# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 31 04:39:34 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: 2-{4-[(4-amino-2-methylpyrimidin-5-yl)methyl]-3-methylthiophen-2-yl}ethyl trihydrogen diphosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(Cc2csc(CCO[P@](O)(=O)O[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
 TPW  TPW  '2-{4-[(4-amino-2-methylpyrimidin-5-yl)methyl]-3-methylthiophen-2-yl}ethyl trihydrogen diphosphate'  ligand  45  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 OK
;

data_comp_TPW
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
 TPW  C2A   C  CH3   0  -0.753  -1.8969   4.2276   4.8438
 TPW  C35   C  CH2   0  -0.581   1.5577   5.4123   0.4698
 TPW  C2    C  CR15  0  -0.552   1.4623   4.2954  -1.7874
 TPW  S1    S  S2    0   0.208   1.4316   2.7459  -2.5094
 TPW  C5    C  CR5   0  -0.196   1.7192   1.9692  -1.0033
 TPW  C4    C  CR5   0   0.157   1.8576   2.8733   0.0114
 TPW  C4A   C  CH3   0  -0.761   2.1379   2.4868   1.4315
 TPW  C5A   C  CH2   0  -0.556   1.6104   0.4813  -0.9043
 TPW  C5B   C  CH2   0  -0.181   0.3440   0.0688  -0.1620
 TPW  O5G   O  O2    0  -0.571  -0.7362   0.8731  -0.6528
 TPW  P1    P  P     0   1.493  -2.2771   0.5940  -0.4284
 TPW  O11   O  O2    0  -0.703  -2.4559   0.1760   1.1132
 TPW  O12   O  OH1   0  -0.727  -2.6143  -0.8368  -1.0370
 TPW  O13   O  O     0  -0.684  -3.0807   1.7389  -0.8905
 TPW  P2    P  P     0   1.446  -2.3672   1.0253   2.5097
 TPW  O21   O  OH1   0  -0.721  -3.4366   0.2476   3.3935
 TPW  O22   O  O     0  -0.687  -0.9842   1.0719   3.0238
 TPW  O23   O  OH1   0  -0.777  -3.1010   2.3717   2.2202
 TPW  N1'   N  N     0  -0.439   0.1306   5.1987   3.9524
 TPW  C2'   C  CR6   0   0.425  -1.0244   4.6229   3.6972
 TPW  N3'   N  N     0  -0.626  -1.4674   4.3317   2.4720
 TPW  C4'   C  CR6   0   0.556  -0.7137   4.6268   1.4036
 TPW  N4'   N  NH2   0  -0.828  -1.2367   4.3888   0.1952
 TPW  C5'   C  CR6   0  -0.032   0.5785   5.1797   1.5906
 TPW  C6'   C  CR16  0  -0.088   0.9139   5.4405   2.8936
 TPW  C3    C  CR5   0   0.115   1.6750   4.2217  -0.4421
 TPW  H2A1  H  HCH3  0   0.260  -2.9400   4.4807   4.6599
 TPW  H2A2  H  HCH3  0   0.261  -1.8428   3.1479   4.9974
 TPW  H2A3  H  HCH3  0   0.262  -1.5669   4.7124   5.7586
 TPW  H351  H  HCH2  0   0.280   1.2632   6.2833  -0.1222
 TPW  H352  H  HCH2  0   0.278   2.5260   5.6612   0.9131
 TPW  H2    H  HCR5  0   0.298   1.2955   5.1846  -2.3775
 TPW  H5A1  H  HCH2  0   0.269   1.6224   0.0307  -1.8980
 TPW  H5A2  H  HCH2  0   0.275   2.4612   0.0578  -0.3645
 TPW  H4A1  H  HCH3  0   0.250   2.7976   3.2076   1.9161
 TPW  H4A2  H  HCH3  0   0.255   1.2291   2.4223   2.0326
 TPW  H4A3  H  HCH3  0   0.249   2.6288   1.5145   1.4827
