# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 08:10:40 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: 1-cyclopropyl-6-fluoro-8-methoxy-7-[(3S)-3-methylpiperazin-1-yl]-4-oxo-1,4-dihydroquinoline-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1c(N2CCN[C@@H](C)C2)c(F)cc3C(=O)C(=CN(C4CC4)c13)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
 GFN  GFN  '1-cyclopropyl-6-fluoro-8-methoxy-7-[(3S)-3-methylpiperazin-1-yl]-4-oxo-1,4-dihydroquinoline-3-carboxylic acid'  ligand  49  27  .  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_GFN
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
 GFN  C01   C  CH3   0  -0.668  -6.0522   0.3635  -1.7698
 GFN  C02   C  CH1   0  -0.119  -4.9379  -0.1859  -0.8965
 GFN  C03   C  CH2   0  -0.268  -3.7411   0.7692  -0.8866
 GFN  N04   N  NT    0  -0.501  -2.7179   0.2571   0.0061
 GFN  C05   C  CH2   0  -0.302  -3.1901   0.0472   1.3667
 GFN  C06   C  CH2   0  -0.321  -4.3875  -0.8912   1.3458
 GFN  N07   N  NH1   0  -0.577  -5.4414  -0.4596   0.4432
 GFN  C08   C  CR6   0   0.075  -1.3755   0.5508  -0.1839
 GFN  C09   C  CR6   0   0.550  -0.9102   1.8047  -0.5952
 GFN  C10   C  CR16  0  -0.505   0.4170   2.0895  -0.7241
 GFN  C11   C  CR66  0  -0.136   1.3705   1.1304  -0.3890
 GFN  C12   C  CR66  0   0.323   0.9680  -0.1558   0.0116
 GFN  C13   C  CR6   0   0.301  -0.4139  -0.4420   0.0733
 GFN  O14   O  O2    0  -0.480  -0.8413  -1.6668   0.4503
 GFN  C15   C  CH3   0  -0.432  -1.4883  -2.4348  -0.5637
 GFN  N16   N  NR6   0  -0.556   1.9702  -1.0720   0.3645
 GFN  C17   C  CR16  0   0.056   3.2321  -0.6498   0.4605
 GFN  C18   C  CR6   0  -0.349   3.6994   0.5922   0.1200
 GFN  C19   C  CR6   0   0.435   2.7835   1.5569  -0.4344
 GFN  O20   O  O     0  -0.442   3.0902   2.6523  -0.8892
 GFN  C21   C  C     0   0.530   5.1409   0.8086   0.3249
 GFN  O22   O  O     0  -0.461   5.8937  -0.0465   0.7424
 GFN  O23   O  OH1   0  -0.586   5.5560   2.0298   0.0248
 GFN  C24   C  CH1   0  -0.089   1.7165  -2.4677   0.6868
 GFN  C25   C  CH2   0  -0.526   2.7562  -3.4923   0.3573
 GFN  C26   C  CH2   0  -0.478   1.4683  -3.4559  -0.3998
 GFN  F27   F  F     0  -0.308  -1.7990   2.7808  -0.8279
 GFN  H011  H  HCH3  0   0.232  -5.7033   0.5281  -2.7897
 GFN  H012  H  HCH3  0   0.238  -6.8927  -0.3293  -1.8084
 GFN  H013  H  HCH3  0   0.221  -6.4187   1.3188  -1.3858
 GFN  H021  H  HCH1  0   0.226  -4.6032  -1.1423  -1.3173
 GFN  H032  H  HCH2  0   0.245  -3.3344   0.8521  -1.8961
 GFN  H031  H  HCH2  0   0.204  -4.1024   1.7637  -0.5841
 GFN  H051  H  HCH2  0   0.255  -2.3938  -0.3709   1.9803
 GFN  H052  H  HCH2  0   0.219  -3.4822   1.0069   1.8216
 GFN  H062  H  HCH2  0   0.226  -4.0531  -1.8868   1.0383
 GFN  H061  H  HCH2  0   0.240  -4.7994  -0.9863   2.3523
 GFN  H071  H  HNH1  0   0.335  -5.8648   0.3868   0.8119
 GFN  H101  H  HCR6  0   0.284   0.7352   3.0785  -1.0241
 GFN  H151  H  HCH3  0   0.244  -1.6739  -3.4184  -0.1391
