# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 04:10:50 2020
#   Inital geometry file: a 43 line input string
#   Ligand name: pyrimidine-2,4,5,6(1H,3H)-tetrone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1NC(=O)C(=O)C(=O)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
 LXN  LXN  pyrimidine-2,4,5,6(1H,3H)-tetrone  ligand  12  10  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LXN
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
 LXN  OAB  O  O     0  -0.372   1.0476  -2.3574   0.0517
 LXN  CAH  C  CR6   0   0.521   0.4716  -1.3037   0.0308
 LXN  CAJ  C  CR6   0   0.196   1.2397   0.0120   0.0212
 LXN  OAD  O  O     0  -0.272   2.4316   0.0193   0.0265
 LXN  CAI  C  CR6   0   0.521   0.4556   1.3182   0.0058
 LXN  OAC  O  O     0  -0.372   1.0186   2.3791   0.0055
 LXN  NAF  N  NR16  0  -0.715  -0.8990   1.1723  -0.0084
 LXN  CAG  C  CR6   0   0.725  -1.6194  -0.0058  -0.0077
 LXN  OAA  O  O     0  -0.416  -2.8217  -0.0133  -0.0229
 LXN  NAE  N  NR16  0  -0.715  -0.8847  -1.1748   0.0135
 LXN  HAE  H  HNR6  0   0.450  -1.4329  -2.0284   0.0166
 LXN  HAF  H  HNR6  0   0.450  -1.4577   2.0189  -0.0201

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
 LXN  OAB  CAH  double  1.201  0.020  1.201
 LXN  CAH  CAJ  single  1.524  0.020  1.524
 LXN  CAH  NAE  single  1.363  0.020  1.363
 LXN  CAJ  OAD  double  1.192  0.020  1.192
 LXN  CAJ  CAI  single  1.524  0.020  1.524
 LXN  CAI  OAC  double  1.201  0.020  1.201
 LXN  CAI  NAF  single  1.363  0.020  1.363
 LXN  NAF  CAG  single  1.381  0.020  1.381
 LXN  CAG  OAA  double  1.202  0.020  1.202
 LXN  CAG  NAE  single  1.381  0.020  1.381
 LXN  NAE  HAE  single  0.860  0.020  1.020
 LXN  NAF  HAF  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
 LXN  NAE  CAH  CAJ  114.84  3.000
 LXN  NAE  CAH  OAB  124.10  3.000
 LXN  CAJ  CAH  OAB  121.07  3.000
 LXN  CAI  CAJ  OAD  120.63  3.000
 LXN  CAI  CAJ  CAH  118.75  3.000
 LXN  OAD  CAJ  CAH  120.62  3.000
 LXN  NAF  CAI  OAC  124.10  3.000
 LXN  NAF  CAI  CAJ  114.83  3.000
 LXN  OAC  CAI  CAJ  121.07  3.000
 LXN  HAF  NAF  CAG  115.13  3.000
 LXN  HAF  NAF  CAI  117.28  3.000
 LXN  CAG  NAF  CAI  127.59  3.000
 LXN  NAE  CAG  OAA  121.80  3.000
 LXN  NAE  CAG  NAF  116.41  3.000
 LXN  OAA  CAG  NAF  121.80  3.000
 LXN  HAE  NAE  CAG  115.15  3.000
 LXN  HAE  NAE  CAH  117.27  3.000
 LXN  CAG  NAE  CAH  127.58  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
 LXN  CONST_01  NAF  CAG  NAE  CAH    0.00  0.0  0
 LXN  CONST_02  CAG  NAE  CAH  CAJ    0.00  0.0  0
 LXN  CONST_03  CAG  NAF  CAI  CAJ    0.00  0.0  0
 LXN  CONST_04  NAE  CAG  NAF  CAI    0.00  0.0  0
 LXN  CONST_05  CAG  NAE  CAH  OAB  180.00  0.0  0
 LXN  CONST_06  OAA  CAG  NAE  CAH  180.00  0.0  0
 LXN  CONST_07  OAA  CAG  NAF  CAI  180.00  0.0  0
 LXN  CONST_08  CAG  NAF  CAI  OAC  180.00  0.0  0
 LXN  CONST_09  HAE  NAE  CAH  CAJ  180.00  0.0  0
 LXN  CONST_10  HAF  NAF  CAI  CAJ  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
 LXN  plan-1  OAB  0.020
 LXN  plan-1  CAH  0.020
 LXN  plan-1  CAJ  0.020
 LXN  plan-1  OAD  0.020
 LXN  plan-1  CAI  0.020
 LXN  plan-1  OAC  0.020
 LXN  plan-1  NAF  0.020
 LXN  plan-1  CAG  0.020
 LXN  plan-1  OAA  0.020
 LXN  plan-1  NAE  0.020
 LXN  plan-1  HAE  0.020
 LXN  plan-1  HAF  0.020

