PRIVILEGED & CONFIDENTIAL ATTORNEY-CLIENT COMMUNICATION ATTORNEY WORK PRODUCT
CALDERWOOD & HARKNESS LLP
Attorneys at Law
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www.calderwoodharkness.com
April 1, 2024
Via Hand Delivery and Email
Marcus Whitfield Vice President, Global Tax Penterra Pharmaceuticals Corp. 2200 Independence Boulevard Princeton Junction, NJ 08550
Re: Examination Resolution Summary — IRS Transfer Pricing Examination of Penterra Pharmaceuticals Corp. (EIN 22-3741856), Tax Years 2017–2020
C&H Matter No. 1018-00009 IRS Exam Team ID: LB&I-NE-TP-2022-00641
Dear Marcus:
We write to you on behalf of Calderwood & Harkness LLP ("C&H") in our capacity as outside tax counsel to Penterra Pharmaceuticals Corp. ("PPC" or the "Company"). This letter, prepared by Leonard Cross, Responsible Partner, Tax Department, and Sylvia Hartwell, Billing Partner, Tax Department, serves as our formal summary of the resolution of the Internal Revenue Service ("IRS") Large Business & International ("LB&I") Division examination of PPC's transfer pricing positions for tax years 2017, 2018, 2019, and 2020 (the "Examination"). As you are aware, the parties executed IRS Form 906 Closing Agreement on March 29, 2024, formally closing the Examination. This letter is provided for PPC's corporate records and to outline the remaining administrative steps that PPC must undertake to implement the settlement and ensure compliance with the terms of the Closing Agreement.
This communication is protected by the attorney-client privilege and the work product doctrine. It should not be disclosed to any third party without the prior written consent of C&H and PPC, except as may be necessary for PPC's financial reporting, credit facility compliance, and coordination with PPC's independent auditor, Crestfield & Associates LLP, and PPC's Irish tax advisors, Thornbury & Keogh, Chartered Tax Advisors, Dublin, each of whom are subject to existing confidentiality arrangements.
1. Background and Examination History
1.1 Examination Opening and Scope
On May 16, 2022, the IRS LB&I Division opened an examination of PPC by issuing Letter 2205-A (Examination Notification). The Examination was conducted by the LB&I Northeast Transfer Pricing Practice, designated as Team ID LB&I-NE-TP-2022-00641. The IRS examination team was led by Supervisory Revenue Agent Gerald Meskill, who served as Team Manager, with Lead Revenue Agent Patricia Dunleavy conducting the day-to-day examination work. The IRS also engaged Dr. Alan Washburne as its examining economist, and IRS Chief Counsel assigned Attorney-Advisor Franklin Rosario and Senior Counsel Donna Hirabayashi to advise the examination team on legal matters.
The tax years under examination were 2017, 2018, 2019, and 2020, as reflected on PPC's consolidated federal income tax returns (Forms 1120) filed for those periods. The Examination focused principally on the transfer pricing methodology employed in the intercompany arrangements between PPC's U.S. operations and its Irish subsidiary, Penterra Biopharma International DAC ("PBI"), a designated activity company organized and tax resident in Ireland. PBI is held through Penterra Holdings Luxembourg S.à r.l. ("PHL"), which is treated as a disregarded entity for U.S. federal income tax purposes under Treasury Regulations § 301.7701-3. As a result, for purposes of the U.S. transfer pricing analysis, the relevant controlled transactions were analyzed as occurring directly between PPC and PBI.
1.2 C&H Engagement
Calderwood & Harkness LLP was engaged as outside tax counsel to PPC effective June 2, 2022, pursuant to an engagement letter executed on that date between PPC and C&H. On June 8, 2022, C&H filed IRS Form 2848, Power of Attorney and Declaration of Representative, on behalf of PPC, authorizing the following C&H attorneys to represent PPC before the IRS in connection with the Examination: Leonard Cross, Sylvia Hartwell, Garrett Simmons, and Leila Nazari.
To support the defense of PPC's transfer pricing positions, Whitmore Valuation Group LLC ("Whitmore") was retained as an independent economic consulting and valuation firm under a Kovel arrangement effective June 20, 2022, referenced internally as C&H Matter No. 1018-00009-KV. The Kovel arrangement ensured that Whitmore's work was performed at the direction of counsel and protected by the attorney-client privilege and work product doctrine to the fullest extent permissible under applicable law. Dr. Helena Vasquez served as Whitmore's lead economist on the engagement, supported by Dr. Rohan Chakrabarti, Senior Director.
Throughout the Examination, C&H coordinated closely with the following additional advisors to PPC and PBI:
• Crestfield & Associates LLP — PPC's independent auditor and the firm that prepared PPC's original contemporaneous transfer pricing documentation. Coordination was conducted primarily through Martin Ogilvy, Engagement Partner (Audit), and Susan Lam, Transfer Pricing Partner.
