# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  3 03:46:02 2021
#   Inital geometry file: a 116 line input string
#   Ligand name: 9-{5-O-[(R)-{[(R)-[(S)-chloro(fluoro)phosphonomethyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2-deoxy-alpha-D-threo-pentofuranosyl}-9H-purin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3C[C@@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)[C@@](F)(Cl)[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
 VA5  VA5  9-{5-O-[(R)-{[(R)-[(S)-chloro(fluoro)phosphonomethyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2-deoxy-alpha-D-threo-pentofuranosyl}-9H-purin-6-amine  ligand  48  32  .  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_VA5
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
 VA5  PA   P   P     0   1.540   4.0681   4.9043  15.3051
 VA5  O1A  O   OH1   0  -0.707   3.5559   6.2537  15.9347
 VA5  O2A  O   O     0  -0.688   4.9766   4.0586  16.1146
 VA5  O3A  O   O2    0  -0.692   2.6264   4.1973  15.0955
 VA5  O5'  O   O2    0  -0.559   4.6590   5.1706  13.8761
 VA5  PB   P   P     0   1.422   2.0422   3.1025  14.0608
 VA5  O2B  O   O     0  -0.656   2.3552   3.3543  12.6399
 VA5  O1B  O   OH1   0  -0.693   0.5315   3.0442  14.4947
 VA5  C3B  C   CT    0  -0.179   2.7463   1.5079  14.6984
 VA5  F3B  F   F     0  -0.316   1.9127   0.5334  14.2227
 VA5  CL1  CL  CL    0  -0.048   4.3392   1.2951  13.9647
 VA5  PG   P   P     0   1.365   2.8257   1.2987  16.5624
 VA5  O1G  O   OH1   0  -0.754   4.2643   1.7569  16.9910
 VA5  O2G  O   OH1   0  -0.720   2.9929  -0.2732  16.7268
 VA5  O3G  O   O     0  -0.671   1.6406   1.9383  17.1667
 VA5  C5'  C   CH2   0  -0.236   4.1685   6.1847  12.9769
 VA5  C4'  C   CH1   0   0.022   4.9587   6.1672  11.6935
 VA5  O4'  O   O2    0  -0.497   6.3421   6.2779  11.9899
 VA5  C1'  C   CH1   0   0.219   7.0984   5.6924  10.9636
 VA5  N9   N   NR5   0  -0.534   8.0277   6.6623  10.4256
 VA5  C4   C   CR56  0   0.489   7.7404   7.8545   9.8219
 VA5  N3   N   N     0  -0.454   6.5493   8.3945   9.5657
 VA5  C2   C   CR16  0   0.040   6.6603   9.5648   8.9626
 VA5  N1   N   N     0  -0.475   7.7674  10.2139   8.6115
 VA5  C6   C   CR6   0   0.457   8.9566   9.6627   8.8773
 VA5  N6   N   NH2   0  -0.817  10.0703  10.3128   8.5367
 VA5  C5   C   CR56  0  -0.004   8.9741   8.4107   9.5201
 VA5  N7   N   N     0  -0.455   9.9957   7.5932   9.9310
 VA5  C8   C   CR15  0   0.112   9.3912   6.5753  10.4663
 VA5  C2'  C   CH2   0  -0.548   6.1007   5.1609   9.9320
 VA5  C3'  C   CH1   0  -0.020   4.8388   4.9603  10.7558
 VA5  O3'  O   OH1   0  -0.688   4.9161   3.7143  11.3914
 VA5  H1   H   HOH1  0   0.523   4.2178   6.7628  16.4272
 VA5  H2   H   HOH1  0   0.523  -0.1055   3.2144  13.7835
 VA5  H3   H   HOH1  0   0.507   4.5580   2.6810  16.7333
