# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 30 08:48:15 2021
#   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  47  31  .  2021-08-05  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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   CR56  0   0.496  62.1546  12.4344  -61.8089
 6NQ  C5   C   CR56  0  -0.010  62.6111  12.0568  -60.5577
 6NQ  C6   C   CR6   0   0.463  63.8894  12.5201  -60.1948
 6NQ  C8   C   CR15  0   0.117  60.6926  11.1934  -60.7477
 6NQ  N1   N   N     0  -0.474  64.5512  13.2811  -61.0745
 6NQ  N3   N   N     0  -0.457  62.7988  13.1887  -62.6938
 6NQ  PG   P   P     0   1.415  56.1251   5.6810  -60.4959
 6NQ  O1G  O   OH1   0  -0.756  56.6374   6.2382  -59.1053
 6NQ  O2G  O   OH1   0  -0.722  55.4820   4.3281  -59.9607
 6NQ  O3G  O   O     0  -0.698  57.0849   5.6097  -61.6151
 6NQ  PB   P   P     0   1.478  54.7609   7.5475  -62.3526
 6NQ  O1B  O   OH1   0  -0.724  53.3804   8.2990  -62.1405
 6NQ  O2B  O   O     0  -0.660  54.9913   6.8744  -63.6369
 6NQ  N3B  N   NH1   0  -0.978  54.8273   6.6702  -60.9434
 6NQ  PA   P   P     0   1.534  56.4488   9.4642  -60.8611
 6NQ  O1A  O   OH1   0  -0.725  55.1087  10.0318  -60.2410
 6NQ  O2A  O   O     0  -0.688  57.3143   8.6483  -59.9801
 6NQ  O3A  O   O2    0  -0.701  55.8979   8.7192  -62.1702
 6NQ  C5'  C   CH2   0  -0.211  56.7033  11.7072  -62.2720
 6NQ  C4'  C   CH1   0  -0.019  57.7147  12.1636  -63.2941
 6NQ  O4'  O   O2    0  -0.487  58.8673  12.6824  -62.6376
 6NQ  C3'  C   CH1   0   0.012  58.2132  11.0680  -64.2627
 6NQ  O3'  O   OH1   0  -0.653  58.5018  11.5915  -65.5258
 6NQ  C2'  C   CH1   0  -0.443  59.5161  10.6711  -63.5904
 6NQ  BR   BR  BR    0  -0.050  60.8077   9.8145  -64.7447
 6NQ  C1'  C   CH1   0   0.252  60.0260  12.0028  -63.0401
 6NQ  N9   N   NR5   0  -0.546  60.9163  11.8643  -61.9245
 6NQ  N7   N   N     0  -0.445  61.6805  11.2828  -59.9115
 6NQ  N6   N   NH2   0  -0.815  64.4543  12.2384  -59.0211
 6NQ  C2   C   CR16  0   0.048  63.9830  13.5660  -62.2424
 6NQ  H1   H   HCR5  0   0.292  59.7747  10.6563  -60.5609
 6NQ  H2   H   HOH1  0   0.502  56.9713   7.1614  -59.2213
 6NQ  H3   H   HOH1  0   0.504  55.1694   3.7376  -60.6591
 6NQ  H4   H   HOH1  0   0.511  52.9435   8.5681  -62.9609
 6NQ  H5   H   HNH1  0   0.450  54.0421   6.7555  -60.3065
 6NQ  H6   H   HOH1  0   0.514  55.1778  10.3513  -59.3294
 6NQ  H7   H   HCH2  0   0.283  56.4340  12.5322  -61.6114
 6NQ  H8   H   HCH2  0   0.263  55.8012  11.3767  -62.7914
 6NQ  H9   H   HCH1  0   0.284  57.2318  12.9626  -63.8676
 6NQ  H10  H   HCH1  0   0.270  57.5135  10.2265  -64.3164
 6NQ  H11  H   HOH1  0   0.466  57.6739  11.8177  -65.9623
 6NQ  H12  H   HCH1  0   0.334  59.3147   9.9657  -62.7837
 6NQ  H13  H   HCH1  0   0.278  60.5724  12.5672  -63.8022
 6NQ  H14  H   HNH2  0   0.405  65.3832  12.5635  -58.8155
