# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 09:25:37 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  52  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  OP    -1  -0.895  -7.9920   2.0759   0.4374
 A5X  P2   P  P      0   1.224  -7.6163   0.6568   0.0357
 A5X  O23  O  O      0  -0.895  -8.0245  -0.4128   1.0362
 A5X  O21  O  OP    -1  -0.893  -7.8630   0.3089  -1.4240
 A5X  O11  O  O2     0  -0.776  -5.8918   0.7154   0.1766
 A5X  P1   P  P      0   1.331  -4.8707  -0.0051  -0.8234
 A5X  O12  O  OP    -1  -0.831  -4.6412   0.7771  -2.0862
 A5X  O13  O  O      0  -0.829  -5.0824  -1.4894  -0.9151
 A5X  O5G  O  O2     0  -0.627  -3.5442   0.2559   0.1653
 A5X  C5B  C  CH2    0  -0.106  -2.2806  -0.0126  -0.3765
 A5X  C5A  C  CH2    0  -0.559  -1.2579   0.0639   0.7543
 A5X  C5   C  CR5    0  -0.305   0.1302  -0.1539   0.2547
 A5X  C4   C  CR5    0   0.486   0.9671   0.7318  -0.3305
 A5X  C4A  C  CH3    0  -0.754   0.6932   2.1702  -0.5851
 A5X  S1   S  S2     0   0.354   0.8646  -1.7073   0.3112
 A5X  C2   C  CR5    0   0.197   2.2872  -1.1454  -0.4198
 A5X  C2B  C  CT     0  -0.081   3.4589  -2.0735  -0.5945
 A5X  P3   P  P      0   0.946   3.9893  -2.7480   1.1169
 A5X  O32  O  O      0  -0.766   4.6390  -1.5370   1.7473
 A5X  O31  O  OP    -1  -0.760   4.7477  -4.0267   0.9077
 A5X  C22  C  CH3    0  -0.658   3.0929  -3.1954  -1.5565
 A5X  O24  O  OH1    0  -0.654   4.6062  -1.4202  -1.0608
 A5X  N3   N  NR5    1  -0.479   2.1689   0.1436  -0.7171
 A5X  C35  C  CH2    0  -0.390   3.1705   0.9420  -1.4302
 A5X  C5'  C  CR6    0  -0.110   4.1248   1.6326  -0.5036
 A5X  C6'  C  CR16   0  -0.042   4.0923   1.5406   0.8657
 A5X  N1'  N  N      0  -0.447   4.9539   2.1647   1.6726
 A5X  C2'  C  CR6    0   0.352   5.8853   2.8960   1.0801
 A5X  C2A  C  CH3    0  -0.727   6.8851   3.5934   1.9475
 A5X  N3'  N  N      0  -0.464   6.0201   3.0595  -0.2303
 A5X  C4'  C  CR6    0   0.491   5.1559   2.4445  -1.0344
 A5X  N4'  N  NH2    0  -0.836   5.3166   2.6088  -2.3555
 A5X  H4   H  HCH2   0   0.200  -2.2329  -1.0082  -0.8369
 A5X  H5   H  HCH2   0   0.203  -2.0139   0.7116  -1.1561
 A5X  H6   H  HCH2   0   0.276  -1.3113   1.0436   1.2342
 A5X  H7   H  HCH2   0   0.276  -1.4992  -0.6732   1.5223
 A5X  H8   H  HCH3   0   0.277   1.4886   2.8114  -0.2054
 A5X  H9   H  HCH3   0   0.286   0.5704   2.3724  -1.6502
 A5X  H10  H  HCH3   0   0.289  -0.2290   2.4608  -0.0884
 A5X  H13  H  HCH3   0   0.256   2.8707  -2.8044  -2.5504
 A5X  H14  H  HCH3   0   0.262   3.9242  -3.8943  -1.6291
 A5X  H15  H  HCH3   0   0.241   2.2212  -3.7509  -1.2111
 A5X  H16  H  HOH1   0   0.455   5.0345  -1.0035  -0.2946
 A5X  H17  H  HCH2   0   0.330   3.6887   0.2939  -2.1306
 A5X  H18  H  HCH2   0   0.317   2.6203   1.6647  -2.0342
 A5X  H19  H  HCR6   0   0.254   3.3409   0.9391   1.3643
 A5X  H20  H  HCH3   0   0.256   7.8644   3.1209   1.8490
