# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 01:27:11 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: 3-({3-[(6-amino-5-bromopyrimidin-4-yl)sulfanyl]propanoyl}amino)-4-methoxy-N-phenylbenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1NC(=O)CCSc2ncnc(N)c2Br)C(=O)Nc3ccccc3
#
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
 AK5  AK5  3-({3-[(6-amino-5-bromopyrimidin-4-yl)sulfanyl]propanoyl}amino)-4-methoxy-N-phenylbenzamide  ligand  51  31  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AK5
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
 AK5  C28   C   CR16  0  -0.317   -7.4881  -2.7820   1.1207
 AK5  C27   C   CR16  0  -0.244   -8.5403  -3.6866   1.1934
 AK5  C26   C   CR16  0  -0.273   -9.6337  -3.5933   0.3459
 AK5  C24   C   CR16  0  -0.356   -8.6305  -1.6616  -0.6788
 AK5  C23   C   CR6   0   0.380   -7.5291  -1.7531   0.1778
 AK5  C16   C   CR16  0  -0.298   -5.1960   1.7517  -0.2235
 AK5  C17   C   CR16  0  -0.373   -4.4302   2.8651  -0.5319
 AK5  O19   O   O2    0  -0.464   -2.2353   3.8701  -0.5904
 AK5  C20   C   C     0   0.535   -5.3857  -0.5970   0.7115
 AK5  C15   C   CR6   0  -0.061   -4.6121   0.6206   0.3337
 AK5  C13   C   CR6   0   0.293   -2.4594   1.7201   0.2747
 AK5  C14   C   CR16  0  -0.310   -3.2426   0.6291   0.6028
 AK5  C9    C   CR16  0   0.067    5.1654  -2.2561  -1.5633
 AK5  C7    C   CR6   0   0.544    7.0720  -1.3231  -0.7518
 AK5  C5    C   CR6   0   0.145    4.9035  -0.4194  -0.2884
 AK5  C6    C   CR6   0  -0.250    6.2775  -0.3434  -0.1254
 AK5  C3    C   C     0   0.562   -0.2006   0.7459   0.3614
 AK5  C2    C   CH2   0  -0.547    2.2236   0.2269  -0.0161
 AK5  C1    C   CH2   0  -0.599    1.2274   1.1210   0.7047
 AK5  BR30  BR  BR    0  -0.002    7.0464   1.0202   0.9093
 AK5  N8    N   N     0  -0.456    6.4767  -2.2844  -1.4754
 AK5  N10   N   N     0  -0.444    4.3392  -1.3811  -1.0153
 AK5  S4    S   S2    0   0.072    3.8819   0.7747   0.4798
 AK5  O12   O   O     0  -0.465   -0.5169  -0.3723   0.0018
 AK5  N11   N   NH1   0  -0.738   -1.0799   1.7668   0.5169
 AK5  C18   C   CR6   0   0.352   -3.0598   2.8550  -0.3059
 AK5  C29   C   CH3   0  -0.440   -2.7733   5.0510  -1.1607
 AK5  O21   O   O     0  -0.464   -4.9828  -1.3626   1.5719
 AK5  N22   N   NH1   0  -0.764   -6.5376  -0.7806   0.0168
 AK5  C25   C   CR16  0  -0.243   -9.6698  -2.5712  -0.5944
 AK5  H28   H   HCR6  0   0.280   -6.6523  -2.8891   1.7913
 AK5  H27   H   HCR6  0   0.259   -8.4938  -4.4784   1.9299
 AK5  H26   H   HCR6  0   0.256  -10.4471  -4.3027   0.4177
 AK5  H24   H   HCR6  0   0.270   -8.6737  -0.8680  -1.4159
 AK5  H16   H   HCR6  0   0.266   -6.2623   1.8110  -0.4008
 AK5  H17   H   HCR6  0   0.294   -4.9176   3.7322  -0.9546
 AK5  H14   H   HCR6  0   0.273   -2.7917  -0.2334   1.0696
