# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 17:31:34 2021
#   Inital geometry file: a 117 line input string
#   Ligand name: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)O2
#
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
 0KX  0KX  2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine  ligand  45  28  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_0KX
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
 0KX  PG   P  P     0   1.460  54.6215  2.2904  7.3819
 0KX  O1G  O  OH1   0  -0.728  53.4937  2.1809  8.4934
 0KX  O2G  O  O     0  -0.683  54.6187  1.2933  6.2997
 0KX  O3G  O  OH1   0  -0.715  55.9493  2.4355  8.2380
 0KX  PB   P  P     0   1.438  53.3825  4.3491  5.7351
 0KX  O1B  O  OH1   0  -0.749  52.7550  5.5703  6.5140
 0KX  O2B  O  O     0  -0.669  54.0685  4.5998  4.4583
 0KX  O3B  O  O2    0  -0.685  54.3715  3.8176  6.9065
 0KX  PA   P  P     0   1.464  51.8161  2.1900  4.3434
 0KX  O1A  O  O     0  -0.677  52.9886  1.9024  3.5040
 0KX  O2A  O  OH1   0  -0.718  51.0214  0.9912  5.0194
 0KX  N3A  N  NH1   0  -0.991  52.1503  3.2242  5.6303
 0KX  O5'  O  O2    0  -0.584  50.5624  2.8397  3.5858
 0KX  C5'  C  CH2   0  -0.226  50.7608  3.9984  2.7706
 0KX  C4'  C  CH1   0   0.015  49.7736  5.0843  3.1157
 0KX  O4'  O  O2    0  -0.497  48.4439  4.6628  2.8526
 0KX  C3'  C  CH1   0   0.025  49.7341  5.5624  4.5664
 0KX  O3'  O  OH1   0  -0.691  50.8164  6.3826  4.9293
 0KX  C2'  C  CH2   0  -0.539  48.3609  6.2143  4.6197
 0KX  C1'  C  CH1   0   0.200  47.5372  5.2955  3.7178
 0KX  N1   N  NR6   0  -0.550  46.8004  4.2728  4.4786
 0KX  C2   C  CR6   0   0.596  45.5984  4.6758  5.0790
 0KX  N3   N  N     0  -0.538  44.8852  3.7631  5.7650
 0KX  C4   C  CR6   0   0.515  45.3238  2.5258  5.9023
 0KX  C5   C  CR16  0  -0.475  46.5607  2.0940  5.3369
 0KX  C6   C  CR16  0   0.083  47.2553  3.0092  4.6290
 0KX  O2   O  O     0  -0.527  45.2457  5.8438  4.9568
 0KX  N4   N  NH2   0  -0.810  44.5773  1.6648  6.5930
 0KX  H1   H  HOH1  0   0.508  53.3320  1.2832  8.8156
 0KX  H2   H  HOH1  0   0.509  56.7669  2.3120  7.7358
 0KX  H3   H  HOH1  0   0.512  52.0352  6.0096  5.9877
 0KX  H4   H  HOH1  0   0.504  51.5848  0.3490  5.4729
 0KX  H5   H  HNH1  0   0.441  51.4836  3.2172  6.3959
 0KX  H6   H  HCH2  0   0.282  50.6467  3.7041  1.7263
 0KX  H7   H  HCH2  0   0.251  51.7671  4.4132  2.8795
 0KX  H8   H  HCH1  0   0.257  50.0300  5.9369  2.4684
 0KX  H9   H  HCH1  0   0.258  49.7645  4.7094  5.2481
 0KX  H10  H  HOH1  0   0.478  50.8474  7.1797  4.3862
 0KX  H11  H  HCH2  0   0.271  48.4041  7.2146  4.1810
 0KX  H12  H  HCH2  0   0.289  47.9559  6.3040  5.6253
 0KX  H13  H  HCH1  0   0.278  46.7979  5.8469  3.1382
 0KX  H14  H  HCR6  0   0.285  46.9249  1.0841  5.4502
 0KX  H15  H  HCR6  0   0.317  48.1925  2.7608  4.1563
 0KX  H16  H  HNH2  0   0.402  43.7009  1.9578  6.9897
 0KX  H17  H  HNH2  0   0.413  44.8614  0.7105  6.7261

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
 0KX  O4'  C4'  single  1.419  0.020  1.419
 0KX  O4'  C1'  single  1.404  0.020  1.404
