# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 02:41:55 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: 3-chloranyl-~{N}-(3-nitropyridin-2-yl)-5-(trifluoromethyl)pyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [O-][N+](=O)c1cccnc1Nc2ncc(cc2Cl)C(F)(F)F
#
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
 99K  99K  3-chloranyl-~{N}-(3-nitropyridin-2-yl)-5-(trifluoromethyl)pyridin-2-amine  ligand  27  21  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_99K
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
 99K  O1   O   O     -1  -0.368   5.1249  -0.9442  -1.0984
 99K  O3   O   O      0  -0.409   3.3037  -1.8466  -0.4634
 99K  C11  C   CR6    0   0.594  -0.1399  -0.1224   0.0381
 99K  C13  C   CR16   0  -0.056  -1.9627   1.1356  -0.5318
 99K  C14  C   CR6    0  -0.329  -2.8545   0.1684  -0.1014
 99K  C15  C   CR16   0  -0.088  -2.3372  -1.0136   0.4190
 99K  C16  C   CR6    0  -0.186  -0.9731  -1.1590   0.4968
 99K  C18  C   CT     0   1.069  -4.3334   0.3398  -0.2058
 99K  N2   N   N      1   0.351   4.0216  -0.8750  -0.6147
 99K  C4   C   CR6    0   0.107   3.5405   0.4148  -0.1898
 99K  C5   C   CR16   0  -0.174   4.4671   1.4465  -0.0952
 99K  C6   C   CR16   0  -0.339   4.0515   2.6943   0.3107
 99K  C7   C   CR16   0  -0.032   2.7059   2.8507   0.6163
 99K  N8   N   N      0  -0.421   1.8161   1.8808   0.5331
 99K  C9   C   CR6    0   0.537   2.1847   0.6709   0.1326
 99K  N10  N   NH1    0  -0.757   1.2256  -0.2989   0.0720
 99K  N12  N   N      0  -0.411  -0.6497   0.9831  -0.4709
 99K  CL   CL  CL     0  -0.085  -0.2957  -2.5996   1.1568
 99K  F19  F   F      0  -0.311  -4.8641  -0.5088  -1.0975
 99K  F20  F   F      0  -0.310  -4.9423   0.0942   0.9614
 99K  F21  F   F      0  -0.299  -4.6761   1.5730  -0.5820
 99K  H1   H   HCR6   0   0.288  -2.3066   2.0698  -0.9577
 99K  H2   H   HCR6   0   0.312  -2.9807  -1.8089   0.7723
 99K  H3   H   HCR6   0   0.317   5.5067   1.2700  -0.3305
 99K  H4   H   HCR6   0   0.290   4.7455   3.5160   0.4021
 99K  H5   H   HCR6   0   0.286   2.3318   3.8084   0.9589
 99K  H6   H   HNH1   0   0.425   1.5725  -1.2471   0.0303

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
 99K  C6   C7   aromatic  1.389  0.020  1.389
 99K  C6   C5   aromatic  1.376  0.020  1.376
 99K  C7   N8   aromatic  1.319  0.020  1.319
 99K  C5   C4   aromatic  1.390  0.020  1.390
 99K  N8   C9   aromatic  1.327  0.020  1.327
 99K  C4   C9   aromatic  1.417  0.020  1.417
 99K  C4   N2   single    1.441  0.020  1.441
 99K  C9   N10  single    1.365  0.020  1.365
 99K  N12  C13  aromatic  1.323  0.020  1.323
 99K  N12  C11  aromatic  1.320  0.020  1.320
 99K  O3   N2   double    1.217  0.020  1.217
 99K  C13  C14  aromatic  1.384  0.020  1.384
 99K  N2   O1   single    1.207  0.020  1.207
 99K  N10  C11  single    1.377  0.020  1.377
 99K  F20  C18  single    1.339  0.020  1.339
 99K  C11  C16  aromatic  1.407  0.020  1.407
 99K  F19  C18  single    1.341  0.020  1.341
 99K  C14  C18  single    1.492  0.020  1.492
 99K  C14  C15  aromatic  1.391  0.020  1.391
 99K  C18  F21  single    1.334  0.020  1.334
 99K  C16  C15  aromatic  1.374  0.020  1.374
 99K  C16  CL   single    1.723  0.020  1.723
 99K  C13  H1   single    0.930  0.020  1.080
 99K  C15  H2   single    0.930  0.020  1.080
 99K  C5   H3   single    0.930  0.020  1.080
 99K  C6   H4   single    0.930  0.020  1.080
 99K  C7   H5   single    0.930  0.020  1.080
 99K  N10  H6   single    0.860  0.020  1.020

