# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 06:56:53 2022
#   Inital geometry file: a 76 line input string
#   Ligand name: 1-[[4-(trifluoromethyl)phenyl]methyl]imidazole-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1nccn1Cc2ccc(cc2)C(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
 HML  HML  "1-[[4-(trifluoromethyl)phenyl]methyl]imidazole-2-carboxylic acid"  ligand  27  19  .  2022-08-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_HML
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
 HML  C10  C  CR6    0   0.121  19.7798  11.8813   6.0915
 HML  C11  C  CR16   0  -0.284  19.2984  11.1175   5.0310
 HML  C12  C  CR16   0  -0.256  18.3038  11.5998   4.2009
 HML  C13  C  CR6    0  -0.212  17.7692  12.8662   4.4225
 HML  C14  C  CR16   0  -0.266  18.2445  13.6373   5.4726
 HML  C15  C  CR16   0  -0.284  19.2462  13.1461   6.2980
 HML  C16  C  CT     0   1.048  16.6510  13.3436   3.5553
 HML  C01  C  CR15   0  -0.219  21.7075  13.3309   9.7823
 HML  C02  C  CR15   0  -0.118  21.9436  12.9388   8.4961
 HML  N03  N  NR5    0  -0.437  21.0202  11.9709   8.2276
 HML  C04  C  CR5    0   0.264  20.2543  11.8158   9.3466
 HML  N05  N  N      0  -0.446  20.6640  12.6293  10.2962
 HML  C06  C  C      0   0.367  19.1020  10.8407   9.4891
 HML  O07  O  O      0  -0.576  18.8175  10.1686   8.4797
 HML  O08  O  OC    -1  -0.578  18.5614  10.8128  10.6052
 HML  C09  C  CH2    0  -0.336  20.8957  11.3295   6.9382
 HML  F17  F  F      0  -0.316  15.5129  12.6793   3.8147
 HML  F18  F  F      0  -0.304  16.3878  14.6437   3.7202
 HML  F19  F  F      0  -0.313  16.9054  13.1580   2.2523
 HML  H1   H  HCR6   0   0.260  19.7009  10.1271   4.8553
 HML  H2   H  HCR6   0   0.271  17.9460  10.9798   3.3885
 HML  H3   H  HCR6   0   0.268  17.8463  14.6242   5.6654
 HML  H4   H  HCR6   0   0.262  19.6027  13.7670   7.1098
 HML  H8   H  HCH2   0   0.281  20.7676  10.2592   7.0696
 HML  H9   H  HCH2   0   0.277  21.8425  11.4771   6.4142
 HML  H5   H  HCR5   0   0.240  22.2382  14.0763  10.3553
 HML  H6   H  HCR5   0   0.284  22.6729  13.2481   7.7651

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
 HML  F19  C16  single    1.341  0.020  1.341
 HML  C16  F18  single    1.337  0.020  1.337
 HML  C16  F17  single    1.343  0.020  1.343
 HML  C16  C13  single    1.493  0.020  1.493
 HML  C12  C13  aromatic  1.392  0.020  1.392
 HML  C12  C11  aromatic  1.382  0.020  1.382
 HML  C13  C14  aromatic  1.387  0.020  1.387
 HML  C11  C10  aromatic  1.393  0.020  1.393
 HML  C14  C15  aromatic  1.388  0.020  1.388
 HML  C10  C15  aromatic  1.388  0.020  1.388
 HML  C10  C09  single    1.506  0.020  1.506
 HML  C09  N03  single    1.445  0.020  1.445
 HML  N03  C02  aromatic  1.364  0.020  1.364
 HML  N03  C04  aromatic  1.365  0.020  1.365
 HML  C02  C01  aromatic  1.365  0.020  1.365
 HML  O07  C06  deloc     1.246  0.020  1.246
