# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 01:34:53 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: N-[6-[[2,3-bis(oxidanyl)phenyl]carbonylamino]hexyl]-2,3-bis(oxidanyl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1cccc(C(=O)NCCCCCCNC(=O)c2cccc(O)c2O)c1O
#
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
 PXJ  PXJ  N-[6-[[2,3-bis(oxidanyl)phenyl]carbonylamino]hexyl]-2,3-bis(oxidanyl)benzamide  ligand  52  28  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_PXJ
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
 PXJ  C1    C  CR16  0  -0.372   -9.1508   1.5450  -0.0631
 PXJ  C2    C  CR6   0   0.285   -9.1827   0.1672   0.0119
 PXJ  C3    C  CR6   0   0.284   -7.9819  -0.5667  -0.0397
 PXJ  C4    C  CR6   0  -0.178   -6.7606   0.1144  -0.1409
 PXJ  C5    C  CR16  0  -0.327   -6.7563   1.5139  -0.2306
 PXJ  C6    C  CR16  0  -0.261   -7.9369   2.2199  -0.1916
 PXJ  C8    C  C     0   0.627   -5.5179  -0.6980  -0.1597
 PXJ  O9    O  O     0  -0.546   -5.5743  -1.9345  -0.2680
 PXJ  N10   N  NH1   0  -0.662   -4.3467  -0.0734  -0.0535
 PXJ  C11   C  CH2   0  -0.238   -3.0778  -0.7771  -0.0471
 PXJ  C12   C  CH2   0  -0.478   -1.9235   0.2110  -0.0720
 PXJ  C13   C  CH2   0  -0.419   -0.5750  -0.4964  -0.0603
 PXJ  C14   C  CH2   0  -0.419    0.5969   0.4767  -0.0671
 PXJ  C15   C  CH2   0  -0.474    1.9455  -0.2304  -0.0611
 PXJ  C16   C  CH2   0  -0.241    3.1001   0.7577  -0.0537
 PXJ  N17   N  NH1   0  -0.663    4.3695   0.0554  -0.0667
 PXJ  C18   C  C     0   0.628    5.5299   0.6470   0.2102
 PXJ  O19   O  O     0  -0.546    5.5795   1.8560   0.4926
 PXJ  C20   C  CR6   0  -0.179    6.7700  -0.1681   0.1721
 PXJ  C21   C  CR6   0   0.284    7.9949   0.5048   0.2868
 PXJ  C22   C  CR6   0   0.284    9.1968  -0.2266   0.2250
 PXJ  C23   C  CR16  0  -0.372    9.1608  -1.5983   0.0775
 PXJ  C24   C  CR16  0  -0.260    7.9412  -2.2698  -0.0091
 PXJ  C25   C  CR16  0  -0.327    6.7609  -1.5641   0.0376
 PXJ  O26   O  OH1   0  -0.631   -8.0797  -1.8950   0.0178
 PXJ  O27   O  OH1   0  -0.627  -10.3144  -0.5557   0.1297
 PXJ  O28   O  OH1   0  -0.631    8.0958   1.8237   0.4525
 PXJ  O29   O  OH1   0  -0.627   10.3334   0.4910   0.3272
 PXJ  H1    H  HCR6  0   0.278  -10.0781   2.1060  -0.0296
 PXJ  H5    H  HCR6  0   0.251   -5.8318   2.0615  -0.3563
 PXJ  H6    H  HCR6  0   0.263   -7.9296   3.2984  -0.2653
 PXJ  HN10  H  HNH1  0   0.414   -4.3263   0.9112   0.1532
 PXJ  H11   H  HCH2  0   0.237   -3.0047  -1.4134   0.8402
 PXJ  H11A  H  HCH2  0   0.241   -3.0241  -1.4346  -0.9171
