diff --git a/ketcher-autotests/tests/Macromolecule-editor/Copy-And-Paste/flex-mode-copy-paste.spec.ts-snapshots/Flex-mode-copy-paste-Copy-paste-selection-with-Shift-Click-and-undo-1-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/Copy-And-Paste/flex-mode-copy-paste.spec.ts-snapshots/Flex-mode-copy-paste-Copy-paste-selection-with-Shift-Click-and-undo-1-chromium-linux.png
index b7e6e9a15e..8a01dda1f1 100644
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diff --git a/ketcher-autotests/tests/Macromolecule-editor/Enumerations/enumerations.spec.ts-snapshots/Enumerations-Remove-a-monomer-from-a-chain-tha-632e4--and-ensure-proper-renumbering-in-both-chains-1-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/Enumerations/enumerations.spec.ts-snapshots/Enumerations-Remove-a-monomer-from-a-chain-tha-632e4--and-ensure-proper-renumbering-in-both-chains-1-chromium-linux.png
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index 8c212ec458..21a7381112 100644
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diff --git a/ketcher-autotests/tests/Macromolecule-editor/Erase-Tool/erase-tool.spec.ts b/ketcher-autotests/tests/Macromolecule-editor/Erase-Tool/erase-tool.spec.ts
index 35a1ac5712..0e0b115018 100644
--- a/ketcher-autotests/tests/Macromolecule-editor/Erase-Tool/erase-tool.spec.ts
+++ b/ketcher-autotests/tests/Macromolecule-editor/Erase-Tool/erase-tool.spec.ts
@@ -19,6 +19,7 @@ import {
   selectMacroBond,
   selectZoomInTool,
   selectZoomOutTool,
+  selectClearCanvasTool,
 } from '@utils';
 import { MacroBondTool } from '@utils/canvas/tools/selectNestedTool/types';
 import {
@@ -377,6 +378,8 @@ test.describe('Erase Tool', () => {
       FileType.KET,
     );
 
