# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 09:47:27 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: 5-(2,5-dimethylphenoxy)-2,2-dimethylpentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(C)c(OCCCC(C)(C)C(O)=O)c1
#
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
 4TX  4TX  '5-(2,5-dimethylphenoxy)-2,2-dimethylpentanoic acid'  ligand  40  18  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4TX
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
 4TX  C8   C  CR16  0  -0.425  -2.9006   1.0877  -0.0064
 4TX  C6   C  CH2   0  -0.161  -0.2235   0.1793  -0.0236
 4TX  C5   C  CH2   0  -0.473   1.0607  -0.6264  -0.0222
 4TX  C1   C  CT    0  -0.241   3.6376  -0.3915  -0.0253
 4TX  C9   C  CR6   0   0.100  -4.2349   1.5014   0.0154
 4TX  C10  C  CR16  0  -0.325  -5.2305   0.5373   0.0532
 4TX  C11  C  CR16  0  -0.274  -4.8949  -0.8140   0.0656
 4TX  O    O  O     0  -0.439   4.5199   1.8742  -0.0252
 4TX  C    C  C     0   0.597   4.7176   0.6838  -0.0288
 4TX  O1   O  OH1   0  -0.595   5.9439   0.1713  -0.0355
 4TX  C2   C  CH3   0  -0.653   3.8150  -1.2623  -1.2770
 4TX  C3   C  CH3   0  -0.653   3.8183  -1.2537   1.2322
 4TX  C4   C  CH2   0  -0.402   2.2678   0.3060  -0.0258
 4TX  C7   C  CR6   0   0.369  -2.5730  -0.2627   0.0059
 4TX  C12  C  CR6   0  -0.019  -3.5785  -1.2434   0.0422
 4TX  C13  C  CH3   0  -0.712  -3.2247  -2.7009   0.0558
 4TX  C14  C  CH3   0  -0.724  -4.5621   2.9668  -0.0182
 4TX  H13  H  HCR6  0   0.269  -2.1272   1.8451  -0.0308
 4TX  H12  H  HCH2  0   0.219  -0.2623   0.8328   0.8562
 4TX  H11  H  HCH2  0   0.219  -0.2682   0.8205  -0.9122
 4TX  H10  H  HCH2  0   0.237   1.0700  -1.2713   0.8596
 4TX  H9   H  HCH2  0   0.237   1.0690  -1.2772  -0.8997
 4TX  H14  H  HCR6  0   0.239  -6.2727   0.8315   0.0745
 4TX  H15  H  HCR6  0   0.244  -5.6842  -1.5559   0.0961
 4TX  H    H  HOH1  0   0.478   6.5976   0.8862  -0.0369
 4TX  H2   H  HCH3  0   0.245   4.7898  -1.7481  -1.2955
 4TX  H3   H  HCH3  0   0.242   3.0647  -2.0523  -1.2985
 4TX  H1   H  HCH3  0   0.237   3.7103  -0.6770  -2.1924
 4TX  H4   H  HCH3  0   0.237   3.7162  -0.6621   2.1438
 4TX  H5   H  HCH3  0   0.242   3.0679  -2.0435   1.2612
 4TX  H6   H  HCH3  0   0.245   4.7931  -1.7396   1.2511
 4TX  H7   H  HCH2  0   0.233   2.2024   0.9579  -0.9018
 4TX  H8   H  HCH2  0   0.233   2.2036   0.9619   0.8473
 4TX  H16  H  HCH3  0   0.239  -2.6854  -2.9974  -0.8461
 4TX  H18  H  HCH3  0   0.239  -2.5886  -2.9592   0.9043
 4TX  H17  H  HCH3  0   0.239  -4.1233  -3.3131   0.1174
 4TX  H19  H  HCH3  0   0.245  -4.3463   3.3959  -0.9987
 4TX  H21  H  HCH3  0   0.242  -5.6150   3.1459   0.1954
 4TX  H20  H  HCH3  0   0.242  -3.9726   3.5240   0.7108
 4TX  O2   O  O2    0  -0.473  -1.3088  -0.7315  -0.0127

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
 4TX  C10  C11  aromatic  1.392  0.020  1.392
 4TX  C10  C9   aromatic  1.386  0.020  1.386
 4TX  C11  C12  aromatic  1.385  0.020  1.385
 4TX  C14  C9   single    1.502  0.020  1.502
