# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 23:55:47 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: 5-chloro-N-methyl-N-{[(3R)-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
 K07  K07  5-chloro-N-methyl-N-{[(3R)-oxolan-3-yl]methyl}pyrimidin-4-amine  ligand  29  15  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_K07
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
 K07  N1   N   N     0  -0.457   1.3863   1.3529  -0.8234
 K07  C4   C   CH2   0  -0.151  -4.3383   0.2017  -0.8474
 K07  C5   C   CH2   0  -0.121  -2.1482  -0.5484  -0.6194
 K07  C6   C   CR6   0   0.619   1.1591   0.5249   0.2048
 K07  C7   C   CR16  0   0.061   2.4952   1.2347  -1.5203
 K07  C8   C   CR16  0  -0.009   3.2405  -0.5199  -0.3571
 K07  N    N   NT    0  -0.481   0.0581   0.7396   0.9545
 K07  C    C   CH3   0  -0.543  -0.0541   0.3426   2.3461
 K07  O    O   O2    0  -0.503  -3.4513  -0.8929  -1.0523
 K07  C1   C   CH2   0  -0.326  -1.0668   1.5031   0.4334
 K07  C2   C   CH1   0  -0.309  -2.3152   0.6439   0.3148
 K07  C3   C   CH2   0  -0.491  -3.4895   1.3635  -0.3425
 K07  C9   C   CR6   0  -0.201   2.0976  -0.5162   0.4110
 K07  N2   N   N     0  -0.422   3.4742   0.3676  -1.3203
 K07  CL   CL  CL    0  -0.100   1.8279  -1.8661   1.4587
 K07  H2   H   HCH2  0   0.208  -5.0979  -0.0789  -0.1100
 K07  H3   H   HCH2  0   0.225  -1.6910  -1.4141  -0.1346
 K07  H4   H   HCH2  0   0.193  -1.5140  -0.2718  -1.4745
 K07  H5   H   HCR6  0   0.262   2.6209   1.9336  -2.3407
 K07  H6   H   HCR6  0   0.289   3.9854  -1.2929  -0.2019
 K07  H7   H   HCH3  0   0.260  -0.6603   1.0904   2.8565
 K07  H8   H   HCH3  0   0.246  -0.5286  -0.6285   2.4890
 K07  H9   H   HCH3  0   0.260   0.9175   0.3329   2.8336
 K07  H10  H   HCH2  0   0.254  -1.2574   2.3557   1.0913
 K07  H11  H   HCH2  0   0.269  -0.8020   1.9059  -0.5419
 K07  H12  H   HCH1  0   0.256  -2.6241   0.2895   1.3043
 K07  H13  H   HCH2  0   0.236  -3.1349   1.9773  -1.1752
 K07  H14  H   HCH2  0   0.257  -4.0375   2.0111   0.3415
 K07  H1   H   HCH2  0   0.219  -4.8545   0.4416  -1.7807

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
 K07  N2  C7   aromatic  1.323  0.020  1.323
 K07  N2  C8   aromatic  1.330  0.020  1.330
 K07  C7  N1   aromatic  1.315  0.020  1.315
 K07  C8  C9   aromatic  1.377  0.020  1.377
 K07  N1  C6   aromatic  1.340  0.020  1.340
 K07  C9  C6   aromatic  1.417  0.020  1.417
 K07  C9  CL   single    1.730  0.020  1.730
 K07  C6  N    single    1.349  0.020  1.349
 K07  N   C1   single    1.456  0.020  1.456
 K07  N   C    single    1.451  0.020  1.451
 K07  C1  C2   single    1.520  0.020  1.520
 K07  C2  C3   single    1.526  0.020  1.526
 K07  C2  C5   single    1.524  0.020  1.524
 K07  C3  C4   single    1.525  0.020  1.525
 K07  C5  O    single    1.416  0.020  1.416
 K07  C4  O    single    1.424  0.020  1.424
 K07  C4  H1   single    0.970  0.020  1.090
 K07  C4  H2   single    0.970  0.020  1.090
 K07  C5  H3   single    0.970  0.020  1.090
 K07  C5  H4   single    0.970  0.020  1.090
 K07  C7  H5   single    0.930  0.020  1.080
 K07  C8  H6   single    0.930  0.020  1.080
 K07  C   H7   single    0.970  0.020  1.090
 K07  C   H8   single    0.970  0.020  1.090
 K07  C   H9   single    0.970  0.020  1.090
 K07  C1  H10  single    0.970  0.020  1.090
 K07  C1  H11  single    0.970  0.020  1.090
