# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 01:50:26 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-2-{(1S)-1-hydroxy-1-[(R)-hydroxy(oxo)-lambda~5~-phosphanyl]ethyl}-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(C[n+]2c(C)c(CCO[P](O)(=O)O[P](O)(O)=O)sc2[C@@](C)(O)[PH](O)=O)c(N)n1
#
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
 A5X  A5X  3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-2-{(1S)-1-hydroxy-1-[(R)-hydroxy(oxo)-lambda~5~-phosphanyl]ethyl}-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium  ligand  56  32  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A5X
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
 A5X  O22  O  OH1   0  -0.718  -7.9789   1.1380   1.3811
 A5X  P2   P  P     0   1.468  -7.4095   0.1236   0.3026
 A5X  O23  O  O     0  -0.677  -7.5733  -1.3163   0.5355
 A5X  O21  O  OH1   0  -0.733  -7.9582   0.5444  -1.1284
 A5X  O11  O  O2    0  -0.682  -5.8771   0.6624   0.3495
 A5X  P1   P  P     0   1.478  -4.7326   0.3885  -0.7567
 A5X  O12  O  OH1   0  -0.720  -4.6576   1.7112  -1.6282
 A5X  O13  O  O     0  -0.686  -4.9273  -0.7994  -1.5985
 A5X  O5G  O  O2    0  -0.573  -3.4903   0.3926   0.2365
 A5X  C5B  C  CH2   0  -0.147  -2.1885   0.0606  -0.2601
 A5X  C5A  C  CH2   0  -0.566  -1.1965   0.3109   0.8665
 A5X  C5   C  CR5   0  -0.307   0.1826  -0.0294   0.4117
 A5X  C4   C  CR5   0   0.505   1.0234   0.7160  -0.3466
 A5X  C4A  C  CH3   0  -0.755   0.7701   2.0852  -0.8618
 A5X  S1   S  S2    0   0.407   0.8976  -1.5424   0.7742
 A5X  C2   C  CR5   0   0.183   2.2881  -1.1737  -0.1001
 A5X  C2B  C  CT    0  -0.108   3.4280  -2.1555  -0.3076
 A5X  P3   P  P     0   0.993   3.4031  -3.4579   1.0358
 A5X  O32  O  O     0  -0.683   3.3800  -2.8492   2.3918
 A5X  O31  O  OH1   0  -0.726   4.7059  -4.2720   0.5990
 A5X  C22  C  CH3   0  -0.669   3.2645  -2.8191  -1.6745
 A5X  O24  O  OH1   0  -0.622   4.6715  -1.5188  -0.2503
 A5X  N3   N  NR5   1  -0.460   2.2004   0.0409  -0.6276
 A5X  C35  C  CH2   0  -0.403   3.2554   0.6995  -1.4016
 A5X  C5'  C  CR6   0  -0.077   4.1282   1.5583  -0.5360
 A5X  C6'  C  CR16  0  -0.071   4.0317   1.6464   0.8305
 A5X  N1'  N  N     0  -0.441   4.8102   2.4243   1.5837
 A5X  C2'  C  CR6   0   0.357   5.7194   3.1405   0.9375
 A5X  C2A  C  CH3   0  -0.730   6.6293   4.0036   1.7519
 A5X  N3'  N  N     0  -0.461   5.9108   3.1368  -0.3747
 A5X  C4'  C  CR6   0   0.496   5.1357   2.3578  -1.1269
 A5X  N4'  N  NH2   0  -0.834   5.3349   2.3837  -2.4516
 A5X  H1   H  HOH1  0   0.512  -8.8492   0.8982   1.7294
