# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 13:14:02 2022
#   Inital geometry file: a 140 line input string
#   Ligand name: (5Z,8Z,11Z,13S,14Z)-13-methylicosa-5,8,11,14-tetraenoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCC\C=C/[C@H](C)/C=C\C\C=C/C\C=C/CCCC(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
 LM8  LM8  '(5Z,8Z,11Z,13S,14Z)-13-methylicosa-5,8,11,14-tetraenoic acid'  ligand  56  23  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_LM8
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
 LM8  C01  C  C1     0  -0.207   2.8563   0.6800  -0.1449
 LM8  C02  C  CH2    0  -0.576   2.1201  -0.6273  -0.0718
 LM8  C03  C  C1     0  -0.198   0.8457  -0.4816   0.7089
 LM8  C04  C  C1     0  -0.208  -0.4004  -0.5687   0.2476
 LM8  C05  C  CH2    0  -0.586  -0.8305  -0.8718  -1.1595
 LM8  C06  C  C1     0  -0.209  -1.3336  -2.2846  -1.2469
 LM8  C07  C  C1     0  -0.174  -2.6004  -2.6884  -1.3146
 LM8  C08  C  CH1    0  -0.388  -3.8330  -1.8278  -1.3490
 LM8  C09  C  C1     0  -0.175  -4.5665  -1.9735  -0.0441
 LM8  C10  C  C1     0  -0.218  -4.8126  -1.0224   0.8552
 LM8  C11  C  C1     0  -0.209   4.0154   0.9873   0.4355
 LM8  C12  C  CH2    0  -0.488   4.8825   0.1020   1.2730
 LM8  C13  C  CH2    0  -0.402   6.2073  -0.2381   0.5837
 LM8  C14  C  CH2    0  -0.490  -4.4415   0.4258   0.7785
 LM8  C15  C  CH2    0  -0.409  -5.6561   1.3157   0.5057
 LM8  C16  C  CH2    0  -0.407  -5.3194   2.8009   0.5167
 LM8  C17  C  CH2    0  -0.418  -6.5219   3.6905   0.2251
 LM8  C18  C  CH3    0  -0.662  -6.1828   5.1743   0.2592
 LM8  C19  C  CH2    0  -0.582   7.1098  -1.0827   1.4665
 LM8  C20  C  C      0   0.410   8.4673  -1.4847   0.8640
 LM8  O21  O  OC    -1  -0.635   9.1912  -2.2046   1.5853
 LM8  O22  O  O      0  -0.609   8.7462  -1.0712  -0.2783
 LM8  C23  C  CH3    0  -0.643  -4.7390  -2.2341  -2.5153
 LM8  H1   H  H      0   0.233   2.3586   1.4495  -0.7283
 LM8  H2   H  HCH2   0   0.249   1.9161  -0.9796  -1.0860
 LM8  H3   H  HCH2   0   0.252   2.7391  -1.3925   0.4022
 LM8  H4   H  H      0   0.238   0.9805  -0.2685   1.7656
 LM8  H5   H  H      0   0.238  -1.2141  -0.4499   0.9579
 LM8  H6   H  HCH2   0   0.252  -1.6055  -0.1622  -1.4569
 LM8  H7   H  HCH2   0   0.254  -0.0029  -0.7378  -1.8585
 LM8  H8   H  H      0   0.237  -0.5604  -3.0462  -1.2046
 LM8  H9   H  H      0   0.233  -2.7881  -3.7600  -1.3317
 LM8  H10  H  HCH1   0   0.243  -3.5499  -0.7842  -1.4941
 LM8  H11  H  H      0   0.231  -4.9247  -2.9787   0.1678
 LM8  H12  H  H      0   0.230  -5.3709  -1.3087   1.7430
 LM8  H13  H  H      0   0.229   4.4031   1.9900   0.2722
 LM8  H14  H  HCH2   0   0.225   5.0994   0.6114   2.2187
 LM8  H15  H  HCH2   0   0.225   4.3659  -0.8227   1.5412
 LM8  H16  H  HCH2   0   0.209   5.9951  -0.7628  -0.3516
 LM8  H17  H  HCH2   0   0.208   6.7176   0.6870   0.3017
