# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 13:58:29 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: 5-[(E)-(2-amino-4-hydroxy-5-methylphenyl)diazenyl]-2,4-dimethylbenzenesulfonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(N=Nc2cc(c(C)cc2C)[S](O)(=O)=O)c(N)cc1O
#
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
 J28  J28  '5-[(E)-(2-amino-4-hydroxy-5-methylphenyl)diazenyl]-2,4-dimethylbenzenesulfonic acid'  ligand  40  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_J28
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
 J28  S     S  S     0   1.471   3.7714  -1.4600   0.2481
 J28  NB    N  N     0  -0.265  -1.2355  -0.1381  -0.0773
 J28  CG    C  CR6   0   0.162  -2.6074  -0.2540  -0.0199
 J28  CH    C  CR6   0   0.191   0.6556   1.0391   0.0417
 J28  CK    C  CR6   0   0.180   3.4704   1.2734  -0.0888
 J28  CN    C  CH3   0  -0.742   4.9540   1.4703  -0.1860
 J28  OT    O  OS    0  -0.713   4.4585  -1.1874   1.6700
 J28  CZ    C  CR6   0   0.341  -5.3572  -0.6489  -0.0102
 J28  OC1   O  OS    0  -0.641   4.8045  -1.5356  -0.7670
 J28  OC2   O  OS    0  -0.633   2.8623  -2.5812   0.3760
 J28  CD1   C  CR6   0   0.310  -3.1257  -1.5451  -0.2817
 J28  CD2   C  CR16  0  -0.326  -3.4899   0.8026   0.2556
 J28  CE1   C  CR16  0  -0.430  -4.5154  -1.7126  -0.2756
 J28  CE2   C  CR6   0  -0.017  -4.8538   0.6442   0.2711
 J28  CI1   C  CR16  0  -0.253   1.4652  -0.0864   0.1667
 J28  CI2   C  CR6   0   0.095   1.2445   2.2982  -0.1243
 J28  CJ1   C  CR6   0  -0.317   2.8418   0.0341   0.1025
 J28  CJ2   C  CR16  0  -0.344   2.6317   2.3773  -0.1902
 J28  HOH   H  HOH1  0   0.486  -7.1855  -0.1076   0.1801
 J28  HOT   H  H     0   0.505   5.2734  -1.7092   1.7740
 J28  HD2   H  HCR6  0   0.265  -3.0687   1.7792   0.4610
 J28  HE1   H  HCR6  0   0.269  -4.9407  -2.6878  -0.4814
 J28  HI1   H  HCR6  0   0.285   1.0014  -1.0501   0.3242
 J28  HJ2   H  HCR6  0   0.261   3.0856   3.3507  -0.3344
 J28  HNL   H  HNH2  0   0.388  -1.3404  -2.4097  -0.7051
 J28  HNLA  H  HNH2  0   0.393  -2.6873  -3.4151  -0.9523
 J28  HM    H  HCH3  0   0.251  -6.4179   1.5929   1.4351
 J28  HMA   H  HCH3  0   0.269  -5.2250   2.6924   0.7712
 J28  HMB   H  HCH3  0   0.252  -6.4481   2.0039  -0.2792
 J28  HN    H  HCH3  0   0.265   5.3661   0.9720  -1.0622
 J28  HNA   H  HCH3  0   0.258   5.1820   2.5307  -0.2678
 J28  HNB   H  HCH3  0   0.255   5.4794   1.0845   0.6874
 J28  HP    H  HCH3  0   0.254  -0.2872   3.6354   0.5772
 J28  HPA   H  HCH3  0   0.248   1.0359   4.4247  -0.2879
 J28  HPB   H  HCH3  0   0.255  -0.1889   3.5110  -1.1657
 J28  NA    N  N     0  -0.280  -0.7436   0.9936   0.0969
 J28  CP    C  CH3   0  -0.718   0.4099   3.5347  -0.2543
 J28  OH    O  OH1   0  -0.614  -6.6748  -0.8976  -0.0294
 J28  NL    N  NH2   0  -0.842  -2.3050  -2.6038  -0.4975
 J28  CM    C  CH3   0  -0.774  -5.7865   1.7836   0.5630

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
 J28  S    OT    single    1.603  0.020  1.603
 J28  S    OC1   double    1.450  0.020  1.450
 J28  S    OC2   double    1.449  0.020  1.449
 J28  S    CJ1   single    1.766  0.020  1.766
 J28  NA   NB    double    1.246  0.020  1.246
 J28  NA   CH    single    1.401  0.020  1.401
 J28  NB   CG    single    1.378  0.020  1.378
 J28  CG   CD1   aromatic  1.416  0.020  1.416
 J28  CG   CD2   aromatic  1.404  0.020  1.404
 J28  CH   CI1   aromatic  1.392  0.020  1.392
