# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 22:25:38 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: [(4R)-4-(3-hydroxyphenyl)-1,6-dimethyl-2-thioxo-1,2,3,4-tetrahydropyrimidin-5-yl](phenyl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=C([C@H](NC1=S)c2cccc(O)c2)C(=O)c3ccccc3)C
#
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
 MOY  MOY  '[(4R)-4-(3-hydroxyphenyl)-1,6-dimethyl-2-thioxo-1,2,3,4-tetrahydropyrimidin-5-yl](phenyl)methanone'  ligand  42  24  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MOY
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
 MOY  S    S  S1    0  -0.390  -2.9910  -2.3689  -5.2794
 MOY  O3   O  O     0  -0.388   1.2334   1.3794  -1.5899
 MOY  O4   O  OH1   0  -0.631  -4.3172   2.9785  -2.2152
 MOY  N1   N  NR16  0  -0.588  -2.0317  -1.7522  -2.9255
 MOY  N2   N  NR6   0  -0.525  -1.1627  -0.5115  -4.6489
 MOY  C1   C  CR6   0   0.384  -2.0223  -1.4896  -4.2299
 MOY  C2   C  CR6   0   0.354  -0.1477  -0.0402  -3.8067
 MOY  C3   C  CR6   0  -0.137  -0.2197  -0.2572  -2.4801
 MOY  C4   C  CR16  0  -0.246  -1.4285  -0.9344  -1.8966
 MOY  C6   C  CH3   0  -0.753   1.0091   0.6257  -4.4860
 MOY  C17  C  C     0   0.342   0.7903   0.2489  -1.5252
 MOY  C18  C  CR6   0  -0.037   1.2431  -0.6696  -0.4446
 MOY  C19  C  CR16  0  -0.269   1.3594  -2.0397  -0.6744
 MOY  C20  C  CR16  0  -0.246   1.8509  -2.8756   0.3168
 MOY  C21  C  CR16  0  -0.245   2.2117  -2.3491   1.5504
 MOY  C22  C  CR16  0  -0.246   2.0959  -0.9842   1.7862
 MOY  C23  C  CR16  0  -0.270   1.6252  -0.1449   0.7892
 MOY  C24  C  CR6   0   0.222  -2.3990   0.0550  -1.2772
 MOY  C25  C  CR16  0  -0.390  -2.9398   1.0933  -2.0269
 MOY  C26  C  CR6   0   0.376  -3.8233   1.9930  -1.4405
 MOY  C27  C  CR16  0  -0.390  -4.1625   1.8575  -0.0942
 MOY  C28  C  CR16  0  -0.226  -3.6167   0.8235   0.6478
 MOY  C29  C  CR16  0  -0.355  -2.7386  -0.0803   0.0638
 MOY  HO4  H  HOH1  0   0.475  -4.8986   3.5511  -1.7025
 MOY  HN1  H  HNR6  0   0.416  -2.6424  -2.4983  -2.6309
 MOY  H4   H  HCR6  0   0.306  -1.1255  -1.6170  -1.1008
 MOY  H51  H  HCH3  0   0.266  -0.8422   0.9243  -6.1332
 MOY  H52  H  HCH3  0   0.273  -2.2194  -0.1311  -6.4010
 MOY  H53  H  HCH3  0   0.256  -0.5883  -0.7453  -6.6787
 MOY  H61  H  HCH3  0   0.278   1.8796   0.6700  -3.8414
 MOY  H62  H  HCH3  0   0.273   0.7672   1.6488  -4.7763
 MOY  H63  H  HCH3  0   0.266   1.2930   0.0846  -5.3874
 MOY  H19  H  HCR6  0   0.271   1.0864  -2.4538  -1.6380
 MOY  H20  H  HCR6  0   0.265   1.9520  -3.9357   0.1266
 MOY  H21  H  HCR6  0   0.266   2.5853  -3.0018   2.3288
 MOY  H22  H  HCR6  0   0.264   2.3783  -0.5753   2.7473
 MOY  H23  H  HCR6  0   0.264   1.5423   0.9186   0.9730
