# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 07:06:33 2022
#   Inital geometry file: a 116 line input string
#   Ligand name: 1-[6-[3-(dimethylcarbamoyl)phenyl]pyridin-2-yl]-5-(trifluoromethyl)pyrazole-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)C(=O)c1cccc(c1)c2cccc(n2)n3ncc(C(O)=O)c3C(F)(F)F
#
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
 5VX  5VX  "1-[6-[3-(dimethylcarbamoyl)phenyl]pyridin-2-yl]-5-(trifluoromethyl)pyrazole-4-carboxylic acid"  ligand  43  29  .  2022-09-15  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_5VX
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
 5VX  C1   C  CH3    0  -0.524   9.0693  63.9975  28.6655
 5VX  C3   C  CH3    0  -0.528  10.1206  66.1911  28.9006
 5VX  C6   C  CR6    0  -0.045  12.0341  65.0307  30.7627
 5VX  C7   C  CR16   0  -0.260  11.5755  65.9772  31.6753
 5VX  C8   C  CR16   0  -0.226  12.4780  66.6577  32.4782
 5VX  C10  C  CR6    0   0.089  14.3089  65.4602  31.4590
 5VX  C11  C  CR16   0  -0.320  13.3955  64.7731  30.6636
 5VX  C12  C  CR6    0   0.222  15.7553  65.1783  31.3453
 5VX  C13  C  CR16   0  -0.337  16.5856  65.1987  32.4629
 5VX  C14  C  CR16   0  -0.142  17.9320  64.9158  32.2987
 5VX  C15  C  CR16   0  -0.338  18.4193  64.6176  31.0391
 5VX  C16  C  CR6    0   0.489  17.5055  64.6314  29.9934
 5VX  N18  N  NR5    0  -0.455  17.9625  64.3991  28.6761
 5VX  C21  C  CR5    0  -0.336  18.1632  63.9949  26.5180
 5VX  C22  C  C      0   0.361  17.9666  63.6589  25.0543
 5VX  C25  C  CR5    0   0.151  17.3351  63.8329  27.6044
 5VX  C26  C  CT     0   1.084  16.0793  63.0322  27.6877
 5VX  N2   N  NT     0  -0.439  10.1005  64.7965  29.2951
 5VX  C4   C  C      0   0.508  11.0814  64.1790  29.9811
 5VX  O5   O  O      0  -0.481  11.1945  62.9604  30.0251
 5VX  C9   C  CR16   0  -0.304  13.8365  66.4038  32.3709
 5VX  N17  N  N      0  -0.450  16.2264  64.9026  30.1298
 5VX  N19  N  N      0  -0.257  19.1466  64.9049  28.3341
 5VX  C20  C  CR15   0  -0.045  19.2839  64.6593  27.0526
 5VX  O23  O  O      0  -0.585  19.0133  63.4173  24.4278
 5VX  O24  O  OC    -1  -0.583  16.8019  63.7045  24.6252
 5VX  F27  F  F      0  -0.312  15.9450  62.4363  28.8792
 5VX  F28  F  F      0  -0.315  14.9782  63.7598  27.4742
 5VX  F29  F  F      0  -0.296  16.0830  62.0525  26.7837
 5VX  H31  H  HCH3   0   0.253   8.8551  63.1071  29.2499
 5VX  H32  H  HCH3   0   0.246   8.1581  64.5902  28.5978
 5VX  H30  H  HCH3   0   0.239   9.3531  63.6923  27.6553
 5VX  H35  H  HCH3   0   0.263  11.0492  66.6731  29.1884
 5VX  H33  H  HCH3   0   0.253  10.0338  66.2623  27.8149
 5VX  H34  H  HCH3   0   0.244   9.2891  66.7405  29.3449
