# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 02:04:15 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: ~{N}4-[(4-fluorophenyl)methyl]-6-(trifluoromethyl)pyridine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1cc(NCc2ccc(F)cc2)cc(n1)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
 HLK  HLK  ~{N}4-[(4-fluorophenyl)methyl]-6-(trifluoromethyl)pyridine-2,4-diamine  ligand  31  20  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HLK
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
 HLK  C10   C  CR16  0  -0.277  -3.8385  -0.2324  -1.2243
 HLK  C15   C  CR16  0  -0.264  -3.6094  -0.1920   1.1598
 HLK  C17   C  CT    0   1.042   3.9745   1.2650   0.0313
 HLK  C02   C  CR6   0   0.449   2.4725  -2.0050   0.1205
 HLK  C04   C  CR6   0  -0.001   2.8908   0.2217   0.0417
 HLK  C05   C  CR16  0  -0.449   1.5699   0.5723  -0.0243
 HLK  C06   C  CR6   0   0.503   0.6154  -0.4752  -0.0141
 HLK  C08   C  CH2   0  -0.339  -1.7387  -1.1704  -0.2046
 HLK  C09   C  CR6   0   0.059  -3.0929  -0.5297  -0.0889
 HLK  C11   C  CR16  0  -0.398  -5.0805   0.3814  -1.1271
 HLK  C12   C  CR6   0   0.518  -5.5604   0.6970   0.1279
 HLK  C14   C  CR16  0  -0.397  -4.8471   0.4206   1.2798
 HLK  C16   C  CR16  0  -0.490   1.0891  -1.7808   0.0513
 HLK  F13   F  F     0  -0.315  -6.7609   1.2886   0.2353
 HLK  F18   F  F     0  -0.315   4.7735   1.1240  -1.0344
 HLK  F19   F  F     0  -0.302   3.4965   2.5124   0.0008
 HLK  F20   F  F     0  -0.313   4.7538   1.1685   1.1151
 HLK  N03   N  N     0  -0.511   3.3656  -1.0187   0.1164
 HLK  N07   N  NH1   0  -0.684  -0.7023  -0.1729  -0.0496
 HLK  H101  H  HCR6  0   0.267  -3.4512  -0.4844  -2.2037
 HLK  H151  H  HCR6  0   0.266  -3.0441  -0.4152   2.0562
 HLK  H051  H  HCR6  0   0.275   1.2456   1.6020  -0.0814
 HLK  H081  H  HCH2  0   0.256  -1.6243  -1.9294   0.5735
 HLK  H082  H  HCH2  0   0.250  -1.6519  -1.6892  -1.1668
 HLK  H111  H  HCR6  0   0.281  -5.6603   0.6072  -2.0124
 HLK  H141  H  HCR6  0   0.282  -5.2509   0.6747   2.2509
 HLK  H161  H  HCR6  0   0.279   0.4168  -2.6279   0.0460
 HLK  H011  H  HNH2  0   0.392   2.3442  -4.0114   0.4479
 HLK  H012  H  HNH2  0   0.384   3.9171  -3.3859   0.4373
 HLK  H071  H  HNH1  0   0.394  -0.9468   0.7734  -0.2921
 HLK  N01   N  NH2   0  -0.840   2.9601  -3.2755   0.1463

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
 HLK  F19  C17   single    1.336  0.020  1.336
 HLK  C17  F20   single    1.338  0.020  1.338
 HLK  C17  F18   single    1.339  0.020  1.339
 HLK  C17  C04   single    1.504  0.020  1.504
 HLK  N03  C04   aromatic  1.330  0.020  1.330
 HLK  N03  C02   aromatic  1.331  0.020  1.331
 HLK  N01  C02   single    1.361  0.020  1.361
 HLK  C04  C05   aromatic  1.368  0.020  1.368
 HLK  C02  C16   aromatic  1.403  0.020  1.403
 HLK  C05  C06   aromatic  1.417  0.020  1.417
