diff --git a/packages/ketcher-core/__tests__/domain/serializers/ket/KetSerializer.test.ts b/packages/ketcher-core/__tests__/domain/serializers/ket/KetSerializer.test.ts
index 0779ec3afe..f0a318ee79 100644
--- a/packages/ketcher-core/__tests__/domain/serializers/ket/KetSerializer.test.ts
+++ b/packages/ketcher-core/__tests__/domain/serializers/ket/KetSerializer.test.ts
@@ -47,7 +47,7 @@ describe('deserialize (ToStruct)', () => {
     const preparedAtoms = parsedPrepareContent.mol0.atoms
     preparedAtoms.forEach((props, id) => {
       const locationWithNegativeY = props.location.map((coordinate, index) => {
-        return index === 1 && props.label ? -coordinate : coordinate
+        return index === 1 ? -coordinate : coordinate
       })
       const relatedAtom = deserData.atoms.get(id)
       const label = props.type === 'rg-label' ? 'R#' : 'C'
@@ -175,9 +175,7 @@ describe('serialize (ToKet)', () => {
   it('correct work with atoms', () => {
     parsedNewPrepareStruct.mol0.atoms.forEach((atom, id) => {
       const relatedAtom = parsedPrepareContent.mol0.atoms[id]
-      if (relatedAtom.label) {
-        relatedAtom.location[1] = -relatedAtom.location[1]
-      }
+      relatedAtom.location[1] = -relatedAtom.location[1]
       expect(atom).toEqual(relatedAtom)
     })
   })
diff --git a/packages/ketcher-core/src/domain/serializers/ket/fromKet/moleculeToStruct.ts b/packages/ketcher-core/src/domain/serializers/ket/fromKet/moleculeToStruct.ts
index e36a65b1d5..500b1bb000 100644
--- a/packages/ketcher-core/src/domain/serializers/ket/fromKet/moleculeToStruct.ts
+++ b/packages/ketcher-core/src/domain/serializers/ket/fromKet/moleculeToStruct.ts
@@ -90,7 +90,7 @@ export function rglabelToStruct(source) {
   params.label = 'R#'
   ifDef(params, 'pp', {
     x: source.location[0],
-    y: source.location[1],
+    y: -source.location[1],
     z: source.location[2] || 0.0
   })
   ifDef(params, 'attpnt', source.attachmentPoints)
@@ -104,7 +104,7 @@ export function atomListToStruct(source) {
   params.label = 'L#'
   ifDef(params, 'pp', {
     x: source.location[0],
-    y: source.location[1],
+    y: -source.location[1],
     z: source.location[2] || 0.0
   })
   ifDef(params, 'attpnt', source.attachmentPoints)
diff --git a/packages/ketcher-core/src/domain/serializers/ket/toKet/moleculeToKet.ts b/packages/ketcher-core/src/domain/serializers/ket/toKet/moleculeToKet.ts
index 3e64a2e77d..f2591a8d35 100644
--- a/packages/ketcher-core/src/domain/serializers/ket/toKet/moleculeToKet.ts
+++ b/packages/ketcher-core/src/domain/serializers/ket/toKet/moleculeToKet.ts
@@ -90,7 +90,7 @@ function rglabelToKet(source) {
   const result = {
     type: 'rg-label'
   }
-  ifDef(result, 'location', [source.pp.x, source.pp.y, source.pp.z])
+  ifDef(result, 'location', [source.pp.x, -source.pp.y, source.pp.z])
   ifDef(result, 'attachmentPoints', source.attpnt, 0)
 
   const refsToRGroups = fromRlabel(source.rglabel).map(
@@ -105,7 +105,7 @@ function atomListToKet(source) {
   const result = {
     type: 'atom-list'
   }
-  ifDef(result, 'location', [source.pp.x, source.pp.y, source.pp.z])
+  ifDef(result, 'location', [source.pp.x, -source.pp.y, source.pp.z])
   ifDef(result, 'attachmentPoints', source.attpnt, 0)
   ifDef(result, 'elements', source.atomList.labelList())
   ifDef(result, 'notList', source.atomList.notList, false)