• Thornbury & Keogh, Chartered Tax Advisors, Dublin — Irish tax advisors to PBI, with Ciarán Thornbury serving as the lead partner on all Irish tax matters relevant to the Examination, including Irish corporate tax compliance, Knowledge Development box ("KDB") claims, and U.S.-Ireland Tax Treaty considerations.
This multi-advisor structure allowed C&H to manage the U.S. tax controversy aspects of the matter while ensuring consistent coordination with PPC's financial reporting advisors and PBI's Irish tax advisors on overlapping issues.
1.3 IRS Positions and Proposed Adjustments
Over the course of the Examination, the IRS challenged two primary categories of intercompany arrangements between PPC and PBI:
(a) Cost-Sharing Arrangement ("CSA"). The IRS examined the qualified cost-sharing arrangement ("CSA") between PPC and PBI, effective July 1, 2012, pursuant to which PBI co-funded research and development costs incurred by PPC in exchange for rights to exploit the resulting pharmaceutical intellectual property outside the Americas territory. The CSA was structured under Treasury Regulations § 1.482-7 and included a platform contribution transaction ("PCT") payment of $312 million from PBI to PPC, representing compensation for PPC's pre-existing intangible property and other platform contributions made available to the CSA at its inception. The IRS challenged both the cost-sharing ratios applied during the 2017–2020 examination period and, to a lesser degree, the adequacy of the PCT payment.
(b) Legacy IP License. The IRS also examined a separate intercompany license agreement under which PBI paid PPC a royalty of 4.5% of net sales for non-Americas territory rights to pre-2012 pharmaceutical compounds (i.e., compounds that predated the CSA and were not covered by the cost-sharing arrangement). The IRS contended that the 4.5% royalty rate was below the arm's-length range and proposed an increase to 11.0% of net sales.
In addition to challenging the pricing of the two principal intercompany arrangements, the IRS raised questions regarding PBI's economic substance and its performance of development, enhancement, maintenance, protection, and exploitation ("DEMPE") functions with respect to the intellectual property rights it held. The IRS contended that PBI's functional profile was more limited than reflected in PPC's transfer pricing documentation, warranting reduced cost-sharing percentages and higher royalty payments flowing from PBI to PPC.
During the course of the Examination, the IRS issued a total of forty-seven (47) Information Document Requests ("IDRs"), spanning from June 2022 through September 2023, covering a broad range of topics including organizational structure, functional analyses, financial data, intercompany agreements, board minutes, employee records, R&D cost allocations, regulatory filings, and comparable company data. C&H, in coordination with PPC's internal teams and Crestfield & Associates, responded to each IDR within the agreed-upon timelines, and no enforcement summonses were issued.
On October 12, 2023, the IRS issued its Notice of Proposed Adjustment ("NOPA"), setting forth the IRS's proposed adjustments in detail. Following PPC's response to the NOPA, the IRS issued a 30-Day Letter on November 8, 2023, formally proposing the adjustments and advising PPC of its right to file a formal administrative protest with the IRS Office of Appeals.
1.4 Proposed Adjustment Detail
The NOPA and 30-Day Letter set forth the following proposed adjustments to PPC's taxable income for tax years 2017 through 2020:
CSA Cost-Sharing Ratio Adjustments. The IRS proposed increasing PBI's cost-sharing percentage by approximately 8 to 12 percentage points for each examination year, thereby reducing PBI's share of R&D costs borne under the CSA and correspondingly increasing the portion of R&D expenditures allocable to PPC. The proposed adjustments to PPC's taxable income resulting from the cost-sharing ratio modifications were as follows:
Legacy IP Royalty Rate Adjustments. The IRS proposed increasing the royalty rate on the legacy IP license from 4.5% to 11.0% of PBI's net sales, representing an incremental 6.5 percentage points applied to PBI's non-Americas net sales of the pre-2012 compounds:
Correlative Offset. The IRS examination team allowed a correlative offset of ($42.65 million) across the four examination years to avoid double-counting of certain cost-sharing payments that would have been affected by both the CSA ratio adjustments and the royalty rate adjustments. This offset reflected the interaction between the two categories of proposed adjustments and was applied to prevent the IRS from effectively taxing the same economic income twice.
Net Proposed Adjustment. After application of the correlative offset, the IRS's total net proposed adjustment to PPC's taxable income for the four examination years was as follows:
• CSA cost-sharing adjustments: $235.01 million
• Legacy IP royalty adjustments: $188.04 million
• Less correlative offset: ($42.65 million)
• Net proposed adjustment: $380.40 million
Proposed Penalty. The IRS also proposed the imposition of a substantial valuation misstatement penalty under IRC § 6662(e) at the 20% rate. The estimated penalty amount was approximately $15.98 million, computed as 20% of the underpayment of tax attributable to the proposed transfer pricing adjustments ($380.4 million × 21% statutory rate × 20% penalty rate = $15.98 million, rounded).
