diff --git a/changes/developer/internal.input-file-parser.md b/changes/developer/internal.input-file-parser.md
index 51e3dd7dc..ae8e56106 100644
--- a/changes/developer/internal.input-file-parser.md
+++ b/changes/developer/internal.input-file-parser.md
@@ -1,2 +1,3 @@
 - prepare celllist input file parser to remove engine dependency
 - prepare constraints input file parser to remove engine dependency
+- prepare files input file parser to remove engine dependency
diff --git a/include/engine/engine.hpp b/include/engine/engine.hpp
index 563cc6781..2abc5d659 100644
--- a/include/engine/engine.hpp
+++ b/include/engine/engine.hpp
@@ -105,14 +105,16 @@ namespace engine
         const std::shared_ptr<simulationBox::CellList> &getCellList() const;
         [[nodiscard]]
         const std::shared_ptr<constraints::Constraints> &getConstraints() const;
+        [[nodiscard]]
+        const std::shared_ptr<
+            intraNonBonded::IntraNonBonded> &getIntraNonBonded() const;
 
-        [[nodiscard]] simulationBox::SimulationBox   &getSimulationBox();
-        [[nodiscard]] physicalData::PhysicalData     &getPhysicalData();
-        [[nodiscard]] physicalData::PhysicalData     &getAveragePhysicalData();
-        [[nodiscard]] forceField::ForceField         &getForceField();
-        [[nodiscard]] intraNonBonded::IntraNonBonded &getIntraNonBonded();
-        [[nodiscard]] virial::Virial                 &getVirial();
-        [[nodiscard]] potential::Potential           &getPotential();
+        [[nodiscard]] simulationBox::SimulationBox &getSimulationBox();
+        [[nodiscard]] physicalData::PhysicalData   &getPhysicalData();
+        [[nodiscard]] physicalData::PhysicalData   &getAveragePhysicalData();
+        [[nodiscard]] forceField::ForceField       &getForceField();
+        [[nodiscard]] virial::Virial               &getVirial();
+        [[nodiscard]] potential::Potential         &getPotential();
 
         /*************************
          * output getter methods *
@@ -133,12 +135,11 @@ namespace engine
          * get pointer methods *
          ***********************/
 
-        [[nodiscard]] forceField::ForceField         *getForceFieldPtr();
-        [[nodiscard]] potential::Potential           *getPotentialPtr();
-        [[nodiscard]] virial::Virial                 *getVirialPtr();
-        [[nodiscard]] simulationBox::SimulationBox   *getSimulationBoxPtr();
-        [[nodiscard]] physicalData::PhysicalData     *getPhysicalDataPtr();
-        [[nodiscard]] intraNonBonded::IntraNonBonded *getIntraNonBondedPtr();
+        [[nodiscard]] forceField::ForceField       *getForceFieldPtr();
+        [[nodiscard]] potential::Potential         *getPotentialPtr();
+        [[nodiscard]] virial::Virial               *getVirialPtr();
+        [[nodiscard]] simulationBox::SimulationBox *getSimulationBoxPtr();
+        [[nodiscard]] physicalData::PhysicalData   *getPhysicalDataPtr();
 
         /******************************
          * get shared pointer methods *
@@ -151,9 +152,6 @@ namespace engine
         [[nodiscard]]
         std::shared_ptr<physicalData::PhysicalData> getSharedPhysicalData(
         ) const;
-        [[nodiscard]]
-        std::shared_ptr<intraNonBonded::IntraNonBonded> getSharedIntraNonBonded(
-        ) const;
         [[nodiscard]] std::shared_ptr<virial::Virial> getSharedVirial() const;
         [[nodiscard]] std::shared_ptr<potential::Potential> getSharedPotential(
         ) const;
diff --git a/include/input/inputFileParser/filesInputParser.hpp b/include/input/inputFileParser/filesInputParser.hpp
index dde429661..187b96a9f 100644
--- a/include/input/inputFileParser/filesInputParser.hpp
+++ b/include/input/inputFileParser/filesInputParser.hpp
@@ -39,11 +39,14 @@ namespace input
     class FilesInputParser : public InputFileParser
     {
        private:
+        std::shared_ptr<intraNonBonded::IntraNonBonded> _intraNonBonded;
+
         bool _validateFilePaths;
 
