# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 05:27:02 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: 5-cyano-N-{3-[(2Z,4R)-5,5-difluoro-2-imino-4-methyl-1,3-oxazinan-4-yl]-4-fluorophenyl}pyridine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@]1(NC(=N)OCC1(F)F)c2cc(NC(=O)c3ccc(cn3)C#N)ccc2F
#
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
 6Z0  6Z0  5-cyano-N-{3-[(2Z,4R)-5,5-difluoro-2-imino-4-methyl-1,3-oxazinan-4-yl]-4-fluorophenyl}pyridine-2-carboxamide  ligand  42  28  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6Z0
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
 6Z0  C2    C  CR16  0  -0.112   6.1919  -0.7249  -0.3236
 6Z0  C3    C  CR16  0  -0.282   5.0626  -1.5210  -0.2765
 6Z0  C4    C  CR6   0   0.145   3.8269  -0.9024  -0.1529
 6Z0  N5    N  N     0  -0.438   3.6787   0.4158  -0.0786
 6Z0  C6    C  CR16  0  -0.016   4.7473   1.1842  -0.1224
 6Z0  N9    N  NH1   0  -0.764   1.4537  -1.0181   0.0236
 6Z0  C15   C  CR6   0   0.534  -2.5451  -2.0952   0.3559
 6Z0  C1    C  CR6   0  -0.080   6.0333   0.6548  -0.2444
 6Z0  C7    C  C     0   0.545   2.5806  -1.7439  -0.0951
 6Z0  O8    O  O     0  -0.449   2.6471  -2.9588  -0.1527
 6Z0  C10   C  CSP   0   0.061   7.1596   1.5272  -0.2849
 6Z0  N11   N  NS    0  -0.232   8.0674   2.2346  -0.3167
 6Z0  C12   C  CR6   0   0.420   0.1318  -1.4569   0.1251
 6Z0  C13   C  CR16  0  -0.304  -0.2660  -2.7880   0.0458
 6Z0  C14   C  CR16  0  -0.399  -1.6123  -3.0921   0.1642
 6Z0  C16   C  CR6   0  -0.072  -2.1874  -0.7525   0.4438
 6Z0  C17   C  CR16  0  -0.393  -0.8339  -0.4699   0.3228
 6Z0  C20   C  CH3   0  -0.670  -4.1664   0.0600   1.8225
 6Z0  O22   O  O2    0  -0.460  -2.8170   2.8107  -0.8803
 6Z0  C23   C  C     0   0.613  -2.4430   2.7991   0.4131
 6Z0  N28   N  NH1   0  -0.676  -2.4684   1.5950   1.0520
 6Z0  C25   C  CT    0   0.748  -3.9128   0.7137  -0.6330
 6Z0  C60   C  CH2   0  -0.288  -3.0492   1.5748  -1.5249
 6Z0  F26   F  F     0  -0.332  -5.0697   1.3791  -0.3688
 6Z0  F27   F  F     0  -0.320  -4.2608  -0.4127  -1.2961
 6Z0  C5    C  CT    0  -0.048  -3.1905   0.3877   0.6850
 6Z0  N24   N  N     0  -0.707  -2.0674   3.8518   1.0125
 6Z0  H2    H  HCR6  0   0.305   7.1755  -1.1634  -0.4193
 6Z0  H3    H  HCR6  0   0.296   5.1429  -2.5964  -0.3331
 6Z0  H6    H  HCR6  0   0.303   4.5953   2.2547  -0.0601
 6Z0  H9    H  HNH1  0   0.428   1.5969  -0.0158   0.0608
 6Z0  H14   H  HCR6  0   0.285  -1.9406  -4.1219   0.1072
 6Z0  H13   H  HCR6  0   0.293   0.4431  -3.5847  -0.1032
 6Z0  H17   H  HCR6  0   0.288  -0.5117   0.5605   0.3947
 6Z0  H201  H  HCH3  0   0.257  -3.6034  -0.2898   2.6882
 6Z0  H202  H  HCH3  0   0.261  -4.7081   0.9564   2.1169
 6Z0  H203  H  HCH3  0   0.259  -4.8915  -0.7053   1.5632
