// Created by libAntimony v2.13.0
model *Bruggeman2005_AmmoniumAssimilation()

  // Compartments and Species:
  compartment compartment_;
  species PII in compartment_, $UTP in compartment_, PIIUMP in compartment_;
  species $PPi in compartment_, GLN in compartment_, PIIUMP2 in compartment_;
  species PIIUMP3 in compartment_, $UMP in compartment_, GS in compartment_;
  species AMP in compartment_, $NH4 in compartment_, $KG in compartment_;
  species $NADPH in compartment_, GLU in compartment_, $NADP in compartment_;
  species AZGLU in compartment_, ATP in compartment_, ADP in compartment_;
  species $AZglu in compartment_, AZGLN in compartment_, $AZgln in compartment_;
  species $P_i in compartment_;

  // Assignment Rules:
  vAPP_GS := (aamp*camp/((1 + 12^n1amp*(AMP/(bamp*GStot))^n1amp)*(1 + 12^n2amp*(AMP/(damp*GStot))^n2amp)))*Vgs;
  nAMP := 12*AMP/GStot;
  PIIKG1 := 3*PII*KG/Kd1/(1 + 3*KG/Kd1 + 3*KG^2/(Kd1*Kd2) + KG^3/(Kd1*Kd2*Kd3));
  PIIUMP3KG3 := PIIUMP3*KG^3/(Kd1piiump*Kd2piiump*Kd3piiump)/(1 + 3*KG/Kd1piiump + 3*KG^2/(Kd1piiump*Kd2piiump) + KG^3/(Kd1piiump*Kd2piiump*Kd3piiump));

