# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 01:24:38 2022
#   Inital geometry file: a 114 line input string
#   Ligand name: 2,4,6-tris(fluoranyl)-~{N}-[6-(1-methylpiperidin-4-yl)carbonylpyridin-2-yl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCC(CC1)C(=O)c2cccc(NC(=O)c3c(F)cc(F)cc3F)n2
#
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
 05X  05X  2,4,6-tris(fluoranyl)-~{N}-[6-(1-methylpiperidin-4-yl)carbonylpyridin-2-yl]benzamide  ligand  45  27  .  2022-03-08  2022-03-08
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_05X
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
 05X  C10  C  CR6   0   0.145  125.3539  132.5118  119.1409
 05X  C13  C  CR16  0  -0.367  127.5727  133.3138  117.7985
 05X  C15  C  CR16  0  -0.303  125.5438  132.0531  117.8463
 05X  C17  C  C     0   0.517  128.3577  134.8240  121.0524
 05X  C20  C  CR6   0   0.597  129.0769  137.1023  121.8251
 05X  C21  C  CR16  0  -0.571  130.0067  138.0800  122.1112
 05X  C22  C  CR6   0   0.570  131.3342  137.7681  121.8834
 05X  C24  C  CR6   0   0.615  130.7663  135.6119  121.1278
 05X  N2   N  NT    0  -0.415  123.0377  134.0200  123.4521
 05X  C3   C  CH2   0  -0.283  122.5887  134.6719  122.2398
 05X  C4   C  CH2   0  -0.432  123.4402  134.2042  121.0548
 05X  C5   C  CH1   0  -0.353  123.8800  132.7328  121.2518
 05X  C6   C  CH2   0  -0.472  122.8166  131.9950  122.0535
 05X  C7   C  CH2   0  -0.261  122.6869  132.6082  123.4501
 05X  C8   C  C     0   0.383  124.1313  132.0957  119.9101
 05X  O9   O  O     0  -0.380  123.3749  131.2842  119.4237
 05X  N11  N  N     0  -0.432  126.2061  133.3313  119.7523
 05X  C12  C  CR6   0   0.507  127.2850  133.7180  119.1064
 05X  C14  C  CR16  0  -0.141  126.6811  132.4722  117.1678
 05X  N16  N  NH1   0  -0.714  128.1718  134.6018  119.7240
 05X  O18  O  O     0  -0.402  127.7632  134.2872  121.9566
 05X  C19  C  CR6   0  -0.499  129.4165  135.8582  121.3175
 05X  C23  C  CR16  0  -0.570  131.7487  136.5418  121.4007
 05X  F26  F  F     0  -0.295  132.2571  138.6931  122.1417
 05X  F27  F  F     0  -0.286  127.7857  137.3643  122.0227
 05X  H1   H  HCR6  0   0.293  128.4725  133.6520  117.3008
 05X  H2   H  HCR6  0   0.277  124.8269  131.3941  117.3787
 05X  H3   H  HCR6  0   0.315  129.7074  139.0474  122.4921
 05X  H4   H  HCH3  0   0.230  122.9210  135.7075  124.6782
 05X  H5   H  HCH3  0   0.188  121.4872  134.6682  124.7666
 05X  H6   H  HCH3  0   0.229  123.0002  134.1658  125.5297
 05X  H8   H  HCH2  0   0.240  122.6979  135.7519  122.3562
 05X  H9   H  HCH2  0   0.197  121.5181  134.4912  122.0457
 05X  H10  H  HCH2  0   0.244  124.3238  134.8332  120.9541
 05X  H11  H  HCH2  0   0.232  122.8596  134.3166  120.1352
 05X  H12  H  HCH1  0   0.267  124.8207  132.7380  121.8090
 05X  H13  H  HCH2  0   0.231  121.8610  132.0530  121.5269
