# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 11:00:07 2021
#   Inital geometry file: a 77 line input string
#   Ligand name: 1-[(1R)-1-(2-fluorophenyl)ethyl]piperazine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](N1CCNCC1)c2ccccc2F
#
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
 WMD  WMD  1-[(1R)-1-(2-fluorophenyl)ethyl]piperazine  ligand  32  15  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_WMD
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
 WMD  C10  C  CR16  0  -0.285  -35.0728  24.4673  -3.7420
 WMD  C13  C  CR16  0  -0.404  -35.4800  22.2207  -5.3059
 WMD  C01  C  CH3   0  -0.662  -33.4182  24.0218  -1.2691
 WMD  C02  C  CH1   0  -0.180  -34.5238  23.0570  -1.6849
 WMD  C04  C  CH2   0  -0.280  -36.5527  21.9862  -0.8529
 WMD  C05  C  CH2   0  -0.293  -37.5338  22.0118   0.3056
 WMD  C07  C  CH2   0  -0.289  -37.4083  24.3908   0.3543
 WMD  C08  C  CH2   0  -0.288  -36.4289  24.3643  -0.8065
 WMD  C09  C  CR6   0  -0.046  -34.8957  23.2144  -3.1533
 WMD  C11  C  CR16  0  -0.259  -35.4500  24.6080  -5.0695
 WMD  C12  C  CR16  0  -0.253  -35.6546  23.4817  -5.8548
 WMD  C14  C  CR6   0   0.505  -35.1091  22.1181  -3.9778
 WMD  F15  F  F     0  -0.318  -34.9415  20.8786  -3.4760
 WMD  N03  N  NT    0  -0.405  -35.6637  23.1313  -0.7754
 WMD  N06  N  NH1   0  -0.599  -38.2949  23.2461   0.2659
 WMD  H1   H  HCR6  0   0.260  -34.9081  25.3598  -3.1524
 WMD  H2   H  HCR6  0   0.275  -35.6255  21.3261  -5.8975
 WMD  H4   H  HCH3  0   0.239  -32.5388  23.8760  -1.8964
 WMD  H5   H  HCH3  0   0.225  -33.7031  25.0710  -1.3473
 WMD  H6   H  HCH1  0   0.254  -34.1170  22.0529  -1.5493
 WMD  H7   H  HCH2  0   0.190  -37.1217  21.9635  -1.7978
 WMD  H8   H  HCH2  0   0.233  -35.9610  21.0696  -0.8054
 WMD  H9   H  HCH2  0   0.231  -38.2144  21.1622   0.2211
 WMD  H10  H  HCH2  0   0.189  -36.9698  21.8911   1.2441
 WMD  H11  H  HCH2  0   0.189  -36.8351  24.4134   1.2949
 WMD  H12  H  HCH2  0   0.230  -37.9966  25.3095   0.3084
 WMD  H13  H  HCH2  0   0.234  -35.7591  25.2218  -0.7218
 WMD  H14  H  HCH2  0   0.196  -36.9912  24.4794  -1.7474
 WMD  H15  H  HCR6  0   0.258  -35.5805  25.5963  -5.4898
 WMD  H16  H  HCR6  0   0.265  -35.9436  23.5802  -6.8926
 WMD  H18  H  HNH1  0   0.352  -38.9583  23.2656   1.0289
 WMD  H3   H  HCH3  0   0.239  -33.1338  23.8309  -0.2344

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
 WMD  C12  C13  aromatic  1.386  0.020  1.386
 WMD  C12  C11  aromatic  1.388  0.020  1.388
 WMD  C13  C14  aromatic  1.383  0.020  1.383
 WMD  C11  C10  aromatic  1.387  0.020  1.387
 WMD  C14  F15  single    1.348  0.020  1.348
 WMD  C14  C09  aromatic  1.388  0.020  1.388
 WMD  C10  C09  aromatic  1.396  0.020  1.396
 WMD  C09  C02  single    1.523  0.020  1.523
 WMD  C02  C01  single    1.525  0.020  1.525
 WMD  C02  N03  single    1.460  0.020  1.460
 WMD  C08  N03  single    1.451  0.020  1.451
 WMD  C08  C07  single    1.519  0.020  1.519
 WMD  N03  C04  single    1.452  0.020  1.452
 WMD  C04  C05  single    1.518  0.020  1.518
 WMD  C07  N06  single    1.451  0.020  1.451
 WMD  N06  C05  single    1.451  0.020  1.451
 WMD  C10  H1   single    0.930  0.020  1.080
 WMD  C13  H2   single    0.930  0.020  1.080
 WMD  C01  H3   single    0.970  0.020  1.090
 WMD  C01  H4   single    0.970  0.020  1.090
 WMD  C01  H5   single    0.970  0.020  1.090
 WMD  C02  H6   single    0.970  0.020  1.090
 WMD  C04  H7   single    0.970  0.020  1.090
 WMD  C04  H8   single    0.970  0.020  1.090
 WMD  C05  H9   single    0.970  0.020  1.090
 WMD  C05  H10  single    0.970  0.020  1.090
 WMD  C07  H11  single    0.970  0.020  1.090
 WMD  C07  H12  single    0.970  0.020  1.090
 WMD  C08  H13  single    0.970  0.020  1.090
 WMD  C08  H14  single    0.970  0.020  1.090
 WMD  C11  H15  single    0.930  0.020  1.080
 WMD  C12  H16  single    0.930  0.020  1.080
 WMD  N06  H18  single    0.890  0.020  1.040

