# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 13:14:33 2020
#   Inital geometry file: a 62 line input string
#   Ligand name: 2-(3-methoxy-4-oxidanyl-phenyl)ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(CC(O)=O)ccc1O
#
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
 YTX  YTX  '2-(3-methoxy-4-oxidanyl-phenyl)ethanoic acid'  ligand  22  13  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_YTX
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
 YTX  C1   C  CR6    0   0.300  -1.5497   0.3298  -0.1329
 YTX  C2   C  CR16   0  -0.420  -0.2236   0.5835  -0.4373
 YTX  C3   C  CR6    0   0.174   0.6905  -0.4595  -0.6148
 YTX  O1   O  OC    -1  -0.627   4.1812   0.5524  -0.0361
 YTX  O2   O  O      0  -0.595   2.4242   0.5221   1.3340
 YTX  C4   C  CH2    0  -0.696   2.1184  -0.1581  -0.9463
 YTX  C5   C  C      0   0.418   2.9808   0.3512   0.2364
 YTX  C6   C  CR16   0  -0.340   0.2343  -1.7608  -0.4752
 YTX  C7   C  CR16   0  -0.332  -1.0968  -2.0284  -0.1618
 YTX  C8   C  CR6    0   0.255  -1.9969  -0.9945   0.0115
 YTX  O3   O  OH1    0  -0.639  -3.2869  -1.2743   0.3094
 YTX  O    O  O2     0  -0.493  -2.5064   1.2707   0.0494
 YTX  C    C  CH3    0  -0.429  -2.1434   2.6314  -0.0567
 YTX  H1   H  HCR6   0   0.266   0.1231   1.6033  -0.5500
 YTX  H3   H  HCH2   0   0.242   2.6008  -1.0475  -1.3627
 YTX  H4   H  HCH2   0   0.241   2.1673   0.5970  -1.7382
 YTX  H5   H  HCR6   0   0.238   0.9184  -2.5900  -0.6100
 YTX  H6   H  HCR6   0   0.255  -1.4394  -3.0505  -0.0536
 YTX  H7   H  HOH1   0   0.468  -3.7822  -0.4550   0.4260
 YTX  H8   H  HCH3   0   0.228  -1.3810   2.9063   0.6765
 YTX  H9   H  HCH3   0   0.228  -1.7742   2.8761  -1.0560
 YTX  H10  H  HCH3   0   0.260  -3.0430   3.2099   0.1380

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
 YTX  O2  C5   deloc     1.242  0.020  1.242
 YTX  C4  C5   single    1.550  0.020  1.550
 YTX  C4  C3   single    1.497  0.020  1.497
 YTX  C5  O1   deloc     1.247  0.020  1.247
 YTX  C   O    single    1.412  0.020  1.412
 YTX  C2  C3   aromatic  1.398  0.020  1.398
 YTX  C2  C1   aromatic  1.384  0.020  1.384
 YTX  C3  C6   aromatic  1.386  0.020  1.386
 YTX  O   C1   single    1.354  0.020  1.354
 YTX  C1  C8   aromatic  1.405  0.020  1.405
 YTX  C6  C7   aromatic  1.393  0.020  1.393
 YTX  C8  C7   aromatic  1.382  0.020  1.382
 YTX  C8  O3   single    1.353  0.020  1.353
 YTX  C2  H1   single    0.930  0.020  1.080
 YTX  C4  H3   single    0.970  0.020  1.090
 YTX  C4  H4   single    0.970  0.020  1.090
 YTX  C6  H5   single    0.930  0.020  1.080
 YTX  C7  H6   single    0.930  0.020  1.080
 YTX  O3  H7   single    0.850  0.020  0.980
