# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 07:22:17 2022
#   Inital geometry file: a 90 line input string
#   Ligand name: 5'-O-sulfocytidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[S](O)(=O)=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
 RQA  RQA  '5'-O-sulfocytidine       '  ligand  33  21  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RQA
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
 RQA  C1   C  CR6    0   0.592  -232.1943  257.9270  286.2409
 RQA  C2   C  CR6    0   0.515  -232.4463  260.2113  286.5947
 RQA  C3   C  CR16   0  -0.479  -233.8631  260.0945  286.7433
 RQA  C4   C  CR16   0   0.098  -234.3754  258.8551  286.6310
 RQA  C5   C  CH1    0   0.199  -234.1869  256.4614  286.2994
 RQA  C6   C  CH1    0  -0.043  -234.8191  255.9646  287.5978
 RQA  C7   C  CH1    0  -0.037  -235.8410  254.9579  287.0622
 RQA  C8   C  CH1    0  -0.008  -236.2876  255.6186  285.7561
 RQA  C9   C  CH2    0  -0.188  -237.5921  256.3818  285.8284
 RQA  N1   N  NR6    0  -0.560  -233.5864  257.7770  286.3957
 RQA  N2   N  N      0  -0.540  -231.6778  259.1687  286.3523
 RQA  N3   N  NH2    0  -0.808  -231.8724  261.4090  286.6988
 RQA  O1   O  OS     0  -0.731  -239.9001  258.0501  286.7498
 RQA  O2   O  O      0  -0.508  -231.5016  256.9447  286.0172
 RQA  O3   O  OH1    0  -0.654  -233.8309  255.4094  288.4192
 RQA  O4   O  OS     0  -0.727  -238.2147  259.3274  288.0200
 RQA  O5   O  OH1    0  -0.667  -235.2152  253.7377  286.7512
 RQA  O6   O  O2     0  -0.495  -235.2272  256.4898  285.3599
 RQA  O7   O  OC2    0  -0.616  -237.5247  257.3434  286.8664
 RQA  S1   S  S      0   1.581  -238.5577  258.6324  286.7832
 RQA  H1   H  HCR6   0   0.285  -234.4967  260.9484  286.9304
 RQA  H2   H  HCR6   0   0.311  -235.4369  258.6742  286.7169
 RQA  H3   H  HCH1   0   0.264  -233.3900  255.7818  285.9913
 RQA  H4   H  HCH1   0   0.255  -235.3464  256.7830  288.0999
 RQA  H5   H  HCH1   0   0.246  -236.6782  254.8112  287.7564
 RQA  H6   H  HCH1   0   0.259  -236.4239  254.8464  284.9902
 RQA  H7   H  HCH2   0   0.238  -237.7781  256.8515  284.8572
 RQA  H8   H  HCH2   0   0.230  -238.4004  255.6665  286.0112
 RQA  H9   H  HNH2   0   0.401  -230.8757  261.5034  286.6008
 RQA  H10  H  HNH2   0   0.413  -232.4108  262.2359  286.8894
 RQA  H12  H  HOH1   0   0.466  -234.1494  255.3996  289.3274
 RQA  H14  H  HOH1   0   0.445  -234.5939  253.5390  287.4625
 RQA  O3S  O  OS    -1  -0.736  -238.1891  259.3423  285.5563

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
 RQA  O6  C8   single  1.428  0.020  1.428
 RQA  O6  C5   single  1.402  0.020  1.402
 RQA  C8  C9   single  1.513  0.020  1.513
 RQA  C8  C7   single  1.530  0.020  1.530
 RQA  O2  C1   double  1.223  0.020  1.223
 RQA  C9  O7   single  1.417  0.020  1.417
 RQA  C1  N2   single  1.349  0.020  1.349
 RQA  C1  N1   single  1.409  0.020  1.409
 RQA  C5  N1   single  1.449  0.020  1.449
 RQA  C5  C6   single  1.527  0.020  1.527
 RQA  N2  C2   double  1.318  0.020  1.318
 RQA  N1  C4   single  1.357  0.020  1.357
 RQA  O7  S1   single  1.654  0.020  1.654
 RQA  S1  O1   deloc   1.464  0.020  1.464
 RQA  S1  O4   deloc   1.460  0.020  1.460
 RQA  C2  N3   single  1.332  0.020  1.332
 RQA  C2  C3   single  1.429  0.020  1.429
 RQA  O5  C7   single  1.406  0.020  1.406
 RQA  C4  C3   double  1.346  0.020  1.346
 RQA  C7  C6   single  1.531  0.020  1.531
 RQA  C6  O3   single  1.400  0.020  1.400
 RQA  C3  H1   single  0.930  0.020  1.080
 RQA  C4  H2   single  0.930  0.020  1.080
 RQA  C5  H3   single  0.970  0.020  1.090
 RQA  C6  H4   single  0.970  0.020  1.090
