# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 12:55:36 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: (2~{S})-2-oxidanyl-2-(3-phenoxyphenyl)ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H](C(O)=O)c1cccc(Oc2ccccc2)c1
#
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
 9F5  9F5  '(2~{S})-2-oxidanyl-2-(3-phenoxyphenyl)ethanoic acid'  ligand  29  18  .  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_9F5
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
 9F5  C10  C  CR6    0   0.328  -0.5216  -1.1500   0.2708
 9F5  C13  C  CR16   0  -0.336  -2.6878   0.2020  -0.9610
 9F5  C15  C  CR16   0  -0.273  -4.7295   1.4360  -0.5789
 9F5  C17  C  CR16   0  -0.332  -3.6863   0.2385   1.2355
 9F5  C02  C  C      0   0.399   3.4013   0.9319   0.8303
 9F5  O03  O  O      0  -0.601   4.6339   0.8157   0.6564
 9F5  C04  C  CH1    0  -0.148   2.5682   0.9003  -0.4857
 9F5  O05  O  OH1    0  -0.687   3.4334   0.8137  -1.5800
 9F5  C06  C  CR6    0   0.113   1.5969  -0.2512  -0.4321
 9F5  C07  C  CR16   0  -0.313   1.9344  -1.5024  -0.9428
 9F5  C08  C  CR16   0  -0.240   1.0493  -2.5653  -0.8345
 9F5  C09  C  CR16   0  -0.338  -0.1901  -2.3985  -0.2308
 9F5  O11  O  O2     0  -0.516  -1.7279  -1.0011   0.9106
 9F5  C12  C  CR6    0   0.359  -2.6761  -0.1816   0.3758
 9F5  C14  C  CR16   0  -0.246  -3.7162   1.0121  -1.4268
 9F5  C16  C  CR16   0  -0.247  -4.7084   1.0415   0.7535
 9F5  C18  C  CR16   0  -0.354   0.3585  -0.0820   0.1766
 9F5  H1   H  HCR6   0   0.276  -1.9121  -0.1234  -1.6419
 9F5  H2   H  HCR6   0   0.254  -5.5275   2.0644  -0.9511
 9F5  H3   H  HCR6   0   0.267  -3.6690  -0.0670   2.2742
 9F5  H5   H  HCH1   0   0.229   1.9922   1.8367  -0.5265
 9F5  H6   H  HOH1   0   0.431   4.3081   0.7546  -1.1486
 9F5  H7   H  HCR6   0   0.247   2.8905  -1.6492  -1.4270
 9F5  H8   H  HCR6   0   0.257   1.3220  -3.5350  -1.2308
 9F5  H9   H  HCR6   0   0.265  -0.8879  -3.2221  -0.1515
 9F5  H10  H  HCR6   0   0.261  -3.7205   1.3076  -2.4680
 9F5  H11  H  HCR6   0   0.260  -5.4899   1.3653   1.4288
 9F5  H12  H  HCR6   0   0.261   0.0764   0.8875   0.5703
 9F5  O01  O  OC    -1  -0.576   2.7859   1.0668   1.8942

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
 9F5  C14  C13  aromatic  1.390  0.020  1.390
 9F5  C14  C15  aromatic  1.388  0.020  1.388
 9F5  C13  C12  aromatic  1.391  0.020  1.391
 9F5  C15  C16  aromatic  1.390  0.020  1.390
 9F5  C12  O11  single    1.363  0.020  1.363
 9F5  C12  C17  aromatic  1.391  0.020  1.391
 9F5  O11  C10  single    1.374  0.020  1.374
 9F5  C16  C17  aromatic  1.386  0.020  1.386
 9F5  C10  C09  aromatic  1.386  0.020  1.386
 9F5  C10  C18  aromatic  1.387  0.020  1.387
 9F5  C09  C08  aromatic  1.389  0.020  1.389
 9F5  C18  C06  aromatic  1.390  0.020  1.390
 9F5  O03  C02  deloc     1.250  0.020  1.250
 9F5  O01  C02  deloc     1.236  0.020  1.236
 9F5  C08  C07  aromatic  1.387  0.020  1.387
 9F5  C02  C04  single    1.558  0.020  1.558
 9F5  C06  C07  aromatic  1.393  0.020  1.393
 9F5  C06  C04  single    1.507  0.020  1.507
 9F5  C04  O05  single    1.398  0.020  1.398
 9F5  C13  H1   single    0.930  0.020  1.080
 9F5  C15  H2   single    0.930  0.020  1.080
 9F5  C17  H3   single    0.930  0.020  1.080
 9F5  C04  H5   single    0.970  0.020  1.090
 9F5  O05  H6   single    0.850  0.020  0.980
 9F5  C07  H7   single    0.930  0.020  1.080
 9F5  C08  H8   single    0.930  0.020  1.080
 9F5  C09  H9   single    0.930  0.020  1.080
 9F5  C14  H10  single    0.930  0.020  1.080
 9F5  C16  H11  single    0.930  0.020  1.080
 9F5  C18  H12  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
 9F5  C18  C10  O11  120.36  3.000
 9F5  C18  C10  C09  121.16  3.000
 9F5  O11  C10  C09  118.45  3.000
 9F5  H1   C13  C14  119.66  3.000
 9F5  H1   C13  C12  121.05  3.000
 9F5  C14  C13  C12  119.29  3.000
