# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 02:06:16 2022
#   Inital geometry file: a 129 line input string
#   Ligand name: ~{N}-[5-[2-[(~{E})-hydroxyiminomethyl]pyridin-1-ium-1-yl]pentyl]-4-methyl-3-nitro-benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(cc1[N+]([O-])=O)C(=O)NCCCCC[n+]2ccccc2\C=N\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
 I1X  I1X  "4-methyl-3-nitro-~{N}-[(2~{E},4~{E})-5-[2-[(oxidanylamino)methyl]pyridin-1-yl]penta-2,4-dienyl]benzamide"
  ligand  50  27  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_I1X
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
 I1X  C10  C  CR16   0   0.059   5.8683   -4.2291  -37.7206
 I1X  C13  C  CR16   0  -0.329   6.1028   -1.5715  -38.2298
 I1X  C14  C  CR6    0   0.390   7.2334   -2.3803  -38.2052
 I1X  C15  C  C1     0  -0.078   8.5658   -1.8331  -38.4531
 I1X  C18  C  CR6    0  -0.049  13.2903   -8.0691  -38.5133
 I1X  C20  C  CR16   0  -0.289  13.5864   -9.5621  -40.3833
 I1X  C02  C  C      0   0.540  12.6817   -7.6599  -37.2058
 I1X  N03  N  NH1    0  -0.642  11.4525   -8.1363  -36.9598
 I1X  C04  C  CH2    0  -0.300  10.6985   -7.8683  -35.7532
 I1X  C05  C  CH2    0  -0.437   9.5634   -6.8728  -35.9685
 I1X  C06  C  CH2    0  -0.441  10.0452   -5.4583  -36.2685
 I1X  C07  C  CH2    0  -0.446   8.9103   -4.4516  -36.4535
 I1X  N09  N  NR6    1  -0.483   7.0845   -3.6990  -37.9471
 I1X  C11  C  CR16   0  -0.331   4.7320   -3.4646  -37.7427
 I1X  C12  C  CR16   0  -0.087   4.8532   -2.1051  -37.9987
 I1X  N16  N  N      0  -0.065   8.6585   -0.5734  -38.5967
 I1X  O17  O  OH1    0  -0.501   9.9015   -0.1581  -38.8467
 I1X  C19  C  CR16   0  -0.257  12.9628   -9.2402  -39.1905
 I1X  C21  C  CR6    0   0.116  14.5691   -8.7556  -40.9538
 I1X  C23  C  CR6    0   0.216  14.8808   -7.5921  -40.2460
 I1X  N24  N  N      1   0.324  15.9009   -6.6738  -40.7342
 I1X  O25  O  O      0  -0.365  16.8678   -7.1395  -41.2878
 I1X  O26  O  O     -1  -0.370  15.7310   -5.4932  -40.5420
 I1X  C27  C  CR16   0  -0.288  14.2619   -7.2433  -39.0568
 I1X  H1   H  HCR6   0   0.349   5.8398   -5.2897  -37.5193
 I1X  H2   H  HCR6   0   0.313   6.2239   -0.5194  -38.4382
 I1X  H3   H  H      0   0.292   9.4340   -2.4789  -38.5330
 I1X  H5   H  HCR6   0   0.277  13.3037  -10.4738  -40.8932
 I1X  H6   H  HCH3   0   0.256  15.2251   -8.3466  -42.9762
 I1X  H7   H  HCH3   0   0.266  16.1919   -9.5435  -42.1261
 I1X  H8   H  HCH3   0   0.256  14.5832   -9.9609  -42.7055
 I1X  H9   H  HNH1   0   0.406  10.9692   -8.6421  -37.6847
 I1X  H10  H  HCH2   0   0.259  10.2914   -8.8129  -35.3882
 I1X  H11  H  HCH2   0   0.248  11.3871   -7.4987  -34.9945
 I1X  H12  H  HCH2   0   0.235   8.9496   -6.8625  -35.0634
 I1X  H13  H  HCH2   0   0.234  10.6811   -5.4524  -37.1579
 I1X  H14  H  HCH2   0   0.261   9.3020   -3.4373  -36.3453
 I1X  H15  H  HCH2   0   0.309   7.8663   -5.6146  -37.9543
 I1X  H16  H  HCR6   0   0.314   3.7757   -3.9316  -37.5616
