# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 04:29:54 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: N-{4-[(4-hydroxy-3-nitrobenzoyl)amino]phenyl}pyridine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc(cc1[N+]([O-])=O)C(=O)Nc2ccc(NC(=O)c3ccccn3)cc2
#
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
 1SE  1SE  N-{4-[(4-hydroxy-3-nitrobenzoyl)amino]phenyl}pyridine-2-carboxamide  ligand  42  28  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1SE
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
 1SE  C1   C  CR16   0  -0.145  -8.9348  -0.2909   0.4561
 1SE  C2   C  CR16   0  -0.319  -9.0268   0.9423  -0.1682
 1SE  C3   C  CR16   0  -0.056  -7.8541   1.5731  -0.5641
 1SE  N4   N  N      0  -0.444  -6.6563   1.0455  -0.3689
 1SE  C5   C  CR6    0   0.125  -6.5708  -0.1368   0.2317
 1SE  C6   C  CR16   0  -0.296  -7.6812  -0.8470   0.6643
 1SE  C7   C  C      0   0.532  -5.1959  -0.7065   0.4394
 1SE  O8   O  O      0  -0.460  -5.0357  -1.7829   0.9903
 1SE  N9   N  NH1    0  -0.757  -4.2156   0.0859  -0.0362
 1SE  C10  C  CR6    0   0.373  -2.8340  -0.1058  -0.0183
 1SE  C11  C  CR16   0  -0.344  -2.0448   0.9111  -0.5540
 1SE  C12  C  CR16   0  -0.300  -0.6640   0.8272  -0.5878
 1SE  C13  C  CR6    0   0.372  -0.0258  -0.3029  -0.0761
 1SE  C14  C  CR16   0  -0.349  -0.8150  -1.3211   0.4571
 1SE  C15  C  CR16   0  -0.302  -2.1952  -1.2364   0.4923
 1SE  N16  N  NH1    0  -0.767   1.3593  -0.5042  -0.0557
 1SE  C17  C  C      0   0.553   2.3458   0.3094  -0.4982
 1SE  O18  O  O      0  -0.461   2.1576   1.4218  -0.9612
 1SE  C19  C  CR6    0  -0.055   3.7278  -0.2410  -0.3691
 1SE  C20  C  CR16   0  -0.267   4.0247  -1.6095  -0.2996
 1SE  C21  C  CR16   0  -0.333   5.3199  -2.0559  -0.2038
 1SE  C22  C  CR6    0   0.375   6.3938  -1.1592  -0.1654
 1SE  C23  C  CR6    0   0.197   6.0889   0.2150  -0.2450
 1SE  C24  C  CR16   0  -0.321   4.7748   0.6571  -0.3564
 1SE  N25  N  N      1   0.366   7.1338   1.2044  -0.2181
 1SE  O26  O  O     -1  -0.422   8.2888   0.8162  -0.1173
 1SE  O27  O  O      0  -0.358   6.8437   2.3695  -0.2939
 1SE  O28  O  OH1    0  -0.590   7.6061  -1.6704  -0.0624
 1SE  H1   H  HCR6   0   0.283  -9.8256  -0.8142   0.7764
 1SE  H2   H  HCR6   0   0.282  -9.9836   1.4118  -0.3487
 1SE  H3   H  HCR6   0   0.275  -7.8866   2.5375  -1.0571
 1SE  H4   H  HCR6   0   0.279  -7.5695  -1.8061   1.1493
 1SE  H5   H  HNH1   0   0.420  -4.5450   0.9462  -0.4583
 1SE  H6   H  HCR6   0   0.274  -2.5174   1.7992  -0.9568
 1SE  H7   H  HCR6   0   0.285  -0.1059   1.6456  -1.0100
 1SE  H8   H  HCR6   0   0.275  -0.3437  -2.2107   0.8584
 1SE  H9   H  HCR6   0   0.284  -2.7540  -2.0539   0.9165
 1SE  H10  H  HNH1   0   0.426   1.6403  -1.3579   0.4007
 1SE  H11  H  HCR6   0   0.281   3.2416  -2.3553  -0.3446
 1SE  H12  H  HCR6   0   0.298   5.5303  -3.1163  -0.1622
 1SE  H13  H  HCR6   0   0.304   4.5735   1.7166  -0.4272
 1SE  H14  H  HOH1   0   0.486   8.2602  -0.9472  -0.0430

