# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 22:54:17 2020
#   Inital geometry file: a 152 line input string
#   Ligand name: (2,3-dimethyl-4-{[2-(prop-2-yn-1-yloxy)-4-{[4-(trifluoromethyl)phenoxy]methyl}phenyl]sulfanyl}phenoxy)acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1c(C)c(Sc2ccc(COc3ccc(cc3)C(F)(F)F)cc2OCC#C)ccc1OCC(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
 D32  D32  '(2,3-dimethyl-4-{[2-(prop-2-yn-1-yloxy)-4-{[4-(trifluoromethyl)phenoxy]methyl}phenyl]sulfanyl}phenoxy)acetic acid'  ligand  58  36  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_D32
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
 D32  O22   O  OC    -1  -0.623   7.5042  -4.7970  -0.5995
 D32  C17   C  C      0   0.383   7.4852  -3.5691  -0.8145
 D32  O21   O  O      0  -0.584   8.1993  -2.9162  -1.5884
 D32  C14   C  CH2    0  -0.314   6.4226  -2.8209   0.0080
 D32  O11   O  O2     0  -0.452   6.4552  -1.4398  -0.2810
 D32  C5    C  CR6    0   0.374   5.5559  -0.6216   0.2913
 D32  C10   C  CR16   0  -0.380   4.6192  -1.0508   1.2281
 D32  C8    C  CR16   0  -0.183   3.7267  -0.1419   1.7685
 D32  C2    C  CR6    0  -0.042   5.6019   0.7278  -0.1009
 D32  C6    C  CH3    0  -0.746   6.6023   1.1714  -1.1350
 D32  C1    C  CR6    0   0.113   4.6996   1.6393   0.4550
 D32  C4    C  CH3    0  -0.725   4.7308   3.0844   0.0463
 D32  C3    C  CR6    0  -0.211   3.7494   1.1861   1.3791
 D32  S7    S  S2     0   0.058   2.5564   2.3062   2.0812
 D32  C13   C  CR6    0  -0.258   1.0460   1.4696   1.7127
 D32  C16   C  CR16   0  -0.208   0.2023   1.0930   2.7458
 D32  C20   C  CR16   0  -0.295  -1.0096   0.4661   2.4852
 D32  C15   C  CR6    0   0.485   0.6655   1.2193   0.3837
 D32  O1    O  O2     0  -0.441   1.5199   1.6322  -0.5650
 D32  C7    C  CH2    0  -0.331   1.2508   1.2878  -1.9095
 D32  C11   C  CSP    0   0.327   2.3495   1.7748  -2.7293
 D32  C19   C  CSP1   0  -0.489   3.2389   2.1684  -3.4321
 D32  C18   C  CR16   0  -0.390  -0.5367   0.5715   0.1287
 D32  C23   C  CR6    0   0.134  -1.3742   0.1938   1.1766
 D32  C24   C  CH2    0  -0.264  -2.6783  -0.4768   0.8687
 D32  O25   O  O2     0  -0.446  -3.6250   0.5485   0.5910
 D32  C26   C  C      0   0.407  -4.8711   0.1973   0.2385
 D32  C28   C  C1     0  -0.307  -5.7565   1.2498  -0.0170
 D32  C30   C  C1     0  -0.225  -7.0553   0.9887  -0.3940
 D32  C27   C  C1     0  -0.347  -5.3164  -1.1158   0.1148
 D32  C29   C  C1     0  -0.250  -6.6275  -1.3679  -0.2677
 D32  C31   C  C      0  -0.207  -7.5032  -0.3266  -0.5262
 D32  C32   C  CT     0   1.051  -8.9175  -0.5719  -0.9304
 D32  F34   F  F      0  -0.313  -9.7880  -0.1253  -0.0100
 D32  F35   F  F      0  -0.312  -9.2280   0.0610  -2.0731
 D32  F33   F  F      0  -0.303  -9.1840  -1.8683  -1.1185
 D32  H14   H  HCH2   0   0.212   5.4351  -3.2412  -0.2208
 D32  H14A  H  HCH2   0   0.211   6.6055  -3.0017   1.0747
 D32  H10   H  HCR6   0   0.250   4.5767  -2.0809   1.5526
