# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sat Jul  4 19:26:50 2020
#   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  42  30  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

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   0.513  -6.3620  -2.8829   0.2756
 VC9  N4   N   NH2    0  -0.809  -6.7289  -4.0374   0.8310
 VC9  C5   C   CR16   0  -0.477  -6.2813  -2.7787  -1.1465
 VC9  C6   C   CR16   0   0.098  -5.9010  -1.5819  -1.6344
 VC9  N3   N   N      0  -0.541  -6.0840  -1.8676   1.0688
 VC9  C2   C   CR6    0   0.602  -5.7096  -0.6713   0.5694
 VC9  O2   O   O      0  -0.505  -5.4497   0.2844   1.2861
 VC9  N1   N   NR6    0  -0.553  -5.6256  -0.5304  -0.8259
 VC9  C1'  C   CH1    0   0.222  -5.1868   0.7248  -1.4271
 VC9  C2'  C   CH2    0  -0.556  -5.9920   1.9724  -1.0520
 VC9  C3'  C   CH1    0   0.023  -5.0214   2.8431  -0.2547
 VC9  O3'  O   OH1    0  -0.671  -5.0842   4.2178  -0.5480
 VC9  O4'  O   O2     0  -0.491  -3.8513   0.9636  -1.0841
 VC9  C4'  C   CH1    0   0.017  -3.6541   2.3089  -0.6870
 VC9  C5'  C   CH2    0  -0.152  -2.6306   2.3761   0.4199
 VC9  O5'  O   O2     0  -0.626  -1.3862   1.9142  -0.0540
 VC9  PA   P   P      0   1.336  -0.0597   2.2286   0.8857
 VC9  O1A  O   OP    -1  -0.802  -0.3863   1.8729   2.3022
 VC9  O2A  O   O      0  -0.810   0.4502   3.6001   0.5569
 VC9  O3A  O   O2     0  -0.739   0.8546   1.0937   0.1570
 VC9  PB   P   P      0   1.336   2.5052   0.9932   0.3030
 VC9  O1B  O   OP    -1  -0.782   3.1045   1.5433  -0.9539
 VC9  O2B  O   O      0  -0.787   2.9084   1.5261   1.6427
 VC9  C3B  C   CT     0  -0.643   2.6865  -0.8547   0.2977
 VC9  BR1  BR  BR     0  -0.148   1.5876  -1.5876   1.7437
 VC9  BR2  BR  BR     0  -0.158   1.9428  -1.5328  -1.3886
 VC9  PG   P   P      0   1.220   4.4696  -1.5408   0.4889
 VC9  O2G  O   OP    -1  -0.871   4.8818  -1.0475   1.8679
 VC9  O1G  O   OP    -1  -0.882   4.2951  -3.0493   0.3758
 VC9  O3G  O   O      0  -0.872   5.2034  -0.8888  -0.6745
 VC9  H1   H   HNH2   0   0.413  -6.9330  -4.8478   0.2737
 VC9  H2   H   HNH2   0   0.402  -6.7610  -4.1299   1.8319
 VC9  H3   H   HCR6   0   0.287  -6.5020  -3.6074  -1.8017
 VC9  H4   H   HCR6   0   0.318  -5.8029  -1.4086  -2.6974
 VC9  H5   H   HCH1   0   0.243  -5.2668   0.5508  -2.5040
 VC9  H6   H   HCH2   0   0.260  -6.2701   2.4951  -1.9692
 VC9  H7   H   HCH2   0   0.270  -6.9102   1.7397  -0.5161
 VC9  H8   H   HCH1   0   0.231  -5.1633   2.6701   0.8154
 VC9  H9   H   HOH1   0   0.455  -5.8384   4.5907  -0.0828
 VC9  H10  H   HCH1   0   0.220  -3.3058   2.9007  -1.5469
 VC9  H11  H   HCH2   0   0.202  -2.5789   3.4205   0.7547
 VC9  H12  H   HCH2   0   0.209  -2.9801   1.7779   1.2684

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  1.222  0.020  1.222
 VC9  C2   N3   single  1.349  0.020  1.349
 VC9  C2   N1   single  1.405  0.020  1.405
 VC9  C2'  C1'  single  1.532  0.020  1.532
 VC9  C2'  C3'  single  1.528  0.020  1.528
 VC9  N3   C4   double  1.318  0.020  1.318
 VC9  C1'  N1   single  1.459  0.020  1.459
 VC9  C1'  O4'  single  1.399  0.020  1.399
 VC9  N1   C6   single  1.355  0.020  1.355
 VC9  O3'  C3'  single  1.407  0.020  1.407
 VC9  C3'  C4'  single  1.530  0.020  1.530
 VC9  C4   N4   single  1.333  0.020  1.333
 VC9  C4   C5   single  1.428  0.020  1.428
 VC9  O4'  C4'  single  1.416  0.020  1.416
 VC9  C4'  C5'  single  1.509  0.020  1.509
 VC9  C6   C5   double  1.347  0.020  1.347
 VC9  O2B  PB   deloc   1.497  0.020  1.497
 VC9  C5'  O5'  single  1.409  0.020  1.409
 VC9  O5'  PA   single  1.656  0.020  1.656
 VC9  O3A  PB   single  1.660  0.020  1.660
 VC9  O3A  PA   single  1.629  0.020  1.629
 VC9  PB   O1B  deloc   1.497  0.020  1.497
 VC9  PB   C3B  single  1.857  0.020  1.857
 VC9  BR2  C3B  single  1.964  0.020  1.964
 VC9  PA   O2A  deloc   1.500  0.020  1.500
 VC9  PA   O1A  deloc   1.497  0.020  1.497
 VC9  C3B  BR1  single  1.958  0.020  1.958
 VC9  C3B  PG   single  1.920  0.020  1.920
 VC9  O3G  PG   deloc   1.522  0.020  1.522
 VC9  PG   O2G  deloc   1.521  0.020  1.521
 VC9  PG   O1G  deloc   1.523  0.020  1.523
 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

