# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 02:13:56 2021
#   Inital geometry file: a 128 line input string
#   Ligand name: (3~{S})-3-[2-[4-(3,4-dimethylphenyl)piperazin-1-yl]ethyl]-2,3-dihydroisoindol-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(cc1C)N2CCN(CC[C@@H]3NC(=O)c4ccccc34)CC2
#
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
 RMZ  RMZ  (3~{S})-3-[2-[4-(3,4-dimethylphenyl)piperazin-1-yl]ethyl]-2,3-dihydroisoindol-1-one  ligand  53  26  .  2022-07-22  2022-07-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_RMZ
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
 RMZ  C10   C  CH2   0  -0.295   4.6510  3.2334  -21.7793
 RMZ  C13   C  CH2   0  -0.315   2.7771  1.1204  -21.9335
 RMZ  C15   C  CH2   0  -0.450   6.6101  2.8896  -19.4595
 RMZ  C17   C  CR56  0   0.130   9.1583  2.8334  -19.7237
 RMZ  C20   C  CR16  0  -0.262  11.4711  3.7279  -20.9647
 RMZ  C21   C  CR16  0  -0.294  11.0993  4.2901  -19.7517
 RMZ  C22   C  CR56  0  -0.089   9.9422  3.8242  -19.1515
 RMZ  C26   C  CH3   0  -0.736   0.0177  4.7577  -26.1369
 RMZ  C01   C  CH3   0  -0.734  -2.2775  2.9848  -25.6687
 RMZ  C02   C  CR6   0   0.040  -0.9997  2.8100  -24.9009
 RMZ  C03   C  CR6   0   0.087   0.0971  3.6602  -25.1155
 RMZ  C04   C  CR16  0  -0.379   1.2671  3.4705  -24.3966
 RMZ  C05   C  CR6   0   0.362   1.4067  2.4533  -23.4413
 RMZ  C06   C  CR16  0  -0.364   0.3098  1.6169  -23.2328
 RMZ  C07   C  CR16  0  -0.288  -0.8608  1.8002  -23.9607
 RMZ  C09   C  CH2   0  -0.305   3.2013  3.4717  -22.1508
 RMZ  C12   C  CH2   0  -0.280   4.2362  0.9141  -21.5729
 RMZ  C16   C  CR15  0  -0.079   7.9706  2.5632  -18.8363
 RMZ  C18   C  CR16  0  -0.329   9.5385  2.2583  -20.9257
 RMZ  C19   C  CR16  0  -0.237  10.6986  2.7195  -21.5392
 RMZ  C23   C  CR5   0   0.515   9.3444  4.2221  -17.8574
 RMZ  N08   N  NT    0  -0.517   2.6239  2.2893  -22.7726
 RMZ  N11   N  NT    0  -0.425   4.7821  2.0809  -20.9093
 RMZ  N25   N  NR15  0  -0.668   8.2490  3.4464  -17.7204
 RMZ  O24   O  O     0  -0.479   9.7546  5.0616  -17.0726
 RMZ  H102  H  HCH2  0   0.196   5.2484  3.1131  -22.7002
 RMZ  H101  H  HCH2  0   0.246   5.0199  4.1273  -21.2740
 RMZ  H131  H  HCH2  0   0.209   2.1791  1.1913  -21.0113
 RMZ  H132  H  HCH2  0   0.249   2.4358  0.2364  -22.4743
 RMZ  H151  H  HCH2  0   0.242   6.6590  3.8939  -19.8876
 RMZ  H152  H  HCH2  0   0.247   5.8669  2.9181  -18.6580
 RMZ  H201  H  HCR6  0   0.264  12.3685  4.0657  -21.4661
 RMZ  H211  H  HCR6  0   0.263  11.6975  5.0634  -19.2865
 RMZ  H261  H  HCH3  0   0.241  -0.8132  5.4367  -25.9355
 RMZ  H263  H  HCH3  0   0.248   0.9319  5.3492  -26.1561
