# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 14:56:30 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: N-{1-[(2,4-dichlorophenoxy)acetyl]piperidin-4-yl}-4-sulfanylbutanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: SCCCC(=O)NC1CCN(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
 20G  20G  N-{1-[(2,4-dichlorophenoxy)acetyl]piperidin-4-yl}-4-sulfanylbutanamide  ligand  47  25  .  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_20G
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
 20G  CL1   CL  CL    0  -0.123    7.5948  -3.0083   0.1724
 20G  CL2   CL  CL    0  -0.094    5.6336   1.8780   1.2591
 20G  C02   C   CR6   0  -0.072    6.2762  -1.8859   0.1525
 20G  C03   C   CR16  0  -0.161    6.4667  -0.6075   0.6559
 20G  C04   C   CR6   0  -0.166    5.4116   0.2842   0.6377
 20G  C06   C   CR6   0   0.474    4.1597  -0.0732   0.1247
 20G  O07   O   O2    0  -0.441    3.2081   0.8680   0.1560
 20G  C08   C   CH2   0  -0.335    1.9463   0.5483  -0.3721
 20G  C09   C   C     0   0.533    1.0744   1.7930  -0.2357
 20G  N10   N   NT    0  -0.455   -0.1775   1.6907  -0.7198
 20G  C11   C   CH2   0  -0.314   -1.1038   2.8078  -0.6393
 20G  C12   C   CH2   0  -0.449   -2.3534   2.4250   0.1435
 20G  C13   C   CH1   0  -0.064   -3.0072   1.1858  -0.4564
 20G  N14   N   NH1   0  -0.648   -4.1729   0.8132   0.3155
 20G  C15   C   C     0   0.563   -5.2502   0.1984  -0.2061
 20G  C16   C   CH2   0  -0.582   -6.3418  -0.1136   0.7999
 20G  C17   C   CH2   0  -0.413   -7.5361  -0.8316   0.1911
 20G  C18   C   CH2   0  -0.553   -8.6117  -1.0718   1.2393
 20G  S19   S   S2    0  -0.257  -10.0183  -1.9325   0.4585
 20G  O20   O   O     0  -0.499   -5.3484  -0.0721  -1.3944
 20G  C21   C   CH2   0  -0.423   -1.9891   0.0512  -0.5531
 20G  C22   C   CH2   0  -0.332   -0.7528   0.5002  -1.3219
 20G  O23   O   O     0  -0.479    1.5196   2.8030   0.2808
 20G  C24   C   CR16  0  -0.388    3.9980  -1.3625  -0.3732
 20G  C25   C   CR16  0  -0.193    5.0512  -2.2670  -0.3608
 20G  H11   H   HCH2  0   0.272   -0.6086   3.6570  -0.1775
 20G  H21   H   HCH2  0   0.232   -1.6970  -0.2679   0.4519
 20G  H11A  H   HCH2  0   0.246   -1.3818   3.1040  -1.6562
 20G  H21A  H   HCH2  0   0.253   -2.4298  -0.8100  -1.0588
 20G  H12   H   HCH2  0   0.236   -2.0831   2.2389   1.1880
 20G  H22   H   HCH2  0   0.254   -1.0198   0.7269  -2.3594
 20G  H12A  H   HCH2  0   0.256   -3.0529   3.2632   0.1310
 20G  H22A  H   HCH2  0   0.279   -0.0319  -0.3112  -1.3615
 20G  H03   H   HCR6  0   0.302    7.4237  -0.3050   1.0581
 20G  H13   H   HCH1  0   0.244   -3.3484   1.4320  -1.4662
 20G  HN14  H   HNH1  0   0.397   -4.1365   0.9509   1.3138
 20G  H24   H   HCR6  0   0.301    3.0506  -1.6898  -0.7779
 20G  H25   H   HCR6  0   0.290    4.9015  -3.2632  -0.7534
 20G  H16   H   HCH2  0   0.269   -5.9126  -0.7124   1.6094