 A5X  H21  H  HCH3   0   0.251   6.9998   4.6344   1.6469
 A5X  H22  H  HCH3   0   0.246   6.5915   3.5538   2.9936
 A5X  H23  H  HNH2   0   0.403   6.0069   3.2636  -2.6824
 A5X  H24  H  HNH2   0   0.419   4.6307   2.3049  -3.0236
 A5X  H25  H  H      0   0.005   2.7402  -3.0207   1.7413

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   deloc     1.502  0.020  1.502
 A5X  O12  P1   deloc     1.503  0.020  1.503
 A5X  C2A  C2'  single    1.496  0.020  1.496
 A5X  P1   O11  single    1.601  0.020  1.601
 A5X  P1   O5G  single    1.675  0.020  1.675
 A5X  O11  P2   single    1.731  0.020  1.731
 A5X  O5G  C5B  single    1.401  0.020  1.401
 A5X  C2'  N1'  aromatic  1.324  0.020  1.324
 A5X  C2'  N3'  aromatic  1.327  0.020  1.327
 A5X  N1'  C6'  aromatic  1.335  0.020  1.335
 A5X  C5B  C5A  single    1.527  0.020  1.527
 A5X  O23  P2   deloc     1.520  0.020  1.520
 A5X  N3'  C4'  aromatic  1.331  0.020  1.331
 A5X  O21  P2   deloc     1.521  0.020  1.521
 A5X  P2   O22  deloc     1.522  0.020  1.522
 A5X  C6'  C5'  aromatic  1.373  0.020  1.373
 A5X  C5A  C5   single    1.491  0.020  1.491
 A5X  C4A  C4   single    1.486  0.020  1.486
 A5X  C4'  C5'  aromatic  1.416  0.020  1.416
 A5X  C4'  N4'  single    1.341  0.020  1.341
 A5X  C5'  C35  single    1.499  0.020  1.499
 A5X  C5   C4   aromatic  1.352  0.020  1.352
 A5X  C5   S1   aromatic  1.719  0.020  1.719
 A5X  C4   N3   aromatic  1.393  0.020  1.393
 A5X  N3   C35  single    1.466  0.020  1.466
 A5X  N3   C2   aromatic  1.328  0.020  1.328
 A5X  S1   C2   aromatic  1.695  0.020  1.695
 A5X  C2   C2B  single    1.505  0.020  1.505
 A5X  C22  C2B  single    1.523  0.020  1.523
 A5X  O24  C2B  single    1.400  0.020  1.400
 A5X  C2B  P3   single    1.914  0.020  1.914
 A5X  P3   O31  deloc     1.501  0.020  1.501
 A5X  P3   O32  deloc     1.512  0.020  1.512
 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  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  O11  P2   O21  104.33  3.000
 A5X  O21  P2   O23  115.29  3.000
 A5X  O11  P2   O23  103.75  3.000
 A5X  O21  P2   O22  115.26  3.000
 A5X  O23  P2   O22  114.58  3.000
 A5X  O11  P2   O22  101.12  3.000
 A5X  P1   O11  P2   124.70  3.000
 A5X  O5G  P1   O13  107.56  3.000
 A5X  O5G  P1   O12  107.10  3.000
 A5X  O13  P1   O12  118.97  3.000
 A5X  O5G  P1   O11   93.80  3.000
 A5X  O12  P1   O11  112.84  3.000
 A5X  O13  P1   O11  113.14  3.000
 A5X  C5B  O5G  P1   117.14  3.000
 A5X  H5   C5B  H4   106.86  3.000
 A5X  H5   C5B  C5A  109.30  3.000
 A5X  H4   C5B  C5A  109.08  3.000
 A5X  H5   C5B  O5G  111.57  3.000
 A5X  H4   C5B  O5G  112.04  3.000
 A5X  C5A  C5B  O5G  107.95  3.000
 A5X  H7   C5A  H6   106.61  3.000
 A5X  H7   C5A  C5   110.05  3.000
 A5X  H6   C5A  C5   108.88  3.000
 A5X  H7   C5A  C5B  109.84  3.000
 A5X  H6   C5A  C5B  109.73  3.000
 A5X  C5   C5A  C5B  111.60  3.000
