# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 18 12:10:07 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: (1R,4R,5R)-3-(3-benzoylphenyl)-1,4,5-trihydroxycyclohex-2-ene-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1C[C@@](O)(C=C([C@H]1O)c2cccc(c2)C(=O)c3ccccc3)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
 N87  N87  '(1R,4R,5R)-3-(3-benzoylphenyl)-1,4,5-trihydroxycyclohex-2-ene-1-carboxylic acid'  ligand  44  26  .  2022-07-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_N87
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
 N87  O1    O  O     0  -0.430  -3.3903   2.5816  -1.2968
 N87  C2    C  C     0   0.532  -3.8168   2.2401  -0.2229
 N87  O3    O  OH1   0  -0.581  -4.2932   3.0794   0.6794
 N87  C4    C  CT    0   0.066  -3.8048   0.7854   0.2690
 N87  O5    O  OH1   0  -0.653  -4.6698   0.5962   1.3618
 N87  C6    C  C1    0  -0.252  -2.3747   0.4869   0.6553
 N87  C7    C  C     0   0.015  -1.7110  -0.6027   0.2752
 N87  C8    C  CH1   0  -0.033  -2.3267  -1.6455  -0.6372
 N87  O9    O  OH1   0  -0.662  -1.9558  -2.9576  -0.2834
 N87  C10   C  CH1   0   0.053  -3.8467  -1.5667  -0.5950
 N87  O11   O  OH1   0  -0.673  -4.4320  -2.3806  -1.5816
 N87  C12   C  CH2   0  -0.491  -4.2746  -0.1349  -0.8548
 N87  C13   C  CR6   0   0.055  -0.2978  -0.7820   0.6836
 N87  C14   C  CR16  0  -0.313   0.6626   0.1069   0.2163
 N87  C15   C  CR6   0  -0.016   2.0040  -0.0308   0.5722
 N87  C16   C  C     0   0.359   2.9798   0.9816   0.0866
 N87  C17   C  CR6   0  -0.037   4.3937   0.5787  -0.1351
 N87  C18   C  CR16  0  -0.280   4.7257  -0.6919  -0.6037
 N87  C19   C  CR16  0  -0.241   6.0494  -1.0150  -0.8658
 N87  C20   C  CR16  0  -0.248   7.0502  -0.0797  -0.6417
 N87  C21   C  CR16  0  -0.244   6.7259   1.1884  -0.1729
 N87  C22   C  CR16  0  -0.269   5.4030   1.5219   0.0644
 N87  C23   C  CR16  0  -0.287   2.3823  -1.0592   1.4315
 N87  C24   C  CR16  0  -0.226   1.4249  -1.9336   1.9249
 N87  C25   C  CR16  0  -0.283   0.0975  -1.8073   1.5460
 N87  O26   O  O     0  -0.389   2.6262   2.1254  -0.1213
 N87  HO3   H  HOH1  0   0.487  -4.2348   3.9887   0.3474
 N87  HO5   H  HOH1  0   0.454  -4.2837   0.9772   2.1583
 N87  H6    H  H     0   0.283  -1.8854   1.2033   1.3105
 N87  H8    H  HCH1  0   0.243  -2.0005  -1.4204  -1.6642
 N87  HO9   H  HOH1  0   0.464  -1.1061  -3.1666  -0.6829
 N87  H10   H  HCH1  0   0.217  -4.1753  -1.8724   0.4095
 N87  HO11  H  HOH1  0   0.449  -4.1563  -3.2892  -1.4210
 N87  H12   H  HCH2  0   0.272  -5.3621  -0.0693  -0.9401
 N87  H12A  H  HCH2  0   0.260  -3.8531   0.1968  -1.8058
 N87  H14   H  HCR6  0   0.261   0.3646   0.9093  -0.4472
 N87  H18   H  HCR6  0   0.271   3.9527  -1.4263  -0.7898
