# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sat Jul  4 19:58:51 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: 4-amino-1-{2-deoxy-5-O-[(R)-{[(R)-[dichloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-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(Cl)(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
 VC8  VC8  4-amino-1-{2-deoxy-5-O-[(R)-{[(R)-[dichloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-alpha-L-threo-pentofuranosyl}pyrimidin-2(1H)-one  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_VC8
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
 VC8  C4   C   CR6    0   0.513  -6.0984  -3.0986  -0.4855
 VC8  N4   N   NH2    0  -0.810  -6.4859  -4.3737  -0.4736
 VC8  C5   C   CR16   0  -0.478  -6.4986  -2.2495  -1.5616
 VC8  C6   C   CR16   0   0.099  -6.0691  -0.9739  -1.5036
 VC8  N3   N   N      0  -0.541  -5.3494  -2.6626   0.5076
 VC8  C2   C   CR6    0   0.599  -4.9248  -1.3828   0.5577
 VC8  O2   O   O      0  -0.511  -4.2236  -0.9628   1.4675
 VC8  N1   N   NR6    0  -0.557  -5.3123  -0.5139  -0.4785
 VC8  C1'  C   CR15   0   0.243  -4.8829   0.8832  -0.4963
 VC8  C2'  C   CH2    0  -0.557  -5.3605   1.7249   0.6879
 VC8  C3'  C   CR15   0  -0.010  -4.2142   2.7143   0.8573
 VC8  O3'  O   OH1    0  -0.673  -4.2822   3.7739  -0.0707
 VC8  O4'  O   O      0  -0.498  -3.4882   0.9815  -0.5366
 VC8  C4'  C   CR15   0   0.009  -3.0241   1.8287   0.5114
 VC8  C5'  C   CH2    0  -0.144  -1.7758   2.5593   0.0767
 VC8  O5'  O   O2     0  -0.624  -0.7307   1.6187  -0.0393
 VC8  PA   P   P      0   1.340   0.7614   2.1944  -0.4654
 VC8  O1A  O   OP    -1  -0.804   1.2145   3.1646   0.5807
 VC8  O2A  O   O      0  -0.815   0.7320   2.6138  -1.9047
 VC8  O3A  O   O2     0  -0.741   1.4717   0.7402  -0.2947
 VC8  PB   P   P      0   1.331   2.9470   0.3232  -0.9342
 VC8  O1B  O   OP    -1  -0.786   2.6916  -0.5405  -2.1310
 VC8  O2B  O   O      0  -0.793   3.7971   1.5513  -1.0452
 VC8  C3B  C   CT     0  -0.552   3.5494  -0.7349   0.4623
 VC8  CL1  CL  CL     0  -0.175   3.5616   0.2753   1.9522
 VC8  CL2  CL  CL     0  -0.183   2.3332  -2.0394   0.7297
 VC8  PG   P   P      0   1.212   5.2685  -1.5406   0.2560
 VC8  O2G  O   OP    -1  -0.878   6.1914  -0.3410   0.0883
 VC8  O1G  O   OP    -1  -0.883   5.4598  -2.3199   1.5508
 VC8  O3G  O   O      0  -0.876   5.1016  -2.3997  -0.9898
 VC8  H1   H   HNH2   0   0.413  -7.0436  -4.7604  -1.2141
 VC8  H2   H   HNH2   0   0.402  -6.1860  -4.9878   0.2641
 VC8  H3   H   HCR6   0   0.287  -7.0999  -2.6014  -2.3859
 VC8  H4   H   HCR6   0   0.317  -6.3138  -0.2588  -2.2768
 VC8  H5   H   HCR5   0   0.245  -5.2929   1.2867  -1.4267
 VC8  H6   H   HCH2   0   0.269  -6.3184   2.2045   0.4833
 VC8  H7   H   HCH2   0   0.270  -5.4690   1.1250   1.5893
 VC8  H8   H   HCR5   0   0.241  -4.1407   3.0852   1.8861
 VC8  H9   H   HOH1   0   0.455  -5.0950   4.2621   0.0918
 VC8  H10  H   HCR5   0   0.229  -2.7858   1.2260   1.3954
 VC8  H11  H   HCH2   0   0.206  -1.9468   3.0812  -0.8705
