# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 17:27:01 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: 2'-deoxy-5'-O-[(R)-hydroxy({(R)-hydroxy[(1S)-1-phosphonoethyl]phosphoryl}oxy)phosphoryl]adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]([P](O)(O)=O)[P](O)(=O)O[P](O)(=O)OC[C@H]1O[C@H](C[C@@H]1O)n2cnc3c(N)ncnc23
#
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
 HGV  HGV  2'-deoxy-5'-O-[(R)-hydroxy({(R)-hydroxy[(1S)-1-phosphonoethyl]phosphoryl}oxy)phosphoryl]adenosine  ligand  47  31  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_HGV
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
 HGV  PA   P  P      0   1.336   1.2968  -1.9615  -1.3789
 HGV  O1A  O  OP    -1  -0.950   0.4004  -0.8927  -1.9383
 HGV  O2A  O  O      0  -0.825   1.9133  -2.9592  -2.3167
 HGV  O3A  O  O2     0  -0.669   2.4209  -1.3764  -0.3768
 HGV  O5'  O  O2     0  -0.635   0.4681  -2.8032  -0.2127
 HGV  PB   P  P      0   1.256   3.2582   0.0906  -0.5851
 HGV  O2B  O  O      0  -0.828   3.4759   0.2288  -2.0692
 HGV  O1B  O  OP    -1  -0.824   4.4452  -0.0846   0.3279
 HGV  C3B  C  CH1    0  -0.752   2.0837   1.3031   0.0776
 HGV  C4B  C  CH3    0  -0.726   1.4713   0.8639   1.4042
 HGV  PG   P  P      0   1.137   2.8312   3.0177   0.2527
 HGV  O1G  O  OP    -1  -0.956   3.6945   3.2321  -0.9963
 HGV  O2G  O  OP    -1  -1.013   1.6113   3.9540   0.3112
 HGV  O3G  O  O      0  -0.809   3.6357   3.0071   1.5572
 HGV  C5'  C  CH2    0  -0.127  -0.9061  -3.0468  -0.3717
 HGV  C4'  C  CH1    0  -0.044  -1.6271  -2.8759   0.9470
 HGV  O4'  O  O2     0  -0.505  -1.4023  -1.5720   1.4862
 HGV  C1'  C  CH1    0   0.236  -2.5996  -0.9230   1.7623
 HGV  N9   N  NR5    0  -0.544  -2.8667   0.0627   0.7038
 HGV  C4   C  CR56   0   0.517  -3.9567   0.8802   0.6385
 HGV  N3   N  N      0  -0.438  -5.0117   0.9271   1.4540
 HGV  C2   C  CR16   0  -0.000  -5.8832   1.8453   1.0771
 HGV  N1   N  N      0  -0.434  -5.8173   2.6735   0.0370
 HGV  C6   C  CR6    0   0.423  -4.7498   2.6211  -0.7673
 HGV  N6   N  NH2    0  -0.750  -4.6797   3.4448  -1.8165
 HGV  C5   C  CR56   0  -0.042  -3.7444   1.6829  -0.4726
 HGV  N7   N  N      0  -0.474  -2.5531   1.3765  -1.0719
 HGV  C8   C  CR15   0   0.102  -2.0543   0.4180  -0.3405
 HGV  C2'  C  CH2    0  -0.593  -3.6617  -2.0086   1.8218
 HGV  C3'  C  CH1    0   0.074  -3.1446  -3.0175   0.8016
 HGV  O3'  O  OH1    0  -0.695  -3.5198  -4.3490   1.0304
 HGV  H3   H  HCH1   0   0.280   1.2803   1.3743  -0.6629
 HGV  H4   H  HCH3   0   0.250   2.2467   0.6546   2.1414
 HGV  H5   H  HCH3   0   0.195   0.8514   1.6653   1.8098
 HGV  H6   H  HCH3   0   0.249   0.8382  -0.0184   1.3041
 HGV  H9   H  HCH2   0   0.228  -1.3530  -2.3764  -1.1130
 HGV  H10  H  HCH2   0   0.180  -1.0866  -4.0727  -0.7184
