# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 31 14:24:13 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: 5-{[(3S)-2-oxo-2,3-dihydro-1H-indol-3-yl]methyl}-1,3-benzodioxole-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1c(C[C@@H]2C(=O)Nc3ccccc23)ccc4OCOc14
#
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
 UJ6  UJ6  '5-{[(3S)-2-oxo-2,3-dihydro-1H-indol-3-yl]methyl}-1,3-benzodioxole-4-carboxylic acid'  ligand  36  23  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_UJ6
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
 UJ6  O1    O  O     0  -0.444   0.6959  -2.2585  -1.1194
 UJ6  C2    C  CR5   0   0.553   1.5899  -1.5237  -0.7595
 UJ6  C3    C  CR15  0  -0.467   1.4572  -0.0907  -0.2453
 UJ6  C4    C  CH2   0  -0.523   0.5718  -0.0041   1.0122
 UJ6  C5    C  CR6   0   0.159  -0.8895  -0.2811   0.7723
 UJ6  C6    C  CR16  0  -0.333  -1.4107  -1.4553   1.2903
 UJ6  C7    C  CR16  0  -0.325  -2.7408  -1.8502   1.1089
 UJ6  C8    C  CR56  0   0.296  -3.5294  -1.0230   0.3587
 UJ6  O9    O  O     0  -0.482  -4.8311  -1.1692   0.0179
 UJ6  C10   C  CH2   0   0.068  -5.2149   0.0411  -0.6147
 UJ6  O11   O  O     0  -0.466  -4.0176   0.7653  -0.8767
 UJ6  C12   C  CR56  0   0.327  -3.0343   0.1506  -0.1909
 UJ6  C13   C  CR6   0  -0.205  -1.7318   0.5725   0.0098
 UJ6  C14   C  C     0   0.489  -1.3381   1.8646  -0.6028
 UJ6  O15   O  OH1   0  -0.590  -0.4165   2.5233   0.0862
 UJ6  O16   O  O     0  -0.426  -1.8299   2.2954  -1.6170
 UJ6  C17   C  CR56  0   0.072   2.8808   0.2982   0.0166
 UJ6  C18   C  CR56  0   0.378   3.7020  -0.7861  -0.2880
 UJ6  N19   N  NR15  0  -0.739   2.9159  -1.8398  -0.7356
 UJ6  C20   C  CR16  0  -0.308   5.0752  -0.7286  -0.1422
 UJ6  C21   C  CR16  0  -0.266   5.6214   0.4644   0.3282
 UJ6  C22   C  CR16  0  -0.265   4.8167   1.5530   0.6390
 UJ6  C23   C  CR16  0  -0.328   3.4323   1.4724   0.4835
 UJ6  H3    H  HCR5  0   0.313   1.0326   0.5155  -1.0515
 UJ6  H4    H  HCH2  0   0.272   0.9449  -0.7214   1.7458
 UJ6  H4A   H  HCH2  0   0.280   0.7171   0.9779   1.4577
 UJ6  H6    H  HCR6  0   0.259  -0.7588  -2.1032   1.8610
 UJ6  H7    H  HCR6  0   0.281  -3.1170  -2.7698   1.5357
 UJ6  H10   H  HCH2  0   0.250  -5.7244  -0.1744  -1.5536
 UJ6  H10A  H  HCH2  0   0.239  -5.8599   0.6249   0.0496
 UJ6  HO15  H  HOH1  0   0.489  -0.1892   3.3464  -0.3730
 UJ6  HN19  H  HNR5  0   0.410   3.2745  -2.7379  -1.0228
 UJ6  H20   H  HCR6  0   0.267   5.7069  -1.5737  -0.3825
 UJ6  H21   H  HCR6  0   0.259   6.6939   0.5389   0.4525
 UJ6  H22   H  HCR6  0   0.255   5.2647   2.4675   1.0033
 UJ6  H23   H  HCR6  0   0.251   2.8048   2.3217   0.7257

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
 UJ6  O1   C2    double    1.212  0.020  1.212
 UJ6  N19  C2    single    1.363  0.020  1.363
 UJ6  C2   C3    single    1.528  0.020  1.528
 UJ6  C3   C17   single    1.499  0.020  1.499
 UJ6  C3   C4    single    1.540  0.020  1.540
 UJ6  C3   H3    single    0.970  0.020  1.090
 UJ6  C4   C5    single    1.507  0.020  1.507
 UJ6  C4   H4    single    0.970  0.020  1.090
 UJ6  C4   H4A   single    0.970  0.020  1.090
 UJ6  C13  C5    aromatic  1.421  0.020  1.421
 UJ6  C5   C6    aromatic  1.385  0.020  1.385
