# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 20:03:36 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: (2~{R})-2-[3-(phenylcarbonyl)phenyl]propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](C(O)=O)c1cccc(c1)C(=O)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
 JGE  JGE  '(2~{R})-2-[3-(phenylcarbonyl)phenyl]propanoic acid'  ligand  33  19  .  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_JGE
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
 JGE  C13   C  CR16  0  -0.244   4.4927  -1.4962   0.3953
 JGE  C15   C  CR16  0  -0.241   2.7780  -2.1431  -1.1638
 JGE  C17   C  C     0   0.575  -3.2207  -1.4020  -0.2437
 JGE  C01   C  CH3   0  -0.650  -3.6774  -0.2691   1.9327
 JGE  C02   C  CH1   0  -0.497  -2.5867  -0.6974   0.9393
 JGE  C03   C  CR6   0   0.203  -1.7255   0.4510   0.4828
 JGE  C04   C  CR16  0  -0.292  -2.2791   1.6411   0.0192
 JGE  C05   C  CR16  0  -0.233  -1.4658   2.6946  -0.3746
 JGE  C06   C  CR16  0  -0.287  -0.0873   2.5759  -0.3111
 JGE  C07   C  CR6   0  -0.016   0.4847   1.3826   0.1240
 JGE  C08   C  CR16  0  -0.352  -0.3422   0.3322   0.5208
 JGE  C09   C  C     0   0.364   1.9654   1.2850   0.2206
 JGE  C11   C  CR6   0  -0.037   2.6242  -0.0277  -0.0134
 JGE  C12   C  CR16  0  -0.270   3.8327  -0.3013   0.6289
 JGE  C14   C  CR16  0  -0.247   3.9677  -2.4178  -0.5039
 JGE  C16   C  CR16  0  -0.279   2.1031  -0.9571  -0.9133
 JGE  O10   O  O     0  -0.391   2.6298   2.2690   0.4806
 JGE  O19   O  OH1   0  -0.592  -3.6673  -2.6062   0.0928
 JGE  H131  H  HCR6  0   0.265   5.4206  -1.7091   0.9093
 JGE  H151  H  HCR6  0   0.266   2.3722  -2.8517  -1.8734
 JGE  H012  H  HCH3  0   0.253  -3.2236   0.2653   2.7660
 JGE  H013  H  HCH3  0   0.237  -4.4133   0.3887   1.4707
 JGE  H011  H  HCH3  0   0.254  -4.2031  -1.1339   2.3344
 JGE  H021  H  HCH1  0   0.298  -1.9486  -1.4263   1.4472
 JGE  H041  H  HCR6  0   0.258  -3.3537   1.7600  -0.0319
 JGE  H051  H  HCR6  0   0.264  -1.9113   3.6133  -0.7321
 JGE  H061  H  HCR6  0   0.264   0.5418   3.4025  -0.6144
 JGE  H081  H  HCR6  0   0.272   0.0957  -0.5878   0.8895
 JGE  H121  H  HCR6  0   0.264   4.2500   0.4154   1.3241
 JGE  H141  H  HCR6  0   0.267   4.4874  -3.3485  -0.6909
 JGE  H161  H  HCR6  0   0.271   1.1803  -0.7502  -1.4390
 JGE  H1    H  HOH1  0   0.482  -4.0941  -3.0278  -0.6685
 JGE  O18   O  O     0  -0.428  -3.3337  -0.9390  -1.3494

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
 JGE  C14  C13   aromatic  1.390  0.020  1.390
 JGE  C14  C15   aromatic  1.388  0.020  1.388
 JGE  C13  C12   aromatic  1.385  0.020  1.385
 JGE  C15  C16   aromatic  1.387  0.020  1.387
 JGE  C12  C11   aromatic  1.396  0.020  1.396
 JGE  O18  C17   double    1.204  0.020  1.204
 JGE  C16  C11   aromatic  1.395  0.020  1.395
 JGE  C11  C09   single    1.487  0.020  1.487
 JGE  O19  C17   single    1.328  0.020  1.328
 JGE  C17  C02   single    1.516  0.020  1.516
