# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 13:32:32 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: {(1Z)-5-fluoro-2-methyl-1-[4-(methylsulfanyl)benzylidene]-1H-inden-3-yl}acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSc1ccc(cc1)/C=C2/C(=C(CC(O)=O)c3cc(F)ccc23)C
#
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
 SFI  SFI  '{(1Z)-5-fluoro-2-methyl-1-[4-(methylsulfanyl)benzylidene]-1H-inden-3-yl}acetic acid'  ligand  40  24  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SFI
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
 SFI  F     F  F      0  -0.322  -2.3386   4.2604   0.1533
 SFI  S     S  S2     0   0.050   6.2505  -0.4405   0.2495
 SFI  C1    C  CR5    0   0.118  -2.9598  -0.5610  -0.5357
 SFI  O1    O  OC    -1  -0.621  -6.5375  -0.3525   0.2177
 SFI  C2    C  CR56   0   0.107  -2.2571   0.6983  -0.2965
 SFI  O2    O  O      0  -0.591  -4.7414  -0.1864   1.5293
 SFI  C3    C  CR5    0  -0.001  -2.0568  -1.5676  -0.4783
 SFI  C4    C  CR56   0   0.035  -0.8863   0.4400  -0.1121
 SFI  C5    C  CR5    0   0.144  -0.7106  -1.0180  -0.2414
 SFI  C6    C  CH2    0  -0.745  -4.4178  -0.6278  -0.8017
 SFI  C7    C  CR16   0  -0.511  -2.7667   1.9827  -0.2097
 SFI  C8    C  CR16   0  -0.333  -0.0311   1.4796   0.2128
 SFI  C9    C  C1     0  -0.401   0.3879  -1.7923  -0.1617
 SFI  C10   C  CH3    0  -0.763  -2.3124  -3.0253  -0.6523
 SFI  C11   C  CR6    0   0.537  -1.8730   3.0002   0.0776
 SFI  C12   C  CR16   0  -0.430  -0.5279   2.7781   0.3058
 SFI  C13   C  CR6    0   0.092   1.7944  -1.4018  -0.0769
 SFI  C14   C  C      0   0.426  -5.3107  -0.3607   0.4385
 SFI  C15   C  CR16   0  -0.285   2.6577  -2.1113   0.7657
 SFI  C16   C  CR16   0  -0.306   2.3454  -0.3967  -0.8704
 SFI  C17   C  CR16   0  -0.253   3.9984  -1.7917   0.8530
 SFI  C18   C  CR16   0  -0.241   3.6918  -0.0742  -0.7997
 SFI  C19   C  CR6    0  -0.121   4.5324  -0.7621   0.0724
 SFI  C20   C  CH3    0  -0.797   6.5404   0.9544  -0.8521
 SFI  H6    H  HCH2   0   0.243  -4.6868   0.0999  -1.5759
 SFI  H6A   H  HCH2   0   0.256  -4.6911  -1.6029  -1.2140
 SFI  H7    H  HCR6   0   0.261  -3.8178   2.1957  -0.3560
 SFI  H8    H  HCR6   0   0.264   1.0197   1.3140   0.4015
 SFI  H9    H  H      0   0.264   0.2239  -2.8662  -0.1659
 SFI  H10   H  HCH3   0   0.242  -1.7334  -3.4400  -1.4802
 SFI  H10A  H  HCH3   0   0.244  -2.0341  -3.5886   0.2414
 SFI  H10B  H  HCH3   0   0.254  -3.3630  -3.2272  -0.8515
 SFI  H12   H  HCR6   0   0.272   0.1274   3.6035   0.5502
 SFI  H15   H  HCR6   0   0.259   2.2682  -2.9201   1.3721
 SFI  H16   H  HCR6   0   0.272   1.7202   0.1322  -1.5782
 SFI  H17   H  HCR6   0   0.266   4.6360  -2.3486   1.5289
 SFI  H18   H  HCR6   0   0.268   4.0725   0.7105  -1.4388
 SFI  H20   H  HCH3   0   0.296   7.5971   1.1960  -0.7561
 SFI  H20A  H  HCH3   0   0.276   6.3355   0.7000  -1.8902
 SFI  H20B  H  HCH3   0   0.277   5.9559   1.8242  -0.5579

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
 SFI  F    C11   single    1.346  0.020  1.346
 SFI  S    C19   single    1.757  0.020  1.757
 SFI  S    C20   single    1.801  0.020  1.801
 SFI  C1   C2    single    1.462  0.020  1.462
 SFI  C1   C3    double    1.354  0.020  1.354
 SFI  C1   C6    single    1.484  0.020  1.484
 SFI  O1   C14   deloc     1.246  0.020  1.246
 SFI  C2   C4    aromatic  1.407  0.020  1.407