 I1X  H17  H  HCR6   0   0.313   3.9811   -1.4664  -38.0222
 I1X  H19  H  HOH1   0   0.493   9.8364    0.8023  -38.9252
 I1X  H20  H  HCR6   0   0.274  12.2297   -9.9300  -38.7921
 I1X  H21  H  HCR6   0   0.292  14.5432   -6.3345  -38.5435
 I1X  H22  H  HCH2   0   0.231   8.9160   -7.2430  -36.7694
 I1X  H23  H  HCH2   0   0.244  10.6746   -5.1155  -35.4441
 I1X  H24  H  HCH2   0   0.255   8.1609   -4.5849  -35.6683
 I1X  H25  H  HCH2   0   0.304   8.9406   -4.4232  -38.6290
 I1X  C08  C  CH2    0  -0.375   8.2447   -4.6057  -37.8134
 I1X  C22  C  CH3    0  -0.715  15.1788   -9.1664  -42.2605
 I1X  O01  O  O      0  -0.478  13.2996   -6.9334  -36.4404

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
 I1X  C22  C21  single    1.499  0.020  1.499
 I1X  O25  N24  double    1.207  0.020  1.207
 I1X  C21  C20  aromatic  1.393  0.020  1.393
 I1X  C21  C23  aromatic  1.397  0.020  1.397
 I1X  O26  N24  single    1.208  0.020  1.208
 I1X  N24  C23  single    1.457  0.020  1.457
 I1X  C20  C19  aromatic  1.384  0.020  1.384
 I1X  C23  C27  aromatic  1.385  0.020  1.385
 I1X  C19  C18  aromatic  1.392  0.020  1.392
 I1X  C27  C18  aromatic  1.386  0.020  1.386
 I1X  C18  C02  single    1.499  0.020  1.499
 I1X  O17  N16  single    1.334  0.020  1.334
 I1X  C15  C14  single    1.462  0.020  1.462
 I1X  C15  N16  double    1.271  0.020  1.271
 I1X  C13  C14  aromatic  1.390  0.020  1.390
 I1X  C13  C12  aromatic  1.378  0.020  1.378
 I1X  C14  N09  aromatic  1.352  0.020  1.352
 I1X  C12  C11  aromatic  1.389  0.020  1.389
 I1X  N09  C08  single    1.479  0.020  1.479
 I1X  N09  C10  aromatic  1.346  0.020  1.346
 I1X  C08  C07  single    1.522  0.020  1.522
 I1X  C11  C10  aromatic  1.370  0.020  1.370
 I1X  C02  N03  single    1.341  0.020  1.341
 I1X  C02  O01  double    1.223  0.020  1.223
 I1X  N03  C04  single    1.448  0.020  1.448
 I1X  C07  C06  single    1.528  0.020  1.528
 I1X  C06  C05  single    1.524  0.020  1.524
 I1X  C05  C04  single    1.525  0.020  1.525
 I1X  C10  H1   single    0.930  0.020  1.080
 I1X  C13  H2   single    0.930  0.020  1.080
 I1X  C15  H3   single    0.930  0.020  1.080
 I1X  C20  H5   single    0.930  0.020  1.080
 I1X  C22  H6   single    0.970  0.020  1.090
 I1X  C22  H7   single    0.970  0.020  1.090
 I1X  C22  H8   single    0.970  0.020  1.090
 I1X  N03  H9   single    0.860  0.020  1.020
 I1X  C04  H10  single    0.970  0.020  1.090
 I1X  C04  H11  single    0.970  0.020  1.090
 I1X  C05  H12  single    0.970  0.020  1.090
 I1X  C06  H13  single    0.970  0.020  1.090
 I1X  C07  H14  single    0.970  0.020  1.090
 I1X  C08  H15  single    0.970  0.020  1.090
 I1X  C11  H16  single    0.930  0.020  1.080
 I1X  C12  H17  single    0.930  0.020  1.080
 I1X  O17  H19  single    0.850  0.020  0.980
 I1X  C19  H20  single    0.930  0.020  1.080
 I1X  C27  H21  single    0.930  0.020  1.080
 I1X  C05  H22  single    0.970  0.020  1.090
