# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 01:59:34 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: 4-chloro-5-nitro-2-[(3,4,5-trifluorobenzyl)amino]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1cc(c(Cl)cc1NCc2cc(F)c(F)c(F)c2)[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
 XA0  XA0  4-chloro-5-nitro-2-[(3,4,5-trifluorobenzyl)amino]benzamide  ligand  33  24  .  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_XA0
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
 XA0  N01   N   NH1    0  -0.682   0.2830  -0.0754   0.0359
 XA0  N02   N   NH2    0  -0.805  -1.7341  -3.7348  -0.0250
 XA0  N03   N   N      1   0.320  -5.3064  -0.1929   0.0206
 XA0  C04   C   CR16   0  -0.330  -3.1552  -1.2852   0.1799
 XA0  C05   C   CR6    0  -0.114  -1.7780  -1.3306   0.1582
 XA0  C06   C   CR6    0   0.419  -1.0528  -0.1102   0.0156
 XA0  C07   C   CR16   0  -0.323  -1.7906   1.0779  -0.1678
 XA0  C08   C   CR6    0  -0.052  -3.1642   1.0884  -0.1806
 XA0  C09   C   CR6    0   0.295  -3.8731  -0.1074   0.0062
 XA0  C11   C   CH2    0  -0.351   1.0701   1.1261  -0.1479
 XA0  C12   C   CR6    0   0.074   2.5300   0.7748  -0.1032
 XA0  C13   C   CR16   0  -0.450   3.2240   0.5223  -1.2803
 XA0  C14   C   CR6    0   0.430   4.5549   0.1637  -1.2182
 XA0  C15   C   CR6    0   0.262   5.2072   0.0430  -0.0051
 XA0  C16   C   CR6    0   0.430   4.5035   0.2948   1.1590
 XA0  C17   C   CR16   0  -0.443   3.1736   0.6580   1.1242
 XA0  O18   O   O      0  -0.496   0.0910  -2.6733   0.7418
 XA0  O19   O   O      0  -0.384  -5.9473   0.6725  -0.5299
 XA0  O20   O   O     -1  -0.395  -5.8099  -1.1483   0.5746
 XA0  CL21  CL  CL     0  -0.055  -3.9168   2.6250  -0.3398
 XA0  F22   F   F      0  -0.298   5.1434   0.1790   2.3225
 XA0  F23   F   F      0  -0.298   5.2428  -0.0759  -2.3344
 XA0  F24   F   F      0  -0.294   6.4904  -0.3063   0.0419
 XA0  HN01  H   HNH1   0   0.418   0.7490  -0.9366   0.2908
 XA0  H102  H   HNH2   0   0.418  -2.5927  -3.7154  -0.5472
 XA0  H202  H   HNH2   0   0.412  -1.2790  -4.6294   0.0625
 XA0  H04   H   HCR6   0   0.299  -3.7155  -2.1959   0.3371
 XA0  H07   H   HCR6   0   0.314  -1.2705   2.0178  -0.2809
 XA0  H111  H   HCH2   0   0.274   0.8281   1.5895  -1.1078
 XA0  H211  H   HCH2   0   0.272   0.8434   1.8609   0.6310
 XA0  H13   H   HCR6   0   0.296   2.7395   0.6109  -2.2442
 XA0  H17   H   HCR6   0   0.298   2.6503   0.8535   2.0515
 XA0  C10   C   C      0   0.538  -1.0613  -2.6284   0.3143

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
 XA0  N01  C06   single    1.336  0.020  1.336
 XA0  N01  C11   single    1.448  0.020  1.448
 XA0  N01  HN01  single    0.860  0.020  1.020
 XA0  N02  C10   single    1.339  0.020  1.339
 XA0  N02  H102  single    0.860  0.020  1.020
 XA0  N02  H202  single    0.860  0.020  1.020
 XA0  N03  O20   single    1.214  0.020  1.214
 XA0  C04  C09   aromatic  1.390  0.020  1.390
 XA0  C04  H04   single    0.930  0.020  1.080
 XA0  C05  C04   aromatic  1.378  0.020  1.378
 XA0  C05  C06   aromatic  1.427  0.020  1.427
 XA0  C06  C07   aromatic  1.410  0.020  1.410
 XA0  C07  C08   aromatic  1.374  0.020  1.374
