# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 15:02:24 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: 5'-O-{(S)-hydroxy[(2-sulfanylethyl)amino]phosphoryl}thymidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CN([C@@H]2C[C@H](O)[C@@H](CO[P](O)(=O)NCCS)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
 08Q  08Q  5'-O-{(S)-hydroxy[(2-sulfanylethyl)amino]phosphoryl}thymidine  ligand  44  24  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_08Q
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
 08Q  P     P  P     0   1.417   3.3879   1.5679  -1.5750
 08Q  OP1   O  O     0  -0.709   4.3840   1.2879  -2.6301
 08Q  C8'   C  CH2   0  -0.574   2.8095  -0.5769   1.5860
 08Q  C7'   C  CH2   0  -0.283   2.8932   0.8393   1.0320
 08Q  C5'   C  CH2   0  -0.195   1.5980  -0.2940  -2.1137
 08Q  O5'   O  O2    0  -0.598   1.8827   1.0827  -1.8600
 08Q  C4'   C  CR15  0  -0.004   0.4796  -0.7633  -1.2186
 08Q  O4'   O  O     0  -0.489  -0.7278  -0.0946  -1.5333
 08Q  C3'   C  CR15  0   0.032   0.1651  -2.2474  -1.3753
 08Q  O3'   O  OH1   0  -0.654   1.0857  -2.9981  -0.6376
 08Q  C2'   C  CH2   0  -0.563  -1.2748  -2.2955  -0.8720
 08Q  C1'   C  CR15  0   0.181  -1.8335  -0.9407  -1.3028
 08Q  N1    N  NR6   0  -0.562  -2.7167  -0.3347  -0.3113
 08Q  C2    C  CR6   0   0.732  -4.0257  -0.0674  -0.6425
 08Q  O2    O  O     0  -0.482  -4.5189  -0.3333  -1.7199
 08Q  N3    N  NR16  0  -0.734  -4.7491   0.5285   0.3573
 08Q  C4    C  CR6   0   0.563  -4.3229   0.8865   1.6229
 08Q  N4    N  NH1   0  -0.779   3.7700   0.8825  -0.1247
 08Q  O4    O  O     0  -0.451  -5.0884   1.4106   2.4102
 08Q  C5    C  CR6   0  -0.181  -2.9307   0.5818   1.8958
 08Q  C7    C  CH3   0  -0.712  -2.3653   0.9311   3.2324
 08Q  C6    C  CR16  0   0.075  -2.2153  -0.0047   0.9227
 08Q  S     S  S2    0  -0.245   1.4800  -0.6465   2.8362
 08Q  OP3   O  OH1   0  -0.739   3.1498   3.1457  -1.4327
 08Q  H1    H  HCH2  0   0.274   2.5786  -1.2849   0.7919
 08Q  H2    H  HCH2  0   0.288   3.7594  -0.8679   2.0348
 08Q  H3    H  HCH2  0   0.245   1.8967   1.1750   0.7422
 08Q  H4    H  HCH2  0   0.269   3.2375   1.5257   1.8095
 08Q  H5    H  HCH2  0   0.260   1.3164  -0.3999  -3.1636
 08Q  H6    H  HCH2  0   0.248   2.4701  -0.9298  -1.9350
 08Q  H7    H  HCR5  0   0.230   0.7518  -0.5778  -0.1690
 08Q  H8    H  HCR5  0   0.237   0.1922  -2.5148  -2.4408
 08Q  H9    H  HOH1  0   0.464   0.9911  -3.9257  -0.8740
 08Q  H10   H  HCH2  0   0.286  -1.8553  -3.1165  -1.2901
 08Q  H11   H  HCH2  0   0.269  -1.2739  -2.4064   0.2156
 08Q  H12   H  HCR5  0   0.284  -2.4150  -1.0198  -2.2185
 08Q  H13   H  HNR6  0   0.426  -5.7164   0.7256   0.1304
 08Q  H14   H  HNH1  0   0.411   4.7571   0.7989   0.0750
 08Q  H15   H  HCH3  0   0.249  -2.4356   2.0026   3.4243
 08Q  H16   H  HCH3  0   0.249  -2.9002   0.4225   4.0355
 08Q  H17   H  HCH3  0   0.243  -1.3160   0.6472   3.2973
 08Q  H18   H  HCR6  0   0.293  -1.1748  -0.2528   1.0906
 08Q  H19   H  HSH1  0   0.235   1.2705  -1.9657   2.7894
 08Q  HOP3  H  HOH1  0   0.492   2.6806   3.4449  -0.6436

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
 08Q  C8'  C7'   single  1.523  0.020  1.523
