# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 12:15:42 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: 5'-O-[(dithiophosphono)]thymidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](S)(S)=O)O2)C(=O)NC1=O
#
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
 THS  THS  5'-O-[(dithiophosphono)]thymidine  ligand  36  21  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_THS
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
 THS  P     P  P     0   1.022   1.0131   0.3586  -3.4431
 THS  O1P   O  O     0  -0.657   1.7139   1.6344  -3.1833
 THS  S2P   S  S2    0  -0.328   2.1882  -1.2963  -3.8964
 THS  S3P   S  S2    0  -0.338  -0.3648   0.6892  -4.9739
 THS  O5'   O  O2    0  -0.576   0.2289  -0.3302  -2.2351
 THS  C5'   C  CH2   0  -0.186  -0.7912   0.3901  -1.5233
 THS  C4'   C  CR15  0   0.018  -1.4780  -0.5640  -0.5817
 THS  O4'   O  O     0  -0.488  -0.5693  -0.9919   0.4141
 THS  C3'   C  CR15  0   0.018  -2.6630   0.0892   0.1354
 THS  O3'   O  OH1   0  -0.667  -3.8300  -0.1692  -0.6023
 THS  C2'   C  CH2   0  -0.559  -2.6176  -0.5671   1.5161
 THS  C1'   C  CR15  0   0.212  -1.1875  -1.0917   1.6658
 THS  N1    N  NR6   0  -0.566  -0.3628  -0.4244   2.6727
 THS  C2    C  CR6   0   0.746  -0.1360   0.9290   2.5874
 THS  O2    O  O     0  -0.475  -0.6094   1.6353   1.7216
 THS  N3    N  NR16  0  -0.733   0.6737   1.4332   3.5710
 THS  C4    C  CR6   0   0.559   1.2737   0.7531   4.6155
 THS  O4    O  O     0  -0.454   1.9666   1.3447   5.4228
 THS  C5    C  CR6   0  -0.184   1.0005  -0.6696   4.6351
 THS  C5M   C  CH3   0  -0.707   1.6062  -1.5077   5.7124
 THS  C6    C  CR16  0   0.059   0.2114  -1.1708   3.6695
 THS  HSP2  H  HSH1  0   0.271   2.8782  -0.6718  -4.8596
 THS  HSP3  H  HSH1  0   0.265  -0.8500  -0.5584  -5.0328
 THS  H5'1  H  HCH2  0   0.249  -1.5265   0.7922  -2.2263
 THS  H5'2  H  HCH2  0   0.257  -0.3449   1.2170  -0.9679
 THS  H4'   H  HCR5  0   0.245  -1.8466  -1.4325  -1.1448
 THS  H3'   H  HCR5  0   0.241  -2.4997   1.1660   0.2307
 THS  HO3'  H  HOH1  0   0.459  -4.5223   0.4190  -0.2869
 THS  H2'1  H  HCH2  0   0.272  -3.2989  -1.4195   1.5251
 THS  H2'2  H  HCH2  0   0.279  -2.9131   0.0999   2.3242
 THS  H1'   H  HCR5  0   0.260  -1.2080  -2.1358   1.9854
 THS  HN3   H  HNR6  0   0.426   0.8478   2.4295   3.5159
 THS  HM51  H  HCH3  0   0.248   2.6949  -1.4411   5.7022
 THS  HM52  H  HCH3  0   0.248   1.2725  -1.1880   6.7003
 THS  HM53  H  HCH3  0   0.247   1.3336  -2.5547   5.5909
 THS  H6    H  HCR6  0   0.317  -0.0205  -2.2268   3.6376

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
 THS  P    O1P   double  1.479  0.020  1.479
 THS  P    S2P   single  2.080  0.020  2.080
 THS  P    S3P   single  2.086  0.020  2.086
 THS  P    O5'   single  1.596  0.020  1.596
 THS  S2P  HSP2  single  1.200  0.020  1.300
 THS  S3P  HSP3  single  1.200  0.020  1.300
 THS  O5'  C5'   single  1.437  0.020  1.437
 THS  C5'  C4'   single  1.506  0.020  1.506
 THS  C5'  H5'1  single  0.970  0.020  1.090
 THS  C5'  H5'2  single  0.970  0.020  1.090
 THS  C4'  O4'   single  1.414  0.020  1.414
 THS  C4'  C3'   single  1.531  0.020  1.531
 THS  C4'  H4'   single  0.970  0.020  1.090
 THS  O4'  C1'   single  1.400  0.020  1.400
 THS  C3'  O3'   single  1.405  0.020  1.405
 THS  C3'  C2'   single  1.529  0.020  1.529
 THS  C3'  H3'   single  0.970  0.020  1.090
 THS  O3'  HO3'  single  0.850  0.020  0.980
 THS  C2'  C1'   single  1.531  0.020  1.531
 THS  C2'  H2'1  single  0.970  0.020  1.090
 THS  C2'  H2'2  single  0.970  0.020  1.090
 THS  C1'  N1    single  1.463  0.020  1.463
 THS  C1'  H1'   single  0.970  0.020  1.090
 THS  N1   C2    single  1.375  0.020  1.375
 THS  N1   C6    single  1.371  0.020  1.371
 THS  C2   O2    double  1.214  0.020  1.214
 THS  C2   N3    single  1.370  0.020  1.370
 THS  N3   C4    single  1.383  0.020  1.383
 THS  N3   HN3   single  0.860  0.020  1.020
 THS  C4   O4    double  1.217  0.020  1.217
