# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 04:07:24 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: 3-chloro-2,6-dimethyl-5-{4-[4-(trifluoromethoxy)phenoxy]phenyl}pyridin-4-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nc(C)c(c(O)c1Cl)c2ccc(Oc3ccc(OC(F)(F)F)cc3)cc2
#
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
 4X9  4X9  3-chloro-2,6-dimethyl-5-{4-[4-(trifluoromethoxy)phenoxy]phenyl}pyridin-4-ol  ligand  43  28  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4X9
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
 4X9  C1    C   CT    0   1.072  -6.7960   1.1216   0.7396
 4X9  O3    O   O2    0  -0.523  -6.2433   0.8467  -0.4474
 4X9  C4    C   CR6   0   0.294  -5.0518   0.1269  -0.4529
 4X9  C5    C   CR16  0  -0.288  -3.8470   0.8022  -0.4250
 4X9  C6    C   CR16  0  -0.339  -2.6559   0.0911  -0.4863
 4X9  C7    C   CR6   0   0.374  -2.6875  -1.2957  -0.5739
 4X9  C8    C   CR16  0  -0.327  -3.9074  -1.9663  -0.6105
 4X9  C9    C   CR16  0  -0.288  -5.0919  -1.2549  -0.5507
 4X9  O10   O   O2    0  -0.509  -1.5765  -2.0746  -0.6461
 4X9  C11   C   CR6   0   0.291  -0.3388  -1.4915  -0.5237
 4X9  C12   C   CR16  0  -0.286   0.1760  -1.2257   0.7359
 4X9  C13   C   CR16  0  -0.277   1.4420  -0.6716   0.8466
 4X9  C14   C   CR6   0   0.057   2.1954  -0.3805  -0.2875
 4X9  C15   C   CR16  0  -0.277   1.6622  -0.6631  -1.5412
 4X9  C16   C   CR16  0  -0.293   0.3938  -1.2119  -1.6661
 4X9  C17   C   CR6   0  -0.141   3.5378   0.2323  -0.1576
 4X9  C18   C   CR6   0   0.523   4.6767  -0.5720  -0.1686
 4X9  C19   C   CR6   0  -0.254   5.9180   0.0475  -0.0298
 4X9  C20   C   CR6   0   0.263   6.0010   1.4262   0.1101
 4X9  C22   C   CR6   0   0.213   3.7064   1.6073  -0.0163
 4X9  F23   F   F     0  -0.300  -6.0088   1.8687   1.5163
 4X9  F24   F   F     0  -0.278  -7.9158   1.7923   0.5173
 4X9  F25   F   F     0  -0.299  -7.0949   0.0246   1.4374
 4X9  C26   C   CH3   0  -0.732   7.3187   2.1177   0.2624
 4X9  CL    CL  CL    0  -0.109   7.3456  -0.9334  -0.0327
 4X9  O28   O   OH1   0  -0.584   4.5209  -1.8850  -0.3072
 4X9  C29   C   CH3   0  -0.742   2.5204   2.5235  -0.0049
 4X9  N30   N   N     0  -0.465   4.9040   2.1751   0.1117
 4X9  H5    H   HCR6  0   0.286  -3.8192   1.8825  -0.3726
 4X9  H6    H   HCR6  0   0.287  -1.7222   0.6366  -0.4674
 4X9  H8    H   HCR6  0   0.281  -3.9280  -3.0455  -0.6870
 4X9  H9    H   HCR6  0   0.284  -6.0367  -1.7799  -0.5946
 4X9  H12   H   HCR6  0   0.278  -0.4020  -1.4513   1.6231
 4X9  H13   H   HCR6  0   0.263   1.8455  -0.4595   1.8286
 4X9  H15   H   HCR6  0   0.261   2.2357  -0.4438  -2.4329
 4X9  H16   H   HCR6  0   0.276  -0.0178  -1.4258  -2.6441
 4X9  H26   H   HCH3  0   0.257   7.9543   1.9620  -0.6108
 4X9  H26A  H   HCH3  0   0.258   7.1620   3.1862   0.3874
 4X9  H26B  H   HCH3  0   0.255   7.8675   1.7444   1.1280
 4X9  HO28  H   HOH1  0   0.476   5.3723  -2.3437  -0.3150
