# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 23:20:09 2021
#   Inital geometry file: a 69 line input string
#   Ligand name: (4~{R})-4-(3-fluoranylpyridin-2-yl)-1-methyl-piperazin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCN(CC1=O)c2ncccc2F
#
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
 SZE  SZE  (4~{R})-4-(3-fluoranylpyridin-2-yl)-1-methyl-piperazin-2-one  ligand  27  15  .  2022-07-22  2022-07-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_SZE
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
 SZE  N1   N  NT    0  -0.505  -38.3593  2.9243   0.0389
 SZE  C4   C  C     0   0.531  -37.8007  3.3611  -2.3378
 SZE  C5   C  CR6   0   0.356  -39.1252  2.2659   0.9833
 SZE  C6   C  CR16  0  -0.073  -41.0347  1.0885   1.4929
 SZE  C7   C  CR16  0  -0.335  -40.6586  0.8829   2.8040
 SZE  C8   C  CR16  0  -0.297  -39.4230  1.3813   3.2095
 SZE  C9   C  CR6   0   0.420  -38.6576  2.0496   2.2903
 SZE  N2   N  N     0  -0.450  -40.2960  1.7665   0.6185
 SZE  C2   C  CH2   0  -0.346  -37.8328  4.2488   0.3208
 SZE  C1   C  CH2   0  -0.260  -36.5863  4.4558  -0.5020
 SZE  C3   C  CH2   0  -0.388  -38.8038  2.8271  -1.3319
 SZE  O    O  O     0  -0.513  -37.9460  3.0614  -3.5169
 SZE  N    N  NT    0  -0.458  -36.8231  4.1750  -1.9067
 SZE  C    C  CH3   0  -0.522  -35.8099  4.6349  -2.8343
 SZE  H1   H  HCR6  0   0.265  -41.9746  0.6973   1.1219
 SZE  H2   H  HCR6  0   0.276  -41.2940  0.3402   3.4889
 SZE  H3   H  HCR6  0   0.295  -39.0508  1.2232   4.2135
 SZE  H4   H  HCH2  0   0.281  -37.5815  4.3678   1.3698
 SZE  H5   H  HCH2  0   0.248  -38.5813  5.0162   0.0808
 SZE  H6   H  HCH2  0   0.245  -35.7757  3.8258  -0.1221
 SZE  H7   H  HCH2  0   0.253  -36.2647  5.4943  -0.4068
 SZE  H8   H  HCH2  0   0.260  -39.7487  3.3613  -1.5081
 SZE  H9   H  HCH2  0   0.283  -38.9846  1.7842  -1.5897
 SZE  H10  H  HCH3  0   0.243  -35.4279  5.5960  -2.4954
 SZE  H11  H  HCH3  0   0.242  -34.9732  3.9353  -2.8958
 SZE  H12  H  HCH3  0   0.257  -36.2286  4.7627  -3.8280
 SZE  F    F  F     0  -0.307  -37.4321  2.4746   2.6372

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
 SZE  O   C4   double    1.225  0.020  1.225
 SZE  C   N    single    1.449  0.020  1.449
 SZE  C4  N    single    1.343  0.020  1.343
 SZE  C4  C3   single    1.518  0.020  1.518
 SZE  N   C1   single    1.452  0.020  1.452
 SZE  C3  N1   single    1.444  0.020  1.444
 SZE  C1  C2   single    1.508  0.020  1.508
 SZE  N1  C2   single    1.453  0.020  1.453
 SZE  N1  C5   single    1.383  0.020  1.383
 SZE  N2  C5   aromatic  1.324  0.020  1.324
 SZE  N2  C6   aromatic  1.330  0.020  1.330
 SZE  C5  C9   aromatic  1.405  0.020  1.405
 SZE  C6  C7   aromatic  1.379  0.020  1.379
 SZE  C9  F    single    1.343  0.020  1.343
 SZE  C9  C8   aromatic  1.370  0.020  1.370
 SZE  C7  C8   aromatic  1.393  0.020  1.393
 SZE  C6  H1   single    0.930  0.020  1.080
 SZE  C7  H2   single    0.930  0.020  1.080
 SZE  C8  H3   single    0.930  0.020  1.080
 SZE  C2  H4   single    0.970  0.020  1.090
 SZE  C2  H5   single    0.970  0.020  1.090
 SZE  C1  H6   single    0.970  0.020  1.090
 SZE  C1  H7   single    0.970  0.020  1.090
 SZE  C3  H8   single    0.970  0.020  1.090
 SZE  C3  H9   single    0.970  0.020  1.090
 SZE  C   H10  single    0.970  0.020  1.090
 SZE  C   H11  single    0.970  0.020  1.090
 SZE  C   H12  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
