# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 30 02:50:56 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-4-methyl-5-[2-(phosphonooxy)ethyl]-1,3-thiazol-3-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(C[n+]2csc(CCO[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
 TPS  TPS  3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-4-methyl-5-[2-(phosphonooxy)ethyl]-1,3-thiazol-3-ium  ligand  40  22  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_TPS
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
 TPS  CM2   C  CH3   0  -0.731   6.1900   2.2592   1.4074
 TPS  N3    N  NR5   1  -0.387   1.3685  -1.0580  -0.9918
 TPS  C2    C  CR15  0  -0.144   1.1724  -2.3267  -0.7074
 TPS  S1    S  S2    0   0.408  -0.1649  -2.5666   0.2626
 TPS  C5    C  CR5   0  -0.331  -0.4911  -0.8777   0.2903
 TPS  C4    C  CR5   0   0.539   0.4286  -0.2009  -0.4452
 TPS  CM4   C  CH3   0  -0.748   0.4618   1.2639  -0.6852
 TPS  C6    C  CH2   0  -0.563  -1.6872  -0.3314   0.9950
 TPS  C7    C  CH2   0  -0.143  -2.8748  -0.2628   0.0447
 TPS  O7    O  O2    0  -0.586  -3.9783   0.2676   0.7784
 TPS  N1A   N  N     0  -0.436   4.6290   2.1590  -0.4348
 TPS  C2A   C  CR6   0   0.366   5.2761   1.4870   0.5120
 TPS  N3A   N  N     0  -0.456   5.1719   0.1854   0.7378
 TPS  C4A   C  CR6   0   0.476   4.3365  -0.5267  -0.0165
 TPS  N4A   N  NH2   0  -0.823   4.2659  -1.8514   0.2251
 TPS  C5A   C  CR6   0  -0.038   3.5389   0.1062  -0.9946
 TPS  C6A   C  CR16  0  -0.066   3.7676   1.4544  -1.1609
 TPS  C7A   C  CH2   0  -0.471   2.5141  -0.6117  -1.8114
 TPS  P1    P  P     0   1.458  -5.3264   0.6437   0.0034
 TPS  O1    O  O     0  -0.708  -5.8281  -0.3589  -0.9536
 TPS  O2    O  OH1   0  -0.730  -6.1987   0.9582   1.2973
 TPS  O3    O  OH1   0  -0.739  -5.0547   2.0212  -0.7575
 TPS  HM21  H  HCH3  0   0.263   5.6957   2.4515   2.3621
 TPS  HM22  H  HCH3  0   0.255   7.0980   1.6982   1.6212
 TPS  HM23  H  HCH3  0   0.251   6.4509   3.2179   0.9663
 TPS  H2    H  HCR5  0   0.378   1.7985  -3.1235  -1.0783
 TPS  HM41  H  HCH3  0   0.284   0.5641   1.4955  -1.7452
 TPS  HM42  H  HCH3  0   0.288  -0.4649   1.7183  -0.3440
 TPS  HM43  H  HCH3  0   0.289   1.2786   1.7401  -0.1443
 TPS  H61   H  HCH2  0   0.300  -1.9369  -0.9555   1.8549
 TPS  H62   H  HCH2  0   0.295  -1.4537   0.6615   1.3819
 TPS  H71   H  HCH2  0   0.246  -2.6320   0.3738  -0.8110
 TPS  H72   H  HCH2  0   0.254  -3.1178  -1.2581  -0.3336
 TPS  H41N  H  HNH2  0   0.405   4.9583  -2.2292   0.8533
 TPS  H42N  H  HNH2  0   0.400   3.9998  -2.4801  -0.5137
 TPS  H6A   H  HCR6  0   0.279   3.2212   1.9988  -1.9255
 TPS  H7A1  H  HCH2  0   0.329   2.9068  -1.4997  -2.3071
 TPS  H7A2  H  HCH2  0   0.337   2.1259   0.0347  -2.5977
 TPS  HO2   H  HOH1  0   0.506  -7.1269   1.1570   1.1124
 TPS  HO3   H  HOH1  0   0.497  -4.7790   2.7618  -0.2003

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
 TPS  CM2  C2A   single    1.494  0.020  1.494
 TPS  CM2  HM21  single    0.970  0.020  1.090
 TPS  CM2  HM22  single    0.970  0.020  1.090
 TPS  CM2  HM23  single    0.970  0.020  1.090
 TPS  N3   C2    aromatic  1.315  0.020  1.315
 TPS  N3   C4    aromatic  1.384  0.020  1.384
 TPS  N3   C7A   single    1.478  0.020  1.478
 TPS  C2   S1    aromatic  1.669  0.020  1.669
