# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 17:12:55 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: 4-{2-[(6-methoxy-5-nitropyrimidin-4-yl)amino]ethyl}benzenesulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ncnc(NCCc2ccc(cc2)[S](N)(=O)=O)c1[N+]([O-])=O
#
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
 JS7  JS7  4-{2-[(6-methoxy-5-nitropyrimidin-4-yl)amino]ethyl}benzenesulfonamide  ligand  39  24  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_JS7
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
 JS7  N1    N  N      0  -0.483   4.4715  -1.5875   0.9932
 JS7  C2    C  CR16   0   0.094   3.1557  -1.7336   0.9364
 JS7  N3    N  N      0  -0.469   2.3052  -1.0378   0.2308
 JS7  C4    C  CR6    0   0.550   2.7873  -0.0576  -0.5560
 JS7  C5    C  CR6    0   0.009   4.1992   0.1599  -0.6113
 JS7  C6    C  CR6    0   0.567   5.0006  -0.6534   0.2272
 JS7  N7    N  NH1    0  -0.640   1.8885   0.6228  -1.2555
 JS7  C8    C  CR6    0   0.134  -1.6733   0.7080   0.0249
 JS7  C9    C  CR16   0  -0.291  -2.1371  -0.4309   0.6765
 JS7  C10   C  CR16   0  -0.219  -3.4835  -0.7625   0.6661
 JS7  C11   C  CR6    0  -0.225  -4.3729   0.0596  -0.0081
 JS7  C12   C  CR16   0  -0.200  -3.9362   1.2004  -0.6708
 JS7  C13   C  CR16   0  -0.294  -2.5896   1.5161  -0.6489
 JS7  S14   S  S      0   1.360  -6.0914  -0.3504  -0.0524
 JS7  O15   O  OS     0  -0.668  -6.6230  -0.0874  -1.3825
 JS7  O16   O  OS     0  -0.653  -6.2466  -1.6917   0.4958
 JS7  N17   N  NC2    0  -0.887  -6.7238   0.8248   0.9216
 JS7  N18   N  N      1   0.355   4.7741   1.1384  -1.4681
 JS7  O19   O  O     -1  -0.432   4.0387   1.9885  -1.9485
 JS7  O20   O  O      0  -0.386   5.9588   1.1061  -1.7069
 JS7  O21   O  O2     0  -0.430   6.2944  -0.4668   0.2735
 JS7  C22   C  CH3    0  -0.420   7.0739  -1.2751   1.1597
 JS7  C23   C  CH2    0  -0.286   0.4663   0.3620  -1.2013
 JS7  C24   C  CH2    0  -0.526  -0.2078   1.0263   0.0039
 JS7  H2    H  HCR6   0   0.275   2.7372  -2.5195   1.5561
 JS7  HN7   H  HNH1   0   0.425   2.2093   1.4073  -1.7989
 JS7  H9    H  HCR6   0   0.264  -1.4400  -1.0686   1.2061
 JS7  H10   H  HCR6   0   0.283  -3.8244  -1.6508   1.1795
 JS7  H12   H  HCR6   0   0.284  -4.6318   1.8410  -1.1968
 JS7  H13   H  HCR6   0   0.266  -2.2468   2.4082  -1.1586
 JS7  HN17  H  HNC2   0   0.419  -7.7292   0.9056   0.7980
 JS7  HN1A  H  HNC2   0   0.415  -6.5028   0.6831   1.9021
 JS7  H22   H  HCH3   0   0.258   8.1010  -0.9615   1.0002
 JS7  H22A  H  HCH3   0   0.245   6.7951  -1.1061   2.1985
 JS7  H22B  H  HCH3   0   0.246   6.9720  -2.3335   0.9268
 JS7  H23   H  HCH2   0   0.273   0.0395   0.7496  -2.1259
 JS7  H23A  H  HCH2   0   0.262   0.2913  -0.7124  -1.1837
 JS7  H24   H  HCH2   0   0.261  -0.0538   2.1059  -0.0460
 JS7  H24A  H  HCH2   0   0.266   0.2650   0.6680   0.9195

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
 JS7  N1   C2    aromatic  1.325  0.020  1.325
 JS7  N1   C6    aromatic  1.319  0.020  1.319
 JS7  C2   N3    aromatic  1.306  0.020  1.306
 JS7  N3   C4    aromatic  1.346  0.020  1.346
 JS7  C4   C5    aromatic  1.430  0.020  1.430
 JS7  C4   N7    single    1.327  0.020  1.327
 JS7  C5   C6    aromatic  1.417  0.020  1.417
 JS7  C5   N18   single    1.422  0.020  1.422
 JS7  C6   O21   single    1.308  0.020  1.308
 JS7  N7   C23   single    1.447  0.020  1.447
