# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 09:38:27 2022
#   Inital geometry file: a 124 line input string
#   Ligand name: 4-({[6-(benzylamino)-5-nitropyrimidin-4-yl]amino}methyl)benzenesulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[S](=O)(=O)c1ccc(CNc2ncnc(NCc3ccccc3)c2[N+]([O-])=O)cc1
#
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
 J75  J75  4-({[6-(benzylamino)-5-nitropyrimidin-4-yl]amino}methyl)benzenesulfonamide  ligand  47  29  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_J75
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
 J75  N1    N  N      0  -0.493   3.1703  -2.3319  -0.0813
 J75  C2    C  CR16   0   0.093   2.0840  -3.0690  -0.0337
 J75  N3    N  N      0  -0.495   0.8394  -2.6790   0.1301
 J75  C4    C  CR6    0   0.548   0.6157  -1.3643   0.2582
 J75  C5    C  CR6    0   0.043   1.7148  -0.4437   0.2190
 J75  C6    C  CR6    0   0.541   3.0239  -1.0046   0.0435
 J75  N7    N  NH1    0  -0.646  -0.6523  -1.0036   0.4163
 J75  C8    C  CR6    0   0.070  -3.0461  -1.2155   0.2682
 J75  C9    C  CR16   0  -0.267  -3.3573  -0.6719  -0.9746
 J75  C10   C  CR16   0  -0.220  -4.5383   0.0271  -1.1659
 J75  C11   C  CR6    0  -0.217  -5.4112   0.1751  -0.0979
 J75  C12   C  CR16   0  -0.200  -5.1219  -0.3586   1.1502
 J75  C13   C  CR16   0  -0.285  -3.9355  -1.0515   1.3256
 J75  S14   S  S      0   1.361  -6.9162   1.0837  -0.3090
 J75  O15   O  OS     0  -0.665  -7.1763   1.8732   0.8859
 J75  O16   O  OS     0  -0.650  -6.8447   1.7728  -1.5904
 J75  N17   N  NC2    0  -0.887  -8.0270  -0.1383  -0.2925
 J75  N18   N  N      1   0.369   1.5188   0.9399   0.3442
 J75  O19   O  O     -1  -0.441   0.3867   1.3827   0.4857
 J75  O20   O  O      0  -0.439   2.4809   1.6947   0.3099
 J75  N21   N  NH1    0  -0.639   4.1431  -0.2956  -0.0081
 J75  C22   C  CH2    0  -0.321   5.4547  -0.8993  -0.1853
 J75  C23   C  CR6    0   0.048   6.4968   0.1836  -0.2121
 J75  C24   C  CR16   0  -0.289   7.1904   0.5289   0.9435
 J75  C25   C  CR16   0  -0.241   8.1339   1.5480   0.9218
 J75  C26   C  CR16   0  -0.262   8.3879   2.2348  -0.2579
 J75  C27   C  CR16   0  -0.241   7.6979   1.8977  -1.4157
 J75  C28   C  CR16   0  -0.281   6.7574   0.8774  -1.3912
 J75  C29   C  CH2    0  -0.322  -1.7495  -1.9521   0.4624
 J75  H2    H  HCR6   0   0.267   2.2340  -4.1390  -0.1391
 J75  HN7   H  HNH1   0   0.425  -0.8427  -0.0265   0.5734
 J75  H9    H  HCR6   0   0.273  -2.6738  -0.7945  -1.8056
 J75  H10   H  HCR6   0   0.286  -4.7680   0.4448  -2.1362
 J75  H12   H  HCR6   0   0.287  -5.8043  -0.2387   1.9810
 J75  H13   H  HCR6   0   0.273  -3.6989  -1.4643   2.2979
 J75  HN17  H  HNC2   0   0.416  -8.0181  -0.6876  -1.1460
 J75  HN1A  H  HNC2   0   0.420  -8.9633   0.2131  -0.1128
 J75  HN21  H  HNH1   0   0.422   4.0736   0.7046   0.0881
 J75  H22   H  HCH2   0   0.264   5.6519  -1.6023   0.6260
 J75  H22A  H  HCH2   0   0.264   5.4742  -1.4722  -1.1144
 J75  H24   H  HCR6   0   0.255   6.9963  -0.0059   1.8658
 J75  H25   H  HCR6   0   0.259   8.6717   1.8035   1.8256
 J75  H26   H  HCR6   0   0.259   9.1240   3.0278  -0.2763
 J75  H27   H  HCR6   0   0.259   7.8939   2.4278  -2.3388
 J75  H28   H  HCR6   0   0.256   6.2250   0.6133  -2.2976