2. Defense and Protest
2.1 Key Defense Strategies Employed
C&H, together with Whitmore Valuation Group and in coordination with PPC's internal tax team, developed and executed a comprehensive defense strategy addressing each of the IRS's proposed adjustments. The defense was built upon the following principal pillars:
Functional Analysis and PBI Substance. C&H prepared and submitted to the IRS a comprehensive functional analysis demonstrating that PBI maintained substantive operations in Ireland sufficient to support its participation in the CSA and its entitlement to residual profits attributable to the non-Americas exploitation of PPC's pharmaceutical intellectual property. Key substance evidence included the following:
• PBI employed 185 full-time employees as of December 31, 2020, an increase from 52 employees at the time of PBI's incorporation in 2012, reflecting significant organic growth in PBI's operational capacity during the intervening years.
• PBI's board of directors held a total of 42 formally convened board meetings in Dublin during the 2017–2020 examination period, with detailed minutes documenting strategic decision-making, budget approvals, regulatory submissions, and commercial planning activities.
• PBI incurred cumulative regulatory expenditures of approximately €47.2 million during the examination years, reflecting its direct involvement in obtaining and maintaining marketing authorizations across 68 country markets outside the Americas.
• PBI maintained independent pricing authority and responsibility for commercial operations across its 68-country territory, including the establishment of local pricing strategies, distribution channel management, and government tender negotiations.
• PBI occupied approximately 18,000 square feet of office space at Sandyford Business Park, Dublin 18, Ireland, housing its commercial, regulatory, medical affairs, and finance teams.
• C&H conducted and submitted to the IRS detailed interviews with 12 key PBI employees, including PBI's Managing Director, Chief Commercial Officer, Vice President of Regulatory Affairs, and Head of Medical Affairs, each of whom provided testimony regarding PBI's autonomous decision-making functions and DEMPE contributions.
Whitmore Valuation Group Economic Analyses. Dr. Helena Vasquez and Dr. Rohan Chakrabarti of Whitmore Valuation Group prepared comprehensive economic analyses rebutting each element of the IRS's proposed adjustments. These analyses included the following:
• Comparable Uncontrolled Transaction ("CUT") Analysis. Whitmore identified and analyzed 14 comparable pharmaceutical license agreements sourced from publicly available databases and SEC filings. The resulting interquartile range of royalty rates for comparable non-exclusive territorial pharmaceutical licenses was 3.1% to 6.8% of net sales, with a median of 4.4%. PPC's legacy IP royalty rate of 4.5% fell within the arm's-length range established by these comparables, and in fact was slightly above the median, undermining the IRS's position that the rate should be increased to 11.0%.
• Comparable Profits Method ("CPM") / Transactional Net Margin Method ("TNMM") Analysis. Whitmore performed a CPM/TNMM analysis using a set of 22 comparable companies to benchmark PBI's operating profitability. The analysis demonstrated that PBI's operating margins were within the interquartile range of comparable company results for all four examination years, confirming that PBI's profit levels were consistent with arm's-length outcomes and did not reflect an excessive allocation of profits away from PPC.
• PCT Income Method / Discounted Cash Flow ("DCF") Analysis. Whitmore prepared a DCF analysis to evaluate the arm's-length value of the PCT payment. Using a weighted average cost of capital ("WACC") of 9.8% — reflecting the risk profile of pharmaceutical R&D intangibles at the early-stage development phase — Whitmore determined an arm's-length range for the PCT payment of $278 million to $361 million. PPC's actual PCT payment of $312 million fell comfortably within this range. The IRS economist, Dr. Washburne, had applied a lower WACC of 7.2%, which Whitmore demonstrated was inappropriate given the risk characteristics of the underlying intangible development activities and the stage of development of the relevant compounds at the CSA inception date.
Contemporaneous Transfer Pricing Documentation and Penalty Protection. PPC maintained contemporaneous transfer pricing documentation prepared by Crestfield & Associates LLP in accordance with Treasury Regulations § 1.482-7 (applicable to cost-sharing arrangements) and § 1.482-4 (applicable to transfers of intangible property). This documentation was prepared and in existence prior to the filing of PPC's federal income tax returns for each of the examination years. C&H submitted this documentation to the IRS examination team and argued that it established reasonable-cause penalty protection under IRC § 6662(e)(3)(B), which provides a defense to the substantial valuation misstatement penalty where the taxpayer maintained contemporaneous documentation and acted in a reasonable manner with respect to its transfer pricing methodology.
Rebuttal of IRS Economist's Analysis. Dr. Vasquez and Dr. Chakrabarti prepared a detailed written rebuttal of the economic analysis performed by Dr. Washburne on behalf of the IRS. The rebuttal identified a number of methodological deficiencies in Dr. Washburne's work, including the use of an inappropriately low discount rate in the PCT valuation, the exclusion of comparable license agreements that supported PPC's royalty rate, the reliance on functionally dissimilar comparable companies in the CPM/TNMM analysis, and the failure to account for PBI's significant and growing DEMPE contributions. This rebuttal was submitted to the IRS examination team and subsequently to IRS Appeals as part of C&H's comprehensive defense presentation.
