# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 22 13:27:23 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: (5Z,9alpha,13E,15S)-9,15-dihydroxy-11-oxoprosta-5,13-dien-1-oic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCC[C@H](O)/C=C/[C@@H]1[C@@H](C\C=C/CCCC(O)=O)[C@@H](O)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
 PG2  PG2  '(5Z,9alpha,13E,15S)-9,15-dihydroxy-11-oxoprosta-5,13-dien-1-oic acid'  ligand  57  25  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PG2
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
 PG2  C1    C  C     0   0.549  -4.3195   4.0793   0.1993
 PG2  C2    C  CH2   0  -0.580  -3.6828   2.8633   0.8116
 PG2  C3    C  CH2   0  -0.419  -4.1799   1.5483   0.2352
 PG2  C4    C  CH2   0  -0.493  -3.4955   0.3562   0.9056
 PG2  C5    C  C1    0  -0.208  -3.9757  -0.9488   0.3527
 PG2  C6    C  C1    0  -0.218  -3.2592  -1.8517  -0.3160
 PG2  C7    C  CH2   0  -0.485  -1.7987  -1.7731  -0.6388
 PG2  C8    C  CH1   0  -0.250  -0.9509  -2.7072   0.2196
 PG2  C9    C  CH1   0   0.022  -1.2765  -4.2013   0.1089
 PG2  C10   C  CH2   0  -0.596  -0.0644  -4.8599   0.7575
 PG2  C11   C  C     0   0.429   1.0948  -3.9703   0.3765
 PG2  C12   C  CH1   0  -0.446   0.5514  -2.6286  -0.1020
 PG2  C13   C  C1    0  -0.167   1.2532  -1.4653   0.5166
 PG2  C14   C  C1    0  -0.264   1.7932  -0.4657  -0.1712
 PG2  C15   C  CH1   0   0.006   2.4979   0.7240   0.4189
 PG2  C16   C  CH2   0  -0.460   3.8514   0.9289  -0.2629
 PG2  C17   C  CH2   0  -0.412   4.5863   2.1867   0.1835
 PG2  C18   C  CH2   0  -0.407   5.8744   2.4149  -0.5967
 PG2  C19   C  CH2   0  -0.419   6.6330   3.6619  -0.1584
 PG2  C20   C  CH3   0  -0.661   7.9059   3.8918  -0.9608
 PG2  O1    O  OH1   0  -0.598  -3.8368   5.2040   0.7210
 PG2  O2    O  O     0  -0.445  -5.1661   4.0664  -0.6596
 PG2  O3    O  OH1   0  -0.671  -1.3637  -4.5254  -1.2612
 PG2  O4    O  O     0  -0.392   2.2645  -4.2527   0.4575
 PG2  O5    O  OH1   0  -0.662   2.6061   0.6618   1.8218
 PG2  H21   H  HCH2  0   0.278  -3.8540   2.8984   1.8926
 PG2  H22   H  HCH2  0   0.277  -2.5982   2.9480   0.6883
 PG2  H31   H  HCH2  0   0.234  -3.9880   1.5143  -0.8398
 PG2  H32   H  HCH2  0   0.232  -5.2624   1.4675   0.3619
 PG2  H41   H  HCH2  0   0.236  -3.7011   0.3882   1.9811
 PG2  H42   H  HCH2  0   0.232  -2.4126   0.4542   0.8022
 PG2  H5    H  H     0   0.231  -5.0317  -1.1551   0.5080
 PG2  H6    H  H     0   0.233  -3.7695  -2.7478  -0.6573
 PG2  H71   H  HCH2  0   0.242  -1.4254  -0.7559  -0.5048
 PG2  H72   H  HCH2  0   0.240  -1.6440  -2.0148  -1.6938
 PG2  H8    H  HCH1  0   0.255  -1.0917  -2.4301   1.2718
 PG2  H9    H  HCH1  0   0.233  -2.2037  -4.4532   0.6363
 PG2  H101  H  HCH2  0   0.283  -0.1588  -4.8187   1.8489
 PG2  H102  H  HCH2  0   0.283   0.0924  -5.9060   0.4882
 PG2  H12   H  HCH1  0   0.296   0.6841  -2.6034  -1.1917
 PG2  H13   H  H     0   0.244   1.2760  -1.4517   1.6031
 PG2  H14   H  H     0   0.243   1.7452  -0.4805  -1.2575
