# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 03:05:34 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: 4-{[(4,6-dimethylpyrimidin-2-yl)sulfanyl]acetyl}benzenesulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(C)nc(SCC(=O)c2ccc(cc2)[S](N)(=O)=O)n1
#
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
 E65  E65  4-{[(4,6-dimethylpyrimidin-2-yl)sulfanyl]acetyl}benzenesulfonamide  ligand  37  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_E65
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
 E65  N1    N  N     0  -0.441   5.2114  -0.6621   0.0434
 E65  C2    C  CR6   0   0.221   3.9634  -0.2176   0.0206
 E65  N3    N  N     0  -0.428   3.5640   1.0376  -0.0248
 E65  C4    C  CR6   0   0.302   4.5200   1.9694  -0.0531
 E65  C5    C  CR16  0  -0.402   5.8590   1.6116  -0.0343
 E65  C6    C  CR6   0   0.286   6.1723   0.2571   0.0151
 E65  S7    S  S2    0   0.079   2.7780  -1.5151   0.0538
 E65  C8    C  CH2   0  -0.709   1.2373  -0.5729   0.0179
 E65  C9    C  C     0   0.398   0.0851  -1.5424   0.0024
 E65  O10   O  O     0  -0.370   0.2750  -2.7370   0.0012
 E65  C11   C  CH3   0  -0.718   4.0776   3.3944  -0.0952
 E65  C12   C  CH3   0  -0.720   7.5847  -0.2269   0.0216
 E65  C13   C  CR6   0   0.011  -1.2960  -0.9813  -0.0149
 E65  C14   C  CR16  0  -0.244  -2.3740  -1.8628  -0.0710
 E65  C15   C  CR16  0  -0.221  -3.6727  -1.3844  -0.0930
 E65  C16   C  CR6   0  -0.201  -3.8857  -0.0144  -0.0477
 E65  C17   C  CR16  0  -0.201  -2.8286   0.8814   0.0077
 E65  C18   C  CR16  0  -0.279  -1.5344   0.3919   0.0207
 E65  S19   S  S     0   1.367  -5.5438   0.6220  -0.0591
 E65  O20   O  OS    0  -0.659  -5.5448   1.9329  -0.6890
 E65  O21   O  OS    0  -0.644  -6.4104  -0.4166  -0.5948
 E65  N22   N  NC2   0  -0.888  -5.7859   0.8888   1.5496
 E65  H5    H  HCR6  0   0.274   6.6363   2.3622  -0.0558
 E65  H8    H  HCH2  0   0.320   1.1716   0.0833   0.8879
 E65  H8A   H  HCH2  0   0.322   1.2032   0.0659  -0.8670
 E65  H11   H  HCH3  0   0.263   3.5596   3.6540   0.8293
 E65  H11A  H  HCH3  0   0.251   4.9180   4.0738  -0.2187
 E65  H11B  H  HCH3  0   0.261   3.3748   3.5525  -0.9134
 E65  H12   H  HCH3  0   0.265   7.8208  -0.7014  -0.9325
 E65  H12A  H  HCH3  0   0.252   8.2889   0.5873   0.1780
 E65  H12B  H  HCH3  0   0.260   7.7318  -0.9758   0.7993
 E65  H14   H  HCR6  0   0.281  -2.2042  -2.9301  -0.1026
 E65  H15   H  HCR6  0   0.292  -4.4998  -2.0784  -0.1446
 E65  H17   H  HCR6  0   0.295  -2.9980   1.9489   0.0368
 E65  H18   H  HCR6  0   0.283  -0.7211   1.1030   0.0596
 E65  HN22  H  HNC2  0   0.423  -6.4889   1.6035   1.7117
 E65  HN2A  H  HNC2  0   0.420  -6.0109   0.0433   2.0636

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
 E65  N1   C2    aromatic  1.325  0.020  1.325
 E65  N1   C6    aromatic  1.330  0.020  1.330
 E65  S7   C2    single    1.758  0.020  1.758
 E65  C2   N3    aromatic  1.318  0.020  1.318
 E65  N3   C4    aromatic  1.335  0.020  1.335
 E65  C5   C4    aromatic  1.386  0.020  1.386
 E65  C4   C11   single    1.493  0.020  1.493
 E65  C6   C5    aromatic  1.391  0.020  1.391
 E65  C5   H5    single    0.930  0.020  1.080
