# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 23:42:31 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: 4-chloro-2-{[(6-chloropyridin-3-yl)methyl]amino}-5-nitrobenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1cc(c(Cl)cc1NCc2ccc(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
 X75  X75  4-chloro-2-{[(6-chloropyridin-3-yl)methyl]amino}-5-nitrobenzamide  ligand  32  22  .  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_X75
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
 X75  N01   N   NH1    0  -0.688   0.4528  -0.0591   0.0898
 X75  N02   N   NH2    0  -0.805  -1.5116  -3.7107  -0.3701
 X75  N03   N   N      0  -0.386   4.8653   0.8416   0.9826
 X75  N04   N   N      1   0.320  -5.1358  -0.2322   0.0505
 X75  C05   C   CR16   0  -0.329  -2.9730  -1.3129   0.0379
 X75  C06   C   CR6    0  -0.115  -1.5952  -1.3385   0.0481
 X75  C07   C   CR6    0   0.421  -0.8846  -0.1021   0.0443
 X75  C08   C   CR16   0  -0.322  -1.6346   1.0889  -0.0409
 X75  C09   C   CR6    0  -0.053  -3.0086   1.0855  -0.0490
 X75  C10   C   CR6    0   0.296  -3.7036  -0.1308   0.0060
 X75  C12   C   CH2    0  -0.352   1.2263   1.1629   0.1037
 X75  C13   C   CR6    0  -0.013   2.6870   0.8425  -0.0077
 X75  C14   C   CR16   0  -0.089   3.5618   1.1019   1.0352
 X75  C15   C   CR6    0   0.161   5.3343   0.3073  -0.1159
 X75  C16   C   CR16   0  -0.261   4.5687  -0.0063  -1.2306
 X75  C17   C   CR16   0  -0.160   3.2173   0.2721  -1.1626
 X75  O18   O   O      0  -0.495   0.2694  -2.7140   0.5691
 X75  O19   O   O      0  -0.383  -5.7753   0.7149   0.4455
 X75  O20   O   O     -1  -0.394  -5.6383  -1.2801  -0.2995
 X75  CL21  CL  CL     0  -0.055  -3.7806   2.6139  -0.1960
 X75  CL22  CL  CL     0  -0.103   7.0377  -0.0216  -0.1530
 X75  HN01  H   HNH1   0   0.417   0.9126  -0.9271   0.3330
 X75  H102  H   HNH2   0   0.419  -2.3559  -3.6466  -0.9116
 X75  H202  H   HNH2   0   0.413  -1.0532  -4.6076  -0.3500
 X75  H05   H   HCR6   0   0.300  -3.5239  -2.2413   0.0939
 X75  H08   H   HCR6   0   0.313  -1.1259   2.0408  -0.0896
 X75  H112  H   HCH2   0   0.273   0.9351   1.7932  -0.7407
 X75  H212  H   HCH2   0   0.270   1.0380   1.7422   1.0137
 X75  H14   H   HCR6   0   0.278   3.1991   1.5427   1.9574
 X75  H16   H   HCR6   0   0.297   5.0117  -0.4444  -2.1130
 X75  H17   H   HCR6   0   0.287   2.5798   0.0499  -2.0095
 X75  C11   C   C      0   0.538  -0.8661  -2.6382   0.1033

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
 X75  N01  C07   single    1.339  0.020  1.339
 X75  N01  C12   single    1.446  0.020  1.446
 X75  N01  HN01  single    0.860  0.020  1.020
 X75  N02  C11   single    1.338  0.020  1.338
 X75  N02  H102  single    0.860  0.020  1.020
 X75  N02  H202  single    0.860  0.020  1.020
 X75  N03  C15   aromatic  1.309  0.020  1.309
 X75  N04  O20   single    1.214  0.020  1.214
 X75  C05  C10   aromatic  1.390  0.020  1.390
 X75  C05  H05   single    0.930  0.020  1.080
 X75  C06  C05   aromatic  1.378  0.020  1.378