 0KX  C4'  C5'  single  1.508  0.020  1.508
 0KX  C4'  C3'  single  1.528  0.020  1.528
 0KX  C5'  O5'  single  1.431  0.020  1.431
 0KX  C1'  N1   single  1.472  0.020  1.472
 0KX  C1'  C2'  single  1.528  0.020  1.528
 0KX  O5'  PA   single  1.602  0.020  1.602
 0KX  O1A  PA   double  1.470  0.020  1.470
 0KX  O2   C2   double  1.226  0.020  1.226
 0KX  N1   C2   single  1.403  0.020  1.403
 0KX  N1   C6   single  1.351  0.020  1.351
 0KX  C3'  C2'  single  1.521  0.020  1.521
 0KX  C3'  O3'  single  1.406  0.020  1.406
 0KX  C2   N3   single  1.346  0.020  1.346
 0KX  C6   C5   double  1.349  0.020  1.349
 0KX  O2B  PB   double  1.471  0.020  1.471
 0KX  PA   O2A  single  1.589  0.020  1.589
 0KX  PA   N3A  single  1.684  0.020  1.684
 0KX  N3   C4   double  1.320  0.020  1.320
 0KX  C5   C4   single  1.427  0.020  1.427
 0KX  C4   N4   single  1.333  0.020  1.333
 0KX  O2G  PG   double  1.472  0.020  1.472
 0KX  PB   N3A  single  1.672  0.020  1.672
 0KX  PB   O1B  single  1.579  0.020  1.579
 0KX  PB   O3B  single  1.623  0.020  1.623
 0KX  PG   O3B  single  1.619  0.020  1.619
 0KX  PG   O3G  single  1.587  0.020  1.587
 0KX  PG   O1G  single  1.587  0.020  1.587
 0KX  O1G  H1   single  0.850  0.020  0.980
 0KX  O3G  H2   single  0.850  0.020  0.980
 0KX  O1B  H3   single  0.850  0.020  0.980
 0KX  O2A  H4   single  0.850  0.020  0.980
 0KX  N3A  H5   single  0.860  0.020  1.020
 0KX  C5'  H6   single  0.970  0.020  1.090
 0KX  C5'  H7   single  0.970  0.020  1.090
 0KX  C4'  H8   single  0.970  0.020  1.090
 0KX  C3'  H9   single  0.970  0.020  1.090
 0KX  O3'  H10  single  0.850  0.020  0.980
 0KX  C2'  H11  single  0.970  0.020  1.090
 0KX  C2'  H12  single  0.970  0.020  1.090
 0KX  C1'  H13  single  0.970  0.020  1.090
 0KX  C5   H14  single  0.930  0.020  1.080
 0KX  C6   H15  single  0.930  0.020  1.080
 0KX  N4   H16  single  0.860  0.020  1.020
 0KX  N4   H17  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
 0KX  O3B  PG   O3G  101.62  3.000
 0KX  O3G  PG   O2G  117.41  3.000
 0KX  O3B  PG   O2G  115.02  3.000
 0KX  O3G  PG   O1G  102.89  3.000
 0KX  O3B  PG   O1G   99.27  3.000
 0KX  O2G  PG   O1G  117.83  3.000
 0KX  H1   O1G  PG   114.59  3.000
 0KX  H2   O3G  PG   114.55  3.000
 0KX  N3A  PB   O3B  105.91  3.000
 0KX  O3B  PB   O2B  113.47  3.000
 0KX  N3A  PB   O2B  113.83  3.000
 0KX  O3B  PB   O1B   98.02  3.000
 0KX  N3A  PB   O1B  104.98  3.000
 0KX  O2B  PB   O1B  118.81  3.000
 0KX  H3   O1B  PB   111.62  3.000
 0KX  PB   O3B  PG   127.96  3.000
 0KX  O5'  PA   N3A  105.52  3.000
 0KX  N3A  PA   O2A  103.73  3.000
 0KX  O5'  PA   O2A   96.64  3.000
 0KX  N3A  PA   O1A  113.46  3.000
 0KX  O2A  PA   O1A  119.60  3.000
 0KX  O5'  PA   O1A  115.67  3.000
 0KX  H4   O2A  PA   114.14  3.000
 0KX  H5   N3A  PA   116.21  3.000
 0KX  H5   N3A  PB   116.19  3.000
 0KX  PA   N3A  PB   127.39  3.000
 0KX  C5'  O5'  PA   119.29  3.000
 0KX  H7   C5'  H6   107.09  3.000
 0KX  H7   C5'  C4'  107.85  3.000
 0KX  H6   C5'  C4'  110.18  3.000
 0KX  H7   C5'  O5'  112.21  3.000
