# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 15:08:28 2020
#   Inital geometry file: a 61 line input string
#   Ligand name: 4-phenylpyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nccc(n1)c2ccccc2
#
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
 F3E  F3E  4-phenylpyrimidin-2-amine  ligand  22  13  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_F3E
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
 F3E  C10  C  CR16  0  -0.257  -3.8243   0.3527  -0.0265
 F3E  C02  C  CR6   0   0.542   2.4908   0.5709  -0.1110
 F3E  C04  C  CR16  0  -0.020   2.3307  -1.6522   0.2228
 F3E  C05  C  CR16  0  -0.400   0.9487  -1.5824   0.2179
 F3E  C06  C  CR6   0   0.286   0.3958  -0.3185   0.0182
 F3E  C07  C  CR6   0   0.057  -1.0653  -0.0946  -0.0059
 F3E  C08  C  CR16  0  -0.280  -1.5807   1.1776   0.2467
 F3E  C09  C  CR16  0  -0.239  -2.9491   1.3977   0.2424
 F3E  C11  C  CR16  0  -0.238  -3.3209  -0.9143  -0.2903
 F3E  C12  C  CR16  0  -0.313  -1.9522  -1.1372  -0.2775
 F3E  N03  N  N     0  -0.455   3.1156  -0.6010   0.0592
 F3E  N13  N  N     0  -0.485   1.1683   0.7485  -0.1423
 F3E  H1   H  HCR6  0   0.262  -4.8926   0.5252  -0.0325
 F3E  H2   H  HCR6  0   0.271   2.8268  -2.6056   0.3717
 F3E  H3   H  HCR6  0   0.267   0.3502  -2.4658   0.3792
 F3E  H4   H  HCR6  0   0.256  -0.9032   1.9944   0.4553
 F3E  H5   H  HCR6  0   0.260  -3.3337   2.3874   0.4514
 F3E  H6   H  HCR6  0   0.262  -3.9948  -1.7319  -0.5102
 F3E  H7   H  HCR6  0   0.257  -1.5809  -2.1288  -0.5023
 F3E  H8   H  HNH2  0   0.396   2.8413   2.5285  -0.5402
 F3E  H9   H  HNH2  0   0.396   4.2483   1.5552  -0.3919
 F3E  N01  N  NH2   0  -0.824   3.2618   1.6675  -0.2380

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
 F3E  N03  C04  aromatic  1.322  0.020  1.322
 F3E  N03  C02  aromatic  1.339  0.020  1.339
 F3E  C04  C05  aromatic  1.384  0.020  1.384
 F3E  N01  C02  single    1.347  0.020  1.347
 F3E  C02  N13  aromatic  1.335  0.020  1.335
 F3E  C05  C06  aromatic  1.394  0.020  1.394
 F3E  N13  C06  aromatic  1.327  0.020  1.327
 F3E  C06  C07  single    1.478  0.020  1.478
 F3E  C07  C08  aromatic  1.396  0.020  1.396
 F3E  C07  C12  aromatic  1.395  0.020  1.395
 F3E  C08  C09  aromatic  1.386  0.020  1.386
 F3E  C12  C11  aromatic  1.387  0.020  1.387
 F3E  C09  C10  aromatic  1.389  0.020  1.389
 F3E  C11  C10  aromatic  1.389  0.020  1.389
 F3E  C10  H1   single    0.930  0.020  1.080
 F3E  C04  H2   single    0.930  0.020  1.080
 F3E  C05  H3   single    0.930  0.020  1.080
 F3E  C08  H4   single    0.930  0.020  1.080
 F3E  C09  H5   single    0.930  0.020  1.080
 F3E  C11  H6   single    0.930  0.020  1.080
 F3E  C12  H7   single    0.930  0.020  1.080
 F3E  N01  H8   single    0.890  0.020  1.040
 F3E  N01  H9   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
 F3E  H1   C10  C11  120.15  3.000
 F3E  H1   C10  C09  120.20  3.000
 F3E  C11  C10  C09  119.65  3.000
 F3E  N13  C02  N03  125.58  3.000
 F3E  N13  C02  N01  117.18  3.000
 F3E  N03  C02  N01  117.23  3.000
 F3E  H2   C04  N03  116.37  3.000
