# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 16:42:36 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: 5-nitro-2-[(pyridin-2-ylmethyl)amino]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1cc(ccc1NCc2ccccn2)[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
 Z02  Z02  5-nitro-2-[(pyridin-2-ylmethyl)amino]benzamide  ligand  32  20  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Z02
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
 Z02  N01   N  N      1   0.319   4.6398  -0.7344  -0.0078
 Z02  N02   N  NH2    0  -0.804   1.5138   3.2438   0.4666
 Z02  N03   N  NH1    0  -0.702  -0.8968  -0.1062  -0.0824
 Z02  N04   N  N      0  -0.451  -3.4442   0.5170   0.1811
 Z02  C05   C  CR16   0  -0.314   2.6601   0.6562   0.3087
 Z02  C06   C  CR6    0  -0.122   1.2929   0.8526   0.2831
 Z02  C07   C  CR6    0   0.422   0.4326  -0.2288  -0.0835
 Z02  C08   C  CR16   0  -0.364   1.0404  -1.4450  -0.4809
 Z02  C09   C  CR16   0  -0.256   2.3994  -1.6109  -0.4646
 Z02  C10   C  CR6    0   0.233   3.2207  -0.5607  -0.0546
 Z02  C11   C  C      0   0.522   0.7281   2.1772   0.6705
 Z02  C12   C  CH2    0  -0.316  -1.8057  -1.1499  -0.4650
 Z02  C13   C  CR6    0   0.240  -3.2333  -0.6788  -0.3452
 Z02  C14   C  CR16   0  -0.057  -4.6962   0.9479   0.3098
 Z02  C15   C  CR16   0  -0.337  -5.7946   0.2032  -0.0796
 Z02  C16   C  CR16   0  -0.145  -5.5723  -1.0526  -0.6316
 Z02  C17   C  CR16   0  -0.328  -4.2720  -1.5028  -0.7693
 Z02  O18   O  O      0  -0.493  -0.3958   2.2805   1.1552
 Z02  O19   O  O     -1  -0.405   5.3277   0.1937   0.3668
 Z02  O20   O  O      0  -0.403   5.1005  -1.8051  -0.3480
 Z02  HN02  H  HNH2   0   0.416   2.3590   3.2044  -0.0757
 Z02  HN0A  H  HNH2   0   0.409   1.1724   4.1595   0.7104
 Z02  HN03  H  HNH1   0   0.425  -1.3112   0.7310   0.3117
 Z02  H05   H  HCR6   0   0.293   3.3071   1.4581   0.6357
 Z02  H08   H  HCR6   0   0.294   0.4273  -2.2781  -0.7927
 Z02  H09   H  HCR6   0   0.297   2.8167  -2.5612  -0.7646
 Z02  H12   H  HCH2   0   0.269  -1.6215  -1.4725  -1.4951
 Z02  H12A  H  HCH2   0   0.270  -1.6773  -2.0396   0.1638
 Z02  H14   H  HCR6   0   0.267  -4.8238   1.9327   0.7445
 Z02  H15   H  HCR6   0   0.274  -6.7941   0.5952   0.0458
 Z02  H16   H  HCR6   0   0.277  -6.4024  -1.6701  -0.9486
 Z02  H17   H  HCR6   0   0.271  -4.0585  -2.4743  -1.1963

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
 Z02  N01  C10   single    1.430  0.020  1.430
 Z02  N01  O19   single    1.214  0.020  1.214
 Z02  N01  O20   double    1.214  0.020  1.214
 Z02  N02  C11   single    1.340  0.020  1.340
 Z02  N02  HN02  single    0.860  0.020  1.020
 Z02  N02  HN0A  single    0.860  0.020  1.020
 Z02  N03  C07   single    1.335  0.020  1.335
 Z02  N03  C12   single    1.436  0.020  1.436
 Z02  N03  HN03  single    0.860  0.020  1.020
 Z02  N04  C13   aromatic  1.323  0.020  1.323
 Z02  N04  C14   aromatic  1.330  0.020  1.330
 Z02  C05  C06   aromatic  1.382  0.020  1.382
 Z02  C05  C10   aromatic  1.388  0.020  1.388
