# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Aug  3 03:29:03 2022
#   Inital geometry file: a 117 line input string
#   Ligand name: [[[(2~{R},3~{S},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-sulfanyl-phosphinic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(S)=O)[C@@H](O)[C@H]2O
#
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
 UFQ  UFQ  "Cytosine 5'-[gamma-thio]triphosphate"  ligand  42  29  .  2022-08-11  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_UFQ
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
 UFQ  N1   N  NR6    0  -0.558  -11.5730  17.2728  -31.6479
 UFQ  N3   N  NH2    0  -0.808  -10.2399  14.0821  -33.7151
 UFQ  C4   C  CR16   0   0.100  -10.2530  16.9668  -31.6024
 UFQ  C5   C  CH1    0   0.201  -12.0686  18.4088  -30.8930
 UFQ  C6   C  CH1    0  -0.046  -11.9597  18.2510  -29.3787
 UFQ  C7   C  CH1    0  -0.029  -11.9505  19.7148  -28.9330
 UFQ  C8   C  CH1    0  -0.024  -11.1280  20.3636  -30.0409
 UFQ  C1   C  CR6    0   0.592  -12.4597  16.5010  -32.4247
 UFQ  C2   C  CR6    0   0.514  -10.6738  15.1426  -33.0354
 UFQ  C3   C  CR16   0  -0.475   -9.7452  15.9158  -32.2716
 UFQ  C9   C  CH2    0  -0.190   -9.6386  20.4685  -29.7438
 UFQ  N2   N  N      0  -0.540  -11.9550  15.4438  -33.0951
 UFQ  O1   O  O      0  -0.507  -13.6441  16.8007  -32.4680
 UFQ  O10  O  O      0  -0.776  -10.3213  23.2521  -31.8415
 UFQ  O11  O  O2     0  -0.730   -9.3803  25.4611  -31.1098
 UFQ  O12  O  OP    -1  -0.773   -8.6079  26.6403  -28.9479
 UFQ  O13  O  O      0  -0.758  -10.7657  27.4306  -30.2232
 UFQ  O2   O  OH1    0  -0.653  -13.0331  17.4931  -28.9012
 UFQ  O3   O  O2     0  -0.500  -11.3077  19.5442  -31.2024
 UFQ  O4   O  OH1    0  -0.666  -13.2490  20.2534  -28.9625
 UFQ  O5   O  O2     0  -0.624   -9.4634  21.4111  -28.7109
 UFQ  O6   O  O      0  -0.791   -6.9353  21.7108  -29.0614
 UFQ  O7   O  OP    -1  -0.783   -8.3246  23.2692  -27.4892
 UFQ  O8   O  O2     0  -0.756   -8.5138  23.3634  -30.0693
 UFQ  O9   O  OP    -1  -0.800  -10.8913  24.1785  -29.4636
 UFQ  P1   P  P      0   1.352   -8.1909  22.4552  -28.7327
 UFQ  P2   P  P      0   1.374   -9.9375  23.9926  -30.5995
 UFQ  P3   P  P      0   1.178   -9.3984  26.8318  -30.2000
 UFQ  S1   S  S2     0  -0.518   -8.1066  28.0328  -31.4285
 UFQ  H1   H  HNH2   0   0.401  -10.8835  13.5283  -34.2545
 UFQ  H2   H  HNH2   0   0.414   -9.2738  13.8060  -33.6991
 UFQ  H3   H  HCR6   0   0.320   -9.6193  17.6087  -31.0069
 UFQ  H4   H  HCH1   0   0.263  -13.1133  18.5352  -31.1827
 UFQ  H5   H  HCH1   0   0.248  -10.9960  17.7936  -29.1174
 UFQ  H6   H  HCH1   0   0.245  -11.4851  19.8427  -27.9478
 UFQ  H7   H  HCH1   0   0.252  -11.5077  21.3649  -30.2568
 UFQ  H8   H  HCR6   0   0.286   -8.6927  15.6791  -32.2305
 UFQ  H9   H  HCH2   0   0.217   -9.2307  19.4959  -29.4416
 UFQ  H10  H  HCH2   0   0.225   -9.1267  20.7583  -30.6663
 UFQ  H12  H  HOH1   0   0.465  -12.8143  17.1586  -28.0257
 UFQ  H13  H  HOH1   0   0.444  -13.8393  19.6258  -28.5294
 UFQ  H16  H  HSH1   0   0.211   -8.9670  28.3039  -32.4174

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
 UFQ  N3   C2   single  1.332  0.020  1.332
 UFQ  N2   C2   double  1.317  0.020  1.317
 UFQ  N2   C1   single  1.350  0.020  1.350
 UFQ  C2   C3   single  1.430  0.020  1.430
 UFQ  O1   C1   double  1.222  0.020  1.222
 UFQ  C1   N1   single  1.409  0.020  1.409