  // Reactions:
  vut1: PII + $UTP -> PIIUMP + $PPi; compartment_*(kcatut*UT*UTP*PII/(Kutipii*Kututp*(1 + GLN/Kglnut)*(1 + UTP/Kututp + (PII + PIIUMP + PIIUMP2)/Kutipii + UTP*(PII + PIIUMP + PIIUMP2)/(Kutipii*Kututp) + PPi*UTP*(PII + PIIUMP + PIIUMP2)/(Kutipii*Kutippi*Kututp) + Kutpii*(PIIUMP + PIIUMP2 + PIIUMP3)/(Kutipii*Kutpiiump))));
  vur1: PIIUMP -> PII + $UMP; compartment_*(kcatur*UR*PIIUMP/(Kurpiiump*(1 + Kglnur/GLN)*(1 + (1 + UMP/Kurump)*(PIIUMP + PIIUMP2 + PIIUMP3)/Kurpiiump)));
  vut2: PIIUMP + $UTP -> PIIUMP2 + $PPi; compartment_*(kcatut*UT*UTP*PIIUMP/(Kutipii*Kututp*(1 + GLN/Kglnut)*(1 + UTP/Kututp + (PII + PIIUMP + PIIUMP2)/Kutipii + UTP*(PII + PIIUMP + PIIUMP2)/(Kutipii*Kututp) + PPi*UTP*(PII + PIIUMP + PIIUMP2)/(Kutipii*Kutippi*Kututp) + Kutpii*(PIIUMP + PIIUMP2 + PIIUMP3)/(Kutipii*Kutpiiump))));
  vur2: PIIUMP2 -> PIIUMP + $UMP; compartment_*(kcatur*UR*PIIUMP2/(Kurpiiump*(1 + Kglnur/GLN)*(1 + (1 + UMP/Kurump)*(PIIUMP + PIIUMP2 + PIIUMP3)/Kurpiiump)));
  vut3: PIIUMP2 + $UTP -> PIIUMP3 + $PPi; compartment_*(kcatut*UT*UTP*PIIUMP2/(Kutipii*Kututp*(1 + GLN/Kglnut)*(1 + UTP/Kututp + (PII + PIIUMP + PIIUMP2)/Kutipii + UTP*(PII + PIIUMP + PIIUMP2)/(Kutipii*Kututp) + PPi*UTP*(PII + PIIUMP + PIIUMP2)/(Kutipii*Kutippi*Kututp) + Kutpii*(PIIUMP + PIIUMP2 + PIIUMP3)/(Kutipii*Kutpiiump))));
  vur3: PIIUMP3 -> PIIUMP2 + $UMP; compartment_*(kcatur*UR*PIIUMP3/(Kurpiiump*(1 + Kglnur/GLN)*(1 + (1 + UMP/Kurump)*(PIIUMP + PIIUMP2 + PIIUMP3)/Kurpiiump)));
  vad: GS -> AMP; compartment_*(Vad*GS*(b1*GLN/Kadgln + 3*a1*KG*PII/(Kadpiikg*Kd1*(1 + 3*KG/Kd1 + 3*KG^2/(Kd1*Kd2) + KG^3/(Kd1*Kd2*Kd3))) + 3*c1*KG*GLN*PII/(Kadgln*Kadpiikg*Kd1*(1 + 3*KG/Kd1 + 3*KG^2/(Kd1*Kd2) + KG^3/(Kd1*Kd2*Kd3))))/((Kadgs + GS)*(1 + GLN/Kadgln + 3*KG*PII/(Kadpiikg*Kd1*(1 + 3*KG/Kd1 + 3*KG^2/(Kd1*Kd2) + KG^3/(Kd1*Kd2*Kd3))) + 3*KG*GLN*PII/(d1*Kadgln*Kadpiikg*Kd1*(1 + 3*KG/Kd1 + 3*KG^2/(Kd1*Kd2) + KG^3/(Kd1*Kd2*Kd3))))));
  vdead: AMP -> GS; compartment_*(Vdead*AMP*(f1*GLN/Kdeadgln + 3*e1*KG*PII/(Kd1*Kdeadpiikg*(1 + 3*KG/Kd1 + 3*KG^2/(Kd1*Kd2) + KG^3/(Kd1*Kd2*Kd3))) + 3*h1*KG*GLN*PII/(Kd1*Kdeadgln*Kdeadpiikg*(1 + 3*KG/Kd1 + 3*KG^2/(Kd1*Kd2) + KG^3/(Kd1*Kd2*Kd3))) + g1*KG^3*PIIUMP3/(Kd1piiump*Kd2piiump*Kd3piiump*Kdeadpiiu*(1 + 3*KG/Kd1piiump + 3*KG^2/(Kd1piiump*Kd2piiump) + KG^3/(Kd1piiump*Kd2piiump*Kd3piiump))) + j1*KG^3*GLN*PIIUMP3/(Kd1piiump*Kd2piiump*Kd3piiump*Kdeadgln*Kdeadpiiu*(1 + 3*KG/Kd1piiump + 3*KG^2/(Kd1piiump*Kd2piiump) + KG^3/(Kd1piiump*Kd2piiump*Kd3piiump))) + 3*i1*KG^4*PII*PIIUMP3/(Kd1*Kd1piiump*Kd2piiump*Kd3piiump*Kdeadpiikg*Kdeadpiiu*(1 + 3*KG/Kd1 + 3*KG^2/(Kd1*Kd2) + KG^3/(Kd1*Kd2*Kd3))*(1 + 3*KG/Kd1piiump + 3*KG^2/(Kd1piiump*Kd2piiump) + KG^3/(Kd1piiump*Kd2piiump*Kd3piiump))) + 