# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 30 15:50:32 2022
#   Inital geometry file: a 85 line input string
#   Ligand name: 3,4,5-tris(oxidanyl)-~{N}-[(~{E})-1~{H}-pyrrol-2-ylmethylideneamino]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1cc(cc(O)c1O)C(=O)N\N=C\c2[nH]ccc2
#
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
 DZI  DZI  "3,4,5-tris(oxidanyl)-N-[(E)-1H-pyrrol-2-ylmethylideneamino]benzamide"
  ligand  30  19  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DZI
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
 DZI  C11   C  CR6   0  -0.046  70.4132  28.9136  -30.8767
 DZI  C12   C  CR16  0  -0.430  70.1573  28.1817  -32.0316
 DZI  C13   C  CR6   0   0.305  71.1926  27.8125  -32.8762
 DZI  C15   C  CR6   0   0.218  72.5034  28.1934  -32.5818
 DZI  C02   C  C     0   0.536  69.2427  29.2760  -30.0313
 DZI  C05   C  C1    0  -0.097  68.8328  29.9756  -26.6390
 DZI  C06   C  CR5   0   0.295  67.8387  30.3690  -25.6788
 DZI  C07   C  CR15  0  -0.366  67.9629  30.5271  -24.3110
 DZI  C08   C  CR15  0  -0.347  66.7016  30.9200  -23.8172
 DZI  C09   C  CR15  0  -0.047  65.8494  30.9888  -24.8975
 DZI  C17   C  CR6   0   0.294  72.7520  28.9440  -31.4311
 DZI  C19   C  CR16  0  -0.446  71.7170  29.3027  -30.5796
 DZI  N03   N  NH1   0  -0.531  69.5214  29.4972  -28.7193
 DZI  N04   N  N     0  -0.214  68.5401  29.8702  -27.8757
 DZI  N10   N  NR15  0  -0.623  66.5464  30.6558  -26.0081
 DZI  O01   O  O     0  -0.456  68.1156  29.3509  -30.4860
 DZI  O14   O  OH1   0  -0.623  71.0137  27.0905  -33.9987
 DZI  O16   O  OH1   0  -0.616  73.4791  27.8245  -33.4322
 DZI  O18   O  OH1   0  -0.642  74.0434  29.2860  -31.2319
 DZI  H121  H  HCR6  0   0.273  69.1424  27.8884  -32.2715
 DZI  H051  H  H     0   0.255  69.8318  29.7788  -26.2443
 DZI  H071  H  HCR5  0   0.252  68.8675  30.3727  -23.7431
 DZI  H081  H  HCR5  0   0.249  66.4413  31.1297  -22.7922
 DZI  H091  H  HCR5  0   0.275  64.8046  31.2474  -24.9509
 DZI  H191  H  HCR6  0   0.274  71.9469  29.9166  -29.7161
 DZI  H031  H  HNH1  0   0.414  70.4443  29.2980  -28.3504
 DZI  H101  H  HNR5  0   0.411  66.1718  30.6169  -26.9427
 DZI  H141  H  HOH1  0   0.476  70.0801  26.8783  -34.1122
 DZI  H161  H  HOH1  0   0.474  74.3356  28.1327  -33.1119
 DZI  H181  H  HOH1  0   0.483  74.1518  29.7786  -30.4106

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
 DZI  O14  C13   single    1.347  0.020  1.347
 DZI  O16  C15   single    1.346  0.020  1.346
 DZI  C13  C15   aromatic  1.396  0.020  1.396
 DZI  C13  C12   aromatic  1.386  0.020  1.386
 DZI  C15  C17   aromatic  1.396  0.020  1.396
 DZI  C12  C11   aromatic  1.391  0.020  1.391
 DZI  C17  O18   single    1.351  0.020  1.351
 DZI  C17  C19   aromatic  1.387  0.020  1.387
 DZI  C11  C19   aromatic  1.393  0.020  1.393
 DZI  C11  C02   single    1.489  0.020  1.489
 DZI  O01  C02   double    1.218  0.020  1.218
 DZI  C02  N03   single    1.359  0.020  1.359
 DZI  N03  N04   single    1.347  0.020  1.347
 DZI  N04  C05   double    1.275  0.020  1.275
