# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jun  1 20:50:49 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(S)-hydroxy(phosphonoamino)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(C[n+]2csc(CCO[P@](O)(=O)N[P](O)(O)=O)c2C)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
 VNP  VNP  3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(S)-hydroxy(phosphonoamino)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium  ligand  46  26  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VNP
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
 VNP  O2G   O  OH1   0  -0.730   4.3967   2.6900  -0.0450
 VNP  PG    P  P     0   1.446   3.0116   1.9557  -0.3418
 VNP  O3G   O  O     0  -0.692   2.2816   1.7496   0.9248
 VNP  O1G   O  OH1   0  -0.741   2.2653   2.7718  -1.4949
 VNP  N3B   N  NH1   0  -0.977   3.3291   0.5671  -1.2296
 VNP  PB    P  P     0   1.461   4.0352  -0.8006  -0.5703
 VNP  O2B   O  O     0  -0.692   4.6016  -0.5102   0.7586
 VNP  O1B   O  OH1   0  -0.721   5.1101  -1.3306  -1.6095
 VNP  O1    O  O2    0  -0.582   2.9323  -1.9591  -0.6413
 VNP  C7    C  CH2   0  -0.171   1.7228  -1.8578   0.1147
 VNP  C12   C  CH2   0  -0.552   0.5541  -1.5417  -0.8132
 VNP  C11   C  CR5   0  -0.329  -0.7470  -1.6689  -0.0936
 VNP  C10   C  CR5   0   0.544  -1.4301  -0.7268   0.6074
 VNP  CM4   C  CH3   0  -0.767  -1.0350   0.6885   0.8137
 VNP  S1    S  S2    0   0.406  -1.5578  -3.1855  -0.0183
 VNP  C9    C  CR15  0  -0.145  -2.7710  -2.5296   0.9218
 VNP  N5    N  NR5   1  -0.387  -2.5855  -1.2509   1.1634
 VNP  C7A   C  CH2   0  -0.468  -3.5506  -0.4576   1.9514
 VNP  C5A   C  CR6   0  -0.044  -4.2729   0.5418   1.1084
 VNP  C6A   C  CR16  0  -0.061  -4.0930   1.8954   1.2936
 VNP  N1A   N  N     0  -0.437  -4.6717   2.8321   0.5510
 VNP  C2A   C  CR6   0   0.365  -5.4511   2.3941  -0.4334
 VNP  CM2   C  CH3   0  -0.730  -6.0453   3.4151  -1.3487
 VNP  N3A   N  N     0  -0.457  -5.7356   1.1241  -0.6799
 VNP  C4A   C  CR6   0   0.476  -5.1851   0.1871   0.0912
 VNP  N4A   N  NH2   0  -0.822  -5.5107  -1.0944  -0.1714
 VNP  H2G   H  HOH1  0   0.495   4.9568   2.8475  -0.8168
 VNP  H1G   H  HOH1  0   0.505   1.9026   3.6219  -1.2103
 VNP  H3B   H  HNH1  0   0.446   3.0688   0.5609  -2.2097
 VNP  H1B   H  HOH1  0   0.504   4.7860  -1.6821  -2.4499
 VNP  H71   H  HCH2  0   0.270   1.5758  -2.8230   0.5992
 VNP  H72   H  HCH2  0   0.249   1.8030  -1.1053   0.9039
 VNP  H121  H  HCH2  0   0.283   0.6428  -0.5342  -1.2208
 VNP  H122  H  HCH2  0   0.301   0.5718  -2.2253  -1.6641
 VNP  HM41  H  HCH3  0   0.288  -1.6378   1.3665   0.2101
 VNP  HM42  H  HCH3  0   0.279  -1.1325   0.9801   1.8595
 VNP  HM43  H  HCH3  0   0.293   0.0070   0.8343   0.5439
 VNP  H9    H  HCR5  0   0.379  -3.6036  -3.0958   1.3093
