# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 17:44:52 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: 6-[3-hydroxy-2-(hydroxymethyl)prop-1-en-1-yl]-5-methylpyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=C(NC(=O)NC1=O)C=C(CO)CO
#
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
 I51  I51  6-[3-hydroxy-2-(hydroxymethyl)prop-1-en-1-yl]-5-methylpyrimidine-2,4(1H,3H)-dione  ligand  27  15  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_I51
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
 I51  N1   N  NR16  0  -0.714  -0.7226   0.9305   0.8259
 I51  O1   O  O     0  -0.481  -2.2547   2.5642   1.2067
 I51  O2   O  O     0  -0.465  -3.5784  -1.1915  -0.9461
 I51  N2   N  NR16  0  -0.714  -2.8788   0.6691   0.1151
 I51  C1   C  CR6   0   0.662  -1.9738   1.4735   0.7512
 I51  C2   C  CR6   0   0.561  -2.6599  -0.5956  -0.4094
 I51  C3   C  CR6   0  -0.189  -1.3066  -1.0964  -0.2678
 I51  C4   C  CH3   0  -0.733  -0.9567  -2.4465  -0.8142
 I51  C5   C  CR6   0   0.369  -0.3865  -0.3070   0.3376
 I51  C11  C  C1    0  -0.337   1.0044  -0.7343   0.5290
 I51  C12  C  C     0   0.031   2.0844  -0.0679   0.1134
 I51  C13  C  CH2   0  -0.167   3.4688  -0.5789   0.3879
 I51  C14  C  CH2   0  -0.219   2.0300   1.2382  -0.6317
 I51  O3   O  OH1   0  -0.664   3.4319  -1.6596   1.2802
 I51  O4   O  OH1   0  -0.666   2.9986   1.2169  -1.6542
 I51  H1   H  HNR6  0   0.430  -0.0381   1.4505   1.3560
 I51  H2   H  HNR6  0   0.425  -3.8192   1.0360   0.0369
 I51  H3   H  HCH3  0   0.258  -1.8441  -2.9571  -1.1800
 I51  H4   H  HCH3  0   0.249  -0.2498  -2.3761  -1.6422
 I51  H5   H  HCH3  0   0.246  -0.5014  -3.0841  -0.0545
 I51  H6   H  H     0   0.285   1.1258  -1.6854   1.0338
 I51  H7   H  HCH2  0   0.232   3.9356  -0.8582  -0.5641
 I51  H8   H  HCH2  0   0.218   4.0648   0.2564   0.7843
 I51  H9   H  HCH2  0   0.224   1.0281   1.4105  -1.0382
 I51  H10  H  HCH2  0   0.230   2.2273   2.0485   0.0847
 I51  H11  H  HOH1  0   0.464   4.3042  -2.0629   1.2969
 I51  H12  H  HOH1  0   0.464   3.0737   2.1066  -2.0107

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
 I51  C4   C3   single  1.498  0.020  1.498
 I51  O2   C2   double  1.219  0.020  1.219
 I51  O4   C14  single  1.409  0.020  1.409
 I51  C3   C2   single  1.450  0.020  1.450
 I51  C3   C5   double  1.355  0.020  1.355
 I51  C2   N2   single  1.387  0.020  1.387
 I51  C13  C12  single  1.501  0.020  1.501
 I51  C13  O3   single  1.402  0.020  1.402
 I51  C12  C14  single  1.505  0.020  1.505
 I51  C12  C11  double  1.335  0.020  1.335
 I51  C11  C5   single  1.468  0.020  1.468
 I51  C5   N1   single  1.372  0.020  1.372
 I51  N2   C1   single  1.368  0.020  1.368
 I51  N1   C1   single  1.366  0.020  1.366
 I51  C1   O1   double  1.215  0.020  1.215
 I51  N1   H1   single  0.860  0.020  1.020
 I51  N2   H2   single  0.860  0.020  1.020
 I51  C4   H3   single  0.970  0.020  1.090
 I51  C4   H4   single  0.970  0.020  1.090
 I51  C4   H5   single  0.970  0.020  1.090
 I51  C11  H6   single  0.930  0.020  1.080
 I51  C13  H7   single  0.970  0.020  1.090
