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@tdudgeon
Created December 17, 2021 14:09
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{
"cells": [
{
"cell_type": "markdown",
"id": "60273a06",
"metadata": {},
"source": [
"# Mpro amido pyridine structures are the enol tautomer\n",
"\n",
"Amido pyridines are prominant in the Mpro Fragalysis structures and in the Moonshot compounds.\n",
"\n",
"This notebook that suggest that in these structuresthe amide moiety is actually the enol tauromer, not the keto as they are commonly displayed as.\n",
"The key points are:\n",
"1. the enol is the lower energy\n",
"2. the keto is planar with respect to the pyridine ring, the enol is perpendicular to the ring. All Fragalysis structures examined so far correspond to the enol conformation."
]
},
{
"cell_type": "code",
"execution_count": 25,
"id": "b97e0fb6",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"RDKit version: 2021.09.2\n"
]
}
],
"source": [
"from rdkit import Chem\n",
"from rdkit.Chem import AllChem\n",
"from rdkit.Chem import rdMolAlign\n",
"from rdkit.Chem import rdForceFieldHelpers\n",
"from rdkit.Chem import Draw\n",
"from rdkit import rdBase\n",
"from rdkit.Chem import rdFMCS \n",
"from rdkit.Chem.Draw import IPythonConsole\n",
"print('RDKit version:', rdBase.rdkitVersion)"
]
},
{
"cell_type": "code",
"execution_count": 26,
"id": "88c67b58",
"metadata": {},
"outputs": [
{
"data": {
"image/png": 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\n",
"text/plain": [
"<IPython.core.display.Image object>"
]
},
"execution_count": 26,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"x0107_keto_1d = Chem.MolFromSmiles('CC(=O)Nc1cnccc1C')\n",
"x0107_enol_1d = Chem.MolFromSmiles('CC(O)=Nc1cnccc1C')\n",
"Draw.MolsToGridImage([x0107_keto_1d, x0107_enol_1d])"
]
},
{
"cell_type": "code",
"execution_count": 27,
"id": "43859bf0",
"metadata": {},
"outputs": [
{
"data": {
"image/png": 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20bR4gqIY7Qeeew5qNS5ehEyGujokJMDPDwkJePiQvzGl0WjGjBlTUFAQFRUVEhKSmpraszf6l3/BihUA0NiIt9825UcgPVNbW6vVasVi8csvv2xgs06H778HKEYFRjHab0ycCI0GWVmYPRv37yM+HuPGYetW6HQimUyWl5enVquHDx9++vTp+fPnz5o1KzMzswfvsnEjXFwA4OhRHDxo4o9AuislJaWhoSE8PFw/r01bp0+e/J2/f/qLL2LqVPPXRvQoRvuZ0FCkpUGrxdSpKC5GTAwmT0ZS0hOznwwaNIhb6X7+/PkXL17s1usPG4YPP+Qfr12L7k+QQkxp3759AF5p5/bRP3bv/iYj4+CkSeYtijyNYrRfkkpx9iw0Gvj6Ij8fn3wC7oqoo6OjQqEoKipSqVTOzs6pqanTpk2Lioq6ceNG1188Lg7cL+b169iypXc+AOmCxsbGlJQUAEuXLjXYYP/+/Wg/ZInZUIz2V2IxZDLk5+Pzz/Hpp2gzeSmcnZ31PfYlEklSUtL48eNjYmLKy8u78soSCf73f/kXXL8eDx70zgcgndFqtdXV1UFBQb6+vs9uPXfuXGFhoZeXV+izAyqIeVGM9m/29viP/8DzzxvY5OHhoVKpCgoK5HJ5a2urvsd+ewuXtjVrFqKjAaCi4okD0pYWKBS0FqmZdHxGz21dtmyZWEy/xQKjfwALN2rUKLVanZOTI5PJamtr9T32W1tbO97xk0/4+X/bhuaGDdiwAYGB2L+/N4smQGtra3JyMoBl7dyF37t3L+iMvo8QelA/MZ8TJ07Mnj2b+3d3ckrST03Snq++emJq57feYqWlbNEi/q8yGS1X0YuOHj0KYOzYsQa3FhQUAHBzc2tqajJzYeRZdDRqRcLCwtLS0rRa7dSpU+vq6rgnT5w4wdrpsf/WW5g584lnvLxw8CDUajg5ISkJU6fi2LHertpKcefsK7h+vM/YvXs3gKVLl0okErOWRQwSOseJAFpbW2fPvvHoMHMZNyDKYMvTp5lYbGCivOvX+QkwRSIml9OioSam0+mee+45AKfbWZVw+vTpAL7//nszF0YMErGejh0k/dp33+H4cV1BQcHPP8fdu6cFIJVKExISgoKCnmq5cSPy8gBg9my89trj51ta8Nln+Mtf0NSECROwfTuCg81Xv2XLzs4OCwsbMWJEcXFx2xVkOSUlJSNHjnRycrpz586AAQMEqZA8QegcJwKrra1VqVRubm4ARCKRTCa7cuVK13fPyWGTJ/OrOSkUjK7UmcR7770HYO3atQa3fvHFFwCioqLMXBVpD8UoYYyx+/fvKxQK7tCGGxB166mlRNvX0MAUCv7cf+ZMdvlyr1ZqFcaOHQvgp59+Mrj1+eefB7Br1y4zV0XaQzFKHvvll1/kcrmtrS0eDYh60OWb8ZmZzM+PAWzAAKZSMW45qYMHD+bm5jY3N/di0RbnwoULAIYOHdpiaInB8vJyGxsbe3v7qqoq89dGDKIYJU+7fPmyfr1SbkBUtcElgJ5RVcXkcv5+lFTKCgub7OzsuMPbiRMnymQypVKp0Whyc3N13DpTxBClUgkgJibG4Fa1Wg1g8eLFZq6KdIBilBh26tSpxYsXcxfQuQFRDx8+7MqOe/YwDw9ugTzdzJl/8PPze3aYjaura0RERExMzObNm9PT07t+zGsNAgMDARw6dMjg1hdffBHAN998Y+aqSAfoTj3pSGZm5gcffMDNuTdq1Kg//elPb775po2NTcd73bkDuRxpaZVOTpPDw0O+/PLLioqKs2fP5ufn5+Xl5efnFxYWtm1vb29fW1vLXUywcteuXRszZoybm1t5eTl3LN9WVVWVp6dna2traWmph4eHIBUSA4TOcdIPaLXayZMnc/9hAgICNO2tlv6kv//9R2dnZwDDhg1LSUlpu+nOnTupqamJiYm/+93vZs6cOWvWrN4pvP9RqVQAoqOjDW7dvn07gBdeeMHMVZGOUYySLmltbdVoNKNHj+bCNCwsLD09vdO9bt68OWfOHG6X6OjompoaM5Tar7322msA9rQzRJcbX79p0yYzV0U6RjFKuqGxsVGtVg8dOpRLRqlUev78+Y530el0iYmJ9vb2AEaPHt2V8LVyBQUF9fX1jLG7d+8WFRUVFxdzz9fV1Tk5OYlEIv0zpI+gGCXdVlNTo1KpXFxcAIjFYplMdu3atY53ycvL48ZHicXi2NjYLt6tslrV1dUqlcrV1TUkJEQikSiVypaWlj179gAIDQ0VujryNIpR0kN3795VKBQODg541GO/tLS0g/bNzc1KpZK7PTVp0qROD2OtU01NzUcffTSIm6MQ8Pf353qeRUZGxsfH29nZJSQkCF0jeRrFKDHKjRs3Vq5cyXVpGjhwYGxsbHJy8u3bt9trn52dzQ3R0R9kmbPavoy7YOLl5cUFaERExLFjxxhjR44cGTFiBABnZ+fExMSKigqhKyVPoxglJpCfn8/12Nf3wnFzc4uIiJDL5YmJiVqt9u7du/rG9fX1sbGx3EFWWFjY1atXBay8L2hqalKr1d7e3tyPLjQ0VKvVtm1QWVn5m9/8htu6cOHCDr6liCAoRonJpKWl6e8+PcvHx2fx4sXx8fE7d+7Mycn55z//yQWHo6NjYmKidY5r4vo/+Pn5cT+iwMDADjqTaTQad3d3AJ6envv27TNnnaRjFKPElBoaGhQKBXcB1NfX97333pPL5REREU5OTk+lqq2trY+PD3e6yp3D/vLLL0KXbz5cgHLXNwBMnDhRo9F0+l1SWlq6aNEifQeyLg7SJb2NYpSY3okTJ8aMGQPAwcFBpVJxF0Bv3bp14MABlUoVHR09ceLEZ4dCvfLKK0IXbg46ne7AgQNTp07lPvXo0aPVanXXrxHrdDq1