# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 18:22:34 2022
#   Inital geometry file: a 66 line input string
#   Ligand name: 1-(5-amino-1,3-dihydro-2H-isoindol-2-yl)ethan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N1Cc2ccc(N)cc2C1
#
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
 X1J  X1J  1-(5-amino-1,3-dihydro-2H-isoindol-2-yl)ethan-1-one  ligand  25  13  .  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_X1J
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
 X1J  C4   C  CR16  0  -0.390  17.8760  62.1332  -11.6523
 X1J  C5   C  CR56  0   0.058  17.7095  61.9032  -10.2991
 X1J  C6   C  CR56  0   0.018  18.0183  60.6816   -9.7253
 X1J  C7   C  CH2   0  -0.277  17.2071  62.8578   -9.2622
 X1J  C8   C  CH2   0  -0.271  17.7540  60.7008   -8.2521
 X1J  C10  C  CH3   0  -0.791  17.0001  61.6626   -5.6672
 X1J  N1   N  NR5   0  -0.489  17.2669  62.0609   -8.0432
 X1J  C3   C  CR6   0   0.310  18.3670  61.1053  -12.4662
 X1J  C1   C  CR16  0  -0.308  18.5082  59.6570  -10.5194
 X1J  C2   C  CR16  0  -0.323  18.6800  59.8691  -11.8780
 X1J  O1   O  O     0  -0.502  16.4787  63.7292   -6.7699
 X1J  H3   H  HCR6  0   0.250  17.6323  63.0975  -12.0846
 X1J  H4   H  HCH2  0   0.254  17.8328  63.7522   -9.1869
 X1J  H5   H  HCH2  0   0.254  16.1874  63.1959   -9.4699
 X1J  H6   H  HCH2  0   0.254  17.0079  59.9564   -7.9556
 X1J  H7   H  HCH2  0   0.254  18.6584  60.5022   -7.6681
 X1J  H10  H  HCH3  0   0.267  16.6640  62.1812   -4.7730
 X1J  H11  H  HCH3  0   0.262  16.3956  60.7630   -5.7952
 X1J  H12  H  HCH3  0   0.262  18.0304  61.3370   -5.5131
 X1J  H9   H  HNH2  0   0.377  18.5871  62.2376  -14.1368
 X1J  H8   H  HNH2  0   0.377  19.1557  60.6791  -14.2871
 X1J  H1   H  HCR6  0   0.246  18.7615  58.6938  -10.0928
 X1J  H2   H  HCR6  0   0.253  19.0639  59.0696  -12.5008
 X1J  C9   C  C     0   0.517  16.8876  62.5780   -6.8606
 X1J  N2   N  NH2   0  -0.861  18.4916  61.2828  -13.8292

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
 X1J  N2   C3   single    1.380  0.020  1.380
 X1J  C3   C2   aromatic  1.404  0.020  1.404
 X1J  C3   C4   aromatic  1.400  0.020  1.400
 X1J  C2   C1   aromatic  1.386  0.020  1.386
 X1J  C4   C5   aromatic  1.383  0.020  1.383
 X1J  C1   C6   aromatic  1.386  0.020  1.386
 X1J  C5   C6   aromatic  1.384  0.020  1.384
 X1J  C5   C7   single    1.496  0.020  1.496
 X1J  C6   C8   single    1.497  0.020  1.497
 X1J  C7   N1   single    1.458  0.020  1.458
 X1J  C8   N1   single    1.460  0.020  1.460
 X1J  N1   C9   single    1.345  0.020  1.345
 X1J  C9   O1   double    1.225  0.020  1.225
 X1J  C9   C10  single    1.508  0.020  1.508
 X1J  C4   H3   single    0.930  0.020  1.080
 X1J  C7   H4   single    0.970  0.020  1.090
 X1J  C7   H5   single    0.970  0.020  1.090
 X1J  C8   H6   single    0.970  0.020  1.090
 X1J  C8   H7   single    0.970  0.020  1.090
 X1J  C10  H10  single    0.970  0.020  1.090
 X1J  C10  H11  single    0.970  0.020  1.090
 X1J  C10  H12  single    0.970  0.020  1.090
 X1J  N2   H9   single    0.890  0.020  1.040
 X1J  N2   H8   single    0.890  0.020  1.040
 X1J  C1   H1   single    0.930  0.020  1.080
 X1J  C2   H2   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