 A5X  H2   H  HOH1  0   0.503  -8.0274   1.4921  -1.3089
 A5X  H3   H  HOH1  0   0.507  -4.5325   2.5418  -1.1476
 A5X  H4   H  HCH2  0   0.264  -2.1621  -0.9865  -0.5670
 A5X  H5   H  HCH2  0   0.254  -1.9390   0.6776  -1.1275
 A5X  H6   H  HCH2  0   0.302  -1.2263   1.3576   1.1736
 A5X  H7   H  HCH2  0   0.304  -1.4677  -0.2848   1.7394
 A5X  H8   H  HCH3  0   0.287   1.5882   2.7661  -0.6287
 A5X  H9   H  HCH3  0   0.295   0.6272   2.0812  -1.9430
 A5X  H10  H  HCH3  0   0.292  -0.1318   2.4902  -0.4091
 A5X  H12  H  HOH1  0   0.511   4.8252  -5.1137   1.0610
 A5X  H13  H  HCH3  0   0.278   3.2626  -2.0854  -2.4802
 A5X  H14  H  HCH3  0   0.287   4.0809  -3.5170  -1.8526
 A5X  H15  H  HCH3  0   0.266   2.3252  -3.3690  -1.7239
 A5X  H16  H  HOH1  0   0.471   4.8608  -1.1967   0.6408
 A5X  H17  H  HCH2  0   0.330   3.8336  -0.0529  -1.9317
 A5X  H18  H  HCH2  0   0.327   2.7567   1.2949  -2.1680
 A5X  H19  H  HCR6  0   0.261   3.2860   1.0746   1.3757
 A5X  H20  H  HCH3  0   0.261   7.5784   3.4896   1.9192
 A5X  H21  H  HCH3  0   0.252   6.8523   4.9357   1.2364
 A5X  H22  H  HCH3  0   0.249   6.1936   4.2225   2.7238
 A5X  H23  H  HNH2  0   0.406   6.1214   2.8986  -2.8109
 A5X  H24  H  HNH2  0   0.421   4.9140   1.7171  -3.0745
 A5X  H25  H  H     0   0.126   2.3117  -4.2965   0.7441

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
 A5X  O13  P1   double    1.469  0.020  1.469
 A5X  O12  P1   single    1.586  0.020  1.586
 A5X  C2A  C2'  single    1.495  0.020  1.495
 A5X  P1   O11  single    1.615  0.020  1.615
 A5X  P1   O5G  single    1.590  0.020  1.590
 A5X  O11  P2   single    1.625  0.020  1.625
 A5X  O5G  C5B  single    1.432  0.020  1.432
 A5X  C2'  N1'  aromatic  1.326  0.020  1.326
 A5X  C2'  N3'  aromatic  1.326  0.020  1.326
 A5X  N1'  C6'  aromatic  1.334  0.020  1.334
 A5X  C5B  C5A  single    1.522  0.020  1.522
 A5X  O23  P2   double    1.468  0.020  1.468
 A5X  N3'  C4'  aromatic  1.332  0.020  1.332
 A5X  O21  P2   single    1.589  0.020  1.589
 A5X  P2   O22  single    1.586  0.020  1.586
 A5X  C6'  C5'  aromatic  1.373  0.020  1.373
 A5X  C5A  C5   single    1.491  0.020  1.491
 A5X  C4A  C4   single    1.485  0.020  1.485
 A5X  C4'  C5'  aromatic  1.415  0.020  1.415
 A5X  C4'  N4'  single    1.340  0.020  1.340
 A5X  C5'  C35  single    1.500  0.020  1.500
 A5X  C5   C4   aromatic  1.356  0.020  1.356
 A5X  C5   S1   aromatic  1.712  0.020  1.712
 A5X  C4   N3   aromatic  1.386  0.020  1.386
 A5X  N3   C35  single    1.465  0.020  1.465
