# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 12:21:16 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: (4-chlorophenyl)-[(3~{S})-3-oxidanylpiperidin-1-yl]methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1CCCN(C1)C(=O)c2ccc(Cl)cc2
#
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
 M2E  M2E  (4-chlorophenyl)-[(3~{S})-3-oxidanylpiperidin-1-yl]methanone  ligand  30  16  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_M2E
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
 M2E  C10  C   CR6   0  -0.069  -0.5669  -0.8055   0.0662
 M2E  C11  C   CR16  0  -0.261  -1.1575  -0.3105   1.2250
 M2E  O01  O   OH1   0  -0.668   2.5857   2.8874  -0.4918
 M2E  C02  C   CH1   0   0.077   2.5707   1.4816  -0.5746
 M2E  C03  C   CH2   0  -0.472   4.0035   0.9785  -0.5248
 M2E  C04  C   CH2   0  -0.447   4.0393  -0.5462  -0.4968
 M2E  C05  C   CH2   0  -0.318   3.1726  -1.0876   0.6317
 M2E  N06  N   NT    0  -0.449   1.8146  -0.5704   0.5331
 M2E  C07  C   CH2   0  -0.354   1.7554   0.8811   0.5767
 M2E  C08  C   C     0   0.521   0.8223  -1.3633   0.0759
 M2E  O09  O   O     0  -0.483   0.9983  -2.5183  -0.2881
 M2E  C12  C   CR16  0  -0.200  -2.4793   0.1069   1.2217
 M2E  C13  C   CR6   0  -0.041  -3.2038   0.0379   0.0419
 M2E  CL1  CL  CL    0  -0.121  -4.8504   0.5736   0.0236
 M2E  C15  C   CR16  0  -0.202  -2.6352  -0.4533  -1.1235
 M2E  C16  C   CR16  0  -0.277  -1.3198  -0.8894  -1.0999
 M2E  H1   H   HCR6  0   0.279  -0.5917  -0.2550   2.1467
 M2E  H3   H   HCH1  0   0.203   2.1131   1.1463  -1.5182
 M2E  H4   H   HCH2  0   0.247   4.5630   1.3582  -1.3828
 M2E  H5   H   HCH2  0   0.225   4.4857   1.3725   0.3772
 M2E  H6   H   HCH2  0   0.232   3.6873  -0.9519  -1.4497
 M2E  H7   H   HCH2  0   0.248   5.0645  -0.8967  -0.3633
 M2E  H8   H   HCH2  0   0.266   3.1495  -2.1737   0.6266
 M2E  H9   H   HCH2  0   0.247   3.5796  -0.7706   1.5970
 M2E  H10  H   HCH2  0   0.248   2.1650   1.2252   1.5315
 M2E  H11  H   HCH2  0   0.274   0.7252   1.2267   0.5196
 M2E  H12  H   HCR6  0   0.286  -2.9342   0.4812   2.1283
 M2E  H13  H   HCR6  0   0.285  -3.2100  -0.5025  -2.0381
 M2E  H14  H   HCR6  0   0.273  -0.8790  -1.2832  -2.0064
 M2E  H2   H   HOH1  0   0.453   1.7003   3.2147  -0.6789

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
 M2E  CL1  C13  single    1.732  0.020  1.732
 M2E  C12  C13  aromatic  1.386  0.020  1.386
 M2E  C12  C11  aromatic  1.386  0.020  1.386
 M2E  C13  C15  aromatic  1.387  0.020  1.387
 M2E  C11  C10  aromatic  1.392  0.020  1.392
 M2E  C15  C16  aromatic  1.386  0.020  1.386
 M2E  C10  C16  aromatic  1.391  0.020  1.391
 M2E  C10  C08  single    1.497  0.020  1.497
 M2E  O09  C08  double    1.224  0.020  1.224
 M2E  C08  N06  single    1.350  0.020  1.350
 M2E  N06  C07  single    1.453  0.020  1.453
 M2E  N06  C05  single    1.456  0.020  1.456
 M2E  C07  C02  single    1.533  0.020  1.533
 M2E  C05  C04  single    1.522  0.020  1.522
 M2E  C04  C03  single    1.525  0.020  1.525
 M2E  C02  C03  single    1.519  0.020  1.519
 M2E  C02  O01  single    1.408  0.020  1.408
 M2E  C11  H1   single    0.930  0.020  1.080
 M2E  O01  H2   single    0.850  0.020  0.980
 M2E  C02  H3   single    0.970  0.020  1.090
 M2E  C03  H4   single    0.970  0.020  1.090
 M2E  C03  H5   single    0.970  0.020  1.090
 M2E  C04  H6   single    0.970  0.020  1.090
 M2E  C04  H7   single    0.970  0.020  1.090
 M2E  C05  H8   single    0.970  0.020  1.090
 M2E  C05  H9   single    0.970  0.020  1.090
 M2E  C07  H10  single    0.970  0.020  1.090
 M2E  C07  H11  single    0.970  0.020  1.090
 M2E  C12  H12  single    0.930  0.020  1.080
 M2E  C15  H13  single    0.930  0.020  1.080
