// This model generated automatically from SBML
// WARNING: Renamed variable _space_6_minus_Hexanolide to xxx_space_6_minus_Hexanolide due to JSim namespace restrictions
// WARNING: Renamed variable _space_6_minus_Hydroxyhexanoic_space_acid to xxx_space_6_minus_Hydroxyhexanoic_space_acid due to JSim namespace restrictions
// WARNING: Renamed variable _space_5_minus_Carboxy_minus_2_minus_pentenoyl_minus_CoA to xxx_space_5_minus_Carboxy_minus_2_minus_pentenoyl_minus_CoA due to JSim namespace restrictions
// WARNING: Renamed variable _space_3S_space__minus_3_minus_Hydroxyadipyl_minus_CoA to xxx_space_3S_space__minus_3_minus_Hydroxyadipyl_minus_CoA due to JSim namespace restrictions
// WARNING: Renamed variable _space_3_minus_Oxoadipyl_minus_CoA to xxx_space_3_minus_Oxoadipyl_minus_CoA due to JSim namespace restrictions

// unit definitions
import nsrunit;
unit conversion off;

// SBML property definitions
property sbmlRole=string;
property sbmlName=string;
property sbmlCompartment=string;

// SBML reactions
// R03751: _space_6_minus_Hexanolide <=> _space_6_minus_Hydroxyhexanoic_space_acid 
// R05231: _space_6_minus_Hydroxyhexanoic_space_acid <=> Adipate_space_semialdehyde 
// R06942: _space_5_minus_Carboxy_minus_2_minus_pentenoyl_minus_CoA <=> _space_3S_space__minus_3_minus_Hydroxyadipyl_minus_CoA 
// R06941: _space_3S_space__minus_3_minus_Hydroxyadipyl_minus_CoA <=> _space_3_minus_Oxoadipyl_minus_CoA 
// R06940: N_minus_Cyclohexylformamide <=> Cyclohexylamine 

math main {
  realDomain time second;
  time.min=0;
  extern time.max;
  extern time.delta;

  // variable definitions
  real default = 1 L;
  real uVol = 1 L;
  real E3_space_5_space_1_space__minus_ = 0 M;
  real E1_space_1_space_1_space_2 = 0 M;
  real E3_space_1_space_1_space_17 = 0 M;
  real E4_space_2_space_1_space_17 = 0 M;
  real E1_space_1_space_1_space_35 = 0 M;
  real N_minus_Cyclohexylformamide(time) M;
  real Cyclohexylamine(time) M;
  real xxx_space_6_minus_Hexanolide(time) M;
  real xxx_space_6_minus_Hydroxyhexanoic_space_acid(time) M;
  real Adipate_space_semialdehyde(time) M;
  real xxx_space_5_minus_Carboxy_minus_2_minus_pentenoyl_minus_CoA(time) M;
  real xxx_space_3S_space__minus_3_minus_Hydroxyadipyl_minus_CoA(time) M;
  real xxx_space_3_minus_Oxoadipyl_minus_CoA(time) M;
  real R03751(time) katal;
  extern real R03751.kf;
  extern real R03751.kb;
  real R05231(time) katal;
  extern real R05231.kf;
  extern real R05231.kb;
  real R06942(time) katal;
  extern real R06942.kf;
  extern real R06942.kb;
  real R06941(time) katal;
  extern real R06941.kf;
  extern real R06941.kb;
  real R06940(time) katal;
  extern real R06940.kf;
  extern real R06940.kb;

  // equations
  when (time=time.min) N_minus_Cyclohexylformamide = 0;
  (N_minus_Cyclohexylformamide*uVol):time = -1*R06940;
  when (time=time.min) Cyclohexylamine = 0;
  (Cyclohexylamine*uVol):time = R06940;
  when (time=time.min) xxx_space_6_minus_Hexanolide = 0;
  (xxx_space_6_minus_Hexanolide*uVol):time = -1*R03751;
  when (time=time.min) xxx_space_6_minus_Hydroxyhexanoic_space_acid = 0;
  (xxx_space_6_minus_Hydroxyhexanoic_space_acid*uVol):time = R03751 + -1*R05231;
  when (time=time.min) Adipate_space_semialdehyde = 0;
  (Adipate_space_semialdehyde*uVol):time = R05231;
  when (time=time.min) xxx_space_5_minus_Carboxy_minus_2_minus_pentenoyl_minus_CoA = 0;
  (xxx_space_5_minus_Carboxy_minus_2_minus_pentenoyl_minus_CoA*uVol):time = -1*R06942;
  when (time=time.min) xxx_space_3S_space__minus_3_minus_Hydroxyadipyl_minus_CoA = 0;
  (xxx_space_3S_space__minus_3_minus_Hydroxyadipyl_minus_CoA*uVol):time = R06942 + -1*R06941;
  when (time=time.min) xxx_space_3_minus_Oxoadipyl_minus_CoA = 0;
  (xxx_space_3_minus_Oxoadipyl_minus_CoA*uVol):time = R06941;
  R03751 = R03751.kf*_space_6_minus_Hexanolide - R03751.kb*_space_6_minus_Hydroxyhexanoic_space_acid;
  R05231 = R05231.kf*_space_6_minus_Hydroxyhexanoic_space_acid - R05231.kb*Adipate_space_semialdehyde;
  R06942 = R06942.kf*_space_5_minus_Carboxy_minus_2_minus_pentenoyl_minus_CoA - R06942.kb*_space_3S_space__minus_3_minus_Hydroxyadipyl_minus_CoA;
  R06941 = R06941.kf*_space_3S_space__minus_3_minus_Hydroxyadipyl_minus_CoA - R06941.kb*_space_3_minus_Oxoadipyl_minus_CoA;
  R06940 = R06940.kf*N_minus_Cyclohexylformamide - R06940.kb*Cyclohexylamine;

