# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 16:19:32 2020
#   Inital geometry file: a 66 line input string
#   Ligand name: 4-amino-5-fluoro-1-[(2R,5S)-2-(hydroxymethyl)-1,3-oxathiolan-5-yl]pyrimidin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)N(C=C1F)[C@@H]2CS[C@H](CO)O2
#
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
 ETV  ETV  4-amino-5-fluoro-1-[(2R,5S)-2-(hydroxymethyl)-1,3-oxathiolan-5-yl]pyrimidin-2(1H)-one  ligand  26  16  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ETV
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
 ETV  O4    O  OC    0  -0.511   3.5231  -1.7773  -1.4554
 ETV  C9    C  CR6   0   0.609   3.4826  -1.1422  -0.4118
 ETV  N5    N  N     0  -0.533   4.5419  -0.4433   0.0518
 ETV  C10   C  CR6   0   0.408   4.4889   0.2513   1.1661
 ETV  N6    N  NH2   0  -0.802   5.5570   0.9262   1.5735
 ETV  C11   C  CR6   0   0.314   3.2855   0.2825   1.9367
 ETV  F2    F  F     0  -0.300   3.2511   0.9924   3.0744
 ETV  C12   C  CR16  0  -0.072   2.2251  -0.4112   1.5079
 ETV  N4    N  NR6   0  -0.551   2.3011  -1.1180   0.3461
 ETV  C13   C  CH1   0   0.200   1.1332  -1.8593  -0.0886
 ETV  O5    O  O2    0  -0.471   0.7427  -2.7016   0.9670
 ETV  C15   C  CH1   0  -0.101  -0.6402  -2.9148   1.1015
 ETV  C16   C  CH2   0  -0.174  -1.1199  -2.4568   2.4672
 ETV  O6    O  OH1   0  -0.651  -0.9957  -1.0732   2.6682
 ETV  S2    S  S2    0  -0.026  -1.4740  -2.0081  -0.2609
 ETV  C14   C  CH2   0  -0.604  -0.0318  -0.9432  -0.4505
 ETV  HN61  H  HNH2  0   0.413   6.4093   0.8761   1.0407
 ETV  HN62  H  HNH2  0   0.421   5.5696   1.4488   2.4321
 ETV  H12   H  HCR6  0   0.335   1.2949  -0.4371   2.0622
 ETV  H13   H  HCH1  0   0.286   1.4322  -2.4426  -0.9590
 ETV  H15   H  HCH1  0   0.283  -0.8690  -3.9769   0.9766
 ETV  H161  H  HCH2  0   0.246  -0.5165  -2.9528   3.2316
 ETV  H162  H  HCH2  0   0.225  -2.1515  -2.8018   2.5977
 ETV  HO6   H  HOH1  0   0.454  -1.6573  -0.6313   2.1238
 ETV  H141  H  HCH2  0   0.290  -0.0886  -0.0689   0.1988
 ETV  H142  H  HCH2  0   0.310   0.0477  -0.6082  -1.4829

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
 ETV  O4   C9    double    1.222  0.020  1.222
 ETV  C9   N5    aromatic  1.351  0.020  1.351
 ETV  C9   N4    aromatic  1.404  0.020  1.404
 ETV  N5   C10   aromatic  1.314  0.020  1.314
 ETV  C10  N6    single    1.327  0.020  1.327
 ETV  C10  C11   aromatic  1.429  0.020  1.429
 ETV  N6   HN61  single    0.860  0.020  1.020
 ETV  N6   HN62  single    0.860  0.020  1.020
 ETV  C11  F2    single    1.342  0.020  1.342
 ETV  C11  C12   aromatic  1.338  0.020  1.338
 ETV  C12  N4    aromatic  1.362  0.020  1.362
 ETV  C12  H12   single    0.930  0.020  1.080
 ETV  N4   C13   single    1.450  0.020  1.450
 ETV  C13  O5    single    1.406  0.020  1.406
 ETV  C13  C14   single    1.526  0.020  1.526
 ETV  C13  H13   single    0.970  0.020  1.090
 ETV  O5   C15   single    1.406  0.020  1.406
 ETV  C15  C16   single    1.518  0.020  1.518
 ETV  C15  S2    single    1.837  0.020  1.837
 ETV  C15  H15   single    0.970  0.020  1.090
 ETV  C16  O6    single    1.404  0.020  1.404
 ETV  C16  H161  single    0.970  0.020  1.090
 ETV  C16  H162  single    0.970  0.020  1.090
 ETV  O6   HO6   single    0.850  0.020  0.980
 ETV  S2   C14   single    1.803  0.020  1.803
 ETV  C14  H141  single    0.970  0.020  1.090
