# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 22:26:27 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: 6-[(5-bromo-2,3-dioxo-2,3-dihydro-1H-indol-1-yl)methyl]-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1c(CN2C(=O)C(=O)c3cc(Br)ccc23)ccc4OCCOc14
#
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
 CBJ  CBJ  '6-[(5-bromo-2,3-dioxo-2,3-dihydro-1H-indol-1-yl)methyl]-2,3-dihydro-1,4-benzodioxine-5-carboxylic acid'  ligand  38  26  .  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_CBJ
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
 CBJ  O1    O   O     0  -0.393  -0.2259  -3.5309   0.8322
 CBJ  C2    C   CR5   0   0.461   0.5239  -2.6315   0.5556
 CBJ  C3    C   CR5   0   0.267   1.9874  -2.4806   1.0394
 CBJ  O4    O   O     0  -0.324   2.5400  -3.2668   1.7583
 CBJ  C5    C   CR56  0  -0.071   2.4534  -1.2376   0.4382
 CBJ  C6    C   CR16  0  -0.246   3.6719  -0.5897   0.5215
 CBJ  C7    C   CR6   0  -0.129   3.8083   0.6041  -0.1721
 CBJ  BR8   BR  BR    0  -0.023   5.4435   1.5381  -0.1023
 CBJ  C9    C   CR16  0  -0.203   2.7548   1.1259  -0.9177
 CBJ  C10   C   CR16  0  -0.294   1.5294   0.4705  -0.9948
 CBJ  C11   C   CR56  0   0.433   1.3948  -0.7202  -0.3104
 CBJ  N12   N   NR5   0  -0.627   0.2745  -1.5506  -0.2362
 CBJ  C13   C   CH2   0  -0.379  -0.9739  -1.3018  -0.9105
 CBJ  C14   C   CR6   0   0.082  -1.9043  -0.3832  -0.1453
 CBJ  C15   C   CR16  0  -0.313  -1.5132   0.2220   1.0404
 CBJ  C16   C   CR16  0  -0.347  -2.3697   1.0681   1.7282
 CBJ  C17   C   CR6   0   0.321  -3.6455   1.3158   1.2554
 CBJ  O18   O   O2    0  -0.477  -4.4476   2.1597   1.9406
 CBJ  C19   C   CH2   0  -0.230  -5.5674   2.6313   1.2044
 CBJ  C20   C   CH2   0  -0.226  -6.2283   1.4868   0.4781
 CBJ  O21   O   O2    0  -0.471  -5.3058   0.8818  -0.4209
 CBJ  C22   C   CR6   0   0.355  -4.0726   0.6832   0.0824
 CBJ  C23   C   CR6   0  -0.186  -3.2029  -0.1529  -0.6128
 CBJ  C24   C   C     0   0.467  -3.7372  -0.8447  -1.8242
 CBJ  O25   O   O     0  -0.412  -4.6706  -1.6035  -1.8076
 CBJ  O26   O   OH1   0  -0.581  -3.0552  -0.5340  -2.9165
 CBJ  H6    H   HCR6  0   0.298   4.4781  -1.0080   1.1097
 CBJ  H9    H   HCR6  0   0.300   2.8748   2.0591  -1.4513
 CBJ  H10   H   HCR6  0   0.295   0.7271   0.9021  -1.5766
 CBJ  H13   H   HCH2  0   0.296  -0.7467  -0.8896  -1.8942
 CBJ  H13A  H   HCH2  0   0.299  -1.4471  -2.2692  -1.0858
 CBJ  H15   H   HCR6  0   0.256  -0.5278   0.0507   1.4506
 CBJ  H16   H   HCR6  0   0.277  -2.0432   1.5477   2.6423
