SmilesManager.ipynb: Knowledge Management

In [1]:

from xv.chemistry.physical import SmilesManager

In [2]:

ke = SmilesManager()
ke

Out[2]:

2867619582784@SmilesManager

Smiles code of molecules and conversion to rdkit molecule

Minimum Grade: 6
Maximum Grade: 12

Examples
--------
ke = SmilesManager()
ke

ke.printProblemTypes()

ke.getRandomProblem()
ke.getRandomProblem(problem_type = 0)
...

ke.printProblem()
ke.printAnswer()
ke.printSolution()

doc_style: xv_doc

In [3]:

ke.getRandomProblem(problem_type = 0, verbose = True)

Problem Template: _problem_examples_smiles

Out[3]:

Give some examples of the simplified molecular-input line-entry system (SMILES).

Note: Use input parameter 'search' to filter result.

In [4]:

from IPython.display import HTML
n = len(ke._problemTemplates)
max_loop = 1
for j in range(0, max_loop):
    for i in range(n):
        problem_type = i
        display(HTML(f"<h2>problem_type: {problem_type}/{n-1} (loop {j}/{max_loop-1})</h2>"))
        ke.getRandomProblem(problem_type = problem_type, verbose = True)
        display(ke.printProblem())

        display(HTML(f"<h6>Answer:</h6>"))
        display(ke.printAnswer())

        display(HTML(f"<h6>Solution:</h6>"))
        display(ke.printSolution())
        pass

problem_type: 0/25 (loop 0/0)

Problem Template: _problem_examples_smiles

[15:16:29] WARNING: Accepted unusual valence(s): Co(6); Metal was disconnected; Proton(s) added/removed

Give some examples of the simplified molecular-input line-entry system (SMILES).

Note: Use input parameter 'search' to filter result.

Answer:

Examples of SMILES:

Br:

S[Co@@](F)(Cl)(Br)(I)C=O:

[Zr]:

biphenyl: A ring closure digit may be reused if desired.: c1ccccc1c1ccccc1

Solution:

Examples of SMILES:

Br:

smiles_non_kekule:    Br
smiles_kekule:    Br
inchi:    InChI=1S/BrH/h1H
inchiKey:    CPELXLSAUQHCOX-UHFFFAOYSA-N
smarts:    [#35]
smarts_isomeric:    [#35]

S[Co@@](F)(Cl)(Br)(I)C=O:

smiles_non_kekule:    O=C[Co](F)(S)(Cl)(Br)I
smiles_kekule:    O=C[Co](F)(S)(Cl)(Br)I
inchi:    InChI=1S/CHO.BrH.ClH.Co.FH.HI.H2S/c1-2;;;;;;/h1H;2*1H;;2*1H;1H2/q;;;+5;;;/p-5
inchiKey:    OFLGBCHBKKTRSH-UHFFFAOYSA-I
smarts:    [#16]-[Co](-[#9])(-[#17])(-[#35])(-[#53])-[#6]=[#8]
smarts_isomeric:    [#16]-[Co](-[#9])(-[#17])(-[#35])(-[#53])-[#6]=[#8]

[Zr]:

smiles_non_kekule:    [Zr]
smiles_kekule:    [Zr]
inchi:    InChI=1S/Zr
inchiKey:    QCWXUUIWCKQGHC-UHFFFAOYSA-N
smarts:    [Zr]
smarts_isomeric:    [Zr]

biphenyl: A ring closure digit may be reused if desired.: c1ccccc1c1ccccc1

smiles_non_kekule:    c1ccc(-c2ccccc2)cc1
smiles_kekule:    C1=CC=C(C2=CC=CC=C2)C=C1
inchi:    InChI=1S/C12H10/c1-3-7-11(8-4-1)12-9-5-2-6-10-12/h1-10H
inchiKey:    ZUOUZKKEUPVFJK-UHFFFAOYSA-N
smarts:    [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1
smarts_isomeric:    [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1

problem_type: 1/25 (loop 0/0)

Problem Template: _problem_search_smiles

Please pass input parameter 'search'.
For example:
search = "methane"

Answer:

None

Solution:

None

problem_type: 2/25 (loop 0/0)

Problem Template: _problem_draw_smiles

Draw the following smiles:
P

Note: Pass input smiles = 'YOUR SMILE CODE'

Answer:

Solution:

Code to draw smiles:

from rdkit import Chem
rdkit_molecule = Chem.MolFromSmiles('P')
if not rdkit_molecule is None:

display(rdkit_molecule)
pass

problem_type: 3/25 (loop 0/0)

Problem Template: _problem_draw_3d_from_smiles

Draw the following smiles:
N[C@H](C)C(=O)O

Note: Pass input smiles = 'YOUR SMILE CODE'

Answer:

N[C@H](C)C(=O)O

Solution:

N[C@H](C)C(=O)O

Code to draw smiles as 3d:

from xv.chemistry.helper import MoleculeVisualizationHelper
visual_helper = MoleculeVisualizationHelper()
visual_helper.mol_object_to_3d('N[C@H](C)C(=O)O')

problem_type: 4/25 (loop 0/0)

Problem Template: _problem_amino_acids

[15:16:31] WARNING: not removing hydrogen atom without neighbors

Write structure of amino acids molecules.

Answer:

structure of amino acids molecules:

alanine: C

arginine: CCCCNC(N)=N

asparagine: CCC(N)=O

aspartic acid: CC(O)=O

cysteine: CS

glutamic acid: CCC(O)=O

glutamine: CCC(N)=O

glycine: [H]

histidine: CC1=CNC=N1

isoleucine: C(CC)([H])C

leucine: CC(C)C

lysine: CCCCN

methionine: CCSC

phenylalanine: CC1=CC=CC=C1

proline: C2CCCN2

serine: CO

threonine: C(C)([H])O

tryptophan: CCC1=CNC2=C1C=CC=C2

tyrosine: CC1=CC=C(O)C=C1

valine: C(C)C

Solution:

structure of amino acids molecules:

alanine: C

smiles_non_kekule:    C
smiles_kekule:    C
inchi:    InChI=1S/CH4/h1H4
inchiKey:    VNWKTOKETHGBQD-UHFFFAOYSA-N
smarts:    [#6]
smarts_isomeric:    [#6]

arginine: CCCCNC(N)=N

smiles_non_kekule:    CCCCNC(=N)N
smiles_kekule:    CCCCNC(=N)N
inchi:    InChI=1S/C5H13N3/c1-2-3-4-8-5(6)7/h2-4H2,1H3,(H4,6,7,8)
inchiKey:    CGWBIHLHAGNJCX-UHFFFAOYSA-N
smarts:    [#6]-[#6]-[#6]-[#6]-[#7]-[#6](-[#7])=[#7]
smarts_isomeric:    [#6]-[#6]-[#6]-[#6]-[#7]-[#6](-[#7])=[#7]

asparagine: CCC(N)=O

smiles_non_kekule:    CCC(N)=O
smiles_kekule:    CCC(N)=O
inchi:    InChI=1S/C3H7NO/c1-2-3(4)5/h2H2,1H3,(H2,4,5)
inchiKey:    QLNJFJADRCOGBJ-UHFFFAOYSA-N
smarts:    [#6]-[#6]-[#6](-[#7])=[#8]
smarts_isomeric:    [#6]-[#6]-[#6](-[#7])=[#8]

aspartic acid: CC(O)=O

smiles_non_kekule:    CC(=O)O
smiles_kekule:    CC(=O)O
inchi:    InChI=1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)
inchiKey:    QTBSBXVTEAMEQO-UHFFFAOYSA-N
smarts:    [#6]-[#6](-[#8])=[#8]
smarts_isomeric:    [#6]-[#6](-[#8])=[#8]

cysteine: CS

smiles_non_kekule:    CS
smiles_kekule:    CS
inchi:    InChI=1S/CH4S/c1-2/h2H,1H3
inchiKey:    LSDPWZHWYPCBBB-UHFFFAOYSA-N
smarts:    [#6]-[#16]
smarts_isomeric:    [#6]-[#16]

glutamic acid: CCC(O)=O

smiles_non_kekule:    CCC(=O)O
smiles_kekule:    CCC(=O)O
inchi:    InChI=1S/C3H6O2/c1-2-3(4)5/h2H2,1H3,(H,4,5)
inchiKey:    XBDQKXXYIPTUBI-UHFFFAOYSA-N
smarts:    [#6]-[#6]-[#6](-[#8])=[#8]
smarts_isomeric:    [#6]-[#6]-[#6](-[#8])=[#8]

glutamine: CCC(N)=O

glycine: [H]