 D32  H8    H  HCR6   0   0.244   3.0018  -0.4827   2.4971
 D32  H6    H  HCH3   0   0.236   6.1134   1.7153  -1.9440
 D32  H6A   H  HCH3   0   0.230   7.3530   1.8405  -0.7085
 D32  H6B   H  HCH3   0   0.271   7.1296   0.3307  -1.5765
 D32  H4    H  HCH3   0   0.263   3.9529   3.2847  -0.6928
 D32  H4A   H  HCH3   0   0.235   4.5547   3.7502   0.8894
 D32  H4B   H  HCH3   0   0.237   5.6841   3.3672  -0.3923
 D32  H16   H  HCR6   0   0.251   0.5056   1.2805   3.7674
 D32  H20   H  HCR6   0   0.231  -1.6531   0.1749   3.3057
 D32  H7    H  HCH2   0   0.252   1.1590   0.2023  -2.0267
 D32  H7A   H  HCH2   0   0.252   0.3123   1.7360  -2.2545
 D32  H19   H  H      0   0.240   4.0301   2.5210  -4.0532
 D32  H18   H  HCR6   0   0.256  -0.8478   0.3517  -0.8848
 D32  H24   H  HCH2   0   0.223  -2.5724  -1.1395   0.0038
 D32  H24A  H  HCH2   0   0.227  -3.0106  -1.0806   1.7188
 D32  H28   H  H      0   0.249  -5.4128   2.2711   0.0829
 D32  H30   H  H      0   0.247  -7.7185   1.8227  -0.5859
 D32  H27   H  H      0   0.250  -4.6658  -1.9573   0.3064
 D32  H29   H  H      0   0.248  -6.9436  -2.3978  -0.3595

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
 D32  C17  O22   deloc     1.247  0.020  1.247
 D32  O21  C17   deloc     1.239  0.020  1.239
 D32  C17  C14   single    1.538  0.020  1.538
 D32  O11  C14   single    1.411  0.020  1.411
 D32  C14  H14   single    0.939  0.020  1.096
 D32  C14  H14A  single    0.939  0.020  1.096
 D32  O11  C5    single    1.344  0.020  1.344
 D32  C2   C5    aromatic  1.406  0.020  1.406
 D32  C5   C10   aromatic  1.393  0.020  1.393
 D32  C10  C8    aromatic  1.384  0.020  1.384
 D32  C10  H10   single    0.929  0.020  1.085
 D32  C3   C8    aromatic  1.384  0.020  1.384
 D32  C8   H8    single    0.929  0.020  1.085
 D32  C6   C2    single    1.506  0.020  1.506
 D32  C2   C1    aromatic  1.398  0.020  1.398
 D32  C6   H6    single    0.939  0.020  1.096
 D32  C6   H6A   single    0.939  0.020  1.096
 D32  C6   H6B   single    0.939  0.020  1.096
 D32  C4   C1    single    1.502  0.020  1.502
 D32  C1   C3    aromatic  1.401  0.020  1.401
 D32  C4   H4    single    0.939  0.020  1.096
 D32  C4   H4A   single    0.939  0.020  1.096
 D32  C4   H4B   single    0.939  0.020  1.096
 D32  C3   S7    single    1.781  0.020  1.781
 D32  S7   C13   single    1.765  0.020  1.765
 D32  C13  C15   aromatic  1.405  0.020  1.405
 D32  C13  C16   aromatic  1.386  0.020  1.386
 D32  C16  C20   aromatic  1.389  0.020  1.389
 D32  C16  H16   single    0.929  0.020  1.085
 D32  C20  C23   aromatic  1.385  0.020  1.385
 D32  C20  H20   single    0.929  0.020  1.085
 D32  O1   C15   single    1.342  0.020  1.342
 D32  C15  C18   aromatic  1.389  0.020  1.389
 D32  O1   C7    single    1.414  0.020  1.414
 D32  C7   C11   single    1.455  0.020  1.455
 D32  C7   H7    single    0.939  0.020  1.096
 D32  C7   H7A   single    0.939  0.020  1.096