 05X  H14  H  HCH2  0   0.249  123.0521  130.9337  122.1456
 05X  H15  H  HCH2  0   0.196  121.6570  132.4495  123.8116
 05X  H16  H  HCH2  0   0.225  123.3464  132.0896  124.1528
 05X  H17  H  HCR6  0   0.283  126.8715  132.1406  116.1560
 05X  H18  H  HNH1  0   0.435  128.7844  135.1015  119.0956
 05X  H19  H  HCR6  0   0.315  132.7953  136.3182  121.2427
 05X  F25  F  F     0  -0.289  131.1276  134.4144  120.6647
 05X  C1   C  CH3   0  -0.515  122.5834  134.6702  124.6557

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
 05X  C14  C13  aromatic  1.379  0.020  1.379
 05X  C14  C15  aromatic  1.389  0.020  1.389
 05X  C13  C12  aromatic  1.399  0.020  1.399
 05X  C15  C10  aromatic  1.387  0.020  1.387
 05X  C12  N16  single    1.396  0.020  1.396
 05X  C12  N11  aromatic  1.316  0.020  1.316
 05X  O9   C8   double    1.211  0.020  1.211
 05X  C10  N11  aromatic  1.331  0.020  1.331
 05X  C10  C8   single    1.503  0.020  1.503
 05X  N16  C17  single    1.360  0.020  1.360
 05X  F25  C24  single    1.334  0.020  1.334
 05X  C8   C5   single    1.506  0.020  1.506
 05X  C24  C23  aromatic  1.380  0.020  1.380
 05X  C24  C19  aromatic  1.385  0.020  1.385
 05X  C17  C19  single    1.504  0.020  1.504
 05X  C17  O18  double    1.208  0.020  1.208
 05X  C23  C22  aromatic  1.382  0.020  1.382
 05X  C19  C20  aromatic  1.386  0.020  1.386
 05X  C5   C6   single    1.523  0.020  1.523
 05X  C5   C4   single    1.548  0.020  1.548
 05X  C6   C7   single    1.531  0.020  1.531
 05X  C4   C3   single    1.532  0.020  1.532
 05X  C22  F26  single    1.332  0.020  1.332
 05X  C22  C21  aromatic  1.383  0.020  1.383
 05X  C20  C21  aromatic  1.379  0.020  1.379
 05X  C20  F27  single    1.332  0.020  1.332
 05X  C7   N2   single    1.455  0.020  1.455
 05X  C3   N2   single    1.448  0.020  1.448
 05X  N2   C1   single    1.442  0.020  1.442
 05X  C13  H1   single    0.930  0.020  1.080
 05X  C15  H2   single    0.930  0.020  1.080
 05X  C21  H3   single    0.930  0.020  1.080
 05X  C1   H4   single    0.970  0.020  1.090
 05X  C1   H5   single    0.970  0.020  1.090
 05X  C1   H6   single    0.970  0.020  1.090
 05X  C3   H8   single    0.970  0.020  1.090
 05X  C3   H9   single    0.970  0.020  1.090
 05X  C4   H10  single    0.970  0.020  1.090
 05X  C4   H11  single    0.970  0.020  1.090
 05X  C5   H12  single    0.970  0.020  1.090
 05X  C6   H13  single    0.970  0.020  1.090
 05X  C6   H14  single    0.970  0.020  1.090
 05X  C7   H15  single    0.970  0.020  1.090
 05X  C7   H16  single    0.970  0.020  1.090
 05X  C14  H17  single    0.930  0.020  1.080
 05X  N16  H18  single    0.860  0.020  1.020
 05X  C23  H19  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
 05X  N11  C10  C8   117.14  3.000
 05X  C8   C10  C15  119.84  3.000
 05X  N11  C10  C15  123.02  3.000
 05X  H1   C13  C14  121.20  3.000
 05X  H1   C13  C12  120.70  3.000