 A5X  S1   C5   C4   109.99  3.000
 A5X  S1   C5   C5A  121.24  3.000
 A5X  C4   C5   C5A  128.72  3.000
 A5X  N3   C4   C4A  121.35  3.000
 A5X  N3   C4   C5   112.19  3.000
 A5X  C4A  C4   C5   126.46  3.000
 A5X  H10  C4A  H9   107.52  3.000
 A5X  H10  C4A  H8   107.62  3.000
 A5X  H9   C4A  H8   108.25  3.000
 A5X  H10  C4A  C4   109.68  3.000
 A5X  H9   C4A  C4   111.56  3.000
 A5X  H8   C4A  C4   112.03  3.000
 A5X  C2   S1   C5    92.57  3.000
 A5X  N3   C2   C2B  129.94  3.000
 A5X  C2B  C2   S1   119.93  3.000
 A5X  N3   C2   S1   110.09  3.000
 A5X  O24  C2B  C22  109.29  3.000
 A5X  O24  C2B  P3   103.60  3.000
 A5X  C22  C2B  P3   111.83  3.000
 A5X  P3   C2B  C2   109.22  3.000
 A5X  O24  C2B  C2   112.88  3.000
 A5X  C22  C2B  C2   109.92  3.000
 A5X  H25  P3   O31  109.96  3.000
 A5X  H25  P3   O32  110.35  3.000
 A5X  O31  P3   O32  121.55  3.000
 A5X  H25  P3   C2B  102.51  3.000
 A5X  O32  P3   C2B  102.10  3.000
 A5X  O31  P3   C2B  108.39  3.000
 A5X  H15  C22  H14  107.75  3.000
 A5X  H15  C22  H13  107.97  3.000
 A5X  H14  C22  H13  108.96  3.000
 A5X  H15  C22  C2B  111.57  3.000
 A5X  H14  C22  C2B  109.37  3.000
 A5X  H13  C22  C2B  111.13  3.000
 A5X  H16  O24  C2B  107.38  3.000
 A5X  C35  N3   C2   125.21  3.000
 A5X  C2   N3   C4   115.13  3.000
 A5X  C35  N3   C4   119.64  3.000
 A5X  H18  C35  H17  106.20  3.000
 A5X  H18  C35  C5'  110.99  3.000
 A5X  H17  C35  C5'  111.71  3.000
 A5X  H18  C35  N3   106.60  3.000
 A5X  H17  C35  N3   108.35  3.000
 A5X  C5'  C35  N3   112.66  3.000
 A5X  C4'  C5'  C6'  115.45  3.000
 A5X  C4'  C5'  C35  119.75  3.000
 A5X  C6'  C5'  C35  124.80  3.000
 A5X  H19  C6'  N1'  115.38  3.000
 A5X  H19  C6'  C5'  120.83  3.000
 A5X  N1'  C6'  C5'  123.79  3.000
 A5X  C2'  N1'  C6'  116.20  3.000
 A5X  N3'  C2'  C2A  116.56  3.000
 A5X  N3'  C2'  N1'  125.54  3.000
 A5X  C2A  C2'  N1'  117.91  3.000
 A5X  H22  C2A  H21  109.19  3.000
 A5X  H22  C2A  H20  108.26  3.000
 A5X  H21  C2A  H20  107.11  3.000
 A5X  H22  C2A  C2'  111.12  3.000
 A5X  H21  C2A  C2'  110.84  3.000
 A5X  H20  C2A  C2'  110.20  3.000
 A5X  C4'  N3'  C2'  118.27  3.000
 A5X  N4'  C4'  N3'  117.44  3.000
 A5X  N4'  C4'  C5'  121.80  3.000
 A5X  N3'  C4'  C5'  120.75  3.000
 A5X  H24  N4'  H23  116.69  3.000
 A5X  H24  N4'  C4'  122.44  3.000
 A5X  H23  N4'  C4'  118.82  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     89.48  30.0  2
 A5X  Var_02    C6'  C5'  C35  N3      0.29  30.0  2
 A5X  Var_03    C4   C5   C5A  C5B    81.80  30.0  2
 A5X  Var_04    H8   C4A  C4   C5    128.44  30.0  2
 A5X  Var_05    H20  C2A  C2'  N1'   109.04  30.0  2
 A5X  Var_06    C5   C5A  C5B  O5G  -177.61  30.0  3
 A5X  Var_07    O13  P1   O11  P2    -57.82  30.0  1
 A5X  Var_08    C5A  C5B  O5G  P1   -170.54  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

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

