# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 08:05:36 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: 3-oxidanylidene-2-[3-(trifluoromethyl)phenyl]-1~{H}-isoindole-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cccc2CN(C(=O)c12)c3cccc(c3)C(F)(F)F
#
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
 B06  B06  '3-oxidanylidene-2-[3-(trifluoromethyl)phenyl]-1~{H}-isoindole-4-carboxylic acid'  ligand  32  23  .  2022-07-24  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_B06
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
 B06  O01  O  O      0  -0.595   3.6837  -2.6224   1.2068
 B06  C02  C  C      0   0.343   3.5430  -2.0944   0.0918
 B06  O03  O  OC    -1  -0.593   3.3909  -2.6429  -1.0109
 B06  C04  C  C      0  -0.037   3.6183  -0.5765   0.0666
 B06  C05  C  C1     0  -0.316   4.8537   0.0679   0.0674
 B06  C06  C  C1     0  -0.229   4.9511   1.4566   0.0207
 B06  C07  C  C1     0  -0.351   3.8177   2.2617  -0.0147
 B06  C08  C  CR5    0   0.106   2.5905   1.6278  -0.0033
 B06  C09  C  CH2    0  -0.305   1.2208   2.2169  -0.0161
 B06  N10  N  NR5    0  -0.639   0.3552   1.0452   0.0108
 B06  C11  C  CR5    0   0.551   1.0765  -0.1322   0.0530
 B06  O12  O  O      0  -0.455   0.6196  -1.2564   0.1060
 B06  C13  C  CR5    0  -0.090   2.4975   0.2470   0.0334
 B06  C14  C  CR6    0   0.409  -1.0342   1.1818   0.0111
 B06  C15  C  CR16   0  -0.339  -1.5912   2.4656   0.0608
 B06  C16  C  CR16   0  -0.226  -2.9626   2.6448   0.0593
 B06  C17  C  CR16   0  -0.310  -3.8246   1.5608   0.0076
 B06  C18  C  CR6    0  -0.166  -3.2761   0.2886  -0.0488
 B06  C19  C  CR16   0  -0.358  -1.9016   0.0876  -0.0458
 B06  C20  C  CT     0   1.049  -4.1573  -0.9226  -0.0728
 B06  F21  F  F      0  -0.304  -5.4296  -0.6268  -0.3545
 B06  F22  F  F      0  -0.311  -3.7547  -1.8215  -0.9810
 B06  F23  F  F      0  -0.315  -4.1586  -1.5543   1.1117
 B06  H2   H  H      0   0.258   5.7634  -0.5197   0.0998
 B06  H3   H  H      0   0.262   5.9313   1.9164   0.0159
 B06  H4   H  H      0   0.256   3.9009   3.3402  -0.0458
 B06  H5   H  HCH2   0   0.284   1.0515   2.8555   0.8547
 B06  H6   H  HCH2   0   0.285   1.0405   2.8196  -0.9100
 B06  H7   H  HCR6   0   0.293  -0.9619   3.3426   0.1010
 B06  H8   H  HCR6   0   0.271  -3.3620   3.6492   0.1001
 B06  H9   H  HCR6   0   0.271  -4.8934   1.7198   0.0099
 B06  H10  H  HCR6   0   0.301  -1.5056  -0.9134  -0.0909

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
 B06  F21  C20  single    1.336  0.020  1.336
 B06  F23  C20  single    1.342  0.020  1.342
 B06  F22  C20  single    1.340  0.020  1.340
 B06  C20  C18  single    1.498  0.020  1.498
 B06  C18  C17  aromatic  1.386  0.020  1.386
 B06  C18  C19  aromatic  1.389  0.020  1.389
 B06  C17  C16  aromatic  1.386  0.020  1.386
 B06  C19  C14  aromatic  1.397  0.020  1.397
 B06  O12  C11  double    1.215  0.020  1.215