 I1X  C06  H23  single    0.970  0.020  1.090
 I1X  C07  H24  single    0.970  0.020  1.090
 I1X  C08  H25  single    0.970  0.020  1.090

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
 I1X  H1   C10  C11  121.96  3.000
 I1X  H1   C10  N09  116.23  3.000
 I1X  C11  C10  N09  121.81  3.000
 I1X  H2   C13  C12  120.76  3.000
 I1X  H2   C13  C14  118.63  3.000
 I1X  C12  C13  C14  120.61  3.000
 I1X  N09  C14  C15  119.86  3.000
 I1X  N09  C14  C13  118.77  3.000
 I1X  C15  C14  C13  121.37  3.000
 I1X  H3   C15  N16  121.54  3.000
 I1X  H3   C15  C14  121.28  3.000
 I1X  N16  C15  C14  117.17  3.000
 I1X  C27  C18  C19  118.39  3.000
 I1X  C27  C18  C02  117.64  3.000
 I1X  C19  C18  C02  123.95  3.000
 I1X  H5   C20  C21  118.62  3.000
 I1X  H5   C20  C19  118.97  3.000
 I1X  C21  C20  C19  122.41  3.000
 I1X  N03  C02  O01  124.01  3.000
 I1X  O01  C02  C18  120.19  3.000
 I1X  N03  C02  C18  115.80  3.000
 I1X  H9   N03  C04  116.28  3.000
 I1X  H9   N03  C02  119.08  3.000
 I1X  C04  N03  C02  124.37  3.000
 I1X  H11  C04  H10  107.25  3.000
 I1X  H11  C04  C05  110.32  3.000
 I1X  H10  C04  C05  109.55  3.000
 I1X  H11  C04  N03  108.30  3.000
 I1X  H10  C04  N03  108.23  3.000
 I1X  C05  C04  N03  113.00  3.000
 I1X  H22  C05  H12  106.08  3.000
 I1X  H22  C05  C06  110.92  3.000
 I1X  H12  C05  C06  109.36  3.000
 I1X  H22  C05  C04  108.83  3.000
 I1X  H12  C05  C04  107.87  3.000
 I1X  C06  C05  C04  113.47  3.000
 I1X  H23  C06  H13  106.09  3.000
 I1X  H23  C06  C07  108.21  3.000
 I1X  H13  C06  C07  109.26  3.000
 I1X  H23  C06  C05  108.96  3.000
 I1X  H13  C06  C05  110.43  3.000
 I1X  C07  C06  C05  113.60  3.000
 I1X  H24  C07  H14  106.72  3.000
 I1X  H24  C07  C08  109.24  3.000
 I1X  H14  C07  C08  109.83  3.000
 I1X  H24  C07  C06  109.98  3.000
 I1X  H14  C07  C06  109.47  3.000
 I1X  C08  C07  C06  111.48  3.000
 I1X  C08  N09  C14  121.94  3.000
 I1X  C08  N09  C10  116.89  3.000
 I1X  C14  N09  C10  121.05  3.000
 I1X  H16  C11  C12  122.12  3.000
 I1X  H16  C11  C10  119.39  3.000
 I1X  C12  C11  C10  118.49  3.000
 I1X  H17  C12  C11  120.79  3.000
 I1X  H17  C12  C13  119.93  3.000
 I1X  C11  C12  C13  119.27  3.000
 I1X  O17  N16  C15  113.43  3.000
 I1X  H19  O17  N16  105.19  3.000
 I1X  H20  C19  C20  118.30  3.000
 I1X  H20  C19  C18  121.09  3.000
 I1X  C20  C19  C18  120.60  3.000
 I1X  C23  C21  C22  125.38  3.000
 I1X  C23  C21  C20  115.59  3.000
 I1X  C22  C21  C20  119.01  3.000
 I1X  C27  C23  N24  116.22  3.000
 I1X  C27  C23  C21  123.02  3.000
 I1X  N24  C23  C21  120.75  3.000
 I1X  O26  N24  O25  124.22  3.000
 I1X  O26  N24  C23  117.65  3.000
 I1X  O25  N24  C23  118.12  3.000
 I1X  H21  C27  C23  120.21  3.000
 I1X  H21  C27  C18  119.80  3.000
 I1X  C23  C27  C18  119.98  3.000
 I1X  H25  C08  H15  106.34  3.000
 I1X  H25  C08  N09  109.35  3.000
 I1X  H15  C08  N09  106.52  3.000
 I1X  H25  C08  C07  111.92  3.000
 I1X  H15  C08  C07  111.24  3.000
