# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 08:58:48 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: [[(2R,5S)-5-(4-azanyl-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=C1)[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
 1RZ  1RZ  '[[(2R,5S)-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-1,3-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate'  ligand  41  27  .  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_1RZ
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
 1RZ  O3G  O  OH1   0  -0.669  -2.6335  -3.1092  -0.3693
 1RZ  PG   P  P     0   1.468  -3.6009  -1.8492  -0.3910
 1RZ  O1G  O  O     0  -0.845  -4.3352  -1.5055   0.8336
 1RZ  PB   P  P     0   1.471  -1.9893   0.5068   0.0466
 1RZ  O2B  O  O     0  -0.709  -1.4291   0.1615   1.3557
 1RZ  O1B  O  OH1   0  -0.593  -3.1717   1.5468   0.1409
 1RZ  O3A  O  O2    0  -0.648  -0.9466   1.0660  -1.0463
 1RZ  PA   P  P     0   1.490  -0.1771   2.4980  -1.0321
 1RZ  O1A  O  O     0  -0.762  -0.4009   3.3114   0.1691
 1RZ  O2A  O  OH1   0  -0.759  -0.6869   3.2338  -2.3371
 1RZ  O5'  O  O2    0  -0.491   1.2827   1.9506  -1.3194
 1RZ  C5'  C  CH2   0  -0.209   2.4312   2.7849  -1.1468
 1RZ  C4'  C  CH1   0  -0.112   3.3343   2.2102  -0.0833
 1RZ  O4'  O  O2    0  -0.480   3.7360   0.9224  -0.4604
 1RZ  S3'  S  S2    0   0.006   2.5094   2.0738   1.5387
 1RZ  C2'  C  CH2   0  -0.562   3.6141   0.6943   1.9315
 1RZ  C1'  C  CH1   0   0.138   3.9117   0.0021   0.5889
 1RZ  N1   N  NR6   0  -0.420   3.0865  -1.1573   0.3320
 1RZ  C2   C  CR6   0   0.565   3.6752  -2.2922  -0.2611
 1RZ  O2   O  O     0  -0.540   4.8685  -2.2834  -0.5280
 1RZ  N3   N  N     0  -0.533   2.8872  -3.3550  -0.5062
 1RZ  C4   C  CR6   0   0.462   1.5952  -3.3305  -0.2316
 1RZ  N4   N  NH2   0  -0.815   0.8747  -4.4081  -0.5026
 1RZ  C5   C  CR16  0  -0.412   0.9572  -2.1789   0.3257
 1RZ  C6   C  CR16  0   0.006   1.7500  -1.1203   0.5735
 1RZ  O3B  O  O2    0  -0.629  -2.5107  -0.7283  -0.8487
 1RZ  O2C  O  OH1   0  -0.643  -4.5558  -1.9745  -1.6435
 1RZ  H1   H  HOH1  0   0.525  -3.0349  -3.9148  -0.0087
 1RZ  H2   H  HOH1  0   0.489  -3.6005   1.8108  -0.6866
 1RZ  H3   H  HOH1  0   0.486  -0.5137   2.7987  -3.1862
 1RZ  H4   H  HCH2  0   0.268   2.9629   2.8146  -2.0980
 1RZ  H5   H  HCH2  0   0.288   2.1669   3.8118  -0.8867
 1RZ  H6   H  HCH1  0   0.275   4.2001   2.8756   0.0095
 1RZ  H7   H  HCH2  0   0.315   4.5418   1.0657   2.3686
 1RZ  H8   H  HCH2  0   0.349   3.1425   0.0276   2.6502
 1RZ  H9   H  HCH1  0   0.331   4.9399  -0.3537   0.5847
 1RZ  H10  H  HNH2  0   0.391   1.3060  -5.2133  -0.9252
 1RZ  H11  H  HNH2  0   0.395  -0.1198  -4.4218  -0.3664
 1RZ  H12  H  HCR6  0   0.283  -0.0939  -2.1621   0.5712
 1RZ  H13  H  HCR6  0   0.315   1.3545  -0.2078   0.9991
 1RZ  H14  H  HOH1  0   0.516  -4.1669  -2.3013  -2.4699

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