 B06  O01  C02  deloc     1.242  0.020  1.242
 B06  O03  C02  deloc     1.241  0.020  1.241
 B06  C02  C04  single    1.520  0.020  1.520
 B06  C16  C15  aromatic  1.383  0.020  1.383
 B06  C14  C15  aromatic  1.400  0.020  1.400
 B06  C14  N10  single    1.396  0.020  1.396
 B06  C11  N10  single    1.381  0.020  1.381
 B06  C11  C13  single    1.471  0.020  1.471
 B06  N10  C09  single    1.457  0.020  1.457
 B06  C04  C13  aromatic  1.391  0.020  1.391
 B06  C04  C05  aromatic  1.393  0.020  1.393
 B06  C13  C08  aromatic  1.384  0.020  1.384
 B06  C09  C08  single    1.491  0.020  1.491
 B06  C05  C06  aromatic  1.393  0.020  1.393
 B06  C08  C07  aromatic  1.381  0.020  1.381
 B06  C06  C07  aromatic  1.391  0.020  1.391
 B06  C05  H2   single    0.930  0.020  1.080
 B06  C06  H3   single    0.930  0.020  1.080
 B06  C07  H4   single    0.930  0.020  1.080
 B06  C09  H5   single    0.970  0.020  1.090
 B06  C09  H6   single    0.970  0.020  1.090
 B06  C15  H7   single    0.930  0.020  1.080
 B06  C16  H8   single    0.930  0.020  1.080
 B06  C17  H9   single    0.930  0.020  1.080
 B06  C19  H10  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
 B06  C04  C02  O03  115.64  3.000
 B06  C04  C02  O01  115.72  3.000
 B06  O03  C02  O01  128.59  3.000
 B06  C13  C04  C05  116.14  3.000
 B06  C05  C04  C02  120.38  3.000
 B06  C13  C04  C02  123.48  3.000
 B06  H2   C05  C06  118.88  3.000
 B06  H2   C05  C04  119.58  3.000
 B06  C06  C05  C04  121.54  3.000
 B06  H3   C06  C07  119.46  3.000
 B06  H3   C06  C05  119.14  3.000
 B06  C07  C06  C05  121.40  3.000
 B06  H4   C07  C08  121.73  3.000
 B06  H4   C07  C06  121.00  3.000
 B06  C08  C07  C06  117.27  3.000
 B06  C13  C08  C09  109.43  3.000
 B06  C09  C08  C07  129.40  3.000
 B06  C13  C08  C07  121.17  3.000
 B06  H6   C09  H5   107.69  3.000
 B06  H6   C09  N10  111.14  3.000
 B06  H5   C09  N10  111.29  3.000
 B06  H6   C09  C08  112.11  3.000
 B06  H5   C09  C08  111.48  3.000
 B06  N10  C09  C08  103.17  3.000
 B06  C14  N10  C11  127.09  3.000
 B06  C11  N10  C09  112.07  3.000
 B06  C14  N10  C09  120.83  3.000
 B06  C13  C11  O12  127.05  3.000
 B06  C13  C11  N10  106.52  3.000
 B06  O12  C11  N10  126.43  3.000
 B06  C11  C13  C08  108.80  3.000
 B06  C08  C13  C04  122.48  3.000
 B06  C11  C13  C04  128.71  3.000
 B06  C19  C14  C15  118.19  3.000
 B06  C15  C14  N10  119.05  3.000
 B06  C19  C14  N10  122.75  3.000
 B06  H7   C15  C16  118.20  3.000
 B06  H7   C15  C14  120.92  3.000
 B06  C16  C15  C14  120.88  3.000
 B06  H8   C16  C17  119.87  3.000
 B06  H8   C16  C15  119.11  3.000
 B06  C17  C16  C15  121.03  3.000
 B06  H9   C17  C18  121.76  3.000
 B06  H9   C17  C16  120.00  3.000
 B06  C18  C17  C16  118.24  3.000
 B06  C20  C18  C19  117.71  3.000
 B06  C19  C18  C17  121.61  3.000
 B06  C20  C18  C17  120.65  3.000
 B06  H10  C19  C18  119.87  3.000
 B06  H10  C19  C14  120.08  3.000
