# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 00:34:02 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  21  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 GRAND
;

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  C1     0  -0.324  -2.3146  -1.1085  -0.1750
 JMG  C13   C  C1     0  -0.235  -4.0955   0.9633   0.2823
 JMG  O01   O  OC    -1  -0.599   3.5859  -1.4217   0.5424
 JMG  O03   O  O      0  -0.585   4.4195   0.6107   0.1021
 JMG  C04   C  CR5    0  -0.327   2.0993   0.3121   0.1065
 JMG  C05   C  CR15   0  -0.198   1.6533   1.5629  -0.2087
 JMG  C06   C  CR15   0  -0.236   0.2415   1.6503  -0.2667
 JMG  C07   C  CR5    0  -0.216  -0.3829   0.4595   0.0064
 JMG  S08   S  S2     0   0.213   0.7840  -0.7680   0.3405
 JMG  C09   C  C      0   0.145  -1.8183   0.1812   0.0343
 JMG  C11   C  C1     0  -0.236  -3.6783  -1.3584  -0.1496
 JMG  C12   C  C1     0  -0.270  -4.5764  -0.3238   0.0760
 JMG  C14   C  C1     0  -0.324  -2.7324   1.2134   0.2677
 JMG  H101  H  H      0   0.253  -1.6344  -1.9280  -0.3750
 JMG  H131  H  H      0   0.259  -4.7851   1.7772   0.4655
 JMG  H051  H  HCR5   0   0.256   2.3177   2.3935  -0.4011
 JMG  H061  H  HCR5   0   0.258  -0.2927   2.5548  -0.5242
 JMG  H111  H  H      0   0.260  -4.0386  -2.3653  -0.3159
 JMG  H121  H  H      0   0.258  -5.6408  -0.5179   0.0926
 JMG  H141  H  H      0   0.253  -2.3753   2.2177   0.4571
 JMG  C02   C  C      0   0.393   3.4999  -0.2099   0.2641

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  1.398  0.020  1.398
 JMG  C12  C11   aromatic  1.388  0.020  1.388
 JMG  C06  C07   aromatic  1.372  0.020  1.372
 JMG  C06  C05   aromatic  1.416  0.020  1.416
 JMG  C09  C07   single    1.462  0.020  1.462
 JMG  C09  C10   aromatic  1.398  0.020  1.398
 JMG  C07  S08   aromatic  1.726  0.020  1.726
 JMG  C05  C04   aromatic  1.365  0.020  1.365
 JMG  C11  C10   aromatic  1.387  0.020  1.387
 JMG  C04  S08   aromatic  1.718  0.020  1.718
 JMG  C04  C02   single    1.503  0.020  1.503
 JMG  O03  C02   deloc     1.243  0.020  1.243
 JMG  C02  O01   deloc     1.246  0.020  1.246
 JMG  C10  H101  single    0.930  0.020  1.080
 JMG  C13  H131  single    0.930  0.020  1.080
 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  118.98  3.000
 JMG  H101  C10  C09  120.17  3.000
 JMG  C11   C10  C09  120.84  3.000
 JMG  H131  C13  C14  119.52  3.000
 JMG  H131  C13  C12  120.08  3.000
 JMG  C14   C13  C12  120.39  3.000
 JMG  S08   C04  C05  110.94  3.000
 JMG  S08   C04  C02  118.74  3.000
 JMG  C05   C04  C02  130.32  3.000
 JMG  H051  C05  C06  123.93  3.000
 JMG  H051  C05  C04  122.99  3.000
 JMG  C06   C05  C04  113.07  3.000
 JMG  H061  C06  C07  123.26  3.000
 JMG  H061  C06  C05  123.64  3.000
 JMG  C07   C06  C05  113.09  3.000
 JMG  C09   C07  S08  121.63  3.000
 JMG  S08   C07  C06  110.37  3.000
 JMG  C09   C07  C06  128.00  3.000
 JMG  C07   S08  C04   92.53  3.000
 JMG  C14   C09  C07  120.29  3.000
 JMG  C07   C09  C10  121.42  3.000
 JMG  C14   C09  C10  118.30  3.000
 JMG  H111  C11  C12  120.19  3.000
 JMG  H111  C11  C10  119.49  3.000
 JMG  C12   C11  C10  120.32  3.000
 JMG  H121  C12  C11  120.34  3.000
 JMG  H121  C12  C13  120.29  3.000
 JMG  C11   C12  C13  119.38  3.000
 JMG  H141  C14  C09  119.89  3.000
 JMG  H141  C14  C13  119.34  3.000
 JMG  C09   C14  C13  120.77  3.000
 JMG  C04   C02  O03  116.51  3.000
 JMG  O03   C02  O01  128.31  3.000
 JMG  C04   C02  O01  115.17  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  Var_01    C05   C04  C02  O01  -179.03  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  C02   0.020