 PXJ  H12   H  HCH2  0   0.235   -2.0014   0.8422  -0.9627
 PXJ  H12A  H  HCH2  0   0.232   -1.9944   0.8782   0.7938
 PXJ  H13   H  HCH2  0   0.221   -0.5064  -1.1402   0.8228
 PXJ  H13A  H  HCH2  0   0.221   -0.5020  -1.1591  -0.9289
 PXJ  H14   H  HCH2  0   0.221    0.5272   1.1243  -0.9474
 PXJ  H14A  H  HCH2  0   0.221    0.5258   1.1360   0.8043
 PXJ  H15   H  HCH2  0   0.234    2.0195  -0.8806   0.8161
 PXJ  H15A  H  HCH2  0   0.231    2.0219  -0.8788  -0.9405
 PXJ  H16   H  HCH2  0   0.237    3.0276   1.4258  -0.9175
 PXJ  H16A  H  HCH2  0   0.242    3.0467   1.3828   0.8392
 PXJ  HN17  H  HNH1  0   0.414    4.3634  -0.8918  -0.4072
 PXJ  H23   H  HCR6  0   0.278   10.0881  -2.1583   0.0353
 PXJ  H24   H  HCR6  0   0.263    7.9290  -3.3463  -0.1071
 PXJ  H25   H  HCR6  0   0.250    5.8311  -2.1148  -0.0134
 PXJ  HO26  H  HOH1  0   0.476   -7.1559  -2.2381  -0.0959
 PXJ  HO27  H  HOH1  0   0.476  -11.0796   0.0294   0.1531
 PXJ  HO28  H  HOH1  0   0.476    7.1644   2.1568   0.5304
 PXJ  HO29  H  HOH1  0   0.476   11.0987  -0.0918   0.2697

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
 PXJ  C1   C2    aromatic  1.380  0.020  1.380
 PXJ  C1   C6    aromatic  1.395  0.020  1.395
 PXJ  C2   C3    aromatic  1.408  0.020  1.408
 PXJ  C2   O27   single    1.348  0.020  1.348
 PXJ  C3   C4    aromatic  1.402  0.020  1.402
 PXJ  C3   O26   single    1.333  0.020  1.333
 PXJ  C4   C5    aromatic  1.402  0.020  1.402
 PXJ  C4   C8    single    1.485  0.020  1.485
 PXJ  C5   C6    aromatic  1.376  0.020  1.376
 PXJ  C8   O9    double    1.242  0.020  1.242
 PXJ  C8   N10   single    1.332  0.020  1.332
 PXJ  N10  C11   single    1.451  0.020  1.451
 PXJ  C11  C12   single    1.520  0.020  1.520
 PXJ  C12  C13   single    1.523  0.020  1.523
 PXJ  C13  C14   single    1.523  0.020  1.523
 PXJ  C14  C15   single    1.523  0.020  1.523
 PXJ  C15  C16   single    1.520  0.020  1.520
 PXJ  C16  N17   single    1.451  0.020  1.451
 PXJ  N17  C18   single    1.332  0.020  1.332
 PXJ  C18  O19   double    1.243  0.020  1.243
 PXJ  C18  C20   single    1.485  0.020  1.485
 PXJ  C20  C21   aromatic  1.402  0.020  1.402
 PXJ  C20  C25   aromatic  1.402  0.020  1.402
 PXJ  C21  C22   aromatic  1.408  0.020  1.408
 PXJ  C21  O28   single    1.333  0.020  1.333
 PXJ  C22  C23   aromatic  1.380  0.020  1.380
 PXJ  C22  O29   single    1.348  0.020  1.348
 PXJ  C23  C24   aromatic  1.395  0.020  1.395
 PXJ  C24  C25   aromatic  1.376  0.020  1.376
 PXJ  C1   H1    single    0.930  0.020  1.080
 PXJ  C5   H5    single    0.930  0.020  1.080
