# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 20 13:30:23 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: 5-[4-bromo-1-methyl-5-(trifluoromethyl)-1H-pyrazol-3-yl]-2-chloro-4-fluorobenzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1nc(c(Br)c1C(F)(F)F)c2cc(C(O)=O)c(Cl)cc2F
#
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
 OMN  OMN  '5-[4-bromo-1-methyl-5-(trifluoromethyl)-1H-pyrazol-3-yl]-2-chloro-4-fluorobenzoic acid'  ligand  28  22  .  2021-08-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_OMN
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
 OMN  C1    C   CH3   0  -0.532  -2.8934   2.9732  -1.1714
 OMN  N1    N   NR5   0  -0.339  -2.1693   1.8279  -0.6512
 OMN  N2    N   N     0  -0.253  -0.8712   1.7468  -0.8589
 OMN  C2    C   CR5   0   0.328  -0.4736   0.5944  -0.3505
 OMN  C3    C   CR5   0  -0.408  -1.5668  -0.0878   0.2069
 OMN  BR1   BR  BR    0   0.008  -1.4776  -1.6955   1.1242
 OMN  C4    C   CR5   0   0.201  -2.6490   0.7381  -0.0133
 OMN  C5    C   CT    0   1.094  -4.0886   0.5881   0.3380
 OMN  F1    F   F     0  -0.307  -4.8721   0.7789  -0.7294
 OMN  F2    F   F     0  -0.288  -4.3505  -0.6220   0.8169
 OMN  F3    F   F     0  -0.308  -4.4670   1.4795   1.2616
 OMN  C6    C   CR6   0  -0.145   0.9418   0.2153  -0.3722
 OMN  C7    C   CR16  0  -0.285   1.9118   1.0574   0.1522
 OMN  C8    C   CR6   0   0.010   3.2704   0.7492   0.1130
 OMN  C9    C   C     0   0.517   4.2575   1.7292   0.6411
 OMN  O1    O   OH1   0  -0.589   3.7270   2.5104   1.5713
 OMN  O2    O   O     0  -0.418   5.3968   1.8203   0.2646
 OMN  C10   C   CR6   0  -0.055   3.6517  -0.4654  -0.4647
 OMN  CL1   CL  CL    0  -0.080   5.2892  -0.9929  -0.5168
 OMN  C11   C   CR16  0  -0.351   2.7057  -1.3303  -0.9898
 OMN  C12   C   CR6   0   0.557   1.3759  -0.9691  -0.9481
 OMN  F4    F   F     0  -0.283   0.4805  -1.7866  -1.4969
 OMN  H11A  H   HCH3  0   0.277  -3.3860   2.7253  -2.1089
 OMN  H12   H   HCH3  0   0.268  -3.6266   3.3273  -0.4529
 OMN  H13   H   HCH3  0   0.286  -2.1696   3.7621  -1.3447
 OMN  H7    H   HCR6  0   0.291   1.5888   1.9878   0.5978
 OMN  HO1   H   HOH1  0   0.493   4.3748   3.1738   1.8536
 OMN  H11   H   HCR6  0   0.315   2.9988  -2.2702  -1.4369

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
 OMN  C1   N1    single    1.451  0.020  1.451
 OMN  C1   H11A  single    0.970  0.020  1.090
 OMN  C1   H12   single    0.970  0.020  1.090
 OMN  C1   H13   single    0.970  0.020  1.090
 OMN  N1   N2    aromatic  1.317  0.020  1.317
 OMN  N1   C4    aromatic  1.351  0.020  1.351
 OMN  N2   C2    aromatic  1.321  0.020  1.321
 OMN  C2   C3    aromatic  1.404  0.020  1.404
