# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 18:22:51 2022
#   Inital geometry file: a 58 line input string
#   Ligand name: 2-(3-nitropyridin-2-yl)sulfanylethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CSc1ncccc1[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
 U2Q  U2Q  "2-[(3-Nitro-2-pyridyl)thio]acetic acid"  ligand  19  14  .  2022-08-11  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_U2Q
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
 U2Q  N12  N  N      1   0.333  1.5746  -4.0105  5.4424
 U2Q  C01  C  CR16   0  -0.175  1.4799  -6.3318  6.1266
 U2Q  C02  C  CR16   0  -0.334  2.1015  -7.5015  6.5051
 U2Q  C03  C  CR16   0  -0.031  3.4871  -7.4932  6.5749
 U2Q  C05  C  CR6    0   0.072  3.6620  -5.2881  5.9335
 U2Q  C07  C  CH2    0  -0.694  6.3527  -4.6811  5.8759
 U2Q  C08  C  C      0   0.437  7.4212  -3.6014  5.5921
 U2Q  C11  C  CR6    0   0.205  2.2552  -5.2168  5.8373
 U2Q  N04  N  N      0  -0.412  4.2288  -6.4351  6.3018
 U2Q  O09  O  O      0  -0.589  7.0048  -2.4876  5.2249
 U2Q  O10  O  OC    -1  -0.596  8.5949  -3.9675  5.7630
 U2Q  O13  O  O     -1  -0.383  0.3668  -4.0254  5.3634
 U2Q  O14  O  O      0  -0.378  2.2505  -3.0336  5.2067
 U2Q  H1   H  HCR6   0   0.312  0.4030  -6.2820  6.0560
 U2Q  H2   H  HCR6   0   0.287  1.5348  -8.3904  6.7393
 U2Q  H3   H  HCR6   0   0.284  4.0261  -8.3870  6.8679
 U2Q  H4   H  HCH2   0   0.275  6.4997  -5.5433  5.2246
 U2Q  H5   H  HCH2   0   0.274  6.4343  -5.0370  6.9035
 U2Q  S06  S  S2     0   0.113  4.7248  -3.9412  5.5890

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
 U2Q  O13  N12  single    1.210  0.020  1.210
 U2Q  O14  N12  double    1.211  0.020  1.211
 U2Q  O09  C08  deloc     1.244  0.020  1.244
 U2Q  C08  O10  deloc     1.241  0.020  1.241
 U2Q  C08  C07  single    1.545  0.020  1.545
 U2Q  S06  C07  single    1.811  0.020  1.811
 U2Q  S06  C05  single    1.750  0.020  1.750
 U2Q  N12  C11  single    1.440  0.020  1.440
 U2Q  C11  C05  aromatic  1.412  0.020  1.412
 U2Q  C11  C01  aromatic  1.389  0.020  1.389
 U2Q  C05  N04  aromatic  1.331  0.020  1.331
 U2Q  C01  C02  aromatic  1.378  0.020  1.378
 U2Q  N04  C03  aromatic  1.321  0.020  1.321
 U2Q  C02  C03  aromatic  1.387  0.020  1.387
 U2Q  C01  H1   single    0.930  0.020  1.080
 U2Q  C02  H2   single    0.930  0.020  1.080
 U2Q  C03  H3   single    0.930  0.020  1.080
 U2Q  C07  H4   single    0.970  0.020  1.090
 U2Q  C07  H5   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
 U2Q  O14  N12  O13  123.65  3.000
 U2Q  O14  N12  C11  117.73  3.000
 U2Q  O13  N12  C11  118.62  3.000
 U2Q  H1   C01  C11  120.39  3.000
 U2Q  H1   C01  C02  120.45  3.000
 U2Q  C11  C01  C02  119.16  3.000
 U2Q  H2   C02  C03  121.20  3.000
 U2Q  H2   C02  C01  121.45  3.000
 U2Q  C03  C02  C01  117.35  3.000
 U2Q  H3   C03  N04  115.93  3.000
