# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 08:14:25 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: 2'-deoxy-N-(2-sulfanylethyl)cytidine 5'-(dihydrogen phosphate)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC(=NC2=O)NCCS
#
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
 2YR  2YR  '2'-deoxy-N-(2-sulfanylethyl)cytidine 5'-(dihydrogen phosphate)'  ligand  41  23  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_2YR
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
 2YR  P    P  P     0   1.456   4.2996  -1.9393  -0.1792
 2YR  OP1  O  O     0  -0.712   3.6105  -2.9436   0.6526
 2YR  OP2  O  OH1   0  -0.731   4.5834  -2.3005  -1.7052
 2YR  O5'  O  O2    0  -0.591   3.5147  -0.5775  -0.4511
 2YR  C5'  C  CH2   0  -0.188   2.9000   0.1056   0.6489
 2YR  C4'  C  CR15  0   0.022   2.4643   1.4729   0.1915
 2YR  O4'  O  O     0  -0.491   1.4439   1.3601  -0.7795
 2YR  C3'  C  CR15  0   0.018   1.9009   2.3049   1.3463
 2YR  O3'  O  OH1   0  -0.669   2.9468   3.0591   1.9059
 2YR  C2'  C  CH2   0  -0.555   0.8082   3.1254   0.6616
 2YR  C1'  C  CR15  0   0.217   0.4678   2.3534  -0.6162
 2YR  N1   N  NR6   0  -0.558  -0.8592   1.7509  -0.6719
 2YR  C2   C  CR6   0   0.606  -1.2742   0.8303   0.3024
 2YR  O2   O  O     0  -0.505  -0.5211   0.5514   1.2244
 2YR  N3   N  N     0  -0.553  -2.5038   0.2858   0.1861
 2YR  C4   C  CR6   0   0.566  -3.3013   0.6103  -0.8107
 2YR  N4   N  NH1   0  -0.655  -4.5063   0.0408  -0.8720
 2YR  C5   C  CR16  0  -0.481  -2.9138   1.5434  -1.8220
 2YR  C6   C  CR16  0   0.099  -1.6815   2.0717  -1.7022
 2YR  S    S  S2    0  -0.242  -6.9154  -2.6291   0.9265
 2YR  C8   C  CH2   0  -0.598  -6.3661  -1.3992  -0.2988
 2YR  C9   C  CH2   0  -0.236  -4.9834  -0.9141   0.1035
 2YR  H2   H  HOH1  0   0.504   5.0418  -3.1422  -1.8310
 2YR  H3   H  HCH2  0   0.250   2.0386  -0.4604   1.0088
 2YR  H4   H  HCH2  0   0.242   3.6091   0.2270   1.4729
 2YR  H5   H  HCR5  0   0.236   3.3257   2.0079  -0.2338
 2YR  H6   H  HCR5  0   0.238   1.4525   1.6491   2.0973
 2YR  H7   H  HOH1  0   0.457   2.6559   3.3923   2.7596
 2YR  H8   H  HCH2  0   0.274  -0.0592   3.3055   1.2942
 2YR  H9   H  HCH2  0   0.264   1.2188   4.0966   0.3796
 2YR  H10  H  HCR5  0   0.249   0.4933   3.0338  -1.4709
 2YR  H11  H  HNH1  0   0.412  -5.1234   0.3174  -1.6183
 2YR  H12  H  HCR6  0   0.287  -3.5620   1.8112  -2.6426
 2YR  H13  H  HCR6  0   0.319  -1.2955   2.7802  -2.4225
 2YR  H14  H  HSH1  0   0.232  -8.1350  -2.8338   0.4196
 2YR  H15  H  HCH2  0   0.280  -6.3358  -1.8555  -1.2886
 2YR  H16  H  HCH2  0   0.281  -7.0706  -0.5678  -0.3192
 2YR  H17  H  HCH2  0   0.250  -4.2916  -1.7575   0.1641
 2YR  H18  H  HCH2  0   0.249  -5.0206  -0.4567   1.0956
 2YR  OP3  O  OH1   0  -0.741   5.6923  -1.5502   0.5020
 2YR  H20  H  HOH1  0   0.496   6.2413  -0.9250   0.0099

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
