# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 25 17:26:10 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  34  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 OK
;

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  -0.252  -6.8854  -2.6064   0.1280
 RCF  C02  C  CSP   0   0.058  -5.9639  -1.9150   0.0954
 RCF  C03  C  CR6   0  -0.002  -4.8249  -1.0602   0.0556
 RCF  C04  C  CR16  0  -0.395  -5.0033   0.3192  -0.0800
 RCF  C05  C  CR6   0   0.494  -3.8952   1.1249  -0.1168
 RCF  F06  F  F     0  -0.297  -4.0387   2.4460  -0.2489
 RCF  C07  C  CR6   0   0.244  -2.6005   0.6085  -0.0219
 RCF  C08  C  CR16  0  -0.327  -2.4378  -0.7650   0.1121
 RCF  C09  C  CR16  0  -0.239  -3.5448  -1.5962   0.1514
 RCF  O10  O  O2    0  -0.495  -1.6019   1.5072  -0.0584
 RCF  C11  C  CR6   0   0.271  -0.3010   1.0578  -0.1694
 RCF  C12  C  CR16  0  -0.278   0.2075   0.7242  -1.4166
 RCF  C13  C  CR16  0  -0.346   1.5284   0.3362  -1.5321
 RCF  C14  C  CR6   0   0.398   2.3508   0.2744  -0.4051
 RCF  C15  C  CR16  0  -0.372   1.8277   0.6060   0.8412
 RCF  C16  C  CR16  0  -0.290   0.4977   0.9948   0.9548
 RCF  O17  O  O2    0  -0.476   3.6188  -0.1257  -0.6334
 RCF  C18  C  CH1   0  -0.106   4.5747  -0.0820   0.4010
 RCF  C19  C  C     0   0.536   5.7106  -0.9787  -0.0598
 RCF  O20  O  OH1   0  -0.590   6.6362  -1.0773   0.8814
 RCF  O21  O  O     0  -0.422   5.7682  -1.5212  -1.1295
 RCF  C22  C  CH3   0  -0.688   5.0649   1.3380   0.6652
 RCF  H1   H  HCR6  0   0.307  -5.9911   0.7524  -0.1614
 RCF  H2   H  HCR6  0   0.306  -1.4492  -1.1957   0.1917
 RCF  H3   H  HCR6  0   0.292  -3.4072  -2.6630   0.2571
 RCF  H4   H  HCR6  0   0.283  -0.4203   0.7773  -2.2972
 RCF  H5   H  HCR6  0   0.276   1.9338   0.0803  -2.5024
 RCF  H6   H  HCR6  0   0.289   2.4267   0.5704   1.7404
 RCF  H7   H  HCR6  0   0.283   0.0984   1.2577   1.9258
 RCF  H8   H  HCH1  0   0.280   4.1771  -0.5185   1.3260
 RCF  H9   H  HOH1  0   0.490   7.3676  -1.6364   0.5781
 RCF  H10  H  HCH3  0   0.258   4.2392   1.9833   0.9627
 RCF  H11  H  HCH3  0   0.257   5.7940   1.3508   1.4724
 RCF  H12  H  HCH3  0   0.250   5.5249   1.7626  -0.2271

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    1.335  0.020  1.335
 RCF  C04  C05  aromatic  1.371  0.020  1.371
 RCF  C04  C03  aromatic  1.397  0.020  1.397
 RCF  C05  C07  aromatic  1.397  0.020  1.397
 RCF  N01  C02  triple    1.152  0.020  1.152
 RCF  C02  C03  single    1.425  0.020  1.425
 RCF  C03  C09  aromatic  1.391  0.020  1.391
 RCF  C07  O10  single    1.344  0.020  1.344
 RCF  C07  C08  aromatic  1.390  0.020  1.390
 RCF  O10  C11  single    1.381  0.020  1.381
 RCF  C16  C11  aromatic  1.380  0.020  1.380
 RCF  C16  C15  aromatic  1.390  0.020  1.390