 AK5  H9    H   HCR6  0   0.266    4.7056  -3.0411  -2.1545
 AK5  H2    H   HCH2  0   0.290    2.0924  -0.8155   0.2625
 AK5  H2A   H   HCH2  0   0.289    2.1235   0.3151  -1.0967
 AK5  H1    H   HCH2  0   0.279    1.4056   2.1737   0.4744
 AK5  H1A   H   HCH2  0   0.299    1.3393   1.0164   1.7889
 AK5  HN31  H   HNH2  0   0.412    8.9465  -0.6554  -0.2091
 AK5  HN3A  H   HNH2  0   0.409    8.8979  -2.0779  -1.1729
 AK5  HN11  H   HNH1  0   0.413   -0.6918   2.6742   0.7258
 AK5  H29   H   HCH3  0   0.267   -1.9340   5.7221  -1.3207
 AK5  H29A  H   HCH3  0   0.237   -3.2561   4.8510  -2.1198
 AK5  H29B  H   HCH3  0   0.238   -3.4914   5.5307  -0.4921
 AK5  HN22  H   HNH1  0   0.422   -6.7117  -0.1362  -0.7382
 AK5  H25   H   HCR6  0   0.260  -10.5130  -2.4755  -1.2661
 AK5  N31   N   NH2   0  -0.819    8.4016  -1.3684  -0.6609

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
 AK5  C23   C28   aromatic  1.396  0.020  1.396
 AK5  C28   C27   aromatic  1.390  0.020  1.390
 AK5  C28   H28   single    0.930  0.020  1.080
 AK5  C26   C27   aromatic  1.387  0.020  1.387
 AK5  C27   H27   single    0.930  0.020  1.080
 AK5  C25   C26   aromatic  1.389  0.020  1.389
 AK5  C26   H26   single    0.930  0.020  1.080
 AK5  C24   C23   aromatic  1.398  0.020  1.398
 AK5  C24   C25   aromatic  1.384  0.020  1.384
 AK5  C24   H24   single    0.930  0.020  1.080
 AK5  N22   C23   single    1.398  0.020  1.398
 AK5  C17   C16   aromatic  1.386  0.020  1.386
 AK5  C15   C16   aromatic  1.390  0.020  1.390
 AK5  C16   H16   single    0.930  0.020  1.080
 AK5  C18   C17   aromatic  1.389  0.020  1.389
 AK5  C17   H17   single    0.930  0.020  1.080
 AK5  O19   C29   single    1.418  0.020  1.418
 AK5  O19   C18   single    1.338  0.020  1.338
 AK5  C15   C20   single    1.491  0.020  1.491
 AK5  C20   O21   double    1.220  0.020  1.220
 AK5  C20   N22   single    1.358  0.020  1.358
 AK5  C14   C15   aromatic  1.396  0.020  1.396
 AK5  N11   C13   single    1.401  0.020  1.401
 AK5  C13   C18   aromatic  1.409  0.020  1.409
 AK5  C13   C14   aromatic  1.383  0.020  1.383
 AK5  C14   H14   single    0.930  0.020  1.080
 AK5  N8    C9    aromatic  1.314  0.020  1.314
 AK5  C9    N10   aromatic  1.322  0.020  1.322
 AK5  C9    H9    single    0.930  0.020  1.080
 AK5  N31   C7    single    1.333  0.020  1.333
 AK5  C7    C6    aromatic  1.408  0.020  1.408
 AK5  C7    N8    aromatic  1.342  0.020  1.342
 AK5  C6    C5    aromatic  1.386  0.020  1.386
 AK5  C5    S4    single    1.749  0.020  1.749
 AK5  C5    N10   aromatic  1.331  0.020  1.331
 AK5  BR30  C6    single    1.877  0.020  1.877
 AK5  C1    C3    single    1.516  0.020  1.516
 AK5  C3    N11   single    1.356  0.020  1.356
 AK5  C3    O12   double    1.216  0.020  1.216