 N87  H19   H  HCR6  0   0.266   6.2991  -1.9977  -1.2429
 N87  H20   H  HCR6  0   0.267   8.0836  -0.3376  -0.8333
 N87  H21   H  HCR6  0   0.264   7.5058   1.9173   0.0033
 N87  H22   H  HCR6  0   0.265   5.1505   2.5115   0.4222
 N87  H23   H  HCR6  0   0.273   3.4137  -1.1659   1.7409
 N87  H24   H  HCR6  0   0.267   1.7150  -2.7183   2.6108
 N87  H25   H  HCR6  0   0.264  -0.6370  -2.4931   1.9447

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
 N87  C2   O1    double    1.205  0.020  1.205
 N87  C4   C2    single    1.536  0.020  1.536
 N87  C2   O3    single    1.321  0.020  1.321
 N87  O3   HO3   single    0.850  0.020  0.980
 N87  C12  C4    single    1.527  0.020  1.527
 N87  C6   C4    single    1.511  0.020  1.511
 N87  O5   C4    single    1.406  0.020  1.406
 N87  O5   HO5   single    0.850  0.020  0.980
 N87  C7   C6    double    1.331  0.020  1.331
 N87  C6   H6    single    0.930  0.020  1.080
 N87  C8   C7    single    1.516  0.020  1.516
 N87  C13  C7    single    1.482  0.020  1.482
 N87  O9   C8    single    1.409  0.020  1.409
 N87  C8   C10   single    1.523  0.020  1.523
 N87  C8   H8    single    0.970  0.020  1.090
 N87  O9   HO9   single    0.850  0.020  0.980
 N87  O11  C10   single    1.407  0.020  1.407
 N87  C10  C12   single    1.517  0.020  1.517
 N87  C10  H10   single    0.970  0.020  1.090
 N87  O11  HO11  single    0.850  0.020  0.980
 N87  C12  H12   single    0.970  0.020  1.090
 N87  C12  H12A  single    0.970  0.020  1.090
 N87  C14  C13   aromatic  1.390  0.020  1.390
 N87  C13  C25   aromatic  1.397  0.020  1.397
 N87  C15  C14   aromatic  1.395  0.020  1.395
 N87  C14  H14   single    0.930  0.020  1.080
 N87  C16  C15   single    1.488  0.020  1.488
 N87  C15  C23   aromatic  1.393  0.020  1.393
 N87  O26  C16   double    1.215  0.020  1.215
 N87  C16  C17   single    1.487  0.020  1.487
 N87  C18  C17   aromatic  1.394  0.020  1.394
 N87  C17  C22   aromatic  1.396  0.020  1.396
 N87  C18  C19   aromatic  1.388  0.020  1.388
 N87  C18  H18   single    0.930  0.020  1.080
 N87  C19  C20   aromatic  1.388  0.020  1.388
 N87  C19  H19   single    0.930  0.020  1.080
 N87  C20  C21   aromatic  1.390  0.020  1.390
 N87  C20  H20   single    0.930  0.020  1.080
 N87  C22  C21   aromatic  1.385  0.020  1.385
 N87  C21  H21   single    0.930  0.020  1.080
 N87  C22  H22   single    0.930  0.020  1.080
 N87  C23  C24   aromatic  1.387  0.020  1.387
 N87  C23  H23   single    0.930  0.020  1.080
 N87  C24  C25   aromatic  1.386  0.020  1.386
 N87  C24  H24   single    0.930  0.020  1.080
 N87  C25  H25   single    0.930  0.020  1.080

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
 N87  C4    C2   O3   112.69  3.000
 N87  O3    C2   O1   123.80  3.000