 VA5  H4   H   HOH1  0   0.510   2.1664  -0.7532  16.8751
 VA5  H5   H   HCH2  0   0.278   4.2709   7.1597  13.4554
 VA5  H6   H   HCH2  0   0.264   3.1121   6.0254  12.7516
 VA5  H7   H   HCH1  0   0.247   4.6162   7.0489  11.1343
 VA5  H8   H   HCH1  0   0.265   7.7169   4.8901  11.3748
 VA5  H9   H   HCR6  0   0.252   5.7297  10.0670   8.7205
 VA5  H10  H   HNH2  0   0.403  10.0167  11.1797   8.0302
 VA5  H11  H   HNH2  0   0.411  10.9747   9.8974   8.6735
 VA5  H12  H   HCR5  0   0.299   9.8791   5.7187  10.9083
 VA5  H13  H   HCH2  0   0.278   6.4491   4.2456   9.4556
 VA5  H14  H   HCH2  0   0.279   5.9195   5.9027   9.1548
 VA5  H15  H   HCH1  0   0.242   3.9362   5.0516  10.1401
 VA5  H16  H   HOH1  0   0.461   4.0775   3.5360  11.8397

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
 VA5  C2   N1   aromatic  1.331  0.020  1.331
 VA5  C2   N3   aromatic  1.321  0.020  1.321
 VA5  N1   C6   aromatic  1.337  0.020  1.337
 VA5  N3   C4   aromatic  1.333  0.020  1.333
 VA5  C6   N6   single    1.334  0.020  1.334
 VA5  C6   C5   aromatic  1.407  0.020  1.407
 VA5  C4   C5   aromatic  1.387  0.020  1.387
 VA5  C4   N9   aromatic  1.367  0.020  1.367
 VA5  C2'  C3'  single    1.520  0.020  1.520
 VA5  C2'  C1'  single    1.530  0.020  1.530
 VA5  C5   N7   aromatic  1.371  0.020  1.371
 VA5  C3'  O3'  single    1.401  0.020  1.401
 VA5  C3'  C4'  single    1.533  0.020  1.533
 VA5  N9   C1'  single    1.447  0.020  1.447
 VA5  N9   C8   aromatic  1.367  0.020  1.367
 VA5  C1'  O4'  single    1.403  0.020  1.403
 VA5  O4'  C4'  single    1.419  0.020  1.419
 VA5  N7   C8   aromatic  1.299  0.020  1.299
 VA5  C4'  C5'  single    1.507  0.020  1.507
 VA5  O2B  PB   double    1.477  0.020  1.477
 VA5  C5'  O5'  single    1.441  0.020  1.441
 VA5  O5'  PA   single    1.569  0.020  1.569
 VA5  PB   O3A  single    1.616  0.020  1.616
 VA5  PB   O1B  single    1.573  0.020  1.573
 VA5  PB   C3B  single    1.856  0.020  1.856
 VA5  O3A  PA   single    1.619  0.020  1.619
 VA5  F3B  C3B  single    1.368  0.020  1.368
 VA5  PA   O2A  double    1.482  0.020  1.482
 VA5  PA   O1A  single    1.575  0.020  1.575
 VA5  C3B  CL1  single    1.767  0.020  1.767
 VA5  C3B  PG   single    1.877  0.020  1.877
 VA5  O3G  PG   double    1.476  0.020  1.476
 VA5  PG   O1G  single    1.569  0.020  1.569
 VA5  PG   O2G  single    1.589  0.020  1.589
 VA5  O1A  H1   single    0.850  0.020  0.980
 VA5  O1B  H2   single    0.850  0.020  0.980
 VA5  O1G  H3   single    0.850  0.020  0.980
 VA5  O2G  H4   single    0.850  0.020  0.980
 VA5  C5'  H5   single    0.970  0.020  1.090
 VA5  C5'  H6   single    0.970  0.020  1.090
 VA5  C4'  H7   single    0.970  0.020  1.090
 VA5  C1'  H8   single    0.970  0.020  1.090
 VA5  C2   H9   single    0.930  0.020  1.080
 VA5  N6   H10  single    0.860  0.020  1.020