+    await selectClearCanvasTool(page);
+
     await openFileAndAddToCanvasMacro(
       'KET/peptides-flex-chain-expected.ket',
       page,
@@ -396,6 +399,7 @@ test.describe('Erase Tool', () => {
     await selectEraseTool(page);
     await page.getByText('Bal').locator('..').first().click();
     await page.getByText('D-2Nal').locator('..').first().click();
+
     await verifyFileExport(
       page,
       'Molfiles-V3000/peptides-flex-chain-expected.mol',
@@ -403,6 +407,9 @@ test.describe('Erase Tool', () => {
       'v3000',
       [1],
     );
+
+    await selectClearCanvasTool(page);
+
     await openFileAndAddToCanvasMacro(
       'Molfiles-V3000/peptides-flex-chain-expected.mol',
       page,
diff --git a/ketcher-autotests/tests/Macromolecule-editor/Import-Saving-Files/import-saving-helm.spec.ts-snapshots/Import-correct-HELM-sequence-25-Connection--22c42-2-to-Peptide3-R1-Peptide3-R2-to-CHEM3-R1-1-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/Import-Saving-Files/import-saving-helm.spec.ts-snapshots/Import-correct-HELM-sequence-25-Connection--22c42-2-to-Peptide3-R1-Peptide3-R2-to-CHEM3-R1-1-chromium-linux.png
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diff --git a/ketcher-autotests/tests/Macromolecule-editor/Sequence-Mode/sequence-mode-replacement.spec.ts-snapshots/Case-22-13-18-Replace-last-symbol-at-base-to--a0dd3-sphates-on-phosphate-Test-6-Ph-in-edit-mode-2-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/Sequence-Mode/sequence-mode-replacement.spec.ts-snapshots/Case-22-13-18-Replace-last-symbol-at-base-to--a0dd3-sphates-on-phosphate-Test-6-Ph-in-edit-mode-2-chromium-linux.png
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diff --git a/ketcher-autotests/tests/Macromolecule-editor/Sequence-Mode/sequence-mode-replacement.spec.ts-snapshots/Case-22-13-19-Replace-last-symbol-at-base-to--1002a-hosphates-on-nucleotide-AmMC6T-in-edit-mode-2-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/Sequence-Mode/sequence-mode-replacement.spec.ts-snapshots/Case-22-13-19-Replace-last-symbol-at-base-to--1002a-hosphates-on-nucleotide-AmMC6T-in-edit-mode-2-chromium-linux.png
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diff --git a/ketcher-autotests/tests/Macromolecule-editor/Sequence-Mode/sequence-mode-replacement.spec.ts-snapshots/Case-22-13-20-Replace-last-symbol-at-base-to--e0b70-U-w-o-phosphates-on-CHEM-sDBL-in-edit-mode-2-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/Sequence-Mode/sequence-mode-replacement.spec.ts-snapshots/Case-22-13-20-Replace-last-symbol-at-base-to--e0b70-U-w-o-phosphates-on-CHEM-sDBL-in-edit-mode-2-chromium-linux.png
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diff --git a/ketcher-autotests/tests/Macromolecule-editor/Sequence-Mode/sequence-mode-replacement.spec.ts-snapshots/Case-22-14-11-Replace-last-symbol-at-base-to--9bfaa--of-presets-U-on-peptide-Hcy-in-edit-mode-2-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/Sequence-Mode/sequence-mode-replacement.spec.ts-snapshots/Case-22-14-11-Replace-last-symbol-at-base-to--9bfaa--of-presets-U-on-peptide-Hcy-in-edit-mode-2-chromium-linux.png
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diff --git a/ketcher-autotests/tests/Macromolecule-editor/Sequence-Mode/sequence-mode-replacement.spec.ts-snapshots/Case-22-14-12-Replace-last-symbol-at-base-to--9ebce-ide-w-o-natural-analog-Test-6-P-in-edit-mode-2-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/Sequence-Mode/sequence-mode-replacement.spec.ts-snapshots/Case-22-14-12-Replace-last-symbol-at-base-to--9ebce-ide-w-o-natural-analog-Test-6-P-in-edit-mode-2-chromium-linux.png
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diff --git a/ketcher-autotests/tests/Macromolecule-editor/Sequence-Mode/sequence-mode-replacement.spec.ts-snapshots/Case-22-14-13-Replace-last-symbol-at-base-to--1823c-preset-25mo3r-nC6n5C-Test-6-Ph-in-edit-mode-2-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/Sequence-Mode/sequence-mode-replacement.spec.ts-snapshots/Case-22-14-13-Replace-last-symbol-at-base-to--1823c-preset-25mo3r-nC6n5C-Test-6-Ph-in-edit-mode-2-chromium-linux.png
