# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 23:15:52 2022
#   Inital geometry file: a 134 line input string
#   Ligand name: (5Z)-7-{(1R,4S,5R,6R)-6-[(1E,3S)-3-hydroperoxyoct-1-en-1-yl]-2,3-dioxabicyclo[2.2.1]hept-5-yl}hept-5-enoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCC[C@H](OO)/C=C/[C@H]1[C@H]2C[C@H](OO2)[C@@H]1C\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
 PGX  PGX  '(5Z)-7-{(1R,4S,5R,6R)-6-[(1E,3S)-3-hydroperoxyoct-1-en-1-yl]-2,3-dioxabicyclo[2.2.1]hept-5-yl}hept-5-enoic acid'  ligand  57  26  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PGX
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
 PGX  C1    C  C      0   0.411   4.0213   0.0120  -4.8043
 PGX  C2    C  CH2    0  -0.582   2.8468   0.6864  -4.0735
 PGX  C3    C  CH2    0  -0.402   1.4560   0.2605  -4.5128
 PGX  C4    C  CH2    0  -0.488   0.3536   0.9778  -3.7300
 PGX  C5    C  C1     0  -0.205  -1.0159   0.6040  -4.2032
 PGX  C6    C  C1     0  -0.226  -1.9170  -0.1266  -3.5478
 PGX  C7    C  CH2    0  -0.497  -1.7613  -0.7059  -2.1737
 PGX  C8    C  CH1    0  -0.227  -2.4033   0.1582  -1.0916
 PGX  C9    C  CH1    0  -0.025  -3.9075   0.4085  -1.2324
 PGX  C10   C  CH2    0  -0.478  -4.2998   0.8810   0.1595
 PGX  C11   C  CH1    0  -0.003  -3.8005  -0.4229   0.7610
 PGX  C12   C  CH1    0  -0.328  -2.3226  -0.4755   0.3366
 PGX  C13   C  C1     0  -0.172  -1.4061   0.2679   1.2521
 PGX  C14   C  C1     0  -0.282  -0.3293  -0.2771   1.8085
 PGX  C15   C  CH1    0   0.041   0.6575   0.3925   2.7188
 PGX  C16   C  CH2    0  -0.445   0.8168  -0.4118   4.0101
 PGX  C17   C  CH2    0  -0.432   1.8856   0.0848   4.9776
 PGX  C18   C  CH2    0  -0.405   2.1034  -0.8840   6.1347
 PGX  C19   C  CH2    0  -0.420   3.1469  -0.4008   7.1336
 PGX  C20   C  CH3    0  -0.661   3.3440  -1.3683   8.2928
 PGX  O1    O  O      0  -0.609   3.7550  -0.7917  -5.7197
 PGX  O2    O  OC    -1  -0.634   5.1640   0.3365  -4.4163
 PGX  O3    O  O2     0  -0.297  -4.5822  -0.8427  -1.3333
 PGX  O4    O  O2     0  -0.301  -4.5089  -1.3991  -0.0001
 PGX  O5    O  O2     0  -0.311   0.2113   1.7227   2.9456
 PGX  O6    O  OH1    0  -0.451   1.3158   2.5746   3.1252
 PGX  H21   H  HCH2   0   0.219   2.9502   1.7721  -4.1904
 PGX  H22   H  HCH2   0   0.218   2.9622   0.5089  -2.9978
 PGX  H31   H  HCH2   0   0.209   1.3363  -0.8184  -4.3829
 PGX  H32   H  HCH2   0   0.208   1.3269   0.4533  -5.5813
 PGX  H41   H  HCH2   0   0.226   0.4838   2.0600  -3.8431
 PGX  H42   H  HCH2   0   0.221   0.4699   0.7689  -2.6635
 PGX  H51   H  H      0   0.228  -1.2761   0.9562  -5.1979
 PGX  H61   H  H      0   0.230  -2.8702  -0.3138  -4.0342
 PGX  H71   H  HCH2   0   0.243  -0.7060  -0.8324  -1.9206
 PGX  H72   H  HCH2   0   0.241  -2.2014  -1.7060  -2.1485
 PGX  H81   H  HCH1   0   0.252  -1.9023   1.1320  -1.0961
 PGX  H91   H  HCH1   0   0.276  -4.2240   1.0139  -2.0823
 PGX  H101  H  HCH2   0   0.270  -5.3670   1.0572   0.2947
 PGX  H102  H  HCH2   0   0.261  -3.7410   1.7564   0.4875
