# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 30 19:27:05 2021
#   Inital geometry file: a 138 line input string
#   Ligand name: 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-2-[(Z)-2-fluoro-1-hydroxy-2-phosphonoethenyl]-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(O)=C(/F)[P](O)(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
 EN0  EN0  3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-2-[(Z)-2-fluoro-1-hydroxy-2-phosphonoethenyl]-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium  ligand  55  34  .  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_EN0
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
 EN0  C01  C  CH3   0  -0.733  -30.6607  -30.3072  267.7453
 EN0  C02  C  CR6   0   0.373  -31.7714  -30.0028  266.7949
 EN0  N03  N  N     0  -0.423  -32.8422  -29.3874  267.2894
 EN0  C04  C  CR16  0  -0.065  -33.7760  -29.0432  266.4155
 EN0  C05  C  CR6   0  -0.019  -33.6963  -29.3061  265.0608
 EN0  C06  C  CH2   0  -0.488  -34.7255  -28.8002  264.1005
 EN0  N07  N  NR5   1  -0.433  -34.1791  -27.6799  263.2972
 EN0  C08  C  CR5   0   0.103  -33.7172  -27.8203  262.0642
 EN0  C09  C  C     0   0.159  -33.7833  -28.9978  261.1940
 EN0  O10  O  OH1   0  -0.594  -32.6236  -29.4008  260.6494
 EN0  C11  C  C     0   0.100  -34.9362  -29.5473  260.8100
 EN0  F12  F  F     0  -0.287  -36.0872  -29.0094  261.2295
 EN0  P13  P  P     0   1.354  -35.1197  -30.9983  259.7243
 EN0  O14  O  OH1   0  -0.729  -34.1174  -32.0820  260.3225
 EN0  O15  O  OH1   0  -0.723  -34.3096  -30.6577  258.4002
 EN0  O16  O  O     0  -0.671  -36.5462  -31.3560  259.6124
 EN0  S17  S  S2    0   0.446  -32.9542  -26.4250  261.5162
 EN0  C18  C  CR5   0  -0.313  -33.2989  -25.6076  262.9826
 EN0  C19  C  CH2   0  -0.570  -32.9001  -24.1834  263.1686
 EN0  C20  C  CH2   0  -0.182  -33.8879  -23.2551  262.4652
 EN0  O21  O  O2    0  -0.571  -33.5629  -21.8832  262.6966
 EN0  P22  P  P     0   1.494  -32.4443  -21.1302  261.8573
 EN0  O23  O  OH1   0  -0.719  -32.7193  -19.6636  262.3818
 EN0  O24  O  O2    0  -0.698  -32.9782  -21.1891  260.3286
 EN0  P25  P  P     0   1.474  -34.1133  -20.3925  259.4950
 EN0  O26  O  O     0  -0.678  -34.3640  -21.0590  258.2088
 EN0  O27  O  OH1   0  -0.728  -33.6125  -18.8859  259.4366
 EN0  O28  O  OH1   0  -0.737  -35.2749  -20.3406  260.5714
 EN0  O29  O  O     0  -0.671  -31.0718  -21.6562  261.9078
 EN0  C30  C  CR5   0   0.527  -33.9772  -26.4192  263.8363
 EN0  C31  C  CH3   0  -0.758  -34.4586  -26.0489  265.1906
 EN0  C32  C  CR6   0   0.474  -32.5907  -30.0791  264.6690
 EN0  N33  N  NH2   0  -0.863  -32.4436  -30.5379  263.3864
 EN0  N34  N  N     0  -0.448  -31.6270  -30.3782  265.5320
 EN0  H1   H  HCH3  0   0.253  -29.8663  -30.8667  267.2593
 EN0  H2   H  HCH3  0   0.263  -30.2446  -29.3809  268.1440
 EN0  H3   H  HCH3  0   0.262  -31.0319  -30.8818  268.5945
 EN0  H4   H  HCR6  0   0.288  -34.6466  -28.5297  266.8122
 EN0  H5   H  HCH2  0   0.344  -35.6052  -28.4317  264.6247
 EN0  H6   H  HCH2  0   0.329  -35.0815  -29.5688  263.4209
 EN0  H7   H  HOH1  0   0.491  -31.9874  -29.5927  261.3592
 EN0  H8   H  HOH1  0   0.509  -34.5456  -32.7304  260.8986
