# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 23:59:24 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: 2-({5-[(2,4-dimethylphenyl)sulfonyl]-6-oxo-1,6-dihydropyrimidin-2-yl}sulfanyl)-N-[2-(trifluoromethyl)phenyl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(c(C)c1)[S](=O)(=O)C2=CN=C(NC2=O)SCC(=O)Nc3ccccc3C(F)(F)F
#
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
 4ID  4ID  2-({5-[(2,4-dimethylphenyl)sulfonyl]-6-oxo-1,6-dihydropyrimidin-2-yl}sulfanyl)-N-[2-(trifluoromethyl)phenyl]acetamide  ligand  51  33  .  2022-07-23  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_4ID
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
 4ID  C1    C  CR6   0   0.611   2.9146   0.4342   1.3089
 4ID  F1    F  F     0  -0.299  -7.2897  -1.7332   1.6471
 4ID  N1    N  NR16  0  -0.684   1.6363   0.9867   1.3422
 4ID  O1    O  O     0  -0.430   3.8365   0.9533   1.9012
 4ID  S1    S  S2    0   0.135  -0.9198   1.3271   0.9317
 4ID  C2    C  CR6   0   0.398   0.5695   0.4610   0.7088
 4ID  F2    F  F     0  -0.309  -5.3384  -0.8743   1.9030
 4ID  N2    N  NH1   0  -0.761  -4.3663   0.2568  -0.6043
 4ID  O2    O  O     0  -0.450  -3.6062   1.9011   0.7539
 4ID  S2    S  S     0   1.233   4.4741  -1.6492   0.4024
 4ID  C3    C  CH2   0  -0.699  -2.0256   0.3109  -0.0738
 4ID  F3    F  F     0  -0.313  -5.7355  -2.1721   0.2326
 4ID  N3    N  N     0  -0.434   0.6327  -0.6193  -0.0162
 4ID  O3    O  OS    0  -0.645   4.9295  -1.9263   1.7596
 4ID  C4    C  C     0   0.561  -3.4053   0.9128   0.0753
 4ID  O4    O  OS    0  -0.654   4.2470  -2.7884  -0.4827
 4ID  C5    C  CR6   0   0.332  -5.7178   0.6800  -0.5866
 4ID  C6    C  CR6   0  -0.216  -6.6714  -0.0095   0.1657
 4ID  C7    C  CT    0   1.074  -6.2616  -1.1959   0.9864
 4ID  C8    C  CR16  0  -0.314  -7.9933   0.4164   0.1559
 4ID  C9    C  CR16  0  -0.231  -8.3619   1.5309  -0.5835
 4ID  C10   C  CR16  0  -0.256  -7.4124   2.2211  -1.3196
 4ID  C11   C  CR16  0  -0.253  -6.0934   1.7919  -1.3235
 4ID  C12   C  CR16  0   0.012   1.8330  -1.2193  -0.1095
 4ID  C13   C  CR6   0  -0.425   2.9609  -0.7591   0.5025
 4ID  C14   C  CR6   0  -0.266   5.6154  -0.5243  -0.3550
 4ID  C15   C  CR16  0  -0.205   6.6566  -0.0604   0.4382
 4ID  C16   C  CR16  0  -0.316   7.6048   0.7952  -0.0942
 4ID  C17   C  CR6   0   0.133   7.5211   1.2005  -1.4216
 4ID  C18   C  CH3   0  -0.724   8.5492   2.1088  -2.0237
 4ID  C19   C  CR16  0  -0.346   6.4619   0.7272  -2.1925
 4ID  C20   C  CR6   0   0.200   5.4920  -0.1376  -1.6977
 4ID  C21   C  CH3   0  -0.753   4.3837  -0.5767  -2.6098
