# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 23:06:35 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: 2-{[(6-chloropyridin-3-yl)methyl]amino}-5-nitrobenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1cc(ccc1NCc2ccc(Cl)nc2)[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
 X73  X73  2-{[(6-chloropyridin-3-yl)methyl]amino}-5-nitrobenzamide  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 PERFECT
;

data_comp_X73
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
 X73  N01   N   NH1    0  -0.686   0.0727   0.2512   0.1957
 X73  N02   N   NH2    0  -0.803  -2.1352  -3.2339  -0.3118
 X73  N03   N   N      0  -0.386   4.5894   0.7553   0.9067
 X73  N04   N   N      1   0.321  -5.4843   0.5862  -0.1040
 X73  C05   C   CR16   0  -0.316  -3.4435  -0.7433   0.0409
 X73  C06   C   CR6    0  -0.121  -2.0678  -0.8599   0.1024
 X73  C07   C   CR6    0   0.419  -1.2629   0.3202   0.1081
 X73  C08   C   CR16   0  -0.359  -1.9174   1.5685  -0.0050
 X73  C09   C   CR16   0  -0.256  -3.2822   1.6586  -0.0846
 X73  C10   C   CR6    0   0.238  -4.0551   0.4988  -0.0517
 X73  C12   C   CH2    0  -0.346   0.9546   1.3960   0.1955
 X73  C13   C   CR6    0  -0.012   2.3744   0.9435   0.0207
 X73  C14   C   CR16   0  -0.090   3.3186   1.1336   1.0168
 X73  C15   C   CR6    0   0.160   4.9543   0.1684  -0.2043
 X73  C16   C   CR16   0  -0.261   4.1103  -0.0870  -1.2765
 X73  C17   C   CR16   0  -0.161   2.7944   0.3136  -1.1488
 X73  O18   O   O      0  -0.498  -0.3330  -2.3689   0.7104
 X73  O19   O   O     -1  -0.402  -6.1307  -0.4393  -0.0440
 X73  O20   O   O      0  -0.400  -5.9897   1.6846  -0.2071
 X73  CL21  CL  CL     0  -0.103   6.6172  -0.3152  -0.3161
 X73  HN01  H   HNH1   0   0.415   0.4509  -0.6462   0.4705
 X73  H102  H   HNH2   0   0.417  -2.9473  -3.1095  -0.8904
 X73  H202  H   HNH2   0   0.411  -1.7417  -4.1604  -0.2749
 X73  H05   H   HCR6   0   0.294  -4.0602  -1.6304   0.0827
 X73  H08   H   HCR6   0   0.295  -1.3402   2.4820  -0.0073
 X73  H09   H   HCR6   0   0.298  -3.7428   2.6335  -0.1564
 X73  H112  H   HCH2   0   0.272   0.6926   2.0642  -0.6287
 X73  H212  H   HCH2   0   0.267   0.8590   1.9766   1.1192
 X73  H14   H   HCR6   0   0.278   3.0420   1.6166   1.9479
 X73  H16   H   HCR6   0   0.297   4.4686  -0.5743  -2.1716
 X73  H17   H   HCR6   0   0.286   2.0983   0.1416  -1.9603
 X73  C11   C   C      0   0.534  -1.4369  -2.2086   0.1917

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
 X73  N01  C07   single    1.340  0.020  1.340
 X73  N01  C12   single    1.445  0.020  1.445
 X73  N01  HN01  single    0.860  0.020  1.020
 X73  N02  C11   single    1.339  0.020  1.339
 X73  N02  H102  single    0.860  0.020  1.020
 X73  N02  H202  single    0.860  0.020  1.020
 X73  N03  C15   aromatic  1.308  0.020  1.308
 X73  N04  O19   single    1.214  0.020  1.214
 X73  C05  C10   aromatic  1.388  0.020  1.388
 X73  C05  H05   single    0.930  0.020  1.080
 X73  C06  C05   aromatic  1.382  0.020  1.382
 X73  C06  C07   aromatic  1.428  0.020  1.428
 X73  C07  C08   aromatic  1.414  0.020  1.414
