# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 08:52:50 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: 5'-deoxy-5'-[(imidazo[2,1-b][1,3]thiazol-5-ylcarbonyl)amino]cytidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CNC(=O)c3cnc4sccn34)[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
 AO9  AO9  5'-deoxy-5'-[(imidazo[2,1-b][1,3]thiazol-5-ylcarbonyl)amino]cytidine  ligand  43  27  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AO9
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
 AO9  N1    N  NR6   0  -0.567   2.5052  -0.3133   0.6098
 AO9  C2    C  CR6   0   0.616   2.0428  -0.8163  -0.6197
 AO9  O2    O  O     0  -0.522   1.4226  -0.0787  -1.3787
 AO9  N3    N  N     0  -0.532   2.2969  -2.1015  -0.9204
 AO9  C4    C  CR6   0   0.519   2.9737  -2.8801  -0.0973
 AO9  N4    N  NH2   0  -0.805   3.1884  -4.1424  -0.4570
 AO9  C5    C  CR16  0  -0.470   3.4678  -2.4045   1.1554
 AO9  C6    C  CR16  0   0.095   3.1972  -1.1205   1.4547
 AO9  C1'   C  CR15  0   0.246   2.2581   1.0606   1.0173
 AO9  C2'   C  CR15  0  -0.062   2.8868   2.1479   0.1464
 AO9  O2'   O  OH1   0  -0.658   4.2219   2.3318   0.5238
 AO9  C3'   C  CR15  0  -0.028   1.9701   3.3361   0.4724
 AO9  O3'   O  OH1   0  -0.670   2.2942   3.8924   1.7198
 AO9  C30   C  C     0   0.511  -2.3601   1.6521  -0.6718
 AO9  O31   O  O     0  -0.484  -2.9448   2.7183  -0.5364
 AO9  C32   C  CR5   0   0.152  -3.1008   0.3808  -0.6495
 AO9  N33   N  N     0  -0.523  -2.6165  -0.8403  -0.2228
 AO9  C34   C  CR55  0   0.267  -3.6115  -1.7416  -0.4359
 AO9  N35   N  N     0  -0.454  -4.6848  -1.2110  -0.9623
 AO9  C36   C  CR15  0  -0.203  -4.3742   0.1074  -1.0871
 AO9  S37   S  S2    0   0.244  -3.1494  -3.3148   0.1027
 AO9  C38   C  CR15  0  -0.553  -1.6258  -2.6701   0.6463
 AO9  C39   C  CR15  0   0.103  -1.5014  -1.3546   0.4164
 AO9  C4'   C  CR15  0   0.007   0.6178   2.6450   0.5679
 AO9  O4'   O  O     0  -0.491   0.8890   1.3320   1.0642
 AO9  C5'   C  CH2   0  -0.326  -0.0861   2.6058  -0.7926
 AO9  N5'   N  NH1   0  -0.649  -1.0389   1.5325  -0.8776
 AO9  HN4   H  HNH2  0   0.405   2.8386  -4.4843  -1.3360
 AO9  HN4A  H  HNH2  0   0.416   3.7065  -4.7764   0.1253
 AO9  H5    H  HCR6  0   0.293   4.0205  -3.0325   1.8371
 AO9  H6    H  HCR6  0   0.323   3.5208  -0.6770   2.3859
 AO9  H1'   H  HCR5  0   0.249   2.6887   1.1398   2.0223
 AO9  H2'   H  HCR5  0   0.264   2.7979   1.8954  -0.9131
 AO9  HO2'  H  HOH1  0   0.469   4.6993   2.7308  -0.2101
 AO9  H3'   H  HCR5  0   0.249   1.9827   4.0923  -0.3241
 AO9  HO3'  H  HOH1  0   0.448   3.2537   3.9835   1.7615
 AO9  H36   H  HCR5  0   0.278  -5.0715   0.8129  -1.5125
 AO9  H38   H  HCR5  0   0.322  -0.9049  -3.3123   1.1249
 AO9  H39   H  HCR5  0   0.315  -0.6803  -0.7180   0.7046