 XA0  C07  H07   single    0.930  0.020  1.080
 XA0  C08  CL21  single    1.718  0.020  1.718
 XA0  C09  N03   single    1.436  0.020  1.436
 XA0  C09  C08   aromatic  1.403  0.020  1.403
 XA0  C10  C05   single    1.491  0.020  1.491
 XA0  C11  C12   single    1.502  0.020  1.502
 XA0  C11  H111  single    0.970  0.020  1.090
 XA0  C11  H211  single    0.970  0.020  1.090
 XA0  C12  C13   aromatic  1.390  0.020  1.390
 XA0  C13  C14   aromatic  1.380  0.020  1.380
 XA0  C13  H13   single    0.930  0.020  1.080
 XA0  C14  F23   single    1.333  0.020  1.333
 XA0  C15  C14   aromatic  1.383  0.020  1.383
 XA0  C15  F24   single    1.331  0.020  1.331
 XA0  C16  C15   aromatic  1.383  0.020  1.383
 XA0  C17  C12   aromatic  1.391  0.020  1.391
 XA0  C17  C16   aromatic  1.379  0.020  1.379
 XA0  C17  H17   single    0.930  0.020  1.080
 XA0  O18  C10   double    1.230  0.020  1.230
 XA0  O19  N03   double    1.209  0.020  1.209
 XA0  F22  C16   single    1.333  0.020  1.333

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
 XA0  HN01  N01  C11   119.20  3.000
 XA0  HN01  N01  C06   116.24  3.000
 XA0  C11   N01  C06   124.26  3.000
 XA0  H202  N02  H102  116.63  3.000
 XA0  H202  N02  C10   119.00  3.000
 XA0  H102  N02  C10   123.03  3.000
 XA0  O20   N03  O19   123.45  3.000
 XA0  O19   N03  C09   118.80  3.000
 XA0  O20   N03  C09   117.75  3.000
 XA0  H04   C04  C09   117.67  3.000
 XA0  H04   C04  C05   119.51  3.000
 XA0  C09   C04  C05   122.82  3.000
 XA0  C10   C05  C06   120.71  3.000
 XA0  C10   C05  C04   120.50  3.000
 XA0  C06   C05  C04   118.77  3.000
 XA0  C07   C06  C05   117.88  3.000
 XA0  C07   C06  N01   120.20  3.000
 XA0  C05   C06  N01   121.92  3.000
 XA0  H07   C07  C08   118.28  3.000
 XA0  H07   C07  C06   119.65  3.000
 XA0  C08   C07  C06   122.06  3.000
 XA0  CL21  C08  C09   123.60  3.000
 XA0  C09   C08  C07   119.84  3.000
 XA0  CL21  C08  C07   116.47  3.000
 XA0  C08   C09  C04   118.55  3.000
 XA0  C08   C09  N03   123.82  3.000
 XA0  C04   C09  N03   117.63  3.000
 XA0  H211  C11  H111  107.13  3.000
 XA0  H211  C11  C12   109.69  3.000
 XA0  H111  C11  C12   109.90  3.000
 XA0  H211  C11  N01   110.74  3.000
 XA0  H111  C11  N01   110.06  3.000
 XA0  C12   C11  N01   109.30  3.000
 XA0  C17   C12  C13   120.08  3.000
 XA0  C17   C12  C11   119.71  3.000
 XA0  C13   C12  C11   120.17  3.000
 XA0  H13   C13  C14   119.54  3.000
 XA0  H13   C13  C12   121.06  3.000
 XA0  C14   C13  C12   119.40  3.000
 XA0  F23   C14  C15   118.40  3.000
 XA0  C15   C14  C13   121.14  3.000
 XA0  F23   C14  C13   120.46  3.000
 XA0  F24   C15  C16   120.57  3.000
 XA0  C16   C15  C14   118.85  3.000
 XA0  F24   C15  C14   120.58  3.000
 XA0  F22   C16  C17   120.53  3.000
 XA0  F22   C16  C15   118.33  3.000
 XA0  C17   C16  C15   121.15  3.000
 XA0  H17   C17  C16   119.48  3.000
 XA0  H17   C17  C12   121.13  3.000
 XA0  C16   C17  C12   119.39  3.000
 XA0  O18   C10  C05   121.24  3.000
 XA0  O18   C10  N02   121.93  3.000
 XA0  C05   C10  N02   116.83  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
 XA0  CONST_01  C07   C08  C09  C04     0.00   0.0  0