 MOY  H25  H  HCR6  0   0.260  -2.6772   1.2284  -3.0698
 MOY  H27  H  HCR6  0   0.274  -4.8461   2.5586   0.3710
 MOY  H28  H  HCR6  0   0.263  -3.8810   0.7221   1.6923
 MOY  H29  H  HCR6  0   0.252  -2.3157  -0.8859   0.6515
 MOY  C5   C  CH3   0  -0.533  -1.1953  -0.0979  -6.0462

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
 MOY  S    C1   double    1.677  0.020  1.677
 MOY  O3   C17  double    1.216  0.020  1.216
 MOY  O4   C26  single    1.347  0.020  1.347
 MOY  O4   HO4  single    0.850  0.020  0.980
 MOY  N1   C1   single    1.331  0.020  1.331
 MOY  N1   C4   single    1.446  0.020  1.446
 MOY  N1   HN1  single    0.860  0.020  1.020
 MOY  N2   C2   single    1.401  0.020  1.401
 MOY  N2   C1   single    1.368  0.020  1.368
 MOY  N2   C5   single    1.458  0.020  1.458
 MOY  C2   C6   single    1.498  0.020  1.498
 MOY  C2   C3   double    1.346  0.020  1.346
 MOY  C3   C17  single    1.479  0.020  1.479
 MOY  C3   C4   single    1.503  0.020  1.503
 MOY  C4   C24  single    1.518  0.020  1.518
 MOY  C4   H4   single    0.970  0.020  1.090
 MOY  C5   H51  single    0.970  0.020  1.090
 MOY  C5   H52  single    0.970  0.020  1.090
 MOY  C5   H53  single    0.970  0.020  1.090
 MOY  C6   H61  single    0.970  0.020  1.090
 MOY  C6   H62  single    0.970  0.020  1.090
 MOY  C6   H63  single    0.970  0.020  1.090
 MOY  C17  C18  single    1.489  0.020  1.489
 MOY  C18  C23  aromatic  1.394  0.020  1.394
 MOY  C18  C19  aromatic  1.394  0.020  1.394
 MOY  C19  C20  aromatic  1.387  0.020  1.387
 MOY  C19  H19  single    0.930  0.020  1.080
 MOY  C20  C21  aromatic  1.389  0.020  1.389
 MOY  C20  H20  single    0.930  0.020  1.080
 MOY  C21  C22  aromatic  1.390  0.020  1.390
 MOY  C21  H21  single    0.930  0.020  1.080
 MOY  C22  C23  aromatic  1.386  0.020  1.386
 MOY  C22  H22  single    0.930  0.020  1.080
 MOY  C23  H23  single    0.930  0.020  1.080
 MOY  C24  C25  aromatic  1.390  0.020  1.390
 MOY  C24  C29  aromatic  1.390  0.020  1.390
 MOY  C25  C26  aromatic  1.391  0.020  1.391
 MOY  C25  H25  single    0.930  0.020  1.080
 MOY  C26  C27  aromatic  1.395  0.020  1.395
 MOY  C27  C28  aromatic  1.385  0.020  1.385
 MOY  C27  H27  single    0.930  0.020  1.080
 MOY  C28  C29  aromatic  1.389  0.020  1.389
 MOY  C28  H28  single    0.930  0.020  1.080
 MOY  C29  H29  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
 MOY  HO4  O4   C26  110.47  3.000
 MOY  HN1  N1   C4   117.60  3.000
 MOY  HN1  N1   C1   115.90  3.000
 MOY  C4   N1   C1   125.66  3.000
 MOY  C5   N2   C2   119.81  3.000
 MOY  C5   N2   C1   118.85  3.000
 MOY  C2   N2   C1   120.78  3.000
 MOY  N2   C1   N1   116.48  3.000
 MOY  N2   C1   S    123.10  3.000