 D32  C11  C19   triple    1.200  0.020  1.200
 D32  C19  H19   single    0.913  0.020  1.066
 D32  C18  C23   aromatic  1.394  0.020  1.394
 D32  C18  H18   single    0.929  0.020  1.085
 D32  C23  C24   single    1.498  0.020  1.498
 D32  O25  C24   single    1.423  0.020  1.423
 D32  C24  H24   single    0.939  0.020  1.096
 D32  C24  H24A  single    0.939  0.020  1.096
 D32  C26  O25   single    1.342  0.020  1.342
 D32  C27  C26   aromatic  1.392  0.020  1.392
 D32  C26  C28   aromatic  1.399  0.020  1.399
 D32  C30  C28   aromatic  1.377  0.020  1.377
 D32  C28  H28   single    0.929  0.020  1.085
 D32  C31  C30   aromatic  1.396  0.020  1.396
 D32  C30  H30   single    0.929  0.020  1.085
 D32  C29  C27   aromatic  1.389  0.020  1.389
 D32  C27  H27   single    0.929  0.020  1.085
 D32  C29  C31   aromatic  1.385  0.020  1.385
 D32  C29  H29   single    0.929  0.020  1.085
 D32  C32  C31   single    1.491  0.020  1.491
 D32  F35  C32   single    1.343  0.020  1.343
 D32  F33  C32   single    1.337  0.020  1.337
 D32  C32  F34   single    1.343  0.020  1.343

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
 D32  C14   C17  O21  118.42  3.000
 D32  C14   C17  O22  113.42  3.000
 D32  O21   C17  O22  128.16  3.000
 D32  H14A  C14  H14  106.84  3.000
 D32  H14A  C14  O11  110.88  3.000
 D32  H14   C14  O11  110.67  3.000
 D32  H14A  C14  C17  108.94  3.000
 D32  H14   C14  C17  108.90  3.000
 D32  O11   C14  C17  110.52  3.000
 D32  C5    O11  C14  119.55  3.000
 D32  C2    C5   C10  120.36  3.000
 D32  C10   C5   O11  123.30  3.000
 D32  C2    C5   O11  116.34  3.000
 D32  H10   C10  C8   118.91  3.000
 D32  H10   C10  C5   121.48  3.000
 D32  C8    C10  C5   119.61  3.000
 D32  H8    C8   C3   120.15  3.000
 D32  H8    C8   C10  119.20  3.000
 D32  C3    C8   C10  120.65  3.000
 D32  C1    C2   C6   120.66  3.000
 D32  C1    C2   C5   119.59  3.000
 D32  C6    C2   C5   119.74  3.000
 D32  H6B   C6   H6A  107.40  3.000
 D32  H6B   C6   H6   107.59  3.000
 D32  H6A   C6   H6   107.00  3.000
 D32  H6B   C6   C2   111.94  3.000
 D32  H6A   C6   C2   111.65  3.000
 D32  H6    C6   C2   111.01  3.000
 D32  C3    C1   C4   120.32  3.000
 D32  C3    C1   C2   119.29  3.000
 D32  C4    C1   C2   120.38  3.000
 D32  H4B   C4   H4A  107.18  3.000
 D32  H4B   C4   H4   107.70  3.000
 D32  H4A   C4   H4   107.27  3.000
 D32  H4B   C4   C1   112.23  3.000
 D32  H4A   C4   C1   111.98  3.000
 D32  H4    C4   C1   110.24  3.000
 D32  S7    C3   C1   120.73  3.000
 D32  S7    C3   C8   118.79  3.000
 D32  C1    C3   C8   120.47  3.000
 D32  C13   S7   C3   101.12  3.000
 D32  C15   C13  C16  119.46  3.000
 D32  C16   C13  S7   119.60  3.000
 D32  C15   C13  S7   120.91  3.000
 D32  H16   C16  C20  119.99  3.000
 D32  H16   C16  C13  119.08  3.000
 D32  C20   C16  C13  120.92  3.000
 D32  H20   C20  C23  120.43  3.000
 D32  H20   C20  C16  119.85  3.000