 RMZ  H262  H  HCH3  0   0.242  -0.1414  4.3590  -27.1413
 RMZ  H012  H  HCH3  0   0.238  -2.1276  2.8541  -26.7431
 RMZ  H011  H  HCH3  0   0.246  -3.0286  2.2614  -25.3525
 RMZ  H013  H  HCH3  0   0.237  -2.7020  3.9819  -25.5312
 RMZ  H041  H  HCR6  0   0.247   2.1062  4.1238  -24.6057
 RMZ  H061  H  HCR6  0   0.261   0.3409  0.8225  -22.5001
 RMZ  H071  H  HCR6  0   0.240  -1.6946  1.1328  -23.7732
 RMZ  H091  H  HCH2  0   0.253   3.1631  4.3166  -22.8359
 RMZ  H092  H  HCH2  0   0.213   2.6363  3.7553  -21.2499
 RMZ  H121  H  HCH2  0   0.241   4.3057  0.0543  -20.9027
 RMZ  H122  H  HCH2  0   0.195   4.7983  0.6610  -22.4885
 RMZ  H141  H  HCH2  0   0.235   6.2038  0.8690  -20.0243
 RMZ  H142  H  HCH2  0   0.201   6.8363  1.8400  -21.3473
 RMZ  H161  H  HCR5  0   0.277   7.9737  1.5200  -18.4992
 RMZ  H181  H  HCR6  0   0.259   8.9637  1.4641  -21.3829
 RMZ  H191  H  HCR6  0   0.266  11.0091  2.2833  -22.4796
 RMZ  H251  H  HNR5  0   0.402   7.6297  3.5153  -16.9281
 RMZ  C14   C  CH2   0  -0.267   6.1519  1.8605  -20.4839

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
 RMZ  C26  C03   single    1.501  0.020  1.501
 RMZ  C01  C02   single    1.501  0.020  1.501
 RMZ  C03  C02   aromatic  1.404  0.020  1.404
 RMZ  C03  C04   aromatic  1.386  0.020  1.386
 RMZ  C02  C07   aromatic  1.387  0.020  1.387
 RMZ  C04  C05   aromatic  1.402  0.020  1.402
 RMZ  C07  C06   aromatic  1.391  0.020  1.391
 RMZ  C05  C06   aromatic  1.395  0.020  1.395
 RMZ  C05  N08   single    1.398  0.020  1.398
 RMZ  N08  C13   single    1.447  0.020  1.447
 RMZ  N08  C09   single    1.455  0.020  1.455
 RMZ  C13  C12   single    1.517  0.020  1.517
 RMZ  C09  C10   single    1.515  0.020  1.515
 RMZ  C12  N11   single    1.449  0.020  1.449
 RMZ  C10  N11   single    1.450  0.020  1.450
 RMZ  N11  C14   single    1.451  0.020  1.451
 RMZ  C14  C15   single    1.523  0.020  1.523
 RMZ  C15  C16   single    1.532  0.020  1.532
 RMZ  C18  C19   aromatic  1.391  0.020  1.391
 RMZ  C18  C17   aromatic  1.386  0.020  1.386
 RMZ  C19  C20   aromatic  1.394  0.020  1.394
 RMZ  C17  C16   single    1.507  0.020  1.507
 RMZ  C17  C22   aromatic  1.387  0.020  1.387
 RMZ  C16  N25   single    1.450  0.020  1.450
 RMZ  C20  C21   aromatic  1.388  0.020  1.388
 RMZ  C22  C21   aromatic  1.384  0.020  1.384
 RMZ  C22  C23   single    1.480  0.020  1.480
 RMZ  N25  C23   single    1.349  0.020  1.349
 RMZ  C23  O24   double    1.220  0.020  1.220
 RMZ  C10  H102  single    0.970  0.020  1.090
 RMZ  C10  H101  single    0.970  0.020  1.090
 RMZ  C13  H131  single    0.970  0.020  1.090
 RMZ  C13  H132  single    0.970  0.020  1.090