2.2 Formal Protest
On December 22, 2023, within the extended deadline granted by the IRS, C&H filed a Formal Protest on behalf of PPC with the IRS Office of Appeals, contesting the full $380.4 million in proposed adjustments to PPC's taxable income across all four examination years. The Protest set forth detailed legal and economic arguments under IRC § 482 and the applicable Treasury Regulations, including Treasury Regulations §§ 1.482-4 and 1.482-7, and challenged both the IRS's legal theories and the economic methodologies employed by the IRS examination team.
The Formal Protest was supported by five detailed exhibits:
• Exhibit A: PPC-PBI Entity Structure and Organizational Chart
• Exhibit B: CSA Summary, including the PCT Payment Analysis and Cost-Sharing Ratio Computations
• Exhibit C: Whitmore Valuation Group Economic Analyses (CUT, CPM/TNMM, and DCF analyses with supporting data)
• Exhibit D: PBI Substance Evidence (employee data, board minutes, regulatory filings, office lease, key employee interview summaries)
• Exhibit E: Penalty Protection Documentation (contemporaneous transfer pricing reports for TY 2017–2020, engagement letters with Crestfield & Associates, and reasonable-cause narrative)
2.3 Appeals Proceedings
Following the filing of the Formal Protest, the case was assigned to Appeals Officer Noreen Castañeda of the IRS Office of Appeals in January 2024. Appeals Officer Castañeda conducted a thorough review of the administrative file, the Formal Protest, and the supporting exhibits prior to scheduling an appeals conference.
The appeals conference was held on February 28, 2024, at the IRS Appeals Office in Manhattan, New York. The following individuals attended the conference:
• Calderwood & Harkness LLP: Leonard Cross (Responsible Partner), Sylvia Hartwell (Billing Partner), and Garrett Simmons (Senior Associate)
• Penterra Pharmaceuticals Corp.: Marcus Whitfield (Vice President, Global Tax) and Deborah Staines (General Counsel)
• Whitmore Valuation Group LLC: Dr. Helena Vasquez (Lead Economist)
• IRS Office of Appeals: Appeals Officer Noreen Castañeda
During the appeals conference, C&H and Whitmore presented a comprehensive defense of PPC's transfer pricing positions, focusing on the strength of the CUT analysis supporting the legacy IP royalty rate, the CPM/TNMM results confirming PBI's arm's-length profitability, the robustness of the PCT valuation, and the substantial evidence of PBI's DEMPE functions and economic substance. Appeals Officer Castañeda engaged constructively with the presentation and posed a number of questions regarding the comparable license agreements and the WACC assumptions used in the DCF analysis.
Following the appeals conference, C&H submitted a supplemental written submission to Appeals Officer Castañeda on March 8, 2024, providing additional CUT comparables that had been identified through supplemental database searches and further supporting PPC's position that the 4.5% legacy IP royalty rate was within the arm's-length range.
3. Settlement Terms and Resolution
3.1 Settlement Offer and Acceptance
On March 15, 2024, Appeals Officer Castañeda transmitted a formal settlement offer to C&H on behalf of the IRS. The settlement offer reflected Appeals Officer Castañeda's independent evaluation of the hazards of litigation faced by both the IRS and PPC and represented a significant reduction from the IRS examination team's original proposed adjustments.
C&H promptly transmitted the settlement offer to PPC for review and evaluation. Following internal deliberations among PPC's tax, legal, and finance leadership — including discussions with you, Deborah Staines (General Counsel), Rajesh Iyer (Chief Financial Officer), and Catherine Falk (Chief Executive Officer) — PPC's management approved acceptance of the settlement offer on March 22, 2024.
The settlement was formalized through the execution of IRS Form 906, Closing Agreement on Final Determination Covering Specific Matters, on March 29, 2024. The Closing Agreement was signed on behalf of PPC by Rajesh Iyer, Chief Financial Officer, and on behalf of the IRS by Appeals Officer Castañeda and her Team Manager. A copy of the fully executed Form 906 Closing Agreement is enclosed with this letter.
The Examination was formally closed as of March 29, 2024, the date of execution of the Closing Agreement.
3.2 Settlement Adjustment Amount
The total settlement adjustment to PPC's taxable income, as set forth in the Form 906 Closing Agreement, is $47.6 million, representing approximately 12.51% of the IRS's original proposed adjustment of $380.4 million. The settlement adjustment is allocated among the four examination years as follows:
The settlement adjustment encompasses a blended resolution of the IRS's challenges to both the CSA cost-sharing ratios and the legacy IP royalty rate. The Form 906 Closing Agreement does not separately allocate the settlement between the two categories of intercompany arrangements; rather, the agreed-upon amount reflects a global settlement of all transfer pricing issues for the four examination years.
