# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 23:01:02 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: 2-{[(2-aminopyrimidin-5-yl)methyl]amino}-4-chloro-5-nitrobenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1cc(c(Cl)cc1NCc2cnc(N)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
 X6A  X6A  2-{[(2-aminopyrimidin-5-yl)methyl]amino}-4-chloro-5-nitrobenzamide  ligand  33  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_X6A
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
 X6A  N01   N   NH1    0  -0.678   0.9076  -0.0542   0.0840
 X6A  N02   N   NH2    0  -0.805  -1.0776  -3.7083  -0.2932
 X6A  N03   N   N      0  -0.451   5.1037   0.1070  -1.1579
 X6A  N04   N   N      0  -0.451   5.2201   0.6321   1.1588
 X6A  N05   N   N      1   0.320  -4.6806  -0.2129   0.0387
 X6A  N06   N   NH2    0  -0.817   7.0600  -0.1168   0.0154
 X6A  C07   C   CR16   0  -0.330  -2.5218  -1.2981   0.1148
 X6A  C08   C   CR6    0  -0.114  -1.1445  -1.3311   0.0978
 X6A  C09   C   CR6    0   0.419  -0.4273  -0.0983   0.0534
 X6A  C10   C   CR16   0  -0.323  -1.1743   1.0948  -0.0434
 X6A  C11   C   CR6    0  -0.053  -2.5478   1.0960  -0.0630
 X6A  C12   C   CR6    0   0.294  -3.2484  -0.1156   0.0301
 X6A  C14   C   CH2    0  -0.359   1.6889   1.1640  -0.0051
 X6A  C15   C   CR6    0  -0.095   3.1482   0.8405  -0.0052
 X6A  C16   C   CR16   0  -0.017   3.8211   0.4139  -1.1442
 X6A  C17   C   CR6    0   0.555   5.7602   0.2236   0.0043
 X6A  C18   C   CR16   0  -0.025   3.9339   0.9287   1.1356
 X6A  O19   O   O      0  -0.496   0.7238  -2.7071   0.6019
 X6A  O20   O   O      0  -0.396  -5.1760  -1.2114   0.5196
 X6A  O21   O   O     -1  -0.384  -5.3294   0.6867  -0.4434
 X6A  CL22  CL  CL     0  -0.056  -3.3117   2.6351  -0.1109
 X6A  HN01  H   HNH1   0   0.413   1.3811  -0.9202   0.3035
 X6A  H102  H   HNH2   0   0.418  -1.9322  -3.6476  -0.8183
 X6A  H202  H   HNH2   0   0.412  -0.6223  -4.6067  -0.2704
 X6A  H106  H   HNH2   0   0.399   7.6235   0.1220   0.8125
 X6A  H206  H   HNH2   0   0.399   7.5339  -0.2747  -0.8567
 X6A  H07   H   HCR6   0   0.299  -3.0760  -2.2227   0.1962
 X6A  H10   H   HCR6   0   0.314  -0.6609   2.0446  -0.0785
 X6A  H114  H   HCH2   0   0.267   1.4243   1.7034  -0.9191
 X6A  H214  H   HCH2   0   0.265   1.4614   1.8324   0.8322
 X6A  H16   H   HCR6   0   0.271   3.2937   0.3232  -2.0901
 X6A  H18   H   HCR6   0   0.270   3.4986   1.2626   2.0733
 X6A  C13   C   C      0   0.535  -0.4198  -2.6327   0.1563

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
 X6A  N01  C09   single    1.336  0.020  1.336
 X6A  N01  C14   single    1.450  0.020  1.450
 X6A  N01  HN01  single    0.860  0.020  1.020
 X6A  N02  C13   single    1.339  0.020  1.339
 X6A  N02  H102  single    0.860  0.020  1.020
 X6A  N02  H202  single    0.860  0.020  1.020
 X6A  N04  C17   aromatic  1.338  0.020  1.338
 X6A  N05  O20   double    1.214  0.020  1.214
 X6A  N06  H106  single    0.890  0.020  1.040
 X6A  N06  H206  single    0.890  0.020  1.040
 X6A  C07  C12   aromatic  1.391  0.020  1.391
 X6A  C07  H07   single    0.930  0.020  1.080
