# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 06:49:38 2022
#   Inital geometry file: a 50 line input string
#   Ligand name: 2,3-dihydrothieno[3,4-b][1,4]dioxine-5-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1scc2OCCOc12
#
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
 Y34  Y34  '2,3-dihydrothieno[3,4-b][1,4]dioxine-5-carboxylic acid'  ligand  17  12  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Y34
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
 Y34  C4  C  CH2    0  -0.230  -18.9639  13.4740  25.8458
 Y34  C5  C  CR5    0   0.362  -20.9805  12.3968  25.5207
 Y34  C6  C  CR15   0  -0.571  -21.9406  11.7403  24.8155
 Y34  O1  O  O      0  -0.598  -24.9900  12.9927  27.7085
 Y34  O   O  OC    -1  -0.576  -23.3425  13.9922  28.8507
 Y34  C1  C  CR5    0  -0.465  -22.8411  12.8662  26.8492
 Y34  S   S  S2     0   0.186  -23.4748  11.9032  25.5653
 Y34  C2  C  CR5    0   0.356  -21.4939  13.0447  26.6904
 Y34  O3  O  O2     0  -0.474  -19.6747  12.4411  25.1749
 Y34  C3  C  CH2    0  -0.229  -19.3116  13.4954  27.3162
 Y34  O2  O  O2     0  -0.459  -20.6961  13.7575  27.5113
 Y34  H1  H  HCH2   0   0.259  -17.9019  13.2689  25.7162
 Y34  H2  H  HCH2   0   0.239  -19.1862  14.4443  25.3881
 Y34  H3  H  HCR5   0   0.290  -21.8102  11.1779  23.9036
 Y34  H5  H  HCH2   0   0.240  -19.0395  12.5435  27.7857
 Y34  H6  H  HCH2   0   0.258  -18.7637  14.2924  27.8176
 Y34  C   C  C      0   0.411  -23.8056  13.3330  27.9051

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
 Y34  C6  S   aromatic  1.715  0.020  1.715
 Y34  C6  C5  aromatic  1.360  0.020  1.360
 Y34  O3  C5  single    1.352  0.020  1.352
 Y34  O3  C4  single    1.422  0.020  1.422
 Y34  S   C1  aromatic  1.726  0.020  1.726
 Y34  C5  C2  aromatic  1.432  0.020  1.432
 Y34  C4  C3  single    1.511  0.020  1.511
 Y34  C2  C1  aromatic  1.368  0.020  1.368
 Y34  C2  O2  single    1.348  0.020  1.348
 Y34  C1  C   single    1.504  0.020  1.504
 Y34  C3  O2  single    1.423  0.020  1.423
 Y34  O1  C   deloc     1.248  0.020  1.248
 Y34  C   O   deloc     1.242  0.020  1.242
 Y34  C4  H1  single    0.970  0.020  1.090
 Y34  C4  H2  single    0.970  0.020  1.090
 Y34  C6  H3  single    0.930  0.020  1.080
 Y34  C3  H5  single    0.970  0.020  1.090
 Y34  C3  H6  single    0.970  0.020  1.090

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
 Y34  H2  C4  H1  108.35  3.000
 Y34  H2  C4  C3  110.32  3.000
 Y34  H1  C4  C3  110.05  3.000
 Y34  H2  C4  O3  110.16  3.000
 Y34  H1  C4  O3  107.12  3.000
 Y34  C3  C4  O3  110.75  3.000
 Y34  O3  C5  C2  122.71  3.000
 Y34  C2  C5  C6  112.87  3.000
 Y34  O3  C5  C6  124.41  3.000
 Y34  H3  C6  S   121.80  3.000
 Y34  H3  C6  C5  127.17  3.000
 Y34  S   C6  C5  111.03  3.000
 Y34  C2  C1  S   110.37  3.000
 Y34  C2  C1  C   132.24  3.000
 Y34  S   C1  C   117.39  3.000
 Y34  C1  S   C6   92.85  3.000
 Y34  O2  C2  C1  125.51  3.000
 Y34  O2  C2  C5  121.61  3.000
 Y34  C1  C2  C5  112.87  3.000
 Y34  C5  O3  C4  112.71  3.000
 Y34  H6  C3  H5  108.27  3.000
 Y34  H6  C3  O2  106.95  3.000
 Y34  H5  C3  O2  110.06  3.000
 Y34  H6  C3  C4  110.03  3.000
 Y34  H5  C3  C4  110.33  3.000
 Y34  O2  C3  C4  111.10  3.000
 Y34  C3  O2  C2  113.26  3.000
 Y34  C1  C   O   117.38  3.000
 Y34  O   C   O1  128.21  3.000
 Y34  C1  C   O1  114.41  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
 Y34  CONST_01  C1  S   C6  C5    0.00   0.0  0
 Y34  CONST_02  S   C1  C2  C5    0.00   0.0  0
 Y34  CONST_03  C2  C1  S   C6    0.00   0.0  0
 Y34  CONST_04  C1  C2  C5  C6    0.00   0.0  0
 Y34  CONST_05  C2  C5  C6  S     0.00   0.0  0
 Y34  CONST_06  C   C1  C2  C5  180.00   0.0  0
 Y34  CONST_07  C   C1  S   C6  180.00   0.0  0
 Y34  CONST_08  O2  C2  C1  C     0.00   0.0  0
 Y34  CONST_09  H3  C6  S   C1  180.00   0.0  0
 Y34  Var_01    C6  C5  O3  C4  163.53  30.0  1
 Y34  Var_02    C3  C4  O3  C5   45.22  30.0  1
 Y34  Var_03    O2  C3  C4  O3  -61.56  30.0  1
 Y34  Var_04    H5  C3  O2  C2  -77.49  30.0  1
 Y34  Var_05    S   C1  C   O1   -1.88  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
 Y34  plan-1  O1  0.020
 Y34  plan-1  O   0.020
 Y34  plan-1  C1  0.020
 Y34  plan-1  C   0.020
 Y34  plan-2  C5  0.020
 Y34  plan-2  C6  0.020
 Y34  plan-2  C1  0.020
 Y34  plan-2  S   0.020
 Y34  plan-2  C2  0.020
 Y34  plan-2  O3  0.020
 Y34  plan-2  O2  0.020
 Y34  plan-2  H3  0.020
 Y34  plan-2  C   0.020

