# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 21 05:20:13 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: methyl (E)-octadec-9-enoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCC/C=C/CCCCCCCC(=O)OC
#
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
 14Y  14Y  'methyl (E)-octadec-9-enoate'  ligand  57  21  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_14Y
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
 14Y  O2    O  O2    0  -0.457    9.3786   1.0249  -0.4224
 14Y  C1    C  C     0   0.600    8.1638   1.2670   0.0585
 14Y  O1    O  O     0  -0.454    7.8832   2.2692   0.6676
 14Y  C2    C  CH2   0  -0.580    7.2152   0.1405  -0.2491
 14Y  C3    C  CH2   0  -0.417    5.7768   0.4205   0.1547
 14Y  C4    C  CH2   0  -0.415    4.8601  -0.7498  -0.1787
 14Y  C5    C  CH2   0  -0.413    3.4087  -0.5017   0.2101
 14Y  C6    C  CH2   0  -0.414    2.4963  -1.6740  -0.1267
 14Y  C7    C  CH2   0  -0.414    1.0464  -1.4524   0.2840
 14Y  C8    C  CH2   0  -0.480    0.1413  -2.6212  -0.1067
 14Y  C9    C  C1    0  -0.213   -1.2582  -2.4748   0.4008
 14Y  C10   C  C1    0  -0.211   -2.3399  -2.3501  -0.3630
 14Y  C11   C  CH2   0  -0.480   -3.7421  -2.2102   0.1381
 14Y  C12   C  CH2   0  -0.414   -4.3902  -0.8804  -0.2493
 14Y  C13   C  CH2   0  -0.413   -5.8621  -0.8160   0.1383
 14Y  C14   C  CH2   0  -0.412   -6.5280   0.5096  -0.2080
 14Y  C15   C  CH2   0  -0.411   -8.0108   0.5381   0.1421
 14Y  C16   C  CH2   0  -0.407   -8.6887   1.8613  -0.1895
 14Y  C17   C  CH2   0  -0.418  -10.1764   1.8733   0.1413
 14Y  C18   C  CH3   0  -0.663  -10.8470   3.1992  -0.1905
 14Y  CA4   C  CH3   0  -0.425   10.3882   2.0067  -0.1923
 14Y  HA41  H  HCH3  0   0.237   10.5805   2.1412   0.8718
 14Y  HA42  H  HCH3  0   0.251   11.2862   1.6308  -0.6739
 14Y  HA43  H  HCH3  0   0.237   10.1203   2.9670  -0.6326
 14Y  H21C  H  HCH2  0   0.270    7.2783  -0.0841  -1.3181
 14Y  H22C  H  HCH2  0   0.275    7.5856  -0.7564   0.2592
 14Y  H31C  H  HCH2  0   0.224    5.7240   0.6293   1.2264
 14Y  H32C  H  HCH2  0   0.224    5.4174   1.3197  -0.3535
 14Y  H41C  H  HCH2  0   0.212    4.9177  -0.9632  -1.2518
 14Y  H42C  H  HCH2  0   0.212    5.2217  -1.6515   0.3281
 14Y  H51C  H  HCH2  0   0.209    3.3507  -0.2904   1.2836
 14Y  H52C  H  HCH2  0   0.210    3.0442   0.3991  -0.2958
 14Y  H61C  H  HCH2  0   0.209    2.5433  -1.8696  -1.2039
 14Y  H62C  H  HCH2  0   0.210    2.8743  -2.5797   0.3606
 14Y  H71C  H  HCH2  0   0.213    0.9938  -1.2934   1.3665
 14Y  H72C  H  HCH2  0   0.215    0.6661  -0.5354  -0.1774
 14Y  H81C  H  HCH2  0   0.226    0.1336  -2.7277  -1.1957
 14Y  H82C  H  HCH2  0   0.223    0.5732  -3.5462   0.2925
 14Y  H9    H  H     0   0.225   -1.3770  -2.4686   1.4832
 14Y  H10   H  H     0   0.225   -2.2173  -2.3484  -1.4451
 14Y  H111  H  HCH2  0   0.223   -4.3498  -3.0248  -0.2728
 14Y  H112  H  HCH2  0   0.226   -3.7648  -2.3260   1.2261