 HGV  H11  H  HCH1   0   0.289  -1.2672  -3.6086   1.6797
 HGV  H12  H  HCH1   0   0.267  -2.5089  -0.3704   2.6999
 HGV  H13  H  HCR6   0   0.194  -6.7718   1.9410   1.6926
 HGV  H14  H  HNH2   0   0.425  -5.3979   4.1307  -1.9726
 HGV  H15  H  HNH2   0   0.413  -3.8609   3.4710  -2.3984
 HGV  H16  H  HCR5   0   0.296  -1.1027  -0.0598  -0.5364
 HGV  H17  H  HCH2   0   0.276  -3.6493  -2.4552   2.8189
 HGV  H18  H  HCH2   0   0.279  -4.6686  -1.6467   1.6228
 HGV  H19  H  HCH1   0   0.279  -3.4448  -2.6963  -0.2061
 HGV  H20  H  HOH1   0   0.451  -4.4485  -4.4465   0.7989

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
 HGV  C2   N1   aromatic  1.331  0.020  1.331
 HGV  C2   N3   aromatic  1.321  0.020  1.321
 HGV  N1   C6   aromatic  1.338  0.020  1.338
 HGV  N3   C4   aromatic  1.334  0.020  1.334
 HGV  C6   N6   single    1.336  0.020  1.336
 HGV  C6   C5   aromatic  1.406  0.020  1.406
 HGV  C4   C5   aromatic  1.387  0.020  1.387
 HGV  C4   N9   aromatic  1.364  0.020  1.364
 HGV  C2'  C1'  single    1.520  0.020  1.520
 HGV  C2'  C3'  single    1.525  0.020  1.525
 HGV  C1'  N9   single    1.471  0.020  1.471
 HGV  C1'  O4'  single    1.390  0.020  1.390
 HGV  C5   N7   aromatic  1.368  0.020  1.368
 HGV  N9   C8   aromatic  1.370  0.020  1.370
 HGV  O3'  C3'  single    1.402  0.020  1.402
 HGV  C3'  C4'  single    1.531  0.020  1.531
 HGV  O4'  C4'  single    1.429  0.020  1.429
 HGV  N7   C8   aromatic  1.305  0.020  1.305
 HGV  C4'  C5'  single    1.513  0.020  1.513
 HGV  O2B  PB   deloc     1.506  0.020  1.506
 HGV  C5'  O5'  single    1.405  0.020  1.405
 HGV  O5'  PA   single    1.660  0.020  1.660
 HGV  PB   O3A  single    1.702  0.020  1.702
 HGV  PB   O1B  deloc     1.508  0.020  1.508
 HGV  PB   C3B  single    1.814  0.020  1.814
 HGV  O3A  PA   single    1.616  0.020  1.616
 HGV  C3B  C4B  single    1.526  0.020  1.526
 HGV  C3B  PG   single    1.879  0.020  1.879
 HGV  PA   O2A  deloc     1.502  0.020  1.502
 HGV  PA   O1A  deloc     1.503  0.020  1.503
 HGV  O3G  PG   deloc     1.533  0.020  1.533
 HGV  PG   O1G  deloc     1.533  0.020  1.533
 HGV  PG   O2G  deloc     1.539  0.020  1.539
 HGV  C3B  H3   single    0.970  0.020  1.090
 HGV  C4B  H4   single    0.970  0.020  1.090
 HGV  C4B  H5   single    0.970  0.020  1.090
 HGV  C4B  H6   single    0.970  0.020  1.090
 HGV  C5'  H9   single    0.970  0.020  1.090
 HGV  C5'  H10  single    0.970  0.020  1.090
 HGV  C4'  H11  single    0.970  0.020  1.090
 HGV  C1'  H12  single    0.970  0.020  1.090
 HGV  C2   H13  single    0.930  0.020  1.080
 HGV  N6   H14  single    0.860  0.020  1.020
 HGV  N6   H15  single    0.860  0.020  1.020
 HGV  C8   H16  single    0.930  0.020  1.080
 HGV  C2'  H17  single    0.970  0.020  1.090
