# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 17:45:56 2020
#   Inital geometry file: a 143 line input string
#   Ligand name: (2~{S})-2-[4-(4,4-dimethylcyclohexen-1-yl)-2-methyl-5-pyridin-4-yl-thiophen-3-yl]-2-[(2-methylpropan-2-yl)oxy]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1sc(c2ccncc2)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
 9VN  9VN  '(2~{S})-2-[4-(4,4-dimethylcyclohexen-1-yl)-2-methyl-5-pyridin-4-yl-thiophen-3-yl]-2-[(2-methylpropan-2-yl)oxy]ethanoic acid'  ligand  60  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_9VN
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
 9VN  C6   C  CT    0   0.188  -3.8008  -0.1142  -1.1884
 9VN  C7   C  CH3   0  -0.681  -4.5888  -1.0321  -0.2566
 9VN  C8   C  CH3   0  -0.677  -2.8407  -0.9250  -2.0552
 9VN  C9   C  CH3   0  -0.658  -4.7600   0.6714  -2.0729
 9VN  C3   C  C     0   0.538  -2.7518   0.8231   1.8966
 9VN  C1   C  CH1   0  -0.168  -2.1773   0.5100   0.5163
 9VN  O5   O  OH1   0  -0.586  -1.9026   0.4801   2.8562
 9VN  O2   O  O2    0  -0.481  -3.0866   0.8949  -0.4665
 9VN  C22  C  CR5   0   0.191  -0.8611   1.2189   0.3106
 9VN  C23  C  CR5   0   0.197   0.3938   0.5523   0.1285
 9VN  C27  C  C     0  -0.037   0.5927  -0.9144   0.1569
 9VN  C26  C  CH2   0  -0.506   1.0438  -1.5842  -1.1146
 9VN  C28  C  C1    0  -0.251   0.4025  -1.6119   1.2796
 9VN  C29  C  CH2   0  -0.442   0.6488  -3.0821   1.4156
 9VN  C30  C  CT    0  -0.090   0.8126  -3.8182   0.0815
 9VN  C51  C  CH3   0  -0.645   1.5123  -5.1546   0.3157
 9VN  C25  C  CH2   0  -0.410   1.6627  -2.9491  -0.8498
 9VN  C24  C  CH3   0  -0.657  -0.5640  -4.0799  -0.5326
 9VN  C21  C  CR5   0  -0.289   1.4146   1.4387  -0.1219
 9VN  S35  S  S2    0   0.249   0.8402   3.0620  -0.1179
 9VN  C20  C  CR5   0  -0.234  -0.7685   2.5824   0.2182
 9VN  C36  C  CH3   0  -0.734  -1.8241   3.6218   0.4097
 9VN  C38  C  CR6   0   0.152   2.8328   1.1803  -0.3629
 9VN  C42  C  CR16  0  -0.387   3.5592   1.9306  -1.2889
 9VN  C41  C  CR16  0  -0.059   4.9021   1.6525  -1.4820
 9VN  N52  N  N     0  -0.409   5.5590   0.6974  -0.8336
 9VN  C40  C  CR16  0  -0.058   4.8699  -0.0138   0.0522
 9VN  C39  C  CR16  0  -0.373   3.5274   0.1858   0.3268
 9VN  H1   H  HCH3  0   0.225  -3.9401  -1.6313   0.3858
 9VN  H2   H  HCH3  0   0.242  -5.2678  -0.4629   0.3785
 9VN  H3   H  HCH3  0   0.241  -5.1837  -1.7324  -0.8445
 9VN  H4   H  HCH3  0   0.239  -3.3928  -1.6150  -2.6948
 9VN  H5   H  HCH3  0   0.239  -2.2406  -0.2737  -2.6921
 9VN  H6   H  HCH3  0   0.225  -2.1573  -1.5279  -1.4547
 9VN  H7   H  HCH3  0   0.234  -5.4411   1.2752  -1.4712
 9VN  H8   H  HCH3  0   0.233  -4.2189   1.3354  -2.7491
 9VN  H9   H  HCH3  0   0.225  -5.3582  -0.0089  -2.6787
 9VN  H10  H  HCH1  0   0.266  -1.9730  -0.5689   0.5058
