# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 21:14:59 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: 1-[(2,4-dichlorophenoxy)acetyl]-N-(2-sulfanylethyl)piperidine-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: SCCNC(=O)C1CCN(CC1)C(=O)COc2ccc(Cl)cc2Cl
#
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
 20H  20H  1-[(2,4-dichlorophenoxy)acetyl]-N-(2-sulfanylethyl)piperidine-4-carboxamide  ligand  44  24  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_20H
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
 20H  CL1   CL  CL    0  -0.124  -7.4141  -2.4756  -0.7017
 20H  CL2   CL  CL    0  -0.094  -4.8206   2.2205  -1.0506
 20H  C02   C   CR6   0  -0.072  -5.9835  -1.5329  -0.4485
 20H  C03   C   CR16  0  -0.193  -4.8610  -2.1157   0.1081
 20H  C04   C   CR16  0  -0.388  -3.7180  -1.3540   0.3095
 20H  C05   C   CR6   0   0.474  -3.6863  -0.0086  -0.0434
 20H  O06   O   O2    0  -0.441  -2.6362   0.8070   0.1094
 20H  C07   C   CH2   0  -0.333  -1.4610   0.2837   0.6731
 20H  C08   C   C     0   0.531  -0.4435   1.4206   0.7081
 20H  N09   N   NT    0  -0.452   0.7534   1.1265   1.2500
 20H  C10   C   CH2   0  -0.332   1.1615  -0.1853   1.7216
 20H  C11   C   CH2   0  -0.412   2.3049  -0.7318   0.8770
 20H  C12   C   CH1   0  -0.403   3.4753   0.2572   0.8492
 20H  C13   C   C     0   0.579   4.5667  -0.2640  -0.0653
 20H  N14   N   NH1   0  -0.631   5.6581  -0.7440   0.5547
 20H  C15   C   CH2   0  -0.282   6.7921  -1.2917  -0.1494
 20H  C16   C   CH2   0  -0.553   7.7803  -0.2056  -0.5600
 20H  S17   S   S2    0  -0.259   9.1708  -0.9949  -1.4376
 20H  O18   O   O     0  -0.497   4.4403  -0.2704  -1.2822
 20H  C19   C   CH2   0  -0.419   2.9901   1.6351   0.3990
 20H  C20   C   CH2   0  -0.319   1.8276   2.1059   1.2626
 20H  O21   O   O     0  -0.479  -0.7337   2.5190   0.2675
 20H  C22   C   CR6   0  -0.166  -4.8380   0.5538  -0.6055
 20H  C24   C   CR16  0  -0.161  -5.9816  -0.1936  -0.8097
 20H  H10   H   HCH2  0   0.256   1.4816  -0.0934   2.7642
 20H  H20   H   HCH2  0   0.271   1.4506   3.0622   0.9112
 20H  H10A  H   HCH2  0   0.279   0.3299  -0.8843   1.7165
 20H  H20A  H   HCH2  0   0.245   2.1588   2.2456   2.2967
 20H  H11   H   HCH2  0   0.256   2.6240  -1.6898   1.2929
 20H  H11A  H   HCH2  0   0.241   1.9491  -0.9184  -0.1398
 20H  H12   H   HCH1  0   0.257   3.8642   0.3475   1.8706
 20H  H03   H   HCR6  0   0.290  -4.8612  -3.1595   0.3895
 20H  H04   H   HCR6  0   0.301  -2.8547  -1.8354   0.7470
 20H  HN14  H   HNH1  0   0.405   5.7169  -0.6747   1.5572
 20H  H24   H   HCR6  0   0.302  -6.8582   0.2661  -1.2446
 20H  H15   H   HCH2  0   0.264   7.2796  -2.0128   0.5066
 20H  H15A  H   HCH2  0   0.253   6.4421  -1.8335  -1.0287
 20H  H16   H   HCH2  0   0.274   7.2949   0.5157  -1.2159
 20H  H16A  H   HCH2  0   0.271   8.1525   0.3155   0.3216
 20H  H07   H   HCH2  0   0.272  -1.6466  -0.0940   1.6854
 20H  H07A  H   HCH2  0   0.269  -1.0754  -0.5480   0.0713
 20H  H19   H   HCH2  0   0.252   3.8003   2.3644   0.4660
 20H  H19A  H   HCH2  0   0.238   2.6714   1.5957  -0.6450
 20H  HS17  H   HSH1  0   0.229   9.8715   0.1165  -1.6846

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
 20H  CL1   C02   single    1.732  0.020  1.732
 20H  C22   CL2   single    1.725  0.020  1.725
 20H  C03   C02   aromatic  1.382  0.020  1.382
 20H  C02   C24   aromatic  1.387  0.020  1.387
 20H  H03   C03   single    0.930  0.020  1.080
 20H  C03   C04   aromatic  1.388  0.020  1.388
 20H  H04   C04   single    0.930  0.020  1.080
 20H  C04   C05   aromatic  1.391  0.020  1.391