 LM8  H18  H  HCH2   0   0.229  -3.9901   0.7271   1.7297
 LM8  H19  H  HCH2   0   0.224  -3.6852   0.6040   0.0105
 LM8  H20  H  HCH2   0   0.215  -6.0846   1.0411  -0.4633
 LM8  H21  H  HCH2   0   0.214  -6.4312   1.1126   1.2522
 LM8  H22  H  HCH2   0   0.208  -4.8988   3.0689   1.4923
 LM8  H23  H  HCH2   0   0.208  -4.5329   3.0021  -0.2191
 LM8  H24  H  HCH2   0   0.211  -6.9343   3.4317  -0.7550
 LM8  H25  H  HCH2   0   0.210  -7.3121   3.4790   0.9521
 LM8  H26  H  HCH3   0   0.216  -5.4087   5.4196  -0.4706
 LM8  H27  H  HCH3   0   0.226  -7.0544   5.7902   0.0346
 LM8  H28  H  HCH3   0   0.216  -5.8127   5.4711   1.2422
 LM8  H29  H  HCH2   0   0.219   7.2990  -0.5532   2.4082
 LM8  H30  H  HCH2   0   0.218   6.5833  -1.9979   1.7623
 LM8  H32  H  HCH3   0   0.232  -5.6215  -1.5949  -2.5594
 LM8  H33  H  HCH3   0   0.232  -4.2118  -2.1506  -3.4667
 LM8  H34  H  HCH3   0   0.220  -5.0780  -3.2669  -2.4110

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
 LM8  O22  C20  deloc   1.246  0.020  1.246
 LM8  C13  C19  single  1.519  0.020  1.519
 LM8  C13  C12  single  1.532  0.020  1.532
 LM8  C19  C20  single  1.539  0.020  1.539
 LM8  C11  C12  single  1.496  0.020  1.496
 LM8  C11  C01  double  1.332  0.020  1.332
 LM8  C20  O21  deloc   1.250  0.020  1.250
 LM8  C01  C02  single  1.502  0.020  1.502
 LM8  C03  C04  double  1.332  0.020  1.332
 LM8  C03  C02  single  1.502  0.020  1.502
 LM8  C04  C05  single  1.502  0.020  1.502
 LM8  C05  C06  single  1.502  0.020  1.502
 LM8  C06  C07  double  1.331  0.020  1.331
 LM8  C07  C08  single  1.504  0.020  1.504
 LM8  C08  C23  single  1.532  0.020  1.532
 LM8  C08  C09  single  1.504  0.020  1.504
 LM8  C14  C15  single  1.530  0.020  1.530
 LM8  C14  C10  single  1.497  0.020  1.497
 LM8  C16  C17  single  1.524  0.020  1.524
 LM8  C16  C15  single  1.523  0.020  1.523
 LM8  C17  C18  single  1.522  0.020  1.522
 LM8  C09  C10  double  1.332  0.020  1.332
 LM8  C01  H1   single  0.930  0.020  1.080
 LM8  C02  H2   single  0.970  0.020  1.090
 LM8  C02  H3   single  0.970  0.020  1.090
 LM8  C03  H4   single  0.930  0.020  1.080
 LM8  C04  H5   single  0.930  0.020  1.080
 LM8  C05  H6   single  0.970  0.020  1.090
 LM8  C05  H7   single  0.970  0.020  1.090
 LM8  C06  H8   single  0.930  0.020  1.080
 LM8  C07  H9   single  0.930  0.020  1.080
 LM8  C08  H10  single  0.970  0.020  1.090
 LM8  C09  H11  single  0.930  0.020  1.080
 LM8  C10  H12  single  0.930  0.020  1.080
 LM8  C11  H13  single  0.930  0.020  1.080
 LM8  C12  H14  single  0.970  0.020  1.090
 LM8  C12  H15  single  0.970  0.020  1.090
 LM8  C13  H16  single  0.970  0.020  1.090
 LM8  C13  H17  single  0.970  0.020  1.090
 LM8  C14  H18  single  0.970  0.020  1.090
 LM8  C14  H19  single  0.970  0.020  1.090
 LM8  C15  H20  single  0.970  0.020  1.090
 LM8  C15  H21  single  0.970  0.020  1.090