 HGV  C2'  H18  single    0.970  0.020  1.090
 HGV  C3'  H19  single    0.970  0.020  1.090
 HGV  O3'  H20  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
 HGV  O5'  PA   O3A   95.46  3.000
 HGV  O3A  PA   O2A  110.02  3.000
 HGV  O5'  PA   O2A  107.87  3.000
 HGV  O2A  PA   O1A  119.01  3.000
 HGV  O3A  PA   O1A  112.85  3.000
 HGV  O5'  PA   O1A  108.93  3.000
 HGV  PB   O3A  PA   125.35  3.000
 HGV  C5'  O5'  PA   119.79  3.000
 HGV  C3B  PB   O1B  111.49  3.000
 HGV  C3B  PB   O2B  113.10  3.000
 HGV  O1B  PB   O2B  119.57  3.000
 HGV  C3B  PB   O3A  102.29  3.000
 HGV  O1B  PB   O3A  102.30  3.000
 HGV  O2B  PB   O3A  105.71  3.000
 HGV  H3   C3B  PG   107.20  3.000
 HGV  H3   C3B  C4B  108.20  3.000
 HGV  PG   C3B  C4B  109.96  3.000
 HGV  H3   C3B  PB   105.75  3.000
 HGV  PG   C3B  PB   112.74  3.000
 HGV  C4B  C3B  PB   112.66  3.000
 HGV  H6   C4B  H5   107.37  3.000
 HGV  H6   C4B  H4   108.64  3.000
 HGV  H5   C4B  H4   107.07  3.000
 HGV  H6   C4B  C3B  112.71  3.000
 HGV  H5   C4B  C3B  109.86  3.000
 HGV  H4   C4B  C3B  110.96  3.000
 HGV  O3G  PG   O2G  112.83  3.000
 HGV  O2G  PG   O1G  113.09  3.000
 HGV  O3G  PG   O1G  113.50  3.000
 HGV  O2G  PG   C3B  104.09  3.000
 HGV  O1G  PG   C3B  106.00  3.000
 HGV  O3G  PG   C3B  106.37  3.000
 HGV  H10  C5'  H9   106.93  3.000
 HGV  H10  C5'  C4'  107.61  3.000
 HGV  H9   C5'  C4'  109.06  3.000
 HGV  H10  C5'  O5'  111.02  3.000
 HGV  H9   C5'  O5'  111.70  3.000
 HGV  C4'  C5'  O5'  110.36  3.000
 HGV  H11  C4'  C3'  109.08  3.000
 HGV  H11  C4'  O4'  107.81  3.000
 HGV  C3'  C4'  O4'  106.03  3.000
 HGV  H11  C4'  C5'  110.52  3.000
 HGV  O4'  C4'  C5'  110.93  3.000
 HGV  C3'  C4'  C5'  112.28  3.000
 HGV  C1'  O4'  C4'  111.45  3.000
 HGV  H12  C1'  C2'  112.70  3.000
 HGV  H12  C1'  N9   107.09  3.000
 HGV  C2'  C1'  N9   112.33  3.000
 HGV  H12  C1'  O4'  109.59  3.000
 HGV  N9   C1'  O4'  109.05  3.000
 HGV  C2'  C1'  O4'  106.03  3.000
 HGV  C8   N9   C4   106.38  3.000
 HGV  C8   N9   C1'  127.93  3.000
 HGV  C4   N9   C1'  125.53  3.000
 HGV  C5   C4   N3   126.18  3.000
 HGV  C5   C4   N9   105.24  3.000
 HGV  N3   C4   N9   128.58  3.000
 HGV  C2   N3   C4   111.82  3.000
 HGV  H13  C2   N1   115.39  3.000
 HGV  H13  C2   N3   116.09  3.000
 HGV  N1   C2   N3   128.53  3.000
 HGV  C6   N1   C2   119.00  3.000
 HGV  C5   C6   N6   122.58  3.000
 HGV  C5   C6   N1   118.08  3.000
 HGV  N6   C6   N1   119.34  3.000
 HGV  H15  N6   H14  118.32  3.000
 HGV  H15  N6   C6   120.91  3.000
 HGV  H14  N6   C6   120.34  3.000
 HGV  N7   C5   C6   132.84  3.000
 HGV  N7   C5   C4   110.77  3.000
 HGV  C6   C5   C4   116.39  3.000
 HGV  C8   N7   C5   104.58  3.000
 HGV  H16  C8   N7   123.96  3.000
 HGV  H16  C8   N9   123.00  3.000
