# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 08:06:04 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: (3R)-3-(2-carboxyethyl)-6-{(E)-[(2R)-2-hydroxy-2,3-dihydro-1H-inden-1-ylidene]methyl}-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1Cc2ccccc2\C1=C/c3ccc4OC[C@@H](CCC(O)=O)Oc4c3C(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
 5EY  5EY  '(3R)-3-(2-carboxyethyl)-6-{(E)-[(2R)-2-hydroxy-2,3-dihydro-1H-inden-1-ylidene]methyl}-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid'  ligand  49  29  .  2021-08-04  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5EY
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
 5EY  C3    C  CR16  0  -0.257  -3.4596  -1.9062   2.1998
 5EY  C2    C  CR16  0  -0.256  -4.8259  -1.8224   2.4538
 5EY  C4    C  CR16  0  -0.322  -2.8627  -1.0829   1.2557
 5EY  C12   C  CR16  0  -0.297  -1.3387  -1.3456  -1.7071
 5EY  C1    C  CR16  0  -0.321  -5.6151  -0.9064   1.7667
 5EY  C13   C  CR16  0  -0.349  -0.3165  -2.2781  -1.7396
 5EY  C5    C  CR56  0   0.122  -3.6521  -0.1710   0.5596
 5EY  C11   C  CR6   0   0.042  -1.1109  -0.0435  -1.2691
 5EY  C16   C  CR6   0  -0.199   0.1744   0.2991  -0.8421
 5EY  C6    C  CR56  0   0.058  -5.0221  -0.0841   0.8237
 5EY  C14   C  CR6   0   0.316   0.9604  -1.9334  -1.3231
 5EY  C15   C  CR6   0   0.354   1.2037  -0.6384  -0.8608
 5EY  C9    C  CR5   0   0.132  -3.3040   0.8254  -0.4612
 5EY  C10   C  C1    0  -0.383  -2.2255   0.9249  -1.2403
 5EY  C17   C  C     0   0.464   0.4559   1.6451  -0.2635
 5EY  C26   C  C     0   0.555   6.1844   0.9358   1.1828
 5EY  C7    C  CH2   0  -0.525  -5.6599   0.9559  -0.0518
 5EY  C22   C  CH2   0  -0.187   3.2587  -2.3428  -1.2723
 5EY  C8    C  CR15  0  -0.043  -4.4660   1.7970  -0.5311
 5EY  C21   C  CH1   0  -0.020   3.3432  -1.3087  -0.1683
 5EY  C24   C  CH2   0  -0.462   4.7271  -0.7053  -0.0550
 5EY  O19   O  OH1   0  -0.582   0.2602   2.6155  -1.1437
 5EY  O28   O  OH1   0  -0.596   6.2288   1.8525   2.1441
 5EY  O18   O  O     0  -0.416   0.8096   1.8282   0.8719
 5EY  O27   O  O     0  -0.444   7.1416   0.6370   0.5131
 5EY  O23   O  O2    0  -0.480   1.9413  -2.8614  -1.3729
 5EY  O20   O  O2    0  -0.476   2.4278  -0.2525  -0.4537
 5EY  O29   O  OH1   0  -0.663  -4.1680   2.8525   0.3599
 5EY  H3    H  HCR6  0   0.256  -2.8536  -2.6160   2.7476
 5EY  HA    H  HCR6  0   0.256  -5.2754  -2.4697   3.1961
 5EY  H4    H  HCR6  0   0.250  -1.7980  -1.1519   1.0788
 5EY  H1    H  HCR6  0   0.251  -6.6766  -0.8372   1.9716
 5EY  H13   H  HCR6  0   0.274  -0.5033  -3.2837  -2.0954
 5EY  H10   H  H     0   0.266  -2.1743   1.7577  -1.9344
 5EY  H71C  H  HCH2  0   0.261  -6.1479   0.4798  -0.9073
 5EY  H72C  H  HCH2  0   0.260  -6.4202   1.5515   0.4581
 5EY  H8    H  HCR5  0   0.227  -4.6192   2.1718  -1.5491
 5EY  H19   H  HOH1  0   0.487   0.3920   3.4803  -0.7244
 5EY  H251  H  HCH2  0   0.284   4.5344  -0.0966   2.0129
 5EY  H252  H  HCH2  0   0.290   4.1014   1.1524   0.8770
 5EY  H28   H  HOH1  0   0.480   7.1217   2.2231   2.2077
