# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 07:19:13 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: 2-[[2-fluoranyl-4-(3-methoxyphenyl)phenyl]carbamoyl]cyclopentene-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(c1)c2ccc(NC(=O)C3=C(CCC3)C(O)=O)c(F)c2
#
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
 D5H  D5H  '2-[[2-fluoranyl-4-(3-methoxyphenyl)phenyl]carbamoyl]cyclopentene-1-carboxylic acid'  ligand  43  26  .  2021-08-08  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_D5H
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
 D5H  F    F  F      0  -0.317   0.7618   2.1348  -0.6540
 D5H  C9   C  CR6    0   0.494  -0.0364   1.0567  -0.5324
 D5H  C8   C  CR16   0  -0.472  -1.3967   1.2417  -0.5204
 D5H  C7   C  CR6    0   0.090  -2.2438   0.1411  -0.3824
 D5H  C5   C  CR6    0   0.113  -3.7086   0.3173  -0.3622
 D5H  C4   C  CR16   0  -0.337  -4.3224   1.2884  -1.1596
 D5H  C3   C  CR16   0  -0.226  -5.6965   1.4408  -1.1221
 D5H  C2   C  CR16   0  -0.394  -6.4905   0.6454  -0.3031
 D5H  C1   C  CR6    0   0.407  -5.8842  -0.3239   0.4918
 D5H  O    O  O2     0  -0.473  -6.5477  -1.1428   1.3296
 D5H  C    C  CH3    0  -0.437  -7.9526  -1.0191   1.4252
 D5H  C6   C  CR16   0  -0.416  -4.4983  -0.4811   0.4569
 D5H  C12  C  CR16   0  -0.314  -1.6565  -1.1159  -0.2659
 D5H  C11  C  CR16   0  -0.300  -0.2808  -1.2898  -0.2834
 D5H  C10  C  CR6    0   0.205   0.5734  -0.1940  -0.4161
 D5H  N    N  NH1    0  -0.716   1.9598  -0.2456  -0.4603
 D5H  C13  C  C      0   0.511   2.7785  -1.3017  -0.2058
 D5H  O1   O  O      0  -0.466   2.3913  -2.4402  -0.0105
 D5H  C14  C  CR5    0  -0.098   4.2235  -0.9776  -0.3303
 D5H  C15  C  CR5    0  -0.072   4.9807  -0.3354   0.5608
 D5H  C19  C  C      0   0.370   4.5077   0.1983   1.8900
 D5H  O3   O  O      0  -0.588   3.3316  -0.0663   2.2105
 D5H  O2   O  OC    -1  -0.594   5.3418   0.8486   2.5496
 D5H  C18  C  CH2    0  -0.468   5.0205  -1.4903  -1.5010
 D5H  C17  C  CH2    0  -0.464   6.3472  -0.7249  -1.3618
 D5H  C16  C  CH2    0  -0.473   6.4136  -0.2856   0.1094
 D5H  H1   H  HCR6   0   0.278  -1.7877   2.2488  -0.5966
 D5H  H2   H  HCR6   0   0.252  -3.7294   1.9056  -1.8219
 D5H  H3   H  HCR6   0   0.261  -6.1706   2.1891  -1.7441
 D5H  H4   H  HCR6   0   0.279  -7.5611   0.7976  -0.2985
 D5H  H5   H  HCH3   0   0.229  -8.2540  -0.0244   1.7630
 D5H  H6   H  HCH3   0   0.229  -8.4476  -1.2332   0.4743
 D5H  H7   H  HCH3   0   0.260  -8.2777  -1.7508   2.1607
 D5H  H8   H  HCR6   0   0.260  -4.0437  -1.2245   1.1011
 D5H  H9   H  HCR6   0   0.259  -2.2808  -1.9959  -0.1814
 D5H  H10  H  HCR6   0   0.290   0.1236  -2.2847  -0.2017
 D5H  H11  H  HNH1   0   0.414   2.4320   0.6396  -0.5595
 D5H  H13  H  HCH2   0   0.244   5.1561  -2.5739  -1.4173