 14Y  H121  H  HCH2  0   0.215   -3.8441  -0.0599   0.2270
 14Y  H122  H  HCH2  0   0.213   -4.2917  -0.7266  -1.3293
 14Y  H131  H  HCH2  0   0.208   -6.3982  -1.6312  -0.3606
 14Y  H132  H  HCH2  0   0.208   -5.9637  -1.0019   1.2135
 14Y  H141  H  HCH2  0   0.207   -6.0143   1.3239   0.3149
 14Y  H142  H  HCH2  0   0.207   -6.4047   0.7115  -1.2779
 14Y  H151  H  HCH2  0   0.206   -8.5214  -0.2736  -0.3881
 14Y  H152  H  HCH2  0   0.206   -8.1348   0.3250   1.2099
 14Y  H161  H  HCH2  0   0.206   -8.1902   2.6725   0.3529
 14Y  H162  H  HCH2  0   0.205   -8.5544   2.0834  -1.2542
 14Y  H171  H  HCH2  0   0.210  -10.6726   1.0640  -0.4034
 14Y  H172  H  HCH2  0   0.210  -10.3115   1.6490   1.2039
 14Y  H181  H  HCH3  0   0.215  -10.3918   4.0211   0.3655
 14Y  H182  H  HCH3  0   0.215  -10.7551   3.4320  -1.2533
 14Y  H183  H  HCH3  0   0.226  -11.9100   3.1845   0.0525

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
 14Y  O2   C1    single  1.329  0.020  1.329
 14Y  O2   CA4   single  1.427  0.020  1.427
 14Y  C1   O1    double  1.206  0.020  1.206
 14Y  C1   C2    single  1.505  0.020  1.505
 14Y  C2   C3    single  1.520  0.020  1.520
 14Y  C3   C4    single  1.524  0.020  1.524
 14Y  C4   C5    single  1.523  0.020  1.523
 14Y  C5   C6    single  1.523  0.020  1.523
 14Y  C6   C7    single  1.523  0.020  1.523
 14Y  C7   C8    single  1.529  0.020  1.529
 14Y  C8   C9    single  1.496  0.020  1.496
 14Y  C9   C10   double  1.330  0.020  1.330
 14Y  C10  C11   single  1.496  0.020  1.496
 14Y  C11  C12   single  1.529  0.020  1.529
 14Y  C12  C13   single  1.523  0.020  1.523
 14Y  C13  C14   single  1.523  0.020  1.523
 14Y  C14  C15   single  1.524  0.020  1.524
 14Y  C15  C16   single  1.523  0.020  1.523
 14Y  C16  C17   single  1.524  0.020  1.524
 14Y  C17  C18   single  1.522  0.020  1.522
 14Y  CA4  HA41  single  0.970  0.020  1.090
 14Y  CA4  HA42  single  0.970  0.020  1.090
 14Y  CA4  HA43  single  0.970  0.020  1.090
 14Y  C2   H21C  single  0.970  0.020  1.090
 14Y  C2   H22C  single  0.970  0.020  1.090
 14Y  C3   H31C  single  0.970  0.020  1.090
 14Y  C3   H32C  single  0.970  0.020  1.090
 14Y  C4   H41C  single  0.970  0.020  1.090
 14Y  C4   H42C  single  0.970  0.020  1.090
 14Y  C5   H51C  single  0.970  0.020  1.090
 14Y  C5   H52C  single  0.970  0.020  1.090
 14Y  C6   H61C  single  0.970  0.020  1.090
 14Y  C6   H62C  single  0.970  0.020  1.090
 14Y  C7   H71C  single  0.970  0.020  1.090
 14Y  C7   H72C  single  0.970  0.020  1.090
 14Y  C8   H81C  single  0.970  0.020  1.090
 14Y  C8   H82C  single  0.970  0.020  1.090
 14Y  C9   H9    single  0.930  0.020  1.080
 14Y  C10  H10   single  0.930  0.020  1.080
 14Y  C11  H111  single  0.970  0.020  1.090
 14Y  C11  H112  single  0.970  0.020  1.090
 14Y  C12  H121  single  0.970  0.020  1.090
 14Y  C12  H122  single  0.970  0.020  1.090