 J75  H29   H  HCH2   0   0.276  -1.6181  -2.6947  -0.3245
 J75  H29A  H  HCH2   0   0.269  -1.7546  -2.4898   1.4138

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
 J75  N1   C2    aromatic  1.314  0.020  1.314
 J75  N1   C6    aromatic  1.341  0.020  1.341
 J75  C2   N3    aromatic  1.315  0.020  1.315
 J75  N3   C4    aromatic  1.340  0.020  1.340
 J75  C4   C5    aromatic  1.434  0.020  1.434
 J75  C4   N7    single    1.328  0.020  1.328
 J75  C5   C6    aromatic  1.435  0.020  1.435
 J75  C5   N18   single    1.403  0.020  1.403
 J75  C6   N21   single    1.326  0.020  1.326
 J75  N7   C29   single    1.451  0.020  1.451
 J75  C8   C9    aromatic  1.392  0.020  1.392
 J75  C8   C13   aromatic  1.391  0.020  1.391
 J75  C8   C29   single    1.504  0.020  1.504
 J75  C9   C10   aromatic  1.386  0.020  1.386
 J75  C10  C11   aromatic  1.387  0.020  1.387
 J75  C11  C12   aromatic  1.388  0.020  1.388
 J75  C11  S14   single    1.771  0.020  1.771
 J75  C12  C13   aromatic  1.385  0.020  1.385
 J75  S14  O15   double    1.456  0.020  1.456
 J75  S14  O16   double    1.457  0.020  1.457
 J75  S14  N17   single    1.652  0.020  1.652
 J75  N18  O19   single    1.224  0.020  1.224
 J75  N18  O20   double    1.223  0.020  1.223
 J75  N21  C22   single    1.455  0.020  1.455
 J75  C22  C23   single    1.503  0.020  1.503
 J75  C23  C24   aromatic  1.391  0.020  1.391
 J75  C23  C28   aromatic  1.393  0.020  1.393
 J75  C24  C25   aromatic  1.389  0.020  1.389
 J75  C25  C26   aromatic  1.388  0.020  1.388
 J75  C26  C27   aromatic  1.389  0.020  1.389
 J75  C27  C28   aromatic  1.388  0.020  1.388
 J75  C2   H2    single    0.930  0.020  1.080
 J75  N7   HN7   single    0.860  0.020  1.020
 J75  C9   H9    single    0.930  0.020  1.080
 J75  C10  H10   single    0.930  0.020  1.080
 J75  C12  H12   single    0.930  0.020  1.080
 J75  C13  H13   single    0.930  0.020  1.080
 J75  N17  HN17  single    0.890  0.020  1.040
 J75  N17  HN1A  single    0.890  0.020  1.040
 J75  N21  HN21  single    0.860  0.020  1.020
 J75  C22  H22   single    0.970  0.020  1.090
 J75  C22  H22A  single    0.970  0.020  1.090
 J75  C24  H24   single    0.930  0.020  1.080
 J75  C25  H25   single    0.930  0.020  1.080
 J75  C26  H26   single    0.930  0.020  1.080
 J75  C27  H27   single    0.930  0.020  1.080
 J75  C28  H28   single    0.930  0.020  1.080
 J75  C29  H29   single    0.970  0.020  1.090
 J75  C29  H29A  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
 J75  C6    N1   C2    117.50  3.000
 J75  H2    C2   N3    115.80  3.000
 J75  H2    C2   N1    115.81  3.000
 J75  N3    C2   N1    128.39  3.000
 J75  C4    N3   C2    117.46  3.000
 J75  N7    C4   C5    124.10  3.000
 J75  N7    C4   N3    115.94  3.000
 J75  C5    C4   N3    119.95  3.000
 J75  N18   C5   C6    121.59  3.000
 J75  N18   C5   C4    121.57  3.000
 J75  C6    C5   C4    116.84  3.000
 J75  N21   C6   C5    124.46  3.000
 J75  N21   C6   N1    115.69  3.000
 J75  C5    C6   N1    119.85  3.000
 J75  HN7   N7   C29   119.07  3.000
 J75  HN7   N7   C4    117.54  3.000
 J75  C29   N7   C4    123.25  3.000
 J75  C29   C8   C13   120.71  3.000
 J75  C29   C8   C9    119.97  3.000
 J75  C13   C8   C9    119.31  3.000
 J75  H9    C9   C10   119.29  3.000
