# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jun 10 00:22:03 2020
#   Inital geometry file: a 63 line input string
#   Ligand name: 4-(2-methoxyethoxy)-6-methylpyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCCOc1cc(C)nc(N)n1
#
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
 ZZ2  ZZ2  4-(2-methoxyethoxy)-6-methylpyrimidin-2-amine  ligand  26  13  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ZZ2
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
 ZZ2  N2    N  NH2   0  -0.819  -2.6869   2.3480  -0.2018
 ZZ2  C3    C  CR6   0   0.534  -2.1496   1.1162  -0.1021
 ZZ2  N3    N  N     0  -0.518  -0.8206   1.0547   0.0633
 ZZ2  C4    C  CR6   0   0.578  -0.3040  -0.1457   0.1930
 ZZ2  C5    C  CR16  0  -0.480  -1.0761  -1.3124   0.1664
 ZZ2  C2    C  CR6   0   0.289  -2.4337  -1.1334  -0.0084
 ZZ2  C1    C  CH3   0  -0.719  -3.3741  -2.2954  -0.0480
 ZZ2  N1    N  N     0  -0.500  -2.9790   0.0780  -0.1465
 ZZ2  O1    O  O2    0  -0.465   1.0043  -0.2826   0.3564
 ZZ2  C6    C  CH2   0  -0.206   1.8206   0.8851   0.4125
 ZZ2  C7    C  CH2   0  -0.167   3.2506   0.4423   0.5722
 ZZ2  O2    O  O2    0  -0.483   3.6648  -0.2390  -0.5819
 ZZ2  C8    C  CH3   0  -0.395   4.9986  -0.6724  -0.5054
 ZZ2  H21N  H  HNH2  0   0.395  -2.0811   3.1327  -0.3673
 ZZ2  H22N  H  HNH2  0   0.394  -3.6421   2.4344  -0.5019
 ZZ2  H5    H  HCR6  0   0.263  -0.6323  -2.2907   0.2798
 ZZ2  H11C  H  HCH3  0   0.256  -4.0822  -2.2342   0.7795
 ZZ2  H12C  H  HCH3  0   0.254  -3.9554  -2.2828  -0.9705
 ZZ2  H13C  H  HCH3  0   0.246  -2.8493  -3.2461   0.0191
 ZZ2  H61C  H  HCH2  0   0.237   1.6999   1.4856  -0.4925
 ZZ2  H62C  H  HCH2  0   0.239   1.5423   1.5082   1.2658
 ZZ2  H71C  H  HCH2  0   0.214   3.8590   1.3411   0.7465
 ZZ2  H72C  H  HCH2  0   0.210   3.3527  -0.1882   1.4673
 ZZ2  H81C  H  HCH3  0   0.205   5.6958   0.1623  -0.3662
 ZZ2  H82C  H  HCH3  0   0.205   5.1562  -1.3816   0.3160
 ZZ2  H83C  H  HCH3  0   0.234   5.2432  -1.1734  -1.4414

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
 ZZ2  N2  C3    single    1.348  0.020  1.348
 ZZ2  C3  N3    aromatic  1.341  0.020  1.341
 ZZ2  C3  N1    aromatic  1.330  0.020  1.330
 ZZ2  N3  C4    aromatic  1.313  0.020  1.313
 ZZ2  C4  C5    aromatic  1.399  0.020  1.399
 ZZ2  C4  O1    single    1.326  0.020  1.326
 ZZ2  C5  C2    aromatic  1.380  0.020  1.380
 ZZ2  C2  C1    single    1.495  0.020  1.495
 ZZ2  C2  N1    aromatic  1.336  0.020  1.336
 ZZ2  O1  C6    single    1.426  0.020  1.426
 ZZ2  C6  C7    single    1.506  0.020  1.506
 ZZ2  C7  O2    single    1.403  0.020  1.403
 ZZ2  O2  C8    single    1.405  0.020  1.405
 ZZ2  N2  H21N  single    0.890  0.020  1.040
 ZZ2  N2  H22N  single    0.890  0.020  1.040
 ZZ2  C5  H5    single    0.930  0.020  1.080
 ZZ2  C1  H11C  single    0.970  0.020  1.090
 ZZ2  C1  H12C  single    0.970  0.020  1.090
 ZZ2  C1  H13C  single    0.970  0.020  1.090
 ZZ2  C6  H61C  single    0.970  0.020  1.090
 ZZ2  C6  H62C  single    0.970  0.020  1.090
 ZZ2  C7  H71C  single    0.970  0.020  1.090
 ZZ2  C7  H72C  single    0.970  0.020  1.090
