# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 01:16:06 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: 4-{[(4-methyl-6-oxo-1,6-dihydropyrimidin-2-yl)sulfanyl]acetyl}benzenesulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CC(=O)NC(=N1)SCC(=O)c2ccc(cc2)[S](N)(=O)=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
 E59  E59  4-{[(4-methyl-6-oxo-1,6-dihydropyrimidin-2-yl)sulfanyl]acetyl}benzenesulfonamide  ligand  35  22  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_E59
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
 E59  N1    N  NR16  0  -0.689   5.1763   0.6813  -0.0134
 E59  C2    C  CR6   0   0.552   6.2670  -0.1846  -0.0629
 E59  C3    C  CR16  0  -0.490   5.8784  -1.5649  -0.0977
 E59  C4    C  CR6   0   0.292   4.5640  -1.9138  -0.0804
 E59  N5    N  N     0  -0.457   3.5577  -0.9903  -0.0303
 E59  C6    C  CR6   0   0.366   3.8949   0.2545   0.0004
 E59  O7    O  O     0  -0.481   7.4038   0.2591  -0.0737
 E59  C8    C  CH3   0  -0.713   4.1163  -3.3359  -0.1125
 E59  S9    S  S2    0   0.107   2.7044   1.5359   0.0632
 E59  C10   C  CH2   0  -0.704   1.1921   0.5470   0.0392
 E59  C11   C  C     0   0.399   0.0273   1.5026   0.0638
 E59  O12   O  O     0  -0.368   0.2103   2.6973   0.1082
 E59  C13   C  CR6   0   0.012  -1.3454   0.9280   0.0310
 E59  C14   C  CR16  0  -0.276  -1.5671  -0.4448  -0.0173
 E59  C15   C  CR16  0  -0.214  -2.8590  -0.9483  -0.0523
 E59  C16   C  CR6   0  -0.202  -3.9232  -0.0639  -0.0347
 E59  C17   C  CR16  0  -0.205  -3.7247   1.3110   0.0126
 E59  C18   C  CR16  0  -0.246  -2.4346   1.8018   0.0457
 E59  S19   S  S     0   1.367  -5.5858  -0.6866  -0.0959
 E59  O20   O  OS    0  -0.660  -6.3924   0.1906  -0.9299
 E59  O21   O  OS    0  -0.644  -5.5120  -2.0996  -0.4360
 E59  N22   N  NC2   0  -0.887  -6.0740  -0.4195   1.4549
 E59  H1    H  HNR6  0   0.431   5.3822   1.6737   0.0102
 E59  H3    H  HCR6  0   0.277   6.6554  -2.3149  -0.1364
 E59  H8    H  HCH3  0   0.260   3.5369  -3.5675   0.7826
 E59  H8A   H  HCH3  0   0.259   3.4621  -3.5059  -0.9688
 E59  H8B   H  HCH3  0   0.251   4.9558  -4.0243  -0.1714
 E59  H10   H  HCH2  0   0.331   1.1656  -0.0757  -0.8563
 E59  H10A  H  HCH2  0   0.332   1.1631  -0.1181   0.9039
 E59  H14   H  HCR6  0   0.284  -0.7465  -1.1486  -0.0312
 E59  H15   H  HCR6  0   0.295  -3.0172  -2.0166  -0.0939
 E59  H17   H  HCR6  0   0.295  -4.5606   1.9969   0.0234
 E59  H18   H  HCR6  0   0.282  -2.2752   2.8706   0.0805
 E59  HN22  H  HNC2  0   0.424  -7.0853  -0.3561   1.5256
 E59  HN2A  H  HNC2  0   0.420  -5.7133  -1.1047   2.1110

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
 E59  N1   C6    single    1.351  0.020  1.351
 E59  C2   N1    single    1.393  0.020  1.393
 E59  C2   C3    single    1.434  0.020  1.434
 E59  C3   C4    double    1.360  0.020  1.360
 E59  C4   N5    single    1.367  0.020  1.367
 E59  C4   C8    single    1.491  0.020  1.491