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
 1SE  C1   C2   aromatic  1.385  0.020  1.385
 1SE  C1   C6   aromatic  1.387  0.020  1.387
 1SE  C2   C3   aromatic  1.389  0.020  1.389
 1SE  C6   C5   aromatic  1.387  0.020  1.387
 1SE  C3   N4   aromatic  1.323  0.020  1.323
 1SE  C5   N4   aromatic  1.329  0.020  1.329
 1SE  C5   C7   single    1.503  0.020  1.503
 1SE  C7   N9   single    1.347  0.020  1.347
 1SE  C7   O8   double    1.220  0.020  1.220
 1SE  N9   C10  single    1.395  0.020  1.395
 1SE  C11  C10  aromatic  1.394  0.020  1.394
 1SE  C11  C12  aromatic  1.384  0.020  1.384
 1SE  C10  C15  aromatic  1.395  0.020  1.395
 1SE  C12  C13  aromatic  1.395  0.020  1.395
 1SE  O18  C17  double    1.220  0.020  1.220
 1SE  C15  C14  aromatic  1.383  0.020  1.383
 1SE  C13  C14  aromatic  1.394  0.020  1.394
 1SE  C13  N16  single    1.400  0.020  1.400
 1SE  C17  N16  single    1.353  0.020  1.353
 1SE  C17  C19  single    1.493  0.020  1.493
 1SE  C20  C19  aromatic  1.402  0.020  1.402
 1SE  C20  C21  aromatic  1.373  0.020  1.373
 1SE  C19  C24  aromatic  1.379  0.020  1.379
 1SE  C21  C22  aromatic  1.400  0.020  1.400
 1SE  C24  C23  aromatic  1.391  0.020  1.391
 1SE  C22  C23  aromatic  1.410  0.020  1.410
 1SE  C22  O28  single    1.320  0.020  1.320
 1SE  C23  N25  single    1.439  0.020  1.439
 1SE  N25  O27  double    1.203  0.020  1.203
 1SE  N25  O26  single    1.223  0.020  1.223
 1SE  C1   H1   single    0.930  0.020  1.080
 1SE  C2   H2   single    0.930  0.020  1.080
 1SE  C3   H3   single    0.930  0.020  1.080
 1SE  C6   H4   single    0.930  0.020  1.080
 1SE  N9   H5   single    0.860  0.020  1.020
 1SE  C11  H6   single    0.930  0.020  1.080
 1SE  C12  H7   single    0.930  0.020  1.080
 1SE  C14  H8   single    0.930  0.020  1.080
 1SE  C15  H9   single    0.930  0.020  1.080
 1SE  N16  H10  single    0.860  0.020  1.020
 1SE  C20  H11  single    0.930  0.020  1.080
 1SE  C21  H12  single    0.930  0.020  1.080
 1SE  C24  H13  single    0.930  0.020  1.080
 1SE  O28  H14  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
 1SE  H1   C1   C6   120.39  3.000
 1SE  H1   C1   C2   120.63  3.000
 1SE  C6   C1   C2   118.98  3.000
 1SE  H2   C2   C3   120.16  3.000
 1SE  H2   C2   C1   121.38  3.000
 1SE  C3   C2   C1   118.46  3.000
 1SE  H3   C3   N4   116.69  3.000
 1SE  H3   C3   C2   120.56  3.000
 1SE  N4   C3   C2   122.76  3.000
 1SE  C5   N4   C3   118.66  3.000
 1SE  C7   C5   C6   119.68  3.000
 1SE  C7   C5   N4   117.30  3.000
 1SE  C6   C5   N4   123.02  3.000
 1SE  H4   C6   C5   120.77  3.000
 1SE  H4   C6   C1   121.11  3.000
 1SE  C5   C6   C1   118.12  3.000
 1SE  N9   C7   O8   125.65  3.000
 1SE  O8   C7   C5   121.14  3.000
 1SE  N9   C7   C5   113.20  3.000
 1SE  H5   N9   C10  116.36  3.000
 1SE  H5   N9   C7   114.19  3.000
 1SE  C10  N9   C7   129.44  3.000
 1SE  C15  C10  C11  118.20  3.000
