# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 17:59:32 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: 7-[(3R)-3-aminopyrrolidin-1-yl]-8-chloro-1-cyclopropyl-6-fluoro-4-oxo-1,4-dihydroquinoline-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]1CCN(C1)c2c(F)cc3C(=O)C(=CN(C4CC4)c3c2Cl)C(O)=O
#
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
 NFX  NFX  '7-[(3R)-3-aminopyrrolidin-1-yl]-8-chloro-1-cyclopropyl-6-fluoro-4-oxo-1,4-dihydroquinoline-3-carboxylic acid'  ligand  41  25  .  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_NFX
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
 NFX  F     F   F      0  -0.311  -2.1814   2.6843  -0.0678
 NFX  O02   O   O      0  -0.452   2.7377   2.8197   0.0050
 NFX  O03   O   O      0  -0.604   5.7006  -0.1564   0.4739
 NFX  O     O   OC    -1  -0.582   5.3020   1.9883   0.9102
 NFX  N01   N   NR5    0  -0.537  -2.9681   0.0845   0.4716
 NFX  N     N   NR6    0  -0.543   1.7569  -1.1204   0.2624
 NFX  C01   C   CR15   0  -0.128  -5.0080  -0.4549  -0.4863
 NFX  C02   C   CH2    0  -0.496  -5.2716   0.1187   0.9122
 NFX  C03   C   CH2    0  -0.272  -3.5875  -0.9779  -0.3099
 NFX  C04   C   CH2    0  -0.272  -3.9514   0.7997   1.2825
 NFX  N05   N   NH2    0  -0.788  -5.0602   0.5121  -1.5720
 NFX  C06   C   CH1    0  -0.133   1.5505  -2.4994  -0.1242
 NFX  C08   C   CH2    0  -0.482   0.7946  -2.7917  -1.3742
 NFX  C09   C   CH2    0  -0.494   2.2738  -3.0036  -1.3357
 NFX  C11   C   CR6    0   0.286  -1.6444   0.4265   0.3764
 NFX  C12   C   CR66   0   0.459   0.7388  -0.1845   0.3091
 NFX  C13   C   CR6    0  -0.233  -0.6178  -0.5140   0.5127
 NFX  C14   C   CR66   0  -0.147   1.0833   1.1697   0.1954
 NFX  C15   C   CR6    0   0.515  -1.2355   1.7533   0.1394
 NFX  C16   C   CR16   0   0.013   3.0413  -0.7022   0.3569
 NFX  C17   C   CR16   0  -0.475   0.0716   2.1307   0.1093
 NFX  C18   C   CR6    0  -0.366   3.4657   0.5879   0.3985
 NFX  C19   C   CR6    0   0.399   2.4878   1.6315   0.1863
 NFX  C20   C   C      0   0.401   4.9536   0.8365   0.6046
 NFX  H01   H   HCR5   0   0.244  -5.6960  -1.2714  -0.7155
 NFX  H02   H   HCH2   0   0.252  -6.1128   0.8123   0.9333
 NFX  H03   H   HCH2   0   0.246  -3.0667  -1.1195  -1.2588
 NFX  H03A  H   HCH2   0   0.226  -3.6102  -1.9392   0.2121
 NFX  H04   H   HCH2   0   0.239  -3.7298   0.7043   2.3488
 NFX  H04A  H   HCH2   0   0.234  -3.9874   1.8643   1.0534
 NFX  H06   H   HCH1   0   0.289   1.4424  -3.1898   0.7024
 NFX  H08   H   HCH2   0   0.268   0.1341  -3.6478  -1.3623
 NFX  H08A  H   HCH2   0   0.267   0.4264  -1.9512  -1.9493
 NFX  H09   H   HCH2   0   0.267   2.8953  -2.3121  -1.8902
 NFX  H09A  H   HCH2   0   0.268   2.6584  -4.0140  -1.2896
 NFX  H16   H   HCR6   0   0.303   3.7713  -1.4989   0.3835
 NFX  H17   H   HCR6   0   0.281   0.3343   3.1703  -0.0342
 NFX  H02A  H   HCH2   0   0.238  -5.4930  -0.6925   1.6095
 NFX  H05   H   HNH2   0   0.346  -5.9574   0.9821  -1.5664
 NFX  H05A  H   HNH2   0   0.339  -4.3695   1.2371  -1.4162
 NFX  CL    CL  CL     0  -0.064  -1.0650  -2.0586   1.1463

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
 NFX  F    C15   single    1.343  0.020  1.343
 NFX  CL   C13   single    1.728  0.020  1.728
 NFX  O02  C19   double    1.228  0.020  1.228
 NFX  O03  C20   deloc     1.249  0.020  1.249
 NFX  O    C20   deloc     1.242  0.020  1.242
