There are a few issues here.
1. Your data (Amp, Pha) does not agree with closed form transfer function at low frequencies, below 100 rad/s:
R=1682;
C=1.07*10^(-6)
L=46.5*10^(-3)
s=tf('s');
sys=(s^2*L*R*C+s*L+R)/(s^2*L*C+s*R*C);
[mag,ph]=bode(sys,Freq);
semilogx(Freq,20*log10(squeeze(mag)))
semilogx(Freq,20*log10(Amp),'r')
legend('closed form transfer function','data');
2. When import your data into System Identification App, you specify Ts of 0.001. This effectively cuts off your data at 1,000Hz*2*pi=3,142 rad/sec. But if you look at your Freq, it goes to 10 times higher frequency.
3. So to get good results you need to do this: import the data like you do, but specify Ts=1e-4. Then preprocess the data and select to keep the data from 100Hz and up. Now move the resulting dataset to MATLAB workspace. Assume it is called mydataf. Now do this:
mydataf.Ts = 0; % change sampling time to zero, you cannot do it in the app due to a bug
model = tfest(mydataf,2,2)
compare(mydataf, model)
Hope this helps.
