# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 12:14:29 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: [[[[(2R,5S)-5-(4-azanyl-5-fluoranyl-2-oxidanylidene-pyrimidin-1-yl)-1,3-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]amino]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)N(C=C1F)[C@@H]2CS[C@H](CO[P](O)(=O)O[P](O)(=O)N[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
 0G4  0G4  '[[[[(2R,5S)-5-(4-azanyl-5-fluoranyl-2-oxidanylidene-pyrimidin-1-yl)-1,3-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]amino]phosphonic acid'  ligand  38  28  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_0G4
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
 0G4  F5   F  F      0  -0.302  -1.5255   1.9909  -2.0053
 0G4  C5   C  CR6    0   0.331  -2.1942   1.6497  -0.8851
 0G4  C4   C  CR6    0   0.354  -2.4991   2.6766   0.0818
 0G4  N4   N  NH2    0  -0.809  -2.0250   3.8763  -0.0946
 0G4  N3   N  N      0  -0.449  -3.2634   2.3137   1.1339
 0G4  C2   C  CR6    0   0.581  -3.6559   1.0553   1.3438
 0G4  O2   O  O      0  -0.605  -4.3334   0.7124   2.3198
 0G4  C6   C  CR16   0  -0.072  -2.5275   0.3766  -0.6663
 0G4  N1   N  NR6    0  -0.516  -3.2575   0.0548   0.4436
 0G4  C1'  C  CH1    0   0.254  -3.6017  -1.3235   0.7695
 0G4  O4'  O  O2     0  -0.522  -3.4981  -2.1110  -0.3864
 0G4  C2'  C  CH2    0  -0.582  -2.7030  -1.8979   1.8670
 0G4  S3'  S  S2     0   0.041  -2.7102  -3.6728   1.5450
 0G4  C4'  C  CH1    0  -0.152  -2.8093  -3.3305  -0.2445
 0G4  C5'  C  CH2    0  -0.125  -1.4592  -3.3050  -0.9275
 0G4  O5'  O  O2     0  -0.557  -0.6029  -2.4043  -0.2791
 0G4  PA   P  P      0   1.332   0.6694  -1.8152  -1.1607
 0G4  O1A  O  O      0  -0.803   1.5288  -2.9749  -1.5662
 0G4  O2A  O  OP    -1  -0.946   0.1547  -0.8706  -2.2066
 0G4  O3A  O  O2     0  -0.575   1.3255  -1.0141   0.0942
 0G4  PB   P  P      0   1.239   2.3462   0.2982  -0.0687
 0G4  O2B  O  OP    -1  -0.903   3.1917   0.0397  -1.2845
 0G4  O1B  O  O      0  -0.776   2.9934   0.4755   1.2731
 0G4  N3B  N  NH1    0  -0.981   1.2335   1.5436  -0.2943
 0G4  PG   P  P      0   1.167   1.5405   3.1533   0.2218
 0G4  O3G  O  OP    -1  -0.867   0.5662   3.9836  -0.7738
 0G4  O1G  O  O      0  -0.871   1.1008   3.3204   1.6527
 0G4  O2C  O  OP    -1  -0.988   2.9545   3.5385  -0.1357
 0G4  H1   H  HNH2   0   0.409  -0.4117   3.9518  -0.5210
 0G4  H2   H  HNH2   0   0.412  -2.2985   4.4612   0.6885
 0G4  H3   H  HCR6   0   0.334  -2.2343  -0.4068  -1.3449
 0G4  H4   H  HCH1   0   0.319  -4.6395  -1.3292   1.1088
 0G4  H5   H  HCH2   0   0.318  -1.6948  -1.4917   1.8071
 0G4  H6   H  HCH2   0   0.274  -3.1186  -1.6974   2.8513
 0G4  H7   H  HCH1   0   0.260  -3.4062  -4.1233  -0.7033
 0G4  H8   H  HCH2   0   0.204  -1.0581  -4.3252  -0.9173
 0G4  H9   H  HCH2   0   0.252  -1.6242  -3.0360  -1.9800
