# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Aug  4 00:28:31 2022
#   Inital geometry file: a 95 line input string
#   Ligand name: 2-(4-chlorobenzamido)-4,5,6,7-tetrahydro-1-benzothiophene-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1c2CCCCc2sc1NC(=O)c3ccc(Cl)cc3
#
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
 Z5G  Z5G  "2-(4-chlorobenzamido)-4,5,6,7-tetrahydro-1-benzothiophene-3-carboxylic acid"  ligand  35  22  .  2022-08-11  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Z5G
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
 Z5G  C02   C   CR6    0  -0.040   94.1253  100.1960  75.1172
 Z5G  C03   C   CR16   0  -0.198   94.4017  100.6827  73.8483
 Z5G  C04   C   CR16   0  -0.272   95.6885  100.5720  73.3502
 Z5G  C05   C   CR6    0  -0.035   96.7032   99.9951  74.1106
 Z5G  C06   C   CR16   0  -0.297   96.4006   99.5137  75.3832
 Z5G  C07   C   CR16   0  -0.194   95.1150   99.6094  75.8904
 Z5G  C08   C   C      0   0.531   98.0584   99.8760  73.5017
 Z5G  C11   C   CR5    0   0.079  100.3861   99.4643  74.0102
 Z5G  C13   C   CR5    0  -0.283  102.5605   99.0821  72.9218
 Z5G  C14   C   CH2    0  -0.473  103.6792   98.8884  71.9475
 Z5G  C15   C   CH2    0  -0.440  104.8629   98.2256  72.6461
 Z5G  C16   C   CH2    0  -0.447  105.1352   98.8995  73.9843
 Z5G  C17   C   CH2    0  -0.472  103.9637   98.7340  74.9499
 Z5G  C18   C   CR5    0   0.184  102.6470   99.0084  74.2787
 Z5G  C19   C   CR5    0  -0.191  101.3809   99.2209  74.9286
 Z5G  C20   C   C      0   0.443  101.0966   99.1661  76.4084
 Z5G  N10   N   NH1    0  -0.749   99.0759   99.6890  74.3608
 Z5G  O09   O   O      0  -0.469   98.2262   99.9446  72.2903
 Z5G  O21   O   OC    -1  -0.551  102.0098   98.8263  77.1719
 Z5G  O22   O   O      0  -0.612   99.9213   99.4695  76.7673
 Z5G  S12   S   S2     0   0.210  100.9519   99.4300  72.3839
 Z5G  CL01  CL  CL     0  -0.115   92.5171  100.3127  75.7412
 Z5G  H1    H   HCR6   0   0.284   93.6236  101.1395  73.2524
 Z5G  H2    H   HCR6   0   0.270   95.9034  100.9436  72.3575
 Z5G  H3    H   HCR6   0   0.261   97.1520   99.0330  75.9962
 Z5G  H4    H   HCR6   0   0.286   94.8890   99.2235  76.8750
 Z5G  H5    H   HCH2   0   0.238  103.9897   99.8511  71.5271
 Z5G  H6    H   HCH2   0   0.245  103.3515   98.2810  71.0995
 Z5G  H7    H   HCH2   0   0.221  104.6469   97.1651  72.8075
 Z5G  H8    H   HCH2   0   0.233  105.7434   98.2738  72.0022
 Z5G  H9    H   HCH2   0   0.231  106.0413   98.4945  74.4397
 Z5G  H10   H   HCH2   0   0.217  105.3217   99.9649  73.8148
 Z5G  H11   H   HCH2   0   0.224  103.9601   97.7190  75.3593
 Z5G  H12   H   HCH2   0   0.236  104.0905   99.3943  75.8067
 Z5G  H13   H   HNH1   0   0.447   99.0148   99.6928  75.4020

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
 Z5G  C14  C15   single    1.526  0.020  1.526
 Z5G  C14  C13   single    1.496  0.020  1.496
