# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 22:50:25 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: (3R)-3-amino-2-methyl-3-phenyl-2,3-dihydro-1H-isoindol-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)c2ccccc2[C@@]1(N)c3ccccc3
#
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
 IIN  IIN  (3R)-3-amino-2-methyl-3-phenyl-2,3-dihydro-1H-isoindol-1-one  ligand  32  18  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_IIN
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
 IIN  C1    C  C     0   0.518   1.5687   0.3021   1.5054
 IIN  O1    O  O     0  -0.473   2.5071   0.7819   2.1182
 IIN  N2    N  NT    0  -0.509   1.6246  -0.3573   0.3237
 IIN  C3    C  CT    0   0.170   0.3259  -0.8568  -0.1527
 IIN  C3A   C  CR6   0   0.168  -0.5882  -0.3696   0.9500
 IIN  C4    C  CR16  0  -0.318  -1.9530  -0.5364   1.0841
 IIN  C5    C  CR16  0  -0.242  -2.5660   0.0175   2.2031
 IIN  C6    C  CR16  0  -0.260  -1.8282   0.7159   3.1589
 IIN  C7    C  CR16  0  -0.300  -0.4555   0.8716   3.0183
 IIN  C7A   C  CR6   0  -0.066   0.1426   0.3162   1.8998
 IIN  CM2   C  CH3   0  -0.538   2.8421  -0.6601  -0.3797
 IIN  N3    N  NH2   0  -0.776   0.2445  -2.2842  -0.2731
 IIN  C1'   C  CR6   0   0.136  -0.0577  -0.1887  -1.4704
 IIN  C2'   C  CR16  0  -0.292   0.3379   1.1195  -1.7401
 IIN  C3'   C  CR16  0  -0.241  -0.0570   1.7512  -2.9097
 IIN  C4'   C  CR16  0  -0.263  -0.8578   1.0854  -3.8289
 IIN  C5'   C  CR16  0  -0.239  -1.2589  -0.2160  -3.5653
 IIN  C6'   C  CR16  0  -0.304  -0.8631  -0.8488  -2.3932
 IIN  H4    H  HCR6  0   0.261  -2.5305  -1.0749   0.3436
 IIN  H5    H  HCR6  0   0.266  -3.6340  -0.0954   2.3370
 IIN  H6    H  HCR6  0   0.266  -2.3330   1.1373   4.0180
 IIN  H7    H  HCR6  0   0.263   0.1253   1.4053   3.7597
 IIN  HM21  H  HCH3  0   0.264   3.6665  -0.1168   0.0736
 IIN  HM22  H  HCH3  0   0.245   3.0703  -1.7270  -0.3417
 IIN  HM23  H  HCH3  0   0.247   2.7674  -0.3614  -1.4258
 IIN  HN31  H  HNH2  0   0.366   0.8799  -2.6331  -0.9808
 IIN  HN32  H  HNH2  0   0.367   0.4832  -2.7319   0.6030
 IIN  H2'   H  HCR6  0   0.255   0.9630   1.6573  -1.0387
 IIN  H3'   H  HCR6  0   0.258   0.2651   2.7661  -3.1035
 IIN  H4'   H  HCR6  0   0.258  -1.1663   1.5777  -4.7421
 IIN  H5'   H  HCR6  0   0.257  -1.8841  -0.7454  -4.2726
 IIN  H6'   H  HCR6  0   0.258  -1.1877  -1.8608  -2.1951

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
 IIN  C1   O1    double    1.219  0.020  1.219
 IIN  C1   N2    single    1.354  0.020  1.354
 IIN  C1   C7A   single    1.480  0.020  1.480
 IIN  N2   C3    single    1.471  0.020  1.471
 IIN  N2   CM2   single    1.438  0.020  1.438
 IIN  C3   C3A   single    1.513  0.020  1.513
 IIN  C3   N3    single    1.435  0.020  1.435
 IIN  C3   C1'   single    1.526  0.020  1.526
 IIN  C3A  C4    aromatic  1.382  0.020  1.382
