# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sun Jun  7 15:16:47 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: 2'-bromo-2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonoamino)phosphoryl]oxy}phosphoryl]adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3Br
#
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
 6NQ  6NQ  2'-bromo-2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonoamino)phosphoryl]oxy}phosphoryl]adenosine  ligand  43  31  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_6NQ
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
 6NQ  C4   C   CR5    0   0.477   2.7381  -1.4236   0.5545
 6NQ  C5   C   CR5    0   0.002   1.9390  -2.4056  -0.0049
 6NQ  C6   C   C      0   0.431   2.1001  -3.7186   0.4933
 6NQ  C8   C   CR15   0   0.112   1.3370  -0.5833  -0.9089
 6NQ  N1   N   N      0  -0.485   3.0900  -3.9072   1.3897
 6NQ  N3   N   N      0  -0.468   3.6913  -1.5962   1.4676
 6NQ  PG   P   P      0   1.237  -2.2386  -3.9182   0.0242
 6NQ  O1G  O   OP    -1  -0.891  -2.2073  -4.3038   1.4967
 6NQ  O2G  O   OP    -1  -0.875  -1.0902  -4.5712  -0.7963
 6NQ  O3G  O   O      0  -0.889  -3.5995  -4.0838  -0.6437
 6NQ  PB   P   P      0   1.288  -2.9853  -1.0304  -0.3798
 6NQ  O1B  O   OP    -1  -0.826  -4.0385  -1.0462   0.6931
 6NQ  O2B  O   O      0  -0.831  -3.4203  -0.9179  -1.8183
 6NQ  N3B  N   NH1    0  -1.014  -1.8416  -2.2136  -0.0787
 6NQ  PA   P   P      0   1.364  -1.8553   1.5752  -1.0777
 6NQ  O1A  O   OP    -1  -0.806  -1.0835   1.2191  -2.3182
 6NQ  O2A  O   O      0  -0.802  -3.1508   2.3196  -1.1861
 6NQ  O3A  O   O2     0  -0.755  -2.0023   0.3076  -0.0751
 6NQ  C5'  C   CH2    0  -0.154   0.2886   3.0858  -0.5900
 6NQ  C4'  C   CH1    0  -0.041   1.4133   3.0205   0.4345
 6NQ  O4'  O   O2     0  -0.478   1.5772   1.7017   0.9497
 6NQ  C3'  C   CH1    0   0.019   2.7546   3.3792  -0.2057
 6NQ  O3'  O   OH1    0  -0.658   3.6138   3.8465   0.7928
 6NQ  C2'  C   CH1    0  -0.470   3.1470   1.9981  -0.7355
 6NQ  BR   BR  BR     0  -0.061   5.0244   1.7930  -1.1621
 6NQ  C1'  C   CH1    0   0.256   2.6998   1.0714   0.3946
 6NQ  N9   N   NR5    0  -0.541   2.3411  -0.2518  -0.0358
 6NQ  N7   N   N      0  -0.476   1.0834  -1.8557  -0.9278
 6NQ  N6   N   NH2    0  -0.862   1.3365  -4.7389   0.1253
 6NQ  C2   C   C1     0   0.038   3.8061  -2.8712   1.8063
 6NQ  H1   H   HCR5   0   0.296   0.7961   0.1477  -1.4953
 6NQ  H5   H   HNH1   0   0.399  -0.9492  -2.0613  -0.5372
 6NQ  H7   H   HCH2   0   0.210   0.6031   2.6289  -1.5323
 6NQ  H8   H   HCH2   0   0.221   0.1005   4.1456  -0.8045
