# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 19:19:00 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: 6-[3-hydroxy-2-(hydroxymethyl)prop-1-en-1-yl]-1,5-dimethylpyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)NC(=O)C(=C1C=C(CO)CO)C
#
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
 SK7  SK7  6-[3-hydroxy-2-(hydroxymethyl)prop-1-en-1-yl]-1,5-dimethylpyrimidine-2,4(1H,3H)-dione  ligand  30  16  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_SK7
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
 SK7  N1   N  NR6   0  -0.562  -0.9073   1.2266  -0.2308
 SK7  C6   C  CH3   0  -0.530  -0.2598   2.5261  -0.0901
 SK7  O1   O  O     0  -0.487  -2.9852   2.1716  -0.1523
 SK7  O2   O  O     0  -0.463  -2.7497  -2.3273  -0.3752
 SK7  N2   N  NR16  0  -0.718  -2.8137  -0.0755  -0.2667
 SK7  C1   C  CR6   0   0.699  -2.2802   1.1828  -0.2154
 SK7  C2   C  CR6   0   0.569  -2.1358  -1.2737  -0.3454
 SK7  C3   C  CR6   0  -0.239  -0.6948  -1.1543  -0.4038
 SK7  C4   C  CH3   0  -0.719   0.0772  -2.4275  -0.5568
 SK7  C5   C  CR6   0   0.388  -0.1392   0.0845  -0.3445
 SK7  C11  C  C1    0  -0.378   1.3093   0.3045  -0.4983
 SK7  C12  C  C     0   0.046   2.2519  -0.0110   0.3851
 SK7  C14  C  CH2   0  -0.238   2.0062  -0.5863   1.7558
 SK7  C13  C  CH2   0  -0.180   3.7082   0.1932   0.0956
 SK7  O4   O  OH1   0  -0.650   0.7670  -0.2678   2.3311
 SK7  O3   O  OH1   0  -0.660   3.9257   0.4969  -1.2532
 SK7  H1   H  HCH3  0   0.277  -0.9921   3.2552   0.2358
 SK7  H2   H  HCH3  0   0.265   0.5281   2.4625   0.6549
 SK7  H3   H  HCH3  0   0.260   0.1662   2.8577  -1.0356
 SK7  H4   H  HNR6  0   0.423  -3.8247  -0.1205  -0.2459
 SK7  H5   H  HCH3  0   0.252  -0.3281  -3.0287  -1.3712
 SK7  H6   H  HCH3  0   0.252   1.1267  -2.2435  -0.7692
 SK7  H7   H  HCH3  0   0.244   0.0210  -3.0430   0.3440
 SK7  H8   H  H     0   0.291   1.5972   0.7591  -1.4411
 SK7  H11  H  HCH2  0   0.239   2.1740  -1.6711   1.7117
 SK7  H12  H  HCH2  0   0.247   2.7767  -0.1974   2.4287
 SK7  H13  H  HCH2  0   0.228   4.0709   0.9913   0.7592
 SK7  H14  H  HCH2  0   0.221   4.2467  -0.7162   0.4030
 SK7  H15  H  HOH1  0   0.461   0.1047  -0.8891   2.0176
 SK7  H16  H  HOH1  0   0.464   4.8505   0.7365  -1.3612

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
 SK7  O4   C14  single  1.403  0.020  1.403
 SK7  C4   C3   single  1.497  0.020  1.497
 SK7  C13  C12  single  1.499  0.020  1.499
 SK7  C13  O3   single  1.400  0.020  1.400
 SK7  O2   C2   double  1.220  0.020  1.220
 SK7  C12  C14  single  1.507  0.020  1.507
 SK7  C12  C11  double  1.330  0.020  1.330
 SK7  C3   C2   single  1.447  0.020  1.447
 SK7  C3   C5   double  1.359  0.020  1.359
 SK7  C2   N2   single  1.379  0.020  1.379
 SK7  C11  C5   single  1.473  0.020  1.473
 SK7  C5   N1   single  1.381  0.020  1.381
 SK7  N2   C1   single  1.368  0.020  1.368
 SK7  N1   C1   single  1.374  0.020  1.374
 SK7  N1   C6   single  1.459  0.020  1.459
 SK7  C1   O1   double  1.216  0.020  1.216
 SK7  C6   H1   single  0.970  0.020  1.090
 SK7  C6   H2   single  0.970  0.020  1.090
 SK7  C6   H3   single  0.970  0.020  1.090
 SK7  N2   H4   single  0.860  0.020  1.020
 SK7  C4   H5   single  0.970  0.020  1.090
 SK7  C4   H6   single  0.970  0.020  1.090
 SK7  C4   H7   single  0.970  0.020  1.090
 SK7  C11  H8   single  0.930  0.020  1.080
 SK7  C14  H11  single  0.970  0.020  1.090
 SK7  C14  H12  single  0.970  0.020  1.090