 I1X  N09  C08  C07  111.22  3.000
 I1X  H8   C22  H7   107.87  3.000
 I1X  H8   C22  H6   107.71  3.000
 I1X  H7   C22  H6   107.58  3.000
 I1X  H8   C22  C21  109.51  3.000
 I1X  H7   C22  C21  111.43  3.000
 I1X  H6   C22  C21  112.57  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
 I1X  CONST_01  C13  C14  N09  C10     0.00   0.0  0
 I1X  CONST_02  C13  C12  C11  C10     0.00   0.0  0
 I1X  CONST_03  C11  C12  C13  C14     0.00   0.0  0
 I1X  CONST_04  C11  C10  N09  C14     0.00   0.0  0
 I1X  CONST_05  C21  C20  C19  C18     0.00   0.0  0
 I1X  CONST_06  C21  C23  C27  C18     0.00   0.0  0
 I1X  CONST_07  C27  C23  C21  C20     0.00   0.0  0
 I1X  CONST_08  C27  C18  C19  C20     0.00   0.0  0
 I1X  CONST_09  C12  C13  C14  N09     0.00   0.0  0
 I1X  CONST_10  C12  C11  C10  N09     0.00   0.0  0
 I1X  CONST_11  C23  C21  C20  C19     0.00   0.0  0
 I1X  CONST_12  C23  C27  C18  C19     0.00   0.0  0
 I1X  CONST_13  C15  C14  N09  C10   180.00   0.0  0
 I1X  CONST_14  C08  N09  C14  C13   180.00   0.0  0
 I1X  CONST_15  C12  C13  C14  C15   180.00   0.0  0
 I1X  CONST_16  N24  C23  C27  C18   180.00   0.0  0
 I1X  CONST_17  N24  C23  C21  C20   180.00   0.0  0
 I1X  CONST_18  C02  C18  C19  C20   180.00   0.0  0
 I1X  CONST_19  C19  C20  C21  C22   180.00   0.0  0
 I1X  CONST_20  C27  C23  C21  C22   180.00   0.0  0
 I1X  CONST_21  C23  C27  C18  C02   180.00   0.0  0
 I1X  CONST_22  C11  C10  N09  C08   180.00   0.0  0
 I1X  CONST_23  H17  C12  C11  C10   180.00   0.0  0
 I1X  CONST_24  H16  C11  C12  C13   180.00   0.0  0
 I1X  CONST_25  H17  C12  C13  C14   180.00   0.0  0
 I1X  CONST_26  H1   C10  N09  C14   180.00   0.0  0
 I1X  CONST_27  H5   C20  C19  C18   180.00   0.0  0
 I1X  CONST_28  H2   C13  C14  N09   180.00   0.0  0
 I1X  CONST_29  H16  C11  C10  N09   180.00   0.0  0
 I1X  CONST_30  H2   C13  C12  C11   180.00   0.0  0
 I1X  CONST_31  H1   C10  C11  C12   180.00   0.0  0
 I1X  CONST_32  H21  C27  C18  C19   180.00   0.0  0
 I1X  CONST_33  H20  C19  C20  C21   180.00   0.0  0
 I1X  CONST_34  H21  C27  C23  C21   180.00   0.0  0
 I1X  CONST_35  H5   C20  C21  C23   180.00   0.0  0
 I1X  CONST_36  H20  C19  C18  C27   180.00   0.0  0
 I1X  CONST_41  C04  N03  C02  C18   180.00   0.0  0
 I1X  CONST_42  H9   N03  C02  C18     0.00   0.0  0
 I1X  CONST_43  C04  N03  C02  O01     0.00   0.0  0
 I1X  CONST_44  H9   N03  C02  O01   180.00   0.0  0
 I1X  Var_01    C07  C08  N09  C10   -98.37  30.0  2
 I1X  Var_02    N16  C15  C14  C13     4.92  30.0  2
 I1X  Var_03    C07  C08  N09  C14    77.75  30.0  2
 I1X  Var_04    C19  C18  C02  O01   153.64  30.0  2
 I1X  Var_05    C27  C18  C02  O01   -24.63  30.0  2
 I1X  Var_06    C19  C18  C02  N03   -26.51  30.0  2
 I1X  Var_07    C27  C18  C02  N03   155.22  30.0  2
 I1X  Var_08    N16  C15  C14  N09  -175.16  30.0  2
 I1X  Var_09    H15  C08  N09  C10    22.99  30.0  2
 I1X  Var_10    H25  C08  N09  C10   137.52  30.0  2
