diff --git a/Code/GraphMol/ChemReactions/ReactionWriter.cpp b/Code/GraphMol/ChemReactions/ReactionWriter.cpp
index 9e150487f..21317021c 100644
--- a/Code/GraphMol/ChemReactions/ReactionWriter.cpp
+++ b/Code/GraphMol/ChemReactions/ReactionWriter.cpp
@@ -103,14 +103,18 @@ std::string chemicalReactionToRxnToString(const RDKit::ChemicalReaction &rxn,
 }
 
 void write_template(std::ostringstream &res, RDKit::ROMol &tpl) {
-  if (tpl.needsUpdatePropertyCache()) {
-    tpl.updatePropertyCache(false);
+  RDKit::RWMol trwmol(tpl);
+
+  if (trwmol.needsUpdatePropertyCache()) {
+    trwmol.updatePropertyCache(false);
   }
   // to write the mol block, we need ring information:
-  if (!tpl.getRingInfo()->isInitialized()) {
-    RDKit::MolOps::findSSSR(tpl);
+  if (!trwmol.getRingInfo()->isInitialized()) {
+    RDKit::MolOps::findSSSR(trwmol);
   }
-  res << RDKit::FileParserUtils::getV3000CTAB(tpl, -1);
+  RDKit::FileParserUtils::moveAdditionalPropertiesToSGroups(trwmol);
+
+  res << RDKit::FileParserUtils::getV3000CTAB(trwmol, -1);
 }
 
 }  // namespace
diff --git a/Code/GraphMol/ChemReactions/catch_tests.cpp b/Code/GraphMol/ChemReactions/catch_tests.cpp
index 38f22642d..c7809c5f2 100644
--- a/Code/GraphMol/ChemReactions/catch_tests.cpp
+++ b/Code/GraphMol/ChemReactions/catch_tests.cpp
@@ -1584,4 +1584,75 @@ TEST_CASE("problematic in-place example from MolStandardize") {
     rxn->runReactant(*m);
     CHECK(MolToSmiles(*m)=="CN(C)c1cc[nH+]cc1");
   }
+}
+
+TEST_CASE(
+    "github #5819: Support writing detailed SMARTS queries to CTABs using the SMARTSQ mechanism") {
+  SECTION("as reported") {
+    auto rxn = "[C;$(C([#6])=O):1][OH:2]>>[C:1][NH2:2]"_rxnsmarts;
+    REQUIRE(rxn);
+    auto ctab = ChemicalReactionToV3KRxnBlock(*rxn);
+
+    // make sure the templates haven't been modified by that operation
+    CHECK(getSubstanceGroups(*rxn->getReactants()[0]).empty());
+
+    CHECK(ctab.find("SMARTSQ") != std::string::npos);
+    CHECK(ctab.find("FIELDDATA=\"[C&$(C([#6])=O):1]\"") != std::string::npos);
+    CHECK(ctab.find("FIELDDATA=\"[N&H2:2]\"") != std::string::npos);
+
+    // make sure we can properly parse that
+    std::unique_ptr<ChemicalReaction> nrxn{RxnBlockToChemicalReaction(ctab)};
+    REQUIRE(nrxn);
+    CHECK(MolToSmarts(*nrxn->getReactants()[0]) == "[C&$(C([#6])=O):1][O&H1:2]");
+  }
+
+
+SECTION("isotopes are weird"){
+  auto rxnb = R"CTAB($RXN V3000
+
+      Mrv2211  111620231722
+
+M  V30 COUNTS 1 1
+M  V30 BEGIN REACTANT
+M  V30 BEGIN CTAB
+M  V30 COUNTS 4 3 0 0 0
+M  V30 BEGIN ATOM
+M  V30 1 C 6.9035 -10.0923 0 1
+M  V30 2 O 6.9035 -8.5923 0 2 MASS=18
+M  V30 3 Cl 5.6045 -10.8423 0 0
+M  V30 4 C 8.2025 -10.8423 0 4
+M  V30 END ATOM
+M  V30 BEGIN BOND
+M  V30 1 1 1 4
+M  V30 2 2 1 2
+M  V30 3 1 1 3
+M  V30 END BOND
+M  V30 END CTAB
+M  V30 END REACTANT
+M  V30 BEGIN PRODUCT
+M  V30 BEGIN CTAB
+M  V30 COUNTS 4 3 0 0 0
+M  V30 BEGIN ATOM
+M  V30 1 C 22.0416 -9.3829 0 0
+M  V30 2 C 23.3406 -8.6329 0 1
+M  V30 3 O 23.3406 -7.1329 0 2 MASS=18
+M  V30 4 C 24.6396 -9.3829 0 4
+M  V30 END ATOM
+M  V30 BEGIN BOND
+M  V30 1 1 1 2
+M  V30 2 1 2 4
+M  V30 3 2 2 3
+M  V30 END BOND
+M  V30 END CTAB
+M  V30 END PRODUCT
+M  END
+)CTAB";
+  std::unique_ptr<ChemicalReaction> rxn{RxnBlockToChemicalReaction(rxnb)};
+  REQUIRE(rxn);
+  CHECK(rxn->getReactants()[0]->getAtomWithIdx(0)->hasQuery());
+  CHECK(rxn->getReactants()[0]->getAtomWithIdx(1)->hasQuery());
+  auto ctab = ChemicalReactionToV3KRxnBlock(*rxn);
+  CHECK(ctab.find("SMARTSQ") == std::string::npos);
+
+}
 }
\ No newline at end of file
diff --git a/Code/GraphMol/FileParsers/FileParserUtils.h b/Code/GraphMol/FileParsers/FileParserUtils.h
index dd19dcadd..529089741 100644
--- a/Code/GraphMol/FileParsers/FileParserUtils.h
+++ b/Code/GraphMol/FileParsers/FileParserUtils.h
@@ -250,6 +250,8 @@ inline void createAtomStringPropertyList(
                                                missingValueMarker, lineSize));
 }
 
