# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 12:10:11 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: 8-bromoguanosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2n([C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O)c(Br)nc2C(=O)N1
#
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
 BG2  BG2  '8-bromoguanosine         '  ligand  33  21  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BG2
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
 BG2  BR    BR  BR    0   0.035   1.2372   2.2641  -0.4318
 BG2  N1    N   NR16  0  -0.728  -4.3009  -0.3840   0.3882
 BG2  C2    C   CR6   0   0.698  -3.5500  -1.5069   0.5866
 BG2  N2    N   NH2   0  -0.828  -4.2048  -2.6307   0.9028
 BG2  N3    N   N     0  -0.513  -2.2405  -1.5122   0.5152
 BG2  C4    C   CR56  0   0.528  -1.7234  -0.3122   0.2375
 BG2  C5    C   CR56  0  -0.090  -2.3873   0.8793   0.0368
 BG2  C6    C   CR6   0   0.510  -3.8120   0.8938   0.0918
 BG2  O6    O   O     0  -0.466  -4.5718   1.8305  -0.0775
 BG2  N7    N   N     0  -0.413  -1.4987   1.8920  -0.2132
 BG2  C8    C   CR5   0   0.278  -0.3409   1.3278  -0.1677
 BG2  N9    N   NR5   0  -0.565  -0.3928  -0.0216   0.1108
 BG2  C1'   C   CH1   0   0.206   0.6516  -1.0154   0.1714
 BG2  C2'   C   CH1   0   0.009   1.3435  -1.3183  -1.1526
 BG2  O2'   O   OH1   0  -0.652   0.5105  -2.1210  -1.9266
 BG2  C3'   C   CH1   0  -0.062   2.6509  -1.9588  -0.6632
 BG2  O3'   O   OH1   0  -0.664   2.4572  -3.3433  -0.5574
 BG2  C4'   C   CH1   0  -0.014   2.8729  -1.2639   0.6982
 BG2  O4'   O   O2    0  -0.489   1.6587  -0.5885   1.0326
 BG2  C5'   C   CH2   0  -0.156   4.0172  -0.2776   0.6549
 BG2  O5'   O   OH1   0  -0.668   4.1248   0.3553   1.9043
 BG2  HN2   H   HNH2  0   0.417  -5.1973  -2.7085   0.7594
 BG2  HN2A  H   HNH2  0   0.415  -3.6837  -3.4916   0.8946
 BG2  H1'   H   HCH1  0   0.265   0.1603  -1.9292   0.5289
 BG2  H2'   H   HCH1  0   0.241   1.5986  -0.3857  -1.6709
 BG2  HO2'  H   HOH1  0   0.463   0.9398  -2.2950  -2.7702
 BG2  H3'   H   HCH1  0   0.247   3.4744  -1.7246  -1.3510
 BG2  HO3'  H   HOH1  0   0.457   3.2580  -3.7334  -0.1927
 BG2  H4'   H   HCH1  0   0.248   3.0713  -2.0236   1.4645
 BG2  H5'   H   HCH2  0   0.205   4.9252  -0.8431   0.4047
 BG2  H5'A  H   HCH2  0   0.202   3.8503   0.4401  -0.1585
 BG2  HO5'  H   HOH1  0   0.458   4.7595   1.0725   1.8241
 BG2  HN1   H   HNR6  0   0.429  -5.3088  -0.4654   0.4446

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
 BG2  BR   C8    single    1.854  0.020  1.854
 BG2  N1   C2    single    1.365  0.020  1.365
 BG2  N1   C6    single    1.400  0.020  1.400
 BG2  C2   N2    single    1.339  0.020  1.339