 N87  C4    C2   O1   123.45  3.000
 N87  HO3   O3   C2   109.89  3.000
 N87  C12   C4   C6   111.12  3.000
 N87  C6    C4   O5   110.91  3.000
 N87  C12   C4   O5   107.56  3.000
 N87  O5    C4   C2   111.81  3.000
 N87  C6    C4   C2   106.04  3.000
 N87  C12   C4   C2   109.44  3.000
 N87  HO5   O5   C4   110.03  3.000
 N87  H6    C6   C7   119.15  3.000
 N87  H6    C6   C4   116.73  3.000
 N87  C7    C6   C4   124.09  3.000
 N87  C13   C7   C8   118.03  3.000
 N87  C13   C7   C6   119.72  3.000
 N87  C8    C7   C6   122.16  3.000
 N87  H8    C8   C10  108.12  3.000
 N87  H8    C8   O9   110.29  3.000
 N87  C10   C8   O9   107.70  3.000
 N87  H8    C8   C7   107.49  3.000
 N87  C10   C8   C7   110.68  3.000
 N87  O9    C8   C7   112.49  3.000
 N87  HO9   O9   C8   109.31  3.000
 N87  H10   C10  C12  109.54  3.000
 N87  H10   C10  O11  110.81  3.000
 N87  C12   C10  O11  107.98  3.000
 N87  H10   C10  C8   108.00  3.000
 N87  C12   C10  C8   109.01  3.000
 N87  O11   C10  C8   111.47  3.000
 N87  HO11  O11  C10  108.05  3.000
 N87  H12A  C12  H12  107.34  3.000
 N87  H12A  C12  C10  109.09  3.000
 N87  H12   C12  C10  110.54  3.000
 N87  H12A  C12  C4   109.83  3.000
 N87  H12   C12  C4   109.12  3.000
 N87  C10   C12  C4   110.86  3.000
 N87  C25   C13  C14  118.79  3.000
 N87  C25   C13  C7   121.92  3.000
 N87  C14   C13  C7   119.28  3.000
 N87  H14   C14  C15  119.61  3.000
 N87  H14   C14  C13  119.33  3.000
 N87  C15   C14  C13  121.06  3.000
 N87  C23   C15  C16  121.73  3.000
 N87  C23   C15  C14  119.45  3.000
 N87  C16   C15  C14  118.72  3.000
 N87  O26   C16  C17  120.42  3.000
 N87  C17   C16  C15  119.21  3.000
 N87  O26   C16  C15  120.37  3.000
 N87  C22   C17  C18  119.45  3.000
 N87  C22   C17  C16  118.90  3.000
 N87  C18   C17  C16  121.56  3.000
 N87  H18   C18  C19  119.40  3.000
 N87  H18   C18  C17  120.40  3.000
 N87  C19   C18  C17  120.19  3.000
 N87  H19   C19  C20  120.13  3.000
 N87  H19   C19  C18  119.84  3.000
 N87  C20   C19  C18  120.03  3.000
 N87  H20   C20  C21  119.99  3.000
 N87  H20   C20  C19  119.96  3.000
 N87  C21   C20  C19  120.05  3.000
 N87  H21   C21  C22  119.91  3.000
 N87  H21   C21  C20  120.07  3.000
 N87  C22   C21  C20  120.02  3.000
 N87  H22   C22  C21  119.98  3.000
 N87  H22   C22  C17  119.77  3.000
 N87  C21   C22  C17  120.24  3.000
 N87  H23   C23  C24  119.60  3.000
 N87  H23   C23  C15  120.54  3.000
 N87  C24   C23  C15  119.84  3.000
 N87  H24   C24  C25  119.74  3.000
 N87  H24   C24  C23  119.85  3.000
 N87  C25   C24  C23  120.41  3.000
 N87  H25   C25  C24  119.48  3.000
 N87  H25   C25  C13  120.07  3.000
 N87  C24   C25  C13  120.44  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