 D5H  H14  H  HCH2   0   0.244   4.5313  -1.3119  -2.4615
 D5H  H15  H  HCH2   0   0.234   7.2073  -1.3206  -1.6675
 D5H  H16  H  HCH2   0   0.234   6.3220   0.1565  -2.0051
 D5H  H17  H  HCH2   0   0.235   6.8546   0.7044   0.2351
 D5H  H18  H  HCH2   0   0.233   7.0207  -0.9694   0.7121

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
 D5H  C18  C17  single    1.538  0.020  1.538
 D5H  C18  C14  single    1.506  0.020  1.506
 D5H  C17  C16  single    1.537  0.020  1.537
 D5H  O1   C13  double    1.218  0.020  1.218
 D5H  C14  C13  single    1.486  0.020  1.486
 D5H  C14  C15  double    1.334  0.020  1.334
 D5H  C13  N    single    1.360  0.020  1.360
 D5H  C16  C15  single    1.503  0.020  1.503
 D5H  C11  C12  aromatic  1.387  0.020  1.387
 D5H  C11  C10  aromatic  1.396  0.020  1.396
 D5H  C12  C7   aromatic  1.392  0.020  1.392
 D5H  C15  C19  single    1.508  0.020  1.508
 D5H  N    C10  single    1.388  0.020  1.388
 D5H  C10  C9   aromatic  1.396  0.020  1.396
 D5H  C    O    single    1.414  0.020  1.414
 D5H  C7   C5   single    1.475  0.020  1.475
 D5H  C7   C8   aromatic  1.396  0.020  1.396
 D5H  C6   C5   aromatic  1.390  0.020  1.390
 D5H  C6   C1   aromatic  1.395  0.020  1.395
 D5H  C5   C4   aromatic  1.398  0.020  1.398
 D5H  C1   O    single    1.346  0.020  1.346
 D5H  C1   C2   aromatic  1.392  0.020  1.392
 D5H  C4   C3   aromatic  1.383  0.020  1.383
 D5H  C9   C8   aromatic  1.373  0.020  1.373
 D5H  C9   F    single    1.347  0.020  1.347
 D5H  C2   C3   aromatic  1.391  0.020  1.391
 D5H  C19  O3   deloc     1.247  0.020  1.247
 D5H  C19  O2   deloc     1.246  0.020  1.246
 D5H  C8   H1   single    0.930  0.020  1.080
 D5H  C4   H2   single    0.930  0.020  1.080
 D5H  C3   H3   single    0.930  0.020  1.080
 D5H  C2   H4   single    0.930  0.020  1.080
 D5H  C    H5   single    0.970  0.020  1.090
 D5H  C    H6   single    0.970  0.020  1.090
 D5H  C    H7   single    0.970  0.020  1.090
 D5H  C6   H8   single    0.930  0.020  1.080
 D5H  C12  H9   single    0.930  0.020  1.080
 D5H  C11  H10  single    0.930  0.020  1.080
 D5H  N    H11  single    0.860  0.020  1.020
 D5H  C18  H13  single    0.970  0.020  1.090
 D5H  C18  H14  single    0.970  0.020  1.090
 D5H  C17  H15  single    0.970  0.020  1.090
 D5H  C17  H16  single    0.970  0.020  1.090
 D5H  C16  H17  single    0.970  0.020  1.090
 D5H  C16  H18  single    0.970  0.020  1.090

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
 D5H  C10  C9   C8   123.55  3.000
 D5H  C8   C9   F    118.69  3.000
 D5H  C10  C9   F    117.76  3.000
 D5H  H1   C8   C7   121.41  3.000
 D5H  H1   C8   C9   118.84  3.000
 D5H  C7   C8   C9   119.74  3.000
 D5H  C12  C7   C5   121.70  3.000
 D5H  C5   C7   C8   120.65  3.000
