# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 06:51:40 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: [[(2R,3S,5R)-5-(2-azanyl-6-oxo-1H-purin-9-yl)-3-hydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]boranuide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [BH3-][P](O)(=O)OC[C@H]1O[C@H](C[C@@H]1O)n2cnc3C(=O)NC(=Nc23)N
#
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
 BGR  BGR  '[[(2R,3S,5R)-5-(2-azanyl-6-oxo-1H-purin-9-yl)-3-hydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]boranuide'  ligand  39  23  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BGR
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
 BGR  P     P  P      0   1.191  -4.8028  -0.9763   0.5226
 BGR  N1    N  NR16   0  -0.727   5.1933  -0.7028   0.6115
 BGR  C2    C  CR6    0   0.692   4.5993   0.2831   1.3462
 BGR  N2    N  NH2    0  -0.832   5.3337   0.8450   2.3171
 BGR  N3    N  N      0  -0.514   3.3814   0.7079   1.1181
 BGR  C4    C  CR56   0   0.508   2.7842   0.0763   0.0982
 BGR  C5    C  CR56   0  -0.096   3.2905  -0.9330  -0.6998
 BGR  C6    C  CR6    0   0.505   4.6148  -1.3986  -0.4578
 BGR  O6    O  O      0  -0.474   5.2387  -2.2680  -1.0427
 BGR  N7    N  N      0  -0.440   2.3646  -1.3238  -1.6322
 BGR  C8    C  CR15   0   0.097   1.3338  -0.5701  -1.4063
 BGR  N9    N  NR5    0  -0.524   1.5256   0.3047  -0.3656
 BGR  BP    B  B     -1  -0.745  -6.0215   0.4967   0.5131
 BGR  C1'   C  CH1    0   0.171   0.5909   1.2911   0.1449
 BGR  C2'   C  CH2    0  -0.549   0.2497   2.3929  -0.8575
 BGR  C3'   C  CH1    0   0.009  -1.0951   1.9470  -1.4252
 BGR  O3'   O  OH1    0  -0.660  -1.9386   2.9782  -1.8537
 BGR  C4'   C  CH1    0   0.011  -1.7109   1.2416  -0.2203
 BGR  O4'   O  O2     0  -0.491  -0.6164   0.6458   0.4621
 BGR  C5'   C  CH2    0  -0.153  -2.7224   0.1877  -0.5977
 BGR  O5'   O  O2     0  -0.617  -3.2548  -0.3965   0.5723
 BGR  OP1   O  O      0  -0.779  -4.9174  -2.0438  -0.5231
 BGR  OP2   O  OH1    0  -0.777  -4.8115  -1.6977   1.9887
 BGR  H8    H  HCR5   0   0.283   0.4070  -0.6109  -1.9580
 BGR  H1BP  H  H      0   0.001  -5.8501   1.1375  -0.5063
 BGR  H2BP  H  H      0   0.004  -7.1493   0.0417   0.5385
 BGR  H3BP  H  H      0  -0.002  -5.8143   1.1900   1.4906
 BGR  H1'   H  HCH1   0   0.270   1.0580   1.6979   1.0437
 BGR  H2'   H  HCH2   0   0.271   0.1169   3.3371  -0.3252
 BGR  H2'A  H  HCH2   0   0.281   1.0276   2.5323  -1.6073
 BGR  HN2   H  HNH2   0   0.415   6.1715   0.4021   2.6547
 BGR  HN2A  H  HNH2   0   0.413   4.8640   1.4599   2.9600
 BGR  H3'   H  HCH1   0   0.221  -0.9364   1.2159  -2.2309
 BGR  H4'   H  HCH1   0   0.236  -2.1911   1.9925   0.4234
 BGR  H5'   H  HCH2   0   0.220  -3.4951   0.6772  -1.2029
 BGR  H5'A  H  HCH2   0   0.218  -2.2467  -0.5726  -1.2282
 BGR  H15   H  HOH1   0   0.461  -1.6211   3.3006  -2.7024
 BGR  H16   H  HOH1   0   0.477  -5.0219  -1.0821   2.7007
 BGR  HN1   H  HNR6   0   0.426   6.1438  -0.9655   0.8396

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
 BGR  P    BP    single    1.912  0.020  1.912
 BGR  P    O5'   single    1.654  0.020  1.654
 BGR  P    OP1   double    1.499  0.020  1.499
