# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 17:29:26 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: 1,2-dideoxy-1-{2,6-dioxo-5-[(1E)-3-oxobut-1-en-1-yl]-1,2,3,6-tetrahydropyrimidin-4-yl}-D-ribo-hexitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)/C=C/C1=C(CC[C@H](O)[C@H](O)[C@H](O)CO)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
 OYV  OYV  1,2-dideoxy-1-{2,6-dioxo-5-[(1E)-3-oxobut-1-en-1-yl]-1,2,3,6-tetrahydropyrimidin-4-yl}-D-ribo-hexitol  ligand  43  23  .  2021-08-17  2021-08-17  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_OYV
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
 OYV  C1   C  C     0   0.364   2.5977  -3.5332  -0.2919
 OYV  C2   C  C1    0  -0.391   3.0386  -2.1588   0.0089
 OYV  C3   C  C1    0  -0.232   2.2883  -1.1089  -0.3697
 OYV  C4   C  CR6   0  -0.187   2.5188   0.3056  -0.1878
 OYV  C5   C  CR6   0   0.467   1.5774   1.2217  -0.5906
 OYV  C6   C  CH2   0  -0.571   0.2450   0.8928  -1.1860
 OYV  C7   C  CH2   0  -0.448  -0.8097   0.7340  -0.0852
 OYV  C8   C  CH1   0   0.019  -2.1701   0.3285  -0.6490
 OYV  C9   C  CH1   0  -0.018  -3.1747   0.0693   0.4919
 OYV  C10  C  CH1   0  -0.035  -4.6265  -0.0784  -0.0101
 OYV  C11  C  CH2   0  -0.160  -5.5010  -0.8011   1.0063
 OYV  N    N  NR16  0  -0.707   1.7824   2.5482  -0.4035
 OYV  C    C  CH3   0  -0.780   3.4995  -4.6211   0.2227
 OYV  C12  C  CR6   0   0.677   2.8934   3.1052   0.1810
 OYV  C13  C  CR6   0   0.573   3.7407   0.8047   0.4325
 OYV  N1   N  NR16  0  -0.715   3.8194   2.1810   0.5658
 OYV  O1   O  OH1   0  -0.662  -2.6278   1.2511  -1.6068
 OYV  O2   O  OH1   0  -0.658  -2.7398  -1.0327   1.2562
 OYV  O3   O  OH1   0  -0.660  -5.1638   1.1855  -0.3395
 OYV  O4   O  OH1   0  -0.671  -6.8137  -0.8572   0.4968
 OYV  O5   O  O     0  -0.462   3.0267   4.2993   0.3319
 OYV  O6   O  O     0  -0.445   4.6638   0.1200   0.8294
 OYV  H3   H  H     0   0.269   3.9707  -2.0456   0.5405
 OYV  H4   H  H     0   0.249   1.3710  -1.3656  -0.8870
 OYV  H6   H  HCH2  0   0.290  -0.0432   1.6926  -1.8697
 OYV  H7   H  HCH2  0   0.284   0.3019  -0.0123  -1.7888
 OYV  H8   H  HCH2  0   0.253  -0.4789  -0.0185   0.6326
 OYV  H9   H  HCH2  0   0.247  -0.9086   1.6733   0.4692
 OYV  H10  H  HCH1  0   0.229  -2.0532  -0.6194  -1.1930
 OYV  H11  H  HCH1  0   0.231  -3.1559   0.9222   1.1841
 OYV  H12  H  HCH1  0   0.234  -4.6329  -0.6575  -0.9417
 OYV  H13  H  HCH2  0   0.206  -5.1019  -1.8033   1.1899
 OYV  H14  H  HCH2  0   0.190  -5.4644  -0.2626   1.9661
 OYV  H15  H  HCH3  0   0.257   3.1569  -5.6065  -0.0846
 OYV  H16  H  HCH3  0   0.262   4.5215  -4.4676  -0.1287
 OYV  H17  H  HCH3  0   0.265   3.5379  -4.5803   1.3137
 OYV  H18  H  HNR6  0   0.431   4.6604   2.5439   0.9978
 OYV  H19  H  HOH1  0   0.442  -3.0210   2.0053  -1.1556
 OYV  H20  H  HOH1  0   0.449  -2.6729  -1.8044   0.6823
 OYV  H21  H  HOH1  0   0.444  -5.3005   1.6793   0.4769
 OYV  H22  H  HOH1  0   0.455  -7.3488  -1.3568   1.1195
 OYV  O7   O  O     0  -0.427   1.5751  -3.7817  -0.9057
 OYV  H1   H  HNR6  0   0.440   1.0751   3.2002  -0.7161