 PG2  H15   H  HCH1  0   0.236   1.8866   1.6122   0.2141
 PG2  H161  H  HCH2  0   0.225   3.6832   0.9743  -1.3436
 PG2  H162  H  HCH2  0   0.224   4.4805   0.0462  -0.0937
 PG2  H171  H  HCH2  0   0.214   4.8138   2.1283   1.2515
 PG2  H172  H  HCH2  0   0.210   3.9284   3.0539   0.0582
 PG2  H181  H  HCH2  0   0.206   5.6422   2.4895  -1.6649
 PG2  H182  H  HCH2  0   0.208   6.5253   1.5402  -0.4905
 PG2  H191  H  HCH2  0   0.210   6.8803   3.5805   0.9047
 PG2  H192  H  HCH2  0   0.210   5.9783   4.5342  -0.2502
 PG2  H201  H  HCH3  0   0.225   8.4369   4.7831  -0.6241
 PG2  H202  H  HCH3  0   0.216   8.5886   3.0455  -0.8671
 PG2  H203  H  HCH3  0   0.215   7.6858   4.0200  -2.0223
 PG2  HO1   H  HOH1  0   0.478  -4.2687   5.9689   0.3131
 PG2  HO3   H  HOH1  0   0.454  -1.4887  -5.4759  -1.3432
 PG2  HO5   H  HOH1  0   0.444   3.2031  -0.0615   2.0448

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
 PG2  C1   C2    single  1.503  0.020  1.503
 PG2  C1   O1    single  1.330  0.020  1.330
 PG2  C1   O2    double  1.206  0.020  1.206
 PG2  C2   C3    single  1.519  0.020  1.519
 PG2  C2   H21   single  0.970  0.020  1.090
 PG2  C2   H22   single  0.970  0.020  1.090
 PG2  C3   C4    single  1.529  0.020  1.529
 PG2  C3   H31   single  0.970  0.020  1.090
 PG2  C3   H32   single  0.970  0.020  1.090
 PG2  C4   C5    single  1.496  0.020  1.496
 PG2  C4   H41   single  0.970  0.020  1.090
 PG2  C4   H42   single  0.970  0.020  1.090
 PG2  C5   C6    double  1.333  0.020  1.333
 PG2  C5   H5    single  0.930  0.020  1.080
 PG2  C6   C7    single  1.498  0.020  1.498
 PG2  C6   H6    single  0.930  0.020  1.080
 PG2  C7   C8    single  1.526  0.020  1.526
 PG2  C7   H71   single  0.970  0.020  1.090
 PG2  C7   H72   single  0.970  0.020  1.090
 PG2  C8   C9    single  1.533  0.020  1.533
 PG2  C8   C12   single  1.538  0.020  1.538
 PG2  C8   H8    single  0.970  0.020  1.090
 PG2  C9   C10   single  1.524  0.020  1.524
 PG2  C9   O3    single  1.411  0.020  1.411
 PG2  C9   H9    single  0.970  0.020  1.090
 PG2  C10  C11   single  1.510  0.020  1.510
 PG2  C10  H101  single  0.970  0.020  1.090
 PG2  C10  H102  single  0.970  0.020  1.090
 PG2  C11  C12   single  1.525  0.020  1.525
 PG2  C11  O4    double  1.206  0.020  1.206
 PG2  C12  C13   single  1.493  0.020  1.493
 PG2  C12  H12   single  0.970  0.020  1.090
 PG2  C13  C14   double  1.328  0.020  1.328
 PG2  C13  H13   single  0.930  0.020  1.080
 PG2  C14  C15   single  1.503  0.020  1.503
 PG2  C14  H14   single  0.930  0.020  1.080
 PG2  C15  C16   single  1.529  0.020  1.529
 PG2  C15  O5    single  1.408  0.020  1.408
 PG2  C15  H15   single  0.970  0.020  1.090
 PG2  C16  C17   single  1.524  0.020  1.524
 PG2  C16  H161  single  0.970  0.020  1.090
 PG2  C16  H162  single  0.970  0.020  1.090
 PG2  C17  C18   single  1.523  0.020  1.523
 PG2  C17  H171  single  0.970  0.020  1.090
 PG2  C17  H172  single  0.970  0.020  1.090
