# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Aug  1 03:00:36 2021
#   Inital geometry file: a 161 line input string
#   Ligand name: a 2 line input string
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)N(C=C1C#Cc2ccc(cc2)C#C)[C@H]3C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O3
#
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
 0R6  0R6  '2'-deoxy-5-[(4-ethynylphenyl)ethynyl]cytidine 5'-(tetrahydrogen triphosphate)'  ligand  58  38  .  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_0R6
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
 0R6  O2   O  O     0  -0.487  18.1534  -20.5489   -5.7799
 0R6  C2   C  CR6   0   0.567  18.6840  -19.4531   -5.8771
 0R6  N3   N  N     0  -0.550  18.8753  -18.6212   -4.8382
 0R6  C4   C  CR6   0   0.484  19.4155  -17.4334   -5.0013
 0R6  N4   N  NH2   0  -0.808  19.5654  -16.6471   -3.9432
 0R6  C5   C  CR6   0  -0.367  19.8425  -16.9624   -6.2948
 0R6  C29  C  CSP   0   0.076  20.3941  -15.6786   -6.4865
 0R6  C30  C  CSP   0   0.171  20.8551  -14.5720   -6.6316
 0R6  C31  C  CR6   0  -0.075  21.3932  -13.2807   -6.8632
 0R6  C36  C  CR16  0  -0.315  21.4669  -12.3363   -5.8359
 0R6  C35  C  CR16  0  -0.286  21.9925  -11.0827   -6.0738
 0R6  C34  C  CR6   0   0.237  22.4623  -10.7385   -7.3438
 0R6  C37  C  CSP   0   0.111  23.0074   -9.4440   -7.5830
 0R6  C38  C  CSP1  0  -0.542  23.4713   -8.3511   -7.7765
 0R6  C33  C  CR16  0  -0.350  22.3931  -11.6826   -8.3725
 0R6  C32  C  CR16  0  -0.263  21.8672  -12.9375   -8.1355
 0R6  C6   C  CR16  0   0.018  19.6725  -17.8267   -7.3312
 0R6  N1   N  NR6   0  -0.451  19.1151  -19.0345   -7.1536
 0R6  C1'  C  CH1   0   0.188  18.8973  -19.9704   -8.2704
 0R6  C2'  C  CH2   0  -0.587  17.4497  -19.9687   -8.7575
 0R6  C3'  C  CH1   0   0.001  17.4979  -18.9573   -9.8947
 0R6  O3'  O  OH1   0  -0.628  16.4382  -19.0198  -10.8158
 0R6  O4'  O  O2    0  -0.475  19.6815  -19.5773   -9.3625
 0R6  C4'  C  CH1   0   0.028  18.8809  -19.2546  -10.4866
 0R6  C5'  C  CH2   0  -0.288  19.5476  -18.1807  -11.3142
 0R6  O5'  O  O2    0  -0.545  19.6209  -16.9564  -10.5759
 0R6  PA   P  P     0   1.474  19.0137  -15.5705  -11.0362
 0R6  O1A  O  O     0  -0.688  19.5904  -14.9240  -12.2344
 0R6  O2A  O  OH1   0  -0.703  19.1680  -14.8130   -9.6538
 0R6  O3A  O  O2    0  -0.650  17.4240  -15.7970  -11.1545
 0R6  PB   P  P     0   1.467  16.5735  -16.2162  -12.5047
 0R6  O1B  O  O     0  -0.641  17.3672  -17.0741  -13.3891
 0R6  O2B  O  OH1   0  -0.675  15.2426  -16.7560  -11.8631
 0R6  O3B  O  O2    0  -0.576  16.0867  -14.8134  -13.0575
