# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 05:02:29 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: 10-{(1R,2R)-2-[(2E)-hex-2-en-1-yl]cyclopropyl}decanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC/C=C/C[C@H]1C[C@H]1CCCCCCCCCC(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
 OMA  OMA  '10-{(1R,2R)-2-[(2E)-hex-2-en-1-yl]cyclopropyl}decanoic acid'  ligand  54  21  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_OMA
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
 OMA  O1   O  OC    -1  -0.618  -10.4184  -0.7083  -1.1056
 OMA  C18  C  C      0   0.374   -9.5115  -0.0003  -0.6166
 OMA  O    O  O      0  -0.643   -9.6721   1.0218   0.0793
 OMA  C17  C  CH2    0  -0.604   -8.0722  -0.4422  -0.9311
 OMA  C16  C  CH2    0  -0.416   -6.9621   0.3097  -0.2161
 OMA  C15  C  CH2    0  -0.407   -5.5760  -0.2092  -0.5799
 OMA  C14  C  CH2    0  -0.410   -4.4411   0.5558   0.0893
 OMA  C13  C  CH2    0  -0.408   -3.0723  -0.0660  -0.1602
 OMA  C12  C  CH2    0  -0.409   -1.9172   0.7589   0.3949
 OMA  C11  C  CH2    0  -0.409   -0.5748   0.0437   0.3020
 OMA  C10  C  CH2    0  -0.406    0.6077   0.9122   0.7134
 OMA  C9   C  CH2    0  -0.423    1.9252   0.1439   0.7418
 OMA  C8   C  CH1    0  -0.227    3.0983   1.0295   1.0798
 OMA  C7   C  CH2    0  -0.468    3.8718   1.7261  -0.0024
 OMA  C6   C  CH1    0  -0.218    4.5226   0.6421   0.8078
 OMA  C5   C  CH2    0  -0.494    4.9081  -0.6774   0.1759
 OMA  C4   C  C1     0  -0.165    6.2521  -0.5949  -0.4792
 OMA  C3   C  C1     0  -0.184    7.3177  -1.3105  -0.1314
 OMA  C2   C  CH2    0  -0.461    8.6725  -1.2037  -0.7564
 OMA  C1   C  CH2    0  -0.410    9.7399  -0.7441   0.2378
 OMA  C    C  CH3    0  -0.641   11.1300  -0.6862  -0.3794
 OMA  H2   H  HCH2   0   0.245   -7.9856  -1.5145  -0.7223
 OMA  H3   H  HCH2   0   0.229   -7.9279  -0.3570  -2.0156
 OMA  H4   H  HCH2   0   0.212   -7.0262   1.3761  -0.4505
 OMA  H5   H  HCH2   0   0.209   -7.0976   0.2335   0.8674
 OMA  H6   H  HCH2   0   0.201   -5.5047  -1.2694  -0.3108
 OMA  H7   H  HCH2   0   0.204   -5.4454  -0.1698  -1.6675
 OMA  H8   H  HCH2   0   0.204   -4.4444   1.5933  -0.2627
 OMA  H9   H  HCH2   0   0.206   -4.6191   0.6049   1.1696
 OMA  H10  H  HCH2   0   0.206   -3.0507  -1.0684   0.2816
 OMA  H11  H  HCH2   0   0.205   -2.9257  -0.2084  -1.2366
 OMA  H12  H  HCH2   0   0.205   -1.8643   1.7106  -0.1451
 OMA  H13  H  HCH2   0   0.206   -2.1182   1.0151   1.4411
 OMA  H14  H  HCH2   0   0.205   -0.6033  -0.8533   0.9307
 OMA  H15  H  HCH2   0   0.203   -0.4189  -0.3100  -0.7232
 OMA  H16  H  HCH2   0   0.212    0.6946   1.7571   0.0220
 OMA  H17  H  HCH2   0   0.205    0.4182   1.3447   1.7020
 OMA  H18  H  HCH2   0   0.214    1.8527  -0.6696   1.4720
 OMA  H19  H  HCH2   0   0.203    2.0773  -0.3327  -0.2311
