# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 19:59:42 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: 4-chloro-5-nitro-2-[(pyridin-3-ylmethyl)amino]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1cc(c(Cl)cc1NCc2cccnc2)[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
 X4B  X4B  4-chloro-5-nitro-2-[(pyridin-3-ylmethyl)amino]benzamide  ligand  32  21  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_X4B
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
 X4B  N01   N   NH2    0  -0.804   0.6916   3.7197  -0.2257
 X4B  N02   N   NH1    0  -0.681  -1.2738   0.0463   0.0536
 X4B  N03   N   N      0  -0.402  -5.5047  -0.2986  -1.2336
 X4B  N04   N   N      1   0.320   4.3136   0.2368   0.0504
 X4B  C05   C   CR16   0  -0.330   2.1480   1.3078   0.1357
 X4B  C06   C   CR6    0  -0.114   0.7706   1.3337   0.1076
 X4B  C07   C   CR6    0   0.419   0.0612   0.0982   0.0310
 X4B  C08   C   CR16   0  -0.323   0.8151  -1.0882  -0.0899
 X4B  C09   C   CR6    0  -0.052   2.1887  -1.0814  -0.0979
 X4B  C10   C   CR6    0   0.294   2.8818   0.1316   0.0295
 X4B  C11   C   C      0   0.535   0.0374   2.6289   0.1909
 X4B  C12   C   CH2    0  -0.356  -2.0437  -1.1748  -0.0667
 X4B  C13   C   CR6    0  -0.030  -3.5081  -0.8527  -0.0278
 X4B  C14   C   CR16   0  -0.078  -4.2161  -0.6111  -1.2000
 X4B  C15   C   CR16   0  -0.063  -6.1513  -0.2092  -0.0771
 X4B  C16   C   CR16   0  -0.319  -5.5455  -0.4285   1.1513
 X4B  C17   C   CR16   0  -0.168  -4.1994  -0.7562   1.1734
 X4B  O18   O   O      0  -0.496  -1.1107   2.6852   0.6281
 X4B  O19   O   O     -1  -0.384   4.9711  -0.6500  -0.4432
 X4B  O20   O   O      0  -0.395   4.7998   1.2293   0.5528
 X4B  CL21  CL  CL     0  -0.056   2.9612  -2.6145  -0.1797
 X4B  H101  H   HNH2   0   0.419   1.5482   3.6781  -0.7498
 X4B  H201  H   HNH2   0   0.412   0.2296   4.6140  -0.1840
 X4B  HN02  H   HNH1   0   0.415  -1.7527   0.9103   0.2706
 X4B  H05   H   HCR6   0   0.300   2.6960   2.2330   0.2454
 X4B  H08   H   HCR6   0   0.314   0.3076  -2.0397  -0.1561
 X4B  H112  H   HCH2   0   0.269  -1.7971  -1.6796  -1.0049
 X4B  H212  H   HCH2   0   0.268  -1.7973  -1.8679   0.7441
 X4B  H14   H   HCR6   0   0.264  -3.7102  -0.6831  -2.1583
 X4B  H15   H   HCR6   0   0.268  -7.2040   0.0455  -0.1282
 X4B  H16   H   HCR6   0   0.276  -6.1183  -0.3467   2.0645
 X4B  H17   H   HCR6   0   0.276  -3.6938  -0.9417   2.1133

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
 X4B  N01  C11   single    1.338  0.020  1.338
 X4B  N01  H101  single    0.860  0.020  1.020
 X4B  N01  H201  single    0.860  0.020  1.020
 X4B  N02  C07   single    1.336  0.020  1.336
 X4B  N02  C12   single    1.449  0.020  1.449
 X4B  N02  HN02  single    0.860  0.020  1.020
 X4B  N04  O20   double    1.214  0.020  1.214
 X4B  C05  C10   aromatic  1.390  0.020  1.390
 X4B  C05  H05   single    0.930  0.020  1.080
 X4B  C06  C05   aromatic  1.378  0.020  1.378
 X4B  C06  C07   aromatic  1.427  0.020  1.427