smiles_non_kekule:    [H]
smiles_kekule:    [H]
inchi:    InChI=1S/H
inchiKey:    YZCKVEUIGOORGS-UHFFFAOYSA-N
smarts:    [H]
smarts_isomeric:    [H]

histidine: CC1=CNC=N1

smiles_non_kekule:    Cc1c[nH]cn1
smiles_kekule:    CC1=CNC=N1
inchi:    InChI=1S/C4H6N2/c1-4-2-5-3-6-4/h2-3H,1H3,(H,5,6)
inchiKey:    XLSZMDLNRCVEIJ-UHFFFAOYSA-N
smarts:    [#6]-[#6]1:[#6]:[#7H]:[#6]:[#7]:1
smarts_isomeric:    [#6]-[#6]1:[#6]:[#7H]:[#6]:[#7]:1

isoleucine: C(CC)([H])C

smiles_non_kekule:    CCCC
smiles_kekule:    CCCC
inchi:    InChI=1S/C4H10/c1-3-4-2/h3-4H2,1-2H3
inchiKey:    IJDNQMDRQITEOD-UHFFFAOYSA-N
smarts:    [#6H](-[#6]-[#6])-[#6]
smarts_isomeric:    [#6H](-[#6]-[#6])-[#6]

leucine: CC(C)C

smiles_non_kekule:    CC(C)C
smiles_kekule:    CC(C)C
inchi:    InChI=1S/C4H10/c1-4(2)3/h4H,1-3H3
inchiKey:    NNPPMTNAJDCUHE-UHFFFAOYSA-N
smarts:    [#6]-[#6](-[#6])-[#6]
smarts_isomeric:    [#6]-[#6](-[#6])-[#6]

lysine: CCCCN

smiles_non_kekule:    CCCCN
smiles_kekule:    CCCCN
inchi:    InChI=1S/C4H11N/c1-2-3-4-5/h2-5H2,1H3
inchiKey:    HQABUPZFAYXKJW-UHFFFAOYSA-N
smarts:    [#6]-[#6]-[#6]-[#6]-[#7]
smarts_isomeric:    [#6]-[#6]-[#6]-[#6]-[#7]

methionine: CCSC

smiles_non_kekule:    CCSC
smiles_kekule:    CCSC
inchi:    InChI=1S/C3H8S/c1-3-4-2/h3H2,1-2H3
inchiKey:    WXEHBUMAEPOYKP-UHFFFAOYSA-N
smarts:    [#6]-[#6]-[#16]-[#6]
smarts_isomeric:    [#6]-[#6]-[#16]-[#6]

phenylalanine: CC1=CC=CC=C1

smiles_non_kekule:    Cc1ccccc1
smiles_kekule:    CC1=CC=CC=C1
inchi:    InChI=1S/C7H8/c1-7-5-3-2-4-6-7/h2-6H,1H3
inchiKey:    YXFVVABEGXRONW-UHFFFAOYSA-N
smarts:    [#6]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1
smarts_isomeric:    [#6]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1

proline: C2CCCN2

smiles_non_kekule:    C1CCNC1
smiles_kekule:    C1CCNC1
inchi:    InChI=1S/C4H9N/c1-2-4-5-3-1/h5H,1-4H2
inchiKey:    RWRDLPDLKQPQOW-UHFFFAOYSA-N
smarts:    [#6]1-[#6]-[#6]-[#6]-[#7]-1
smarts_isomeric:    [#6]1-[#6]-[#6]-[#6]-[#7]-1

serine: CO

smiles_non_kekule:    CO
smiles_kekule:    CO
inchi:    InChI=1S/CH4O/c1-2/h2H,1H3
inchiKey:    OKKJLVBELUTLKV-UHFFFAOYSA-N
smarts:    [#6]-[#8]
smarts_isomeric:    [#6]-[#8]

threonine: C(C)([H])O

smiles_non_kekule:    CCO
smiles_kekule:    CCO
inchi:    InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3
inchiKey:    LFQSCWFLJHTTHZ-UHFFFAOYSA-N
smarts:    [#6H](-[#6])-[#8]
smarts_isomeric:    [#6H](-[#6])-[#8]

tryptophan: CCC1=CNC2=C1C=CC=C2

smiles_non_kekule:    CCc1c[nH]c2ccccc12
smiles_kekule:    CCC1=CNC2=C1C=CC=C2
inchi:    InChI=1S/C10H11N/c1-2-8-7-11-10-6-4-3-5-9(8)10/h3-7,11H,2H2,1H3
inchiKey:    GOVXKUCVZUROAN-UHFFFAOYSA-N
smarts:    [#6]-[#6]-[#6]1:[#6]:[#7H]:[#6]2:[#6]:1:[#6]:[#6]:[#6]:[#6]:2
smarts_isomeric:    [#6]-[#6]-[#6]1:[#6]:[#7H]:[#6]2:[#6]:1:[#6]:[#6]:[#6]:[#6]:2

tyrosine: CC1=CC=C(O)C=C1

smiles_non_kekule:    Cc1ccc(O)cc1
smiles_kekule:    CC1=CC=C(O)C=C1
inchi:    InChI=1S/C7H8O/c1-6-2-4-7(8)5-3-6/h2-5,8H,1H3
inchiKey:    IWDCLRJOBJJRNH-UHFFFAOYSA-N
smarts:    [#6]-[#6]1:[#6]:[#6]:[#6](-[#8]):[#6]:[#6]:1
smarts_isomeric:    [#6]-[#6]1:[#6]:[#6]:[#6](-[#8]):[#6]:[#6]:1

valine: C(C)C

smiles_non_kekule:    CCC
smiles_kekule:    CCC
inchi:    InChI=1S/C3H8/c1-3-2/h3H2,1-2H3
inchiKey:    ATUOYWHBWRKTHZ-UHFFFAOYSA-N
smarts:    [#6](-[#6])-[#6]
smarts_isomeric:    [#6](-[#6])-[#6]

problem_type: 5/25 (loop 0/0)

Problem Template: _problem_braf_kinase_inhibitors_for_cancer

Write structure of braf kinase inhibitors for cancer molecules.

Answer:

structure of braf kinase inhibitors for cancer molecules:

imidazole: C1=CN=CN1

pyrazole-1-ethanol: OCCN1N=CC=C1

acetonitrile: C#N

2-(tert-butyl)thiazole: CC(C)(C)C1=NC=CS1

pyridine: C1=CC=NC=C1

1-isopropyl-pyrazole: CC(C)N1N=CC=C1

isoindoline: C12=CC=CC=C1CNC2

pyrrolopyridine: C12=CC=CN=C1C=CN2

Solution:

structure of braf kinase inhibitors for cancer molecules:

imidazole: C1=CN=CN1

smiles_non_kekule:    c1c[nH]cn1
smiles_kekule:    C1=CNC=N1
inchi:    InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5)
inchiKey:    RAXXELZNTBOGNW-UHFFFAOYSA-N
smarts:    [#6]1:[#6]:[#7]:[#6]:[#7H]:1
smarts_isomeric:    [#6]1:[#6]:[#7]:[#6]:[#7H]:1

pyrazole-1-ethanol: OCCN1N=CC=C1

smiles_non_kekule:    OCCn1cccn1
smiles_kekule:    OCCN1C=CC=N1
inchi:    InChI=1S/C5H8N2O/c8-5-4-7-3-1-2-6-7/h1-3,8H,4-5H2
inchiKey:    DXFBKDSQMUFYLD-UHFFFAOYSA-N
smarts:    [#8]-[#6]-[#6]-[#7]1:[#7]:[#6]:[#6]:[#6]:1
smarts_isomeric:    [#8]-[#6]-[#6]-[#7]1:[#7]:[#6]:[#6]:[#6]:1

acetonitrile: C#N

smiles_non_kekule:    C#N
smiles_kekule:    C#N
inchi:    InChI=1S/CHN/c1-2/h1H
inchiKey:    LELOWRISYMNNSU-UHFFFAOYSA-N
smarts:    [#6]#[#7]
smarts_isomeric:    [#6]#[#7]

2-(tert-butyl)thiazole: CC(C)(C)C1=NC=CS1

smiles_non_kekule:    CC(C)(C)c1nccs1
smiles_kekule:    CC(C)(C)C1=NC=CS1
inchi:    InChI=1S/C7H11NS/c1-7(2,3)6-8-4-5-9-6/h4-5H,1-3H3
inchiKey:    DQAIZGWCKXJRSP-UHFFFAOYSA-N
smarts:    [#6]-[#6](-[#6])(-[#6])-[#6]1:[#7]:[#6]:[#6]:[#16]:1
smarts_isomeric:    [#6]-[#6](-[#6])(-[#6])-[#6]1:[#7]:[#6]:[#6]:[#16]:1

pyridine: C1=CC=NC=C1

smiles_non_kekule:    c1ccncc1
smiles_kekule:    C1=CC=NC=C1
inchi:    InChI=1S/C5H5N/c1-2-4-6-5-3-1/h1-5H
inchiKey:    JUJWROOIHBZHMG-UHFFFAOYSA-N
smarts:    [#6]1:[#6]:[#6]:[#7]:[#6]:[#6]:1
smarts_isomeric:    [#6]1:[#6]:[#6]:[#7]:[#6]:[#6]:1

