# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 20 18:19:43 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: 8-[(1R,5R)-4-oxo-5-pent-2-en-1-ylcyclopent-2-en-1-yl]octanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC=CC[C@@H]1[C@H](CCCCCCCC(O)=O)C=CC1=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
 OPD  OPD  '8-[(1R,5R)-4-oxo-5-pent-2-en-1-ylcyclopent-2-en-1-yl]octanoic acid'  ligand  49  21  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_OPD
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
 OPD  C8    C  C1    0  -0.207  -3.3949   1.2922  -1.4848
 OPD  C7    C  C1    0  -0.179  -2.6856   0.5168  -0.6729
 OPD  C5    C  CR15  0  -0.367  -0.2790  -0.1476  -0.2740
 OPD  C1    C  CR5   0   0.380   0.2153  -0.2152  -1.7126
 OPD  O6    O  O     0  -0.408  -0.4706  -0.1480  -2.7094
 OPD  C2    C  CR15  0  -0.334   1.6705  -0.4052  -1.6706
 OPD  C3    C  CR15  0  -0.160   2.0978  -0.3228  -0.4093
 OPD  C4    C  CR15  0  -0.300   1.0084  -0.0181   0.5755
 OPD  C11   C  CH2   0  -0.417   1.2289   1.3452   1.2448
 OPD  C12   C  CH2   0  -0.422   2.5229   1.4267   2.0472
 OPD  C13   C  CH2   0  -0.411   2.6318   2.7173   2.8501
 OPD  C14   C  CH2   0  -0.413   3.9110   2.8026   3.6735
 OPD  C15   C  CH2   0  -0.415   4.0006   4.0711   4.5127
 OPD  C16   C  CH2   0  -0.417   5.2676   4.1335   5.3572
 OPD  C17   C  CH2   0  -0.579   5.3272   5.3995   6.1963
 OPD  C18   C  C     0   0.549   6.5591   5.5060   7.0510
 OPD  O20   O  OH1   0  -0.599   6.5858   6.6424   7.7431
 OPD  O19   O  O     0  -0.446   7.4332   4.6777   7.1203
 OPD  C6    C  CH2   0  -0.496  -1.3828   0.8862  -0.0374
 OPD  C9    C  CH2   0  -0.483  -4.6972   0.9094  -2.1139
 OPD  C10   C  CH3   0  -0.657  -4.5857   0.8109  -3.6342
 OPD  H81   H  H     0   0.220  -3.0012   2.2699  -1.7576
 OPD  H71   H  H     0   0.224  -3.0747  -0.4670  -0.4136
 OPD  H51   H  HCR5  0   0.288  -0.6994  -1.1403  -0.0664
 OPD  H21   H  HCR5  0   0.266   2.2803  -0.5763  -2.5473
 OPD  H31   H  HCR5  0   0.279   3.1308  -0.4355  -0.1049
 OPD  H41   H  HCR5  0   0.261   1.0143  -0.7721   1.3703
 OPD  H111  H  HCH2  0   0.225   1.2092   2.1373   0.4898
 OPD  H112  H  HCH2  0   0.234   0.3922   1.5373   1.9218
 OPD  H121  H  HCH2  0   0.219   3.3886   1.3442   1.3832
 OPD  H122  H  HCH2  0   0.214   2.5787   0.5715   2.7301
 OPD  H131  H  HCH2  0   0.210   1.7670   2.7998   3.5177
 OPD  H132  H  HCH2  0   0.211   2.5758   3.5756   2.1719
 OPD  H141  H  HCH2  0   0.209   3.9741   1.9295   4.3323
 OPD  H142  H  HCH2  0   0.210   4.7789   2.7447   3.0077
 OPD  H151  H  HCH2  0   0.213   3.9543   4.9474   3.8571
 OPD  H152  H  HCH2  0   0.212   3.1240   4.1337   5.1666
 OPD  H161  H  HCH2  0   0.224   6.1436   4.0798   4.7051
 OPD  H162  H  HCH2  0   0.224   5.3117   3.2559   6.0077
 OPD  H171  H  HCH2  0   0.275   4.4536   5.4657   6.8533
 OPD  H172  H  HCH2  0   0.274   5.2785   6.2879   5.5583
 OPD  H201  H  HOH1  0   0.478   7.3896   6.6807   8.2826
 OPD  H61   H  HCH2  0   0.242  -1.0633   1.8762  -0.3728
 OPD  H62   H  HCH2  0   0.248  -1.5391   0.9624   1.0435
 OPD  H91   H  HCH2  0   0.226  -5.0412  -0.0440  -1.7047
 OPD  H92   H  HCH2  0   0.225  -5.4629   1.6499  -1.8617
 OPD  H101  H  HCH3  0   0.223  -3.8515   0.0573  -3.9212
 OPD  H102  H  HCH3  0   0.227  -5.5417   0.5416  -4.0851
 OPD  H103  H  HCH3  0   0.219  -4.2712   1.7609  -4.0698

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
 OPD  C8   C7    double  1.328  0.020  1.328