 VNP  H7A1  H  HCH2  0   0.328  -4.2201  -1.1695   2.4348
 VNP  H7A2  H  HCH2  0   0.338  -2.9988   0.0379   2.7495
 VNP  H6A   H  HCR6  0   0.278  -3.4421   2.2444   2.0904
 VNP  HM21  H  HCH3  0   0.263  -5.4003   3.5472  -2.2203
 VNP  HM22  H  HCH3  0   0.253  -7.0217   3.0993  -1.7102
 VNP  HM23  H  HCH3  0   0.252  -6.1341   4.3798  -0.8546
 VNP  H4A1  H  HNH2  0   0.400  -5.4646  -1.7824   0.5604
 VNP  H4A2  H  HNH2  0   0.404  -6.2646  -1.2417  -0.8244

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
 VNP  O2G  PG    single    1.596  0.020  1.596
 VNP  O2G  H2G   single    0.850  0.020  0.980
 VNP  PG   O3G   double    1.476  0.020  1.476
 VNP  PG   O1G   single    1.598  0.020  1.598
 VNP  PG   N3B   single    1.678  0.020  1.678
 VNP  O1G  H1G   single    0.850  0.020  0.980
 VNP  N3B  PB    single    1.674  0.020  1.674
 VNP  N3B  H3B   single    0.860  0.020  1.020
 VNP  PB   O2B   double    1.473  0.020  1.473
 VNP  PB   O1B   single    1.586  0.020  1.586
 VNP  PB   O1    single    1.601  0.020  1.601
 VNP  O1B  H1B   single    0.850  0.020  0.980
 VNP  O1   C7    single    1.430  0.020  1.430
 VNP  C7   C12   single    1.525  0.020  1.525
 VNP  C7   H71   single    0.970  0.020  1.090
 VNP  C7   H72   single    0.970  0.020  1.090
 VNP  C12  C11   single    1.492  0.020  1.492
 VNP  C12  H121  single    0.970  0.020  1.090
 VNP  C12  H122  single    0.970  0.020  1.090
 VNP  C11  C10   aromatic  1.358  0.020  1.358
 VNP  C11  S1    aromatic  1.721  0.020  1.721
 VNP  C10  CM4   single    1.484  0.020  1.484
 VNP  C10  N5    aromatic  1.385  0.020  1.385
 VNP  CM4  HM41  single    0.970  0.020  1.090
 VNP  CM4  HM42  single    0.970  0.020  1.090
 VNP  CM4  HM43  single    0.970  0.020  1.090
 VNP  S1   C9    aromatic  1.669  0.020  1.669
 VNP  C9   N5    aromatic  1.314  0.020  1.314
 VNP  C9   H9    single    0.930  0.020  1.080
 VNP  N5   C7A   single    1.477  0.020  1.477
 VNP  C7A  C5A   single    1.494  0.020  1.494
 VNP  C7A  H7A1  single    0.970  0.020  1.090
 VNP  C7A  H7A2  single    0.970  0.020  1.090
 VNP  C5A  C6A   aromatic  1.378  0.020  1.378
 VNP  C5A  C4A   aromatic  1.412  0.020  1.412
 VNP  C6A  N1A   aromatic  1.328  0.020  1.328
 VNP  C6A  H6A   single    0.930  0.020  1.080
 VNP  N1A  C2A   aromatic  1.330  0.020  1.330
 VNP  C2A  CM2   single    1.494  0.020  1.494
 VNP  C2A  N3A   aromatic  1.325  0.020  1.325
 VNP  CM2  HM21  single    0.970  0.020  1.090
 VNP  CM2  HM22  single    0.970  0.020  1.090
 VNP  CM2  HM23  single    0.970  0.020  1.090
 VNP  N3A  C4A   aromatic  1.332  0.020  1.332
 VNP  C4A  N4A   single    1.348  0.020  1.348
 VNP  N4A  H4A1  single    0.890  0.020  1.040
 VNP  N4A  H4A2  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
 VNP  H2G   O2G  PG    115.43  3.000
