# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 07:39:16 2020
#   Inital geometry file: a 63 line input string
#   Ligand name: 5-chloranyl-~{N}-(oxan-4-yl)pyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cnc(NC2CCOCC2)nc1
#
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
 EQW  EQW  5-chloranyl-~{N}-(oxan-4-yl)pyrimidin-2-amine  ligand  26  14  .  2021-08-08  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_EQW
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
 EQW  C2   C   CR6   0  -0.172  -3.0466   0.0745   0.0104
 EQW  C3   C   CR16  0   0.033  -2.0390   0.9153   0.4506
 EQW  N4   N   N     0  -0.456  -0.7682   0.5615   0.4175
 EQW  C5   C   CR6   0   0.609  -0.4867  -0.6573  -0.0570
 EQW  C7   C   CH1   0  -0.065   1.9266  -0.2111   0.2406
 EQW  C8   C   CH2   0  -0.469   3.1242  -1.0755   0.6191
 EQW  C11  C   CH2   0  -0.185   3.5861   1.4728  -0.5869
 EQW  C12  C   CH2   0  -0.456   2.3096   0.7143  -0.9149
 EQW  C14  C   CR16  0   0.019  -2.6582  -1.1676  -0.4720
 EQW  CL1  CL  CL    0  -0.122  -4.7034   0.5492   0.0519
 EQW  N6   N   NH1   0  -0.660   0.7958  -1.0565  -0.0744
 EQW  C9   C   CH2   0  -0.184   4.3478  -0.2035   0.8556
 EQW  O10  O   O2    0  -0.483   4.6487   0.6033  -0.2610
 EQW  N13  N   N     0  -0.453  -1.3954  -1.5367  -0.5087
 EQW  H15  H   HCR6  0   0.288  -2.2693   1.9024   0.8373
 EQW  H17  H   HCH1  0   0.245   1.6528   0.4012   1.1042
 EQW  H18  H   HCH2  0   0.250   2.9109  -1.6514   1.5225
 EQW  H19  H   HCH2  0   0.231   3.3318  -1.7906  -0.1839
 EQW  H23  H   HCH2  0   0.239   3.9100   2.0659  -1.4436
 EQW  H22  H   HCH2  0   0.199   3.3977   2.1717   0.2419
 EQW  H24  H   HCH2  0   0.226   2.4522   0.1187  -1.8218
 EQW  H25  H   HCH2  0   0.243   1.5070   1.4284  -1.1131
 EQW  H26  H   HCR6  0   0.290  -3.3942  -1.8766  -0.8367
 EQW  H16  H   HNH1  0   0.391   0.9789  -1.9335  -0.5366
 EQW  H20  H   HCH2  0   0.200   4.1850   0.4212   1.7465
 EQW  H21  H   HCH2  0   0.240   5.2246  -0.8233   1.0484

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
 EQW  O10  C11  single    1.411  0.020  1.411
 EQW  O10  C9   single    1.410  0.020  1.410
 EQW  C11  C12  single    1.521  0.020  1.521
 EQW  C12  C7   single    1.529  0.020  1.529
 EQW  C9   C8   single    1.521  0.020  1.521
 EQW  C8   C7   single    1.525  0.020  1.525
 EQW  C7   N6   single    1.447  0.020  1.447
 EQW  N6   C5   single    1.343  0.020  1.343
 EQW  C5   N13  aromatic  1.343  0.020  1.343
 EQW  C5   N4   aromatic  1.338  0.020  1.338
 EQW  N13  C14  aromatic  1.316  0.020  1.316
 EQW  N4   C3   aromatic  1.320  0.020  1.320
 EQW  C14  C2   aromatic  1.388  0.020  1.388
 EQW  C3   C2   aromatic  1.384  0.020  1.384
 EQW  C2   CL1  single    1.724  0.020  1.724
 EQW  C3   H15  single    0.930  0.020  1.080
 EQW  C7   H17  single    0.970  0.020  1.090
 EQW  C8   H18  single    0.970  0.020  1.090
 EQW  C8   H19  single    0.970  0.020  1.090
 EQW  C11  H23  single    0.970  0.020  1.090
 EQW  C11  H22  single    0.970  0.020  1.090
 EQW  C12  H24  single    0.970  0.020  1.090
 EQW  C12  H25  single    0.970  0.020  1.090
 EQW  C14  H26  single    0.930  0.020  1.080
 EQW  N6   H16  single    0.860  0.020  1.020
 EQW  C9   H20  single    0.970  0.020  1.090
 EQW  C9   H21  single    0.970  0.020  1.090

