# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 23:29:18 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: (2~{R})-2-[2-[(3~{R})-3-(4-fluorophenyl)pyrrolidin-1-yl]ethyl]-1,4-dimethyl-piperazine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCN(C)[C@H](CCN2CC[C@@H](C2)c3ccc(F)cc3)C1
#
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
 HJQ  HJQ  (2~{R})-2-[2-[(3~{R})-3-(4-fluorophenyl)pyrrolidin-1-yl]ethyl]-1,4-dimethyl-piperazine  ligand  50  22  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_HJQ
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
 HJQ  C01  C  CH2   0  -0.279  -0.4670  -1.6449  -0.7911
 HJQ  C03  C  CH2   0  -0.465  -1.9721  -1.9059  -0.6113
 HJQ  C05  C  CR15  0  -0.361  -2.4220  -0.8978   0.4643
 HJQ  C07  C  CH2   0  -0.238  -1.3269   0.1626   0.3839
 HJQ  C09  C  CH2   0  -0.477   2.3155  -0.7130  -0.0641
 HJQ  C10  C  CH1   0  -0.095   3.5853   0.0813  -0.3401
 HJQ  C11  C  CH2   0  -0.257   4.8077  -0.8374  -0.3811
 HJQ  C13  C  CH2   0  -0.286   6.2230   1.0170   0.1767
 HJQ  C14  C  CH2   0  -0.327   4.9910   1.9118   0.2187
 HJQ  C16  C  CR6   0   0.177  -3.8224  -0.3733   0.3145
 HJQ  C17  C  CR16  0  -0.318  -4.7364  -0.4939   1.3578
 HJQ  C18  C  CR16  0  -0.395  -6.0350  -0.0127   1.2489
 HJQ  C19  C  CR6   0   0.505  -6.4122   0.5985   0.0711
 HJQ  C20  C  CR16  0  -0.394  -5.5387   0.7406  -0.9906
 HJQ  C21  C  CR16  0  -0.304  -4.2482   0.2502  -0.8587
 HJQ  F22  F  F     0  -0.319  -7.6664   1.0692  -0.0483
 HJQ  N02  N  NR5   0  -0.434  -0.1319  -0.6320   0.2029
 HJQ  N04  N  NT    0  -0.415   6.0027  -0.0921  -0.7325
 HJQ  N06  N  NT    0  -0.410   3.7726   1.2043   0.5759
 HJQ  H1   H  HCH2  0   0.230   0.1340  -2.5453  -0.6492
 HJQ  H2   H  HCH2  0   0.197  -0.2666  -1.2862  -1.8131
 HJQ  H3   H  HCH2  0   0.239  -2.4979  -1.7312  -1.5504
 HJQ  H4   H  HCH2  0   0.250  -2.1897  -2.9306  -0.3110
 HJQ  H5   H  HCR5  0   0.257  -2.3436  -1.3744   1.4452
 HJQ  H6   H  HCH2  0   0.191  -1.5120   0.8491  -0.4623
 HJQ  H7   H  HCH2  0   0.240  -1.2625   0.7728   1.2881
 HJQ  H10  H  HCH2  0   0.223   2.3819  -1.2425   0.8918
 HJQ  H11  H  HCH2  0   0.243   2.2471  -1.4876  -0.8333
 HJQ  H12  H  HCH1  0   0.224   3.4892   0.5215  -1.3418
 HJQ  H13  H  HCH2  0   0.185   4.9163  -1.3607   0.5870
 HJQ  H14  H  HCH2  0   0.231   4.6476  -1.6121  -1.1366
 HJQ  H15  H  HCH3  0   0.229   6.9799  -1.7480  -1.5430
 HJQ  H16  H  HCH3  0   0.229   8.0252  -0.3808  -1.1618
 HJQ  H17  H  HCH3  0   0.188   7.4272  -1.4223   0.1392
 HJQ  H18  H  HCH2  0   0.232   7.0804   1.5980  -0.1739
 HJQ  H19  H  HCH2  0   0.190   6.4729   0.6689   1.1948
 HJQ  H20  H  HCH2  0   0.235   5.1520   2.7296   0.9247
 HJQ  H21  H  HCH2  0   0.227   4.8507   2.3605  -0.7703
 HJQ  H22  H  HCH3  0   0.235   3.9385   1.7473   2.5747
