# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 23:25:49 2021
#   Inital geometry file: a 142 line input string
#   Ligand name: 3-methyl-5-[[(4~{R})-4-methyl-4-oxidanyl-1,2-oxazolidin-2-yl]carbonyl]-6-[[5-methyl-3-(trifluoromethyl)-1~{H}-pyrazol-4-yl]methyl]-1-propan-2-yl-thieno[2,3-d]pyrimidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)N1C(=O)N(C)C(=O)c2c1sc(Cc3c(C)[nH]nc3C(F)(F)F)c2C(=O)N4C[C@@](C)(O)CO4
#
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
 EY0  EY0  3-methyl-5-[[(4~{R})-4-methyl-4-oxidanyl-1,2-oxazolidin-2-yl]carbonyl]-6-[[5-methyl-3-(trifluoromethyl)-1~{H}-pyrazol-4-yl]methyl]-1-propan-2-yl-thieno[2,3-d]pyrimidine-2,4-dione  ligand  59  35  .  2022-03-18  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EY0
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
 EY0  C2   C  CR56  0   0.130  108.7412  110.7401  106.6122
 EY0  C3   C  CR56  0  -0.022  109.3201  111.7641  107.3130
 EY0  C4   C  CR6   0   0.571  108.7043  112.2664  108.5090
 EY0  C6   C  CR6   0   0.772  106.9559  110.5621  108.1597
 EY0  C13  C  CH3   0  -0.654  106.4469  109.5321  104.8730
 EY0  C14  C  CH3   0  -0.664  107.8217  107.8029  106.1467
 EY0  C17  C  CR5   0  -0.166  112.7269  110.4710  104.3719
 EY0  C18  C  CR5   0   0.412  113.5366  109.7519  105.2296
 EY0  C21  C  CR5   0  -0.051  112.6899  109.6829  103.2068
 EY0  C22  C  CT    0   1.068  111.9623  109.9718  101.9460
 EY0  C26  C  CH3   0  -0.747  113.9859  110.0341  106.6165
 EY0  C30  C  CH2   0  -0.182  111.0951  116.7282  107.2611
 EY0  C31  C  CT    0   0.152  110.2650  116.4868  105.9958
 EY0  C32  C  CH2   0  -0.311  109.9375  114.9952  106.1879
 EY0  C35  C  CH3   0  -0.666  111.0843  116.7135  104.7359
 EY0  C8   C  CR5   0  -0.173  110.8505  111.5667  105.5859
 EY0  C9   C  CR5   0  -0.029  110.5307  112.2326  106.7190
 EY0  F23  F  F     0  -0.302  112.0590  108.9769  101.0671
 EY0  F24  F  F     0  -0.318  110.6547  110.1835  102.1734
 EY0  F25  F  F     0  -0.316  112.4225  111.0815  101.3483
 EY0  N1   N  NR6   0  -0.605  107.5821  110.1361  107.0000
 EY0  N19  N  NR15  0  -0.470  113.9063  108.6527  104.5459
 EY0  N20  N  N     0  -0.270  113.4095  108.5860  103.3245
 EY0  N28  N  NT    0  -0.176  111.1136  114.5163  106.8884
 EY0  N5   N  NR6   0  -0.600  107.5381  111.6028  108.8639
 EY0  O10  O  O     0  -0.453  109.1523  113.1923  109.1608
 EY0  O11  O  O     0  -0.478  105.9284  110.0543  108.5589
 EY0  O29  O  O2    0  -0.383  111.8812  115.5556  107.3974
 EY0  O33  O  O     0  -0.460  112.3368  113.0194  108.0592
 EY0  S7   S  S2    0   0.272  109.6724  110.3415  105.2195
 EY0  H2   H  HCH3  0   0.250  105.7978  110.4000  104.9826
 EY0  H3   H  HCH3  0   0.230  107.2495  109.7877  104.1814
 EY0  H4   H  HCH3  0   0.253  105.8646  108.7369  104.4079
 EY0  H5   H  HCH3  0   0.251  108.2118  107.5307  107.1270
 EY0  H6   H  HCH3  0   0.256  107.2107  106.9742  105.7901
 EY0  H7   H  HCH3  0   0.234  108.6579  107.8999  105.4557
