# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 04:07:36 2022
#   Inital geometry file: a 56 line input string
#   Ligand name: methyl 2,4-bis(oxidanyl)benzoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)c1ccc(O)cc1O
#
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
 HF9  HF9  "methyl 2,4-bis(oxidanyl)benzoate"  ligand  20  12  .  2022-08-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HF9
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
 HF9  C1   C  CR6   0   0.390  -2.4154  -10.6650  5.7586
 HF9  C6   C  CR16  0  -0.349  -3.4640   -9.8834  5.2523
 HF9  C5   C  CR16  0  -0.250  -3.5888   -8.5815  5.6705
 HF9  C3   C  CR6   0   0.390  -1.6493   -8.8089  7.0933
 HF9  C2   C  CR16  0  -0.475  -1.5182  -10.1299  6.6711
 HF9  C4   C  CR6   0  -0.262  -2.6982   -8.0111  6.5907
 HF9  O7   O  OH1   0  -0.614  -2.3298  -11.9269  5.3239
 HF9  O8   O  OH1   0  -0.622  -0.7580   -8.3539  7.9705
 HF9  O10  O  O2    0  -0.449  -3.8265   -5.9697  6.5068
 HF9  O11  O  O     0  -0.499  -2.0517   -6.1154  7.8469
 HF9  C12  C  CH3   0  -0.422  -4.0145   -4.6054  6.8852
 HF9  H1   H  HCR6  0   0.268  -4.1607  -10.3071  4.5415
 HF9  H2   H  HCR6  0   0.269  -4.3999   -7.9860  5.2748
 HF9  H3   H  HCR6  0   0.281  -0.7059  -10.7297  7.0668
 HF9  H4   H  HOH1  0   0.480  -1.5827  -12.3839  5.7295
 HF9  H5   H  HOH1  0   0.476  -0.9790   -7.4177  8.1692
 HF9  H6   H  HCH3  0   0.255  -4.8885   -4.2657  6.3379
 HF9  H7   H  HCH3  0   0.243  -4.1974   -4.5103  7.9548
 HF9  H8   H  HCH3  0   0.243  -3.1547   -3.9954  6.6100
 HF9  C9   C  C     0   0.648  -2.8181   -6.6271  7.0422

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
 HF9  C6   C5   aromatic  1.373  0.020  1.373
 HF9  C6   C1   aromatic  1.402  0.020  1.402
 HF9  O7   C1   single    1.337  0.020  1.337
 HF9  C5   C4   aromatic  1.402  0.020  1.402
 HF9  C1   C2   aromatic  1.387  0.020  1.387
 HF9  O10  C12  single    1.428  0.020  1.428
 HF9  O10  C9   single    1.317  0.020  1.317
 HF9  C4   C9   single    1.461  0.020  1.461
 HF9  C4   C3   aromatic  1.410  0.020  1.410
 HF9  C2   C3   aromatic  1.393  0.020  1.393
 HF9  C9   O11  double    1.223  0.020  1.223
 HF9  C3   O8   single    1.331  0.020  1.331
 HF9  C6   H1   single    0.930  0.020  1.080
 HF9  C5   H2   single    0.930  0.020  1.080
 HF9  C2   H3   single    0.930  0.020  1.080
 HF9  O7   H4   single    0.850  0.020  0.980
 HF9  O8   H5   single    0.850  0.020  0.980
 HF9  C12  H6   single    0.970  0.020  1.090
 HF9  C12  H7   single    0.970  0.020  1.090
 HF9  C12  H8   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
 HF9  O7   C1   C2   122.44  3.000
 HF9  C2   C1   C6   120.41  3.000
 HF9  O7   C1   C6   117.15  3.000
 HF9  H1   C6   C5   120.86  3.000
 HF9  H1   C6   C1   120.04  3.000
