# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 19:57:13 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: (2S)-2-(2-carboxyethyl)-6-{(E)-[(2E)-2-(hydroxyimino)-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\N=C\1Cc2ccccc2C\1=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
 K5Q  K5Q  '(2S)-2-(2-carboxyethyl)-6-{(E)-[(2E)-2-(hydroxyimino)-2,3-dihydro-1H-inden-1-ylidene]methyl}-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid'  ligand  49  30  .  2022-07-25  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_K5Q
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
 K5Q  C1    C  CR16  0  -0.252  -2.3619  -3.4598   1.2421
 K5Q  C2    C  CR16  0  -0.256  -3.6346  -4.0139   1.3505
 K5Q  C3    C  CR16  0  -0.330  -2.1826  -2.1989   0.6936
 K5Q  C4    C  CR16  0  -0.314  -0.4132  -0.4573  -1.4158
 K5Q  C5    C  CR16  0  -0.307  -4.7466  -3.3013   0.9223
 K5Q  C6    C  CR16  0  -0.344   0.9592  -0.6326  -1.4277
 K5Q  C7    C  CR56  0   0.092  -3.2929  -1.4865   0.2438
 K5Q  C8    C  CR6   0   0.067  -1.0019   0.5561  -0.6605
 K5Q  C9    C  CR6   0  -0.192  -0.1663   1.4169   0.0522
 K5Q  C10   C  CR56  0   0.033  -4.5704  -2.0402   0.3780
 K5Q  C11   C  CR6   0   0.319   1.7821   0.2111  -0.6947
 K5Q  C12   C  CR6   0   0.361   1.2112   1.2491   0.0444
 K5Q  C13   C  CR5   0   0.133  -3.3977  -0.1368  -0.3302
 K5Q  C14   C  CR5   0   0.152  -4.8500   0.1200  -0.4829
 K5Q  C15   C  C1    0  -0.394  -2.4573   0.7601  -0.6624
 K5Q  C16   C  C     0   0.443  -0.7369   2.5125   0.8936
 K5Q  C17   C  C     0   0.555   7.3151  -0.8909  -0.3335
 K5Q  C18   C  CH2   0  -0.544  -5.6375  -1.1009  -0.0974
 K5Q  C19   C  CH2   0  -0.185   3.3450   2.0943   0.4530
 K5Q  C20   C  CH1   0  -0.023   3.8415   0.6681   0.3245
 K5Q  C22   C  CH2   0  -0.461   5.3161   0.6093  -0.0114
 K5Q  N23   N  N     0  -0.149  -5.2932   1.2346  -0.8948
 K5Q  O24   O  OH1   0  -0.576  -0.9697   3.6035   0.1833
 K5Q  O25   O  O     0  -0.444   8.0432   0.0589  -0.4804
 K5Q  O26   O  O     0  -0.412  -0.9634   2.4047   2.0698
 K5Q  O27   O  OH1   0  -0.596   7.7486  -2.1471  -0.3522
 K5Q  O28   O  O2    0  -0.477   1.9588   2.1107   0.7651
 K5Q  O29   O  O2    0  -0.483   3.1164   0.0126  -0.7149
 K5Q  O30   O  OH1   0  -0.545  -6.6532   1.2602  -0.9725
 K5Q  H1    H  HCR6  0   0.259  -1.5011  -4.0159   1.5899
 K5Q  H2    H  HCR6  0   0.260  -3.7590  -4.9999   1.7790
 K5Q  H3    H  HCR6  0   0.259  -1.1864  -1.7868   0.6278
 K5Q  H5    H  HCR6  0   0.256  -5.7390  -3.7229   1.0236
 K5Q  H4    H  HCR6  0   0.266  -1.0408  -1.1219  -1.9948
 K5Q  H6    H  HCR6  0   0.276   1.4061  -1.4279  -2.0109
 K5Q  H15   H  H     0   0.268  -2.8059   1.7349  -0.9928
 K5Q  H181  H  HCH2  0   0.288  -6.1888  -1.5005  -0.9542
 K5Q  H182  H  HCH2  0   0.286  -6.3785  -0.8871   0.6774
 K5Q  H24   H  HOH1  0   0.490  -1.3572   4.2950   0.7433
 K5Q  H211  H  HCH2  0   0.291   5.3420  -1.3592  -0.9279
 K5Q  H212  H  HCH2  0   0.282   5.5920  -1.3783   0.7973
 K5Q  H27   H  HOH1  0   0.480   8.7065  -2.1644  -0.4964
