begin name
xie1
end name

begin reactions
re1 {1.0}CC + {1.0}PT = {1.0}CCPT
re10 {1.0}$EXTERNAL = {1.0}CLK
re15 {1.0}perm = {1.0}$EXTERNAL
re17 {1.0}$EXTERNAL = {1.0}PER
re2 {1.0}CC = {1.0}$EXTERNAL
re20 {1.0}$EXTERNAL = {1.0}perm
re28 {1.0}$EXTERNAL = {1.0}vrim
re3 {1.0}CCPT = {1.0}$EXTERNAL
re30 {1.0}vrim = {1.0}$EXTERNAL
re31 {1.0}$EXTERNAL = {1.0}VRI
re32 {1.0}VRI = {1.0}$EXTERNAL
re35 {1.0}$EXTERNAL = {1.0}pdpm
re37 {1.0}pdpm = {1.0}$EXTERNAL
re38 {1.0}$EXTERNAL = {1.0}PDP
re39 {1.0}PDP = {1.0}$EXTERNAL
re4 {1.0}PT = {1.0}$EXTERNAL
re42 {1.0}$EXTERNAL = {1.0}clkm
re43 {1.0}CLK + {1.0}$CYC = {1.0}CC
re44 {1.0}CLK = {1.0}$EXTERNAL
re45 {1.0}CC = {1.0}CLK + {1.0}$CYC
re46 {1.0}PER + {1.0}TIM = {1.0}PT
re47 {1.0}PT = {1.0}PER + {1.0}TIM
re48 {1.0}PER = {1.0}$EXTERNAL
re51 {1.0}$EXTERNAL = {1.0}timm
re53 {1.0}timm = {1.0}$EXTERNAL
re54 {1.0}$EXTERNAL = {1.0}TIM
re55 {1.0}TIM = {1.0}$EXTERNAL
re56 {1.0}CCPT = {1.0}CC + {1.0}PT
re57 {1.0}$EXTERNAL = {1.0}prcper
re58 {1.0}prcper = {1.0}$EXTERNAL
re59 {1.0}prcv = {1.0}$EXTERNAL
re60 {1.0}$EXTERNAL = {1.0}prcv
re61 {1.0}prcpdp = {1.0}$EXTERNAL
re62 {1.0}$EXTERNAL = {1.0}prcpdp
re63 {1.0}$EXTERNAL = {1.0}prvc
re64 {1.0}prvc = {1.0}$EXTERNAL
re65 {1.0}$EXTERNAL = {1.0}prpc
re66 {1.0}prpc = {1.0}$EXTERNAL
re68 {1.0}$EXTERNAL = {1.0}prct
re69 {1.0}prct = {1.0}$EXTERNAL
re9 {1.0}clkm = {1.0}$EXTERNAL
end reactions

begin rate equations
re1 = bccpt*wholeCell*CC[t]*PT[t]
re10 = tlclk*wholeCell*clkm[t]
re15 = dperm*wholeCell*perm[t]
re17 = tlper*wholeCell*perm[t]
re2 = dcc*wholeCell*CC[t]
re20 = wholeCell*perp[t]*(tcccperp*(1 - (1 - prcper[t])^npt) + tcdvpmt*(1 - prcper[t])^npt)
re28 = wholeCell*(tcccvrip*(1 - (1 - prcv[t])^nvri) + tcdvpmt*(1 - prcv[t])^nvri)*vrip[t]
re3 = dccpt*wholeCell*CCPT[t]
re30 = dvrim*wholeCell*vrim[t]
re31 = tlvri*wholeCell*vrim[t]
re32 = dvri*wholeCell*VRI[t]
re35 = wholeCell*pdpp[t]*(tcccpdpp*(1 - (1 - prcpdp[t])^npdp) + tcdvpmt*(1 - prcpdp[t])^npdp)
re37 = dpdpm*wholeCell*pdpm[t]
re38 = tlpdp*wholeCell*pdpm[t]
re39 = dpdp*wholeCell*PDP[t]
re4 = dpt*wholeCell*PT[t]
re42 = wholeCell*clkp[t]*(tcpdpclkp*prpc[t] + tcclkp*(1 - prpc[t] - prvc[t]) + tcvriclkp*prvc[t])
re43 = bcc*CYC*wholeCell*CLK[t]
re44 = dclk*wholeCell*CLK[t]
re45 = ubcc*wholeCell*CC[t]
re46 = bpt*wholeCell*PER[t]*TIM[t]
re47 = ubpt*wholeCell*PT[t]
re48 = dper*wholeCell*PER[t]
re51 = wholeCell*(tccctimp*(1 - (1 - prct[t])^npt) + tcdvpmt*(1 - prct[t])^npt)*timp[t]
re53 = dtimm*wholeCell*timm[t]
re54 = tltim*wholeCell*timm[t]
re55 = dtim*wholeCell*TIM[t]
re56 = ubccpt*wholeCell*CCPT[t]
re57 = bccperp*wholeCell*CC[t]*(1 - prcper[t])
re58 = ubccperp*wholeCell*prcper[t]
re59 = ubccvrip*wholeCell*prcv[t]
re60 = bccvrip*wholeCell*CC[t]*(1 - prcv[t])
re61 = ubccpdpp*wholeCell*prcpdp[t]
re62 = bccpdpp*wholeCell*CC[t]*(1 - prcpdp[t])
re63 = bvriclkp*wholeCell*(1 - prpc[t] - prvc[t])*VRI[t]
re64 = ubvriclkp*wholeCell*prvc[t]
re65 = bpdpclkp*wholeCell*PDP[t]*(1 - prpc[t] - prvc[t])
re66 = ubpdpclkp*wholeCell*prpc[t]
re68 = bcctimp*wholeCell*CC[t]*(1 - prct[t])
re69 = ubcctimp*wholeCell*prct[t]
re9 = dclkm*wholeCell*clkm[t]
end rate equations