        public:
         explicit FilesInputParser(
             engine::Engine &,
+            std::shared_ptr<intraNonBonded::IntraNonBonded> intraNonBonded,
             bool validateFilePaths = true
         );
 
diff --git a/src/engine/engine.cpp b/src/engine/engine.cpp
index d2b96999b..e821d5304 100644
--- a/src/engine/engine.cpp
+++ b/src/engine/engine.cpp
@@ -184,9 +184,12 @@ ForceField &Engine::getForceField() { return *_forceField; }
 /**
  * @brief get the reference to the intra non bonded interactions
  *
- * @return IntraNonBonded&
+ * @return const std::shared_ptr<IntraNonBonded>&
  */
-IntraNonBonded &Engine::getIntraNonBonded() { return *_intraNonBonded; }
+const std::shared_ptr<IntraNonBonded> &Engine::getIntraNonBonded() const
+{
+    return _intraNonBonded;
+}
 
 /**
  * @brief get the reference to the virial
@@ -237,13 +240,6 @@ SimulationBox *Engine::getSimulationBoxPtr() { return _simulationBox.get(); }
  */
 PhysicalData *Engine::getPhysicalDataPtr() { return _physicalData.get(); }
 
-/**
- * @brief get the pointer to the intra non bonded interactions
- *
- * @return IntraNonBonded*
- */
-IntraNonBonded *Engine::getIntraNonBondedPtr() { return _intraNonBonded.get(); }
-
 /**
  * @brief set the inter-water interactions handler
  *
@@ -391,16 +387,6 @@ const std::shared_ptr<Constraints> &Engine::getConstraints() const
     return _constraints;
 }
 
-/**
- * @brief get the shared pointer to the intra non bonded interactions
- *
- * @return std::shared_ptr<IntraNonBonded>
- */
-std::shared_ptr<IntraNonBonded> Engine::getSharedIntraNonBonded() const
-{
-    return _intraNonBonded;
-}
-
 /**
  * @brief get the shared pointer to the virial
  *
diff --git a/src/engine/hessianEngine.cpp b/src/engine/hessianEngine.cpp
index a202d1252..58b82aa7f 100644
--- a/src/engine/hessianEngine.cpp
+++ b/src/engine/hessianEngine.cpp
@@ -105,7 +105,7 @@ std::shared_ptr<Evaluator> HessianEngine::setupEvaluator()
     evaluator->setPotential(getSharedPotential());
     evaluator->setForceField(getSharedForceField());
     evaluator->setConstraints(getConstraints());
-    evaluator->setIntraNonBonded(getSharedIntraNonBonded());
+    evaluator->setIntraNonBonded(getIntraNonBonded());
     evaluator->setVirial(getSharedVirial());
     evaluator->setPhysicalData(getSharedPhysicalData());
     evaluator->setPhysicalDataOld(getSharedPhysicalDataOld());
diff --git a/src/input/inputFileParser/filesInputParser.cpp b/src/input/inputFileParser/filesInputParser.cpp
index 43536b370..2682295df 100644
--- a/src/input/inputFileParser/filesInputParser.cpp
+++ b/src/input/inputFileParser/filesInputParser.cpp
@@ -50,8 +50,14 @@ using namespace utilities;
  *
  * @param engine
  */
-FilesInputParser::FilesInputParser(Engine &engine, const bool validateFilePaths)
-    : InputFileParser(engine), _validateFilePaths(validateFilePaths)
+FilesInputParser::FilesInputParser(
+    Engine                                         &engine,
+    std::shared_ptr<intraNonBonded::IntraNonBonded> intraNonBonded,
+    const bool                                      validateFilePaths
+)
+    : InputFileParser(engine),
+      _intraNonBonded(intraNonBonded),
+      _validateFilePaths(validateFilePaths)
 {
     addKeyword(
         std::string("intra-nonBonded_file"),
@@ -144,7 +150,7 @@ void FilesInputParser::parseIntraNonBondedFile(
             std::format("Intra non bonded file \"{}\" File not found", fileName)
         );
 
-    _engine.getIntraNonBonded().activate();
+    _intraNonBonded->activate();
 
