% '3-keto-adipyl-CoA'


config('3-keto-adipyl-CoA',[
        substituent('3-keto-adipyl'),
        substituent('coenzymeA-yl'),
        linkage(from('3-keto-adipyl',car(1)),
                to('coenzymeA-yl',sul(1)),
                right,single)]).

%%%% Substituent Config Rules for compound '3-keto-adipyl-CoA' %%%%

config('3-keto-adipyl',[
        chain([
                car(1,oxy~~),
                methandiyl,
                keto,
                methandiyl,
                methandiyl,
                carboxyl])]).

config('coenzymeA-yl',[
        substituent('R-pantothenyl'),
        substituent('3''-phospho-ADP-beta-yl'),
        substituent('beta-mercaptoethylamine-N-S-diyl'),
        linkage(from('beta-mercaptoethylamine-N-S-diyl',nit(1)),
                to('R-pantothenyl',car(1)),
                trans(car(2),car(2)),cn_resonant),
        linkage(from('R-pantothenyl',oxy(4)),
                to('3''-phospho-ADP-beta-yl',pho(3)),
                right,single)]).

%%%% Substituent Config Rules for compound 'coenzymeA-yl' %%%%

config('3''-phospho-ADP-beta-yl',[
        substituent('D-1-dehydroxy-3-phospho-5-oxy-ribofuranosyl'),
        substituent(adenyl),
        substituent(diphosphopentaoxygen),
        linkage(from('D-1-dehydroxy-3-phospho-5-oxy-ribofuranosyl',car(1)),
                to(adenyl,nit(9)),
                up,single),
        linkage(from('D-1-dehydroxy-3-phospho-5-oxy-ribofuranosyl',attach_to([oxy,car(5)])),
                to(diphosphopentaoxygen,pho(1)),
                nil,single)]).

%%%% Substituent Config Rules for compound '3''-phospho-ADP-beta-yl' %%%%

config('D-1-dehydroxy-3-phospho-5-oxy-ribofuranosyl',[
        ring([
                oxy,
                anomeric(1,hyd),
                car(2,hyd&&hydroxyl),
                car(3,hyd&&phosphate),
                car(4,oxymethyl&&hyd)])]).

config(adenyl,[
        model(adenine,[
                diff(nit(9,hyd),nit(9))])]).

%%%% Model/Diff Config Rules for compound adenyl %%%%

config(adenine,[
        model(purine,[
                diff(car(6,hyd),car(6,amine(10)))])]).

%%%% Model/Diff Config Rules for compound adenine %%%%

config(purine,[
        ring_system([
                ring([
                        car(6,hyd)&,
                        car(5)&,
                        car(4)&,
                        nit(3)&,
                        car(2,hyd)&,
                        nit(1)&]),
                ring([
                        nit(7)&,
                        car(8,hyd)&,
                        nit(9,hyd)&,
                        car(4)&,
                        car(5)&])],
                conjugate(1,pseudopos([car(4),car(5)]),2,pseudopos([car(4),car(5)]))])]).

config('R-pantothenyl',[
        chain([
                car(1,oxy?),
                car(2,hyd&&hyd),
                car(3,hyd&&hyd),
                nit(1,hyd)#,
                car(4,oxy?),
                car(5,hydroxyl&&hyd),
                car(6,methyl&&methyl),
                oxymethyl]),
        trans(car(3),car(5),bond(nit(1),car(4)))]).

config('beta-mercaptoethylamine-N-S-diyl',[
        chain([
                sul(1),
                car(1,hyd&&hyd),
                car(2,hyd&&hyd),
                nit(1,hyd)])]).