 IIN  C3A  C7A   aromatic  1.381  0.020  1.381
 IIN  C4   C5    aromatic  1.391  0.020  1.391
 IIN  C4   H4    single    0.930  0.020  1.080
 IIN  C5   C6    aromatic  1.395  0.020  1.395
 IIN  C5   H5    single    0.930  0.020  1.080
 IIN  C6   C7    aromatic  1.389  0.020  1.389
 IIN  C6   H6    single    0.930  0.020  1.080
 IIN  C7   C7A   aromatic  1.385  0.020  1.385
 IIN  C7   H7    single    0.930  0.020  1.080
 IIN  CM2  HM21  single    0.970  0.020  1.090
 IIN  CM2  HM22  single    0.970  0.020  1.090
 IIN  CM2  HM23  single    0.970  0.020  1.090
 IIN  N3   HN31  single    0.890  0.020  1.040
 IIN  N3   HN32  single    0.890  0.020  1.040
 IIN  C1'  C2'   aromatic  1.393  0.020  1.393
 IIN  C1'  C6'   aromatic  1.391  0.020  1.391
 IIN  C2'  C3'   aromatic  1.387  0.020  1.387
 IIN  C2'  H2'   single    0.930  0.020  1.080
 IIN  C3'  C4'   aromatic  1.389  0.020  1.389
 IIN  C3'  H3'   single    0.930  0.020  1.080
 IIN  C4'  C5'   aromatic  1.387  0.020  1.387
 IIN  C4'  H4'   single    0.930  0.020  1.080
 IIN  C5'  C6'   aromatic  1.390  0.020  1.390
 IIN  C5'  H5'   single    0.930  0.020  1.080
 IIN  C6'  H6'   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
 IIN  C7A   C1   N2    106.08  3.000
 IIN  C7A   C1   O1    127.16  3.000
 IIN  N2    C1   O1    126.76  3.000
 IIN  CM2   N2   C3    121.16  3.000
 IIN  CM2   N2   C1    124.34  3.000
 IIN  C3    N2   C1    114.30  3.000
 IIN  C1'   C3   N3    110.41  3.000
 IIN  C1'   C3   C3A   109.66  3.000
 IIN  N3    C3   C3A   110.32  3.000
 IIN  C1'   C3   N2    110.67  3.000
 IIN  N3    C3   N2    114.53  3.000
 IIN  C3A   C3   N2    100.84  3.000
 IIN  C7A   C3A  C4    121.07  3.000
 IIN  C7A   C3A  C3    109.97  3.000
 IIN  C4    C3A  C3    128.96  3.000
 IIN  H4    C4   C5    120.89  3.000
 IIN  H4    C4   C3A   121.38  3.000
 IIN  C5    C4   C3A   117.73  3.000
 IIN  H5    C5   C6    119.30  3.000
 IIN  H5    C5   C4    119.53  3.000
 IIN  C6    C5   C4    121.17  3.000
 IIN  H6    C6   C7    119.87  3.000
 IIN  H6    C6   C5    119.49  3.000
 IIN  C7    C6   C5    120.63  3.000
 IIN  H7    C7   C7A   121.29  3.000
 IIN  H7    C7   C6    121.08  3.000
 IIN  C7A   C7   C6    117.63  3.000
 IIN  C7    C7A  C3A   121.76  3.000
 IIN  C7    C7A  C1    129.45  3.000
 IIN  C3A   C7A  C1    108.78  3.000
 IIN  HM23  CM2  HM22  108.38  3.000
 IIN  HM23  CM2  HM21  108.38  3.000
 IIN  HM22  CM2  HM21  108.40  3.000
 IIN  HM23  CM2  N2    110.70  3.000
 IIN  HM22  CM2  N2    111.45  3.000
 IIN  HM21  CM2  N2    109.45  3.000
 IIN  HN32  N3   HN31  107.72  3.000
 IIN  HN32  N3   C3    110.73  3.000
 IIN  HN31  N3   C3    111.45  3.000
 IIN  C6'   C1'  C2'   118.79  3.000
 IIN  C6'   C1'  C3    120.69  3.000
 IIN  C2'   C1'  C3    120.45  3.000
 IIN  H2'   C2'  C3'   118.99  3.000
 IIN  H2'   C2'  C1'   120.34  3.000
