# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  2 20:09:36 2021
#   Inital geometry file: a 116 line input string
#   Ligand name: 9-{2-deoxy-5-O-[(S)-{[(S)-[difluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-alpha-D-erythro-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)(F)[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
 VA6  VA6  9-{2-deoxy-5-O-[(S)-{[(S)-[difluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-alpha-D-erythro-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_VA6
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
 VA6  N1   N  N     0  -0.474  -14.0331   -9.3822  63.8211
 VA6  C2   C  CR16  0   0.041  -13.2831   -8.3491  63.4462
 VA6  N3   N  N     0  -0.454  -12.5655   -7.5372  64.2022
 VA6  C4   C  CR56  0   0.493  -12.6559   -7.8537  65.4930
 VA6  C5   C  CR56  0  -0.004  -13.3964   -8.8946  66.0321
 VA6  C6   C  CR6   0   0.456  -14.1156   -9.6888  65.1200
 VA6  N6   N  NH2   0  -0.816  -14.8769  -10.7158  65.5031
 VA6  N7   N  N     0  -0.454  -13.2560   -8.9438  67.3956
 VA6  C8   C  CR15  0   0.113  -12.4492   -7.9625  67.6664
 VA6  N9   N  NR5   0  -0.534  -12.0546   -7.2552  66.5649
 VA6  PA   P  P     0   1.525   -6.5844   -3.7469  65.3069
 VA6  PB   P  P     0   1.332   -7.7676   -1.5634  63.7670
 VA6  PG   P  P     0   1.305   -4.8123   -0.9216  62.7037
 VA6  C1'  C  CH1   0   0.208  -11.1413   -6.1345  66.5602
 VA6  O1A  O  O     0  -0.711   -5.5951   -3.9358  64.2132
 VA6  O2B  O  OH1   0  -0.711   -8.9464   -0.6832  64.3496
 VA6  O1G  O  OH1   0  -0.761   -4.0967   -1.9062  63.7032
 VA6  C2'  C  CH2   0  -0.558  -11.7325   -4.8573  65.9645
 VA6  O2A  O  OH1   0  -0.689   -6.0588   -3.5079  66.7676
 VA6  O1B  O  O     0  -0.635   -7.9642   -2.3703  62.5556
 VA6  O2G  O  OH1   0  -0.729   -3.8627    0.3472  62.8570
 VA6  C3'  C  CH1   0   0.020  -10.5353   -4.2623  65.2292
 VA6  O3'  O  OH1   0  -0.658  -10.8315   -3.4329  64.1428
 VA6  O3A  O  O2    0  -0.689   -7.4215   -2.3713  65.1281
 VA6  C3B  C  CT    0   0.250   -6.3511   -0.3663  63.6069
 VA6  F1B  F  F     0  -0.338   -6.8574    0.6824  62.8954
 VA6  F2B  F  F     0  -0.325   -6.0226    0.0956  64.8379
 VA6  O3G  O  O     0  -0.672   -5.1525   -1.3706  61.3410
 VA6  C4'  C  CH1   0   0.022   -9.8548   -5.5354  64.7326
 VA6  O4'  O  O2    0  -0.494   -9.9960   -6.4491  65.8051
 VA6  C5'  C  CH2   0  -0.236   -8.4062   -5.4109  64.3447
 VA6  O5'  O  O2    0  -0.557   -7.6532   -4.8867  65.4588
 VA6  H1   H  HCR6  0   0.252  -13.2599   -8.1533  62.3795
 VA6  H2   H  HNH2  0   0.403  -15.3034  -11.3106  64.8136
 VA6  H3   H  HNH2  0   0.410  -14.8845  -11.0223  66.4601
 VA6  H4   H  HCR5  0   0.300  -12.1027   -7.6912  68.6531
 VA6  H5   H  HCH1  0   0.271  -10.8512   -5.9884  67.6036
 VA6  H6   H  HOH1  0   0.520   -9.5186   -0.2633  63.6905
