# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 00:57:40 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: 1-[4-(benzenecarbonyl)piperazin-1-yl]-2-(4-bromo-7-fluoro-1H-indol-3-yl)ethane-1,2-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccc(Br)c2c1[nH]cc2C(=O)C(=O)N3CCN(CC3)C(=O)c4ccccc4
#
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
 JYS  JYS  1-[4-(benzenecarbonyl)piperazin-1-yl]-2-(4-bromo-7-fluoro-1H-indol-3-yl)ethane-1,2-dione  ligand  46  29  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_JYS
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
 JYS  C01  C   CR16  0  -0.447   5.4513   0.0067  -1.5296
 JYS  C02  C   CR6   0   0.542   4.5757  -1.0342  -1.6787
 JYS  C03  C   CR56  0   0.199   3.4773  -1.1282  -0.8385
 JYS  C04  C   CR56  0   0.220   3.2169  -0.1912   0.1848
 JYS  C05  C   CR6   0  -0.317   4.1057   0.8915   0.2904
 JYS  C06  C   CR16  0  -0.227   5.2034   0.9699  -0.5458
 JYS  C07  C   CR15  0   0.019   1.6099  -1.7885   0.1353
 JYS  C08  C   CR5   0  -0.150   1.9969  -0.6476   0.8181
 JYS  C09  C   C     0   0.220   1.2649  -0.1985   1.9843
 JYS  C10  C   C     0   0.420  -0.0855  -0.8795   2.2228
 JYS  C11  C   CH2   0  -0.310  -2.4777  -0.9209   1.7631
 JYS  C12  C   CH2   0  -0.326  -3.0281  -1.3262   0.4003
 JYS  C13  C   CH2   0  -0.319  -1.6510   0.3547  -0.6587
 JYS  C14  C   CH2   0  -0.326  -1.1039   0.7799   0.6965
 JYS  C15  C   C     0   0.524  -4.0636   0.5399  -0.8769
 JYS  C16  C   CR6   0  -0.074  -5.4097  -0.1044  -0.7817
 JYS  C17  C   CR16  0  -0.271  -6.4399   0.5853  -0.1488
 JYS  C18  C   CR16  0  -0.246  -7.7182   0.0478  -0.1136
 JYS  C19  C   CR16  0  -0.252  -7.9816  -1.1645  -0.7383
 JYS  C20  C   CR16  0  -0.243  -6.9609  -1.8442  -1.3901
 JYS  C21  C   CR16  0  -0.260  -5.6759  -1.3206  -1.4057
 JYS  F22  F   F     0  -0.302   4.7504  -1.9672  -2.6207
 JYS  N23  N   NR15  0  -0.665   2.4862  -2.0698  -0.8327
 JYS  N24  N   NT    0  -0.438  -1.1527  -0.3441   1.6161
 JYS  N25  N   NT    0  -0.455  -2.9861  -0.1983  -0.5165
 JYS  O26  O   O     0  -0.375   1.6424   0.5984   2.8168
 JYS  O27  O   O     0  -0.480  -0.1120  -1.8426   2.9734
 JYS  O28  O   O     0  -0.477  -3.9713   1.6789  -1.3109
 JYS  BR   BR  BR    0  -0.041   3.8423   2.3134   1.4947
 JYS  H1   H   HCR6  0   0.296   6.3160   0.0951  -2.1732
 JYS  H2   H   HCR6  0   0.289   5.8926   1.7983  -0.4587
 JYS  H3   H   HCR5  0   0.320   0.7676  -2.4408   0.3040
 JYS  H4   H   HCH2  0   0.262  -3.1395  -0.1832   2.2268
 JYS  H5   H   HCH2  0   0.283  -2.4318  -1.7882   2.4167
