# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 18 05:12:48 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  42  25  .  2022-09-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  -0.303  -2.3023   2.3912  -0.7403
 NFX  O02   O   O     0  -0.426   2.6005   2.7765  -0.5297
 NFX  O03   O   O     0  -0.457   5.6170   0.1885   0.8907
 NFX  O     O   OH1   0  -0.581   5.1083   2.2866   0.3592
 NFX  N01   N   NT    0  -0.523  -2.9889  -0.1591   0.0959
 NFX  N     N   NR6   0  -0.546   1.8006  -1.1209   0.3259
 NFX  C01   C   CH1   0  -0.145  -5.2737   0.0714  -0.4831
 NFX  C02   C   CH2   0  -0.473  -5.1117  -0.3141   0.9947
 NFX  C03   C   CH2   0  -0.270  -3.8842  -0.2257  -1.0580
 NFX  C04   C   CH2   0  -0.278  -3.7053   0.1599   1.3222
 NFX  N05   N   NH2   0  -0.793  -5.6338   1.4631  -0.7172
 NFX  C06   C   CH1   0  -0.139   1.7008  -2.5626   0.1826
 NFX  C08   C   CH2   0  -0.479   1.1483  -3.1203  -1.0831
 NFX  C09   C   CH2   0  -0.499   2.6112  -3.2320  -0.8014
 NFX  C11   C   CR6   0   0.220  -1.6666   0.2415  -0.0466
 NFX  C12   C   CR66  0   0.466   0.7264  -0.2532   0.1325
 NFX  C13   C   CR6   0  -0.196  -0.6238  -0.6288   0.2735
 NFX  C14   C   CR66  0  -0.125   1.0089   1.0802  -0.2005
 NFX  C15   C   CR6   0   0.572  -1.3167   1.5336  -0.4509
 NFX  C16   C   CR16  0   0.059   3.0336  -0.6208   0.4574
 NFX  C17   C   CR16  0  -0.479  -0.0234   1.9657  -0.5047
 NFX  C18   C   CR6   0  -0.353   3.3818   0.6924   0.2977
 NFX  C19   C   CR6   0   0.438   2.3866   1.6250  -0.1803
 NFX  C20   C   C     0   0.536   4.7997   1.0133   0.5411
 NFX  H01   H   HCH1  0   0.246  -6.0290  -0.5508  -0.9675
 NFX  H02   H   HCH2  0   0.245  -5.8729   0.1365   1.6331
 NFX  H03   H   HCH2  0   0.232  -3.6326   0.4892  -1.8460
 NFX  H03A  H   HCH2  0   0.235  -3.8476  -1.2232  -1.5066
 NFX  H04   H   HCH2  0   0.240  -3.2722  -0.3616   2.1785
 NFX  H04A  H   HCH2  0   0.209  -3.6939   1.2338   1.5557
 NFX  H06   H   HCH1  0   0.301   1.4975  -3.0878   1.1060
 NFX  H08   H   HCH2  0   0.273   0.5200  -3.9965  -1.0019
 NFX  H08A  H   HCH2  0   0.272   0.8449  -2.4201  -1.8515
 NFX  H09   H   HCH2  0   0.272   3.2816  -2.6175  -1.3888
 NFX  H09A  H   HCH2  0   0.275   3.0199  -4.1899  -0.5094
 NFX  H16   H   HCR6  0   0.331   3.7960  -1.3549   0.6780
 NFX  H17   H   HCR6  0   0.292   0.2052   2.9909  -0.7624
 NFX  H02A  H   HCH2  0   0.235  -5.1739  -1.3988   1.1113
 NFX  HO    H   HOH1  0   0.481   6.0511   2.4095   0.5473
 NFX  H05   H   HNH2  0   0.345  -6.4856   1.6797  -0.2134
 NFX  H05A  H   HNH2  0   0.339  -4.9260   2.0788  -0.3346
 NFX  CL    CL  CL    0  -0.050  -1.0972  -2.1316   0.9668

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    1.338  0.020  1.338
 NFX  CL   C13   single    1.721  0.020  1.721
 NFX  O02  C19   double    1.222  0.020  1.222
 NFX  O03  C20   double    1.213  0.020  1.213
 NFX  O    C20   single    1.323  0.020  1.323
 NFX  N01  C03   single    1.462  0.020  1.462
 NFX  N01  C04   single    1.456  0.020  1.456
 NFX  N01  C11   single    1.389  0.020  1.389
 NFX  N    C06   single    1.452  0.020  1.452
 NFX  N    C12   single    1.394  0.020  1.394
 NFX  N    C16   single    1.337  0.020  1.337
 NFX  C01  C02   single    1.536  0.020  1.536
 NFX  C01  C03   single    1.533  0.020  1.533
 NFX  C01  N05   single    1.457  0.020  1.457
 NFX  C01  H01   single    0.970  0.020  1.090
 NFX  C02  C04   single    1.520  0.020  1.520
 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    1.489  0.020  1.489
 NFX  C06  C09   single    1.498  0.020  1.498
 NFX  C06  H06   single    0.970  0.020  1.090
 NFX  C08  C09   single    1.494  0.020  1.494
 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  1.396  0.020  1.396
 NFX  C11  C15   aromatic  1.398  0.020  1.398
 NFX  C12  C13   aromatic  1.408  0.020  1.408
 NFX  C12  C14   aromatic  1.403  0.020  1.403
 NFX  C14  C17   aromatic  1.394  0.020  1.394
 NFX  C14  C19   single    1.482  0.020  1.482
 NFX  C15  C17   aromatic  1.365  0.020  1.365
 NFX  C16  C18   double    1.368  0.020  1.368