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
 WMD  H1   C10  C11  118.62  3.000
 WMD  H1   C10  C09  119.42  3.000
 WMD  C11  C10  C09  121.96  3.000
 WMD  H2   C13  C14  119.98  3.000
 WMD  H2   C13  C12  121.24  3.000
 WMD  C14  C13  C12  118.78  3.000
 WMD  H5   C01  H4   107.36  3.000
 WMD  H5   C01  H3   107.76  3.000
 WMD  H4   C01  H3   108.20  3.000
 WMD  H5   C01  C02  113.57  3.000
 WMD  H4   C01  C02  110.08  3.000
 WMD  H3   C01  C02  109.70  3.000
 WMD  H6   C02  N03  105.09  3.000
 WMD  H6   C02  C09  107.80  3.000
 WMD  N03  C02  C09  113.87  3.000
 WMD  H6   C02  C01  106.13  3.000
 WMD  N03  C02  C01  111.34  3.000
 WMD  C09  C02  C01  111.99  3.000
 WMD  H8   C04  H7   107.42  3.000
 WMD  H8   C04  N03  109.15  3.000
 WMD  H7   C04  N03  112.20  3.000
 WMD  H8   C04  C05  109.33  3.000
 WMD  H7   C04  C05  108.69  3.000
 WMD  N03  C04  C05  109.98  3.000
 WMD  H10  C05  H9   107.45  3.000
 WMD  H10  C05  N06  112.65  3.000
 WMD  H9   C05  N06  109.45  3.000
 WMD  H10  C05  C04  108.50  3.000
 WMD  H9   C05  C04  109.31  3.000
 WMD  N06  C05  C04  109.42  3.000
 WMD  H12  C07  H11  107.39  3.000
 WMD  H12  C07  N06  109.39  3.000
 WMD  H11  C07  N06  112.72  3.000
 WMD  H12  C07  C08  109.27  3.000
 WMD  H11  C07  C08  108.51  3.000
 WMD  N06  C07  C08  109.50  3.000
 WMD  H14  C08  H13  107.30  3.000
 WMD  H14  C08  N03  112.09  3.000
 WMD  H13  C08  N03  110.02  3.000
 WMD  H14  C08  C07  108.76  3.000
 WMD  H13  C08  C07  108.82  3.000
 WMD  N03  C08  C07  109.78  3.000
 WMD  C14  C09  C02  121.91  3.000
 WMD  C02  C09  C10  122.04  3.000
 WMD  C14  C09  C10  116.04  3.000
 WMD  H15  C11  C12  120.24  3.000
 WMD  H15  C11  C10  119.82  3.000
 WMD  C12  C11  C10  119.94  3.000
 WMD  H16  C12  C11  120.55  3.000
 WMD  H16  C12  C13  119.75  3.000
 WMD  C11  C12  C13  119.70  3.000
 WMD  F15  C14  C09  119.08  3.000
 WMD  C09  C14  C13  123.58  3.000
 WMD  F15  C14  C13  117.33  3.000
 WMD  C08  N03  C04  110.25  3.000
 WMD  C04  N03  C02  113.87  3.000
 WMD  C08  N03  C02  116.20  3.000
 WMD  H18  N06  C07  109.86  3.000
 WMD  H18  N06  C05  109.88  3.000
 WMD  C07  N06  C05  110.43  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
 WMD  CONST_01  C13  C12  C11  C10    0.00   0.0  0
 WMD  CONST_02  C13  C14  C09  C10    0.00   0.0  0
 WMD  CONST_03  C12  C13  C14  C09    0.00   0.0  0
 WMD  CONST_04  C12  C11  C10  C09    0.00   0.0  0
 WMD  CONST_05  C14  C13  C12  C11    0.00   0.0  0
 WMD  CONST_06  C14  C09  C10  C11    0.00   0.0  0
 WMD  CONST_07  F15  C14  C09  C10  180.00   0.0  0
 WMD  CONST_08  C02  C09  C14  C13  180.00   0.0  0
 WMD  CONST_09  C11  C10  C09  C02  180.00   0.0  0
 WMD  CONST_10  F15  C14  C13  C12  180.00   0.0  0
 WMD  CONST_11  H16  C12  C11  C10  180.00   0.0  0
 WMD  CONST_12  H15  C11  C12  C13  180.00   0.0  0
 WMD  CONST_13  H2   C13  C14  C09  180.00   0.0  0
 WMD  CONST_14  H1   C10  C11  C12  180.00   0.0  0
 WMD  Var_01    C07  C08  N03  C04   58.80  30.0  1
 WMD  Var_02    C07  N06  C05  C04  -59.29  30.0  1
 WMD  Var_03    C08  N03  C04  C05  -58.79  30.0  1
 WMD  Var_04    C08  C07  N06  C05   59.47  30.0  1
 WMD  Var_05    N06  C07  C08  N03  -58.78  30.0  1
 WMD  Var_06    N06  C05  C04  N03   58.58  30.0  1

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
 WMD  chir_01  C02  C09  C01  N03  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
 WMD  plan-1  C10  0.020
 WMD  plan-1  C13  0.020
 WMD  plan-1  C02  0.020
 WMD  plan-1  C09  0.020
 WMD  plan-1  C11  0.020
 WMD  plan-1  C12  0.020
 WMD  plan-1  C14  0.020
 WMD  plan-1  F15  0.020
 WMD  plan-1  H1   0.020
 WMD  plan-1  H2   0.020
 WMD  plan-1  H15  0.020
 WMD  plan-1  H16  0.020