 4TX  C9   C8   aromatic  1.397  0.020  1.397
 4TX  C12  C13  single    1.500  0.020  1.500
 4TX  C12  C7   aromatic  1.405  0.020  1.405
 4TX  C8   C7   aromatic  1.390  0.020  1.390
 4TX  C7   O2   single    1.348  0.020  1.348
 4TX  O2   C6   single    1.417  0.020  1.417
 4TX  C6   C5   single    1.516  0.020  1.516
 4TX  C5   C4   single    1.525  0.020  1.525
 4TX  C4   C1   single    1.537  0.020  1.537
 4TX  C3   C1   single    1.535  0.020  1.535
 4TX  C2   C1   single    1.535  0.020  1.535
 4TX  C1   C    single    1.524  0.020  1.524
 4TX  C    O    double    1.207  0.020  1.207
 4TX  C    O1   single    1.329  0.020  1.329
 4TX  C8   H13  single    0.930  0.020  1.080
 4TX  C6   H12  single    0.970  0.020  1.090
 4TX  C6   H11  single    0.970  0.020  1.090
 4TX  C5   H10  single    0.970  0.020  1.090
 4TX  C5   H9   single    0.970  0.020  1.090
 4TX  C10  H14  single    0.930  0.020  1.080
 4TX  C11  H15  single    0.930  0.020  1.080
 4TX  O1   H    single    0.850  0.020  0.980
 4TX  C2   H2   single    0.970  0.020  1.090
 4TX  C2   H3   single    0.970  0.020  1.090
 4TX  C2   H1   single    0.970  0.020  1.090
 4TX  C3   H4   single    0.970  0.020  1.090
 4TX  C3   H5   single    0.970  0.020  1.090
 4TX  C3   H6   single    0.970  0.020  1.090
 4TX  C4   H7   single    0.970  0.020  1.090
 4TX  C4   H8   single    0.970  0.020  1.090
 4TX  C13  H16  single    0.970  0.020  1.090
 4TX  C13  H18  single    0.970  0.020  1.090
 4TX  C13  H17  single    0.970  0.020  1.090
 4TX  C14  H19  single    0.970  0.020  1.090
 4TX  C14  H21  single    0.970  0.020  1.090
 4TX  C14  H20  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
 4TX  H13  C8   C7   120.77  3.000
 4TX  H13  C8   C9   118.38  3.000
 4TX  C7   C8   C9   120.84  3.000
 4TX  H11  C6   H12  107.47  3.000
 4TX  H11  C6   O2   110.54  3.000
 4TX  H12  C6   O2   110.47  3.000
 4TX  H11  C6   C5   110.24  3.000
 4TX  H12  C6   C5   110.24  3.000
 4TX  O2   C6   C5   107.89  3.000
 4TX  H9   C5   H10  107.25  3.000
 4TX  H9   C5   C4   110.87  3.000
 4TX  H10  C5   C4   110.85  3.000
 4TX  H9   C5   C6   108.80  3.000
 4TX  H10  C5   C6   108.77  3.000
 4TX  C4   C5   C6   110.21  3.000
 4TX  C4   C1   C3   111.10  3.000
 4TX  C3   C1   C2   109.61  3.000
 4TX  C4   C1   C2   111.11  3.000
 4TX  C2   C1   C    108.45  3.000
 4TX  C3   C1   C    108.35  3.000
 4TX  C4   C1   C    108.14  3.000
 4TX  C14  C9   C10  121.51  3.000
 4TX  C14  C9   C8   119.78  3.000
 4TX  C10  C9   C8   118.71  3.000
 4TX  H14  C10  C11  119.69  3.000
 4TX  H14  C10  C9   120.17  3.000
 4TX  C11  C10  C9   120.13  3.000
 4TX  H15  C11  C12  118.72  3.000
 4TX  H15  C11  C10  119.28  3.000
 4TX  C12  C11  C10  122.00  3.000
 4TX  O1   C    O    122.11  3.000
 4TX  O1   C    C1   112.44  3.000
 4TX  O    C    C1   125.45  3.000
 4TX  H    O1   C    109.76  3.000
 4TX  H1   C2   H3   107.83  3.000
 4TX  H1   C2   H2   108.10  3.000
 4TX  H3   C2   H2   107.01  3.000
 4TX  H1   C2   C1   111.62  3.000
 4TX  H3   C2   C1   110.35  3.000