3.3 Tax, Interest, and Penalty
The financial consequences of the settlement are summarized as follows:
Federal Income Tax. The additional federal income tax resulting from the settlement adjustment is approximately $10.0 million ($47.6 million × 21% = $9,996,000, rounded to $10.0 million). We note that although tax year 2017 was subject to the pre-Tax Cuts and Jobs Act ("TCJA") corporate income tax rate of 35%, the blended computation as specified in the terms of the Form 906 Closing Agreement applies the 21% statutory rate to the settlement adjustment for all four years. This treatment reflects the agreed-upon methodology negotiated with Appeals and set forth in the Closing Agreement.
Underpayment Interest. Estimated federal underpayment interest on the settlement amount is approximately $2.84 million, computed at the applicable federal underpayment rate prescribed under IRC § 6621 over the relevant periods for each examination year, from the original due date of each return through the anticipated payment date. This estimate is subject to minor adjustment by the IRS upon processing of PPC's amended returns, as the final interest computation will depend on the precise date of payment.
Substantial Valuation Misstatement Penalty. The IRC § 6662(e) substantial valuation misstatement penalty has been fully abated. Appeals Officer Castañeda accepted PPC's reasonable-cause defense and determined that PPC's contemporaneous transfer pricing documentation, prepared by Crestfield & Associates in accordance with Treasury Regulations §§ 1.482-4 and 1.482-7, satisfied the requirements for penalty protection under IRC § 6662(e)(3)(B). The full abatement of the proposed penalty, which the IRS had estimated at approximately $15.98 million, represents a significant component of the favorable outcome achieved in this matter.
Total Cash Cost of Settlement. The total cash cost to PPC of the settlement, inclusive of additional federal income tax and estimated underpayment interest, is approximately $12.84 million.
3.4 Comparison to Proposed Adjustments
The settlement represents a highly favorable outcome for PPC when compared to the IRS's original proposed assessment. The following summary illustrates the magnitude of the savings achieved:
Including the estimated interest component, the total potential exposure under the IRS's proposed assessment would have been substantially in excess of $95.86 million, while PPC's actual total cash outlay under the settlement is approximately $12.84 million. The settlement thus represents a reduction of approximately $83.02 million, or approximately 86.6%, from the total proposed assessment (excluding interest on the proposed assessment, which would have been substantially higher than the interest on the settlement amount).
4. Total Engagement Cost Summary
4.1 Professional Fees
The professional fees incurred by PPC in connection with the Examination defense, from inception of the C&H engagement through matter closure on March 29, 2024, are as follows:
The Calderwood & Harkness fees reflect the aggregate of all professional time billed to C&H Matter No. 1018-00009 from June 2, 2022, through March 29, 2024, including attorney and paralegal time, and are exclusive of disbursements, which will be reflected on the final invoice transmitted under separate cover. The Whitmore Valuation Group fees reflect all economic consulting and expert services rendered under the Kovel arrangement. The Thornbury & Keogh fees have been converted from euros to U.S. dollars at the average USD/EUR exchange rate over the engagement period.
4.2 Total Cost to PPC
The total cost to PPC of the Examination, inclusive of all professional fees, settlement tax payments, and interest, is summarized as follows:
We note that this total cost should be considered in the context of the approximately $95.86 million in total potential exposure (tax and penalties, excluding interest) that PPC faced under the IRS's original proposed assessment. The net savings to PPC, after deducting all professional fees and settlement costs, remains highly favorable.
5. Impact on Financial Reporting and Reserves
5.1 FIN 48 / ASC 740-10 Reserve Adjustment
Prior to the settlement, PPC maintained a reserve for uncertain tax positions under Financial Accounting Standards Board ("FASB") Accounting Standards Codification ("ASC") 740-10 (formerly FIN 48) related to the Irish IP structure and the intercompany arrangements at issue in the Examination. As of PPC's most recent financial statements preceding the settlement, the FIN 48 reserve attributable to these positions was $62.4 million.
Following execution of the Closing Agreement, PPC's reserve should be reduced to reflect the actual settlement amount and the resolution of the uncertainty with respect to tax years 2017 through 2020. Based on our analysis, the post-settlement reserve should be adjusted to approximately $14.8 million, reflecting the residual uncertain tax positions for tax years not covered by the Closing Agreement (i.e., TY 2021 and subsequent years, for which similar intercompany arrangements remain in place and may be subject to future IRS examination).
We recommend that PPC coordinate promptly with Crestfield & Associates LLP (Martin Ogilvy, Engagement Partner) to finalize the reserve adjustment for inclusion in PPC's next quarterly financial statements (Form 10-Q). The reserve release of approximately $47.6 million will have a favorable impact on PPC's effective tax rate and net income for the reporting period in which it is recognized, and appropriate disclosure of the underlying events should accompany the reserve adjustment.
