# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Aug  1 23:57:57 2021
#   Inital geometry file: a 119 line input string
#   Ligand name: [[[(2~{R},3~{S},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]methylphosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)C[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
 SFV  SFV  '[[[(2~{R},3~{S},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]methylphosphonic acid'  ligand  46  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
;

data_comp_SFV
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
 SFV  C3B  C  CH2   0  -1.034   4.6178   1.2205  14.7387
 SFV  O2B  O  OH1   0  -0.728   2.7189   3.1382  14.2122
 SFV  PA   P  P     0   1.505   5.1983   5.2448  14.7474
 SFV  O1A  O  OH1   0  -0.733   3.9043   5.4112  15.6449
 SFV  O2A  O  O     0  -0.659   6.5191   5.4408  15.3541
 SFV  O3A  O  O2    0  -0.704   5.1099   3.7703  14.0802
 SFV  O5'  O  O2    0  -0.579   4.9214   6.2444  13.5554
 SFV  PB   P  P     0   1.423   4.1098   2.5791  13.6777
 SFV  O1B  O  O     0  -0.671   4.1877   2.2664  12.2298
 SFV  PG   P  P     0   1.395   4.1490   1.3277  16.4843
 SFV  O1G  O  OH1   0  -0.733   5.1179   0.2937  17.2291
 SFV  O2G  O  O     0  -0.690   2.7049   1.1482  16.7449
 SFV  O3G  O  OH1   0  -0.757   4.7911   2.7474  16.8817
 SFV  C5'  C  CH2   0  -0.227   3.6801   6.4104  12.8570
 SFV  C4'  C  CH1   0   0.016   3.9243   6.5120  11.3739
 SFV  O4'  O  O2    0  -0.501   4.7733   7.6133  11.0842
 SFV  C1'  C  CH1   0   0.202   5.5204   7.3680   9.9220
 SFV  N1   N  NR6   0  -0.549   6.9569   7.4634  10.2365
 SFV  C6   C  CR16  0   0.082   7.4358   7.3284  11.4915
 SFV  C2   C  CR6   0   0.594   7.8301   7.6635   9.1571
 SFV  O2   O  O     0  -0.528   7.3598   7.7361   8.0268
 SFV  N3   N  N     0  -0.539   9.1492   7.7657   9.4084
 SFV  C4   C  CR6   0   0.514   9.6160   7.6414  10.6366
 SFV  N4   N  NH2   0  -0.811  10.9324   7.7410  10.8232
 SFV  C5   C  CR16  0  -0.477   8.7586   7.4019  11.7508
 SFV  C2'  C  CH2   0  -0.534   5.1190   5.9800   9.4282
 SFV  C3'  C  CH1   0   0.003   4.5782   5.3106  10.6852
 SFV  O3'  O  OH1   0  -0.696   3.6717   4.2867  10.4051
 SFV  H1   H  HCH2  0   0.349   4.1623   0.3085  14.3429
 SFV  H2   H  HCH2  0   0.351   5.6994   1.1029  14.6373
 SFV  H3   H  HOH1  0   0.513   1.9441   2.6084  13.9745
 SFV  H4   H  HOH1  0   0.499   3.8389   4.8103  16.4014
 SFV  H5   H  HOH1  0   0.502   4.6737  -0.5091  17.5336
 SFV  H6   H  HOH1  0   0.508   4.7925   2.9349  17.8324
 SFV  H7   H  HCH2  0   0.282   3.2032   7.3157  13.2346
 SFV  H8   H  HCH2  0   0.250   2.9917   5.5805  13.0319
 SFV  H9   H  HCH1  0   0.249   2.9358   6.6701  10.9190
 SFV  H10  H  HCH1  0   0.271   5.3157   8.1422   9.1833
 SFV  H11  H  HCR6  0   0.318   6.7176   7.1712  12.2798
 SFV  H12  H  HNH2  0   0.401  11.5377   7.9508  10.0479
 SFV  H13  H  HNH2  0   0.412  11.3378   7.6967  11.7413
 SFV  H14  H  HCR6  0   0.283   9.1359   7.2995  12.7571
 SFV  H15  H  HCH2  0   0.262   4.3152   6.0752   8.6942
 SFV  H16  H  HCH2  0   0.278   5.9401   5.4392   8.9619
 SFV  H17  H  HCH1  0   0.226   5.4175   4.9470  11.2929
 SFV  H18  H  HOH1  0   0.460   3.8257   3.5452  11.0153

