# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 02:27:42 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: (2S)-2-[3-(benzenecarbonyl)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
 9KL  9KL  '(2S)-2-[3-(benzenecarbonyl)phenyl]propanoic acid'  ligand  33  19  .  2021-08-06  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9KL
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
 9KL  C10   C  CR16  0  -0.229  -0.6452   1.6969  -1.5408
 9KL  O13   O  O     0  -0.392   1.5559  -2.2544  -0.2610
 9KL  C01   C  CH3   0  -0.647  -4.2584  -0.7587  -1.3451
 9KL  C02   C  CH1   0  -0.505  -3.3397  -0.5834  -0.1279
 9KL  C03   C  C     0   0.578  -3.9982   0.2576   0.9482
 9KL  C06   C  CR6   0   0.203  -1.9950  -0.0198  -0.5055
 9KL  C07   C  CR16  0  -0.347  -0.8374  -0.7237  -0.2150
 9KL  C08   C  CR6   0  -0.016   0.4198  -0.2195  -0.5539
 9KL  C09   C  CR16  0  -0.294   0.5109   0.9979  -1.2216
 9KL  C11   C  CR16  0  -0.287  -1.8850   1.1987  -1.1761
 9KL  C12   C  C     0   0.360   1.6238  -1.0409  -0.2589
 9KL  C14   C  CR6   0  -0.036   2.9126  -0.3611   0.0390
 9KL  C15   C  CR16  0  -0.270   4.1062  -0.9999  -0.3006
 9KL  C16   C  CR16  0  -0.244   5.3230  -0.4129   0.0038
 9KL  C17   C  CR16  0  -0.248   5.3603   0.8042   0.6749
 9KL  C18   C  CR16  0  -0.241   4.1777   1.4343   1.0369
 9KL  C19   C  CR16  0  -0.279   2.9574   0.8593   0.7123
 9KL  O04   O  O     0  -0.431  -3.5358   1.2630   1.4238
 9KL  O05   O  OH1   0  -0.591  -5.1617  -0.2564   1.3265
 9KL  H101  H  HCR6  0   0.265  -0.5760   2.6362  -2.0732
 9KL  H012  H  HCH3  0   0.252  -5.1738  -1.2836  -1.0792
 9KL  H011  H  HCH3  0   0.236  -4.5332   0.1995  -1.7859
 9KL  H021  H  HCH1  0   0.307  -3.1837  -1.5744   0.3126
 9KL  H071  H  HCR6  0   0.261  -0.9060  -1.6752   0.2992
 9KL  H091  H  HCR6  0   0.272   1.4735   1.3936  -1.5171
 9KL  H111  H  HCR6  0   0.259  -2.7740   1.7655  -1.4248
 9KL  H151  H  HCR6  0   0.264   4.0809  -1.9503  -0.8180
 9KL  H161  H  HCR6  0   0.265   6.2446  -0.9052  -0.2768
 9KL  H171  H  HCR6  0   0.267   6.3120   1.2594   0.9161
 9KL  H181  H  HCR6  0   0.266   4.2037   2.3743   1.5719
 9KL  H191  H  HCR6  0   0.272   2.0415   1.3541   1.0080
 9KL  H1    H  HOH1  0   0.482  -5.5587   0.2939   2.0183
 9KL  H013  H  HCH3  0   0.250  -3.7463  -1.3451  -2.1064

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
 9KL  C18  C17   aromatic  1.388  0.020  1.388
 9KL  C18  C19   aromatic  1.387  0.020  1.387
 9KL  C17  C16   aromatic  1.390  0.020  1.390
 9KL  C19  C14   aromatic  1.395  0.020  1.395
 9KL  C16  C15   aromatic  1.385  0.020  1.385
 9KL  C14  C15   aromatic  1.396  0.020  1.396
 9KL  C14  C12   single    1.487  0.020  1.487
 9KL  C12  O13   double    1.215  0.020  1.215
 9KL  C12  C08   single    1.487  0.020  1.487
 9KL  C01  C02   single    1.535  0.020  1.535
 9KL  C08  C07   aromatic  1.396  0.020  1.396