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diff --git a/ketcher-autotests/tests/Macromolecule-editor/Sequence-Mode/sequence-mode-replacement.spec.ts-snapshots/Case-22-14-15-Replace-last-symbol-at-base-to--4131d-without-base-25mo3r-Test-6-Ph-in-edit-mode-2-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/Sequence-Mode/sequence-mode-replacement.spec.ts-snapshots/Case-22-14-15-Replace-last-symbol-at-base-to--4131d-without-base-25mo3r-Test-6-Ph-in-edit-mode-2-chromium-linux.png
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diff --git a/ketcher-autotests/tests/Macromolecule-editor/Sequence-Mode/sequence-mode-replacement.spec.ts-snapshots/Case-22-14-18-Replace-last-symbol-at-base-to--b6ad0-ets-U-on-phosphate-Test-6-Ph-in-edit-mode-2-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/Sequence-Mode/sequence-mode-replacement.spec.ts-snapshots/Case-22-14-18-Replace-last-symbol-at-base-to--b6ad0-ets-U-on-phosphate-Test-6-Ph-in-edit-mode-2-chromium-linux.png
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diff --git a/ketcher-autotests/tests/Macromolecule-editor/Sequence-Mode/sequence-mode-replacement.spec.ts-snapshots/Case-22-14-19-Replace-last-symbol-at-base-to--a4dcc-esets-U-on-nucleotide-AmMC6T-in-edit-mode-2-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/Sequence-Mode/sequence-mode-replacement.spec.ts-snapshots/Case-22-14-19-Replace-last-symbol-at-base-to--a4dcc-esets-U-on-nucleotide-AmMC6T-in-edit-mode-2-chromium-linux.png
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diff --git a/ketcher-autotests/tests/Macromolecule-editor/Sequence-Mode/sequence-mode-replacement.spec.ts-snapshots/Case-22-14-20-Replace-last-symbol-at-base-to--6bc47-es-of-presets-U-on-CHEM-sDBL-in-edit-mode-2-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/Sequence-Mode/sequence-mode-replacement.spec.ts-snapshots/Case-22-14-20-Replace-last-symbol-at-base-to--6bc47-es-of-presets-U-on-CHEM-sDBL-in-edit-mode-2-chromium-linux.png
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diff --git a/ketcher-autotests/tests/Macromolecule-editor/Sequence-Mode/sequence-mode-replacement.spec.ts-snapshots/Case-22-18-13-Replace-last-symbol-at-phosphat-412b7-preset-25mo3r-nC6n5C-Test-6-Ph-in-edit-mode-2-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/Sequence-Mode/sequence-mode-replacement.spec.ts-snapshots/Case-22-18-13-Replace-last-symbol-at-phosphat-412b7-preset-25mo3r-nC6n5C-Test-6-Ph-in-edit-mode-2-chromium-linux.png
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diff --git a/ketcher-autotests/tests/Macromolecule-editor/Sequence-Mode/sequence-mode.spec.ts-snapshots/Sequence-Mode-Switch-from-flex-view-to-sequence-view-to-snake-view-and-back-to-flex-3-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/Sequence-Mode/sequence-mode.spec.ts-snapshots/Sequence-Mode-Switch-from-flex-view-to-sequence-view-to-snake-view-and-back-to-flex-3-chromium-linux.png
index ef4e4279a2..a2103ac0b2 100644
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diff --git a/ketcher-autotests/tests/Macromolecule-editor/Undo-Redo/undo-redo.spec.ts-snapshots/Undo-Redo-Undo-redo-for-imported-structure-1-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/Undo-Redo/undo-redo.spec.ts-snapshots/Undo-Redo-Undo-redo-for-imported-structure-1-chromium-linux.png
index 408b398ae6..037e8216a1 100644
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diff --git a/ketcher-autotests/tests/Macromolecule-editor/Undo-Redo/undo-redo.spec.ts-snapshots/Undo-Redo-Undo-redo-for-imported-structure-2-chromium-linux.png b/ketcher-autotests/tests/Macromolecule-editor/Undo-Redo/undo-redo.spec.ts-snapshots/Undo-Redo-Undo-redo-for-imported-structure-2-chromium-linux.png
index b364c72569..dbd7ccdbf3 100644
Binary files a/ketcher-autotests/tests/Macromolecule-editor/Undo-Redo/undo-redo.spec.ts-snapshots/Undo-Redo-Undo-redo-for-imported-structure-2-chromium-linux.png and b/ketcher-autotests/tests/Macromolecule-editor/Undo-Redo/undo-redo.spec.ts-snapshots/Undo-Redo-Undo-redo-for-imported-structure-2-chromium-linux.png differ
diff --git a/ketcher-autotests/tests/test-data/Molfiles-V3000/Base-Templates/01 - (R1) - Left only-expected.mol b/ketcher-autotests/tests/test-data/Molfiles-V3000/Base-Templates/01 - (R1) - Left only-expected.mol
index 5bc8500e6c..63f70dcc35 100644
--- a/ketcher-autotests/tests/test-data/Molfiles-V3000/Base-Templates/01 - (R1) - Left only-expected.mol	
+++ b/ketcher-autotests/tests/test-data/Molfiles-V3000/Base-Templates/01 - (R1) - Left only-expected.mol	
@@ -1,11 +1,11 @@
 