 RMZ  C15  H151  single    0.970  0.020  1.090
 RMZ  C15  H152  single    0.970  0.020  1.090
 RMZ  C20  H201  single    0.930  0.020  1.080
 RMZ  C21  H211  single    0.930  0.020  1.080
 RMZ  C26  H261  single    0.970  0.020  1.090
 RMZ  C26  H263  single    0.970  0.020  1.090
 RMZ  C26  H262  single    0.970  0.020  1.090
 RMZ  C01  H012  single    0.970  0.020  1.090
 RMZ  C01  H011  single    0.970  0.020  1.090
 RMZ  C01  H013  single    0.970  0.020  1.090
 RMZ  C04  H041  single    0.930  0.020  1.080
 RMZ  C06  H061  single    0.930  0.020  1.080
 RMZ  C07  H071  single    0.930  0.020  1.080
 RMZ  C09  H091  single    0.970  0.020  1.090
 RMZ  C09  H092  single    0.970  0.020  1.090
 RMZ  C12  H121  single    0.970  0.020  1.090
 RMZ  C12  H122  single    0.970  0.020  1.090
 RMZ  C14  H141  single    0.970  0.020  1.090
 RMZ  C14  H142  single    0.970  0.020  1.090
 RMZ  C16  H161  single    0.970  0.020  1.090
 RMZ  C18  H181  single    0.930  0.020  1.080
 RMZ  C19  H191  single    0.930  0.020  1.080
 RMZ  N25  H251  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
 RMZ  H101  C10  H102  107.01  3.000
 RMZ  H101  C10  N11   110.04  3.000
 RMZ  H102  C10  N11   111.40  3.000
 RMZ  H101  C10  C09   107.95  3.000
 RMZ  H102  C10  C09   109.28  3.000
 RMZ  N11   C10  C09   111.01  3.000
 RMZ  H132  C13  H131  107.30  3.000
 RMZ  H132  C13  N08   109.51  3.000
 RMZ  H131  C13  N08   112.09  3.000
 RMZ  H132  C13  C12   107.97  3.000
 RMZ  H131  C13  C12   109.39  3.000
 RMZ  N08   C13  C12   110.46  3.000
 RMZ  H152  C15  H151  107.08  3.000
 RMZ  H152  C15  C16   108.12  3.000
 RMZ  H151  C15  C16   108.39  3.000
 RMZ  H152  C15  C14   107.84  3.000
 RMZ  H151  C15  C14   111.78  3.000
 RMZ  C16   C15  C14   113.39  3.000
 RMZ  C18   C17  C16   130.75  3.000
 RMZ  C16   C17  C22   109.30  3.000
 RMZ  C18   C17  C22   119.95  3.000
 RMZ  H201  C20  C19   119.63  3.000
 RMZ  H201  C20  C21   120.05  3.000
 RMZ  C19   C20  C21   120.31  3.000
 RMZ  H211  C21  C22   121.06  3.000
 RMZ  H211  C21  C20   121.12  3.000
 RMZ  C22   C21  C20   117.82  3.000
 RMZ  C23   C22  C21   128.78  3.000
 RMZ  C23   C22  C17   108.93  3.000
 RMZ  C21   C22  C17   122.27  3.000
 RMZ  H262  C26  H263  107.72  3.000
 RMZ  H262  C26  H261  106.60  3.000
 RMZ  H263  C26  H261  107.71  3.000
 RMZ  H262  C26  C03   111.50  3.000
 RMZ  H263  C26  C03   111.39  3.000
 RMZ  H261  C26  C03   111.68  3.000
 RMZ  H013  C01  H011  107.56  3.000
 RMZ  H013  C01  H012  106.63  3.000
 RMZ  H011  C01  H012  107.48  3.000
 RMZ  H013  C01  C02   111.89  3.000
 RMZ  H011  C01  C02   111.17  3.000