 K5Q  H191  H  HCH2  0   0.266   3.8566   2.6035   1.2679
 K5Q  H192  H  HCH2  0   0.245   3.5267   2.6482  -0.4744
 K5Q  H20   H  HCH1  0   0.257   3.6538   0.1426   1.2705
 K5Q  H221  H  HCH2  0   0.251   5.5033   1.1512  -0.9414
 K5Q  H222  H  HCH2  0   0.256   5.8542   1.1398   0.7771
 K5Q  H30   H  HOH1  0   0.479  -6.8600   2.1508  -1.2758
 K5Q  C21   C  CH2   0  -0.583   5.8299  -0.8185  -0.1122

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
 K5Q  C1   C2    aromatic  1.392  0.020  1.392
 K5Q  C1   C3    aromatic  1.387  0.020  1.387
 K5Q  C2   C5    aromatic  1.388  0.020  1.388
 K5Q  C3   C7    aromatic  1.394  0.020  1.394
 K5Q  C4   C6    aromatic  1.384  0.020  1.384
 K5Q  C4   C8    aromatic  1.394  0.020  1.394
 K5Q  C5   C10   aromatic  1.385  0.020  1.385
 K5Q  C6   C11   aromatic  1.388  0.020  1.388
 K5Q  C7   C10   aromatic  1.399  0.020  1.399
 K5Q  C7   C13   single    1.470  0.020  1.470
 K5Q  C8   C9    aromatic  1.395  0.020  1.395
 K5Q  C8   C15   single    1.470  0.020  1.470
 K5Q  C9   C12   aromatic  1.388  0.020  1.388
 K5Q  C9   C16   single    1.495  0.020  1.495
 K5Q  C10  C18   single    1.499  0.020  1.499
 K5Q  C11  C12   aromatic  1.396  0.020  1.396
 K5Q  C11  O29   single    1.349  0.020  1.349
 K5Q  C12  O28   single    1.349  0.020  1.349
 K5Q  C13  C14   single    1.483  0.020  1.483
 K5Q  C13  C15   double    1.341  0.020  1.341
 K5Q  C14  C18   single    1.503  0.020  1.503
 K5Q  C14  N23   double    1.268  0.020  1.268
 K5Q  C16  O24   single    1.323  0.020  1.323
 K5Q  C16  O26   double    1.203  0.020  1.203
 K5Q  C17  C21   single    1.503  0.020  1.503
 K5Q  C17  O25   double    1.206  0.020  1.206
 K5Q  C17  O27   single    1.329  0.020  1.329
 K5Q  C19  C20   single    1.516  0.020  1.516
 K5Q  C19  O28   single    1.421  0.020  1.421
 K5Q  C20  C22   single    1.513  0.020  1.513
 K5Q  C20  O29   single    1.427  0.020  1.427
 K5Q  C21  C22   single    1.521  0.020  1.521
 K5Q  N23  O30   single    1.362  0.020  1.362
 K5Q  C1   H1    single    0.930  0.020  1.080
 K5Q  C2   H2    single    0.930  0.020  1.080
 K5Q  C3   H3    single    0.930  0.020  1.080
 K5Q  C5   H5    single    0.930  0.020  1.080
 K5Q  C4   H4    single    0.930  0.020  1.080
 K5Q  C6   H6    single    0.930  0.020  1.080
 K5Q  C15  H15   single    0.930  0.020  1.080
 K5Q  C18  H181  single    0.970  0.020  1.090
 K5Q  C18  H182  single    0.970  0.020  1.090
 K5Q  O24  H24   single    0.850  0.020  0.980
 K5Q  C21  H211  single    0.970  0.020  1.090
 K5Q  C21  H212  single    0.970  0.020  1.090
 K5Q  O27  H27   single    0.850  0.020  0.980
 K5Q  C19  H191  single    0.970  0.020  1.090
 K5Q  C19  H192  single    0.970  0.020  1.090
 K5Q  C20  H20   single    0.970  0.020  1.090
 K5Q  C22  H221  single    0.970  0.020  1.090
 K5Q  C22  H222  single    0.970  0.020  1.090
 K5Q  O30  H30   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
 K5Q  H1    C1   C3    119.44  3.000
 K5Q  H1    C1   C2    119.83  3.000
