# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 05:18:03 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: 2-[3-(3,4-difluorophenyl)-5-hydroxy-1H-pyrazol-1-yl]-1,3-thiazole-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1csc(n1)n2nc(cc2O)c3ccc(F)c(F)c3
#
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
 9YD  9YD  '2-[3-(3,4-difluorophenyl)-5-hydroxy-1H-pyrazol-1-yl]-1,3-thiazole-4-carboxylic acid'  ligand  29  22  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9YD
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
 9YD  C2   C  CR6   0   0.392  -5.1085   0.5668   0.0391
 9YD  C3   C  CR6   0   0.432  -4.0046   1.4030   0.1033
 9YD  C4   C  CR16  0  -0.451  -2.7291   0.8903   0.0827
 9YD  C5   C  CR6   0   0.060  -2.5407  -0.4910  -0.0021
 9YD  C6   C  CR16  0  -0.319  -3.6550  -1.3235  -0.0661
 9YD  C12  C  CR5   0   0.632   0.5364  -2.4015  -0.0545
 9YD  C13  C  CR15  0  -0.625  -0.8287  -2.4210  -0.0459
 9YD  C15  C  CR5   0   0.291   2.2097  -0.5819  -0.0411
 9YD  O21  O  OH1   0  -0.584   3.4003   3.2063  -0.0081
 9YD  F1   F  F     0  -0.301  -6.3325   1.0997   0.0609
 9YD  C7   C  CR16  0  -0.389  -4.9385  -0.7977  -0.0461
 9YD  F8   F  F     0  -0.305  -4.1971   2.7227   0.1883
 9YD  C9   C  CR5   0   0.351  -1.1887  -1.0510  -0.0227
 9YD  N10  N  N     0  -0.321  -0.1372  -0.2641  -0.0175
 9YD  N11  N  NR5   0  -0.423   0.9247  -1.0949  -0.0375
 9YD  S16  S  S2    0   0.288   3.6186  -1.6009  -0.0597
 9YD  C17  C  CR15  0  -0.493   4.5828  -0.1931  -0.0524
 9YD  C18  C  CR5   0   0.215   3.7927   0.9120  -0.0365
 9YD  N19  N  N     0  -0.394   2.4475   0.6820  -0.0303
 9YD  C20  C  C     0   0.500   4.3431   2.2815  -0.0271
 9YD  O22  O  O     0  -0.433   5.5275   2.5130  -0.0359
 9YD  H1   H  HCR6  0   0.290  -1.8857   1.5664   0.1351
 9YD  H2   H  HCR6  0   0.271  -3.5366  -2.3960  -0.1341
 9YD  H3   H  HCR5  0   0.296  -1.4654  -3.2895  -0.0502
 9YD  H5   H  HOH1  0   0.491   3.8043   4.0873  -0.0004
 9YD  H6   H  HCR6  0   0.298  -5.8023  -1.4468  -0.0975
 9YD  H7   H  HCR5  0   0.328   5.6596  -0.2534  -0.0607
 9YD  H4   H  HOH1  0   0.510   1.0821  -4.2172  -0.0890
 9YD  O14  O  OH1   0  -0.607   1.4722  -3.3336  -0.0728

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
 9YD  O22  C20  double    1.207  0.020  1.207
 9YD  C20  O21  single    1.321  0.020  1.321
 9YD  C20  C18  single    1.476  0.020  1.476
 9YD  C18  C17  aromatic  1.359  0.020  1.359
 9YD  C18  N19  aromatic  1.365  0.020  1.365
 9YD  C17  S16  aromatic  1.706  0.020  1.706
 9YD  N19  C15  aromatic  1.286  0.020  1.286
 9YD  S16  C15  aromatic  1.739  0.020  1.739
 9YD  C15  N11  single    1.384  0.020  1.384
 9YD  N11  C12  aromatic  1.363  0.020  1.363
 9YD  N11  N10  aromatic  1.348  0.020  1.348
 9YD  O14  C12  single    1.321  0.020  1.321
 9YD  C12  C13  aromatic  1.365  0.020  1.365
 9YD  N10  C9   aromatic  1.313  0.020  1.313
 9YD  C6   C7   aromatic  1.387  0.020  1.387
