# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Aug  4 00:20:33 2022
#   Inital geometry file: a 125 line input string
#   Ligand name: 2-({1-[2-(4-fluorophenyl)-2-oxoethyl]piperidin-4-yl}methyl)-2,3-dihydro-1H-isoindol-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccc(cc1)C(=O)CN2CCC(CC2)CN3Cc4ccccc4C3=O
#
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
 YT7  YT7  "Roluperidone"
  ligand  50  27  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_YT7
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
 YT7  C5   C  CH2   0  -0.271  -0.8729  -24.4850  31.5472
 YT7  C6   C  CH2   0  -0.279  -1.2056  -26.6614  32.7801
 YT7  C7   C  CR56  0   0.090  -0.9110  -28.0771  32.3977
 YT7  C8   C  CR16  0  -0.319  -1.0936  -29.2539  33.1027
 YT7  C9   C  CR16  0  -0.241  -0.7155  -30.4448  32.4924
 YT7  C10  C  CR16  0  -0.258  -0.1685  -30.4581  31.2089
 YT7  C3   C  CH2   0  -0.424   1.5124  -24.1954  32.3665
 YT7  C2   C  CH2   0  -0.279   2.4241  -23.3813  33.2714
 YT7  C1   C  CH2   0  -0.286   0.9220  -21.5178  33.2394
 YT7  O1   O  O     0  -0.382   3.0927  -19.5808  31.9203
 YT7  N1   N  NR5   0  -0.508  -0.7850  -25.9223  31.6087
 YT7  C4   C  CH1   0  -0.270   0.0581  -23.7694  32.5245
 YT7  C11  C  CR16  0  -0.302   0.0116  -29.2749  30.5067
 YT7  C15  C  C     0   0.359   3.5841  -19.8647  32.9896
 YT7  C13  C  CR5   0   0.543  -0.2875  -26.7063  30.6204
 YT7  C12  C  CR56  0  -0.070  -0.3686  -28.0944  31.1239
 YT7  C16  C  CR6   0  -0.027   4.5610  -18.9440  33.6373
 YT7  N    N  NT    0  -0.415   2.2845  -21.9610  33.0004
 YT7  C    C  CH2   0  -0.421  -0.0547  -22.2588  32.3409
 YT7  O    O  O     0  -0.477   0.1353  -26.3355  29.5374
 YT7  C17  C  CR16  0  -0.241   4.8417  -17.7256  33.0150
 YT7  C18  C  CR16  0  -0.396   5.7621  -16.8443  33.5510
 YT7  C19  C  CR6   0   0.537   6.4082  -17.1972  34.7225
 YT7  C20  C  CR16  0  -0.394   6.1562  -18.3903  35.3719
 YT7  C21  C  CR16  0  -0.274   5.2277  -19.2601  34.8219
 YT7  F    F  F     0  -0.305   7.3079  -16.3538  35.2405
 YT7  H1   H  HCH2  0   0.249  -0.6351  -24.1823  30.5263
 YT7  H2   H  HCH2  0   0.250  -1.9071  -24.1807  31.7384
 YT7  H3   H  HCH2  0   0.270  -0.6472  -26.3567  33.6703
 YT7  H4   H  HCH2  0   0.271  -2.2675  -26.4979  32.9883
 YT7  H5   H  HCR6  0   0.258  -1.5161  -29.2548  34.0995
 YT7  H6   H  HCR6  0   0.263  -0.8470  -31.3795  33.0221
 YT7  H7   H  HCR6  0   0.261   0.1166  -31.4009  30.7608
 YT7  H8   H  HCH2  0   0.235   1.6346  -25.2555  32.6022
 YT7  H9   H  HCH2  0   0.216   1.8242  -24.0602  31.3254
 YT7  H10  H  HCH2  0   0.188   2.1988  -23.6214  34.3255
 YT7  H11  H  HCH2  0   0.238   3.4628  -23.6721  33.0985
 YT7  H12  H  HCH2  0   0.241   0.8479  -20.4466  33.0479
 YT7  H13  H  HCH2  0   0.190   0.6367  -21.6696  34.2962
 YT7  H14  H  HCH1  0   0.227  -0.2585  -24.0030  33.5498
 YT7  H15  H  HCR6  0   0.257   0.4353  -29.2745  29.5104
 YT7  H16  H  HCH2  0   0.281   4.1930  -21.7266  33.7777
 YT7  H17  H  HCH2  0   0.242   2.9639  -20.9419  34.7413