 6NQ  H15  H   HNH2  0   0.412  64.0010  11.6384  -58.3548
 6NQ  H16  H   HCR6  0   0.254  64.5713  14.1890  -62.9074
 6NQ  O5'  O   O2    0  -0.572  57.2787  10.6576  -61.4801

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    1.397  0.020  1.397
 6NQ  BR   C2'  single    1.932  0.020  1.932
 6NQ  C3'  C2'  single    1.519  0.020  1.519
 6NQ  C3'  C4'  single    1.545  0.020  1.545
 6NQ  C2'  C1'  single    1.528  0.020  1.528
 6NQ  C4'  O4'  single    1.424  0.020  1.424
 6NQ  C4'  C5'  single    1.509  0.020  1.509
 6NQ  O2B  PB   double    1.468  0.020  1.468
 6NQ  C1'  O4'  single    1.402  0.020  1.402
 6NQ  C1'  N9   single    1.434  0.020  1.434
 6NQ  N3   C2   aromatic  1.322  0.020  1.322
 6NQ  N3   C4   aromatic  1.329  0.020  1.329
 6NQ  C2   N1   aromatic  1.330  0.020  1.330
 6NQ  C5'  O5'  single    1.435  0.020  1.435
 6NQ  N9   C4   aromatic  1.368  0.020  1.368
 6NQ  N9   C8   aromatic  1.373  0.020  1.373
 6NQ  C4   C5   aromatic  1.384  0.020  1.384
 6NQ  O3G  PG   double    1.476  0.020  1.476
 6NQ  O3A  PB   single    1.643  0.020  1.643
 6NQ  O3A  PA   single    1.604  0.020  1.604
 6NQ  PB   O1B  single    1.586  0.020  1.586
 6NQ  PB   N3B  single    1.661  0.020  1.661
 6NQ  O5'  PA   single    1.580  0.020  1.580
 6NQ  N1   C6   aromatic  1.338  0.020  1.338
 6NQ  O2G  PG   single    1.591  0.020  1.591
 6NQ  PA   O2A  double    1.480  0.020  1.480
 6NQ  PA   O1A  single    1.582  0.020  1.582
 6NQ  PG   N3B  single    1.692  0.020  1.692
 6NQ  PG   O1G  single    1.583  0.020  1.583
 6NQ  C8   N7   aromatic  1.297  0.020  1.297
 6NQ  C5   C6   aromatic  1.407  0.020  1.407
 6NQ  C5   N7   aromatic  1.372  0.020  1.372
 6NQ  C6   N6   single    1.333  0.020  1.333
 6NQ  C8   H1   single    0.930  0.020  1.080
 6NQ  O1G  H2   single    0.850  0.020  0.980
 6NQ  O2G  H3   single    0.850  0.020  0.980
 6NQ  O1B  H4   single    0.850  0.020  0.980
 6NQ  N3B  H5   single    0.860  0.020  1.020
 6NQ  O1A  H6   single    0.850  0.020  0.980
 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    0.860  0.020  1.020
 6NQ  N6   H15  single    0.860  0.020  1.020
 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   128.23  3.000
 6NQ  N9   C4   C5   105.14  3.000
 6NQ  N3   C4   C5   126.63  3.000
 6NQ  N7   C5   C6   132.87  3.000
 6NQ  N7   C5   C4   110.85  3.000
 6NQ  C6   C5   C4   116.29  3.000
 6NQ  N6   C6   N1   119.31  3.000
 6NQ  N6   C6   C5   122.86  3.000
 6NQ  N1   C6   C5   117.83  3.000
 6NQ  H1   C8   N7   124.75  3.000
 6NQ  H1   C8   N9   122.00  3.000
 6NQ  N7   C8   N9   113.25  3.000
 6NQ  C2   N1   C6   119.21  3.000
 6NQ  C2   N3   C4   111.63  3.000
 6NQ  N3B  PG   O3G  109.05  3.000
 6NQ  N3B  PG   O2G  106.03  3.000
 6NQ  O3G  PG   O2G  118.48  3.000
 6NQ  N3B  PG   O1G  105.95  3.000
 6NQ  O2G  PG   O1G   97.74  3.000
