# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 15:27:58 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: (2S,4aR,6R,7R,7aS)-6-(6-amino-2-chloro-9H-purin-9-yl)-7-hydroxy-2-sulfanyltetrahydro-2H,4H-2lambda~5~-furo[3,2-d][1,3,2]dioxaphosphinin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(Cl)nc2n(cnc12)[C@@H]3O[C@@H]4CO[P@@](S)(=O)O[C@H]4[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
 75G  75G  (2S,4aR,6R,7R,7aS)-6-(6-amino-2-chloro-9H-purin-9-yl)-7-hydroxy-2-sulfanyltetrahydro-2H,4H-2lambda~5~-furo[3,2-d][1,3,2]dioxaphosphinin-2-one  ligand  34  23  .  2021-08-05  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_75G
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
 75G  C1   C   CR6   0   0.277   4.2270  -0.7140   0.3475
 75G  C2   C   CR56  0   0.508   2.4184   0.3492  -0.2232
 75G  C3   C   CR56  0   0.007   2.9203   1.5621   0.2143
 75G  C4   C   CR6   0   0.481   4.2189   1.5342   0.7597
 75G  P1   P   P     0   1.246  -4.1941  -0.1694   0.5683
 75G  O1   O   O     0  -0.640  -5.3823  -0.9897   0.8411
 75G  O2   O   O2    0  -0.568  -4.2291   0.4743  -0.8984
 75G  C5   C   CH2   0  -0.217  -3.0613   1.0200  -1.5389
 75G  C6   C   CR15  0   0.015  -2.0064  -0.0616  -1.4448
 75G  O3   O   O     0  -0.489  -0.7424   0.3045  -1.9540
 75G  C7   C   CR15  0   0.155   0.2581  -0.3710  -1.2300
 75G  C8   C   CR15  0  -0.066  -0.4423  -1.1930  -0.1091
 75G  O4   O   OH1   0  -0.650  -0.7816  -2.4729  -0.5398
 75G  C9   C   CR15  0  -0.020  -1.7047  -0.3664   0.0125
 75G  O5   O   O2    0  -0.568  -2.8036  -0.9809   0.6611
 75G  N1   N   NR5   0  -0.537   1.1711   0.6208  -0.6934
 75G  C10  C   CR15  0   0.104   0.9822   1.9679  -0.5184
 75G  N2   N   N     0  -0.443   2.0065   2.5617   0.0187
 75G  N3   N   NH2   0  -0.810   4.8351   2.6156   1.2216
 75G  N4   N   N     0  -0.452   4.8492   0.3518   0.8079
 75G  CL1  CL  CL    0  -0.108   5.1362  -2.1884   0.4584
 75G  N5   N   N     0  -0.434   3.0332  -0.8338  -0.1788
 75G  H3   H   HCH2  0   0.253  -2.7489   1.9418  -1.0399
 75G  H4   H   HCR5  0   0.277  -2.3815  -0.9586  -1.9525
 75G  H5   H   HCR5  0   0.300   0.8339  -1.0310  -1.8851
 75G  H6   H   HCR5  0   0.291   0.1572  -1.2012   0.8068
 75G  H7   H   HOH1  0   0.471   0.0051  -3.0281  -0.5268
 75G  H8   H   HCR5  0   0.270  -1.4412   0.5653   0.5310
 75G  H9   H   HCR5  0   0.302   0.0723   2.4636  -0.8182
 75G  H10  H   HNH2  0   0.419   4.3840   3.5140   1.2116
 75G  H11  H   HNH2  0   0.411   5.7533   2.5475   1.6268
 75G  H12  H   HSH1  0   0.279  -4.9234   2.0842   1.5921
 75G  H2   H   HCH2  0   0.292  -3.3488   1.2516  -2.5620
 75G  S1   S   S2    0  -0.357  -3.8187   1.3902   1.8992

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
 75G  N3   C4   single    1.328  0.020  1.328
 75G  N4   C4   aromatic  1.341  0.020  1.341
 75G  N4   C1   aromatic  1.317  0.020  1.317
 75G  C4   C3   aromatic  1.409  0.020  1.409
 75G  CL1  C1   single    1.736  0.020  1.736
 75G  C1   N5   aromatic  1.310  0.020  1.310