 YT7  H19  H  HCH2  0   0.218   0.1521  -21.9980  31.2976
 YT7  H20  H  HCH2  0   0.233  -1.0716  -21.9220  32.5587
 YT7  H21  H  HCR6  0   0.273   4.3353  -17.4616  32.0966
 YT7  H22  H  HCR6  0   0.285   5.9783  -15.9009  33.0674
 YT7  H23  H  HCR6  0   0.287   6.6758  -18.6396  36.2875
 YT7  H24  H  HCR6  0   0.276   5.0400  -20.1933  35.3353
 YT7  C14  C  CH2   0  -0.401   3.2552  -21.1651  33.7007

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
 YT7  O    C13  double    1.220  0.020  1.220
 YT7  C11  C10  aromatic  1.388  0.020  1.388
 YT7  C11  C12  aromatic  1.385  0.020  1.385
 YT7  C13  C12  single    1.479  0.020  1.479
 YT7  C13  N1   single    1.356  0.020  1.356
 YT7  C10  C9   aromatic  1.395  0.020  1.395
 YT7  C12  C7   aromatic  1.385  0.020  1.385
 YT7  C5   N1   single    1.441  0.020  1.441
 YT7  C5   C4   single    1.528  0.020  1.528
 YT7  N1   C6   single    1.448  0.020  1.448
 YT7  C9   C8   aromatic  1.391  0.020  1.391
 YT7  O1   C15  double    1.211  0.020  1.211
 YT7  C7   C6   single    1.496  0.020  1.496
 YT7  C7   C8   aromatic  1.384  0.020  1.384
 YT7  C    C4   single    1.526  0.020  1.526
 YT7  C    C1   single    1.520  0.020  1.520
 YT7  C4   C3   single    1.524  0.020  1.524
 YT7  C3   C2   single    1.521  0.020  1.521
 YT7  C17  C18  aromatic  1.382  0.020  1.382
 YT7  C17  C16  aromatic  1.397  0.020  1.397
 YT7  C15  C16  single    1.491  0.020  1.491
 YT7  C15  C14  single    1.518  0.020  1.518
 YT7  N    C1   single    1.453  0.020  1.453
 YT7  N    C2   single    1.453  0.020  1.453
 YT7  N    C14  single    1.437  0.020  1.437
 YT7  C18  C19  aromatic  1.384  0.020  1.384
 YT7  C16  C21  aromatic  1.396  0.020  1.396
 YT7  C19  F    single    1.338  0.020  1.338
 YT7  C19  C20  aromatic  1.382  0.020  1.382
 YT7  C21  C20  aromatic  1.386  0.020  1.386
 YT7  C5   H1   single    0.970  0.020  1.090
 YT7  C5   H2   single    0.970  0.020  1.090
 YT7  C6   H3   single    0.970  0.020  1.090
 YT7  C6   H4   single    0.970  0.020  1.090
 YT7  C8   H5   single    0.930  0.020  1.080
 YT7  C9   H6   single    0.930  0.020  1.080
 YT7  C10  H7   single    0.930  0.020  1.080
 YT7  C3   H8   single    0.970  0.020  1.090
 YT7  C3   H9   single    0.970  0.020  1.090
 YT7  C2   H10  single    0.970  0.020  1.090
 YT7  C2   H11  single    0.970  0.020  1.090
 YT7  C1   H12  single    0.970  0.020  1.090
 YT7  C1   H13  single    0.970  0.020  1.090
 YT7  C4   H14  single    0.970  0.020  1.090
 YT7  C11  H15  single    0.930  0.020  1.080
 YT7  C14  H16  single    0.970  0.020  1.090
 YT7  C14  H17  single    0.970  0.020  1.090
 YT7  C    H19  single    0.970  0.020  1.090
 YT7  C    H20  single    0.970  0.020  1.090
 YT7  C17  H21  single    0.930  0.020  1.080
 YT7  C18  H22  single    0.930  0.020  1.080
 YT7  C20  H23  single    0.930  0.020  1.080
 YT7  C21  H24  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
 YT7  H2   C5   H1   106.98  3.000
 YT7  H2   C5   C4   109.50  3.000
