Document:

EX-10.1

Adopted on December 19, 2007

FEDERAL HOME LOAN BANK OF TOPEKA

Executive Short Term Incentive Plan

	 	 	 	 	 	 	 	 	 
	1.01
	 	Purpose
	 		1	
	1.02
	 	Administration
	 		1	
	1.03
	 	Eligibility
	 		2	
	1.04
	 	Goal Setting
	 		3	
	1.05
	 	Shareholder Safeguard
	 		3	
	1.06
	 	Timing and Form of Awards
	 		3	
	1.07
	 	Forfeiture of Awards
	 		3	
	1.08
	 	Change of Control
	 		4	
	1.09
	 	Plan Period
	 		4	
	1.10
	 	Duration of the Plan
	 		4	
	1.11
	 	Recordkeeping
	 		5	
	1.12
	 	Debts
	 		5	
	1.13
	 	Absence of Liability
	 		5	
	1.14
	 	Limitations
	 		5	
	2.01
	 	Target Awards
	 		5	
	2.02
	 	Goal Metrics
	 		6	
	2.03
	 	Performance Ranges
	 		6	
	2.04
	 	Annual Awards
	 		7	
	2.05
	 	Quarterly Awards
	 		8	

Article 1: Administration

1.01: Purpose. The purpose of the Executive Short Term Incentive Plan (“Plan”) of the Federal
Home Loan Bank of Topeka (“Bank”) is to promote the mission and financial performance of the Bank
by providing incentives to key employees for accomplishing annual goals that are aligned with the
Bank’s mission and business objectives and approved by the Compensation Committee of the Board of
Directors (“Committee”), pursuant to the terms and conditions described in Article 1.

1.02: Administration. (a) Except as otherwise noted, the Committee shall administer the Plan and
shall have full authority to construe, interpret, implement, and administer the Plan.

(b) Decisions and determinations by the Committee shall be final and binding upon all participants
in the Plan (“Participants”). The Committee shall have the authority to interpret the Plan, to
adopt and revise rules and regulations relating to the Plan and make any other determinations that
it believes necessary or advisable for the administration of the Plan.

(c) Such determinations may include, but not be limited to, the 1) metrics against which
Participants’ performance will be evaluated, 2) weights assigned metrics in determining
Participants’ annual awards, 3) annual threshold, target, and optimum levels of performance
associated with each metric, including interim quarterly performance levels against which quarterly
progress payments may be computed, 4) annual awards due Participants for their goal-related
performance, 5) formula for determining the quarterly awards due Participants for their
goal-related performance, 6) shareholder safeguard level of performance below which Participants
may not be entitled to awards, and 7) all policy determining the ongoing administration of the
Plan.

(d) The conditions subject to which any amounts may become payable under the Plan may be based upon
such consideration as the Committee deems appropriate. These conditions may include, but not be
limited to, the results of operations of the Bank and the terms and conditions of the elective
deferred compensation plan maintained for Plan Participants.

(e) For purposes of effective and efficient Plan administration, the Committee shall delegate to
the Chief Executive Officer or his designee responsibility and authority to 1) ensure that all goal
metrics, metric weights, and metric performance ranges defined by threshold, target, and optimum
levels of performance on the metrics are submitted to the Committee for review and approval prior
to the beginning of the Plan period, 2) ensure that Plan Participants receive award summaries
outlining their annual award potential under the Plan before the beginning of the Plan period, 3)
compute the quarterly awards earned by Participants for their year-to-date performance against
their goal metrics at the end of each quarter, subject to the terms and conditions stated herein,
4) distribute quarterly reports to the Committee showing the quarterly awards earned by
Participants, 5) compute the total awards earned by Participants for their annual performance
against their goal metrics by February 15 following the end of the Plan period, subject to the
terms and conditions stated herein, and 6) submit the total awards earned by Participants to the
Compensation Committee by March 1 following the end of the Plan period.

1.03: Eligibility. (a) The Plan establishes a participating group of employees (“Executive
Group”) comprised of top executives of the Bank. The Committee, in its sole discretion, shall
determine each year the identity of employees assigned to the Executive Group.

