# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 12:08:07 2022
#   Inital geometry file: a 120 line input string
#   Ligand name: {(1Z)-5-fluoro-2-methyl-1-[4-(methylsulfonyl)benzylidene]-1H-inden-3-yl}acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC\1=C(CC(O)=O)c2cc(F)ccc2C\1=C\c3ccc(cc3)[S](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
 SLO  SLO  '{(1Z)-5-fluoro-2-methyl-1-[4-(methylsulfonyl)benzylidene]-1H-inden-3-yl}acetic acid'  ligand  42  26  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SLO
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
 SLO  F     F  F      0  -0.320  -2.9763  -4.2304  -0.0549
 SLO  S     S  S      0   1.215   5.6686   0.0990  -0.1899
 SLO  C1    C  CR5    0   0.121  -3.4823   0.6170   0.5373
 SLO  O1    O  OC    -1  -0.619  -7.0372   0.4751  -0.3144
 SLO  C2    C  CR5    0   0.154  -1.2188   1.0090   0.2720
 SLO  O2    O  O      0  -0.591  -5.2049   0.2363  -1.5630
 SLO  C3    C  CR5    0  -0.000  -2.5535   1.5987   0.4817
 SLO  O3    O  OS     0  -0.668   5.7854  -1.2905   0.2479
 SLO  C4    C  CR56   0   0.113  -2.8090  -0.6658   0.3299
 SLO  O4    O  OS     0  -0.669   6.1542   0.4614  -1.5200
 SLO  C5    C  CR56   0   0.039  -1.4304  -0.4468   0.1598
 SLO  C6    C  CH2    0  -0.745  -4.9434   0.7255   0.7658
 SLO  C7    C  C1     0  -0.406  -0.1011   1.7521   0.1952
 SLO  C8    C  CR16   0  -0.510  -3.3508  -1.9367   0.2598
 SLO  C9    C  CR16   0  -0.330  -0.5973  -1.5125  -0.1325
 SLO  C10   C  CH3    0  -0.763  -2.7715   3.0654   0.6255
 SLO  C11   C  CR6    0   0.113   1.2927   1.3111   0.1032
 SLO  C12   C  CR6    0   0.541  -2.4792  -2.9826   0.0049
 SLO  C13   C  CR16   0  -0.429  -1.1263  -2.7998  -0.2075
 SLO  C14   C  CR16   0  -0.282   2.1481   1.9463  -0.8011
 SLO  C15   C  CR16   0  -0.310   1.8157   0.3259   0.9437
 SLO  C16   C  CR6    0  -0.216   3.9644   0.5760  -0.0735
 SLO  C17   C  C      0   0.427  -5.8048   0.4499  -0.4959
 SLO  C18   C  CR16   0  -0.218   3.4774   1.5766  -0.9034
 SLO  C19   C  CR16   0  -0.209   3.1445  -0.0504   0.8553
 SLO  C20   C  CH3    0  -0.790   6.4851   1.1332   1.0037
 SLO  H6    H  HCH2   0   0.245  -5.2515   0.0236   1.5492
 SLO  H6A   H  HCH2   0   0.257  -5.2018   1.7171   1.1469
 SLO  H7    H  H      0   0.274  -0.2276   2.8304   0.1956
 SLO  H8    H  HCR6   0   0.263  -4.4089  -2.1200   0.3952
 SLO  H9    H  HCR6   0   0.263   0.4598  -1.3795  -0.3108
 SLO  H10   H  HCH3   0   0.244  -2.1833   3.4825   1.4457
 SLO  H10A  H  HCH3   0   0.245  -2.4793   3.6025  -0.2798
 SLO  H10B  H  HCH3   0   0.256  -3.8169   3.2974   0.8197
 SLO  H13   H  HCR6   0   0.275  -0.4892  -3.6461  -0.4271
