# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 04:40:07 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  48  27  .  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_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  -0.667  -5.8514  -0.2423  -1.9755
 GFN  C02   C  CH1    0  -0.117  -4.8841  -0.4449  -0.8227
 GFN  C03   C  CH2    0  -0.261  -3.5764   0.3086  -1.0643
 GFN  N04   N  NT     0  -0.490  -2.7004   0.1476   0.0837
 GFN  C05   C  CH2    0  -0.290  -3.2937   0.5881   1.3359
 GFN  C06   C  CH2    0  -0.322  -4.6009  -0.1589   1.5567
 GFN  N07   N  NH1    0  -0.579  -5.5189  -0.0687   0.4345
 GFN  C08   C  CR6    0   0.004  -1.3403   0.4620  -0.0758
 GFN  C09   C  CR6    0   0.567  -0.8884   1.7392  -0.4305
 GFN  C10   C  CR16   0  -0.511   0.4311   2.0822  -0.4475
 GFN  C11   C  CR6    0  -0.126   1.3927   1.1182  -0.1345
 GFN  C12   C  CR6    0   0.293   1.0003  -0.1971   0.1434
 GFN  C13   C  CR6    0   0.329  -0.3810  -0.5028   0.2306
 GFN  O14   O  O2     0  -0.479  -0.7275  -1.7011   0.7270
 GFN  C15   C  CH3    0  -0.409  -1.6446  -2.5363   0.0287
 GFN  N16   N  NT     0  -0.538   1.9914  -1.1429   0.3750
 GFN  C17   C  C1     0   0.013   3.2581  -0.7249   0.5704
 GFN  C18   C  C      0  -0.379   3.7138   0.5540   0.4494
 GFN  C19   C  C      0   0.397   2.8075   1.5505  -0.0644
 GFN  O20   O  O      0  -0.458   3.1135   2.6852  -0.4219
 GFN  C21   C  C      0   0.404   5.1704   0.8196   0.7992
 GFN  O22   O  O      0  -0.605   5.8819  -0.1884   0.9977
 GFN  O23   O  OC    -1  -0.588   5.5330   2.0054   0.8839
 GFN  C24   C  CH1    0  -0.102   1.7722  -2.5676   0.2326
 GFN  C25   C  CH2    0  -0.508   2.7507  -3.3482  -0.5883
 GFN  C26   C  CH2    0  -0.485   1.3675  -3.1018  -1.1008
 GFN  F27   F  F      0  -0.311  -1.8061   2.6808  -0.7038
 GFN  H011  H  HCH3   0   0.230  -5.4139  -0.5767  -2.9166
 GFN  H012  H  HCH3   0   0.236  -6.7705  -0.8053  -1.8121
 GFN  H013  H  HCH3   0   0.220  -6.1171   0.8113  -2.0893
 GFN  H021  H  HCH1   0   0.222  -4.6441  -1.5123  -0.7510
 GFN  H032  H  HCH2   0   0.238  -3.0760  -0.0959  -1.9476
 GFN  H031  H  HCH2   0   0.199  -3.8169   1.3618  -1.2740
 GFN  H051  H  HCH2   0   0.243  -2.6028   0.3724   2.1535
 GFN  H052  H  HCH2   0   0.205  -3.4818   1.6736   1.3461
 GFN  H062  H  HCH2   0   0.222  -4.3763  -1.2150   1.7376
 GFN  H061  H  HCH2   0   0.239  -5.0955   0.2218   2.4524
 GFN  H071  H  HNH1   0   0.335  -5.8605   0.8851   0.3607
 GFN  H101  H  HCR6   0   0.276   0.7369   3.0940  -0.6759
 GFN  H151  H  HCH3   0   0.239  -1.3025  -3.5612   0.1688
 GFN  H153  H  HCH3   0   0.241  -2.6515  -2.4368   0.4285
 GFN  H152  H  HCH3   0   0.223  -1.6644  -2.3163  -1.0396
 GFN  H171  H  H      0   0.304   3.9593  -1.5051   0.8299
 GFN  H241  H  HCH1   0   0.284   1.3759  -3.0557   1.1131
 GFN  H252  H  HCH2   0   0.267   3.5647  -2.8241  -1.0722
