# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 24 13:34:04 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: 3-{[(4-fluorophenyl)methyl]amino}pyridine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccncc1NCc2ccc(F)cc2
#
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
 QC1  QC1  '3-{[(4-fluorophenyl)methyl]amino}pyridine-4-carboxylic acid'  ligand  29  18  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QC1
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
 QC1  F18  F  F     0  -0.314  -5.6329   0.8322   0.0387
 QC1  C15  C  CR6   0   0.519  -4.4102   0.2787   0.0099
 QC1  C14  C  CR16  0  -0.397  -3.8077   0.0542  -1.2130
 QC1  C13  C  CR16  0  -0.265  -2.5465  -0.5232  -1.2319
 QC1  C16  C  CR16  0  -0.398  -3.7986  -0.0535   1.2032
 QC1  C17  C  CR16  0  -0.267  -2.5375  -0.6308   1.1612
 QC1  C12  C  CR6   0   0.045  -1.9000  -0.8763  -0.0510
 QC1  C11  C  CH2   0  -0.339  -0.5168  -1.4623  -0.0837
 QC1  N10  N  NH1   0  -0.690   0.4573  -0.3914  -0.0591
 QC1  C2   C  CR6   0   0.334   1.7902  -0.5772  -0.0498
 QC1  C1   C  CR6   0  -0.099   2.7275   0.4826   0.0236
 QC1  C7   C  C     0   0.569   2.2824   1.8859   0.1027
 QC1  O9   O  OH1   0  -0.589   3.2810   2.7538   0.1474
 QC1  O8   O  O     0  -0.459   1.1192   2.2354   0.1244
 QC1  C3   C  CR16  0  -0.170   2.3330  -1.8853  -0.1202
 QC1  N4   N  N     0  -0.371   3.6179  -2.1547  -0.1208
 QC1  C5   C  CR16  0  -0.109   4.4919  -1.1503  -0.0511
 QC1  C6   C  CR16  0  -0.322   4.0864   0.1645   0.0210
 QC1  H1   H  HCR6  0   0.282  -4.3116   0.3208  -2.1327
 QC1  H2   H  HCR6  0   0.266  -2.0660  -0.7066  -2.1849
 QC1  H3   H  HCR6  0   0.282  -4.2950   0.1320   2.1466
 QC1  H4   H  HCR6  0   0.267  -2.0500  -0.8965   2.0910
 QC1  H5   H  HCH2  0   0.256  -0.3762  -2.1334   0.7702
 QC1  H6   H  HOH1  0   0.491   2.9300   3.6557   0.1944
 QC1  H7   H  HCR6  0   0.278   1.6661  -2.7376  -0.1775
 QC1  H8   H  HCR6  0   0.260   5.5436  -1.4073  -0.0538
 QC1  H9   H  HCR6  0   0.278   4.8349   0.9416   0.0764
 QC1  H10  H  HCH2  0   0.256  -0.3948  -2.0716  -0.9849
 QC1  H11  H  HNH1  0   0.407   0.1266   0.5563   0.0325

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
 QC1  C14  C13  aromatic  1.387  0.020  1.387
 QC1  C14  C15  aromatic  1.382  0.020  1.382
 QC1  C13  C12  aromatic  1.392  0.020  1.392
 QC1  F18  C15  single    1.342  0.020  1.342
 QC1  C15  C16  aromatic  1.381  0.020  1.381
 QC1  C12  C11  single    1.503  0.020  1.503
 QC1  C12  C17  aromatic  1.391  0.020  1.391
 QC1  C11  N10  single    1.448  0.020  1.448
 QC1  N10  C2   single    1.346  0.020  1.346