 UFQ  O10  P2   deloc   1.496  0.020  1.496
 UFQ  C3   C4   double  1.345  0.020  1.345
 UFQ  O11  P2   single  1.651  0.020  1.651
 UFQ  O11  P3   single  1.645  0.020  1.645
 UFQ  N1   C4   single  1.356  0.020  1.356
 UFQ  N1   C5   single  1.451  0.020  1.451
 UFQ  O13  P3   deloc   1.493  0.020  1.493
 UFQ  P2   O8   single  1.644  0.020  1.644
 UFQ  P2   O9   deloc   1.495  0.020  1.495
 UFQ  O3   C5   single  1.401  0.020  1.401
 UFQ  O3   C8   single  1.433  0.020  1.433
 UFQ  S1   P3   single  2.149  0.020  2.149
 UFQ  P3   O12  deloc   1.493  0.020  1.493
 UFQ  C5   C6   single  1.526  0.020  1.526
 UFQ  O8   P1   single  1.648  0.020  1.648
 UFQ  C8   C9   single  1.522  0.020  1.522
 UFQ  C8   C7   single  1.525  0.020  1.525
 UFQ  C9   O5   single  1.409  0.020  1.409
 UFQ  C6   C7   single  1.530  0.020  1.530
 UFQ  C6   O2   single  1.398  0.020  1.398
 UFQ  O5   P1   single  1.646  0.020  1.646
 UFQ  P1   O6   deloc   1.496  0.020  1.496
 UFQ  P1   O7   deloc   1.492  0.020  1.492
 UFQ  C7   O4   single  1.406  0.020  1.406
 UFQ  N3   H1   single  0.860  0.020  1.020
 UFQ  N3   H2   single  0.860  0.020  1.020
 UFQ  C4   H3   single  0.930  0.020  1.080
 UFQ  C5   H4   single  0.970  0.020  1.090
 UFQ  C6   H5   single  0.970  0.020  1.090
 UFQ  C7   H6   single  0.970  0.020  1.090
 UFQ  C8   H7   single  0.970  0.020  1.090
 UFQ  C3   H8   single  0.930  0.020  1.080
 UFQ  C9   H9   single  0.970  0.020  1.090
 UFQ  C9   H10  single  0.970  0.020  1.090
 UFQ  O2   H12  single  0.850  0.020  0.980
 UFQ  O4   H13  single  0.850  0.020  0.980
 UFQ  S1   H16  single  1.200  0.020  1.300

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
 UFQ  C1   N1   C5   120.04  3.000
 UFQ  C5   N1   C4   119.46  3.000
 UFQ  C1   N1   C4   120.50  3.000
 UFQ  H2   N3   H1   118.18  3.000
 UFQ  H2   N3   C2   121.58  3.000
 UFQ  H1   N3   C2   120.23  3.000
 UFQ  H3   C4   C3   121.11  3.000
 UFQ  H3   C4   N1   117.08  3.000
 UFQ  C3   C4   N1   121.81  3.000
 UFQ  H4   C5   O3   111.55  3.000
 UFQ  H4   C5   C6   110.09  3.000
 UFQ  O3   C5   C6   105.31  3.000
 UFQ  H4   C5   N1   106.23  3.000
 UFQ  C6   C5   N1   114.26  3.000
 UFQ  O3   C5   N1   109.51  3.000
 UFQ  H5   C6   O2   111.51  3.000
 UFQ  H5   C6   C7   108.90  3.000
 UFQ  O2   C6   C7   115.07  3.000
 UFQ  H5   C6   C5   109.98  3.000
 UFQ  O2   C6   C5   109.88  3.000
 UFQ  C7   C6   C5   100.98  3.000
 UFQ  H6   C7   O4   111.46  3.000
 UFQ  H6   C7   C8   111.96  3.000
 UFQ  O4   C7   C8   108.66  3.000
 UFQ  H6   C7   C6   112.07  3.000
 UFQ  O4   C7   C6   110.78  3.000
 UFQ  C8   C7   C6   101.46  3.000
 UFQ  H7   C8   O3   108.69  3.000
 UFQ  H7   C8   C9   108.39  3.000
 UFQ  O3   C8   C9   108.68  3.000
 UFQ  H7   C8   C7   110.25  3.000
 UFQ  C9   C8   C7   114.54  3.000
 UFQ  O3   C8   C7   106.14  3.000
 UFQ  O1   C1   N2   122.46  3.000
 UFQ  O1   C1   N1   119.67  3.000
 UFQ  N2   C1   N1   117.87  3.000
 UFQ  N2   C2   C3   122.16  3.000
 UFQ  C3   C2   N3   119.45  3.000
 UFQ  N2   C2   N3   118.39  3.000
 UFQ  H8   C3   C2   122.35  3.000
 UFQ  H8   C3   C4   121.35  3.000
 UFQ  C2   C3   C4   116.30  3.000
 UFQ  H10  C9   H9   107.04  3.000
 UFQ  H10  C9   O5   112.50  3.000
 UFQ  H9   C9   O5   110.17  3.000
 UFQ  H10  C9   C8   108.15  3.000
 UFQ  H9   C9   C8   110.87  3.000
 UFQ  O5   C9   C8   108.11  3.000