 08Q  C8'  S     single  1.826  0.020  1.826
 08Q  C7'  N4    single  1.452  0.020  1.452
 08Q  N4   P     single  1.649  0.020  1.649
 08Q  O5'  C5'   single  1.428  0.020  1.428
 08Q  O5'  P     single  1.607  0.020  1.607
 08Q  C5'  C4'   single  1.507  0.020  1.507
 08Q  O3'  C3'   single  1.398  0.020  1.398
 08Q  P    OP1   double  1.478  0.020  1.478
 08Q  C3'  C4'   single  1.525  0.020  1.525
 08Q  C3'  C2'   single  1.526  0.020  1.526
 08Q  C4'  O4'   single  1.416  0.020  1.416
 08Q  O4'  C1'   single  1.411  0.020  1.411
 08Q  C2'  C1'   single  1.528  0.020  1.528
 08Q  C1'  N1    single  1.460  0.020  1.460
 08Q  N1   C6    single  1.372  0.020  1.372
 08Q  N1   C2    single  1.377  0.020  1.377
 08Q  C6   C5    double  1.343  0.020  1.343
 08Q  O2   C2    double  1.214  0.020  1.214
 08Q  C2   N3    single  1.370  0.020  1.370
 08Q  C5   C7    single  1.493  0.020  1.493
 08Q  C5   C4    single  1.451  0.020  1.451
 08Q  N3   C4    single  1.383  0.020  1.383
 08Q  C4   O4    double  1.217  0.020  1.217
 08Q  P    OP3   single  1.602  0.020  1.602
 08Q  C8'  H1    single  0.970  0.020  1.090
 08Q  C8'  H2    single  0.970  0.020  1.090
 08Q  C7'  H3    single  0.970  0.020  1.090
 08Q  C7'  H4    single  0.970  0.020  1.090
 08Q  C5'  H5    single  0.970  0.020  1.090
 08Q  C5'  H6    single  0.970  0.020  1.090
 08Q  C4'  H7    single  0.970  0.020  1.090
 08Q  C3'  H8    single  0.970  0.020  1.090
 08Q  O3'  H9    single  0.850  0.020  0.980
 08Q  C2'  H10   single  0.970  0.020  1.090
 08Q  C2'  H11   single  0.970  0.020  1.090
 08Q  C1'  H12   single  0.970  0.020  1.090
 08Q  N3   H13   single  0.860  0.020  1.020
 08Q  N4   H14   single  0.890  0.020  1.040
 08Q  C7   H15   single  0.970  0.020  1.090
 08Q  C7   H16   single  0.970  0.020  1.090
 08Q  C7   H17   single  0.970  0.020  1.090
 08Q  C6   H18   single  0.930  0.020  1.080
 08Q  S    H19   single  1.200  0.020  1.300
 08Q  OP3  HOP3  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
 08Q  OP3   P    N4   111.45  3.000
 08Q  OP3   P    O5'  100.01  3.000
 08Q  N4    P    O5'  104.33  3.000
 08Q  OP3   P    OP1  110.50  3.000
 08Q  O5'   P    OP1  116.58  3.000
 08Q  N4    P    OP1  113.14  3.000
 08Q  H2    C8'  H1   108.15  3.000
 08Q  H2    C8'  S    110.02  3.000
 08Q  H1    C8'  S    108.67  3.000
 08Q  H2    C8'  C7'  110.50  3.000
 08Q  H1    C8'  C7'  110.55  3.000
 08Q  S     C8'  C7'  108.94  3.000
 08Q  H4    C7'  H3   106.47  3.000
 08Q  H4    C7'  N4   110.97  3.000
 08Q  H3    C7'  N4   109.32  3.000
 08Q  H4    C7'  C8'  110.03  3.000
 08Q  H3    C7'  C8'  109.43  3.000
 08Q  N4    C7'  C8'  110.53  3.000
 08Q  H6    C5'  H5   107.83  3.000
 08Q  H6    C5'  C4'  108.27  3.000
 08Q  H5    C5'  C4'  110.44  3.000
 08Q  H6    C5'  O5'  111.86  3.000
 08Q  H5    C5'  O5'  108.40  3.000
 08Q  C4'   C5'  O5'  110.02  3.000
 08Q  C5'   O5'  P    120.61  3.000
 08Q  H7    C4'  C3'  108.25  3.000
 08Q  H7    C4'  O4'  110.09  3.000
 08Q  C3'   C4'  O4'  105.12  3.000
 08Q  H7    C4'  C5'  109.30  3.000
 08Q  O4'   C4'  C5'  110.72  3.000
 08Q  C3'   C4'  C5'  113.26  3.000
 08Q  C1'   O4'  C4'  110.41  3.000
