# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 09:39:49 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: 5-{[(4,6-dimethylpyrimidin-2-yl)sulfanyl]methyl}-1,2-oxazole-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(C)nc(SCc2onc(c2)C(N)=O)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
 A0C  A0C  5-{[(4,6-dimethylpyrimidin-2-yl)sulfanyl]methyl}-1,2-oxazole-3-carboxamide  ligand  30  18  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A0C
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
 A0C  O1    O  O     0  -0.463   5.5164  -0.1578   1.6281
 A0C  C9    C  C     0   0.492   5.2402   0.0888   0.4656
 A0C  N3    N  NH2   0  -0.804   6.1131   0.4854  -0.4622
 A0C  C8    C  CR5   0   0.144   3.8289  -0.0503   0.0039
 A0C  C7    C  CR15  0  -0.479   2.7226  -0.4422   0.7925
 A0C  N2    N  N     0  -0.153   3.4745   0.1885  -1.2257
 A0C  O     O  O     0  -0.317   2.1468  -0.0366  -1.2875
 A0C  C6    C  CR5   0   0.462   1.6932  -0.4165  -0.0845
 A0C  C5    C  CH2   0  -0.653   0.2492  -0.7110   0.0462
 A0C  S     S  S2    0   0.068  -0.6777   0.8508  -0.1067
 A0C  C4    C  CR6   0   0.218  -2.3377   0.2845   0.0166
 A0C  N     N  N     0  -0.436  -3.2265   1.2635  -0.0385
 A0C  C3    C  CR6   0   0.287  -4.5060   0.9090   0.0547
 A0C  C10   C  CH3   0  -0.720  -5.5235   2.0003   0.0109
 A0C  C2    C  CR16  0  -0.400  -4.8643  -0.4273   0.1982
 A0C  N1    N  N     0  -0.428  -2.5711  -1.0046   0.1509
 A0C  C1    C  CR6   0   0.305  -3.8514  -1.3730   0.2419
 A0C  C     C  CH3   0  -0.719  -4.1288  -2.8326   0.3829
 A0C  H31N  H  HNH2  0   0.414   7.0856   0.5994  -0.2267
 A0C  H32N  H  HNH2  0   0.417   5.8348   0.6724  -1.4111
 A0C  H7    H  HCR5  0   0.296   2.6990  -0.6984   1.8374
 A0C  H51C  H  HCH2  0   0.320  -0.0806  -1.4066  -0.7252
 A0C  H52C  H  HCH2  0   0.318   0.0594  -1.1584   1.0193
 A0C  H101  H  HCH3  0   0.263  -5.3945   2.6089  -0.8842
 A0C  H102  H  HCH3  0   0.252  -6.5371   1.6059   0.0211
 A0C  H103  H  HCH3  0   0.265  -5.4037   2.6608   0.8706
 A0C  H2    H  HCR6  0   0.274  -5.9020  -0.7195   0.2775
 A0C  HC1   H  HCH3  0   0.265  -3.8421  -3.3588  -0.5291
 A0C  HC2   H  HCH3  0   0.262  -3.5399  -3.2550   1.1971
 A0C  HC3   H  HCH3  0   0.252  -5.1818  -3.0267   0.5735

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
 A0C  O1   C9    double    1.220  0.020  1.220
 A0C  C9   N3    single    1.334  0.020  1.334
 A0C  C9   C8    single    1.491  0.020  1.491
 A0C  C8   C7    aromatic  1.414  0.020  1.414
 A0C  C8   N2    aromatic  1.302  0.020  1.302
 A0C  C7   C6    aromatic  1.353  0.020  1.353
 A0C  N2   O     aromatic  1.348  0.020  1.348
 A0C  O    C6    aromatic  1.341  0.020  1.341
 A0C  C6   C5    single    1.479  0.020  1.479
 A0C  C5   S     single    1.823  0.020  1.823
 A0C  S    C4    single    1.758  0.020  1.758
 A0C  C4   N     aromatic  1.323  0.020  1.323
 A0C  C4   N1    aromatic  1.317  0.020  1.317
 A0C  N    C3    aromatic  1.331  0.020  1.331
 A0C  C3   C10   single    1.493  0.020  1.493
 A0C  C3   C2    aromatic  1.391  0.020  1.391
 A0C  C2   C1    aromatic  1.386  0.020  1.386
 A0C  N1   C1    aromatic  1.335  0.020  1.335
 A0C  C1   C     single    1.492  0.020  1.492
 A0C  N3   H31N  single    0.860  0.020  1.020
 A0C  N3   H32N  single    0.860  0.020  1.020
 A0C  C7   H7    single    0.930  0.020  1.080
 A0C  C5   H51C  single    0.970  0.020  1.090
 A0C  C5   H52C  single    0.970  0.020  1.090
 A0C  C10  H101  single    0.970  0.020  1.090
 A0C  C10  H102  single    0.970  0.020  1.090
 A0C  C10  H103  single    0.970  0.020  1.090
 A0C  C2   H2    single    0.930  0.020  1.080
 A0C  C    HC1   single    0.970  0.020  1.090
 A0C  C    HC2   single    0.970  0.020  1.090
 A0C  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
 A0C  C8    C9   N3    115.56  3.000
 A0C  C8    C9   O1    119.37  3.000
 A0C  N3    C9   O1    125.07  3.000
 A0C  H32N  N3   H31N  117.81  3.000
 A0C  H32N  N3   C9    122.01  3.000
