# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 21:51:46 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: cyclopropyl-[4-(4-fluorophenyl)piperazin-1-yl]methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccc(cc1)N2CCN(CC2)C(=O)C3CC3
#
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
 GX4  GX4  cyclopropyl-[4-(4-fluorophenyl)piperazin-1-yl]methanone  ligand  35  18  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_GX4
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
 GX4  N1   N  NT    0  -0.472  -2.2161   0.5853   0.4554
 GX4  C4   C  CR16  0  -0.304   2.8638   1.2192   0.0936
 GX4  C5   C  CR16  0  -0.398   4.2108   1.0120  -0.1441
 GX4  C6   C  CH2   0  -0.300  -0.2026  -0.7317   0.8704
 GX4  C7   C  CH2   0  -0.325  -1.5406  -0.2601   1.4193
 GX4  C8   C  CH2   0  -0.325  -1.3989   1.7336   0.1092
 GX4  C10  C  C     0   0.592  -3.3228   0.2835  -0.2650
 GX4  C13  C  CH2   0  -0.462  -5.5766  -0.9311  -0.2228
 GX4  O    O  O     0  -0.512  -3.6948   0.9927  -1.1946
 GX4  C11  C  CH1   0  -0.428  -4.1073  -0.9275   0.1076
 GX4  C12  C  CH2   0  -0.464  -4.6485  -1.7699  -1.0215
 GX4  C9   C  CH2   0  -0.301  -0.0581   1.2860  -0.4451
 GX4  N    N  NT    0  -0.518   0.6194   0.3999   0.4947
 GX4  C3   C  CR6   0   0.350   1.9725   0.1467   0.2348
 GX4  C2   C  CR16  0  -0.335   2.4920  -1.1468   0.1355
 GX4  C1   C  CR16  0  -0.400   3.8468  -1.3651  -0.0866
 GX4  C    C  CR6   0   0.495   4.6869  -0.2835  -0.2288
 GX4  F    F  F     0  -0.323   5.9998  -0.4878  -0.4505
 GX4  H2   H  HCR6  0   0.277   4.8844   1.8529  -0.2464
 GX4  H3   H  HCH2  0   0.260   0.3019  -1.3002   1.6537
 GX4  H4   H  HCH2  0   0.218  -0.3831  -1.4187   0.0285
 GX4  H5   H  HCH2  0   0.252  -1.3768   0.3160   2.3347
 GX4  H6   H  HCH2  0   0.273  -2.1341  -1.1270   1.6897
 GX4  H7   H  HCH2  0   0.272  -1.9127   2.3531  -0.6198
 GX4  H8   H  HCH2  0   0.249  -1.2421   2.3326   1.0112
 GX4  H9   H  HCH2  0   0.261  -6.2284  -1.4186   0.4902
 GX4  H10  H  HCH2  0   0.256  -5.9872  -0.0433  -0.6840
 GX4  H11  H  HCH1  0   0.285  -3.8371  -1.4677   1.0021
 GX4  H12  H  HCH2  0   0.261  -4.6527  -2.8413  -0.8716
 GX4  H13  H  HCH2  0   0.257  -4.4173  -1.4528  -2.0298
 GX4  H14  H  HCH2  0   0.224  -0.2115   0.7887  -1.4146
 GX4  H15  H  HCH2  0   0.260   0.5481   2.1715  -0.6286
 GX4  H16  H  HCR6  0   0.278   1.8486  -2.0113   0.2197
 GX4  H17  H  HCR6  0   0.277   4.2302  -2.3745  -0.1612
 GX4  H1   H  HCR6  0   0.271   2.5068   2.2364   0.1895

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
 GX4  C1   C2   aromatic  1.390  0.020  1.390
 GX4  C1   C    aromatic  1.377  0.020  1.377
 GX4  C2   C3   aromatic  1.397  0.020  1.397
 GX4  F    C    single    1.347  0.020  1.347
 GX4  C    C5   aromatic  1.383  0.020  1.383
 GX4  C6   C7   single    1.521  0.020  1.521
 GX4  C6   N    single    1.448  0.020  1.448
 GX4  C3   N    single    1.401  0.020  1.401
