# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 17:25:32 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: 2-nitro-5-sulfanylbenzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cc(S)ccc1[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
 MNB  MNB  '2-nitro-5-sulfanylbenzoic acid'  ligand  17  13  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MNB
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
 MNB  C6   C  CR16   0  -0.303   0.9140  -0.0485  -1.0547
 MNB  C1   C  CR6    0  -0.048   0.5881   0.0340   0.2911
 MNB  C2   C  CR6    0   0.186  -0.7552  -0.0843   0.6286
 MNB  C3   C  CR16   0  -0.237  -1.7499  -0.2487  -0.3192
 MNB  C4   C  CR16   0  -0.271  -1.4048  -0.3203  -1.6574
 MNB  C5   C  CR6    0  -0.096  -0.0667  -0.2216  -2.0297
 MNB  S5   S  S2     0  -0.145   0.4569  -0.3008  -3.7075
 MNB  C10  C  C      0   0.408   1.6740   0.3812   1.3107
 MNB  O12  O  OC    -1  -0.579   2.8017  -0.0847   1.0897
 MNB  O11  O  O      0  -0.585   1.3104   1.1338   2.2287
 MNB  N7   N  N      1   0.342  -1.1590  -0.1131   2.0246
 MNB  O9   O  O      0  -0.384  -2.0424   0.6365   2.3695
 MNB  O8   O  O     -1  -0.379  -0.6284  -0.9231   2.7436
 MNB  HC6  H  HCR6   0   0.274   1.9544   0.0431  -1.3415
 MNB  HC3  H  HCR6   0   0.292  -2.7871  -0.3451  -0.0270
 MNB  HC4  H  HCR6   0   0.278  -2.1788  -0.4555  -2.4005
 MNB  HS5  H  HSH1   0   0.249  -0.7479  -0.4504  -4.2675

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
 MNB  C6   C1   aromatic  1.387  0.020  1.387
 MNB  C6   C5   aromatic  1.394  0.020  1.394
 MNB  C6   HC6  single    0.930  0.020  1.080
 MNB  C1   C2   aromatic  1.390  0.020  1.390
 MNB  C1   C10  single    1.529  0.020  1.529
 MNB  C2   C3   aromatic  1.384  0.020  1.384
 MNB  C2   N7   single    1.453  0.020  1.453
 MNB  C3   C4   aromatic  1.384  0.020  1.384
 MNB  C3   HC3  single    0.930  0.020  1.080
 MNB  C4   C5   aromatic  1.392  0.020  1.392
 MNB  C4   HC4  single    0.930  0.020  1.080
 MNB  C5   S5   single    1.759  0.020  1.759
 MNB  S5   HS5  single    1.200  0.020  1.300
 MNB  C10  O12  deloc     1.240  0.020  1.240
 MNB  C10  O11  deloc     1.242  0.020  1.242
 MNB  N7   O9   double    1.209  0.020  1.209
 MNB  N7   O8   single    1.206  0.020  1.206

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
 MNB  HC6  C6   C5   120.07  3.000
 MNB  HC6  C6   C1   118.53  3.000
 MNB  C5   C6   C1   121.39  3.000
 MNB  C10  C1   C2   122.93  3.000
 MNB  C10  C1   C6   119.57  3.000
 MNB  C2   C1   C6   117.23  3.000
 MNB  N7   C2   C3   117.12  3.000
 MNB  N7   C2   C1   120.22  3.000
 MNB  C3   C2   C1   122.58  3.000
 MNB  HC3  C3   C4   119.71  3.000
 MNB  HC3  C3   C2   120.98  3.000
 MNB  C4   C3   C2   119.29  3.000
 MNB  HC4  C4   C5   120.86  3.000
 MNB  HC4  C4   C3   119.50  3.000
 MNB  C5   C4   C3   119.64  3.000
 MNB  S5   C5   C4   122.53  3.000
 MNB  S5   C5   C6   117.60  3.000
 MNB  C4   C5   C6   119.86  3.000
 MNB  HS5  S5   C5    97.84  3.000
 MNB  O11  C10  O12  128.75  3.000
 MNB  O11  C10  C1   115.00  3.000
 MNB  O12  C10  C1   116.21  3.000
 MNB  O8   N7   O9   124.60  3.000
 MNB  O8   N7   C2   117.62  3.000
 MNB  O9   N7   C2   117.70  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
 MNB  CONST_01  C3   C2   C1  C6    0.00   0.0  0
 MNB  CONST_02  C3   C4   C5  C6    0.00   0.0  0
 MNB  CONST_03  C4   C5   C6  C1    0.00   0.0  0
 MNB  CONST_04  C4   C3   C2  C1    0.00   0.0  0
 MNB  CONST_05  C5   C6   C1  C2    0.00   0.0  0
 MNB  CONST_06  C5   C4   C3  C2    0.00   0.0  0
 MNB  CONST_07  N7   C2   C1  C6  180.00   0.0  0
 MNB  CONST_08  S5   C5   C6  C1  180.00   0.0  0
 MNB  CONST_09  C10  C1   C2  C3  180.00   0.0  0
 MNB  CONST_10  S5   C5   C4  C3  180.00   0.0  0
 MNB  CONST_11  N7   C2   C3  C4  180.00   0.0  0
 MNB  CONST_12  C10  C1   C6  C5  180.00   0.0  0
 MNB  CONST_13  HC4  C4   C5  C6  180.00   0.0  0
 MNB  CONST_14  HC3  C3   C2  C1  180.00   0.0  0
 MNB  CONST_15  HC6  C6   C1  C2  180.00   0.0  0
 MNB  Var_01    O12  C10  C1  C6  -36.56  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
 MNB  plan-1  C6   0.020
 MNB  plan-1  C1   0.020
 MNB  plan-1  C2   0.020
 MNB  plan-1  C3   0.020
 MNB  plan-1  C4   0.020
 MNB  plan-1  C5   0.020
 MNB  plan-1  S5   0.020
 MNB  plan-1  C10  0.020
 MNB  plan-1  N7   0.020
 MNB  plan-1  HC6  0.020
 MNB  plan-1  HC3  0.020
 MNB  plan-1  HC4  0.020
 MNB  plan-2  C2   0.020
 MNB  plan-2  N7   0.020
 MNB  plan-2  O9   0.020
 MNB  plan-2  O8   0.020
 MNB  plan-3  C1   0.020
 MNB  plan-3  C10  0.020
 MNB  plan-3  O12  0.020
 MNB  plan-3  O11  0.020