 D5H  C12  C7   C8   117.65  3.000
 D5H  C6   C5   C4   119.04  3.000
 D5H  C4   C5   C7   120.72  3.000
 D5H  C6   C5   C7   120.23  3.000
 D5H  H2   C4   C3   119.88  3.000
 D5H  H2   C4   C5   120.29  3.000
 D5H  C3   C4   C5   119.82  3.000
 D5H  H3   C3   C2   118.93  3.000
 D5H  H3   C3   C4   119.72  3.000
 D5H  C2   C3   C4   121.34  3.000
 D5H  H4   C2   C1   121.78  3.000
 D5H  H4   C2   C3   119.16  3.000
 D5H  C1   C2   C3   119.06  3.000
 D5H  C6   C1   O    115.88  3.000
 D5H  O    C1   C2   124.34  3.000
 D5H  C6   C1   C2   119.78  3.000
 D5H  C    O    C1   118.59  3.000
 D5H  H7   C    H6   108.75  3.000
 D5H  H7   C    H5   108.72  3.000
 D5H  H6   C    H5   108.80  3.000
 D5H  H7   C    O    106.50  3.000
 D5H  H6   C    O    111.96  3.000
 D5H  H5   C    O    112.00  3.000
 D5H  H8   C6   C1   118.63  3.000
 D5H  H8   C6   C5   120.39  3.000
 D5H  C1   C6   C5   120.96  3.000
 D5H  H9   C12  C11  118.12  3.000
 D5H  H9   C12  C7   119.82  3.000
 D5H  C11  C12  C7   122.05  3.000
 D5H  H10  C11  C10  120.17  3.000
 D5H  H10  C11  C12  119.17  3.000
 D5H  C10  C11  C12  120.66  3.000
 D5H  N    C10  C11  125.81  3.000
 D5H  N    C10  C9   117.83  3.000
 D5H  C11  C10  C9   116.35  3.000
 D5H  H11  N    C13  114.72  3.000
 D5H  H11  N    C10  116.00  3.000
 D5H  C13  N    C10  128.61  3.000
 D5H  C14  C13  O1   121.75  3.000
 D5H  C14  C13  N    113.59  3.000
 D5H  O1   C13  N    124.35  3.000
 D5H  C18  C14  C15  112.50  3.000
 D5H  C15  C14  C13  126.93  3.000
 D5H  C18  C14  C13  120.36  3.000
 D5H  C16  C15  C19  123.50  3.000
 D5H  C19  C15  C14  125.52  3.000
 D5H  C16  C15  C14  110.88  3.000
 D5H  O2   C19  O3   127.28  3.000
 D5H  O2   C19  C15  116.17  3.000
 D5H  O3   C19  C15  116.55  3.000
 D5H  H14  C18  H13  106.51  3.000
 D5H  H14  C18  C17  112.61  3.000
 D5H  H13  C18  C17  112.25  3.000
 D5H  H14  C18  C14  113.00  3.000
 D5H  H13  C18  C14  110.05  3.000
 D5H  C17  C18  C14  102.51  3.000
 D5H  H16  C17  H15  107.11  3.000
 D5H  H16  C17  C16  109.53  3.000
 D5H  H15  C17  C16  112.99  3.000
 D5H  H16  C17  C18  109.18  3.000
 D5H  H15  C17  C18  112.54  3.000
 D5H  C16  C17  C18  105.44  3.000
 D5H  H18  C16  H17  106.20  3.000
 D5H  H18  C16  C17  111.86  3.000
 D5H  H17  C16  C17  112.78  3.000
 D5H  H18  C16  C15  110.03  3.000
 D5H  H17  C16  C15  112.38  3.000
 D5H  C17  C16  C15  103.70  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
 D5H  CONST_01  C12  C11  C10  C9     0.00   0.0  0
 D5H  CONST_02  C12  C7   C8   C9     0.00   0.0  0
 D5H  CONST_03  C5   C7   C8   C9   180.00   0.0  0
 D5H  CONST_04  C11  C12  C7   C8     0.00   0.0  0
 D5H  CONST_07  C11  C10  C9   C8     0.00   0.0  0
 D5H  CONST_08  C10  C11  C12  C7     0.00   0.0  0
