# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 11:02:30 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: (9S,10E)-9-hydroxy-11-[(2R,3R)-3-pentyloxiran-2-yl]undec-10-enoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCC[C@H]1O[C@@H]1/C=C/[C@@H](O)CCCCCCCC(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
 9OH  9OH  '(9S,10E)-9-hydroxy-11-[(2R,3R)-3-pentyloxiran-2-yl]undec-10-enoic acid'  ligand  53  22  .  2022-09-16  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_9OH
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
 9OH  C1    C  C      0   0.410   1.8362   0.1098  -8.7599
 9OH  C2    C  CH2    0  -0.582   1.8586  -0.2431  -7.2630
 9OH  C3    C  CH2    0  -0.403   0.5788   0.0180  -6.4859
 9OH  C4    C  CH2    0  -0.409   0.7184  -0.3190  -5.0065
 9OH  C5    C  CH2    0  -0.411  -0.5461  -0.0640  -4.1962
 9OH  C6    C  CH2    0  -0.412  -0.3694  -0.3633  -2.7134
 9OH  C7    C  CH2    0  -0.412  -1.6230  -0.1114  -1.8847
 9OH  C8    C  CH2    0  -0.464  -1.3814  -0.3376  -0.3983
 9OH  C9    C  CH1    0   0.009  -2.6287  -0.1847   0.4766
 9OH  C10   C  C1     0  -0.243  -2.2747  -0.4555   1.9113
 9OH  C11   C  C1     0  -0.275  -2.4872   0.3774   2.9237
 9OH  C12   C  CH1    0  -0.051  -2.0662   0.1261   4.3182
 9OH  C13   C  CH1    0   0.012  -0.6585   0.2071   4.7202
 9OH  C14   C  CH2    0  -0.464  -0.2202   0.6164   6.0949
 9OH  C15   C  CH2    0  -0.421   1.0267  -0.1300   6.5612
 9OH  C16   C  CH2    0  -0.408   1.5324   0.3570   7.9127
 9OH  C17   C  CH2    0  -0.419   2.7730  -0.3858   8.3940
 9OH  C18   C  CH3    0  -0.663   3.2807   0.1188   9.7375
 9OH  O19   O  O      0  -0.610   0.7834   0.5789  -9.2353
 9OH  O20   O  OC    -1  -0.636   2.8964  -0.1045  -9.3866
 9OH  O21   O  OH1    0  -0.663  -3.2733   1.0525   0.2881
 9OH  O22   O  O2     0  -0.488  -1.3189  -1.0460   4.5877
 9OH  H21   H  HCH2   0   0.215   2.6859   0.3063  -6.7978
 9OH  H22   H  HCH2   0   0.216   2.1370  -1.2993  -7.1651
 9OH  H31   H  HCH2   0   0.200  -0.2441  -0.5622  -6.9145
 9OH  H32   H  HCH2   0   0.200   0.2897   1.0678  -6.5907
 9OH  H41   H  HCH2   0   0.201   1.5425   0.2640  -4.5786
 9OH  H42   H  HCH2   0   0.202   1.0107  -1.3699  -4.8972
 9OH  H51   H  HCH2   0   0.205  -1.3670  -0.6684  -4.5983
 9OH  H52   H  HCH2   0   0.205  -0.8526   0.9807  -4.3201
 9OH  H61   H  HCH2   0   0.207   0.4515   0.2475  -2.3203
 9OH  H62   H  HCH2   0   0.208  -0.0538  -1.4049  -2.5872
 9OH  H71   H  HCH2   0   0.211  -2.4302  -0.7659  -2.2321
 9OH  H72   H  HCH2   0   0.213  -1.9659   0.9132  -2.0539
 9OH  H81   H  HCH2   0   0.223  -0.6043   0.3499  -0.0425
 9OH  H82   H  HCH2   0   0.227  -0.9828  -1.3448  -0.2417
 9OH  H91   H  HCH1   0   0.235  -3.3550  -0.9426   0.1569
 9OH  H101  H  H      0   0.248  -1.7877  -1.4095   2.0941