 A5X  N3   C2   aromatic  1.327  0.020  1.327
 A5X  S1   C2   aromatic  1.683  0.020  1.683
 A5X  C2   C2B  single    1.519  0.020  1.519
 A5X  C22  C2B  single    1.528  0.020  1.528
 A5X  O24  C2B  single    1.398  0.020  1.398
 A5X  C2B  P3   single    1.871  0.020  1.871
 A5X  P3   O31  single    1.597  0.020  1.597
 A5X  P3   O32  double    1.487  0.020  1.487
 A5X  O22  H1   single    0.832  0.020  0.971
 A5X  O21  H2   single    0.832  0.020  0.971
 A5X  O12  H3   single    0.832  0.020  0.971
 A5X  C5B  H4   single    0.939  0.020  1.096
 A5X  C5B  H5   single    0.939  0.020  1.096
 A5X  C5A  H6   single    0.939  0.020  1.096
 A5X  C5A  H7   single    0.939  0.020  1.096
 A5X  C4A  H8   single    0.939  0.020  1.096
 A5X  C4A  H9   single    0.939  0.020  1.096
 A5X  C4A  H10  single    0.939  0.020  1.096
 A5X  O31  H12  single    0.832  0.020  0.971
 A5X  C22  H13  single    0.939  0.020  1.096
 A5X  C22  H14  single    0.939  0.020  1.096
 A5X  C22  H15  single    0.939  0.020  1.096
 A5X  O24  H16  single    0.832  0.020  0.971
 A5X  C35  H17  single    0.939  0.020  1.096
 A5X  C35  H18  single    0.939  0.020  1.096
 A5X  C6'  H19  single    0.929  0.020  1.085
 A5X  C2A  H20  single    0.939  0.020  1.096
 A5X  C2A  H21  single    0.939  0.020  1.096
 A5X  C2A  H22  single    0.939  0.020  1.096
 A5X  N4'  H23  single    0.868  0.020  1.013
 A5X  N4'  H24  single    0.868  0.020  1.013
 A5X  P3   H25  single    1.209  0.020  1.412

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
 A5X  H1   O22  P2   114.15  3.000
 A5X  O11  P2   O21  105.29  3.000
 A5X  O21  P2   O23  111.35  3.000
 A5X  O11  P2   O23  115.21  3.000
 A5X  O21  P2   O22  108.60  3.000
 A5X  O23  P2   O22  118.65  3.000
 A5X  O11  P2   O22   96.13  3.000
 A5X  H2   O21  P2   116.88  3.000
 A5X  P1   O11  P2   126.32  3.000
 A5X  O5G  P1   O13  117.61  3.000
 A5X  O5G  P1   O12  107.71  3.000
 A5X  O13  P1   O12  111.46  3.000
 A5X  O5G  P1   O11   97.20  3.000
 A5X  O12  P1   O11  105.57  3.000
 A5X  O13  P1   O11  115.83  3.000
 A5X  H3   O12  P1   116.68  3.000
 A5X  C5B  O5G  P1   119.52  3.000
 A5X  H5   C5B  H4   108.23  3.000
 A5X  H5   C5B  C5A  110.23  3.000
 A5X  H4   C5B  C5A  110.50  3.000
 A5X  H5   C5B  O5G  110.58  3.000
 A5X  H4   C5B  O5G  109.99  3.000
 A5X  C5A  C5B  O5G  107.32  3.000
 A5X  H7   C5A  H6   106.96  3.000
 A5X  H7   C5A  C5   110.44  3.000
 A5X  H6   C5A  C5   109.26  3.000
 A5X  H7   C5A  C5B  109.90  3.000
 A5X  H6   C5A  C5B  110.39  3.000
 A5X  C5   C5A  C5B  109.84  3.000
