# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 06:34:31 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: 11-[(2R,3S)-3-pentyloxiran-2-yl]undecanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCC[C@@H]1O[C@@H]1CCCCCCCCCCC(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
 EOD  EOD  '11-[(2R,3S)-3-pentyloxiran-2-yl]undecanoic acid'  ligand  55  21  .  2022-09-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EOD
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
 EOD  O1    O  O     0  -0.446   -9.3398   1.9322  -0.2490
 EOD  C1    C  C     0   0.549   -9.3823   0.7343  -0.3827
 EOD  O2    O  OH1   0  -0.599  -10.5224   0.0664  -0.5422
 EOD  C2    C  CH2   0  -0.579   -8.1923  -0.1838  -0.3906
 EOD  C3    C  CH2   0  -0.418   -6.8610   0.5271  -0.2137
 EOD  C4    C  CH2   0  -0.414   -5.6941  -0.4525  -0.2242
 EOD  C5    C  CH2   0  -0.413   -4.3442   0.2246  -0.0236
 EOD  C6    C  CH2   0  -0.412   -3.1807  -0.7590  -0.0414
 EOD  C7    C  CH2   0  -0.413   -1.8291  -0.1105   0.2316
 EOD  C8    C  CH2   0  -0.412   -0.6749  -1.1050   0.1813
 EOD  C9    C  CH2   0  -0.415    0.6596  -0.5129   0.6147
 EOD  C10   C  CH2   0  -0.421    1.8181  -1.4943   0.4850
 EOD  C11   C  CH2   0  -0.466    3.1222  -0.9498   1.0615
 EOD  C12   C  CH1   0   0.004    4.2727  -1.8928   0.8496
 EOD  O3    O  O2    0  -0.505    4.9142  -1.8742  -0.4215
 EOD  C13   C  CH1   0   0.005    5.6717  -1.4877   0.7218
 EOD  C14   C  CH2   0  -0.469    6.1642  -0.0708   0.7960
 EOD  C15   C  CH2   0  -0.418    7.3340   0.1896  -0.1489
 EOD  C16   C  CH2   0  -0.408    7.8973   1.5975  -0.0089
 EOD  C17   C  CH2   0  -0.419    9.0616   1.8775  -0.9514
 EOD  C18   C  CH3   0  -0.662    9.6259   3.2818  -0.7868
 EOD  HO2   H  HOH1  0   0.478  -11.2704   0.6816  -0.5253
 EOD  H21   H  HCH2  0   0.275   -8.2057  -0.7493  -1.3283
 EOD  H22   H  HCH2  0   0.275   -8.3356  -0.9292   0.3985
 EOD  H31   H  HCH2  0   0.224   -6.8598   1.0831   0.7279
 EOD  H32   H  HCH2  0   0.225   -6.7241   1.2642  -1.0091
 EOD  H41   H  HCH2  0   0.212   -5.6889  -1.0040  -1.1710
 EOD  H42   H  HCH2  0   0.212   -5.8409  -1.2012   0.5619
 EOD  H51   H  HCH2  0   0.208   -4.3488   0.7653   0.9296
 EOD  H52   H  HCH2  0   0.209   -4.1952   0.9810  -0.8017
 EOD  H61   H  HCH2  0   0.207   -3.1537  -1.2708  -1.0100
 EOD  H62   H  HCH2  0   0.207   -3.3576  -1.5386   0.7076
 EOD  H71   H  HCH2  0   0.206   -1.8539   0.3697   1.2164
 EOD  H72   H  HCH2  0   0.208   -1.6519   0.6914  -0.4930
 EOD  H81   H  HCH2  0   0.208   -0.5887  -1.5068  -0.8343
 EOD  H82   H  HCH2  0   0.207   -0.9097  -1.9603   0.8245
 EOD  H91   H  HCH2  0   0.209    0.5810  -0.1762   1.6543
 EOD  H92   H  HCH2  0   0.210    0.8806   0.3825   0.0234
 EOD  H101  H  HCH2  0   0.219    1.9608  -1.7462  -0.5706
 EOD  H102  H  HCH2  0   0.215    1.5623  -2.4312   0.9916
 EOD  H111  H  HCH2  0   0.229    3.0039  -0.7899   2.1377
