# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 14:30:05 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: 8-bromoadenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n([C@@H]3O[C@H](CO)[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
 GBA  GBA  '8-bromoadenosine         '  ligand  32  20  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GBA
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
 GBA  C4   C   CR56  0   0.507   1.8007  -0.7509  -0.2932
 GBA  C5   C   CR56  0  -0.001   2.6436   0.3370  -0.1678
 GBA  C6   C   CR6   0   0.463   4.0255   0.0710  -0.2004
 GBA  C8   C   CR5   0   0.288   0.6903   1.1108  -0.0692
 GBA  N1   N   N     0  -0.471   4.4091  -1.2013  -0.3531
 GBA  N3   N   N     0  -0.458   2.1672  -2.0183  -0.4485
 GBA  O2'  O   OH1   0  -0.651  -0.6963  -2.0666   1.8896
 GBA  C2'  C   CH1   0  -0.002  -1.4065  -1.2300   1.0371
 GBA  C3'  C   CH1   0  -0.060  -2.7475  -1.7511   0.5127
 GBA  O3'  O   OH1   0  -0.667  -2.5999  -3.1203   0.2441
 GBA  C4'  C   CH1   0  -0.028  -2.9101  -0.9059  -0.7576
 GBA  C5'  C   CH2   0  -0.152  -3.7473   0.3295  -0.4982
 GBA  O5'  O   OH1   0  -0.667  -3.7502   1.1357  -1.6470
 GBA  O4'  O   O2    0  -0.492  -1.5839  -0.5596  -1.1836
 GBA  C1'  C   CH1   0   0.224  -0.6550  -1.0753  -0.2808
 GBA  N9   N   NR5   0  -0.567   0.5269  -0.2433  -0.2285
 GBA  BR8  BR  BR    0   0.049  -0.7147   2.3090   0.0490
 GBA  N7   N   N     0  -0.423   1.9241   1.4950  -0.0330
 GBA  C2   C   CR16  0   0.049   3.4830  -2.1483  -0.4688
 GBA  N6   N   NH2   0  -0.815   4.9473   1.0248  -0.0815
 GBA  H1   H   HOH1  0   0.464  -1.1109  -2.0488   2.7578
 GBA  H2   H   HCH1  0   0.240  -1.5787  -0.2412   1.4834
 GBA  H3   H   HCH1  0   0.255  -3.5650  -1.5668   1.2217
 GBA  H4   H   HOH1  0   0.457  -3.4249  -3.4491  -0.1268
 GBA  H5   H   HCH1  0   0.255  -3.3807  -1.4923  -1.5546
 GBA  H6   H   HCH2  0   0.211  -4.7563  -0.0174  -0.2374
 GBA  H7   H   HCH2  0   0.198  -3.3626   0.8638   0.3793
 GBA  H8   H   HOH1  0   0.457  -4.2058   1.9550  -1.4353
 GBA  H9   H   HCH1  0   0.261  -0.2817  -2.0568  -0.5950
 GBA  H10  H   HCR6  0   0.256   3.8602  -3.1573  -0.5950
 GBA  H11  H   HNH2  0   0.414   4.6890   1.9927  -0.0032
 GBA  H12  H   HNH2  0   0.406   5.9248   0.7945  -0.1292

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
 GBA  N6   C6   single    1.332  0.020  1.332
 GBA  N1   C6   aromatic  1.338  0.020  1.338
 GBA  N1   C2   aromatic  1.330  0.020  1.330
 GBA  C6   C5   aromatic  1.408  0.020  1.408
 GBA  C2   N3   aromatic  1.322  0.020  1.322
 GBA  C5   N7   aromatic  1.370  0.020  1.370
 GBA  C5   C4   aromatic  1.382  0.020  1.382
 GBA  N7   C8   aromatic  1.293  0.020  1.293
