# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 15:47:01 2022
#   Inital geometry file: a 132 line input string
#   Ligand name: ~{N}-[3-[(3~{R},6~{R})-5-azanyl-3,6-dimethyl-6-(trifluoromethyl)-2~{H}-1,4-oxazin-3-yl]-4-fluoranyl-phenyl]-5-cyano-3-methyl-pyridine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(cnc1C(=O)Nc2ccc(F)c(c2)[C@]3(C)CO[C@](C)(C(=N3)N)C(F)(F)F)C#N
#
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
 SLK  SLK  ~{N}-[3-[(3~{R},6~{R})-5-azanyl-3,6-dimethyl-6-(trifluoromethyl)-2~{H}-1,4-oxazin-3-yl]-4-fluoranyl-phenyl]-5-cyano-3-methyl-pyridine-2-carboxamide  ligand  51  32  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_SLK
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
 SLK  C1   C  CR6   0   0.421  29.9536  75.5477  20.2264
 SLK  C2   C  CR16  0  -0.315  31.0299  75.9804  20.9968
 SLK  C3   C  CR16  0  -0.391  31.7041  75.0585  21.7826
 SLK  C11  C  CH2   0  -0.196  30.9051  70.8525  20.6219
 SLK  C14  C  CT    0  -0.056  30.1338  70.8704  18.3577
 SLK  C15  C  CT    0   1.031  30.2003  69.4076  17.8610
 SLK  C16  C  C     0   0.417  28.7855  71.1646  19.0197
 SLK  C21  C  CH3   0  -0.676  30.3713  71.8391  17.1973
 SLK  C22  C  CR6   0  -0.067  26.3746  78.9003  16.3735
 SLK  C23  C  CR16  0  -0.159  27.2621  79.8653  16.8270
 SLK  C24  C  CR6   0   0.080  28.2589  79.5399  17.7428
 SLK  C25  C  CR6   0   0.107  28.2971  78.2011  18.1569
 SLK  C27  C  CR16  0  -0.025  26.4985  77.5997  16.8570
 SLK  C28  C  CSP   0   0.052  25.3561  79.2249  15.4302
 SLK  C4   C  CR6   0   0.505  31.3146  73.7369  21.8002
 SLK  C5   C  CR6   0  -0.024  30.2503  73.2588  21.0416
 SLK  C6   C  CR16  0  -0.433  29.5862  74.2005  20.2675
 SLK  F7   F  F     0  -0.316  32.0128  72.8997  22.5932
 SLK  N8   N  NH1   0  -0.761  29.1875  76.3690  19.3963
 SLK  C9   C  CT    0  -0.039  29.7960  71.7967  21.0683
 SLK  N10  N  N     0  -0.416  28.6494  71.6292  20.1967
 SLK  O13  O  O2    0  -0.487  31.1926  71.0602  19.2531
 SLK  F18  F  F     0  -0.299  31.4482  69.0741  17.5318
 SLK  F19  F  F     0  -0.301  29.7927  68.5387  18.7951
 SLK  F20  F  F     0  -0.303  29.4483  69.1922  16.7757
 SLK  N26  N  N     0  -0.444  27.4365  77.2842  17.7195
 SLK  O30  O  O     0  -0.442  30.1828  78.4067  19.6119
 SLK  N32  N  NS    0  -0.229  24.5338  79.4825  14.6667
 SLK  H1   H  HCR6  0   0.286  31.3502  77.0086  20.9997
 SLK  H2   H  HCR6  0   0.278  32.5422  75.3761  22.3896
 SLK  H3   H  HCH2  0   0.233  30.5922  69.8221  20.8231
 SLK  H4   H  HCH2  0   0.259  31.8407  71.0142  21.1520
 SLK  H5   H  HCH3  0   0.234  30.1267  71.4828  23.2139
 SLK  H6   H  HCH3  0   0.239  28.5168  72.0726  22.7904
 SLK  H7   H  HCH3  0   0.237  28.9544  70.3928  22.4761
 SLK  H8   H  HCH3  0   0.268  30.3157  72.8600  17.5731
 SLK  H9   H  HCH3  0   0.267  31.3653  71.6887  16.7768
 SLK  H10  H  HCH3  0   0.251  29.6455  71.7355  16.3945
 SLK  H11  H  HCR6  0   0.298  27.1801  80.8823  16.4654
 SLK  H12  H  HCR6  0   0.297  25.8257  76.8140  16.5353
 SLK  H13  H  HCR6  0   0.284  28.7373  73.8777  19.6790
 SLK  H14  H  HNH1  0   0.426  28.4243  75.9225  18.9016
 SLK  H15  H  HNH2  0   0.390  26.8136  71.2444  18.6456
