# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 09:50:58 2022
#   Inital geometry file: a 112 line input string
#   Ligand name: N-{[(2R)-piperidin-2-yl]methyl}-2,5-bis(2,2,2-trifluoroethoxy)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(F)COc1ccc(OCC(F)(F)F)c(c1)C(=O)NC[C@H]2CCCCN2
#
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
 K4D  K4D  N-{[(2R)-piperidin-2-yl]methyl}-2,5-bis(2,2,2-trifluoroethoxy)benzamide  ligand  48  28  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_K4D
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
 K4D  C10  C  C     0   0.504   1.4717  -0.1077   0.4508
 K4D  N12  N  NH1   0  -0.627   1.8931  -0.9283  -0.5266
 K4D  C13  C  CH2   0  -0.269   3.1782  -1.5924  -0.5464
 K4D  C15  C  C     0  -0.416   4.4444  -3.7440  -0.6130
 K4D  C17  C  C     0  -0.427   3.5720  -5.6830   0.7118
 K4D  C20  C  CR6   0   0.374  -0.0836   1.8377   0.1025
 K4D  C22  C  CH2   0  -0.377   0.9056   3.9820   0.0118
 K4D  C28  C  CR16  0  -0.363  -2.4600   1.4804  -0.1166
 K4D  C02  C  CT    0   0.993  -5.4913  -1.5406   0.0754
 K4D  C05  C  CH2   0  -0.376  -4.5969  -0.3325  -0.0736
 K4D  C07  C  CR6   0   0.385  -2.2788   0.1127   0.0044
 K4D  C08  C  CR16  0  -0.343  -0.9887  -0.3934   0.1569
 K4D  C09  C  CR6   0  -0.154   0.1008   0.4551   0.2156
 K4D  C14  C  CR16  0  -0.083   3.0587  -3.1110  -0.5332
 K4D  C16  C  C     0  -0.446   4.3602  -5.2642  -0.5239
 K4D  C18  C  C     0  -0.295   2.2182  -4.9901   0.7339
 K4D  C23  C  CT    0   0.994   2.2979   4.5536   0.1399
 K4D  C27  C  CR16  0  -0.367  -1.3629   2.3378  -0.0721
 K4D  F01  F  F     0  -0.306  -5.3058  -2.4318  -0.9034
 K4D  F03  F  F     0  -0.305  -5.2865  -2.1801   1.2308
 K4D  F04  F  F     0  -0.308  -6.7749  -1.1663   0.0427
 K4D  F24  F  F     0  -0.304   2.8492   4.2810   1.3256
 K4D  F25  F  F     0  -0.306   3.1271   4.0824  -0.7961
 K4D  F26  F  F     0  -0.309   2.2590   5.8850   0.0097
 K4D  N19  N  NR16  0  -0.601   2.3954  -3.5473   0.6821
 K4D  O11  O  O     0  -0.466   2.1062   0.1587   1.4566
 K4D  O21  O  O2    0  -0.465   1.0350   2.5939   0.1447
 K4D  H1   H  HNH1  0   0.407   1.3185  -1.0088  -1.3510
 K4D  H2   H  HCH2  0   0.247   3.7224  -1.2807  -1.4411
 K4D  H3   H  HCH2  0   0.245   3.7470  -1.2594   0.3207
 K4D  H4   H  H     0   0.226   4.9289  -3.4420  -1.5451
 K4D  H5   H  H     0   0.211   5.0576  -3.3590   0.2090
 K4D  H6   H  H     0   0.225   3.4329  -6.7663   0.7331
 K4D  H7   H  H     0   0.211   4.1284  -5.4119   1.6142
 K4D  H8   H  HCH2  0   0.272   0.2736   4.4175   0.7938
 K4D  H9   H  HCH2  0   0.272   0.4913   4.2690  -0.9613
 K4D  H10  H  HCR6  0   0.294  -3.4396   1.9180  -0.2543
 K4D  H11  H  HCH2  0   0.272  -4.8222   0.1598  -1.0263