 GFN  H153  H  HCH3  0   0.251  -2.4363  -1.9889  -0.8574
 GFN  H152  H  HCH3  0   0.230  -0.8546  -2.5382  -1.4452
 GFN  H171  H  HCR6  0   0.325   3.9302  -1.3815   0.8376
 GFN  H2    H  HOH1  0   0.480   6.5085   2.0862   0.1950
 GFN  H241  H  HCH1  0   0.296   1.1894  -2.6036   1.6211
 GFN  H252  H  HCH2  0   0.270   3.6505  -3.2057  -0.1803
 GFN  H251  H  HCH2  0   0.276   2.9133  -4.2696   1.0931
 GFN  H262  H  HCH2  0   0.268   0.7278  -4.2239  -0.2245
 GFN  H261  H  HCH2  0   0.268   1.5189  -3.0997  -1.4211

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
 GFN  C01  C02   single    1.519  0.020  1.519
 GFN  N07  C02   single    1.457  0.020  1.457
 GFN  N07  C06   single    1.453  0.020  1.453
 GFN  C02  C03   single    1.531  0.020  1.531
 GFN  C06  C05   single    1.521  0.020  1.521
 GFN  C03  N04   single    1.451  0.020  1.451
 GFN  C15  O14   single    1.427  0.020  1.427
 GFN  C05  N04   single    1.455  0.020  1.455
 GFN  O14  C13   single    1.351  0.020  1.351
 GFN  C25  C24   single    1.496  0.020  1.496
 GFN  C25  C26   single    1.494  0.020  1.494
 GFN  N04  C08   single    1.387  0.020  1.387
 GFN  C24  C26   single    1.490  0.020  1.490
 GFN  C24  N16   single    1.455  0.020  1.455
 GFN  C13  C08   aromatic  1.406  0.020  1.406
 GFN  C13  C12   aromatic  1.413  0.020  1.413
 GFN  C08  C09   aromatic  1.399  0.020  1.399
 GFN  N16  C12   single    1.403  0.020  1.403
 GFN  N16  C17   single    1.334  0.020  1.334
 GFN  C12  C11   aromatic  1.406  0.020  1.406
 GFN  C09  F27   single    1.341  0.020  1.341
 GFN  C09  C10   aromatic  1.363  0.020  1.363
 GFN  C17  C18   double    1.370  0.020  1.370
 GFN  C11  C10   aromatic  1.393  0.020  1.393
 GFN  C11  C19   single    1.477  0.020  1.477
 GFN  C18  C19   single    1.441  0.020  1.441
 GFN  C18  C21   single    1.472  0.020  1.472
 GFN  C19  O20   double    1.225  0.020  1.225
 GFN  O22  C21   double    1.213  0.020  1.213
 GFN  C21  O23   single    1.324  0.020  1.324
 GFN  C01  H011  single    0.970  0.020  1.090
 GFN  C01  H012  single    0.970  0.020  1.090
 GFN  C01  H013  single    0.970  0.020  1.090
 GFN  C02  H021  single    0.970  0.020  1.090
 GFN  C03  H032  single    0.970  0.020  1.090
 GFN  C03  H031  single    0.970  0.020  1.090
 GFN  C05  H051  single    0.970  0.020  1.090
 GFN  C05  H052  single    0.970  0.020  1.090
 GFN  C06  H062  single    0.970  0.020  1.090
 GFN  C06  H061  single    0.970  0.020  1.090
 GFN  N07  H071  single    0.890  0.020  1.040
 GFN  C10  H101  single    0.930  0.020  1.080
 GFN  C15  H151  single    0.970  0.020  1.090
 GFN  C15  H153  single    0.970  0.020  1.090
 GFN  C15  H152  single    0.970  0.020  1.090
 GFN  C17  H171  single    0.930  0.020  1.080
 GFN  O23  H2    single    0.850  0.020  0.980
 GFN  C24  H241  single    0.970  0.020  1.090
 GFN  C25  H252  single    0.970  0.020  1.090
 GFN  C25  H251  single    0.970  0.020  1.090