 BGR  P    OP2   single    1.634  0.020  1.634
 BGR  N1   C2    single    1.366  0.020  1.366
 BGR  N1   C6    single    1.401  0.020  1.401
 BGR  N1   HN1   single    0.860  0.020  1.020
 BGR  C2   N2    single    1.341  0.020  1.341
 BGR  C2   N3    double    1.310  0.020  1.310
 BGR  N2   HN2   single    0.890  0.020  1.040
 BGR  N2   HN2A  single    0.890  0.020  1.040
 BGR  N3   C4    single    1.340  0.020  1.340
 BGR  C4   C5    aromatic  1.383  0.020  1.383
 BGR  C4   N9    aromatic  1.361  0.020  1.361
 BGR  C5   C6    single    1.424  0.020  1.424
 BGR  C5   N7    aromatic  1.371  0.020  1.371
 BGR  C6   O6    double    1.220  0.020  1.220
 BGR  N7   C8    aromatic  1.297  0.020  1.297
 BGR  C8   N9    aromatic  1.373  0.020  1.373
 BGR  C8   H8    single    0.929  0.020  1.085
 BGR  N9   C1'   single    1.452  0.020  1.452
 BGR  BP   H1BP  single    1.040  0.020  1.214
 BGR  BP   H2BP  single    1.040  0.020  1.214
 BGR  BP   H3BP  single    1.040  0.020  1.214
 BGR  C1'  C2'   single    1.528  0.020  1.528
 BGR  C1'  O4'   single    1.405  0.020  1.405
 BGR  C1'  H1'   single    0.970  0.020  1.090
 BGR  C2'  C3'   single    1.526  0.020  1.526
 BGR  C2'  H2'   single    0.970  0.020  1.090
 BGR  C2'  H2'A  single    0.970  0.020  1.090
 BGR  C3'  O3'   single    1.399  0.020  1.399
 BGR  C3'  C4'   single    1.526  0.020  1.526
 BGR  C3'  H3'   single    0.970  0.020  1.090
 BGR  C4'  O4'   single    1.421  0.020  1.421
 BGR  C4'  C5'   single    1.509  0.020  1.509
 BGR  C4'  H4'   single    0.970  0.020  1.090
 BGR  C5'  O5'   single    1.412  0.020  1.412
 BGR  C5'  H5'   single    0.970  0.020  1.090
 BGR  C5'  H5'A  single    0.970  0.020  1.090
 BGR  O3'  H15   single    0.850  0.020  0.980
 BGR  OP2  H16   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
 BGR  OP2   P    OP1   108.13  3.000
 BGR  OP2   P    O5'    97.63  3.000
 BGR  OP1   P    O5'   110.02  3.000
 BGR  OP2   P    BP    109.95  3.000
 BGR  OP1   P    BP    119.77  3.000
 BGR  O5'   P    BP    109.07  3.000
 BGR  HN1   N1   C6    115.53  3.000
 BGR  HN1   N1   C2    118.34  3.000
 BGR  C6    N1   C2    126.14  3.000
 BGR  N3    C2   N2    119.97  3.000
 BGR  N3    C2   N1    123.02  3.000
 BGR  N2    C2   N1    116.99  3.000
 BGR  HN2A  N2   HN2   116.33  3.000
 BGR  HN2A  N2   C2    117.59  3.000
 BGR  HN2   N2   C2    120.98  3.000
 BGR  C4    N3   C2    113.21  3.000
 BGR  N9    C4   C5    105.34  3.000
 BGR  N9    C4   N3    126.33  3.000
 BGR  C5    C4   N3    128.33  3.000
 BGR  N7    C5   C6    130.57  3.000
 BGR  N7    C5   C4    110.69  3.000
 BGR  C6    C5   C4    118.74  3.000
 BGR  O6    C6   C5    128.84  3.000
 BGR  O6    C6   N1    120.60  3.000
 BGR  C5    C6   N1    110.57  3.000
 BGR  C8    N7   C5    104.64  3.000
 BGR  H8    C8   N9    122.10  3.000
 BGR  H8    C8   N7    124.85  3.000
 BGR  N9    C8   N7    113.04  3.000
 BGR  C1'   N9   C8    127.56  3.000
 BGR  C1'   N9   C4    126.14  3.000
 BGR  C8    N9   C4    106.29  3.000
 BGR  H3BP  BP   H2BP  110.76  3.000
 BGR  H3BP  BP   H1BP  110.44  3.000
 BGR  H2BP  BP   H1BP  110.20  3.000