 05X  C14  C13  C12  118.10  3.000
 05X  H2   C15  C14  121.07  3.000
 05X  H2   C15  C10  121.00  3.000
 05X  C14  C15  C10  117.93  3.000
 05X  C19  C17  O18  121.35  3.000
 05X  O18  C17  N16  126.26  3.000
 05X  C19  C17  N16  112.39  3.000
 05X  F27  C20  C19  117.93  3.000
 05X  F27  C20  C21  118.89  3.000
 05X  C19  C20  C21  123.17  3.000
 05X  H3   C21  C22  121.69  3.000
 05X  H3   C21  C20  121.36  3.000
 05X  C22  C21  C20  116.95  3.000
 05X  F26  C22  C23  118.44  3.000
 05X  F26  C22  C21  118.47  3.000
 05X  C23  C22  C21  123.08  3.000
 05X  F25  C24  C23  118.74  3.000
 05X  C23  C24  C19  123.15  3.000
 05X  F25  C24  C19  118.10  3.000
 05X  C7   N2   C3   111.17  3.000
 05X  C3   N2   C1   113.47  3.000
 05X  C7   N2   C1   111.28  3.000
 05X  H9   C3   H8   106.14  3.000
 05X  H9   C3   C4   110.69  3.000
 05X  H8   C3   C4   109.19  3.000
 05X  H9   C3   N2   112.00  3.000
 05X  H8   C3   N2   108.97  3.000
 05X  C4   C3   N2   109.74  3.000
 05X  H11  C4   H10  107.08  3.000
 05X  H11  C4   C5   110.83  3.000
 05X  H10  C4   C5   109.27  3.000
 05X  H11  C4   C3   108.91  3.000
 05X  H10  C4   C3   110.24  3.000
 05X  C5   C4   C3   110.45  3.000
 05X  H12  C5   C8   108.21  3.000
 05X  H12  C5   C6   109.57  3.000
 05X  C8   C5   C6   112.37  3.000
 05X  H12  C5   C4   107.74  3.000
 05X  C6   C5   C4   109.21  3.000
 05X  C8   C5   C4   109.63  3.000
 05X  H14  C6   H13  106.33  3.000
 05X  H14  C6   C7   109.32  3.000
 05X  H13  C6   C7   110.14  3.000
 05X  H14  C6   C5   111.41  3.000
 05X  H13  C6   C5   109.35  3.000
 05X  C7   C6   C5   110.21  3.000
 05X  H16  C7   H15  106.50  3.000
 05X  H16  C7   C6   110.18  3.000
 05X  H15  C7   C6   108.69  3.000
 05X  H16  C7   N2   108.28  3.000
 05X  H15  C7   N2   111.37  3.000
 05X  C6   C7   N2   111.69  3.000
 05X  O9   C8   C5   122.47  3.000
 05X  C5   C8   C10  118.31  3.000
 05X  O9   C8   C10  119.20  3.000
 05X  C12  N11  C10  118.72  3.000
 05X  N16  C12  N11  119.33  3.000
 05X  N11  C12  C13  122.88  3.000
 05X  N16  C12  C13  117.77  3.000
 05X  H17  C14  C15  120.57  3.000
 05X  H17  C14  C13  120.07  3.000
 05X  C15  C14  C13  119.35  3.000
 05X  H18  N16  C12  115.04  3.000
 05X  H18  N16  C17  116.37  3.000
 05X  C12  N16  C17  128.50  3.000
 05X  C24  C19  C20  116.65  3.000
 05X  C20  C19  C17  120.63  3.000
 05X  C24  C19  C17  122.67  3.000
 05X  H19  C23  C24  121.38  3.000
 05X  H19  C23  C22  121.65  3.000
 05X  C24  C23  C22  116.98  3.000
 05X  H6   C1   H5   107.36  3.000
 05X  H6   C1   H4   107.73  3.000
 05X  H5   C1   H4   107.91  3.000
 05X  H6   C1   N2   109.86  3.000
 05X  H5   C1   N2   113.38  3.000
 05X  H4   C1   N2   110.40  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
 05X  CONST_01  C13  C14  C15  C10     0.00   0.0  0
 05X  CONST_02  C13  C12  N11  C10     0.00   0.0  0
