# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 13:40:26 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  47  30  .  2022-07-25  2022-07-26
;
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  -2.5825  -3.6949   1.0900
 K5Q  C2    C  CR16   0  -0.261  -3.8819  -4.1929   1.1204
 K5Q  C3    C  CR16   0  -0.344  -2.3258  -2.4081   0.6408
 K5Q  C4    C  CR16   0  -0.327  -0.3964  -0.5993  -1.1722
 K5Q  C5    C  CR16   0  -0.307  -4.9435  -3.3937   0.7168
 K5Q  C6    C  CR16   0  -0.364   0.9747  -0.7645  -1.2077
 K5Q  C7    C  CR56   0   0.089  -3.3836  -1.6070   0.2131
 K5Q  C8    C  CR6    0   0.043  -0.9766   0.4744  -0.4906
 K5Q  C9    C  CR6    0  -0.194  -0.1442   1.4252   0.1110
 K5Q  C10   C  CR56   0   0.029  -4.6895  -2.1065   0.2743
 K5Q  C11   C  CR6    0   0.310   1.8024   0.1554  -0.5728
 K5Q  C12   C  CR6    0   0.313   1.2334   1.2552   0.0713
 K5Q  C13   C  CR5    0   0.113  -3.4072  -0.2116  -0.2539
 K5Q  C14   C  CR5    0   0.150  -4.8415   0.1269  -0.4179
 K5Q  C15   C  C1     0  -0.366  -2.4262   0.6794  -0.4823
 K5Q  C16   C  C      0   0.344  -0.7157   2.6405   0.8303
 K5Q  C17   C  C      0   0.416   7.4568  -0.8158  -0.2903
 K5Q  C18   C  CH2    0  -0.544  -5.6965  -1.0807  -0.1501
 K5Q  C19   C  CH2    0  -0.188   3.3649   2.1755   0.2618
 K5Q  C20   C  CH1    0  -0.012   3.9049   0.7598   0.2897
 K5Q  C22   C  CH2    0  -0.445   5.3603   0.6839  -0.1188
 K5Q  N23   N  N      0  -0.158  -5.2282   1.2884  -0.7520
 K5Q  O24   O  OC    -1  -0.595  -1.0241   3.6027   0.1060
 K5Q  O25   O  O      0  -0.607   8.0918   0.2454  -0.4466
 K5Q  O26   O  O      0  -0.586  -0.8248   2.5413   2.0630
 K5Q  O27   O  OC    -1  -0.630   7.9271  -1.9720  -0.3267
 K5Q  O28   O  O2     0  -0.479   2.0070   2.1998   0.6665
 K5Q  O29   O  O2     0  -0.485   3.1376  -0.0437  -0.6076
 K5Q  O30   O  OH1    0  -0.550  -6.5874   1.3774  -0.8543
 K5Q  H1    H  HCR6   0   0.257  -1.7601  -4.3167   1.4197
 K5Q  H2    H  HCR6   0   0.257  -4.0669  -5.2013   1.4673
 K5Q  H3    H  HCR6   0   0.263  -1.3091  -2.0435   0.6332
 K5Q  H5    H  HCR6   0   0.253  -5.9586  -3.7694   0.7581
 K5Q  H4    H  HCR6   0   0.258  -1.0255  -1.3130  -1.6884
 K5Q  H6    H  HCR6   0   0.261   1.4175  -1.6025  -1.7313
 K5Q  H15   H  H      0   0.253  -2.7495   1.6927  -0.7031
 K5Q  H181  H  HCH2   0   0.285  -6.2438  -1.3825  -1.0485
 K5Q  H182  H  HCH2   0   0.283  -6.4465  -0.8913   0.6226
 K5Q  H211  H  HCH2   0   0.228   5.4236  -1.4061  -0.6753
 K5Q  H212  H  HCH2   0   0.225   5.7677  -1.1033   1.0022
 K5Q  H191  H  HCH2   0   0.255   3.9144   2.8052   0.9604
 K5Q  H192  H  HCH2   0   0.231   3.4718   2.5997  -0.7441
 K5Q  H20   H  HCH1   0   0.238   3.7853   0.3607   1.3066
 K5Q  H221  H  HCH2   0   0.223   5.4724   1.0691  -1.1364
 K5Q  H222  H  HCH2   0   0.229   5.9190   1.3639   0.5280