 Z5G  O09  C08   double    1.225  0.020  1.225
 Z5G  S12  C13   aromatic  1.732  0.020  1.732
 Z5G  S12  C11   aromatic  1.722  0.020  1.722
 Z5G  C15  C16   single    1.523  0.020  1.523
 Z5G  C13  C18   aromatic  1.362  0.020  1.362
 Z5G  C04  C03   aromatic  1.384  0.020  1.384
 Z5G  C04  C05   aromatic  1.393  0.020  1.393
 Z5G  C08  C05   single    1.491  0.020  1.491
 Z5G  C08  N10   single    1.345  0.020  1.345
 Z5G  C03  C02   aromatic  1.387  0.020  1.387
 Z5G  C11  N10   single    1.375  0.020  1.375
 Z5G  C11  C19   aromatic  1.376  0.020  1.376
 Z5G  C16  C17   single    1.527  0.020  1.527
 Z5G  C05  C06   aromatic  1.394  0.020  1.394
 Z5G  C18  C19   aromatic  1.439  0.020  1.439
 Z5G  C18  C17   single    1.503  0.020  1.503
 Z5G  C19  C20   single    1.508  0.020  1.508
 Z5G  C02  CL01  single    1.729  0.020  1.729
 Z5G  C02  C07   aromatic  1.386  0.020  1.386
 Z5G  C06  C07   aromatic  1.385  0.020  1.385
 Z5G  C20  O22   deloc     1.266  0.020  1.266
 Z5G  C20  O21   deloc     1.238  0.020  1.238
 Z5G  C03  H1    single    0.930  0.020  1.080
 Z5G  C04  H2    single    0.930  0.020  1.080
 Z5G  C06  H3    single    0.930  0.020  1.080
 Z5G  C07  H4    single    0.930  0.020  1.080
 Z5G  C14  H5    single    0.970  0.020  1.090
 Z5G  C14  H6    single    0.970  0.020  1.090
 Z5G  C15  H7    single    0.970  0.020  1.090
 Z5G  C15  H8    single    0.970  0.020  1.090
 Z5G  C16  H9    single    0.970  0.020  1.090
 Z5G  C16  H10   single    0.970  0.020  1.090
 Z5G  C17  H11   single    0.970  0.020  1.090
 Z5G  C17  H12   single    0.970  0.020  1.090
 Z5G  N10  H13   single    0.860  0.020  1.020

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
 Z5G  CL01  C02  C07  119.43  3.000
 Z5G  C07   C02  C03  121.11  3.000
 Z5G  CL01  C02  C03  119.46  3.000
 Z5G  H1    C03  C04  120.30  3.000
 Z5G  H1    C03  C02  120.60  3.000
 Z5G  C04   C03  C02  119.10  3.000
 Z5G  H2    C04  C05  119.91  3.000
 Z5G  H2    C04  C03  119.17  3.000
 Z5G  C05   C04  C03  120.92  3.000
 Z5G  C08   C05  C06  122.87  3.000
 Z5G  C06   C05  C04  118.90  3.000
 Z5G  C08   C05  C04  118.19  3.000
 Z5G  H3    C06  C07  117.88  3.000
 Z5G  H3    C06  C05  121.32  3.000
 Z5G  C07   C06  C05  120.79  3.000
 Z5G  H4    C07  C06  120.17  3.000
 Z5G  H4    C07  C02  120.64  3.000
 Z5G  C06   C07  C02  119.18  3.000
 Z5G  O09   C08  N10  122.41  3.000
 Z5G  N10   C08  C05  115.98  3.000
 Z5G  O09   C08  C05  121.61  3.000
 Z5G  S12   C11  N10  123.86  3.000
 Z5G  N10   C11  C19  123.22  3.000
 Z5G  S12   C11  C19  112.92  3.000
 Z5G  S12   C13  C18  112.30  3.000
 Z5G  C18   C13  C14  126.48  3.000
 Z5G  S12   C13  C14  121.23  3.000
 Z5G  H6    C14  H5   105.99  3.000
 Z5G  H6    C14  C15  110.26  3.000
 Z5G  H5    C14  C15  109.73  3.000
 Z5G  H6    C14  C13  110.67  3.000
 Z5G  H5    C14  C13  110.37  3.000
 Z5G  C15   C14  C13  109.76  3.000
 Z5G  H8    C15  H7   106.80  3.000
