# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 07:07:22 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: N-phenyl-6-[(sulfanylacetyl)amino]hexanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: SCC(=O)NCCCCCC(=O)Nc1ccccc1
#
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
 9Z8  9Z8  N-phenyl-6-[(sulfanylacetyl)amino]hexanamide  ligand  39  19  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_9Z8
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
 9Z8  O01   O  O     0  -0.491   6.0674  -1.4384  -0.0124
 9Z8  C02   C  C     0   0.567   5.8048  -0.2452  -0.0165
 9Z8  C03   C  CH2   0  -0.687   6.8911   0.8127  -0.0480
 9Z8  S04   S  S2    0  -0.225   8.4993  -0.0243  -0.0191
 9Z8  N05   N  NH1   0  -0.638   4.5584   0.2385   0.0050
 9Z8  C06   C  CH2   0  -0.232   3.3801  -0.6065   0.0365
 9Z8  C07   C  CH2   0  -0.477   2.1201   0.2430   0.0218
 9Z8  C08   C  CH2   0  -0.421   0.8555  -0.6041   0.0682
 9Z8  C09   C  CH2   0  -0.413  -0.4066   0.2491   0.0351
 9Z8  C10   C  CH2   0  -0.597  -1.6667  -0.5968   0.1108
 9Z8  C11   C  C     0   0.557  -2.9453   0.2139   0.0619
 9Z8  O12   O  O     0  -0.468  -2.9578   1.4311   0.0783
 9Z8  N13   N  NH1   0  -0.747  -4.0681  -0.5523   0.0058
 9Z8  C14   C  CR6   0   0.370  -5.4113  -0.1653  -0.0077
 9Z8  C15   C  CR16  0  -0.319  -5.8512   1.1576  -0.0894
 9Z8  C16   C  CR16  0  -0.244  -7.2138   1.4295  -0.1017
 9Z8  C17   C  CR16  0  -0.275  -8.1540   0.4124  -0.0358
 9Z8  C18   C  CR16  0  -0.245  -7.7143  -0.9030   0.0429
 9Z8  C19   C  CR16  0  -0.348  -6.3606  -1.1903   0.0569
 9Z8  H031  H  HCH2  0   0.305   6.7921   1.4207  -0.9491
 9Z8  H032  H  HCH2  0   0.303   6.7890   1.4785   0.8104
 9Z8  H05   H  HNH1  0   0.406   4.4261   1.2377   0.0002
 9Z8  H061  H  HCH2  0   0.234   3.3831  -1.2806  -0.8244
 9Z8  H062  H  HCH2  0   0.233   3.3957  -1.2331   0.9330
 9Z8  H071  H  HCH2  0   0.232   2.1308   0.9268   0.8767
 9Z8  H072  H  HCH2  0   0.232   2.1110   0.8653  -0.8790
 9Z8  H081  H  HCH2  0   0.221   0.8496  -1.3012  -0.7762
 9Z8  H082  H  HCH2  0   0.221   0.8610  -1.2193   0.9743
 9Z8  H091  H  HCH2  0   0.226  -0.3848   0.9575   0.8669
 9Z8  H092  H  HCH2  0   0.226  -0.4139   0.8468  -0.8805
 9Z8  H101  H  HCH2  0   0.269  -1.6808  -1.3296  -0.7024
 9Z8  H102  H  HCH2  0   0.275  -1.6701  -1.1843   1.0359
 9Z8  H13   H  HNH1  0   0.415  -3.9190  -1.5506   0.0101
 9Z8  H15   H  HCR6  0   0.279  -5.1482   1.9714  -0.1443
 9Z8  H19   H  HCR6  0   0.267  -6.0326  -2.2215   0.1203
 9Z8  H16   H  HCR6  0   0.257  -7.5368   2.4608  -0.1666
 9Z8  H17   H  HCR6  0   0.254  -9.2121   0.6378  -0.0462
 9Z8  H18   H  HCR6  0   0.259  -8.4281  -1.7147   0.0938
 9Z8  H32   H  HSH1  0   0.218   9.2316   1.0952  -0.0485

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
 9Z8  O01  C02   double    1.222  0.020  1.222
 9Z8  C02  C03   single    1.517  0.020  1.517
 9Z8  C02  N05   single    1.337  0.020  1.337
 9Z8  C03  S04   single    1.813  0.020  1.813
 9Z8  N05  C06   single    1.450  0.020  1.450
 9Z8  C06  C07   single    1.520  0.020  1.520
 9Z8  C07  C08   single    1.523  0.020  1.523
