# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 04:58:35 2022
#   Inital geometry file: a 96 line input string
#   Ligand name: ~{N}-[2-(2-fluorophenyl)ethyl]-4-methyl-piperidine-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1CCN(CC1)C(=O)NCCc2ccccc2F
#
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
 U9T  U9T  "~{N}-[2-(2-fluorophenyl)ethyl]-4-methyl-piperidine-1-carboxamide"
  ligand  40  19  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_U9T
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
 U9T  C4   C  CH2   0  -0.290  -16.4429  -29.3803   0.3332
 U9T  C14  C  CH2   0  -0.310  -16.1840  -29.3513   2.7644
 U9T  C5   C  C     0   0.728  -14.2929  -28.7118   1.2605
 U9T  C6   C  CH2   0  -0.255  -12.2617  -27.7903   2.2810
 U9T  C11  C  CR16  0  -0.253   -7.4677  -26.6492   3.8903
 U9T  C7   C  CH2   0  -0.498  -11.5403  -28.0515   3.5947
 U9T  C8   C  CR6   0  -0.087  -10.1252  -27.5436   3.6529
 U9T  C9   C  CR16  0  -0.301   -9.4852  -26.8907   2.6027
 U9T  C10  C  CR16  0  -0.250   -8.1734  -26.4445   2.7153
 U9T  C12  C  CR16  0  -0.403   -8.0754  -27.3013   4.9558
 U9T  C13  C  CR6   0   0.521   -9.3793  -27.7267   4.8115
 U9T  N1   N  NT    0  -0.496  -15.5474  -29.2128   1.4663
 U9T  N2   N  NH1   0  -0.697  -13.6068  -28.3101   2.3703
 U9T  C3   C  CH2   0  -0.415  -17.1897  -30.7032   0.4061
 U9T  C1   C  CH3   0  -0.650  -18.6735  -32.1768   1.8257
 U9T  C2   C  CH1   0  -0.242  -17.9388  -30.8488   1.7252
 U9T  O1   O  O     0  -0.543  -13.7857  -28.6625   0.1429
 U9T  F1   F  F     0  -0.314   -9.9671  -28.3558   5.8468
 U9T  C15  C  CH2   0  -0.408  -16.9453  -30.6674   2.8665
 U9T  H1   H  HCH2  0   0.257  -15.8653  -29.3238  -0.5847
 U9T  H2   H  HCH2  0   0.218  -17.1650  -28.5531   0.3129
 U9T  H3   H  HCH2  0   0.246  -15.4421  -29.3335   3.5587
 U9T  H4   H  HCH2  0   0.227  -16.8720  -28.5141   2.9383
 U9T  H5   H  HCH2  0   0.246  -11.7483  -28.2940   1.4636
 U9T  H6   H  HCH2  0   0.228  -12.2616  -26.7191   2.0493
 U9T  H8   H  HCH2  0   0.253  -12.1128  -27.6032   4.4135
 U9T  H9   H  HCH2  0   0.258  -11.5472  -29.1291   3.7816
 U9T  H10  H  HCR6  0   0.265  -10.0116  -26.7236   1.6722
 U9T  H11  H  HCR6  0   0.258   -7.7070  -25.9375   1.8810
 U9T  H12  H  HCR6  0   0.274   -7.5475  -27.4727   5.8851
 U9T  H13  H  HNH1  0   0.396  -14.1231  -28.0199   3.1840
 U9T  H14  H  HCH2  0   0.231  -17.8795  -30.7683  -0.4393
 U9T  H15  H  HCH2  0   0.215  -16.4745  -31.5265   0.3015
 U9T  H16  H  HCH3  0   0.225  -19.1877  -32.2737   2.7839
 U9T  H17  H  HCH3  0   0.225  -19.4195  -32.2806   1.0359
 U9T  H18  H  HCH3  0   0.214  -17.9776  -33.0143   1.7369
 U9T  H19  H  HCH1  0   0.213  -18.6754  -30.0368   1.7892
 U9T  H20  H  HCH2  0   0.234  -17.4565  -30.6999   3.8320
 U9T  H21  H  HCH2  0   0.217  -16.2294  -31.4961   2.8578