 4TX  H2   C2   C1   111.73  3.000
 4TX  H6   C3   H5   107.01  3.000
 4TX  H6   C3   H4   108.12  3.000
 4TX  H5   C3   H4   107.84  3.000
 4TX  H6   C3   C1   111.71  3.000
 4TX  H5   C3   C1   110.35  3.000
 4TX  H4   C3   C1   111.63  3.000
 4TX  H8   C4   H7   106.17  3.000
 4TX  H8   C4   C1   108.91  3.000
 4TX  H7   C4   C1   108.90  3.000
 4TX  H8   C4   C5   108.56  3.000
 4TX  H7   C4   C5   108.59  3.000
 4TX  C1   C4   C5   115.33  3.000
 4TX  C12  C7   O2   115.38  3.000
 4TX  O2   C7   C8   123.97  3.000
 4TX  C12  C7   C8   120.65  3.000
 4TX  C13  C12  C7   120.65  3.000
 4TX  C7   C12  C11  117.66  3.000
 4TX  C13  C12  C11  121.70  3.000
 4TX  H17  C13  H18  107.69  3.000
 4TX  H17  C13  H16  107.55  3.000
 4TX  H18  C13  H16  106.86  3.000
 4TX  H17  C13  C12  110.61  3.000
 4TX  H18  C13  C12  111.99  3.000
 4TX  H16  C13  C12  111.89  3.000
 4TX  H20  C14  H21  107.90  3.000
 4TX  H20  C14  H19  107.02  3.000
 4TX  H21  C14  H19  107.61  3.000
 4TX  H20  C14  C9   111.46  3.000
 4TX  H21  C14  C9   111.51  3.000
 4TX  H19  C14  C9   111.13  3.000
 4TX  C7   O2   C6   119.66  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
 4TX  CONST_01  C11  C10  C9   C8      0.00   0.0  0
 4TX  CONST_02  C11  C12  C7   C8      0.00   0.0  0
 4TX  CONST_03  C12  C11  C10  C9      0.00   0.0  0
 4TX  CONST_04  C12  C7   C8   C9      0.00   0.0  0
 4TX  CONST_05  C7   C12  C11  C10     0.00   0.0  0
 4TX  CONST_06  C7   C8   C9   C10     0.00   0.0  0
 4TX  CONST_07  C13  C12  C7   C8    180.00   0.0  0
 4TX  CONST_08  O2   C7   C8   C9    180.00   0.0  0
 4TX  CONST_09  C13  C12  C11  C10   180.00   0.0  0
 4TX  CONST_10  C14  C9   C10  C11   180.00   0.0  0
 4TX  CONST_11  O2   C7   C12  C11   180.00   0.0  0
 4TX  CONST_12  C14  C9   C8   C7    180.00   0.0  0
 4TX  CONST_13  H14  C10  C9   C8    180.00   0.0  0
 4TX  CONST_14  H15  C11  C10  C9    180.00   0.0  0
 4TX  CONST_15  H13  C8   C9   C10   180.00   0.0  0
 4TX  CONST_16  H    O1   C    C1    180.00   0.0  0
 4TX  Var_01    C12  C7   O2   C6   -178.80  30.0  3
 4TX  Var_02    H19  C14  C9   C8     70.86  30.0  2
 4TX  Var_03    H16  C13  C12  C11   118.09  30.0  2
 4TX  Var_04    H12  C6   O2   C7     58.58  30.0  3
 4TX  Var_05    C1   C4   C5   C6   -179.98  30.0  3
 4TX  Var_06    C3   C1   C4   C5    -61.21  30.0  3
 4TX  Var_07    C4   C1   C    O       0.37  30.0  2
 4TX  Var_08    O2   C6   C5   C4   -179.68  30.0  1
 4TX  Var_09    H4   C3   C1   C      60.81  30.0  3
 4TX  Var_10    H2   C2   C1   C      60.29  30.0  3

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
 4TX  plan-1  C8   0.020
 4TX  plan-1  C9   0.020
 4TX  plan-1  C10  0.020
 4TX  plan-1  C11  0.020
 4TX  plan-1  C7   0.020
 4TX  plan-1  C12  0.020
 4TX  plan-1  C13  0.020
 4TX  plan-1  C14  0.020
 4TX  plan-1  H13  0.020
 4TX  plan-1  H14  0.020
 4TX  plan-1  H15  0.020
 4TX  plan-1  O2   0.020
 4TX  plan-2  C1   0.020
 4TX  plan-2  O    0.020
 4TX  plan-2  C    0.020
 4TX  plan-2  O1   0.020
 4TX  plan-2  H    0.020

