# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 21:30:39 2020
#   Inital geometry file: a 109 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] phosphono hydrogen phosphate
#   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)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
 1RY  1RY  '[[(2R,5S)-5-(4-azanyl-5-fluoranyl-2-oxidanylidene-pyrimidin-1-yl)-1,3-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate'  ligand  41  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_1RY
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
 1RY  OAC  O  OH1   0  -0.763   1.6739   0.4340  -2.2031
 1RY  PAZ  P  P     0   1.468   1.7564  -0.9197  -1.4177
 1RY  OAF  O  OH1   0  -0.714   0.3807  -1.6582  -1.7108
 1RY  OAG  O  O     0  -0.681   2.9781  -1.7097  -1.6253
 1RY  OAQ  O  O2    0  -0.708   1.5152  -0.4984   0.1565
 1RY  PBB  P  P     0   1.493   2.4249   0.4074   1.1164
 1RY  OAI  O  OH1   0  -0.697   2.6581  -0.4360   2.4200
 1RY  OAE  O  O     0  -0.656   3.6444   0.9590   0.5249
 1RY  OAR  O  O2    0  -0.675   1.3275   1.5090   1.5989
 1RY  PBA  P  P     0   1.528   0.6208   2.5970   0.6407
 1RY  OAH  O  O     0  -0.699   1.0580   2.5273  -0.7735
 1RY  OAD  O  OH1   0  -0.693   0.9538   4.0111   1.2435
 1RY  OAO  O  O2    0  -0.565  -0.8901   2.2479   0.9544
 1RY  CAL  C  CH2   0  -0.226  -1.9828   2.9040   0.2958
 1RY  CAW  C  CH1   0  -0.084  -2.6940   1.9813  -0.6630
 1RY  OAP  O  O2    0  -0.477  -3.2883   0.8909   0.0188
 1RY  SAS  S  S2    0   0.008  -1.6045   1.2661  -1.9218
 1RY  CAM  C  CH2   0  -0.608  -2.8344  -0.0320  -2.1273
 1RY  CAX  C  CH1   0   0.223  -3.3240  -0.3008  -0.7048
 1RY  NAY  N  NR6   0  -0.543  -2.4935  -1.3095  -0.0226
 1RY  CAK  C  CR16  0  -0.056  -1.6830  -0.9924   1.0100
 1RY  CAU  C  CR6   0   0.311  -0.9452  -1.9474   1.5935
 1RY  FAJ  F  F     0  -0.318  -0.1438  -1.6610   2.6426
 1RY  CAV  C  CR6   0   0.603  -2.5934  -2.6313  -0.4748
 1RY  OAB  O  O     0  -0.518  -3.3831  -2.8882  -1.3752
 1RY  NAN  N  N     0  -0.533  -1.8073  -3.5665   0.0976
 1RY  CAT  C  CR6   0   0.407  -0.9990  -3.2773   1.0960
 1RY  NAA  N  NH2   0  -0.806  -0.2386  -4.2309   1.6245
 1RY  H1   H  HOH1  0   0.507   1.3514   1.2473  -1.7243
 1RY  H2   H  HOH1  0   0.504   0.4490  -2.6223  -1.7370
 1RY  H3   H  HOH1  0   0.504   1.9004  -0.8945   2.8114
 1RY  H4   H  HOH1  0   0.517   0.6727   4.1831   2.1547
 1RY  H5   H  HCH2  0   0.301  -2.6703   3.2292   1.0758
 1RY  H6   H  HCH2  0   0.281  -1.6600   3.7923  -0.2509
 1RY  H7   H  HCH1  0   0.294  -3.4767   2.5732  -1.1506
 1RY  H8   H  HCH2  0   0.300  -3.6646   0.3145  -2.7439
 1RY  H9   H  HCH2  0   0.316  -2.3857  -0.9004  -2.5991
 1RY  H10  H  HCH1  0   0.291  -4.3464  -0.6813  -0.7201
 1RY  H11  H  HCR6  0   0.335  -1.6654   0.0277   1.3570
 1RY  H12  H  HNH2  0   0.419   0.3542  -4.0698   2.4198
 1RY  H13  H  HNH2  0   0.412  -0.3170  -5.1737   1.2819