 2YR  S    C8   single  1.821  0.020  1.821
 2YR  C8   C9   single  1.520  0.020  1.520
 2YR  N4   C9   single  1.446  0.020  1.446
 2YR  N4   C4   single  1.334  0.020  1.334
 2YR  C4   N3   double  1.317  0.020  1.317
 2YR  C4   C5   single  1.430  0.020  1.430
 2YR  N3   C2   single  1.350  0.020  1.350
 2YR  C5   C6   double  1.346  0.020  1.346
 2YR  C2   O2   double  1.223  0.020  1.223
 2YR  C2   N1   single  1.403  0.020  1.403
 2YR  C6   N1   single  1.357  0.020  1.357
 2YR  N1   C1'  single  1.458  0.020  1.458
 2YR  C2'  C3'  single  1.528  0.020  1.528
 2YR  C2'  C1'  single  1.531  0.020  1.531
 2YR  C3'  O3'  single  1.406  0.020  1.406
 2YR  C3'  C4'  single  1.531  0.020  1.531
 2YR  C1'  O4'  single  1.402  0.020  1.402
 2YR  O4'  C4'  single  1.413  0.020  1.413
 2YR  C4'  C5'  single  1.506  0.020  1.506
 2YR  C5'  O5'  single  1.433  0.020  1.433
 2YR  O5'  P    single  1.595  0.020  1.595
 2YR  OP2  P    single  1.594  0.020  1.594
 2YR  P    OP1  double  1.475  0.020  1.475
 2YR  OP2  H2   single  0.850  0.020  0.980
 2YR  C5'  H3   single  0.970  0.020  1.090
 2YR  C5'  H4   single  0.970  0.020  1.090
 2YR  C4'  H5   single  0.970  0.020  1.090
 2YR  C3'  H6   single  0.970  0.020  1.090
 2YR  O3'  H7   single  0.850  0.020  0.980
 2YR  C2'  H8   single  0.970  0.020  1.090
 2YR  C2'  H9   single  0.970  0.020  1.090
 2YR  C1'  H10  single  0.970  0.020  1.090
 2YR  N4   H11  single  0.860  0.020  1.020
 2YR  C5   H12  single  0.930  0.020  1.080
 2YR  C6   H13  single  0.930  0.020  1.080
 2YR  S    H14  single  1.200  0.020  1.300
 2YR  C8   H15  single  0.970  0.020  1.090
 2YR  C8   H16  single  0.970  0.020  1.090
 2YR  C9   H17  single  0.970  0.020  1.090
 2YR  C9   H18  single  0.970  0.020  1.090
 2YR  P    OP3  single  1.598  0.020  1.598
 2YR  OP3  H20  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
 2YR  OP3  P    O5'  107.07  3.000
 2YR  OP3  P    OP2  107.94  3.000
 2YR  O5'  P    OP2   96.77  3.000
 2YR  OP3  P    OP1  109.42  3.000
 2YR  OP2  P    OP1  117.96  3.000
 2YR  O5'  P    OP1  116.59  3.000
 2YR  H2   OP2  P    113.98  3.000
 2YR  C5'  O5'  P    119.15  3.000
 2YR  H4   C5'  H3   108.71  3.000
 2YR  H4   C5'  C4'  108.39  3.000
 2YR  H3   C5'  C4'  110.03  3.000
 2YR  H4   C5'  O5'  110.67  3.000
 2YR  H3   C5'  O5'  110.14  3.000
 2YR  C4'  C5'  O5'  108.88  3.000
 2YR  H5   C4'  C3'  108.40  3.000
 2YR  H5   C4'  O4'  109.80  3.000
 2YR  C3'  C4'  O4'  107.22  3.000
 2YR  H5   C4'  C5'  109.42  3.000
 2YR  O4'  C4'  C5'  110.19  3.000
 2YR  C3'  C4'  C5'  111.76  3.000
 2YR  C1'  O4'  C4'  111.47  3.000
 2YR  H6   C3'  C2'  109.66  3.000
 2YR  H6   C3'  O3'  110.70  3.000
 2YR  C2'  C3'  O3'  114.98  3.000
 2YR  H6   C3'  C4'  110.07  3.000
 2YR  O3'  C3'  C4'  108.55  3.000
 2YR  C2'  C3'  C4'  102.53  3.000
 2YR  H7   O3'  C3'  108.32  3.000
 2YR  H9   C2'  H8   107.62  3.000
