# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 18:39:38 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: 5-chloranyl-~{N}-methyl-~{N}-[[(3~{S})-oxolan-3-yl]methyl]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C[C@@H]1CCOC1)c2ncncc2Cl
#
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
 GWY  GWY  5-chloranyl-~{N}-methyl-~{N}-[[(3~{S})-oxolan-3-yl]methyl]pyrimidin-4-amine  ligand  29  15  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_GWY
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
 GWY  N1   N   N     0  -0.457   2.3219  -1.0701   0.9474
 GWY  C4   C   CH2   0  -0.151  -4.4896   0.2690  -0.3582
 GWY  C5   C   CH2   0  -0.117  -2.4015   0.8384   0.5018
 GWY  C6   C   CR6   0   0.603   1.3006  -0.6152   0.2132
 GWY  C7   C   CR16  0   0.060   3.5609  -0.8573   0.5567
 GWY  C8   C   CR16  0  -0.009   2.9601   0.2777  -1.2675
 GWY  C9   C   CR6   0  -0.178   1.6297   0.1464  -0.9356
 GWY  N2   N   N     0  -0.415   3.9498  -0.2332  -0.5406
 GWY  N    N   NT    0  -0.482   0.0516  -0.8882   0.6722
 GWY  C    C   CH3   0  -0.535  -0.0425  -1.5118   1.9833
 GWY  C1   C   CH2   0  -0.301  -1.0548  -1.2313  -0.2208
 GWY  C2   C   CR15  0  -0.337  -2.3931  -0.6597   0.2250
 GWY  O    O   O     0  -0.504  -3.7498   1.2538   0.3545
 GWY  C3   C   CH2   0  -0.486  -3.4796  -0.7624  -0.8423
 GWY  H2   H   HCH2  0   0.220  -5.0334   0.7388  -1.1815
 GWY  H3   H   HCH2  0   0.224  -2.0578   1.0841   1.5090
 GWY  H4   H   HCH2  0   0.193  -1.7565   1.3688  -0.2090
 GWY  H5   H   HCR6  0   0.263   4.3405  -1.2448   1.2040
 GWY  H6   H   HCR6  0   0.291   3.2346   0.8404  -2.1530
 GWY  H7   H   HCH3  0   0.256   0.5607  -0.9785   2.7121
 GWY  H8   H   HCH3  0   0.251  -1.0774  -1.4740   2.3126
 GWY  H9   H   HCH3  0   0.237   0.2731  -2.5580   1.9680
 GWY  H10  H   HCH2  0   0.254  -0.8378  -0.8958  -1.2296
 GWY  H11  H   HCH2  0   0.260  -1.1319  -2.3233  -0.2730
 GWY  H12  H   HCR5  0   0.257  -2.7443  -1.1852   1.1191
 GWY  H13  H   HCH2  0   0.257  -3.9113  -1.7596  -0.9280
 GWY  H14  H   HCH2  0   0.235  -3.0770  -0.4841  -1.8202
 GWY  CL   CL  CL    0  -0.095   0.4932   1.0240  -1.9002
 GWY  H1   H   HCH2  0   0.206  -5.2268  -0.1915   0.3087

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
 GWY  N2  C8   aromatic  1.330  0.020  1.330
 GWY  N2  C7   aromatic  1.321  0.020  1.321
 GWY  C8  C9   aromatic  1.377  0.020  1.377
 GWY  C7  N1   aromatic  1.316  0.020  1.316
 GWY  C9  CL   single    1.730  0.020  1.730
 GWY  C9  C6   aromatic  1.417  0.020  1.417
 GWY  N1  C6   aromatic  1.338  0.020  1.338
 GWY  C6  N    single    1.358  0.020  1.358
 GWY  N   C    single    1.455  0.020  1.455
 GWY  N   C1   single    1.463  0.020  1.463
 GWY  C1  C2   single    1.522  0.020  1.522
 GWY  C2  C3   single    1.526  0.020  1.526
 GWY  C2  C5   single    1.524  0.020  1.524
 GWY  C3  C4   single    1.523  0.020  1.523
 GWY  C5  O    single    1.419  0.020  1.419
 GWY  C4  O    single    1.423  0.020  1.423
 GWY  C4  H1   single    0.970  0.020  1.090
 GWY  C4  H2   single    0.970  0.020  1.090
 GWY  C5  H3   single    0.970  0.020  1.090
 GWY  C5  H4   single    0.970  0.020  1.090
 GWY  C7  H5   single    0.930  0.020  1.080
 GWY  C8  H6   single    0.930  0.020  1.080
 GWY  C   H7   single    0.970  0.020  1.090
 GWY  C   H8   single    0.970  0.020  1.090
 GWY  C   H9   single    0.970  0.020  1.090
 GWY  C1  H10  single    0.970  0.020  1.090
 GWY  C1  H11  single    0.970  0.020  1.090
