# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 12 16:07:20 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: 3-[4-(4-phenylthiophen-2-yl)phenyl]propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCc1ccc(cc1)c2scc(c2)c3ccccc3
#
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
 03J  03J  '3-[4-(4-phenylthiophen-2-yl)phenyl]propanoic acid'  ligand  37  22  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_03J
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
 03J  O2    O  O      0  -0.606  -7.4384  -0.6892  -0.6541
 03J  S7    S  S2     0   0.236   1.6484   2.3543   0.1429
 03J  C11   C  C      0   0.414  -6.8366  -0.9231   0.4118
 03J  C12   C  CH2    0  -0.576  -5.3285  -0.6151   0.4721
 03J  C13   C  CH2    0  -0.498  -4.7270  -0.0226  -0.8003
 03J  C14   C  CR16   0  -0.291  -2.3262  -0.7502  -1.0590
 03J  C15   C  CR16   0  -0.310  -1.3975   1.5653   0.1198
 03J  C16   C  CR6    0   0.138  -0.4733   0.6016  -0.2905
 03J  C17   C  CR16   0  -0.313  -0.9650  -0.5604  -0.8902
 03J  C18   C  CR5    0  -0.204   0.9650   0.7860  -0.1033
 03J  C19   C  CR15   0  -0.297   1.9488  -0.1618  -0.1067
 03J  C20   C  CR5    0   0.217   3.2597   0.3654   0.0869
 03J  C21   C  C      0   0.102   4.4823  -0.4504   0.1222
 03J  C22   C  C1     0  -0.319   5.7234   0.0993  -0.2083
 03J  C23   C  C1     0  -0.237   6.8760  -0.6693  -0.1616
 03J  C24   C  C1     0  -0.269   6.8125  -2.0071   0.2082
 03J  C25   C  C1     0  -0.236   5.5841  -2.5671   0.5314
 03J  C26   C  C1     0  -0.327   4.4312  -1.7962   0.4907
 03J  C27   C  CR6    0   0.121  -3.2507   0.2108  -0.6543
 03J  C28   C  CR16   0  -0.290  -2.7569   1.3729  -0.0650
 03J  C29   C  CR15   0  -0.577   3.2327   1.7245   0.2418
 03J  H12   H  HCH2   0   0.229  -5.1494   0.0651   1.3121
 03J  H12A  H  HCH2   0   0.230  -4.7970  -1.5370   0.7337
 03J  H13   H  HCH2   0   0.230  -4.9090  -0.6963  -1.6401
 03J  H13A  H  HCH2   0   0.231  -5.2274   0.9186  -1.0387
 03J  H14   H  HCR6   0   0.248  -2.6770  -1.6632  -1.5263
 03J  H15   H  HCR6   0   0.249  -1.0620   2.4770   0.6005
 03J  H17   H  HCR6   0   0.251  -0.2807  -1.3208  -1.2451
 03J  H19   H  HCR5   0   0.264   1.7455  -1.2141  -0.2491
 03J  H22   H  H      0   0.251   5.7902   1.1340  -0.5208
 03J  H23   H  H      0   0.258   7.8266  -0.2231  -0.4236
 03J  H24   H  H      0   0.258   7.7117  -2.6081   0.2428
 03J  H25   H  H      0   0.258   5.5205  -3.6079   0.8217
 03J  H26   H  H      0   0.253   3.4858  -2.2481   0.7628
 03J  H28   H  HCR6   0   0.248  -3.4463   2.1435   0.2605
 03J  H29   H  HCR5   0   0.294   4.0619   2.3898   0.4286
 03J  OXT   O  OC    -1  -0.629  -7.3340  -1.3918   1.4570

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
 03J  O2   C11   deloc     1.246  0.020  1.246
 03J  S7   C18   aromatic  1.728  0.020  1.728
 03J  S7   C29   aromatic  1.708  0.020  1.708
 03J  C11  C12   single    1.540  0.020  1.540
 03J  C12  C13   single    1.527  0.020  1.527
 03J  C12  H12   single    0.970  0.020  1.090
 03J  C12  H12A  single    0.970  0.020  1.090
 03J  C13  C27   single    1.502  0.020  1.502
 03J  C13  H13   single    0.970  0.020  1.090
 03J  C13  H13A  single    0.970  0.020  1.090
 03J  C14  C17   aromatic  1.385  0.020  1.385
 03J  C14  C27   aromatic  1.394  0.020  1.394
 03J  C14  H14   single    0.930  0.020  1.080
 03J  C15  C16   aromatic  1.397  0.020  1.397
