# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 19:25:32 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: (5R,6E,8Z,11Z,14Z,17Z)-5-hydroxyicosa-6,8,11,14,17-pentaenoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC\C=C/C/C=C\C\C=C/C/C=C\C=C\[C@H](O)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
 5HE  5HE  '(5R,6E,8Z,11Z,14Z,17Z)-5-hydroxyicosa-6,8,11,14,17-pentaenoic acid'  ligand  53  23  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5HE
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
 5HE  C1    C  CH3   0  -0.658  -11.0179  -0.9754   0.5872
 5HE  C2    C  CH2   0  -0.489   -9.6451  -1.6405   0.6729
 5HE  C3    C  C1    0  -0.208   -8.9510  -1.6575  -0.6528
 5HE  C4    C  C1    0  -0.208   -7.7852  -1.0985  -0.9736
 5HE  C5    C  CH2   0  -0.579   -6.8536  -0.3451  -0.0675
 5HE  C6    C  C1    0  -0.201   -5.6230  -1.1604   0.2101
 5HE  C7    C  C1    0  -0.206   -4.3766  -0.9042  -0.1826
 5HE  C8    C  CH2   0  -0.583   -3.8899   0.2860  -0.9601
 5HE  C9    C  C1    0  -0.205   -3.0936   1.1904  -0.0634
 5HE  C10   C  C1    0  -0.200   -1.7718   1.3494  -0.0404
 5HE  C11   C  CH2   0  -0.582   -0.7584   0.6946  -0.9359
 5HE  C13   C  C1    0  -0.208   -0.0094   1.7286  -1.7239
 5HE  C14   C  C1    0  -0.250    1.2652   2.1022  -1.5568
 5HE  C16   C  C1    0  -0.260    2.1970   1.5598  -0.5819
 5HE  C17   C  C1    0  -0.234    3.4671   1.9574  -0.4694
 5HE  C18   C  CH1   0  -0.023    4.4467   1.3775   0.5069
 5HE  C19   C  CH2   0  -0.456    5.5467   0.6149  -0.2300
 5HE  C20   C  CH2   0  -0.419    6.5346  -0.0844   0.6947
 5HE  C21   C  CH2   0  -0.581    7.5650  -0.8692  -0.1013
 5HE  C22   C  C     0   0.550    8.5545  -1.6126   0.7520
 5HE  O23   O  OH1   0  -0.598    9.4004  -2.3299   0.0170
 5HE  O24   O  O     0  -0.446    8.5990  -1.5801   1.9567
 5HE  O3    O  OH1   0  -0.666    4.9691   2.3753   1.3667
 5HE  H1C1  H  HCH3  0   0.223  -10.9290   0.0705   0.2912
 5HE  H1C2  H  HCH3  0   0.221  -11.6542  -1.4741  -0.1458
 5HE  H1C3  H  HCH3  0   0.230  -11.5311  -1.0091   1.5488
 5HE  H2C1  H  HCH2  0   0.232   -9.0411  -1.1382   1.4303
 5HE  H2C2  H  HCH2  0   0.233   -9.7736  -2.6714   1.0177
 5HE  H3    H  H     0   0.231   -9.4854  -2.1818  -1.4415
 5HE  H4    H  H     0   0.236   -7.4315  -1.2131  -1.9944
 5HE  H5C1  H  HCH2  0   0.251   -6.5884   0.6074  -0.5312
 5HE  H5C2  H  HCH2  0   0.253   -7.3421  -0.1025   0.8788
 5HE  H6    H  H     0   0.239   -5.7977  -2.0685   0.7802
 5HE  H7    H  H     0   0.239   -3.5992  -1.6055   0.1073
 5HE  H8C1  H  HCH2  0   0.255   -3.2876  -0.0584  -1.8036
 5HE  H8C2  H  HCH2  0   0.255   -4.7270   0.8437  -1.3852
 5HE  H9    H  H     0   0.241   -3.6813   1.7347   0.6702
 5HE  H10   H  H     0   0.242   -1.3553   2.0306   0.6962
 5HE  H111  H  HCH2  0   0.258   -0.0758   0.0984  -0.3263