 ZZ2  C8  H81C  single    0.970  0.020  1.090
 ZZ2  C8  H82C  single    0.970  0.020  1.090
 ZZ2  C8  H83C  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
 ZZ2  H22N  N2  H21N  117.17  3.000
 ZZ2  H22N  N2  C3    118.66  3.000
 ZZ2  H21N  N2  C3    119.05  3.000
 ZZ2  N1    C3  N3    125.92  3.000
 ZZ2  N1    C3  N2    117.55  3.000
 ZZ2  N3    C3  N2    116.51  3.000
 ZZ2  C4    N3  C3    116.37  3.000
 ZZ2  O1    C4  C5    117.44  3.000
 ZZ2  O1    C4  N3    119.66  3.000
 ZZ2  C5    C4  N3    122.90  3.000
 ZZ2  H5    C5  C2    122.33  3.000
 ZZ2  H5    C5  C4    121.76  3.000
 ZZ2  C2    C5  C4    115.91  3.000
 ZZ2  N1    C2  C1    116.44  3.000
 ZZ2  N1    C2  C5    122.16  3.000
 ZZ2  C1    C2  C5    121.40  3.000
 ZZ2  H13C  C1  H12C  108.62  3.000
 ZZ2  H13C  C1  H11C  108.38  3.000
 ZZ2  H12C  C1  H11C  107.17  3.000
 ZZ2  H13C  C1  C2    111.96  3.000
 ZZ2  H12C  C1  C2    110.41  3.000
 ZZ2  H11C  C1  C2    110.15  3.000
 ZZ2  C2    N1  C3    116.75  3.000
 ZZ2  C6    O1  C4    119.03  3.000
 ZZ2  H62C  C6  H61C  107.78  3.000
 ZZ2  H62C  C6  C7    109.07  3.000
 ZZ2  H61C  C6  C7    110.76  3.000
 ZZ2  H62C  C6  O1    110.61  3.000
 ZZ2  H61C  C6  O1    110.74  3.000
 ZZ2  C7    C6  O1    107.88  3.000
 ZZ2  H72C  C7  H71C  106.76  3.000
 ZZ2  H72C  C7  O2    111.33  3.000
 ZZ2  H71C  C7  O2    111.36  3.000
 ZZ2  H72C  C7  C6    110.07  3.000
 ZZ2  H71C  C7  C6    107.58  3.000
 ZZ2  O2    C7  C6    109.63  3.000
 ZZ2  C8    O2  C7    112.67  3.000
 ZZ2  H83C  C8  H82C  108.30  3.000
 ZZ2  H83C  C8  H81C  108.45  3.000
 ZZ2  H82C  C8  H81C  107.81  3.000
 ZZ2  H83C  C8  O2    107.96  3.000
 ZZ2  H82C  C8  O2    112.13  3.000
 ZZ2  H81C  C8  O2    112.08  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
 ZZ2  CONST_01  C5    C4  N3  C3     0.00   0.0  0
 ZZ2  CONST_02  C5    C2  N1  C3     0.00   0.0  0
 ZZ2  CONST_03  C2    N1  C3  N3     0.00   0.0  0
 ZZ2  CONST_04  C2    C5  C4  N3     0.00   0.0  0
 ZZ2  CONST_05  N1    C3  N3  C4     0.00   0.0  0
 ZZ2  CONST_06  N1    C2  C5  C4     0.00   0.0  0
 ZZ2  CONST_07  C4    N3  C3  N2   180.00   0.0  0
 ZZ2  CONST_08  C2    N1  C3  N2   180.00   0.0  0
 ZZ2  CONST_09  O1    C4  N3  C3   180.00   0.0  0
 ZZ2  CONST_10  C1    C2  N1  C3   180.00   0.0  0
 ZZ2  CONST_11  C1    C2  C5  C4   180.00   0.0  0
 ZZ2  CONST_12  O1    C4  C5  C2   180.00   0.0  0
 ZZ2  CONST_13  H5    C5  C4  N3   180.00   0.0  0
 ZZ2  CONST_14  H21N  N2  C3  N3     0.00   0.0  0
 ZZ2  CONST_15  H22N  N2  C3  N3   180.00   0.0  0
 ZZ2  Var_01    H11C  C1  C2  C5   117.50  30.0  2
 ZZ2  Var_02    C7    C6  O1  C4  -178.83  30.0  3
 ZZ2  Var_03    O2    C7  C6  O1    66.02  30.0  3
 ZZ2  Var_04    H81C  C8  O2  C7   -59.70  30.0  3

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
 ZZ2  plan-1  N2    0.020
 ZZ2  plan-1  C3    0.020
 ZZ2  plan-1  N3    0.020
 ZZ2  plan-1  C4    0.020
 ZZ2  plan-1  C5    0.020
 ZZ2  plan-1  C2    0.020
 ZZ2  plan-1  C1    0.020
 ZZ2  plan-1  N1    0.020
 ZZ2  plan-1  O1    0.020
 ZZ2  plan-1  H5    0.020
 ZZ2  plan-2  N2    0.020
 ZZ2  plan-2  C3    0.020
 ZZ2  plan-2  H21N  0.020
 ZZ2  plan-2  H22N  0.020