 SLK  H16  H  HNH2  0   0.398  27.7352  70.9332  17.2646
 SLK  H17  H  HCH3  0   0.259  29.1484  80.7652  19.2763
 SLK  H18  H  HCH3  0   0.259  30.2210  80.4104  17.9361
 SLK  H19  H  HCH3  0   0.249  28.9087  81.5672  17.7259
 SLK  N17  N  NH2   0  -0.817  27.6837  70.9013  18.2687
 SLK  C12  C  CH3   0  -0.642  29.3290  71.4172  22.4773
 SLK  C29  C  C     0   0.526  29.3271  77.6846  19.1338
 SLK  C31  C  CH3   0  -0.715  29.1870  80.6264  18.1978

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
 SLK  N32  C28  triple    1.151  0.020  1.151
 SLK  C28  C22  single    1.426  0.020  1.426
 SLK  C22  C23  aromatic  1.387  0.020  1.387
 SLK  C22  C27  aromatic  1.393  0.020  1.393
 SLK  C23  C24  aromatic  1.392  0.020  1.392
 SLK  F20  C15  single    1.338  0.020  1.338
 SLK  C21  C14  single    1.530  0.020  1.530
 SLK  C27  N26  aromatic  1.313  0.020  1.313
 SLK  F18  C15  single    1.333  0.020  1.333
 SLK  C24  C31  single    1.500  0.020  1.500
 SLK  C24  C25  aromatic  1.402  0.020  1.402
 SLK  C15  C14  single    1.546  0.020  1.546
 SLK  C15  F19  single    1.339  0.020  1.339
 SLK  N26  C25  aromatic  1.331  0.020  1.331
 SLK  C14  C16  single    1.531  0.020  1.531
 SLK  C14  O13  single    1.400  0.020  1.400
 SLK  C25  C29  single    1.511  0.020  1.511
 SLK  N17  C16  single    1.359  0.020  1.359
 SLK  C16  N10  double    1.273  0.020  1.273
 SLK  O13  C11  single    1.414  0.020  1.414
 SLK  C29  N8   single    1.349  0.020  1.349
 SLK  C29  O30  double    1.217  0.020  1.217
 SLK  N8   C1   single    1.397  0.020  1.397
 SLK  N10  C9   single    1.450  0.020  1.450
 SLK  C6   C1   aromatic  1.397  0.020  1.397
 SLK  C6   C5   aromatic  1.388  0.020  1.388
 SLK  C11  C9   single    1.523  0.020  1.523
 SLK  C1   C2   aromatic  1.393  0.020  1.393
 SLK  C9   C5   single    1.531  0.020  1.531
 SLK  C9   C12  single    1.532  0.020  1.532
 SLK  C5   C4   aromatic  1.392  0.020  1.392
 SLK  C2   C3   aromatic  1.386  0.020  1.386
 SLK  C4   C3   aromatic  1.378  0.020  1.378
 SLK  C4   F7   single    1.348  0.020  1.348
 SLK  C2   H1   single    0.930  0.020  1.080
 SLK  C3   H2   single    0.930  0.020  1.080
 SLK  C11  H3   single    0.970  0.020  1.090
 SLK  C11  H4   single    0.970  0.020  1.090
 SLK  C12  H5   single    0.970  0.020  1.090
 SLK  C12  H6   single    0.970  0.020  1.090
 SLK  C12  H7   single    0.970  0.020  1.090
 SLK  C21  H8   single    0.970  0.020  1.090
 SLK  C21  H9   single    0.970  0.020  1.090
 SLK  C21  H10  single    0.970  0.020  1.090
 SLK  C23  H11  single    0.930  0.020  1.080
 SLK  C27  H12  single    0.930  0.020  1.080
 SLK  C6   H13  single    0.930  0.020  1.080
 SLK  N8   H14  single    0.860  0.020  1.020
 SLK  N17  H15  single    0.890  0.020  1.040
 SLK  N17  H16  single    0.890  0.020  1.040
 SLK  C31  H17  single    0.970  0.020  1.090
 SLK  C31  H18  single    0.970  0.020  1.090
 SLK  C31  H19  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
 SLK  N8   C1   C6   116.13  3.000
 SLK  C6   C1   C2   119.12  3.000
 SLK  N8   C1   C2   124.76  3.000
 SLK  H1   C2   C3   119.26  3.000
 SLK  H1   C2   C1   121.87  3.000