 0KX  H6   C5'  O5'  108.21  3.000
 0KX  C4'  C5'  O5'  111.23  3.000
 0KX  H8   C4'  C3'  108.78  3.000
 0KX  H8   C4'  O4'  109.83  3.000
 0KX  C3'  C4'  O4'  104.16  3.000
 0KX  H8   C4'  C5'  105.71  3.000
 0KX  C3'  C4'  C5'  117.36  3.000
 0KX  O4'  C4'  C5'  110.92  3.000
 0KX  C1'  O4'  C4'  110.91  3.000
 0KX  H9   C3'  C2'  109.75  3.000
 0KX  H9   C3'  O3'  105.84  3.000
 0KX  C2'  C3'  O3'  115.85  3.000
 0KX  H9   C3'  C4'  110.33  3.000
 0KX  O3'  C3'  C4'  114.07  3.000
 0KX  C2'  C3'  C4'  100.99  3.000
 0KX  H10  O3'  C3'  111.18  3.000
 0KX  H12  C2'  H11  108.08  3.000
 0KX  H12  C2'  C1'  113.23  3.000
 0KX  H11  C2'  C1'  109.55  3.000
 0KX  H12  C2'  C3'  113.82  3.000
 0KX  H11  C2'  C3'  110.03  3.000
 0KX  C1'  C2'  C3'  102.02  3.000
 0KX  H13  C1'  N1   106.68  3.000
 0KX  H13  C1'  C2'  112.05  3.000
 0KX  N1   C1'  C2'  112.48  3.000
 0KX  H13  C1'  O4'  109.79  3.000
 0KX  C2'  C1'  O4'  106.65  3.000
 0KX  N1   C1'  O4'  109.18  3.000
 0KX  C6   N1   C2   120.63  3.000
 0KX  C6   N1   C1'  122.59  3.000
 0KX  C2   N1   C1'  116.77  3.000
 0KX  O2   C2   N3   122.97  3.000
 0KX  N3   C2   N1   118.51  3.000
 0KX  O2   C2   N1   118.52  3.000
 0KX  C4   N3   C2   120.83  3.000
 0KX  N4   C4   C5   119.70  3.000
 0KX  N4   C4   N3   118.26  3.000
 0KX  C5   C4   N3   122.04  3.000
 0KX  H14  C5   C6   121.06  3.000
 0KX  H14  C5   C4   122.27  3.000
 0KX  C6   C5   C4   116.67  3.000
 0KX  H15  C6   C5   121.39  3.000
 0KX  H15  C6   N1   117.32  3.000
 0KX  C5   C6   N1   121.28  3.000
 0KX  H17  N4   H16  118.10  3.000
 0KX  H17  N4   C4   121.61  3.000
 0KX  H16  N4   C4   120.30  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
 0KX  CONST_01  N3   C2   N1   C1'   180.00   0.0  0
 0KX  CONST_02  C4   N3   C2   N1      0.00   0.0  0
 0KX  CONST_03  C5   C4   N3   C2      0.00   0.0  0
 0KX  CONST_04  C6   N1   C2   N3      0.00   0.0  0
 0KX  CONST_05  O2   C2   N1   C1'     0.00   0.0  0
 0KX  CONST_06  N4   C4   N3   C2    180.00   0.0  0
 0KX  CONST_07  O2   C2   N3   C4    180.00   0.0  0
 0KX  CONST_08  O2   C2   N1   C6    180.00   0.0  0
 0KX  CONST_09  H16  N4   C4   N3      0.00   0.0  0
 0KX  CONST_10  H17  N4   C4   N3    180.00   0.0  0
 0KX  Var_01    C4'  C5'  O5'  PA   -129.67  30.0  1
 0KX  Var_02    O2B  PB   O3B  PG    -97.85  30.0  1
 0KX  Var_03    O5'  PA   N3A  PB   -102.91  30.0  2
 0KX  Var_04    PA   N3A  PB   O1B   143.40  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
 0KX  chir_03  C4'  O4'  C5'  C3'  positiv
 0KX  chir_04  C3'  O3'  C4'  C2'  positiv
 0KX  chir_05  C1'  O4'  N1   C2'  negativ
 0KX  chir_06  PB   N3A  O1B  O3B  both
 0KX  chir_07  PA   O1A  O2A  N3A  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
 0KX  plan-1  C1'  0.020
 0KX  plan-1  N1   0.020
 0KX  plan-1  C2   0.020
 0KX  plan-1  N3   0.020
 0KX  plan-1  C4   0.020
 0KX  plan-1  C5   0.020
 0KX  plan-1  C6   0.020
 0KX  plan-1  O2   0.020
 0KX  plan-1  N4   0.020
 0KX  plan-1  H14  0.020
 0KX  plan-1  H15  0.020
 0KX  plan-1  H16  0.020
 0KX  plan-1  H17  0.020

