# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 20:49:08 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: (2R)-2-[4-(4-cyano-2-fluorophenoxy)phenoxy]propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](Oc1ccc(Oc2ccc(cc2F)C#N)cc1)C(O)=O
#
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
 RCF  RCF  '(2R)-2-[4-(4-cyano-2-fluorophenoxy)phenoxy]propanoic acid'  ligand  33  22  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RCF
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
 RCF  N01  N  NS     0  -0.253  -6.7040  -2.7122   0.4736
 RCF  C02  C  CSP    0   0.058  -5.8143  -1.9890   0.3562
 RCF  C03  C  CR6    0  -0.003  -4.7131  -1.0967   0.2127
 RCF  C04  C  CR16   0  -0.395  -4.9482   0.2761   0.0956
 RCF  C05  C  CR6    0   0.493  -3.8750   1.1174  -0.0396
 RCF  F06  F  F      0  -0.298  -4.0721   2.4335  -0.1555
 RCF  C07  C  CR6    0   0.246  -2.5599   0.6445  -0.0633
 RCF  C08  C  CR16   0  -0.329  -2.3414  -0.7233   0.0517
 RCF  C09  C  CR16   0  -0.238  -3.4128  -1.5902   0.1898
 RCF  O10  O  O2     0  -0.495  -1.5998   1.5747  -0.1943
 RCF  C11  C  C      0   0.260  -0.2835   1.1629  -0.2962
 RCF  C12  C  C1     0  -0.279   0.2529   0.8869  -1.5452
 RCF  C13  C  C1     0  -0.355   1.5802   0.5175  -1.6499
 RCF  C14  C  C      0   0.401   2.3892   0.4134  -0.5124
 RCF  C15  C  C1     0  -0.382   1.8331   0.6965   0.7356
 RCF  C16  C  C1     0  -0.285   0.4976   1.0676   0.8384
 RCF  O17  O  O2     0  -0.471   3.6552   0.0321  -0.7305
 RCF  C18  C  CH1    0  -0.123   4.5700  -0.1092   0.3517
 RCF  C19  C  C      0   0.401   5.7210  -1.0379  -0.0981
 RCF  O20  O  OC    -1  -0.616   6.5342  -1.3096   0.8065
 RCF  O21  O  O      0  -0.591   5.7410  -1.4189  -1.2778
 RCF  C22  C  CH3    0  -0.685   5.1026   1.2478   0.7924
 RCF  H1   H  HCR6   0   0.307  -5.9531   0.6767   0.1076
 RCF  H2   H  HCR6   0   0.306  -1.3365  -1.1216   0.0360
 RCF  H3   H  HCR6   0   0.291  -3.2320  -2.6520   0.2796
 RCF  H4   H  H      0   0.277  -0.3599   0.9648  -2.4345
 RCF  H5   H  H      0   0.268   2.0037   0.3004  -2.6224
 RCF  H6   H  H      0   0.283   2.4160   0.6371   1.6435
 RCF  H7   H  H      0   0.279   0.0787   1.2893   1.8117
 RCF  H8   H  HCH1   0   0.226   4.0694  -0.5999   1.1956
 RCF  H10  H  HCH3   0   0.233   4.3077   1.9151   1.1283
 RCF  H11  H  HCH3   0   0.237   5.7990   1.1206   1.6188
 RCF  H12  H  HCH3   0   0.230   5.6312   1.7411  -0.0252

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
 RCF  F06  C05  single    1.336  0.020  1.336
 RCF  C04  C05  aromatic  1.370  0.020  1.370
 RCF  C04  C03  aromatic  1.398  0.020  1.398
 RCF  C05  C07  aromatic  1.398  0.020  1.398
 RCF  N01  C02  triple    1.153  0.020  1.153
 RCF  C02  C03  single    1.425  0.020  1.425
 RCF  C03  C09  aromatic  1.391  0.020  1.391