 EY0  H13  H  HCH3  0   0.267  115.0376  110.3229  106.6389
 EY0  H14  H  HCH3  0   0.264  113.4086  110.8467  107.0517
 EY0  H15  H  HCH3  0   0.266  113.8669  109.1609  107.2576
 EY0  H16  H  HCH2  0   0.266  111.7785  117.5730  107.1844
 EY0  H17  H  HCH2  0   0.243  110.4435  116.8671  108.1332
 EY0  H18  H  HCH2  0   0.277  109.0392  114.8751  106.8005
 EY0  H19  H  HCH2  0   0.287  109.7952  114.4680  105.2451
 EY0  H20  H  HCH3  0   0.240  111.9820  116.0951  104.7321
 EY0  H21  H  HCH3  0   0.249  110.5020  116.4602  103.8492
 EY0  H22  H  HCH3  0   0.249  111.3951  117.7560  104.6591
 EY0  H23  H  HNR5  0   0.427  114.5038  107.9097  104.8763
 EY0  C12  C  CH1   0  -0.155  106.9436  109.0453  106.2275
 EY0  C15  C  CH3   0  -0.528  106.8336  112.0106  110.0754
 EY0  C16  C  CH2   0  -0.633  112.0241  111.7575  104.6754
 EY0  C27  C  C     0   0.470  111.4055  113.2872  107.3178
 EY0  O34  O  OH1   0  -0.660  109.1297  117.2962  105.9098
 EY0  H1   H  HCH1  0   0.292  106.0709  108.7794  106.8153
 EY0  H8   H  HCH3  0   0.269  107.3680  112.8381  110.5252
 EY0  H9   H  HCH3  0   0.259  105.8212  112.3299  109.8400
 EY0  H10  H  HCH3  0   0.260  106.7922  111.1890  110.7868
 EY0  H11  H  HCH2  0   0.291  112.7182  112.4527  105.1514
 EY0  H12  H  HCH2  0   0.294  111.7024  112.2501  103.7550
 EY0  H24  H  HOH1  0   0.454  108.5946  117.1944  106.7055

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
 EY0  F23  C22  single    1.331  0.020  1.331
 EY0  F24  C22  single    1.344  0.020  1.344
 EY0  C22  F25  single    1.342  0.020  1.342
 EY0  C22  C21  single    1.484  0.020  1.484
 EY0  N20  C21  aromatic  1.317  0.020  1.317
 EY0  N20  N19  aromatic  1.320  0.020  1.320
 EY0  C21  C17  aromatic  1.407  0.020  1.407
 EY0  N19  C18  aromatic  1.346  0.020  1.346
 EY0  C17  C16  single    1.497  0.020  1.497
 EY0  C17  C18  aromatic  1.381  0.020  1.381
 EY0  C16  C8   single    1.498  0.020  1.498
 EY0  C35  C31  single    1.520  0.020  1.520
 EY0  C18  C26  single    1.485  0.020  1.485
 EY0  C13  C12  single    1.523  0.020  1.523
 EY0  S7   C8   aromatic  1.739  0.020  1.739
 EY0  S7   C2   aromatic  1.722  0.020  1.722
 EY0  C8   C9   aromatic  1.353  0.020  1.353
 EY0  C31  O34  single    1.397  0.020  1.397
 EY0  C31  C32  single    1.539  0.020  1.539
 EY0  C31  C30  single    1.532  0.020  1.532
 EY0  C32  N28  single    1.450  0.020  1.450
 EY0  C12  C14  single    1.524  0.020  1.524
 EY0  C12  N1   single    1.481  0.020  1.481
 EY0  C9   C27  single    1.495  0.020  1.495
 EY0  C9   C3   aromatic  1.427  0.020  1.427
 EY0  C2   N1   single    1.363  0.020  1.363
 EY0  C2   C3   aromatic  1.369  0.020  1.369
 EY0  N28  C27  single    1.334  0.020  1.334
 EY0  N28  O29  single    1.389  0.020  1.389
 EY0  C27  O33  double    1.220  0.020  1.220
 EY0  C30  O29  single    1.418  0.020  1.418
 EY0  N1   C6   single    1.385  0.020  1.385
 EY0  C3   C4   single    1.436  0.020  1.436