3*k1*KG^4*GLN*PII*PIIUMP3/(Kd1*Kd1piiump*Kd2piiump*Kd3piiump*Kdeadgln*Kdeadpiikg*Kdeadpiiu*(1 + 3*KG/Kd1 + 3*KG^2/(Kd1*Kd2) + KG^3/(Kd1*Kd2*Kd3))*(1 + 3*KG/Kd1piiump + 3*KG^2/(Kd1piiump*Kd2piiump) + KG^3/(Kd1piiump*Kd2piiump*Kd3piiump))))/((Kdeadgsa + AMP)*(1 + GLN/Kdeadgln + 3*KG*PII/(Kd1*Kdeadpiikg*(1 + 3*KG/Kd1 + 3*KG^2/(Kd1*Kd2) + KG^3/(Kd1*Kd2*Kd3))) + 3*KG*GLN*PII/(Kd1*Kdeadgln*Kdeadpiikg*(1 + 3*KG/Kd1 + 3*KG^2/(Kd1*Kd2) + KG^3/(Kd1*Kd2*Kd3))*l1) + KG^3*PIIUMP3/(Kd1piiump*Kd2piiump*Kd3piiump*Kdeadpiiu*(1 + 3*KG/Kd1piiump + 3*KG^2/(Kd1piiump*Kd2piiump) + KG^3/(Kd1piiump*Kd2piiump*Kd3piiump))) + KG^3*GLN*PIIUMP3/(Kd1piiump*Kd2piiump*Kd3piiump*Kdeadgln*Kdeadpiiu*(1 + 3*KG/Kd1piiump + 3*KG^2/(Kd1piiump*Kd2piiump) + KG^3/(Kd1piiump*Kd2piiump*Kd3piiump))*n1) + 3*KG^4*PII*PIIUMP3/(Kd1*Kd1piiump*Kd2piiump*Kd3piiump*Kdeadpiikg*Kdeadpiiu*(1 + 3*KG/Kd1 + 3*KG^2/(Kd1*Kd2) + KG^3/(Kd1*Kd2*Kd3))*(1 + 3*KG/Kd1piiump + 3*KG^2/(Kd1piiump*Kd2piiump) + KG^3/(Kd1piiump*Kd2piiump*Kd3piiump))*m1) + 3*KG^4*GLN*PII*PIIUMP3/(Kd1*Kd1piiump*Kd2piiump*Kd3piiump*Kdeadgln*Kdeadpiikg*Kdeadpiiu*(1 + 3*KG/Kd1 + 3*KG^2/(Kd1*Kd2) + KG^3/(Kd1*Kd2*Kd3))*(1 + 3*KG/Kd1piiump + 3*KG^2/(Kd1piiump*Kd2piiump) + KG^3/(Kd1piiump*Kd2piiump*Kd3piiump))*o1))));
  vgdh: $NH4 + $KG + $NADPH -> GLU + $NADP; compartment_*(Vgdh*(KG*NADPH*NH4 - NADP*GLU/Keqgdh)/(Kgdhkg*Kgdhnadph*Kgdhnh*(1 + NADP/Kgdhnadp + NADPH/Kgdhnadph)*(1 + NH4/Kgdhnh)*(1 + KG/Kgdhkg + GLU/Kgdhglu)));
  vgog: GLN + $NADPH + $KG -> 2 GLU + $NADP; compartment_*(KG*NADPH*Vgog*GLN/(Kgoggln*Kgogkg*Kgognadph*(1 + NADP/Kgognadp + NADPH/Kgognadph)*(1 + AZGLU/Kgogaz)*(1 + KG/Kgogkg + GLU/Kgogglu)*(1 + GLN/Kgoggln + GLU/Kgogglu)));
  vgs: GLU + ATP + $NH4 -> $P_i + GLN + ADP; compartment_*(aamp*camp*Vgs*(-(P_i*ADP*GLN/Keq) + NH4*ATP*GLU)/(Kgsatp*Kgsglu*Kgsnh*(1 + P_i/Kgspi + ADP/Kgsadp + P_i*ADP/(Kgsadp*Kgspi) + ATP/Kgsatp)*(1 + NH4/Kgsnh + GLN/Kgsgln + NH4*GLN/(Kgsgln*Kgsnh) + GLU/Kgsglu + NH4*GLU/(Kgsglu*Kgsnh))*(1 + 12^n1amp*(AMP/(bamp*GStot))^n1amp)*(1 + 12^n2amp*(AMP/(damp*GStot))^n2amp)));
  vgludem: GLU -> AZGLU; compartment_*(Vgludem*(-(AZGLU/Kgludemeq) + GLU)/(Kgludemglu*(1 + AZGLU/Kgludemazglu + GLU/Kgludemglu)));
  vazgludem: AZGLU -> $AZglu; compartment_*(Vazgludem*(-(AZglu/Kazgludemeq) + AZGLU)/(Kazgludemazglu*(1 + AZglu/Kazgludemazinter + AZGLU/Kazgludemazglu)));
  vglndem: GLN -> AZGLN; compartment_*(Vglndem*(-(AZGLN/Kglndemeq) + GLN)/(Kglndemgln*(1 + AZGLN/Kglndemazgln + GLN/Kglndemgln)));
  vazglndem: AZGLN -> $AZgln; compartment_*(Vazglndem*(-(AZgln/Kazglndemeq) + AZGLN)/(Kazglndemazgln*(1 + AZgln/Kazglndemazinter + AZGLN/Kazglndemazgln)));
  vatpase: ADP -> ATP; compartment_*(Vadp*ADP/(Kadp + ADP));