 E65  C12  C6    single    1.493  0.020  1.493
 E65  S7   C8    single    1.806  0.020  1.806
 E65  C8   C9    single    1.506  0.020  1.506
 E65  C8   H8    single    0.970  0.020  1.090
 E65  C8   H8A   single    0.970  0.020  1.090
 E65  O10  C9    double    1.210  0.020  1.210
 E65  C9   C13   single    1.491  0.020  1.491
 E65  C11  H11   single    0.970  0.020  1.090
 E65  C11  H11A  single    0.970  0.020  1.090
 E65  C11  H11B  single    0.970  0.020  1.090
 E65  C12  H12   single    0.970  0.020  1.090
 E65  C12  H12A  single    0.970  0.020  1.090
 E65  C12  H12B  single    0.970  0.020  1.090
 E65  C13  C14   aromatic  1.394  0.020  1.394
 E65  C13  C18   aromatic  1.394  0.020  1.394
 E65  C14  C15   aromatic  1.384  0.020  1.384
 E65  C14  H14   single    0.930  0.020  1.080
 E65  C15  C16   aromatic  1.387  0.020  1.387
 E65  C15  H15   single    0.930  0.020  1.080
 E65  C17  C16   aromatic  1.387  0.020  1.387
 E65  C16  S19   single    1.776  0.020  1.776
 E65  C18  C17   aromatic  1.384  0.020  1.384
 E65  C17  H17   single    0.930  0.020  1.080
 E65  C18  H18   single    0.930  0.020  1.080
 E65  N22  S19   single    1.649  0.020  1.649
 E65  O20  S19   double    1.454  0.020  1.454
 E65  S19  O21   double    1.455  0.020  1.455
 E65  N22  HN22  single    0.890  0.020  1.040
 E65  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
 E65  C6    N1   C2    116.64  3.000
 E65  S7    C2   N3    119.95  3.000
 E65  N3    C2   N1    127.26  3.000
 E65  S7    C2   N1    112.79  3.000
 E65  C4    N3   C2    116.64  3.000
 E65  C11   C4   C5    122.22  3.000
 E65  C11   C4   N3    117.04  3.000
 E65  C5    C4   N3    120.74  3.000
 E65  H5    C5   C6    120.99  3.000
 E65  H5    C5   C4    121.02  3.000
 E65  C6    C5   C4    117.99  3.000
 E65  C12   C6   C5    121.93  3.000
 E65  C12   C6   N1    117.34  3.000
 E65  C5    C6   N1    120.73  3.000
 E65  C8    S7   C2    100.94  3.000
 E65  H8A   C8   H8    106.99  3.000
 E65  H8A   C8   C9    110.15  3.000
 E65  H8    C8   C9    110.43  3.000
 E65  H8A   C8   S7    110.36  3.000
 E65  H8    C8   S7    110.43  3.000
 E65  C9    C8   S7    108.48  3.000
 E65  C13   C9   O10   121.14  3.000
 E65  C13   C9   C8    117.81  3.000
 E65  O10   C9   C8    121.05  3.000
 E65  H11B  C11  H11A  108.80  3.000
 E65  H11B  C11  H11   107.18  3.000
 E65  H11A  C11  H11   108.32  3.000
 E65  H11B  C11  C4    110.53  3.000
 E65  H11A  C11  C4    111.75  3.000
 E65  H11   C11  C4    110.12  3.000
 E65  H12B  C12  H12A  108.94  3.000
 E65  H12B  C12  H12   107.21  3.000
 E65  H12A  C12  H12   108.12  3.000
 E65  H12B  C12  C6    110.71  3.000
 E65  H12A  C12  C6    111.74  3.000
 E65  H12   C12  C6    109.99  3.000
 E65  C18   C13  C14   119.45  3.000
 E65  C18   C13  C9    121.93  3.000
 E65  C14   C13  C9    118.62  3.000
 E65  H14   C14  C15   119.22  3.000
 E65  H14   C14  C13   120.26  3.000
 E65  C15   C14  C13   120.52  3.000
 E65  H15   C15  C16   121.21  3.000
 E65  H15   C15  C14   119.78  3.000
 E65  C16   C15  C14   119.01  3.000
 E65  S19   C16  C17   118.71  3.000
 E65  S19   C16  C15   119.80  3.000