 E59  C6   N5    double    1.290  0.020  1.290
 E59  C6   S9    single    1.750  0.020  1.750
 E59  O7   C2    double    1.220  0.020  1.220
 E59  C10  S9    single    1.807  0.020  1.807
 E59  C10  C11   single    1.507  0.020  1.507
 E59  C11  C13   single    1.488  0.020  1.488
 E59  O12  C11   double    1.209  0.020  1.209
 E59  C13  C18   aromatic  1.397  0.020  1.397
 E59  C13  C14   aromatic  1.391  0.020  1.391
 E59  C14  C15   aromatic  1.387  0.020  1.387
 E59  C15  C16   aromatic  1.384  0.020  1.384
 E59  C16  S19   single    1.776  0.020  1.776
 E59  C17  C16   aromatic  1.390  0.020  1.390
 E59  C18  C17   aromatic  1.381  0.020  1.381
 E59  S19  O21   double    1.455  0.020  1.455
 E59  O20  S19   double    1.454  0.020  1.454
 E59  N22  S19   single    1.648  0.020  1.648
 E59  N1   H1    single    0.860  0.020  1.020
 E59  C3   H3    single    0.930  0.020  1.080
 E59  C8   H8    single    0.970  0.020  1.090
 E59  C8   H8A   single    0.970  0.020  1.090
 E59  C8   H8B   single    0.970  0.020  1.090
 E59  C10  H10   single    0.970  0.020  1.090
 E59  C10  H10A  single    0.970  0.020  1.090
 E59  C14  H14   single    0.930  0.020  1.080
 E59  C15  H15   single    0.930  0.020  1.080
 E59  C17  H17   single    0.930  0.020  1.080
 E59  C18  H18   single    0.930  0.020  1.080
 E59  N22  HN22  single    0.890  0.020  1.040
 E59  N22  HN2A  single    0.890  0.020  1.040

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
 E59  H1    N1   C6    120.11  3.000
 E59  H1    N1   C2    116.75  3.000
 E59  C6    N1   C2    123.13  3.000
 E59  O7    C2   C3    127.01  3.000
 E59  O7    C2   N1    120.23  3.000
 E59  C3    C2   N1    112.75  3.000
 E59  H3    C3   C4    121.15  3.000
 E59  H3    C3   C2    118.29  3.000
 E59  C4    C3   C2    120.56  3.000
 E59  C8    C4   N5    115.09  3.000
 E59  C8    C4   C3    122.32  3.000
 E59  N5    C4   C3    122.60  3.000
 E59  C6    N5   C4    117.41  3.000
 E59  S9    C6   N5    121.97  3.000
 E59  S9    C6   N1    114.48  3.000
 E59  N5    C6   N1    123.55  3.000
 E59  H8B   C8   H8A   108.77  3.000
 E59  H8B   C8   H8    108.66  3.000
 E59  H8A   C8   H8    107.01  3.000
 E59  H8B   C8   C4    111.91  3.000
 E59  H8A   C8   C4    110.22  3.000
 E59  H8    C8   C4    110.13  3.000
 E59  C10   S9   C6     99.68  3.000
 E59  H10A  C10  H10   107.57  3.000
 E59  H10A  C10  C11   110.67  3.000
 E59  H10   C10  C11   110.89  3.000
 E59  H10A  C10  S9    110.20  3.000
 E59  H10   C10  S9    110.09  3.000
 E59  C11   C10  S9    107.44  3.000
 E59  C13   C11  O12   121.45  3.000
 E59  O12   C11  C10   120.67  3.000
 E59  C13   C11  C10   117.89  3.000
 E59  C18   C13  C14   119.57  3.000
 E59  C14   C13  C11   121.91  3.000
 E59  C18   C13  C11   118.52  3.000
 E59  H14   C14  C15   118.06  3.000
 E59  H14   C14  C13   121.45  3.000
 E59  C15   C14  C13   120.49  3.000
 E59  H15   C15  C16   121.30  3.000
 E59  H15   C15  C14   119.75  3.000
