# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 19:21:43 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 2-(4,6-dimethylpyrimidin-2-yl)sulfanyl-~{N}-(4-phenylsulfanylphenyl)ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(C)nc(SCC(=O)Nc2ccc(Sc3ccccc3)cc2)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
 A2X  A2X  2-(4,6-dimethylpyrimidin-2-yl)sulfanyl-~{N}-(4-phenylsulfanylphenyl)ethanamide  ligand  45  26  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A2X
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
 A2X  C01   C  CR16  0  -0.243   8.1860   0.9021  -1.2873
 A2X  C02   C  CR16  0  -0.267   7.4614   1.9247  -1.8860
 A2X  C03   C  CR16  0  -0.242   6.1225   2.0929  -1.5591
 A2X  C04   C  CR16  0  -0.235   5.5079   1.2542  -0.6393
 A2X  C05   C  CR6   0  -0.116   6.2348   0.2249  -0.0491
 A2X  C06   C  CR16  0  -0.266   7.5779   0.0496  -0.3777
 A2X  S07   S  S2    0   0.073   5.5564  -0.8746   1.1635
 A2X  C08   C  CR6   0  -0.192   3.8152  -0.7586   0.8857
 A2X  C09   C  CR16  0  -0.199   3.2310  -1.3369  -0.2389
 A2X  C10   C  CR16  0  -0.340   1.8652  -1.2702  -0.4224
 A2X  C11   C  CR6   0   0.382   1.0436  -0.6443   0.5218
 A2X  C12   C  CR16  0  -0.306   1.6257  -0.0755   1.6544
 A2X  C13   C  CR16  0  -0.217   3.0028  -0.1331   1.8208
 A2X  N14   N  NH1   0  -0.744  -0.3254  -0.6448   0.2525
 A2X  C15   C  C     0   0.569  -1.3376  -0.0769   0.9522
 A2X  O16   O  O     0  -0.451  -1.2021   0.5717   1.9709
 A2X  C17   C  CH2   0  -0.700  -2.6969  -0.3388   0.3392
 A2X  S18   S  S2    0   0.072  -3.9062   0.6631   1.2305
 A2X  C19   C  CR6   0   0.219  -5.3780   0.2702   0.3549
 A2X  N20   N  N     0  -0.440  -6.4402   0.9098   0.8227
 A2X  C21   C  CR6   0   0.285  -7.5982   0.6657   0.2161
 A2X  C22   C  CR16  0  -0.400  -7.6680  -0.2217  -0.8531
 A2X  C23   C  CR6   0   0.300  -6.4967  -0.8385  -1.2638
 A2X  N24   N  N     0  -0.429  -5.3393  -0.5852  -0.6475
 A2X  C25   C  CH3   0  -0.718  -6.4628  -1.8058  -2.4004
 A2X  C26   C  CH3   0  -0.721  -8.8024   1.3878   0.7233
 A2X  H011  H  HCR6  0   0.262   9.2292   0.7564  -1.5360
 A2X  H021  H  HCR6  0   0.258   7.9362   2.5825  -2.6019
 A2X  H031  H  HCR6  0   0.261   5.5468   2.8870  -2.0167
 A2X  H041  H  HCR6  0   0.265   4.4664   1.4064  -0.3886
 A2X  H061  H  HCR6  0   0.265   8.1490  -0.7547   0.0701
 A2X  H091  H  HCR6  0   0.277   3.8440  -1.8365  -0.9777
 A2X  H101  H  HCR6  0   0.280   1.4262  -1.7169  -1.3065
 A2X  H121  H  HCR6  0   0.288   1.0298   0.4155   2.4053
 A2X  H131  H  HCR6  0   0.275   3.4427   0.3214   2.6987
 A2X  H141  H  HNH1  0   0.427  -0.5904  -1.1356  -0.5892
 A2X  H171  H  HCH2  0   0.317  -2.7016  -0.0902  -0.7228
 A2X  H172  H  HCH2  0   0.325  -2.9415  -1.3994   0.4262
 A2X  H221  H  HCR6  0   0.272  -8.6082  -0.4235  -1.3470
 A2X  H252  H  HCH3  0   0.263  -5.8128  -1.4347  -3.1940
 A2X  H253  H  HCH3  0   0.262  -6.0565  -2.7631  -2.0726
 A2X  H251  H  HCH3  0   0.251  -7.4536  -1.9719  -2.8176
 A2X  H262  H  HCH3  0   0.265  -8.7180   2.4544   0.5091