 PXJ  C6   H6    single    0.930  0.020  1.080
 PXJ  N10  HN10  single    0.860  0.020  1.020
 PXJ  C11  H11   single    0.970  0.020  1.090
 PXJ  C11  H11A  single    0.970  0.020  1.090
 PXJ  C12  H12   single    0.970  0.020  1.090
 PXJ  C12  H12A  single    0.970  0.020  1.090
 PXJ  C13  H13   single    0.970  0.020  1.090
 PXJ  C13  H13A  single    0.970  0.020  1.090
 PXJ  C14  H14   single    0.970  0.020  1.090
 PXJ  C14  H14A  single    0.970  0.020  1.090
 PXJ  C15  H15   single    0.970  0.020  1.090
 PXJ  C15  H15A  single    0.970  0.020  1.090
 PXJ  C16  H16   single    0.970  0.020  1.090
 PXJ  C16  H16A  single    0.970  0.020  1.090
 PXJ  N17  HN17  single    0.860  0.020  1.020
 PXJ  C23  H23   single    0.930  0.020  1.080
 PXJ  C24  H24   single    0.930  0.020  1.080
 PXJ  C25  H25   single    0.930  0.020  1.080
 PXJ  O26  HO26  single    0.850  0.020  0.980
 PXJ  O27  HO27  single    0.850  0.020  0.980
 PXJ  O28  HO28  single    0.850  0.020  0.980
 PXJ  O29  HO29  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
 PXJ  H1    C1   C6   119.79  3.000
 PXJ  H1    C1   C2   119.67  3.000
 PXJ  C6    C1   C2   120.54  3.000
 PXJ  O27   C2   C3   116.08  3.000
 PXJ  O27   C2   C1   124.02  3.000
 PXJ  C3    C2   C1   119.90  3.000
 PXJ  O26   C3   C4   123.43  3.000
 PXJ  O26   C3   C2   117.07  3.000
 PXJ  C4    C3   C2   119.49  3.000
 PXJ  C8    C4   C5   122.87  3.000
 PXJ  C8    C4   C3   117.66  3.000
 PXJ  C5    C4   C3   119.47  3.000
 PXJ  H5    C5   C6   118.47  3.000
 PXJ  H5    C5   C4   121.01  3.000
 PXJ  C6    C5   C4   120.50  3.000
 PXJ  H6    C6   C5   120.27  3.000
 PXJ  H6    C6   C1   119.66  3.000
 PXJ  C5    C6   C1   120.06  3.000
 PXJ  N10   C8   O9   120.90  3.000
 PXJ  N10   C8   C4   118.59  3.000
 PXJ  O9    C8   C4   120.51  3.000
 PXJ  HN10  N10  C11  117.13  3.000
 PXJ  HN10  N10  C8   119.55  3.000
 PXJ  C11   N10  C8   122.82  3.000
 PXJ  H11A  C11  H11  107.01  3.000
 PXJ  H11A  C11  C12  109.94  3.000
 PXJ  H11   C11  C12  109.92  3.000
 PXJ  H11A  C11  N10  109.36  3.000
 PXJ  H11   C11  N10  110.12  3.000
 PXJ  C12   C11  N10  110.42  3.000
 PXJ  H12A  C12  H12  106.70  3.000
 PXJ  H12A  C12  C13  109.52  3.000
 PXJ  H12   C12  C13  109.71  3.000
 PXJ  H12A  C12  C11  109.50  3.000
 PXJ  H12   C12  C11  109.53  3.000
 PXJ  C13   C12  C11  111.75  3.000
 PXJ  H13A  C13  H13  106.24  3.000
 PXJ  H13A  C13  C14  109.38  3.000
 PXJ  H13   C13  C14  109.33  3.000
 PXJ  H13A  C13  C12  109.51  3.000
 PXJ  H13   C13  C12  109.56  3.000
 PXJ  C14   C13  C12  112.62  3.000
