# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 02:32:22 2021
#   Inital geometry file: a 107 line input string
#   Ligand name: (3R,4S,5R)-5-[(1R)-1-carboxy-2,2-difluoro-1-(phosphonooxy)ethoxy]-4-hydroxy-3-(phosphonooxy)cyclohex-1-ene-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1[C@@H](CC(=C[C@H]1O[P](O)(O)=O)C(O)=O)O[C@](O[P](O)(O)=O)(C(F)F)C(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
 GG9  GG9  '(3R,4S,5R)-5-[(1R)-1-carboxy-2,2-difluoro-1-(phosphonooxy)ethoxy]-4-hydroxy-3-(phosphonooxy)cyclohex-1-ene-1-carboxylic acid'  ligand  42  28  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_GG9
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
 GG9  C1    C  C     0  -0.073  56.6271  11.8042  28.0505
 GG9  C2    C  C1    0  -0.188  55.5262  11.1220  28.3616
 GG9  C3    C  CH1   0  -0.106  55.5447   9.9112  29.2347
 GG9  C4    C  CH1   0   0.031  56.8621   9.7448  29.9895
 GG9  C5    C  CH1   0  -0.008  58.0412   9.9850  29.0475
 GG9  C6    C  CH2   0  -0.518  57.9954  11.4176  28.5295
 GG9  C7    C  C     0   0.538  56.4637  13.0202  27.2024
 GG9  O1    O  O2    0  -0.598  55.3691   8.7463  28.4027
 GG9  O2    O  OH1   0  -0.657  56.9115   8.5208  30.6657
 GG9  O3    O  O2    0  -0.503  59.2597   9.8415  29.7847
 GG9  O4    O  O     0  -0.433  55.4140  13.3915  26.7365
 GG9  O5    O  OH1   0  -0.587  57.6082  13.6609  27.0202
 GG9  P1    P  P     0   1.468  53.9769   7.9742  28.2383
 GG9  O6    O  OH1   0  -0.740  52.9997   9.1797  27.8861
 GG9  O7    O  OH1   0  -0.743  53.4973   7.5704  29.7077
 GG9  O8    O  O     0  -0.690  54.1050   6.8674  27.2753
 GG9  C8    C  CT    0   0.339  60.1703   8.8543  29.4910
 GG9  C9    C  CH1   0   0.528  59.6818   7.4274  29.8255
 GG9  C10   C  C     0   0.519  61.3790   9.1512  30.4059
 GG9  O9    O  O     0  -0.410  62.4790   9.3771  29.9841
 GG9  O10   O  OH1   0  -0.566  61.0271   9.1115  31.6680
 GG9  O11   O  O     0  -0.679  62.6965   9.2070  26.7985
 GG9  O12   O  OH1   0  -0.735  61.4942  11.2185  28.0046
 GG9  O13   O  OH1   0  -0.727  60.3965  10.2356  26.1207
 GG9  O14   O  O2    0  -0.623  60.5593   8.8032  28.1599
 GG9  F1    F  F     0  -0.328  58.8200   6.9851  28.8805
 GG9  F2    F  F     0  -0.331  60.7616   6.6043  29.7950
 GG9  H2    H  H     0   0.285  54.5625  11.4397  27.9845
 GG9  H3    H  HCH1  0   0.292  54.7366   9.9777  29.9700
 GG9  H4    H  HCH1  0   0.271  56.8868  10.5225  30.7609
 GG9  H5    H  HCH1  0   0.265  58.0059   9.2913  28.2017
 GG9  H61   H  HCH2  0   0.279  58.7203  11.5385  27.7264
 GG9  H62   H  HCH2  0   0.275  58.3047  12.0951  29.3325
 GG9  HO2   H  HOH1  0   0.445  56.6935   7.8128  30.0494
 GG9  HO5   H  HOH1  0   0.489  57.4672  14.4436  26.4664
 GG9  HO6   H  HOH1  0   0.507  52.0660   8.9437  27.7970
 GG9  HO7   H  HOH1  0   0.502  53.7242   6.6668  29.9657
