# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 00:57:01 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: (3~{a}~{R},5~{S},7~{a}~{S})-5-phenyl-3~{a},4,5,6,7,7~{a}-hexahydroisoindole-1,3-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1NC(=O)[C@@H]2C[C@H](CC[C@H]12)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
 A8H  A8H  (3~{a}~{R},5~{S},7~{a}~{S})-5-phenyl-3~{a},4,5,6,7,7~{a}-hexahydroisoindole-1,3-dione  ligand  32  17  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A8H
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
 A8H  C12  C  CR16  0  -0.237   4.2861   0.7710  -0.9507
 A8H  C13  C  CR16  0  -0.339   2.9009   0.7012  -1.0376
 A8H  C11  C  CR16  0  -0.275   4.9589   0.0565   0.0303
 A8H  C10  C  CR16  0  -0.239   4.2355  -0.7272   0.9213
 A8H  C9   C  CR16  0  -0.320   2.8522  -0.7925   0.8308
 A8H  C8   C  CR6   0   0.201   2.1635  -0.0787  -0.1506
 A8H  C7   C  CH1   0  -0.402  -2.1264  -0.9546   0.4764
 A8H  C4   C  CH1   0  -0.350   0.6607  -0.1415  -0.2499
 A8H  C5   C  CH2   0  -0.415   0.1467  -1.5649  -0.4770
 A8H  C6   C  CH2   0  -0.440  -1.3556  -1.5577  -0.7118
 A8H  C3   C  CH2   0  -0.414   0.0021   0.4486   0.9978
 A8H  C2   C  CH1   0  -0.405  -1.5154   0.3572   0.9816
 A8H  C1   C  C     0   0.572  -2.2365   1.4068   0.1639
 A8H  O1   O  O     0  -0.421  -1.9073   2.5481  -0.0447
 A8H  N    N  NH1   0  -0.673  -3.4087   0.8299  -0.2708
 A8H  C    C  C     0   0.559  -3.4824  -0.5244  -0.0333
 A8H  O    O  O     0  -0.423  -4.4433  -1.2155  -0.2683
 A8H  H1   H  HCR6  0   0.253   4.8389   1.3839  -1.6514
 A8H  H2   H  HCR6  0   0.247   2.3854   1.2593  -1.8109
 A8H  H3   H  HCR6  0   0.253   6.0378   0.1089   0.1017
 A8H  H4   H  HCR6  0   0.253   4.7508  -1.2872   1.6913
 A8H  H5   H  HCR6  0   0.246   2.3076  -1.4084   1.5377
 A8H  H6   H  HCH1  0   0.300  -2.2227  -1.6967   1.2698
 A8H  H7   H  HCH1  0   0.245   0.3601   0.4567  -1.1185
 A8H  H8   H  HCH2  0   0.249   0.6446  -2.0083  -1.3421
 A8H  H9   H  HCH2  0   0.226   0.3887  -2.1948   0.3849
 A8H  H10  H  HCH2  0   0.263  -1.7231  -2.5683  -0.8955
 A8H  H11  H  HCH2  0   0.238  -1.5590  -0.9839  -1.6226
 A8H  H12  H  HCH2  0   0.247   0.3639  -0.0894   1.8784
 A8H  H13  H  HCH2  0   0.255   0.3006   1.4905   1.1339
 A8H  H14  H  HCH1  0   0.326  -1.8735   0.5228   2.0057
 A8H  H15  H  HNH1  0   0.421  -4.1377   1.3482  -0.7447

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
 A8H  C12  C13  aromatic  1.390  0.020  1.390
 A8H  C12  C11  aromatic  1.388  0.020  1.388
 A8H  C13  C8   aromatic  1.392  0.020  1.392
 A8H  C11  C10  aromatic  1.390  0.020  1.390
 A8H  C8   C4   single    1.507  0.020  1.507
