# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 10:46:42 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: 5-{[(4,6-dimethylpyrimidin-2-yl)sulfanyl]methyl}-N-[(2-methylpyridin-4-yl)methyl]-1,2-oxazole-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(CNC(=O)c2cc(CSc3nc(C)cc(C)n3)on2)ccn1
#
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
 KXU  KXU  5-{[(4,6-dimethylpyrimidin-2-yl)sulfanyl]methyl}-N-[(2-methylpyridin-4-yl)methyl]-1,2-oxazole-3-carboxamide  ligand  45  26  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_KXU
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
 KXU  O1    O  O     0  -0.473   2.4399  -1.8916   2.3391
 KXU  C9    C  C     0   0.547   2.4175  -1.3070   1.2680
 KXU  N3    N  NH1   0  -0.647   3.5016  -0.8447   0.6397
 KXU  C10   C  CH2   0  -0.313   4.8317  -1.0051   1.1979
 KXU  C11   C  CR6   0   0.142   5.8374  -0.3405   0.3015
 KXU  C15   C  CR16  0  -0.373   6.1666   0.9971   0.4663
 KXU  C14   C  CR6   0   0.250   7.0877   1.5941  -0.3911
 KXU  C16   C  CH3   0  -0.718   7.4930   3.0255  -0.2136
 KXU  N4    N  N     0  -0.426   7.6639   0.9161  -1.3821
 KXU  C13   C  CR16  0  -0.066   7.3451  -0.3618  -1.5437
 KXU  C12   C  CR16  0  -0.364   6.4442  -1.0366  -0.7361
 KXU  C8    C  CR5   0   0.147   1.1189  -1.0678   0.5787
 KXU  C7    C  CR15  0  -0.479  -0.1633  -1.4198   1.0600
 KXU  N2    N  N     0  -0.155   1.0465  -0.4831  -0.5821
 KXU  O     O  O     0  -0.318  -0.2625  -0.4338  -0.9000
 KXU  C6    C  CR5   0   0.462  -0.9894  -0.9940   0.0774
 KXU  C5    C  CH2   0  -0.655  -2.4594  -1.0254  -0.0866
 KXU  S     S  S2    0   0.068  -3.0826   0.6853  -0.0039
 KXU  C4    C  CR6   0   0.218  -4.8163   0.4325  -0.1506
 KXU  N     N  N     0  -0.437  -5.5089   1.5605  -0.1273
 KXU  C3    C  CR6   0   0.288  -6.8310   1.4464  -0.2233
 KXU  C17   C  CH3   0  -0.721  -7.6314   2.7062  -0.2220
 KXU  C2    C  CR16  0  -0.400  -7.4297   0.1955  -0.3361
 KXU  N1    N  N     0  -0.428  -5.2825  -0.7936  -0.2607
 KXU  C1    C  CR6   0   0.305  -6.6089  -0.9212  -0.3548
 KXU  C     C  CH3   0  -0.718  -7.1500  -2.3061  -0.4820
 KXU  H3    H  HNH1  0   0.417   3.3951  -0.3625  -0.2399
 KXU  H101  H  HCH2  0   0.268   4.8700  -0.5643   2.1963
 KXU  H102  H  HCH2  0   0.268   5.0672  -2.0666   1.3027
 KXU  H15   H  HCR6  0   0.265   5.7169   1.5793   1.2617
 KXU  H12   H  HCR6  0   0.269   6.2251  -2.0811  -0.9155
 KXU  H161  H  HCH3  0   0.255   8.4380   3.0877   0.3303
 KXU  H162  H  HCH3  0   0.250   7.6409   3.5113  -1.1771
 KXU  H163  H  HCH3  0   0.245   6.7512   3.5881   0.3507
 KXU  H13   H  HCR6  0   0.263   7.8333  -0.8816  -2.3608
 KXU  H7    H  HCR5  0   0.296  -0.4245  -1.9077   1.9828
 KXU  H51C  H  HCH2  0   0.320  -2.7409  -1.4688  -1.0419
 KXU  H52C  H  HCH2  0   0.318  -2.8971  -1.6185   0.7132
 KXU  H171  H  HCH3  0   0.266  -7.5150   3.2224  -1.1768
 KXU  H172  H  HCH3  0   0.252  -8.6911   2.5095  -0.0739
 KXU  H173  H  HCH3  0   0.260  -7.2837   3.3847   0.5560
