# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 12:55:54 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: 5'-amino-8-bromo-5'-deoxyadenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2c(Br)nc3c(N)ncnc23
#
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
 5NB  5NB  5'-amino-8-bromo-5'-deoxyadenosine  ligand  33  20  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5NB
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
 5NB  O2'  O   OH1   0  -0.670  -1.1857   2.8810  -1.4253
 5NB  C2'  C   CH1   0  -0.042  -1.2651   1.5002  -1.2163
 5NB  C3'  C   CH1   0  -0.022  -2.7204   1.0475  -0.9462
 5NB  O3'  O   OH1   0  -0.660  -3.6654   1.9927  -1.3721
 5NB  C4'  C   CH1   0   0.032  -2.7648   0.8953   0.5730
 5NB  C5'  C   CH2   0  -0.302  -3.8003  -0.0921   1.0603
 5NB  N5'  N   NH2   0  -0.798  -3.8387  -0.1534   2.5108
 5NB  O4'  O   O2    0  -0.485  -1.4612   0.4586   0.9170
 5NB  C1'  C   CH1   0   0.195  -0.5461   1.1338   0.1034
 5NB  N9   N   NR5   0  -0.564   0.6389   0.3198  -0.0307
 5NB  C8   C   CR5   0   0.288   0.7927  -0.9598  -0.5006
 5NB  BR8  BR  BR    0   0.046  -0.6224  -1.9890  -1.1056
 5NB  N7   N   N     0  -0.422   2.0095  -1.3927  -0.4777
 5NB  C5   C   CR56  0  -0.001   2.7284  -0.3456   0.0382
 5NB  C4   C   CR56  0   0.508   1.9003   0.7231   0.3272
 5NB  N3   N   N     0  -0.459   2.2681   1.8904   0.8427
 5NB  C2   C   CR16  0   0.050   3.5709   1.9367   1.0670
 5NB  N1   N   N     0  -0.470   4.4825   0.9969   0.8366
 5NB  C6   C   CR6   0   0.463   4.0976  -0.1730   0.3146
 5NB  N6   N   NH2   0  -0.814   5.0053  -1.1215   0.0883
 5NB  H1   H   HOH1  0   0.449  -2.0860   3.1885  -1.6053
 5NB  H2   H   HCH1  0   0.247  -0.8318   0.9637  -2.0681
 5NB  H3   H   HCH1  0   0.246  -2.8972   0.0754  -1.4159
 5NB  H4   H   HOH1  0   0.473  -3.9513   1.7727  -2.2645
 5NB  H5   H   HCH1  0   0.233  -2.9624   1.8839   1.0185
 5NB  H6   H   HCH2  0   0.212  -4.7561   0.1932   0.5985
 5NB  H7   H   HCH2  0   0.224  -3.5510  -1.0833   0.6720
 5NB  H8   H   HNH2  0   0.342  -4.1865   0.7253   2.8755
 5NB  H9   H   HNH2  0   0.352  -4.5149  -0.8508   2.7940
 5NB  H11  H   HCH1  0   0.268  -0.2012   2.0637   0.5689
 5NB  H12  H   HCR6  0   0.257   3.9491   2.8599   1.4920
 5NB  H13  H   HNH2  0   0.406   5.9811  -0.9323   0.2411
 5NB  H14  H   HNH2  0   0.414   4.7562  -1.9771  -0.3764

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
 5NB  N6   C6   single    1.332  0.020  1.332
 5NB  C6   N1   aromatic  1.338  0.020  1.338
 5NB  C6   C5   aromatic  1.408  0.020  1.408
 5NB  N1   C2   aromatic  1.329  0.020  1.329
 5NB  N7   C5   aromatic  1.371  0.020  1.371
 5NB  N7   C8   aromatic  1.292  0.020  1.292
 5NB  C5   C4   aromatic  1.383  0.020  1.383
 5NB  C2   N3   aromatic  1.323  0.020  1.323
 5NB  C8   BR8  single    1.851  0.020  1.851