(b) The Committee may add additional persons to, and remove persons from, the Executive Group
during each Plan period.

(c) A member of the Executive Group whose employment by the Bank is terminated for any reason other
than death shall not participate in the Plan from the date of termination until the end of the Plan
period, and shall not be eligible to receive awards or holdbacks for the quarter during which he is
terminated or for subsequent quarters of that Plan period.

(d) Independent contractors are ineligible to participate in the Plan, regardless of whether they
are later reclassified as common law employees.

1.04: Goal Setting. The purpose of the Plan is to promote the Bank’s mission and financial goals.
Consistent with this purpose, the Committee shall delegate to the Chief Executive Officer
responsibility and authority to determine in close collaboration with the Committee’s designee and
any other qualified third parties the 1) goal metrics against which Participants’ performance will
be evaluated, 2) weights assigned metrics in determining Participants’ total awards, and 3) annual
threshold, target, and optimum levels of performance associated with each Plan metric (“Performance
Range”), including interim quarterly performance levels against which quarterly progress payments
may be computed. The Chief Executive Officer shall submit the metrics, metric weights, and metric
performance ranges so developed to the Committee for review and approval prior to the beginning of
the Plan period.

1.05: Shareholder Safeguard. The Committee shall delegate to the Chief Executive Officer
responsibility and authority to determine in close collaboration with the Committee’s designee and
any other qualified third parties the 1) shareholder safeguard metric that will be used to evaluate
the Bank’s ability to pay awards earned under the Plan, and 2) annual threshold level of
performance on the identified metric below which no awards earned under the Plan will be paid. The
Chief Executive Officer shall submit the threshold measure so developed to the Committee for review
and approval before the beginning of the Plan period.

1.06: Timing and Form of Awards. (a) If the Bank’s performance on the Committee-approved
shareholder safeguard metric is at least equal to threshold for the Plan period, the total annual
awards earned under the Plan will 1) be paid in full, in cash, by March 15 following the close of
the Plan period unless deferred subject to the terms and conditions of the Bank’s Benefits
Equalization Plan, the terms of which are included by reference herein, and 2) not include a
vesting requirement.

(b) Subject to the terms and conditions stated herein, Participants may earn quarterly awards for
year-to-date performance against Plan metrics that do not exceed, in aggregate, the awards they
would otherwise be entitled to for their full Plan period performance against these same metrics.
If Participants receive quarterly awards that exceed, in aggregate, the total awards they are
entitled to for a full Plan period, the amount of the award excess will be 1) credited against any
future awards the Participants earn in subsequent Plan periods, and 2) deducted from those
quarterly awards before they are paid.

1.07: Forfeiture of Awards. (a) Notwithstanding any other provisions of the Plan, payment of any
award hereunder to a Participant will, at the discretion of the Committee, be discontinued and
forfeited, and the Bank will have no further obligation hereunder to such Participant if the
Participant 1) is discharged from employment with the Bank for Good Cause as defined in Section
1.07(c) below; 2) engages in competition with the Bank or interferes with the business
relationships of the Bank during his employment or following his termination of employment with the
Bank; or 3) discloses any types of confidential information of the Bank to any third party by any
means, or refuses to report to the Bank any discoveries, inventions or improvements conceived by
him during the course of his employment that are in any way applicable to the business of the Bank.

(b) The Committee shall have the sole discretion with respect to the application of the provisions
of this section, and such exercise of discretion shall be conclusive and binding upon all
participants and all other persons.

(c) For purposes of this section, “Good Cause” shall mean a Participant’s 1) conviction of any
criminal violation involving dishonesty, fraud, or breach of trust; 2) willful engagement in any
misconduct in the performance of his duty that materially injures the Bank; 3) performance of any
act which, if known to the stockholders of the Bank, would materially and adversely impact the
business of the Bank; or 4) willful and substantial nonperformance of assigned duties, provided
that such nonperformance continues more than ten (10) days after the Bank has given written notice
of such nonperformance and of its intention to terminate the Participant’s employment because of
such nonperformance.

