# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 20:42:03 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: (9E,12R)-12-hydroxyoctadec-9-enoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCC[C@@H](O)C/C=C/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
 RCL  RCL  '(9E,12R)-12-hydroxyoctadec-9-enoic acid'  ligand  54  21  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_RCL
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
 RCL  O1    O  OC    -1  -0.636   1.1993   0.4057  -10.1157
 RCL  C1    C  C      0   0.410   1.4494   0.1428   -8.9194
 RCL  O2    O  O      0  -0.610   2.5338  -0.2770   -8.4695
 RCL  C2    C  CH2    0  -0.582   0.2975   0.3742   -7.9265
 RCL  C3    C  CH2    0  -0.402   0.5641  -0.0138   -6.4818
 RCL  C4    C  CH2    0  -0.409  -0.6288   0.2602   -5.5732
 RCL  C5    C  CH2    0  -0.410  -0.3922  -0.1312   -4.1202
 RCL  C6    C  CH2    0  -0.412  -1.5905   0.1558   -3.2243
 RCL  C7    C  CH2    0  -0.412  -1.3799  -0.2550   -1.7729
 RCL  C8    C  CH2    0  -0.482  -2.5851   0.0711   -0.8899
 RCL  C9    C  C1     0  -0.208  -2.4322  -0.4245    0.5128
 RCL  C10   C  C1     0  -0.196  -2.3586   0.3480    1.5920
 RCL  C11   C  CH2    0  -0.521  -2.1990  -0.1439    2.9936
 RCL  C12   C  CH1    0   0.043  -0.8546   0.2426    3.6182
 RCL  O12   O  OH1    0  -0.663   0.2287  -0.2726    2.8729
 RCL  C13   C  CH2    0  -0.444  -0.7969  -0.1685    5.0864
 RCL  C14   C  CH2    0  -0.410   0.5041   0.1958    5.7895
 RCL  C15   C  CH2    0  -0.412   0.4802  -0.1461    7.2746
 RCL  C16   C  CH2    0  -0.407   1.7804   0.1906    7.9929
 RCL  C17   C  CH2    0  -0.418   1.7460  -0.1320    9.4819
 RCL  C18   C  CH3    0  -0.663   3.0522   0.1986   10.1903
 RCL  H21   H  HCH2   0   0.214  -0.5848  -0.1626   -8.2945
 RCL  H22   H  HCH2   0   0.216   0.0187   1.4341   -7.9742
 RCL  H31   H  HCH2   0   0.200   1.4367   0.5285   -6.1056
 RCL  H32   H  HCH2   0   0.199   0.8242  -1.0752   -6.4236
 RCL  H41   H  HCH2   0   0.202  -1.5063  -0.2767   -5.9521
 RCL  H42   H  HCH2   0   0.202  -0.8864   1.3246   -5.6235
 RCL  H51   H  HCH2   0   0.205   0.4853   0.4016   -3.7368
 RCL  H52   H  HCH2   0   0.205  -0.1447  -1.1972   -4.0665
 RCL  H61   H  HCH2   0   0.207  -2.4710  -0.3626   -3.6205
 RCL  H62   H  HCH2   0   0.207  -1.8263   1.2250   -3.2687
 RCL  H71   H  HCH2   0   0.214  -0.4938   0.2458   -1.3699
 RCL  H72   H  HCH2   0   0.212  -1.1706  -1.3291   -1.7243
 RCL  H81   H  HCH2   0   0.222  -3.4778  -0.3797   -1.3384
 RCL  H82   H  HCH2   0   0.225  -2.7520   1.1524   -0.8867
 RCL  H9    H  H      0   0.223  -2.3699  -1.5045    0.6364
 RCL  H10   H  H      0   0.226  -2.4114   1.4282    1.4667
 RCL  H111  H  HCH2   0   0.231  -2.3136  -1.2338    3.0291
 RCL  H112  H  HCH2   0   0.233  -2.9955   0.2716    3.6196