 VNP  N3B   PG   O1G    97.42  3.000
 VNP  N3B   PG   O3G   115.58  3.000
 VNP  O1G   PG   O3G   117.35  3.000
 VNP  N3B   PG   O2G   108.36  3.000
 VNP  O1G   PG   O2G   107.74  3.000
 VNP  O3G   PG   O2G   109.51  3.000
 VNP  H1G   O1G  PG    114.32  3.000
 VNP  H3B   N3B  PB    118.94  3.000
 VNP  H3B   N3B  PG    117.88  3.000
 VNP  PB    N3B  PG    123.18  3.000
 VNP  O1    PB   O1B   101.30  3.000
 VNP  O1    PB   O2B   116.58  3.000
 VNP  O1B   PB   O2B   113.34  3.000
 VNP  O1    PB   N3B   106.45  3.000
 VNP  O1B   PB   N3B   107.50  3.000
 VNP  O2B   PB   N3B   110.87  3.000
 VNP  H1B   O1B  PB    117.63  3.000
 VNP  C7    O1   PB    120.52  3.000
 VNP  H72   C7   H71   107.37  3.000
 VNP  H72   C7   C12   110.65  3.000
 VNP  H71   C7   C12   110.52  3.000
 VNP  H72   C7   O1    111.61  3.000
 VNP  H71   C7   O1    106.64  3.000
 VNP  C12   C7   O1    109.94  3.000
 VNP  H122  C12  H121  106.62  3.000
 VNP  H122  C12  C11   109.67  3.000
 VNP  H121  C12  C11   109.27  3.000
 VNP  H122  C12  C7    109.39  3.000
 VNP  H121  C12  C7    110.88  3.000
 VNP  C11   C12  C7    110.91  3.000
 VNP  S1    C11  C10   110.58  3.000
 VNP  S1    C11  C12   120.46  3.000
 VNP  C10   C11  C12   128.91  3.000
 VNP  N5    C10  CM4   121.81  3.000
 VNP  N5    C10  C11   111.35  3.000
 VNP  CM4   C10  C11   126.82  3.000
 VNP  HM43  CM4  HM42  106.75  3.000
 VNP  HM43  CM4  HM41  108.03  3.000
 VNP  HM42  CM4  HM41  108.39  3.000
 VNP  HM43  CM4  C10   110.42  3.000
 VNP  HM42  CM4  C10   111.39  3.000
 VNP  HM41  CM4  C10   111.67  3.000
 VNP  C9    S1   C11    91.19  3.000
 VNP  H9    C9   N5    123.60  3.000
 VNP  H9    C9   S1    123.85  3.000
 VNP  N5    C9   S1    112.53  3.000
 VNP  C7A   N5   C9    121.89  3.000
 VNP  C7A   N5   C10   123.77  3.000
 VNP  C9    N5   C10   114.33  3.000
 VNP  H7A2  C7A  H7A1  106.45  3.000
 VNP  H7A2  C7A  C5A   110.74  3.000
 VNP  H7A1  C7A  C5A   112.96  3.000
 VNP  H7A2  C7A  N5    107.71  3.000
 VNP  H7A1  C7A  N5    106.68  3.000
 VNP  C5A   C7A  N5    111.98  3.000
 VNP  C4A   C5A  C6A   115.34  3.000
 VNP  C4A   C5A  C7A   123.44  3.000
 VNP  C6A   C5A  C7A   121.21  3.000
 VNP  H6A   C6A  N1A   116.40  3.000
 VNP  H6A   C6A  C5A   119.49  3.000
 VNP  N1A   C6A  C5A   124.11  3.000
 VNP  C2A   N1A  C6A   115.91  3.000
 VNP  N3A   C2A  CM2   117.11  3.000
 VNP  N3A   C2A  N1A   125.41  3.000
 VNP  CM2   C2A  N1A   117.48  3.000
 VNP  HM23  CM2  HM22  109.58  3.000
 VNP  HM23  CM2  HM21  107.67  3.000
 VNP  HM22  CM2  HM21  107.45  3.000
 VNP  HM23  CM2  C2A   111.11  3.000
 VNP  HM22  CM2  C2A   111.22  3.000
 VNP  HM21  CM2  C2A   109.67  3.000
 VNP  C4A   N3A  C2A   118.54  3.000
 VNP  N4A   C4A  N3A   117.12  3.000
 VNP  N4A   C4A  C5A   122.37  3.000
 VNP  N3A   C4A  C5A   120.48  3.000