 OMN  C2   C6    single    1.465  0.020  1.465
 OMN  C3   BR1   single    1.853  0.020  1.853
 OMN  C3   C4    aromatic  1.379  0.020  1.379
 OMN  C4   C5    single    1.489  0.020  1.489
 OMN  C5   F1    single    1.338  0.020  1.338
 OMN  C5   F2    single    1.327  0.020  1.327
 OMN  C5   F3    single    1.338  0.020  1.338
 OMN  C6   C7    aromatic  1.387  0.020  1.387
 OMN  C6   C12   aromatic  1.387  0.020  1.387
 OMN  C7   C8    aromatic  1.394  0.020  1.394
 OMN  C7   H7    single    0.930  0.020  1.080
 OMN  C8   C9    single    1.488  0.020  1.488
 OMN  C8   C10   aromatic  1.398  0.020  1.398
 OMN  C9   O1    single    1.325  0.020  1.325
 OMN  C9   O2    double    1.203  0.020  1.203
 OMN  O1   HO1   single    0.850  0.020  0.980
 OMN  C10  CL1   single    1.721  0.020  1.721
 OMN  C10  C11   aromatic  1.385  0.020  1.385
 OMN  C11  C12   aromatic  1.379  0.020  1.379
 OMN  C11  H11   single    0.930  0.020  1.080
 OMN  C12  F4    single    1.331  0.020  1.331

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
 OMN  H13   C1   H12   108.61  3.000
 OMN  H13   C1   H11A  109.28  3.000
 OMN  H12   C1   H11A  109.81  3.000
 OMN  H13   C1   N1    107.35  3.000
 OMN  H12   C1   N1    110.92  3.000
 OMN  H11A  C1   N1    110.79  3.000
 OMN  C4    N1   N2    112.01  3.000
 OMN  C4    N1   C1    128.96  3.000
 OMN  N2    N1   C1    118.93  3.000
 OMN  C2    N2   N1    106.84  3.000
 OMN  C6    C2   C3    129.22  3.000
 OMN  C6    C2   N2    120.71  3.000
 OMN  C3    C2   N2    110.02  3.000
 OMN  C4    C3   BR1   129.52  3.000
 OMN  C4    C3   C2    104.87  3.000
 OMN  BR1   C3   C2    125.49  3.000
 OMN  C5    C4   C3    131.34  3.000
 OMN  C5    C4   N1    122.40  3.000
 OMN  C3    C4   N1    106.26  3.000
 OMN  F3    C5   F2    107.60  3.000
 OMN  F3    C5   F1    106.86  3.000
 OMN  F2    C5   F1    107.59  3.000
 OMN  F3    C5   C4    111.66  3.000
 OMN  F2    C5   C4    111.57  3.000
 OMN  F1    C5   C4    111.32  3.000
 OMN  C12   C6   C7    117.16  3.000
 OMN  C12   C6   C2    121.97  3.000
 OMN  C7    C6   C2    120.84  3.000
 OMN  H7    C7   C8    119.55  3.000
 OMN  H7    C7   C6    117.99  3.000
 OMN  C8    C7   C6    122.46  3.000
 OMN  C10   C8   C9    122.55  3.000
 OMN  C10   C8   C7    118.01  3.000
 OMN  C9    C8   C7    119.41  3.000
 OMN  O2    C9   O1    123.64  3.000
 OMN  O2    C9   C8    124.53  3.000
 OMN  O1    C9   C8    111.83  3.000
 OMN  HO1   O1   C9    109.90  3.000
 OMN  C11   C10  CL1   116.54  3.000
 OMN  C11   C10  C8    120.86  3.000
 OMN  CL1   C10  C8    122.57  3.000
 OMN  H11   C11  C12   120.11  3.000
 OMN  H11   C11  C10   120.96  3.000
 OMN  C12   C11  C10   118.93  3.000
 OMN  F4    C12  C11   118.40  3.000
