# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 11:10:45 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: 3-chloro-6-(hydroxymethyl)-2-methyl-5-{4-[3-(trifluoromethoxy)phenoxy]phenyl}pyridin-4-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nc(CO)c(c(O)c1Cl)c2ccc(Oc3cccc(OC(F)(F)F)c3)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
 G8U  G8U  3-chloro-6-(hydroxymethyl)-2-methyl-5-{4-[3-(trifluoromethoxy)phenoxy]phenyl}pyridin-4-ol  ligand  44  29  .  2021-08-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_G8U
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
 G8U  C1    C   CT    0   1.073  -7.1957  -0.7886  -0.6416
 G8U  F1    F   F     0  -0.299  -6.6491  -1.7805  -1.3474
 G8U  F2    F   F     0  -0.298  -7.3150   0.2523  -1.4673
 G8U  F3    F   F     0  -0.277  -8.4077  -1.1648  -0.2665
 G8U  C4    C   CR6   0   0.329  -5.2007  -0.0278   0.3129
 G8U  C5    C   CR16  0  -0.382  -4.1656  -0.9422   0.3031
 G8U  C6    C   CR6   0   0.379  -2.8593  -0.4697   0.2096
 G8U  C7    C   CR16  0  -0.334  -2.6075   0.8949   0.1236
 G8U  C8    C   CR16  0  -0.246  -3.6745   1.7829   0.1435
 G8U  C9    C   CR16  0  -0.315  -4.9835   1.3382   0.2367
 G8U  O10   O   O2    0  -0.511  -1.8890  -1.4199   0.2085
 G8U  C11   C   CR6   0   0.288  -0.5755  -1.0281   0.1067
 G8U  C12   C   CR16  0  -0.289   0.1489  -0.7522   1.2549
 G8U  C13   C   CR16  0  -0.265   1.4822  -0.3850   1.1452
 G8U  C14   C   CR6   0   0.034   2.0935  -0.2909  -0.1020
 G8U  C15   C   CR16  0  -0.275   1.3484  -0.5837  -1.2420
 G8U  C16   C   CR16  0  -0.289   0.0139  -0.9453  -1.1452
 G8U  C17   C   CR6   0  -0.112   3.5131   0.1132  -0.2203
 G8U  C18   C   CR6   0   0.523   4.4754  -0.8318  -0.5916
 G8U  C19   C   CR6   0  -0.251   5.8009  -0.4169  -0.6832
 G8U  C20   C   CR6   0   0.262   6.1484   0.9027  -0.4148
 G8U  C22   C   CR6   0   0.196   3.9461   1.4108   0.0258
 G8U  O23   O   OH1   0  -0.583   4.0787  -2.0770  -0.8300
 G8U  C24   C   CH2   0  -0.228   2.9852   2.4860   0.4529
 G8U  O25   O   OH1   0  -0.664   2.9450   2.4874   1.8648
 G8U  CL    CL  CL    0  -0.104   7.0044  -1.5762  -1.1341
 G8U  C27   C   CH3   0  -0.732   7.5654   1.3719  -0.5080
 G8U  N28   N   N     0  -0.458   5.2208   1.7846  -0.0692
 G8U  O29   O   O2    0  -0.524  -6.5007  -0.4973   0.4649
 G8U  H5    H   HCR6  0   0.292  -4.3556  -2.0047   0.3855
 G8U  H9    H   HCR6  0   0.280  -5.8081   2.0365   0.2655
 G8U  H7    H   HCR6  0   0.284  -1.5984   1.2768   0.0504
 G8U  H8    H   HCR6  0   0.276  -3.4765   2.8446   0.0849
 G8U  H12   H   HCR6  0   0.277  -0.3205  -0.8263   2.2277
 G8U  H16   H   HCR6  0   0.277  -0.5616  -1.1632  -2.0359
 G8U  H13   H   HCR6  0   0.260   2.0482  -0.1688   2.0409
 G8U  H15   H   HCR6  0   0.261   1.8076  -0.5125  -2.2198
 G8U  H23   H   HOH1  0   0.477   4.8210  -2.6424  -1.0852
 G8U  H271  H   HCH3  0   0.257   7.9771   1.2021  -1.5038
 G8U  H272  H   HCH3  0   0.259   7.6173   2.4357  -0.2892
