# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 11:26:54 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: 4-{[(6-methoxy-5-nitropyrimidin-4-yl)amino]methyl}benzenesulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ncnc(NCc2ccc(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
 J71  J71  4-{[(6-methoxy-5-nitropyrimidin-4-yl)amino]methyl}benzenesulfonamide  ligand  36  23  .  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_J71
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
 J71  N1    N  N      0  -0.483  -5.1623  -1.2396   0.1326
 J71  C2    C  CR16   0   0.100  -4.2121  -2.1611   0.1573
 J71  N3    N  N      0  -0.477  -2.9197  -1.9763   0.0905
 J71  C4    C  CR6    0   0.550  -2.4693  -0.7126  -0.0017
 J71  C5    C  CR6    0   0.020  -3.4035   0.3701  -0.0001
 J71  C6    C  CR6    0   0.567  -4.7751   0.0197   0.0535
 J71  N7    N  NH1    0  -0.641  -1.1527  -0.5744  -0.0734
 J71  C8    C  CR6    0   0.059   1.1739  -1.1838  -0.0331
 J71  C9    C  CR16   0  -0.275   1.8496  -1.0072   1.1714
 J71  C10   C  CR16   0  -0.207   3.1403  -0.5075   1.1910
 J71  C11   C  CR6    0  -0.210   3.7507  -0.1733  -0.0104
 J71  C12   C  CR16   0  -0.219   3.0948  -0.3318  -1.2213
 J71  C13   C  CR16   0  -0.267   1.8051  -0.8420  -1.2241
 J71  S14   S  S      0   1.362   5.4022   0.4658   0.0180
 J71  O15   O  OS     0  -0.650   5.6397   1.1383  -1.2517
 J71  O16   O  OS     0  -0.665   5.6083   1.2155   1.2484
 J71  N17   N  NC2    0  -0.887   6.2790  -0.9237   0.1823
 J71  N18   N  N      1   0.357  -2.9790   1.7259  -0.0452
 J71  O19   O  O     -1  -0.436  -1.7996   1.9556  -0.2775
 J71  O20   O  O      0  -0.385  -3.7754   2.6132   0.1509
 J71  O21   O  O2     0  -0.427  -5.6914   0.9504   0.0057
 J71  C22   C  CH3    0  -0.420  -7.0677   0.5614   0.0294
 J71  C23   C  CH2    0  -0.321  -0.2371  -1.7024  -0.0427
 J71  H2    H  HCR6   0   0.276  -4.5478  -3.1893   0.2372
 J71  HN7   H  HNH1   0   0.425  -0.7851   0.3577  -0.1813
 J71  H9    H  HCR6   0   0.273   1.3666  -1.2657   2.1050
 J71  H10   H  HCR6   0   0.287   3.6539  -0.3781   2.1341
 J71  H12   H  HCR6   0   0.286   3.5715  -0.0681  -2.1551
 J71  H13   H  HCR6   0   0.273   1.2910  -0.9770  -2.1674
 J71  HN17  H  HNC2   0   0.417   6.3482  -1.4489  -0.6834
 J71  HN1A  H  HNC2   0   0.421   7.2046  -0.7382   0.5573
 J71  H22   H  HCH3   0   0.245  -7.3142  -0.0845  -0.8115
 J71  H22A  H  HCH3   0   0.246  -7.3200   0.0551   0.9597
 J71  H22B  H  HCH3   0   0.258  -7.6252   1.4902  -0.0452
 J71  H23   H  HCH2   0   0.272  -0.4229  -2.3100   0.8438
 J71  H23A  H  HCH2   0   0.272  -0.3994  -2.3442  -0.9114

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
 J71  N1   C2    aromatic  1.324  0.020  1.324
 J71  N1   C6    aromatic  1.320  0.020  1.320
 J71  C2   N3    aromatic  1.307  0.020  1.307
 J71  N3   C4    aromatic  1.345  0.020  1.345
 J71  C4   C5    aromatic  1.430  0.020  1.430
 J71  C4   N7    single    1.326  0.020  1.326
 J71  C5   C6    aromatic  1.417  0.020  1.417
 J71  C5   N18   single    1.421  0.020  1.421
 J71  C6   O21   single    1.307  0.020  1.307
 J71  N7   C23   single    1.453  0.020  1.453
 J71  C8   C9    aromatic  1.392  0.020  1.392
