# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 12:14:02 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: (2E)-N-[(1S)-2-hydroxy-1-({(R)-[(methylsulfanyl)methyl]sulfinyl}methyl)ethyl]-3-(6-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)prop-2-enamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSC[S@](=O)C[C@H](CO)NC(=O)/C=C/C1=C(C)NC(=O)NC1=O
#
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
 SPS  SPS  (2E)-N-[(1S)-2-hydroxy-1-({(R)-[(methylsulfanyl)methyl]sulfinyl}methyl)ethyl]-3-(6-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)prop-2-enamide  ligand  42  23  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_SPS
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
 SPS  C1    C  CR6   0   0.590   3.8160   0.7775   1.0669
 SPS  O1    O  OC    0  -0.495   3.0265   0.8119   1.9929
 SPS  N2    N  NR16  0  -0.443   5.0328   1.4313   1.1959
 SPS  C3    C  CR6   0   0.573   6.0492   1.4755   0.2894
 SPS  O3    O  OC    0  -0.568   7.0934   2.0628   0.4699
 SPS  N4    N  NR16  0  -0.674   5.7743   0.7899  -0.8697
 SPS  C5    C  CR6   0   0.241   4.6178   0.1357  -1.1314
 SPS  C7    C  CH3   0  -0.706   4.5490  -0.5264  -2.4690
 SPS  C6    C  CR6   0  -0.132   3.6040   0.1094  -0.2064
 SPS  C8    C  C1    0  -0.240   2.3681  -0.5758  -0.5152
 SPS  C9    C  C1    0  -0.431   1.2619  -0.7249   0.2276
 SPS  C10   C  C     0   0.594   0.1037  -1.4554  -0.3336
 SPS  O10   O  O     0  -0.562   0.0874  -1.9353  -1.4616
 SPS  N11   N  NH1   0  -0.652  -0.9510  -1.5291   0.5073
 SPS  C12   C  CH1   0  -0.120  -2.1880  -2.2038   0.1822
 SPS  C13   C  CH2   0  -0.143  -2.2302  -3.6240   0.7232
 SPS  O13   O  OH1   0  -0.655  -2.1532  -3.5773   2.1278
 SPS  C14   C  CH2   0  -0.618  -3.3680  -1.3829   0.6871
 SPS  S15   S  S3    0   0.698  -3.2535   0.3099   0.0269
 SPS  O15   O  O     0  -0.705  -3.2742   0.1798  -1.4771
 SPS  C16   C  CH2   0  -0.702  -4.9159   0.8384   0.5425
 SPS  S17   S  S2    0   0.013  -5.1984   2.5717   0.1607
 SPS  C18   C  CH3   0  -0.764  -5.6471   2.4916  -1.5901
 SPS  HN2   H  HNR6  0   0.476   5.1933   1.9168   2.0701
 SPS  HN4   H  HNR6  0   0.377   6.5018   0.7980  -1.5700
 SPS  H71   H  HCH3  0   0.254   5.4953  -0.4582  -3.0027
 SPS  H72   H  HCH3  0   0.308   4.3000  -1.5811  -2.3650
 SPS  H73   H  HCH3  0   0.277   3.7810  -0.0647  -3.0889
 SPS  H81   H  H     0   0.276   2.3300  -1.0257  -1.5012
 SPS  H91   H  H     0   0.315   1.1723  -0.3287   1.2277
 SPS  HN11  H  HNH1  0   0.419  -0.8284  -1.2024   1.4532
 SPS  H121  H  HCH1  0   0.288  -2.2528  -2.2689  -0.9022
 SPS  H131  H  HCH2  0   0.227  -3.1553  -4.1024   0.3774
 SPS  H132  H  HCH2  0   0.191  -1.3933  -4.1841   0.2882
 SPS  HO13  H  HOH1  0   0.465  -2.2101  -4.4760   2.4637
 SPS  H141  H  HCH2  0   0.275  -4.3102  -1.8275   0.3591
 SPS  H142  H  HCH2  0   0.293  -3.3782  -1.3003   1.7754
 SPS  H161  H  HCH2  0   0.296  -5.6608   0.1958   0.0676
 SPS  H162  H  HCH2  0   0.344  -4.9795   0.7219   1.6257
 SPS  H181  H  HCH3  0   0.254  -5.9638   3.4920  -1.8765
 SPS  H182  H  HCH3  0   0.291  -4.8050   2.1914  -2.2055
 SPS  H183  H  HCH3  0   0.277  -6.4784   1.8052  -1.7421

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
 SPS  C1   O1    double    1.217  0.020  1.217
 SPS  C1   N2    aromatic  1.387  0.020  1.387
 SPS  C1   C6    aromatic  1.453  0.020  1.453
