# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 11:12:23 2021
#   Inital geometry file: a 151 line input string
#   Ligand name: ~{N}-[6-(4-azanylbutylamino)-1-[(4-bromophenyl)methyl]-2,4-bis(oxidanylidene)pyrimidin-5-yl]-~{N}-methyl-benzenesulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C1=C(NCCCCN)N(Cc2ccc(Br)cc2)C(=O)NC1=O)[S](=O)(=O)c3ccccc3
#
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
 MBK  MBK  ~{N}-[6-(4-azanylbutylamino)-1-[(4-bromophenyl)methyl]-2,4-bis(oxidanylidene)pyrimidin-5-yl]-~{N}-methyl-benzenesulfonamide  ligand  59  33  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MBK
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
 MBK  C1   C   CR6   0   0.710  -12.3034  11.7041  38.8628
 MBK  C10  C   CR16  0  -0.238  -10.8628   4.5366  39.9935
 MBK  C11  C   CR16  0  -0.256   -9.9650   5.5748  40.2083
 MBK  C12  C   CR16  0  -0.207  -10.4266   6.8516  40.4862
 MBK  C13  C   CR6   0   0.085  -11.6069  14.7002  39.2929
 MBK  C14  C   CR16  0  -0.293  -12.3853  15.8045  39.6194
 MBK  C15  C   CR16  0  -0.211  -12.1656  16.5168  40.7892
 MBK  C16  C   CR6   0  -0.122  -11.1529  16.1095  41.6435
 MBK  C17  C   CR16  0  -0.210  -10.3620  15.0115  41.3387
 MBK  C18  C   CR16  0  -0.273  -10.5925  14.3156  40.1612
 MBK  C19  C   CH2   0  -0.254  -13.8512  11.8421  40.8212
 MBK  C2   C   CR6   0  -0.051  -11.9766  10.3597  38.9235
 MBK  C20  C   CH2   0  -0.468  -14.4664  13.0384  41.5301
 MBK  C21  C   CH2   0  -0.449  -14.8740  12.7083  42.9626
 MBK  C22  C   CH2   0  -0.302  -15.8414  11.5391  43.0993
 MBK  C3   C   CR6   0   0.560  -10.8977   9.8398  38.1463
 MBK  C4   C   CR6   0   0.724  -10.4895  12.1077  37.2935
 MBK  C6   C   CH3   0  -0.537  -13.8610   8.8036  38.7252
 MBK  C7   C   CR6   0  -0.151  -11.7947   7.0729  40.5587
 MBK  C8   C   CR16  0  -0.246  -12.7030   6.0396  40.3648
 MBK  C9   C   CR16  0  -0.248  -12.2291   4.7697  40.0697
 MBK  N1   N   NR6   0  -0.612  -11.5676  12.5506  38.0454
 MBK  N2   N   NR16  0  -0.735  -10.2025  10.7851  37.4083
 MBK  N3   N   NH1   0  -0.678  -13.3157  12.2651  39.5326
 MBK  N4   N   N     0  -0.628  -12.8469   9.4493  39.5505
 MBK  O1   O   O     0  -0.475   -9.8350  12.8501  36.5902
 MBK  O2   O   O     0  -0.464  -10.5765   8.6642  38.0849
 MBK  O3   O   OS    0  -0.653  -13.6148   8.4853  41.7353
 MBK  O4   O   OS    0  -0.648  -11.3099   9.4703  41.5214
 MBK  S1   S   S     0   1.361  -12.4007   8.6922  40.9567
 MBK  BR1  BR  BR    0  -0.044  -10.8497  17.0580  43.2474
 MBK  N5   N   NH2   0  -0.794  -17.0257  11.7328  42.2778
 MBK  H2   H   HCR6  0   0.269   -8.9001   5.3917  40.1585
 MBK  H3   H   HCR6  0   0.275   -9.7242   7.6564  40.6476
 MBK  H4   H   HCR6  0   0.272  -13.1854  16.1178  38.9592
 MBK  H5   H   HCR6  0   0.283  -12.7885  17.3697  41.0224
 MBK  H6   H   HCR6  0   0.283   -9.5714  14.6893  42.0028
 MBK  H7   H   HCR6  0   0.264   -9.9696  13.4572  39.9428