 TPW  H5B1  H  HCH2  0   0.256   0.1465  -0.9932  -0.3226
 TPW  H5B2  H  HCH2  0   0.251   0.4522   0.2418   0.9085
 TPW  H12   H  HOH1  0   0.506  -2.7030  -0.8434  -2.0001
 TPW  H21   H  HOH1  0   0.504  -3.1126  -0.5748   3.7851
 TPW  H23   H  HOH1  0   0.515  -2.5094   3.2296   2.3318
 TPW  H6'   H  HCR6  0   0.270   1.8904   5.8620   3.1123
 TPW  H4'1  H  HNH2  0   0.398  -2.0835   3.8490   0.1054
 TPW  H4'2  H  HNH2  0   0.426  -0.6450   4.3992  -0.6196

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
 TPW  C2   S1    aromatic  1.710  0.020  1.710
 TPW  S1   C5    aromatic  1.719  0.020  1.719
 TPW  C5   C4    aromatic  1.366  0.020  1.366
 TPW  C4   C4A   single    1.498  0.020  1.498
 TPW  C5   C5A   single    1.495  0.020  1.495
 TPW  C5A  C5B   single    1.525  0.020  1.525
 TPW  C5B  O5G   single    1.433  0.020  1.433
 TPW  O5G  P1    single    1.582  0.020  1.582
 TPW  P1   O11   single    1.607  0.020  1.607
 TPW  P1   O12   single    1.591  0.020  1.591
 TPW  P1   O13   double    1.473  0.020  1.473
 TPW  O11  P2    single    1.637  0.020  1.637
 TPW  P2   O21   single    1.590  0.020  1.590
 TPW  P2   O22   double    1.476  0.020  1.476
 TPW  P2   O23   single    1.560  0.020  1.560
 TPW  C2A  C2'   single    1.494  0.020  1.494
 TPW  N1'  C2'   aromatic  1.316  0.020  1.316
 TPW  C2'  N3'   aromatic  1.335  0.020  1.335
 TPW  N3'  C4'   aromatic  1.340  0.020  1.340
 TPW  C4'  N4'   single    1.338  0.020  1.338
 TPW  C35  C5'   single    1.506  0.020  1.506
 TPW  C4'  C5'   aromatic  1.418  0.020  1.418
 TPW  N1'  C6'   aromatic  1.339  0.020  1.339
 TPW  C5'  C6'   aromatic  1.371  0.020  1.371
 TPW  C35  C3    single    1.504  0.020  1.504
 TPW  C2   C3    aromatic  1.364  0.020  1.364
 TPW  C4   C3    aromatic  1.434  0.020  1.434
 TPW  C2A  H2A1  single    0.970  0.020  1.090
 TPW  C2A  H2A2  single    0.970  0.020  1.090
 TPW  C2A  H2A3  single    0.970  0.020  1.090
 TPW  C35  H351  single    0.970  0.020  1.090
 TPW  C35  H352  single    0.970  0.020  1.090
 TPW  C2   H2    single    0.930  0.020  1.080
 TPW  C5A  H5A1  single    0.970  0.020  1.090
 TPW  C5A  H5A2  single    0.970  0.020  1.090
 TPW  C4A  H4A1  single    0.970  0.020  1.090
 TPW  C4A  H4A2  single    0.970  0.020  1.090
 TPW  C4A  H4A3  single    0.970  0.020  1.090
 TPW  C5B  H5B1  single    0.970  0.020  1.090
 TPW  C5B  H5B2  single    0.970  0.020  1.090
 TPW  O12  H12   single    0.850  0.020  0.980
 TPW  O21  H21   single    0.850  0.020  0.980
 TPW  O23  H23   single    0.850  0.020  0.980
 TPW  C6'  H6'   single    0.930  0.020  1.080
 TPW  N4'  H4'1  single    0.890  0.020  1.040
 TPW  N4'  H4'2  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
 TPW  H2A3  C2A  H2A2  107.92  3.000