 HGV  N7   C8   N9   113.03  3.000
 HGV  H18  C2'  H17  108.26  3.000
 HGV  H18  C2'  C3'  114.29  3.000
 HGV  H17  C2'  C3'  109.64  3.000
 HGV  H18  C2'  C1'  113.70  3.000
 HGV  H17  C2'  C1'  108.65  3.000
 HGV  C3'  C2'  C1'  102.09  3.000
 HGV  H19  C3'  O3'  110.73  3.000
 HGV  H19  C3'  C2'  109.10  3.000
 HGV  O3'  C3'  C2'  115.36  3.000
 HGV  H19  C3'  C4'  109.31  3.000
 HGV  O3'  C3'  C4'  109.73  3.000
 HGV  C2'  C3'  C4'  102.20  3.000
 HGV  H20  O3'  C3'  108.37  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
 HGV  CONST_01  C2   N3   C4   N9    180.00   0.0  0
 HGV  CONST_02  C6   C5   C4   N9    180.00   0.0  0
 HGV  CONST_03  N7   C5   C4   N9      0.00   0.0  0
 HGV  CONST_04  C5   N7   C8   N9      0.00   0.0  0
 HGV  CONST_05  N1   C2   N3   C4      0.00   0.0  0
 HGV  CONST_06  N1   C6   C5   C4      0.00   0.0  0
 HGV  CONST_07  C8   N7   C5   C4      0.00   0.0  0
 HGV  CONST_08  N7   C8   N9   C4      0.00   0.0  0
 HGV  CONST_09  C6   N1   C2   N3      0.00   0.0  0
 HGV  CONST_10  C6   C5   C4   N3      0.00   0.0  0
 HGV  CONST_11  N7   C5   C4   N3    180.00   0.0  0
 HGV  CONST_12  C8   N9   C4   N3    180.00   0.0  0
 HGV  CONST_13  C5   C6   N1   C2      0.00   0.0  0
 HGV  CONST_14  C5   C4   N3   C2      0.00   0.0  0
 HGV  CONST_15  N7   C5   C6   N1    180.00   0.0  0
 HGV  CONST_16  C8   N7   C5   C6    180.00   0.0  0
 HGV  CONST_17  C8   N9   C4   C5      0.00   0.0  0
 HGV  CONST_18  N3   C4   N9   C1'     0.00   0.0  0
 HGV  CONST_19  C5   C4   N9   C1'   180.00   0.0  0
 HGV  CONST_20  N7   C8   N9   C1'   180.00   0.0  0
 HGV  CONST_21  N6   C6   C5   C4    180.00   0.0  0
 HGV  CONST_22  N6   C6   N1   C2    180.00   0.0  0
 HGV  CONST_23  N7   C5   C6   N6      0.00   0.0  0
 HGV  CONST_24  H16  C8   N9   C1'     0.00   0.0  0
 HGV  CONST_25  H13  C2   N3   C4    180.00   0.0  0
 HGV  CONST_26  H14  N6   C6   N1      0.00   0.0  0
 HGV  CONST_27  H15  N6   C6   N1    180.00   0.0  0
 HGV  Var_01    C4'  C5'  O5'  PA   -139.68  30.0  1
 HGV  Var_02    O2B  PB   O3A  PA    -36.15  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
 HGV  chir_03  C3B  PB   C4B  PG   negativ
 HGV  chir_04  C4'  O4'  C3'  C5'  negativ
 HGV  chir_05  C1'  O4'  N9   C2'  negativ
 HGV  chir_06  C3'  O3'  C4'  C2'  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
 HGV  plan-1  C1'  0.020
 HGV  plan-1  N9   0.020
 HGV  plan-1  C4   0.020
 HGV  plan-1  N3   0.020
 HGV  plan-1  C2   0.020
 HGV  plan-1  N1   0.020
 HGV  plan-1  C6   0.020
 HGV  plan-1  N6   0.020
 HGV  plan-1  C5   0.020
 HGV  plan-1  N7   0.020
 HGV  plan-1  C8   0.020
 HGV  plan-1  H13  0.020
 HGV  plan-1  H16  0.020
 HGV  plan-2  C6   0.020
 HGV  plan-2  N6   0.020
 HGV  plan-2  H14  0.020
 HGV  plan-2  H15  0.020

