# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 23:36:36 2022
#   Inital geometry file: a 90 line input string
#   Ligand name: 4-methyl-~{N}-[4-(trifluoromethyl)phenyl]piperidine-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1CCN(CC1)C(=O)Nc2ccc(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
 U9Z  U9Z  "4-methyl-~{N}-[4-(trifluoromethyl)phenyl]piperidine-1-carboxamide"
  ligand  37  20  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_U9Z
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
 U9Z  C4   C  CH2   0  -0.324  -15.8290  -30.1900   2.6642
 U9Z  C14  C  CH2   0  -0.465  -17.5756  -29.9393   0.5351
 U9Z  C5   C  C     0   0.735  -14.1697  -28.9486   1.2984
 U9Z  C6   C  CR6   0   0.399  -12.3770  -28.0429   2.7733
 U9Z  C11  C  CR16  0  -0.269  -10.0968  -27.4689   2.2395
 U9Z  C7   C  CR16  0  -0.350  -12.1162  -27.6846   4.1031
 U9Z  C8   C  CR16  0  -0.256  -10.8725  -27.2386   4.4916
 U9Z  C9   C  CR6   0  -0.223   -9.8435  -27.1286   3.5607
 U9Z  C10  C  CT    0   1.048   -8.4860  -26.7184   4.0170
 U9Z  C12  C  CR16  0  -0.308  -11.3461  -27.9164   1.8380
 U9Z  C13  C  CH2   0  -0.286  -16.0924  -29.9410   0.2002
 U9Z  N1   N  NT    0  -0.491  -15.3179  -29.6580   1.4034
 U9Z  N2   N  NH1   0  -0.802  -13.6460  -28.5272   2.5053
 U9Z  C3   C  CH2   0  -0.460  -16.7214  -31.3902   2.4005
 U9Z  C1   C  CH3   0  -0.664  -18.5107  -32.2781   0.8791
 U9Z  C2   C  CH1   0  -0.215  -17.9466  -31.0342   1.5524
 U9Z  O1   O  O     0  -0.517  -13.6403  -28.6872   0.2266
 U9Z  F1   F  F     0  -0.306   -7.7144  -26.2772   3.0178
 U9Z  F2   F  F     0  -0.313   -8.5343  -25.7432   4.9360
 U9Z  F3   F  F     0  -0.319   -7.8243  -27.7394   4.5917
 U9Z  H1   H  HCH2  0   0.258  -14.9957  -30.5089   3.2923
 U9Z  H2   H  HCH2  0   0.240  -16.3869  -29.4264   3.2204
 U9Z  H3   H  HCH2  0   0.238  -17.8356  -28.9528   0.9272
 U9Z  H4   H  HCH2  0   0.244  -18.1460  -30.0625  -0.3884
 U9Z  H5   H  HCR6  0   0.269   -9.3208  -27.3925   1.4894
 U9Z  H6   H  HCR6  0   0.276  -12.9013  -27.7689   4.8452
 U9Z  H7   H  HCR6  0   0.272  -10.7159  -26.9810   5.5311
 U9Z  H8   H  HCR6  0   0.285  -11.5035  -28.1659   0.8023
 U9Z  H9   H  HCH2  0   0.231  -15.7971  -30.9017  -0.2361
 U9Z  H10  H  HCH2  0   0.256  -15.8788  -29.1776  -0.5449
 U9Z  H11  H  HNH1  0   0.430  -14.2446  -28.5747   3.3147
 U9Z  H12  H  HCH2  0   0.253  -17.0302  -31.8140   3.3576
 U9Z  H13  H  HCH2  0   0.232  -16.1272  -32.1617   1.9004
 U9Z  H14  H  HCH3  0   0.226  -18.7294  -33.0583   1.6105
 U9Z  H15  H  HCH3  0   0.228  -19.4341  -32.0544   0.3432
 U9Z  H16  H  HCH3  0   0.218  -17.7991  -32.6916   0.1601
