# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 19:37:40 2022
#   Inital geometry file: a 64 line input string
#   Ligand name: 3-fluoro-5-[(2S)-1-methylpyrrolidin-2-yl]pyridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCC[C@H]1c2cncc(F)c2
#
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
 FN1  FN1  3-fluoro-5-[(2S)-1-methylpyrrolidin-2-yl]pyridine  ligand  26  13  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_FN1
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
 FN1  F13   F  F     0  -0.304  -3.5473  -1.4173  -0.2754
 FN1  C4    C  CR6   0   0.444  -2.5269  -0.5538  -0.1946
 FN1  C3    C  CR16  0  -0.359  -1.2399  -1.0259  -0.0360
 FN1  C2    C  CR6   0   0.043  -0.2131  -0.0972   0.0441
 FN1  C1    C  CR16  0  -0.087  -0.5522   1.2520  -0.0492
 FN1  N1    N  N     0  -0.386  -1.7931   1.6886  -0.2069
 FN1  C5    C  CR16  0  -0.214  -2.7783   0.8016  -0.2779
 FN1  C6    C  CH1   0  -0.112   1.2107  -0.5261   0.2592
 FN1  C7    C  CH2   0  -0.446   1.7044  -0.2924   1.6941
 FN1  C8    C  CH2   0  -0.468   3.2244  -0.1002   1.5436
 FN1  C9    C  CH2   0  -0.278   3.4568  -0.0596   0.0295
 FN1  N2    N  NT    0  -0.422   2.1523   0.2432  -0.5326
 FN1  C10   C  CH3   0  -0.523   2.0708   0.0067  -1.9534
 FN1  H3    H  HCR6  0   0.289  -1.0431  -2.0900   0.0202
 FN1  H1    H  HCR6  0   0.260   0.2278   2.0030  -0.0015
 FN1  H5    H  HCR6  0   0.281  -3.7895   1.1713  -0.4085
 FN1  H6    H  HCH1  0   0.223   1.2862  -1.6042   0.0264
 FN1  H72   H  HCH2  0   0.240   1.2414   0.6064   2.1047
 FN1  H71   H  HCH2  0   0.246   1.4359  -1.1227   2.3463
 FN1  H81   H  HCH2  0   0.240   3.5457   0.8245   2.0220
 FN1  H82   H  HCH2  0   0.238   3.7882  -0.9121   2.0012
 FN1  H91   H  HCH2  0   0.235   4.1915   0.6884  -0.2757
 FN1  H92   H  HCH2  0   0.195   3.8244  -1.0385  -0.3207
 FN1  H103  H  HCH3  0   0.236   1.0852   0.2774  -2.3342
 FN1  H102  H  HCH3  0   0.237   2.8042   0.6237  -2.4737
 FN1  H101  H  HCH3  0   0.195   2.2611  -1.0437  -2.2238

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
 FN1  F13  C4    single    1.339  0.020  1.339
 FN1  C4   C5    aromatic  1.381  0.020  1.381
 FN1  C4   C3    aromatic  1.380  0.020  1.380
 FN1  C5   N1    aromatic  1.328  0.020  1.328
 FN1  C3   C2    aromatic  1.387  0.020  1.387
 FN1  N1   C1    aromatic  1.325  0.020  1.325
 FN1  C2   C1    aromatic  1.394  0.020  1.394
 FN1  C2   C6    single    1.502  0.020  1.502
 FN1  C6   C7    single    1.535  0.020  1.535
 FN1  C6   N2    single    1.451  0.020  1.451
 FN1  C7   C8    single    1.540  0.020  1.540
 FN1  N2   C10   single    1.443  0.020  1.443
 FN1  N2   C9    single    1.452  0.020  1.452
 FN1  C8   C9    single    1.532  0.020  1.532
 FN1  C3   H3    single    0.930  0.020  1.080
 FN1  C1   H1    single    0.930  0.020  1.080
 FN1  C5   H5    single    0.930  0.020  1.080
 FN1  C6   H6    single    0.970  0.020  1.090
 FN1  C7   H72   single    0.970  0.020  1.090
 FN1  C7   H71   single    0.970  0.020  1.090
 FN1  C8   H81   single    0.970  0.020  1.090
 FN1  C8   H82   single    0.970  0.020  1.090
 FN1  C9   H91   single    0.970  0.020  1.090
 FN1  C9   H92   single    0.970  0.020  1.090
 FN1  C10  H103  single    0.970  0.020  1.090