 PXJ  H14A  C14  H14  106.22  3.000
 PXJ  H14A  C14  C15  109.51  3.000
 PXJ  H14   C14  C15  109.53  3.000
 PXJ  H14A  C14  C13  109.33  3.000
 PXJ  H14   C14  C13  109.42  3.000
 PXJ  C15   C14  C13  112.63  3.000
 PXJ  H15A  C15  H15  106.69  3.000
 PXJ  H15A  C15  C16  109.62  3.000
 PXJ  H15   C15  C16  109.33  3.000
 PXJ  H15A  C15  C14  109.48  3.000
 PXJ  H15   C15  C14  109.81  3.000
 PXJ  C16   C15  C14  111.78  3.000
 PXJ  H16A  C16  H16  107.03  3.000
 PXJ  H16A  C16  N17  109.12  3.000
 PXJ  H16   C16  N17  110.27  3.000
 PXJ  H16A  C16  C15  109.83  3.000
 PXJ  H16   C16  C15  110.04  3.000
 PXJ  N17   C16  C15  110.49  3.000
 PXJ  HN17  N17  C18  119.58  3.000
 PXJ  HN17  N17  C16  116.95  3.000
 PXJ  C18   N17  C16  123.06  3.000
 PXJ  C20   C18  O19  120.45  3.000
 PXJ  C20   C18  N17  118.60  3.000
 PXJ  O19   C18  N17  120.95  3.000
 PXJ  C25   C20  C21  119.42  3.000
 PXJ  C25   C20  C18  122.93  3.000
 PXJ  C21   C20  C18  117.65  3.000
 PXJ  O28   C21  C22  117.04  3.000
 PXJ  O28   C21  C20  123.44  3.000
 PXJ  C22   C21  C20  119.51  3.000
 PXJ  O29   C22  C23  124.00  3.000
 PXJ  O29   C22  C21  116.09  3.000
 PXJ  C23   C22  C21  119.91  3.000
 PXJ  H23   C23  C24  119.79  3.000
 PXJ  H23   C23  C22  119.69  3.000
 PXJ  C24   C23  C22  120.53  3.000
 PXJ  H24   C24  C25  120.28  3.000
 PXJ  H24   C24  C23  119.66  3.000
 PXJ  C25   C24  C23  120.06  3.000
 PXJ  H25   C25  C24  118.33  3.000
 PXJ  H25   C25  C20  121.12  3.000
 PXJ  C24   C25  C20  120.54  3.000
 PXJ  HO26  O26  C3   105.74  3.000
 PXJ  HO27  O27  C2   110.07  3.000
 PXJ  HO28  O28  C21  105.71  3.000
 PXJ  HO29  O29  C22  110.07  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
 PXJ  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 PXJ  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 PXJ  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 PXJ  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 PXJ  CONST_05  C6    C1   C2   C3      0.00   0.0  0
 PXJ  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 PXJ  CONST_07  C23   C22  C21  C20     0.00   0.0  0
 PXJ  CONST_08  C23   C24  C25  C20     0.00   0.0  0
 PXJ  CONST_09  C24   C25  C20  C21     0.00   0.0  0
 PXJ  CONST_10  C24   C23  C22  C21     0.00   0.0  0
 PXJ  CONST_11  C25   C20  C21  C22     0.00   0.0  0
 PXJ  CONST_12  C25   C24  C23  C22     0.00   0.0  0
 PXJ  CONST_13  O26   C3   C2   C1    180.00   0.0  0
 PXJ  CONST_14  C8    C4   C3   C2    180.00   0.0  0
 PXJ  CONST_15  O27   C2   C3   C4    180.00   0.0  0
 PXJ  CONST_16  O26   C3   C4   C5    180.00   0.0  0
