# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 07:26:22 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: 2-{difluoro[(4-methylpyrimidin-2-yl)sulfanyl]methyl}-1,3-benzoxazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccnc(SC(F)(F)c2oc3ccccc3n2)n1
#
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
 YKN  YKN  2-{difluoro[(4-methylpyrimidin-2-yl)sulfanyl]methyl}-1,3-benzoxazole  ligand  29  20  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_YKN
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
 YKN  F10   F  F     0  -0.308  -0.2472   1.6350  -1.0876
 YKN  C9    C  CT    0   0.538   0.0128   0.8853   0.0009
 YKN  F11   F  F     0  -0.310  -0.2421   1.6604   1.0744
 YKN  S12   S  S2    0   0.085  -0.9608  -0.6379   0.0209
 YKN  C13   C  CR6   0   0.241  -2.6305  -0.0434   0.0050
 YKN  N15   N  N     0  -0.428  -3.4863  -1.0467   0.0019
 YKN  C16   C  CR6   0   0.285  -4.7826  -0.7365  -0.0030
 YKN  C17   C  CH3   0  -0.718  -5.7582  -1.8643   0.0012
 YKN  C18   C  CR16  0  -0.368  -5.1821   0.5966  -0.0038
 YKN  C19   C  CR16  0  -0.000  -4.1882   1.5556  -0.0042
 YKN  N20   N  N     0  -0.395  -2.8951   1.2443   0.0000
 YKN  C8    C  CR5   0   0.427   1.4788   0.5457   0.0003
 YKN  N7    N  N     0  -0.416   2.4278   1.3979  -0.0588
 YKN  C6    C  CR56  0   0.150   3.5738   0.6215  -0.0298
 YKN  C5    C  CR16  0  -0.311   4.9201   0.9676  -0.0677
 YKN  C4    C  CR16  0  -0.261   5.8340  -0.0711  -0.0212
 YKN  C3    C  CR16  0  -0.262   5.4259  -1.4102   0.0559
 YKN  C2    C  CR16  0  -0.333   4.0866  -1.7686   0.0910
 YKN  C1    C  CR56  0   0.356   3.1967  -0.7142   0.0472
 YKN  O14   O  O     0  -0.442   1.8376  -0.7450   0.0660
 YKN  H171  H  HCH3  0   0.268  -5.6727  -2.4312   0.9294
 YKN  H172  H  HCH3  0   0.255  -6.7818  -1.5100  -0.0926
 YKN  H173  H  HCH3  0   0.266  -5.5475  -2.5537  -0.8164
 YKN  H18   H  HCR6  0   0.286  -6.2263   0.8735  -0.0042
 YKN  H19   H  HCR6  0   0.289  -4.4315   2.6113  -0.0105
 YKN  H5    H  HCR6  0   0.276   5.2345   2.0000  -0.1379
 YKN  H4    H  HCR6  0   0.269   6.8921   0.1519  -0.0437
 YKN  H3    H  HCR6  0   0.274   6.1773  -2.1874   0.0854
 YKN  H2    H  HCR6  0   0.286   3.7677  -2.8001   0.1473

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
 YKN  F10  C9    single    1.347  0.020  1.347
 YKN  C9   F11   single    1.348  0.020  1.348
 YKN  C9   S12   single    1.808  0.020  1.808
 YKN  C9   C8    single    1.505  0.020  1.505
 YKN  S12  C13   single    1.772  0.020  1.772
 YKN  C13  N15   aromatic  1.319  0.020  1.319
 YKN  C13  N20   aromatic  1.315  0.020  1.315
 YKN  N15  C16   aromatic  1.333  0.020  1.333
 YKN  C16  C17   single    1.491  0.020  1.491
 YKN  C16  C18   aromatic  1.392  0.020  1.392
 YKN  C18  C19   aromatic  1.381  0.020  1.381
 YKN  C19  N20   aromatic  1.330  0.020  1.330
