Hi Lucy,

if I execute you code I do get the desired/expected result (i.e. similar to FEL.tiff). Maybe you need to make a clean start (e.g. by executing ClearAll["Global`*"] at the beginning of you notebook). And the PlotRange option is not really needed.

Regards -- Henrik

Well, strange, I do not have any idea of what the problem could be here. I was trying this successfully on v11.3 and v12.0. Instead of using ListContourPlot: Does probably ContourPlot work for you?, e.g.

fel = Interpolation[{{#1, #2}, #3} & @@@ arrayData];
ContourPlot[fel[\[FormalX], \[FormalY]], 
 Evaluate[Sequence @@ 
   MapThread[Prepend, {First[fel], {\[FormalX], \[FormalY]}}]], 
 ColorFunction -> ColorData["Rainbow"], ContourStyle -> None, 
 FrameLabel -> {"PC2", "PC3"}, GridLines -> Automatic, 
 LabelStyle -> {FontSize -> 20, FontFamily -> "Times", Black, Bold},
 PlotRange -> All, 
 FrameTicks -> {{{0.4, 0.6, 0.8, 1.0, 1.2, 1.4}, 
    None}, {{0.4, 0.6, 0.8, 1.0, 1.2, 1.4}, None}}, 
 PlotLabel -> Style["FEL: Amber/Tip4p-eW", FontSize -> 18], 
 PlotLegends -> 
  BarLegend[All, LegendLabel -> "kJ/mol", 
   LabelStyle -> {Bold, Black, "Times", Bold[0.3], 18}]]

EDIT:

What happens when you use your original code with:

ListContourPlot[(*bla bla*), PlotRange->All]