 XA0  CONST_02  C07   C06  C05  C04     0.00   0.0  0
 XA0  CONST_03  C08   C09  C04  C05     0.00   0.0  0
 XA0  CONST_04  C08   C07  C06  C05     0.00   0.0  0
 XA0  CONST_05  C09   C04  C05  C06     0.00   0.0  0
 XA0  CONST_06  C09   C08  C07  C06     0.00   0.0  0
 XA0  CONST_07  C15   C14  C13  C12     0.00   0.0  0
 XA0  CONST_08  C15   C16  C17  C12     0.00   0.0  0
 XA0  CONST_09  C16   C17  C12  C13     0.00   0.0  0
 XA0  CONST_10  C16   C15  C14  C13     0.00   0.0  0
 XA0  CONST_11  C17   C12  C13  C14     0.00   0.0  0
 XA0  CONST_12  C17   C16  C15  C14     0.00   0.0  0
 XA0  CONST_13  C04   C05  C06  N01   180.00   0.0  0
 XA0  CONST_14  C08   C07  C06  N01   180.00   0.0  0
 XA0  CONST_15  C05   C04  C09  N03   180.00   0.0  0
 XA0  CONST_16  C07   C08  C09  N03   180.00   0.0  0
 XA0  CONST_17  CL21  C08  C09  C04   180.00   0.0  0
 XA0  CONST_18  CL21  C08  C07  C06   180.00   0.0  0
 XA0  CONST_19  C10   C05  C06  C07   180.00   0.0  0
 XA0  CONST_20  C10   C05  C04  C09   180.00   0.0  0
 XA0  CONST_21  C14   C13  C12  C11   180.00   0.0  0
 XA0  CONST_22  C16   C17  C12  C11   180.00   0.0  0
 XA0  CONST_23  F23   C14  C13  C12   180.00   0.0  0
 XA0  CONST_24  F22   C16  C17  C12   180.00   0.0  0
 XA0  CONST_25  F24   C15  C14  C13   180.00   0.0  0
 XA0  CONST_26  F22   C16  C15  C14   180.00   0.0  0
 XA0  CONST_27  F23   C14  C15  C16   180.00   0.0  0
 XA0  CONST_28  F24   C15  C16  C17   180.00   0.0  0
 XA0  CONST_29  H07   C07  C06  C05   180.00   0.0  0
 XA0  CONST_30  H04   C04  C05  C06   180.00   0.0  0
 XA0  CONST_31  H17   C17  C12  C13   180.00   0.0  0
 XA0  CONST_32  H13   C13  C14  C15   180.00   0.0  0
 XA0  CONST_35  C11   N01  C06  C05   180.00   0.0  0
 XA0  CONST_36  C11   N01  C06  C07     0.00   0.0  0
 XA0  CONST_39  HN01  N01  C06  C05     0.00   0.0  0
 XA0  CONST_40  H102  N02  C10  C05     0.00   0.0  0
 XA0  CONST_41  H202  N02  C10  C05   180.00   0.0  0
 XA0  Var_01    C13   C12  C11  N01    94.37  30.0  2
 XA0  Var_02    C04   C05  C10  N02    24.42  30.0  2
 XA0  Var_03    C12   C11  N01  C06  -178.32  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
 XA0  plan-1  N01   0.020
 XA0  plan-1  N03   0.020
 XA0  plan-1  C04   0.020
 XA0  plan-1  C05   0.020
 XA0  plan-1  C06   0.020
 XA0  plan-1  C07   0.020
 XA0  plan-1  C08   0.020
 XA0  plan-1  C09   0.020
 XA0  plan-1  CL21  0.020
 XA0  plan-1  H04   0.020
 XA0  plan-1  H07   0.020
 XA0  plan-1  C10   0.020
 XA0  plan-2  C11   0.020
 XA0  plan-2  C12   0.020
 XA0  plan-2  C13   0.020
 XA0  plan-2  C14   0.020
 XA0  plan-2  C15   0.020
 XA0  plan-2  C16   0.020
 XA0  plan-2  C17   0.020
 XA0  plan-2  F22   0.020
 XA0  plan-2  F23   0.020
 XA0  plan-2  F24   0.020
 XA0  plan-2  H13   0.020
 XA0  plan-2  H17   0.020
 XA0  plan-3  N02   0.020
 XA0  plan-3  C05   0.020
 XA0  plan-3  O18   0.020
 XA0  plan-3  H102  0.020
 XA0  plan-3  H202  0.020
 XA0  plan-3  C10   0.020
 XA0  plan-4  N01   0.020
 XA0  plan-4  C06   0.020
 XA0  plan-4  C11   0.020
 XA0  plan-4  HN01  0.020
 XA0  plan-5  N03   0.020
 XA0  plan-5  C09   0.020
 XA0  plan-5  O19   0.020
 XA0  plan-5  O20   0.020

