# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 21:39:35 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  47  29  .  2021-08-04  2022-09-22
;
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  -4.1616  -2.2644   1.9896
 5EY  C2    C  CR16   0  -0.260  -5.5421  -2.0879   2.0279
 5EY  C4    C  CR16   0  -0.332  -3.3566  -1.4019   1.2580
 5EY  C12   C  CR16   0  -0.319  -1.3045  -1.4394  -1.2273
 5EY  C1    C  CR16   0  -0.321  -6.1344  -1.0344   1.3397
 5EY  C13   C  CR16   0  -0.367  -0.2684  -2.3481  -1.3344
 5EY  C5    C  CR56   0   0.114  -3.9461  -0.3522   0.5585
 5EY  C11   C  CR6    0   0.033  -1.0621  -0.1100  -0.8747
 5EY  C16   C  CR6    0  -0.196   0.2531   0.3041  -0.6458
 5EY  C6    C  CR56   0   0.054  -5.3322  -0.1704   0.6136
 5EY  C14   C  CR66   0   0.305   1.0384  -1.9415  -1.0904
 5EY  C15   C  CR66   0   0.313   1.2920  -0.6128  -0.7491
 5EY  C9    C  CR5    0   0.111  -3.3552   0.7359  -0.2320
 5EY  C10   C  C1     0  -0.358  -2.1519   0.8720  -0.8008
 5EY  C17   C  C      0   0.349   0.5728   1.7468  -0.2771
 5EY  C26   C  C      0   0.416   6.5231   1.1170   0.7732
 5EY  C7    C  CH2    0  -0.523  -5.7319   1.0288  -0.1969
 5EY  C22   C  C      0  -0.183   3.3412  -2.3061  -1.2488
 5EY  C8    C  CR15   0  -0.046  -4.4176   1.8148  -0.3232
 5EY  C21   C  CR16   0  -0.014   3.5057  -1.1935  -0.2325
 5EY  C24   C  CH2    0  -0.446   4.8914  -0.5827  -0.2808
 5EY  O19   O  OC    -1  -0.602   0.7950   2.5099  -1.2343
 5EY  O28   O  OC    -1  -0.631   6.7263   1.9907   1.6423
 5EY  O18   O  O      0  -0.586   0.5599   2.0191   0.9331
 5EY  O27   O  O      0  -0.608   7.3490   0.6993  -0.0620
 5EY  O23   O  O      0  -0.485   2.0330  -2.8533  -1.2004
 5EY  O20   O  O      0  -0.479   2.5525  -0.1726  -0.5093
 5EY  O29   O  OH1    0  -0.664  -4.2166   2.6852   0.7735
 5EY  H3    H  HCR6   0   0.254  -3.7090  -3.0802   2.5385
 5EY  HA    H  HCR6   0   0.254  -6.1557  -2.7691   2.6033
 5EY  H4    H  HCR6   0   0.254  -2.2850  -1.5478   1.2448
 5EY  H1    H  HCR6   0   0.248  -7.2072  -0.8887   1.3802
 5EY  H13   H  HCR6   0   0.259  -0.4617  -3.3754  -1.6172
 5EY  H10   H  H      0   0.245  -1.9487   1.8259  -1.2814
 5EY  H71C  H  HCH2   0   0.258  -6.0765   0.7183  -1.1880
 5EY  H72C  H  HCH2   0   0.257  -6.5372   1.6136   0.2529
 5EY  H8    H  HCR5   0   0.223  -4.3628   2.3607  -1.2717
 5EY  H251  H  HCH2   0   0.221   4.8828   0.1292   1.7502
 5EY  H252  H  HCH2   0   0.235   4.3922   1.3290   0.5914
 5EY  H21   H  HCR6   0   0.234   3.3119  -1.5975   0.7719
 5EY  H29   H  HOH1   0   0.449  -4.9270   3.3353   0.7699
 5EY  H241  H  HCH2   0   0.227   5.6119  -1.3874  -0.1129
 5EY  H242  H  HCH2   0   0.222   5.0839  -0.2066  -1.2896
 5EY  H22A  H  H      0   0.230   3.5548  -1.9276  -2.2556