 J75  H9    C9   C8    119.99  3.000
 J75  C10   C9   C8    120.73  3.000
 J75  H10   C10  C11   121.07  3.000
 J75  H10   C10  C9    119.99  3.000
 J75  C11   C10  C9    118.94  3.000
 J75  S14   C11  C12   118.80  3.000
 J75  S14   C11  C10   119.85  3.000
 J75  C12   C11  C10   121.34  3.000
 J75  H12   C12  C13   119.90  3.000
 J75  H12   C12  C11   121.10  3.000
 J75  C13   C12  C11   119.00  3.000
 J75  H13   C13  C12   119.45  3.000
 J75  H13   C13  C8    119.86  3.000
 J75  C12   C13  C8    120.68  3.000
 J75  N17   S14  O16   113.07  3.000
 J75  N17   S14  O15   105.84  3.000
 J75  O16   S14  O15   118.32  3.000
 J75  N17   S14  C11   101.00  3.000
 J75  O16   S14  C11   107.82  3.000
 J75  O15   S14  C11   109.41  3.000
 J75  HN1A  N17  HN17  110.12  3.000
 J75  HN1A  N17  S14   111.45  3.000
 J75  HN17  N17  S14   112.71  3.000
 J75  O20   N18  O19   120.50  3.000
 J75  O20   N18  C5    119.75  3.000
 J75  O19   N18  C5    119.76  3.000
 J75  HN21  N21  C22   119.07  3.000
 J75  HN21  N21  C6    117.97  3.000
 J75  C22   N21  C6    122.95  3.000
 J75  H22A  C22  H22   106.94  3.000
 J75  H22A  C22  C23   110.52  3.000
 J75  H22   C22  C23   110.61  3.000
 J75  H22A  C22  N21   109.73  3.000
 J75  H22   C22  N21   109.85  3.000
 J75  C23   C22  N21   109.17  3.000
 J75  C28   C23  C24   119.10  3.000
 J75  C28   C23  C22   120.25  3.000
 J75  C24   C23  C22   120.64  3.000
 J75  H24   C24  C25   119.80  3.000
 J75  H24   C24  C23   119.68  3.000
 J75  C25   C24  C23   120.52  3.000
 J75  H25   C25  C26   120.12  3.000
 J75  H25   C25  C24   119.85  3.000
 J75  C26   C25  C24   120.03  3.000
 J75  H26   C26  C27   120.10  3.000
 J75  H26   C26  C25   120.09  3.000
 J75  C27   C26  C25   119.81  3.000
 J75  H27   C27  C28   119.85  3.000
 J75  H27   C27  C26   120.13  3.000
 J75  C28   C27  C26   120.02  3.000
 J75  H28   C28  C27   119.82  3.000
 J75  H28   C28  C23   119.65  3.000
 J75  C27   C28  C23   120.53  3.000
 J75  H29A  C29  H29   107.09  3.000
 J75  H29A  C29  C8    110.45  3.000
 J75  H29   C29  C8    110.15  3.000
 J75  H29A  C29  N7    110.66  3.000
 J75  H29   C29  N7    109.34  3.000
 J75  C8    C29  N7    109.13  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
 J75  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 J75  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 J75  CONST_03  C5    C6   N1   C2      0.00   0.0  0
 J75  CONST_04  C5    C4   N3   C2      0.00   0.0  0
 J75  CONST_05  C6    N1   C2   N3      0.00   0.0  0
 J75  CONST_06  C6    C5   C4   N3      0.00   0.0  0
 J75  CONST_07  C11   C10  C9   C8      0.00   0.0  0
 J75  CONST_08  C11   C12  C13  C8      0.00   0.0  0
 J75  CONST_09  C12   C13  C8   C9      0.00   0.0  0
 J75  CONST_10  C12   C11  C10  C9      0.00   0.0  0
 J75  CONST_11  C13   C8   C9   C10     0.00   0.0  0
 J75  CONST_12  C13   C12  C11  C10     0.00   0.0  0
 J75  CONST_13  C26   C25  C24  C23     0.00   0.0  0
 J75  CONST_14  C26   C27  C28  C23     0.00   0.0  0
 J75  CONST_15  C27   C28  C23  C24     0.00   0.0  0
 J75  CONST_16  C27   C26  C25  C24     0.00   0.0  0
 J75  CONST_17  C28   C23  C24  C25     0.00   0.0  0
 J75  CONST_18  C28   C27  C26  C25     0.00   0.0  0
 J75  CONST_19  N18   C5   C6   N1    180.00   0.0  0