 HF9  C5   C6   C1   119.10  3.000
 HF9  H2   C5   C4   119.51  3.000
 HF9  H2   C5   C6   118.61  3.000
 HF9  C4   C5   C6   121.87  3.000
 HF9  O8   C3   C4   122.65  3.000
 HF9  O8   C3   C2   117.45  3.000
 HF9  C4   C3   C2   119.89  3.000
 HF9  H3   C2   C3   118.97  3.000
 HF9  H3   C2   C1   120.74  3.000
 HF9  C3   C2   C1   120.29  3.000
 HF9  C9   C4   C3   119.13  3.000
 HF9  C3   C4   C5   118.43  3.000
 HF9  C9   C4   C5   122.43  3.000
 HF9  H4   O7   C1   111.08  3.000
 HF9  H5   O8   C3   107.97  3.000
 HF9  C12  O10  C9   118.01  3.000
 HF9  H8   C12  H7   109.37  3.000
 HF9  H8   C12  H6   109.44  3.000
 HF9  H7   C12  H6   109.41  3.000
 HF9  H8   C12  O10  111.35  3.000
 HF9  H7   C12  O10  111.45  3.000
 HF9  H6   C12  O10  105.74  3.000
 HF9  O11  C9   O10  122.56  3.000
 HF9  O11  C9   C4   123.24  3.000
 HF9  O10  C9   C4   114.20  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
 HF9  CONST_01  C4   C5   C6   C1      0.00   0.0  0
 HF9  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 HF9  CONST_03  C3   C4   C5   C6      0.00   0.0  0
 HF9  CONST_04  C3   C2   C1   C6      0.00   0.0  0
 HF9  CONST_05  C2   C1   C6   C5      0.00   0.0  0
 HF9  CONST_06  C2   C3   C4   C5      0.00   0.0  0
 HF9  CONST_07  O8   C3   C2   C1    180.00   0.0  0
 HF9  CONST_08  C9   C4   C5   C6    180.00   0.0  0
 HF9  CONST_09  O7   C1   C6   C5    180.00   0.0  0
 HF9  CONST_10  O8   C3   C4   C5    180.00   0.0  0
 HF9  CONST_11  O7   C1   C2   C3    180.00   0.0  0
 HF9  CONST_12  C2   C3   C4   C9    180.00   0.0  0
 HF9  CONST_13  H2   C5   C6   C1    180.00   0.0  0
 HF9  CONST_14  H3   C2   C1   C6    180.00   0.0  0
 HF9  CONST_15  H2   C5   C4   C3    180.00   0.0  0
 HF9  CONST_16  H1   C6   C1   C2    180.00   0.0  0
 HF9  CONST_17  H1   C6   C5   C4    180.00   0.0  0
 HF9  CONST_18  H3   C2   C3   C4    180.00   0.0  0
 HF9  Var_01    O10  C9   C4   C5     -0.24  30.0  2
 HF9  Var_02    O11  C9   C4   C5    179.80  30.0  2
 HF9  Var_03    O10  C9   C4   C3    179.68  30.0  2
 HF9  Var_04    O11  C9   C4   C3     -0.28  30.0  2
 HF9  Var_05    C12  O10  C9   C4   -179.60  30.0  1
 HF9  Var_06    C12  O10  C9   O11     0.36  30.0  1
 HF9  Var_07    H6   C12  O10  C9   -179.78  30.0  3
 HF9  Var_08    H7   C12  O10  C9    -60.98  30.0  3
 HF9  Var_09    H8   C12  O10  C9     61.45  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
 HF9  plan-1  C1   0.020
 HF9  plan-1  C6   0.020
 HF9  plan-1  C5   0.020
 HF9  plan-1  C3   0.020
 HF9  plan-1  C2   0.020
 HF9  plan-1  C4   0.020
 HF9  plan-1  O7   0.020
 HF9  plan-1  O8   0.020
 HF9  plan-1  H1   0.020
 HF9  plan-1  H2   0.020
 HF9  plan-1  H3   0.020
 HF9  plan-1  C9   0.020
 HF9  plan-2  C4   0.020
 HF9  plan-2  O10  0.020
 HF9  plan-2  O11  0.020
 HF9  plan-2  C9   0.020