 VA6  H7   H  HOH1  0   0.506   -4.5645   -2.7770  63.8564
 VA6  H8   H  HCH2  0   0.278  -12.1422   -4.2085  66.7373
 VA6  H9   H  HCH2  0   0.272  -12.5235   -5.0812  65.2467
 VA6  H10  H  HOH1  0   0.524   -5.3534   -4.1052  67.0588
 VA6  H11  H  HOH1  0   0.509   -3.8368    0.9201  62.0786
 VA6  H12  H  HCH1  0   0.230   -9.8870   -3.7528  65.9531
 VA6  H13  H  HOH1  0   0.459  -11.1529   -2.5904  64.4770
 VA6  H14  H  HCH1  0   0.248  -10.3892   -5.8974  63.8430
 VA6  H15  H  HCH2  0   0.286   -7.9821   -6.3804  64.0846
 VA6  H16  H  HCH2  0   0.265   -8.3376   -4.7639  63.4681

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
 VA6  O3'  C3'  single    1.399  0.020  1.399
 VA6  C4'  C5'  single    1.505  0.020  1.505
 VA6  C4'  O4'  single    1.416  0.020  1.416
 VA6  C4'  C3'  single    1.526  0.020  1.526
 VA6  C5'  O5'  single    1.443  0.020  1.443
 VA6  O1B  PB   double    1.469  0.020  1.469
 VA6  O4'  C1'  single    1.407  0.020  1.407
 VA6  C3'  C2'  single    1.526  0.020  1.526
 VA6  C2'  C1'  single    1.528  0.020  1.528
 VA6  O2B  PB   single    1.582  0.020  1.582
 VA6  O3G  PG   double    1.475  0.020  1.475
 VA6  C1'  N9   single    1.446  0.020  1.446
 VA6  PB   O3A  single    1.620  0.020  1.620
 VA6  PB   C3B  single    1.861  0.020  1.861
 VA6  O1A  PA   double    1.487  0.020  1.487
 VA6  O5'  PA   single    1.570  0.020  1.570
 VA6  O1G  PG   single    1.575  0.020  1.575
 VA6  N3   C2   aromatic  1.321  0.020  1.321
 VA6  N3   C4   aromatic  1.332  0.020  1.332
 VA6  O3A  PA   single    1.620  0.020  1.620
 VA6  PA   O2A  single    1.571  0.020  1.571
 VA6  PG   C3B  single    1.869  0.020  1.869
 VA6  PG   O2G  single    1.592  0.020  1.592
 VA6  F1B  C3B  single    1.365  0.020  1.365
 VA6  N9   C4   aromatic  1.367  0.020  1.367
 VA6  N9   C8   aromatic  1.367  0.020  1.367
 VA6  C3B  F2B  single    1.355  0.020  1.355
 VA6  C2   N1   aromatic  1.331  0.020  1.331
 VA6  C4   C5   aromatic  1.386  0.020  1.386
 VA6  C8   N7   aromatic  1.299  0.020  1.299
 VA6  N1   C6   aromatic  1.337  0.020  1.337
 VA6  C5   N7   aromatic  1.372  0.020  1.372
 VA6  C5   C6   aromatic  1.407  0.020  1.407
 VA6  C6   N6   single    1.335  0.020  1.335
 VA6  C2   H1   single    0.930  0.020  1.080
 VA6  N6   H2   single    0.860  0.020  1.020
 VA6  N6   H3   single    0.860  0.020  1.020
 VA6  C8   H4   single    0.930  0.020  1.080
 VA6  C1'  H5   single    0.970  0.020  1.090
 VA6  O2B  H6   single    0.850  0.020  0.980
 VA6  O1G  H7   single    0.850  0.020  0.980
 VA6  C2'  H8   single    0.970  0.020  1.090
 VA6  C2'  H9   single    0.970  0.020  1.090
 VA6  O2A  H10  single    0.850  0.020  0.980
 VA6  O2G  H11  single    0.850  0.020  0.980
 VA6  C3'  H12  single    0.970  0.020  1.090