 4ID  HN1   H  HNR6  0   0.446   1.5322   1.8325   1.8938
 4ID  HN2   H  HNH1  0   0.425  -4.1206  -0.5566  -1.1499
 4ID  H3    H  HCH2  0   0.337  -1.7081   0.3234  -1.1171
 4ID  H3A   H  HCH2  0   0.333  -2.0081  -0.7228   0.2725
 4ID  H8    H  HCR6  0   0.279  -8.7462  -0.1064   0.7281
 4ID  H9    H  HCR6  0   0.275  -9.3931   1.8560  -0.5806
 4ID  H10   H  HCR6  0   0.275  -7.6955   3.0915  -1.8960
 4ID  H11   H  HCR6  0   0.278  -5.3494   2.3148  -1.9095
 4ID  H12   H  HCR6  0   0.311   1.8612  -2.1158  -0.7175
 4ID  H15   H  HCR6  0   0.278   6.7340  -0.3593   1.4734
 4ID  H16   H  HCR6  0   0.261   8.4102   1.1542   0.5340
 4ID  H18   H  HCH3  0   0.258   9.2617   1.5370  -2.6215
 4ID  H18A  H  HCH3  0   0.251   8.0921   2.8454  -2.6841
 4ID  H18B  H  HCH3  0   0.250   9.1143   2.6386  -1.2586
 4ID  H19   H  HCR6  0   0.256   6.3843   1.0453  -3.2260
 4ID  H21   H  HCH3  0   0.254   3.4077  -0.2470  -2.2510
 4ID  H21A  H  HCH3  0   0.261   4.5235  -0.1471  -3.5995
 4ID  H21B  H  HCH3  0   0.266   4.3431  -1.6583  -2.7172

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
 4ID  C1   N1    single    1.393  0.020  1.393
 4ID  C1   O1    double    1.213  0.020  1.213
 4ID  C1   C13   single    1.441  0.020  1.441
 4ID  F1   C7    single    1.335  0.020  1.335
 4ID  N1   C2    single    1.347  0.020  1.347
 4ID  S1   C2    single    1.737  0.020  1.737
 4ID  S1   C3    single    1.807  0.020  1.807
 4ID  C2   N3    double    1.303  0.020  1.303
 4ID  F2   C7    single    1.340  0.020  1.340
 4ID  N2   C4    single    1.347  0.020  1.347
 4ID  N2   C5    single    1.416  0.020  1.416
 4ID  O2   C4    double    1.216  0.020  1.216
 4ID  S2   O3    double    1.458  0.020  1.458
 4ID  S2   O4    double    1.460  0.020  1.460
 4ID  S2   C13   single    1.758  0.020  1.758
 4ID  S2   C14   single    1.772  0.020  1.772
 4ID  C3   C4    single    1.513  0.020  1.513
 4ID  F3   C7    single    1.341  0.020  1.341
 4ID  N3   C12   single    1.345  0.020  1.345
 4ID  C5   C6    aromatic  1.397  0.020  1.397
 4ID  C5   C11   aromatic  1.386  0.020  1.386
 4ID  C6   C7    single    1.500  0.020  1.500
 4ID  C6   C8    aromatic  1.389  0.020  1.389
 4ID  C8   C9    aromatic  1.387  0.020  1.387
 4ID  C9   C10   aromatic  1.386  0.020  1.386
 4ID  C10  C11   aromatic  1.387  0.020  1.387
 4ID  C12  C13   double    1.363  0.020  1.363
 4ID  C14  C15   aromatic  1.389  0.020  1.389
 4ID  C14  C20   aromatic  1.403  0.020  1.403
 4ID  C15  C16   aromatic  1.384  0.020  1.384
 4ID  C16  C17   aromatic  1.390  0.020  1.390
 4ID  C17  C18   single    1.498  0.020  1.498
 4ID  C17  C19   aromatic  1.393  0.020  1.393
