# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 22:41:42 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: ethyl (4S)-4-(3-hydroxyphenyl)-6-methyl-2-thioxo-1,2,3,4-tetrahydropyrimidine-5-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOC(=O)C1=C(C)NC(=S)N[C@H]1c2cccc(O)c2
#
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
 NAT  NAT  'ethyl (4S)-4-(3-hydroxyphenyl)-6-methyl-2-thioxo-1,2,3,4-tetrahydropyrimidine-5-carboxylate'  ligand  36  20  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_NAT
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
 NAT  C1    C  CR16  0  -0.322   0.2057  -1.3789  -1.1486
 NAT  C2    C  CR6   0   0.195   0.5840  -0.9256   0.1127
 NAT  C3    C  CR16  0  -0.396   1.7234  -1.4320   0.7179
 NAT  C4    C  CR6   0   0.368   2.5004  -2.3898   0.0680
 NAT  C5    C  CR16  0  -0.393   2.1232  -2.8432  -1.1925
 NAT  C6    C  CR16  0  -0.228   0.9774  -2.3347  -1.7897
 NAT  C7    C  CH1   0  -0.195  -0.2621   0.0999   0.8463
 NAT  N8    N  NH1   0  -0.584  -1.5148  -0.5013   1.2851
 NAT  C9    C  C     0   0.362  -2.6992  -0.3538   0.7099
 NAT  N10   N  NH1   0  -0.669  -2.7813   0.6219  -0.2330
 NAT  C11   C  C     0   0.374  -1.7749   1.5131  -0.5285
 NAT  C12   C  C     0  -0.196  -0.5461   1.3178  -0.0006
 NAT  O13   O  OH1   0  -0.633   3.6016  -2.8367   0.7038
 NAT  C14   C  C     0   0.591   0.5688   2.2215  -0.2909
 NAT  O15   O  O2    0  -0.464   1.6425   1.8944   0.4192
 NAT  C16   C  CH2   0  -0.175   2.8595   2.6170   0.2002
 NAT  C17   C  CH3   0  -0.684   3.9330   1.9636   1.0370
 NAT  C18   C  CH3   0  -0.730  -2.1997   2.6222  -1.4381
 NAT  O19   O  O     0  -0.463   0.5560   3.1456  -1.0754
 NAT  S20   S  S1    0  -0.385  -4.0433  -1.2631   1.1144
 NAT  H1    H  HCR6  0   0.252  -0.6796  -0.9888  -1.6361
 NAT  H3    H  HCR6  0   0.258   2.0224  -1.0767   1.6976
 NAT  H5    H  HCR6  0   0.272   2.7210  -3.5850  -1.7096
 NAT  H6    H  HCR6  0   0.261   0.6914  -2.6907  -2.7708
 NAT  H7    H  HCH1  0   0.295   0.2694   0.3964   1.7524
 NAT  HN8   H  HNH1  0   0.418  -1.4493  -1.2192   1.9905
 NAT  HN10  H  HNH1  0   0.422  -3.6921   0.7645  -0.6408
 NAT  HO13  H  HOH1  0   0.474   4.0610  -3.4877   0.1620
 NAT  H161  H  HCH2  0   0.233   2.7246   3.6636   0.4823
 NAT  H162  H  HCH2  0   0.233   3.1209   2.5876  -0.8597
 NAT  H171  H  HCH3  0   0.234   3.7012   2.0155   2.1010
 NAT  H172  H  HCH3  0   0.235   4.0693   0.9176   0.7613
 NAT  H173  H  HCH3  0   0.238   4.8781   2.4812   0.8754
 NAT  H181  H  HCH3  0   0.274  -1.7454   2.5112  -2.4219
 NAT  H182  H  HCH3  0   0.255  -3.2812   2.6212  -1.5638
 NAT  H183  H  HCH3  0   0.274  -1.9046   3.5927  -1.0500

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
 NAT  C1   C2    aromatic  1.393  0.020  1.393
 NAT  C1   C6    aromatic  1.386  0.020  1.386
 NAT  C1   H1    single    0.930  0.020  1.080
 NAT  C2   C3    aromatic  1.386  0.020  1.386
 NAT  C2   C7    single    1.518  0.020  1.518
 NAT  C3   C4    aromatic  1.394  0.020  1.394