+RDKIT_FILEPARSERS_EXPORT void moveAdditionalPropertiesToSGroups(RWMol &mol);
+
 }  // namespace FileParserUtils
 }  // namespace RDKit
 
diff --git a/Code/GraphMol/FileParsers/MolFileParser.cpp b/Code/GraphMol/FileParsers/MolFileParser.cpp
index 296acc7ac..6f8eeace2 100644
--- a/Code/GraphMol/FileParsers/MolFileParser.cpp
+++ b/Code/GraphMol/FileParsers/MolFileParser.cpp
@@ -1541,7 +1541,6 @@ Atom *ParseMolFileAtomLine(const std::string_view text, RDGeom::Point3D &pos,
           << " has a negative isotope offset. line:  " << line << std::endl;
     }
     res->setIsotope(dIso);
-    res->setProp(common_properties::_hasMassQuery, true);
   }
 
   if (text.size() >= 42 && text.substr(39, 3) != "  0") {
diff --git a/Code/GraphMol/FileParsers/MolFileWriter.cpp b/Code/GraphMol/FileParsers/MolFileWriter.cpp
index c0d29d80d..579e82363 100644
--- a/Code/GraphMol/FileParsers/MolFileWriter.cpp
+++ b/Code/GraphMol/FileParsers/MolFileWriter.cpp
@@ -1,5 +1,5 @@
 //
-//  Copyright (C) 2003-2021 Greg Landrum and other RDKit contributors
+//  Copyright (C) 2003-2023 Greg Landrum and other RDKit contributors
 //
 //   @@ All Rights Reserved @@
 //  This file is part of the RDKit.
@@ -1037,28 +1037,55 @@ int BondStereoCodeV2000ToV3000(int dirCode) {
 