 SLO  H14   H  HCR6   0   0.271   1.7634   2.7302  -1.4412
 SLO  H15   H  HCR6   0   0.282   1.1817  -0.1443   1.6835
 SLO  H18   H  HCR6   0   0.286   4.1200   2.0670  -1.6218
 SLO  H19   H  HCR6   0   0.287   3.5294  -0.8216   1.5090
 SLO  H20   H  HCH3   0   0.311   7.5497   0.9057   0.9561
 SLO  H20A  H  HCH3   0   0.296   6.3147   2.1776   0.7532
 SLO  H20B  H  HCH3   0   0.296   6.1005   0.9131   1.9969

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
 SLO  F    C12   single    1.344  0.020  1.344
 SLO  S    O3    double    1.462  0.020  1.462
 SLO  S    O4    double    1.462  0.020  1.462
 SLO  S    C16   single    1.773  0.020  1.773
 SLO  S    C20   single    1.778  0.020  1.778
 SLO  C1   C3    double    1.353  0.020  1.353
 SLO  C1   C4    single    1.464  0.020  1.464
 SLO  C1   C6    single    1.483  0.020  1.483
 SLO  O1   C17   deloc     1.246  0.020  1.246
 SLO  C2   C3    single    1.474  0.020  1.474
 SLO  C2   C5    single    1.475  0.020  1.475
 SLO  C2   C7    double    1.344  0.020  1.344
 SLO  O2   C17   deloc     1.243  0.020  1.243
 SLO  C3   C10   single    1.490  0.020  1.490
 SLO  C4   C5    aromatic  1.406  0.020  1.406
 SLO  C4   C8    aromatic  1.383  0.020  1.383
 SLO  C5   C9    aromatic  1.384  0.020  1.384
 SLO  C6   C17   single    1.552  0.020  1.552
 SLO  C7   C11   single    1.465  0.020  1.465
 SLO  C8   C12   aromatic  1.385  0.020  1.385
 SLO  C9   C13   aromatic  1.394  0.020  1.394
 SLO  C11  C14   aromatic  1.398  0.020  1.398
 SLO  C11  C15   aromatic  1.397  0.020  1.397
 SLO  C12  C13   aromatic  1.382  0.020  1.382
 SLO  C14  C18   aromatic  1.384  0.020  1.384
 SLO  C15  C19   aromatic  1.384  0.020  1.384
 SLO  C16  C18   aromatic  1.388  0.020  1.388
 SLO  C16  C19   aromatic  1.388  0.020  1.388
 SLO  C6   H6    single    0.970  0.020  1.090
 SLO  C6   H6A   single    0.970  0.020  1.090
 SLO  C7   H7    single    0.930  0.020  1.080
 SLO  C8   H8    single    0.930  0.020  1.080
 SLO  C9   H9    single    0.930  0.020  1.080
 SLO  C10  H10   single    0.970  0.020  1.090
 SLO  C10  H10A  single    0.970  0.020  1.090
 SLO  C10  H10B  single    0.970  0.020  1.090
 SLO  C13  H13   single    0.930  0.020  1.080
 SLO  C14  H14   single    0.930  0.020  1.080
 SLO  C15  H15   single    0.930  0.020  1.080
 SLO  C18  H18   single    0.930  0.020  1.080
 SLO  C19  H19   single    0.930  0.020  1.080
 SLO  C20  H20   single    0.970  0.020  1.090
 SLO  C20  H20A  single    0.970  0.020  1.090
 SLO  C20  H20B  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
 SLO  C20   S    C16   103.93  3.000
 SLO  C20   S    O4    108.31  3.000
 SLO  C16   S    O4    108.20  3.000
