# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 15:04:00 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: 2-(4,6-dimethylpyrimidin-2-yl)sulfanyl-~{N}-[3-(phenoxymethyl)phenyl]ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(C)nc(SCC(=O)Nc2cccc(COc3ccccc3)c2)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
 A2I  A2I  2-(4,6-dimethylpyrimidin-2-yl)sulfanyl-~{N}-[3-(phenoxymethyl)phenyl]ethanamide  ligand  48  27  .  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_A2I
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
 A2I  C11   C  CR16  0  -0.234  -2.5187  -3.3160  -0.2903
 A2I  C14   C  CR16  0  -0.400  -2.0754  -0.7595   0.6369
 A2I  N15   N  NH1   0  -0.746   0.2774  -0.9541   0.3447
 A2I  C16   C  C     0   0.566   1.4649  -1.3914  -0.1345
 A2I  C22   C  CR6   0   0.300   5.8521   2.0954   0.7265
 A2I  C23   C  CR16  0  -0.400   7.1715   1.8596   0.3721
 A2I  C24   C  CR6   0   0.285   7.4726   0.6565  -0.2581
 A2I  C1    C  CR16  0  -0.282  -8.5521   2.4141  -0.1515
 A2I  C2    C  CR16  0  -0.241  -7.9350   2.0496  -1.3445
 A2I  C3    C  CR16  0  -0.344  -6.7828   1.2839  -1.3376
 A2I  C4    C  CR6   0   0.384  -6.2255   0.8666  -0.1265
 A2I  C5    C  CR16  0  -0.382  -6.8348   1.2307   1.0718
 A2I  C6    C  CR16  0  -0.240  -7.9941   2.0003   1.0470
 A2I  C8    C  CH2   0  -0.272  -4.5248  -0.3815   0.9791
 A2I  C9    C  CR6   0   0.119  -3.3698  -1.2491   0.5792
 A2I  C10   C  CR16  0  -0.304  -3.5934  -2.5398   0.1080
 A2I  C12   C  CR16  0  -0.319  -1.2170  -2.8337  -0.2318
 A2I  C13   C  CR6   0   0.397  -0.9886  -1.5406   0.2356
 A2I  O17   O  O     0  -0.456   1.6357  -2.4365  -0.7326
 A2I  C18   C  CH2   0  -0.700   2.6025  -0.4305   0.1428
 A2I  S19   S  S2    0   0.071   4.1133  -1.1601  -0.5242
 A2I  C20   C  CR6   0   0.219   5.2899   0.0846  -0.1341
 A2I  N21   N  N     0  -0.428   4.9034   1.1919   0.4682
 A2I  N25   N  N     0  -0.440   6.5193  -0.2351  -0.5122
 A2I  C27   C  CH3   0  -0.718   5.4211   3.3573   1.3976
 A2I  H111  H  HCR6  0   0.262  -2.6873  -4.3219  -0.6521
 A2I  H141  H  HCR6  0   0.271  -1.9027   0.2489   0.9987
 A2I  H151  H  HNH1  0   0.425   0.2890  -0.0546   0.8035
 A2I  H231  H  HCR6  0   0.272   7.9427   2.5883   0.5789
 A2I  H021  H  HCR6  0   0.257  -8.3567   2.3607  -2.2916
 A2I  H031  H  HCR6  0   0.261  -6.3047   1.0029  -2.2678
 A2I  H051  H  HCR6  0   0.281  -6.4278   0.9311   2.0279
 A2I  H061  H  HCR6  0   0.259  -8.4597   2.2721   1.9856
 A2I  H082  H  HCH2  0   0.244  -4.1890   0.4414   1.6186
 A2I  H081  H  HCH2  0   0.243  -5.2604  -0.9654   1.5419
 A2I  H101  H  HCR6  0   0.255  -4.6002  -2.9359   0.0594
 A2I  H121  H  HCR6  0   0.282  -0.4025  -3.4668  -0.5426
 A2I  H182  H  HCH2  0   0.320   2.4031   0.5347  -0.3259
 A2I  H181  H  HCH2  0   0.319   2.7029  -0.2568   1.2155
 A2I  H273  H  HCH3  0   0.263   4.7650   3.9276   0.7381
 A2I  H271  H  HCH3  0   0.261   4.8548   3.1342   2.3019
 A2I  H272  H  HCH3  0   0.251   6.2698   3.9845   1.6621
 A2I  C26   C  CH3   0  -0.721   8.8648   0.3031  -0.6661
 A2I  O7    O  O2    0  -0.469  -5.1043   0.1208  -0.2164
 A2I  H011  H  HCR6  0   0.253  -9.4538   3.0118  -0.1605
