# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 17:44:03 2022
#   Inital geometry file: a 129 line input string
#   Ligand name: 1-cyclopropyl-6-fluoro-8-methoxy-7-[(4aS,7aS)-octahydro-6H-pyrrolo[3,4-b]pyridin-6-yl]-4-oxo-1,4-dihydroquinoline-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1c(N2C[C@@H]3CCCN[C@@H]3C2)c(F)cc4C(=O)C(=CN(C5CC5)c14)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
 MFX  MFX  '1-cyclopropyl-6-fluoro-8-methoxy-7-[(4aS,7aS)-octahydro-6H-pyrrolo[3,4-b]pyridin-6-yl]-4-oxo-1,4-dihydroquinoline-3-carboxylic acid'  ligand  52  29  .  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_MFX
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
 MFX  F     F  F      0  -0.315   0.9966  -2.8564  -1.7031
 MFX  O02   O  O      0  -0.461  -3.8487  -2.3044  -1.1996
 MFX  O03   O  OC    -1  -0.584  -6.1412  -1.6998   0.3616
 MFX  O     O  O      0  -0.607  -6.1521   0.3645   1.1861
 MFX  N01   N  NT     0  -0.515   2.2364  -0.7321  -0.4072
 MFX  N02   N  NH1    0  -0.578   4.6889   0.7914  -1.0590
 MFX  N     N  NR6    0  -0.550  -2.2317   1.0409   0.4754
 MFX  C01   C  CH1    0  -0.277   4.3199  -0.9103   0.6509
 MFX  C02   C  CH1    0  -0.114   4.5222  -0.6322  -0.8407
 MFX  C03   C  CH2    0  -0.231   2.8706  -0.4830   0.8799
 MFX  C04   C  CH2    0  -0.260   3.2057  -1.1198  -1.4222
 MFX  C05   C  CH2    0  -0.438   5.3450  -0.2238   1.5469
 MFX  C06   C  CH1    0  -0.089  -1.8511   2.4015   0.7994
 MFX  C07   C  CH2    0  -0.432   5.5849   1.2296   1.1516
 MFX  C08   C  CH2    0  -0.481  -1.5597   3.3649  -0.3011
 MFX  C09   C  CH2    0  -0.518  -2.8206   3.5002   0.4901
 MFX  C10   C  CH2    0  -0.288   5.8278   1.3383  -0.3442
 MFX  C11   C  CR6    0   0.116   0.8725  -0.7861  -0.5684
 MFX  C12   C  CR66   0   0.308  -1.3690   0.0955  -0.0748
 MFX  C13   C  CR6    0   0.269   0.0389   0.2253  -0.0617
 MFX  C14   C  CR66   0  -0.147  -1.9429  -1.0573  -0.6359
 MFX  C15   C  CR6    0   0.518   0.2353  -1.8739  -1.1902
 MFX  C16   C  CR16   0   0.011  -3.5253   0.7057   0.6630
 MFX  C17   C  CR16   0  -0.507  -1.1175  -2.0132  -1.2335
 MFX  C18   C  CR6    0  -0.378  -4.1465  -0.4282   0.2361
 MFX  C19   C  CR6    0   0.394  -3.3915  -1.3425  -0.5853
 MFX  C20   C  C      0   0.399  -5.6074  -0.6081   0.6187
 MFX  C     C  CH3    0  -0.453   1.3677   2.1519  -0.3559
 MFX  H01   H  HCH1   0   0.246   4.3912  -1.9926   0.7962
 MFX  H02   H  HCH1   0   0.222   5.3652  -1.2202  -1.2366
 MFX  H03   H  HCH2   0   0.224   2.8229   0.5667   1.1806
 MFX  H03A  H  HCH2   0   0.230   2.3979  -1.0680   1.6741
 MFX  H04   H  HCH2   0   0.223   3.2710  -2.2008  -1.5743
 MFX  H04A  H  HCH2   0   0.234   2.9747  -0.6596  -2.3870
 MFX  H05   H  HCH2   0   0.233   5.0355  -0.2945   2.5932
 MFX  H05A  H  HCH2   0   0.224   6.2891  -0.7725   1.4730
 MFX  H06   H  HCH1   0   0.282  -1.2845   2.5025   1.7154
 MFX  H07   H  HCH2   0   0.217   4.7229   1.8477   1.4158
 MFX  H07A  H  HCH2   0   0.229   6.4408   1.6278   1.7011
 MFX  HN02  H  HNH1   0   0.349   4.7843   0.9689  -2.0506
 MFX  H08   H  HCH2   0   0.261  -0.7648   4.0822  -0.1516
