# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 07:56:21 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: [[(2S,5R)-5-(4-azanyl-5-fluoranyl-2-oxidanylidene-pyrimidin-1-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)N(C=C1F)[C@H]2CC[C@@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)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
 4Y3  4Y3  '[[(2S,5R)-5-(4-azanyl-5-fluoranyl-2-oxidanylidene-pyrimidin-1-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate'  ligand  43  28  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_4Y3
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
 4Y3  N1   N  NR6   0  -0.507   3.2507  -0.0775   0.5622
 4Y3  C2   C  CR6   0   0.614   2.3767  -0.5858  -0.3819
 4Y3  C4   C  CR6   0   0.438   2.7596  -2.7525   0.4446
 4Y3  C5   C  CR6   0   0.210   3.7668  -2.2399   1.3103
 4Y3  PA   P  P     0   1.444  -1.3199   2.1678   1.5838
 4Y3  PB   P  P     0   1.508  -2.9181   0.0761   0.3585
 4Y3  PG   P  P     0   1.492  -1.3007  -1.4172  -1.4953
 4Y3  C5'  C  CH2   0  -0.200   0.2823   2.6425  -0.5156
 4Y3  O5'  O  O2    0  -0.526  -0.6137   1.8017   0.2120
 4Y3  C4'  C  CH1   0   0.047   1.6000   2.8801   0.2047
 4Y3  O4'  O  O2    0  -0.526   1.9354   1.7732   1.0262
 4Y3  S    C  CH2   0  -0.441   2.7437   3.0564  -0.8002
 4Y3  C2'  C  CH2   0  -0.512   3.9016   2.2805  -0.1755
 4Y3  C1'  C  CH1   0   0.156   3.2534   1.3689   0.8636
 4Y3  O1A  O  OH1   0  -0.754  -0.3626   1.8309   2.7906
 4Y3  O1B  O  O     0  -0.735  -3.5251   0.8635  -0.7206
 4Y3  O1G  O  OH1   0  -0.711  -0.3068  -2.5759  -1.2068
 4Y3  O2   O  O     0  -0.458   1.8540   0.1628  -1.1981
 4Y3  O2A  O  O     0  -0.816  -1.8832   3.5216   1.7022
 4Y3  O2B  O  OH1   0  -0.711  -3.9407  -0.9102   1.0420
 4Y3  O2G  O  O     0  -0.680  -2.5335  -1.8109  -2.1956
 4Y3  N3   N  N     0  -0.516   2.0960  -1.9173  -0.3413
 4Y3  O3A  O  O2    0  -0.655  -2.4279   0.9819   1.6128
 4Y3  O3B  O  O2    0  -0.629  -1.6330  -0.8264   0.0290
 4Y3  O3G  O  OH1   0  -0.665  -0.5344  -0.2281  -2.2048
 4Y3  N4   N  NH2   0  -0.834   2.4747  -4.0436   0.4379
 4Y3  C6   C  CR16  0  -0.038   3.9436  -0.9134   1.3801
 4Y3  F    F  F     0  -0.303   4.4539  -3.0886   2.0833
 4Y3  H1   H  HCH2  0   0.264   0.4335   2.1171  -1.4534
 4Y3  H2   H  HCH2  0   0.309  -0.1846   3.6013  -0.7474
 4Y3  H3   H  HCH1  0   0.232   1.5055   3.7575   0.8558
 4Y3  H4   H  HCH2  0   0.209   2.4733   2.6384  -1.7697
 4Y3  H5   H  HCH2  0   0.288   2.9884   4.1058  -0.9517
 4Y3  H6   H  HCH2  0   0.271   4.4862   1.7223  -0.9048
 4Y3  H7   H  HCH2  0   0.270   4.5761   2.9559   0.3493
 4Y3  H8   H  HCH1  0   0.325   3.7857   1.4354   1.8129
 4Y3  H9   H  HOH1  0   0.478   0.1516   1.0152   2.7112
 4Y3  H10  H  HOH1  0   0.480   0.6386  -2.3422  -0.8875
 4Y3  H11  H  HOH1  0   0.491  -3.5575  -1.6807   1.4843
 4Y3  H12  H  HOH1  0   0.520   0.3611  -0.0248  -1.8441
 4Y3  H13  H  HNH2  0   0.394   1.7547  -4.4112  -0.1615
 4Y3  H14  H  HNH2  0   0.418   2.9283  -4.6911   1.0599