 5EY  H21   H  HCH1  0   0.257   3.0571  -1.7752   0.7837
 5EY  H29   H  HOH1  0   0.451  -4.9390   3.4278   0.4055
 5EY  H241  H  HCH2  0   0.256   5.4290  -1.5171   0.1480
 5EY  H242  H  HCH2  0   0.249   5.0136  -0.2714  -1.0164
 5EY  H22A  H  HCH2  0   0.241   3.5631  -1.9017  -2.2280
 5EY  H12   H  HCR6  0   0.260  -2.3307  -1.6316  -2.0300
 5EY  H22B  H  HCH2  0   0.264   3.9144  -3.1847  -1.0552
 5EY  C25   C  CH2   0  -0.585   4.8113   0.3389   1.0475

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
 5EY  C3   C2    aromatic  1.392  0.020  1.392
 5EY  C3   C4    aromatic  1.388  0.020  1.388
 5EY  C2   C1    aromatic  1.391  0.020  1.391
 5EY  C4   C5    aromatic  1.393  0.020  1.393
 5EY  C12  C13   aromatic  1.384  0.020  1.384
 5EY  C12  C11   aromatic  1.392  0.020  1.392
 5EY  C1   C6    aromatic  1.385  0.020  1.385
 5EY  C13  C14   aromatic  1.387  0.020  1.387
 5EY  C5   C6    aromatic  1.398  0.020  1.398
 5EY  C5   C9    single    1.468  0.020  1.468
 5EY  C11  C16   aromatic  1.397  0.020  1.397
 5EY  C11  C10   single    1.477  0.020  1.477
 5EY  C16  C15   aromatic  1.392  0.020  1.392
 5EY  C16  C17   single    1.492  0.020  1.492
 5EY  C6   C7    single    1.502  0.020  1.502
 5EY  C14  C15   aromatic  1.396  0.020  1.396
 5EY  C14  O23   single    1.351  0.020  1.351
 5EY  C15  O20   single    1.346  0.020  1.346
 5EY  C9   C10   double    1.334  0.020  1.334
 5EY  C9   C8    single    1.516  0.020  1.516
 5EY  C17  O19   single    1.325  0.020  1.325
 5EY  C17  O18   double    1.203  0.020  1.203
 5EY  C26  C25   single    1.503  0.020  1.503
 5EY  C26  O28   single    1.329  0.020  1.329
 5EY  C26  O27   double    1.206  0.020  1.206
 5EY  C7   C8    single    1.537  0.020  1.537
 5EY  C22  C21   single    1.515  0.020  1.515
 5EY  C22  O23   single    1.419  0.020  1.419
 5EY  C8   O29   single    1.413  0.020  1.413
 5EY  C21  C24   single    1.514  0.020  1.514
 5EY  C21  O20   single    1.427  0.020  1.427
 5EY  C25  C24   single    1.521  0.020  1.521
 5EY  C3   H3    single    0.930  0.020  1.080
 5EY  C2   HA    single    0.930  0.020  1.080
 5EY  C4   H4    single    0.930  0.020  1.080
 5EY  C1   H1    single    0.930  0.020  1.080
 5EY  C13  H13   single    0.930  0.020  1.080
 5EY  C10  H10   single    0.930  0.020  1.080
 5EY  C7   H71C  single    0.970  0.020  1.090
 5EY  C7   H72C  single    0.970  0.020  1.090
 5EY  C8   H8    single    0.970  0.020  1.090
 5EY  O19  H19   single    0.850  0.020  0.980
 5EY  C25  H251  single    0.970  0.020  1.090
 5EY  C25  H252  single    0.970  0.020  1.090
 5EY  O28  H28   single    0.850  0.020  0.980
 5EY  C21  H21   single    0.970  0.020  1.090
 5EY  O29  H29   single    0.850  0.020  0.980
 5EY  C24  H241  single    0.970  0.020  1.090
 5EY  C24  H242  single    0.970  0.020  1.090
 5EY  C22  H22A  single    0.970  0.020  1.090
 5EY  C12  H12   single    0.930  0.020  1.080
 5EY  C22  H22B  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
 5EY  H3    C3   C4    119.52  3.000