 QC1  C16  C17  aromatic  1.388  0.020  1.388
 QC1  C3   C2   aromatic  1.418  0.020  1.418
 QC1  C3   N4   aromatic  1.313  0.020  1.313
 QC1  C2   C1   aromatic  1.417  0.020  1.417
 QC1  O8   C7   double    1.215  0.020  1.215
 QC1  N4   C5   aromatic  1.333  0.020  1.333
 QC1  C1   C7   single    1.474  0.020  1.474
 QC1  C1   C6   aromatic  1.396  0.020  1.396
 QC1  C7   O9   single    1.324  0.020  1.324
 QC1  C5   C6   aromatic  1.378  0.020  1.378
 QC1  C14  H1   single    0.930  0.020  1.080
 QC1  C13  H2   single    0.930  0.020  1.080
 QC1  C16  H3   single    0.930  0.020  1.080
 QC1  C17  H4   single    0.930  0.020  1.080
 QC1  C11  H5   single    0.970  0.020  1.090
 QC1  O9   H6   single    0.850  0.020  0.980
 QC1  C3   H7   single    0.930  0.020  1.080
 QC1  C5   H8   single    0.930  0.020  1.080
 QC1  C6   H9   single    0.930  0.020  1.080
 QC1  C11  H10  single    0.970  0.020  1.090
 QC1  N10  H11  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
 QC1  C16  C15  C14  122.17  3.000
 QC1  C16  C15  F18  118.94  3.000
 QC1  C14  C15  F18  118.89  3.000
 QC1  H1   C14  C13  120.95  3.000
 QC1  H1   C14  C15  120.61  3.000
 QC1  C13  C14  C15  118.44  3.000
 QC1  H2   C13  C12  119.84  3.000
 QC1  H2   C13  C14  119.07  3.000
 QC1  C12  C13  C14  121.08  3.000
 QC1  H3   C16  C17  120.97  3.000
 QC1  H3   C16  C15  120.59  3.000
 QC1  C17  C16  C15  118.44  3.000
 QC1  H4   C17  C12  119.90  3.000
 QC1  H4   C17  C16  119.03  3.000
 QC1  C12  C17  C16  121.07  3.000
 QC1  C11  C12  C17  120.63  3.000
 QC1  C17  C12  C13  118.79  3.000
 QC1  C11  C12  C13  120.53  3.000
 QC1  H10  C11  H5   106.65  3.000
 QC1  H10  C11  N10  110.53  3.000
 QC1  H5   C11  N10  110.71  3.000
 QC1  H10  C11  C12  109.73  3.000
 QC1  H5   C11  C12  109.89  3.000
 QC1  N10  C11  C12  109.30  3.000
 QC1  H11  N10  C2   117.01  3.000
 QC1  H11  N10  C11  118.44  3.000
 QC1  C2   N10  C11  124.35  3.000
 QC1  C3   C2   C1   116.06  3.000
 QC1  C1   C2   N10  123.52  3.000
 QC1  C3   C2   N10  120.41  3.000
 QC1  C6   C1   C7   120.73  3.000
 QC1  C6   C1   C2   118.27  3.000
 QC1  C7   C1   C2   121.00  3.000
 QC1  O8   C7   O9   122.21  3.000
 QC1  O9   C7   C1   113.46  3.000
 QC1  O8   C7   C1   124.33  3.000
 QC1  H6   O9   C7   109.80  3.000
 QC1  H7   C3   N4   116.16  3.000
 QC1  H7   C3   C2   119.51  3.000
 QC1  N4   C3   C2   124.34  3.000
 QC1  C5   N4   C3   119.14  3.000
 QC1  H8   C5   C6   120.83  3.000
 QC1  H8   C5   N4   117.25  3.000
 QC1  C6   C5   N4   121.92  3.000
 QC1  H9   C6   C5   119.03  3.000
 QC1  H9   C6   C1   120.70  3.000
 QC1  C5   C6   C1   120.27  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
