# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 09:01:24 2021
#   Inital geometry file: a 89 line input string
#   Ligand name: 4-{[(5-fluoro-2-hydroxyphenyl)methyl]amino}-1H-isoindole-1,3(2H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc(F)cc1CNc2cccc3C(=O)NC(=O)c23
#
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
 VXM  VXM  4-{[(5-fluoro-2-hydroxyphenyl)methyl]amino}-1H-isoindole-1,3(2H)-dione  ligand  32  21  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VXM
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
 VXM  C02  C  CR5   0   0.566  -37.4972  -22.2679  -17.4553
 VXM  N03  N  NR15  0  -0.743  -36.2764  -22.0065  -16.8710
 VXM  C04  C  CR5   0   0.574  -36.1710  -22.5294  -15.5913
 VXM  C08  C  CH2   0  -0.325  -37.5382  -24.6415  -11.8631
 VXM  C09  C  CR6   0  -0.021  -36.3957  -24.7280  -10.8926
 VXM  C10  C  CR16  0  -0.438  -36.3044  -23.8215   -9.8440
 VXM  C11  C  CR6   0   0.514  -35.2459  -23.8914   -8.9606
 VXM  C13  C  CR16  0  -0.404  -34.2603  -24.8468   -9.0896
 VXM  C15  C  CR6   0   0.335  -35.3993  -25.6991  -11.0411
 VXM  C17  C  CR16  0  -0.355  -39.1940  -24.4095  -14.2572
 VXM  C20  C  CR56  0  -0.063  -38.2599  -23.0468  -16.4440
 VXM  C05  C  CR56  0  -0.134  -37.4482  -23.1998  -15.3265
 VXM  C06  C  CR6   0   0.393  -37.8777  -23.8907  -14.1872
 VXM  C14  C  CR16  0  -0.362  -34.3429  -25.7531  -10.1367
 VXM  C18  C  CR16  0  -0.237  -39.9802  -24.2445  -15.3813
 VXM  C19  C  CR16  0  -0.342  -39.5328  -23.5544  -16.5148
 VXM  F12  F  F     0  -0.321  -35.1771  -23.0029   -7.9515
 VXM  N07  N  NH1   0  -0.684  -37.0872  -24.0549  -13.1079
 VXM  O01  O  O     0  -0.403  -37.8478  -21.9242  -18.5571
 VXM  O16  O  OH1   0  -0.621  -35.5131  -26.5585  -12.0721
 VXM  O21  O  O     0  -0.421  -35.2011  -22.4243  -14.8734
 VXM  H1   H  HNR5  0   0.424  -35.5399  -21.4799  -17.3192
 VXM  H2   H  HCH2  0   0.258  -38.3432  -24.0453  -11.4198
 VXM  H3   H  HCH2  0   0.258  -37.9500  -25.6371  -12.0492
 VXM  H4   H  HCR6  0   0.279  -37.0645  -23.0601   -9.7206
 VXM  H5   H  HCR6  0   0.285  -33.4368  -24.8912   -8.3892
 VXM  H6   H  HCR6  0   0.289  -39.6072  -24.9460  -13.4144
 VXM  H7   H  HCR6  0   0.283  -33.5739  -26.5087  -10.2477
 VXM  H8   H  HCR6  0   0.274  -40.9780  -24.6634  -15.3754
 VXM  H9   H  HCR6  0   0.268  -40.1617  -23.4308  -17.3852
 VXM  H10  H  HNH1  0   0.397  -36.2215  -23.5403  -13.0873
 VXM  H11  H  HOH1  0   0.478  -34.7827  -27.1871  -12.0676

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
 VXM  O01  C02  double    1.206  0.020  1.206
 VXM  C02  N03  single    1.378  0.020  1.378
 VXM  C02  C20  single    1.487  0.020  1.487
 VXM  N03  C04  single    1.386  0.020  1.386
 VXM  C20  C19  aromatic  1.372  0.020  1.372
 VXM  C20  C05  aromatic  1.390  0.020  1.390
 VXM  C19  C18  aromatic  1.400  0.020  1.400
 VXM  C04  C05  single    1.467  0.020  1.467
 VXM  C04  O21  double    1.211  0.020  1.211
