# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 05:24:09 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  37  26  .  2021-08-07  2021-08-07  
;
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  -0.408   0.4718  -3.7877   1.3761
 CBJ  C2    C   CR5    0   0.459   0.8926  -2.7703   0.8860
 CBJ  C3    C   CR5    0   0.268   2.3142  -2.1904   1.0876
 CBJ  O4    O   O      0  -0.328   3.1632  -2.7133   1.7566
 CBJ  C5    C   CR56   0  -0.088   2.3274  -0.9567   0.3134
 CBJ  C6    C   CR16   0  -0.250   3.3259  -0.0213   0.1163
 CBJ  C7    C   CR6    0  -0.128   3.0295   1.0625  -0.6970
 CBJ  BR8   BR  BR     0  -0.030   4.3446   2.3776  -1.0088
 CBJ  C9    C   CR16   0  -0.215   1.7763   1.1949  -1.2889
 CBJ  C10   C   CR16   0  -0.299   0.7737   0.2496  -1.0887
 CBJ  C11   C   CR56   0   0.437   1.0683  -0.8286  -0.2767
 CBJ  N12   N   NR5    0  -0.614   0.2426  -1.9022   0.0655
 CBJ  C13   C   CH2    0  -0.418  -1.1344  -2.0333  -0.3664
 CBJ  C14   C   C      0   0.065  -2.0268  -0.9851   0.2545
 CBJ  C15   C   C1     0  -0.296  -2.0258  -0.8163   1.6383
 CBJ  C16   C   C1     0  -0.365  -2.8284   0.1357   2.2374
 CBJ  C17   C   C      0   0.308  -3.6580   0.9337   1.4576
 CBJ  O18   O   O2     0  -0.481  -4.4273   1.8640   2.0727
 CBJ  C19   C   CH2    0  -0.225  -4.9744   2.8405   1.1999
 CBJ  C20   C   CH2    0  -0.225  -5.5139   2.1834  -0.0470
 CBJ  O21   O   O2     0  -0.477  -4.4737   1.5046  -0.7304
 CBJ  C22   C   C      0   0.312  -3.6739   0.7571   0.0745
 CBJ  C23   C   C      0  -0.194  -2.8647  -0.1998  -0.5312
 CBJ  C24   C   C      0   0.354  -2.9398  -0.3547  -2.0448
 CBJ  O25   O   O      0  -0.584  -3.7187  -1.2247  -2.4636
 CBJ  O26   O   OC    -1  -0.578  -2.2022   0.3975  -2.7088
 CBJ  H6    H   HCR6   0   0.295   4.2948  -0.1420   0.5832
 CBJ  H9    H   HCR6   0   0.295   1.5625   2.0460  -1.9218
 CBJ  H10   H   HCR6   0   0.316  -0.1918   0.3783  -1.5646
 CBJ  H13   H   HCH2   0   0.287  -1.1586  -1.9932  -1.4558
 CBJ  H13A  H   HCH2   0   0.296  -1.4620  -3.0353  -0.0870
 CBJ  H15   H   H      0   0.248  -1.3886  -1.4297   2.2639
 CBJ  H16   H   H      0   0.262  -2.8202   0.2708   3.3118
 CBJ  H19   H   HCH2   0   0.259  -5.7736   3.3450   1.7410
 CBJ  H19A  H   HCH2   0   0.242  -4.2117   3.5829   0.9411
 CBJ  H20   H   HCH2   0   0.241  -6.3184   1.4845   0.2073
 CBJ  H20A  H   HCH2   0   0.259  -5.9141   2.9334  -0.7280

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    1.205  0.020  1.205
 CBJ  C2   C3    single    1.549  0.020  1.549
 CBJ  C2   N12   single    1.360  0.020  1.360
 CBJ  C3   O4    double    1.201  0.020  1.201
 CBJ  C3   C5    single    1.457  0.020  1.457
 CBJ  C5   C6    aromatic  1.382  0.020  1.382
 CBJ  C5   C11   aromatic  1.396  0.020  1.396
 CBJ  C6   C7    aromatic  1.387  0.020  1.387
 CBJ  C7   BR8   single    1.886  0.020  1.886
 CBJ  C7   C9    aromatic  1.392  0.020  1.392
 CBJ  C9   C10   aromatic  1.392  0.020  1.392
 CBJ  C10  C11   aromatic  1.381  0.020  1.381
 CBJ  C11  N12   single    1.397  0.020  1.397
 CBJ  N12  C13   single    1.449  0.020  1.449
 CBJ  C13  C14   single    1.510  0.020  1.510
 CBJ  C14  C15   aromatic  1.394  0.020  1.394
 CBJ  C14  C23   aromatic  1.391  0.020  1.391
 CBJ  C15  C16   aromatic  1.382  0.020  1.382
 CBJ  C16  C17   aromatic  1.390  0.020  1.390
 CBJ  C17  O18   single    1.355  0.020  1.355