 4X9  H29   H   HCH3  0   0.255   1.8836   2.3425   0.8629
 4X9  H29A  H   HCH3  0   0.255   2.8486   3.5600   0.0238
 4X9  H29B  H   HCH3  0   0.252   1.8952   2.3801  -0.8871

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
 4X9  C1   O3    single    1.338  0.020  1.338
 4X9  C1   F23   single    1.335  0.020  1.335
 4X9  C1   F24   single    1.324  0.020  1.324
 4X9  C1   F25   single    1.334  0.020  1.334
 4X9  O3   C4    single    1.392  0.020  1.392
 4X9  C4   C5    aromatic  1.382  0.020  1.382
 4X9  C4   C9    aromatic  1.386  0.020  1.386
 4X9  C5   C6    aromatic  1.389  0.020  1.389
 4X9  C6   C7    aromatic  1.390  0.020  1.390
 4X9  C7   C8    aromatic  1.393  0.020  1.393
 4X9  C7   O10   single    1.359  0.020  1.359
 4X9  C8   C9    aromatic  1.383  0.020  1.383
 4X9  O10  C11   single    1.374  0.020  1.374
 4X9  C11  C12   aromatic  1.386  0.020  1.386
 4X9  C11  C16   aromatic  1.386  0.020  1.386
 4X9  C12  C13   aromatic  1.386  0.020  1.386
 4X9  C13  C14   aromatic  1.392  0.020  1.392
 4X9  C14  C15   aromatic  1.391  0.020  1.391
 4X9  C14  C17   single    1.481  0.020  1.481
 4X9  C15  C16   aromatic  1.388  0.020  1.388
 4X9  C17  C18   aromatic  1.394  0.020  1.394
 4X9  C17  C22   aromatic  1.392  0.020  1.392
 4X9  C18  C19   aromatic  1.394  0.020  1.394
 4X9  C18  O28   single    1.329  0.020  1.329
 4X9  C19  C20   aromatic  1.388  0.020  1.388
 4X9  C19  CL    single    1.732  0.020  1.732
 4X9  C20  C26   single    1.496  0.020  1.496
 4X9  C20  N30   aromatic  1.328  0.020  1.328
 4X9  C22  C29   single    1.499  0.020  1.499
 4X9  C22  N30   aromatic  1.332  0.020  1.332
 4X9  C5   H5    single    0.930  0.020  1.080
 4X9  C6   H6    single    0.930  0.020  1.080
 4X9  C8   H8    single    0.930  0.020  1.080
 4X9  C9   H9    single    0.930  0.020  1.080
 4X9  C12  H12   single    0.930  0.020  1.080
 4X9  C13  H13   single    0.930  0.020  1.080
 4X9  C15  H15   single    0.930  0.020  1.080
 4X9  C16  H16   single    0.930  0.020  1.080
 4X9  C26  H26   single    0.970  0.020  1.090
 4X9  C26  H26A  single    0.970  0.020  1.090
 4X9  C26  H26B  single    0.970  0.020  1.090
 4X9  O28  HO28  single    0.850  0.020  0.980
 4X9  C29  H29   single    0.970  0.020  1.090
 4X9  C29  H29A  single    0.970  0.020  1.090
 4X9  C29  H29B  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
 4X9  F25   C1   F24   108.35  3.000
 4X9  F25   C1   F23   106.74  3.000
 4X9  F24   C1   F23   108.24  3.000
 4X9  F25   C1   O3    112.81  3.000
 4X9  F24   C1   O3    107.73  3.000
 4X9  F23   C1   O3    112.81  3.000
 4X9  C4    O3   C1    117.61  3.000
 4X9  C9    C4   C5    120.93  3.000
 4X9  C9    C4   O3    119.41  3.000
 4X9  C5    C4   O3    119.58  3.000
 4X9  H5    C5   C6    119.44  3.000
 4X9  H5    C5   C4    120.76  3.000
 4X9  C6    C5   C4    119.79  3.000
 4X9  H6    C6   C7    121.60  3.000