 UJ6  C6   C7    aromatic  1.399  0.020  1.399
 UJ6  C6   H6    single    0.930  0.020  1.080
 UJ6  C8   C7    aromatic  1.367  0.020  1.367
 UJ6  C7   H7    single    0.930  0.020  1.080
 UJ6  C12  C8    aromatic  1.387  0.020  1.387
 UJ6  C8   O9    single    1.354  0.020  1.354
 UJ6  C10  O9    single    1.419  0.020  1.419
 UJ6  O11  C10   single    1.424  0.020  1.424
 UJ6  C10  H10   single    0.970  0.020  1.090
 UJ6  C10  H10A  single    0.970  0.020  1.090
 UJ6  O11  C12   single    1.347  0.020  1.347
 UJ6  C13  C12   aromatic  1.384  0.020  1.384
 UJ6  C14  C13   single    1.483  0.020  1.483
 UJ6  O16  C14   double    1.207  0.020  1.207
 UJ6  O15  C14   single    1.326  0.020  1.326
 UJ6  O15  HO15  single    0.850  0.020  0.980
 UJ6  C18  C17   aromatic  1.394  0.020  1.394
 UJ6  C17  C23   aromatic  1.379  0.020  1.379
 UJ6  N19  C18   single    1.389  0.020  1.389
 UJ6  C18  C20   aromatic  1.382  0.020  1.382
 UJ6  N19  HN19  single    0.860  0.020  1.020
 UJ6  C20  C21   aromatic  1.394  0.020  1.394
 UJ6  C20  H20   single    0.930  0.020  1.080
 UJ6  C21  C22   aromatic  1.389  0.020  1.389
 UJ6  C21  H21   single    0.930  0.020  1.080
 UJ6  C23  C22   aromatic  1.395  0.020  1.395
 UJ6  C22  H22   single    0.930  0.020  1.080
 UJ6  C23  H23   single    0.930  0.020  1.080

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
 UJ6  N19   C2   C3   107.21  3.000
 UJ6  C3    C2   O1   127.19  3.000
 UJ6  N19   C2   O1   125.60  3.000
 UJ6  H3    C3   C17  110.70  3.000
 UJ6  H3    C3   C4   110.32  3.000
 UJ6  C17   C3   C4   112.87  3.000
 UJ6  H3    C3   C2   107.77  3.000
 UJ6  C4    C3   C2   112.17  3.000
 UJ6  C17   C3   C2   102.69  3.000
 UJ6  H4A   C4   H4   105.79  3.000
 UJ6  H4A   C4   C5   111.14  3.000
 UJ6  H4    C4   C5   108.52  3.000
 UJ6  H4A   C4   C3   107.96  3.000
 UJ6  H4    C4   C3   108.37  3.000
 UJ6  C5    C4   C3   114.65  3.000
 UJ6  C13   C5   C6   119.13  3.000
 UJ6  C6    C5   C4   117.47  3.000
 UJ6  C13   C5   C4   123.36  3.000
 UJ6  H6    C6   C7   118.17  3.000
 UJ6  H6    C6   C5   118.56  3.000
 UJ6  C7    C6   C5   123.27  3.000
 UJ6  H7    C7   C8   122.04  3.000
 UJ6  H7    C7   C6   121.30  3.000
 UJ6  C8    C7   C6   116.66  3.000
 UJ6  C12   C8   O9   109.57  3.000
 UJ6  O9    C8   C7   128.87  3.000
 UJ6  C12   C8   C7   121.56  3.000
 UJ6  C10   O9   C8   106.27  3.000
 UJ6  H10A  C10  H10  110.66  3.000
 UJ6  H10A  C10  O11  109.64  3.000
 UJ6  H10   C10  O11  109.59  3.000
 UJ6  H10A  C10  O9   110.11  3.000
 UJ6  H10   C10  O9   109.99  3.000
 UJ6  O11   C10  O9   106.77  3.000
 UJ6  C12   O11  C10  106.74  3.000
 UJ6  C13   C12  O11  128.44  3.000
 UJ6  C13   C12  C8   122.44  3.000
 UJ6  O11   C12  C8   109.10  3.000
 UJ6  C14   C13  C12  117.10  3.000
 UJ6  C14   C13  C5   125.98  3.000
 UJ6  C12   C13  C5   116.91  3.000
 UJ6  O16   C14  O15  122.87  3.000
 UJ6  O15   C14  C13  113.74  3.000
 UJ6  O16   C14  C13  123.37  3.000
 UJ6  HO15  O15  C14  109.79  3.000
 UJ6  C23   C17  C18  120.06  3.000
 UJ6  C23   C17  C3   131.31  3.000
 UJ6  C18   C17  C3   108.63  3.000
 UJ6  C20   C18  N19  128.91  3.000
 UJ6  C20   C18  C17  122.00  3.000
 UJ6  N19   C18  C17  109.10  3.000
 UJ6  HN19  N19  C18  124.47  3.000