 A2X  H263  H  HCH3  0   0.252  -9.7164   1.0200   0.2625
 A2X  H261  H  HCH3  0   0.261  -8.8855   1.2812   1.8046

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
 A2X  C04  C03   aromatic  1.388  0.020  1.388
 A2X  C04  C05   aromatic  1.392  0.020  1.392
 A2X  C03  C02   aromatic  1.388  0.020  1.388
 A2X  S07  C05   single    1.772  0.020  1.772
 A2X  S07  C08   single    1.767  0.020  1.767
 A2X  C05  C06   aromatic  1.394  0.020  1.394
 A2X  C02  C01   aromatic  1.389  0.020  1.389
 A2X  C09  C08   aromatic  1.393  0.020  1.393
 A2X  C09  C10   aromatic  1.380  0.020  1.380
 A2X  C06  C01   aromatic  1.387  0.020  1.387
 A2X  C08  C13   aromatic  1.388  0.020  1.388
 A2X  C10  C11   aromatic  1.399  0.020  1.399
 A2X  C25  C23   single    1.493  0.020  1.493
 A2X  C13  C12   aromatic  1.388  0.020  1.388
 A2X  C11  C12   aromatic  1.395  0.020  1.395
 A2X  C11  N14   single    1.395  0.020  1.395
 A2X  C23  C22   aromatic  1.386  0.020  1.386
 A2X  C23  N24   aromatic  1.335  0.020  1.335
 A2X  C22  C21   aromatic  1.391  0.020  1.391
 A2X  N14  C15   single    1.355  0.020  1.355
 A2X  N24  C19   aromatic  1.318  0.020  1.318
 A2X  C21  C26   single    1.493  0.020  1.493
 A2X  C21  N20   aromatic  1.330  0.020  1.330
 A2X  C15  O16   double    1.215  0.020  1.215
 A2X  C15  C17   single    1.514  0.020  1.514
 A2X  C19  N20   aromatic  1.325  0.020  1.325
 A2X  C19  S18   single    1.757  0.020  1.757
 A2X  C17  S18   single    1.806  0.020  1.806
 A2X  C01  H011  single    0.930  0.020  1.080
 A2X  C02  H021  single    0.930  0.020  1.080
 A2X  C03  H031  single    0.930  0.020  1.080
 A2X  C04  H041  single    0.930  0.020  1.080
 A2X  C06  H061  single    0.930  0.020  1.080
 A2X  C09  H091  single    0.930  0.020  1.080
 A2X  C10  H101  single    0.930  0.020  1.080
 A2X  C12  H121  single    0.930  0.020  1.080
 A2X  C13  H131  single    0.930  0.020  1.080
 A2X  N14  H141  single    0.860  0.020  1.020
 A2X  C17  H171  single    0.970  0.020  1.090
 A2X  C17  H172  single    0.970  0.020  1.090
 A2X  C22  H221  single    0.930  0.020  1.080
 A2X  C25  H252  single    0.970  0.020  1.090
 A2X  C25  H253  single    0.970  0.020  1.090
 A2X  C25  H251  single    0.970  0.020  1.090
 A2X  C26  H262  single    0.970  0.020  1.090
 A2X  C26  H263  single    0.970  0.020  1.090
 A2X  C26  H261  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
 A2X  H011  C01  C06   119.37  3.000
 A2X  H011  C01  C02   120.20  3.000
 A2X  C06   C01  C02   120.43  3.000
 A2X  H021  C02  C03   120.36  3.000
 A2X  H021  C02  C01   120.25  3.000
 A2X  C03   C02  C01   119.39  3.000
 A2X  H031  C03  C04   119.20  3.000
 A2X  H031  C03  C02   120.14  3.000
 A2X  C04   C03  C02   120.65  3.000
 A2X  H041  C04  C05   120.57  3.000
 A2X  H041  C04  C03   119.65  3.000
 A2X  C05   C04  C03   119.78  3.000
 A2X  S07   C05  C06   116.89  3.000
 A2X  C06   C05  C04   119.76  3.000
 A2X  S07   C05  C04   123.32  3.000
 A2X  H061  C06  C05   120.26  3.000
 A2X  H061  C06  C01   119.75  3.000