 D32  C23   C20  C16  119.70  3.000
 D32  C18   C15  O1   124.38  3.000
 D32  C18   C15  C13  119.42  3.000
 D32  O1    C15  C13  116.20  3.000
 D32  C7    O1   C15  118.44  3.000
 D32  H7A   C7   H7   107.44  3.000
 D32  H7A   C7   C11  109.42  3.000
 D32  H7    C7   C11  109.55  3.000
 D32  H7A   C7   O1   111.27  3.000
 D32  H7    C7   O1   111.03  3.000
 D32  C11   C7   O1   108.10  3.000
 D32  C19   C11  C7   180.00  3.000
 D32  H19   C19  C11  180.00  3.000
 D32  H18   C18  C23  118.44  3.000
 D32  H18   C18  C15  121.01  3.000
 D32  C23   C18  C15  120.55  3.000
 D32  C24   C23  C18  119.33  3.000
 D32  C24   C23  C20  120.74  3.000
 D32  C18   C23  C20  119.92  3.000
 D32  H24A  C24  H24  108.00  3.000
 D32  H24A  C24  O25  110.31  3.000
 D32  H24   C24  O25  110.26  3.000
 D32  H24A  C24  C23  110.59  3.000
 D32  H24   C24  C23  110.43  3.000
 D32  O25   C24  C23  107.26  3.000
 D32  C26   O25  C24  118.72  3.000
 D32  C27   C26  C28  119.40  3.000
 D32  C28   C26  O25  116.03  3.000
 D32  C27   C26  O25  124.57  3.000
 D32  H28   C28  C30  120.24  3.000
 D32  H28   C28  C26  119.48  3.000
 D32  C30   C28  C26  120.28  3.000
 D32  H30   C30  C31  120.83  3.000
 D32  H30   C30  C28  118.69  3.000
 D32  C31   C30  C28  120.47  3.000
 D32  H27   C27  C29  118.41  3.000
 D32  H27   C27  C26  121.74  3.000
 D32  C29   C27  C26  119.85  3.000
 D32  H29   C29  C31  121.04  3.000
 D32  H29   C29  C27  118.18  3.000
 D32  C31   C29  C27  120.78  3.000
 D32  C32   C31  C29  121.77  3.000
 D32  C32   C31  C30  119.02  3.000
 D32  C29   C31  C30  119.21  3.000
 D32  F33   C32  F35  106.94  3.000
 D32  F33   C32  F34  106.84  3.000
 D32  F35   C32  F34  106.06  3.000
 D32  F34   C32  C31  111.97  3.000
 D32  F33   C32  C31  112.75  3.000
 D32  F35   C32  C31  111.87  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
 D32  CONST_01  C3   C1   C2   C5      0.00   0.0  0
 D32  CONST_02  C3   C8   C10  C5      0.00   0.0  0
 D32  CONST_03  C1   C2   C5   C10     0.00   0.0  0
 D32  CONST_04  C1   C3   C8   C10     0.00   0.0  0
 D32  CONST_05  C2   C5   C10  C8      0.00   0.0  0
 D32  CONST_06  C2   C1   C3   C8      0.00   0.0  0
 D32  CONST_07  C23  C18  C15  C13     0.00   0.0  0
 D32  CONST_08  C23  C20  C16  C13     0.00   0.0  0
 D32  CONST_09  C18  C15  C13  C16     0.00   0.0  0
 D32  CONST_10  C18  C23  C20  C16     0.00   0.0  0
 D32  CONST_11  C15  C13  C16  C20     0.00   0.0  0
 D32  CONST_12  C15  C18  C23  C20     0.00   0.0  0
 D32  CONST_13  C31  C29  C27  C26     0.00   0.0  0
 D32  CONST_14  C31  C30  C28  C26     0.00   0.0  0
 D32  CONST_15  C29  C27  C26  C28     0.00   0.0  0
 D32  CONST_16  C29  C31  C30  C28     0.00   0.0  0
 D32  CONST_17  C27  C26  C28  C30     0.00   0.0  0
 D32  CONST_18  C27  C29  C31  C30     0.00   0.0  0
 D32  CONST_19  C1   C2   C5   O11   180.00   0.0  0
 D32  CONST_20  C8   C10  C5   O11   180.00   0.0  0
 D32  CONST_21  C4   C1   C2   C5    180.00   0.0  0