 5VX  H36  H  HCR6   0   0.270  10.5154  66.1769  31.7704
 5VX  H37  H  HCR6   0   0.264  12.1219  67.3924  33.1879
 5VX  H39  H  HCR6   0   0.261  13.7516  64.0231  29.9705
 5VX  H40  H  HCR6   0   0.278  16.1878  65.4101  33.4456
 5VX  H41  H  HCR6   0   0.282  18.5964  64.9116  33.1522
 5VX  H42  H  HCR6   0   0.287  19.4600  64.3803  30.8752
 5VX  H38  H  HCR6   0   0.262  14.5301  66.9588  32.9898
 5VX  H43  H  HCR5   0   0.272  20.1712  64.9798  26.5286

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
 5VX  O23  C22  deloc     1.244  0.020  1.244
 5VX  O24  C22  deloc     1.242  0.020  1.242
 5VX  C22  C21  single    1.515  0.020  1.515
 5VX  C21  C20  aromatic  1.408  0.020  1.408
 5VX  C21  C25  aromatic  1.376  0.020  1.376
 5VX  F29  C26  single    1.333  0.020  1.333
 5VX  C20  N19  aromatic  1.312  0.020  1.312
 5VX  C25  C26  single    1.492  0.020  1.492
 5VX  C25  N18  aromatic  1.365  0.020  1.365
 5VX  F28  C26  single    1.337  0.020  1.337
 5VX  C26  F27  single    1.339  0.020  1.339
 5VX  N19  N18  aromatic  1.332  0.020  1.332
 5VX  C1   N2   single    1.449  0.020  1.449
 5VX  N18  C16  single    1.414  0.020  1.414
 5VX  C3   N2   single    1.449  0.020  1.449
 5VX  N2   C4   single    1.347  0.020  1.347
 5VX  C16  N17  aromatic  1.315  0.020  1.315
 5VX  C16  C15  aromatic  1.389  0.020  1.389
 5VX  N17  C12  aromatic  1.332  0.020  1.332
 5VX  C4   O5   double    1.225  0.020  1.225
 5VX  C4   C6   single    1.498  0.020  1.498
 5VX  C11  C6   aromatic  1.389  0.020  1.389
 5VX  C11  C10  aromatic  1.392  0.020  1.392
 5VX  C15  C14  aromatic  1.383  0.020  1.383
 5VX  C6   C7   aromatic  1.392  0.020  1.392
 5VX  C12  C10  single    1.478  0.020  1.478
 5VX  C12  C13  aromatic  1.392  0.020  1.392
 5VX  C10  C9   aromatic  1.395  0.020  1.395
 5VX  C7   C8   aromatic  1.386  0.020  1.386
 5VX  C9   C8   aromatic  1.386  0.020  1.386
 5VX  C14  C13  aromatic  1.386  0.020  1.386
 5VX  C1   H31  single    0.970  0.020  1.090
 5VX  C1   H32  single    0.970  0.020  1.090
 5VX  C1   H30  single    0.970  0.020  1.090
 5VX  C3   H35  single    0.970  0.020  1.090
 5VX  C3   H33  single    0.970  0.020  1.090
 5VX  C3   H34  single    0.970  0.020  1.090
 5VX  C7   H36  single    0.930  0.020  1.080
 5VX  C8   H37  single    0.930  0.020  1.080
 5VX  C11  H39  single    0.930  0.020  1.080
 5VX  C13  H40  single    0.930  0.020  1.080
 5VX  C14  H41  single    0.930  0.020  1.080
 5VX  C15  H42  single    0.930  0.020  1.080
 5VX  C9   H38  single    0.930  0.020  1.080
 5VX  C20  H43  single    0.930  0.020  1.080

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
