# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 21:33:16 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: 4-chloro-2-{[(2-chloropyrimidin-5-yl)methyl]amino}-5-nitrobenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1cc(c(Cl)cc1NCc2cnc(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
 X62  X62  4-chloro-2-{[(2-chloropyrimidin-5-yl)methyl]amino}-5-nitrobenzamide  ligand  31  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_X62
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
 X62  N01   N   NH1    0  -0.686   0.4598  -0.0303   0.0752
 X62  N02   N   NH2    0  -0.805  -1.5077  -3.6884  -0.3244
 X62  N03   N   N      0  -0.368   4.8001   0.6457   1.0709
 X62  N04   N   N      0  -0.369   4.5997   0.1584  -1.2302
 X62  N05   N   N      1   0.320  -5.1288  -0.2049  -0.0279
 X62  C06   C   CR16   0  -0.329  -2.9665  -1.2830   0.0641
 X62  C07   C   CR6    0  -0.113  -1.5886  -1.3101   0.0618
 X62  C08   C   CR6    0   0.421  -0.8780  -0.0742   0.0354
 X62  C09   C   CR16   0  -0.321  -1.6267   1.1167  -0.0508
 X62  C10   C   CR6    0  -0.053  -3.0006   1.1128  -0.0876
 X62  C11   C   CR6    0   0.296  -3.6956  -0.1025  -0.0180
 X62  C13   C   CH2    0  -0.352   1.2285   1.1940   0.0508
 X62  C14   C   CR6    0  -0.060   2.6889   0.8702  -0.0034
 X62  C15   C   CR16   0  -0.016   3.5067   0.9442   1.1129
 X62  C16   C   CR6    0   0.304   5.2602   0.2699  -0.0993
 X62  C17   C   CR16   0  -0.005   3.3096   0.4605  -1.1758
 X62  O18   O   O      0  -0.496   0.2846  -2.6755   0.5746
 X62  O19   O   O     -1  -0.382  -5.7726   0.6904  -0.5234
 X62  O20   O   O      0  -0.393  -5.6261  -1.2027   0.4512
 X62  CL21  CL  CL     0  -0.054  -3.7717   2.6479  -0.1229
 X62  CL22  CL  CL     0  -0.084   6.9405  -0.1238  -0.1628
 X62  HN01  H   HNH1   0   0.417   0.9218  -0.8967   0.3207
 X62  H102  H   HNH2   0   0.419  -2.3609  -3.6346  -0.8525
 X62  H202  H   HNH2   0   0.413  -1.0469  -4.5839  -0.2982
 X62  H06   H   HCR6   0   0.300  -3.5190  -2.2095   0.1328
 X62  H09   H   HCR6   0   0.315  -1.1179   2.0697  -0.0642
 X62  H113  H   HCH2   0   0.279   0.9572   1.7883  -0.8257
 X62  H213  H   HCH2   0   0.275   1.0213   1.8121   0.9307
 X62  H15   H   HCR6   0   0.294   3.1117   1.2582   2.0728
 X62  H17   H   HCR6   0   0.295   2.7519   0.3772  -2.1026
 X62  C12   C   C      0   0.539  -0.8578  -2.6083   0.1242

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
 X62  N01  C08   single    1.339  0.020  1.339
 X62  N01  C13   single    1.446  0.020  1.446
 X62  N01  HN01  single    0.860  0.020  1.020
 X62  N02  C12   single    1.338  0.020  1.338
 X62  N02  H102  single    0.860  0.020  1.020
 X62  N02  H202  single    0.860  0.020  1.020
 X62  N03  C16   aromatic  1.312  0.020  1.312
 X62  N05  O20   double    1.213  0.020  1.213
 X62  C06  C11   aromatic  1.390  0.020  1.390
 X62  C06  H06   single    0.930  0.020  1.080
 X62  C07  C06   aromatic  1.378  0.020  1.378
