# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 08:27:20 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: 1-[4-[(4-fluorophenyl)methyl]piperidin-1-yl]ethanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N1CCC(CC1)Cc2ccc(F)cc2
#
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
 SVF  SVF  1-[4-[(4-fluorophenyl)methyl]piperidin-1-yl]ethanone  ligand  35  17  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_SVF
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
 SVF  C01  C  CR16  0  -0.299  -2.4847  -0.3494   1.3428
 SVF  C02  C  CR16  0  -0.397  -3.7042  -0.9336   1.0226
 SVF  C03  C  CR6   0   0.130  -1.9691   0.7087   0.5998
 SVF  C04  C  CR6   0   0.505  -4.4069  -0.4414  -0.0585
 SVF  C05  C  CR16  0  -0.289  -2.7126   1.1734  -0.4845
 SVF  C06  C  CR16  0  -0.396  -3.9326   0.6076  -0.8231
 SVF  C08  C  CH2   0  -0.502  -0.6370   1.3263   0.9225
 SVF  C09  C  CH1   0  -0.241   0.4779   0.8833  -0.0304
 SVF  C10  C  CH2   0  -0.414   0.7897  -0.6060   0.0930
 SVF  C11  C  CH2   0  -0.416   1.7498   1.6965   0.1977
 SVF  C12  C  CH2   0  -0.308   1.9477  -1.0088  -0.8111
 SVF  C13  C  CH2   0  -0.318   2.8777   1.2299  -0.7141
 SVF  N14  N  NT    0  -0.434   3.1194  -0.1914  -0.5463
 SVF  C15  C  C     0   0.514   4.2634  -0.7355  -0.0795
 SVF  O16  O  O     0  -0.514   4.3874  -1.9425   0.1006
 SVF  C17  C  CH3   0  -0.807   5.4139   0.2032   0.2070
 SVF  F07  F  F     0  -0.320  -5.5904  -0.9964  -0.3766
 SVF  H1   H  HCR6  0   0.257  -1.9285  -0.7289   2.1913
 SVF  H2   H  HCR6  0   0.276  -4.0992  -1.7549   1.6069
 SVF  H3   H  HCR6  0   0.257  -2.3340   1.9980  -1.0772
 SVF  H4   H  HCR6  0   0.276  -4.5049   0.9799  -1.6628
 SVF  H5   H  HCH2  0   0.247  -0.7234   2.4161   0.8778
 SVF  H6   H  HCH2  0   0.240  -0.3511   1.0803   1.9497
 SVF  H7   H  HCH1  0   0.226   0.1422   1.0748  -1.0592
 SVF  H8   H  HCH2  0   0.220   1.0436  -0.8416   1.1324
 SVF  H9   H  HCH2  0   0.240  -0.0859  -1.2066  -0.1648
 SVF  H10  H  HCH2  0   0.239   1.5595   2.7565   0.0109
 SVF  H11  H  HCH2  0   0.223   2.0697   1.6054   1.2415
 SVF  H12  H  HCH2  0   0.262   2.2013  -2.0562  -0.6743
 SVF  H13  H  HCH2  0   0.235   1.6601  -0.8746  -1.8602
 SVF  H14  H  HCH2  0   0.240   2.6042   1.4152  -1.7587
 SVF  H15  H  HCH2  0   0.273   3.7809   1.8005  -0.5192
 SVF  H16  H  HCH3  0   0.263   5.1621   0.9387   0.9720
 SVF  H17  H  HCH3  0   0.267   6.2623  -0.3773   0.5595
 SVF  H18  H  HCH3  0   0.264   5.7202   0.7521  -0.6843

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
 SVF  C01  C02  aromatic  1.390  0.020  1.390
 SVF  C01  C03  aromatic  1.392  0.020  1.392
 SVF  C08  C03  single    1.503  0.020  1.503
 SVF  C08  C09  single    1.532  0.020  1.532
 SVF  C10  C09  single    1.527  0.020  1.527
 SVF  C10  C12  single    1.523  0.020  1.523