 I1X  Var_11    H3   C15  C14  C13  -173.75  30.0  2
 I1X  Var_12    H15  C08  N09  C14  -160.88  30.0  2
 I1X  Var_13    H25  C08  N09  C14   -46.35  30.0  2
 I1X  Var_14    H6   C22  C21  C20   132.79  30.0  2
 I1X  Var_15    H7   C22  C21  C20  -106.25  30.0  2
 I1X  Var_16    H8   C22  C21  C20    13.01  30.0  2
 I1X  Var_17    H3   C15  C14  N09     6.17  30.0  2
 I1X  Var_18    H6   C22  C21  C23   -45.72  30.0  2
 I1X  Var_19    H7   C22  C21  C23    75.24  30.0  2
 I1X  Var_20    H8   C22  C21  C23  -165.50  30.0  2
 I1X  Var_21    O17  N16  C15  C14  -178.68   0.0  2
 I1X  Var_22    N09  C08  C07  C06   175.76  30.0  1
 I1X  Var_23    H14  C07  C08  N09   -62.73  30.0  3
 I1X  Var_24    H24  C07  C08  N09    54.00  30.0  3
 I1X  Var_25    C05  C04  N03  C02   105.56  30.0  3
 I1X  Var_26    C06  C05  C04  N03   -68.27  30.0  2
 I1X  Var_27    C07  C06  C05  C04  -178.69  30.0  2
 I1X  Var_28    C08  C07  C06  C05   -76.23  30.0  1
 I1X  Var_29    H3   C15  N16  O17    -0.02   0.0  2
 I1X  Var_30    H10  C04  N03  C02  -132.94  30.0  3
 I1X  Var_31    H11  C04  N03  C02   -16.97  30.0  3
 I1X  Var_32    H12  C05  C04  N03   170.40  30.0  2
 I1X  Var_33    H22  C05  C04  N03    55.73  30.0  2
 I1X  Var_34    H13  C06  C05  C04    58.16  30.0  2
 I1X  Var_35    H23  C06  C05  C04   -57.98  30.0  2
 I1X  Var_36    H14  C07  C06  C05   162.05  30.0  1
 I1X  Var_37    H24  C07  C06  C05    45.10  30.0  1
 I1X  Var_38    H9   N03  C04  C05   -68.40  30.0  2
 I1X  Var_39    H15  C08  C07  C06    57.20  30.0  1
 I1X  Var_40    H25  C08  C07  C06   -61.60  30.0  1
 I1X  Var_41    H10  C04  C05  C06   170.98  30.0  3
 I1X  Var_42    H11  C04  C05  C06    53.13  30.0  3
 I1X  Var_43    H12  C05  C06  C07   -58.21  30.0  3
 I1X  Var_44    H22  C05  C06  C07    58.45  30.0  3
 I1X  Var_45    H13  C06  C07  C08    47.56  30.0  3
 I1X  Var_46    H23  C06  C07  C08   162.65  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
 I1X  plan-1  C10  0.020
 I1X  plan-1  C13  0.020
 I1X  plan-1  C14  0.020
 I1X  plan-1  C15  0.020
 I1X  plan-1  N09  0.020
 I1X  plan-1  C11  0.020
 I1X  plan-1  C12  0.020
 I1X  plan-1  H1   0.020
 I1X  plan-1  H2   0.020
 I1X  plan-1  H16  0.020
 I1X  plan-1  H17  0.020
 I1X  plan-1  C08  0.020
 I1X  plan-2  C18  0.020
 I1X  plan-2  C20  0.020
 I1X  plan-2  C02  0.020
 I1X  plan-2  C19  0.020
 I1X  plan-2  C21  0.020
 I1X  plan-2  C23  0.020
 I1X  plan-2  N24  0.020
 I1X  plan-2  C27  0.020
 I1X  plan-2  H5   0.020
 I1X  plan-2  H20  0.020
 I1X  plan-2  H21  0.020
 I1X  plan-2  C22  0.020
 I1X  plan-3  C18  0.020
 I1X  plan-3  C02  0.020
 I1X  plan-3  N03  0.020
 I1X  plan-3  C04  0.020
 I1X  plan-3  H9   0.020
 I1X  plan-3  O01  0.020
 I1X  plan-4  C23  0.020
 I1X  plan-4  N24  0.020
 I1X  plan-4  O25  0.020
 I1X  plan-4  O26  0.020
 I1X  plan-5  C14  0.020
 I1X  plan-5  C15  0.020
 I1X  plan-5  N16  0.020
 I1X  plan-5  O17  0.020
 I1X  plan-5  H3   0.020

