# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 07:37:56 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  42  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 PERFECT
;

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  -0.305  -1.0858   2.4259  -1.7608
 0G4  C5   C  CR6   0   0.332  -1.8911   2.0425  -0.7571
 0G4  C4   C  CR6   0   0.416  -2.5665   3.0324   0.0193
 0G4  N4   N  NH2   0  -0.803  -2.4025   4.3210  -0.2527
 0G4  N3   N  N     0  -0.533  -3.3590   2.6686   1.0025
 0G4  C2   C  CR6   0   0.608  -3.5527   1.3722   1.3288
 0G4  O2   O  O     0  -0.512  -4.2610   1.0293   2.2649
 0G4  C6   C  CR16  0  -0.084  -2.0713   0.7515  -0.4608
 0G4  N1   N  NR6   0  -0.556  -2.9011   0.3972   0.5590
 0G4  C1'  C  CH1   0   0.209  -3.0319  -1.0048   0.9215
 0G4  O4'  O  O2    0  -0.477  -3.1666  -1.7498  -0.2634
 0G4  C2'  C  CH2   0  -0.618  -1.8174  -1.5093   1.6916
 0G4  S3'  S  S2    0   0.002  -1.8564  -3.2884   1.4179
 0G4  C4'  C  CH1   0  -0.109  -2.5966  -3.0340  -0.2365
 0G4  C5'  C  CH2   0  -0.179  -1.6039  -3.1829  -1.3665
 0G4  O5'  O  O2    0  -0.586  -0.5912  -2.1831  -1.2324
 0G4  PA   P  P     0   1.494   0.9346  -2.4722  -1.5764
 0G4  O1A  O  O     0  -0.673   1.6077  -3.5464  -0.8382
 0G4  O2A  O  OH1   0  -0.718   1.0442  -2.6780  -3.1431
 0G4  O3A  O  O2    0  -0.697   1.5216  -0.9799  -1.3654
 0G4  PB   P  P     0   1.477   2.0756  -0.3072   0.0086
 0G4  O2B  O  OH1   0  -0.714   3.6504  -0.4788  -0.0477
 0G4  O1B  O  O     0  -0.667   1.5251  -0.8845   1.2430
 0G4  N3B  N  NH1   0  -0.960   1.6877   1.2758  -0.3499
 0G4  PG   P  P     0   1.442   1.9885   2.5281   0.7251
 0G4  O3G  O  OH1   0  -0.723   0.5396   3.1812   0.8415
 0G4  O1G  O  O     0  -0.694   2.6399   2.0164   1.9442
 0G4  O2C  O  OH1   0  -0.727   2.9075   3.5984  -0.0167
 0G4  H1   H  HNH2  0   0.420  -1.7873   4.6444  -0.9786
 0G4  H2   H  HNH2  0   0.412  -2.8729   5.0111   0.3088
 0G4  H3   H  HCR6  0   0.333  -1.5808  -0.0333  -1.0182
 0G4  H4   H  HCH1  0   0.285  -3.9291  -1.0939   1.5340
 0G4  H5   H  HCH2  0   0.304  -0.8824  -1.0769   1.3390
 0G4  H6   H  HCH2  0   0.304  -1.9242  -1.2985   2.7544
 0G4  H7   H  HCH1  0   0.299  -3.3701  -3.7953  -0.3712
 0G4  H8   H  HCH2  0   0.263  -1.1886  -4.1924  -1.3443
 0G4  H9   H  HCH2  0   0.276  -2.1075  -3.0423  -2.3255
 0G4  H10  H  HOH1  0   0.506   0.5983  -2.0336  -3.7104
 0G4  H11  H  HOH1  0   0.503   4.1024  -0.0674  -0.7976
 0G4  H12  H  HNH1  0   0.444   1.3299   1.4851  -1.2749
 0G4  H13  H  HOH1  0   0.505   0.5049   4.0128   1.3358
 0G4  H14  H  HOH1  0   0.499   2.4847   4.1541  -0.6848

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   double  1.470  0.020  1.470
 0G4  O1G  PG   double  1.474  0.020  1.474
 0G4  N3B  PB   single  1.669  0.020  1.669
 0G4  N3B  PG   single  1.678  0.020  1.678
 0G4  PB   O2B  single  1.585  0.020  1.585
 0G4  PB   O3A  single  1.627  0.020  1.627
 0G4  O3G  PG   single  1.594  0.020  1.594
 0G4  PG   O2C  single  1.594  0.020  1.594
 0G4  O3A  PA   single  1.617  0.020  1.617
 0G4  PA   O1A  double  1.467  0.020  1.467
 0G4  PA   O2A  single  1.584  0.020  1.584
 0G4  PA   O5'  single  1.591  0.020  1.591
 0G4  F5   C5   single  1.343  0.020  1.343
 0G4  N4   C4   single  1.327  0.020  1.327
 0G4  O5'  C5'  single  1.429  0.020  1.429
 0G4  C5   C4   single  1.428  0.020  1.428
 0G4  C5   C6   double  1.337  0.020  1.337
 0G4  C5'  C4'  single  1.511  0.020  1.511
 0G4  C4   N3   double  1.314  0.020  1.314
 0G4  C6   N1   single  1.362  0.020  1.362
 0G4  O4'  C4'  single  1.405  0.020  1.405
 0G4  O4'  C1'  single  1.406  0.020  1.406
 0G4  N3   C2   single  1.351  0.020  1.351
 0G4  N1   C2   single  1.403  0.020  1.403
 0G4  N1   C1'  single  1.454  0.020  1.454