 SVF  C02  C04  aromatic  1.380  0.020  1.380
 SVF  C03  C05  aromatic  1.394  0.020  1.394
 SVF  C09  C11  single    1.527  0.020  1.527
 SVF  C12  N14  single    1.453  0.020  1.453
 SVF  C11  C13  single    1.524  0.020  1.524
 SVF  N14  C15  single    1.350  0.020  1.350
 SVF  N14  C13  single    1.451  0.020  1.451
 SVF  O16  C15  double    1.227  0.020  1.227
 SVF  C04  F07  single    1.345  0.020  1.345
 SVF  C04  C06  aromatic  1.382  0.020  1.382
 SVF  C05  C06  aromatic  1.387  0.020  1.387
 SVF  C15  C17  single    1.512  0.020  1.512
 SVF  C01  H1   single    0.930  0.020  1.080
 SVF  C02  H2   single    0.930  0.020  1.080
 SVF  C05  H3   single    0.930  0.020  1.080
 SVF  C06  H4   single    0.930  0.020  1.080
 SVF  C08  H5   single    0.970  0.020  1.090
 SVF  C08  H6   single    0.970  0.020  1.090
 SVF  C09  H7   single    0.970  0.020  1.090
 SVF  C10  H8   single    0.970  0.020  1.090
 SVF  C10  H9   single    0.970  0.020  1.090
 SVF  C11  H10  single    0.970  0.020  1.090
 SVF  C11  H11  single    0.970  0.020  1.090
 SVF  C12  H12  single    0.970  0.020  1.090
 SVF  C12  H13  single    0.970  0.020  1.090
 SVF  C13  H14  single    0.970  0.020  1.090
 SVF  C13  H15  single    0.970  0.020  1.090
 SVF  C17  H16  single    0.970  0.020  1.090
 SVF  C17  H17  single    0.970  0.020  1.090
 SVF  C17  H18  single    0.970  0.020  1.090

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
 SVF  H1   C01  C03  119.62  3.000
 SVF  H1   C01  C02  118.93  3.000
 SVF  C03  C01  C02  121.45  3.000
 SVF  H2   C02  C04  120.51  3.000
 SVF  H2   C02  C01  120.98  3.000
 SVF  C04  C02  C01  118.51  3.000
 SVF  C08  C03  C05  120.16  3.000
 SVF  C05  C03  C01  118.09  3.000
 SVF  C08  C03  C01  121.73  3.000
 SVF  F07  C04  C06  118.96  3.000
 SVF  C06  C04  C02  121.96  3.000
 SVF  F07  C04  C02  119.08  3.000
 SVF  H3   C05  C06  118.96  3.000
 SVF  H3   C05  C03  119.51  3.000
 SVF  C06  C05  C03  121.52  3.000
 SVF  H4   C06  C05  120.94  3.000
 SVF  H4   C06  C04  120.59  3.000
 SVF  C05  C06  C04  118.46  3.000
 SVF  H6   C08  H5   106.43  3.000
 SVF  H6   C08  C09  109.19  3.000
 SVF  H5   C08  C09  108.67  3.000
 SVF  H6   C08  C03  109.92  3.000
 SVF  H5   C08  C03  109.29  3.000
 SVF  C09  C08  C03  113.11  3.000
 SVF  H7   C09  C11  107.54  3.000
 SVF  H7   C09  C10  107.94  3.000
 SVF  C11  C09  C10  109.72  3.000
 SVF  H7   C09  C08  108.03  3.000
 SVF  C11  C09  C08  111.06  3.000
 SVF  C10  C09  C08  112.36  3.000
 SVF  H9   C10  H8   106.94  3.000
 SVF  H9   C10  C12  108.89  3.000
 SVF  H8   C10  C12  109.27  3.000
 SVF  H9   C10  C09  110.70  3.000
 SVF  H8   C10  C09  109.50  3.000
 SVF  C12  C10  C09  111.42  3.000
 SVF  H11  C11  H10  107.11  3.000
 SVF  H11  C11  C13  109.18  3.000
 SVF  H10  C11  C13  108.89  3.000
 SVF  H11  C11  C09  109.95  3.000
