# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 01:13:21 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: (2R)-2-(2-carboxyethyl)-6-{(E)-[(2S)-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/c3ccc4O[C@H](CCC(O)=O)COc4c3C(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
 EE2  EE2  '(2R)-2-(2-carboxyethyl)-6-{(E)-[(2S)-2-hydroxy-2,3-dihydro-1H-inden-1-ylidene]methyl}-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid'  ligand  47  29  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EE2
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
 EE2  C1    C  CR16   0  -0.253  -3.0990  -3.3410   1.2823
 EE2  C2    C  CR16   0  -0.261  -4.4378  -3.5833   1.5743
 EE2  C3    C  CR16   0  -0.349  -2.7191  -2.2027   0.5843
 EE2  C4    C  CR16   0  -0.330  -0.5398  -0.6321  -1.3015
 EE2  C5    C  CR16   0  -0.312  -5.4129  -2.6742   1.1814
 EE2  C6    C  CR16   0  -0.369   0.8194  -0.8719  -1.2109
 EE2  C7    C  CR56   0   0.128  -3.6933  -1.2945   0.1719
 EE2  C8    C  CR6    0   0.027  -1.1171   0.4784  -0.6835
 EE2  C9    C  CR6    0  -0.186  -0.3042   1.3591   0.0349
 EE2  C10   C  CR56   0   0.042  -5.0354  -1.5346   0.4910
 EE2  C11   C  CR66   0   0.307   1.6295  -0.0030  -0.4902
 EE2  C12   C  CR66   0   0.310   1.0574   1.1034   0.1405
 EE2  C13   C  CR5    0   0.111  -3.5950  -0.0135  -0.5404
 EE2  C14   C  C1     0  -0.366  -2.5509   0.7666  -0.8427
 EE2  C15   C  C      0   0.345  -0.8900   2.5857   0.7211
 EE2  C16   C  C      0   0.416   7.2822  -0.8527  -0.5313
 EE2  C17   C  CH2    0  -0.522  -5.9064  -0.3956   0.0499
 EE2  C18   C  C      0  -0.186   3.0929   1.4767   1.2166
 EE2  C19   C  CR15   0  -0.046  -5.0085   0.4062  -0.9020
 EE2  C20   C  CR16   0  -0.013   3.7689   0.8239   0.0284
 EE2  C22   C  CH2    0  -0.445   5.1415   0.2817   0.3725
 EE2  O23   O  OC    -1  -0.598  -1.0942   3.5689  -0.0133
 EE2  O24   O  O      0  -0.607   7.7418  -0.6977   0.6168
 EE2  O25   O  O      0  -0.587  -1.1158   2.4790   1.9366
 EE2  O26   O  OC    -1  -0.631   7.8694  -1.3810  -1.4988
 EE2  O27   O  O      0  -0.479   1.8140   1.9720   0.8598
 EE2  O28   O  O      0  -0.487   2.9566  -0.2557  -0.4298
 EE2  O29   O  OH1    0  -0.667  -5.2016   0.0392  -2.2559
 EE2  H1    H  HCR6   0   0.254  -2.3432  -4.0493   1.5967
 EE2  H2    H  HCR6   0   0.254  -4.7195  -4.4792   2.1125
 EE2  H3    H  HCR6   0   0.263  -1.6742  -2.0381   0.3661
 EE2  H5    H  HCR6   0   0.249  -6.4545  -2.8535   1.4189
 EE2  H4    H  HCR6   0   0.254  -1.1605  -1.3052  -1.8796
 EE2  H6    H  HCR6   0   0.259   1.2659  -1.7263  -1.7040
 EE2  H14   H  H      0   0.250  -2.7850   1.7445  -1.2564
 EE2  H171  H  HCH2   0   0.257  -6.8357  -0.7178  -0.4244
 EE2  H172  H  HCH2   0   0.259  -6.1885   0.2124   0.9143
 EE2  H19   H  HCR5   0   0.223  -5.1473   1.4852  -0.7705
 EE2  H211  H  HCH2   0   0.223   5.8973   0.3588  -1.6419
 EE2  H212  H  HCH2   0   0.231   5.2716  -1.2010  -1.1916