 YT7  H1   C5   C4   109.62  3.000
 YT7  H2   C5   N1   109.11  3.000
 YT7  H1   C5   N1   107.66  3.000
 YT7  C4   C5   N1   113.75  3.000
 YT7  H4   C6   H3   107.38  3.000
 YT7  H4   C6   N1   111.08  3.000
 YT7  H3   C6   N1   111.59  3.000
 YT7  H4   C6   C7   112.41  3.000
 YT7  H3   C6   C7   111.78  3.000
 YT7  N1   C6   C7   102.66  3.000
 YT7  C12  C7   C8   120.65  3.000
 YT7  C8   C7   C6   130.44  3.000
 YT7  C12  C7   C6   108.91  3.000
 YT7  H5   C8   C9   120.63  3.000
 YT7  H5   C8   C7   121.42  3.000
 YT7  C9   C8   C7   117.95  3.000
 YT7  H6   C9   C10  119.31  3.000
 YT7  H6   C9   C8   119.45  3.000
 YT7  C10  C9   C8   121.23  3.000
 YT7  H7   C10  C11  119.95  3.000
 YT7  H7   C10  C9   119.51  3.000
 YT7  C11  C10  C9   120.55  3.000
 YT7  H9   C3   H8   107.03  3.000
 YT7  H9   C3   C4   109.62  3.000
 YT7  H8   C3   C4   110.83  3.000
 YT7  H9   C3   C2   109.20  3.000
 YT7  H8   C3   C2   108.90  3.000
 YT7  C4   C3   C2   111.15  3.000
 YT7  H11  C2   H10  106.69  3.000
 YT7  H11  C2   N    108.79  3.000
 YT7  H10  C2   N    111.78  3.000
 YT7  H11  C2   C3   109.47  3.000
 YT7  H10  C2   C3   109.22  3.000
 YT7  N    C2   C3   110.79  3.000
 YT7  H13  C1   H12  106.58  3.000
 YT7  H13  C1   C    109.42  3.000
 YT7  H12  C1   C    109.35  3.000
 YT7  H13  C1   N    110.95  3.000
 YT7  H12  C1   N    109.54  3.000
 YT7  C    C1   N    110.90  3.000
 YT7  C13  N1   C6   113.65  3.000
 YT7  C6   N1   C5   121.73  3.000
 YT7  C13  N1   C5   124.60  3.000
 YT7  H14  C4   C    107.55  3.000
 YT7  H14  C4   C3   108.21  3.000
 YT7  C    C4   C3   109.57  3.000
 YT7  H14  C4   C5   108.78  3.000
 YT7  C3   C4   C5   112.60  3.000
 YT7  C    C4   C5   109.98  3.000
 YT7  H15  C11  C12  121.14  3.000
 YT7  H15  C11  C10  121.11  3.000
 YT7  C12  C11  C10  117.75  3.000
 YT7  C16  C15  C14  117.88  3.000
 YT7  C14  C15  O1   121.78  3.000
 YT7  C16  C15  O1   120.33  3.000
 YT7  O    C13  C12  127.33  3.000
 YT7  C12  C13  N1   105.93  3.000
 YT7  O    C13  N1   126.74  3.000
 YT7  C13  C12  C11  129.28  3.000
 YT7  C13  C12  C7   108.84  3.000
 YT7  C11  C12  C7   121.87  3.000
 YT7  C21  C16  C17  118.67  3.000
 YT7  C21  C16  C15  122.82  3.000
 YT7  C17  C16  C15  118.49  3.000
 YT7  C14  N    C1   112.60  3.000
 YT7  C14  N    C2   112.68  3.000
 YT7  C1   N    C2   110.96  3.000
 YT7  H20  C    H19  106.99  3.000
 YT7  H20  C    C4   110.48  3.000
 YT7  H19  C    C4   109.66  3.000
 YT7  H20  C    C1   109.25  3.000
 YT7  H19  C    C1   109.01  3.000
 YT7  C4   C    C1   111.35  3.000
 YT7  H21  C17  C18  119.03  3.000
 YT7  H21  C17  C16  119.82  3.000
 YT7  C18  C17  C16  121.15  3.000
 YT7  H22  C18  C19  120.50  3.000
 YT7  H22  C18  C17  121.04  3.000
 YT7  C19  C18  C17  118.46  3.000
 YT7  F    C19  C20  119.02  3.000
 YT7  C20  C19  C18  122.21  3.000
 YT7  F    C19  C18  118.76  3.000
 YT7  H23  C20  C21  120.86  3.000
 YT7  H23  C20  C19  120.61  3.000
 YT7  C21  C20  C19  118.53  3.000
 YT7  H24  C21  C20  117.99  3.000
