# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 12 00:01:40 2022
#   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  44  32  .  2022-09-15  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_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  -0.476  -7.1031  -2.6858  -0.5545
 H84  C2   C   C1     0   0.042  -7.5332  -1.4543  -0.2906
 H84  N3   N   N      0  -0.459  -6.8260  -0.3440  -0.1750
 H84  C4   C   CR5    0   0.484  -5.5261  -0.5646  -0.3649
 H84  C5   C   CR5    0  -0.012  -4.9322  -1.7842  -0.6482
 H84  C6   C   C      0   0.449  -5.7945  -2.8905  -0.7430
 H84  N6   N   NH2    0  -0.817  -5.3591  -4.1213  -1.0267
 H84  N7   N   N      0  -0.451  -3.5759  -1.6448  -0.7846
 H84  C8   C   CR15   0   0.100  -3.3549  -0.3786  -0.5841
 H84  N9   N   NR5    0  -0.541  -4.4983   0.3321  -0.3234
 H84  PA   P   P      0   1.370   0.2690   1.9259  -1.8723
 H84  PB   P   P      0   1.341   1.1066  -0.4851  -0.3490
 H84  PG   P   P      0   1.216   2.1572  -1.4254   2.5369
 H84  C1'  C   CH1    0   0.229  -4.6248   1.7541  -0.0851
 H84  O1A  O   OP    -1  -0.801   1.2960   2.8920  -1.3777
 H84  O2B  O   O      0  -0.790   2.4747  -0.1259  -0.8416
 H84  O1G  O   OP    -1  -0.872   3.5578  -1.0504   2.0737
 H84  C2'  C   CH2    0  -0.567  -4.0818   2.2196   1.2622
 H84  O2A  O   O      0  -0.804   0.3099   1.4130  -3.2783
 H84  O1B  O   OP    -1  -0.775   0.4862  -1.8006  -0.7004
 H84  O2G  O   OP    -1  -0.883   1.8355  -1.0490   3.9772
 H84  C3'  C   CH1    0  -0.001  -3.6297   3.6397   0.9429
 H84  O3'  O   OH1    0  -0.671  -4.7076   4.5438   0.8830
 H84  O3A  O   O2     0  -0.751   0.0425   0.6847  -0.8321
 H84  C3B  C   CT     0  -0.653   1.0359  -0.2662   1.4965
 H84  BR1  BR  BR     0  -0.140   1.5009   1.5839   1.9275
 H84  BR2  BR  BR     0  -0.142  -0.8210  -0.5325   2.0776
 H84  O3G  O   O      0  -0.872   1.6929  -2.8137   2.1188
 H84  C4'  C   CH1    0  -0.038  -3.0830   3.4570  -0.4688
 H84  O4'  O   O2     0  -0.491  -3.9005   2.4509  -1.0630
 H84  C5'  C   CH2    0  -0.159  -1.6251   3.0370  -0.4263
 H84  O5'  O   O2     0  -0.621  -1.2297   2.5979  -1.7020
 H84  H1   H   H      0   0.249  -8.6046  -1.3552  -0.1515
 H84  H2   H   HNH2   0   0.401  -5.9941  -4.9001  -0.9940
 H84  H3   H   HNH2   0   0.409  -4.3750  -4.3168  -1.0826
 H84  H4   H   HCR5   0   0.317  -2.3813   0.0876  -0.6252
 H84  H5   H   HCH1   0   0.256  -5.6932   1.9732  -0.1713
 H84  H8   H   HCH2   0   0.283  -4.8308   2.1655   2.0525
 H84  H9   H   HCH2   0   0.259  -3.2313   1.6088   1.5744
 H84  H12  H   HCH1   0   0.248  -2.8519   3.9851   1.6352
 H84  H13  H   HOH1   0   0.454  -5.1297   4.5709   1.7477
 H84  H14  H   HCH1   0   0.252  -3.1909   4.3681  -1.0649
 H84  H15  H   HCH2   0   0.215  -1.0324   3.8969  -0.0917
 H84  H16  H   HCH2   0   0.215  -1.4842   2.2479   0.3215

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  1.321  0.020  1.321
 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  1.365  0.020  1.365
 H84  C6   C5   aromatic  1.406  0.020  1.406
 H84  C6   N6   single    1.336  0.020  1.336
 H84  C2'  C1'  single    1.525  0.020  1.525
 H84  C2'  C3'  single    1.524  0.020  1.524
 H84  C1'  N9   single    1.447  0.020  1.447
 H84  C1'  O4'  single    1.402  0.020  1.402
 H84  C5   N7   aromatic  1.370  0.020  1.370
 H84  N9   C8   aromatic  1.371  0.020  1.371
 H84  O3'  C3'  single    1.408  0.020  1.408
 H84  C3'  C4'  single    1.525  0.020  1.525
 H84  O4'  C4'  single    1.426  0.020  1.426
 H84  C4'  C5'  single    1.518  0.020  1.518
 H84  N7   C8   aromatic  1.301  0.020  1.301
 H84  O2B  PB   deloc     1.498  0.020  1.498
 H84  C5'  O5'  single    1.406  0.020  1.406
 H84  O5'  PA   single    1.651  0.020  1.651
 H84  PB   O3A  single    1.654  0.020  1.654
 H84  PB   O1B  deloc     1.496  0.020  1.496
