# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  2 17:20:39 2021
#   Inital geometry file: a 119 line input string
#   Ligand name: 2'-deoxy-5'-O-[(R)-{[(R)-[dibromo(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)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)O[P](O)(=O)C(Br)(Br)[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
 VC9  VC9  2'-deoxy-5'-O-[(R)-{[(R)-[dibromo(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine  ligand  46  30  .  2022-07-22  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VC9
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
 VC9  C4   C   CR6   0   0.515   9.3659   7.6574  11.2108
 VC9  N4   N   NH2   0  -0.811  10.6700   7.7797  11.4589
 VC9  C5   C   CR16  0  -0.476   8.4647   7.3735  12.2790
 VC9  C6   C   CR16  0   0.081   7.1562   7.2823  11.9593
 VC9  N3   N   N     0  -0.539   8.9515   7.8059   9.9664
 VC9  C2   C   CR6   0   0.594   7.6466   7.6893   9.6548
 VC9  O2   O   O     0  -0.528   7.2244   7.7885   8.5076
 VC9  N1   N   NR6   0  -0.550   6.7310   7.4414  10.6878
 VC9  C1'  C   CH1   0   0.203   5.3109   7.3360  10.3064
 VC9  C2'  C   CH2   0  -0.533   4.9561   5.9657   9.7352
 VC9  C3'  C   CH1   0  -0.000   4.3774   5.2317  10.9382
 VC9  O3'  O   OH1   0  -0.692   3.4955   4.2086  10.5814
 VC9  O4'  O   O2    0  -0.500   4.5093   7.5180  11.4435
 VC9  C4'  C   CH1   0   0.015   3.6749   6.3882  11.6544
 VC9  C5'  C   CH2   0  -0.231   3.3834   6.2130  13.1224
 VC9  O5'  O   O2    0  -0.576   4.6064   6.0336  13.8483
 VC9  PA   P   P     0   1.522   4.8407   5.0224  15.0450
 VC9  O1A  O   OH1   0  -0.729   3.5114   4.9488  15.8994
 VC9  O2A  O   O     0  -0.653   6.1194   5.2686  15.7160
 VC9  O3A  O   O2    0  -0.697   4.8064   3.5659  14.3286
 VC9  PB   P   P     0   1.475   3.8758   2.3938  13.7865
 VC9  O1B  O   OH1   0  -0.707   2.4263   2.8223  14.2460
 VC9  O2B  O   O     0  -0.650   4.0799   2.1061  12.3520
 VC9  C3B  C   CT    0  -0.759   4.3635   0.9826  14.8622
 VC9  BR1  BR  BR    0   0.072   6.2098   0.5786  14.4805
 VC9  BR2  BR  BR    0   0.056   3.2269  -0.4978  14.3339
 VC9  PG   P   P     0   1.439   4.0909   1.2053  16.6871
 VC9  O2G  O   OH1   0  -0.720   5.1725   2.3291  16.9696
 VC9  O1G  O   OH1   0  -0.720   4.7395  -0.1027  17.3202
 VC9  O3G  O   O     0  -0.658   2.6806   1.4739  17.0164
 VC9  H1   H   HNH2  0   0.402  11.3081   7.9990  10.7132
 VC9  H2   H   HNH2  0   0.413  11.0402   7.6926  12.3888
 VC9  H3   H   HCR6  0   0.283   8.7991   7.2517  13.2981
 VC9  H4   H   HCR6  0   0.320   6.4075   7.0911  12.7109
 VC9  H5   H   HCH1  0   0.271   5.1245   8.1385   9.5933
 VC9  H6   H   HCH2  0   0.262   4.1807   6.0803   8.9741
 VC9  H7   H   HCH2  0   0.278   5.8049   5.4594   9.2802
 VC9  H8   H   HCH1  0   0.229   5.1984   4.8515  11.5596
 VC9  H9   H   HOH1  0   0.461   3.6810   3.4263  11.1223
 VC9  H10  H   HCH1  0   0.251   2.6998   6.5471  11.1718
 VC9  H11  H   HCH2  0   0.284   2.8766   7.0901  13.5268
 VC9  H12  H   HCH2  0   0.247   2.7054   5.3637  13.2356
 VC9  H13  H   HOH1  0   0.515   3.4211   5.6329  16.5787
 VC9  H14  H   HOH1  0   0.519   1.6914   2.4760  13.7184
 VC9  H15  H   HOH1  0   0.513   5.1275   2.7338  17.8490
