# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 18:45:36 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: ethyl N-[(5-methylthiophen-3-yl)carbonyl]glycinate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOC(=O)CNC(=O)c1csc(C)c1
#
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
 56E  56E  'ethyl N-[(5-methylthiophen-3-yl)carbonyl]glycinate'  ligand  28  15  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_56E
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
 56E  C1   C  C     0   0.553  -0.5187   0.9712   0.1145
 56E  C4   C  CH2   0  -0.370   1.8977   0.7833   0.0424
 56E  C7   C  CR5   0  -0.163  -4.1553   0.2132  -0.0448
 56E  C8   C  CR5   0   0.058  -1.8270   0.2761   0.0379
 56E  C9   C  CR15  0  -0.218  -3.0528   1.0064   0.0130
 56E  C11  C  C     0   0.567   2.9349  -0.3033  -0.1027
 56E  C14  C  CH2   0  -0.184   5.2675  -0.7081  -0.1259
 56E  C15  C  CH3   0  -0.689   6.5286   0.1015   0.0451
 56E  O11  O  O     0  -0.490  -0.4590   2.1789   0.3081
 56E  C12  C  CR15  0  -0.548  -2.0335  -1.0738   0.0047
 56E  S11  S  S2    0   0.247  -3.6961  -1.4518  -0.0615
 56E  N7   N  NH1   0  -0.672   0.5807   0.2167  -0.0389
 56E  O13  O  O     0  -0.446   2.6781  -1.4686  -0.2747
 56E  O12  O  O2    0  -0.450   4.1503   0.1954  -0.0180
 56E  H1   H  HCH2  0   0.289   2.0539   1.2921   0.9980
 56E  H2   H  HCH2  0   0.289   2.0644   1.5316  -0.7389
 56E  H3   H  HCR5  0   0.264  -3.1075   2.0855   0.0345
 56E  H4   H  HCH3  0   0.256  -6.1551   0.2005   0.7406
 56E  H5   H  HCH3  0   0.259  -5.6672   1.7030  -0.0403
 56E  H6   H  HCH3  0   0.257  -6.0714   0.2908  -1.0141
 56E  H7   H  HCH2  0   0.242   5.2436  -1.1994  -1.1002
 56E  H8   H  HCH2  0   0.242   5.1879  -1.4768   0.6446
 56E  H9   H  HCH3  0   0.239   6.5631   0.5878   1.0199
 56E  H10  H  HCH3  0   0.242   7.3894  -0.5625  -0.0275
 56E  H11  H  HCH3  0   0.239   6.6274   0.8621  -0.7292
 56E  H12  H  HCR5  0   0.298  -1.3102  -1.8748   0.0307
 56E  H13  H  HNH1  0   0.406   0.5119  -0.7698  -0.2322
 56E  C10  C  CH3   0  -0.714  -5.5888   0.6183  -0.0925

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
 56E  C14  C15  single    1.508  0.020  1.508
 56E  C14  O12  single    1.441  0.020  1.441
 56E  C10  C7   single    1.490  0.020  1.490
 56E  C4   C11  single    1.509  0.020  1.509
 56E  C4   N7   single    1.436  0.020  1.436
 56E  O12  C11  single    1.316  0.020  1.316
 56E  C11  O13  double    1.206  0.020  1.206
 56E  N7   C1   single    1.342  0.020  1.342
 56E  C9   C7   aromatic  1.359  0.020  1.359
 56E  C9   C8   aromatic  1.427  0.020  1.427
 56E  C7   S11  aromatic  1.727  0.020  1.727
 56E  C1   C8   single    1.484  0.020  1.484
 56E  C1   O11  double    1.225  0.020  1.225
 56E  C8   C12  aromatic  1.366  0.020  1.366
 56E  S11  C12  aromatic  1.706  0.020  1.706
 56E  C4   H1   single    0.970  0.020  1.090
 56E  C4   H2   single    0.970  0.020  1.090
 56E  C9   H3   single    0.930  0.020  1.080
 56E  C10  H4   single    0.970  0.020  1.090
 56E  C10  H5   single    0.970  0.020  1.090
 56E  C10  H6   single    0.970  0.020  1.090
 56E  C14  H7   single    0.970  0.020  1.090
 56E  C14  H8   single    0.970  0.020  1.090
 56E  C15  H9   single    0.970  0.020  1.090
 56E  C15  H10  single    0.970  0.020  1.090
 56E  C15  H11  single    0.970  0.020  1.090
 56E  C12  H12  single    0.930  0.020  1.080
