# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 01:43:53 2020
#   Inital geometry file: a 147 line input string
#   Ligand name: (4~{Z},7~{Z},10~{Z},13~{Z},19~{Z})-17-oxidanylidenedocosa-4,7,10,13,19-pentaenoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC\C=C/CC(=O)CC\C=C/C/C=C\C\C=C/C\C=C/CCC(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
 4M5  4M5  '(4~{Z},7~{Z},10~{Z},13~{Z},19~{Z})-17-oxidanylidenedocosa-4,7,10,13,19-pentaenoic acid'  ligand  56  25  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4M5
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
 4M5  O23  O  O      0  -0.402    6.6007  -1.3747  -1.0296
 4M5  C17  C  C      0   0.415    6.5816  -0.8908   0.0785
 4M5  C18  C  CH2    0  -0.642    7.7920  -0.2161   0.6877
 4M5  C19  C  C1     0  -0.201    8.9281  -0.0267  -0.2634
 4M5  C20  C  C1     0  -0.203    9.4716   1.1322  -0.6294
 4M5  C21  C  CH2    0  -0.492    9.0933   2.5115  -0.1885
 4M5  C22  C  CH3    0  -0.660   10.2432   3.2100   0.5352
 4M5  C16  C  CH2    0  -0.557    5.3551  -0.9168   0.9540
 4M5  C15  C  CH2    0  -0.494    4.2163  -1.7911   0.4388
 4M5  C14  C  C1     0  -0.215    3.0748  -1.7928   1.4073
 4M5  C13  C  C1     0  -0.203    1.8382  -1.3417   1.2045
 4M5  C12  C  CH2    0  -0.579    1.2704  -0.7579  -0.0581
 4M5  C11  C  C1     0  -0.209    0.1911  -1.6511  -0.5988
 4M5  C10  C  C1     0  -0.201   -1.1205  -1.4205  -0.6213
 4M5  C9   C  CH2    0  -0.573   -1.8442  -0.1901  -0.1561
 4M5  C8   C  C1     0  -0.207   -2.6251   0.4240  -1.2816
 4M5  C7   C  C1     0  -0.205   -3.9485   0.5393  -1.3790
 4M5  C6   C  CH2    0  -0.574   -4.9821   0.1309  -0.3692
 4M5  C5   C  C1     0  -0.212   -5.6676   1.3432   0.1947
 4M5  C4   C  C1     0  -0.207   -6.9501   1.6821   0.0680
 4M5  C3   C  CH2    0  -0.481   -8.0459   0.9270  -0.6160
 4M5  C2   C  CH2    0  -0.579   -9.1500   0.5456   0.3655
 4M5  C1   C  C      0   0.413  -10.3549  -0.1979  -0.2393
 4M5  O25  O  OC    -1  -0.631  -11.2079  -0.6025   0.5788
 4M5  O24  O  O      0  -0.607  -10.3955  -0.3326  -1.4776
 4M5  H1   H  HCH2   0   0.279    7.4691   0.7197   1.1499
 4M5  H2   H  HCH2   0   0.286    8.1036  -0.8502   1.5279
 4M5  H3   H  H      0   0.240    9.3486  -0.9364  -0.6788
 4M5  H4   H  H      0   0.233   10.3073   1.0909  -1.3234
 4M5  H5   H  HCH2   0   0.236    8.8198   3.0993  -1.0702
 4M5  H6   H  HCH2   0   0.233    8.2116   2.4981   0.4540
 4M5  H7   H  HCH3   0   0.231    9.9686   4.2271   0.8159
 4M5  H8   H  HCH3   0   0.224   10.5167   2.6737   1.4445
 4M5  H9   H  HCH3   0   0.222   11.1316   3.2681  -0.0958
 4M5  H10  H  HCH2   0   0.266    5.6569  -1.2230   1.9614
 4M5  H11  H  HCH2   0   0.279    5.0159   0.1197   1.0657
 4M5  H12  H  HCH2   0   0.244    3.8983  -1.4508  -0.5468
 4M5  H13  H  HCH2   0   0.244    4.5808  -2.8149   0.3125
 4M5  H14  H  H      0   0.236    3.3066  -2.1935   2.3909
 4M5  H15  H  H      0   0.238    1.1318  -1.4138   2.0265