 6NQ  H9   H   HCH1   0   0.267   1.1937   3.6839   1.2752
 6NQ  H10  H   HCH1   0   0.274   2.6376   4.0987  -1.0238
 6NQ  H11  H   HOH1   0   0.461   4.4199   4.1811   0.3861
 6NQ  H12  H   HCH1   0   0.331   2.6050   1.7828  -1.6586
 6NQ  H13  H   HCH1   0   0.273   3.4859   0.9485   1.1459
 6NQ  H14  H   HNH2   0   0.440   0.3480  -4.6097  -0.2817
 6NQ  H15  H   HNH2   0   0.365   1.5083  -5.5998   0.6216
 6NQ  H16  H   H      0   0.242   4.5832  -3.1014   2.5288
 6NQ  O5'  O   O2     0  -0.622  -0.8622   2.4633  -0.0849

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
 6NQ  O3'  C3'  single    1.398  0.020  1.398
 6NQ  BR   C2'  single    1.936  0.020  1.936
 6NQ  C3'  C2'  single    1.530  0.020  1.530
 6NQ  C3'  C4'  single    1.529  0.020  1.529
 6NQ  C2'  C1'  single    1.528  0.020  1.528
 6NQ  C4'  O4'  single    1.425  0.020  1.425
 6NQ  C4'  C5'  single    1.523  0.020  1.523
 6NQ  O2B  PB   deloc     1.507  0.020  1.507
 6NQ  C1'  O4'  single    1.402  0.020  1.402
 6NQ  C1'  N9   single    1.437  0.020  1.437
 6NQ  N3   C2   aromatic  1.324  0.020  1.324
 6NQ  N3   C4   aromatic  1.331  0.020  1.331
 6NQ  C2   N1   aromatic  1.326  0.020  1.326
 6NQ  C5'  O5'  single    1.402  0.020  1.402
 6NQ  N9   C4   aromatic  1.371  0.020  1.371
 6NQ  N9   C8   aromatic  1.371  0.020  1.371
 6NQ  C4   C5   aromatic  1.384  0.020  1.384
 6NQ  O3G  PG   deloc     1.525  0.020  1.525
 6NQ  O3A  PB   single    1.688  0.020  1.688
 6NQ  O3A  PA   single    1.623  0.020  1.623
 6NQ  PB   O1B  deloc     1.504  0.020  1.504
 6NQ  PB   N3B  single    1.673  0.020  1.673
 6NQ  O5'  PA   single    1.662  0.020  1.662
 6NQ  N1   C6   aromatic  1.349  0.020  1.349
 6NQ  O2G  PG   deloc     1.555  0.020  1.555
 6NQ  PA   O2A  deloc     1.498  0.020  1.498
 6NQ  PA   O1A  deloc     1.504  0.020  1.504
 6NQ  PG   N3B  single    1.753  0.020  1.753
 6NQ  PG   O1G  deloc     1.522  0.020  1.522
 6NQ  C8   N7   aromatic  1.298  0.020  1.298
 6NQ  C5   C6   aromatic  1.414  0.020  1.414
 6NQ  C5   N7   aromatic  1.373  0.020  1.373
 6NQ  C6   N6   single    1.326  0.020  1.326
 6NQ  C8   H1   single    0.930  0.020  1.080
 6NQ  N3B  H5   single    0.890  0.020  1.040
 6NQ  C5'  H7   single    0.970  0.020  1.090
 6NQ  C5'  H8   single    0.970  0.020  1.090
 6NQ  C4'  H9   single    0.970  0.020  1.090
 6NQ  C3'  H10  single    0.970  0.020  1.090
 6NQ  O3'  H11  single    0.850  0.020  0.980
 6NQ  C2'  H12  single    0.970  0.020  1.090
 6NQ  C1'  H13  single    0.970  0.020  1.090
 6NQ  N6   H14  single    0.890  0.020  1.040
 6NQ  N6   H15  single    0.890  0.020  1.040