 1SE  C15  C10  N9   124.71  3.000
 1SE  C11  C10  N9   117.09  3.000
 1SE  H6   C11  C12  118.41  3.000
 1SE  H6   C11  C10  119.59  3.000
 1SE  C12  C11  C10  122.00  3.000
 1SE  H7   C12  C13  121.49  3.000
 1SE  H7   C12  C11  118.73  3.000
 1SE  C13  C12  C11  119.78  3.000
 1SE  N16  C13  C14  116.71  3.000
 1SE  N16  C13  C12  125.07  3.000
 1SE  C14  C13  C12  118.22  3.000
 1SE  H8   C14  C15  118.34  3.000
 1SE  H8   C14  C13  119.66  3.000
 1SE  C15  C14  C13  122.00  3.000
 1SE  H9   C15  C14  118.76  3.000
 1SE  H9   C15  C10  121.43  3.000
 1SE  C14  C15  C10  119.81  3.000
 1SE  H10  N16  C17  117.01  3.000
 1SE  H10  N16  C13  113.84  3.000
 1SE  C17  N16  C13  129.06  3.000
 1SE  C19  C17  O18  120.79  3.000
 1SE  C19  C17  N16  115.14  3.000
 1SE  O18  C17  N16  124.06  3.000
 1SE  C24  C19  C20  118.31  3.000
 1SE  C24  C19  C17  117.60  3.000
 1SE  C20  C19  C17  124.06  3.000
 1SE  H11  C20  C21  117.47  3.000
 1SE  H11  C20  C19  121.15  3.000
 1SE  C21  C20  C19  121.36  3.000
 1SE  H12  C21  C22  118.54  3.000
 1SE  H12  C21  C20  120.31  3.000
 1SE  C22  C21  C20  121.15  3.000
 1SE  O28  C22  C23  125.49  3.000
 1SE  O28  C22  C21  117.31  3.000
 1SE  C23  C22  C21  117.20  3.000
 1SE  N25  C23  C24  117.96  3.000
 1SE  N25  C23  C22  120.80  3.000
 1SE  C24  C23  C22  121.24  3.000
 1SE  H13  C24  C23  119.52  3.000
 1SE  H13  C24  C19  119.76  3.000
 1SE  C23  C24  C19  120.72  3.000
 1SE  O27  N25  O26  122.71  3.000
 1SE  O26  N25  C23  117.97  3.000
 1SE  O27  N25  C23  119.32  3.000
 1SE  H14  O28  C22  109.29  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
 1SE  CONST_01  N4   C3   C2   C1     0.00   0.0  0
 1SE  CONST_02  N4   C5   C6   C1     0.00   0.0  0
 1SE  CONST_03  C5   C6   C1   C2     0.00   0.0  0
 1SE  CONST_04  C5   N4   C3   C2     0.00   0.0  0
 1SE  CONST_05  C6   C1   C2   C3     0.00   0.0  0
 1SE  CONST_06  C6   C5   N4   C3     0.00   0.0  0
 1SE  CONST_07  C13  C12  C11  C10    0.00   0.0  0
 1SE  CONST_08  C13  C14  C15  C10    0.00   0.0  0
 1SE  CONST_09  C14  C15  C10  C11    0.00   0.0  0
 1SE  CONST_10  C14  C13  C12  C11    0.00   0.0  0
 1SE  CONST_11  C15  C10  C11  C12    0.00   0.0  0
 1SE  CONST_12  C15  C14  C13  C12    0.00   0.0  0
 1SE  CONST_13  C22  C21  C20  C19    0.00   0.0  0
 1SE  CONST_14  C22  C23  C24  C19    0.00   0.0  0
 1SE  CONST_15  C23  C24  C19  C20    0.00   0.0  0
 1SE  CONST_16  C23  C22  C21  C20    0.00   0.0  0
 1SE  CONST_17  C24  C19  C20  C21    0.00   0.0  0
 1SE  CONST_18  C24  C23  C22  C21    0.00   0.0  0
 1SE  CONST_19  C7   C5   C6   C1   180.00   0.0  0
 1SE  CONST_20  C7   C5   N4   C3   180.00   0.0  0
 1SE  CONST_21  C12  C11  C10  N9   180.00   0.0  0
 1SE  CONST_22  C14  C15  C10  N9   180.00   0.0  0
 1SE  CONST_23  N16  C13  C12  C11  180.00   0.0  0
 1SE  CONST_24  N16  C13  C14  C15  180.00   0.0  0
 1SE  CONST_25  C21  C20  C19  C17  180.00   0.0  0
 1SE  CONST_26  C23  C24  C19  C17  180.00   0.0  0
