# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 12:43:47 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: (5R)-5-(4-chlorophenyl)-2,5-dihydro-3H-imidazo[2,1-a]isoindol-5-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@]1(N2CCN=C2c3ccccc13)c4ccc(Cl)cc4
#
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
 29Q  29Q  (5R)-5-(4-chlorophenyl)-2,5-dihydro-3H-imidazo[2,1-a]isoindol-5-ol  ligand  33  20  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_29Q
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
 29Q  CL   CL  CL    0  -0.125  -4.9588  -0.3173   0.7901
 29Q  C13  C   CR6   0  -0.050  -3.3197  -0.1894   0.2449
 29Q  C12  C   CR16  0  -0.196  -2.3137   0.0698   1.1636
 29Q  C11  C   CR16  0  -0.284  -1.0064   0.1771   0.7191
 29Q  C14  C   CR16  0  -0.198  -3.0318  -0.3467  -1.0997
 29Q  C15  C   CR16  0  -0.301  -1.7157  -0.2408  -1.5285
 29Q  C10  C   CR6   0   0.065  -0.6905   0.0282  -0.6292
 29Q  C    C   CR5   0   0.362   0.7628   0.0710  -1.0862
 29Q  O    O   OH1   0  -0.634   0.8721   0.2766  -2.4664
 29Q  C5   C   CR56  0   0.039   1.5998   1.0644  -0.2861
 29Q  C6   C   CR16  0  -0.321   1.5243   2.4437  -0.2768
 29Q  C7   C   CR16  0  -0.243   2.4045   3.1414   0.5448
 29Q  C8   C   CR16  0  -0.256   3.3325   2.4711   1.3394
 29Q  C9   C   CR16  0  -0.312   3.4047   1.0843   1.3294
 29Q  C4   C   CR56  0   0.049   2.5300   0.3989   0.5034
 29Q  C1   C   CR55  0   0.443   2.3293  -1.0276   0.2739
 29Q  N    N   N     0  -0.531   1.4444  -1.1601  -0.7714
 29Q  C3   C   CH2   0  -0.307   0.9383  -2.5190  -0.7293
 29Q  C2   C   CH2   0  -0.354   2.0472  -3.1800   0.1294
 29Q  N1   N   N     0  -0.449   2.7200  -2.0905   0.8482
 29Q  H1   H   HCR6  0   0.283  -2.5425   0.1910   2.2136
 29Q  H2   H   HCR6  0   0.268  -0.2306   0.3810   1.4471
 29Q  H3   H   HCR6  0   0.282  -3.8198  -0.5506  -1.8118
 29Q  H4   H   HCR6  0   0.271  -1.5073  -0.3746  -2.5815
 29Q  H5   H   HOH1  0   0.460   0.4044   1.0844  -2.7098
 29Q  H6   H   HCR6  0   0.263   0.7978   2.9788  -0.8757
 29Q  H7   H   HCR6  0   0.269   2.3657   4.2226   0.5705
 29Q  H8   H   HCR6  0   0.268   4.0025   3.0400   1.9700
 29Q  H9   H   HCR6  0   0.263   4.1231   0.5577   1.9439
 29Q  H10  H   HCH2  0   0.237  -0.0416  -2.5663  -0.2424
 29Q  H11  H   HCH2  0   0.242   1.6447  -3.9152   0.8266
 29Q  H12  H   HCH2  0   0.256   0.8512  -2.9615  -1.7203
 29Q  H13  H   HCH2  0   0.242   2.7713  -3.7008  -0.5041

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
 29Q  CL   C13  single    1.732  0.020  1.732
 29Q  C14  C13  aromatic  1.384  0.020  1.384
 29Q  C14  C15  aromatic  1.388  0.020  1.388
 29Q  C13  C12  aromatic  1.387  0.020  1.387
 29Q  C15  C10  aromatic  1.390  0.020  1.390
 29Q  C12  C11  aromatic  1.385  0.020  1.385
 29Q  C10  C11  aromatic  1.393  0.020  1.393
 29Q  C10  C    single    1.524  0.020  1.524
 29Q  O    C    single    1.400  0.020  1.400
 29Q  C    C5   single    1.526  0.020  1.526
