# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 14:02:01 2021
#   Inital geometry file: a 151 line input string
#   Ligand name: ~{N}-[1-[(4-bromophenyl)methyl]-6-[3-(methylamino)propylamino]-2,4-bis(oxidanylidene)pyrimidin-5-yl]-~{N}-methyl-benzenesulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNCCCNC1=C(N(C)[S](=O)(=O)c2ccccc2)C(=O)NC(=O)N1Cc3ccc(Br)cc3
#
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
 NVQ  NVQ  ~{N}-[1-[(4-bromophenyl)methyl]-6-[3-(methylamino)propylamino]-2,4-bis(oxidanylidene)pyrimidin-5-yl]-~{N}-methyl-benzenesulfonamide  ligand  59  33  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_NVQ
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
 NVQ  N1   N   NR6   0  -0.593  -0.0659   9.2524  21.8485
 NVQ  C1   C   CR6   0   0.678  -0.8643   8.6648  22.8121
 NVQ  C2   C   CR6   0  -0.099  -0.7733   7.3147  23.0624
 NVQ  C3   C   CR6   0   0.591   0.0236   6.4717  22.2164
 NVQ  N2   N   NR16  0  -0.735   0.6641   7.1459  21.1861
 NVQ  C4   C   CR6   0   0.706   0.6899   8.4890  20.9659
 NVQ  O1   O   O     0  -0.464   1.3449   8.9834  20.0734
 NVQ  O2   O   O     0  -0.451   0.1153   5.2610  22.3026
 NVQ  C5   C   CH2   0  -0.391   0.2980  10.6640  21.9657
 NVQ  N3   N   NH1   0  -0.632  -1.6818   9.4803  23.5129
 NVQ  N4   N   N     0  -0.635  -1.6054   6.7361  24.0435
 NVQ  S1   S   S     0   1.369  -0.9355   6.5877  25.5650
 NVQ  C6   C   CH3   0  -0.529  -2.6062   5.7496  23.6343
 NVQ  C7   C   CR6   0  -0.170   0.3930   5.4331  25.4272
 NVQ  C8   C   CR16  0  -0.231   1.6779   5.9022  25.1895
 NVQ  C9   C   CR16  0  -0.240   2.7056   4.9873  25.0225
 NVQ  C10  C   CR16  0  -0.237   2.4447   3.6256  25.0975
 NVQ  C11  C   CR16  0  -0.244   1.1563   3.1709  25.3481
 NVQ  C12  C   CR16  0  -0.236   0.1195   4.0748  25.5166
 NVQ  O3   O   OS    0  -0.640  -0.3663   7.8830  25.8964
 NVQ  O4   O   OS    0  -0.650  -1.9659   6.0128  26.4145
 NVQ  C13  C   CR6   0   0.137   1.1070  10.9621  23.2020
 NVQ  C14  C   CR16  0  -0.269   1.9197  10.0149  23.8121
 NVQ  C15  C   CR16  0  -0.208   2.6813  10.3380  24.9261
 NVQ  C16  C   CR6   0  -0.124   2.6312  11.6278  25.4306
 NVQ  C17  C   CR16  0  -0.215   1.8335  12.5941  24.8358
 NVQ  C18  C   CR16  0  -0.308   1.0764  12.2495  23.7272
 NVQ  BR1  BR  BR    0  -0.045   3.6609  12.0749  26.9486
 NVQ  C19  C   CH2   0  -0.332  -2.6635  10.3570  22.8701
 NVQ  C20  C   CH2   0  -0.464  -2.8109  11.6700  23.6190
 NVQ  C21  C   CH2   0  -0.310  -3.8670  12.5897  23.0010
 NVQ  N5   N   NH1   0  -0.589  -3.6237  13.0701  21.6552
 NVQ  C22  C   CH3   0  -0.525  -2.4416  13.8880  21.5000
 NVQ  H1   H   HNR6  0   0.427   1.2032   6.5842  20.5389
 NVQ  H2   H   HCH2  0   0.318   0.8685  10.9196  21.0758
 NVQ  H3   H   HCH2  0   0.275  -0.5835  11.2986  21.9381
 NVQ  H4   H   HNH1  0   0.395  -2.0627   9.0190  24.3255