 VNP  H4A2  N4A  H4A1  113.93  3.000
 VNP  H4A2  N4A  C4A   116.47  3.000
 VNP  H4A1  N4A  C4A   119.84  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
 VNP  CONST_01  C9    N5   C10  C11     0.00   0.0  0
 VNP  CONST_02  N5    C9   S1   C11     0.00   0.0  0
 VNP  CONST_03  C9    S1   C11  C10     0.00   0.0  0
 VNP  CONST_04  S1    C9   N5   C10     0.00   0.0  0
 VNP  CONST_05  N5    C10  C11  S1      0.00   0.0  0
 VNP  CONST_06  C2A   N1A  C6A  C5A     0.00   0.0  0
 VNP  CONST_07  C2A   N3A  C4A  C5A     0.00   0.0  0
 VNP  CONST_08  N3A   C4A  C5A  C6A     0.00   0.0  0
 VNP  CONST_09  N3A   C2A  N1A  C6A     0.00   0.0  0
 VNP  CONST_10  C4A   C5A  C6A  N1A     0.00   0.0  0
 VNP  CONST_11  C4A   N3A  C2A  N1A     0.00   0.0  0
 VNP  CONST_12  N5    C10  C11  C12   180.00   0.0  0
 VNP  CONST_13  C9    S1   C11  C12   180.00   0.0  0
 VNP  CONST_14  C7A   N5   C10  C11   180.00   0.0  0
 VNP  CONST_15  S1    C11  C10  CM4   180.00   0.0  0
 VNP  CONST_16  C9    N5   C10  CM4   180.00   0.0  0
 VNP  CONST_17  C7A   N5   C9   S1    180.00   0.0  0
 VNP  CONST_18  N1A   C6A  C5A  C7A   180.00   0.0  0
 VNP  CONST_19  N3A   C4A  C5A  C7A   180.00   0.0  0
 VNP  CONST_20  N4A   C4A  C5A  C6A   180.00   0.0  0
 VNP  CONST_21  CM2   C2A  N1A  C6A   180.00   0.0  0
 VNP  CONST_22  N4A   C4A  N3A  C2A   180.00   0.0  0
 VNP  CONST_23  C4A   N3A  C2A  CM2   180.00   0.0  0
 VNP  CONST_24  H9    C9   S1   C11   180.00   0.0  0
 VNP  CONST_25  H6A   C6A  N1A  C2A   180.00   0.0  0
 VNP  CONST_27  H4A2  N4A  C4A  C5A   180.00   0.0  0
 VNP  Var_01    C5A   C7A  N5   C10    68.35  30.0  2
 VNP  Var_02    C6A   C5A  C7A  N5   -113.79  30.0  2
 VNP  Var_03    C10   C11  C12  C7     89.28  30.0  2
 VNP  Var_04    HM41  CM4  C10  C11   105.80  30.0  2
 VNP  Var_05    HM21  CM2  C2A  N1A    93.39  30.0  2
 VNP  Var_06    C11   C12  C7   O1    169.95  30.0  3
 VNP  Var_07    PB    N3B  PG   O2G    72.74  30.0  3
 VNP  Var_08    O2B   PB   N3B  PG    -12.91  30.0  3
 VNP  Var_09    C12   C7   O1   PB    106.62  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
 VNP  chir_01  PB  O2B  O1B  O1  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
 VNP  plan-1  C12   0.020
 VNP  plan-1  C11   0.020
 VNP  plan-1  C10   0.020
 VNP  plan-1  CM4   0.020
 VNP  plan-1  S1    0.020
 VNP  plan-1  C9    0.020
 VNP  plan-1  N5    0.020
 VNP  plan-1  C7A   0.020
 VNP  plan-1  H9    0.020
 VNP  plan-2  C7A   0.020
 VNP  plan-2  C5A   0.020
 VNP  plan-2  C6A   0.020
 VNP  plan-2  N1A   0.020
 VNP  plan-2  C2A   0.020
 VNP  plan-2  CM2   0.020
 VNP  plan-2  N3A   0.020
 VNP  plan-2  C4A   0.020
 VNP  plan-2  N4A   0.020
 VNP  plan-2  H6A   0.020
 VNP  plan-3  C4A   0.020
 VNP  plan-3  N4A   0.020
 VNP  plan-3  H4A1  0.020
 VNP  plan-3  H4A2  0.020

