# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 11:42:44 2020
#   Inital geometry file: a 180 line input string
#   Ligand name: N,N'-{[(2-{[(2,3-dihydroxyphenyl)carbonyl]amino}ethyl)imino]diethane-2,1-diyl}bis(1-hydroxy-6-oxo-1,6-dihydropyridine-2-carboxamide)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ON1C(=O)C=CC=C1C(=O)NCCN(CCNC(=O)C2=CC=CC(=O)N2O)CCNC(=O)c3cccc(O)c3O
#
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
 QED  QED  N,N'-{[(2-{[(2,3-dihydroxyphenyl)carbonyl]amino}ethyl)imino]diethane-2,1-diyl}bis(1-hydroxy-6-oxo-1,6-dihydropyridine-2-carboxamide)  ligand  68  40  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QED
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
 QED  C1    C  CR6   0  -0.173  -5.8024   2.0696   0.4156
 QED  C2    C  CR6   0   0.251  -6.7909   1.5505   1.2619
 QED  C3    C  CR6   0   0.307  -7.9287   2.3192   1.5676
 QED  C4    C  CR16  0  -0.343  -8.0747   3.5769   1.0183
 QED  C5    C  CR16  0  -0.259  -7.1008   4.0875   0.1614
 QED  C6    C  CR16  0  -0.329  -5.9793   3.3453  -0.1371
 QED  O7    O  OH1   0  -0.649  -6.7264   0.3380   1.8211
 QED  O8    O  OH1   0  -0.634  -8.8809   1.8376   2.3909
 QED  C9    C  C     0   0.635  -4.6121   1.2224   0.1535
 QED  O10   O  O     0  -0.544  -4.5638   0.0597   0.5893
 QED  N11   N  NH1   0  -0.655  -3.6077   1.7347  -0.5573
 QED  C12   C  CH2   0  -0.299  -2.3842   1.0132  -0.8346
 QED  C13   C  CH2   0  -0.302  -1.3722   1.1260   0.3028
 QED  N14   N  NT    0  -0.432  -0.1703   0.3733  -0.0061
 QED  C15   C  CH2   0  -0.298   1.0431   0.9981   0.4860
 QED  C16   C  CH2   0  -0.300   1.5028   2.0982  -0.4668
 QED  N17   N  NH1   0  -0.617   2.6870   2.7795   0.0109
 QED  C18   C  C     0   0.509   3.9221   2.3190  -0.2009
 QED  O19   O  O     0  -0.460   4.2008   1.3195  -0.8381
 QED  C21   C  CH2   0  -0.335  -0.2797  -1.0300   0.3393
 QED  C22   C  CH2   0  -0.251   0.5400  -1.8870  -0.6145
 QED  N23   N  NH1   0  -0.629   0.4688  -3.2775  -0.2126
 QED  C24   C  C     0   0.520   0.9953  -4.2609  -0.9424
 QED  N25   N  NR6   0  -0.261   6.0027   3.6122  -0.2810
 QED  C26   C  CR6   0   0.545   7.1110   4.3034   0.1871
 QED  C27   C  CR16  0  -0.451   7.1341   4.4746   1.6017
 QED  C28   C  CR16  0  -0.103   6.1230   4.0021   2.3852
 QED  C29   C  CR16  0  -0.403   5.0266   3.3224   1.8221
 QED  O30   O  OH1   0  -0.528   5.9284   3.4673  -1.6250
 QED  O31   O  O     0  -0.531   7.9312   4.6941  -0.6483
 QED  O32   O  O     0  -0.464   1.5915  -4.1085  -1.9936
 QED  C33   C  CR6   0   0.278   0.7332  -5.6337  -0.3856
 QED  N34   N  NR6   0  -0.260   1.7789  -6.4544  -0.1753
 QED  C35   C  CR6   0   0.545   1.7074  -7.7717   0.2546
 QED  C36   C  CR16  0  -0.450   0.3783  -8.2456   0.4549
 QED  C37   C  CR16  0  -0.104  -0.6979  -7.4336   0.2494
 QED  C38   C  CR16  0  -0.402  -0.5314  -6.1017  -0.1734
 QED  O39   O  OH1   0  -0.528   3.0281  -5.9575  -0.3359
 QED  O40   O  O     0  -0.531   2.7716  -8.3734   0.4243
 QED  C41   C  CR6   0   0.286   4.9945   3.1338   0.4706
 QED  H4    H  HCR6  0   0.272  -8.9550   4.1605   1.2575
 QED  H5    H  HCR6  0   0.262  -7.2320   5.0699  -0.2704
 QED  H6    H  HCR6  0   0.251  -5.2513   3.7697  -0.8151