 5VX  H30  C1   H32  108.17  3.000
 5VX  H30  C1   H31  108.63  3.000
 5VX  H32  C1   H31  108.33  3.000
 5VX  H30  C1   N2   111.78  3.000
 5VX  H32  C1   N2   108.81  3.000
 5VX  H31  C1   N2   111.02  3.000
 5VX  H34  C3   H33  108.15  3.000
 5VX  H34  C3   H35  108.70  3.000
 5VX  H33  C3   H35  107.63  3.000
 5VX  H34  C3   N2   111.29  3.000
 5VX  H33  C3   N2   109.41  3.000
 5VX  H35  C3   N2   111.53  3.000
 5VX  C4   C6   C11  118.73  3.000
 5VX  C11  C6   C7   119.71  3.000
 5VX  C4   C6   C7   121.26  3.000
 5VX  H36  C7   C8   119.72  3.000
 5VX  H36  C7   C6   120.35  3.000
 5VX  C8   C7   C6   119.92  3.000
 5VX  H37  C8   C9   119.85  3.000
 5VX  H37  C8   C7   119.94  3.000
 5VX  C9   C8   C7   120.21  3.000
 5VX  C9   C10  C12  120.72  3.000
 5VX  C9   C10  C11  119.02  3.000
 5VX  C12  C10  C11  120.25  3.000
 5VX  H39  C11  C10  119.49  3.000
 5VX  H39  C11  C6   119.80  3.000
 5VX  C10  C11  C6   120.70  3.000
 5VX  N17  C12  C13  121.63  3.000
 5VX  C13  C12  C10  121.26  3.000
 5VX  N17  C12  C10  117.11  3.000
 5VX  H40  C13  C14  120.35  3.000
 5VX  H40  C13  C12  120.87  3.000
 5VX  C14  C13  C12  118.77  3.000
 5VX  H41  C14  C15  120.09  3.000
 5VX  H41  C14  C13  120.27  3.000
 5VX  C15  C14  C13  119.63  3.000
 5VX  H42  C15  C16  121.46  3.000
 5VX  H42  C15  C14  121.68  3.000
 5VX  C16  C15  C14  116.85  3.000
 5VX  N17  C16  N18  116.43  3.000
 5VX  N17  C16  C15  124.34  3.000
 5VX  N18  C16  C15  119.17  3.000
 5VX  N19  N18  C25  111.38  3.000
 5VX  N19  N18  C16  117.66  3.000
 5VX  C25  N18  C16  130.64  3.000
 5VX  C20  C21  C25  103.58  3.000
 5VX  C25  C21  C22  131.22  3.000
 5VX  C20  C21  C22  125.09  3.000
 5VX  O24  C22  O23  128.49  3.000
 5VX  O24  C22  C21  116.58  3.000
 5VX  O23  C22  C21  114.88  3.000
 5VX  C26  C25  C21  127.89  3.000
 5VX  C26  C25  N18  124.46  3.000
 5VX  C21  C25  N18  107.13  3.000
 5VX  F29  C26  F28  107.09  3.000
 5VX  F28  C26  F27  107.56  3.000
 5VX  F29  C26  F27  106.06  3.000
 5VX  F27  C26  C25  111.91  3.000
 5VX  F28  C26  C25  113.09  3.000
 5VX  F29  C26  C25  110.75  3.000
 5VX  C4   N2   C3   124.73  3.000
 5VX  C4   N2   C1   119.14  3.000
 5VX  C3   N2   C1   114.98  3.000
 5VX  O5   C4   N2   122.81  3.000
 5VX  O5   C4   C6   119.23  3.000
 5VX  N2   C4   C6   117.92  3.000
 5VX  H38  C9   C10  120.24  3.000
 5VX  H38  C9   C8   119.32  3.000
 5VX  C10  C9   C8   120.43  3.000
 5VX  C16  N17  C12  118.77  3.000
 5VX  C20  N19  N18  105.83  3.000
 5VX  H43  C20  N19  120.31  3.000
 5VX  H43  C20  C21  127.60  3.000
 5VX  N19  C20  C21  112.08  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
 5VX  CONST_01  C12  C10  C11  C6    180.00   0.0  0
