# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 19:50:22 2022
#   Inital geometry file: a 80 line input string
#   Ligand name: 2-{4-[(1S)-2,2-dichlorocyclopropyl]phenoxy}-2-methylpropanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(Oc1ccc(cc1)[C@@H]2CC2(Cl)Cl)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
 C5F  C5F  '2-{4-[(1S)-2,2-dichlorocyclopropyl]phenoxy}-2-methylpropanoic acid'  ligand  31  18  .  2022-09-16  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_C5F
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
 C5F  C06  C   CH1    0  -0.273  -15.7727   8.7108  33.0682
 C5F  C07  C   CT     0  -0.103  -15.8249   9.7352  34.1573
 C5F  C08  C   CH2    0  -0.449  -16.7251   9.8782  32.9894
 C5F  C09  C   CR6    0   0.093  -14.5830   8.5864  32.1869
 C5F  C10  C   CR16   0  -0.295  -14.5159   9.1730  30.9278
 C5F  C11  C   CR16   0  -0.277  -13.4881   7.8416  32.6125
 C5F  C12  C   CR16   0  -0.348  -13.3959   9.0231  30.1290
 C5F  C13  C   CR16   0  -0.354  -12.3570   7.6826  31.8262
 C5F  C14  C   CR6    0   0.389  -12.2946   8.2810  30.5647
 C5F  C15  C   CT     0   0.083  -10.0478   7.5225  29.9989
 C5F  C16  C   CH3    0  -0.660  -10.2639   6.0142  29.9692
 C5F  C17  C   CH3    0  -0.668   -9.1217   7.9174  28.8508
 C5F  C18  C   C      0   0.397   -9.4032   8.0619  31.3148
 C5F  O03  O   O2     0  -0.489  -11.2751   8.2058  29.6993
 C5F  O04  O   OC    -1  -0.588   -9.5440   9.2774  31.5304
 C5F  O05  O   O      0  -0.587   -8.7617   7.2363  31.9906
 C5F  CL1  CL  CL     0  -0.067  -14.4882  10.8528  34.3333
 C5F  CL2  CL  CL     0  -0.073  -16.5122   9.2777  35.7075
 C5F  H16  H   HCH1   0   0.304  -16.2303   7.7663  33.3473
 C5F  H82  H   HCH2   0   0.288  -16.5083  10.6823  32.2971
 C5F  H81  H   HCH2   0   0.293  -17.7798   9.6871  33.1376
 C5F  H10  H   HCR6   0   0.245  -15.3491   9.7551  30.5534
 C5F  H11  H   HCR6   0   0.250  -13.5103   7.3681  33.5872
 C5F  H21  H   HCR6   0   0.252  -13.3639   9.4891  29.1519
 C5F  H31  H   HCR6   0   0.269  -11.5403   7.0952  32.2196
 C5F  H62  H   HCH3   0   0.231  -10.8852   5.6446  30.7839
 C5F  H61  H   HCH3   0   0.219  -10.7353   5.7221  29.0288
 C5F  H63  H   HCH3   0   0.230   -9.3088   5.4959  30.0324
 C5F  H72  H   HCH3   0   0.233   -8.9771   8.9973  28.8146
 C5F  H71  H   HCH3   0   0.227   -8.1455   7.4500  28.9807
 C5F  H73  H   HCH3   0   0.229   -9.5239   7.5887  27.8903

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
 C5F  C17  C15  single    1.527  0.020  1.527
 C5F  C16  C15  single    1.524  0.020  1.524
 C5F  C15  O03  single    1.436  0.020  1.436
 C5F  C15  C18  single    1.561  0.020  1.561
 C5F  O03  C14  single    1.339  0.020  1.339
 C5F  C12  C14  aromatic  1.398  0.020  1.398
 C5F  C12  C10  aromatic  1.384  0.020  1.384
 C5F  C14  C13  aromatic  1.398  0.020  1.398
 C5F  C10  C09  aromatic  1.391  0.020  1.391
 C5F  C18  O05  deloc     1.245  0.020  1.245
 C5F  C18  O04  deloc     1.242  0.020  1.242
 C5F  C13  C11  aromatic  1.387  0.020  1.387
 C5F  C09  C11  aromatic  1.391  0.020  1.391
 C5F  C09  C06  single    1.486  0.020  1.486
 C5F  C08  C06  single    1.509  0.020  1.509
 C5F  C08  C07  single    1.481  0.020  1.481
 C5F  C06  C07  single    1.496  0.020  1.496
 C5F  CL1  C07  single    1.751  0.020  1.751
 C5F  C07  CL2  single    1.756  0.020  1.756
 C5F  C06  H16  single    0.970  0.020  1.090
 C5F  C08  H82  single    0.970  0.020  1.090
 C5F  C08  H81  single    0.970  0.020  1.090
 C5F  C10  H10  single    0.930  0.020  1.080
 C5F  C11  H11  single    0.930  0.020  1.080
 C5F  C12  H21  single    0.930  0.020  1.080
 C5F  C13  H31  single    0.930  0.020  1.080
 C5F  C16  H62  single    0.970  0.020  1.090
 C5F  C16  H61  single    0.970  0.020  1.090
 C5F  C16  H63  single    0.970  0.020  1.090
 C5F  C17  H72  single    0.970  0.020  1.090