 29Q  C    N    single    1.442  0.020  1.442
 29Q  C6   C5   aromatic  1.381  0.020  1.381
 29Q  C6   C7   aromatic  1.392  0.020  1.392
 29Q  C5   C4   aromatic  1.390  0.020  1.390
 29Q  C7   C8   aromatic  1.394  0.020  1.394
 29Q  N    C3   single    1.451  0.020  1.451
 29Q  N    C1   single    1.376  0.020  1.376
 29Q  C3   C2   single    1.550  0.020  1.550
 29Q  C4   C1   single    1.459  0.020  1.459
 29Q  C4   C9   aromatic  1.385  0.020  1.385
 29Q  C1   N1   double    1.270  0.020  1.270
 29Q  C8   C9   aromatic  1.389  0.020  1.389
 29Q  C2   N1   single    1.468  0.020  1.468
 29Q  C12  H1   single    0.930  0.020  1.080
 29Q  C11  H2   single    0.930  0.020  1.080
 29Q  C14  H3   single    0.930  0.020  1.080
 29Q  C15  H4   single    0.930  0.020  1.080
 29Q  O    H5   single    0.850  0.020  0.980
 29Q  C6   H6   single    0.930  0.020  1.080
 29Q  C7   H7   single    0.930  0.020  1.080
 29Q  C8   H8   single    0.930  0.020  1.080
 29Q  C9   H9   single    0.930  0.020  1.080
 29Q  C3   H10  single    0.970  0.020  1.090
 29Q  C2   H11  single    0.970  0.020  1.090
 29Q  C3   H12  single    0.970  0.020  1.090
 29Q  C2   H13  single    0.970  0.020  1.090

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
 29Q  C14  C13  C12  120.93  3.000
 29Q  C12  C13  CL   119.46  3.000
 29Q  C14  C13  CL   119.62  3.000
 29Q  H1   C12  C11  120.17  3.000
 29Q  H1   C12  C13  120.70  3.000
 29Q  C11  C12  C13  119.12  3.000
 29Q  H2   C11  C10  120.55  3.000
 29Q  H2   C11  C12  118.35  3.000
 29Q  C10  C11  C12  121.09  3.000
 29Q  H3   C14  C15  120.12  3.000
 29Q  H3   C14  C13  120.63  3.000
 29Q  C15  C14  C13  119.25  3.000
 29Q  H4   C15  C10  120.78  3.000
 29Q  H4   C15  C14  118.29  3.000
 29Q  C10  C15  C14  120.94  3.000
 29Q  C    C10  C15  120.98  3.000
 29Q  C    C10  C11  120.23  3.000
 29Q  C15  C10  C11  118.67  3.000
 29Q  N    C    C5   100.49  3.000
 29Q  N    C    O    107.69  3.000
 29Q  C5   C    O    112.25  3.000
 29Q  N    C    C10  111.18  3.000
 29Q  C5   C    C10  112.59  3.000
 29Q  O    C    C10  111.98  3.000
 29Q  H5   O    C    109.51  3.000
 29Q  C4   C5   C6   120.72  3.000
 29Q  C4   C5   C    110.69  3.000
 29Q  C6   C5   C    128.59  3.000
 29Q  H6   C6   C7   120.20  3.000
 29Q  H6   C6   C5   121.75  3.000
 29Q  C7   C6   C5   118.04  3.000
 29Q  H7   C7   C8   119.40  3.000
 29Q  H7   C7   C6   119.49  3.000
 29Q  C8   C7   C6   121.11  3.000
 29Q  H8   C8   C9   119.81  3.000
 29Q  H8   C8   C7   119.47  3.000
 29Q  C9   C8   C7   120.72  3.000
 29Q  H9   C9   C4   121.15  3.000
 29Q  H9   C9   C8   121.09  3.000
 29Q  C4   C9   C8   117.76  3.000
 29Q  C1   C4   C9   131.67  3.000
 29Q  C9   C4   C5   121.65  3.000
 29Q  C1   C4   C5   106.67  3.000
 29Q  N1   C1   N    117.44  3.000
 29Q  N1   C1   C4   134.84  3.000
 29Q  N    C1   C4   107.59  3.000
 29Q  C3   N    C1   107.01  3.000
 29Q  C1   N    C    112.80  3.000
 29Q  C3   N    C    129.88  3.000