 9YD  C6   C5   aromatic  1.392  0.020  1.392
 9YD  C9   C13  aromatic  1.417  0.020  1.417
 9YD  C9   C5   single    1.464  0.020  1.464
 9YD  C7   C2   aromatic  1.378  0.020  1.378
 9YD  C5   C4   aromatic  1.397  0.020  1.397
 9YD  C2   F1   single    1.335  0.020  1.335
 9YD  C2   C3   aromatic  1.386  0.020  1.386
 9YD  C4   C3   aromatic  1.375  0.020  1.375
 9YD  C3   F8   single    1.336  0.020  1.336
 9YD  C4   H1   single    0.930  0.020  1.080
 9YD  C6   H2   single    0.930  0.020  1.080
 9YD  C13  H3   single    0.930  0.020  1.080
 9YD  O21  H5   single    0.850  0.020  0.980
 9YD  C7   H6   single    0.930  0.020  1.080
 9YD  C17  H7   single    0.930  0.020  1.080
 9YD  O14  H4   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
 9YD  C7   C2   F1   120.62  3.000
 9YD  F1   C2   C3   119.25  3.000
 9YD  C7   C2   C3   120.13  3.000
 9YD  F8   C3   C4   120.19  3.000
 9YD  F8   C3   C2   118.94  3.000
 9YD  C4   C3   C2   120.87  3.000
 9YD  H1   C4   C5   121.05  3.000
 9YD  H1   C4   C3   119.29  3.000
 9YD  C5   C4   C3   119.66  3.000
 9YD  C9   C5   C6   120.66  3.000
 9YD  C9   C5   C4   120.26  3.000
 9YD  C6   C5   C4   119.08  3.000
 9YD  H2   C6   C7   118.57  3.000
 9YD  H2   C6   C5   120.55  3.000
 9YD  C7   C6   C5   120.88  3.000
 9YD  O14  C12  N11  118.34  3.000
 9YD  O14  C12  C13  134.29  3.000
 9YD  N11  C12  C13  107.37  3.000
 9YD  H3   C13  C9   129.03  3.000
 9YD  H3   C13  C12  127.06  3.000
 9YD  C9   C13  C12  103.91  3.000
 9YD  N19  C15  S16  115.22  3.000
 9YD  S16  C15  N11  122.36  3.000
 9YD  N19  C15  N11  122.42  3.000
 9YD  H5   O21  C20  109.82  3.000
 9YD  H6   C7   C6   120.71  3.000
 9YD  H6   C7   C2   119.92  3.000
 9YD  C6   C7   C2   119.37  3.000
 9YD  N10  C9   C13  112.09  3.000
 9YD  C13  C9   C5   127.23  3.000
 9YD  N10  C9   C5   120.68  3.000
 9YD  N11  N10  C9   105.14  3.000
 9YD  N10  N11  C15  120.19  3.000
 9YD  N10  N11  C12  111.50  3.000
 9YD  C15  N11  C12  128.31  3.000
 9YD  C17  S16  C15   88.53  3.000
 9YD  H7   C17  C18  128.77  3.000
 9YD  H7   C17  S16  121.20  3.000
 9YD  C18  C17  S16  110.03  3.000
 9YD  C20  C18  N19  121.60  3.000
 9YD  N19  C18  C17  115.86  3.000
 9YD  C20  C18  C17  122.54  3.000
 9YD  C18  N19  C15  110.36  3.000
 9YD  O22  C20  C18  122.95  3.000
 9YD  C18  C20  O21  112.55  3.000
 9YD  O22  C20  O21  124.49  3.000
 9YD  H4   O14  C12  111.08  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
 9YD  CONST_01  C5   C6   C7   C2      0.00   0.0  0
 9YD  CONST_02  C5   C4   C3   C2      0.00   0.0  0
 9YD  CONST_03  C6   C7   C2   C3      0.00   0.0  0
 9YD  CONST_04  C6   C5   C4   C3      0.00   0.0  0
 9YD  CONST_05  C9   C5   C4   C3    180.00   0.0  0
 9YD  CONST_06  C7   C6   C5   C4      0.00   0.0  0
 9YD  CONST_07  N10  C9   C5   C4      0.00   0.0  0
 9YD  CONST_08  C13  C9   C5   C4    180.00   0.0  0
 9YD  CONST_09  C7   C2   C3   C4      0.00   0.0  0