 A2X  C05   C06  C01   119.99  3.000
 A2X  C08   S07  C05   103.24  3.000
 A2X  C13   C08  C09   119.05  3.000
 A2X  C13   C08  S07   120.04  3.000
 A2X  C09   C08  S07   120.85  3.000
 A2X  H091  C09  C10   119.48  3.000
 A2X  H091  C09  C08   120.35  3.000
 A2X  C10   C09  C08   120.16  3.000
 A2X  H101  C10  C11   119.81  3.000
 A2X  H101  C10  C09   119.33  3.000
 A2X  C11   C10  C09   120.87  3.000
 A2X  N14   C11  C12   124.50  3.000
 A2X  N14   C11  C10   116.47  3.000
 A2X  C12   C11  C10   119.03  3.000
 A2X  H121  C12  C13   118.96  3.000
 A2X  H121  C12  C11   121.41  3.000
 A2X  C13   C12  C11   119.63  3.000
 A2X  H131  C13  C12   118.88  3.000
 A2X  H131  C13  C08   119.87  3.000
 A2X  C12   C13  C08   121.24  3.000
 A2X  H141  N14  C15   115.98  3.000
 A2X  H141  N14  C11   114.74  3.000
 A2X  C15   N14  C11   129.28  3.000
 A2X  C17   C15  O16   122.13  3.000
 A2X  C17   C15  N14   112.90  3.000
 A2X  O16   C15  N14   124.97  3.000
 A2X  H172  C17  H171  107.33  3.000
 A2X  H172  C17  S18   110.46  3.000
 A2X  H171  C17  S18   110.56  3.000
 A2X  H172  C17  C15   109.69  3.000
 A2X  H171  C17  C15   111.02  3.000
 A2X  S18   C17  C15   107.79  3.000
 A2X  C19   S18  C17   101.01  3.000
 A2X  N24   C19  N20   127.24  3.000
 A2X  N20   C19  S18   112.80  3.000
 A2X  N24   C19  S18   119.96  3.000
 A2X  C21   N20  C19   116.63  3.000
 A2X  C26   C21  C22   121.95  3.000
 A2X  C26   C21  N20   117.29  3.000
 A2X  C22   C21  N20   120.76  3.000
 A2X  H221  C22  C23   121.10  3.000
 A2X  H221  C22  C21   120.92  3.000
 A2X  C23   C22  C21   117.98  3.000
 A2X  C25   C23  N24   117.04  3.000
 A2X  N24   C23  C22   120.74  3.000
 A2X  C25   C23  C22   122.22  3.000
 A2X  C23   N24  C19   116.65  3.000
 A2X  H251  C25  H253  108.70  3.000
 A2X  H251  C25  H252  108.40  3.000
 A2X  H253  C25  H252  107.18  3.000
 A2X  H251  C25  C23   111.73  3.000
 A2X  H253  C25  C23   110.39  3.000
 A2X  H252  C25  C23   110.30  3.000
 A2X  H261  C26  H263  108.86  3.000
 A2X  H261  C26  H262  107.23  3.000
 A2X  H263  C26  H262  108.21  3.000
 A2X  H261  C26  C21   110.57  3.000
 A2X  H263  C26  C21   111.73  3.000
 A2X  H262  C26  C21   110.10  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
 A2X  CONST_01  C04   C03  C02  C01     0.00   0.0  0
 A2X  CONST_02  C04   C05  C06  C01     0.00   0.0  0
 A2X  CONST_03  C05   C04  C03  C02     0.00   0.0  0
 A2X  CONST_04  C05   C06  C01  C02     0.00   0.0  0
 A2X  CONST_05  C06   C05  C04  C03     0.00   0.0  0
 A2X  CONST_06  C06   C01  C02  C03     0.00   0.0  0
 A2X  CONST_07  C11   C10  C09  C08     0.00   0.0  0
 A2X  CONST_08  C11   C12  C13  C08     0.00   0.0  0
 A2X  CONST_09  C12   C13  C08  C09     0.00   0.0  0
 A2X  CONST_10  C12   C11  C10  C09     0.00   0.0  0
 A2X  CONST_11  C13   C08  C09  C10     0.00   0.0  0
 A2X  CONST_12  C13   C12  C11  C10     0.00   0.0  0
 A2X  CONST_13  C22   C23  N24  C19     0.00   0.0  0
 A2X  CONST_14  C22   C21  N20  C19     0.00   0.0  0
 A2X  CONST_15  C23   C22  C21  N20     0.00   0.0  0