 TPW  H2A3  C2A  H2A1  109.23  3.000
 TPW  H2A2  C2A  H2A1  107.52  3.000
 TPW  H2A3  C2A  C2'   110.53  3.000
 TPW  H2A2  C2A  C2'   109.92  3.000
 TPW  H2A1  C2A  C2'   111.61  3.000
 TPW  H352  C35  H351  106.06  3.000
 TPW  H352  C35  C3    110.90  3.000
 TPW  H351  C35  C3    108.86  3.000
 TPW  H352  C35  C5'   108.01  3.000
 TPW  H351  C35  C5'   110.53  3.000
 TPW  C3    C35  C5'   112.30  3.000
 TPW  H2    C2   C3    127.40  3.000
 TPW  H2    C2   S1    120.84  3.000
 TPW  C3    C2   S1    111.73  3.000
 TPW  C5    S1   C2     92.10  3.000
 TPW  C5A   C5   C4    128.08  3.000
 TPW  C5A   C5   S1    119.71  3.000
 TPW  C4    C5   S1    111.63  3.000
 TPW  C3    C4   C4A   124.48  3.000
 TPW  C3    C4   C5    111.99  3.000
 TPW  C4A   C4   C5    123.52  3.000
 TPW  H4A3  C4A  H4A2  107.23  3.000
 TPW  H4A3  C4A  H4A1  107.22  3.000
 TPW  H4A2  C4A  H4A1  107.33  3.000
 TPW  H4A3  C4A  C4    111.03  3.000
 TPW  H4A2  C4A  C4    112.42  3.000
 TPW  H4A1  C4A  C4    111.34  3.000
 TPW  H5A2  C5A  H5A1  106.34  3.000
 TPW  H5A2  C5A  C5B   107.53  3.000
 TPW  H5A1  C5A  C5B   109.92  3.000
 TPW  H5A2  C5A  C5    111.20  3.000
 TPW  H5A1  C5A  C5    110.48  3.000
 TPW  C5B   C5A  C5    111.22  3.000
 TPW  H5B2  C5B  H5B1  108.47  3.000
 TPW  H5B2  C5B  O5G   108.79  3.000
 TPW  H5B1  C5B  O5G   111.04  3.000
 TPW  H5B2  C5B  C5A   110.66  3.000
 TPW  H5B1  C5B  C5A   109.98  3.000
 TPW  O5G   C5B  C5A   107.91  3.000
 TPW  P1    O5G  C5B   125.91  3.000
 TPW  O13   P1   O12   117.60  3.000
 TPW  O13   P1   O11   116.25  3.000
 TPW  O12   P1   O11    96.28  3.000
 TPW  O13   P1   O5G   110.47  3.000
 TPW  O12   P1   O5G   108.11  3.000
 TPW  O11   P1   O5G   106.87  3.000
 TPW  P2    O11  P1    132.63  3.000
 TPW  H12   O12  P1    113.98  3.000
 TPW  O23   P2   O22   118.55  3.000
 TPW  O23   P2   O21   102.05  3.000
 TPW  O22   P2   O21   116.86  3.000
 TPW  O23   P2   O11   105.30  3.000
 TPW  O22   P2   O11   111.36  3.000
 TPW  O21   P2   O11   100.60  3.000
 TPW  H21   O21  P2    114.56  3.000
 TPW  H23   O23  P2    114.90  3.000
 TPW  C6'   N1'  C2'   116.05  3.000
 TPW  N3'   C2'  N1'   124.39  3.000
 TPW  N3'   C2'  C2A   116.92  3.000
 TPW  N1'   C2'  C2A   118.66  3.000
 TPW  C4'   N3'  C2'   119.79  3.000
 TPW  C5'   C4'  N4'   123.00  3.000
 TPW  C5'   C4'  N3'   119.55  3.000
 TPW  N4'   C4'  N3'   117.44  3.000
 TPW  H4'2  N4'  H4'1  115.28  3.000
 TPW  H4'2  N4'  C4'   119.94  3.000
 TPW  H4'1  N4'  C4'   120.26  3.000
 TPW  C6'   C5'  C4'   115.00  3.000
 TPW  C6'   C5'  C35   121.26  3.000
 TPW  C4'   C5'  C35   123.68  3.000
 TPW  H6'   C6'  C5'   119.04  3.000
 TPW  H6'   C6'  N1'   115.90  3.000
 TPW  C5'   C6'  N1'   125.05  3.000
 TPW  C4    C3   C2    112.49  3.000