 SFI  C2   C7    aromatic  1.385  0.020  1.385
 SFI  O2   C14   deloc     1.243  0.020  1.243
 SFI  C3   C5    single    1.473  0.020  1.473
 SFI  C3   C10   single    1.490  0.020  1.490
 SFI  C4   C5    single    1.474  0.020  1.474
 SFI  C4   C8    aromatic  1.385  0.020  1.385
 SFI  C5   C9    double    1.346  0.020  1.346
 SFI  C6   C14   single    1.551  0.020  1.551
 SFI  C7   C11   aromatic  1.384  0.020  1.384
 SFI  C8   C12   aromatic  1.393  0.020  1.393
 SFI  C9   C13   single    1.462  0.020  1.462
 SFI  C11  C12   aromatic  1.382  0.020  1.382
 SFI  C13  C15   aromatic  1.400  0.020  1.400
 SFI  C13  C16   aromatic  1.394  0.020  1.394
 SFI  C15  C17   aromatic  1.381  0.020  1.381
 SFI  C16  C18   aromatic  1.386  0.020  1.386
 SFI  C17  C19   aromatic  1.398  0.020  1.398
 SFI  C18  C19   aromatic  1.393  0.020  1.393
 SFI  C6   H6    single    0.970  0.020  1.090
 SFI  C6   H6A   single    0.970  0.020  1.090
 SFI  C7   H7    single    0.930  0.020  1.080
 SFI  C8   H8    single    0.930  0.020  1.080
 SFI  C9   H9    single    0.930  0.020  1.080
 SFI  C10  H10   single    0.970  0.020  1.090
 SFI  C10  H10A  single    0.970  0.020  1.090
 SFI  C10  H10B  single    0.970  0.020  1.090
 SFI  C12  H12   single    0.930  0.020  1.080
 SFI  C15  H15   single    0.930  0.020  1.080
 SFI  C16  H16   single    0.930  0.020  1.080
 SFI  C17  H17   single    0.930  0.020  1.080
 SFI  C18  H18   single    0.930  0.020  1.080
 SFI  C20  H20   single    0.970  0.020  1.090
 SFI  C20  H20A  single    0.970  0.020  1.090
 SFI  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
 SFI  C20   S    C19   103.74  3.000
 SFI  C6    C1   C3    129.03  3.000
 SFI  C6    C1   C2    122.72  3.000
 SFI  C3    C1   C2    108.25  3.000
 SFI  C7    C2   C4    121.37  3.000
 SFI  C7    C2   C1    129.24  3.000
 SFI  C4    C2   C1    109.37  3.000
 SFI  C10   C3   C5    122.72  3.000
 SFI  C10   C3   C1    127.46  3.000
 SFI  C5    C3   C1    109.81  3.000
 SFI  C8    C4   C5    133.59  3.000
 SFI  C8    C4   C2    119.64  3.000
 SFI  C5    C4   C2    106.63  3.000
 SFI  C9    C5   C4    131.36  3.000
 SFI  C9    C5   C3    122.72  3.000
 SFI  C4    C5   C3    105.91  3.000
 SFI  H6A   C6   H6    105.33  3.000
 SFI  H6A   C6   C14   108.13  3.000
 SFI  H6    C6   C14   108.01  3.000
 SFI  H6A   C6   C1    110.69  3.000
 SFI  H6    C6   C1    109.75  3.000
 SFI  C14   C6   C1    114.49  3.000
 SFI  H7    C7   C11   120.69  3.000
 SFI  H7    C7   C2    122.11  3.000
 SFI  C11   C7   C2    117.21  3.000
 SFI  H8    C8   C12   118.55  3.000
 SFI  H8    C8   C4    121.77  3.000
 SFI  C12   C8   C4    119.68  3.000
 SFI  H9    C9   C13   114.17  3.000
 SFI  H9    C9   C5    116.43  3.000
 SFI  C13   C9   C5    129.40  3.000
 SFI  H10B  C10  H10A  107.46  3.000
 SFI  H10B  C10  H10   107.61  3.000
 SFI  H10A  C10  H10   106.81  3.000
 SFI  H10B  C10  C3    111.62  3.000
 SFI  H10A  C10  C3    111.42  3.000
 SFI  H10   C10  C3    111.66  3.000
 SFI  C12   C11  C7    122.98  3.000
 SFI  C12   C11  F     118.55  3.000
 SFI  C7    C11  F     118.46  3.000
 SFI  H12   C12  C11   120.27  3.000
 SFI  H12   C12  C8    120.67  3.000
 SFI  C11   C12  C8    119.06  3.000
 SFI  C16   C13  C15   117.67  3.000
 SFI  C16   C13  C9    122.67  3.000
 SFI  C15   C13  C9    119.53  3.000
 SFI  C6    C14  O2    117.53  3.000