 4ID  C19  C20   aromatic  1.391  0.020  1.391
 4ID  C20  C21   single    1.501  0.020  1.501
 4ID  N1   HN1   single    0.860  0.020  1.020
 4ID  N2   HN2   single    0.860  0.020  1.020
 4ID  C3   H3    single    0.970  0.020  1.090
 4ID  C3   H3A   single    0.970  0.020  1.090
 4ID  C8   H8    single    0.930  0.020  1.080
 4ID  C9   H9    single    0.930  0.020  1.080
 4ID  C10  H10   single    0.930  0.020  1.080
 4ID  C11  H11   single    0.930  0.020  1.080
 4ID  C12  H12   single    0.930  0.020  1.080
 4ID  C15  H15   single    0.930  0.020  1.080
 4ID  C16  H16   single    0.930  0.020  1.080
 4ID  C18  H18   single    0.970  0.020  1.090
 4ID  C18  H18A  single    0.970  0.020  1.090
 4ID  C18  H18B  single    0.970  0.020  1.090
 4ID  C19  H19   single    0.930  0.020  1.080
 4ID  C21  H21   single    0.970  0.020  1.090
 4ID  C21  H21A  single    0.970  0.020  1.090
 4ID  C21  H21B  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
 4ID  C13   C1   O1    127.12  3.000
 4ID  C13   C1   N1    111.80  3.000
 4ID  O1    C1   N1    121.08  3.000
 4ID  HN1   N1   C2    119.96  3.000
 4ID  HN1   N1   C1    115.95  3.000
 4ID  C2    N1   C1    124.09  3.000
 4ID  C3    S1   C2     99.95  3.000
 4ID  N3    C2   S1    121.77  3.000
 4ID  N3    C2   N1    123.15  3.000
 4ID  S1    C2   N1    115.08  3.000
 4ID  HN2   N2   C5    118.66  3.000
 4ID  HN2   N2   C4    119.41  3.000
 4ID  C5    N2   C4    121.92  3.000
 4ID  C14   S2   C13   104.90  3.000
 4ID  C14   S2   O4    109.65  3.000
 4ID  C13   S2   O4    107.19  3.000
 4ID  C14   S2   O3    108.49  3.000
 4ID  C13   S2   O3    108.18  3.000
 4ID  O4    S2   O3    117.67  3.000
 4ID  H3A   C3   H3    108.06  3.000
 4ID  H3A   C3   C4    111.14  3.000
 4ID  H3    C3   C4    110.81  3.000
 4ID  H3A   C3   S1    110.28  3.000
 4ID  H3    C3   S1    110.34  3.000
 4ID  C4    C3   S1    106.23  3.000
 4ID  C12   N3   C2    116.86  3.000
 4ID  C3    C4   O2    121.96  3.000
 4ID  C3    C4   N2    114.02  3.000
 4ID  O2    C4   N2    124.02  3.000
 4ID  C11   C5   C6    119.83  3.000
 4ID  C11   C5   N2    119.45  3.000
 4ID  C6    C5   N2    120.72  3.000
 4ID  C8    C6   C7    120.43  3.000
 4ID  C8    C6   C5    119.65  3.000
 4ID  C7    C6   C5    119.91  3.000
 4ID  C6    C7   F3    112.05  3.000
 4ID  C6    C7   F2    111.88  3.000
 4ID  F3    C7   F2    106.80  3.000
 4ID  C6    C7   F1    112.26  3.000
 4ID  F3    C7   F1    106.70  3.000
 4ID  F2    C7   F1    106.78  3.000
 4ID  H8    C8   C9    119.06  3.000
 4ID  H8    C8   C6    120.74  3.000
 4ID  C9    C8   C6    120.20  3.000