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   122.08  3.000
 VC9  C5   C4   N4   119.60  3.000
 VC9  N3   C4   N4   118.33  3.000
 VC9  H2   N4   H1   118.13  3.000
 VC9  H2   N4   C4   120.22  3.000
 VC9  H1   N4   C4   121.57  3.000
 VC9  H3   C5   C6   121.34  3.000
 VC9  H3   C5   C4   122.47  3.000
 VC9  C6   C5   C4   116.19  3.000
 VC9  H4   C6   N1   116.35  3.000
 VC9  H4   C6   C5   121.59  3.000
 VC9  N1   C6   C5   122.06  3.000
 VC9  C2   N3   C4   121.24  3.000
 VC9  N1   C2   O2   119.41  3.000
 VC9  N1   C2   N3   118.24  3.000
 VC9  O2   C2   N3   122.35  3.000
 VC9  C1'  N1   C2   120.89  3.000
 VC9  C1'  N1   C6   118.87  3.000
 VC9  C2   N1   C6   120.18  3.000
 VC9  H5   C1'  O4'  109.77  3.000
 VC9  H5   C1'  C2'  109.41  3.000
 VC9  O4'  C1'  C2'  107.62  3.000
 VC9  H5   C1'  N1   104.29  3.000
 VC9  O4'  C1'  N1   109.43  3.000
 VC9  C2'  C1'  N1   116.22  3.000
 VC9  H7   C2'  H6   107.53  3.000
 VC9  H7   C2'  C3'  113.62  3.000
 VC9  H6   C2'  C3'  109.11  3.000
 VC9  H7   C2'  C1'  112.95  3.000
 VC9  H6   C2'  C1'  108.55  3.000
 VC9  C3'  C2'  C1'  104.95  3.000
 VC9  H8   C3'  C4'  109.71  3.000
 VC9  H8   C3'  O3'  110.66  3.000
 VC9  C4'  C3'  O3'  108.79  3.000
 VC9  H8   C3'  C2'  109.76  3.000
 VC9  C4'  C3'  C2'  102.78  3.000
 VC9  O3'  C3'  C2'  114.80  3.000
 VC9  H9   O3'  C3'  108.25  3.000
 VC9  C4'  O4'  C1'  111.32  3.000
 VC9  H10  C4'  C5'  109.54  3.000
 VC9  H10  C4'  O4'  109.62  3.000
 VC9  C5'  C4'  O4'  110.02  3.000
 VC9  H10  C4'  C3'  108.41  3.000
 VC9  C5'  C4'  C3'  112.53  3.000
 VC9  O4'  C4'  C3'  106.64  3.000
 VC9  H12  C5'  H11  107.36  3.000
 VC9  H12  C5'  O5'  111.29  3.000
 VC9  H11  C5'  O5'  111.88  3.000
 VC9  H12  C5'  C4'  109.11  3.000
 VC9  H11  C5'  C4'  107.34  3.000
 VC9  O5'  C5'  C4'  109.73  3.000
 VC9  PA   O5'  C5'  117.02  3.000
 VC9  O3A  PA   O2A  110.38  3.000
 VC9  O2A  PA   O1A  119.94  3.000
 VC9  O3A  PA   O1A  112.34  3.000
 VC9  O1A  PA   O5'  108.49  3.000
 VC9  O2A  PA   O5'  108.76  3.000
 VC9  O3A  PA   O5'   93.64  3.000
 VC9  PB   O3A  PA   124.11  3.000
 VC9  C3B  PB   O2B  109.30  3.000
 VC9  C3B  PB   O1B  108.92  3.000
 VC9  O2B  PB   O1B  120.84  3.000
 VC9  C3B  PB   O3A   99.04  3.000
 VC9  O1B  PB   O3A  107.57  3.000
 VC9  O2B  PB   O3A  108.96  3.000
 VC9  PG   C3B  BR2  108.29  3.000
 VC9  PG   C3B  BR1  108.29  3.000
 VC9  BR2  C3B  BR1  107.00  3.000
 VC9  PG   C3B  PB   116.49  3.000
 VC9  BR1  C3B  PB   108.39  3.000
 VC9  BR2  C3B  PB   108.01  3.000
 VC9  O3G  PG   O1G  115.01  3.000
 VC9  O1G  PG   O2G  114.80  3.000
 VC9  O3G  PG   O2G  115.04  3.000
 VC9  O1G  PG   C3B  103.90  3.000
 VC9  O2G  PG   C3B  103.06  3.000
 VC9  O3G  PG   C3B  102.63  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     0.00   0.0  0
 VC9  CONST_10  H2   N4   C4   C5   180.00   0.0  0
 VC9  Var_01    O3A  PA   O5'  C5'  161.93  30.0  3
 VC9  Var_02    O2B  PB   O3A  PA    29.85  30.0  3
 VC9  Var_03    BR2  C3B  PB   O3A   59.29  30.0  3
 VC9  Var_04    O3G  PG   C3B  PB   -57.09  30.0  3
 VC9  Var_05    H11  C5'  O5'  PA    47.29  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

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