 F3E  H2   C04  C05  120.09  3.000
 F3E  N03  C04  C05  123.53  3.000
 F3E  H3   C05  C06  122.94  3.000
 F3E  H3   C05  C04  120.80  3.000
 F3E  C06  C05  C04  116.26  3.000
 F3E  N13  C06  C07  116.85  3.000
 F3E  C07  C06  C05  122.12  3.000
 F3E  N13  C06  C05  121.03  3.000
 F3E  C12  C07  C08  118.79  3.000
 F3E  C12  C07  C06  121.21  3.000
 F3E  C08  C07  C06  120.00  3.000
 F3E  H4   C08  C09  119.95  3.000
 F3E  H4   C08  C07  119.47  3.000
 F3E  C09  C08  C07  120.58  3.000
 F3E  H5   C09  C08  119.70  3.000
 F3E  H5   C09  C10  120.09  3.000
 F3E  C08  C09  C10  120.21  3.000
 F3E  H6   C11  C12  119.68  3.000
 F3E  H6   C11  C10  120.15  3.000
 F3E  C12  C11  C10  120.18  3.000
 F3E  H7   C12  C11  118.94  3.000
 F3E  H7   C12  C07  120.46  3.000
 F3E  C11  C12  C07  120.59  3.000
 F3E  C04  N03  C02  115.76  3.000
 F3E  C06  N13  C02  117.83  3.000
 F3E  H9   N01  H8   117.43  3.000
 F3E  H9   N01  C02  119.05  3.000
 F3E  H8   N01  C02  119.12  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
 F3E  CONST_01  C07  C08  C09  C10    0.00  0.0  0
 F3E  CONST_02  C07  C12  C11  C10    0.00  0.0  0
 F3E  CONST_03  C05  C04  N03  C02    0.00  0.0  0
 F3E  CONST_04  C05  C06  N13  C02    0.00  0.0  0
 F3E  CONST_05  C07  C06  N13  C02  180.00  0.0  0
 F3E  CONST_06  N13  C02  N03  C04    0.00  0.0  0
 F3E  CONST_07  N13  C06  C05  C04    0.00  0.0  0
 F3E  CONST_08  C07  C06  C05  C04  180.00  0.0  0
 F3E  CONST_11  N03  C04  C05  C06    0.00  0.0  0
 F3E  CONST_12  N03  C02  N13  C06    0.00  0.0  0
 F3E  CONST_13  C09  C08  C07  C06  180.00  0.0  0
 F3E  CONST_14  C11  C12  C07  C06  180.00  0.0  0
 F3E  CONST_16  C11  C12  C07  C08    0.00  0.0  0
 F3E  CONST_17  C11  C10  C09  C08    0.00  0.0  0
 F3E  CONST_18  C12  C07  C08  C09    0.00  0.0  0
 F3E  CONST_19  C12  C11  C10  C09    0.00  0.0  0
 F3E  CONST_21  N01  C02  N03  C04  180.00  0.0  0
 F3E  CONST_22  N01  C02  N13  C06  180.00  0.0  0
 F3E  CONST_23  H4   C08  C09  C10  180.00  0.0  0
 F3E  CONST_24  H7   C12  C11  C10  180.00  0.0  0
 F3E  CONST_25  H2   C04  N03  C02  180.00  0.0  0
 F3E  CONST_26  H3   C05  C06  C07    0.00  0.0  0
 F3E  CONST_27  H5   C09  C08  C07  180.00  0.0  0
 F3E  CONST_28  H6   C11  C12  C07  180.00  0.0  0
 F3E  CONST_29  H1   C10  C09  C08  180.00  0.0  0
 F3E  CONST_30  H8   N01  C02  N03  180.00  0.0  0
 F3E  CONST_31  H9   N01  C02  N03    0.00  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
 F3E  plan-1  C10  0.020
 F3E  plan-1  C06  0.020
 F3E  plan-1  C07  0.020
 F3E  plan-1  C08  0.020
 F3E  plan-1  C09  0.020
 F3E  plan-1  C11  0.020
 F3E  plan-1  C12  0.020
 F3E  plan-1  H1   0.020
 F3E  plan-1  H4   0.020
 F3E  plan-1  H5   0.020
 F3E  plan-1  H6   0.020
 F3E  plan-1  H7   0.020
 F3E  plan-2  C02  0.020
 F3E  plan-2  C04  0.020
 F3E  plan-2  C05  0.020
 F3E  plan-2  C06  0.020
 F3E  plan-2  C07  0.020
 F3E  plan-2  N03  0.020
 F3E  plan-2  N13  0.020
 F3E  plan-2  H2   0.020
 F3E  plan-2  H3   0.020
 F3E  plan-2  N01  0.020
 F3E  plan-3  C02  0.020
 F3E  plan-3  H8   0.020
 F3E  plan-3  H9   0.020
 F3E  plan-3  N01  0.020

