# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 30 22:35:55 2020
#   Inital geometry file: a 51 line input string
#   Ligand name: 2,6-dimethylphenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc(C)c1O
#
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
 2MY  2MY  '2,6-dimethylphenol       '  ligand  19  9  .  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_2MY
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
 2MY  C8   C  CH3   0  -0.773   2.4491  -0.7393   0.0628
 2MY  C6   C  CR6   0  -0.003   1.1617   0.0353   0.0394
 2MY  C5   C  CR16  0  -0.315   1.1608   1.4254  -0.0285
 2MY  C4   C  CR16  0  -0.261  -0.0247   2.1432  -0.0499
 2MY  C3   C  CR16  0  -0.306  -1.2335   1.4626  -0.0042
 2MY  C2   C  CR6   0   0.008  -1.2796   0.0751   0.0647
 2MY  C7   C  CH3   0  -0.711  -2.5862  -0.6609   0.1169
 2MY  C1   C  CR6   0   0.279  -0.0697  -0.6263   0.0862
 2MY  O1   O  OH1   0  -0.624  -0.1552  -1.9751   0.1542
 2MY  H8   H  HCH3  0   0.250   2.5594  -1.3314   0.9752
 2MY  H8A  H  HCH3  0   0.252   2.5370  -1.4246  -0.7846
 2MY  H8B  H  HCH3  0   0.265   3.3035  -0.0664   0.0170
 2MY  H5   H  HCR6  0   0.247   2.1093   1.9479  -0.0653
 2MY  H4   H  HCR6  0   0.245  -0.0078   3.2238  -0.1012
 2MY  H3   H  HCR6  0   0.244  -2.1644   2.0171  -0.0215
 2MY  H7   H  HCH3  0   0.241  -2.7025  -1.3435  -0.7270
 2MY  H7A  H  HCH3  0   0.241  -2.6778  -1.2607   1.0243
 2MY  H7B  H  HCH3  0   0.241  -3.4219   0.0372   0.0953
 2MY  HO1  H  HOH1  0   0.480   0.7200  -2.3751   0.1865

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
 2MY  C8  C6   single    1.503  0.020  1.503
 2MY  C6  C5   aromatic  1.392  0.020  1.392
 2MY  C6  C1   aromatic  1.399  0.020  1.399
 2MY  C5  C4   aromatic  1.386  0.020  1.386
 2MY  C4  C3   aromatic  1.388  0.020  1.388
 2MY  C3  C2   aromatic  1.390  0.020  1.390
 2MY  C2  C7   single    1.501  0.020  1.501
 2MY  C2  C1   aromatic  1.399  0.020  1.399
 2MY  C1  O1   single    1.353  0.020  1.353
 2MY  C8  H8   single    0.970  0.020  1.090
 2MY  C8  H8A  single    0.970  0.020  1.090
 2MY  C8  H8B  single    0.970  0.020  1.090
 2MY  C5  H5   single    0.930  0.020  1.080
 2MY  C4  H4   single    0.930  0.020  1.080
 2MY  C3  H3   single    0.930  0.020  1.080
 2MY  C7  H7   single    0.970  0.020  1.090
 2MY  C7  H7A  single    0.970  0.020  1.090
 2MY  C7  H7B  single    0.970  0.020  1.090
 2MY  O1  HO1  single    0.850  0.020  0.980

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
 2MY  H8B  C8  H8A  106.97  3.000
 2MY  H8B  C8  H8   106.90  3.000
 2MY  H8A  C8  H8   107.42  3.000
 2MY  H8B  C8  C6   110.68  3.000
 2MY  H8A  C8  C6   112.32  3.000
 2MY  H8   C8  C6   112.25  3.000
 2MY  C1   C6  C5   118.26  3.000
 2MY  C1   C6  C8   120.66  3.000
 2MY  C5   C6  C8   121.08  3.000
 2MY  H5   C5  C4   119.90  3.000
 2MY  H5   C5  C6   118.86  3.000
 2MY  C4   C5  C6   121.24  3.000
 2MY  H4   C4  C3   120.33  3.000
 2MY  H4   C4  C5   120.30  3.000
 2MY  C3   C4  C5   119.37  3.000
 2MY  H3   C3  C2   118.88  3.000
 2MY  H3   C3  C4   119.79  3.000
 2MY  C2   C3  C4   121.33  3.000
 2MY  C1   C2  C7   120.44  3.000
 2MY  C1   C2  C3   118.21  3.000
 2MY  C7   C2  C3   121.35  3.000
 2MY  H7B  C7  H7A  107.72  3.000
 2MY  H7B  C7  H7   107.68  3.000
 2MY  H7A  C7  H7   106.86  3.000
 2MY  H7B  C7  C2   110.67  3.000
 2MY  H7A  C7  C2   111.81  3.000
 2MY  H7   C7  C2   111.87  3.000
 2MY  O1   C1  C2   116.49  3.000
 2MY  O1   C1  C6   121.92  3.000
 2MY  C2   C1  C6   121.59  3.000
 2MY  HO1  O1  C1   111.00  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
 2MY  CONST_01  C3  C4  C5  C6    0.00   0.0  0
 2MY  CONST_02  C3  C2  C1  C6    0.00   0.0  0
 2MY  CONST_03  C2  C1  C6  C5    0.00   0.0  0
 2MY  CONST_04  C2  C3  C4  C5    0.00   0.0  0
 2MY  CONST_05  C1  C6  C5  C4    0.00   0.0  0
 2MY  CONST_06  C1  C2  C3  C4    0.00   0.0  0
 2MY  CONST_07  C4  C5  C6  C8  180.00   0.0  0
 2MY  CONST_08  C2  C1  C6  C8  180.00   0.0  0
 2MY  CONST_09  C7  C2  C1  C6  180.00   0.0  0
 2MY  CONST_10  O1  C1  C6  C5  180.00   0.0  0
 2MY  CONST_11  C7  C2  C3  C4  180.00   0.0  0
 2MY  CONST_12  O1  C1  C2  C3  180.00   0.0  0
 2MY  CONST_13  H4  C4  C5  C6  180.00   0.0  0
 2MY  CONST_14  H3  C3  C4  C5  180.00   0.0  0
 2MY  CONST_15  H5  C5  C4  C3  180.00   0.0  0
 2MY  Var_01    H8  C8  C6  C5  119.16  30.0  2
 2MY  Var_02    H7  C7  C2  C3  119.94  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
 2MY  plan-1  C8  0.020
 2MY  plan-1  C6  0.020
 2MY  plan-1  C5  0.020
 2MY  plan-1  C4  0.020
 2MY  plan-1  C3  0.020
 2MY  plan-1  C2  0.020
 2MY  plan-1  C7  0.020
 2MY  plan-1  C1  0.020
 2MY  plan-1  O1  0.020
 2MY  plan-1  H5  0.020
 2MY  plan-1  H4  0.020
 2MY  plan-1  H3  0.020