 A0C  H31N  N3   C9    120.18  3.000
 A0C  N2    C8   C7    111.39  3.000
 A0C  N2    C8   C9    122.21  3.000
 A0C  C7    C8   C9    126.41  3.000
 A0C  H7    C7   C6    128.13  3.000
 A0C  H7    C7   C8    128.66  3.000
 A0C  C6    C7   C8    103.21  3.000
 A0C  O     N2   C8    106.31  3.000
 A0C  C6    O    N2    109.84  3.000
 A0C  C5    C6   O     117.77  3.000
 A0C  C5    C6   C7    132.98  3.000
 A0C  O     C6   C7    109.25  3.000
 A0C  H52C  C5   H51C  108.53  3.000
 A0C  H52C  C5   S     109.80  3.000
 A0C  H51C  C5   S     109.49  3.000
 A0C  H52C  C5   C6    109.34  3.000
 A0C  H51C  C5   C6    111.10  3.000
 A0C  S     C5   C6    108.57  3.000
 A0C  C4    S    C5    101.44  3.000
 A0C  N1    C4   N     127.54  3.000
 A0C  N1    C4   S     119.33  3.000
 A0C  N     C4   S     113.14  3.000
 A0C  C3    N    C4    116.47  3.000
 A0C  C2    C3   C10   121.99  3.000
 A0C  C2    C3   N     120.71  3.000
 A0C  C10   C3   N     117.29  3.000
 A0C  H103  C10  H102  108.33  3.000
 A0C  H103  C10  H101  107.23  3.000
 A0C  H102  C10  H101  108.69  3.000
 A0C  H103  C10  C3    110.16  3.000
 A0C  H102  C10  C3    111.71  3.000
 A0C  H101  C10  C3    110.58  3.000
 A0C  H2    C2   C1    120.97  3.000
 A0C  H2    C2   C3    120.96  3.000
 A0C  C1    C2   C3    118.06  3.000
 A0C  C1    N1   C4    116.55  3.000
 A0C  C     C1   N1    117.03  3.000
 A0C  C     C1   C2    122.30  3.000
 A0C  N1    C1   C2    120.67  3.000
 A0C  HC3   C    HC2   108.85  3.000
 A0C  HC3   C    HC1   108.35  3.000
 A0C  HC2   C    HC1   107.19  3.000
 A0C  HC3   C    C1    111.78  3.000
 A0C  HC2   C    C1    110.44  3.000
 A0C  HC1   C    C1    110.11  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
 A0C  CONST_01  O     C6   C7  C8     0.00   0.0  0
 A0C  CONST_02  C6    O    N2  C8     0.00   0.0  0
 A0C  CONST_03  O     N2   C8  C7     0.00   0.0  0
 A0C  CONST_04  N2    O    C6  C7     0.00   0.0  0
 A0C  CONST_05  C6    C7   C8  N2     0.00   0.0  0
 A0C  CONST_06  C2    C3   N   C4     0.00   0.0  0
 A0C  CONST_07  C2    C1   N1  C4     0.00   0.0  0
 A0C  CONST_08  C1    N1   C4  N      0.00   0.0  0
 A0C  CONST_09  C1    C2   C3  N      0.00   0.0  0
 A0C  CONST_10  N1    C4   N   C3     0.00   0.0  0
 A0C  CONST_11  N1    C1   C2  C3     0.00   0.0  0
 A0C  CONST_12  C6    C7   C8  C9   180.00   0.0  0
 A0C  CONST_13  O     N2   C8  C9   180.00   0.0  0
 A0C  CONST_14  C5    C6   C7  C8   180.00   0.0  0
 A0C  CONST_15  C5    C6   O   N2   180.00   0.0  0
 A0C  CONST_16  C3    N    C4  S    180.00   0.0  0
 A0C  CONST_17  C1    N1   C4  S    180.00   0.0  0
 A0C  CONST_18  C10   C3   N   C4   180.00   0.0  0
 A0C  CONST_19  C     C1   N1  C4   180.00   0.0  0
 A0C  CONST_20  C     C1   C2  C3   180.00   0.0  0
 A0C  CONST_21  C1    C2   C3  C10  180.00   0.0  0
 A0C  CONST_22  H7    C7   C8  N2   180.00   0.0  0
 A0C  CONST_23  H2    C2   C3  N    180.00   0.0  0
 A0C  CONST_24  H31N  N3   C9  C8   180.00   0.0  0
 A0C  CONST_25  H32N  N3   C9  C8     0.00   0.0  0
 A0C  Var_01    C7    C8   C9  O1     0.53  30.0  2
 A0C  Var_02    S     C5   C6  C7   110.30  30.0  2
 A0C  Var_03    N     C4   S   C5   178.58  30.0  2
 A0C  Var_04    H101  C10  C3  N     54.66  30.0  2
 A0C  Var_05    HC1   C    C1  C2   113.05  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
 A0C  plan-1  C9    0.020
 A0C  plan-1  C8    0.020
 A0C  plan-1  C7    0.020
 A0C  plan-1  N2    0.020
 A0C  plan-1  O     0.020
 A0C  plan-1  C6    0.020
 A0C  plan-1  C5    0.020
 A0C  plan-1  H7    0.020
 A0C  plan-2  S     0.020
 A0C  plan-2  C4    0.020
 A0C  plan-2  N     0.020
 A0C  plan-2  C3    0.020
 A0C  plan-2  C10   0.020
 A0C  plan-2  C2    0.020
 A0C  plan-2  N1    0.020
 A0C  plan-2  C1    0.020
 A0C  plan-2  C     0.020
 A0C  plan-2  H2    0.020
 A0C  plan-3  O1    0.020
 A0C  plan-3  C9    0.020
 A0C  plan-3  N3    0.020
 A0C  plan-3  C8    0.020
 A0C  plan-3  H31N  0.020
 A0C  plan-3  H32N  0.020