 GFN  H251  H  HCH2   0   0.269   3.0084  -4.3362  -0.2310
 GFN  H262  H  HCH2   0   0.264   0.6606  -3.9198  -1.1230
 GFN  H261  H  HCH2   0   0.265   1.2595  -2.3925  -1.9122

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    1.518  0.020  1.518
 GFN  N07  C02   single    1.458  0.020  1.458
 GFN  N07  C06   single    1.453  0.020  1.453
 GFN  C02  C03   single    1.529  0.020  1.529
 GFN  C06  C05   single    1.522  0.020  1.522
 GFN  C03  N04   single    1.453  0.020  1.453
 GFN  C15  O14   single    1.424  0.020  1.424
 GFN  C05  N04   single    1.454  0.020  1.454
 GFN  O14  C13   single    1.343  0.020  1.343
 GFN  C25  C24   single    1.497  0.020  1.497
 GFN  C25  C26   single    1.496  0.020  1.496
 GFN  N04  C08   single    1.405  0.020  1.405
 GFN  C24  C26   single    1.492  0.020  1.492
 GFN  C24  N16   single    1.449  0.020  1.449
 GFN  C13  C08   aromatic  1.395  0.020  1.395
 GFN  C13  C12   aromatic  1.417  0.020  1.417
 GFN  C08  C09   aromatic  1.400  0.020  1.400
 GFN  N16  C12   single    1.389  0.020  1.389
 GFN  N16  C17   single    1.348  0.020  1.348
 GFN  C12  C11   aromatic  1.400  0.020  1.400
 GFN  C09  F27   single    1.343  0.020  1.343
 GFN  C09  C10   aromatic  1.363  0.020  1.363
 GFN  C17  C18   double    1.363  0.020  1.363
 GFN  C11  C10   aromatic  1.397  0.020  1.397
 GFN  C11  C19   single    1.481  0.020  1.481
 GFN  C18  C19   single    1.442  0.020  1.442
 GFN  C18  C21   single    1.521  0.020  1.521
 GFN  C19  O20   double    1.228  0.020  1.228
 GFN  O22  C21   deloc     1.250  0.020  1.250
 GFN  C21  O23   deloc     1.243  0.020  1.243
 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  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  107.97  3.000
 GFN  H013  C01  H011  107.66  3.000
 GFN  H012  C01  H011  108.02  3.000
 GFN  H013  C01  C02   111.26  3.000
 GFN  H012  C01  C02   110.76  3.000
 GFN  H011  C01  C02   111.03  3.000
 GFN  H021  C02  N07   106.87  3.000
 GFN  H021  C02  C03   107.63  3.000
 GFN  N07   C02  C03   112.44  3.000
 GFN  H021  C02  C01   108.60  3.000
 GFN  C03   C02  C01   111.05  3.000
 GFN  N07   C02  C01   110.06  3.000
 GFN  H031  C03  H032  107.47  3.000
 GFN  H031  C03  N04   112.86  3.000
 GFN  H032  C03  N04   108.76  3.000
 GFN  H031  C03  C02   108.36  3.000
 GFN  H032  C03  C02   109.69  3.000
 GFN  N04   C03  C02   109.65  3.000
 GFN  C08   N04  C05   115.15  3.000
 GFN  C08   N04  C03   117.97  3.000
 GFN  C05   N04  C03   113.63  3.000
 GFN  H052  C05  H051  107.20  3.000
 GFN  H052  C05  C06   109.62  3.000
 GFN  H051  C05  C06   109.75  3.000
 GFN  H052  C05  N04   112.09  3.000
 GFN  H051  C05  N04   109.08  3.000
 GFN  C06   C05  N04   109.07  3.000
 GFN  H061  C06  H062  107.09  3.000
 GFN  H061  C06  N07   109.01  3.000
 GFN  H062  C06  N07   108.49  3.000
 GFN  H061  C06  C05   109.69  3.000
 GFN  H062  C06  C05   108.74  3.000
