# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Aug  1 15:36:15 2021
#   Inital geometry file: a 114 line input string
#   Ligand name: [[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-sulfanyl-phosphoryl] phosphono hydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P@@](S)(=O)O[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
#
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
 P5E  P5E  '[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-sulfanyl-phosphoryl] phosphono hydrogen phosphate'  ligand  44  29  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_P5E
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
 P5E  PA   P  P     0   1.285  45.3189  60.9009  70.6022
 P5E  O2A  O  O     0  -0.629  44.5738  59.7347  71.0975
 P5E  O3A  O  O2    0  -0.695  44.5721  61.8564  69.5329
 P5E  O5'  O  O2    0  -0.594  45.7204  61.9935  71.6956
 P5E  PB   P  P     0   1.518  43.6654  63.1771  69.7590
 P5E  O1B  O  O     0  -0.635  44.4067  64.4388  69.8460
 P5E  O2B  O  OH1   0  -0.732  42.7854  62.7165  70.9889
 P5E  O3B  O  O2    0  -0.673  42.7470  63.1194  68.4522
 P5E  PG   P  P     0   1.480  41.4717  62.1796  68.0301
 P5E  O1G  O  OH1   0  -0.723  40.3367  62.5556  69.0648
 P5E  O2G  O  O     0  -0.668  41.2229  62.3576  66.5943
 P5E  O3G  O  OH1   0  -0.727  41.8213  60.7393  68.5838
 P5E  C5'  C  CH2   0  -0.205  46.3300  61.5770  72.9284
 P5E  C4'  C  CR15  0  -0.017  46.8780  62.7766  73.6604
 P5E  O4'  O  O     0  -0.491  47.9613  63.3473  72.9314
 P5E  C1'  C  CR15  0   0.182  47.7546  64.7212  72.7486
 P5E  C2'  C  CR15  0  -0.024  46.2442  64.9222  72.8368
 P5E  O2'  O  OH1   0  -0.651  45.9736  66.2603  73.1083
 P5E  C3'  C  CR15  0  -0.052  45.8748  63.9153  73.9285
 P5E  O3'  O  OH1   0  -0.663  46.0992  64.5272  75.1700
 P5E  N1   N  NR6   0  -0.567  48.3336  65.1117  71.4764
 P5E  C6   C  CR16  0   0.123  47.9497  64.4633  70.3352
 P5E  C2   C  CR6   0   0.739  49.2987  66.1016  71.4419
 P5E  O2   O  O     0  -0.474  49.6882  66.6904  72.4273
 P5E  N3   N  NR16  0  -0.735  49.7872  66.3740  70.1917
 P5E  C4   C  CR6   0   0.572  49.4477  65.7754  68.9881
 P5E  O4   O  O     0  -0.460  49.9741  66.1293  67.9505
 P5E  C5   C  CR16  0  -0.515  48.4489  64.7425  69.1227
 P5E  S1A  S  S2    0  -0.331  47.0054  60.4733  69.4781
 P5E  H1   H  HOH1  0   0.516  42.3293  63.4241  71.4673
 P5E  H2   H  HOH1  0   0.512  39.8924  63.3973  68.8919
 P5E  H3   H  HOH1  0   0.513  42.3059  60.1743  67.9659
 P5E  H4   H  HCH2  0   0.271  45.5891  61.0808  73.5571
 P5E  H5   H  HCH2  0   0.263  47.1395  60.8695  72.7286
 P5E  H6   H  HCR5  0   0.275  47.2495  62.3882  74.6155
 P5E  H7   H  HCR5  0   0.278  48.2544  65.3114  73.5196
 P5E  H8   H  HCR5  0   0.260  45.7714  64.6006  71.9016
 P5E  H9   H  HOH1  0   0.462  45.0284  66.4124  73.0141
 P5E  H10  H  HCR5  0   0.253  44.8386  63.5674  73.8349
 P5E  H11  H  HOH1  0   0.458  45.8774  63.8978  75.8634
 P5E  H12  H  HCR6  0   0.297  47.2071  63.6923  70.4665
 P5E  H13  H  HNR6  0   0.428  50.4905  67.1020  70.1560
 P5E  H14  H  HCR6  0   0.293  48.1145  64.2032  68.2501