 5NB  C8   N9   aromatic  1.372  0.020  1.372
 5NB  C4   N3   aromatic  1.328  0.020  1.328
 5NB  C4   N9   aromatic  1.372  0.020  1.372
 5NB  O2'  C2'  single    1.399  0.020  1.399
 5NB  N9   C1'  single    1.444  0.020  1.444
 5NB  C2'  C1'  single    1.547  0.020  1.547
 5NB  C2'  C3'  single    1.548  0.020  1.548
 5NB  C1'  O4'  single    1.398  0.020  1.398
 5NB  C3'  O3'  single    1.403  0.020  1.403
 5NB  C3'  C4'  single    1.527  0.020  1.527
 5NB  O4'  C4'  single    1.417  0.020  1.417
 5NB  C4'  C5'  single    1.511  0.020  1.511
 5NB  C5'  N5'  single    1.452  0.020  1.452
 5NB  O2'  H1   single    0.850  0.020  0.980
 5NB  C2'  H2   single    0.970  0.020  1.090
 5NB  C3'  H3   single    0.970  0.020  1.090
 5NB  O3'  H4   single    0.850  0.020  0.980
 5NB  C4'  H5   single    0.970  0.020  1.090
 5NB  C5'  H6   single    0.970  0.020  1.090
 5NB  C5'  H7   single    0.970  0.020  1.090
 5NB  N5'  H8   single    0.890  0.020  1.040
 5NB  N5'  H9   single    0.890  0.020  1.040
 5NB  C1'  H11  single    0.970  0.020  1.090
 5NB  C2   H12  single    0.930  0.020  1.080
 5NB  N6   H13  single    0.860  0.020  1.020
 5NB  N6   H14  single    0.860  0.020  1.020

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
 5NB  H1   O2'  C2'  106.76  3.000
 5NB  H2   C2'  C1'  111.30  3.000
 5NB  H2   C2'  C3'  111.36  3.000
 5NB  C1'  C2'  C3'  102.64  3.000
 5NB  H2   C2'  O2'  110.16  3.000
 5NB  C3'  C2'  O2'  111.60  3.000
 5NB  C1'  C2'  O2'  109.57  3.000
 5NB  H3   C3'  C4'  109.50  3.000
 5NB  H3   C3'  O3'  111.07  3.000
 5NB  C4'  C3'  O3'  110.46  3.000
 5NB  H3   C3'  C2'  109.69  3.000
 5NB  C4'  C3'  C2'  103.30  3.000
 5NB  O3'  C3'  C2'  112.54  3.000
 5NB  H4   O3'  C3'  109.12  3.000
 5NB  H5   C4'  O4'  110.07  3.000
 5NB  H5   C4'  C5'  109.44  3.000
 5NB  O4'  C4'  C5'  110.52  3.000
 5NB  H5   C4'  C3'  108.53  3.000
 5NB  C5'  C4'  C3'  113.93  3.000
 5NB  O4'  C4'  C3'  104.20  3.000
 5NB  H7   C5'  H6   106.52  3.000
 5NB  H7   C5'  N5'  108.81  3.000
 5NB  H6   C5'  N5'  114.05  3.000
 5NB  H7   C5'  C4'  108.75  3.000
 5NB  H6   C5'  C4'  106.90  3.000
 5NB  N5'  C5'  C4'  111.58  3.000
 5NB  H9   N5'  H8   105.53  3.000
 5NB  H9   N5'  C5'  109.05  3.000
 5NB  H8   N5'  C5'  109.39  3.000
 5NB  C1'  O4'  C4'  108.18  3.000
 5NB  H11  C1'  N9   105.04  3.000
 5NB  H11  C1'  O4'  111.63  3.000
 5NB  N9   C1'  O4'  108.60  3.000
 5NB  H11  C1'  C2'  107.93  3.000
 5NB  O4'  C1'  C2'  107.86  3.000
 5NB  N9   C1'  C2'  115.83  3.000
 5NB  C4   N9   C8   105.10  3.000
 5NB  C4   N9   C1'  124.38  3.000
 5NB  C8   N9   C1'  130.52  3.000
 5NB  N7   C8   BR8  122.65  3.000
 5NB  BR8  C8   N9   123.01  3.000
 5NB  N7   C8   N9   114.34  3.000
 5NB  C5   N7   C8   104.16  3.000
 5NB  C6   C5   C4   116.54  3.000