1.08: Change of Control. (a) A change of control shall have occurred if (1) individuals who are
members of the Board on the first day of the Plan period no longer constitute a majority of the
Board; or (2) the Bank merges or consolidates with any other entity and is, itself, not a surviving
entity; or (3) substantially all of the assets of the Bank have been sold, liquidated or dissolved.

(b) In the event of a change of control, the Chief Executive Officer or his designee, in close
collaboration with the Committee’s designee, shall 1) evaluate the Bank’s performance against its
shareholder safeguard metric from the first day of the Plan period to the date of Change of
Control, 2) evaluate Participants’ year-to-date performance against all Plan metrics from the first
day of the Plan period to the date of Change of Control, and 3) apply the formula for calculating
final, Fourth Quarter Payouts defined under Article 2, Section 2.05(b) below to determine any final
awards earned by Participants if the Bank’s shareholder safeguard has been met. The Chief
Executive Officer shall submit any final awards so determined to the Compensation Committee for
review and approval subject to the terms and conditions stated herein.

(c) Final awards due Participants shall be paid, in cash, within thirty (30) days of Change of
Control.

1.09: Plan Period. The plan year will coincide with the Bank’s fiscal year.

1.10: Duration of the Plan. The policies and procedures described in the Plan apply to successive
one-year periods beginning January 1, 2008 and ending when changed by the Committee. Participants
have no vested right to receive any award or benefit under the Plan until it has actually been
paid.

1.11: Recordkeeping. The books and records to be maintained for the purpose of the Plan shall be
maintained by the employees of Bank at its expense, and subject to the supervision and control of
the Chief Executive Officer. All expenses of administering the Plan shall be paid by the Bank.

1.12: Debts. To the extent permitted by law, the right of any participant or any beneficiary to
any payment hereunder shall not be subject in any manner to attachment or

other legal process for the debts of the Participant or beneficiary; and any such payment shall not
be subject to anticipation, alienation, sale, transfer, assignment or encumbrance.

1.13: Absence of Liability. Neither the Chief Executive Officer, nor members of the Compensation
Committee shall be liable to any person for any action taken or omitted in connection with the
administration of this Plan unless attributable to the Chief Executive Officer’s or Committee
member’s own fraud or willful misconduct; nor shall the Bank be liable to any person for any such
action unless attributable to fraud or willful misconduct on the part of an officer or employee of
the Bank.

1.14: Limitations. This Plan is not to be construed as constituting a contract of employment.
The Plan does not limit or impair the right of the Bank to terminate any employee of the Bank with
or without cause at any time. No person shall, because of the Plan, acquire any right to an
accounting or to examine the books or the affairs of the Bank.

Article 2: Awards

2.01: Target Award. (a) Award potential under the Plan corresponds with the values of
Participants’ job responsibilities in the labor market consisting of 1) Government Sponsored
Enterprises (“GSE”), using the Bank’s GSE Asset Normalization Model to determine the appropriate
GSE asset size against which to assess market job values, and 2) financial service organizations in
the Midwest, using the Bank’s Financial Service Asset Normalization Model to determine the
appropriate asset size of financial service organizations against which to assess market job
values.

(b) Award potential under the Plan also corresponds with the expected impact of Participants’ job
responsibilities on the financial performance of the Bank, such that Participants in jobs that are
expected to have the greatest impact are eligible for the largest awards.

	 	(c)	 	Participants’ assigned impact levels and corresponding target award potential under
the Plan are shown below.

	 	 	 	 	 	 	 	 	 
	Impact	 	 	 	 	 	Target Award
	Level
	 	Job Title	 	(% of Earned Base)1 
	1
	 	Chief Executive Officer	 	 	55.0	%
	2
	 	Chief Operating Officer	 	 	45.0	%
	2
	 	Chief Financial Officer	 	 	45.0	%
	2
	 	General Counsel	 	 	45.0	%
	3
	 	Director of Financial	 	 	35.0	%
	 
	 	Operations and Risk	 	 	 	 
	 
	 	Analysis	 	 	 	 

1Earned base represents the portion of participants’ annual base wage earned from
the beginning of the Plan period to the end of the quarter in which an award is paid.