1-isopropyl-pyrazole: CC(C)N1N=CC=C1

smiles_non_kekule:    CC(C)n1cccn1
smiles_kekule:    CC(C)N1C=CC=N1
inchi:    InChI=1S/C6H10N2/c1-6(2)8-5-3-4-7-8/h3-6H,1-2H3
inchiKey:    ANMVTDVBEDVFRB-UHFFFAOYSA-N
smarts:    [#6]-[#6](-[#6])-[#7]1:[#7]:[#6]:[#6]:[#6]:1
smarts_isomeric:    [#6]-[#6](-[#6])-[#7]1:[#7]:[#6]:[#6]:[#6]:1

isoindoline: C12=CC=CC=C1CNC2

smiles_non_kekule:    c1ccc2c(c1)CNC2
smiles_kekule:    C1=CC=C2CNCC2=C1
inchi:    InChI=1S/C8H9N/c1-2-4-8-6-9-5-7(8)3-1/h1-4,9H,5-6H2
inchiKey:    GWVMLCQWXVFZCN-UHFFFAOYSA-N
smarts:    [#6]12:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6]-[#7]-[#6]-2
smarts_isomeric:    [#6]12:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6]-[#7]-[#6]-2

pyrrolopyridine: C12=CC=CN=C1C=CN2

smiles_non_kekule:    c1cnc2cc[nH]c2c1
smiles_kekule:    C1=CN=C2C=CNC2=C1
inchi:    InChI=1S/C7H6N2/c1-2-6-7(8-4-1)3-5-9-6/h1-5,9H
inchiKey:    XWIYUCRMWCHYJR-UHFFFAOYSA-N
smarts:    [#6]12:[#6]:[#6]:[#6]:[#7]:[#6]:1:[#6]:[#6]:[#7H]:2
smarts_isomeric:    [#6]12:[#6]:[#6]:[#6]:[#7]:[#6]:1:[#6]:[#6]:[#7H]:2

problem_type: 6/25 (loop 0/0)

[15:16:38] WARNING: Omitted undefined stereo

[15:16:38] WARNING: Omitted undefined stereo

[15:16:38] WARNING: Charges were rearranged

[15:16:38] WARNING: Omitted undefined stereo

[15:16:38] WARNING: Omitted undefined stereo

[15:16:38] WARNING: Omitted undefined stereo

[15:16:38] WARNING: Omitted undefined stereo

[15:16:38] WARNING: Omitted undefined stereo

Problem Template: _problem_chemical_adsorption_on_montmorillonite_clays

Write structure of chemical adsorption on montmorillonite clays molecules.

Answer:

structure of chemical adsorption on montmorillonite clays molecules:

3,3′,4,4′,5-pentachlorobiphenyl: C1=CC(=C(C=C1C2=CC(=C(C(=C2)Cl)Cl)Cl)Cl)Cl

3,4,3′,4′-tetrachlorobiphenyl: C1=CC(=C(C=C1C2=CC(=C(C=C2)Cl)Cl)Cl)Cl

2,2′,4,4′,5,5′-hexachlorobiphenyl: C1=C(C(=CC(=C1Cl)Cl)Cl)C2=CC(=C(C=C2Cl)Cl)Cl

bisphenol A: CC(C)(C1=CC=C(C=C1)O)C2=CC=C(C=C2)O

2,3,3′,4,4′,5′-hexachlorobiphenyl: C1=CC(=C(C=C1C2=CC(=C(C(=C2Cl)Cl)Cl)Cl)Cl)Cl

2,2′,4,4′,6,6′-hexachlorobiphenyl: C1=C(C=C(C(=C1Cl)C2=CC(=C(C=C2Cl)Cl)Cl)Cl)Cl

2,2′,4,4′,5,6′-hexachlorobiphenyl: C1=CC=C(C(=C1)C2=C(C(=C(C(=C2Cl)Cl)Cl)Cl)Cl)Cl

lindane: C1(C(C(C(C(C1Cl)Cl)Cl)Cl)Cl)Cl

naphthalene: C1=CC=C2C=CC=CC2=C1

benz[e]acephenanthrylene: C1=CC=C2C3=C4C(=CC=C3)C5=CC=CC=C5C4=CC2=C1

dieldrin: C1C2C3C(C1C4C2O4)C5(C(=C(C3(C5(Cl)Cl)Cl)Cl)Cl)Cl

linuron: CN(C(=O)NC1=CC(=C(C=C1)Cl)Cl)OC

trifluralin: CCCN(CCC)C1=C(C=C(C=C1[N+](=O)[O-])C(F)(F)F)[N+](=O)[O-]

toluene: CC1=CC=CC=C1

benzene: C1=CC=CC=C1

bisphenol S: C1=CC(=CC=C1O)S(=O)(=O)C2=CC=C(C=C2)O

bisphenol F: c1cc(ccc1Cc2ccc(cc2)O)O

benzo[a]pyrene: C1=CC=C2C3=C4C(=CC2=C1)C=CC5=C4C(=CC=C5)C=C3

2,4-dichlorophenoxyacetic acid: C1=CC(=C(C=C1Cl)Cl)OCC(=O)O

clofenotane (DDT): C1=CC(=CC=C1C(C2=CC=C(C=C2)Cl)C(Cl)(Cl)Cl)Cl

pyrene: C1=CC2=C3C(=C1)C=CC4=CC=CC(=C43)C=C2

deoxynivalenol (vomitoxin): CC1=CC2C(C(C1=O)O)(C3(CC(C(C34CO4)O2)O)C)CO

glyphosate: C(C(=O)O)NCP(=O)(O)O

fumonisin-B1: CCCCC(C)C(C(CC(C)CC(CCCCC(CC(C(C)N)O)O)O)OC(=O)CC(CC(=O)O)C(=O)O)OC(=O)CC(CC(=O)O)C(=O)O

aflatoxin-B1: COC1=C2C3=C(C(=O)CC3)C(=O)OC2=C4C5C=COC5OC4=C1

2,4,6-trichlorophenol: C1=C(C=C(C(=C1Cl)O)Cl)Cl

diazinon: CCOP(=S)(OCC)OC1=NC(=NC(=C1)C)C(C)C

paraquat: C[N+]1=CC=C(C=C1)C2=CC=[N+](C=C2)C

phenol: C1=CC=C(C=C1)O

aminomethylphosphonic acid: C(N)P(=O)(O)O

chlorpyriphos: CCOP(=S)(OCC)OC1=NC(=C(C=C1Cl)Cl)Cl

xearalenone: CC1CCCC(=O)CCCC=CC2=C(C(=CC(=C2)O)O)C(=O)O1

aldicarb: CC(C)(C=NOC(=O)NC)SC

Solution:

structure of chemical adsorption on montmorillonite clays molecules:

3,3′,4,4′,5-pentachlorobiphenyl: C1=CC(=C(C=C1C2=CC(=C(C(=C2)Cl)Cl)Cl)Cl)Cl

smiles_non_kekule:    Clc1ccc(-c2cc(Cl)c(Cl)c(Cl)c2)cc1Cl
smiles_kekule:    ClC1=C(Cl)C=C(C2=CC(Cl)=C(Cl)C(Cl)=C2)C=C1
inchi:    InChI=1S/C12H5Cl5/c13-8-2-1-6(3-9(8)14)7-4-10(15)12(17)11(16)5-7/h1-5H
inchiKey:    REHONNLQRWTIFF-UHFFFAOYSA-N
smarts:    [#6]1:[#6]:[#6](:[#6](:[#6]:[#6]:1-[#6]1:[#6]:[#6](:[#6](:[#6](:[#6]:1)-[#17])-[#17])-[#17])-[#17])-[#17]
smarts_isomeric:    [#6]1:[#6]:[#6](:[#6](:[#6]:[#6]:1-[#6]1:[#6]:[#6](:[#6](:[#6](:[#6]:1)-[#17])-[#17])-[#17])-[#17])-[#17]