-  -INDIGO-01202510502D
+  -INDIGO-02052512442D
 
   0  0  0  0  0  0  0  0  0  0  0 V3000
 M  V30 BEGIN CTAB
 M  V30 COUNTS 1 0 0 0 0
 M  V30 BEGIN ATOM
-M  V30 1 (R1)_-_Left_only 11.9 -8.325 0.0 0 CLASS=BASE
+M  V30 1 (R1)_-_Left_only 11.025 -7.45 0.0 0 CLASS=BASE
 M  V30 END ATOM
 M  V30 BEGIN BOND
 M  V30 END BOND
diff --git a/packages/ketcher-core/src/application/editor/Editor.ts b/packages/ketcher-core/src/application/editor/Editor.ts
index f5c545c9eb..ab97ff0648 100644
--- a/packages/ketcher-core/src/application/editor/Editor.ts
+++ b/packages/ketcher-core/src/application/editor/Editor.ts
@@ -73,10 +73,6 @@ interface ICoreEditorConstructorParams {
   monomersLibraryUpdate?: string | JSON;
 }
 
-function isMouseMainButtonPressed(event: MouseEvent) {
-  return event.button === 0;
-}
-
 let persistentMonomersLibrary: MonomerItemType[] = [];
 let persistentMonomersLibraryParsedJson: IKetMacromoleculesContent | null =
   null;
@@ -669,6 +665,10 @@ export class CoreEditor {
     return trackedDomEvents;
   }
 
+  private isMouseMainButtonPressed(event) {
+    return event?.button === 0;
+  }
+
   private domEventSetup() {
     this.trackedDomEvents.forEach(({ target, eventName, toolEventHandler }) => {
       this.events[eventName] = new DOMSubscription();
@@ -681,7 +681,7 @@ export class CoreEditor {
 
         if (
           ['mouseup', 'mousedown', 'click', 'dbclick'].includes(event.type) &&
-          !isMouseMainButtonPressed(event)
+          !this.isMouseMainButtonPressed(event)
         ) {
           return true;
         }
diff --git a/packages/ketcher-core/src/application/editor/MacromoleculesConverter.ts b/packages/ketcher-core/src/application/editor/MacromoleculesConverter.ts
index 27d872d0d4..5b8e34175b 100644
--- a/packages/ketcher-core/src/application/editor/MacromoleculesConverter.ts
+++ b/packages/ketcher-core/src/application/editor/MacromoleculesConverter.ts
@@ -672,7 +672,7 @@ export class MacromoleculesConverter {
     });
 
     drawingEntitiesManager.setMicromoleculesHiddenEntities(struct);
-    drawingEntitiesManager.detectCycles();
+    drawingEntitiesManager.detectBondsOverlappedByMonomers();
 
     if (editor) {
       editor.viewModel.initialize([...drawingEntitiesManager.bonds.values()]);
diff --git a/packages/ketcher-core/src/application/editor/tools/Bond.ts b/packages/ketcher-core/src/application/editor/tools/Bond.ts
index 7c476d6f45..055e321b6f 100644
--- a/packages/ketcher-core/src/application/editor/tools/Bond.ts
+++ b/packages/ketcher-core/src/application/editor/tools/Bond.ts
@@ -320,6 +320,11 @@ class PolymerBond implements BaseTool {
       }
       const modelChanges = this.finishBondCreation(renderer.monomer);
       this.history.update(modelChanges);
+      if (modelChanges.operations[0]?.polymerBond) {
+        this.editor.drawingEntitiesManager.detectBondsOverlappedByMonomers([
+          modelChanges.operations[0].polymerBond,
+        ]);
+      }
       this.editor.renderersContainer.update(modelChanges);
       this.editor.renderersContainer.deletePolymerBond(
         this.bondRenderer.polymerBond,
@@ -377,6 +382,7 @@ class PolymerBond implements BaseTool {
         'You have connected monomers with attachment points of the same group',
       );
     }
+
     return this.editor.drawingEntitiesManager.finishPolymerBondCreation(
       this.bondRenderer.polymerBond,
       secondMonomer,
@@ -437,6 +443,11 @@ class PolymerBond implements BaseTool {
 
       // This logic so far is only for no-modal connections. Maybe then we can chain it after modal invoke
       const modelChanges = this.finishBondCreation(renderer.monomer);
+      if (modelChanges.operations[0]?.polymerBond) {
+        this.editor.drawingEntitiesManager.detectBondsOverlappedByMonomers([
+          modelChanges.operations[0].polymerBond,
+        ]);
+      }
       this.editor.renderersContainer.update(modelChanges);
       this.editor.renderersContainer.deletePolymerBond(
         this.bondRenderer.polymerBond,
diff --git a/packages/ketcher-core/src/application/editor/tools/SelectRectangle.ts b/packages/ketcher-core/src/application/editor/tools/SelectRectangle.ts
index 0fc92d1b8a..2864d726b6 100644
--- a/packages/ketcher-core/src/application/editor/tools/SelectRectangle.ts
+++ b/packages/ketcher-core/src/application/editor/tools/SelectRectangle.ts
@@ -232,7 +232,7 @@ class SelectRectangle implements BaseTool {
       this.mousePositionAfterMove = this.editor.lastCursorPositionOfCanvas;
       requestAnimationFrame(() => {
         this.editor.renderersContainer.update(modelChanges);
-        this.editor.drawingEntitiesManager.rerenderPolymerBonds();
+        this.editor.drawingEntitiesManager.rerenderBondsOverlappedByMonomers();
       });
     }
   }
@@ -284,6 +284,10 @@ class SelectRectangle implements BaseTool {
   }
 
