# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 21:23:32 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: 6-[3-hydroxy-2-(hydroxymethyl)prop-1-en-1-yl]-4-methoxy-1,5-dimethylpyrimidin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC1=NC(=O)N(C)C(=C1C)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
 I43  I43  6-[3-hydroxy-2-(hydroxymethyl)prop-1-en-1-yl]-4-methoxy-1,5-dimethylpyrimidin-2(1H)-one  ligand  33  17  .  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_I43
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
 I43  N1   N  NR6   0  -0.553  -0.4367   1.4623  -0.8102
 I43  C01  C  CH3   0  -0.528   0.4132   2.5853  -1.1834
 I43  O1   O  O     0  -0.513  -2.2431   2.7885  -1.1400
 I43  O2   O  O2    0  -0.449  -2.9133  -1.4334   0.3296
 I43  C02  C  CH3   0  -0.419  -4.3111  -1.1747   0.4182
 I43  N2   N  N     0  -0.532  -2.6181   0.6949  -0.3788
 I43  C1   C  CR6   0   0.587  -1.8088   1.6987  -0.7948
 I43  C2   C  CR6   0   0.564  -2.1149  -0.4619  -0.0743
 I43  C3   C  CR6   0  -0.169  -0.7329  -0.7963  -0.1452
 I43  C4   C  CH3   0  -0.715  -0.2761  -2.1877   0.1677
 I43  C5   C  CR6   0   0.399   0.0878   0.2334  -0.5137
 I43  C11  C  C1    0  -0.388   1.5410   0.0696  -0.6868
 I43  C12  C  C     0   0.051   2.4124  -0.1941   0.2863
 I43  C13  C  CH2   0  -0.217   2.0383  -0.2649   1.7385
 I43  C14  C  CH2   0  -0.161   3.8751  -0.3766   0.0090
 I43  O3   O  OH1   0  -0.666   2.4927  -1.4902   2.2684
 I43  O4   O  OH1   0  -0.664   4.1660  -0.1385  -1.3410
 I43  H1   H  HCH3  0   0.267   1.4321   2.3996  -0.8621
 I43  H2   H  HCH3  0   0.258   0.4049   2.7414  -2.2616
 I43  H3   H  HCH3  0   0.264   0.0592   3.4894  -0.6973
 I43  H4   H  HCH3  0   0.237  -4.5255  -0.3865   1.1394
 I43  H5   H  HCH3  0   0.238  -4.7283  -0.8924  -0.5481
 I43  H6   H  HCH3  0   0.252  -4.7622  -2.1052   0.7511
 I43  H7   H  HCH3  0   0.249  -0.8620  -2.9261  -0.3801
 I43  H8   H  HCH3  0   0.251   0.7680  -2.3310  -0.0943
 I43  H9   H  HCH3  0   0.245  -0.3801  -2.4143   1.2303
 I43  H10  H  H     0   0.294   1.8975   0.1940  -1.7043
 I43  H13  H  HCH2  0   0.230   2.5134   0.5872   2.2450
 I43  H14  H  HCH2  0   0.222   0.9583  -0.1412   1.8630
 I43  H15  H  HCH2  0   0.214   4.4317   0.3009   0.6735
 I43  H16  H  HCH2  0   0.228   4.1550  -1.3937   0.3108
 I43  H17  H  HOH1  0   0.461   2.3797  -1.4603   3.2228
 I43  H18  H  HOH1  0   0.464   5.0898  -0.3574  -1.4911

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
 I43  O4   C14  single  1.401  0.020  1.401
 I43  C14  C12  single  1.500  0.020  1.500
 I43  O2   C2   single  1.321  0.020  1.321
 I43  O2   C02  single  1.424  0.020  1.424
 I43  N2   C2   double  1.298  0.020  1.298
 I43  N2   C1   single  1.355  0.020  1.355
 I43  C2   C3   single  1.424  0.020  1.424
 I43  O1   C1   double  1.223  0.020  1.223
 I43  C1   N1   single  1.392  0.020  1.392
 I43  C3   C4   single  1.498  0.020  1.498
 I43  C3   C5   double  1.367  0.020  1.367
 I43  C12  C13  single  1.501  0.020  1.501
 I43  C12  C11  double  1.333  0.020  1.333
 I43  N1   C5   single  1.369  0.020  1.369
 I43  N1   C01  single  1.457  0.020  1.457
 I43  C5   C11  single  1.473  0.020  1.473
 I43  C13  O3   single  1.410  0.020  1.410
 I43  C01  H1   single  0.970  0.020  1.090
 I43  C01  H2   single  0.970  0.020  1.090
 I43  C01  H3   single  0.970  0.020  1.090
 I43  C02  H4   single  0.970  0.020  1.090
 I43  C02  H5   single  0.970  0.020  1.090
 I43  C02  H6   single  0.970  0.020  1.090
 I43  C4   H7   single  0.970  0.020  1.090
 I43  C4   H8   single  0.970  0.020  1.090
 I43  C4   H9   single  0.970  0.020  1.090
