# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 23:26:59 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: 2-(5-acetamido-2-oxidanyl-phenyl)pyridine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)Nc1ccc(O)c(c1)c2cc(ccn2)C(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
 S2X  S2X  '2-(5-acetamido-2-oxidanyl-phenyl)pyridine-4-carboxylic acid'  ligand  31  20  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_S2X
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
 S2X  O3   O  O      0  -0.482   2.3079   2.7409   0.0244
 S2X  C1   C  C      0   0.512   3.4122   2.2395  -0.1179
 S2X  C    C  CH3    0  -0.781   4.6585   3.0850  -0.2040
 S2X  N    N  NH1    0  -0.740   3.6300   0.9073  -0.2190
 S2X  C2   C  CR6    0   0.388   2.7131  -0.1540  -0.1750
 S2X  C7   C  CR16   0  -0.437   1.3395  -0.0074  -0.0656
 S2X  C6   C  CR6    0  -0.071   0.4778  -1.1116  -0.0296
 S2X  C5   C  CR6    0   0.335   1.0292  -2.4068  -0.1074
 S2X  O2   O  OH1    0  -0.644   0.2978  -3.5243  -0.0794
 S2X  C4   C  CR16   0  -0.336   2.4148  -2.5460  -0.2199
 S2X  C3   C  CR16   0  -0.339   3.2411  -1.4463  -0.2526
 S2X  C8   C  CR6    0   0.403  -0.9823  -0.9061   0.0838
 S2X  N1   N  N      0  -0.574  -1.7401  -2.0096   0.1065
 S2X  C12  C  CR16   0  -0.023  -3.0596  -1.9085   0.2030
 S2X  C11  C  CR16   0  -0.391  -3.7135  -0.6950   0.2829
 S2X  C10  C  CR6    0   0.027  -2.9544   0.4709   0.2624
 S2X  C9   C  CR16   0  -0.397  -1.5779   0.3548   0.1621
 S2X  C13  C  C      0   0.416  -3.6176   1.8480   0.3455
 S2X  O1   O  O      0  -0.579  -2.8536   2.8275   0.3060
 S2X  O    O  OC    -1  -0.581  -4.8564   1.8500   0.4432
 S2X  HC1  H  HCH3   0   0.270   4.7075   3.7404   0.6650
 S2X  HC2  H  HCH3   0   0.253   5.5814   2.5105  -0.2557
 S2X  HC3  H  HCH3   0   0.271   4.6002   3.7204  -1.0880
 S2X  H    H  HNH1   0   0.413   4.5901   0.6239  -0.3354
 S2X  H7   H  HCR6   0   0.283   0.9282   0.9850  -0.0061
 S2X  H3   H  HCR6   0   0.274   4.3120  -1.5901  -0.3391
 S2X  H4   H  HCR6   0   0.265   2.8371  -3.5411  -0.2815
 S2X  H9   H  HCR6   0   0.260  -0.9870   1.2588   0.1453
 S2X  H12  H  HCR6   0   0.272  -3.6114  -2.8407   0.2165
 S2X  H11  H  HCR6   0   0.263  -4.7905  -0.6582   0.3591
 S2X  H21  H  HOH1   0   0.472  -0.6551  -3.2387  -0.0046

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
 S2X  O3   C1   double    1.221  0.020  1.221
 S2X  C1   C    single    1.508  0.020  1.508
 S2X  C1   N    single    1.354  0.020  1.354
 S2X  N    C2   single    1.403  0.020  1.403
 S2X  C2   C7   aromatic  1.386  0.020  1.386
 S2X  C2   C3   aromatic  1.398  0.020  1.398
 S2X  C7   C6   aromatic  1.401  0.020  1.401
 S2X  C6   C5   aromatic  1.410  0.020  1.410
 S2X  C6   C8   single    1.479  0.020  1.479
 S2X  C5   O2   single    1.336  0.020  1.336
 S2X  C5   C4   aromatic  1.397  0.020  1.397
 S2X  C4   C3   aromatic  1.376  0.020  1.376