   public mouseOverPolymerBond(event) {
+    if (event.buttons === 1) {
+      return;
+    }
+
     const renderer: DeprecatedFlexModeOrSnakeModePolymerBondRenderer =
       event.target.__data__;
 
diff --git a/packages/ketcher-core/src/application/render/renderers/PolymerBondRenderer/FlexModePolymerBondRenderer.ts b/packages/ketcher-core/src/application/render/renderers/PolymerBondRenderer/FlexModePolymerBondRenderer.ts
index 796f9fd7d1..4aec27be4c 100644
--- a/packages/ketcher-core/src/application/render/renderers/PolymerBondRenderer/FlexModePolymerBondRenderer.ts
+++ b/packages/ketcher-core/src/application/render/renderers/PolymerBondRenderer/FlexModePolymerBondRenderer.ts
@@ -86,7 +86,7 @@ export class FlexModePolymerBondRenderer extends BaseRenderer {
 
   // TODO: Specify the types.
   public appendBond(rootElement) {
-    if (this.polymerBond.isCyclicOverlappingBond) {
+    if (this.polymerBond.isOverlappedByMonomer) {
       this.generateEnvelopingBondPath();
     } else {
       this.generateLinearBondPath();
diff --git a/packages/ketcher-core/src/application/render/renderers/PolymerBondRenderer/SnakeModePolymerBondRenderer.ts b/packages/ketcher-core/src/application/render/renderers/PolymerBondRenderer/SnakeModePolymerBondRenderer.ts
index 120c2a9867..bcdc1c1123 100644
--- a/packages/ketcher-core/src/application/render/renderers/PolymerBondRenderer/SnakeModePolymerBondRenderer.ts
+++ b/packages/ketcher-core/src/application/render/renderers/PolymerBondRenderer/SnakeModePolymerBondRenderer.ts
@@ -464,7 +464,7 @@ export class SnakeModePolymerBondRenderer extends BaseRenderer {
   private get isSideChainLikeBackbone() {
     return (
       !this.polymerBond.isSideChainConnection &&
-      this.polymerBond.isCyclicOverlappingBond
+      this.polymerBond.isOverlappedByMonomer
     );
   }
 
diff --git a/packages/ketcher-core/src/application/render/renderers/RenderersManager.ts b/packages/ketcher-core/src/application/render/renderers/RenderersManager.ts
index 69bf12cc21..44bbf7d1b9 100644
--- a/packages/ketcher-core/src/application/render/renderers/RenderersManager.ts
+++ b/packages/ketcher-core/src/application/render/renderers/RenderersManager.ts
@@ -401,7 +401,7 @@ export class RenderersManager {
     this.polymerBonds.forEach((polymerBondRenderer) => {
       if (
         !polymerBondRenderer.polymerBond.isSideChainConnection &&
-        !polymerBondRenderer.polymerBond.isCyclicOverlappingBond
+        !polymerBondRenderer.polymerBond.isOverlappedByMonomer
       ) {
         return;
       }
diff --git a/packages/ketcher-core/src/domain/entities/BaseBond.ts b/packages/ketcher-core/src/domain/entities/BaseBond.ts
index 5f5bead245..0f7ccc113b 100644
--- a/packages/ketcher-core/src/domain/entities/BaseBond.ts
+++ b/packages/ketcher-core/src/domain/entities/BaseBond.ts
@@ -3,12 +3,12 @@ import { Vec2 } from 'domain/entities/vec2';
 
 export abstract class BaseBond extends DrawingEntity {
   public endPosition: Vec2 = new Vec2();
+  private _isOverlappedByMonomer = false;
 
   abstract get firstEndEntity(): DrawingEntity;
   abstract get secondEndEntity(): DrawingEntity | undefined;
   abstract get isHorizontal(): boolean;
   abstract get isVertical(): boolean;
-  abstract get isCyclicOverlappingBond(): boolean;
 
