# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 02:32:39 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: 4-chloro-5-nitro-2-[(pyrimidin-5-ylmethyl)amino]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1cc(c(Cl)cc1NCc2cncnc2)[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
 X72  X72  4-chloro-5-nitro-2-[(pyrimidin-5-ylmethyl)amino]benzamide  ligand  31  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_X72
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
 X72  N01   N   NH1    0  -0.684   1.2446  -0.0497   0.0177
 X72  N02   N   NH2    0  -0.812  -0.7696  -3.7380  -0.1848
 X72  N03   N   N      0  -0.389   5.4368   0.1880  -1.2184
 X72  N04   N   N      0  -0.389   5.5391   0.5604   1.1143
 X72  N05   N   N      1   0.320  -4.3415  -0.1955   0.0619
 X72  C06   C   CR16   0  -0.331  -2.1862  -1.2890   0.0414
 X72  C07   C   CR6    0  -0.113  -0.8077  -1.3286   0.0358
 X72  C08   C   CR6    0   0.419  -0.0912  -0.0946  -0.0082
 X72  C09   C   CR16   0  -0.323  -0.8361   1.1002  -0.1060
 X72  C10   C   CR6    0  -0.055  -2.2087   1.1071  -0.0905
 X72  C11   C   CR6    0   0.301  -2.9095  -0.1042  -0.0039
 X72  C13   C   CH2    0  -0.354   2.0169   1.1728  -0.0308
 X72  C14   C   CR6    0  -0.059   3.4783   0.8473  -0.0393
 X72  C15   C   CR16   0  -0.022   4.1471   0.4936  -1.2034
 X72  C16   C   CR16   0   0.059   6.0689   0.2355  -0.0549
 X72  C17   C   CR16   0  -0.029   4.2470   0.8622   1.1148
 X72  O18   O   O      0  -0.498   1.0987  -2.6788   0.4578
 X72  O19   O   O     -1  -0.394  -4.8566  -1.2423  -0.2721
 X72  O20   O   O      0  -0.383  -4.9676   0.7596   0.4591
 X72  CL21  CL  CL     0  -0.054  -2.9750   2.6359  -0.2564
 X72  HN01  H   HNH1   0   0.418   1.7114  -0.9283   0.2065
 X72  H102  H   HNH2   0   0.420  -1.6730  -3.7321  -0.6246
 X72  H202  H   HNH2   0   0.413  -0.2969  -4.6267  -0.1440
 X72  H06   H   HCR6   0   0.295  -2.7491  -2.2071   0.1198
 X72  H09   H   HCR6   0   0.315  -0.3206   2.0464  -0.1873
 X72  H113  H   HCH2   0   0.275   1.7650   1.7420  -0.9300
 X72  H213  H   HCH2   0   0.273   1.7881   1.8148   0.8261
 X72  H15   H   HCR6   0   0.282   3.6226   0.4630  -2.1537
 X72  H16   H   HCR6   0   0.269   7.1243  -0.0132  -0.0618
 X72  H17   H   HCR6   0   0.282   3.8048   1.1333   2.0684
 X72  C12   C   C      0   0.550  -0.0826  -2.6290   0.1160

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
 X72  N01  C08   single    1.337  0.020  1.337
 X72  N01  C13   single    1.447  0.020  1.447
 X72  N01  HN01  single    0.860  0.020  1.020
 X72  N02  C12   single    1.339  0.020  1.339
 X72  N02  H102  single    0.860  0.020  1.020
 X72  N02  H202  single    0.860  0.020  1.020
 X72  N04  C16   aromatic  1.324  0.020  1.324
 X72  N05  O19   single    1.214  0.020  1.214
 X72  C06  C11   aromatic  1.389  0.020  1.389
 X72  C06  H06   single    0.930  0.020  1.080
 X72  C07  C06   aromatic  1.379  0.020  1.379