 HJQ  H23  H  HCH3  0   0.235   2.7064   0.5405   2.2576
 HJQ  H24  H  HCH3  0   0.204   4.4042   0.0694   2.3042
 HJQ  H25  H  HCR6  0   0.259  -4.4329  -0.9745   2.2802
 HJQ  H26  H  HCR6  0   0.277  -6.7372  -0.1137   2.0662
 HJQ  H27  H  HCR6  0   0.276  -5.8594   1.2228  -1.9047
 HJQ  H28  H  HCR6  0   0.256  -3.5668   0.3596  -1.6937
 HJQ  C08  C  CH2   0  -0.249   1.0547   0.1396  -0.0858
 HJQ  C12  C  CH3   0  -0.513   7.1593  -0.9505  -0.8199
 HJQ  C15  C  CH3   0  -0.540   3.7127   0.8590   1.9836
 HJQ  H8   H  HCH2  0   0.232   1.1344   0.9299   0.6640
 HJQ  H9   H  HCH2  0   0.182   0.9818   0.6470  -1.0655

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
 HJQ  F22  C19  single    1.345  0.020  1.345
 HJQ  C19  C20  aromatic  1.382  0.020  1.382
 HJQ  C19  C18  aromatic  1.380  0.020  1.380
 HJQ  C20  C21  aromatic  1.387  0.020  1.387
 HJQ  C15  N06  single    1.451  0.020  1.451
 HJQ  C18  C17  aromatic  1.389  0.020  1.389
 HJQ  C13  C14  single    1.523  0.020  1.523
 HJQ  C13  N04  single    1.451  0.020  1.451
 HJQ  C21  C16  aromatic  1.395  0.020  1.395
 HJQ  C12  N04  single    1.443  0.020  1.443
 HJQ  C17  C16  aromatic  1.392  0.020  1.392
 HJQ  C14  N06  single    1.454  0.020  1.454
 HJQ  N06  C10  single    1.461  0.020  1.461
 HJQ  C11  N04  single    1.452  0.020  1.452
 HJQ  C11  C10  single    1.530  0.020  1.530
 HJQ  C16  C05  single    1.503  0.020  1.503
 HJQ  C08  C09  single    1.522  0.020  1.522
 HJQ  C08  N02  single    1.445  0.020  1.445
 HJQ  C10  C09  single    1.523  0.020  1.523
 HJQ  C03  C05  single    1.541  0.020  1.541
 HJQ  C03  C01  single    1.538  0.020  1.538
 HJQ  C05  C07  single    1.526  0.020  1.526
 HJQ  N02  C01  single    1.458  0.020  1.458
 HJQ  N02  C07  single    1.446  0.020  1.446
 HJQ  C01  H1   single    0.970  0.020  1.090
 HJQ  C01  H2   single    0.970  0.020  1.090
 HJQ  C03  H3   single    0.970  0.020  1.090
 HJQ  C03  H4   single    0.970  0.020  1.090
 HJQ  C05  H5   single    0.970  0.020  1.090
 HJQ  C07  H6   single    0.970  0.020  1.090
 HJQ  C07  H7   single    0.970  0.020  1.090
 HJQ  C08  H8   single    0.970  0.020  1.090
 HJQ  C08  H9   single    0.970  0.020  1.090
 HJQ  C09  H10  single    0.970  0.020  1.090
 HJQ  C09  H11  single    0.970  0.020  1.090
 HJQ  C10  H12  single    0.970  0.020  1.090
 HJQ  C11  H13  single    0.970  0.020  1.090
 HJQ  C11  H14  single    0.970  0.020  1.090
 HJQ  C12  H15  single    0.970  0.020  1.090
 HJQ  C12  H16  single    0.970  0.020  1.090
 HJQ  C12  H17  single    0.970  0.020  1.090
 HJQ  C13  H18  single    0.970  0.020  1.090
 HJQ  C13  H19  single    0.970  0.020  1.090
 HJQ  C14  H20  single    0.970  0.020  1.090
 HJQ  C14  H21  single    0.970  0.020  1.090
 HJQ  C15  H22  single    0.970  0.020  1.090