 6NQ  C2   H16  single    0.930  0.020  1.080

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
 6NQ  N9   C4   N3   127.84  3.000
 6NQ  N9   C4   C5   105.38  3.000
 6NQ  N3   C4   C5   126.78  3.000
 6NQ  N7   C5   C6   132.83  3.000
 6NQ  N7   C5   C4   110.31  3.000
 6NQ  C6   C5   C4   116.79  3.000
 6NQ  N6   C6   N1   119.96  3.000
 6NQ  N6   C6   C5   123.44  3.000
 6NQ  N1   C6   C5   116.61  3.000
 6NQ  H1   C8   N7   123.84  3.000
 6NQ  H1   C8   N9   123.21  3.000
 6NQ  N7   C8   N9   112.92  3.000
 6NQ  C2   N1   C6   119.72  3.000
 6NQ  C2   N3   C4   111.24  3.000
 6NQ  N3B  PG   O3G  106.37  3.000
 6NQ  N3B  PG   O2G  102.12  3.000
 6NQ  O3G  PG   O2G  112.48  3.000
 6NQ  N3B  PG   O1G  107.36  3.000
 6NQ  O2G  PG   O1G  112.88  3.000
 6NQ  O3G  PG   O1G  114.48  3.000
 6NQ  O3A  PB   N3B   97.47  3.000
 6NQ  N3B  PB   O2B  114.96  3.000
 6NQ  O3A  PB   O2B  106.33  3.000
 6NQ  N3B  PB   O1B  110.06  3.000
 6NQ  O3A  PB   O1B  106.70  3.000
 6NQ  O2B  PB   O1B  118.67  3.000
 6NQ  H5   N3B  PB   114.44  3.000
 6NQ  H5   N3B  PG   111.81  3.000
 6NQ  PB   N3B  PG   122.92  3.000
 6NQ  O5'  PA   O3A   95.88  3.000
 6NQ  O5'  PA   O2A  107.13  3.000
 6NQ  O3A  PA   O2A  110.76  3.000
 6NQ  O2A  PA   O1A  120.12  3.000
 6NQ  O5'  PA   O1A  108.23  3.000
 6NQ  O3A  PA   O1A  111.79  3.000
 6NQ  PA   O3A  PB   124.08  3.000
 6NQ  H8   C5'  H7   106.52  3.000
 6NQ  H8   C5'  C4'  107.43  3.000
 6NQ  H7   C5'  C4'  110.45  3.000
 6NQ  H8   C5'  O5'  111.00  3.000
 6NQ  H7   C5'  O5'  111.16  3.000
 6NQ  C4'  C5'  O5'  110.16  3.000
 6NQ  H9   C4'  C3'  110.85  3.000
 6NQ  H9   C4'  O4'  107.85  3.000
 6NQ  C3'  C4'  O4'  105.52  3.000
 6NQ  H9   C4'  C5'  110.06  3.000
 6NQ  O4'  C4'  C5'  111.58  3.000
 6NQ  C3'  C4'  C5'  110.86  3.000
 6NQ  C1'  O4'  C4'  111.40  3.000
 6NQ  H10  C3'  C2'  111.19  3.000
 6NQ  H10  C3'  O3'  112.30  3.000
 6NQ  C2'  C3'  O3'  113.04  3.000
 6NQ  H10  C3'  C4'  111.90  3.000
 6NQ  C2'  C3'  C4'   99.10  3.000
 6NQ  O3'  C3'  C4'  108.58  3.000
 6NQ  H11  O3'  C3'  109.22  3.000
 6NQ  H12  C2'  C1'  111.12  3.000
 6NQ  H12  C2'  BR   105.92  3.000
 6NQ  C1'  C2'  BR   112.48  3.000
 6NQ  H12  C2'  C3'  110.08  3.000
 6NQ  C1'  C2'  C3'  102.48  3.000
 6NQ  BR   C2'  C3'  114.87  3.000
 6NQ  H13  C1'  N9   106.35  3.000
 6NQ  H13  C1'  C2'  111.44  3.000
 6NQ  N9   C1'  C2'  114.20  3.000
 6NQ  H13  C1'  O4'  110.72  3.000
 6NQ  N9   C1'  O4'  109.43  3.000
 6NQ  C2'  C1'  O4'  104.74  3.000
 6NQ  C1'  N9   C8   126.59  3.000
 6NQ  C8   N9   C4   106.23  3.000
 6NQ  C1'  N9   C4   125.87  3.000