 9KL  C08  C09   aromatic  1.392  0.020  1.392
 9KL  C07  C06   aromatic  1.386  0.020  1.386
 9KL  C09  C10   aromatic  1.388  0.020  1.388
 9KL  C06  C02   single    1.506  0.020  1.506
 9KL  C06  C11   aromatic  1.395  0.020  1.395
 9KL  C02  C03   single    1.516  0.020  1.516
 9KL  C10  C11   aromatic  1.385  0.020  1.385
 9KL  C03  O04   double    1.205  0.020  1.205
 9KL  C03  O05   single    1.327  0.020  1.327
 9KL  C10  H101  single    0.930  0.020  1.080
 9KL  C01  H013  single    0.970  0.020  1.090
 9KL  C01  H012  single    0.970  0.020  1.090
 9KL  C01  H011  single    0.970  0.020  1.090
 9KL  C02  H021  single    0.970  0.020  1.090
 9KL  C07  H071  single    0.930  0.020  1.080
 9KL  C09  H091  single    0.930  0.020  1.080
 9KL  C11  H111  single    0.930  0.020  1.080
 9KL  C15  H151  single    0.930  0.020  1.080
 9KL  C16  H161  single    0.930  0.020  1.080
 9KL  C17  H171  single    0.930  0.020  1.080
 9KL  C18  H181  single    0.930  0.020  1.080
 9KL  C19  H191  single    0.930  0.020  1.080
 9KL  O05  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
 9KL  H101  C10  C11   119.94  3.000
 9KL  H101  C10  C09   119.80  3.000
 9KL  C11   C10  C09   120.25  3.000
 9KL  H011  C01  H012  108.11  3.000
 9KL  H011  C01  H013  108.02  3.000
 9KL  H012  C01  H013  107.86  3.000
 9KL  H011  C01  C02   111.79  3.000
 9KL  H012  C01  C02   111.40  3.000
 9KL  H013  C01  C02   109.54  3.000
 9KL  H021  C02  C06   108.18  3.000
 9KL  H021  C02  C03   106.15  3.000
 9KL  C06   C02  C03   110.99  3.000
 9KL  H021  C02  C01   107.50  3.000
 9KL  C03   C02  C01   111.48  3.000
 9KL  C06   C02  C01   112.23  3.000
 9KL  O05   C03  O04   123.18  3.000
 9KL  O05   C03  C02   111.61  3.000
 9KL  O04   C03  C02   125.21  3.000
 9KL  C11   C06  C07   118.59  3.000
 9KL  C11   C06  C02   121.17  3.000
 9KL  C07   C06  C02   120.22  3.000
 9KL  H071  C07  C08   119.29  3.000
 9KL  H071  C07  C06   119.51  3.000
 9KL  C08   C07  C06   121.19  3.000
 9KL  C12   C08  C09   121.70  3.000
 9KL  C09   C08  C07   119.43  3.000
 9KL  C12   C08  C07   118.78  3.000
 9KL  H091  C09  C08   120.61  3.000
 9KL  H091  C09  C10   119.61  3.000
 9KL  C08   C09  C10   119.76  3.000
 9KL  H111  C11  C06   120.18  3.000
 9KL  H111  C11  C10   119.07  3.000
 9KL  C06   C11  C10   120.75  3.000
 9KL  C14   C12  C08   119.27  3.000
 9KL  C08   C12  O13   120.39  3.000
 9KL  C14   C12  O13   120.34  3.000
 9KL  C19   C14  C15   119.37  3.000
 9KL  C15   C14  C12   118.89  3.000
 9KL  C19   C14  C12   121.64  3.000
 9KL  H151  C15  C16   119.86  3.000
 9KL  H151  C15  C14   119.88  3.000
 9KL  C16   C15  C14   120.26  3.000
 9KL  H161  C16  C17   120.04  3.000
 9KL  H161  C16  C15   119.91  3.000
 9KL  C17   C16  C15   120.05  3.000
 9KL  H171  C17  C18   120.01  3.000
 9KL  H171  C17  C16   119.96  3.000
 9KL  C18   C17  C16   120.03  3.000
 9KL  H181  C18  C19   119.80  3.000