 4M5  H16  H  HCH2   0   0.253    0.8802   0.2401   0.1547
 4M5  H17  H  HCH2   0   0.253    2.0488  -0.6329  -0.8144
 4M5  H18  H  H      0   0.239    0.5402  -2.6073  -0.9779
 4M5  H19  H  H      0   0.239   -1.7605  -2.1969  -1.0315
 4M5  H20  H  HCH2   0   0.252   -2.5066  -0.4555   0.6714
 4M5  H21  H  HCH2   0   0.252   -1.1417   0.5460   0.2415
 4M5  H22  H  H      0   0.238   -2.0248   0.7910  -2.1095
 4M5  H23  H  H      0   0.238   -4.3488   1.0068  -2.2741
 4M5  H24  H  HCH2   0   0.252   -5.7050  -0.5340  -0.8467
 4M5  H25  H  HCH2   0   0.248   -4.5263  -0.4389   0.4441
 4M5  H26  H  H      0   0.232   -5.0161   2.0166   0.7451
 4M5  H27  H  H      0   0.226   -7.2621   2.6116   0.5393
 4M5  H28  H  HCH2   0   0.223   -8.4718   1.5540  -1.4050
 4M5  H29  H  HCH2   0   0.222   -7.6645   0.0329  -1.1114
 4M5  H30  H  HCH2   0   0.223   -8.7304  -0.0661   1.1710
 4M5  H31  H  HCH2   0   0.224   -9.5251   1.4490   0.8612

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
 4M5  C16  C15  single  1.525  0.020  1.525
 4M5  C16  C17  single  1.507  0.020  1.507
 4M5  C15  C14  single  1.497  0.020  1.497
 4M5  O23  C17  double  1.209  0.020  1.209
 4M5  C17  C18  single  1.514  0.020  1.514
 4M5  C14  C13  double  1.332  0.020  1.332
 4M5  C19  C18  single  1.494  0.020  1.494
 4M5  C19  C20  double  1.331  0.020  1.331
 4M5  O24  C1   deloc   1.246  0.020  1.246
 4M5  O25  C1   deloc   1.249  0.020  1.249
 4M5  C1   C2   single  1.540  0.020  1.540
 4M5  C13  C12  single  1.502  0.020  1.502
 4M5  C20  C21  single  1.497  0.020  1.497
 4M5  C12  C11  single  1.502  0.020  1.502
 4M5  C3   C2   single  1.526  0.020  1.526
 4M5  C3   C4   single  1.496  0.020  1.496
 4M5  C9   C8   single  1.501  0.020  1.501
 4M5  C9   C10  single  1.501  0.020  1.501
 4M5  C4   C5   double  1.333  0.020  1.333
 4M5  C11  C10  double  1.332  0.020  1.332
 4M5  C21  C22  single  1.528  0.020  1.528
 4M5  C6   C5   single  1.503  0.020  1.503
 4M5  C6   C7   single  1.502  0.020  1.502
 4M5  C8   C7   double  1.332  0.020  1.332
 4M5  C18  H1   single  0.970  0.020  1.090
 4M5  C18  H2   single  0.970  0.020  1.090
 4M5  C19  H3   single  0.930  0.020  1.080
 4M5  C20  H4   single  0.930  0.020  1.080
 4M5  C21  H5   single  0.970  0.020  1.090
 4M5  C21  H6   single  0.970  0.020  1.090
 4M5  C22  H7   single  0.970  0.020  1.090
 4M5  C22  H8   single  0.970  0.020  1.090
 4M5  C22  H9   single  0.970  0.020  1.090
 4M5  C16  H10  single  0.970  0.020  1.090
 4M5  C16  H11  single  0.970  0.020  1.090
 4M5  C15  H12  single  0.970  0.020  1.090
 4M5  C15  H13  single  0.970  0.020  1.090
 4M5  C14  H14  single  0.930  0.020  1.080
 4M5  C13  H15  single  0.930  0.020  1.080
 4M5  C12  H16  single  0.970  0.020  1.090
 4M5  C12  H17  single  0.970  0.020  1.090
 4M5  C11  H18  single  0.930  0.020  1.080
 4M5  C10  H19  single  0.930  0.020  1.080
 4M5  C9   H20  single  0.970  0.020  1.090
 4M5  C9   H21  single  0.970  0.020  1.090