 RCF  C07  O10  single    1.343  0.020  1.343
 RCF  C07  C08  aromatic  1.390  0.020  1.390
 RCF  O10  C11  single    1.383  0.020  1.383
 RCF  C16  C11  aromatic  1.381  0.020  1.381
 RCF  C16  C15  aromatic  1.390  0.020  1.390
 RCF  C09  C08  aromatic  1.385  0.020  1.385
 RCF  C11  C12  aromatic  1.387  0.020  1.387
 RCF  C15  C14  aromatic  1.395  0.020  1.395
 RCF  C12  C13  aromatic  1.382  0.020  1.382
 RCF  O21  C19  deloc     1.240  0.020  1.240
 RCF  C14  C13  aromatic  1.400  0.020  1.400
 RCF  C14  O17  single    1.340  0.020  1.340
 RCF  C19  C18  single    1.546  0.020  1.546
 RCF  C19  O20  deloc     1.246  0.020  1.246
 RCF  C18  O17  single    1.424  0.020  1.424
 RCF  C18  C22  single    1.523  0.020  1.523
 RCF  C04  H1   single    0.930  0.020  1.080
 RCF  C08  H2   single    0.930  0.020  1.080
 RCF  C09  H3   single    0.930  0.020  1.080
 RCF  C12  H4   single    0.930  0.020  1.080
 RCF  C13  H5   single    0.930  0.020  1.080
 RCF  C15  H6   single    0.930  0.020  1.080
 RCF  C16  H7   single    0.930  0.020  1.080
 RCF  C18  H8   single    0.970  0.020  1.090
 RCF  C22  H10  single    0.970  0.020  1.090
 RCF  C22  H11  single    0.970  0.020  1.090
 RCF  C22  H12  single    0.970  0.020  1.090

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
 RCF  C03  C02  N01  180.00  3.000
 RCF  C09  C03  C04  120.28  3.000
 RCF  C09  C03  C02  120.14  3.000
 RCF  C04  C03  C02  119.58  3.000
 RCF  H1   C04  C05  120.08  3.000
 RCF  H1   C04  C03  121.26  3.000
 RCF  C05  C04  C03  118.66  3.000
 RCF  C07  C05  F06  118.08  3.000
 RCF  C07  C05  C04  122.06  3.000
 RCF  F06  C05  C04  119.86  3.000
 RCF  O10  C07  C08  125.26  3.000
 RCF  C08  C07  C05  118.65  3.000
 RCF  O10  C07  C05  116.09  3.000
 RCF  H2   C08  C09  119.33  3.000
 RCF  H2   C08  C07  120.49  3.000
 RCF  C09  C08  C07  120.17  3.000
 RCF  H3   C09  C08  119.59  3.000
 RCF  H3   C09  C03  120.23  3.000
 RCF  C08  C09  C03  120.18  3.000
 RCF  C11  O10  C07  118.77  3.000
 RCF  C16  C11  C12  120.49  3.000
 RCF  C12  C11  O10  119.59  3.000
 RCF  C16  C11  O10  119.89  3.000
 RCF  H4   C12  C13  120.04  3.000
 RCF  H4   C12  C11  120.42  3.000
 RCF  C13  C12  C11  119.54  3.000
 RCF  H5   C13  C14  119.27  3.000
 RCF  H5   C13  C12  119.83  3.000
 RCF  C14  C13  C12  120.89  3.000
 RCF  O17  C14  C15  125.44  3.000
 RCF  O17  C14  C13  115.78  3.000
 RCF  C15  C14  C13  118.78  3.000
 RCF  H6   C15  C16  118.09  3.000
 RCF  H6   C15  C14  121.69  3.000
 RCF  C16  C15  C14  120.22  3.000
 RCF  H7   C16  C15  119.53  3.000
 RCF  H7   C16  C11  120.39  3.000
 RCF  C15  C16  C11  120.08  3.000
 RCF  C18  O17  C14  120.76  3.000
 RCF  H8   C18  C22  109.61  3.000
 RCF  H8   C18  C19  107.16  3.000
 RCF  C22  C18  C19  111.05  3.000
 RCF  H8   C18  O17  109.62  3.000
 RCF  C22  C18  O17  110.86  3.000