 HML  C04  C06  single    1.516  0.020  1.516
 HML  C04  N05  aromatic  1.316  0.020  1.316
 HML  C06  O08  deloc     1.240  0.020  1.240
 HML  C01  N05  aromatic  1.358  0.020  1.358
 HML  C11  H1   single    0.930  0.020  1.080
 HML  C12  H2   single    0.930  0.020  1.080
 HML  C14  H3   single    0.930  0.020  1.080
 HML  C15  H4   single    0.930  0.020  1.080
 HML  C01  H5   single    0.930  0.020  1.080
 HML  C02  H6   single    0.930  0.020  1.080
 HML  C09  H8   single    0.970  0.020  1.090
 HML  C09  H9   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
 HML  C09  C10  C15  122.35  3.000
 HML  C09  C10  C11  118.91  3.000
 HML  C15  C10  C11  118.69  3.000
 HML  H1   C11  C12  119.27  3.000
 HML  H1   C11  C10  119.76  3.000
 HML  C12  C11  C10  120.97  3.000
 HML  H2   C12  C13  120.88  3.000
 HML  H2   C12  C11  119.25  3.000
 HML  C13  C12  C11  119.87  3.000
 HML  C16  C13  C14  121.24  3.000
 HML  C14  C13  C12  119.64  3.000
 HML  C16  C13  C12  119.07  3.000
 HML  H3   C14  C15  118.87  3.000
 HML  H3   C14  C13  121.07  3.000
 HML  C15  C14  C13  120.06  3.000
 HML  H4   C15  C14  118.74  3.000
 HML  H4   C15  C10  120.50  3.000
 HML  C14  C15  C10  120.76  3.000
 HML  F19  C16  F18  106.97  3.000
 HML  F18  C16  F17  106.88  3.000
 HML  F19  C16  F17  106.26  3.000
 HML  F17  C16  C13  111.36  3.000
 HML  F18  C16  C13  112.75  3.000
 HML  F19  C16  C13  112.21  3.000
 HML  H5   C01  N05  122.24  3.000
 HML  H5   C01  C02  127.83  3.000
 HML  N05  C01  C02  109.93  3.000
 HML  H6   C02  N03  121.87  3.000
 HML  H6   C02  C01  132.34  3.000
 HML  N03  C02  C01  105.79  3.000
 HML  C09  N03  C04  129.24  3.000
 HML  C04  N03  C02  107.40  3.000
 HML  C09  N03  C02  123.27  3.000
 HML  C06  C04  N05  124.50  3.000
 HML  N05  C04  N03  110.29  3.000
 HML  C06  C04  N03  125.21  3.000
 HML  C04  N05  C01  106.59  3.000
 HML  O08  C06  O07  128.13  3.000
 HML  O08  C06  C04  115.48  3.000
 HML  O07  C06  C04  116.39  3.000
 HML  H9   C09  H8   107.07  3.000
 HML  H9   C09  N03  107.06  3.000
 HML  H8   C09  N03  109.85  3.000
 HML  H9   C09  C10  108.85  3.000
 HML  H8   C09  C10  109.99  3.000
 HML  N03  C09  C10  113.76  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
 HML  CONST_01  C13  C12  C11  C10     0.00   0.0  0
 HML  CONST_02  C13  C14  C15  C10     0.00   0.0  0
 HML  CONST_03  C14  C13  C12  C11     0.00   0.0  0
 HML  CONST_04  C14  C15  C10  C11     0.00   0.0  0
 HML  CONST_05  C15  C14  C13  C12     0.00   0.0  0
 HML  CONST_06  C15  C10  C11  C12     0.00   0.0  0
 HML  CONST_07  C04  N03  C02  C01     0.00   0.0  0
 HML  CONST_08  N03  C04  N05  C01     0.00   0.0  0
 HML  CONST_09  N05  C04  N03  C02     0.00   0.0  0
 HML  CONST_10  C04  N05  C01  C02     0.00   0.0  0
 HML  CONST_11  N05  C01  C02  N03     0.00   0.0  0
 HML  CONST_12  C16  C13  C12  C11   180.00   0.0  0