 4ID  H9    C9   C10   120.34  3.000
 4ID  H9    C9   C8    119.58  3.000
 4ID  C10   C9   C8    120.08  3.000
 4ID  H10   C10  C11   119.76  3.000
 4ID  H10   C10  C9    120.30  3.000
 4ID  C11   C10  C9    119.93  3.000
 4ID  H11   C11  C10   120.39  3.000
 4ID  H11   C11  C5    119.31  3.000
 4ID  C10   C11  C5    120.30  3.000
 4ID  H12   C12  C13   120.64  3.000
 4ID  H12   C12  N3    115.54  3.000
 4ID  C13   C12  N3    123.82  3.000
 4ID  C12   C13  S2    121.03  3.000
 4ID  C12   C13  C1    120.28  3.000
 4ID  S2    C13  C1    118.60  3.000
 4ID  C20   C14  C15   121.37  3.000
 4ID  C20   C14  S2    121.82  3.000
 4ID  C15   C14  S2    116.79  3.000
 4ID  H15   C15  C16   119.39  3.000
 4ID  H15   C15  C14   120.57  3.000
 4ID  C16   C15  C14   120.04  3.000
 4ID  H16   C16  C17   120.14  3.000
 4ID  H16   C16  C15   119.44  3.000
 4ID  C17   C16  C15   120.42  3.000
 4ID  C19   C17  C18   120.36  3.000
 4ID  C19   C17  C16   118.37  3.000
 4ID  C18   C17  C16   121.27  3.000
 4ID  H18B  C18  H18A  108.33  3.000
 4ID  H18B  C18  H18   107.52  3.000
 4ID  H18A  C18  H18   107.21  3.000
 4ID  H18B  C18  C17   111.64  3.000
 4ID  H18A  C18  C17   111.43  3.000
 4ID  H18   C18  C17   110.51  3.000
 4ID  H19   C19  C20   118.15  3.000
 4ID  H19   C19  C17   118.84  3.000
 4ID  C20   C19  C17   123.01  3.000
 4ID  C21   C20  C19   118.73  3.000
 4ID  C21   C20  C14   124.47  3.000
 4ID  C19   C20  C14   116.79  3.000
 4ID  H21B  C21  H21A  107.92  3.000
 4ID  H21B  C21  H21   107.44  3.000
 4ID  H21A  C21  H21   107.15  3.000
 4ID  H21B  C21  C20   112.23  3.000
 4ID  H21A  C21  C20   110.02  3.000
 4ID  H21   C21  C20   111.85  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
 4ID  CONST_01  C9   C8   C6   C5      0.00   0.0  0
 4ID  CONST_02  C9   C10  C11  C5      0.00   0.0  0
 4ID  CONST_03  C10  C11  C5   C6      0.00   0.0  0
 4ID  CONST_04  C10  C9   C8   C6      0.00   0.0  0
 4ID  CONST_05  C11  C5   C6   C8      0.00   0.0  0
 4ID  CONST_06  C11  C10  C9   C8      0.00   0.0  0
 4ID  CONST_07  C17  C16  C15  C14     0.00   0.0  0
 4ID  CONST_08  C17  C19  C20  C14     0.00   0.0  0
 4ID  CONST_09  C19  C20  C14  C15     0.00   0.0  0
 4ID  CONST_10  C19  C17  C16  C15     0.00   0.0  0
 4ID  CONST_11  C20  C14  C15  C16     0.00   0.0  0
 4ID  CONST_12  C20  C19  C17  C16     0.00   0.0  0
 4ID  CONST_13  N3   C2   N1   C1      0.00   0.0  0
 4ID  CONST_14  C12  N3   C2   N1      0.00   0.0  0
 4ID  CONST_15  C13  C1   N1   C2      0.00   0.0  0
 4ID  CONST_16  C8   C6   C5   N2    180.00   0.0  0
 4ID  CONST_17  C10  C11  C5   N2    180.00   0.0  0