 J28  CH   CI2   aromatic  1.400  0.020  1.400
 J28  OH   CZ    single    1.341  0.020  1.341
 J28  OH   HOH   single    0.850  0.020  0.980
 J28  CK   CN    single    1.500  0.020  1.500
 J28  CK   CJ1   aromatic  1.403  0.020  1.403
 J28  CK   CJ2   aromatic  1.390  0.020  1.390
 J28  NL   CD1   single    1.357  0.020  1.357
 J28  NL   HNL   single    0.890  0.020  1.040
 J28  NL   HNLA  single    0.890  0.020  1.040
 J28  CM   CE2   single    1.501  0.020  1.501
 J28  CM   HM    single    0.970  0.020  1.090
 J28  CM   HMA   single    0.970  0.020  1.090
 J28  CM   HMB   single    0.970  0.020  1.090
 J28  CN   HN    single    0.970  0.020  1.090
 J28  CN   HNA   single    0.970  0.020  1.090
 J28  CN   HNB   single    0.970  0.020  1.090
 J28  CP   CI2   single    1.498  0.020  1.498
 J28  CP   HP    single    0.970  0.020  1.090
 J28  CP   HPA   single    0.970  0.020  1.090
 J28  CP   HPB   single    0.970  0.020  1.090
 J28  OT   HOT   single    0.850  0.020  0.980
 J28  CZ   CE1   aromatic  1.382  0.020  1.382
 J28  CZ   CE2   aromatic  1.416  0.020  1.416
 J28  CD1  CE1   aromatic  1.400  0.020  1.400
 J28  CD2  CE2   aromatic  1.373  0.020  1.373
 J28  CD2  HD2   single    0.930  0.020  1.080
 J28  CE1  HE1   single    0.930  0.020  1.080
 J28  CI1  CJ1   aromatic  1.383  0.020  1.383
 J28  CI1  HI1   single    0.930  0.020  1.080
 J28  CI2  CJ2   aromatic  1.391  0.020  1.391
 J28  CJ2  HJ2   single    0.930  0.020  1.080

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
 J28  CJ1   S    OC2  109.38  3.000
 J28  CJ1   S    OC1  111.19  3.000
 J28  OC2   S    OC1  117.93  3.000
 J28  CJ1   S    OT    98.91  3.000
 J28  OC2   S    OT   108.80  3.000
 J28  OC1   S    OT   108.93  3.000
 J28  CG    NB   NA   117.61  3.000
 J28  CD2   CG   CD1  119.50  3.000
 J28  CD2   CG   NB   124.80  3.000
 J28  CD1   CG   NB   115.69  3.000
 J28  CI2   CH   CI1  119.55  3.000
 J28  CI2   CH   NA   117.00  3.000
 J28  CI1   CH   NA   123.43  3.000
 J28  CJ2   CK   CJ1  116.18  3.000
 J28  CJ2   CK   CN   119.20  3.000
 J28  CJ1   CK   CN   124.62  3.000
 J28  HNB   CN   HNA  107.72  3.000
 J28  HNB   CN   HN   107.48  3.000
 J28  HNA   CN   HN   107.84  3.000
 J28  HNB   CN   CK   112.24  3.000
 J28  HNA   CN   CK   109.89  3.000
 J28  HN    CN   CK   111.50  3.000
 J28  HOT   OT   S    111.26  3.000
 J28  CE2   CZ   CE1  121.63  3.000
 J28  CE2   CZ   OH   121.44  3.000
 J28  CE1   CZ   OH   116.93  3.000
 J28  CE1   CD1  NL   120.52  3.000
 J28  CE1   CD1  CG   118.15  3.000
 J28  NL    CD1  CG   121.30  3.000
 J28  HD2   CD2  CE2  119.22  3.000
 J28  HD2   CD2  CG   118.12  3.000
 J28  CE2   CD2  CG   122.67  3.000
 J28  HE1   CE1  CD1  119.77  3.000
 J28  HE1   CE1  CZ   119.34  3.000
 J28  CD1   CE1  CZ   120.89  3.000
 J28  CD2   CE2  CZ   117.14  3.000
 J28  CD2   CE2  CM   122.13  3.000
 J28  CZ    CE2  CM   120.73  3.000
 J28  HI1   CI1  CJ1  120.75  3.000
 J28  HI1   CI1  CH   118.97  3.000
 J28  CJ1   CI1  CH   120.27  3.000
 J28  CJ2   CI2  CP   120.31  3.000
 J28  CJ2   CI2  CH   118.45  3.000
 J28  CP    CI2  CH   121.23  3.000
 J28  CI1   CJ1  CK   121.96  3.000
 J28  CI1   CJ1  S    116.51  3.000
 J28  CK    CJ1  S    121.53  3.000
 J28  HJ2   CJ2  CI2  118.37  3.000
 J28  HJ2   CJ2  CK   118.06  3.000
 J28  CI2   CJ2  CK   123.58  3.000
 J28  CH    NA   NB   114.72  3.000
 J28  HPB   CP   HPA  107.91  3.000