 SLK  C3   C2   C1   118.87  3.000
 SLK  H2   C3   C4   119.55  3.000
 SLK  H2   C3   C2   119.95  3.000
 SLK  C4   C3   C2   120.50  3.000
 SLK  H4   C11  H3   107.22  3.000
 SLK  H4   C11  O13  105.97  3.000
 SLK  H3   C11  O13  111.96  3.000
 SLK  H4   C11  C9   113.04  3.000
 SLK  H3   C11  C9   108.73  3.000
 SLK  O13  C11  C9   109.91  3.000
 SLK  O13  C14  C21  106.37  3.000
 SLK  O13  C14  C16  111.32  3.000
 SLK  C21  C14  C16  110.06  3.000
 SLK  O13  C14  C15  107.54  3.000
 SLK  C16  C14  C15  111.02  3.000
 SLK  C21  C14  C15  110.41  3.000
 SLK  F20  C15  F19  106.87  3.000
 SLK  F19  C15  F18  107.15  3.000
 SLK  F20  C15  F18  106.60  3.000
 SLK  F19  C15  C14  112.13  3.000
 SLK  F18  C15  C14  110.87  3.000
 SLK  F20  C15  C14  112.87  3.000
 SLK  N17  C16  N10  119.67  3.000
 SLK  N10  C16  C14  124.36  3.000
 SLK  N17  C16  C14  115.97  3.000
 SLK  H10  C21  H9   108.11  3.000
 SLK  H10  C21  H8   108.06  3.000
 SLK  H9   C21  H8   108.00  3.000
 SLK  H10  C21  C14  113.33  3.000
 SLK  H9   C21  C14  110.29  3.000
 SLK  H8   C21  C14  108.90  3.000
 SLK  C28  C22  C27  120.38  3.000
 SLK  C27  C22  C23  118.62  3.000
 SLK  C28  C22  C23  121.00  3.000
 SLK  H11  C23  C24  119.57  3.000
 SLK  H11  C23  C22  119.72  3.000
 SLK  C24  C23  C22  120.70  3.000
 SLK  C31  C24  C25  125.83  3.000
 SLK  C25  C24  C23  115.92  3.000
 SLK  C31  C24  C23  118.26  3.000
 SLK  N26  C25  C29  114.69  3.000
 SLK  C29  C25  C24  122.42  3.000
 SLK  N26  C25  C24  122.89  3.000
 SLK  H12  C27  N26  117.68  3.000
 SLK  H12  C27  C22  121.26  3.000
 SLK  N26  C27  C22  121.06  3.000
 SLK  N32  C28  C22  180.00  3.000
 SLK  F7   C4   C5   120.22  3.000
 SLK  F7   C4   C3   117.18  3.000
 SLK  C5   C4   C3   122.60  3.000
 SLK  C9   C5   C6   121.03  3.000
 SLK  C9   C5   C4   123.05  3.000
 SLK  C6   C5   C4   115.89  3.000
 SLK  H13  C6   C5   118.43  3.000
 SLK  H13  C6   C1   118.55  3.000
 SLK  C5   C6   C1   123.01  3.000
 SLK  H14  N8   C29  114.38  3.000
 SLK  H14  N8   C1   116.37  3.000
 SLK  C29  N8   C1   129.23  3.000
 SLK  N10  C9   C5   109.53  3.000
 SLK  C5   C9   C12  110.06  3.000
 SLK  N10  C9   C12  106.45  3.000
 SLK  C12  C9   C11  109.75  3.000
 SLK  C5   C9   C11  111.76  3.000
 SLK  N10  C9   C11  109.15  3.000
 SLK  C9   N10  C16  120.90  3.000
 SLK  C14  O13  C11  116.47  3.000
 SLK  C27  N26  C25  120.81  3.000
 SLK  H16  N17  H15  113.98  3.000
 SLK  H16  N17  C16  120.26  3.000
 SLK  H15  N17  C16  115.28  3.000
 SLK  H7   C12  H6   108.01  3.000
 SLK  H7   C12  H5   108.01  3.000
 SLK  H6   C12  H5   108.41  3.000
 SLK  H7   C12  C9   109.65  3.000
 SLK  H6   C12  C9   110.03  3.000
 SLK  H5   C12  C9   112.60  3.000
 SLK  O30  C29  N8   125.09  3.000
 SLK  O30  C29  C25  122.03  3.000
 SLK  N8   C29  C25  112.88  3.000
 SLK  H19  C31  H18  108.07  3.000
 SLK  H19  C31  H17  108.08  3.000
 SLK  H18  C31  H17  107.30  3.000
 SLK  H19  C31  C24  109.66  3.000
 SLK  H18  C31  C24  111.80  3.000
 SLK  H17  C31  C24  111.79  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
 SLK  CONST_01  C4   C5   C6   C1      0.00   0.0  0