     FileSettings::setIntraNonBondedFileName(fileName);
     FileSettings::setIsIntraNonBondedFileNameSet();
diff --git a/src/input/inputFileReader.cpp b/src/input/inputFileReader.cpp
index c27724821..4479a51fa 100644
--- a/src/input/inputFileReader.cpp
+++ b/src/input/inputFileReader.cpp
@@ -88,7 +88,11 @@ InputFileReader::InputFileReader(
     );
     _parsers.push_back(make_unique<CoulombLongRangeInputParser>(_engine));
     _parsers.push_back(
-        make_unique<FilesInputParser>(_engine, validateFilePaths)
+        make_unique<FilesInputParser>(
+            _engine,
+            _engine.getIntraNonBonded(),
+            validateFilePaths
+        )
     );
     _parsers.push_back(make_unique<MMInputParser>(_engine));
     _parsers.push_back(make_unique<GeneralInputParser>(_engine));
diff --git a/src/input/intraNonBondedReader.cpp b/src/input/intraNonBondedReader.cpp
index 68de65571..7253a3b1a 100644
--- a/src/input/intraNonBondedReader.cpp
+++ b/src/input/intraNonBondedReader.cpp
@@ -33,7 +33,6 @@
 #include "engine.hpp"                    // for Engine
 #include "exceptions.hpp"                // for IntraNonBondedException
 #include "fileSettings.hpp"              // for FileSettings
-#include "intraNonBonded.hpp"            // for IntraNonBonded
 #include "intraNonBondedContainer.hpp"   // for IntraNonBondedContainer
 #include "mathUtilities.hpp"             // for sign, utilities
 #include "simulationBox.hpp"             // for SimulationBox
@@ -92,7 +91,9 @@ IntraNonBondedReader::IntraNonBondedReader(
     const std::string &fileName,
     Engine            &engine
 )
-    : _fileName(fileName), _fp(fileName), _engine(engine){};
+    : _fileName(fileName), _fp(fileName), _engine(engine)
+{
+}
 
 /**
  * @brief reads the intra non bonded interactions from the intraNonBonded file
@@ -285,7 +286,7 @@ void IntraNonBondedReader::processMolecule(const size_t moleculeType)
 
     const auto container = IntraNonBondedContainer(moleculeType, atomIndices);
 
-    _engine.getIntraNonBonded().addIntraNonBondedContainer(container);
+    _engine.getIntraNonBonded()->addIntraNonBondedContainer(container);
 }
 
 /**
@@ -297,8 +298,8 @@ void IntraNonBondedReader::processMolecule(const size_t moleculeType)
  */
 void IntraNonBondedReader::checkDuplicates() const
 {
-    auto      &intraNonBonded = _engine.getIntraNonBonded();
-    const auto nonBondedCont  = intraNonBonded.getIntraNonBondedContainers();
+    const auto &intraNonBonded = _engine.getIntraNonBonded();
+    const auto  nonBondedCont  = intraNonBonded->getIntraNonBondedContainers();
 
     auto transform = [](const auto &container)
     { return container.getMolType(); };
@@ -333,4 +334,4 @@ void IntraNonBondedReader::setFileName(const std::string_view &fileName)
 /**
  * @brief reinitializes the file pointer
  */
-void IntraNonBondedReader::reInitializeFp() { _fp = std::ifstream(_fileName); }
\ No newline at end of file
+void IntraNonBondedReader::reInitializeFp() { _fp = std::ifstream(_fileName); }
diff --git a/src/setup/intraNonBondedSetup.cpp b/src/setup/intraNonBondedSetup.cpp
index 480b1984f..bae69d5e2 100644
--- a/src/setup/intraNonBondedSetup.cpp
+++ b/src/setup/intraNonBondedSetup.cpp
@@ -22,9 +22,8 @@
 
 #include "intraNonBondedSetup.hpp"
 
-#include "engine.hpp"           // for Engine
-#include "intraNonBonded.hpp"   // for IntraNonBonded
-#include "potential.hpp"        // for Potential
+#include "engine.hpp"      // for Engine
+#include "potential.hpp"   // for Potential
 
 using namespace setup;
 using namespace engine;
@@ -52,7 +51,7 @@ void setup::setupIntraNonBonded(engine::Engine &engine)
  *
  * @param engine
  */
-IntraNonBondedSetup::IntraNonBondedSetup(Engine &engine) : _engine(engine){};
+IntraNonBondedSetup::IntraNonBondedSetup(Engine &engine) : _engine(engine) {}
 