 U9Z  H17  H  HCH1  0   0.232  -18.7136  -30.6283   2.2185

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
 U9Z  C13  C14  single    1.521  0.020  1.521
 U9Z  C13  N1   single    1.459  0.020  1.459
 U9Z  C14  C2   single    1.540  0.020  1.540
 U9Z  O1   C5   double    1.224  0.020  1.224
 U9Z  C1   C2   single    1.523  0.020  1.523
 U9Z  C2   C3   single    1.532  0.020  1.532
 U9Z  C5   N1   single    1.354  0.020  1.354
 U9Z  C5   N2   single    1.381  0.020  1.381
 U9Z  N1   C4   single    1.461  0.020  1.461
 U9Z  C12  C11  aromatic  1.386  0.020  1.386
 U9Z  C12  C6   aromatic  1.398  0.020  1.398
 U9Z  C11  C9   aromatic  1.388  0.020  1.388
 U9Z  C3   C4   single    1.519  0.020  1.519
 U9Z  N2   C6   single    1.384  0.020  1.384
 U9Z  C6   C7   aromatic  1.402  0.020  1.402
 U9Z  F1   C10  single    1.337  0.020  1.337
 U9Z  C9   C10  single    1.490  0.020  1.490
 U9Z  C9   C8   aromatic  1.392  0.020  1.392
 U9Z  C10  F3   single    1.346  0.020  1.346
 U9Z  C10  F2   single    1.341  0.020  1.341
 U9Z  C7   C8   aromatic  1.377  0.020  1.377
 U9Z  C4   H1   single    0.970  0.020  1.090
 U9Z  C4   H2   single    0.970  0.020  1.090
 U9Z  C14  H3   single    0.970  0.020  1.090
 U9Z  C14  H4   single    0.970  0.020  1.090
 U9Z  C11  H5   single    0.930  0.020  1.080
 U9Z  C7   H6   single    0.930  0.020  1.080
 U9Z  C8   H7   single    0.930  0.020  1.080
 U9Z  C12  H8   single    0.930  0.020  1.080
 U9Z  C13  H9   single    0.970  0.020  1.090
 U9Z  C13  H10  single    0.970  0.020  1.090
 U9Z  N2   H11  single    0.860  0.020  1.020
 U9Z  C3   H12  single    0.970  0.020  1.090
 U9Z  C3   H13  single    0.970  0.020  1.090
 U9Z  C1   H14  single    0.970  0.020  1.090
 U9Z  C1   H15  single    0.970  0.020  1.090
 U9Z  C1   H16  single    0.970  0.020  1.090
 U9Z  C2   H17  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
 U9Z  H2   C4   H1   107.45  3.000
 U9Z  H2   C4   C3   109.83  3.000
 U9Z  H1   C4   C3   108.53  3.000
 U9Z  H2   C4   N1   111.22  3.000
 U9Z  H1   C4   N1   109.64  3.000
 U9Z  C3   C4   N1   110.09  3.000
 U9Z  H4   C14  H3   106.31  3.000
 U9Z  H4   C14  C2   110.64  3.000
 U9Z  H3   C14  C2   110.33  3.000
 U9Z  H4   C14  C13  108.85  3.000
 U9Z  H3   C14  C13  108.18  3.000
 U9Z  C2   C14  C13  112.32  3.000
 U9Z  O1   C5   N2   122.42  3.000
 U9Z  N2   C5   N1   114.43  3.000
 U9Z  O1   C5   N1   123.15  3.000
 U9Z  N2   C6   C12  125.32  3.000
 U9Z  N2   C6   C7   116.33  3.000
 U9Z  C12  C6   C7   118.33  3.000
 U9Z  H5   C11  C12  117.92  3.000
 U9Z  H5   C11  C9   120.78  3.000
 U9Z  C12  C11  C9   121.29  3.000
 U9Z  H6   C7   C8   119.10  3.000