3,4,3′,4′-tetrachlorobiphenyl: C1=CC(=C(C=C1C2=CC(=C(C=C2)Cl)Cl)Cl)Cl

smiles_non_kekule:    Clc1ccc(-c2ccc(Cl)c(Cl)c2)cc1Cl
smiles_kekule:    ClC1=C(Cl)C=C(C2=CC(Cl)=C(Cl)C=C2)C=C1
inchi:    InChI=1S/C12H6Cl4/c13-9-3-1-7(5-11(9)15)8-2-4-10(14)12(16)6-8/h1-6H
inchiKey:    UQMGJOKDKOLIDP-UHFFFAOYSA-N
smarts:    [#6]1:[#6]:[#6](:[#6](:[#6]:[#6]:1-[#6]1:[#6]:[#6](:[#6](:[#6]:[#6]:1)-[#17])-[#17])-[#17])-[#17]
smarts_isomeric:    [#6]1:[#6]:[#6](:[#6](:[#6]:[#6]:1-[#6]1:[#6]:[#6](:[#6](:[#6]:[#6]:1)-[#17])-[#17])-[#17])-[#17]

2,2′,4,4′,5,5′-hexachlorobiphenyl: C1=C(C(=CC(=C1Cl)Cl)Cl)C2=CC(=C(C=C2Cl)Cl)Cl

smiles_non_kekule:    Clc1cc(Cl)c(-c2cc(Cl)c(Cl)cc2Cl)cc1Cl
smiles_kekule:    ClC1=C(Cl)C=C(C2=CC(Cl)=C(Cl)C=C2Cl)C(Cl)=C1
inchi:    InChI=1S/C12H4Cl6/c13-7-3-11(17)9(15)1-5(7)6-2-10(16)12(18)4-8(6)14/h1-4H
inchiKey:    MVWHGTYKUMDIHL-UHFFFAOYSA-N
smarts:    [#6]1:[#6](:[#6](:[#6]:[#6](:[#6]:1-[#17])-[#17])-[#17])-[#6]1:[#6]:[#6](:[#6](:[#6]:[#6]:1-[#17])-[#17])-[#17]
smarts_isomeric:    [#6]1:[#6](:[#6](:[#6]:[#6](:[#6]:1-[#17])-[#17])-[#17])-[#6]1:[#6]:[#6](:[#6](:[#6]:[#6]:1-[#17])-[#17])-[#17]

bisphenol A: CC(C)(C1=CC=C(C=C1)O)C2=CC=C(C=C2)O

smiles_non_kekule:    CC(C)(c1ccc(O)cc1)c1ccc(O)cc1
smiles_kekule:    CC(C)(C1=CC=C(O)C=C1)C1=CC=C(O)C=C1
inchi:    InChI=1S/C15H16O2/c1-15(2,11-3-7-13(16)8-4-11)12-5-9-14(17)10-6-12/h3-10,16-17H,1-2H3
inchiKey:    IISBACLAFKSPIT-UHFFFAOYSA-N
smarts:    [#6]-[#6](-[#6])(-[#6]1:[#6]:[#6]:[#6](:[#6]:[#6]:1)-[#8])-[#6]1:[#6]:[#6]:[#6](:[#6]:[#6]:1)-[#8]
smarts_isomeric:    [#6]-[#6](-[#6])(-[#6]1:[#6]:[#6]:[#6](:[#6]:[#6]:1)-[#8])-[#6]1:[#6]:[#6]:[#6](:[#6]:[#6]:1)-[#8]

2,3,3′,4,4′,5′-hexachlorobiphenyl: C1=CC(=C(C=C1C2=CC(=C(C(=C2Cl)Cl)Cl)Cl)Cl)Cl

smiles_non_kekule:    Clc1ccc(-c2cc(Cl)c(Cl)c(Cl)c2Cl)cc1Cl
smiles_kekule:    ClC1=C(Cl)C=C(C2=CC(Cl)=C(Cl)C(Cl)=C2Cl)C=C1
inchi:    InChI=1S/C12H4Cl6/c13-7-2-1-5(3-8(7)14)6-4-9(15)11(17)12(18)10(6)16/h1-4H
inchiKey:    LCXMEXLGMKFLQO-UHFFFAOYSA-N
smarts:    [#6]1:[#6]:[#6](:[#6](:[#6]:[#6]:1-[#6]1:[#6]:[#6](:[#6](:[#6](:[#6]:1-[#17])-[#17])-[#17])-[#17])-[#17])-[#17]
smarts_isomeric:    [#6]1:[#6]:[#6](:[#6](:[#6]:[#6]:1-[#6]1:[#6]:[#6](:[#6](:[#6](:[#6]:1-[#17])-[#17])-[#17])-[#17])-[#17])-[#17]

2,2′,4,4′,6,6′-hexachlorobiphenyl: C1=C(C=C(C(=C1Cl)C2=CC(=C(C=C2Cl)Cl)Cl)Cl)Cl

smiles_non_kekule:    Clc1cc(Cl)c(-c2cc(Cl)c(Cl)cc2Cl)c(Cl)c1
smiles_kekule:    ClC1=CC(Cl)=C(C2=CC(Cl)=C(Cl)C=C2Cl)C(Cl)=C1
inchi:    InChI=1S/C12H4Cl6/c13-5-1-10(17)12(11(18)2-5)6-3-8(15)9(16)4-7(6)14/h1-4H
inchiKey:    QXZHEJWDLVUFFB-UHFFFAOYSA-N
smarts:    [#6]1:[#6](:[#6]:[#6](:[#6](:[#6]:1-[#17])-[#6]1:[#6]:[#6](:[#6](:[#6]:[#6]:1-[#17])-[#17])-[#17])-[#17])-[#17]
smarts_isomeric:    [#6]1:[#6](:[#6]:[#6](:[#6](:[#6]:1-[#17])-[#6]1:[#6]:[#6](:[#6](:[#6]:[#6]:1-[#17])-[#17])-[#17])-[#17])-[#17]

2,2′,4,4′,5,6′-hexachlorobiphenyl: C1=CC=C(C(=C1)C2=C(C(=C(C(=C2Cl)Cl)Cl)Cl)Cl)Cl

smiles_non_kekule:    Clc1ccccc1-c1c(Cl)c(Cl)c(Cl)c(Cl)c1Cl
smiles_kekule:    ClC1=CC=CC=C1C1=C(Cl)C(Cl)=C(Cl)C(Cl)=C1Cl
inchi:    InChI=1S/C12H4Cl6/c13-6-4-2-1-3-5(6)7-8(14)10(16)12(18)11(17)9(7)15/h1-4H
inchiKey:    RUEIBQJFGMERJD-UHFFFAOYSA-N
smarts:    [#6]1:[#6]:[#6]:[#6](:[#6](:[#6]:1)-[#6]1:[#6](:[#6](:[#6](:[#6](:[#6]:1-[#17])-[#17])-[#17])-[#17])-[#17])-[#17]
smarts_isomeric:    [#6]1:[#6]:[#6]:[#6](:[#6](:[#6]:1)-[#6]1:[#6](:[#6](:[#6](:[#6](:[#6]:1-[#17])-[#17])-[#17])-[#17])-[#17])-[#17]

lindane: C1(C(C(C(C(C1Cl)Cl)Cl)Cl)Cl)Cl

smiles_non_kekule:    ClC1C(Cl)C(Cl)C(Cl)C(Cl)C1Cl
smiles_kekule:    ClC1C(Cl)C(Cl)C(Cl)C(Cl)C1Cl
inchi:    InChI=1S/C6H6Cl6/c7-1-2(8)4(10)6(12)5(11)3(1)9/h1-6H
inchiKey:    JLYXXMFPNIAWKQ-UHFFFAOYSA-N
smarts:    [#6]1(-[#6](-[#6](-[#6](-[#6](-[#6]-1-[#17])-[#17])-[#17])-[#17])-[#17])-[#17]
smarts_isomeric:    [#6]1(-[#6](-[#6](-[#6](-[#6](-[#6]-1-[#17])-[#17])-[#17])-[#17])-[#17])-[#17]

naphthalene: C1=CC=C2C=CC=CC2=C1

smiles_non_kekule:    c1ccc2ccccc2c1
smiles_kekule:    C1=CC=C2C=CC=CC2=C1
inchi:    InChI=1S/C10H8/c1-2-6-10-8-4-3-7-9(10)5-1/h1-8H
inchiKey:    UFWIBTONFRDIAS-UHFFFAOYSA-N
smarts:    [#6]1:[#6]:[#6]:[#6]2:[#6]:[#6]:[#6]:[#6]:[#6]:2:[#6]:1
smarts_isomeric:    [#6]1:[#6]:[#6]:[#6]2:[#6]:[#6]:[#6]:[#6]:[#6]:2:[#6]:1