 HLK  C16  C06   aromatic  1.390  0.020  1.390
 HLK  C06  N07   single    1.352  0.020  1.352
 HLK  F13  C12   single    1.343  0.020  1.343
 HLK  C12  C14   aromatic  1.383  0.020  1.383
 HLK  C12  C11   aromatic  1.380  0.020  1.380
 HLK  C14  C15   aromatic  1.386  0.020  1.386
 HLK  C11  C10   aromatic  1.389  0.020  1.389
 HLK  N07  C08   single    1.447  0.020  1.447
 HLK  C15  C09   aromatic  1.393  0.020  1.393
 HLK  C10  C09   aromatic  1.390  0.020  1.390
 HLK  C09  C08   single    1.503  0.020  1.503
 HLK  C10  H101  single    0.930  0.020  1.080
 HLK  C15  H151  single    0.930  0.020  1.080
 HLK  C05  H051  single    0.930  0.020  1.080
 HLK  C08  H081  single    0.970  0.020  1.090
 HLK  C08  H082  single    0.970  0.020  1.090
 HLK  C11  H111  single    0.930  0.020  1.080
 HLK  C14  H141  single    0.930  0.020  1.080
 HLK  C16  H161  single    0.930  0.020  1.080
 HLK  N01  H011  single    0.890  0.020  1.040
 HLK  N01  H012  single    0.890  0.020  1.040
 HLK  N07  H071  single    0.890  0.020  1.040

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
 HLK  H101  C10  C11   119.08  3.000
 HLK  H101  C10  C09   119.80  3.000
 HLK  C11   C10  C09   121.12  3.000
 HLK  H151  C15  C14   119.04  3.000
 HLK  H151  C15  C09   119.90  3.000
 HLK  C14   C15  C09   121.06  3.000
 HLK  F20   C17  F19   107.10  3.000
 HLK  F20   C17  F18   106.82  3.000
 HLK  F19   C17  F18   107.07  3.000
 HLK  F18   C17  C04   111.24  3.000
 HLK  F20   C17  C04   111.34  3.000
 HLK  F19   C17  C04   112.95  3.000
 HLK  N03   C02  N01   116.84  3.000
 HLK  N01   C02  C16   120.21  3.000
 HLK  N03   C02  C16   122.91  3.000
 HLK  N03   C04  C05   125.89  3.000
 HLK  C05   C04  C17   121.16  3.000
 HLK  N03   C04  C17   112.95  3.000
 HLK  H051  C05  C06   120.15  3.000
 HLK  H051  C05  C04   122.43  3.000
 HLK  C06   C05  C04   117.42  3.000
 HLK  N07   C06  C16   122.89  3.000
 HLK  N07   C06  C05   119.40  3.000
 HLK  C16   C06  C05   117.71  3.000
 HLK  H082  C08  H081  106.73  3.000
 HLK  H082  C08  N07   111.31  3.000
 HLK  H081  C08  N07   109.12  3.000
 HLK  H082  C08  C09   109.92  3.000
 HLK  H081  C08  C09   109.62  3.000
 HLK  N07   C08  C09   110.08  3.000
 HLK  C08   C09  C15   120.44  3.000
 HLK  C08   C09  C10   120.77  3.000
 HLK  C15   C09  C10   118.77  3.000
 HLK  H111  C11  C12   120.65  3.000
 HLK  H111  C11  C10   120.94  3.000
 HLK  C12   C11  C10   118.40  3.000
 HLK  F13   C12  C14   118.86  3.000
 HLK  C14   C12  C11   122.17  3.000
 HLK  F13   C12  C11   118.97  3.000
 HLK  H141  C14  C12   120.55  3.000
 HLK  H141  C14  C15   120.98  3.000
 HLK  C12   C14  C15   118.48  3.000
 HLK  H161  C16  C06   121.57  3.000
 HLK  H161  C16  C02   119.21  3.000
 HLK  C06   C16  C02   119.22  3.000
 HLK  C04   N03  C02   116.85  3.000
 HLK  H071  N07  C08   116.62  3.000
 HLK  H071  N07  C06   116.93  3.000