 VC9  H16  H   HOH1  0   0.508   4.1055  -0.7905  17.5666

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
 VC9  O2   C2   double  1.226  0.020  1.226
 VC9  C2   N3   single  1.347  0.020  1.347
 VC9  C2   N1   single  1.402  0.020  1.402
 VC9  C2'  C1'  single  1.526  0.020  1.526
 VC9  C2'  C3'  single  1.523  0.020  1.523
 VC9  N3   C4   double  1.320  0.020  1.320
 VC9  C1'  N1   single  1.474  0.020  1.474
 VC9  C1'  O4'  single  1.403  0.020  1.403
 VC9  N1   C6   single  1.350  0.020  1.350
 VC9  O3'  C3'  single  1.397  0.020  1.397
 VC9  C3'  C4'  single  1.531  0.020  1.531
 VC9  C4   N4   single  1.333  0.020  1.333
 VC9  C4   C5   single  1.426  0.020  1.426
 VC9  O4'  C4'  single  1.420  0.020  1.420
 VC9  C4'  C5'  single  1.507  0.020  1.507
 VC9  C6   C5   double  1.350  0.020  1.350
 VC9  O2B  PB   double  1.477  0.020  1.477
 VC9  C5'  O5'  single  1.433  0.020  1.433
 VC9  O5'  PA   single  1.584  0.020  1.584
 VC9  O3A  PB   single  1.592  0.020  1.592
 VC9  O3A  PA   single  1.623  0.020  1.623
 VC9  PB   O1B  single  1.580  0.020  1.580
 VC9  PB   C3B  single  1.840  0.020  1.840
 VC9  BR2  C3B  single  1.940  0.020  1.940
 VC9  PA   O2A  double  1.465  0.020  1.465
 VC9  PA   O1A  single  1.582  0.020  1.582
 VC9  C3B  BR1  single  1.928  0.020  1.928
 VC9  C3B  PG   single  1.858  0.020  1.858
 VC9  O3G  PG   double  1.473  0.020  1.473
 VC9  PG   O2G  single  1.585  0.020  1.585
 VC9  PG   O1G  single  1.591  0.020  1.591
 VC9  N4   H1   single  0.860  0.020  1.020
 VC9  N4   H2   single  0.860  0.020  1.020
 VC9  C5   H3   single  0.930  0.020  1.080
 VC9  C6   H4   single  0.930  0.020  1.080
 VC9  C1'  H5   single  0.970  0.020  1.090
 VC9  C2'  H6   single  0.970  0.020  1.090
 VC9  C2'  H7   single  0.970  0.020  1.090
 VC9  C3'  H8   single  0.970  0.020  1.090
 VC9  O3'  H9   single  0.850  0.020  0.980
 VC9  C4'  H10  single  0.970  0.020  1.090
 VC9  C5'  H11  single  0.970  0.020  1.090
 VC9  C5'  H12  single  0.970  0.020  1.090
 VC9  O1A  H13  single  0.850  0.020  0.980
 VC9  O1B  H14  single  0.850  0.020  0.980
 VC9  O2G  H15  single  0.850  0.020  0.980
 VC9  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
 VC9  N3   C4   C5   122.02  3.000
 VC9  C5   C4   N4   119.80  3.000
 VC9  N3   C4   N4   118.18  3.000
 VC9  H2   N4   H1   118.12  3.000
 VC9  H2   N4   C4   121.65  3.000
 VC9  H1   N4   C4   120.18  3.000
 VC9  H3   C5   C6   121.07  3.000
 VC9  H3   C5   C4   122.27  3.000
 VC9  C6   C5   C4   116.65  3.000
 VC9  H4   C6   N1   117.31  3.000
 VC9  H4   C6   C5   121.33  3.000
 VC9  N1   C6   C5   121.35  3.000
 VC9  C2   N3   C4   120.84  3.000
 VC9  N1   C2   O2   118.59  3.000
 VC9  N1   C2   N3   118.52  3.000
 VC9  O2   C2   N3   122.89  3.000
 VC9  C1'  N1   C2   116.80  3.000
 VC9  C1'  N1   C6   122.59  3.000
 VC9  C2   N1   C6   120.59  3.000
 VC9  H5   C1'  O4'  109.70  3.000
 VC9  H5   C1'  C2'  112.11  3.000
 VC9  O4'  C1'  C2'  106.67  3.000
 VC9  H5   C1'  N1   106.35  3.000
 VC9  O4'  C1'  N1   109.36  3.000
 VC9  C2'  C1'  N1   112.64  3.000
 VC9  H7   C2'  H6   108.13  3.000
 VC9  H7   C2'  C3'  113.72  3.000
 VC9  H6   C2'  C3'  109.33  3.000
 VC9  H7   C2'  C1'  113.14  3.000
 VC9  H6   C2'  C1'  109.36  3.000