2.02: Goal Metrics. (a) The Plan assumes that Participants will be held accountable for
metrics that 1) are measurable, 2) promote the Bank’s mission and financial goals, and 3) are
consistent with Participants’ formal responsibilities.

(b) If Participants are held accountable for performance against more than one metric, each metric
will be weighted to reflect its relative impact on the Bank’s mission and financial performance.

(c) Prior to the beginning of each Plan period, the Chief Executive Officer, in collaboration with
the Executive Group, the Committee’s designee, and any other qualified third parties, shall 1)
determine the metrics that will be used to evaluate Participants’ performance during the Plan
period, 2) determine the weight assigned to each metric, and 3) submit the metrics and metric
weights to the Committee for review and approval.

2.03: Performance Ranges (a) Under the Plan, Participants’ goals are more than just “points” of
annual performance. Instead, Participants’ performance against a goal metric can vary within a
range (“Performance Range”), from threshold, to target, to optimum performance.

(b) Within a Performance Range 1) threshold represents the lowest acceptable, or rewardable, level
of annual performance against the goal metric, 2) target represents the expected level of annual
performance against the goal metric, and 3) optimum represents the best attainable level of annual
performance against the goal metric.

2.04: Annual Awards. (a) The annual award for achieving a particular level of annual performance
against goal metrics varies depending upon its location within the goal metrics’ performance
ranges. Under the Plan, the Participants may earn the following awards, expressed as a percent of
their earned base, for performance that is between threshold and optimum, inclusively, on all goal
metrics:

	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	 	 	 	 	 	 	Threshold	 	Target	 	 	 	 
	 	 	 	 	 	 	Award	 	Award	 	 	 	 
	 
	 	 	 	 	 	(% Earned	 	(% Earned	 	Optimum
	Impact
	 	 	 	 	 	Base)1	 	Base)1	 	Award
	Level
	 	Job Title	 				 				 	(% Earned Base)1 
	1
	 	Chief Executive Officer
	 		27.5	%	 		55.0	%	 		82.5	%
	2
	 	Chief Operating Officer
	 		22.5	%	 		45.0	%	 		67.5	%
	2
	 	Chief Financial Officer
	 		22.5	%	 		45.0	%	 		67.5	%
	2
	 	General Counsel
	 		22.5	%	 		45.0	%	 		67.5	%
	3
	 	Director of Financial
	 		17.5	%	 		35.0	%	 		52.5	%
	 
	 	Operations and Risk
	 	 	 	 	 	 	 	 	 	 	 	 
	 
	 	Analysis
	 	 	 	 	 	 	 	 	 	 	 	 

1Earned base represents the portion of participants’ annual base wage earned from
the beginning of the Plan period to the end of the quarter in which an award is paid.

 (b) Awards may be earned for performance anywhere within a goal metric’s performance
range, from threshold to optimum. For performance between threshold and target, or between target
and optimum, linear interpolation is used to ensure that the annual award earned is consistent with
the annual level of performance achieved. For example, if a Participant is assigned to Impact
Level 2, and his annual level of performance on a goal metric is midway between threshold and
target, he would earn an annual award that is midway between threshold and target in the above
table, or 33.75% of his earned base.

(c) If participants’ performance is evaluated against more than one annual goal metric, then the
annual awards they earn for their performance against each metric are reduced proportionately to
reflect the metric’s weight. For example, if the Participant in the example in Section 2.04(b)
above achieved an annual level of performance on a goal metric that is midway between threshold and
target, and the goal metric’s weight is 50%, then the Participant would earn an annual award for
his performance against that metric equal to 16.88% of his earned wage, rather than 33.75%, (i.e.,
50% x 33.75% = 16.88%).

(d) Consistent with Article 1, Section 1.02(e) above, the Chief Executive Officer, in close
collaboration with the Committee’s designee, shall 1) compute the total annual award earned by each
Participant subject to the terms and conditions stated herein by February 15 following the end of
the Plan period, and 2) submit the calculated awards to the Committee for final review and approval
by March 1 following the end of the Plan period.

