# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 25 13:45:24 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  55  21  .  2021-08-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  OH1   0  -0.599   1.2373   0.4094  -10.0697
 RCL  C1    C  C     0   0.550   1.5231   0.0723   -8.8144
 RCL  O2    O  O     0  -0.446   2.5933  -0.3751   -8.4842
 RCL  C2    C  CH2   0  -0.580   0.3627   0.3220   -7.8924
 RCL  C3    C  CH2   0  -0.418   0.6230  -0.0674   -6.4470
 RCL  C4    C  CH2   0  -0.414  -0.5837   0.2205   -5.5629
 RCL  C5    C  CH2   0  -0.413  -0.3631  -0.1612   -4.1052
 RCL  C6    C  CH2   0  -0.414  -1.5706   0.1374   -3.2262
 RCL  C7    C  CH2   0  -0.413  -1.3743  -0.2613   -1.7694
 RCL  C8    C  CH2   0  -0.482  -2.5848   0.0784   -0.8991
 RCL  C9    C  C1    0  -0.208  -2.4470  -0.4156    0.5058
 RCL  C10   C  C1    0  -0.196  -2.3690   0.3581    1.5837
 RCL  C11   C  CH2   0  -0.522  -2.2188  -0.1334    2.9864
 RCL  C12   C  CH1   0   0.042  -0.8692   0.2345    3.6114
 RCL  O12   O  OH1   0  -0.662   0.2071  -0.2983    2.8680
 RCL  C13   C  CH2   0  -0.444  -0.8184  -0.1749    5.0801
 RCL  C14   C  CH2   0  -0.410   0.4839   0.1798    5.7857
 RCL  C15   C  CH2   0  -0.412   0.4542  -0.1603    7.2710
 RCL  C16   C  CH2   0  -0.407   1.7550   0.1679    7.9920
 RCL  C17   C  CH2   0  -0.418   1.7164  -0.1571    9.4803
 RCL  C18   C  CH3   0  -0.663   3.0219   0.1685   10.1923
 RCL  HO1   H  HOH1  0   0.478   1.9997   0.2357  -10.6416
 RCL  H21   H  HCH2  0   0.275  -0.5045  -0.2176   -8.2863
 RCL  H22   H  HCH2  0   0.275   0.0984   1.3824   -7.9619
 RCL  H31   H  HCH2  0   0.225   1.4918   0.4761   -6.0659
 RCL  H32   H  HCH2  0   0.224   0.8726  -1.1302   -6.3872
 RCL  H41   H  HCH2  0   0.212  -1.4563  -0.3174   -5.9499
 RCL  H42   H  HCH2  0   0.212  -0.8346   1.2852   -5.6254
 RCL  H51   H  HCH2  0   0.210   0.5115   0.3720   -3.7165
 RCL  H52   H  HCH2  0   0.209  -0.1205  -1.2276   -4.0409
 RCL  H61   H  HCH2  0   0.209  -2.4482  -0.3823   -3.6269
 RCL  H62   H  HCH2  0   0.209  -1.8026   1.2068   -3.2823
 RCL  H71   H  HCH2  0   0.215  -0.4892   0.2392   -1.3639
 RCL  H72   H  HCH2  0   0.213  -1.1702  -1.3358   -1.7096
 RCL  H81   H  HCH2  0   0.222  -3.4775  -0.3651   -1.3546
 RCL  H82   H  HCH2  0   0.225  -2.7415   1.1613   -0.8996
 RCL  H9    H  H     0   0.223  -2.3993  -1.4960    0.6317
 RCL  H10   H  H     0   0.226  -2.4092   1.4387    1.4563
 RCL  H111  H  HCH2  0   0.231  -2.3486  -1.2215    3.0235
 RCL  H112  H  HCH2  0   0.234  -3.0095   0.2946    3.6114
 RCL  H12   H  HCH1  0   0.216  -0.7459   1.3224    3.5526
 RCL  HO12  H  HOH1  0   0.436   0.1133  -1.2568    2.8515
 RCL  H131  H  HCH2  0   0.213  -0.9998  -1.2542    5.1627
 RCL  H132  H  HCH2  0   0.217  -1.6530   0.3098    5.5973
 RCL  H141  H  HCH2  0   0.207   0.6858   1.2501    5.6649
 RCL  H142  H  HCH2  0   0.212   1.3187  -0.3431    5.3107