 J71  C8   C13   aromatic  1.391  0.020  1.391
 J71  C8   C23   single    1.503  0.020  1.503
 J71  C9   C10   aromatic  1.384  0.020  1.384
 J71  C10  C11   aromatic  1.388  0.020  1.388
 J71  C11  C12   aromatic  1.386  0.020  1.386
 J71  C11  S14   single    1.771  0.020  1.771
 J71  C12  C13   aromatic  1.387  0.020  1.387
 J71  S14  O15   double    1.456  0.020  1.456
 J71  S14  O16   double    1.455  0.020  1.455
 J71  S14  N17   single    1.651  0.020  1.651
 J71  N18  O19   single    1.224  0.020  1.224
 J71  N18  O20   double    1.208  0.020  1.208
 J71  O21  C22   single    1.430  0.020  1.430
 J71  C2   H2    single    0.930  0.020  1.080
 J71  N7   HN7   single    0.860  0.020  1.020
 J71  C9   H9    single    0.930  0.020  1.080
 J71  C10  H10   single    0.930  0.020  1.080
 J71  C12  H12   single    0.930  0.020  1.080
 J71  C13  H13   single    0.930  0.020  1.080
 J71  N17  HN17  single    0.890  0.020  1.040
 J71  N17  HN1A  single    0.890  0.020  1.040
 J71  C22  H22   single    0.970  0.020  1.090
 J71  C22  H22A  single    0.970  0.020  1.090
 J71  C22  H22B  single    0.970  0.020  1.090
 J71  C23  H23   single    0.970  0.020  1.090
 J71  C23  H23A  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
 J71  C6    N1   C2    117.04  3.000
 J71  H2    C2   N3    116.35  3.000
 J71  H2    C2   N1    116.05  3.000
 J71  N3    C2   N1    127.60  3.000
 J71  C4    N3   C2    117.87  3.000
 J71  N7    C4   C5    124.74  3.000
 J71  N7    C4   N3    115.74  3.000
 J71  C5    C4   N3    119.51  3.000
 J71  N18   C5   C6    121.76  3.000
 J71  N18   C5   C4    121.81  3.000
 J71  C6    C5   C4    116.44  3.000
 J71  O21   C6   C5    120.08  3.000
 J71  O21   C6   N1    118.42  3.000
 J71  C5    C6   N1    121.49  3.000
 J71  HN7   N7   C23   119.36  3.000
 J71  HN7   N7   C4    117.68  3.000
 J71  C23   N7   C4    122.93  3.000
 J71  C23   C8   C13   120.36  3.000
 J71  C23   C8   C9    120.31  3.000
 J71  C13   C8   C9    119.31  3.000
 J71  H9    C9   C10   119.34  3.000
 J71  H9    C9   C8    119.96  3.000
 J71  C10   C9   C8    120.70  3.000
 J71  H10   C10  C11   121.12  3.000
 J71  H10   C10  C9    119.89  3.000
 J71  C11   C10  C9    118.99  3.000
 J71  S14   C11  C12   119.77  3.000
 J71  S14   C11  C10   118.88  3.000
 J71  C12   C11  C10   121.35  3.000
 J71  H12   C12  C13   119.87  3.000
 J71  H12   C12  C11   121.20  3.000
 J71  C13   C12  C11   118.94  3.000
 J71  H13   C13  C12   119.29  3.000
 J71  H13   C13  C8    120.00  3.000
 J71  C12   C13  C8    120.71  3.000
 J71  N17   S14  O16   105.91  3.000
 J71  N17   S14  O15   112.88  3.000
 J71  O16   S14  O15   118.43  3.000
 J71  N17   S14  C11   101.13  3.000
 J71  O16   S14  C11   109.36  3.000
 J71  O15   S14  C11   107.74  3.000
 J71  HN1A  N17  HN17  110.32  3.000
 J71  HN1A  N17  S14   111.52  3.000
 J71  HN17  N17  S14   112.76  3.000
 J71  O20   N18  O19   121.88  3.000
 J71  O20   N18  C5    119.90  3.000
 J71  O19   N18  C5    118.22  3.000
 J71  C22   O21  C6    118.71  3.000
 J71  H22B  C22  H22A  109.73  3.000
 J71  H22B  C22  H22   109.77  3.000
 J71  H22A  C22  H22   109.37  3.000
 J71  H22B  C22  O21   105.08  3.000
 J71  H22A  C22  O21   111.32  3.000