 A8H  C8   C9   aromatic  1.395  0.020  1.395
 A8H  C4   C5   single    1.530  0.020  1.530
 A8H  C4   C3   single    1.529  0.020  1.529
 A8H  C5   C6   single    1.521  0.020  1.521
 A8H  C10  C9   aromatic  1.388  0.020  1.388
 A8H  C6   C7   single    1.539  0.020  1.539
 A8H  C3   C2   single    1.520  0.020  1.520
 A8H  C7   C2   single    1.533  0.020  1.533
 A8H  C7   C    single    1.511  0.020  1.511
 A8H  C2   C1   single    1.513  0.020  1.513
 A8H  C    O    double    1.207  0.020  1.207
 A8H  C    N    single    1.377  0.020  1.377
 A8H  C1   N    single    1.377  0.020  1.377
 A8H  C1   O1   double    1.206  0.020  1.206
 A8H  C12  H1   single    0.930  0.020  1.080
 A8H  C13  H2   single    0.930  0.020  1.080
 A8H  C11  H3   single    0.930  0.020  1.080
 A8H  C10  H4   single    0.930  0.020  1.080
 A8H  C9   H5   single    0.930  0.020  1.080
 A8H  C7   H6   single    0.970  0.020  1.090
 A8H  C4   H7   single    0.970  0.020  1.090
 A8H  C5   H8   single    0.970  0.020  1.090
 A8H  C5   H9   single    0.970  0.020  1.090
 A8H  C6   H10  single    0.970  0.020  1.090
 A8H  C6   H11  single    0.970  0.020  1.090
 A8H  C3   H12  single    0.970  0.020  1.090
 A8H  C3   H13  single    0.970  0.020  1.090
 A8H  C2   H14  single    0.970  0.020  1.090
 A8H  N    H15  single    0.860  0.020  1.020

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
 A8H  H1   C12  C11  120.09  3.000
 A8H  H1   C12  C13  119.80  3.000
 A8H  C11  C12  C13  120.11  3.000
 A8H  H2   C13  C8   119.41  3.000
 A8H  H2   C13  C12  119.52  3.000
 A8H  C8   C13  C12  121.08  3.000
 A8H  H3   C11  C10  120.25  3.000
 A8H  H3   C11  C12  120.33  3.000
 A8H  C10  C11  C12  119.42  3.000
 A8H  H4   C10  C9   119.76  3.000
 A8H  H4   C10  C11  120.00  3.000
 A8H  C9   C10  C11  120.24  3.000
 A8H  H5   C9   C8   120.08  3.000
 A8H  H5   C9   C10  119.01  3.000
 A8H  C8   C9   C10  120.91  3.000
 A8H  C4   C8   C9   121.14  3.000
 A8H  C9   C8   C13  118.24  3.000
 A8H  C4   C8   C13  120.62  3.000
 A8H  H6   C7   C    111.09  3.000
 A8H  H6   C7   C2   112.19  3.000
 A8H  C    C7   C2   103.02  3.000
 A8H  H6   C7   C6   109.83  3.000
 A8H  C    C7   C6   107.49  3.000
 A8H  C2   C7   C6   112.96  3.000
 A8H  H7   C4   C3   108.52  3.000
 A8H  H7   C4   C5   107.32  3.000
 A8H  C3   C4   C5   109.60  3.000
 A8H  H7   C4   C8   107.62  3.000
 A8H  C3   C4   C8   111.07  3.000
 A8H  C5   C4   C8   112.54  3.000
 A8H  H9   C5   H8   106.82  3.000
 A8H  H9   C5   C6   110.04  3.000
 A8H  H8   C5   C6   109.27  3.000
 A8H  H9   C5   C4   110.13  3.000
 A8H  H8   C5   C4   110.00  3.000
 A8H  C6   C5   C4   110.51  3.000
 A8H  H11  C6   H10  106.42  3.000