 EE2  H181  H  H      0   0.230   3.0064   0.7591   2.0417
 EE2  H182  H  H      0   0.253   3.6770   2.3287   1.5628
 EE2  H29   H  HOH1   0   0.449  -6.1019   0.2782  -2.5010
 EE2  H221  H  HCH2   0   0.228   5.7351   1.1169   0.7523
 EE2  H222  H  HCH2   0   0.222   5.0525  -0.4320   1.1961
 EE2  H20   H  HCR6   0   0.237   3.8569   1.5656  -0.7781
 EE2  C21   C  CH2    0  -0.589   5.8522  -0.3554  -0.8116

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
 EE2  C1   C2    aromatic  1.392  0.020  1.392
 EE2  C1   C3    aromatic  1.388  0.020  1.388
 EE2  C2   C5    aromatic  1.390  0.020  1.390
 EE2  C3   C7    aromatic  1.394  0.020  1.394
 EE2  C4   C6    aromatic  1.383  0.020  1.383
 EE2  C4   C8    aromatic  1.396  0.020  1.396
 EE2  C5   C10   aromatic  1.385  0.020  1.385
 EE2  C6   C11   aromatic  1.389  0.020  1.389
 EE2  C7   C10   aromatic  1.400  0.020  1.400
 EE2  C7   C13   single    1.469  0.020  1.469
 EE2  C8   C9    aromatic  1.397  0.020  1.397
 EE2  C8   C14   single    1.471  0.020  1.471
 EE2  C9   C12   aromatic  1.389  0.020  1.389
 EE2  C9   C15   single    1.523  0.020  1.523
 EE2  C10  C17   single    1.500  0.020  1.500
 EE2  C11  C12   aromatic  1.396  0.020  1.396
 EE2  C11  O28   single    1.352  0.020  1.352
 EE2  C12  O27   single    1.358  0.020  1.358
 EE2  C13  C14   double    1.338  0.020  1.338
 EE2  C13  C19   single    1.518  0.020  1.518
 EE2  C15  O23   deloc     1.244  0.020  1.244
 EE2  C15  O25   deloc     1.241  0.020  1.241
 EE2  C16  C21   single    1.540  0.020  1.540
 EE2  C16  O24   deloc     1.246  0.020  1.246
 EE2  C16  O26   deloc     1.249  0.020  1.249
 EE2  C17  C19   single    1.535  0.020  1.535
 EE2  C18  C20   single    1.515  0.020  1.515
 EE2  C18  O27   single    1.417  0.020  1.417
 EE2  C19  O29   single    1.416  0.020  1.416
 EE2  C20  C22   single    1.515  0.020  1.515
 EE2  C20  O28   single    1.427  0.020  1.427
 EE2  C21  C22   single    1.521  0.020  1.521
 EE2  C1   H1    single    0.930  0.020  1.080
 EE2  C2   H2    single    0.930  0.020  1.080
 EE2  C3   H3    single    0.930  0.020  1.080
 EE2  C5   H5    single    0.930  0.020  1.080
 EE2  C4   H4    single    0.930  0.020  1.080
 EE2  C6   H6    single    0.930  0.020  1.080
 EE2  C14  H14   single    0.930  0.020  1.080
 EE2  C17  H171  single    0.970  0.020  1.090
 EE2  C17  H172  single    0.970  0.020  1.090
 EE2  C19  H19   single    0.970  0.020  1.090
 EE2  C21  H211  single    0.970  0.020  1.090
 EE2  C21  H212  single    0.970  0.020  1.090
 EE2  C18  H181  single    0.970  0.020  1.090
 EE2  C18  H182  single    0.970  0.020  1.090
 EE2  O29  H29   single    0.850  0.020  0.980
 EE2  C22  H221  single    0.970  0.020  1.090
 EE2  C22  H222  single    0.970  0.020  1.090
 EE2  C20  H20   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
 EE2  H1    C1   C3    119.44  3.000