 OPD  C8   C9    single  1.496  0.020  1.496
 OPD  C8   H81   single  0.930  0.020  1.080
 OPD  C7   C6    single  1.496  0.020  1.496
 OPD  C7   H71   single  0.930  0.020  1.080
 OPD  C5   C1    single  1.523  0.020  1.523
 OPD  C5   C4    single  1.548  0.020  1.548
 OPD  C5   C6    single  1.531  0.020  1.531
 OPD  C5   H51   single  0.970  0.020  1.090
 OPD  C1   O6    double  1.212  0.020  1.212
 OPD  C1   C2    single  1.468  0.020  1.468
 OPD  C2   C3    double  1.334  0.020  1.334
 OPD  C2   H21   single  0.930  0.020  1.080
 OPD  C3   C4    single  1.500  0.020  1.500
 OPD  C3   H31   single  0.930  0.020  1.080
 OPD  C4   C11   single  1.535  0.020  1.535
 OPD  C4   H41   single  0.970  0.020  1.090
 OPD  C11  C12   single  1.525  0.020  1.525
 OPD  C11  H111  single  0.970  0.020  1.090
 OPD  C11  H112  single  0.970  0.020  1.090
 OPD  C12  C13   single  1.524  0.020  1.524
 OPD  C12  H121  single  0.970  0.020  1.090
 OPD  C12  H122  single  0.970  0.020  1.090
 OPD  C13  C14   single  1.524  0.020  1.524
 OPD  C13  H131  single  0.970  0.020  1.090
 OPD  C13  H132  single  0.970  0.020  1.090
 OPD  C14  C15   single  1.524  0.020  1.524
 OPD  C14  H141  single  0.970  0.020  1.090
 OPD  C14  H142  single  0.970  0.020  1.090
 OPD  C15  C16   single  1.524  0.020  1.524
 OPD  C15  H151  single  0.970  0.020  1.090
 OPD  C15  H152  single  0.970  0.020  1.090
 OPD  C16  C17   single  1.520  0.020  1.520
 OPD  C16  H161  single  0.970  0.020  1.090
 OPD  C16  H162  single  0.970  0.020  1.090
 OPD  C17  C18   single  1.503  0.020  1.503
 OPD  C17  H171  single  0.970  0.020  1.090
 OPD  C17  H172  single  0.970  0.020  1.090
 OPD  C18  O20   single  1.331  0.020  1.331
 OPD  C18  O19   double  1.206  0.020  1.206
 OPD  O20  H201  single  0.850  0.020  0.980
 OPD  C6   H61   single  0.970  0.020  1.090
 OPD  C6   H62   single  0.970  0.020  1.090
 OPD  C9   C10   single  1.528  0.020  1.528
 OPD  C9   H91   single  0.970  0.020  1.090
 OPD  C9   H92   single  0.970  0.020  1.090
 OPD  C10  H101  single  0.970  0.020  1.090
 OPD  C10  H102  single  0.970  0.020  1.090
 OPD  C10  H103  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
 OPD  H81   C8   C9    116.05  3.000
 OPD  H81   C8   C7    118.97  3.000
 OPD  C9    C8   C7    124.94  3.000
 OPD  H71   C7   C6    115.66  3.000
 OPD  H71   C7   C8    118.82  3.000
 OPD  C6    C7   C8    125.50  3.000
 OPD  H51   C5   C6    107.78  3.000
 OPD  H51   C5   C4    106.88  3.000
 OPD  C6    C5   C4    117.28  3.000
 OPD  H51   C5   C1    105.24  3.000
 OPD  C6    C5   C1    114.21  3.000
 OPD  C4    C5   C1    104.61  3.000
 OPD  C2    C1   O6    126.28  3.000
 OPD  C2    C1   C5    107.49  3.000
 OPD  O6    C1   C5    126.22  3.000
 OPD  H21   C2   C3    126.54  3.000
 OPD  H21   C2   C1    123.79  3.000
 OPD  C3    C2   C1    109.66  3.000
 OPD  H31   C3   C4    121.97  3.000
 OPD  H31   C3   C2    124.39  3.000
 OPD  C4    C3   C2    113.62  3.000
 OPD  H41   C4   C11   107.11  3.000
 OPD  H41   C4   C3    109.43  3.000
 OPD  C11   C4   C3    111.25  3.000
 OPD  H41   C4   C5    110.18  3.000
 OPD  C11   C4   C5    115.67  3.000
 OPD  C3    C4   C5    103.11  3.000
 OPD  H112  C11  H111  106.63  3.000
 OPD  H112  C11  C12   108.31  3.000
 OPD  H111  C11  C12   109.85  3.000
 OPD  H112  C11  C4    108.43  3.000
 OPD  H111  C11  C4    109.85  3.000
 OPD  C12   C11  C4    113.51  3.000
 OPD  H122  C12  H121  106.20  3.000
