# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 11:54:38 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: 5-bromo-N-[3-chloro-2-(4-prop-2-yn-1-ylpiperazin-1-yl)phenyl]furan-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cccc(NC(=O)c2oc(Br)cc2)c1N3CCN(CC3)CC#C
#
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
 JK3  JK3  5-bromo-N-[3-chloro-2-(4-prop-2-yn-1-ylpiperazin-1-yl)phenyl]furan-2-carboxamide  ligand  42  25  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JK3
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
 JK3  CL15  CL  CL    0  -0.109  -5.0483   1.7400   0.5804
 JK3  C01   C   CR15  0  -0.300   3.4978   0.9261  -0.7633
 JK3  C02   C   CR15  0  -0.301   3.8631  -0.4438  -0.8586
 JK3  C03   C   CR5   0   0.189   2.7114  -1.1334  -0.6663
 JK3  O05   O   O     0  -0.415   1.6780  -0.3122  -0.4630
 JK3  C06   C   CR5   0   0.224   2.1619   0.9551  -0.5222
 JK3  C07   C   C     0   0.491   1.2484   2.0909  -0.3411
 JK3  O08   O   O     0  -0.455   1.6782   3.2308  -0.3969
 JK3  C10   C   CR6   0   0.348  -1.1585   2.5444   0.0549
 JK3  C11   C   CR16  0  -0.321  -1.1490   3.9370   0.0775
 JK3  C12   C   CR16  0  -0.258  -2.3412   4.6215   0.2564
 JK3  C13   C   CR16  0  -0.245  -3.5422   3.9515   0.4111
 JK3  C14   C   CR6   0  -0.082  -3.5373   2.5644   0.3884
 JK3  C16   C   CR6   0   0.299  -2.3680   1.8319   0.2167
 JK3  N17   N   NT    0  -0.553  -2.2808   0.4231   0.1911
 JK3  C18   C   CH2   0  -0.291  -2.8437  -0.2731  -0.9558
 JK3  C19   C   CH2   0  -0.293  -2.2455  -1.6650  -1.0335
 JK3  C20   C   CH2   0  -0.294  -2.4809  -0.2867   1.4454
 JK3  C21   C   CH2   0  -0.291  -1.8918  -1.6798   1.3293
 JK3  N22   N   NT    0  -0.424  -2.4787  -2.3862   0.2045
 JK3  C23   C   CH2   0  -0.408  -1.9912  -3.7510   0.1451
 JK3  C24   C   CSP   0   0.281  -2.7296  -4.5645  -0.8180
 JK3  C25   C   CSP1  0  -0.551  -3.3186  -5.2444  -1.6151
 JK3  H01   H   HCR5  0   0.287   4.1503   1.7777  -0.8635
 JK3  H02   H   HCR5  0   0.294   4.8402  -0.8568  -1.0437
 JK3  HN09  H   HNH1  0   0.416  -0.2957   0.7583  -0.0945
 JK3  H11   H   HCR6  0   0.284  -0.2310   4.4876  -0.0432
 JK3  H12   H   HCR6  0   0.271  -2.3314   5.7029   0.2740
 JK3  H13   H   HCR6  0   0.281  -4.4667   4.4944   0.5492
 JK3  H18   H   HCH2  0   0.221  -3.9358  -0.3523  -0.9012
 JK3  H18A  H   HCH2  0   0.254  -2.5924   0.2753  -1.8644
 JK3  H19   H   HCH2  0   0.253  -2.7152  -2.2017  -1.8600
 JK3  H19A  H   HCH2  0   0.196  -1.1678  -1.5898  -1.2619
 JK3  H20   H   HCH2  0   0.255  -1.9716   0.2525   2.2455
 JK3  H20A  H   HCH2  0   0.221  -3.5408  -0.3629   1.7170
 JK3  H21   H   HCH2  0   0.197  -0.7940  -1.6050   1.2386
 JK3  H21A  H   HCH2  0   0.251  -2.1051  -2.2312   2.2475
 JK3  H23   H   HCH2  0   0.235  -0.9175  -3.8045  -0.1023