 5HE  H112  H  HCH2  0   0.258   -1.2429  -0.0009  -1.6251
 5HE  H13   H  H     0   0.247   -0.5898   2.2347  -2.4886
 5HE  H14   H  H     0   0.243    1.6558   2.8828  -2.2032
 5HE  H16   H  H     0   0.246    1.8368   0.7848   0.0884
 5HE  H17   H  H     0   0.249    3.8510   2.7319  -1.1325
 5HE  H18   H  HCH1  0   0.235    3.9182   0.6758   1.1614
 5HE  H191  H  HCH2  0   0.234    5.0655  -0.1249  -0.8766
 5HE  H192  H  HCH2  0   0.225    6.0782   1.3016  -0.9007
 5HE  HA    H  HOH1  0   0.443    5.4992   2.9818   0.8375
 5HE  H201  H  HCH2  0   0.232    7.0373   0.6467   1.3301
 5HE  H202  H  HCH2  0   0.228    5.9906  -0.7590   1.3616
 5HE  H211  H  HCH2  0   0.275    7.0744  -1.5907  -0.7626
 5HE  H212  H  HCH2  0   0.278    8.1262  -0.2027  -0.7647
 5HE  H23   H  HOH1  0   0.478   10.0256  -2.7965   0.5917

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
 5HE  C1   C2    single  1.528  0.020  1.528
 5HE  C2   C3    single  1.497  0.020  1.497
 5HE  C3   C4    double  1.332  0.020  1.332
 5HE  C4   C5    single  1.502  0.020  1.502
 5HE  C5   C6    single  1.502  0.020  1.502
 5HE  C6   C7    double  1.332  0.020  1.332
 5HE  C7   C8    single  1.503  0.020  1.503
 5HE  C8   C9    single  1.502  0.020  1.502
 5HE  C9   C10   double  1.332  0.020  1.332
 5HE  C10  C11   single  1.503  0.020  1.503
 5HE  C11  C13   single  1.500  0.020  1.500
 5HE  C13  C14   double  1.339  0.020  1.339
 5HE  C14  C16   single  1.454  0.020  1.454
 5HE  C16  C17   double  1.336  0.020  1.336
 5HE  C17  C18   single  1.500  0.020  1.500
 5HE  C18  C19   single  1.528  0.020  1.528
 5HE  C18  O3    single  1.417  0.020  1.417
 5HE  C19  C20   single  1.523  0.020  1.523
 5HE  C20  C21   single  1.520  0.020  1.520
 5HE  C21  C22   single  1.503  0.020  1.503
 5HE  C22  O23   single  1.331  0.020  1.331
 5HE  C22  O24   double  1.206  0.020  1.206
 5HE  C1   H1C1  single  0.970  0.020  1.090
 5HE  C1   H1C2  single  0.970  0.020  1.090
 5HE  C1   H1C3  single  0.970  0.020  1.090
 5HE  C2   H2C1  single  0.970  0.020  1.090
 5HE  C2   H2C2  single  0.970  0.020  1.090
 5HE  C3   H3    single  0.930  0.020  1.080
 5HE  C4   H4    single  0.930  0.020  1.080
 5HE  C5   H5C1  single  0.970  0.020  1.090
 5HE  C5   H5C2  single  0.970  0.020  1.090
 5HE  C6   H6    single  0.930  0.020  1.080
 5HE  C7   H7    single  0.930  0.020  1.080
 5HE  C8   H8C1  single  0.970  0.020  1.090
 5HE  C8   H8C2  single  0.970  0.020  1.090
 5HE  C9   H9    single  0.930  0.020  1.080
 5HE  C10  H10   single  0.930  0.020  1.080
 5HE  C11  H111  single  0.970  0.020  1.090
 5HE  C11  H112  single  0.970  0.020  1.090
 5HE  C13  H13   single  0.930  0.020  1.080
 5HE  C14  H14   single  0.930  0.020  1.080
 5HE  C16  H16   single  0.930  0.020  1.080
 5HE  C17  H17   single  0.930  0.020  1.080
 5HE  C18  H18   single  0.970  0.020  1.090
 5HE  C19  H191  single  0.970  0.020  1.090