5.2 SEC Disclosure Considerations
The settlement resolution should be reflected in PPC's next quarterly filing on Form 10-Q with the Securities and Exchange Commission ("SEC"). We recommend that PPC update its contingent liability disclosures under ASC 450-20 (formerly SFAS No. 5) and its income tax disclosures under ASC 740-10 to reflect the resolution of the Examination, including the following elements:
• The execution of the Form 906 Closing Agreement and the closure of the IRS transfer pricing examination for TY 2017–2020;
• The total settlement adjustment of $47.6 million and the associated tax payment of approximately $10.0 million;
• The full abatement of the proposed IRC § 6662(e) penalty;
• The reduction in the uncertain tax position reserve from $62.4 million to approximately $14.8 million; and
• Any residual exposure related to transfer pricing positions for tax years subsequent to the Examination period.
We note that Ridgeview Capital Management LP, which holds approximately 8.3% of PPC's outstanding common stock, and other institutional investors are known to monitor ASC 740-10 disclosures closely, particularly with respect to multinational pharmaceutical companies with significant cross-border intellectual property arrangements. Accordingly, we recommend that the disclosures be prepared with care and reviewed by PPC's disclosure committee and outside auditor prior to filing.
5.3 Hargrove Credit Facility
PPC maintains a $1.5 billion revolving credit facility (the "Credit Facility") with Hargrove National Bank, N.A. ("Hargrove"), with Christine Bellucci serving as PPC's relationship manager. The Credit Facility contains certain tax-related covenants, including a tax-indemnity provision and a material-tax-event reporting covenant.
We recommend that PPC confirm with Hargrove, or through its own review of the Credit Facility documentation, that the Examination settlement does not trigger any reporting obligations or covenant compliance issues under the tax-indemnity or material-tax-event provisions. Based on our prior analysis of the Credit Facility agreement (conducted in connection with the Examination defense), the settlement amount of $47.6 million and the associated tax payment of approximately $10.0 million should not constitute a "material tax event" as defined in the Credit Facility, as the threshold for such events under the agreement is generally tied to tax liabilities or assessments that would have a material adverse effect on PPC's consolidated financial condition. However, we strongly recommend that PPC obtain formal confirmation of this conclusion, either through internal analysis by PPC's treasury team or through a direct communication with Hargrove.
6. Next Steps and Required Actions
6.1 Amended Federal Income Tax Returns
PPC is required to file amended federal income tax returns on Form 1120X for each of tax years 2017, 2018, 2019, and 2020 to reflect the $47.6 million settlement adjustment, allocated among the examination years as set forth in the Closing Agreement (TY 2017: $11.2 million; TY 2018: $12.4 million; TY 2019: $12.8 million; TY 2020: $11.2 million). The amended returns should incorporate the adjusted income figures and recompute PPC's federal income tax liability for each year accordingly.
C&H has prepared a separate detailed memorandum, authored by Garrett Simmons and dated April 5, 2024, setting forth comprehensive filing instructions for the preparation of the amended returns, including the specific line items to be adjusted, the supporting schedules to be attached, and the narrative explanation to be included with each amended return. We recommend that PPC coordinate with Crestfield & Associates LLP for the actual preparation and filing of the amended returns, using the C&H memorandum as a guide.
The amended returns should be filed within approximately 90 days of the execution of the Closing Agreement, consistent with customary practice and the expectations set forth in the Form 906. Based on the March 29, 2024 execution date, the target filing deadline is approximately June 27, 2024. We recommend that PPC commence preparation promptly to ensure timely filing.
6.2 Tax and Interest Payment
PPC should remit payment of the additional federal income tax of $10.0 million plus estimated underpayment interest of approximately $2.84 million to the IRS. Payment should be made via the Electronic Federal Tax Payment System ("EFTPS") or by certified check, as appropriate. C&H can provide PPC with detailed payment instructions, including the applicable IRS remittance address and account designation information.
We note that the estimated interest amount of $2.84 million is subject to finalization by the IRS upon processing of PPC's amended returns. The IRS will compute the exact interest amount based on the underpayment rate in effect for each relevant period and the precise date of payment. Any difference between the estimated and actual interest amount is expected to be minor and will be communicated to PPC by the IRS following processing.
6.3 State Tax Considerations
The federal settlement adjustment of $47.6 million may have state income tax consequences in the states in which PPC files income tax returns, including, most significantly, the State of New Jersey, where PPC is headquartered. The federal adjustment may affect PPC's state taxable income through federal-state conformity provisions, state apportionment factors, and state-specific addback or subtraction modifications.
C&H has prepared a separate analysis of the state tax implications of the settlement, authored by Leila Nazari and dated April 10, 2024, addressing the potential impact on PPC's state apportionment calculations and identifying the states in which amended state income tax returns may need to be filed. We recommend that PPC review this analysis promptly and coordinate with PPC's state tax team to determine the appropriate course of action.