 9F5  H2   C15  C16  120.40  3.000
 9F5  H2   C15  C14  120.39  3.000
 9F5  C16  C15  C14  119.21  3.000
 9F5  H3   C17  C16  120.58  3.000
 9F5  H3   C17  C12  119.73  3.000
 9F5  C16  C17  C12  119.69  3.000
 9F5  C04  C02  O03  114.07  3.000
 9F5  C04  C02  O01  117.58  3.000
 9F5  O03  C02  O01  128.35  3.000
 9F5  H5   C04  C06  108.31  3.000
 9F5  H5   C04  O05  110.36  3.000
 9F5  C06  C04  O05  112.29  3.000
 9F5  H5   C04  C02  107.10  3.000
 9F5  O05  C04  C02  109.37  3.000
 9F5  C06  C04  C02  109.27  3.000
 9F5  H6   O05  C04  102.25  3.000
 9F5  C18  C06  C07  119.06  3.000
 9F5  C07  C06  C04  121.13  3.000
 9F5  C18  C06  C04  119.77  3.000
 9F5  H7   C07  C08  119.66  3.000
 9F5  H7   C07  C06  120.01  3.000
 9F5  C08  C07  C06  120.33  3.000
 9F5  H8   C08  C09  119.45  3.000
 9F5  H8   C08  C07  119.80  3.000
 9F5  C09  C08  C07  120.75  3.000
 9F5  H9   C09  C08  121.06  3.000
 9F5  H9   C09  C10  120.32  3.000
 9F5  C08  C09  C10  118.63  3.000
 9F5  C12  O11  C10  119.57  3.000
 9F5  O11  C12  C17  116.37  3.000
 9F5  C17  C12  C13  120.29  3.000
 9F5  O11  C12  C13  123.31  3.000
 9F5  H10  C14  C15  120.11  3.000
 9F5  H10  C14  C13  118.98  3.000
 9F5  C15  C14  C13  120.91  3.000
 9F5  H11  C16  C17  119.25  3.000
 9F5  H11  C16  C15  120.15  3.000
 9F5  C17  C16  C15  120.59  3.000
 9F5  H12  C18  C06  119.99  3.000
 9F5  H12  C18  C10  119.93  3.000
 9F5  C06  C18  C10  120.08  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
 9F5  CONST_01  C07  C08  C09  C10    0.00   0.0  0
 9F5  CONST_02  C07  C06  C18  C10    0.00   0.0  0
 9F5  CONST_03  C16  C15  C14  C13    0.00   0.0  0
 9F5  CONST_04  C16  C17  C12  C13    0.00   0.0  0
 9F5  CONST_05  C12  C13  C14  C15    0.00   0.0  0
 9F5  CONST_06  C12  C17  C16  C15    0.00   0.0  0
 9F5  CONST_07  C14  C13  C12  C17    0.00   0.0  0
 9F5  CONST_08  C14  C15  C16  C17    0.00   0.0  0
 9F5  CONST_09  C09  C10  C18  C06    0.00   0.0  0
 9F5  CONST_10  C09  C08  C07  C06    0.00   0.0  0
 9F5  CONST_11  C18  C10  C09  C08    0.00   0.0  0
 9F5  CONST_12  C18  C06  C07  C08    0.00   0.0  0
 9F5  CONST_13  C04  C06  C18  C10  180.00   0.0  0
 9F5  CONST_14  C08  C07  C06  C04  180.00   0.0  0
 9F5  CONST_15  O11  C10  C18  C06  180.00   0.0  0
 9F5  CONST_16  O11  C10  C09  C08  180.00   0.0  0
 9F5  CONST_17  C14  C13  C12  O11  180.00   0.0  0
 9F5  CONST_18  C16  C17  C12  O11  180.00   0.0  0
 9F5  CONST_19  H8   C08  C09  C10  180.00   0.0  0
 9F5  CONST_20  H2   C15  C14  C13  180.00   0.0  0
 9F5  CONST_21  H3   C17  C12  C13  180.00   0.0  0
 9F5  CONST_22  H1   C13  C14  C15  180.00   0.0  0
 9F5  CONST_23  H9   C09  C08  C07  180.00   0.0  0
 9F5  CONST_24  H12  C18  C06  C07  180.00   0.0  0
 9F5  CONST_25  H7   C07  C08  C09  180.00   0.0  0
 9F5  CONST_26  H10  C14  C13  C12  180.00   0.0  0
 9F5  CONST_27  H11  C16  C17  C12  180.00   0.0  0
 9F5  Var_01    C13  C12  O11  C10   20.40  30.0  3
 9F5  Var_02    C18  C10  O11  C12   66.64  30.0  2

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
 9F5  chir_01  C04  C02  C06  O05  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
 9F5  plan-1  C10  0.020
 9F5  plan-1  C04  0.020
 9F5  plan-1  C06  0.020
 9F5  plan-1  C07  0.020
 9F5  plan-1  C08  0.020
 9F5  plan-1  C09  0.020
 9F5  plan-1  O11  0.020
 9F5  plan-1  C18  0.020
 9F5  plan-1  H7   0.020
 9F5  plan-1  H8   0.020
 9F5  plan-1  H9   0.020
 9F5  plan-1  H12  0.020
 9F5  plan-2  C13  0.020
 9F5  plan-2  C15  0.020
 9F5  plan-2  C17  0.020
 9F5  plan-2  O11  0.020
 9F5  plan-2  C12  0.020
 9F5  plan-2  C14  0.020
 9F5  plan-2  C16  0.020
 9F5  plan-2  H1   0.020
 9F5  plan-2  H2   0.020
 9F5  plan-2  H3   0.020
 9F5  plan-2  H10  0.020
 9F5  plan-2  H11  0.020
 9F5  plan-3  C02  0.020
 9F5  plan-3  O03  0.020
 9F5  plan-3  C04  0.020
 9F5  plan-3  O01  0.020

