Use get on the axes handle to see its structure - You will find that the YAxis is stored as 2x1 Numeric Ruler (1 for each side).
Use the appropriate index to make changes to the corresponding y-axis.
F = openfig('energy vs time.fig','visible');
hold on;
% Get the current axes handle
ax = gca;
get(ax)
ALim: [0 1]
ALimMode: 'auto'
AlphaScale: 'linear'
Alphamap: [0 0.0159 0.0317 0.0476 0.0635 0.0794 0.0952 0.1111 0.1270 0.1429 0.1587 0.1746 0.1905 0.2063 0.2222 0.2381 0.2540 0.2698 0.2857 0.3016 0.3175 0.3333 … ] (1×64 double)
AmbientLightColor: [1 1 1]
BeingDeleted: off
Box: on
BoxStyle: 'back'
BusyAction: 'queue'
ButtonDownFcn: ''
CLim: [0 1]
CLimMode: 'auto'
CameraPosition: [47.5000 -57350 8.1603]
CameraPositionMode: 'auto'
CameraTarget: [47.5000 -57350 -0.5000]
CameraTargetMode: 'auto'
CameraUpVector: [0 1 0]
CameraUpVectorMode: 'auto'
CameraViewAngle: 6.6086
CameraViewAngleMode: 'auto'
Children: [1×1 Line]
Clipping: on
ClippingStyle: 'rectangle'
Color: [1 1 1]
ColorOrder: [0 0 0]
ColorOrderIndex: 1
ColorScale: 'linear'
Colormap: [256×3 double]
ContextMenu: [0×0 GraphicsPlaceholder]
CreateFcn: ''
CurrentPoint: [2×3 double]
DataAspectRatio: [105 3300 1]
DataAspectRatioMode: 'auto'
DeleteFcn: ''
FontAngle: 'normal'
FontName: 'Helvetica'
FontSize: 14
FontSizeMode: 'manual'
FontSmoothing: on
FontUnits: 'points'
FontWeight: 'bold'
GridAlpha: 0.5000
GridAlphaMode: 'manual'
GridColor: [0.1500 0.1500 0.1500]
GridColorMode: 'auto'
GridLineStyle: '-'
GridLineWidth: 1.5000
GridLineWidthMode: 'auto'
HandleVisibility: 'on'
HitTest: on
InnerPosition: [0.1300 0.1100 0.7750 0.8150]
InteractionOptions: [1×1 matlab.graphics.interaction.interactionoptions.InteractionOptions]
Interactions: [1×1 matlab.graphics.interaction.interface.DefaultAxesInteractionSet]
Interruptible: on
LabelFontSizeMultiplier: 1.1000
Layer: 'bottom'
Layout: [0×0 matlab.ui.layout.LayoutOptions]
Legend: [1×1 Legend]
LineStyleCyclingMethod: 'aftercolor'
LineStyleOrder: [7×2 char]
LineStyleOrderIndex: 1
LineWidth: 1.5000
MinorGridAlpha: 0.5000
MinorGridAlphaMode: 'manual'
MinorGridColor: [0.1000 0.1000 0.1000]
MinorGridColorMode: 'auto'
MinorGridLineStyle: ':'
MinorGridLineWidth: 1.5000
MinorGridLineWidthMode: 'auto'
NextPlot: 'add'
NextSeriesIndex: 0
OuterPosition: [0 0 1 1]
Parent: [1×1 Figure]
PickableParts: 'visible'
PlotBoxAspectRatio: [1 1 1]
PlotBoxAspectRatioMode: 'manual'
Position: [0.1300 0.1100 0.7750 0.8150]
PositionConstraint: 'outerposition'
Projection: 'orthographic'
Selected: off
SelectionHighlight: on
SortMethod: 'childorder'
Subtitle: [1×1 Text]
SubtitleFontWeight: 'normal'
Tag: ''
TickDir: 'in'
TickDirMode: 'auto'
TickLabelInterpreter: 'tex'
TickLength: [0.0100 0.0250]
TightInset: [0 0.0603 0 0.0675]
Title: [1×1 Text]
TitleFontSizeMultiplier: 1.1000
TitleFontWeight: 'bold'
TitleHorizontalAlignment: 'center'
Toolbar: [1×1 AxesToolbar]
Type: 'axes'
Units: 'normalized'
UserData: []
View: [0 90]
Visible: on
XAxis: [1×1 NumericRuler]
XAxisLocation: 'bottom'
XColor: [0.1500 0.1500 0.1500]
XColorMode: 'auto'
XDir: 'normal'
XGrid: off
XLabel: [1×1 Text]
XLim: [-5 100]
XLimMode: 'manual'
XLimitMethod: 'tickaligned'
XMinorGrid: off
XMinorTick: on
XScale: 'linear'
XTick: [0 20 40 60 80 100]
XTickLabel: {6×1 cell}
XTickLabelMode: 'auto'
XTickLabelRotation: 0
XTickLabelRotationMode: 'auto'
XTickMode: 'manual'
YAxis: [2×1 NumericRuler]
YAxisLocation: 'left'
YColor: [0 0 0]
YColorMode: 'manual'
YDir: 'normal'
YGrid: off
YLabel: [1×1 Text]
YLim: [0 2700]
YLimMode: 'manual'
YLimitMethod: 'tickaligned'
YMinorGrid: off
YMinorTick: on
YScale: 'linear'
YTick: [0 500 1000 1500 2000 2500]
YTickLabel: {6×1 cell}
YTickLabelMode: 'auto'
YTickLabelRotation: 0
YTickLabelRotationMode: 'auto'
YTickMode: 'auto'
ZAxis: [1×1 NumericRuler]
ZColor: [0.1500 0.1500 0.1500]
ZColorMode: 'auto'
ZDir: 'normal'
ZGrid: off
ZLabel: [1×1 Text]
ZLim: [-1 0]
ZLimMode: 'manual'
ZLimitMethod: 'tickaligned'
ZMinorGrid: off
ZMinorTick: on
ZScale: 'linear'
ZTick: [-1 -0.5000 0]
ZTickLabel: ''
ZTickLabelMode: 'auto'
ZTickLabelRotation: 0
ZTickLabelRotationMode: 'auto'
ZTickMode: 'auto'
%Change the exponent of the 2nd y-axis
ax.YAxis(2).Exponent = 0;