 6NQ  O3G  PG   O1G  118.20  3.000
 6NQ  H2   O1G  PG   109.57  3.000
 6NQ  H3   O2G  PG   114.04  3.000
 6NQ  O3A  PB   N3B  104.76  3.000
 6NQ  N3B  PB   O2B  119.58  3.000
 6NQ  O3A  PB   O2B  108.39  3.000
 6NQ  N3B  PB   O1B   99.88  3.000
 6NQ  O3A  PB   O1B  104.45  3.000
 6NQ  O2B  PB   O1B  118.08  3.000
 6NQ  H4   O1B  PB   114.30  3.000
 6NQ  H5   N3B  PB   117.21  3.000
 6NQ  H5   N3B  PG   118.46  3.000
 6NQ  PB   N3B  PG   124.31  3.000
 6NQ  O5'  PA   O3A  102.21  3.000
 6NQ  O5'  PA   O2A  110.02  3.000
 6NQ  O3A  PA   O2A  115.51  3.000
 6NQ  O2A  PA   O1A  117.38  3.000
 6NQ  O5'  PA   O1A  109.12  3.000
 6NQ  O3A  PA   O1A  101.28  3.000
 6NQ  H6   O1A  PA   115.27  3.000
 6NQ  PA   O3A  PB   131.27  3.000
 6NQ  H8   C5'  H7   108.25  3.000
 6NQ  H8   C5'  C4'  108.85  3.000
 6NQ  H7   C5'  C4'  110.30  3.000
 6NQ  H8   C5'  O5'  111.86  3.000
 6NQ  H7   C5'  O5'  108.54  3.000
 6NQ  C4'  C5'  O5'  109.04  3.000
 6NQ  H9   C4'  C3'  109.34  3.000
 6NQ  H9   C4'  O4'  109.41  3.000
 6NQ  C3'  C4'  O4'  106.63  3.000
 6NQ  H9   C4'  C5'  106.25  3.000
 6NQ  O4'  C4'  C5'  109.90  3.000
 6NQ  C3'  C4'  C5'  115.24  3.000
 6NQ  C1'  O4'  C4'  111.08  3.000
 6NQ  H10  C3'  C2'  111.64  3.000
 6NQ  H10  C3'  O3'  112.04  3.000
 6NQ  C2'  C3'  O3'  108.71  3.000
 6NQ  H10  C3'  C4'  111.67  3.000
 6NQ  C2'  C3'  C4'  100.64  3.000
 6NQ  O3'  C3'  C4'  111.57  3.000
 6NQ  H11  O3'  C3'  108.67  3.000
 6NQ  H12  C2'  C1'  111.03  3.000
 6NQ  H12  C2'  BR   106.18  3.000
 6NQ  C1'  C2'  BR   112.22  3.000
 6NQ  H12  C2'  C3'  109.76  3.000
 6NQ  C1'  C2'  C3'  102.58  3.000
 6NQ  BR   C2'  C3'  115.14  3.000
 6NQ  H13  C1'  N9   106.35  3.000
 6NQ  H13  C1'  C2'  111.42  3.000
 6NQ  N9   C1'  C2'  113.77  3.000
 6NQ  H13  C1'  O4'  111.25  3.000
 6NQ  N9   C1'  O4'  109.66  3.000
 6NQ  C2'  C1'  O4'  104.48  3.000
 6NQ  C1'  N9   C8   127.79  3.000
 6NQ  C8   N9   C4   106.18  3.000
 6NQ  C1'  N9   C4   125.98  3.000
 6NQ  C8   N7   C5   104.58  3.000
 6NQ  H15  N6   H14  118.32  3.000
 6NQ  H15  N6   C6   121.27  3.000
 6NQ  H14  N6   C6   120.22  3.000
 6NQ  H16  C2   N3   116.12  3.000
 6NQ  H16  C2   N1   115.46  3.000
 6NQ  N3   C2   N1   128.42  3.000
 6NQ  C5'  O5'  PA   123.91  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_26  H14  N6   C6   C5    180.00   0.0  0
 6NQ  CONST_27  H15  N6   C6   C5      0.00   0.0  0
 6NQ  Var_01    C4'  C5'  O5'  PA   -147.84  30.0  1
 6NQ  Var_02    O2B  PB   N3B  PG     52.70  30.0  2
 6NQ  Var_03    PB   N3B  PG   O1G   121.70  30.0  3
 6NQ  Var_04    O5'  PA   O3A  PB   -168.29  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
 6NQ  chir_07  PB   O3A  O1B  N3B  both
 6NQ  chir_08  PA   O5'  O2A  O1A  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
 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