 NVQ  H5   H   HCH3  0   0.264  -3.4266   5.7286  24.3454
 NVQ  H6   H   HCH3  0   0.265  -3.0027   6.0722  22.6746
 NVQ  H7   H   HCH3  0   0.246  -2.1977   4.7456  23.5188
 NVQ  H8   H   HCR6  0   0.276   1.8796   6.9637  25.1409
 NVQ  H9   H   HCR6  0   0.271   3.7115   5.3394  24.8379
 NVQ  H10  H   HCR6  0   0.271   3.2501   2.9147  24.9692
 NVQ  H11  H   HCR6  0   0.272   0.9577   2.1100  25.4186
 NVQ  H12  H   HCR6  0   0.280  -0.8807   3.7194  25.7238
 NVQ  H13  H   HCR6  0   0.243   1.9787   9.0017  23.4357
 NVQ  H14  H   HCR6  0   0.280   3.3061   9.5838  25.3849
 NVQ  H15  H   HCR6  0   0.283   1.7884  13.6025  25.2243
 NVQ  H16  H   HCR6  0   0.265   0.4532  13.0065  23.2651
 NVQ  H17  H   HCH2  0   0.250  -2.3845  10.5136  21.8284
 NVQ  H18  H   HCH2  0   0.269  -3.6256   9.8360  22.8400
 NVQ  H19  H   HCH2  0   0.243  -3.1016  11.4592  24.6519
 NVQ  H20  H   HCH2  0   0.229  -1.8425  12.1754  23.6770
 NVQ  H21  H   HCH2  0   0.233  -3.9857  13.4603  23.6520
 NVQ  H22  H   HCH2  0   0.230  -4.8313  12.0730  23.0033
 NVQ  H23  H   HNH1  0   0.349  -3.6121  12.3050  20.9942
 NVQ  H25  H   HCH3  0   0.238  -2.3802  14.2545  20.4752
 NVQ  H26  H   HCH3  0   0.226  -2.5096  14.7582  22.1564
 NVQ  H27  H   HCH3  0   0.187  -1.4852  13.3932  21.7221

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
 NVQ  O1   C4   double    1.212  0.020  1.212
 NVQ  C4   N2   single    1.361  0.020  1.361
 NVQ  C4   N1   single    1.390  0.020  1.390
 NVQ  N2   C3   single    1.388  0.020  1.388
 NVQ  C5   N1   single    1.463  0.020  1.463
 NVQ  C5   C13  single    1.507  0.020  1.507
 NVQ  N1   C1   single    1.382  0.020  1.382
 NVQ  C3   O2   double    1.217  0.020  1.217
 NVQ  C3   C2   single    1.436  0.020  1.436
 NVQ  C18  C13  aromatic  1.391  0.020  1.391
 NVQ  C18  C17  aromatic  1.386  0.020  1.386
 NVQ  C13  C14  aromatic  1.389  0.020  1.389
 NVQ  C1   C2   double    1.376  0.020  1.376
 NVQ  C1   N3   single    1.351  0.020  1.351
 NVQ  C6   N4   single    1.464  0.020  1.464
 NVQ  C19  N3   single    1.465  0.020  1.465
 NVQ  C19  C20  single    1.519  0.020  1.519
 NVQ  C2   N4   single    1.411  0.020  1.411
 NVQ  N5   C21  single    1.450  0.020  1.450
 NVQ  N5   C22  single    1.446  0.020  1.446
 NVQ  C17  C16  aromatic  1.387  0.020  1.387
 NVQ  C14  C15  aromatic  1.388  0.020  1.388
 NVQ  N4   S1   single    1.669  0.020  1.669
 NVQ  C21  C20  single    1.531  0.020  1.531
 NVQ  C16  C15  aromatic  1.386  0.020  1.386
 NVQ  C16  BR1  single    1.888  0.020  1.888
 NVQ  S1   O4   double    1.454  0.020  1.454
 NVQ  S1   C7   single    1.766  0.020  1.766
 NVQ  S1   O3   double    1.453  0.020  1.453
 NVQ  C7   C8   aromatic  1.388  0.020  1.388
 NVQ  C7   C12  aromatic  1.388  0.020  1.388
 NVQ  C8   C9   aromatic  1.386  0.020  1.386
 NVQ  C12  C11  aromatic  1.386  0.020  1.386
