# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 12:21:06 2021
#   Inital geometry file: a 72 line input string
#   Ligand name: 3,5-dimethyl-4-[(6-methylpyrimidin-4-yl)sulfanylmethyl]-1,2-oxazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1onc(C)c1CSc2cc(C)ncn2
#
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
 QGQ  QGQ  3,5-dimethyl-4-[(6-methylpyrimidin-4-yl)sulfanylmethyl]-1,2-oxazole  ligand  29  16  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_QGQ
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
 QGQ  N1   N  N     0  -0.405  29.9814  15.4083  -2.6756
 QGQ  C4   C  CH2   0  -0.706  30.2380  15.2938   0.1980
 QGQ  C5   C  CR5   0  -0.108  31.3091  16.3162   0.1227
 QGQ  C6   C  CR5   0   0.256  31.3742  17.5453   0.8411
 QGQ  C7   C  CH3   0  -0.744  30.3859  18.0743   1.8162
 QGQ  C8   C  CR5   0   0.418  32.4507  16.3129  -0.6121
 QGQ  C10  C  CR16  0   0.053  30.1000  15.4778  -3.9943
 QGQ  C9   C  CH3   0  -0.749  33.0521  15.3449  -1.5553
 QGQ  O    O  O     0  -0.351  33.1332  17.4348  -0.3617
 QGQ  N    N  N     0  -0.184  32.4564  18.2013   0.5450
 QGQ  S    S  S2    0   0.076  28.6305  15.8848  -0.4265
 QGQ  C3   C  CR6   0   0.131  28.8940  15.9531  -2.1558
 QGQ  C2   C  CR16  0  -0.347  27.9276  16.5663  -2.9500
 QGQ  N2   N  N     0  -0.427  29.2490  16.0234  -4.8397
 QGQ  C1   C  CR6   0   0.282  28.1461  16.5741  -4.3165
 QGQ  C    C  CH3   0  -0.720  27.1692  17.1859  -5.2653
 QGQ  H1   H  HCH2  0   0.316  30.0204  15.0234   1.2333
 QGQ  H2   H  HCH2  0   0.312  30.5097  14.3795  -0.3263
 QGQ  H3   H  HCH3  0   0.263  30.7232  19.0143   2.2479
 QGQ  H4   H  HCH3  0   0.258  29.4222  18.2401   1.3342
 QGQ  H5   H  HCH3  0   0.258  30.2248  17.3606   2.6249
 QGQ  H6   H  HCR6  0   0.261  30.9948  15.0333  -4.4171
 QGQ  H7   H  HCH3  0   0.265  33.2251  15.8006  -2.5308
 QGQ  H8   H  HCH3  0   0.267  34.0098  14.9797  -1.1820
 QGQ  H9   H  HCH3  0   0.266  32.3872  14.4982  -1.6962
 QGQ  H10  H  HCR6  0   0.285  27.0448  17.0201  -2.5203
 QGQ  H11  H  HCH3  0   0.264  26.6957  16.4092  -5.8683
 QGQ  H12  H  HCH3  0   0.251  26.3870  17.7327  -4.7435
 QGQ  H13  H  HCH3  0   0.260  27.6754  17.8636  -5.9527

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
 QGQ  C    C1   single    1.493  0.020  1.493
 QGQ  N2   C1   aromatic  1.339  0.020  1.339
 QGQ  N2   C10  aromatic  1.318  0.020  1.318
 QGQ  C1   C2   aromatic  1.384  0.020  1.384
 QGQ  C10  N1   aromatic  1.326  0.020  1.326
 QGQ  C2   C3   aromatic  1.393  0.020  1.393
 QGQ  N1   C3   aromatic  1.323  0.020  1.323
 QGQ  C3   S    single    1.751  0.020  1.751
 QGQ  C9   C8   single    1.479  0.020  1.479
 QGQ  C8   O    aromatic  1.337  0.020  1.337
 QGQ  C8   C5   aromatic  1.358  0.020  1.358
 QGQ  O    N    aromatic  1.367  0.020  1.367
 QGQ  S    C4   single    1.823  0.020  1.823
 QGQ  C5   C4   single    1.483  0.020  1.483
 QGQ  C5   C6   aromatic  1.425  0.020  1.425
 QGQ  N    C6   aromatic  1.300  0.020  1.300
 QGQ  C6   C7   single    1.486  0.020  1.486
 QGQ  C4   H1   single    0.970  0.020  1.090
 QGQ  C4   H2   single    0.970  0.020  1.090
 QGQ  C7   H3   single    0.970  0.020  1.090
 QGQ  C7   H4   single    0.970  0.020  1.090
 QGQ  C7   H5   single    0.970  0.020  1.090
 QGQ  C10  H6   single    0.930  0.020  1.080
 QGQ  C9   H7   single    0.970  0.020  1.090
 QGQ  C9   H8   single    0.970  0.020  1.090
 QGQ  C9   H9   single    0.970  0.020  1.090
 QGQ  C2   H10  single    0.930  0.020  1.080
 QGQ  C    H11  single    0.970  0.020  1.090
 QGQ  C    H12  single    0.970  0.020  1.090
 QGQ  C    H13  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
 QGQ  C3   N1   C10  116.29  3.000
 QGQ  H2   C4   H1   107.37  3.000