 UJ6  HN19  N19  C2   123.17  3.000
 UJ6  C18   N19  C2   112.35  3.000
 UJ6  H20   C20  C21  120.98  3.000
 UJ6  H20   C20  C18  121.60  3.000
 UJ6  C21   C20  C18  117.42  3.000
 UJ6  H21   C21  C22  119.63  3.000
 UJ6  H21   C21  C20  119.08  3.000
 UJ6  C22   C21  C20  121.29  3.000
 UJ6  H22   C22  C23  119.82  3.000
 UJ6  H22   C22  C21  119.88  3.000
 UJ6  C23   C22  C21  120.31  3.000
 UJ6  H23   C23  C22  120.30  3.000
 UJ6  H23   C23  C17  120.77  3.000
 UJ6  C22   C23  C17  118.93  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
 UJ6  CONST_01  C8    C12  C13  C5      0.00   0.0  0
 UJ6  CONST_02  C8    C7   C6   C5      0.00   0.0  0
 UJ6  CONST_03  C12   C13  C5   C6      0.00   0.0  0
 UJ6  CONST_04  C12   C8   C7   C6      0.00   0.0  0
 UJ6  CONST_05  C13   C5   C6   C7      0.00   0.0  0
 UJ6  CONST_06  C13   C12  C8   C7      0.00   0.0  0
 UJ6  CONST_07  C21   C20  C18  C17     0.00   0.0  0
 UJ6  CONST_08  C21   C22  C23  C17     0.00   0.0  0
 UJ6  CONST_09  C22   C23  C17  C18     0.00   0.0  0
 UJ6  CONST_10  C22   C21  C20  C18     0.00   0.0  0
 UJ6  CONST_11  C23   C17  C18  C20     0.00   0.0  0
 UJ6  CONST_12  C23   C22  C21  C20     0.00   0.0  0
 UJ6  CONST_13  C18   N19  C2   C3      0.00   0.0  0
 UJ6  CONST_14  C12   C13  C5   C4    180.00   0.0  0
 UJ6  CONST_15  C7    C6   C5   C4    180.00   0.0  0
 UJ6  CONST_16  C14   C13  C5   C6    180.00   0.0  0
 UJ6  CONST_17  C14   C13  C12  C8    180.00   0.0  0
 UJ6  CONST_18  C14   C13  C12  O11     0.00   0.0  0
 UJ6  CONST_19  C18   N19  C2   O1    180.00   0.0  0
 UJ6  CONST_20  H23   C23  C17  C3      0.00   0.0  0
 UJ6  CONST_21  H7    C7   C6   C5    180.00   0.0  0
 UJ6  CONST_22  H6    C6   C7   C8    180.00   0.0  0
 UJ6  CONST_23  H20   C20  C18  C17   180.00   0.0  0
 UJ6  CONST_24  H22   C22  C23  C17   180.00   0.0  0
 UJ6  CONST_25  H21   C21  C20  C18   180.00   0.0  0
 UJ6  CONST_26  HN19  N19  C2   C3    180.00   0.0  0
 UJ6  CONST_27  HO15  O15  C14  C13   180.00   0.0  0
 UJ6  Var_01    O11   C10  O9   C8     12.19  30.0  1
 UJ6  Var_02    C12   C8   O9   C10    -7.97  30.0  1
 UJ6  Var_03    C13   C12  O11  C10  -171.08  30.0  1
 UJ6  Var_04    C13   C5   C4   C3    -67.29  30.0  2
 UJ6  Var_05    O16   C14  C13  C5    149.76  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
 UJ6  chir_01  C3  C2  C17  C4  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
 UJ6  plan-1  C4    0.020
 UJ6  plan-1  C5    0.020
 UJ6  plan-1  C6    0.020
 UJ6  plan-1  C7    0.020
 UJ6  plan-1  C8    0.020
 UJ6  plan-1  O9    0.020
 UJ6  plan-1  O11   0.020
 UJ6  plan-1  C12   0.020
 UJ6  plan-1  C13   0.020
 UJ6  plan-1  C14   0.020
 UJ6  plan-1  H6    0.020
 UJ6  plan-1  H7    0.020
 UJ6  plan-2  O1    0.020
 UJ6  plan-2  C2    0.020
 UJ6  plan-2  C3    0.020
 UJ6  plan-2  C17   0.020
 UJ6  plan-2  C18   0.020
 UJ6  plan-2  N19   0.020
 UJ6  plan-2  C20   0.020
 UJ6  plan-2  C21   0.020
 UJ6  plan-2  C22   0.020
 UJ6  plan-2  C23   0.020
 UJ6  plan-2  HN19  0.020
 UJ6  plan-2  H20   0.020
 UJ6  plan-2  H21   0.020
 UJ6  plan-2  H22   0.020
 UJ6  plan-2  H23   0.020
 UJ6  plan-3  C13   0.020
 UJ6  plan-3  C14   0.020
 UJ6  plan-3  O15   0.020
 UJ6  plan-3  O16   0.020
 UJ6  plan-3  HO15  0.020

