# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  2 20:04:44 2021
#   Inital geometry file: a 119 line input string
#   Ligand name: 4-amino-1-{5-O-[(R)-{[(R)-[(S)-chloro(fluoro)phosphonomethyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2-deoxy-alpha-L-threo-pentofuranosyl}pyrimidin-2(1H)-one
#   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)O[P](O)(=O)[C@@](F)(Cl)[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
 VC6  VC6  4-amino-1-{5-O-[(R)-{[(R)-[(S)-chloro(fluoro)phosphonomethyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2-deoxy-alpha-L-threo-pentofuranosyl}pyrimidin-2(1H)-one  ligand  46  30  .  2022-11-18  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_VC6
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
 VC6  C4   C   CR6   0   0.515   9.6126  5.9939  10.8391
 VC6  N4   N   NH2   0  -0.810  10.8637  5.5879  10.6260
 VC6  C5   C   CR16  0  -0.467   8.8406  5.3905  11.8773
 VC6  C6   C   CR16  0   0.090   7.5844  5.8545  12.0417
 VC6  N3   N   N     0  -0.538   9.1293  6.9552  10.0755
 VC6  C2   C   CR6   0   0.596   7.8697  7.4018  10.2412
 VC6  O2   O   O     0  -0.526   7.3796  8.2867   9.5484
 VC6  N1   N   NR6   0  -0.550   7.0831  6.8287  11.2506
 VC6  C1'  C   CR15  0   0.182   5.7039  7.3425  11.4002
 VC6  C2'  C   CH2   0  -0.520   4.7641  6.7793  10.3447
 VC6  C3'  C   CR15  0   0.001   4.3122  5.4778  10.9847
 VC6  O3'  O   OH1   0  -0.656   3.0974  5.0355  10.4516
 VC6  O4'  O   O     0  -0.489   5.1850  6.9386  12.6314
 VC6  C4'  C   CR15  0  -0.042   4.2724  5.8549  12.4800
 VC6  C5'  C   CH2   0  -0.210   2.8967  6.2647  12.9657
 VC6  O5'  O   O2    0  -0.567   2.9263  6.4545  14.3926
 VC6  PA   P   P     0   1.515   2.4445  5.3474  15.4166
 VC6  O1A  O   OH1   0  -0.739   1.0017  4.8500  14.9830
 VC6  O2A  O   O     0  -0.651   2.6761  5.7499  16.8064
 VC6  O3A  O   O2    0  -0.720   3.2948  4.0168  15.0044
 VC6  PB   P   P     0   1.431   2.9971  2.6891  14.1512
 VC6  O1B  O   OH1   0  -0.705   2.1576  1.8176  15.1663
 VC6  O2B  O   O     0  -0.647   2.4773  2.8817  12.7856
 VC6  C3B  C   CT    0  -0.172   4.7028  1.9380  14.1945
 VC6  CL1  CL  CL    0  -0.046   5.5429  2.3137  12.6874
 VC6  F4B  F   F     0  -0.320   4.5223  0.5821  14.2496
 VC6  PG   P   P     0   1.402   5.7554  2.3740  15.6623
 VC6  O2G  O   OH1   0  -0.725   6.2485  3.8246  15.2497
 VC6  O1G  O   OH1   0  -0.720   7.0572  1.4897  15.4250
 VC6  O3G  O   O     0  -0.666   5.0256  2.1876  16.9292
 VC6  H1   H   HNH2  0   0.403  11.4177  6.0128   9.9023
 VC6  H2   H   HNH2  0   0.414  11.2823  4.8586  11.1754
 VC6  H3   H   HCR6  0   0.287   9.2362  4.6118  12.5118
 VC6  H4   H   HCR6  0   0.305   6.9469  5.4661  12.8224
 VC6  H5   H   HCR5  0   0.284   5.7657  8.4291  11.3793
 VC6  H6   H   HCH2  0   0.268   3.9156  7.4581  10.2209
 VC6  H7   H   HCH2  0   0.284   5.2357  6.6459   9.3739
 VC6  H8   H   HCR5  0   0.238   5.0926  4.7173  10.8452
 VC6  H9   H   HOH1  0   0.455   2.8981  4.1670  10.8215
 VC6  H10  H   HCR5  0   0.230   4.6400  5.0282  13.0905
 VC6  H11  H   HCH2  0   0.277   2.5932  7.2180  12.5334
 VC6  H12  H   HCH2  0   0.252   2.1466  5.5241  12.6906
 VC6  H13  H   HOH1  0   0.517   0.2690  5.4428  15.2067
 VC6  H14  H   HOH1  0   0.519   1.5306  1.1999  14.7615