 4X9  H6    C6   C5    118.78  3.000
 4X9  C7    C6   C5    119.62  3.000
 4X9  O10   C7   C8    116.03  3.000
 4X9  O10   C7   C6    123.83  3.000
 4X9  C8    C7   C6    120.14  3.000
 4X9  H8    C8   C9    119.98  3.000
 4X9  H8    C8   C7    119.92  3.000
 4X9  C9    C8   C7    120.10  3.000
 4X9  H9    C9   C8    119.78  3.000
 4X9  H9    C9   C4    120.79  3.000
 4X9  C8    C9   C4    119.42  3.000
 4X9  C11   O10  C7    119.25  3.000
 4X9  C16   C11  C12   120.93  3.000
 4X9  C16   C11  O10   119.25  3.000
 4X9  C12   C11  O10   119.79  3.000
 4X9  H12   C12  C13   120.35  3.000
 4X9  H12   C12  C11   120.43  3.000
 4X9  C13   C12  C11   119.22  3.000
 4X9  H13   C13  C14   119.75  3.000
 4X9  H13   C13  C12   119.40  3.000
 4X9  C14   C13  C12   120.84  3.000
 4X9  C17   C14  C15   120.68  3.000
 4X9  C17   C14  C13   120.36  3.000
 4X9  C15   C14  C13   118.96  3.000
 4X9  H15   C15  C16   119.35  3.000
 4X9  H15   C15  C14   119.87  3.000
 4X9  C16   C15  C14   120.78  3.000
 4X9  H16   C16  C15   120.47  3.000
 4X9  H16   C16  C11   120.26  3.000
 4X9  C15   C16  C11   119.27  3.000
 4X9  C22   C17  C18   118.13  3.000
 4X9  C22   C17  C14   121.81  3.000
 4X9  C18   C17  C14   120.06  3.000
 4X9  O28   C18  C19   123.62  3.000
 4X9  O28   C18  C17   118.34  3.000
 4X9  C19   C18  C17   118.04  3.000
 4X9  CL    C19  C20   120.88  3.000
 4X9  CL    C19  C18   118.82  3.000
 4X9  C20   C19  C18   120.30  3.000
 4X9  N30   C20  C26   117.82  3.000
 4X9  N30   C20  C19   120.71  3.000
 4X9  C26   C20  C19   121.47  3.000
 4X9  N30   C22  C29   116.76  3.000
 4X9  N30   C22  C17   122.67  3.000
 4X9  C29   C22  C17   120.57  3.000
 4X9  H26B  C26  H26A  108.53  3.000
 4X9  H26B  C26  H26   107.04  3.000
 4X9  H26A  C26  H26   108.43  3.000
 4X9  H26B  C26  C20   111.46  3.000
 4X9  H26A  C26  C20   109.82  3.000
 4X9  H26   C26  C20   111.45  3.000
 4X9  HO28  O28  C18   111.47  3.000
 4X9  H29B  C29  H29A  108.64  3.000
 4X9  H29B  C29  H29   106.67  3.000
 4X9  H29A  C29  H29   108.25  3.000
 4X9  H29B  C29  C22   111.53  3.000
 4X9  H29A  C29  C22   110.12  3.000
 4X9  H29   C29  C22   111.49  3.000
 4X9  C22   N30  C20   120.15  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
 4X9  CONST_01  C7   C6   C5   C4     0.00   0.0  0
 4X9  CONST_02  C7   C8   C9   C4     0.00   0.0  0
 4X9  CONST_03  C8   C9   C4   C5     0.00   0.0  0
 4X9  CONST_04  C8   C7   C6   C5     0.00   0.0  0
 4X9  CONST_05  C9   C4   C5   C6     0.00   0.0  0
 4X9  CONST_06  C9   C8   C7   C6     0.00   0.0  0
 4X9  CONST_07  C14  C13  C12  C11    0.00   0.0  0
 4X9  CONST_08  C14  C15  C16  C11    0.00   0.0  0
 4X9  CONST_09  C15  C16  C11  C12    0.00   0.0  0
 4X9  CONST_10  C15  C14  C13  C12    0.00   0.0  0
 4X9  CONST_11  C17  C14  C13  C12  180.00   0.0  0
 4X9  CONST_12  C16  C11  C12  C13    0.00   0.0  0
 4X9  CONST_13  C16  C15  C14  C13    0.00   0.0  0