 SLO  C20   S    O3    108.37  3.000
 SLO  C16   S    O3    108.23  3.000
 SLO  O4    S    O3    118.80  3.000
 SLO  C6    C1   C4    122.64  3.000
 SLO  C6    C1   C3    129.04  3.000
 SLO  C4    C1   C3    108.32  3.000
 SLO  C7    C2   C5    131.33  3.000
 SLO  C7    C2   C3    122.66  3.000
 SLO  C5    C2   C3    106.00  3.000
 SLO  C10   C3   C2    122.69  3.000
 SLO  C10   C3   C1    127.59  3.000
 SLO  C2    C3   C1    109.71  3.000
 SLO  C8    C4   C5    121.40  3.000
 SLO  C8    C4   C1    129.21  3.000
 SLO  C5    C4   C1    109.37  3.000
 SLO  C9    C5   C4    119.72  3.000
 SLO  C9    C5   C2    133.59  3.000
 SLO  C4    C5   C2    106.57  3.000
 SLO  H6A   C6   H6    105.39  3.000
 SLO  H6A   C6   C17   108.24  3.000
 SLO  H6    C6   C17   108.13  3.000
 SLO  H6A   C6   C1    110.67  3.000
 SLO  H6    C6   C1    109.90  3.000
 SLO  C17   C6   C1    114.11  3.000
 SLO  H7    C7   C11   114.19  3.000
 SLO  H7    C7   C2    116.89  3.000
 SLO  C11   C7   C2    128.92  3.000
 SLO  H8    C8   C12   120.68  3.000
 SLO  H8    C8   C4    122.15  3.000
 SLO  C12   C8   C4    117.16  3.000
 SLO  H9    C9   C13   118.44  3.000
 SLO  H9    C9   C5    121.95  3.000
 SLO  C13   C9   C5    119.61  3.000
 SLO  H10B  C10  H10A  107.46  3.000
 SLO  H10B  C10  H10   107.57  3.000
 SLO  H10A  C10  H10   106.89  3.000
 SLO  H10B  C10  C3    111.58  3.000
 SLO  H10A  C10  C3    111.40  3.000
 SLO  H10   C10  C3    111.70  3.000
 SLO  C15   C11  C14   118.74  3.000
 SLO  C15   C11  C7    122.07  3.000
 SLO  C14   C11  C7    119.09  3.000
 SLO  C13   C12  C8    123.00  3.000
 SLO  C13   C12  F     118.56  3.000
 SLO  C8    C12  F     118.44  3.000
 SLO  H13   C13  C12   120.29  3.000
 SLO  H13   C13  C9    120.66  3.000
 SLO  C12   C13  C9    119.05  3.000
 SLO  H14   C14  C18   119.41  3.000
 SLO  H14   C14  C11   119.62  3.000
 SLO  C18   C14  C11   120.96  3.000
 SLO  H15   C15  C19   119.22  3.000
 SLO  H15   C15  C11   119.91  3.000
 SLO  C19   C15  C11   120.86  3.000
 SLO  C19   C16  C18   121.20  3.000
 SLO  C19   C16  S     119.34  3.000
 SLO  C18   C16  S     119.46  3.000
 SLO  C6    C17  O2    117.42  3.000
 SLO  C6    C17  O1    115.27  3.000
 SLO  O2    C17  O1    127.31  3.000
 SLO  H18   C18  C16   121.03  3.000
 SLO  H18   C18  C14   119.93  3.000
 SLO  C16   C18  C14   119.05  3.000
 SLO  H19   C19  C16   121.05  3.000
 SLO  H19   C19  C15   119.79  3.000
 SLO  C16   C19  C15   119.15  3.000
 SLO  H20B  C20  H20A  110.45  3.000
 SLO  H20B  C20  H20   110.07  3.000
 SLO  H20A  C20  H20   110.08  3.000
 SLO  H20B  C20  S     109.45  3.000
 SLO  H20A  C20  S     109.39  3.000