 K4D  H12  H  HCH2  0   0.272  -4.8202   0.3710   0.7358
 K4D  H13  H  HCR6  0   0.274  -0.8493  -1.4644   0.2471
 K4D  H14  H  HCR6  0   0.194   2.5002  -3.4218  -1.4360
 K4D  H15  H  H     0   0.216   3.8610  -5.6502  -1.4187
 K4D  H16  H  H     0   0.234   5.3624  -5.6980  -0.5107
 K4D  H17  H  H     0   0.191   1.6126  -5.3685  -0.1063
 K4D  H18  H  H     0   0.234   1.6800  -5.2405   1.6505
 K4D  H19  H  HCR6  0   0.301  -1.5438   3.3982  -0.1818
 K4D  H20  H  HNR6  0   0.348   1.4864  -3.1062   0.7424
 K4D  O06  O  O2    0  -0.481  -3.2780  -0.8018  -0.0176

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
 K4D  C18  C17  single    1.521  0.020  1.521
 K4D  C18  N19  single    1.455  0.020  1.455
 K4D  C17  C16  single    1.524  0.020  1.524
 K4D  N19  C14  single    1.452  0.020  1.452
 K4D  C16  C15  single    1.525  0.020  1.525
 K4D  C13  N12  single    1.447  0.020  1.447
 K4D  C13  C14  single    1.523  0.020  1.523
 K4D  N12  C10  single    1.344  0.020  1.344
 K4D  C14  C15  single    1.526  0.020  1.526
 K4D  F04  C02  single    1.337  0.020  1.337
 K4D  C10  C09  single    1.501  0.020  1.501
 K4D  C10  O11  double    1.219  0.020  1.219
 K4D  C08  C09  aromatic  1.382  0.020  1.382
 K4D  C08  C07  aromatic  1.394  0.020  1.394
 K4D  O06  C07  single    1.355  0.020  1.355
 K4D  O06  C05  single    1.401  0.020  1.401
 K4D  C09  C20  aromatic  1.399  0.020  1.399
 K4D  C07  C28  aromatic  1.385  0.020  1.385
 K4D  C02  F03  single    1.336  0.020  1.336
 K4D  C02  C05  single    1.510  0.020  1.510
 K4D  C02  F01  single    1.337  0.020  1.337
 K4D  F24  C23  single    1.336  0.020  1.336
 K4D  C22  C23  single    1.511  0.020  1.511
 K4D  C22  O21  single    1.400  0.020  1.400
 K4D  F26  C23  single    1.338  0.020  1.338
 K4D  C23  F25  single    1.336  0.020  1.336
 K4D  C20  C27  aromatic  1.385  0.020  1.385
 K4D  C20  O21  single    1.351  0.020  1.351
 K4D  C28  C27  aromatic  1.393  0.020  1.393
 K4D  N12  H1   single    0.860  0.020  1.020
 K4D  C13  H2   single    0.970  0.020  1.090
 K4D  C13  H3   single    0.970  0.020  1.090
 K4D  C15  H4   single    0.970  0.020  1.090
 K4D  C15  H5   single    0.970  0.020  1.090
 K4D  C17  H6   single    0.970  0.020  1.090
 K4D  C17  H7   single    0.970  0.020  1.090
 K4D  C22  H8   single    0.970  0.020  1.090
 K4D  C22  H9   single    0.970  0.020  1.090
 K4D  C28  H10  single    0.930  0.020  1.080
 K4D  C05  H11  single    0.970  0.020  1.090
 K4D  C05  H12  single    0.970  0.020  1.090
 K4D  C08  H13  single    0.930  0.020  1.080
 K4D  C14  H14  single    0.970  0.020  1.090
 K4D  C16  H15  single    0.970  0.020  1.090
 K4D  C16  H16  single    0.970  0.020  1.090
 K4D  C18  H17  single    0.970  0.020  1.090