 0G4  H12  H  HNH1   0   0.321   0.6162   1.4284  -1.0865

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
 0G4  O1B  PB   deloc   1.500  0.020  1.500
 0G4  O1G  PG   deloc   1.506  0.020  1.506
 0G4  N3B  PB   single  1.685  0.020  1.685
 0G4  N3B  PG   single  1.718  0.020  1.718
 0G4  PB   O2B  deloc   1.503  0.020  1.503
 0G4  PB   O3A  single  1.670  0.020  1.670
 0G4  O3G  PG   deloc   1.622  0.020  1.622
 0G4  PG   O2C  deloc   1.508  0.020  1.508
 0G4  O3A  PA   single  1.627  0.020  1.627
 0G4  PA   O1A  deloc   1.499  0.020  1.499
 0G4  PA   O2A  deloc   1.500  0.020  1.500
 0G4  PA   O5'  single  1.656  0.020  1.656
 0G4  F5   C5   single  1.349  0.020  1.349
 0G4  N4   C4   single  1.302  0.020  1.302
 0G4  O5'  C5'  single  1.402  0.020  1.402
 0G4  C5   C4   single  1.443  0.020  1.443
 0G4  C5   C6   double  1.334  0.020  1.334
 0G4  C5'  C4'  single  1.513  0.020  1.513
 0G4  C4   N3   double  1.350  0.020  1.350
 0G4  C6   N1   single  1.367  0.020  1.367
 0G4  O4'  C4'  single  1.408  0.020  1.408
 0G4  O4'  C1'  single  1.403  0.020  1.403
 0G4  N3   C2   single  1.335  0.020  1.335
 0G4  N1   C2   single  1.404  0.020  1.404
 0G4  N1   C1'  single  1.458  0.020  1.458
 0G4  C4'  S3'  single  1.825  0.020  1.825
 0G4  C2   O2   double  1.237  0.020  1.237
 0G4  C1'  C2'  single  1.530  0.020  1.530
 0G4  S3'  C2'  single  1.804  0.020  1.804
 0G4  N4   H1   single  0.890  0.020  1.040
 0G4  N4   H2   single  0.890  0.020  1.040
 0G4  C6   H3   single  0.930  0.020  1.080
 0G4  C1'  H4   single  0.970  0.020  1.090
 0G4  C2'  H5   single  0.970  0.020  1.090
 0G4  C2'  H6   single  0.970  0.020  1.090
 0G4  C4'  H7   single  0.970  0.020  1.090
 0G4  C5'  H8   single  0.970  0.020  1.090
 0G4  C5'  H9   single  0.970  0.020  1.090
 0G4  N3B  H12  single  0.890  0.020  1.040

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
 0G4  C6   C5   C4   121.09  3.000
 0G4  C6   C5   F5   120.11  3.000
 0G4  C4   C5   F5   118.77  3.000
 0G4  N3   C4   N4   124.02  3.000
 0G4  N3   C4   C5   116.77  3.000
 0G4  N4   C4   C5   119.21  3.000
 0G4  H2   N4   H1   115.54  3.000
 0G4  H2   N4   C4   109.17  3.000
 0G4  H1   N4   C4   115.34  3.000
 0G4  C2   N3   C4   122.85  3.000
 0G4  N1   C2   O2   117.65  3.000
 0G4  O2   C2   N3   123.13  3.000
 0G4  N1   C2   N3   119.19  3.000
 0G4  H3   C6   N1   119.06  3.000
 0G4  H3   C6   C5   121.52  3.000
 0G4  N1   C6   C5   119.42  3.000
 0G4  C1'  N1   C6   122.03  3.000
 0G4  C1'  N1   C2   117.62  3.000
 0G4  C6   N1   C2   120.30  3.000
 0G4  H4   C1'  C2'  109.48  3.000
 0G4  H4   C1'  O4'  108.87  3.000
 0G4  C2'  C1'  O4'  109.69  3.000
 0G4  H4   C1'  N1   107.39  3.000
 0G4  C2'  C1'  N1   112.12  3.000
 0G4  O4'  C1'  N1   109.22  3.000
 0G4  C4'  O4'  C1'  116.07  3.000
