# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 00:06:52 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  32  19  .  2021-08-06  2021-08-06  
;
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  -0.234  -0.6613   1.7017  -1.4984
 9KL  O13   O  O      0  -0.396   1.5671  -2.2508  -0.2618
 9KL  C01   C  CH3    0  -0.646  -4.2153  -0.8373  -1.3296
 9KL  C02   C  CH1    0  -0.500  -3.3441  -0.5987  -0.0946
 9KL  C03   C  C      0   0.437  -4.0843   0.2594   0.9680
 9KL  C06   C  CR6    0   0.236  -2.0023  -0.0347  -0.4682
 9KL  C07   C  CR16   0  -0.370  -0.8337  -0.7312  -0.2001
 9KL  C08   C  CR6    0  -0.014   0.4209  -0.2175  -0.5414
 9KL  C09   C  CR16   0  -0.306   0.5033   1.0075  -1.1964
 9KL  C11   C  CR16   0  -0.293  -1.8944   1.1932  -1.1267
 9KL  C12   C  C      0   0.355   1.6290  -1.0360  -0.2661
 9KL  C14   C  CR6    0  -0.035   2.9247  -0.3555   0.0059
 9KL  C15   C  CR16   0  -0.271   4.1108  -0.9901  -0.3663
 9KL  C16   C  CR16   0  -0.244   5.3343  -0.4050  -0.0853
 9KL  C17   C  CR16   0  -0.249   5.3868   0.8059   0.5958
 9KL  C18   C  CR16   0  -0.242   4.2123   1.4317   0.9904
 9KL  C19   C  CR16   0  -0.280   2.9850   0.8588   0.6887
 9KL  O04   O  O      0  -0.595  -3.4516   1.1882   1.5026
 9KL  O05   O  OC    -1  -0.611  -5.2582  -0.0793   1.2141
 9KL  H101  H  HCR6   0   0.257  -0.6018   2.6474  -2.0215
 9KL  H011  H  HCH3   0   0.215  -4.4795   0.0994  -1.8244
 9KL  H021  H  HCH1   0   0.247  -3.1711  -1.5767   0.3720
 9KL  H071  H  HCR6   0   0.248  -0.8920  -1.6900   0.3023
 9KL  H091  H  HCR6   0   0.266   1.4613   1.4112  -1.4959
 9KL  H111  H  HCR6   0   0.248  -2.7893   1.7581  -1.3580
 9KL  H151  H  HCR6   0   0.263   4.0740  -1.9358  -0.8916
 9KL  H161  H  HCR6   0   0.264   6.2494  -0.8945  -0.3912
 9KL  H171  H  HCR6   0   0.266   6.3436   1.2593   0.8196
 9KL  H181  H  HCR6   0   0.265   4.2500   2.3668   1.5333
 9KL  H191  H  HCR6   0   0.271   2.0758   1.3505   1.0085
 9KL  H013  H  HCH3   0   0.220  -3.7014  -1.4640  -2.0600
 9KL  H012  H  HCH3   0   0.230  -5.1422  -1.3364  -1.0528

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  1.388  0.020  1.388
 9KL  C17  C16   aromatic  1.390  0.020  1.390
 9KL  C19  C14   aromatic  1.394  0.020  1.394
 9KL  C16  C15   aromatic  1.385  0.020  1.385
 9KL  C14  C15   aromatic  1.396  0.020  1.396
 9KL  C14  C12   single    1.489  0.020  1.489
 9KL  C12  O13   double    1.216  0.020  1.216
 9KL  C12  C08   single    1.485  0.020  1.485
 9KL  C01  C02   single    1.530  0.020  1.530
 9KL  C08  C07   aromatic  1.398  0.020  1.398
 9KL  C08  C09   aromatic  1.392  0.020  1.392
 9KL  C07  C06   aromatic  1.387  0.020  1.387
 9KL  C09  C10   aromatic  1.389  0.020  1.389
 9KL  C06  C02   single    1.503  0.020  1.503
 9KL  C06  C11   aromatic  1.398  0.020  1.398
 9KL  C02  C03   single    1.554  0.020  1.554
 9KL  C10  C11   aromatic  1.385  0.020  1.385
 9KL  C03  O04   deloc     1.244  0.020  1.244
 9KL  C03  O05   deloc     1.246  0.020  1.246
 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

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   119.98  3.000
 9KL  H101  C10  C09   119.71  3.000
 9KL  C11   C10  C09   120.32  3.000
 9KL  H011  C01  H012  107.61  3.000
 9KL  H011  C01  H013  107.66  3.000
 9KL  H012  C01  H013  107.93  3.000
 9KL  H011  C01  C02   111.70  3.000
 9KL  H012  C01  C02   110.55  3.000
 9KL  H013  C01  C02   111.21  3.000
 9KL  H021  C02  C06   107.43  3.000
 9KL  H021  C02  C03   106.05  3.000
 9KL  C06   C02  C03   112.84  3.000
 9KL  H021  C02  C01   107.10  3.000
 9KL  C03   C02  C01   111.53  3.000
 9KL  C06   C02  C01   111.49  3.000
 9KL  O05   C03  O04   126.65  3.000
 9KL  O05   C03  C02   115.70  3.000
 9KL  O04   C03  C02   117.64  3.000
 9KL  C11   C06  C07   117.87  3.000
 9KL  C11   C06  C02   121.05  3.000
 9KL  C07   C06  C02   121.06  3.000
 9KL  H071  C07  C08   119.11  3.000
 9KL  H071  C07  C06   119.25  3.000
 9KL  C08   C07  C06   121.64  3.000
 9KL  C12   C08  C09   121.62  3.000
 9KL  C09   C08  C07   119.44  3.000
 9KL  C12   C08  C07   118.84  3.000
 9KL  H091  C09  C08   120.74  3.000
 9KL  H091  C09  C10   119.72  3.000
 9KL  C08   C09  C10   119.51  3.000
 9KL  H111  C11  C06   119.67  3.000
 9KL  H111  C11  C10   119.13  3.000
 9KL  C06   C11  C10   121.19  3.000
 9KL  C14   C12  C08   119.34  3.000
 9KL  C08   C12  O13   120.64  3.000
 9KL  C14   C12  O13   120.01  3.000
 9KL  C19   C14  C15   119.33  3.000
 9KL  C15   C14  C12   118.89  3.000
 9KL  C19   C14  C12   121.68  3.000
 9KL  H151  C15  C16   119.84  3.000
 9KL  H151  C15  C14   119.85  3.000
 9KL  C16   C15  C14   120.30  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   120.03  3.000
 9KL  H171  C17  C16   119.97  3.000
 9KL  C18   C17  C16   120.00  3.000
 9KL  H181  C18  C19   119.79  3.000
 9KL  H181  C18  C17   120.19  3.000
 9KL  C19   C18  C17   120.03  3.000
 9KL  H191  C19  C18   119.43  3.000
 9KL  H191  C19  C14   120.27  3.000
 9KL  C18   C19  C14   120.28  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  Var_01    C14   C12  C08  C07  -151.05  30.0  2
 9KL  Var_02    C19   C14  C12  C08    34.49  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