 S2X  C8   N1   aromatic  1.339  0.020  1.339
 S2X  C8   C9   aromatic  1.397  0.020  1.397
 S2X  N1   C12  aromatic  1.327  0.020  1.327
 S2X  C12  C11  aromatic  1.381  0.020  1.381
 S2X  C11  C10  aromatic  1.391  0.020  1.391
 S2X  C10  C9   aromatic  1.385  0.020  1.385
 S2X  C10  C13  single    1.531  0.020  1.531
 S2X  C13  O1   deloc     1.243  0.020  1.243
 S2X  C13  O    deloc     1.243  0.020  1.243
 S2X  O2   H21  single    0.850  0.020  0.980
 S2X  C    HC1  single    0.970  0.020  1.090
 S2X  C    HC2  single    0.970  0.020  1.090
 S2X  C    HC3  single    0.970  0.020  1.090
 S2X  N    H    single    0.860  0.020  1.020
 S2X  C7   H7   single    0.930  0.020  1.080
 S2X  C3   H3   single    0.930  0.020  1.080
 S2X  C4   H4   single    0.930  0.020  1.080
 S2X  C9   H9   single    0.930  0.020  1.080
 S2X  C12  H12  single    0.930  0.020  1.080
 S2X  C11  H11  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
 S2X  N    C1   C    114.49  3.000
 S2X  N    C1   O3   123.93  3.000
 S2X  C    C1   O3   121.58  3.000
 S2X  HC3  C    HC2  108.33  3.000
 S2X  HC3  C    HC1  107.37  3.000
 S2X  HC2  C    HC1  108.50  3.000
 S2X  HC3  C    C1   109.19  3.000
 S2X  HC2  C    C1   114.05  3.000
 S2X  HC1  C    C1   109.20  3.000
 S2X  H    N    C2   114.42  3.000
 S2X  H    N    C1   116.02  3.000
 S2X  C2   N    C1   129.56  3.000
 S2X  C3   C2   C7   118.46  3.000
 S2X  C3   C2   N    116.78  3.000
 S2X  C7   C2   N    124.76  3.000
 S2X  H7   C7   C6   119.37  3.000
 S2X  H7   C7   C2   118.75  3.000
 S2X  C6   C7   C2   121.89  3.000
 S2X  C8   C6   C5   121.20  3.000
 S2X  C8   C6   C7   119.98  3.000
 S2X  C5   C6   C7   118.82  3.000
 S2X  C4   C5   O2   117.48  3.000
 S2X  C4   C5   C6   118.93  3.000
 S2X  O2   C5   C6   123.59  3.000
 S2X  H21  O2   C5   106.56  3.000
 S2X  H4   C4   C3   119.93  3.000
 S2X  H4   C4   C5   118.88  3.000
 S2X  C3   C4   C5   121.19  3.000
 S2X  H3   C3   C4   119.29  3.000
 S2X  H3   C3   C2   120.00  3.000
 S2X  C4   C3   C2   120.71  3.000
 S2X  C9   C8   N1   120.12  3.000
 S2X  C9   C8   C6   123.42  3.000
 S2X  N1   C8   C6   116.46  3.000
 S2X  C12  N1   C8   120.08  3.000
 S2X  H12  C12  C11  120.95  3.000
 S2X  H12  C12  N1   116.23  3.000
 S2X  C11  C12  N1   122.83  3.000
 S2X  H11  C11  C10  121.08  3.000
 S2X  H11  C11  C12  120.41  3.000
 S2X  C10  C11  C12  118.50  3.000
 S2X  C13  C10  C9   120.66  3.000
 S2X  C13  C10  C11  121.11  3.000
 S2X  C9   C10  C11  118.23  3.000
 S2X  H9   C9   C10  118.34  3.000
 S2X  H9   C9   C8   121.43  3.000
 S2X  C10  C9   C8   120.23  3.000
 S2X  O    C13  O1   127.88  3.000
 S2X  O    C13  C10  115.95  3.000
 S2X  O1   C13  C10  116.17  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
 S2X  CONST_01  C5   C6   C7   C2      0.00   0.0  0
 S2X  CONST_02  C8   C6   C7   C2    180.00   0.0  0