 MBK  H8   H   HCH2  0   0.250  -14.5935  11.0556  40.6948
 MBK  H9   H   HCH2  0   0.233  -13.0373  11.4487  41.4294
 MBK  H10  H   HCH2  0   0.236  -13.7414  13.8574  41.5519
 MBK  H11  H   HCH2  0   0.235  -15.3328  13.3921  40.9660
 MBK  H12  H   HCH2  0   0.226  -13.9811  12.4873  43.5548
 MBK  H13  H   HCH2  0   0.231  -15.3204  13.6004  43.4119
 MBK  H14  H   HCH2  0   0.219  -15.3516  10.6162  42.7778
 MBK  H15  H   HCH2  0   0.207  -16.0648  11.4043  44.1670
 MBK  H18  H   HCH3  0   0.260  -14.6089   8.3130  39.3449
 MBK  H19  H   HCH3  0   0.269  -14.3733   9.5707  38.1481
 MBK  H20  H   HCH3  0   0.250  -13.4266   8.0724  38.0414
 MBK  H21  H   HCR6  0   0.283  -13.7684   6.2054  40.4478
 MBK  H22  H   HCR6  0   0.270  -12.9308   3.9620  39.9117
 MBK  H23  H   HNR6  0   0.425   -9.4193  10.4547  36.8594
 MBK  H24  H   HNH1  0   0.422  -13.6075  13.1857  39.2525
 MBK  H25  H   HNH2  0   0.347  -17.6361  10.9312  42.3692
 MBK  H26  H   HNH2  0   0.336  -17.5546  12.5212  42.6310
 MBK  C5   C   CH2   0  -0.433  -11.8676  13.9771  37.9952
 MBK  H1   H   HCR6  0   0.270  -10.4965   3.5430  39.7716
 MBK  H16  H   HCH2  0   0.328  -11.2471  14.4020  37.2103
 MBK  H17  H   HCH2  0   0.296  -12.8968  14.1289  37.6616

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
 MBK  O2   C3   double    1.220  0.020  1.220
 MBK  N2   C3   single    1.386  0.020  1.386
 MBK  N2   C4   single    1.358  0.020  1.358
 MBK  O1   C4   double    1.214  0.020  1.214
 MBK  C6   N4   single    1.458  0.020  1.458
 MBK  C3   C2   single    1.428  0.020  1.428
 MBK  C4   N1   single    1.387  0.020  1.387
 MBK  C2   N4   single    1.407  0.020  1.407
 MBK  C2   C1   double    1.385  0.020  1.385
 MBK  N1   C1   single    1.388  0.020  1.388
 MBK  N1   C5   single    1.459  0.020  1.459
 MBK  N4   S1   single    1.658  0.020  1.658
 MBK  C1   N3   single    1.337  0.020  1.337
 MBK  C5   C13  single    1.508  0.020  1.508
 MBK  N3   C19  single    1.458  0.020  1.458
 MBK  C9   C8   aromatic  1.387  0.020  1.387
 MBK  C9   C10  aromatic  1.388  0.020  1.388
 MBK  C8   C7   aromatic  1.389  0.020  1.389
 MBK  C13  C18  aromatic  1.390  0.020  1.390
 MBK  C13  C14  aromatic  1.390  0.020  1.390
 MBK  C10  C11  aromatic  1.389  0.020  1.389
 MBK  C7   S1   single    1.774  0.020  1.774
 MBK  C7   C12  aromatic  1.388  0.020  1.388
 MBK  S1   O3   double    1.457  0.020  1.457
 MBK  S1   O4   double    1.454  0.020  1.454
 MBK  C11  C12  aromatic  1.386  0.020  1.386
 MBK  C18  C17  aromatic  1.387  0.020  1.387
 MBK  C14  C15  aromatic  1.387  0.020  1.387
 MBK  C19  C20  single    1.521  0.020  1.521
 MBK  C20  C21  single    1.526  0.020  1.526
 MBK  C17  C16  aromatic  1.387  0.020  1.387
 MBK  C15  C16  aromatic  1.386  0.020  1.386
 MBK  C21  C22  single    1.524  0.020  1.524
 MBK  C16  BR1  single    1.888  0.020  1.888
 MBK  N5   C22  single    1.454  0.020  1.454