 JGE  C09  O10   double    1.215  0.020  1.215
 JGE  C09  C07   single    1.487  0.020  1.487
 JGE  C08  C07   aromatic  1.394  0.020  1.394
 JGE  C08  C03   aromatic  1.389  0.020  1.389
 JGE  C02  C01   single    1.536  0.020  1.536
 JGE  C02  C03   single    1.506  0.020  1.506
 JGE  C07  C06   aromatic  1.393  0.020  1.393
 JGE  C03  C04   aromatic  1.392  0.020  1.392
 JGE  C06  C05   aromatic  1.385  0.020  1.385
 JGE  C04  C05   aromatic  1.388  0.020  1.388
 JGE  C13  H131  single    0.930  0.020  1.080
 JGE  C15  H151  single    0.930  0.020  1.080
 JGE  C01  H012  single    0.970  0.020  1.090
 JGE  C01  H013  single    0.970  0.020  1.090
 JGE  C01  H011  single    0.970  0.020  1.090
 JGE  C02  H021  single    0.970  0.020  1.090
 JGE  C04  H041  single    0.930  0.020  1.080
 JGE  C05  H051  single    0.930  0.020  1.080
 JGE  C06  H061  single    0.930  0.020  1.080
 JGE  C08  H081  single    0.930  0.020  1.080
 JGE  C12  H121  single    0.930  0.020  1.080
 JGE  C14  H141  single    0.930  0.020  1.080
 JGE  C16  H161  single    0.930  0.020  1.080
 JGE  O19  H1    single    0.850  0.020  0.980

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
 JGE  H131  C13  C14   120.04  3.000
 JGE  H131  C13  C12   119.89  3.000
 JGE  C14   C13  C12   120.07  3.000
 JGE  H151  C15  C16   119.73  3.000
 JGE  H151  C15  C14   120.25  3.000
 JGE  C16   C15  C14   120.02  3.000
 JGE  O19   C17  O18   123.36  3.000
 JGE  O19   C17  C02   111.37  3.000
 JGE  O18   C17  C02   125.25  3.000
 JGE  H011  C01  H013  108.05  3.000
 JGE  H011  C01  H012  107.98  3.000
 JGE  H013  C01  H012  108.03  3.000
 JGE  H011  C01  C02   111.10  3.000
 JGE  H013  C01  C02   111.94  3.000
 JGE  H012  C01  C02   109.62  3.000
 JGE  H021  C02  C03   108.37  3.000
 JGE  H021  C02  C01   107.44  3.000
 JGE  C03   C02  C01   112.92  3.000
 JGE  H021  C02  C17   107.25  3.000
 JGE  C03   C02  C17   110.91  3.000
 JGE  C01   C02  C17   109.71  3.000
 JGE  C08   C03  C04   118.58  3.000
 JGE  C04   C03  C02   121.69  3.000
 JGE  C08   C03  C02   119.73  3.000
 JGE  H041  C04  C05   119.01  3.000
 JGE  H041  C04  C03   120.29  3.000
 JGE  C05   C04  C03   120.69  3.000
 JGE  H051  C05  C06   119.85  3.000
 JGE  H051  C05  C04   119.81  3.000
 JGE  C06   C05  C04   120.34  3.000
 JGE  H061  C06  C07   120.21  3.000
 JGE  H061  C06  C05   120.02  3.000
 JGE  C07   C06  C05   119.76  3.000
 JGE  C09   C07  C08   121.50  3.000
 JGE  C08   C07  C06   119.39  3.000
 JGE  C09   C07  C06   119.04  3.000
 JGE  H081  C08  C07   119.78  3.000
 JGE  H081  C08  C03   118.98  3.000
 JGE  C07   C08  C03   121.22  3.000
 JGE  O10   C09  C11   120.40  3.000
 JGE  O10   C09  C07   120.34  3.000
 JGE  C11   C09  C07   119.26  3.000
 JGE  C16   C11  C12   119.33  3.000
 JGE  C16   C11  C09   121.61  3.000
 JGE  C12   C11  C09   118.96  3.000
 JGE  H121  C12  C11   119.98  3.000
 JGE  H121  C12  C13   119.74  3.000
 JGE  C11   C12  C13   120.28  3.000