 QC1  CONST_01  C12  C13  C14  C15    0.00   0.0  0
 QC1  CONST_02  C12  C17  C16  C15    0.00   0.0  0
 QC1  CONST_03  C17  C12  C13  C14    0.00   0.0  0
 QC1  CONST_04  C17  C16  C15  C14    0.00   0.0  0
 QC1  CONST_05  C16  C15  C14  C13    0.00   0.0  0
 QC1  CONST_06  C16  C17  C12  C13    0.00   0.0  0
 QC1  CONST_07  C5   N4   C3   C2     0.00   0.0  0
 QC1  CONST_08  C5   C6   C1   C2     0.00   0.0  0
 QC1  CONST_09  N4   C3   C2   C1     0.00   0.0  0
 QC1  CONST_10  N4   C5   C6   C1     0.00   0.0  0
 QC1  CONST_11  C6   C1   C2   C3     0.00   0.0  0
 QC1  CONST_12  C6   C5   N4   C3     0.00   0.0  0
 QC1  CONST_13  C13  C14  C15  F18  180.00   0.0  0
 QC1  CONST_14  C17  C16  C15  F18  180.00   0.0  0
 QC1  CONST_15  C11  C12  C13  C14  180.00   0.0  0
 QC1  CONST_16  C11  C12  C17  C16  180.00   0.0  0
 QC1  CONST_17  N4   C3   C2   N10  180.00   0.0  0
 QC1  CONST_18  C6   C1   C2   N10  180.00   0.0  0
 QC1  CONST_19  C3   C2   C1   C7   180.00   0.0  0
 QC1  CONST_20  C5   C6   C1   C7   180.00   0.0  0
 QC1  CONST_21  H2   C13  C14  C15  180.00   0.0  0
 QC1  CONST_22  H4   C17  C16  C15  180.00   0.0  0
 QC1  CONST_23  H3   C16  C15  C14  180.00   0.0  0
 QC1  CONST_24  H1   C14  C15  C16  180.00   0.0  0
 QC1  CONST_25  H9   C6   C1   C2   180.00   0.0  0
 QC1  CONST_26  H7   C3   C2   C1   180.00   0.0  0
 QC1  CONST_27  H8   C5   C6   C1   180.00   0.0  0
 QC1  CONST_28  C3   C2   N10  C11    0.00   0.0  0
 QC1  CONST_29  C1   C2   N10  C11  180.00   0.0  0
 QC1  CONST_30  H11  N10  C2   C1     0.00   0.0  0
 QC1  CONST_31  H6   O9   C7   C1   180.00   0.0  0
 QC1  Var_01    N10  C11  C12  C13   87.98  30.0  2
 QC1  Var_02    C2   N10  C11  C12  178.53  30.0  3
 QC1  Var_03    O8   C7   C1   C2     0.76  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
 QC1  plan-1  F18  0.020
 QC1  plan-1  C15  0.020
 QC1  plan-1  C14  0.020
 QC1  plan-1  C13  0.020
 QC1  plan-1  C16  0.020
 QC1  plan-1  C17  0.020
 QC1  plan-1  C12  0.020
 QC1  plan-1  C11  0.020
 QC1  plan-1  H1   0.020
 QC1  plan-1  H2   0.020
 QC1  plan-1  H3   0.020
 QC1  plan-1  H4   0.020
 QC1  plan-2  N10  0.020
 QC1  plan-2  C2   0.020
 QC1  plan-2  C1   0.020
 QC1  plan-2  C7   0.020
 QC1  plan-2  C3   0.020
 QC1  plan-2  N4   0.020
 QC1  plan-2  C5   0.020
 QC1  plan-2  C6   0.020
 QC1  plan-2  H7   0.020
 QC1  plan-2  H8   0.020
 QC1  plan-2  H9   0.020
 QC1  plan-3  C11  0.020
 QC1  plan-3  N10  0.020
 QC1  plan-3  C2   0.020
 QC1  plan-3  H11  0.020
 QC1  plan-4  C1   0.020
 QC1  plan-4  C7   0.020
 QC1  plan-4  O9   0.020
 QC1  plan-4  O8   0.020
 QC1  plan-4  H6   0.020