 MOY  N1   C1   S    120.39  3.000
 MOY  C6   C2   C3   124.06  3.000
 MOY  C3   C2   N2   119.97  3.000
 MOY  C6   C2   N2   115.89  3.000
 MOY  C17  C3   C4   116.91  3.000
 MOY  C4   C3   C2   119.87  3.000
 MOY  C17  C3   C2   122.99  3.000
 MOY  H4   C4   C24  106.71  3.000
 MOY  H4   C4   C3   109.97  3.000
 MOY  C24  C4   C3   112.26  3.000
 MOY  H4   C4   N1   106.31  3.000
 MOY  C24  C4   N1   113.10  3.000
 MOY  C3   C4   N1   108.30  3.000
 MOY  H63  C6   H62  107.68  3.000
 MOY  H63  C6   H61  107.65  3.000
 MOY  H62  C6   H61  107.34  3.000
 MOY  H63  C6   C2   110.85  3.000
 MOY  H62  C6   C2   111.50  3.000
 MOY  H61  C6   C2   111.63  3.000
 MOY  C18  C17  C3   117.72  3.000
 MOY  C18  C17  O3   120.09  3.000
 MOY  C3   C17  O3   122.17  3.000
 MOY  C23  C18  C19  119.53  3.000
 MOY  C19  C18  C17  120.80  3.000
 MOY  C23  C18  C17  119.57  3.000
 MOY  H19  C19  C20  119.64  3.000
 MOY  H19  C19  C18  120.07  3.000
 MOY  C20  C19  C18  120.28  3.000
 MOY  H20  C20  C21  120.22  3.000
 MOY  H20  C20  C19  119.88  3.000
 MOY  C21  C20  C19  119.90  3.000
 MOY  H21  C21  C22  119.93  3.000
 MOY  H21  C21  C20  119.99  3.000
 MOY  C22  C21  C20  120.08  3.000
 MOY  H22  C22  C23  119.93  3.000
 MOY  H22  C22  C21  120.00  3.000
 MOY  C23  C22  C21  120.07  3.000
 MOY  H23  C23  C22  119.93  3.000
 MOY  H23  C23  C18  119.94  3.000
 MOY  C22  C23  C18  120.13  3.000
 MOY  C29  C24  C25  119.87  3.000
 MOY  C29  C24  C4   119.11  3.000
 MOY  C25  C24  C4   121.03  3.000
 MOY  H25  C25  C26  118.62  3.000
 MOY  H25  C25  C24  121.18  3.000
 MOY  C26  C25  C24  120.20  3.000
 MOY  C27  C26  C25  119.91  3.000
 MOY  C27  C26  O4   122.47  3.000
 MOY  C25  C26  O4   117.62  3.000
 MOY  H27  C27  C28  120.10  3.000
 MOY  H27  C27  C26  120.31  3.000
 MOY  C28  C27  C26  119.59  3.000
 MOY  H28  C28  C29  119.95  3.000
 MOY  H28  C28  C27  119.40  3.000
 MOY  C29  C28  C27  120.65  3.000
 MOY  H29  C29  C28  120.18  3.000
 MOY  H29  C29  C24  120.03  3.000
 MOY  C28  C29  C24  119.79  3.000
 MOY  H53  C5   H52  108.54  3.000
 MOY  H53  C5   H51  109.38  3.000
 MOY  H52  C5   H51  108.06  3.000
 MOY  H53  C5   N2   112.04  3.000
 MOY  H52  C5   N2   109.03  3.000
 MOY  H51  C5   N2   109.69  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
 MOY  CONST_01  C21  C22  C23  C18     0.00   0.0  0
 MOY  CONST_02  C21  C20  C19  C18     0.00   0.0  0
 MOY  CONST_03  C22  C23  C18  C19     0.00   0.0  0
 MOY  CONST_04  C22  C21  C20  C19     0.00   0.0  0
 MOY  CONST_05  C23  C18  C19  C20     0.00   0.0  0
 MOY  CONST_06  C23  C22  C21  C20     0.00   0.0  0
 MOY  CONST_07  C27  C26  C25  C24     0.00   0.0  0
 MOY  CONST_08  C27  C28  C29  C24     0.00   0.0  0