 5VX  CONST_02  C9   C10  C11  C6      0.00   0.0  0
 5VX  CONST_03  C9   C8   C7   C6      0.00   0.0  0
 5VX  CONST_04  C10  C11  C6   C7      0.00   0.0  0
 5VX  CONST_05  C10  C9   C8   C7      0.00   0.0  0
 5VX  CONST_06  C11  C6   C7   C8      0.00   0.0  0
 5VX  CONST_07  C11  C10  C9   C8      0.00   0.0  0
 5VX  CONST_08  C12  C10  C9   C8    180.00   0.0  0
 5VX  CONST_09  C16  N17  C12  C10   180.00   0.0  0
 5VX  CONST_10  C14  C13  C12  C10   180.00   0.0  0
 5VX  CONST_13  N18  C16  N17  C12   180.00   0.0  0
 5VX  CONST_14  C15  C16  N17  C12     0.00   0.0  0
 5VX  CONST_15  C15  C14  C13  C12     0.00   0.0  0
 5VX  CONST_16  C16  N17  C12  C13     0.00   0.0  0
 5VX  CONST_18  C16  C15  C14  C13     0.00   0.0  0
 5VX  CONST_19  N18  C16  C15  C14   180.00   0.0  0
 5VX  CONST_20  N17  C16  C15  C14     0.00   0.0  0
 5VX  CONST_21  N17  C12  C13  C14     0.00   0.0  0
 5VX  CONST_24  C21  C25  N18  C16   180.00   0.0  0
 5VX  CONST_25  C20  N19  N18  C16   180.00   0.0  0
 5VX  CONST_26  C20  C21  C25  N18     0.00   0.0  0
 5VX  CONST_27  C21  C20  N19  N18     0.00   0.0  0
 5VX  CONST_28  N19  N18  C25  C21     0.00   0.0  0
 5VX  CONST_29  N19  C20  C21  C25     0.00   0.0  0
 5VX  CONST_30  C20  N19  N18  C25     0.00   0.0  0
 5VX  CONST_34  C4   C6   C7   C8    180.00   0.0  0
 5VX  CONST_35  C4   C6   C11  C10   180.00   0.0  0
 5VX  CONST_36  C26  C25  N18  C16     0.00   0.0  0
 5VX  CONST_37  C22  C21  C25  N18   180.00   0.0  0
 5VX  CONST_38  N19  C20  C21  C22   180.00   0.0  0
 5VX  CONST_39  C20  C21  C25  C26   180.00   0.0  0
 5VX  CONST_40  N19  N18  C25  C26   180.00   0.0  0
 5VX  CONST_41  H37  C8   C7   C6    180.00   0.0  0
 5VX  CONST_42  H39  C11  C6   C7    180.00   0.0  0
 5VX  CONST_43  H38  C9   C8   C7    180.00   0.0  0
 5VX  CONST_44  H40  C13  C12  C10     0.00   0.0  0
 5VX  CONST_45  H37  C8   C9   C10   180.00   0.0  0
 5VX  CONST_46  H36  C7   C6   C11   180.00   0.0  0
 5VX  CONST_47  H38  C9   C10  C11   180.00   0.0  0
 5VX  CONST_48  H39  C11  C10  C12     0.00   0.0  0
 5VX  CONST_49  H38  C9   C10  C12     0.00   0.0  0
 5VX  CONST_50  H41  C14  C13  C12   180.00   0.0  0
 5VX  CONST_51  H42  C15  C14  C13   180.00   0.0  0
 5VX  CONST_52  H40  C13  C14  C15   180.00   0.0  0
 5VX  CONST_53  H41  C14  C15  C16   180.00   0.0  0
 5VX  CONST_54  H43  C20  N19  N18   180.00   0.0  0
 5VX  CONST_55  H42  C15  C16  N18     0.00   0.0  0
 5VX  CONST_56  H43  C20  C21  C25   180.00   0.0  0
 5VX  CONST_57  H39  C11  C10  C9    180.00   0.0  0
 5VX  CONST_58  H36  C7   C8   C9    180.00   0.0  0
 5VX  CONST_59  H42  C15  C16  N17   180.00   0.0  0