 14Y  C13  H131  single  0.970  0.020  1.090
 14Y  C13  H132  single  0.970  0.020  1.090
 14Y  C14  H141  single  0.970  0.020  1.090
 14Y  C14  H142  single  0.970  0.020  1.090
 14Y  C15  H151  single  0.970  0.020  1.090
 14Y  C15  H152  single  0.970  0.020  1.090
 14Y  C16  H161  single  0.970  0.020  1.090
 14Y  C16  H162  single  0.970  0.020  1.090
 14Y  C17  H171  single  0.970  0.020  1.090
 14Y  C17  H172  single  0.970  0.020  1.090
 14Y  C18  H181  single  0.970  0.020  1.090
 14Y  C18  H182  single  0.970  0.020  1.090
 14Y  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
 14Y  CA4   O2   C1    117.59  3.000
 14Y  C2    C1   O1    125.37  3.000
 14Y  C2    C1   O2    111.47  3.000
 14Y  O1    C1   O2    123.16  3.000
 14Y  H22C  C2   H21C  105.42  3.000
 14Y  H22C  C2   C3    110.34  3.000
 14Y  H21C  C2   C3    110.61  3.000
 14Y  H22C  C2   C1    107.76  3.000
 14Y  H21C  C2   C1    108.49  3.000
 14Y  C3    C2   C1    113.85  3.000
 14Y  H32C  C3   H31C  106.42  3.000
 14Y  H32C  C3   C4    109.40  3.000
 14Y  H31C  C3   C4    109.40  3.000
 14Y  H32C  C3   C2    109.82  3.000
 14Y  H31C  C3   C2    109.96  3.000
 14Y  C4    C3   C2    111.70  3.000
 14Y  H42C  C4   H41C  105.98  3.000
 14Y  H42C  C4   C5    109.30  3.000
 14Y  H41C  C4   C5    109.39  3.000
 14Y  H42C  C4   C3    109.41  3.000
 14Y  H41C  C4   C3    109.41  3.000
 14Y  C5    C4   C3    113.10  3.000
 14Y  H52C  C5   H51C  106.05  3.000
 14Y  H52C  C5   C6    109.35  3.000
 14Y  H51C  C5   C6    109.47  3.000
 14Y  H52C  C5   C4    109.46  3.000
 14Y  H51C  C5   C4    109.39  3.000
 14Y  C6    C5   C4    112.89  3.000
 14Y  H62C  C6   H61C  105.95  3.000
 14Y  H62C  C6   C7    109.19  3.000
 14Y  H61C  C6   C7    109.38  3.000
 14Y  H62C  C6   C5    109.34  3.000
 14Y  H61C  C6   C5    109.22  3.000
 14Y  C7    C6   C5    113.49  3.000
 14Y  H72C  C7   H71C  106.16  3.000
 14Y  H72C  C7   C8    109.08  3.000
 14Y  H71C  C7   C8    109.58  3.000
 14Y  H72C  C7   C6    109.81  3.000
 14Y  H71C  C7   C6    109.47  3.000
 14Y  C8    C7   C6    112.54  3.000
 14Y  H82C  C8   H81C  106.45  3.000
 14Y  H82C  C8   C9    109.13  3.000
 14Y  H81C  C8   C9    109.91  3.000
 14Y  H82C  C8   C7    108.59  3.000
 14Y  H81C  C8   C7    109.44  3.000
 14Y  C9    C8   C7    113.10  3.000
 14Y  H9    C9   C10   118.79  3.000
 14Y  H9    C9   C8    116.09  3.000
 14Y  C10   C9   C8    125.12  3.000
 14Y  H10   C10  C11   116.00  3.000
 14Y  H10   C10  C9    118.63  3.000
 14Y  C11   C10  C9    125.37  3.000
 14Y  H112  C11  H111  106.41  3.000
 14Y  H112  C11  C12   109.58  3.000
 14Y  H111  C11  C12   108.44  3.000
 14Y  H112  C11  C10   110.04  3.000
 14Y  H111  C11  C10   108.94  3.000
 14Y  C12   C11  C10   113.19  3.000
 14Y  H122  C12  H121  106.19  3.000
 14Y  H122  C12  C13   109.38  3.000
 14Y  H121  C12  C13   109.85  3.000
 14Y  H122  C12  C11   109.50  3.000