 9Z8  C08  C09   single    1.524  0.020  1.524
 9Z8  C09  C10   single    1.520  0.020  1.520
 9Z8  C10  C11   single    1.515  0.020  1.515
 9Z8  C11  O12   double    1.217  0.020  1.217
 9Z8  C11  N13   single    1.360  0.020  1.360
 9Z8  N13  C14   single    1.398  0.020  1.398
 9Z8  C14  C15   aromatic  1.397  0.020  1.397
 9Z8  C14  C19   aromatic  1.399  0.020  1.399
 9Z8  C15  C16   aromatic  1.390  0.020  1.390
 9Z8  C16  C17   aromatic  1.387  0.020  1.387
 9Z8  C17  C18   aromatic  1.389  0.020  1.389
 9Z8  C18  C19   aromatic  1.384  0.020  1.384
 9Z8  C03  H031  single    0.970  0.020  1.090
 9Z8  C03  H032  single    0.970  0.020  1.090
 9Z8  N05  H05   single    0.860  0.020  1.020
 9Z8  C06  H061  single    0.970  0.020  1.090
 9Z8  C06  H062  single    0.970  0.020  1.090
 9Z8  C07  H071  single    0.970  0.020  1.090
 9Z8  C07  H072  single    0.970  0.020  1.090
 9Z8  C08  H081  single    0.970  0.020  1.090
 9Z8  C08  H082  single    0.970  0.020  1.090
 9Z8  C09  H091  single    0.970  0.020  1.090
 9Z8  C09  H092  single    0.970  0.020  1.090
 9Z8  C10  H101  single    0.970  0.020  1.090
 9Z8  C10  H102  single    0.970  0.020  1.090
 9Z8  N13  H13   single    0.860  0.020  1.020
 9Z8  C15  H15   single    0.930  0.020  1.080
 9Z8  C19  H19   single    0.930  0.020  1.080
 9Z8  C16  H16   single    0.930  0.020  1.080
 9Z8  C17  H17   single    0.930  0.020  1.080
 9Z8  C18  H18   single    0.930  0.020  1.080
 9Z8  S04  H32   single    1.200  0.020  1.300

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
 9Z8  N05   C02  C03   114.56  3.000
 9Z8  N05   C02  O01   123.61  3.000
 9Z8  C03   C02  O01   121.83  3.000
 9Z8  H032  C03  H031  107.52  3.000
 9Z8  H032  C03  S04   110.62  3.000
 9Z8  H031  C03  S04   110.54  3.000
 9Z8  H032  C03  C02   110.01  3.000
 9Z8  H031  C03  C02   109.92  3.000
 9Z8  S04   C03  C02   108.24  3.000
 9Z8  H32   S04  C03    95.67  3.000
 9Z8  H05   N05  C06   118.11  3.000
 9Z8  H05   N05  C02   118.74  3.000
 9Z8  C06   N05  C02   123.16  3.000
 9Z8  H062  C06  H061  106.98  3.000
 9Z8  H062  C06  C07   109.87  3.000
 9Z8  H061  C06  C07   109.83  3.000
 9Z8  H062  C06  N05   109.87  3.000
 9Z8  H061  C06  N05   109.87  3.000
 9Z8  C07   C06  N05   110.35  3.000
 9Z8  H072  C07  H071  106.71  3.000
 9Z8  H072  C07  C08   109.53  3.000
 9Z8  H071  C07  C08   109.37  3.000
 9Z8  H072  C07  C06   109.43  3.000
 9Z8  H071  C07  C06   109.48  3.000
 9Z8  C08   C07  C06   112.17  3.000
 9Z8  H082  C08  H081  106.29  3.000
 9Z8  H082  C08  C09   109.67  3.000
 9Z8  H081  C08  C09   109.58  3.000
 9Z8  H082  C08  C07   109.48  3.000
 9Z8  H081  C08  C07   109.58  3.000
 9Z8  C09   C08  C07   112.07  3.000
 9Z8  H092  C09  H091  106.45  3.000
 9Z8  H092  C09  C10   109.91  3.000
 9Z8  H091  C09  C10   109.84  3.000
 9Z8  H092  C09  C08   109.26  3.000
 9Z8  H091  C09  C08   109.26  3.000
 9Z8  C10   C09  C08   111.97  3.000
 9Z8  H102  C10  H101  105.55  3.000
 9Z8  H102  C10  C11   108.15  3.000
 9Z8  H101  C10  C11   108.87  3.000
 9Z8  H102  C10  C09   110.07  3.000
 9Z8  H101  C10  C09   110.26  3.000