 A2I  H261  H  HCH3  0   0.264   9.2240  -0.5429  -0.0782
 A2I  H263  H  HCH3  0   0.261   8.8922   0.0030  -1.7134
 A2I  H262  H  HCH3  0   0.252   9.5514   1.1343  -0.5221

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
 A2I  C2   C3    aromatic  1.383  0.020  1.383
 A2I  C2   C1    aromatic  1.392  0.020  1.392
 A2I  C3   C4    aromatic  1.397  0.020  1.397
 A2I  C1   C6    aromatic  1.385  0.020  1.385
 A2I  C4   O7    single    1.350  0.020  1.350
 A2I  C4   C5    aromatic  1.393  0.020  1.393
 A2I  C11  C10   aromatic  1.384  0.020  1.384
 A2I  C11  C12   aromatic  1.389  0.020  1.389
 A2I  C10  C9    aromatic  1.392  0.020  1.392
 A2I  O7   C8    single    1.420  0.020  1.420
 A2I  C6   C5    aromatic  1.392  0.020  1.392
 A2I  C12  C13   aromatic  1.394  0.020  1.394
 A2I  C9   C8    single    1.499  0.020  1.499
 A2I  C9   C14   aromatic  1.385  0.020  1.385
 A2I  C27  C22   single    1.493  0.020  1.493
 A2I  C13  C14   aromatic  1.397  0.020  1.397
 A2I  C13  N15   single    1.400  0.020  1.400
 A2I  C22  C23   aromatic  1.386  0.020  1.386
 A2I  C22  N21   aromatic  1.335  0.020  1.335
 A2I  C23  C24   aromatic  1.391  0.020  1.391
 A2I  N15  C16   single    1.353  0.020  1.353
 A2I  N21  C20   aromatic  1.318  0.020  1.318
 A2I  C24  C26   single    1.493  0.020  1.493
 A2I  C24  N25   aromatic  1.330  0.020  1.330
 A2I  C16  O17   double    1.216  0.020  1.216
 A2I  C16  C18   single    1.515  0.020  1.515
 A2I  C20  N25   aromatic  1.325  0.020  1.325
 A2I  C20  S19   single    1.757  0.020  1.757
 A2I  C18  S19   single    1.805  0.020  1.805
 A2I  C11  H111  single    0.930  0.020  1.080
 A2I  C14  H141  single    0.930  0.020  1.080
 A2I  N15  H151  single    0.860  0.020  1.020
 A2I  C23  H231  single    0.930  0.020  1.080
 A2I  C1   H011  single    0.930  0.020  1.080
 A2I  C2   H021  single    0.930  0.020  1.080
 A2I  C3   H031  single    0.930  0.020  1.080
 A2I  C5   H051  single    0.930  0.020  1.080
 A2I  C6   H061  single    0.930  0.020  1.080
 A2I  C8   H082  single    0.970  0.020  1.090
 A2I  C8   H081  single    0.970  0.020  1.090
 A2I  C10  H101  single    0.930  0.020  1.080
 A2I  C12  H121  single    0.930  0.020  1.080
 A2I  C18  H182  single    0.970  0.020  1.090
 A2I  C18  H181  single    0.970  0.020  1.090
 A2I  C26  H261  single    0.970  0.020  1.090
 A2I  C26  H263  single    0.970  0.020  1.090
 A2I  C26  H262  single    0.970  0.020  1.090
 A2I  C27  H273  single    0.970  0.020  1.090
 A2I  C27  H271  single    0.970  0.020  1.090
 A2I  C27  H272  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
 A2I  H111  C11  C12   118.86  3.000
 A2I  H111  C11  C10   119.76  3.000
 A2I  C12   C11  C10   121.37  3.000
 A2I  H141  C14  C13   119.44  3.000
 A2I  H141  C14  C9    119.41  3.000
 A2I  C13   C14  C9    121.15  3.000
 A2I  H151  N15  C13   114.78  3.000
 A2I  H151  N15  C16   116.02  3.000
 A2I  C13   N15  C16   129.11  3.000
 A2I  C18   C16  O17   121.99  3.000
 A2I  C18   C16  N15   112.91  3.000
 A2I  O17   C16  N15   125.10  3.000
 A2I  C27   C22  N21   116.98  3.000
 A2I  N21   C22  C23   120.78  3.000
 A2I  C27   C22  C23   122.24  3.000
 A2I  H231  C23  C24   121.01  3.000