(e) Plan Participants will not receive any awards, at any time, for performance against goal
metrics that is not at least equal to the metrics’ annual threshold levels of performance or the
interim quarterly performance levels against which quarterly progress payments may be computed.
Alternatively, if Plan Participants’ performance exceeds their goal metrics’ annual optimum levels
of performance, the Committee will review the circumstances surrounding the Participants’
above-optimum performance and reward it accordingly.

2.05: Quarterly Awards. (a) Plan participants may receive quarterly awards for year-to-date
performance against their goal metrics that exceeds the metrics’ interim quarterly performance
levels for the goal metric against which quarterly progress payments are computed. In aggregate,
any quarterly awards Participants received for such performance may not exceed the value of the
annual awards they would otherwise be entitled to.

(b) The formula for determining quarterly awards (QAs) earned for performance against a single
goal’s metric during the first, second and third quarters of the Plan period is:

QA = [(Earned Base)(Award %)(Metric Weight)(100% — Holdback%)] – Previous Awards

Where: QA = Award Earned at the end of the first, second, or third quarter of the

Plan period

Earned Base = Portion of Participant’s annual base wage earned from the

beginning of the Plan period to the end of the quarter in which the award

is paid

Award % = Award potential resulting from year-to-date performance

against the interim quarterly performance levels for the goal metric
against which quarterly progress payments are computed if the metric
accounted for 100% of the Participant’s award

Metric Weight = Weight assigned to the metric as a percent of the

Participant’s total award potential

Holdback % = 20%

Previous Awards = Cumulative value of awards paid during previous

quarters of the Plan period for performance against the metric.

An example using this formula for determining a quarterly award is shown in Exhibit I. The
formula for determining the fourth quarter, final, award earned (FA) for performance against a
single goal metric during the Plan period is:

FA = [(Earned Base)(Award %)(Metric Weight)] – Previous Awards

In this formula, the 1) Final Award represents the award earned for performance during the
entire Plan period, 2) holdback % is eliminated, and 3) definition of all remaining variables
remains the same as defined above. An example using this formula for determining a final, fourth
quarter award is shown in Exhibit I.

(c) Except as otherwise noted, within thirty (30) days following the completion of each quarter,
the Chief Executive Officer shall distribute to members of the Committee a report showing the
quarterly awards paid Plan Participants.

EXHIBIT I: QUARTERLY AWARDS

Quarterly Awards

The formula for determining quarterly awards (QAs) earned for performance against a single goal’s
metric during the first, second, and third quarters of the Plan period is:

QA = [(Earned Base)(Award % )(Metric Weight)(100% — Holdback%)] – Previous Awards

Where: QA = Award Earned at the end of the first, second, or third quarter of the

Plan period

Earned Base = Portion of Participant’s annual base wage earned from the

beginning of the Plan period to the end of the quarter in which the award

is paid

Award % = Award potential resulting from year-to-date performance

against the interim quarterly performance levels for the goal metric
against which quarterly progress payments are computed if the metric
accounted for 100% of the Participant’s award

Metric Weight = Weight assigned to the metric as a percent of the

Participant’s total award potential

Holdback % = 20%

Previous Awards = Cumulative value of awards paid for performance

	 	 	 	against this metric during previous quarters of the Plan period

For example, assume that a Plan Participant assigned to Impact Level 2 is evaluated against
several metrics including the Bank’s return on class B stock, and, at the end of the second quarter
of the Plan Period, the:

	 	•	 	Bank’s year-to-date return on class B stock is 6.05%, midway between the target and
optimum performance levels set for this goal metric,

	 	•	 	Plan Participant would have an award opportunity of 56.25% of his earned base based
upon the Bank’s year-to-date return on class B stock, which is midway between his total
target and total optimum award opportunities, if this were the only metric he was
evaluated on,

	 	•	 	Goal metric is worth 50.00% of the Plan Participant’s total award opportunity,

	 	•	 	Plan Participant has already been paid $200,000, and

	 	•	 	Plan Participant has already received a $35,000 award at the end of the first quarter
for the Bank’s performance on this metric.