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
 1RY  OAG  PAZ  double  1.470  0.020  1.470
 1RY  FAJ  CAU  single  1.351  0.020  1.351
 1RY  OAF  PAZ  single  1.589  0.020  1.589
 1RY  OAH  PBA  double  1.482  0.020  1.482
 1RY  PAZ  OAC  single  1.567  0.020  1.567
 1RY  PAZ  OAQ  single  1.647  0.020  1.647
 1RY  NAA  CAT  single  1.329  0.020  1.329
 1RY  OAD  PBA  single  1.573  0.020  1.573
 1RY  CAU  CAT  single  1.421  0.020  1.421
 1RY  CAU  CAK  double  1.341  0.020  1.341
 1RY  PBA  OAR  single  1.613  0.020  1.613
 1RY  PBA  OAO  single  1.582  0.020  1.582
 1RY  OAR  PBB  single  1.628  0.020  1.628
 1RY  OAQ  PBB  single  1.603  0.020  1.603
 1RY  CAT  NAN  double  1.317  0.020  1.317
 1RY  CAK  NAY  single  1.350  0.020  1.350
 1RY  PBB  OAE  double  1.463  0.020  1.463
 1RY  PBB  OAI  single  1.570  0.020  1.570
 1RY  OAO  CAL  single  1.435  0.020  1.435
 1RY  NAN  CAV  single  1.349  0.020  1.349
 1RY  NAY  CAV  single  1.401  0.020  1.401
 1RY  NAY  CAX  single  1.474  0.020  1.474
 1RY  CAV  OAB  double  1.225  0.020  1.225
 1RY  SAS  CAM  single  1.800  0.020  1.800
 1RY  SAS  CAW  single  1.812  0.020  1.812
 1RY  CAL  CAW  single  1.509  0.020  1.509
 1RY  CAM  CAX  single  1.528  0.020  1.528
 1RY  CAX  OAP  single  1.395  0.020  1.395
 1RY  OAP  CAW  single  1.417  0.020  1.417
 1RY  OAC  H1   single  0.850  0.020  0.980
 1RY  OAF  H2   single  0.850  0.020  0.980
 1RY  OAI  H3   single  0.850  0.020  0.980
 1RY  OAD  H4   single  0.850  0.020  0.980
 1RY  CAL  H5   single  0.970  0.020  1.090
 1RY  CAL  H6   single  0.970  0.020  1.090
 1RY  CAW  H7   single  0.970  0.020  1.090
 1RY  CAM  H8   single  0.970  0.020  1.090
 1RY  CAM  H9   single  0.970  0.020  1.090
 1RY  CAX  H10  single  0.970  0.020  1.090
 1RY  CAK  H11  single  0.930  0.020  1.080
 1RY  NAA  H12  single  0.860  0.020  1.020
 1RY  NAA  H13  single  0.860  0.020  1.020

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
 1RY  H1   OAC  PAZ  118.74  3.000
 1RY  OAQ  PAZ  OAG  113.21  3.000
 1RY  OAQ  PAZ  OAF   99.69  3.000
 1RY  OAG  PAZ  OAF  116.36  3.000
 1RY  OAQ  PAZ  OAC  104.50  3.000
 1RY  OAF  PAZ  OAC  105.28  3.000
 1RY  OAG  PAZ  OAC  115.93  3.000
 1RY  H2   OAF  PAZ  114.04  3.000
 1RY  PBB  OAQ  PAZ  129.32  3.000
 1RY  OAR  PBB  OAE  115.25  3.000
 1RY  OAE  PBB  OAI  114.48  3.000
 1RY  OAR  PBB  OAI  102.56  3.000
 1RY  OAI  PBB  OAQ  106.14  3.000
 1RY  OAE  PBB  OAQ  116.35  3.000
 1RY  OAR  PBB  OAQ  100.21  3.000
 1RY  H3   OAI  PBB  118.28  3.000
 1RY  PBA  OAR  PBB  125.15  3.000
 1RY  OAO  PBA  OAD  108.94  3.000
 1RY  OAO  PBA  OAH  117.43  3.000
 1RY  OAD  PBA  OAH  110.21  3.000
 1RY  OAO  PBA  OAR   98.73  3.000
 1RY  OAD  PBA  OAR  106.62  3.000
 1RY  OAH  PBA  OAR  113.96  3.000
 1RY  H4   OAD  PBA  117.29  3.000
 1RY  CAL  OAO  PBA  122.37  3.000
 1RY  H6   CAL  H5   107.59  3.000
