# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 22:13:20 2020
#   Inital geometry file: a 47 line input string
#   Ligand name: 2,5-dimethylpyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(C)c(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
 PYD  PYD  2,5-dimethylpyrimidin-4-amine  ligand  18  9  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PYD
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
 PYD  N1'   N  N     0  -0.451   1.2627   0.0226   1.1601
 PYD  C2'   C  CR6   0   0.347  -0.0169   0.0006   1.4954
 PYD  CM2   C  CH3   0  -0.728  -0.3595   0.0032   2.9533
 PYD  N3'   N  N     0  -0.471  -1.0388  -0.0093   0.6463
 PYD  C4'   C  CR6   0   0.463  -0.7701   0.0069  -0.6589
 PYD  N4'   N  NH2   0  -0.833  -1.8101   0.0097  -1.5059
 PYD  C5'   C  CR6   0  -0.052   0.5636   0.0321  -1.1343
 PYD  C6'   C  CR16  0  -0.090   1.5222   0.0383  -0.1535
 PYD  C7'   C  CH3   0  -0.746   0.8873   0.0498  -2.5935
 PYD  HM21  H  HCH3  0   0.252  -0.7952   0.9628   3.2380
 PYD  HM22  H  HCH3  0   0.247  -1.0988  -0.7641   3.1821
 PYD  HM23  H  HCH3  0   0.243   0.5252  -0.1626   3.5633
 PYD  HN41  H  HNH2  0   0.397  -2.7462  -0.0649  -1.1474
 PYD  HN42  H  HNH2  0   0.413  -1.6854  -0.0513  -2.5000
 PYD  HC6'  H  HCR6  0   0.254   2.5715   0.0564  -0.4342
 PYD  HC71  H  HCH3  0   0.248   0.4993  -0.8332  -3.1078
 PYD  HC72  H  HCH3  0   0.248   0.4643   0.9249  -3.0930
 PYD  HC73  H  HCH3  0   0.258   1.9651   0.0721  -2.7490

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
 PYD  N1'  C2'   aromatic  1.323  0.020  1.323
 PYD  N1'  C6'   aromatic  1.339  0.020  1.339
 PYD  C2'  CM2   single    1.498  0.020  1.498
 PYD  C2'  N3'   aromatic  1.329  0.020  1.329
 PYD  CM2  HM21  single    0.970  0.020  1.090
 PYD  CM2  HM22  single    0.970  0.020  1.090
 PYD  CM2  HM23  single    0.970  0.020  1.090
 PYD  N3'  C4'   aromatic  1.333  0.020  1.333
 PYD  C4'  N4'   single    1.341  0.020  1.341
 PYD  C4'  C5'   aromatic  1.416  0.020  1.416
 PYD  N4'  HN41  single    0.860  0.020  1.020
 PYD  N4'  HN42  single    0.860  0.020  1.020
 PYD  C5'  C6'   aromatic  1.371  0.020  1.371
 PYD  C5'  C7'   single    1.495  0.020  1.495
 PYD  C6'  HC6'  single    0.930  0.020  1.080
 PYD  C7'  HC71  single    0.970  0.020  1.090
 PYD  C7'  HC72  single    0.970  0.020  1.090
 PYD  C7'  HC73  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
 PYD  C6'   N1'  C2'   115.86  3.000
 PYD  N3'   C2'  CM2   116.50  3.000
 PYD  N3'   C2'  N1'   125.60  3.000
 PYD  CM2   C2'  N1'   117.90  3.000
 PYD  HM23  CM2  HM22  109.08  3.000
 PYD  HM23  CM2  HM21  108.21  3.000
 PYD  HM22  CM2  HM21  107.06  3.000
 PYD  HM23  CM2  C2'   111.08  3.000
 PYD  HM22  CM2  C2'   111.00  3.000
 PYD  HM21  CM2  C2'   110.28  3.000
 PYD  C4'   N3'  C2'   118.08  3.000
 PYD  C5'   C4'  N4'   121.21  3.000
 PYD  C5'   C4'  N3'   121.26  3.000
 PYD  N4'   C4'  N3'   117.53  3.000
 PYD  HN42  N4'  HN41  117.67  3.000
 PYD  HN42  N4'  C4'   121.94  3.000
 PYD  HN41  N4'  C4'   119.78  3.000
 PYD  C7'   C5'  C6'   123.14  3.000
 PYD  C7'   C5'  C4'   122.13  3.000
 PYD  C6'   C5'  C4'   114.73  3.000
 PYD  HC6'  C6'  C5'   119.37  3.000
 PYD  HC6'  C6'  N1'   116.15  3.000
 PYD  C5'   C6'  N1'   124.47  3.000
 PYD  HC73  C7'  HC72  107.54  3.000
 PYD  HC73  C7'  HC71  107.49  3.000
 PYD  HC72  C7'  HC71  107.12  3.000
 PYD  HC73  C7'  C5'   110.73  3.000
 PYD  HC72  C7'  C5'   111.83  3.000
 PYD  HC71  C7'  C5'   111.89  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
 PYD  CONST_01  C4'   N3'  C2'  N1'    0.00   0.0  0
 PYD  CONST_02  C4'   C5'  C6'  N1'    0.00   0.0  0
 PYD  CONST_03  C5'   C6'  N1'  C2'    0.00   0.0  0
 PYD  CONST_04  C5'   C4'  N3'  C2'    0.00   0.0  0
 PYD  CONST_05  C6'   N1'  C2'  N3'    0.00   0.0  0
 PYD  CONST_06  C6'   C5'  C4'  N3'    0.00   0.0  0
 PYD  CONST_07  C7'   C5'  C6'  N1'  180.00   0.0  0
 PYD  CONST_08  N4'   C4'  N3'  C2'  180.00   0.0  0
 PYD  CONST_09  C6'   N1'  C2'  CM2  180.00   0.0  0
 PYD  CONST_10  C4'   N3'  C2'  CM2  180.00   0.0  0
 PYD  CONST_11  C7'   C5'  C4'  N3'  180.00   0.0  0
 PYD  CONST_12  C6'   C5'  C4'  N4'  180.00   0.0  0
 PYD  CONST_13  HC6'  C6'  N1'  C2'  180.00   0.0  0
 PYD  CONST_14  HN41  N4'  C4'  N3'    0.00   0.0  0
 PYD  CONST_15  HN42  N4'  C4'  N3'  180.00   0.0  0
 PYD  Var_01    HM21  CM2  C2'  N1'  109.40  30.0  2
 PYD  Var_02    HC71  C7'  C5'  C4'  -60.32  30.0  2

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
 PYD  plan-1  N1'   0.020
 PYD  plan-1  C2'   0.020
 PYD  plan-1  CM2   0.020
 PYD  plan-1  N3'   0.020
 PYD  plan-1  C4'   0.020
 PYD  plan-1  N4'   0.020
 PYD  plan-1  C5'   0.020
 PYD  plan-1  C6'   0.020
 PYD  plan-1  C7'   0.020
 PYD  plan-1  HC6'  0.020
 PYD  plan-2  C4'   0.020
 PYD  plan-2  N4'   0.020
 PYD  plan-2  HN41  0.020
 PYD  plan-2  HN42  0.020