 YT7  H24  C21  C16  121.03  3.000
 YT7  C20  C21  C16  120.97  3.000
 YT7  H17  C14  H16  105.26  3.000
 YT7  H17  C14  N    113.15  3.000
 YT7  H16  C14  N    109.18  3.000
 YT7  H17  C14  C15  109.01  3.000
 YT7  H16  C14  C15  106.64  3.000
 YT7  N    C14  C15  113.10  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
 YT7  CONST_01  C10  C11  C12  C7      0.00   0.0  0
 YT7  CONST_02  C10  C9   C8   C7      0.00   0.0  0
 YT7  CONST_03  C11  C10  C9   C8      0.00   0.0  0
 YT7  CONST_04  C11  C12  C7   C8      0.00   0.0  0
 YT7  CONST_05  C12  C11  C10  C9      0.00   0.0  0
 YT7  CONST_06  C12  C7   C8   C9      0.00   0.0  0
 YT7  CONST_07  C19  C18  C17  C16     0.00   0.0  0
 YT7  CONST_08  C19  C20  C21  C16     0.00   0.0  0
 YT7  CONST_09  C20  C19  C18  C17     0.00   0.0  0
 YT7  CONST_10  C20  C21  C16  C17     0.00   0.0  0
 YT7  CONST_11  C21  C16  C17  C18     0.00   0.0  0
 YT7  CONST_12  C21  C20  C19  C18     0.00   0.0  0
 YT7  CONST_13  C12  C13  N1   C6      0.00   0.0  0
 YT7  CONST_14  C18  C17  C16  C15   180.00   0.0  0
 YT7  CONST_15  C20  C21  C16  C15   180.00   0.0  0
 YT7  CONST_16  F    C19  C18  C17   180.00   0.0  0
 YT7  CONST_17  F    C19  C20  C21   180.00   0.0  0
 YT7  CONST_18  C12  C13  N1   C5    180.00   0.0  0
 YT7  CONST_19  O    C13  N1   C6    180.00   0.0  0
 YT7  CONST_20  H5   C8   C7   C6      0.00   0.0  0
 YT7  CONST_21  H15  C11  C12  C7    180.00   0.0  0
 YT7  CONST_22  H6   C9   C8   C7    180.00   0.0  0
 YT7  CONST_23  H7   C10  C9   C8    180.00   0.0  0
 YT7  CONST_24  H15  C11  C10  C9    180.00   0.0  0
 YT7  CONST_25  H5   C8   C9   C10   180.00   0.0  0
 YT7  CONST_26  H6   C9   C10  C11   180.00   0.0  0
 YT7  CONST_27  H15  C11  C12  C13     0.00   0.0  0
 YT7  CONST_28  H7   C10  C11  C12   180.00   0.0  0
 YT7  CONST_29  H5   C8   C7   C12   180.00   0.0  0
 YT7  CONST_30  H22  C18  C17  C16   180.00   0.0  0
 YT7  CONST_31  H23  C20  C21  C16   180.00   0.0  0
 YT7  CONST_32  H24  C21  C16  C17   180.00   0.0  0
 YT7  CONST_33  H23  C20  C19  C18   180.00   0.0  0
 YT7  CONST_34  H21  C17  C18  C19   180.00   0.0  0
 YT7  CONST_35  H24  C21  C20  C19   180.00   0.0  0
 YT7  CONST_36  H22  C18  C19  C20   180.00   0.0  0
 YT7  CONST_37  H21  C17  C16  C21   180.00   0.0  0
 YT7  CONST_38  O    C13  N1   C5      0.00   0.0  0
 YT7  Var_01    C1   N    C2   C3     60.64  30.0  1
 YT7  Var_02    C    C1   N    C2    -60.30  30.0  1
 YT7  Var_03    N    C1   C    C4     56.41  30.0  1
 YT7  Var_04    N    C2   C3   C4    -57.08  30.0  1
 YT7  Var_05    C4   C5   N1   C6     66.28  30.0  2
 YT7  Var_06    C14  N    C2   C3   -172.04  30.0  1
 YT7  Var_07    C13  N1   C5   C4   -112.21  30.0  3
 YT7  Var_08    C    C1   N    C14   172.34  30.0  1
 YT7  Var_09    H3   C6   C7   C8     60.22  30.0  1
 YT7  Var_10    H4   C6   C7   C8    -60.62  30.0  1
 YT7  Var_11    H12  C1   N    C2    178.92  30.0  1
 YT7  Var_12    H13  C1   N    C2     61.52  30.0  1