 JGE  H141  C14  C15   119.98  3.000
 JGE  H141  C14  C13   120.03  3.000
 JGE  C15   C14  C13   119.99  3.000
 JGE  H161  C16  C11   120.32  3.000
 JGE  H161  C16  C15   119.38  3.000
 JGE  C11   C16  C15   120.29  3.000
 JGE  H1    O19  C17   110.09  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
 JGE  CONST_01  C16   C15  C14  C13     0.00   0.0  0
 JGE  CONST_02  C16   C11  C12  C13     0.00   0.0  0
 JGE  CONST_03  C12   C13  C14  C15     0.00   0.0  0
 JGE  CONST_04  C12   C11  C16  C15     0.00   0.0  0
 JGE  CONST_05  C06   C07  C08  C03     0.00   0.0  0
 JGE  CONST_06  C06   C05  C04  C03     0.00   0.0  0
 JGE  CONST_07  C07   C08  C03  C04     0.00   0.0  0
 JGE  CONST_08  C07   C06  C05  C04     0.00   0.0  0
 JGE  CONST_09  C08   C07  C06  C05     0.00   0.0  0
 JGE  CONST_10  C08   C03  C04  C05     0.00   0.0  0
 JGE  CONST_11  C14   C13  C12  C11     0.00   0.0  0
 JGE  CONST_12  C14   C15  C16  C11     0.00   0.0  0
 JGE  CONST_13  C09   C11  C12  C13   180.00   0.0  0
 JGE  CONST_14  C09   C11  C16  C15   180.00   0.0  0
 JGE  CONST_15  C07   C08  C03  C02   180.00   0.0  0
 JGE  CONST_16  C05   C04  C03  C02   180.00   0.0  0
 JGE  CONST_17  C09   C07  C08  C03   180.00   0.0  0
 JGE  CONST_18  C09   C07  C06  C05   180.00   0.0  0
 JGE  CONST_19  H151  C15  C14  C13   180.00   0.0  0
 JGE  CONST_20  H131  C13  C14  C15   180.00   0.0  0
 JGE  CONST_21  H051  C05  C04  C03   180.00   0.0  0
 JGE  CONST_22  H081  C08  C03  C04   180.00   0.0  0
 JGE  CONST_23  H061  C06  C05  C04   180.00   0.0  0
 JGE  CONST_24  H041  C04  C05  C06   180.00   0.0  0
 JGE  CONST_25  H141  C14  C13  C12   180.00   0.0  0
 JGE  CONST_26  H161  C16  C11  C12   180.00   0.0  0
 JGE  CONST_27  H121  C12  C13  C14   180.00   0.0  0
 JGE  CONST_28  H1    O19  C17  C02   180.00   0.0  0
 JGE  Var_01    C11   C09  C07  C06  -148.68  30.0  2
 JGE  Var_02    C12   C11  C09  C07  -151.11  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 JGE  chir_01  C02  C17  C01  C03  positiv

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
 JGE  plan-1  C02   0.020
 JGE  plan-1  C03   0.020
 JGE  plan-1  C04   0.020
 JGE  plan-1  C05   0.020
 JGE  plan-1  C06   0.020
 JGE  plan-1  C07   0.020
 JGE  plan-1  C08   0.020
 JGE  plan-1  C09   0.020
 JGE  plan-1  H041  0.020
 JGE  plan-1  H051  0.020
 JGE  plan-1  H061  0.020
 JGE  plan-1  H081  0.020
 JGE  plan-2  C13   0.020
 JGE  plan-2  C15   0.020
 JGE  plan-2  C09   0.020
 JGE  plan-2  C11   0.020
 JGE  plan-2  C12   0.020
 JGE  plan-2  C14   0.020
 JGE  plan-2  C16   0.020
 JGE  plan-2  H131  0.020
 JGE  plan-2  H151  0.020
 JGE  plan-2  H121  0.020
 JGE  plan-2  H141  0.020
 JGE  plan-2  H161  0.020
 JGE  plan-3  C07   0.020
 JGE  plan-3  C09   0.020
 JGE  plan-3  C11   0.020
 JGE  plan-3  O10   0.020
 JGE  plan-4  C17   0.020
 JGE  plan-4  C02   0.020
 JGE  plan-4  O19   0.020
 JGE  plan-4  H1    0.020
 JGE  plan-4  O18   0.020

