# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 07:50:31 2021
#   Inital geometry file: a 116 line input string
#   Ligand name: 2'-deoxy-5'-O-[(R)-{[(R)-[dibromo(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]adenosine
#   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(Br)(Br)[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
 H84  H84  2'-deoxy-5'-O-[(R)-{[(R)-[dibromo(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]adenosine  ligand  48  32  .  2022-09-15  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_H84
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
 H84  N1   N   N     0  -0.475   9.8072   8.8085   8.4840
 H84  C2   C   CR16  0   0.042   8.6242   8.7585   7.8769
 H84  N3   N   N     0  -0.460   7.4574   8.3956   8.3802
 H84  C4   C   CR56  0   0.486   7.5615   8.0533   9.6636
 H84  C5   C   CR56  0  -0.005   8.7183   8.0507  10.4269
 H84  C6   C   CR6   0   0.456   9.8951   8.4601   9.7728
 H84  N6   N   NH2   0  -0.817  11.0803   8.5104  10.3821
 H84  N7   N   N     0  -0.452   8.4537   7.6405  11.7067
 H84  C8   C   CR15  0   0.102   7.1737   7.4014  11.7122
 H84  N9   N   NR5   0  -0.528   6.5739   7.6354  10.5057
 H84  PA   P   P     0   1.522   4.7929   5.4216  15.0074
 H84  PB   P   P     0   1.475   3.7791   2.7262  13.9526
 H84  PG   P   P     0   1.438   3.9825   1.7105  16.9157
 H84  C1'  C   CH1   0   0.186   5.1769   7.4622  10.1301
 H84  O1A  O   OH1   0  -0.728   3.4778   5.4464  15.8866
 H84  O2B  O   O     0  -0.649   3.9722   2.3587  12.5351
 H84  O1G  O   OH1   0  -0.721   5.0907   2.8245  17.1267
 H84  C2'  C   CH2   0  -0.537   4.8529   6.0551   9.6358
 H84  O2A  O   O     0  -0.654   6.0866   5.7120  15.6306
 H84  O1B  O   OH1   0  -0.707   2.3409   3.2097  14.3926
 H84  O2G  O   OH1   0  -0.720   4.6067   0.4299  17.6247
 H84  C3'  C   CH1   0   0.001   4.2963   5.3723  10.8787
 H84  O3'  O   OH1   0  -0.689   3.4353   4.3156  10.5735
 H84  O3A  O   O2    0  -0.695   4.7338   3.9031  14.4383
 H84  C3B  C   CT    0  -0.758   4.2404   1.3693  15.1066
 H84  BR1  BR  BR    0   0.056   3.0675  -0.1131  14.6724
 H84  BR2  BR  BR    0   0.072   6.0750   0.9000  14.7441
 H84  O3G  O   O     0  -0.658   2.5806   2.0308  17.2344
 H84  C4'  C   CH1   0   0.015   3.5750   6.5532  11.5388
 H84  O4'  O   O2    0  -0.495   4.3818   7.6884  11.2625
 H84  C5'  C   CH2   0  -0.232   3.3103   6.4545  13.0181
 H84  O5'  O   O2    0  -0.576   4.5501   6.3178  13.7242
 H84  H1   H   HCR6  0   0.251   8.6236   9.0546   6.8331
 H84  H2   H   HNH2  0   0.403  11.8947   8.8207   9.8813
 H84  H3   H   HNH2  0   0.411  11.1769   8.2786  11.3548
 H84  H4   H   HCR5  0   0.289   6.6165   7.0677  12.5723
 H84  H5   H   HCH1  0   0.273   4.9794   8.2151   9.3636
 H84  H6   H   HOH1  0   0.515   3.3999   6.2022  16.4869