 NFX  N01  C03   single    1.457  0.020  1.457
 NFX  N01  C04   single    1.462  0.020  1.462
 NFX  N01  C11   single    1.371  0.020  1.371
 NFX  N    C06   single    1.447  0.020  1.447
 NFX  N    C12   single    1.384  0.020  1.384
 NFX  N    C16   single    1.354  0.020  1.354
 NFX  C01  C02   single    1.534  0.020  1.534
 NFX  C01  C03   single    1.524  0.020  1.524
 NFX  C01  N05   single    1.455  0.020  1.455
 NFX  C01  H01   single    0.970  0.020  1.090
 NFX  C02  C04   single    1.531  0.020  1.531
 NFX  C02  H02   single    0.970  0.020  1.090
 NFX  C03  H03   single    0.970  0.020  1.090
 NFX  C03  H03A  single    0.970  0.020  1.090
 NFX  C04  H04   single    0.970  0.020  1.090
 NFX  C04  H04A  single    0.970  0.020  1.090
 NFX  C06  C08   single    1.490  0.020  1.490
 NFX  C06  C09   single    1.498  0.020  1.498
 NFX  C06  H06   single    0.970  0.020  1.090
 NFX  C08  C09   single    1.495  0.020  1.495
 NFX  C08  H08   single    0.970  0.020  1.090
 NFX  C08  H08A  single    0.970  0.020  1.090
 NFX  C09  H09   single    0.970  0.020  1.090
 NFX  C09  H09A  single    0.970  0.020  1.090
 NFX  C11  C13   aromatic  1.399  0.020  1.399
 NFX  C11  C15   aromatic  1.408  0.020  1.408
 NFX  C12  C13   aromatic  1.411  0.020  1.411
 NFX  C12  C14   aromatic  1.402  0.020  1.402
 NFX  C14  C17   aromatic  1.398  0.020  1.398
 NFX  C14  C19   single    1.478  0.020  1.478
 NFX  C15  C17   aromatic  1.361  0.020  1.361
 NFX  C16  C18   double    1.359  0.020  1.359
 NFX  C16  H16   single    0.930  0.020  1.080
 NFX  C17  H17   single    0.930  0.020  1.080
 NFX  C18  C19   single    1.446  0.020  1.446
 NFX  C18  C20   single    1.522  0.020  1.522
 NFX  C02  H02A  single    0.970  0.020  1.090
 NFX  N05  H05   single    0.890  0.020  1.040
 NFX  N05  H05A  single    0.890  0.020  1.040

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
 NFX  C11   N01  C04  124.49  3.000
 NFX  C11   N01  C03  123.73  3.000
 NFX  C04   N01  C03  111.62  3.000
 NFX  C16   N    C12  119.12  3.000
 NFX  C16   N    C06  116.63  3.000
 NFX  C12   N    C06  123.28  3.000
 NFX  H01   C01  N05  108.52  3.000
 NFX  H01   C01  C03  110.79  3.000
 NFX  N05   C01  C03  110.36  3.000
 NFX  H01   C01  C02  111.26  3.000
 NFX  N05   C01  C02  115.18  3.000
 NFX  C03   C01  C02  100.54  3.000
 NFX  H02A  C02  H02  107.68  3.000
 NFX  H02A  C02  C04  110.54  3.000
 NFX  H02   C02  C04  112.18  3.000
 NFX  H02A  C02  C01  109.82  3.000
 NFX  H02   C02  C01  112.82  3.000
 NFX  C04   C02  C01  103.80  3.000
 NFX  H03A  C03  H03  108.10  3.000
 NFX  H03A  C03  C01  109.72  3.000
 NFX  H03   C03  C01  112.87  3.000
 NFX  H03A  C03  N01  113.17  3.000
 NFX  H03   C03  N01  110.98  3.000
 NFX  C01   C03  N01  102.01  3.000
 NFX  H04A  C04  H04  107.28  3.000
 NFX  H04A  C04  C02  110.81  3.000
 NFX  H04   C04  C02  111.83  3.000
 NFX  H04A  C04  N01  112.56  3.000
 NFX  H04   C04  N01  111.23  3.000
 NFX  C02   C04  N01  103.19  3.000
 NFX  H05A  N05  H05  105.72  3.000
 NFX  H05A  N05  C01  109.66  3.000
 NFX  H05   N05  C01  109.64  3.000
 NFX  H06   C06  C09  116.81  3.000
 NFX  H06   C06  C08  117.71  3.000
 NFX  C09   C06  C08   60.03  3.000
 NFX  H06   C06  N    114.71  3.000
 NFX  C09   C06  N    117.90  3.000
 NFX  C08   C06  N    118.91  3.000
 NFX  H08A  C08  H08  114.37  3.000