 0R6  PG   P  P     0   1.400  16.7970  -13.8625  -14.2220
 0R6  O3G  O  OH1   0  -0.688  17.9936  -13.1926  -13.4518
 0R6  O1G  O  O     0  -0.700  17.0206  -14.5811  -15.4753
 0R6  O2G  O  OH1   0  -0.699  15.7547  -12.6618  -14.2398
 0R6  H1   H  HNH2  0   0.399  19.3058  -16.9713   -3.0293
 0R6  H2   H  HNH2  0   0.410  20.0185  -15.7530   -4.0047
 0R6  H3   H  HCR6  0   0.250  21.1111  -12.5850   -4.8463
 0R6  H4   H  HCR6  0   0.272  22.0412  -10.3628   -5.2690
 0R6  H5   H  H     0   0.300  23.8850   -7.3832   -7.9341
 0R6  H6   H  HCR6  0   0.244  22.7574  -11.4274   -9.3585
 0R6  H7   H  HCR6  0   0.259  21.8300  -13.6679   -8.9327
 0R6  H8   H  HCR6  0   0.321  19.9882  -17.5594   -8.3263
 0R6  H9   H  HCH1  0   0.314  19.2137  -20.9528   -7.9216
 0R6  H10  H  HCH2  0   0.318  16.7314  -19.7293   -7.9768
 0R6  H11  H  HCH2  0   0.310  17.1986  -20.9620   -9.1423
 0R6  H12  H  HCH1  0   0.207  17.4683  -17.9435   -9.4885
 0R6  H13  H  HOH1  0   0.471  16.4065  -19.8827  -11.2415
 0R6  H14  H  HCH1  0   0.210  18.8033  -20.1334  -11.1483
 0R6  H15  H  HCH2  0   0.274  19.0091  -18.0619  -12.2546
 0R6  H16  H  HCH2  0   0.284  20.5700  -18.4785  -11.5492
 0R6  H17  H  HOH1  0   0.452  19.1008  -13.8525   -9.6987
 0R6  H18  H  HOH1  0   0.506  15.3882  -17.6325  -11.4552
 0R6  H19  H  HOH1  0   0.517  18.7140  -13.7985  -13.1490
 0R6  H20  H  HOH1  0   0.494  15.2349  -12.6504  -15.0506

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
 0R6  O1G  PG   double    1.462  0.020  1.462
 0R6  O3G  PG   single    1.573  0.020  1.573
 0R6  PG   O2G  single    1.590  0.020  1.590
 0R6  PG   O3B  single    1.663  0.020  1.663
 0R6  O1B  PB   double    1.466  0.020  1.466
 0R6  O1A  PA   double    1.479  0.020  1.479
 0R6  O3B  PB   single    1.584  0.020  1.584
 0R6  PB   O2B  single    1.573  0.020  1.573
 0R6  PB   O3A  single    1.650  0.020  1.650
 0R6  C5'  O5'  single    1.432  0.020  1.432
 0R6  C5'  C4'  single    1.511  0.020  1.511
 0R6  PA   O3A  single    1.610  0.020  1.610
 0R6  PA   O5'  single    1.582  0.020  1.582
 0R6  PA   O2A  single    1.584  0.020  1.584
 0R6  O3'  C3'  single    1.405  0.020  1.405
 0R6  C4'  C3'  single    1.533  0.020  1.533
 0R6  C4'  O4'  single    1.417  0.020  1.417
 0R6  C3'  C2'  single    1.523  0.020  1.523
 0R6  O4'  C1'  single    1.401  0.020  1.401
 0R6  C2'  C1'  single    1.527  0.020  1.527
 0R6  C33  C32  aromatic  1.381  0.020  1.381
 0R6  C33  C34  aromatic  1.398  0.020  1.398
 0R6  C1'  N1   single    1.473  0.020  1.473