 OMN  F4    C12  C6    119.03  3.000
 OMN  C11   C12  C6    122.57  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
 OMN  CONST_01  C3    C2   N2   N1     0.00   0.0  0
 OMN  CONST_02  C6    C2   N2   N1   180.00   0.0  0
 OMN  CONST_03  C2    C3   C4   N1     0.00   0.0  0
 OMN  CONST_04  C3    C4   N1   N2     0.00   0.0  0
 OMN  CONST_05  C4    C3   C2   N2     0.00   0.0  0
 OMN  CONST_08  C4    N1   N2   C2     0.00   0.0  0
 OMN  CONST_09  C8    C7   C6   C2   180.00   0.0  0
 OMN  CONST_10  C11   C12  C6   C2   180.00   0.0  0
 OMN  CONST_13  C6    C2   C3   C4   180.00   0.0  0
 OMN  CONST_14  C10   C8   C7   C6     0.00   0.0  0
 OMN  CONST_15  C10   C11  C12  C6     0.00   0.0  0
 OMN  CONST_16  C11   C12  C6   C7     0.00   0.0  0
 OMN  CONST_17  C11   C10  C8   C7     0.00   0.0  0
 OMN  CONST_18  C12   C6   C7   C8     0.00   0.0  0
 OMN  CONST_19  C12   C11  C10  C8     0.00   0.0  0
 OMN  CONST_20  C2    N2   N1   C1   180.00   0.0  0
 OMN  CONST_21  C3    C4   N1   C1   180.00   0.0  0
 OMN  CONST_22  BR1   C3   C4   N1   180.00   0.0  0
 OMN  CONST_23  C5    C4   N1   N2   180.00   0.0  0
 OMN  CONST_24  BR1   C3   C2   N2   180.00   0.0  0
 OMN  CONST_25  C5    C4   C3   C2   180.00   0.0  0
 OMN  CONST_26  F4    C12  C6   C2     0.00   0.0  0
 OMN  CONST_27  C6    C2   C3   BR1    0.00   0.0  0
 OMN  CONST_28  C9    C8   C7   C6   180.00   0.0  0
 OMN  CONST_29  F4    C12  C6   C7   180.00   0.0  0
 OMN  CONST_30  CL1   C10  C8   C7   180.00   0.0  0
 OMN  CONST_31  C11   C10  C8   C9   180.00   0.0  0
 OMN  CONST_32  F4    C12  C11  C10  180.00   0.0  0
 OMN  CONST_33  C12   C11  C10  CL1  180.00   0.0  0
 OMN  CONST_34  H7    C7   C6   C2     0.00   0.0  0
 OMN  CONST_35  H11   C11  C12  C6   180.00   0.0  0
 OMN  CONST_36  HO1   O1   C9   C8   180.00   0.0  0
 OMN  Var_01    F1    C5   C4   N1    52.52  30.0  2
 OMN  Var_02    O1    C9   C8   C7    26.64  30.0  2
 OMN  Var_03    H11A  C1   N1   N2    98.76  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
 OMN  plan-1  C1   0.020
 OMN  plan-1  N1   0.020
 OMN  plan-1  N2   0.020
 OMN  plan-1  C2   0.020
 OMN  plan-1  C3   0.020
 OMN  plan-1  BR1  0.020
 OMN  plan-1  C4   0.020
 OMN  plan-1  C5   0.020
 OMN  plan-1  C6   0.020
 OMN  plan-2  C2   0.020
 OMN  plan-2  C6   0.020
 OMN  plan-2  C7   0.020
 OMN  plan-2  C8   0.020
 OMN  plan-2  C9   0.020
 OMN  plan-2  C10  0.020
 OMN  plan-2  CL1  0.020
 OMN  plan-2  C11  0.020
 OMN  plan-2  C12  0.020
 OMN  plan-2  F4   0.020
 OMN  plan-2  H7   0.020
 OMN  plan-2  H11  0.020
 OMN  plan-3  C8   0.020
 OMN  plan-3  C9   0.020
 OMN  plan-3  O1   0.020
 OMN  plan-3  O2   0.020
 OMN  plan-3  HO1  0.020

