# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 04:35:17 2020
#   Inital geometry file: a 143 line input string
#   Ligand name: (2~{S})-2-[4-(4,4-dimethylcyclohexen-1-yl)-2-methyl-5-pyridin-2-yl-thiophen-3-yl]-2-[(2-methylpropan-2-yl)oxy]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1sc(c2ccccn2)c(C3=CCC(C)(C)CC3)c1[C@H](OC(C)(C)C)C(O)=O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 9VK  9VK  '(2~{S})-2-[4-(4,4-dimethylcyclohexen-1-yl)-2-methyl-5-pyridin-2-yl-thiophen-3-yl]-2-[(2-methylpropan-2-yl)oxy]ethanoic acid'  ligand  59  29  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9VK
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 9VK  O4   O  OC    -1  -0.600   2.0834  -0.0706  -2.8182
 9VK  C3   C  C      0   0.397   2.8349   0.2920  -1.8873
 9VK  O5   O  O      0  -0.583   3.9783   0.7591  -1.9887
 9VK  C1   C  CH1    0  -0.154   2.2149   0.1381  -0.4733
 9VK  O2   O  O2     0  -0.492   3.1096   0.4032   0.5796
 9VK  C6   C  CT     0   0.205   3.7587  -0.6912   1.2162
 9VK  C9   C  CH3    0  -0.681   4.4585  -1.6230   0.2265
 9VK  C8   C  CH3    0  -0.658   4.7990  -0.0398   2.1208
 9VK  C7   C  CH3    0  -0.663   2.7655  -1.4853   2.0690
 9VK  C22  C  CR5    0   0.199   1.0379   1.0713  -0.3295
 9VK  C23  C  CR5    0   0.175  -0.3114   0.6278  -0.1364
 9VK  C26  C  C      0   0.034  -0.6771  -0.8042  -0.0833
 9VK  C25  C  CH2    0  -0.529  -0.8396  -1.5123  -1.3972
 9VK  C27  C  C1     0  -0.250  -0.8088  -1.4347   1.0826
 9VK  C28  C  CH2    0  -0.436  -1.1340  -2.8918   1.2151
 9VK  C29  C  CT     0  -0.092  -1.6624  -3.5230  -0.0790
 9VK  C54  C  CH3    0  -0.670  -3.1201  -3.1133  -0.2959
 9VK  C53  C  CH3    0  -0.643  -1.5773  -5.0437   0.0197
 9VK  C24  C  CH2    0  -0.408  -0.7958  -3.0266  -1.2409
 9VK  C21  C  CR5    0  -0.322  -1.1931   1.6666   0.0136
 9VK  S43  S  S2     0   0.204  -0.3716   3.1834  -0.0721
 9VK  C20  C  CR5    0  -0.241   1.1562   2.4341  -0.3148
 9VK  C34  C  CH3    0  -0.722   2.3680   3.2828  -0.5182
 9VK  C35  C  CR6    0   0.205  -2.6424   1.6335   0.2193
 9VK  C39  C  CR16   0  -0.340  -3.2799   2.6076   0.9935
 9VK  C38  C  CR16   0  -0.158  -4.6541   2.5531   1.1462
 9VK  C37  C  CR16   0  -0.324  -5.3569   1.5240   0.5374
 9VK  C40  C  CR16   0  -0.078  -4.6365   0.5991  -0.2039
 9VK  N36  N  N      0  -0.406  -3.3226   0.6496  -0.3690
 9VK  H2   H  HCH1   0   0.223   1.8251  -0.8851  -0.4090
 9VK  H3   H  HCH3   0   0.239   5.1350  -1.0693  -0.4230
 9VK  H4   H  HCH3   0   0.226   5.0382  -2.3705   0.7710
 9VK  H5   H  HCH3   0   0.218   3.7513  -2.1655  -0.4041
 9VK  H6   H  HCH3   0   0.224   4.3276   0.6348   2.8383
 9VK  H7   H  HCH3   0   0.216   5.3482  -0.7952   2.6833
 9VK  H8   H  HCH3   0   0.228   5.5183   0.5349   1.5351