 K5Q  H30   H  HOH1   0   0.477  -6.7485   2.2969  -1.0912
 K5Q  C21   C  CH2    0  -0.588   5.9464  -0.7155  -0.0080

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  1.389  0.020  1.389
 K5Q  C3   C7    aromatic  1.394  0.020  1.394
 K5Q  C4   C6    aromatic  1.381  0.020  1.381
 K5Q  C4   C8    aromatic  1.398  0.020  1.398
 K5Q  C5   C10   aromatic  1.385  0.020  1.385
 K5Q  C6   C11   aromatic  1.391  0.020  1.391
 K5Q  C7   C10   aromatic  1.400  0.020  1.400
 K5Q  C7   C13   single    1.472  0.020  1.472
 K5Q  C8   C9    aromatic  1.400  0.020  1.400
 K5Q  C8   C15   single    1.464  0.020  1.464
 K5Q  C9   C12   aromatic  1.389  0.020  1.389
 K5Q  C9   C16   single    1.523  0.020  1.523
 K5Q  C10  C18   single    1.499  0.020  1.499
 K5Q  C11  C12   aromatic  1.396  0.020  1.396
 K5Q  C11  O29   single    1.350  0.020  1.350
 K5Q  C12  O28   single    1.358  0.020  1.358
 K5Q  C13  C14   single    1.483  0.020  1.483
 K5Q  C13  C15   double    1.345  0.020  1.345
 K5Q  C14  C18   single    1.504  0.020  1.504
 K5Q  C14  N23   double    1.269  0.020  1.269
 K5Q  C16  O24   deloc     1.243  0.020  1.243
 K5Q  C16  O26   deloc     1.241  0.020  1.241
 K5Q  C17  C21   single    1.540  0.020  1.540
 K5Q  C17  O25   deloc     1.247  0.020  1.247
 K5Q  C17  O27   deloc     1.249  0.020  1.249
 K5Q  C19  C20   single    1.515  0.020  1.515
 K5Q  C19  O28   single    1.417  0.020  1.417
 K5Q  C20  C22   single    1.514  0.020  1.514
 K5Q  C20  O29   single    1.428  0.020  1.428
 K5Q  C21  C22   single    1.521  0.020  1.521
 K5Q  N23  O30   single    1.366  0.020  1.366
 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  C21  H211  single    0.970  0.020  1.090
 K5Q  C21  H212  single    0.970  0.020  1.090
 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    119.41  3.000
 K5Q  H1    C1   C2    119.81  3.000
 K5Q  C3    C1   C2    120.78  3.000
 K5Q  H2    C2   C5    119.91  3.000
 K5Q  H2    C2   C1    119.99  3.000
 K5Q  C5    C2   C1    120.09  3.000
 K5Q  H3    C3   C7    121.21  3.000
 K5Q  H3    C3   C1    119.32  3.000
 K5Q  C7    C3   C1    119.48  3.000
 K5Q  H4    C4   C8    119.85  3.000
 K5Q  H4    C4   C6    119.06  3.000
 K5Q  C8    C4   C6    121.08  3.000
 K5Q  H5    C5   C10   120.43  3.000
 K5Q  H5    C5   C2    120.38  3.000
 K5Q  C10   C5   C2    119.19  3.000
 K5Q  H6    C6   C11   119.29  3.000
 K5Q  H6    C6   C4    120.72  3.000
 K5Q  C11   C6   C4    119.99  3.000
 K5Q  C13   C7   C10   109.71  3.000
 K5Q  C13   C7   C3    130.87  3.000
 K5Q  C10   C7   C3    119.31  3.000
 K5Q  C15   C8   C9    119.42  3.000
 K5Q  C15   C8   C4    121.42  3.000
 K5Q  C9    C8   C4    118.98  3.000
 K5Q  C16   C9   C12   118.90  3.000
 K5Q  C16   C9   C8    121.45  3.000
 K5Q  C12   C9   C8    119.64  3.000
 K5Q  C18   C10  C7    111.73  3.000