 56E  N7   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
 56E  N7   C1   O11  122.18  3.000
 56E  O11  C1   C8   120.88  3.000
 56E  N7   C1   C8   116.94  3.000
 56E  H2   C4   H1   106.49  3.000
 56E  H2   C4   N7   111.66  3.000
 56E  H1   C4   N7   111.34  3.000
 56E  H2   C4   C11  108.60  3.000
 56E  H1   C4   C11  108.71  3.000
 56E  N7   C4   C11  109.92  3.000
 56E  S11  C7   C10  121.16  3.000
 56E  S11  C7   C9   110.32  3.000
 56E  C10  C7   C9   128.52  3.000
 56E  C12  C8   C9   112.05  3.000
 56E  C12  C8   C1   126.70  3.000
 56E  C9   C8   C1   121.24  3.000
 56E  H3   C9   C8   123.65  3.000
 56E  H3   C9   C7   122.84  3.000
 56E  C8   C9   C7   113.50  3.000
 56E  O12  C11  O13  124.89  3.000
 56E  O13  C11  C4   124.28  3.000
 56E  O12  C11  C4   110.83  3.000
 56E  H8   C14  H7   108.15  3.000
 56E  H8   C14  O12  109.41  3.000
 56E  H7   C14  O12  109.39  3.000
 56E  H8   C14  C15  111.04  3.000
 56E  H7   C14  C15  111.17  3.000
 56E  O12  C14  C15  107.65  3.000
 56E  H11  C15  H10  107.84  3.000
 56E  H11  C15  H9   108.74  3.000
 56E  H10  C15  H9   107.85  3.000
 56E  H11  C15  C14  111.70  3.000
 56E  H10  C15  C14  109.02  3.000
 56E  H9   C15  C14  111.55  3.000
 56E  H12  C12  S11  119.30  3.000
 56E  H12  C12  C8   129.15  3.000
 56E  S11  C12  C8   111.54  3.000
 56E  C12  S11  C7    92.59  3.000
 56E  H13  N7   C4   117.38  3.000
 56E  H13  N7   C1   121.09  3.000
 56E  C4   N7   C1   121.53  3.000
 56E  C14  O12  C11  118.27  3.000
 56E  H6   C10  H5   107.93  3.000
 56E  H6   C10  H4   107.50  3.000
 56E  H5   C10  H4   107.91  3.000
 56E  H6   C10  C7   111.78  3.000
 56E  H5   C10  C7   109.79  3.000
 56E  H4   C10  C7   111.77  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
 56E  CONST_01  C12  C8   C9   C7      0.00   0.0  0
 56E  CONST_02  C8   C12  S11  C7      0.00   0.0  0
 56E  CONST_03  S11  C7   C9   C8      0.00   0.0  0
 56E  CONST_04  C12  S11  C7   C9      0.00   0.0  0
 56E  CONST_05  S11  C12  C8   C9      0.00   0.0  0
 56E  CONST_06  C7   C9   C8   C1    180.00   0.0  0
 56E  CONST_07  S11  C12  C8   C1    180.00   0.0  0
 56E  CONST_08  C10  C7   C9   C8    180.00   0.0  0
 56E  CONST_09  C12  S11  C7   C10   180.00   0.0  0
 56E  CONST_10  H12  C12  S11  C7    180.00   0.0  0
 56E  CONST_11  H3   C9   C8   C12   180.00   0.0  0
 56E  CONST_12  C8   C1   N7   C4    180.00   0.0  0
 56E  CONST_13  H13  N7   C1   C8      0.00   0.0  0
 56E  CONST_14  O11  C1   N7   C4      0.00   0.0  0
 56E  Var_01    N7   C1   C8   C9   -171.73  30.0  2
 56E  Var_02    H4   C10  C7   C9   -121.64  30.0  2
 56E  Var_03    C11  C4   N7   C1    177.33  30.0  1
 56E  Var_04    C15  C14  O12  C11  -178.29  30.0  2
 56E  Var_05    O13  C11  O12  C14    -0.55  30.0  3
 56E  Var_06    O12  C11  C4   N7   -179.40  30.0  3
 56E  Var_07    H9   C15  C14  O12    60.71  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
 56E  plan-1  C1   0.020
 56E  plan-1  C7   0.020
 56E  plan-1  C8   0.020
 56E  plan-1  C9   0.020
 56E  plan-1  C12  0.020
 56E  plan-1  S11  0.020
 56E  plan-1  H3   0.020
 56E  plan-1  H12  0.020
 56E  plan-1  C10  0.020
 56E  plan-2  C1   0.020
 56E  plan-2  C4   0.020
 56E  plan-2  C8   0.020
 56E  plan-2  O11  0.020
 56E  plan-2  N7   0.020
 56E  plan-2  H13  0.020
 56E  plan-3  C4   0.020
 56E  plan-3  C11  0.020
 56E  plan-3  O13  0.020
 56E  plan-3  O12  0.020