 X62  C07  C08   aromatic  1.426  0.020  1.426
 X62  C08  C09   aromatic  1.409  0.020  1.409
 X62  C09  C10   aromatic  1.374  0.020  1.374
 X62  C09  H09   single    0.930  0.020  1.080
 X62  C10  CL21  single    1.718  0.020  1.718
 X62  C11  N05   single    1.437  0.020  1.437
 X62  C11  C10   aromatic  1.402  0.020  1.402
 X62  C12  C07   single    1.491  0.020  1.491
 X62  C13  C14   single    1.497  0.020  1.497
 X62  C13  H113  single    0.970  0.020  1.090
 X62  C13  H213  single    0.970  0.020  1.090
 X62  C14  C17   aromatic  1.388  0.020  1.388
 X62  C15  C14   aromatic  1.386  0.020  1.386
 X62  C15  N03   aromatic  1.328  0.020  1.328
 X62  C15  H15   single    0.930  0.020  1.080
 X62  C16  N04   aromatic  1.314  0.020  1.314
 X62  C16  CL22  single    1.727  0.020  1.727
 X62  C17  N04   aromatic  1.326  0.020  1.326
 X62  C17  H17   single    0.930  0.020  1.080
 X62  O18  C12   double    1.230  0.020  1.230
 X62  O19  N05   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
 X62  HN01  N01  C13   119.09  3.000
 X62  HN01  N01  C08   115.80  3.000
 X62  C13   N01  C08   123.94  3.000
 X62  H202  N02  H102  116.72  3.000
 X62  H202  N02  C12   119.12  3.000
 X62  H102  N02  C12   123.05  3.000
 X62  C16   N03  C15   115.73  3.000
 X62  C17   N04  C16   115.73  3.000
 X62  O20   N05  O19   123.54  3.000
 X62  O19   N05  C11   118.76  3.000
 X62  O20   N05  C11   117.69  3.000
 X62  H06   C06  C11   117.62  3.000
 X62  H06   C06  C07   119.62  3.000
 X62  C11   C06  C07   122.75  3.000
 X62  C12   C07  C08   120.74  3.000
 X62  C12   C07  C06   120.47  3.000
 X62  C08   C07  C06   118.77  3.000
 X62  C09   C08  C07   117.96  3.000
 X62  C09   C08  N01   120.32  3.000
 X62  C07   C08  N01   121.72  3.000
 X62  H09   C09  C10   118.22  3.000
 X62  H09   C09  C08   119.74  3.000
 X62  C10   C09  C08   122.02  3.000
 X62  CL21  C10  C11   123.58  3.000
 X62  C11   C10  C09   119.79  3.000
 X62  CL21  C10  C09   116.53  3.000
 X62  C10   C11  C06   118.64  3.000
 X62  C10   C11  N05   123.78  3.000
 X62  C06   C11  N05   117.58  3.000
 X62  H213  C13  H113  106.89  3.000
 X62  H213  C13  C14   109.62  3.000
 X62  H113  C13  C14   109.31  3.000
 X62  H213  C13  N01   111.34  3.000
 X62  H113  C13  N01   109.99  3.000
 X62  C14   C13  N01   109.64  3.000
 X62  C17   C14  C15   115.61  3.000
 X62  C15   C14  C13   122.35  3.000
 X62  C17   C14  C13   122.04  3.000
 X62  H15   C15  C14   120.90  3.000
 X62  H15   C15  N03   116.61  3.000
 X62  C14   C15  N03   122.50  3.000
 X62  CL22  C16  N04   115.97  3.000
 X62  CL22  C16  N03   116.05  3.000
 X62  N04   C16  N03   127.97  3.000
 X62  H17   C17  C14   120.95  3.000
 X62  H17   C17  N04   116.58  3.000
 X62  C14   C17  N04   122.46  3.000
 X62  O18   C12  C07   121.21  3.000
 X62  O18   C12  N02   122.00  3.000
 X62  C07   C12  N02   116.79  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