 9OH  H111  H  H      0   0.246  -2.9970   1.3233   2.7683
 9OH  H121  H  HCH1   0   0.254  -2.8108   0.3724   5.0765
 9OH  H131  H  HCH1   0   0.243   0.0639   0.4060   3.9272
 9OH  H141  H  HCH2   0   0.233  -1.0355   0.4702   6.8102
 9OH  H142  H  HCH2   0   0.231  -0.0154   1.6913   6.0727
 9OH  H151  H  HCH2   0   0.217   1.8200  -0.0157   5.8143
 9OH  H152  H  HCH2   0   0.219   0.8097  -1.2012   6.6159
 9OH  H161  H  HCH2   0   0.210   0.7365   0.2556   8.6590
 9OH  H162  H  HCH2   0   0.209   1.7536   1.4282   7.8507
 9OH  H171  H  HCH2   0   0.211   3.5644  -0.2931   7.6437
 9OH  H172  H  HCH2   0   0.211   2.5486  -1.4545   8.4654
 9OH  H181  H  HCH3   0   0.226   4.1590  -0.4367  10.0684
 9OH  H182  H  HCH3   0   0.216   3.5584   1.1732   9.6849
 9OH  H183  H  HCH3   0   0.216   2.5166   0.0184  10.5106
 9OH  H211  H  HOH1   0   0.445  -2.6359   1.7556   0.4578

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
 9OH  C1   C2    single  1.538  0.020  1.538
 9OH  C1   O19   deloc   1.247  0.020  1.247
 9OH  C1   O20   deloc   1.250  0.020  1.250
 9OH  C2   C3    single  1.520  0.020  1.520
 9OH  C2   H21   single  0.970  0.020  1.090
 9OH  C2   H22   single  0.970  0.020  1.090
 9OH  C3   C4    single  1.524  0.020  1.524
 9OH  C3   H31   single  0.970  0.020  1.090
 9OH  C3   H32   single  0.970  0.020  1.090
 9OH  C4   C5    single  1.523  0.020  1.523
 9OH  C4   H41   single  0.970  0.020  1.090
 9OH  C4   H42   single  0.970  0.020  1.090
 9OH  C5   C6    single  1.523  0.020  1.523
 9OH  C5   H51   single  0.970  0.020  1.090
 9OH  C5   H52   single  0.970  0.020  1.090
 9OH  C6   C7    single  1.524  0.020  1.524
 9OH  C6   H61   single  0.970  0.020  1.090
 9OH  C6   H62   single  0.970  0.020  1.090
 9OH  C7   C8    single  1.523  0.020  1.523
 9OH  C7   H71   single  0.970  0.020  1.090
 9OH  C7   H72   single  0.970  0.020  1.090
 9OH  C8   C9    single  1.531  0.020  1.531
 9OH  C8   H81   single  0.970  0.020  1.090
 9OH  C8   H82   single  0.970  0.020  1.090
 9OH  C9   C10   single  1.502  0.020  1.502
 9OH  C9   O21   single  1.408  0.020  1.408
 9OH  C9   H91   single  0.970  0.020  1.090
 9OH  C10  C11   double  1.328  0.020  1.328
 9OH  C10  H101  single  0.930  0.020  1.080
 9OH  C11  C12   single  1.478  0.020  1.478
 9OH  C11  H111  single  0.930  0.020  1.080
 9OH  C12  C13   single  1.466  0.020  1.466
 9OH  C12  O22   single  1.416  0.020  1.416
 9OH  C12  H121  single  0.970  0.020  1.090
 9OH  C13  C14   single  1.500  0.020  1.500
 9OH  C13  O22   single  1.423  0.020  1.423
 9OH  C13  H131  single  0.970  0.020  1.090
 9OH  C14  C15   single  1.526  0.020  1.526
 9OH  C14  H141  single  0.970  0.020  1.090
 9OH  C14  H142  single  0.970  0.020  1.090
 9OH  C15  C16   single  1.523  0.020  1.523
 9OH  C15  H151  single  0.970  0.020  1.090