 BG2  C2   N3    double    1.311  0.020  1.311
 BG2  N3   C4    single    1.336  0.020  1.336
 BG2  C4   C5    aromatic  1.379  0.020  1.379
 BG2  C4   N9    aromatic  1.368  0.020  1.368
 BG2  C5   C6    single    1.426  0.020  1.426
 BG2  C5   N7    aromatic  1.370  0.020  1.370
 BG2  C6   O6    double    1.218  0.020  1.218
 BG2  N7   C8    aromatic  1.289  0.020  1.289
 BG2  C8   N9    aromatic  1.379  0.020  1.379
 BG2  N9   C1'   single    1.443  0.020  1.443
 BG2  C1'  C2'   single    1.524  0.020  1.524
 BG2  C1'  O4'   single    1.392  0.020  1.392
 BG2  C2'  O2'   single    1.392  0.020  1.392
 BG2  C2'  C3'   single    1.536  0.020  1.536
 BG2  C3'  O3'   single    1.402  0.020  1.402
 BG2  C3'  C4'   single    1.545  0.020  1.545
 BG2  C4'  O4'   single    1.429  0.020  1.429
 BG2  C4'  C5'   single    1.511  0.020  1.511
 BG2  C5'  O5'   single    1.405  0.020  1.405
 BG2  N1   HN1   single    0.860  0.020  1.020
 BG2  N2   HN2   single    0.890  0.020  1.040
 BG2  N2   HN2A  single    0.890  0.020  1.040
 BG2  C1'  H1'   single    0.970  0.020  1.090
 BG2  C2'  H2'   single    0.970  0.020  1.090
 BG2  O2'  HO2'  single    0.850  0.020  0.980
 BG2  C3'  H3'   single    0.970  0.020  1.090
 BG2  O3'  HO3'  single    0.850  0.020  0.980
 BG2  C4'  H4'   single    0.970  0.020  1.090
 BG2  C5'  H5'   single    0.970  0.020  1.090
 BG2  C5'  H5'A  single    0.970  0.020  1.090
 BG2  O5'  HO5'  single    0.850  0.020  0.980

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
 BG2  HN1   N1   C6   115.64  3.000
 BG2  HN1   N1   C2   118.24  3.000
 BG2  C6    N1   C2   126.11  3.000
 BG2  N3    C2   N2   119.87  3.000
 BG2  N3    C2   N1   122.99  3.000
 BG2  N2    C2   N1   117.11  3.000
 BG2  HN2A  N2   HN2  116.34  3.000
 BG2  HN2A  N2   C2   117.58  3.000
 BG2  HN2   N2   C2   120.93  3.000
 BG2  C4    N3   C2   113.22  3.000
 BG2  N9    C4   C5   105.75  3.000
 BG2  N9    C4   N3   125.92  3.000
 BG2  C5    C4   N3   128.33  3.000
 BG2  N7    C5   C6   130.36  3.000
 BG2  N7    C5   C4   110.67  3.000
 BG2  C6    C5   C4   118.97  3.000
 BG2  O6    C6   C5   128.74  3.000
 BG2  O6    C6   N1   120.90  3.000
 BG2  C5    C6   N1   110.36  3.000
 BG2  C8    N7   C5   104.64  3.000
 BG2  N9    C8   N7   113.69  3.000
 BG2  N9    C8   BR   123.72  3.000
 BG2  N7    C8   BR   122.59  3.000
 BG2  C1'   N9   C8   130.94  3.000
 BG2  C1'   N9   C4   123.64  3.000
 BG2  C8    N9   C4   105.26  3.000
 BG2  H1'   C1'  O4'  112.20  3.000
 BG2  H1'   C1'  C2'  108.71  3.000
 BG2  O4'   C1'  C2'  105.66  3.000
 BG2  H1'   C1'  N9   105.25  3.000
 BG2  O4'   C1'  N9   109.78  3.000
 BG2  C2'   C1'  N9   115.39  3.000