6.4 Irish Tax Coordination
PPC should coordinate with Thornbury & Keogh (Ciarán Thornbury, lead partner) regarding any Irish tax implications of the U.S. settlement for PBI. Specific areas of potential impact include:
• Knowledge Development box ("KDB") Claims. PBI has claimed the benefit of the Irish KDB regime, which provides an effective tax rate of 6.25% on qualifying income derived from qualifying assets. To the extent the U.S. settlement adjustments alter the economic profile of the intercompany arrangements, there may be consequential effects on PBI's KDB computations and the quantum of income eligible for the reduced rate.
• Standard Trading Income. Adjustments to the intercompany pricing may also affect PBI's standard trading income subject to the Irish corporate tax rate of 12.5%, and PBI should confirm that its Irish tax filings remain consistent with the post-settlement economic arrangements.
• Mutual Agreement Procedure ("MAP"). PPC and PBI should consider whether a request for competent authority assistance under the Mutual Agreement Procedure provisions of the U.S.-Ireland Income Tax Treaty (Article 25) is warranted to address potential double taxation arising from the U.S. settlement adjustment. A MAP request could provide PBI with a corresponding adjustment in Ireland, thereby eliminating or reducing the economic double taxation that would otherwise result from the U.S. adjustment. C&H and Thornbury & Keogh are available to advise PPC and PBI on the advisability and mechanics of a MAP request.
6.5 Going-Forward Transfer Pricing Considerations
In light of the issues raised during the Examination and the areas of IRS focus, C&H is preparing several additional memoranda addressing PPC's transfer pricing posture for tax years 2021 and forward. These memoranda will be transmitted under separate cover and include the following:
• Transfer Pricing Documentation and Cost-Sharing Recommendations. A memorandum from Leonard Cross and Sylvia Hartwell, dated April 15, 2024, setting forth specific recommendations for enhancements to PPC's annual transfer pricing documentation, adjustments to the CSA cost-sharing calculations, and modifications to PBI's operational and DEMPE substance, designed to reduce the risk of adverse IRS examination outcomes in future periods.
• Bilateral Advance Pricing Agreement ("APA") Analysis. A memorandum from Leonard Cross, dated April 20, 2024, analyzing the potential benefits, costs, and procedural requirements of pursuing a bilateral APA between PPC and the IRS, on the one hand, and PBI and Irish Revenue, on the other hand. A bilateral APA would provide prospective certainty regarding the arm's-length pricing of the intercompany arrangements and would substantially reduce PPC's and PBI's exposure to future transfer pricing controversies.
• PBI Operational Substance Enhancements. A memorandum from Garrett Simmons, dated April 22, 2024, providing detailed recommendations for further enhancements to PBI's operational substance in Ireland, including headcount expansion, increased local decision-making authority, and enhanced documentation of PBI's DEMPE functions, to strengthen PBI's functional profile in the event of future examination.
6.6 Document Retention
PPC should retain all documents, files, and records related to the Examination in accordance with PPC's corporate document retention policies and all applicable statutory and regulatory requirements. Documents to be retained include, without limitation:
• The executed IRS Form 906 Closing Agreement (dated March 29, 2024);
• All IDR responses and supporting documentation provided to the IRS during the Examination;
• The Formal Protest filed December 22, 2023, together with all supporting exhibits;
• All economic analyses prepared by Whitmore Valuation Group;
• All correspondence with the IRS examination team, IRS Appeals, and IRS Chief Counsel;
• PPC's contemporaneous transfer pricing documentation for TY 2017–2020; and
• All internal PPC memoranda and communications related to the Examination.
We also note that PPC issued a litigation hold and document preservation notice on June 6, 2022, at C&H's recommendation, in connection with the commencement of the Examination. With the execution of the Closing Agreement and the formal closure of the Examination for TY 2017–2020, the litigation hold may be lifted with respect to documents specifically related to the TY 2017–2020 Examination, subject to PPC's assessment of whether any related open matters (including potential state tax examinations, MAP proceedings, or future IRS examinations of subsequent tax years) would warrant continuation of the hold in whole or in part. We recommend that PPC consult with its General Counsel's office before formally lifting the hold.
7. Matter Closure
C&H Matter Number 1018-00009 is now closed effective March 29, 2024, the date of execution of the Form 906 Closing Agreement. All final invoices for professional services rendered by Calderwood & Harkness LLP in connection with this matter will be transmitted to PPC under separate cover.
C&H remains available to assist PPC with any questions or matters arising from the implementation of the settlement terms, including the preparation and filing of amended federal and state income tax returns, remittance of tax and interest payments, coordination with Irish tax advisors on MAP and KDB considerations, and all going-forward transfer pricing planning matters as described in Section 6.5 above. Should PPC require assistance with any of these matters, new engagement arrangements will be established as appropriate.