 GG9  H9    H  HCH1  0   0.228  59.2074   7.3675  30.8031
 GG9  HO10  H  HOH1  0   0.503  61.7851   9.2878  32.2486
 GG9  HO12  H  HOH1  0   0.505  62.2893  11.3513  28.5378
 GG9  HO13  H  HOH1  0   0.505  60.2370   9.5578  25.4500
 GG9  P2    P  P     0   1.468  61.4385   9.8219  27.2512

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
 GG9  C1   C7    single  1.492  0.020  1.492
 GG9  C1   C2    double  1.332  0.020  1.332
 GG9  C1   C6    single  1.500  0.020  1.500
 GG9  C2   C3    single  1.493  0.020  1.493
 GG9  C2   H2    single  0.930  0.020  1.080
 GG9  C3   O1    single  1.442  0.020  1.442
 GG9  C3   C4    single  1.527  0.020  1.527
 GG9  C3   H3    single  0.970  0.020  1.090
 GG9  C4   C5    single  1.528  0.020  1.528
 GG9  C4   O2    single  1.399  0.020  1.399
 GG9  C4   H4    single  0.970  0.020  1.090
 GG9  C5   C6    single  1.524  0.020  1.524
 GG9  C5   O3    single  1.431  0.020  1.431
 GG9  C5   H5    single  0.970  0.020  1.090
 GG9  C6   H61   single  0.970  0.020  1.090
 GG9  C6   H62   single  0.970  0.020  1.090
 GG9  C7   O4    double  1.207  0.020  1.207
 GG9  C7   O5    single  1.324  0.020  1.324
 GG9  O1   P1    single  1.600  0.020  1.600
 GG9  O2   HO2   single  0.850  0.020  0.980
 GG9  O3   C8    single  1.375  0.020  1.375
 GG9  O5   HO5   single  0.850  0.020  0.980
 GG9  P1   O8    double  1.473  0.020  1.473
 GG9  P1   O6    single  1.591  0.020  1.591
 GG9  P1   O7    single  1.598  0.020  1.598
 GG9  O6   HO6   single  0.850  0.020  0.980
 GG9  O7   HO7   single  0.850  0.020  0.980
 GG9  C8   O14   single  1.388  0.020  1.388
 GG9  C8   C9    single  1.545  0.020  1.545
 GG9  C8   C10   single  1.545  0.020  1.545
 GG9  C9   F1    single  1.353  0.020  1.353
 GG9  C9   F2    single  1.358  0.020  1.358
 GG9  C9   H9    single  0.970  0.020  1.090
 GG9  C10  O9    double  1.200  0.020  1.200
 GG9  C10  O10   single  1.311  0.020  1.311
 GG9  O10  HO10  single  0.850  0.020  0.980
 GG9  P2   O11   double  1.472  0.020  1.472
 GG9  P2   O13   single  1.592  0.020  1.592
 GG9  P2   O12   single  1.588  0.020  1.588
 GG9  P2   O14   single  1.624  0.020  1.624
 GG9  O12  HO12  single  0.850  0.020  0.980
 GG9  O13  HO13  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
 GG9  C7    C1   C6   119.44  3.000
 GG9  C6    C1   C2   123.18  3.000
 GG9  C7    C1   C2   117.37  3.000
 GG9  H2    C2   C3   116.92  3.000
 GG9  H2    C2   C1   120.28  3.000
 GG9  C3    C2   C1   122.80  3.000
 GG9  H3    C3   O1   110.28  3.000
 GG9  H3    C3   C4   108.15  3.000
 GG9  O1    C3   C4   107.58  3.000
 GG9  H3    C3   C2   109.54  3.000
 GG9  C4    C3   C2   112.84  3.000
 GG9  O1    C3   C2   108.43  3.000
 GG9  H4    C4   O2   106.26  3.000
 GG9  H4    C4   C5   107.76  3.000
 GG9  O2    C4   C5   114.09  3.000
 GG9  H4    C4   C3   106.86  3.000
 GG9  O2    C4   C3   111.38  3.000