 NFX  C16  H16   single    0.930  0.020  1.080
 NFX  C17  H17   single    0.930  0.020  1.080
 NFX  C18  C19   single    1.445  0.020  1.445
 NFX  C18  C20   single    1.474  0.020  1.474
 NFX  C02  H02A  single    0.970  0.020  1.090
 NFX  O    HO    single    0.850  0.020  0.980
 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  HO    O    C20  108.80  3.000
 NFX  C11   N01  C04  119.46  3.000
 NFX  C11   N01  C03  121.00  3.000
 NFX  C04   N01  C03  111.94  3.000
 NFX  C16   N    C12  119.43  3.000
 NFX  C16   N    C06  116.38  3.000
 NFX  C12   N    C06  123.45  3.000
 NFX  H01   C01  N05  107.59  3.000
 NFX  H01   C01  C03  110.50  3.000
 NFX  N05   C01  C03  110.43  3.000
 NFX  H01   C01  C02  110.90  3.000
 NFX  N05   C01  C02  114.87  3.000
 NFX  C03   C01  C02  102.51  3.000
 NFX  H02A  C02  H02  107.93  3.000
 NFX  H02A  C02  C04  109.84  3.000
 NFX  H02   C02  C04  113.00  3.000
 NFX  H02A  C02  C01  110.23  3.000
 NFX  H02   C02  C01  112.69  3.000
 NFX  C04   C02  C01  103.10  3.000
 NFX  H03A  C03  H03  107.04  3.000
 NFX  H03A  C03  C01  111.15  3.000
 NFX  H03   C03  C01  110.62  3.000
 NFX  H03A  C03  N01  110.15  3.000
 NFX  H03   C03  N01  113.46  3.000
 NFX  C01   C03  N01  104.49  3.000
 NFX  H04A  C04  H04  107.22  3.000
 NFX  H04A  C04  C02  111.10  3.000
 NFX  H04   C04  C02  112.77  3.000
 NFX  H04A  C04  N01  112.83  3.000
 NFX  H04   C04  N01  111.14  3.000
 NFX  C02   C04  N01  101.86  3.000
 NFX  H05A  N05  H05  105.64  3.000
 NFX  H05A  N05  C01  110.32  3.000
 NFX  H05   N05  C01  109.40  3.000
 NFX  H06   C06  C09  117.25  3.000
 NFX  H06   C06  C08  118.29  3.000
 NFX  C09   C06  C08   60.00  3.000
 NFX  H06   C06  N    114.25  3.000
 NFX  C09   C06  N    117.81  3.000
 NFX  C08   C06  N    118.76  3.000
 NFX  H08A  C08  H08  114.48  3.000
 NFX  H08A  C08  C09  117.16  3.000
 NFX  H08   C08  C09  119.62  3.000
 NFX  H08A  C08  C06  117.70  3.000
 NFX  H08   C08  C06  117.07  3.000
 NFX  C09   C08  C06   60.30  3.000
 NFX  H09A  C09  H09  114.53  3.000
 NFX  H09A  C09  C08  119.16  3.000
 NFX  H09   C09  C08  117.49  3.000
 NFX  H09A  C09  C06  116.61  3.000
 NFX  H09   C09  C06  118.61  3.000
 NFX  C08   C09  C06   59.70  3.000
 NFX  C15   C11  C13  117.11  3.000
 NFX  C15   C11  N01  122.30  3.000
 NFX  C13   C11  N01  120.53  3.000
 NFX  C14   C12  C13  118.05  3.000
 NFX  C14   C12  N    117.98  3.000
 NFX  C13   C12  N    123.96  3.000
 NFX  C12   C13  C11  121.80  3.000
 NFX  C12   C13  CL   122.47  3.000
 NFX  C11   C13  CL   115.55  3.000
 NFX  C19   C14  C17  117.26  3.000
 NFX  C19   C14  C12  122.24  3.000
 NFX  C17   C14  C12  120.43  3.000
 NFX  C17   C15  C11  122.76  3.000
 NFX  C17   C15  F    119.11  3.000
 NFX  C11   C15  F    118.07  3.000
 NFX  H16   C16  C18  119.75  3.000
 NFX  H16   C16  N    114.61  3.000
 NFX  C18   C16  N    125.61  3.000
 NFX  H17   C17  C15  120.66  3.000
 NFX  H17   C17  C14  119.85  3.000
 NFX  C15   C17  C14  119.48  3.000
 NFX  C20   C18  C19  125.21  3.000
 NFX  C20   C18  C16  115.76  3.000
 NFX  C19   C18  C16  118.87  3.000
 NFX  C18   C19  C14  114.05  3.000
 NFX  C18   C19  O02  125.59  3.000
 NFX  C14   C19  O02  120.35  3.000
 NFX  C18   C20  O    114.29  3.000
 NFX  C18   C20  O03  123.22  3.000
 NFX  O     C20  O03  122.49  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_14  N    C12  C13  CL      0.00   0.0  0
 NFX  CONST_15  C14  C12  C13  CL    180.00   0.0  0
 NFX  CONST_16  H17  C17  C15  C11   180.00   0.0  0
 NFX  CONST_17  HO   O    C20  C18   180.00   0.0  0
 NFX  Var_01    C01  C02  C04  N01   -38.08  30.0  1
 NFX  Var_02    C09  C08  C06  N     107.32  30.0  1
 NFX  Var_03    C04  N01  C03  C01    -0.35  30.0  1
 NFX  Var_04    C03  N01  C04  C02    24.25  30.0  1
 NFX  Var_05    C13  C11  N01  C03  -118.17  30.0  2
 NFX  Var_06    C12  N    C06  C08    53.43  30.0  1
 NFX  Var_07    C16  C18  C20  O03    -1.62  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
 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
 NFX  plan-2  HO   0.020

