# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 11:37:05 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: (2R,4aR,6R,7R,7aS)-6-(6-amino-8-bromo-9H-purin-9-yl)tetrahydro-4H-furo[3,2-d][1,3,2]dioxaphosphinine-2,7-diol 2-sulfide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n([C@@H]3O[C@@H]4CO[P@@](O)(=S)O[C@H]4[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
 RP2  RP2  '(2R,4aR,6R,7R,7aS)-6-(6-amino-8-bromo-9H-purin-9-yl)tetrahydro-4H-furo[3,2-d][1,3,2]dioxaphosphinine-2,7-diol 2-sulfide'  ligand  34  23  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RP2
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
 RP2  P     P   P     0   1.212  -4.1884  -0.2019   0.1822
 RP2  BR    BR  BR    0   0.053   0.7044   2.3486   0.4170
 RP2  N1    N   N     0  -0.470   5.5189  -1.5677  -0.0524
 RP2  C2    C   CR16  0   0.053   4.5344  -2.3873  -0.4056
 RP2  N3    N   N     0  -0.460   3.2405  -2.1254  -0.4983
 RP2  C4    C   CR56  0   0.510   2.9744  -0.8631  -0.1858
 RP2  C5    C   CR56  0   0.003   3.8854   0.1011   0.1984
 RP2  C6    C   CR6   0   0.467   5.2340  -0.2983   0.2610
 RP2  N6    N   NH2   0  -0.813   6.2157   0.5248   0.6217
 RP2  N7    N   N     0  -0.418   3.2558   1.2921   0.4480
 RP2  C8    C   CR5   0   0.291   2.0072   1.0482   0.2273
 RP2  N9    N   NR5   0  -0.568   1.7484  -0.2431  -0.1679
 RP2  C1'   C   CH1   0   0.175   0.5214  -0.9226  -0.4973
 RP2  S1P   S   S1    0  -0.466  -5.8270  -1.1688   0.3577
 RP2  C2'   C   CH1   0  -0.075  -0.4258  -1.2675   0.7048
 RP2  O2'   O   OH1   0  -0.648  -0.7567  -2.6214   0.7193
 RP2  O2P   O   OH1   0  -0.722  -4.0539   1.1761   0.9835
 RP2  C3'   C   CH1   0  -0.003  -1.6548  -0.4597   0.3185
 RP2  O3'   O   O2    0  -0.565  -2.9005  -0.9847   0.7531
 RP2  C4'   C   CH1   0   0.006  -1.5638  -0.4427  -1.1990
 RP2  O4'   O   O2    0  -0.480  -0.2075  -0.1455  -1.4202
 RP2  C5'   C   CH2   0  -0.220  -2.5314   0.5696  -1.7685
 RP2  O5'   O   O2    0  -0.573  -3.8419   0.1350  -1.3511
 RP2  HN6   H   HNH2  0   0.408   7.1697   0.2066   0.6206
 RP2  HN6A  H   HNH2  0   0.415   6.0378   1.4941   0.8190
 RP2  H1'   H   HCH1  0   0.288   0.8323  -1.8690  -0.9521
 RP2  H2'   H   HCH1  0   0.283   0.0090  -0.9387   1.6541
 RP2  HO2'  H   HOH1  0   0.469  -0.0261  -3.1187   1.1008
 RP2  HO2P  H   HOH1  0   0.505  -4.7604   1.8150   0.8141
 RP2  H3'   H   HCH1  0   0.275  -1.5295   0.5571   0.7026
 RP2  H4'   H   HCH1  0   0.271  -1.8184  -1.4348  -1.5994
 RP2  H5'   H   HCH2  0   0.253  -2.3242   1.5794  -1.4044
 RP2  H5'A  H   HCH2  0   0.287  -2.5435   0.5825  -2.8565
 RP2  H2    H   HCR6  0   0.258   4.8342  -3.4008  -0.6473

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
 RP2  P    S1P   double    1.911  0.020  1.911
 RP2  P    O2P   single    1.600  0.020  1.600
 RP2  P    O3'   single    1.612  0.020  1.612
 RP2  P    O5'   single    1.608  0.020  1.608
 RP2  BR   C8    single    1.851  0.020  1.851
 RP2  N1   C2    aromatic  1.329  0.020  1.329
 RP2  N1   C6    aromatic  1.338  0.020  1.338
 RP2  C2   N3    aromatic  1.323  0.020  1.323