 1RY  H6   CAL  CAW  108.59  3.000
 1RY  H5   CAL  CAW  109.88  3.000
 1RY  H6   CAL  OAO  112.13  3.000
 1RY  H5   CAL  OAO  106.77  3.000
 1RY  CAW  CAL  OAO  111.78  3.000
 1RY  H7   CAW  SAS  109.48  3.000
 1RY  H7   CAW  OAP  109.29  3.000
 1RY  SAS  CAW  OAP  106.43  3.000
 1RY  H7   CAW  CAL  106.81  3.000
 1RY  OAP  CAW  CAL  111.26  3.000
 1RY  SAS  CAW  CAL  113.54  3.000
 1RY  CAX  OAP  CAW  114.75  3.000
 1RY  CAM  SAS  CAW   87.31  3.000
 1RY  H9   CAM  H8   108.85  3.000
 1RY  H9   CAM  CAX  113.34  3.000
 1RY  H8   CAM  CAX  109.77  3.000
 1RY  H9   CAM  SAS  110.13  3.000
 1RY  H8   CAM  SAS  110.83  3.000
 1RY  CAX  CAM  SAS  103.86  3.000
 1RY  H10  CAX  NAY  107.21  3.000
 1RY  H10  CAX  CAM  110.40  3.000
 1RY  NAY  CAX  CAM  111.76  3.000
 1RY  H10  CAX  OAP  109.23  3.000
 1RY  CAM  CAX  OAP  108.93  3.000
 1RY  NAY  CAX  OAP  109.28  3.000
 1RY  CAV  NAY  CAK  120.76  3.000
 1RY  CAV  NAY  CAX  117.14  3.000
 1RY  CAK  NAY  CAX  122.09  3.000
 1RY  H11  CAK  CAU  121.68  3.000
 1RY  H11  CAK  NAY  118.58  3.000
 1RY  CAU  CAK  NAY  119.73  3.000
 1RY  CAT  CAU  FAJ  119.53  3.000
 1RY  CAT  CAU  CAK  119.57  3.000
 1RY  FAJ  CAU  CAK  120.90  3.000
 1RY  NAN  CAV  OAB  122.83  3.000
 1RY  OAB  CAV  NAY  118.77  3.000
 1RY  NAN  CAV  NAY  118.40  3.000
 1RY  CAT  NAN  CAV  121.81  3.000
 1RY  NAA  CAT  NAN  119.67  3.000
 1RY  NAN  CAT  CAU  119.63  3.000
 1RY  NAA  CAT  CAU  120.70  3.000
 1RY  H13  NAA  H12  117.75  3.000
 1RY  H13  NAA  CAT  119.49  3.000
 1RY  H12  NAA  CAT  122.49  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
 1RY  CONST_01  NAN  CAV  NAY  CAX  180.00   0.0  0
 1RY  CONST_02  CAT  NAN  CAV  NAY    0.00   0.0  0
 1RY  CONST_03  NAN  CAV  NAY  CAK    0.00   0.0  0
 1RY  CONST_04  CAV  NAN  CAT  CAU    0.00   0.0  0
 1RY  CONST_05  OAB  CAV  NAY  CAX    0.00   0.0  0
 1RY  CONST_06  OAB  CAV  NAY  CAK  180.00   0.0  0
 1RY  CONST_07  NAA  CAT  NAN  CAV  180.00   0.0  0
 1RY  CONST_08  CAT  NAN  CAV  OAB  180.00   0.0  0
 1RY  CONST_09  H12  NAA  CAT  CAU    0.00   0.0  0
 1RY  CONST_10  H13  NAA  CAT  CAU  180.00   0.0  0
 1RY  Var_01    CAX  CAM  SAS  CAW  -38.53  30.0  1
 1RY  Var_02    CAW  CAL  OAO  PBA  109.39  30.0  3
 1RY  Var_03    OAR  PBB  OAQ  PAZ  125.54  30.0  3
 1RY  Var_04    OAH  PBA  OAR  PBB   -0.13  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
 1RY  chir_03  CAW  SAS  CAL  OAP  positiv
 1RY  chir_04  CAX  OAP  NAY  CAM  positiv
 1RY  chir_05  PBB  OAQ  OAE  OAI  both
 1RY  chir_06  PBA  OAD  OAR  OAO  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
 1RY  plan-1  CAX  0.020
 1RY  plan-1  NAY  0.020
 1RY  plan-1  CAK  0.020
 1RY  plan-1  CAU  0.020
 1RY  plan-1  FAJ  0.020
 1RY  plan-1  CAV  0.020
 1RY  plan-1  OAB  0.020
 1RY  plan-1  NAN  0.020
 1RY  plan-1  CAT  0.020
 1RY  plan-1  NAA  0.020
 1RY  plan-1  H11  0.020
 1RY  plan-1  H12  0.020
 1RY  plan-1  H13  0.020