 EOD  H112  H  HCH2  0   0.230    3.3397   0.0275   0.6232
 EOD  H12   H  HCH1  0   0.233    4.0898  -2.8985   1.2332
 EOD  H13   H  HCH1  0   0.235    6.4222  -2.2245   1.0146
 EOD  H141  H  HCH2  0   0.228    6.4810   0.1156   1.8272
 EOD  H142  H  HCH2  0   0.232    5.3593   0.6381   0.5882
 EOD  H151  H  HCH2  0   0.218    7.0120   0.0260  -1.1822
 EOD  H152  H  HCH2  0   0.215    8.1283  -0.5403   0.0431
 EOD  H161  H  HCH2  0   0.209    8.2217   1.7563   1.0257
 EOD  H162  H  HCH2  0   0.209    7.1016   2.3289  -0.1907
 EOD  H171  H  HCH2  0   0.211    8.7326   1.7317  -1.9850
 EOD  H172  H  HCH2  0   0.211    9.8526   1.1410  -0.7788
 EOD  H181  H  HCH3  0   0.216    8.8628   4.0379  -0.9823
 EOD  H182  H  HCH3  0   0.216    9.9925   3.4407   0.2291
 EOD  H183  H  HCH3  0   0.226   10.4551   3.4659  -1.4707

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
 EOD  O1   C1    double  1.206  0.020  1.206
 EOD  C1   O2    single  1.331  0.020  1.331
 EOD  C1   C2    single  1.503  0.020  1.503
 EOD  O2   HO2   single  0.850  0.020  0.980
 EOD  C2   C3    single  1.520  0.020  1.520
 EOD  C2   H21   single  0.970  0.020  1.090
 EOD  C2   H22   single  0.970  0.020  1.090
 EOD  C3   C4    single  1.524  0.020  1.524
 EOD  C3   H31   single  0.970  0.020  1.090
 EOD  C3   H32   single  0.970  0.020  1.090
 EOD  C4   C5    single  1.523  0.020  1.523
 EOD  C4   H41   single  0.970  0.020  1.090
 EOD  C4   H42   single  0.970  0.020  1.090
 EOD  C5   C6    single  1.524  0.020  1.524
 EOD  C5   H51   single  0.970  0.020  1.090
 EOD  C5   H52   single  0.970  0.020  1.090
 EOD  C6   C7    single  1.524  0.020  1.524
 EOD  C6   H61   single  0.970  0.020  1.090
 EOD  C6   H62   single  0.970  0.020  1.090
 EOD  C7   C8    single  1.524  0.020  1.524
 EOD  C7   H71   single  0.970  0.020  1.090
 EOD  C7   H72   single  0.970  0.020  1.090
 EOD  C8   C9    single  1.523  0.020  1.523
 EOD  C8   H81   single  0.970  0.020  1.090
 EOD  C8   H82   single  0.970  0.020  1.090
 EOD  C9   C10   single  1.524  0.020  1.524
 EOD  C9   H91   single  0.970  0.020  1.090
 EOD  C9   H92   single  0.970  0.020  1.090
 EOD  C10  C11   single  1.526  0.020  1.526
 EOD  C10  H101  single  0.970  0.020  1.090
 EOD  C10  H102  single  0.970  0.020  1.090
 EOD  C11  C12   single  1.503  0.020  1.503
 EOD  C11  H111  single  0.970  0.020  1.090
 EOD  C11  H112  single  0.970  0.020  1.090
 EOD  C12  O3    single  1.424  0.020  1.424
 EOD  C12  C13   single  1.462  0.020  1.462
 EOD  C12  H12   single  0.970  0.020  1.090
 EOD  O3   C13   single  1.425  0.020  1.425
 EOD  C13  C14   single  1.502  0.020  1.502
 EOD  C13  H13   single  0.970  0.020  1.090
 EOD  C14  C15   single  1.526  0.020  1.526
 EOD  C14  H141  single  0.970  0.020  1.090
 EOD  C14  H142  single  0.970  0.020  1.090
 EOD  C15  C16   single  1.523  0.020  1.523