 QED  HO7   H  HOH1  0   0.483  -5.8917  -0.0792   1.4748
 QED  HO8   H  HOH1  0   0.474  -8.6484   0.9493   2.6879
 QED  HN11  H  HNH1  0   0.417  -3.6359   2.7016  -0.8324
 QED  H12   H  HCH2  0   0.251  -2.6239  -0.0299  -1.0423
 QED  H12A  H  HCH2  0   0.260  -1.9514   1.4308  -1.7431
 QED  H13   H  HCH2  0   0.246  -1.1158   2.1795   0.4309
 QED  H13A  H  HCH2  0   0.230  -1.8262   0.8032   1.2503
 QED  H15   H  HCH2  0   0.224   0.9193   1.4061   1.5000
 QED  H15A  H  HCH2  0   0.247   1.8335   0.2477   0.5503
 QED  H16   H  HCH2  0   0.253   1.6992   1.6701  -1.4498
 QED  H16A  H  HCH2  0   0.261   0.7275   2.8544  -0.5915
 QED  HN17  H  HNH1  0   0.420   2.5657   3.6229   0.5492
 QED  H21   H  HCH2  0   0.228   0.0242  -1.2226   1.3803
 QED  H21A  H  HCH2  0   0.255  -1.3263  -1.3350   0.2641
 QED  H22   H  HCH2  0   0.250   0.1485  -1.7732  -1.6269
 QED  H22A  H  HCH2  0   0.243   1.5834  -1.5590  -0.6321
 QED  HN23  H  HNH1  0   0.418   0.0616  -3.5031   0.6823
 QED  H27   H  HCR6  0   0.288   7.9788   4.9989   2.0258
 QED  H28   H  HCR6  0   0.288   6.1618   4.1490   3.4562
 QED  H29   H  HCR6  0   0.292   4.2331   2.9286   2.4395
 QED  HO30  H  HOH1  0   0.484   6.7423   3.9207  -1.9304
 QED  H36   H  HCR6  0   0.288   0.2581  -9.2682   0.7838
 QED  H37   H  HCR6  0   0.288  -1.6962  -7.8162   0.4134
 QED  H38   H  HCR6  0   0.295  -1.3803  -5.4594  -0.3540
 QED  HO39  H  HOH1  0   0.484   3.5913  -6.7148  -0.0712

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
 QED  C2   C1    aromatic  1.401  0.020  1.401
 QED  C1   C9    single    1.484  0.020  1.484
 QED  C1   C6    aromatic  1.402  0.020  1.402
 QED  O7   C2    single    1.337  0.020  1.337
 QED  C3   C2    aromatic  1.407  0.020  1.407
 QED  O8   C3    single    1.348  0.020  1.348
 QED  C3   C4    aromatic  1.380  0.020  1.380
 QED  C4   C5    aromatic  1.394  0.020  1.394
 QED  C4   H4    single    0.930  0.020  1.080
 QED  C5   C6    aromatic  1.378  0.020  1.378
 QED  C5   H5    single    0.930  0.020  1.080
 QED  C6   H6    single    0.930  0.020  1.080
 QED  O7   HO7   single    0.850  0.020  0.980
 QED  O8   HO8   single    0.850  0.020  0.980
 QED  C9   O10   double    1.243  0.020  1.243
 QED  C9   N11   single    1.333  0.020  1.333
 QED  N11  C12   single    1.447  0.020  1.447
 QED  N11  HN11  single    0.860  0.020  1.020
 QED  C12  C13   single    1.527  0.020  1.527
 QED  C12  H12   single    0.970  0.020  1.090
 QED  C12  H12A  single    0.970  0.020  1.090
 QED  N14  C13   single    1.451  0.020  1.451
 QED  C13  H13   single    0.970  0.020  1.090
 QED  C13  H13A  single    0.970  0.020  1.090
 QED  C15  N14   single    1.451  0.020  1.451
 QED  N14  C21   single    1.449  0.020  1.449
 QED  C16  C15   single    1.526  0.020  1.526
 QED  C15  H15   single    0.970  0.020  1.090
 QED  C15  H15A  single    0.970  0.020  1.090
 QED  N17  C16   single    1.447  0.020  1.447
 QED  C16  H16   single    0.970  0.020  1.090
 QED  C16  H16A  single    0.970  0.020  1.090
 QED  C18  N17   single    1.335  0.020  1.335
 QED  N17  HN17  single    0.860  0.020  1.020
 QED  O19  C18   double    1.218  0.020  1.218
 QED  C41  C18   single    1.505  0.020  1.505