 VC8  H12  H   HCH2   0   0.207  -1.5437   3.3181   0.8339

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
 VC8  O2   C2   double  1.223  0.020  1.223
 VC8  C2   N3   single  1.349  0.020  1.349
 VC8  C2   N1   single  1.407  0.020  1.407
 VC8  C2'  C1'  single  1.529  0.020  1.529
 VC8  C2'  C3'  single  1.524  0.020  1.524
 VC8  N3   C4   double  1.318  0.020  1.318
 VC8  C1'  N1   single  1.462  0.020  1.462
 VC8  C1'  O4'  single  1.399  0.020  1.399
 VC8  N1   C6   single  1.355  0.020  1.355
 VC8  O3'  C3'  single  1.410  0.020  1.410
 VC8  C3'  C4'  single  1.523  0.020  1.523
 VC8  C4   N4   single  1.333  0.020  1.333
 VC8  C4   C5   single  1.428  0.020  1.428
 VC8  O4'  C4'  single  1.425  0.020  1.425
 VC8  C6   C5   double  1.347  0.020  1.347
 VC8  C4'  C5'  single  1.510  0.020  1.510
 VC8  O2B  PB   deloc   1.498  0.020  1.498
 VC8  C5'  O5'  single  1.411  0.020  1.411
 VC8  PB   O3A  single  1.661  0.020  1.661
 VC8  PB   O1B  deloc   1.498  0.020  1.498
 VC8  PB   C3B  single  1.853  0.020  1.853
 VC8  O3A  PA   single  1.627  0.020  1.627
 VC8  O5'  PA   single  1.655  0.020  1.655
 VC8  CL2  C3B  single  1.803  0.020  1.803
 VC8  PA   O2A  deloc   1.499  0.020  1.499
 VC8  PA   O1A  deloc   1.497  0.020  1.497
 VC8  C3B  CL1  single  1.800  0.020  1.800
 VC8  C3B  PG   single  1.910  0.020  1.910
 VC8  O3G  PG   deloc   1.522  0.020  1.522
 VC8  PG   O2G  deloc   1.523  0.020  1.523
 VC8  PG   O1G  deloc   1.523  0.020  1.523
 VC8  N4   H1   single  0.860  0.020  1.020
 VC8  N4   H2   single  0.860  0.020  1.020
 VC8  C5   H3   single  0.930  0.020  1.080
 VC8  C6   H4   single  0.930  0.020  1.080
 VC8  C1'  H5   single  0.970  0.020  1.090
 VC8  C2'  H6   single  0.970  0.020  1.090
 VC8  C2'  H7   single  0.970  0.020  1.090
 VC8  C3'  H8   single  0.970  0.020  1.090
 VC8  O3'  H9   single  0.850  0.020  0.980
 VC8  C4'  H10  single  0.970  0.020  1.090
 VC8  C5'  H11  single  0.970  0.020  1.090
 VC8  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
 VC8  N3   C4   C5   122.03  3.000
 VC8  C5   C4   N4   119.62  3.000
 VC8  N3   C4   N4   118.36  3.000
 VC8  H2   N4   H1   118.12  3.000
 VC8  H2   N4   C4   120.27  3.000
 VC8  H1   N4   C4   121.55  3.000
 VC8  H3   C5   C6   121.28  3.000
 VC8  H3   C5   C4   122.53  3.000
 VC8  C6   C5   C4   116.18  3.000
 VC8  H4   C6   N1   116.29  3.000
 VC8  H4   C6   C5   121.55  3.000
 VC8  N1   C6   C5   122.16  3.000
 VC8  C2   N3   C4   121.36  3.000
 VC8  N1   C2   O2   119.59  3.000
 VC8  N1   C2   N3   118.16  3.000
 VC8  O2   C2   N3   122.25  3.000
 VC8  C1'  N1   C2   121.23  3.000
 VC8  C1'  N1   C6   118.65  3.000
 VC8  C2   N1   C6   120.10  3.000
 VC8  H5   C1'  O4'  108.86  3.000
 VC8  H5   C1'  C2'  109.79  3.000
 VC8  O4'  C1'  C2'  107.15  3.000
 VC8  H5   C1'  N1   104.65  3.000
 VC8  O4'  C1'  N1   111.13  3.000
 VC8  C2'  C1'  N1   115.15  3.000
 VC8  H7   C2'  H6   108.07  3.000
 VC8  H7   C2'  C3'  109.93  3.000
 VC8  H6   C2'  C3'  113.33  3.000
 VC8  H7   C2'  C1'  111.66  3.000
 VC8  H6   C2'  C1'  111.78  3.000