 6Z0  H601  H  HCH2  0   0.297  -3.5631   1.7953  -2.4603
 6Z0  H602  H  HCH2  0   0.270  -2.1115   1.0629  -1.7595
 6Z0  H24   H  H     0   0.338  -2.0355   4.6403   0.3781
 6Z0  H28   H  HNH1  0   0.408  -2.1974   1.6543   2.0221
 6Z0  F18   F  F     0  -0.310  -3.8285  -2.4758   0.4607

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
 6Z0  C2   C3    aromatic  1.383  0.020  1.383
 6Z0  C2   C1    aromatic  1.391  0.020  1.391
 6Z0  C3   C4    aromatic  1.387  0.020  1.387
 6Z0  C4   N5    aromatic  1.329  0.020  1.329
 6Z0  C4   C7    single    1.505  0.020  1.505
 6Z0  N5   C6    aromatic  1.317  0.020  1.317
 6Z0  C6   C1    aromatic  1.396  0.020  1.396
 6Z0  N9   C7    single    1.346  0.020  1.346
 6Z0  N9   C12   single    1.397  0.020  1.397
 6Z0  C15  C14   aromatic  1.379  0.020  1.379
 6Z0  C15  C16   aromatic  1.392  0.020  1.392
 6Z0  C15  F18   single    1.343  0.020  1.343
 6Z0  C1   C10   single    1.425  0.020  1.425
 6Z0  C7   O8    double    1.218  0.020  1.218
 6Z0  C10  N11   triple    1.151  0.020  1.151
 6Z0  C12  C13   aromatic  1.392  0.020  1.392
 6Z0  C12  C17   aromatic  1.395  0.020  1.395
 6Z0  C13  C14   aromatic  1.385  0.020  1.385
 6Z0  C16  C17   aromatic  1.388  0.020  1.388
 6Z0  C16  C5    single    1.538  0.020  1.538
 6Z0  C20  C5    single    1.534  0.020  1.534
 6Z0  O22  C23   single    1.346  0.020  1.346
 6Z0  O22  C60   single    1.413  0.020  1.413
 6Z0  C23  N24   double    1.268  0.020  1.268
 6Z0  C23  N28   single    1.363  0.020  1.363
 6Z0  C25  F26   single    1.360  0.020  1.360
 6Z0  C25  C60   single    1.511  0.020  1.511
 6Z0  C25  F27   single    1.353  0.020  1.353
 6Z0  C25  C5    single    1.538  0.020  1.538
 6Z0  N28  C5    single    1.454  0.020  1.454
 6Z0  C2   H2    single    0.930  0.020  1.080
 6Z0  C3   H3    single    0.930  0.020  1.080
 6Z0  C6   H6    single    0.930  0.020  1.080
 6Z0  N9   H9    single    0.860  0.020  1.020
 6Z0  C14  H14   single    0.930  0.020  1.080
 6Z0  C13  H13   single    0.930  0.020  1.080
 6Z0  C17  H17   single    0.930  0.020  1.080
 6Z0  C20  H201  single    0.970  0.020  1.090
 6Z0  C20  H202  single    0.970  0.020  1.090
 6Z0  C20  H203  single    0.970  0.020  1.090
 6Z0  C60  H601  single    0.970  0.020  1.090
 6Z0  C60  H602  single    0.970  0.020  1.090
 6Z0  N24  H24   single    0.890  0.020  1.040
 6Z0  N28  H28   single    0.890  0.020  1.040

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
 6Z0  H2    C2   C1    120.74  3.000
 6Z0  H2    C2   C3    120.84  3.000
 6Z0  C1    C2   C3    118.43  3.000
 6Z0  H3    C3   C4    121.00  3.000
 6Z0  H3    C3   C2    120.72  3.000
 6Z0  C4    C3   C2    118.28  3.000
 6Z0  C7    C4   N5    117.41  3.000
 6Z0  C7    C4   C3    119.45  3.000
 6Z0  N5    C4   C3    123.14  3.000