 X4B  C07  C08   aromatic  1.411  0.020  1.411
 X4B  C08  C09   aromatic  1.374  0.020  1.374
 X4B  C08  H08   single    0.930  0.020  1.080
 X4B  C09  CL21  single    1.719  0.020  1.719
 X4B  C10  N04   single    1.436  0.020  1.436
 X4B  C10  C09   aromatic  1.403  0.020  1.403
 X4B  C11  C06   single    1.491  0.020  1.491
 X4B  C12  C13   single    1.500  0.020  1.500
 X4B  C12  H112  single    0.970  0.020  1.090
 X4B  C12  H212  single    0.970  0.020  1.090
 X4B  C13  C14   aromatic  1.391  0.020  1.391
 X4B  C14  N03   aromatic  1.326  0.020  1.326
 X4B  C14  H14   single    0.930  0.020  1.080
 X4B  C15  N03   aromatic  1.328  0.020  1.328
 X4B  C15  H15   single    0.930  0.020  1.080
 X4B  C16  C15   aromatic  1.387  0.020  1.387
 X4B  C16  H16   single    0.930  0.020  1.080
 X4B  C17  C13   aromatic  1.389  0.020  1.389
 X4B  C17  C16   aromatic  1.386  0.020  1.386
 X4B  C17  H17   single    0.930  0.020  1.080
 X4B  O18  C11   double    1.230  0.020  1.230
 X4B  O19  N04   single    1.209  0.020  1.209

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
 X4B  H201  N01  H101  116.69  3.000
 X4B  H201  N01  C11   119.11  3.000
 X4B  H101  N01  C11   123.03  3.000
 X4B  HN02  N02  C12   119.10  3.000
 X4B  HN02  N02  C07   116.33  3.000
 X4B  C12   N02  C07   124.22  3.000
 X4B  C15   N03  C14   117.83  3.000
 X4B  O20   N04  O19   123.42  3.000
 X4B  O19   N04  C10   118.84  3.000
 X4B  O20   N04  C10   117.73  3.000
 X4B  H05   C05  C10   117.66  3.000
 X4B  H05   C05  C06   119.53  3.000
 X4B  C10   C05  C06   122.81  3.000
 X4B  C11   C06  C07   120.72  3.000
 X4B  C11   C06  C05   120.46  3.000
 X4B  C07   C06  C05   118.80  3.000
 X4B  C08   C07  C06   117.85  3.000
 X4B  C08   C07  N02   120.18  3.000
 X4B  C06   C07  N02   121.97  3.000
 X4B  H08   C08  C09   118.27  3.000
 X4B  H08   C08  C07   119.66  3.000
 X4B  C09   C08  C07   122.05  3.000
 X4B  CL21  C09  C10   123.61  3.000
 X4B  C10   C09  C08   119.86  3.000
 X4B  CL21  C09  C08   116.44  3.000
 X4B  C09   C10  C05   118.53  3.000
 X4B  C09   C10  N04   123.88  3.000
 X4B  C05   C10  N04   117.59  3.000
 X4B  O18   C11  C06   121.25  3.000
 X4B  O18   C11  N01   121.98  3.000
 X4B  C06   C11  N01   116.77  3.000
 X4B  H212  C12  H112  107.01  3.000
 X4B  H212  C12  C13   109.66  3.000
 X4B  H112  C12  C13   109.97  3.000
 X4B  H212  C12  N02   110.65  3.000
 X4B  H112  C12  N02   109.91  3.000
 X4B  C13   C12  N02   109.62  3.000
 X4B  C17   C13  C14   117.61  3.000
 X4B  C17   C13  C12   121.55  3.000
 X4B  C14   C13  C12   120.83  3.000
 X4B  H14   C14  C13   119.68  3.000
 X4B  H14   C14  N03   116.47  3.000
 X4B  C13   C14  N03   123.84  3.000
 X4B  H15   C15  C16   120.20  3.000
 X4B  C16   C15  N03   123.23  3.000
 X4B  H15   C15  N03   116.58  3.000
 X4B  H16   C16  C17   121.27  3.000
 X4B  C17   C16  C15   118.41  3.000
 X4B  H16   C16  C15   120.31  3.000
 X4B  H17   C17  C16   120.51  3.000
 X4B  H17   C17  C13   120.40  3.000