 MBK  C10  H1   single    0.930  0.020  1.080
 MBK  C11  H2   single    0.930  0.020  1.080
 MBK  C12  H3   single    0.930  0.020  1.080
 MBK  C14  H4   single    0.930  0.020  1.080
 MBK  C15  H5   single    0.930  0.020  1.080
 MBK  C17  H6   single    0.930  0.020  1.080
 MBK  C18  H7   single    0.930  0.020  1.080
 MBK  C19  H8   single    0.970  0.020  1.090
 MBK  C19  H9   single    0.970  0.020  1.090
 MBK  C20  H10  single    0.970  0.020  1.090
 MBK  C20  H11  single    0.970  0.020  1.090
 MBK  C21  H12  single    0.970  0.020  1.090
 MBK  C21  H13  single    0.970  0.020  1.090
 MBK  C22  H14  single    0.970  0.020  1.090
 MBK  C22  H15  single    0.970  0.020  1.090
 MBK  C5   H16  single    0.970  0.020  1.090
 MBK  C5   H17  single    0.970  0.020  1.090
 MBK  C6   H18  single    0.970  0.020  1.090
 MBK  C6   H19  single    0.970  0.020  1.090
 MBK  C6   H20  single    0.970  0.020  1.090
 MBK  C8   H21  single    0.930  0.020  1.080
 MBK  C9   H22  single    0.930  0.020  1.080
 MBK  N2   H23  single    0.860  0.020  1.020
 MBK  N3   H24  single    0.860  0.020  1.020
 MBK  N5   H25  single    0.890  0.020  1.040
 MBK  N5   H26  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
 MBK  N3   C1   N1   116.14  3.000
 MBK  N3   C1   C2   124.33  3.000
 MBK  N1   C1   C2   119.52  3.000
 MBK  H1   C10  C9   119.91  3.000
 MBK  H1   C10  C11  119.95  3.000
 MBK  C9   C10  C11  120.14  3.000
 MBK  H2   C11  C12  119.54  3.000
 MBK  H2   C11  C10  120.17  3.000
 MBK  C12  C11  C10  120.28  3.000
 MBK  H3   C12  C7   120.95  3.000
 MBK  H3   C12  C11  119.99  3.000
 MBK  C7   C12  C11  119.06  3.000
 MBK  C5   C13  C18  122.08  3.000
 MBK  C18  C13  C14  118.81  3.000
 MBK  C5   C13  C14  119.09  3.000
 MBK  H4   C14  C15  118.83  3.000
 MBK  H4   C14  C13  120.01  3.000
 MBK  C15  C14  C13  121.16  3.000
 MBK  H5   C15  C16  121.31  3.000
 MBK  H5   C15  C14  119.70  3.000
 MBK  C16  C15  C14  118.98  3.000
 MBK  BR1  C16  C17  119.53  3.000
 MBK  BR1  C16  C15  119.56  3.000
 MBK  C17  C16  C15  120.92  3.000
 MBK  H6   C17  C18  119.55  3.000
 MBK  H6   C17  C16  121.18  3.000
 MBK  C18  C17  C16  119.27  3.000
 MBK  H7   C18  C17  118.26  3.000
 MBK  H7   C18  C13  120.89  3.000
 MBK  C17  C18  C13  120.85  3.000
 MBK  H9   C19  H8   108.25  3.000
 MBK  H9   C19  N3   108.89  3.000
 MBK  H8   C19  N3   110.93  3.000
 MBK  H9   C19  C20  109.03  3.000
 MBK  H8   C19  C20  110.28  3.000
 MBK  N3   C19  C20  109.41  3.000
 MBK  N4   C2   C3   118.33  3.000
 MBK  N4   C2   C1   120.11  3.000
 MBK  C3   C2   C1   120.53  3.000
 MBK  H11  C20  H10  107.06  3.000
 MBK  H11  C20  C21  110.06  3.000
 MBK  H10  C20  C21  108.68  3.000
 MBK  H11  C20  C19  109.56  3.000
 MBK  H10  C20  C19  109.28  3.000
 MBK  C21  C20  C19  112.07  3.000
 MBK  H13  C21  H12  105.99  3.000
 MBK  H13  C21  C22  109.26  3.000
 MBK  H12  C21  C22  108.34  3.000