 9YD  CONST_10  N11  N10  C9   C5    180.00   0.0  0
 9YD  CONST_11  C12  C13  C9   C5    180.00   0.0  0
 9YD  CONST_12  N10  C9   C5   C6    180.00   0.0  0
 9YD  CONST_13  C13  C9   C5   C6      0.00   0.0  0
 9YD  CONST_14  N19  C15  N11  C12   180.00   0.0  0
 9YD  CONST_15  S16  C15  N11  C12     0.00   0.0  0
 9YD  CONST_16  C9   N10  N11  C12     0.00   0.0  0
 9YD  CONST_17  N10  C9   C13  C12     0.00   0.0  0
 9YD  CONST_18  C15  N11  C12  C13   180.00   0.0  0
 9YD  CONST_19  N10  N11  C12  C13     0.00   0.0  0
 9YD  CONST_20  N11  N10  C9   C13     0.00   0.0  0
 9YD  CONST_21  C17  C18  N19  C15     0.00   0.0  0
 9YD  CONST_22  C18  C17  S16  C15     0.00   0.0  0
 9YD  CONST_23  C9   N10  N11  C15   180.00   0.0  0
 9YD  CONST_24  C9   C5   C6   C7    180.00   0.0  0
 9YD  CONST_25  N11  C12  C13  C9      0.00   0.0  0
 9YD  CONST_26  N19  C15  N11  N10     0.00   0.0  0
 9YD  CONST_27  S16  C15  N11  N10   180.00   0.0  0
 9YD  CONST_28  C18  N19  C15  N11   180.00   0.0  0
 9YD  CONST_29  C17  S16  C15  N11   180.00   0.0  0
 9YD  CONST_30  N19  C18  C17  S16     0.00   0.0  0
 9YD  CONST_31  C18  N19  C15  S16     0.00   0.0  0
 9YD  CONST_32  N19  C15  S16  C17     0.00   0.0  0
 9YD  CONST_33  F1   C2   C3   C4    180.00   0.0  0
 9YD  CONST_34  F8   C3   C4   C5    180.00   0.0  0
 9YD  CONST_35  F1   C2   C7   C6    180.00   0.0  0
 9YD  CONST_36  C20  C18  N19  C15   180.00   0.0  0
 9YD  CONST_37  O14  C12  N11  C15     0.00   0.0  0
 9YD  CONST_38  F8   C3   C2   C7    180.00   0.0  0
 9YD  CONST_39  O14  C12  C13  C9    180.00   0.0  0
 9YD  CONST_40  O14  C12  N11  N10   180.00   0.0  0
 9YD  CONST_41  C20  C18  C17  S16   180.00   0.0  0
 9YD  CONST_42  H2   C6   C7   C2    180.00   0.0  0
 9YD  CONST_43  H1   C4   C3   C2    180.00   0.0  0
 9YD  CONST_44  H6   C7   C2   C3    180.00   0.0  0
 9YD  CONST_45  H3   C13  C9   C5      0.00   0.0  0
 9YD  CONST_46  H7   C17  S16  C15   180.00   0.0  0
 9YD  CONST_47  H5   O21  C20  C18   180.00   0.0  0
 9YD  Var_01    C17  C18  C20  O21  -179.83  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
 9YD  plan-1  C5   0.020
 9YD  plan-1  C12  0.020
 9YD  plan-1  C13  0.020
 9YD  plan-1  C15  0.020
 9YD  plan-1  C9   0.020
 9YD  plan-1  N10  0.020
 9YD  plan-1  N11  0.020
 9YD  plan-1  H3   0.020
 9YD  plan-1  O14  0.020
 9YD  plan-2  C15  0.020
 9YD  plan-2  N11  0.020
 9YD  plan-2  S16  0.020
 9YD  plan-2  C17  0.020
 9YD  plan-2  C18  0.020
 9YD  plan-2  N19  0.020
 9YD  plan-2  C20  0.020
 9YD  plan-2  H7   0.020
 9YD  plan-3  C2   0.020
 9YD  plan-3  C3   0.020
 9YD  plan-3  C4   0.020
 9YD  plan-3  C5   0.020
 9YD  plan-3  C6   0.020
 9YD  plan-3  F1   0.020
 9YD  plan-3  C7   0.020
 9YD  plan-3  F8   0.020
 9YD  plan-3  C9   0.020
 9YD  plan-3  H1   0.020
 9YD  plan-3  H2   0.020
 9YD  plan-3  H6   0.020
 9YD  plan-4  O21  0.020
 9YD  plan-4  C18  0.020
 9YD  plan-4  C20  0.020
 9YD  plan-4  O22  0.020
 9YD  plan-4  H5   0.020

