# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 17 17:03:07 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: 7-(2-fluoranyl-6-oxidanyl-phenyl)-3-[(3~{R})-1-propanoylpyrrolidin-3-yl]-4~{H}-2,6-naphthyridin-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)N1CC[C@H](C1)C2=NC(=O)c3cc(ncc3C2)c4c(O)cccc4F
#
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
 MZN  MZN  7-(2-fluoranyl-6-oxidanyl-phenyl)-3-[(3~{R})-1-propanoylpyrrolidin-3-yl]-4~{H}-2,6-naphthyridin-1-one  ligand  48  28  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MZN
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
 MZN  N1   N  N     0  -0.393  -2.9258   1.4841   0.6539
 MZN  C4   C  CR66  0   0.014  -0.9750  -0.2481  -0.2542
 MZN  C5   C  CR6   0   0.447   0.0855  -1.1640  -0.7427
 MZN  C8   C  CR6   0   0.325   1.7494   0.2296   0.0913
 MZN  C10  C  CH2   0  -0.216   4.1571  -0.6134  -0.0173
 MZN  C13  C  CH2   0  -0.483   3.7789   1.7523  -0.1325
 MZN  C17  C  CH3   0  -0.654   9.1243  -0.5426  -0.1756
 MZN  C20  C  CR16  0  -0.105  -1.6481   1.8007   0.7406
 MZN  C21  C  CR6   0  -0.285  -4.7108   0.0039   0.0257
 MZN  C22  C  CR6   0   0.366  -5.5702   0.7733  -0.7677
 MZN  C24  C  CR16  0  -0.232  -7.4296  -0.6055  -0.1146
 MZN  C26  C  CR6   0   0.546  -5.2636  -1.0566   0.7254
 MZN  C16  C  CH2   0  -0.583   7.8487   0.2812  -0.1803
 MZN  O15  O  O     0  -0.511   6.6261  -1.7854  -0.3016
 MZN  N11  N  NR5   0  -0.482   5.4281   0.0944  -0.0599
 MZN  C12  C  CH2   0  -0.267   5.2728   1.5391   0.0638
 MZN  C9   C  CR15  0  -0.389   3.1815   0.4619   0.4448
 MZN  C18  C  C     0  -0.599   0.8133   1.3523   0.4005
 MZN  N7   N  N     0  -0.450   1.4151  -0.8886  -0.4307
 MZN  O6   O  O     0  -0.387  -0.1819  -2.1533  -1.3852
 MZN  C3   C  CR16  0  -0.342  -2.3195  -0.5849  -0.3558
 MZN  C19  C  CR66  0   0.052  -0.6203   0.9683   0.3032
 MZN  C2   C  CR6   0   0.255  -3.2652   0.3118   0.1141
 MZN  F27  F  F     0  -0.304  -4.4457  -1.7926   1.4932
 MZN  C25  C  CR16  0  -0.434  -6.6036  -1.3852   0.6818
 MZN  C23  C  CR16  0  -0.396  -6.9269   0.4645  -0.8368
 MZN  O28  O  OH1   0  -0.611  -5.0224   1.7841  -1.4571
 MZN  H1   H  HCH2  0   0.241   3.8850  -0.9970  -1.0039
 MZN  H2   H  HCH2  0   0.255   4.1960  -1.4598   0.6681
 MZN  H3   H  HCH2  0   0.273   3.4274   2.6553   0.3638
 MZN  H4   H  HCH2  0   0.261   3.5426   1.8330  -1.1963
 MZN  H5   H  HCH3  0   0.227   9.1949  -1.1813  -1.0550
 MZN  H6   H  HCH3  0   0.231   9.9926   0.1155  -0.1733
 MZN  H7   H  HCH3  0   0.226   9.1884  -1.1786   0.7068
 MZN  H8   H  HCR6  0   0.275  -1.4116   2.7626   1.1844
 MZN  H9   H  HCR6  0   0.275  -8.4844  -0.8373  -0.1748
 MZN  H10  H  HCH2  0   0.261   7.8293   0.9519   0.6841
 MZN  H11  H  HCH2  0   0.267   7.8308   0.9381  -1.0559
 MZN  H12  H  HCH2  0   0.260   5.8595   2.0752  -0.6824
 MZN  H13  H  HCH2  0   0.247   5.5882   1.8853   1.0526
 MZN  H14  H  HCR5  0   0.304   3.2179   0.5362   1.5399
 MZN  H15  H  H     0   0.313   1.0517   1.7564   1.3883