 JK3  H23A  H   HCH2  0   0.281  -2.0998  -4.2021   1.1350
 JK3  H25   H   H     0   0.280  -3.8451  -5.8417  -2.3237
 JK3  N09   N   NH1   0  -0.754  -0.0395   1.7427  -0.1229
 JK3  BR04  BR  BR    0   0.039   2.3616  -2.9412  -0.6425

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
 JK3  C01  C06   aromatic  1.358  0.020  1.358
 JK3  C02  C01   aromatic  1.421  0.020  1.421
 JK3  C02  C03   aromatic  1.356  0.020  1.356
 JK3  C03  BR04  single    1.842  0.020  1.842
 JK3  C03  O05   aromatic  1.336  0.020  1.336
 JK3  C06  O05   aromatic  1.358  0.020  1.358
 JK3  C06  C07   single    1.469  0.020  1.469
 JK3  C07  N09   single    1.352  0.020  1.352
 JK3  O08  C07   double    1.220  0.020  1.220
 JK3  N09  C10   single    1.388  0.020  1.388
 JK3  C10  C16   aromatic  1.413  0.020  1.413
 JK3  C11  C10   aromatic  1.393  0.020  1.393
 JK3  C11  C12   aromatic  1.386  0.020  1.386
 JK3  C12  C13   aromatic  1.384  0.020  1.384
 JK3  C13  C14   aromatic  1.387  0.020  1.387
 JK3  C14  CL15  single    1.732  0.020  1.732
 JK3  C16  C14   aromatic  1.390  0.020  1.390
 JK3  C16  N17   single    1.412  0.020  1.412
 JK3  N17  C18   single    1.455  0.020  1.455
 JK3  C18  C19   single    1.517  0.020  1.517
 JK3  C20  N17   single    1.455  0.020  1.455
 JK3  C20  C21   single    1.517  0.020  1.517
 JK3  C21  N22   single    1.452  0.020  1.452
 JK3  N22  C19   single    1.452  0.020  1.452
 JK3  N22  C23   single    1.450  0.020  1.450
 JK3  C24  C23   single    1.461  0.020  1.461
 JK3  C25  C24   triple    1.202  0.020  1.202
 JK3  C01  H01   single    0.929  0.020  1.085
 JK3  C02  H02   single    0.929  0.020  1.085
 JK3  N09  HN09  single    0.868  0.020  1.013
 JK3  C11  H11   single    0.929  0.020  1.085
 JK3  C12  H12   single    0.929  0.020  1.085
 JK3  C13  H13   single    0.929  0.020  1.085
 JK3  C18  H18   single    0.939  0.020  1.096
 JK3  C18  H18A  single    0.939  0.020  1.096
 JK3  C19  H19   single    0.939  0.020  1.096
 JK3  C19  H19A  single    0.939  0.020  1.096
 JK3  C20  H20   single    0.939  0.020  1.096
 JK3  C20  H20A  single    0.939  0.020  1.096
 JK3  C21  H21   single    0.939  0.020  1.096
 JK3  C21  H21A  single    0.939  0.020  1.096
 JK3  C23  H23   single    0.939  0.020  1.096
 JK3  C23  H23A  single    0.939  0.020  1.096
 JK3  C25  H25   single    0.913  0.020  1.066

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
 JK3  H01   C01  C06   126.54  3.000
 JK3  H01   C01  C02   126.87  3.000
 JK3  C06   C01  C02   106.58  3.000
 JK3  H02   C02  C03   126.87  3.000
 JK3  H02   C02  C01   127.92  3.000
 JK3  C03   C02  C01   105.22  3.000
 JK3  BR04  C03  O05   117.04  3.000
 JK3  O05   C03  C02   111.48  3.000
 JK3  BR04  C03  C02   131.48  3.000