 9VN  H11  H  HOH1  0   0.485  -2.2823   0.6779   3.7258
 9VN  H12  H  HCH2  0   0.247   0.1891  -1.6722  -1.7964
 9VN  H13  H  HCH2  0   0.252   1.7609  -0.9488  -1.6390
 9VN  H14  H  H     0   0.245   0.0949  -1.0908   2.1802
 9VN  H15  H  HCH2  0   0.242   1.5499  -3.2124   2.0287
 9VN  H16  H  HCH2  0   0.238  -0.1591  -3.5391   1.9976
 9VN  H17  H  HCH3  0   0.223   0.9637  -5.7651   1.0372
 9VN  H18  H  HCH3  0   0.224   1.5871  -5.7259  -0.6121
 9VN  H19  H  HCH3  0   0.222   2.5243  -5.0123   0.7015
 9VN  H20  H  HCH2  0   0.228   1.8296  -3.4707  -1.7967
 9VN  H21  H  HCH2  0   0.224   2.6499  -2.8060  -0.3953
 9VN  H22  H  HCH3  0   0.228  -1.1602  -3.1691  -0.6037
 9VN  H23  H  HCH3  0   0.225  -0.4767  -4.5002  -1.5371
 9VN  H24  H  HCH3  0   0.228  -1.1286  -4.7870   0.0790
 9VN  H25  H  HCH3  0   0.259  -1.9700   3.8404   1.4694
 9VN  H26  H  HCH3  0   0.258  -1.5564   4.5572  -0.0795
 9VN  H27  H  HCH3  0   0.269  -2.7764   3.2914   0.0035
 9VN  H28  H  HCR6  0   0.268   3.0891   2.7110  -1.8739
 9VN  H29  H  HCR6  0   0.266   5.4698   2.2279  -2.2045
 9VN  H30  H  HCR6  0   0.265   5.4151  -0.7859   0.5835
 9VN  H31  H  HCR6  0   0.277   3.0371  -0.4203   1.0753
 9VN  O4   O  O     0  -0.424  -3.8308   1.3109   2.0973

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
 9VN  O4   C3   double    1.201  0.020  1.201
 9VN  C29  C28  single    1.497  0.020  1.497
 9VN  C29  C30  single    1.532  0.020  1.532
 9VN  O5   C3   single    1.326  0.020  1.326
 9VN  C28  C27  double    1.335  0.020  1.335
 9VN  C51  C30  single    1.527  0.020  1.527
 9VN  C3   C1   single    1.527  0.020  1.527
 9VN  C30  C24  single    1.530  0.020  1.530
 9VN  C30  C25  single    1.531  0.020  1.531
 9VN  C40  C39  aromatic  1.385  0.020  1.385
 9VN  C40  N52  aromatic  1.329  0.020  1.329
 9VN  C39  C38  aromatic  1.395  0.020  1.395
 9VN  C27  C23  single    1.480  0.020  1.480
 9VN  C27  C26  single    1.506  0.020  1.506
 9VN  C1   C22  single    1.509  0.020  1.509
 9VN  C1   O2   single    1.393  0.020  1.393
 9VN  C23  C22  aromatic  1.433  0.020  1.433
 9VN  C23  C21  aromatic  1.375  0.020  1.375
 9VN  N52  C41  aromatic  1.328  0.020  1.328
 9VN  C25  C26  single    1.522  0.020  1.522
 9VN  C22  C20  aromatic  1.370  0.020  1.370
 9VN  C38  C21  single    1.462  0.020  1.462
 9VN  C38  C42  aromatic  1.396  0.020  1.396
 9VN  C21  S35  aromatic  1.722  0.020  1.722
 9VN  C20  S35  aromatic  1.712  0.020  1.712
 9VN  C20  C36  single    1.494  0.020  1.494
 9VN  O2   C6   single    1.432  0.020  1.432
 9VN  C41  C42  aromatic  1.385  0.020  1.385
 9VN  C9   C6   single    1.523  0.020  1.523
 9VN  C6   C7   single    1.527  0.020  1.527
 9VN  C6   C8   single    1.527  0.020  1.527