 M2E  C16  H14  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
 M2E  C16  C10  C08  119.04  3.000
 M2E  C08  C10  C11  121.39  3.000
 M2E  C16  C10  C11  119.34  3.000
 M2E  H1   C11  C12  119.00  3.000
 M2E  H1   C11  C10  120.35  3.000
 M2E  C12  C11  C10  120.65  3.000
 M2E  H2   O01  C02  108.56  3.000
 M2E  H3   C02  C07  107.65  3.000
 M2E  H3   C02  C03  108.61  3.000
 M2E  C07  C02  C03  110.31  3.000
 M2E  H3   C02  O01  111.03  3.000
 M2E  C03  C02  O01  108.58  3.000
 M2E  C07  C02  O01  110.64  3.000
 M2E  H5   C03  H4   107.22  3.000
 M2E  H5   C03  C04  109.50  3.000
 M2E  H4   C03  C04  110.47  3.000
 M2E  H5   C03  C02  108.84  3.000
 M2E  H4   C03  C02  110.01  3.000
 M2E  C04  C03  C02  110.72  3.000
 M2E  H7   C04  H6   106.85  3.000
 M2E  H7   C04  C05  109.26  3.000
 M2E  H6   C04  C05  109.30  3.000
 M2E  H7   C04  C03  110.20  3.000
 M2E  H6   C04  C03  110.31  3.000
 M2E  C05  C04  C03  110.83  3.000
 M2E  H9   C05  H8   107.55  3.000
 M2E  H9   C05  N06  107.67  3.000
 M2E  H8   C05  N06  109.57  3.000
 M2E  H9   C05  C04  109.82  3.000
 M2E  H8   C05  C04  111.36  3.000
 M2E  N06  C05  C04  110.76  3.000
 M2E  C08  N06  C07  124.53  3.000
 M2E  C07  N06  C05  112.99  3.000
 M2E  C08  N06  C05  119.98  3.000
 M2E  H11  C07  H10  107.47  3.000
 M2E  H11  C07  N06  110.74  3.000
 M2E  H10  C07  N06  108.96  3.000
 M2E  H11  C07  C02  109.85  3.000
 M2E  H10  C07  C02  109.45  3.000
 M2E  N06  C07  C02  110.31  3.000
 M2E  O09  C08  N06  123.32  3.000
 M2E  N06  C08  C10  117.74  3.000
 M2E  O09  C08  C10  118.90  3.000
 M2E  H12  C12  C13  120.73  3.000
 M2E  H12  C12  C11  120.23  3.000
 M2E  C13  C12  C11  119.04  3.000
 M2E  C15  C13  CL1  119.38  3.000
 M2E  C15  C13  C12  121.24  3.000
 M2E  CL1  C13  C12  119.38  3.000
 M2E  H13  C15  C16  120.30  3.000
 M2E  H13  C15  C13  120.60  3.000
 M2E  C16  C15  C13  119.10  3.000
 M2E  H14  C16  C15  119.13  3.000
 M2E  H14  C16  C10  120.26  3.000
 M2E  C15  C16  C10  120.60  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
 M2E  CONST_01  C13  C12  C11  C10    0.00   0.0  0
 M2E  CONST_02  C13  C15  C16  C10    0.00   0.0  0
 M2E  CONST_03  C15  C13  C12  C11    0.00   0.0  0
 M2E  CONST_04  C15  C16  C10  C11    0.00   0.0  0
 M2E  CONST_05  C16  C15  C13  C12    0.00   0.0  0
 M2E  CONST_06  C16  C10  C11  C12    0.00   0.0  0
 M2E  CONST_07  CL1  C13  C12  C11  180.00   0.0  0
 M2E  CONST_08  C12  C11  C10  C08  180.00   0.0  0
 M2E  CONST_09  C15  C16  C10  C08  180.00   0.0  0
 M2E  CONST_10  C16  C15  C13  CL1  180.00   0.0  0
 M2E  CONST_12  C05  N06  C08  C10  180.00   0.0  0
 M2E  CONST_13  H12  C12  C11  C10  180.00   0.0  0
 M2E  CONST_14  H13  C15  C16  C10  180.00   0.0  0
 M2E  CONST_15  H14  C16  C10  C11  180.00   0.0  0
 M2E  CONST_16  H1   C11  C12  C13  180.00   0.0  0
 M2E  CONST_17  O09  C08  N06  C05    0.00   0.0  0
 M2E  Var_01    C05  N06  C07  C02   59.25  30.0  1
 M2E  Var_02    C05  C04  C03  C02  -53.44  30.0  1
 M2E  Var_03    N06  C05  C04  C03   54.77  30.0  1
 M2E  Var_04    C07  N06  C05  C04  -58.63  30.0  1
 M2E  Var_05    N06  C08  C10  C11  -56.09  30.0  2

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
 M2E  chir_01  C02  C07  C03  O01  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
 M2E  plan-1  C10  0.020
 M2E  plan-1  C11  0.020
 M2E  plan-1  C08  0.020
 M2E  plan-1  C12  0.020
 M2E  plan-1  C13  0.020
 M2E  plan-1  CL1  0.020
 M2E  plan-1  C15  0.020
 M2E  plan-1  C16  0.020
 M2E  plan-1  H1   0.020
 M2E  plan-1  H12  0.020
 M2E  plan-1  H13  0.020
 M2E  plan-1  H14  0.020
 M2E  plan-2  C10  0.020
 M2E  plan-2  C05  0.020
 M2E  plan-2  N06  0.020
 M2E  plan-2  C07  0.020
 M2E  plan-2  C08  0.020
 M2E  plan-2  O09  0.020