 U9T  H7   H  HCR6  0   0.263   -6.4458  -26.3067   3.9845

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
 U9T  O1   C5   double    1.228  0.020  1.228
 U9T  C4   C3   single    1.521  0.020  1.521
 U9T  C4   N1   single    1.454  0.020  1.454
 U9T  C3   C2   single    1.524  0.020  1.524
 U9T  C5   N1   single    1.366  0.020  1.366
 U9T  C5   N2   single    1.365  0.020  1.365
 U9T  N1   C14  single    1.452  0.020  1.452
 U9T  C2   C1   single    1.521  0.020  1.521
 U9T  C2   C15  single    1.524  0.020  1.524
 U9T  C6   N2   single    1.445  0.020  1.445
 U9T  C6   C7   single    1.521  0.020  1.521
 U9T  C9   C10  aromatic  1.390  0.020  1.390
 U9T  C9   C8   aromatic  1.392  0.020  1.392
 U9T  C10  C11  aromatic  1.386  0.020  1.386
 U9T  C15  C14  single    1.524  0.020  1.524
 U9T  C7   C8   single    1.505  0.020  1.505
 U9T  C8   C13  aromatic  1.390  0.020  1.390
 U9T  C11  C12  aromatic  1.389  0.020  1.389
 U9T  C13  C12  aromatic  1.379  0.020  1.379
 U9T  C13  F1   single    1.347  0.020  1.347
 U9T  C4   H1   single    0.970  0.020  1.090
 U9T  C4   H2   single    0.970  0.020  1.090
 U9T  C14  H3   single    0.970  0.020  1.090
 U9T  C14  H4   single    0.970  0.020  1.090
 U9T  C6   H5   single    0.970  0.020  1.090
 U9T  C6   H6   single    0.970  0.020  1.090
 U9T  C11  H7   single    0.930  0.020  1.080
 U9T  C7   H8   single    0.970  0.020  1.090
 U9T  C7   H9   single    0.970  0.020  1.090
 U9T  C9   H10  single    0.930  0.020  1.080
 U9T  C10  H11  single    0.930  0.020  1.080
 U9T  C12  H12  single    0.930  0.020  1.080
 U9T  N2   H13  single    0.890  0.020  1.040
 U9T  C3   H14  single    0.970  0.020  1.090
 U9T  C3   H15  single    0.970  0.020  1.090
 U9T  C1   H16  single    0.970  0.020  1.090
 U9T  C1   H17  single    0.970  0.020  1.090
 U9T  C1   H18  single    0.970  0.020  1.090
 U9T  C2   H19  single    0.970  0.020  1.090
 U9T  C15  H20  single    0.970  0.020  1.090
 U9T  C15  H21  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
 U9T  H2   C4   H1   107.15  3.000
 U9T  H2   C4   C3   109.47  3.000
 U9T  H1   C4   C3   110.29  3.000
 U9T  H2   C4   N1   109.43  3.000
 U9T  H1   C4   N1   108.97  3.000
 U9T  C3   C4   N1   111.43  3.000
 U9T  H4   C14  H3   107.43  3.000
 U9T  H4   C14  C15  109.57  3.000
 U9T  H3   C14  C15  107.83  3.000
 U9T  H4   C14  N1   110.09  3.000
 U9T  H3   C14  N1   110.63  3.000
 U9T  C15  C14  N1   111.18  3.000
 U9T  O1   C5   N2   121.36  3.000
 U9T  N2   C5   N1   116.54  3.000
 U9T  O1   C5   N1   122.06  3.000
 U9T  H6   C6   H5   107.06  3.000
 U9T  H6   C6   N2   111.39  3.000
 U9T  H5   C6   N2   108.60  3.000
 U9T  H6   C6   C7   110.51  3.000
 U9T  H5   C6   C7   110.20  3.000
 U9T  N2   C6   C7   109.04  3.000
 U9T  H7   C11  C12  119.67  3.000
 U9T  H7   C11  C10  120.54  3.000
