# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 18:18:37 2020
#   Inital geometry file: a 41 line input string
#   Ligand name: N-methylpyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNc1ncccn1
#
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
 JH4  JH4  N-methylpyrimidin-2-amine  ligand  15  8  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_JH4
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
 JH4  C01   C  CH3   0  -0.509   2.7884   0.4121   0.0237
 JH4  N02   N  NH1   0  -0.643   1.7264  -0.5598   0.0229
 JH4  C03   C  CR6   0   0.589   0.4225  -0.2422   0.0184
 JH4  N04   N  N     0  -0.462   0.0975   1.0556   0.0287
 JH4  C05   C  CR16  0  -0.011  -1.1959   1.3393   0.0252
 JH4  C06   C  CR16  0  -0.394  -2.1828   0.3690   0.0116
 JH4  C07   C  CR16  0  -0.021  -1.7294  -0.9436   0.0017
 JH4  N08   N  N     0  -0.460  -0.4495  -1.2640   0.0049
 JH4  H011  H  HCH3  0   0.249   3.7355  -0.1203   0.0338
 JH4  H012  H  HCH3  0   0.232   2.7636   1.0482  -0.8629
 JH4  H013  H  HCH3  0   0.233   2.7500   1.0576   0.9024
 JH4  H021  H  HNH1  0   0.396   1.9577  -1.5380   0.0028
 JH4  H051  H  HCR6  0   0.266  -1.4559   2.3927   0.0337
 JH4  H061  H  HCR6  0   0.268  -3.2339   0.6140   0.0085
 JH4  H071  H  HCR6  0   0.268  -2.4330  -1.7696  -0.0094

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
 JH4  C05  C06   aromatic  1.384  0.020  1.384
 JH4  C05  N04   aromatic  1.324  0.020  1.324
 JH4  C06  C07   aromatic  1.389  0.020  1.389
 JH4  N04  C03   aromatic  1.338  0.020  1.338
 JH4  C07  N08   aromatic  1.319  0.020  1.319
 JH4  C03  N08   aromatic  1.343  0.020  1.343
 JH4  C03  N02   single    1.342  0.020  1.342
 JH4  C01  N02   single    1.440  0.020  1.440
 JH4  C01  H011  single    0.970  0.020  1.090
 JH4  C01  H012  single    0.970  0.020  1.090
 JH4  C01  H013  single    0.970  0.020  1.090
 JH4  N02  H021  single    0.860  0.020  1.020
 JH4  C05  H051  single    0.930  0.020  1.080
 JH4  C06  H061  single    0.930  0.020  1.080
 JH4  C07  H071  single    0.930  0.020  1.080

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
 JH4  H013  C01  H012  107.98  3.000
 JH4  H013  C01  H011  108.25  3.000
 JH4  H012  C01  H011  108.24  3.000
 JH4  H013  C01  N02   111.96  3.000
 JH4  H012  C01  N02   112.10  3.000
 JH4  H011  C01  N02   108.19  3.000
 JH4  H021  N02  C03   116.98  3.000
 JH4  H021  N02  C01   119.16  3.000
 JH4  C03   N02  C01   123.84  3.000
 JH4  N08   C03  N04   125.46  3.000
 JH4  N08   C03  N02   116.79  3.000
 JH4  N04   C03  N02   117.75  3.000
 JH4  C05   N04  C03   116.43  3.000
 JH4  H051  C05  C06   120.65  3.000
 JH4  H051  C05  N04   116.23  3.000
 JH4  C06   C05  N04   123.12  3.000
 JH4  H061  C06  C07   122.17  3.000
 JH4  H061  C06  C05   122.37  3.000
 JH4  C07   C06  C05   115.46  3.000
 JH4  H071  C07  N08   116.37  3.000
 JH4  H071  C07  C06   120.53  3.000
 JH4  N08   C07  C06   123.11  3.000
 JH4  C07   N08  C03   116.42  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
 JH4  CONST_01  C06   C05  N04  C03    0.00   0.0  0
 JH4  CONST_02  C06   C07  N08  C03    0.00   0.0  0
 JH4  CONST_03  C07   C06  C05  N04    0.00   0.0  0
 JH4  CONST_04  C07   N08  C03  N04    0.00   0.0  0
 JH4  CONST_05  N08   C07  C06  C05    0.00   0.0  0
 JH4  CONST_06  N08   C03  N04  C05    0.00   0.0  0
 JH4  CONST_07  C05   N04  C03  N02  180.00   0.0  0
 JH4  CONST_08  C07   N08  C03  N02  180.00   0.0  0
 JH4  CONST_09  H051  C05  N04  C03  180.00   0.0  0
 JH4  CONST_10  H071  C07  N08  C03  180.00   0.0  0
 JH4  CONST_11  H061  C06  C05  N04  180.00   0.0  0
 JH4  CONST_12  N04   C03  N02  C01    0.00   0.0  0
 JH4  CONST_13  N08   C03  N02  C01  180.00   0.0  0
 JH4  CONST_14  H021  N02  C03  N04  180.00   0.0  0
 JH4  Var_01    H011  C01  N02  C03  179.66  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
 JH4  plan-1  N02   0.020
 JH4  plan-1  C03   0.020
 JH4  plan-1  N04   0.020
 JH4  plan-1  C05   0.020
 JH4  plan-1  C06   0.020
 JH4  plan-1  C07   0.020
 JH4  plan-1  N08   0.020
 JH4  plan-1  H051  0.020
 JH4  plan-1  H061  0.020
 JH4  plan-1  H071  0.020
 JH4  plan-2  C01   0.020
 JH4  plan-2  N02   0.020
 JH4  plan-2  C03   0.020
 JH4  plan-2  H021  0.020