 EN0  H9   H  HOH1  0   0.507  -34.7332  -30.0038  257.8269
 EN0  H10  H  HCH2  0   0.300  -32.8667  -23.9531  264.2337
 EN0  H11  H  HCH2  0   0.305  -31.8899  -24.0327  262.7853
 EN0  H12  H  HCH2  0   0.252  -33.9323  -23.4704  261.3943
 EN0  H13  H  HCH2  0   0.282  -34.8905  -23.3952  262.8665
 EN0  H14  H  HOH1  0   0.513  -31.9744  -19.0538  262.2837
 EN0  H15  H  HOH1  0   0.506  -33.0598  -18.6776  258.6706
 EN0  H16  H  HOH1  0   0.512  -36.1179  -19.9898  260.2503
 EN0  H17  H  HCH3  0   0.288  -35.4734  -26.3997  265.3713
 EN0  H18  H  HCH3  0   0.291  -33.8092  -26.4482  265.9691
 EN0  H19  H  HCH3  0   0.295  -34.4684  -24.9676  265.2968
 EN0  H20  H  HNH2  0   0.408  -31.6817  -31.1971  263.2938
 EN0  H21  H  HNH2  0   0.396  -33.2853  -30.9103  262.9680

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
 EN0  O16  P13  double    1.475  0.020  1.475
 EN0  O15  P13  single    1.589  0.020  1.589
 EN0  O26  P25  double    1.470  0.020  1.470
 EN0  P13  C11  single    1.821  0.020  1.821
 EN0  P13  O14  single    1.593  0.020  1.593
 EN0  O27  P25  single    1.589  0.020  1.589
 EN0  P25  O28  single    1.585  0.020  1.585
 EN0  P25  O24  single    1.618  0.020  1.618
 EN0  F12  C11  single    1.338  0.020  1.338
 EN0  C11  C09  double    1.334  0.020  1.334
 EN0  S17  C08  aromatic  1.682  0.020  1.682
 EN0  S17  C18  aromatic  1.714  0.020  1.714
 EN0  C09  O10  single    1.343  0.020  1.343
 EN0  C09  C08  single    1.466  0.020  1.466
 EN0  O24  P22  single    1.620  0.020  1.620
 EN0  C08  N07  aromatic  1.324  0.020  1.324
 EN0  C18  C19  single    1.491  0.020  1.491
 EN0  C18  C30  aromatic  1.359  0.020  1.359
 EN0  C19  C20  single    1.527  0.020  1.527
 EN0  C20  O21  single    1.429  0.020  1.429
 EN0  P22  O29  double    1.471  0.020  1.471
 EN0  P22  O23  single    1.582  0.020  1.582
 EN0  P22  O21  single    1.588  0.020  1.588
 EN0  N07  C30  aromatic  1.386  0.020  1.386
 EN0  N07  C06  single    1.483  0.020  1.483
 EN0  N33  C32  single    1.370  0.020  1.370
 EN0  C30  C31  single    1.484  0.020  1.484
 EN0  C06  C05  single    1.496  0.020  1.496
 EN0  C32  C05  aromatic  1.405  0.020  1.405
 EN0  C32  N34  aromatic  1.328  0.020  1.328
 EN0  C05  C04  aromatic  1.382  0.020  1.382
 EN0  N34  C02  aromatic  1.325  0.020  1.325
 EN0  C04  N03  aromatic  1.325  0.020  1.325
 EN0  C02  N03  aromatic  1.330  0.020  1.330
 EN0  C02  C01  single    1.493  0.020  1.493
 EN0  C01  H1   single    0.970  0.020  1.090
 EN0  C01  H2   single    0.970  0.020  1.090
 EN0  C01  H3   single    0.970  0.020  1.090
 EN0  C04  H4   single    0.930  0.020  1.080
 EN0  C06  H5   single    0.970  0.020  1.090
 EN0  C06  H6   single    0.970  0.020  1.090
 EN0  O10  H7   single    0.850  0.020  0.980
 EN0  O14  H8   single    0.850  0.020  0.980
 EN0  O15  H9   single    0.850  0.020  0.980
 EN0  C19  H10  single    0.970  0.020  1.090
 EN0  C19  H11  single    0.970  0.020  1.090
 EN0  C20  H12  single    0.970  0.020  1.090
 EN0  C20  H13  single    0.970  0.020  1.090
 EN0  O23  H14  single    0.850  0.020  0.980
 EN0  O27  H15  single    0.850  0.020  0.980
 EN0  O28  H16  single    0.850  0.020  0.980
 EN0  C31  H17  single    0.970  0.020  1.090