 N87  CONST_01  C23  C15  C14  C13     0.00   0.0  0
 N87  CONST_02  C23  C24  C25  C13     0.00   0.0  0
 N87  CONST_03  C24  C25  C13  C14     0.00   0.0  0
 N87  CONST_04  C24  C23  C15  C14     0.00   0.0  0
 N87  CONST_05  C25  C13  C14  C15     0.00   0.0  0
 N87  CONST_06  C25  C24  C23  C15     0.00   0.0  0
 N87  CONST_07  C20  C19  C18  C17     0.00   0.0  0
 N87  CONST_08  C20  C21  C22  C17     0.00   0.0  0
 N87  CONST_09  C21  C22  C17  C18     0.00   0.0  0
 N87  CONST_10  C21  C20  C19  C18     0.00   0.0  0
 N87  CONST_11  C22  C17  C18  C19     0.00   0.0  0
 N87  CONST_12  C22  C21  C20  C19     0.00   0.0  0
 N87  CONST_13  C15  C14  C13  C7    180.00   0.0  0
 N87  CONST_14  C24  C25  C13  C7    180.00   0.0  0
 N87  CONST_15  C16  C15  C14  C13   180.00   0.0  0
 N87  CONST_16  C24  C23  C15  C16   180.00   0.0  0
 N87  CONST_17  C19  C18  C17  C16   180.00   0.0  0
 N87  CONST_18  C21  C22  C17  C16   180.00   0.0  0
 N87  CONST_19  H14  C14  C13  C7      0.00   0.0  0
 N87  CONST_20  H25  C25  C13  C7      0.00   0.0  0
 N87  CONST_21  H24  C24  C25  C13   180.00   0.0  0
 N87  CONST_22  H23  C23  C15  C14   180.00   0.0  0
 N87  CONST_23  H19  C19  C18  C17   180.00   0.0  0
 N87  CONST_24  H21  C21  C22  C17   180.00   0.0  0
 N87  CONST_25  H22  C22  C17  C18   180.00   0.0  0
 N87  CONST_26  H20  C20  C19  C18   180.00   0.0  0
 N87  CONST_27  H18  C18  C19  C20   180.00   0.0  0
 N87  CONST_28  HO3  O3   C2   C4    180.00   0.0  0
 N87  Var_01    C8   C7   C6   C4      2.10  30.0  1
 N87  Var_02    C14  C13  C7   C6    -64.55  30.0  2
 N87  Var_03    C17  C16  C15  C14  -150.91  30.0  3
 N87  Var_04    C18  C17  C16  C15    34.93  30.0  2

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
 N87  chir_01  C4   C12  C6   O5   positiv
 N87  chir_02  C8   O9   C10  C7   negativ
 N87  chir_03  C10  O11  C8   C12  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
 N87  plan-1  C7   0.020
 N87  plan-1  C13  0.020
 N87  plan-1  C14  0.020
 N87  plan-1  C15  0.020
 N87  plan-1  C16  0.020
 N87  plan-1  C23  0.020
 N87  plan-1  C24  0.020
 N87  plan-1  C25  0.020
 N87  plan-1  H14  0.020
 N87  plan-1  H23  0.020
 N87  plan-1  H24  0.020
 N87  plan-1  H25  0.020
 N87  plan-2  C16  0.020
 N87  plan-2  C17  0.020
 N87  plan-2  C18  0.020
 N87  plan-2  C19  0.020
 N87  plan-2  C20  0.020
 N87  plan-2  C21  0.020
 N87  plan-2  C22  0.020
 N87  plan-2  H18  0.020
 N87  plan-2  H19  0.020
 N87  plan-2  H20  0.020
 N87  plan-2  H21  0.020
 N87  plan-2  H22  0.020
 N87  plan-3  O1   0.020
 N87  plan-3  C2   0.020
 N87  plan-3  O3   0.020
 N87  plan-3  C4   0.020
 N87  plan-3  HO3  0.020
 N87  plan-4  C15  0.020
 N87  plan-4  C16  0.020
 N87  plan-4  C17  0.020
 N87  plan-4  O26  0.020