 B06  C18  C19  C14  120.06  3.000
 B06  F23  C20  F22  106.43  3.000
 B06  F22  C20  F21  106.96  3.000
 B06  F23  C20  F21  106.81  3.000
 B06  F22  C20  C18  112.12  3.000
 B06  F23  C20  C18  111.52  3.000
 B06  F21  C20  C18  112.61  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
 B06  CONST_01  C07  C08  C13  C04    0.00   0.0  0
 B06  CONST_02  C07  C06  C05  C04    0.00   0.0  0
 B06  CONST_03  C08  C13  C04  C05    0.00   0.0  0
 B06  CONST_04  C08  C07  C06  C05    0.00   0.0  0
 B06  CONST_05  C13  C04  C05  C06    0.00   0.0  0
 B06  CONST_06  C13  C08  C07  C06    0.00   0.0  0
 B06  CONST_07  C17  C18  C19  C14    0.00   0.0  0
 B06  CONST_08  C17  C16  C15  C14    0.00   0.0  0
 B06  CONST_09  C18  C17  C16  C15    0.00   0.0  0
 B06  CONST_10  C18  C19  C14  C15    0.00   0.0  0
 B06  CONST_11  C19  C18  C17  C16    0.00   0.0  0
 B06  CONST_12  C19  C14  C15  C16    0.00   0.0  0
 B06  CONST_13  C18  C19  C14  N10  180.00   0.0  0
 B06  CONST_14  C16  C15  C14  N10  180.00   0.0  0
 B06  CONST_15  C13  C11  N10  C09    0.00   0.0  0
 B06  CONST_16  C14  N10  C11  C13  180.00   0.0  0
 B06  CONST_17  C11  C13  C04  C02    0.00   0.0  0
 B06  CONST_18  C08  C13  C04  C02  180.00   0.0  0
 B06  CONST_19  C06  C05  C04  C02  180.00   0.0  0
 B06  CONST_20  C20  C18  C19  C14  180.00   0.0  0
 B06  CONST_21  C20  C18  C17  C16  180.00   0.0  0
 B06  CONST_22  O12  C11  N10  C09  180.00   0.0  0
 B06  CONST_23  C14  N10  C11  O12    0.00   0.0  0
 B06  CONST_24  H3   C06  C05  C04  180.00   0.0  0
 B06  CONST_25  H4   C07  C06  C05  180.00   0.0  0
 B06  CONST_26  H2   C05  C06  C07  180.00   0.0  0
 B06  CONST_27  H10  C19  C14  N10    0.00   0.0  0
 B06  CONST_28  H7   C15  C14  N10    0.00   0.0  0
 B06  CONST_29  H8   C16  C15  C14  180.00   0.0  0
 B06  CONST_30  H9   C17  C16  C15  180.00   0.0  0
 B06  Var_01    C19  C14  N10  C09  175.99  30.0  2
 B06  Var_02    H5   C09  C08  C07  -60.29  30.0  1
 B06  Var_03    C13  C04  C02  O01  -99.57  30.0  2
 B06  Var_04    F21  C20  C18  C17   14.97  30.0  3

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
 B06  plan-1  N10  0.020
 B06  plan-1  C14  0.020
 B06  plan-1  C15  0.020
 B06  plan-1  C16  0.020
 B06  plan-1  C17  0.020
 B06  plan-1  C18  0.020
 B06  plan-1  C19  0.020
 B06  plan-1  C20  0.020
 B06  plan-1  H7   0.020
 B06  plan-1  H8   0.020
 B06  plan-1  H9   0.020
 B06  plan-1  H10  0.020
 B06  plan-2  C02  0.020
 B06  plan-2  C04  0.020
 B06  plan-2  C05  0.020
 B06  plan-2  C06  0.020
 B06  plan-2  C07  0.020
 B06  plan-2  C08  0.020
 B06  plan-2  C09  0.020
 B06  plan-2  N10  0.020
 B06  plan-2  C11  0.020
 B06  plan-2  O12  0.020
 B06  plan-2  C13  0.020
 B06  plan-2  C14  0.020
 B06  plan-2  H2   0.020
 B06  plan-2  H3   0.020
 B06  plan-2  H4   0.020
 B06  plan-3  O01  0.020
 B06  plan-3  C02  0.020
 B06  plan-3  O03  0.020
 B06  plan-3  C04  0.020