 X75  C06  C07   aromatic  1.426  0.020  1.426
 X75  C07  C08   aromatic  1.410  0.020  1.410
 X75  C08  C09   aromatic  1.374  0.020  1.374
 X75  C08  H08   single    0.930  0.020  1.080
 X75  C09  CL21  single    1.719  0.020  1.719
 X75  C10  N04   single    1.436  0.020  1.436
 X75  C10  C09   aromatic  1.402  0.020  1.402
 X75  C11  C06   single    1.491  0.020  1.491
 X75  C12  C13   single    1.500  0.020  1.500
 X75  C12  H112  single    0.970  0.020  1.090
 X75  C12  H212  single    0.970  0.020  1.090
 X75  C13  C17   aromatic  1.393  0.020  1.393
 X75  C14  C13   aromatic  1.386  0.020  1.386
 X75  C14  N03   aromatic  1.330  0.020  1.330
 X75  C14  H14   single    0.930  0.020  1.080
 X75  C15  C16   aromatic  1.388  0.020  1.388
 X75  C15  CL22  single    1.735  0.020  1.735
 X75  C16  H16   single    0.930  0.020  1.080
 X75  C17  C16   aromatic  1.381  0.020  1.381
 X75  C17  H17   single    0.930  0.020  1.080
 X75  O18  C11   double    1.230  0.020  1.230
 X75  O19  N04   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
 X75  HN01  N01  C12   118.64  3.000
 X75  HN01  N01  C07   115.75  3.000
 X75  C12   N01  C07   124.18  3.000
 X75  H202  N02  H102  116.73  3.000
 X75  H202  N02  C11   119.13  3.000
 X75  H102  N02  C11   123.00  3.000
 X75  C15   N03  C14   117.66  3.000
 X75  O20   N04  O19   123.47  3.000
 X75  O19   N04  C10   118.82  3.000
 X75  O20   N04  C10   117.70  3.000
 X75  H05   C05  C10   117.63  3.000
 X75  H05   C05  C06   119.55  3.000
 X75  C10   C05  C06   122.78  3.000
 X75  C11   C06  C07   120.80  3.000
 X75  C11   C06  C05   120.35  3.000
 X75  C07   C06  C05   118.82  3.000
 X75  C08   C07  C06   117.87  3.000
 X75  C08   C07  N01   120.41  3.000
 X75  C06   C07  N01   121.71  3.000
 X75  H08   C08  C09   118.22  3.000
 X75  H08   C08  C07   119.77  3.000
 X75  C09   C08  C07   122.01  3.000
 X75  CL21  C09  C10   123.52  3.000
 X75  C10   C09  C08   119.85  3.000
 X75  CL21  C09  C08   116.58  3.000
 X75  C09   C10  C05   118.56  3.000
 X75  C09   C10  N04   123.83  3.000
 X75  C05   C10  N04   117.60  3.000
 X75  H212  C12  H112  106.92  3.000
 X75  H212  C12  C13   110.01  3.000
 X75  H112  C12  C13   108.98  3.000
 X75  H212  C12  N01   111.29  3.000
 X75  H112  C12  N01   109.71  3.000
 X75  C13   C12  N01   109.87  3.000
 X75  C17   C13  C14   117.40  3.000
 X75  C14   C13  C12   121.27  3.000
 X75  C17   C13  C12   121.33  3.000
 X75  H14   C14  C13   120.32  3.000
 X75  H14   C14  N03   116.15  3.000
 X75  C13   C14  N03   123.52  3.000
 X75  CL22  C15  C16   118.78  3.000
 X75  CL22  C15  N03   116.56  3.000
 X75  C16   C15  N03   124.66  3.000
 X75  H16   C16  C17   121.54  3.000
 X75  C17   C16  C15   117.03  3.000
 X75  H16   C16  C15   121.43  3.000
 X75  H17   C17  C16   119.74  3.000
 X75  H17   C17  C13   120.54  3.000
 X75  C16   C17  C13   119.72  3.000
 X75  O18   C11  C06   121.28  3.000
 X75  O18   C11  N02   122.01  3.000
 X75  C06   C11  N02   116.71  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
