# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 12:44:01 2022
#   Inital geometry file: a 115 line input string
#   Ligand name: (3S)-9-fluoro-3-methyl-10-(4-methylpiperazin-1-yl)-7-oxo-2,3-dihydro-7H-[1,4]oxazino[2,3,4-ij]quinoline-6-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1COc2c(N3CCN(C)CC3)c(F)cc4C(=O)C(=CN1c24)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
 LFX  LFX  '(3S)-9-fluoro-3-methyl-10-(4-methylpiperazin-1-yl)-7-oxo-2,3-dihydro-7H-[1,4]oxazino[2,3,4-ij]quinoline-6-carboxylic acid'  ligand  45  26  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_LFX
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
 LFX  C     C  C      0   0.406   5.2821  -0.4243   0.0729
 LFX  N     N  NT     0  -0.403  -5.5408   0.2247   0.0257
 LFX  O     O  O      0  -0.605   5.9255   0.6421   0.1810
 LFX  C01   C  CH2    0  -0.295  -3.4438  -0.2391  -1.2395
 LFX  N01   N  NT     0  -0.481  -2.6832   0.0399  -0.0305
 LFX  O01   O  O2     0  -0.449  -0.7558   1.9218   0.2459
 LFX  C02   C  CH2    0  -0.295  -3.3962  -0.2556   1.2033
 LFX  N02   N  NR6    0  -0.535   1.9627   1.3003   0.1579
 LFX  C03   C  CH1    0  -0.169   1.5305   2.6981   0.1411
 LFX  O03   O  OC    -1  -0.583   5.7640  -1.5661  -0.0060
 LFX  C04   C  CR6    0  -0.026  -1.3293  -0.3361  -0.0460
 LFX  C05   C  CR66   0   0.339   1.0109   0.3110   0.0649
 LFX  C06   C  CR6    0   0.324  -0.3584   0.6472   0.0925
 LFX  C07   C  CH2    0  -0.323  -4.7725   0.5069  -1.1736
 LFX  C08   C  CH2    0  -0.324  -4.7303   0.4835   1.2020
 LFX  C09   C  CH2    0  -0.214   0.2029   2.7636   0.8683
 LFX  C10   C  CR66   0  -0.124   1.4111  -1.0191  -0.0661
 LFX  C11   C  CR6    0   0.575  -0.8833  -1.6596  -0.1760
 LFX  C12   C  CR16   0   0.020   3.2636   0.9817   0.1427
 LFX  C13   C  CR16   0  -0.525   0.4369  -2.0151  -0.1849
 LFX  C14   C  CH3    0  -0.646   1.4657   3.2389  -1.2792
 LFX  C15   C  CR6    0   0.401   2.8439  -1.3939  -0.0869
 LFX  C17   C  CR6    0  -0.401   3.7658  -0.2859   0.0441
 LFX  H01   H  HCH2   0   0.243  -2.8785   0.1202  -2.1019
 LFX  H01A  H  HCH2   0   0.206  -3.6246  -1.3110  -1.3971
 LFX  H02   H  HCH2   0   0.207  -3.5592  -1.3336   1.3494
 LFX  H02A  H  HCH2   0   0.244  -2.7990   0.0940   2.0479
 LFX  H03   H  HCH1   0   0.293   2.2551   3.2702   0.7232
 LFX  H07   H  HCH2   0   0.236  -5.3726   0.2623  -2.0531
 LFX  H07A  H  HCH2   0   0.229  -4.5706   1.5824  -1.2066
 LFX  H08   H  HCH2   0   0.229  -4.5300   1.5587   1.2515
 LFX  H08A  H  HCH2   0   0.236  -5.2967   0.2168   2.0972
 LFX  H09   H  HCH2   0   0.270  -0.1980   3.7747   0.8379
 LFX  H09A  H  HCH2   0   0.261   0.3320   2.4728   1.9161
 LFX  H12   H  HCR6   0   0.300   3.9440   1.8196   0.2160