 A2I  H231  C23  C22   121.03  3.000
 A2I  C24   C23  C22   117.96  3.000
 A2I  C26   C24  N25   117.23  3.000
 A2I  N25   C24  C23   120.75  3.000
 A2I  C26   C24  C23   122.02  3.000
 A2I  H011  C1   C6    120.53  3.000
 A2I  H011  C1   C2    120.47  3.000
 A2I  C6    C1   C2    118.99  3.000
 A2I  H021  C2   C3    119.20  3.000
 A2I  H021  C2   C1    120.14  3.000
 A2I  C3    C2   C1    120.66  3.000
 A2I  H031  C3   C4    119.41  3.000
 A2I  H031  C3   C2    120.46  3.000
 A2I  C4    C3   C2    120.13  3.000
 A2I  O7    C4   C5    124.42  3.000
 A2I  C5    C4   C3    119.55  3.000
 A2I  O7    C4   C3    116.03  3.000
 A2I  H051  C5   C6    118.85  3.000
 A2I  H051  C5   C4    121.57  3.000
 A2I  C6    C5   C4    119.58  3.000
 A2I  H061  C6   C5    118.80  3.000
 A2I  H061  C6   C1    120.12  3.000
 A2I  C5    C6   C1    121.08  3.000
 A2I  H081  C8   H082  107.85  3.000
 A2I  H081  C8   C9    110.25  3.000
 A2I  H082  C8   C9    110.77  3.000
 A2I  H081  C8   O7    110.31  3.000
 A2I  H082  C8   O7    110.55  3.000
 A2I  C9    C8   O7    107.13  3.000
 A2I  C10   C9   C8    120.21  3.000
 A2I  C8    C9   C14   120.29  3.000
 A2I  C10   C9   C14   119.47  3.000
 A2I  H101  C10  C9    120.24  3.000
 A2I  H101  C10  C11   120.25  3.000
 A2I  C9    C10  C11   119.51  3.000
 A2I  H121  C12  C13   121.20  3.000
 A2I  H121  C12  C11   119.48  3.000
 A2I  C13   C12  C11   119.32  3.000
 A2I  C12   C13  N15   124.27  3.000
 A2I  N15   C13  C14   116.55  3.000
 A2I  C12   C13  C14   119.18  3.000
 A2I  H181  C18  H182  107.35  3.000
 A2I  H181  C18  S19   110.51  3.000
 A2I  H182  C18  S19   110.59  3.000
 A2I  H181  C18  C16   110.49  3.000
 A2I  H182  C18  C16   110.20  3.000
 A2I  S19   C18  C16   107.72  3.000
 A2I  C20   S19  C18   101.08  3.000
 A2I  N25   C20  N21   127.22  3.000
 A2I  N25   C20  S19   112.77  3.000
 A2I  N21   C20  S19   120.01  3.000
 A2I  C20   N21  C22   116.64  3.000
 A2I  C20   N25  C24   116.66  3.000
 A2I  H272  C27  H271  108.76  3.000
 A2I  H272  C27  H273  108.34  3.000
 A2I  H271  C27  H273  107.22  3.000
 A2I  H272  C27  C22   111.80  3.000
 A2I  H271  C27  C22   110.48  3.000
 A2I  H273  C27  C22   110.11  3.000
 A2I  H262  C26  H263  108.77  3.000
 A2I  H262  C26  H261  108.27  3.000
 A2I  H263  C26  H261  107.22  3.000
 A2I  H262  C26  C24   111.81  3.000
 A2I  H263  C26  C24   110.56  3.000
 A2I  H261  C26  C24   110.07  3.000
 A2I  C8    O7   C4    118.58  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
 A2I  CONST_01  C14   C9   C10  C11    0.00   0.0  0
 A2I  CONST_02  C14   C13  C12  C11    0.00   0.0  0
 A2I  CONST_03  N25   C24  C23  C22    0.00   0.0  0
 A2I  CONST_04  N25   C20  N21  C22    0.00   0.0  0
 A2I  CONST_05  C20   N21  C22  C23    0.00   0.0  0
 A2I  CONST_06  C20   N25  C24  C23    0.00   0.0  0
 A2I  CONST_07  N21   C22  C23  C24    0.00   0.0  0
 A2I  CONST_08  N21   C20  N25  C24    0.00   0.0  0
 A2I  CONST_09  C4    C3   C2   C1     0.00   0.0  0
 A2I  CONST_10  C4    C5   C6   C1     0.00   0.0  0
 A2I  CONST_11  C5    C4   C3   C2     0.00   0.0  0
 A2I  CONST_12  C5    C6   C1   C2     0.00   0.0  0
 A2I  CONST_13  C6    C1   C2   C3     0.00   0.0  0