 GFN  C26  H262  single    0.970  0.020  1.090
 GFN  C26  H261  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
 GFN  H013  C01  H012  108.03  3.000
 GFN  H013  C01  H011  107.69  3.000
 GFN  H012  C01  H011  108.04  3.000
 GFN  H013  C01  C02   111.12  3.000
 GFN  H012  C01  C02   110.87  3.000
 GFN  H011  C01  C02   110.95  3.000
 GFN  H021  C02  N07   107.11  3.000
 GFN  H021  C02  C03   107.92  3.000
 GFN  N07   C02  C03   112.42  3.000
 GFN  H021  C02  C01   108.58  3.000
 GFN  C03   C02  C01   110.59  3.000
 GFN  N07   C02  C01   110.06  3.000
 GFN  H031  C03  H032  107.93  3.000
 GFN  H031  C03  N04   112.41  3.000
 GFN  H032  C03  N04   109.45  3.000
 GFN  H031  C03  C02   107.99  3.000
 GFN  H032  C03  C02   109.43  3.000
 GFN  N04   C03  C02   109.57  3.000
 GFN  C08   N04  C05   118.20  3.000
 GFN  C08   N04  C03   121.56  3.000
 GFN  C05   N04  C03   113.40  3.000
 GFN  H052  C05  H051  107.21  3.000
 GFN  H052  C05  C06   109.53  3.000
 GFN  H051  C05  C06   110.27  3.000
 GFN  H052  C05  N04   110.27  3.000
 GFN  H051  C05  N04   110.18  3.000
 GFN  C06   C05  N04   109.36  3.000
 GFN  H061  C06  H062  107.17  3.000
 GFN  H061  C06  N07   108.96  3.000
 GFN  H062  C06  N07   108.49  3.000
 GFN  H061  C06  C05   109.76  3.000
 GFN  H062  C06  C05   108.94  3.000
 GFN  N07   C06  C05   113.34  3.000
 GFN  H071  N07  C06   108.92  3.000
 GFN  H071  N07  C02   108.74  3.000
 GFN  C06   N07  C02   112.10  3.000
 GFN  C13   C08  C09   117.33  3.000
 GFN  C09   C08  N04   123.49  3.000
 GFN  C13   C08  N04   119.17  3.000
 GFN  F27   C09  C10   118.48  3.000
 GFN  C10   C09  C08   122.59  3.000
 GFN  F27   C09  C08   118.89  3.000
 GFN  H101  C10  C11   119.66  3.000
 GFN  H101  C10  C09   120.24  3.000
 GFN  C11   C10  C09   119.98  3.000
 GFN  C19   C11  C12   123.16  3.000
 GFN  C19   C11  C10   116.65  3.000
 GFN  C12   C11  C10   120.15  3.000
 GFN  N16   C12  C13   123.75  3.000
 GFN  N16   C12  C11   117.68  3.000
 GFN  C13   C12  C11   118.55  3.000
 GFN  O14   C13  C12   120.36  3.000
 GFN  C12   C13  C08   121.20  3.000
 GFN  O14   C13  C08   118.36  3.000
 GFN  C15   O14  C13   115.66  3.000
 GFN  H152  C15  H153  109.08  3.000
 GFN  H152  C15  H151  109.21  3.000
 GFN  H153  C15  H151  109.11  3.000
 GFN  H152  C15  O14   111.22  3.000
 GFN  H153  C15  O14   111.49  3.000
 GFN  H151  C15  O14   106.67  3.000
 GFN  C24   N16  C17   116.91  3.000
 GFN  C17   N16  C12   119.15  3.000
 GFN  C24   N16  C12   123.90  3.000
 GFN  H171  C17  C18   118.74  3.000
 GFN  H171  C17  N16   114.99  3.000
 GFN  C18   C17  N16   126.27  3.000
 GFN  C21   C18  C19   125.27  3.000
 GFN  C21   C18  C17   115.64  3.000
 GFN  C19   C18  C17   119.06  3.000
 GFN  O20   C19  C18   125.60  3.000
 GFN  O20   C19  C11   120.62  3.000
 GFN  C18   C19  C11   113.76  3.000
 GFN  O23   C21  O22   122.23  3.000
 GFN  O23   C21  C18   114.27  3.000
 GFN  O22   C21  C18   123.49  3.000