 AK5  S4    C2    single    1.816  0.020  1.816
 AK5  C1    C2    single    1.520  0.020  1.520
 AK5  C2    H2    single    0.970  0.020  1.090
 AK5  C2    H2A   single    0.970  0.020  1.090
 AK5  C1    H1    single    0.970  0.020  1.090
 AK5  C1    H1A   single    0.970  0.020  1.090
 AK5  N31   HN31  single    0.860  0.020  1.020
 AK5  N31   HN3A  single    0.860  0.020  1.020
 AK5  N11   HN11  single    0.860  0.020  1.020
 AK5  C29   H29   single    0.970  0.020  1.090
 AK5  C29   H29A  single    0.970  0.020  1.090
 AK5  C29   H29B  single    0.970  0.020  1.090
 AK5  N22   HN22  single    0.860  0.020  1.020
 AK5  C25   H25   single    0.930  0.020  1.080

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
 AK5  H28   C28  C23   121.11  3.000
 AK5  H28   C28  C27   119.37  3.000
 AK5  C23   C28  C27   119.53  3.000
 AK5  H27   C27  C26   119.94  3.000
 AK5  H27   C27  C28   118.64  3.000
 AK5  C26   C27  C28   121.42  3.000
 AK5  H26   C26  C25   120.52  3.000
 AK5  H26   C26  C27   120.55  3.000
 AK5  C25   C26  C27   118.93  3.000
 AK5  H24   C24  C25   119.53  3.000
 AK5  H24   C24  C23   119.73  3.000
 AK5  C25   C24  C23   120.75  3.000
 AK5  N22   C23  C24   116.27  3.000
 AK5  N22   C23  C28   124.72  3.000
 AK5  C24   C23  C28   119.02  3.000
 AK5  H16   C16  C15   121.61  3.000
 AK5  H16   C16  C17   117.63  3.000
 AK5  C15   C16  C17   120.72  3.000
 AK5  H17   C17  C18   120.96  3.000
 AK5  H17   C17  C16   118.84  3.000
 AK5  C18   C17  C16   120.20  3.000
 AK5  C29   O19  C18   118.92  3.000
 AK5  N22   C20  O21   123.79  3.000
 AK5  N22   C20  C15   114.90  3.000
 AK5  O21   C20  C15   121.31  3.000
 AK5  C14   C15  C20   117.72  3.000
 AK5  C14   C15  C16   119.00  3.000
 AK5  C20   C15  C16   123.24  3.000
 AK5  C18   C13  N11   117.63  3.000
 AK5  C18   C13  C14   119.47  3.000
 AK5  N11   C13  C14   122.89  3.000
 AK5  H14   C14  C13   119.77  3.000
 AK5  H14   C14  C15   119.24  3.000
 AK5  C13   C14  C15   120.99  3.000
 AK5  H9    C9   N10   116.09  3.000
 AK5  H9    C9   N8    116.33  3.000
 AK5  N10   C9   N8    127.57  3.000
 AK5  N8    C7   N31   117.04  3.000
 AK5  N8    C7   C6    119.19  3.000
 AK5  N31   C7   C6    123.76  3.000
 AK5  S4    C5   N10   119.04  3.000
 AK5  N10   C5   C6    121.62  3.000
 AK5  S4    C5   C6    119.34  3.000
 AK5  BR30  C6   C5    120.73  3.000
 AK5  BR30  C6   C7    121.31  3.000
 AK5  C5    C6   C7    117.96  3.000
 AK5  N11   C3   O12   123.86  3.000
 AK5  O12   C3   C1    122.64  3.000
 AK5  N11   C3   C1    113.49  3.000
 AK5  H2A   C2   H2    108.72  3.000
 AK5  H2A   C2   S4    109.31  3.000
 AK5  H2    C2   S4    109.24  3.000
 AK5  H2A   C2   C1    111.27  3.000
 AK5  H2    C2   C1    111.31  3.000
 AK5  S4    C2   C1    106.95  3.000