 HJQ  C15  H23  single    0.970  0.020  1.090
 HJQ  C15  H24  single    0.970  0.020  1.090
 HJQ  C17  H25  single    0.930  0.020  1.080
 HJQ  C18  H26  single    0.930  0.020  1.080
 HJQ  C20  H27  single    0.930  0.020  1.080
 HJQ  C21  H28  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
 HJQ  H2   C01  H1   106.80  3.000
 HJQ  H2   C01  N02  111.37  3.000
 HJQ  H1   C01  N02  110.97  3.000
 HJQ  H2   C01  C03  109.98  3.000
 HJQ  H1   C01  C03  112.55  3.000
 HJQ  N02  C01  C03  105.25  3.000
 HJQ  H4   C03  H3   106.96  3.000
 HJQ  H4   C03  C05  111.37  3.000
 HJQ  H3   C03  C05  110.82  3.000
 HJQ  H4   C03  C01  112.78  3.000
 HJQ  H3   C03  C01  110.12  3.000
 HJQ  C05  C03  C01  104.85  3.000
 HJQ  H5   C05  C16  107.96  3.000
 HJQ  H5   C05  C07  107.37  3.000
 HJQ  C16  C05  C07  114.88  3.000
 HJQ  H5   C05  C03  108.66  3.000
 HJQ  C07  C05  C03  102.02  3.000
 HJQ  C16  C05  C03  115.51  3.000
 HJQ  H7   C07  H6   107.26  3.000
 HJQ  H7   C07  N02  111.20  3.000
 HJQ  H6   C07  N02  112.56  3.000
 HJQ  H7   C07  C05  112.75  3.000
 HJQ  H6   C07  C05  110.59  3.000
 HJQ  N02  C07  C05  102.57  3.000
 HJQ  H11  C09  H10  105.98  3.000
 HJQ  H11  C09  C10  107.10  3.000
 HJQ  H10  C09  C10  111.10  3.000
 HJQ  H11  C09  C08  109.56  3.000
 HJQ  H10  C09  C08  109.49  3.000
 HJQ  C10  C09  C08  113.33  3.000
 HJQ  H12  C10  N06  105.95  3.000
 HJQ  H12  C10  C11  106.63  3.000
 HJQ  N06  C10  C11  112.08  3.000
 HJQ  H12  C10  C09  107.53  3.000
 HJQ  C11  C10  C09  110.97  3.000
 HJQ  N06  C10  C09  113.21  3.000
 HJQ  H14  C11  H13  106.50  3.000
 HJQ  H14  C11  N04  108.47  3.000
 HJQ  H13  C11  N04  111.97  3.000
 HJQ  H14  C11  C10  109.08  3.000
 HJQ  H13  C11  C10  109.83  3.000
 HJQ  N04  C11  C10  110.85  3.000
 HJQ  H19  C13  H18  106.59  3.000
 HJQ  H19  C13  N04  111.78  3.000
 HJQ  H18  C13  N04  108.93  3.000
 HJQ  H19  C13  C14  110.04  3.000
 HJQ  H18  C13  C14  109.33  3.000
 HJQ  N04  C13  C14  110.09  3.000
 HJQ  H21  C14  H20  107.20  3.000
 HJQ  H21  C14  N06  108.30  3.000
 HJQ  H20  C14  N06  109.22  3.000
 HJQ  H21  C14  C13  108.63  3.000
 HJQ  H20  C14  C13  109.79  3.000
 HJQ  N06  C14  C13  113.51  3.000
 HJQ  C21  C16  C17  117.94  3.000
 HJQ  C17  C16  C05  120.45  3.000
 HJQ  C21  C16  C05  121.61  3.000
 HJQ  H25  C17  C18  118.83  3.000
 HJQ  H25  C17  C16  119.51  3.000
 HJQ  C18  C17  C16  121.66  3.000
 HJQ  H26  C18  C19  120.58  3.000
 HJQ  H26  C18  C17  120.99  3.000
 HJQ  C19  C18  C17  118.43  3.000
 HJQ  F22  C19  C20  119.03  3.000
 HJQ  C20  C19  C18  121.91  3.000
 HJQ  F22  C19  C18  119.07  3.000
 HJQ  H27  C20  C21  120.92  3.000
 HJQ  H27  C20  C19  120.49  3.000
 HJQ  C21  C20  C19  118.60  3.000
 HJQ  H28  C21  C20  118.44  3.000
 HJQ  H28  C21  C16  120.09  3.000
 HJQ  C20  C21  C16  121.47  3.000