 EY0  C6   O11  double    1.214  0.020  1.214
 EY0  C6   N5   single    1.385  0.020  1.385
 EY0  C4   N5   single    1.388  0.020  1.388
 EY0  C4   O10  double    1.218  0.020  1.218
 EY0  N5   C15  single    1.460  0.020  1.460
 EY0  C12  H1   single    0.970  0.020  1.090
 EY0  C13  H2   single    0.970  0.020  1.090
 EY0  C13  H3   single    0.970  0.020  1.090
 EY0  C13  H4   single    0.970  0.020  1.090
 EY0  C14  H5   single    0.970  0.020  1.090
 EY0  C14  H6   single    0.970  0.020  1.090
 EY0  C14  H7   single    0.970  0.020  1.090
 EY0  C15  H8   single    0.970  0.020  1.090
 EY0  C15  H9   single    0.970  0.020  1.090
 EY0  C15  H10  single    0.970  0.020  1.090
 EY0  C16  H11  single    0.970  0.020  1.090
 EY0  C16  H12  single    0.970  0.020  1.090
 EY0  C26  H13  single    0.970  0.020  1.090
 EY0  C26  H14  single    0.970  0.020  1.090
 EY0  C26  H15  single    0.970  0.020  1.090
 EY0  C30  H16  single    0.970  0.020  1.090
 EY0  C30  H17  single    0.970  0.020  1.090
 EY0  C32  H18  single    0.970  0.020  1.090
 EY0  C32  H19  single    0.970  0.020  1.090
 EY0  C35  H20  single    0.970  0.020  1.090
 EY0  C35  H21  single    0.970  0.020  1.090
 EY0  C35  H22  single    0.970  0.020  1.090
 EY0  N19  H23  single    0.860  0.020  1.020
 EY0  O34  H24  single    0.850  0.020  0.980

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
 EY0  S7   C2   N1   125.96  3.000
 EY0  N1   C2   C3   123.04  3.000
 EY0  S7   C2   C3   111.00  3.000
 EY0  C9   C3   C4   126.55  3.000
 EY0  C4   C3   C2   120.44  3.000
 EY0  C9   C3   C2   113.01  3.000
 EY0  O10  C4   N5   122.40  3.000
 EY0  O10  C4   C3   123.64  3.000
 EY0  N5   C4   C3   113.96  3.000
 EY0  O11  C6   N5   120.21  3.000
 EY0  N5   C6   N1   117.83  3.000
 EY0  O11  C6   N1   121.96  3.000
 EY0  H4   C13  H3   107.08  3.000
 EY0  H4   C13  H2   107.81  3.000
 EY0  H3   C13  H2   108.41  3.000
 EY0  H4   C13  C12  108.71  3.000
 EY0  H3   C13  C12  113.53  3.000
 EY0  H2   C13  C12  111.08  3.000
 EY0  H7   C14  H6   106.89  3.000
 EY0  H7   C14  H5   108.55  3.000
 EY0  H6   C14  H5   107.76  3.000
 EY0  H7   C14  C12  113.80  3.000
 EY0  H6   C14  C12  108.32  3.000
 EY0  H5   C14  C12  111.25  3.000
 EY0  C21  C17  C18  103.77  3.000
 EY0  C18  C17  C16  126.63  3.000
 EY0  C21  C17  C16  129.56  3.000
 EY0  N19  C18  C26  123.12  3.000
 EY0  C26  C18  C17  131.17  3.000
 EY0  N19  C18  C17  105.70  3.000
 EY0  N20  C21  C22  120.39  3.000
 EY0  N20  C21  C17  112.21  3.000
 EY0  C22  C21  C17  127.39  3.000
 EY0  F25  C22  F24  106.19  3.000
 EY0  F25  C22  F23  107.41  3.000
 EY0  F24  C22  F23  107.47  3.000
 EY0  F25  C22  C21  111.79  3.000
 EY0  F24  C22  C21  111.34  3.000
 EY0  F23  C22  C21  112.32  3.000
 EY0  H15  C26  H14  107.77  3.000
 EY0  H15  C26  H13  107.78  3.000
 EY0  H14  C26  H13  107.81  3.000
 EY0  H15  C26  C18  111.36  3.000
 EY0  H14  C26  C18  110.80  3.000
 EY0  H13  C26  C18  111.17  3.000