 4Y3  H15  H  HCR6  0   0.359   4.6483  -0.4680   2.0709

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
 4Y3  O2G  PG   double  1.471  0.020  1.471
 4Y3  O3G  PG   single  1.583  0.020  1.583
 4Y3  PG   O3B  single  1.668  0.020  1.668
 4Y3  PG   O1G  single  1.554  0.020  1.554
 4Y3  O3B  PB   single  1.604  0.020  1.604
 4Y3  O1B  PB   double  1.467  0.020  1.467
 4Y3  PB   O2B  single  1.577  0.020  1.577
 4Y3  PB   O3A  single  1.623  0.020  1.623
 4Y3  O3A  PA   single  1.623  0.020  1.623
 4Y3  PA   O2A  double  1.471  0.020  1.471
 4Y3  PA   O5'  single  1.586  0.020  1.586
 4Y3  PA   O1A  single  1.577  0.020  1.577
 4Y3  O5'  C5'  single  1.428  0.020  1.428
 4Y3  S    C2'  single  1.527  0.020  1.527
 4Y3  S    C4'  single  1.533  0.020  1.533
 4Y3  C5'  C4'  single  1.520  0.020  1.520
 4Y3  C2'  C1'  single  1.527  0.020  1.527
 4Y3  C4'  O4'  single  1.419  0.020  1.419
 4Y3  C1'  O4'  single  1.388  0.020  1.388
 4Y3  C1'  N1   single  1.477  0.020  1.477
 4Y3  C6   N1   single  1.359  0.020  1.359
 4Y3  C6   C5   double  1.340  0.020  1.340
 4Y3  F    C5   single  1.338  0.020  1.338
 4Y3  N1   C2   single  1.383  0.020  1.383
 4Y3  C5   C4   single  1.424  0.020  1.424
 4Y3  C2   O2   double  1.225  0.020  1.225
 4Y3  C2   N3   single  1.361  0.020  1.361
 4Y3  C4   N3   double  1.325  0.020  1.325
 4Y3  C4   N4   single  1.322  0.020  1.322
 4Y3  C5'  H1   single  0.970  0.020  1.090
 4Y3  C5'  H2   single  0.970  0.020  1.090
 4Y3  C4'  H3   single  0.970  0.020  1.090
 4Y3  S    H4   single  0.970  0.020  1.090
 4Y3  S    H5   single  0.970  0.020  1.090
 4Y3  C2'  H6   single  0.970  0.020  1.090
 4Y3  C2'  H7   single  0.970  0.020  1.090
 4Y3  C1'  H8   single  0.970  0.020  1.090
 4Y3  O1A  H9   single  0.850  0.020  0.980
 4Y3  O1G  H10  single  0.850  0.020  0.980
 4Y3  O2B  H11  single  0.850  0.020  0.980
 4Y3  O3G  H12  single  0.850  0.020  0.980
 4Y3  N4   H13  single  0.860  0.020  1.020
 4Y3  N4   H14  single  0.860  0.020  1.020
 4Y3  C6   H15  single  0.930  0.020  1.080

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
 4Y3  C6   N1   C1'  118.58  3.000
 4Y3  C6   N1   C2   120.45  3.000
 4Y3  C1'  N1   C2   120.01  3.000
 4Y3  N3   C2   O2   121.99  3.000
 4Y3  N3   C2   N1   117.99  3.000
 4Y3  O2   C2   N1   119.99  3.000
 4Y3  N4   C4   N3   120.30  3.000
 4Y3  N4   C4   C5   120.48  3.000
 4Y3  N3   C4   C5   119.22  3.000
 4Y3  F    C5   C6   122.01  3.000
 4Y3  F    C5   C4   119.09  3.000
 4Y3  C6   C5   C4   118.78  3.000
 4Y3  O3A  PA   O2A  114.17  3.000
 4Y3  O2A  PA   O1A  111.56  3.000
 4Y3  O3A  PA   O1A  104.16  3.000
 4Y3  O1A  PA   O5'  110.02  3.000
 4Y3  O2A  PA   O5'  116.92  3.000
 4Y3  O3A  PA   O5'   98.67  3.000
 4Y3  O3B  PB   O3A  103.34  3.000
 4Y3  O3A  PB   O2B  102.12  3.000
 4Y3  O3B  PB   O2B  104.87  3.000
 4Y3  O3A  PB   O1B  113.20  3.000
 4Y3  O2B  PB   O1B  112.72  3.000
 4Y3  O3B  PB   O1B  118.82  3.000
 4Y3  O3G  PG   O3B  103.88  3.000
 4Y3  O3B  PG   O2G  111.27  3.000
 4Y3  O3G  PG   O2G  113.16  3.000