 SPS  N2   C3    aromatic  1.363  0.020  1.363
 SPS  N2   HN2   single    0.860  0.020  1.020
 SPS  C3   O3    double    1.212  0.020  1.212
 SPS  C3   N4    aromatic  1.374  0.020  1.374
 SPS  N4   C5    aromatic  1.354  0.020  1.354
 SPS  N4   HN4   single    0.860  0.020  1.020
 SPS  C5   C7    single    1.494  0.020  1.494
 SPS  C5   C6    aromatic  1.373  0.020  1.373
 SPS  C7   H71   single    0.970  0.020  1.090
 SPS  C7   H72   single    0.970  0.020  1.090
 SPS  C7   H73   single    0.970  0.020  1.090
 SPS  C6   C8    single    1.447  0.020  1.447
 SPS  C8   C9    double    1.341  0.020  1.341
 SPS  C8   H81   single    0.930  0.020  1.080
 SPS  C9   C10   single    1.480  0.020  1.480
 SPS  C9   H91   single    0.930  0.020  1.080
 SPS  C10  O10   double    1.226  0.020  1.226
 SPS  C10  N11   single    1.351  0.020  1.351
 SPS  N11  C12   single    1.446  0.020  1.446
 SPS  N11  HN11  single    0.860  0.020  1.020
 SPS  C12  C13   single    1.520  0.020  1.520
 SPS  C12  C14   single    1.524  0.020  1.524
 SPS  C12  H121  single    0.970  0.020  1.090
 SPS  C13  O13   single    1.407  0.020  1.407
 SPS  C13  H131  single    0.970  0.020  1.090
 SPS  C13  H132  single    0.970  0.020  1.090
 SPS  O13  HO13  single    0.850  0.020  0.980
 SPS  C14  S15   single    1.821  0.020  1.821
 SPS  C14  H141  single    0.970  0.020  1.090
 SPS  C14  H142  single    0.970  0.020  1.090
 SPS  S15  O15   double    1.510  0.020  1.510
 SPS  S15  C16   single    1.819  0.020  1.819
 SPS  C16  S17   single    1.797  0.020  1.797
 SPS  C16  H161  single    0.970  0.020  1.090
 SPS  C16  H162  single    0.970  0.020  1.090
 SPS  S17  C18   single    1.809  0.020  1.809
 SPS  C18  H181  single    0.970  0.020  1.090
 SPS  C18  H182  single    0.970  0.020  1.090
 SPS  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
 SPS  C6    C1   N2    115.22  3.000
 SPS  C6    C1   O1    125.78  3.000
 SPS  N2    C1   O1    119.00  3.000
 SPS  HN2   N2   C3    116.13  3.000
 SPS  HN2   N2   C1    116.44  3.000
 SPS  C3    N2   C1    127.42  3.000
 SPS  N4    C3   O3    122.68  3.000
 SPS  N4    C3   N2    113.31  3.000
 SPS  O3    C3   N2    124.02  3.000
 SPS  HN4   N4   C5    119.02  3.000
 SPS  HN4   N4   C3    115.89  3.000
 SPS  C5    N4   C3    125.08  3.000
 SPS  C6    C5   C7    124.11  3.000
 SPS  C6    C5   N4    120.65  3.000
 SPS  C7    C5   N4    115.24  3.000
 SPS  H73   C7   H72   107.68  3.000
 SPS  H73   C7   H71   107.90  3.000
 SPS  H72   C7   H71   107.84  3.000
 SPS  H73   C7   C5    110.73  3.000
 SPS  H72   C7   C5    110.75  3.000
 SPS  H71   C7   C5    111.78  3.000
 SPS  C8    C6   C5    119.75  3.000
 SPS  C8    C6   C1    121.96  3.000
 SPS  C5    C6   C1    118.28  3.000
 SPS  H81   C8   C9    115.38  3.000
 SPS  H81   C8   C6    114.87  3.000
 SPS  C9    C8   C6    129.75  3.000
 SPS  H91   C9   C10   117.88  3.000
 SPS  H91   C9   C8    122.75  3.000
 SPS  C10   C9   C8    119.38  3.000
 SPS  N11   C10  O10   122.75  3.000
 SPS  N11   C10  C9    113.70  3.000
 SPS  O10   C10  C9    123.54  3.000
 SPS  HN11  N11  C12   117.79  3.000
 SPS  HN11  N11  C10   118.12  3.000
 SPS  C12   N11  C10   123.60  3.000
 SPS  H121  C12  C14   108.44  3.000
 SPS  H121  C12  C13   107.28  3.000
 SPS  C14   C12  C13   111.33  3.000
 SPS  H121  C12  N11   107.63  3.000
 SPS  C14   C12  N11   109.67  3.000
 SPS  C13   C12  N11   112.31  3.000