 JS7  C8   C9    aromatic  1.392  0.020  1.392
 JS7  C8   C13   aromatic  1.395  0.020  1.395
 JS7  C8   C24   single    1.500  0.020  1.500
 JS7  C9   C10   aromatic  1.387  0.020  1.387
 JS7  C10  C11   aromatic  1.386  0.020  1.386
 JS7  C11  C12   aromatic  1.390  0.020  1.390
 JS7  C11  S14   single    1.767  0.020  1.767
 JS7  C12  C13   aromatic  1.383  0.020  1.383
 JS7  S14  O15   double    1.456  0.020  1.456
 JS7  S14  O16   double    1.457  0.020  1.457
 JS7  S14  N17   single    1.652  0.020  1.652
 JS7  N18  O19   single    1.222  0.020  1.222
 JS7  N18  O20   double    1.209  0.020  1.209
 JS7  O21  C22   single    1.430  0.020  1.430
 JS7  C23  C24   single    1.532  0.020  1.532
 JS7  C2   H2    single    0.930  0.020  1.080
 JS7  N7   HN7   single    0.860  0.020  1.020
 JS7  C9   H9    single    0.930  0.020  1.080
 JS7  C10  H10   single    0.930  0.020  1.080
 JS7  C12  H12   single    0.930  0.020  1.080
 JS7  C13  H13   single    0.930  0.020  1.080
 JS7  N17  HN17  single    0.890  0.020  1.040
 JS7  N17  HN1A  single    0.890  0.020  1.040
 JS7  C22  H22   single    0.970  0.020  1.090
 JS7  C22  H22A  single    0.970  0.020  1.090
 JS7  C22  H22B  single    0.970  0.020  1.090
 JS7  C23  H23   single    0.970  0.020  1.090
 JS7  C23  H23A  single    0.970  0.020  1.090
 JS7  C24  H24   single    0.970  0.020  1.090
 JS7  C24  H24A  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
 JS7  C6    N1   C2    116.85  3.000
 JS7  H2    C2   N3    116.32  3.000
 JS7  H2    C2   N1    116.00  3.000
 JS7  N3    C2   N1    127.67  3.000
 JS7  C4    N3   C2    118.07  3.000
 JS7  N7    C4   C5    124.80  3.000
 JS7  N7    C4   N3    116.04  3.000
 JS7  C5    C4   N3    119.14  3.000
 JS7  N18   C5   C6    121.53  3.000
 JS7  N18   C5   C4    121.82  3.000
 JS7  C6    C5   C4    116.65  3.000
 JS7  O21   C6   C5    119.91  3.000
 JS7  O21   C6   N1    118.51  3.000
 JS7  C5    C6   N1    121.56  3.000
 JS7  HN7   N7   C23   118.29  3.000
 JS7  HN7   N7   C4    117.93  3.000
 JS7  C23   N7   C4    123.62  3.000
 JS7  C24   C8   C13   120.80  3.000
 JS7  C24   C8   C9    120.39  3.000
 JS7  C13   C8   C9    118.77  3.000
 JS7  H9    C9   C10   119.19  3.000
 JS7  H9    C9   C8    119.75  3.000
 JS7  C10   C9   C8    121.05  3.000
 JS7  H10   C10  C11   121.06  3.000
 JS7  H10   C10  C9    119.94  3.000
 JS7  C11   C10  C9    119.00  3.000
 JS7  S14   C11  C12   118.95  3.000
 JS7  S14   C11  C10   119.90  3.000
 JS7  C12   C11  C10   121.14  3.000
 JS7  H12   C12  C13   119.89  3.000
 JS7  H12   C12  C11   121.05  3.000
 JS7  C13   C12  C11   119.06  3.000
 JS7  H13   C13  C12   119.25  3.000
 JS7  H13   C13  C8    119.77  3.000
 JS7  C12   C13  C8    120.98  3.000
 JS7  N17   S14  O16   113.09  3.000
 JS7  N17   S14  O15   105.68  3.000
 JS7  O16   S14  O15   118.09  3.000
 JS7  N17   S14  C11   101.09  3.000
 JS7  O16   S14  C11   107.92  3.000
 JS7  O15   S14  C11   109.63  3.000
 JS7  HN1A  N17  HN17  110.12  3.000
 JS7  HN1A  N17  S14   112.76  3.000
 JS7  HN17  N17  S14   111.32  3.000
 JS7  O20   N18  O19   122.04  3.000
 JS7  O20   N18  C5    119.79  3.000
 JS7  O19   N18  C5    118.17  3.000
 JS7  C22   O21  C6    118.71  3.000
 JS7  H22B  C22  H22A  109.33  3.000
 JS7  H22B  C22  H22   109.76  3.000
 JS7  H22A  C22  H22   109.73  3.000
