# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 03:26:38 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: 5-phenylthiophene-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1sc(cc1)c2ccccc2
#
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
 JMG  JMG  '5-phenylthiophene-2-carboxylic acid'  ligand  22  14  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JMG
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
 JMG  C10   C  CR16  0  -0.315  -2.2867  -1.1175  -0.2863
 JMG  C13   C  CR16  0  -0.235  -4.0637   0.9128   0.3545
 JMG  O01   O  OH1   0  -0.601   3.6159  -1.3743   0.4313
 JMG  O03   O  O     0  -0.435   4.4373   0.6585  -0.0358
 JMG  C04   C  CR5   0  -0.326   2.1041   0.3235   0.0178
 JMG  C05   C  CR15  0  -0.151   1.6501   1.5798  -0.2807
 JMG  C06   C  CR15  0  -0.223   0.2446   1.6538  -0.3173
 JMG  C07   C  CR5   0  -0.202  -0.3639   0.4515  -0.0478
 JMG  S08   S  S2    0   0.285   0.8023  -0.7727   0.2630
 JMG  C09   C  CR6   0   0.139  -1.7957   0.1593  -0.0034
 JMG  C11   C  CR16  0  -0.236  -3.6481  -1.3747  -0.2436
 JMG  C12   C  CR16  0  -0.261  -4.5422  -0.3610   0.0745
 JMG  C14   C  CR16  0  -0.312  -2.7028   1.1715   0.3204
 JMG  H101  H  HCR6  0   0.258  -1.6082  -1.9169  -0.5601
 JMG  H131  H  HCR6  0   0.264  -4.7520   1.7080   0.6099
 JMG  H1    H  HOH1  0   0.493   4.5495  -1.6238   0.5017
 JMG  H051  H  HCR5  0   0.282   2.3055   2.4168  -0.4748
 JMG  H061  H  HCR5  0   0.274  -0.3013   2.5552  -0.5561
 JMG  H111  H  HCR6  0   0.264  -4.0105  -2.3687  -0.4701
 JMG  H121  H  HCR6  0   0.263  -5.6050  -0.5618   0.1048
 JMG  H141  H  HCR6  0   0.260  -2.3429   2.1621   0.5668
 JMG  C02   C  C     0   0.516   3.5015  -0.0870   0.1286

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
 JMG  C13  C14   aromatic  1.386  0.020  1.386
 JMG  C13  C12   aromatic  1.389  0.020  1.389
 JMG  C14  C09   aromatic  1.397  0.020  1.397
 JMG  C12  C11   aromatic  1.389  0.020  1.389
 JMG  C06  C07   aromatic  1.374  0.020  1.374
 JMG  C06  C05   aromatic  1.408  0.020  1.408
 JMG  C09  C07   single    1.462  0.020  1.462
 JMG  C09  C10   aromatic  1.397  0.020  1.397
 JMG  C07  S08   aromatic  1.719  0.020  1.719
 JMG  C05  C04   aromatic  1.369  0.020  1.369
 JMG  C11  C10   aromatic  1.386  0.020  1.386
 JMG  C04  S08   aromatic  1.719  0.020  1.719
 JMG  C04  C02   single    1.461  0.020  1.461
 JMG  O03  C02   double    1.208  0.020  1.208
 JMG  C02  O01   single    1.327  0.020  1.327
 JMG  C10  H101  single    0.930  0.020  1.080
 JMG  C13  H131  single    0.930  0.020  1.080
 JMG  O01  H1    single    0.850  0.020  0.980
 JMG  C05  H051  single    0.930  0.020  1.080
 JMG  C06  H061  single    0.930  0.020  1.080
 JMG  C11  H111  single    0.930  0.020  1.080
 JMG  C12  H121  single    0.930  0.020  1.080
 JMG  C14  H141  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
 JMG  H101  C10  C11  119.06  3.000
 JMG  H101  C10  C09  120.35  3.000
 JMG  C11   C10  C09  120.57  3.000
 JMG  H131  C13  C14  119.56  3.000
 JMG  H131  C13  C12  120.15  3.000
 JMG  C14   C13  C12  120.29  3.000
 JMG  H1    O01  C02  110.45  3.000
 JMG  S08   C04  C05  111.42  3.000