 20H  C05   O06   single    1.338  0.020  1.338
 20H  C05   C22   aromatic  1.400  0.020  1.400
 20H  C07   O06   single    1.405  0.020  1.405
 20H  H07   C07   single    0.970  0.020  1.090
 20H  C07   H07A  single    0.970  0.020  1.090
 20H  C07   C08   single    1.526  0.020  1.526
 20H  N09   C08   single    1.346  0.020  1.346
 20H  C08   O21   double    1.219  0.020  1.219
 20H  C10   N09   single    1.453  0.020  1.453
 20H  N09   C20   single    1.454  0.020  1.454
 20H  C11   C10   single    1.523  0.020  1.523
 20H  H10   C10   single    0.970  0.020  1.090
 20H  C10   H10A  single    0.970  0.020  1.090
 20H  H11A  C11   single    0.970  0.020  1.090
 20H  H11   C11   single    0.970  0.020  1.090
 20H  C11   C12   single    1.533  0.020  1.533
 20H  C13   C12   single    1.516  0.020  1.516
 20H  C12   H12   single    0.970  0.020  1.090
 20H  C12   C19   single    1.529  0.020  1.529
 20H  O18   C13   double    1.224  0.020  1.224
 20H  N14   C13   single    1.344  0.020  1.344
 20H  C15   N14   single    1.443  0.020  1.443
 20H  N14   HN14  single    0.860  0.020  1.020
 20H  C16   C15   single    1.525  0.020  1.525
 20H  H15   C15   single    0.970  0.020  1.090
 20H  C15   H15A  single    0.970  0.020  1.090
 20H  S17   C16   single    1.824  0.020  1.824
 20H  H16A  C16   single    0.970  0.020  1.090
 20H  C16   H16   single    0.970  0.020  1.090
 20H  S17   HS17  single    1.200  0.020  1.300
 20H  H19A  C19   single    0.970  0.020  1.090
 20H  C19   H19   single    0.970  0.020  1.090
 20H  C19   C20   single    1.523  0.020  1.523
 20H  C20   H20   single    0.970  0.020  1.090
 20H  C20   H20A  single    0.970  0.020  1.090
 20H  C24   C22   aromatic  1.381  0.020  1.381
 20H  C24   H24   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
 20H  C24   C02  C03  120.73  3.000
 20H  C24   C02  CL1  119.25  3.000
 20H  C03   C02  CL1  120.02  3.000
 20H  H03   C03  C04  119.49  3.000
 20H  C04   C03  C02  119.73  3.000
 20H  H03   C03  C02  120.79  3.000
 20H  H04   C04  C05  121.01  3.000
 20H  C05   C04  C03  120.83  3.000
 20H  H04   C04  C03  118.16  3.000
 20H  C22   C05  O06  116.53  3.000
 20H  C22   C05  C04  118.15  3.000
 20H  O06   C05  C04  125.32  3.000
 20H  C07   O06  C05  118.38  3.000
 20H  H07A  C07  H07  107.76  3.000
 20H  H07A  C07  C08  110.06  3.000
 20H  H07   C07  C08  110.39  3.000
 20H  C08   C07  O06  106.83  3.000
 20H  H07A  C07  O06  110.89  3.000
 20H  H07   C07  O06  110.93  3.000
 20H  O21   C08  N09  123.65  3.000
 20H  O21   C08  C07  120.29  3.000
 20H  N09   C08  C07  116.06  3.000
 20H  C20   N09  C10  113.45  3.000
 20H  C20   N09  C08  120.88  3.000
 20H  C10   N09  C08  125.29  3.000
 20H  H10A  C10  H10  106.40  3.000
 20H  H10A  C10  C11  109.95  3.000
 20H  H10   C10  C11  109.81  3.000
 20H  H10A  C10  N09  111.38  3.000
 20H  H10   C10  N09  108.40  3.000
 20H  C11   C10  N09  110.79  3.000
 20H  H11A  C11  H11  107.43  3.000
 20H  H11   C11  C12  110.48  3.000
 20H  H11A  C11  C12  109.99  3.000
 20H  C12   C11  C10  110.60  3.000
 20H  H11   C11  C10  108.84  3.000
 20H  H11A  C11  C10  109.43  3.000
 20H  H12   C12  C19  108.22  3.000
 20H  C19   C12  C13  111.15  3.000
 20H  H12   C12  C13  109.56  3.000
 20H  C19   C12  C11  110.16  3.000
 20H  H12   C12  C11  107.88  3.000
 20H  C13   C12  C11  109.81  3.000
 20H  O18   C13  N14  122.74  3.000
 20H  N14   C13  C12  115.41  3.000
 20H  O18   C13  C12  121.82  3.000
 20H  HN14  N14  C15  117.79  3.000
 20H  HN14  N14  C13  118.84  3.000
 20H  C15   N14  C13  123.28  3.000