 BGR  H3BP  BP   P     109.06  3.000
 BGR  H2BP  BP   P     107.62  3.000
 BGR  H1BP  BP   P     108.68  3.000
 BGR  H1'   C1'  O4'   110.67  3.000
 BGR  H1'   C1'  C2'   111.53  3.000
 BGR  O4'   C1'  C2'   106.70  3.000
 BGR  H1'   C1'  N9    105.50  3.000
 BGR  O4'   C1'  N9    108.70  3.000
 BGR  C2'   C1'  N9    113.76  3.000
 BGR  H2'A  C2'  H2'   108.16  3.000
 BGR  H2'A  C2'  C3'   114.24  3.000
 BGR  H2'   C2'  C3'   109.07  3.000
 BGR  H2'A  C2'  C1'   112.60  3.000
 BGR  H2'   C2'  C1'   109.32  3.000
 BGR  C3'   C2'  C1'   103.30  3.000
 BGR  H3'   C3'  C4'   109.23  3.000
 BGR  H3'   C3'  O3'   110.64  3.000
 BGR  C4'   C3'  O3'   109.82  3.000
 BGR  H3'   C3'  C2'   109.86  3.000
 BGR  C4'   C3'  C2'   101.36  3.000
 BGR  O3'   C3'  C2'   115.45  3.000
 BGR  H15   O3'  C3'   108.55  3.000
 BGR  H4'   C4'  C5'   109.32  3.000
 BGR  H4'   C4'  O4'   109.97  3.000
 BGR  C5'   C4'  O4'   110.10  3.000
 BGR  H4'   C4'  C3'   108.84  3.000
 BGR  C5'   C4'  C3'   113.33  3.000
 BGR  O4'   C4'  C3'   105.20  3.000
 BGR  C4'   O4'  C1'   111.15  3.000
 BGR  H5'A  C5'  H5'   107.33  3.000
 BGR  H5'A  C5'  O5'   110.69  3.000
 BGR  H5'   C5'  O5'   112.10  3.000
 BGR  H5'A  C5'  C4'   109.72  3.000
 BGR  H5'   C5'  C4'   107.37  3.000
 BGR  O5'   C5'  C4'   109.54  3.000
 BGR  C5'   O5'  P     118.24  3.000
 BGR  H16   OP2  P     112.45  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
 BGR  CONST_01  C8    N7   C5   C4     0.00   0.0  0
 BGR  CONST_02  N7    C8   N9   C4     0.00   0.0  0
 BGR  CONST_03  C8    N9   C4   C5     0.00   0.0  0
 BGR  CONST_04  N9    C8   N7   C5     0.00   0.0  0
 BGR  CONST_05  N9    C4   C5   N7     0.00   0.0  0
 BGR  CONST_06  C1'   N9   C4   N3     0.00   0.0  0
 BGR  CONST_07  C1'   N9   C4   C5   180.00   0.0  0
 BGR  CONST_08  C1'   N9   C8   N7   180.00   0.0  0
 BGR  CONST_09  C4    N3   C2   N1     0.00   0.0  0
 BGR  CONST_10  C5    C6   N1   C2     0.00   0.0  0
 BGR  CONST_11  C6    N1   C2   N3     0.00   0.0  0
 BGR  CONST_12  O6    C6   N1   C2   180.00   0.0  0
 BGR  CONST_13  C6    N1   C2   N2   180.00   0.0  0
 BGR  CONST_14  C4    N3   C2   N2   180.00   0.0  0
 BGR  CONST_15  H8    C8   N9   C4   180.00   0.0  0
 BGR  CONST_16  HN1   N1   C2   N3   180.00   0.0  0
 BGR  CONST_18  HN2A  N2   C2   N1   180.00   0.0  0
 BGR  Var_01    C4'   C5'  O5'  P    150.37  30.0  2
 BGR  Var_02    OP1   P    O5'  C5'   59.78  30.0  1
 BGR  Var_03    H1BP  BP   P    O5'   63.74  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
 BGR  chir_02  C1'  N9   C2'  O4'  negativ
 BGR  chir_03  C3'  O3'  C4'  C2'  positiv
 BGR  chir_04  C4'  O4'  C3'  C5'  negativ
 BGR  chir_05  P    O5'  OP1  OP2  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
 BGR  plan-1  N1    0.020
 BGR  plan-1  C2    0.020
 BGR  plan-1  N2    0.020
 BGR  plan-1  N3    0.020
 BGR  plan-1  C4    0.020
 BGR  plan-1  C5    0.020
 BGR  plan-1  C6    0.020
 BGR  plan-1  O6    0.020
 BGR  plan-1  N7    0.020
 BGR  plan-1  C8    0.020
 BGR  plan-1  N9    0.020
 BGR  plan-1  C1'   0.020
 BGR  plan-1  H8    0.020
 BGR  plan-1  HN2   0.020
 BGR  plan-1  HN2A  0.020
 BGR  plan-1  HN1   0.020