 AO9  H4'   H  HCR5  0   0.261  -0.0334   3.1432   1.2912
 AO9  H5'   H  HCH2  0   0.269  -0.5809   3.5624  -0.9562
 AO9  H5'A  H  HCH2  0   0.261   0.6327   2.4758  -1.6011
 AO9  HN5'  H  HNH1  0   0.417  -0.6412   0.6388  -1.1235

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
 AO9  C1'  N1    single    1.454  0.020  1.454
 AO9  N1   C6    single    1.358  0.020  1.358
 AO9  N1   C2    single    1.407  0.020  1.407
 AO9  O2   C2    double    1.227  0.020  1.227
 AO9  C2   N3    single    1.344  0.020  1.344
 AO9  N3   C4    double    1.320  0.020  1.320
 AO9  C5   C4    single    1.428  0.020  1.428
 AO9  C4   N4    single    1.330  0.020  1.330
 AO9  N4   HN4   single    0.860  0.020  1.020
 AO9  N4   HN4A  single    0.860  0.020  1.020
 AO9  C6   C5    double    1.346  0.020  1.346
 AO9  C5   H5    single    0.930  0.020  1.080
 AO9  C6   H6    single    0.930  0.020  1.080
 AO9  O4'  C1'   single    1.397  0.020  1.397
 AO9  C2'  C1'   single    1.528  0.020  1.528
 AO9  C1'  H1'   single    0.970  0.020  1.090
 AO9  C3'  C2'   single    1.536  0.020  1.536
 AO9  C2'  O2'   single    1.400  0.020  1.400
 AO9  C2'  H2'   single    0.970  0.020  1.090
 AO9  O2'  HO2'  single    0.850  0.020  0.980
 AO9  C4'  C3'   single    1.522  0.020  1.522
 AO9  O3'  C3'   single    1.404  0.020  1.404
 AO9  C3'  H3'   single    0.970  0.020  1.090
 AO9  O3'  HO3'  single    0.850  0.020  0.980
 AO9  C32  C30   single    1.472  0.020  1.472
 AO9  O31  C30   double    1.224  0.020  1.224
 AO9  C30  N5'   single    1.342  0.020  1.342
 AO9  N33  C32   aromatic  1.381  0.020  1.381
 AO9  C32  C36   aromatic  1.374  0.020  1.374
 AO9  C39  N33   aromatic  1.384  0.020  1.384
 AO9  C34  N33   aromatic  1.359  0.020  1.359
 AO9  S37  C34   aromatic  1.726  0.020  1.726
 AO9  C34  N35   aromatic  1.308  0.020  1.308
 AO9  N35  C36   aromatic  1.360  0.020  1.360
 AO9  C36  H36   single    0.930  0.020  1.080
 AO9  C38  S37   aromatic  1.741  0.020  1.741
 AO9  C38  C39   aromatic  1.341  0.020  1.341
 AO9  C38  H38   single    0.930  0.020  1.080
 AO9  C39  H39   single    0.930  0.020  1.080
 AO9  C5'  C4'   single    1.532  0.020  1.532
 AO9  C4'  O4'   single    1.430  0.020  1.430
 AO9  C4'  H4'   single    0.970  0.020  1.090
 AO9  N5'  C5'   single    1.438  0.020  1.438
 AO9  C5'  H5'   single    0.970  0.020  1.090
 AO9  C5'  H5'A  single    0.970  0.020  1.090
 AO9  N5'  HN5'  single    0.860  0.020  1.020

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
 AO9  C1'   N1   C6   118.28  3.000
 AO9  C6    N1   C2   119.92  3.000
 AO9  C1'   N1   C2   121.80  3.000
 AO9  N3    C2   O2   122.14  3.000
 AO9  N3    C2   N1   118.38  3.000
 AO9  O2    C2   N1   119.47  3.000
 AO9  C4    N3   C2   121.43  3.000
 AO9  C5    C4   N4   119.83  3.000
 AO9  N4    C4   N3   118.30  3.000
