# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 05:07:22 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: 5'-azido-8-bromo-5'-deoxyadenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n([C@@H]3O[C@H](CN=[N+]=[N-])[C@@H](O)[C@H]3O)c(Br)nc12
#
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
 Z8B  Z8B  5'-azido-8-bromo-5'-deoxyadenosine  ligand  33  22  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Z8B
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
 Z8B  N1    N   N      0  -0.471  -4.5739  -0.6640   1.1929
 Z8B  C2    C   CR16   0   0.052  -3.7537  -1.7086   1.2485
 Z8B  N3    N   N      0  -0.459  -2.4800  -1.7731   0.8973
 Z8B  C4    C   CR56   0   0.510  -2.0357  -0.6065   0.4448
 Z8B  C5    C   CR56   0  -0.001  -2.7643   0.5615   0.3325
 Z8B  C6    C   CR6    0   0.466  -4.1124   0.5048   0.7340
 Z8B  N6    N   NH2    0  -0.814  -4.9285   1.5545   0.6739
 Z8B  N7    N   N      0  -0.419  -1.9845   1.5738  -0.1622
 Z8B  C8    C   CR5    0   0.295  -0.8284   1.0280  -0.3443
 Z8B  BR8   BR  BR     0   0.045   0.6137   1.9896  -0.9957
 Z8B  N9    N   NR5    0  -0.571  -0.7724  -0.3020  -0.0015
 Z8B  C1'   C   CH1    0   0.215   0.3013  -1.2636  -0.0365
 Z8B  C2'   C   CH1    0  -0.001   0.8844  -1.5808  -1.4100
 Z8B  O2'   O   OH1    0  -0.651  -0.0106  -2.3676  -2.1248
 Z8B  C3'   C   CH1    0  -0.058   2.2038  -2.2426  -0.9970
 Z8B  O3'   O   OH1    0  -0.663   1.9373  -3.5858  -0.6976
 Z8B  C4'   C   CH1    0   0.004   2.5830  -1.4248   0.2515
 Z8B  C5'   C   CH2    0  -0.334   3.6185  -0.3511  -0.0278
 Z8B  O5'   O   O2     0  -0.496   1.3804  -0.8164   0.7321
 Z8B  N51   N   N      0  -0.359   3.9526   0.4042   1.1778
 Z8B  N52   N   N      1   0.361   3.1828   1.2817   1.5256
 Z8B  N53   N   N     -1  -0.218   2.5640   2.1244   1.9376
 Z8B  H2    H   HCR6   0   0.257  -4.1895  -2.6247   1.6316
 Z8B  H1N6  H   HNH2   0   0.415  -4.6118   2.4440   0.3299
 Z8B  H2N6  H   HNH2   0   0.407  -5.8835   1.4735   0.9780
 Z8B  H1'   H   HCH1   0   0.267  -0.1376  -2.1786   0.3784
 Z8B  H2'   H   HCH1   0   0.245   1.1262  -0.6541  -1.9423
 Z8B  HO2'  H   HOH1   0   0.465   0.2819  -2.4193  -3.0399
 Z8B  H3'   H   HCH1   0   0.257   2.9677  -2.1467  -1.7787
 Z8B  HO3'  H   HOH1   0   0.459   2.7559  -4.0028  -0.4106
 Z8B  H4'   H   HCH1   0   0.263   2.9790  -2.0867   1.0290
 Z8B  H15'  H   HCH2   0   0.279   4.5430  -0.8346  -0.3391
 Z8B  H25'  H   HCH2   0   0.254   3.3062   0.3087  -0.8422

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
 Z8B  N53  N52   double    1.124  0.020  1.124
 Z8B  N52  N51   double    1.218  0.020  1.218
 Z8B  N51  C5'   single    1.461  0.020  1.461
 Z8B  N6   C6    single    1.331  0.020  1.331
 Z8B  N7   C5    aromatic  1.370  0.020  1.370
 Z8B  N7   C8    aromatic  1.291  0.020  1.291
 Z8B  C6   C5    aromatic  1.408  0.020  1.408
 Z8B  C6   N1    aromatic  1.338  0.020  1.338
 Z8B  C5   C4    aromatic  1.381  0.020  1.381