 LFX  H13   H  HCR6   0   0.274   0.7281  -3.0520  -0.2817
 LFX  H14   H  HCH3   0   0.251   2.4437   3.1856  -1.7568
 LFX  H14A  H  HCH3   0   0.241   0.7570   2.6843  -1.8944
 LFX  H14B  H  HCH3   0   0.248   1.1581   4.2844  -1.2637
 LFX  H16   H  HCH3   0   0.199  -5.4841  -1.9399   0.0108
 LFX  H16A  H  HCH3   0   0.231  -6.7959  -1.1816   0.9136
 LFX  H16B  H  HCH3   0   0.231  -6.8199  -1.1703  -0.8466
 LFX  O02   O  O      0  -0.459   3.1498  -2.5779  -0.2101
 LFX  F     F  F      0  -0.311  -1.8127  -2.6237  -0.2779
 LFX  C16   C  CH3    0  -0.526  -6.1693  -1.0814   0.0253

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
 LFX  C17   C     single    1.523  0.020  1.523
 LFX  C     O03   deloc     1.242  0.020  1.242
 LFX  C     O     deloc     1.250  0.020  1.250
 LFX  F     C11   single    1.343  0.020  1.343
 LFX  C16   N     single    1.450  0.020  1.450
 LFX  C08   N     single    1.452  0.020  1.452
 LFX  N     C07   single    1.452  0.020  1.452
 LFX  H01   C01   single    0.970  0.020  1.090
 LFX  C07   C01   single    1.525  0.020  1.525
 LFX  C01   H01A  single    0.970  0.020  1.090
 LFX  C01   N01   single    1.455  0.020  1.455
 LFX  C02   N01   single    1.455  0.020  1.455
 LFX  N01   C04   single    1.405  0.020  1.405
 LFX  O01   C06   single    1.344  0.020  1.344
 LFX  O01   C09   single    1.420  0.020  1.420
 LFX  C08   C02   single    1.525  0.020  1.525
 LFX  H02A  C02   single    0.970  0.020  1.090
 LFX  C02   H02   single    0.970  0.020  1.090
 LFX  C05   N02   single    1.376  0.020  1.376
 LFX  C03   N02   single    1.463  0.020  1.463
 LFX  N02   C12   single    1.339  0.020  1.339
 LFX  C15   O02   double    1.229  0.020  1.229
 LFX  C09   C03   single    1.515  0.020  1.515
 LFX  C03   C14   single    1.521  0.020  1.521
 LFX  C03   H03   single    0.970  0.020  1.090
 LFX  C04   C11   aromatic  1.403  0.020  1.403
 LFX  C04   C06   aromatic  1.389  0.020  1.389
 LFX  C06   C05   aromatic  1.410  0.020  1.410
 LFX  C05   C10   aromatic  1.395  0.020  1.395
 LFX  H07A  C07   single    0.970  0.020  1.090
 LFX  C07   H07   single    0.970  0.020  1.090
 LFX  H08   C08   single    0.970  0.020  1.090
 LFX  H08A  C08   single    0.970  0.020  1.090
 LFX  H09A  C09   single    0.970  0.020  1.090
 LFX  H09   C09   single    0.970  0.020  1.090
 LFX  C13   C10   aromatic  1.398  0.020  1.398
 LFX  C10   C15   single    1.481  0.020  1.481
 LFX  C11   C13   aromatic  1.367  0.020  1.367
 LFX  C12   C17   double    1.367  0.020  1.367
 LFX  C12   H12   single    0.930  0.020  1.080
 LFX  C13   H13   single    0.930  0.020  1.080
 LFX  H14   C14   single    0.970  0.020  1.090
 LFX  C14   H14A  single    0.970  0.020  1.090
 LFX  C14   H14B  single    0.970  0.020  1.090