 U9T  C12  C11  C10  119.80  3.000
 U9T  H9   C7   H8   105.80  3.000
 U9T  H9   C7   C8   109.39  3.000
 U9T  H8   C7   C8   108.94  3.000
 U9T  H9   C7   C6   108.28  3.000
 U9T  H8   C7   C6   109.12  3.000
 U9T  C8   C7   C6   114.92  3.000
 U9T  C13  C8   C9   116.34  3.000
 U9T  C13  C8   C7   119.50  3.000
 U9T  C9   C8   C7   124.15  3.000
 U9T  H10  C9   C10  118.63  3.000
 U9T  H10  C9   C8   119.83  3.000
 U9T  C10  C9   C8   121.55  3.000
 U9T  H11  C10  C9   119.65  3.000
 U9T  H11  C10  C11  120.23  3.000
 U9T  C9   C10  C11  120.11  3.000
 U9T  H12  C12  C13  120.14  3.000
 U9T  H12  C12  C11  121.30  3.000
 U9T  C13  C12  C11  118.57  3.000
 U9T  F1   C13  C12  118.45  3.000
 U9T  F1   C13  C8   117.91  3.000
 U9T  C12  C13  C8   123.64  3.000
 U9T  C5   N1   C14  124.89  3.000
 U9T  C14  N1   C4   114.55  3.000
 U9T  C5   N1   C4   119.37  3.000
 U9T  H13  N2   C6   115.08  3.000
 U9T  H13  N2   C5   118.97  3.000
 U9T  C6   N2   C5   121.56  3.000
 U9T  H15  C3   H14  107.06  3.000
 U9T  H15  C3   C2   109.38  3.000
 U9T  H14  C3   C2   110.71  3.000
 U9T  H15  C3   C4   109.18  3.000
 U9T  H14  C3   C4   108.94  3.000
 U9T  C2   C3   C4   111.47  3.000
 U9T  H18  C1   H17  107.68  3.000
 U9T  H18  C1   H16  107.66  3.000
 U9T  H17  C1   H16  107.74  3.000
 U9T  H18  C1   C2   110.87  3.000
 U9T  H17  C1   C2   111.43  3.000
 U9T  H16  C1   C2   111.29  3.000
 U9T  H19  C2   C15  107.80  3.000
 U9T  H19  C2   C1   108.53  3.000
 U9T  C15  C2   C1   111.67  3.000
 U9T  H19  C2   C3   108.03  3.000
 U9T  C15  C2   C3   108.45  3.000
 U9T  C1   C2   C3   112.21  3.000
 U9T  H21  C15  H20  106.87  3.000
 U9T  H21  C15  C2   109.28  3.000
 U9T  H20  C15  C2   110.68  3.000
 U9T  H21  C15  C14  109.05  3.000
 U9T  H20  C15  C14  108.58  3.000
 U9T  C2   C15  C14  112.23  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
 U9T  CONST_01  C8   C9   C10  C11     0.00   0.0  0
 U9T  CONST_02  C8   C13  C12  C11     0.00   0.0  0
 U9T  CONST_03  C12  C11  C10  C9      0.00   0.0  0
 U9T  CONST_04  C12  C13  C8   C9      0.00   0.0  0
 U9T  CONST_05  C13  C8   C9   C10     0.00   0.0  0
 U9T  CONST_06  C13  C12  C11  C10     0.00   0.0  0
 U9T  CONST_07  F1   C13  C12  C11   180.00   0.0  0
 U9T  CONST_08  C10  C9   C8   C7    180.00   0.0  0
 U9T  CONST_09  C12  C13  C8   C7    180.00   0.0  0
 U9T  CONST_10  F1   C13  C8   C9    180.00   0.0  0
 U9T  CONST_11  H10  C9   C10  C11   180.00   0.0  0
 U9T  CONST_12  H11  C10  C9   C8    180.00   0.0  0
 U9T  CONST_13  H12  C12  C13  C8    180.00   0.0  0
 U9T  CONST_14  H7   C11  C10  C9    180.00   0.0  0
 U9T  CONST_15  H12  C12  C11  C10   180.00   0.0  0
 U9T  CONST_16  H11  C10  C11  C12   180.00   0.0  0
 U9T  CONST_17  H10  C9   C8   C13   180.00   0.0  0
 U9T  CONST_18  H7   C11  C12  C13   180.00   0.0  0