 A5X  S1   C5   C4   110.20  3.000
 A5X  S1   C5   C5A  121.55  3.000
 A5X  C4   C5   C5A  128.21  3.000
 A5X  N3   C4   C4A  121.59  3.000
 A5X  N3   C4   C5   111.86  3.000
 A5X  C4A  C4   C5   126.54  3.000
 A5X  H10  C4A  H9   107.78  3.000
 A5X  H10  C4A  H8   107.52  3.000
 A5X  H9   C4A  H8   108.23  3.000
 A5X  H10  C4A  C4   109.91  3.000
 A5X  H9   C4A  C4   111.28  3.000
 A5X  H8   C4A  C4   111.96  3.000
 A5X  C2   S1   C5    92.37  3.000
 A5X  N3   C2   C2B  125.94  3.000
 A5X  C2B  C2   S1   123.32  3.000
 A5X  N3   C2   S1   110.63  3.000
 A5X  O24  C2B  C22  109.24  3.000
 A5X  O24  C2B  P3   107.41  3.000
 A5X  C22  C2B  P3   109.79  3.000
 A5X  P3   C2B  C2   109.99  3.000
 A5X  O24  C2B  C2   111.56  3.000
 A5X  C22  C2B  C2   108.83  3.000
 A5X  H25  P3   O31  105.80  3.000
 A5X  H25  P3   O32  114.90  3.000
 A5X  O31  P3   O32  118.09  3.000
 A5X  H25  P3   C2B  106.04  3.000
 A5X  O32  P3   C2B  111.72  3.000
 A5X  O31  P3   C2B   98.49  3.000
 A5X  H12  O31  P3   114.43  3.000
 A5X  H15  C22  H14  108.39  3.000
 A5X  H15  C22  H13  107.75  3.000
 A5X  H14  C22  H13  108.18  3.000
 A5X  H15  C22  C2B  110.60  3.000
 A5X  H14  C22  C2B  110.15  3.000
 A5X  H13  C22  C2B  111.66  3.000
 A5X  H16  O24  C2B  111.34  3.000
 A5X  C35  N3   C2   125.02  3.000
 A5X  C2   N3   C4   114.92  3.000
 A5X  C35  N3   C4   119.99  3.000
 A5X  H18  C35  H17  106.16  3.000
 A5X  H18  C35  C5'  111.04  3.000
 A5X  H17  C35  C5'  111.61  3.000
 A5X  H18  C35  N3   106.69  3.000
 A5X  H17  C35  N3   109.24  3.000
 A5X  C5'  C35  N3   111.82  3.000
 A5X  C4'  C5'  C6'  115.43  3.000
 A5X  C4'  C5'  C35  119.79  3.000
 A5X  C6'  C5'  C35  124.78  3.000
 A5X  H19  C6'  N1'  115.10  3.000
 A5X  H19  C6'  C5'  120.94  3.000
 A5X  N1'  C6'  C5'  123.96  3.000
 A5X  C2'  N1'  C6'  116.11  3.000
 A5X  N3'  C2'  C2A  116.92  3.000
 A5X  N3'  C2'  N1'  125.44  3.000
 A5X  C2A  C2'  N1'  117.63  3.000
 A5X  H22  C2A  H21  109.45  3.000
 A5X  H22  C2A  H20  107.82  3.000
 A5X  H21  C2A  H20  107.31  3.000
 A5X  H22  C2A  C2'  111.05  3.000
 A5X  H21  C2A  C2'  111.17  3.000
 A5X  H20  C2A  C2'  109.91  3.000
 A5X  C4'  N3'  C2'  118.47  3.000
 A5X  N4'  C4'  N3'  117.43  3.000
 A5X  N4'  C4'  C5'  121.97  3.000
 A5X  N3'  C4'  C5'  120.58  3.000
 A5X  H24  N4'  H23  116.46  3.000
 A5X  H24  N4'  C4'  122.54  3.000
 A5X  H23  N4'  C4'  118.62  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
 A5X  CONST_01  C2   N3   C4   C5     0.00   0.0  0
 A5X  CONST_02  N3   C2   S1   C5     0.00   0.0  0