 RCL  H12   H  HCH1   0   0.216  -0.7475   1.3323    3.5616
 RCL  HO12  H  HOH1   0   0.436   0.1496  -1.2325    2.8548
 RCL  H131  H  HCH2   0   0.213  -0.9700  -1.2491    5.1691
 RCL  H132  H  HCH2   0   0.217  -1.6342   0.3097    5.6054
 RCL  H141  H  HCH2   0   0.207   0.6972   1.2678    5.6695
 RCL  H142  H  HCH2   0   0.212   1.3418  -0.3201    5.3121
 RCL  H151  H  HCH2   0   0.207   0.2645  -1.2135    7.3971
 RCL  H152  H  HCH2   0   0.206  -0.3484   0.3852    7.7561
 RCL  H161  H  HCH2   0   0.206   2.0059   1.2547    7.8596
 RCL  H162  H  HCH2   0   0.206   2.6074  -0.3532    7.5227
 RCL  H171  H  HCH2   0   0.210   1.5132  -1.1930    9.6158
 RCL  H172  H  HCH2   0   0.210   0.9241   0.4185    9.9504
 RCL  H181  H  HCH3   0   0.226   3.0075  -0.0464   11.2519
 RCL  H182  H  HCH3   0   0.215   3.8864  -0.3568    9.7573
 RCL  H183  H  HCH3   0   0.215   3.2878   1.2614   10.1066

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
 RCL  O1   C1    deloc   1.250  0.020  1.250
 RCL  C1   O2    deloc   1.247  0.020  1.247
 RCL  C1   C2    single  1.538  0.020  1.538
 RCL  C2   C3    single  1.519  0.020  1.519
 RCL  C2   H21   single  0.970  0.020  1.090
 RCL  C2   H22   single  0.970  0.020  1.090
 RCL  C3   C4    single  1.524  0.020  1.524
 RCL  C3   H31   single  0.970  0.020  1.090
 RCL  C3   H32   single  0.970  0.020  1.090
 RCL  C4   C5    single  1.523  0.020  1.523
 RCL  C4   H41   single  0.970  0.020  1.090
 RCL  C4   H42   single  0.970  0.020  1.090
 RCL  C5   C6    single  1.523  0.020  1.523
 RCL  C5   H51   single  0.970  0.020  1.090
 RCL  C5   H52   single  0.970  0.020  1.090
 RCL  C6   C7    single  1.523  0.020  1.523
 RCL  C6   H61   single  0.970  0.020  1.090
 RCL  C6   H62   single  0.970  0.020  1.090
 RCL  C7   C8    single  1.529  0.020  1.529
 RCL  C7   H71   single  0.970  0.020  1.090
 RCL  C7   H72   single  0.970  0.020  1.090
 RCL  C8   C9    single  1.495  0.020  1.495
 RCL  C8   H81   single  0.970  0.020  1.090
 RCL  C8   H82   single  0.970  0.020  1.090
 RCL  C9   C10   double  1.329  0.020  1.329
 RCL  C9   H9    single  0.930  0.020  1.080
 RCL  C10  C11   single  1.494  0.020  1.494
 RCL  C10  H10   single  0.930  0.020  1.080
 RCL  C11  C12   single  1.532  0.020  1.532
 RCL  C11  H111  single  0.970  0.020  1.090
 RCL  C11  H112  single  0.970  0.020  1.090
 RCL  C12  O12   single  1.412  0.020  1.412
 RCL  C12  C13   single  1.526  0.020  1.526
 RCL  C12  H12   single  0.970  0.020  1.090
 RCL  O12  HO12  single  0.850  0.020  0.980
 RCL  C13  C14   single  1.523  0.020  1.523
 RCL  C13  H131  single  0.970  0.020  1.090
 RCL  C13  H132  single  0.970  0.020  1.090
 RCL  C14  C15   single  1.524  0.020  1.524
 RCL  C14  H141  single  0.970  0.020  1.090