 CBJ  H19   H   HCH2  0   0.267  -6.2568   3.0783   1.9185
 CBJ  H19A  H   HCH2  0   0.248  -5.2534   3.4048   0.4957
 CBJ  H20   H   HCH2  0   0.252  -6.6011   0.7412   1.1871
 CBJ  H20A  H   HCH2  0   0.266  -7.0651   1.8448  -0.1192
 CBJ  HO26  H   HOH1  0   0.490  -3.3896  -1.0357  -3.6771

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
 CBJ  O1   C2    double    1.203  0.020  1.203
 CBJ  C2   C3    single    1.549  0.020  1.549
 CBJ  C2   N12   single    1.363  0.020  1.363
 CBJ  C3   O4    double    1.200  0.020  1.200
 CBJ  C3   C5    single    1.457  0.020  1.457
 CBJ  C5   C6    aromatic  1.383  0.020  1.383
 CBJ  C5   C11   aromatic  1.396  0.020  1.396
 CBJ  C6   C7    aromatic  1.387  0.020  1.387
 CBJ  C7   BR8   single    1.885  0.020  1.885
 CBJ  C7   C9    aromatic  1.392  0.020  1.392
 CBJ  C9   C10   aromatic  1.392  0.020  1.392
 CBJ  C10  C11   aromatic  1.380  0.020  1.380
 CBJ  C11  N12   single    1.397  0.020  1.397
 CBJ  N12  C13   single    1.441  0.020  1.441
 CBJ  C13  C14   single    1.515  0.020  1.515
 CBJ  C14  C15   aromatic  1.388  0.020  1.388
 CBJ  C14  C23   aromatic  1.399  0.020  1.399
 CBJ  C15  C16   aromatic  1.387  0.020  1.387
 CBJ  C16  C17   aromatic  1.383  0.020  1.383
 CBJ  C17  O18   single    1.351  0.020  1.351
 CBJ  C17  C22   aromatic  1.400  0.020  1.400
 CBJ  O18  C19   single    1.421  0.020  1.421
 CBJ  C19  C20   single    1.508  0.020  1.508
 CBJ  C20  O21   single    1.423  0.020  1.423
 CBJ  O21  C22   single    1.347  0.020  1.347
 CBJ  C22  C23   aromatic  1.392  0.020  1.392
 CBJ  C23  C24   single    1.494  0.020  1.494
 CBJ  C24  O25   double    1.203  0.020  1.203
 CBJ  C24  O26   single    1.325  0.020  1.325
 CBJ  C6   H6    single    0.930  0.020  1.080
 CBJ  C9   H9    single    0.930  0.020  1.080
 CBJ  C10  H10   single    0.930  0.020  1.080
 CBJ  C13  H13   single    0.970  0.020  1.090
 CBJ  C13  H13A  single    0.970  0.020  1.090
 CBJ  C15  H15   single    0.930  0.020  1.080
 CBJ  C16  H16   single    0.930  0.020  1.080
 CBJ  C19  H19   single    0.970  0.020  1.090
 CBJ  C19  H19A  single    0.970  0.020  1.090
 CBJ  C20  H20   single    0.970  0.020  1.090
 CBJ  C20  H20A  single    0.970  0.020  1.090
 CBJ  O26  HO26  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
 CBJ  N12   C2   C3   106.09  3.000
 CBJ  N12   C2   O1   127.76  3.000
 CBJ  C3    C2   O1   126.15  3.000
 CBJ  C5    C3   O4   131.20  3.000
 CBJ  C5    C3   C2   104.86  3.000
 CBJ  O4    C3   C2   123.94  3.000
 CBJ  C11   C5   C6   121.80  3.000