 K4D  C18  H18  single    0.970  0.020  1.090
 K4D  C27  H19  single    0.930  0.020  1.080
 K4D  N19  H20  single    0.890  0.020  1.040

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
 K4D  O11  C10  C09  121.54  3.000
 K4D  O11  C10  N12  124.78  3.000
 K4D  C09  C10  N12  113.67  3.000
 K4D  H1   N12  C13  117.29  3.000
 K4D  H1   N12  C10  117.69  3.000
 K4D  C13  N12  C10  124.66  3.000
 K4D  H3   C13  H2   107.73  3.000
 K4D  H3   C13  C14  109.81  3.000
 K4D  H2   C13  C14  109.30  3.000
 K4D  H3   C13  N12  108.22  3.000
 K4D  H2   C13  N12  108.83  3.000
 K4D  C14  C13  N12  112.82  3.000
 K4D  H5   C15  H4   107.13  3.000
 K4D  H5   C15  C16  109.72  3.000
 K4D  H4   C15  C16  110.47  3.000
 K4D  H5   C15  C14  108.86  3.000
 K4D  H4   C15  C14  109.42  3.000
 K4D  C16  C15  C14  111.13  3.000
 K4D  H7   C17  H6   107.12  3.000
 K4D  H7   C17  C18  109.13  3.000
 K4D  H6   C17  C18  109.76  3.000
 K4D  H7   C17  C16  109.73  3.000
 K4D  H6   C17  C16  110.74  3.000
 K4D  C18  C17  C16  110.30  3.000
 K4D  O21  C20  C27  124.53  3.000
 K4D  O21  C20  C09  116.20  3.000
 K4D  C27  C20  C09  119.25  3.000
 K4D  H9   C22  H8   108.16  3.000
 K4D  H9   C22  O21  112.26  3.000
 K4D  H8   C22  O21  112.30  3.000
 K4D  H9   C22  C23  108.95  3.000
 K4D  H8   C22  C23  108.70  3.000
 K4D  O21  C22  C23  106.37  3.000
 K4D  H10  C28  C27  117.92  3.000
 K4D  H10  C28  C07  121.95  3.000
 K4D  C27  C28  C07  120.13  3.000
 K4D  F04  C02  F03  107.59  3.000
 K4D  F03  C02  F01  107.03  3.000
 K4D  F04  C02  F01  107.56  3.000
 K4D  F01  C02  C05  112.26  3.000
 K4D  F03  C02  C05  112.17  3.000
 K4D  F04  C02  C05  110.00  3.000
 K4D  H12  C05  H11  108.17  3.000
 K4D  H12  C05  O06  112.18  3.000
 K4D  H11  C05  O06  112.26  3.000
 K4D  H12  C05  C02  108.67  3.000
 K4D  H11  C05  C02  108.87  3.000
 K4D  O06  C05  C02  106.60  3.000
 K4D  O06  C07  C08  116.05  3.000
 K4D  O06  C07  C28  124.66  3.000
 K4D  C08  C07  C28  119.28  3.000
 K4D  H13  C08  C09  120.11  3.000
 K4D  H13  C08  C07  119.14  3.000
 K4D  C09  C08  C07  120.74  3.000
 K4D  C08  C09  C20  119.95  3.000
 K4D  C20  C09  C10  120.24  3.000
 K4D  C08  C09  C10  119.77  3.000
 K4D  H14  C14  N19  111.60  3.000
 K4D  H14  C14  C15  107.42  3.000
 K4D  N19  C14  C15  109.52  3.000
 K4D  H14  C14  C13  108.22  3.000
 K4D  C15  C14  C13  110.00  3.000
 K4D  N19  C14  C13  110.04  3.000
 K4D  H16  C16  H15  106.76  3.000
 K4D  H16  C16  C17  110.83  3.000
 K4D  H15  C16  C17  109.26  3.000
 K4D  H16  C16  C15  110.25  3.000
 K4D  H15  C16  C15  109.19  3.000
 K4D  C17  C16  C15  110.47  3.000
 K4D  H18  C18  H17  106.87  3.000
 K4D  H18  C18  N19  108.50  3.000
 K4D  H17  C18  N19  112.34  3.000
 K4D  H18  C18  C17  110.27  3.000
