# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 12:34:03 2021
#   Inital geometry file: a 72 line input string
#   Ligand name: 3-fluoro-N-[(oxan-4-yl)methyl]pyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1cccnc1NCC2CCOCC2
#
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
 WGS  WGS  3-fluoro-N-[(oxan-4-yl)methyl]pyridin-2-amine  ligand  30  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_WGS
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
 WGS  N1   N  NH1   0  -0.677  3.5285  -16.7446   -9.7931
 WGS  C4   C  CR6   0   0.407  3.6812  -16.2125   -8.5596
 WGS  C5   C  CH2   0  -0.270  4.2572  -16.3363  -10.9699
 WGS  C6   C  CH1   0  -0.229  3.4336  -15.4957  -11.9418
 WGS  C7   C  CH2   0  -0.459  2.8656  -14.2241  -11.2913
 WGS  C8   C  CH2   0  -0.185  2.7029  -13.1132  -12.3312
 WGS  C10  C  CH2   0  -0.512  4.2726  -15.1110  -13.1556
 WGS  N    N  N     0  -0.470  4.5881  -15.2675   -8.3451
 WGS  C    C  CR6   0   0.374  2.8878  -16.6676   -7.4844
 WGS  O    O  O2    0  -0.495  2.3549  -13.6433  -13.5921
 WGS  C1   C  CR16  0  -0.300  3.0323  -16.1532   -6.2298
 WGS  C2   C  CR16  0  -0.359  3.9945  -15.1581   -6.0287
 WGS  C3   C  CR16  0  -0.074  4.7358  -14.7631   -7.1209
 WGS  C9   C  CH2   0  -0.153  3.4157  -14.3705  -14.1842
 WGS  F    F  F     0  -0.317  1.9762  -17.6295   -7.7324
 WGS  H3   H  HNH1  0   0.393  2.8131  -17.4403   -9.9181
 WGS  H5   H  HCH2  0   0.241  5.1372  -15.7777  -10.6523
 WGS  H4   H  HCH2  0   0.244  4.6152  -17.2329  -11.4836
 WGS  H6   H  HCH1  0   0.229  2.5969  -16.1112  -12.2929
 WGS  H7   H  HCH2  0   0.231  1.9080  -14.4476  -10.8171
 WGS  H8   H  HCH2  0   0.230  3.5303  -13.8690  -10.4988
 WGS  H9   H  HCH2  0   0.236  1.9084  -12.4221  -12.0446
 WGS  H10  H  HCH2  0   0.201  3.6253  -12.5209  -12.4016
 WGS  H13  H  HCH2  0   0.247  4.7101  -15.9946  -13.6264
 WGS  H14  H  HCH2  0   0.232  5.1135  -14.4896  -12.8305
 WGS  H    H  HCR6  0   0.289  2.4115  -16.5126   -5.4189
 WGS  H1   H  HCR6  0   0.265  4.1481  -14.7156   -5.0553
 WGS  H2   H  HCR6  0   0.256  5.4939  -13.9948   -7.0177
 WGS  H11  H  HCH2  0   0.220  2.9507  -15.0850  -14.8677
 WGS  H12  H  HCH2  0   0.204  4.0486  -13.7046  -14.7854

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
 WGS  C    F    single    1.348  0.020  1.348
 WGS  C    C1   aromatic  1.364  0.020  1.364
 WGS  C1   C2   aromatic  1.399  0.020  1.399
 WGS  C2   C3   aromatic  1.378  0.020  1.378
 WGS  C3   N    aromatic  1.332  0.020  1.332
 WGS  N    C4   aromatic  1.327  0.020  1.327
 WGS  C4   C    aromatic  1.412  0.020  1.412
 WGS  N1   C4   single    1.352  0.020  1.352
 WGS  C5   N1   single    1.443  0.020  1.443
 WGS  C6   C5   single    1.526  0.020  1.526
 WGS  C6   C7   single    1.537  0.020  1.537
 WGS  C7   C8   single    1.530  0.020  1.530
 WGS  C8   O    single    1.411  0.020  1.411
 WGS  O    C9   single    1.416  0.020  1.416
 WGS  C9   C10  single    1.530  0.020  1.530
 WGS  C10  C6   single    1.525  0.020  1.525
 WGS  N1   H3   single    0.860  0.020  1.020
 WGS  C5   H5   single    0.970  0.020  1.090
 WGS  C5   H4   single    0.970  0.020  1.090
 WGS  C6   H6   single    0.970  0.020  1.090
 WGS  C7   H7   single    0.970  0.020  1.090
 WGS  C7   H8   single    0.970  0.020  1.090
 WGS  C8   H9   single    0.970  0.020  1.090
 WGS  C8   H10  single    0.970  0.020  1.090
 WGS  C10  H13  single    0.970  0.020  1.090
 WGS  C10  H14  single    0.970  0.020  1.090
 WGS  C1   H    single    0.930  0.020  1.080
 WGS  C2   H1   single    0.930  0.020  1.080
 WGS  C3   H2   single    0.930  0.020  1.080