 03J  C15  C28   aromatic  1.385  0.020  1.385
 03J  C15  H15   single    0.930  0.020  1.080
 03J  C16  C17   aromatic  1.397  0.020  1.397
 03J  C16  C18   single    1.462  0.020  1.462
 03J  C17  H17   single    0.930  0.020  1.080
 03J  C18  C19   aromatic  1.366  0.020  1.366
 03J  C19  C20   aromatic  1.426  0.020  1.426
 03J  C19  H19   single    0.930  0.020  1.080
 03J  C20  C21   single    1.470  0.020  1.470
 03J  C20  C29   aromatic  1.368  0.020  1.368
 03J  C21  C22   aromatic  1.397  0.020  1.397
 03J  C21  C26   aromatic  1.396  0.020  1.396
 03J  C22  C23   aromatic  1.386  0.020  1.386
 03J  C22  H22   single    0.930  0.020  1.080
 03J  C23  C24   aromatic  1.389  0.020  1.389
 03J  C23  H23   single    0.930  0.020  1.080
 03J  C24  C25   aromatic  1.388  0.020  1.388
 03J  C24  H24   single    0.930  0.020  1.080
 03J  C25  C26   aromatic  1.387  0.020  1.387
 03J  C25  H25   single    0.930  0.020  1.080
 03J  C26  H26   single    0.930  0.020  1.080
 03J  C27  C28   aromatic  1.393  0.020  1.393
 03J  C28  H28   single    0.930  0.020  1.080
 03J  C29  H29   single    0.930  0.020  1.080
 03J  C11  OXT   deloc     1.249  0.020  1.249

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
 03J  C29   S7   C18   92.31  3.000
 03J  OXT   C11  C12  115.61  3.000
 03J  OXT   C11  O2   126.44  3.000
 03J  C12   C11  O2   117.95  3.000
 03J  H12A  C12  H12  105.07  3.000
 03J  H12A  C12  C13  109.53  3.000
 03J  H12   C12  C13  109.49  3.000
 03J  H12A  C12  C11  108.42  3.000
 03J  H12   C12  C11  108.31  3.000
 03J  C13   C12  C11  115.50  3.000
 03J  H13A  C13  H13  106.70  3.000
 03J  H13A  C13  C27  109.74  3.000
 03J  H13   C13  C27  109.55  3.000
 03J  H13A  C13  C12  109.62  3.000
 03J  H13   C13  C12  109.62  3.000
 03J  C27   C13  C12  111.50  3.000
 03J  H14   C14  C27  119.43  3.000
 03J  H14   C14  C17  119.09  3.000
 03J  C27   C14  C17  121.48  3.000
 03J  H15   C15  C28  118.67  3.000
 03J  H15   C15  C16  120.38  3.000
 03J  C28   C15  C16  120.95  3.000
 03J  C18   C16  C17  120.40  3.000
 03J  C18   C16  C15  121.75  3.000
 03J  C17   C16  C15  117.85  3.000
 03J  H17   C17  C16  120.17  3.000
 03J  H17   C17  C14  119.01  3.000
 03J  C16   C17  C14  120.82  3.000
 03J  C19   C18  C16  128.36  3.000
 03J  C19   C18  S7   110.20  3.000
 03J  C16   C18  S7   121.44  3.000
 03J  H19   C19  C20  123.40  3.000
 03J  H19   C19  C18  122.70  3.000
 03J  C20   C19  C18  113.90  3.000
 03J  C29   C20  C21  124.39  3.000
 03J  C29   C20  C19  111.38  3.000
 03J  C21   C20  C19  124.23  3.000
 03J  C26   C21  C22  118.31  3.000
 03J  C26   C21  C20  120.71  3.000
 03J  C22   C21  C20  120.98  3.000
 03J  H22   C22  C23  119.23  3.000
 03J  H22   C22  C21  119.93  3.000
 03J  C23   C22  C21  120.84  3.000
 03J  H23   C23  C24  120.11  3.000
 03J  H23   C23  C22  119.58  3.000
 03J  C24   C23  C22  120.32  3.000
 03J  H24   C24  C25  120.26  3.000
 03J  H24   C24  C23  120.35  3.000
 03J  C25   C24  C23  119.40  3.000
 03J  H25   C25  C26  119.56  3.000
 03J  H25   C25  C24  120.15  3.000
 03J  C26   C25  C24  120.29  3.000
 03J  H26   C26  C25  119.10  3.000
 03J  H26   C26  C21  120.04  3.000
 03J  C25   C26  C21  120.86  3.000
 03J  C28   C27  C14  117.57  3.000
 03J  C28   C27  C13  121.27  3.000
 03J  C14   C27  C13  121.12  3.000
 03J  H28   C28  C27  119.63  3.000