 Z02  C05  H05   single    0.930  0.020  1.080
 Z02  C06  C07   aromatic  1.430  0.020  1.430
 Z02  C06  C11   single    1.491  0.020  1.491
 Z02  C07  C08   aromatic  1.417  0.020  1.417
 Z02  C08  C09   aromatic  1.369  0.020  1.369
 Z02  C08  H08   single    0.930  0.020  1.080
 Z02  C09  C10   aromatic  1.395  0.020  1.395
 Z02  C09  H09   single    0.930  0.020  1.080
 Z02  C11  O18   double    1.228  0.020  1.228
 Z02  C12  C13   single    1.508  0.020  1.508
 Z02  C12  H12   single    0.970  0.020  1.090
 Z02  C12  H12A  single    0.970  0.020  1.090
 Z02  C13  C17   aromatic  1.392  0.020  1.392
 Z02  C14  C15   aromatic  1.383  0.020  1.383
 Z02  C14  H14   single    0.930  0.020  1.080
 Z02  C15  C16   aromatic  1.390  0.020  1.390
 Z02  C15  H15   single    0.930  0.020  1.080
 Z02  C16  C17   aromatic  1.383  0.020  1.383
 Z02  C16  H16   single    0.930  0.020  1.080
 Z02  C17  H17   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
 Z02  O20   N01  O19   123.05  3.000
 Z02  O20   N01  C10   118.31  3.000
 Z02  O19   N01  C10   118.63  3.000
 Z02  HN0A  N02  HN02  116.83  3.000
 Z02  HN0A  N02  C11   119.21  3.000
 Z02  HN02  N02  C11   122.94  3.000
 Z02  HN03  N03  C12   116.42  3.000
 Z02  HN03  N03  C07   118.89  3.000
 Z02  C12   N03  C07   124.29  3.000
 Z02  C14   N04  C13   118.76  3.000
 Z02  H05   C05  C10   119.20  3.000
 Z02  H05   C05  C06   119.50  3.000
 Z02  C10   C05  C06   121.29  3.000
 Z02  C11   C06  C07   120.71  3.000
 Z02  C11   C06  C05   119.76  3.000
 Z02  C07   C06  C05   119.52  3.000
 Z02  C08   C07  C06   117.60  3.000
 Z02  C08   C07  N03   120.41  3.000
 Z02  C06   C07  N03   121.97  3.000
 Z02  H08   C08  C09   118.25  3.000
 Z02  H08   C08  C07   119.98  3.000
 Z02  C09   C08  C07   121.77  3.000
 Z02  H09   C09  C10   121.09  3.000
 Z02  H09   C09  C08   119.12  3.000
 Z02  C10   C09  C08   119.78  3.000
 Z02  C09   C10  C05   119.95  3.000
 Z02  C09   C10  N01   120.16  3.000
 Z02  C05   C10  N01   119.90  3.000
 Z02  O18   C11  C06   121.59  3.000
 Z02  O18   C11  N02   121.97  3.000
 Z02  C06   C11  N02   116.45  3.000
 Z02  H12A  C12  H12   106.29  3.000
 Z02  H12A  C12  C13   108.58  3.000
 Z02  H12   C12  C13   109.02  3.000
 Z02  H12A  C12  N03   111.26  3.000
 Z02  H12   C12  N03   111.00  3.000
 Z02  C13   C12  N03   110.55  3.000
 Z02  C17   C13  C12   119.82  3.000
 Z02  C17   C13  N04   122.48  3.000
 Z02  C12   C13  N04   117.69  3.000
 Z02  H14   C14  C15   120.57  3.000
 Z02  H14   C14  N04   116.35  3.000
 Z02  C15   C14  N04   123.08  3.000
 Z02  H15   C15  C16   121.45  3.000
 Z02  H15   C15  C14   120.43  3.000
 Z02  C16   C15  C14   118.12  3.000
 Z02  H16   C16  C17   120.42  3.000
 Z02  H16   C16  C15   120.62  3.000
 Z02  C17   C16  C15   118.96  3.000
 Z02  H17   C17  C16   121.13  3.000
 Z02  H17   C17  C13   120.28  3.000
 Z02  C16   C17  C13   118.59  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
 Z02  CONST_01  C16   C17  C13  N04    0.00   0.0  0