 A2I  CONST_14  C6    C5   C4   C3     0.00   0.0  0
 A2I  CONST_15  C12   C11  C10  C9     0.00   0.0  0
 A2I  CONST_16  C12   C13  C14  C9     0.00   0.0  0
 A2I  CONST_17  C13   C12  C11  C10    0.00   0.0  0
 A2I  CONST_18  C13   C14  C9   C10    0.00   0.0  0
 A2I  CONST_19  C8    C9   C10  C11  180.00   0.0  0
 A2I  CONST_20  N15   C13  C12  C11  180.00   0.0  0
 A2I  CONST_21  C9    C14  C13  N15  180.00   0.0  0
 A2I  CONST_22  C26   C24  C23  C22  180.00   0.0  0
 A2I  CONST_23  S19   C20  N21  C22  180.00   0.0  0
 A2I  CONST_24  C27   C22  C23  C24  180.00   0.0  0
 A2I  CONST_25  S19   C20  N25  C24  180.00   0.0  0
 A2I  CONST_26  O7    C4   C3   C2   180.00   0.0  0
 A2I  CONST_27  O7    C4   C5   C6   180.00   0.0  0
 A2I  CONST_28  C13   C14  C9   C8   180.00   0.0  0
 A2I  CONST_29  C27   C22  N21  C20  180.00   0.0  0
 A2I  CONST_30  C26   C24  N25  C20  180.00   0.0  0
 A2I  CONST_31  H101  C10  C9   C14  180.00   0.0  0
 A2I  CONST_32  H121  C12  C13  C14  180.00   0.0  0
 A2I  CONST_33  H031  C3   C2   C1   180.00   0.0  0
 A2I  CONST_34  H051  C5   C6   C1   180.00   0.0  0
 A2I  CONST_35  H061  C6   C1   C2   180.00   0.0  0
 A2I  CONST_36  H011  C1   C2   C3   180.00   0.0  0
 A2I  CONST_37  H021  C2   C3   C4   180.00   0.0  0
 A2I  CONST_38  H111  C11  C10  C9   180.00   0.0  0
 A2I  CONST_39  H141  C14  C9   C10  180.00   0.0  0
 A2I  CONST_40  H231  C23  C22  N21  180.00   0.0  0
 A2I  CONST_41  C16   N15  C13  C14  180.00   0.0  0
 A2I  CONST_42  C12   C13  N15  C16    0.00   0.0  0
 A2I  CONST_43  H151  N15  C13  C14    0.00   0.0  0
 A2I  CONST_44  O17   C16  N15  C13    0.00   0.0  0
 A2I  CONST_45  C18   C16  N15  C13  180.00   0.0  0
 A2I  Var_01    O7    C8   C9   C14   99.96  30.0  2
 A2I  Var_02    C9    C8   O7   C4   175.76  30.0  3
 A2I  Var_03    N21   C20  S19  C18   -1.33  30.0  3
 A2I  Var_04    H273  C27  C22  C23  114.02  30.0  2
 A2I  Var_05    H261  C26  C24  C23  113.36  30.0  2
 A2I  Var_06    H182  C18  S19  C20   58.75  30.0  1
 A2I  Var_07    S19   C18  C16  N15  178.98  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
 A2I  plan-1  C11   0.020
 A2I  plan-1  C14   0.020
 A2I  plan-1  N15   0.020
 A2I  plan-1  C8    0.020
 A2I  plan-1  C9    0.020
 A2I  plan-1  C10   0.020
 A2I  plan-1  C12   0.020
 A2I  plan-1  C13   0.020
 A2I  plan-1  H111  0.020
 A2I  plan-1  H141  0.020
 A2I  plan-1  H101  0.020
 A2I  plan-1  H121  0.020
 A2I  plan-2  C22   0.020
 A2I  plan-2  C23   0.020
 A2I  plan-2  C24   0.020
 A2I  plan-2  S19   0.020
 A2I  plan-2  C20   0.020
 A2I  plan-2  N21   0.020
 A2I  plan-2  N25   0.020
 A2I  plan-2  C27   0.020
 A2I  plan-2  H231  0.020
 A2I  plan-2  C26   0.020
 A2I  plan-3  C1    0.020
 A2I  plan-3  C2    0.020
 A2I  plan-3  C3    0.020
 A2I  plan-3  C4    0.020
 A2I  plan-3  C5    0.020
 A2I  plan-3  C6    0.020
 A2I  plan-3  H021  0.020
 A2I  plan-3  H031  0.020
 A2I  plan-3  H051  0.020
 A2I  plan-3  H061  0.020
 A2I  plan-3  O7    0.020
 A2I  plan-3  H011  0.020
 A2I  plan-4  N15   0.020
 A2I  plan-4  C16   0.020
 A2I  plan-4  C13   0.020
 A2I  plan-4  O17   0.020
 A2I  plan-4  C18   0.020
 A2I  plan-4  H151  0.020