 RP2  N3   C4    aromatic  1.327  0.020  1.327
 RP2  C4   C5    aromatic  1.381  0.020  1.381
 RP2  C4   N9    aromatic  1.374  0.020  1.374
 RP2  C5   C6    aromatic  1.408  0.020  1.408
 RP2  C5   N7    aromatic  1.370  0.020  1.370
 RP2  C6   N6    single    1.331  0.020  1.331
 RP2  N7   C8    aromatic  1.291  0.020  1.291
 RP2  C8   N9    aromatic  1.375  0.020  1.375
 RP2  N9   C1'   single    1.441  0.020  1.441
 RP2  C1'  C2'   single    1.569  0.020  1.569
 RP2  C1'  O4'   single    1.410  0.020  1.410
 RP2  C2'  O2'   single    1.394  0.020  1.394
 RP2  C2'  C3'   single    1.521  0.020  1.521
 RP2  C3'  O3'   single    1.420  0.020  1.420
 RP2  C3'  C4'   single    1.520  0.020  1.520
 RP2  C4'  O4'   single    1.406  0.020  1.406
 RP2  C4'  C5'   single    1.512  0.020  1.512
 RP2  C5'  O5'   single    1.442  0.020  1.442
 RP2  C2   H2    single    0.930  0.020  1.080
 RP2  N6   HN6   single    0.860  0.020  1.020
 RP2  N6   HN6A  single    0.860  0.020  1.020
 RP2  C1'  H1'   single    0.970  0.020  1.090
 RP2  C2'  H2'   single    0.970  0.020  1.090
 RP2  O2'  HO2'  single    0.850  0.020  0.980
 RP2  O2P  HO2P  single    0.850  0.020  0.980
 RP2  C3'  H3'   single    0.970  0.020  1.090
 RP2  C4'  H4'   single    0.970  0.020  1.090
 RP2  C5'  H5'   single    0.970  0.020  1.090
 RP2  C5'  H5'A  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
 RP2  O5'   P    O3'  105.51  3.000
 RP2  O5'   P    O2P  106.21  3.000
 RP2  O3'   P    O2P  100.01  3.000
 RP2  O5'   P    S1P  112.24  3.000
 RP2  O3'   P    S1P  114.02  3.000
 RP2  O2P   P    S1P  117.52  3.000
 RP2  C6    N1   C2   119.31  3.000
 RP2  H2    C2   N3   116.09  3.000
 RP2  H2    C2   N1   115.53  3.000
 RP2  N3    C2   N1   128.38  3.000
 RP2  C4    N3   C2   111.58  3.000
 RP2  N9    C4   C5   105.66  3.000
 RP2  N9    C4   N3   127.67  3.000
 RP2  C5    C4   N3   126.67  3.000
 RP2  N7    C5   C6   132.73  3.000
 RP2  N7    C5   C4   110.76  3.000
 RP2  C6    C5   C4   116.50  3.000
 RP2  N6    C6   C5   122.90  3.000
 RP2  N6    C6   N1   119.54  3.000
 RP2  C5    C6   N1   117.55  3.000
 RP2  HN6A  N6   HN6  118.25  3.000
 RP2  HN6A  N6   C6   121.27  3.000
 RP2  HN6   N6   C6   120.25  3.000
 RP2  C8    N7   C5   104.41  3.000
 RP2  N9    C8   N7   114.12  3.000
 RP2  N9    C8   BR   123.84  3.000
 RP2  N7    C8   BR   122.04  3.000
 RP2  C1'   N9   C8   131.99  3.000
 RP2  C1'   N9   C4   122.96  3.000
 RP2  C8    N9   C4   105.04  3.000
 RP2  H1'   C1'  O4'  110.57  3.000
 RP2  H1'   C1'  C2'  107.44  3.000
 RP2  O4'   C1'  C2'  108.10  3.000
 RP2  H1'   C1'  N9   105.12  3.000
 RP2  O4'   C1'  N9   109.27  3.000
 RP2  C2'   C1'  N9   116.28  3.000
 RP2  H2'   C2'  C3'  112.45  3.000
 RP2  H2'   C2'  O2'  112.15  3.000
 RP2  C3'   C2'  O2'  109.07  3.000
 RP2  H2'   C2'  C1'  111.01  3.000
 RP2  C3'   C2'  C1'  100.17  3.000
 RP2  O2'   C2'  C1'  111.40  3.000
 RP2  HO2'  O2'  C2'  109.01  3.000
 RP2  HO2P  O2P  P    114.81  3.000
 RP2  H3'   C3'  C4'  109.46  3.000
 RP2  H3'   C3'  O3'  109.67  3.000
 RP2  C4'   C3'  O3'  111.23  3.000