 X72  C07  C08   aromatic  1.428  0.020  1.428
 X72  C08  C09   aromatic  1.411  0.020  1.411
 X72  C09  C10   aromatic  1.373  0.020  1.373
 X72  C09  H09   single    0.930  0.020  1.080
 X72  C10  CL21  single    1.718  0.020  1.718
 X72  C11  N05   single    1.436  0.020  1.436
 X72  C11  C10   aromatic  1.402  0.020  1.402
 X72  C12  C07   single    1.491  0.020  1.491
 X72  C13  C14   single    1.497  0.020  1.497
 X72  C13  H113  single    0.970  0.020  1.090
 X72  C13  H213  single    0.970  0.020  1.090
 X72  C14  C15   aromatic  1.388  0.020  1.388
 X72  C15  N03   aromatic  1.325  0.020  1.325
 X72  C15  H15   single    0.930  0.020  1.080
 X72  C16  N03   aromatic  1.325  0.020  1.325
 X72  C16  H16   single    0.930  0.020  1.080
 X72  C17  C14   aromatic  1.387  0.020  1.387
 X72  C17  N04   aromatic  1.327  0.020  1.327
 X72  C17  H17   single    0.930  0.020  1.080
 X72  O18  C12   double    1.231  0.020  1.231
 X72  O20  N05   double    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
 X72  HN01  N01  C13   119.55  3.000
 X72  HN01  N01  C08   115.79  3.000
 X72  C13   N01  C08   124.13  3.000
 X72  H202  N02  H102  116.41  3.000
 X72  H202  N02  C12   118.74  3.000
 X72  H102  N02  C12   123.70  3.000
 X72  C16   N03  C15   116.49  3.000
 X72  C17   N04  C16   116.47  3.000
 X72  O20   N05  O19   123.51  3.000
 X72  O20   N05  C11   118.76  3.000
 X72  O19   N05  C11   117.73  3.000
 X72  H06   C06  C11   117.14  3.000
 X72  H06   C06  C07   119.80  3.000
 X72  C11   C06  C07   123.02  3.000
 X72  C12   C07  C08   120.76  3.000
 X72  C12   C07  C06   120.72  3.000
 X72  C08   C07  C06   118.49  3.000
 X72  C09   C08  C07   117.97  3.000
 X72  C09   C08  N01   120.02  3.000
 X72  C07   C08  N01   122.00  3.000
 X72  H09   C09  C10   118.26  3.000
 X72  H09   C09  C08   119.65  3.000
 X72  C10   C09  C08   122.08  3.000
 X72  CL21  C10  C11   123.49  3.000
 X72  C11   C10  C09   119.75  3.000
 X72  CL21  C10  C09   116.70  3.000
 X72  C10   C11  C06   118.60  3.000
 X72  C10   C11  N05   123.78  3.000
 X72  C06   C11  N05   117.61  3.000
 X72  H213  C13  H113  106.87  3.000
 X72  H213  C13  C14   109.62  3.000
 X72  H113  C13  C14   109.47  3.000
 X72  H213  C13  N01   110.96  3.000
 X72  H113  C13  N01   110.15  3.000
 X72  C14   C13  N01   109.72  3.000
 X72  C17   C14  C15   115.69  3.000
 X72  C17   C14  C13   122.28  3.000
 X72  C15   C14  C13   122.03  3.000
 X72  H15   C15  C14   120.55  3.000
 X72  H15   C15  N03   116.97  3.000
 X72  C14   C15  N03   122.47  3.000
 X72  H16   C16  N04   116.83  3.000
 X72  H16   C16  N03   116.78  3.000
 X72  N04   C16  N03   126.39  3.000
 X72  H17   C17  C14   120.53  3.000
 X72  H17   C17  N04   116.99  3.000
 X72  C14   C17  N04   122.48  3.000
 X72  O18   C12  C07   121.13  3.000
 X72  O18   C12  N02   121.43  3.000
 X72  C07   C12  N02   117.44  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