 TPS  C2   H2    single    0.930  0.020  1.080
 TPS  S1   C5    aromatic  1.720  0.020  1.720
 TPS  C5   C4    aromatic  1.358  0.020  1.358
 TPS  C5   C6    single    1.492  0.020  1.492
 TPS  C4   CM4   single    1.485  0.020  1.485
 TPS  CM4  HM41  single    0.970  0.020  1.090
 TPS  CM4  HM42  single    0.970  0.020  1.090
 TPS  CM4  HM43  single    0.970  0.020  1.090
 TPS  C6   C7    single    1.523  0.020  1.523
 TPS  C6   H61   single    0.970  0.020  1.090
 TPS  C6   H62   single    0.970  0.020  1.090
 TPS  C7   O7    single    1.427  0.020  1.427
 TPS  C7   H71   single    0.970  0.020  1.090
 TPS  C7   H72   single    0.970  0.020  1.090
 TPS  O7   P1    single    1.600  0.020  1.600
 TPS  N1A  C2A   aromatic  1.329  0.020  1.329
 TPS  N1A  C6A   aromatic  1.329  0.020  1.329
 TPS  C2A  N3A   aromatic  1.325  0.020  1.325
 TPS  N3A  C4A   aromatic  1.332  0.020  1.332
 TPS  C4A  N4A   single    1.348  0.020  1.348
 TPS  C4A  C5A   aromatic  1.412  0.020  1.412
 TPS  N4A  H41N  single    0.890  0.020  1.040
 TPS  N4A  H42N  single    0.890  0.020  1.040
 TPS  C5A  C6A   aromatic  1.377  0.020  1.377
 TPS  C5A  C7A   single    1.494  0.020  1.494
 TPS  C6A  H6A   single    0.930  0.020  1.080
 TPS  C7A  H7A1  single    0.970  0.020  1.090
 TPS  C7A  H7A2  single    0.970  0.020  1.090
 TPS  P1   O1    double    1.474  0.020  1.474
 TPS  P1   O2    single    1.592  0.020  1.592
 TPS  P1   O3    single    1.597  0.020  1.597
 TPS  O2   HO2   single    0.850  0.020  0.980
 TPS  O3   HO3   single    0.850  0.020  0.980

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
 TPS  HM23  CM2  HM22  109.51  3.000
 TPS  HM23  CM2  HM21  107.94  3.000
 TPS  HM22  CM2  HM21  107.26  3.000
 TPS  HM23  CM2  C2A   111.06  3.000
 TPS  HM22  CM2  C2A   111.19  3.000
 TPS  HM21  CM2  C2A   109.75  3.000
 TPS  C7A   N3   C4    123.94  3.000
 TPS  C7A   N3   C2    121.80  3.000
 TPS  C4    N3   C2    114.25  3.000
 TPS  H2    C2   S1    123.94  3.000
 TPS  H2    C2   N3    123.48  3.000
 TPS  S1    C2   N3    112.57  3.000
 TPS  C5    S1   C2     91.16  3.000
 TPS  C6    C5   C4    128.04  3.000
 TPS  C6    C5   S1    121.27  3.000
 TPS  C4    C5   S1    110.61  3.000
 TPS  CM4   C4   C5    126.46  3.000
 TPS  CM4   C4   N3    122.13  3.000
 TPS  C5    C4   N3    111.41  3.000
 TPS  HM43  CM4  HM42  107.49  3.000
 TPS  HM43  CM4  HM41  108.64  3.000
 TPS  HM42  CM4  HM41  107.25  3.000
 TPS  HM43  CM4  C4    111.58  3.000
 TPS  HM42  CM4  C4    110.04  3.000
 TPS  HM41  CM4  C4    111.66  3.000
 TPS  H62   C6   H61   106.86  3.000
 TPS  H62   C6   C7    110.32  3.000
 TPS  H61   C6   C7    109.82  3.000
 TPS  H62   C6   C5    109.22  3.000
 TPS  H61   C6   C5    110.25  3.000
 TPS  C7    C6   C5    110.31  3.000
 TPS  H72   C7   H71   107.99  3.000
 TPS  H72   C7   O7    110.16  3.000
 TPS  H71   C7   O7    110.95  3.000
 TPS  H72   C7   C6    110.40  3.000
 TPS  H71   C7   C6    109.96  3.000
 TPS  O7    C7   C6    107.39  3.000
 TPS  P1    O7   C7    119.33  3.000
 TPS  C6A   N1A  C2A   115.90  3.000
 TPS  N3A   C2A  N1A   125.42  3.000
 TPS  N3A   C2A  CM2   116.97  3.000
 TPS  N1A   C2A  CM2   117.60  3.000
 TPS  C4A   N3A  C2A   118.55  3.000
 TPS  C5A   C4A  N4A   122.34  3.000
 TPS  C5A   C4A  N3A   120.46  3.000
 TPS  N4A   C4A  N3A   117.17  3.000
 TPS  H42N  N4A  H41N  113.89  3.000