 RMZ  H012  C01  C02   111.85  3.000
 RMZ  C07   C02  C03   117.79  3.000
 RMZ  C07   C02  C01   121.12  3.000
 RMZ  C03   C02  C01   121.08  3.000
 RMZ  C04   C03  C02   119.81  3.000
 RMZ  C04   C03  C26   119.83  3.000
 RMZ  C02   C03  C26   120.35  3.000
 RMZ  H041  C04  C05   119.45  3.000
 RMZ  H041  C04  C03   118.09  3.000
 RMZ  C05   C04  C03   122.45  3.000
 RMZ  N08   C05  C06   122.86  3.000
 RMZ  N08   C05  C04   119.83  3.000
 RMZ  C06   C05  C04   117.28  3.000
 RMZ  H061  C06  C07   118.41  3.000
 RMZ  H061  C06  C05   121.28  3.000
 RMZ  C07   C06  C05   120.31  3.000
 RMZ  H071  C07  C06   118.41  3.000
 RMZ  H071  C07  C02   119.23  3.000
 RMZ  C06   C07  C02   122.35  3.000
 RMZ  H092  C09  H091  107.29  3.000
 RMZ  H092  C09  N08   110.82  3.000
 RMZ  H091  C09  N08   110.35  3.000
 RMZ  H092  C09  C10   109.33  3.000
 RMZ  H091  C09  C10   108.06  3.000
 RMZ  N08   C09  C10   110.89  3.000
 RMZ  H122  C12  H121  107.22  3.000
 RMZ  H122  C12  N11   111.88  3.000
 RMZ  H121  C12  N11   109.20  3.000
 RMZ  H122  C12  C13   108.90  3.000
 RMZ  H121  C12  C13   108.30  3.000
 RMZ  N11   C12  C13   111.20  3.000
 RMZ  H161  C16  N25   110.02  3.000
 RMZ  H161  C16  C17   110.45  3.000
 RMZ  N25   C16  C17   101.11  3.000
 RMZ  H161  C16  C15   109.29  3.000
 RMZ  N25   C16  C15   110.73  3.000
 RMZ  C17   C16  C15   114.97  3.000
 RMZ  H181  C18  C19   120.02  3.000
 RMZ  H181  C18  C17   121.70  3.000
 RMZ  C19   C18  C17   118.28  3.000
 RMZ  H191  C19  C18   119.27  3.000
 RMZ  H191  C19  C20   119.38  3.000
 RMZ  C18   C19  C20   121.35  3.000
 RMZ  O24   C23  N25   127.10  3.000
 RMZ  O24   C23  C22   127.70  3.000
 RMZ  N25   C23  C22   105.20  3.000
 RMZ  C09   N08  C05   117.02  3.000
 RMZ  C09   N08  C13   111.50  3.000
 RMZ  C05   N08  C13   117.66  3.000
 RMZ  C14   N11  C12   111.56  3.000
 RMZ  C14   N11  C10   112.45  3.000
 RMZ  C12   N11  C10   109.34  3.000
 RMZ  H251  N25  C23   122.64  3.000
 RMZ  H251  N25  C16   121.90  3.000
 RMZ  C23   N25  C16   115.34  3.000
 RMZ  H142  C14  H141  106.42  3.000
 RMZ  H142  C14  N11   111.07  3.000
 RMZ  H141  C14  N11   107.79  3.000
 RMZ  H142  C14  C15   110.66  3.000
 RMZ  H141  C14  C15   108.40  3.000
 RMZ  N11   C14  C15   112.25  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
 RMZ  CONST_01  C20   C19  C18  C17     0.00   0.0  0
 RMZ  CONST_02  C20   C21  C22  C17     0.00   0.0  0
 RMZ  CONST_03  C18   C19  C20  C21     0.00   0.0  0
 RMZ  CONST_04  C18   C17  C22  C21     0.00   0.0  0
 RMZ  CONST_05  C19   C18  C17  C22     0.00   0.0  0
 RMZ  CONST_06  C19   C20  C21  C22     0.00   0.0  0