 9KL  H181  C18  C17   120.19  3.000
 9KL  C19   C18  C17   120.01  3.000
 9KL  H191  C19  C18   119.40  3.000
 9KL  H191  C19  C14   120.32  3.000
 9KL  C18   C19  C14   120.26  3.000
 9KL  H1    O05  C03   110.04  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
 9KL  CONST_01  C07   C08  C09  C10     0.00   0.0  0
 9KL  CONST_02  C07   C06  C11  C10     0.00   0.0  0
 9KL  CONST_03  C09   C08  C07  C06     0.00   0.0  0
 9KL  CONST_04  C09   C10  C11  C06     0.00   0.0  0
 9KL  CONST_05  C11   C06  C07  C08     0.00   0.0  0
 9KL  CONST_06  C11   C10  C09  C08     0.00   0.0  0
 9KL  CONST_07  C17   C18  C19  C14     0.00   0.0  0
 9KL  CONST_08  C17   C16  C15  C14     0.00   0.0  0
 9KL  CONST_09  C18   C17  C16  C15     0.00   0.0  0
 9KL  CONST_10  C18   C19  C14  C15     0.00   0.0  0
 9KL  CONST_11  C19   C18  C17  C16     0.00   0.0  0
 9KL  CONST_12  C19   C14  C15  C16     0.00   0.0  0
 9KL  CONST_13  C12   C08  C09  C10   180.00   0.0  0
 9KL  CONST_14  C02   C06  C11  C10   180.00   0.0  0
 9KL  CONST_15  C08   C07  C06  C02   180.00   0.0  0
 9KL  CONST_16  C12   C08  C07  C06   180.00   0.0  0
 9KL  CONST_17  C18   C19  C14  C12   180.00   0.0  0
 9KL  CONST_18  C16   C15  C14  C12   180.00   0.0  0
 9KL  CONST_19  H101  C10  C11  C06   180.00   0.0  0
 9KL  CONST_20  H091  C09  C08  C07   180.00   0.0  0
 9KL  CONST_21  H111  C11  C06  C07   180.00   0.0  0
 9KL  CONST_22  H071  C07  C08  C09   180.00   0.0  0
 9KL  CONST_23  H181  C18  C19  C14   180.00   0.0  0
 9KL  CONST_24  H161  C16  C15  C14   180.00   0.0  0
 9KL  CONST_25  H171  C17  C16  C15   180.00   0.0  0
 9KL  CONST_26  H191  C19  C14  C15   180.00   0.0  0
 9KL  CONST_27  H151  C15  C16  C17   180.00   0.0  0
 9KL  CONST_28  H1    O05  C03  C02   180.00   0.0  0
 9KL  Var_01    C14   C12  C08  C07  -149.88  30.0  2
 9KL  Var_02    C19   C14  C12  C08    33.68  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
 9KL  chir_01  C02  C01  C06  C03  negativ

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
 9KL  plan-1  C10   0.020
 9KL  plan-1  C02   0.020
 9KL  plan-1  C06   0.020
 9KL  plan-1  C07   0.020
 9KL  plan-1  C08   0.020
 9KL  plan-1  C09   0.020
 9KL  plan-1  C11   0.020
 9KL  plan-1  C12   0.020
 9KL  plan-1  H101  0.020
 9KL  plan-1  H071  0.020
 9KL  plan-1  H091  0.020
 9KL  plan-1  H111  0.020
 9KL  plan-2  C12   0.020
 9KL  plan-2  C14   0.020
 9KL  plan-2  C15   0.020
 9KL  plan-2  C16   0.020
 9KL  plan-2  C17   0.020
 9KL  plan-2  C18   0.020
 9KL  plan-2  C19   0.020
 9KL  plan-2  H151  0.020
 9KL  plan-2  H161  0.020
 9KL  plan-2  H171  0.020
 9KL  plan-2  H181  0.020
 9KL  plan-2  H191  0.020
 9KL  plan-3  O13   0.020
 9KL  plan-3  C08   0.020
 9KL  plan-3  C12   0.020
 9KL  plan-3  C14   0.020
 9KL  plan-4  C02   0.020
 9KL  plan-4  C03   0.020
 9KL  plan-4  O04   0.020
 9KL  plan-4  O05   0.020
 9KL  plan-4  H1    0.020