 P5E  H15  H  HSH1  0   0.281  47.3250  59.3703  70.1678

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
 P5E  O2G  PG   double  1.468  0.020  1.468
 P5E  O3B  PG   single  1.639  0.020  1.639
 P5E  O3B  PB   single  1.598  0.020  1.598
 P5E  O4   C4   double  1.216  0.020  1.216
 P5E  PG   O3G  single  1.582  0.020  1.582
 P5E  PG   O1G  single  1.581  0.020  1.581
 P5E  S1A  PA   single  2.071  0.020  2.071
 P5E  O3A  PB   single  1.618  0.020  1.618
 P5E  O3A  PA   single  1.617  0.020  1.617
 P5E  C5   C4   single  1.443  0.020  1.443
 P5E  C5   C6   double  1.341  0.020  1.341
 P5E  C4   N3   single  1.386  0.020  1.386
 P5E  PB   O1B  double  1.466  0.020  1.466
 P5E  PB   O2B  single  1.581  0.020  1.581
 P5E  PA   O2A  double  1.470  0.020  1.470
 P5E  PA   O5'  single  1.597  0.020  1.597
 P5E  C6   N1   single  1.367  0.020  1.367
 P5E  N3   C2   single  1.370  0.020  1.370
 P5E  O5'  C5'  single  1.437  0.020  1.437
 P5E  N1   C2   single  1.383  0.020  1.383
 P5E  N1   C1'  single  1.451  0.020  1.451
 P5E  C2   O2   double  1.212  0.020  1.212
 P5E  C5'  C4'  single  1.508  0.020  1.508
 P5E  C2'  C1'  single  1.526  0.020  1.526
 P5E  C2'  O2'  single  1.392  0.020  1.392
 P5E  C2'  C3'  single  1.530  0.020  1.530
 P5E  C1'  O4'  single  1.401  0.020  1.401
 P5E  O4'  C4'  single  1.425  0.020  1.425
 P5E  C4'  C3'  single  1.541  0.020  1.541
 P5E  C3'  O3'  single  1.402  0.020  1.402
 P5E  O2B  H1   single  0.850  0.020  0.980
 P5E  O1G  H2   single  0.850  0.020  0.980
 P5E  O3G  H3   single  0.850  0.020  0.980
 P5E  C5'  H4   single  0.970  0.020  1.090
 P5E  C5'  H5   single  0.970  0.020  1.090
 P5E  C4'  H6   single  0.970  0.020  1.090
 P5E  C1'  H7   single  0.970  0.020  1.090
 P5E  C2'  H8   single  0.970  0.020  1.090
 P5E  O2'  H9   single  0.850  0.020  0.980
 P5E  C3'  H10  single  0.970  0.020  1.090
 P5E  O3'  H11  single  0.850  0.020  0.980
 P5E  C6   H12  single  0.930  0.020  1.080
 P5E  N3   H13  single  0.860  0.020  1.020
 P5E  C5   H14  single  0.930  0.020  1.080
 P5E  S1A  H15  single  1.200  0.020  1.300

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
 P5E  S1A  PA   O5'  107.95  3.000
 P5E  O5'  PA   O3A   99.47  3.000
 P5E  S1A  PA   O3A   98.00  3.000
 P5E  O5'  PA   O2A  116.07  3.000
 P5E  O3A  PA   O2A  117.23  3.000
 P5E  S1A  PA   O2A  115.58  3.000
 P5E  PB   O3A  PA   130.46  3.000
 P5E  C5'  O5'  PA   119.72  3.000
 P5E  O3B  PB   O2B  107.80  3.000
 P5E  O2B  PB   O1B  119.08  3.000
 P5E  O3B  PB   O1B  111.73  3.000
 P5E  O2B  PB   O3A  100.53  3.000
 P5E  O1B  PB   O3A  115.31  3.000
 P5E  O3B  PB   O3A  100.27  3.000
 P5E  H1   O2B  PB   115.70  3.000
 P5E  PG   O3B  PB   132.70  3.000
 P5E  O3G  PG   O2G  119.35  3.000
 P5E  O3G  PG   O1G   98.40  3.000
 P5E  O2G  PG   O1G  119.31  3.000
 P5E  O1G  PG   O3B  104.69  3.000
 P5E  O3G  PG   O3B  105.06  3.000
 P5E  O2G  PG   O3B  108.31  3.000
 P5E  H2   O1G  PG   114.82  3.000
 P5E  H3   O3G  PG   114.76  3.000
 P5E  H5   C5'  H4   108.29  3.000
 P5E  H5   C5'  C4'  109.53  3.000
 P5E  H4   C5'  C4'  109.19  3.000
