# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 09:51:10 2020
#   Inital geometry file: a 44 line input string
#   Ligand name: benzaldehyde
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=Cc1ccccc1
#
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
 HBX  HBX  'benzaldehyde             '  ligand  14  8  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HBX
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
 HBX  C1'  C  C1    0   0.120   1.9341   0.5134   0.0147
 HBX  O1'  O  O     0  -0.384   2.8103  -0.3196   0.0410
 HBX  C1   C  CR6   0  -0.013   0.4945   0.2134   0.0001
 HBX  C2   C  CR16  0  -0.275  -0.4099   1.2721  -0.0359
 HBX  C3   C  CR16  0  -0.241  -1.7741   1.0225  -0.0517
 HBX  C4   C  CR16  0  -0.241  -2.2335  -0.2876  -0.0306
 HBX  C5   C  CR16  0  -0.241  -1.3331  -1.3494   0.0058
 HBX  C6   C  CR16  0  -0.264   0.0281  -1.1020   0.0208
 HBX  H1'  H  H     0   0.198   2.1767   1.5909  -0.0013
 HBX  H2   H  HCR6  0   0.269  -0.0437   2.2922  -0.0529
 HBX  H3   H  HCR6  0   0.268  -2.4770   1.8440  -0.0802
 HBX  H4   H  HCR6  0   0.270  -3.2977  -0.4842  -0.0424
 HBX  H5   H  HCR6  0   0.267  -1.6982  -2.3678   0.0226
 HBX  H6   H  HCR6  0   0.268   0.7308  -1.9248   0.0485

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
 HBX  C1   C1'  single    1.471  0.020  1.471
 HBX  C1'  O1'  double    1.209  0.020  1.209
 HBX  C1'  H1'  single    0.930  0.020  1.080
 HBX  C6   C1   aromatic  1.396  0.020  1.396
 HBX  C2   C1   aromatic  1.393  0.020  1.393
 HBX  C3   C2   aromatic  1.387  0.020  1.387
 HBX  C2   H2   single    0.930  0.020  1.080
 HBX  C4   C3   aromatic  1.388  0.020  1.388
 HBX  C3   H3   single    0.930  0.020  1.080
 HBX  C4   C5   aromatic  1.393  0.020  1.393
 HBX  C4   H4   single    0.930  0.020  1.080
 HBX  C5   C6   aromatic  1.384  0.020  1.384
 HBX  C5   H5   single    0.930  0.020  1.080
 HBX  C6   H6   single    0.930  0.020  1.080

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
 HBX  H1'  C1'  C1   114.45  3.000
 HBX  H1'  C1'  O1'  120.88  3.000
 HBX  C1   C1'  O1'  124.68  3.000
 HBX  C6   C1   C2   119.98  3.000
 HBX  C2   C1   C1'  118.74  3.000
 HBX  C6   C1   C1'  121.28  3.000
 HBX  H2   C2   C3   120.10  3.000
 HBX  H2   C2   C1   119.75  3.000
 HBX  C3   C2   C1   120.14  3.000
 HBX  H3   C3   C4   120.14  3.000
 HBX  H3   C3   C2   120.19  3.000
 HBX  C4   C3   C2   119.67  3.000
 HBX  H4   C4   C5   119.84  3.000
 HBX  H4   C4   C3   119.77  3.000
 HBX  C5   C4   C3   120.39  3.000
 HBX  H5   C5   C6   120.01  3.000
 HBX  H5   C5   C4   119.99  3.000
 HBX  C6   C5   C4   120.00  3.000
 HBX  H6   C6   C5   120.20  3.000
 HBX  H6   C6   C1   119.99  3.000
 HBX  C5   C6   C1   119.81  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
 HBX  CONST_01  C4  C5  C6   C1     0.00   0.0  0
 HBX  CONST_02  C4  C3  C2   C1     0.00   0.0  0
 HBX  CONST_03  C5  C6  C1   C2     0.00   0.0  0
 HBX  CONST_04  C5  C4  C3   C2     0.00   0.0  0
 HBX  CONST_05  C6  C1  C2   C3     0.00   0.0  0
 HBX  CONST_06  C6  C5  C4   C3     0.00   0.0  0
 HBX  CONST_07  C5  C6  C1   C1'  180.00   0.0  0
 HBX  CONST_08  C3  C2  C1   C1'  180.00   0.0  0
 HBX  CONST_09  H5  C5  C6   C1   180.00   0.0  0
 HBX  CONST_10  H3  C3  C2   C1   180.00   0.0  0
 HBX  CONST_11  H6  C6  C1   C2   180.00   0.0  0
 HBX  CONST_12  H4  C4  C3   C2   180.00   0.0  0
 HBX  CONST_13  H2  C2  C3   C4   180.00   0.0  0
 HBX  Var_01    C6  C1  C1'  O1'    0.23  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
 HBX  plan-1  C1'  0.020
 HBX  plan-1  C1   0.020
 HBX  plan-1  C2   0.020
 HBX  plan-1  C3   0.020
 HBX  plan-1  C4   0.020
 HBX  plan-1  C5   0.020
 HBX  plan-1  C6   0.020
 HBX  plan-1  H2   0.020
 HBX  plan-1  H3   0.020
 HBX  plan-1  H4   0.020
 HBX  plan-1  H5   0.020
 HBX  plan-1  H6   0.020
 HBX  plan-2  C1'  0.020
 HBX  plan-2  O1'  0.020
 HBX  plan-2  C1   0.020
 HBX  plan-2  H1'  0.020