 SVF  H10  C11  C09  110.24  3.000
 SVF  C13  C11  C09  111.36  3.000
 SVF  H13  C12  H12  107.45  3.000
 SVF  H13  C12  N14  108.49  3.000
 SVF  H12  C12  N14  109.35  3.000
 SVF  H13  C12  C10  109.65  3.000
 SVF  H12  C12  C10  110.95  3.000
 SVF  N14  C12  C10  110.86  3.000
 SVF  H15  C13  H14  106.85  3.000
 SVF  H15  C13  N14  110.81  3.000
 SVF  H14  C13  N14  108.51  3.000
 SVF  H15  C13  C11  110.32  3.000
 SVF  H14  C13  C11  109.51  3.000
 SVF  N14  C13  C11  110.73  3.000
 SVF  C15  N14  C13  125.15  3.000
 SVF  C13  N14  C12  113.30  3.000
 SVF  C15  N14  C12  121.30  3.000
 SVF  C17  C15  O16  120.41  3.000
 SVF  C17  C15  N14  117.38  3.000
 SVF  O16  C15  N14  122.21  3.000
 SVF  H18  C17  H17  108.34  3.000
 SVF  H18  C17  H16  107.38  3.000
 SVF  H17  C17  H16  108.23  3.000
 SVF  H18  C17  C15  111.79  3.000
 SVF  H17  C17  C15  108.89  3.000
 SVF  H16  C17  C15  112.08  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
 SVF  CONST_01  C06  C04  C02  C01    0.00   0.0  0
 SVF  CONST_02  C06  C05  C03  C01    0.00   0.0  0
 SVF  CONST_03  C05  C03  C01  C02    0.00   0.0  0
 SVF  CONST_04  C05  C06  C04  C02    0.00   0.0  0
 SVF  CONST_05  C04  C02  C01  C03    0.00   0.0  0
 SVF  CONST_06  C04  C06  C05  C03    0.00   0.0  0
 SVF  CONST_07  F07  C04  C02  C01  180.00   0.0  0
 SVF  CONST_08  C08  C03  C01  C02  180.00   0.0  0
 SVF  CONST_09  F07  C04  C06  C05  180.00   0.0  0
 SVF  CONST_10  C08  C03  C05  C06  180.00   0.0  0
 SVF  CONST_11  H3   C05  C03  C01  180.00   0.0  0
 SVF  CONST_12  H4   C06  C04  C02  180.00   0.0  0
 SVF  CONST_13  H2   C02  C01  C03  180.00   0.0  0
 SVF  CONST_14  H1   C01  C02  C04  180.00   0.0  0
 SVF  CONST_15  O16  C15  N14  C12    0.00   0.0  0
 SVF  CONST_16  C17  C15  N14  C12  180.00   0.0  0
 SVF  CONST_17  O16  C15  N14  C13  180.00   0.0  0
 SVF  CONST_18  C17  C15  N14  C13    0.00   0.0  0
 SVF  Var_01    N14  C12  C10  C09   54.96  30.0  1
 SVF  Var_02    N14  C13  C11  C09  -55.41  30.0  1
 SVF  Var_03    C13  N14  C12  C10  -57.78  30.0  1
 SVF  Var_04    C12  N14  C13  C11   57.97  30.0  1
 SVF  Var_05    C09  C08  C03  C01  102.95  30.0  2
 SVF  Var_06    H16  C17  C15  N14   61.09  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
 SVF  chir_01  C09  C08  C10  C11  positiv

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
 SVF  plan-1  C01  0.020
 SVF  plan-1  C02  0.020
 SVF  plan-1  C03  0.020
 SVF  plan-1  C04  0.020
 SVF  plan-1  C05  0.020
 SVF  plan-1  C06  0.020
 SVF  plan-1  C08  0.020
 SVF  plan-1  F07  0.020
 SVF  plan-1  H1   0.020
 SVF  plan-1  H2   0.020
 SVF  plan-1  H3   0.020
 SVF  plan-1  H4   0.020
 SVF  plan-2  C12  0.020
 SVF  plan-2  C13  0.020
 SVF  plan-2  N14  0.020
 SVF  plan-2  C15  0.020
 SVF  plan-2  O16  0.020
 SVF  plan-2  C17  0.020