 GFN  N07   C06  C05   113.60  3.000
 GFN  H071  N07  C06   109.08  3.000
 GFN  H071  N07  C02   109.03  3.000
 GFN  C06   N07  C02   112.02  3.000
 GFN  C13   C08  C09   117.69  3.000
 GFN  C09   C08  N04   123.04  3.000
 GFN  C13   C08  N04   119.08  3.000
 GFN  F27   C09  C10   118.84  3.000
 GFN  C10   C09  C08   123.01  3.000
 GFN  F27   C09  C08   118.07  3.000
 GFN  H101  C10  C11   119.88  3.000
 GFN  H101  C10  C09   120.77  3.000
 GFN  C11   C10  C09   119.33  3.000
 GFN  C19   C11  C12   122.17  3.000
 GFN  C19   C11  C10   117.82  3.000
 GFN  C12   C11  C10   119.98  3.000
 GFN  N16   C12  C13   122.56  3.000
 GFN  N16   C12  C11   118.20  3.000
 GFN  C13   C12  C11   119.19  3.000
 GFN  O14   C13  C12   117.82  3.000
 GFN  C12   C13  C08   120.51  3.000
 GFN  O14   C13  C08   121.42  3.000
 GFN  C15   O14  C13   120.57  3.000
 GFN  H152  C15  H153  108.94  3.000
 GFN  H152  C15  H151  108.75  3.000
 GFN  H153  C15  H151  109.23  3.000
 GFN  H152  C15  O14   111.94  3.000
 GFN  H153  C15  O14   111.24  3.000
 GFN  H151  C15  O14   106.65  3.000
 GFN  C24   N16  C17   117.48  3.000
 GFN  C17   N16  C12   118.90  3.000
 GFN  C24   N16  C12   123.04  3.000
 GFN  H171  C17  C18   118.80  3.000
 GFN  H171  C17  N16   114.88  3.000
 GFN  C18   C17  N16   126.31  3.000
 GFN  C21   C18  C19   124.27  3.000
 GFN  C21   C18  C17   117.62  3.000
 GFN  C19   C18  C17   118.03  3.000
 GFN  O20   C19  C18   125.84  3.000
 GFN  O20   C19  C11   119.59  3.000
 GFN  C18   C19  C11   114.56  3.000
 GFN  O23   C21  O22   126.35  3.000
 GFN  O23   C21  C18   117.49  3.000
 GFN  O22   C21  C18   116.15  3.000
 GFN  H241  C24  C26   117.80  3.000
 GFN  H241  C24  C25   116.78  3.000
 GFN  C26   C24  C25    60.04  3.000
 GFN  H241  C24  N16   114.78  3.000
 GFN  C26   C24  N16   118.74  3.000
 GFN  C25   C24  N16   117.90  3.000
 GFN  H251  C25  H252  114.26  3.000
 GFN  H251  C25  C26   118.95  3.000
 GFN  H252  C25  C26   117.55  3.000
 GFN  H251  C25  C24   116.80  3.000
 GFN  H252  C25  C24   118.96  3.000
 GFN  C26   C25  C24    59.83  3.000
 GFN  H261  C26  H262  114.51  3.000
 GFN  H261  C26  C25   117.19  3.000
 GFN  H262  C26  C25   119.14  3.000
 GFN  H261  C26  C24   117.52  3.000
 GFN  H262  C26  C24   117.80  3.000
 GFN  C25   C26  C24    60.13  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  Var_01    C05   C06  N07  C02    52.03  30.0  1
 GFN  Var_02    C05   N04  C03  C02   -56.94  30.0  1
 GFN  Var_03    C06   C05  N04  C03    56.35  30.0  1
 GFN  Var_04    C13   C08  N04  C03  -124.49  30.0  2
 GFN  Var_05    N07   C06  C05  N04   -53.15  30.0  1
 GFN  Var_06    C25   C24  N16  C12   129.85  30.0  2
 GFN  Var_07    C26   C25  C24  N16  -108.84  30.0  1
 GFN  Var_08    O22   C21  C18  C17     9.31  30.0  2
 GFN  Var_09    H151  C15  O14  C13   143.19  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