 VA6  O3'  H13  single    0.850  0.020  0.980
 VA6  C4'  H14  single    0.970  0.020  1.090
 VA6  C5'  H15  single    0.970  0.020  1.090
 VA6  C5'  H16  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
 VA6  C6   N1   C2   119.11  3.000
 VA6  H1   C2   N3   116.11  3.000
 VA6  H1   C2   N1   115.42  3.000
 VA6  N3   C2   N1   128.47  3.000
 VA6  C4   N3   C2   111.81  3.000
 VA6  N9   C4   C5   105.00  3.000
 VA6  C5   C4   N3   126.25  3.000
 VA6  N9   C4   N3   128.74  3.000
 VA6  N7   C5   C6   132.57  3.000
 VA6  C6   C5   C4   116.40  3.000
 VA6  N7   C5   C4   111.02  3.000
 VA6  N6   C6   C5   122.67  3.000
 VA6  N6   C6   N1   119.37  3.000
 VA6  C5   C6   N1   117.95  3.000
 VA6  H3   N6   H2   118.00  3.000
 VA6  H3   N6   C6   120.82  3.000
 VA6  H2   N6   C6   120.02  3.000
 VA6  C8   N7   C5   104.11  3.000
 VA6  H4   C8   N9   120.88  3.000
 VA6  H4   C8   N7   125.40  3.000
 VA6  N9   C8   N7   113.71  3.000
 VA6  C1'  N9   C8   125.87  3.000
 VA6  C8   N9   C4   106.15  3.000
 VA6  C1'  N9   C4   127.93  3.000
 VA6  O5'  PA   O3A  105.98  3.000
 VA6  O3A  PA   O2A   98.42  3.000
 VA6  O5'  PA   O2A  104.38  3.000
 VA6  O2A  PA   O1A  118.74  3.000
 VA6  O3A  PA   O1A  111.74  3.000
 VA6  O5'  PA   O1A  115.59  3.000
 VA6  C3B  PB   O3A  103.32  3.000
 VA6  C3B  PB   O1B  112.59  3.000
 VA6  O3A  PB   O1B  116.58  3.000
 VA6  C3B  PB   O2B  103.94  3.000
 VA6  O3A  PB   O2B   97.31  3.000
 VA6  O1B  PB   O2B  120.64  3.000
 VA6  O3G  PG   C3B  110.31  3.000
 VA6  C3B  PG   O2G  101.99  3.000
 VA6  O3G  PG   O2G  117.98  3.000
 VA6  O2G  PG   O1G   99.56  3.000
 VA6  C3B  PG   O1G  104.67  3.000
 VA6  O3G  PG   O1G  120.06  3.000
 VA6  H5   C1'  O4'  109.03  3.000
 VA6  H5   C1'  C2'  111.30  3.000
 VA6  O4'  C1'  C2'  107.01  3.000
 VA6  H5   C1'  N9   105.56  3.000
 VA6  C2'  C1'  N9   113.88  3.000
 VA6  O4'  C1'  N9   110.03  3.000
 VA6  H6   O2B  PB   115.52  3.000
 VA6  H7   O1G  PG   115.39  3.000
 VA6  H9   C2'  H8   108.44  3.000
 VA6  H9   C2'  C3'  109.38  3.000
 VA6  H8   C2'  C3'  113.89  3.000
 VA6  H9   C2'  C1'  111.42  3.000
 VA6  H8   C2'  C1'  111.52  3.000
 VA6  C3'  C2'  C1'  102.13  3.000
 VA6  H10  O2A  PA   115.42  3.000
 VA6  H11  O2G  PG   114.25  3.000
 VA6  H12  C3'  C4'  109.79  3.000
 VA6  H12  C3'  O3'  111.24  3.000
 VA6  C4'  C3'  O3'  109.65  3.000
 VA6  H12  C3'  C2'  109.07  3.000
 VA6  C4'  C3'  C2'  100.45  3.000
 VA6  O3'  C3'  C2'  116.06  3.000
 VA6  H13  O3'  C3'  108.69  3.000
 VA6  PB   O3A  PA   128.79  3.000
 VA6  F2B  C3B  F1B  107.55  3.000
 VA6  F2B  C3B  PG   109.92  3.000
 VA6  F1B  C3B  PG   106.37  3.000
 VA6  F2B  C3B  PB   108.99  3.000
 VA6  F1B  C3B  PB   104.88  3.000
 VA6  PG   C3B  PB   118.50  3.000
 VA6  H14  C4'  C5'  106.66  3.000
 VA6  H14  C4'  O4'  110.61  3.000
