# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 13:32:35 2021
#   Inital geometry file: a 105 line input string
#   Ligand name: {[(S)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]amino}acetic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)NCC(O)=O)[C@@H](O)[C@H]3O
#
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
 V2G  V2G  '{[(S)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]amino}acetic acid (non-preferred name)'  ligand  44  27  .  2022-11-18  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_V2G
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
 V2G  N    N  NH1   0  -0.758  12.1444  4.7193  23.2696
 V2G  CA   C  CH2   0  -0.396  13.0860  3.6327  23.3398
 V2G  C    C  C     0   0.534  13.6580  3.4864  24.7321
 V2G  OXT  O  OH1   0  -0.593  14.5560  2.5113  24.7687
 V2G  O    O  O     0  -0.432  13.3542  4.1624  25.6785
 V2G  P    P  P     0   1.429  10.7519  4.6799  22.3955
 V2G  O1   O  OH1   0  -0.746  10.0087  3.3216  22.8143
 V2G  O2   O  O     0  -0.711   9.9581  5.9242  22.5017
 V2G  O5'  O  O2    0  -0.595  11.2019  4.2742  20.9081
 V2G  C5'  C  CH2   0  -0.195  10.2795  4.3445  19.8216
 V2G  C4'  C  CH1   0   0.015  10.4348  5.6446  19.0710
 V2G  O4'  O  O2    0  -0.495  11.7552  5.7554  18.5448
 V2G  C3'  C  CH1   0  -0.037   9.5175  5.7482  17.8562
 V2G  O3'  O  OH1   0  -0.654   8.2582  6.2204  18.2364
 V2G  C2'  C  CH1   0  -0.045  10.3062  6.7124  16.9632
 V2G  O2'  O  OH1   0  -0.662  10.1863  8.0316  17.4173
 V2G  C1'  C  CH1   0   0.177  11.7386  6.2630  17.2449
 V2G  N9   N  NR5   0  -0.537  12.1642  5.2194  16.3181
 V2G  C8   C  CR15  0   0.101  12.3667  3.8874  16.5544
 V2G  N7   N  N     0  -0.451  12.7720  3.2333  15.5045
 V2G  C5   C  CR56  0  -0.002  12.8488  4.1821  14.5199
 V2G  C4   C  CR56  0   0.487  12.4793  5.4254  15.0073
 V2G  N3   N  N     0  -0.459  12.4469  6.5699  14.3266
 V2G  C2   C  CR16  0   0.039  12.8218  6.3985  13.0709
 V2G  N1   N  N     0  -0.474  13.1972  5.2744  12.4659
 V2G  C6   C  CR6   0   0.458  13.2238  4.1334  13.1638
 V2G  N6   N  NH2   0  -0.816  13.6047  3.0073  12.5603
 V2G  H1   H  HNH1  0   0.412  12.5418  5.6393  23.3985
 V2G  H2   H  HCH2  0   0.292  12.6014  2.6903  23.0766
 V2G  H3   H  HCH2  0   0.288  13.9142  3.7525  22.6342
 V2G  H4   H  HOH1  0   0.486  14.9279  2.4296  25.6598
 V2G  H5   H  HOH1  0   0.495   9.5852  3.3598  23.6825
 V2G  H6   H  HCH2  0   0.254   9.2419  4.2535  20.1555
 V2G  H7   H  HCH2  0   0.252  10.4853  3.4913  19.1724
 V2G  H8   H  HCH1  0   0.254  10.2456  6.4821  19.7529
 V2G  H9   H  HCH1  0   0.246   9.4498  4.7713  17.3580
 V2G  H10  H  HOH1  0   0.470   7.6218  6.0016  17.5478