 Z8B  BR8  C8    single    1.852  0.020  1.852
 Z8B  C8   N9    aromatic  1.375  0.020  1.375
 Z8B  N1   C2    aromatic  1.329  0.020  1.329
 Z8B  O5'  C4'   single    1.431  0.020  1.431
 Z8B  O5'  C1'   single    1.398  0.020  1.398
 Z8B  C5'  C4'   single    1.518  0.020  1.518
 Z8B  C4   N9    aromatic  1.374  0.020  1.374
 Z8B  C4   N3    aromatic  1.328  0.020  1.328
 Z8B  N9   C1'   single    1.442  0.020  1.442
 Z8B  C2   N3    aromatic  1.323  0.020  1.323
 Z8B  C4'  C3'   single    1.540  0.020  1.540
 Z8B  C1'  C2'   single    1.525  0.020  1.525
 Z8B  C2'  C3'   single    1.533  0.020  1.533
 Z8B  C2'  O2'   single    1.390  0.020  1.390
 Z8B  C3'  O3'   single    1.402  0.020  1.402
 Z8B  C2   H2    single    0.930  0.020  1.080
 Z8B  N6   H1N6  single    0.860  0.020  1.020
 Z8B  N6   H2N6  single    0.860  0.020  1.020
 Z8B  C1'  H1'   single    0.970  0.020  1.090
 Z8B  C2'  H2'   single    0.970  0.020  1.090
 Z8B  O2'  HO2'  single    0.850  0.020  0.980
 Z8B  C3'  H3'   single    0.970  0.020  1.090
 Z8B  O3'  HO3'  single    0.850  0.020  0.980
 Z8B  C4'  H4'   single    0.970  0.020  1.090
 Z8B  C5'  H15'  single    0.970  0.020  1.090
 Z8B  C5'  H25'  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
 Z8B  C6    N1   C2    119.21  3.000
 Z8B  H2    C2   N3    116.07  3.000
 Z8B  H2    C2   N1    115.51  3.000
 Z8B  N3    C2   N1    128.41  3.000
 Z8B  C4    N3   C2    111.71  3.000
 Z8B  N9    C4   C5    105.74  3.000
 Z8B  N9    C4   N3    127.81  3.000
 Z8B  C5    C4   N3    126.45  3.000
 Z8B  N7    C5   C6    132.66  3.000
 Z8B  C6    C5   C4    116.61  3.000
 Z8B  N7    C5   C4    110.73  3.000
 Z8B  N6    C6   C5    122.86  3.000
 Z8B  C5    C6   N1    117.60  3.000
 Z8B  N6    C6   N1    119.54  3.000
 Z8B  H2N6  N6   H1N6  118.31  3.000
 Z8B  H2N6  N6   C6    120.34  3.000
 Z8B  H1N6  N6   C6    121.35  3.000
 Z8B  C8    N7   C5    104.36  3.000
 Z8B  N9    C8   BR8   123.95  3.000
 Z8B  N9    C8   N7    114.22  3.000
 Z8B  BR8   C8   N7    121.82  3.000
 Z8B  C1'   N9   C8    132.04  3.000
 Z8B  C1'   N9   C4    123.01  3.000
 Z8B  C8    N9   C4    104.94  3.000
 Z8B  H1'   C1'  O5'   111.58  3.000
 Z8B  H1'   C1'  C2'   108.68  3.000
 Z8B  O5'   C1'  C2'   105.45  3.000
 Z8B  H1'   C1'  N9    104.44  3.000
 Z8B  C2'   C1'  N9    116.43  3.000
 Z8B  O5'   C1'  N9    110.36  3.000
 Z8B  H2'   C2'  C3'   107.82  3.000
 Z8B  H2'   C2'  O2'   111.79  3.000
 Z8B  C3'   C2'  O2'   116.65  3.000
 Z8B  H2'   C2'  C1'   110.24  3.000
 Z8B  O2'   C2'  C1'   109.55  3.000
 Z8B  C3'   C2'  C1'   100.15  3.000
 Z8B  HO2'  O2'  C2'   108.89  3.000
 Z8B  H3'   C3'  C4'   111.09  3.000
 Z8B  H3'   C3'  O3'   111.61  3.000
 Z8B  C4'   C3'  O3'   112.50  3.000
 Z8B  H3'   C3'  C2'   111.69  3.000
 Z8B  O3'   C3'  C2'   107.92  3.000
 Z8B  C4'   C3'  C2'   101.60  3.000
 Z8B  HO3'  O3'  C3'   108.49  3.000
 Z8B  H4'   C4'  O5'   108.81  3.000
 Z8B  H4'   C4'  C5'   108.15  3.000
