
+++ b/Code/GraphMol/FileParsers/MolFileWriter.cpp
@@ -530,9 +530,12 @@ bool hasNonDefaultValence(const Atom *atom) {
   if (atom->getNumRadicalElectrons() != 0) {
     return true;
   }
-  if (atom->hasQuery()) {
+  // for queries and atoms which don't have computed properties, the answer is
+  // always no:
+  if (atom->hasQuery() || atom->needsUpdatePropertyCache()) {
     return false;
   }
+
   if (atom->getAtomicNum() == 1 ||
       SmilesWrite ::inOrganicSubset(atom->getAtomicNum())) {
     // for the ones we "know", we may have to specify the valence if it's