 AK5  H1A   C1   H1    106.51  3.000
 AK5  H1A   C1   C2    110.26  3.000
 AK5  H1    C1   C2    111.09  3.000
 AK5  H1A   C1   C3    107.27  3.000
 AK5  H1    C1   C3    110.15  3.000
 AK5  C2    C1   C3    111.37  3.000
 AK5  C7    N8   C9    117.58  3.000
 AK5  C5    N10  C9    116.07  3.000
 AK5  C2    S4   C5    101.98  3.000
 AK5  HN11  N11  C3    116.84  3.000
 AK5  HN11  N11  C13   116.39  3.000
 AK5  C3    N11  C13   126.39  3.000
 AK5  C13   C18  O19   115.85  3.000
 AK5  C13   C18  C17   119.56  3.000
 AK5  O19   C18  C17   124.59  3.000
 AK5  H29B  C29  H29A  109.10  3.000
 AK5  H29B  C29  H29   109.07  3.000
 AK5  H29A  C29  H29   108.98  3.000
 AK5  H29B  C29  O19   111.66  3.000
 AK5  H29A  C29  O19   111.63  3.000
 AK5  H29   C29  O19   106.30  3.000
 AK5  HN22  N22  C20   116.32  3.000
 AK5  HN22  N22  C23   114.12  3.000
 AK5  C20   N22  C23   129.56  3.000
 AK5  H25   C25  C24   119.29  3.000
 AK5  H25   C25  C26   120.36  3.000
 AK5  C24   C25  C26   120.35  3.000
 AK5  HN3A  N31  HN31  117.51  3.000
 AK5  HN3A  N31  C7    118.76  3.000
 AK5  HN31  N31  C7    123.19  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
 AK5  CONST_01  C25   C24  C23  C28      0.00   0.0  0
 AK5  CONST_02  C25   C26  C27  C28      0.00   0.0  0
 AK5  CONST_03  C24   C23  C28  C27      0.00   0.0  0
 AK5  CONST_04  C24   C25  C26  C27      0.00   0.0  0
 AK5  CONST_05  C23   C28  C27  C26      0.00   0.0  0
 AK5  CONST_06  C23   C24  C25  C26      0.00   0.0  0
 AK5  CONST_07  C13   C18  C17  C16      0.00   0.0  0
 AK5  CONST_08  C13   C14  C15  C16      0.00   0.0  0
 AK5  CONST_09  C14   C15  C16  C17      0.00   0.0  0
 AK5  CONST_10  C14   C13  C18  C17      0.00   0.0  0
 AK5  CONST_11  C18   C17  C16  C15      0.00   0.0  0
 AK5  CONST_12  C18   C13  C14  C15      0.00   0.0  0
 AK5  CONST_13  C6    C7   N8   C9       0.00   0.0  0
 AK5  CONST_14  C6    C5   N10  C9       0.00   0.0  0
 AK5  CONST_15  N10   C5   C6   C7       0.00   0.0  0
 AK5  CONST_16  N10   C9   N8   C7       0.00   0.0  0
 AK5  CONST_17  N8    C7   C6   C5       0.00   0.0  0
 AK5  CONST_18  N8    C9   N10  C5       0.00   0.0  0
 AK5  CONST_19  N22   C23  C28  C27    180.00   0.0  0
 AK5  CONST_20  O19   C18  C17  C16    180.00   0.0  0
 AK5  CONST_21  C20   C15  C16  C17    180.00   0.0  0
 AK5  CONST_22  N11   C13  C18  C17    180.00   0.0  0
 AK5  CONST_23  C14   C13  C18  O19    180.00   0.0  0
 AK5  CONST_24  C13   C14  C15  C20    180.00   0.0  0
 AK5  CONST_25  N11   C13  C14  C15    180.00   0.0  0
 AK5  CONST_26  N31   C7   N8   C9     180.00   0.0  0
 AK5  CONST_27  S4    C5   N10  C9     180.00   0.0  0
 AK5  CONST_28  S4    C5   C6   C7     180.00   0.0  0
 AK5  CONST_29  N31   C7   C6   C5     180.00   0.0  0
 AK5  CONST_30  N8    C7   C6   BR30   180.00   0.0  0