 VA5  N6   H11  single    0.860  0.020  1.020
 VA5  C8   H12  single    0.930  0.020  1.080
 VA5  C2'  H13  single    0.970  0.020  1.090
 VA5  C2'  H14  single    0.970  0.020  1.090
 VA5  C3'  H15  single    0.970  0.020  1.090
 VA5  O3'  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
 VA5  O5'  PA   O3A  106.94  3.000
 VA5  O3A  PA   O2A  111.55  3.000
 VA5  O5'  PA   O2A  111.32  3.000
 VA5  O2A  PA   O1A  118.04  3.000
 VA5  O3A  PA   O1A   97.83  3.000
 VA5  O5'  PA   O1A  109.95  3.000
 VA5  H1   O1A  PA   115.53  3.000
 VA5  PB   O3A  PA   134.48  3.000
 VA5  C5'  O5'  PA   124.01  3.000
 VA5  C3B  PB   O1B  103.75  3.000
 VA5  C3B  PB   O2B  113.37  3.000
 VA5  O1B  PB   O2B  118.38  3.000
 VA5  C3B  PB   O3A  103.00  3.000
 VA5  O1B  PB   O3A  101.29  3.000
 VA5  O2B  PB   O3A  115.09  3.000
 VA5  H2   O1B  PB   114.96  3.000
 VA5  PG   C3B  CL1  111.15  3.000
 VA5  PG   C3B  F3B  106.96  3.000
 VA5  CL1  C3B  F3B  108.62  3.000
 VA5  PG   C3B  PB   116.93  3.000
 VA5  CL1  C3B  PB   107.63  3.000
 VA5  F3B  C3B  PB   105.16  3.000
 VA5  O3G  PG   O2G  118.08  3.000
 VA5  O2G  PG   O1G   99.45  3.000
 VA5  O3G  PG   O1G  119.84  3.000
 VA5  O2G  PG   C3B  102.56  3.000
 VA5  O1G  PG   C3B  106.10  3.000
 VA5  O3G  PG   C3B  108.92  3.000
 VA5  H3   O1G  PG   117.85  3.000
 VA5  H4   O2G  PG   114.63  3.000
 VA5  H6   C5'  H5   108.17  3.000
 VA5  H6   C5'  C4'  109.25  3.000
 VA5  H5   C5'  C4'  109.55  3.000
 VA5  H6   C5'  O5'  110.81  3.000
 VA5  H5   C5'  O5'  108.86  3.000
 VA5  C4'  C5'  O5'  110.16  3.000
 VA5  H7   C4'  C3'  107.22  3.000
 VA5  H7   C4'  O4'  110.33  3.000
 VA5  C3'  C4'  O4'  105.39  3.000
 VA5  H7   C4'  C5'  105.11  3.000
 VA5  O4'  C4'  C5'  109.41  3.000
 VA5  C3'  C4'  C5'  119.27  3.000
 VA5  C1'  O4'  C4'  109.89  3.000
 VA5  H8   C1'  C2'  111.56  3.000
 VA5  H8   C1'  N9   105.57  3.000
 VA5  C2'  C1'  N9   113.63  3.000
 VA5  H8   C1'  O4'  109.64  3.000
 VA5  N9   C1'  O4'  109.78  3.000
 VA5  C2'  C1'  O4'  106.66  3.000
 VA5  C8   N9   C4   106.16  3.000
 VA5  C8   N9   C1'  125.94  3.000
 VA5  C4   N9   C1'  127.87  3.000
 VA5  C5   C4   N3   126.22  3.000
 VA5  C5   C4   N9   105.02  3.000
 VA5  N3   C4   N9   128.77  3.000
 VA5  C2   N3   C4   111.82  3.000
 VA5  H9   C2   N1   115.40  3.000
 VA5  H9   C2   N3   116.10  3.000
 VA5  N1   C2   N3   128.50  3.000
 VA5  C6   N1   C2   119.10  3.000
 VA5  C5   C6   N6   122.67  3.000
 VA5  C5   C6   N1   117.94  3.000
 VA5  N6   C6   N1   119.39  3.000
 VA5  H11  N6   H10  118.23  3.000
 VA5  H11  N6   C6   121.02  3.000
 VA5  H10  N6   C6   120.29  3.000
 VA5  N7   C5   C6   132.56  3.000
 VA5  N7   C5   C4   111.01  3.000
 VA5  C6   C5   C4   116.44  3.000
 VA5  C8   N7   C5   104.11  3.000
 VA5  H12  C8   N7   125.42  3.000
 VA5  H12  C8   N9   120.88  3.000
