# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 09:51:47 2021
#   Inital geometry file: a 101 line input string
#   Ligand name: 4-{[3-(2-hydroxyphenyl)propyl]amino}-1H-isoindole-1,3(2H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccccc1CCCNc2cccc3C(=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
 VXS  VXS  4-{[3-(2-hydroxyphenyl)propyl]amino}-1H-isoindole-1,3(2H)-dione  ligand  38  22  .  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_VXS
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
 VXS  C10  C  CH2   0  -0.452  43.5561   -7.9686  -36.8235
 VXS  C11  C  CR6   0   0.014  43.4107   -6.4701  -36.8953
 VXS  C12  C  CR16  0  -0.310  42.8261   -5.8094  -37.9695
 VXS  C13  C  CR16  0  -0.271  42.7082   -4.4235  -38.0067
 VXS  C14  C  CR16  0  -0.259  43.1848   -3.6702  -36.9471
 VXS  C15  C  CR16  0  -0.380  43.7741   -4.3012  -35.8597
 VXS  C16  C  CR6   0   0.324  43.8859   -5.6867  -35.8328
 VXS  C18  C  CR16  0  -0.353  43.5699  -12.9466  -36.8209
 VXS  C19  C  CR16  0  -0.238  43.6878  -14.2303  -36.3245
 VXS  C20  C  CR16  0  -0.344  42.8559  -14.7229  -35.3108
 VXS  C21  C  CR56  0  -0.061  41.9082  -13.8510  -34.8380
 VXS  C02  C  CR5   0   0.565  40.8782  -14.0579  -33.7863
 VXS  C04  C  CR5   0   0.574  40.6644  -11.9138  -34.5976
 VXS  C05  C  CR56  0  -0.140  41.7696  -12.5541  -35.3181
 VXS  C06  C  CR6   0   0.400  42.5979  -12.0422  -36.3245
 VXS  C08  C  CH2   0  -0.276  43.2131  -10.2375  -37.8973
 VXS  C09  C  CH2   0  -0.501  42.9966   -8.7371  -38.0139
 VXS  N03  N  NR15  0  -0.743  40.1902  -12.8662  -33.7080
 VXS  N07  N  NH1   0  -0.694  42.4807  -10.7770  -36.7732
 VXS  O17  O  OH1   0  -0.628  44.4532   -6.3369  -34.7937
 VXS  O22  O  O     0  -0.422  40.2211  -10.7931  -34.7205
 VXS  H1   H  HCH2  0   0.240  43.0846   -8.3262  -35.9027
 VXS  H2   H  HCH2  0   0.242  44.6168   -8.2212  -36.7161
 VXS  H3   H  HCR6  0   0.254  42.4456   -6.3809  -38.8061
 VXS  H4   H  HCR6  0   0.248  42.2469   -3.9439  -38.8596
 VXS  H5   H  HCR6  0   0.255  43.1023   -2.5911  -36.9574
 VXS  H6   H  HCR6  0   0.265  44.1502   -3.7136  -35.0289
 VXS  H7   H  HCR6  0   0.286  44.2403  -12.6359  -37.6103
 VXS  H8   H  HCR6  0   0.273  44.4497  -14.8737  -36.7449
 VXS  H9   H  HCR6  0   0.267  42.9585  -15.7309  -34.9346
 VXS  H10  H  HCH2  0   0.247  42.9099  -10.7242  -38.8311
 VXS  H11  H  HCH2  0   0.237  44.2806  -10.4348  -37.7670
 VXS  H12  H  HCH2  0   0.252  43.4826   -8.4113  -38.9360
 VXS  H13  H  HCH2  0   0.240  41.9287   -8.5332  -38.1409
 VXS  H14  H  HNR5  0   0.424  39.4169  -12.7055  -33.0779
 VXS  H15  H  HNH1  0   0.394  41.6760  -10.2582  -36.4585
 VXS  H16  H  HOH1  0   0.474  44.7212   -5.7083  -34.1145
 VXS  O01  O  O     0  -0.404  40.6676  -15.0464  -33.1277

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
 VXS  C09  C08  single    1.520  0.020  1.520
 VXS  C09  C10  single    1.523  0.020  1.523
 VXS  C08  N07  single    1.446  0.020  1.446
 VXS  C10  C11  single    1.507  0.020  1.507
 VXS  N07  C06  single    1.348  0.020  1.348
 VXS  C12  C11  aromatic  1.390  0.020  1.390
 VXS  C12  C13  aromatic  1.391  0.020  1.391
 VXS  C11  C16  aromatic  1.403  0.020  1.403
 VXS  C13  C14  aromatic  1.385  0.020  1.385
 VXS  C06  C18  aromatic  1.417  0.020  1.417