 Z8B  O5'   C4'  C5'   109.54  3.000
 Z8B  H4'   C4'  C3'   110.10  3.000
 Z8B  C5'   C4'  C3'   113.24  3.000
 Z8B  O5'   C4'  C3'   106.93  3.000
 Z8B  H25'  C5'  H15'  107.31  3.000
 Z8B  H25'  C5'  N51   111.58  3.000
 Z8B  H15'  C5'  N51   105.74  3.000
 Z8B  H25'  C5'  C4'   111.66  3.000
 Z8B  H15'  C5'  C4'   108.54  3.000
 Z8B  N51   C5'  C4'   111.70  3.000
 Z8B  C4'   O5'  C1'   109.15  3.000
 Z8B  N52   N51  C5'   117.61  3.000
 Z8B  N53   N52  N51   173.20  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
 Z8B  CONST_01  N7    C5   C6   N1   180.00   0.0  0
 Z8B  CONST_02  C4    C5   C6   N1     0.00   0.0  0
 Z8B  CONST_03  C4    N3   C2   N1     0.00   0.0  0
 Z8B  CONST_04  C5    C6   N1   C2     0.00   0.0  0
 Z8B  CONST_05  C5    C4   N3   C2     0.00   0.0  0
 Z8B  CONST_06  N9    C4   N3   C2   180.00   0.0  0
 Z8B  CONST_07  N7    C5   C4   N3   180.00   0.0  0
 Z8B  CONST_08  C6    C5   C4   N3     0.00   0.0  0
 Z8B  CONST_09  C8    N9   C4   N3   180.00   0.0  0
 Z8B  CONST_10  C6    N1   C2   N3     0.00   0.0  0
 Z8B  CONST_11  C8    N7   C5   C4     0.00   0.0  0
 Z8B  CONST_12  N7    C8   N9   C4     0.00   0.0  0
 Z8B  CONST_13  N9    C8   N7   C5     0.00   0.0  0
 Z8B  CONST_14  C8    N9   C4   C5     0.00   0.0  0
 Z8B  CONST_15  C8    N7   C5   C6   180.00   0.0  0
 Z8B  CONST_16  N9    C4   C5   C6   180.00   0.0  0
 Z8B  CONST_17  N9    C4   C5   N7     0.00   0.0  0
 Z8B  CONST_18  C1'   N9   C4   N3     0.00   0.0  0
 Z8B  CONST_19  C1'   N9   C4   C5   180.00   0.0  0
 Z8B  CONST_20  C1'   N9   C8   N7   180.00   0.0  0
 Z8B  CONST_21  N6    C6   N1   C2   180.00   0.0  0
 Z8B  CONST_22  N6    C6   C5   C4   180.00   0.0  0
 Z8B  CONST_23  BR8   C8   N9   C4   180.00   0.0  0
 Z8B  CONST_24  BR8   C8   N7   C5   180.00   0.0  0
 Z8B  CONST_25  N7    C5   C6   N6     0.00   0.0  0
 Z8B  CONST_26  C1'   N9   C8   BR8    0.00   0.0  0
 Z8B  CONST_27  H2    C2   N3   C4   180.00   0.0  0
 Z8B  CONST_28  H1N6  N6   C6   N1   180.00   0.0  0
 Z8B  CONST_29  H2N6  N6   C6   N1     0.00   0.0  0
 Z8B  Var_01    H15'  C5'  N51  N52  162.30  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
 Z8B  chir_01  C1'  O5'  N9   C2'  negativ
 Z8B  chir_02  C2'  O2'  C1'  C3'  negativ
 Z8B  chir_03  C3'  O3'  C4'  C2'  positiv
 Z8B  chir_04  C4'  O5'  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
 Z8B  plan-1  N1    0.020
 Z8B  plan-1  C2    0.020
 Z8B  plan-1  N3    0.020
 Z8B  plan-1  C4    0.020
 Z8B  plan-1  C5    0.020
 Z8B  plan-1  C6    0.020
 Z8B  plan-1  N6    0.020
 Z8B  plan-1  N7    0.020
 Z8B  plan-1  C8    0.020
 Z8B  plan-1  BR8   0.020
 Z8B  plan-1  N9    0.020
 Z8B  plan-1  C1'   0.020
 Z8B  plan-1  H2    0.020
 Z8B  plan-2  C6    0.020
 Z8B  plan-2  N6    0.020
 Z8B  plan-2  H1N6  0.020
 Z8B  plan-2  H2N6  0.020
 Z8B  plan-3  C5'   0.020
 Z8B  plan-3  N51   0.020
 Z8B  plan-3  N52   0.020
 Z8B  plan-3  N53   0.020

