# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 02:12:01 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: 1,3-dimethyl-6-(2-methylpropoxy)pyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)COC1=CC(=O)N(C)C(=O)N1C
#
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
 6HP  6HP  1,3-dimethyl-6-(2-methylpropoxy)pyrimidine-2,4(1H,3H)-dione  ligand  31  15  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_6HP
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
 6HP  C1   C  CH3   0  -0.656   3.9766  -0.9445  -0.9597
 6HP  C2   C  CH1   0  -0.284   3.7490  -0.0656   0.2651
 6HP  C3   C  CH3   0  -0.662   4.8399   0.9946   0.3845
 6HP  C6   C  CR6   0   0.718   0.1177   0.0164   0.1068
 6HP  C7   C  CR16  0  -0.622  -0.3339   1.2950   0.0514
 6HP  C8   C  CR6   0   0.589  -1.7321   1.5627  -0.0496
 6HP  O9   O  O     0  -0.490  -2.2114   2.6852  -0.1079
 6HP  C12  C  CR6   0   0.762  -2.1094  -0.8612   0.0052
 6HP  C4   C  CH2   0  -0.164   2.4044   0.6355   0.2209
 6HP  O5   O  O2    0  -0.445   1.3734  -0.3566   0.2035
 6HP  N10  N  NR6   0  -0.588  -2.5578   0.4345  -0.0731
 6HP  O13  O  O     0  -0.486  -2.8831  -1.7980   0.0130
 6HP  N14  N  NR6   0  -0.597  -0.7410  -1.0482   0.0679
 6HP  H18  H  HCH3  0   0.218   3.9540  -0.3494  -1.8760
 6HP  H17  H  HCH3  0   0.234   4.9535  -1.4269  -0.9065
 6HP  H16  H  HCH3  0   0.236   3.2286  -1.7319  -1.0522
 6HP  H19  H  HCH1  0   0.241   3.7770  -0.6913   1.1634
 6HP  H22  H  HCH3  0   0.223   4.8401   1.6555  -0.4847
 6HP  H21  H  HCH3  0   0.234   4.7116   1.6110   1.2756
 6HP  H20  H  HCH3  0   0.240   5.8228   0.5271   0.4429
 6HP  H25  H  HCR6  0   0.299   0.3374   2.1378   0.0835
 6HP  H27  H  HCH3  0   0.265  -4.2184   1.6552  -0.3065
 6HP  H28  H  HCH3  0   0.254  -4.3993   0.0437  -1.0066
 6HP  H26  H  HCH3  0   0.253  -4.4901   0.2635   0.7483
 6HP  H31  H  HCH3  0   0.262   0.2153  -2.6225   1.0979
 6HP  H30  H  HCH3  0   0.275  -1.0277  -3.1025  -0.0593
 6HP  H29  H  HCH3  0   0.264   0.5406  -2.5556  -0.6459
 6HP  H23  H  HCH2  0   0.252   2.2724   1.2788   1.0964
 6HP  H24  H  HCH2  0   0.238   2.3281   1.2582  -0.6770
 6HP  C11  C  CH3   0  -0.529  -4.0021   0.6039  -0.1634
 6HP  C15  C  CH3   0  -0.534  -0.2154  -2.4102   0.1213

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
 6HP  C3   C2   single  1.526  0.020  1.526
 6HP  C2   C1   single  1.525  0.020  1.525
 6HP  C2   C4   single  1.517  0.020  1.517
 6HP  O5   C4   single  1.431  0.020  1.431
 6HP  O5   C6   single  1.313  0.020  1.313
 6HP  C7   C6   double  1.357  0.020  1.357
 6HP  C7   C8   single  1.427  0.020  1.427
 6HP  C6   N14  single  1.368  0.020  1.368
 6HP  O9   C8   double  1.222  0.020  1.222
 6HP  C8   N10  single  1.398  0.020  1.398
 6HP  N14  C15  single  1.461  0.020  1.461
 6HP  N14  C12  single  1.382  0.020  1.382
 6HP  N10  C12  single  1.373  0.020  1.373
 6HP  N10  C11  single  1.457  0.020  1.457
 6HP  C12  O13  double  1.215  0.020  1.215
 6HP  C1   H18  single  0.970  0.020  1.090
 6HP  C1   H17  single  0.970  0.020  1.090
 6HP  C1   H16  single  0.970  0.020  1.090
 6HP  C2   H19  single  0.970  0.020  1.090
 6HP  C3   H22  single  0.970  0.020  1.090
 6HP  C3   H21  single  0.970  0.020  1.090
 6HP  C3   H20  single  0.970  0.020  1.090
 6HP  C7   H25  single  0.930  0.020  1.080
 6HP  C11  H27  single  0.970  0.020  1.090
 6HP  C11  H28  single  0.970  0.020  1.090
 6HP  C11  H26  single  0.970  0.020  1.090
 6HP  C15  H31  single  0.970  0.020  1.090