 I51  C13  H8   single  0.970  0.020  1.090
 I51  C14  H9   single  0.970  0.020  1.090
 I51  C14  H10  single  0.970  0.020  1.090
 I51  O3   H11  single  0.850  0.020  0.980
 I51  O4   H12  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
 I51  H1   N1   C5   119.02  3.000
 I51  H1   N1   C1   116.41  3.000
 I51  C5   N1   C1   124.29  3.000
 I51  H2   N2   C2   116.61  3.000
 I51  H2   N2   C1   115.94  3.000
 I51  C2   N2   C1   127.44  3.000
 I51  N2   C1   O1   123.32  3.000
 I51  O1   C1   N1   123.24  3.000
 I51  N2   C1   N1   113.44  3.000
 I51  C3   C2   N2   115.18  3.000
 I51  N2   C2   O2   119.56  3.000
 I51  C3   C2   O2   125.25  3.000
 I51  C5   C3   C4   121.96  3.000
 I51  C5   C3   C2   118.43  3.000
 I51  C4   C3   C2   119.59  3.000
 I51  H5   C4   H4   107.20  3.000
 I51  H5   C4   H3   107.48  3.000
 I51  H4   C4   H3   107.68  3.000
 I51  H5   C4   C3   111.73  3.000
 I51  H4   C4   C3   111.72  3.000
 I51  H3   C4   C3   110.81  3.000
 I51  C11  C5   C3   122.15  3.000
 I51  C11  C5   N1   116.64  3.000
 I51  C3   C5   N1   121.20  3.000
 I51  H6   C11  C12  119.50  3.000
 I51  H6   C11  C5   115.00  3.000
 I51  C12  C11  C5   125.49  3.000
 I51  C14  C12  C13  114.80  3.000
 I51  C14  C12  C11  123.92  3.000
 I51  C13  C12  C11  121.27  3.000
 I51  H8   C13  H7   106.00  3.000
 I51  H8   C13  O3   111.73  3.000
 I51  H7   C13  O3   111.56  3.000
 I51  H8   C13  C12  107.89  3.000
 I51  H7   C13  C12  108.70  3.000
 I51  O3   C13  C12  110.77  3.000
 I51  H10  C14  H9   106.87  3.000
 I51  H10  C14  O4   111.14  3.000
 I51  H9   C14  O4   111.23  3.000
 I51  H10  C14  C12  108.10  3.000
 I51  H9   C14  C12  110.71  3.000
 I51  O4   C14  C12  108.75  3.000
 I51  H11  O3   C13  108.10  3.000
 I51  H12  O4   C14  108.00  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
 I51  CONST_01  C2   N2   C1   N1      0.00   0.0  0
 I51  CONST_02  C5   N1   C1   N2      0.00   0.0  0
 I51  CONST_03  C3   C2   N2   C1      0.00   0.0  0
 I51  CONST_04  C2   N2   C1   O1    180.00   0.0  0
 I51  CONST_05  C5   N1   C1   O1    180.00   0.0  0
 I51  CONST_06  C1   N2   C2   O2    180.00   0.0  0
 I51  CONST_07  H2   N2   C1   N1    180.00   0.0  0
 I51  CONST_08  H1   N1   C1   N2    180.00   0.0  0
 I51  CONST_09  C13  C12  C11  C5    180.00   0.0  0
 I51  CONST_10  C14  C12  C11  C5      0.00   0.0  0
 I51  CONST_11  H6   C11  C12  C13     0.00   0.0  0
 I51  Var_01    C12  C11  C5   N1    -56.51  30.0  3
 I51  Var_02    H3   C4   C3   C2     -6.31  30.0  3
 I51  Var_03    O3   C13  C12  C11    -9.55  30.0  2
 I51  Var_04    O4   C14  C12  C11  -139.23  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
 I51  plan-1  N1   0.020
 I51  plan-1  O1   0.020
 I51  plan-1  O2   0.020
 I51  plan-1  N2   0.020
 I51  plan-1  C1   0.020
 I51  plan-1  C2   0.020
 I51  plan-1  C3   0.020
 I51  plan-1  C4   0.020
 I51  plan-1  C5   0.020
 I51  plan-1  C11  0.020
 I51  plan-1  H1   0.020
 I51  plan-1  H2   0.020
 I51  plan-2  C5   0.020
 I51  plan-2  C11  0.020
 I51  plan-2  C12  0.020
 I51  plan-2  C13  0.020
 I51  plan-2  C14  0.020
 I51  plan-2  H6   0.020