 NFX  H08A  C08  C09  117.40  3.000
 NFX  H08   C08  C09  119.46  3.000
 NFX  H08A  C08  C06  117.77  3.000
 NFX  H08   C08  C06  117.12  3.000
 NFX  C09   C08  C06   60.27  3.000
 NFX  H09A  C09  H09  114.47  3.000
 NFX  H09A  C09  C08  119.03  3.000
 NFX  H09   C09  C08  117.66  3.000
 NFX  H09A  C09  C06  116.83  3.000
 NFX  H09   C09  C06  118.45  3.000
 NFX  C08   C09  C06   59.70  3.000
 NFX  C15   C11  C13  115.90  3.000
 NFX  C15   C11  N01  121.82  3.000
 NFX  C13   C11  N01  122.29  3.000
 NFX  C14   C12  C13  118.27  3.000
 NFX  C14   C12  N    118.02  3.000
 NFX  C13   C12  N    123.67  3.000
 NFX  C12   C13  C11  122.31  3.000
 NFX  C12   C13  CL   120.69  3.000
 NFX  C11   C13  CL   116.53  3.000
 NFX  C19   C14  C17  118.19  3.000
 NFX  C19   C14  C12  122.38  3.000
 NFX  C17   C14  C12  119.42  3.000
 NFX  C17   C15  C11  122.94  3.000
 NFX  C17   C15  F    118.73  3.000
 NFX  C11   C15  F    118.33  3.000
 NFX  H16   C16  C18  119.22  3.000
 NFX  H16   C16  N    114.50  3.000
 NFX  C18   C16  N    126.28  3.000
 NFX  H17   C17  C15  120.18  3.000
 NFX  H17   C17  C14  119.54  3.000
 NFX  C15   C17  C14  120.20  3.000
 NFX  C20   C18  C19  124.26  3.000
 NFX  C20   C18  C16  117.67  3.000
 NFX  C19   C18  C16  118.00  3.000
 NFX  C18   C19  C14  114.60  3.000
 NFX  C18   C19  O02  125.63  3.000
 NFX  C14   C19  O02  119.77  3.000
 NFX  C18   C20  O    117.33  3.000
 NFX  C18   C20  O03  116.13  3.000
 NFX  O     C20  O03  126.53  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
 NFX  CONST_01  C14  C12  C13  C11    0.00   0.0  0
 NFX  CONST_02  C14  C17  C15  C11    0.00   0.0  0
 NFX  CONST_03  C15  C11  C13  C12    0.00   0.0  0
 NFX  CONST_04  C15  C17  C14  C12    0.00   0.0  0
 NFX  CONST_05  C17  C15  C11  C13    0.00   0.0  0
 NFX  CONST_06  C17  C14  C12  C13    0.00   0.0  0
 NFX  CONST_07  C12  C13  C11  N01  180.00   0.0  0
 NFX  CONST_08  C17  C15  C11  N01  180.00   0.0  0
 NFX  CONST_09  N01  C11  C15  F      0.00   0.0  0
 NFX  CONST_10  C13  C11  C15  F    180.00   0.0  0
 NFX  CONST_11  C14  C17  C15  F    180.00   0.0  0
 NFX  CONST_12  N01  C11  C13  CL     0.00   0.0  0
 NFX  CONST_13  C15  C11  C13  CL   180.00   0.0  0
 NFX  CONST_16  H17  C17  C15  C11  180.00   0.0  0
 NFX  Var_01    C01  C02  C04  N01  -24.74  30.0  1
 NFX  Var_02    C09  C08  C06  N    107.37  30.0  1
 NFX  Var_03    C04  N01  C03  C01   27.37  30.0  1
 NFX  Var_04    C03  N01  C04  C02   -1.65  30.0  1
 NFX  Var_05    C13  C11  N01  C03  -53.05  30.0  2
 NFX  Var_06    C12  N    C06  C08   49.26  30.0  2
 NFX  Var_07    C16  C18  C20  O03   12.75  30.0  2

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
 NFX  chir_01  C01  C02  C03  N05  positiv
 NFX  chir_02  C06  N    C08  C09  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
 NFX  plan-1  F    0.020
 NFX  plan-1  O02  0.020
 NFX  plan-1  N01  0.020
 NFX  plan-1  N    0.020
 NFX  plan-1  C06  0.020
 NFX  plan-1  C11  0.020
 NFX  plan-1  C12  0.020
 NFX  plan-1  C13  0.020
 NFX  plan-1  C14  0.020
 NFX  plan-1  C15  0.020
 NFX  plan-1  C16  0.020
 NFX  plan-1  C17  0.020
 NFX  plan-1  C18  0.020
 NFX  plan-1  C19  0.020
 NFX  plan-1  C20  0.020
 NFX  plan-1  H16  0.020
 NFX  plan-1  H17  0.020
 NFX  plan-1  CL   0.020
 NFX  plan-2  O03  0.020
 NFX  plan-2  O    0.020
 NFX  plan-2  C18  0.020
 NFX  plan-2  C20  0.020