 6Z0  C6    N5   C4    119.12  3.000
 6Z0  H6    C6   C1    120.61  3.000
 6Z0  H6    C6   N5    117.45  3.000
 6Z0  C1    C6   N5    121.95  3.000
 6Z0  H9    N9   C12   116.23  3.000
 6Z0  H9    N9   C7    114.74  3.000
 6Z0  C12   N9   C7    129.02  3.000
 6Z0  F18   C15  C16   120.93  3.000
 6Z0  F18   C15  C14   116.91  3.000
 6Z0  C16   C15  C14   122.16  3.000
 6Z0  C10   C1   C6    119.89  3.000
 6Z0  C10   C1   C2    121.02  3.000
 6Z0  C6    C1   C2    119.09  3.000
 6Z0  O8    C7   N9    126.01  3.000
 6Z0  O8    C7   C4    120.71  3.000
 6Z0  N9    C7   C4    113.28  3.000
 6Z0  N11   C10  C1    180.00  3.000
 6Z0  C17   C12  C13   119.14  3.000
 6Z0  C17   C12  N9    116.31  3.000
 6Z0  C13   C12  N9    124.55  3.000
 6Z0  H13   C13  C14   119.29  3.000
 6Z0  H13   C13  C12   121.82  3.000
 6Z0  C14   C13  C12   118.88  3.000
 6Z0  H14   C14  C13   119.94  3.000
 6Z0  H14   C14  C15   119.35  3.000
 6Z0  C13   C14  C15   120.71  3.000
 6Z0  C5    C16  C17   119.93  3.000
 6Z0  C5    C16  C15   123.87  3.000
 6Z0  C17   C16  C15   116.19  3.000
 6Z0  H17   C17  C16   118.58  3.000
 6Z0  H17   C17  C12   118.50  3.000
 6Z0  C16   C17  C12   122.91  3.000
 6Z0  H203  C20  H202  108.24  3.000
 6Z0  H203  C20  H201  107.96  3.000
 6Z0  H202  C20  H201  107.85  3.000
 6Z0  H203  C20  C5    113.48  3.000
 6Z0  H202  C20  C5    109.96  3.000
 6Z0  H201  C20  C5    109.19  3.000
 6Z0  C60   O22  C23   118.44  3.000
 6Z0  N24   C23  N28   121.14  3.000
 6Z0  N28   C23  O22   116.91  3.000
 6Z0  N24   C23  O22   121.94  3.000
 6Z0  H28   N28  C5    115.15  3.000
 6Z0  H28   N28  C23   113.18  3.000
 6Z0  C5    N28  C23   128.64  3.000
 6Z0  C5    C25  F27   111.37  3.000
 6Z0  C5    C25  F26   109.67  3.000
 6Z0  F27   C25  F26   106.48  3.000
 6Z0  C5    C25  C60   111.00  3.000
 6Z0  F27   C25  C60   109.40  3.000
 6Z0  F26   C25  C60   108.78  3.000
 6Z0  H602  C60  H601  108.36  3.000
 6Z0  H602  C60  C25   110.48  3.000
 6Z0  H601  C60  C25   110.63  3.000
 6Z0  H602  C60  O22   111.49  3.000
 6Z0  H601  C60  O22   106.98  3.000
 6Z0  C25   C60  O22   108.85  3.000
 6Z0  C25   C5   N28   105.88  3.000
 6Z0  N28   C5   C20   107.82  3.000
 6Z0  C25   C5   C20   112.45  3.000
 6Z0  N28   C5   C16   109.35  3.000
 6Z0  C25   C5   C16   109.22  3.000
 6Z0  C20   C5   C16   111.89  3.000
 6Z0  H24   N24  C23   111.08  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
 6Z0  CONST_01  N5   C4   C3   C2      0.00   0.0  0
 6Z0  CONST_02  N5   C6   C1   C2      0.00   0.0  0
 6Z0  CONST_03  C6   C1   C2   C3      0.00   0.0  0
 6Z0  CONST_04  C6   N5   C4   C3      0.00   0.0  0
 6Z0  CONST_05  C1   C2   C3   C4      0.00   0.0  0
 6Z0  CONST_06  C1   C6   N5   C4      0.00   0.0  0
 6Z0  CONST_07  C12  C13  C14  C15     0.00   0.0  0