 NAT  C3   H3    single    0.930  0.020  1.080
 NAT  C4   C5    aromatic  1.392  0.020  1.392
 NAT  C4   O13   single    1.348  0.020  1.348
 NAT  C5   C6    aromatic  1.389  0.020  1.389
 NAT  C5   H5    single    0.930  0.020  1.080
 NAT  C6   H6    single    0.930  0.020  1.080
 NAT  C7   N8    single    1.457  0.020  1.457
 NAT  C7   C12   single    1.510  0.020  1.510
 NAT  C7   H7    single    0.970  0.020  1.090
 NAT  N8   C9    single    1.325  0.020  1.325
 NAT  N8   HN8   single    0.860  0.020  1.020
 NAT  C9   N10   single    1.359  0.020  1.359
 NAT  C9   S20   double    1.672  0.020  1.672
 NAT  N10  C11   single    1.376  0.020  1.376
 NAT  N10  HN10  single    0.860  0.020  1.020
 NAT  C11  C12   double    1.352  0.020  1.352
 NAT  C11  C18   single    1.496  0.020  1.496
 NAT  C12  C14   single    1.464  0.020  1.464
 NAT  O13  HO13  single    0.850  0.020  0.980
 NAT  C14  O15   single    1.328  0.020  1.328
 NAT  C14  O19   double    1.212  0.020  1.212
 NAT  O15  C16   single    1.432  0.020  1.432
 NAT  C16  C17   single    1.510  0.020  1.510
 NAT  C16  H161  single    0.970  0.020  1.090
 NAT  C16  H162  single    0.970  0.020  1.090
 NAT  C17  H171  single    0.970  0.020  1.090
 NAT  C17  H172  single    0.970  0.020  1.090
 NAT  C17  H173  single    0.970  0.020  1.090
 NAT  C18  H181  single    0.970  0.020  1.090
 NAT  C18  H182  single    0.970  0.020  1.090
 NAT  C18  H183  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
 NAT  H1    C1   C6    119.69  3.000
 NAT  H1    C1   C2    120.82  3.000
 NAT  C6    C1   C2    119.49  3.000
 NAT  C7    C2   C3    119.59  3.000
 NAT  C7    C2   C1    120.40  3.000
 NAT  C3    C2   C1    119.99  3.000
 NAT  H3    C3   C4    119.52  3.000
 NAT  H3    C3   C2    120.10  3.000
 NAT  C4    C3   C2    120.37  3.000
 NAT  O13   C4   C5    122.73  3.000
 NAT  O13   C4   C3    117.60  3.000
 NAT  C5    C4   C3    119.67  3.000
 NAT  H5    C5   C6    120.04  3.000
 NAT  H5    C5   C4    120.37  3.000
 NAT  C6    C5   C4    119.60  3.000
 NAT  H6    C6   C5    119.18  3.000
 NAT  H6    C6   C1    119.94  3.000
 NAT  C5    C6   C1    120.88  3.000
 NAT  H7    C7   C12   109.75  3.000
 NAT  H7    C7   N8    106.30  3.000
 NAT  C12   C7   N8    109.87  3.000
 NAT  H7    C7   C2    108.25  3.000
 NAT  C12   C7   C2    112.24  3.000
 NAT  N8    C7   C2    110.24  3.000
 NAT  HN8   N8   C9    116.17  3.000
 NAT  HN8   N8   C7    116.64  3.000
 NAT  C9    N8   C7    126.29  3.000
 NAT  S20   C9   N10   120.63  3.000
 NAT  S20   C9   N8    123.57  3.000
 NAT  N10   C9   N8    115.79  3.000
 NAT  HN10  N10  C11   118.83  3.000
 NAT  HN10  N10  C9    115.89  3.000
 NAT  C11   N10  C9    124.72  3.000
 NAT  C18   C11  C12   127.07  3.000
 NAT  C18   C11  N10   113.77  3.000
 NAT  C12   C11  N10   119.16  3.000
 NAT  C14   C12  C11   121.71  3.000
 NAT  C14   C12  C7    117.76  3.000
 NAT  C11   C12  C7    120.43  3.000
 NAT  HO13  O13  C4    110.39  3.000
 NAT  O19   C14  O15   122.84  3.000