 IIN  C3'   C2'  C1'   120.68  3.000
 IIN  H3'   C3'  C4'   120.17  3.000
 IIN  H3'   C3'  C2'   119.57  3.000
 IIN  C4'   C3'  C2'   120.26  3.000
 IIN  H4'   C4'  C5'   120.31  3.000
 IIN  H4'   C4'  C3'   120.30  3.000
 IIN  C5'   C4'  C3'   119.38  3.000
 IIN  H5'   C5'  C6'   119.54  3.000
 IIN  H5'   C5'  C4'   120.12  3.000
 IIN  C6'   C5'  C4'   120.35  3.000
 IIN  H6'   C6'  C5'   119.69  3.000
 IIN  H6'   C6'  C1'   119.76  3.000
 IIN  C5'   C6'  C1'   120.55  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
 IIN  CONST_01  C6    C5   C4   C3A    0.00   0.0  0
 IIN  CONST_02  C6    C7   C7A  C3A    0.00   0.0  0
 IIN  CONST_03  C7    C7A  C3A  C4     0.00   0.0  0
 IIN  CONST_04  C7    C6   C5   C4     0.00   0.0  0
 IIN  CONST_05  C7A   C3A  C4   C5     0.00   0.0  0
 IIN  CONST_06  C7A   C7   C6   C5     0.00   0.0  0
 IIN  CONST_07  C4'   C3'  C2'  C1'    0.00   0.0  0
 IIN  CONST_08  C4'   C5'  C6'  C1'    0.00   0.0  0
 IIN  CONST_09  C5'   C6'  C1'  C2'    0.00   0.0  0
 IIN  CONST_10  C5'   C4'  C3'  C2'    0.00   0.0  0
 IIN  CONST_11  C6'   C1'  C2'  C3'    0.00   0.0  0
 IIN  CONST_12  C6'   C5'  C4'  C3'    0.00   0.0  0
 IIN  CONST_13  C3'   C2'  C1'  C3   180.00   0.0  0
 IIN  CONST_14  C5'   C6'  C1'  C3   180.00   0.0  0
 IIN  CONST_15  C7A   C1   N2   C3     0.00   0.0  0
 IIN  CONST_16  C3    N2   C1   O1   180.00   0.0  0
 IIN  CONST_17  CM2   N2   C1   C7A  180.00   0.0  0
 IIN  CONST_18  H7    C7   C7A  C1     0.00   0.0  0
 IIN  CONST_19  H4    C4   C3A  C3     0.00   0.0  0
 IIN  CONST_20  H2'   C2'  C1'  C3     0.00   0.0  0
 IIN  CONST_21  H6'   C6'  C1'  C3     0.00   0.0  0
 IIN  CONST_22  H5    C5   C4   C3A  180.00   0.0  0
 IIN  CONST_23  H6    C6   C5   C4   180.00   0.0  0
 IIN  CONST_24  H3'   C3'  C2'  C1'  180.00   0.0  0
 IIN  CONST_25  H5'   C5'  C6'  C1'  180.00   0.0  0
 IIN  CONST_26  H4'   C4'  C3'  C2'  180.00   0.0  0
 IIN  CONST_27  CM2   N2   C1   O1     0.00   0.0  0
 IIN  Var_01    HM21  CM2  N2   C1   -11.08  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 IIN  chir_01  C3  C3A  N2  C1'  positiv

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
 IIN  plan-1  C3   0.020
 IIN  plan-1  C1'  0.020
 IIN  plan-1  C2'  0.020
 IIN  plan-1  C3'  0.020
 IIN  plan-1  C4'  0.020
 IIN  plan-1  C5'  0.020
 IIN  plan-1  C6'  0.020
 IIN  plan-1  H2'  0.020
 IIN  plan-1  H3'  0.020
 IIN  plan-1  H4'  0.020
 IIN  plan-1  H5'  0.020
 IIN  plan-1  H6'  0.020
 IIN  plan-2  C1   0.020
 IIN  plan-2  O1   0.020
 IIN  plan-2  N2   0.020
 IIN  plan-2  C3   0.020
 IIN  plan-2  C3A  0.020
 IIN  plan-2  C4   0.020
 IIN  plan-2  C5   0.020
 IIN  plan-2  C6   0.020
 IIN  plan-2  C7   0.020
 IIN  plan-2  C7A  0.020
 IIN  plan-2  CM2  0.020
 IIN  plan-2  H4   0.020
 IIN  plan-2  H5   0.020
 IIN  plan-2  H6   0.020
 IIN  plan-2  H7   0.020