 U9Z  H6   C7   C6   119.67  3.000
 U9Z  C8   C7   C6   121.22  3.000
 U9Z  H7   C8   C9   121.10  3.000
 U9Z  H7   C8   C7   118.60  3.000
 U9Z  C9   C8   C7   120.30  3.000
 U9Z  C10  C9   C8   119.38  3.000
 U9Z  C8   C9   C11  118.84  3.000
 U9Z  C10  C9   C11  121.70  3.000
 U9Z  F3   C10  F2   106.07  3.000
 U9Z  F2   C10  F1   107.03  3.000
 U9Z  F3   C10  F1   106.60  3.000
 U9Z  F2   C10  C9   112.17  3.000
 U9Z  F3   C10  C9   111.72  3.000
 U9Z  F1   C10  C9   112.82  3.000
 U9Z  H8   C12  C11  119.01  3.000
 U9Z  H8   C12  C6   120.99  3.000
 U9Z  C11  C12  C6   120.00  3.000
 U9Z  H10  C13  H9   106.83  3.000
 U9Z  H10  C13  N1   108.94  3.000
 U9Z  H9   C13  N1   110.82  3.000
 U9Z  H10  C13  C14  109.98  3.000
 U9Z  H9   C13  C14  110.58  3.000
 U9Z  N1   C13  C14  109.64  3.000
 U9Z  C13  N1   C5   119.21  3.000
 U9Z  C5   N1   C4   123.68  3.000
 U9Z  C13  N1   C4   117.10  3.000
 U9Z  H11  N2   C6   113.92  3.000
 U9Z  H11  N2   C5   117.52  3.000
 U9Z  C6   N2   C5   128.55  3.000
 U9Z  H13  C3   H12  106.30  3.000
 U9Z  H13  C3   C2   110.17  3.000
 U9Z  H12  C3   C2   110.45  3.000
 U9Z  H13  C3   C4   108.50  3.000
 U9Z  H12  C3   C4   108.72  3.000
 U9Z  C2   C3   C4   112.48  3.000
 U9Z  H16  C1   H15  107.79  3.000
 U9Z  H16  C1   H14  107.51  3.000
 U9Z  H15  C1   H14  107.83  3.000
 U9Z  H16  C1   C2   111.02  3.000
 U9Z  H15  C1   C2   111.30  3.000
 U9Z  H14  C1   C2   111.21  3.000
 U9Z  H17  C2   C1   108.21  3.000
 U9Z  H17  C2   C3   108.05  3.000
 U9Z  C1   C2   C3   110.56  3.000
 U9Z  H17  C2   C14  107.90  3.000
 U9Z  C3   C2   C14  109.77  3.000
 U9Z  C1   C2   C14  112.20  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
 U9Z  CONST_01  C9   C11  C12  C6      0.00   0.0  0
 U9Z  CONST_02  C9   C8   C7   C6      0.00   0.0  0
 U9Z  CONST_03  C7   C6   C12  C11     0.00   0.0  0
 U9Z  CONST_04  C7   C8   C9   C11     0.00   0.0  0
 U9Z  CONST_05  C12  C11  C9   C8      0.00   0.0  0
 U9Z  CONST_06  C12  C6   C7   C8      0.00   0.0  0
 U9Z  CONST_07  N2   C6   C12  C11   180.00   0.0  0
 U9Z  CONST_08  C10  C9   C8   C7    180.00   0.0  0
 U9Z  CONST_09  N2   C6   C7   C8    180.00   0.0  0
 U9Z  CONST_10  C12  C11  C9   C10   180.00   0.0  0
 U9Z  CONST_11  H5   C11  C12  C6    180.00   0.0  0
 U9Z  CONST_12  H7   C8   C7   C6    180.00   0.0  0
 U9Z  CONST_13  H7   C8   C9   C11   180.00   0.0  0
 U9Z  CONST_14  H8   C12  C6   C7    180.00   0.0  0
 U9Z  CONST_15  H5   C11  C9   C8    180.00   0.0  0
 U9Z  CONST_16  H8   C12  C11  C9    180.00   0.0  0
 U9Z  CONST_17  H6   C7   C8   C9    180.00   0.0  0
 U9Z  CONST_18  H6   C7   C6   C12   180.00   0.0  0