 /**
  * @brief Setup intra non bonded interactions
@@ -71,8 +70,8 @@ void IntraNonBondedSetup::setup()
     const auto &nonCoulombPot  = potential.getNonCoulombPotSharedPtr();
     const auto &coulombPot     = potential.getCoulombPotSharedPtr();
 
-    intraNonBonded.setNonCoulombPotential(nonCoulombPot);
-    intraNonBonded.setCoulombPotential(coulombPot);
+    intraNonBonded->setNonCoulombPotential(nonCoulombPot);
+    intraNonBonded->setCoulombPotential(coulombPot);
 
-    intraNonBonded.fillIntraNonBondedMaps(_engine.getSimulationBox());
-}
\ No newline at end of file
+    intraNonBonded->fillIntraNonBondedMaps(_engine.getSimulationBox());
+}
diff --git a/src/setup/optimizerSetup.cpp b/src/setup/optimizerSetup.cpp
index 3bc981bdd..7520d4f71 100644
--- a/src/setup/optimizerSetup.cpp
+++ b/src/setup/optimizerSetup.cpp
@@ -240,7 +240,7 @@ std::shared_ptr<Evaluator> OptimizerSetup::setupEvaluator()
     evaluator->setPotential(_optEngine.getSharedPotential());
     evaluator->setForceField(_optEngine.getSharedForceField());
     evaluator->setConstraints(_optEngine.getConstraints());
-    evaluator->setIntraNonBonded(_optEngine.getSharedIntraNonBonded());
+    evaluator->setIntraNonBonded(_optEngine.getIntraNonBonded());
     evaluator->setVirial(_optEngine.getSharedVirial());
     evaluator->setSimulationBox(_optEngine.getSharedSimulationBox());
     evaluator->setPhysicalData(_optEngine.getSharedPhysicalData());
diff --git a/tests/include/input/testIntraNonBondedReader.hpp b/tests/include/input/testIntraNonBondedReader.hpp
index ce712f5f9..4611d4d03 100644
--- a/tests/include/input/testIntraNonBondedReader.hpp
+++ b/tests/include/input/testIntraNonBondedReader.hpp
@@ -58,7 +58,7 @@ class TestIntraNonBondedReader : public ::testing::Test
         _engine = new engine::MMMDEngine();
 
         _engine->getSimulationBox().addMoleculeType(molecule1);
-        _engine->getIntraNonBonded().activate();
+        _engine->getIntraNonBonded()->activate();
 
         _intraNonBondedReader =
             new input::intraNonBondedReader::IntraNonBondedReader(
@@ -75,4 +75,4 @@ class TestIntraNonBondedReader : public ::testing::Test
     }
 };
 
-#endif   // _TEST_INTRA_NON_BONDED_READER_HPP_
\ No newline at end of file
+#endif   // _TEST_INTRA_NON_BONDED_READER_HPP_
diff --git a/tests/src/input/inputFileParsing/testFilesParser.cpp b/tests/src/input/inputFileParsing/testFilesParser.cpp
index 6930c9e0d..7e9d8284a 100644
--- a/tests/src/input/inputFileParsing/testFilesParser.cpp
+++ b/tests/src/input/inputFileParsing/testFilesParser.cpp
@@ -43,7 +43,7 @@ using namespace input;
  */
 TEST_F(TestInputFileReader, testParseTopologyFilename)
 {
-    FilesInputParser parser(*_engine);
+    FilesInputParser parser(*_engine, _engine->getIntraNonBonded());
 
     std::vector<std::string> lineElements = {
         "topology_file",
@@ -73,7 +73,7 @@ TEST_F(TestInputFileReader, testParseTopologyFilename)
  */
 TEST_F(TestInputFileReader, testParseParameterFilename)
 {
-    FilesInputParser parser(*_engine);
+    FilesInputParser parser(*_engine, _engine->getIntraNonBonded());
 