 PG2  C18  C19   single  1.524  0.020  1.524
 PG2  C18  H181  single  0.970  0.020  1.090
 PG2  C18  H182  single  0.970  0.020  1.090
 PG2  C19  C20   single  1.522  0.020  1.522
 PG2  C19  H191  single  0.970  0.020  1.090
 PG2  C19  H192  single  0.970  0.020  1.090
 PG2  C20  H201  single  0.970  0.020  1.090
 PG2  C20  H202  single  0.970  0.020  1.090
 PG2  C20  H203  single  0.970  0.020  1.090
 PG2  O1   HO1   single  0.850  0.020  0.980
 PG2  O3   HO3   single  0.850  0.020  0.980
 PG2  O5   HO5   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
 PG2  O2    C1   O1    122.88  3.000
 PG2  O2    C1   C2    125.37  3.000
 PG2  O1    C1   C2    111.75  3.000
 PG2  H22   C2   H21   105.28  3.000
 PG2  H22   C2   C3    110.39  3.000
 PG2  H21   C2   C3    110.55  3.000
 PG2  H22   C2   C1    108.13  3.000
 PG2  H21   C2   C1    108.06  3.000
 PG2  C3    C2   C1    114.02  3.000
 PG2  H32   C3   H31   106.61  3.000
 PG2  H32   C3   C4    109.56  3.000
 PG2  H31   C3   C4    109.17  3.000
 PG2  H32   C3   C2    110.13  3.000
 PG2  H31   C3   C2    110.05  3.000
 PG2  C4    C3   C2    111.22  3.000
 PG2  H42   C4   H41   106.05  3.000
 PG2  H42   C4   C5    111.19  3.000
 PG2  H41   C4   C5    109.14  3.000
 PG2  H42   C4   C3    109.40  3.000
 PG2  H41   C4   C3    108.88  3.000
 PG2  C5    C4   C3    111.98  3.000
 PG2  H5    C5   C6    117.74  3.000
 PG2  H5    C5   C4    115.11  3.000
 PG2  C6    C5   C4    127.13  3.000
 PG2  H6    C6   C7    115.70  3.000
 PG2  H6    C6   C5    117.64  3.000
 PG2  C7    C6   C5    126.65  3.000
 PG2  H72   C7   H71   106.02  3.000
 PG2  H72   C7   C8    109.20  3.000
 PG2  H71   C7   C8    108.14  3.000
 PG2  H72   C7   C6    109.53  3.000
 PG2  H71   C7   C6    110.84  3.000
 PG2  C8    C7   C6    112.86  3.000
 PG2  H8    C8   C12   108.23  3.000
 PG2  H8    C8   C9    106.74  3.000
 PG2  C12   C8   C9    104.01  3.000
 PG2  H8    C8   C7    108.28  3.000
 PG2  C12   C8   C7    113.19  3.000
 PG2  C9    C8   C7    115.98  3.000
 PG2  H9    C9   O3    111.24  3.000
 PG2  H9    C9   C10   111.64  3.000
 PG2  O3    C9   C10   111.29  3.000
 PG2  H9    C9   C8    111.65  3.000
 PG2  O3    C9   C8    107.88  3.000
 PG2  C10   C9   C8    102.80  3.000
 PG2  H102  C10  H101  107.09  3.000
 PG2  H102  C10  C11   113.08  3.000
 PG2  H101  C10  C11   107.16  3.000
 PG2  H102  C10  C9    115.05  3.000
 PG2  H101  C10  C9    109.81  3.000
 PG2  C11   C10  C9    104.39  3.000
 PG2  O4    C11  C12   124.95  3.000
 PG2  O4    C11  C10   126.14  3.000
 PG2  C12   C11  C10   108.90  3.000
 PG2  H12   C12  C13   109.66  3.000
 PG2  H12   C12  C11   106.77  3.000
 PG2  C13   C12  C11   112.84  3.000
 PG2  H12   C12  C8    109.07  3.000
 PG2  C13   C12  C8    114.35  3.000
 PG2  C11   C12  C8    103.74  3.000
 PG2  H13   C13  C14   119.98  3.000
 PG2  H13   C13  C12   115.71  3.000
 PG2  C14   C13  C12   124.27  3.000
 PG2  H14   C14  C15   115.06  3.000
 PG2  H14   C14  C13   119.28  3.000
 PG2  C15   C14  C13   125.65  3.000
