# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 09:41:00 2020
#   Inital geometry file: a 35 line input string
#   Ligand name: pyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncccn1
#
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
 LGA  LGA  'pyrimidin-2-amine        '  ligand  12  7  .  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_LGA
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
 LGA  N2    N  NH2   0  -0.819  61.8332  33.5573  26.1974
 LGA  C1    C  CR6   0   0.548  62.8499  33.9561  25.4103
 LGA  N1    N  N     0  -0.454  64.0928  33.7394  25.8579
 LGA  C4    C  CR16  0  -0.018  65.0796  34.1022  25.0559
 LGA  C5    C  CR16  0  -0.385  64.8708  34.6784  23.8130
 LGA  C3    C  CR16  0  -0.018  63.5440  34.8623  23.4568
 LGA  N7    N  N     0  -0.454  62.5332  34.5120  24.2340
 LGA  H2N1  H  HNH2  0   0.396  62.0247  33.2919  27.1476
 LGA  H2N2  H  HNH2  0   0.396  60.8985  33.8538  25.9782
 LGA  H4    H  HCR6  0   0.270  66.0857  33.9265  25.4219
 LGA  H5    H  HCR6  0   0.269  65.6860  34.9685  23.1679
 LGA  H3    H  HCR6  0   0.270  63.2836  35.3123  22.5046

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
 LGA  N2  C1    single    1.346  0.020  1.346
 LGA  C1  N1    aromatic  1.339  0.020  1.339
 LGA  C1  N7    aromatic  1.339  0.020  1.339
 LGA  N1  C4    aromatic  1.322  0.020  1.322
 LGA  C4  C5    aromatic  1.386  0.020  1.386
 LGA  C5  C3    aromatic  1.386  0.020  1.386
 LGA  C3  N7    aromatic  1.322  0.020  1.322
 LGA  N2  H2N1  single    0.890  0.020  1.040
 LGA  N2  H2N2  single    0.890  0.020  1.040
 LGA  C4  H4    single    0.930  0.020  1.080
 LGA  C5  H5    single    0.930  0.020  1.080
 LGA  C3  H3    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
 LGA  H2N2  N2  H2N1  117.48  3.000
 LGA  H2N2  N2  C1    119.18  3.000
 LGA  H2N1  N2  C1    119.15  3.000
 LGA  N7    C1  N1    125.49  3.000
 LGA  N7    C1  N2    117.26  3.000
 LGA  N1    C1  N2    117.24  3.000
 LGA  C4    N1  C1    116.46  3.000
 LGA  H4    C4  C5    120.64  3.000
 LGA  H4    C4  N1    116.30  3.000
 LGA  C5    C4  N1    123.06  3.000
 LGA  H5    C5  C3    122.26  3.000
 LGA  H5    C5  C4    122.27  3.000
 LGA  C3    C5  C4    115.46  3.000
 LGA  H3    C3  N7    116.25  3.000
 LGA  H3    C3  C5    120.69  3.000
 LGA  N7    C3  C5    123.06  3.000
 LGA  C3    N7  C1    116.46  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
 LGA  CONST_01  C5    C4  N1  C1    0.00  0.0  0
 LGA  CONST_02  C5    C3  N7  C1    0.00  0.0  0
 LGA  CONST_03  C3    N7  C1  N1    0.00  0.0  0
 LGA  CONST_04  C3    C5  C4  N1    0.00  0.0  0
 LGA  CONST_05  N7    C1  N1  C4    0.00  0.0  0
 LGA  CONST_06  N7    C3  C5  C4    0.00  0.0  0
 LGA  CONST_07  C4    N1  C1  N2  180.00  0.0  0
 LGA  CONST_08  C3    N7  C1  N2  180.00  0.0  0
 LGA  CONST_09  H4    C4  N1  C1  180.00  0.0  0
 LGA  CONST_10  H3    C3  N7  C1  180.00  0.0  0
 LGA  CONST_11  H5    C5  C4  N1  180.00  0.0  0
 LGA  CONST_12  H2N1  N2  C1  N1    0.00  0.0  0
 LGA  CONST_13  H2N2  N2  C1  N1  180.00  0.0  0

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
 LGA  plan-1  N2    0.020
 LGA  plan-1  C1    0.020
 LGA  plan-1  N1    0.020
 LGA  plan-1  C4    0.020
 LGA  plan-1  C5    0.020
 LGA  plan-1  C3    0.020
 LGA  plan-1  N7    0.020
 LGA  plan-1  H4    0.020
 LGA  plan-1  H5    0.020
 LGA  plan-1  H3    0.020
 LGA  plan-2  N2    0.020
 LGA  plan-2  C1    0.020
 LGA  plan-2  H2N1  0.020
 LGA  plan-2  H2N2  0.020