 P5E  H5   C5'  O5'  110.17  3.000
 P5E  H4   C5'  O5'  109.76  3.000
 P5E  C4'  C5'  O5'  109.87  3.000
 P5E  H6   C4'  C3'  109.32  3.000
 P5E  H6   C4'  O4'  109.27  3.000
 P5E  C3'  C4'  O4'  106.74  3.000
 P5E  H6   C4'  C5'  105.32  3.000
 P5E  C3'  C4'  C5'  115.82  3.000
 P5E  O4'  C4'  C5'  110.27  3.000
 P5E  C1'  O4'  C4'  110.32  3.000
 P5E  H7   C1'  N1   106.91  3.000
 P5E  H7   C1'  C2'  109.94  3.000
 P5E  N1   C1'  C2'  114.21  3.000
 P5E  H7   C1'  O4'  111.73  3.000
 P5E  C2'  C1'  O4'  105.52  3.000
 P5E  N1   C1'  O4'  108.62  3.000
 P5E  H8   C2'  C3'  108.14  3.000
 P5E  H8   C2'  O2'  111.38  3.000
 P5E  C3'  C2'  O2'  116.51  3.000
 P5E  H8   C2'  C1'  109.81  3.000
 P5E  C3'  C2'  C1'  101.15  3.000
 P5E  O2'  C2'  C1'  109.29  3.000
 P5E  H9   O2'  C2'  108.90  3.000
 P5E  H10  C3'  O3'  111.41  3.000
 P5E  H10  C3'  C2'  112.07  3.000
 P5E  O3'  C3'  C2'  107.81  3.000
 P5E  H10  C3'  C4'  111.45  3.000
 P5E  O3'  C3'  C4'  111.86  3.000
 P5E  C2'  C3'  C4'  101.82  3.000
 P5E  H11  O3'  C3'  108.40  3.000
 P5E  C2   N1   C6   120.97  3.000
 P5E  C2   N1   C1'  119.53  3.000
 P5E  C6   N1   C1'  119.47  3.000
 P5E  H12  C6   C5   121.02  3.000
 P5E  H12  C6   N1   115.51  3.000
 P5E  C5   C6   N1   123.47  3.000
 P5E  N3   C2   O2   122.06  3.000
 P5E  O2   C2   N1   123.49  3.000
 P5E  N3   C2   N1   114.45  3.000
 P5E  H13  N3   C4   116.73  3.000
 P5E  H13  N3   C2   115.01  3.000
 P5E  C4   N3   C2   128.26  3.000
 P5E  C5   C4   O4   125.98  3.000
 P5E  C5   C4   N3   113.42  3.000
 P5E  O4   C4   N3   120.60  3.000
 P5E  H14  C5   C4   119.79  3.000
 P5E  H14  C5   C6   120.79  3.000
 P5E  C4   C5   C6   119.42  3.000
 P5E  H15  S1A  PA    94.86  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
 P5E  CONST_01  N3   C2   N1   C1'   180.00   0.0  0
 P5E  CONST_02  C4   N3   C2   N1      0.00   0.0  0
 P5E  CONST_03  N3   C2   N1   C6      0.00   0.0  0
 P5E  CONST_04  C5   C4   N3   C2      0.00   0.0  0
 P5E  CONST_05  O2   C2   N1   C1'     0.00   0.0  0
 P5E  CONST_06  O2   C2   N1   C6    180.00   0.0  0
 P5E  CONST_07  O4   C4   N3   C2    180.00   0.0  0
 P5E  CONST_08  C4   N3   C2   O2    180.00   0.0  0
 P5E  CONST_09  H13  N3   C2   N1    180.00   0.0  0
 P5E  Var_01    C4'  C5'  O5'  PA    168.09  30.0  3
 P5E  Var_02    O3B  PB   O3A  PA   -153.34  30.0  3
 P5E  Var_03    O2G  PG   O3B  PB   -166.94  30.0  3
 P5E  Var_04    S1A  PA   O3A  PB   -144.09  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
 P5E  chir_03  C4'  C5'  O4'  C3'  negativ
 P5E  chir_04  C1'  O4'  N1   C2'  negativ
 P5E  chir_05  C2'  O2'  C1'  C3'  negativ
 P5E  chir_06  C3'  O3'  C4'  C2'  positiv
 P5E  chir_07  PA   O3A  O2A  O5'  both
 P5E  chir_08  PB   O3A  O1B  O2B  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
 P5E  plan-1  C1'  0.020
 P5E  plan-1  N1   0.020
 P5E  plan-1  C6   0.020
 P5E  plan-1  C2   0.020
 P5E  plan-1  O2   0.020
 P5E  plan-1  N3   0.020
 P5E  plan-1  C4   0.020
 P5E  plan-1  O4   0.020
 P5E  plan-1  C5   0.020
 P5E  plan-1  H12  0.020
 P5E  plan-1  H13  0.020
 P5E  plan-1  H14  0.020