 5VX  CONST_60  H40  C13  C12  N17   180.00   0.0  0
 5VX  CONST_61  C6   C4   N2   C1    180.00   0.0  0
 5VX  CONST_63  O5   C4   N2   C1      0.00   0.0  0
 5VX  Var_01    N2   C4   C6   C7     52.42  30.0  2
 5VX  Var_02    O5   C4   C6   C7   -125.18  30.0  2
 5VX  Var_03    N2   C4   C6   C11  -133.91  30.0  2
 5VX  Var_04    O5   C4   C6   C11    48.49  30.0  2
 5VX  Var_05    F29  C26  C25  N18  -145.53  30.0  2
 5VX  Var_06    F28  C26  C25  N18    94.26  30.0  2
 5VX  Var_07    F27  C26  C25  N18   -27.41  30.0  2
 5VX  Var_08    F29  C26  C25  C21    25.10  30.0  2
 5VX  Var_09    F28  C26  C25  C21   -95.11  30.0  2
 5VX  Var_10    F27  C26  C25  C21   143.22  30.0  2
 5VX  Var_11    O23  C22  C21  C25  -152.35  30.0  3
 5VX  Var_12    O24  C22  C21  C25    30.06  30.0  3
 5VX  Var_13    O23  C22  C21  C20    32.12  30.0  3
 5VX  Var_14    O24  C22  C21  C20  -145.47  30.0  3
 5VX  Var_15    H35  C3   N2   C1   -165.01  30.0  3
 5VX  Var_16    H33  C3   N2   C1    -46.05  30.0  3
 5VX  Var_17    H34  C3   N2   C1     73.41  30.0  3
 5VX  Var_18    H31  C1   N2   C3   -158.31  30.0  3
 5VX  Var_19    H32  C1   N2   C3    -39.18  30.0  3
 5VX  Var_20    H30  C1   N2   C3     80.21  30.0  3
 5VX  Var_21    H31  C1   N2   C4     33.38  30.0  3
 5VX  Var_22    H32  C1   N2   C4    152.51  30.0  3
 5VX  Var_23    H30  C1   N2   C4    -88.09  30.0  3
 5VX  Var_24    H35  C3   N2   C4      2.54  30.0  3
 5VX  Var_25    H33  C3   N2   C4    121.51  30.0  3
 5VX  Var_26    H34  C3   N2   C4   -119.03  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
 5VX  plan-1  C16  0.020
 5VX  plan-1  N18  0.020
 5VX  plan-1  C21  0.020
 5VX  plan-1  C22  0.020
 5VX  plan-1  C25  0.020
 5VX  plan-1  C26  0.020
 5VX  plan-1  N19  0.020
 5VX  plan-1  C20  0.020
 5VX  plan-1  H43  0.020
 5VX  plan-2  C6   0.020
 5VX  plan-2  C7   0.020
 5VX  plan-2  C8   0.020
 5VX  plan-2  C10  0.020
 5VX  plan-2  C11  0.020
 5VX  plan-2  C12  0.020
 5VX  plan-2  C4   0.020
 5VX  plan-2  C9   0.020
 5VX  plan-2  H36  0.020
 5VX  plan-2  H37  0.020
 5VX  plan-2  H39  0.020
 5VX  plan-2  H38  0.020
 5VX  plan-3  C10  0.020
 5VX  plan-3  C12  0.020
 5VX  plan-3  C13  0.020
 5VX  plan-3  C14  0.020
 5VX  plan-3  C15  0.020
 5VX  plan-3  C16  0.020
 5VX  plan-3  N18  0.020
 5VX  plan-3  N17  0.020
 5VX  plan-3  H40  0.020
 5VX  plan-3  H41  0.020
 5VX  plan-3  H42  0.020
 5VX  plan-4  C1   0.020
 5VX  plan-4  C3   0.020
 5VX  plan-4  C6   0.020
 5VX  plan-4  N2   0.020
 5VX  plan-4  C4   0.020
 5VX  plan-4  O5   0.020
 5VX  plan-5  C21  0.020
 5VX  plan-5  C22  0.020
 5VX  plan-5  O23  0.020
 5VX  plan-5  O24  0.020