 JYS  H6   H   HCH2  0   0.262  -2.4315  -2.1441  -0.0122
 JYS  H7   H   HCH2  0   0.289  -4.0438  -1.6905   0.5245
 JYS  H8   H   HCH2  0   0.283  -1.6658   1.2022  -1.3377
 JYS  H9   H   HCH2  0   0.258  -1.0032  -0.4139  -1.0911
 JYS  H10  H   HCH2  0   0.282  -0.0889   1.1547   0.5801
 JYS  H11  H   HCH2  0   0.274  -1.7044   1.5991   1.1014
 JYS  H12  H   HCR6  0   0.263  -6.2405   1.5360   0.3286
 JYS  H13  H   HCR6  0   0.263  -8.5108   0.5790   0.3968
 JYS  H14  H   HCR6  0   0.263  -8.9819  -1.5770  -0.7208
 JYS  H15  H   HCR6  0   0.263  -7.1642  -2.7832  -1.8875
 JYS  H16  H   HCR6  0   0.270  -4.8849  -1.8553  -1.9172
 JYS  H17  H   HNR5  0   0.438   2.4239  -2.8649  -1.4499

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
 JYS  C20  C19  aromatic  1.389  0.020  1.389
 JYS  C20  C21  aromatic  1.388  0.020  1.388
 JYS  C01  C06  aromatic  1.399  0.020  1.399
 JYS  C01  C02  aromatic  1.368  0.020  1.368
 JYS  C06  C05  aromatic  1.382  0.020  1.382
 JYS  C19  C18  aromatic  1.389  0.020  1.389
 JYS  C21  C16  aromatic  1.393  0.020  1.393
 JYS  F22  C02  single    1.337  0.020  1.337
 JYS  C02  C03  aromatic  1.386  0.020  1.386
 JYS  BR   C05  single    1.882  0.020  1.882
 JYS  C05  C04  aromatic  1.405  0.020  1.405
 JYS  C18  C17  aromatic  1.387  0.020  1.387
 JYS  C16  C17  aromatic  1.392  0.020  1.392
 JYS  C16  C15  single    1.495  0.020  1.495
 JYS  C03  C04  aromatic  1.412  0.020  1.412
 JYS  C03  N23  aromatic  1.367  0.020  1.367
 JYS  C04  C08  aromatic  1.448  0.020  1.448
 JYS  C13  N25  single    1.452  0.020  1.452
 JYS  C13  C14  single    1.522  0.020  1.522
 JYS  C15  N25  single    1.355  0.020  1.355
 JYS  C15  O28  double    1.222  0.020  1.222
 JYS  N25  C12  single    1.454  0.020  1.454
 JYS  O27  C10  double    1.221  0.020  1.221
 JYS  N23  C07  aromatic  1.336  0.020  1.336
 JYS  C14  N24  single    1.453  0.020  1.453
 JYS  C08  C07  aromatic  1.385  0.020  1.385
 JYS  C08  C09  single    1.448  0.020  1.448
 JYS  C10  N24  single    1.339  0.020  1.339
 JYS  C10  C09  single    1.531  0.020  1.531
 JYS  N24  C11  single    1.453  0.020  1.453
 JYS  C12  C11  single    1.525  0.020  1.525
 JYS  C09  O26  double    1.213  0.020  1.213
 JYS  C01  H1   single    0.930  0.020  1.080
 JYS  C06  H2   single    0.930  0.020  1.080
 JYS  C07  H3   single    0.930  0.020  1.080
 JYS  C11  H4   single    0.970  0.020  1.090
 JYS  C11  H5   single    0.970  0.020  1.090
 JYS  C12  H6   single    0.970  0.020  1.090
 JYS  C12  H7   single    0.970  0.020  1.090