  // Species initializations:
  PII = 0.003;
  UTP = 0.5;
  PIIUMP = 0;
  PPi = 0.05;
  GLN = 1;
  PIIUMP2 = 0;
  PIIUMP3 = 0;
  UMP = 0.01;
  GS = 0.014;
  AMP = 0;
  NH4 = 0.05;
  KG = 0.2;
  NADPH = 0.15;
  GLU = 1;
  NADP = 0.05;
  AZGLU = 1;
  ATP = 2.685;
  ADP = 2.685;
  AZglu = 0.1;
  AZGLN = 1;
  AZgln = 0.1;
  P_i = 10;

  // Compartment initializations:
  compartment_ = 1;

  // Variable initializations:
  UT = 0.0006;
  kcatut = 137;
  Kglnut = 0.07;
  Kutipii = 0.0018;
  Kutpii = 0.003;
  Kutpiiump = 0.0035;
  Kututp = 0.04;
  Kutippi = 0.1135;
  UR = 0.0006;
  kcatur = 5.5;
  Kurpiiump = 0.0023;
  Kurump = 8.4;
  Kglnur = 0.07;
  a1 = 1e-22;
  b1 = 0.5166;
  c1 = 0.5974;
  d1 = 0.0387;
  Vad = 0.5;
  Kadpiikg = 1.052e-05;
  Kadgln = 0.9714;
  Kadgs = 0.001703;
  e1 = 1e-22;
  f1 = 2.766;
  g1 = 3.323;
  h1 = 0.2148;
  i1 = 1e-22;
  j1 = 1e-22;
  k1 = 1e-22;
  l1 = 0.02316;
  m1 = 0.8821;
  n1 = 8.491;
  o1 = 0.8791;
  Vdead = 0.5;
  Kdeadpiikg = 2.274e-06;
  Kdeadgln = 0.04444;
  Kdeadpiiu = 1.805e-05;
  Kdeadgsa = 0.0002015;
  Vgdh = 360;
  Kgdhkg = 0.32;
  Kgdhnh = 1.1;
  Kgdhglu = 10;
  Kgdhnadph = 0.04;
  Kgdhnadp = 0.042;
  Keqgdh = 1290;
  Kgdhazglu = 2.5;
  Vgog = 85;
  Kgoggln = 0.175;
  Kgogkg = 0.007;
  Kgognadph = 0.0015;
  Kgogglu = 11;
  Kgognadp = 0.0037;
  Kgogaz = 0.65;
  Vgs = 600;
  aamp = 10;
  bamp = 2.3667;
  camp = 0.1012;
  damp = 10.8688;
  n1amp = 1.1456;
  n2amp = 19.2166;
  Kgseq = 460;
  Kgsatp = 0.35;
  Kgsglu = 4.1;
  Kgsnh = 0.1;
  Kgsadp = 0.0585;
  Kgspi = 3.7;
  Kgsgln = 5.65;
  Keq = 460;
  Keq has dimensionless;
  Vgludem = 120;
  Kgludemglu = 8;
  Kgludemeq = 10000000000;
  Kgludemazglu = 0.5;
  Vglndem = 70;
  Kglndemgln = 2;
  Kglndemeq = 10000000000;
  Kglndemazgln = 0.25;
  Vazglndem = 20;
  Kazglndemazgln = 1;
  Kazglndemeq = 10000000000;
  Kazglndemazinter = 0.5;
  Vazgludem = 30;
  Kazgludemazglu = 0.3;
  Kazgludemeq = 10000000000;
  Kazgludemeq has dimensionless;
  Kazgludemazinter = 0.5;
  Kazgludemazinter has dimensionless;
  Vadp = 100;
  Kadp = 0.5;
  ATPtot = 5.37;
  GStot = 0.014;
  PIItot = 0.003;
  Kd1 = 0.005;
  Kd2 = 0.15;
  Kd3 = 0.15;
  Kd1piiump = 0.025;
  Kd2piiump = 0.15;
  Kd3piiump = 0.15;