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
 SFV  O2   C2   double  1.226  0.020  1.226
 SFV  C2   N3   single  1.347  0.020  1.347
 SFV  C2   N1   single  1.403  0.020  1.403
 SFV  N3   C4   double  1.320  0.020  1.320
 SFV  C2'  C1'  single  1.527  0.020  1.527
 SFV  C2'  C3'  single  1.523  0.020  1.523
 SFV  C1'  N1   single  1.474  0.020  1.474
 SFV  C1'  O4'  single  1.403  0.020  1.403
 SFV  N1   C6   single  1.350  0.020  1.350
 SFV  C4   N4   single  1.333  0.020  1.333
 SFV  C4   C5   single  1.426  0.020  1.426
 SFV  O3'  C3'  single  1.396  0.020  1.396
 SFV  C3'  C4'  single  1.531  0.020  1.531
 SFV  O4'  C4'  single  1.420  0.020  1.420
 SFV  C4'  C5'  single  1.507  0.020  1.507
 SFV  C6   C5   double  1.350  0.020  1.350
 SFV  O1B  PB   double  1.483  0.020  1.483
 SFV  C5'  O5'  single  1.434  0.020  1.434
 SFV  O5'  PA   single  1.580  0.020  1.580
 SFV  PB   O3A  single  1.607  0.020  1.607
 SFV  PB   O2B  single  1.591  0.020  1.591
 SFV  PB   C3B  single  1.797  0.020  1.797
 SFV  O3A  PA   single  1.621  0.020  1.621
 SFV  C3B  PG   single  1.811  0.020  1.811
 SFV  PA   O2A  double  1.467  0.020  1.467
 SFV  PA   O1A  single  1.584  0.020  1.584
 SFV  PG   O2G  double  1.478  0.020  1.478
 SFV  PG   O3G  single  1.608  0.020  1.608
 SFV  PG   O1G  single  1.601  0.020  1.601
 SFV  C3B  H1   single  0.970  0.020  1.090
 SFV  C3B  H2   single  0.970  0.020  1.090
 SFV  O2B  H3   single  0.850  0.020  0.980
 SFV  O1A  H4   single  0.850  0.020  0.980
 SFV  O1G  H5   single  0.850  0.020  0.980
 SFV  O3G  H6   single  0.850  0.020  0.980
 SFV  C5'  H7   single  0.970  0.020  1.090
 SFV  C5'  H8   single  0.970  0.020  1.090
 SFV  C4'  H9   single  0.970  0.020  1.090
 SFV  C1'  H10  single  0.970  0.020  1.090
 SFV  C6   H11  single  0.930  0.020  1.080
 SFV  N4   H12  single  0.860  0.020  1.020
 SFV  N4   H13  single  0.860  0.020  1.020
 SFV  C5   H14  single  0.930  0.020  1.080
 SFV  C2'  H15  single  0.970  0.020  1.090
 SFV  C2'  H16  single  0.970  0.020  1.090
 SFV  C3'  H17  single  0.970  0.020  1.090
 SFV  O3'  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
 SFV  H2   C3B  H1   106.80  3.000
 SFV  H2   C3B  PG   110.62  3.000
 SFV  H1   C3B  PG   106.89  3.000
 SFV  H2   C3B  PB   107.84  3.000
 SFV  H1   C3B  PB   107.40  3.000
 SFV  PG   C3B  PB   116.82  3.000
 SFV  H3   O2B  PB   115.13  3.000
 SFV  O5'  PA   O3A  104.79  3.000
 SFV  O3A  PA   O2A  109.94  3.000
 SFV  O5'  PA   O2A  112.67  3.000
 SFV  O2A  PA   O1A  119.17  3.000
 SFV  O3A  PA   O1A  106.52  3.000
 SFV  O5'  PA   O1A  102.58  3.000
 SFV  H4   O1A  PA   115.64  3.000
 SFV  PB   O3A  PA   144.25  3.000
 SFV  C5'  O5'  PA   126.32  3.000
 SFV  O1B  PB   O3A  111.60  3.000
 SFV  O3A  PB   O2B  101.51  3.000
 SFV  O1B  PB   O2B  116.60  3.000
 SFV  O2B  PB   C3B  108.32  3.000
 SFV  O3A  PB   C3B  103.69  3.000
 SFV  O1B  PB   C3B  113.71  3.000
 SFV  O3G  PG   O2G  116.98  3.000
 SFV  O3G  PG   O1G  102.33  3.000
 SFV  O2G  PG   O1G  115.52  3.000
 SFV  O1G  PG   C3B  104.69  3.000
 SFV  O3G  PG   C3B  100.79  3.000
 SFV  O2G  PG   C3B  114.56  3.000
 SFV  H5   O1G  PG   113.88  3.000
 SFV  H6   O3G  PG   114.45  3.000
