In[132]:=
nc=13;

k1=k2=k3=k4=1.0;

sig1=sig2=sig3=0.3;

z=7.0;

a=Table[{0,0,0},{nc}];

b=Table[{0,0,0},{nc}];

c=Table[{0,0,0},{nc}];



(* N,N He shell*)

T = 2*2.25*k1/R1^2;

Vee=2*3.0*sig1/R1;

Vne=-2*3.0*z/R1;



(* bonding and lone pairs *)

T = T + 2.25*(2*k2/R2^2+k3/R3^2)+4*1.125*k4/R4^2;



Vee=Vee+3.0*(2*sig2/R2+sig3/R3);



c[[1,1]]=-2;      c[[1,2]]=z;  c[[1,3]]=R1;

c[[2,1]]=-2;      c[[2,2]]=z;  c[[2,3]]=R1;

c[[3,1]]=-2;      c[[3,2]]=0;  c[[3,3]]=R2;

c[[4,1]]=-2;      c[[4,2]]=0;  c[[4,3]]=R2;

c[[5,1]]=-2;      c[[5,2]]=0;  c[[5,3]]=R3;

c[[6,1]]=-0.5;      c[[6,2]]=0;  c[[6,3]]=R4;

c[[7,1]]=-0.5;      c[[7,2]]=0;  c[[7,3]]=R4;

c[[8,1]]=-0.5;      c[[8,2]]=0;  c[[8,3]]=R4;

c[[9,1]]=-0.5;      c[[9,2]]=0;  c[[9,3]]=R4;

c[[10,1]]=-0.5;      c[[10,2]]=0;  c[[10,3]]=R4;

c[[11,1]]=-0.5;      c[[11,2]]=0;  c[[11,3]]=R4;

c[[12,1]]=-0.5;      c[[12,2]]=0;  c[[12,3]]=R4;

c[[13,1]]=-0.5;      c[[13,2]]=0;  c[[13,3]]=R4;

d1=R1+R3;               

d2=R1+R3+R1+R2;

b[[1,1]]=d1;

b[[2,1]]=-d1;



a[[1,1]]=d1;

a[[2,1]]=-d1;

a[[3,1]]=d2;

a[[4,1]]=-d2;

a[[5,1]]=0.0;             

a[[6,1]]=d1;     a[[6,2]]=R4;

a[[7,1]]=d1;                                      a[[7,3]]=R4;

a[[8,1]]=-d1;  a[[8,2]]=R4;

a[[9,1]]=-d1;                                   a[[9,3]]=R4;

a[[10,1]]=d1;     a[[10,2]]=-R4;

a[[11,1]]=d1;                                      a[[11,3]]=-R4;

a[[12,1]]=-d1;  a[[12,2]]=-R4;

a[[13,1]]=-d1;                                   a[[13,3]]=-R4;





For[i=1,i<nc,i++,

  For[j=i+1,j<=nc,j++,

    d=Sqrt[(a[[i,1]]-a[[j,1]])^2+(a[[i,2]]-a[[j,2]])^2+(a[[i,3]]-a[[j,3]])^2];

    If[d!=0, Vee=Vee+c[[i,1]]*c[[j,1]]/d]]];



Vee=Vee-4*0.25/(2*R4);



Vnn=z*z/(2*d1);



 For[i=1,i<=nc,i++,

  For[j=1,j<=nc,j++,      d=Sqrt[(a[[i,1]]-b[[j,1]])^2+(a[[i,2]]-b[[j,2]]^2)+(a[[i,3]]-b[[j,3]])^2];

       If[d!=0, Vne=Vne+c[[i,1]]*c[[j,2]]/d]]];



Ekin=T;

Epot=Vne+Vee+Vnn;

func=Ekin+Epot;



t=FindMinimum[func,{R1,0.19},{R2,0.7},{R3,0.6},{R4,2.0},{Method-> "Newton",MaxIterations->500}]

Out[258]= {-89.793888,{R1->0.2238806,R2->1.8185434*10^7,R3->4.6207805*10^7,R4->18.}}