 SLO  H20   C20  S     107.33  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
 SLO  CONST_01  C13  C9   C5   C4      0.00   0.0  0
 SLO  CONST_02  C13  C12  C8   C4      0.00   0.0  0
 SLO  CONST_03  C12  C8   C4   C5      0.00   0.0  0
 SLO  CONST_04  C12  C13  C9   C5      0.00   0.0  0
 SLO  CONST_05  C9   C5   C4   C8      0.00   0.0  0
 SLO  CONST_06  C9   C13  C12  C8      0.00   0.0  0
 SLO  CONST_07  C16  C18  C14  C11     0.00   0.0  0
 SLO  CONST_08  C16  C19  C15  C11     0.00   0.0  0
 SLO  CONST_09  C19  C15  C11  C14     0.00   0.0  0
 SLO  CONST_10  C19  C16  C18  C14     0.00   0.0  0
 SLO  CONST_11  C18  C14  C11  C15     0.00   0.0  0
 SLO  CONST_12  C18  C16  C19  C15     0.00   0.0  0
 SLO  CONST_13  C4   C8   C12  F     180.00   0.0  0
 SLO  CONST_14  C9   C13  C12  F     180.00   0.0  0
 SLO  CONST_15  C14  C18  C16  S     180.00   0.0  0
 SLO  CONST_16  C15  C19  C16  S     180.00   0.0  0
 SLO  CONST_17  C18  C14  C11  C7    180.00   0.0  0
 SLO  CONST_18  C19  C15  C11  C7    180.00   0.0  0
 SLO  CONST_19  H8   C8   C4   C1      0.00   0.0  0
 SLO  CONST_20  H9   C9   C5   C2      0.00   0.0  0
 SLO  CONST_21  H13  C13  C9   C5    180.00   0.0  0
 SLO  CONST_22  H18  C18  C14  C11   180.00   0.0  0
 SLO  CONST_23  H19  C19  C15  C11   180.00   0.0  0
 SLO  CONST_24  H15  C15  C11  C14   180.00   0.0  0
 SLO  CONST_25  H14  C14  C11  C15   180.00   0.0  0
 SLO  Var_01    C11  C7   C2   C3    174.37   0.0  2
 SLO  Var_02    C14  C11  C7   C2    136.31  30.0  2
 SLO  Var_03    C17  C6   C1   C3    108.00  30.0  3
 SLO  Var_04    C18  C16  S    O3   -153.26  30.0  2
 SLO  Var_05    H10  C10  C3   C1    122.05  30.0  3
 SLO  Var_06    O1   C17  C6   C1    176.86  30.0  3
 SLO  Var_07    H20  C20  S    C16  -178.26  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
 SLO  plan-1  S    0.020
 SLO  plan-1  C7   0.020
 SLO  plan-1  C11  0.020
 SLO  plan-1  C14  0.020
 SLO  plan-1  C15  0.020
 SLO  plan-1  C16  0.020
 SLO  plan-1  C18  0.020
 SLO  plan-1  C19  0.020
 SLO  plan-1  H14  0.020
 SLO  plan-1  H15  0.020
 SLO  plan-1  H18  0.020
 SLO  plan-1  H19  0.020
 SLO  plan-2  O1   0.020
 SLO  plan-2  O2   0.020
 SLO  plan-2  C6   0.020
 SLO  plan-2  C17  0.020
 SLO  plan-3  F    0.020
 SLO  plan-3  C1   0.020
 SLO  plan-3  C2   0.020
 SLO  plan-3  C3   0.020
 SLO  plan-3  C4   0.020
 SLO  plan-3  C5   0.020
 SLO  plan-3  C6   0.020
 SLO  plan-3  C7   0.020
 SLO  plan-3  C8   0.020
 SLO  plan-3  C9   0.020
 SLO  plan-3  C10  0.020
 SLO  plan-3  C11  0.020
 SLO  plan-3  C12  0.020
 SLO  plan-3  C13  0.020
 SLO  plan-3  H7   0.020
 SLO  plan-3  H8   0.020
 SLO  plan-3  H9   0.020
 SLO  plan-3  H13  0.020