 VXM  C05  C06  aromatic  1.400  0.020  1.400
 VXM  C18  C17  aromatic  1.382  0.020  1.382
 VXM  C06  C17  aromatic  1.417  0.020  1.417
 VXM  C06  N07  single    1.348  0.020  1.348
 VXM  N07  C08  single    1.448  0.020  1.448
 VXM  O16  C15  single    1.347  0.020  1.347
 VXM  C08  C09  single    1.502  0.020  1.502
 VXM  C15  C09  aromatic  1.399  0.020  1.399
 VXM  C15  C14  aromatic  1.392  0.020  1.392
 VXM  C09  C10  aromatic  1.389  0.020  1.389
 VXM  C14  C13  aromatic  1.387  0.020  1.387
 VXM  C10  C11  aromatic  1.380  0.020  1.380
 VXM  C13  C11  aromatic  1.379  0.020  1.379
 VXM  C11  F12  single    1.346  0.020  1.346
 VXM  N03  H1   single    0.860  0.020  1.020
 VXM  C08  H2   single    0.970  0.020  1.090
 VXM  C08  H3   single    0.970  0.020  1.090
 VXM  C10  H4   single    0.930  0.020  1.080
 VXM  C13  H5   single    0.930  0.020  1.080
 VXM  C17  H6   single    0.930  0.020  1.080
 VXM  C14  H7   single    0.930  0.020  1.080
 VXM  C18  H8   single    0.930  0.020  1.080
 VXM  C19  H9   single    0.930  0.020  1.080
 VXM  N07  H10  single    0.860  0.020  1.020
 VXM  O16  H11  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
 VXM  O01  C02  C20  128.41  3.000
 VXM  C20  C02  N03  105.39  3.000
 VXM  O01  C02  N03  126.20  3.000
 VXM  H1   N03  C04  123.41  3.000
 VXM  H1   N03  C02  123.81  3.000
 VXM  C04  N03  C02  112.77  3.000
 VXM  O21  C04  C05  129.05  3.000
 VXM  O21  C04  N03  125.11  3.000
 VXM  C05  C04  N03  105.83  3.000
 VXM  H3   C08  H2   106.72  3.000
 VXM  H3   C08  N07  109.87  3.000
 VXM  H2   C08  N07  110.87  3.000
 VXM  H3   C08  C09  110.13  3.000
 VXM  H2   C08  C09  109.20  3.000
 VXM  N07  C08  C09  109.99  3.000
 VXM  C15  C09  C10  119.10  3.000
 VXM  C10  C09  C08  120.02  3.000
 VXM  C15  C09  C08  120.88  3.000
 VXM  H4   C10  C11  120.05  3.000
 VXM  H4   C10  C09  119.92  3.000
 VXM  C11  C10  C09  120.03  3.000
 VXM  F12  C11  C13  119.40  3.000
 VXM  F12  C11  C10  119.04  3.000
 VXM  C13  C11  C10  121.55  3.000
 VXM  H5   C13  C14  120.47  3.000
 VXM  H5   C13  C11  120.79  3.000
 VXM  C14  C13  C11  118.74  3.000
 VXM  O16  C15  C14  122.46  3.000
 VXM  C14  C15  C09  119.90  3.000
 VXM  O16  C15  C09  117.64  3.000
 VXM  H6   C17  C18  118.42  3.000
 VXM  H6   C17  C06  119.89  3.000
 VXM  C18  C17  C06  121.68  3.000
 VXM  C19  C20  C05  122.86  3.000
 VXM  C05  C20  C02  107.76  3.000
 VXM  C19  C20  C02  129.38  3.000
 VXM  C06  C05  C20  121.98  3.000
 VXM  C06  C05  C04  129.77  3.000
 VXM  C20  C05  C04  108.25  3.000
 VXM  N07  C06  C05  122.13  3.000
 VXM  N07  C06  C17  122.68  3.000
 VXM  C05  C06  C17  115.19  3.000
 VXM  H7   C14  C15  119.94  3.000
 VXM  H7   C14  C13  119.37  3.000
 VXM  C15  C14  C13  120.69  3.000
 VXM  H8   C18  C19  119.32  3.000
 VXM  H8   C18  C17  118.29  3.000
 VXM  C19  C18  C17  122.39  3.000
 VXM  H9   C19  C18  121.48  3.000
