# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 02:18:02 2020
#   Inital geometry file: a 46 line input string
#   Ligand name: benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccccc1
#
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
 BOX  BOX  'benzoic acid             '  ligand  14  9  .  2022-03-15  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_BOX
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
 BOX  C1   C  CR6    0  -0.098  -0.0285  -0.0004   0.1821
 BOX  C2   C  CR16   0  -0.290  -1.1995  -0.0149  -0.5728
 BOX  C3   C  CR16   0  -0.246  -1.1529  -0.0218  -1.9605
 BOX  C4   C  CR16   0  -0.265   0.0719  -0.0158  -2.6165
 BOX  C5   C  CR16   0  -0.246   1.2469  -0.0013  -1.8748
 BOX  C6   C  CR16   0  -0.290   1.1937   0.0065  -0.4875
 BOX  C1'  C  C      0   0.395  -0.0824   0.0097   1.7054
 BOX  O1'  O  O      0  -0.595  -1.2151  -0.0051   2.2246
 BOX  O2'  O  OC    -1  -0.595   1.0112   0.0330   2.3023
 BOX  H2   H  HCR6   0   0.242  -2.1560  -0.0205  -0.0663
 BOX  H3   H  HCR6   0   0.248  -2.0720  -0.0333  -2.5332
 BOX  H4   H  HCR6   0   0.251   0.1107  -0.0219  -3.6984
 BOX  H5   H  HCR6   0   0.247   2.2051   0.0043  -2.3795
 BOX  H6   H  HCR6   0   0.242   2.1108   0.0186   0.0871

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
 BOX  C1   C2   aromatic  1.393  0.020  1.393
 BOX  C1   C6   aromatic  1.394  0.020  1.394
 BOX  C1   C1'  single    1.524  0.020  1.524
 BOX  C2   C3   aromatic  1.389  0.020  1.389
 BOX  C2   H2   single    0.930  0.020  1.080
 BOX  C3   C4   aromatic  1.389  0.020  1.389
 BOX  C3   H3   single    0.930  0.020  1.080
 BOX  C4   C5   aromatic  1.390  0.020  1.390
 BOX  C4   H4   single    0.930  0.020  1.080
 BOX  C5   C6   aromatic  1.388  0.020  1.388
 BOX  C5   H5   single    0.930  0.020  1.080
 BOX  C6   H6   single    0.930  0.020  1.080
 BOX  C1'  O1'  deloc     1.246  0.020  1.246
 BOX  C1'  O2'  deloc     1.246  0.020  1.246

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
 BOX  C1'  C1   C6   120.74  3.000
 BOX  C1'  C1   C2   120.78  3.000
 BOX  C6   C1   C2   118.48  3.000
 BOX  H2   C2   C3   119.82  3.000
 BOX  H2   C2   C1   119.29  3.000
 BOX  C3   C2   C1   120.88  3.000
 BOX  H3   C3   C4   119.90  3.000
 BOX  H3   C3   C2   120.00  3.000
 BOX  C4   C3   C2   120.09  3.000
 BOX  H4   C4   C5   120.21  3.000
 BOX  H4   C4   C3   120.23  3.000
 BOX  C5   C4   C3   119.57  3.000
 BOX  H5   C5   C6   119.97  3.000
 BOX  H5   C5   C4   119.97  3.000
 BOX  C6   C5   C4   120.07  3.000
 BOX  H6   C6   C5   119.87  3.000
 BOX  H6   C6   C1   119.22  3.000
 BOX  C5   C6   C1   120.91  3.000
 BOX  O2'  C1'  O1'  126.76  3.000
 BOX  O2'  C1'  C1   116.60  3.000
 BOX  O1'  C1'  C1   116.64  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
 BOX  CONST_01  C4   C3   C2  C1    0.00   0.0  0
 BOX  CONST_02  C4   C5   C6  C1    0.00   0.0  0
 BOX  CONST_03  C5   C6   C1  C2    0.00   0.0  0
 BOX  CONST_04  C5   C4   C3  C2    0.00   0.0  0
 BOX  CONST_05  C6   C1   C2  C3    0.00   0.0  0
 BOX  CONST_06  C6   C5   C4  C3    0.00   0.0  0
 BOX  CONST_07  C1'  C1   C2  C3  180.00   0.0  0
 BOX  CONST_08  C1'  C1   C6  C5  180.00   0.0  0
 BOX  CONST_09  H3   C3   C2  C1  180.00   0.0  0
 BOX  CONST_10  H5   C5   C6  C1  180.00   0.0  0
 BOX  CONST_11  H6   C6   C1  C2  180.00   0.0  0
 BOX  CONST_12  H4   C4   C3  C2  180.00   0.0  0
 BOX  CONST_13  H2   C2   C3  C4  180.00   0.0  0
 BOX  Var_01    O1'  C1'  C1  C2    0.49  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
 BOX  plan-1  C1   0.020
 BOX  plan-1  C2   0.020
 BOX  plan-1  C3   0.020
 BOX  plan-1  C4   0.020
 BOX  plan-1  C5   0.020
 BOX  plan-1  C6   0.020
 BOX  plan-1  C1'  0.020
 BOX  plan-1  H2   0.020
 BOX  plan-1  H3   0.020
 BOX  plan-1  H4   0.020
 BOX  plan-1  H5   0.020
 BOX  plan-1  H6   0.020
 BOX  plan-2  C1   0.020
 BOX  plan-2  C1'  0.020
 BOX  plan-2  O1'  0.020
 BOX  plan-2  O2'  0.020

