# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 23:50:53 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: 2-[(chloroacetyl)amino]-5-[(E)-(4-sulfophenyl)diazenyl]benzenesulfonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[S](=O)(=O)c1ccc(cc1)N=Nc2ccc(NC(=O)CCl)c(c2)[S](O)(=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
 5J5  5J5  '2-[(chloroacetyl)amino]-5-[(E)-(4-sulfophenyl)diazenyl]benzenesulfonic acid'  ligand  39  27  .  2021-08-04  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5J5
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
 5J5  O5   O   OS    0  -0.713  -4.2587  -2.7063   1.0965
 5J5  S1   S   S     0   1.477  -3.5698  -2.4185  -0.3203
 5J5  O4   O   OS    0  -0.620  -2.6966  -3.5185  -0.6648
 5J5  O6   O   OS    0  -0.624  -4.5838  -2.0103  -1.2692
 5J5  C13  C   CR6   0  -0.281  -2.5896  -1.0276   0.1563
 5J5  C2   C   CR6   0   0.430  -3.1842   0.1870   0.5128
 5J5  N    N   NH1   0  -0.756  -4.5696   0.3024   0.6511
 5J5  C    C   C     0   0.546  -5.3123   1.2422   0.0002
 5J5  C1   C   CH2   0  -0.597  -6.7979   1.0513   0.2388
 5J5  CL   CL  CL    0  -0.118  -7.7394   2.3715  -0.4673
 5J5  O    O   O     0  -0.421  -4.8431   2.1065  -0.6991
 5J5  C12  C   CR16  0  -0.281  -1.2134  -1.1496   0.0599
 5J5  C5   C   CR6   0   0.255  -0.4054  -0.0458   0.2926
 5J5  C4   C   CR16  0  -0.248  -0.9872   1.1748   0.6377
 5J5  C3   C   CR16  0  -0.261  -2.3569   1.2834   0.7522
 5J5  N1   N   N     0  -0.254   0.9720  -0.2718   0.1521
 5J5  N2   N   N     0  -0.258   1.6865   0.7270   0.2989
 5J5  C6   C   CR6   0   0.254   3.0674   0.4964   0.1527
 5J5  C11  C   CR16  0  -0.272   3.8718   1.6260   0.2617
 5J5  C10  C   CR16  0  -0.210   5.2457   1.5232   0.1231
 5J5  C9   C   CR6   0  -0.237   5.7971   0.2749  -0.1205
 5J5  S    S   S     0   1.475   7.5446   0.1286  -0.3024
 5J5  O3   O   OS    0  -0.634   8.1035   1.3998  -0.7142
 5J5  O2   O   OS    0  -0.713   7.8946  -0.1332   1.2358
 5J5  O1   O   OS    0  -0.634   7.8596  -1.0556  -1.0752
 5J5  C8   C   CR16  0  -0.212   5.0080  -0.8660  -0.2281
 5J5  C7   C   CR16  0  -0.252   3.6392  -0.7538  -0.0912
 5J5  H1   H   HNH1  0   0.423  -5.0551  -0.4194   1.1650
 5J5  H2   H   HCH2  0   0.327  -7.1234   0.1131  -0.2123
 5J5  H3   H   HCH2  0   0.325  -7.0090   1.0035   1.3068
 5J5  H4   H   HCR6  0   0.304  -0.7512  -2.0887  -0.2125
 5J5  H5   H   HCR6  0   0.294  -0.3651   2.0367   0.8344
 5J5  H6   H   HCR6  0   0.297  -2.7928   2.2230   1.0585
 5J5  H7   H   HCR6  0   0.287   3.4132   2.5870   0.4517
 5J5  H8   H   HCR6  0   0.297   5.8645   2.4063   0.2006
 5J5  H9   H   HCR6  0   0.297   5.4491  -1.8335  -0.4247
 5J5  H10  H   HCR6  0   0.288   3.0163  -1.6327  -0.1771
 5J5  H11  H   H     0   0.513  -5.0275  -3.2996   1.0118
 5J5  H12  H   H     0   0.507   8.8500  -0.2657   1.3710

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
 5J5  CL   C1   single    1.769  0.020  1.769
 5J5  C1   C    single    1.517  0.020  1.517
 5J5  C    O    double    1.207  0.020  1.207
 5J5  C    N    single    1.363  0.020  1.363
 5J5  N    C2   single    1.397  0.020  1.397
 5J5  O6   S1   double    1.448  0.020  1.448
 5J5  C2   C3   aromatic  1.394  0.020  1.394
 5J5  C2   C13  aromatic  1.399  0.020  1.399
 5J5  O4   S1   double    1.446  0.020  1.446