 2YR  H9   C2'  C1'  108.46  3.000
 2YR  H8   C2'  C1'  113.03  3.000
 2YR  H9   C2'  C3'  108.93  3.000
 2YR  H8   C2'  C3'  113.47  3.000
 2YR  C1'  C2'  C3'  105.20  3.000
 2YR  H10  C1'  N1   104.39  3.000
 2YR  H10  C1'  C2'  109.50  3.000
 2YR  N1   C1'  C2'  116.26  3.000
 2YR  H10  C1'  O4'  109.49  3.000
 2YR  C2'  C1'  O4'  107.43  3.000
 2YR  N1   C1'  O4'  109.65  3.000
 2YR  C6   N1   C2   120.21  3.000
 2YR  C6   N1   C1'  118.87  3.000
 2YR  C2   N1   C1'  120.90  3.000
 2YR  N3   C2   O2   122.28  3.000
 2YR  O2   C2   N1   119.41  3.000
 2YR  N3   C2   N1   118.31  3.000
 2YR  C4   N3   C2   121.16  3.000
 2YR  C5   C4   N4   119.40  3.000
 2YR  C5   C4   N3   122.14  3.000
 2YR  N4   C4   N3   118.46  3.000
 2YR  H11  N4   C9   118.62  3.000
 2YR  H11  N4   C4   118.05  3.000
 2YR  C9   N4   C4   123.29  3.000
 2YR  H12  C5   C6   121.33  3.000
 2YR  H12  C5   C4   122.47  3.000
 2YR  C6   C5   C4   116.20  3.000
 2YR  H13  C6   C5   121.64  3.000
 2YR  H13  C6   N1   116.38  3.000
 2YR  C5   C6   N1   121.97  3.000
 2YR  H14  S    C8    97.09  3.000
 2YR  H16  C8   H15  108.67  3.000
 2YR  H16  C8   C9   110.46  3.000
 2YR  H15  C8   C9   110.40  3.000
 2YR  H16  C8   S    109.44  3.000
 2YR  H15  C8   S    109.67  3.000
 2YR  C9   C8   S    108.18  3.000
 2YR  H18  C9   H17  107.11  3.000
 2YR  H18  C9   C8   110.06  3.000
 2YR  H17  C9   C8   110.15  3.000
 2YR  H18  C9   N4   110.31  3.000
 2YR  H17  C9   N4   109.77  3.000
 2YR  C8   C9   N4   109.42  3.000
 2YR  H20  OP3  P    115.81  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
 2YR  CONST_01  N3   C2   N1   C1'   180.00   0.0  0
 2YR  CONST_02  C4   N3   C2   N1      0.00   0.0  0
 2YR  CONST_03  C5   C4   N3   C2      0.00   0.0  0
 2YR  CONST_04  C6   N1   C2   N3      0.00   0.0  0
 2YR  CONST_05  O2   C2   N1   C1'     0.00   0.0  0
 2YR  CONST_06  N4   C4   N3   C2    180.00   0.0  0
 2YR  CONST_07  C4   N3   C2   O2    180.00   0.0  0
 2YR  CONST_08  C6   N1   C2   O2    180.00   0.0  0
 2YR  CONST_09  C9   N4   C4   N3      0.00   0.0  0
 2YR  CONST_10  C9   N4   C4   C5    180.00   0.0  0
 2YR  CONST_11  H11  N4   C4   N3    180.00   0.0  0
 2YR  Var_01    C4'  C5'  O5'  P     169.11  30.0  1
 2YR  Var_02    C8   C9   N4   C4   -177.79  30.0  3
 2YR  Var_03    OP3  P    O5'  C5'   -75.27  30.0  3
 2YR  Var_04    S    C8   C9   N4    178.57  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
 2YR  chir_01  C4'  C3'  O4'  C5'  positiv
 2YR  chir_02  C3'  O3'  C2'  C4'  negativ
 2YR  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
 2YR  plan-1  C1'  0.020
 2YR  plan-1  N1   0.020
 2YR  plan-1  C2   0.020
 2YR  plan-1  O2   0.020
 2YR  plan-1  N3   0.020
 2YR  plan-1  C4   0.020
 2YR  plan-1  N4   0.020
 2YR  plan-1  C5   0.020
 2YR  plan-1  C6   0.020
 2YR  plan-1  C9   0.020
 2YR  plan-1  H11  0.020
 2YR  plan-1  H12  0.020
 2YR  plan-1  H13  0.020