 AO9  C5    C4   N3   121.87  3.000
 AO9  HN4A  N4   HN4  118.12  3.000
 AO9  HN4A  N4   C4   121.69  3.000
 AO9  HN4   N4   C4   120.18  3.000
 AO9  H5    C5   C6   121.17  3.000
 AO9  H5    C5   C4   122.52  3.000
 AO9  C6    C5   C4   116.31  3.000
 AO9  H6    C6   C5   121.52  3.000
 AO9  H6    C6   N1   116.40  3.000
 AO9  C5    C6   N1   122.08  3.000
 AO9  H1'   C1'  O4'  109.89  3.000
 AO9  H1'   C1'  C2'  108.03  3.000
 AO9  O4'   C1'  C2'  106.51  3.000
 AO9  H1'   C1'  N1   104.98  3.000
 AO9  C2'   C1'  N1   116.27  3.000
 AO9  O4'   C1'  N1   111.08  3.000
 AO9  H2'   C2'  C3'  109.63  3.000
 AO9  H2'   C2'  O2'  111.68  3.000
 AO9  C3'   C2'  O2'  114.24  3.000
 AO9  H2'   C2'  C1'  110.77  3.000
 AO9  O2'   C2'  C1'  109.40  3.000
 AO9  C3'   C2'  C1'  100.60  3.000
 AO9  HO2'  O2'  C2'  108.79  3.000
 AO9  H3'   C3'  C4'  111.62  3.000
 AO9  H3'   C3'  O3'  111.65  3.000
 AO9  C4'   C3'  O3'  109.23  3.000
 AO9  H3'   C3'  C2'  111.83  3.000
 AO9  O3'   C3'  C2'  110.94  3.000
 AO9  C4'   C3'  C2'  101.09  3.000
 AO9  HO3'  O3'  C3'  107.78  3.000
 AO9  N5'   C30  C32  114.88  3.000
 AO9  N5'   C30  O31  124.40  3.000
 AO9  C32   C30  O31  120.70  3.000
 AO9  C36   C32  N33  104.33  3.000
 AO9  C36   C32  C30  129.32  3.000
 AO9  N33   C32  C30  126.29  3.000
 AO9  C39   N33  C34  114.56  3.000
 AO9  C34   N33  C32  106.32  3.000
 AO9  C39   N33  C32  138.90  3.000
 AO9  S37   C34  N35  135.65  3.000
 AO9  N35   C34  N33  113.25  3.000
 AO9  S37   C34  N33  111.07  3.000
 AO9  C36   N35  C34  104.05  3.000
 AO9  H36   C36  N35  121.48  3.000
 AO9  H36   C36  C32  126.46  3.000
 AO9  N35   C36  C32  112.04  3.000
 AO9  C38   S37  C34   89.67  3.000
 AO9  H38   C38  C39  126.77  3.000
 AO9  H38   C38  S37  120.22  3.000
 AO9  C39   C38  S37  113.01  3.000
 AO9  H39   C39  C38  127.16  3.000
 AO9  H39   C39  N33  121.16  3.000
 AO9  C38   C39  N33  111.64  3.000
 AO9  H4'   C4'  C5'  108.99  3.000
 AO9  H4'   C4'  O4'  107.57  3.000
 AO9  C5'   C4'  O4'  111.83  3.000
 AO9  H4'   C4'  C3'  111.34  3.000
 AO9  O4'   C4'  C3'  105.69  3.000
 AO9  C5'   C4'  C3'  111.35  3.000
 AO9  C4'   O4'  C1'  110.66  3.000
 AO9  H5'A  C5'  H5'  107.04  3.000
 AO9  H5'A  C5'  N5'  107.71  3.000
 AO9  H5'   C5'  N5'  110.22  3.000
 AO9  H5'A  C5'  C4'  111.03  3.000
 AO9  H5'   C5'  C4'  108.63  3.000
 AO9  N5'   C5'  C4'  112.08  3.000
 AO9  HN5'  N5'  C5'  114.50  3.000
 AO9  HN5'  N5'  C30  120.29  3.000
 AO9  C5'   N5'  C30  125.21  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
 AO9  CONST_01  C38   C39  N33  C32   180.00   0.0  0
 AO9  CONST_02  S37   C34  N33  C32   180.00   0.0  0
 AO9  CONST_03  N35   C34  N33  C32     0.00   0.0  0
 AO9  CONST_04  C34   N35  C36  C32     0.00   0.0  0
 AO9  CONST_05  N35   C36  C32  N33     0.00   0.0  0