 E65  C17   C16  C15   121.48  3.000
 E65  H17   C17  C18   119.70  3.000
 E65  H17   C17  C16   121.30  3.000
 E65  C18   C17  C16   119.00  3.000
 E65  H18   C18  C17   118.12  3.000
 E65  H18   C18  C13   121.34  3.000
 E65  C17   C18  C13   120.54  3.000
 E65  N22   S19  O21   112.79  3.000
 E65  O21   S19  O20   118.92  3.000
 E65  N22   S19  O20   106.06  3.000
 E65  O21   S19  C16   107.61  3.000
 E65  O20   S19  C16   109.05  3.000
 E65  N22   S19  C16   100.88  3.000
 E65  HN2A  N22  HN22  110.61  3.000
 E65  HN2A  N22  S19   113.08  3.000
 E65  HN22  N22  S19   111.79  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
 E65  CONST_01  C4    N3   C2   N1     0.00   0.0  0
 E65  CONST_02  C4    C5   C6   N1     0.00   0.0  0
 E65  CONST_03  C5    C6   N1   C2     0.00   0.0  0
 E65  CONST_04  C5    C4   N3   C2     0.00   0.0  0
 E65  CONST_05  C6    N1   C2   N3     0.00   0.0  0
 E65  CONST_06  C6    C5   C4   N3     0.00   0.0  0
 E65  CONST_07  C16   C15  C14  C13    0.00   0.0  0
 E65  CONST_08  C16   C17  C18  C13    0.00   0.0  0
 E65  CONST_09  C17   C18  C13  C14    0.00   0.0  0
 E65  CONST_10  C17   C16  C15  C14    0.00   0.0  0
 E65  CONST_11  C18   C13  C14  C15    0.00   0.0  0
 E65  CONST_12  C18   C17  C16  C15    0.00   0.0  0
 E65  CONST_13  C12   C6   N1   C2   180.00   0.0  0
 E65  CONST_14  C11   C4   N3   C2   180.00   0.0  0
 E65  CONST_15  S7    C2   N3   C4   180.00   0.0  0
 E65  CONST_16  C12   C6   C5   C4   180.00   0.0  0
 E65  CONST_17  S7    C2   N1   C6   180.00   0.0  0
 E65  CONST_18  C11   C4   C5   C6   180.00   0.0  0
 E65  CONST_19  C15   C14  C13  C9   180.00   0.0  0
 E65  CONST_20  C17   C18  C13  C9   180.00   0.0  0
 E65  CONST_21  S19   C16  C15  C14  180.00   0.0  0
 E65  CONST_22  S19   C16  C17  C18  180.00   0.0  0
 E65  CONST_23  H5    C5   C6   N1   180.00   0.0  0
 E65  CONST_24  H15   C15  C14  C13  180.00   0.0  0
 E65  CONST_25  H17   C17  C18  C13  180.00   0.0  0
 E65  CONST_26  H18   C18  C13  C14  180.00   0.0  0
 E65  CONST_27  H14   C14  C15  C16  180.00   0.0  0
 E65  Var_01    C14   C13  C9   C8   178.05  30.0  2
 E65  Var_02    N22   S19  C16  C15   98.12  30.0  2
 E65  Var_03    H12   C12  C6   N1    70.22  30.0  2
 E65  Var_04    H11   C11  C4   N3    65.40  30.0  2
 E65  Var_05    C9    C8   S7   C2   178.44  30.0  3
 E65  Var_06    C13   C9   C8   S7   179.44  30.0  3
 E65  Var_07    HN22  N22  S19  C16  155.15  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
 E65  plan-1  N1   0.020
 E65  plan-1  C2   0.020
 E65  plan-1  N3   0.020
 E65  plan-1  C4   0.020
 E65  plan-1  C5   0.020
 E65  plan-1  C6   0.020
 E65  plan-1  S7   0.020
 E65  plan-1  C11  0.020
 E65  plan-1  C12  0.020
 E65  plan-1  H5   0.020
 E65  plan-2  C9   0.020
 E65  plan-2  C13  0.020
 E65  plan-2  C14  0.020
 E65  plan-2  C15  0.020
 E65  plan-2  C16  0.020
 E65  plan-2  C17  0.020
 E65  plan-2  C18  0.020
 E65  plan-2  S19  0.020
 E65  plan-2  H14  0.020
 E65  plan-2  H15  0.020
 E65  plan-2  H17  0.020
 E65  plan-2  H18  0.020
 E65  plan-3  C8   0.020
 E65  plan-3  C9   0.020
 E65  plan-3  O10  0.020
 E65  plan-3  C13  0.020