 5HE  C19  H192  single  0.970  0.020  1.090
 5HE  O3   HA    single  0.850  0.020  0.980
 5HE  C20  H201  single  0.970  0.020  1.090
 5HE  C20  H202  single  0.970  0.020  1.090
 5HE  C21  H211  single  0.970  0.020  1.090
 5HE  C21  H212  single  0.970  0.020  1.090
 5HE  O23  H23   single  0.850  0.020  0.980

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
 5HE  H1C3  C1   H1C2  107.68  3.000
 5HE  H1C3  C1   H1C1  107.90  3.000
 5HE  H1C2  C1   H1C1  107.66  3.000
 5HE  H1C3  C1   C2    111.10  3.000
 5HE  H1C2  C1   C2    111.26  3.000
 5HE  H1C1  C1   C2    111.07  3.000
 5HE  H2C2  C2   H2C1  106.25  3.000
 5HE  H2C2  C2   C3    108.83  3.000
 5HE  H2C1  C2   C3    111.31  3.000
 5HE  H2C2  C2   C1    108.80  3.000
 5HE  H2C1  C2   C1    109.63  3.000
 5HE  C3    C2   C1    111.84  3.000
 5HE  H3    C3   C4    117.25  3.000
 5HE  H3    C3   C2    114.83  3.000
 5HE  C4    C3   C2    127.91  3.000
 5HE  H4    C4   C5    114.69  3.000
 5HE  H4    C4   C3    117.83  3.000
 5HE  C5    C4   C3    127.45  3.000
 5HE  H5C2  C5   H5C1  106.42  3.000
 5HE  H5C2  C5   C6    109.08  3.000
 5HE  H5C1  C5   C6    110.67  3.000
 5HE  H5C2  C5   C4    110.89  3.000
 5HE  H5C1  C5   C4    109.39  3.000
 5HE  C6    C5   C4    110.33  3.000
 5HE  H6    C6   C7    117.78  3.000
 5HE  H6    C6   C5    114.77  3.000
 5HE  C7    C6   C5    127.44  3.000
 5HE  H7    C7   C8    114.69  3.000
 5HE  H7    C7   C6    117.83  3.000
 5HE  C8    C7   C6    127.45  3.000
 5HE  H8C2  C8   H8C1  106.44  3.000
 5HE  H8C2  C8   C9    109.35  3.000
 5HE  H8C1  C8   C9    111.02  3.000
 5HE  H8C2  C8   C7    110.96  3.000
 5HE  H8C1  C8   C7    109.17  3.000
 5HE  C9    C8   C7    109.86  3.000
 5HE  H9    C9   C10   117.75  3.000
 5HE  H9    C9   C8    114.72  3.000
 5HE  C10   C9   C8    127.48  3.000
 5HE  H10   C10  C11   114.76  3.000
 5HE  H10   C10  C9    117.85  3.000
 5HE  C11   C10  C9    127.39  3.000
 5HE  H112  C11  H111  106.36  3.000
 5HE  H112  C11  C13   109.19  3.000
 5HE  H111  C11  C13   110.94  3.000
 5HE  H112  C11  C10   110.75  3.000
 5HE  H111  C11  C10   109.07  3.000
 5HE  C13   C11  C10   110.45  3.000
 5HE  H13   C13  C14   117.84  3.000
 5HE  H13   C13  C11   115.12  3.000
 5HE  C14   C13  C11   127.02  3.000
 5HE  H14   C14  C16   115.90  3.000
 5HE  H14   C14  C13   117.95  3.000
 5HE  C16   C14  C13   126.15  3.000
 5HE  H16   C16  C17   118.42  3.000
 5HE  H16   C16  C14   117.87  3.000
 5HE  C17   C16  C14   123.71  3.000
 5HE  H17   C17  C18   116.16  3.000
 5HE  H17   C17  C16   119.70  3.000
 5HE  C18   C17  C16   124.11  3.000
 5HE  H18   C18  O3    105.45  3.000
 5HE  H18   C18  C19   108.41  3.000
 5HE  O3    C18  C19   112.25  3.000
 5HE  H18   C18  C17   108.76  3.000
 5HE  O3    C18  C17   111.32  3.000
 5HE  C19   C18  C17   110.44  3.000
 5HE  H192  C19  H191  105.96  3.000