 H84  H7   H   HOH1  0   0.513   5.0398   3.3021  17.9684
 H84  H8   H   HCH2  0   0.268   4.0711   6.1140   8.8750
 H84  H9   H   HCH2  0   0.282   5.7152   5.5532   9.1992
 H84  H10  H   HOH1  0   0.518   1.5942   2.8352  13.9022
 H84  H11  H   HOH1  0   0.508   3.9609  -0.2317  17.9092
 H84  H12  H   HCH1  0   0.231   5.1279   5.0377  11.5126
 H84  H13  H   HOH1  0   0.460   3.5935   3.5853  11.1910
 H84  H14  H   HCH1  0   0.251   2.5911   6.6638  11.0612
 H84  H15  H   HCH2  0   0.285   2.8063   7.3503  13.3833
 H84  H16  H   HCH2  0   0.247   2.6383   5.6101  13.1884

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
 H84  C2   N3   aromatic  1.322  0.020  1.322
 H84  C2   N1   aromatic  1.331  0.020  1.331
 H84  N3   C4   aromatic  1.332  0.020  1.332
 H84  N1   C6   aromatic  1.338  0.020  1.338
 H84  C4   C5   aromatic  1.386  0.020  1.386
 H84  C4   N9   aromatic  1.363  0.020  1.363
 H84  C6   C5   aromatic  1.407  0.020  1.407
 H84  C6   N6   single    1.334  0.020  1.334
 H84  C2'  C1'  single    1.526  0.020  1.526
 H84  C2'  C3'  single    1.523  0.020  1.523
 H84  C1'  N9   single    1.457  0.020  1.457
 H84  C1'  O4'  single    1.402  0.020  1.402
 H84  C5   N7   aromatic  1.370  0.020  1.370
 H84  N9   C8   aromatic  1.368  0.020  1.368
 H84  O3'  C3'  single    1.397  0.020  1.397
 H84  C3'  C4'  single    1.533  0.020  1.533
 H84  O4'  C4'  single    1.420  0.020  1.420
 H84  C4'  C5'  single    1.506  0.020  1.506
 H84  N7   C8   aromatic  1.302  0.020  1.302
 H84  O2B  PB   double    1.477  0.020  1.477
 H84  C5'  O5'  single    1.433  0.020  1.433
 H84  O5'  PA   single    1.584  0.020  1.584
 H84  PB   O3A  single    1.591  0.020  1.591
 H84  PB   O1B  single    1.580  0.020  1.580
 H84  PB   C3B  single    1.840  0.020  1.840
 H84  O3A  PA   single    1.623  0.020  1.623
 H84  BR1  C3B  single    1.940  0.020  1.940
 H84  PA   O2A  double    1.465  0.020  1.465
 H84  PA   O1A  single    1.582  0.020  1.582
 H84  C3B  BR2  single    1.928  0.020  1.928
 H84  C3B  PG   single    1.859  0.020  1.859
 H84  O3G  PG   double    1.473  0.020  1.473
 H84  PG   O1G  single    1.586  0.020  1.586
 H84  PG   O2G  single    1.591  0.020  1.591
 H84  C2   H1   single    0.930  0.020  1.080
 H84  N6   H2   single    0.860  0.020  1.020
 H84  N6   H3   single    0.860  0.020  1.020
 H84  C8   H4   single    0.930  0.020  1.080
 H84  C1'  H5   single    0.970  0.020  1.090
 H84  O1A  H6   single    0.850  0.020  0.980
 H84  O1G  H7   single    0.850  0.020  0.980
 H84  C2'  H8   single    0.970  0.020  1.090
 H84  C2'  H9   single    0.970  0.020  1.090
 H84  O1B  H10  single    0.850  0.020  0.980
 H84  O2G  H11  single    0.850  0.020  0.980
 H84  C3'  H12  single    0.970  0.020  1.090