 Z02  CONST_02  C16   C15  C14  N04    0.00   0.0  0
 Z02  CONST_03  C08   C07  C06  C05    0.00   0.0  0
 Z02  CONST_04  C08   C09  C10  C05    0.00   0.0  0
 Z02  CONST_05  C09   C10  C05  C06    0.00   0.0  0
 Z02  CONST_06  C09   C08  C07  C06    0.00   0.0  0
 Z02  CONST_07  C10   C05  C06  C07    0.00   0.0  0
 Z02  CONST_08  C10   C09  C08  C07    0.00   0.0  0
 Z02  CONST_09  C15   C14  N04  C13    0.00   0.0  0
 Z02  CONST_10  C15   C16  C17  C13    0.00   0.0  0
 Z02  CONST_11  C17   C13  N04  C14    0.00   0.0  0
 Z02  CONST_12  C17   C16  C15  C14    0.00   0.0  0
 Z02  CONST_13  C06   C05  C10  N01  180.00   0.0  0
 Z02  CONST_14  C08   C09  C10  N01  180.00   0.0  0
 Z02  CONST_15  C05   C06  C07  N03  180.00   0.0  0
 Z02  CONST_16  C09   C08  C07  N03  180.00   0.0  0
 Z02  CONST_17  C11   C06  C07  C08  180.00   0.0  0
 Z02  CONST_18  C11   C06  C05  C10  180.00   0.0  0
 Z02  CONST_19  C14   N04  C13  C12  180.00   0.0  0
 Z02  CONST_20  C16   C17  C13  C12  180.00   0.0  0
 Z02  CONST_21  H17   C17  C13  N04  180.00   0.0  0
 Z02  CONST_22  H15   C15  C14  N04  180.00   0.0  0
 Z02  CONST_23  H09   C09  C10  C05  180.00   0.0  0
 Z02  CONST_24  H08   C08  C07  C06  180.00   0.0  0
 Z02  CONST_25  H05   C05  C06  C07  180.00   0.0  0
 Z02  CONST_26  H14   C14  N04  C13  180.00   0.0  0
 Z02  CONST_27  H16   C16  C17  C13  180.00   0.0  0
 Z02  CONST_28  O19   N01  C10  C05    0.00   0.0  0
 Z02  CONST_29  O20   N01  C10  C05  180.00   0.0  0
 Z02  CONST_30  C12   N03  C07  C06  180.00   0.0  0
 Z02  CONST_31  C12   N03  C07  C08    0.00   0.0  0
 Z02  CONST_32  O19   N01  C10  C09  180.00   0.0  0
 Z02  CONST_33  O20   N01  C10  C09    0.00   0.0  0
 Z02  CONST_34  HN03  N03  C07  C06    0.00   0.0  0
 Z02  CONST_35  HN02  N02  C11  C06    0.00   0.0  0
 Z02  CONST_36  HN0A  N02  C11  C06  180.00   0.0  0
 Z02  Var_01    C05   C06  C11  N02   28.18  30.0  2
 Z02  Var_02    N04   C13  C12  N03   -5.74  30.0  2
 Z02  Var_03    C13   C12  N03  C07  179.88  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
 Z02  plan-1  N04   0.020
 Z02  plan-1  C12   0.020
 Z02  plan-1  C13   0.020
 Z02  plan-1  C14   0.020
 Z02  plan-1  C15   0.020
 Z02  plan-1  C16   0.020
 Z02  plan-1  C17   0.020
 Z02  plan-1  H14   0.020
 Z02  plan-1  H15   0.020
 Z02  plan-1  H16   0.020
 Z02  plan-1  H17   0.020
 Z02  plan-2  N01   0.020
 Z02  plan-2  N03   0.020
 Z02  plan-2  C05   0.020
 Z02  plan-2  C06   0.020
 Z02  plan-2  C07   0.020
 Z02  plan-2  C08   0.020
 Z02  plan-2  C09   0.020
 Z02  plan-2  C10   0.020
 Z02  plan-2  C11   0.020
 Z02  plan-2  H05   0.020
 Z02  plan-2  H08   0.020
 Z02  plan-2  H09   0.020
 Z02  plan-3  N02   0.020
 Z02  plan-3  C06   0.020
 Z02  plan-3  C11   0.020
 Z02  plan-3  O18   0.020
 Z02  plan-3  HN02  0.020
 Z02  plan-3  HN0A  0.020
 Z02  plan-4  N01   0.020
 Z02  plan-4  C10   0.020
 Z02  plan-4  O19   0.020
 Z02  plan-4  O20   0.020
 Z02  plan-5  N03   0.020
 Z02  plan-5  C07   0.020
 Z02  plan-5  C12   0.020
 Z02  plan-5  HN03  0.020