 HLK  C08   N07  C06   123.14  3.000
 HLK  H012  N01  H011  114.54  3.000
 HLK  H012  N01  C02   116.65  3.000
 HLK  H011  N01  C02   117.98  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
 HLK  CONST_01  C14   C12  C11  C10    0.00   0.0  0
 HLK  CONST_02  C14   C15  C09  C10    0.00   0.0  0
 HLK  CONST_03  C11   C12  C14  C15    0.00   0.0  0
 HLK  CONST_04  C11   C10  C09  C15    0.00   0.0  0
 HLK  CONST_05  C05   C04  N03  C02    0.00   0.0  0
 HLK  CONST_06  C05   C06  C16  C02    0.00   0.0  0
 HLK  CONST_07  C16   C02  N03  C04    0.00   0.0  0
 HLK  CONST_08  C16   C06  C05  C04    0.00   0.0  0
 HLK  CONST_09  N03   C04  C05  C06    0.00   0.0  0
 HLK  CONST_10  N03   C02  C16  C06    0.00   0.0  0
 HLK  CONST_11  C12   C14  C15  C09    0.00   0.0  0
 HLK  CONST_12  C12   C11  C10  C09    0.00   0.0  0
 HLK  CONST_13  F13   C12  C11  C10  180.00   0.0  0
 HLK  CONST_14  F13   C12  C14  C15  180.00   0.0  0
 HLK  CONST_15  C02   N03  C04  C17  180.00   0.0  0
 HLK  CONST_16  C06   C05  C04  C17  180.00   0.0  0
 HLK  CONST_17  N07   C06  C16  C02  180.00   0.0  0
 HLK  CONST_18  N01   C02  N03  C04  180.00   0.0  0
 HLK  CONST_19  N07   C06  C05  C04  180.00   0.0  0
 HLK  CONST_20  N01   C02  C16  C06  180.00   0.0  0
 HLK  CONST_21  C14   C15  C09  C08  180.00   0.0  0
 HLK  CONST_22  C11   C10  C09  C08  180.00   0.0  0
 HLK  CONST_23  H151  C15  C09  C10  180.00   0.0  0
 HLK  CONST_24  H101  C10  C09  C15  180.00   0.0  0
 HLK  CONST_25  H161  C16  C06  C05  180.00   0.0  0
 HLK  CONST_26  H141  C14  C15  C09  180.00   0.0  0
 HLK  CONST_27  H111  C11  C10  C09  180.00   0.0  0
 HLK  CONST_28  H051  C05  C06  C16  180.00   0.0  0
 HLK  CONST_29  C08   N07  C06  C05  180.00   0.0  0
 HLK  CONST_30  C16   C06  N07  C08    0.00   0.0  0
 HLK  CONST_31  H071  N07  C06  C05    0.00   0.0  0
 HLK  Var_01    N07   C08  C09  C10  100.61  30.0  2
 HLK  Var_02    F19   C17  C04  C05    2.22  30.0  3
 HLK  Var_03    C09   C08  N07  C06  175.23  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
 HLK  plan-1  C10   0.020
 HLK  plan-1  C15   0.020
 HLK  plan-1  C08   0.020
 HLK  plan-1  C09   0.020
 HLK  plan-1  C11   0.020
 HLK  plan-1  C12   0.020
 HLK  plan-1  C14   0.020
 HLK  plan-1  F13   0.020
 HLK  plan-1  H101  0.020
 HLK  plan-1  H151  0.020
 HLK  plan-1  H111  0.020
 HLK  plan-1  H141  0.020
 HLK  plan-2  C17   0.020
 HLK  plan-2  C02   0.020
 HLK  plan-2  C04   0.020
 HLK  plan-2  C05   0.020
 HLK  plan-2  C06   0.020
 HLK  plan-2  C16   0.020
 HLK  plan-2  N03   0.020
 HLK  plan-2  N07   0.020
 HLK  plan-2  H051  0.020
 HLK  plan-2  H161  0.020
 HLK  plan-2  N01   0.020
 HLK  plan-3  C06   0.020
 HLK  plan-3  C08   0.020
 HLK  plan-3  N07   0.020
 HLK  plan-3  H071  0.020
 HLK  plan-4  C02   0.020
 HLK  plan-4  H011  0.020
 HLK  plan-4  H012  0.020
 HLK  plan-4  N01   0.020