 29Q  H12  C3   H10  108.39  3.000
 29Q  H12  C3   C2   112.83  3.000
 29Q  H10  C3   C2   112.04  3.000
 29Q  H12  C3   N    112.47  3.000
 29Q  H10  C3   N    111.44  3.000
 29Q  C2   C3   N     99.55  3.000
 29Q  H13  C2   H11  107.07  3.000
 29Q  H13  C2   N1   109.48  3.000
 29Q  H11  C2   N1   110.88  3.000
 29Q  H13  C2   C3   110.83  3.000
 29Q  H11  C2   C3   112.19  3.000
 29Q  N1   C2   C3   106.41  3.000
 29Q  C2   N1   C1   104.99  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
 29Q  CONST_01  C10  C15  C14  C13     0.00   0.0  0
 29Q  CONST_02  C10  C11  C12  C13     0.00   0.0  0
 29Q  CONST_03  C15  C14  C13  C12     0.00   0.0  0
 29Q  CONST_04  C15  C10  C11  C12     0.00   0.0  0
 29Q  CONST_05  C14  C13  C12  C11     0.00   0.0  0
 29Q  CONST_06  C14  C15  C10  C11     0.00   0.0  0
 29Q  CONST_07  C8   C7   C6   C5      0.00   0.0  0
 29Q  CONST_08  C8   C9   C4   C5      0.00   0.0  0
 29Q  CONST_09  C9   C4   C5   C6      0.00   0.0  0
 29Q  CONST_10  C9   C8   C7   C6      0.00   0.0  0
 29Q  CONST_11  C4   C5   C6   C7      0.00   0.0  0
 29Q  CONST_12  C4   C9   C8   C7      0.00   0.0  0
 29Q  CONST_13  C    C10  C11  C12   180.00   0.0  0
 29Q  CONST_14  C    C10  C15  C14   180.00   0.0  0
 29Q  CONST_16  C4   C1   N    C       0.00   0.0  0
 29Q  CONST_19  C2   N1   C1   C4    180.00   0.0  0
 29Q  CONST_21  C3   C2   N1   C1      0.00   0.0  0
 29Q  CONST_23  C2   N1   C1   N       0.00   0.0  0
 29Q  CONST_24  N1   C1   N    C3      0.00   0.0  0
 29Q  CONST_25  C15  C14  C13  CL    180.00   0.0  0
 29Q  CONST_26  C11  C12  C13  CL    180.00   0.0  0
 29Q  CONST_27  H4   C15  C14  C13   180.00   0.0  0
 29Q  CONST_28  H2   C11  C12  C13   180.00   0.0  0
 29Q  CONST_29  H3   C14  C13  C12   180.00   0.0  0
 29Q  CONST_30  H1   C12  C13  C14   180.00   0.0  0
 29Q  CONST_31  H6   C6   C5   C       0.00   0.0  0
 29Q  CONST_32  H7   C7   C6   C5    180.00   0.0  0
 29Q  CONST_33  H9   C9   C4   C5    180.00   0.0  0
 29Q  CONST_34  H8   C8   C7   C6    180.00   0.0  0
 29Q  Var_01    H10  C3   N    C     -42.89  30.0  1
 29Q  Var_02    H11  C2   N1   C1   -135.89  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
 29Q  chir_01  C  C10  C5  N  negativ

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
 29Q  plan-1  CL   0.020
 29Q  plan-1  C13  0.020
 29Q  plan-1  C12  0.020
 29Q  plan-1  C11  0.020
 29Q  plan-1  C14  0.020
 29Q  plan-1  C15  0.020
 29Q  plan-1  C10  0.020
 29Q  plan-1  C    0.020
 29Q  plan-1  H1   0.020
 29Q  plan-1  H2   0.020
 29Q  plan-1  H3   0.020
 29Q  plan-1  H4   0.020
 29Q  plan-2  C    0.020
 29Q  plan-2  C5   0.020
 29Q  plan-2  C6   0.020
 29Q  plan-2  C7   0.020
 29Q  plan-2  C8   0.020
 29Q  plan-2  C9   0.020
 29Q  plan-2  C4   0.020
 29Q  plan-2  C1   0.020
 29Q  plan-2  N    0.020
 29Q  plan-2  C3   0.020
 29Q  plan-2  C2   0.020
 29Q  plan-2  N1   0.020
 29Q  plan-2  H6   0.020
 29Q  plan-2  H7   0.020
 29Q  plan-2  H8   0.020
 29Q  plan-2  H9   0.020