 MFX  H08A  H  HCH2   0   0.263  -1.6578   3.0072  -1.3186
 MFX  H09   H  HCH2   0   0.266  -3.7493   3.2620  -0.0116
 MFX  H09A  H  HCH2   0   0.268  -2.9014   4.2971   1.2175
 MFX  H10   H  HCH2   0   0.182   6.7709   0.8243  -0.5967
 MFX  H10A  H  HCH2   0   0.232   5.9513   2.3838  -0.6326
 MFX  H16   H  HCR6   0   0.303  -4.1102   1.4350   1.2029
 MFX  H17   H  HCR6   0   0.273  -1.5568  -2.8976  -1.6750
 MFX  H     H  HCH3   0   0.238   1.5204   3.0882   0.1771
 MFX  HA    H  HCH3   0   0.268   2.3395   1.7159  -0.5955
 MFX  HB    H  HCH3   0   0.224   0.8299   2.3590  -1.2835
 MFX  O01   O  O2     0  -0.483   0.5982   1.3158   0.5082

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
 MFX  F    C15   single    1.345  0.020  1.345
 MFX  O01  C13   single    1.352  0.020  1.352
 MFX  O01  C     single    1.428  0.020  1.428
 MFX  O02  C19   double    1.229  0.020  1.229
 MFX  O03  C20   deloc     1.242  0.020  1.242
 MFX  O    C20   deloc     1.251  0.020  1.251
 MFX  N01  C03   single    1.456  0.020  1.456
 MFX  N01  C04   single    1.456  0.020  1.456
 MFX  N01  C11   single    1.374  0.020  1.374
 MFX  N02  C02   single    1.450  0.020  1.450
 MFX  N02  C10   single    1.452  0.020  1.452
 MFX  N02  HN02  single    0.890  0.020  1.040
 MFX  N    C06   single    1.450  0.020  1.450
 MFX  N    C12   single    1.393  0.020  1.393
 MFX  N    C16   single    1.349  0.020  1.349
 MFX  C01  C02   single    1.531  0.020  1.531
 MFX  C01  C03   single    1.528  0.020  1.528
 MFX  C01  C05   single    1.525  0.020  1.525
 MFX  C01  H01   single    0.970  0.020  1.090
 MFX  C02  C04   single    1.520  0.020  1.520
 MFX  C02  H02   single    0.970  0.020  1.090
 MFX  C03  H03   single    0.970  0.020  1.090
 MFX  C03  H03A  single    0.970  0.020  1.090
 MFX  C04  H04   single    0.970  0.020  1.090
 MFX  C04  H04A  single    0.970  0.020  1.090
 MFX  C05  C07   single    1.525  0.020  1.525
 MFX  C05  H05   single    0.970  0.020  1.090
 MFX  C05  H05A  single    0.970  0.020  1.090
 MFX  C06  C08   single    1.491  0.020  1.491
 MFX  C06  C09   single    1.498  0.020  1.498
 MFX  C06  H06   single    0.970  0.020  1.090
 MFX  C07  C10   single    1.519  0.020  1.519
 MFX  C07  H07   single    0.970  0.020  1.090
 MFX  C07  H07A  single    0.970  0.020  1.090
 MFX  C08  C09   single    1.495  0.020  1.495
 MFX  C08  H08   single    0.970  0.020  1.090
 MFX  C08  H08A  single    0.970  0.020  1.090
 MFX  C09  H09   single    0.970  0.020  1.090
 MFX  C09  H09A  single    0.970  0.020  1.090
 MFX  C10  H10   single    0.970  0.020  1.090
 MFX  C10  H10A  single    0.970  0.020  1.090
 MFX  C11  C13   aromatic  1.405  0.020  1.405
 MFX  C11  C15   aromatic  1.406  0.020  1.406
 MFX  C12  C13   aromatic  1.414  0.020  1.414
 MFX  C12  C14   aromatic  1.405  0.020  1.405
 MFX  C14  C17   aromatic  1.397  0.020  1.397
 MFX  C14  C19   single    1.477  0.020  1.477
 MFX  C15  C17   aromatic  1.361  0.020  1.361
 MFX  C16  C18   double    1.362  0.020  1.362
 MFX  C16  H16   single    0.930  0.020  1.080
 MFX  C17  H17   single    0.930  0.020  1.080
