# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 17:20:11 2022
#   Inital geometry file: a 127 line input string
#   Ligand name: 1-cyclopropyl-6-fluoro-8-methyl-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: Cc1c(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
 8MX  8MX  '1-cyclopropyl-6-fluoro-8-methyl-7-[(4aS,7aS)-octahydro-6H-pyrrolo[3,4-b]pyridin-6-yl]-4-oxo-1,4-dihydroquinoline-3-carboxylic acid'  ligand  51  28  .  2022-09-16  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_8MX
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
 8MX  C01   C  CH3    0  -0.740   0.6214   1.9017   0.7328
 8MX  C02   C  CR6    0   0.030   0.0396   0.6200   0.2067
 8MX  C03   C  CR6    0   0.316  -1.3523   0.3631   0.1620
 8MX  C04   C  CR6    0  -0.119  -1.8244  -0.9453  -0.0151
 8MX  C05   C  CR16   0  -0.502  -0.9249  -1.9653  -0.3373
 8MX  C06   C  CR6    0   0.564   0.4015  -1.6714  -0.4399
 8MX  C07   C  CR6    0   0.106   0.9220  -0.4075  -0.1295
 8MX  N08   N  NT     0  -0.537   2.3019  -0.1749  -0.1385
 8MX  C09   C  CH2    0  -0.264   3.1971  -0.9520   0.7161
 8MX  C10   C  CH1    0  -0.280   4.5113  -1.0184  -0.0687
 8MX  C11   C  CH2    0  -0.438   5.7717  -1.0205   0.7895
 8MX  C12   C  CH2    0  -0.448   6.0499   0.3501   1.3979
 8MX  C13   C  CH2    0  -0.315   6.0046   1.4272   0.3201
 8MX  N14   N  NH1    0  -0.582   4.7433   1.4645  -0.4045
 8MX  C15   C  CH1    0  -0.127   4.4142   0.1867  -1.0212
 8MX  C16   C  CH2    0  -0.276   2.9451   0.1502  -1.4059
 8MX  F17   F  F      0  -0.314   1.2585  -2.6346  -0.8192
 8MX  C18   C  C      0   0.394  -3.2479  -1.3108   0.1693
 8MX  O19   O  O      0  -0.458  -3.6167  -2.4589  -0.0665
 8MX  C20   C  C      0  -0.375  -4.0911  -0.2342   0.6320
 8MX  C21   C  C1     0   0.014  -3.5794   1.0271   0.6139
 8MX  N22   N  NT     0  -0.540  -2.3011   1.3647   0.3419
 8MX  C23   C  CH1    0  -0.132  -2.0485   2.7478   0.0022
 8MX  C24   C  CH2    0  -0.483  -1.5520   3.0760  -1.3672
 8MX  C25   C  CH2    0  -0.498  -2.9575   3.4106  -0.9864
 8MX  C26   C  C      0   0.403  -5.5371  -0.4033   1.0702
 8MX  O27   O  OC    -1  -0.587  -5.9371  -1.5594   1.2885
 8MX  O28   O  O      0  -0.604  -6.2007   0.6471   1.2029
 8MX  H011  H  HCH3   0   0.255   0.7294   2.6737  -0.0287
 8MX  H013  H  HCH3   0   0.246   0.0189   2.3087   1.5420
 8MX  H012  H  HCH3   0   0.270   1.6144   1.7021   1.1279
 8MX  H051  H  HCR6   0   0.275  -1.2879  -2.9681  -0.5190
 8MX  H091  H  HCH2   0   0.223   3.3241  -0.4460   1.6810
 8MX  H092  H  HCH2   0   0.233   2.8273  -1.9547   0.9419
 8MX  H101  H  HCH1   0   0.243   4.4972  -1.9262  -0.6809
 8MX  H111  H  HCH2   0   0.232   5.6902  -1.7815   1.5705
 8MX  H112  H  HCH2   0   0.225   6.6222  -1.3142   0.1666
 8MX  H122  H  HCH2   0   0.214   5.3045   0.5821   2.1658
 8MX  H121  H  HCH2   0   0.229   7.0222   0.3514   1.8971
 8MX  H132  H  HCH2   0   0.235   6.1842   2.4139   0.7524
 8MX  H131  H  HCH2   0   0.213   6.8079   1.2535  -0.4046
 8MX  H141  H  HNH1   0   0.341   4.0042   1.7136   0.2443
 8MX  H151  H  HCH1   0   0.240   5.0627   0.0491  -1.8922