 GX4  C3   C4   aromatic  1.402  0.020  1.402
 GX4  C7   N1   single    1.449  0.020  1.449
 GX4  C5   C4   aromatic  1.383  0.020  1.383
 GX4  N    C9   single    1.459  0.020  1.459
 GX4  O    C10  double    1.227  0.020  1.227
 GX4  N1   C10  single    1.355  0.020  1.355
 GX4  N1   C8   single    1.451  0.020  1.451
 GX4  C9   C8   single    1.518  0.020  1.518
 GX4  C10  C11  single    1.490  0.020  1.490
 GX4  C11  C13  single    1.506  0.020  1.506
 GX4  C11  C12  single    1.509  0.020  1.509
 GX4  C13  C12  single    1.484  0.020  1.484
 GX4  C4   H1   single    0.930  0.020  1.080
 GX4  C5   H2   single    0.930  0.020  1.080
 GX4  C6   H3   single    0.970  0.020  1.090
 GX4  C6   H4   single    0.970  0.020  1.090
 GX4  C7   H5   single    0.970  0.020  1.090
 GX4  C7   H6   single    0.970  0.020  1.090
 GX4  C8   H7   single    0.970  0.020  1.090
 GX4  C8   H8   single    0.970  0.020  1.090
 GX4  C13  H9   single    0.970  0.020  1.090
 GX4  C13  H10  single    0.970  0.020  1.090
 GX4  C11  H11  single    0.970  0.020  1.090
 GX4  C12  H12  single    0.970  0.020  1.090
 GX4  C12  H13  single    0.970  0.020  1.090
 GX4  C9   H14  single    0.970  0.020  1.090
 GX4  C9   H15  single    0.970  0.020  1.090
 GX4  C2   H16  single    0.930  0.020  1.080
 GX4  C1   H17  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
 GX4  C10  N1   C8   120.63  3.000
 GX4  C8   N1   C7   110.96  3.000
 GX4  C10  N1   C7   127.20  3.000
 GX4  H1   C4   C3   120.03  3.000
 GX4  H1   C4   C5   118.50  3.000
 GX4  C3   C4   C5   121.45  3.000
 GX4  H2   C5   C    120.52  3.000
 GX4  H2   C5   C4   120.39  3.000
 GX4  C    C5   C4   119.09  3.000
 GX4  H4   C6   H3   107.42  3.000
 GX4  H4   C6   N    112.46  3.000
 GX4  H3   C6   N    109.32  3.000
 GX4  H4   C6   C7   108.97  3.000
 GX4  H3   C6   C7   108.00  3.000
 GX4  N    C6   C7   110.53  3.000
 GX4  H6   C7   H5   107.11  3.000
 GX4  H6   C7   C6   108.87  3.000
 GX4  H5   C7   C6   109.48  3.000
 GX4  H6   C7   N1   112.15  3.000
 GX4  H5   C7   N1   108.61  3.000
 GX4  C6   C7   N1   110.54  3.000
 GX4  H8   C8   H7   107.99  3.000
 GX4  H8   C8   C9   109.62  3.000
 GX4  H7   C8   C9   109.93  3.000
 GX4  H8   C8   N1   108.50  3.000
 GX4  H7   C8   N1   110.19  3.000
 GX4  C9   C8   N1   110.56  3.000
 GX4  C11  C10  O    119.97  3.000
 GX4  C11  C10  N1   118.57  3.000
 GX4  O    C10  N1   121.45  3.000
 GX4  H10  C13  H9   114.97  3.000
 GX4  H10  C13  C12  118.16  3.000
 GX4  H9   C13  C12  118.47  3.000
 GX4  H10  C13  C11  117.52  3.000
 GX4  H9   C13  C11  116.37  3.000
 GX4  C12  C13  C11   60.61  3.000
 GX4  H11  C11  C12  115.50  3.000
 GX4  H11  C11  C13  115.14  3.000
 GX4  C12  C11  C13   58.98  3.000
 GX4  H11  C11  C10  118.82  3.000
 GX4  C12  C11  C10  117.09  3.000
 GX4  C13  C11  C10  117.43  3.000
 GX4  H13  C12  H12  114.85  3.000
 GX4  H13  C12  C11  117.19  3.000
 GX4  H12  C12  C11  116.78  3.000