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
 99K  N12  C11  N10  119.99  3.000
 99K  N10  C11  C16  119.00  3.000
 99K  N12  C11  C16  120.95  3.000
 99K  H1   C13  N12  115.64  3.000
 99K  H1   C13  C14  121.37  3.000
 99K  N12  C13  C14  122.98  3.000
 99K  C18  C14  C15  119.48  3.000
 99K  C15  C14  C13  118.06  3.000
 99K  C18  C14  C13  122.44  3.000
 99K  H2   C15  C16  119.60  3.000
 99K  H2   C15  C14  121.69  3.000
 99K  C16  C15  C14  118.70  3.000
 99K  CL   C16  C15  120.02  3.000
 99K  CL   C16  C11  120.53  3.000
 99K  C15  C16  C11  119.44  3.000
 99K  F21  C18  F20  107.37  3.000
 99K  F21  C18  F19  107.21  3.000
 99K  F20  C18  F19  106.48  3.000
 99K  F21  C18  C14  112.36  3.000
 99K  F19  C18  C14  111.48  3.000
 99K  F20  C18  C14  111.63  3.000
 99K  C4   N2   O3   118.74  3.000
 99K  O3   N2   O1   122.90  3.000
 99K  C4   N2   O1   118.36  3.000
 99K  C9   C4   C5   119.23  3.000
 99K  C9   C4   N2   123.26  3.000
 99K  C5   C4   N2   117.51  3.000
 99K  H3   C5   C6   120.19  3.000
 99K  H3   C5   C4   120.36  3.000
 99K  C6   C5   C4   119.45  3.000
 99K  H4   C6   C7   121.23  3.000
 99K  H4   C6   C5   121.40  3.000
 99K  C7   C6   C5   117.36  3.000
 99K  H5   C7   N8   115.91  3.000
 99K  H5   C7   C6   120.24  3.000
 99K  N8   C7   C6   123.85  3.000
 99K  C9   N8   C7   120.15  3.000
 99K  N10  C9   N8   117.78  3.000
 99K  N10  C9   C4   122.26  3.000
 99K  N8   C9   C4   119.96  3.000
 99K  H6   N10  C9   115.29  3.000
 99K  H6   N10  C11  117.36  3.000
 99K  C9   N10  C11  127.34  3.000
 99K  C13  N12  C11  119.85  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
 99K  CONST_01  C14  C13  N12  C11     0.00   0.0  0
 99K  CONST_02  C14  C15  C16  C11     0.00   0.0  0
 99K  CONST_03  C16  C11  N12  C13     0.00   0.0  0
 99K  CONST_04  C16  C15  C14  C13     0.00   0.0  0
 99K  CONST_05  N12  C13  C14  C15     0.00   0.0  0
 99K  CONST_06  N12  C11  C16  C15     0.00   0.0  0
 99K  CONST_07  C7   C6   C5   C4      0.00   0.0  0
 99K  CONST_08  C7   N8   C9   C4      0.00   0.0  0
 99K  CONST_09  N8   C7   C6   C5      0.00   0.0  0
 99K  CONST_10  N8   C9   C4   C5      0.00   0.0  0
 99K  CONST_11  C9   N8   C7   C6      0.00   0.0  0
 99K  CONST_12  C9   C4   C5   C6      0.00   0.0  0
 99K  CONST_13  N10  C11  N12  C13   180.00   0.0  0
 99K  CONST_14  CL   C16  C15  C14   180.00   0.0  0
 99K  CONST_15  N10  C11  C16  C15   180.00   0.0  0
 99K  CONST_16  C18  C14  C15  C16   180.00   0.0  0
 99K  CONST_17  N12  C13  C14  C18   180.00   0.0  0
 99K  CONST_18  C6   C5   C4   N2    180.00   0.0  0
 99K  CONST_19  N8   C9   C4   N2    180.00   0.0  0
 99K  CONST_20  N10  C9   C4   C5    180.00   0.0  0
 99K  CONST_21  N10  C9   N8   C7    180.00   0.0  0
 99K  CONST_22  CL   C16  C11  N12   180.00   0.0  0
 99K  CONST_23  H1   C13  N12  C11   180.00   0.0  0
 99K  CONST_24  H2   C15  C16  C11   180.00   0.0  0
 99K  CONST_25  H4   C6   C5   C4    180.00   0.0  0
 99K  CONST_26  H5   C7   C6   C5    180.00   0.0  0
 99K  CONST_27  H3   C5   C6   C7    180.00   0.0  0
 99K  CONST_28  C5   C4   N2   O1      0.00   0.0  0
 99K  CONST_29  C9   C4   N2   O1    180.00   0.0  0
 99K  CONST_30  C5   C4   N2   O3    180.00   0.0  0
 99K  CONST_31  C9   C4   N2   O3      0.00   0.0  0
 99K  Var_01    N8   C9   N10  C11    18.39  30.0  1
 99K  Var_02    C9   N10  C11  C16  -155.14  30.0  3
 99K  Var_03    F20  C18  C14  C13  -129.06  30.0  2

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
 99K  plan-1  N2   0.020
 99K  plan-1  C4   0.020
 99K  plan-1  C5   0.020
 99K  plan-1  C6   0.020
 99K  plan-1  C7   0.020
 99K  plan-1  N8   0.020
 99K  plan-1  C9   0.020
 99K  plan-1  N10  0.020
 99K  plan-1  H3   0.020
 99K  plan-1  H4   0.020
 99K  plan-1  H5   0.020
 99K  plan-2  C11  0.020
 99K  plan-2  C13  0.020
 99K  plan-2  C14  0.020
 99K  plan-2  C15  0.020
 99K  plan-2  C16  0.020
 99K  plan-2  C18  0.020
 99K  plan-2  N10  0.020
 99K  plan-2  N12  0.020
 99K  plan-2  CL   0.020
 99K  plan-2  H1   0.020
 99K  plan-2  H2   0.020
 99K  plan-3  O1   0.020
 99K  plan-3  O3   0.020
 99K  plan-3  N2   0.020
 99K  plan-3  C4   0.020