 NVQ  C9   C10  aromatic  1.389  0.020  1.389
 NVQ  C11  C10  aromatic  1.389  0.020  1.389
 NVQ  N2   H1   single    0.860  0.020  1.020
 NVQ  C5   H2   single    0.970  0.020  1.090
 NVQ  C5   H3   single    0.970  0.020  1.090
 NVQ  N3   H4   single    0.890  0.020  1.040
 NVQ  C6   H5   single    0.970  0.020  1.090
 NVQ  C6   H6   single    0.970  0.020  1.090
 NVQ  C6   H7   single    0.970  0.020  1.090
 NVQ  C8   H8   single    0.930  0.020  1.080
 NVQ  C9   H9   single    0.930  0.020  1.080
 NVQ  C10  H10  single    0.930  0.020  1.080
 NVQ  C11  H11  single    0.930  0.020  1.080
 NVQ  C12  H12  single    0.930  0.020  1.080
 NVQ  C14  H13  single    0.930  0.020  1.080
 NVQ  C15  H14  single    0.930  0.020  1.080
 NVQ  C17  H15  single    0.930  0.020  1.080
 NVQ  C18  H16  single    0.930  0.020  1.080
 NVQ  C19  H17  single    0.970  0.020  1.090
 NVQ  C19  H18  single    0.970  0.020  1.090
 NVQ  C20  H19  single    0.970  0.020  1.090
 NVQ  C20  H20  single    0.970  0.020  1.090
 NVQ  C21  H21  single    0.970  0.020  1.090
 NVQ  C21  H22  single    0.970  0.020  1.090
 NVQ  N5   H23  single    0.890  0.020  1.040
 NVQ  C22  H25  single    0.970  0.020  1.090
 NVQ  C22  H26  single    0.970  0.020  1.090
 NVQ  C22  H27  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
 NVQ  C5   N1   C4   116.46  3.000
 NVQ  C5   N1   C1   119.87  3.000
 NVQ  C4   N1   C1   121.54  3.000
 NVQ  N3   C1   C2   122.55  3.000
 NVQ  N3   C1   N1   117.04  3.000
 NVQ  C2   C1   N1   120.37  3.000
 NVQ  N4   C2   C3   119.76  3.000
 NVQ  N4   C2   C1   119.34  3.000
 NVQ  C3   C2   C1   120.37  3.000
 NVQ  O2   C3   N2   120.07  3.000
 NVQ  O2   C3   C2   125.74  3.000
 NVQ  N2   C3   C2   114.10  3.000
 NVQ  H1   N2   C4   115.72  3.000
 NVQ  H1   N2   C3   116.79  3.000
 NVQ  C4   N2   C3   127.45  3.000
 NVQ  O1   C4   N2   122.11  3.000
 NVQ  N2   C4   N1   115.39  3.000
 NVQ  O1   C4   N1   122.49  3.000
 NVQ  H3   C5   H2   105.52  3.000
 NVQ  H3   C5   C13  109.93  3.000
 NVQ  H2   C5   C13  110.07  3.000
 NVQ  H3   C5   N1   111.09  3.000
 NVQ  H2   C5   N1   106.96  3.000
 NVQ  C13  C5   N1   112.96  3.000
 NVQ  H4   N3   C19  111.97  3.000
 NVQ  H4   N3   C1   111.73  3.000
 NVQ  C19  N3   C1   122.64  3.000
 NVQ  C6   N4   S1   117.99  3.000
 NVQ  S1   N4   C2   115.71  3.000
 NVQ  C6   N4   C2   119.03  3.000
 NVQ  O4   S1   O3   119.79  3.000
 NVQ  O3   S1   C7   107.82  3.000
 NVQ  O4   S1   C7   108.68  3.000
 NVQ  O3   S1   N4   106.61  3.000
 NVQ  C7   S1   N4   106.80  3.000
 NVQ  O4   S1   N4   106.46  3.000
 NVQ  H7   C6   H6   108.45  3.000
 NVQ  H7   C6   H5   109.55  3.000
 NVQ  H6   C6   H5   107.95  3.000
 NVQ  H7   C6   N4   113.22  3.000
 NVQ  H6   C6   N4   107.23  3.000
 NVQ  H5   C6   N4   110.28  3.000
 NVQ  C12  C7   C8   121.60  3.000
 NVQ  C12  C7   S1   119.11  3.000