 4M5  C8   H22  single  0.930  0.020  1.080
 4M5  C7   H23  single  0.930  0.020  1.080
 4M5  C6   H24  single  0.970  0.020  1.090
 4M5  C6   H25  single  0.970  0.020  1.090
 4M5  C5   H26  single  0.930  0.020  1.080
 4M5  C4   H27  single  0.930  0.020  1.080
 4M5  C3   H28  single  0.970  0.020  1.090
 4M5  C3   H29  single  0.970  0.020  1.090
 4M5  C2   H30  single  0.970  0.020  1.090
 4M5  C2   H31  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
 4M5  C16  C17  C18  115.13  3.000
 4M5  C18  C17  O23  122.31  3.000
 4M5  C16  C17  O23  122.57  3.000
 4M5  H2   C18  H1   104.76  3.000
 4M5  H2   C18  C19  110.16  3.000
 4M5  H1   C18  C19  112.68  3.000
 4M5  H2   C18  C17  106.11  3.000
 4M5  H1   C18  C17  108.40  3.000
 4M5  C19  C18  C17  114.11  3.000
 4M5  H3   C19  C20  117.80  3.000
 4M5  H3   C19  C18  115.62  3.000
 4M5  C20  C19  C18  126.58  3.000
 4M5  H4   C20  C21  114.67  3.000
 4M5  H4   C20  C19  117.15  3.000
 4M5  C21  C20  C19  128.17  3.000
 4M5  H6   C21  H5   106.20  3.000
 4M5  H6   C21  C22  109.57  3.000
 4M5  H5   C21  C22  108.91  3.000
 4M5  H6   C21  C20  111.50  3.000
 4M5  H5   C21  C20  108.71  3.000
 4M5  C22  C21  C20  111.76  3.000
 4M5  H9   C22  H8   107.71  3.000
 4M5  H9   C22  H7   107.71  3.000
 4M5  H8   C22  H7   107.89  3.000
 4M5  H9   C22  C21  111.30  3.000
 4M5  H8   C22  C21  111.03  3.000
 4M5  H7   C22  C21  111.03  3.000
 4M5  H11  C16  H10  104.83  3.000
 4M5  H11  C16  C15  110.20  3.000
 4M5  H10  C16  C15  110.87  3.000
 4M5  H11  C16  C17  107.13  3.000
 4M5  H10  C16  C17  108.35  3.000
 4M5  C15  C16  C17  114.91  3.000
 4M5  H13  C15  H12  106.55  3.000
 4M5  H13  C15  C14  109.13  3.000
 4M5  H12  C15  C14  111.28  3.000
 4M5  H13  C15  C16  109.06  3.000
 4M5  H12  C15  C16  110.14  3.000
 4M5  C14  C15  C16  110.58  3.000
 4M5  H14  C14  C13  117.43  3.000
 4M5  H14  C14  C15  115.04  3.000
 4M5  C13  C14  C15  127.52  3.000
 4M5  H15  C13  C12  114.58  3.000
 4M5  H15  C13  C14  117.78  3.000
 4M5  C12  C13  C14  127.62  3.000
 4M5  H17  C12  H16  106.55  3.000
 4M5  H17  C12  C11  109.32  3.000
 4M5  H16  C12  C11  110.90  3.000
 4M5  H17  C12  C13  110.92  3.000
 4M5  H16  C12  C13  109.04  3.000
 4M5  C11  C12  C13  110.06  3.000
 4M5  H18  C11  C10  117.58  3.000
 4M5  H18  C11  C12  114.73  3.000
 4M5  C10  C11  C12  127.65  3.000
 4M5  H19  C10  C9   114.75  3.000
 4M5  H19  C10  C11  117.56  3.000
 4M5  C9   C10  C11  127.69  3.000
 4M5  H21  C9   H20  106.14  3.000
 4M5  H21  C9   C8   109.37  3.000
 4M5  H20  C9   C8   110.60  3.000
 4M5  H21  C9   C10  110.80  3.000
 4M5  H20  C9   C10  109.14  3.000
 4M5  C8   C9   C10  110.71  3.000
 4M5  H22  C8   C7   117.65  3.000
 4M5  H22  C8   C9   114.96  3.000
 4M5  C7   C8   C9   127.37  3.000
 4M5  H23  C7   C6   114.68  3.000
 4M5  H23  C7   C8   117.62  3.000
 4M5  C6   C7   C8   127.68  3.000
 4M5  H25  C6   H24  106.50  3.000
 4M5  H25  C6   C5   109.38  3.000