     std::vector<std::string> lineElements = {
         "parameter_file",
@@ -104,7 +104,7 @@ TEST_F(TestInputFileReader, testParseParameterFilename)
  */
 TEST_F(TestInputFileReader, parseIntraNonBondedFile)
 {
-    FilesInputParser         parser(*_engine);
+    FilesInputParser         parser(*_engine, _engine->getIntraNonBonded());
     std::vector<std::string> lineElements = {
         "intra-nonBonded_file",
         "=",
@@ -134,7 +134,7 @@ TEST_F(TestInputFileReader, parseIntraNonBondedFile)
  */
 TEST_F(TestInputFileReader, testStartFileName)
 {
-    FilesInputParser         parser(*_engine);
+    FilesInputParser         parser(*_engine, _engine->getIntraNonBonded());
     std::vector<std::string> lineElements = {
         "startFile_name",
         "=",
@@ -160,7 +160,7 @@ TEST_F(TestInputFileReader, testStartFileName)
  */
 TEST_F(TestInputFileReader, testMoldescriptorFileName)
 {
-    FilesInputParser         parser(*_engine);
+    FilesInputParser         parser(*_engine, _engine->getIntraNonBonded());
     std::vector<std::string> lineElements = {
         "moldescriptorFile_name",
         "=",
@@ -191,7 +191,7 @@ TEST_F(TestInputFileReader, testMoldescriptorFileName)
  */
 TEST_F(TestInputFileReader, testGuffPath)
 {
-    FilesInputParser               parser(*_engine);
+    FilesInputParser parser(*_engine, _engine->getIntraNonBonded());
     const std::vector<std::string> lineElements = {"guff_path", "=", "guff"};
     EXPECT_THROW_MSG(
         parser.parseGuffPath(lineElements, 0),
@@ -206,7 +206,7 @@ TEST_F(TestInputFileReader, testGuffPath)
  */
 TEST_F(TestInputFileReader, guffDatFilename)
 {
-    FilesInputParser         parser(*_engine);
+    FilesInputParser         parser(*_engine, _engine->getIntraNonBonded());
     std::vector<std::string> lineElements = {"guffdat_file", "=", "guff.dat"};
     EXPECT_THROW_MSG(
         parser.parseGuffDatFilename(lineElements, 0),
@@ -227,7 +227,7 @@ TEST_F(TestInputFileReader, guffDatFilename)
  */
 TEST_F(TestInputFileReader, testRpmdStartFileName)
 {
-    FilesInputParser         parser(*_engine);
+    FilesInputParser         parser(*_engine, _engine->getIntraNonBonded());
     std::vector<std::string> lineElements = {
         "rpmd_start_file",
         "=",
@@ -256,7 +256,7 @@ TEST_F(TestInputFileReader, testRpmdStartFileName)
  */
 TEST_F(TestInputFileReader, testMShakeFileName)
 {
-    FilesInputParser         parser(*_engine);
+    FilesInputParser         parser(*_engine, _engine->getIntraNonBonded());
     std::vector<std::string> lineElements = {"mshake_file", "=", "mshake.dat"};
 
     EXPECT_THROW_MSG(
@@ -278,7 +278,7 @@ TEST_F(TestInputFileReader, testMShakeFileName)
  */
 TEST_F(TestInputFileReader, testDFTBFileName)
 {
-    FilesInputParser         parser(*_engine);
+    FilesInputParser         parser(*_engine, _engine->getIntraNonBonded());
     std::vector<std::string> lineElements = {
         "dftb_file",
         "=",
@@ -304,7 +304,7 @@ TEST_F(TestInputFileReader, testDFTBFileName)
  */
 TEST_F(TestInputFileReader, testTMFileName)
 {
-    FilesInputParser         parser(*_engine);
+    FilesInputParser         parser(*_engine, _engine->getIntraNonBonded());
     std::vector<std::string> lineElements = {
         "turbomole_file",
         "=",
@@ -327,4 +327,4 @@ TEST_F(TestInputFileReader, testTMFileName)
         settings::FileSettings::getTMFileName(),
         "data/turbomoleReader/tm_define.template"
     );
-}
\ No newline at end of file
+}
diff --git a/tests/src/input/testIntraNonBondedReader.cpp b/tests/src/input/testIntraNonBondedReader.cpp
index 9a1fb5622..4ad059e48 100644
--- a/tests/src/input/testIntraNonBondedReader.cpp
+++ b/tests/src/input/testIntraNonBondedReader.cpp
@@ -68,7 +68,7 @@ TEST_F(TestIntraNonBondedReader, noFileSetByUser)
 TEST_F(TestIntraNonBondedReader, readingNotNeeded)
 {
     _intraNonBondedReader->setFileName("");
-    _engine->getIntraNonBonded().deactivate();
+    _engine->getIntraNonBonded()->deactivate();
     EXPECT_NO_THROW(_intraNonBondedReader->read());
 }
 