 KXU  H2    H  HCR6  0   0.274  -8.5040   0.0972  -0.4049
 KXU  HC1   H  HCH3  0   0.264  -6.8067  -2.7601  -1.4129
 KXU  HC2   H  HCH3  0   0.262  -6.7888  -2.9323   0.3340
 KXU  HC3   H  HCH3  0   0.252  -8.2377  -2.3164  -0.4753

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
 KXU  O1   C9    double    1.220  0.020  1.220
 KXU  C9   N3    single    1.336  0.020  1.336
 KXU  C9   C8    single    1.490  0.020  1.490
 KXU  N3   C10   single    1.451  0.020  1.451
 KXU  C10  C11   single    1.502  0.020  1.502
 KXU  C11  C15   aromatic  1.387  0.020  1.387
 KXU  C11  C12   aromatic  1.389  0.020  1.389
 KXU  C15  C14   aromatic  1.393  0.020  1.393
 KXU  C14  C16   single    1.498  0.020  1.498
 KXU  C14  N4    aromatic  1.332  0.020  1.332
 KXU  N4   C13   aromatic  1.327  0.020  1.327
 KXU  C13  C12   aromatic  1.385  0.020  1.385
 KXU  C8   C7    aromatic  1.414  0.020  1.414
 KXU  C8   N2    aromatic  1.302  0.020  1.302
 KXU  C7   C6    aromatic  1.353  0.020  1.353
 KXU  N2   O     aromatic  1.348  0.020  1.348
 KXU  O    C6    aromatic  1.341  0.020  1.341
 KXU  C6   C5    single    1.479  0.020  1.479
 KXU  C5   S     single    1.823  0.020  1.823
 KXU  S    C4    single    1.758  0.020  1.758
 KXU  C4   N     aromatic  1.324  0.020  1.324
 KXU  C4   N1    aromatic  1.316  0.020  1.316
 KXU  N    C3    aromatic  1.331  0.020  1.331
 KXU  C3   C17   single    1.493  0.020  1.493
 KXU  C3   C2    aromatic  1.391  0.020  1.391
 KXU  C2   C1    aromatic  1.386  0.020  1.386
 KXU  N1   C1    aromatic  1.336  0.020  1.336
 KXU  C1   C     single    1.492  0.020  1.492
 KXU  N3   H3    single    0.860  0.020  1.020
 KXU  C10  H101  single    0.970  0.020  1.090
 KXU  C10  H102  single    0.970  0.020  1.090
 KXU  C15  H15   single    0.930  0.020  1.080
 KXU  C12  H12   single    0.930  0.020  1.080
 KXU  C16  H161  single    0.970  0.020  1.090
 KXU  C16  H162  single    0.970  0.020  1.090
 KXU  C16  H163  single    0.970  0.020  1.090
 KXU  C13  H13   single    0.930  0.020  1.080
 KXU  C7   H7    single    0.930  0.020  1.080
 KXU  C5   H51C  single    0.970  0.020  1.090
 KXU  C5   H52C  single    0.970  0.020  1.090
 KXU  C17  H171  single    0.970  0.020  1.090
 KXU  C17  H172  single    0.970  0.020  1.090
 KXU  C17  H173  single    0.970  0.020  1.090
 KXU  C2   H2    single    0.930  0.020  1.080
 KXU  C    HC1   single    0.970  0.020  1.090
 KXU  C    HC2   single    0.970  0.020  1.090
 KXU  C    HC3   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
 KXU  C8    C9   N3    115.75  3.000
 KXU  C8    C9   O1    119.94  3.000
 KXU  N3    C9   O1    124.32  3.000
 KXU  H3    N3   C10   119.01  3.000
 KXU  H3    N3   C9    119.34  3.000
 KXU  C10   N3   C9    121.65  3.000
 KXU  H102  C10  H101  107.28  3.000
 KXU  H102  C10  C11   110.05  3.000
 KXU  H101  C10  C11   110.09  3.000
 KXU  H102  C10  N3    109.99  3.000
 KXU  H101  C10  N3    109.83  3.000
 KXU  C11   C10  N3    109.58  3.000