 0G4  H6   C2'  H5   109.59  3.000
 0G4  H6   C2'  S3'  109.97  3.000
 0G4  H5   C2'  S3'  111.16  3.000
 0G4  H6   C2'  C1'  110.82  3.000
 0G4  H5   C2'  C1'  111.37  3.000
 0G4  S3'  C2'  C1'  103.82  3.000
 0G4  C4'  S3'  C2'   89.47  3.000
 0G4  H7   C4'  C5'  108.05  3.000
 0G4  H7   C4'  S3'  107.77  3.000
 0G4  C5'  C4'  S3'  113.42  3.000
 0G4  H7   C4'  O4'  108.58  3.000
 0G4  S3'  C4'  O4'  106.73  3.000
 0G4  C5'  C4'  O4'  112.11  3.000
 0G4  H9   C5'  H8   106.96  3.000
 0G4  H9   C5'  O5'  112.18  3.000
 0G4  H8   C5'  O5'  111.72  3.000
 0G4  H9   C5'  C4'  107.61  3.000
 0G4  H8   C5'  C4'  107.85  3.000
 0G4  O5'  C5'  C4'  110.31  3.000
 0G4  PA   O5'  C5'  116.84  3.000
 0G4  O3A  PA   O2A  111.47  3.000
 0G4  O2A  PA   O1A  119.67  3.000
 0G4  O3A  PA   O1A  111.00  3.000
 0G4  O2A  PA   O5'  109.36  3.000
 0G4  O1A  PA   O5'  108.01  3.000
 0G4  O3A  PA   O5'   94.26  3.000
 0G4  PB   O3A  PA   123.92  3.000
 0G4  N3B  PB   O1B  108.49  3.000
 0G4  N3B  PB   O2B  112.96  3.000
 0G4  O1B  PB   O2B  120.07  3.000
 0G4  O2B  PB   O3A  106.71  3.000
 0G4  N3B  PB   O3A  100.96  3.000
 0G4  O1B  PB   O3A  105.62  3.000
 0G4  H12  N3B  PG   116.82  3.000
 0G4  H12  N3B  PB   115.08  3.000
 0G4  PG   N3B  PB   122.29  3.000
 0G4  O2C  PG   O1G  118.06  3.000
 0G4  O2C  PG   O3G  106.67  3.000
 0G4  O1G  PG   O3G  110.55  3.000
 0G4  O2C  PG   N3B  109.60  3.000
 0G4  O3G  PG   N3B  100.83  3.000
 0G4  O1G  PG   N3B  109.70  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
 0G4  CONST_01  C2   N3   C4   C5      0.00   0.0  0
 0G4  CONST_02  N1   C2   N3   C4      0.00   0.0  0
 0G4  CONST_03  C6   N1   C2   N3      0.00   0.0  0
 0G4  CONST_04  C1'  N1   C2   N3    180.00   0.0  0
 0G4  CONST_05  O2   C2   N3   C4    180.00   0.0  0
 0G4  CONST_06  C2   N3   C4   N4    180.00   0.0  0
 0G4  CONST_07  C6   N1   C2   O2    180.00   0.0  0
 0G4  CONST_08  C1'  N1   C2   O2      0.00   0.0  0
 0G4  CONST_10  H2   N4   C4   C5    180.00   0.0  0
 0G4  Var_01    H5   C2'  S3'  C4'   -85.67  30.0  1
 0G4  Var_02    O3A  PA   O5'  C5'  -174.70  30.0  1
 0G4  Var_03    O1B  PB   O3A  PA   -164.95  30.0  2
 0G4  Var_04    PG   N3B  PB   O3A   149.40  30.0  1
 0G4  Var_05    O1G  PG   N3B  PB    -87.65  30.0  3
 0G4  Var_06    H8   C5'  O5'  PA     82.23  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
 0G4  chir_01  C1'  O4'  N1   C2'  positiv
 0G4  chir_02  C4'  S3'  O4'  C5'  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
 0G4  plan-1  F5   0.020
 0G4  plan-1  C5   0.020
 0G4  plan-1  C4   0.020
 0G4  plan-1  N4   0.020
 0G4  plan-1  N3   0.020
 0G4  plan-1  C2   0.020
 0G4  plan-1  O2   0.020
 0G4  plan-1  C6   0.020
 0G4  plan-1  N1   0.020
 0G4  plan-1  C1'  0.020
 0G4  plan-1  H1   0.020
 0G4  plan-1  H2   0.020
 0G4  plan-1  H3   0.020