 J28  HPB   CP   HP   106.76  3.000
 J28  HPA   CP   HP   108.42  3.000
 J28  HPB   CP   CI2  111.13  3.000
 J28  HPA   CP   CI2  110.93  3.000
 J28  HP    CP   CI2  111.51  3.000
 J28  HOH   OH   CZ   111.44  3.000
 J28  HNLA  NL   HNL  115.28  3.000
 J28  HNLA  NL   CD1  118.13  3.000
 J28  HNL   NL   CD1  117.55  3.000
 J28  HMB   CM   HMA  106.93  3.000
 J28  HMB   CM   HM   107.46  3.000
 J28  HMA   CM   HM   106.92  3.000
 J28  HMB   CM   CE2  112.28  3.000
 J28  HMA   CM   CE2  110.52  3.000
 J28  HM    CM   CE2  112.43  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
 J28  CONST_01  CZ   CE1  CD1  CG     0.00   0.0  0
 J28  CONST_02  CZ   CE2  CD2  CG     0.00   0.0  0
 J28  CONST_03  CK   CJ1  CI1  CH     0.00   0.0  0
 J28  CONST_04  CK   CJ2  CI2  CH     0.00   0.0  0
 J28  CONST_05  CE2  CD2  CG   CD1    0.00   0.0  0
 J28  CONST_06  CE2  CZ   CE1  CD1    0.00   0.0  0
 J28  CONST_07  CE1  CD1  CG   CD2    0.00   0.0  0
 J28  CONST_08  CE1  CZ   CE2  CD2    0.00   0.0  0
 J28  CONST_09  CJ2  CI2  CH   CI1    0.00   0.0  0
 J28  CONST_10  CJ2  CK   CJ1  CI1    0.00   0.0  0
 J28  CONST_11  CJ1  CI1  CH   CI2    0.00   0.0  0
 J28  CONST_12  CJ1  CK   CJ2  CI2    0.00   0.0  0
 J28  CONST_13  CJ2  CK   CJ1  S    180.00   0.0  0
 J28  CONST_14  CH   CI1  CJ1  S    180.00   0.0  0
 J28  CONST_15  CJ1  CI1  CH   NA   180.00   0.0  0
 J28  CONST_16  CJ2  CI2  CH   NA   180.00   0.0  0
 J28  CONST_17  CE1  CD1  CG   NB   180.00   0.0  0
 J28  CONST_18  CE2  CD2  CG   NB   180.00   0.0  0
 J28  CONST_19  CM   CE2  CD2  CG   180.00   0.0  0
 J28  CONST_20  CD1  CE1  CZ   OH   180.00   0.0  0
 J28  CONST_21  CD2  CE2  CZ   OH   180.00   0.0  0
 J28  CONST_22  CP   CI2  CJ2  CK   180.00   0.0  0
 J28  CONST_23  CD2  CG   CD1  NL   180.00   0.0  0
 J28  CONST_24  CZ   CE1  CD1  NL   180.00   0.0  0
 J28  CONST_25  CE1  CZ   CE2  CM   180.00   0.0  0
 J28  CONST_26  CI1  CJ1  CK   CN   180.00   0.0  0
 J28  CONST_27  CI2  CJ2  CK   CN   180.00   0.0  0
 J28  CONST_28  CI1  CH   CI2  CP   180.00   0.0  0
 J28  CONST_29  HE1  CE1  CD1  CG   180.00   0.0  0
 J28  CONST_30  HJ2  CJ2  CI2  CH   180.00   0.0  0
 J28  CONST_31  HI1  CI1  CJ1  CK   180.00   0.0  0
 J28  CONST_32  HD2  CD2  CE2  CZ   180.00   0.0  0
 J28  CONST_33  CD1  CG   NB   NA   180.00   0.0  0
 J28  CONST_34  CD2  CG   NB   NA     0.00   0.0  0
 J28  Var_01    OT   S    CJ1  CK    68.95  30.0  3
 J28  Var_02    HP   CP   CI2  CH    54.09  30.0  2
 J28  Var_03    HM   CM   CE2  CZ    59.68  30.0  2
 J28  Var_04    HN   CN   CK   CJ1   64.21  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
 J28  plan-1  NB    0.020
 J28  plan-1  CG    0.020
 J28  plan-1  CH    0.020
 J28  plan-1  CZ    0.020
 J28  plan-1  CD1   0.020
 J28  plan-1  CD2   0.020
 J28  plan-1  CE1   0.020
 J28  plan-1  CE2   0.020
 J28  plan-1  HD2   0.020
 J28  plan-1  HE1   0.020
 J28  plan-1  NA    0.020
 J28  plan-1  OH    0.020
 J28  plan-1  NL    0.020
 J28  plan-1  CM    0.020
 J28  plan-2  S     0.020
 J28  plan-2  NB    0.020
 J28  plan-2  CH    0.020
 J28  plan-2  CK    0.020
 J28  plan-2  CN    0.020
 J28  plan-2  CI1   0.020
 J28  plan-2  CI2   0.020
 J28  plan-2  CJ1   0.020
 J28  plan-2  CJ2   0.020
 J28  plan-2  HI1   0.020
 J28  plan-2  HJ2   0.020
 J28  plan-2  NA    0.020
 J28  plan-2  CP    0.020
 J28  plan-3  CD1   0.020
 J28  plan-3  HNL   0.020
 J28  plan-3  HNLA  0.020
 J28  plan-3  NL    0.020