   public get finished() {
     return Boolean(this.firstEndEntity && this.secondEndEntity);
@@ -44,4 +44,12 @@ export abstract class BaseBond extends DrawingEntity {
       ? this.secondEndEntity
       : this.firstEndEntity;
   }
+
+  public get isOverlappedByMonomer() {
+    return this._isOverlappedByMonomer;
+  }
+
+  public set isOverlappedByMonomer(value: boolean) {
+    this._isOverlappedByMonomer = value;
+  }
 }
diff --git a/packages/ketcher-core/src/domain/entities/DrawingEntitiesManager.ts b/packages/ketcher-core/src/domain/entities/DrawingEntitiesManager.ts
index 4bc2ef827c..c917901474 100644
--- a/packages/ketcher-core/src/domain/entities/DrawingEntitiesManager.ts
+++ b/packages/ketcher-core/src/domain/entities/DrawingEntitiesManager.ts
@@ -119,10 +119,10 @@ type RnaPresetAdditionParams = {
 export class DrawingEntitiesManager {
   public monomers: Map<number, BaseMonomer> = new Map();
   public polymerBonds: Map<number, PolymerBond | HydrogenBond> = new Map();
+  private bondsMonomersOverlaps: Map<number, BaseMonomer> = new Map();
   public atoms: Map<number, Atom> = new Map();
   public bonds: Map<number, Bond> = new Map();
   public monomerToAtomBonds: Map<number, MonomerToAtomBond> = new Map();
-  public cycles: Chain[] = [];
 
   public micromoleculesHiddenEntities: Struct = new Struct();
   public canvasMatrix?: CanvasMatrix;
@@ -378,6 +378,8 @@ export class DrawingEntitiesManager {
       drawingEntity instanceof HydrogenBond
     ) {
       drawingEntity.moveToLinkedEntities();
+      drawingEntity.isOverlappedByMonomer =
+        this.checkBondForOverlapsByMonomers(drawingEntity);
     } else if (drawingEntity instanceof Bond) {
       drawingEntity.moveToLinkedAtoms();
     } else if (drawingEntity instanceof MonomerToAtomBond) {
@@ -2162,6 +2164,8 @@ export class DrawingEntitiesManager {
       command.merge(this.redrawBonds());
     }
 
+    this.detectBondsOverlappedByMonomers();
+
     this.monomers.forEach((monomer) => {
       editor.renderersContainer.deleteMonomer(monomer);
       editor.renderersContainer.addMonomer(monomer);
@@ -2180,12 +2184,34 @@ export class DrawingEntitiesManager {
     return command;
   }
 
-  public rerenderPolymerBonds() {
+  public rerenderBondsOverlappedByMonomers() {
     const editor = CoreEditor.provideEditorInstance();
 
-    this.polymerBonds.forEach((polymerBond) => {
-      editor.renderersContainer.deletePolymerBond(polymerBond, false, false);
-      editor.renderersContainer.addPolymerBond(polymerBond, false);
+    if (editor.mode instanceof SequenceMode) {
+      return;
+    }
+
+    const monomersToCheck = this.selectedEntities
+      .filter(([, entity]) => entity instanceof BaseMonomer)
+      .map(([, entity]) => entity as BaseMonomer);
+    const outstandingBonds = this.polymerBondsArray.filter((polymerBond) =>
+      monomersToCheck.some(
+        (monomer) =>
+          polymerBond.firstMonomer !== monomer &&
+          polymerBond.secondMonomer !== monomer,
+      ),
+    );
+
+    outstandingBonds.forEach((polymerBond) => {
+      const previousIsOverlappedByMonomer = polymerBond.isOverlappedByMonomer;
+      polymerBond.isOverlappedByMonomer = this.checkBondForOverlapsByMonomers(
+        polymerBond,
+        monomersToCheck,
+      );
+      if (polymerBond.isOverlappedByMonomer !== previousIsOverlappedByMonomer) {
+        editor.renderersContainer.deletePolymerBond(polymerBond, false, false);
+        editor.renderersContainer.addPolymerBond(polymerBond, false);
+      }
     });
   }
 
@@ -3029,6 +3055,10 @@ export class DrawingEntitiesManager {
     return [...this.monomers.values()];
   }
 
+  public get polymerBondsArray() {
+    return [...this.polymerBonds.values()];
+  }
+
   public get molecules() {
     return this.monomersArray.filter((monomer) => {
       return (
@@ -3038,10 +3068,70 @@ export class DrawingEntitiesManager {
     });
   }
 