 9VK  H9   H  HCH3   0   0.234   1.9854  -1.9545   1.4664
 9VK  H10  H  HCH3   0   0.221   3.2806  -2.2788   2.6138
 9VK  H11  H  HCH3   0   0.222   2.2768  -0.8395   2.8010
 9VK  H12  H  HCH2   0   0.241  -1.7868  -1.1875  -1.8412
 9VK  H13  H  HCH2   0   0.254  -0.0546  -1.1805  -2.0827
 9VK  H14  H  H      0   0.220  -0.6505  -0.8802   2.0026
 9VK  H15  H  HCH2   0   0.231  -0.2325  -3.4252   1.5445
 9VK  H16  H  HCH2   0   0.228  -1.8630  -3.0345   2.0206
 9VK  H17  H  HCH3   0   0.217  -3.7560  -3.5165   0.4957
 9VK  H18  H  HCH3   0   0.261  -3.2377  -2.0293  -0.2978
 9VK  H19  H  HCH3   0   0.215  -3.4970  -3.4943  -1.2487
 9VK  H20  H  HCH3   0   0.220  -2.1580  -5.4167   0.8669
 9VK  H21  H  HCH3   0   0.220  -1.9665  -5.5201  -0.8835
 9VK  H22  H  HCH3   0   0.218  -0.5455  -5.3777   0.1520
 9VK  H23  H  HCH2   0   0.220  -1.1111  -3.5061  -2.1731
 9VK  H24  H  HCH2   0   0.215   0.2406  -3.3402  -1.0673
 9VK  H25  H  HCH3   0   0.248   2.5300   3.4889  -1.5777
 9VK  H26  H  HCH3   0   0.240   2.2749   4.2420  -0.0091
 9VK  H27  H  HCH3   0   0.268   3.2548   2.7790  -0.1453
 9VK  H28  H  HCR6   0   0.266  -2.7078   3.3869   1.4802
 9VK  H29  H  HCR6   0   0.273  -5.1665   3.2986   1.7398
 9VK  H30  H  HCR6   0   0.269  -6.4304   1.4371   0.6311
 9VK  H31  H  HCR6   0   0.258  -5.1485  -0.2205  -0.6968

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 9VK  O5   C3   deloc     1.239  0.020  1.239
 9VK  C24  C25  single    1.523  0.020  1.523
 9VK  C24  C29  single    1.532  0.020  1.532
 9VK  C25  C26  single    1.501  0.020  1.501
 9VK  O4   C3   deloc     1.250  0.020  1.250
 9VK  C54  C29  single    1.530  0.020  1.530
 9VK  C3   C1   single    1.552  0.020  1.552
 9VK  C29  C53  single    1.526  0.020  1.526
 9VK  C29  C28  single    1.534  0.020  1.534
 9VK  C39  C38  aromatic  1.384  0.020  1.384
 9VK  C39  C35  aromatic  1.398  0.020  1.398
 9VK  C38  C37  aromatic  1.387  0.020  1.387
 9VK  C26  C23  single    1.479  0.020  1.479
 9VK  C26  C27  double    1.332  0.020  1.332
 9VK  C1   C22  single    1.509  0.020  1.509
 9VK  C1   O2   single    1.407  0.020  1.407
 9VK  C28  C27  single    1.499  0.020  1.499
 9VK  C23  C22  aromatic  1.433  0.020  1.433
 9VK  C23  C21  aromatic  1.371  0.020  1.371
 9VK  C22  C20  aromatic  1.368  0.020  1.368
 9VK  C21  C35  single    1.464  0.020  1.464
 9VK  C21  S43  aromatic  1.727  0.020  1.727
 9VK  C35  N36  aromatic  1.333  0.020  1.333
 9VK  C20  C34  single    1.493  0.020  1.493
 9VK  C20  S43  aromatic  1.719  0.020  1.719
 9VK  C37  C40  aromatic  1.387  0.020  1.387
 9VK  O2   C6   single    1.423  0.020  1.423
 9VK  N36  C40  aromatic  1.325  0.020  1.325
 9VK  C7   C6   single    1.531  0.020  1.531
 9VK  C6   C9   single    1.529  0.020  1.529