 4ID  CONST_18  C16  C15  C14  S2    180.00   0.0  0
 4ID  CONST_19  C19  C20  C14  S2    180.00   0.0  0
 4ID  CONST_20  C11  C5   C6   C7    180.00   0.0  0
 4ID  CONST_21  C9   C8   C6   C7    180.00   0.0  0
 4ID  CONST_22  C21  C20  C14  C15   180.00   0.0  0
 4ID  CONST_23  C18  C17  C16  C15   180.00   0.0  0
 4ID  CONST_24  C21  C20  C19  C17   180.00   0.0  0
 4ID  CONST_25  C20  C19  C17  C18   180.00   0.0  0
 4ID  CONST_26  S1   C2   N1   C1    180.00   0.0  0
 4ID  CONST_27  C2   N1   C1   O1    180.00   0.0  0
 4ID  CONST_28  C12  N3   C2   S1    180.00   0.0  0
 4ID  CONST_29  H8   C8   C6   C5    180.00   0.0  0
 4ID  CONST_30  H10  C10  C11  C5    180.00   0.0  0
 4ID  CONST_31  H11  C11  C5   C6    180.00   0.0  0
 4ID  CONST_32  H9   C9   C8   C6    180.00   0.0  0
 4ID  CONST_33  H16  C16  C15  C14   180.00   0.0  0
 4ID  CONST_34  H19  C19  C20  C14   180.00   0.0  0
 4ID  CONST_35  H15  C15  C16  C17   180.00   0.0  0
 4ID  CONST_36  HN1  N1   C2   N3    180.00   0.0  0
 4ID  CONST_40  C5   N2   C4   O2      0.00   0.0  0
 4ID  CONST_41  C5   N2   C4   C3    180.00   0.0  0
 4ID  Var_01    C14  S2   C13  C1    -62.72  30.0  3
 4ID  Var_02    C15  C14  S2   C13   112.32  30.0  2
 4ID  Var_03    C5   C6   C7   F1    179.68  30.0  3
 4ID  Var_04    N3   C2   S1   C3     -0.87  30.0  3
 4ID  Var_05    H21  C21  C20  C14    61.63  30.0  2
 4ID  Var_06    H18  C18  C17  C16   100.72  30.0  2
 4ID  Var_07    C4   C3   S1   C2    177.35  30.0  3
 4ID  Var_08    N2   C4   C3   S1   -179.13  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
 4ID  plan-1  C1   0.020
 4ID  plan-1  N1   0.020
 4ID  plan-1  O1   0.020
 4ID  plan-1  S1   0.020
 4ID  plan-1  C2   0.020
 4ID  plan-1  S2   0.020
 4ID  plan-1  N3   0.020
 4ID  plan-1  C12  0.020
 4ID  plan-1  C13  0.020
 4ID  plan-1  HN1  0.020
 4ID  plan-1  H12  0.020
 4ID  plan-2  N2   0.020
 4ID  plan-2  C5   0.020
 4ID  plan-2  C6   0.020
 4ID  plan-2  C7   0.020
 4ID  plan-2  C8   0.020
 4ID  plan-2  C9   0.020
 4ID  plan-2  C10  0.020
 4ID  plan-2  C11  0.020
 4ID  plan-2  H8   0.020
 4ID  plan-2  H9   0.020
 4ID  plan-2  H10  0.020
 4ID  plan-2  H11  0.020
 4ID  plan-3  S2   0.020
 4ID  plan-3  C14  0.020
 4ID  plan-3  C15  0.020
 4ID  plan-3  C16  0.020
 4ID  plan-3  C17  0.020
 4ID  plan-3  C18  0.020
 4ID  plan-3  C19  0.020
 4ID  plan-3  C20  0.020
 4ID  plan-3  C21  0.020
 4ID  plan-3  H15  0.020
 4ID  plan-3  H16  0.020
 4ID  plan-3  H19  0.020
 4ID  plan-4  N2   0.020
 4ID  plan-4  O2   0.020
 4ID  plan-4  C3   0.020
 4ID  plan-4  C4   0.020
 4ID  plan-4  C5   0.020
 4ID  plan-4  HN2  0.020