 20G  H16A  H   HCH2  0   0.270   -6.6617   0.8249   1.2639
 20G  H17   H   HCH2  0   0.240   -7.9491  -0.2383  -0.6272
 20G  H17A  H   HCH2  0   0.240   -7.2209  -1.7866  -0.2344
 20G  H08   H   HCH2  0   0.272    2.0296   0.2565  -1.4251
 20G  H18   H   HCH2  0   0.265   -8.2249  -1.6836   2.0548
 20G  H08A  H   HCH2  0   0.270    1.4962  -0.2889   0.1741
 20G  H18A  H   HCH2  0   0.264   -8.9560  -0.1256   1.6577
 20G  HS19  H   HSH1  0   0.223  -10.7715  -2.0834   1.5533

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
 20G  CL1   C02   single    1.732  0.020  1.732
 20G  C04   CL2   single    1.725  0.020  1.725
 20G  C25   C02   aromatic  1.382  0.020  1.382
 20G  C02   C03   aromatic  1.387  0.020  1.387
 20G  C03   C04   aromatic  1.382  0.020  1.382
 20G  C03   H03   single    0.930  0.020  1.080
 20G  C06   C04   aromatic  1.399  0.020  1.399
 20G  C24   C06   aromatic  1.392  0.020  1.392
 20G  C06   O07   single    1.339  0.020  1.339
 20G  C08   O07   single    1.405  0.020  1.405
 20G  H08   C08   single    0.970  0.020  1.090
 20G  C08   H08A  single    0.970  0.020  1.090
 20G  C08   C09   single    1.526  0.020  1.526
 20G  N10   C09   single    1.346  0.020  1.346
 20G  C09   O23   double    1.219  0.020  1.219
 20G  C22   N10   single    1.453  0.020  1.453
 20G  N10   C11   single    1.453  0.020  1.453
 20G  C12   C11   single    1.523  0.020  1.523
 20G  C11   H11   single    0.970  0.020  1.090
 20G  C11   H11A  single    0.970  0.020  1.090
 20G  C13   C12   single    1.524  0.020  1.524
 20G  H12   C12   single    0.970  0.020  1.090
 20G  C12   H12A  single    0.970  0.020  1.090
 20G  N14   C13   single    1.447  0.020  1.447
 20G  C21   C13   single    1.528  0.020  1.528
 20G  C13   H13   single    0.970  0.020  1.090
 20G  C15   N14   single    1.346  0.020  1.346
 20G  HN14  N14   single    0.860  0.020  1.020
 20G  C16   C15   single    1.517  0.020  1.517
 20G  C15   O20   double    1.223  0.020  1.223
 20G  C17   C16   single    1.521  0.020  1.521
 20G  H16A  C16   single    0.970  0.020  1.090
 20G  C16   H16   single    0.970  0.020  1.090
 20G  C18   C17   single    1.521  0.020  1.521
 20G  C17   H17   single    0.970  0.020  1.090
 20G  C17   H17A  single    0.970  0.020  1.090
 20G  S19   C18   single    1.825  0.020  1.825
 20G  H18A  C18   single    0.970  0.020  1.090
 20G  H18   C18   single    0.970  0.020  1.090
 20G  S19   HS19  single    1.200  0.020  1.300
 20G  H21   C21   single    0.970  0.020  1.090
 20G  H21A  C21   single    0.970  0.020  1.090
 20G  C21   C22   single    1.524  0.020  1.524
 20G  H22A  C22   single    0.970  0.020  1.090
 20G  C22   H22   single    0.970  0.020  1.090
 20G  H24   C24   single    0.930  0.020  1.080
 20G  C25   C24   aromatic  1.388  0.020  1.388