 9VK  C6   C8   single    1.525  0.020  1.525
 9VK  C1   H2   single    0.970  0.020  1.090
 9VK  C9   H3   single    0.970  0.020  1.090
 9VK  C9   H4   single    0.970  0.020  1.090
 9VK  C9   H5   single    0.970  0.020  1.090
 9VK  C8   H6   single    0.970  0.020  1.090
 9VK  C8   H7   single    0.970  0.020  1.090
 9VK  C8   H8   single    0.970  0.020  1.090
 9VK  C7   H9   single    0.970  0.020  1.090
 9VK  C7   H10  single    0.970  0.020  1.090
 9VK  C7   H11  single    0.970  0.020  1.090
 9VK  C25  H12  single    0.970  0.020  1.090
 9VK  C25  H13  single    0.970  0.020  1.090
 9VK  C27  H14  single    0.930  0.020  1.080
 9VK  C28  H15  single    0.970  0.020  1.090
 9VK  C28  H16  single    0.970  0.020  1.090
 9VK  C54  H17  single    0.970  0.020  1.090
 9VK  C54  H18  single    0.970  0.020  1.090
 9VK  C54  H19  single    0.970  0.020  1.090
 9VK  C53  H20  single    0.970  0.020  1.090
 9VK  C53  H21  single    0.970  0.020  1.090
 9VK  C53  H22  single    0.970  0.020  1.090
 9VK  C24  H23  single    0.970  0.020  1.090
 9VK  C24  H24  single    0.970  0.020  1.090
 9VK  C34  H25  single    0.970  0.020  1.090
 9VK  C34  H26  single    0.970  0.020  1.090
 9VK  C34  H27  single    0.970  0.020  1.090
 9VK  C39  H28  single    0.930  0.020  1.080
 9VK  C38  H29  single    0.930  0.020  1.080
 9VK  C37  H30  single    0.930  0.020  1.080
 9VK  C40  H31  single    0.930  0.020  1.080

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 9VK  C1   C3   O5   118.72  3.000
 9VK  C1   C3   O4   114.19  3.000
 9VK  O5   C3   O4   127.08  3.000
 9VK  H2   C1   C22  107.11  3.000
 9VK  H2   C1   O2   110.97  3.000
 9VK  C22  C1   O2   107.95  3.000
 9VK  H2   C1   C3   106.73  3.000
 9VK  O2   C1   C3   114.15  3.000
 9VK  C22  C1   C3   109.71  3.000
 9VK  C6   O2   C1   118.69  3.000
 9VK  C7   C6   C8   109.49  3.000
 9VK  C8   C6   C9   109.40  3.000
 9VK  C7   C6   C9   109.96  3.000
 9VK  C8   C6   O2   104.36  3.000
 9VK  C9   C6   O2   112.83  3.000
 9VK  C7   C6   O2   110.63  3.000
 9VK  H5   C9   H4   106.97  3.000
 9VK  H5   C9   H3   108.09  3.000
 9VK  H4   C9   H3   108.40  3.000
 9VK  H5   C9   C6   112.35  3.000
 9VK  H4   C9   C6   109.74  3.000
 9VK  H3   C9   C6   111.13  3.000
 9VK  H8   C8   H7   108.04  3.000
 9VK  H8   C8   H6   108.18  3.000
 9VK  H7   C8   H6   107.84  3.000
 9VK  H8   C8   C6   110.88  3.000
 9VK  H7   C8   C6   110.72  3.000
 9VK  H6   C8   C6   111.05  3.000
 9VK  H11  C7   H10  107.85  3.000
 9VK  H11  C7   H9   107.72  3.000
 9VK  H10  C7   H9   107.47  3.000
 9VK  H11  C7   C6   110.92  3.000
 9VK  H10  C7   C6   110.42  3.000
 9VK  H9   C7   C6   112.27  3.000
 9VK  C20  C22  C23  112.84  3.000
 9VK  C20  C22  C1   123.34  3.000
 9VK  C23  C22  C1   123.77  3.000