 KXU  C12   C11  C15   117.92  3.000
 KXU  C12   C11  C10   121.10  3.000
 KXU  C15   C11  C10   120.96  3.000
 KXU  H15   C15  C14   119.74  3.000
 KXU  H15   C15  C11   120.46  3.000
 KXU  C14   C15  C11   119.80  3.000
 KXU  N4    C14  C16   117.23  3.000
 KXU  N4    C14  C15   121.73  3.000
 KXU  C16   C14  C15   121.03  3.000
 KXU  H163  C16  H162  108.70  3.000
 KXU  H163  C16  H161  107.57  3.000
 KXU  H162  C16  H161  107.31  3.000
 KXU  H163  C16  C14   111.77  3.000
 KXU  H162  C16  C14   110.99  3.000
 KXU  H161  C16  C14   110.33  3.000
 KXU  C13   N4   C14   118.48  3.000
 KXU  H13   C13  C12   119.90  3.000
 KXU  H13   C13  N4    116.44  3.000
 KXU  C12   C13  N4    123.67  3.000
 KXU  H12   C12  C13   120.34  3.000
 KXU  H12   C12  C11   121.27  3.000
 KXU  C13   C12  C11   118.39  3.000
 KXU  N2    C8   C7    111.40  3.000
 KXU  N2    C8   C9    122.22  3.000
 KXU  C7    C8   C9    126.38  3.000
 KXU  H7    C7   C6    128.13  3.000
 KXU  H7    C7   C8    128.68  3.000
 KXU  C6    C7   C8    103.19  3.000
 KXU  O     N2   C8    106.30  3.000
 KXU  C6    O    N2    109.84  3.000
 KXU  C5    C6   O     117.83  3.000
 KXU  C5    C6   C7    132.90  3.000
 KXU  O     C6   C7    109.27  3.000
 KXU  H52C  C5   H51C  108.58  3.000
 KXU  H52C  C5   S     109.93  3.000
 KXU  H51C  C5   S     109.46  3.000
 KXU  H52C  C5   C6    109.27  3.000
 KXU  H51C  C5   C6    111.25  3.000
 KXU  S     C5   C6    108.35  3.000
 KXU  C4    S    C5    101.45  3.000
 KXU  N1    C4   N     127.58  3.000
 KXU  N1    C4   S     119.35  3.000
 KXU  N     C4   S     113.07  3.000
 KXU  C3    N    C4    116.45  3.000
 KXU  C2    C3   C17   121.88  3.000
 KXU  C2    C3   N     120.70  3.000
 KXU  C17   C3   N     117.41  3.000
 KXU  H173  C17  H172  109.05  3.000
 KXU  H173  C17  H171  107.23  3.000
 KXU  H172  C17  H171  107.96  3.000
 KXU  H173  C17  C3    110.80  3.000
 KXU  H172  C17  C3    111.71  3.000
 KXU  H171  C17  C3    109.95  3.000
 KXU  H2    C2   C1    120.96  3.000
 KXU  H2    C2   C3    120.97  3.000
 KXU  C1    C2   C3    118.08  3.000
 KXU  C1    N1   C4    116.52  3.000
 KXU  C     C1   N1    117.04  3.000
 KXU  C     C1   C2    122.29  3.000
 KXU  N1    C1   C2    120.67  3.000
 KXU  HC3   C    HC2   108.73  3.000
 KXU  HC3   C    HC1   108.42  3.000
 KXU  HC2   C    HC1   107.18  3.000
 KXU  HC3   C    C1    111.77  3.000
 KXU  HC2   C    C1    110.44  3.000
 KXU  HC1   C    C1    110.17  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
 KXU  CONST_01  N4    C14  C15  C11     0.00   0.0  0
 KXU  CONST_02  N4    C13  C12  C11     0.00   0.0  0
 KXU  CONST_03  C13   C12  C11  C15     0.00   0.0  0
 KXU  CONST_04  C13   N4   C14  C15     0.00   0.0  0
 KXU  CONST_05  C12   C11  C15  C14     0.00   0.0  0
 KXU  CONST_06  C12   C13  N4   C14     0.00   0.0  0
 KXU  CONST_07  O     C6   C7   C8      0.00   0.0  0
 KXU  CONST_08  C6    O    N2   C8      0.00   0.0  0
 KXU  CONST_09  O     N2   C8   C7      0.00   0.0  0