 RCL  H151  H  HCH2  0   0.207   0.2301  -1.2260    7.3945
 RCL  H152  H  HCH2  0   0.206  -0.3717   0.3774    7.7501
 RCL  H161  H  HCH2  0   0.206   1.9864   1.2311    7.8609
 RCL  H162  H  HCH2  0   0.206   2.5798  -0.3794    7.5220
 RCL  H171  H  HCH2  0   0.210   1.4808  -1.2178    9.6118
 RCL  H172  H  HCH2  0   0.210   0.8947   0.3944    9.9480
 RCL  H181  H  HCH3  0   0.226   2.9710  -0.0692   11.2555
 RCL  H182  H  HCH3  0   0.215   3.8539  -0.3957    9.7665
 RCL  H183  H  HCH3  0   0.215   3.2660   1.2290   10.1031

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    single  1.331  0.020  1.331
 RCL  O1   HO1   single  0.850  0.020  0.980
 RCL  C1   O2    double  1.206  0.020  1.206
 RCL  C1   C2    single  1.503  0.020  1.503
 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  1.523  0.020  1.523
 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  1.496  0.020  1.496
 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  HO1   O1   C1    110.03  3.000
 RCL  C2    C1   O2    125.37  3.000
 RCL  C2    C1   O1    111.76  3.000
 RCL  O2    C1   O1    122.87  3.000
 RCL  H22   C2   H21   105.27  3.000
 RCL  H22   C2   C3    110.48  3.000
 RCL  H21   C2   C3    110.59  3.000
 RCL  H22   C2   C1    107.96  3.000
 RCL  H21   C2   C1    108.00  3.000
 RCL  C3    C2   C1    114.12  3.000
 RCL  H32   C3   H31   106.42  3.000
 RCL  H32   C3   C4    109.44  3.000
 RCL  H31   C3   C4    109.46  3.000
 RCL  H32   C3   C2    109.90  3.000
 RCL  H31   C3   C2    109.90  3.000
 RCL  C4    C3   C2    111.59  3.000
 RCL  H42   C4   H41   105.93  3.000
 RCL  H42   C4   C5    109.35  3.000
 RCL  H41   C4   C5    109.29  3.000
 RCL  H42   C4   C3    109.38  3.000
 RCL  H41   C4   C3    109.45  3.000
 RCL  C5    C4   C3    113.17  3.000
 RCL  H52   C5   H51   106.03  3.000
 RCL  H52   C5   C6    109.42  3.000
 RCL  H51   C5   C6    109.43  3.000
 RCL  H52   C5   C4    109.40  3.000
 RCL  H51   C5   C4    109.47  3.000
 RCL  C6    C5   C4    112.86  3.000
 RCL  H62   C6   H61   105.94  3.000
 RCL  H62   C6   C7    109.37  3.000
 RCL  H61   C6   C7    109.20  3.000
 RCL  H62   C6   C5    109.25  3.000
 RCL  H61   C6   C5    109.32  3.000
 RCL  C7    C6   C5    113.48  3.000
 RCL  H72   C7   H71   106.12  3.000
 RCL  H72   C7   C8    109.53  3.000
 RCL  H71   C7   C8    109.13  3.000
 RCL  H72   C7   C6    109.45  3.000
 RCL  H71   C7   C6    109.81  3.000
 RCL  C8    C7   C6    112.60  3.000
 RCL  H82   C8   H81   106.48  3.000
 RCL  H82   C8   C9    109.91  3.000
 RCL  H81   C8   C9    109.38  3.000
 RCL  H82   C8   C7    109.45  3.000
 RCL  H81   C8   C7    108.56  3.000
 RCL  C9    C8   C7    112.85  3.000
 RCL  H9    C9   C10   118.77  3.000
 RCL  H9    C9   C8    116.13  3.000
 RCL  C10   C9   C8    125.10  3.000
 RCL  H10   C10  C11   116.11  3.000
 RCL  H10   C10  C9    118.73  3.000