 Z5G  H8    C15  C16  110.76  3.000
 Z5G  H7    C15  C16  109.54  3.000
 Z5G  H8    C15  C14  109.66  3.000
 Z5G  H7    C15  C14  109.60  3.000
 Z5G  C16   C15  C14  110.41  3.000
 Z5G  H10   C16  H9   106.51  3.000
 Z5G  H10   C16  C17  109.51  3.000
 Z5G  H9    C16  C17  109.43  3.000
 Z5G  H10   C16  C15  108.96  3.000
 Z5G  H9    C16  C15  110.53  3.000
 Z5G  C17   C16  C15  111.75  3.000
 Z5G  H12   C17  H11  105.57  3.000
 Z5G  H12   C17  C18  110.03  3.000
 Z5G  H11   C17  C18  109.47  3.000
 Z5G  H12   C17  C16  110.03  3.000
 Z5G  H11   C17  C16  109.85  3.000
 Z5G  C18   C17  C16  111.71  3.000
 Z5G  C19   C18  C17  126.59  3.000
 Z5G  C17   C18  C13  120.69  3.000
 Z5G  C19   C18  C13  112.72  3.000
 Z5G  C20   C19  C18  127.14  3.000
 Z5G  C20   C19  C11  121.69  3.000
 Z5G  C18   C19  C11  111.15  3.000
 Z5G  O22   C20  O21  125.17  3.000
 Z5G  O21   C20  C19  118.43  3.000
 Z5G  O22   C20  C19  116.40  3.000
 Z5G  H13   N10  C11  108.12  3.000
 Z5G  H13   N10  C08  126.37  3.000
 Z5G  C11   N10  C08  125.51  3.000
 Z5G  C13   S12  C11   90.91  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
 Z5G  CONST_01  C05   C04  C03  C02     0.00   0.0  0
 Z5G  CONST_02  C05   C06  C07  C02     0.00   0.0  0
 Z5G  CONST_03  C06   C05  C04  C03     0.00   0.0  0
 Z5G  CONST_04  C06   C07  C02  C03     0.00   0.0  0
 Z5G  CONST_05  C07   C02  C03  C04     0.00   0.0  0
 Z5G  CONST_06  C07   C06  C05  C04     0.00   0.0  0
 Z5G  CONST_07  C18   C13  S12  C11     0.00   0.0  0
 Z5G  CONST_08  C13   C18  C19  C11     0.00   0.0  0
 Z5G  CONST_09  C19   C11  S12  C13     0.00   0.0  0
 Z5G  CONST_10  S12   C11  C19  C18     0.00   0.0  0
 Z5G  CONST_11  S12   C13  C18  C19     0.00   0.0  0
 Z5G  CONST_12  C08   C05  C04  C03   180.00   0.0  0
 Z5G  CONST_13  CL01  C02  C03  C04   180.00   0.0  0
 Z5G  CONST_14  CL01  C02  C07  C06   180.00   0.0  0
 Z5G  CONST_15  C08   C05  C06  C07   180.00   0.0  0
 Z5G  CONST_16  N10   C11  S12  C13   180.00   0.0  0
 Z5G  CONST_17  C20   C19  C18  C13   180.00   0.0  0
 Z5G  CONST_18  C20   C19  C18  C17     0.00   0.0  0
 Z5G  CONST_19  N10   C11  C19  C18   180.00   0.0  0
 Z5G  CONST_20  S12   C11  C19  C20   180.00   0.0  0
 Z5G  CONST_21  H2    C04  C03  C02   180.00   0.0  0
 Z5G  CONST_22  H3    C06  C07  C02   180.00   0.0  0
 Z5G  CONST_23  H4    C07  C02  C03   180.00   0.0  0
 Z5G  CONST_24  H3    C06  C05  C04   180.00   0.0  0
 Z5G  CONST_25  H1    C03  C04  C05   180.00   0.0  0
 Z5G  CONST_26  H4    C07  C06  C05   180.00   0.0  0
 Z5G  CONST_27  H2    C04  C05  C06   180.00   0.0  0
 Z5G  CONST_28  H1    C03  C02  C07   180.00   0.0  0
 Z5G  CONST_29  C11   N10  C08  C05   180.00   0.0  0
 Z5G  CONST_30  S12   C11  N10  C08     0.00   0.0  0
 Z5G  CONST_31  C19   C11  N10  C08   180.00   0.0  0
 Z5G  CONST_32  H13   N10  C11  C19     0.00   0.0  0
 Z5G  CONST_33  H13   N10  C11  S12   180.00   0.0  0
