# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 15:16:44 2021
#   Inital geometry file: a 70 line input string
#   Ligand name: 4-[(thiophen-2-yl)methyl]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccc(Cc2sccc2)cc1
#
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
 R7T  R7T  '4-[(thiophen-2-yl)methyl]benzoic acid'  ligand  25  15  .  2022-03-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_R7T
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
 R7T  O1   O  OH1   0  -0.594  6.6128  48.0157  17.1525
 R7T  C7   C  C     0   0.530  5.5593  47.7531  16.3911
 R7T  O2   O  O     0  -0.441  4.8381  46.8001  16.5699
 R7T  C4   C  CR6   0  -0.097  5.3643  48.7455  15.3080
 R7T  C5   C  CR16  0  -0.242  4.2873  48.5773  14.4363
 R7T  C6   C  CR16  0  -0.275  4.0707  49.4795  13.4127
 R7T  C3   C  CR16  0  -0.242  6.2184  49.8307  15.1299
 R7T  C2   C  CR16  0  -0.308  5.9957  50.7305  14.0981
 R7T  C1   C  CR6   0   0.155  4.9233  50.5678  13.2294
 R7T  C8   C  CH2   0  -0.585  4.6673  51.5554  12.1211
 R7T  C9   C  CR5   0  -0.148  3.4256  52.3591  12.3739
 R7T  S    S  S2    0   0.204  2.0899  52.3040  11.2911
 R7T  C12  C  CR15  0  -0.477  1.1757  53.3959  12.2441
 R7T  C11  C  CR15  0  -0.179  1.8698  53.7830  13.3499
 R7T  C10  C  CR15  0  -0.222  3.1582  53.1874  13.4242
 R7T  H1   H  HOH1  0   0.487  6.7017  47.3379  17.8388
 R7T  H2   H  HCR6  0   0.265  3.6163  47.7377  14.5584
 R7T  H3   H  HCR6  0   0.256  3.2287  49.3408  12.7449
 R7T  H4   H  HCR6  0   0.268  7.0614  49.9854  15.7887
 R7T  H5   H  HCR6  0   0.261  6.6696  51.5685  13.9701
 R7T  H6   H  HCH2  0   0.281  4.5843  51.0235  11.1705
 R7T  H7   H  HCH2  0   0.284  5.5217  52.2284  12.0208
 R7T  H8   H  HCR5  0   0.293  0.1845  53.6940  11.9395
 R7T  H9   H  HCR5  0   0.265  1.4775  54.4680  14.0880
 R7T  H10  H  HCR5  0   0.258  3.8597  53.3618  14.2289

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
 R7T  S    C12  aromatic  1.713  0.020  1.713
 R7T  S    C9   aromatic  1.720  0.020  1.720
 R7T  C8   C9   single    1.501  0.020  1.501
 R7T  C8   C1   single    1.506  0.020  1.506
 R7T  C12  C11  aromatic  1.362  0.020  1.362
 R7T  C9   C10  aromatic  1.364  0.020  1.364
 R7T  C1   C6   aromatic  1.395  0.020  1.395
 R7T  C1   C2   aromatic  1.390  0.020  1.390
 R7T  C6   C5   aromatic  1.382  0.020  1.382
 R7T  C11  C10  aromatic  1.421  0.020  1.421
 R7T  C2   C3   aromatic  1.387  0.020  1.387
 R7T  C5   C4   aromatic  1.396  0.020  1.396
 R7T  C3   C4   aromatic  1.392  0.020  1.392
 R7T  C4   C7   single    1.482  0.020  1.482
 R7T  C7   O2   double    1.208  0.020  1.208
 R7T  C7   O1   single    1.326  0.020  1.326
 R7T  O1   H1   single    0.850  0.020  0.980
 R7T  C5   H2   single    0.930  0.020  1.080
 R7T  C6   H3   single    0.930  0.020  1.080
 R7T  C3   H4   single    0.930  0.020  1.080
 R7T  C2   H5   single    0.930  0.020  1.080
 R7T  C8   H6   single    0.970  0.020  1.090
 R7T  C8   H7   single    0.970  0.020  1.090
 R7T  C12  H8   single    0.930  0.020  1.080
 R7T  C11  H9   single    0.930  0.020  1.080
 R7T  C10  H10  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
 R7T  H1   O1   C7   109.94  3.000
 R7T  C4   C7   O2   123.90  3.000
 R7T  O2   C7   O1   123.05  3.000
 R7T  C4   C7   O1   113.05  3.000
 R7T  C3   C4   C5   119.16  3.000
 R7T  C3   C4   C7   122.32  3.000
 R7T  C5   C4   C7   118.51  3.000
