# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 05:27:18 2020
#   Inital geometry file: a 45 line input string
#   Ligand name: 5-aminopyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=CNC(=O)NC1=O
#
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
 WBU  WBU  5-aminopyrimidine-2,4(1H,3H)-dione  ligand  14  9  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_WBU
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
 WBU  N1    N  NR16  0  -0.666  -1.2437   0.0090  -1.1125
 WBU  C2    C  CR6   0   0.670   0.0113  -0.0466  -1.6205
 WBU  O2    O  OC    0  -0.496   0.2672  -0.0996  -2.8096
 WBU  N3    N  NR16  0  -0.714   0.9906  -0.0398  -0.6517
 WBU  C4    C  CR6   0   0.544   0.8282   0.0284   0.7149
 WBU  O4    O  OC    0  -0.461   1.7873   0.0247   1.4660
 WBU  C5    C  CR6   0   0.070  -0.5573   0.0903   1.1671
 WBU  C6    C  CR16  0  -0.022  -1.5260   0.0617   0.2324
 WBU  N01   N  NH2   0  -0.847  -0.7645   0.2372   2.5322
 WBU  H1    H  HNR6  0   0.433  -2.0090   0.0011  -1.7690
 WBU  H3    H  HNR6  0   0.426   1.9441  -0.0876  -0.9895
 WBU  H6    H  HCR6  0   0.313  -2.5771   0.0924   0.4799
 WBU  H011  H  HNH2  0   0.375  -0.0900  -0.2646   3.0914
 WBU  H012  H  HNH2  0   0.376  -1.6996  -0.0003   2.8271

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
 WBU  N1   C2    aromatic  1.355  0.020  1.355
 WBU  N1   C6    aromatic  1.375  0.020  1.375
 WBU  N1   H1    single    0.860  0.020  1.020
 WBU  C2   O2    double    1.218  0.020  1.218
 WBU  C2   N3    aromatic  1.377  0.020  1.377
 WBU  N3   C4    aromatic  1.378  0.020  1.378
 WBU  N3   H3    single    0.860  0.020  1.020
 WBU  C4   O4    double    1.218  0.020  1.218
 WBU  C4   C5    aromatic  1.459  0.020  1.459
 WBU  C5   C6    aromatic  1.346  0.020  1.346
 WBU  C5   N01   single    1.389  0.020  1.389
 WBU  C6   H6    single    0.930  0.020  1.080
 WBU  N01  H011  single    0.890  0.020  1.040
 WBU  N01  H012  single    0.890  0.020  1.040

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
 WBU  H1    N1   C6    118.77  3.000
 WBU  H1    N1   C2    117.29  3.000
 WBU  C6    N1   C2    123.94  3.000
 WBU  N3    C2   O2    122.53  3.000
 WBU  N3    C2   N1    113.24  3.000
 WBU  O2    C2   N1    124.23  3.000
 WBU  H3    N3   C4    116.36  3.000
 WBU  H3    N3   C2    115.76  3.000
 WBU  C4    N3   C2    127.88  3.000
 WBU  C5    C4   O4    123.84  3.000
 WBU  C5    C4   N3    114.92  3.000
 WBU  O4    C4   N3    121.24  3.000
 WBU  N01   C5   C6    125.27  3.000
 WBU  N01   C5   C4    116.80  3.000
 WBU  C6    C5   C4    117.86  3.000
 WBU  H6    C6   C5    122.70  3.000
 WBU  H6    C6   N1    115.15  3.000
 WBU  C5    C6   N1    122.15  3.000
 WBU  H012  N01  H011  109.90  3.000
 WBU  H012  N01  C5    113.62  3.000
 WBU  H011  N01  C5    113.09  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
 WBU  CONST_01  C4   N3  C2  N1    0.00  0.0  0
 WBU  CONST_02  C4   C5  C6  N1    0.00  0.0  0
 WBU  CONST_03  C5   C6  N1  C2    0.00  0.0  0
 WBU  CONST_04  C5   C4  N3  C2    0.00  0.0  0
 WBU  CONST_05  C6   N1  C2  N3    0.00  0.0  0
 WBU  CONST_06  C6   C5  C4  N3    0.00  0.0  0
 WBU  CONST_07  N01  C5  C6  N1  180.00  0.0  0
 WBU  CONST_08  O4   C4  N3  C2  180.00  0.0  0
 WBU  CONST_09  C6   N1  C2  O2  180.00  0.0  0
 WBU  CONST_10  C4   N3  C2  O2  180.00  0.0  0
 WBU  CONST_11  N01  C5  C4  N3  180.00  0.0  0
 WBU  CONST_12  C6   C5  C4  O4  180.00  0.0  0
 WBU  CONST_13  H3   N3  C2  N1  180.00  0.0  0
 WBU  CONST_14  H6   C6  N1  C2  180.00  0.0  0
 WBU  CONST_15  H1   N1  C2  N3  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
 WBU  plan-1  N1    0.020
 WBU  plan-1  C2    0.020
 WBU  plan-1  O2    0.020
 WBU  plan-1  N3    0.020
 WBU  plan-1  C4    0.020
 WBU  plan-1  O4    0.020
 WBU  plan-1  C5    0.020
 WBU  plan-1  C6    0.020
 WBU  plan-1  N01   0.020
 WBU  plan-1  H1    0.020
 WBU  plan-1  H3    0.020
 WBU  plan-1  H6    0.020
 WBU  plan-2  C5    0.020
 WBU  plan-2  N01   0.020
 WBU  plan-2  H011  0.020
 WBU  plan-2  H012  0.020