 5EY  H3    C3   C2    119.78  3.000
 5EY  C4    C3   C2    120.70  3.000
 5EY  HA    C2   C1    119.80  3.000
 5EY  HA    C2   C3    119.77  3.000
 5EY  C1    C2   C3    120.42  3.000
 5EY  H4    C4   C5    121.21  3.000
 5EY  H4    C4   C3    119.79  3.000
 5EY  C5    C4   C3    119.00  3.000
 5EY  H12   C12  C11   119.41  3.000
 5EY  H12   C12  C13   119.48  3.000
 5EY  C11   C12  C13   121.11  3.000
 5EY  H1    C1   C6    120.70  3.000
 5EY  H1    C1   C2    120.31  3.000
 5EY  C6    C1   C2    118.99  3.000
 5EY  H13   C13  C14   119.24  3.000
 5EY  H13   C13  C12   120.39  3.000
 5EY  C14   C13  C12   120.37  3.000
 5EY  C9    C5   C6    108.75  3.000
 5EY  C9    C5   C4    131.11  3.000
 5EY  C6    C5   C4    120.12  3.000
 5EY  C10   C11  C16   121.84  3.000
 5EY  C10   C11  C12   119.73  3.000
 5EY  C16   C11  C12   118.42  3.000
 5EY  C17   C16  C15   118.25  3.000
 5EY  C17   C16  C11   120.89  3.000
 5EY  C15   C16  C11   120.72  3.000
 5EY  C7    C6   C5    110.43  3.000
 5EY  C7    C6   C1    128.80  3.000
 5EY  C5    C6   C1    120.76  3.000
 5EY  O23   C14  C15   121.50  3.000
 5EY  O23   C14  C13   119.12  3.000
 5EY  C15   C14  C13   119.37  3.000
 5EY  O20   C15  C14   121.63  3.000
 5EY  O20   C15  C16   118.36  3.000
 5EY  C14   C15  C16   120.00  3.000
 5EY  C8    C9   C10   123.01  3.000
 5EY  C8    C9   C5    106.57  3.000
 5EY  C10   C9   C5    130.41  3.000
 5EY  H10   C10  C9    117.96  3.000
 5EY  H10   C10  C11   117.08  3.000
 5EY  C9    C10  C11   124.93  3.000
 5EY  O18   C17  O19   123.98  3.000
 5EY  O18   C17  C16   123.97  3.000
 5EY  O19   C17  C16   112.05  3.000
 5EY  O27   C26  O28   123.10  3.000
 5EY  O27   C26  C25   125.22  3.000
 5EY  O28   C26  C25   111.68  3.000
 5EY  H72C  C7   H71C  106.97  3.000
 5EY  H72C  C7   C8    112.83  3.000
 5EY  H71C  C7   C8    109.93  3.000
 5EY  H72C  C7   C6    113.65  3.000
 5EY  H71C  C7   C6    110.12  3.000
 5EY  C8    C7   C6    103.35  3.000
 5EY  H22B  C22  H22A  108.53  3.000
 5EY  H22B  C22  O23   106.89  3.000
 5EY  H22A  C22  O23   110.06  3.000
 5EY  H22B  C22  C21   110.42  3.000
 5EY  H22A  C22  C21   110.21  3.000
 5EY  O23   C22  C21   110.66  3.000
 5EY  H8    C8   O29   111.09  3.000
 5EY  H8    C8   C7    111.61  3.000
 5EY  O29   C8   C7    112.08  3.000
 5EY  H8    C8   C9    111.67  3.000
 5EY  O29   C8   C9    106.74  3.000
 5EY  C7    C8   C9    103.31  3.000
 5EY  H21   C21  O20   108.72  3.000
 5EY  H21   C21  C24   110.04  3.000
 5EY  O20   C21  C24   107.84  3.000
 5EY  H21   C21  C22   109.10  3.000
 5EY  O20   C21  C22   108.89  3.000
 5EY  C24   C21  C22   112.18  3.000
 5EY  H242  C24  H241  106.87  3.000
 5EY  H242  C24  C25   110.52  3.000
 5EY  H241  C24  C25   109.88  3.000
 5EY  H242  C24  C21   109.39  3.000
 5EY  H241  C24  C21   107.76  3.000
 5EY  C25   C24  C21   112.24  3.000
 5EY  H19   O19  C17   110.23  3.000
 5EY  H28   O28  C26   110.00  3.000
 5EY  C22   O23  C14   114.85  3.000
 5EY  C21   O20  C15   115.57  3.000
 5EY  H29   O29  C8    107.90  3.000
