# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 19:24:18 2022
#   Inital geometry file: a 76 line input string
#   Ligand name: 2-(4-chlorophenyl)sulfanyl-~{N}-(3-sulfanylpropyl)ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: SCCCNC(=O)CSc1ccc(Cl)cc1
#
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
 T4Z  T4Z  2-(4-chlorophenyl)sulfanyl-~{N}-(3-sulfanylpropyl)ethanamide  ligand  30  16  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_T4Z
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
 T4Z  C1   C   CH2   0  -0.453  20.7771  19.0456  -0.8785
 T4Z  C2   C   CH2   0  -0.289  19.7646  18.2519  -1.6962
 T4Z  C4   C   CH2   0  -0.696  16.1255  19.3183  -1.6607
 T4Z  C6   C   CR16  0  -0.229  16.8308  21.2871   0.8568
 T4Z  C7   C   CR16  0  -0.205  17.7534  21.7295   1.7906
 T4Z  C9   C   CR16  0  -0.203  17.4614  19.6806   3.0366
 T4Z  N    N   NH1   0  -0.617  18.4895  18.9276  -1.7832
 T4Z  C    C   CH2   0  -0.546  20.3762  19.2936   0.5662
 T4Z  O    O   O     0  -0.475  17.1722  17.2779  -0.9567
 T4Z  C10  C   CR16  0  -0.239  16.5560  19.2374   2.0837
 T4Z  C3   C   C     0   0.559  17.3110  18.3966  -1.4225
 T4Z  C5   C   CR6   0  -0.141  16.2386  20.0338   0.9896
 T4Z  C8   C   CR6   0  -0.045  18.0625  20.9171   2.8725
 T4Z  S    S   S2    0  -0.264  20.3209  17.7184   1.4900
 T4Z  S1   S   S2    0   0.041  15.0630  19.4461  -0.1975
 T4Z  CL   CL  CL    0  -0.119  19.2406  21.4463   4.0238
 T4Z  H1   H   HCH2  0   0.249  21.7376  18.5262  -0.9193
 T4Z  H2   H   HCH2  0   0.254  20.9370  20.0184  -1.3523
 T4Z  H3   H   HCH2  0   0.253  19.5989  17.2647  -1.2683
 T4Z  H4   H   HCH2  0   0.257  20.1644  18.0980  -2.7015
 T4Z  H5   H   HCH2  0   0.293  16.4247  20.3113  -1.9949
 T4Z  H6   H   HCH2  0   0.320  15.4931  18.8878  -2.4407
 T4Z  H8   H   HCR6  0   0.284  18.2246  22.6961   1.6745
 T4Z  H9   H   HCR6  0   0.287  17.7084  19.0550   3.8837
 T4Z  H10  H   HNH1  0   0.402  18.4957  19.8618  -2.1626
 T4Z  H11  H   HCH2  0   0.276  21.0995  19.9547   1.0416
 T4Z  H12  H   HCH2  0   0.270  19.3985  19.7708   0.6166
 T4Z  H13  H   HCR6  0   0.278  16.1035  18.2609   2.1941
 T4Z  H14  H   HSH1  0   0.220  19.9994  18.2322   2.6820
 T4Z  H7   H   HCR6  0   0.281  16.5805  21.9230   0.0171

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
 T4Z  C4   C3   single    1.520  0.020  1.520
 T4Z  C4   S1   single    1.813  0.020  1.813
 T4Z  C3   N    single    1.342  0.020  1.342
 T4Z  C3   O    double    1.220  0.020  1.220
 T4Z  N    C2   single    1.446  0.020  1.446
 T4Z  C2   C1   single    1.524  0.020  1.524
 T4Z  C1   C    single    1.520  0.020  1.520
 T4Z  S1   C5   single    1.771  0.020  1.771
 T4Z  C5   C6   aromatic  1.392  0.020  1.392
 T4Z  C5   C10  aromatic  1.390  0.020  1.390
 T4Z  C6   C7   aromatic  1.385  0.020  1.385
 T4Z  C    S    single    1.827  0.020  1.827
 T4Z  C10  C9   aromatic  1.387  0.020  1.387
 T4Z  C7   C8   aromatic  1.388  0.020  1.388
 T4Z  C9   C8   aromatic  1.385  0.020  1.385
 T4Z  C8   CL   single    1.730  0.020  1.730
 T4Z  C1   H1   single    0.970  0.020  1.090
 T4Z  C1   H2   single    0.970  0.020  1.090
 T4Z  C2   H3   single    0.970  0.020  1.090
 T4Z  C2   H4   single    0.970  0.020  1.090
 T4Z  C4   H5   single    0.970  0.020  1.090
 T4Z  C4   H6   single    0.970  0.020  1.090
 T4Z  C6   H7   single    0.930  0.020  1.080
 T4Z  C7   H8   single    0.930  0.020  1.080
 T4Z  C9   H9   single    0.930  0.020  1.080
 T4Z  N    H10  single    0.860  0.020  1.020
 T4Z  C    H11  single    0.970  0.020  1.090
 T4Z  C    H12  single    0.970  0.020  1.090