 A5X  CONST_03  C2   S1   C5   C4     0.00   0.0  0
 A5X  CONST_04  S1   C2   N3   C4     0.00   0.0  0
 A5X  CONST_05  N3   C4   C5   S1     0.00   0.0  0
 A5X  CONST_06  C2'  N1'  C6'  C5'    0.00   0.0  0
 A5X  CONST_07  C2'  N3'  C4'  C5'    0.00   0.0  0
 A5X  CONST_08  N3'  C2'  N1'  C6'    0.00   0.0  0
 A5X  CONST_09  N3'  C4'  C5'  C6'    0.00   0.0  0
 A5X  CONST_10  C4'  N3'  C2'  N1'    0.00   0.0  0
 A5X  CONST_11  C4'  C5'  C6'  N1'    0.00   0.0  0
 A5X  CONST_12  N3   C4   C5   C5A  180.00   0.0  0
 A5X  CONST_13  C2   S1   C5   C5A  180.00   0.0  0
 A5X  CONST_14  C35  N3   C4   C5   180.00   0.0  0
 A5X  CONST_15  C2B  C2   S1   C5   180.00   0.0  0
 A5X  CONST_16  C2B  C2   N3   C4   180.00   0.0  0
 A5X  CONST_17  S1   C5   C4   C4A  180.00   0.0  0
 A5X  CONST_18  C2   N3   C4   C4A  180.00   0.0  0
 A5X  CONST_19  C35  N3   C2   S1   180.00   0.0  0
 A5X  CONST_20  N1'  C6'  C5'  C35  180.00   0.0  0
 A5X  CONST_21  N3'  C4'  C5'  C35  180.00   0.0  0
 A5X  CONST_22  C2A  C2'  N1'  C6'  180.00   0.0  0
 A5X  CONST_23  N4'  C4'  C5'  C6'  180.00   0.0  0
 A5X  CONST_24  N4'  C4'  N3'  C2'  180.00   0.0  0
 A5X  CONST_25  C4'  N3'  C2'  C2A  180.00   0.0  0
 A5X  CONST_26  H19  C6'  N1'  C2'  180.00   0.0  0
 A5X  CONST_27  H23  N4'  C4'  C5'  180.00   0.0  0
 A5X  CONST_28  H24  N4'  C4'  C5'    0.00   0.0  0
 A5X  Var_01    C5'  C35  N3   C4    83.75  30.0  2
 A5X  Var_02    C6'  C5'  C35  N3     4.82  30.0  2
 A5X  Var_03    C4   C5   C5A  C5B   79.92  30.0  2
 A5X  Var_04    H8   C4A  C4   C5   128.81  30.0  2
 A5X  Var_05    H20  C2A  C2'  N1'   97.53  30.0  2
 A5X  Var_06    C5   C5A  C5B  O5G  179.52  30.0  3
 A5X  Var_07    O13  P1   O11  P2   -22.98  30.0  1
 A5X  Var_08    C5A  C5B  O5G  P1   173.37  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
 A5X  chir_02  C2B  C2   O24  P3   negativ
 A5X  chir_03  P1   O12  O11  O5G  both
 A5X  chir_04  P3   C2B  O31  O32  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
 A5X  plan-1  C5A  0.020
 A5X  plan-1  C5   0.020
 A5X  plan-1  C4   0.020
 A5X  plan-1  C4A  0.020
 A5X  plan-1  S1   0.020
 A5X  plan-1  C2   0.020
 A5X  plan-1  C2B  0.020
 A5X  plan-1  N3   0.020
 A5X  plan-1  C35  0.020
 A5X  plan-2  C35  0.020
 A5X  plan-2  C5'  0.020
 A5X  plan-2  C6'  0.020
 A5X  plan-2  N1'  0.020
 A5X  plan-2  C2'  0.020
 A5X  plan-2  C2A  0.020
 A5X  plan-2  N3'  0.020
 A5X  plan-2  C4'  0.020
 A5X  plan-2  N4'  0.020
 A5X  plan-2  H19  0.020
 A5X  plan-3  C4'  0.020
 A5X  plan-3  N4'  0.020
 A5X  plan-3  H23  0.020
 A5X  plan-3  H24  0.020