 20G  H25   C25   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
 20G  C25   C02  C03  120.71  3.000
 20G  C03   C02  CL1  119.25  3.000
 20G  C25   C02  CL1  120.03  3.000
 20G  H03   C03  C04  120.02  3.000
 20G  H03   C03  C02  120.95  3.000
 20G  C04   C03  C02  119.02  3.000
 20G  C06   C04  C03  121.55  3.000
 20G  C06   C04  CL2  118.89  3.000
 20G  C03   C04  CL2  119.56  3.000
 20G  C24   C06  O07  125.25  3.000
 20G  O07   C06  C04  116.60  3.000
 20G  C24   C06  C04  118.15  3.000
 20G  C08   O07  C06  118.01  3.000
 20G  H08A  C08  H08  107.86  3.000
 20G  H08A  C08  C09  110.11  3.000
 20G  H08   C08  C09  110.27  3.000
 20G  C09   C08  O07  107.10  3.000
 20G  H08A  C08  O07  110.81  3.000
 20G  H08   C08  O07  110.70  3.000
 20G  O23   C09  N10  123.72  3.000
 20G  O23   C09  C08  120.35  3.000
 20G  N10   C09  C08  115.93  3.000
 20G  C22   N10  C11  113.60  3.000
 20G  C11   N10  C09  120.96  3.000
 20G  C22   N10  C09  125.42  3.000
 20G  H11A  C11  H11  107.40  3.000
 20G  H11A  C11  C12  109.69  3.000
 20G  H11   C11  C12  110.61  3.000
 20G  H11A  C11  N10  108.56  3.000
 20G  H11   C11  N10  109.51  3.000
 20G  C12   C11  N10  110.98  3.000
 20G  H12A  C12  H12  107.43  3.000
 20G  H12A  C12  C13  110.17  3.000
 20G  H12   C12  C13  110.07  3.000
 20G  H12A  C12  C11  109.08  3.000
 20G  H12   C12  C11  109.29  3.000
 20G  C13   C12  C11  110.73  3.000
 20G  H13   C13  C21  108.45  3.000
 20G  H13   C13  N14  107.41  3.000
 20G  C21   C13  N14  112.30  3.000
 20G  H13   C13  C12  108.31  3.000
 20G  C21   C13  C12  110.06  3.000
 20G  N14   C13  C12  110.19  3.000
 20G  HN14  N14  C15  118.36  3.000
 20G  HN14  N14  C13  117.64  3.000
 20G  C15   N14  C13  123.77  3.000
 20G  O20   C15  C16  122.77  3.000
 20G  O20   C15  N14  122.83  3.000
 20G  C16   C15  N14  114.39  3.000
 20G  H16A  C16  H16  105.67  3.000
 20G  H16   C16  C17  110.23  3.000
 20G  H16A  C16  C17  110.18  3.000
 20G  H16   C16  C15  108.71  3.000
 20G  H16A  C16  C15  108.36  3.000
 20G  C17   C16  C15  113.37  3.000
 20G  H17A  C17  H17  107.00  3.000
 20G  H17A  C17  C18  109.55  3.000
 20G  H17   C17  C18  109.56  3.000
 20G  H17A  C17  C16  110.01  3.000
 20G  H17   C17  C16  109.90  3.000
 20G  C18   C17  C16  110.73  3.000
 20G  H18A  C18  H18  108.17  3.000
 20G  H18   C18  S19  109.20  3.000
 20G  H18A  C18  S19  109.28  3.000
 20G  H18   C18  C17  110.68  3.000
 20G  H18A  C18  C17  110.53  3.000
 20G  S19   C18  C17  108.95  3.000
 20G  HS19  S19  C18   97.88  3.000
 20G  H21A  C21  H21  107.65  3.000
 20G  H21A  C21  C22  109.05  3.000
 20G  H21   C21  C22  109.44  3.000
 20G  C22   C21  C13  110.73  3.000
 20G  H21A  C21  C13  110.26  3.000
 20G  H21   C21  C13  109.65  3.000
 20G  H22A  C22  H22  106.38  3.000
 20G  H22   C22  C21  109.95  3.000
 20G  H22A  C22  C21  109.68  3.000