 MFX  C18  C19   single    1.442  0.020  1.442
 MFX  C18  C20   single    1.521  0.020  1.521
 MFX  C    H     single    0.970  0.020  1.090
 MFX  C    HA    single    0.970  0.020  1.090
 MFX  C    HB    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
 MFX  C11   N01  C04  124.64  3.000
 MFX  C11   N01  C03  122.85  3.000
 MFX  C04   N01  C03  111.82  3.000
 MFX  HN02  N02  C10  110.03  3.000
 MFX  HN02  N02  C02  109.30  3.000
 MFX  C10   N02  C02  112.71  3.000
 MFX  C16   N    C12  118.68  3.000
 MFX  C16   N    C06  116.99  3.000
 MFX  C12   N    C06  124.24  3.000
 MFX  H01   C01  C05  108.88  3.000
 MFX  H01   C01  C03  108.56  3.000
 MFX  C05   C01  C03  115.07  3.000
 MFX  H01   C01  C02  107.49  3.000
 MFX  C05   C01  C02  113.70  3.000
 MFX  C03   C01  C02  102.74  3.000
 MFX  H02   C02  C04  110.74  3.000
 MFX  H02   C02  C01  110.76  3.000
 MFX  C04   C02  C01  101.55  3.000
 MFX  H02   C02  N02  112.46  3.000
 MFX  C04   C02  N02  110.92  3.000
 MFX  C01   C02  N02  109.89  3.000
 MFX  H03A  C03  H03  107.16  3.000
 MFX  H03A  C03  C01  111.66  3.000
 MFX  H03   C03  C01  110.56  3.000
 MFX  H03A  C03  N01  111.22  3.000
 MFX  H03   C03  N01  112.86  3.000
 MFX  C01   C03  N01  103.46  3.000
 MFX  H04A  C04  H04  107.81  3.000
 MFX  H04A  C04  C02  112.68  3.000
 MFX  H04   C04  C02  108.58  3.000
 MFX  H04A  C04  N01  111.25  3.000
 MFX  H04   C04  N01  113.57  3.000
 MFX  C02   C04  N01  102.97  3.000
 MFX  H05A  C05  H05  106.04  3.000
 MFX  H05A  C05  C07  108.94  3.000
 MFX  H05   C05  C07  110.74  3.000
 MFX  H05A  C05  C01  108.33  3.000
 MFX  H05   C05  C01  110.05  3.000
 MFX  C07   C05  C01  112.49  3.000
 MFX  H06   C06  C09  116.45  3.000
 MFX  H06   C06  C08  117.53  3.000
 MFX  C09   C06  C08   60.01  3.000
 MFX  H06   C06  N    114.48  3.000
 MFX  C09   C06  N    118.19  3.000
 MFX  C08   C06  N    119.52  3.000
 MFX  H07A  C07  H07  106.87  3.000
 MFX  H07A  C07  C10  110.12  3.000
 MFX  H07   C07  C10  108.89  3.000
 MFX  H07A  C07  C05  109.89  3.000
 MFX  H07   C07  C05  110.62  3.000
 MFX  C10   C07  C05  110.39  3.000
 MFX  H08A  C08  H08  114.56  3.000
 MFX  H08A  C08  C09  116.80  3.000
 MFX  H08   C08  C09  119.14  3.000
 MFX  H08A  C08  C06  117.54  3.000
 MFX  H08   C08  C06  118.05  3.000
 MFX  C09   C08  C06   60.20  3.000
 MFX  H09A  C09  H09  114.19  3.000
 MFX  H09A  C09  C08  119.05  3.000
 MFX  H09   C09  C08  117.29  3.000
 MFX  H09A  C09  C06  116.74  3.000
 MFX  H09   C09  C06  119.34  3.000
 MFX  C08   C09  C06   59.79  3.000
 MFX  H10A  C10  H10  106.80  3.000
 MFX  H10A  C10  C07  110.28  3.000
 MFX  H10   C10  C07  109.19  3.000
 MFX  H10A  C10  N02  108.63  3.000
 MFX  H10   C10  N02  112.49  3.000
 MFX  C07   C10  N02  109.42  3.000
 MFX  C15   C11  C13  116.59  3.000
 MFX  C15   C11  N01  122.15  3.000
 MFX  C13   C11  N01  121.21  3.000
 MFX  C14   C12  C13  119.07  3.000
 MFX  C14   C12  N    117.50  3.000
 MFX  C13   C12  N    123.41  3.000
 MFX  C12   C13  C11  121.42  3.000
 MFX  C12   C13  O01  119.34  3.000
 MFX  C11   C13  O01  119.16  3.000
 MFX  C19   C14  C17  117.51  3.000
 MFX  C19   C14  C12  123.05  3.000