 EOD  C15  H151  single  0.970  0.020  1.090
 EOD  C15  H152  single  0.970  0.020  1.090
 EOD  C16  C17   single  1.524  0.020  1.524
 EOD  C16  H161  single  0.970  0.020  1.090
 EOD  C16  H162  single  0.970  0.020  1.090
 EOD  C17  C18   single  1.522  0.020  1.522
 EOD  C17  H171  single  0.970  0.020  1.090
 EOD  C17  H172  single  0.970  0.020  1.090
 EOD  C18  H181  single  0.970  0.020  1.090
 EOD  C18  H182  single  0.970  0.020  1.090
 EOD  C18  H183  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
 EOD  C2    C1   O2    111.78  3.000
 EOD  C2    C1   O1    125.41  3.000
 EOD  O2    C1   O1    122.81  3.000
 EOD  HO2   O2   C1    109.92  3.000
 EOD  H22   C2   H21   105.31  3.000
 EOD  H22   C2   C3    110.44  3.000
 EOD  H21   C2   C3    110.61  3.000
 EOD  H22   C2   C1    107.96  3.000
 EOD  H21   C2   C1    108.08  3.000
 EOD  C3    C2   C1    114.03  3.000
 EOD  H32   C3   H31   106.48  3.000
 EOD  H32   C3   C4    109.43  3.000
 EOD  H31   C3   C4    109.39  3.000
 EOD  H32   C3   C2    109.90  3.000
 EOD  H31   C3   C2    109.82  3.000
 EOD  C4    C3   C2    111.68  3.000
 EOD  H42   C4   H41   106.07  3.000
 EOD  H42   C4   C5    109.15  3.000
 EOD  H41   C4   C5    109.47  3.000
 EOD  H42   C4   C3    109.38  3.000
 EOD  H41   C4   C3    109.46  3.000
 EOD  C5    C4   C3    113.07  3.000
 EOD  H52   C5   H51   106.12  3.000
 EOD  H52   C5   C6    109.49  3.000
 EOD  H51   C5   C6    109.38  3.000
 EOD  H52   C5   C4    109.51  3.000
 EOD  H51   C5   C4    109.27  3.000
 EOD  C6    C5   C4    112.84  3.000
 EOD  H62   C6   H61   106.02  3.000
 EOD  H62   C6   C7    108.88  3.000
 EOD  H61   C6   C7    109.59  3.000
 EOD  H62   C6   C5    109.15  3.000
 EOD  H61   C6   C5    109.31  3.000
 EOD  C7    C6   C5    113.61  3.000
 EOD  H72   C7   H71   106.10  3.000
 EOD  H72   C7   C8    109.47  3.000
 EOD  H71   C7   C8    109.43  3.000
 EOD  H72   C7   C6    109.67  3.000
 EOD  H71   C7   C6    109.11  3.000
 EOD  C8    C7   C6    112.83  3.000
 EOD  H82   C8   H81   105.95  3.000
 EOD  H82   C8   C9    108.92  3.000
 EOD  H81   C8   C9    109.72  3.000
 EOD  H82   C8   C7    109.12  3.000
 EOD  H81   C8   C7    109.23  3.000
 EOD  C9    C8   C7    113.60  3.000
 EOD  H92   C9   H91   105.99  3.000
 EOD  H92   C9   C10   109.09  3.000
 EOD  H91   C9   C10   109.46  3.000
 EOD  H92   C9   C8    109.93  3.000
 EOD  H91   C9   C8    109.07  3.000
 EOD  C10   C9   C8    113.05  3.000
 EOD  H102  C10  H101  106.24  3.000
 EOD  H102  C10  C11   109.27  3.000
 EOD  H101  C10  C11   109.57  3.000
 EOD  H102  C10  C9    109.51  3.000
 EOD  H101  C10  C9    109.23  3.000
 EOD  C11   C10  C9    112.81  3.000
 EOD  H112  C11  H111  106.57  3.000
 EOD  H112  C11  C12   110.63  3.000
 EOD  H111  C11  C12   108.25  3.000
 EOD  H112  C11  C10   109.73  3.000
 EOD  H111  C11  C10   109.34  3.000
 EOD  C12   C11  C10   112.15  3.000
 EOD  H12   C12  C13   116.50  3.000
