diff --git a/energy_protein/energies.txt b/energy_protein/energies.txt
new file mode 100644
index 0000000..0e39f83
--- /dev/null
+++ b/energy_protein/energies.txt
@@ -0,0 +1 @@
+9.215018106863146841e+02
diff --git a/moleculeLists/fileList.txt b/moleculeLists/fileList.txt
new file mode 100644
index 0000000..dd5a523
--- /dev/null
+++ b/moleculeLists/fileList.txt
@@ -0,0 +1,1497 @@
+Abacavir
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+Ethinyl_Estradiol
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+Gadobenate_Dimeglumine
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+Glutathione
+Glutethimide
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+Glycodiazine
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+Griseofulvin
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+Guanadrel_Sulfate
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+Guanidine
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+Halobetasol_Propionate
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+Haloprogin
+Halothane
+Heptabarbital
+Heroin
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+Hetacillin
+Hexachlorophene
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+Hexobarbital
+Hexylcaine
+Histamine_Phosphate
+Homatropine_Methylbromide
+Homoharringtonine
+Hydralazine
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+Hydrocodone
+Hydrocortamate
+Hydrocortisone
+Hydroflumethiazide
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+Hydroxocobalamin
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+Hydroxyproline
+Hydroxystilbamidine_Isethionate
+Hydroxyurea
+Hydroxyzine
+Hyoscyamine
+Ibandronate
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+Icosapent
+Icosapent_ethyl
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+L-Alanine
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+L-Asparagine
+L-Aspartic_Acid
+L-Carnitine
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+L-Cysteine
+L-Cystine
+L-Glutamic_Acid
+L-Glutamine
+L-Histidine
+L-Isoleucine
+L-Leucine
+L-Lysine
+L-Methionine
+L-Ornithine
+L-Phenylalanine
+L-Proline
+L-Serine
+L-Threonine
+L-Tryptophan
+L-Tyrosine
+L-Valine
+Labetalol
+Lacosamide
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+Linezolid
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+Magnesium_Sulfate
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+Methylscopolamine
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+Metocurine_Iodide
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+Metrizamide
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+Niflumic_Acid
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+Nisoldipine
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+Nitrazepam
+Nitrendipine
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+Nitrofurazone
+Nitroglycerin
+Nitroprusside
+Nitroxoline
+Nizatidine
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+Norepinephrine
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+Olsalazine
+Omeprazole
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+Orphenadrine
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+Ospemifene
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+Oxybenzone
+Oxybuprocaine
+Oxybutynin
+Oxycodone
+Oxymetazoline
+Oxymorphone
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+Oxyphenonium
+Oxytetracycline
+Paclitaxel
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+Palonosetron
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+Pantoprazole