 KXU  CONST_10  N2    O    C6   C7      0.00   0.0  0
 KXU  CONST_11  C6    C7   C8   N2      0.00   0.0  0
 KXU  CONST_12  C2    C3   N    C4      0.00   0.0  0
 KXU  CONST_13  C2    C1   N1   C4      0.00   0.0  0
 KXU  CONST_14  C1    N1   C4   N       0.00   0.0  0
 KXU  CONST_15  C1    C2   C3   N       0.00   0.0  0
 KXU  CONST_16  N1    C4   N    C3      0.00   0.0  0
 KXU  CONST_17  N1    C1   C2   C3      0.00   0.0  0
 KXU  CONST_18  C6    C7   C8   C9    180.00   0.0  0
 KXU  CONST_19  O     N2   C8   C9    180.00   0.0  0
 KXU  CONST_20  C14   C15  C11  C10   180.00   0.0  0
 KXU  CONST_21  C13   C12  C11  C10   180.00   0.0  0
 KXU  CONST_22  C16   C14  C15  C11   180.00   0.0  0
 KXU  CONST_23  C13   N4   C14  C16   180.00   0.0  0
 KXU  CONST_24  C5    C6   C7   C8    180.00   0.0  0
 KXU  CONST_25  C5    C6   O    N2    180.00   0.0  0
 KXU  CONST_26  C3    N    C4   S     180.00   0.0  0
 KXU  CONST_27  C1    N1   C4   S     180.00   0.0  0
 KXU  CONST_28  C17   C3   N    C4    180.00   0.0  0
 KXU  CONST_29  C     C1   N1   C4    180.00   0.0  0
 KXU  CONST_30  C     C1   C2   C3    180.00   0.0  0
 KXU  CONST_31  C1    C2   C3   C17   180.00   0.0  0
 KXU  CONST_32  H13   C13  C12  C11   180.00   0.0  0
 KXU  CONST_33  H12   C12  C11  C15   180.00   0.0  0
 KXU  CONST_34  H15   C15  C14  N4    180.00   0.0  0
 KXU  CONST_35  H7    C7   C8   N2    180.00   0.0  0
 KXU  CONST_36  H2    C2   C3   N     180.00   0.0  0
 KXU  CONST_37  C8    C9   N3   C10   180.00   0.0  0
 KXU  CONST_38  H3    N3   C9   C8      0.00   0.0  0
 KXU  CONST_39  C10   N3   C9   O1      0.00   0.0  0
 KXU  Var_01    C7    C8   C9   O1      2.13  30.0  2
 KXU  Var_02    C15   C11  C10  N3     88.88  30.0  2
 KXU  Var_03    S     C5   C6   C7    111.70  30.0  2
 KXU  Var_04    N     C4   S    C5   -179.51  30.0  2
 KXU  Var_05    H161  C16  C14  C15    97.94  30.0  2
 KXU  Var_06    H171  C17  C3   N      73.25  30.0  2
 KXU  Var_07    HC1   C    C1   C2    116.08  30.0  2
 KXU  Var_08    C11   C10  N3   C9   -177.74  30.0  3

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
 KXU  plan-1  C9   0.020
 KXU  plan-1  C8   0.020
 KXU  plan-1  C7   0.020
 KXU  plan-1  N2   0.020
 KXU  plan-1  O    0.020
 KXU  plan-1  C6   0.020
 KXU  plan-1  C5   0.020
 KXU  plan-1  H7   0.020
 KXU  plan-2  C10  0.020
 KXU  plan-2  C11  0.020
 KXU  plan-2  C15  0.020
 KXU  plan-2  C14  0.020
 KXU  plan-2  C16  0.020
 KXU  plan-2  N4   0.020
 KXU  plan-2  C13  0.020
 KXU  plan-2  C12  0.020
 KXU  plan-2  H15  0.020
 KXU  plan-2  H12  0.020
 KXU  plan-2  H13  0.020
 KXU  plan-3  S    0.020
 KXU  plan-3  C4   0.020
 KXU  plan-3  N    0.020
 KXU  plan-3  C3   0.020
 KXU  plan-3  C17  0.020
 KXU  plan-3  C2   0.020
 KXU  plan-3  N1   0.020
 KXU  plan-3  C1   0.020
 KXU  plan-3  C    0.020
 KXU  plan-3  H2   0.020
 KXU  plan-4  O1   0.020
 KXU  plan-4  C9   0.020
 KXU  plan-4  N3   0.020
 KXU  plan-4  C10  0.020
 KXU  plan-4  C8   0.020
 KXU  plan-4  H3   0.020