 8MX  H162  H  HCH2   0   0.220   2.7758  -0.6088  -2.1814
 8MX  H161  H  HCH2   0   0.238   2.5915   1.1097  -1.7939
 8MX  H211  H  H      0   0.301  -4.2356   1.8621   0.8165
 8MX  H231  H  HCH1   0   0.288  -1.6956   3.3651   0.8184
 8MX  H241  H  HCH2   0   0.267  -0.8252   3.8726  -1.4561
 8MX  H242  H  HCH2   0   0.269  -1.4080   2.2565  -2.0602
 8MX  H252  H  HCH2   0   0.268  -3.7492   2.8217  -1.4318
 8MX  H251  H  HCH2   0   0.270  -3.2198   4.4424  -0.7944

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
 8MX  C12  C13   single    1.524  0.020  1.524
 8MX  C12  C11   single    1.525  0.020  1.525
 8MX  C13  N14   single    1.455  0.020  1.455
 8MX  C11  C10   single    1.525  0.020  1.525
 8MX  N14  C15   single    1.457  0.020  1.457
 8MX  C10  C15   single    1.539  0.020  1.539
 8MX  C10  C09   single    1.532  0.020  1.532
 8MX  C15  C16   single    1.519  0.020  1.519
 8MX  C09  N08   single    1.461  0.020  1.461
 8MX  C01  C02   single    1.503  0.020  1.503
 8MX  N08  C16   single    1.458  0.020  1.458
 8MX  N08  C07   single    1.399  0.020  1.399
 8MX  C25  C24   single    1.494  0.020  1.494
 8MX  C25  C23   single    1.498  0.020  1.498
 8MX  C24  C23   single    1.493  0.020  1.493
 8MX  C02  C07   aromatic  1.396  0.020  1.396
 8MX  C02  C03   aromatic  1.416  0.020  1.416
 8MX  C07  C06   aromatic  1.402  0.020  1.402
 8MX  C23  N22   single    1.446  0.020  1.446
 8MX  C03  N22   single    1.391  0.020  1.391
 8MX  C03  C04   aromatic  1.402  0.020  1.402
 8MX  N22  C21   single    1.350  0.020  1.350
 8MX  C06  F17   single    1.344  0.020  1.344
 8MX  C06  C05   aromatic  1.362  0.020  1.362
 8MX  C04  C05   aromatic  1.398  0.020  1.398
 8MX  C04  C18   single    1.481  0.020  1.481
 8MX  C21  C20   double    1.361  0.020  1.361
 8MX  C20  C18   single    1.444  0.020  1.444
 8MX  C20  C26   single    1.520  0.020  1.520
 8MX  C18  O19   double    1.229  0.020  1.229
 8MX  O28  C26   deloc     1.250  0.020  1.250
 8MX  C26  O27   deloc     1.243  0.020  1.243
 8MX  C01  H011  single    0.970  0.020  1.090
 8MX  C01  H013  single    0.970  0.020  1.090
 8MX  C01  H012  single    0.970  0.020  1.090
 8MX  C05  H051  single    0.930  0.020  1.080
 8MX  C09  H091  single    0.970  0.020  1.090
 8MX  C09  H092  single    0.970  0.020  1.090
 8MX  C10  H101  single    0.970  0.020  1.090
 8MX  C11  H111  single    0.970  0.020  1.090
 8MX  C11  H112  single    0.970  0.020  1.090
 8MX  C12  H122  single    0.970  0.020  1.090
 8MX  C12  H121  single    0.970  0.020  1.090
 8MX  C13  H132  single    0.970  0.020  1.090
 8MX  C13  H131  single    0.970  0.020  1.090
 8MX  N14  H141  single    0.890  0.020  1.040
 8MX  C15  H151  single    0.970  0.020  1.090
 8MX  C16  H162  single    0.970  0.020  1.090
 8MX  C16  H161  single    0.970  0.020  1.090
 8MX  C21  H211  single    0.930  0.020  1.080
 8MX  C23  H231  single    0.970  0.020  1.090
 8MX  C24  H241  single    0.970  0.020  1.090
 8MX  C24  H242  single    0.970  0.020  1.090
 8MX  C25  H252  single    0.970  0.020  1.090