 SLK  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 SLK  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 SLK  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 SLK  CONST_05  C6   C1   C2   C3      0.00   0.0  0
 SLK  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 SLK  CONST_07  C25  C24  C23  C22     0.00   0.0  0
 SLK  CONST_08  C25  N26  C27  C22     0.00   0.0  0
 SLK  CONST_09  N26  C27  C22  C23     0.00   0.0  0
 SLK  CONST_10  N26  C25  C24  C23     0.00   0.0  0
 SLK  CONST_11  C27  C22  C23  C24     0.00   0.0  0
 SLK  CONST_12  C27  N26  C25  C24     0.00   0.0  0
 SLK  CONST_13  C9   C5   C6   C1    180.00   0.0  0
 SLK  CONST_14  C9   C5   C4   C3    180.00   0.0  0
 SLK  CONST_15  C9   N10  C16  C14     0.00   0.0  0
 SLK  CONST_16  F7   C4   C3   C2    180.00   0.0  0
 SLK  CONST_17  N8   C1   C2   C3    180.00   0.0  0
 SLK  CONST_18  C31  C24  C23  C22   180.00   0.0  0
 SLK  CONST_19  C29  C25  C24  C23   180.00   0.0  0
 SLK  CONST_20  C28  C22  C23  C24   180.00   0.0  0
 SLK  CONST_21  C29  C25  N26  C27   180.00   0.0  0
 SLK  CONST_22  N26  C27  C22  C28   180.00   0.0  0
 SLK  CONST_23  N8   C1   C6   C5    180.00   0.0  0
 SLK  CONST_24  F7   C4   C5   C6    180.00   0.0  0
 SLK  CONST_25  C9   C5   C4   F7      0.00   0.0  0
 SLK  CONST_26  C31  C24  C25  N26   180.00   0.0  0
 SLK  CONST_27  N17  C16  N10  C9    180.00   0.0  0
 SLK  CONST_28  H2   C3   C2   C1    180.00   0.0  0
 SLK  CONST_29  H13  C6   C1   C2    180.00   0.0  0
 SLK  CONST_30  H12  C27  C22  C23   180.00   0.0  0
 SLK  CONST_31  H11  C23  C24  C25   180.00   0.0  0
 SLK  CONST_32  H1   C2   C3   C4    180.00   0.0  0
 SLK  CONST_33  C25  C29  N8   C1    180.00   0.0  0
 SLK  CONST_34  C29  N8   C1   C2      0.00   0.0  0
 SLK  CONST_35  C6   C1   N8   C29   180.00   0.0  0
 SLK  CONST_36  H14  N8   C1   C2    180.00   0.0  0
 SLK  CONST_37  H15  N17  C16  C14   180.00   0.0  0
 SLK  CONST_39  O30  C29  N8   C1      0.00   0.0  0
 SLK  Var_01    C9   C11  O13  C14   -59.20  30.0  1
 SLK  Var_02    N8   C29  C25  C24  -179.94  30.0  2
 SLK  Var_03    H17  C31  C24  C23   120.98  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
 SLK  chir_01  C14  C15  C16  O13  negativ
 SLK  chir_02  C9   C11  C5   N10  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
 SLK  plan-1  C22  0.020
 SLK  plan-1  C23  0.020
 SLK  plan-1  C24  0.020
 SLK  plan-1  C25  0.020
 SLK  plan-1  C27  0.020
 SLK  plan-1  C28  0.020
 SLK  plan-1  N26  0.020
 SLK  plan-1  N32  0.020
 SLK  plan-1  H11  0.020
 SLK  plan-1  H12  0.020
 SLK  plan-1  C29  0.020
 SLK  plan-1  C31  0.020
 SLK  plan-2  C1   0.020
 SLK  plan-2  C2   0.020
 SLK  plan-2  C3   0.020
 SLK  plan-2  C4   0.020
 SLK  plan-2  C5   0.020
 SLK  plan-2  C6   0.020
 SLK  plan-2  F7   0.020
 SLK  plan-2  N8   0.020
 SLK  plan-2  C9   0.020
 SLK  plan-2  H1   0.020
 SLK  plan-2  H2   0.020
 SLK  plan-2  H13  0.020
 SLK  plan-3  C1   0.020
 SLK  plan-3  C25  0.020
 SLK  plan-3  N8   0.020
 SLK  plan-3  O30  0.020
 SLK  plan-3  H14  0.020
 SLK  plan-3  C29  0.020
 SLK  plan-4  C14  0.020
 SLK  plan-4  C16  0.020
 SLK  plan-4  C9   0.020
 SLK  plan-4  N10  0.020
 SLK  plan-4  H15  0.020
 SLK  plan-4  H16  0.020
 SLK  plan-4  N17  0.020