 EY0  H17  C30  H16  109.28  3.000
 EY0  H17  C30  O29  110.94  3.000
 EY0  H16  C30  O29  107.47  3.000
 EY0  H17  C30  C31  110.76  3.000
 EY0  H16  C30  C31  113.82  3.000
 EY0  O29  C30  C31  104.44  3.000
 EY0  O34  C31  C35  107.49  3.000
 EY0  O34  C31  C32  113.35  3.000
 EY0  C35  C31  C32  111.26  3.000
 EY0  C32  C31  C30   99.49  3.000
 EY0  O34  C31  C30  113.57  3.000
 EY0  C35  C31  C30  111.65  3.000
 EY0  H19  C32  H18  108.92  3.000
 EY0  H19  C32  N28  111.35  3.000
 EY0  H18  C32  N28  111.05  3.000
 EY0  H19  C32  C31  112.88  3.000
 EY0  H18  C32  C31  110.55  3.000
 EY0  N28  C32  C31  101.99  3.000
 EY0  H22  C35  H21  108.48  3.000
 EY0  H22  C35  H20  107.90  3.000
 EY0  H21  C35  H20  107.76  3.000
 EY0  H22  C35  C31  110.77  3.000
 EY0  H21  C35  C31  110.58  3.000
 EY0  H20  C35  C31  111.24  3.000
 EY0  S7   C8   C9   111.30  3.000
 EY0  C9   C8   C16  129.19  3.000
 EY0  S7   C8   C16  119.52  3.000
 EY0  C8   C9   C27  122.98  3.000
 EY0  C27  C9   C3   124.12  3.000
 EY0  C8   C9   C3   112.80  3.000
 EY0  C12  N1   C6   117.92  3.000
 EY0  C6   N1   C2   119.09  3.000
 EY0  C12  N1   C2   122.98  3.000
 EY0  H23  N19  N20  119.24  3.000
 EY0  H23  N19  C18  126.70  3.000
 EY0  N20  N19  C18  114.07  3.000
 EY0  N19  N20  C21  104.25  3.000
 EY0  O29  N28  C32  112.22  3.000
 EY0  O29  N28  C27  116.78  3.000
 EY0  C32  N28  C27  129.57  3.000
 EY0  C15  N5   C6   115.41  3.000
 EY0  C15  N5   C4   118.96  3.000
 EY0  C6   N5   C4   125.63  3.000
 EY0  N28  O29  C30  106.09  3.000
 EY0  C8   S7   C2    91.88  3.000
 EY0  H1   C12  N1   104.16  3.000
 EY0  H1   C12  C14  107.00  3.000
 EY0  N1   C12  C14  112.31  3.000
 EY0  H1   C12  C13  107.33  3.000
 EY0  N1   C12  C13  111.66  3.000
 EY0  C14  C12  C13  113.68  3.000
 EY0  H10  C15  H9   109.15  3.000
 EY0  H10  C15  H8   108.93  3.000
 EY0  H9   C15  H8   108.97  3.000
 EY0  H10  C15  N5   110.50  3.000
 EY0  H9   C15  N5   110.59  3.000
 EY0  H8   C15  N5   108.67  3.000
 EY0  H12  C16  H11  105.51  3.000
 EY0  H12  C16  C8   109.81  3.000
 EY0  H11  C16  C8   108.32  3.000
 EY0  H12  C16  C17  110.79  3.000
 EY0  H11  C16  C17  109.71  3.000
 EY0  C8   C16  C17  112.43  3.000
 EY0  O33  C27  N28  124.39  3.000
 EY0  O33  C27  C9   122.34  3.000
 EY0  N28  C27  C9   113.13  3.000
 EY0  H24  O34  C31  109.82  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
 EY0  CONST_01  C9   C8   S7   C2      0.00   0.0  0
 EY0  CONST_02  C8   C9   C3   C2      0.00   0.0  0
 EY0  CONST_03  S7   C8   C9   C3      0.00   0.0  0
 EY0  CONST_04  C8   S7   C2   C3      0.00   0.0  0
 EY0  CONST_05  N19  N20  C21  C17     0.00   0.0  0
 EY0  CONST_06  N20  N19  C18  C17     0.00   0.0  0
 EY0  CONST_07  C21  N20  N19  C18     0.00   0.0  0
 EY0  CONST_08  N20  C21  C17  C18     0.00   0.0  0
 EY0  CONST_09  N19  C18  C17  C21     0.00   0.0  0
 EY0  CONST_10  S7   C2   C3   C9      0.00   0.0  0
 EY0  CONST_11  N5   C6   N1   C2      0.00   0.0  0
