# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 04:24:46 2020
#   Inital geometry file: a 40 line input string
#   Ligand name: 1,3-diazinan-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1NCCCN1
#
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
 L60  L60  '1,3-diazinan-2-one       '  ligand  15  7  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_L60
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
 L60  O   O  O     0  -0.561  -2.2795   0.0289   0.0068
 L60  C   C  C     0   0.637  -1.0481   0.0186   0.0260
 L60  N1  N  NH1   0  -0.652  -0.3226   1.1648   0.0099
 L60  C3  C  CH2   0  -0.265   1.1148   1.2389   0.1690
 L60  C2  C  CH2   0  -0.484   1.7523  -0.0082  -0.4117
 L60  C1  C  CH2   0  -0.266   1.0930  -1.2353   0.1870
 L60  N   N  NH1   0  -0.652  -0.3422  -1.1401   0.0203
 L60  H1  H  HNH1  0   0.393  -0.8544   2.0153   0.0914
 L60  H2  H  HCH2  0   0.253   1.4747   2.1295  -0.3463
 L60  H3  H  HCH2  0   0.227   1.3909   1.3440   1.2240
 L60  H4  H  HCH2  0   0.243   1.6351  -0.0155  -1.4979
 L60  H5  H  HCH2  0   0.254   2.8200  -0.0155  -0.1953
 L60  H6  H  HCH2  0   0.253   1.4399  -2.1401  -0.3120
 L60  H7  H  HCH2  0   0.227   1.3635  -1.3267   1.2448
 L60  H8  H  HNH1  0   0.393  -0.8882  -1.9809   0.1068

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
 L60  C3  C2  single  1.516  0.020  1.516
 L60  C3  N1  single  1.448  0.020  1.448
 L60  C2  C1  single  1.516  0.020  1.516
 L60  C1  N   single  1.448  0.020  1.448
 L60  N1  C   single  1.357  0.020  1.357
 L60  N   C   single  1.357  0.020  1.357
 L60  C   O   double  1.232  0.020  1.232
 L60  N1  H1  single  0.860  0.020  1.020
 L60  C3  H2  single  0.970  0.020  1.090
 L60  C3  H3  single  0.970  0.020  1.090
 L60  C2  H4  single  0.970  0.020  1.090
 L60  C2  H5  single  0.970  0.020  1.090
 L60  C1  H6  single  0.970  0.020  1.090
 L60  C1  H7  single  0.970  0.020  1.090
 L60  N   H8  single  0.860  0.020  1.020

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
 L60  N   C   N1  116.31  3.000
 L60  N   C   O   121.82  3.000
 L60  N1  C   O   121.83  3.000
 L60  H1  N1  C3  118.19  3.000
 L60  H1  N1  C   115.50  3.000
 L60  C3  N1  C   124.94  3.000
 L60  H3  C3  H2  107.07  3.000
 L60  H3  C3  C2  109.98  3.000
 L60  H2  C3  C2  110.62  3.000
 L60  H3  C3  N1  111.15  3.000
 L60  H2  C3  N1  108.52  3.000
 L60  C2  C3  N1  109.46  3.000
 L60  H5  C2  H4  107.61  3.000
 L60  H5  C2  C1  110.02  3.000
 L60  H4  C2  C1  109.91  3.000
 L60  H5  C2  C3  109.97  3.000
 L60  H4  C2  C3  109.95  3.000
 L60  C1  C2  C3  109.37  3.000
 L60  H7  C1  H6  107.10  3.000
 L60  H7  C1  N   111.19  3.000
 L60  H6  C1  N   108.50  3.000
 L60  H7  C1  C2  109.96  3.000
 L60  H6  C1  C2  110.65  3.000
 L60  N   C1  C2  109.41  3.000
 L60  H8  N   C1  118.23  3.000
 L60  H8  N   C   115.53  3.000
 L60  C1  N   C   124.84  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
 L60  CONST_01  C1  N   C   N1    0.00   0.0  0
 L60  CONST_02  N   C   N1  C3    0.00   0.0  0
 L60  CONST_03  C3  N1  C   O   180.00   0.0  0
 L60  CONST_04  C1  N   C   O   180.00   0.0  0
 L60  CONST_05  H8  N   C   N1  180.00   0.0  0
 L60  CONST_06  H1  N1  C   N   180.00   0.0  0
 L60  Var_01    C2  C3  N1  C    31.87  30.0  1
 L60  Var_02    C2  C1  N   C   -32.46  30.0  1
 L60  Var_03    C1  C2  C3  N1  -52.61  30.0  1
 L60  Var_04    N   C1  C2  C3   52.88  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
 L60  plan-1  O   0.020
 L60  plan-1  C   0.020
 L60  plan-1  N1  0.020
 L60  plan-1  C3  0.020
 L60  plan-1  C1  0.020
 L60  plan-1  N   0.020
 L60  plan-1  H1  0.020
 L60  plan-1  H8  0.020