 namespace {
 void createSMARTSQSubstanceGroups(ROMol &mol) {
+  auto isRedundantQuery = [](const auto query) {
+    if (query->getDescription() == "AtomAnd" &&
+        (query->endChildren() - query->beginChildren() == 2) &&
+        (*query->beginChildren())->getDescription() == "AtomAtomicNum" &&
+        !(*query->beginChildren())->getNegation() &&
+        !(*(query->beginChildren() + 1))->getNegation() &&
+        ((*(query->beginChildren() + 1))->getDescription() == "AtomIsotope" ||
+         (*(query->beginChildren() + 1))->getDescription() ==
+             "AtomFormalCharge")) {
+      return true;
+    }
+    return false;
+  };
   for (const auto atom : mol.atoms()) {
-    std::string sma;
-    if (atom->hasQuery() &&
-        atom->getPropIfPresent(common_properties::MRV_SMA, sma) &&
-        !sma.empty()) {
-      SubstanceGroup sg(&mol, "DAT");
-      sg.setProp("QUERYTYPE", "SMARTSQ");
-      sg.setProp("QUERYOP", "=");
-      std::vector<std::string> dataFields{sma};
-      sg.setProp("DATAFIELDS", dataFields);
-      sg.addAtomWithIdx(atom->getIdx());
-      addSubstanceGroup(mol, sg);
+    if (atom->hasQuery()) {
+      std::string sma;
+
+      if (!atom->getPropIfPresent(common_properties::MRV_SMA, sma) &&
+          !isAtomListQuery(atom) &&
+          atom->getQuery()->getDescription() != "AtomNull" &&
+          // we may want to re-think this next one.
+          // including AtomType queries will result in an entry
+          // for every atom that comes from SMARTS, and I don't think
+          // we want that.
+          !boost::starts_with(atom->getQuery()->getDescription(), "AtomType") &&
+          !boost::starts_with(atom->getQuery()->getDescription(),
+                              "AtomAtomicNum") &&
+          !isRedundantQuery(atom->getQuery())) {
+        sma = SmartsWrite::GetAtomSmarts(static_cast<const QueryAtom *>(atom));
+      }
+      if (!sma.empty()) {
+        SubstanceGroup sg(&mol, "DAT");
+        sg.setProp("QUERYTYPE", "SMARTSQ");
+        sg.setProp("QUERYOP", "=");
+        std::vector<std::string> dataFields{sma};
+        sg.setProp("DATAFIELDS", dataFields);
+        sg.addAtomWithIdx(atom->getIdx());
+        addSubstanceGroup(mol, sg);
+      }
     }
   }
 }
 }  // namespace
-
+namespace FileParserUtils {
 void moveAdditionalPropertiesToSGroups(RWMol &mol) {
   GenericGroups::convertGenericQueriesToSubstanceGroups(mol);
   createSMARTSQSubstanceGroups(mol);
 }
-
+}  // namespace FileParserUtils
 const std::string GetV3000MolFileBondLine(const Bond *bond,
                                           const INT_MAP_INT &wedgeBonds,
                                           const Conformer *conf) {
@@ -1374,7 +1401,7 @@ std::string MolToMolBlock(const ROMol &mol, bool includeStereo, int confId,
       MolOps::assignStereochemistry(trwmol);
     }
 #endif
-  moveAdditionalPropertiesToSGroups(trwmol);
+  FileParserUtils::moveAdditionalPropertiesToSGroups(trwmol);
 
   try {
     return outputMolToMolBlock(trwmol, confId, forceV3000);
diff --git a/Code/GraphMol/FileParsers/file_parsers_catch.cpp b/Code/GraphMol/FileParsers/file_parsers_catch.cpp
index 0f4e44140..b46fe9e46 100644
--- a/Code/GraphMol/FileParsers/file_parsers_catch.cpp
+++ b/Code/GraphMol/FileParsers/file_parsers_catch.cpp
@@ -6804,4 +6804,27 @@ TEST_CASE(
   REQUIRE(bond2->getBondType() == Bond::DOUBLE);
   CHECK(bond2->getStereo() == Bond::BondStereo::STEREONONE);
   CHECK(bond2->getBondDir() == Bond::BondDir::NONE);
+}
+
+TEST_CASE(
+    "github #5819: Support writing detailed SMARTS queries to CTABs using the SMARTSQ mechanism") {
+  SECTION("as reported") {
+    auto m = "[C,N,O]C[#6]*[$(C(=O)O)]"_smarts;
+    REQUIRE(m);
+    auto ctab = MolToV3KMolBlock(*m);
+    // std::cerr << ctab << std::endl;
+    // make sure we still do list queries correctly
+    CHECK(ctab.find("V30 1 [C,N,O]") != std::string::npos);
+    CHECK(ctab.find("FIELDDATA=\"[C,N,O]") == std::string::npos);
+    CHECK(ctab.find("FIELDDATA=\"C\"") == std::string::npos);
+    CHECK(ctab.find("FIELDDATA=\"[#6]\"") == std::string::npos);
+    CHECK(ctab.find("FIELDDATA=\"*\"") == std::string::npos);
+    CHECK(ctab.find("SMARTSQ") != std::string::npos);
+    CHECK(ctab.find("[$(C(=O)O)]") != std::string::npos);
+
+    // make sure we can properly parse that
+    std::unique_ptr<RWMol> nm{MolBlockToMol(ctab)};
+    REQUIRE(nm);
+    CHECK(MolToSmarts(*nm) == "[#6,#7,#8][#6][#6]*[$(C(=O)O)]");
+  }
 }
\ No newline at end of file
diff --git a/Code/GraphMol/MarvinParse/MarvinParser.cpp b/Code/GraphMol/MarvinParse/MarvinParser.cpp
index f5eb1f2cc..ead8127f0 100644
--- a/Code/GraphMol/MarvinParse/MarvinParser.cpp
+++ b/Code/GraphMol/MarvinParse/MarvinParser.cpp
@@ -192,7 +192,6 @@ class MarvinCMLReader {
 
       if (marvinAtom->isotope != 0) {
         res->setIsotope(marvinAtom->isotope);
-        res->setProp(common_properties::_hasMassQuery, true);
       }
 
       // mrvValence and hydrogenCount both set the number of explicit hydrogens