 G8U  H273  H   HCH3  0   0.258   8.2066   0.8430   0.1990
 G8U  H241  H   HCH2  0   0.221   3.3433   3.4435   0.0587
 G8U  H242  H   HCH2  0   0.214   1.9965   2.3020   0.0204
 G8U  H25   H   HOH1  0   0.459   2.2736   3.1202   2.1387

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
 G8U  C1   F1    single    1.335  0.020  1.335
 G8U  C1   F2    single    1.334  0.020  1.334
 G8U  C1   F3    single    1.323  0.020  1.323
 G8U  C1   O29   single    1.339  0.020  1.339
 G8U  C4   C5    aromatic  1.381  0.020  1.381
 G8U  C4   C9    aromatic  1.385  0.020  1.385
 G8U  C4   O29   single    1.391  0.020  1.391
 G8U  C5   C6    aromatic  1.392  0.020  1.392
 G8U  C6   C7    aromatic  1.390  0.020  1.390
 G8U  C6   O10   single    1.358  0.020  1.358
 G8U  C7   C8    aromatic  1.388  0.020  1.388
 G8U  C8   C9    aromatic  1.386  0.020  1.386
 G8U  O10  C11   single    1.374  0.020  1.374
 G8U  C11  C12   aromatic  1.385  0.020  1.385
 G8U  C11  C16   aromatic  1.386  0.020  1.386
 G8U  C12  C13   aromatic  1.387  0.020  1.387
 G8U  C13  C14   aromatic  1.392  0.020  1.392
 G8U  C14  C15   aromatic  1.393  0.020  1.393
 G8U  C14  C17   single    1.481  0.020  1.481
 G8U  C15  C16   aromatic  1.386  0.020  1.386
 G8U  C17  C18   aromatic  1.399  0.020  1.399
 G8U  C17  C22   aromatic  1.390  0.020  1.390
 G8U  C18  C19   aromatic  1.392  0.020  1.392
 G8U  C18  O23   single    1.328  0.020  1.328
 G8U  C19  C20   aromatic  1.391  0.020  1.391
 G8U  C19  CL    single    1.731  0.020  1.731
 G8U  C20  C27   single    1.496  0.020  1.496
 G8U  C20  N28   aromatic  1.326  0.020  1.326
 G8U  C22  C24   single    1.504  0.020  1.504
 G8U  C22  N28   aromatic  1.332  0.020  1.332
 G8U  C24  O25   single    1.413  0.020  1.413
 G8U  C5   H5    single    0.930  0.020  1.080
 G8U  C9   H9    single    0.930  0.020  1.080
 G8U  C7   H7    single    0.930  0.020  1.080
 G8U  C8   H8    single    0.930  0.020  1.080
 G8U  C12  H12   single    0.930  0.020  1.080
 G8U  C16  H16   single    0.930  0.020  1.080
 G8U  C13  H13   single    0.930  0.020  1.080
 G8U  C15  H15   single    0.930  0.020  1.080
 G8U  O23  H23   single    0.850  0.020  0.980
 G8U  C27  H271  single    0.970  0.020  1.090
 G8U  C27  H272  single    0.970  0.020  1.090
 G8U  C27  H273  single    0.970  0.020  1.090
 G8U  C24  H241  single    0.970  0.020  1.090
 G8U  C24  H242  single    0.970  0.020  1.090
 G8U  O25  H25   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
 G8U  O29   C1   F3    107.64  3.000
 G8U  O29   C1   F2    112.85  3.000
 G8U  F3    C1   F2    108.39  3.000
 G8U  O29   C1   F1    112.72  3.000
 G8U  F3    C1   F1    108.28  3.000
 G8U  F2    C1   F1    106.82  3.000
 G8U  O29   C4   C9    119.05  3.000
 G8U  O29   C4   C5    118.55  3.000
 G8U  C9    C4   C5    122.34  3.000
 G8U  H5    C5   C6    120.19  3.000
 G8U  H5    C5   C4    121.18  3.000
 G8U  C6    C5   C4    118.62  3.000
 G8U  O10   C6   C7    123.86  3.000