 GFN  H2    O23  C21   108.78  3.000
 GFN  H241  C24  C26   117.75  3.000
 GFN  H241  C24  C25   116.29  3.000
 GFN  C26   C24  C25    60.06  3.000
 GFN  H241  C24  N16   113.40  3.000
 GFN  C26   C24  N16   120.26  3.000
 GFN  C25   C24  N16   119.14  3.000
 GFN  H251  C25  H252  114.10  3.000
 GFN  H251  C25  C26   119.16  3.000
 GFN  H252  C25  C26   117.01  3.000
 GFN  H251  C25  C24   116.30  3.000
 GFN  H252  C25  C24   120.15  3.000
 GFN  C26   C25  C24    59.74  3.000
 GFN  H261  C26  H262  114.75  3.000
 GFN  H261  C26  C25   116.46  3.000
 GFN  H262  C26  C25   119.39  3.000
 GFN  H261  C26  C24   117.52  3.000
 GFN  H262  C26  C24   117.84  3.000
 GFN  C25   C26  C24    60.20  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
 GFN  CONST_01  C11   C12  C13  C08     0.00   0.0  0
 GFN  CONST_02  C11   C10  C09  C08     0.00   0.0  0
 GFN  CONST_03  C12   C13  C08  C09     0.00   0.0  0
 GFN  CONST_04  C12   C11  C10  C09     0.00   0.0  0
 GFN  CONST_05  C13   C08  C09  C10     0.00   0.0  0
 GFN  CONST_06  C13   C12  C11  C10     0.00   0.0  0
 GFN  CONST_07  C12   C13  C08  N04   180.00   0.0  0
 GFN  CONST_08  C10   C09  C08  N04   180.00   0.0  0
 GFN  CONST_09  O14   C13  C08  N04     0.00   0.0  0
 GFN  CONST_10  F27   C09  C08  N04     0.00   0.0  0
 GFN  CONST_11  O14   C13  C08  C09   180.00   0.0  0
 GFN  CONST_12  O14   C13  C12  C11   180.00   0.0  0
 GFN  CONST_13  F27   C09  C10  C11   180.00   0.0  0
 GFN  CONST_14  F27   C09  C08  C13   180.00   0.0  0
 GFN  CONST_15  N16   C12  C13  O14     0.00   0.0  0
 GFN  CONST_16  H101  C10  C09  C08   180.00   0.0  0
 GFN  CONST_17  H2    O23  C21  C18   180.00   0.0  0
 GFN  Var_01    C05   C06  N07  C02    51.95  30.0  1
 GFN  Var_02    C05   N04  C03  C02   -57.03  30.0  1
 GFN  Var_03    C06   C05  N04  C03    56.54  30.0  1
 GFN  Var_04    C13   C08  N04  C03  -142.32  30.0  2
 GFN  Var_05    N07   C06  C05  N04   -53.15  30.0  1
 GFN  Var_06    C25   C24  N16  C12   148.25  30.0  1
 GFN  Var_07    C26   C25  C24  N16  -110.16  30.0  1
 GFN  Var_08    O22   C21  C18  C17     1.35  30.0  2
 GFN  Var_09    H151  C15  O14  C13   174.14  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
 GFN  chir_01  C02  C01  N07  C03  positiv
 GFN  chir_02  C24  C25  C26  N16  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
 GFN  plan-1  N04   0.020
 GFN  plan-1  C08   0.020
 GFN  plan-1  C09   0.020
 GFN  plan-1  C10   0.020
 GFN  plan-1  C11   0.020
 GFN  plan-1  C12   0.020
 GFN  plan-1  C13   0.020
 GFN  plan-1  O14   0.020
 GFN  plan-1  N16   0.020
 GFN  plan-1  C17   0.020
 GFN  plan-1  C18   0.020
 GFN  plan-1  C19   0.020
 GFN  plan-1  O20   0.020
 GFN  plan-1  C21   0.020
 GFN  plan-1  C24   0.020
 GFN  plan-1  F27   0.020
 GFN  plan-1  H101  0.020
 GFN  plan-1  H171  0.020
 GFN  plan-2  C18   0.020
 GFN  plan-2  C21   0.020
 GFN  plan-2  O22   0.020
 GFN  plan-2  O23   0.020
 GFN  plan-2  H2    0.020

