# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 04:39:51 2020
#   Inital geometry file: a 67 line input string
#   Ligand name: 6-(3-hydroxypropyl)-5-methylpyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=C(CCCO)NC(=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
 HPT  HPT  6-(3-hydroxypropyl)-5-methylpyrimidine-2,4(1H,3H)-dione  ligand  25  13  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HPT
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
 HPT  O2    O  O     0  -0.467   1.9964  -0.5206   2.7580
 HPT  C3    C  CR6   0  -0.211   1.1218   0.2343   0.6835
 HPT  C4    C  CH3   0  -0.743   2.4716   0.4176   0.0568
 HPT  C5    C  CR6   0   0.432  -0.0328   0.4886   0.0230
 HPT  C1    C  CR6   0   0.663  -1.4197  -0.1524   1.8998
 HPT  N1    N  NR16  0  -0.712  -1.2490   0.2980   0.6229
 HPT  C2    C  CR6   0   0.563   1.0417  -0.2496   2.0488
 HPT  N2    N  NR16  0  -0.715  -0.2423  -0.4044   2.5477
 HPT  O3    O  OH1   0  -0.672  -0.4635  -0.9310  -4.6242
 HPT  C11   C  CH2   0  -0.547  -0.0932   0.9306  -1.4031
 HPT  C12   C  CH2   0  -0.458  -0.2426  -0.2626  -2.3523
 HPT  C13   C  CH2   0  -0.139  -0.2964   0.1979  -3.7962
 HPT  H43   H  HCH3  0   0.260   3.2574   0.2554   0.7903
 HPT  H42   H  HCH3  0   0.247   2.6414  -0.2841  -0.7615
 HPT  H41   H  HCH3  0   0.249   2.6029   1.4239  -0.3428
 HPT  H1    H  HNR6  0   0.430  -2.0910   0.5063   0.1050
 HPT  H2    H  HNR6  0   0.423  -0.3222  -0.7411   3.4990
 HPT  H3    H  HOH1  0   0.455  -0.4754  -0.6326  -5.5379
 HPT  H112  H  HCH2  0   0.275  -0.9322   1.6188  -1.5378
 HPT  H111  H  HCH2  0   0.273   0.8098   1.4887  -1.6492
 HPT  H122  H  HCH2  0   0.245   0.5966  -0.9498  -2.2153
 HPT  H121  H  HCH2  0   0.241  -1.1546  -0.8152  -2.1115
 HPT  H132  H  HCH2  0   0.194  -1.1223   0.9120  -3.9168
 HPT  H131  H  HCH2  0   0.196   0.6279   0.7396  -4.0369
 HPT  O1    O  O     0  -0.483  -2.5103  -0.3119   2.4116

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
 HPT  O2   C2    double  1.220  0.020  1.220
 HPT  C3   C4    single  1.499  0.020  1.499
 HPT  C3   C5    double  1.354  0.020  1.354
 HPT  C3   C2    single  1.451  0.020  1.451
 HPT  C4   H43   single  0.970  0.020  1.090
 HPT  C4   H42   single  0.970  0.020  1.090
 HPT  C4   H41   single  0.970  0.020  1.090
 HPT  C5   N1    single  1.370  0.020  1.370
 HPT  C5   C11   single  1.494  0.020  1.494
 HPT  C1   N1    single  1.365  0.020  1.365
 HPT  C1   N2    single  1.367  0.020  1.367
 HPT  C1   O1    double  1.215  0.020  1.215
 HPT  N1   H1    single  0.860  0.020  1.020
 HPT  C2   N2    single  1.386  0.020  1.386
 HPT  N2   H2    single  0.860  0.020  1.020
 HPT  O3   C13   single  1.410  0.020  1.410
 HPT  O3   H3    single  0.850  0.020  0.980
 HPT  C11  C12   single  1.532  0.020  1.532
 HPT  C11  H112  single  0.970  0.020  1.090
 HPT  C11  H111  single  0.970  0.020  1.090