 5J5  C3   C4   aromatic  1.379  0.020  1.379
 5J5  S1   C13  single    1.767  0.020  1.767
 5J5  S1   O5   single    1.602  0.020  1.602
 5J5  C13  C12  aromatic  1.385  0.020  1.385
 5J5  C4   C5   aromatic  1.396  0.020  1.396
 5J5  C12  C5   aromatic  1.388  0.020  1.388
 5J5  C5   N1   single    1.403  0.020  1.403
 5J5  N1   N2   double    1.237  0.020  1.237
 5J5  N2   C6   single    1.408  0.020  1.408
 5J5  C6   C11  aromatic  1.391  0.020  1.391
 5J5  C6   C7   aromatic  1.396  0.020  1.396
 5J5  C11  C10  aromatic  1.385  0.020  1.385
 5J5  C7   C8   aromatic  1.380  0.020  1.380
 5J5  C10  C9   aromatic  1.386  0.020  1.386
 5J5  C8   C9   aromatic  1.391  0.020  1.391
 5J5  C9   S    single    1.763  0.020  1.763
 5J5  S    O3   double    1.448  0.020  1.448
 5J5  S    O1   double    1.449  0.020  1.449
 5J5  S    O2   single    1.599  0.020  1.599
 5J5  N    H1   single    0.860  0.020  1.020
 5J5  C1   H2   single    0.970  0.020  1.090
 5J5  C1   H3   single    0.970  0.020  1.090
 5J5  C12  H4   single    0.930  0.020  1.080
 5J5  C4   H5   single    0.930  0.020  1.080
 5J5  C3   H6   single    0.930  0.020  1.080
 5J5  C11  H7   single    0.930  0.020  1.080
 5J5  C10  H8   single    0.930  0.020  1.080
 5J5  C8   H9   single    0.930  0.020  1.080
 5J5  C7   H10  single    0.930  0.020  1.080
 5J5  O5   H11  single    0.850  0.020  0.980
 5J5  O2   H12  single    0.850  0.020  0.980

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
 5J5  H11  O5   S1   111.82  3.000
 5J5  C13  S1   O6   110.08  3.000
 5J5  C13  S1   O4   109.15  3.000
 5J5  O6   S1   O4   118.78  3.000
 5J5  C13  S1   O5    98.13  3.000
 5J5  O4   S1   O5   109.50  3.000
 5J5  O6   S1   O5   109.22  3.000
 5J5  C12  C13  C2   121.11  3.000
 5J5  C12  C13  S1   117.58  3.000
 5J5  C2   C13  S1   121.10  3.000
 5J5  C3   C2   N    120.43  3.000
 5J5  C3   C2   C13  118.32  3.000
 5J5  N    C2   C13  121.24  3.000
 5J5  H1   N    C    118.26  3.000
 5J5  H1   N    C2   117.89  3.000
 5J5  C    N    C2   123.36  3.000
 5J5  O    C    C1   124.21  3.000
 5J5  O    C    N    123.96  3.000
 5J5  C1   C    N    111.82  3.000
 5J5  H3   C1   H2   108.05  3.000
 5J5  H3   C1   CL   108.72  3.000
 5J5  H2   C1   CL   108.55  3.000
 5J5  H3   C1   C    110.45  3.000
 5J5  H2   C1   C    109.60  3.000
 5J5  CL   C1   C    111.39  3.000
 5J5  H4   C12  C5   118.96  3.000
 5J5  H4   C12  C13  121.24  3.000
 5J5  C5   C12  C13  119.79  3.000
 5J5  N1   C5   C4   125.10  3.000
 5J5  N1   C5   C12  115.26  3.000
 5J5  C4   C5   C12  119.64  3.000
 5J5  H5   C4   C3   119.59  3.000
 5J5  H5   C4   C5   120.16  3.000
 5J5  C3   C4   C5   120.24  3.000
 5J5  H6   C3   C4   119.54  3.000
 5J5  H6   C3   C2   119.55  3.000
 5J5  C4   C3   C2   120.88  3.000
 5J5  N2   N1   C5   115.16  3.000
 5J5  C6   N2   N1   114.97  3.000
 5J5  C7   C6   C11  120.27  3.000
 5J5  C7   C6   N2   124.51  3.000
 5J5  C11  C6   N2   115.22  3.000
 5J5  H7   C11  C10  120.28  3.000
 5J5  H7   C11  C6   119.35  3.000
 5J5  C10  C11  C6   120.37  3.000
 5J5  H8   C10  C9   121.37  3.000
 5J5  H8   C10  C11  120.01  3.000
 5J5  C9   C10  C11  118.63  3.000
 5J5  C8   C9   S    119.08  3.000
 5J5  S    C9   C10  119.15  3.000
 5J5  C8   C9   C10  121.77  3.000
 5J5  O1   S    O2   109.37  3.000