 K5Q  C3    C1   C2    120.72  3.000
 K5Q  H2    C2   C5    119.84  3.000
 K5Q  H2    C2   C1    119.90  3.000
 K5Q  C5    C2   C1    120.25  3.000
 K5Q  H3    C3   C7    121.33  3.000
 K5Q  H3    C3   C1    119.36  3.000
 K5Q  C7    C3   C1    119.30  3.000
 K5Q  H4    C4   C8    119.43  3.000
 K5Q  H4    C4   C6    119.53  3.000
 K5Q  C8    C4   C6    121.03  3.000
 K5Q  H5    C5   C10   120.52  3.000
 K5Q  H5    C5   C2    120.35  3.000
 K5Q  C10   C5   C2    119.12  3.000
 K5Q  H6    C6   C11   119.10  3.000
 K5Q  H6    C6   C4    120.47  3.000
 K5Q  C11   C6   C4    120.44  3.000
 K5Q  C13   C7   C10   109.62  3.000
 K5Q  C13   C7   C3    130.69  3.000
 K5Q  C10   C7   C3    119.62  3.000
 K5Q  C15   C8   C9    120.54  3.000
 K5Q  C15   C8   C4    121.22  3.000
 K5Q  C9    C8   C4    118.18  3.000
 K5Q  C16   C9   C12   118.08  3.000
 K5Q  C16   C9   C8    120.74  3.000
 K5Q  C12   C9   C8    121.13  3.000
 K5Q  C18   C10  C7    111.81  3.000
 K5Q  C18   C10  C5    127.21  3.000
 K5Q  C7    C10  C5    120.96  3.000
 K5Q  O29   C11  C12   121.44  3.000
 K5Q  O29   C11  C6    119.28  3.000
 K5Q  C12   C11  C6    119.28  3.000
 K5Q  O28   C12  C11   122.07  3.000
 K5Q  O28   C12  C9    118.02  3.000
 K5Q  C11   C12  C9    119.91  3.000
 K5Q  C15   C13  C14   123.06  3.000
 K5Q  C15   C13  C7    131.33  3.000
 K5Q  C14   C13  C7    105.60  3.000
 K5Q  N23   C14  C18   127.88  3.000
 K5Q  N23   C14  C13   121.87  3.000
 K5Q  C18   C14  C13   110.25  3.000
 K5Q  H15   C15  C13   116.75  3.000
 K5Q  H15   C15  C8    116.27  3.000
 K5Q  C13   C15  C8    126.96  3.000
 K5Q  O26   C16  O24   124.47  3.000
 K5Q  O26   C16  C9    123.83  3.000
 K5Q  O24   C16  C9    111.69  3.000
 K5Q  O27   C17  O25   123.09  3.000
 K5Q  O27   C17  C21   111.71  3.000
 K5Q  O25   C17  C21   125.21  3.000
 K5Q  H182  C18  H181  106.55  3.000
 K5Q  H182  C18  C14   112.21  3.000
 K5Q  H181  C18  C14   111.08  3.000
 K5Q  H182  C18  C10   112.35  3.000
 K5Q  H181  C18  C10   112.22  3.000
 K5Q  C14   C18  C10   102.55  3.000
 K5Q  H192  C19  H191  108.62  3.000
 K5Q  H192  C19  O28   110.00  3.000
 K5Q  H191  C19  O28   106.77  3.000
 K5Q  H192  C19  C20   110.48  3.000
 K5Q  H191  C19  C20   110.47  3.000
 K5Q  O28   C19  C20   110.43  3.000
 K5Q  H20   C20  O29   108.71  3.000
 K5Q  H20   C20  C22   109.82  3.000
 K5Q  O29   C20  C22   108.40  3.000
 K5Q  H20   C20  C19   108.74  3.000
 K5Q  O29   C20  C19   109.12  3.000
 K5Q  C22   C20  C19   112.00  3.000
 K5Q  H222  C22  H221  106.81  3.000
 K5Q  H222  C22  C21   109.72  3.000
 K5Q  H221  C22  C21   110.57  3.000
 K5Q  H222  C22  C20   107.51  3.000
 K5Q  H221  C22  C20   109.67  3.000
 K5Q  C21   C22  C20   112.36  3.000
 K5Q  O30   N23  C14   112.58  3.000
 K5Q  H24   O24  C16   110.38  3.000
 K5Q  H27   O27  C17   109.96  3.000
 K5Q  C19   O28  C12   114.57  3.000
 K5Q  C20   O29  C11   115.10  3.000
 K5Q  H30   O30  N23   104.46  3.000
 K5Q  H212  C21  H211  105.67  3.000
 K5Q  H212  C21  C22   110.60  3.000
 K5Q  H211  C21  C22   111.28  3.000