 X73  C08  C09   aromatic  1.370  0.020  1.370
 X73  C08  H08   single    0.930  0.020  1.080
 X73  C09  H09   single    0.930  0.020  1.080
 X73  C10  N04   single    1.433  0.020  1.433
 X73  C10  C09   aromatic  1.394  0.020  1.394
 X73  C11  C06   single    1.492  0.020  1.492
 X73  C12  C13   single    1.500  0.020  1.500
 X73  C12  H112  single    0.970  0.020  1.090
 X73  C12  H212  single    0.970  0.020  1.090
 X73  C13  C17   aromatic  1.393  0.020  1.393
 X73  C14  C13   aromatic  1.386  0.020  1.386
 X73  C14  N03   aromatic  1.330  0.020  1.330
 X73  C14  H14   single    0.930  0.020  1.080
 X73  C15  C16   aromatic  1.388  0.020  1.388
 X73  C15  CL21  single    1.735  0.020  1.735
 X73  C16  H16   single    0.930  0.020  1.080
 X73  C17  C16   aromatic  1.381  0.020  1.381
 X73  C17  H17   single    0.930  0.020  1.080
 X73  O18  C11   double    1.230  0.020  1.230
 X73  O20  N04   double    1.213  0.020  1.213

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
 X73  HN01  N01  C12   118.32  3.000
 X73  HN01  N01  C07   115.84  3.000
 X73  C12   N01  C07   124.57  3.000
 X73  H202  N02  H102  116.79  3.000
 X73  H202  N02  C11   119.13  3.000
 X73  H102  N02  C11   122.91  3.000
 X73  C15   N03  C14   117.66  3.000
 X73  O20   N04  O19   123.18  3.000
 X73  O20   N04  C10   118.28  3.000
 X73  O19   N04  C10   118.54  3.000
 X73  H05   C05  C10   119.05  3.000
 X73  H05   C05  C06   119.79  3.000
 X73  C10   C05  C06   121.15  3.000
 X73  C11   C06  C07   120.56  3.000
 X73  C11   C06  C05   120.00  3.000
 X73  C07   C06  C05   119.43  3.000
 X73  C08   C07  C06   117.92  3.000
 X73  C08   C07  N01   120.79  3.000
 X73  C06   C07  N01   121.28  3.000
 X73  H08   C08  C09   118.45  3.000
 X73  H08   C08  C07   119.95  3.000
 X73  C09   C08  C07   121.59  3.000
 X73  H09   C09  C10   121.05  3.000
 X73  C10   C09  C08   119.75  3.000
 X73  H09   C09  C08   119.19  3.000
 X73  C09   C10  C05   120.12  3.000
 X73  C09   C10  N04   120.09  3.000
 X73  C05   C10  N04   119.79  3.000
 X73  H212  C12  H112  106.91  3.000
 X73  H212  C12  C13   109.92  3.000
 X73  H112  C12  C13   108.86  3.000
 X73  H212  C12  N01   111.51  3.000
 X73  H112  C12  N01   109.76  3.000
 X73  C13   C12  N01   109.79  3.000
 X73  C17   C13  C14   117.39  3.000
 X73  C14   C13  C12   121.32  3.000
 X73  C17   C13  C12   121.29  3.000
 X73  H14   C14  C13   120.29  3.000
 X73  H14   C14  N03   116.18  3.000
 X73  C13   C14  N03   123.53  3.000
 X73  CL21  C15  C16   118.79  3.000
 X73  CL21  C15  N03   116.55  3.000
 X73  C16   C15  N03   124.66  3.000
 X73  H16   C16  C17   121.56  3.000
 X73  C17   C16  C15   117.02  3.000
 X73  H16   C16  C15   121.42  3.000
 X73  H17   C17  C16   119.80  3.000
 X73  H17   C17  C13   120.47  3.000
 X73  C16   C17  C13   119.73  3.000
 X73  O18   C11  C06   121.51  3.000
 X73  O18   C11  N02   121.79  3.000
 X73  C06   C11  N02   116.70  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
 X73  CONST_01  C17   C16  C15  N03     0.00   0.0  0
 X73  CONST_02  C17   C13  C14  N03     0.00   0.0  0