 OMA  H20  H  HCH1   0   0.229    2.9560   1.6062   1.9900
 OMA  H21  H  HCH2   0   0.219    3.6077   1.4892  -1.0283
 OMA  H22  H  HCH2   0   0.237    4.1842   2.7522   0.1473
 OMA  H23  H  HCH1   0   0.238    5.2380   0.9849   1.5499
 OMA  H24  H  HCH2   0   0.225    4.9083  -1.4678   0.9325
 OMA  H25  H  HCH2   0   0.216    4.1613  -0.9615  -0.5717
 OMA  H26  H  H      0   0.207    6.3427   0.1279  -1.2882
 OMA  H27  H  H      0   0.204    7.2242  -2.0246   0.6854
 OMA  H28  H  HCH2   0   0.215    8.9690  -2.1792  -1.1587
 OMA  H29  H  HCH2   0   0.214    8.6396  -0.5139  -1.6054
 OMA  H30  H  HCH2   0   0.216    9.4649   0.2400   0.6272
 OMA  H31  H  HCH2   0   0.208    9.7489  -1.4209   1.0977
 OMA  H32  H  HCH3   0   0.211   11.4426  -1.6676  -0.7409
 OMA  H33  H  HCH3   0   0.210   11.1589   0.0010  -1.2270
 OMA  H34  H  HCH3   0   0.223   11.8724  -0.3492   0.3450

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
 OMA  O    C18  deloc   1.247  0.020  1.247
 OMA  C18  O1   deloc   1.250  0.020  1.250
 OMA  C18  C17  single  1.538  0.020  1.538
 OMA  C16  C15  single  1.524  0.020  1.524
 OMA  C16  C17  single  1.520  0.020  1.520
 OMA  C15  C14  single  1.524  0.020  1.524
 OMA  C8   C6   single  1.501  0.020  1.501
 OMA  C8   C7   single  1.502  0.020  1.502
 OMA  C8   C9   single  1.508  0.020  1.508
 OMA  C6   C7   single  1.502  0.020  1.502
 OMA  C6   C5   single  1.513  0.020  1.513
 OMA  C12  C13  single  1.524  0.020  1.524
 OMA  C12  C11  single  1.524  0.020  1.524
 OMA  C14  C13  single  1.524  0.020  1.524
 OMA  C10  C9   single  1.525  0.020  1.525
 OMA  C10  C11  single  1.524  0.020  1.524
 OMA  C5   C4   single  1.497  0.020  1.497
 OMA  C4   C3   double  1.330  0.020  1.330
 OMA  C3   C2   single  1.496  0.020  1.496
 OMA  C2   C1   single  1.529  0.020  1.529
 OMA  C1   C    single  1.522  0.020  1.522
 OMA  C17  H2   single  0.970  0.020  1.090
 OMA  C17  H3   single  0.970  0.020  1.090
 OMA  C16  H4   single  0.970  0.020  1.090
 OMA  C16  H5   single  0.970  0.020  1.090
 OMA  C15  H6   single  0.970  0.020  1.090
 OMA  C15  H7   single  0.970  0.020  1.090
 OMA  C14  H8   single  0.970  0.020  1.090
 OMA  C14  H9   single  0.970  0.020  1.090
 OMA  C13  H10  single  0.970  0.020  1.090
 OMA  C13  H11  single  0.970  0.020  1.090
 OMA  C12  H12  single  0.970  0.020  1.090
 OMA  C12  H13  single  0.970  0.020  1.090
 OMA  C11  H14  single  0.970  0.020  1.090
 OMA  C11  H15  single  0.970  0.020  1.090
 OMA  C10  H16  single  0.970  0.020  1.090
 OMA  C10  H17  single  0.970  0.020  1.090
 OMA  C9   H18  single  0.970  0.020  1.090
 OMA  C9   H19  single  0.970  0.020  1.090
 OMA  C8   H20  single  0.970  0.020  1.090
 OMA  C7   H21  single  0.970  0.020  1.090
 OMA  C7   H22  single  0.970  0.020  1.090