 08Q  H8    C3'  C2'  109.59  3.000
 08Q  H8    C3'  O3'  111.39  3.000
 08Q  C2'   C3'  O3'  115.48  3.000
 08Q  H8    C3'  C4'  109.35  3.000
 08Q  C2'   C3'  C4'  101.03  3.000
 08Q  O3'   C3'  C4'  109.42  3.000
 08Q  H9    O3'  C3'  108.86  3.000
 08Q  H11   C2'  H10  107.81  3.000
 08Q  H11   C2'  C1'  111.77  3.000
 08Q  H10   C2'  C1'  111.43  3.000
 08Q  H11   C2'  C3'  109.30  3.000
 08Q  H10   C2'  C3'  113.59  3.000
 08Q  C1'   C2'  C3'  102.95  3.000
 08Q  H12   C1'  N1   106.18  3.000
 08Q  H12   C1'  C2'  111.62  3.000
 08Q  N1    C1'  C2'  113.45  3.000
 08Q  H12   C1'  O4'  108.97  3.000
 08Q  N1    C1'  O4'  109.64  3.000
 08Q  C2'   C1'  O4'  106.93  3.000
 08Q  C6    N1   C2   121.14  3.000
 08Q  C2    N1   C1'  119.51  3.000
 08Q  C6    N1   C1'  119.32  3.000
 08Q  N3    C2   O2   121.88  3.000
 08Q  N3    C2   N1   114.26  3.000
 08Q  O2    C2   N1   123.86  3.000
 08Q  H13   N3   C4   116.68  3.000
 08Q  H13   N3   C2   115.17  3.000
 08Q  C4    N3   C2   128.15  3.000
 08Q  C5    C4   O4   124.91  3.000
 08Q  O4    C4   N3   120.66  3.000
 08Q  C5    C4   N3   114.43  3.000
 08Q  H14   N4   C7'  115.46  3.000
 08Q  H14   N4   P    115.76  3.000
 08Q  C7'   N4   P    124.96  3.000
 08Q  C6    C5   C7   123.32  3.000
 08Q  C7    C5   C4   118.86  3.000
 08Q  C6    C5   C4   117.82  3.000
 08Q  H17   C7   H16  107.88  3.000
 08Q  H17   C7   H15  107.92  3.000
 08Q  H16   C7   H15  107.27  3.000
 08Q  H17   C7   C5   110.94  3.000
 08Q  H16   C7   C5   111.37  3.000
 08Q  H15   C7   C5   111.28  3.000
 08Q  H18   C6   C5   119.98  3.000
 08Q  H18   C6   N1   115.82  3.000
 08Q  C5    C6   N1   124.20  3.000
 08Q  H19   S    C8'   97.34  3.000
 08Q  HOP3  OP3  P    116.75  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
 08Q  CONST_01  N3   C2   N1   C1'   180.00   0.0  0
 08Q  CONST_02  C4   N3   C2   N1      0.00   0.0  0
 08Q  CONST_03  C5   C4   N3   C2      0.00   0.0  0
 08Q  CONST_04  C6   N1   C2   N3      0.00   0.0  0
 08Q  CONST_05  O2   C2   N1   C1'     0.00   0.0  0
 08Q  CONST_06  O4   C4   N3   C2    180.00   0.0  0
 08Q  CONST_07  C6   N1   C2   O2    180.00   0.0  0
 08Q  CONST_08  C4   N3   C2   O2    180.00   0.0  0
 08Q  CONST_09  H13  N3   C2   N1    180.00   0.0  0
 08Q  Var_01    H15  C7   C5   C4    -59.83  30.0  3
 08Q  Var_02    C4'  C5'  O5'  P     129.04  30.0  3
 08Q  Var_03    C8'  C7'  N4   P     129.95  30.0  2
 08Q  Var_04    C7'  N4   P    OP1  -171.29  30.0  1
 08Q  Var_05    N4   P    O5'  C5'   -67.12  30.0  3
 08Q  Var_06    S    C8'  C7'  N4   -169.94  30.0  1

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
 08Q  chir_02  C4'  C5'  C3'  O4'  positiv
 08Q  chir_03  C3'  O3'  C2'  C4'  negativ
 08Q  chir_04  C1'  O4'  N1   C2'  positiv
 08Q  chir_05  P    O5'  OP1  OP3  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
 08Q  plan-1  C1'  0.020
 08Q  plan-1  N1   0.020
 08Q  plan-1  C2   0.020
 08Q  plan-1  O2   0.020
 08Q  plan-1  N3   0.020
 08Q  plan-1  C4   0.020
 08Q  plan-1  O4   0.020
 08Q  plan-1  C5   0.020
 08Q  plan-1  C7   0.020
 08Q  plan-1  C6   0.020
 08Q  plan-1  H13  0.020
 08Q  plan-1  H18  0.020