 PGX  H111  H  HCH1   0   0.277  -4.0110  -0.6223   1.8120
 PGX  H121  H  HCH1   0   0.260  -1.9995  -1.5193   0.2762
 PGX  H131  H  H      0   0.247  -1.6455   1.3114   1.4345
 PGX  H141  H  H      0   0.256  -0.1041  -1.3216   1.6084
 PGX  H151  H  HCH1   0   0.237   1.6265   0.4249   2.2021
 PGX  H161  H  HCH2   0   0.228   1.0623  -1.4383   3.7191
 PGX  H162  H  HCH2   0   0.230  -0.1506  -0.4641   4.5201
 PGX  H171  H  HCH2   0   0.205   1.6056   1.0562   5.3970
 PGX  H172  H  HCH2   0   0.219   2.8299   0.2355   4.4446
 PGX  H181  H  HCH2   0   0.211   2.4036  -1.8608   5.7394
 PGX  H182  H  HCH2   0   0.210   1.1528  -1.0467   6.6548
 PGX  H191  H  HCH2   0   0.211   2.8500   0.5785   7.5222
 PGX  H192  H  HCH2   0   0.212   4.0987  -0.2454   6.6164
 PGX  H201  H  HCH3   0   0.226   4.0798  -0.9961   9.0066
 PGX  H202  H  HCH3   0   0.216   2.4090  -1.5259   8.8340
 PGX  H203  H  HCH3   0   0.216   3.6881  -2.3428   7.9414
 PGX  HO61  H  HOH1   0   0.471   1.3268   2.7148   4.0818

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
 PGX  C1   C2    single  1.539  0.020  1.539
 PGX  C1   O1    deloc   1.247  0.020  1.247
 PGX  C1   O2    deloc   1.250  0.020  1.250
 PGX  C2   C3    single  1.519  0.020  1.519
 PGX  C2   H21   single  0.970  0.020  1.090
 PGX  C2   H22   single  0.970  0.020  1.090
 PGX  C3   C4    single  1.531  0.020  1.531
 PGX  C3   H31   single  0.970  0.020  1.090
 PGX  C3   H32   single  0.970  0.020  1.090
 PGX  C4   C5    single  1.496  0.020  1.496
 PGX  C4   H41   single  0.970  0.020  1.090
 PGX  C4   H42   single  0.970  0.020  1.090
 PGX  C5   C6    double  1.332  0.020  1.332
 PGX  C5   H51   single  0.930  0.020  1.080
 PGX  C6   C7    single  1.499  0.020  1.499
 PGX  C6   H61   single  0.930  0.020  1.080
 PGX  C7   C8    single  1.526  0.020  1.526
 PGX  C7   H71   single  0.970  0.020  1.090
 PGX  C7   H72   single  0.970  0.020  1.090
 PGX  C8   C9    single  1.531  0.020  1.531
 PGX  C8   C12   single  1.565  0.020  1.565
 PGX  C8   H81   single  0.970  0.020  1.090
 PGX  C9   C10   single  1.521  0.020  1.521
 PGX  C9   O3    single  1.425  0.020  1.425
 PGX  C9   H91   single  0.970  0.020  1.090
 PGX  C10  C11   single  1.520  0.020  1.520
 PGX  C10  H101  single  0.970  0.020  1.090
 PGX  C10  H102  single  0.970  0.020  1.090
 PGX  C11  C12   single  1.539  0.020  1.539
 PGX  C11  O4    single  1.426  0.020  1.426
 PGX  C11  H111  single  0.970  0.020  1.090
 PGX  C12  C13   single  1.494  0.020  1.494
 PGX  C12  H121  single  0.970  0.020  1.090
 PGX  C13  C14   double  1.329  0.020  1.329
 PGX  C13  H131  single  0.930  0.020  1.080
 PGX  C14  C15   single  1.500  0.020  1.500
 PGX  C14  H141  single  0.930  0.020  1.080
 PGX  C15  C16   single  1.530  0.020  1.530
 PGX  C15  O5    single  1.421  0.020  1.421
 PGX  C15  H151  single  0.970  0.020  1.090
 PGX  C16  C17   single  1.525  0.020  1.525
 PGX  C16  H161  single  0.970  0.020  1.090
 PGX  C16  H162  single  0.970  0.020  1.090
 PGX  C17  C18   single  1.525  0.020  1.525
