How to determine the price for custom software?

I am working for a company that has just entered the field of software development, and we do not know how to price out custom software.

There are so many factors at play, and man hours (to develop the software) are only a fraction of determining the cost. I think we must look at how this will benefit the customer, and how much they value the software. But, we also don't want to scare them, or ask for anything outrageous.

The current project is a web application built with Laravel. It's pretty complex - there's an administrator backend, which has a lot of administrative tasks, such as adding users, adding projects, adding calendars, etc. Then, there's a frontend for the employees, where they are able to download and view calendars, handbooks, and other downloads. They can also submit time off requests, update personnel records, submit VA-4 and W-4, direct deposit, and other forms. Then, there is a frontend for the contractors. The contractors portion of the site is for their contractors and subcontractors to login and view/download project plans. And, finally, there is an extremely complex portion that is for tracking equipment usage, employee time on job sites, materials (expenses) for job sites, and other things. They use to do this through Excel, but then they decided to bring everything web-based, so that their employees can work on this in the field on iPads. As such, this portion of the application mimics excel, and is laid out as spreadsheets. The application as a whole tracks user activity (what they are doing, pages they are viewing, actions they make) and has notifications for essentially everything.

I've only briefly explained the project above, and this is the first custom software we have developed for a client. We don't know what to charge them, and we believe that somewhere between $75,000 and $100,000 is reasonable. Without knowing too many details, and from my brief explanation, does this sound fair? What is necessary to determine the cost of custom software? How do most software companies do this?