 6Z0  CONST_08  C12  C17  C16  C15     0.00   0.0  0
 6Z0  CONST_09  C16  C17  C12  C13     0.00   0.0  0
 6Z0  CONST_10  C16  C15  C14  C13     0.00   0.0  0
 6Z0  CONST_11  C17  C16  C15  C14     0.00   0.0  0
 6Z0  CONST_12  C17  C12  C13  C14     0.00   0.0  0
 6Z0  CONST_13  C5   C16  C17  C12   180.00   0.0  0
 6Z0  CONST_14  C5   C16  C15  C14   180.00   0.0  0
 6Z0  CONST_16  C7   C4   C3   C2    180.00   0.0  0
 6Z0  CONST_17  C10  C1   C2   C3    180.00   0.0  0
 6Z0  CONST_18  C10  C1   C6   N5    180.00   0.0  0
 6Z0  CONST_19  C7   C4   N5   C6    180.00   0.0  0
 6Z0  CONST_20  C14  C13  C12  N9    180.00   0.0  0
 6Z0  CONST_21  C16  C17  C12  N9    180.00   0.0  0
 6Z0  CONST_22  F18  C15  C14  C13   180.00   0.0  0
 6Z0  CONST_23  F18  C15  C16  C17   180.00   0.0  0
 6Z0  CONST_24  C5   C16  C15  F18     0.00   0.0  0
 6Z0  CONST_26  H6   C6   C1   C2    180.00   0.0  0
 6Z0  CONST_27  H2   C2   C3   C4    180.00   0.0  0
 6Z0  CONST_28  H3   C3   C4   N5    180.00   0.0  0
 6Z0  CONST_29  H13  C13  C14  C15   180.00   0.0  0
 6Z0  CONST_30  H17  C17  C16  C15   180.00   0.0  0
 6Z0  CONST_31  H14  C14  C13  C12   180.00   0.0  0
 6Z0  CONST_32  H28  N28  C23  O22   180.00   0.0  0
 6Z0  CONST_33  C12  N9   C7   C4    180.00   0.0  0
 6Z0  CONST_34  C13  C12  N9   C7      0.00   0.0  0
 6Z0  CONST_35  C17  C12  N9   C7    180.00   0.0  0
 6Z0  CONST_36  H9   N9   C12  C13   180.00   0.0  0
 6Z0  CONST_37  H24  N24  C23  O22     0.00   0.0  0
 6Z0  CONST_38  C12  N9   C7   O8      0.00   0.0  0
 6Z0  Var_01    C5   C25  C60  O22   -63.19  30.0  1
 6Z0  Var_02    C25  C60  O22  C23    47.04  30.0  1
 6Z0  Var_03    N24  C23  O22  C60   171.63  30.0  1
 6Z0  Var_04    N9   C7   C4   C3   -179.93  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
 6Z0  chir_01  C5  C16  C25  N28  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
 6Z0  plan-1  C2   0.020
 6Z0  plan-1  C3   0.020
 6Z0  plan-1  C4   0.020
 6Z0  plan-1  N5   0.020
 6Z0  plan-1  C6   0.020
 6Z0  plan-1  C1   0.020
 6Z0  plan-1  C7   0.020
 6Z0  plan-1  C10  0.020
 6Z0  plan-1  N11  0.020
 6Z0  plan-1  H2   0.020
 6Z0  plan-1  H3   0.020
 6Z0  plan-1  H6   0.020
 6Z0  plan-2  N9   0.020
 6Z0  plan-2  C15  0.020
 6Z0  plan-2  C12  0.020
 6Z0  plan-2  C13  0.020
 6Z0  plan-2  C14  0.020
 6Z0  plan-2  C16  0.020
 6Z0  plan-2  C17  0.020
 6Z0  plan-2  C5   0.020
 6Z0  plan-2  H14  0.020
 6Z0  plan-2  H13  0.020
 6Z0  plan-2  H17  0.020
 6Z0  plan-2  F18  0.020
 6Z0  plan-3  C4   0.020
 6Z0  plan-3  N9   0.020
 6Z0  plan-3  C7   0.020
 6Z0  plan-3  O8   0.020
 6Z0  plan-3  C12  0.020
 6Z0  plan-3  H9   0.020
 6Z0  plan-4  O22  0.020
 6Z0  plan-4  C23  0.020
 6Z0  plan-4  N28  0.020
 6Z0  plan-4  C5   0.020
 6Z0  plan-4  N24  0.020
 6Z0  plan-4  H24  0.020
 6Z0  plan-4  H28  0.020