 R7T  H2   C5   C6   119.55  3.000
 R7T  H2   C5   C4   120.11  3.000
 R7T  C6   C5   C4   120.34  3.000
 R7T  H3   C6   C1   119.60  3.000
 R7T  H3   C6   C5   119.66  3.000
 R7T  C1   C6   C5   120.74  3.000
 R7T  H4   C3   C2   119.05  3.000
 R7T  H4   C3   C4   120.79  3.000
 R7T  C2   C3   C4   120.15  3.000
 R7T  H5   C2   C1   119.79  3.000
 R7T  H5   C2   C3   119.34  3.000
 R7T  C1   C2   C3   120.86  3.000
 R7T  C8   C1   C2   120.95  3.000
 R7T  C2   C1   C6   118.75  3.000
 R7T  C8   C1   C6   120.29  3.000
 R7T  H7   C8   H6   106.23  3.000
 R7T  H7   C8   C9   109.44  3.000
 R7T  H6   C8   C9   110.15  3.000
 R7T  H7   C8   C1   109.79  3.000
 R7T  H6   C8   C1   109.51  3.000
 R7T  C9   C8   C1   111.58  3.000
 R7T  C10  C9   S    110.60  3.000
 R7T  C10  C9   C8   128.11  3.000
 R7T  S    C9   C8   121.28  3.000
 R7T  C12  S    C9    92.51  3.000
 R7T  H8   C12  C11  128.24  3.000
 R7T  H8   C12  S    120.61  3.000
 R7T  C11  C12  S    111.15  3.000
 R7T  H9   C11  C10  123.99  3.000
 R7T  H9   C11  C12  123.35  3.000
 R7T  C10  C11  C12  112.67  3.000
 R7T  H10  C10  C11  124.00  3.000
 R7T  H10  C10  C9   122.93  3.000
 R7T  C11  C10  C9   113.07  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
 R7T  CONST_01  C1   C6   C5   C4      0.00   0.0  0
 R7T  CONST_02  C1   C2   C3   C4      0.00   0.0  0
 R7T  CONST_03  C2   C1   C6   C5      0.00   0.0  0
 R7T  CONST_04  C2   C3   C4   C5      0.00   0.0  0
 R7T  CONST_05  C3   C2   C1   C6      0.00   0.0  0
 R7T  CONST_06  C3   C4   C5   C6      0.00   0.0  0
 R7T  CONST_07  C11  C12  S    C9      0.00   0.0  0
 R7T  CONST_08  C12  C11  C10  C9      0.00   0.0  0
 R7T  CONST_09  C10  C11  C12  S       0.00   0.0  0
 R7T  CONST_10  C11  C10  C9   S       0.00   0.0  0
 R7T  CONST_11  C10  C9   S    C12     0.00   0.0  0
 R7T  CONST_12  C6   C5   C4   C7    180.00   0.0  0
 R7T  CONST_13  C2   C3   C4   C7    180.00   0.0  0
 R7T  CONST_14  C8   C1   C6   C5    180.00   0.0  0
 R7T  CONST_15  C8   C1   C2   C3    180.00   0.0  0
 R7T  CONST_16  C12  S    C9   C8    180.00   0.0  0
 R7T  CONST_17  C11  C10  C9   C8    180.00   0.0  0
 R7T  CONST_18  H3   C6   C5   C4    180.00   0.0  0
 R7T  CONST_19  H5   C2   C3   C4    180.00   0.0  0
 R7T  CONST_20  H4   C3   C4   C5    180.00   0.0  0
 R7T  CONST_21  H2   C5   C4   C3    180.00   0.0  0
 R7T  CONST_22  H8   C12  S    C9    180.00   0.0  0
 R7T  CONST_23  H9   C11  C10  C9    180.00   0.0  0
 R7T  CONST_24  H10  C10  C9   S     180.00   0.0  0
 R7T  CONST_25  H1   O1   C7   C4    180.00   0.0  0
 R7T  Var_01    C9   C8   C1   C6     68.40  30.0  2
 R7T  Var_02    S    C9   C8   C1   -118.82  30.0  2
 R7T  Var_03    C5   C4   C7   O1    179.93  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
 R7T  plan-1  C8   0.020
 R7T  plan-1  C9   0.020
 R7T  plan-1  S    0.020
 R7T  plan-1  C12  0.020
 R7T  plan-1  C11  0.020
 R7T  plan-1  C10  0.020
 R7T  plan-1  H8   0.020
 R7T  plan-1  H9   0.020
 R7T  plan-1  H10  0.020
 R7T  plan-2  C7   0.020
 R7T  plan-2  C4   0.020
 R7T  plan-2  C5   0.020
 R7T  plan-2  C6   0.020
 R7T  plan-2  C3   0.020
 R7T  plan-2  C2   0.020
 R7T  plan-2  C1   0.020
 R7T  plan-2  C8   0.020
 R7T  plan-2  H2   0.020
 R7T  plan-2  H3   0.020
 R7T  plan-2  H4   0.020
 R7T  plan-2  H5   0.020
 R7T  plan-3  O1   0.020
 R7T  plan-3  C7   0.020
 R7T  plan-3  O2   0.020
 R7T  plan-3  C4   0.020
 R7T  plan-3  H1   0.020