 U2Q  H3   C03  C02  120.34  3.000
 U2Q  N04  C03  C02  123.73  3.000
 U2Q  S06  C05  N04  117.32  3.000
 U2Q  N04  C05  C11  119.11  3.000
 U2Q  S06  C05  C11  123.56  3.000
 U2Q  H5   C07  H4   107.14  3.000
 U2Q  H5   C07  S06  110.48  3.000
 U2Q  H4   C07  S06  110.46  3.000
 U2Q  H5   C07  C08  110.44  3.000
 U2Q  H4   C07  C08  110.46  3.000
 U2Q  S06  C07  C08  107.87  3.000
 U2Q  O10  C08  O09  128.38  3.000
 U2Q  O10  C08  C07  114.99  3.000
 U2Q  O09  C08  C07  116.63  3.000
 U2Q  C05  C11  C01  120.10  3.000
 U2Q  C01  C11  N12  117.77  3.000
 U2Q  C05  C11  N12  122.13  3.000
 U2Q  C05  N04  C03  120.55  3.000
 U2Q  C07  S06  C05  101.55  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
 U2Q  CONST_01  N04  C05  C11  C01     0.00   0.0  0
 U2Q  CONST_02  N04  C03  C02  C01     0.00   0.0  0
 U2Q  CONST_03  C05  C11  C01  C02     0.00   0.0  0
 U2Q  CONST_04  C05  N04  C03  C02     0.00   0.0  0
 U2Q  CONST_05  C11  C05  N04  C03     0.00   0.0  0
 U2Q  CONST_06  C11  C01  C02  C03     0.00   0.0  0
 U2Q  CONST_07  N04  C05  C11  N12   180.00   0.0  0
 U2Q  CONST_08  C02  C01  C11  N12   180.00   0.0  0
 U2Q  CONST_09  S06  C05  C11  C01   180.00   0.0  0
 U2Q  CONST_10  S06  C05  N04  C03   180.00   0.0  0
 U2Q  CONST_11  H3   C03  C02  C01   180.00   0.0  0
 U2Q  CONST_12  H1   C01  C02  C03   180.00   0.0  0
 U2Q  CONST_13  H1   C01  C11  C05   180.00   0.0  0
 U2Q  CONST_14  H3   C03  N04  C05   180.00   0.0  0
 U2Q  CONST_15  H2   C02  C01  C11   180.00   0.0  0
 U2Q  CONST_16  H2   C02  C03  N04   180.00   0.0  0
 U2Q  CONST_17  O13  N12  C11  C01     0.00   0.0  0
 U2Q  CONST_18  O14  N12  C11  C01   180.00   0.0  0
 U2Q  CONST_19  O13  N12  C11  C05   180.00   0.0  0
 U2Q  CONST_20  O14  N12  C11  C05     0.00   0.0  0
 U2Q  Var_01    C11  C05  S06  C07  -179.38  30.0  2
 U2Q  Var_02    N04  C05  S06  C07     0.46  30.0  2
 U2Q  Var_03    C08  C07  S06  C05   179.36  30.0  3
 U2Q  Var_04    H4   C07  S06  C05    58.54  30.0  3
 U2Q  Var_05    H5   C07  S06  C05   -59.83  30.0  3
 U2Q  Var_06    S06  C07  C08  O09    -0.74  30.0  3
 U2Q  Var_07    S06  C07  C08  O10   179.29  30.0  3
 U2Q  Var_08    H4   C07  C08  O09   120.08  30.0  3
 U2Q  Var_09    H5   C07  C08  O09  -121.57  30.0  3
 U2Q  Var_10    H4   C07  C08  O10   -59.88  30.0  3
 U2Q  Var_11    H5   C07  C08  O10    58.46  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
 U2Q  plan-1  N12  0.020
 U2Q  plan-1  C01  0.020
 U2Q  plan-1  C02  0.020
 U2Q  plan-1  C03  0.020
 U2Q  plan-1  C05  0.020
 U2Q  plan-1  C11  0.020
 U2Q  plan-1  N04  0.020
 U2Q  plan-1  H1   0.020
 U2Q  plan-1  H2   0.020
 U2Q  plan-1  H3   0.020
 U2Q  plan-1  S06  0.020
 U2Q  plan-2  N12  0.020
 U2Q  plan-2  C11  0.020
 U2Q  plan-2  O13  0.020
 U2Q  plan-2  O14  0.020
 U2Q  plan-3  C07  0.020
 U2Q  plan-3  C08  0.020
 U2Q  plan-3  O09  0.020
 U2Q  plan-3  O10  0.020