 EN0  C31  H18  single    0.970  0.020  1.090
 EN0  C31  H19  single    0.970  0.020  1.090
 EN0  N33  H20  single    0.890  0.020  1.040
 EN0  N33  H21  single    0.890  0.020  1.040

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
 EN0  H3   C01  H2   107.02  3.000
 EN0  H3   C01  H1   109.02  3.000
 EN0  H2   C01  H1   108.77  3.000
 EN0  H3   C01  C02  110.48  3.000
 EN0  H2   C01  C02  110.08  3.000
 EN0  H1   C01  C02  111.36  3.000
 EN0  N34  C02  N03  124.95  3.000
 EN0  N03  C02  C01  117.15  3.000
 EN0  N34  C02  C01  117.89  3.000
 EN0  C04  N03  C02  116.26  3.000
 EN0  H4   C04  C05  119.62  3.000
 EN0  H4   C04  N03  116.56  3.000
 EN0  C05  C04  N03  123.82  3.000
 EN0  C32  C05  C06  123.27  3.000
 EN0  C32  C05  C04  115.05  3.000
 EN0  C06  C05  C04  121.68  3.000
 EN0  H6   C06  H5   106.03  3.000
 EN0  H6   C06  N07  108.45  3.000
 EN0  H5   C06  N07  107.64  3.000
 EN0  H6   C06  C05  112.83  3.000
 EN0  H5   C06  C05  111.19  3.000
 EN0  N07  C06  C05  110.47  3.000
 EN0  C30  N07  C08  114.07  3.000
 EN0  C30  N07  C06  122.02  3.000
 EN0  C08  N07  C06  123.56  3.000
 EN0  S17  C08  C09  119.57  3.000
 EN0  C09  C08  N07  128.49  3.000
 EN0  S17  C08  N07  111.94  3.000
 EN0  C11  C09  O10  120.40  3.000
 EN0  O10  C09  C08  116.29  3.000
 EN0  C11  C09  C08  122.75  3.000
 EN0  H7   O10  C09  109.16  3.000
 EN0  P13  C11  F12  114.86  3.000
 EN0  F12  C11  C09  119.19  3.000
 EN0  P13  C11  C09  125.94  3.000
 EN0  O16  P13  O15  118.80  3.000
 EN0  O15  P13  O14   97.93  3.000
 EN0  O16  P13  O14  118.17  3.000
 EN0  O14  P13  C11  104.76  3.000
 EN0  O15  P13  C11  105.94  3.000
 EN0  O16  P13  C11  109.63  3.000
 EN0  H8   O14  P13  113.65  3.000
 EN0  H9   O15  P13  114.55  3.000
 EN0  C18  S17  C08   91.47  3.000
 EN0  C30  C18  C19  128.73  3.000
 EN0  C30  C18  S17  110.67  3.000
 EN0  C19  C18  S17  120.57  3.000
 EN0  H11  C19  H10  106.60  3.000
 EN0  H11  C19  C20  110.68  3.000
 EN0  H10  C19  C20  109.97  3.000
 EN0  H11  C19  C18  109.62  3.000
 EN0  H10  C19  C18  109.38  3.000
 EN0  C20  C19  C18  110.50  3.000
 EN0  H13  C20  H12  107.35  3.000
 EN0  H13  C20  O21  105.86  3.000
 EN0  H12  C20  O21  110.91  3.000
 EN0  H13  C20  C19  110.34  3.000
 EN0  H12  C20  C19  110.97  3.000
 EN0  O21  C20  C19  111.22  3.000
 EN0  P22  O21  C20  122.00  3.000
 EN0  O29  P22  O24  109.08  3.000
 EN0  O29  P22  O23  118.85  3.000
 EN0  O24  P22  O23  106.81  3.000
 EN0  O23  P22  O21   98.16  3.000
 EN0  O29  P22  O21  118.01  3.000
 EN0  O24  P22  O21  104.43  3.000
 EN0  H14  O23  P22  114.64  3.000
 EN0  P25  O24  P22  134.38  3.000
 EN0  O28  P25  O27  103.00  3.000
 EN0  O28  P25  O26  118.96  3.000
 EN0  O27  P25  O26  116.84  3.000
 EN0  O28  P25  O24  100.40  3.000
 EN0  O27  P25  O24  105.35  3.000
 EN0  O26  P25  O24  110.32  3.000
 EN0  H15  O27  P25  114.42  3.000
 EN0  H16  O28  P25  115.15  3.000
 EN0  C31  C30  C18  125.87  3.000
 EN0  C31  C30  N07  122.32  3.000
 EN0  C18  C30  N07  111.81  3.000
 EN0  H19  C31  H18  107.47  3.000
 EN0  H19  C31  H17  107.21  3.000
 EN0  H18  C31  H17  108.60  3.000
 EN0  H19  C31  C30  109.90  3.000
 EN0  H18  C31  C30  111.54  3.000