 PXJ  CONST_17  O27   C2   C1   C6    180.00   0.0  0
 PXJ  CONST_18  C8    C4   C5   C6    180.00   0.0  0
 PXJ  CONST_19  C22   C21  C20  C18   180.00   0.0  0
 PXJ  CONST_20  C24   C25  C20  C18   180.00   0.0  0
 PXJ  CONST_21  O29   C22  C21  C20   180.00   0.0  0
 PXJ  CONST_22  O28   C21  C22  C23   180.00   0.0  0
 PXJ  CONST_23  O29   C22  C23  C24   180.00   0.0  0
 PXJ  CONST_24  O28   C21  C20  C25   180.00   0.0  0
 PXJ  CONST_25  H5    C5   C6   C1    180.00   0.0  0
 PXJ  CONST_26  H6    C6   C1   C2    180.00   0.0  0
 PXJ  CONST_27  H1    C1   C2   C3    180.00   0.0  0
 PXJ  CONST_28  H24   C24  C25  C20   180.00   0.0  0
 PXJ  CONST_29  H25   C25  C20  C21   180.00   0.0  0
 PXJ  CONST_30  H23   C23  C22  C21   180.00   0.0  0
 PXJ  CONST_31  C11   N10  C8   C4    180.00   0.0  0
 PXJ  CONST_32  C20   C18  N17  C16   180.00   0.0  0
 PXJ  CONST_33  HN10  N10  C8   C4      0.00   0.0  0
 PXJ  CONST_34  HN17  N17  C18  C20     0.00   0.0  0
 PXJ  CONST_35  C11   N10  C8   O9      0.00   0.0  0
 PXJ  CONST_36  O19   C18  N17  C16     0.00   0.0  0
 PXJ  Var_01    O9    C8   C4   C3      9.67  30.0  2
 PXJ  Var_02    C21   C20  C18  N17   171.54  30.0  2
 PXJ  Var_03    C12   C11  N10  C8    173.62  30.0  3
 PXJ  Var_04    C13   C12  C11  N10   179.77  30.0  3
 PXJ  Var_05    C14   C13  C12  C11  -179.27  30.0  3
 PXJ  Var_06    C15   C14  C13  C12  -179.77  30.0  3
 PXJ  Var_07    C16   C15  C14  C13  -179.42  30.0  3
 PXJ  Var_08    N17   C16  C15  C14  -179.21  30.0  3
 PXJ  Var_09    C18   N17  C16  C15  -165.77  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
 PXJ  plan-1  C1    0.020
 PXJ  plan-1  C2    0.020
 PXJ  plan-1  C3    0.020
 PXJ  plan-1  C4    0.020
 PXJ  plan-1  C5    0.020
 PXJ  plan-1  C6    0.020
 PXJ  plan-1  C8    0.020
 PXJ  plan-1  O26   0.020
 PXJ  plan-1  O27   0.020
 PXJ  plan-1  H1    0.020
 PXJ  plan-1  H5    0.020
 PXJ  plan-1  H6    0.020
 PXJ  plan-2  C18   0.020
 PXJ  plan-2  C20   0.020
 PXJ  plan-2  C21   0.020
 PXJ  plan-2  C22   0.020
 PXJ  plan-2  C23   0.020
 PXJ  plan-2  C24   0.020
 PXJ  plan-2  C25   0.020
 PXJ  plan-2  O28   0.020
 PXJ  plan-2  O29   0.020
 PXJ  plan-2  H23   0.020
 PXJ  plan-2  H24   0.020
 PXJ  plan-2  H25   0.020
 PXJ  plan-3  C4    0.020
 PXJ  plan-3  C8    0.020
 PXJ  plan-3  O9    0.020
 PXJ  plan-3  N10   0.020
 PXJ  plan-3  C11   0.020
 PXJ  plan-3  HN10  0.020
 PXJ  plan-4  C16   0.020
 PXJ  plan-4  N17   0.020
 PXJ  plan-4  C18   0.020
 PXJ  plan-4  O19   0.020
 PXJ  plan-4  C20   0.020
 PXJ  plan-4  HN17  0.020