 5EY  H12   H  HCR6   0   0.249  -2.3147  -1.7635  -1.4411
 5EY  H22B  H  H      0   0.253   4.0322  -3.1210  -1.0360
 5EY  C25   C  CH2    0  -0.589   5.1066   0.5152   0.7491

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  1.392  0.020  1.392
 5EY  C12  C13   aromatic  1.382  0.020  1.382
 5EY  C12  C11   aromatic  1.397  0.020  1.397
 5EY  C1   C6    aromatic  1.385  0.020  1.385
 5EY  C13  C14   aromatic  1.390  0.020  1.390
 5EY  C5   C6    aromatic  1.399  0.020  1.399
 5EY  C5   C9    single    1.469  0.020  1.469
 5EY  C11  C16   aromatic  1.398  0.020  1.398
 5EY  C11  C10   single    1.469  0.020  1.469
 5EY  C16  C15   aromatic  1.389  0.020  1.389
 5EY  C16  C17   single    1.523  0.020  1.523
 5EY  C6   C7    single    1.502  0.020  1.502
 5EY  C14  C15   aromatic  1.395  0.020  1.395
 5EY  C14  O23   single    1.354  0.020  1.354
 5EY  C15  O20   single    1.357  0.020  1.357
 5EY  C9   C10   double    1.338  0.020  1.338
 5EY  C9   C8    single    1.517  0.020  1.517
 5EY  C17  O19   deloc     1.244  0.020  1.244
 5EY  C17  O18   deloc     1.241  0.020  1.241
 5EY  C26  C25   single    1.539  0.020  1.539
 5EY  C26  O28   deloc     1.249  0.020  1.249
 5EY  C26  O27   deloc     1.247  0.020  1.247
 5EY  C7   C8    single    1.537  0.020  1.537
 5EY  C22  C21   single    1.516  0.020  1.516
 5EY  C22  O23   single    1.419  0.020  1.419
 5EY  C8   O29   single    1.415  0.020  1.415
 5EY  C21  C24   single    1.515  0.020  1.515
 5EY  C21  O20   single    1.424  0.020  1.424
 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  C25  H251  single    0.970  0.020  1.090
 5EY  C25  H252  single    0.970  0.020  1.090
 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    119.54  3.000
 5EY  H3    C3   C2    119.75  3.000
 5EY  C4    C3   C2    120.71  3.000
 5EY  HA    C2   C1    119.89  3.000
 5EY  HA    C2   C3    119.80  3.000
 5EY  C1    C2   C3    120.31  3.000
 5EY  H4    C4   C5    121.01  3.000
 5EY  H4    C4   C3    119.81  3.000
 5EY  C5    C4   C3    119.18  3.000
 5EY  H12   C12  C11   119.79  3.000
 5EY  H12   C12  C13   119.18  3.000
 5EY  C11   C12  C13   121.02  3.000
 5EY  H1    C1   C6    120.62  3.000
 5EY  H1    C1   C2    120.33  3.000
 5EY  C6    C1   C2    119.04  3.000
 5EY  H13   C13  C14   119.41  3.000
 5EY  H13   C13  C12   120.67  3.000
 5EY  C14   C13  C12   119.92  3.000
 5EY  C9    C5   C6    108.88  3.000
 5EY  C9    C5   C4    131.18  3.000
 5EY  C6    C5   C4    119.84  3.000
 5EY  C10   C11  C16   119.46  3.000
 5EY  C10   C11  C12   121.36  3.000
 5EY  C16   C11  C12   119.12  3.000
 5EY  C17   C16  C15   119.09  3.000
 5EY  C17   C16  C11   121.18  3.000
 5EY  C15   C16  C11   119.73  3.000
 5EY  C7    C6   C5    110.25  3.000
 5EY  C7    C6   C1    128.84  3.000