 SK7  C13  H13  single  0.970  0.020  1.090
 SK7  C13  H14  single  0.970  0.020  1.090
 SK7  O4   H15  single  0.850  0.020  0.980
 SK7  O3   H16  single  0.850  0.020  0.980

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
 SK7  C5   N1   C1   122.03  3.000
 SK7  C1   N1   C6   118.10  3.000
 SK7  C5   N1   C6   119.86  3.000
 SK7  H3   C6   H2   109.25  3.000
 SK7  H3   C6   H1   108.71  3.000
 SK7  H2   C6   H1   108.87  3.000
 SK7  H3   C6   N1   111.17  3.000
 SK7  H2   C6   N1   109.63  3.000
 SK7  H1   C6   N1   109.17  3.000
 SK7  H4   N2   C2   116.98  3.000
 SK7  H4   N2   C1   115.45  3.000
 SK7  C2   N2   C1   127.57  3.000
 SK7  N2   C1   O1   121.59  3.000
 SK7  O1   C1   N1   123.65  3.000
 SK7  N2   C1   N1   114.76  3.000
 SK7  C3   C2   N2   114.84  3.000
 SK7  N2   C2   O2   120.30  3.000
 SK7  C3   C2   O2   124.85  3.000
 SK7  C5   C3   C4   124.68  3.000
 SK7  C5   C3   C2   118.72  3.000
 SK7  C4   C3   C2   116.59  3.000
 SK7  H7   C4   H6   107.84  3.000
 SK7  H7   C4   H5   106.62  3.000
 SK7  H6   C4   H5   107.85  3.000
 SK7  H7   C4   C3   111.62  3.000
 SK7  H6   C4   C3   111.97  3.000
 SK7  H5   C4   C3   110.71  3.000
 SK7  C11  C5   C3   122.25  3.000
 SK7  C11  C5   N1   115.59  3.000
 SK7  C3   C5   N1   122.01  3.000
 SK7  H8   C11  C12  119.23  3.000
 SK7  H8   C11  C5   114.46  3.000
 SK7  C12  C11  C5   126.31  3.000
 SK7  C13  C12  C14  112.72  3.000
 SK7  C14  C12  C11  125.40  3.000
 SK7  C13  C12  C11  121.87  3.000
 SK7  H12  C14  H11  105.55  3.000
 SK7  H12  C14  O4   106.80  3.000
 SK7  H11  C14  O4   112.06  3.000
 SK7  H12  C14  C12  107.99  3.000
 SK7  H11  C14  C12  108.40  3.000
 SK7  O4   C14  C12  115.50  3.000
 SK7  H14  C13  H13  105.65  3.000
 SK7  H14  C13  O3   111.86  3.000
 SK7  H13  C13  O3   111.89  3.000
 SK7  H14  C13  C12  107.99  3.000
 SK7  H13  C13  C12  107.63  3.000
 SK7  O3   C13  C12  111.52  3.000
 SK7  H15  O4   C14  109.17  3.000
 SK7  H16  O3   C13  108.17  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
 SK7  CONST_01  C2   N2   C1   N1     0.00   0.0  0
 SK7  CONST_02  C5   N1   C1   N2     0.00   0.0  0
 SK7  CONST_03  C3   C2   N2   C1     0.00   0.0  0
 SK7  CONST_04  N2   C1   N1   C6   180.00   0.0  0
 SK7  CONST_05  C2   N2   C1   O1   180.00   0.0  0
 SK7  CONST_06  C5   N1   C1   O1   180.00   0.0  0
 SK7  CONST_07  C1   N2   C2   O2   180.00   0.0  0
 SK7  CONST_08  H4   N2   C1   N1   180.00   0.0  0
 SK7  CONST_09  O1   C1   N1   C6     0.00   0.0  0
 SK7  CONST_10  C13  C12  C11  C5   180.00   0.0  0
 SK7  CONST_11  C14  C12  C11  C5     0.00   0.0  0
 SK7  CONST_12  H8   C11  C12  C14  180.00   0.0  0
 SK7  Var_01    C12  C11  C5   N1   112.66  30.0  2
 SK7  Var_02    H1   C6   N1   C1    12.93  30.0  3
 SK7  Var_03    H5   C4   C3   C2    49.46  30.0  3
 SK7  Var_04    O3   C13  C12  C11  -11.12  30.0  2
 SK7  Var_05    O4   C14  C12  C11  -26.76  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
 SK7  plan-1  N1   0.020
 SK7  plan-1  C6   0.020
 SK7  plan-1  O1   0.020
 SK7  plan-1  O2   0.020
 SK7  plan-1  N2   0.020
 SK7  plan-1  C1   0.020
 SK7  plan-1  C2   0.020
 SK7  plan-1  C3   0.020
 SK7  plan-1  C4   0.020
 SK7  plan-1  C5   0.020
 SK7  plan-1  C11  0.020
 SK7  plan-1  H4   0.020
 SK7  plan-2  C5   0.020
 SK7  plan-2  C11  0.020
 SK7  plan-2  C12  0.020
 SK7  plan-2  C14  0.020
 SK7  plan-2  C13  0.020
 SK7  plan-2  H8   0.020