 VXM  H9   C19  C20  122.61  3.000
 VXM  C18  C19  C20  115.90  3.000
 VXM  H10  N07  C06  117.27  3.000
 VXM  H10  N07  C08  117.20  3.000
 VXM  C06  N07  C08  123.71  3.000
 VXM  H11  O16  C15  110.40  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
 VXM  CONST_01  C13  C14  C15  C09    0.00   0.0  0
 VXM  CONST_02  C13  C11  C10  C09    0.00   0.0  0
 VXM  CONST_03  C14  C15  C09  C10    0.00   0.0  0
 VXM  CONST_04  C14  C13  C11  C10    0.00   0.0  0
 VXM  CONST_05  C15  C09  C10  C11    0.00   0.0  0
 VXM  CONST_06  C15  C14  C13  C11    0.00   0.0  0
 VXM  CONST_07  C20  C19  C18  C17    0.00   0.0  0
 VXM  CONST_08  C20  C05  C06  C17    0.00   0.0  0
 VXM  CONST_09  C18  C19  C20  C05    0.00   0.0  0
 VXM  CONST_10  C18  C17  C06  C05    0.00   0.0  0
 VXM  CONST_11  C19  C20  C05  C06    0.00   0.0  0
 VXM  CONST_12  C19  C18  C17  C06    0.00   0.0  0
 VXM  CONST_13  C20  C02  N03  C04    0.00   0.0  0
 VXM  CONST_14  N07  C06  C05  C04    0.00   0.0  0
 VXM  CONST_15  C14  C15  C09  C08  180.00   0.0  0
 VXM  CONST_16  C11  C10  C09  C08  180.00   0.0  0
 VXM  CONST_17  F12  C11  C10  C09  180.00   0.0  0
 VXM  CONST_18  O16  C15  C09  C10  180.00   0.0  0
 VXM  CONST_19  O16  C15  C14  C13  180.00   0.0  0
 VXM  CONST_20  N07  C06  C05  C20  180.00   0.0  0
 VXM  CONST_21  F12  C11  C13  C14  180.00   0.0  0
 VXM  CONST_22  N07  C06  C17  C18  180.00   0.0  0
 VXM  CONST_23  O01  C02  N03  C04  180.00   0.0  0
 VXM  CONST_24  H9   C19  C20  C02    0.00   0.0  0
 VXM  CONST_25  H7   C14  C15  C09  180.00   0.0  0
 VXM  CONST_26  H5   C13  C11  C10  180.00   0.0  0
 VXM  CONST_27  H4   C10  C11  C13  180.00   0.0  0
 VXM  CONST_28  H8   C18  C19  C20  180.00   0.0  0
 VXM  CONST_29  H6   C17  C06  C05  180.00   0.0  0
 VXM  CONST_30  H1   N03  C02  C20  180.00   0.0  0
 VXM  CONST_31  C05  C06  N07  C08  180.00   0.0  0
 VXM  CONST_32  C17  C06  N07  C08    0.00   0.0  0
 VXM  CONST_33  H10  N07  C06  C17  180.00   0.0  0
 VXM  Var_01    C06  N07  C08  C09  177.62  30.0  1
 VXM  Var_02    N07  C08  C09  C10  103.72  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
 VXM  plan-1  C08  0.020
 VXM  plan-1  C09  0.020
 VXM  plan-1  C10  0.020
 VXM  plan-1  C11  0.020
 VXM  plan-1  C13  0.020
 VXM  plan-1  C15  0.020
 VXM  plan-1  C14  0.020
 VXM  plan-1  F12  0.020
 VXM  plan-1  O16  0.020
 VXM  plan-1  H4   0.020
 VXM  plan-1  H5   0.020
 VXM  plan-1  H7   0.020
 VXM  plan-2  C02  0.020
 VXM  plan-2  N03  0.020
 VXM  plan-2  C04  0.020
 VXM  plan-2  C17  0.020
 VXM  plan-2  C20  0.020
 VXM  plan-2  C05  0.020
 VXM  plan-2  C06  0.020
 VXM  plan-2  C18  0.020
 VXM  plan-2  C19  0.020
 VXM  plan-2  N07  0.020
 VXM  plan-2  O01  0.020
 VXM  plan-2  O21  0.020
 VXM  plan-2  H1   0.020
 VXM  plan-2  H6   0.020
 VXM  plan-2  H8   0.020
 VXM  plan-2  H9   0.020
 VXM  plan-3  C08  0.020
 VXM  plan-3  C06  0.020
 VXM  plan-3  N07  0.020
 VXM  plan-3  H10  0.020