 VC9  C3'  C2'  C1'  103.02  3.000
 VC9  H8   C3'  C4'  109.88  3.000
 VC9  H8   C3'  O3'  111.29  3.000
 VC9  C4'  C3'  O3'  112.51  3.000
 VC9  H8   C3'  C2'  109.26  3.000
 VC9  C4'  C3'  C2'  100.36  3.000
 VC9  O3'  C3'  C2'  113.02  3.000
 VC9  H9   O3'  C3'  109.14  3.000
 VC9  C4'  O4'  C1'  110.66  3.000
 VC9  H10  C4'  C5'  105.83  3.000
 VC9  H10  C4'  O4'  109.93  3.000
 VC9  C5'  C4'  O4'  110.54  3.000
 VC9  H10  C4'  C3'  108.11  3.000
 VC9  C5'  C4'  C3'  117.17  3.000
 VC9  O4'  C4'  C3'  105.18  3.000
 VC9  H12  C5'  H11  107.36  3.000
 VC9  H12  C5'  O5'  112.31  3.000
 VC9  H11  C5'  O5'  108.02  3.000
 VC9  H12  C5'  C4'  108.14  3.000
 VC9  H11  C5'  C4'  110.95  3.000
 VC9  O5'  C5'  C4'  110.05  3.000
 VC9  PA   O5'  C5'  126.06  3.000
 VC9  O3A  PA   O2A  111.80  3.000
 VC9  O2A  PA   O1A  119.60  3.000
 VC9  O3A  PA   O1A  100.30  3.000
 VC9  O1A  PA   O5'  108.26  3.000
 VC9  O2A  PA   O5'  111.59  3.000
 VC9  O3A  PA   O5'  103.66  3.000
 VC9  H13  O1A  PA   115.12  3.000
 VC9  PB   O3A  PA   145.41  3.000
 VC9  C3B  PB   O2B  112.44  3.000
 VC9  C3B  PB   O1B  106.33  3.000
 VC9  O2B  PB   O1B  117.52  3.000
 VC9  C3B  PB   O3A  102.16  3.000
 VC9  O1B  PB   O3A  103.75  3.000
 VC9  O2B  PB   O3A  113.16  3.000
 VC9  H14  O1B  PB   116.15  3.000
 VC9  PG   C3B  BR2  105.84  3.000
 VC9  PG   C3B  BR1  111.10  3.000
 VC9  BR2  C3B  BR1  110.32  3.000
 VC9  PG   C3B  PB   116.31  3.000
 VC9  BR1  C3B  PB   107.38  3.000
 VC9  BR2  C3B  PB   105.71  3.000
 VC9  O3G  PG   O1G  116.82  3.000
 VC9  O1G  PG   O2G  103.51  3.000
 VC9  O3G  PG   O2G  118.96  3.000
 VC9  O1G  PG   C3B  103.44  3.000
 VC9  O2G  PG   C3B   99.20  3.000
 VC9  O3G  PG   C3B  112.45  3.000
 VC9  H15  O2G  PG   115.22  3.000
 VC9  H16  O1G  PG   114.75  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
 VC9  CONST_01  N1   C2   N3   C4     0.00   0.0  0
 VC9  CONST_02  C2   N3   C4   C5     0.00   0.0  0
 VC9  CONST_03  N3   C2   N1   C6     0.00   0.0  0
 VC9  CONST_04  C1'  N1   C2   N3   180.00   0.0  0
 VC9  CONST_05  O2   C2   N3   C4   180.00   0.0  0
 VC9  CONST_06  C2   N3   C4   N4   180.00   0.0  0
 VC9  CONST_07  O2   C2   N1   C6   180.00   0.0  0
 VC9  CONST_08  C1'  N1   C2   O2     0.00   0.0  0
 VC9  CONST_09  H1   N4   C4   C5   180.00   0.0  0
 VC9  CONST_10  H2   N4   C4   C5     0.00   0.0  0
 VC9  Var_01    O3A  PA   O5'  C5'   70.03  30.0  3
 VC9  Var_02    O2B  PB   O3A  PA   121.99  30.0  3
 VC9  Var_03    BR2  C3B  PB   O3A  177.68  30.0  3
 VC9  Var_04    O3G  PG   C3B  PB    58.56  30.0  3
 VC9  Var_05    H11  C5'  O5'  PA    98.98  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
 VC9  chir_01  C1'  C2'  N1   O4'  positiv
 VC9  chir_02  C3'  O3'  C4'  C2'  positiv
 VC9  chir_03  C4'  O4'  C3'  C5'  negativ
 VC9  chir_04  PA   O3A  O2A  O1A  both
 VC9  chir_05  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
 VC9  plan-1  C4   0.020
 VC9  plan-1  N4   0.020
 VC9  plan-1  C5   0.020
 VC9  plan-1  C6   0.020
 VC9  plan-1  N3   0.020
 VC9  plan-1  C2   0.020
 VC9  plan-1  O2   0.020
 VC9  plan-1  N1   0.020
 VC9  plan-1  C1'  0.020
 VC9  plan-1  H1   0.020
 VC9  plan-1  H2   0.020
 VC9  plan-1  H3   0.020
 VC9  plan-1  H4   0.020