 A2X  CONST_16  C23   N24  C19  N20     0.00   0.0  0
 A2X  CONST_17  N24   C23  C22  C21     0.00   0.0  0
 A2X  CONST_18  N24   C19  N20  C21     0.00   0.0  0
 A2X  CONST_19  S07   C05  C06  C01   180.00   0.0  0
 A2X  CONST_20  S07   C05  C04  C03   180.00   0.0  0
 A2X  CONST_21  C10   C09  C08  S07   180.00   0.0  0
 A2X  CONST_22  C12   C13  C08  S07   180.00   0.0  0
 A2X  CONST_23  N14   C11  C10  C09   180.00   0.0  0
 A2X  CONST_24  N14   C11  C12  C13   180.00   0.0  0
 A2X  CONST_25  C23   N24  C19  S18   180.00   0.0  0
 A2X  CONST_26  C21   N20  C19  S18   180.00   0.0  0
 A2X  CONST_27  C25   C23  N24  C19   180.00   0.0  0
 A2X  CONST_28  C26   C21  N20  C19   180.00   0.0  0
 A2X  CONST_29  C25   C23  C22  C21   180.00   0.0  0
 A2X  CONST_30  C26   C21  C22  C23   180.00   0.0  0
 A2X  CONST_31  H031  C03  C02  C01   180.00   0.0  0
 A2X  CONST_32  H041  C04  C03  C02   180.00   0.0  0
 A2X  CONST_33  H061  C06  C01  C02   180.00   0.0  0
 A2X  CONST_34  H011  C01  C02  C03   180.00   0.0  0
 A2X  CONST_35  H021  C02  C03  C04   180.00   0.0  0
 A2X  CONST_36  H101  C10  C09  C08   180.00   0.0  0
 A2X  CONST_37  H121  C12  C13  C08   180.00   0.0  0
 A2X  CONST_38  H131  C13  C08  C09   180.00   0.0  0
 A2X  CONST_39  H091  C09  C10  C11   180.00   0.0  0
 A2X  CONST_40  H221  C22  C21  N20   180.00   0.0  0
 A2X  CONST_41  C15   N14  C11  C10   180.00   0.0  0
 A2X  CONST_42  C15   N14  C11  C12     0.00   0.0  0
 A2X  CONST_43  H141  N14  C11  C10     0.00   0.0  0
 A2X  CONST_44  O16   C15  N14  C11     0.00   0.0  0
 A2X  CONST_45  C17   C15  N14  C11   180.00   0.0  0
 A2X  Var_01    C09   C08  S07  C05    72.47  30.0  2
 A2X  Var_02    N24   C19  S18  C17     0.86  30.0  3
 A2X  Var_03    H262  C26  C21  N20    67.83  30.0  2
 A2X  Var_04    H252  C25  C23  C22   118.84  30.0  2
 A2X  Var_05    H171  C17  S18  C19    56.67  30.0  1
 A2X  Var_06    S18   C17  C15  N14  -172.03  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
 A2X  plan-1  C01   0.020
 A2X  plan-1  C02   0.020
 A2X  plan-1  C03   0.020
 A2X  plan-1  C04   0.020
 A2X  plan-1  C05   0.020
 A2X  plan-1  C06   0.020
 A2X  plan-1  S07   0.020
 A2X  plan-1  H011  0.020
 A2X  plan-1  H021  0.020
 A2X  plan-1  H031  0.020
 A2X  plan-1  H041  0.020
 A2X  plan-1  H061  0.020
 A2X  plan-2  S07   0.020
 A2X  plan-2  C08   0.020
 A2X  plan-2  C09   0.020
 A2X  plan-2  C10   0.020
 A2X  plan-2  C11   0.020
 A2X  plan-2  C12   0.020
 A2X  plan-2  C13   0.020
 A2X  plan-2  N14   0.020
 A2X  plan-2  H091  0.020
 A2X  plan-2  H101  0.020
 A2X  plan-2  H121  0.020
 A2X  plan-2  H131  0.020
 A2X  plan-3  S18   0.020
 A2X  plan-3  C19   0.020
 A2X  plan-3  N20   0.020
 A2X  plan-3  C21   0.020
 A2X  plan-3  C22   0.020
 A2X  plan-3  C23   0.020
 A2X  plan-3  N24   0.020
 A2X  plan-3  C25   0.020
 A2X  plan-3  C26   0.020
 A2X  plan-3  H221  0.020
 A2X  plan-4  C11   0.020
 A2X  plan-4  N14   0.020
 A2X  plan-4  C15   0.020
 A2X  plan-4  O16   0.020
 A2X  plan-4  C17   0.020
 A2X  plan-4  H141  0.020