 H84  O3'  H13  single    0.850  0.020  0.980
 H84  C4'  H14  single    0.970  0.020  1.090
 H84  C5'  H15  single    0.970  0.020  1.090
 H84  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
 H84  C6   N1   C2   119.22  3.000
 H84  H1   C2   N3   116.16  3.000
 H84  H1   C2   N1   115.41  3.000
 H84  N3   C2   N1   128.43  3.000
 H84  C4   N3   C2   111.62  3.000
 H84  N9   C4   C5   105.30  3.000
 H84  N9   C4   N3   128.10  3.000
 H84  C5   C4   N3   126.60  3.000
 H84  N7   C5   C6   133.08  3.000
 H84  N7   C5   C4   110.72  3.000
 H84  C6   C5   C4   116.20  3.000
 H84  N6   C6   C5   122.81  3.000
 H84  N6   C6   N1   119.25  3.000
 H84  C5   C6   N1   117.94  3.000
 H84  H3   N6   H2   118.41  3.000
 H84  H3   N6   C6   121.28  3.000
 H84  H2   N6   C6   120.27  3.000
 H84  C8   N7   C5   104.41  3.000
 H84  H4   C8   N9   122.02  3.000
 H84  H4   C8   N7   124.64  3.000
 H84  N9   C8   N7   113.33  3.000
 H84  C1'  N9   C8   128.88  3.000
 H84  C8   N9   C4   106.24  3.000
 H84  C1'  N9   C4   124.87  3.000
 H84  O5'  PA   O3A  103.88  3.000
 H84  O3A  PA   O2A  111.52  3.000
 H84  O5'  PA   O2A  111.58  3.000
 H84  O2A  PA   O1A  119.64  3.000
 H84  O3A  PA   O1A  100.33  3.000
 H84  O5'  PA   O1A  108.30  3.000
 H84  C3B  PB   O3A  101.74  3.000
 H84  C3B  PB   O1B  106.21  3.000
 H84  O3A  PB   O1B  103.58  3.000
 H84  C3B  PB   O2B  112.68  3.000
 H84  O1B  PB   O2B  117.55  3.000
 H84  O3A  PB   O2B  113.49  3.000
 H84  O3G  PG   C3B  112.49  3.000
 H84  O3G  PG   O2G  116.87  3.000
 H84  C3B  PG   O2G  103.39  3.000
 H84  O2G  PG   O1G  103.41  3.000
 H84  O3G  PG   O1G  118.92  3.000
 H84  C3B  PG   O1G   99.29  3.000
 H84  H5   C1'  O4'  110.67  3.000
 H84  H5   C1'  C2'  111.71  3.000
 H84  O4'  C1'  C2'  106.86  3.000
 H84  H5   C1'  N9   105.80  3.000
 H84  O4'  C1'  N9   108.44  3.000
 H84  C2'  C1'  N9   113.37  3.000
 H84  H6   O1A  PA   115.06  3.000
 H84  H7   O1G  PG   115.16  3.000
 H84  H9   C2'  H8   108.20  3.000
 H84  H9   C2'  C3'  114.19  3.000
 H84  H8   C2'  C3'  109.32  3.000
 H84  H9   C2'  C1'  112.74  3.000
 H84  H8   C2'  C1'  109.13  3.000
 H84  C3'  C2'  C1'  103.09  3.000
 H84  H10  O1B  PB   116.26  3.000
 H84  H11  O2G  PG   114.80  3.000
 H84  H12  C3'  C4'  110.03  3.000
 H84  H12  C3'  O3'  111.25  3.000
 H84  C4'  C3'  O3'  112.76  3.000
 H84  H12  C3'  C2'  109.32  3.000
 H84  C4'  C3'  C2'  100.25  3.000
 H84  O3'  C3'  C2'  112.71  3.000
 H84  H13  O3'  C3'  109.28  3.000
 H84  PB   O3A  PA   145.18  3.000
 H84  BR2  C3B  BR1  110.32  3.000
 H84  BR2  C3B  PG   111.08  3.000
 H84  BR1  C3B  PG   105.91  3.000
 H84  PG   C3B  PB   116.12  3.000
 H84  BR2  C3B  PB   107.47  3.000
 H84  BR1  C3B  PB   105.76  3.000
 H84  H14  C4'  C5'  106.03  3.000
 H84  H14  C4'  O4'  110.10  3.000