 5EY  C5    C6   C1    120.90  3.000
 5EY  O23   C14  C15   121.86  3.000
 5EY  O23   C14  C13   118.64  3.000
 5EY  C15   C14  C13   119.49  3.000
 5EY  O20   C15  C14   121.41  3.000
 5EY  O20   C15  C16   117.87  3.000
 5EY  C14   C15  C16   120.72  3.000
 5EY  C8    C9   C10   122.14  3.000
 5EY  C8    C9   C5    106.11  3.000
 5EY  C10   C9   C5    131.75  3.000
 5EY  H10   C10  C9    116.44  3.000
 5EY  H10   C10  C11   115.19  3.000
 5EY  C9    C10  C11   128.37  3.000
 5EY  O18   C17  O19   128.16  3.000
 5EY  O18   C17  C16   116.22  3.000
 5EY  O19   C17  C16   115.61  3.000
 5EY  O27   C26  O28   126.35  3.000
 5EY  O27   C26  C25   117.91  3.000
 5EY  O28   C26  C25   115.74  3.000
 5EY  H72C  C7   H71C  107.02  3.000
 5EY  H72C  C7   C8    113.00  3.000
 5EY  H71C  C7   C8    109.88  3.000
 5EY  H72C  C7   C6    113.67  3.000
 5EY  H71C  C7   C6    110.25  3.000
 5EY  C8    C7   C6    103.02  3.000
 5EY  H22B  C22  H22A  108.30  3.000
 5EY  H22B  C22  O23   106.83  3.000
 5EY  H22A  C22  O23   110.12  3.000
 5EY  H22B  C22  C21   110.44  3.000
 5EY  H22A  C22  C21   109.94  3.000
 5EY  O23   C22  C21   111.12  3.000
 5EY  H8    C8   O29   110.94  3.000
 5EY  H8    C8   C7    111.64  3.000
 5EY  O29   C8   C7    111.88  3.000
 5EY  H8    C8   C9    111.80  3.000
 5EY  O29   C8   C9    106.95  3.000
 5EY  C7    C8   C9    103.32  3.000
 5EY  H21   C21  O20   108.84  3.000
 5EY  H21   C21  C24   109.78  3.000
 5EY  O20   C21  C24   108.48  3.000
 5EY  H21   C21  C22   108.88  3.000
 5EY  O20   C21  C22   108.86  3.000
 5EY  C24   C21  C22   111.95  3.000
 5EY  H242  C24  H241  106.19  3.000
 5EY  H242  C24  C25   110.58  3.000
 5EY  H241  C24  C25   109.53  3.000
 5EY  H242  C24  C21   109.21  3.000
 5EY  H241  C24  C21   107.53  3.000
 5EY  C25   C24  C21   113.51  3.000
 5EY  C22   O23  C14   114.86  3.000
 5EY  C21   O20  C15   115.07  3.000
 5EY  H29   O29  C8    107.92  3.000
 5EY  H252  C25  H251  105.08  3.000
 5EY  H252  C25  C24   110.31  3.000
 5EY  H251  C25  C24   109.60  3.000
 5EY  H252  C25  C26   108.19  3.000
 5EY  H251  C25  C26   108.13  3.000
 5EY  C24   C25  C26   115.04  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  Var_01    C8   C9   C5   C4   -160.18  30.0  1
 5EY  Var_02    C8   C7   C6   C1    160.78  30.0  1
 5EY  Var_03    C21  C22  O23  C14    42.85  30.0  1
 5EY  Var_04    C9   C10  C11  C12    45.58  30.0  2
 5EY  Var_05    C11  C10  C9   C5      4.68  30.0  2
 5EY  Var_06    O19  C17  C16  C11   -90.00  30.0  2
 5EY  Var_07    C21  C24  C25  C26   177.38  30.0  3
 5EY  Var_08    O28  C26  C25  C24  -177.85  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-4  C26  0.020
 5EY  plan-4  O28  0.020
 5EY  plan-4  O27  0.020
 5EY  plan-4  C25  0.020