+Papaverine
+Paramethadione
+Paramethasone
+Pargyline
+Paricalcitol
+Paromomycin
+Paroxetine
+Pazopanib
+Pefloxacin
+Pemetrexed
+Pemirolast
+Penbutolol
+Penciclovir
+Penicillamine
+Penicillin_G
+Penicillin_V
+Pentagastrin
+Pentamidine
+Pentazocine
+Pentobarbital
+Pentolinium
+Pentosan_Polysulfate
+Pentostatin
+Pentoxifylline
+Perflutren
+Pergolide
+Perhexiline
+Perindopril
+Permethrin
+Perphenazine
+Phenacemide
+Phenazopyridine
+Phendimetrazine
+Phenelzine
+Phenformin
+Phenindamine
+Phenindione
+Pheniramine
+Phenmetrazine
+Phenobarbital
+Phenol
+Phenoxybenzamine
+Phenprocoumon
+Phensuximide
+Phentermine
+Phentolamine
+Phenylbutazone
+Phenylephrine
+Phenylpropanolamine
+Phenytoin
+Phosphatidylserine
+Physostigmine
+Phytonadione
+Picrotoxin
+Pilocarpine
+Pimecrolimus
+Pimozide
+Pindolol
+Pioglitazone
+Pipazethate
+Pipecuronium
+Piperacillin
+Piperazine
+Pipobroman
+Pipotiazine
+Pirbuterol
+Pirenzepine
+Piroxicam
+Pitavastatin
+Pivampicillin
+Pivmecillinam
+Plerixafor
+Plicamycin
+Podofilox
+Polidocanol
+Polymyxin_B_Sulfate
+Polythiazide
+Pomalidomide
+Ponatinib
+Posaconazole
+Potassium_Chloride
+Potassium_Iodide
+Practolol
+Pralatrexate
+Pralidoxime
+Pramipexole
+Pranlukast
+Prasugrel
+Pravastatin
+Prazepam
+Praziquantel
+Prazosin
+Prednicarbate
+Prednisolone
+Prednisone
+Pregabalin
+Prilocaine
+Primaquine
+Primidone
+Probenecid
+Probucol
+Procainamide
+Procaine
+Procarbazine
+Procaterol
+Prochlorperazine
+Procyclidine
+Proflavine
+Progabide
+Progesterone
+Proguanil
+Promazine
+Promethazine
+Propafenone
+Propantheline
+Proparacaine
+Propericiazine
+Propiomazine
+Propofol
+Propoxyphene
+Propranolol
+Propylhexedrine
+Propylthiouracil
+Protriptyline
+Pseudoephedrine
+Pyrazinamide
+Pyridostigmine
+Pyridoxal
+Pyridoxine
+Pyrimethamine
+Pyruvic_acid
+Quazepam
+Quetiapine
+Quinacrine
+Quinapril
+Quinestrol
+Quinethazone
+Quinidine
+Quinidine_barbiturate
+Quinine
+Quinupristin
+Rabeprazole
+Raloxifene
+Raltitrexed
+Ramelteon
+Ramipril
+Ranitidine
+Ranolazine
+Rasagiline
+Reboxetine
+Regadenoson
+Regorafenib
+Remifentanil
+Remikiren
+Remoxipride
+Repaglinide
+Rescinnamine
+Reserpine
+Retapamulin
+Ribavirin
+Riboflavin
+Ridogrel
+Rifabutin
+Rifampin
+Rifapentine
+Rifaximin
+Rilpivirine
+Riluzole
+Rimantadine
+Rimexolone
+Rimonabant
+Risedronate
+Risperidone
+Ritodrine
+Ritonavir
+Rivaroxaban
+Rivastigmine
+Rizatriptan
+Rocuronium
+Roflumilast
+Rolitetracycline
+Ropinirole
+Ropivacaine
+Rosiglitazone
+Rosoxacin
+Rosuvastatin
+Rotigotine
+Roxatidine_acetate
+Roxithromycin
+Rufinamide
+Ruxolitinib
+S-Adenosylmethionine
+Salbutamol
+Salicyclic_acid
+Salicylamide
+Salicylate-sodium
+Salmeterol
+Salsalate
+Saprisartan
+Saquinavir
+Saxagliptin
+Scopolamine
+Secobarbital
+Selegiline
+Selenium_Sulfide
+Sertaconazole
+Sertindole
+Sertraline
+Sevelamer
+Sevoflurane
+Sibutramine
+Sildenafil
+Silodosin
+Silver_sulfadiazine
+Simvastatin
+Sirolimus
+Sitagliptin
+Sitaxentan
+Sodium_bicarbonate
+Sodium_lauryl_sulfate
+Sodium_stibogluconate
+Sodium_Tetradecyl_Sulfate
+Solifenacin
+Sorafenib
+Sotalol
+Spaglumic_Acid
+Sparfloxacin
+Spectinomycin
+Spermine
+Spinosad
+Spirapril
+Spironolactone
+Stanozolol
+Stavudine
+Stepronin
+Streptomycin
+Streptozocin
+Succimer
+Succinic_acid
+Succinylcholine
+Sucralfate
+Sufentanil
+Sulfacetamide
+Sulfacytine
+Sulfadiazine
+Sulfadimethoxine
+Sulfadoxine
+Sulfamerazine
+Sulfamethazine
+Sulfamethizole
+Sulfamethoxazole
+Sulfametopyrazine
+Sulfamoxole
+Sulfanilamide
+Sulfaphenazole
+Sulfapyridine
+Sulfasalazine