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
 EQW  CL1  C2   C14  121.58  3.000
 EQW  CL1  C2   C3   121.64  3.000
 EQW  C14  C2   C3   116.78  3.000
 EQW  H15  C3   N4   117.22  3.000
 EQW  H15  C3   C2   120.77  3.000
 EQW  N4   C3   C2   122.01  3.000
 EQW  C5   N4   C3   117.12  3.000
 EQW  N13  C5   N6   116.56  3.000
 EQW  N13  C5   N4   125.00  3.000
 EQW  N6   C5   N4   118.44  3.000
 EQW  H17  C7   N6   107.67  3.000
 EQW  H17  C7   C12  108.70  3.000
 EQW  N6   C7   C12  112.63  3.000
 EQW  H17  C7   C8   108.55  3.000
 EQW  N6   C7   C8   109.68  3.000
 EQW  C12  C7   C8   109.51  3.000
 EQW  H19  C8   H18  107.40  3.000
 EQW  H19  C8   C9   109.62  3.000
 EQW  H18  C8   C9   109.31  3.000
 EQW  H19  C8   C7   109.70  3.000
 EQW  H18  C8   C7   110.54  3.000
 EQW  C9   C8   C7   110.21  3.000
 EQW  H22  C11  H23  107.27  3.000
 EQW  H22  C11  O10  110.26  3.000
 EQW  H23  C11  O10  107.02  3.000
 EQW  H22  C11  C12  109.60  3.000
 EQW  H23  C11  C12  110.54  3.000
 EQW  O10  C11  C12  112.00  3.000
 EQW  H25  C12  H24  107.53  3.000
 EQW  H25  C12  C11  109.26  3.000
 EQW  H24  C12  C11  109.93  3.000
 EQW  H25  C12  C7   110.40  3.000
 EQW  H24  C12  C7   109.24  3.000
 EQW  C11  C12  C7   110.43  3.000
 EQW  H26  C14  N13  117.27  3.000
 EQW  H26  C14  C2   120.78  3.000
 EQW  N13  C14  C2   121.95  3.000
 EQW  H16  N6   C7   117.79  3.000
 EQW  H16  N6   C5   115.97  3.000
 EQW  C7   N6   C5   124.74  3.000
 EQW  H21  C9   H20  107.36  3.000
 EQW  H21  C9   O10  107.07  3.000
 EQW  H20  C9   O10  110.37  3.000
 EQW  H21  C9   C8   110.39  3.000
 EQW  H20  C9   C8   109.41  3.000
 EQW  O10  C9   C8   112.12  3.000
 EQW  C9   O10  C11  112.01  3.000
 EQW  C14  N13  C5   117.15  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
 EQW  CONST_01  C5   N13  C14  C2     0.00   0.0  0
 EQW  CONST_02  C5   N4   C3   C2     0.00   0.0  0
 EQW  CONST_03  N13  C5   N4   C3     0.00   0.0  0
 EQW  CONST_04  N13  C14  C2   C3     0.00   0.0  0
 EQW  CONST_05  C14  N13  C5   N4     0.00   0.0  0
 EQW  CONST_06  C14  C2   C3   N4     0.00   0.0  0
 EQW  CONST_07  N6   C5   N4   C3   180.00   0.0  0
 EQW  CONST_08  CL1  C2   C3   N4   180.00   0.0  0
 EQW  CONST_09  N6   C5   N13  C14  180.00   0.0  0
 EQW  CONST_10  N13  C14  C2   CL1  180.00   0.0  0
 EQW  CONST_11  C7   N6   C5   N4     0.00   0.0  0
 EQW  CONST_12  N13  C5   N6   C7   180.00   0.0  0
 EQW  CONST_13  H26  C14  C2   C3   180.00   0.0  0
 EQW  CONST_14  H15  C3   N4   C5   180.00   0.0  0
 EQW  CONST_15  H16  N6   C5   N4   180.00   0.0  0
 EQW  Var_01    O10  C11  C12  C7    55.70  30.0  1
 EQW  Var_02    O10  C9   C8   C7   -56.22  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 EQW  chir_01  C7  C12  C8  N6  positiv

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
 EQW  plan-1  C2   0.020
 EQW  plan-1  C3   0.020
 EQW  plan-1  N4   0.020
 EQW  plan-1  C5   0.020
 EQW  plan-1  C14  0.020
 EQW  plan-1  CL1  0.020
 EQW  plan-1  N6   0.020
 EQW  plan-1  N13  0.020
 EQW  plan-1  H15  0.020
 EQW  plan-1  H26  0.020
 EQW  plan-2  C5   0.020
 EQW  plan-2  C7   0.020
 EQW  plan-2  N6   0.020
 EQW  plan-2  H16  0.020