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
 OYV  O4   C11  single  1.409  0.020  1.409
 OYV  C11  C10  single  1.523  0.020  1.523
 OYV  O2   C9   single  1.410  0.020  1.410
 OYV  C7   C8   single  1.527  0.020  1.527
 OYV  C7   C6   single  1.533  0.020  1.533
 OYV  C8   C9   single  1.542  0.020  1.542
 OYV  C8   O1   single  1.406  0.020  1.406
 OYV  C10  C9   single  1.543  0.020  1.543
 OYV  C10  O3   single  1.412  0.020  1.412
 OYV  O5   C12  double  1.211  0.020  1.211
 OYV  N    C12  single  1.373  0.020  1.373
 OYV  N    C5   single  1.355  0.020  1.355
 OYV  C6   C5   single  1.496  0.020  1.496
 OYV  C12  N1   single  1.364  0.020  1.364
 OYV  C5   C4   double  1.374  0.020  1.374
 OYV  N1   C13  single  1.385  0.020  1.385
 OYV  C4   C13  single  1.458  0.020  1.458
 OYV  C4   C3   single  1.445  0.020  1.445
 OYV  C13  O6   double  1.216  0.020  1.216
 OYV  C3   C2   double  1.345  0.020  1.345
 OYV  C    C1   single  1.504  0.020  1.504
 OYV  C2   C1   single  1.474  0.020  1.474
 OYV  C2   H3   single  0.930  0.020  1.080
 OYV  C3   H4   single  0.930  0.020  1.080
 OYV  C6   H6   single  0.970  0.020  1.090
 OYV  C6   H7   single  0.970  0.020  1.090
 OYV  C7   H8   single  0.970  0.020  1.090
 OYV  C7   H9   single  0.970  0.020  1.090
 OYV  C8   H10  single  0.970  0.020  1.090
 OYV  C9   H11  single  0.970  0.020  1.090
 OYV  C10  H12  single  0.970  0.020  1.090
 OYV  C11  H13  single  0.970  0.020  1.090
 OYV  C11  H14  single  0.970  0.020  1.090
 OYV  C    H15  single  0.970  0.020  1.090
 OYV  C    H16  single  0.970  0.020  1.090
 OYV  C    H17  single  0.970  0.020  1.090
 OYV  N1   H18  single  0.860  0.020  1.020
 OYV  O1   H19  single  0.850  0.020  0.980
 OYV  O2   H20  single  0.850  0.020  0.980
 OYV  O3   H21  single  0.850  0.020  0.980
 OYV  O4   H22  single  0.850  0.020  0.980
 OYV  C1   O7   double  1.218  0.020  1.218
 OYV  N    H1   single  0.860  0.020  1.020

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
 OYV  O7   C1   C    121.88  3.000
 OYV  O7   C1   C2   122.95  3.000
 OYV  C    C1   C2   115.16  3.000
 OYV  H3   C2   C3   122.60  3.000
 OYV  H3   C2   C1   117.17  3.000
 OYV  C3   C2   C1   120.23  3.000
 OYV  H4   C3   C4   115.28  3.000
 OYV  H4   C3   C2   114.94  3.000
 OYV  C4   C3   C2   129.79  3.000
 OYV  C13  C4   C5   118.07  3.000
 OYV  C13  C4   C3   121.49  3.000
 OYV  C5   C4   C3   120.44  3.000
 OYV  N    C5   C6   113.89  3.000
 OYV  C6   C5   C4   125.48  3.000
 OYV  N    C5   C4   120.56  3.000
 OYV  H7   C6   H6   106.03  3.000
 OYV  H7   C6   C7   110.33  3.000
 OYV  H6   C6   C7   110.13  3.000
 OYV  H7   C6   C5   110.89  3.000
 OYV  H6   C6   C5   108.88  3.000
 OYV  C7   C6   C5   110.48  3.000
 OYV  H9   C7   H8   106.60  3.000
 OYV  H9   C7   C8   109.52  3.000
 OYV  H8   C7   C8   109.25  3.000
 OYV  H9   C7   C6   109.68  3.000
 OYV  H8   C7   C6   109.58  3.000
 OYV  C8   C7   C6   112.04  3.000
 OYV  H10  C8   O1   105.27  3.000
 OYV  H10  C8   C9   106.88  3.000
 OYV  O1   C8   C9   113.71  3.000
 OYV  H10  C8   C7   108.48  3.000
 OYV  O1   C8   C7   111.54  3.000