benz[e]acephenanthrylene: C1=CC=C2C3=C4C(=CC=C3)C5=CC=CC=C5C4=CC2=C1

smiles_non_kekule:    c1ccc2c(c1)-c1cccc3c1c-2cc1ccccc13
smiles_kekule:    C1=CC=C2C(=C1)C1=CC=CC3=C1C2=CC1=CC=CC=C13
inchi:    InChI=1S/C20H12/c1-2-7-14-13(6-1)12-19-16-9-4-3-8-15(16)18-11-5-10-17(14)20(18)19/h1-12H
inchiKey:    FTOVXSOBNPWTSH-UHFFFAOYSA-N
smarts:    [#6]1:[#6]:[#6]:[#6]2:[#6]3:[#6]4:[#6](:[#6]:[#6]:[#6]:3)-[#6]3:[#6]:[#6]:[#6]:[#6]:[#6]:3-[#6]:4:[#6]:[#6]:2:[#6]:1
smarts_isomeric:    [#6]1:[#6]:[#6]:[#6]2:[#6]3:[#6]4:[#6](:[#6]:[#6]:[#6]:3)-[#6]3:[#6]:[#6]:[#6]:[#6]:[#6]:3-[#6]:4:[#6]:[#6]:2:[#6]:1

dieldrin: C1C2C3C(C1C4C2O4)C5(C(=C(C3(C5(Cl)Cl)Cl)Cl)Cl)Cl

smiles_non_kekule:    ClC1=C(Cl)C2(Cl)C3C4CC(C5OC45)C3C1(Cl)C2(Cl)Cl
smiles_kekule:    ClC1=C(Cl)C2(Cl)C3C4CC(C5OC45)C3C1(Cl)C2(Cl)Cl
inchi:    InChI=1S/C12H8Cl6O/c13-8-9(14)11(16)5-3-1-2(6-7(3)19-6)4(5)10(8,15)12(11,17)18/h2-7H,1H2
inchiKey:    DFBKLUNHFCTMDC-UHFFFAOYSA-N
smarts:    [#6]1-[#6]2-[#6]3-[#6](-[#6]-1-[#6]1-[#6]-2-[#8]-1)-[#6]1(-[#6](=[#6](-[#6]-3(-[#6]-1(-[#17])-[#17])-[#17])-[#17])-[#17])-[#17]
smarts_isomeric:    [#6]1-[#6]2-[#6]3-[#6](-[#6]-1-[#6]1-[#6]-2-[#8]-1)-[#6]1(-[#6](=[#6](-[#6]-3(-[#6]-1(-[#17])-[#17])-[#17])-[#17])-[#17])-[#17]

linuron: CN(C(=O)NC1=CC(=C(C=C1)Cl)Cl)OC

smiles_non_kekule:    CON(C)C(=O)Nc1ccc(Cl)c(Cl)c1
smiles_kekule:    CON(C)C(=O)NC1=CC(Cl)=C(Cl)C=C1
inchi:    InChI=1S/C9H10Cl2N2O2/c1-13(15-2)9(14)12-6-3-4-7(10)8(11)5-6/h3-5H,1-2H3,(H,12,14)
inchiKey:    XKJMBINCVNINCA-UHFFFAOYSA-N
smarts:    [#6]-[#7](-[#6](=[#8])-[#7]-[#6]1:[#6]:[#6](:[#6](:[#6]:[#6]:1)-[#17])-[#17])-[#8]-[#6]
smarts_isomeric:    [#6]-[#7](-[#6](=[#8])-[#7]-[#6]1:[#6]:[#6](:[#6](:[#6]:[#6]:1)-[#17])-[#17])-[#8]-[#6]

trifluralin: CCCN(CCC)C1=C(C=C(C=C1[N+](=O)[O-])C(F)(F)F)[N+](=O)[O-]

smiles_non_kekule:    CCCN(CCC)c1c([N+](=O)[O-])cc(C(F)(F)F)cc1[N+](=O)[O-]
smiles_kekule:    CCCN(CCC)C1=C([N+](=O)[O-])C=C(C(F)(F)F)C=C1[N+](=O)[O-]
inchi:    InChI=1S/C13H16F3N3O4/c1-3-5-17(6-4-2)12-10(18(20)21)7-9(13(14,15)16)8-11(12)19(22)23/h7-8H,3-6H2,1-2H3
inchiKey:    ZSDSQXJSNMTJDA-UHFFFAOYSA-N
smarts:    [#6]-[#6]-[#6]-[#7](-[#6]-[#6]-[#6])-[#6]1:[#6](:[#6]:[#6](:[#6]:[#6]:1-[#7+](=[#8])-[#8-])-[#6](-[#9])(-[#9])-[#9])-[#7+](=[#8])-[#8-]
smarts_isomeric:    [#6]-[#6]-[#6]-[#7](-[#6]-[#6]-[#6])-[#6]1:[#6](:[#6]:[#6](:[#6]:[#6]:1-[#7+](=[#8])-[#8-])-[#6](-[#9])(-[#9])-[#9])-[#7+](=[#8])-[#8-]

toluene: CC1=CC=CC=C1

benzene: C1=CC=CC=C1

smiles_non_kekule:    c1ccccc1
smiles_kekule:    C1=CC=CC=C1
inchi:    InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H
inchiKey:    UHOVQNZJYSORNB-UHFFFAOYSA-N
smarts:    [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1
smarts_isomeric:    [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1

bisphenol S: C1=CC(=CC=C1O)S(=O)(=O)C2=CC=C(C=C2)O

smiles_non_kekule:    O=S(=O)(c1ccc(O)cc1)c1ccc(O)cc1
smiles_kekule:    O=S(=O)(C1=CC=C(O)C=C1)C1=CC=C(O)C=C1
inchi:    InChI=1S/C12H10O4S/c13-9-1-5-11(6-2-9)17(15,16)12-7-3-10(14)4-8-12/h1-8,13-14H
inchiKey:    VPWNQTHUCYMVMZ-UHFFFAOYSA-N
smarts:    [#6]1:[#6]:[#6](:[#6]:[#6]:[#6]:1-[#8])-[#16](=[#8])(=[#8])-[#6]1:[#6]:[#6]:[#6](:[#6]:[#6]:1)-[#8]
smarts_isomeric:    [#6]1:[#6]:[#6](:[#6]:[#6]:[#6]:1-[#8])-[#16](=[#8])(=[#8])-[#6]1:[#6]:[#6]:[#6](:[#6]:[#6]:1)-[#8]

bisphenol F: c1cc(ccc1Cc2ccc(cc2)O)O

smiles_non_kekule:    Oc1ccc(Cc2ccc(O)cc2)cc1
smiles_kekule:    OC1=CC=C(CC2=CC=C(O)C=C2)C=C1
inchi:    InChI=1S/C13H12O2/c14-12-5-1-10(2-6-12)9-11-3-7-13(15)8-4-11/h1-8,14-15H,9H2
inchiKey:    PXKLMJQFEQBVLD-UHFFFAOYSA-N
smarts:    [#6]1:[#6]:[#6](:[#6]:[#6]:[#6]:1-[#6]-[#6]1:[#6]:[#6]:[#6](:[#6]:[#6]:1)-[#8])-[#8]
smarts_isomeric:    [#6]1:[#6]:[#6](:[#6]:[#6]:[#6]:1-[#6]-[#6]1:[#6]:[#6]:[#6](:[#6]:[#6]:1)-[#8])-[#8]

benzo[a]pyrene: C1=CC=C2C3=C4C(=CC2=C1)C=CC5=C4C(=CC=C5)C=C3

smiles_non_kekule:    c1ccc2c(c1)cc1ccc3cccc4ccc2c1c34
smiles_kekule:    C1=CC=C2C(=C1)C=C1C=CC3=C4C(=CC=C3)C=CC2=C14
inchi:    InChI=1S/C20H12/c1-2-7-17-15(4-1)12-16-9-8-13-5-3-6-14-10-11-18(17)20(16)19(13)14/h1-12H
inchiKey:    FMMWHPNWAFZXNH-UHFFFAOYSA-N
smarts:    [#6]1:[#6]:[#6]:[#6]2:[#6]3:[#6]4:[#6](:[#6]:[#6]:2:[#6]:1):[#6]:[#6]:[#6]1:[#6]:4:[#6](:[#6]:[#6]:[#6]:1):[#6]:[#6]:3
smarts_isomeric:    [#6]1:[#6]:[#6]:[#6]2:[#6]3:[#6]4:[#6](:[#6]:[#6]:2:[#6]:1):[#6]:[#6]:[#6]1:[#6]:4:[#6](:[#6]:[#6]:[#6]:1):[#6]:[#6]:3