 0G4  C4'  S3'  single  1.830  0.020  1.830
 0G4  C2   O2   double  1.223  0.020  1.223
 0G4  C1'  C2'  single  1.524  0.020  1.524
 0G4  S3'  C2'  single  1.800  0.020  1.800
 0G4  N4   H1   single  0.860  0.020  1.020
 0G4  N4   H2   single  0.860  0.020  1.020
 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  O2A  H10  single  0.850  0.020  0.980
 0G4  O2B  H11  single  0.850  0.020  0.980
 0G4  N3B  H12  single  0.860  0.020  1.020
 0G4  O3G  H13  single  0.850  0.020  0.980
 0G4  O2C  H14  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
 0G4  C6   C5   C4   119.03  3.000
 0G4  C6   C5   F5   121.48  3.000
 0G4  C4   C5   F5   119.49  3.000
 0G4  N3   C4   N4   119.78  3.000
 0G4  N3   C4   C5   120.01  3.000
 0G4  N4   C4   C5   120.21  3.000
 0G4  H2   N4   H1   117.93  3.000
 0G4  H2   N4   C4   119.59  3.000
 0G4  H1   N4   C4   122.42  3.000
 0G4  C2   N3   C4   122.20  3.000
 0G4  N1   C2   O2   119.62  3.000
 0G4  O2   C2   N3   122.48  3.000
 0G4  N1   C2   N3   117.90  3.000
 0G4  H3   C6   N1   118.30  3.000
 0G4  H3   C6   C5   121.74  3.000
 0G4  N1   C6   C5   119.96  3.000
 0G4  C1'  N1   C6   119.50  3.000
 0G4  C1'  N1   C2   119.44  3.000
 0G4  C6   N1   C2   120.88  3.000
 0G4  H4   C1'  C2'  110.18  3.000
 0G4  H4   C1'  O4'  110.57  3.000
 0G4  C2'  C1'  O4'  109.07  3.000
 0G4  H4   C1'  N1   107.04  3.000
 0G4  C2'  C1'  N1   111.93  3.000
 0G4  O4'  C1'  N1   108.02  3.000
 0G4  C4'  O4'  C1'  115.41  3.000
 0G4  H6   C2'  H5   108.88  3.000
 0G4  H6   C2'  S3'  109.73  3.000
 0G4  H5   C2'  S3'  111.21  3.000
 0G4  H6   C2'  C1'  110.54  3.000
 0G4  H5   C2'  C1'  112.90  3.000
 0G4  S3'  C2'  C1'  103.47  3.000
 0G4  C4'  S3'  C2'   90.51  3.000
 0G4  H7   C4'  C5'  107.69  3.000
 0G4  H7   C4'  S3'  107.50  3.000
 0G4  C5'  C4'  S3'  113.36  3.000
 0G4  H7   C4'  O4'  110.30  3.000
 0G4  S3'  C4'  O4'  107.96  3.000
 0G4  C5'  C4'  O4'  110.00  3.000
 0G4  H9   C5'  H8   108.20  3.000
 0G4  H9   C5'  O5'  108.61  3.000
 0G4  H8   C5'  O5'  112.04  3.000
 0G4  H9   C5'  C4'  109.93  3.000
 0G4  H8   C5'  C4'  109.00  3.000
 0G4  O5'  C5'  C4'  109.04  3.000
 0G4  PA   O5'  C5'  122.16  3.000
 0G4  O3A  PA   O2A  102.93  3.000
 0G4  O2A  PA   O1A  111.77  3.000
 0G4  O3A  PA   O1A  116.32  3.000
 0G4  O2A  PA   O5'  107.69  3.000
 0G4  O1A  PA   O5'  117.67  3.000
 0G4  O3A  PA   O5'   98.76  3.000
 0G4  H10  O2A  PA   117.49  3.000
 0G4  PB   O3A  PA   127.96  3.000
 0G4  N3B  PB   O1B  117.77  3.000
 0G4  N3B  PB   O2B  109.02  3.000
 0G4  O1B  PB   O2B  111.07  3.000
 0G4  O2B  PB   O3A  105.28  3.000
 0G4  N3B  PB   O3A   97.56  3.000
 0G4  O1B  PB   O3A  114.80  3.000
 0G4  H11  O2B  PB   116.47  3.000
 0G4  H12  N3B  PG   119.59  3.000
 0G4  H12  N3B  PB   118.29  3.000
 0G4  PG   N3B  PB   121.93  3.000
 0G4  O2C  PG   O1G  111.30  3.000
 0G4  O2C  PG   O3G  106.44  3.000
 0G4  O1G  PG   O3G  118.93  3.000
 0G4  O2C  PG   N3B  107.84  3.000
 0G4  O3G  PG   N3B  100.94  3.000
 0G4  O1G  PG   N3B  110.49  3.000
 0G4  H13  O3G  PG   114.96  3.000
 0G4  H14  O2C  PG   117.11  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_09  H1   N4   C4   C5     0.00   0.0  0
 0G4  CONST_10  H2   N4   C4   C5   180.00   0.0  0
 0G4  Var_01    H5   C2'  S3'  C4'  -89.76  30.0  1
 0G4  Var_02    O3A  PA   O5'  C5'  175.11  30.0  1
 0G4  Var_03    O1B  PB   O3A  PA   -25.36  30.0  1
 0G4  Var_04    PG   N3B  PB   O3A  178.84  30.0  1
 0G4  Var_05    O1G  PG   N3B  PB     1.22  30.0  3
 0G4  Var_06    H8   C5'  O5'  PA    21.86  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
 0G4  chir_03  PA   O1A  O2A  O5'  both
 0G4  chir_04  PB   O2B  O1B  N3B  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
 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