 SPS  H132  C13  H131  107.19  3.000
 SPS  H132  C13  O13   111.77  3.000
 SPS  H131  C13  O13   112.03  3.000
 SPS  H132  C13  C12   108.33  3.000
 SPS  H131  C13  C12   108.57  3.000
 SPS  O13   C13  C12   108.82  3.000
 SPS  HO13  O13  C13   108.33  3.000
 SPS  H142  C14  H141  108.80  3.000
 SPS  H142  C14  S15   106.96  3.000
 SPS  H141  C14  S15   108.89  3.000
 SPS  H142  C14  C12   112.24  3.000
 SPS  H141  C14  C12   110.44  3.000
 SPS  S15   C14  C12   109.39  3.000
 SPS  C16   S15  O15   107.15  3.000
 SPS  C16   S15  C14    96.31  3.000
 SPS  O15   S15  C14   106.27  3.000
 SPS  H162  C16  H161  109.21  3.000
 SPS  H162  C16  S17   107.74  3.000
 SPS  H161  C16  S17   111.58  3.000
 SPS  H162  C16  S15   107.67  3.000
 SPS  H161  C16  S15   109.21  3.000
 SPS  S17   C16  S15   111.32  3.000
 SPS  C18   S17  C16   101.64  3.000
 SPS  H183  C18  H182  109.81  3.000
 SPS  H183  C18  H181  108.71  3.000
 SPS  H182  C18  H181  109.33  3.000
 SPS  H183  C18  S17   110.63  3.000
 SPS  H182  C18  S17   111.62  3.000
 SPS  H181  C18  S17   106.64  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
 SPS  CONST_01  N4    C3   N2   C1     0.00   0.0  0
 SPS  CONST_02  N4    C5   C6   C1     0.00   0.0  0
 SPS  CONST_03  C5    C6   C1   N2     0.00   0.0  0
 SPS  CONST_04  C5    N4   C3   N2     0.00   0.0  0
 SPS  CONST_05  C6    C1   N2   C3     0.00   0.0  0
 SPS  CONST_06  C6    C5   N4   C3     0.00   0.0  0
 SPS  CONST_07  O3    C3   N2   C1   180.00   0.0  0
 SPS  CONST_08  C7    C5   C6   C1   180.00   0.0  0
 SPS  CONST_09  C3    N2   C1   O1   180.00   0.0  0
 SPS  CONST_10  C5    C6   C1   O1   180.00   0.0  0
 SPS  CONST_11  C8    C6   C1   N2   180.00   0.0  0
 SPS  CONST_12  C7    C5   N4   C3   180.00   0.0  0
 SPS  CONST_13  C5    N4   C3   O3   180.00   0.0  0
 SPS  CONST_14  C8    C6   C5   N4   180.00   0.0  0
 SPS  CONST_15  HN4   N4   C3   N2   180.00   0.0  0
 SPS  CONST_16  HN2   N2   C3   N4   180.00   0.0  0
 SPS  CONST_17  C12   N11  C10  C9   180.00   0.0  0
 SPS  CONST_18  C12   N11  C10  O10    0.00   0.0  0
 SPS  CONST_19  HN11  N11  C10  C9     0.00   0.0  0
 SPS  Var_01    C9    C8   C6   C1     0.21  30.0  2
 SPS  Var_02    H71   C7   C5   N4     5.43  30.0  2
 SPS  Var_03    C10   C9   C8   C6   178.67   0.0  2
 SPS  Var_04    O10   C10  C9   C8    -0.53  30.0  2
 SPS  Var_05    O15   S15  C14  C12   59.54  30.0  3
 SPS  Var_06    S17   C16  S15  C14  176.28  30.0  3
 SPS  Var_07    H181  C18  S17  C16  172.76  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
 SPS  chir_01  C12  N11  C13  C14  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
 SPS  plan-1  C1    0.020
 SPS  plan-1  O1    0.020
 SPS  plan-1  N2    0.020
 SPS  plan-1  C3    0.020
 SPS  plan-1  O3    0.020
 SPS  plan-1  N4    0.020
 SPS  plan-1  C5    0.020
 SPS  plan-1  C7    0.020
 SPS  plan-1  C6    0.020
 SPS  plan-1  C8    0.020
 SPS  plan-1  HN2   0.020
 SPS  plan-1  HN4   0.020
 SPS  plan-2  C6    0.020
 SPS  plan-2  C8    0.020
 SPS  plan-2  C9    0.020
 SPS  plan-2  C10   0.020
 SPS  plan-2  H81   0.020
 SPS  plan-2  H91   0.020
 SPS  plan-3  C14   0.020
 SPS  plan-3  S15   0.020
 SPS  plan-3  O15   0.020
 SPS  plan-3  C16   0.020
 SPS  plan-4  C9    0.020
 SPS  plan-4  C10   0.020
 SPS  plan-4  O10   0.020
 SPS  plan-4  N11   0.020
 SPS  plan-4  C12   0.020
 SPS  plan-4  HN11  0.020