 QED  C21  C22   single    1.522  0.020  1.522
 QED  C21  H21   single    0.970  0.020  1.090
 QED  C21  H21A  single    0.970  0.020  1.090
 QED  N23  C22   single    1.449  0.020  1.449
 QED  C22  H22   single    0.970  0.020  1.090
 QED  C22  H22A  single    0.970  0.020  1.090
 QED  N23  C24   single    1.333  0.020  1.333
 QED  N23  HN23  single    0.860  0.020  1.020
 QED  C33  C24   single    1.504  0.020  1.504
 QED  C24  O32   double    1.218  0.020  1.218
 QED  C26  N25   single    1.387  0.020  1.387
 QED  C41  N25   single    1.345  0.020  1.345
 QED  N25  O30   single    1.354  0.020  1.354
 QED  C27  C26   single    1.425  0.020  1.425
 QED  C26  O31   double    1.234  0.020  1.234
 QED  C28  C27   double    1.364  0.020  1.364
 QED  C27  H27   single    0.930  0.020  1.080
 QED  C28  C29   single    1.408  0.020  1.408
 QED  C28  H28   single    0.930  0.020  1.080
 QED  C29  C41   double    1.365  0.020  1.365
 QED  C29  H29   single    0.930  0.020  1.080
 QED  O30  HO30  single    0.850  0.020  0.980
 QED  N34  C33   single    1.346  0.020  1.346
 QED  C38  C33   double    1.365  0.020  1.365
 QED  C35  N34   single    1.388  0.020  1.388
 QED  N34  O39   single    1.354  0.020  1.354
 QED  O40  C35   double    1.234  0.020  1.234
 QED  C36  C35   single    1.425  0.020  1.425
 QED  C36  C37   double    1.364  0.020  1.364
 QED  C36  H36   single    0.930  0.020  1.080
 QED  C37  C38   single    1.407  0.020  1.407
 QED  C37  H37   single    0.930  0.020  1.080
 QED  C38  H38   single    0.930  0.020  1.080
 QED  O39  HO39  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
 QED  C9    C1   C6   123.44  3.000
 QED  C6    C1   C2   119.10  3.000
 QED  C9    C1   C2   117.45  3.000
 QED  O7    C2   C3   116.34  3.000
 QED  C3    C2   C1   119.97  3.000
 QED  O7    C2   C1   123.69  3.000
 QED  O8    C3   C4   119.60  3.000
 QED  C4    C3   C2   119.80  3.000
 QED  O8    C3   C2   120.59  3.000
 QED  H4    C4   C5   120.41  3.000
 QED  H4    C4   C3   119.28  3.000
 QED  C5    C4   C3   120.30  3.000
 QED  H5    C5   C6   120.12  3.000
 QED  H5    C5   C4   119.58  3.000
 QED  C6    C5   C4   120.30  3.000
 QED  H6    C6   C5   118.19  3.000
 QED  H6    C6   C1   121.29  3.000
 QED  C5    C6   C1   120.51  3.000
 QED  HO7   O7   C2   105.97  3.000
 QED  HO8   O8   C3   110.28  3.000
 QED  N11   C9   O10  121.15  3.000
 QED  N11   C9   C1   118.63  3.000
 QED  O10   C9   C1   120.22  3.000
 QED  HN11  N11  C12  116.79  3.000
 QED  HN11  N11  C9   119.62  3.000
 QED  C12   N11  C9   123.21  3.000
 QED  H12A  C12  H12  107.17  3.000
 QED  H12A  C12  C13  109.24  3.000
 QED  H12   C12  C13  111.00  3.000
 QED  H12A  C12  N11  107.73  3.000
 QED  H12   C12  N11  109.13  3.000
 QED  C13   C12  N11  112.38  3.000
 QED  H13A  C13  H13  106.22  3.000
 QED  H13A  C13  N14  111.92  3.000
 QED  H13   C13  N14  109.33  3.000
 QED  H13A  C13  C12  110.28  3.000
 QED  H13   C13  C12  108.32  3.000
 QED  N14   C13  C12  110.61  3.000
 QED  C21   N14  C15  113.53  3.000
 QED  C21   N14  C13  112.89  3.000
 QED  C15   N14  C13  113.39  3.000
 QED  H15A  C15  H15  106.39  3.000
 QED  H15A  C15  C16  108.31  3.000
 QED  H15   C15  C16  110.00  3.000
 QED  H15A  C15  N14  109.24  3.000