 E59  C16   C15  C14   118.95  3.000
 E59  S19   C16  C17   118.79  3.000
 E59  C17   C16  C15   121.52  3.000
 E59  S19   C16  C15   119.69  3.000
 E59  H17   C17  C18   119.78  3.000
 E59  H17   C17  C16   121.15  3.000
 E59  C18   C17  C16   119.07  3.000
 E59  H18   C18  C17   119.34  3.000
 E59  H18   C18  C13   120.26  3.000
 E59  C17   C18  C13   120.41  3.000
 E59  N22   S19  O21   113.10  3.000
 E59  N22   S19  O20   106.12  3.000
 E59  O21   S19  O20   118.66  3.000
 E59  N22   S19  C16   100.84  3.000
 E59  O20   S19  C16   109.11  3.000
 E59  O21   S19  C16   107.52  3.000
 E59  HN2A  N22  HN22  110.55  3.000
 E59  HN2A  N22  S19   113.18  3.000
 E59  HN22  N22  S19   111.76  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
 E59  CONST_01  C16   C17  C18  C13     0.00   0.0  0
 E59  CONST_02  C16   C15  C14  C13     0.00   0.0  0
 E59  CONST_03  C17   C18  C13  C14     0.00   0.0  0
 E59  CONST_04  C17   C16  C15  C14     0.00   0.0  0
 E59  CONST_05  C18   C13  C14  C15     0.00   0.0  0
 E59  CONST_06  C18   C17  C16  C15     0.00   0.0  0
 E59  CONST_07  C4    N5   C6   N1      0.00   0.0  0
 E59  CONST_08  N5    C6   N1   C2      0.00   0.0  0
 E59  CONST_09  C6    N1   C2   C3      0.00   0.0  0
 E59  CONST_10  C17   C18  C13  C11   180.00   0.0  0
 E59  CONST_11  C15   C14  C13  C11   180.00   0.0  0
 E59  CONST_12  S19   C16  C15  C14   180.00   0.0  0
 E59  CONST_13  S19   C16  C17  C18   180.00   0.0  0
 E59  CONST_14  S9    C6   N1   C2    180.00   0.0  0
 E59  CONST_15  S9    C6   N5   C4    180.00   0.0  0
 E59  CONST_16  O7    C2   N1   C6    180.00   0.0  0
 E59  CONST_17  H17   C17  C18  C13   180.00   0.0  0
 E59  CONST_18  H15   C15  C14  C13   180.00   0.0  0
 E59  CONST_19  H18   C18  C13  C14   180.00   0.0  0
 E59  CONST_20  H14   C14  C15  C16   180.00   0.0  0
 E59  CONST_21  H1    N1   C2   C3    180.00   0.0  0
 E59  Var_01    C18   C13  C11  C10  -179.65  30.0  2
 E59  Var_02    O21   S19  C16  C15   -11.59  30.0  2
 E59  Var_03    H8    C8   C4   C3    119.78  30.0  3
 E59  Var_04    C11   C10  S9   C6   -179.01  30.0  1
 E59  Var_05    C13   C11  C10  S9    179.16  30.0  3
 E59  Var_06    HN22  N22  S19  C16   156.70  30.0  3

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
 E59  plan-1  N1   0.020
 E59  plan-1  C2   0.020
 E59  plan-1  C3   0.020
 E59  plan-1  C4   0.020
 E59  plan-1  N5   0.020
 E59  plan-1  C6   0.020
 E59  plan-1  O7   0.020
 E59  plan-1  C8   0.020
 E59  plan-1  S9   0.020
 E59  plan-1  H1   0.020
 E59  plan-1  H3   0.020
 E59  plan-2  C11  0.020
 E59  plan-2  C13  0.020
 E59  plan-2  C14  0.020
 E59  plan-2  C15  0.020
 E59  plan-2  C16  0.020
 E59  plan-2  C17  0.020
 E59  plan-2  C18  0.020
 E59  plan-2  S19  0.020
 E59  plan-2  H14  0.020
 E59  plan-2  H15  0.020
 E59  plan-2  H17  0.020
 E59  plan-2  H18  0.020
 E59  plan-3  C10  0.020
 E59  plan-3  C11  0.020
 E59  plan-3  O12  0.020
 E59  plan-3  C13  0.020