 TPW  C4    C3   C35   124.22  3.000
 TPW  C2    C3   C35   122.88  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
 TPW  CONST_01  C4    C5   S1   C2      0.00   0.0  0
 TPW  CONST_02  C5    C4   C3   C2      0.00   0.0  0
 TPW  CONST_03  C4    C3   C2   S1      0.00   0.0  0
 TPW  CONST_04  C3    C4   C5   S1      0.00   0.0  0
 TPW  CONST_05  C3    C2   S1   C5      0.00   0.0  0
 TPW  CONST_06  C4'   N3'  C2'  N1'     0.00   0.0  0
 TPW  CONST_07  C4'   C5'  C6'  N1'     0.00   0.0  0
 TPW  CONST_08  C5'   C6'  N1'  C2'     0.00   0.0  0
 TPW  CONST_09  C5'   C4'  N3'  C2'     0.00   0.0  0
 TPW  CONST_10  C6'   N1'  C2'  N3'     0.00   0.0  0
 TPW  CONST_11  C6'   C5'  C4'  N3'     0.00   0.0  0
 TPW  CONST_12  C6'   N1'  C2'  C2A   180.00   0.0  0
 TPW  CONST_13  C4'   N3'  C2'  C2A   180.00   0.0  0
 TPW  CONST_14  N3'   C4'  C5'  C35   180.00   0.0  0
 TPW  CONST_15  N1'   C6'  C5'  C35   180.00   0.0  0
 TPW  CONST_16  S1    C2   C3   C35   180.00   0.0  0
 TPW  CONST_17  C5    C4   C3   C35   180.00   0.0  0
 TPW  CONST_18  C5A   C5   S1   C2    180.00   0.0  0
 TPW  CONST_19  C4A   C4   C3   C2    180.00   0.0  0
 TPW  CONST_20  C4A   C4   C5   S1    180.00   0.0  0
 TPW  CONST_21  C3    C4   C5   C5A   180.00   0.0  0
 TPW  CONST_22  N4'   C4'  N3'  C2'   180.00   0.0  0
 TPW  CONST_23  C6'   C5'  C4'  N4'   180.00   0.0  0
 TPW  CONST_24  H2    C2   S1   C5    180.00   0.0  0
 TPW  CONST_25  H6'   C6'  N1'  C2'   180.00   0.0  0
 TPW  CONST_26  H4'1  N4'  C4'  N3'     0.00   0.0  0
 TPW  CONST_27  H4'2  N4'  C4'  N3'   180.00   0.0  0
 TPW  Var_01    C5'   C35  C3   C2    124.03  30.0  3
 TPW  Var_02    C3    C35  C5'  C4'   -46.70  30.0  1
 TPW  Var_03    C5B   C5A  C5   S1   -106.54  30.0  2
 TPW  Var_04    H4A1  C4A  C4   C5    143.94  30.0  2
 TPW  Var_05    H2A1  C2A  C2'  N1'   136.87  30.0  2
 TPW  Var_06    O5G   C5B  C5A  C5     44.06  30.0  3
 TPW  Var_07    O11   P1   O5G  C5B    43.66  30.0  3
 TPW  Var_08    O21   P2   O11  P1    147.57  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
 TPW  chir_01  P1  O11  O12  O13  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
 TPW  plan-1  C35   0.020
 TPW  plan-1  C2    0.020
 TPW  plan-1  S1    0.020
 TPW  plan-1  C5    0.020
 TPW  plan-1  C4    0.020
 TPW  plan-1  C4A   0.020
 TPW  plan-1  C5A   0.020
 TPW  plan-1  C3    0.020
 TPW  plan-1  H2    0.020
 TPW  plan-2  C2A   0.020
 TPW  plan-2  C35   0.020
 TPW  plan-2  N1'   0.020
 TPW  plan-2  C2'   0.020
 TPW  plan-2  N3'   0.020
 TPW  plan-2  C4'   0.020
 TPW  plan-2  N4'   0.020
 TPW  plan-2  C5'   0.020
 TPW  plan-2  C6'   0.020
 TPW  plan-2  H6'   0.020
 TPW  plan-3  C4'   0.020
 TPW  plan-3  N4'   0.020
 TPW  plan-3  H4'1  0.020
 TPW  plan-3  H4'2  0.020