begin parameters
bcc = 2.349
bccpdpp = 0.062
bccperp = 0.069
bccpt = 51.0
bcctimp = 0.069
bccvrip = 0.1
bpdpclkp = 1.155
bpt = 1.1
bvriclkp = 1.858
dcc = 0.184
dccpt = 15.06
dclk = 0.2
dclkm = 0.643
dpdp = 0.156
dpdpm = 0.06
dper = 0.62
dperm = 0.053
dpt = 0.279
dtim = 0.62
dtimm = 0.053
dvri = 1.226
dvrim = 0.07
npdp = 6.0
npt = 5.0
nvri = 4.0
tcccpdpp = 9.831
tcccperp = 11.0
tccctimp = 11.0
tcccvrip = 16.86
tcclkp = 1.42
tcdvpmt = 0.028
tcpdpclkp = 125.54
tcvriclkp = 0.053
tlclk = 35.0
tlpdp = 1.87
tlper = 36.0
tltim = 36.0
tlvri = 14.68
ubcc = 0.89
ubccpdpp = 0.145
ubccperp = 0.262
ubccpt = 7.89
ubcctimp = 0.262
ubccvrip = 0.276
ubpdpclkp = 0.952
ubpt = 2.93
ubvriclkp = 1.043
CYC = 1.0
wholeCell = 1.0
end parameters

begin initial conditions
CC[0] = CCi
CCPT[0] = CCPTi
CLK[0] = CLKi
PDP[0] = PDPi
PER[0] = PERi
PT[0] = PTi
TIM[0] = TIMi
VRI[0] = VRIi
clkm[0] = clkmi
clkp[0] = clkpi
pdpm[0] = pdpmi
pdpp[0] = pdppi
perm[0] = permi
perp[0] = perpi
prcpdp[0] = prcpdpi
prcper[0] = prcperi
prct[0] = prcti
prcv[0] = prcvi
prpc[0] = prpci
prvc[0] = prvci
timm[0] = timmi
timp[0] = timpi
vrim[0] = vrimi
vrip[0] = vripi
end initial conditions

begin initial values
CCi = 0.5566
CCPTi = 0.4982
CLKi = 3.6628
PDPi = 4.1953
PERi = 2.7527
PTi = 0.4014
TIMi = 2.7527
VRIi = 3.175
clkmi = 0.2583
clkpi = 0.003185
pdpmi = 0.3175
pdppi = 0.003185
permi = 0.2395
perpi = 0.003185
prcpdpi = 0.0
prcperi = 0.0
prcti = 0.0
prcvi = 0.0
prpci = 0.0
prvci = 0.0
timmi = 0.2395
timpi = 0.003185
vrimi = 0.2571
vripi = 0.003185
end initial values

begin assignment rules
end assignment rules

begin function definitions
end function definitions

begin events
end events

begin process annotations
end process annotations

begin species annotations
VRI http://identifiers.org/uniprot/Q9VMS4
end species annotations

begin units
end units