 U9T  CONST_20  O1   C5   N1   C14   180.00   0.0  0
 U9T  CONST_21  N2   C5   N1   C4    180.00   0.0  0
 U9T  CONST_22  N2   C5   N1   C14     0.00   0.0  0
 U9T  CONST_23  N1   C5   N2   C6    180.00   0.0  0
 U9T  CONST_25  O1   C5   N2   C6      0.00   0.0  0
 U9T  Var_01    C15  C14  N1   C4     53.44  30.0  1
 U9T  Var_02    C3   C4   N1   C14   -54.41  30.0  1
 U9T  Var_03    C2   C3   C4   N1     55.20  30.0  1
 U9T  Var_04    C2   C15  C14  N1    -53.87  30.0  1
 U9T  Var_05    C3   C4   N1   C5    137.46  30.0  1
 U9T  Var_06    C15  C14  N1   C5   -139.18  30.0  1
 U9T  Var_07    H3   C14  N1   C4    173.23  30.0  1
 U9T  Var_08    H4   C14  N1   C4    -68.18  30.0  1
 U9T  Var_09    H1   C4   N1   C14  -176.34  30.0  1
 U9T  Var_10    H2   C4   N1   C14    66.79  30.0  1
 U9T  Var_11    H14  C3   C4   N1    177.66  30.0  1
 U9T  Var_12    H15  C3   C4   N1    -65.75  30.0  1
 U9T  Var_13    H20  C15  C14  N1   -176.54  30.0  1
 U9T  Var_14    H21  C15  C14  N1     67.36  30.0  1
 U9T  Var_15    H1   C4   C3   C2    176.36  30.0  1
 U9T  Var_16    H2   C4   C3   C2    -65.98  30.0  1
 U9T  Var_17    H3   C14  C15  C2   -175.31  30.0  1
 U9T  Var_18    H4   C14  C15  C2     68.06  30.0  1
 U9T  Var_19    C9   C8   C7   C6     -0.56  30.0  2
 U9T  Var_20    C13  C8   C7   C6    179.75  30.0  2
 U9T  Var_21    H1   C4   N1   C5     15.53  30.0  1
 U9T  Var_22    H2   C4   N1   C5   -101.34  30.0  1
 U9T  Var_23    H3   C14  N1   C5    -19.39  30.0  1
 U9T  Var_24    H4   C14  N1   C5     99.20  30.0  1
 U9T  Var_25    H8   C7   C8   C9   -123.33  30.0  3
 U9T  Var_26    H9   C7   C8   C9    121.46  30.0  3
 U9T  Var_27    H8   C7   C8   C13    56.98  30.0  3
 U9T  Var_28    H9   C7   C8   C13   -58.23  30.0  3
 U9T  Var_29    N2   C6   C7   C8   -179.21  30.0  1
 U9T  Var_30    H5   C6   C7   C8     61.68  30.0  1
 U9T  Var_31    H6   C6   C7   C8    -56.44  30.0  1
 U9T  Var_32    C7   C6   N2   C5   -153.21  30.0  2
 U9T  Var_33    H5   C6   N2   C5    -33.11  30.0  2
 U9T  Var_34    H6   C6   N2   C5     84.56  30.0  2
 U9T  Var_35    H13  N2   C6   C7     50.58  30.0  3
 U9T  Var_36    H8   C7   C6   N2    -56.53  30.0  3
 U9T  Var_37    H9   C7   C6   N2     58.17  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
 U9T  chir_01  C2  C3  C1  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
 U9T  plan-1  C11  0.020
 U9T  plan-1  C7   0.020
 U9T  plan-1  C8   0.020
 U9T  plan-1  C9   0.020
 U9T  plan-1  C10  0.020
 U9T  plan-1  C12  0.020
 U9T  plan-1  C13  0.020
 U9T  plan-1  F1   0.020
 U9T  plan-1  H10  0.020
 U9T  plan-1  H11  0.020
 U9T  plan-1  H12  0.020
 U9T  plan-1  H7   0.020
 U9T  plan-2  C4   0.020
 U9T  plan-2  C14  0.020
 U9T  plan-2  C5   0.020
 U9T  plan-2  C6   0.020
 U9T  plan-2  N1   0.020
 U9T  plan-2  N2   0.020
 U9T  plan-2  O1   0.020
 U9T  plan-2  H13  0.020