 QGQ  H2   C4   S    109.11  3.000
 QGQ  H1   C4   S    103.26  3.000
 QGQ  H2   C4   C5   111.99  3.000
 QGQ  H1   C4   C5   111.28  3.000
 QGQ  S    C4   C5   113.33  3.000
 QGQ  C8   C5   C6   103.68  3.000
 QGQ  C6   C5   C4   127.02  3.000
 QGQ  C8   C5   C4   129.29  3.000
 QGQ  N    C6   C7   121.58  3.000
 QGQ  C7   C6   C5   127.42  3.000
 QGQ  N    C6   C5   111.01  3.000
 QGQ  H5   C7   H4   107.26  3.000
 QGQ  H5   C7   H3   108.48  3.000
 QGQ  H4   C7   H3   108.55  3.000
 QGQ  H5   C7   C6   110.61  3.000
 QGQ  H4   C7   C6   110.61  3.000
 QGQ  H3   C7   C6   111.21  3.000
 QGQ  O    C8   C9   117.45  3.000
 QGQ  O    C8   C5   109.02  3.000
 QGQ  C9   C8   C5   133.51  3.000
 QGQ  H6   C10  N2   116.88  3.000
 QGQ  H6   C10  N1   116.11  3.000
 QGQ  N2   C10  N1   127.01  3.000
 QGQ  H9   C9   H8   108.72  3.000
 QGQ  H9   C9   H7   107.88  3.000
 QGQ  H8   C9   H7   107.87  3.000
 QGQ  H9   C9   C8   110.12  3.000
 QGQ  H8   C9   C8   110.96  3.000
 QGQ  H7   C9   C8   111.19  3.000
 QGQ  N    O    C8   110.01  3.000
 QGQ  O    N    C6   106.28  3.000
 QGQ  C3   S    C4   102.61  3.000
 QGQ  C2   C3   S    118.42  3.000
 QGQ  S    C3   N1   119.73  3.000
 QGQ  C2   C3   N1   121.84  3.000
 QGQ  H10  C2   C1   121.25  3.000
 QGQ  H10  C2   C3   121.63  3.000
 QGQ  C1   C2   C3   117.12  3.000
 QGQ  C1   N2   C10  116.83  3.000
 QGQ  C    C1   N2   117.33  3.000
 QGQ  N2   C1   C2   120.90  3.000
 QGQ  C    C1   C2   121.77  3.000
 QGQ  H13  C    H12  108.90  3.000
 QGQ  H13  C    H11  107.19  3.000
 QGQ  H12  C    H11  108.11  3.000
 QGQ  H13  C    C1   110.59  3.000
 QGQ  H12  C    C1   111.82  3.000
 QGQ  H11  C    C1   110.09  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
 QGQ  CONST_01  C1   N2   C10  N1      0.00   0.0  0
 QGQ  CONST_02  C1   C2   C3   N1      0.00   0.0  0
 QGQ  CONST_03  N    O    C8   C5      0.00   0.0  0
 QGQ  CONST_04  O    N    C6   C5      0.00   0.0  0
 QGQ  CONST_05  O    C8   C5   C6      0.00   0.0  0
 QGQ  CONST_06  C8   O    N    C6      0.00   0.0  0
 QGQ  CONST_07  N    C6   C5   C8      0.00   0.0  0
 QGQ  CONST_08  C2   C1   N2   C10     0.00   0.0  0
 QGQ  CONST_09  C2   C3   N1   C10     0.00   0.0  0
 QGQ  CONST_10  N2   C1   C2   C3      0.00   0.0  0
 QGQ  CONST_11  N2   C10  N1   C3      0.00   0.0  0
 QGQ  CONST_12  O    C8   C5   C4    180.00   0.0  0
 QGQ  CONST_13  N    C6   C5   C4    180.00   0.0  0
 QGQ  CONST_14  C9   C8   C5   C6    180.00   0.0  0
 QGQ  CONST_15  C8   C5   C6   C7    180.00   0.0  0
 QGQ  CONST_16  O    N    C6   C7    180.00   0.0  0
 QGQ  CONST_17  C    C1   N2   C10   180.00   0.0  0
 QGQ  CONST_18  S    C3   N1   C10   180.00   0.0  0
 QGQ  CONST_19  N    O    C8   C9    180.00   0.0  0
 QGQ  CONST_20  C1   C2   C3   S     180.00   0.0  0
 QGQ  CONST_21  C    C1   C2   C3    180.00   0.0  0
 QGQ  CONST_22  H10  C2   C3   N1    180.00   0.0  0
 QGQ  CONST_23  H6   C10  N1   C3    180.00   0.0  0
 QGQ  Var_01    C2   C3   S    C4   -170.22  30.0  1
 QGQ  Var_02    S    C4   C5   C6     65.40  30.0  2
 QGQ  Var_03    H7   C9   C8   C5    122.94  30.0  2
 QGQ  Var_04    H3   C7   C6   C5    177.03  30.0  2
 QGQ  Var_05    H11  C    C1   C2   -111.47  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
 QGQ  plan-1  C4   0.020
 QGQ  plan-1  C5   0.020
 QGQ  plan-1  C6   0.020
 QGQ  plan-1  C7   0.020
 QGQ  plan-1  C8   0.020
 QGQ  plan-1  C9   0.020
 QGQ  plan-1  O    0.020
 QGQ  plan-1  N    0.020
 QGQ  plan-2  N1   0.020
 QGQ  plan-2  C10  0.020
 QGQ  plan-2  S    0.020
 QGQ  plan-2  C3   0.020
 QGQ  plan-2  C2   0.020
 QGQ  plan-2  N2   0.020
 QGQ  plan-2  C1   0.020
 QGQ  plan-2  C    0.020
 QGQ  plan-2  H6   0.020
 QGQ  plan-2  H10  0.020