 9VK  C21  C23  C26  124.80  3.000
 9VK  C21  C23  C22  112.69  3.000
 9VK  C26  C23  C22  122.49  3.000
 9VK  C27  C26  C25  122.14  3.000
 9VK  C27  C26  C23  120.94  3.000
 9VK  C25  C26  C23  116.88  3.000
 9VK  H13  C25  H12  106.06  3.000
 9VK  H13  C25  C24  110.20  3.000
 9VK  H12  C25  C24  111.18  3.000
 9VK  H13  C25  C26  109.13  3.000
 9VK  H12  C25  C26  107.97  3.000
 9VK  C24  C25  C26  112.09  3.000
 9VK  H14  C27  C28  116.95  3.000
 9VK  H14  C27  C26  119.04  3.000
 9VK  C28  C27  C26  123.99  3.000
 9VK  H16  C28  H15  105.21  3.000
 9VK  H16  C28  C29  109.72  3.000
 9VK  H15  C28  C29  109.63  3.000
 9VK  H16  C28  C27  109.63  3.000
 9VK  H15  C28  C27  108.70  3.000
 9VK  C29  C28  C27  113.59  3.000
 9VK  C24  C29  C53  109.90  3.000
 9VK  C53  C29  C54  109.22  3.000
 9VK  C24  C29  C54  110.16  3.000
 9VK  C53  C29  C28  109.65  3.000
 9VK  C54  C29  C28  109.74  3.000
 9VK  C24  C29  C28  108.16  3.000
 9VK  H19  C54  H18  107.92  3.000
 9VK  H19  C54  H17  107.59  3.000
 9VK  H18  C54  H17  107.78  3.000
 9VK  H19  C54  C29  111.03  3.000
 9VK  H18  C54  C29  111.67  3.000
 9VK  H17  C54  C29  110.68  3.000
 9VK  H22  C53  H21  107.65  3.000
 9VK  H22  C53  H20  107.68  3.000
 9VK  H21  C53  H20  107.62  3.000
 9VK  H22  C53  C29  111.41  3.000
 9VK  H21  C53  C29  111.17  3.000
 9VK  H20  C53  C29  111.14  3.000
 9VK  H24  C24  H23  106.37  3.000
 9VK  H24  C24  C29  108.77  3.000
 9VK  H23  C24  C29  109.94  3.000
 9VK  H24  C24  C25  109.13  3.000
 9VK  H23  C24  C25  109.87  3.000
 9VK  C29  C24  C25  112.56  3.000
 9VK  C35  C21  S43  119.84  3.000
 9VK  S43  C21  C23  110.74  3.000
 9VK  C35  C21  C23  129.42  3.000
 9VK  C20  S43  C21   92.69  3.000
 9VK  C34  C20  S43  119.52  3.000
 9VK  S43  C20  C22  111.03  3.000
 9VK  C34  C20  C22  129.41  3.000
 9VK  H27  C34  H26  108.52  3.000
 9VK  H27  C34  H25  107.44  3.000
 9VK  H26  C34  H25  107.45  3.000
 9VK  H27  C34  C20  110.62  3.000
 9VK  H26  C34  C20  111.55  3.000
 9VK  H25  C34  C20  111.10  3.000
 9VK  N36  C35  C39  121.73  3.000
 9VK  N36  C35  C21  117.37  3.000
 9VK  C39  C35  C21  120.89  3.000
 9VK  H28  C39  C38  120.24  3.000
 9VK  H28  C39  C35  120.64  3.000
 9VK  C38  C39  C35  119.11  3.000
 9VK  H29  C38  C37  120.80  3.000
 9VK  H29  C38  C39  120.25  3.000
 9VK  C37  C38  C39  118.95  3.000
 9VK  H30  C37  C40  120.56  3.000
 9VK  H30  C37  C38  121.65  3.000
 9VK  C40  C37  C38  117.79  3.000
 9VK  H31  C40  N36  116.12  3.000
 9VK  H31  C40  C37  120.09  3.000
 9VK  N36  C40  C37  123.79  3.000
 9VK  C40  N36  C35  118.63  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 9VK  CONST_01  C35  C21  C23  C22   180.00   0.0  0
 9VK  CONST_02  S43  C21  C23  C22     0.00   0.0  0
 9VK  CONST_03  C21  S43  C20  C22     0.00   0.0  0
