# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 09:29:16 2022
#   Inital geometry file: a 50 line input string
#   Ligand name: 5-chloro-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C1=C(Cl)C(=O)NC(=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
 HRO  HRO  '5-chloro-2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylic acid'  ligand  14  12  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_HRO
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
 HRO  OAA  O   OC    -1  -0.537   2.6637   0.8294  -0.0767
 HRO  CAH  C   C      0   0.431   1.5960   1.4374  -0.0083
 HRO  OAD  O   O      0  -0.581   1.3844   2.6607   0.0525
 HRO  CAI  C   C      0   0.292   0.3023   0.5899  -0.0018
 HRO  CAJ  C   C      0  -0.302   0.1849  -0.7564   0.0061
 HRO  CL   CL  CL     0  -0.089   1.4965  -1.8610   0.0246
 HRO  CAL  C   C      0   0.613  -1.1317  -1.3806   0.0061
 HRO  OAC  O   O      0  -0.444  -1.3334  -2.5780   0.0143
 HRO  NAG  N   NH1    0  -0.716  -2.1809  -0.4839  -0.0056
 HRO  CAK  C   C      0   0.668  -2.1037   0.8865  -0.0107
 HRO  OAB  O   O      0  -0.479  -3.0835   1.6039  -0.0173
 HRO  NAF  N   NH1    0  -0.710  -0.8255   1.3536  -0.0080
 HRO  H3   H   HNH1   0   0.430  -3.1138  -0.8781  -0.0124
 HRO  H2   H   HNH1   0   0.425  -0.6627   2.3556   0.0008

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
 HRO  CL   CAJ  single  1.715  0.020  1.715
 HRO  OAC  CAL  double  1.214  0.020  1.214
 HRO  CAL  CAJ  single  1.457  0.020  1.457
 HRO  CAL  NAG  single  1.380  0.020  1.380
 HRO  CAJ  CAI  double  1.351  0.020  1.351
 HRO  NAG  CAK  single  1.373  0.020  1.373
 HRO  OAD  CAH  deloc   1.243  0.020  1.243
 HRO  OAA  CAH  deloc   1.231  0.020  1.231
 HRO  CAI  CAH  single  1.547  0.020  1.547
 HRO  CAI  NAF  single  1.362  0.020  1.362
 HRO  CAK  NAF  single  1.361  0.020  1.361
 HRO  CAK  OAB  double  1.214  0.020  1.214
 HRO  NAG  H3   single  0.860  0.020  1.020
 HRO  NAF  H2   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
 HRO  CAI  CAH  OAD  113.37  3.000
 HRO  CAI  CAH  OAA  117.08  3.000
 HRO  OAD  CAH  OAA  129.55  3.000
 HRO  NAF  CAI  CAJ  119.12  3.000
 HRO  NAF  CAI  CAH  112.67  3.000
 HRO  CAJ  CAI  CAH  128.21  3.000
 HRO  CAL  CAJ  CL   114.53  3.000
 HRO  CAL  CAJ  CAI  120.35  3.000
 HRO  CL   CAJ  CAI  125.12  3.000
 HRO  NAG  CAL  OAC  120.96  3.000
 HRO  NAG  CAL  CAJ  114.11  3.000
 HRO  OAC  CAL  CAJ  124.93  3.000
 HRO  H3   NAG  CAK  116.14  3.000
 HRO  H3   NAG  CAL  116.57  3.000
 HRO  CAK  NAG  CAL  127.29  3.000
 HRO  NAF  CAK  OAB  123.71  3.000
 HRO  OAB  CAK  NAG  122.98  3.000
 HRO  NAF  CAK  NAG  113.30  3.000
 HRO  H2   NAF  CAK  119.30  3.000
 HRO  H2   NAF  CAI  114.88  3.000
 HRO  CAK  NAF  CAI  125.82  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
 HRO  CONST_01  NAG  CAK  NAF  CAI    0.00   0.0  0
 HRO  CONST_02  CAK  NAG  CAL  CAJ    0.00   0.0  0
 HRO  CONST_03  NAF  CAK  NAG  CAL    0.00   0.0  0
 HRO  CONST_04  OAB  CAK  NAF  CAI  180.00   0.0  0
 HRO  CONST_05  OAB  CAK  NAG  CAL  180.00   0.0  0
 HRO  CONST_06  CAK  NAG  CAL  OAC  180.00   0.0  0
 HRO  CONST_07  H3   NAG  CAL  CAJ  180.00   0.0  0
 HRO  CONST_08  H2   NAF  CAK  NAG  180.00   0.0  0
 HRO  Var_01    CAJ  CAI  CAH  OAA    3.70  30.0  2

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
 HRO  plan-1  CAH  0.020
 HRO  plan-1  CAI  0.020
 HRO  plan-1  CAJ  0.020
 HRO  plan-1  CL   0.020
 HRO  plan-1  CAL  0.020
 HRO  plan-1  OAC  0.020
 HRO  plan-1  NAG  0.020
 HRO  plan-1  CAK  0.020
 HRO  plan-1  OAB  0.020
 HRO  plan-1  NAF  0.020
 HRO  plan-1  H3   0.020
 HRO  plan-1  H2   0.020
 HRO  plan-2  OAA  0.020
 HRO  plan-2  CAH  0.020
 HRO  plan-2  OAD  0.020
 HRO  plan-2  CAI  0.020