 OMA  C6   H23  single  0.970  0.020  1.090
 OMA  C5   H24  single  0.970  0.020  1.090
 OMA  C5   H25  single  0.970  0.020  1.090
 OMA  C4   H26  single  0.930  0.020  1.080
 OMA  C3   H27  single  0.930  0.020  1.080
 OMA  C2   H28  single  0.970  0.020  1.090
 OMA  C2   H29  single  0.970  0.020  1.090
 OMA  C1   H30  single  0.970  0.020  1.090
 OMA  C1   H31  single  0.970  0.020  1.090
 OMA  C    H32  single  0.970  0.020  1.090
 OMA  C    H33  single  0.970  0.020  1.090
 OMA  C    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
 OMA  C17  C18  O    118.04  3.000
 OMA  C17  C18  O1   115.86  3.000
 OMA  O    C18  O1   126.10  3.000
 OMA  H3   C17  H2   104.71  3.000
 OMA  H3   C17  C16  109.31  3.000
 OMA  H2   C17  C16  109.68  3.000
 OMA  H3   C17  C18  107.62  3.000
 OMA  H2   C17  C18  108.43  3.000
 OMA  C16  C17  C18  116.44  3.000
 OMA  H5   C16  H4   105.83  3.000
 OMA  H5   C16  C15  108.97  3.000
 OMA  H4   C16  C15  109.51  3.000
 OMA  H5   C16  C17  109.94  3.000
 OMA  H4   C16  C17  109.81  3.000
 OMA  C15  C16  C17  112.55  3.000
 OMA  H7   C15  H6   105.70  3.000
 OMA  H7   C15  C14  109.21  3.000
 OMA  H6   C15  C14  109.23  3.000
 OMA  H7   C15  C16  109.45  3.000
 OMA  H6   C15  C16  109.26  3.000
 OMA  C14  C15  C16  113.68  3.000
 OMA  H9   C14  H8   105.89  3.000
 OMA  H9   C14  C13  109.00  3.000
 OMA  H8   C14  C13  109.66  3.000
 OMA  H9   C14  C15  109.54  3.000
 OMA  H8   C14  C15  109.40  3.000
 OMA  C13  C14  C15  113.10  3.000
 OMA  H11  C13  H10  105.94  3.000
 OMA  H11  C13  C12  109.07  3.000
 OMA  H10  C13  C12  109.48  3.000
 OMA  H11  C13  C14  109.52  3.000
 OMA  H10  C13  C14  108.97  3.000
 OMA  C12  C13  C14  113.60  3.000
 OMA  H13  C12  H12  106.04  3.000
 OMA  H13  C12  C11  109.24  3.000
 OMA  H12  C12  C11  109.58  3.000
 OMA  H13  C12  C13  109.59  3.000
 OMA  H12  C12  C13  109.10  3.000
 OMA  C11  C12  C13  113.04  3.000
 OMA  H15  C11  H14  106.04  3.000
 OMA  H15  C11  C10  109.04  3.000
 OMA  H14  C11  C10  109.38  3.000
 OMA  H15  C11  C12  109.51  3.000
 OMA  H14  C11  C12  109.05  3.000
 OMA  C10  C11  C12  113.56  3.000
 OMA  H17  C10  H16  106.19  3.000
 OMA  H17  C10  C9   109.35  3.000
 OMA  H16  C10  C9   109.38  3.000
 OMA  H17  C10  C11  109.54  3.000
 OMA  H16  C10  C11  109.32  3.000
 OMA  C9   C10  C11  112.84  3.000
 OMA  H19  C9   H18  106.17  3.000
 OMA  H19  C9   C8   110.30  3.000
 OMA  H18  C9   C8   109.77  3.000
 OMA  H19  C9   C10  108.84  3.000
 OMA  H18  C9   C10  109.22  3.000
 OMA  C8   C9   C10  112.35  3.000
 OMA  H20  C8   C6   114.39  3.000
 OMA  H20  C8   C7   115.14  3.000
 OMA  C6   C8   C7    60.02  3.000
 OMA  H20  C8   C9   113.42  3.000
 OMA  C7   C8   C9   120.77  3.000
 OMA  C6   C8   C9   123.09  3.000
 OMA  H22  C7   H21  114.05  3.000