 20G  H22   C22  N10  108.64  3.000
 20G  H22A  C22  N10  111.38  3.000
 20G  C21   C22  N10  110.71  3.000
 20G  H24   C24  C25  118.09  3.000
 20G  C25   C24  C06  120.82  3.000
 20G  H24   C24  C06  121.09  3.000
 20G  H25   C25  C24  119.47  3.000
 20G  H25   C25  C02  120.78  3.000
 20G  C24   C25  C02  119.75  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
 20G  CONST_01  C06   C24  C25  C02     0.00   0.0  0
 20G  CONST_02  C06   C04  C03  C02     0.00   0.0  0
 20G  CONST_03  C24   C25  C02  C03     0.00   0.0  0
 20G  CONST_04  C24   C06  C04  C03     0.00   0.0  0
 20G  CONST_05  C25   C02  C03  C04     0.00   0.0  0
 20G  CONST_06  C25   C24  C06  C04     0.00   0.0  0
 20G  CONST_07  C24   C25  C02  CL1   180.00   0.0  0
 20G  CONST_08  C04   C03  C02  CL1   180.00   0.0  0
 20G  CONST_09  C02   C03  C04  CL2   180.00   0.0  0
 20G  CONST_10  C24   C06  C04  CL2   180.00   0.0  0
 20G  CONST_11  O07   C06  C04  C03   180.00   0.0  0
 20G  CONST_12  C25   C24  C06  O07   180.00   0.0  0
 20G  CONST_13  H24   C24  C25  C02   180.00   0.0  0
 20G  CONST_14  H25   C25  C02  C03   180.00   0.0  0
 20G  CONST_15  H03   C03  C04  C06   180.00   0.0  0
 20G  CONST_16  C22   N10  C09  C08     0.00   0.0  0
 20G  CONST_17  C11   N10  C09  C08   180.00   0.0  0
 20G  CONST_18  O23   C09  N10  C11     0.00   0.0  0
 20G  CONST_19  O23   C09  N10  C22   180.00   0.0  0
 20G  CONST_20  C16   C15  N14  C13   180.00   0.0  0
 20G  CONST_21  O20   C15  N14  C13     0.00   0.0  0
 20G  CONST_22  HN14  N14  C15  C16     0.00   0.0  0
 20G  Var_01    C13   C21  C22  N10    55.44  30.0  1
 20G  Var_02    C13   C12  C11  N10   -55.06  30.0  1
 20G  Var_03    C21   C22  N10  C11   -57.52  30.0  1
 20G  Var_04    C22   N10  C11  C12    57.39  30.0  1
 20G  Var_05    C24   C06  O07  C08    -1.05  30.0  2
 20G  Var_06    C09   C08  O07  C06  -178.90  30.0  2
 20G  Var_07    N10   C09  C08  O07   178.56  30.0  3
 20G  Var_08    C17   C16  C15  N14  -178.89  30.0  1
 20G  Var_09    C18   C17  C16  C15  -178.05  30.0  1
 20G  Var_10    S19   C18  C17  C16   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
 20G  chir_01  C13  C12  N14  C21  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
 20G  plan-1  CL1   0.020
 20G  plan-1  CL2   0.020
 20G  plan-1  C02   0.020
 20G  plan-1  C03   0.020
 20G  plan-1  C04   0.020
 20G  plan-1  C06   0.020
 20G  plan-1  O07   0.020
 20G  plan-1  C24   0.020
 20G  plan-1  C25   0.020
 20G  plan-1  H03   0.020
 20G  plan-1  H24   0.020
 20G  plan-1  H25   0.020
 20G  plan-2  C13   0.020
 20G  plan-2  N14   0.020
 20G  plan-2  C15   0.020
 20G  plan-2  C16   0.020
 20G  plan-2  O20   0.020
 20G  plan-2  HN14  0.020
 20G  plan-3  C08   0.020
 20G  plan-3  C09   0.020
 20G  plan-3  N10   0.020
 20G  plan-3  C11   0.020
 20G  plan-3  C22   0.020
 20G  plan-3  O23   0.020