 PGX  C17  H171  single  0.970  0.020  1.090
 PGX  C17  H172  single  0.970  0.020  1.090
 PGX  C18  C19   single  1.523  0.020  1.523
 PGX  C18  H181  single  0.970  0.020  1.090
 PGX  C18  H182  single  0.970  0.020  1.090
 PGX  C19  C20   single  1.523  0.020  1.523
 PGX  C19  H191  single  0.970  0.020  1.090
 PGX  C19  H192  single  0.970  0.020  1.090
 PGX  C20  H201  single  0.970  0.020  1.090
 PGX  C20  H202  single  0.970  0.020  1.090
 PGX  C20  H203  single  0.970  0.020  1.090
 PGX  O3   O4    single  1.447  0.020  1.447
 PGX  O5   O6    single  1.406  0.020  1.406
 PGX  O6   HO61  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
 PGX  O2    C1   O1    126.20  3.000
 PGX  O2    C1   C2    115.89  3.000
 PGX  O1    C1   C2    117.91  3.000
 PGX  H22   C2   H21   104.77  3.000
 PGX  H22   C2   C3    109.55  3.000
 PGX  H21   C2   C3    109.45  3.000
 PGX  H22   C2   C1    108.34  3.000
 PGX  H21   C2   C1    108.13  3.000
 PGX  C3    C2   C1    116.00  3.000
 PGX  H32   C3   H31   106.09  3.000
 PGX  H32   C3   C4    109.40  3.000
 PGX  H31   C3   C4    108.84  3.000
 PGX  H32   C3   C2    109.95  3.000
 PGX  H31   C3   C2    110.03  3.000
 PGX  C4    C3   C2    112.34  3.000
 PGX  H42   C4   H41   106.08  3.000
 PGX  H42   C4   C5    110.99  3.000
 PGX  H41   C4   C5    108.83  3.000
 PGX  H42   C4   C3    109.44  3.000
 PGX  H41   C4   C3    108.93  3.000
 PGX  C5    C4   C3    112.36  3.000
 PGX  H51   C5   C6    117.77  3.000
 PGX  H51   C5   C4    115.32  3.000
 PGX  C6    C5   C4    126.90  3.000
 PGX  H61   C6   C7    115.78  3.000
 PGX  H61   C6   C5    117.88  3.000
 PGX  C7    C6   C5    126.33  3.000
 PGX  H72   C7   H71   106.12  3.000
 PGX  H72   C7   C8    109.41  3.000
 PGX  H71   C7   C8    107.91  3.000
 PGX  H72   C7   C6    109.44  3.000
 PGX  H71   C7   C6    110.94  3.000
 PGX  C8    C7   C6    112.79  3.000
 PGX  H81   C8   C12   109.90  3.000
 PGX  H81   C8   C9    107.67  3.000
 PGX  C12   C8   C9    101.58  3.000
 PGX  H81   C8   C7    107.94  3.000
 PGX  C12   C8   C7    113.34  3.000
 PGX  C9    C8   C7    116.14  3.000
 PGX  H91   C9   O3    107.15  3.000
 PGX  H91   C9   C10   117.77  3.000
 PGX  O3    C9   C10   102.44  3.000
 PGX  H91   C9   C8    116.59  3.000
 PGX  O3    C9   C8    109.14  3.000
 PGX  C10   C9   C8    102.70  3.000
 PGX  H102  C10  H101  109.58  3.000
 PGX  H102  C10  C11   113.69  3.000
 PGX  H101  C10  C11   114.27  3.000
 PGX  H102  C10  C9    113.14  3.000
 PGX  H101  C10  C9    114.59  3.000
 PGX  C11   C10  C9     90.63  3.000
 PGX  H111  C11  O4    107.06  3.000
 PGX  H111  C11  C12   116.43  3.000
 PGX  O4    C11  C12   107.85  3.000
 PGX  H111  C11  C10   118.35  3.000
 PGX  O4    C11  C10   102.29  3.000
 PGX  C12   C11  C10   103.63  3.000
 PGX  H121  C12  C13   109.11  3.000
 PGX  H121  C12  C11   109.36  3.000
 PGX  C13   C12  C11   113.79  3.000
 PGX  H121  C12  C8    110.56  3.000
 PGX  C13   C12  C8    112.93  3.000
 PGX  C11   C12  C8    100.86  3.000
 PGX  H131  C13  C14   120.15  3.000