 CBJ  C11   C5   C3   107.15  3.000
 CBJ  C6    C5   C3   131.05  3.000
 CBJ  H6    C6   C7   122.08  3.000
 CBJ  H6    C6   C5   120.55  3.000
 CBJ  C7    C6   C5   117.37  3.000
 CBJ  C9    C7   BR8  119.39  3.000
 CBJ  C9    C7   C6   121.06  3.000
 CBJ  BR8   C7   C6   119.55  3.000
 CBJ  H9    C9   C10  118.47  3.000
 CBJ  H9    C9   C7   120.24  3.000
 CBJ  C10   C9   C7   121.29  3.000
 CBJ  H10   C10  C11  122.62  3.000
 CBJ  H10   C10  C9   119.69  3.000
 CBJ  C11   C10  C9   117.70  3.000
 CBJ  N12   C11  C10  128.15  3.000
 CBJ  N12   C11  C5   111.07  3.000
 CBJ  C10   C11  C5   120.78  3.000
 CBJ  C13   N12  C11  124.58  3.000
 CBJ  C13   N12  C2   124.58  3.000
 CBJ  C11   N12  C2   110.84  3.000
 CBJ  H13A  C13  H13  106.30  3.000
 CBJ  H13A  C13  C14  110.63  3.000
 CBJ  H13   C13  C14  110.75  3.000
 CBJ  H13A  C13  N12  107.33  3.000
 CBJ  H13   C13  N12  107.88  3.000
 CBJ  C14   C13  N12  113.61  3.000
 CBJ  C23   C14  C15  118.38  3.000
 CBJ  C23   C14  C13  120.07  3.000
 CBJ  C15   C14  C13  121.53  3.000
 CBJ  H15   C15  C16  118.14  3.000
 CBJ  H15   C15  C14  120.80  3.000
 CBJ  C16   C15  C14  121.06  3.000
 CBJ  H16   C16  C17  119.18  3.000
 CBJ  H16   C16  C15  120.19  3.000
 CBJ  C17   C16  C15  120.64  3.000
 CBJ  C22   C17  O18  121.76  3.000
 CBJ  C22   C17  C16  119.15  3.000
 CBJ  O18   C17  C16  119.10  3.000
 CBJ  C19   O18  C17  114.37  3.000
 CBJ  H19A  C19  H19  108.42  3.000
 CBJ  H19A  C19  C20  110.49  3.000
 CBJ  H19   C19  C20  110.49  3.000
 CBJ  H19A  C19  O18  110.11  3.000
 CBJ  H19   C19  O18  107.19  3.000
 CBJ  C20   C19  O18  110.07  3.000
 CBJ  H20A  C20  H20  108.52  3.000
 CBJ  H20A  C20  O21  106.95  3.000
 CBJ  H20   C20  O21  109.90  3.000
 CBJ  H20A  C20  C19  110.58  3.000
 CBJ  H20   C20  C19  110.75  3.000
 CBJ  O21   C20  C19  110.05  3.000
 CBJ  C22   O21  C20  114.85  3.000
 CBJ  C23   C22  O21  118.29  3.000
 CBJ  C23   C22  C17  119.96  3.000
 CBJ  O21   C22  C17  121.73  3.000
 CBJ  C24   C23  C22  117.36  3.000
 CBJ  C24   C23  C14  121.78  3.000
 CBJ  C22   C23  C14  120.78  3.000
 CBJ  O26   C24  O25  123.97  3.000
 CBJ  O26   C24  C23  112.08  3.000
 CBJ  O25   C24  C23  123.95  3.000
 CBJ  HO26  O26  C24  110.34  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
 CBJ  CONST_01  C9    C7   C6   C5     0.00   0.0  0
 CBJ  CONST_02  C9    C10  C11  C5     0.00   0.0  0
 CBJ  CONST_03  C10   C11  C5   C6     0.00   0.0  0
 CBJ  CONST_04  C10   C9   C7   C6     0.00   0.0  0
 CBJ  CONST_05  C11   C5   C6   C7     0.00   0.0  0