 X6A  C08  C07   aromatic  1.378  0.020  1.378
 X6A  C08  C09   aromatic  1.427  0.020  1.427
 X6A  C09  C10   aromatic  1.411  0.020  1.411
 X6A  C10  C11   aromatic  1.374  0.020  1.374
 X6A  C10  H10   single    0.930  0.020  1.080
 X6A  C11  CL22  single    1.719  0.020  1.719
 X6A  C12  N05   single    1.436  0.020  1.436
 X6A  C12  C11   aromatic  1.403  0.020  1.403
 X6A  C13  C08   single    1.491  0.020  1.491
 X6A  C14  C15   single    1.495  0.020  1.495
 X6A  C14  H114  single    0.970  0.020  1.090
 X6A  C14  H214  single    0.970  0.020  1.090
 X6A  C15  C16   aromatic  1.390  0.020  1.390
 X6A  C16  N03   aromatic  1.319  0.020  1.319
 X6A  C16  H16   single    0.930  0.020  1.080
 X6A  C17  N03   aromatic  1.340  0.020  1.340
 X6A  C17  N06   single    1.344  0.020  1.344
 X6A  C18  C15   aromatic  1.388  0.020  1.388
 X6A  C18  N04   aromatic  1.320  0.020  1.320
 X6A  C18  H18   single    0.930  0.020  1.080
 X6A  O19  C13   double    1.230  0.020  1.230
 X6A  O21  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
 X6A  HN01  N01  C14   118.72  3.000
 X6A  HN01  N01  C09   116.40  3.000
 X6A  C14   N01  C09   124.39  3.000
 X6A  H202  N02  H102  116.75  3.000
 X6A  H202  N02  C13   119.14  3.000
 X6A  H102  N02  C13   123.01  3.000
 X6A  C17   N03  C16   116.57  3.000
 X6A  C18   N04  C17   116.53  3.000
 X6A  O21   N05  O20   123.43  3.000
 X6A  O21   N05  C12   118.84  3.000
 X6A  O20   N05  C12   117.73  3.000
 X6A  H206  N06  H106  117.47  3.000
 X6A  H206  N06  C17   119.26  3.000
 X6A  H106  N06  C17   119.26  3.000
 X6A  H07   C07  C12   117.65  3.000
 X6A  H07   C07  C08   119.53  3.000
 X6A  C12   C07  C08   122.82  3.000
 X6A  C13   C08  C09   120.74  3.000
 X6A  C13   C08  C07   120.42  3.000
 X6A  C09   C08  C07   118.83  3.000
 X6A  C10   C09  C08   117.81  3.000
 X6A  C10   C09  N01   120.17  3.000
 X6A  C08   C09  N01   122.01  3.000
 X6A  H10   C10  C11   118.30  3.000
 X6A  H10   C10  C09   119.61  3.000
 X6A  C11   C10  C09   122.08  3.000
 X6A  CL22  C11  C12   123.59  3.000
 X6A  C12   C11  C10   119.85  3.000
 X6A  CL22  C11  C10   116.46  3.000
 X6A  C11   C12  C07   118.53  3.000
 X6A  C11   C12  N05   123.87  3.000
 X6A  C07   C12  N05   117.60  3.000
 X6A  H214  C14  H114  106.71  3.000
 X6A  H214  C14  C15   109.56  3.000
 X6A  H114  C14  C15   110.05  3.000
 X6A  H214  C14  N01   110.73  3.000
 X6A  H114  C14  N01   109.60  3.000
 X6A  C15   C14  N01   110.14  3.000
 X6A  C18   C15  C16   114.77  3.000
 X6A  C18   C15  C14   122.60  3.000
 X6A  C16   C15  C14   122.62  3.000
 X6A  H16   C16  C15   120.26  3.000
 X6A  H16   C16  N03   116.33  3.000
 X6A  C15   C16  N03   123.41  3.000
 X6A  N06   C17  N04   117.43  3.000
 X6A  N06   C17  N03   117.33  3.000
 X6A  N04   C17  N03   125.24  3.000
 X6A  H18   C18  C15   120.14  3.000
 X6A  H18   C18  N04   116.38  3.000
 X6A  C15   C18  N04   123.48  3.000
 X6A  O19   C13  C08   121.28  3.000
 X6A  O19   C13  N02   122.01  3.000
 X6A  C08   C13  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
 X6A  CONST_01  C18   C15  C16  N03     0.00   0.0  0