 VXS  C06  C05  aromatic  1.400  0.020  1.400
 VXS  C18  C19  aromatic  1.381  0.020  1.381
 VXS  O22  C04  double    1.211  0.020  1.211
 VXS  C16  O17  single    1.351  0.020  1.351
 VXS  C16  C15  aromatic  1.390  0.020  1.390
 VXS  C14  C15  aromatic  1.388  0.020  1.388
 VXS  C05  C04  single    1.466  0.020  1.466
 VXS  C05  C21  aromatic  1.390  0.020  1.390
 VXS  C04  N03  single    1.387  0.020  1.387
 VXS  C19  C20  aromatic  1.401  0.020  1.401
 VXS  C21  C20  aromatic  1.372  0.020  1.372
 VXS  C21  C02  single    1.487  0.020  1.487
 VXS  N03  C02  single    1.378  0.020  1.378
 VXS  C02  O01  double    1.206  0.020  1.206
 VXS  C10  H1   single    0.970  0.020  1.090
 VXS  C10  H2   single    0.970  0.020  1.090
 VXS  C12  H3   single    0.930  0.020  1.080
 VXS  C13  H4   single    0.930  0.020  1.080
 VXS  C14  H5   single    0.930  0.020  1.080
 VXS  C15  H6   single    0.930  0.020  1.080
 VXS  C18  H7   single    0.930  0.020  1.080
 VXS  C19  H8   single    0.930  0.020  1.080
 VXS  C20  H9   single    0.930  0.020  1.080
 VXS  C08  H10  single    0.970  0.020  1.090
 VXS  C08  H11  single    0.970  0.020  1.090
 VXS  C09  H12  single    0.970  0.020  1.090
 VXS  C09  H13  single    0.970  0.020  1.090
 VXS  N03  H14  single    0.860  0.020  1.020
 VXS  N07  H15  single    0.860  0.020  1.020
 VXS  O17  H16  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
 VXS  H2   C10  H1   105.02  3.000
 VXS  H2   C10  C09  108.41  3.000
 VXS  H1   C10  C09  109.54  3.000
 VXS  H2   C10  C11  109.10  3.000
 VXS  H1   C10  C11  108.87  3.000
 VXS  C09  C10  C11  115.40  3.000
 VXS  C16  C11  C12  117.53  3.000
 VXS  C16  C11  C10  119.11  3.000
 VXS  C12  C11  C10  123.36  3.000
 VXS  H3   C12  C13  118.39  3.000
 VXS  H3   C12  C11  119.62  3.000
 VXS  C13  C12  C11  121.99  3.000
 VXS  H4   C13  C14  120.59  3.000
 VXS  H4   C13  C12  119.92  3.000
 VXS  C14  C13  C12  119.49  3.000
 VXS  H5   C14  C15  119.54  3.000
 VXS  H5   C14  C13  120.59  3.000
 VXS  C15  C14  C13  119.88  3.000
 VXS  H6   C15  C16  119.81  3.000
 VXS  H6   C15  C14  120.05  3.000
 VXS  C16  C15  C14  120.14  3.000
 VXS  O17  C16  C15  121.89  3.000
 VXS  C15  C16  C11  120.97  3.000
 VXS  O17  C16  C11  117.13  3.000
 VXS  H7   C18  C06  119.84  3.000
 VXS  H7   C18  C19  118.45  3.000
 VXS  C06  C18  C19  121.71  3.000
 VXS  H8   C19  C20  119.35  3.000
 VXS  H8   C19  C18  118.23  3.000
 VXS  C20  C19  C18  122.42  3.000
 VXS  H9   C20  C21  122.57  3.000
 VXS  H9   C20  C19  121.57  3.000
 VXS  C21  C20  C19  115.86  3.000
 VXS  C05  C21  C02  107.77  3.000
 VXS  C02  C21  C20  129.35  3.000
 VXS  C05  C21  C20  122.89  3.000
 VXS  O01  C02  N03  126.18  3.000
 VXS  O01  C02  C21  128.41  3.000
 VXS  N03  C02  C21  105.41  3.000
 VXS  O22  C04  N03  125.12  3.000
 VXS  N03  C04  C05  105.84  3.000
 VXS  O22  C04  C05  129.04  3.000
 VXS  C06  C05  C04  129.74  3.000
 VXS  C04  C05  C21  108.24  3.000
 VXS  C06  C05  C21  122.03  3.000
 VXS  N07  C06  C05  122.08  3.000
 VXS  C05  C06  C18  115.09  3.000
 VXS  N07  C06  C18  122.82  3.000
 VXS  H11  C08  H10  106.95  3.000
 VXS  H11  C08  N07  109.54  3.000
 VXS  H10  C08  N07  110.89  3.000
 VXS  H11  C08  C09  109.05  3.000
 VXS  H10  C08  C09  109.48  3.000