 6NQ  C8   N7   C5   105.14  3.000
 6NQ  H15  N6   H14  116.41  3.000
 6NQ  H15  N6   C6   114.97  3.000
 6NQ  H14  N6   C6   122.76  3.000
 6NQ  H16  C2   N3   115.88  3.000
 6NQ  H16  C2   N1   115.45  3.000
 6NQ  N3   C2   N1   128.67  3.000
 6NQ  C5'  O5'  PA   120.83  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
 6NQ  CONST_01  N1   C2   N3   C4      0.00   0.0  0
 6NQ  CONST_02  N7   C8   N9   C4      0.00   0.0  0
 6NQ  CONST_03  N1   C6   C5   C4      0.00   0.0  0
 6NQ  CONST_04  C8   N7   C5   C4      0.00   0.0  0
 6NQ  CONST_05  C2   N3   C4   C5      0.00   0.0  0
 6NQ  CONST_06  C8   N9   C4   C5      0.00   0.0  0
 6NQ  CONST_07  C2   N1   C6   C5      0.00   0.0  0
 6NQ  CONST_08  N9   C8   N7   C5      0.00   0.0  0
 6NQ  CONST_09  N3   C2   N1   C6      0.00   0.0  0
 6NQ  CONST_10  N3   C4   C5   C6      0.00   0.0  0
 6NQ  CONST_11  N9   C4   C5   C6    180.00   0.0  0
 6NQ  CONST_12  C8   N7   C5   C6    180.00   0.0  0
 6NQ  CONST_13  N3   C4   N9   C8    180.00   0.0  0
 6NQ  CONST_14  N7   C5   C6   N1    180.00   0.0  0
 6NQ  CONST_15  N7   C5   C4   N3    180.00   0.0  0
 6NQ  CONST_16  C2   N3   C4   N9    180.00   0.0  0
 6NQ  CONST_17  N7   C5   C4   N9      0.00   0.0  0
 6NQ  CONST_18  C1'  N9   C4   C5    180.00   0.0  0
 6NQ  CONST_19  C1'  N9   C4   N3      0.00   0.0  0
 6NQ  CONST_20  N7   C8   N9   C1'   180.00   0.0  0
 6NQ  CONST_21  N6   C6   C5   C4    180.00   0.0  0
 6NQ  CONST_22  N6   C6   C5   N7      0.00   0.0  0
 6NQ  CONST_23  C2   N1   C6   N6    180.00   0.0  0
 6NQ  CONST_24  H16  C2   N3   C4    180.00   0.0  0
 6NQ  CONST_25  H1   C8   N9   C4    180.00   0.0  0
 6NQ  CONST_27  H15  N6   C6   C5    180.00   0.0  0
 6NQ  Var_01    C4'  C5'  O5'  PA   -143.02  30.0  2
 6NQ  Var_02    O2B  PB   N3B  PG    -77.40  30.0  1
 6NQ  Var_03    PB   N3B  PG   O1G  -104.84  30.0  3
 6NQ  Var_04    O5'  PA   O3A  PB    176.32  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
 6NQ  chir_03  C4'  C3'  O4'  C5'  positiv
 6NQ  chir_04  C3'  O3'  C2'  C4'  negativ
 6NQ  chir_05  C2'  BR   C1'  C3'  negativ
 6NQ  chir_06  C1'  O4'  N9   C2'  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
 6NQ  plan-1  C4   0.020
 6NQ  plan-1  C5   0.020
 6NQ  plan-1  C6   0.020
 6NQ  plan-1  C8   0.020
 6NQ  plan-1  N1   0.020
 6NQ  plan-1  N3   0.020
 6NQ  plan-1  C1'  0.020
 6NQ  plan-1  N9   0.020
 6NQ  plan-1  N7   0.020
 6NQ  plan-1  N6   0.020
 6NQ  plan-1  C2   0.020
 6NQ  plan-1  H1   0.020
 6NQ  plan-1  H16  0.020
 6NQ  plan-2  C6   0.020
 6NQ  plan-2  N6   0.020
 6NQ  plan-2  H14  0.020
 6NQ  plan-2  H15  0.020

