# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 16:14:47 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: 2-methylbenzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccccc1C(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
 3SK  3SK  '2-methylbenzoic acid     '  ligand  18  10  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_3SK
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
 3SK  O8   O  O     0  -0.429   2.3725  -0.6796   0.1884
 3SK  C1   C  C     0   0.524   1.6571   0.2822   0.0481
 3SK  O9   O  OH1   0  -0.586   2.1529   1.5120  -0.0794
 3SK  C2   C  CR6   0  -0.123   0.1738   0.2539   0.0053
 3SK  C3   C  CR16  0  -0.231  -0.5268   1.4635   0.0113
 3SK  C4   C  CR16  0  -0.234  -1.9085   1.4924  -0.0042
 3SK  C5   C  CR16  0  -0.203  -2.6099   0.2982  -0.0333
 3SK  C6   C  CR16  0  -0.276  -1.9232  -0.9041  -0.0463
 3SK  C7   C  CR6   0   0.128  -0.5314  -0.9635  -0.0243
 3SK  C10  C  CH3   0  -0.698   0.1118  -2.3210  -0.0401
 3SK  H1   H  HOH1  0   0.460   3.1155   1.4668  -0.0185
 3SK  H2   H  HCR6  0   0.254   0.0105   2.4001   0.0360
 3SK  H3   H  HCR6  0   0.242  -2.4303   2.4392   0.0085
 3SK  H4   H  HCR6  0   0.235  -3.6917   0.3009  -0.0456
 3SK  H5   H  HCR6  0   0.226  -2.4835  -1.8303  -0.0738
 3SK  H6   H  HCH3  0   0.245   0.6708  -2.5179   0.8735
 3SK  H7   H  HCH3  0   0.222  -0.6535  -3.0902  -0.1342
 3SK  H8   H  HCH3  0   0.243   0.8079  -2.4395  -0.8689

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
 3SK  C4   C3   aromatic  1.382  0.020  1.382
 3SK  C4   C5   aromatic  1.385  0.020  1.385
 3SK  C3   C2   aromatic  1.398  0.020  1.398
 3SK  O8   C1   double    1.207  0.020  1.207
 3SK  C5   C6   aromatic  1.385  0.020  1.385
 3SK  C2   C1   single    1.484  0.020  1.484
 3SK  C2   C7   aromatic  1.407  0.020  1.407
 3SK  C1   O9   single    1.332  0.020  1.332
 3SK  C6   C7   aromatic  1.393  0.020  1.393
 3SK  C7   C10  single    1.502  0.020  1.502
 3SK  O9   H1   single    0.850  0.020  0.980
 3SK  C3   H2   single    0.930  0.020  1.080
 3SK  C4   H3   single    0.930  0.020  1.080
 3SK  C5   H4   single    0.930  0.020  1.080
 3SK  C6   H5   single    0.930  0.020  1.080
 3SK  C10  H6   single    0.970  0.020  1.090
 3SK  C10  H7   single    0.970  0.020  1.090
 3SK  C10  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
 3SK  C2   C1   O9  112.76  3.000
 3SK  O9   C1   O8  121.75  3.000
 3SK  C2   C1   O8  125.49  3.000
 3SK  H1   O9   C1  108.77  3.000
 3SK  C7   C2   C3  119.84  3.000
 3SK  C7   C2   C1  121.20  3.000
 3SK  C3   C2   C1  118.96  3.000
 3SK  H2   C3   C4  118.65  3.000
 3SK  H2   C3   C2  120.08  3.000
 3SK  C4   C3   C2  121.27  3.000
 3SK  H3   C4   C5  120.72  3.000
 3SK  H3   C4   C3  120.04  3.000
 3SK  C5   C4   C3  119.23  3.000
 3SK  H4   C5   C6  119.86  3.000
 3SK  H4   C5   C4  120.29  3.000
 3SK  C6   C5   C4  119.85  3.000
 3SK  H5   C6   C7  118.74  3.000
 3SK  H5   C6   C5  119.10  3.000
 3SK  C7   C6   C5  122.16  3.000
 3SK  C10  C7   C6  117.78  3.000
 3SK  C10  C7   C2  124.57  3.000
 3SK  C6   C7   C2  117.65  3.000
 3SK  H8   C10  H7  107.85  3.000
 3SK  H8   C10  H6  106.90  3.000
 3SK  H7   C10  H6  107.79  3.000
 3SK  H8   C10  C7  112.34  3.000
 3SK  H7   C10  C7  109.77  3.000
 3SK  H6   C10  C7  111.98  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
 3SK  CONST_01  C5   C4   C3  C2    0.00   0.0  0
 3SK  CONST_02  C5   C6   C7  C2    0.00   0.0  0
 3SK  CONST_03  C6   C5   C4  C3    0.00   0.0  0
 3SK  CONST_04  C6   C7   C2  C3    0.00   0.0  0
 3SK  CONST_05  C7   C2   C3  C4    0.00   0.0  0
 3SK  CONST_06  C7   C6   C5  C4    0.00   0.0  0
 3SK  CONST_07  C4   C3   C2  C1  180.00   0.0  0
 3SK  CONST_08  C6   C7   C2  C1  180.00   0.0  0
 3SK  CONST_09  C10  C7   C2  C3  180.00   0.0  0
 3SK  CONST_10  C10  C7   C6  C5  180.00   0.0  0
 3SK  CONST_11  H3   C4   C3  C2  180.00   0.0  0
 3SK  CONST_12  H5   C6   C7  C2  180.00   0.0  0
 3SK  CONST_13  H4   C5   C4  C3  180.00   0.0  0
 3SK  CONST_14  H2   C3   C4  C5  180.00   0.0  0
 3SK  CONST_15  H1   O9   C1  C2  180.00   0.0  0
 3SK  Var_01    C3   C2   C1  O8  171.78  30.0  2
 3SK  Var_02    H6   C10  C7  C2   64.31  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
 3SK  plan-1  C1   0.020
 3SK  plan-1  C2   0.020
 3SK  plan-1  C3   0.020
 3SK  plan-1  C4   0.020
 3SK  plan-1  C5   0.020
 3SK  plan-1  C6   0.020
 3SK  plan-1  C7   0.020
 3SK  plan-1  C10  0.020
 3SK  plan-1  H2   0.020
 3SK  plan-1  H3   0.020
 3SK  plan-1  H4   0.020
 3SK  plan-1  H5   0.020
 3SK  plan-2  O8   0.020
 3SK  plan-2  C1   0.020
 3SK  plan-2  O9   0.020
 3SK  plan-2  C2   0.020
 3SK  plan-2  H1   0.020