 K5Q  H212  C21  C17   108.21  3.000
 K5Q  H211  C21  C17   107.89  3.000
 K5Q  C22   C21  C17   112.88  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
 K5Q  CONST_01  C10  C5   C2   C1      0.00   0.0  0
 K5Q  CONST_02  C10  C7   C3   C1      0.00   0.0  0
 K5Q  CONST_03  C7   C3   C1   C2      0.00   0.0  0
 K5Q  CONST_04  C7   C10  C5   C2      0.00   0.0  0
 K5Q  CONST_05  C5   C2   C1   C3      0.00   0.0  0
 K5Q  CONST_06  C5   C10  C7   C3      0.00   0.0  0
 K5Q  CONST_07  C12  C11  C6   C4      0.00   0.0  0
 K5Q  CONST_08  C12  C9   C8   C4      0.00   0.0  0
 K5Q  CONST_09  C9   C8   C4   C6      0.00   0.0  0
 K5Q  CONST_10  C9   C12  C11  C6      0.00   0.0  0
 K5Q  CONST_11  C11  C6   C4   C8      0.00   0.0  0
 K5Q  CONST_12  C11  C12  C9   C8      0.00   0.0  0
 K5Q  CONST_13  C16  C9   C8   C4    180.00   0.0  0
 K5Q  CONST_14  C15  C8   C4   C6    180.00   0.0  0
 K5Q  CONST_15  C16  C9   C12  C11   180.00   0.0  0
 K5Q  CONST_16  C15  C8   C9   C12   180.00   0.0  0
 K5Q  CONST_17  O28  C12  C9   C16     0.00   0.0  0
 K5Q  CONST_18  H5   C5   C2   C1    180.00   0.0  0
 K5Q  CONST_19  H3   C3   C1   C2    180.00   0.0  0
 K5Q  CONST_20  H2   C2   C1   C3    180.00   0.0  0
 K5Q  CONST_21  H1   C1   C2   C5    180.00   0.0  0
 K5Q  CONST_22  H6   C6   C4   C8    180.00   0.0  0
 K5Q  CONST_23  H4   C4   C8   C9    180.00   0.0  0
 K5Q  CONST_24  H24  O24  C16  C9    180.00   0.0  0
 K5Q  CONST_25  H27  O27  C17  C21   180.00   0.0  0
 K5Q  Var_01    C14  C13  C7   C3   -174.26  30.0  1
 K5Q  Var_02    C14  C18  C10  C5    176.23  30.0  1
 K5Q  Var_03    C18  C14  C13  C7     -4.00  30.0  1
 K5Q  Var_04    C13  C14  C18  C10     3.88  30.0  1
 K5Q  Var_05    C20  C19  O28  C12   -44.32  30.0  1
 K5Q  Var_06    C13  C15  C8   C4     57.48  30.0  2
 K5Q  Var_07    C8   C15  C13  C7      6.98  30.0  2
 K5Q  Var_08    O24  C16  C9   C8    -85.71  30.0  2
 K5Q  Var_09    C20  C22  C21  C17  -175.28  30.0  3
 K5Q  Var_10    O25  C17  C21  C22    -3.19  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
 K5Q  chir_01  C20  C19  C22  O29  positiv

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
 K5Q  plan-1  C1   0.020
 K5Q  plan-1  C2   0.020
 K5Q  plan-1  C3   0.020
 K5Q  plan-1  C5   0.020
 K5Q  plan-1  C7   0.020
 K5Q  plan-1  C10  0.020
 K5Q  plan-1  C13  0.020
 K5Q  plan-1  C18  0.020
 K5Q  plan-1  H1   0.020
 K5Q  plan-1  H2   0.020
 K5Q  plan-1  H3   0.020
 K5Q  plan-1  H5   0.020
 K5Q  plan-2  C4   0.020
 K5Q  plan-2  C6   0.020
 K5Q  plan-2  C8   0.020
 K5Q  plan-2  C9   0.020
 K5Q  plan-2  C11  0.020
 K5Q  plan-2  C12  0.020
 K5Q  plan-2  C15  0.020
 K5Q  plan-2  C16  0.020
 K5Q  plan-2  O28  0.020
 K5Q  plan-2  O29  0.020
 K5Q  plan-2  H4   0.020
 K5Q  plan-2  H6   0.020
 K5Q  plan-3  C9   0.020
 K5Q  plan-3  C16  0.020
 K5Q  plan-3  O24  0.020
 K5Q  plan-3  O26  0.020
 K5Q  plan-3  H24  0.020
 K5Q  plan-4  C17  0.020
 K5Q  plan-4  O25  0.020
 K5Q  plan-4  O27  0.020
 K5Q  plan-4  H27  0.020
 K5Q  plan-4  C21  0.020