 D5H  CONST_09  C1   C6   C5   C7   180.00   0.0  0
 D5H  CONST_10  C3   C4   C5   C7   180.00   0.0  0
 D5H  CONST_11  C10  C9   C8   C7     0.00   0.0  0
 D5H  CONST_12  C11  C12  C7   C5   180.00   0.0  0
 D5H  CONST_13  C2   C1   C6   C5     0.00   0.0  0
 D5H  CONST_14  C2   C3   C4   C5     0.00   0.0  0
 D5H  CONST_16  C1   C6   C5   C4     0.00   0.0  0
 D5H  CONST_17  C1   C2   C3   C4     0.00   0.0  0
 D5H  CONST_18  C6   C5   C4   C3     0.00   0.0  0
 D5H  CONST_19  C6   C1   C2   C3     0.00   0.0  0
 D5H  CONST_21  C11  C10  C9   F    180.00   0.0  0
 D5H  CONST_22  C7   C8   C9   F    180.00   0.0  0
 D5H  CONST_23  N    C10  C9   C8   180.00   0.0  0
 D5H  CONST_24  O    C1   C6   C5   180.00   0.0  0
 D5H  CONST_25  O    C1   C2   C3   180.00   0.0  0
 D5H  CONST_26  N    C10  C11  C12  180.00   0.0  0
 D5H  CONST_27  H10  C11  C10  C9   180.00   0.0  0
 D5H  CONST_28  H9   C12  C7   C8   180.00   0.0  0
 D5H  CONST_29  H8   C6   C5   C7     0.00   0.0  0
 D5H  CONST_30  H2   C4   C5   C7     0.00   0.0  0
 D5H  CONST_31  H1   C8   C7   C5     0.00   0.0  0
 D5H  CONST_32  H3   C3   C4   C5   180.00   0.0  0
 D5H  CONST_33  H4   C2   C3   C4   180.00   0.0  0
 D5H  CONST_34  C14  C13  N    C10  180.00   0.0  0
 D5H  CONST_35  C13  N    C10  C9   180.00   0.0  0
 D5H  CONST_36  C13  N    C10  C11    0.00   0.0  0
 D5H  CONST_37  H11  N    C10  C9     0.00   0.0  0
 D5H  CONST_38  O1   C13  N    C10    0.00   0.0  0
 D5H  Var_01    C16  C17  C18  C14   21.39  30.0  1
 D5H  Var_02    C17  C16  C15  C14   12.58  30.0  1
 D5H  Var_03    C17  C18  C14  C15  -14.66  30.0  1
 D5H  Var_04    C18  C17  C16  C15  -20.94  30.0  1
 D5H  Var_05    C16  C15  C14  C18    1.39  30.0  1
 D5H  Var_06    C6   C1   O    C    179.07  30.0  3
 D5H  Var_07    O3   C19  C15  C14    5.02  30.0  2
 D5H  Var_08    H5   C    O    C1   -60.19  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
 D5H  plan-1  C7   0.020
 D5H  plan-1  C5   0.020
 D5H  plan-1  C4   0.020
 D5H  plan-1  C3   0.020
 D5H  plan-1  C2   0.020
 D5H  plan-1  C1   0.020
 D5H  plan-1  O    0.020
 D5H  plan-1  C6   0.020
 D5H  plan-1  H2   0.020
 D5H  plan-1  H3   0.020
 D5H  plan-1  H4   0.020
 D5H  plan-1  H8   0.020
 D5H  plan-2  F    0.020
 D5H  plan-2  C9   0.020
 D5H  plan-2  C8   0.020
 D5H  plan-2  C7   0.020
 D5H  plan-2  C5   0.020
 D5H  plan-2  C12  0.020
 D5H  plan-2  C11  0.020
 D5H  plan-2  C10  0.020
 D5H  plan-2  N    0.020
 D5H  plan-2  H1   0.020
 D5H  plan-2  H9   0.020
 D5H  plan-2  H10  0.020
 D5H  plan-3  C10  0.020
 D5H  plan-3  N    0.020
 D5H  plan-3  C13  0.020
 D5H  plan-3  O1   0.020
 D5H  plan-3  C14  0.020
 D5H  plan-3  H11  0.020
 D5H  plan-4  C15  0.020
 D5H  plan-4  C19  0.020
 D5H  plan-4  O3   0.020
 D5H  plan-4  O2   0.020