 I43  C11  H10  single  0.930  0.020  1.080
 I43  C13  H13  single  0.970  0.020  1.090
 I43  C13  H14  single  0.970  0.020  1.090
 I43  C14  H15  single  0.970  0.020  1.090
 I43  C14  H16  single  0.970  0.020  1.090
 I43  O3   H17  single  0.850  0.020  0.980
 I43  O4   H18  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
 I43  C5   N1   C1   121.85  3.000
 I43  C5   N1   C01  121.60  3.000
 I43  C1   N1   C01  116.54  3.000
 I43  H3   C01  H2   108.74  3.000
 I43  H3   C01  H1   108.44  3.000
 I43  H2   C01  H1   108.96  3.000
 I43  H3   C01  N1   109.69  3.000
 I43  H2   C01  N1   111.07  3.000
 I43  H1   C01  N1   109.89  3.000
 I43  C2   O2   C02  118.60  3.000
 I43  H6   C02  H5   109.55  3.000
 I43  H6   C02  H4   109.58  3.000
 I43  H5   C02  H4   108.92  3.000
 I43  H6   C02  O2   105.73  3.000
 I43  H5   C02  O2   111.57  3.000
 I43  H4   C02  O2   111.45  3.000
 I43  C2   N2   C1   120.06  3.000
 I43  N2   C1   O1   122.33  3.000
 I43  O1   C1   N1   119.88  3.000
 I43  N2   C1   N1   117.79  3.000
 I43  C3   C2   N2   125.03  3.000
 I43  C3   C2   O2   115.42  3.000
 I43  N2   C2   O2   119.54  3.000
 I43  C5   C3   C4   124.96  3.000
 I43  C5   C3   C2   114.78  3.000
 I43  C4   C3   C2   120.26  3.000
 I43  H9   C4   H8   107.40  3.000
 I43  H9   C4   H7   107.30  3.000
 I43  H8   C4   H7   107.83  3.000
 I43  H9   C4   C3   111.54  3.000
 I43  H8   C4   C3   111.44  3.000
 I43  H7   C4   C3   111.13  3.000
 I43  C11  C5   C3   122.69  3.000
 I43  C11  C5   N1   116.91  3.000
 I43  C3   C5   N1   120.30  3.000
 I43  H10  C11  C12  119.50  3.000
 I43  H10  C11  C5   114.94  3.000
 I43  C12  C11  C5   125.55  3.000
 I43  C14  C12  C13  114.59  3.000
 I43  C13  C12  C11  123.55  3.000
 I43  C14  C12  C11  121.79  3.000
 I43  H14  C13  H13  106.65  3.000
 I43  H14  C13  O3   111.93  3.000
 I43  H13  C13  O3   111.17  3.000
 I43  H14  C13  C12  110.53  3.000
 I43  H13  C13  C12  107.54  3.000
 I43  O3   C13  C12  108.91  3.000
 I43  H16  C14  H15  106.00  3.000
 I43  H16  C14  O4   111.68  3.000
 I43  H15  C14  O4   111.86  3.000
 I43  H16  C14  C12  108.10  3.000
 I43  H15  C14  C12  107.87  3.000
 I43  O4   C14  C12  111.09  3.000
 I43  H17  O3   C13  107.95  3.000
 I43  H18  O4   C14  108.14  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
 I43  CONST_01  C2   N2   C1   N1     0.00   0.0  0
 I43  CONST_02  C5   N1   C1   N2     0.00   0.0  0
 I43  CONST_03  N2   C1   N1   C01  180.00   0.0  0
 I43  CONST_04  C2   N2   C1   O1   180.00   0.0  0
 I43  CONST_05  C5   N1   C1   O1   180.00   0.0  0
 I43  CONST_06  O1   C1   N1   C01    0.00   0.0  0
 I43  CONST_07  C14  C12  C11  C5   180.00   0.0  0
 I43  CONST_08  C13  C12  C11  C5     0.00   0.0  0
 I43  CONST_09  H10  C11  C12  C13  180.00   0.0  0
 I43  Var_01    C12  C11  C5   N1   116.46  30.0  2
 I43  Var_02    N2   C2   O2   C02   -0.03  30.0  3
 I43  Var_03    H1   C01  N1   C1   161.92  30.0  3
 I43  Var_04    H7   C4   C3   C2    49.87  30.0  3
 I43  Var_05    H4   C02  O2   C2   -61.83  30.0  3
 I43  Var_06    O4   C14  C12  C11    4.21  30.0  2
 I43  Var_07    O3   C13  C12  C11  127.31  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
 I43  plan-1  N1   0.020
 I43  plan-1  C01  0.020
 I43  plan-1  O1   0.020
 I43  plan-1  O2   0.020
 I43  plan-1  N2   0.020
 I43  plan-1  C1   0.020
 I43  plan-1  C2   0.020
 I43  plan-1  C3   0.020
 I43  plan-1  C4   0.020
 I43  plan-1  C5   0.020
 I43  plan-1  C11  0.020
 I43  plan-2  C5   0.020
 I43  plan-2  C11  0.020
 I43  plan-2  C12  0.020
 I43  plan-2  C13  0.020
 I43  plan-2  C14  0.020
 I43  plan-2  H10  0.020