 K4D  H17  C18  C17  108.75  3.000
 K4D  N19  C18  C17  110.05  3.000
 K4D  F26  C23  F25  107.50  3.000
 K4D  F25  C23  F24  107.08  3.000
 K4D  F26  C23  F24  107.54  3.000
 K4D  F25  C23  C22  112.27  3.000
 K4D  F26  C23  C22  109.97  3.000
 K4D  F24  C23  C22  112.24  3.000
 K4D  H19  C27  C28  117.94  3.000
 K4D  H19  C27  C20  121.43  3.000
 K4D  C28  C27  C20  120.63  3.000
 K4D  H20  N19  C18  108.71  3.000
 K4D  H20  N19  C14  109.22  3.000
 K4D  C18  N19  C14  112.56  3.000
 K4D  C22  O21  C20  118.38  3.000
 K4D  C07  O06  C05  117.96  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
 K4D  CONST_01  C07  C08  C09  C20    0.00   0.0  0
 K4D  CONST_02  C07  C28  C27  C20    0.00   0.0  0
 K4D  CONST_03  C09  C08  C07  C28    0.00   0.0  0
 K4D  CONST_04  C09  C20  C27  C28    0.00   0.0  0
 K4D  CONST_05  C27  C20  C09  C08    0.00   0.0  0
 K4D  CONST_06  C27  C28  C07  C08    0.00   0.0  0
 K4D  CONST_07  C07  C08  C09  C10  180.00   0.0  0
 K4D  CONST_08  C27  C20  C09  C10  180.00   0.0  0
 K4D  CONST_09  O21  C20  C27  C28  180.00   0.0  0
 K4D  CONST_10  O21  C20  C09  C08  180.00   0.0  0
 K4D  CONST_11  O06  C07  C08  C09  180.00   0.0  0
 K4D  CONST_12  O06  C07  C28  C27  180.00   0.0  0
 K4D  CONST_13  H13  C08  C09  C20  180.00   0.0  0
 K4D  CONST_14  H10  C28  C27  C20  180.00   0.0  0
 K4D  CONST_15  H19  C27  C28  C07  180.00   0.0  0
 K4D  CONST_16  C09  C10  N12  C13  180.00   0.0  0
 K4D  CONST_17  H1   N12  C10  C09    0.00   0.0  0
 K4D  CONST_18  O11  C10  N12  C13    0.00   0.0  0
 K4D  Var_01    C18  C17  C16  C15   53.28  30.0  1
 K4D  Var_02    C14  N19  C18  C17   61.53  30.0  1
 K4D  Var_03    C14  C15  C16  C17  -53.14  30.0  1
 K4D  Var_04    N19  C18  C17  C16  -56.73  30.0  1
 K4D  Var_05    C08  C09  C10  N12   63.24  30.0  2
 K4D  Var_06    C09  C20  O21  C22  178.89  30.0  2
 K4D  Var_07    C08  C07  O06  C05  175.56  30.0  2
 K4D  Var_08    C14  C13  N12  C10  118.11  30.0  1
 K4D  Var_09    C23  C22  O21  C20  178.29  30.0  1
 K4D  Var_10    H11  C05  O06  C07   67.32  30.0  3
 K4D  Var_11    O06  C05  C02  F01  -60.79  30.0  3
 K4D  Var_12    O21  C22  C23  F24  -60.94  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
 K4D  chir_01  C14  N19  C13  C15  negativ

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
 K4D  plan-1  C10  0.020
 K4D  plan-1  C20  0.020
 K4D  plan-1  C28  0.020
 K4D  plan-1  C07  0.020
 K4D  plan-1  C08  0.020
 K4D  plan-1  C09  0.020
 K4D  plan-1  C27  0.020
 K4D  plan-1  O21  0.020
 K4D  plan-1  H10  0.020
 K4D  plan-1  H13  0.020
 K4D  plan-1  H19  0.020
 K4D  plan-1  O06  0.020
 K4D  plan-2  C10  0.020
 K4D  plan-2  N12  0.020
 K4D  plan-2  C13  0.020
 K4D  plan-2  C09  0.020
 K4D  plan-2  O11  0.020
 K4D  plan-2  H1   0.020

