# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 16:36:14 2022
#   Inital geometry file: a 38 line input string
#   Ligand name: 5-fluoranylpyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ccc(F)cn1
#
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
 U1Q  U1Q  "5-fluoranylpyridin-2-amine"
  ligand  13  8  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_U1Q
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
 U1Q  C02  C  CR6   0   0.442  -1.3831  4.5520   9.2279
 U1Q  C03  C  CR16  0  -0.360  -2.6860  4.3014   9.6961
 U1Q  C04  C  CR16  0  -0.295  -2.8598  3.4379  10.7542
 U1Q  C05  C  CR6   0   0.394  -1.7349  2.8524  11.3118
 U1Q  C07  C  CR16  0  -0.202  -0.4921  3.1353  10.7955
 U1Q  F06  F  F     0  -0.314  -1.8569  2.0090  12.3524
 U1Q  N01  N  NH2   0  -0.833  -1.1594  5.4485   8.2212
 U1Q  N08  N  N     0  -0.442  -0.3210  3.9664   9.7723
 U1Q  H1   H  HCR6  0   0.278  -3.5384  4.7795   9.2317
 U1Q  H2   H  HCR6  0   0.290  -3.8487  3.2216  11.1378
 U1Q  H3   H  HCR6  0   0.273   0.3977  2.6766  11.2148
 U1Q  H4   H  HNH2  0   0.381  -0.2701  5.3753   7.7544
 U1Q  H5   H  HNH2  0   0.389  -1.9271  5.6518   7.6029

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
 U1Q  N01  C02  single    1.367  0.020  1.367
 U1Q  C02  N08  aromatic  1.330  0.020  1.330
 U1Q  C02  C03  aromatic  1.407  0.020  1.407
 U1Q  N08  C07  aromatic  1.329  0.020  1.329
 U1Q  C03  C04  aromatic  1.377  0.020  1.377
 U1Q  C07  C05  aromatic  1.375  0.020  1.375
 U1Q  C04  C05  aromatic  1.385  0.020  1.385
 U1Q  C05  F06  single    1.345  0.020  1.345
 U1Q  C03  H1   single    0.930  0.020  1.080
 U1Q  C04  H2   single    0.930  0.020  1.080
 U1Q  C07  H3   single    0.930  0.020  1.080
 U1Q  N01  H4   single    0.890  0.020  1.040
 U1Q  N01  H5   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
 U1Q  N08  C02  N01  117.38  3.000
 U1Q  N08  C02  C03  121.68  3.000
 U1Q  N01  C02  C03  120.91  3.000
 U1Q  H1   C03  C04  120.50  3.000
 U1Q  H1   C03  C02  120.53  3.000
 U1Q  C04  C03  C02  118.97  3.000
 U1Q  H2   C04  C05  120.98  3.000
 U1Q  H2   C04  C03  120.86  3.000
 U1Q  C05  C04  C03  118.16  3.000
 U1Q  F06  C05  C07  120.09  3.000
 U1Q  F06  C05  C04  120.19  3.000
 U1Q  C07  C05  C04  119.72  3.000
 U1Q  H3   C07  N08  117.14  3.000
 U1Q  H3   C07  C05  120.59  3.000
 U1Q  N08  C07  C05  122.27  3.000
 U1Q  H5   N01  H4   113.80  3.000
 U1Q  H5   N01  C02  117.40  3.000
 U1Q  H4   N01  C02  116.00  3.000
 U1Q  C07  N08  C02  119.19  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
 U1Q  CONST_01  C05  C07  N08  C02    0.00  0.0  0
 U1Q  CONST_02  C05  C04  C03  C02    0.00  0.0  0
 U1Q  CONST_03  C07  N08  C02  C03    0.00  0.0  0
 U1Q  CONST_04  C07  C05  C04  C03    0.00  0.0  0
 U1Q  CONST_05  N08  C02  C03  C04    0.00  0.0  0
 U1Q  CONST_06  N08  C07  C05  C04    0.00  0.0  0
 U1Q  CONST_07  F06  C05  C04  C03  180.00  0.0  0
 U1Q  CONST_08  N01  C02  C03  C04  180.00  0.0  0
 U1Q  CONST_09  N01  C02  N08  C07  180.00  0.0  0
 U1Q  CONST_10  N08  C07  C05  F06  180.00  0.0  0
 U1Q  CONST_11  H3   C07  N08  C02  180.00  0.0  0
 U1Q  CONST_12  H2   C04  C03  C02  180.00  0.0  0
 U1Q  CONST_13  H3   C07  C05  C04  180.00  0.0  0
 U1Q  CONST_14  H1   C03  C04  C05  180.00  0.0  0
 U1Q  CONST_15  H2   C04  C05  C07  180.00  0.0  0
 U1Q  CONST_16  H1   C03  C02  N08  180.00  0.0  0

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
 U1Q  plan-1  C02  0.020
 U1Q  plan-1  C03  0.020
 U1Q  plan-1  C04  0.020
 U1Q  plan-1  C05  0.020
 U1Q  plan-1  C07  0.020
 U1Q  plan-1  F06  0.020
 U1Q  plan-1  N01  0.020
 U1Q  plan-1  N08  0.020
 U1Q  plan-1  H1   0.020
 U1Q  plan-1  H2   0.020
 U1Q  plan-1  H3   0.020
 U1Q  plan-2  C02  0.020
 U1Q  plan-2  N01  0.020
 U1Q  plan-2  H4   0.020
 U1Q  plan-2  H5   0.020

