TI-OPA381 output voltage issue
D1 output polarity is correct but the circuit is unusual.
D1 current source polarity appears be wrong.
ie Swap V2 polarity and see what happens.
Circuit operation explained below as it is not quite the usual arrangement.



The OPA381 ( superb data sheet here) is a precision single supply transconductance op amp.
It can swing its output close to but not completely to ground, so   


the purpose of the R10/R9 divider is to provide a pseudo ground reference 0.3V above true ground and this is the point that Vout should be measured with respect to.


The divider works like this:


OA+ is biased to 0.3V by R10/R9.
Vss = 3V3.
R10/R9 junction is at 3V3 x R9/(R9 + R10) = 0.3V.  

This is a "pseudo ground" reference point so the op amp effectively has a +3V positive supply and a -0.3V negative supply relative to this point.


Negative feedback will now cause the opamp to adjust OA- to 0.3V - ie same as OA+.
For this to happen OA output must be > 0.3V so D1 will be negative biased in the typical reverse biased detector mode.

D1 current = R12 current =
(V_out - V_OA-) / R12 = (2.892 - 0.3) / 5.12MegOhm
=  493 nA 

THe D1 model is probably wrong;y driven as it may assume as shown that D1 is forward biased. Swapping polarity of V2 should give 9 nA diode current is the source model is correct to produce as 9 nA diode current.
I_R2 = 50 mA and it is not 100% obvious how that translates to 9 nA.  

IF I_D! = 9NA then IR12= 9nA so
V_R1 = IR = 9E-9 x 5.2E6 = 46.8 mV
So Vout = 0.3V + 0.0468V = 0.3468V.



Note: D1 current will also flow in R 9 but the resulting error voltage is so small as to be negligible.