# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 07:37:52 2020
#   Inital geometry file: a 54 line input string
#   Ligand name: (2S)-(3,5-difluorophenyl)(hydroxy)acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H](C(O)=O)c1cc(F)cc(F)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
 CXJ  CXJ  '(2S)-(3,5-difluorophenyl)(hydroxy)acetic acid'  ligand  18  13  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CXJ
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
 CXJ  C7  C  CR16   0  -0.469  -0.6157   1.2037  -0.3735
 CXJ  C4  C  CR6    0   0.559  -1.7189  -1.2584   0.1450
 CXJ  C5  C  CR16   0  -0.573  -2.5204  -0.1439   0.2956
 CXJ  C6  C  CR6    0   0.552  -1.9302   1.0764   0.0230
 CXJ  C3  C  CR16   0  -0.481  -0.3986  -1.1915  -0.2543
 CXJ  C2  C  CR6    0   0.120   0.1609   0.0558  -0.5125
 CXJ  C1  C  C      0   0.403   2.4545   0.5130   0.3656
 CXJ  F1  F  F      0  -0.314  -2.6782   2.1831   0.1509
 CXJ  F   F  F      0  -0.314  -2.2557  -2.4624   0.3972
 CXJ  C   C  CH1    0  -0.141   1.6123   0.1757  -0.9039
 CXJ  O   O  OH1    0  -0.682   2.0996  -0.9942  -1.4886
 CXJ  H5  H  HCR6   0   0.270  -0.2045   2.1827  -0.5812
 CXJ  H4  H  HCR6   0   0.297  -3.5551  -0.2219   0.6019
 CXJ  H3  H  HCR6   0   0.273   0.1793  -2.0980  -0.3697
 CXJ  H1  H  HCH1   0   0.238   1.7124   1.0214  -1.5983
 CXJ  H   H  HOH1   0   0.433   2.7973  -1.2683  -0.8617
 CXJ  O1  O  OC    -1  -0.572   2.1958   1.5622   0.9642
 CXJ  O2  O  O      0  -0.598   3.3233  -0.3435   0.6389

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
 CXJ  O   C   single    1.396  0.020  1.396
 CXJ  C   C1  single    1.560  0.020  1.560
 CXJ  C   C2  single    1.508  0.020  1.508
 CXJ  O2  C1  deloc     1.250  0.020  1.250
 CXJ  C1  O1  deloc     1.235  0.020  1.235
 CXJ  C2  C7  aromatic  1.393  0.020  1.393
 CXJ  C2  C3  aromatic  1.391  0.020  1.391
 CXJ  C7  C6  aromatic  1.379  0.020  1.379
 CXJ  C3  C4  aromatic  1.381  0.020  1.381
 CXJ  C6  F1  single    1.342  0.020  1.342
 CXJ  C6  C5  aromatic  1.383  0.020  1.383
 CXJ  C4  C5  aromatic  1.381  0.020  1.381
 CXJ  C4  F   single    1.342  0.020  1.342
 CXJ  C7  H5  single    0.930  0.020  1.080
 CXJ  C5  H4  single    0.930  0.020  1.080
 CXJ  C3  H3  single    0.930  0.020  1.080
 CXJ  C   H1  single    0.970  0.020  1.090
 CXJ  O   H   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
 CXJ  H5  C7  C2  120.97  3.000
 CXJ  H5  C7  C6  120.07  3.000
 CXJ  C2  C7  C6  118.95  3.000
 CXJ  F   C4  C3  118.70  3.000
 CXJ  F   C4  C5  118.12  3.000
 CXJ  C3  C4  C5  123.18  3.000
 CXJ  H4  C5  C6  121.84  3.000
 CXJ  H4  C5  C4  121.86  3.000
 CXJ  C6  C5  C4  116.30  3.000
 CXJ  F1  C6  C5  118.11  3.000
 CXJ  C5  C6  C7  123.03  3.000
 CXJ  F1  C6  C7  118.86  3.000
 CXJ  H3  C3  C2  121.13  3.000
 CXJ  H3  C3  C4  120.08  3.000
 CXJ  C2  C3  C4  118.79  3.000
 CXJ  C   C2  C3  120.43  3.000
 CXJ  C3  C2  C7  119.74  3.000
 CXJ  C   C2  C7  119.80  3.000
 CXJ  O2  C1  O1  128.43  3.000
 CXJ  O1  C1  C   117.70  3.000
 CXJ  O2  C1  C   113.88  3.000
 CXJ  H1  C   O   110.40  3.000
 CXJ  H1  C   C1  107.38  3.000
 CXJ  O   C   C1  109.49  3.000
 CXJ  H1  C   C2  108.23  3.000
 CXJ  C1  C   C2  109.00  3.000
 CXJ  O   C   C2  112.22  3.000
 CXJ  H   O   C   102.45  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
 CXJ  CONST_01  C4  C3  C2  C7    0.00  0.0  0
 CXJ  CONST_02  C4  C5  C6  C7    0.00  0.0  0
 CXJ  CONST_03  C2  C7  C6  C5    0.00  0.0  0
 CXJ  CONST_04  C2  C3  C4  C5    0.00  0.0  0
 CXJ  CONST_05  C3  C2  C7  C6    0.00  0.0  0
 CXJ  CONST_06  C3  C4  C5  C6    0.00  0.0  0
 CXJ  CONST_07  C   C2  C3  C4  180.00  0.0  0
 CXJ  CONST_08  F1  C6  C5  C4  180.00  0.0  0
 CXJ  CONST_09  C   C2  C7  C6  180.00  0.0  0
 CXJ  CONST_10  F   C4  C5  C6  180.00  0.0  0
 CXJ  CONST_11  F1  C6  C7  C2  180.00  0.0  0
 CXJ  CONST_12  F   C4  C3  C2  180.00  0.0  0
 CXJ  CONST_13  H3  C3  C2  C7  180.00  0.0  0
 CXJ  CONST_14  H4  C5  C6  C7  180.00  0.0  0
 CXJ  CONST_15  H5  C7  C6  C5  180.00  0.0  0

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
 CXJ  chir_01  C  O  C1  C2  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
 CXJ  plan-1  C7  0.020
 CXJ  plan-1  C4  0.020
 CXJ  plan-1  C5  0.020
 CXJ  plan-1  C6  0.020
 CXJ  plan-1  C3  0.020
 CXJ  plan-1  C2  0.020
 CXJ  plan-1  F1  0.020
 CXJ  plan-1  F   0.020
 CXJ  plan-1  C   0.020
 CXJ  plan-1  H5  0.020
 CXJ  plan-1  H4  0.020
 CXJ  plan-1  H3  0.020
 CXJ  plan-2  C1  0.020
 CXJ  plan-2  C   0.020
 CXJ  plan-2  O1  0.020
 CXJ  plan-2  O2  0.020