 4M5  H24  C6   C5   110.69  3.000
 4M5  H25  C6   C7   110.81  3.000
 4M5  H24  C6   C7   109.10  3.000
 4M5  C5   C6   C7   110.30  3.000
 4M5  H26  C5   C4   117.88  3.000
 4M5  H26  C5   C6   114.62  3.000
 4M5  C4   C5   C6   127.49  3.000
 4M5  H27  C4   C3   114.78  3.000
 4M5  H27  C4   C5   116.88  3.000
 4M5  C3   C4   C5   128.32  3.000
 4M5  H29  C3   H28  106.16  3.000
 4M5  H29  C3   C2   109.89  3.000
 4M5  H28  C3   C2   108.99  3.000
 4M5  H29  C3   C4   111.42  3.000
 4M5  H28  C3   C4   109.00  3.000
 4M5  C2   C3   C4   111.23  3.000
 4M5  H31  C2   H30  105.00  3.000
 4M5  H31  C2   C1   107.92  3.000
 4M5  H30  C2   C1   108.60  3.000
 4M5  H31  C2   C3   109.42  3.000
 4M5  H30  C2   C3   109.61  3.000
 4M5  C1   C2   C3   115.74  3.000
 4M5  O24  C1   O25  126.40  3.000
 4M5  O25  C1   C2   115.69  3.000
 4M5  O24  C1   C2   117.90  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
 4M5  Var_01  C21  C20  C19  C18    0.15   0.0  2
 4M5  Var_02  C12  C13  C14  C15    2.02   0.0  2
 4M5  Var_03  C9   C10  C11  C12    2.35   0.0  2
 4M5  Var_04  C6   C7   C8   C9     2.43   0.0  2
 4M5  Var_05  C3   C4   C5   C6     2.60   0.0  2
 4M5  Var_06  C15  C16  C17  O23    9.54  30.0  2
 4M5  Var_07  C19  C18  C17  O23    8.48  30.0  3
 4M5  Var_08  C14  C15  C16  C17  177.57  30.0  3
 4M5  Var_09  C20  C19  C18  C17  119.45  30.0  1
 4M5  Var_10  C22  C21  C20  C19  118.29  30.0  3
 4M5  Var_11  C13  C14  C15  C16  116.95  30.0  3
 4M5  Var_12  C11  C12  C13  C14  114.73  30.0  3
 4M5  Var_13  C10  C11  C12  C13  109.16  30.0  3
 4M5  Var_14  C8   C9   C10  C11  120.84  30.0  2
 4M5  Var_15  C7   C8   C9   C10  114.86  30.0  3
 4M5  Var_16  C5   C6   C7   C8   112.46  30.0  2
 4M5  Var_17  C4   C5   C6   C7   115.31  30.0  3
 4M5  Var_18  C2   C3   C4   C5   118.35  30.0  1
 4M5  Var_19  C1   C2   C3   C4   178.11  30.0  3
 4M5  Var_20  O24  C1   C2   C3    -5.84  30.0  2
 4M5  Var_21  H7   C22  C21  C20  177.74  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
 4M5  plan-1  C9   0.020
 4M5  plan-1  C8   0.020
 4M5  plan-1  C7   0.020
 4M5  plan-1  C6   0.020
 4M5  plan-1  H22  0.020
 4M5  plan-1  H23  0.020
 4M5  plan-2  O23  0.020
 4M5  plan-2  C17  0.020
 4M5  plan-2  C18  0.020
 4M5  plan-2  C16  0.020
 4M5  plan-3  C2   0.020
 4M5  plan-3  C1   0.020
 4M5  plan-3  O25  0.020
 4M5  plan-3  O24  0.020
 4M5  plan-4  C15  0.020
 4M5  plan-4  C14  0.020
 4M5  plan-4  C13  0.020
 4M5  plan-4  C12  0.020
 4M5  plan-4  H14  0.020
 4M5  plan-4  H15  0.020
 4M5  plan-5  C18  0.020
 4M5  plan-5  C19  0.020
 4M5  plan-5  C20  0.020
 4M5  plan-5  C21  0.020
 4M5  plan-5  H3   0.020
 4M5  plan-5  H4   0.020
 4M5  plan-6  C6   0.020
 4M5  plan-6  C5   0.020
 4M5  plan-6  C4   0.020
 4M5  plan-6  C3   0.020
 4M5  plan-6  H26  0.020
 4M5  plan-6  H27  0.020
 4M5  plan-7  C12  0.020
 4M5  plan-7  C11  0.020
 4M5  plan-7  C10  0.020
 4M5  plan-7  C9   0.020
 4M5  plan-7  H18  0.020
 4M5  plan-7  H19  0.020