 QED  H15   C15  N14  112.22  3.000
 QED  C16   C15  N14  110.52  3.000
 QED  H16A  C16  H16  107.31  3.000
 QED  H16A  C16  N17  107.04  3.000
 QED  H16   C16  N17  109.58  3.000
 QED  H16A  C16  C15  110.93  3.000
 QED  H16   C16  C15  109.52  3.000
 QED  N17   C16  C15  112.32  3.000
 QED  HN17  N17  C18  119.00  3.000
 QED  HN17  N17  C16  118.14  3.000
 QED  C18   N17  C16  122.83  3.000
 QED  C41   C18  O19  120.99  3.000
 QED  C41   C18  N17  113.68  3.000
 QED  O19   C18  N17  125.30  3.000
 QED  H21A  C21  H21  106.29  3.000
 QED  H21A  C21  C22  108.40  3.000
 QED  H21   C21  C22  110.20  3.000
 QED  H21A  C21  N14  109.03  3.000
 QED  H21   C21  N14  111.94  3.000
 QED  C22   C21  N14  110.81  3.000
 QED  H22A  C22  H22  107.22  3.000
 QED  H22A  C22  N23  109.82  3.000
 QED  H22   C22  N23  109.86  3.000
 QED  H22A  C22  C21  110.79  3.000
 QED  H22   C22  C21  109.23  3.000
 QED  N23   C22  C21  109.88  3.000
 QED  HN23  N23  C24  118.69  3.000
 QED  HN23  N23  C22  118.72  3.000
 QED  C24   N23  C22  122.45  3.000
 QED  C33   C24  O32  121.25  3.000
 QED  O32   C24  N23  124.99  3.000
 QED  C33   C24  N23  113.69  3.000
 QED  C41   N25  O30  118.38  3.000
 QED  O30   N25  C26  115.60  3.000
 QED  C41   N25  C26  125.96  3.000
 QED  O31   C26  C27  128.54  3.000
 QED  O31   C26  N25  117.40  3.000
 QED  C27   C26  N25  114.06  3.000
 QED  H27   C27  C28  121.48  3.000
 QED  H27   C27  C26  117.42  3.000
 QED  C28   C27  C26  121.10  3.000
 QED  H28   C28  C29  119.31  3.000
 QED  H28   C28  C27  119.68  3.000
 QED  C29   C28  C27  121.01  3.000
 QED  H29   C29  C41  119.90  3.000
 QED  H29   C29  C28  121.32  3.000
 QED  C41   C29  C28  118.76  3.000
 QED  HO30  O30  N25  102.37  3.000
 QED  C38   C33  N34  119.11  3.000
 QED  C38   C33  C24  122.12  3.000
 QED  N34   C33  C24  118.62  3.000
 QED  O39   N34  C35  115.64  3.000
 QED  O39   N34  C33  118.33  3.000
 QED  C35   N34  C33  125.97  3.000
 QED  O40   C35  C36  128.51  3.000
 QED  C36   C35  N34  114.03  3.000
 QED  O40   C35  N34  117.45  3.000
 QED  H36   C36  C37  121.43  3.000
 QED  H36   C36  C35  117.45  3.000
 QED  C37   C36  C35  121.12  3.000
 QED  H37   C37  C38  119.31  3.000
 QED  H37   C37  C36  119.67  3.000
 QED  C38   C37  C36  121.03  3.000
 QED  H38   C38  C37  121.35  3.000
 QED  H38   C38  C33  119.90  3.000
 QED  C37   C38  C33  118.74  3.000
 QED  HO39  O39  N34  102.39  3.000
 QED  C29   C41  N25  119.10  3.000
 QED  C29   C41  C18  122.23  3.000
 QED  N25   C41  C18  118.50  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
 QED  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 QED  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 QED  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 QED  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 QED  CONST_05  C6    C1   C2   C3      0.00   0.0  0
 QED  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 QED  CONST_07  C41   N25  C26  C27     0.00   0.0  0
 QED  CONST_08  C36   C35  N34  C33     0.00   0.0  0
 QED  CONST_09  O8    C3   C2   C1    180.00   0.0  0
 QED  CONST_10  C9    C1   C2   C3    180.00   0.0  0
 QED  CONST_11  O7    C2   C3   C4    180.00   0.0  0