 GWY  C2  H12  single    0.970  0.020  1.090
 GWY  C3  H13  single    0.970  0.020  1.090
 GWY  C3  H14  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
 GWY  C7   N1  C6   120.05  3.000
 GWY  H2   C4  H1   107.72  3.000
 GWY  H2   C4  C3   112.44  3.000
 GWY  H1   C4  C3   110.80  3.000
 GWY  H2   C4  O    109.79  3.000
 GWY  H1   C4  O    109.63  3.000
 GWY  C3   C4  O    106.45  3.000
 GWY  H4   C5  H3   107.69  3.000
 GWY  H4   C5  O    110.49  3.000
 GWY  H3   C5  O    109.20  3.000
 GWY  H4   C5  C2   110.77  3.000
 GWY  H3   C5  C2   112.77  3.000
 GWY  O    C5  C2   105.92  3.000
 GWY  N    C6  C9   126.54  3.000
 GWY  N    C6  N1   116.63  3.000
 GWY  C9   C6  N1   116.78  3.000
 GWY  H5   C7  N2   116.93  3.000
 GWY  H5   C7  N1   116.19  3.000
 GWY  N2   C7  N1   126.87  3.000
 GWY  H6   C8  N2   117.21  3.000
 GWY  H6   C8  C9   119.38  3.000
 GWY  N2   C8  C9   123.40  3.000
 GWY  CL   C9  C8   116.87  3.000
 GWY  CL   C9  C6   124.90  3.000
 GWY  C8   C9  C6   118.09  3.000
 GWY  C8   N2  C7   114.61  3.000
 GWY  C1   N   C    113.62  3.000
 GWY  C1   N   C6   122.44  3.000
 GWY  C    N   C6   116.75  3.000
 GWY  H9   C   H8   108.21  3.000
 GWY  H9   C   H7   108.60  3.000
 GWY  H8   C   H7   107.97  3.000
 GWY  H9   C   N    112.28  3.000
 GWY  H8   C   N    108.65  3.000
 GWY  H7   C   N    111.00  3.000
 GWY  H11  C1  H10  106.13  3.000
 GWY  H11  C1  C2   109.04  3.000
 GWY  H10  C1  C2   109.39  3.000
 GWY  H11  C1  N    108.42  3.000
 GWY  H10  C1  N    110.11  3.000
 GWY  C2   C1  N    113.47  3.000
 GWY  H12  C2  C3   108.08  3.000
 GWY  H12  C2  C1   109.93  3.000
 GWY  C3   C2  C1   113.32  3.000
 GWY  H12  C2  C5   108.77  3.000
 GWY  C3   C2  C5   100.91  3.000
 GWY  C1   C2  C5   115.30  3.000
 GWY  C5   O   C4   110.09  3.000
 GWY  H14  C3  H13  107.96  3.000
 GWY  H14  C3  C2   110.25  3.000
 GWY  H13  C3  C2   113.48  3.000
 GWY  H14  C3  C4   110.87  3.000
 GWY  H13  C3  C4   112.46  3.000
 GWY  C2   C3  C4   101.79  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
 GWY  CONST_01  C8  N2  C7  N1     0.00   0.0  0
 GWY  CONST_02  C8  C9  C6  N1     0.00   0.0  0
 GWY  CONST_03  N2  C8  C9  C6     0.00   0.0  0
 GWY  CONST_04  N2  C7  N1  C6     0.00   0.0  0
 GWY  CONST_05  C9  C8  N2  C7     0.00   0.0  0
 GWY  CONST_06  C9  C6  N1  C7     0.00   0.0  0
 GWY  CONST_07  CL  C9  C6  N1   180.00   0.0  0
 GWY  CONST_08  N   C6  N1  C7   180.00   0.0  0
 GWY  CONST_09  N   C6  C9  C8   180.00   0.0  0
 GWY  CONST_10  N2  C8  C9  CL   180.00   0.0  0
 GWY  CONST_11  H6  C8  C9  C6   180.00   0.0  0
 GWY  CONST_12  H5  C7  N1  C6   180.00   0.0  0
 GWY  CONST_13  C   N   C6  N1     0.00   0.0  0
 GWY  CONST_15  C   N   C6  C9   180.00   0.0  0
 GWY  Var_01    C2  C5  O   C4   -17.17  30.0  1
 GWY  Var_02    C3  C4  O   C5    -7.44  30.0  1
 GWY  Var_03    O   C4  C3  C2    28.56  30.0  1
 GWY  Var_04    C2  C1  N   C6  -143.01  30.0  3
 GWY  Var_05    H7  C   N   C6    49.27  30.0  3

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
 GWY  chir_01  C2  C1  C3  C5  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
 GWY  plan-1  N1  0.020
 GWY  plan-1  C6  0.020
 GWY  plan-1  C7  0.020
 GWY  plan-1  C8  0.020
 GWY  plan-1  C9  0.020
 GWY  plan-1  N2  0.020
 GWY  plan-1  N   0.020
 GWY  plan-1  H5  0.020
 GWY  plan-1  H6  0.020
 GWY  plan-1  CL  0.020
 GWY  plan-2  C6  0.020
 GWY  plan-2  N   0.020
 GWY  plan-2  C   0.020
 GWY  plan-2  C1  0.020