 LFX  C15   C17   single    1.447  0.020  1.447
 LFX  H16A  C16   single    0.970  0.020  1.090
 LFX  H16B  C16   single    0.970  0.020  1.090
 LFX  C16   H16   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
 LFX  C17   C    O03   117.95  3.000
 LFX  O03   C    O     126.16  3.000
 LFX  C17   C    O     115.89  3.000
 LFX  C16   N    C08   113.76  3.000
 LFX  C08   N    C07   109.83  3.000
 LFX  C16   N    C07   113.85  3.000
 LFX  H01A  C01  H01   107.04  3.000
 LFX  H01A  C01  C07   109.88  3.000
 LFX  H01   C01  C07   108.92  3.000
 LFX  H01A  C01  N01   113.10  3.000
 LFX  C07   C01  N01   109.00  3.000
 LFX  H01   C01  N01   108.81  3.000
 LFX  C04   N01  C02   115.28  3.000
 LFX  C04   N01  C01   116.30  3.000
 LFX  C02   N01  C01   114.16  3.000
 LFX  C09   O01  C06   114.38  3.000
 LFX  H02A  C02  H02   106.99  3.000
 LFX  H02   C02  C08   110.21  3.000
 LFX  H02A  C02  C08   108.90  3.000
 LFX  H02   C02  N01   112.59  3.000
 LFX  H02A  C02  N01   108.83  3.000
 LFX  C08   C02  N01   109.23  3.000
 LFX  C12   N02  C05   120.01  3.000
 LFX  C12   N02  C03   120.92  3.000
 LFX  C05   N02  C03   118.80  3.000
 LFX  H03   C03  C14   109.87  3.000
 LFX  H03   C03  C09   107.65  3.000
 LFX  C14   C03  C09   113.29  3.000
 LFX  H03   C03  N02   107.37  3.000
 LFX  C14   C03  N02   111.28  3.000
 LFX  C09   C03  N02   107.13  3.000
 LFX  C11   C04  C06   117.06  3.000
 LFX  C06   C04  N01   118.89  3.000
 LFX  C11   C04  N01   124.04  3.000
 LFX  C10   C05  C06   120.51  3.000
 LFX  C10   C05  N02   119.56  3.000
 LFX  C06   C05  N02   119.93  3.000
 LFX  C05   C06  C04   120.54  3.000
 LFX  C05   C06  O01   121.02  3.000
 LFX  C04   C06  O01   118.44  3.000
 LFX  H07A  C07  H07   107.27  3.000
 LFX  H07   C07  C01   109.53  3.000
 LFX  H07A  C07  C01   108.57  3.000
 LFX  H07   C07  N     109.32  3.000
 LFX  H07A  C07  N     108.26  3.000
 LFX  C01   C07  N     113.68  3.000
 LFX  H08A  C08  H08   107.32  3.000
 LFX  H08A  C08  C02   109.54  3.000
 LFX  H08   C08  C02   108.41  3.000
 LFX  H08A  C08  N     109.33  3.000
 LFX  H08   C08  N     108.29  3.000
 LFX  C02   C08  N     113.75  3.000
 LFX  H09A  C09  H09   108.48  3.000
 LFX  H09   C09  C03   110.46  3.000
 LFX  H09A  C09  C03   110.15  3.000
 LFX  H09   C09  O01   106.85  3.000
 LFX  H09A  C09  O01   109.98  3.000
 LFX  C03   C09  O01   110.84  3.000
 LFX  C15   C10  C13   119.51  3.000
 LFX  C15   C10  C05   121.34  3.000
 LFX  C13   C10  C05   119.15  3.000
 LFX  C13   C11  C04   123.57  3.000
 LFX  C13   C11  F     118.76  3.000
 LFX  C04   C11  F     117.66  3.000
 LFX  H12   C12  C17   119.47  3.000
 LFX  H12   C12  N02   115.21  3.000
 LFX  C17   C12  N02   125.32  3.000
 LFX  H13   C13  C11   120.66  3.000