 G8U  O10   C6   C5    115.66  3.000
 G8U  C7    C6   C5    120.48  3.000
 G8U  H7    C7   C8    119.49  3.000
 G8U  H7    C7   C6    121.32  3.000
 G8U  C8    C7   C6    119.19  3.000
 G8U  H8    C8   C9    119.45  3.000
 G8U  H8    C8   C7    119.10  3.000
 G8U  C9    C8   C7    121.45  3.000
 G8U  H9    C9   C8    121.00  3.000
 G8U  H9    C9   C4    121.06  3.000
 G8U  C8    C9   C4    117.93  3.000
 G8U  C11   O10  C6    118.91  3.000
 G8U  C16   C11  C12   120.95  3.000
 G8U  C16   C11  O10   119.35  3.000
 G8U  C12   C11  O10   119.68  3.000
 G8U  H12   C12  C13   120.38  3.000
 G8U  H12   C12  C11   120.29  3.000
 G8U  C13   C12  C11   119.32  3.000
 G8U  H13   C13  C14   119.91  3.000
 G8U  H13   C13  C12   119.37  3.000
 G8U  C14   C13  C12   120.71  3.000
 G8U  C17   C14  C15   120.32  3.000
 G8U  C17   C14  C13   120.73  3.000
 G8U  C15   C14  C13   118.95  3.000
 G8U  H15   C15  C16   119.26  3.000
 G8U  H15   C15  C14   119.89  3.000
 G8U  C16   C15  C14   120.84  3.000
 G8U  H16   C16  C15   120.45  3.000
 G8U  H16   C16  C11   120.33  3.000
 G8U  C15   C16  C11   119.21  3.000
 G8U  C22   C17  C18   117.60  3.000
 G8U  C22   C17  C14   122.64  3.000
 G8U  C18   C17  C14   119.76  3.000
 G8U  O23   C18  C19   123.51  3.000
 G8U  O23   C18  C17   118.38  3.000
 G8U  C19   C18  C17   118.11  3.000
 G8U  CL    C19  C20   120.81  3.000
 G8U  CL    C19  C18   118.66  3.000
 G8U  C20   C19  C18   120.54  3.000
 G8U  N28   C20  C27   118.06  3.000
 G8U  N28   C20  C19   120.44  3.000
 G8U  C27   C20  C19   121.49  3.000
 G8U  N28   C22  C24   115.54  3.000
 G8U  N28   C22  C17   123.20  3.000
 G8U  C24   C22  C17   121.24  3.000
 G8U  H23   O23  C18   111.47  3.000
 G8U  H242  C24  H241  107.46  3.000
 G8U  H242  C24  O25   111.67  3.000
 G8U  H241  C24  O25   111.60  3.000
 G8U  H242  C24  C22   110.16  3.000
 G8U  H241  C24  C22   108.29  3.000
 G8U  O25   C24  C22   107.62  3.000
 G8U  H25   O25  C24   107.76  3.000
 G8U  H273  C27  H272  108.41  3.000
 G8U  H273  C27  H271  107.11  3.000
 G8U  H272  C27  H271  108.54  3.000
 G8U  H273  C27  C20   111.36  3.000
 G8U  H272  C27  C20   109.86  3.000
 G8U  H271  C27  C20   111.45  3.000
 G8U  C22   N28  C20   120.10  3.000
 G8U  C4    O29  C1    117.93  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
 G8U  CONST_01  C7    C6   C5   C4     0.00   0.0  0
 G8U  CONST_02  C7    C8   C9   C4     0.00   0.0  0
 G8U  CONST_03  C8    C9   C4   C5     0.00   0.0  0
 G8U  CONST_04  C8    C7   C6   C5     0.00   0.0  0
 G8U  CONST_05  C9    C4   C5   C6     0.00   0.0  0
 G8U  CONST_06  C9    C8   C7   C6     0.00   0.0  0
 G8U  CONST_07  C14   C13  C12  C11    0.00   0.0  0
 G8U  CONST_08  C14   C15  C16  C11    0.00   0.0  0
 G8U  CONST_09  C15   C16  C11  C12    0.00   0.0  0
 G8U  CONST_10  C15   C14  C13  C12    0.00   0.0  0
 G8U  CONST_11  C17   C14  C13  C12  180.00   0.0  0
 G8U  CONST_12  C16   C11  C12  C13    0.00   0.0  0