+Sulfathiazole
+Sulfinpyrazone
+Sulfisoxazole
+Sulfoxone
+Sulindac
+Sulpiride
+Sumatriptan
+Sunitinib
+Suprofen
+Suramin
+Tacrine
+Tacrolimus
+Tadalafil
+Tafluprost
+Talbutal
+Tamibarotene
+Tamoxifen
+Tamsulosin
+Tapentadol
+Tasosartan
+Tauroursodeoxycholic_acid
+Tazarotene
+Tazobactam
+Telaprevir
+Telavancin
+Telbivudine
+Telithromycin
+Telmisartan
+Temazepam
+Temozolomide
+Temsirolimus
+Teniposide
+Tenofovir
+Tenoxicam
+Terazosin
+Terbinafine
+Terbutaline
+Terconazole
+Terfenadine
+Terlipressin
+Testolactone
+Testosterone
+Testosterone_Propionate
+Tetrabenazine
+Tetracycline
+Tetrahydrobiopterin
+Tetrahydrofolic_acid
+Thalidomide
+Theobromine
+Theophylline
+Thiabendazole
+Thiamine
+Thiamylal
+Thiethylperazine
+Thioguanine
+Thiopental
+Thioproperazine
+Thioridazine
+Thiotepa
+Thiothixene
+Tiagabine
+Tiaprofenic_acid
+Ticagrelor
+Ticarcillin
+Ticlopidine
+Tigecycline
+Tiludronate
+Timolol
+Tinidazole
+Tioconazole
+Tiotropium
+Tipranavir
+Tirofiban
+Tizanidine
+Tobramycin
+Tocainide
+Tofisopam
+Tolazamide
+Tolazoline
+Tolbutamide
+Tolcapone
+Tolmetin
+Tolnaftate
+Tolterodine
+Tolvaptan
+Topiramate
+Topotecan
+Torasemide
+Toremifene
+Trabectedin
+Tramadol
+Trametinib
+Trandolapril
+Tranexamic_Acid
+Tranylcypromine
+Travoprost
+Trazodone
+Treprostinil
+Tretinoin
+Triamcinolone
+Triamterene
+Triazolam
+Trichlormethiazide
+Tridihexethyl
+Trifluoperazine
+Triflupromazine
+Trifluridine
+Trihexyphenidyl
+Trilostane
+Trimeprazine
+Trimethadione
+Trimethaphan
+Trimethobenzamide
+Trimethoprim
+Trimetrexate
+Trimipramine
+Trioxsalen
+Tripelennamine
+Triprolidine
+Trisalicylate-choline
+Troleandomycin
+Tropicamide
+Trospium
+Trovafloxacin
+Tubocurarine
+Tymazoline
+Udenafil
+Uracil_mustard
+Ursodeoxycholic_acid
+Valaciclovir
+Valganciclovir
+Valproic_Acid
+Valrubicin
+Valsartan
+Vancomycin
+Vandetanib
+Vapreotide
+Vardenafil
+Varenicline
+Vecuronium
+Vemurafenib
+Venlafaxine
+Verapamil
+Verteporfin
+Vidarabine
+Vigabatrin
+Vilazodone
+Vildagliptin
+Vinblastine
+Vincristine
+Vindesine
+Vinorelbine
+Vismodegib
+Vitamin_A
+Vitamin_C
+Vitamin_E
+Voacamine
+Voglibose
+Voriconazole
+Vorinostat
+Warfarin
+Xanthophyll
+Ximelagatran
+Xylometazoline
+Yohimbine
+Zafirlukast
+Zalcitabine
+Zaleplon
+Zanamivir
+Zidovudine
+Zileuton
+Zinc
+Ziprasidone
+Zoledronate
+Zolmitriptan
+Zolpidem
+Zonisamide
+Zopiclone
+Zuclopenthixol
\ No newline at end of file
diff --git a/xyzFromSmiles.py b/xyzFromSmiles.py
new file mode 100644
index 0000000..32c5333
--- /dev/null
+++ b/xyzFromSmiles.py
@@ -0,0 +1,24 @@
+from rdkit import Chem
+from rdkit.Chem import AllChem
+
+###########################################################
+#                                                         #
+# This program generates the xyz coordinates for the      #
+# molecules using SMILES. It tries for upto 20 iterations #
+# inside the rdkit MM force field optimizer and only      #
+# returns a geometry if converged. Most of the molecules  #
+# were converged with an exception of four to five.       #
+#                                                         #
+###########################################################
+def xyzFromSmiles(smiles, fileName):
+    mol = Chem.MolFromSmiles(smiles)
+    mol = Chem.AddHs(mol)
+    AllChem.EmbedMolecule(mol, useRandomCoords=True)
+    try:
+        AllChem.MMFFOptimizeMolecule(mol, maxIters=20)
+        writer = Chem.rdmolfiles.SDWriter(fileName + '.sd')
+        writer.write(mol)
+    except:
+        print('Skipping ', fileName)
+        return
+