 VA6  C5'  C4'  O4'  110.15  3.000
 VA6  H14  C4'  C3'  108.74  3.000
 VA6  O4'  C4'  C3'  104.32  3.000
 VA6  C5'  C4'  C3'  116.36  3.000
 VA6  C4'  O4'  C1'  110.07  3.000
 VA6  H16  C5'  H15  108.13  3.000
 VA6  H16  C5'  O5'  111.82  3.000
 VA6  H15  C5'  O5'  107.72  3.000
 VA6  H16  C5'  C4'  108.45  3.000
 VA6  H15  C5'  C4'  111.26  3.000
 VA6  O5'  C5'  C4'  109.47  3.000
 VA6  C5'  O5'  PA   122.97  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
 VA6  CONST_01  C4   N3   C2   N1     0.00   0.0  0
 VA6  CONST_02  C4   C5   C6   N1     0.00   0.0  0
 VA6  CONST_03  N7   C5   C6   N1   180.00   0.0  0
 VA6  CONST_04  N9   C4   N3   C2   180.00   0.0  0
 VA6  CONST_05  C5   C4   N3   C2     0.00   0.0  0
 VA6  CONST_06  C5   C6   N1   C2     0.00   0.0  0
 VA6  CONST_07  C6   N1   C2   N3     0.00   0.0  0
 VA6  CONST_08  C8   N9   C4   N3   180.00   0.0  0
 VA6  CONST_09  N7   C5   C4   N3   180.00   0.0  0
 VA6  CONST_10  C6   C5   C4   N3     0.00   0.0  0
 VA6  CONST_11  N7   C8   N9   C4     0.00   0.0  0
 VA6  CONST_12  C8   N7   C5   C4     0.00   0.0  0
 VA6  CONST_13  C8   N9   C4   C5     0.00   0.0  0
 VA6  CONST_14  N9   C8   N7   C5     0.00   0.0  0
 VA6  CONST_15  N9   C4   C5   C6   180.00   0.0  0
 VA6  CONST_16  C8   N7   C5   C6   180.00   0.0  0
 VA6  CONST_17  N9   C4   C5   N7     0.00   0.0  0
 VA6  CONST_18  C1'  N9   C4   N3     0.00   0.0  0
 VA6  CONST_19  C1'  N9   C4   C5   180.00   0.0  0
 VA6  CONST_20  C1'  N9   C8   N7   180.00   0.0  0
 VA6  CONST_21  N6   C6   N1   C2   180.00   0.0  0
 VA6  CONST_22  N6   C6   C5   C4   180.00   0.0  0
 VA6  CONST_23  N7   C5   C6   N6     0.00   0.0  0
 VA6  CONST_24  H1   C2   N3   C4   180.00   0.0  0
 VA6  CONST_25  H4   C8   N9   C4   180.00   0.0  0
 VA6  CONST_26  H2   N6   C6   N1     0.00   0.0  0
 VA6  CONST_27  H3   N6   C6   N1   180.00   0.0  0
 VA6  Var_01    C4'  C5'  O5'  PA  -134.97  30.0  1
 VA6  Var_02    O1B  PB   O3A  PA    32.69  30.0  1
 VA6  Var_03    O1A  PA   O3A  PB    27.09  30.0  3
 VA6  Var_04    O3G  PG   C3B  PB    56.28  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
 VA6  chir_03  C1'  O4'  C2'  N9   negativ
 VA6  chir_04  C3'  O3'  C4'  C2'  positiv
 VA6  chir_05  C4'  O4'  C3'  C5'  negativ
 VA6  chir_06  PA   O5'  O3A  O2A  both
 VA6  chir_07  PB   O2B  O3A  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
 VA6  plan-1  N1   0.020
 VA6  plan-1  C2   0.020
 VA6  plan-1  N3   0.020
 VA6  plan-1  C4   0.020
 VA6  plan-1  C5   0.020
 VA6  plan-1  C6   0.020
 VA6  plan-1  N6   0.020
 VA6  plan-1  N7   0.020
 VA6  plan-1  C8   0.020
 VA6  plan-1  N9   0.020
 VA6  plan-1  C1'  0.020
 VA6  plan-1  H1   0.020
 VA6  plan-1  H4   0.020
 VA6  plan-2  C6   0.020
 VA6  plan-2  N6   0.020
 VA6  plan-2  H2   0.020
 VA6  plan-2  H3   0.020