 UFQ  C2   N2   C1   121.35  3.000
 UFQ  P3   O11  P2   124.49  3.000
 UFQ  H12  O2   C6   108.94  3.000
 UFQ  C8   O3   C5   110.64  3.000
 UFQ  H13  O4   C7   107.85  3.000
 UFQ  P1   O5   C9   120.70  3.000
 UFQ  P2   O8   P1   129.94  3.000
 UFQ  O8   P1   O7   110.96  3.000
 UFQ  O7   P1   O6   121.98  3.000
 UFQ  O8   P1   O6   105.09  3.000
 UFQ  O7   P1   O5   105.41  3.000
 UFQ  O6   P1   O5   109.63  3.000
 UFQ  O8   P1   O5   102.06  3.000
 UFQ  O9   P2   O8   110.79  3.000
 UFQ  O9   P2   O11  109.85  3.000
 UFQ  O8   P2   O11   98.50  3.000
 UFQ  O9   P2   O10  121.92  3.000
 UFQ  O8   P2   O10  107.48  3.000
 UFQ  O11  P2   O10  105.68  3.000
 UFQ  S1   P3   O13  108.51  3.000
 UFQ  S1   P3   O12  103.46  3.000
 UFQ  O13  P3   O12  123.32  3.000
 UFQ  O12  P3   O11  110.55  3.000
 UFQ  S1   P3   O11   98.21  3.000
 UFQ  O13  P3   O11  109.61  3.000
 UFQ  H16  S1   P3    98.58  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
 UFQ  CONST_01  C2   N2   C1   N1      0.00   0.0  0
 UFQ  CONST_02  N2   C1   N1   C4      0.00   0.0  0
 UFQ  CONST_03  N2   C1   N1   C5    180.00   0.0  0
 UFQ  CONST_04  C3   C2   N2   C1      0.00   0.0  0
 UFQ  CONST_05  C1   N2   C2   N3    180.00   0.0  0
 UFQ  CONST_06  O1   C1   N1   C4    180.00   0.0  0
 UFQ  CONST_07  O1   C1   N1   C5      0.00   0.0  0
 UFQ  CONST_08  O1   C1   N2   C2    180.00   0.0  0
 UFQ  CONST_09  H1   N3   C2   C3    180.00   0.0  0
 UFQ  CONST_10  H2   N3   C2   C3      0.00   0.0  0
 UFQ  CONST_11  H1   N3   C2   N2      0.00   0.0  0
 UFQ  CONST_12  H2   N3   C2   N2    180.00   0.0  0
 UFQ  Var_01    H8   C3   C4   N1    179.97  30.0  1
 UFQ  Var_02    H3   C4   N1   C5     -1.06  30.0  1
 UFQ  Var_03    H3   C4   N1   C1    178.67  30.0  1
 UFQ  Var_04    H3   C4   C3   C2   -179.51  30.0  1
 UFQ  Var_05    H8   C3   C2   N2   -179.21  30.0  1
 UFQ  Var_06    H8   C3   C2   N3      0.66  30.0  1
 UFQ  Var_07    P1   O5   C9   C8   -141.40  30.0  3
 UFQ  Var_08    O8   P1   O5   C9     64.88  30.0  3
 UFQ  Var_09    O6   P1   O5   C9    -46.15  30.0  3
 UFQ  Var_10    O7   P1   O5   C9   -179.12  30.0  3
 UFQ  Var_11    P3   O11  P2   O10   154.39  30.0  1
 UFQ  Var_12    P1   O8   P2   O10  -110.65  30.0  3
 UFQ  Var_13    P1   O8   P2   O11   139.87  30.0  3
 UFQ  Var_14    P2   O11  P3   O12    59.36  30.0  2
 UFQ  Var_15    P2   O11  P3   O13   -79.79  30.0  2
 UFQ  Var_16    P2   O8   P1   O5     42.09  30.0  2
 UFQ  Var_17    P2   O8   P1   O6    156.51  30.0  2
 UFQ  Var_18    P2   O8   P1   O7    -69.80  30.0  2
 UFQ  Var_19    P3   O11  P2   O8    -94.67  30.0  1
 UFQ  Var_20    P3   O11  P2   O9     21.15  30.0  1
 UFQ  Var_21    P1   O8   P2   O9     24.79  30.0  3
 UFQ  Var_22    S1   P3   O11  P2    167.14  30.0  3
 UFQ  Var_23    H9   C9   O5   P1     97.30  30.0  2
 UFQ  Var_24    H10  C9   O5   P1    -22.05  30.0  2

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
 UFQ  chir_01  C5  N1  O3  C6  positiv
 UFQ  chir_02  C6  O2  C5  C7  negativ
 UFQ  chir_03  C7  O4  C8  C6  positiv
 UFQ  chir_04  C8  O3  C7  C9  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
 UFQ  plan-1  N1  0.020
 UFQ  plan-1  N3  0.020
 UFQ  plan-1  C4  0.020
 UFQ  plan-1  C5  0.020
 UFQ  plan-1  C1  0.020
 UFQ  plan-1  C2  0.020
 UFQ  plan-1  C3  0.020
 UFQ  plan-1  N2  0.020
 UFQ  plan-1  O1  0.020
 UFQ  plan-1  H1  0.020
 UFQ  plan-1  H2  0.020