 ETV  C14  H142  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
 ETV  N4    C9   N5    117.75  3.000
 ETV  N4    C9   O4    119.85  3.000
 ETV  N5    C9   O4    122.39  3.000
 ETV  C10   N5   C9    122.19  3.000
 ETV  C11   C10  N6    120.06  3.000
 ETV  C11   C10  N5    120.17  3.000
 ETV  N6    C10  N5    119.77  3.000
 ETV  HN62  N6   HN61  117.87  3.000
 ETV  HN62  N6   C10   122.45  3.000
 ETV  HN61  N6   C10   119.57  3.000
 ETV  C12   C11  F2    121.73  3.000
 ETV  C12   C11  C10   118.90  3.000
 ETV  F2    C11  C10   119.37  3.000
 ETV  H12   C12  N4    118.17  3.000
 ETV  H12   C12  C11   121.95  3.000
 ETV  N4    C12  C11   119.88  3.000
 ETV  C13   N4   C12   118.43  3.000
 ETV  C13   N4   C9    120.48  3.000
 ETV  C12   N4   C9    121.09  3.000
 ETV  H13   C13  C14   109.97  3.000
 ETV  H13   C13  O5    110.81  3.000
 ETV  C14   C13  O5    109.01  3.000
 ETV  H13   C13  N4    106.99  3.000
 ETV  C14   C13  N4    112.28  3.000
 ETV  O5    C13  N4    107.76  3.000
 ETV  C15   O5   C13   115.85  3.000
 ETV  H15   C15  S2    107.44  3.000
 ETV  H15   C15  C16   109.24  3.000
 ETV  S2    C15  C16   112.02  3.000
 ETV  H15   C15  O5    110.01  3.000
 ETV  S2    C15  O5    107.51  3.000
 ETV  C16   C15  O5    110.56  3.000
 ETV  H162  C16  H161  107.08  3.000
 ETV  H162  C16  O6    112.13  3.000
 ETV  H161  C16  O6    107.36  3.000
 ETV  H162  C16  C15   108.04  3.000
 ETV  H161  C16  C15   108.53  3.000
 ETV  O6    C16  C15   113.46  3.000
 ETV  HO6   O6   C16   108.07  3.000
 ETV  C14   S2   C15    90.37  3.000
 ETV  H142  C14  H141  108.77  3.000
 ETV  H142  C14  S2    109.88  3.000
 ETV  H141  C14  S2    111.67  3.000
 ETV  H142  C14  C13   110.74  3.000
 ETV  H141  C14  C13   112.33  3.000
 ETV  S2    C14  C13   103.37  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
 ETV  CONST_01  C11   C10  N5   C9     0.00   0.0  0
 ETV  CONST_02  C11   C12  N4   C9     0.00   0.0  0
 ETV  CONST_03  C12   N4   C9   N5     0.00   0.0  0
 ETV  CONST_04  C12   C11  C10  N5     0.00   0.0  0
 ETV  CONST_05  N4    C9   N5   C10    0.00   0.0  0
 ETV  CONST_06  N4    C12  C11  C10    0.00   0.0  0
 ETV  CONST_07  C13   N4   C9   N5   180.00   0.0  0
 ETV  CONST_08  C13   N4   C12  C11  180.00   0.0  0
 ETV  CONST_09  C10   N5   C9   O4   180.00   0.0  0
 ETV  CONST_10  C12   N4   C9   O4   180.00   0.0  0
 ETV  CONST_11  C13   N4   C9   O4     0.00   0.0  0
 ETV  CONST_12  N6    C10  N5   C9   180.00   0.0  0
 ETV  CONST_13  F2    C11  C10  N5   180.00   0.0  0
 ETV  CONST_14  C12   C11  C10  N6   180.00   0.0  0
 ETV  CONST_15  N4    C12  C11  F2   180.00   0.0  0
 ETV  CONST_16  H12   C12  N4   C9   180.00   0.0  0
 ETV  CONST_17  HN61  N6   C10  N5     0.00   0.0  0
 ETV  CONST_18  HN62  N6   C10  N5   180.00   0.0  0
 ETV  Var_01    H141  C14  S2   C15  -88.48  30.0  1

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
 ETV  chir_01  C13  N4  O5  C14  negativ
 ETV  chir_02  C15  S2  O5  C16  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
 ETV  plan-1  O4    0.020
 ETV  plan-1  C9    0.020
 ETV  plan-1  N5    0.020
 ETV  plan-1  C10   0.020
 ETV  plan-1  N6    0.020
 ETV  plan-1  C11   0.020
 ETV  plan-1  F2    0.020
 ETV  plan-1  C12   0.020
 ETV  plan-1  N4    0.020
 ETV  plan-1  C13   0.020
 ETV  plan-1  H12   0.020
 ETV  plan-2  C10   0.020
 ETV  plan-2  N6    0.020
 ETV  plan-2  HN61  0.020
 ETV  plan-2  HN62  0.020