 V2G  H11  H  HCH1  0   0.264  10.0422  6.6178  15.9033
 V2G  H12  H  HOH1  0   0.453   9.2620  8.1857  17.6478
 V2G  H13  H  HCH1  0   0.286  12.4455  7.0915  17.1486
 V2G  H14  H  HCR5  0   0.295  12.2140  3.4482  17.5272
 V2G  H15  H  HCR6  0   0.252  12.8261  7.2862  12.4473
 V2G  H16  H  HNH2  0   0.404  13.8416  3.0100  11.5832
 V2G  H17  H  HNH2  0   0.412  13.6033  2.1291  13.0486

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
 V2G  N6   C6   single    1.333  0.020  1.333
 V2G  N1   C6   aromatic  1.338  0.020  1.338
 V2G  N1   C2   aromatic  1.331  0.020  1.331
 V2G  C6   C5   aromatic  1.408  0.020  1.408
 V2G  C5   N7   aromatic  1.370  0.020  1.370
 V2G  C5   C4   aromatic  1.386  0.020  1.386
 V2G  C2   N3   aromatic  1.322  0.020  1.322
 V2G  N7   C8   aromatic  1.302  0.020  1.302
 V2G  C4   N3   aromatic  1.332  0.020  1.332
 V2G  C4   N9   aromatic  1.364  0.020  1.364
 V2G  C8   N9   aromatic  1.368  0.020  1.368
 V2G  N9   C1'  single    1.459  0.020  1.459
 V2G  O2'  C2'  single    1.400  0.020  1.400
 V2G  C2'  C1'  single    1.527  0.020  1.527
 V2G  C2'  C3'  single    1.533  0.020  1.533
 V2G  C1'  O4'  single    1.396  0.020  1.396
 V2G  C3'  O3'  single    1.398  0.020  1.398
 V2G  C3'  C4'  single    1.526  0.020  1.526
 V2G  O4'  C4'  single    1.426  0.020  1.426
 V2G  C4'  C5'  single    1.509  0.020  1.509
 V2G  C5'  O5'  single    1.427  0.020  1.427
 V2G  O2   P    double    1.480  0.020  1.480
 V2G  O5'  P    single    1.606  0.020  1.606
 V2G  P    N    single    1.645  0.020  1.645
 V2G  P    O1   single    1.604  0.020  1.604
 V2G  N    CA   single    1.440  0.020  1.440
 V2G  O    C    double    1.202  0.020  1.202
 V2G  C    CA   single    1.512  0.020  1.512
 V2G  C    OXT  single    1.326  0.020  1.326
 V2G  N    H1   single    0.890  0.020  1.040
 V2G  CA   H2   single    0.970  0.020  1.090
 V2G  CA   H3   single    0.970  0.020  1.090
 V2G  OXT  H4   single    0.850  0.020  0.980
 V2G  O1   H5   single    0.850  0.020  0.980
 V2G  C5'  H6   single    0.970  0.020  1.090
 V2G  C5'  H7   single    0.970  0.020  1.090
 V2G  C4'  H8   single    0.970  0.020  1.090
 V2G  C3'  H9   single    0.970  0.020  1.090
 V2G  O3'  H10  single    0.850  0.020  0.980
 V2G  C2'  H11  single    0.970  0.020  1.090
 V2G  O2'  H12  single    0.850  0.020  0.980
 V2G  C1'  H13  single    0.970  0.020  1.090
 V2G  C8   H14  single    0.930  0.020  1.080
 V2G  C2   H15  single    0.930  0.020  1.080
 V2G  N6   H16  single    0.860  0.020  1.020
 V2G  N6   H17  single    0.860  0.020  1.020

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
 V2G  H1   N    P    115.00  3.000