 VC6  H15  H   HOH1  0   0.513   6.3864  4.4374  15.9866
 VC6  H16  H   HOH1  0   0.509   7.0656  0.6422  15.8913

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
 VC6  O2   C2   double  1.226  0.020  1.226
 VC6  C2   N3   single  1.347  0.020  1.347
 VC6  C2   N1   single  1.402  0.020  1.402
 VC6  C2'  C1'  single  1.521  0.020  1.521
 VC6  C2'  C3'  single  1.519  0.020  1.519
 VC6  N3   C4   double  1.319  0.020  1.319
 VC6  C1'  N1   single  1.479  0.020  1.479
 VC6  C1'  O4'  single  1.396  0.020  1.396
 VC6  N1   C6   single  1.351  0.020  1.351
 VC6  O3'  C3'  single  1.398  0.020  1.398
 VC6  C3'  C4'  single  1.543  0.020  1.543
 VC6  C4   N4   single  1.332  0.020  1.332
 VC6  C4   C5   single  1.428  0.020  1.428
 VC6  O4'  C4'  single  1.425  0.020  1.425
 VC6  C6   C5   double  1.349  0.020  1.349
 VC6  C4'  C5'  single  1.515  0.020  1.515
 VC6  O2B  PB   double  1.474  0.020  1.474
 VC6  C5'  O5'  single  1.440  0.020  1.440
 VC6  PB   O3A  single  1.606  0.020  1.606
 VC6  PB   O1B  single  1.579  0.020  1.579
 VC6  PB   C3B  single  1.864  0.020  1.864
 VC6  O3A  PA   single  1.632  0.020  1.632
 VC6  O5'  PA   single  1.583  0.020  1.583
 VC6  F4B  C3B  single  1.369  0.020  1.369
 VC6  C3B  CL1  single  1.766  0.020  1.766
 VC6  C3B  PG   single  1.858  0.020  1.858
 VC6  PA   O2A  double  1.465  0.020  1.465
 VC6  PA   O1A  single  1.587  0.020  1.587
 VC6  O3G  PG   double  1.474  0.020  1.474
 VC6  PG   O2G  single  1.587  0.020  1.587
 VC6  PG   O1G  single  1.592  0.020  1.592
 VC6  N4   H1   single  0.860  0.020  1.020
 VC6  N4   H2   single  0.860  0.020  1.020
 VC6  C5   H3   single  0.930  0.020  1.080
 VC6  C6   H4   single  0.930  0.020  1.080
 VC6  C1'  H5   single  0.970  0.020  1.090
 VC6  C2'  H6   single  0.970  0.020  1.090
 VC6  C2'  H7   single  0.970  0.020  1.090
 VC6  C3'  H8   single  0.970  0.020  1.090
 VC6  O3'  H9   single  0.850  0.020  0.980
 VC6  C4'  H10  single  0.970  0.020  1.090
 VC6  C5'  H11  single  0.970  0.020  1.090
 VC6  C5'  H12  single  0.970  0.020  1.090
 VC6  O1A  H13  single  0.850  0.020  0.980
 VC6  O1B  H14  single  0.850  0.020  0.980
 VC6  O2G  H15  single  0.850  0.020  0.980
 VC6  O1G  H16  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
 VC6  N3   C4   C5   122.06  3.000
 VC6  C5   C4   N4   119.69  3.000
 VC6  N3   C4   N4   118.25  3.000
 VC6  H2   N4   H1   118.08  3.000
 VC6  H2   N4   C4   121.68  3.000
 VC6  H1   N4   C4   120.24  3.000
 VC6  H3   C5   C6   121.17  3.000
 VC6  H3   C5   C4   122.29  3.000
 VC6  C6   C5   C4   116.54  3.000
 VC6  H4   C6   N1   117.61  3.000
 VC6  H4   C6   C5   120.92  3.000
 VC6  N1   C6   C5   121.46  3.000
 VC6  C2   N3   C4   120.86  3.000
 VC6  N1   C2   O2   118.53  3.000
 VC6  N1   C2   N3   118.54  3.000
 VC6  O2   C2   N3   122.93  3.000
 VC6  C1'  N1   C2   116.99  3.000
 VC6  C1'  N1   C6   122.48  3.000
 VC6  C2   N1   C6   120.53  3.000
 VC6  H5   C1'  O4'  109.08  3.000
 VC6  H5   C1'  C2'  113.03  3.000
 VC6  O4'  C1'  C2'  105.98  3.000
 VC6  H5   C1'  N1   106.97  3.000
 VC6  O4'  C1'  N1   109.59  3.000
 VC6  C2'  C1'  N1   112.16  3.000
 VC6  H7   C2'  H6   108.15  3.000
 VC6  H7   C2'  C3'  113.57  3.000
 VC6  H6   C2'  C3'  110.41  3.000