 RCF  C19  C18  O17  108.47  3.000
 RCF  O21  C19  O20  127.81  3.000
 RCF  O20  C19  C18  113.93  3.000
 RCF  O21  C19  C18  118.26  3.000
 RCF  H12  C22  H11  108.17  3.000
 RCF  H12  C22  H10  107.88  3.000
 RCF  H11  C22  H10  107.69  3.000
 RCF  H12  C22  C18  110.81  3.000
 RCF  H11  C22  C18  109.84  3.000
 RCF  H10  C22  C18  112.30  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
 RCF  CONST_01  C07  C05  C04  C03    0.00   0.0  0
 RCF  CONST_02  C07  C08  C09  C03    0.00   0.0  0
 RCF  CONST_03  C08  C07  C05  C04    0.00   0.0  0
 RCF  CONST_04  C08  C09  C03  C04    0.00   0.0  0
 RCF  CONST_05  C09  C03  C04  C05    0.00   0.0  0
 RCF  CONST_06  C09  C08  C07  C05    0.00   0.0  0
 RCF  CONST_07  C14  C15  C16  C11    0.00   0.0  0
 RCF  CONST_08  C14  C13  C12  C11    0.00   0.0  0
 RCF  CONST_09  C15  C16  C11  C12    0.00   0.0  0
 RCF  CONST_10  C15  C14  C13  C12    0.00   0.0  0
 RCF  CONST_11  C16  C11  C12  C13    0.00   0.0  0
 RCF  CONST_12  C16  C15  C14  C13    0.00   0.0  0
 RCF  CONST_13  C05  C04  C03  C02  180.00   0.0  0
 RCF  CONST_14  C08  C09  C03  C02  180.00   0.0  0
 RCF  CONST_15  F06  C05  C04  C03  180.00   0.0  0
 RCF  CONST_16  O10  C07  C05  C04  180.00   0.0  0
 RCF  CONST_17  C08  C07  C05  F06  180.00   0.0  0
 RCF  CONST_18  O10  C07  C08  C09  180.00   0.0  0
 RCF  CONST_19  C15  C16  C11  O10  180.00   0.0  0
 RCF  CONST_20  C13  C12  C11  O10  180.00   0.0  0
 RCF  CONST_21  O17  C14  C13  C12  180.00   0.0  0
 RCF  CONST_22  O17  C14  C15  C16  180.00   0.0  0
 RCF  CONST_23  H2   C08  C09  C03  180.00   0.0  0
 RCF  CONST_24  H3   C09  C03  C04  180.00   0.0  0
 RCF  CONST_25  H1   C04  C05  C07  180.00   0.0  0
 RCF  CONST_26  H6   C15  C16  C11  180.00   0.0  0
 RCF  CONST_27  H5   C13  C12  C11  180.00   0.0  0
 RCF  CONST_28  H7   C16  C11  C12  180.00   0.0  0
 RCF  CONST_29  H4   C12  C13  C14  180.00   0.0  0
 RCF  Var_01    C16  C11  O10  C07  -92.76  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
 RCF  chir_01  C18  C19  O17  C22  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
 RCF  plan-1  N01  0.020
 RCF  plan-1  C02  0.020
 RCF  plan-1  C03  0.020
 RCF  plan-1  C04  0.020
 RCF  plan-1  C05  0.020
 RCF  plan-1  F06  0.020
 RCF  plan-1  C07  0.020
 RCF  plan-1  C08  0.020
 RCF  plan-1  C09  0.020
 RCF  plan-1  O10  0.020
 RCF  plan-1  H1   0.020
 RCF  plan-1  H2   0.020
 RCF  plan-1  H3   0.020
 RCF  plan-2  O10  0.020
 RCF  plan-2  C11  0.020
 RCF  plan-2  C12  0.020
 RCF  plan-2  C13  0.020
 RCF  plan-2  C14  0.020
 RCF  plan-2  C15  0.020
 RCF  plan-2  C16  0.020
 RCF  plan-2  O17  0.020
 RCF  plan-2  H4   0.020
 RCF  plan-2  H5   0.020
 RCF  plan-2  H6   0.020
 RCF  plan-2  H7   0.020
 RCF  plan-3  C18  0.020
 RCF  plan-3  C19  0.020
 RCF  plan-3  O20  0.020
 RCF  plan-3  O21  0.020