 V2G  H1   N    CA   115.08  3.000
 V2G  P    N    CA   124.17  3.000
 V2G  H3   CA   H2   105.96  3.000
 V2G  H3   CA   C    108.54  3.000
 V2G  H2   CA   C    107.84  3.000
 V2G  H3   CA   N    112.38  3.000
 V2G  H2   CA   N    110.45  3.000
 V2G  C    CA   N    111.43  3.000
 V2G  O    C    OXT  124.26  3.000
 V2G  OXT  C    CA   110.65  3.000
 V2G  O    C    CA   125.09  3.000
 V2G  H4   OXT  C    110.32  3.000
 V2G  O5'  P    O2   115.41  3.000
 V2G  O5'  P    O1    99.08  3.000
 V2G  O2   P    O1   116.41  3.000
 V2G  O1   P    N    105.89  3.000
 V2G  O5'  P    N    105.13  3.000
 V2G  O2   P    N    113.32  3.000
 V2G  H5   O1   P    113.83  3.000
 V2G  C5'  O5'  P    120.77  3.000
 V2G  H7   C5'  H6   107.18  3.000
 V2G  H7   C5'  C4'  110.98  3.000
 V2G  H6   C5'  C4'  108.73  3.000
 V2G  H7   C5'  O5'  107.01  3.000
 V2G  H6   C5'  O5'  112.13  3.000
 V2G  C4'  C5'  O5'  110.76  3.000
 V2G  H8   C4'  C3'  109.85  3.000
 V2G  H8   C4'  O4'  109.27  3.000
 V2G  C3'  C4'  O4'  104.93  3.000
 V2G  H8   C4'  C5'  109.33  3.000
 V2G  O4'  C4'  C5'  110.24  3.000
 V2G  C3'  C4'  C5'  113.12  3.000
 V2G  C1'  O4'  C4'  111.16  3.000
 V2G  H9   C3'  C2'  109.08  3.000
 V2G  H9   C3'  O3'  111.60  3.000
 V2G  C2'  C3'  O3'  114.18  3.000
 V2G  H9   C3'  C4'  109.74  3.000
 V2G  O3'  C3'  C4'  110.37  3.000
 V2G  C2'  C3'  C4'  101.38  3.000
 V2G  H10  O3'  C3'  108.93  3.000
 V2G  H11  C2'  C1'  112.25  3.000
 V2G  H11  C2'  O2'  111.97  3.000
 V2G  C1'  C2'  O2'  107.32  3.000
 V2G  H11  C2'  C3'  112.65  3.000
 V2G  C1'  C2'  C3'  100.95  3.000
 V2G  O2'  C2'  C3'  111.08  3.000
 V2G  H12  O2'  C2'  108.05  3.000
 V2G  H13  C1'  N9   107.31  3.000
 V2G  H13  C1'  C2'  111.54  3.000
 V2G  N9   C1'  C2'  111.52  3.000
 V2G  H13  C1'  O4'  110.48  3.000
 V2G  C2'  C1'  O4'  106.85  3.000
 V2G  N9   C1'  O4'  109.15  3.000
 V2G  C4   N9   C8   106.20  3.000
 V2G  C8   N9   C1'  129.04  3.000
 V2G  C4   N9   C1'  124.74  3.000
 V2G  H14  C8   N7   124.55  3.000
 V2G  H14  C8   N9   122.11  3.000
 V2G  N7   C8   N9   113.34  3.000
 V2G  C5   N7   C8   104.43  3.000
 V2G  C6   C5   C4   116.16  3.000
 V2G  C4   C5   N7   110.72  3.000
 V2G  C6   C5   N7   133.12  3.000
 V2G  N3   C4   C5   126.71  3.000
 V2G  N3   C4   N9   127.98  3.000
 V2G  C5   C4   N9   105.32  3.000
 V2G  C2   N3   C4   111.54  3.000
 V2G  H15  C2   N1   115.39  3.000
 V2G  H15  C2   N3   116.18  3.000
 V2G  N1   C2   N3   128.43  3.000
 V2G  C6   N1   C2   119.27  3.000
 V2G  N6   C6   N1   119.34  3.000
 V2G  N1   C6   C5   117.89  3.000
 V2G  N6   C6   C5   122.78  3.000
 V2G  H17  N6   H16  118.36  3.000