 0R6  C32  C31  aromatic  1.401  0.020  1.401
 0R6  C38  C37  triple    1.203  0.020  1.203
 0R6  C37  C34  single    1.425  0.020  1.425
 0R6  C34  C35  aromatic  1.397  0.020  1.397
 0R6  C6   N1   single    1.342  0.020  1.342
 0R6  C6   C5   double    1.360  0.020  1.360
 0R6  N1   C2   single    1.411  0.020  1.411
 0R6  C31  C30  single    1.418  0.020  1.418
 0R6  C31  C36  aromatic  1.397  0.020  1.397
 0R6  C30  C29  triple    1.208  0.020  1.208
 0R6  C29  C5   single    1.410  0.020  1.410
 0R6  C5   C4   single    1.441  0.020  1.441
 0R6  C35  C36  aromatic  1.380  0.020  1.380
 0R6  C2   O2   double    1.221  0.020  1.221
 0R6  C2   N3   single    1.345  0.020  1.345
 0R6  C4   N3   double    1.315  0.020  1.315
 0R6  C4   N4   single    1.327  0.020  1.327
 0R6  N4   H1   single    0.868  0.020  1.013
 0R6  N4   H2   single    0.868  0.020  1.013
 0R6  C36  H3   single    0.929  0.020  1.085
 0R6  C35  H4   single    0.929  0.020  1.085
 0R6  C38  H5   single    0.913  0.020  1.066
 0R6  C33  H6   single    0.929  0.020  1.085
 0R6  C32  H7   single    0.929  0.020  1.085
 0R6  C6   H8   single    0.930  0.020  1.086
 0R6  C1'  H9   single    0.939  0.020  1.096
 0R6  C2'  H10  single    0.939  0.020  1.096
 0R6  C2'  H11  single    0.939  0.020  1.096
 0R6  C3'  H12  single    0.939  0.020  1.096
 0R6  O3'  H13  single    0.832  0.020  0.971
 0R6  C4'  H14  single    0.939  0.020  1.096
 0R6  C5'  H15  single    0.939  0.020  1.096
 0R6  C5'  H16  single    0.939  0.020  1.096
 0R6  O2A  H17  single    0.832  0.020  0.971
 0R6  O2B  H18  single    0.832  0.020  0.971
 0R6  O3G  H19  single    0.832  0.020  0.971
 0R6  O2G  H20  single    0.832  0.020  0.971

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
 0R6  N1   C2   N3   118.17  3.000
 0R6  N3   C2   O2   123.74  3.000
 0R6  N1   C2   O2   118.10  3.000
 0R6  C4   N3   C2   121.43  3.000
 0R6  C5   C4   N4   119.25  3.000
 0R6  N4   C4   N3   118.87  3.000
 0R6  C5   C4   N3   121.88  3.000
 0R6  H2   N4   H1   117.39  3.000
 0R6  H2   N4   C4   121.99  3.000
 0R6  H1   N4   C4   120.36  3.000
 0R6  C6   C5   C29  121.58  3.000
 0R6  C29  C5   C4   122.36  3.000
 0R6  C6   C5   C4   116.05  3.000
 0R6  C30  C29  C5   180.00  3.000
 0R6  C31  C30  C29  180.00  3.000
 0R6  C32  C31  C36  118.98  3.000
 0R6  C36  C31  C30  121.03  3.000
 0R6  C32  C31  C30  120.00  3.000
 0R6  H3   C36  C35  119.50  3.000
 0R6  H3   C36  C31  120.02  3.000
 0R6  C35  C36  C31  120.48  3.000
 0R6  H4   C35  C34  119.84  3.000
 0R6  H4   C35  C36  119.59  3.000