 J75  CONST_20  N21   C6   N1   C2    180.00   0.0  0
 J75  CONST_21  N7    C4   N3   C2    180.00   0.0  0
 J75  CONST_22  N18   C5   C4   N3    180.00   0.0  0
 J75  CONST_23  N21   C6   C5   C4    180.00   0.0  0
 J75  CONST_24  N7    C4   C5   C6    180.00   0.0  0
 J75  CONST_25  S14   C11  C10  C9    180.00   0.0  0
 J75  CONST_26  C29   C8   C9   C10   180.00   0.0  0
 J75  CONST_27  C29   C8   C13  C12   180.00   0.0  0
 J75  CONST_28  S14   C11  C12  C13   180.00   0.0  0
 J75  CONST_29  C25   C24  C23  C22   180.00   0.0  0
 J75  CONST_30  C27   C28  C23  C22   180.00   0.0  0
 J75  CONST_31  H2    C2   N3   C4    180.00   0.0  0
 J75  CONST_32  H10   C10  C9   C8    180.00   0.0  0
 J75  CONST_33  H12   C12  C13  C8    180.00   0.0  0
 J75  CONST_34  H13   C13  C8   C9    180.00   0.0  0
 J75  CONST_35  H9    C9   C10  C11   180.00   0.0  0
 J75  CONST_36  H25   C25  C24  C23   180.00   0.0  0
 J75  CONST_37  H27   C27  C28  C23   180.00   0.0  0
 J75  CONST_38  H28   C28  C23  C24   180.00   0.0  0
 J75  CONST_39  H26   C26  C25  C24   180.00   0.0  0
 J75  CONST_40  H24   C24  C25  C26   180.00   0.0  0
 J75  CONST_41  C22   N21  C6   N1      0.00   0.0  0
 J75  CONST_42  C29   N7   C4   N3      0.00   0.0  0
 J75  CONST_43  O19   N18  C5   C4      0.00   0.0  0
 J75  CONST_44  O20   N18  C5   C4    180.00   0.0  0
 J75  CONST_45  C29   N7   C4   C5    180.00   0.0  0
 J75  CONST_46  C22   N21  C6   C5    180.00   0.0  0
 J75  CONST_47  O19   N18  C5   C6    180.00   0.0  0
 J75  CONST_48  O20   N18  C5   C6      0.00   0.0  0
 J75  CONST_49  HN21  N21  C6   N1    180.00   0.0  0
 J75  CONST_50  HN7   N7   C4   N3    180.00   0.0  0
 J75  Var_01    C8    C29  N7   C4   -164.52  30.0  3
 J75  Var_02    C23   C22  N21  C6    179.48  30.0  3
 J75  Var_03    C9    C8   C29  N7     70.13  30.0  2
 J75  Var_04    O15   S14  C11  C10  -141.13  30.0  2
 J75  Var_05    C24   C23  C22  N21    95.51  30.0  2
 J75  Var_06    HN17  N17  S14  C11   -73.41  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
 J75  plan-1  N1    0.020
 J75  plan-1  C2    0.020
 J75  plan-1  N3    0.020
 J75  plan-1  C4    0.020
 J75  plan-1  C5    0.020
 J75  plan-1  C6    0.020
 J75  plan-1  N7    0.020
 J75  plan-1  N18   0.020
 J75  plan-1  N21   0.020
 J75  plan-1  H2    0.020
 J75  plan-2  C8    0.020
 J75  plan-2  C9    0.020
 J75  plan-2  C10   0.020
 J75  plan-2  C11   0.020
 J75  plan-2  C12   0.020
 J75  plan-2  C13   0.020
 J75  plan-2  S14   0.020
 J75  plan-2  C29   0.020
 J75  plan-2  H9    0.020
 J75  plan-2  H10   0.020
 J75  plan-2  H12   0.020
 J75  plan-2  H13   0.020
 J75  plan-3  C22   0.020
 J75  plan-3  C23   0.020
 J75  plan-3  C24   0.020
 J75  plan-3  C25   0.020
 J75  plan-3  C26   0.020
 J75  plan-3  C27   0.020
 J75  plan-3  C28   0.020
 J75  plan-3  H24   0.020
 J75  plan-3  H25   0.020
 J75  plan-3  H26   0.020
 J75  plan-3  H27   0.020
 J75  plan-3  H28   0.020
 J75  plan-4  C4    0.020
 J75  plan-4  N7    0.020
 J75  plan-4  C29   0.020
 J75  plan-4  HN7   0.020
 J75  plan-5  C5    0.020
 J75  plan-5  N18   0.020
 J75  plan-5  O19   0.020
 J75  plan-5  O20   0.020
 J75  plan-6  C6    0.020
 J75  plan-6  N21   0.020
 J75  plan-6  C22   0.020
 J75  plan-6  HN21  0.020