 V2G  H17  N6   C6   121.19  3.000
 V2G  H16  N6   C6   120.33  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
 V2G  CONST_01  C6   C5   C4   N9    180.00   0.0  0
 V2G  CONST_02  N7   C5   C4   N9      0.00   0.0  0
 V2G  CONST_03  C2   N3   C4   N9    180.00   0.0  0
 V2G  CONST_04  C5   N7   C8   N9      0.00   0.0  0
 V2G  CONST_05  C6   C5   N7   C8    180.00   0.0  0
 V2G  CONST_06  C4   C5   N7   C8      0.00   0.0  0
 V2G  CONST_07  C5   C4   N9   C8      0.00   0.0  0
 V2G  CONST_08  N3   C4   N9   C8    180.00   0.0  0
 V2G  CONST_09  N1   C6   C5   N7    180.00   0.0  0
 V2G  CONST_10  N3   C4   C5   N7    180.00   0.0  0
 V2G  CONST_11  C4   N9   C8   N7      0.00   0.0  0
 V2G  CONST_12  C2   N1   C6   C5      0.00   0.0  0
 V2G  CONST_13  C2   N3   C4   C5      0.00   0.0  0
 V2G  CONST_14  N1   C6   C5   C4      0.00   0.0  0
 V2G  CONST_15  N1   C2   N3   C4      0.00   0.0  0
 V2G  CONST_16  C6   N1   C2   N3      0.00   0.0  0
 V2G  CONST_17  C6   C5   C4   N3      0.00   0.0  0
 V2G  CONST_18  C5   C4   N9   C1'   180.00   0.0  0
 V2G  CONST_19  N3   C4   N9   C1'     0.00   0.0  0
 V2G  CONST_20  N7   C8   N9   C1'   180.00   0.0  0
 V2G  CONST_21  N6   C6   C5   N7      0.00   0.0  0
 V2G  CONST_22  N6   C6   C5   C4    180.00   0.0  0
 V2G  CONST_23  N6   C6   N1   C2    180.00   0.0  0
 V2G  CONST_24  H14  C8   N9   C1'     0.00   0.0  0
 V2G  CONST_25  H15  C2   N3   C4    180.00   0.0  0
 V2G  CONST_26  H16  N6   C6   C5    180.00   0.0  0
 V2G  CONST_27  H17  N6   C6   C5      0.00   0.0  0
 V2G  CONST_28  H4   OXT  C    CA    180.00   0.0  0
 V2G  Var_01    C4'  C5'  O5'  P      96.47  30.0  2
 V2G  Var_02    O    C    CA   N       1.59  30.0  2
 V2G  Var_03    O2   P    N    CA    179.61  30.0  1
 V2G  Var_04    P    N    CA   C    -141.42  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
 V2G  chir_02  C4'  C3'  O4'  C5'  positiv
 V2G  chir_03  C3'  O3'  C2'  C4'  negativ
 V2G  chir_04  C2'  O2'  C1'  C3'  negativ
 V2G  chir_05  C1'  O4'  N9   C2'  negativ
 V2G  chir_06  P    O5'  N    O1   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
 V2G  plan-1  C1'  0.020
 V2G  plan-1  N9   0.020
 V2G  plan-1  C8   0.020
 V2G  plan-1  N7   0.020
 V2G  plan-1  C5   0.020
 V2G  plan-1  C4   0.020
 V2G  plan-1  N3   0.020
 V2G  plan-1  C2   0.020
 V2G  plan-1  N1   0.020
 V2G  plan-1  C6   0.020
 V2G  plan-1  N6   0.020
 V2G  plan-1  H14  0.020
 V2G  plan-1  H15  0.020
 V2G  plan-2  C6   0.020
 V2G  plan-2  N6   0.020
 V2G  plan-2  H16  0.020
 V2G  plan-2  H17  0.020
 V2G  plan-3  CA   0.020
 V2G  plan-3  C    0.020
 V2G  plan-3  OXT  0.020
 V2G  plan-3  O    0.020
 V2G  plan-3  H4   0.020