 14Y  H121  C12  C11   109.27  3.000
 14Y  C13   C12  C11   112.44  3.000
 14Y  H132  C13  H131  105.97  3.000
 14Y  H132  C13  C14   109.27  3.000
 14Y  H131  C13  C14   109.27  3.000
 14Y  H132  C13  C12   109.40  3.000
 14Y  H131  C13  C12   108.99  3.000
 14Y  C14   C13  C12   113.66  3.000
 14Y  H142  C14  H141  106.04  3.000
 14Y  H142  C14  C15   109.29  3.000
 14Y  H141  C14  C15   109.44  3.000
 14Y  H142  C14  C13   109.45  3.000
 14Y  H141  C14  C13   109.47  3.000
 14Y  C15   C14  C13   112.92  3.000
 14Y  H152  C15  H151  105.94  3.000
 14Y  H152  C15  C16   109.32  3.000
 14Y  H151  C15  C16   109.31  3.000
 14Y  H152  C15  C14   109.29  3.000
 14Y  H151  C15  C14   109.17  3.000
 14Y  C16   C15  C14   113.53  3.000
 14Y  H162  C16  H161  105.97  3.000
 14Y  H162  C16  C17   109.20  3.000
 14Y  H161  C16  C17   109.32  3.000
 14Y  H162  C16  C15   109.46  3.000
 14Y  H161  C16  C15   109.44  3.000
 14Y  C17   C16  C15   113.20  3.000
 14Y  H172  C17  H171  106.01  3.000
 14Y  H172  C17  C18   109.62  3.000
 14Y  H171  C17  C18   109.62  3.000
 14Y  H172  C17  C16   109.24  3.000
 14Y  H171  C17  C16   109.19  3.000
 14Y  C18   C17  C16   112.92  3.000
 14Y  H183  C18  H182  107.56  3.000
 14Y  H183  C18  H181  107.64  3.000
 14Y  H182  C18  H181  107.47  3.000
 14Y  H183  C18  C17   111.66  3.000
 14Y  H182  C18  C17   111.15  3.000
 14Y  H181  C18  C17   111.16  3.000
 14Y  HA43  CA4  HA42  109.22  3.000
 14Y  HA43  CA4  HA41  109.21  3.000
 14Y  HA42  CA4  HA41  109.26  3.000
 14Y  HA43  CA4  O2    111.54  3.000
 14Y  HA42  CA4  O2    105.98  3.000
 14Y  HA41  CA4  O2    111.54  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
 14Y  Var_01  C11   C10  C9   C8    179.68   0.0  2
 14Y  Var_02  C3    C2   C1   O2   -174.25  30.0  3
 14Y  Var_03  C4    C3   C2   C1    179.99  30.0  3
 14Y  Var_04  C5    C4   C3   C2   -179.87  30.0  3
 14Y  Var_05  C6    C5   C4   C3    179.93  30.0  3
 14Y  Var_06  C7    C6   C5   C4    178.75  30.0  3
 14Y  Var_07  C8    C7   C6   C5    178.04  30.0  3
 14Y  Var_08  C9    C8   C7   C6    174.70  30.0  3
 14Y  Var_09  C10   C9   C8   C7    116.08  30.0  3
 14Y  Var_10  C12   C11  C10  C9    117.30  30.0  3
 14Y  Var_11  C13   C12  C11  C10   173.85  30.0  3
 14Y  Var_12  C14   C13  C12  C11   178.74  30.0  3
 14Y  Var_13  C15   C14  C13  C12   177.98  30.0  3
 14Y  Var_14  C16   C15  C14  C13   179.60  30.0  3
 14Y  Var_15  C17   C16  C15  C14   179.01  30.0  3
 14Y  Var_16  C18   C17  C16  C15   179.91  30.0  3
 14Y  Var_17  HA41  CA4  O2   C1     62.19  30.0  3
 14Y  Var_18  H181  C18  C17  C16   -59.87  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
 14Y  plan-1  O2   0.020
 14Y  plan-1  C1   0.020
 14Y  plan-1  O1   0.020
 14Y  plan-1  C2   0.020
 14Y  plan-2  C8   0.020
 14Y  plan-2  C9   0.020
 14Y  plan-2  C10  0.020
 14Y  plan-2  C11  0.020
 14Y  plan-2  H9   0.020
 14Y  plan-2  H10  0.020