2,4-dichlorophenoxyacetic acid: C1=CC(=C(C=C1Cl)Cl)OCC(=O)O

smiles_non_kekule:    O=C(O)COc1ccc(Cl)cc1Cl
smiles_kekule:    O=C(O)COC1=C(Cl)C=C(Cl)C=C1
inchi:    InChI=1S/C8H6Cl2O3/c9-5-1-2-7(6(10)3-5)13-4-8(11)12/h1-3H,4H2,(H,11,12)
inchiKey:    OVSKIKFHRZPJSS-UHFFFAOYSA-N
smarts:    [#6]1:[#6]:[#6](:[#6](:[#6]:[#6]:1-[#17])-[#17])-[#8]-[#6]-[#6](=[#8])-[#8]
smarts_isomeric:    [#6]1:[#6]:[#6](:[#6](:[#6]:[#6]:1-[#17])-[#17])-[#8]-[#6]-[#6](=[#8])-[#8]

clofenotane (DDT): C1=CC(=CC=C1C(C2=CC=C(C=C2)Cl)C(Cl)(Cl)Cl)Cl

smiles_non_kekule:    Clc1ccc(C(c2ccc(Cl)cc2)C(Cl)(Cl)Cl)cc1
smiles_kekule:    ClC1=CC=C(C(C2=CC=C(Cl)C=C2)C(Cl)(Cl)Cl)C=C1
inchi:    InChI=1S/C14H9Cl5/c15-11-5-1-9(2-6-11)13(14(17,18)19)10-3-7-12(16)8-4-10/h1-8,13H
inchiKey:    YVGGHNCTFXOJCH-UHFFFAOYSA-N
smarts:    [#6]1:[#6]:[#6](:[#6]:[#6]:[#6]:1-[#6](-[#6]1:[#6]:[#6]:[#6](:[#6]:[#6]:1)-[#17])-[#6](-[#17])(-[#17])-[#17])-[#17]
smarts_isomeric:    [#6]1:[#6]:[#6](:[#6]:[#6]:[#6]:1-[#6](-[#6]1:[#6]:[#6]:[#6](:[#6]:[#6]:1)-[#17])-[#6](-[#17])(-[#17])-[#17])-[#17]

pyrene: C1=CC2=C3C(=C1)C=CC4=CC=CC(=C43)C=C2

smiles_non_kekule:    c1cc2ccc3cccc4ccc(c1)c2c34
smiles_kekule:    C1=CC2=C3C(=C1)C=CC1=CC=CC(=C13)C=C2
inchi:    InChI=1S/C16H10/c1-3-11-7-9-13-5-2-6-14-10-8-12(4-1)15(11)16(13)14/h1-10H
inchiKey:    BBEAQIROQSPTKN-UHFFFAOYSA-N
smarts:    [#6]1:[#6]:[#6]2:[#6]3:[#6](:[#6]:1):[#6]:[#6]:[#6]1:[#6]:[#6]:[#6]:[#6](:[#6]:3:1):[#6]:[#6]:2
smarts_isomeric:    [#6]1:[#6]:[#6]2:[#6]3:[#6](:[#6]:1):[#6]:[#6]:[#6]1:[#6]:[#6]:[#6]:[#6](:[#6]:3:1):[#6]:[#6]:2

deoxynivalenol (vomitoxin): CC1=CC2C(C(C1=O)O)(C3(CC(C(C34CO4)O2)O)C)CO

smiles_non_kekule:    CC1=CC2OC3C(O)CC(C)(C34CO4)C2(CO)C(O)C1=O
smiles_kekule:    CC1=CC2OC3C(O)CC(C)(C34CO4)C2(CO)C(O)C1=O
inchi:    InChI=1S/C15H20O6/c1-7-3-9-14(5-16,11(19)10(7)18)13(2)4-8(17)12(21-9)15(13)6-20-15/h3,8-9,11-12,16-17,19H,4-6H2,1-2H3
inchiKey:    LINOMUASTDIRTM-UHFFFAOYSA-N
smarts:    [#6]-[#6]1=[#6]-[#6]2-[#6](-[#6](-[#6]-1=[#8])-[#8])(-[#6]1(-[#6]-[#6](-[#6](-[#6]-13-[#6]-[#8]-3)-[#8]-2)-[#8])-[#6])-[#6]-[#8]
smarts_isomeric:    [#6]-[#6]1=[#6]-[#6]2-[#6](-[#6](-[#6]-1=[#8])-[#8])(-[#6]1(-[#6]-[#6](-[#6](-[#6]-13-[#6]-[#8]-3)-[#8]-2)-[#8])-[#6])-[#6]-[#8]

glyphosate: C(C(=O)O)NCP(=O)(O)O

smiles_non_kekule:    O=C(O)CNCP(=O)(O)O
smiles_kekule:    O=C(O)CNCP(=O)(O)O
inchi:    InChI=1S/C3H8NO5P/c5-3(6)1-4-2-10(7,8)9/h4H,1-2H2,(H,5,6)(H2,7,8,9)
inchiKey:    XDDAORKBJWWYJS-UHFFFAOYSA-N
smarts:    [#6](-[#6](=[#8])-[#8])-[#7]-[#6]-[#15](=[#8])(-[#8])-[#8]
smarts_isomeric:    [#6](-[#6](=[#8])-[#8])-[#7]-[#6]-[#15](=[#8])(-[#8])-[#8]

fumonisin-B1: CCCCC(C)C(C(CC(C)CC(CCCCC(CC(C(C)N)O)O)O)OC(=O)CC(CC(=O)O)C(=O)O)OC(=O)CC(CC(=O)O)C(=O)O

smiles_non_kekule:    CCCCC(C)C(OC(=O)CC(CC(=O)O)C(=O)O)C(CC(C)CC(O)CCCCC(O)CC(O)C(C)N)OC(=O)CC(CC(=O)O)C(=O)O
smiles_kekule:    CCCCC(C)C(OC(=O)CC(CC(=O)O)C(=O)O)C(CC(C)CC(O)CCCCC(O)CC(O)C(C)N)OC(=O)CC(CC(=O)O)C(=O)O
inchi:    InChI=1S/C34H59NO15/c1-5-6-9-20(3)32(50-31(44)17-23(34(47)48)15-29(41)42)27(49-30(43)16-22(33(45)46)14-28(39)40)13-19(2)12-24(36)10-7-8-11-25(37)18-26(38)21(4)35/h19-27,32,36-38H,5-18,35H2,1-4H3,(H,39,40)(H,41,42)(H,45,46)(H,47,48)
inchiKey:    UVBUBMSSQKOIBE-UHFFFAOYSA-N
smarts:    [#6]-[#6]-[#6]-[#6]-[#6](-[#6])-[#6](-[#6](-[#6]-[#6](-[#6])-[#6]-[#6](-[#6]-[#6]-[#6]-[#6]-[#6](-[#6]-[#6](-[#6](-[#6])-[#7])-[#8])-[#8])-[#8])-[#8]-[#6](=[#8])-[#6]-[#6](-[#6]-[#6](=[#8])-[#8])-[#6](=[#8])-[#8])-[#8]-[#6](=[#8])-[#6]-[#6](-[#6]-[#6](=[#8])-[#8])-[#6](=[#8])-[#8]
smarts_isomeric:    [#6]-[#6]-[#6]-[#6]-[#6](-[#6])-[#6](-[#6](-[#6]-[#6](-[#6])-[#6]-[#6](-[#6]-[#6]-[#6]-[#6]-[#6](-[#6]-[#6](-[#6](-[#6])-[#7])-[#8])-[#8])-[#8])-[#8]-[#6](=[#8])-[#6]-[#6](-[#6]-[#6](=[#8])-[#8])-[#6](=[#8])-[#8])-[#8]-[#6](=[#8])-[#6]-[#6](-[#6]-[#6](=[#8])-[#8])-[#6](=[#8])-[#8]

aflatoxin-B1: COC1=C2C3=C(C(=O)CC3)C(=O)OC2=C4C5C=COC5OC4=C1

smiles_non_kekule:    COc1cc2c(c3oc(=O)c4c(c13)CCC4=O)C1C=COC1O2
smiles_kekule:    COC1=C2C3=C(C(=O)CC3)C(=O)OC2=C2C(=C1)OC1OC=CC21
inchi:    InChI=1S/C17H12O6/c1-20-10-6-11-14(8-4-5-21-17(8)22-11)15-13(10)7-2-3-9(18)12(7)16(19)23-15/h4-6,8,17H,2-3H2,1H3
inchiKey:    OQIQSTLJSLGHID-UHFFFAOYSA-N
smarts:    [#6]-[#8]-[#6]1:[#6]2:[#6]3:[#6](-[#6](=[#8])-[#6]-[#6]-3):[#6](=[#8]):[#8]:[#6]:2:[#6]2-[#6]3-[#6]=[#6]-[#8]-[#6]-3-[#8]-[#6]:2:[#6]:1
smarts_isomeric:    [#6]-[#8]-[#6]1:[#6]2:[#6]3:[#6](-[#6](=[#8])-[#6]-[#6]-3):[#6](=[#8]):[#8]:[#6]:2:[#6]2-[#6]3-[#6]=[#6]-[#8]-[#6]-3-[#8]-[#6]:2:[#6]:1