-  public detectCycles() {
-    const chainsCollection = ChainsCollection.fromMonomers(this.monomersArray);
-    // TODO: Detect cycles properly with side-chains/hydrogen bonds
-    this.cycles = chainsCollection.chains.filter((chain) => chain.isCyclic);
+  private checkBondForOverlapsByMonomers(
+    polymerBond: PolymerBond,
+    monomers?: BaseMonomer[],
+  ) {
+    const editor = CoreEditor.provideEditorInstance();
+    if (!editor || editor.mode instanceof SequenceMode) {
+      return false;
+    }
+
+    const secondMonomer = polymerBond.secondMonomer;
+    if (!secondMonomer) {
+      return false;
+    }
+
+    if (!polymerBond.isHorizontal && !polymerBond.isVertical) {
+      return false;
+    }
+
+    const monomersToUse = monomers ?? this.monomersArray;
+    // Skip processing for large structures for now as in worst case its has O(n^2) complexity and may freeze the app
+    // Further optimization might be needed to allow that
+    if (monomersToUse.length > 500) {
+      return false;
+    }
+
+    const previousOverlap = this.bondsMonomersOverlaps.get(polymerBond.id);
+    const monomersToUseWithPreviousOverlap = previousOverlap
+      ? [previousOverlap, ...monomersToUse]
+      : monomersToUse;
+
+    const overlappingMonomer = monomersToUseWithPreviousOverlap.find(
+      (monomer) => {
+        if (
+          monomer.id === polymerBond.firstMonomer.id ||
+          monomer.id === secondMonomer.id
+        ) {
+          return false;
+        }
+
+        const distanceFromMonomerToLine =
+          monomer.center.calculateDistanceToLine([
+            polymerBond.firstMonomer.center,
+            secondMonomer.center,
+          ]);
+
+        return distanceFromMonomerToLine < 0.375;
+      },
+    );
+
+    if (overlappingMonomer) {
+      this.bondsMonomersOverlaps.set(polymerBond.id, overlappingMonomer);
+    }
+
+    return Boolean(overlappingMonomer);
+  }
+
+  public detectBondsOverlappedByMonomers(
+    polymerBonds?: Array<PolymerBond | HydrogenBond>,
+  ) {
+    const bondsToCheck = polymerBonds ?? this.polymerBondsArray;
+    bondsToCheck.forEach((polymerBond) => {
+      polymerBond.isOverlappedByMonomer =
+        this.checkBondForOverlapsByMonomers(polymerBond);
+    });
   }
 }
 
diff --git a/packages/ketcher-core/src/domain/entities/HydrogenBond.ts b/packages/ketcher-core/src/domain/entities/HydrogenBond.ts
index a7f6056cfa..188835a054 100644
--- a/packages/ketcher-core/src/domain/entities/HydrogenBond.ts
+++ b/packages/ketcher-core/src/domain/entities/HydrogenBond.ts
@@ -56,10 +56,6 @@ export class HydrogenBond extends BaseBond {
     return super.getAnotherEntity(monomer) as BaseMonomer;
   }
 
-  public get isCyclicOverlappingBond() {
-    return false;
-  }
-
   public get isHorizontal() {
     return false;
   }
diff --git a/packages/ketcher-core/src/domain/entities/MonomerToAtomBond.ts b/packages/ketcher-core/src/domain/entities/MonomerToAtomBond.ts
index 3fd99207be..71dac1e06e 100644
--- a/packages/ketcher-core/src/domain/entities/MonomerToAtomBond.ts
+++ b/packages/ketcher-core/src/domain/entities/MonomerToAtomBond.ts
@@ -29,10 +29,6 @@ export class MonomerToAtomBond extends BaseBond {
     return this.atom;
   }
 
-  public get isCyclicOverlappingBond() {
-    return false;
-  }
-
   public get isHorizontal() {
     return false;
   }
diff --git a/packages/ketcher-core/src/domain/entities/PolymerBond.ts b/packages/ketcher-core/src/domain/entities/PolymerBond.ts
index 05fbfead5a..029e1ab802 100644
--- a/packages/ketcher-core/src/domain/entities/PolymerBond.ts
+++ b/packages/ketcher-core/src/domain/entities/PolymerBond.ts
@@ -11,7 +11,6 @@ import {
 import { AttachmentPointName } from 'domain/types';
 import { BaseMonomer } from './BaseMonomer';
 import { BaseBond } from 'domain/entities/BaseBond';
-import { CoreEditor } from 'application/editor';
 
 export type FlexOrSequenceOrSnakeModePolymerBondRenderer =
   | BackBoneBondSequenceRenderer
@@ -61,52 +60,6 @@ export class PolymerBond extends BaseBond {
     return this.secondMonomer?.getAttachmentPointByBond(this);
   }
 