 D32  CONST_22  C6   C2   C5   C10   180.00   0.0  0
 D32  CONST_23  S7   C3   C8   C10   180.00   0.0  0
 D32  CONST_24  C4   C1   C3   C8    180.00   0.0  0
 D32  CONST_25  S7   C3   C1   C2    180.00   0.0  0
 D32  CONST_26  C3   C1   C2   C6    180.00   0.0  0
 D32  CONST_27  C18  C15  C13  S7    180.00   0.0  0
 D32  CONST_28  C20  C16  C13  S7    180.00   0.0  0
 D32  CONST_29  O1   C15  C13  C16   180.00   0.0  0
 D32  CONST_30  C24  C23  C20  C16   180.00   0.0  0
 D32  CONST_31  C24  C23  C18  C15   180.00   0.0  0
 D32  CONST_32  C23  C18  C15  O1    180.00   0.0  0
 D32  CONST_33  C29  C27  C26  O25   180.00   0.0  0
 D32  CONST_34  C30  C28  C26  O25   180.00   0.0  0
 D32  CONST_35  C32  C31  C30  C28   180.00   0.0  0
 D32  CONST_36  C32  C31  C29  C27   180.00   0.0  0
 D32  CONST_37  H8   C8   C10  C5    180.00   0.0  0
 D32  CONST_38  H10  C10  C5   C2    180.00   0.0  0
 D32  CONST_39  H18  C18  C15  C13   180.00   0.0  0
 D32  CONST_40  H20  C20  C16  C13   180.00   0.0  0
 D32  CONST_41  H16  C16  C13  C15   180.00   0.0  0
 D32  CONST_42  H29  C29  C27  C26   180.00   0.0  0
 D32  CONST_43  H30  C30  C28  C26   180.00   0.0  0
 D32  CONST_44  H27  C27  C26  C28   180.00   0.0  0
 D32  CONST_45  H28  C28  C26  C27   180.00   0.0  0
 D32  Var_01    C15  C13  S7   C3    -61.44  30.0  2
 D32  Var_02    C2   C5   O11  C14  -176.55  30.0  2
 D32  Var_03    O25  C24  C23  C20    94.62  30.0  2
 D32  Var_04    C18  C15  O1   C7     -5.92  30.0  2
 D32  Var_05    C27  C26  O25  C24    -0.33  30.0  2
 D32  Var_06    F35  C32  C31  C30    54.60  30.0  3
 D32  Var_07    H6   C6   C2   C5    127.47  30.0  2
 D32  Var_08    H4   C4   C1   C2     99.63  30.0  2
 D32  Var_09    C11  C7   O1   C15  -176.65  30.0  3
 D32  Var_10    H14  C14  O11  C5     56.08  30.0  3
 D32  Var_11    O11  C14  C17  O22   179.94  30.0  3

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
 D32  plan-1  O11  0.020
 D32  plan-1  C5   0.020
 D32  plan-1  C10  0.020
 D32  plan-1  C8   0.020
 D32  plan-1  C2   0.020
 D32  plan-1  C6   0.020
 D32  plan-1  C1   0.020
 D32  plan-1  C4   0.020
 D32  plan-1  C3   0.020
 D32  plan-1  S7   0.020
 D32  plan-1  H10  0.020
 D32  plan-1  H8   0.020
 D32  plan-2  S7   0.020
 D32  plan-2  C13  0.020
 D32  plan-2  C16  0.020
 D32  plan-2  C20  0.020
 D32  plan-2  C15  0.020
 D32  plan-2  O1   0.020
 D32  plan-2  C18  0.020
 D32  plan-2  C23  0.020
 D32  plan-2  C24  0.020
 D32  plan-2  H16  0.020
 D32  plan-2  H20  0.020
 D32  plan-2  H18  0.020
 D32  plan-3  O25  0.020
 D32  plan-3  C26  0.020
 D32  plan-3  C28  0.020
 D32  plan-3  C30  0.020
 D32  plan-3  C27  0.020
 D32  plan-3  C29  0.020
 D32  plan-3  C31  0.020
 D32  plan-3  C32  0.020
 D32  plan-3  H28  0.020
 D32  plan-3  H30  0.020
 D32  plan-3  H27  0.020
 D32  plan-3  H29  0.020
 D32  plan-4  O22  0.020
 D32  plan-4  C17  0.020
 D32  plan-4  O21  0.020
 D32  plan-4  C14  0.020