 S2X  CONST_03  C5   C4   C3   C2      0.00   0.0  0
 S2X  CONST_04  C4   C3   C2   C7      0.00   0.0  0
 S2X  CONST_05  C4   C5   C6   C7      0.00   0.0  0
 S2X  CONST_06  N1   C8   C6   C7    180.00   0.0  0
 S2X  CONST_07  C9   C8   C6   C7      0.00   0.0  0
 S2X  CONST_08  C3   C2   C7   C6      0.00   0.0  0
 S2X  CONST_09  C3   C4   C5   C6      0.00   0.0  0
 S2X  CONST_10  C12  N1   C8   C6    180.00   0.0  0
 S2X  CONST_11  C10  C9   C8   C6    180.00   0.0  0
 S2X  CONST_12  N1   C8   C6   C5      0.00   0.0  0
 S2X  CONST_13  C9   C8   C6   C5    180.00   0.0  0
 S2X  CONST_14  C8   C6   C5   C4    180.00   0.0  0
 S2X  CONST_15  C11  C12  N1   C8      0.00   0.0  0
 S2X  CONST_16  C11  C10  C9   C8      0.00   0.0  0
 S2X  CONST_17  C10  C9   C8   N1      0.00   0.0  0
 S2X  CONST_18  C10  C11  C12  N1      0.00   0.0  0
 S2X  CONST_19  C9   C8   N1   C12     0.00   0.0  0
 S2X  CONST_20  C9   C10  C11  C12     0.00   0.0  0
 S2X  CONST_21  C6   C7   C2   N     180.00   0.0  0
 S2X  CONST_22  C4   C3   C2   N     180.00   0.0  0
 S2X  CONST_23  O2   C5   C6   C7    180.00   0.0  0
 S2X  CONST_24  C8   C6   C5   O2      0.00   0.0  0
 S2X  CONST_25  C3   C4   C5   O2    180.00   0.0  0
 S2X  CONST_26  C13  C10  C9   C8    180.00   0.0  0
 S2X  CONST_27  C13  C10  C11  C12   180.00   0.0  0
 S2X  CONST_28  H4   C4   C3   C2    180.00   0.0  0
 S2X  CONST_29  H3   C3   C2   C7    180.00   0.0  0
 S2X  CONST_30  H9   C9   C8   C6      0.00   0.0  0
 S2X  CONST_31  H7   C7   C6   C5    180.00   0.0  0
 S2X  CONST_32  H12  C12  N1   C8    180.00   0.0  0
 S2X  CONST_33  H11  C11  C12  N1    180.00   0.0  0
 S2X  CONST_34  C7   C2   N    C1      0.00   0.0  0
 S2X  CONST_35  C3   C2   N    C1    180.00   0.0  0
 S2X  CONST_36  H    N    C2   C7    180.00   0.0  0
 S2X  CONST_37  C2   N    C1   O3      0.00   0.0  0
 S2X  CONST_38  C2   N    C1   C     180.00   0.0  0
 S2X  Var_01    O1   C13  C10  C11  -179.31  30.0  2
 S2X  Var_02    HC1  C    C1   O3     54.13  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
 S2X  plan-1  N    0.020
 S2X  plan-1  C2   0.020
 S2X  plan-1  C7   0.020
 S2X  plan-1  C6   0.020
 S2X  plan-1  C5   0.020
 S2X  plan-1  O2   0.020
 S2X  plan-1  C4   0.020
 S2X  plan-1  C3   0.020
 S2X  plan-1  C8   0.020
 S2X  plan-1  H7   0.020
 S2X  plan-1  H3   0.020
 S2X  plan-1  H4   0.020
 S2X  plan-2  C6   0.020
 S2X  plan-2  C8   0.020
 S2X  plan-2  N1   0.020
 S2X  plan-2  C12  0.020
 S2X  plan-2  C11  0.020
 S2X  plan-2  C10  0.020
 S2X  plan-2  C9   0.020
 S2X  plan-2  C13  0.020
 S2X  plan-2  H9   0.020
 S2X  plan-2  H12  0.020
 S2X  plan-2  H11  0.020
 S2X  plan-3  O3   0.020
 S2X  plan-3  C1   0.020
 S2X  plan-3  C    0.020
 S2X  plan-3  N    0.020
 S2X  plan-3  C2   0.020
 S2X  plan-3  H    0.020
 S2X  plan-4  C10  0.020
 S2X  plan-4  C13  0.020
 S2X  plan-4  O1   0.020
 S2X  plan-4  O    0.020