 CBJ  CONST_06  C11   C10  C9   C7     0.00   0.0  0
 CBJ  CONST_07  C17   C16  C15  C14    0.00   0.0  0
 CBJ  CONST_08  C17   C22  C23  C14    0.00   0.0  0
 CBJ  CONST_09  C22   C23  C14  C15    0.00   0.0  0
 CBJ  CONST_10  C22   C17  C16  C15    0.00   0.0  0
 CBJ  CONST_11  C23   C14  C15  C16    0.00   0.0  0
 CBJ  CONST_12  C23   C22  C17  C16    0.00   0.0  0
 CBJ  CONST_13  C11   N12  C2   C3     0.00   0.0  0
 CBJ  CONST_14  BR8   C7   C6   C5   180.00   0.0  0
 CBJ  CONST_15  C10   C9   C7   BR8  180.00   0.0  0
 CBJ  CONST_16  C16   C15  C14  C13  180.00   0.0  0
 CBJ  CONST_17  C22   C23  C14  C13  180.00   0.0  0
 CBJ  CONST_18  C24   C23  C14  C15  180.00   0.0  0
 CBJ  CONST_19  C24   C23  C22  C17  180.00   0.0  0
 CBJ  CONST_20  C24   C23  C22  O21    0.00   0.0  0
 CBJ  CONST_21  C11   N12  C2   O1   180.00   0.0  0
 CBJ  CONST_22  C13   N12  C2   C3   180.00   0.0  0
 CBJ  CONST_23  H6    C6   C5   C3     0.00   0.0  0
 CBJ  CONST_24  H10   C10  C11  C5   180.00   0.0  0
 CBJ  CONST_25  H9    C9   C7   C6   180.00   0.0  0
 CBJ  CONST_26  H16   C16  C15  C14  180.00   0.0  0
 CBJ  CONST_27  H15   C15  C16  C17  180.00   0.0  0
 CBJ  CONST_28  C13   N12  C2   O1     0.00   0.0  0
 CBJ  CONST_29  HO26  O26  C24  C23  180.00   0.0  0
 CBJ  Var_01    C20   C19  O18  C17   45.50  30.0  1
 CBJ  Var_02    O21   C20  C19  O18  -59.91  30.0  1
 CBJ  Var_03    C22   C17  O18  C19  -16.69  30.0  1
 CBJ  Var_04    C23   C22  O21  C20  166.34  30.0  1
 CBJ  Var_05    C14   C13  N12  C2    95.52  30.0  3
 CBJ  Var_06    C15   C14  C13  N12    4.59  30.0  2
 CBJ  Var_07    O25   C24  C23  C14  116.76  30.0  2

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
 CBJ  plan-1  O1    0.020
 CBJ  plan-1  C2    0.020
 CBJ  plan-1  C3    0.020
 CBJ  plan-1  O4    0.020
 CBJ  plan-1  C5    0.020
 CBJ  plan-1  C6    0.020
 CBJ  plan-1  C7    0.020
 CBJ  plan-1  BR8   0.020
 CBJ  plan-1  C9    0.020
 CBJ  plan-1  C10   0.020
 CBJ  plan-1  C11   0.020
 CBJ  plan-1  N12   0.020
 CBJ  plan-1  C13   0.020
 CBJ  plan-1  H6    0.020
 CBJ  plan-1  H9    0.020
 CBJ  plan-1  H10   0.020
 CBJ  plan-2  C13   0.020
 CBJ  plan-2  C14   0.020
 CBJ  plan-2  C15   0.020
 CBJ  plan-2  C16   0.020
 CBJ  plan-2  C17   0.020
 CBJ  plan-2  O18   0.020
 CBJ  plan-2  O21   0.020
 CBJ  plan-2  C22   0.020
 CBJ  plan-2  C23   0.020
 CBJ  plan-2  C24   0.020
 CBJ  plan-2  H15   0.020
 CBJ  plan-2  H16   0.020
 CBJ  plan-3  C23   0.020
 CBJ  plan-3  C24   0.020
 CBJ  plan-3  O25   0.020
 CBJ  plan-3  O26   0.020
 CBJ  plan-3  HO26  0.020