 X75  CONST_01  C17   C16  C15  N03     0.00   0.0  0
 X75  CONST_02  C17   C13  C14  N03     0.00   0.0  0
 X75  CONST_03  C08   C09  C10  C05     0.00   0.0  0
 X75  CONST_04  C08   C07  C06  C05     0.00   0.0  0
 X75  CONST_05  C09   C10  C05  C06     0.00   0.0  0
 X75  CONST_06  C09   C08  C07  C06     0.00   0.0  0
 X75  CONST_07  C10   C05  C06  C07     0.00   0.0  0
 X75  CONST_08  C10   C09  C08  C07     0.00   0.0  0
 X75  CONST_09  C15   C16  C17  C13     0.00   0.0  0
 X75  CONST_10  C15   N03  C14  C13     0.00   0.0  0
 X75  CONST_11  C16   C17  C13  C14     0.00   0.0  0
 X75  CONST_12  C16   C15  N03  C14     0.00   0.0  0
 X75  CONST_13  C05   C06  C07  N01   180.00   0.0  0
 X75  CONST_14  C09   C08  C07  N01   180.00   0.0  0
 X75  CONST_15  C12   C13  C14  N03   180.00   0.0  0
 X75  CONST_16  C06   C05  C10  N04   180.00   0.0  0
 X75  CONST_17  C08   C09  C10  N04   180.00   0.0  0
 X75  CONST_18  CL21  C09  C10  C05   180.00   0.0  0
 X75  CONST_19  CL21  C09  C08  C07   180.00   0.0  0
 X75  CONST_20  C11   C06  C07  C08   180.00   0.0  0
 X75  CONST_21  C11   C06  C05  C10   180.00   0.0  0
 X75  CONST_22  C16   C17  C13  C12   180.00   0.0  0
 X75  CONST_23  CL22  C15  N03  C14   180.00   0.0  0
 X75  CONST_24  CL22  C15  C16  C17   180.00   0.0  0
 X75  CONST_25  H16   C16  C15  N03   180.00   0.0  0
 X75  CONST_26  H08   C08  C07  C06   180.00   0.0  0
 X75  CONST_27  H05   C05  C06  C07   180.00   0.0  0
 X75  CONST_28  H17   C17  C13  C14   180.00   0.0  0
 X75  CONST_29  H14   C14  N03  C15   180.00   0.0  0
 X75  CONST_32  C12   N01  C07  C06   180.00   0.0  0
 X75  CONST_33  C12   N01  C07  C08     0.00   0.0  0
 X75  CONST_36  HN01  N01  C07  C06     0.00   0.0  0
 X75  CONST_37  H102  N02  C11  C06     0.00   0.0  0
 X75  CONST_38  H202  N02  C11  C06   180.00   0.0  0
 X75  Var_01    C17   C13  C12  N01    65.98  30.0  2
 X75  Var_02    C05   C06  C11  N02    25.26  30.0  2
 X75  Var_03    C13   C12  N01  C07  -173.29  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
 X75  plan-1  N03   0.020
 X75  plan-1  C12   0.020
 X75  plan-1  C13   0.020
 X75  plan-1  C14   0.020
 X75  plan-1  C15   0.020
 X75  plan-1  C16   0.020
 X75  plan-1  C17   0.020
 X75  plan-1  CL22  0.020
 X75  plan-1  H14   0.020
 X75  plan-1  H16   0.020
 X75  plan-1  H17   0.020
 X75  plan-2  N01   0.020
 X75  plan-2  N04   0.020
 X75  plan-2  C05   0.020
 X75  plan-2  C06   0.020
 X75  plan-2  C07   0.020
 X75  plan-2  C08   0.020
 X75  plan-2  C09   0.020
 X75  plan-2  C10   0.020
 X75  plan-2  CL21  0.020
 X75  plan-2  H05   0.020
 X75  plan-2  H08   0.020
 X75  plan-2  C11   0.020
 X75  plan-3  N02   0.020
 X75  plan-3  C06   0.020
 X75  plan-3  O18   0.020
 X75  plan-3  H102  0.020
 X75  plan-3  H202  0.020
 X75  plan-3  C11   0.020
 X75  plan-4  N01   0.020
 X75  plan-4  C07   0.020
 X75  plan-4  C12   0.020
 X75  plan-4  HN01  0.020
 X75  plan-5  N04   0.020
 X75  plan-5  C10   0.020
 X75  plan-5  O19   0.020
 X75  plan-5  O20   0.020

