# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 21:26:44 2020
#   Inital geometry file: a 49 line input string
#   Ligand name: 1,4-dimethylbenzene
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(C)cc1
#
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
 PXY  PXY  '1,4-dimethylbenzene      '  ligand  18  8  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_PXY
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
 PXY  C1    C  CR6   0   0.079   0.0167  -0.0224   1.3876
 PXY  C2    C  CR16  0  -0.285   1.2028  -0.0343   0.6564
 PXY  C3    C  CR16  0  -0.284   1.1911  -0.0112  -0.7309
 PXY  C4    C  CR6   0   0.079  -0.0075   0.0201  -1.4410
 PXY  C5    C  CR16  0  -0.287  -1.1927   0.0307  -0.7105
 PXY  C6    C  CR16  0  -0.286  -1.1809   0.0082   0.6780
 PXY  C1'   C  CH3   0  -0.720   0.0318  -0.0110   2.8891
 PXY  C4'   C  CH3   0  -0.720  -0.0176   0.0119  -2.9426
 PXY  H2    H  HCR6  0   0.242   2.1522  -0.0619   1.1794
 PXY  H3    H  HCR6  0   0.242   2.1315  -0.0189  -1.2707
 PXY  H5    H  HCR6  0   0.242  -2.1420   0.0572  -1.2333
 PXY  H6    H  HCR6  0   0.242  -2.1213   0.0153   1.2176
 PXY  H1'1  H  HCH3  0   0.245   0.0863   1.0098   3.2736
 PXY  H1'2  H  HCH3  0   0.241  -0.8692  -0.4635   3.3023
 PXY  H1'3  H  HCH3  0   0.241   0.8923  -0.5504   3.2848
 PXY  H4'1  H  HCH3  0   0.245   0.0716  -1.0050  -3.3310
 PXY  H4'2  H  HCH3  0   0.241  -0.9423   0.4300  -3.3394
 PXY  H4'3  H  HCH3  0   0.241   0.8148   0.5849  -3.3514

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
 PXY  C1   C2    aromatic  1.393  0.020  1.393
 PXY  C1   C6    aromatic  1.392  0.020  1.392
 PXY  C1   C1'   single    1.502  0.020  1.502
 PXY  C2   C3    aromatic  1.387  0.020  1.387
 PXY  C2   H2    single    0.930  0.020  1.080
 PXY  C3   C4    aromatic  1.394  0.020  1.394
 PXY  C3   H3    single    0.930  0.020  1.080
 PXY  C4   C5    aromatic  1.392  0.020  1.392
 PXY  C4   C4'   single    1.502  0.020  1.502
 PXY  C5   C6    aromatic  1.389  0.020  1.389
 PXY  C5   H5    single    0.930  0.020  1.080
 PXY  C6   H6    single    0.930  0.020  1.080
 PXY  C1'  H1'1  single    0.970  0.020  1.090
 PXY  C1'  H1'2  single    0.970  0.020  1.090
 PXY  C1'  H1'3  single    0.970  0.020  1.090
 PXY  C4'  H4'1  single    0.970  0.020  1.090
 PXY  C4'  H4'2  single    0.970  0.020  1.090
 PXY  C4'  H4'3  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
 PXY  C1'   C1   C6    121.20  3.000
 PXY  C1'   C1   C2    121.08  3.000
 PXY  C6    C1   C2    117.70  3.000
 PXY  H2    C2   C3    119.34  3.000
 PXY  H2    C2   C1    119.50  3.000
 PXY  C3    C2   C1    121.15  3.000
 PXY  H3    C3   C4    119.50  3.000
 PXY  H3    C3   C2    119.36  3.000
 PXY  C4    C3   C2    121.14  3.000
 PXY  C4'   C4   C5    121.27  3.000
 PXY  C4'   C4   C3    121.01  3.000
 PXY  C5    C4   C3    117.71  3.000
 PXY  H5    C5   C6    119.34  3.000
 PXY  H5    C5   C4    119.51  3.000
 PXY  C6    C5   C4    121.15  3.000
 PXY  H6    C6   C5    119.35  3.000
 PXY  H6    C6   C1    119.51  3.000
 PXY  C5    C6   C1    121.14  3.000
 PXY  H1'3  C1'  H1'2  108.04  3.000
 PXY  H1'3  C1'  H1'1  107.17  3.000
 PXY  H1'2  C1'  H1'1  107.21  3.000
 PXY  H1'3  C1'  C1    111.54  3.000
 PXY  H1'2  C1'  C1    111.58  3.000
 PXY  H1'1  C1'  C1    111.08  3.000
 PXY  H4'3  C4'  H4'2  108.05  3.000
 PXY  H4'3  C4'  H4'1  107.08  3.000
 PXY  H4'2  C4'  H4'1  107.27  3.000
 PXY  H4'3  C4'  C4    111.53  3.000
 PXY  H4'2  C4'  C4    111.58  3.000
 PXY  H4'1  C4'  C4    111.11  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
 PXY  CONST_01  C4    C3   C2  C1    0.00   0.0  0
 PXY  CONST_02  C4    C5   C6  C1    0.00   0.0  0
 PXY  CONST_03  C5    C6   C1  C2    0.00   0.0  0
 PXY  CONST_04  C5    C4   C3  C2    0.00   0.0  0
 PXY  CONST_05  C6    C1   C2  C3    0.00   0.0  0
 PXY  CONST_06  C6    C5   C4  C3    0.00   0.0  0
 PXY  CONST_07  C4'   C4   C3  C2  180.00   0.0  0
 PXY  CONST_08  C1'   C1   C2  C3  180.00   0.0  0
 PXY  CONST_09  C1'   C1   C6  C5  180.00   0.0  0
 PXY  CONST_10  C4'   C4   C5  C6  180.00   0.0  0
 PXY  CONST_11  H3    C3   C2  C1  180.00   0.0  0
 PXY  CONST_12  H5    C5   C6  C1  180.00   0.0  0
 PXY  CONST_13  H6    C6   C1  C2  180.00   0.0  0
 PXY  CONST_14  H2    C2   C3  C4  180.00   0.0  0
 PXY  Var_01    H1'1  C1'  C1  C2   87.46  30.0  2
 PXY  Var_02    H4'1  C4'  C4  C3   83.15  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
 PXY  plan-1  C1   0.020
 PXY  plan-1  C2   0.020
 PXY  plan-1  C3   0.020
 PXY  plan-1  C4   0.020
 PXY  plan-1  C5   0.020
 PXY  plan-1  C6   0.020
 PXY  plan-1  C1'  0.020
 PXY  plan-1  C4'  0.020
 PXY  plan-1  H2   0.020
 PXY  plan-1  H3   0.020
 PXY  plan-1  H5   0.020
 PXY  plan-1  H6   0.020