 X4B  C16   C17  C13   119.08  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
 X4B  CONST_01  C17   C13  C14  N03     0.00   0.0  0
 X4B  CONST_02  C17   C16  C15  N03     0.00   0.0  0
 X4B  CONST_03  C08   C09  C10  C05     0.00   0.0  0
 X4B  CONST_04  C08   C07  C06  C05     0.00   0.0  0
 X4B  CONST_05  C09   C10  C05  C06     0.00   0.0  0
 X4B  CONST_06  C09   C08  C07  C06     0.00   0.0  0
 X4B  CONST_07  C10   C05  C06  C07     0.00   0.0  0
 X4B  CONST_08  C10   C09  C08  C07     0.00   0.0  0
 X4B  CONST_09  C15   N03  C14  C13     0.00   0.0  0
 X4B  CONST_10  C15   C16  C17  C13     0.00   0.0  0
 X4B  CONST_11  C16   C17  C13  C14     0.00   0.0  0
 X4B  CONST_12  C16   C15  N03  C14     0.00   0.0  0
 X4B  CONST_13  C05   C06  C07  N02   180.00   0.0  0
 X4B  CONST_14  C09   C08  C07  N02   180.00   0.0  0
 X4B  CONST_15  C12   C13  C14  N03   180.00   0.0  0
 X4B  CONST_16  C06   C05  C10  N04   180.00   0.0  0
 X4B  CONST_17  C08   C09  C10  N04   180.00   0.0  0
 X4B  CONST_18  CL21  C09  C10  C05   180.00   0.0  0
 X4B  CONST_19  CL21  C09  C08  C07   180.00   0.0  0
 X4B  CONST_20  C11   C06  C07  C08   180.00   0.0  0
 X4B  CONST_21  C11   C06  C05  C10   180.00   0.0  0
 X4B  CONST_22  C16   C17  C13  C12   180.00   0.0  0
 X4B  CONST_23  H16   C16  C15  N03   180.00   0.0  0
 X4B  CONST_24  H08   C08  C07  C06   180.00   0.0  0
 X4B  CONST_25  H05   C05  C06  C07   180.00   0.0  0
 X4B  CONST_26  H17   C17  C13  C14   180.00   0.0  0
 X4B  CONST_27  H15   C15  N03  C14   180.00   0.0  0
 X4B  CONST_28  H14   C14  N03  C15   180.00   0.0  0
 X4B  CONST_31  C12   N02  C07  C06   180.00   0.0  0
 X4B  CONST_32  C12   N02  C07  C08     0.00   0.0  0
 X4B  CONST_35  HN02  N02  C07  C06     0.00   0.0  0
 X4B  CONST_36  H101  N01  C11  C06     0.00   0.0  0
 X4B  CONST_37  H201  N01  C11  C06   180.00   0.0  0
 X4B  Var_01    C05   C06  C11  N01    25.42  30.0  2
 X4B  Var_02    C14   C13  C12  N02    91.56  30.0  2
 X4B  Var_03    C13   C12  N02  C07  -178.86  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
 X4B  plan-1  N02   0.020
 X4B  plan-1  N04   0.020
 X4B  plan-1  C05   0.020
 X4B  plan-1  C06   0.020
 X4B  plan-1  C07   0.020
 X4B  plan-1  C08   0.020
 X4B  plan-1  C09   0.020
 X4B  plan-1  C10   0.020
 X4B  plan-1  C11   0.020
 X4B  plan-1  CL21  0.020
 X4B  plan-1  H05   0.020
 X4B  plan-1  H08   0.020
 X4B  plan-2  N03   0.020
 X4B  plan-2  C12   0.020
 X4B  plan-2  C13   0.020
 X4B  plan-2  C14   0.020
 X4B  plan-2  C15   0.020
 X4B  plan-2  C16   0.020
 X4B  plan-2  C17   0.020
 X4B  plan-2  H14   0.020
 X4B  plan-2  H15   0.020
 X4B  plan-2  H16   0.020
 X4B  plan-2  H17   0.020
 X4B  plan-3  N01   0.020
 X4B  plan-3  C06   0.020
 X4B  plan-3  C11   0.020
 X4B  plan-3  O18   0.020
 X4B  plan-3  H101  0.020
 X4B  plan-3  H201  0.020
 X4B  plan-4  N02   0.020
 X4B  plan-4  C07   0.020
 X4B  plan-4  C12   0.020
 X4B  plan-4  HN02  0.020
 X4B  plan-5  N04   0.020
 X4B  plan-5  C10   0.020
 X4B  plan-5  O19   0.020
 X4B  plan-5  O20   0.020