 1SE  CONST_27  N25  C23  C24  C19  180.00   0.0  0
 1SE  CONST_28  O28  C22  C21  C20  180.00   0.0  0
 1SE  CONST_29  N25  C23  C22  C21  180.00   0.0  0
 1SE  CONST_30  O28  C22  C23  C24  180.00   0.0  0
 1SE  CONST_31  H3   C3   C2   C1   180.00   0.0  0
 1SE  CONST_32  H4   C6   C1   C2   180.00   0.0  0
 1SE  CONST_33  H1   C1   C2   C3   180.00   0.0  0
 1SE  CONST_34  H2   C2   C3   N4   180.00   0.0  0
 1SE  CONST_35  H7   C12  C11  C10  180.00   0.0  0
 1SE  CONST_36  H8   C14  C15  C10  180.00   0.0  0
 1SE  CONST_37  H9   C15  C10  C11  180.00   0.0  0
 1SE  CONST_38  H6   C11  C12  C13  180.00   0.0  0
 1SE  CONST_39  H12  C21  C20  C19  180.00   0.0  0
 1SE  CONST_40  H13  C24  C19  C20  180.00   0.0  0
 1SE  CONST_41  H11  C20  C21  C22  180.00   0.0  0
 1SE  CONST_42  C10  N9   C7   C5   180.00   0.0  0
 1SE  CONST_43  C19  C17  N16  C13  180.00   0.0  0
 1SE  CONST_44  C11  C10  N9   C7   180.00   0.0  0
 1SE  CONST_45  C15  C10  N9   C7     0.00   0.0  0
 1SE  CONST_46  C17  N16  C13  C12    0.00   0.0  0
 1SE  CONST_47  C17  N16  C13  C14  180.00   0.0  0
 1SE  CONST_48  O27  N25  C23  C22  180.00   0.0  0
 1SE  CONST_49  O26  N25  C23  C22    0.00   0.0  0
 1SE  CONST_50  O27  N25  C23  C24    0.00   0.0  0
 1SE  CONST_51  O26  N25  C23  C24  180.00   0.0  0
 1SE  CONST_52  H5   N9   C10  C11    0.00   0.0  0
 1SE  CONST_53  H10  N16  C13  C12  180.00   0.0  0
 1SE  CONST_54  C10  N9   C7   O8     0.00   0.0  0
 1SE  CONST_55  O18  C17  N16  C13    0.00   0.0  0
 1SE  Var_01    N9   C7   C5   N4    -0.39  30.0  2
 1SE  Var_02    C20  C19  C17  N16   23.71  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
 1SE  plan-1  C1   0.020
 1SE  plan-1  C2   0.020
 1SE  plan-1  C3   0.020
 1SE  plan-1  N4   0.020
 1SE  plan-1  C5   0.020
 1SE  plan-1  C6   0.020
 1SE  plan-1  C7   0.020
 1SE  plan-1  H1   0.020
 1SE  plan-1  H2   0.020
 1SE  plan-1  H3   0.020
 1SE  plan-1  H4   0.020
 1SE  plan-2  N9   0.020
 1SE  plan-2  C10  0.020
 1SE  plan-2  C11  0.020
 1SE  plan-2  C12  0.020
 1SE  plan-2  C13  0.020
 1SE  plan-2  C14  0.020
 1SE  plan-2  C15  0.020
 1SE  plan-2  N16  0.020
 1SE  plan-2  H6   0.020
 1SE  plan-2  H7   0.020
 1SE  plan-2  H8   0.020
 1SE  plan-2  H9   0.020
 1SE  plan-3  C17  0.020
 1SE  plan-3  C19  0.020
 1SE  plan-3  C20  0.020
 1SE  plan-3  C21  0.020
 1SE  plan-3  C22  0.020
 1SE  plan-3  C23  0.020
 1SE  plan-3  C24  0.020
 1SE  plan-3  N25  0.020
 1SE  plan-3  O28  0.020
 1SE  plan-3  H11  0.020
 1SE  plan-3  H12  0.020
 1SE  plan-3  H13  0.020
 1SE  plan-4  C5   0.020
 1SE  plan-4  C7   0.020
 1SE  plan-4  O8   0.020
 1SE  plan-4  N9   0.020
 1SE  plan-4  C10  0.020
 1SE  plan-4  H5   0.020
 1SE  plan-5  C13  0.020
 1SE  plan-5  N16  0.020
 1SE  plan-5  C17  0.020
 1SE  plan-5  O18  0.020
 1SE  plan-5  C19  0.020
 1SE  plan-5  H10  0.020
 1SE  plan-6  C23  0.020
 1SE  plan-6  N25  0.020
 1SE  plan-6  O26  0.020
 1SE  plan-6  O27  0.020