 NAT  O19   C14  C12   126.21  3.000
 NAT  O15   C14  C12   110.95  3.000
 NAT  C16   O15  C14   118.74  3.000
 NAT  H162  C16  H161  107.82  3.000
 NAT  H162  C16  C17   110.86  3.000
 NAT  H161  C16  C17   111.06  3.000
 NAT  H162  C16  O15   109.77  3.000
 NAT  H161  C16  O15   109.82  3.000
 NAT  C17   C16  O15   107.52  3.000
 NAT  H173  C17  H172  108.05  3.000
 NAT  H173  C17  H171  107.85  3.000
 NAT  H172  C17  H171  108.60  3.000
 NAT  H173  C17  C16   109.21  3.000
 NAT  H172  C17  C16   111.34  3.000
 NAT  H171  C17  C16   111.66  3.000
 NAT  H183  C18  H182  108.17  3.000
 NAT  H183  C18  H181  107.49  3.000
 NAT  H182  C18  H181  108.05  3.000
 NAT  H183  C18  C11   111.60  3.000
 NAT  H182  C18  C11   110.59  3.000
 NAT  H181  C18  C11   110.80  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
 NAT  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 NAT  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 NAT  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 NAT  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 NAT  CONST_05  C6    C1   C2   C3      0.00   0.0  0
 NAT  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 NAT  CONST_07  C7    C2   C3   C4    180.00   0.0  0
 NAT  CONST_08  C7    C2   C1   C6    180.00   0.0  0
 NAT  CONST_09  N10   C9   N8   C7      0.00   0.0  0
 NAT  CONST_10  C11   N10  C9   N8      0.00   0.0  0
 NAT  CONST_11  O13   C4   C3   C2    180.00   0.0  0
 NAT  CONST_12  O13   C4   C5   C6    180.00   0.0  0
 NAT  CONST_13  S20   C9   N8   C7    180.00   0.0  0
 NAT  CONST_14  S20   C9   N10  C11   180.00   0.0  0
 NAT  CONST_15  H3    C3   C2   C1    180.00   0.0  0
 NAT  CONST_16  H5    C5   C6   C1    180.00   0.0  0
 NAT  CONST_17  H6    C6   C1   C2    180.00   0.0  0
 NAT  CONST_18  H1    C1   C2   C3    180.00   0.0  0
 NAT  CONST_19  HN10  N10  C9   N8    180.00   0.0  0
 NAT  CONST_20  HN8   N8   C9   N10   180.00   0.0  0
 NAT  Var_01    N10   C11  C12  C7      3.05  30.0  1
 NAT  Var_02    C12   C11  N10  C9      9.88  30.0  1
 NAT  Var_03    O15   C14  C12  C7     -8.73  30.0  2
 NAT  Var_04    H181  C18  C11  N10  -109.80  30.0  3
 NAT  Var_05    C17   C16  O15  C14  -174.99  30.0  3
 NAT  Var_06    H171  C17  C16  O15   -61.93  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
 NAT  chir_01  C7  C2  N8  C12  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
 NAT  plan-1  C1    0.020
 NAT  plan-1  C2    0.020
 NAT  plan-1  C3    0.020
 NAT  plan-1  C4    0.020
 NAT  plan-1  C5    0.020
 NAT  plan-1  C6    0.020
 NAT  plan-1  C7    0.020
 NAT  plan-1  O13   0.020
 NAT  plan-1  H1    0.020
 NAT  plan-1  H3    0.020
 NAT  plan-1  H5    0.020
 NAT  plan-1  H6    0.020
 NAT  plan-2  C7    0.020
 NAT  plan-2  N8    0.020
 NAT  plan-2  C9    0.020
 NAT  plan-2  N10   0.020
 NAT  plan-2  C11   0.020
 NAT  plan-2  S20   0.020
 NAT  plan-2  HN8   0.020
 NAT  plan-2  HN10  0.020
 NAT  plan-3  C12   0.020
 NAT  plan-3  C14   0.020
 NAT  plan-3  O15   0.020
 NAT  plan-3  O19   0.020

