# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 08:00:09 2021
#   Inital geometry file: a 43 line input string
#   Ligand name: 1,4,5,6-tetrahydropyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NCCCN1
#
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
 W3J  W3J  1,4,5,6-tetrahydropyrimidin-2-amine  ligand  16  7  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_W3J
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
 W3J  N1  N  NH1   0  -0.674  6.6830  22.6354  18.0648
 W3J  N   N  NH2   0  -0.857  4.9708  21.1794  17.6079
 W3J  C   C  C     0   0.617  5.6099  22.3374  17.2816
 W3J  N2  N  N     0  -0.525  5.1829  23.0399  16.2905
 W3J  C3  C  CH2   0  -0.302  5.9020  24.2558  15.9849
 W3J  C2  C  CH2   0  -0.492  7.3735  24.2161  16.3805
 W3J  C1  C  CH2   0  -0.250  7.4820  23.8180  17.8412
 W3J  H1  H  HNH1  0   0.387  6.9266  22.0271  18.8265
 W3J  H2  H  HNH2  0   0.383  4.1532  20.9146  17.0913
 W3J  H3  H  HNH2  0   0.389  5.2476  20.6081  18.3842
 W3J  H4  H  HCH2  0   0.210  5.8201  24.4511  14.9112
 W3J  H5  H  HCH2  0   0.194  5.4313  25.1209  16.4741
 W3J  H6  H  HCH2  0   0.226  7.9047  23.4879  15.7607
 W3J  H7  H  HCH2  0   0.234  7.8460  25.1864  16.2200
 W3J  H8  H  HCH2  0   0.242  8.5158  23.5990  18.1122
 W3J  H9  H  HCH2  0   0.217  7.1501  24.6471  18.4769

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
 W3J  C3  N2  single  1.445  0.020  1.445
 W3J  C3  C2  single  1.524  0.020  1.524
 W3J  N2  C   double  1.288  0.020  1.288
 W3J  C2  C1  single  1.518  0.020  1.518
 W3J  C   N   single  1.362  0.020  1.362
 W3J  C   N1  single  1.362  0.020  1.362
 W3J  C1  N1  single  1.445  0.020  1.445
 W3J  N1  H1  single  0.860  0.020  1.020
 W3J  N   H2  single  0.860  0.020  1.020
 W3J  N   H3  single  0.860  0.020  1.020
 W3J  C3  H4  single  0.970  0.020  1.090
 W3J  C3  H5  single  0.970  0.020  1.090
 W3J  C2  H6  single  0.970  0.020  1.090
 W3J  C2  H7  single  0.970  0.020  1.090
 W3J  C1  H8  single  0.970  0.020  1.090
 W3J  C1  H9  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
 W3J  H1  N1  C1  118.61  3.000
 W3J  H1  N1  C   119.64  3.000
 W3J  C1  N1  C   121.74  3.000
 W3J  H3  N   H2  118.26  3.000
 W3J  H3  N   C   122.70  3.000
 W3J  H2  N   C   118.92  3.000
 W3J  N2  C   N   119.51  3.000
 W3J  N   C   N1  114.71  3.000
 W3J  N2  C   N1  125.78  3.000
 W3J  C3  N2  C   117.18  3.000
 W3J  H5  C3  H4  105.31  3.000
 W3J  H5  C3  C2  108.56  3.000
 W3J  H4  C3  C2  109.36  3.000
 W3J  H5  C3  N2  110.78  3.000
 W3J  H4  C3  N2  108.68  3.000
 W3J  C2  C3  N2  113.80  3.000
 W3J  H7  C2  H6  107.36  3.000
 W3J  H7  C2  C1  110.11  3.000
 W3J  H6  C2  C1  109.63  3.000
 W3J  H7  C2  C3  110.90  3.000
 W3J  H6  C2  C3  109.82  3.000
 W3J  C1  C2  C3  109.00  3.000
 W3J  H9  C1  H8  107.14  3.000
 W3J  H9  C1  C2  109.75  3.000
 W3J  H8  C1  C2  111.06  3.000
 W3J  H9  C1  N1  111.22  3.000
 W3J  H8  C1  N1  108.74  3.000
 W3J  C2  C1  N1  108.91  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
 W3J  CONST_01  C3  N2  C   N1    0.00   0.0  0
 W3J  CONST_02  C1  N1  C   N2    0.00   0.0  0
 W3J  CONST_03  C3  N2  C   N   180.00   0.0  0
 W3J  CONST_04  C1  N1  C   N   180.00   0.0  0
 W3J  CONST_05  H1  N1  C   N2  180.00   0.0  0
 W3J  CONST_06  H2  N   C   N1  180.00   0.0  0
 W3J  CONST_07  H3  N   C   N1    0.00   0.0  0
 W3J  Var_01    C3  C2  C1  N1   49.75  30.0  1
 W3J  Var_02    C2  C3  N2  C    28.04  30.0  1
 W3J  Var_03    C2  C1  N1  C   -26.01  30.0  1
 W3J  Var_04    C1  C2  C3  N2  -53.06  30.0  1

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
 W3J  plan-1  N1  0.020
 W3J  plan-1  N   0.020
 W3J  plan-1  C   0.020
 W3J  plan-1  N2  0.020
 W3J  plan-1  C3  0.020
 W3J  plan-1  C1  0.020
 W3J  plan-1  H1  0.020
 W3J  plan-1  H2  0.020
 W3J  plan-1  H3  0.020