 AK5  CONST_31  N10   C5   C6   BR30   180.00   0.0  0
 AK5  CONST_32  C25   C24  C23  N22    180.00   0.0  0
 AK5  CONST_33  H24   C24  C23  C28    180.00   0.0  0
 AK5  CONST_34  H26   C26  C27  C28    180.00   0.0  0
 AK5  CONST_35  H25   C25  C26  C27    180.00   0.0  0
 AK5  CONST_36  H28   C28  C27  C26    180.00   0.0  0
 AK5  CONST_37  H27   C27  C28  C23    180.00   0.0  0
 AK5  CONST_38  H14   C14  C15  C16    180.00   0.0  0
 AK5  CONST_39  H17   C17  C16  C15    180.00   0.0  0
 AK5  CONST_40  H16   C16  C15  C14    180.00   0.0  0
 AK5  CONST_41  H9    C9   N8   C7     180.00   0.0  0
 AK5  CONST_42  C15   C20  N22  C23    180.00   0.0  0
 AK5  CONST_43  C20   N22  C23  C28      0.00   0.0  0
 AK5  CONST_44  C20   N22  C23  C24    180.00   0.0  0
 AK5  CONST_47  HN22  N22  C23  C28    180.00   0.0  0
 AK5  CONST_49  HN31  N31  C7   C6       0.00   0.0  0
 AK5  CONST_50  HN3A  N31  C7   C6     180.00   0.0  0
 AK5  CONST_51  O21   C20  N22  C23      0.00   0.0  0
 AK5  CONST_52  C1    C3   N11  C13    180.00   0.0  0
 AK5  CONST_53  O12   C3   N11  C13      0.00   0.0  0
 AK5  Var_01    O21   C20  C15  C16   -154.97  30.0  2
 AK5  Var_02    N10   C5   S4   C2       0.59  30.0  1
 AK5  Var_03    C1    C2   S4   C5     174.80  30.0  3
 AK5  Var_04    H29   C29  O19  C18   -179.04  30.0  3
 AK5  Var_05    S4    C2   C1   C3    -179.90  30.0  3
 AK5  Var_06    N11   C3   C1   C2    -155.40  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
 AK5  plan-1  C28   0.020
 AK5  plan-1  C27   0.020
 AK5  plan-1  C26   0.020
 AK5  plan-1  C24   0.020
 AK5  plan-1  C23   0.020
 AK5  plan-1  N22   0.020
 AK5  plan-1  C25   0.020
 AK5  plan-1  H28   0.020
 AK5  plan-1  H27   0.020
 AK5  plan-1  H26   0.020
 AK5  plan-1  H24   0.020
 AK5  plan-1  H25   0.020
 AK5  plan-2  C16   0.020
 AK5  plan-2  C17   0.020
 AK5  plan-2  O19   0.020
 AK5  plan-2  C20   0.020
 AK5  plan-2  C15   0.020
 AK5  plan-2  C13   0.020
 AK5  plan-2  C14   0.020
 AK5  plan-2  N11   0.020
 AK5  plan-2  C18   0.020
 AK5  plan-2  H16   0.020
 AK5  plan-2  H17   0.020
 AK5  plan-2  H14   0.020
 AK5  plan-3  C9    0.020
 AK5  plan-3  C7    0.020
 AK5  plan-3  C5    0.020
 AK5  plan-3  C6    0.020
 AK5  plan-3  BR30  0.020
 AK5  plan-3  N8    0.020
 AK5  plan-3  N10   0.020
 AK5  plan-3  S4    0.020
 AK5  plan-3  H9    0.020
 AK5  plan-3  N31   0.020
 AK5  plan-4  C23   0.020
 AK5  plan-4  C20   0.020
 AK5  plan-4  C15   0.020
 AK5  plan-4  O21   0.020
 AK5  plan-4  N22   0.020
 AK5  plan-4  HN22  0.020
 AK5  plan-5  C13   0.020
 AK5  plan-5  C3    0.020
 AK5  plan-5  C1    0.020
 AK5  plan-5  O12   0.020
 AK5  plan-5  N11   0.020
 AK5  plan-5  HN11  0.020
 AK5  plan-6  C7    0.020
 AK5  plan-6  HN31  0.020
 AK5  plan-6  HN3A  0.020
 AK5  plan-6  N31   0.020