 4X9  CONST_16  C19  C18  C17  C14  180.00   0.0  0
 4X9  CONST_17  N30  C22  C17  C14  180.00   0.0  0
 4X9  CONST_20  C17  C14  C15  C16  180.00   0.0  0
 4X9  CONST_21  C20  C19  C18  C17    0.00   0.0  0
 4X9  CONST_22  C20  N30  C22  C17    0.00   0.0  0
 4X9  CONST_23  N30  C22  C17  C18    0.00   0.0  0
 4X9  CONST_24  N30  C20  C19  C18    0.00   0.0  0
 4X9  CONST_25  C22  C17  C18  C19    0.00   0.0  0
 4X9  CONST_26  C22  N30  C20  C19    0.00   0.0  0
 4X9  CONST_27  C6   C5   C4   O3   180.00   0.0  0
 4X9  CONST_28  C8   C9   C4   O3   180.00   0.0  0
 4X9  CONST_29  O10  C7   C6   C5   180.00   0.0  0
 4X9  CONST_30  O10  C7   C8   C9   180.00   0.0  0
 4X9  CONST_31  C13  C12  C11  O10  180.00   0.0  0
 4X9  CONST_32  C15  C16  C11  O10  180.00   0.0  0
 4X9  CONST_33  O28  C18  C17  C14    0.00   0.0  0
 4X9  CONST_34  C29  C22  C17  C14    0.00   0.0  0
 4X9  CONST_35  CL   C19  C18  C17  180.00   0.0  0
 4X9  CONST_36  C29  C22  C17  C18  180.00   0.0  0
 4X9  CONST_37  C26  C20  C19  C18  180.00   0.0  0
 4X9  CONST_38  O28  C18  C19  C20  180.00   0.0  0
 4X9  CONST_39  C29  C22  N30  C20  180.00   0.0  0
 4X9  CONST_40  O28  C18  C17  C22  180.00   0.0  0
 4X9  CONST_41  C26  C20  N30  C22  180.00   0.0  0
 4X9  CONST_42  N30  C20  C19  CL   180.00   0.0  0
 4X9  CONST_43  H6   C6   C5   C4   180.00   0.0  0
 4X9  CONST_44  H8   C8   C9   C4   180.00   0.0  0
 4X9  CONST_45  H9   C9   C4   C5   180.00   0.0  0
 4X9  CONST_46  H5   C5   C6   C7   180.00   0.0  0
 4X9  CONST_47  H13  C13  C12  C11  180.00   0.0  0
 4X9  CONST_48  H15  C15  C16  C11  180.00   0.0  0
 4X9  CONST_49  H16  C16  C11  C12  180.00   0.0  0
 4X9  CONST_50  H12  C12  C13  C14  180.00   0.0  0
 4X9  Var_01    C12  C11  O10  C7    82.61  30.0  2
 4X9  Var_02    C5   C4   O3   C1   -90.98  30.0  2
 4X9  Var_03    H29  C29  C22  C17   64.88  30.0  2
 4X9  Var_04    H26  C26  C20  C19   61.53  30.0  2
 4X9  Var_05    F23  C1   O3   C4    61.26  30.0  3

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
 4X9  plan-1  O3   0.020
 4X9  plan-1  C4   0.020
 4X9  plan-1  C5   0.020
 4X9  plan-1  C6   0.020
 4X9  plan-1  C7   0.020
 4X9  plan-1  C8   0.020
 4X9  plan-1  C9   0.020
 4X9  plan-1  O10  0.020
 4X9  plan-1  H5   0.020
 4X9  plan-1  H6   0.020
 4X9  plan-1  H8   0.020
 4X9  plan-1  H9   0.020
 4X9  plan-2  O10  0.020
 4X9  plan-2  C11  0.020
 4X9  plan-2  C12  0.020
 4X9  plan-2  C13  0.020
 4X9  plan-2  C14  0.020
 4X9  plan-2  C15  0.020
 4X9  plan-2  C16  0.020
 4X9  plan-2  C17  0.020
 4X9  plan-2  H12  0.020
 4X9  plan-2  H13  0.020
 4X9  plan-2  H15  0.020
 4X9  plan-2  H16  0.020
 4X9  plan-3  C14  0.020
 4X9  plan-3  C17  0.020
 4X9  plan-3  C18  0.020
 4X9  plan-3  C19  0.020
 4X9  plan-3  C20  0.020
 4X9  plan-3  C22  0.020
 4X9  plan-3  C26  0.020
 4X9  plan-3  CL   0.020
 4X9  plan-3  O28  0.020
 4X9  plan-3  C29  0.020
 4X9  plan-3  N30  0.020