 MZN  H16  H  H     0   0.328   1.0289   2.1682  -0.3011
 MZN  H17  H  HCR6  0   0.279  -2.6234  -1.5222  -0.8016
 MZN  H18  H  HCR6  0   0.278  -6.9868  -2.2211   1.2506
 MZN  H19  H  HCR6  0   0.278  -7.5853   1.0558  -1.4620
 MZN  H20  H  HOH1  0   0.481  -5.6915   2.2341  -1.9857
 MZN  C14  C  C     0   0.561   6.5926  -0.5654  -0.1867

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
 MZN  O28  C22  single    1.341  0.020  1.341
 MZN  C23  C22  aromatic  1.393  0.020  1.393
 MZN  C23  C24  aromatic  1.385  0.020  1.385
 MZN  C22  C21  aromatic  1.400  0.020  1.400
 MZN  C20  N1   aromatic  1.319  0.020  1.319
 MZN  C20  C19  aromatic  1.393  0.020  1.393
 MZN  N1   C2   aromatic  1.334  0.020  1.334
 MZN  C13  C12  single    1.522  0.020  1.522
 MZN  C13  C9   single    1.535  0.020  1.535
 MZN  C12  N11  single    1.458  0.020  1.458
 MZN  C18  C19  single    1.487  0.020  1.487
 MZN  C18  C8   single    1.494  0.020  1.494
 MZN  C19  C4   aromatic  1.384  0.020  1.384
 MZN  C24  C25  aromatic  1.387  0.020  1.387
 MZN  C21  C2   single    1.481  0.020  1.481
 MZN  C21  C26  aromatic  1.386  0.020  1.386
 MZN  C2   C3   aromatic  1.385  0.020  1.385
 MZN  C16  C14  single    1.515  0.020  1.515
 MZN  C16  C17  single    1.518  0.020  1.518
 MZN  N11  C14  single    1.344  0.020  1.344
 MZN  N11  C10  single    1.455  0.020  1.455
 MZN  C8   C9   single    1.493  0.020  1.493
 MZN  C8   N7   double    1.279  0.020  1.279
 MZN  C9   C10  single    1.524  0.020  1.524
 MZN  C4   C3   aromatic  1.390  0.020  1.390
 MZN  C4   C5   single    1.484  0.020  1.484
 MZN  C14  O15  double    1.226  0.020  1.226
 MZN  C25  C26  aromatic  1.380  0.020  1.380
 MZN  C26  F27  single    1.342  0.020  1.342
 MZN  N7   C5   single    1.393  0.020  1.393
 MZN  C5   O6   double    1.210  0.020  1.210
 MZN  C10  H1   single    0.970  0.020  1.090
 MZN  C10  H2   single    0.970  0.020  1.090
 MZN  C13  H3   single    0.970  0.020  1.090
 MZN  C13  H4   single    0.970  0.020  1.090
 MZN  C17  H5   single    0.970  0.020  1.090
 MZN  C17  H6   single    0.970  0.020  1.090
 MZN  C17  H7   single    0.970  0.020  1.090
 MZN  C20  H8   single    0.930  0.020  1.080
 MZN  C24  H9   single    0.930  0.020  1.080
 MZN  C16  H10  single    0.970  0.020  1.090
 MZN  C16  H11  single    0.970  0.020  1.090
 MZN  C12  H12  single    0.970  0.020  1.090
 MZN  C12  H13  single    0.970  0.020  1.090
 MZN  C9   H14  single    0.970  0.020  1.090
 MZN  C18  H15  single    0.970  0.020  1.090
 MZN  C18  H16  single    0.970  0.020  1.090
 MZN  C3   H17  single    0.930  0.020  1.080
 MZN  C25  H18  single    0.930  0.020  1.080
 MZN  C23  H19  single    0.930  0.020  1.080
 MZN  O28  H20  single    0.850  0.020  0.980

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
 MZN  C2   N1   C20  118.93  3.000
 MZN  C19  C4   C3   119.36  3.000
 MZN  C3   C4   C5   121.18  3.000
 MZN  C19  C4   C5   119.46  3.000
 MZN  O6   C5   N7   119.44  3.000
 MZN  O6   C5   C4   121.45  3.000
 MZN  N7   C5   C4   119.10  3.000
 MZN  N7   C8   C18  125.30  3.000