 TPS  H42N  N4A  C4A   119.75  3.000
 TPS  H41N  N4A  C4A   116.35  3.000
 TPS  C7A   C5A  C6A   121.21  3.000
 TPS  C7A   C5A  C4A   123.42  3.000
 TPS  C6A   C5A  C4A   115.38  3.000
 TPS  H6A   C6A  C5A   119.48  3.000
 TPS  H6A   C6A  N1A   116.42  3.000
 TPS  C5A   C6A  N1A   124.10  3.000
 TPS  H7A2  C7A  H7A1  106.47  3.000
 TPS  H7A2  C7A  C5A   110.73  3.000
 TPS  H7A1  C7A  C5A   113.13  3.000
 TPS  H7A2  C7A  N3    107.65  3.000
 TPS  H7A1  C7A  N3    106.59  3.000
 TPS  C5A   C7A  N3    111.94  3.000
 TPS  O3    P1   O2    108.06  3.000
 TPS  O3    P1   O1    109.58  3.000
 TPS  O2    P1   O1    118.40  3.000
 TPS  O3    P1   O7    106.87  3.000
 TPS  O2    P1   O7     96.57  3.000
 TPS  O1    P1   O7    116.20  3.000
 TPS  HO2   O2   P1    114.28  3.000
 TPS  HO3   O3   P1    115.76  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
 TPS  CONST_01  C5    S1   C2   N3      0.00   0.0  0
 TPS  CONST_02  S1    C5   C4   N3      0.00   0.0  0
 TPS  CONST_03  C5    C4   N3   C2      0.00   0.0  0
 TPS  CONST_04  C4    C5   S1   C2      0.00   0.0  0
 TPS  CONST_05  C4    N3   C2   S1      0.00   0.0  0
 TPS  CONST_06  C4A   N3A  C2A  N1A     0.00   0.0  0
 TPS  CONST_07  C4A   C5A  C6A  N1A     0.00   0.0  0
 TPS  CONST_08  C5A   C6A  N1A  C2A     0.00   0.0  0
 TPS  CONST_09  C5A   C4A  N3A  C2A     0.00   0.0  0
 TPS  CONST_10  C6A   N1A  C2A  N3A     0.00   0.0  0
 TPS  CONST_11  C6A   C5A  C4A  N3A     0.00   0.0  0
 TPS  CONST_12  C6A   N1A  C2A  CM2   180.00   0.0  0
 TPS  CONST_13  C4A   N3A  C2A  CM2   180.00   0.0  0
 TPS  CONST_14  C6    C5   C4   N3    180.00   0.0  0
 TPS  CONST_15  CM4   C4   N3   C2    180.00   0.0  0
 TPS  CONST_16  C6    C5   S1   C2    180.00   0.0  0
 TPS  CONST_17  C7A   N3   C2   S1    180.00   0.0  0
 TPS  CONST_18  CM4   C4   C5   S1    180.00   0.0  0
 TPS  CONST_19  C7A   N3   C4   C5    180.00   0.0  0
 TPS  CONST_20  C7A   C5A  C6A  N1A   180.00   0.0  0
 TPS  CONST_21  N4A   C4A  N3A  C2A   180.00   0.0  0
 TPS  CONST_22  C7A   C5A  C4A  N3A   180.00   0.0  0
 TPS  CONST_23  C6A   C5A  C4A  N4A   180.00   0.0  0
 TPS  CONST_24  H2    C2   S1   C5    180.00   0.0  0
 TPS  CONST_25  H6A   C6A  N1A  C2A   180.00   0.0  0
 TPS  CONST_26  H41N  N4A  C4A  N3A     0.00   0.0  0
 TPS  Var_01    C4A   C5A  C7A  N3     68.21  30.0  2
 TPS  Var_02    C5A   C7A  N3   C2   -108.55  30.0  2
 TPS  Var_03    C7    C6   C5   S1    -90.14  30.0  2
 TPS  Var_04    HM41  CM4  C4   N3     49.38  30.0  2
 TPS  Var_05    HM21  CM2  C2A  N1A   100.83  30.0  2
 TPS  Var_06    O7    C7   C6   C5   -179.90  30.0  3
 TPS  Var_07    O1    P1   O7   C7     46.39  30.0  3

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
 TPS  plan-1  N3    0.020
 TPS  plan-1  C2    0.020
 TPS  plan-1  S1    0.020
 TPS  plan-1  C5    0.020
 TPS  plan-1  C4    0.020
 TPS  plan-1  CM4   0.020
 TPS  plan-1  C6    0.020
 TPS  plan-1  C7A   0.020
 TPS  plan-1  H2    0.020
 TPS  plan-2  CM2   0.020
 TPS  plan-2  N1A   0.020
 TPS  plan-2  C2A   0.020
 TPS  plan-2  N3A   0.020
 TPS  plan-2  C4A   0.020
 TPS  plan-2  N4A   0.020
 TPS  plan-2  C5A   0.020
 TPS  plan-2  C6A   0.020
 TPS  plan-2  C7A   0.020
 TPS  plan-2  H6A   0.020
 TPS  plan-3  C4A   0.020
 TPS  plan-3  N4A   0.020
 TPS  plan-3  H41N  0.020
 TPS  plan-3  H42N  0.020