 T4Z  C10  H13  single    0.930  0.020  1.080
 T4Z  S    H14  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
 T4Z  H2   C1   H1   106.15  3.000
 T4Z  H2   C1   C    107.77  3.000
 T4Z  H1   C1   C    110.18  3.000
 T4Z  H2   C1   C2   109.14  3.000
 T4Z  H1   C1   C2   108.44  3.000
 T4Z  C    C1   C2   114.81  3.000
 T4Z  H4   C2   H3   106.83  3.000
 T4Z  H4   C2   N    109.46  3.000
 T4Z  H3   C2   N    108.25  3.000
 T4Z  H4   C2   C1   108.90  3.000
 T4Z  H3   C2   C1   111.25  3.000
 T4Z  N    C2   C1   112.01  3.000
 T4Z  H6   C4   H5   107.40  3.000
 T4Z  H6   C4   S1   105.35  3.000
 T4Z  H5   C4   S1   110.13  3.000
 T4Z  H6   C4   C3   108.93  3.000
 T4Z  H5   C4   C3   112.74  3.000
 T4Z  S1   C4   C3   111.92  3.000
 T4Z  H7   C6   C5   120.28  3.000
 T4Z  H7   C6   C7   119.29  3.000
 T4Z  C5   C6   C7   120.42  3.000
 T4Z  H8   C7   C8   120.65  3.000
 T4Z  H8   C7   C6   120.21  3.000
 T4Z  C8   C7   C6   119.14  3.000
 T4Z  H9   C9   C8   120.68  3.000
 T4Z  H9   C9   C10  120.14  3.000
 T4Z  C8   C9   C10  119.16  3.000
 T4Z  H10  N    C3   118.24  3.000
 T4Z  H10  N    C2   116.76  3.000
 T4Z  C3   N    C2   124.99  3.000
 T4Z  H12  C    H11  108.06  3.000
 T4Z  H12  C    S    109.10  3.000
 T4Z  H11  C    S    108.83  3.000
 T4Z  H12  C    C1   110.63  3.000
 T4Z  H11  C    C1   109.81  3.000
 T4Z  S    C    C1   110.37  3.000
 T4Z  H13  C10  C5   120.13  3.000
 T4Z  H13  C10  C9   119.43  3.000
 T4Z  C5   C10  C9   120.44  3.000
 T4Z  O    C3   N    124.44  3.000
 T4Z  O    C3   C4   121.81  3.000
 T4Z  N    C3   C4   113.75  3.000
 T4Z  S1   C5   C10  119.28  3.000
 T4Z  C10  C5   C6   119.58  3.000
 T4Z  S1   C5   C6   121.13  3.000
 T4Z  CL   C8   C9   119.33  3.000
 T4Z  CL   C8   C7   119.43  3.000
 T4Z  C9   C8   C7   121.23  3.000
 T4Z  H14  S    C     97.28  3.000
 T4Z  C5   S1   C4   100.10  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
 T4Z  CONST_01  C9   C10  C5   C6      0.00   0.0  0
 T4Z  CONST_02  C9   C8   C7   C6      0.00   0.0  0
 T4Z  CONST_03  C10  C5   C6   C7      0.00   0.0  0
 T4Z  CONST_04  C10  C9   C8   C7      0.00   0.0  0
 T4Z  CONST_05  C8   C7   C6   C5      0.00   0.0  0
 T4Z  CONST_06  C8   C9   C10  C5      0.00   0.0  0
 T4Z  CONST_07  CL   C8   C7   C6    180.00   0.0  0
 T4Z  CONST_08  S1   C5   C6   C7    180.00   0.0  0
 T4Z  CONST_09  S1   C5   C10  C9    180.00   0.0  0
 T4Z  CONST_10  CL   C8   C9   C10   180.00   0.0  0
 T4Z  CONST_11  H13  C10  C5   C6    180.00   0.0  0
 T4Z  CONST_12  H9   C9   C8   C7    180.00   0.0  0
 T4Z  CONST_13  H8   C7   C8   C9    180.00   0.0  0
 T4Z  CONST_14  H7   C6   C5   C10   180.00   0.0  0
 T4Z  CONST_15  C4   C3   N    C2    180.00   0.0  0
 T4Z  CONST_16  O    C3   N    C2      0.00   0.0  0
 T4Z  CONST_17  H10  N    C3   C4      0.00   0.0  0
 T4Z  Var_01    C6   C5   S1   C4     65.21  30.0  2
 T4Z  Var_02    H5   C4   S1   C5    -68.46  30.0  1
 T4Z  Var_03    C3   N    C2   C1   -124.50  30.0  1
 T4Z  Var_04    S    C    C1   C2     66.17  30.0  3
 T4Z  Var_05    S1   C4   C3   N    -130.67  30.0  2
 T4Z  Var_06    C    C1   C2   N      60.92  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
 T4Z  plan-1  C6   0.020
 T4Z  plan-1  C7   0.020
 T4Z  plan-1  C9   0.020
 T4Z  plan-1  C10  0.020
 T4Z  plan-1  C5   0.020
 T4Z  plan-1  C8   0.020
 T4Z  plan-1  S1   0.020
 T4Z  plan-1  CL   0.020
 T4Z  plan-1  H8   0.020
 T4Z  plan-1  H9   0.020
 T4Z  plan-1  H13  0.020
 T4Z  plan-1  H7   0.020
 T4Z  plan-2  C2   0.020
 T4Z  plan-2  C4   0.020
 T4Z  plan-2  N    0.020
 T4Z  plan-2  O    0.020
 T4Z  plan-2  C3   0.020
 T4Z  plan-2  H10  0.020