-  // TODO: Consider moving to DrawingEntitiesManager/RenderersManager to track the state of the bond and avoid excessive calls
-  public get isCyclicOverlappingBond() {
-    const secondMonomer = this.secondMonomer;
-    if (!secondMonomer) {
-      return false;
-    }
-
-    if (!this.isHorizontal && !this.isVertical) {
-      return false;
-    }
-
-    const editor = CoreEditor.provideEditorInstance();
-
-    const cyclesWithThisBond = editor.drawingEntitiesManager.cycles.filter(
-      (chain) => {
-        return (
-          chain.monomers.includes(this.firstMonomer) &&
-          chain.monomers.includes(secondMonomer)
-        );
-      },
-    );
-
-    if (!cyclesWithThisBond.length) {
-      return false;
-    }
-
-    return cyclesWithThisBond.some((chain) => {
-      return chain.monomers.some((monomer) => {
-        if (
-          monomer.id === this.firstMonomer.id ||
-          monomer.id === secondMonomer.id
-        ) {
-          return false;
-        }
-
-        const distanceFromMonomerToLine =
-          monomer.center.calculateDistanceToLine([
-            this.firstMonomer.center,
-            secondMonomer.center,
-          ]);
-
-        return distanceFromMonomerToLine < 0.375;
-      });
-    });
-  }
-
   public get isSideChainConnection() {
     const firstMonomerAttachmentPoint = this.firstMonomerAttachmentPoint;
     const secondMonomerAttachmentPoint = this.secondMonomerAttachmentPoint;
diff --git a/packages/ketcher-core/src/domain/entities/canvas-matrix/CanvasMatrix.ts b/packages/ketcher-core/src/domain/entities/canvas-matrix/CanvasMatrix.ts
index d17f4a8932..15471bc41e 100644
--- a/packages/ketcher-core/src/domain/entities/canvas-matrix/CanvasMatrix.ts
+++ b/packages/ketcher-core/src/domain/entities/canvas-matrix/CanvasMatrix.ts
@@ -223,7 +223,7 @@ export class CanvasMatrix {
 
         if (
           (polymerBond.isSideChainConnection ||
-            polymerBond.isCyclicOverlappingBond) &&
+            polymerBond.isOverlappedByMonomer) &&
           !handledConnections.has(polymerBond)
         ) {
           const anotherMonomer = polymerBond.getAnotherMonomer(
diff --git a/packages/ketcher-macromolecules/src/components/modal/Open/Open.tsx b/packages/ketcher-macromolecules/src/components/modal/Open/Open.tsx
index b3f28404a5..b104378689 100644
--- a/packages/ketcher-macromolecules/src/components/modal/Open/Open.tsx
+++ b/packages/ketcher-macromolecules/src/components/modal/Open/Open.tsx
@@ -194,7 +194,7 @@ const addToCanvas = ({
     }
   }
 
-  editor.drawingEntitiesManager.detectCycles();
+  editor.drawingEntitiesManager.detectBondsOverlappedByMonomers();
 
   editor.renderersContainer.update(modelChanges);
   editorHistory.update(modelChanges);
diff --git a/packages/ketcher-macromolecules/src/components/modal/save/Save.test.tsx b/packages/ketcher-macromolecules/src/components/modal/save/Save.test.tsx
index e330622416..2c539a6703 100644
--- a/packages/ketcher-macromolecules/src/components/modal/save/Save.test.tsx
+++ b/packages/ketcher-macromolecules/src/components/modal/save/Save.test.tsx
@@ -38,7 +38,7 @@ describe('Save modal', () => {
             mergeInto: jest.fn(),
           },
           setMicromoleculesHiddenEntities: jest.fn(),
-          detectCycles: jest.fn(),
+          detectBondsOverlappedByMonomers: jest.fn(),
           monomers: [],
           polymerBonds: [],
           bonds: [],