 U9Z  CONST_19  O1   C5   N1   C4    180.00   0.0  0
 U9Z  CONST_20  O1   C5   N1   C13     0.00   0.0  0
 U9Z  CONST_21  C12  C6   N2   C5      0.00   0.0  0
 U9Z  CONST_22  C7   C6   N2   C5    180.00   0.0  0
 U9Z  CONST_23  N1   C5   N2   C6    180.00   0.0  0
 U9Z  CONST_24  N2   C5   N1   C4      0.00   0.0  0
 U9Z  CONST_25  N2   C5   N1   C13   180.00   0.0  0
 U9Z  CONST_26  H11  N2   C6   C7      0.00   0.0  0
 U9Z  CONST_27  H11  N2   C6   C12   180.00   0.0  0
 U9Z  CONST_29  H11  N2   C5   N1      0.00   0.0  0
 U9Z  Var_01    C14  C13  N1   C4     35.33  30.0  1
 U9Z  Var_02    C3   C4   N1   C13    23.78  30.0  1
 U9Z  Var_03    C2   C14  C13  N1    -62.17  30.0  1
 U9Z  Var_04    C2   C3   C4   N1    -61.50  30.0  1
 U9Z  Var_05    C5   N1   C13  C14  -145.79  30.0  1
 U9Z  Var_06    C3   C4   N1   C5   -155.04  30.0  1
 U9Z  Var_07    H9   C13  N1   C4    -87.02  30.0  1
 U9Z  Var_08    H10  C13  N1   C4    155.72  30.0  1
 U9Z  Var_09    H1   C4   N1   C13   143.11  30.0  1
 U9Z  Var_10    H2   C4   N1   C13   -98.20  30.0  1
 U9Z  Var_11    H3   C14  C13  N1     59.84  30.0  1
 U9Z  Var_12    H4   C14  C13  N1    174.95  30.0  1
 U9Z  Var_13    H12  C3   C4   N1    175.85  30.0  1
 U9Z  Var_14    H13  C3   C4   N1     60.64  30.0  1
 U9Z  Var_15    H9   C13  C14  C2     60.32  30.0  1
 U9Z  Var_16    H10  C13  C14  C2    178.07  30.0  1
 U9Z  Var_17    H1   C4   C3   C2    178.50  30.0  1
 U9Z  Var_18    H2   C4   C3   C2     61.30  30.0  1
 U9Z  Var_19    F1   C10  C9   C11    21.65  30.0  2
 U9Z  Var_20    F3   C10  C9   C11   -98.43  30.0  2
 U9Z  Var_21    F2   C10  C9   C11   142.62  30.0  2
 U9Z  Var_22    F1   C10  C9   C8   -161.58  30.0  2
 U9Z  Var_23    F3   C10  C9   C8     78.34  30.0  2
 U9Z  Var_24    F2   C10  C9   C8    -40.61  30.0  2
 U9Z  Var_25    H9   C13  N1   C5     91.86  30.0  1
 U9Z  Var_26    H10  C13  N1   C5    -25.40  30.0  1
 U9Z  Var_27    H1   C4   N1   C5    -35.72  30.0  1
 U9Z  Var_28    H2   C4   N1   C5     82.98  30.0  1

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
 U9Z  chir_01  C2  C14  C1  C3  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
 U9Z  plan-1  C6   0.020
 U9Z  plan-1  C11  0.020
 U9Z  plan-1  C7   0.020
 U9Z  plan-1  C8   0.020
 U9Z  plan-1  C9   0.020
 U9Z  plan-1  C10  0.020
 U9Z  plan-1  C12  0.020
 U9Z  plan-1  N2   0.020
 U9Z  plan-1  H5   0.020
 U9Z  plan-1  H6   0.020
 U9Z  plan-1  H7   0.020
 U9Z  plan-1  H8   0.020
 U9Z  plan-2  C4   0.020
 U9Z  plan-2  C5   0.020
 U9Z  plan-2  C6   0.020
 U9Z  plan-2  C13  0.020
 U9Z  plan-2  N1   0.020
 U9Z  plan-2  N2   0.020
 U9Z  plan-2  O1   0.020
 U9Z  plan-2  H11  0.020

