Entity Framework - Parent Child relational table

I have an Organization entity table

public class Organization
{
    public int OrganizationId { get; set; } 
    public string Name { get; set; }        
    public int OrganizationTypeId { get; set; } 
    public OrganizationType OrganizationType { get; set; }
    public ICollection<OrganizationRelation> OrganizationRelations { get; set; }        
}

then I have my relational table with a self-referencing parent column

public class OrganizationRelation
{
    public int OrganizationRelationId { get; set; }
    public int OrganizationId { get; set; }        
    public int? ParentOrganizationId { get; set; }
    public Organization Organization { get; set; }
    public Organization ParentOrganization { get; set; }
}

public class OrganizationRelationModelConfiguration : IEntityTypeConfiguration<OrganizationRelation>
{
    public void Configure(EntityTypeBuilder<OrganizationRelation> builder)
    {
        builder.HasKey(c => c.OrganizationRelationId);
        builder.Property(c => c.OrganizationRelationId).ValueGeneratedOnAdd();
        builder.Property(c => c.OrganizationId).IsRequired();
        builder.Property(c => c.ParentOrganizationId);            
        builder.HasOne(r => r.Organization).WithMany().HasForeignKey(fk => fk.OrganizationId);
        builder.HasOne(r => r.ParentOrganization).WithMany().HasForeignKey(fk => fk.ParentOrganizationId);
        builder.ToTable("OrganizationRelation", "dbo");
    }
}

When I deploy my db with migration, I see this table created:

CREATE TABLE [mdo].[OrganizationRelation](
[OrganizationRelationId] [int] IDENTITY(1,1) NOT NULL,
[OrganizationId] [int] NOT NULL,
[ParentOrganizationId] [int] NULL,
[OrganizationId1] [int] NULL,
 CONSTRAINT [PK_OrganizationRelation] PRIMARY KEY CLUSTERED
(
[OrganizationRelationId] ASC
)WITH (PAD_INDEX = OFF, STATISTICS_NORECOMPUTE = OFF, IGNORE_DUP_KEY = OFF, ALLOW_ROW_LOCKS = ON, ALLOW_PAGE_LOCKS = ON) ON [PRIMARY]
) ON [PRIMARY]
GO

I'm using EF 5.0 I don't get it why is creating the column OrganizationId1

You didn't map OrganizationRelation.ParentOrganization to Organization.OrganizationRelations, so EF is adding an additional FK to OrganizationRelation for the second navigation property.

But that model seems overly complex. Why not just

public class Organization
{
    public int OrganizationId { get; set; }
    public string Name { get; set; }
    public int OrganizationTypeId { get; set; }
    public int? ParentOrganizationId { get; set; }
    public Organization ParentOrganization { get; set; }
    public ICollection<Organization> ChildOrganizations{ get; } = new HashSet<Organization>();
}

which creates

  CREATE TABLE [Organization] (
      [OrganizationId] int NOT NULL IDENTITY,
      [Name] nvarchar(max) NULL,
      [OrganizationTypeId] int NOT NULL,
      [ParentOrganizationId] int NULL,
      CONSTRAINT [PK_Organization] PRIMARY KEY ([OrganizationId]),
      CONSTRAINT [FK_Organization_Organization_ParentOrganizationId] FOREIGN KEY ([ParentOrganizationId]) REFERENCES [Organization] ([OrganizationId]) ON DELETE NO ACTION
  );

  CREATE INDEX [IX_Organization_ParentOrganizationId] ON [Organization] ([ParentOrganizationId]);

?

To factor a foreign key out into a separate table, you just introduce a 1-1 dependent table, where the dependent table's FK and PK are the same as the main table's PK.

So to do the same thing with a separate entity would look like this:

public class Organization
{
    public int OrganizationId { get; set; }
    public string Name { get; set; }
    public int OrganizationTypeId { get; set; }
    public OrganizationRelation OrganizationRelation { get; set; }
    public ICollection<OrganizationRelation> ChildOrganizations { get; } = new HashSet<OrganizationRelation>();
}
public class OrganizationRelation
{
    public int OrganizationId { get; set; }
    public int ParentOrganizationId { get; set; }
    public Organization Organization { get; set; }
    public Organization ParentOrganization { get; set; }
}

protected override void OnModelCreating(ModelBuilder builder)
{
    base.OnModelCreating(builder);

    builder.Entity<OrganizationRelation>().HasKey(c => c.OrganizationId);

    builder.Entity<OrganizationRelation>()
           .HasOne(r => r.Organization)
           .WithOne(o => o.OrganizationRelation)
           .HasForeignKey(nameof(OrganizationRelation), nameof(OrganizationRelation.OrganizationId));

    builder.Entity<OrganizationRelation>()
           .HasOne(r => r.ParentOrganization)
           .WithMany(o => o.ChildOrganizations)
           .HasForeignKey(r => r.ParentOrganizationId)
           .OnDelete(DeleteBehavior.Restrict);

    builder.Entity<OrganizationRelation>().ToTable("OrganizationRelation", "dbo");


    base.OnModelCreating(builder);

}