 EN0  H17  C31  C30  111.92  3.000
 EN0  N34  C32  N33  117.07  3.000
 EN0  N34  C32  C05  120.93  3.000
 EN0  N33  C32  C05  121.99  3.000
 EN0  H21  N33  H20  110.44  3.000
 EN0  H21  N33  C32  114.92  3.000
 EN0  H20  N33  C32  112.62  3.000
 EN0  C32  N34  C02  118.45  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
 EN0  CONST_01  C05  C32  N34  C02     0.00   0.0  0
 EN0  CONST_02  C05  C04  N03  C02     0.00   0.0  0
 EN0  CONST_03  C32  C05  C04  N03     0.00   0.0  0
 EN0  CONST_04  C32  N34  C02  N03     0.00   0.0  0
 EN0  CONST_05  N34  C32  C05  C04     0.00   0.0  0
 EN0  CONST_06  N34  C02  N03  C04     0.00   0.0  0
 EN0  CONST_07  C18  S17  C08  N07     0.00   0.0  0
 EN0  CONST_08  S17  C18  C30  N07     0.00   0.0  0
 EN0  CONST_09  C30  C18  S17  C08     0.00   0.0  0
 EN0  CONST_10  C18  C30  N07  C08     0.00   0.0  0
 EN0  CONST_11  C30  N07  C08  S17     0.00   0.0  0
 EN0  CONST_12  C32  N34  C02  C01   180.00   0.0  0
 EN0  CONST_13  C04  N03  C02  C01   180.00   0.0  0
 EN0  CONST_14  N33  C32  N34  C02   180.00   0.0  0
 EN0  CONST_15  C06  C05  C04  N03   180.00   0.0  0
 EN0  CONST_16  N33  C32  C05  C04   180.00   0.0  0
 EN0  CONST_17  S17  C08  N07  C06   180.00   0.0  0
 EN0  CONST_18  C18  C30  N07  C06   180.00   0.0  0
 EN0  CONST_19  N34  C32  C05  C06   180.00   0.0  0
 EN0  CONST_20  C19  C18  C30  N07   180.00   0.0  0
 EN0  CONST_21  C19  C18  S17  C08   180.00   0.0  0
 EN0  CONST_22  C31  C30  N07  C08   180.00   0.0  0
 EN0  CONST_23  C18  S17  C08  C09   180.00   0.0  0
 EN0  CONST_24  C30  N07  C08  C09   180.00   0.0  0
 EN0  CONST_25  C31  C30  C18  S17   180.00   0.0  0
 EN0  CONST_26  H4   C04  N03  C02   180.00   0.0  0
 EN0  CONST_27  H20  N33  C32  C05   180.00   0.0  0
 EN0  Var_01    N07  C06  C05  C04   106.37  30.0  2
 EN0  Var_02    C08  N07  C06  C05    99.47  30.0  2
 EN0  Var_03    C11  C09  C08  N07    60.27  30.0  2
 EN0  Var_04    C20  C19  C18  S17    79.12  30.0  2
 EN0  Var_05    H1   C01  C02  N03   176.20  30.0  2
 EN0  Var_06    H17  C31  C30  N07   -44.01  30.0  2
 EN0  Var_07    P13  C11  C09  C08   179.52   0.0  2
 EN0  Var_08    O21  C20  C19  C18   176.73  30.0  3
 EN0  Var_09    O16  P13  C11  C09   176.01  30.0  2
 EN0  Var_10    O24  P22  O21  C20    61.28  30.0  2
 EN0  Var_11    O26  P25  O24  P22  -167.83  30.0  2

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
 EN0  chir_01  P22  O29  O23  O21  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
 EN0  plan-1  C06  0.020
 EN0  plan-1  N07  0.020
 EN0  plan-1  C08  0.020
 EN0  plan-1  C09  0.020
 EN0  plan-1  S17  0.020
 EN0  plan-1  C18  0.020
 EN0  plan-1  C19  0.020
 EN0  plan-1  C30  0.020
 EN0  plan-1  C31  0.020
 EN0  plan-2  C01  0.020
 EN0  plan-2  C02  0.020
 EN0  plan-2  N03  0.020
 EN0  plan-2  C04  0.020
 EN0  plan-2  C05  0.020
 EN0  plan-2  C06  0.020
 EN0  plan-2  C32  0.020
 EN0  plan-2  N33  0.020
 EN0  plan-2  N34  0.020
 EN0  plan-2  H4   0.020
 EN0  plan-3  C32  0.020
 EN0  plan-3  N33  0.020
 EN0  plan-3  H20  0.020
 EN0  plan-3  H21  0.020
 EN0  plan-4  C08  0.020
 EN0  plan-4  C09  0.020
 EN0  plan-4  O10  0.020
 EN0  plan-4  C11  0.020
 EN0  plan-4  F12  0.020
 EN0  plan-4  P13  0.020