 DZI  C05  C06   single    1.437  0.020  1.437
 DZI  N10  C06   aromatic  1.364  0.020  1.364
 DZI  N10  C09   aromatic  1.353  0.020  1.353
 DZI  C06  C07   aromatic  1.382  0.020  1.382
 DZI  C09  C08   aromatic  1.378  0.020  1.378
 DZI  C07  C08   aromatic  1.410  0.020  1.410
 DZI  C12  H121  single    0.930  0.020  1.080
 DZI  C05  H051  single    0.930  0.020  1.080
 DZI  C07  H071  single    0.930  0.020  1.080
 DZI  C08  H081  single    0.930  0.020  1.080
 DZI  C09  H091  single    0.930  0.020  1.080
 DZI  C19  H191  single    0.930  0.020  1.080
 DZI  N03  H031  single    0.860  0.020  1.020
 DZI  N10  H101  single    0.860  0.020  1.020
 DZI  O14  H141  single    0.850  0.020  0.980
 DZI  O16  H161  single    0.850  0.020  0.980
 DZI  O18  H181  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
 DZI  C19   C11  C02  123.16  3.000
 DZI  C02   C11  C12  117.06  3.000
 DZI  C19   C11  C12  119.76  3.000
 DZI  H121  C12  C13  119.51  3.000
 DZI  H121  C12  C11  119.91  3.000
 DZI  C13   C12  C11  120.57  3.000
 DZI  O14   C13  C15  116.53  3.000
 DZI  C15   C13  C12  120.00  3.000
 DZI  O14   C13  C12  123.47  3.000
 DZI  O16   C15  C17  122.62  3.000
 DZI  C17   C15  C13  119.18  3.000
 DZI  O16   C15  C13  118.20  3.000
 DZI  O01   C02  N03  122.70  3.000
 DZI  N03   C02  C11  115.25  3.000
 DZI  O01   C02  C11  122.05  3.000
 DZI  H051  C05  N04  123.06  3.000
 DZI  H051  C05  C06  116.15  3.000
 DZI  N04   C05  C06  120.79  3.000
 DZI  N10   C06  C07  107.45  3.000
 DZI  C07   C06  C05  129.07  3.000
 DZI  N10   C06  C05  123.48  3.000
 DZI  H071  C07  C08  127.24  3.000
 DZI  H071  C07  C06  125.43  3.000
 DZI  C08   C07  C06  107.33  3.000
 DZI  H081  C08  C09  125.91  3.000
 DZI  H081  C08  C07  127.08  3.000
 DZI  C09   C08  C07  107.01  3.000
 DZI  H091  C09  N10  121.19  3.000
 DZI  H091  C09  C08  130.58  3.000
 DZI  N10   C09  C08  108.23  3.000
 DZI  O18   C17  C19  123.87  3.000
 DZI  C19   C17  C15  120.79  3.000
 DZI  O18   C17  C15  115.34  3.000
 DZI  H191  C19  C17  118.49  3.000
 DZI  H191  C19  C11  121.78  3.000
 DZI  C17   C19  C11  119.69  3.000
 DZI  H031  N03  N04  119.33  3.000
 DZI  H031  N03  C02  120.40  3.000
 DZI  N04   N03  C02  120.02  3.000
 DZI  N03   N04  C05  117.59  3.000
 DZI  H101  N10  C09  125.41  3.000
 DZI  H101  N10  C06  124.61  3.000
 DZI  C09   N10  C06  109.98  3.000
 DZI  H141  O14  C13  110.17  3.000
 DZI  H161  O16  C15  110.25  3.000
 DZI  H181  O18  C17  111.26  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
 DZI  CONST_01  C15   C13  C12  C11    0.00   0.0  0
 DZI  CONST_02  C15   C17  C19  C11    0.00   0.0  0
 DZI  CONST_03  C17   C15  C13  C12    0.00   0.0  0
 DZI  CONST_04  C17   C19  C11  C12    0.00   0.0  0
 DZI  CONST_05  C19   C17  C15  C13    0.00   0.0  0
 DZI  CONST_06  C19   C11  C12  C13    0.00   0.0  0
 DZI  CONST_07  C08   C09  N10  C06    0.00   0.0  0
 DZI  CONST_08  C09   C08  C07  C06    0.00   0.0  0
 DZI  CONST_09  C09   N10  C06  C07    0.00   0.0  0