 LM8  C16  H22  single  0.970  0.020  1.090
 LM8  C16  H23  single  0.970  0.020  1.090
 LM8  C17  H24  single  0.970  0.020  1.090
 LM8  C17  H25  single  0.970  0.020  1.090
 LM8  C18  H26  single  0.970  0.020  1.090
 LM8  C18  H27  single  0.970  0.020  1.090
 LM8  C18  H28  single  0.970  0.020  1.090
 LM8  C19  H29  single  0.970  0.020  1.090
 LM8  C19  H30  single  0.970  0.020  1.090
 LM8  C23  H32  single  0.970  0.020  1.090
 LM8  C23  H33  single  0.970  0.020  1.090
 LM8  C23  H34  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
 LM8  H1   C01  C11  117.98  3.000
 LM8  H1   C01  C02  114.71  3.000
 LM8  C11  C01  C02  127.30  3.000
 LM8  H3   C02  H2   106.42  3.000
 LM8  H3   C02  C03  108.86  3.000
 LM8  H2   C02  C03  110.82  3.000
 LM8  H3   C02  C01  110.67  3.000
 LM8  H2   C02  C01  109.08  3.000
 LM8  C03  C02  C01  110.90  3.000
 LM8  H4   C03  C04  117.77  3.000
 LM8  H4   C03  C02  114.80  3.000
 LM8  C04  C03  C02  127.42  3.000
 LM8  H5   C04  C05  114.83  3.000
 LM8  H5   C04  C03  117.85  3.000
 LM8  C05  C04  C03  127.27  3.000
 LM8  H7   C05  H6   106.50  3.000
 LM8  H7   C05  C06  109.40  3.000
 LM8  H6   C05  C06  110.95  3.000
 LM8  H7   C05  C04  110.98  3.000
 LM8  H6   C05  C04  109.09  3.000
 LM8  C06  C05  C04  109.88  3.000
 LM8  H8   C06  C07  117.83  3.000
 LM8  H8   C06  C05  114.75  3.000
 LM8  C07  C06  C05  127.36  3.000
 LM8  H9   C07  C08  114.96  3.000
 LM8  H9   C07  C06  117.62  3.000
 LM8  C08  C07  C06  127.42  3.000
 LM8  H10  C08  C23  107.81  3.000
 LM8  H10  C08  C09  109.55  3.000
 LM8  C23  C08  C09  110.27  3.000
 LM8  H10  C08  C07  109.74  3.000
 LM8  C09  C08  C07  108.94  3.000
 LM8  C23  C08  C07  110.51  3.000
 LM8  H11  C09  C10  117.87  3.000
 LM8  H11  C09  C08  114.77  3.000
 LM8  C10  C09  C08  127.36  3.000
 LM8  H12  C10  C14  115.08  3.000
 LM8  H12  C10  C09  117.28  3.000
 LM8  C14  C10  C09  127.62  3.000
 LM8  H13  C11  C12  115.04  3.000
 LM8  H13  C11  C01  117.23  3.000
 LM8  C12  C11  C01  127.72  3.000
 LM8  H15  C12  H14  105.97  3.000
 LM8  H15  C12  C13  109.36  3.000
 LM8  H14  C12  C13  108.69  3.000
 LM8  H15  C12  C11  111.36  3.000
 LM8  H14  C12  C11  108.83  3.000
 LM8  C13  C12  C11  112.39  3.000
 LM8  H17  C13  H16  106.02  3.000
 LM8  H17  C13  C19  110.06  3.000
 LM8  H16  C13  C19  110.22  3.000
 LM8  H17  C13  C12  109.38  3.000
 LM8  H16  C13  C12  108.89  3.000
 LM8  C19  C13  C12  112.08  3.000
 LM8  H19  C14  H18  106.28  3.000
 LM8  H19  C14  C15  109.22  3.000
 LM8  H18  C14  C15  108.79  3.000
 LM8  H19  C14  C10  111.43  3.000
 LM8  H18  C14  C10  108.90  3.000
 LM8  C15  C14  C10  112.02  3.000
 LM8  H21  C15  H20  106.25  3.000
 LM8  H21  C15  C16  109.42  3.000
 LM8  H20  C15  C16  109.73  3.000
 LM8  H21  C15  C14  109.41  3.000
 LM8  H20  C15  C14  108.82  3.000
 LM8  C16  C15  C14  112.98  3.000
 LM8  H23  C16  H22  106.12  3.000