 5NB  C4   C5   N7   110.80  3.000
 5NB  C6   C5   N7   132.66  3.000
 5NB  N3   C4   C5   126.49  3.000
 5NB  N3   C4   N9   127.91  3.000
 5NB  C5   C4   N9   105.60  3.000
 5NB  C2   N3   C4   111.68  3.000
 5NB  H12  C2   N1   115.50  3.000
 5NB  H12  C2   N3   116.09  3.000
 5NB  N1   C2   N3   128.41  3.000
 5NB  C6   N1   C2   119.25  3.000
 5NB  N6   C6   N1   119.53  3.000
 5NB  N1   C6   C5   117.63  3.000
 5NB  N6   C6   C5   122.83  3.000
 5NB  H14  N6   H13  118.09  3.000
 5NB  H14  N6   C6   121.05  3.000
 5NB  H13  N6   C6   120.09  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
 5NB  CONST_01  C5   N7   C8   N9     0.00   0.0  0
 5NB  CONST_02  C6   C5   C4   N9   180.00   0.0  0
 5NB  CONST_03  N7   C5   C4   N9     0.00   0.0  0
 5NB  CONST_04  C2   N3   C4   N9   180.00   0.0  0
 5NB  CONST_05  C6   C5   N7   C8   180.00   0.0  0
 5NB  CONST_06  C4   C5   N7   C8     0.00   0.0  0
 5NB  CONST_07  C5   C4   N9   C8     0.00   0.0  0
 5NB  CONST_08  N3   C4   N9   C8   180.00   0.0  0
 5NB  CONST_09  N1   C6   C5   N7   180.00   0.0  0
 5NB  CONST_10  N3   C4   C5   N7   180.00   0.0  0
 5NB  CONST_11  C4   N9   C8   N7     0.00   0.0  0
 5NB  CONST_12  C2   N1   C6   C5     0.00   0.0  0
 5NB  CONST_13  C2   N3   C4   C5     0.00   0.0  0
 5NB  CONST_14  N1   C6   C5   C4     0.00   0.0  0
 5NB  CONST_15  N1   C2   N3   C4     0.00   0.0  0
 5NB  CONST_16  C6   N1   C2   N3     0.00   0.0  0
 5NB  CONST_17  C6   C5   C4   N3     0.00   0.0  0
 5NB  CONST_18  N7   C8   N9   C1'  180.00   0.0  0
 5NB  CONST_19  C5   C4   N9   C1'  180.00   0.0  0
 5NB  CONST_20  N3   C4   N9   C1'    0.00   0.0  0
 5NB  CONST_21  BR8  C8   N9   C1'    0.00   0.0  0
 5NB  CONST_22  C5   N7   C8   BR8  180.00   0.0  0
 5NB  CONST_23  C4   N9   C8   BR8  180.00   0.0  0
 5NB  CONST_24  N6   C6   C5   N7     0.00   0.0  0
 5NB  CONST_25  N6   C6   C5   C4   180.00   0.0  0
 5NB  CONST_26  N6   C6   N1   C2   180.00   0.0  0
 5NB  CONST_27  H12  C2   N3   C4   180.00   0.0  0
 5NB  CONST_28  H13  N6   C6   C5   180.00   0.0  0
 5NB  CONST_29  H14  N6   C6   C5     0.00   0.0  0
 5NB  Var_01    H8   N5'  C5'  C4'   67.38  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
 5NB  chir_01  C2'  O2'  C1'  C3'  negativ
 5NB  chir_02  C3'  O3'  C4'  C2'  positiv
 5NB  chir_03  C4'  O4'  C3'  C5'  negativ
 5NB  chir_04  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
 5NB  plan-1  C1'  0.020
 5NB  plan-1  N9   0.020
 5NB  plan-1  C8   0.020
 5NB  plan-1  BR8  0.020
 5NB  plan-1  N7   0.020
 5NB  plan-1  C5   0.020
 5NB  plan-1  C4   0.020
 5NB  plan-1  N3   0.020
 5NB  plan-1  C2   0.020
 5NB  plan-1  N1   0.020
 5NB  plan-1  C6   0.020
 5NB  plan-1  N6   0.020
 5NB  plan-1  H12  0.020
 5NB  plan-2  C6   0.020
 5NB  plan-2  N6   0.020
 5NB  plan-2  H13  0.020
 5NB  plan-2  H14  0.020