 75G  C3   N2   aromatic  1.368  0.020  1.368
 75G  C3   C2   aromatic  1.384  0.020  1.384
 75G  N2   C10  aromatic  1.300  0.020  1.300
 75G  N5   C2   aromatic  1.334  0.020  1.334
 75G  C2   N1   aromatic  1.360  0.020  1.360
 75G  C10  N1   aromatic  1.371  0.020  1.371
 75G  N1   C7   single    1.451  0.020  1.451
 75G  C7   O3   single    1.408  0.020  1.408
 75G  C7   C8   single    1.556  0.020  1.556
 75G  O3   C6   single    1.411  0.020  1.411
 75G  C8   C9   single    1.514  0.020  1.514
 75G  C8   O4   single    1.392  0.020  1.392
 75G  S1   P1   single    2.084  0.020  2.084
 75G  C9   C6   single    1.519  0.020  1.519
 75G  C9   O5   single    1.416  0.020  1.416
 75G  C5   C6   single    1.514  0.020  1.514
 75G  C5   O2   single    1.439  0.020  1.439
 75G  O5   P1   single    1.613  0.020  1.613
 75G  P1   O2   single    1.602  0.020  1.602
 75G  P1   O1   double    1.469  0.020  1.469
 75G  C5   H2   single    0.970  0.020  1.090
 75G  C5   H3   single    0.970  0.020  1.090
 75G  C6   H4   single    0.970  0.020  1.090
 75G  C7   H5   single    0.970  0.020  1.090
 75G  C8   H6   single    0.970  0.020  1.090
 75G  O4   H7   single    0.850  0.020  0.980
 75G  C9   H8   single    0.970  0.020  1.090
 75G  C10  H9   single    0.930  0.020  1.080
 75G  N3   H10  single    0.860  0.020  1.020
 75G  N3   H11  single    0.860  0.020  1.020
 75G  S1   H12  single    1.200  0.020  1.300

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
 75G  N5   C1   CL1  115.17  3.000
 75G  N5   C1   N4   130.15  3.000
 75G  CL1  C1   N4   114.68  3.000
 75G  N5   C2   N1   127.68  3.000
 75G  N1   C2   C3   105.47  3.000
 75G  N5   C2   C3   126.85  3.000
 75G  N2   C3   C4   133.27  3.000
 75G  N2   C3   C2   110.66  3.000
 75G  C4   C3   C2   116.06  3.000
 75G  N4   C4   N3   119.18  3.000
 75G  N4   C4   C3   117.70  3.000
 75G  N3   C4   C3   123.12  3.000
 75G  O5   P1   O2   105.88  3.000
 75G  O2   P1   O1   112.12  3.000
 75G  O5   P1   O1   113.93  3.000
 75G  O1   P1   S1   116.41  3.000
 75G  O2   P1   S1   106.73  3.000
 75G  O5   P1   S1   100.63  3.000
 75G  C5   O2   P1   122.82  3.000
 75G  H3   C5   H2   108.97  3.000
 75G  H3   C5   C6   112.01  3.000
 75G  H2   C5   C6   113.26  3.000
 75G  H3   C5   O2   110.38  3.000
 75G  H2   C5   O2   106.55  3.000
 75G  C6   C5   O2   105.48  3.000
 75G  H4   C6   C9   110.36  3.000
 75G  H4   C6   O3   110.58  3.000
 75G  C9   C6   O3   102.73  3.000
 75G  H4   C6   C5   108.49  3.000
 75G  C9   C6   C5   109.96  3.000
 75G  O3   C6   C5   114.61  3.000
 75G  C7   O3   C6   109.06  3.000
 75G  H5   C7   N1   107.62  3.000
 75G  H5   C7   C8   110.46  3.000
 75G  N1   C7   C8   112.20  3.000
 75G  H5   C7   O3   110.84  3.000
 75G  C8   C7   O3   107.70  3.000
 75G  N1   C7   O3   108.02  3.000
 75G  H6   C8   C9   113.17  3.000
 75G  H6   C8   O4   112.66  3.000
 75G  C9   C8   O4   108.88  3.000
 75G  H6   C8   C7   111.11  3.000
 75G  O4   C8   C7   111.86  3.000
 75G  C9   C8   C7    98.32  3.000