 H84  C5'  C4'  O4'  110.08  3.000
 H84  H14  C4'  C3'  108.15  3.000
 H84  C5'  C4'  C3'  117.07  3.000
 H84  O4'  C4'  C3'  105.35  3.000
 H84  C4'  O4'  C1'  110.51  3.000
 H84  H16  C5'  H15  107.35  3.000
 H84  H16  C5'  O5'  112.43  3.000
 H84  H15  C5'  O5'  108.24  3.000
 H84  H16  C5'  C4'  108.17  3.000
 H84  H15  C5'  C4'  110.87  3.000
 H84  O5'  C5'  C4'  109.76  3.000
 H84  C5'  O5'  PA   125.85  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
 H84  CONST_01  C4   N3   C2   N1     0.00   0.0  0
 H84  CONST_02  C4   C5   C6   N1     0.00   0.0  0
 H84  CONST_03  N7   C5   C6   N1   180.00   0.0  0
 H84  CONST_04  C5   C4   N3   C2     0.00   0.0  0
 H84  CONST_05  N9   C4   N3   C2   180.00   0.0  0
 H84  CONST_06  C5   C6   N1   C2     0.00   0.0  0
 H84  CONST_07  C6   N1   C2   N3     0.00   0.0  0
 H84  CONST_08  C6   C5   C4   N3     0.00   0.0  0
 H84  CONST_09  N7   C5   C4   N3   180.00   0.0  0
 H84  CONST_10  C8   N9   C4   N3   180.00   0.0  0
 H84  CONST_11  C8   N7   C5   C4     0.00   0.0  0
 H84  CONST_12  N7   C8   N9   C4     0.00   0.0  0
 H84  CONST_13  C8   N9   C4   C5     0.00   0.0  0
 H84  CONST_14  N9   C8   N7   C5     0.00   0.0  0
 H84  CONST_15  N9   C4   C5   C6   180.00   0.0  0
 H84  CONST_16  C8   N7   C5   C6   180.00   0.0  0
 H84  CONST_17  N9   C4   C5   N7     0.00   0.0  0
 H84  CONST_18  C1'  N9   C4   N3     0.00   0.0  0
 H84  CONST_19  C1'  N9   C4   C5   180.00   0.0  0
 H84  CONST_20  C1'  N9   C8   N7   180.00   0.0  0
 H84  CONST_21  N6   C6   N1   C2   180.00   0.0  0
 H84  CONST_22  N6   C6   C5   C4   180.00   0.0  0
 H84  CONST_23  N7   C5   C6   N6     0.00   0.0  0
 H84  CONST_24  H1   C2   N3   C4   180.00   0.0  0
 H84  CONST_25  H4   C8   N9   C4   180.00   0.0  0
 H84  CONST_26  H2   N6   C6   N1     0.00   0.0  0
 H84  CONST_27  H3   N6   C6   N1   180.00   0.0  0
 H84  Var_01    C4'  C5'  O5'  PA  -142.84  30.0  1
 H84  Var_02    O2B  PB   O3A  PA   116.96  30.0  1
 H84  Var_03    O5'  PA   O3A  PB   -77.74  30.0  3
 H84  Var_04    O3G  PG   C3B  PB    58.64  30.0  3

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
 H84  chir_03  C1'  C2'  N9   O4'  positiv
 H84  chir_04  C3'  O3'  C4'  C2'  positiv
 H84  chir_05  C4'  O4'  C3'  C5'  negativ
 H84  chir_06  PA   O3A  O2A  O1A  both
 H84  chir_07  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
 H84  plan-1  N1   0.020
 H84  plan-1  C2   0.020
 H84  plan-1  N3   0.020
 H84  plan-1  C4   0.020
 H84  plan-1  C5   0.020
 H84  plan-1  C6   0.020
 H84  plan-1  N6   0.020
 H84  plan-1  N7   0.020
 H84  plan-1  C8   0.020
 H84  plan-1  N9   0.020
 H84  plan-1  C1'  0.020
 H84  plan-1  H1   0.020
 H84  plan-1  H4   0.020
 H84  plan-2  C6   0.020
 H84  plan-2  N6   0.020
 H84  plan-2  H2   0.020
 H84  plan-2  H3   0.020