 9VK  CONST_04  S43  C20  C22  C23     0.00   0.0  0
 9VK  CONST_07  C20  S43  C21  C23     0.00   0.0  0
 9VK  CONST_08  C20  C22  C23  C21     0.00   0.0  0
 9VK  CONST_09  C38  C39  C35  C21   180.00   0.0  0
 9VK  CONST_10  C40  N36  C35  C21   180.00   0.0  0
 9VK  CONST_13  C35  C21  S43  C20   180.00   0.0  0
 9VK  CONST_14  C37  C38  C39  C35     0.00   0.0  0
 9VK  CONST_15  C37  C40  N36  C35     0.00   0.0  0
 9VK  CONST_16  C40  C37  C38  C39     0.00   0.0  0
 9VK  CONST_17  C40  N36  C35  C39     0.00   0.0  0
 9VK  CONST_18  N36  C35  C39  C38     0.00   0.0  0
 9VK  CONST_19  N36  C40  C37  C38     0.00   0.0  0
 9VK  CONST_20  C20  C22  C23  C26   180.00   0.0  0
 9VK  CONST_21  C35  C21  C23  C26     0.00   0.0  0
 9VK  CONST_22  S43  C21  C23  C26   180.00   0.0  0
 9VK  CONST_23  C26  C23  C22  C1      0.00   0.0  0
 9VK  CONST_24  C21  C23  C22  C1    180.00   0.0  0
 9VK  CONST_25  S43  C20  C22  C1    180.00   0.0  0
 9VK  CONST_26  C34  C20  C22  C23   180.00   0.0  0
 9VK  CONST_27  C34  C20  S43  C21   180.00   0.0  0
 9VK  CONST_28  H28  C39  C35  C21     0.00   0.0  0
 9VK  CONST_29  H29  C38  C39  C35   180.00   0.0  0
 9VK  CONST_30  H31  C40  N36  C35   180.00   0.0  0
 9VK  CONST_31  H30  C37  C38  C39   180.00   0.0  0
 9VK  Var_01    C25  C26  C23  C22   -81.36  30.0  2
 9VK  Var_02    C24  C25  C26  C23   162.75  30.0  1
 9VK  Var_03    C28  C27  C26  C23  -177.99  30.0  1
 9VK  Var_04    C29  C24  C25  C26    46.04  30.0  1
 9VK  Var_05    C29  C28  C27  C26   -15.15  30.0  1
 9VK  Var_06    C28  C29  C24  C25   -60.48  30.0  1
 9VK  Var_07    C24  C29  C28  C27    43.70  30.0  1
 9VK  Var_08    H25  C34  C20  C22    86.98  30.0  2
 9VK  Var_09    H17  C54  C29  C28   -64.56  30.0  3
 9VK  Var_10    H20  C53  C29  C28    59.04  30.0  3
 9VK  Var_11    C7   C6   O2   C1    -71.36  30.0  3
 9VK  Var_12    H9   C7   C6   O2     64.28  30.0  3
 9VK  Var_13    H3   C9   C6   O2     53.25  30.0  3
 9VK  Var_14    H6   C8   C6   O2     58.88  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 9VK  chir_01  C1  C3  C22  O2  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 9VK  plan-1  C1   0.020
 9VK  plan-1  C22  0.020
 9VK  plan-1  C23  0.020
 9VK  plan-1  C26  0.020
 9VK  plan-1  C21  0.020
 9VK  plan-1  S43  0.020
 9VK  plan-1  C20  0.020
 9VK  plan-1  C34  0.020
 9VK  plan-1  C35  0.020
 9VK  plan-2  C21  0.020
 9VK  plan-2  C35  0.020
 9VK  plan-2  C39  0.020
 9VK  plan-2  C38  0.020
 9VK  plan-2  C37  0.020
 9VK  plan-2  C40  0.020
 9VK  plan-2  N36  0.020
 9VK  plan-2  H28  0.020
 9VK  plan-2  H29  0.020
 9VK  plan-2  H30  0.020
 9VK  plan-2  H31  0.020
 9VK  plan-3  O4   0.020
 9VK  plan-3  C3   0.020
 9VK  plan-3  O5   0.020
 9VK  plan-3  C1   0.020