 JYS  C13  H8   single    0.970  0.020  1.090
 JYS  C13  H9   single    0.970  0.020  1.090
 JYS  C14  H10  single    0.970  0.020  1.090
 JYS  C14  H11  single    0.970  0.020  1.090
 JYS  C17  H12  single    0.930  0.020  1.080
 JYS  C18  H13  single    0.930  0.020  1.080
 JYS  C19  H14  single    0.930  0.020  1.080
 JYS  C20  H15  single    0.930  0.020  1.080
 JYS  C21  H16  single    0.930  0.020  1.080
 JYS  N23  H17  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
 JYS  H1   C01  C06  120.25  3.000
 JYS  H1   C01  C02  120.59  3.000
 JYS  C06  C01  C02  119.15  3.000
 JYS  F22  C02  C03  118.89  3.000
 JYS  C03  C02  C01  119.51  3.000
 JYS  F22  C02  C01  121.60  3.000
 JYS  N23  C03  C04  108.68  3.000
 JYS  N23  C03  C02  128.60  3.000
 JYS  C04  C03  C02  122.72  3.000
 JYS  C08  C04  C05  137.98  3.000
 JYS  C08  C04  C03  105.26  3.000
 JYS  C05  C04  C03  116.70  3.000
 JYS  BR   C05  C06  117.09  3.000
 JYS  BR   C05  C04  122.81  3.000
 JYS  C06  C05  C04  120.05  3.000
 JYS  H2   C06  C05  120.07  3.000
 JYS  H2   C06  C01  118.12  3.000
 JYS  C05  C06  C01  121.81  3.000
 JYS  H3   C07  N23  119.89  3.000
 JYS  H3   C07  C08  129.75  3.000
 JYS  N23  C07  C08  110.33  3.000
 JYS  C09  C08  C07  120.75  3.000
 JYS  C09  C08  C04  132.85  3.000
 JYS  C07  C08  C04  106.23  3.000
 JYS  O26  C09  C10  117.38  3.000
 JYS  O26  C09  C08  126.82  3.000
 JYS  C10  C09  C08  115.68  3.000
 JYS  O27  C10  N24  125.20  3.000
 JYS  N24  C10  C09  117.03  3.000
 JYS  O27  C10  C09  117.75  3.000
 JYS  H5   C11  H4   107.98  3.000
 JYS  H5   C11  N24  109.83  3.000
 JYS  H4   C11  N24  109.08  3.000
 JYS  H5   C11  C12  109.91  3.000
 JYS  H4   C11  C12  109.86  3.000
 JYS  N24  C11  C12  110.14  3.000
 JYS  H7   C12  H6   107.61  3.000
 JYS  H7   C12  N25  111.06  3.000
 JYS  H6   C12  N25  109.07  3.000
 JYS  H7   C12  C11  108.94  3.000
 JYS  H6   C12  C11  109.82  3.000
 JYS  N25  C12  C11  110.30  3.000
 JYS  H9   C13  H8   108.01  3.000
 JYS  H9   C13  N25  108.39  3.000
 JYS  H8   C13  N25  110.24  3.000
 JYS  H9   C13  C14  109.58  3.000
 JYS  H8   C13  C14  110.09  3.000
 JYS  N25  C13  C14  110.47  3.000
 JYS  H11  C14  H10  107.09  3.000
 JYS  H11  C14  N24  109.06  3.000
 JYS  H10  C14  N24  111.43  3.000
 JYS  H11  C14  C13  109.97  3.000
 JYS  H10  C14  C13  109.65  3.000
 JYS  N24  C14  C13  109.59  3.000
 JYS  O28  C15  N25  122.82  3.000
 JYS  O28  C15  C16  119.47  3.000
 JYS  N25  C15  C16  117.66  3.000
 JYS  C21  C16  C17  119.67  3.000
 JYS  C17  C16  C15  118.80  3.000