 CBJ  C17  C22   aromatic  1.394  0.020  1.394
 CBJ  O18  C19   single    1.419  0.020  1.419
 CBJ  C19  C20   single    1.509  0.020  1.509
 CBJ  C20  O21   single    1.418  0.020  1.418
 CBJ  O21  C22   single    1.359  0.020  1.359
 CBJ  C22  C23   aromatic  1.392  0.020  1.392
 CBJ  C23  C24   single    1.523  0.020  1.523
 CBJ  C24  O25   deloc     1.241  0.020  1.241
 CBJ  C24  O26   deloc     1.245  0.020  1.245
 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

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   106.16  3.000
 CBJ  N12   C2   O1   128.13  3.000
 CBJ  C3    C2   O1   125.72  3.000
 CBJ  C5    C3   O4   131.19  3.000
 CBJ  C5    C3   C2   104.85  3.000
 CBJ  O4    C3   C2   123.95  3.000
 CBJ  C11   C5   C6   121.94  3.000
 CBJ  C11   C5   C3   107.11  3.000
 CBJ  C6    C5   C3   130.95  3.000
 CBJ  H6    C6   C7   122.10  3.000
 CBJ  H6    C6   C5   120.64  3.000
 CBJ  C7    C6   C5   117.26  3.000
 CBJ  C9    C7   BR8  119.42  3.000
 CBJ  C9    C7   C6   121.06  3.000
 CBJ  BR8   C7   C6   119.53  3.000
 CBJ  H9    C9   C10  118.42  3.000
 CBJ  H9    C9   C7   120.09  3.000
 CBJ  C10   C9   C7   121.50  3.000
 CBJ  H10   C10  C11  122.72  3.000
 CBJ  H10   C10  C9   119.84  3.000
 CBJ  C11   C10  C9   117.44  3.000
 CBJ  N12   C11  C10  128.15  3.000
 CBJ  N12   C11  C5   111.03  3.000
 CBJ  C10   C11  C5   120.81  3.000
 CBJ  C13   N12  C11  123.93  3.000
 CBJ  C13   N12  C2   125.19  3.000
 CBJ  C11   N12  C2   110.85  3.000
 CBJ  H13A  C13  H13  106.45  3.000
 CBJ  H13A  C13  C14  110.78  3.000
 CBJ  H13   C13  C14  111.85  3.000
 CBJ  H13A  C13  N12  106.99  3.000
 CBJ  H13   C13  N12  108.39  3.000
 CBJ  C14   C13  N12  112.10  3.000
 CBJ  C23   C14  C15  119.52  3.000
 CBJ  C23   C14  C13  121.02  3.000
 CBJ  C15   C14  C13  119.46  3.000
 CBJ  H15   C15  C16  118.77  3.000
 CBJ  H15   C15  C14  120.34  3.000
 CBJ  C16   C15  C14  120.89  3.000
 CBJ  H16   C16  C17  119.30  3.000
 CBJ  H16   C16  C15  120.78  3.000
 CBJ  C17   C16  C15  119.92  3.000
 CBJ  C22   C17  O18  122.06  3.000
 CBJ  C22   C17  C16  119.37  3.000
 CBJ  O18   C17  C16  118.57  3.000
 CBJ  C19   O18  C17  114.34  3.000
 CBJ  H19A  C19  H19  108.33  3.000
 CBJ  H19A  C19  C20  110.41  3.000
 CBJ  H19   C19  C20  110.48  3.000
 CBJ  H19A  C19  O18  110.07  3.000
 CBJ  H19   C19  O18  107.22  3.000
 CBJ  C20   C19  O18  110.26  3.000
 CBJ  H20A  C20  H20  108.33  3.000
 CBJ  H20A  C20  O21  107.33  3.000
 CBJ  H20   C20  O21  110.20  3.000
 CBJ  H20A  C20  C19  110.36  3.000
 CBJ  H20   C20  C19  110.39  3.000
 CBJ  O21   C20  C19  110.15  3.000
 CBJ  C22   O21  C20  114.19  3.000
 CBJ  C23   C22  O21  117.56  3.000
 CBJ  C23   C22  C17  120.80  3.000
 CBJ  O21   C22  C17  121.64  3.000
 CBJ  C24   C23  C22  118.27  3.000
 CBJ  C24   C23  C14  122.23  3.000
 CBJ  C22   C23  C14  119.49  3.000
 CBJ  O26   C24  O25  127.99  3.000
 CBJ  O26   C24  C23  116.05  3.000
 CBJ  O25   C24  C23  115.96  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  Var_01    C20  C19  O18  C17   44.10  30.0  1
 CBJ  Var_02    O21  C20  C19  O18  -60.40  30.0  1
 CBJ  Var_03    C22  C17  O18  C19  -14.99  30.0  1
 CBJ  Var_04    C23  C22  O21  C20  163.63  30.0  1
 CBJ  Var_05    C14  C13  N12  C2   110.13  30.0  3
 CBJ  Var_06    C15  C14  C13  N12  -52.38  30.0  2
 CBJ  Var_07    O25  C24  C23  C14   85.44  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