 JK3  C06   O05  C03   106.94  3.000
 JK3  C07   C06  O05   119.65  3.000
 JK3  C07   C06  C01   130.56  3.000
 JK3  O05   C06  C01   109.79  3.000
 JK3  N09   C07  O08   125.73  3.000
 JK3  O08   C07  C06   119.86  3.000
 JK3  N09   C07  C06   114.41  3.000
 JK3  C16   C10  C11   120.54  3.000
 JK3  C11   C10  N09   125.04  3.000
 JK3  C16   C10  N09   114.42  3.000
 JK3  H11   C11  C12   119.67  3.000
 JK3  H11   C11  C10   120.99  3.000
 JK3  C12   C11  C10   119.33  3.000
 JK3  H12   C12  C13   119.35  3.000
 JK3  H12   C12  C11   119.20  3.000
 JK3  C13   C12  C11   121.44  3.000
 JK3  H13   C13  C14   120.48  3.000
 JK3  H13   C13  C12   120.89  3.000
 JK3  C14   C13  C12   118.63  3.000
 JK3  C16   C14  C13   122.12  3.000
 JK3  C16   C14  CL15  119.78  3.000
 JK3  C13   C14  CL15  118.10  3.000
 JK3  N17   C16  C14   125.45  3.000
 JK3  N17   C16  C10   116.63  3.000
 JK3  C14   C16  C10   117.93  3.000
 JK3  C20   N17  C18   113.14  3.000
 JK3  C20   N17  C16   117.55  3.000
 JK3  C18   N17  C16   117.90  3.000
 JK3  H18A  C18  H18   107.90  3.000
 JK3  H18A  C18  C19   109.14  3.000
 JK3  H18   C18  C19   109.22  3.000
 JK3  H18A  C18  N17   109.08  3.000
 JK3  H18   C18  N17   112.38  3.000
 JK3  C19   C18  N17   109.08  3.000
 JK3  H19A  C19  H19   107.26  3.000
 JK3  H19A  C19  N22   111.53  3.000
 JK3  H19   C19  N22   109.41  3.000
 JK3  H19A  C19  C18   109.45  3.000
 JK3  H19   C19  C18   108.67  3.000
 JK3  N22   C19  C18   110.42  3.000
 JK3  H20A  C20  H20   107.69  3.000
 JK3  H20A  C20  C21   109.29  3.000
 JK3  H20   C20  C21   109.19  3.000
 JK3  H20A  C20  N17   112.35  3.000
 JK3  H20   C20  N17   109.08  3.000
 JK3  C21   C20  N17   109.18  3.000
 JK3  H21A  C21  H21   107.30  3.000
 JK3  H21A  C21  N22   109.07  3.000
 JK3  H21   C21  N22   111.79  3.000
 JK3  H21A  C21  C20   108.87  3.000
 JK3  H21   C21  C20   109.28  3.000
 JK3  N22   C21  C20   110.44  3.000
 JK3  C23   N22  C21   110.71  3.000
 JK3  C23   N22  C19   112.24  3.000
 JK3  C21   N22  C19   110.73  3.000
 JK3  H23A  C23  H23   106.25  3.000
 JK3  H23A  C23  C24   108.47  3.000
 JK3  H23   C23  C24   108.49  3.000
 JK3  H23A  C23  N22   108.53  3.000
 JK3  H23   C23  N22   112.46  3.000
 JK3  C24   C23  N22   112.40  3.000
 JK3  C25   C24  C23   180.00  3.000
 JK3  H25   C25  C24   180.00  3.000
 JK3  HN09  N09  C10   110.63  3.000
 JK3  HN09  N09  C07   119.57  3.000
 JK3  C10   N09  C07   129.79  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
 JK3  CONST_01  C03   O05  C06  C01      0.00   0.0  0
 JK3  CONST_02  O05   C03  C02  C01      0.00   0.0  0
 JK3  CONST_03  O05   C06  C01  C02      0.00   0.0  0
 JK3  CONST_04  C06   O05  C03  C02      0.00   0.0  0
 JK3  CONST_05  C06   C01  C02  C03      0.00   0.0  0