2,4,6-trichlorophenol: C1=C(C=C(C(=C1Cl)O)Cl)Cl

smiles_non_kekule:    Oc1c(Cl)cc(Cl)cc1Cl
smiles_kekule:    OC1=C(Cl)C=C(Cl)C=C1Cl
inchi:    InChI=1S/C6H3Cl3O/c7-3-1-4(8)6(10)5(9)2-3/h1-2,10H
inchiKey:    LINPIYWFGCPVIE-UHFFFAOYSA-N
smarts:    [#6]1:[#6](:[#6]:[#6](:[#6](:[#6]:1-[#17])-[#8])-[#17])-[#17]
smarts_isomeric:    [#6]1:[#6](:[#6]:[#6](:[#6](:[#6]:1-[#17])-[#8])-[#17])-[#17]

diazinon: CCOP(=S)(OCC)OC1=NC(=NC(=C1)C)C(C)C

smiles_non_kekule:    CCOP(=S)(OCC)Oc1cc(C)nc(C(C)C)n1
smiles_kekule:    CCOP(=S)(OCC)OC1=NC(C(C)C)=NC(C)=C1
inchi:    InChI=1S/C12H21N2O3PS/c1-6-15-18(19,16-7-2)17-11-8-10(5)13-12(14-11)9(3)4/h8-9H,6-7H2,1-5H3
inchiKey:    FHIVAFMUCKRCQO-UHFFFAOYSA-N
smarts:    [#6]-[#6]-[#8]-[#15](=[#16])(-[#8]-[#6]-[#6])-[#8]-[#6]1:[#7]:[#6](:[#7]:[#6](:[#6]:1)-[#6])-[#6](-[#6])-[#6]
smarts_isomeric:    [#6]-[#6]-[#8]-[#15](=[#16])(-[#8]-[#6]-[#6])-[#8]-[#6]1:[#7]:[#6](:[#7]:[#6](:[#6]:1)-[#6])-[#6](-[#6])-[#6]

paraquat: C[N+]1=CC=C(C=C1)C2=CC=[N+](C=C2)C

smiles_non_kekule:    C[n+]1ccc(-c2cc[n+](C)cc2)cc1
smiles_kekule:    C[N+]1=CC=C(C2=CC=[N+](C)C=C2)C=C1
inchi:    InChI=1S/C12H14N2/c1-13-7-3-11(4-8-13)12-5-9-14(2)10-6-12/h3-10H,1-2H3/q+2
inchiKey:    INFDPOAKFNIJBF-UHFFFAOYSA-N
smarts:    [#6]-[#7+]1:[#6]:[#6]:[#6](:[#6]:[#6]:1)-[#6]1:[#6]:[#6]:[#7+](:[#6]:[#6]:1)-[#6]
smarts_isomeric:    [#6]-[#7+]1:[#6]:[#6]:[#6](:[#6]:[#6]:1)-[#6]1:[#6]:[#6]:[#7+](:[#6]:[#6]:1)-[#6]

phenol: C1=CC=C(C=C1)O

smiles_non_kekule:    Oc1ccccc1
smiles_kekule:    OC1=CC=CC=C1
inchi:    InChI=1S/C6H6O/c7-6-4-2-1-3-5-6/h1-5,7H
inchiKey:    ISWSIDIOOBJBQZ-UHFFFAOYSA-N
smarts:    [#6]1:[#6]:[#6]:[#6](:[#6]:[#6]:1)-[#8]
smarts_isomeric:    [#6]1:[#6]:[#6]:[#6](:[#6]:[#6]:1)-[#8]

aminomethylphosphonic acid: C(N)P(=O)(O)O

smiles_non_kekule:    NCP(=O)(O)O
smiles_kekule:    NCP(=O)(O)O
inchi:    InChI=1S/CH6NO3P/c2-1-6(3,4)5/h1-2H2,(H2,3,4,5)
inchiKey:    MGRVRXRGTBOSHW-UHFFFAOYSA-N
smarts:    [#6](-[#7])-[#15](=[#8])(-[#8])-[#8]
smarts_isomeric:    [#6](-[#7])-[#15](=[#8])(-[#8])-[#8]

chlorpyriphos: CCOP(=S)(OCC)OC1=NC(=C(C=C1Cl)Cl)Cl

smiles_non_kekule:    CCOP(=S)(OCC)Oc1nc(Cl)c(Cl)cc1Cl
smiles_kekule:    CCOP(=S)(OCC)OC1=NC(Cl)=C(Cl)C=C1Cl
inchi:    InChI=1S/C9H11Cl3NO3PS/c1-3-14-17(18,15-4-2)16-9-7(11)5-6(10)8(12)13-9/h5H,3-4H2,1-2H3
inchiKey:    SBPBAQFWLVIOKP-UHFFFAOYSA-N
smarts:    [#6]-[#6]-[#8]-[#15](=[#16])(-[#8]-[#6]-[#6])-[#8]-[#6]1:[#7]:[#6](:[#6](:[#6]:[#6]:1-[#17])-[#17])-[#17]
smarts_isomeric:    [#6]-[#6]-[#8]-[#15](=[#16])(-[#8]-[#6]-[#6])-[#8]-[#6]1:[#7]:[#6](:[#6](:[#6]:[#6]:1-[#17])-[#17])-[#17]

xearalenone: CC1CCCC(=O)CCCC=CC2=C(C(=CC(=C2)O)O)C(=O)O1

smiles_non_kekule:    CC1CCCC(=O)CCCC=Cc2cc(O)cc(O)c2C(=O)O1
smiles_kekule:    CC1CCCC(=O)CCCC=CC2=C(C(=O)O1)C(O)=CC(O)=C2
inchi:    InChI=1S/C18H22O5/c1-12-6-5-9-14(19)8-4-2-3-7-13-10-15(20)11-16(21)17(13)18(22)23-12/h3,7,10-12,20-21H,2,4-6,8-9H2,1H3
inchiKey:    MBMQEIFVQACCCH-UHFFFAOYSA-N
smarts:    [#6]-[#6]1-[#6]-[#6]-[#6]-[#6](=[#8])-[#6]-[#6]-[#6]-[#6]=[#6]-[#6]2:[#6](:[#6](:[#6]:[#6](:[#6]:2)-[#8])-[#8])-[#6](=[#8])-[#8]-1
smarts_isomeric:    [#6]-[#6]1-[#6]-[#6]-[#6]-[#6](=[#8])-[#6]-[#6]-[#6]-[#6]=[#6]-[#6]2:[#6](:[#6](:[#6]:[#6](:[#6]:2)-[#8])-[#8])-[#6](=[#8])-[#8]-1

aldicarb: CC(C)(C=NOC(=O)NC)SC

smiles_non_kekule:    CNC(=O)ON=CC(C)(C)SC
smiles_kekule:    CNC(=O)ON=CC(C)(C)SC
inchi:    InChI=1S/C7H14N2O2S/c1-7(2,12-4)5-9-11-6(10)8-3/h5H,1-4H3,(H,8,10)
inchiKey:    QGLZXHRNAYXIBU-UHFFFAOYSA-N
smarts:    [#6]-[#6](-[#6])(-[#6]=[#7]-[#8]-[#6](=[#8])-[#7]-[#6])-[#16]-[#6]
smarts_isomeric:    [#6]-[#6](-[#6])(-[#6]=[#7]-[#8]-[#6](=[#8])-[#7]-[#6])-[#16]-[#6]

problem_type: 7/25 (loop 0/0)

Problem Template: _problem_common_amino_acid_protecting_groups

[15:16:45] WARNING: Charges were rearranged

Write structure of common amino acid protecting groups molecules.