 HPT  C12  C13   single  1.517  0.020  1.517
 HPT  C12  H122  single  0.970  0.020  1.090
 HPT  C12  H121  single  0.970  0.020  1.090
 HPT  C13  H132  single  0.970  0.020  1.090
 HPT  C13  H131  single  0.970  0.020  1.090

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
 HPT  C2    C3   C5    118.33  3.000
 HPT  C2    C3   C4    118.93  3.000
 HPT  C5    C3   C4    122.73  3.000
 HPT  H41   C4   H42   107.44  3.000
 HPT  H41   C4   H43   107.33  3.000
 HPT  H42   C4   H43   107.31  3.000
 HPT  H41   C4   C3    111.98  3.000
 HPT  H42   C4   C3    112.02  3.000
 HPT  H43   C4   C3    110.52  3.000
 HPT  C11   C5   N1    115.05  3.000
 HPT  C11   C5   C3    123.74  3.000
 HPT  N1    C5   C3    121.16  3.000
 HPT  O1    C1   N2    123.30  3.000
 HPT  O1    C1   N1    123.34  3.000
 HPT  N2    C1   N1    113.36  3.000
 HPT  H1    N1   C1    116.33  3.000
 HPT  H1    N1   C5    119.14  3.000
 HPT  C1    N1   C5    124.53  3.000
 HPT  N2    C2   C3    115.28  3.000
 HPT  N2    C2   O2    119.40  3.000
 HPT  C3    C2   O2    125.32  3.000
 HPT  H2    N2   C2    116.64  3.000
 HPT  H2    N2   C1    116.02  3.000
 HPT  C2    N2   C1    127.34  3.000
 HPT  H3    O3   C13   108.13  3.000
 HPT  H111  C11  H112  106.60  3.000
 HPT  H111  C11  C12   109.86  3.000
 HPT  H112  C11  C12   109.81  3.000
 HPT  H111  C11  C5    109.48  3.000
 HPT  H112  C11  C5    109.56  3.000
 HPT  C12   C11  C5    111.40  3.000
 HPT  H121  C12  H122  107.16  3.000
 HPT  H121  C12  C13   109.49  3.000
 HPT  H122  C12  C13   109.72  3.000
 HPT  H121  C12  C11   109.79  3.000
 HPT  H122  C12  C11   109.69  3.000
 HPT  C13   C12  C11   110.91  3.000
 HPT  H131  C13  H132  106.75  3.000
 HPT  H131  C13  C12   109.19  3.000
 HPT  H132  C13  C12   109.18  3.000
 HPT  H131  C13  O3    111.47  3.000
 HPT  H132  C13  O3    111.53  3.000
 HPT  C12   C13  O3    108.68  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
 HPT  CONST_01  C1   N2   C2   C3     0.00   0.0  0
 HPT  CONST_02  N2   C1   N1   C5     0.00   0.0  0
 HPT  CONST_03  C2   N2   C1   N1     0.00   0.0  0
 HPT  CONST_04  C1   N2   C2   O2   180.00   0.0  0
 HPT  CONST_05  O1   C1   N1   C5   180.00   0.0  0
 HPT  CONST_06  O1   C1   N2   C2   180.00   0.0  0
 HPT  CONST_07  H2   N2   C2   C3   180.00   0.0  0
 HPT  CONST_08  H1   N1   C1   N2   180.00   0.0  0
 HPT  Var_01    C12  C11  C5   C3    92.70  30.0  3
 HPT  Var_02    H43  C4   C3   C5   174.23  30.0  3
 HPT  Var_03    C13  C12  C11  C5  -179.74  30.0  3
 HPT  Var_04    C11  C12  C13  O3  -178.72  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
 HPT  plan-1  O2   0.020
 HPT  plan-1  C3   0.020
 HPT  plan-1  C4   0.020
 HPT  plan-1  C5   0.020
 HPT  plan-1  C1   0.020
 HPT  plan-1  N1   0.020
 HPT  plan-1  C2   0.020
 HPT  plan-1  N2   0.020
 HPT  plan-1  C11  0.020
 HPT  plan-1  H1   0.020
 HPT  plan-1  H2   0.020
 HPT  plan-1  O1   0.020