 MZN  N7   C8   C9   118.91  3.000
 MZN  C18  C8   C9   115.78  3.000
 MZN  H2   C10  H1   107.70  3.000
 MZN  H2   C10  C9   112.35  3.000
 MZN  H1   C10  C9   111.22  3.000
 MZN  H2   C10  N11  111.41  3.000
 MZN  H1   C10  N11  111.20  3.000
 MZN  C9   C10  N11  102.99  3.000
 MZN  H4   C13  H3   108.22  3.000
 MZN  H4   C13  C9   110.13  3.000
 MZN  H3   C13  C9   113.59  3.000
 MZN  H4   C13  C12  110.38  3.000
 MZN  H3   C13  C12  111.98  3.000
 MZN  C9   C13  C12  102.46  3.000
 MZN  H7   C17  H6   107.70  3.000
 MZN  H7   C17  H5   107.92  3.000
 MZN  H6   C17  H5   107.72  3.000
 MZN  H7   C17  C16  111.63  3.000
 MZN  H6   C17  C16  109.98  3.000
 MZN  H5   C17  C16  111.72  3.000
 MZN  H8   C20  C19  119.82  3.000
 MZN  H8   C20  N1   116.78  3.000
 MZN  C19  C20  N1   123.40  3.000
 MZN  C2   C21  C26  121.23  3.000
 MZN  C26  C21  C22  117.51  3.000
 MZN  C2   C21  C22  121.26  3.000
 MZN  O28  C22  C23  122.65  3.000
 MZN  C23  C22  C21  120.27  3.000
 MZN  O28  C22  C21  117.06  3.000
 MZN  H9   C24  C23  119.36  3.000
 MZN  H9   C24  C25  119.48  3.000
 MZN  C23  C24  C25  121.16  3.000
 MZN  C25  C26  F27  118.64  3.000
 MZN  F27  C26  C21  117.75  3.000
 MZN  C25  C26  C21  123.61  3.000
 MZN  H11  C16  H10  105.29  3.000
 MZN  H11  C16  C14  108.56  3.000
 MZN  H10  C16  C14  109.34  3.000
 MZN  H11  C16  C17  109.98  3.000
 MZN  H10  C16  C17  110.18  3.000
 MZN  C14  C16  C17  113.16  3.000
 MZN  C12  N11  C14  125.91  3.000
 MZN  C14  N11  C10  121.36  3.000
 MZN  C12  N11  C10  112.73  3.000
 MZN  H13  C12  H12  107.93  3.000
 MZN  H13  C12  N11  111.06  3.000
 MZN  H12  C12  N11  111.83  3.000
 MZN  H13  C12  C13  110.81  3.000
 MZN  H12  C12  C13  111.79  3.000
 MZN  N11  C12  C13  103.44  3.000
 MZN  H14  C9   C13  107.78  3.000
 MZN  H14  C9   C10  109.20  3.000
 MZN  C13  C9   C10  103.30  3.000
 MZN  H14  C9   C8   106.16  3.000
 MZN  C10  C9   C8   115.63  3.000
 MZN  C13  C9   C8   114.52  3.000
 MZN  H16  C18  H15  105.06  3.000
 MZN  H16  C18  C19  109.85  3.000
 MZN  H15  C18  C19  111.38  3.000
 MZN  H16  C18  C8   107.65  3.000
 MZN  H15  C18  C8   109.15  3.000
 MZN  C19  C18  C8   113.35  3.000
 MZN  C8   N7   C5   120.92  3.000
 MZN  H17  C3   C2   120.60  3.000
 MZN  H17  C3   C4   120.79  3.000
 MZN  C2   C3   C4   118.60  3.000
 MZN  C18  C19  C20  122.44  3.000
 MZN  C18  C19  C4   120.01  3.000
 MZN  C20  C19  C4   117.55  3.000
 MZN  C3   C2   C21  120.77  3.000
 MZN  C3   C2   N1   122.16  3.000
 MZN  C21  C2   N1   117.07  3.000
 MZN  H18  C25  C26  120.76  3.000
 MZN  H18  C25  C24  121.70  3.000
 MZN  C26  C25  C24  117.54  3.000
 MZN  H19  C23  C24  120.12  3.000
 MZN  H19  C23  C22  119.96  3.000
 MZN  C24  C23  C22  119.91  3.000
 MZN  H20  O28  C22  110.51  3.000
 MZN  N11  C14  O15  121.40  3.000
 MZN  O15  C14  C16  122.27  3.000
 MZN  N11  C14  C16  116.33  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
 MZN  CONST_01  C4   C19  C20  N1      0.00   0.0  0
 MZN  CONST_04  C4   C3   C2   N1      0.00   0.0  0