 NVQ  C8   C7   S1   119.26  3.000
 NVQ  H8   C8   C9   120.27  3.000
 NVQ  H8   C8   C7   120.79  3.000
 NVQ  C9   C8   C7   118.93  3.000
 NVQ  H9   C9   C10  120.21  3.000
 NVQ  H9   C9   C8   119.69  3.000
 NVQ  C10  C9   C8   120.10  3.000
 NVQ  H10  C10  C11  119.79  3.000
 NVQ  H10  C10  C9   119.88  3.000
 NVQ  C11  C10  C9   120.33  3.000
 NVQ  H11  C11  C12  119.64  3.000
 NVQ  H11  C11  C10  120.20  3.000
 NVQ  C12  C11  C10  120.16  3.000
 NVQ  H12  C12  C11  120.06  3.000
 NVQ  H12  C12  C7   121.06  3.000
 NVQ  C11  C12  C7   118.88  3.000
 NVQ  C18  C13  C14  118.57  3.000
 NVQ  C14  C13  C5   122.64  3.000
 NVQ  C18  C13  C5   118.75  3.000
 NVQ  H13  C14  C15  117.86  3.000
 NVQ  H13  C14  C13  121.16  3.000
 NVQ  C15  C14  C13  120.99  3.000
 NVQ  H14  C15  C16  121.03  3.000
 NVQ  H14  C15  C14  119.68  3.000
 NVQ  C16  C15  C14  119.29  3.000
 NVQ  BR1  C16  C17  119.57  3.000
 NVQ  BR1  C16  C15  119.56  3.000
 NVQ  C17  C16  C15  120.87  3.000
 NVQ  H15  C17  C18  119.76  3.000
 NVQ  H15  C17  C16  121.30  3.000
 NVQ  C18  C17  C16  118.94  3.000
 NVQ  H16  C18  C17  118.77  3.000
 NVQ  H16  C18  C13  119.88  3.000
 NVQ  C17  C18  C13  121.34  3.000
 NVQ  H18  C19  H17  105.49  3.000
 NVQ  H18  C19  C20  109.86  3.000
 NVQ  H17  C19  C20  111.84  3.000
 NVQ  H18  C19  N3   108.44  3.000
 NVQ  H17  C19  N3   109.50  3.000
 NVQ  C20  C19  N3   111.48  3.000
 NVQ  H20  C20  H19  105.92  3.000
 NVQ  H20  C20  C21  110.77  3.000
 NVQ  H19  C20  C21  108.29  3.000
 NVQ  H20  C20  C19  109.85  3.000
 NVQ  H19  C20  C19  108.96  3.000
 NVQ  C21  C20  C19  112.79  3.000
 NVQ  H22  C21  H21  106.20  3.000
 NVQ  H22  C21  N5   107.84  3.000
 NVQ  H21  C21  N5   107.88  3.000
 NVQ  H22  C21  C20  108.88  3.000
 NVQ  H21  C21  C20  108.24  3.000
 NVQ  N5   C21  C20  117.27  3.000
 NVQ  H23  N5   C22  110.39  3.000
 NVQ  H23  N5   C21  110.98  3.000
 NVQ  C22  N5   C21  115.11  3.000
 NVQ  H27  C22  H26  106.94  3.000
 NVQ  H27  C22  H25  106.99  3.000
 NVQ  H26  C22  H25  107.50  3.000
 NVQ  H27  C22  N5   115.78  3.000
 NVQ  H26  C22  N5   109.59  3.000
 NVQ  H25  C22  N5   109.71  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
 NVQ  CONST_01  C10  C9   C8   C7      0.00   0.0  0
 NVQ  CONST_02  C10  C11  C12  C7      0.00   0.0  0
 NVQ  CONST_03  C11  C12  C7   C8      0.00   0.0  0
 NVQ  CONST_04  C11  C10  C9   C8      0.00   0.0  0
 NVQ  CONST_05  C12  C7   C8   C9      0.00   0.0  0
 NVQ  CONST_06  C12  C11  C10  C9      0.00   0.0  0
 NVQ  CONST_07  C16  C17  C18  C13     0.00   0.0  0
 NVQ  CONST_08  C16  C15  C14  C13     0.00   0.0  0
 NVQ  CONST_09  C17  C18  C13  C14     0.00   0.0  0
 NVQ  CONST_10  C17  C16  C15  C14     0.00   0.0  0
 NVQ  CONST_11  C18  C13  C14  C15     0.00   0.0  0
 NVQ  CONST_12  C18  C17  C16  C15     0.00   0.0  0
 NVQ  CONST_13  C3   N2   C4   N1      0.00   0.0  0