 VXS  N07  C08  C09  110.84  3.000
 VXS  H13  C09  H12  106.30  3.000
 VXS  H13  C09  C08  109.37  3.000
 VXS  H12  C09  C08  107.20  3.000
 VXS  H13  C09  C10  110.79  3.000
 VXS  H12  C09  C10  110.23  3.000
 VXS  C08  C09  C10  112.68  3.000
 VXS  H14  N03  C04  123.54  3.000
 VXS  H14  N03  C02  123.71  3.000
 VXS  C04  N03  C02  112.74  3.000
 VXS  H15  N07  C08  117.07  3.000
 VXS  H15  N07  C06  116.66  3.000
 VXS  C08  N07  C06  124.41  3.000
 VXS  H16  O17  C16  110.19  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
 VXS  CONST_01  C14  C13  C12  C11     0.00   0.0  0
 VXS  CONST_02  C14  C15  C16  C11     0.00   0.0  0
 VXS  CONST_03  C15  C16  C11  C12     0.00   0.0  0
 VXS  CONST_04  C15  C14  C13  C12     0.00   0.0  0
 VXS  CONST_05  C16  C11  C12  C13     0.00   0.0  0
 VXS  CONST_06  C16  C15  C14  C13     0.00   0.0  0
 VXS  CONST_07  C21  C05  C06  C18     0.00   0.0  0
 VXS  CONST_08  C21  C20  C19  C18     0.00   0.0  0
 VXS  CONST_09  C05  C06  C18  C19     0.00   0.0  0
 VXS  CONST_10  C05  C21  C20  C19     0.00   0.0  0
 VXS  CONST_11  C06  C18  C19  C20     0.00   0.0  0
 VXS  CONST_12  C06  C05  C21  C20     0.00   0.0  0
 VXS  CONST_13  C04  N03  C02  C21     0.00   0.0  0
 VXS  CONST_14  C13  C12  C11  C10   180.00   0.0  0
 VXS  CONST_15  C15  C16  C11  C10   180.00   0.0  0
 VXS  CONST_16  O17  C16  C11  C12   180.00   0.0  0
 VXS  CONST_17  O17  C16  C15  C14   180.00   0.0  0
 VXS  CONST_18  N07  C06  C18  C19   180.00   0.0  0
 VXS  CONST_19  N07  C06  C05  C21   180.00   0.0  0
 VXS  CONST_20  N07  C06  C05  C04     0.00   0.0  0
 VXS  CONST_21  O01  C02  N03  C04   180.00   0.0  0
 VXS  CONST_22  H4   C13  C12  C11   180.00   0.0  0
 VXS  CONST_23  H6   C15  C16  C11   180.00   0.0  0
 VXS  CONST_24  H5   C14  C13  C12   180.00   0.0  0
 VXS  CONST_25  H3   C12  C13  C14   180.00   0.0  0
 VXS  CONST_26  H9   C20  C19  C18   180.00   0.0  0
 VXS  CONST_27  H7   C18  C19  C20   180.00   0.0  0
 VXS  CONST_28  H8   C19  C20  C21   180.00   0.0  0
 VXS  CONST_29  H14  N03  C02  C21   180.00   0.0  0
 VXS  CONST_30  C08  N07  C06  C18     0.00   0.0  0
 VXS  CONST_31  C08  N07  C06  C05   180.00   0.0  0
 VXS  CONST_32  H15  N07  C06  C18   180.00   0.0  0
 VXS  Var_01    C09  C10  C11  C12    -0.79  30.0  2
 VXS  Var_02    C08  C09  C10  C11   178.27  30.0  2
 VXS  Var_03    C09  C08  N07  C06  -171.95  30.0  2
 VXS  Var_04    N07  C08  C09  C10    64.57  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
 VXS  plan-1  C10  0.020
 VXS  plan-1  C11  0.020
 VXS  plan-1  C12  0.020
 VXS  plan-1  C13  0.020
 VXS  plan-1  C14  0.020
 VXS  plan-1  C15  0.020
 VXS  plan-1  C16  0.020
 VXS  plan-1  O17  0.020
 VXS  plan-1  H3   0.020
 VXS  plan-1  H4   0.020
 VXS  plan-1  H5   0.020
 VXS  plan-1  H6   0.020
 VXS  plan-2  C18  0.020
 VXS  plan-2  C19  0.020
 VXS  plan-2  C20  0.020
 VXS  plan-2  C21  0.020
 VXS  plan-2  C02  0.020
 VXS  plan-2  C04  0.020
 VXS  plan-2  C05  0.020
 VXS  plan-2  C06  0.020
 VXS  plan-2  N03  0.020
 VXS  plan-2  N07  0.020
 VXS  plan-2  O22  0.020
 VXS  plan-2  H7   0.020
 VXS  plan-2  H8   0.020
 VXS  plan-2  H9   0.020
 VXS  plan-2  H14  0.020
 VXS  plan-2  O01  0.020
 VXS  plan-3  C06  0.020
 VXS  plan-3  C08  0.020
 VXS  plan-3  N07  0.020
 VXS  plan-3  H15  0.020