 PG2  H15   C15  O5    105.33  3.000
 PG2  H15   C15  C16   107.54  3.000
 PG2  O5    C15  C16   112.46  3.000
 PG2  H15   C15  C14   107.82  3.000
 PG2  O5    C15  C14   113.09  3.000
 PG2  C16   C15  C14   110.23  3.000
 PG2  H162  C16  H161  105.89  3.000
 PG2  H162  C16  C17   110.02  3.000
 PG2  H161  C16  C17   109.21  3.000
 PG2  H162  C16  C15   109.33  3.000
 PG2  H161  C16  C15   108.05  3.000
 PG2  C17   C16  C15   114.01  3.000
 PG2  H172  C17  H171  106.19  3.000
 PG2  H172  C17  C18   109.31  3.000
 PG2  H171  C17  C18   109.41  3.000
 PG2  H172  C17  C16   109.28  3.000
 PG2  H171  C17  C16   110.03  3.000
 PG2  C18   C17  C16   112.43  3.000
 PG2  H182  C18  H181  105.95  3.000
 PG2  H182  C18  C19   109.25  3.000
 PG2  H181  C18  C19   109.28  3.000
 PG2  H182  C18  C17   109.46  3.000
 PG2  H181  C18  C17   109.29  3.000
 PG2  C19   C18  C17   113.35  3.000
 PG2  H192  C19  H191  106.01  3.000
 PG2  H192  C19  C20   109.61  3.000
 PG2  H191  C19  C20   109.54  3.000
 PG2  H192  C19  C18   109.28  3.000
 PG2  H191  C19  C18   109.33  3.000
 PG2  C20   C19  C18   112.85  3.000
 PG2  H203  C20  H202  107.50  3.000
 PG2  H203  C20  H201  107.60  3.000
 PG2  H202  C20  H201  107.61  3.000
 PG2  H203  C20  C19   111.21  3.000
 PG2  H202  C20  C19   111.15  3.000
 PG2  H201  C20  C19   111.58  3.000
 PG2  HO1   O1   C1    109.92  3.000
 PG2  HO3   O3   C9    108.53  3.000
 PG2  HO5   O5   C15   108.13  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
 PG2  CONST_01  HO1   O1   C1   C2    180.00   0.0  0
 PG2  Var_01    C12   C11  C10  C9     16.70  30.0  1
 PG2  Var_02    C15   C14  C13  C12   179.56   0.0  2
 PG2  Var_03    C8    C7   C6   C5    105.65  30.0  3
 PG2  Var_04    C7    C6   C5   C4      1.42   0.0  2
 PG2  Var_05    C4    C3   C2   C1   -179.80  30.0  3
 PG2  Var_06    C5    C4   C3   C2    179.85  30.0  3
 PG2  Var_07    O1    C1   C2   C3   -179.00  30.0  2
 PG2  Var_08    C6    C5   C4   C3    115.90  30.0  3
 PG2  Var_09    C18   C17  C16  C15  -175.40  30.0  3
 PG2  Var_10    C19   C18  C17  C16  -179.50  30.0  3
 PG2  Var_11    C20   C19  C18  C17  -179.04  30.0  3
 PG2  Var_12    H201  C20  C19  C18  -179.45  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
 PG2  chir_01  C8   C7  C9   C12  negativ
 PG2  chir_02  C9   O3  C8   C10  positiv
 PG2  chir_03  C12  C8  C11  C13  positiv
 PG2  chir_04  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
 PG2  plan-1  C10  0.020
 PG2  plan-1  C11  0.020
 PG2  plan-1  C12  0.020
 PG2  plan-1  O4   0.020
 PG2  plan-2  C1   0.020
 PG2  plan-2  C2   0.020
 PG2  plan-2  O1   0.020
 PG2  plan-2  O2   0.020
 PG2  plan-2  HO1  0.020
 PG2  plan-3  C4   0.020
 PG2  plan-3  C5   0.020
 PG2  plan-3  C6   0.020
 PG2  plan-3  C7   0.020
 PG2  plan-3  H5   0.020
 PG2  plan-3  H6   0.020
 PG2  plan-4  C12  0.020
 PG2  plan-4  C13  0.020
 PG2  plan-4  C14  0.020
 PG2  plan-4  C15  0.020
 PG2  plan-4  H13  0.020
 PG2  plan-4  H14  0.020

