# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 15:41:40 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: 5-nitro-2-[(pyridin-3-ylmethyl)amino]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1cc(ccc1NCc2cccnc2)[N+]([O-])=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
 X07  X07  5-nitro-2-[(pyridin-3-ylmethyl)amino]benzamide  ligand  32  20  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_X07
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
 X07  C1    C  CR16   0  -0.359  -1.0496  -1.5610  -0.0442
 X07  C2    C  CR16   0  -0.256  -2.4115  -1.6810  -0.1299
 X07  C3    C  CR6    0   0.237  -3.2105  -0.5390  -0.0909
 X07  C4    C  CR16   0  -0.316  -2.6266   0.7156   0.0123
 X07  C5    C  CR6    0  -0.121  -1.2542   0.8626   0.0805
 X07  C6    C  CR6    0   0.419  -0.4229  -0.2993   0.0829
 X07  N7    N  NH1    0  -0.684   0.9097  -0.2025   0.1785
 X07  C8    C  C      0   0.534  -0.6541   2.2244   0.1802
 X07  N9    N  NH2    0  -0.804  -1.3718   3.2364  -0.3231
 X07  O10   O  O      0  -0.498   0.4433   2.4065   0.7054
 X07  N11   N  N      1   0.321  -4.6368  -0.6579  -0.1492
 X07  O12   O  O      0  -0.400  -5.1171  -1.7663  -0.2646
 X07  O13   O  O     -1  -0.403  -5.3068   0.3522  -0.0815
 X07  C14   C  CH2    0  -0.345   1.8164  -1.3285   0.1782
 X07  C15   C  CR16   0  -0.064   5.8182  -0.0206  -0.1404
 X07  N16   N  N      0  -0.400   5.4298  -0.6442   0.9641
 X07  C17   C  CR16   0  -0.095   4.1648  -1.0411   1.0400
 X07  C18   C  CR6    0  -0.019   3.2303  -0.8464   0.0313
 X07  C19   C  CR16   0  -0.168   3.6532  -0.1893  -1.1198
 X07  C20   C  CR16   0  -0.318   4.9685   0.2316  -1.2093
 X07  H1    H  HCR6   0   0.295  -0.4517  -2.4609  -0.0526
 X07  H2    H  HCR6   0   0.298  -2.8494  -2.6654  -0.2121
 X07  H4    H  HCR6   0   0.294  -3.2628   1.5885   0.0561
 X07  HN7   H  HNH1   0   0.414   1.2679   0.7023   0.4550
 X07  HN9   H  HNH2   0   0.417  -2.1827   3.0985  -0.9001
 X07  HN9A  H  HNH2   0   0.411  -1.0013   4.1719  -0.2764
 X07  H14   H  HCH2   0   0.264   1.7164  -1.9218   1.0935
 X07  H14A  H  HCH2   0   0.268   1.5780  -1.9930  -0.6563
 X07  H17   H  HCR6   0   0.264   3.8710  -1.5483   1.9543
 X07  H19   H  HCR6   0   0.275   2.9629  -0.0153  -1.9365
 X07  H20   H  HCR6   0   0.275   5.3351   0.7420  -2.0891
 X07  H15   H  HCR6   0   0.267   6.8548   0.2946  -0.1817

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
 X07  C1   C2    aromatic  1.370  0.020  1.370
 X07  C1   C6    aromatic  1.414  0.020  1.414
 X07  C1   H1    single    0.930  0.020  1.080
 X07  C2   C3    aromatic  1.394  0.020  1.394
 X07  C2   H2    single    0.930  0.020  1.080
 X07  C3   C4    aromatic  1.388  0.020  1.388
 X07  C3   N11   single    1.432  0.020  1.432
 X07  C4   C5    aromatic  1.382  0.020  1.382
 X07  C4   H4    single    0.930  0.020  1.080
 X07  C5   C6    aromatic  1.429  0.020  1.429
 X07  C5   C8    single    1.492  0.020  1.492
 X07  C6   N7    single    1.339  0.020  1.339