 1RZ  O1G  PG   double  1.469  0.020  1.469
 1RZ  O1A  PA   double  1.468  0.020  1.468
 1RZ  O2C  PG   single  1.580  0.020  1.580
 1RZ  PG   O3G  single  1.589  0.020  1.589
 1RZ  PG   O3B  single  1.629  0.020  1.629
 1RZ  N4   C4   single  1.324  0.020  1.324
 1RZ  PA   O2A  single  1.583  0.020  1.583
 1RZ  PA   O3A  single  1.626  0.020  1.626
 1RZ  PA   O5'  single  1.585  0.020  1.585
 1RZ  C5   C4   single  1.430  0.020  1.430
 1RZ  C5   C6   double  1.346  0.020  1.346
 1RZ  O3B  PB   single  1.612  0.020  1.612
 1RZ  O3A  PB   single  1.611  0.020  1.611
 1RZ  C4   N3   double  1.321  0.020  1.321
 1RZ  C6   N1   single  1.359  0.020  1.359
 1RZ  PB   O2B  double  1.465  0.020  1.465
 1RZ  PB   O1B  single  1.577  0.020  1.577
 1RZ  O5'  C5'  single  1.430  0.020  1.430
 1RZ  N3   C2   single  1.346  0.020  1.346
 1RZ  N1   C2   single  1.409  0.020  1.409
 1RZ  N1   C1'  single  1.446  0.020  1.446
 1RZ  C2   O2   double  1.223  0.020  1.223
 1RZ  C5'  C4'  single  1.509  0.020  1.509
 1RZ  S3'  C2'  single  1.811  0.020  1.811
 1RZ  S3'  C4'  single  1.825  0.020  1.825
 1RZ  C2'  C1'  single  1.540  0.020  1.540
 1RZ  C4'  O4'  single  1.401  0.020  1.401
 1RZ  C1'  O4'  single  1.407  0.020  1.407
 1RZ  O3G  H1   single  0.850  0.020  0.980
 1RZ  O1B  H2   single  0.850  0.020  0.980
 1RZ  O2A  H3   single  0.850  0.020  0.980
 1RZ  C5'  H4   single  0.970  0.020  1.090
 1RZ  C5'  H5   single  0.970  0.020  1.090
 1RZ  C4'  H6   single  0.970  0.020  1.090
 1RZ  C2'  H7   single  0.970  0.020  1.090
 1RZ  C2'  H8   single  0.970  0.020  1.090
 1RZ  C1'  H9   single  0.970  0.020  1.090
 1RZ  N4   H10  single  0.860  0.020  1.020
 1RZ  N4   H11  single  0.860  0.020  1.020
 1RZ  C5   H12  single  0.930  0.020  1.080
 1RZ  C6   H13  single  0.930  0.020  1.080
 1RZ  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
 1RZ  H1   O3G  PG   114.32  3.000
 1RZ  O2C  PG   O3B  103.67  3.000
 1RZ  O3B  PG   O1G  114.06  3.000
 1RZ  O2C  PG   O1G  112.17  3.000
 1RZ  O3B  PG   O3G   98.17  3.000
 1RZ  O2C  PG   O3G  108.42  3.000
 1RZ  O1G  PG   O3G  118.60  3.000
 1RZ  O3B  PB   O3A   95.65  3.000
 1RZ  O3A  PB   O1B  107.27  3.000
 1RZ  O3B  PB   O1B  107.21  3.000
 1RZ  O1B  PB   O2B  112.87  3.000
 1RZ  O3A  PB   O2B  116.14  3.000
 1RZ  O3B  PB   O2B  116.06  3.000
 1RZ  H2   O1B  PB   117.42  3.000
 1RZ  PA   O3A  PB   127.32  3.000
 1RZ  O5'  PA   O2A  107.93  3.000
 1RZ  O5'  PA   O1A  118.69  3.000
 1RZ  O2A  PA   O1A  111.60  3.000
 1RZ  O5'  PA   O3A   97.48  3.000
 1RZ  O2A  PA   O3A  104.47  3.000
 1RZ  O1A  PA   O3A  115.03  3.000
 1RZ  H3   O2A  PA   117.12  3.000
 1RZ  C5'  O5'  PA   121.08  3.000
 1RZ  H5   C5'  H4   107.48  3.000
 1RZ  H5   C5'  C4'  109.58  3.000
 1RZ  H4   C5'  C4'  109.47  3.000
 1RZ  H5   C5'  O5'  112.53  3.000
 1RZ  H4   C5'  O5'  107.60  3.000
 1RZ  C4'  C5'  O5'  110.09  3.000