 PGX  H131  C13  C12   116.48  3.000
 PGX  C14   C13  C12   123.35  3.000
 PGX  H141  C14  C15   113.84  3.000
 PGX  H141  C14  C13   119.00  3.000
 PGX  C15   C14  C13   127.15  3.000
 PGX  H151  C15  O5    108.93  3.000
 PGX  H151  C15  C16   108.71  3.000
 PGX  O5    C15  C16   112.96  3.000
 PGX  H151  C15  C14   107.94  3.000
 PGX  O5    C15  C14   107.94  3.000
 PGX  C16   C15  C14   110.24  3.000
 PGX  H162  C16  H161  106.09  3.000
 PGX  H162  C16  C17   109.84  3.000
 PGX  H161  C16  C17   108.47  3.000
 PGX  H162  C16  C15   109.05  3.000
 PGX  H161  C16  C15   106.98  3.000
 PGX  C17   C16  C15   115.94  3.000
 PGX  H172  C17  H171  106.56  3.000
 PGX  H172  C17  C18   109.49  3.000
 PGX  H171  C17  C18   108.04  3.000
 PGX  H172  C17  C16   109.91  3.000
 PGX  H171  C17  C16   110.66  3.000
 PGX  C18   C17  C16   112.01  3.000
 PGX  H182  C18  H181  106.05  3.000
 PGX  H182  C18  C19   109.28  3.000
 PGX  H181  C18  C19   109.38  3.000
 PGX  H182  C18  C17   109.30  3.000
 PGX  H181  C18  C17   109.38  3.000
 PGX  C19   C18  C17   113.20  3.000
 PGX  H192  C19  H191  106.06  3.000
 PGX  H192  C19  C20   109.72  3.000
 PGX  H191  C19  C20   109.47  3.000
 PGX  H192  C19  C18   109.32  3.000
 PGX  H191  C19  C18   109.32  3.000
 PGX  C20   C19  C18   112.73  3.000
 PGX  H203  C20  H202  107.50  3.000
 PGX  H203  C20  H201  107.62  3.000
 PGX  H202  C20  H201  107.62  3.000
 PGX  H203  C20  C19   111.28  3.000
 PGX  H202  C20  C19   110.99  3.000
 PGX  H201  C20  C19   111.64  3.000
 PGX  O4    O3   C9    104.39  3.000
 PGX  O3    O4   C11   104.70  3.000
 PGX  O6    O5   C15   109.92  3.000
 PGX  HO61  O6   O5    102.89  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
 PGX  Var_01  C15   C14  C13  C12   178.96   0.0  2
 PGX  Var_02  C8    C7   C6   C5     97.21  30.0  3
 PGX  Var_03  C7    C6   C5   C4      1.59   0.0  2
 PGX  Var_04  C4    C3   C2   C1    179.81  30.0  3
 PGX  Var_05  C5    C4   C3   C2    177.47  30.0  3
 PGX  Var_06  O1    C1   C2   C3      2.20  30.0  2
 PGX  Var_07  C6    C5   C4   C3    110.03  30.0  3
 PGX  Var_08  C18   C17  C16  C15  -172.04  30.0  3
 PGX  Var_09  C19   C18  C17  C16  -178.85  30.0  3
 PGX  Var_10  C20   C19  C18  C17   179.32  30.0  3
 PGX  Var_11  H201  C20  C19  C18  -178.89  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
 PGX  chir_01  C8   C7   C9   C12  negativ
 PGX  chir_02  C9   O3   C8   C10  positiv
 PGX  chir_03  C11  O4   C12  C10  negativ
 PGX  chir_04  C12  C13  C11  C8   negativ
 PGX  chir_05  C15  O5   C16  C14  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
 PGX  plan-1  C1    0.020
 PGX  plan-1  C2    0.020
 PGX  plan-1  O1    0.020
 PGX  plan-1  O2    0.020
 PGX  plan-2  C4    0.020
 PGX  plan-2  C5    0.020
 PGX  plan-2  C6    0.020
 PGX  plan-2  C7    0.020
 PGX  plan-2  H51   0.020
 PGX  plan-2  H61   0.020
 PGX  plan-3  C12   0.020
 PGX  plan-3  C13   0.020
 PGX  plan-3  C14   0.020
 PGX  plan-3  C15   0.020
 PGX  plan-3  H131  0.020
 PGX  plan-3  H141  0.020