 5J5  O2   S    O3   109.43  3.000
 5J5  O1   S    O3   118.81  3.000
 5J5  O2   S    C9    97.54  3.000
 5J5  O1   S    C9   109.78  3.000
 5J5  O3   S    C9   109.81  3.000
 5J5  H12  O2   S    111.74  3.000
 5J5  H9   C8   C7   119.69  3.000
 5J5  H9   C8   C9   121.09  3.000
 5J5  C7   C8   C9   119.22  3.000
 5J5  H10  C7   C8   119.85  3.000
 5J5  H10  C7   C6   120.40  3.000
 5J5  C8   C7   C6   119.75  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
 5J5  CONST_01  C4   C3   C2   C13    0.00   0.0  0
 5J5  CONST_02  C4   C5   C12  C13    0.00   0.0  0
 5J5  CONST_03  C5   C4   C3   C2     0.00   0.0  0
 5J5  CONST_04  C5   C12  C13  C2     0.00   0.0  0
 5J5  CONST_05  C3   C2   C13  C12    0.00   0.0  0
 5J5  CONST_06  C3   C4   C5   C12    0.00   0.0  0
 5J5  CONST_07  C9   C10  C11  C6     0.00   0.0  0
 5J5  CONST_08  C9   C8   C7   C6     0.00   0.0  0
 5J5  CONST_09  C8   C7   C6   C11    0.00   0.0  0
 5J5  CONST_10  C8   C9   C10  C11    0.00   0.0  0
 5J5  CONST_11  C7   C6   C11  C10    0.00   0.0  0
 5J5  CONST_12  C7   C8   C9   C10    0.00   0.0  0
 5J5  CONST_13  C3   C2   C13  S1   180.00   0.0  0
 5J5  CONST_14  C5   C12  C13  S1   180.00   0.0  0
 5J5  CONST_15  N1   C5   C12  C13  180.00   0.0  0
 5J5  CONST_16  C4   C3   C2   N    180.00   0.0  0
 5J5  CONST_17  C12  C13  C2   N    180.00   0.0  0
 5J5  CONST_18  N1   C5   C4   C3   180.00   0.0  0
 5J5  CONST_19  C10  C11  C6   N2   180.00   0.0  0
 5J5  CONST_20  C8   C7   C6   N2   180.00   0.0  0
 5J5  CONST_21  S    C9   C10  C11  180.00   0.0  0
 5J5  CONST_22  C7   C8   C9   S    180.00   0.0  0
 5J5  CONST_23  H6   C3   C2   C13  180.00   0.0  0
 5J5  CONST_24  H5   C4   C3   C2   180.00   0.0  0
 5J5  CONST_25  H4   C12  C13  C2   180.00   0.0  0
 5J5  CONST_26  H8   C10  C11  C6   180.00   0.0  0
 5J5  CONST_27  H9   C8   C7   C6   180.00   0.0  0
 5J5  CONST_28  H10  C7   C6   C11  180.00   0.0  0
 5J5  CONST_29  H7   C11  C10  C9   180.00   0.0  0
 5J5  CONST_30  N2   N1   C5   C12  180.00   0.0  0
 5J5  CONST_31  N2   N1   C5   C4     0.00   0.0  0
 5J5  CONST_32  C11  C6   N2   N1   180.00   0.0  0
 5J5  CONST_33  C7   C6   N2   N1     0.00   0.0  0
 5J5  CONST_37  C1   C    N    C2   180.00   0.0  0
 5J5  CONST_38  O    C    N    C2     0.00   0.0  0
 5J5  Var_01    C2   C13  S1   O5   -67.43  30.0  2
 5J5  Var_02    O3   S    C9   C10  -23.75  30.0  2
 5J5  Var_03    CL   C1   C    N    174.00  30.0  2

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
 5J5  plan-1  S1   0.020
 5J5  plan-1  C13  0.020
 5J5  plan-1  C2   0.020
 5J5  plan-1  N    0.020
 5J5  plan-1  C12  0.020
 5J5  plan-1  C5   0.020
 5J5  plan-1  C4   0.020
 5J5  plan-1  C3   0.020
 5J5  plan-1  N1   0.020
 5J5  plan-1  N2   0.020
 5J5  plan-1  C6   0.020
 5J5  plan-1  H4   0.020
 5J5  plan-1  H5   0.020
 5J5  plan-1  H6   0.020
 5J5  plan-2  N1   0.020
 5J5  plan-2  N2   0.020
 5J5  plan-2  C6   0.020
 5J5  plan-2  C11  0.020
 5J5  plan-2  C10  0.020
 5J5  plan-2  C9   0.020
 5J5  plan-2  S    0.020
 5J5  plan-2  C8   0.020
 5J5  plan-2  C7   0.020
 5J5  plan-2  H7   0.020
 5J5  plan-2  H8   0.020
 5J5  plan-2  H9   0.020
 5J5  plan-2  H10  0.020
 5J5  plan-3  C2   0.020
 5J5  plan-3  N    0.020
 5J5  plan-3  C    0.020
 5J5  plan-3  C1   0.020
 5J5  plan-3  O    0.020
 5J5  plan-3  H1   0.020

