# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 26 14:17:45 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  32  20  .  2022-03-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  -0.475   2.2909   2.7522   0.0546
 S2X  C1   C  C     0   0.499   3.3988   2.2620  -0.0867
 S2X  C    C  CH3   0  -0.787   4.6568   3.0927  -0.1496
 S2X  N    N  NH1   0  -0.733   3.6250   0.9287  -0.1920
 S2X  C2   C  CR6   0   0.395   2.7146  -0.1362  -0.1630
 S2X  C7   C  CR16  0  -0.439   1.3402   0.0029  -0.0672
 S2X  C6   C  CR6   0  -0.066   0.4831  -1.1066  -0.0497
 S2X  C5   C  CR6   0   0.338   1.0397  -2.3991  -0.1243
 S2X  O2   O  OH1   0  -0.639   0.3188  -3.5234  -0.1084
 S2X  C4   C  CR16  0  -0.333   2.4275  -2.5306  -0.2223
 S2X  C3   C  CR16  0  -0.337   3.2481  -1.4274  -0.2414
 S2X  C8   C  CR6   0   0.409  -0.9762  -0.9064   0.0404
 S2X  N1   N  N     0  -0.561  -1.7359  -2.0065   0.0830
 S2X  C12  C  CR16  0  -0.012  -3.0546  -1.9147   0.1631
 S2X  C11  C  CR16  0  -0.368  -3.7215  -0.7052   0.2075
 S2X  C10  C  CR6   0   0.052  -2.9539   0.4540   0.1610
 S2X  C9   C  CR16  0  -0.367  -1.5765   0.3551   0.0761
 S2X  C13  C  C     0   0.552  -3.5599   1.8188   0.1940
 S2X  O1   O  O     0  -0.420  -2.9107   2.8308   0.1208
 S2X  O    O  OH1   0  -0.585  -4.8743   1.7862   0.3114
 S2X  HC1  H  HCH3  0   0.266   4.4061   4.1494  -0.1721
 S2X  HC2  H  HCH3  0   0.272   5.2843   2.9028   0.7228
 S2X  HC3  H  HCH3  0   0.267   5.2473   2.8520  -1.0342
 S2X  H    H  HNH1  0   0.416   4.5888   0.6536  -0.3045
 S2X  H7   H  HCR6  0   0.282   0.9264   0.9941  -0.0032
 S2X  H3   H  HCR6  0   0.276   4.3205  -1.5664  -0.3162
 S2X  H4   H  HCR6  0   0.269   2.8552  -3.5233  -0.2833
 S2X  H9   H  HCR6  0   0.281  -0.9870   1.2587   0.0360
 S2X  H12  H  HCR6  0   0.288  -3.6024  -2.8479   0.1930
 S2X  H11  H  HCR6  0   0.287  -4.7990  -0.6882   0.2720
 S2X  HA   H  HOH1  0   0.495  -5.2323   2.6869   0.3302
 S2X  H21  H  HOH1  0   0.476  -0.6340  -3.2581  -0.0283

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    1.220  0.020  1.220
 S2X  C1   C    single    1.509  0.020  1.509
 S2X  C1   N    single    1.357  0.020  1.357
 S2X  N    C2   single    1.401  0.020  1.401
 S2X  C2   C7   aromatic  1.385  0.020  1.385
 S2X  C2   C3   aromatic  1.399  0.020  1.399
 S2X  C7   C6   aromatic  1.402  0.020  1.402
 S2X  C6   C5   aromatic  1.409  0.020  1.409
 S2X  C6   C8   single    1.476  0.020  1.476
 S2X  C5   O2   single    1.336  0.020  1.336
 S2X  C5   C4   aromatic  1.397  0.020  1.397
 S2X  C4   C3   aromatic  1.375  0.020  1.375
 S2X  C8   N1   aromatic  1.338  0.020  1.338
 S2X  C8   C9   aromatic  1.398  0.020  1.398
 S2X  N1   C12  aromatic  1.324  0.020  1.324
 S2X  C12  C11  aromatic  1.382  0.020  1.382
 S2X  C11  C10  aromatic  1.391  0.020  1.391
 S2X  C10  C9   aromatic  1.383  0.020  1.383
 S2X  C10  C13  single    1.494  0.020  1.494
 S2X  C13  O1   double    1.205  0.020  1.205
 S2X  C13  O    single    1.320  0.020  1.320
 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
 S2X  O    HA   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
 S2X  N    C1   C    113.51  3.000
 S2X  N    C1   O3   123.74  3.000
 S2X  C    C1   O3   122.75  3.000
 S2X  HC3  C    HC2  107.38  3.000
 S2X  HC3  C    HC1  108.84  3.000
 S2X  HC2  C    HC1  108.58  3.000
 S2X  HC3  C    C1   111.33  3.000
 S2X  HC2  C    C1   110.50  3.000
 S2X  HC1  C    C1   110.12  3.000
 S2X  H    N    C2   114.58  3.000
 S2X  H    N    C1   115.85  3.000
 S2X  C2   N    C1   129.57  3.000
 S2X  C3   C2   C7   118.36  3.000
 S2X  C3   C2   N    116.90  3.000
 S2X  C7   C2   N    124.74  3.000
 S2X  H7   C7   C6   119.54  3.000
 S2X  H7   C7   C2   118.58  3.000
 S2X  C6   C7   C2   121.88  3.000
 S2X  C8   C6   C5   121.21  3.000
 S2X  C8   C6   C7   119.86  3.000
 S2X  C5   C6   C7   118.92  3.000
 S2X  C4   C5   O2   117.24  3.000
 S2X  C4   C5   C6   118.83  3.000
 S2X  O2   C5   C6   123.93  3.000
 S2X  H21  O2   C5   107.11  3.000
 S2X  H4   C4   C3   119.94  3.000
 S2X  H4   C4   C5   118.85  3.000
 S2X  C3   C4   C5   121.21  3.000
 S2X  H3   C3   C4   119.24  3.000
 S2X  H3   C3   C2   119.96  3.000
 S2X  C4   C3   C2   120.80  3.000
 S2X  C9   C8   N1   119.84  3.000
 S2X  C9   C8   C6   123.28  3.000
 S2X  N1   C8   C6   116.87  3.000
 S2X  C12  N1   C8   120.69  3.000
 S2X  H12  C12  C11  120.62  3.000
 S2X  H12  C12  N1   116.48  3.000
 S2X  C11  C12  N1   122.90  3.000
 S2X  H11  C11  C10  122.65  3.000
 S2X  H11  C11  C12  119.83  3.000
 S2X  C10  C11  C12  117.52  3.000
 S2X  C13  C10  C9   118.07  3.000
 S2X  C13  C10  C11  122.47  3.000
 S2X  C9   C10  C11  119.46  3.000
 S2X  H9   C9   C10  119.09  3.000
 S2X  H9   C9   C8   121.33  3.000
 S2X  C10  C9   C8   119.58  3.000
 S2X  O    C13  O1   124.25  3.000
 S2X  O    C13  C10  112.54  3.000
 S2X  O1   C13  C10  123.21  3.000
 S2X  HA   O    C13  110.27  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  CONST_39  HA   O    C13  C10   180.00   0.0  0
 S2X  Var_01    O1   C13  C10  C11  -178.08  30.0  2
 S2X  Var_02    HC1  C    C1   O3     -6.77  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
 S2X  plan-4  HA   0.020