Answer:

structure of common amino acid protecting groups molecules:

tert-butyloxycarbonyl: O=COC(C)(C)C

trityl: C(C1=CC=CC=C1)(C2=CC=CC=C2)C3=CC=CC=C3

3,5-dimethoxyphenylisoproxycarbonyl: COC1=CC(C(C)(OC=O)C)=CC(OC)=C1

2-(4-biphenyl)isopropoxycarbonyl: CC(C)(OC=O)C(C=C1)=CC=C1C2=CC=CC=C2

2-nitrophenylsulfenyl: SC1=CC=CC=C1[N+]([O-])=O

Solution:

structure of common amino acid protecting groups molecules:

tert-butyloxycarbonyl: O=COC(C)(C)C

smiles_non_kekule:    CC(C)(C)OC=O
smiles_kekule:    CC(C)(C)OC=O
inchi:    InChI=1S/C5H10O2/c1-5(2,3)7-4-6/h4H,1-3H3
inchiKey:    RUPAXCPQAAOIPB-UHFFFAOYSA-N
smarts:    [#8]=[#6]-[#8]-[#6](-[#6])(-[#6])-[#6]
smarts_isomeric:    [#8]=[#6]-[#8]-[#6](-[#6])(-[#6])-[#6]

trityl: C(C1=CC=CC=C1)(C2=CC=CC=C2)C3=CC=CC=C3

smiles_non_kekule:    c1ccc(C(c2ccccc2)c2ccccc2)cc1
smiles_kekule:    C1=CC=C(C(C2=CC=CC=C2)C2=CC=CC=C2)C=C1
inchi:    InChI=1S/C19H16/c1-4-10-16(11-5-1)19(17-12-6-2-7-13-17)18-14-8-3-9-15-18/h1-15,19H
inchiKey:    AAAQKTZKLRYKHR-UHFFFAOYSA-N
smarts:    [#6](-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1)(-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1)-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1
smarts_isomeric:    [#6](-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1)(-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1)-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1

3,5-dimethoxyphenylisoproxycarbonyl: COC1=CC(C(C)(OC=O)C)=CC(OC)=C1

smiles_non_kekule:    COc1cc(OC)cc(C(C)(C)OC=O)c1
smiles_kekule:    COC1=CC(C(C)(C)OC=O)=CC(OC)=C1
inchi:    InChI=1S/C12H16O4/c1-12(2,16-8-13)9-5-10(14-3)7-11(6-9)15-4/h5-8H,1-4H3
inchiKey:    LROBWYQGENSLEK-UHFFFAOYSA-N
smarts:    [#6]-[#8]-[#6]1:[#6]:[#6](-[#6](-[#6])(-[#8]-[#6]=[#8])-[#6]):[#6]:[#6](-[#8]-[#6]):[#6]:1
smarts_isomeric:    [#6]-[#8]-[#6]1:[#6]:[#6](-[#6](-[#6])(-[#8]-[#6]=[#8])-[#6]):[#6]:[#6](-[#8]-[#6]):[#6]:1

2-(4-biphenyl)isopropoxycarbonyl: CC(C)(OC=O)C(C=C1)=CC=C1C2=CC=CC=C2

smiles_non_kekule:    CC(C)(OC=O)c1ccc(-c2ccccc2)cc1
smiles_kekule:    CC(C)(OC=O)C1=CC=C(C2=CC=CC=C2)C=C1
inchi:    InChI=1S/C16H16O2/c1-16(2,18-12-17)15-10-8-14(9-11-15)13-6-4-3-5-7-13/h3-12H,1-2H3
inchiKey:    VXLGMNUZTLZKHW-UHFFFAOYSA-N
smarts:    [#6]-[#6](-[#6])(-[#8]-[#6]=[#8])-[#6]1:[#6]:[#6]:[#6](:[#6]:[#6]:1)-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1
smarts_isomeric:    [#6]-[#6](-[#6])(-[#8]-[#6]=[#8])-[#6]1:[#6]:[#6]:[#6](:[#6]:[#6]:1)-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1

2-nitrophenylsulfenyl: SC1=CC=CC=C1[N+]([O-])=O

smiles_non_kekule:    O=[N+]([O-])c1ccccc1S
smiles_kekule:    O=[N+]([O-])C1=CC=CC=C1S
inchi:    InChI=1S/C6H5NO2S/c8-7(9)5-3-1-2-4-6(5)10/h1-4,10H
inchiKey:    JKIFPWHZEZQCQA-UHFFFAOYSA-N
smarts:    [#16]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#7+](-[#8-])=[#8]
smarts_isomeric:    [#16]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#7+](-[#8-])=[#8]

problem_type: 8/25 (loop 0/0)

Problem Template: _problem_common_electrophilic_warheads_for_kinases

[15:16:47] SMILES Parse Error: syntax error while parsing: C/C=N/\/NC(OC(C)(C)C)=O
[15:16:47] SMILES Parse Error: Failed parsing SMILES 'C/C=N/\/NC(OC(C)(C)C)=O' for input: 'C/C=N/\/NC(OC(C)(C)C)=O'
[15:16:47] WARNING: Omitted undefined stereo

[15:16:47] WARNING: Omitted undefined stereo

[15:16:47] WARNING: Omitted undefined stereo

Write structure of common electrophilic warheads for kinases molecules.

Answer:

structure of common electrophilic warheads for kinases molecules:

methylacrylamide: CNC(C=C)=O

methyl acrylate: COC(C=C)=O

methyl propiolate: COC(C#C)=O

2-cyanoacrylamide: N#CC(C(N)=O)=C

n-methylmaleimide: CN1C(C=CC1=O)=O

n-ethylmaleimide: O=C(C=CC1=O)N1CC

crotonamide: C/C=C/C(N)=O

ethyl crotonate: C/C=C/C(OCC)=O

crotononitrile: C/C=C/C#N

methyl methylpropiolate: CC#CC(OC)=O

isothiocyanatomethane: CN=C=S

isothiocyanatoethane: CCN=C=S

prop-1-ene: CC=C

prop-1-yne: CC#C

acetonitrile: CC#N

n-methylchloroacetamide: CNC(CCl)=O

n-methyl-2-chloropropanamide: CNC(C(C)Cl)=O

n-methyl-2-bromopropanamide: CNC(C(C)Br)=O

bromoacetone: CC(CBr)=O

2-methyloxirane: CC1OC1

fluoromethane: CF

methylsulfane: CS

aldehyde: CC=O

Solution:

structure of common electrophilic warheads for kinases molecules:

methylacrylamide: CNC(C=C)=O

smiles_non_kekule:    C=CC(=O)NC
smiles_kekule:    C=CC(=O)NC
inchi:    InChI=1S/C4H7NO/c1-3-4(6)5-2/h3H,1H2,2H3,(H,5,6)
inchiKey:    YPHQUSNPXDGUHL-UHFFFAOYSA-N
smarts:    [#6]-[#7]-[#6](-[#6]=[#6])=[#8]
smarts_isomeric:    [#6]-[#7]-[#6](-[#6]=[#6])=[#8]

methyl acrylate: COC(C=C)=O

smiles_non_kekule:    C=CC(=O)OC
smiles_kekule:    C=CC(=O)OC
inchi:    InChI=1S/C4H6O2/c1-3-4(5)6-2/h3H,1H2,2H3
inchiKey:    BAPJBEWLBFYGME-UHFFFAOYSA-N
smarts:    [#6]-[#8]-[#6](-[#6]=[#6])=[#8]
smarts_isomeric:    [#6]-[#8]-[#6](-[#6]=[#6])=[#8]

methyl propiolate: COC(C#C)=O

smiles_non_kekule:    C#CC(=O)OC
smiles_kekule:    C#CC(=O)OC
inchi:    InChI=1S/C4H4O2/c1-3-4(5)6-2/h1H,2H3
inchiKey:    IMAKHNTVDGLIRY-UHFFFAOYSA-N
smarts:    [#6]-[#8]-[#6](-[#6]#[#6])=[#8]
smarts_isomeric:    [#6]-[#8]-[#6](-[#6]#[#6])=[#8]

2-cyanoacrylamide: N#CC(C(N)=O)=C

smiles_non_kekule:    C=C(C#N)C(N)=O
smiles_kekule:    C=C(C#N)C(N)=O
inchi:    InChI=1S/C4H4N2O/c1-3(2-5)4(6)7/h1H2,(H2,6,7)
inchiKey:    HGBFVOSZYVRIHY-UHFFFAOYSA-N
smarts:    [#7]#[#6]-[#6](-[#6](-[#7])=[#8])=[#6]
smarts_isomeric:    [#7]#[#6]-[#6](-[#6](-[#7])=[#8])=[#6]

n-methylmaleimide: CN1C(C=CC1=O)=O

smiles_non_kekule:    CN1C(=O)C=CC1=O
smiles_kekule:    CN1C(=O)C=CC1=O
inchi:    InChI=1S/C5H5NO2/c1-6-4(7)2-3-5(6)8/h2-3H,1H3
inchiKey:    SEEYREPSKCQBBF-UHFFFAOYSA-N
smarts:    [#6]-[#7]1-[#6](-[#6]=[#6]-[#6]-1=[#8])=[#8]
smarts_isomeric:    [#6]-[#7]1-[#6](-[#6]=[#6]-[#6]-1=[#8])=[#8]