Ws19Lfn4+KSlpfVqtaQrKEZJr6irq9NfAA0PD3/2Amh9ff2ZM2e+/fbbd999d/bs2Y6OjpcuXRKkVHPSarXBj2a3HjlypFqt7tn0V/n5+dwE+NSBrC+gGCW96NChQ3QBlJORkaFfT9DT07PrU720p7m5WaVScWsxUQcyYVGMkt5VUVGhv8u8YMGCkpISoSsytxMnTsybN4/7CQwZMkSlUnGDlEzi5MmT3AXWttdPiJlRjBJz0Gg0gwcP5jpCbd++XehyzCQnJ0cmk3EB6u7urlQqe2Ou5bYdyMLDwzsdUUZMjmKUmElZWdmSJUu4TJHJZPfu3RO6ol6Um5urn/p64MCBCoWit7vNHz58mLt+4uLiolare/W9yFMoRolZbdu2beDAgQC8vLySk5OFLsf0fv755+joaK4fgqOjY2xsbFlZmXneuqKi4vXXX+e+qJYtW9Z2yAPpVRSjxNxu3LjB3WwRiURyudxiZs+7efOmfiUrOzs7uVwuyHAjjUbDDcn39PSkhezNg2KUCKClpUWlUnGz5/n7+x8/fkLoioxSXMxiYtisWb8GIJFI1qxZI+xQgqKiorlz5+p76VvMF1WfRTFKBJObm8vNnhcRcTM2lvXHvo+lpSw2ltnbM4CNHZu/atWqwsJCoYti7FEvfUdHR66Hf3trNROToBglQmpsbExIOGhjwwA2eTLLyRG6oC67d48plczZmQFMJGIyGbt8WeianqGf5tXGxkahUDQ2NgpdkWWiGCXCy85m48YxgEkkTKlkfbzvY00NU6mYq+vjpaTPnRO6pvY1NTXpp3kNDAzM6UffVP0HxSjpE+rrmULBxGIGsNBQVlAgdEGG1NYylYoNGvQ4QE+dErqmrsnKymo7y0Fra6vQFVkUilHSh2i17LnnGMAGDGAqFes7v+yNjUytZl5efIBGRLBjx4SuqZvaznIwb948WtDJhChGSd9SWcnkcj6t5s9ngk+e19TE1Grm7c2XFBrKDhwQuCRj/PDDD8OHDwfg6upKvfRNhWKU9EW7d7MhQxjAXF2ZUL/sra1Mo2F+fnyABgay9qdU7k/u3LmzdOlSrjvUihUrLHs4mXlQjJI+qrycLV3KR9iKFcycQ3K4AB07ln/3iROZRsMsbHYqfS/9oUOHWuRwMnMSMcYMLPhASN+QlISYGFRUwNMTW7fi5Zef2JqSgkuX+Mdr1sDVtd3XOXcOWi0ATJ2KBQvabcYYDh7EX/6CCxcAYPRoxMfjzTfxzBzTlqCoqGjVqlVpaWkikWj16tWff/75s4sUkC4ROscJ6cTNm2zuXP7AMDqatV04Y9Uq/nmAvfNORy+yaRPfbM2adttotSw4mG82ciRTq1mPplTuT3Q6XWJiIjeczNfXNyMjQ+iK+iWx0DFOSCdGjcLRo1Cr4eiI7dsRGIhjxww027IF2dk9fIvMTMyZg/nzcfYsPD2hUqGgAHI5bG2NKbwfEIlEcXFxZ8+enTZtWmFh4dy5c+Pj45uamoSuq5+hGCX9gEgEuRxnzmD6dBQVYd48xMSgvv6JNjodYmLQ0tK9V87KglSKyEikp2PIEKhUuHkTCgUcHExYfl8XEBBw8uRJpVLJGEtISJg1a9bly5eFLqo/oRgl/caECThxAkolbGywdSuOHn28ycMDAC5exObNXX21ixcRFYXwcBw9Cnd3KJW4fh0KBQYMMH3lfZ9EIlm3bl1GRoa/v//p06eDgoISEhJ0Op3QdfUTQl9VIKTbTp1if/oTY22ujX76KT8/iLOz4a6mT10bjY5mIhEDmIsLUypZZaVZ6+/Lqqqq5HI5Fw5SqdSqVr3uMToaJf3PjBn46KMnnvHxwZo1AFBTg7VrO38FHx8MGIDYWFy5gnXrOrrFb224yfNTUlKGDRuWmpo6adKk7du3C11UX0cxSiyEUokhQwBgzx4kJ3fS+I9/RGEhvvwSQ4eaobT+Z+HChRcuXHj55ZerqqpWrlwZFRX14MEDoYvquyhGiYUYNAj//d/843feQV1dR41dXChAO+Hp6bl//35u0ZekpKSAgICUlBShi+qjKEaJ5ZDLMWUKABQX43/+R+hqLMLKlSsvXLgQHh5eVla2ePHiuLi4xsZGoYvqcyhGieWwscGmTRCJAOCzz5CXJ3RBFsHPzy8jIyMxMVEikZw+fdrW4jvTdh/FKLEokZFYuRIAmpuxZg1oqLNJiMXiuLi47Ozs7du321jkwFjjUIwSS7NhAwYNAoDMTHz3ncDFWJJp06b5+fkJXUVfRDFKLI2n5+MLo/HxqKoStBpiBShGiQVaswYhIQBw587TPUwJMTmKUWKBxGJs2gSxGAC+/BJXrwpdELFoFKPEMs2YAW5MY1MT4uOFroZYNIpRYrE+/hiengCwdy+OHxe6GmK5KEaJxRo0CAkJ/OP/+z9BSyEWjWKUWLLf/hZz5gCgDqSkF1GMEksmEuGrryCRCF0HsWgUo8TCBQTg978Xughi0ShGieVbtw7e3kIXQSwXLbBM+rGbN3H/PgD4+vIDQNtTXIy7dwHAwwMjR5qjNmI9KEYJIcQoNOcV6cdUKlRXA0BsLLy8OmpZUoItWwDA3R1//KM5aiPWg45GST82fDhKSwEgJweTJ3fU8tQpfpT96NEoLDRHbcR60C0mQggxCsUoIYQYhWKUEEKMQjFKCCFGoRglhBCjUIwSQohRKEYJIcQoFKOEEGIUGsVELMGiRZ3MhtfUZK5SiPWhGCWW4NYtoSsgVoxilFiC2bPh4tJRg8pKZGSYqxpiZShGiSXYuLGrY+oJMTm6xUQIIUahGCWEEKNQjBJCiFEoRgkhxCgUo4QQYhSKUUIIMQrFKCGEGIVilBBCjEIxSgghRqGVQUk/lp+P5mYAGDcODg4dtWxowJUrAGBvj/HjzVEbsR4Uo4QQYhQ6qSeEEKNQjBJCiFEoRgkhxCgUo4QQYhSKUUIIMcr/A+1tQFg1gBZSAAABHXpUWHRyZGtpdFBLTCByZGtpdCAyMDIxLjA5LjIAAHice79v7T0GIOBlQABuKG5gZGNIANKMzGwMGkCamYUDQjOxM2SAaUY2B4gEmwNYgJmRHSLADBdAYkCVQs3kZmRgYGLUYGJmVGBhVmBlyWBiY01gZ8tg4mBP4OTIYOJkSeDiZBBhZGPh5GBnYxXvA+mCYgbuPysVHVnC9PZ352xxvO8v7PhnZeFe6/urHYWaJRwfVpXYNx9Y7qi44Z+D2zbj/db3Vzhqxjx2yJj4dq/llgWO05zfOwhEWO6TZJnmyKR93SGMb61dWlqf4+2fmxxeqhXax+2aADRnicO89+320vqzHaX19zrIRrHYp6UtdrTlWu9w+6ecfZLAekcxABJVRpNT7celAAABWHpUWHRNT0wgcmRraXQgMjAyMS4wOS4yAAB4nH2SQW7EIAxF9zmFL1Bkgw14OZmMqqqaRGqnvUP3c3/VEFLCpglSHOfF2P8zQbk+lvefJ/xdYZkmAPxnqSp8B0Sc7lACmG+vbytcH5f5yFy3r/XxCURlYblH9vLY7keG4AqEjpCtJLygi5lK5L0TKdv0n72h6jymRqJoJclx5oEMsBkpwdesU5EKWhR1ABlWSPZdW8mEvpUkHEmxzZNlpZFEsdXEnAcyVpLT0SbtA1F2SfxAJts9uuT35l0ItRAlV55nMFtJcaKhzcO+VUSlAdQKEu87Oow7qC7o2CRhJZWaREKpjcNeRpIqyWlvyUVPTaKcR39u6zJYu5s9b+vSzSZzkbqh3qzy3TUyQ3z3hkx17gawSStdZTb9YpeSTaXUBWPTIndZuEysp+lrQk5D1sNKwzDn1sv7ccYtnn4BErubBTeD98YAAACvelRYdFNNSUxFUyByZGtpdCAyMDIxLjA5LjIAAHicHY5BDgJBCAS/4nFNRkIzMEA2nvauj5i7L/DxgidCpWj6uo7n+/7a2J+9N67b9wATWMeDaQWGCJnNM0nYm7HlEJCGFrMpgynNhtRYeXot2ZqztAZuBrZmwGqPI4qp/+NQLxDkJuciF624OWPAKU4jy9n5Ku1wohC0DohXoaSZbSW6hcE7XcUKqRdZgu4QMe/fHzq9L5W6MrT8AAAAAElFTkSuQmCC\n",
"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x7fb851d537c0>"
]
},
"execution_count": 27,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# this is the Fragalysis molfile\n",
"x0107_keto_3d = Chem.MolFromMolFile('../frag-merge/Mpro-x0107/Mpro-x0107_0A.mol')\n",
"x0107_keto_3d"
]
},
{
"cell_type": "code",
"execution_count": 28,
"id": "23db8726",
"metadata": {},
"outputs": [
{
"data": {
"image/png": 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\n",
"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x7fb851a3eac0>"
]
},
"execution_count": 28,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# This is the Fragalysis molfile tweaked to be the enol form\n",
"x0107_enol_3d = Chem.MolFromMolFile('../frag-merge/Mpro-x0107/Mpro-x0107_0A_enol.mol')\n",