 8MX  C25  H251  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
 8MX  H012  C01  H013  107.71  3.000
 8MX  H012  C01  H011  107.07  3.000
 8MX  H013  C01  H011  108.04  3.000
 8MX  H012  C01  C02   108.92  3.000
 8MX  H013  C01  C02   111.42  3.000
 8MX  H011  C01  C02   113.45  3.000
 8MX  C07   C02  C03   118.71  3.000
 8MX  C03   C02  C01   123.11  3.000
 8MX  C07   C02  C01   117.88  3.000
 8MX  N22   C03  C04   117.29  3.000
 8MX  C04   C03  C02   120.28  3.000
 8MX  N22   C03  C02   122.38  3.000
 8MX  C18   C04  C05   117.85  3.000
 8MX  C18   C04  C03   122.56  3.000
 8MX  C05   C04  C03   119.57  3.000
 8MX  H051  C05  C06   120.93  3.000
 8MX  H051  C05  C04   119.95  3.000
 8MX  C06   C05  C04   119.11  3.000
 8MX  F17   C06  C07   118.16  3.000
 8MX  F17   C06  C05   119.17  3.000
 8MX  C07   C06  C05   122.64  3.000
 8MX  N08   C07  C06   120.98  3.000
 8MX  C06   C07  C02   118.84  3.000
 8MX  N08   C07  C02   120.18  3.000
 8MX  C16   N08  C09   110.89  3.000
 8MX  C16   N08  C07   118.53  3.000
 8MX  C09   N08  C07   120.79  3.000
 8MX  H092  C09  H091  106.31  3.000
 8MX  H092  C09  C10   110.88  3.000
 8MX  H091  C09  C10   111.80  3.000
 8MX  H092  C09  N08   113.68  3.000
 8MX  H091  C09  N08   109.88  3.000
 8MX  C10   C09  N08   104.42  3.000
 8MX  H101  C10  C15   107.60  3.000
 8MX  H101  C10  C11   108.91  3.000
 8MX  C15   C10  C11   113.67  3.000
 8MX  H101  C10  C09   108.14  3.000
 8MX  C15   C10  C09   103.24  3.000
 8MX  C11   C10  C09   114.88  3.000
 8MX  H112  C11  H111  106.12  3.000
 8MX  H112  C11  C12   109.06  3.000
 8MX  H111  C11  C12   110.74  3.000
 8MX  H112  C11  C10   108.81  3.000
 8MX  H111  C11  C10   109.96  3.000
 8MX  C12   C11  C10   111.96  3.000
 8MX  H121  C12  H122  106.56  3.000
 8MX  H121  C12  C13   110.40  3.000
 8MX  H122  C12  C13   109.02  3.000
 8MX  H121  C12  C11   110.21  3.000
 8MX  H122  C12  C11   110.24  3.000
 8MX  C13   C12  C11   110.34  3.000
 8MX  H131  C13  H132  106.53  3.000
 8MX  H131  C13  N14   108.07  3.000
 8MX  H132  C13  N14   108.45  3.000
 8MX  H131  C13  C12   109.50  3.000
 8MX  H132  C13  C12   110.71  3.000
 8MX  N14   C13  C12   113.33  3.000
 8MX  H141  N14  C15   108.76  3.000
 8MX  H141  N14  C13   108.63  3.000
 8MX  C15   N14  C13   112.59  3.000
 8MX  H151  C15  C16   111.62  3.000
 8MX  H151  C15  N14   108.26  3.000
 8MX  C16   C15  N14   110.29  3.000
 8MX  H151  C15  C10   110.90  3.000
 8MX  C16   C15  C10   101.47  3.000
 8MX  N14   C15  C10   114.24  3.000
 8MX  H161  C16  H162  107.81  3.000
 8MX  H161  C16  C15   112.43  3.000
 8MX  H162  C16  C15   110.15  3.000
 8MX  H161  C16  N08   111.19  3.000
 8MX  H162  C16  N08   113.06  3.000
 8MX  C15   C16  N08   102.23  3.000
 8MX  C20   C18  O19   125.66  3.000
 8MX  O19   C18  C04   119.68  3.000
 8MX  C20   C18  C04   114.66  3.000
 8MX  C26   C20  C21   117.67  3.000
 8MX  C26   C20  C18   124.40  3.000
 8MX  C21   C20  C18   117.85  3.000
 8MX  H211  C21  N22   114.79  3.000
 8MX  H211  C21  C20   119.01  3.000
 8MX  N22   C21  C20   126.19  3.000