 X72  CONST_01  C17   C14  C15  N03     0.00   0.0  0
 X72  CONST_02  C17   N04  C16  N03     0.00   0.0  0
 X72  CONST_03  C15   N03  C16  N04     0.00   0.0  0
 X72  CONST_04  C15   C14  C17  N04     0.00   0.0  0
 X72  CONST_05  C09   C10  C11  C06     0.00   0.0  0
 X72  CONST_06  C09   C08  C07  C06     0.00   0.0  0
 X72  CONST_07  C10   C11  C06  C07     0.00   0.0  0
 X72  CONST_08  C10   C09  C08  C07     0.00   0.0  0
 X72  CONST_09  C11   C06  C07  C08     0.00   0.0  0
 X72  CONST_10  C11   C10  C09  C08     0.00   0.0  0
 X72  CONST_11  C16   N03  C15  C14     0.00   0.0  0
 X72  CONST_12  C16   N04  C17  C14     0.00   0.0  0
 X72  CONST_13  C06   C07  C08  N01   180.00   0.0  0
 X72  CONST_14  C10   C09  C08  N01   180.00   0.0  0
 X72  CONST_15  C13   C14  C15  N03   180.00   0.0  0
 X72  CONST_16  C13   C14  C17  N04   180.00   0.0  0
 X72  CONST_17  C07   C06  C11  N05   180.00   0.0  0
 X72  CONST_18  C09   C10  C11  N05   180.00   0.0  0
 X72  CONST_19  CL21  C10  C11  C06   180.00   0.0  0
 X72  CONST_20  CL21  C10  C09  C08   180.00   0.0  0
 X72  CONST_21  C12   C07  C08  C09   180.00   0.0  0
 X72  CONST_22  C12   C07  C06  C11   180.00   0.0  0
 X72  CONST_23  H09   C09  C08  C07   180.00   0.0  0
 X72  CONST_24  H06   C06  C07  C08   180.00   0.0  0
 X72  CONST_25  H17   C17  C14  C15   180.00   0.0  0
 X72  CONST_26  H16   C16  N03  C15   180.00   0.0  0
 X72  CONST_27  H15   C15  N03  C16   180.00   0.0  0
 X72  CONST_30  C13   N01  C08  C07   180.00   0.0  0
 X72  CONST_31  C13   N01  C08  C09     0.00   0.0  0
 X72  CONST_34  HN01  N01  C08  C07     0.00   0.0  0
 X72  CONST_35  H102  N02  C12  C07     0.00   0.0  0
 X72  CONST_36  H202  N02  C12  C07   180.00   0.0  0
 X72  Var_01    C15   C14  C13  N01    82.15  30.0  2
 X72  Var_02    C06   C07  C12  N02    18.45  30.0  2
 X72  Var_03    C14   C13  N01  C08  -177.70  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
 X72  plan-1  N03   0.020
 X72  plan-1  N04   0.020
 X72  plan-1  C13   0.020
 X72  plan-1  C14   0.020
 X72  plan-1  C15   0.020
 X72  plan-1  C16   0.020
 X72  plan-1  C17   0.020
 X72  plan-1  H15   0.020
 X72  plan-1  H16   0.020
 X72  plan-1  H17   0.020
 X72  plan-2  N01   0.020
 X72  plan-2  N05   0.020
 X72  plan-2  C06   0.020
 X72  plan-2  C07   0.020
 X72  plan-2  C08   0.020
 X72  plan-2  C09   0.020
 X72  plan-2  C10   0.020
 X72  plan-2  C11   0.020
 X72  plan-2  CL21  0.020
 X72  plan-2  H06   0.020
 X72  plan-2  H09   0.020
 X72  plan-2  C12   0.020
 X72  plan-3  N02   0.020
 X72  plan-3  C07   0.020
 X72  plan-3  O18   0.020
 X72  plan-3  H102  0.020
 X72  plan-3  H202  0.020
 X72  plan-3  C12   0.020
 X72  plan-4  N01   0.020
 X72  plan-4  C08   0.020
 X72  plan-4  C13   0.020
 X72  plan-4  HN01  0.020
 X72  plan-5  N05   0.020
 X72  plan-5  C11   0.020
 X72  plan-5  O19   0.020
 X72  plan-5  O20   0.020