 Z5G  CONST_34  O09   C08  N10  C11     0.00   0.0  0
 Z5G  CONST_35  H13   N10  C08  C05     0.00   0.0  0
 Z5G  CONST_36  H13   N10  C08  O09   180.00   0.0  0
 Z5G  Var_01    C16   C15  C14  C13   -45.90  30.0  1
 Z5G  Var_02    C16   C17  C18  C13    13.74  30.0  1
 Z5G  Var_03    C17   C16  C15  C14    63.55  30.0  1
 Z5G  Var_04    S12   C13  C14  C15  -164.33  30.0  1
 Z5G  Var_05    C18   C13  C14  C15    15.28  30.0  1
 Z5G  Var_06    C18   C17  C16  C15   -45.46  30.0  1
 Z5G  Var_07    C19   C18  C17  C16  -166.07  30.0  1
 Z5G  Var_08    H7    C15  C14  C13    74.86  30.0  1
 Z5G  Var_09    H8    C15  C14  C13  -168.21  30.0  1
 Z5G  Var_10    H11   C17  C18  C13  -108.15  30.0  1
 Z5G  Var_11    H12   C17  C18  C13   136.26  30.0  1
 Z5G  Var_12    H9    C16  C15  C14  -174.32  30.0  1
 Z5G  Var_13    H10   C16  C15  C14   -57.61  30.0  1
 Z5G  Var_14    H11   C17  C16  C15    76.22  30.0  1
 Z5G  Var_15    H12   C17  C16  C15  -167.98  30.0  1
 Z5G  Var_16    H5    C14  C15  C16    75.56  30.0  1
 Z5G  Var_17    H6    C14  C15  C16  -168.06  30.0  1
 Z5G  Var_18    H7    C15  C16  C17   -57.24  30.0  1
 Z5G  Var_19    H8    C15  C16  C17  -174.79  30.0  1
 Z5G  Var_20    H5    C14  C13  C18  -105.79  30.0  1
 Z5G  Var_21    H6    C14  C13  C18   137.20  30.0  1
 Z5G  Var_22    H9    C16  C17  C18  -168.22  30.0  1
 Z5G  Var_23    H10   C16  C17  C18    75.38  30.0  1
 Z5G  Var_24    H11   C17  C18  C19    72.03  30.0  1
 Z5G  Var_25    H12   C17  C18  C19   -43.56  30.0  1
 Z5G  Var_26    H5    C14  C13  S12    74.60  30.0  1
 Z5G  Var_27    H6    C14  C13  S12   -42.41  30.0  1
 Z5G  Var_28    O09   C08  C05  C04   -18.74  30.0  2
 Z5G  Var_29    N10   C08  C05  C04   161.30  30.0  2
 Z5G  Var_30    O09   C08  C05  C06   158.96  30.0  2
 Z5G  Var_31    N10   C08  C05  C06   -21.00  30.0  2
 Z5G  Var_32    O22   C20  C19  C11    -5.92  30.0  2
 Z5G  Var_33    O21   C20  C19  C11   173.68  30.0  2
 Z5G  Var_34    O22   C20  C19  C18   175.69  30.0  2
 Z5G  Var_35    O21   C20  C19  C18    -4.72  30.0  2

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
 Z5G  plan-1  C02   0.020
 Z5G  plan-1  C03   0.020
 Z5G  plan-1  C04   0.020
 Z5G  plan-1  C05   0.020
 Z5G  plan-1  C06   0.020
 Z5G  plan-1  C07   0.020
 Z5G  plan-1  C08   0.020
 Z5G  plan-1  CL01  0.020
 Z5G  plan-1  H1    0.020
 Z5G  plan-1  H2    0.020
 Z5G  plan-1  H3    0.020
 Z5G  plan-1  H4    0.020
 Z5G  plan-2  C11   0.020
 Z5G  plan-2  C13   0.020
 Z5G  plan-2  C14   0.020
 Z5G  plan-2  C17   0.020
 Z5G  plan-2  C18   0.020
 Z5G  plan-2  C19   0.020
 Z5G  plan-2  C20   0.020
 Z5G  plan-2  N10   0.020
 Z5G  plan-2  S12   0.020
 Z5G  plan-3  C05   0.020
 Z5G  plan-3  C08   0.020
 Z5G  plan-3  C11   0.020
 Z5G  plan-3  N10   0.020
 Z5G  plan-3  O09   0.020
 Z5G  plan-3  H13   0.020
 Z5G  plan-4  C19   0.020
 Z5G  plan-4  C20   0.020
 Z5G  plan-4  O21   0.020
 Z5G  plan-4  O22   0.020