 MBK  H13  C21  C20  108.56  3.000
 MBK  H12  C21  C20  109.51  3.000
 MBK  C22  C21  C20  114.83  3.000
 MBK  H15  C22  H14  105.86  3.000
 MBK  H15  C22  N5   113.55  3.000
 MBK  H14  C22  N5   108.13  3.000
 MBK  H15  C22  C21  108.08  3.000
 MBK  H14  C22  C21  109.69  3.000
 MBK  N5   C22  C21  111.35  3.000
 MBK  O2   C3   N2   119.88  3.000
 MBK  N2   C3   C2   114.87  3.000
 MBK  O2   C3   C2   125.25  3.000
 MBK  O1   C4   N2   122.04  3.000
 MBK  O1   C4   N1   122.53  3.000
 MBK  N2   C4   N1   115.43  3.000
 MBK  H20  C6   H19  109.11  3.000
 MBK  H20  C6   H18  109.17  3.000
 MBK  H19  C6   H18  107.24  3.000
 MBK  H20  C6   N4   111.99  3.000
 MBK  H19  C6   N4   108.38  3.000
 MBK  H18  C6   N4   110.81  3.000
 MBK  S1   C7   C8   119.13  3.000
 MBK  S1   C7   C12  119.61  3.000
 MBK  C8   C7   C12  121.23  3.000
 MBK  H21  C8   C9   119.55  3.000
 MBK  H21  C8   C7   121.29  3.000
 MBK  C9   C8   C7   119.16  3.000
 MBK  H22  C9   C8   119.54  3.000
 MBK  H22  C9   C10  120.35  3.000
 MBK  C8   C9   C10  120.11  3.000
 MBK  C5   N1   C4   116.97  3.000
 MBK  C5   N1   C1   120.51  3.000
 MBK  C4   N1   C1   122.45  3.000
 MBK  H23  N2   C4   115.83  3.000
 MBK  H23  N2   C3   117.02  3.000
 MBK  C4   N2   C3   127.09  3.000
 MBK  H24  N3   C19  113.90  3.000
 MBK  H24  N3   C1   117.66  3.000
 MBK  C19  N3   C1   126.79  3.000
 MBK  S1   N4   C6   117.71  3.000
 MBK  S1   N4   C2   120.46  3.000
 MBK  C6   N4   C2   117.67  3.000
 MBK  O4   S1   O3   119.58  3.000
 MBK  O4   S1   N4   106.67  3.000
 MBK  O3   S1   N4   107.08  3.000
 MBK  O4   S1   C7   108.62  3.000
 MBK  O3   S1   C7   105.96  3.000
 MBK  N4   S1   C7   108.56  3.000
 MBK  H26  N5   H25  105.67  3.000
 MBK  H26  N5   C22  109.39  3.000
 MBK  H25  N5   C22  109.55  3.000
 MBK  H17  C5   H16  105.25  3.000
 MBK  H17  C5   N1   109.89  3.000
 MBK  H16  C5   N1   106.84  3.000
 MBK  H17  C5   C13  111.04  3.000
 MBK  H16  C5   C13  109.58  3.000
 MBK  N1   C5   C13  113.81  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
 MBK  CONST_01  C7   C8   C9   C10     0.00   0.0  0
 MBK  CONST_02  C7   C12  C11  C10     0.00   0.0  0
 MBK  CONST_03  C8   C9   C10  C11     0.00   0.0  0
 MBK  CONST_04  C8   C7   C12  C11     0.00   0.0  0
 MBK  CONST_05  C9   C8   C7   C12     0.00   0.0  0
 MBK  CONST_06  C9   C10  C11  C12     0.00   0.0  0
 MBK  CONST_07  C16  C17  C18  C13     0.00   0.0  0
 MBK  CONST_08  C16  C15  C14  C13     0.00   0.0  0
 MBK  CONST_09  C17  C18  C13  C14     0.00   0.0  0
 MBK  CONST_10  C17  C16  C15  C14     0.00   0.0  0
 MBK  CONST_11  C18  C13  C14  C15     0.00   0.0  0
 MBK  CONST_12  C18  C17  C16  C15     0.00   0.0  0
 MBK  CONST_13  N2   C4   N1   C1      0.00   0.0  0
 MBK  CONST_14  C4   N2   C3   C2      0.00   0.0  0
 MBK  CONST_15  C4   N1   C1   C2      0.00   0.0  0
 MBK  CONST_16  N1   C4   N2   C3      0.00   0.0  0