 1RZ  H6   C4'  S3'  109.10  3.000
 1RZ  H6   C4'  O4'  110.76  3.000
 1RZ  S3'  C4'  O4'  107.47  3.000
 1RZ  H6   C4'  C5'  107.53  3.000
 1RZ  O4'  C4'  C5'  109.40  3.000
 1RZ  S3'  C4'  C5'  112.60  3.000
 1RZ  C1'  O4'  C4'  115.88  3.000
 1RZ  C2'  S3'  C4'   88.50  3.000
 1RZ  H8   C2'  H7   108.22  3.000
 1RZ  H8   C2'  C1'  112.61  3.000
 1RZ  H7   C2'  C1'  109.77  3.000
 1RZ  H8   C2'  S3'  110.23  3.000
 1RZ  H7   C2'  S3'  110.27  3.000
 1RZ  C1'  C2'  S3'  105.74  3.000
 1RZ  H9   C1'  N1   106.05  3.000
 1RZ  H9   C1'  C2'  109.45  3.000
 1RZ  N1   C1'  C2'  113.89  3.000
 1RZ  H9   C1'  O4'  109.22  3.000
 1RZ  C2'  C1'  O4'  109.40  3.000
 1RZ  N1   C1'  O4'  108.71  3.000
 1RZ  C6   N1   C2   120.51  3.000
 1RZ  C2   N1   C1'  118.81  3.000
 1RZ  C6   N1   C1'  120.53  3.000
 1RZ  N3   C2   O2   122.50  3.000
 1RZ  O2   C2   N1   119.58  3.000
 1RZ  N3   C2   N1   117.91  3.000
 1RZ  C4   N3   C2   121.34  3.000
 1RZ  C5   C4   N4   119.50  3.000
 1RZ  C5   C4   N3   122.17  3.000
 1RZ  N4   C4   N3   118.32  3.000
 1RZ  H11  N4   H10  118.07  3.000
 1RZ  H11  N4   C4   121.48  3.000
 1RZ  H10  N4   C4   120.25  3.000
 1RZ  H12  C5   C6   121.30  3.000
 1RZ  H12  C5   C4   122.40  3.000
 1RZ  C6   C5   C4   116.26  3.000
 1RZ  H13  C6   C5   121.37  3.000
 1RZ  H13  C6   N1   116.91  3.000
 1RZ  C5   C6   N1   121.70  3.000
 1RZ  PB   O3B  PG   125.98  3.000
 1RZ  H14  O2C  PG   117.37  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
 1RZ  CONST_01  N3   C2   N1   C1'  180.00   0.0  0
 1RZ  CONST_02  C4   N3   C2   N1     0.00   0.0  0
 1RZ  CONST_03  C5   C4   N3   C2     0.00   0.0  0
 1RZ  CONST_04  C6   N1   C2   N3     0.00   0.0  0
 1RZ  CONST_05  O2   C2   N1   C1'    0.00   0.0  0
 1RZ  CONST_06  N4   C4   N3   C2   180.00   0.0  0
 1RZ  CONST_07  C4   N3   C2   O2   180.00   0.0  0
 1RZ  CONST_08  C6   N1   C2   O2   180.00   0.0  0
 1RZ  CONST_09  H10  N4   C4   N3     0.00   0.0  0
 1RZ  CONST_10  H11  N4   C4   N3   180.00   0.0  0
 1RZ  Var_01    C1'  C2'  S3'  C4'  -31.33  30.0  1
 1RZ  Var_02    C4'  C5'  O5'  PA   118.00  30.0  3
 1RZ  Var_03    O3A  PB   O3B  PG   177.92  30.0  3
 1RZ  Var_04    O2C  PG   O3B  PB   135.17  30.0  1
 1RZ  Var_05    O1A  PA   O3A  PB     4.73  30.0  1
 1RZ  Var_06    O3B  PB   O3A  PA   167.65  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
 1RZ  chir_03  C4'  C5'  S3'  O4'  negativ
 1RZ  chir_04  C1'  O4'  N1   C2'  positiv
 1RZ  chir_05  PB   O3A  O2B  O1B  both
 1RZ  chir_06  PA   O2A  O3A  O5'  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
 1RZ  plan-1  C1'  0.020
 1RZ  plan-1  N1   0.020
 1RZ  plan-1  C2   0.020
 1RZ  plan-1  O2   0.020
 1RZ  plan-1  N3   0.020
 1RZ  plan-1  C4   0.020
 1RZ  plan-1  N4   0.020
 1RZ  plan-1  C5   0.020
 1RZ  plan-1  C6   0.020
 1RZ  plan-1  H10  0.020
 1RZ  plan-1  H11  0.020
 1RZ  plan-1  H12  0.020
 1RZ  plan-1  H13  0.020