 03J  H28   C28  C15  119.03  3.000
 03J  C27   C28  C15  121.34  3.000
 03J  H29   C29  C20  128.08  3.000
 03J  H29   C29  S7   119.69  3.000
 03J  C20   C29  S7   112.21  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
 03J  CONST_03  C20  C19  C18  S7      0.00   0.0  0
 03J  CONST_04  C19  C20  C29  S7      0.00   0.0  0
 03J  CONST_05  C21  C20  C29  S7    180.00   0.0  0
 03J  CONST_06  C15  C16  C17  C14     0.00   0.0  0
 03J  CONST_07  C18  C16  C17  C14   180.00   0.0  0
 03J  CONST_08  C15  C28  C27  C14     0.00   0.0  0
 03J  CONST_10  C27  C28  C15  C16     0.00   0.0  0
 03J  CONST_11  C27  C14  C17  C16     0.00   0.0  0
 03J  CONST_12  C29  S7   C18  C16   180.00   0.0  0
 03J  CONST_13  C20  C19  C18  C16   180.00   0.0  0
 03J  CONST_14  C28  C27  C14  C17     0.00   0.0  0
 03J  CONST_15  C28  C15  C16  C17     0.00   0.0  0
 03J  CONST_17  C20  C29  S7   C18     0.00   0.0  0
 03J  CONST_18  C28  C15  C16  C18   180.00   0.0  0
 03J  CONST_19  C21  C20  C19  C18   180.00   0.0  0
 03J  CONST_20  C29  C20  C19  C18     0.00   0.0  0
 03J  CONST_21  C29  S7   C18  C19     0.00   0.0  0
 03J  CONST_24  C23  C22  C21  C20   180.00   0.0  0
 03J  CONST_25  C25  C26  C21  C20   180.00   0.0  0
 03J  CONST_26  C24  C23  C22  C21     0.00   0.0  0
 03J  CONST_27  C24  C25  C26  C21     0.00   0.0  0
 03J  CONST_29  C25  C26  C21  C22     0.00   0.0  0
 03J  CONST_30  C25  C24  C23  C22     0.00   0.0  0
 03J  CONST_31  C26  C21  C22  C23     0.00   0.0  0
 03J  CONST_32  C26  C25  C24  C23     0.00   0.0  0
 03J  CONST_34  C17  C14  C27  C13   180.00   0.0  0
 03J  CONST_35  C15  C28  C27  C13   180.00   0.0  0
 03J  CONST_36  H19  C19  C18  S7    180.00   0.0  0
 03J  CONST_37  H28  C28  C27  C14   180.00   0.0  0
 03J  CONST_38  H17  C17  C16  C15   180.00   0.0  0
 03J  CONST_39  H14  C14  C17  C16   180.00   0.0  0
 03J  CONST_40  H15  C15  C16  C17   180.00   0.0  0
 03J  CONST_41  H29  C29  S7   C18   180.00   0.0  0
 03J  CONST_42  H22  C22  C21  C20     0.00   0.0  0
 03J  CONST_43  H26  C26  C21  C20     0.00   0.0  0
 03J  CONST_44  H23  C23  C22  C21   180.00   0.0  0
 03J  CONST_45  H25  C25  C26  C21   180.00   0.0  0
 03J  CONST_46  H24  C24  C23  C22   180.00   0.0  0
 03J  Var_01    C14  C27  C13  C12    93.34  30.0  2
 03J  Var_02    C27  C13  C12  C11  -178.61  30.0  3
 03J  Var_03    C13  C12  C11  O2      0.99  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
 03J  plan-1  S7   0.020
 03J  plan-1  C16  0.020
 03J  plan-1  C18  0.020
 03J  plan-1  C19  0.020
 03J  plan-1  C20  0.020
 03J  plan-1  C21  0.020
 03J  plan-1  C29  0.020
 03J  plan-1  H19  0.020
 03J  plan-1  H29  0.020
 03J  plan-2  C13  0.020
 03J  plan-2  C14  0.020
 03J  plan-2  C15  0.020
 03J  plan-2  C16  0.020
 03J  plan-2  C17  0.020
 03J  plan-2  C18  0.020
 03J  plan-2  C27  0.020
 03J  plan-2  C28  0.020
 03J  plan-2  H14  0.020
 03J  plan-2  H15  0.020
 03J  plan-2  H17  0.020
 03J  plan-2  H28  0.020
 03J  plan-3  C20  0.020
 03J  plan-3  C21  0.020
 03J  plan-3  C22  0.020
 03J  plan-3  C23  0.020
 03J  plan-3  C24  0.020
 03J  plan-3  C25  0.020
 03J  plan-3  C26  0.020
 03J  plan-3  H22  0.020
 03J  plan-3  H23  0.020
 03J  plan-3  H24  0.020
 03J  plan-3  H25  0.020
 03J  plan-3  H26  0.020
 03J  plan-4  O2   0.020
 03J  plan-4  C11  0.020
 03J  plan-4  C12  0.020
 03J  plan-4  OXT  0.020