 9VN  C7   H1   single    0.970  0.020  1.090
 9VN  C7   H2   single    0.970  0.020  1.090
 9VN  C7   H3   single    0.970  0.020  1.090
 9VN  C8   H4   single    0.970  0.020  1.090
 9VN  C8   H5   single    0.970  0.020  1.090
 9VN  C8   H6   single    0.970  0.020  1.090
 9VN  C9   H7   single    0.970  0.020  1.090
 9VN  C9   H8   single    0.970  0.020  1.090
 9VN  C9   H9   single    0.970  0.020  1.090
 9VN  C1   H10  single    0.970  0.020  1.090
 9VN  O5   H11  single    0.850  0.020  0.980
 9VN  C26  H12  single    0.970  0.020  1.090
 9VN  C26  H13  single    0.970  0.020  1.090
 9VN  C28  H14  single    0.930  0.020  1.080
 9VN  C29  H15  single    0.970  0.020  1.090
 9VN  C29  H16  single    0.970  0.020  1.090
 9VN  C51  H17  single    0.970  0.020  1.090
 9VN  C51  H18  single    0.970  0.020  1.090
 9VN  C51  H19  single    0.970  0.020  1.090
 9VN  C25  H20  single    0.970  0.020  1.090
 9VN  C25  H21  single    0.970  0.020  1.090
 9VN  C24  H22  single    0.970  0.020  1.090
 9VN  C24  H23  single    0.970  0.020  1.090
 9VN  C24  H24  single    0.970  0.020  1.090
 9VN  C36  H25  single    0.970  0.020  1.090
 9VN  C36  H26  single    0.970  0.020  1.090
 9VN  C36  H27  single    0.970  0.020  1.090
 9VN  C42  H28  single    0.930  0.020  1.080
 9VN  C41  H29  single    0.930  0.020  1.080
 9VN  C40  H30  single    0.930  0.020  1.080
 9VN  C39  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
 9VN  O2   C6   C9   104.09  3.000
 9VN  C9   C6   C8   109.89  3.000
 9VN  O2   C6   C8   110.30  3.000
 9VN  C8   C6   C7   110.60  3.000
 9VN  C9   C6   C7   109.84  3.000
 9VN  O2   C6   C7   111.93  3.000
 9VN  H3   C7   H2   108.03  3.000
 9VN  H3   C7   H1   106.78  3.000
 9VN  H2   C7   H1   108.29  3.000
 9VN  H3   C7   C6   109.78  3.000
 9VN  H2   C7   C6   111.29  3.000
 9VN  H1   C7   C6   112.48  3.000
 9VN  H6   C8   H5   107.86  3.000
 9VN  H6   C8   H4   106.86  3.000
 9VN  H5   C8   H4   108.29  3.000
 9VN  H6   C8   C6   112.01  3.000
 9VN  H5   C8   C6   111.13  3.000
 9VN  H4   C8   C6   110.52  3.000
 9VN  H9   C9   H8   107.91  3.000
 9VN  H9   C9   H7   108.02  3.000
 9VN  H8   C9   H7   108.33  3.000
 9VN  H9   C9   C6   110.28  3.000
 9VN  H8   C9   C6   111.19  3.000
 9VN  H7   C9   C6   111.00  3.000
 9VN  O5   C3   O4   124.00  3.000
 9VN  O5   C3   C1   111.10  3.000
 9VN  O4   C3   C1   124.90  3.000
 9VN  H10  C1   C22  107.34  3.000
 9VN  H10  C1   O2   112.71  3.000
 9VN  C22  C1   O2   110.08  3.000
 9VN  H10  C1   C3   106.26  3.000
 9VN  O2   C1   C3   109.59  3.000
 9VN  C22  C1   C3   110.79  3.000
 9VN  H11  O5   C3   110.21  3.000
 9VN  C1   O2   C6   119.12  3.000
 9VN  C20  C22  C23  113.29  3.000
 9VN  C20  C22  C1   122.40  3.000
 9VN  C23  C22  C1   124.25  3.000