 RCL  C11   C10  C9    125.16  3.000
 RCL  H112  C11  H111  106.44  3.000
 RCL  H112  C11  C12   108.03  3.000
 RCL  H111  C11  C12   109.20  3.000
 RCL  H112  C11  C10   109.56  3.000
 RCL  H111  C11  C10   110.26  3.000
 RCL  C12   C11  C10   113.12  3.000
 RCL  H12   C12  C13   108.31  3.000
 RCL  H12   C12  O12   105.09  3.000
 RCL  C13   C12  O12   112.34  3.000
 RCL  H12   C12  C11   108.39  3.000
 RCL  C13   C12  C11   110.95  3.000
 RCL  O12   C12  C11   111.47  3.000
 RCL  HO12  O12  C12   108.07  3.000
 RCL  H132  C13  H131  105.89  3.000
 RCL  H132  C13  C14   109.26  3.000
 RCL  H131  C13  C14   109.60  3.000
 RCL  H132  C13  C12   108.09  3.000
 RCL  H131  C13  C12   109.32  3.000
 RCL  C14   C13  C12   114.33  3.000
 RCL  H142  C14  H141  106.17  3.000
 RCL  H142  C14  C15   109.36  3.000
 RCL  H141  C14  C15   109.21  3.000
 RCL  H142  C14  C13   109.89  3.000
 RCL  H141  C14  C13   109.51  3.000
 RCL  C15   C14  C13   112.51  3.000
 RCL  H152  C15  H151  105.89  3.000
 RCL  H152  C15  C16   109.32  3.000
 RCL  H151  C15  C16   109.32  3.000
 RCL  H152  C15  C14   109.35  3.000
 RCL  H151  C15  C14   109.32  3.000
 RCL  C16   C15  C14   113.37  3.000
 RCL  H162  C16  H161  105.92  3.000
 RCL  H162  C16  C17   109.36  3.000
 RCL  H161  C16  C17   109.22  3.000
 RCL  H162  C16  C15   109.40  3.000
 RCL  H161  C16  C15   109.44  3.000
 RCL  C17   C16  C15   113.25  3.000
 RCL  H172  C17  H171  105.99  3.000
 RCL  H172  C17  C18   109.64  3.000
 RCL  H171  C17  C18   109.62  3.000
 RCL  H172  C17  C16   109.20  3.000
 RCL  H171  C17  C16   109.24  3.000
 RCL  C18   C17  C16   112.92  3.000
 RCL  H183  C18  H182  107.44  3.000
 RCL  H183  C18  H181  107.56  3.000
 RCL  H182  C18  H181  107.64  3.000
 RCL  H183  C18  C17   111.18  3.000
 RCL  H182  C18  C17   111.14  3.000
 RCL  H181  C18  C17   111.67  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  CONST_01  HO1   O1   C1   O2      0.00   0.0  0
 RCL  Var_01    C11   C10  C9   C8   -179.41   0.0  2
 RCL  Var_02    C3    C2   C1   O1    179.00  30.0  3
 RCL  Var_03    C4    C3   C2   C1    179.51  30.0  3
 RCL  Var_04    C5    C4   C3   C2    179.81  30.0  3
 RCL  Var_05    C6    C5   C4   C3    179.65  30.0  3
 RCL  Var_06    C7    C6   C5   C4    179.00  30.0  3
 RCL  Var_07    C8    C7   C6   C5    178.60  30.0  3
 RCL  Var_08    C9    C8   C7   C6    175.06  30.0  3
 RCL  Var_09    C10   C9   C8   C7    115.21  30.0  3
 RCL  Var_10    C12   C11  C10  C9    113.20  30.0  3
 RCL  Var_11    C15   C14  C13  C12   176.07  30.0  3
 RCL  Var_12    C16   C15  C14  C13   179.16  30.0  3
 RCL  Var_13    C17   C16  C15  C14   179.29  30.0  3
 RCL  Var_14    C18   C17  C16  C15   179.76  30.0  3
 RCL  Var_15    H181  C18  C17  C16   179.85  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-1  HO1  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

