# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 13:48:33 2020
#   Inital geometry file: a 44 line input string
#   Ligand name: methyl thiophene-2-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)c1sccc1
#
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
 54D  54D  'methyl thiophene-2-carboxylate'  ligand  15  9  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_54D
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
 54D  O8   O  O     0  -0.444   1.8234  -1.5894   0.0194
 54D  C6   C  C     0   0.583   1.2434  -0.5309  -0.0006
 54D  O7   O  O2    0  -0.464   1.8392   0.6521  -0.0226
 54D  C9   C  CH3   0  -0.421   3.2676   0.6747  -0.0232
 54D  C2   C  CR5   0  -0.324  -0.2134  -0.3980  -0.0036
 54D  S3   S  S2    0   0.271  -0.9982   1.1333  -0.0260
 54D  C4   C  CR15  0  -0.449  -2.5362   0.3969  -0.0193
 54D  C5   C  CR15  0  -0.176  -2.4552  -0.9665  -0.0005
 54D  C1   C  CR15  0  -0.181  -1.1182  -1.4244   0.0083
 54D  H9   H  HCH3  0   0.255   3.5477   1.7231  -0.0550
 54D  H9A  H  HCH3  0   0.243   3.6708   0.2182   0.8802
 54D  H9B  H  HCH3  0   0.243   3.6711   0.1649  -0.8975
 54D  H4   H  HCR5  0   0.308  -3.4283   1.0045  -0.0289
 54D  H5   H  HCR5  0   0.278  -3.3179  -1.6160   0.0044
 54D  H1   H  HCR5  0   0.279  -0.8340  -2.4668   0.0213

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
 54D  O8  C6   double    1.207  0.020  1.207
 54D  C6  O7   single    1.325  0.020  1.325
 54D  C6  C2   single    1.463  0.020  1.463
 54D  O7  C9   single    1.429  0.020  1.429
 54D  C2  S3   aromatic  1.721  0.020  1.721
 54D  C2  C1   aromatic  1.368  0.020  1.368
 54D  S3  C4   aromatic  1.705  0.020  1.705
 54D  C4  C5   aromatic  1.366  0.020  1.366
 54D  C5  C1   aromatic  1.413  0.020  1.413
 54D  C9  H9   single    0.970  0.020  1.090
 54D  C9  H9A  single    0.970  0.020  1.090
 54D  C9  H9B  single    0.970  0.020  1.090
 54D  C4  H4   single    0.930  0.020  1.080
 54D  C5  H5   single    0.930  0.020  1.080
 54D  C1  H1   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
 54D  C2   C6  O7   111.51  3.000
 54D  C2   C6  O8   123.94  3.000
 54D  O7   C6  O8   124.55  3.000
 54D  C9   O7  C6   117.64  3.000
 54D  H9B  C9  H9A  109.40  3.000
 54D  H9B  C9  H9   109.44  3.000
 54D  H9A  C9  H9   109.48  3.000
 54D  H9B  C9  O7   111.30  3.000
 54D  H9A  C9  O7   111.29  3.000
 54D  H9   C9  O7   105.86  3.000
 54D  C1   C2  S3   111.47  3.000
 54D  C1   C2  C6   126.18  3.000
 54D  S3   C2  C6   122.35  3.000
 54D  C4   S3  C2    91.55  3.000
 54D  H4   C4  C5   127.66  3.000
 54D  H4   C4  S3   120.15  3.000
 54D  C5   C4  S3   112.19  3.000
 54D  H5   C5  C1   124.11  3.000
 54D  H5   C5  C4   123.58  3.000
 54D  C1   C5  C4   112.30  3.000
 54D  H1   C1  C5   124.15  3.000
 54D  H1   C1  C2   123.36  3.000
 54D  C5   C1  C2   112.49  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
 54D  CONST_01  C5  C4  S3  C2     0.00   0.0  0
 54D  CONST_02  C4  C5  C1  C2     0.00   0.0  0
 54D  CONST_03  C5  C1  C2  S3     0.00   0.0  0
 54D  CONST_04  C1  C5  C4  S3     0.00   0.0  0
 54D  CONST_05  C1  C2  S3  C4     0.00   0.0  0
 54D  CONST_06  C4  S3  C2  C6   180.00   0.0  0
 54D  CONST_07  C5  C1  C2  C6   180.00   0.0  0
 54D  CONST_08  H4  C4  S3  C2   180.00   0.0  0
 54D  CONST_09  H5  C5  C1  C2   180.00   0.0  0
 54D  CONST_10  H1  C1  C2  S3   180.00   0.0  0
 54D  Var_01    S3  C2  C6  O8   179.74  30.0  2
 54D  Var_02    C2  C6  O7  C9  -179.97  30.0  1
 54D  Var_03    H9  C9  O7  C6   179.33  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
 54D  plan-1  C6  0.020
 54D  plan-1  C2  0.020
 54D  plan-1  S3  0.020
 54D  plan-1  C4  0.020
 54D  plan-1  C5  0.020
 54D  plan-1  C1  0.020
 54D  plan-1  H4  0.020
 54D  plan-1  H5  0.020
 54D  plan-1  H1  0.020
 54D  plan-2  O8  0.020
 54D  plan-2  C6  0.020
 54D  plan-2  O7  0.020
 54D  plan-2  C2  0.020