 HML  CONST_13  C09  C10  C11  C12   180.00   0.0  0
 HML  CONST_14  C09  C10  C15  C14   180.00   0.0  0
 HML  CONST_15  C16  C13  C14  C15   180.00   0.0  0
 HML  CONST_16  C09  N03  C02  C01   180.00   0.0  0
 HML  CONST_17  C06  C04  N05  C01   180.00   0.0  0
 HML  CONST_18  C06  C04  N03  C02   180.00   0.0  0
 HML  CONST_19  C09  N03  C04  N05   180.00   0.0  0
 HML  CONST_20  H2   C12  C11  C10   180.00   0.0  0
 HML  CONST_21  H3   C14  C15  C10   180.00   0.0  0
 HML  CONST_22  H4   C15  C10  C11   180.00   0.0  0
 HML  CONST_23  H3   C14  C13  C12   180.00   0.0  0
 HML  CONST_24  H1   C11  C12  C13   180.00   0.0  0
 HML  CONST_25  H4   C15  C14  C13   180.00   0.0  0
 HML  CONST_26  H2   C12  C13  C14   180.00   0.0  0
 HML  CONST_27  H1   C11  C10  C15   180.00   0.0  0
 HML  CONST_28  H5   C01  C02  N03   180.00   0.0  0
 HML  CONST_29  H6   C02  N03  C04   180.00   0.0  0
 HML  CONST_30  H5   C01  N05  C04   180.00   0.0  0
 HML  CONST_31  H6   C02  C01  N05   180.00   0.0  0
 HML  Var_01    C02  N03  C09  C10   -99.88  30.0  2
 HML  Var_02    C04  N03  C09  C10    76.29  30.0  2
 HML  Var_03    N03  C09  C10  C11  -161.00  30.0  2
 HML  Var_04    N03  C09  C10  C15    21.47  30.0  2
 HML  Var_05    F19  C16  C13  C12   -48.41  30.0  3
 HML  Var_06    F18  C16  C13  C12  -169.29  30.0  3
 HML  Var_07    F17  C16  C13  C12    70.57  30.0  3
 HML  Var_08    F19  C16  C13  C14   134.20  30.0  3
 HML  Var_09    F18  C16  C13  C14    13.33  30.0  3
 HML  Var_10    F17  C16  C13  C14  -106.81  30.0  3
 HML  Var_11    O07  C06  C04  N03    -2.56  30.0  2
 HML  Var_12    O08  C06  C04  N03   177.30  30.0  2
 HML  Var_13    O07  C06  C04  N05   177.98  30.0  2
 HML  Var_14    O08  C06  C04  N05    -2.15  30.0  2
 HML  Var_15    H8   C09  C10  C11   -37.30  30.0  2
 HML  Var_16    H9   C09  C10  C11    79.72  30.0  2
 HML  Var_17    H8   C09  C10  C15   145.18  30.0  2
 HML  Var_18    H9   C09  C10  C15   -97.81  30.0  2
 HML  Var_19    H8   C09  N03  C02   136.34  30.0  2
 HML  Var_20    H9   C09  N03  C02    20.42  30.0  2
 HML  Var_21    H8   C09  N03  C04   -47.50  30.0  2
 HML  Var_22    H9   C09  N03  C04  -163.42  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
 HML  plan-1  C01  0.020
 HML  plan-1  C02  0.020
 HML  plan-1  N03  0.020
 HML  plan-1  C04  0.020
 HML  plan-1  N05  0.020
 HML  plan-1  C06  0.020
 HML  plan-1  C09  0.020
 HML  plan-1  H5   0.020
 HML  plan-1  H6   0.020
 HML  plan-2  C10  0.020
 HML  plan-2  C11  0.020
 HML  plan-2  C12  0.020
 HML  plan-2  C13  0.020
 HML  plan-2  C14  0.020
 HML  plan-2  C15  0.020
 HML  plan-2  C16  0.020
 HML  plan-2  C09  0.020
 HML  plan-2  H1   0.020
 HML  plan-2  H2   0.020
 HML  plan-2  H3   0.020
 HML  plan-2  H4   0.020
 HML  plan-3  C04  0.020
 HML  plan-3  C06  0.020
 HML  plan-3  O07  0.020
 HML  plan-3  O08  0.020