 6HP  C15  H30  single  0.970  0.020  1.090
 6HP  C15  H29  single  0.970  0.020  1.090
 6HP  C4   H23  single  0.970  0.020  1.090
 6HP  C4   H24  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
 6HP  H16  C1   H17  107.41  3.000
 6HP  H16  C1   H18  107.94  3.000
 6HP  H17  C1   H18  107.48  3.000
 6HP  H16  C1   C2   112.47  3.000
 6HP  H17  C1   C2   110.45  3.000
 6HP  H18  C1   C2   110.89  3.000
 6HP  H19  C2   C4   108.09  3.000
 6HP  H19  C2   C3   108.33  3.000
 6HP  C4   C2   C3   108.35  3.000
 6HP  H19  C2   C1   109.02  3.000
 6HP  C4   C2   C1   112.04  3.000
 6HP  C3   C2   C1   110.90  3.000
 6HP  H20  C3   H21  107.73  3.000
 6HP  H20  C3   H22  107.59  3.000
 6HP  H21  C3   H22  107.95  3.000
 6HP  H20  C3   C2   110.54  3.000
 6HP  H21  C3   C2   111.86  3.000
 6HP  H22  C3   C2   111.00  3.000
 6HP  N14  C6   O5   112.40  3.000
 6HP  N14  C6   C7   121.53  3.000
 6HP  O5   C6   C7   126.06  3.000
 6HP  H25  C7   C8   117.75  3.000
 6HP  H25  C7   C6   121.88  3.000
 6HP  C8   C7   C6   120.37  3.000
 6HP  N10  C8   O9   120.58  3.000
 6HP  N10  C8   C7   115.36  3.000
 6HP  O9   C8   C7   124.05  3.000
 6HP  N14  C12  O13  121.72  3.000
 6HP  O13  C12  N10  121.32  3.000
 6HP  N14  C12  N10  116.96  3.000
 6HP  H24  C4   H23  108.26  3.000
 6HP  H24  C4   O5   109.52  3.000
 6HP  H23  C4   O5   109.28  3.000
 6HP  H24  C4   C2   110.39  3.000
 6HP  H23  C4   C2   110.81  3.000
 6HP  O5   C4   C2   108.58  3.000
 6HP  C4   O5   C6   119.53  3.000
 6HP  C12  N10  C11  115.90  3.000
 6HP  C11  N10  C8   119.51  3.000
 6HP  C12  N10  C8   124.58  3.000
 6HP  C15  N14  C12  118.94  3.000
 6HP  C12  N14  C6   121.15  3.000
 6HP  C15  N14  C6   119.90  3.000
 6HP  H26  C11  H28  108.94  3.000
 6HP  H26  C11  H27  108.94  3.000
 6HP  H28  C11  H27  108.95  3.000
 6HP  H26  C11  N10  110.86  3.000
 6HP  H28  C11  N10  110.50  3.000
 6HP  H27  C11  N10  108.61  3.000
 6HP  H29  C15  H30  108.58  3.000
 6HP  H29  C15  H31  109.39  3.000
 6HP  H30  C15  H31  108.78  3.000
 6HP  H29  C15  N14  110.44  3.000
 6HP  H30  C15  N14  108.67  3.000
 6HP  H31  C15  N14  110.92  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
 6HP  CONST_01  N10  C12  N14  C6     0.00   0.0  0
 6HP  CONST_02  C12  N10  C8   C7     0.00   0.0  0
 6HP  CONST_03  N14  C12  N10  C8     0.00   0.0  0
 6HP  CONST_04  O13  C12  N14  C6   180.00   0.0  0
 6HP  CONST_05  C11  N10  C8   C7   180.00   0.0  0
 6HP  CONST_06  O13  C12  N10  C8   180.00   0.0  0
 6HP  CONST_07  C12  N10  C8   O9   180.00   0.0  0
 6HP  CONST_08  N14  C12  N10  C11  180.00   0.0  0
 6HP  CONST_09  N10  C12  N14  C15  180.00   0.0  0
 6HP  CONST_10  C11  N10  C8   O9     0.00   0.0  0
 6HP  CONST_11  O13  C12  N10  C11    0.00   0.0  0
 6HP  CONST_12  O13  C12  N14  C15    0.00   0.0  0
 6HP  Var_01    N14  C6   O5   C4   178.38  30.0  3
 6HP  Var_02    H31  C15  N14  C6    68.24  30.0  3
 6HP  Var_03    H27  C11  N10  C8     5.92  30.0  3
 6HP  Var_04    H23  C4   O5   C6    61.96  30.0  3
 6HP  Var_05    O5   C4   C2   C1    61.34  30.0  3
 6HP  Var_06    H22  C3   C2   C1    61.33  30.0  3
 6HP  Var_07    H18  C1   C2   C3   -60.85  30.0  3

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
 6HP  plan-1  C6   0.020
 6HP  plan-1  C7   0.020
 6HP  plan-1  C8   0.020
 6HP  plan-1  O9   0.020
 6HP  plan-1  C12  0.020
 6HP  plan-1  O5   0.020
 6HP  plan-1  N10  0.020
 6HP  plan-1  O13  0.020
 6HP  plan-1  N14  0.020
 6HP  plan-1  H25  0.020
 6HP  plan-1  C11  0.020
 6HP  plan-1  C15  0.020