 20H  H15A  C15  H15  107.47  3.000
 20H  H15A  C15  C16  110.17  3.000
 20H  H15   C15  C16  110.09  3.000
 20H  H15A  C15  N14  109.26  3.000
 20H  H15   C15  N14  107.99  3.000
 20H  C16   C15  N14  111.74  3.000
 20H  H16A  C16  H16  108.83  3.000
 20H  H16   C16  S17  109.67  3.000
 20H  H16A  C16  S17  109.62  3.000
 20H  H16   C16  C15  110.19  3.000
 20H  H16A  C16  C15  110.13  3.000
 20H  S17   C16  C15  108.39  3.000
 20H  HS17  S17  C16   97.40  3.000
 20H  H19A  C19  H19  107.41  3.000
 20H  H19   C19  C20  108.97  3.000
 20H  H19A  C19  C20  109.30  3.000
 20H  C20   C19  C12  110.73  3.000
 20H  H19   C19  C12  110.39  3.000
 20H  H19A  C19  C12  109.97  3.000
 20H  H20A  C20  H20  107.34  3.000
 20H  H20A  C20  C19  110.13  3.000
 20H  H20   C20  C19  110.71  3.000
 20H  H20A  C20  N09  108.53  3.000
 20H  H20   C20  N09  109.50  3.000
 20H  C19   C20  N09  110.55  3.000
 20H  C24   C22  C05  121.55  3.000
 20H  C24   C22  CL2  119.53  3.000
 20H  C05   C22  CL2  118.92  3.000
 20H  H24   C24  C22  120.04  3.000
 20H  H24   C24  C02  120.94  3.000
 20H  C22   C24  C02  119.02  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
 20H  CONST_01  C05   C04  C03  C02    0.00   0.0  0
 20H  CONST_02  C05   C22  C24  C02    0.00   0.0  0
 20H  CONST_03  C22   C24  C02  C03    0.00   0.0  0
 20H  CONST_04  C22   C05  C04  C03    0.00   0.0  0
 20H  CONST_05  C24   C02  C03  C04    0.00   0.0  0
 20H  CONST_06  C24   C22  C05  C04    0.00   0.0  0
 20H  CONST_07  C04   C03  C02  CL1  180.00   0.0  0
 20H  CONST_08  C22   C24  C02  CL1  180.00   0.0  0
 20H  CONST_09  C04   C05  C22  CL2  180.00   0.0  0
 20H  CONST_10  C02   C24  C22  CL2  180.00   0.0  0
 20H  CONST_11  O06   C05  C04  C03  180.00   0.0  0
 20H  CONST_12  C24   C22  C05  O06  180.00   0.0  0
 20H  CONST_13  H04   C04  C03  C02  180.00   0.0  0
 20H  CONST_14  H24   C24  C02  C03  180.00   0.0  0
 20H  CONST_15  H03   C03  C04  C05  180.00   0.0  0
 20H  CONST_16  C10   N09  C08  C07    0.00   0.0  0
 20H  CONST_17  C20   N09  C08  C07  180.00   0.0  0
 20H  CONST_18  O21   C08  N09  C10  180.00   0.0  0
 20H  CONST_19  O21   C08  N09  C20    0.00   0.0  0
 20H  CONST_20  C15   N14  C13  C12  180.00   0.0  0
 20H  CONST_21  HN14  N14  C13  C12    0.00   0.0  0
 20H  CONST_22  O18   C13  N14  C15    0.00   0.0  0
 20H  Var_01    C12   C11  C10  N09   55.23  30.0  1
 20H  Var_02    C12   C19  C20  N09  -55.63  30.0  1
 20H  Var_03    C19   C20  N09  C10   58.47  30.0  1
 20H  Var_04    C20   N09  C10  C11  -58.39  30.0  1
 20H  Var_05    C22   C05  O06  C07  179.84  30.0  2
 20H  Var_06    C08   C07  O06  C05  179.34  30.0  1
 20H  Var_07    N09   C08  C07  O06  178.45  30.0  3
 20H  Var_08    C16   C15  N14  C13   85.90  30.0  1
 20H  Var_09    S17   C16  C15  N14  179.97  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
 20H  chir_01  C12  C11  C13  C19  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
 20H  plan-1  CL1   0.020
 20H  plan-1  CL2   0.020
 20H  plan-1  C02   0.020
 20H  plan-1  C03   0.020
 20H  plan-1  C04   0.020
 20H  plan-1  C05   0.020
 20H  plan-1  O06   0.020
 20H  plan-1  C22   0.020
 20H  plan-1  C24   0.020
 20H  plan-1  H03   0.020
 20H  plan-1  H04   0.020
 20H  plan-1  H24   0.020
 20H  plan-2  C07   0.020
 20H  plan-2  C08   0.020
 20H  plan-2  N09   0.020
 20H  plan-2  C10   0.020
 20H  plan-2  C20   0.020
 20H  plan-2  O21   0.020
 20H  plan-3  C12   0.020
 20H  plan-3  C13   0.020
 20H  plan-3  N14   0.020
 20H  plan-3  C15   0.020
 20H  plan-3  O18   0.020
 20H  plan-3  HN14  0.020