 X73  CONST_03  C08   C09  C10  C05     0.00   0.0  0
 X73  CONST_04  C08   C07  C06  C05     0.00   0.0  0
 X73  CONST_05  C09   C10  C05  C06     0.00   0.0  0
 X73  CONST_06  C09   C08  C07  C06     0.00   0.0  0
 X73  CONST_07  C10   C05  C06  C07     0.00   0.0  0
 X73  CONST_08  C10   C09  C08  C07     0.00   0.0  0
 X73  CONST_09  C15   C16  C17  C13     0.00   0.0  0
 X73  CONST_10  C15   N03  C14  C13     0.00   0.0  0
 X73  CONST_11  C16   C17  C13  C14     0.00   0.0  0
 X73  CONST_12  C16   C15  N03  C14     0.00   0.0  0
 X73  CONST_13  C05   C06  C07  N01   180.00   0.0  0
 X73  CONST_14  C09   C08  C07  N01   180.00   0.0  0
 X73  CONST_15  C12   C13  C14  N03   180.00   0.0  0
 X73  CONST_16  C06   C05  C10  N04   180.00   0.0  0
 X73  CONST_17  C08   C09  C10  N04   180.00   0.0  0
 X73  CONST_18  C11   C06  C07  C08   180.00   0.0  0
 X73  CONST_19  C11   C06  C05  C10   180.00   0.0  0
 X73  CONST_20  C16   C17  C13  C12   180.00   0.0  0
 X73  CONST_21  CL21  C15  N03  C14   180.00   0.0  0
 X73  CONST_22  CL21  C15  C16  C17   180.00   0.0  0
 X73  CONST_23  H16   C16  C15  N03   180.00   0.0  0
 X73  CONST_24  H09   C09  C10  C05   180.00   0.0  0
 X73  CONST_25  H08   C08  C07  C06   180.00   0.0  0
 X73  CONST_26  H05   C05  C06  C07   180.00   0.0  0
 X73  CONST_27  H17   C17  C13  C14   180.00   0.0  0
 X73  CONST_28  H14   C14  N03  C15   180.00   0.0  0
 X73  CONST_29  O19   N04  C10  C05     0.00   0.0  0
 X73  CONST_30  O20   N04  C10  C05   180.00   0.0  0
 X73  CONST_31  C12   N01  C07  C06   180.00   0.0  0
 X73  CONST_32  C12   N01  C07  C08     0.00   0.0  0
 X73  CONST_33  O19   N04  C10  C09   180.00   0.0  0
 X73  CONST_34  O20   N04  C10  C09     0.00   0.0  0
 X73  CONST_35  HN01  N01  C07  C06     0.00   0.0  0
 X73  CONST_36  H102  N02  C11  C06     0.00   0.0  0
 X73  CONST_37  H202  N02  C11  C06   180.00   0.0  0
 X73  Var_01    C17   C13  C12  N01    64.19  30.0  2
 X73  Var_02    C05   C06  C11  N02    25.89  30.0  2
 X73  Var_03    C13   C12  N01  C07  -168.33  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
 X73  plan-1  N03   0.020
 X73  plan-1  C12   0.020
 X73  plan-1  C13   0.020
 X73  plan-1  C14   0.020
 X73  plan-1  C15   0.020
 X73  plan-1  C16   0.020
 X73  plan-1  C17   0.020
 X73  plan-1  CL21  0.020
 X73  plan-1  H14   0.020
 X73  plan-1  H16   0.020
 X73  plan-1  H17   0.020
 X73  plan-2  N01   0.020
 X73  plan-2  N04   0.020
 X73  plan-2  C05   0.020
 X73  plan-2  C06   0.020
 X73  plan-2  C07   0.020
 X73  plan-2  C08   0.020
 X73  plan-2  C09   0.020
 X73  plan-2  C10   0.020
 X73  plan-2  H05   0.020
 X73  plan-2  H08   0.020
 X73  plan-2  H09   0.020
 X73  plan-2  C11   0.020
 X73  plan-3  N02   0.020
 X73  plan-3  C06   0.020
 X73  plan-3  O18   0.020
 X73  plan-3  H102  0.020
 X73  plan-3  H202  0.020
 X73  plan-3  C11   0.020
 X73  plan-4  N01   0.020
 X73  plan-4  C07   0.020
 X73  plan-4  C12   0.020
 X73  plan-4  HN01  0.020
 X73  plan-5  N04   0.020
 X73  plan-5  C10   0.020
 X73  plan-5  O19   0.020
 X73  plan-5  O20   0.020

