(* Kimball model and energy derived from experimental molecule data source, ES Febuary 2013 *)

ChemicalData["Adenosine","MoleculePlot"]

t1=0.01889726*ChemicalData["Adenosine","AtomPositions"];
(*MatrixForm[t]*)

(*ChemicalData["Adenosine","BondTally"]*)

u=ChemicalData["Adenosine","VertexTypes"]

n=Length[u]

un=Table[If[u[[i]]=="H","Z",u[[i]]],{i,1,n}]

num=Table[i,{i,1,n}];

um=Table[{un[[i]],num[[i]]},{i,1,n}];

us=Sort[um]

num=Table[us[[i,2]],{i,1,n}]

For[i=1,i<n+1,i++,If[us[[i,1]]=="Z",us[[i,1]]="H"]];

u1=Table[If[us[[i,1]]=="C",0.255,If[us[[i,1]]=="H",0.1,If[us[[i,1]]=="N",0.213,If[us[[i,1]]=="O",0.178]]]],{i,1,n}]
u2=Table[If[us[[i,1]]=="C",0.255,If[us[[i,1]]=="H",0.579,If[us[[i,1]]=="N",0.213,If[us[[i,1]]=="O",0.178]]]],{i,1,n}]

u=Table[us[[i,1]],{i,1,n}]

cn=Table[If[u[[i]]=="C",6.0,If[u[[i]]=="H",1.0,If[u[[i]]=="N",7.0,If[u[[i]]=="O",8.0]]]],{i,1,n}]

bc=0;
For[i=1, i<n+1,i++,If[u[[i]]≠"H", bc=bc+1]];
bc
bh=n-bc

ChemicalData["Adenosine","MolecularFormulaString"]

v=0.01889726*ChemicalData["Adenosine","VertexCoordinates"];
t=Table[t1[[num[[i]]]],{i,1,n}];

Plot1=Table[Graphics3D[{If[u[[i]]=="N",Lighter[Blue],If[u[[i]]=="O",Lighter[Red],Lighter[Brown]]],Sphere[{t[[i,1]],t[[i,2]],t[[i,3]]},u1[[i]]]}],{i,1,n}];

Plot2=Table[Graphics3D[Text[i,{t[[i,1]]-0.3,t[[i,2]],t[[i,3]]} ,{1,0}]],{i,1,n}];

ChemicalData["Adenosine","CHStructureDiagram"]

x=Table[t[[i,1]],{i,1,n}];
y=Table[t[[i,2]],{i,1,n}];
z=Table[t[[i,3]],{i,1,n}];

(* Distance matrix Bohr *)
Dij=Table[If[i≥j,If[sq=Sqrt[(x[[i]]-x[[j]])^2+(y[[i]]-y[[j]])^2+(z[[i]]-z[[j]])^2]; sq<3.0,sq,0]," "],{i,1,n},{j,1,n}];
(*MatrixForm[Dij]*)

Fij=Dij-u2;
(*MatrixForm[Fij];*)
Gij=Table[If[i≥j,If[Fij[[i,j]]>0,Fij[[i,j]],0]," "],{i,1,n},{j,1,n}];
(*MatrixForm[Gij];*)

Hij=Transpose[Gij];
(*MatrixForm[Hij];*)

Kij=Hij-u2;
(*MatrixForm[Kij];*)
Lij=Table[If[i≤j,If[Kij[[i,j]]>0,Kij[[i,j]],0]," "],{i,1,n},{j,1,n}];
(*MatrixForm[Lij];*)

Lij=Table[If[i≤j,If[Lij[[i,j]]>0,If[u[[j]]≠"H",0.5*Lij[[i,j]],Lij[[i,j]]],0]," "],{i,1,n},{j,1,n}];  
Qij=Lij;
(*MatrixForm[Lij];*)

Nij=Table[If[i≤j,If[Lij[[i,j]]>0,2.25/Lij[[i,j]]^2,0]," "],{i,1,n},{j,1,n}];
(*MatrixForm[Nij]*)

Tval=Sum[If[i≤j,Nij[[i,j]],0],{i,1,n},{j,1,n}]

TvalH=Sum[If[(i≤j && u[[j]]== "H"),Nij[[i,j]],0],{i,1,n},{j,1,n}]

TvalC=Tval-TvalH

Tcor=Sum[If[u[[i]]≠"H",2.25/u2[[i]]^2,0],{i,1,n}]