 RQA  C7  H5   single  0.970  0.020  1.090
 RQA  C8  H6   single  0.970  0.020  1.090
 RQA  C9  H7   single  0.970  0.020  1.090
 RQA  C9  H8   single  0.970  0.020  1.090
 RQA  N3  H9   single  0.860  0.020  1.020
 RQA  N3  H10  single  0.860  0.020  1.020
 RQA  O3  H12  single  0.850  0.020  0.980
 RQA  O5  H14  single  0.850  0.020  0.980
 RQA  S1  O3S  deloc   1.465  0.020  1.465

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
 RQA  O2   C1  N2  122.51  3.000
 RQA  N2   C1  N1  117.85  3.000
 RQA  O2   C1  N1  119.63  3.000
 RQA  N3   C2  N2  118.33  3.000
 RQA  N3   C2  C3  119.50  3.000
 RQA  N2   C2  C3  122.18  3.000
 RQA  H1   C3  C4  121.30  3.000
 RQA  H1   C3  C2  122.35  3.000
 RQA  C4   C3  C2  116.35  3.000
 RQA  H2   C4  N1  116.89  3.000
 RQA  H2   C4  C3  121.44  3.000
 RQA  N1   C4  C3  121.67  3.000
 RQA  H3   C5  O6  111.41  3.000
 RQA  H3   C5  N1  106.34  3.000
 RQA  O6   C5  N1  109.48  3.000
 RQA  H3   C5  C6  109.86  3.000
 RQA  N1   C5  C6  114.23  3.000
 RQA  O6   C5  C6  105.61  3.000
 RQA  H4   C6  O3  111.55  3.000
 RQA  H4   C6  C7  109.29  3.000
 RQA  O3   C6  C7  114.56  3.000
 RQA  H4   C6  C5  110.24  3.000
 RQA  O3   C6  C5  109.61  3.000
 RQA  C7   C6  C5  101.11  3.000
 RQA  H5   C7  O5  111.32  3.000
 RQA  H5   C7  C8  112.02  3.000
 RQA  O5   C7  C8  108.41  3.000
 RQA  H5   C7  C6  112.07  3.000
 RQA  O5   C7  C6  110.54  3.000
 RQA  C8   C7  C6  102.09  3.000
 RQA  H6   C8  O6  109.16  3.000
 RQA  H6   C8  C9  106.35  3.000
 RQA  O6   C8  C9  110.22  3.000
 RQA  H6   C8  C7  109.18  3.000
 RQA  C9   C8  C7  115.38  3.000
 RQA  O6   C8  C7  106.47  3.000
 RQA  H8   C9  H7  107.64  3.000
 RQA  H8   C9  O7  110.87  3.000
 RQA  H7   C9  O7  111.53  3.000
 RQA  H8   C9  C8  108.36  3.000
 RQA  H7   C9  C8  108.69  3.000
 RQA  O7   C9  C8  109.66  3.000
 RQA  C5   N1  C4  119.47  3.000
 RQA  C4   N1  C1  120.61  3.000
 RQA  C5   N1  C1  119.92  3.000
 RQA  C2   N2  C1  121.33  3.000
 RQA  H10  N3  H9  118.16  3.000
 RQA  H10  N3  C2  121.59  3.000
 RQA  H9   N3  C2  120.24  3.000
 RQA  H12  O3  C6  108.91  3.000
 RQA  H14  O5  C7  107.59  3.000
 RQA  C8   O6  C5  110.65  3.000
 RQA  S1   O7  C9  117.54  3.000
 RQA  O3S  S1  O7  105.23  3.000
 RQA  O3S  S1  O4  114.83  3.000
 RQA  O7   S1  O4  100.47  3.000
 RQA  O3S  S1  O1  113.87  3.000
 RQA  O4   S1  O1  115.10  3.000
 RQA  O7   S1  O1  105.30  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
 RQA  CONST_01  C3   C2  N2  C1    0.00   0.0  0
 RQA  CONST_02  N1   C1  N2  C2    0.00   0.0  0
 RQA  CONST_03  N2   C1  N1  C4    0.00   0.0  0
 RQA  CONST_04  N2   C1  N1  C5  180.00   0.0  0
 RQA  CONST_05  N3   C2  N2  C1  180.00   0.0  0
 RQA  CONST_06  O2   C1  N2  C2  180.00   0.0  0
 RQA  CONST_07  O2   C1  N1  C4  180.00   0.0  0
 RQA  CONST_08  O2   C1  N1  C5    0.00   0.0  0
 RQA  CONST_09  H9   N3  C2  C3  180.00   0.0  0
 RQA  CONST_10  H10  N3  C2  C3    0.00   0.0  0
 RQA  Var_01    O1   S1  O7  C9   58.06  30.0  3
 RQA  Var_02    H7   C9  O7  S1   37.45  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
 RQA  chir_01  C5  O6  N1  C6  negativ
 RQA  chir_02  C6  O3  C5  C7  negativ
 RQA  chir_03  C7  O5  C8  C6  positiv
 RQA  chir_04  C8  O6  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
 RQA  plan-1  C1   0.020
 RQA  plan-1  C2   0.020
 RQA  plan-1  C3   0.020
 RQA  plan-1  C4   0.020
 RQA  plan-1  C5   0.020
 RQA  plan-1  N1   0.020
 RQA  plan-1  N2   0.020
 RQA  plan-1  N3   0.020
 RQA  plan-1  O2   0.020
 RQA  plan-1  H1   0.020
 RQA  plan-1  H2   0.020
 RQA  plan-1  H9   0.020
 RQA  plan-1  H10  0.020