 RCL  C14  H142  single  0.970  0.020  1.090
 RCL  C15  C16   single  1.523  0.020  1.523
 RCL  C15  H151  single  0.970  0.020  1.090
 RCL  C15  H152  single  0.970  0.020  1.090
 RCL  C16  C17   single  1.524  0.020  1.524
 RCL  C16  H161  single  0.970  0.020  1.090
 RCL  C16  H162  single  0.970  0.020  1.090
 RCL  C17  C18   single  1.522  0.020  1.522
 RCL  C17  H171  single  0.970  0.020  1.090
 RCL  C17  H172  single  0.970  0.020  1.090
 RCL  C18  H181  single  0.970  0.020  1.090
 RCL  C18  H182  single  0.970  0.020  1.090
 RCL  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
 RCL  C2    C1   O2    117.97  3.000
 RCL  C2    C1   O1    115.86  3.000
 RCL  O2    C1   O1    126.17  3.000
 RCL  H22   C2   H21   104.71  3.000
 RCL  H22   C2   C3    109.43  3.000
 RCL  H21   C2   C3    109.59  3.000
 RCL  H22   C2   C1    107.91  3.000
 RCL  H21   C2   C1    108.19  3.000
 RCL  C3    C2   C1    116.36  3.000
 RCL  H32   C3   H31   105.83  3.000
 RCL  H32   C3   C4    109.19  3.000
 RCL  H31   C3   C4    109.28  3.000
 RCL  H32   C3   C2    109.87  3.000
 RCL  H31   C3   C2    109.89  3.000
 RCL  C4    C3   C2    112.55  3.000
 RCL  H42   C4   H41   105.76  3.000
 RCL  H42   C4   C5    109.25  3.000
 RCL  H41   C4   C5    109.15  3.000
 RCL  H42   C4   C3    109.33  3.000
 RCL  H41   C4   C3    109.41  3.000
 RCL  C5    C4   C3    113.63  3.000
 RCL  H52   C5   H51   105.96  3.000
 RCL  H52   C5   C6    109.40  3.000
 RCL  H51   C5   C6    109.42  3.000
 RCL  H52   C5   C4    109.38  3.000
 RCL  H51   C5   C4    109.46  3.000
 RCL  C6    C5   C4    112.98  3.000
 RCL  H62   C6   H61   105.90  3.000
 RCL  H62   C6   C7    109.37  3.000
 RCL  H61   C6   C7    109.15  3.000
 RCL  H62   C6   C5    109.22  3.000
 RCL  H61   C6   C5    109.28  3.000
 RCL  C7    C6   C5    113.63  3.000
 RCL  H72   C7   H71   106.12  3.000
 RCL  H72   C7   C8    109.52  3.000
 RCL  H71   C7   C8    109.14  3.000
 RCL  H72   C7   C6    109.46  3.000
 RCL  H71   C7   C6    109.83  3.000
 RCL  C8    C7   C6    112.57  3.000
 RCL  H82   C8   H81   106.46  3.000
 RCL  H82   C8   C9    109.90  3.000
 RCL  H81   C8   C9    109.32  3.000
 RCL  H82   C8   C7    109.43  3.000
 RCL  H81   C8   C7    108.54  3.000
 RCL  C9    C8   C7    112.98  3.000
 RCL  H9    C9   C10   118.76  3.000
 RCL  H9    C9   C8    116.17  3.000
 RCL  C10   C9   C8    125.07  3.000
 RCL  H10   C10  C11   116.09  3.000
 RCL  H10   C10  C9    118.71  3.000
 RCL  C11   C10  C9    125.19  3.000
 RCL  H112  C11  H111  106.42  3.000
 RCL  H112  C11  C12   108.03  3.000
 RCL  H111  C11  C12   109.22  3.000
 RCL  H112  C11  C10   109.50  3.000
 RCL  H111  C11  C10   110.27  3.000
 RCL  C12   C11  C10   113.15  3.000
 RCL  H12   C12  C13   108.29  3.000