 K5Q  C18   C10  C5    127.12  3.000
 K5Q  C7    C10  C5    121.12  3.000
 K5Q  O29   C11  C12   122.08  3.000
 K5Q  O29   C11  C6    118.63  3.000
 K5Q  C12   C11  C6    119.29  3.000
 K5Q  O28   C12  C11   121.20  3.000
 K5Q  O28   C12  C9    117.87  3.000
 K5Q  C11   C12  C9    120.93  3.000
 K5Q  C15   C13  C14   122.38  3.000
 K5Q  C15   C13  C7    132.10  3.000
 K5Q  C14   C13  C7    105.49  3.000
 K5Q  N23   C14  C18   127.50  3.000
 K5Q  N23   C14  C13   122.20  3.000
 K5Q  C18   C14  C13   110.30  3.000
 K5Q  H15   C15  C13   115.81  3.000
 K5Q  H15   C15  C8    115.10  3.000
 K5Q  C13   C15  C8    129.08  3.000
 K5Q  O26   C16  O24   128.21  3.000
 K5Q  O26   C16  C9    115.98  3.000
 K5Q  O24   C16  C9    115.81  3.000
 K5Q  O27   C17  O25   126.35  3.000
 K5Q  O27   C17  C21   115.79  3.000
 K5Q  O25   C17  C21   117.85  3.000
 K5Q  H182  C18  H181  106.55  3.000
 K5Q  H182  C18  C14   112.14  3.000
 K5Q  H181  C18  C14   111.08  3.000
 K5Q  H182  C18  C10   112.29  3.000
 K5Q  H181  C18  C10   112.31  3.000
 K5Q  C14   C18  C10   102.60  3.000
 K5Q  H192  C19  H191  108.38  3.000
 K5Q  H192  C19  O28   110.41  3.000
 K5Q  H191  C19  O28   106.87  3.000
 K5Q  H192  C19  C20   110.09  3.000
 K5Q  H191  C19  C20   110.39  3.000
 K5Q  O28   C19  C20   110.62  3.000
 K5Q  H20   C20  O29   108.58  3.000
 K5Q  H20   C20  C22   109.64  3.000
 K5Q  O29   C20  C22   108.60  3.000
 K5Q  H20   C20  C19   108.51  3.000
 K5Q  O29   C20  C19   108.82  3.000
 K5Q  C22   C20  C19   112.61  3.000
 K5Q  H222  C22  H221  106.22  3.000
 K5Q  H222  C22  C21   109.42  3.000
 K5Q  H221  C22  C21   110.62  3.000
 K5Q  H222  C22  C20   107.51  3.000
 K5Q  H221  C22  C20   109.39  3.000
 K5Q  C21   C22  C20   113.39  3.000
 K5Q  O30   N23  C14   112.50  3.000
 K5Q  C19   O28  C12   114.12  3.000
 K5Q  C20   O29  C11   115.60  3.000
 K5Q  H30   O30  N23   104.31  3.000
 K5Q  H212  C21  H211  105.13  3.000
 K5Q  H212  C21  C22   109.24  3.000
 K5Q  H211  C21  C22   110.63  3.000
 K5Q  H212  C21  C17   107.80  3.000
 K5Q  H211  C21  C17   108.42  3.000
 K5Q  C22   C21  C17   115.12  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  Var_01    C14  C13  C7   C3   -173.67  30.0  1
 K5Q  Var_02    C14  C18  C10  C5    175.93  30.0  1
 K5Q  Var_03    C18  C14  C13  C7     -4.05  30.0  1
 K5Q  Var_04    C13  C14  C18  C10     3.97  30.0  1
 K5Q  Var_05    C20  C19  O28  C12   -47.00  30.0  1
 K5Q  Var_06    C13  C15  C8   C4     46.97  30.0  2
 K5Q  Var_07    C8   C15  C13  C7      8.54  30.0  2
 K5Q  Var_08    O24  C16  C9   C8    -82.57  30.0  2
 K5Q  Var_09    C20  C22  C21  C17  -174.67  30.0  3
 K5Q  Var_10    O25  C17  C21  C22     7.12  30.0  3

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-4  C17  0.020
 K5Q  plan-4  O25  0.020
 K5Q  plan-4  O27  0.020
 K5Q  plan-4  C21  0.020