 RP2  H3'   C3'  C2'  108.18  3.000
 RP2  C4'   C3'  C2'  102.19  3.000
 RP2  O3'   C3'  C2'  115.78  3.000
 RP2  C3'   O3'  P    114.40  3.000
 RP2  H4'   C4'  C5'  108.59  3.000
 RP2  H4'   C4'  O4'  110.89  3.000
 RP2  C5'   C4'  O4'  114.62  3.000
 RP2  H4'   C4'  C3'  109.85  3.000
 RP2  C5'   C4'  C3'  110.20  3.000
 RP2  O4'   C4'  C3'  102.54  3.000
 RP2  C4'   O4'  C1'  106.21  3.000
 RP2  H5'A  C5'  H5'  108.92  3.000
 RP2  H5'A  C5'  O5'  106.43  3.000
 RP2  H5'   C5'  O5'  110.74  3.000
 RP2  H5'A  C5'  C4'  113.06  3.000
 RP2  H5'   C5'  C4'  111.82  3.000
 RP2  O5'   C5'  C4'  105.71  3.000
 RP2  C5'   O5'  P    122.34  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
 RP2  CONST_01  C4    N3   C2   N1     0.00   0.0  0
 RP2  CONST_02  C4    C5   C6   N1     0.00   0.0  0
 RP2  CONST_03  N7    C5   C6   N1   180.00   0.0  0
 RP2  CONST_04  C5    C6   N1   C2     0.00   0.0  0
 RP2  CONST_05  C5    C4   N3   C2     0.00   0.0  0
 RP2  CONST_06  N9    C4   N3   C2   180.00   0.0  0
 RP2  CONST_07  C6    N1   C2   N3     0.00   0.0  0
 RP2  CONST_08  C6    C5   C4   N3     0.00   0.0  0
 RP2  CONST_09  N7    C5   C4   N3   180.00   0.0  0
 RP2  CONST_10  C8    N9   C4   N3   180.00   0.0  0
 RP2  CONST_11  C8    N7   C5   C4     0.00   0.0  0
 RP2  CONST_12  N7    C8   N9   C4     0.00   0.0  0
 RP2  CONST_13  C8    N9   C4   C5     0.00   0.0  0
 RP2  CONST_14  N9    C8   N7   C5     0.00   0.0  0
 RP2  CONST_15  N9    C4   C5   C6   180.00   0.0  0
 RP2  CONST_16  C8    N7   C5   C6   180.00   0.0  0
 RP2  CONST_17  N9    C4   C5   N7     0.00   0.0  0
 RP2  CONST_18  C1'   N9   C4   N3     0.00   0.0  0
 RP2  CONST_19  C1'   N9   C4   C5   180.00   0.0  0
 RP2  CONST_20  C1'   N9   C8   N7   180.00   0.0  0
 RP2  CONST_21  C5    N7   C8   BR   180.00   0.0  0
 RP2  CONST_22  C4    N9   C8   BR   180.00   0.0  0
 RP2  CONST_23  C1'   N9   C8   BR     0.00   0.0  0
 RP2  CONST_24  N6    C6   N1   C2   180.00   0.0  0
 RP2  CONST_25  N6    C6   C5   C4   180.00   0.0  0
 RP2  CONST_26  N7    C5   C6   N6     0.00   0.0  0
 RP2  CONST_27  H2    C2   N3   C4   180.00   0.0  0
 RP2  CONST_28  HN6   N6   C6   N1     0.00   0.0  0
 RP2  CONST_29  HN6A  N6   C6   N1   180.00   0.0  0
 RP2  Var_01    C4'   C5'  O5'  P     51.48  30.0  1
 RP2  Var_02    O5'   P    O3'  C3'   40.33  30.0  1

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
 RP2  chir_02  C1'  N9   C2'  O4'  negativ
 RP2  chir_03  C2'  O2'  C3'  C1'  positiv
 RP2  chir_04  C3'  O3'  C4'  C2'  positiv
 RP2  chir_05  C4'  O4'  C3'  C5'  negativ
 RP2  chir_06  P    O2P  O3'  O5'  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
 RP2  plan-1  BR    0.020
 RP2  plan-1  N1    0.020
 RP2  plan-1  C2    0.020
 RP2  plan-1  N3    0.020
 RP2  plan-1  C4    0.020
 RP2  plan-1  C5    0.020
 RP2  plan-1  C6    0.020
 RP2  plan-1  N6    0.020
 RP2  plan-1  N7    0.020
 RP2  plan-1  C8    0.020
 RP2  plan-1  N9    0.020
 RP2  plan-1  C1'   0.020
 RP2  plan-1  H2    0.020
 RP2  plan-2  C6    0.020
 RP2  plan-2  N6    0.020
 RP2  plan-2  HN6   0.020
 RP2  plan-2  HN6A  0.020