 RCL  H12   C12  O12   105.09  3.000
 RCL  C13   C12  O12   112.37  3.000
 RCL  H12   C12  C11   108.39  3.000
 RCL  C13   C12  C11   110.95  3.000
 RCL  O12   C12  C11   111.46  3.000
 RCL  HO12  O12  C12   108.08  3.000
 RCL  H132  C13  H131  105.88  3.000
 RCL  H132  C13  C14   109.26  3.000
 RCL  H131  C13  C14   109.60  3.000
 RCL  H132  C13  C12   108.03  3.000
 RCL  H131  C13  C12   109.38  3.000
 RCL  C14   C13  C12   114.33  3.000
 RCL  H142  C14  H141  106.19  3.000
 RCL  H142  C14  C15   109.36  3.000
 RCL  H141  C14  C15   109.20  3.000
 RCL  H142  C14  C13   109.88  3.000
 RCL  H141  C14  C13   109.51  3.000
 RCL  C15   C14  C13   112.51  3.000
 RCL  H152  C15  H151  105.92  3.000
 RCL  H152  C15  C16   109.34  3.000
 RCL  H151  C15  C16   109.31  3.000
 RCL  H152  C15  C14   109.34  3.000
 RCL  H151  C15  C14   109.30  3.000
 RCL  C16   C15  C14   113.37  3.000
 RCL  H162  C16  H161  105.92  3.000
 RCL  H162  C16  C17   109.34  3.000
 RCL  H161  C16  C17   109.21  3.000
 RCL  H162  C16  C15   109.40  3.000
 RCL  H161  C16  C15   109.45  3.000
 RCL  C17   C16  C15   113.25  3.000
 RCL  H172  C17  H171  105.99  3.000
 RCL  H172  C17  C18   109.63  3.000
 RCL  H171  C17  C18   109.64  3.000
 RCL  H172  C17  C16   109.19  3.000
 RCL  H171  C17  C16   109.24  3.000
 RCL  C18   C17  C16   112.92  3.000
 RCL  H183  C18  H182  107.45  3.000
 RCL  H183  C18  H181  107.59  3.000
 RCL  H182  C18  H181  107.65  3.000
 RCL  H183  C18  C17   111.16  3.000
 RCL  H182  C18  C17   111.14  3.000
 RCL  H181  C18  C17   111.66  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
 RCL  Var_01  C11   C10  C9   C8   -179.67   0.0  2
 RCL  Var_02  C3    C2   C1   O1    176.75  30.0  3
 RCL  Var_03  C4    C3   C2   C1    179.61  30.0  3
 RCL  Var_04  C5    C4   C3   C2    179.50  30.0  3
 RCL  Var_05  C6    C5   C4   C3    179.69  30.0  3
 RCL  Var_06  C7    C6   C5   C4    178.87  30.0  3
 RCL  Var_07  C8    C7   C6   C5    178.77  30.0  3
 RCL  Var_08  C9    C8   C7   C6    175.49  30.0  3
 RCL  Var_09  C10   C9   C8   C7    115.54  30.0  3
 RCL  Var_10  C12   C11  C10  C9    113.50  30.0  3
 RCL  Var_11  C15   C14  C13  C12   176.04  30.0  3
 RCL  Var_12  C16   C15  C14  C13   179.11  30.0  3
 RCL  Var_13  C17   C16  C15  C14   179.09  30.0  3
 RCL  Var_14  C18   C17  C16  C15   179.61  30.0  3
 RCL  Var_15  H181  C18  C17  C16  -179.61  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
 RCL  chir_01  C12  C11  O12  C13  positiv

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
 RCL  plan-1  O1   0.020
 RCL  plan-1  C1   0.020
 RCL  plan-1  O2   0.020
 RCL  plan-1  C2   0.020
 RCL  plan-2  C8   0.020
 RCL  plan-2  C9   0.020
 RCL  plan-2  C10  0.020
 RCL  plan-2  C11  0.020
 RCL  plan-2  H9   0.020
 RCL  plan-2  H10  0.020