 JYS  C21  C16  C15  121.32  3.000
 JYS  H12  C17  C18  119.93  3.000
 JYS  H12  C17  C16  119.96  3.000
 JYS  C18  C17  C16  120.11  3.000
 JYS  H13  C18  C19  120.11  3.000
 JYS  H13  C18  C17  119.79  3.000
 JYS  C19  C18  C17  120.10  3.000
 JYS  H14  C19  C20  120.03  3.000
 JYS  H14  C19  C18  120.05  3.000
 JYS  C20  C19  C18  119.92  3.000
 JYS  H15  C20  C21  119.76  3.000
 JYS  H15  C20  C19  120.16  3.000
 JYS  C21  C20  C19  120.08  3.000
 JYS  H16  C21  C20  119.69  3.000
 JYS  H16  C21  C16  120.21  3.000
 JYS  C20  C21  C16  120.10  3.000
 JYS  H17  N23  C07  124.69  3.000
 JYS  H17  N23  C03  125.82  3.000
 JYS  C07  N23  C03  109.49  3.000
 JYS  C14  N24  C11  113.70  3.000
 JYS  C11  N24  C10  121.48  3.000
 JYS  C14  N24  C10  124.69  3.000
 JYS  C15  N25  C13  119.84  3.000
 JYS  C15  N25  C12  124.56  3.000
 JYS  C13  N25  C12  112.57  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
 JYS  CONST_01  C04  C05  C06  C01    0.00   0.0  0
 JYS  CONST_02  C04  C03  C02  C01    0.00   0.0  0
 JYS  CONST_03  N23  C03  C02  C01  180.00   0.0  0
 JYS  CONST_04  C05  C06  C01  C02    0.00   0.0  0
 JYS  CONST_05  C05  C04  C03  C02    0.00   0.0  0
 JYS  CONST_06  C08  C04  C03  C02  180.00   0.0  0
 JYS  CONST_07  C07  N23  C03  C02  180.00   0.0  0
 JYS  CONST_08  C06  C01  C02  C03    0.00   0.0  0
 JYS  CONST_09  C06  C05  C04  C03    0.00   0.0  0
 JYS  CONST_10  C07  C08  C04  C03    0.00   0.0  0
 JYS  CONST_11  C08  C07  N23  C03    0.00   0.0  0
 JYS  CONST_12  C07  N23  C03  C04    0.00   0.0  0
 JYS  CONST_13  N23  C07  C08  C04    0.00   0.0  0
 JYS  CONST_14  N23  C03  C04  C05  180.00   0.0  0
 JYS  CONST_15  C07  C08  C04  C05  180.00   0.0  0
 JYS  CONST_16  C08  C04  C05  C06  180.00   0.0  0
 JYS  CONST_17  N23  C03  C04  C08    0.00   0.0  0
 JYS  CONST_18  C19  C20  C21  C16    0.00   0.0  0
 JYS  CONST_19  C19  C18  C17  C16    0.00   0.0  0
 JYS  CONST_20  C20  C19  C18  C17    0.00   0.0  0
 JYS  CONST_21  C20  C21  C16  C17    0.00   0.0  0
 JYS  CONST_22  C21  C20  C19  C18    0.00   0.0  0
 JYS  CONST_23  C21  C16  C17  C18    0.00   0.0  0
 JYS  CONST_24  BR   C05  C06  C01  180.00   0.0  0
 JYS  CONST_25  BR   C05  C04  C03  180.00   0.0  0
 JYS  CONST_26  C09  C08  C04  C03  180.00   0.0  0
 JYS  CONST_27  F22  C02  C03  C04  180.00   0.0  0
 JYS  CONST_28  C09  C08  C04  C05    0.00   0.0  0
 JYS  CONST_29  F22  C02  C01  C06  180.00   0.0  0
 JYS  CONST_30  BR   C05  C04  C08    0.00   0.0  0
 JYS  CONST_31  N23  C07  C08  C09  180.00   0.0  0