 X62  CONST_01  C17   N04  C16  N03     0.00   0.0  0
 X62  CONST_02  C17   C14  C15  N03     0.00   0.0  0
 X62  CONST_03  C15   N03  C16  N04     0.00   0.0  0
 X62  CONST_04  C15   C14  C17  N04     0.00   0.0  0
 X62  CONST_05  C09   C10  C11  C06     0.00   0.0  0
 X62  CONST_06  C09   C08  C07  C06     0.00   0.0  0
 X62  CONST_07  C10   C11  C06  C07     0.00   0.0  0
 X62  CONST_08  C10   C09  C08  C07     0.00   0.0  0
 X62  CONST_09  C11   C06  C07  C08     0.00   0.0  0
 X62  CONST_10  C11   C10  C09  C08     0.00   0.0  0
 X62  CONST_11  C16   N04  C17  C14     0.00   0.0  0
 X62  CONST_12  C16   N03  C15  C14     0.00   0.0  0
 X62  CONST_13  C06   C07  C08  N01   180.00   0.0  0
 X62  CONST_14  C10   C09  C08  N01   180.00   0.0  0
 X62  CONST_15  C13   C14  C15  N03   180.00   0.0  0
 X62  CONST_16  C13   C14  C17  N04   180.00   0.0  0
 X62  CONST_17  C07   C06  C11  N05   180.00   0.0  0
 X62  CONST_18  C09   C10  C11  N05   180.00   0.0  0
 X62  CONST_19  CL21  C10  C11  C06   180.00   0.0  0
 X62  CONST_20  CL21  C10  C09  C08   180.00   0.0  0
 X62  CONST_21  C12   C07  C08  C09   180.00   0.0  0
 X62  CONST_22  C12   C07  C06  C11   180.00   0.0  0
 X62  CONST_23  CL22  C16  N03  C15   180.00   0.0  0
 X62  CONST_24  CL22  C16  N04  C17   180.00   0.0  0
 X62  CONST_25  H09   C09  C08  C07   180.00   0.0  0
 X62  CONST_26  H06   C06  C07  C08   180.00   0.0  0
 X62  CONST_27  H17   C17  C14  C15   180.00   0.0  0
 X62  CONST_28  H15   C15  N03  C16   180.00   0.0  0
 X62  CONST_31  C13   N01  C08  C07   180.00   0.0  0
 X62  CONST_32  C13   N01  C08  C09     0.00   0.0  0
 X62  CONST_35  HN01  N01  C08  C07     0.00   0.0  0
 X62  CONST_36  H102  N02  C12  C07     0.00   0.0  0
 X62  CONST_37  H202  N02  C12  C07   180.00   0.0  0
 X62  Var_01    C17   C14  C13  N01    77.25  30.0  2
 X62  Var_02    C06   C07  C12  N02    24.92  30.0  2
 X62  Var_03    C14   C13  N01  C08  -175.44  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
 X62  plan-1  N03   0.020
 X62  plan-1  N04   0.020
 X62  plan-1  C13   0.020
 X62  plan-1  C14   0.020
 X62  plan-1  C15   0.020
 X62  plan-1  C16   0.020
 X62  plan-1  C17   0.020
 X62  plan-1  CL22  0.020
 X62  plan-1  H15   0.020
 X62  plan-1  H17   0.020
 X62  plan-2  N01   0.020
 X62  plan-2  N05   0.020
 X62  plan-2  C06   0.020
 X62  plan-2  C07   0.020
 X62  plan-2  C08   0.020
 X62  plan-2  C09   0.020
 X62  plan-2  C10   0.020
 X62  plan-2  C11   0.020
 X62  plan-2  CL21  0.020
 X62  plan-2  H06   0.020
 X62  plan-2  H09   0.020
 X62  plan-2  C12   0.020
 X62  plan-3  N02   0.020
 X62  plan-3  C07   0.020
 X62  plan-3  O18   0.020
 X62  plan-3  H102  0.020
 X62  plan-3  H202  0.020
 X62  plan-3  C12   0.020
 X62  plan-4  N01   0.020
 X62  plan-4  C08   0.020
 X62  plan-4  C13   0.020
 X62  plan-4  HN01  0.020
 X62  plan-5  N05   0.020
 X62  plan-5  C11   0.020
 X62  plan-5  O19   0.020
 X62  plan-5  O20   0.020