 JS7  H22B  C22  O21   111.46  3.000
 JS7  H22A  C22  O21   111.33  3.000
 JS7  H22   C22  O21   105.15  3.000
 JS7  H23A  C23  H23   107.56  3.000
 JS7  H23A  C23  C24   110.14  3.000
 JS7  H23   C23  C24   109.94  3.000
 JS7  H23A  C23  N7    109.66  3.000
 JS7  H23   C23  N7    106.80  3.000
 JS7  C24   C23  N7    112.56  3.000
 JS7  H24A  C24  H24   107.58  3.000
 JS7  H24A  C24  C23   109.09  3.000
 JS7  H24   C24  C23   109.31  3.000
 JS7  H24A  C24  C8    110.00  3.000
 JS7  H24   C24  C8    110.38  3.000
 JS7  C23   C24  C8    110.42  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
 JS7  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 JS7  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 JS7  CONST_03  C5    C6   N1   C2      0.00   0.0  0
 JS7  CONST_04  C5    C4   N3   C2      0.00   0.0  0
 JS7  CONST_05  C6    N1   C2   N3      0.00   0.0  0
 JS7  CONST_06  C6    C5   C4   N3      0.00   0.0  0
 JS7  CONST_07  C11   C10  C9   C8      0.00   0.0  0
 JS7  CONST_08  C11   C12  C13  C8      0.00   0.0  0
 JS7  CONST_09  C12   C13  C8   C9      0.00   0.0  0
 JS7  CONST_10  C12   C11  C10  C9      0.00   0.0  0
 JS7  CONST_11  C13   C8   C9   C10     0.00   0.0  0
 JS7  CONST_12  C13   C12  C11  C10     0.00   0.0  0
 JS7  CONST_13  N18   C5   C6   N1    180.00   0.0  0
 JS7  CONST_14  O21   C6   N1   C2    180.00   0.0  0
 JS7  CONST_15  N7    C4   N3   C2    180.00   0.0  0
 JS7  CONST_16  N18   C5   C4   N3    180.00   0.0  0
 JS7  CONST_17  O21   C6   C5   C4    180.00   0.0  0
 JS7  CONST_18  N7    C4   C5   C6    180.00   0.0  0
 JS7  CONST_19  S14   C11  C10  C9    180.00   0.0  0
 JS7  CONST_20  C24   C8   C9   C10   180.00   0.0  0
 JS7  CONST_21  C24   C8   C13  C12   180.00   0.0  0
 JS7  CONST_22  S14   C11  C12  C13   180.00   0.0  0
 JS7  CONST_23  H2    C2   N3   C4    180.00   0.0  0
 JS7  CONST_24  H10   C10  C9   C8    180.00   0.0  0
 JS7  CONST_25  H12   C12  C13  C8    180.00   0.0  0
 JS7  CONST_26  H13   C13  C8   C9    180.00   0.0  0
 JS7  CONST_27  H9    C9   C10  C11   180.00   0.0  0
 JS7  CONST_28  C23   N7   C4   N3      0.00   0.0  0
 JS7  CONST_31  C23   N7   C4   C5    180.00   0.0  0
 JS7  CONST_34  HN7   N7   C4   N3    180.00   0.0  0
 JS7  Var_01    C23   C24  C8   C9     88.84  30.0  2
 JS7  Var_02    O15   S14  C11  C10  -139.20  30.0  2
 JS7  Var_03    C24   C23  N7   C4     82.02  30.0  3
 JS7  Var_04    C8    C24  C23  N7   -179.12  30.0  3
 JS7  Var_05    H22   C22  O21  C6    178.33  30.0  3
 JS7  Var_06    HN17  N17  S14  C11   163.55  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
 JS7  plan-1  N1   0.020
 JS7  plan-1  C2   0.020
 JS7  plan-1  N3   0.020
 JS7  plan-1  C4   0.020
 JS7  plan-1  C5   0.020
 JS7  plan-1  C6   0.020
 JS7  plan-1  N7   0.020
 JS7  plan-1  N18  0.020
 JS7  plan-1  O21  0.020
 JS7  plan-1  H2   0.020
 JS7  plan-2  C8   0.020
 JS7  plan-2  C9   0.020
 JS7  plan-2  C10  0.020
 JS7  plan-2  C11  0.020
 JS7  plan-2  C12  0.020
 JS7  plan-2  C13  0.020
 JS7  plan-2  S14  0.020
 JS7  plan-2  C24  0.020
 JS7  plan-2  H9   0.020
 JS7  plan-2  H10  0.020
 JS7  plan-2  H12  0.020
 JS7  plan-2  H13  0.020
 JS7  plan-3  C4   0.020
 JS7  plan-3  N7   0.020
 JS7  plan-3  C23  0.020
 JS7  plan-3  HN7  0.020
 JS7  plan-4  C5   0.020
 JS7  plan-4  N18  0.020
 JS7  plan-4  O19  0.020
 JS7  plan-4  O20  0.020

