I added a small animation to show how the heatmap is built rather than just showing the final picture. The atoms are added in order of decreasing Topological Steric Effect Index, so the most sterically crowded parts of idarubicin contribute first. This makes the plot readable in a different way: one can see which atomic neighborhoods dominate.

ClearAll["Global`*"];

mol2 = Molecule[Entity["Chemical", "Idarubicin"]];

coords2da =
  MoleculeValue[
   mol2,
   "AtomDiagramCoordinates",
   IncludeHydrogens -> None
   ];

coords2daAll =
  MoleculeValue[
   mol2,
   "AtomDiagramCoordinates",
   IncludeHydrogens -> All
   ];

rot = RotationTransform[-Pi/2, Mean[coords2da]];

coords2daV = rot /@ coords2da;
coords2daAllV = rot /@ coords2daAll;

mol2V = Molecule[
   mol2,
   AtomDiagramCoordinates -> coords2daAllV
   ];

topid =
  MoleculeValue[
   mol2,
   "TopologicalStericEffectIndex",
   IncludeHydrogens -> None
   ];

order = Ordering[topid, All, Greater];

{{xm, xp}, {ym, yp}} =
  MinMax[#, Scaled[0.1]] & /@ Transpose[coords2daV];

gauss[u_?NumericQ] := If[u > 40, 0., Exp[-u]];

hmfun2[n_Integer][x_?NumericQ, y_?NumericQ] :=
 With[
  {sc = 0.3, ii = order[[;; n]]},
  Total[
   MapThread[
    #2 gauss[
       SquaredEuclideanDistance[{x, y}, #1]/(2 sc^2)
       ] &,
    {coords2daV[[ii]], topid[[ii]]}
    ],
   Method -> "CompensatedSummation"
   ]
  ];

Manipulate[
 Show[
  DensityPlot[
   hmfun2[n][x, y],
   {x, xm, xp},
   {y, ym, yp},
   PerformanceGoal->"Quality",
   AspectRatio -> Automatic,
   ColorFunction->"ValentineTones",
   Frame -> None,
   PlotPoints -> 100,
   PlotRange -> All,
   PlotRangePadding->0,
   ImageSize->550
   ],
  MoleculePlot[mol2V,ColorRules -> {_ -> Directive[White,Thickness[.005]]}]
  ],
 {{n, Length[topid], "atoms included"}, 0, Length[topid], 1,
  Appearance -> "Labeled"}
 ]

frnsTM=ParallelTable[
 Show[
  DensityPlot[
   hmfun2[n][x, y],
   {x, xm, xp},
   {y, ym, yp},
   PerformanceGoal->"Quality",
   AspectRatio -> Automatic,
   ColorFunction->"LightTemperatureMap",
   Frame -> None,
   PlotPoints -> 100,
   PlotRange -> All,
   PlotRangePadding->0,
   ImageSize->550
   ],
  MoleculePlot[mol2V,ColorRules -> {_ -> Directive[Black,Thickness[.005]]}]
  ],
 {n, 0, Length[topid], 1}
 ];//AbsoluteTiming

frnsSC=ParallelTable[
 Show[
  DensityPlot[
   hmfun2[n][x, y],
   {x, xm, xp},
   {y, ym, yp},
   PerformanceGoal->"Quality",
   AspectRatio -> Automatic,
   ColorFunction->"SolarColors",
   Frame -> None,
   PlotPoints -> 100,
   PlotRange -> All,
   PlotRangePadding->0,
   ImageSize->550
   ],
  MoleculePlot[mol2V,ColorRules -> {_ -> Directive[White,Thickness[.005]]}]
  ],
 {n, 0, Length[topid], 1}
 ];//AbsoluteTiming

Export["mollights.gif", ImageAssemble /@ Transpose[{frnsTM, frnsSC}], 
 ImageSize -> 900]

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