 J71  H22   C22  O21   111.50  3.000
 J71  H23A  C23  H23   107.09  3.000
 J71  H23A  C23  C8    110.32  3.000
 J71  H23   C23  C8    110.29  3.000
 J71  H23A  C23  N7    110.23  3.000
 J71  H23   C23  N7    110.02  3.000
 J71  C8    C23  N7    108.89  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
 J71  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 J71  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 J71  CONST_03  C5    C6   N1   C2      0.00   0.0  0
 J71  CONST_04  C5    C4   N3   C2      0.00   0.0  0
 J71  CONST_05  C6    N1   C2   N3      0.00   0.0  0
 J71  CONST_06  C6    C5   C4   N3      0.00   0.0  0
 J71  CONST_07  C11   C10  C9   C8      0.00   0.0  0
 J71  CONST_08  C11   C12  C13  C8      0.00   0.0  0
 J71  CONST_09  C12   C13  C8   C9      0.00   0.0  0
 J71  CONST_10  C12   C11  C10  C9      0.00   0.0  0
 J71  CONST_11  C13   C8   C9   C10     0.00   0.0  0
 J71  CONST_12  C13   C12  C11  C10     0.00   0.0  0
 J71  CONST_13  N18   C5   C6   N1    180.00   0.0  0
 J71  CONST_14  O21   C6   N1   C2    180.00   0.0  0
 J71  CONST_15  N7    C4   N3   C2    180.00   0.0  0
 J71  CONST_16  N18   C5   C4   N3    180.00   0.0  0
 J71  CONST_17  O21   C6   C5   C4    180.00   0.0  0
 J71  CONST_18  N7    C4   C5   C6    180.00   0.0  0
 J71  CONST_19  S14   C11  C10  C9    180.00   0.0  0
 J71  CONST_20  C23   C8   C9   C10   180.00   0.0  0
 J71  CONST_21  C23   C8   C13  C12   180.00   0.0  0
 J71  CONST_22  S14   C11  C12  C13   180.00   0.0  0
 J71  CONST_23  H2    C2   N3   C4    180.00   0.0  0
 J71  CONST_24  H10   C10  C9   C8    180.00   0.0  0
 J71  CONST_25  H12   C12  C13  C8    180.00   0.0  0
 J71  CONST_26  H13   C13  C8   C9    180.00   0.0  0
 J71  CONST_27  H9    C9   C10  C11   180.00   0.0  0
 J71  CONST_28  C23   N7   C4   N3      0.00   0.0  0
 J71  CONST_29  O19   N18  C5   C4      0.00   0.0  0
 J71  CONST_30  O20   N18  C5   C4    180.00   0.0  0
 J71  CONST_31  C23   N7   C4   C5    180.00   0.0  0
 J71  CONST_32  O19   N18  C5   C6    180.00   0.0  0
 J71  CONST_33  O20   N18  C5   C6      0.00   0.0  0
 J71  CONST_34  HN7   N7   C4   N3    180.00   0.0  0
 J71  Var_01    C8    C23  N7   C4   -175.55  30.0  3
 J71  Var_02    C9    C8   C23  N7     94.37  30.0  2
 J71  Var_03    O15   S14  C11  C10  -161.34  30.0  2
 J71  Var_04    H22   C22  O21  C6    -59.72  30.0  3
 J71  Var_05    HN17  N17  S14  C11    76.49  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
 J71  plan-1  N1   0.020
 J71  plan-1  C2   0.020
 J71  plan-1  N3   0.020
 J71  plan-1  C4   0.020
 J71  plan-1  C5   0.020
 J71  plan-1  C6   0.020
 J71  plan-1  N7   0.020
 J71  plan-1  N18  0.020
 J71  plan-1  O21  0.020
 J71  plan-1  H2   0.020
 J71  plan-2  C8   0.020
 J71  plan-2  C9   0.020
 J71  plan-2  C10  0.020
 J71  plan-2  C11  0.020
 J71  plan-2  C12  0.020
 J71  plan-2  C13  0.020
 J71  plan-2  S14  0.020
 J71  plan-2  C23  0.020
 J71  plan-2  H9   0.020
 J71  plan-2  H10  0.020
 J71  plan-2  H12  0.020
 J71  plan-2  H13  0.020
 J71  plan-3  C4   0.020
 J71  plan-3  N7   0.020
 J71  plan-3  C23  0.020
 J71  plan-3  HN7  0.020
 J71  plan-4  C5   0.020
 J71  plan-4  N18  0.020
 J71  plan-4  O19  0.020
 J71  plan-4  O20  0.020