 EE2  H1    C1   C2    119.79  3.000
 EE2  C3    C1   C2    120.77  3.000
 EE2  H2    C2   C5    119.96  3.000
 EE2  H2    C2   C1    119.93  3.000
 EE2  C5    C2   C1    120.11  3.000
 EE2  H3    C3   C7    121.12  3.000
 EE2  H3    C3   C1    119.43  3.000
 EE2  C7    C3   C1    119.45  3.000
 EE2  H4    C4   C8    119.59  3.000
 EE2  H4    C4   C6    119.38  3.000
 EE2  C8    C4   C6    121.02  3.000
 EE2  H5    C5   C10   120.50  3.000
 EE2  H5    C5   C2    120.29  3.000
 EE2  C10   C5   C2    119.21  3.000
 EE2  H6    C6   C11   119.29  3.000
 EE2  H6    C6   C4    120.81  3.000
 EE2  C11   C6   C4    119.90  3.000
 EE2  C13   C7   C10   108.91  3.000
 EE2  C13   C7   C3    131.66  3.000
 EE2  C10   C7   C3    119.38  3.000
 EE2  C14   C8   C9    119.94  3.000
 EE2  C14   C8   C4    120.74  3.000
 EE2  C9    C8   C4    119.24  3.000
 EE2  C15   C9   C12   119.41  3.000
 EE2  C15   C9   C8    121.04  3.000
 EE2  C12   C9   C8    119.55  3.000
 EE2  C17   C10  C7    111.06  3.000
 EE2  C17   C10  C5    127.81  3.000
 EE2  C7    C10  C5    121.06  3.000
 EE2  O28   C11  C12   122.01  3.000
 EE2  O28   C11  C6    118.58  3.000
 EE2  C12   C11  C6    119.40  3.000
 EE2  O27   C12  C11   121.19  3.000
 EE2  O27   C12  C9    117.94  3.000
 EE2  C11   C12  C9    120.87  3.000
 EE2  C19   C13  C14   120.77  3.000
 EE2  C19   C13  C7    107.11  3.000
 EE2  C14   C13  C7    132.08  3.000
 EE2  H14   C14  C13   116.25  3.000
 EE2  H14   C14  C8    115.29  3.000
 EE2  C13   C14  C8    128.45  3.000
 EE2  O25   C15  O23   128.05  3.000
 EE2  O25   C15  C9    116.25  3.000
 EE2  O23   C15  C9    115.71  3.000
 EE2  O26   C16  O24   126.36  3.000
 EE2  O26   C16  C21   115.61  3.000
 EE2  O24   C16  C21   118.03  3.000
 EE2  H172  C17  H171  106.73  3.000
 EE2  H172  C17  C19   110.53  3.000
 EE2  H171  C17  C19   112.49  3.000
 EE2  H172  C17  C10   109.85  3.000
 EE2  H171  C17  C10   113.44  3.000
 EE2  C19   C17  C10   103.85  3.000
 EE2  H182  C18  H181  108.35  3.000
 EE2  H182  C18  O27   106.89  3.000
 EE2  H181  C18  O27   110.29  3.000
 EE2  H182  C18  C20   110.30  3.000
 EE2  H181  C18  C20   110.08  3.000
 EE2  O27   C18  C20   110.85  3.000
 EE2  H19   C19  O29   110.65  3.000
 EE2  H19   C19  C17   111.47  3.000
 EE2  O29   C19  C17   112.20  3.000
 EE2  H19   C19  C13   111.20  3.000
 EE2  O29   C19  C13   106.44  3.000
 EE2  C17   C19  C13   104.63  3.000
 EE2  H20   C20  O28   108.70  3.000
 EE2  H20   C20  C22   109.61  3.000
 EE2  O28   C20  C22   108.53  3.000
 EE2  H20   C20  C18   108.69  3.000
 EE2  O28   C20  C18   108.90  3.000
 EE2  C22   C20  C18   112.35  3.000
 EE2  H222  C22  H221  106.34  3.000
 EE2  H222  C22  C21   110.55  3.000
 EE2  H221  C22  C21   109.69  3.000
 EE2  H222  C22  C20   109.32  3.000
 EE2  H221  C22  C20   107.30  3.000
 EE2  C21   C22  C20   113.35  3.000
 EE2  C18   O27  C12   114.37  3.000
 EE2  C20   O28  C11   115.57  3.000