 SFV  H8   C5'  H7   107.43  3.000
 SFV  H8   C5'  C4'  108.12  3.000
 SFV  H7   C5'  C4'  110.84  3.000
 SFV  H8   C5'  O5'  112.31  3.000
 SFV  H7   C5'  O5'  107.82  3.000
 SFV  C4'  C5'  O5'  110.30  3.000
 SFV  H9   C4'  C3'  108.10  3.000
 SFV  H9   C4'  O4'  109.96  3.000
 SFV  C3'  C4'  O4'  105.15  3.000
 SFV  H9   C4'  C5'  105.74  3.000
 SFV  O4'  C4'  C5'  110.49  3.000
 SFV  C3'  C4'  C5'  117.33  3.000
 SFV  C1'  O4'  C4'  110.59  3.000
 SFV  H10  C1'  C2'  112.16  3.000
 SFV  H10  C1'  N1   106.37  3.000
 SFV  C2'  C1'  N1   112.59  3.000
 SFV  H10  C1'  O4'  109.71  3.000
 SFV  N1   C1'  O4'  109.33  3.000
 SFV  C2'  C1'  O4'  106.67  3.000
 SFV  C2   N1   C6   120.58  3.000
 SFV  C6   N1   C1'  122.53  3.000
 SFV  C2   N1   C1'  116.87  3.000
 SFV  H11  C6   C5   121.35  3.000
 SFV  H11  C6   N1   117.26  3.000
 SFV  C5   C6   N1   121.38  3.000
 SFV  N3   C2   O2   122.90  3.000
 SFV  N3   C2   N1   118.49  3.000
 SFV  O2   C2   N1   118.61  3.000
 SFV  C4   N3   C2   120.86  3.000
 SFV  C5   C4   N4   119.79  3.000
 SFV  C5   C4   N3   122.02  3.000
 SFV  N4   C4   N3   118.19  3.000
 SFV  H13  N4   H12  118.09  3.000
 SFV  H13  N4   C4   121.53  3.000
 SFV  H12  N4   C4   120.13  3.000
 SFV  H14  C5   C4   122.28  3.000
 SFV  H14  C5   C6   121.09  3.000
 SFV  C4   C5   C6   116.62  3.000
 SFV  H16  C2'  H15  108.09  3.000
 SFV  H16  C2'  C3'  113.77  3.000
 SFV  H15  C2'  C3'  109.35  3.000
 SFV  H16  C2'  C1'  113.08  3.000
 SFV  H15  C2'  C1'  109.36  3.000
 SFV  C3'  C2'  C1'  103.05  3.000
 SFV  H17  C3'  O3'  111.38  3.000
 SFV  H17  C3'  C2'  109.32  3.000
 SFV  O3'  C3'  C2'  112.78  3.000
 SFV  H17  C3'  C4'  109.71  3.000
 SFV  O3'  C3'  C4'  112.86  3.000
 SFV  C2'  C3'  C4'  100.25  3.000
 SFV  H18  O3'  C3'  109.30  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
 SFV  CONST_01  N3   C2   N1   C1'   180.00   0.0  0
 SFV  CONST_02  C4   N3   C2   N1      0.00   0.0  0
 SFV  CONST_03  N3   C2   N1   C6      0.00   0.0  0
 SFV  CONST_04  C5   C4   N3   C2      0.00   0.0  0
 SFV  CONST_05  O2   C2   N1   C1'     0.00   0.0  0
 SFV  CONST_06  O2   C2   N1   C6    180.00   0.0  0
 SFV  CONST_07  N4   C4   N3   C2    180.00   0.0  0
 SFV  CONST_08  C4   N3   C2   O2    180.00   0.0  0
 SFV  CONST_09  H12  N4   C4   N3      0.00   0.0  0
 SFV  CONST_10  H13  N4   C4   N3    180.00   0.0  0
 SFV  Var_01    C4'  C5'  O5'  PA   -136.86  30.0  1
 SFV  Var_02    PG   C3B  PB   O2B   -32.73  30.0  3
 SFV  Var_03    O1B  PB   O3A  PA    122.51  30.0  2
 SFV  Var_04    O2G  PG   C3B  PB     70.73  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
 SFV  chir_03  C4'  C3'  O4'  C5'  positiv
 SFV  chir_04  C1'  O4'  N1   C2'  negativ
 SFV  chir_05  C3'  O3'  C4'  C2'  positiv
 SFV  chir_06  PA   O3A  O2A  O1A  both
 SFV  chir_07  PB   O3A  O2B  C3B  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
 SFV  plan-1  C1'  0.020
 SFV  plan-1  N1   0.020
 SFV  plan-1  C6   0.020
 SFV  plan-1  C2   0.020
 SFV  plan-1  O2   0.020
 SFV  plan-1  N3   0.020
 SFV  plan-1  C4   0.020
 SFV  plan-1  N4   0.020
 SFV  plan-1  C5   0.020
 SFV  plan-1  H11  0.020
 SFV  plan-1  H12  0.020
 SFV  plan-1  H13  0.020
 SFV  plan-1  H14  0.020