In this example, the Participant would receive an award of $10,000 at the end of the second quarter
for the Bank’s performance against this metric:

QA = [($200,000)(56.25%)(50%)(80%)] — $35,000

= $45,000 — $35,000

= $10,000

Final Awards

The formula for determining the fourth quarter, final, award earned (FA) for performance against a
single metric during the Plan period is:

FA = [(Earned Base)(Award %)(Metric Weight)] – Previous Awards

Where: FA = Award Earned at the end of the Plan period

Earned Base = Portion of Participant’s annual base wage earned from the

beginning of the Plan period to the end of the Plan period

Award % = Award potential resulting from annual performance

against the goal metric if the metric accounted for 100% of the

Participant’s award

Metric Weight = Weight assigned to the metric as a percent of the

Participant’s total award potential

Previous Awards = Cumulative value of awards paid for performance

against this metric during previous quarters of the Plan period

For example, assume that a Plan Participant assigned to Impact Level 2 is evaluated against
several metrics including the Bank’s return on class B stock, and, at the end of the Plan period,
the:

	 	•	 	Bank’s annual return on class B stock is now 5.85%, which is the annual target level
performance set for this goal metric,

	 	•	 	Plan Participant would have an award opportunity of 45.00% of his earned base based
upon the Bank’s annual return on class B stock, which is his total target award
opportunity, if this were the only metric he was evaluated on,

	 	•	 	Goal metric is worth 50.00% of the Plan Participant’s total award opportunity,

	 	•	 	Plan Participant has been paid $400,000 for the entire year, and

	 	•	 	Plan Participant has already received a total of $75,000 in awards at the end of the
first, second, and third quarters for the Bank’s performance on this metric.

In this example, the Participant would receive an award of $15,000 at the end of the year for the
Bank’s full Plan period performance against this metric:

FA = [($400,000)(45.00%)(50.00%)] — $75,000

= $90,000 — $75,000

= $15,000EX-10.2

FIRST AMENDMENT TO BENEFIT EQUALIZATION PLAN

This amendment to the Federal Home Loan Bank of Topeka Benefit Equalization Plan is adopted by
the Federal Home Loan Bank of Topeka as of the date last written below, the same to be effective as
of January 1, 2008.

WHEREAS, Federal Home Loan Bank of Topeka (hereinafter, the “Bank”), previously established
the Federal Home Loan Bank of Topeka Benefit Equalization Plan (hereinafter, the “Plan”) for the
exclusive benefit of its members and their beneficiaries, which Plan was most recently amended and
restated effective as of March 23, 2006; and

WHEREAS, the Bank retained the power to amend and/or terminate the Plan; and

WHEREAS, the Bank now desires to amend the Plan to clarify or change provisions regarding the
deferral of Members’ Incentive Compensation and employer contributions matching Members’ deferred
amounts;

NOW, THEREFORE, the Plan is hereby amended, effective January 1, 2008, as follows:

	1.	 	Notwithstanding any language in the Plan to the Contrary, Members shall be allowed to make
deferrals under Sections 4.01 or 4.02 from Incentive Compensation; provided, the Member must
make a deferral election before December 31 of the calendar year preceding the calendar year
in which the Incentive Compensation is earned. The Member shall elect the amount to be
deferred, which may be expressed as a dollar amount or a percentage of the Member’s total
Incentive Compensation, as well as the time and form of payment of the amount deferred.

	2.	 	Notwithstanding any language in the Plan to the contrary, a Member’s matching contribution
credited under Section 4.05(a) shall be calculated based on the Member’s total annual
compensation (other than Incentive Compensation) and actual deferral elections for the
applicable Plan Year, disregarding IRC Limitations. The matching amount shall be offset by
any matching contribution actually made to the Thrift Plan, but the amount of the offset shall
not exceed the dollar limit under IRC Section 402(g) for that Plan Year.

IN WITNESS WHEREOF, the Bank has caused this First Amendment to be signed by its duly
authorized officer on this 19th day of December, 2007.

FEDERAL HOME LOAN BANK OF TOPEKA

By: /s/ Patrick C. Doran

Name: Patrick C. Doran

Title: Senior Vice President and General Counsel

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