 YKN  C8   N7    aromatic  1.277  0.020  1.277
 YKN  C8   O14   aromatic  1.341  0.020  1.341
 YKN  N7   C6    aromatic  1.385  0.020  1.385
 YKN  C6   C5    aromatic  1.391  0.020  1.391
 YKN  C6   C1    aromatic  1.390  0.020  1.390
 YKN  C5   C4    aromatic  1.384  0.020  1.384
 YKN  C4   C3    aromatic  1.402  0.020  1.402
 YKN  C3   C2    aromatic  1.387  0.020  1.387
 YKN  C2   C1    aromatic  1.380  0.020  1.380
 YKN  C1   O14   aromatic  1.360  0.020  1.360
 YKN  C17  H171  single    0.970  0.020  1.090
 YKN  C17  H172  single    0.970  0.020  1.090
 YKN  C17  H173  single    0.970  0.020  1.090
 YKN  C18  H18   single    0.930  0.020  1.080
 YKN  C19  H19   single    0.930  0.020  1.080
 YKN  C5   H5    single    0.930  0.020  1.080
 YKN  C4   H4    single    0.930  0.020  1.080
 YKN  C3   H3    single    0.930  0.020  1.080
 YKN  C2   H2    single    0.930  0.020  1.080

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
 YKN  C8    C9   S12   109.54  3.000
 YKN  C8    C9   F11   108.31  3.000
 YKN  S12   C9   F11   111.94  3.000
 YKN  C8    C9   F10   108.26  3.000
 YKN  S12   C9   F10   111.96  3.000
 YKN  F11   C9   F10   106.67  3.000
 YKN  C13   S12  C9    102.98  3.000
 YKN  N20   C13  N15   127.93  3.000
 YKN  N20   C13  S12   121.21  3.000
 YKN  N15   C13  S12   110.86  3.000
 YKN  C16   N15  C13   117.00  3.000
 YKN  C18   C16  C17   122.46  3.000
 YKN  C18   C16  N15   120.14  3.000
 YKN  C17   C16  N15   117.40  3.000
 YKN  H173  C17  H172  108.87  3.000
 YKN  H173  C17  H171  107.12  3.000
 YKN  H172  C17  H171  108.45  3.000
 YKN  H173  C17  C16   110.47  3.000
 YKN  H172  C17  C16   111.67  3.000
 YKN  H171  C17  C16   110.13  3.000
 YKN  H18   C18  C19   121.17  3.000
 YKN  H18   C18  C16   121.54  3.000
 YKN  C19   C18  C16   117.30  3.000
 YKN  H19   C19  N20   116.51  3.000
 YKN  H19   C19  C18   121.00  3.000
 YKN  N20   C19  C18   122.49  3.000
 YKN  C19   N20  C13   115.14  3.000
 YKN  O14   C8   N7    116.47  3.000
 YKN  O14   C8   C9    118.54  3.000
 YKN  N7    C8   C9    124.99  3.000
 YKN  C6    N7   C8    103.88  3.000
 YKN  C1    C6   C5    120.22  3.000
 YKN  C1    C6   N7    108.39  3.000
 YKN  C5    C6   N7    131.39  3.000
 YKN  H5    C5   C4    121.78  3.000
 YKN  H5    C5   C6    121.38  3.000
 YKN  C4    C5   C6    116.84  3.000
 YKN  H4    C4   C3    118.87  3.000
 YKN  H4    C4   C5    119.37  3.000
 YKN  C3    C4   C5    121.76  3.000
 YKN  H3    C3   C2    118.98  3.000
 YKN  H3    C3   C4    119.06  3.000
 YKN  C2    C3   C4    121.96  3.000
 YKN  H2    C2   C1    122.70  3.000
 YKN  H2    C2   C3    122.19  3.000
 YKN  C1    C2   C3    115.11  3.000
 YKN  O14   C1   C2    128.80  3.000
 YKN  O14   C1   C6    107.08  3.000
 YKN  C2    C1   C6    124.11  3.000