 G8U  CONST_13  C16   C15  C14  C13    0.00   0.0  0
 G8U  CONST_16  C19   C18  C17  C14  180.00   0.0  0
 G8U  CONST_17  N28   C22  C17  C14  180.00   0.0  0
 G8U  CONST_20  C17   C14  C15  C16  180.00   0.0  0
 G8U  CONST_21  C20   C19  C18  C17    0.00   0.0  0
 G8U  CONST_22  C20   N28  C22  C17    0.00   0.0  0
 G8U  CONST_23  N28   C22  C17  C18    0.00   0.0  0
 G8U  CONST_24  N28   C20  C19  C18    0.00   0.0  0
 G8U  CONST_25  C22   C17  C18  C19    0.00   0.0  0
 G8U  CONST_26  C22   N28  C20  C19    0.00   0.0  0
 G8U  CONST_27  O10   C6   C5   C4   180.00   0.0  0
 G8U  CONST_28  O29   C4   C5   C6   180.00   0.0  0
 G8U  CONST_29  O10   C6   C7   C8   180.00   0.0  0
 G8U  CONST_30  O29   C4   C9   C8   180.00   0.0  0
 G8U  CONST_31  C13   C12  C11  O10  180.00   0.0  0
 G8U  CONST_32  C15   C16  C11  O10  180.00   0.0  0
 G8U  CONST_33  O23   C18  C17  C14    0.00   0.0  0
 G8U  CONST_34  C24   C22  C17  C14    0.00   0.0  0
 G8U  CONST_35  CL    C19  C18  C17  180.00   0.0  0
 G8U  CONST_36  C24   C22  C17  C18  180.00   0.0  0
 G8U  CONST_37  C27   C20  C19  C18  180.00   0.0  0
 G8U  CONST_38  O23   C18  C19  C20  180.00   0.0  0
 G8U  CONST_39  C24   C22  N28  C20  180.00   0.0  0
 G8U  CONST_40  O23   C18  C17  C22  180.00   0.0  0
 G8U  CONST_41  C27   C20  N28  C22  180.00   0.0  0
 G8U  CONST_42  N28   C20  C19  CL   180.00   0.0  0
 G8U  CONST_43  H8    C8   C9   C4   180.00   0.0  0
 G8U  CONST_44  H9    C9   C4   C5   180.00   0.0  0
 G8U  CONST_45  H7    C7   C6   C5   180.00   0.0  0
 G8U  CONST_46  H5    C5   C6   C7   180.00   0.0  0
 G8U  CONST_47  H13   C13  C12  C11  180.00   0.0  0
 G8U  CONST_48  H15   C15  C16  C11  180.00   0.0  0
 G8U  CONST_49  H16   C16  C11  C12  180.00   0.0  0
 G8U  CONST_50  H12   C12  C13  C14  180.00   0.0  0
 G8U  Var_01    C12   C11  O10  C6    89.57  30.0  2
 G8U  Var_02    C5    C4   O29  C1   -91.13  30.0  3
 G8U  Var_03    O25   C24  C22  C17   90.85  30.0  2
 G8U  Var_04    H271  C27  C20  C19   58.00  30.0  2

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
 G8U  plan-1  C4   0.020
 G8U  plan-1  C5   0.020
 G8U  plan-1  C6   0.020
 G8U  plan-1  C7   0.020
 G8U  plan-1  C8   0.020
 G8U  plan-1  C9   0.020
 G8U  plan-1  O10  0.020
 G8U  plan-1  O29  0.020
 G8U  plan-1  H5   0.020
 G8U  plan-1  H9   0.020
 G8U  plan-1  H7   0.020
 G8U  plan-1  H8   0.020
 G8U  plan-2  O10  0.020
 G8U  plan-2  C11  0.020
 G8U  plan-2  C12  0.020
 G8U  plan-2  C13  0.020
 G8U  plan-2  C14  0.020
 G8U  plan-2  C15  0.020
 G8U  plan-2  C16  0.020
 G8U  plan-2  C17  0.020
 G8U  plan-2  H12  0.020
 G8U  plan-2  H16  0.020
 G8U  plan-2  H13  0.020
 G8U  plan-2  H15  0.020
 G8U  plan-3  C14  0.020
 G8U  plan-3  C17  0.020
 G8U  plan-3  C18  0.020
 G8U  plan-3  C19  0.020
 G8U  plan-3  C20  0.020
 G8U  plan-3  C22  0.020
 G8U  plan-3  O23  0.020
 G8U  plan-3  C24  0.020
 G8U  plan-3  CL   0.020
 G8U  plan-3  C27  0.020
 G8U  plan-3  N28  0.020