 9OH  C15  H152  single  0.970  0.020  1.090
 9OH  C16  C17   single  1.524  0.020  1.524
 9OH  C16  H161  single  0.970  0.020  1.090
 9OH  C16  H162  single  0.970  0.020  1.090
 9OH  C17  C18   single  1.522  0.020  1.522
 9OH  C17  H171  single  0.970  0.020  1.090
 9OH  C17  H172  single  0.970  0.020  1.090
 9OH  C18  H181  single  0.970  0.020  1.090
 9OH  C18  H182  single  0.970  0.020  1.090
 9OH  C18  H183  single  0.970  0.020  1.090
 9OH  O21  H211  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
 9OH  O20   C1   O19   126.12  3.000
 9OH  O20   C1   C2    115.86  3.000
 9OH  O19   C1   C2    118.02  3.000
 9OH  H22   C2   H21   104.66  3.000
 9OH  H22   C2   C3    109.49  3.000
 9OH  H21   C2   C3    109.41  3.000
 9OH  H22   C2   C1    108.15  3.000
 9OH  H21   C2   C1    107.99  3.000
 9OH  C3    C2   C1    116.48  3.000
 9OH  H32   C3   H31   105.82  3.000
 9OH  H32   C3   C4    109.23  3.000
 9OH  H31   C3   C4    109.38  3.000
 9OH  H32   C3   C2    109.78  3.000
 9OH  H31   C3   C2    110.00  3.000
 9OH  C4    C3   C2    112.41  3.000
 9OH  H42   C4   H41   105.69  3.000
 9OH  H42   C4   C5    109.20  3.000
 9OH  H41   C4   C5    109.11  3.000
 9OH  H42   C4   C3    109.46  3.000
 9OH  H41   C4   C3    109.28  3.000
 9OH  C5    C4   C3    113.79  3.000
 9OH  H52   C5   H51   105.95  3.000
 9OH  H52   C5   C6    109.26  3.000
 9OH  H51   C5   C6    109.62  3.000
 9OH  H52   C5   C4    109.37  3.000
 9OH  H51   C5   C4    109.54  3.000
 9OH  C6    C5   C4    112.87  3.000
 9OH  H62   C6   H61   105.83  3.000
 9OH  H62   C6   C7    109.36  3.000
 9OH  H61   C6   C7    109.20  3.000
 9OH  H62   C6   C5    109.41  3.000
 9OH  H61   C6   C5    109.06  3.000
 9OH  C7    C6   C5    113.68  3.000
 9OH  H72   C7   H71   106.24  3.000
 9OH  H72   C7   C8    109.87  3.000
 9OH  H71   C7   C8    109.73  3.000
 9OH  H72   C7   C6    109.19  3.000
 9OH  H71   C7   C6    109.57  3.000
 9OH  C8    C7   C6    112.07  3.000
 9OH  H82   C8   H81   105.80  3.000
 9OH  H82   C8   C9    107.87  3.000
 9OH  H81   C8   C9    109.22  3.000
 9OH  H82   C8   C7    109.52  3.000
 9OH  H81   C8   C7    109.63  3.000
 9OH  C9    C8   C7    114.43  3.000
 9OH  H91   C9   O21   105.36  3.000
 9OH  H91   C9   C10   108.04  3.000
 9OH  O21   C9   C10   113.21  3.000
 9OH  H91   C9   C8    107.68  3.000
 9OH  O21   C9   C8    112.60  3.000
 9OH  C10   C9   C8    109.62  3.000
 9OH  H101  C10  C11   119.60  3.000
 9OH  H101  C10  C9    115.12  3.000
 9OH  C11   C10  C9    125.26  3.000
 9OH  H111  C11  C12   114.64  3.000
 9OH  H111  C11  C10   120.82  3.000
 9OH  C12   C11  C10   124.54  3.000
 9OH  H121  C12  O22   114.51  3.000
 9OH  H121  C12  C13   116.89  3.000
 9OH  O22   C12  C13    59.13  3.000
 9OH  H121  C12  C11   115.02  3.000
 9OH  O22   C12  C11   118.07  3.000