 MOY  CONST_09  C28  C29  C24  C25     0.00   0.0  0
 MOY  CONST_10  C28  C27  C26  C25     0.00   0.0  0
 MOY  CONST_11  C29  C24  C25  C26     0.00   0.0  0
 MOY  CONST_12  C29  C28  C27  C26     0.00   0.0  0
 MOY  CONST_13  C26  C25  C24  C4    180.00   0.0  0
 MOY  CONST_14  C28  C29  C24  C4    180.00   0.0  0
 MOY  CONST_15  C2   N2   C1   N1      0.00   0.0  0
 MOY  CONST_16  C4   N1   C1   N2      0.00   0.0  0
 MOY  CONST_17  C24  C25  C26  O4    180.00   0.0  0
 MOY  CONST_18  C28  C27  C26  O4    180.00   0.0  0
 MOY  CONST_19  C22  C23  C18  C17   180.00   0.0  0
 MOY  CONST_20  C20  C19  C18  C17   180.00   0.0  0
 MOY  CONST_21  C4   N1   C1   S     180.00   0.0  0
 MOY  CONST_23  C5   N2   C1   N1    180.00   0.0  0
 MOY  CONST_24  H25  C25  C24  C4      0.00   0.0  0
 MOY  CONST_25  H29  C29  C24  C4      0.00   0.0  0
 MOY  CONST_26  H22  C22  C23  C18   180.00   0.0  0
 MOY  CONST_27  H20  C20  C19  C18   180.00   0.0  0
 MOY  CONST_28  H23  C23  C18  C19   180.00   0.0  0
 MOY  CONST_29  H21  C21  C20  C19   180.00   0.0  0
 MOY  CONST_30  H19  C19  C20  C21   180.00   0.0  0
 MOY  CONST_31  H28  C28  C29  C24   180.00   0.0  0
 MOY  CONST_32  H27  C27  C26  C25   180.00   0.0  0
 MOY  CONST_33  HN1  N1   C1   N2    180.00   0.0  0
 MOY  CONST_34  C5   N2   C1   S       0.00   0.0  0
 MOY  Var_01    C4   C3   C2   N2     -3.57  30.0  1
 MOY  Var_02    C3   C2   N2   C1    -18.33  30.0  1
 MOY  Var_03    C18  C17  C3   C2   -137.24  30.0  2
 MOY  Var_04    C23  C18  C17  C3   -148.67  30.0  2
 MOY  Var_05    H61  C6   C2   N2   -161.32  30.0  3
 MOY  Var_06    H51  C5   N2   C1    153.84  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
 MOY  chir_01  C4  N1  C3  C24  negativ

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
 MOY  plan-1  C17  0.020
 MOY  plan-1  C18  0.020
 MOY  plan-1  C19  0.020
 MOY  plan-1  C20  0.020
 MOY  plan-1  C21  0.020
 MOY  plan-1  C22  0.020
 MOY  plan-1  C23  0.020
 MOY  plan-1  H19  0.020
 MOY  plan-1  H20  0.020
 MOY  plan-1  H21  0.020
 MOY  plan-1  H22  0.020
 MOY  plan-1  H23  0.020
 MOY  plan-2  O4   0.020
 MOY  plan-2  C4   0.020
 MOY  plan-2  C24  0.020
 MOY  plan-2  C25  0.020
 MOY  plan-2  C26  0.020
 MOY  plan-2  C27  0.020
 MOY  plan-2  C28  0.020
 MOY  plan-2  C29  0.020
 MOY  plan-2  H25  0.020
 MOY  plan-2  H27  0.020
 MOY  plan-2  H28  0.020
 MOY  plan-2  H29  0.020
 MOY  plan-3  S    0.020
 MOY  plan-3  N1   0.020
 MOY  plan-3  N2   0.020
 MOY  plan-3  C1   0.020
 MOY  plan-3  C2   0.020
 MOY  plan-3  C4   0.020
 MOY  plan-3  HN1  0.020
 MOY  plan-3  C5   0.020
 MOY  plan-4  O3   0.020
 MOY  plan-4  C3   0.020
 MOY  plan-4  C17  0.020
 MOY  plan-4  C18  0.020