 BG2  H2'   C2'  C3'  107.89  3.000
 BG2  H2'   C2'  O2'  111.51  3.000
 BG2  C3'   C2'  O2'  116.49  3.000
 BG2  H2'   C2'  C1'  110.31  3.000
 BG2  C3'   C2'  C1'  101.10  3.000
 BG2  O2'   C2'  C1'  109.03  3.000
 BG2  HO2'  O2'  C2'  108.96  3.000
 BG2  H3'   C3'  C4'  110.38  3.000
 BG2  H3'   C3'  O3'  111.19  3.000
 BG2  C4'   C3'  O3'  113.43  3.000
 BG2  H3'   C3'  C2'  110.48  3.000
 BG2  C4'   C3'  C2'  102.45  3.000
 BG2  O3'   C3'  C2'  108.56  3.000
 BG2  HO3'  O3'  C3'  108.29  3.000
 BG2  H4'   C4'  C5'  109.57  3.000
 BG2  H4'   C4'  O4'  108.51  3.000
 BG2  C5'   C4'  O4'  109.97  3.000
 BG2  H4'   C4'  C3'  109.28  3.000
 BG2  C5'   C4'  C3'  112.16  3.000
 BG2  O4'   C4'  C3'  107.27  3.000
 BG2  C4'   O4'  C1'  108.96  3.000
 BG2  H5'A  C5'  H5'  107.07  3.000
 BG2  H5'A  C5'  O5'  112.10  3.000
 BG2  H5'   C5'  O5'  111.79  3.000
 BG2  H5'A  C5'  C4'  109.44  3.000
 BG2  H5'   C5'  C4'  107.24  3.000
 BG2  O5'   C5'  C4'  109.06  3.000
 BG2  HO5'  O5'  C5'  108.22  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
 BG2  CONST_01  C8    N7  C5  C4    0.00  0.0  0
 BG2  CONST_02  N7    C8  N9  C4    0.00  0.0  0
 BG2  CONST_03  C8    N9  C4  C5    0.00  0.0  0
 BG2  CONST_04  N9    C8  N7  C5    0.00  0.0  0
 BG2  CONST_05  N9    C4  C5  N7    0.00  0.0  0
 BG2  CONST_06  C1'   N9  C4  N3    0.00  0.0  0
 BG2  CONST_07  C1'   N9  C4  C5  180.00  0.0  0
 BG2  CONST_08  C1'   N9  C8  N7  180.00  0.0  0
 BG2  CONST_09  C4    N3  C2  N1    0.00  0.0  0
 BG2  CONST_10  C5    C6  N1  C2    0.00  0.0  0
 BG2  CONST_11  C6    N1  C2  N3    0.00  0.0  0
 BG2  CONST_12  C5    N7  C8  BR  180.00  0.0  0
 BG2  CONST_13  C4    N9  C8  BR  180.00  0.0  0
 BG2  CONST_14  C1'   N9  C8  BR    0.00  0.0  0
 BG2  CONST_15  O6    C6  N1  C2  180.00  0.0  0
 BG2  CONST_16  C6    N1  C2  N2  180.00  0.0  0
 BG2  CONST_17  C4    N3  C2  N2  180.00  0.0  0
 BG2  CONST_18  HN1   N1  C2  N3  180.00  0.0  0
 BG2  CONST_20  HN2A  N2  C2  N1  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
 BG2  chir_01  C1'  N9   C2'  O4'  negativ
 BG2  chir_02  C2'  O2'  C3'  C1'  positiv
 BG2  chir_03  C3'  O3'  C4'  C2'  positiv
 BG2  chir_04  C4'  O4'  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
 BG2  plan-1  BR    0.020
 BG2  plan-1  N1    0.020
 BG2  plan-1  C2    0.020
 BG2  plan-1  N2    0.020
 BG2  plan-1  N3    0.020
 BG2  plan-1  C4    0.020
 BG2  plan-1  C5    0.020
 BG2  plan-1  C6    0.020
 BG2  plan-1  O6    0.020
 BG2  plan-1  N7    0.020
 BG2  plan-1  C8    0.020
 BG2  plan-1  N9    0.020
 BG2  plan-1  C1'   0.020
 BG2  plan-1  HN2   0.020
 BG2  plan-1  HN2A  0.020
 BG2  plan-1  HN1   0.020