Vnn=0.0;
For[ i=1,i<n,i++,
For[j=i+1,j<n+1,j++,
Vnn=Vnn+cn[[i]]*cn[[j]]/Sqrt[(x[[i]]-x[[j]])^2+(y[[i]]-y[[j]])^2+(z[[i]]-z[[j]])^2]]];
Vnn

Mij=Prepend[Qij,u];
Oij=Transpose[Mij];
Pij=Prepend[Oij,Prepend[u," "]];

(*MatrixForm[Pij];*)

(* sigma bond cloud radii *)

For[i=2,i<n+2,i++,
For[j=2,j≤i,j++,
If[Pij[[i,j]]>0,Print[u[[i-1]],i-1," ",u[[j-1]],j-1,"  ",Extract[Pij,{i,j}]]]]]

DeleteFile[ "C:\\Kimb_Mathem\\tmp4"];
For[i=2,i<n+2,i++,
For[j=2,j≤i,j++,
If[Pij[[i,j]]>0,{i-1,j-1,Extract[Pij,{i,j}]}>>> "C:\\Kimb_Mathem\\tmp4"]]]

a=ReadList["C:\\Kimb_Mathem\\tmp4"]
nb=Length[a]

wx=Table[If[u[[a[[i,1]]]]≠"H",(a[[i,3]]+u2[[a[[i,1]]]])/(u2[[a[[i,1]]]]+2*a[[i,3]]+u2[[a[[i,2]]]])*(x[[a[[i,2]]]]-x[[a[[i,1]]]])+x[[a[[i,1]]]],0],{i,1,nb}];
wy=Table[If[u[[a[[i,1]]]]≠"H",(a[[i,3]]+u2[[a[[i,1]]]])/(u2[[a[[i,1]]]]+2*a[[i,3]]+u2[[a[[i,2]]]])*(y[[a[[i,2]]]]-y[[a[[i,1]]]])+y[[a[[i,1]]]],0],{i,1,nb}];   
wz=Table[If[u[[a[[i,1]]]]≠"H",(a[[i,3]]+u2[[a[[i,1]]]])/(u2[[a[[i,1]]]]+2*a[[i,3]]+u2[[a[[i,2]]]])*(z[[a[[i,2]]]]-z[[a[[i,1]]]])+z[[a[[i,1]]]],0],{i,1,nb}];
Plot7=Table[Graphics3D[{Darker[Gray],{Opacity[0.5],If[wx[[i]]≠0,Sphere[{wx[[i]],wy[[i]],wz[[i]]},a[[i,3]]]]}}],{i,1,nb}];
wx=Table[If[u[[a[[i,1]]]]=="H",(a[[i,3]]+u2[[a[[i,2]]]])/(u2[[a[[i,1]]]]+a[[i,3]]+u2[[a[[i,2]]]])*(x[[a[[i,1]]]]-x[[a[[i,2]]]])+x[[a[[i,2]]]],0],{i,1,nb}];
wy=Table[If[u[[a[[i,1]]]]=="H",(a[[i,3]]+u2[[a[[i,2]]]])/(u2[[a[[i,1]]]]+a[[i,3]]+u2[[a[[i,2]]]])*(y[[a[[i,1]]]]-y[[a[[i,2]]]])+y[[a[[i,2]]]],0],{i,1,nb}];
wz=Table[If[u[[a[[i,1]]]]=="H",(a[[i,3]]+u2[[a[[i,2]]]])/(u2[[a[[i,1]]]]+a[[i,3]]+u2[[a[[i,2]]]])*(z[[a[[i,1]]]]-z[[a[[i,2]]]])+z[[a[[i,2]]]],0],{i,1,nb}];
Plot8=Table[Graphics3D[{Opacity[0.5],If[wx[[i]]≠0,Sphere[{wx[[i]],wy[[i]],wz[[i]]},a[[i,3]]]]}],{i,1,nb}];

Plot9= Table[Graphics3D[{Darker[Red,0.8],Cylinder[{{x[[a[[i,1]]]],y[[a[[i,1]]]],z[[a[[i,1]]]]},{x[[a[[i,2]]]],y[[a[[i,2]]]],z[[a[[i,2]]]]}},0.05]}],{i,1,nb}];
Show[Plot1,Plot7,Plot8,Plot9,{AspectRatio->Automatic,Boxed->False}]
Show[Plot1,Plot2,Plot9,{AspectRatio->Automatic}]