 C5F  C17  H71  single    0.970  0.020  1.090
 C5F  C17  H73  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
 C5F  H16  C06  C09  114.65  3.000
 C5F  H16  C06  C08  114.86  3.000
 C5F  C09  C06  C08  122.63  3.000
 C5F  H16  C06  C07  113.19  3.000
 C5F  C08  C06  C07   59.08  3.000
 C5F  C09  C06  C07  121.13  3.000
 C5F  CL2  C07  CL1  112.10  3.000
 C5F  CL2  C07  C08  118.89  3.000
 C5F  CL1  C07  C08  118.78  3.000
 C5F  CL2  C07  C06  118.54  3.000
 C5F  CL1  C07  C06  118.92  3.000
 C5F  C08  C07  C06   60.88  3.000
 C5F  H81  C08  H82  114.45  3.000
 C5F  H81  C08  C07  117.86  3.000
 C5F  H82  C08  C07  116.99  3.000
 C5F  H81  C08  C06  118.13  3.000
 C5F  H82  C08  C06  118.78  3.000
 C5F  C07  C08  C06   60.03  3.000
 C5F  C11  C09  C10  117.70  3.000
 C5F  C11  C09  C06  119.58  3.000
 C5F  C10  C09  C06  122.71  3.000
 C5F  H10  C10  C12  118.77  3.000
 C5F  H10  C10  C09  120.17  3.000
 C5F  C12  C10  C09  121.06  3.000
 C5F  H11  C11  C13  118.46  3.000
 C5F  H11  C11  C09  119.53  3.000
 C5F  C13  C11  C09  122.01  3.000
 C5F  H21  C12  C14  119.11  3.000
 C5F  H21  C12  C10  119.87  3.000
 C5F  C14  C12  C10  121.02  3.000
 C5F  H31  C13  C14  121.86  3.000
 C5F  H31  C13  C11  118.20  3.000
 C5F  C14  C13  C11  119.94  3.000
 C5F  O03  C14  C13  126.38  3.000
 C5F  C13  C14  C12  118.26  3.000
 C5F  O03  C14  C12  115.35  3.000
 C5F  O03  C15  C18  111.36  3.000
 C5F  C18  C15  C17  107.09  3.000
 C5F  O03  C15  C17  103.79  3.000
 C5F  C18  C15  C16  114.64  3.000
 C5F  O03  C15  C16  110.22  3.000
 C5F  C17  C15  C16  109.11  3.000
 C5F  H63  C16  H61  107.54  3.000
 C5F  H63  C16  H62  107.19  3.000
 C5F  H61  C16  H62  107.89  3.000
 C5F  H63  C16  C15  110.22  3.000
 C5F  H61  C16  C15  110.05  3.000
 C5F  H62  C16  C15  113.71  3.000
 C5F  H73  C17  H71  107.79  3.000
 C5F  H73  C17  H72  108.53  3.000
 C5F  H71  C17  H72  108.06  3.000
 C5F  H73  C17  C15  111.11  3.000
 C5F  H71  C17  C15  110.04  3.000
 C5F  H72  C17  C15  111.20  3.000
 C5F  O05  C18  O04  127.80  3.000
 C5F  O04  C18  C15  115.94  3.000
 C5F  O05  C18  C15  116.17  3.000
 C5F  C15  O03  C14  122.84  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
 C5F  CONST_01  C14  C12  C10  C09     0.00   0.0  0
 C5F  CONST_02  C14  C13  C11  C09     0.00   0.0  0
 C5F  CONST_03  C13  C14  C12  C10     0.00   0.0  0
 C5F  CONST_04  C13  C11  C09  C10     0.00   0.0  0
 C5F  CONST_05  C12  C14  C13  C11     0.00   0.0  0
 C5F  CONST_06  C12  C10  C09  C11     0.00   0.0  0
 C5F  CONST_07  C12  C10  C09  C06   180.00   0.0  0
 C5F  CONST_08  C13  C11  C09  C06   180.00   0.0  0
 C5F  CONST_09  O03  C14  C12  C10   180.00   0.0  0
 C5F  CONST_10  O03  C14  C13  C11   180.00   0.0  0
 C5F  CONST_11  H10  C10  C09  C06     0.00   0.0  0
 C5F  CONST_12  H11  C11  C09  C06     0.00   0.0  0
 C5F  CONST_13  H21  C12  C10  C09   180.00   0.0  0
 C5F  CONST_14  H31  C13  C11  C09   180.00   0.0  0
 C5F  Var_01    C09  C06  C08  C07  -109.40  30.0  1
 C5F  Var_02    C10  C09  C06  C07   -97.38  30.0  2
 C5F  Var_03    CL1  C07  C08  C06   109.00  30.0  1
 C5F  Var_04    C17  C15  O03  C14  -170.03  30.0  2
 C5F  Var_05    O05  C18  C15  C16    21.96  30.0  3
 C5F  Var_06    H72  C17  C15  C16   177.61  30.0  3
 C5F  Var_07    H62  C16  C15  C17   177.72  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
 C5F  chir_01  C06  C09  C08  C07  both

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
 C5F  plan-1  C06  0.020
 C5F  plan-1  C09  0.020
 C5F  plan-1  C10  0.020
 C5F  plan-1  C11  0.020
 C5F  plan-1  C12  0.020
 C5F  plan-1  C13  0.020
 C5F  plan-1  C14  0.020
 C5F  plan-1  O03  0.020
 C5F  plan-1  H10  0.020
 C5F  plan-1  H11  0.020
 C5F  plan-1  H21  0.020
 C5F  plan-1  H31  0.020
 C5F  plan-2  C15  0.020
 C5F  plan-2  C18  0.020
 C5F  plan-2  O04  0.020
 C5F  plan-2  O05  0.020