 YTX  C   H8   single    0.970  0.020  1.090
 YTX  C   H9   single    0.970  0.020  1.090
 YTX  C   H10  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
 YTX  O    C1  C8  114.59  3.000
 YTX  C8   C1  C2  120.02  3.000
 YTX  O    C1  C2  125.39  3.000
 YTX  H1   C2  C3  118.68  3.000
 YTX  H1   C2  C1  120.14  3.000
 YTX  C3   C2  C1  121.17  3.000
 YTX  C6   C3  C4  121.70  3.000
 YTX  C6   C3  C2  118.19  3.000
 YTX  C4   C3  C2  120.11  3.000
 YTX  H4   C4  H3  105.40  3.000
 YTX  H4   C4  C5  107.48  3.000
 YTX  H3   C4  C5  108.19  3.000
 YTX  H4   C4  C3  109.98  3.000
 YTX  H3   C4  C3  109.95  3.000
 YTX  C5   C4  C3  115.35  3.000
 YTX  C4   C5  O2  118.04  3.000
 YTX  C4   C5  O1  114.95  3.000
 YTX  O2   C5  O1  127.02  3.000
 YTX  H5   C6  C7  118.96  3.000
 YTX  H5   C6  C3  119.88  3.000
 YTX  C7   C6  C3  121.16  3.000
 YTX  H6   C7  C8  119.16  3.000
 YTX  H6   C7  C6  120.38  3.000
 YTX  C8   C7  C6  120.45  3.000
 YTX  O3   C8  C7  119.60  3.000
 YTX  O3   C8  C1  121.39  3.000
 YTX  C7   C8  C1  119.01  3.000
 YTX  H7   O3  C8  109.91  3.000
 YTX  C    O   C1  118.54  3.000
 YTX  H10  C   H9  108.91  3.000
 YTX  H10  C   H8  108.86  3.000
 YTX  H9   C   H8  108.75  3.000
 YTX  H10  C   O   106.65  3.000
 YTX  H9   C   O   111.79  3.000
 YTX  H8   C   O   111.79  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
 YTX  CONST_01  C6  C3  C2  C1    0.00   0.0  0
 YTX  CONST_02  C6  C7  C8  C1    0.00   0.0  0
 YTX  CONST_03  C7  C6  C3  C2    0.00   0.0  0
 YTX  CONST_04  C7  C8  C1  C2    0.00   0.0  0
 YTX  CONST_05  C8  C1  C2  C3    0.00   0.0  0
 YTX  CONST_06  C8  C7  C6  C3    0.00   0.0  0
 YTX  CONST_07  C4  C3  C2  C1  180.00   0.0  0
 YTX  CONST_08  O3  C8  C1  C2  180.00   0.0  0
 YTX  CONST_09  O   C1  C2  C3  180.00   0.0  0
 YTX  CONST_10  C7  C6  C3  C4  180.00   0.0  0
 YTX  CONST_11  O3  C8  C7  C6  180.00   0.0  0
 YTX  CONST_12  O   C1  C8  C7  180.00   0.0  0
 YTX  CONST_13  H6  C7  C8  C1  180.00   0.0  0
 YTX  CONST_14  H5  C6  C3  C2  180.00   0.0  0
 YTX  CONST_15  H1  C2  C3  C6  180.00   0.0  0
 YTX  Var_01    C5  C4  C3  C2   75.71  30.0  2
 YTX  Var_02    O2  C5  C4  C3   -2.92  30.0  3
 YTX  Var_03    H8  C   O   C1  -60.22  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
 YTX  plan-1  C1  0.020
 YTX  plan-1  C2  0.020
 YTX  plan-1  C3  0.020
 YTX  plan-1  C4  0.020
 YTX  plan-1  C6  0.020
 YTX  plan-1  C7  0.020
 YTX  plan-1  C8  0.020
 YTX  plan-1  O3  0.020
 YTX  plan-1  O   0.020
 YTX  plan-1  H1  0.020
 YTX  plan-1  H5  0.020
 YTX  plan-1  H6  0.020
 YTX  plan-2  O1  0.020
 YTX  plan-2  O2  0.020
 YTX  plan-2  C4  0.020
 YTX  plan-2  C5  0.020