 9VN  C21  C23  C27  122.85  3.000
 9VN  C21  C23  C22  111.93  3.000
 9VN  C27  C23  C22  125.19  3.000
 9VN  C28  C27  C26  121.34  3.000
 9VN  C26  C27  C23  117.69  3.000
 9VN  C28  C27  C23  120.96  3.000
 9VN  H13  C26  H12  105.06  3.000
 9VN  H13  C26  C25  109.78  3.000
 9VN  H12  C26  C25  110.67  3.000
 9VN  H13  C26  C27  110.07  3.000
 9VN  H12  C26  C27  109.09  3.000
 9VN  C25  C26  C27  111.94  3.000
 9VN  H14  C28  C29  116.29  3.000
 9VN  H14  C28  C27  119.17  3.000
 9VN  C29  C28  C27  124.47  3.000
 9VN  H16  C29  H15  105.02  3.000
 9VN  H16  C29  C30  109.93  3.000
 9VN  H15  C29  C30  109.97  3.000
 9VN  H16  C29  C28  109.67  3.000
 9VN  H15  C29  C28  107.60  3.000
 9VN  C30  C29  C28  114.22  3.000
 9VN  C24  C30  C25  110.64  3.000
 9VN  C25  C30  C51  109.61  3.000
 9VN  C24  C30  C51  108.92  3.000
 9VN  C25  C30  C29  108.43  3.000
 9VN  C24  C30  C29  109.60  3.000
 9VN  C51  C30  C29  109.63  3.000
 9VN  H19  C51  H18  107.74  3.000
 9VN  H19  C51  H17  107.74  3.000
 9VN  H18  C51  H17  107.65  3.000
 9VN  H19  C51  C30  111.39  3.000
 9VN  H18  C51  C30  111.04  3.000
 9VN  H17  C51  C30  111.12  3.000
 9VN  H21  C25  H20  106.48  3.000
 9VN  H21  C25  C30  108.78  3.000
 9VN  H20  C25  C30  109.91  3.000
 9VN  H21  C25  C26  108.74  3.000
 9VN  H20  C25  C26  109.82  3.000
 9VN  C30  C25  C26  112.90  3.000
 9VN  H24  C24  H23  107.89  3.000
 9VN  H24  C24  H22  107.13  3.000
 9VN  H23  C24  H22  107.76  3.000
 9VN  H24  C24  C30  110.56  3.000
 9VN  H23  C24  C30  111.28  3.000
 9VN  H22  C24  C30  112.03  3.000
 9VN  C38  C21  S35  119.39  3.000
 9VN  S35  C21  C23  111.08  3.000
 9VN  C38  C21  C23  129.52  3.000
 9VN  C20  S35  C21   92.86  3.000
 9VN  C36  C20  S35  119.62  3.000
 9VN  C36  C20  C22  129.51  3.000
 9VN  S35  C20  C22  110.83  3.000
 9VN  H27  C36  H26  107.98  3.000
 9VN  H27  C36  H25  107.85  3.000
 9VN  H26  C36  H25  107.27  3.000
 9VN  H27  C36  C20  111.09  3.000
 9VN  H26  C36  C20  111.49  3.000
 9VN  H25  C36  C20  110.99  3.000
 9VN  C39  C38  C42  116.87  3.000
 9VN  C42  C38  C21  121.29  3.000
 9VN  C39  C38  C21  121.84  3.000
 9VN  H28  C42  C41  119.37  3.000
 9VN  H28  C42  C38  121.33  3.000
 9VN  C41  C42  C38  119.28  3.000
 9VN  H29  C41  N52  116.62  3.000
 9VN  H29  C41  C42  119.60  3.000
 9VN  N52  C41  C42  123.78  3.000
 9VN  C40  N52  C41  116.99  3.000
 9VN  H30  C40  C39  119.54  3.000
 9VN  H30  C40  N52  116.55  3.000
 9VN  C39  C40  N52  123.91  3.000
 9VN  H31  C39  C40  119.76  3.000
 9VN  H31  C39  C38  121.07  3.000
 9VN  C40  C39  C38  119.17  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
 9VN  CONST_01  C38  C21  C23  C22   180.00   0.0  0
 9VN  CONST_02  S35  C21  C23  C22     0.00   0.0  0
 9VN  CONST_03  C21  S35  C20  C22     0.00   0.0  0