 A8H  H11  C6   C5   108.32  3.000
 A8H  H10  C6   C5   110.76  3.000
 A8H  H11  C6   C7   110.10  3.000
 A8H  H10  C6   C7   108.92  3.000
 A8H  C5   C6   C7   112.17  3.000
 A8H  H13  C3   H12  106.17  3.000
 A8H  H13  C3   C2   109.36  3.000
 A8H  H12  C3   C2   108.01  3.000
 A8H  H13  C3   C4   110.61  3.000
 A8H  H12  C3   C4   108.95  3.000
 A8H  C2   C3   C4   113.45  3.000
 A8H  H14  C2   C1   104.12  3.000
 A8H  H14  C2   C3   107.86  3.000
 A8H  C1   C2   C3   116.08  3.000
 A8H  H14  C2   C7   107.86  3.000
 A8H  C1   C2   C7   103.04  3.000
 A8H  C3   C2   C7   116.93  3.000
 A8H  N    C1   O1   125.05  3.000
 A8H  O1   C1   C2   128.30  3.000
 A8H  N    C1   C2   106.60  3.000
 A8H  H15  N    C    123.07  3.000
 A8H  H15  N    C1   123.12  3.000
 A8H  C    N    C1   113.78  3.000
 A8H  O    C    N    124.91  3.000
 A8H  N    C    C7   106.86  3.000
 A8H  O    C    C7   128.11  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
 A8H  CONST_01  C9   C8   C13  C12    0.00   0.0  0
 A8H  CONST_02  C9   C10  C11  C12    0.00   0.0  0
 A8H  CONST_03  C10  C11  C12  C13    0.00   0.0  0
 A8H  CONST_04  C10  C9   C8   C13    0.00   0.0  0
 A8H  CONST_05  C8   C13  C12  C11    0.00   0.0  0
 A8H  CONST_06  C8   C9   C10  C11    0.00   0.0  0
 A8H  CONST_07  C4   C8   C13  C12  180.00   0.0  0
 A8H  CONST_08  C4   C8   C9   C10  180.00   0.0  0
 A8H  CONST_09  C    N    C1   C2     0.00   0.0  0
 A8H  CONST_10  C    N    C1   O1   180.00   0.0  0
 A8H  CONST_11  H4   C10  C11  C12  180.00   0.0  0
 A8H  CONST_12  H3   C11  C12  C13  180.00   0.0  0
 A8H  CONST_13  H5   C9   C8   C13  180.00   0.0  0
 A8H  CONST_14  H2   C13  C12  C11  180.00   0.0  0
 A8H  CONST_15  H1   C12  C11  C10  180.00   0.0  0
 A8H  CONST_16  H15  N    C1   C2   180.00   0.0  0
 A8H  Var_01    C4   C5   C6   C7   -59.29  30.0  1
 A8H  Var_02    C1   N    C    C7    -7.57  30.0  1

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
 A8H  chir_01  C7  C6  C2  C   negativ
 A8H  chir_02  C4  C3  C5  C8  positiv
 A8H  chir_03  C2  C3  C7  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
 A8H  plan-1  C12  0.020
 A8H  plan-1  C13  0.020
 A8H  plan-1  C11  0.020
 A8H  plan-1  C10  0.020
 A8H  plan-1  C9   0.020
 A8H  plan-1  C8   0.020
 A8H  plan-1  C4   0.020
 A8H  plan-1  H1   0.020
 A8H  plan-1  H2   0.020
 A8H  plan-1  H3   0.020
 A8H  plan-1  H4   0.020
 A8H  plan-1  H5   0.020
 A8H  plan-2  C7   0.020
 A8H  plan-2  N    0.020
 A8H  plan-2  C    0.020
 A8H  plan-2  O    0.020
 A8H  plan-3  C2   0.020
 A8H  plan-3  C1   0.020
 A8H  plan-3  O1   0.020
 A8H  plan-3  N    0.020
 A8H  plan-3  C    0.020
 A8H  plan-3  H15  0.020