 RMZ  CONST_07  C05   C04  C03  C02     0.00   0.0  0
 RMZ  CONST_08  C05   C06  C07  C02     0.00   0.0  0
 RMZ  CONST_09  C06   C07  C02  C03     0.00   0.0  0
 RMZ  CONST_10  C06   C05  C04  C03     0.00   0.0  0
 RMZ  CONST_11  C07   C02  C03  C04     0.00   0.0  0
 RMZ  CONST_12  C07   C06  C05  C04     0.00   0.0  0
 RMZ  CONST_13  N08   C05  C04  C03   180.00   0.0  0
 RMZ  CONST_14  N08   C05  C06  C07   180.00   0.0  0
 RMZ  CONST_15  C16   N25  C23  C22     0.00   0.0  0
 RMZ  CONST_16  C07   C02  C03  C26   180.00   0.0  0
 RMZ  CONST_17  C05   C04  C03  C26   180.00   0.0  0
 RMZ  CONST_18  C04   C03  C02  C01   180.00   0.0  0
 RMZ  CONST_19  C06   C07  C02  C01   180.00   0.0  0
 RMZ  CONST_20  O24   C23  N25  C16   180.00   0.0  0
 RMZ  CONST_21  H191  C19  C18  C17   180.00   0.0  0
 RMZ  CONST_22  H211  C21  C22  C17   180.00   0.0  0
 RMZ  CONST_23  H181  C18  C19  C20   180.00   0.0  0
 RMZ  CONST_24  H201  C20  C21  C22   180.00   0.0  0
 RMZ  CONST_25  H041  C04  C03  C02   180.00   0.0  0
 RMZ  CONST_26  H061  C06  C07  C02   180.00   0.0  0
 RMZ  CONST_27  H071  C07  C02  C03   180.00   0.0  0
 RMZ  CONST_28  H251  N25  C23  C22   180.00   0.0  0
 RMZ  Var_01    C05   N08  C09  C10  -165.66  30.0  1
 RMZ  Var_02    C13   C12  N11  C10   -58.67  30.0  1
 RMZ  Var_03    C04   C05  N08  C13  -171.81  30.0  3
 RMZ  Var_04    C12   C13  N08  C05   165.79  30.0  1
 RMZ  Var_05    C12   N11  C10  C09    58.15  30.0  1
 RMZ  Var_06    N11   C12  C13  N08    57.34  30.0  1
 RMZ  Var_07    N11   C10  C09  N08   -56.50  30.0  1
 RMZ  Var_08    C15   C14  N11  C10    72.94  30.0  3
 RMZ  Var_09    N11   C14  C15  C16   171.33  30.0  1
 RMZ  Var_10    H261  C26  C03  C02    57.35  30.0  2
 RMZ  Var_11    H012  C01  C02  C03    61.67  30.0  2

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
 RMZ  chir_01  C16  C15  C17  N25  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
 RMZ  plan-1  C26   0.020
 RMZ  plan-1  C01   0.020
 RMZ  plan-1  C02   0.020
 RMZ  plan-1  C03   0.020
 RMZ  plan-1  C04   0.020
 RMZ  plan-1  C05   0.020
 RMZ  plan-1  C06   0.020
 RMZ  plan-1  C07   0.020
 RMZ  plan-1  N08   0.020
 RMZ  plan-1  H041  0.020
 RMZ  plan-1  H061  0.020
 RMZ  plan-1  H071  0.020
 RMZ  plan-2  C17   0.020
 RMZ  plan-2  C20   0.020
 RMZ  plan-2  C21   0.020
 RMZ  plan-2  C22   0.020
 RMZ  plan-2  C16   0.020
 RMZ  plan-2  C18   0.020
 RMZ  plan-2  C19   0.020
 RMZ  plan-2  C23   0.020
 RMZ  plan-2  N25   0.020
 RMZ  plan-2  O24   0.020
 RMZ  plan-2  H201  0.020
 RMZ  plan-2  H211  0.020
 RMZ  plan-2  H181  0.020
 RMZ  plan-2  H191  0.020
 RMZ  plan-2  H251  0.020