 EY0  CONST_12  C6   N5   C4   C3      0.00   0.0  0
 EY0  CONST_13  N1   C6   N5   C4      0.00   0.0  0
 EY0  CONST_14  C16  C8   S7   C2    180.00   0.0  0
 EY0  CONST_15  C27  C9   C3   C2    180.00   0.0  0
 EY0  CONST_16  C16  C8   C9   C3    180.00   0.0  0
 EY0  CONST_17  C27  C9   C3   C4      0.00   0.0  0
 EY0  CONST_18  N20  C21  C17  C16   180.00   0.0  0
 EY0  CONST_19  N19  C18  C17  C16   180.00   0.0  0
 EY0  CONST_20  C22  C21  C17  C18   180.00   0.0  0
 EY0  CONST_21  C26  C18  C17  C21   180.00   0.0  0
 EY0  CONST_22  N19  N20  C21  C22   180.00   0.0  0
 EY0  CONST_23  N20  N19  C18  C26   180.00   0.0  0
 EY0  CONST_24  S7   C8   C9   C27   180.00   0.0  0
 EY0  CONST_25  C9   C27  N28  C32     0.00   0.0  0
 EY0  CONST_26  O29  N28  C27  C9    180.00   0.0  0
 EY0  CONST_27  O11  C6   N1   C2    180.00   0.0  0
 EY0  CONST_28  C15  N5   C4   C3    180.00   0.0  0
 EY0  CONST_29  O11  C6   N5   C4    180.00   0.0  0
 EY0  CONST_30  O10  C4   N5   C6    180.00   0.0  0
 EY0  CONST_31  N5   C6   N1   C12   180.00   0.0  0
 EY0  CONST_32  N1   C6   N5   C15   180.00   0.0  0
 EY0  CONST_33  H23  N19  C18  C17   180.00   0.0  0
 EY0  CONST_34  O33  C27  N28  C32   180.00   0.0  0
 EY0  CONST_35  O33  C27  N28  O29     0.00   0.0  0
 EY0  CONST_36  O11  C6   N1   C12     0.00   0.0  0
 EY0  CONST_37  O11  C6   N5   C15     0.00   0.0  0
 EY0  CONST_38  O10  C4   N5   C15     0.00   0.0  0
 EY0  Var_01    C32  N28  O29  C30    10.79  30.0  1
 EY0  Var_02    O29  N28  C32  C31    14.75  30.0  1
 EY0  Var_03    N28  C27  C9   C3    -92.29  30.0  2
 EY0  Var_04    S7   C8   C16  C17   -49.89  30.0  2
 EY0  Var_05    C8   C16  C17  C18   -73.39  30.0  2
 EY0  Var_06    H16  C30  O29  N28  -153.22  30.0  1
 EY0  Var_07    C13  C12  N1   C2    -65.91  30.0  2
 EY0  Var_08    F23  C22  C21  C17  -175.65  30.0  3
 EY0  Var_09    H8   C15  N5   C4      0.98  30.0  3
 EY0  Var_10    H13  C26  C18  C17  -106.75  30.0  2
 EY0  Var_11    H2   C13  C12  N1    -53.56  30.0  3
 EY0  Var_12    H5   C14  C12  N1     47.98  30.0  3

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
 EY0  chir_01  C31  O34  C32  C30  positiv

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
 EY0  plan-1  C17  0.020
 EY0  plan-1  C18  0.020
 EY0  plan-1  C21  0.020
 EY0  plan-1  C22  0.020
 EY0  plan-1  C26  0.020
 EY0  plan-1  N19  0.020
 EY0  plan-1  N20  0.020
 EY0  plan-1  H23  0.020
 EY0  plan-1  C16  0.020
 EY0  plan-2  C2   0.020
 EY0  plan-2  C3   0.020
 EY0  plan-2  C4   0.020
 EY0  plan-2  C6   0.020
 EY0  plan-2  C8   0.020
 EY0  plan-2  C9   0.020
 EY0  plan-2  N1   0.020
 EY0  plan-2  N5   0.020
 EY0  plan-2  O10  0.020
 EY0  plan-2  O11  0.020
 EY0  plan-2  S7   0.020
 EY0  plan-2  C12  0.020
 EY0  plan-2  C15  0.020
 EY0  plan-2  C16  0.020
 EY0  plan-2  C27  0.020
 EY0  plan-3  C32  0.020
 EY0  plan-3  C9   0.020
 EY0  plan-3  N28  0.020
 EY0  plan-3  O29  0.020
 EY0  plan-3  O33  0.020
 EY0  plan-3  C27  0.020