 EOD  H12   C12  O3    113.65  3.000
 EOD  C13   C12  O3     59.15  3.000
 EOD  H12   C12  C11   113.60  3.000
 EOD  C13   C12  C11   124.82  3.000
 EOD  O3    C12  C11   117.55  3.000
 EOD  C13   O3   C12    61.76  3.000
 EOD  H13   C13  C14   113.45  3.000
 EOD  H13   C13  O3    113.43  3.000
 EOD  C14   C13  O3    118.02  3.000
 EOD  H13   C13  C12   116.58  3.000
 EOD  C14   C13  C12   124.81  3.000
 EOD  O3    C13  C12    59.09  3.000
 EOD  H142  C14  H141  106.37  3.000
 EOD  H142  C14  C15   109.65  3.000
 EOD  H141  C14  C15   109.41  3.000
 EOD  H142  C14  C13   111.18  3.000
 EOD  H141  C14  C13   107.58  3.000
 EOD  C15   C14  C13   112.44  3.000
 EOD  H152  C15  H151  106.21  3.000
 EOD  H152  C15  C16   109.37  3.000
 EOD  H151  C15  C16   109.50  3.000
 EOD  H152  C15  C14   109.48  3.000
 EOD  H151  C15  C14   109.48  3.000
 EOD  C16   C15  C14   112.61  3.000
 EOD  H162  C16  H161  105.95  3.000
 EOD  H162  C16  C17   109.24  3.000
 EOD  H161  C16  C17   109.34  3.000
 EOD  H162  C16  C15   109.46  3.000
 EOD  H161  C16  C15   109.29  3.000
 EOD  C17   C16  C15   113.30  3.000
 EOD  H172  C17  H171  106.06  3.000
 EOD  H172  C17  C18   109.62  3.000
 EOD  H171  C17  C18   109.66  3.000
 EOD  H172  C17  C16   109.33  3.000
 EOD  H171  C17  C16   109.27  3.000
 EOD  C18   C17  C16   112.69  3.000
 EOD  H183  C18  H182  107.68  3.000
 EOD  H183  C18  H181  107.59  3.000
 EOD  H182  C18  H181  107.49  3.000
 EOD  H183  C18  C17   111.70  3.000
 EOD  H182  C18  C17   111.06  3.000
 EOD  H181  C18  C17   111.12  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
 EOD  CONST_01  HO2   O2   C1   O1      0.00   0.0  0
 EOD  Var_01    C14   C13  O3   C12  -115.79  30.0  1
 EOD  Var_02    O3    C12  C11  C10    81.46  30.0  3
 EOD  Var_03    C15   C14  C13  C12  -144.39  30.0  3
 EOD  Var_04    C12   C11  C10  C9   -176.44  30.0  3
 EOD  Var_05    C16   C15  C14  C13  -176.11  30.0  3
 EOD  Var_06    C3    C2   C1   O1     -0.14  30.0  3
 EOD  Var_07    C4    C3   C2   C1    179.77  30.0  3
 EOD  Var_08    C5    C4   C3   C2   -178.96  30.0  3
 EOD  Var_09    C6    C5   C4   C3   -179.74  30.0  3
 EOD  Var_10    C7    C6   C5   C4   -176.92  30.0  3
 EOD  Var_11    C8    C7   C6   C5   -178.81  30.0  3
 EOD  Var_12    C9    C8   C7   C6   -173.05  30.0  3
 EOD  Var_13    C10   C9   C8   C7   -176.76  30.0  3
 EOD  Var_14    C11   C10  C9   C8   -173.73  30.0  3
 EOD  Var_15    C17   C16  C15  C14  -179.66  30.0  3
 EOD  Var_16    C18   C17  C16  C15  -179.23  30.0  3
 EOD  Var_17    H181  C18  C17  C16   -59.64  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 EOD  chir_01  C12  C11  O3   C13  both
 EOD  chir_02  C13  O3   C14  C12  both

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
 EOD  plan-1  O1   0.020
 EOD  plan-1  C1   0.020
 EOD  plan-1  O2   0.020
 EOD  plan-1  C2   0.020
 EOD  plan-1  HO2  0.020