 JYS  CONST_32  C20  C21  C16  C15  180.00   0.0  0
 JYS  CONST_33  C18  C17  C16  C15  180.00   0.0  0
 JYS  CONST_34  N23  C03  C02  F22    0.00   0.0  0
 JYS  CONST_36  C16  C15  N25  C13  180.00   0.0  0
 JYS  CONST_37  H2   C06  C01  C02  180.00   0.0  0
 JYS  CONST_38  H17  N23  C03  C02    0.00   0.0  0
 JYS  CONST_39  H1   C01  C02  C03  180.00   0.0  0
 JYS  CONST_40  H3   C07  N23  C03  180.00   0.0  0
 JYS  CONST_41  H15  C20  C21  C16  180.00   0.0  0
 JYS  CONST_42  H13  C18  C17  C16  180.00   0.0  0
 JYS  CONST_43  H14  C19  C18  C17  180.00   0.0  0
 JYS  CONST_44  H16  C21  C16  C17  180.00   0.0  0
 JYS  CONST_45  H12  C17  C18  C19  180.00   0.0  0
 JYS  CONST_46  C14  N24  C10  C09    0.00   0.0  0
 JYS  CONST_47  C11  N24  C10  C09  180.00   0.0  0
 JYS  CONST_48  O27  C10  N24  C11    0.00   0.0  0
 JYS  CONST_50  O28  C15  N25  C13    0.00   0.0  0
 JYS  CONST_51  O27  C10  N24  C14  180.00   0.0  0
 JYS  Var_01    C13  C14  N24  C11  -55.91  30.0  1
 JYS  Var_02    C13  N25  C12  C11   56.44  30.0  1
 JYS  Var_03    C14  C13  N25  C12  -57.22  30.0  1
 JYS  Var_04    C14  N24  C11  C12   55.54  30.0  1
 JYS  Var_05    N25  C13  C14  N24   55.12  30.0  1
 JYS  Var_06    N25  C12  C11  N24  -53.99  30.0  1
 JYS  Var_07    N25  C15  C16  C17  131.46  30.0  2
 JYS  Var_08    C10  C09  C08  C04  173.52  30.0  2
 JYS  Var_09    N24  C10  C09  C08  -87.50  30.0  1

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
 JYS  plan-1  C15  0.020
 JYS  plan-1  C16  0.020
 JYS  plan-1  C17  0.020
 JYS  plan-1  C18  0.020
 JYS  plan-1  C19  0.020
 JYS  plan-1  C20  0.020
 JYS  plan-1  C21  0.020
 JYS  plan-1  H12  0.020
 JYS  plan-1  H13  0.020
 JYS  plan-1  H14  0.020
 JYS  plan-1  H15  0.020
 JYS  plan-1  H16  0.020
 JYS  plan-2  C01  0.020
 JYS  plan-2  C02  0.020
 JYS  plan-2  C03  0.020
 JYS  plan-2  C04  0.020
 JYS  plan-2  C05  0.020
 JYS  plan-2  C06  0.020
 JYS  plan-2  C07  0.020
 JYS  plan-2  C08  0.020
 JYS  plan-2  C09  0.020
 JYS  plan-2  F22  0.020
 JYS  plan-2  N23  0.020
 JYS  plan-2  BR   0.020
 JYS  plan-2  H1   0.020
 JYS  plan-2  H2   0.020
 JYS  plan-2  H3   0.020
 JYS  plan-2  H17  0.020
 JYS  plan-3  C12  0.020
 JYS  plan-3  C13  0.020
 JYS  plan-3  C15  0.020
 JYS  plan-3  C16  0.020
 JYS  plan-3  N25  0.020
 JYS  plan-3  O28  0.020
 JYS  plan-4  C08  0.020
 JYS  plan-4  C09  0.020
 JYS  plan-4  C10  0.020
 JYS  plan-4  O26  0.020
 JYS  plan-5  C09  0.020
 JYS  plan-5  C10  0.020
 JYS  plan-5  C11  0.020
 JYS  plan-5  C14  0.020
 JYS  plan-5  N24  0.020
 JYS  plan-5  O27  0.020