 LM8  H23  C16  C17  109.32  3.000
 LM8  H22  C16  C17  109.30  3.000
 LM8  H23  C16  C15  109.44  3.000
 LM8  H22  C16  C15  109.26  3.000
 LM8  C17  C16  C15  113.17  3.000
 LM8  H25  C17  H24  106.10  3.000
 LM8  H25  C17  C18  109.53  3.000
 LM8  H24  C17  C18  109.54  3.000
 LM8  H25  C17  C16  109.25  3.000
 LM8  H24  C17  C16  109.31  3.000
 LM8  C18  C17  C16  112.88  3.000
 LM8  H28  C18  H27  107.63  3.000
 LM8  H28  C18  H26  107.49  3.000
 LM8  H27  C18  H26  107.58  3.000
 LM8  H28  C18  C17  111.15  3.000
 LM8  H27  C18  C17  111.57  3.000
 LM8  H26  C18  C17  111.22  3.000
 LM8  H30  C19  H29  104.72  3.000
 LM8  H30  C19  C20  108.13  3.000
 LM8  H29  C19  C20  108.06  3.000
 LM8  H30  C19  C13  109.61  3.000
 LM8  H29  C19  C13  109.45  3.000
 LM8  C20  C19  C13  116.23  3.000
 LM8  O22  C20  O21  126.18  3.000
 LM8  O21  C20  C19  115.81  3.000
 LM8  O22  C20  C19  118.00  3.000
 LM8  H34  C23  H33  107.80  3.000
 LM8  H34  C23  H32  107.87  3.000
 LM8  H33  C23  H32  108.12  3.000
 LM8  H34  C23  C08  111.21  3.000
 LM8  H33  C23  C08  110.97  3.000
 LM8  H32  C23  C08  110.73  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
 LM8  Var_01  C12  C11  C01  C02    1.55   0.0  2
 LM8  Var_02  C05  C04  C03  C02    1.83   0.0  2
 LM8  Var_03  C08  C07  C06  C05    1.38   0.0  2
 LM8  Var_04  C14  C10  C09  C08    1.14   0.0  2
 LM8  Var_05  C13  C12  C11  C01  111.85  30.0  3
 LM8  Var_06  C04  C03  C02  C01  112.34  30.0  1
 LM8  Var_07  C06  C05  C04  C03  104.65  30.0  3
 LM8  Var_08  C11  C01  C02  C03  111.58  30.0  2
 LM8  Var_09  C07  C06  C05  C04  103.53  30.0  3
 LM8  Var_10  C15  C14  C10  C09  106.83  30.0  2
 LM8  Var_11  C16  C15  C14  C10  176.12  30.0  3
 LM8  Var_12  C19  C13  C12  C11  177.29  30.0  2
 LM8  Var_13  C20  C19  C13  C12  179.78  30.0  3
 LM8  Var_14  O22  C20  C19  C13    1.64  30.0  3
 LM8  Var_15  C17  C16  C15  C14  179.15  30.0  2
 LM8  Var_16  C18  C17  C16  C15  179.10  30.0  3
 LM8  Var_17  H26  C18  C17  C16   59.09  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
 LM8  chir_01  C08  C07  C23  C09  negativ

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
 LM8  plan-1  C19  0.020
 LM8  plan-1  C20  0.020
 LM8  plan-1  O21  0.020
 LM8  plan-1  O22  0.020
 LM8  plan-2  C01  0.020
 LM8  plan-2  C02  0.020
 LM8  plan-2  C11  0.020
 LM8  plan-2  C12  0.020
 LM8  plan-2  H1   0.020
 LM8  plan-2  H13  0.020
 LM8  plan-3  C02  0.020
 LM8  plan-3  C03  0.020
 LM8  plan-3  C04  0.020
 LM8  plan-3  C05  0.020
 LM8  plan-3  H4   0.020
 LM8  plan-3  H5   0.020
 LM8  plan-4  C05  0.020
 LM8  plan-4  C06  0.020
 LM8  plan-4  C07  0.020
 LM8  plan-4  C08  0.020
 LM8  plan-4  H8   0.020
 LM8  plan-4  H9   0.020
 LM8  plan-5  C08  0.020
 LM8  plan-5  C09  0.020
 LM8  plan-5  C10  0.020
 LM8  plan-5  C14  0.020
 LM8  plan-5  H11  0.020
 LM8  plan-5  H12  0.020