 YT7  Var_13    H10  C2   N    C1    -61.42  30.0  1
 YT7  Var_14    H11  C2   N    C1   -178.98  30.0  1
 YT7  Var_15    H12  C1   C    C4    177.31  30.0  1
 YT7  Var_16    H13  C1   C    C4    -66.31  30.0  1
 YT7  Var_17    H10  C2   C3   C4     66.46  30.0  1
 YT7  Var_18    H11  C2   C3   C4   -177.06  30.0  1
 YT7  Var_19    H3   C6   N1   C13   119.48  30.0  1
 YT7  Var_20    H4   C6   N1   C13  -120.73  30.0  1
 YT7  Var_21    H3   C6   C7   C12  -119.44  30.0  1
 YT7  Var_22    H4   C6   C7   C12   119.72  30.0  1
 YT7  Var_23    H19  C    C1   N     -64.70  30.0  1
 YT7  Var_24    H20  C    C1   N     178.70  30.0  1
 YT7  Var_25    H8   C3   C2   N    -179.46  30.0  1
 YT7  Var_26    H9   C3   C2   N      63.98  30.0  1
 YT7  Var_27    C15  C14  N    C2    152.49  30.0  3
 YT7  Var_28    C15  C14  N    C1    -81.07  30.0  3
 YT7  Var_29    C17  C16  C15  O1      3.08  30.0  2
 YT7  Var_30    C21  C16  C15  O1   -175.48  30.0  2
 YT7  Var_31    C17  C16  C15  C14  -178.05  30.0  2
 YT7  Var_32    C21  C16  C15  C14     3.39  30.0  2
 YT7  Var_33    N    C14  C15  C16   178.85  30.0  3
 YT7  Var_34    H3   C6   N1   C5    -59.17  30.0  1
 YT7  Var_35    H4   C6   N1   C5     60.63  30.0  1
 YT7  Var_36    H1   C5   N1   C6   -172.05  30.0  2
 YT7  Var_37    H2   C5   N1   C6    -56.29  30.0  2
 YT7  Var_38    H16  C14  N    C2     33.93  30.0  3
 YT7  Var_39    H17  C14  N    C2    -82.93  30.0  3
 YT7  Var_40    H16  C14  N    C1    160.37  30.0  3
 YT7  Var_41    H17  C14  N    C1     43.51  30.0  3
 YT7  Var_42    H12  C1   N    C14    51.55  30.0  1
 YT7  Var_43    H13  C1   N    C14   -65.84  30.0  1
 YT7  Var_44    H10  C2   N    C14    65.90  30.0  1
 YT7  Var_45    H11  C2   N    C14   -51.66  30.0  1
 YT7  Var_46    H1   C5   N1   C13     9.46  30.0  2
 YT7  Var_47    H2   C5   N1   C13   125.22  30.0  2
 YT7  Var_48    N    C14  C15  O1     -2.30  30.0  3
 YT7  Var_49    H16  C14  C15  C16   -61.13  30.0  3
 YT7  Var_50    H17  C14  C15  C16    52.05  30.0  3
 YT7  Var_51    H16  C14  C15  O1    117.72  30.0  3
 YT7  Var_52    H17  C14  C15  O1   -129.10  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
 YT7  chir_01  C4  C5  C  C3  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
 YT7  plan-1  C15  0.020
 YT7  plan-1  C16  0.020
 YT7  plan-1  C17  0.020
 YT7  plan-1  C18  0.020
 YT7  plan-1  C19  0.020
 YT7  plan-1  C20  0.020
 YT7  plan-1  C21  0.020
 YT7  plan-1  F    0.020
 YT7  plan-1  H21  0.020
 YT7  plan-1  H22  0.020
 YT7  plan-1  H23  0.020
 YT7  plan-1  H24  0.020
 YT7  plan-2  O1   0.020
 YT7  plan-2  C15  0.020
 YT7  plan-2  C16  0.020
 YT7  plan-2  C14  0.020
 YT7  plan-3  C5   0.020
 YT7  plan-3  C6   0.020
 YT7  plan-3  C7   0.020
 YT7  plan-3  C8   0.020
 YT7  plan-3  C9   0.020
 YT7  plan-3  C10  0.020
 YT7  plan-3  N1   0.020
 YT7  plan-3  C11  0.020
 YT7  plan-3  C13  0.020
 YT7  plan-3  C12  0.020
 YT7  plan-3  O    0.020
 YT7  plan-3  H5   0.020
 YT7  plan-3  H6   0.020
 YT7  plan-3  H7   0.020
 YT7  plan-3  H15  0.020

