# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 29 22:59:30 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: (3Z)-4-(2-methoxyphenyl)-2-oxobut-3-enoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccccc1\C=C/C(=O)C(O)=O
#
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
 TOM  TOM  '(3Z)-4-(2-methoxyphenyl)-2-oxobut-3-enoic acid'  ligand  25  15  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_TOM
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
 TOM  O8    O  O     0  -0.358   5.6293  -4.4443   4.2633
 TOM  C9    C  C     0   0.260   5.7988  -4.2186   3.0850
 TOM  C10   C  C     0   0.505   7.0387  -4.7991   2.3869
 TOM  O11   O  OH1   0  -0.614   7.7755  -5.5025   3.2173
 TOM  O10   O  O     0  -0.405   7.2786  -4.6225   1.2212
 TOM  C8    C  C1    0  -0.392   4.9213  -3.4270   2.2365
 TOM  C7    C  C1    0  -0.187   3.8420  -2.8140   2.7598
 TOM  C1    C  CR6   0  -0.002   2.8568  -2.0342   2.0353
 TOM  C6    C  CR16  0  -0.215   2.8996  -1.8929   0.6426
 TOM  C5    C  CR16  0  -0.280   1.9181  -1.2106  -0.0470
 TOM  C4    C  CR16  0  -0.210   0.8536  -0.6568   0.6567
 TOM  C3    C  CR16  0  -0.263   0.7721  -0.7827   2.0333
 TOM  C2    C  CR6   0   0.259   1.7714  -1.4589   2.7318
 TOM  O2    O  O2    0  -0.484   1.7881  -1.5565   4.0684
 TOM  C11   C  CH3   0  -0.427   0.5759  -1.3883   4.7859
 TOM  HO11  H  HOH1  0   0.481   8.5556  -5.8541   2.7610
 TOM  H8    H  H     0   0.281   5.1695  -3.3601   1.1867
 TOM  H7    H  H     0   0.297   3.6660  -2.9395   3.8219
 TOM  H6    H  HCR6  0   0.262   3.7112  -2.3436   0.0867
 TOM  H5    H  HCR6  0   0.246   1.9725  -1.1179  -1.1228
 TOM  H4    H  HCR6  0   0.281   0.0767  -0.1175   0.1309
 TOM  H3    H  HCR6  0   0.283  -0.0586  -0.3279   2.5557
 TOM  H111  H  HCH3  0   0.210  -0.2257  -1.9995   4.3660
 TOM  H112  H  HCH3  0   0.233   0.2570  -0.3447   4.8138
 TOM  H113  H  HCH3  0   0.240   0.7759  -1.7152   5.8030

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
 TOM  O8   C9    double    1.212  0.020  1.212
 TOM  C9   C10   single    1.537  0.020  1.537
 TOM  C9   C8    single    1.455  0.020  1.455
 TOM  C10  O10   double    1.203  0.020  1.203
 TOM  C10  O11   single    1.314  0.020  1.314
 TOM  O11  HO11  single    0.850  0.020  0.980
 TOM  C8   C7    double    1.347  0.020  1.347
 TOM  C8   H8    single    0.930  0.020  1.080
 TOM  C7   C1    single    1.450  0.020  1.450
 TOM  C7   H7    single    0.930  0.020  1.080
 TOM  C1   C2    aromatic  1.412  0.020  1.412
 TOM  C1   C6    aromatic  1.400  0.020  1.400
 TOM  C6   C5    aromatic  1.380  0.020  1.380
 TOM  C6   H6    single    0.930  0.020  1.080
 TOM  C5   C4    aromatic  1.391  0.020  1.391
 TOM  C5   H5    single    0.930  0.020  1.080
 TOM  C4   C3    aromatic  1.385  0.020  1.385
 TOM  C4   H4    single    0.930  0.020  1.080
 TOM  C3   C2    aromatic  1.394  0.020  1.394
 TOM  C3   H3    single    0.930  0.020  1.080
 TOM  C2   O2    single    1.340  0.020  1.340
 TOM  O2   C11   single    1.419  0.020  1.419
 TOM  C11  H111  single    0.970  0.020  1.090
 TOM  C11  H112  single    0.970  0.020  1.090
 TOM  C11  H113  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
 TOM  C8    C9   C10   115.29  3.000