 X07  N7   C14   single    1.446  0.020  1.446
 X07  N7   HN7   single    0.860  0.020  1.020
 X07  C8   N9    single    1.339  0.020  1.339
 X07  C8   O10   double    1.230  0.020  1.230
 X07  N9   HN9   single    0.860  0.020  1.020
 X07  N9   HN9A  single    0.860  0.020  1.020
 X07  N11  O12   double    1.214  0.020  1.214
 X07  N11  O13   single    1.214  0.020  1.214
 X07  C14  C18   single    1.501  0.020  1.501
 X07  C14  H14   single    0.970  0.020  1.090
 X07  C14  H14A  single    0.970  0.020  1.090
 X07  C15  N16   aromatic  1.326  0.020  1.326
 X07  C15  C20   aromatic  1.389  0.020  1.389
 X07  C15  H15   single    0.930  0.020  1.080
 X07  N16  C17   aromatic  1.328  0.020  1.328
 X07  C17  C18   aromatic  1.389  0.020  1.389
 X07  C17  H17   single    0.930  0.020  1.080
 X07  C18  C19   aromatic  1.391  0.020  1.391
 X07  C19  C20   aromatic  1.384  0.020  1.384
 X07  C19  H19   single    0.930  0.020  1.080
 X07  C20  H20   single    0.930  0.020  1.080

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
 X07  H1    C1   C6   119.90  3.000
 X07  H1    C1   C2   118.47  3.000
 X07  C6    C1   C2   121.62  3.000
 X07  H2    C2   C3   121.07  3.000
 X07  H2    C2   C1   119.18  3.000
 X07  C3    C2   C1   119.75  3.000
 X07  N11   C3   C4   119.80  3.000
 X07  N11   C3   C2   120.10  3.000
 X07  C4    C3   C2   120.10  3.000
 X07  H4    C4   C5   119.77  3.000
 X07  H4    C4   C3   119.04  3.000
 X07  C5    C4   C3   121.18  3.000
 X07  C8    C5   C6   120.55  3.000
 X07  C8    C5   C4   120.00  3.000
 X07  C6    C5   C4   119.44  3.000
 X07  N7    C6   C5   121.35  3.000
 X07  N7    C6   C1   120.77  3.000
 X07  C5    C6   C1   117.87  3.000
 X07  HN7   N7   C14  118.33  3.000
 X07  HN7   N7   C6   115.88  3.000
 X07  C14   N7   C6   124.59  3.000
 X07  O10   C8   N9   121.79  3.000
 X07  O10   C8   C5   121.51  3.000
 X07  N9    C8   C5   116.70  3.000
 X07  HN9A  N9   HN9  116.80  3.000
 X07  HN9A  N9   C8   119.17  3.000
 X07  HN9   N9   C8   123.01  3.000
 X07  O13   N11  O12  123.15  3.000
 X07  O13   N11  C3   118.57  3.000
 X07  O12   N11  C3   118.28  3.000
 X07  H14A  C14  H14  106.78  3.000
 X07  H14A  C14  C18  109.02  3.000
 X07  H14   C14  C18  109.98  3.000
 X07  H14A  C14  N7   109.69  3.000
 X07  H14   C14  N7   111.37  3.000
 X07  C18   C14  N7   109.92  3.000
 X07  H15   C15  C20  120.19  3.000
 X07  H15   C15  N16  116.64  3.000
 X07  C20   C15  N16  123.18  3.000
 X07  C17   N16  C15  117.84  3.000
 X07  H17   C17  C18  119.67  3.000
 X07  H17   C17  N16  116.45  3.000
 X07  C18   C17  N16  123.88  3.000
 X07  C19   C18  C17  117.56  3.000
 X07  C19   C18  C14  121.27  3.000
 X07  C17   C18  C14  121.18  3.000
 X07  H19   C19  C20  120.53  3.000
 X07  H19   C19  C18  120.39  3.000
 X07  C20   C19  C18  119.08  3.000
 X07  H20   C20  C19  121.23  3.000
 X07  H20   C20  C15  120.31  3.000
 X07  C19   C20  C15  118.46  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
 X07  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 X07  CONST_02  C4    C5   C6   C1     0.00   0.0  0