@@ -137,11 +137,11 @@ TEST_F(TestIntraNonBondedReader, readIntraNonBondedFile)
     input::intraNonBondedReader::readIntraNonBondedFile(*_engine);
 
     const auto container =
-        _engine->getIntraNonBonded().getIntraNonBondedContainers()[0];
+        _engine->getIntraNonBonded()->getIntraNonBondedContainers()[0];
     EXPECT_EQ(container.getMolType(), 0);
     const auto &atomIndices = container.getAtomIndices();
 
     EXPECT_EQ(atomIndices[0], std::vector<int>({1, -2}));
     EXPECT_EQ(atomIndices[1], std::vector<int>({}));
     EXPECT_EQ(atomIndices[2], std::vector<int>({1}));
-}
\ No newline at end of file
+}
diff --git a/tests/src/setup/testIntraNonBondedSetup.cpp b/tests/src/setup/testIntraNonBondedSetup.cpp
index 8e5bfb922..5ca6dd3f6 100644
--- a/tests/src/setup/testIntraNonBondedSetup.cpp
+++ b/tests/src/setup/testIntraNonBondedSetup.cpp
@@ -20,36 +20,38 @@
 <GPL_HEADER>
 ******************************************************************************/
 
+#include <gtest/gtest.h>   // for InitGoogleTest, RUN_ALL_TESTS
+
+#include <vector>   // for vector, allocator
+
 #include "engine.hpp"                    // for Engine
+#include "gtest/gtest.h"                 // for Message, TestPartResult
 #include "intraNonBondedContainer.hpp"   // for IntraNonBondedContainer
 #include "intraNonBondedSetup.hpp"       // for setupIntraNonBonded
 #include "molecule.hpp"                  // for Molecule
 #include "testSetup.hpp"                 // for TestSetup
 
-#include "gtest/gtest.h"   // for Message, TestPartResult
-#include <gtest/gtest.h>   // for InitGoogleTest, RUN_ALL_TESTS
-#include <vector>          // for vector, allocator
-
 /**
  * @brief tests the setup of the intra non bonded interactions
  *
  */
 TEST_F(TestSetup, setupIntraNonBonded)
 {
+    auto molecule = simulationBox::Molecule(1);
+    auto intraNonBondedContainer =
+        intraNonBonded::IntraNonBondedContainer(1, {{-1}});
 
-    auto molecule                = simulationBox::Molecule(1);
-    auto intraNonBondedContainer = intraNonBonded::IntraNonBondedContainer(1, {{-1}});
-
-    _engine->getIntraNonBonded().addIntraNonBondedContainer(intraNonBondedContainer);
+    const auto& intraNonBonded = _engine->getIntraNonBonded();
+    intraNonBonded->addIntraNonBondedContainer(intraNonBondedContainer);
     _engine->getSimulationBox().addMolecule(molecule);
 
-    _engine->getIntraNonBonded().deactivate();
+    intraNonBonded->deactivate();
     setup::setupIntraNonBonded(*_engine);
 
-    EXPECT_EQ(_engine->getIntraNonBonded().getIntraNonBondedMaps().size(), 0);
+    EXPECT_EQ(intraNonBonded->getIntraNonBondedMaps().size(), 0);
 
-    _engine->getIntraNonBonded().activate();
+    intraNonBonded->activate();
     setup::setupIntraNonBonded(*_engine);
 
-    EXPECT_EQ(_engine->getIntraNonBonded().getIntraNonBondedMaps().size(), 1);
-}
\ No newline at end of file
+    EXPECT_EQ(intraNonBonded->getIntraNonBondedMaps().size(), 1);
+}