 K07  C2  H12  single    0.970  0.020  1.090
 K07  C3  H13  single    0.970  0.020  1.090
 K07  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
 K07  C7   N1  C6   119.62  3.000
 K07  H2   C4  H1   107.68  3.000
 K07  H2   C4  C3   111.00  3.000
 K07  H1   C4  C3   112.23  3.000
 K07  H2   C4  O    109.39  3.000
 K07  H1   C4  O    109.88  3.000
 K07  C3   C4  O    106.65  3.000
 K07  H4   C5  H3   107.64  3.000
 K07  H4   C5  C2   110.06  3.000
 K07  H3   C5  C2   113.19  3.000
 K07  H4   C5  O    110.74  3.000
 K07  H3   C5  O    109.16  3.000
 K07  C2   C5  O    106.08  3.000
 K07  C9   C6  N    125.22  3.000
 K07  N    C6  N1   117.81  3.000
 K07  C9   C6  N1   116.97  3.000
 K07  H5   C7  N2   116.79  3.000
 K07  H5   C7  N1   116.13  3.000
 K07  N2   C7  N1   127.07  3.000
 K07  H6   C8  N2   117.29  3.000
 K07  H6   C8  C9   119.47  3.000
 K07  N2   C8  C9   123.22  3.000
 K07  C1   N   C    115.27  3.000
 K07  C    N   C6   123.53  3.000
 K07  C1   N   C6   121.00  3.000
 K07  H9   C   H8   108.80  3.000
 K07  H9   C   H7   107.06  3.000
 K07  H8   C   H7   107.93  3.000
 K07  H9   C   N    111.30  3.000
 K07  H8   C   N    113.76  3.000
 K07  H7   C   N    107.72  3.000
 K07  C5   O   C4   110.02  3.000
 K07  H11  C1  H10  107.04  3.000
 K07  H11  C1  C2   109.83  3.000
 K07  H10  C1  C2   110.15  3.000
 K07  H11  C1  N    109.09  3.000
 K07  H10  C1  N    109.16  3.000
 K07  C2   C1  N    111.47  3.000
 K07  H12  C2  C3   108.94  3.000
 K07  H12  C2  C1   110.12  3.000
 K07  C3   C2  C1   113.52  3.000
 K07  H12  C2  C5   109.36  3.000
 K07  C3   C2  C5   100.91  3.000
 K07  C1   C2  C5   113.58  3.000
 K07  H14  C3  H13  107.90  3.000
 K07  H14  C3  C2   113.38  3.000
 K07  H13  C3  C2   110.06  3.000
 K07  H14  C3  C4   112.38  3.000
 K07  H13  C3  C4   110.86  3.000
 K07  C2   C3  C4   102.23  3.000
 K07  CL   C9  C8   117.72  3.000
 K07  CL   C9  C6   123.93  3.000
 K07  C8   C9  C6   118.07  3.000
 K07  C8   N2  C7   114.63  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
 K07  CONST_01  C8  N2  C7  N1    0.00   0.0  0
 K07  CONST_02  C8  C9  C6  N1    0.00   0.0  0
 K07  CONST_03  N2  C7  N1  C6    0.00   0.0  0
 K07  CONST_04  N2  C8  C9  C6    0.00   0.0  0
 K07  CONST_05  C9  C8  N2  C7    0.00   0.0  0
 K07  CONST_06  C9  C6  N1  C7    0.00   0.0  0
 K07  CONST_07  CL  C9  C6  N1  180.00   0.0  0
 K07  CONST_08  N   C6  N1  C7  180.00   0.0  0
 K07  CONST_09  N   C6  C9  C8  180.00   0.0  0
 K07  CONST_10  CL  C9  C8  N2  180.00   0.0  0
 K07  CONST_11  H5  C7  N1  C6  180.00   0.0  0
 K07  CONST_12  H6  C8  C9  C6  180.00   0.0  0
 K07  Var_01    C2  C5  O   C4   19.14  30.0  1
 K07  Var_02    C3  C4  O   C5    4.65  30.0  1
 K07  Var_03    C2  C3  C4  O   -26.13  30.0  1
 K07  Var_04    C2  C1  N   C6  115.90  30.0  3
 K07  Var_05    H7  C   N   C6  145.62  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
 K07  chir_01  C2  C1  C3  C5  negativ

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
 K07  plan-1  N1  0.020
 K07  plan-1  C6  0.020
 K07  plan-1  C7  0.020
 K07  plan-1  C8  0.020
 K07  plan-1  N   0.020
 K07  plan-1  C9  0.020
 K07  plan-1  N2  0.020
 K07  plan-1  CL  0.020
 K07  plan-1  H5  0.020
 K07  plan-1  H6  0.020
 K07  plan-2  C6  0.020
 K07  plan-2  N   0.020
 K07  plan-2  C   0.020
 K07  plan-2  C1  0.020