 SZE  C3   N1  C2   110.91  3.000
 SZE  C2   N1  C5   120.15  3.000
 SZE  C3   N1  C5   116.47  3.000
 SZE  N    C4  O    122.92  3.000
 SZE  N    C4  C3   118.79  3.000
 SZE  O    C4  C3   118.25  3.000
 SZE  N2   C5  C9   119.51  3.000
 SZE  C9   C5  N1   121.63  3.000
 SZE  N2   C5  N1   118.76  3.000
 SZE  H1   C6  N2   116.14  3.000
 SZE  H1   C6  C7   120.54  3.000
 SZE  N2   C6  C7   123.32  3.000
 SZE  H2   C7  C8   121.13  3.000
 SZE  H2   C7  C6   121.14  3.000
 SZE  C8   C7  C6   117.73  3.000
 SZE  H3   C8  C9   120.10  3.000
 SZE  H3   C8  C7   121.53  3.000
 SZE  C9   C8  C7   118.34  3.000
 SZE  F    C9  C8   119.40  3.000
 SZE  C8   C9  C5   120.89  3.000
 SZE  F    C9  C5   119.70  3.000
 SZE  C6   N2  C5   120.14  3.000
 SZE  H5   C2  H4   107.00  3.000
 SZE  H5   C2  C1   110.38  3.000
 SZE  H4   C2  C1   108.73  3.000
 SZE  H5   C2  N1   110.33  3.000
 SZE  H4   C2  N1   111.80  3.000
 SZE  C1   C2  N1   108.59  3.000
 SZE  H7   C1  H6   107.41  3.000
 SZE  H7   C1  N    108.45  3.000
 SZE  H6   C1  N    110.19  3.000
 SZE  H7   C1  C2   109.06  3.000
 SZE  H6   C1  C2   110.11  3.000
 SZE  N    C1  C2   111.51  3.000
 SZE  H9   C3  H8   106.53  3.000
 SZE  H9   C3  C4   106.84  3.000
 SZE  H8   C3  C4   106.91  3.000
 SZE  H9   C3  N1   109.88  3.000
 SZE  H8   C3  N1   112.57  3.000
 SZE  C4   C3  N1   113.70  3.000
 SZE  C    N   C1   116.37  3.000
 SZE  C1   N   C4   123.12  3.000
 SZE  C    N   C4   119.73  3.000
 SZE  H12  C   H11  108.62  3.000
 SZE  H12  C   H10  108.44  3.000
 SZE  H11  C   H10  108.31  3.000
 SZE  H12  C   N    110.72  3.000
 SZE  H11  C   N    111.62  3.000
 SZE  H10  C   N    109.05  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
 SZE  CONST_01  C7   C6  N2  C5    0.00   0.0  0
 SZE  CONST_02  C7   C8  C9  C5    0.00   0.0  0
 SZE  CONST_03  C9   C5  N2  C6    0.00   0.0  0
 SZE  CONST_04  C9   C8  C7  C6    0.00   0.0  0
 SZE  CONST_05  N2   C5  C9  C8    0.00   0.0  0
 SZE  CONST_06  N2   C6  C7  C8    0.00   0.0  0
 SZE  CONST_07  C6   N2  C5  N1  180.00   0.0  0
 SZE  CONST_08  C8   C9  C5  N1  180.00   0.0  0
 SZE  CONST_09  C3   C4  N   C1    0.00   0.0  0
 SZE  CONST_10  F    C9  C5  N1    0.00   0.0  0
 SZE  CONST_11  F    C9  C8  C7  180.00   0.0  0
 SZE  CONST_12  N2   C5  C9  F   180.00   0.0  0
 SZE  CONST_13  O    C4  N   C1  180.00   0.0  0
 SZE  CONST_14  C    N   C4  C3  180.00   0.0  0
 SZE  CONST_15  H1   C6  N2  C5  180.00   0.0  0
 SZE  CONST_16  H3   C8  C9  C5  180.00   0.0  0
 SZE  CONST_17  H2   C7  C8  C9  180.00   0.0  0
 SZE  CONST_18  C    N   C4  O     0.00   0.0  0
 SZE  Var_01    N    C4  C3  N1  -18.05  30.0  1
 SZE  Var_02    N    C1  C2  N1   52.24  30.0  1
 SZE  Var_03    C2   C1  N   C4  -24.32  30.0  1
 SZE  Var_04    C2   N1  C3  C4   47.74  30.0  1
 SZE  Var_05    C1   C2  N1  C5  153.87  30.0  1
 SZE  Var_06    C3   N1  C5  C9  166.54  30.0  3
 SZE  Var_07    H10  C   N   C4  152.59  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
 SZE  plan-1  N1  0.020
 SZE  plan-1  C5  0.020
 SZE  plan-1  C6  0.020
 SZE  plan-1  C7  0.020
 SZE  plan-1  C8  0.020
 SZE  plan-1  C9  0.020
 SZE  plan-1  N2  0.020
 SZE  plan-1  H1  0.020
 SZE  plan-1  H2  0.020
 SZE  plan-1  H3  0.020
 SZE  plan-1  F   0.020
 SZE  plan-2  C4  0.020
 SZE  plan-2  C1  0.020
 SZE  plan-2  C3  0.020
 SZE  plan-2  O   0.020
 SZE  plan-2  N   0.020
 SZE  plan-2  C   0.020