 X07  CONST_03  C5    C6   C1   C2     0.00   0.0  0
 X07  CONST_04  C5    C4   C3   C2     0.00   0.0  0
 X07  CONST_05  C6    C1   C2   C3     0.00   0.0  0
 X07  CONST_06  C6    C5   C4   C3     0.00   0.0  0
 X07  CONST_07  C18   C17  N16  C15    0.00   0.0  0
 X07  CONST_08  C18   C19  C20  C15    0.00   0.0  0
 X07  CONST_09  C19   C20  C15  N16    0.00   0.0  0
 X07  CONST_10  C19   C18  C17  N16    0.00   0.0  0
 X07  CONST_11  C20   C15  N16  C17    0.00   0.0  0
 X07  CONST_12  C20   C19  C18  C17    0.00   0.0  0
 X07  CONST_13  N11   C3   C2   C1   180.00   0.0  0
 X07  CONST_14  C8    C5   C6   C1   180.00   0.0  0
 X07  CONST_15  N7    C6   C1   C2   180.00   0.0  0
 X07  CONST_16  C8    C5   C4   C3   180.00   0.0  0
 X07  CONST_17  N7    C6   C5   C4   180.00   0.0  0
 X07  CONST_18  N11   C3   C4   C5   180.00   0.0  0
 X07  CONST_19  N16   C17  C18  C14  180.00   0.0  0
 X07  CONST_20  C20   C19  C18  C14  180.00   0.0  0
 X07  CONST_21  H4    C4   C3   C2   180.00   0.0  0
 X07  CONST_22  H1    C1   C2   C3   180.00   0.0  0
 X07  CONST_23  H2    C2   C3   C4   180.00   0.0  0
 X07  CONST_24  H17   C17  N16  C15  180.00   0.0  0
 X07  CONST_25  H19   C19  C20  C15  180.00   0.0  0
 X07  CONST_26  H20   C20  C15  N16  180.00   0.0  0
 X07  CONST_27  H15   C15  N16  C17  180.00   0.0  0
 X07  CONST_28  C14   N7   C6   C1     0.00   0.0  0
 X07  CONST_29  O12   N11  C3   C2     0.00   0.0  0
 X07  CONST_30  O13   N11  C3   C2   180.00   0.0  0
 X07  CONST_31  O12   N11  C3   C4   180.00   0.0  0
 X07  CONST_32  O13   N11  C3   C4     0.00   0.0  0
 X07  CONST_33  C14   N7   C6   C5   180.00   0.0  0
 X07  CONST_34  HN7   N7   C6   C1   180.00   0.0  0
 X07  CONST_35  HN9   N9   C8   C5     0.00   0.0  0
 X07  CONST_36  HN9A  N9   C8   C5   180.00   0.0  0
 X07  Var_01    N9    C8   C5   C4   -26.04  30.0  2
 X07  Var_02    C18   C14  N7   C6   169.04  30.0  3
 X07  Var_03    C17   C18  C14  N7   116.16  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
 X07  plan-1  C1    0.020
 X07  plan-1  C2    0.020
 X07  plan-1  C3    0.020
 X07  plan-1  C4    0.020
 X07  plan-1  C5    0.020
 X07  plan-1  C6    0.020
 X07  plan-1  N7    0.020
 X07  plan-1  C8    0.020
 X07  plan-1  N11   0.020
 X07  plan-1  H1    0.020
 X07  plan-1  H2    0.020
 X07  plan-1  H4    0.020
 X07  plan-2  C14   0.020
 X07  plan-2  C15   0.020
 X07  plan-2  N16   0.020
 X07  plan-2  C17   0.020
 X07  plan-2  C18   0.020
 X07  plan-2  C19   0.020
 X07  plan-2  C20   0.020
 X07  plan-2  H17   0.020
 X07  plan-2  H19   0.020
 X07  plan-2  H20   0.020
 X07  plan-2  H15   0.020
 X07  plan-3  C5    0.020
 X07  plan-3  C8    0.020
 X07  plan-3  N9    0.020
 X07  plan-3  O10   0.020
 X07  plan-3  HN9   0.020
 X07  plan-3  HN9A  0.020
 X07  plan-4  C6    0.020
 X07  plan-4  N7    0.020
 X07  plan-4  C14   0.020
 X07  plan-4  HN7   0.020
 X07  plan-5  C3    0.020
 X07  plan-5  N11   0.020
 X07  plan-5  O12   0.020
 X07  plan-5  O13   0.020