 VA5  N7   C8   N9   113.71  3.000
 VA5  H14  C2'  H13  108.26  3.000
 VA5  H14  C2'  C3'  109.78  3.000
 VA5  H13  C2'  C3'  113.06  3.000
 VA5  H14  C2'  C1'  110.66  3.000
 VA5  H13  C2'  C1'  112.22  3.000
 VA5  C3'  C2'  C1'  102.81  3.000
 VA5  H15  C3'  O3'  111.98  3.000
 VA5  H15  C3'  C2'  111.59  3.000
 VA5  O3'  C3'  C2'  108.50  3.000
 VA5  H15  C3'  C4'  110.02  3.000
 VA5  O3'  C3'  C4'  114.74  3.000
 VA5  C2'  C3'  C4'   99.36  3.000
 VA5  H16  O3'  C3'  109.04  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
 VA5  CONST_01  C2   N3   C4   N9    180.00   0.0  0
 VA5  CONST_02  C6   C5   C4   N9    180.00   0.0  0
 VA5  CONST_03  N7   C5   C4   N9      0.00   0.0  0
 VA5  CONST_04  C5   N7   C8   N9      0.00   0.0  0
 VA5  CONST_05  N1   C2   N3   C4      0.00   0.0  0
 VA5  CONST_06  N1   C6   C5   C4      0.00   0.0  0
 VA5  CONST_07  C8   N7   C5   C4      0.00   0.0  0
 VA5  CONST_08  N7   C8   N9   C4      0.00   0.0  0
 VA5  CONST_09  C6   N1   C2   N3      0.00   0.0  0
 VA5  CONST_10  C6   C5   C4   N3      0.00   0.0  0
 VA5  CONST_11  N7   C5   C4   N3    180.00   0.0  0
 VA5  CONST_12  C8   N9   C4   N3    180.00   0.0  0
 VA5  CONST_13  C5   C6   N1   C2      0.00   0.0  0
 VA5  CONST_14  C5   C4   N3   C2      0.00   0.0  0
 VA5  CONST_15  N7   C5   C6   N1    180.00   0.0  0
 VA5  CONST_16  C8   N7   C5   C6    180.00   0.0  0
 VA5  CONST_17  C8   N9   C4   C5      0.00   0.0  0
 VA5  CONST_18  N3   C4   N9   C1'     0.00   0.0  0
 VA5  CONST_19  C5   C4   N9   C1'   180.00   0.0  0
 VA5  CONST_20  N7   C8   N9   C1'   180.00   0.0  0
 VA5  CONST_21  N6   C6   C5   C4    180.00   0.0  0
 VA5  CONST_22  N6   C6   N1   C2    180.00   0.0  0
 VA5  CONST_23  N7   C5   C6   N6      0.00   0.0  0
 VA5  CONST_24  H12  C8   N9   C1'     0.00   0.0  0
 VA5  CONST_25  H9   C2   N3   C4    180.00   0.0  0
 VA5  CONST_26  H10  N6   C6   N1      0.00   0.0  0
 VA5  CONST_27  H11  N6   C6   N1    180.00   0.0  0
 VA5  Var_01    C4'  C5'  O5'  PA   -179.95  30.0  2
 VA5  Var_02    O2B  PB   O3A  PA    -47.60  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
 VA5  chir_03  C3B  F3B  CL1  PG   positiv
 VA5  chir_04  C4'  O4'  C3'  C5'  negativ
 VA5  chir_05  C1'  O4'  N9   C2'  positiv
 VA5  chir_06  C3'  O3'  C4'  C2'  negativ
 VA5  chir_07  PA   O3A  O2A  O1A  both
 VA5  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
 VA5  plan-1  C1'  0.020
 VA5  plan-1  N9   0.020
 VA5  plan-1  C4   0.020
 VA5  plan-1  N3   0.020
 VA5  plan-1  C2   0.020
 VA5  plan-1  N1   0.020
 VA5  plan-1  C6   0.020
 VA5  plan-1  N6   0.020
 VA5  plan-1  C5   0.020
 VA5  plan-1  N7   0.020
 VA5  plan-1  C8   0.020
 VA5  plan-1  H9   0.020
 VA5  plan-1  H12  0.020
 VA5  plan-2  C6   0.020
 VA5  plan-2  N6   0.020
 VA5  plan-2  H10  0.020
 VA5  plan-2  H11  0.020