 05X  CONST_03  C12  C13  C14  C15     0.00   0.0  0
 05X  CONST_04  C12  N11  C10  C15     0.00   0.0  0
 05X  CONST_05  C23  C24  C19  C20     0.00   0.0  0
 05X  CONST_06  C23  C22  C21  C20     0.00   0.0  0
 05X  CONST_07  C24  C23  C22  C21     0.00   0.0  0
 05X  CONST_08  C24  C19  C20  C21     0.00   0.0  0
 05X  CONST_09  C19  C24  C23  C22     0.00   0.0  0
 05X  CONST_10  C19  C20  C21  C22     0.00   0.0  0
 05X  CONST_11  C14  C13  C12  N11     0.00   0.0  0
 05X  CONST_12  C14  C15  C10  N11     0.00   0.0  0
 05X  CONST_13  N16  C12  N11  C10   180.00   0.0  0
 05X  CONST_14  C23  C24  C19  C17   180.00   0.0  0
 05X  CONST_15  C21  C20  C19  C17   180.00   0.0  0
 05X  CONST_16  F25  C24  C19  C20   180.00   0.0  0
 05X  CONST_17  F26  C22  C21  C20   180.00   0.0  0
 05X  CONST_18  F25  C24  C23  C22   180.00   0.0  0
 05X  CONST_19  F27  C20  C21  C22   180.00   0.0  0
 05X  CONST_20  F26  C22  C23  C24   180.00   0.0  0
 05X  CONST_21  F27  C20  C19  C24   180.00   0.0  0
 05X  CONST_22  C14  C15  C10  C8    180.00   0.0  0
 05X  CONST_23  C12  N11  C10  C8    180.00   0.0  0
 05X  CONST_24  N16  C12  C13  C14   180.00   0.0  0
 05X  CONST_25  H17  C14  C15  C10   180.00   0.0  0
 05X  CONST_26  H2   C15  C14  C13   180.00   0.0  0
 05X  CONST_27  H1   C13  C14  C15   180.00   0.0  0
 05X  CONST_28  H19  C23  C22  C21   180.00   0.0  0
 05X  CONST_29  H3   C21  C20  C19   180.00   0.0  0
 05X  CONST_30  C19  C17  N16  C12   180.00   0.0  0
 05X  CONST_34  O18  C17  N16  C12     0.00   0.0  0
 05X  Var_01    C5   C6   C7   N2     28.59  30.0  1
 05X  Var_02    C5   C4   C3   N2     32.88  30.0  1
 05X  Var_03    C6   C7   N2   C3     37.14  30.0  1
 05X  Var_04    C7   N2   C3   C4    -71.04  30.0  1
 05X  Var_05    C5   C8   C10  C15  -173.27  30.0  2
 05X  Var_06    N16  C17  C19  C20   110.37  30.0  2
 05X  Var_07    H4   C1   N2   C3    -58.15  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 05X  chir_01  C5  C8  C6  C4  positiv

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
 05X  plan-1  C17  0.020
 05X  plan-1  C20  0.020
 05X  plan-1  C21  0.020
 05X  plan-1  C22  0.020
 05X  plan-1  C24  0.020
 05X  plan-1  C19  0.020
 05X  plan-1  C23  0.020
 05X  plan-1  F26  0.020
 05X  plan-1  F27  0.020
 05X  plan-1  H3   0.020
 05X  plan-1  H19  0.020
 05X  plan-1  F25  0.020
 05X  plan-2  C10  0.020
 05X  plan-2  C13  0.020
 05X  plan-2  C15  0.020
 05X  plan-2  C8   0.020
 05X  plan-2  N11  0.020
 05X  plan-2  C12  0.020
 05X  plan-2  C14  0.020
 05X  plan-2  N16  0.020
 05X  plan-2  H1   0.020
 05X  plan-2  H2   0.020
 05X  plan-2  H17  0.020
 05X  plan-3  C17  0.020
 05X  plan-3  C12  0.020
 05X  plan-3  N16  0.020
 05X  plan-3  O18  0.020
 05X  plan-3  C19  0.020
 05X  plan-3  H18  0.020
 05X  plan-4  C10  0.020
 05X  plan-4  C5   0.020
 05X  plan-4  C8   0.020
 05X  plan-4  O9   0.020