 5HE  H192  C19  C20   110.14  3.000
 5HE  H191  C19  C20   109.49  3.000
 5HE  H192  C19  C18   109.34  3.000
 5HE  H191  C19  C18   107.81  3.000
 5HE  C20   C19  C18   113.78  3.000
 5HE  H202  C20  H201  106.70  3.000
 5HE  H202  C20  C21   109.75  3.000
 5HE  H201  C20  C21   109.78  3.000
 5HE  H202  C20  C19   109.32  3.000
 5HE  H201  C20  C19   110.16  3.000
 5HE  C21   C20  C19   111.02  3.000
 5HE  H212  C21  H211  105.36  3.000
 5HE  H212  C21  C22   107.91  3.000
 5HE  H211  C21  C22   108.18  3.000
 5HE  H212  C21  C20   110.50  3.000
 5HE  H211  C21  C20   110.66  3.000
 5HE  C22   C21  C20   113.84  3.000
 5HE  O24   C22  O23   122.88  3.000
 5HE  O24   C22  C21   125.31  3.000
 5HE  O23   C22  C21   111.81  3.000
 5HE  H23   O23  C22   110.01  3.000
 5HE  HA    O3   C18   108.23  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
 5HE  CONST_01  H23   O23  C22  C21   180.00   0.0  0
 5HE  Var_01    C5    C4   C3   C2      2.10   0.0  2
 5HE  Var_02    C8    C7   C6   C5      2.21   0.0  2
 5HE  Var_03    C11   C10  C9   C8      2.11   0.0  2
 5HE  Var_04    C16   C14  C13  C11     1.10   0.0  2
 5HE  Var_05    C18   C17  C16  C14  -178.21   0.0  2
 5HE  Var_06    C4    C3   C2   C1    119.58  30.0  3
 5HE  Var_07    C6    C5   C4   C3    108.28  30.0  3
 5HE  Var_08    C7    C6   C5   C4    112.75  30.0  3
 5HE  Var_09    C9    C8   C7   C6    107.89  30.0  3
 5HE  Var_10    C10   C9   C8   C7    105.57  30.0  3
 5HE  Var_11    C13   C11  C10  C9    118.62  30.0  3
 5HE  Var_12    C14   C13  C11  C10   108.37  30.0  3
 5HE  Var_13    C17   C16  C14  C13   179.06  30.0  2
 5HE  Var_14    C21   C20  C19  C18   177.63  30.0  3
 5HE  Var_15    C22   C21  C20  C19  -178.64  30.0  3
 5HE  Var_16    O23   C22  C21  C20   177.32  30.0  3
 5HE  Var_17    H1C1  C1   C2   C3    -62.42  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
 5HE  chir_01  C18  C17  C19  O3  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
 5HE  plan-1  C21  0.020
 5HE  plan-1  C22  0.020
 5HE  plan-1  O23  0.020
 5HE  plan-1  O24  0.020
 5HE  plan-1  H23  0.020
 5HE  plan-2  C2   0.020
 5HE  plan-2  C3   0.020
 5HE  plan-2  C4   0.020
 5HE  plan-2  C5   0.020
 5HE  plan-2  H3   0.020
 5HE  plan-2  H4   0.020
 5HE  plan-3  C5   0.020
 5HE  plan-3  C6   0.020
 5HE  plan-3  C7   0.020
 5HE  plan-3  C8   0.020
 5HE  plan-3  H6   0.020
 5HE  plan-3  H7   0.020
 5HE  plan-4  C8   0.020
 5HE  plan-4  C9   0.020
 5HE  plan-4  C10  0.020
 5HE  plan-4  C11  0.020
 5HE  plan-4  H9   0.020
 5HE  plan-4  H10  0.020
 5HE  plan-5  C11  0.020
 5HE  plan-5  C13  0.020
 5HE  plan-5  C14  0.020
 5HE  plan-5  C16  0.020
 5HE  plan-5  H13  0.020
 5HE  plan-5  H14  0.020
 5HE  plan-6  C14  0.020
 5HE  plan-6  C16  0.020
 5HE  plan-6  C17  0.020
 5HE  plan-6  C18  0.020
 5HE  plan-6  H16  0.020
 5HE  plan-6  H17  0.020