 NVQ  CONST_14  N2   C4   N1   C1      0.00   0.0  0
 NVQ  CONST_15  C4   N2   C3   C2      0.00   0.0  0
 NVQ  CONST_16  C4   N1   C1   C2      0.00   0.0  0
 NVQ  CONST_17  C17  C18  C13  C5    180.00   0.0  0
 NVQ  CONST_18  C15  C14  C13  C5    180.00   0.0  0
 NVQ  CONST_19  C9   C8   C7   S1    180.00   0.0  0
 NVQ  CONST_20  C11  C12  C7   S1    180.00   0.0  0
 NVQ  CONST_21  BR1  C16  C15  C14   180.00   0.0  0
 NVQ  CONST_22  BR1  C16  C17  C18   180.00   0.0  0
 NVQ  CONST_23  O1   C4   N1   C1    180.00   0.0  0
 NVQ  CONST_25  O1   C4   N2   C3    180.00   0.0  0
 NVQ  CONST_27  O2   C3   N2   C4    180.00   0.0  0
 NVQ  CONST_28  N3   C1   N1   C4    180.00   0.0  0
 NVQ  CONST_29  H9   C9   C8   C7    180.00   0.0  0
 NVQ  CONST_30  H11  C11  C12  C7    180.00   0.0  0
 NVQ  CONST_31  H12  C12  C7   C8    180.00   0.0  0
 NVQ  CONST_32  H10  C10  C9   C8    180.00   0.0  0
 NVQ  CONST_33  H8   C8   C9   C10   180.00   0.0  0
 NVQ  CONST_34  H15  C17  C18  C13   180.00   0.0  0
 NVQ  CONST_35  H14  C15  C14  C13   180.00   0.0  0
 NVQ  CONST_36  H16  C18  C13  C14   180.00   0.0  0
 NVQ  CONST_37  H13  C14  C15  C16   180.00   0.0  0
 NVQ  CONST_38  H1   N2   C4   N1    180.00   0.0  0
 NVQ  CONST_43  H4   N3   C1   N1    180.00   0.0  0
 NVQ  Var_01    C18  C13  C5   N1   -154.84  30.0  2
 NVQ  Var_02    C13  C5   N1   C1     62.23  30.0  3
 NVQ  Var_03    C6   N4   C2   C1    115.44  30.0  2
 NVQ  Var_04    C7   S1   N4   C2    -65.67  30.0  3
 NVQ  Var_05    C8   C7   S1   N4     93.02  30.0  2
 NVQ  Var_06    C20  C19  N3   C1   -144.64  30.0  2
 NVQ  Var_07    H5   C6   N4   C2   -154.60  30.0  3
 NVQ  Var_08    C21  C20  C19  N3   -177.95  30.0  3
 NVQ  Var_09    N5   C21  C20  C19   -63.55  30.0  1
 NVQ  Var_10    C22  N5   C21  C20   -62.21  30.0  1
 NVQ  Var_11    H25  C22  N5   C21  -176.23  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
 NVQ  plan-1  N1   0.020
 NVQ  plan-1  C1   0.020
 NVQ  plan-1  C2   0.020
 NVQ  plan-1  C3   0.020
 NVQ  plan-1  N2   0.020
 NVQ  plan-1  C4   0.020
 NVQ  plan-1  O1   0.020
 NVQ  plan-1  O2   0.020
 NVQ  plan-1  C5   0.020
 NVQ  plan-1  N3   0.020
 NVQ  plan-1  N4   0.020
 NVQ  plan-1  C19  0.020
 NVQ  plan-1  H1   0.020
 NVQ  plan-1  H4   0.020
 NVQ  plan-2  S1   0.020
 NVQ  plan-2  C7   0.020
 NVQ  plan-2  C8   0.020
 NVQ  plan-2  C9   0.020
 NVQ  plan-2  C10  0.020
 NVQ  plan-2  C11  0.020
 NVQ  plan-2  C12  0.020
 NVQ  plan-2  H8   0.020
 NVQ  plan-2  H9   0.020
 NVQ  plan-2  H10  0.020
 NVQ  plan-2  H11  0.020
 NVQ  plan-2  H12  0.020
 NVQ  plan-3  C5   0.020
 NVQ  plan-3  C13  0.020
 NVQ  plan-3  C14  0.020
 NVQ  plan-3  C15  0.020
 NVQ  plan-3  C16  0.020
 NVQ  plan-3  C17  0.020
 NVQ  plan-3  C18  0.020
 NVQ  plan-3  BR1  0.020
 NVQ  plan-3  H13  0.020
 NVQ  plan-3  H14  0.020
 NVQ  plan-3  H15  0.020
 NVQ  plan-3  H16  0.020

