Does IntelliJ come with a Tomcat container with it?

IDE does not bundled any application servers.

What Run/Debug Configuration do you use for starting in IDE?

What error do you get when run it from command line?

Make sure you have all the needed dependencies configured for the Gradle project. Check related tutorials and a sample project (e.g. Spring Initializ) and https://spring.io/guides/gs/spring-boot/

My main class:

@SpringBootApplication
@Import({WebConfigurer.class})
@ComponentScan("com.jde.nlu.qe")
@PropertySource({"classpath:boot.properties", "classpath:important.properties", "classpath:jss.properties",
        "classpath:system.properties", "classpath:ump.properties"})
@EnableAutoConfiguration
public class JnluQEWebStart extends SpringBootServletInitializer {

    public static void main(String[] args) {

        SpringApplication.run(JnluQEWebStart.class, args);
    }
}

When I run "JnluQEWebStart" I received the following error message:

Error starting ApplicationContext. To display the conditions report re-run your application with 'debug' enabled.
2018-09-16 at 00:44:28.164 [main] ERROR org.springframework.boot.SpringApplication [863] [reportFailure] - Application run failed org.springframework.context.ApplicationContextException: Unable to start web server; nested exception is org.springframework.context.ApplicationContextException: Unable to start ServletWebServerApplicationContext due to missing ServletWebServerFactory bean.
    at org.springframework.boot.web.servlet.context.ServletWebServerApplicationContext.onRefresh(ServletWebServerApplicationContext.java:155) ~[spring-boot-2.0.5.RELEASE.jar:2.0.5.RELEASE]
    at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:544) ~[spring-context-5.0.9.RELEASE.jar:5.0.9.RELEASE]
    at org.springframework.boot.web.servlet.context.ServletWebServerApplicationContext.refresh(ServletWebServerApplicationContext.java:140) ~[spring-boot-2.0.5.RELEASE.jar:2.0.5.RELEASE]
    at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:780) [spring-boot-2.0.5.RELEASE.jar:2.0.5.RELEASE]
    at org.springframework.boot.SpringApplication.refreshContext(SpringApplication.java:412) [spring-boot-2.0.5.RELEASE.jar:2.0.5.RELEASE]
    at org.springframework.boot.SpringApplication.run(SpringApplication.java:333) [spring-boot-2.0.5.RELEASE.jar:2.0.5.RELEASE]
    at org.springframework.boot.SpringApplication.run(SpringApplication.java:1277) [spring-boot-2.0.5.RELEASE.jar:2.0.5.RELEASE]
    at org.springframework.boot.SpringApplication.run(SpringApplication.java:1265) [spring-boot-2.0.5.RELEASE.jar:2.0.5.RELEASE]
    at com.jde.nlu.qe.boot.JnluQEWebStart.main(JnluQEWebStart.java:22) [classes/:?]
Caused by: org.springframework.context.ApplicationContextException: Unable to start ServletWebServerApplicationContext due to missing ServletWebServerFactory bean.
    at org.springframework.boot.web.servlet.context.ServletWebServerApplicationContext.getWebServerFactory(ServletWebServerApplicationContext.java:204) ~[spring-boot-2.0.5.RELEASE.jar:2.0.5.RELEASE]
    at org.springframework.boot.web.servlet.context.ServletWebServerApplicationContext.createWebServer(ServletWebServerApplicationContext.java:178) ~[spring-boot-2.0.5.RELEASE.jar:2.0.5.RELEASE]
    at org.springframework.boot.web.servlet.context.ServletWebServerApplicationContext.onRefresh(ServletWebServerApplicationContext.java:152) ~[spring-boot-2.0.5.RELEASE.jar:2.0.5.RELEASE]
    ... 8 more

It may have nothing to do with Tomcat. 

Please ask the question on a Spring Boot related forums. You will have better chance to get the answer which rather relates to the Spring Boot than to IDE functionality. See e.g. https://stackoverflow.com/a/50232382/2000323.