 9OH  C13   C12  C11   121.51  3.000
 9OH  H131  C13  O22   113.59  3.000
 9OH  H131  C13  C14   115.02  3.000
 9OH  O22   C13  C14   117.47  3.000
 9OH  H131  C13  C12   116.53  3.000
 9OH  O22   C13  C12    58.68  3.000
 9OH  C14   C13  C12   123.16  3.000
 9OH  H142  C14  H141  106.49  3.000
 9OH  H142  C14  C15   109.49  3.000
 9OH  H141  C14  C15   110.10  3.000
 9OH  H142  C14  C13   107.70  3.000
 9OH  H141  C14  C13   110.18  3.000
 9OH  C15   C14  C13   112.67  3.000
 9OH  H152  C15  H151  106.24  3.000
 9OH  H152  C15  C16   109.54  3.000
 9OH  H151  C15  C16   109.34  3.000
 9OH  H152  C15  C14   109.39  3.000
 9OH  H151  C15  C14   109.41  3.000
 9OH  C16   C15  C14   112.71  3.000
 9OH  H162  C16  H161  106.00  3.000
 9OH  H162  C16  C17   109.28  3.000
 9OH  H161  C16  C17   109.33  3.000
 9OH  H162  C16  C15   109.24  3.000
 9OH  H161  C16  C15   109.49  3.000
 9OH  C17   C16  C15   113.25  3.000
 9OH  H172  C17  H171  106.01  3.000
 9OH  H172  C17  C18   109.54  3.000
 9OH  H171  C17  C18   109.62  3.000
 9OH  H172  C17  C16   109.25  3.000
 9OH  H171  C17  C16   109.31  3.000
 9OH  C18   C17  C16   112.87  3.000
 9OH  H183  C18  H182  107.52  3.000
 9OH  H183  C18  H181  107.57  3.000
 9OH  H182  C18  H181  107.56  3.000
 9OH  H183  C18  C17   111.17  3.000
 9OH  H182  C18  C17   111.26  3.000
 9OH  H181  C18  C17   111.57  3.000
 9OH  H211  O21  C9    108.34  3.000
 9OH  C13   O22  C12    62.20  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
 9OH  Var_01  O22   C13  C12  C11  -106.05  30.0  1
 9OH  Var_02  C14   C13  O22  C12   113.90  30.0  1
 9OH  Var_03  C13   C12  C11  C10    72.91  30.0  3
 9OH  Var_04  C15   C14  C13  C12   144.69  30.0  3
 9OH  Var_05  C12   C11  C10  C9   -176.51   0.0  2
 9OH  Var_06  C16   C15  C14  C13   175.77  30.0  3
 9OH  Var_07  C4    C3   C2   C1   -178.04  30.0  3
 9OH  Var_08  C5    C4   C3   C2    179.79  30.0  3
 9OH  Var_09  O19   C1   C2   C3     -0.13  30.0  2
 9OH  Var_10  C6    C5   C4   C3   -178.07  30.0  3
 9OH  Var_11  C7    C6   C5   C4    179.87  30.0  3
 9OH  Var_12  C8    C7   C6   C5   -176.40  30.0  3
 9OH  Var_13  C9    C8   C7   C6   -176.36  30.0  3
 9OH  Var_14  C17   C16  C15  C14   179.66  30.0  3
 9OH  Var_15  C18   C17  C16  C15   179.32  30.0  3
 9OH  Var_16  H181  C18  C17  C16   179.15  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
 9OH  chir_01  C9   C8   C10  O21  negativ
 9OH  chir_02  C12  C11  C13  O22  both
 9OH  chir_03  C13  O22  C12  C14  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
 9OH  plan-1  C1    0.020
 9OH  plan-1  C2    0.020
 9OH  plan-1  O19   0.020
 9OH  plan-1  O20   0.020
 9OH  plan-2  C9    0.020
 9OH  plan-2  C10   0.020
 9OH  plan-2  C11   0.020
 9OH  plan-2  C12   0.020
 9OH  plan-2  H101  0.020
 9OH  plan-2  H111  0.020