 VC8  C3'  C2'  C1'  102.04  3.000
 VC8  H8   C3'  C4'  110.95  3.000
 VC8  H8   C3'  O3'  111.51  3.000
 VC8  C4'  C3'  O3'  108.97  3.000
 VC8  H8   C3'  C2'  112.00  3.000
 VC8  C4'  C3'  C2'  100.66  3.000
 VC8  O3'  C3'  C2'  112.24  3.000
 VC8  H9   O3'  C3'  108.12  3.000
 VC8  C4'  O4'  C1'  110.20  3.000
 VC8  H10  C4'  C5'  108.57  3.000
 VC8  H10  C4'  O4'  109.69  3.000
 VC8  C5'  C4'  O4'  110.18  3.000
 VC8  H10  C4'  C3'  107.84  3.000
 VC8  C5'  C4'  C3'  115.46  3.000
 VC8  O4'  C4'  C3'  104.96  3.000
 VC8  H12  C5'  H11  107.49  3.000
 VC8  H12  C5'  O5'  111.17  3.000
 VC8  H11  C5'  O5'  111.24  3.000
 VC8  H12  C5'  C4'  108.11  3.000
 VC8  H11  C5'  C4'  110.52  3.000
 VC8  O5'  C5'  C4'  108.27  3.000
 VC8  PA   O5'  C5'  117.20  3.000
 VC8  O3A  PA   O2A  111.05  3.000
 VC8  O2A  PA   O1A  119.70  3.000
 VC8  O3A  PA   O1A  111.95  3.000
 VC8  O1A  PA   O5'  108.57  3.000
 VC8  O2A  PA   O5'  109.07  3.000
 VC8  O3A  PA   O5'   93.19  3.000
 VC8  PB   O3A  PA   124.86  3.000
 VC8  C3B  PB   O2B  109.85  3.000
 VC8  C3B  PB   O1B  109.17  3.000
 VC8  O2B  PB   O1B  120.69  3.000
 VC8  C3B  PB   O3A   98.16  3.000
 VC8  O1B  PB   O3A  107.51  3.000
 VC8  O2B  PB   O3A  109.07  3.000
 VC8  PG   C3B  CL2  108.54  3.000
 VC8  PG   C3B  CL1  108.67  3.000
 VC8  CL2  C3B  CL1  106.73  3.000
 VC8  PG   C3B  PB   116.89  3.000
 VC8  CL1  C3B  PB   107.79  3.000
 VC8  CL2  C3B  PB   107.79  3.000
 VC8  O3G  PG   O1G  114.87  3.000
 VC8  O1G  PG   O2G  114.86  3.000
 VC8  O3G  PG   O2G  114.89  3.000
 VC8  O1G  PG   C3B  103.71  3.000
 VC8  O2G  PG   C3B  103.01  3.000
 VC8  O3G  PG   C3B  103.17  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
 VC8  CONST_01  N1   C2   N3   C4     0.00   0.0  0
 VC8  CONST_02  C2   N3   C4   C5     0.00   0.0  0
 VC8  CONST_03  N3   C2   N1   C6     0.00   0.0  0
 VC8  CONST_04  C1'  N1   C2   N3   180.00   0.0  0
 VC8  CONST_05  O2   C2   N3   C4   180.00   0.0  0
 VC8  CONST_06  C2   N3   C4   N4   180.00   0.0  0
 VC8  CONST_07  O2   C2   N1   C6   180.00   0.0  0
 VC8  CONST_08  C1'  N1   C2   O2     0.00   0.0  0
 VC8  CONST_09  H1   N4   C4   C5     0.00   0.0  0
 VC8  CONST_10  H2   N4   C4   C5   180.00   0.0  0
 VC8  Var_01    O3A  PA   O5'  C5'  175.27  30.0  3
 VC8  Var_02    O2B  PB   O3A  PA    28.81  30.0  1
 VC8  Var_03    CL2  C3B  PB   O3A   56.67  30.0  3
 VC8  Var_04    O3G  PG   C3B  PB   -60.08  30.0  3
 VC8  Var_05    H11  C5'  O5'  PA    60.09  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
 VC8  chir_01  C1'  C2'  N1   O4'  positiv
 VC8  chir_02  C3'  O3'  C4'  C2'  positiv
 VC8  chir_03  C4'  O4'  C3'  C5'  positiv

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
 VC8  plan-1  C4   0.020
 VC8  plan-1  N4   0.020
 VC8  plan-1  C5   0.020
 VC8  plan-1  C6   0.020
 VC8  plan-1  N3   0.020
 VC8  plan-1  C2   0.020
 VC8  plan-1  O2   0.020
 VC8  plan-1  N1   0.020
 VC8  plan-1  C1'  0.020
 VC8  plan-1  H1   0.020
 VC8  plan-1  H2   0.020
 VC8  plan-1  H3   0.020
 VC8  plan-1  H4   0.020