 MFX  C17   C14  C12  119.41  3.000
 MFX  C17   C15  C11  122.96  3.000
 MFX  C17   C15  F    118.42  3.000
 MFX  C11   C15  F    118.52  3.000
 MFX  H16   C16  C18  118.18  3.000
 MFX  H16   C16  N    114.90  3.000
 MFX  C18   C16  N    126.91  3.000
 MFX  H17   C17  C15  120.04  3.000
 MFX  H17   C17  C14  119.60  3.000
 MFX  C15   C17  C14  120.24  3.000
 MFX  C20   C18  C19  124.83  3.000
 MFX  C20   C18  C16  117.25  3.000
 MFX  C19   C18  C16  117.88  3.000
 MFX  C18   C19  C14  114.23  3.000
 MFX  C18   C19  O02  125.86  3.000
 MFX  C14   C19  O02  119.91  3.000
 MFX  C18   C20  O    116.14  3.000
 MFX  C18   C20  O03  117.69  3.000
 MFX  O     C20  O03  126.17  3.000
 MFX  HB    C    HA   109.13  3.000
 MFX  HB    C    H    108.79  3.000
 MFX  HA    C    H    109.04  3.000
 MFX  HB    C    O01  111.08  3.000
 MFX  HA    C    O01  112.26  3.000
 MFX  H     C    O01  106.44  3.000
 MFX  C     O01  C13  116.13  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
 MFX  CONST_01  C14  C12  C13  C11     0.00   0.0  0
 MFX  CONST_02  C14  C17  C15  C11     0.00   0.0  0
 MFX  CONST_03  C15  C11  C13  C12     0.00   0.0  0
 MFX  CONST_04  C15  C17  C14  C12     0.00   0.0  0
 MFX  CONST_05  C17  C15  C11  C13     0.00   0.0  0
 MFX  CONST_06  C17  C14  C12  C13     0.00   0.0  0
 MFX  CONST_07  C12  C13  C11  N01   180.00   0.0  0
 MFX  CONST_08  C17  C15  C11  N01   180.00   0.0  0
 MFX  CONST_09  N01  C11  C15  F       0.00   0.0  0
 MFX  CONST_10  C13  C11  C15  F     180.00   0.0  0
 MFX  CONST_11  C14  C17  C15  F     180.00   0.0  0
 MFX  CONST_12  N01  C11  C13  O01     0.00   0.0  0
 MFX  CONST_13  C15  C11  C13  O01   180.00   0.0  0
 MFX  CONST_14  N    C12  C13  O01     0.00   0.0  0
 MFX  CONST_15  C14  C12  C13  O01   180.00   0.0  0
 MFX  CONST_16  H17  C17  C15  C11   180.00   0.0  0
 MFX  Var_01    C05  C07  C10  N02    57.83  30.0  1
 MFX  Var_02    C09  C08  C06  N     107.47  30.0  1
 MFX  Var_03    C04  N01  C03  C01    -6.67  30.0  1
 MFX  Var_04    C10  C07  C05  C01   -48.65  30.0  1
 MFX  Var_05    C07  C10  N02  C02   -65.19  30.0  1
 MFX  Var_06    C03  N01  C04  C02   -19.29  30.0  1
 MFX  Var_07    C13  C11  N01  C03    49.72  30.0  2
 MFX  Var_08    C12  N    C06  C08    69.55  30.0  1
 MFX  Var_09    C16  C18  C20  O03  -172.31  30.0  3
 MFX  Var_10    H    C    O01  C13   165.65  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
 MFX  chir_01  C01  C02  C03  C05  positiv
 MFX  chir_02  C02  N02  C04  C01  positiv
 MFX  chir_03  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
 MFX  plan-1  F    0.020
 MFX  plan-1  O02  0.020
 MFX  plan-1  N01  0.020
 MFX  plan-1  N    0.020
 MFX  plan-1  C06  0.020
 MFX  plan-1  C11  0.020
 MFX  plan-1  C12  0.020
 MFX  plan-1  C13  0.020
 MFX  plan-1  C14  0.020
 MFX  plan-1  C15  0.020
 MFX  plan-1  C16  0.020
 MFX  plan-1  C17  0.020
 MFX  plan-1  C18  0.020
 MFX  plan-1  C19  0.020
 MFX  plan-1  C20  0.020
 MFX  plan-1  H16  0.020
 MFX  plan-1  H17  0.020
 MFX  plan-1  O01  0.020
 MFX  plan-2  O03  0.020
 MFX  plan-2  O    0.020
 MFX  plan-2  C18  0.020
 MFX  plan-2  C20  0.020