  // Other declarations:
  var vAPP_GS, nAMP, PIIKG1, PIIUMP3KG3;
  const compartment_, UT, kcatut, Kglnut, Kutipii, Kutpii, Kutpiiump, Kututp;
  const Kutippi, UR, kcatur, Kurpiiump, Kurump, Kglnur, a1, b1, c1, d1, Vad;
  const Kadpiikg, Kadgln, Kadgs, e1, f1, g1, h1, i1, j1, k1, l1, m1, n1, o1;
  const Vdead, Kdeadpiikg, Kdeadgln, Kdeadpiiu, Kdeadgsa, Vgdh, Kgdhkg, Kgdhnh;
  const Kgdhglu, Kgdhnadph, Kgdhnadp, Keqgdh, Kgdhazglu, Vgog, Kgoggln, Kgogkg;
  const Kgognadph, Kgogglu, Kgognadp, Kgogaz, Vgs, aamp, bamp, camp, damp;
  const n1amp, n2amp, Kgseq, Kgsatp, Kgsglu, Kgsnh, Kgsadp, Kgspi, Kgsgln;
  const Keq, Vgludem, Kgludemglu, Kgludemeq, Kgludemazglu, Vglndem, Kglndemgln;
  const Kglndemeq, Kglndemazgln, Vazglndem, Kazglndemazgln, Kazglndemeq, Kazglndemazinter;
  const Vazgludem, Kazgludemazglu, Kazgludemeq, Kazgludemazinter, Vadp, Kadp;
  const ATPtot, GStot, PIItot, Kd1, Kd2, Kd3, Kd1piiump, Kd2piiump, Kd3piiump;

  // Unit definitions:
  unit time_unit = 60 second;
  unit milliMolar = 1e-3 mole / litre;

  // Display Names:
  time_unit is "mins";
  milliMolar is "mM";
  compartment_ is "compartment";
  vAPP_GS is "maxRateGS";
  nAMP is "AdenylationStateGS";

  // CV terms:
  PII hypernym "http://identifiers.org/uniprot/P0A9Z1"
  UTP hypernym "http://identifiers.org/obo.chebi/CHEBI:15713",
               "http://identifiers.org/kegg.compound/C00075"
  PPi hypernym "http://identifiers.org/obo.chebi/CHEBI:18361",
               "http://identifiers.org/kegg.compound/C00013"
  GLN hypernym "http://identifiers.org/obo.chebi/CHEBI:30011",
               "http://identifiers.org/kegg.compound/C00303"
  UMP hypernym "http://identifiers.org/obo.chebi/CHEBI:16695",
               "http://identifiers.org/kegg.compound/C00105"
  GS hypernym "http://identifiers.org/uniprot/P0A9C5"
  AMP hypernym "http://identifiers.org/obo.chebi/CHEBI:16027",
               "http://identifiers.org/kegg.compound/C00020"
  NH4 hypernym "http://identifiers.org/obo.chebi/CHEBI:28938",
               "http://identifiers.org/kegg.compound/C01342"
  KG hypernym "http://identifiers.org/uniprot/P0AEX3"
  NADPH hypernym "http://identifiers.org/obo.chebi/CHEBI:16474",
                 "http://identifiers.org/kegg.compound/C00005"
  GLU hypernym "http://identifiers.org/obo.chebi/CHEBI:16015",
               "http://identifiers.org/kegg.compound/C00025"
  NADP hypernym "http://identifiers.org/obo.chebi/CHEBI:18009",
                "http://identifiers.org/kegg.compound/C00006"
  ATP hypernym "http://identifiers.org/obo.chebi/CHEBI:15422",
               "http://identifiers.org/kegg.compound/C00002"
  ADP hypernym "http://identifiers.org/obo.chebi/CHEBI:16761",
               "http://identifiers.org/kegg.compound/C00008"
  P_i hypernym "http://identifiers.org/obo.chebi/CHEBI:43474"
  vut1 hypernym "http://identifiers.org/obo.go/GO:0008773"
  vur1 hypernym "http://identifiers.org/obo.go/GO:0008773"
  vut2 hypernym "http://identifiers.org/obo.go/GO:0008773"
  vur2 hypernym "http://identifiers.org/obo.go/GO:0008773"
  vut3 hypernym "http://identifiers.org/obo.go/GO:0008773"
  vur3 hypernym "http://identifiers.org/obo.go/GO:0008773"
  vad hypernym "http://identifiers.org/obo.go/GO:0018117"
end

Bruggeman2005_AmmoniumAssimilation is "Bruggeman2005_AmmoniumAssimilation"

Bruggeman2005_AmmoniumAssimilation model_entity_is "http://identifiers.org/biomodels.db/MODEL3579243073"
Bruggeman2005_AmmoniumAssimilation model_entity_is "http://identifiers.org/biomodels.db/BIOMD0000000217"
Bruggeman2005_AmmoniumAssimilation description "http://identifiers.org/pubmed/15819889"
Bruggeman2005_AmmoniumAssimilation hypernym "http://identifiers.org/obo.go/GO:0019676"
Bruggeman2005_AmmoniumAssimilation taxon "http://identifiers.org/taxonomy/562"