 OYV  C9   C8   C7   110.59  3.000
 OYV  H11  C9   O2   105.07  3.000
 OYV  H11  C9   C10  107.18  3.000
 OYV  O2   C9   C10  113.06  3.000
 OYV  H11  C9   C8   108.94  3.000
 OYV  C10  C9   C8   112.85  3.000
 OYV  O2   C9   C8   109.36  3.000
 OYV  H12  C10  O3   105.80  3.000
 OYV  H12  C10  C11  108.23  3.000
 OYV  O3   C10  C11  111.21  3.000
 OYV  H12  C10  C9   109.40  3.000
 OYV  O3   C10  C9   110.37  3.000
 OYV  C11  C10  C9   111.62  3.000
 OYV  H14  C11  H13  106.83  3.000
 OYV  H14  C11  O4   111.45  3.000
 OYV  H13  C11  O4   111.34  3.000
 OYV  H14  C11  C10  109.30  3.000
 OYV  H13  C11  C10  109.70  3.000
 OYV  O4   C11  C10  108.20  3.000
 OYV  H1   N    C12  115.83  3.000
 OYV  H1   N    C5   118.84  3.000
 OYV  C12  N    C5   125.32  3.000
 OYV  H17  C    H16  106.45  3.000
 OYV  H17  C    H15  109.09  3.000
 OYV  H16  C    H15  109.35  3.000
 OYV  H17  C    C1   109.62  3.000
 OYV  H16  C    C1   110.46  3.000
 OYV  H15  C    C1   111.71  3.000
 OYV  O5   C12  N1   123.94  3.000
 OYV  N1   C12  N    113.23  3.000
 OYV  O5   C12  N    122.83  3.000
 OYV  O6   C13  N1   119.01  3.000
 OYV  O6   C13  C4   125.61  3.000
 OYV  N1   C13  C4   115.38  3.000
 OYV  H18  N1   C13  116.38  3.000
 OYV  H18  N1   C12  116.19  3.000
 OYV  C13  N1   C12  127.43  3.000
 OYV  H19  O1   C8   109.12  3.000
 OYV  H20  O2   C9   108.93  3.000
 OYV  H21  O3   C10  108.36  3.000
 OYV  H22  O4   C11  107.76  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
 OYV  CONST_01  C12  N1   C13  C4      0.00   0.0  0
 OYV  CONST_02  N1   C12  N    C5      0.00   0.0  0
 OYV  CONST_03  C13  N1   C12  N       0.00   0.0  0
 OYV  CONST_04  O5   C12  N    C5    180.00   0.0  0
 OYV  CONST_05  O6   C13  N1   C12   180.00   0.0  0
 OYV  CONST_06  O5   C12  N1   C13   180.00   0.0  0
 OYV  CONST_07  H18  N1   C13  C4    180.00   0.0  0
 OYV  CONST_08  H1   N    C12  N1    180.00   0.0  0
 OYV  CONST_09  C4   C3   C2   C1    180.00   0.0  0
 OYV  CONST_10  H3   C2   C3   C4      0.00   0.0  0
 OYV  CONST_11  H4   C3   C2   C1      0.00   0.0  0
 OYV  Var_01    C5   C4   C3   C2   -176.30  30.0  2
 OYV  Var_02    C7   C6   C5   C4     89.16  30.0  1
 OYV  Var_03    C8   C7   C6   C5   -177.14  30.0  1
 OYV  Var_04    C    C1   C2   C3   -178.07  30.0  2
 OYV  Var_05    H15  C    C1   C2   -176.32  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 OYV  chir_01  C8   C7  C9   O1   negativ
 OYV  chir_02  C9   O2  C10  C8   positiv
 OYV  chir_03  C10  O3  C9   C11  negativ

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
 OYV  plan-1  C3   0.020
 OYV  plan-1  C4   0.020
 OYV  plan-1  C5   0.020
 OYV  plan-1  C6   0.020
 OYV  plan-1  N    0.020
 OYV  plan-1  C12  0.020
 OYV  plan-1  C13  0.020
 OYV  plan-1  N1   0.020
 OYV  plan-1  O5   0.020
 OYV  plan-1  O6   0.020
 OYV  plan-1  H18  0.020
 OYV  plan-1  H1   0.020
 OYV  plan-2  C1   0.020
 OYV  plan-2  C2   0.020
 OYV  plan-2  C    0.020
 OYV  plan-2  O7   0.020
 OYV  plan-3  C1   0.020
 OYV  plan-3  C2   0.020
 OYV  plan-3  C3   0.020
 OYV  plan-3  C4   0.020
 OYV  plan-3  H3   0.020
 OYV  plan-3  H4   0.020