 VC6  H7   C2'  C1'  113.38  3.000
 VC6  H6   C2'  C1'  109.15  3.000
 VC6  C3'  C2'  C1'  102.04  3.000
 VC6  H8   C3'  C4'  108.10  3.000
 VC6  H8   C3'  O3'  110.48  3.000
 VC6  C4'  C3'  O3'  115.12  3.000
 VC6  H8   C3'  C2'  109.16  3.000
 VC6  C4'  C3'  C2'  101.92  3.000
 VC6  O3'  C3'  C2'  111.64  3.000
 VC6  H9   O3'  C3'  108.54  3.000
 VC6  C4'  O4'  C1'  111.37  3.000
 VC6  H10  C4'  C5'  109.35  3.000
 VC6  H10  C4'  O4'  107.52  3.000
 VC6  C5'  C4'  O4'  109.98  3.000
 VC6  H10  C4'  C3'  110.38  3.000
 VC6  C5'  C4'  C3'  113.59  3.000
 VC6  O4'  C4'  C3'  105.81  3.000
 VC6  H12  C5'  H11  107.62  3.000
 VC6  H12  C5'  O5'  110.73  3.000
 VC6  H11  C5'  O5'  106.47  3.000
 VC6  H12  C5'  C4'  111.12  3.000
 VC6  H11  C5'  C4'  111.24  3.000
 VC6  O5'  C5'  C4'  109.55  3.000
 VC6  PA   O5'  C5'  122.86  3.000
 VC6  O3A  PA   O2A  112.41  3.000
 VC6  O2A  PA   O1A  119.28  3.000
 VC6  O3A  PA   O1A   98.58  3.000
 VC6  O1A  PA   O5'  108.61  3.000
 VC6  O2A  PA   O5'  111.92  3.000
 VC6  O3A  PA   O5'  104.37  3.000
 VC6  H13  O1A  PA   115.66  3.000
 VC6  PB   O3A  PA   135.37  3.000
 VC6  C3B  PB   O2B  113.38  3.000
 VC6  C3B  PB   O1B  104.43  3.000
 VC6  O2B  PB   O1B  118.70  3.000
 VC6  C3B  PB   O3A   98.69  3.000
 VC6  O1B  PB   O3A  102.31  3.000
 VC6  O2B  PB   O3A  116.71  3.000
 VC6  H14  O1B  PB   115.29  3.000
 VC6  PG   C3B  F4B  105.98  3.000
 VC6  PG   C3B  CL1  110.78  3.000
 VC6  F4B  C3B  CL1  107.92  3.000
 VC6  PG   C3B  PB   116.24  3.000
 VC6  CL1  C3B  PB   109.25  3.000
 VC6  F4B  C3B  PB   106.22  3.000
 VC6  O3G  PG   O1G  117.58  3.000
 VC6  O1G  PG   O2G  102.41  3.000
 VC6  O3G  PG   O2G  119.54  3.000
 VC6  O1G  PG   C3B  102.43  3.000
 VC6  O2G  PG   C3B  100.67  3.000
 VC6  O3G  PG   C3B  111.64  3.000
 VC6  H15  O2G  PG   115.15  3.000
 VC6  H16  O1G  PG   114.96  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
 VC6  CONST_01  N1   C2   N3   C4     0.00   0.0  0
 VC6  CONST_02  C2   N3   C4   C5     0.00   0.0  0
 VC6  CONST_03  N3   C2   N1   C6     0.00   0.0  0
 VC6  CONST_04  C1'  N1   C2   N3   180.00   0.0  0
 VC6  CONST_05  O2   C2   N3   C4   180.00   0.0  0
 VC6  CONST_06  C2   N3   C4   N4   180.00   0.0  0
 VC6  CONST_07  O2   C2   N1   C6   180.00   0.0  0
 VC6  CONST_08  C1'  N1   C2   O2     0.00   0.0  0
 VC6  CONST_09  H1   N4   C4   C5   180.00   0.0  0
 VC6  CONST_10  H2   N4   C4   C5     0.00   0.0  0
 VC6  Var_01    O3A  PA   O5'  C5'   53.69  30.0  3
 VC6  Var_02    O2B  PB   O3A  PA    53.17  30.0  1
 VC6  Var_03    H11  C5'  O5'  PA   141.42  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
 VC6  chir_01  C1'  C2'  N1   O4'  positiv
 VC6  chir_02  C3'  O3'  C4'  C2'  positiv
 VC6  chir_03  C4'  O4'  C3'  C5'  positiv
 VC6  chir_06  C3B  F4B  CL1  PG   positiv
 VC6  chir_07  PA   O5'  O2A  O1A  both
 VC6  chir_08  PB   O3A  O1B  C3B  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
 VC6  plan-1  C4   0.020
 VC6  plan-1  N4   0.020
 VC6  plan-1  C5   0.020
 VC6  plan-1  C6   0.020
 VC6  plan-1  N3   0.020
 VC6  plan-1  C2   0.020
 VC6  plan-1  O2   0.020
 VC6  plan-1  N1   0.020
 VC6  plan-1  C1'  0.020
 VC6  plan-1  H1   0.020
 VC6  plan-1  H2   0.020
 VC6  plan-1  H3   0.020
 VC6  plan-1  H4   0.020