 0R6  C34  C35  C36  120.57  3.000
 0R6  C33  C34  C37  120.59  3.000
 0R6  C37  C34  C35  120.34  3.000
 0R6  C33  C34  C35  119.07  3.000
 0R6  C38  C37  C34  180.00  3.000
 0R6  H5   C38  C37  180.00  3.000
 0R6  H6   C33  C32  119.94  3.000
 0R6  H6   C33  C34  119.65  3.000
 0R6  C32  C33  C34  120.41  3.000
 0R6  H7   C32  C33  120.01  3.000
 0R6  H7   C32  C31  119.50  3.000
 0R6  C33  C32  C31  120.49  3.000
 0R6  H8   C6   N1   117.85  3.000
 0R6  H8   C6   C5   120.62  3.000
 0R6  N1   C6   C5   121.53  3.000
 0R6  C1'  N1   C6   122.19  3.000
 0R6  C6   N1   C2   120.91  3.000
 0R6  C1'  N1   C2   116.88  3.000
 0R6  H9   C1'  O4'  109.88  3.000
 0R6  H9   C1'  C2'  112.23  3.000
 0R6  O4'  C1'  C2'  106.36  3.000
 0R6  H9   C1'  N1   106.69  3.000
 0R6  C2'  C1'  N1   112.40  3.000
 0R6  O4'  C1'  N1   109.27  3.000
 0R6  H11  C2'  H10  107.50  3.000
 0R6  H11  C2'  C3'  110.33  3.000
 0R6  H10  C2'  C3'  114.26  3.000
 0R6  H11  C2'  C1'  109.18  3.000
 0R6  H10  C2'  C1'  113.41  3.000
 0R6  C3'  C2'  C1'  102.06  3.000
 0R6  H12  C3'  C4'  110.35  3.000
 0R6  H12  C3'  O3'  105.34  3.000
 0R6  C4'  C3'  O3'  114.74  3.000
 0R6  H12  C3'  C2'  109.74  3.000
 0R6  C4'  C3'  C2'  100.84  3.000
 0R6  O3'  C3'  C2'  115.85  3.000
 0R6  H13  O3'  C3'  110.77  3.000
 0R6  C4'  O4'  C1'  111.47  3.000
 0R6  H14  C4'  C5'  105.60  3.000
 0R6  H14  C4'  O4'  109.52  3.000
 0R6  C5'  C4'  O4'  110.31  3.000
 0R6  H14  C4'  C3'  108.82  3.000
 0R6  O4'  C4'  C3'  104.33  3.000
 0R6  C5'  C4'  C3'  118.14  3.000
 0R6  H16  C5'  H15  107.88  3.000
 0R6  H16  C5'  O5'  107.26  3.000
 0R6  H15  C5'  O5'  112.15  3.000
 0R6  H16  C5'  C4'  109.73  3.000
 0R6  H15  C5'  C4'  109.39  3.000
 0R6  O5'  C5'  C4'  110.36  3.000
 0R6  PA   O5'  C5'  125.43  3.000
 0R6  O3A  PA   O2A  103.16  3.000
 0R6  O2A  PA   O1A  117.40  3.000
 0R6  O3A  PA   O1A  112.77  3.000
 0R6  O2A  PA   O5'   97.33  3.000
 0R6  O3A  PA   O5'  106.09  3.000
 0R6  O1A  PA   O5'  117.99  3.000
 0R6  H17  O2A  PA   115.41  3.000
 0R6  PB   O3A  PA   127.22  3.000
 0R6  O3B  PB   O2B  100.73  3.000
 0R6  O2B  PB   O1B  120.23  3.000
 0R6  O3B  PB   O1B  118.30  3.000
 0R6  O2B  PB   O3A  100.93  3.000
 0R6  O3B  PB   O3A  102.65  3.000
 0R6  O1B  PB   O3A  111.31  3.000
 0R6  H18  O2B  PB   110.60  3.000
 0R6  PG   O3B  PB   128.28  3.000
 0R6  O2G  PG   O1G  117.51  3.000
 0R6  O2G  PG   O3G  100.52  3.000
 0R6  O1G  PG   O3G  120.85  3.000
 0R6  O2G  PG   O3B   99.19  3.000
 0R6  O3G  PG   O3B  103.04  3.000
 0R6  O1G  PG   O3B  112.62  3.000