 FN1  C10  H102  single    0.970  0.020  1.090
 FN1  C10  H101  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
 FN1  C5    C4   C3    120.83  3.000
 FN1  C3    C4   F13   119.80  3.000
 FN1  C5    C4   F13   119.37  3.000
 FN1  H3    C3   C2    121.35  3.000
 FN1  H3    C3   C4    120.75  3.000
 FN1  C2    C3   C4    117.91  3.000
 FN1  C6    C2   C1    121.08  3.000
 FN1  C6    C2   C3    121.25  3.000
 FN1  C1    C2   C3    117.66  3.000
 FN1  H1    C1   N1    116.80  3.000
 FN1  H1    C1   C2    119.51  3.000
 FN1  N1    C1   C2    123.68  3.000
 FN1  C5    N1   C1    118.77  3.000
 FN1  H5    C5   N1    118.07  3.000
 FN1  H5    C5   C4    120.77  3.000
 FN1  N1    C5   C4    121.16  3.000
 FN1  H6    C6   N2    110.96  3.000
 FN1  H6    C6   C7    108.86  3.000
 FN1  N2    C6   C7    102.75  3.000
 FN1  H6    C6   C2    108.24  3.000
 FN1  N2    C6   C2    112.68  3.000
 FN1  C7    C6   C2    113.27  3.000
 FN1  H71   C7   H72   107.33  3.000
 FN1  H71   C7   C8    113.39  3.000
 FN1  H72   C7   C8    110.66  3.000
 FN1  H71   C7   C6    111.37  3.000
 FN1  H72   C7   C6    109.91  3.000
 FN1  C8    C7   C6    104.19  3.000
 FN1  H82   C8   H81   107.19  3.000
 FN1  H82   C8   C9    110.88  3.000
 FN1  H81   C8   C9    111.51  3.000
 FN1  H82   C8   C7    112.14  3.000
 FN1  H81   C8   C7    110.74  3.000
 FN1  C9    C8   C7    104.46  3.000
 FN1  H92   C9   H91   107.16  3.000
 FN1  H92   C9   N2    111.19  3.000
 FN1  H91   C9   N2    110.69  3.000
 FN1  H92   C9   C8    109.93  3.000
 FN1  H91   C9   C8    113.35  3.000
 FN1  N2    C9   C8    104.58  3.000
 FN1  C10   N2   C9    113.44  3.000
 FN1  C9    N2   C6    105.14  3.000
 FN1  C10   N2   C6    114.45  3.000
 FN1  H101  C10  H102  107.83  3.000
 FN1  H101  C10  H103  107.89  3.000
 FN1  H102  C10  H103  107.51  3.000
 FN1  H101  C10  N2    112.85  3.000
 FN1  H102  C10  N2    109.82  3.000
 FN1  H103  C10  N2    110.74  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
 FN1  CONST_01  C1    N1   C5  C4     0.00   0.0  0
 FN1  CONST_02  C1    C2   C3  C4     0.00   0.0  0
 FN1  CONST_03  N1    C5   C4  C3     0.00   0.0  0
 FN1  CONST_04  N1    C1   C2  C3     0.00   0.0  0
 FN1  CONST_05  C5    C4   C3  C2     0.00   0.0  0
 FN1  CONST_06  C5    N1   C1  C2     0.00   0.0  0
 FN1  CONST_07  C6    C2   C3  C4   180.00   0.0  0
 FN1  CONST_08  C6    C2   C1  N1   180.00   0.0  0
 FN1  CONST_09  N1    C5   C4  F13  180.00   0.0  0
 FN1  CONST_10  C2    C3   C4  F13  180.00   0.0  0
 FN1  CONST_11  H5    C5   C4  C3   180.00   0.0  0
 FN1  CONST_12  H1    C1   C2  C3   180.00   0.0  0
 FN1  CONST_13  H3    C3   C2  C1   180.00   0.0  0
 FN1  Var_01    C9    C8   C7  C6     6.98  30.0  1
 FN1  Var_02    C8    C9   N2  C6   -39.83  30.0  1
 FN1  Var_03    N2    C9   C8  C7    19.06  30.0  1
 FN1  Var_04    H103  C10  N2  C6    61.14  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
 FN1  chir_01  C6  C2  C7  N2  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
 FN1  plan-1  F13  0.020
 FN1  plan-1  C4   0.020
 FN1  plan-1  C3   0.020
 FN1  plan-1  C2   0.020
 FN1  plan-1  C1   0.020
 FN1  plan-1  N1   0.020
 FN1  plan-1  C5   0.020
 FN1  plan-1  C6   0.020
 FN1  plan-1  H3   0.020
 FN1  plan-1  H1   0.020
 FN1  plan-1  H5   0.020