 9Z8  C11   C10  C09   113.61  3.000
 9Z8  N13   C11  O12   123.72  3.000
 9Z8  N13   C11  C10   113.36  3.000
 9Z8  O12   C11  C10   122.91  3.000
 9Z8  H13   N13  C14   114.57  3.000
 9Z8  H13   N13  C11   115.78  3.000
 9Z8  C14   N13  C11   129.61  3.000
 9Z8  C19   C14  C15   118.89  3.000
 9Z8  C19   C14  N13   116.67  3.000
 9Z8  C15   C14  N13   124.44  3.000
 9Z8  H15   C15  C16   119.47  3.000
 9Z8  H15   C15  C14   120.88  3.000
 9Z8  C16   C15  C14   119.66  3.000
 9Z8  H16   C16  C17   119.95  3.000
 9Z8  H16   C16  C15   118.65  3.000
 9Z8  C17   C16  C15   121.40  3.000
 9Z8  H17   C17  C18   120.49  3.000
 9Z8  H17   C17  C16   120.66  3.000
 9Z8  C18   C17  C16   118.85  3.000
 9Z8  H18   C18  C19   119.28  3.000
 9Z8  H18   C18  C17   120.27  3.000
 9Z8  C19   C18  C17   120.44  3.000
 9Z8  H19   C19  C18   119.60  3.000
 9Z8  H19   C19  C14   119.64  3.000
 9Z8  C18   C19  C14   120.76  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
 9Z8  CONST_01  C17  C16  C15  C14     0.00   0.0  0
 9Z8  CONST_02  C17  C18  C19  C14     0.00   0.0  0
 9Z8  CONST_03  C18  C19  C14  C15     0.00   0.0  0
 9Z8  CONST_04  C18  C17  C16  C15     0.00   0.0  0
 9Z8  CONST_05  C19  C14  C15  C16     0.00   0.0  0
 9Z8  CONST_06  C19  C18  C17  C16     0.00   0.0  0
 9Z8  CONST_07  C16  C15  C14  N13   180.00   0.0  0
 9Z8  CONST_08  C18  C19  C14  N13   180.00   0.0  0
 9Z8  CONST_09  H16  C16  C15  C14   180.00   0.0  0
 9Z8  CONST_10  H18  C18  C19  C14   180.00   0.0  0
 9Z8  CONST_11  H19  C19  C14  C15   180.00   0.0  0
 9Z8  CONST_12  H17  C17  C16  C15   180.00   0.0  0
 9Z8  CONST_13  H15  C15  C16  C17   180.00   0.0  0
 9Z8  CONST_14  C15  C14  N13  C11     0.00   0.0  0
 9Z8  CONST_15  C19  C14  N13  C11   180.00   0.0  0
 9Z8  CONST_16  H13  N13  C14  C15   180.00   0.0  0
 9Z8  CONST_17  C14  N13  C11  C10   180.00   0.0  0
 9Z8  CONST_18  C14  N13  C11  O12     0.00   0.0  0
 9Z8  CONST_19  C06  N05  C02  O01     0.00   0.0  0
 9Z8  CONST_20  C06  N05  C02  C03   180.00   0.0  0
 9Z8  CONST_21  H05  N05  C02  O01   180.00   0.0  0
 9Z8  Var_01    S04  C03  C02  O01    -1.87  30.0  3
 9Z8  Var_02    C07  C06  N05  C02  -178.66  30.0  3
 9Z8  Var_03    C08  C07  C06  N05  -179.42  30.0  3
 9Z8  Var_04    C09  C08  C07  C06  -179.26  30.0  3
 9Z8  Var_05    C10  C09  C08  C07  -178.80  30.0  3
 9Z8  Var_06    C11  C10  C09  C08  -179.23  30.0  3
 9Z8  Var_07    O12  C11  C10  C09    -6.05  30.0  3

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
 9Z8  plan-1  N13  0.020
 9Z8  plan-1  C14  0.020
 9Z8  plan-1  C15  0.020
 9Z8  plan-1  C16  0.020
 9Z8  plan-1  C17  0.020
 9Z8  plan-1  C18  0.020
 9Z8  plan-1  C19  0.020
 9Z8  plan-1  H15  0.020
 9Z8  plan-1  H19  0.020
 9Z8  plan-1  H16  0.020
 9Z8  plan-1  H17  0.020
 9Z8  plan-1  H18  0.020
 9Z8  plan-2  O01  0.020
 9Z8  plan-2  C02  0.020
 9Z8  plan-2  C03  0.020
 9Z8  plan-2  N05  0.020
 9Z8  plan-2  C06  0.020
 9Z8  plan-2  H05  0.020
 9Z8  plan-3  C10  0.020
 9Z8  plan-3  C11  0.020
 9Z8  plan-3  O12  0.020
 9Z8  plan-3  N13  0.020
 9Z8  plan-3  C14  0.020
 9Z8  plan-3  H13  0.020