 OMA  H22  C7   C6   118.97  3.000
 OMA  H21  C7   C6   117.25  3.000
 OMA  H22  C7   C8   119.24  3.000
 OMA  H21  C7   C8   117.04  3.000
 OMA  C6   C7   C8    59.97  3.000
 OMA  H23  C6   C5   113.13  3.000
 OMA  H23  C6   C7   115.22  3.000
 OMA  C5   C6   C7   120.97  3.000
 OMA  H23  C6   C8   114.82  3.000
 OMA  C5   C6   C8   122.86  3.000
 OMA  C7   C6   C8    60.01  3.000
 OMA  H25  C5   H24  106.56  3.000
 OMA  H25  C5   C4   109.15  3.000
 OMA  H24  C5   C4   110.01  3.000
 OMA  H25  C5   C6   109.75  3.000
 OMA  H24  C5   C6   109.95  3.000
 OMA  C4   C5   C6   111.31  3.000
 OMA  H26  C4   C3   119.01  3.000
 OMA  H26  C4   C5   115.87  3.000
 OMA  C3   C4   C5   125.11  3.000
 OMA  H27  C3   C2   115.97  3.000
 OMA  H27  C3   C4   118.70  3.000
 OMA  C2   C3   C4   125.31  3.000
 OMA  H29  C2   H28  106.51  3.000
 OMA  H29  C2   C1   109.62  3.000
 OMA  H28  C2   C1   108.50  3.000
 OMA  H29  C2   C3   110.00  3.000
 OMA  H28  C2   C3   109.56  3.000
 OMA  C1   C2   C3   112.46  3.000
 OMA  H31  C1   H30  106.19  3.000
 OMA  H31  C1   C    109.55  3.000
 OMA  H30  C1   C    109.87  3.000
 OMA  H31  C1   C2   109.31  3.000
 OMA  H30  C1   C2   109.05  3.000
 OMA  C    C1   C2   112.66  3.000
 OMA  H34  C    H33  107.65  3.000
 OMA  H34  C    H32  107.63  3.000
 OMA  H33  C    H32  107.54  3.000
 OMA  H34  C    C1   111.35  3.000
 OMA  H33  C    C1   111.28  3.000
 OMA  H32  C    C1   111.20  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
 OMA  Var_01  C7   C6   C8   C9    109.21  30.0  1
 OMA  Var_02  C5   C6   C7   C8    112.60  30.0  1
 OMA  Var_03  C6   C8   C9   C10  -162.41  30.0  2
 OMA  Var_04  C4   C5   C6   C8    156.86  30.0  3
 OMA  Var_05  C8   C9   C10  C11   177.00  30.0  3
 OMA  Var_06  C3   C4   C5   C6    117.78  30.0  3
 OMA  Var_07  C2   C3   C4   C5   -178.13   0.0  2
 OMA  Var_08  C16  C17  C18  O1   -173.19  30.0  3
 OMA  Var_09  C15  C16  C17  C18   179.36  30.0  2
 OMA  Var_10  C14  C15  C16  C17   178.18  30.0  3
 OMA  Var_11  C13  C14  C15  C16   173.69  30.0  3
 OMA  Var_12  C12  C13  C14  C15   174.68  30.0  3
 OMA  Var_13  C11  C12  C13  C14   172.48  30.0  1
 OMA  Var_14  C10  C11  C12  C13   173.77  30.0  3
 OMA  Var_15  C9   C10  C11  C12   174.54  30.0  1
 OMA  Var_16  C1   C2   C3   C4    117.37  30.0  3
 OMA  Var_17  C    C1   C2   C3    177.76  30.0  3
 OMA  Var_18  H32  C    C1   C2    -60.40  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
 OMA  chir_01  C8  C6  C7  C9  both
 OMA  chir_02  C6  C8  C7  C5  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
 OMA  plan-1  O1   0.020
 OMA  plan-1  C18  0.020
 OMA  plan-1  O    0.020
 OMA  plan-1  C17  0.020
 OMA  plan-2  C5   0.020
 OMA  plan-2  C4   0.020
 OMA  plan-2  C3   0.020
 OMA  plan-2  C2   0.020
 OMA  plan-2  H26  0.020
 OMA  plan-2  H27  0.020