 TOM  C8    C9   O8    125.75  3.000
 TOM  C10   C9   O8    118.96  3.000
 TOM  O10   C10  O11   125.37  3.000
 TOM  O11   C10  C9    111.56  3.000
 TOM  O10   C10  C9    123.07  3.000
 TOM  HO11  O11  C10   110.35  3.000
 TOM  H8    C8   C7    122.21  3.000
 TOM  H8    C8   C9    117.50  3.000
 TOM  C7    C8   C9    120.29  3.000
 TOM  H7    C7   C1    116.20  3.000
 TOM  H7    C7   C8    117.26  3.000
 TOM  C1    C7   C8    126.51  3.000
 TOM  C2    C1   C6    118.22  3.000
 TOM  C6    C1   C7    122.02  3.000
 TOM  C2    C1   C7    119.66  3.000
 TOM  H6    C6   C5    118.86  3.000
 TOM  H6    C6   C1    119.46  3.000
 TOM  C5    C6   C1    121.67  3.000
 TOM  H5    C5   C4    120.52  3.000
 TOM  H5    C5   C6    120.25  3.000
 TOM  C4    C5   C6    119.23  3.000
 TOM  H4    C4   C3    119.08  3.000
 TOM  H4    C4   C5    120.14  3.000
 TOM  C3    C4   C5    120.78  3.000
 TOM  H3    C3   C2    120.83  3.000
 TOM  H3    C3   C4    119.15  3.000
 TOM  C2    C3   C4    119.99  3.000
 TOM  O2    C2   C3    122.94  3.000
 TOM  O2    C2   C1    116.91  3.000
 TOM  C3    C2   C1    120.10  3.000
 TOM  C11   O2   C2    119.02  3.000
 TOM  H113  C11  H112  108.50  3.000
 TOM  H113  C11  H111  109.06  3.000
 TOM  H112  C11  H111  109.30  3.000
 TOM  H113  C11  O2    106.28  3.000
 TOM  H112  C11  O2    112.09  3.000
 TOM  H111  C11  O2    111.50  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
 TOM  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 TOM  CONST_02  C4    C5   C6   C1     0.00   0.0  0
 TOM  CONST_03  C3    C2   C1   C6     0.00   0.0  0
 TOM  CONST_04  C3    C4   C5   C6     0.00   0.0  0
 TOM  CONST_05  C2    C1   C6   C5     0.00   0.0  0
 TOM  CONST_06  C2    C3   C4   C5     0.00   0.0  0
 TOM  CONST_07  C3    C2   C1   C7   180.00   0.0  0
 TOM  CONST_08  C5    C6   C1   C7   180.00   0.0  0
 TOM  CONST_09  O2    C2   C1   C6   180.00   0.0  0
 TOM  CONST_10  O2    C2   C3   C4   180.00   0.0  0
 TOM  CONST_11  H3    C3   C2   C1   180.00   0.0  0
 TOM  CONST_12  H5    C5   C6   C1   180.00   0.0  0
 TOM  CONST_13  H4    C4   C5   C6   180.00   0.0  0
 TOM  CONST_14  H6    C6   C5   C4   180.00   0.0  0
 TOM  CONST_15  HO11  O11  C10  C9   180.00   0.0  0
 TOM  Var_01    C2    C1   C7   C8   179.62  30.0  2
 TOM  Var_02    C1    C7   C8   C9  -177.74   0.0  2
 TOM  Var_03    H111  C11  O2   C2    49.39  30.0  3
 TOM  Var_04    O10   C10  C9   O8   179.93  30.0  2
 TOM  Var_05    C7    C8   C9   O8     3.29  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
 TOM  plan-1  C7    0.020
 TOM  plan-1  C1    0.020
 TOM  plan-1  C6    0.020
 TOM  plan-1  C5    0.020
 TOM  plan-1  C4    0.020
 TOM  plan-1  C3    0.020
 TOM  plan-1  C2    0.020
 TOM  plan-1  O2    0.020
 TOM  plan-1  H6    0.020
 TOM  plan-1  H5    0.020
 TOM  plan-1  H4    0.020
 TOM  plan-1  H3    0.020
 TOM  plan-2  O8    0.020
 TOM  plan-2  C9    0.020
 TOM  plan-2  C10   0.020
 TOM  plan-2  C8    0.020
 TOM  plan-3  C9    0.020
 TOM  plan-3  C10   0.020
 TOM  plan-3  O11   0.020
 TOM  plan-3  O10   0.020
 TOM  plan-3  HO11  0.020
 TOM  plan-4  C9    0.020
 TOM  plan-4  C8    0.020
 TOM  plan-4  C7    0.020
 TOM  plan-4  C1    0.020
 TOM  plan-4  H8    0.020
 TOM  plan-4  H7    0.020