 THS  C4   C5    single  1.449  0.020  1.449
 THS  C5   C5M   single  1.493  0.020  1.493
 THS  C5   C6    double  1.344  0.020  1.344
 THS  C5M  HM51  single  0.970  0.020  1.090
 THS  C5M  HM52  single  0.970  0.020  1.090
 THS  C5M  HM53  single  0.970  0.020  1.090
 THS  C6   H6    single  0.930  0.020  1.080

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
 THS  O5'   P    S3P   107.41  3.000
 THS  O5'   P    S2P    95.69  3.000
 THS  S3P   P    S2P   109.84  3.000
 THS  O5'   P    O1P   118.18  3.000
 THS  S3P   P    O1P   107.77  3.000
 THS  S2P   P    O1P   117.20  3.000
 THS  HSP2  S2P  P      94.41  3.000
 THS  HSP3  S3P  P      97.12  3.000
 THS  C5'   O5'  P     120.47  3.000
 THS  H5'2  C5'  H5'1  108.87  3.000
 THS  H5'2  C5'  C4'   110.38  3.000
 THS  H5'1  C5'  C4'   109.15  3.000
 THS  H5'2  C5'  O5'   109.96  3.000
 THS  H5'1  C5'  O5'   110.06  3.000
 THS  C4'   C5'  O5'   108.41  3.000
 THS  H4'   C4'  C3'   108.51  3.000
 THS  H4'   C4'  O4'   109.71  3.000
 THS  C3'   C4'  O4'   107.25  3.000
 THS  H4'   C4'  C5'   109.47  3.000
 THS  C3'   C4'  C5'   112.05  3.000
 THS  O4'   C4'  C5'   109.81  3.000
 THS  C1'   O4'  C4'   111.56  3.000
 THS  H3'   C3'  C2'   109.85  3.000
 THS  H3'   C3'  O3'   110.55  3.000
 THS  C2'   C3'  O3'   114.83  3.000
 THS  H3'   C3'  C4'   110.20  3.000
 THS  C2'   C3'  C4'   102.52  3.000
 THS  O3'   C3'  C4'   108.57  3.000
 THS  HO3'  O3'  C3'   108.26  3.000
 THS  H2'2  C2'  H2'1  107.64  3.000
 THS  H2'2  C2'  C1'   113.01  3.000
 THS  H2'1  C2'  C1'   108.35  3.000
 THS  H2'2  C2'  C3'   113.52  3.000
 THS  H2'1  C2'  C3'   108.91  3.000
 THS  C1'   C2'  C3'   105.26  3.000
 THS  H1'   C1'  N1    104.20  3.000
 THS  H1'   C1'  C2'   109.80  3.000
 THS  N1    C1'  C2'   115.97  3.000
 THS  H1'   C1'  O4'   109.76  3.000
 THS  N1    C1'  O4'   109.52  3.000
 THS  C2'   C1'  O4'   107.50  3.000
 THS  C6    N1   C2    120.78  3.000
 THS  C6    N1   C1'   119.22  3.000
 THS  C2    N1   C1'   119.96  3.000
 THS  N3    C2   O2    121.91  3.000
 THS  N3    C2   N1    114.53  3.000
 THS  O2    C2   N1    123.56  3.000
 THS  HN3   N3   C4    116.75  3.000
 THS  HN3   N3   C2    115.12  3.000
 THS  C4    N3   C2    128.13  3.000
 THS  C5    C4   O4    125.14  3.000
 THS  C5    C4   N3    114.28  3.000
 THS  O4    C4   N3    120.58  3.000
 THS  C6    C5   C5M   123.17  3.000
 THS  C6    C5   C4    117.85  3.000
 THS  C5M   C5   C4    118.97  3.000
 THS  HM53  C5M  HM52  107.84  3.000
 THS  HM53  C5M  HM51  107.92  3.000
 THS  HM52  C5M  HM51  107.22  3.000
 THS  HM53  C5M  C5    110.96  3.000
 THS  HM52  C5M  C5    111.40  3.000
 THS  HM51  C5M  C5    111.34  3.000
 THS  H6    C6   C5    120.74  3.000
 THS  H6    C6   N1    114.85  3.000
 THS  C5    C6   N1    124.41  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
 THS  CONST_01  N3    C2   N1   C1'  180.00   0.0  0
 THS  CONST_02  C4    N3   C2   N1     0.00   0.0  0
 THS  CONST_03  C5    C4   N3   C2     0.00   0.0  0
 THS  CONST_04  C6    N1   C2   N3     0.00   0.0  0
 THS  CONST_05  O2    C2   N1   C1'    0.00   0.0  0
 THS  CONST_06  O4    C4   N3   C2   180.00   0.0  0
 THS  CONST_07  C6    N1   C2   O2   180.00   0.0  0
 THS  CONST_08  C4    N3   C2   O2   180.00   0.0  0
 THS  CONST_09  HN3   N3   C2   N1   180.00   0.0  0
 THS  Var_01    HM51  C5M  C5   C4   -58.60  30.0  3
 THS  Var_02    C4'   C5'  O5'  P    172.20  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
 THS  chir_01  C4'  C5'  O4'  C3'  negativ
 THS  chir_02  C3'  O3'  C4'  C2'  positiv
 THS  chir_03  C1'  O4'  N1   C2'  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
 THS  plan-1  C1'  0.020
 THS  plan-1  N1   0.020
 THS  plan-1  C2   0.020
 THS  plan-1  O2   0.020
 THS  plan-1  N3   0.020
 THS  plan-1  C4   0.020
 THS  plan-1  O4   0.020
 THS  plan-1  C5   0.020
 THS  plan-1  C5M  0.020
 THS  plan-1  C6   0.020
 THS  plan-1  HN3  0.020
 THS  plan-1  H6   0.020