 EE2  H29   O29  C19   107.84  3.000
 EE2  H212  C21  H211  105.21  3.000
 EE2  H212  C21  C22   110.26  3.000
 EE2  H211  C21  C22   109.64  3.000
 EE2  H212  C21  C16   107.85  3.000
 EE2  H211  C21  C16   108.06  3.000
 EE2  C22   C21  C16   115.31  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
 EE2  CONST_01  C10  C5   C2   C1      0.00   0.0  0
 EE2  CONST_02  C10  C7   C3   C1      0.00   0.0  0
 EE2  CONST_03  C7   C3   C1   C2      0.00   0.0  0
 EE2  CONST_04  C7   C10  C5   C2      0.00   0.0  0
 EE2  CONST_05  C5   C2   C1   C3      0.00   0.0  0
 EE2  CONST_06  C5   C10  C7   C3      0.00   0.0  0
 EE2  CONST_07  C12  C11  C6   C4      0.00   0.0  0
 EE2  CONST_08  C12  C9   C8   C4      0.00   0.0  0
 EE2  CONST_09  C9   C8   C4   C6      0.00   0.0  0
 EE2  CONST_10  C9   C12  C11  C6      0.00   0.0  0
 EE2  CONST_11  C11  C6   C4   C8      0.00   0.0  0
 EE2  CONST_12  C11  C12  C9   C8      0.00   0.0  0
 EE2  CONST_13  C15  C9   C8   C4    180.00   0.0  0
 EE2  CONST_14  C14  C8   C4   C6    180.00   0.0  0
 EE2  CONST_15  C15  C9   C12  C11   180.00   0.0  0
 EE2  CONST_16  C14  C8   C9   C12   180.00   0.0  0
 EE2  CONST_17  O27  C12  C9   C15     0.00   0.0  0
 EE2  CONST_18  H5   C5   C2   C1    180.00   0.0  0
 EE2  CONST_19  H3   C3   C1   C2    180.00   0.0  0
 EE2  CONST_20  H2   C2   C1   C3    180.00   0.0  0
 EE2  CONST_21  H1   C1   C2   C5    180.00   0.0  0
 EE2  CONST_22  H6   C6   C4   C8    180.00   0.0  0
 EE2  CONST_23  H4   C4   C8   C9    180.00   0.0  0
 EE2  Var_01    C19  C13  C7   C3    171.12  30.0  1
 EE2  Var_02    C19  C17  C10  C5   -168.59  30.0  1
 EE2  Var_03    C20  C18  O27  C12    46.20  30.0  1
 EE2  Var_04    C13  C14  C8   C4     57.78  30.0  2
 EE2  Var_05    C8   C14  C13  C7      8.43  30.0  2
 EE2  Var_06    O23  C15  C9   C8    -80.73  30.0  2
 EE2  Var_07    C20  C22  C21  C16   176.79  30.0  3
 EE2  Var_08    O24  C16  C21  C22    -0.14  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
 EE2  chir_01  C19  C13  C17  O29  positiv
 EE2  chir_02  C20  C18  C22  O28  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
 EE2  plan-1  C1   0.020
 EE2  plan-1  C2   0.020
 EE2  plan-1  C3   0.020
 EE2  plan-1  C5   0.020
 EE2  plan-1  C7   0.020
 EE2  plan-1  C10  0.020
 EE2  plan-1  C13  0.020
 EE2  plan-1  C17  0.020
 EE2  plan-1  H1   0.020
 EE2  plan-1  H2   0.020
 EE2  plan-1  H3   0.020
 EE2  plan-1  H5   0.020
 EE2  plan-2  C4   0.020
 EE2  plan-2  C6   0.020
 EE2  plan-2  C8   0.020
 EE2  plan-2  C9   0.020
 EE2  plan-2  C11  0.020
 EE2  plan-2  C12  0.020
 EE2  plan-2  C14  0.020
 EE2  plan-2  C15  0.020
 EE2  plan-2  O27  0.020
 EE2  plan-2  O28  0.020
 EE2  plan-2  H4   0.020
 EE2  plan-2  H6   0.020
 EE2  plan-3  C9   0.020
 EE2  plan-3  C15  0.020
 EE2  plan-3  O23  0.020
 EE2  plan-3  O25  0.020
 EE2  plan-4  C16  0.020
 EE2  plan-4  O24  0.020
 EE2  plan-4  O26  0.020
 EE2  plan-4  C21  0.020

