EO.Pdf can digitally sign a PDF file with X509 certificate. The following code demonstrates how to digitally sign a PDF file:

//Create a PdfSigner object
PdfSigner signer = new PdfSigner(your_x509_certificate);

//Sign the PDF file
signer.Sign(pdf_file_name);

'Create a PdfSigner object
Dim signer As New PdfSigner(your_x509_certificate)

'Sign the PDF file
signer.Sign(pdf_file_name)

The above code signs and overwrites the original PDF file with the digitally signed file. There are multiple overloaded versions of the Sign method that take different parameter types. For example, one takes two strings allowing you to write the signed file as a new file instead of overwriting the existing file, another takes a byte array allowing you to sign the file contents in memory without reading/writing any physical files, etc. Please see the reference for the Sign methods for more details.