 JK3  CONST_06  C13   C14  C16  C10      0.00   0.0  0
 JK3  CONST_07  C13   C12  C11  C10      0.00   0.0  0
 JK3  CONST_08  C14   C16  C10  C11      0.00   0.0  0
 JK3  CONST_09  C14   C13  C12  C11      0.00   0.0  0
 JK3  CONST_10  C16   C10  C11  C12      0.00   0.0  0
 JK3  CONST_11  C16   C14  C13  C12      0.00   0.0  0
 JK3  CONST_12  N17   C16  C10  C11    180.00   0.0  0
 JK3  CONST_13  N17   C16  C14  C13    180.00   0.0  0
 JK3  CONST_14  C12   C13  C14  CL15   180.00   0.0  0
 JK3  CONST_15  C10   C16  C14  CL15   180.00   0.0  0
 JK3  CONST_16  N17   C16  C14  CL15     0.00   0.0  0
 JK3  CONST_17  BR04  C03  C02  C01    180.00   0.0  0
 JK3  CONST_18  C07   C06  C01  C02    180.00   0.0  0
 JK3  CONST_19  C07   C06  O05  C03    180.00   0.0  0
 JK3  CONST_20  BR04  C03  O05  C06    180.00   0.0  0
 JK3  CONST_21  C14   C16  C10  N09    180.00   0.0  0
 JK3  CONST_22  N17   C16  C10  N09      0.00   0.0  0
 JK3  CONST_23  C12   C11  C10  N09    180.00   0.0  0
 JK3  CONST_24  H01   C01  C02  C03    180.00   0.0  0
 JK3  CONST_25  H02   C02  C03  O05    180.00   0.0  0
 JK3  CONST_26  H12   C12  C11  C10    180.00   0.0  0
 JK3  CONST_27  H13   C13  C12  C11    180.00   0.0  0
 JK3  CONST_28  H11   C11  C12  C13    180.00   0.0  0
 JK3  CONST_29  C10   N09  C07  C06    180.00   0.0  0
 JK3  CONST_30  C16   C10  N09  C07    180.00   0.0  0
 JK3  CONST_31  C11   C10  N09  C07      0.00   0.0  0
 JK3  CONST_32  HN09  N09  C10  C11    180.00   0.0  0
 JK3  CONST_33  C10   N09  C07  O08      0.00   0.0  0
 JK3  Var_01    C18   N17  C16  C10   -110.17  30.0  2
 JK3  Var_02    C19   C18  N17  C16    160.64  30.0  1
 JK3  Var_03    C21   C20  N17  C16   -160.61  30.0  1
 JK3  Var_04    N22   C19  C18  N17     56.69  30.0  1
 JK3  Var_05    N22   C21  C20  N17    -56.42  30.0  1
 JK3  Var_06    C21   N22  C19  C18    -59.10  30.0  1
 JK3  Var_07    C20   C21  N22  C19     58.94  30.0  1
 JK3  Var_08    N09   C07  C06  C01    179.60  30.0  2
 JK3  Var_09    C24   C23  N22  C19    -65.96  30.0  3

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
 JK3  plan-1  C01   0.020
 JK3  plan-1  C02   0.020
 JK3  plan-1  C03   0.020
 JK3  plan-1  O05   0.020
 JK3  plan-1  C06   0.020
 JK3  plan-1  C07   0.020
 JK3  plan-1  H01   0.020
 JK3  plan-1  H02   0.020
 JK3  plan-1  BR04  0.020
 JK3  plan-2  CL15  0.020
 JK3  plan-2  C10   0.020
 JK3  plan-2  C11   0.020
 JK3  plan-2  C12   0.020
 JK3  plan-2  C13   0.020
 JK3  plan-2  C14   0.020
 JK3  plan-2  C16   0.020
 JK3  plan-2  N17   0.020
 JK3  plan-2  H11   0.020
 JK3  plan-2  H12   0.020
 JK3  plan-2  H13   0.020
 JK3  plan-2  N09   0.020
 JK3  plan-3  C06   0.020
 JK3  plan-3  C07   0.020
 JK3  plan-3  O08   0.020
 JK3  plan-3  C10   0.020
 JK3  plan-3  HN09  0.020
 JK3  plan-3  N09   0.020