 8MX  C23   N22  C21   116.87  3.000
 8MX  C21   N22  C03   119.46  3.000
 8MX  C23   N22  C03   122.61  3.000
 8MX  H231  C23  C25   116.31  3.000
 8MX  H231  C23  C24   117.24  3.000
 8MX  C25   C23  C24    59.94  3.000
 8MX  H231  C23  N22   115.16  3.000
 8MX  C24   C23  N22   118.93  3.000
 8MX  C25   C23  N22   118.18  3.000
 8MX  H242  C24  H241  114.54  3.000
 8MX  H242  C24  C25   117.24  3.000
 8MX  H241  C24  C25   119.20  3.000
 8MX  H242  C24  C23   117.70  3.000
 8MX  H241  C24  C23   117.43  3.000
 8MX  C25   C24  C23    60.18  3.000
 8MX  H251  C25  H252  114.49  3.000
 8MX  H251  C25  C24   119.14  3.000
 8MX  H252  C25  C24   117.47  3.000
 8MX  H251  C25  C23   116.89  3.000
 8MX  H252  C25  C23   118.33  3.000
 8MX  C24   C25  C23    59.88  3.000
 8MX  O28   C26  O27   126.34  3.000
 8MX  O27   C26  C20   117.40  3.000
 8MX  O28   C26  C20   116.24  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
 8MX  CONST_01  C05   C06  C07  C02     0.00   0.0  0
 8MX  CONST_02  C05   C04  C03  C02     0.00   0.0  0
 8MX  CONST_03  C06   C07  C02  C03     0.00   0.0  0
 8MX  CONST_04  C06   C05  C04  C03     0.00   0.0  0
 8MX  CONST_05  C07   C02  C03  C04     0.00   0.0  0
 8MX  CONST_06  C07   C06  C05  C04     0.00   0.0  0
 8MX  CONST_07  N08   C07  C02  C03   180.00   0.0  0
 8MX  CONST_08  N08   C07  C06  C05   180.00   0.0  0
 8MX  CONST_09  N08   C07  C02  C01     0.00   0.0  0
 8MX  CONST_10  C06   C07  C02  C01   180.00   0.0  0
 8MX  CONST_11  N22   C03  C02  C01     0.00   0.0  0
 8MX  CONST_13  F17   C06  C07  C02   180.00   0.0  0
 8MX  CONST_14  F17   C06  C05  C04   180.00   0.0  0
 8MX  CONST_15  F17   C06  C07  N08     0.00   0.0  0
 8MX  CONST_16  H051  C05  C04  C03   180.00   0.0  0
 8MX  Var_01    C09   N08  C07  C02   120.84  30.0  1
 8MX  Var_02    C25   C23  N22  C03   121.93  30.0  2
 8MX  Var_03    C10   C09  N08  C07   149.17  30.0  1
 8MX  Var_04    C15   C16  N08  C07  -174.60  30.0  1
 8MX  Var_05    C13   C12  C11  C10   -50.47  30.0  1
 8MX  Var_06    N14   C13  C12  C11    56.81  30.0  1
 8MX  Var_07    C15   N14  C13  C12   -56.66  30.0  1
 8MX  Var_08    C24   C25  C23  N22  -108.90  30.0  1
 8MX  Var_09    O28   C26  C20  C18  -167.07  30.0  2
 8MX  Var_10    H011  C01  C02  C03   -88.99  30.0  2

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
 8MX  chir_01  C10  C11  C15  C09  positiv
 8MX  chir_02  C15  N14  C16  C10  positiv
 8MX  chir_03  C23  C25  C24  N22  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
 8MX  plan-1  C01   0.020
 8MX  plan-1  C02   0.020
 8MX  plan-1  C03   0.020
 8MX  plan-1  C04   0.020
 8MX  plan-1  C05   0.020
 8MX  plan-1  C06   0.020
 8MX  plan-1  C07   0.020
 8MX  plan-1  N08   0.020
 8MX  plan-1  F17   0.020
 8MX  plan-1  C18   0.020
 8MX  plan-1  O19   0.020
 8MX  plan-1  C20   0.020
 8MX  plan-1  C21   0.020
 8MX  plan-1  N22   0.020
 8MX  plan-1  C23   0.020
 8MX  plan-1  C26   0.020
 8MX  plan-1  H051  0.020
 8MX  plan-1  H211  0.020
 8MX  plan-2  C20   0.020
 8MX  plan-2  C26   0.020
 8MX  plan-2  O27   0.020
 8MX  plan-2  O28   0.020