  // variable properties
  default.sbmlRole="compartment";
  uVol.sbmlRole="compartment";
  E3_space_5_space_1_space__minus_.sbmlRole="species";
  E3_space_5_space_1_space__minus_.sbmlCompartment="uVol";
  E1_space_1_space_1_space_2.sbmlRole="species";
  E1_space_1_space_1_space_2.sbmlCompartment="uVol";
  E3_space_1_space_1_space_17.sbmlRole="species";
  E3_space_1_space_1_space_17.sbmlCompartment="uVol";
  E4_space_2_space_1_space_17.sbmlRole="species";
  E4_space_2_space_1_space_17.sbmlCompartment="uVol";
  E1_space_1_space_1_space_35.sbmlRole="species";
  E1_space_1_space_1_space_35.sbmlCompartment="uVol";
  N_minus_Cyclohexylformamide.sbmlRole="species";
  N_minus_Cyclohexylformamide.sbmlCompartment="uVol";
  Cyclohexylamine.sbmlRole="species";
  Cyclohexylamine.sbmlCompartment="uVol";
  xxx_space_6_minus_Hexanolide.sbmlRole="species";
  xxx_space_6_minus_Hexanolide.sbmlName="_space_6_minus_Hexanolide";
  xxx_space_6_minus_Hexanolide.sbmlCompartment="uVol";
  xxx_space_6_minus_Hydroxyhexanoic_space_acid.sbmlRole="species";
  xxx_space_6_minus_Hydroxyhexanoic_space_acid.sbmlName="_space_6_minus_Hydroxyhexanoic_space_acid";
  xxx_space_6_minus_Hydroxyhexanoic_space_acid.sbmlCompartment="uVol";
  Adipate_space_semialdehyde.sbmlRole="species";
  Adipate_space_semialdehyde.sbmlCompartment="uVol";
  xxx_space_5_minus_Carboxy_minus_2_minus_pentenoyl_minus_CoA.sbmlRole="species";
  xxx_space_5_minus_Carboxy_minus_2_minus_pentenoyl_minus_CoA.sbmlName="_space_5_minus_Carboxy_minus_2_minus_pentenoyl_minus_CoA";
  xxx_space_5_minus_Carboxy_minus_2_minus_pentenoyl_minus_CoA.sbmlCompartment="uVol";
  xxx_space_3S_space__minus_3_minus_Hydroxyadipyl_minus_CoA.sbmlRole="species";
  xxx_space_3S_space__minus_3_minus_Hydroxyadipyl_minus_CoA.sbmlName="_space_3S_space__minus_3_minus_Hydroxyadipyl_minus_CoA";
  xxx_space_3S_space__minus_3_minus_Hydroxyadipyl_minus_CoA.sbmlCompartment="uVol";
  xxx_space_3_minus_Oxoadipyl_minus_CoA.sbmlRole="species";
  xxx_space_3_minus_Oxoadipyl_minus_CoA.sbmlName="_space_3_minus_Oxoadipyl_minus_CoA";
  xxx_space_3_minus_Oxoadipyl_minus_CoA.sbmlCompartment="uVol";
  R03751.sbmlRole="rate";
  R03751.kf.sbmlRole="rate";
  R03751.kb.sbmlRole="rate";
  R05231.sbmlRole="rate";
  R05231.kf.sbmlRole="rate";
  R05231.kb.sbmlRole="rate";
  R06942.sbmlRole="rate";
  R06942.kf.sbmlRole="rate";
  R06942.kb.sbmlRole="rate";
  R06941.sbmlRole="rate";
  R06941.kf.sbmlRole="rate";
  R06941.kb.sbmlRole="rate";
  R06940.sbmlRole="rate";
  R06940.kf.sbmlRole="rate";
  R06940.kb.sbmlRole="rate";
}