 SFI  C6    C14  O1    115.21  3.000
 SFI  O2    C14  O1    127.26  3.000
 SFI  H15   C15  C17   119.11  3.000
 SFI  H15   C15  C13   119.58  3.000
 SFI  C17   C15  C13   121.30  3.000
 SFI  H16   C16  C18   118.73  3.000
 SFI  H16   C16  C13   119.74  3.000
 SFI  C18   C16  C13   121.50  3.000
 SFI  H17   C17  C19   120.15  3.000
 SFI  H17   C17  C15   119.46  3.000
 SFI  C19   C17  C15   120.40  3.000
 SFI  H18   C18  C19   121.06  3.000
 SFI  H18   C18  C16   118.73  3.000
 SFI  C19   C18  C16   120.21  3.000
 SFI  C18   C19  C17   118.86  3.000
 SFI  C18   C19  S     124.25  3.000
 SFI  C17   C19  S     116.88  3.000
 SFI  H20B  C20  H20A  110.10  3.000
 SFI  H20B  C20  H20   108.68  3.000
 SFI  H20A  C20  H20   108.60  3.000
 SFI  H20B  C20  S     111.54  3.000
 SFI  H20A  C20  S     111.84  3.000
 SFI  H20   C20  S     105.92  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
 SFI  CONST_01  C12  C8   C4   C2     0.00   0.0  0
 SFI  CONST_02  C12  C11  C7   C2     0.00   0.0  0
 SFI  CONST_03  C11  C7   C2   C4     0.00   0.0  0
 SFI  CONST_04  C11  C12  C8   C4     0.00   0.0  0
 SFI  CONST_05  C8   C4   C2   C7     0.00   0.0  0
 SFI  CONST_06  C8   C12  C11  C7     0.00   0.0  0
 SFI  CONST_07  C19  C17  C15  C13    0.00   0.0  0
 SFI  CONST_08  C19  C18  C16  C13    0.00   0.0  0
 SFI  CONST_09  C18  C16  C13  C15    0.00   0.0  0
 SFI  CONST_10  C18  C19  C17  C15    0.00   0.0  0
 SFI  CONST_11  C17  C15  C13  C16    0.00   0.0  0
 SFI  CONST_12  C17  C19  C18  C16    0.00   0.0  0
 SFI  CONST_13  C2   C7   C11  F    180.00   0.0  0
 SFI  CONST_14  C8   C12  C11  F    180.00   0.0  0
 SFI  CONST_15  C15  C17  C19  S    180.00   0.0  0
 SFI  CONST_16  C16  C18  C19  S    180.00   0.0  0
 SFI  CONST_17  C17  C15  C13  C9   180.00   0.0  0
 SFI  CONST_18  C18  C16  C13  C9   180.00   0.0  0
 SFI  CONST_19  H7   C7   C2   C1     0.00   0.0  0
 SFI  CONST_20  H8   C8   C4   C2   180.00   0.0  0
 SFI  CONST_21  H12  C12  C8   C4   180.00   0.0  0
 SFI  CONST_22  H17  C17  C15  C13  180.00   0.0  0
 SFI  CONST_23  H18  C18  C16  C13  180.00   0.0  0
 SFI  CONST_24  H16  C16  C13  C15  180.00   0.0  0
 SFI  CONST_25  H15  C15  C13  C16  180.00   0.0  0
 SFI  Var_01    C13  C9   C5   C3   172.70  30.0  2
 SFI  Var_02    C15  C13  C9   C5   140.34  30.0  2
 SFI  Var_03    C14  C6   C1   C2   -72.79  30.0  3
 SFI  Var_04    H10  C10  C3   C1   120.96  30.0  3
 SFI  Var_05    O1   C14  C6   C1   176.84  30.0  3
 SFI  Var_06    H20  C20  S    C19  179.01  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
 SFI  plan-1  S    0.020
 SFI  plan-1  C9   0.020
 SFI  plan-1  C13  0.020
 SFI  plan-1  C15  0.020
 SFI  plan-1  C16  0.020
 SFI  plan-1  C17  0.020
 SFI  plan-1  C18  0.020
 SFI  plan-1  C19  0.020
 SFI  plan-1  H15  0.020
 SFI  plan-1  H16  0.020
 SFI  plan-1  H17  0.020
 SFI  plan-1  H18  0.020
 SFI  plan-2  F    0.020
 SFI  plan-2  C1   0.020
 SFI  plan-2  C2   0.020
 SFI  plan-2  C3   0.020
 SFI  plan-2  C4   0.020
 SFI  plan-2  C5   0.020
 SFI  plan-2  C6   0.020
 SFI  plan-2  C7   0.020
 SFI  plan-2  C8   0.020
 SFI  plan-2  C9   0.020
 SFI  plan-2  C10  0.020
 SFI  plan-2  C11  0.020
 SFI  plan-2  C12  0.020
 SFI  plan-2  H7   0.020
 SFI  plan-2  H8   0.020
 SFI  plan-2  H12  0.020
 SFI  plan-3  O1   0.020
 SFI  plan-3  O2   0.020
 SFI  plan-3  C6   0.020
 SFI  plan-3  C14  0.020