 GBA  N3   C4   aromatic  1.328  0.020  1.328
 GBA  C4   N9   aromatic  1.373  0.020  1.373
 GBA  C8   N9   aromatic  1.373  0.020  1.373
 GBA  C8   BR8  single    1.850  0.020  1.850
 GBA  N9   C1'  single    1.446  0.020  1.446
 GBA  O5'  C5'  single    1.403  0.020  1.403
 GBA  O4'  C1'  single    1.394  0.020  1.394
 GBA  O4'  C4'  single    1.435  0.020  1.435
 GBA  C1'  C2'  single    1.525  0.020  1.525
 GBA  C5'  C4'  single    1.515  0.020  1.515
 GBA  C4'  C3'  single    1.534  0.020  1.534
 GBA  C2'  C3'  single    1.531  0.020  1.531
 GBA  C2'  O2'  single    1.390  0.020  1.390
 GBA  C3'  O3'  single    1.403  0.020  1.403
 GBA  O2'  H1   single    0.850  0.020  0.980
 GBA  C2'  H2   single    0.970  0.020  1.090
 GBA  C3'  H3   single    0.970  0.020  1.090
 GBA  O3'  H4   single    0.850  0.020  0.980
 GBA  C4'  H5   single    0.970  0.020  1.090
 GBA  C5'  H6   single    0.970  0.020  1.090
 GBA  C5'  H7   single    0.970  0.020  1.090
 GBA  O5'  H8   single    0.850  0.020  0.980
 GBA  C1'  H9   single    0.970  0.020  1.090
 GBA  C2   H10  single    0.930  0.020  1.080
 GBA  N6   H11  single    0.860  0.020  1.020
 GBA  N6   H12  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
 GBA  N9   C4   N3   127.90  3.000
 GBA  N9   C4   C5   105.70  3.000
 GBA  N3   C4   C5   126.40  3.000
 GBA  N7   C5   C6   132.66  3.000
 GBA  N7   C5   C4   110.73  3.000
 GBA  C6   C5   C4   116.61  3.000
 GBA  N6   C6   N1   119.54  3.000
 GBA  N1   C6   C5   117.64  3.000
 GBA  N6   C6   C5   122.82  3.000
 GBA  N7   C8   BR8  122.04  3.000
 GBA  BR8  C8   N9   123.75  3.000
 GBA  N7   C8   N9   114.20  3.000
 GBA  C2   N1   C6   119.19  3.000
 GBA  C2   N3   C4   111.73  3.000
 GBA  H1   O2'  C2'  108.80  3.000
 GBA  H2   C2'  C1'  109.70  3.000
 GBA  H2   C2'  C3'  107.96  3.000
 GBA  C1'  C2'  C3'   99.80  3.000
 GBA  H2   C2'  O2'  111.88  3.000
 GBA  C3'  C2'  O2'  116.92  3.000
 GBA  C1'  C2'  O2'  109.84  3.000
 GBA  H3   C3'  C4'  111.30  3.000
 GBA  H3   C3'  O3'  111.46  3.000
 GBA  C4'  C3'  O3'  112.96  3.000
 GBA  H3   C3'  C2'  111.95  3.000
 GBA  O3'  C3'  C2'  107.80  3.000
 GBA  C4'  C3'  C2'  100.88  3.000
 GBA  H4   O3'  C3'  108.48  3.000
 GBA  H5   C4'  O4'  108.06  3.000
 GBA  H5   C4'  C5'  108.88  3.000
 GBA  O4'  C4'  C5'  111.39  3.000
 GBA  H5   C4'  C3'  110.66  3.000
 GBA  C5'  C4'  C3'  111.48  3.000
 GBA  O4'  C4'  C3'  106.30  3.000
 GBA  H7   C5'  H6   106.62  3.000
 GBA  H7   C5'  O5'  112.07  3.000
 GBA  H6   C5'  O5'  111.95  3.000
 GBA  H7   C5'  C4'  109.90  3.000
 GBA  H6   C5'  C4'  106.90  3.000
 GBA  O5'  C5'  C4'  109.24  3.000
 GBA  H8   O5'  C5'  108.08  3.000
 GBA  C1'  O4'  C4'  109.52  3.000