 4Y3  O3B  PG   O1G  102.82  3.000
 4Y3  O3G  PG   O1G  109.51  3.000
 4Y3  O2G  PG   O1G  115.14  3.000
 4Y3  H2   C5'  H1   107.54  3.000
 4Y3  H2   C5'  C4'  109.52  3.000
 4Y3  H1   C5'  C4'  111.36  3.000
 4Y3  H2   C5'  O5'  110.92  3.000
 4Y3  H1   C5'  O5'  104.04  3.000
 4Y3  C4'  C5'  O5'  113.23  3.000
 4Y3  C5'  O5'  PA   125.75  3.000
 4Y3  H3   C4'  S    111.20  3.000
 4Y3  H3   C4'  O4'  107.51  3.000
 4Y3  S    C4'  O4'  107.04  3.000
 4Y3  H3   C4'  C5'  109.37  3.000
 4Y3  O4'  C4'  C5'  110.93  3.000
 4Y3  S    C4'  C5'  110.74  3.000
 4Y3  C1'  O4'  C4'  112.57  3.000
 4Y3  H5   S    H4   107.56  3.000
 4Y3  H5   S    C2'  112.11  3.000
 4Y3  H4   S    C2'  110.92  3.000
 4Y3  H5   S    C4'  111.72  3.000
 4Y3  H4   S    C4'  110.73  3.000
 4Y3  C2'  S    C4'  103.84  3.000
 4Y3  H7   C2'  H6   107.95  3.000
 4Y3  H7   C2'  C1'  107.78  3.000
 4Y3  H6   C2'  C1'  112.20  3.000
 4Y3  H7   C2'  S    110.58  3.000
 4Y3  H6   C2'  S    113.17  3.000
 4Y3  C1'  C2'  S    105.06  3.000
 4Y3  H8   C1'  C2'  110.42  3.000
 4Y3  H8   C1'  O4'  110.11  3.000
 4Y3  C2'  C1'  O4'  108.00  3.000
 4Y3  H8   C1'  N1   103.78  3.000
 4Y3  O4'  C1'  N1   107.89  3.000
 4Y3  C2'  C1'  N1   116.52  3.000
 4Y3  H9   O1A  PA   116.10  3.000
 4Y3  H10  O1G  PG   118.54  3.000
 4Y3  H11  O2B  PB   116.07  3.000
 4Y3  C4   N3   C2   122.06  3.000
 4Y3  PB   O3A  PA   126.87  3.000
 4Y3  PG   O3B  PB   123.12  3.000
 4Y3  H12  O3G  PG   115.50  3.000
 4Y3  H14  N4   H13  117.11  3.000
 4Y3  H14  N4   C4   121.89  3.000
 4Y3  H13  N4   C4   120.92  3.000
 4Y3  H15  C6   C5   121.76  3.000
 4Y3  H15  C6   N1   117.56  3.000
 4Y3  C5   C6   N1   120.67  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
 4Y3  CONST_01  C4   N3   C2   N1     0.00   0.0  0
 4Y3  CONST_02  C5   C4   N3   C2     0.00   0.0  0
 4Y3  CONST_04  C6   N1   C2   N3     0.00   0.0  0
 4Y3  CONST_05  N4   C4   N3   C2   180.00   0.0  0
 4Y3  CONST_06  O2   C2   N3   C4   180.00   0.0  0
 4Y3  CONST_08  C6   N1   C2   O2   180.00   0.0  0
 4Y3  CONST_09  H13  N4   C4   C5   180.00   0.0  0
 4Y3  CONST_10  H14  N4   C4   C5     0.00   0.0  0
 4Y3  Var_01    C1'  C2'  S    C4'   17.57  30.0  1
 4Y3  Var_02    C4'  C5'  O5'  PA    67.09  30.0  3
 4Y3  Var_03    O3B  PB   O3A  PA    69.08  30.0  1
 4Y3  Var_04    O2G  PG   O3B  PB   -37.29  30.0  3
 4Y3  Var_05    O2A  PA   O3A  PB   107.09  30.0  3
 4Y3  Var_06    O3A  PA   O5'  C5'  166.30  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
 4Y3  chir_03  C4'  S    C5'  O4'  negativ
 4Y3  chir_04  C1'  O4'  N1   C2'  negativ
 4Y3  chir_05  PA   O2A  O5'  O1A  both
 4Y3  chir_06  PB   O2B  O1B  O3B  both

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
 4Y3  plan-1  N1   0.020
 4Y3  plan-1  C2   0.020
 4Y3  plan-1  C4   0.020
 4Y3  plan-1  C5   0.020
 4Y3  plan-1  C1'  0.020
 4Y3  plan-1  O2   0.020
 4Y3  plan-1  N3   0.020
 4Y3  plan-1  N4   0.020
 4Y3  plan-1  C6   0.020
 4Y3  plan-1  F    0.020
 4Y3  plan-1  H13  0.020
 4Y3  plan-1  H14  0.020
 4Y3  plan-1  H15  0.020