 YKN  C1    O14  C8    104.18  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
 YKN  CONST_01  C18   C16  N15  C13     0.00   0.0  0
 YKN  CONST_02  C18   C19  N20  C13     0.00   0.0  0
 YKN  CONST_03  C19   N20  C13  N15     0.00   0.0  0
 YKN  CONST_04  C19   C18  C16  N15     0.00   0.0  0
 YKN  CONST_05  N20   C13  N15  C16     0.00   0.0  0
 YKN  CONST_06  N20   C19  C18  C16     0.00   0.0  0
 YKN  CONST_07  C5    C6   N7   C8    180.00   0.0  0
 YKN  CONST_08  C1    C6   N7   C8      0.00   0.0  0
 YKN  CONST_09  C6    C1   O14  C8      0.00   0.0  0
 YKN  CONST_10  C2    C1   O14  C8    180.00   0.0  0
 YKN  CONST_11  C1    O14  C8   N7      0.00   0.0  0
 YKN  CONST_12  C4    C5   C6   N7    180.00   0.0  0
 YKN  CONST_13  C2    C1   C6   N7    180.00   0.0  0
 YKN  CONST_14  O14   C1   C6   N7      0.00   0.0  0
 YKN  CONST_15  O14   C8   N7   C6      0.00   0.0  0
 YKN  CONST_16  C3    C4   C5   C6      0.00   0.0  0
 YKN  CONST_17  C3    C2   C1   C6      0.00   0.0  0
 YKN  CONST_18  C2    C1   C6   C5      0.00   0.0  0
 YKN  CONST_19  O14   C1   C6   C5    180.00   0.0  0
 YKN  CONST_20  C2    C3   C4   C5      0.00   0.0  0
 YKN  CONST_21  C1    C6   C5   C4      0.00   0.0  0
 YKN  CONST_22  C1    C2   C3   C4      0.00   0.0  0
 YKN  CONST_23  O14   C1   C2   C3    180.00   0.0  0
 YKN  CONST_24  C6    N7   C8   C9    180.00   0.0  0
 YKN  CONST_25  C1    O14  C8   C9    180.00   0.0  0
 YKN  CONST_26  C16   N15  C13  S12   180.00   0.0  0
 YKN  CONST_27  C19   N20  C13  S12   180.00   0.0  0
 YKN  CONST_28  C17   C16  N15  C13   180.00   0.0  0
 YKN  CONST_29  C19   C18  C16  C17   180.00   0.0  0
 YKN  CONST_30  H19   C19  N20  C13   180.00   0.0  0
 YKN  CONST_31  H18   C18  C16  N15   180.00   0.0  0
 YKN  CONST_32  H5    C5   C6   N7      0.00   0.0  0
 YKN  CONST_33  H4    C4   C5   C6    180.00   0.0  0
 YKN  CONST_34  H2    C2   C1   C6    180.00   0.0  0
 YKN  CONST_35  H3    C3   C4   C5    180.00   0.0  0
 YKN  Var_01    N7    C8   C9   F10    55.10  30.0  2
 YKN  Var_02    N15   C13  S12  C9    179.28  30.0  2
 YKN  Var_03    C8    C9   S12  C13  -179.53  30.0  1
 YKN  Var_04    H171  C17  C16  N15    64.52  30.0  2

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
 YKN  plan-1  S12  0.020
 YKN  plan-1  C13  0.020
 YKN  plan-1  N15  0.020
 YKN  plan-1  C16  0.020
 YKN  plan-1  C17  0.020
 YKN  plan-1  C18  0.020
 YKN  plan-1  C19  0.020
 YKN  plan-1  N20  0.020
 YKN  plan-1  H18  0.020
 YKN  plan-1  H19  0.020
 YKN  plan-2  C9   0.020
 YKN  plan-2  C8   0.020
 YKN  plan-2  N7   0.020
 YKN  plan-2  C6   0.020
 YKN  plan-2  C5   0.020
 YKN  plan-2  C4   0.020
 YKN  plan-2  C3   0.020
 YKN  plan-2  C2   0.020
 YKN  plan-2  C1   0.020
 YKN  plan-2  O14  0.020
 YKN  plan-2  H5   0.020
 YKN  plan-2  H4   0.020
 YKN  plan-2  H3   0.020
 YKN  plan-2  H2   0.020