 X6A  CONST_02  C18   N04  C17  N03     0.00   0.0  0
 X6A  CONST_03  C16   N03  C17  N04     0.00   0.0  0
 X6A  CONST_04  C16   C15  C18  N04     0.00   0.0  0
 X6A  CONST_05  C10   C11  C12  C07     0.00   0.0  0
 X6A  CONST_06  C10   C09  C08  C07     0.00   0.0  0
 X6A  CONST_07  C11   C12  C07  C08     0.00   0.0  0
 X6A  CONST_08  C11   C10  C09  C08     0.00   0.0  0
 X6A  CONST_09  C12   C07  C08  C09     0.00   0.0  0
 X6A  CONST_10  C12   C11  C10  C09     0.00   0.0  0
 X6A  CONST_11  C17   N03  C16  C15     0.00   0.0  0
 X6A  CONST_12  C17   N04  C18  C15     0.00   0.0  0
 X6A  CONST_13  C07   C08  C09  N01   180.00   0.0  0
 X6A  CONST_14  C11   C10  C09  N01   180.00   0.0  0
 X6A  CONST_15  C14   C15  C16  N03   180.00   0.0  0
 X6A  CONST_16  C14   C15  C18  N04   180.00   0.0  0
 X6A  CONST_17  C08   C07  C12  N05   180.00   0.0  0
 X6A  CONST_18  C10   C11  C12  N05   180.00   0.0  0
 X6A  CONST_19  C18   N04  C17  N06   180.00   0.0  0
 X6A  CONST_20  C16   N03  C17  N06   180.00   0.0  0
 X6A  CONST_21  CL22  C11  C12  C07   180.00   0.0  0
 X6A  CONST_22  CL22  C11  C10  C09   180.00   0.0  0
 X6A  CONST_23  C13   C08  C09  C10   180.00   0.0  0
 X6A  CONST_24  C13   C08  C07  C12   180.00   0.0  0
 X6A  CONST_25  H10   C10  C09  C08   180.00   0.0  0
 X6A  CONST_26  H07   C07  C08  C09   180.00   0.0  0
 X6A  CONST_27  H18   C18  C15  C16   180.00   0.0  0
 X6A  CONST_28  H16   C16  N03  C17   180.00   0.0  0
 X6A  CONST_31  C14   N01  C09  C08   180.00   0.0  0
 X6A  CONST_32  C14   N01  C09  C10     0.00   0.0  0
 X6A  CONST_35  H106  N06  C17  N03   180.00   0.0  0
 X6A  CONST_36  H206  N06  C17  N03     0.00   0.0  0
 X6A  CONST_37  HN01  N01  C09  C08     0.00   0.0  0
 X6A  CONST_38  H102  N02  C13  C08     0.00   0.0  0
 X6A  CONST_39  H202  N02  C13  C08   180.00   0.0  0
 X6A  Var_01    C16   C15  C14  N01    80.37  30.0  2
 X6A  Var_02    C07   C08  C13  N02    25.46  30.0  2
 X6A  Var_03    C15   C14  N01  C09  -177.28  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
 X6A  plan-1  N03   0.020
 X6A  plan-1  N04   0.020
 X6A  plan-1  N06   0.020
 X6A  plan-1  C14   0.020
 X6A  plan-1  C15   0.020
 X6A  plan-1  C16   0.020
 X6A  plan-1  C17   0.020
 X6A  plan-1  C18   0.020
 X6A  plan-1  H16   0.020
 X6A  plan-1  H18   0.020
 X6A  plan-2  N01   0.020
 X6A  plan-2  N05   0.020
 X6A  plan-2  C07   0.020
 X6A  plan-2  C08   0.020
 X6A  plan-2  C09   0.020
 X6A  plan-2  C10   0.020
 X6A  plan-2  C11   0.020
 X6A  plan-2  C12   0.020
 X6A  plan-2  CL22  0.020
 X6A  plan-2  H07   0.020
 X6A  plan-2  H10   0.020
 X6A  plan-2  C13   0.020
 X6A  plan-3  N02   0.020
 X6A  plan-3  C08   0.020
 X6A  plan-3  O19   0.020
 X6A  plan-3  H102  0.020
 X6A  plan-3  H202  0.020
 X6A  plan-3  C13   0.020
 X6A  plan-4  N01   0.020
 X6A  plan-4  C09   0.020
 X6A  plan-4  C14   0.020
 X6A  plan-4  HN01  0.020
 X6A  plan-5  N05   0.020
 X6A  plan-5  C12   0.020
 X6A  plan-5  O20   0.020
 X6A  plan-5  O21   0.020
 X6A  plan-6  N06   0.020
 X6A  plan-6  C17   0.020
 X6A  plan-6  H106  0.020
 X6A  plan-6  H206  0.020