Closing
We wish to express our sincere appreciation for the opportunity to represent Penterra Pharmaceuticals Corp. in this significant matter. The resolution achieved — a settlement at 12.51% of the IRS's proposed adjustment, with full abatement of the proposed IRC § 6662(e) substantial valuation misstatement penalty — represents a highly favorable outcome that reflects the strength of PPC's transfer pricing positions and the quality of the defense effort.
This outcome was made possible by the collaborative efforts of PPC's exceptional internal team, including your leadership, Marcus, throughout the Examination, as well as the invaluable contributions of Deborah Staines and Rajesh Iyer. We also wish to acknowledge the outstanding work of our co-advisors — Dr. Helena Vasquez and the team at Whitmore Valuation Group, Martin Ogilvy and Susan Lam at Crestfield & Associates, and Ciarán Thornbury at Thornbury & Keogh — each of whom contributed essential expertise that strengthened our defense and contributed to the favorable resolution.
We look forward to continuing to serve PPC and remain at your disposal for any questions regarding this matter or any related tax planning matters.
Very truly yours,
CALDERWOOD & HARKNESS LLP
By: ________
Leonard Cross Partner, Tax Department
By: ________
Sylvia Hartwell Partner, Tax Department
Calderwood & Harkness LLP 1735 Market Street, Suite 3100 Philadelphia, PA 19103
cc:
Deborah Staines, General Counsel, Penterra Pharmaceuticals Corp. Rajesh Iyer, Chief Financial Officer, Penterra Pharmaceuticals Corp. Catherine Falk, Chief Executive Officer, Penterra Pharmaceuticals Corp. (per client instructions) Garrett Simmons, Calderwood & Harkness LLP Leila Nazari, Calderwood & Harkness LLP
Enclosures:
1. Copy of executed IRS Form 906 Closing Agreement (dated March 29, 2024)
2. Settlement financial impact analysis workbook
3. Summary of settlement allocation by tax year
PRIVILEGED & CONFIDENTIAL — ATTORNEY-CLIENT COMMUNICATION — ATTORNEY WORK PRODUCT This communication is intended solely for the use of the addressee and the individuals copied herein. Any dissemination, distribution, or copying of this communication without the prior written consent of Calderwood & Harkness LLP and Penterra Pharmaceuticals Corp. is strictly prohibited.
| Tax Year | PPC CSA % (As Filed) | IRS Proposed CSA % | Total R&D Pool | Proposed Adjustment |
| 2017 | 38.2% | 48.2% | $487.3M | $48.73 million |
| 2018 | 39.6% | 50.6% | $523.8M | $57.61 million |
| 2019 | 41.1% | 52.3% | $561.2M | $62.85 million |
| 2020 | 42.7% | 53.7% | $598.4M | $65.82 million |
| Subtotal CSA | $235.01 million | |||
| Tax Year | PBI Net Sales (Legacy IP) | Incremental Rate | Proposed Adjustment | |
| 2017 | $814.6M | 6.5% | $52.95 million | |
| 2018 | $762.3M | 6.5% | $49.55 million | |
| 2019 | $691.8M | 6.5% | $44.97 million | |
| 2020 | $624.1M | 6.5% | $40.57 million | |
| Subtotal Royalty | $188.04 million | |||
| Tax Year | Settlement Adjustment | |||
| 2017 | $11.2 million | |||
| 2018 | $12.4 million | |||
| 2019 | $12.8 million | |||
| 2020 | $11.2 million | |||
| Total | $47.6 million | |||
| Component | Amount | |||
| Additional federal income tax | $10,000,000 | |||
| Estimated underpayment interest | $2,840,000 | |||
| Penalty | $0 | |||
| Total cash cost | $12,840,000 | |||
| Metric | Proposed Assessment | Settlement | Savings | |
| Taxable income adjustment | $380.4 million | $47.6 million | $332.8 million |
| Federal income tax | $79.88 million | $10.00 million | $69.88 million |
| § 6662(e) penalty | $15.98 million | $0 | $15.98 million |
| Total (excl. interest) | $95.86 million | $10.00 million | $85.86 million |
| Advisor | Fees | ||
| Calderwood & Harkness LLP — legal fees | $5,837,420 | ||
| Whitmore Valuation Group LLC — expert/economist fees | $2,146,800 | ||
| Thornbury & Keogh — Irish tax coordination fees | €312,500 (~$341,200) | ||
| Total professional fees | ~$8,325,420 | ||
| Component | Amount | ||
| Professional fees (C&H, Whitmore, T&K) | ~$8,325,420 | ||
| Federal income tax settlement payment | $10,000,000 | ||
| Estimated underpayment interest | $2,840,000 | ||
| Penalties | $0 (fully abated) | ||
| Total cost of Examination | ~$21,165,420 |