 GBA  H9   C1'  N9   104.31  3.000
 GBA  H9   C1'  O4'  111.87  3.000
 GBA  N9   C1'  O4'  110.80  3.000
 GBA  H9   C1'  C2'  108.95  3.000
 GBA  O4'  C1'  C2'  105.59  3.000
 GBA  N9   C1'  C2'  115.46  3.000
 GBA  C1'  N9   C8   131.96  3.000
 GBA  C1'  N9   C4   122.95  3.000
 GBA  C8   N9   C4   105.05  3.000
 GBA  C8   N7   C5   104.32  3.000
 GBA  H10  C2   N3   116.06  3.000
 GBA  H10  C2   N1   115.50  3.000
 GBA  N3   C2   N1   128.44  3.000
 GBA  H12  N6   H11  118.31  3.000
 GBA  H12  N6   C6   120.31  3.000
 GBA  H11  N6   C6   121.26  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
 GBA  CONST_01  N1   C6  C5  C4     0.00  0.0  0
 GBA  CONST_02  C8   N7  C5  C4     0.00  0.0  0
 GBA  CONST_03  N1   C2  N3  C4     0.00  0.0  0
 GBA  CONST_04  N7   C8  N9  C4     0.00  0.0  0
 GBA  CONST_05  C2   N1  C6  C5     0.00  0.0  0
 GBA  CONST_06  N9   C8  N7  C5     0.00  0.0  0
 GBA  CONST_07  C2   N3  C4  C5     0.00  0.0  0
 GBA  CONST_08  C8   N9  C4  C5     0.00  0.0  0
 GBA  CONST_09  N3   C2  N1  C6     0.00  0.0  0
 GBA  CONST_10  C8   N7  C5  C6   180.00  0.0  0
 GBA  CONST_11  N3   C4  C5  C6     0.00  0.0  0
 GBA  CONST_12  N9   C4  C5  C6   180.00  0.0  0
 GBA  CONST_13  N3   C4  N9  C8   180.00  0.0  0
 GBA  CONST_14  N7   C5  C6  N1   180.00  0.0  0
 GBA  CONST_15  N7   C5  C4  N3   180.00  0.0  0
 GBA  CONST_16  N7   C5  C4  N9     0.00  0.0  0
 GBA  CONST_17  C2   N3  C4  N9   180.00  0.0  0
 GBA  CONST_18  C1'  N9  C4  C5   180.00  0.0  0
 GBA  CONST_19  C1'  N9  C4  N3     0.00  0.0  0
 GBA  CONST_20  N7   C8  N9  C1'  180.00  0.0  0
 GBA  CONST_21  N6   C6  C5  C4   180.00  0.0  0
 GBA  CONST_22  BR8  C8  N9  C4   180.00  0.0  0
 GBA  CONST_23  BR8  C8  N7  C5   180.00  0.0  0
 GBA  CONST_24  BR8  C8  N9  C1'    0.00  0.0  0
 GBA  CONST_25  N6   C6  C5  N7     0.00  0.0  0
 GBA  CONST_26  N6   C6  N1  C2   180.00  0.0  0
 GBA  CONST_27  H10  C2  N3  C4   180.00  0.0  0
 GBA  CONST_28  H11  N6  C6  C5     0.00  0.0  0
 GBA  CONST_29  H12  N6  C6  C5   180.00  0.0  0

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
 GBA  chir_01  C2'  C1'  C3'  O2'  negativ
 GBA  chir_02  C3'  O3'  C4'  C2'  positiv
 GBA  chir_03  C4'  O4'  C3'  C5'  negativ
 GBA  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
 GBA  plan-1  C4   0.020
 GBA  plan-1  C5   0.020
 GBA  plan-1  C6   0.020
 GBA  plan-1  C8   0.020
 GBA  plan-1  N1   0.020
 GBA  plan-1  N3   0.020
 GBA  plan-1  C1'  0.020
 GBA  plan-1  N9   0.020
 GBA  plan-1  BR8  0.020
 GBA  plan-1  N7   0.020
 GBA  plan-1  C2   0.020
 GBA  plan-1  N6   0.020
 GBA  plan-1  H10  0.020
 GBA  plan-2  C6   0.020
 GBA  plan-2  N6   0.020
 GBA  plan-2  H11  0.020
 GBA  plan-2  H12  0.020