 OPD  H122  C12  C13   109.20  3.000
 OPD  H121  C12  C13   109.09  3.000
 OPD  H122  C12  C11   109.24  3.000
 OPD  H121  C12  C11   110.37  3.000
 OPD  C13   C12  C11   112.53  3.000
 OPD  H132  C13  H131  106.14  3.000
 OPD  H132  C13  C14   109.49  3.000
 OPD  H131  C13  C14   109.22  3.000
 OPD  H132  C13  C12   109.49  3.000
 OPD  H131  C13  C12   109.17  3.000
 OPD  C14   C13  C12   113.09  3.000
 OPD  H142  C14  H141  106.13  3.000
 OPD  H142  C14  C15   109.40  3.000
 OPD  H141  C14  C15   109.20  3.000
 OPD  H142  C14  C13   109.49  3.000
 OPD  H141  C14  C13   109.19  3.000
 OPD  C15   C14  C13   113.18  3.000
 OPD  H152  C15  H151  106.12  3.000
 OPD  H152  C15  C16   109.40  3.000
 OPD  H151  C15  C16   109.52  3.000
 OPD  H152  C15  C14   109.23  3.000
 OPD  H151  C15  C14   109.51  3.000
 OPD  C16   C15  C14   112.85  3.000
 OPD  H162  C16  H161  106.45  3.000
 OPD  H162  C16  C17   109.78  3.000
 OPD  H161  C16  C17   109.80  3.000
 OPD  H162  C16  C15   109.29  3.000
 OPD  H161  C16  C15   109.49  3.000
 OPD  C17   C16  C15   111.88  3.000
 OPD  H172  C17  H171  105.37  3.000
 OPD  H172  C17  C18   108.07  3.000
 OPD  H171  C17  C18   107.96  3.000
 OPD  H172  C17  C16   110.64  3.000
 OPD  H171  C17  C16   110.51  3.000
 OPD  C18   C17  C16   113.90  3.000
 OPD  O19   C18  O20   122.82  3.000
 OPD  O19   C18  C17   125.30  3.000
 OPD  O20   C18  C17   111.88  3.000
 OPD  H201  O20  C18   109.87  3.000
 OPD  H62   C6   H61   106.36  3.000
 OPD  H62   C6   C5    107.60  3.000
 OPD  H61   C6   C5    110.70  3.000
 OPD  H62   C6   C7    108.20  3.000
 OPD  H61   C6   C7    110.36  3.000
 OPD  C5    C6   C7    113.30  3.000
 OPD  H92   C9   H91   106.48  3.000
 OPD  H92   C9   C10   108.90  3.000
 OPD  H91   C9   C10   109.83  3.000
 OPD  H92   C9   C8    109.81  3.000
 OPD  H91   C9   C8    109.86  3.000
 OPD  C10   C9   C8    111.81  3.000
 OPD  H103  C10  H102  107.61  3.000
 OPD  H103  C10  H101  107.60  3.000
 OPD  H102  C10  H101  108.10  3.000
 OPD  H103  C10  C9    111.23  3.000
 OPD  H102  C10  C9    111.31  3.000
 OPD  H101  C10  C9    110.83  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
 OPD  CONST_01  H201  O20  C18  C17   180.00   0.0  0
 OPD  Var_01    C3    C2   C1   C5     -6.14  30.0  1
 OPD  Var_02    C4    C3   C2   C1     -2.06  30.0  1
 OPD  Var_03    C5    C6   C7   C8   -127.50  30.0  3
 OPD  Var_04    C13   C12  C11  C4   -172.40  30.0  3
 OPD  Var_05    C9    C8   C7   C6    179.99   0.0  2
 OPD  Var_06    C10   C9   C8   C7   -114.79  30.0  3
 OPD  Var_07    C14   C13  C12  C11   179.13  30.0  3
 OPD  Var_08    C15   C14  C13  C12  -178.09  30.0  3
 OPD  Var_09    C16   C15  C14  C13   178.68  30.0  3
 OPD  Var_10    C17   C16  C15  C14  -179.37  30.0  3
 OPD  Var_11    C18   C17  C16  C15   179.86  30.0  3
 OPD  Var_12    O20   C18  C17  C16   178.49  30.0  3
 OPD  Var_13    H101  C10  C9   C8     60.24  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
 OPD  chir_01  C5  C1   C4  C6  negativ
 OPD  chir_02  C4  C11  C3  C5  positiv

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
 OPD  plan-1  C5    0.020
 OPD  plan-1  C1    0.020
 OPD  plan-1  O6    0.020
 OPD  plan-1  C2    0.020
 OPD  plan-2  C17   0.020
 OPD  plan-2  C18   0.020
 OPD  plan-2  O20   0.020
 OPD  plan-2  O19   0.020
 OPD  plan-2  H201  0.020
 OPD  plan-3  C8    0.020
 OPD  plan-3  C7    0.020
 OPD  plan-3  C6    0.020
 OPD  plan-3  C9    0.020
 OPD  plan-3  H81   0.020
 OPD  plan-3  H71   0.020