 MBK  CONST_17  S1   C7   C12  C11   180.00   0.0  0
 MBK  CONST_18  BR1  C16  C15  C14   180.00   0.0  0
 MBK  CONST_19  C5   C13  C14  C15   180.00   0.0  0
 MBK  CONST_20  C5   C13  C18  C17   180.00   0.0  0
 MBK  CONST_21  BR1  C16  C17  C18   180.00   0.0  0
 MBK  CONST_22  S1   C7   C8   C9    180.00   0.0  0
 MBK  CONST_23  O1   C4   N1   C1    180.00   0.0  0
 MBK  CONST_24  C5   N1   C1   C2    180.00   0.0  0
 MBK  CONST_25  O1   C4   N2   C3    180.00   0.0  0
 MBK  CONST_26  O2   C3   N2   C4    180.00   0.0  0
 MBK  CONST_27  N3   C1   N1   C4    180.00   0.0  0
 MBK  CONST_28  N2   C4   N1   C5    180.00   0.0  0
 MBK  CONST_29  H21  C8   C9   C10   180.00   0.0  0
 MBK  CONST_30  H3   C12  C11  C10   180.00   0.0  0
 MBK  CONST_31  H22  C9   C10  C11   180.00   0.0  0
 MBK  CONST_32  H1   C10  C11  C12   180.00   0.0  0
 MBK  CONST_33  H6   C17  C18  C13   180.00   0.0  0
 MBK  CONST_34  H5   C15  C14  C13   180.00   0.0  0
 MBK  CONST_35  H7   C18  C13  C14   180.00   0.0  0
 MBK  CONST_36  H4   C14  C15  C16   180.00   0.0  0
 MBK  CONST_37  H2   C11  C12  C7    180.00   0.0  0
 MBK  CONST_38  H23  N2   C3   C2    180.00   0.0  0
 MBK  CONST_41  O1   C4   N1   C5      0.00   0.0  0
 MBK  CONST_42  N3   C1   N1   C5      0.00   0.0  0
 MBK  CONST_43  H24  N3   C1   C2    180.00   0.0  0
 MBK  Var_01    C13  C5   N1   C1     65.43  30.0  3
 MBK  Var_02    N1   C5   C13  C14  -149.36  30.0  3
 MBK  Var_03    C6   N4   C2   C1     90.59  30.0  2
 MBK  Var_04    N4   S1   C7   C12    99.53  30.0  2
 MBK  Var_05    C7   S1   N4   C2    -98.30  30.0  3
 MBK  Var_06    C20  C19  N3   C1    152.64  30.0  3
 MBK  Var_07    H18  C6   N4   C2   -166.73  30.0  3
 MBK  Var_08    C22  C21  C20  C19   -56.62  30.0  3
 MBK  Var_09    N5   C22  C21  C20   -54.19  30.0  3
 MBK  Var_10    N3   C19  C20  C21  -172.16  30.0  1
 MBK  Var_11    H25  N5   C22  C21   178.46  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
 MBK  plan-1  C13  0.020
 MBK  plan-1  C14  0.020
 MBK  plan-1  C15  0.020
 MBK  plan-1  C16  0.020
 MBK  plan-1  C17  0.020
 MBK  plan-1  C18  0.020
 MBK  plan-1  BR1  0.020
 MBK  plan-1  H4   0.020
 MBK  plan-1  H5   0.020
 MBK  plan-1  H6   0.020
 MBK  plan-1  H7   0.020
 MBK  plan-1  C5   0.020
 MBK  plan-2  C10  0.020
 MBK  plan-2  C11  0.020
 MBK  plan-2  C12  0.020
 MBK  plan-2  C7   0.020
 MBK  plan-2  C8   0.020
 MBK  plan-2  C9   0.020
 MBK  plan-2  S1   0.020
 MBK  plan-2  H2   0.020
 MBK  plan-2  H3   0.020
 MBK  plan-2  H21  0.020
 MBK  plan-2  H22  0.020
 MBK  plan-2  H1   0.020
 MBK  plan-3  C1   0.020
 MBK  plan-3  C19  0.020
 MBK  plan-3  C2   0.020
 MBK  plan-3  C3   0.020
 MBK  plan-3  C4   0.020
 MBK  plan-3  N1   0.020
 MBK  plan-3  N2   0.020
 MBK  plan-3  N3   0.020
 MBK  plan-3  N4   0.020
 MBK  plan-3  O1   0.020
 MBK  plan-3  O2   0.020
 MBK  plan-3  H23  0.020
 MBK  plan-3  H24  0.020
 MBK  plan-3  C5   0.020