 H84  PB   C3B  single    1.860  0.020  1.860
 H84  O3A  PA   single    1.635  0.020  1.635
 H84  BR1  C3B  single    1.956  0.020  1.956
 H84  PA   O2A  deloc     1.497  0.020  1.497
 H84  PA   O1A  deloc     1.494  0.020  1.494
 H84  C3B  BR2  single    1.964  0.020  1.964
 H84  C3B  PG   single    1.919  0.020  1.919
 H84  O3G  PG   deloc     1.522  0.020  1.522
 H84  PG   O1G  deloc     1.522  0.020  1.522
 H84  PG   O2G  deloc     1.523  0.020  1.523
 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  C2'  H8   single    0.970  0.020  1.090
 H84  C2'  H9   single    0.970  0.020  1.090
 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   119.05  3.000
 H84  H1   C2   N3   116.14  3.000
 H84  H1   C2   N1   115.40  3.000
 H84  N3   C2   N1   128.46  3.000
 H84  C4   N3   C2   111.76  3.000
 H84  N9   C4   C5   105.18  3.000
 H84  N9   C4   N3   128.45  3.000
 H84  C5   C4   N3   126.37  3.000
 H84  N7   C5   C6   132.88  3.000
 H84  N7   C5   C4   110.79  3.000
 H84  C6   C5   C4   116.33  3.000
 H84  N6   C6   C5   122.64  3.000
 H84  N6   C6   N1   119.32  3.000
 H84  C5   C6   N1   118.03  3.000
 H84  H3   N6   H2   118.01  3.000
 H84  H3   N6   C6   120.68  3.000
 H84  H2   N6   C6   120.06  3.000
 H84  C8   N7   C5   104.58  3.000
 H84  H4   C8   N9   122.35  3.000
 H84  H4   C8   N7   124.56  3.000
 H84  N9   C8   N7   113.09  3.000
 H84  C1'  N9   C8   127.83  3.000
 H84  C8   N9   C4   106.36  3.000
 H84  C1'  N9   C4   125.79  3.000
 H84  O5'  PA   O3A   96.75  3.000
 H84  O3A  PA   O2A  109.95  3.000
 H84  O5'  PA   O2A  105.13  3.000
 H84  O2A  PA   O1A  120.90  3.000
 H84  O3A  PA   O1A  112.05  3.000
 H84  O5'  PA   O1A  109.06  3.000
 H84  C3B  PB   O3A  100.50  3.000
 H84  C3B  PB   O1B  108.71  3.000
 H84  O3A  PB   O1B  106.65  3.000
 H84  C3B  PB   O2B  109.44  3.000
 H84  O1B  PB   O2B  120.82  3.000
 H84  O3A  PB   O2B  108.79  3.000
 H84  O3G  PG   C3B  102.93  3.000
 H84  O3G  PG   O2G  114.87  3.000
 H84  C3B  PG   O2G  103.88  3.000
 H84  O2G  PG   O1G  114.91  3.000
 H84  O3G  PG   O1G  114.95  3.000
 H84  C3B  PG   O1G  102.93  3.000
 H84  H5   C1'  O4'  110.48  3.000
 H84  H5   C1'  C2'  110.86  3.000
 H84  O4'  C1'  C2'  106.29  3.000
 H84  H5   C1'  N9   105.61  3.000
 H84  O4'  C1'  N9   109.16  3.000
 H84  C2'  C1'  N9   114.46  3.000
 H84  H9   C2'  H8   107.45  3.000
 H84  H9   C2'  C3'  110.48  3.000
 H84  H8   C2'  C3'  113.70  3.000
 H84  H9   C2'  C1'  111.03  3.000
 H84  H8   C2'  C1'  112.37  3.000
 H84  C3'  C2'  C1'  101.82  3.000
 H84  H12  C3'  C4'  111.57  3.000
 H84  H12  C3'  O3'  111.56  3.000
 H84  C4'  C3'  O3'  108.18  3.000
 H84  H12  C3'  C2'  111.80  3.000
 H84  C4'  C3'  C2'  100.87  3.000
 H84  O3'  C3'  C2'  112.34  3.000
 H84  H13  O3'  C3'  108.39  3.000
 H84  PB   O3A  PA   129.33  3.000
 H84  BR2  C3B  BR1  106.73  3.000
 H84  BR2  C3B  PG   108.07  3.000
 H84  BR1  C3B  PG   108.24  3.000
 H84  PG   C3B  PB   116.40  3.000
 H84  BR2  C3B  PB   108.28  3.000
 H84  BR1  C3B  PB   108.72  3.000
 H84  H14  C4'  C5'  109.90  3.000
 H84  H14  C4'  O4'  107.69  3.000
 H84  C5'  C4'  O4'  111.54  3.000
 H84  H14  C4'  C3'  111.66  3.000
 H84  C5'  C4'  C3'  110.59  3.000
 H84  O4'  C4'  C3'  105.35  3.000
 H84  C4'  O4'  C1'  110.86  3.000
 H84  H16  C5'  H15  106.67  3.000
 H84  H16  C5'  O5'  110.97  3.000
 H84  H15  C5'  O5'  111.70  3.000
 H84  H16  C5'  C4'  109.99  3.000
 H84  H15  C5'  C4'  108.11  3.000
 H84  O5'  C5'  C4'  109.34  3.000
 H84  C5'  O5'  PA   118.42  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  -173.13  30.0  2
 H84  Var_02    O2B  PB   O3A  PA     9.70  30.0  1
 H84  Var_03    O5'  PA   O3A  PB  -177.28  30.0  3
 H84  Var_04    O3G  PG   C3B  PB   -57.61  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

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