 X1J  H3   C4   C3   119.99  3.000
 X1J  H3   C4   C5   120.73  3.000
 X1J  C3   C4   C5   119.28  3.000
 X1J  C7   C5   C6   110.53  3.000
 X1J  C7   C5   C4   127.77  3.000
 X1J  C6   C5   C4   121.70  3.000
 X1J  C1   C6   C8   129.49  3.000
 X1J  C8   C6   C5   110.93  3.000
 X1J  C1   C6   C5   119.59  3.000
 X1J  H5   C7   H4   107.06  3.000
 X1J  H5   C7   N1   111.47  3.000
 X1J  H4   C7   N1   111.47  3.000
 X1J  H5   C7   C5   112.24  3.000
 X1J  H4   C7   C5   112.16  3.000
 X1J  N1   C7   C5   102.53  3.000
 X1J  H7   C8   H6   107.16  3.000
 X1J  H7   C8   N1   111.62  3.000
 X1J  H6   C8   N1   111.55  3.000
 X1J  H7   C8   C6   112.14  3.000
 X1J  H6   C8   C6   112.22  3.000
 X1J  N1   C8   C6   102.22  3.000
 X1J  H12  C10  H11  107.07  3.000
 X1J  H12  C10  H10  108.55  3.000
 X1J  H11  C10  H10  108.57  3.000
 X1J  H12  C10  C9   111.30  3.000
 X1J  H11  C10  C9   111.47  3.000
 X1J  H10  C10  C9   109.78  3.000
 X1J  C9   N1   C8   125.31  3.000
 X1J  C9   N1   C7   120.90  3.000
 X1J  C8   N1   C7   113.79  3.000
 X1J  C2   C3   N2   120.45  3.000
 X1J  C2   C3   C4   118.75  3.000
 X1J  N2   C3   C4   120.75  3.000
 X1J  H1   C1   C2   119.55  3.000
 X1J  H1   C1   C6   120.95  3.000
 X1J  C2   C1   C6   119.50  3.000
 X1J  H2   C2   C1   119.63  3.000
 X1J  H2   C2   C3   119.18  3.000
 X1J  C1   C2   C3   121.18  3.000
 X1J  O1   C9   N1   121.36  3.000
 X1J  O1   C9   C10  122.45  3.000
 X1J  N1   C9   C10  116.19  3.000
 X1J  H8   N2   H9   111.51  3.000
 X1J  H8   N2   C3   115.54  3.000
 X1J  H9   N2   C3   115.59  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
 X1J  CONST_01  C1   C2   C3  C4     0.00   0.0  0
 X1J  CONST_02  C1   C6   C5  C4     0.00   0.0  0
 X1J  CONST_03  C2   C3   C4  C5     0.00   0.0  0
 X1J  CONST_04  C2   C1   C6  C5     0.00   0.0  0
 X1J  CONST_05  C3   C2   C1  C6     0.00   0.0  0
 X1J  CONST_06  C3   C4   C5  C6     0.00   0.0  0
 X1J  CONST_07  N2   C3   C4  C5   180.00   0.0  0
 X1J  CONST_08  C1   C2   C3  N2   180.00   0.0  0
 X1J  CONST_09  H2   C2   C3  C4   180.00   0.0  0
 X1J  CONST_10  H1   C1   C6  C5   180.00   0.0  0
 X1J  CONST_11  H3   C4   C5  C6   180.00   0.0  0
 X1J  CONST_12  O1   C9   N1  C7     0.00   0.0  0
 X1J  CONST_13  C10  C9   N1  C7   180.00   0.0  0
 X1J  CONST_14  O1   C9   N1  C8   180.00   0.0  0
 X1J  CONST_15  C10  C9   N1  C8     0.00   0.0  0
 X1J  Var_01    N1   C7   C5  C4  -179.46  30.0  1
 X1J  Var_02    N1   C8   C6  C5    -0.19  30.0  1
 X1J  Var_03    C8   N1   C7  C5    -0.39  30.0  1
 X1J  Var_04    C7   N1   C8  C6     0.37  30.0  1
 X1J  Var_05    H10  C10  C9  N1  -179.72  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
 X1J  plan-1  C7   0.020
 X1J  plan-1  C8   0.020
 X1J  plan-1  C10  0.020
 X1J  plan-1  N1   0.020
 X1J  plan-1  O1   0.020
 X1J  plan-1  C9   0.020
 X1J  plan-2  C4   0.020
 X1J  plan-2  C5   0.020
 X1J  plan-2  C6   0.020
 X1J  plan-2  C7   0.020
 X1J  plan-2  C8   0.020
 X1J  plan-2  C3   0.020
 X1J  plan-2  C1   0.020
 X1J  plan-2  C2   0.020
 X1J  plan-2  H3   0.020
 X1J  plan-2  H1   0.020
 X1J  plan-2  H2   0.020
 X1J  plan-2  N2   0.020
 X1J  plan-3  C3   0.020
 X1J  plan-3  H9   0.020
 X1J  plan-3  H8   0.020
 X1J  plan-3  N2   0.020