 GG9  C5    C4   C3   110.10  3.000
 GG9  H5    C5   O3   111.22  3.000
 GG9  H5    C5   C6   109.40  3.000
 GG9  O3    C5   C6   107.15  3.000
 GG9  H5    C5   C4   110.60  3.000
 GG9  O3    C5   C4   108.88  3.000
 GG9  C6    C5   C4   109.52  3.000
 GG9  H62   C6   H61  106.51  3.000
 GG9  H62   C6   C5   108.89  3.000
 GG9  H61   C6   C5   109.58  3.000
 GG9  H62   C6   C1   109.40  3.000
 GG9  H61   C6   C1   110.07  3.000
 GG9  C5    C6   C1   112.22  3.000
 GG9  O5    C7   O4   123.35  3.000
 GG9  O5    C7   C1   112.21  3.000
 GG9  O4    C7   C1   124.44  3.000
 GG9  P1    O1   C3   123.70  3.000
 GG9  HO2   O2   C4   109.00  3.000
 GG9  C8    O3   C5   121.72  3.000
 GG9  HO5   O5   C7   110.10  3.000
 GG9  O8    P1   O7   115.95  3.000
 GG9  O7    P1   O6   102.16  3.000
 GG9  O8    P1   O6   118.56  3.000
 GG9  O7    P1   O1   106.77  3.000
 GG9  O6    P1   O1   101.04  3.000
 GG9  O8    P1   O1   110.74  3.000
 GG9  HO6   O6   P1   115.37  3.000
 GG9  HO7   O7   P1   114.28  3.000
 GG9  O14   C8   C10  110.85  3.000
 GG9  C10   C8   C9   107.26  3.000
 GG9  O14   C8   C9   105.21  3.000
 GG9  C10   C8   O3   104.70  3.000
 GG9  C9    C8   O3   114.05  3.000
 GG9  O14   C8   O3   114.65  3.000
 GG9  H9    C9   F2   109.48  3.000
 GG9  H9    C9   F1   109.37  3.000
 GG9  F2    C9   F1   107.01  3.000
 GG9  H9    C9   C8   112.53  3.000
 GG9  F2    C9   C8   107.67  3.000
 GG9  F1    C9   C8   110.61  3.000
 GG9  O10   C10  O9   126.18  3.000
 GG9  O10   C10  C8   110.76  3.000
 GG9  O9    C10  C8   123.06  3.000
 GG9  HO10  O10  C10  111.14  3.000
 GG9  HO12  O12  P2   114.30  3.000
 GG9  HO13  O13  P2   114.74  3.000
 GG9  P2    O14  C8   131.72  3.000
 GG9  O14   P2   O13  101.89  3.000
 GG9  O14   P2   O12  107.77  3.000
 GG9  O13   P2   O12   97.55  3.000
 GG9  O14   P2   O11  111.90  3.000
 GG9  O12   P2   O11  118.91  3.000
 GG9  O13   P2   O11  116.72  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
 GG9  CONST_01  HO5   O5   C7   C1  180.00   0.0  0
 GG9  CONST_02  HO10  O10  C10  C8  180.00   0.0  0
 GG9  Var_01    C5    C6   C1   C2   16.51  30.0  1
 GG9  Var_02    C6    C1   C2   C3    0.79  30.0  1
 GG9  Var_03    O4    C7   C1   C2   -3.26  30.0  2
 GG9  Var_04    O8    P1   O1   C3  177.33  30.0  3
 GG9  Var_05    O11   P2   O14  C8  115.84  30.0  1

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
 GG9  chir_01  C3  C2  O1   C4  negativ
 GG9  chir_02  C4  O2  C3   C5  positiv
 GG9  chir_03  C5  O3  C6   C4  positiv
 GG9  chir_04  C8  O3  C10  C9  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
 GG9  plan-1  C1    0.020
 GG9  plan-1  C7    0.020
 GG9  plan-1  O4    0.020
 GG9  plan-1  O5    0.020
 GG9  plan-1  HO5   0.020
 GG9  plan-2  C8    0.020
 GG9  plan-2  C10   0.020
 GG9  plan-2  O9    0.020
 GG9  plan-2  O10   0.020
 GG9  plan-2  HO10  0.020