 RCF  C09  C08  aromatic  1.385  0.020  1.385
 RCF  C11  C12  aromatic  1.388  0.020  1.388
 RCF  C15  C14  aromatic  1.392  0.020  1.392
 RCF  C12  C13  aromatic  1.381  0.020  1.381
 RCF  O21  C19  double    1.201  0.020  1.201
 RCF  C14  C13  aromatic  1.396  0.020  1.396
 RCF  C14  O17  single    1.349  0.020  1.349
 RCF  C19  C18  single    1.519  0.020  1.519
 RCF  C19  O20  single    1.324  0.020  1.324
 RCF  C18  O17  single    1.409  0.020  1.409
 RCF  C18  C22  single    1.525  0.020  1.525
 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  O20  H9   single    0.850  0.020  0.980
 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  120.30  3.000
 RCF  C09  C03  C02  120.17  3.000
 RCF  C04  C03  C02  119.53  3.000
 RCF  H1   C04  C05  120.06  3.000
 RCF  H1   C04  C03  121.28  3.000
 RCF  C05  C04  C03  118.66  3.000
 RCF  C07  C05  F06  118.16  3.000
 RCF  C07  C05  C04  122.01  3.000
 RCF  F06  C05  C04  119.82  3.000
 RCF  O10  C07  C08  125.21  3.000
 RCF  C08  C07  C05  118.72  3.000
 RCF  O10  C07  C05  116.07  3.000
 RCF  H2   C08  C09  119.32  3.000
 RCF  H2   C08  C07  120.53  3.000
 RCF  C09  C08  C07  120.15  3.000
 RCF  H3   C09  C08  119.56  3.000
 RCF  H3   C09  C03  120.28  3.000
 RCF  C08  C09  C03  120.16  3.000
 RCF  C11  O10  C07  118.99  3.000
 RCF  C16  C11  C12  120.59  3.000
 RCF  C12  C11  O10  119.72  3.000
 RCF  C16  C11  O10  119.63  3.000
 RCF  H4   C12  C13  120.01  3.000
 RCF  H4   C12  C11  120.44  3.000
 RCF  C13  C12  C11  119.54  3.000
 RCF  H5   C13  C14  119.50  3.000
 RCF  H5   C13  C12  119.96  3.000
 RCF  C14  C13  C12  120.53  3.000
 RCF  O17  C14  C15  125.13  3.000
 RCF  O17  C14  C13  115.47  3.000
 RCF  C15  C14  C13  119.40  3.000
 RCF  H6   C15  C16  118.12  3.000
 RCF  H6   C15  C14  121.93  3.000
 RCF  C16  C15  C14  119.95  3.000
 RCF  H7   C16  C15  119.61  3.000
 RCF  H7   C16  C11  120.40  3.000
 RCF  C15  C16  C11  119.98  3.000
 RCF  C18  O17  C14  120.28  3.000
 RCF  H8   C18  C22  109.92  3.000
 RCF  H8   C18  C19  106.97  3.000
 RCF  C22  C18  C19  111.22  3.000
 RCF  H8   C18  O17  111.14  3.000
 RCF  C22  C18  O17  111.97  3.000
 RCF  C19  C18  O17  105.44  3.000
 RCF  O21  C19  O20  124.49  3.000
 RCF  O20  C19  C18  110.56  3.000
 RCF  O21  C19  C18  124.95  3.000
 RCF  H9   O20  C19  110.37  3.000
 RCF  H12  C22  H11  108.67  3.000
 RCF  H12  C22  H10  108.22  3.000
 RCF  H11  C22  H10  107.36  3.000
 RCF  H12  C22  C18  110.88  3.000
 RCF  H11  C22  C18  110.79  3.000
 RCF  H10  C22  C18  110.80  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  CONST_30  H9   O20  C19  C18   180.00   0.0  0
 RCF  Var_01    C16  C11  O10  C07  -100.43  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
 RCF  plan-3  H9   0.020