 DZI  CONST_10  N10   C09  C08  C07    0.00   0.0  0
 DZI  CONST_11  N10   C06  C07  C08    0.00   0.0  0
 DZI  CONST_12  O14   C13  C12  C11  180.00   0.0  0
 DZI  CONST_13  O18   C17  C19  C11  180.00   0.0  0
 DZI  CONST_14  O16   C15  C13  C12  180.00   0.0  0
 DZI  CONST_15  O18   C17  C15  C13  180.00   0.0  0
 DZI  CONST_16  C02   C11  C12  C13  180.00   0.0  0
 DZI  CONST_17  C17   C19  C11  C02  180.00   0.0  0
 DZI  CONST_18  C09   N10  C06  C05  180.00   0.0  0
 DZI  CONST_19  C08   C07  C06  C05  180.00   0.0  0
 DZI  CONST_20  O14   C13  C15  C17  180.00   0.0  0
 DZI  CONST_21  O16   C15  C17  C19  180.00   0.0  0
 DZI  CONST_22  H191  C19  C11  C12  180.00   0.0  0
 DZI  CONST_23  H121  C12  C13  C15  180.00   0.0  0
 DZI  CONST_24  H191  C19  C17  C15  180.00   0.0  0
 DZI  CONST_25  H091  C09  N10  C06  180.00   0.0  0
 DZI  CONST_26  H081  C08  C07  C06  180.00   0.0  0
 DZI  CONST_27  H101  N10  C06  C07  180.00   0.0  0
 DZI  CONST_28  H091  C09  C08  C07  180.00   0.0  0
 DZI  CONST_29  H101  N10  C09  C08  180.00   0.0  0
 DZI  CONST_30  H071  C07  C08  C09  180.00   0.0  0
 DZI  CONST_31  H121  C12  C11  C19  180.00   0.0  0
 DZI  CONST_32  H071  C07  C06  N10  180.00   0.0  0
 DZI  CONST_33  H081  C08  C09  N10  180.00   0.0  0
 DZI  CONST_34  N04   N03  C02  C11  180.00   0.0  0
 DZI  CONST_35  H031  N03  C02  C11    0.00   0.0  0
 DZI  CONST_36  O01   C02  N03  N04    0.00   0.0  0
 DZI  CONST_37  H031  N03  C02  O01  180.00   0.0  0
 DZI  Var_01    O01   C02  C11  C12  -24.02  30.0  2
 DZI  Var_02    N03   C02  C11  C12  155.10  30.0  2
 DZI  Var_03    N04   C05  C06  C07  179.52  30.0  2
 DZI  Var_04    O01   C02  C11  C19  154.19  30.0  2
 DZI  Var_05    N03   C02  C11  C19  -26.69  30.0  2
 DZI  Var_06    N10   C06  C05  N04   -0.25  30.0  2
 DZI  Var_07    H051  C05  C06  C07   -0.50  30.0  2
 DZI  Var_08    H051  C05  C06  N10  179.72  30.0  2
 DZI  Var_09    N03   N04  C05  C06  179.99   0.0  2
 DZI  Var_10    C05   N04  N03  C02  175.27  30.0  3
 DZI  Var_11    H051  C05  N04  N03    0.02   0.0  2
 DZI  Var_12    H031  N03  N04  C05    1.10  30.0  2

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
 DZI  plan-1  C05   0.020
 DZI  plan-1  C06   0.020
 DZI  plan-1  C07   0.020
 DZI  plan-1  C08   0.020
 DZI  plan-1  C09   0.020
 DZI  plan-1  N10   0.020
 DZI  plan-1  H071  0.020
 DZI  plan-1  H081  0.020
 DZI  plan-1  H091  0.020
 DZI  plan-1  H101  0.020
 DZI  plan-2  C11   0.020
 DZI  plan-2  C12   0.020
 DZI  plan-2  C13   0.020
 DZI  plan-2  C15   0.020
 DZI  plan-2  C02   0.020
 DZI  plan-2  C17   0.020
 DZI  plan-2  C19   0.020
 DZI  plan-2  O14   0.020
 DZI  plan-2  O16   0.020
 DZI  plan-2  O18   0.020
 DZI  plan-2  H121  0.020
 DZI  plan-2  H191  0.020
 DZI  plan-3  C11   0.020
 DZI  plan-3  C02   0.020
 DZI  plan-3  N03   0.020
 DZI  plan-3  N04   0.020
 DZI  plan-3  O01   0.020
 DZI  plan-3  H031  0.020
 DZI  plan-4  C05   0.020
 DZI  plan-4  C06   0.020
 DZI  plan-4  N03   0.020
 DZI  plan-4  N04   0.020
 DZI  plan-4  H051  0.020