 HJQ  C08  N02  C07  114.22  3.000
 HJQ  C07  N02  C01  106.09  3.000
 HJQ  C08  N02  C01  115.06  3.000
 HJQ  C13  N04  C12  111.78  3.000
 HJQ  C12  N04  C11  111.65  3.000
 HJQ  C13  N04  C11  111.46  3.000
 HJQ  C15  N06  C14  112.89  3.000
 HJQ  C14  N06  C10  109.11  3.000
 HJQ  C15  N06  C10  114.84  3.000
 HJQ  H9   C08  H8   106.32  3.000
 HJQ  H9   C08  N02  111.59  3.000
 HJQ  H8   C08  N02  108.01  3.000
 HJQ  H9   C08  C09  108.92  3.000
 HJQ  H8   C08  C09  109.57  3.000
 HJQ  N02  C08  C09  112.23  3.000
 HJQ  H17  C12  H16  107.66  3.000
 HJQ  H17  C12  H15  107.69  3.000
 HJQ  H16  C12  H15  107.71  3.000
 HJQ  H17  C12  N04  113.38  3.000
 HJQ  H16  C12  N04  110.14  3.000
 HJQ  H15  C12  N04  110.06  3.000
 HJQ  H24  C15  H23  107.33  3.000
 HJQ  H24  C15  H22  107.29  3.000
 HJQ  H23  C15  H22  107.03  3.000
 HJQ  H24  C15  N06  115.39  3.000
 HJQ  H23  C15  N06  110.57  3.000
 HJQ  H22  C15  N06  108.87  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
 HJQ  CONST_01  C19  C20  C21  C16     0.00   0.0  0
 HJQ  CONST_02  C19  C18  C17  C16     0.00   0.0  0
 HJQ  CONST_03  C20  C19  C18  C17     0.00   0.0  0
 HJQ  CONST_04  C20  C21  C16  C17     0.00   0.0  0
 HJQ  CONST_05  C21  C20  C19  C18     0.00   0.0  0
 HJQ  CONST_06  C21  C16  C17  C18     0.00   0.0  0
 HJQ  CONST_07  C20  C21  C16  C05   180.00   0.0  0
 HJQ  CONST_08  C18  C17  C16  C05   180.00   0.0  0
 HJQ  CONST_09  F22  C19  C18  C17   180.00   0.0  0
 HJQ  CONST_10  F22  C19  C20  C21   180.00   0.0  0
 HJQ  CONST_11  H28  C21  C16  C05     0.00   0.0  0
 HJQ  CONST_12  H25  C17  C16  C05     0.00   0.0  0
 HJQ  CONST_13  H27  C20  C21  C16   180.00   0.0  0
 HJQ  CONST_14  H26  C18  C17  C16   180.00   0.0  0
 HJQ  Var_01    C05  C07  N02  C01    44.24  30.0  1
 HJQ  Var_02    C07  N02  C01  C03   -30.01  30.0  1
 HJQ  Var_03    N02  C01  C03  C05     3.94  30.0  1
 HJQ  Var_04    C13  C14  N06  C10   -55.10  30.0  1
 HJQ  Var_05    C13  N04  C11  C10    56.13  30.0  1
 HJQ  Var_06    C14  C13  N04  C11   -55.39  30.0  1
 HJQ  Var_07    N06  C14  C13  N04    55.94  30.0  1
 HJQ  Var_08    C09  C08  N02  C01   -65.38  30.0  1
 HJQ  Var_09    N02  C08  C09  C10  -178.93  30.0  1
 HJQ  Var_10    H22  C15  N06  C10   175.75  30.0  3
 HJQ  Var_11    H15  C12  N04  C11    56.90  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
 HJQ  chir_01  C05  C16  C03  C07  negativ
 HJQ  chir_02  C10  N06  C11  C09  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
 HJQ  plan-1  C05  0.020
 HJQ  plan-1  C16  0.020
 HJQ  plan-1  C17  0.020
 HJQ  plan-1  C18  0.020
 HJQ  plan-1  C19  0.020
 HJQ  plan-1  C20  0.020
 HJQ  plan-1  C21  0.020
 HJQ  plan-1  F22  0.020
 HJQ  plan-1  H25  0.020
 HJQ  plan-1  H26  0.020
 HJQ  plan-1  H27  0.020
 HJQ  plan-1  H28  0.020