 5EY  H252  C25  H251  105.63  3.000
 5EY  H252  C25  C24   111.21  3.000
 5EY  H251  C25  C24   110.62  3.000
 5EY  H252  C25  C26   108.17  3.000
 5EY  H251  C25  C26   108.04  3.000
 5EY  C24   C25  C26   112.85  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
 5EY  CONST_01  C6   C1   C2   C3      0.00   0.0  0
 5EY  CONST_02  C6   C5   C4   C3      0.00   0.0  0
 5EY  CONST_03  C5   C4   C3   C2      0.00   0.0  0
 5EY  CONST_04  C5   C6   C1   C2      0.00   0.0  0
 5EY  CONST_05  C1   C2   C3   C4      0.00   0.0  0
 5EY  CONST_06  C1   C6   C5   C4      0.00   0.0  0
 5EY  CONST_07  C15  C14  C13  C12     0.00   0.0  0
 5EY  CONST_08  C15  C16  C11  C12     0.00   0.0  0
 5EY  CONST_09  C16  C11  C12  C13     0.00   0.0  0
 5EY  CONST_10  C16  C15  C14  C13     0.00   0.0  0
 5EY  CONST_11  C14  C13  C12  C11     0.00   0.0  0
 5EY  CONST_12  C14  C15  C16  C11     0.00   0.0  0
 5EY  CONST_13  C17  C16  C11  C12   180.00   0.0  0
 5EY  CONST_14  C10  C11  C12  C13   180.00   0.0  0
 5EY  CONST_15  C17  C16  C15  C14   180.00   0.0  0
 5EY  CONST_16  C10  C11  C16  C15   180.00   0.0  0
 5EY  CONST_17  O20  C15  C16  C17     0.00   0.0  0
 5EY  CONST_18  H1   C1   C2   C3    180.00   0.0  0
 5EY  CONST_19  H4   C4   C3   C2    180.00   0.0  0
 5EY  CONST_20  HA   C2   C3   C4    180.00   0.0  0
 5EY  CONST_21  H3   C3   C2   C1    180.00   0.0  0
 5EY  CONST_22  H13  C13  C12  C11   180.00   0.0  0
 5EY  CONST_23  H12  C12  C11  C16   180.00   0.0  0
 5EY  CONST_24  H19  O19  C17  C16   180.00   0.0  0
 5EY  CONST_25  H28  O28  C26  C25   180.00   0.0  0
 5EY  Var_01    C8   C9   C5   C4   -162.71  30.0  1
 5EY  Var_02    C8   C7   C6   C1    163.04  30.0  1
 5EY  Var_03    C21  C22  O23  C14    44.71  30.0  1
 5EY  Var_04    C9   C10  C11  C12    64.89  30.0  2
 5EY  Var_05    C11  C10  C9   C5      2.58  30.0  2
 5EY  Var_06    O19  C17  C16  C11   -63.73  30.0  2
 5EY  Var_07    C21  C24  C25  C26   179.32  30.0  3
 5EY  Var_08    O28  C26  C25  C24   179.46  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
 5EY  chir_01  C8   C9   C7   O29  negativ
 5EY  chir_02  C21  C22  C24  O20  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
 5EY  plan-1  C3   0.020
 5EY  plan-1  C2   0.020
 5EY  plan-1  C4   0.020
 5EY  plan-1  C1   0.020
 5EY  plan-1  C5   0.020
 5EY  plan-1  C6   0.020
 5EY  plan-1  C9   0.020
 5EY  plan-1  C7   0.020
 5EY  plan-1  H3   0.020
 5EY  plan-1  HA   0.020
 5EY  plan-1  H4   0.020
 5EY  plan-1  H1   0.020
 5EY  plan-2  C12  0.020
 5EY  plan-2  C13  0.020
 5EY  plan-2  C11  0.020
 5EY  plan-2  C16  0.020
 5EY  plan-2  C14  0.020
 5EY  plan-2  C15  0.020
 5EY  plan-2  C10  0.020
 5EY  plan-2  C17  0.020
 5EY  plan-2  O23  0.020
 5EY  plan-2  O20  0.020
 5EY  plan-2  H13  0.020
 5EY  plan-2  H12  0.020
 5EY  plan-3  C16  0.020
 5EY  plan-3  C17  0.020
 5EY  plan-3  O19  0.020
 5EY  plan-3  O18  0.020
 5EY  plan-3  H19  0.020
 5EY  plan-4  C26  0.020
 5EY  plan-4  O28  0.020
 5EY  plan-4  O27  0.020
 5EY  plan-4  H28  0.020
 5EY  plan-4  C25  0.020