 GX4  H13  C12  C13  118.00  3.000
 GX4  H12  C12  C13  118.86  3.000
 GX4  C11  C12  C13   60.41  3.000
 GX4  H15  C9   H14  107.26  3.000
 GX4  H15  C9   N    110.13  3.000
 GX4  H14  C9   N    110.97  3.000
 GX4  H15  C9   C8   108.27  3.000
 GX4  H14  C9   C8   109.38  3.000
 GX4  N    C9   C8   110.73  3.000
 GX4  C3   N    C9   116.04  3.000
 GX4  C9   N    C6   112.22  3.000
 GX4  C3   N    C6   117.07  3.000
 GX4  C2   C3   N    122.65  3.000
 GX4  N    C3   C4   119.64  3.000
 GX4  C2   C3   C4   117.69  3.000
 GX4  H16  C2   C1   117.84  3.000
 GX4  H16  C2   C3   120.89  3.000
 GX4  C1   C2   C3   121.27  3.000
 GX4  H17  C1   C    120.62  3.000
 GX4  H17  C1   C2   120.18  3.000
 GX4  C    C1   C2   119.20  3.000
 GX4  F    C    C1   119.51  3.000
 GX4  F    C    C5   119.20  3.000
 GX4  C1   C    C5   121.30  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
 GX4  CONST_01  C1   C2   C3   C4      0.00   0.0  0
 GX4  CONST_02  C1   C    C5   C4      0.00   0.0  0
 GX4  CONST_03  C2   C1   C    C5      0.00   0.0  0
 GX4  CONST_04  C2   C3   C4   C5      0.00   0.0  0
 GX4  CONST_05  C    C1   C2   C3      0.00   0.0  0
 GX4  CONST_06  C    C5   C4   C3      0.00   0.0  0
 GX4  CONST_07  N    C3   C4   C5    180.00   0.0  0
 GX4  CONST_08  C1   C2   C3   N     180.00   0.0  0
 GX4  CONST_09  F    C    C5   C4    180.00   0.0  0
 GX4  CONST_10  F    C    C1   C2    180.00   0.0  0
 GX4  CONST_11  C11  C10  N1   C7      0.00   0.0  0
 GX4  CONST_12  C11  C10  N1   C8    180.00   0.0  0
 GX4  CONST_13  H16  C2   C3   C4    180.00   0.0  0
 GX4  CONST_14  H17  C1   C    C5    180.00   0.0  0
 GX4  CONST_15  H1   C4   C3   N       0.00   0.0  0
 GX4  CONST_16  H2   C5   C4   C3    180.00   0.0  0
 GX4  CONST_17  O    C10  N1   C7    180.00   0.0  0
 GX4  CONST_18  O    C10  N1   C8      0.00   0.0  0
 GX4  Var_01    N    C6   C7   N1     56.28  30.0  1
 GX4  Var_02    N    C9   C8   N1    -55.41  30.0  1
 GX4  Var_03    C6   N    C3   C4   -169.06  30.0  2
 GX4  Var_04    C8   N1   C7   C6    -58.14  30.0  1
 GX4  Var_05    C8   C9   N    C6     54.76  30.0  1
 GX4  Var_06    C3   N    C6   C7    167.14  30.0  1
 GX4  Var_07    C9   C8   N1   C7     57.77  30.0  1
 GX4  Var_08    C13  C11  C10  N1    152.91  30.0  3
 GX4  Var_09    C12  C13  C11  C10   106.65  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
 GX4  chir_01  C11  C10  C13  C12  both

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
 GX4  plan-1  N1   0.020
 GX4  plan-1  C7   0.020
 GX4  plan-1  C8   0.020
 GX4  plan-1  C10  0.020
 GX4  plan-1  O    0.020
 GX4  plan-1  C11  0.020
 GX4  plan-2  C4   0.020
 GX4  plan-2  C5   0.020
 GX4  plan-2  N    0.020
 GX4  plan-2  C3   0.020
 GX4  plan-2  C2   0.020
 GX4  plan-2  C1   0.020
 GX4  plan-2  C    0.020
 GX4  plan-2  F    0.020
 GX4  plan-2  H2   0.020
 GX4  plan-2  H16  0.020
 GX4  plan-2  H17  0.020
 GX4  plan-2  H1   0.020