 9VN  CONST_04  S35  C20  C22  C23     0.00   0.0  0
 9VN  CONST_07  C20  S35  C21  C23     0.00   0.0  0
 9VN  CONST_08  C20  C22  C23  C21     0.00   0.0  0
 9VN  CONST_09  C40  C39  C38  C21   180.00   0.0  0
 9VN  CONST_10  C41  C42  C38  C21   180.00   0.0  0
 9VN  CONST_13  C38  C21  S35  C20   180.00   0.0  0
 9VN  CONST_14  N52  C40  C39  C38     0.00   0.0  0
 9VN  CONST_15  N52  C41  C42  C38     0.00   0.0  0
 9VN  CONST_16  C40  C39  C38  C42     0.00   0.0  0
 9VN  CONST_17  C40  N52  C41  C42     0.00   0.0  0
 9VN  CONST_18  C39  C40  N52  C41     0.00   0.0  0
 9VN  CONST_19  C39  C38  C42  C41     0.00   0.0  0
 9VN  CONST_20  C20  C22  C23  C27   180.00   0.0  0
 9VN  CONST_21  C38  C21  C23  C27     0.00   0.0  0
 9VN  CONST_22  S35  C21  C23  C27   180.00   0.0  0
 9VN  CONST_23  C27  C23  C22  C1      0.00   0.0  0
 9VN  CONST_24  C21  C23  C22  C1    180.00   0.0  0
 9VN  CONST_25  S35  C20  C22  C1    180.00   0.0  0
 9VN  CONST_26  C36  C20  C22  C23   180.00   0.0  0
 9VN  CONST_27  C36  C20  S35  C21   180.00   0.0  0
 9VN  CONST_28  H31  C39  C38  C21     0.00   0.0  0
 9VN  CONST_29  H28  C42  C38  C21     0.00   0.0  0
 9VN  CONST_30  H30  C40  C39  C38   180.00   0.0  0
 9VN  CONST_31  H29  C41  C42  C38   180.00   0.0  0
 9VN  CONST_32  H11  O5   C3   C1    180.00   0.0  0
 9VN  Var_01    C28  C27  C23  C22   -65.99  30.0  2
 9VN  Var_02    C29  C28  C27  C23  -176.68  30.0  1
 9VN  Var_03    C25  C26  C27  C23   160.23  30.0  1
 9VN  Var_04    C30  C29  C28  C27   -14.33  30.0  1
 9VN  Var_05    C30  C25  C26  C27    47.92  30.0  1
 9VN  Var_06    C29  C30  C25  C26   -59.33  30.0  1
 9VN  Var_07    C25  C30  C29  C28    41.20  30.0  1
 9VN  Var_08    H25  C36  C20  C22    81.78  30.0  2
 9VN  Var_09    H17  C51  C30  C29    56.80  30.0  3
 9VN  Var_10    H22  C24  C30  C29    52.76  30.0  3
 9VN  Var_11    H7   C9   C6   C7     59.36  30.0  3
 9VN  Var_12    H4   C8   C6   C7     62.34  30.0  3
 9VN  Var_13    H1   C7   C6   C8     57.45  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
 9VN  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
 9VN  plan-1  C1   0.020
 9VN  plan-1  C22  0.020
 9VN  plan-1  C23  0.020
 9VN  plan-1  C27  0.020
 9VN  plan-1  C21  0.020
 9VN  plan-1  S35  0.020
 9VN  plan-1  C20  0.020
 9VN  plan-1  C36  0.020
 9VN  plan-1  C38  0.020
 9VN  plan-2  C21  0.020
 9VN  plan-2  C38  0.020
 9VN  plan-2  C42  0.020
 9VN  plan-2  C41  0.020
 9VN  plan-2  N52  0.020
 9VN  plan-2  C40  0.020
 9VN  plan-2  C39  0.020
 9VN  plan-2  H28  0.020
 9VN  plan-2  H29  0.020
 9VN  plan-2  H30  0.020
 9VN  plan-2  H31  0.020
 9VN  plan-3  C3   0.020
 9VN  plan-3  C1   0.020
 9VN  plan-3  O5   0.020
 9VN  plan-3  H11  0.020
 9VN  plan-3  O4   0.020