 LFX  H13   C13  C10   120.19  3.000
 LFX  C11   C13  C10   119.15  3.000
 LFX  H14B  C14  H14A  108.20  3.000
 LFX  H14B  C14  H14   107.85  3.000
 LFX  H14A  C14  H14   108.14  3.000
 LFX  H14B  C14  C03   109.86  3.000
 LFX  H14A  C14  C03   111.95  3.000
 LFX  H14   C14  C03   110.71  3.000
 LFX  C17   C15  C10   114.91  3.000
 LFX  C17   C15  O02   126.01  3.000
 LFX  C10   C15  O02   119.07  3.000
 LFX  C15   C17  C12   118.84  3.000
 LFX  C15   C17  C     124.50  3.000
 LFX  C12   C17  C     116.66  3.000
 LFX  H16B  C16  H16A  107.48  3.000
 LFX  H16B  C16  H16   107.32  3.000
 LFX  H16A  C16  H16   107.28  3.000
 LFX  H16   C16  N     115.70  3.000
 LFX  H16B  C16  N     109.40  3.000
 LFX  H16A  C16  N     109.35  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
 LFX  CONST_01  C10   C13  C11  C04     0.00   0.0  0
 LFX  CONST_02  C10   C05  C06  C04     0.00   0.0  0
 LFX  CONST_03  C11   C04  C06  C05     0.00   0.0  0
 LFX  CONST_04  C11   C13  C10  C05     0.00   0.0  0
 LFX  CONST_05  C13   C11  C04  C06     0.00   0.0  0
 LFX  CONST_06  C13   C10  C05  C06     0.00   0.0  0
 LFX  CONST_07  C13   C11  C04  N01   180.00   0.0  0
 LFX  CONST_08  O01   C06  C04  N01     0.00   0.0  0
 LFX  CONST_09  C05   C06  C04  N01   180.00   0.0  0
 LFX  CONST_10  N01   C04  C11  F       0.00   0.0  0
 LFX  CONST_11  C06   C04  C11  F     180.00   0.0  0
 LFX  CONST_12  C10   C13  C11  F     180.00   0.0  0
 LFX  CONST_13  H13   C13  C11  C04   180.00   0.0  0
 LFX  Var_01    N01   C02  C08  N      53.85  30.0  1
 LFX  Var_02    N01   C01  C07  N     -54.47  30.0  1
 LFX  Var_03    C08   N    C07  C01    54.49  30.0  1
 LFX  Var_04    C08   C02  N01  C01   -54.54  30.0  1
 LFX  Var_05    C11   C04  N01  C01   -62.79  30.0  2
 LFX  Var_06    C07   C01  N01  C02    54.79  30.0  1
 LFX  Var_07    C07   N    C08  C02   -54.13  30.0  1
 LFX  Var_08    H09A  C09  O01  C06   -68.15  30.0  1
 LFX  Var_09    C12   C17  C    O      -0.18  30.0  2
 LFX  Var_10    H16A  C16  N    C07  -175.02  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
 LFX  chir_01  C03  N02  C09  C14  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
 LFX  plan-1  C    0.020
 LFX  plan-1  N01  0.020
 LFX  plan-1  O01  0.020
 LFX  plan-1  N02  0.020
 LFX  plan-1  C03  0.020
 LFX  plan-1  C04  0.020
 LFX  plan-1  C05  0.020
 LFX  plan-1  C06  0.020
 LFX  plan-1  C10  0.020
 LFX  plan-1  C11  0.020
 LFX  plan-1  C12  0.020
 LFX  plan-1  C13  0.020
 LFX  plan-1  C15  0.020
 LFX  plan-1  C17  0.020
 LFX  plan-1  H12  0.020
 LFX  plan-1  H13  0.020
 LFX  plan-1  O02  0.020
 LFX  plan-1  F    0.020
 LFX  plan-2  C    0.020
 LFX  plan-2  O    0.020
 LFX  plan-2  O03  0.020
 LFX  plan-2  C17  0.020

