# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 18:11:52 2022
#   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  24  15  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

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  OC    -1  -0.588  6.6669  47.9733  17.2064
 R7T  C7   C  C      0   0.391  5.6723  47.7512  16.4891
 R7T  O2   O  O      0  -0.588  4.8645  46.8079  16.5922
 R7T  C4   C  CR6    0  -0.110  5.4169  48.7435  15.3577
 R7T  C5   C  CR16   0  -0.277  4.3664  48.5549  14.4594
 R7T  C6   C  CR16   0  -0.280  4.1337  49.4536  13.4312
 R7T  C3   C  CR16   0  -0.275  6.2253  49.8632  15.1888
 R7T  C2   C  CR16   0  -0.309  5.9922  50.7682  14.1609
 R7T  C1   C  CR6    0   0.137  4.9446  50.5753  13.2679
 R7T  C8   C  CH2    0  -0.581  4.6735  51.5611  12.1596
 R7T  C9   C  CR5    0  -0.141  3.4267  52.3587  12.4088
 R7T  S    S  S2     0   0.199  2.1058  52.3166  11.3068
 R7T  C12  C  CR15   0  -0.477  1.1775  53.3984  12.2576
 R7T  C11  C  CR15   0  -0.178  1.8570  53.7740  13.3764
 R7T  C10  C  CR15   0  -0.224  3.1440  53.1766  13.4630
 R7T  H2   H  HCR6   0   0.236  3.7241  47.6908  14.5674
 R7T  H3   H  HCR6   0   0.238  3.3116  49.2859  12.7438
 R7T  H4   H  HCR6   0   0.237  7.0473  50.0297  15.8725
 R7T  H5   H  HCR6   0   0.240  6.6360  51.6338  14.0515
 R7T  H6   H  HCH2   0   0.271  4.5932  51.0323  11.2071
 R7T  H7   H  HCH2   0   0.275  5.5214  52.2428  12.0572
 R7T  H8   H  HCR5   0   0.289  0.1913  53.7020  11.9420
 R7T  H9   H  HCR5   0   0.261  1.4554  54.4545  14.1138
 R7T  H10  H  HCR5   0   0.256  3.8348  53.3418  14.2789

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  1.714  0.020  1.714
 R7T  S    C9   aromatic  1.721  0.020  1.721
 R7T  C8   C9   single    1.501  0.020  1.501
 R7T  C8   C1   single    1.508  0.020  1.508
 R7T  C12  C11  aromatic  1.362  0.020  1.362
 R7T  C9   C10  aromatic  1.364  0.020  1.364
 R7T  C1   C6   aromatic  1.394  0.020  1.394
 R7T  C1   C2   aromatic  1.390  0.020  1.390
 R7T  C6   C5   aromatic  1.385  0.020  1.385
 R7T  C11  C10  aromatic  1.422  0.020  1.422
 R7T  C2   C3   aromatic  1.389  0.020  1.389
 R7T  C5   C4   aromatic  1.395  0.020  1.395
 R7T  C3   C4   aromatic  1.391  0.020  1.391
 R7T  C4   C7   single    1.526  0.020  1.526
 R7T  C7   O2   deloc     1.246  0.020  1.246
 R7T  C7   O1   deloc     1.246  0.020  1.246
 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  C4   C7   O2   116.42  3.000
 R7T  O2   C7   O1   127.20  3.000
 R7T  C4   C7   O1   116.38  3.000
 R7T  C3   C4   C5   117.92  3.000
 R7T  C3   C4   C7   121.05  3.000
 R7T  C5   C4   C7   121.03  3.000
 R7T  H2   C5   C6   119.50  3.000
 R7T  H2   C5   C4   119.39  3.000
 R7T  C6   C5   C4   121.11  3.000
 R7T  H3   C6   C1   119.42  3.000
 R7T  H3   C6   C5   119.83  3.000
 R7T  C1   C6   C5   120.75  3.000
 R7T  H4   C3   C2   119.65  3.000
 R7T  H4   C3   C4   119.25  3.000
 R7T  C2   C3   C4   121.10  3.000
 R7T  H5   C2   C1   119.57  3.000
 R7T  H5   C2   C3   119.67  3.000
 R7T  C1   C2   C3   120.76  3.000
 R7T  C8   C1   C2   121.13  3.000
 R7T  C2   C1   C6   118.35  3.000
 R7T  C8   C1   C6   120.51  3.000
 R7T  H7   C8   H6   106.10  3.000
 R7T  H7   C8   C9   109.19  3.000
 R7T  H6   C8   C9   109.94  3.000
 R7T  H7   C8   C1   109.71  3.000
 R7T  H6   C8   C1   109.73  3.000
 R7T  C9   C8   C1   112.01  3.000
 R7T  C10  C9   S    110.52  3.000
 R7T  C10  C9   C8   128.26  3.000
 R7T  S    C9   C8   121.22  3.000
 R7T  C12  S    C9    92.58  3.000
 R7T  H8   C12  C11  128.22  3.000
 R7T  H8   C12  S    120.70  3.000
 R7T  C11  C12  S    111.08  3.000
 R7T  H9   C11  C10  124.02  3.000
 R7T  H9   C11  C12  123.28  3.000
 R7T  C10  C11  C12  112.70  3.000
 R7T  H10  C10  C11  124.05  3.000
 R7T  H10  C10  C9   122.83  3.000
 R7T  C11  C10  C9   113.12  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  Var_01    C9   C8   C1   C6     70.60  30.0  2
 R7T  Var_02    S    C9   C8   C1   -120.18  30.0  2
 R7T  Var_03    C5   C4   C7   O1    177.09  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