 AO9  CONST_06  S37   C38  C39  N33     0.00   0.0  0
 AO9  CONST_07  C38   S37  C34  N33     0.00   0.0  0
 AO9  CONST_08  C36   N35  C34  N33     0.00   0.0  0
 AO9  CONST_09  C36   C32  N33  C34     0.00   0.0  0
 AO9  CONST_10  C38   C39  N33  C34     0.00   0.0  0
 AO9  CONST_11  C39   C38  S37  C34     0.00   0.0  0
 AO9  CONST_12  C39   N33  C34  N35   180.00   0.0  0
 AO9  CONST_13  C38   S37  C34  N35   180.00   0.0  0
 AO9  CONST_14  C39   N33  C32  C36   180.00   0.0  0
 AO9  CONST_15  S37   C34  N35  C36   180.00   0.0  0
 AO9  CONST_16  C39   N33  C34  S37     0.00   0.0  0
 AO9  CONST_17  C4    N3   C2   N1      0.00   0.0  0
 AO9  CONST_18  C5    C4   N3   C2      0.00   0.0  0
 AO9  CONST_19  C1'   N1   C2   N3    180.00   0.0  0
 AO9  CONST_20  C6    N1   C2   N3      0.00   0.0  0
 AO9  CONST_21  C39   N33  C32  C30     0.00   0.0  0
 AO9  CONST_22  C34   N33  C32  C30   180.00   0.0  0
 AO9  CONST_23  N35   C36  C32  C30   180.00   0.0  0
 AO9  CONST_24  N4    C4   N3   C2    180.00   0.0  0
 AO9  CONST_25  C1'   N1   C2   O2      0.00   0.0  0
 AO9  CONST_26  C6    N1   C2   O2    180.00   0.0  0
 AO9  CONST_27  C4    N3   C2   O2    180.00   0.0  0
 AO9  CONST_28  H39   C39  N33  C32     0.00   0.0  0
 AO9  CONST_29  H36   C36  C32  N33   180.00   0.0  0
 AO9  CONST_30  H38   C38  C39  N33   180.00   0.0  0
 AO9  CONST_31  HN4   N4   C4   N3      0.00   0.0  0
 AO9  CONST_32  HN4A  N4   C4   N3    180.00   0.0  0
 AO9  CONST_33  C5'   N5'  C30  C32   180.00   0.0  0
 AO9  CONST_34  HN5'  N5'  C30  C32     0.00   0.0  0
 AO9  CONST_35  C5'   N5'  C30  O31     0.00   0.0  0
 AO9  Var_01    N33   C32  C30  O31  -150.23  30.0  2
 AO9  Var_02    C4'   C5'  N5'  C30    97.35  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
 AO9  chir_01  C1'  N1   O4'  C2'  positiv
 AO9  chir_02  C2'  O2'  C1'  C3'  negativ
 AO9  chir_03  C3'  O3'  C2'  C4'  negativ
 AO9  chir_04  C4'  O4'  C3'  C5'  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
 AO9  plan-1  N1    0.020
 AO9  plan-1  C2    0.020
 AO9  plan-1  O2    0.020
 AO9  plan-1  N3    0.020
 AO9  plan-1  C4    0.020
 AO9  plan-1  N4    0.020
 AO9  plan-1  C5    0.020
 AO9  plan-1  C6    0.020
 AO9  plan-1  C1'   0.020
 AO9  plan-1  HN4   0.020
 AO9  plan-1  HN4A  0.020
 AO9  plan-1  H5    0.020
 AO9  plan-1  H6    0.020
 AO9  plan-2  C30   0.020
 AO9  plan-2  C32   0.020
 AO9  plan-2  N33   0.020
 AO9  plan-2  C34   0.020
 AO9  plan-2  N35   0.020
 AO9  plan-2  C36   0.020
 AO9  plan-2  S37   0.020
 AO9  plan-2  C38   0.020
 AO9  plan-2  C39   0.020
 AO9  plan-2  H36   0.020
 AO9  plan-2  H38   0.020
 AO9  plan-2  H39   0.020
 AO9  plan-3  C30   0.020
 AO9  plan-3  O31   0.020
 AO9  plan-3  C32   0.020
 AO9  plan-3  C5'   0.020
 AO9  plan-3  N5'   0.020
 AO9  plan-3  HN5'  0.020