 WGS  C9   H11  single    0.970  0.020  1.090
 WGS  C9   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
 WGS  H3   N1   C5   116.97  3.000
 WGS  H3   N1   C4   117.78  3.000
 WGS  C5   N1   C4   125.14  3.000
 WGS  C    C4   N    119.37  3.000
 WGS  C    C4   N1   120.30  3.000
 WGS  N    C4   N1   120.32  3.000
 WGS  H4   C5   H5   107.03  3.000
 WGS  H4   C5   C6   109.21  3.000
 WGS  H5   C5   C6   109.82  3.000
 WGS  H4   C5   N1   108.44  3.000
 WGS  H5   C5   N1   108.37  3.000
 WGS  C6   C5   N1   113.74  3.000
 WGS  H6   C6   C10  107.85  3.000
 WGS  H6   C6   C7   108.54  3.000
 WGS  C10  C6   C7   109.36  3.000
 WGS  H6   C6   C5   107.85  3.000
 WGS  C10  C6   C5   110.42  3.000
 WGS  C7   C6   C5   112.68  3.000
 WGS  H8   C7   H7   106.55  3.000
 WGS  H8   C7   C8   108.74  3.000
 WGS  H7   C7   C8   110.52  3.000
 WGS  H8   C7   C6   110.53  3.000
 WGS  H7   C7   C6   109.79  3.000
 WGS  C8   C7   C6   110.62  3.000
 WGS  H10  C8   H9   106.66  3.000
 WGS  H10  C8   O    110.63  3.000
 WGS  H9   C8   O    107.03  3.000
 WGS  H10  C8   C7   110.22  3.000
 WGS  H9   C8   C7   111.02  3.000
 WGS  O    C8   C7   111.14  3.000
 WGS  H14  C10  H13  106.22  3.000
 WGS  H14  C10  C9   110.80  3.000
 WGS  H13  C10  C9   109.02  3.000
 WGS  H14  C10  C6   109.23  3.000
 WGS  H13  C10  C6   111.05  3.000
 WGS  C9   C10  C6   110.44  3.000
 WGS  C3   N    C4   119.60  3.000
 WGS  F    C    C1   120.67  3.000
 WGS  C1   C    C4   121.31  3.000
 WGS  F    C    C4   118.03  3.000
 WGS  C9   O    C8   112.45  3.000
 WGS  H    C1   C2   121.53  3.000
 WGS  H    C1   C    120.20  3.000
 WGS  C2   C1   C    118.27  3.000
 WGS  H1   C2   C3   121.36  3.000
 WGS  H1   C2   C1   121.25  3.000
 WGS  C3   C2   C1   117.39  3.000
 WGS  H2   C3   C2   120.26  3.000
 WGS  H2   C3   N    115.67  3.000
 WGS  C2   C3   N    124.07  3.000
 WGS  H12  C9   H11  107.43  3.000
 WGS  H12  C9   O    110.45  3.000
 WGS  H11  C9   O    106.18  3.000
 WGS  H12  C9   C10  109.80  3.000
 WGS  H11  C9   C10  110.02  3.000
 WGS  O    C9   C10  112.77  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
 WGS  CONST_01  C2   C3  N    C4     0.00   0.0  0
 WGS  CONST_02  C2   C1  C    C4     0.00   0.0  0
 WGS  CONST_03  C1   C2  C3   N      0.00   0.0  0
 WGS  CONST_04  C1   C   C4   N      0.00   0.0  0
 WGS  CONST_05  C3   C2  C1   C      0.00   0.0  0
 WGS  CONST_06  C3   N   C4   C      0.00   0.0  0
 WGS  CONST_07  C3   N   C4   N1   180.00   0.0  0
 WGS  CONST_08  C1   C   C4   N1   180.00   0.0  0
 WGS  CONST_09  F    C   C4   N    180.00   0.0  0
 WGS  CONST_10  F    C   C1   C2   180.00   0.0  0
 WGS  CONST_11  H2   C3  N    C4   180.00   0.0  0
 WGS  CONST_12  H    C1  C    C4   180.00   0.0  0
 WGS  CONST_13  H1   C2  C3   N    180.00   0.0  0
 WGS  CONST_14  N    C4  N1   C5     0.00   0.0  0
 WGS  CONST_15  C    C4  N1   C5   180.00   0.0  0
 WGS  CONST_16  H3   N1  C4   N    180.00   0.0  0
 WGS  Var_01    O    C8  C7   C6    33.88  30.0  1
 WGS  Var_02    O    C9  C10  C6    29.69  30.0  1
 WGS  Var_03    C10  C9  O    C8    34.21  30.0  1
 WGS  Var_04    C6   C5  N1   C4  -104.97  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
 WGS  chir_01  C6  C5  C7  C10  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
 WGS  plan-1  N1  0.020
 WGS  plan-1  C4  0.020
 WGS  plan-1  N   0.020
 WGS  plan-1  C   0.020
 WGS  plan-1  C1  0.020
 WGS  plan-1  C2  0.020
 WGS  plan-1  C3  0.020
 WGS  plan-1  F   0.020
 WGS  plan-1  H   0.020
 WGS  plan-1  H1  0.020
 WGS  plan-1  H2  0.020
 WGS  plan-2  N1  0.020
 WGS  plan-2  C4  0.020
 WGS  plan-2  C5  0.020
 WGS  plan-2  H3  0.020