 75G  H7   O4   C8   109.07  3.000
 75G  H8   C9   O5   109.75  3.000
 75G  H8   C9   C8   107.53  3.000
 75G  O5   C9   C8   116.54  3.000
 75G  H8   C9   C6   109.29  3.000
 75G  O5   C9   C6   111.85  3.000
 75G  C8   C9   C6   101.43  3.000
 75G  C9   O5   P1   115.11  3.000
 75G  C10  N1   C7   129.19  3.000
 75G  C7   N1   C2   124.63  3.000
 75G  C10  N1   C2   106.16  3.000
 75G  H9   C10  N2   124.72  3.000
 75G  H9   C10  N1   122.15  3.000
 75G  N2   C10  N1   113.12  3.000
 75G  C10  N2   C3   104.57  3.000
 75G  H11  N3   H10  118.30  3.000
 75G  H11  N3   C4   120.58  3.000
 75G  H10  N3   C4   121.07  3.000
 75G  C4   N4   C1   118.61  3.000
 75G  C2   N5   C1   110.63  3.000
 75G  H12  S1   P1    95.32  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
 75G  CONST_01  C3   C4   N4  C1     0.00   0.0  0
 75G  CONST_02  C3   C2   N5  C1     0.00   0.0  0
 75G  CONST_03  N1   C2   N5  C1   180.00   0.0  0
 75G  CONST_04  N4   C4   C3  C2     0.00   0.0  0
 75G  CONST_05  C10  N2   C3  C2     0.00   0.0  0
 75G  CONST_06  N4   C1   N5  C2     0.00   0.0  0
 75G  CONST_07  N2   C10  N1  C2     0.00   0.0  0
 75G  CONST_08  N1   C10  N2  C3     0.00   0.0  0
 75G  CONST_09  C10  N1   C2  C3     0.00   0.0  0
 75G  CONST_10  N5   C1   N4  C4     0.00   0.0  0
 75G  CONST_11  C10  N2   C3  C4   180.00   0.0  0
 75G  CONST_12  N5   C2   C3  C4     0.00   0.0  0
 75G  CONST_13  N1   C2   C3  C4   180.00   0.0  0
 75G  CONST_14  N2   C3   C2  N1     0.00   0.0  0
 75G  CONST_15  N5   C2   N1  C10  180.00   0.0  0
 75G  CONST_16  N4   C4   C3  N2   180.00   0.0  0
 75G  CONST_17  N5   C2   C3  N2   180.00   0.0  0
 75G  CONST_18  C7   N1   C2  C3   180.00   0.0  0
 75G  CONST_19  N5   C2   N1  C7     0.00   0.0  0
 75G  CONST_20  N2   C10  N1  C7   180.00   0.0  0
 75G  CONST_21  N3   C4   N4  C1   180.00   0.0  0
 75G  CONST_22  N3   C4   C3  C2   180.00   0.0  0
 75G  CONST_23  CL1  C1   N5  C2   180.00   0.0  0
 75G  CONST_24  CL1  C1   N4  C4   180.00   0.0  0
 75G  CONST_25  N3   C4   C3  N2     0.00   0.0  0
 75G  CONST_26  H9   C10  N1  C2   180.00   0.0  0
 75G  CONST_27  H10  N3   C4  C3     0.00   0.0  0
 75G  CONST_28  H11  N3   C4  C3   180.00   0.0  0
 75G  Var_01    C6   C5   O2  P1    51.53  30.0  1
 75G  Var_02    O5   P1   O2  C5   -38.62  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
 75G  chir_02  C6  O3  C9  C5  negativ
 75G  chir_03  C7  O3  N1  C8  negativ
 75G  chir_04  C8  O4  C7  C9  negativ
 75G  chir_05  C9  O5  C8  C6  negativ
 75G  chir_06  P1  O5  O2  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
 75G  plan-1  C1   0.020
 75G  plan-1  C2   0.020
 75G  plan-1  C3   0.020
 75G  plan-1  C4   0.020
 75G  plan-1  C7   0.020
 75G  plan-1  N1   0.020
 75G  plan-1  C10  0.020
 75G  plan-1  N2   0.020
 75G  plan-1  N3   0.020
 75G  plan-1  N4   0.020
 75G  plan-1  CL1  0.020
 75G  plan-1  N5   0.020
 75G  plan-1  H9   0.020
 75G  plan-2  C4   0.020
 75G  plan-2  N3   0.020
 75G  plan-2  H10  0.020
 75G  plan-2  H11  0.020