 0R6  H19  O3G  PG   116.31  3.000
 0R6  H20  O2G  PG   111.85  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
 0R6  CONST_01  C34  C33  C32  C31    0.00   0.0  0
 0R6  CONST_02  C34  C35  C36  C31    0.00   0.0  0
 0R6  CONST_03  C33  C32  C31  C36    0.00   0.0  0
 0R6  CONST_04  C33  C34  C35  C36    0.00   0.0  0
 0R6  CONST_05  C32  C33  C34  C35    0.00   0.0  0
 0R6  CONST_06  C32  C31  C36  C35    0.00   0.0  0
 0R6  CONST_07  C5   C4   N3   C2     0.00   0.0  0
 0R6  CONST_08  C1'  N1   C2   N3   180.00   0.0  0
 0R6  CONST_09  C6   N1   C2   N3     0.00   0.0  0
 0R6  CONST_10  N1   C2   N3   C4     0.00   0.0  0
 0R6  CONST_11  C33  C32  C31  C30  180.00   0.0  0
 0R6  CONST_12  C35  C36  C31  C30  180.00   0.0  0
 0R6  CONST_13  C37  C34  C35  C36  180.00   0.0  0
 0R6  CONST_14  C32  C33  C34  C37  180.00   0.0  0
 0R6  CONST_15  C1'  N1   C2   O2     0.00   0.0  0
 0R6  CONST_16  C6   N1   C2   O2   180.00   0.0  0
 0R6  CONST_17  C4   N3   C2   O2   180.00   0.0  0
 0R6  CONST_18  N4   C4   N3   C2   180.00   0.0  0
 0R6  CONST_19  H6   C33  C32  C31  180.00   0.0  0
 0R6  CONST_20  H4   C35  C36  C31  180.00   0.0  0
 0R6  CONST_21  H7   C32  C31  C36  180.00   0.0  0
 0R6  CONST_22  H3   C36  C35  C34  180.00   0.0  0
 0R6  CONST_23  H1   N4   C4   N3     0.00   0.0  0
 0R6  CONST_24  H2   N4   C4   N3   180.00   0.0  0
 0R6  Var_01    O1A  PA   O5'  C5'  -65.71  30.0  1
 0R6  Var_02    O1B  PB   O3A  PA    32.21  30.0  1
 0R6  Var_03    O1G  PG   O3B  PB    54.44  30.0  2
 0R6  Var_04    H15  C5'  O5'  PA    -0.33  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
 0R6  chir_01  C1'  O4'  C2'  N1   positiv
 0R6  chir_02  C3'  O3'  C4'  C2'  positiv
 0R6  chir_03  C4'  O4'  C3'  C5'  negativ
 0R6  chir_04  PA   O3A  O5'  O2A  both
 0R6  chir_05  PB   O2B  O3B  O1B  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
 0R6  plan-1  C29  0.020
 0R6  plan-1  C30  0.020
 0R6  plan-1  C31  0.020
 0R6  plan-1  C36  0.020
 0R6  plan-1  C35  0.020
 0R6  plan-1  C34  0.020
 0R6  plan-1  C37  0.020
 0R6  plan-1  C38  0.020
 0R6  plan-1  C33  0.020
 0R6  plan-1  C32  0.020
 0R6  plan-1  H3   0.020
 0R6  plan-1  H4   0.020
 0R6  plan-1  H6   0.020
 0R6  plan-1  H7   0.020
 0R6  plan-2  O2   0.020
 0R6  plan-2  C2   0.020
 0R6  plan-2  N3   0.020
 0R6  plan-2  C4   0.020
 0R6  plan-2  N4   0.020
 0R6  plan-2  C5   0.020
 0R6  plan-2  C29  0.020
 0R6  plan-2  C30  0.020
 0R6  plan-2  C6   0.020
 0R6  plan-2  N1   0.020
 0R6  plan-2  C1'  0.020
 0R6  plan-2  H1   0.020
 0R6  plan-2  H2   0.020
 0R6  plan-2  H8   0.020