 MZN  CONST_05  C21  C2   C3   C4    180.00   0.0  0
 MZN  CONST_06  C21  C2   N1   C20   180.00   0.0  0
 MZN  CONST_07  C3   C2   N1   C20     0.00   0.0  0
 MZN  CONST_08  C3   C4   C19  C20     0.00   0.0  0
 MZN  CONST_09  C24  C23  C22  C21     0.00   0.0  0
 MZN  CONST_10  C24  C25  C26  C21     0.00   0.0  0
 MZN  CONST_11  C25  C24  C23  C22     0.00   0.0  0
 MZN  CONST_13  C25  C26  C21  C22     0.00   0.0  0
 MZN  CONST_14  C23  C22  C21  C26     0.00   0.0  0
 MZN  CONST_16  C23  C24  C25  C26     0.00   0.0  0
 MZN  CONST_17  C2   N1   C20  C19     0.00   0.0  0
 MZN  CONST_18  C2   C3   C4   C19     0.00   0.0  0
 MZN  CONST_19  C23  C22  C21  C2    180.00   0.0  0
 MZN  CONST_20  C25  C26  C21  C2    180.00   0.0  0
 MZN  CONST_21  F27  C26  C21  C22   180.00   0.0  0
 MZN  CONST_22  O28  C22  C23  C24   180.00   0.0  0
 MZN  CONST_23  F27  C26  C25  C24   180.00   0.0  0
 MZN  CONST_24  O28  C22  C21  C26   180.00   0.0  0
 MZN  CONST_25  O28  C22  C21  C2      0.00   0.0  0
 MZN  CONST_26  F27  C26  C21  C2      0.00   0.0  0
 MZN  CONST_27  H17  C3   C2   N1    180.00   0.0  0
 MZN  CONST_28  H8   C20  C19  C4    180.00   0.0  0
 MZN  CONST_29  H19  C23  C22  C21   180.00   0.0  0
 MZN  CONST_30  H18  C25  C26  C21   180.00   0.0  0
 MZN  CONST_31  H9   C24  C23  C22   180.00   0.0  0
 MZN  CONST_32  C16  C14  N11  C10   180.00   0.0  0
 MZN  CONST_33  O15  C14  N11  C10     0.00   0.0  0
 MZN  CONST_34  C12  N11  C14  C16     0.00   0.0  0
 MZN  CONST_35  C12  N11  C14  O15   180.00   0.0  0
 MZN  Var_01    C8   C18  C19  C4    -10.62  30.0  1
 MZN  Var_02    C18  C8   N7   C5     -1.19  30.0  1
 MZN  Var_03    C13  C12  N11  C10   -12.70  30.0  1
 MZN  Var_04    C9   C13  C12  N11    31.50  30.0  1
 MZN  Var_05    C9   C10  N11  C12   -11.75  30.0  1
 MZN  Var_06    C19  C18  C8   C9   -167.68  30.0  1
 MZN  Var_07    C19  C4   C5   N7     10.71  30.0  1
 MZN  Var_08    O6   C5   N7   C8    170.78  30.0  1
 MZN  Var_09    N11  C14  C16  C17   173.75  30.0  3
 MZN  Var_10    H5   C17  C16  C14    60.31  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
 MZN  chir_01  C9  C13  C8  C10  negativ

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
 MZN  plan-1  C21  0.020
 MZN  plan-1  C22  0.020
 MZN  plan-1  C24  0.020
 MZN  plan-1  C26  0.020
 MZN  plan-1  C2   0.020
 MZN  plan-1  F27  0.020
 MZN  plan-1  C25  0.020
 MZN  plan-1  C23  0.020
 MZN  plan-1  O28  0.020
 MZN  plan-1  H9   0.020
 MZN  plan-1  H18  0.020
 MZN  plan-1  H19  0.020
 MZN  plan-2  N1   0.020
 MZN  plan-2  C4   0.020
 MZN  plan-2  C5   0.020
 MZN  plan-2  C20  0.020
 MZN  plan-2  C21  0.020
 MZN  plan-2  C18  0.020
 MZN  plan-2  C3   0.020
 MZN  plan-2  C19  0.020
 MZN  plan-2  C2   0.020
 MZN  plan-2  H8   0.020
 MZN  plan-2  H17  0.020
 MZN  plan-3  C10  0.020
 MZN  plan-3  C16  0.020
 MZN  plan-3  O15  0.020
 MZN  plan-3  N11  0.020
 MZN  plan-3  C12  0.020
 MZN  plan-3  C14  0.020
 MZN  plan-4  C4   0.020
 MZN  plan-4  C5   0.020
 MZN  plan-4  N7   0.020
 MZN  plan-4  O6   0.020