"x0107_enol_3d"
]
},
{
"cell_type": "code",
"execution_count": 29,
"id": "cfe5f969",
"metadata": {},
"outputs": [],
"source": [
"# energy minimisation using MMFF94\n",
"def miminize_mol(mol):\n",
" # calc energy\n",
" ff = rdForceFieldHelpers.MMFFGetMoleculeForceField(mol, AllChem.MMFFGetMoleculeProperties(mol))\n",
" energy1 = ff.CalcEnergy()\n",
" # energy minimize\n",
" converged = rdForceFieldHelpers.MMFFOptimizeMolecule(mol, maxIters=500)\n",
" print('Converged?',converged)\n",
" ff = rdForceFieldHelpers.MMFFGetMoleculeForceField(mol, AllChem.MMFFGetMoleculeProperties(mol))\n",
" energy2 = ff.CalcEnergy()\n",
" print('Energy before:', energy1, 'after:', energy2)"
]
},
{
"cell_type": "code",
"execution_count": 30,
"id": "b0900d9f",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Converged? 0\n",
"Energy before: 45.78218216848276 after: 16.321839388513137\n"
]
},
{
"data": {
"image/png": 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\n",
"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x7fb851a39e80>"
]
},
"execution_count": 30,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"keto = Chem.AddHs(x0107_keto_3d, addCoords=True)\n",
"miminize_mol(keto)\n",
"Chem.RemoveHs(keto)\n",
"# molecule is now planar. This seems to make sense - N pi electrons above and below the plane\n",
"# delocalising with the aromatic ring"
]
},
{
"cell_type": "code",
"execution_count": 31,
"id": "7343f298",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Converged? 0\n",
"Energy before: 48.684058137191485 after: 12.94702004001868\n"
]
},
{
"data": {
"image/png": 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\n",
"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x7fb851a39dc0>"
]
},
"execution_count": 31,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"enol = Chem.AddHs(x0107_enol_3d, addCoords=True)\n",
"miminize_mol(enol)\n",
"Chem.RemoveHs(enol)\n",
"# conformation mostly unchanged. Energy is 3.4 kCal/mol lower\n",
"# lone pair electrons on the N delocalising with the aromatic ring?\n",
"# All Fragalysis structures I've looked at so far have this conformation, not the planar one.\n",
"# N now becomes H-bond acceptor and can form H-bond with Cys145 thiol."
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "92e44577",
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.12"
}
},
"nbformat": 4,
"nbformat_minor": 5
}
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