@Entity
@Table(name = "Company")
public class Company
{
    @Id
    @GeneratedValue(strategy = SEQUENCE, generator = company_id_seq")
    @Column(name = "company_id")
    @NotNull
    private long                          companyId;

...

    @OneToMany(mappedBy = "accountCompany")
    private Collection<CompanyCompetitor> competitors;

    @OneToMany(mappedBy = "competitorCompany")
    private Collection<CompanyCompetitor> accounts;

...

//Original mapping:

    @ManyToMany
    @JoinTable(name = "Company_Competitor", joinColumns = @JoinColumn(name = "company_id"), inverseJoinColumns = @JoinColumn(name = "competitor_company_id"))
    private Collection<Company>            competitors;

    @ManyToMany
    @JoinTable(name = "Company_Competitor", joinColumns = @JoinColumn(name = "competitor_company_id"), inverseJoinColumns =  @JoinColumn(name = "company_id"))
    private Collection<Company>                accounts;

@Entity
@Table(name = "Company_Competitor")
public class CompanyCompetitor
{
    @Embeddable
    public static class Id implements Serializable
    {
        private static final long serialVersionUID = 1L;

        @Column(name = "account_company_id")
        private Long accountCompanyId;

        @Column(name = "competitor_company_id")
        private Long competitorCompanyId;

        public Id()
        {           
        }

        public Id(Long accountCompanyId, Long competitorCompanyId)
        {
            this.accountCompanyId = accountCompanyId;
            this.competitorCompanyId = competitorCompanyId;
        }

        @Override
        public int hashCode()
        {
            final int prime = 31;
            int result = 1;
            result = prime * result + ((accountCompanyId == null) ? 0 : accountCompanyId.hashCode());
            result = prime * result + ((competitorCompanyId == null) ? 0 : competitorCompanyId.hashCode());
            return result;
        }

        @Override
        public boolean equals(Object obj)
        {
            if (this == obj) return true;
            if (obj == null) return false;
            if (getClass() != obj.getClass()) return false;
            final Id other = (Id) obj;
            if (accountCompanyId == null)
            {
                if (other.accountCompanyId != null) return false;
            }
            else if (!accountCompanyId.equals(other.accountCompanyId)) return false;
            if (competitorCompanyId == null)
            {
                if (other.competitorCompanyId != null) return false;
            }
            else if (!competitorCompanyId.equals(other.competitorCompanyId)) return false;
            return true;
        }
    }

    @EmbeddedId
    private Id      id = new Id();

    @ManyToOne
    @JoinColumn(name = "competitor_company_id", insertable = false, updatable = false)
    private Company competitorCompany;

    @ManyToOne
    @JoinColumn(name = "account_company_id", insertable = false, updatable = false)
    private Company accountCompany;

    @Column(name = "market_share")
    @Min(0)
    @Max(100)
    private Long    marketShare;

    public CompanyCompetitor()
    {
        this.id = new Id();
    }

    public CompanyCompetitor(Company competitor, Company accountCompany, long marketShare)
    {
        this.id.competitorCompanyId = competitor.getCompanyId();
        this.id.accountCompanyId = accountCompany.getCompanyId();

        competitor.getAccounts().add(this);
        accountCompany.getCompetitors().add(this);
    }

    @Override
    public int hashCode()
    {
        final int prime = 31;
        int result = 1;
        result = prime * result + (int) (marketShare ^ (marketShare >>> 32));
        result = prime * result + ((competitorCompany == null) ? 0 : competitorCompany.hashCode());
        result = prime * result + ((accountCompany == null) ? 0 : accountCompany.hashCode());
        return result;
    }

    @Override
    public boolean equals(Object obj)
    {
        if (this == obj) return true;
        if (obj == null) return false;
        if (getClass() != obj.getClass()) return false;
        final CompanyCompetitor other = (CompanyCompetitor) obj;
        if (marketShare != other.marketShare) return false;
        if (competitorCompany == null)
        {
            if (other.competitorCompany != null) return false;
        }
        else if (!competitorCompany.equals(other.competitorCompany)) return false;
        return true;
    }

    @Override
    public String toString()
    {
        return competitorCompany.getCompanyId() + "," + accountCompany.getCompanyId() + "," + marketShare;
    }

    public Company getCompetitorCompany()
    {
        if (competitorCompany == null) competitorCompany = new Company();
        return competitorCompany;
    }

    public void setCompetitorCompany(Company competitorCompany)
    {
        this.competitorCompany = competitorCompany;
    }

    public Company getAccountCompany()
    {
        if (accountCompany == null) accountCompany = new Company();
        return accountCompany;
    }

    public void setAccountCompany(Company accountCompany)
    {
        this.accountCompany = accountCompany;
    }

    public long getMarketShare()
    {
        if (marketShare == null) marketShare = (long) 0;
        return marketShare;
    }

    public void setMarketShare(long marketShare)
    {
        this.marketShare = marketShare;
    }

    public Id getId()
    {
        return id;
    }

    public void setId(Id id)
    {
        this.id = id;
    }
}

Hibernate:
    select
        companymar_.account_company_id,
        companymar_.competitor_company_id,
        companymar_.market_share as market3_21_
    from
        Company_Market_Share companymar_
    where
        companymar_.account_company_id=?
        and companymar_.competitor_company_id=?
Hibernate:
    select
        companymar_.account_company_id,
        companymar_.competitor_company_id,
        companymar_.market_share as market3_21_
    from
        Company_Market_Share companymar_
    where
        companymar_.account_company_id=?
        and companymar_.competitor_company_id=?
Hibernate:
    select
        companymar_.account_company_id,
        companymar_.competitor_company_id,
        companymar_.market_share as market3_21_
    from
        Company_Market_Share companymar_
    where
        companymar_.account_company_id=?
        and companymar_.competitor_company_id=?
Hibernate:
    insert
    into
        Company_Market_Share
        (market_share, account_company_id, competitor_company_id)
    values
        (?, ?, ?)
Hibernate:
    update
        Company
    set

Hibernate:
    update
        Company
    set
        update_dttm=?,
        update_user_name=?,
        address1=?,
        address2=?,
        city=?,
        country=?,
        postal_code=?,
        state=?,
        alter_market_share=?,
        company_name=?,
        company_status_id=?,
        company_type_id=?,
        email=?,
        fax=?,
        notes=?,
        parent_company_id=?,
        phone=?,
        service_priority_id=?,
        url=?
    where
        company_id=?
Hibernate:
    delete
    from
        Company_Branch
    where
        company_id=?
Hibernate:
    delete
    from
        Company_Trader
    where
        company_id=?
Hibernate:
    insert
    into
        Company_Branch
        (company_id, branch)
    values
        (?, ?)
Hibernate:
    insert
    into
        Company_Trader
        (company_id, trader_id)
    values
        (?, ?)