 QED  CONST_12  O8    C3   C4   C5    180.00   0.0  0
 QED  CONST_13  C9    C1   C6   C5    180.00   0.0  0
 QED  CONST_14  O7    C2   C1   C6    180.00   0.0  0
 QED  CONST_15  O30   N25  C26  C27   180.00   0.0  0
 QED  CONST_16  C41   N25  C26  O31   180.00   0.0  0
 QED  CONST_17  O40   C35  N34  C33   180.00   0.0  0
 QED  CONST_18  O39   N34  C35  C36   180.00   0.0  0
 QED  CONST_19  H5    C5   C6   C1    180.00   0.0  0
 QED  CONST_20  H6    C6   C1   C2    180.00   0.0  0
 QED  CONST_21  H4    C4   C3   C2    180.00   0.0  0
 QED  CONST_22  O31   C26  N25  O30     0.00   0.0  0
 QED  CONST_23  O40   C35  N34  O39     0.00   0.0  0
 QED  CONST_24  C12   N11  C9   C1    180.00   0.0  0
 QED  CONST_25  C41   C18  N17  C16   180.00   0.0  0
 QED  CONST_26  C33   C24  N23  C22   180.00   0.0  0
 QED  CONST_27  HN11  N11  C9   C1      0.00   0.0  0
 QED  CONST_28  HN23  N23  C24  C33     0.00   0.0  0
 QED  CONST_29  HN17  N17  C18  C41     0.00   0.0  0
 QED  CONST_30  C12   N11  C9   O10     0.00   0.0  0
 QED  CONST_31  O19   C18  N17  C16     0.00   0.0  0
 QED  CONST_32  O32   C24  N23  C22     0.00   0.0  0
 QED  Var_01    O10   C9   C1   C2      5.63  30.0  2
 QED  Var_02    N25   C41  C18  N17  -125.52  30.0  3
 QED  Var_03    N34   C33  C24  N23  -126.55  30.0  2
 QED  Var_04    C13   C12  N11  C9    -84.22  30.0  3
 QED  Var_05    N14   C13  C12  N11   179.14  30.0  3
 QED  Var_06    C15   N14  C13  C12   144.48  30.0  3
 QED  Var_07    C16   C15  N14  C13   -81.25  30.0  3
 QED  Var_08    C22   C21  N14  C13   148.38  30.0  3
 QED  Var_09    N17   C16  C15  N14   178.01  30.0  1
 QED  Var_10    N23   C22  C21  N14   177.25  30.0  3
 QED  Var_11    C18   N17  C16  C15    84.33  30.0  2
 QED  Var_12    C24   N23  C22  C21   173.75  30.0  1

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
 QED  plan-1  C1    0.020
 QED  plan-1  C2    0.020
 QED  plan-1  C3    0.020
 QED  plan-1  C4    0.020
 QED  plan-1  C5    0.020
 QED  plan-1  C6    0.020
 QED  plan-1  O7    0.020
 QED  plan-1  O8    0.020
 QED  plan-1  C9    0.020
 QED  plan-1  H4    0.020
 QED  plan-1  H5    0.020
 QED  plan-1  H6    0.020
 QED  plan-2  C18   0.020
 QED  plan-2  N25   0.020
 QED  plan-2  C26   0.020
 QED  plan-2  C27   0.020
 QED  plan-2  C28   0.020
 QED  plan-2  C29   0.020
 QED  plan-2  O30   0.020
 QED  plan-2  O31   0.020
 QED  plan-2  C41   0.020
 QED  plan-2  H27   0.020
 QED  plan-2  H28   0.020
 QED  plan-2  H29   0.020
 QED  plan-3  C24   0.020
 QED  plan-3  C33   0.020
 QED  plan-3  N34   0.020
 QED  plan-3  C35   0.020
 QED  plan-3  C36   0.020
 QED  plan-3  C37   0.020
 QED  plan-3  C38   0.020
 QED  plan-3  O39   0.020
 QED  plan-3  O40   0.020
 QED  plan-3  H36   0.020
 QED  plan-3  H37   0.020
 QED  plan-3  H38   0.020
 QED  plan-4  C1    0.020
 QED  plan-4  C9    0.020
 QED  plan-4  O10   0.020
 QED  plan-4  N11   0.020
 QED  plan-4  C12   0.020
 QED  plan-4  HN11  0.020
 QED  plan-5  C16   0.020
 QED  plan-5  N17   0.020
 QED  plan-5  C18   0.020
 QED  plan-5  O19   0.020
 QED  plan-5  C41   0.020
 QED  plan-5  HN17  0.020
 QED  plan-6  C22   0.020
 QED  plan-6  N23   0.020
 QED  plan-6  C24   0.020
 QED  plan-6  O32   0.020
 QED  plan-6  C33   0.020
 QED  plan-6  HN23  0.020