 JMG  S08   C04  C02  122.30  3.000
 JMG  C05   C04  C02  126.28  3.000
 JMG  H051  C05  C06  124.06  3.000
 JMG  H051  C05  C04  123.29  3.000
 JMG  C06   C05  C04  112.64  3.000
 JMG  H061  C06  C07  123.33  3.000
 JMG  H061  C06  C05  123.63  3.000
 JMG  C07   C06  C05  113.02  3.000
 JMG  C09   C07  S08  121.10  3.000
 JMG  S08   C07  C06  110.98  3.000
 JMG  C09   C07  C06  127.92  3.000
 JMG  C07   S08  C04   91.94  3.000
 JMG  C14   C09  C07  119.87  3.000
 JMG  C07   C09  C10  121.38  3.000
 JMG  C14   C09  C10  118.74  3.000
 JMG  H111  C11  C12  120.20  3.000
 JMG  H111  C11  C10  119.54  3.000
 JMG  C12   C11  C10  120.26  3.000
 JMG  H121  C12  C11  120.22  3.000
 JMG  H121  C12  C13  120.19  3.000
 JMG  C11   C12  C13  119.59  3.000
 JMG  H141  C14  C09  119.99  3.000
 JMG  H141  C14  C13  119.46  3.000
 JMG  C09   C14  C13  120.54  3.000
 JMG  C04   C02  O03  123.89  3.000
 JMG  O03   C02  O01  124.26  3.000
 JMG  C04   C02  O01  111.86  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
 JMG  CONST_01  C13   C14  C09  C10    0.00   0.0  0
 JMG  CONST_04  C13   C12  C11  C10    0.00   0.0  0
 JMG  CONST_05  C07   C09  C14  C13  180.00   0.0  0
 JMG  CONST_06  C07   C06  C05  C04    0.00   0.0  0
 JMG  CONST_07  C06   C07  S08  C04    0.00   0.0  0
 JMG  CONST_08  C09   C07  S08  C04  180.00   0.0  0
 JMG  CONST_09  C09   C07  C06  C05  180.00   0.0  0
 JMG  CONST_10  S08   C07  C06  C05    0.00   0.0  0
 JMG  CONST_11  C07   S08  C04  C05    0.00   0.0  0
 JMG  CONST_13  S08   C04  C05  C06    0.00   0.0  0
 JMG  CONST_14  C11   C10  C09  C07  180.00   0.0  0
 JMG  CONST_16  C12   C13  C14  C09    0.00   0.0  0
 JMG  CONST_17  C12   C11  C10  C09    0.00   0.0  0
 JMG  CONST_18  C14   C13  C12  C11    0.00   0.0  0
 JMG  CONST_19  C14   C09  C10  C11    0.00   0.0  0
 JMG  CONST_20  C06   C05  C04  C02  180.00   0.0  0
 JMG  CONST_21  C07   S08  C04  C02  180.00   0.0  0
 JMG  CONST_22  H141  C14  C09  C10  180.00   0.0  0
 JMG  CONST_23  H121  C12  C11  C10  180.00   0.0  0
 JMG  CONST_24  H111  C11  C12  C13  180.00   0.0  0
 JMG  CONST_25  H061  C06  C05  C04  180.00   0.0  0
 JMG  CONST_26  H051  C05  C06  C07  180.00   0.0  0
 JMG  CONST_27  H101  C10  C09  C07    0.00   0.0  0
 JMG  CONST_28  H131  C13  C14  C09  180.00   0.0  0
 JMG  CONST_29  H1    O01  C02  C04  180.00   0.0  0
 JMG  Var_01    C05   C04  C02  O01  179.97  30.0  2

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
 JMG  plan-1  C04   0.020
 JMG  plan-1  C05   0.020
 JMG  plan-1  C06   0.020
 JMG  plan-1  C07   0.020
 JMG  plan-1  S08   0.020
 JMG  plan-1  C09   0.020
 JMG  plan-1  H051  0.020
 JMG  plan-1  H061  0.020
 JMG  plan-1  C02   0.020
 JMG  plan-2  C10   0.020
 JMG  plan-2  C13   0.020
 JMG  plan-2  C07   0.020
 JMG  plan-2  C09   0.020
 JMG  plan-2  C11   0.020
 JMG  plan-2  C12   0.020
 JMG  plan-2  C14   0.020
 JMG  plan-2  H101  0.020
 JMG  plan-2  H131  0.020
 JMG  plan-2  H111  0.020
 JMG  plan-2  H121  0.020
 JMG  plan-2  H141  0.020
 JMG  plan-3  O01   0.020
 JMG  plan-3  O03   0.020
 JMG  plan-3  C04   0.020
 JMG  plan-3  H1    0.020
 JMG  plan-3  C02   0.020

