# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 19:00:34 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: (2R,4aR,6R,7R,7aS)-6-(6-amino-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(cnc12)[C@@H]3O[C@@H]4CO[P@@](O)(=S)O[C@H]4[C@H]3O
#
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
 RP1  RP1  '(2R,4aR,6R,7R,7aS)-6-(6-amino-9H-purin-9-yl)tetrahydro-4H-furo[3,2-d][1,3,2]dioxaphosphinine-2,7-diol 2-sulfide'  ligand  34  22  .  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_RP1
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
 RP1  P     P  P     0   1.186  -3.5045   0.2586   0.8673
 RP1  S1P   S  S1    0  -0.586  -5.2026  -0.4930   1.2997
 RP1  O2P   O  OH1   0  -0.668  -2.8165   1.2116   1.9565
 RP1  O5'   O  O2    0  -0.517  -3.5338   1.1068  -0.4987
 RP1  C5'   C  CH2   0  -0.314  -2.3292   1.5280  -1.1668
 RP1  C4'   C  CR15  0  -0.004  -1.4921   0.2784  -1.3315
 RP1  O4'   O  O     0  -0.477  -0.2164   0.4926  -1.8961
 RP1  C3'   C  CR15  0  -0.014  -1.1671  -0.3142   0.0280
 RP1  O3'   O  O2    0  -0.506  -2.3248  -0.8235   0.6651
 RP1  C2'   C  CR15  0  -0.123  -0.0909  -1.3153  -0.3361
 RP1  O2'   O  OH1   0  -0.683  -0.6827  -2.4141  -0.9538
 RP1  C1'   C  CR15  0   0.193   0.6914  -0.4345  -1.3520
 RP1  N9    N  NR5   0  -0.557   1.7631   0.3041  -0.7109
 RP1  C8    C  CR15  0   0.145   1.8386   1.6412  -0.4215
 RP1  N7    N  N     0  -0.458   2.9472   1.9763   0.1694
 RP1  C5    C  CR56  0  -0.146   3.6445   0.8032   0.2784
 RP1  C6    C  CR6   0   0.500   4.8997   0.4791   0.8216
 RP1  N6    N  NH2   0  -0.784   5.7066   1.3945   1.3628
 RP1  N1    N  N     0  -0.483   5.2918  -0.7982   0.7755
 RP1  C2    C  CR16  0   0.041   4.4952  -1.7030   0.2145
 RP1  N3    N  N     0  -0.426   3.3019  -1.5251  -0.3244
 RP1  C4    C  CR56  0   0.538   2.9266  -0.2496  -0.2639
 RP1  HOP2  H  HOH1  0   0.522  -3.3803   1.9215   2.2876
 RP1  H5'1  H  HCH2  0   0.325  -1.8116   2.2948  -0.5833
 RP1  H5'2  H  HCH2  0   0.315  -2.6384   1.9603  -2.1159
 RP1  H4'   H  HCR5  0   0.276  -2.0614  -0.4409  -1.9330
 RP1  H3'   H  HCR5  0   0.281  -0.6985   0.4499   0.6617
 RP1  H2'   H  HCR5  0   0.283   0.5357  -1.5986   0.5156
 RP1  HO2'  H  HOH1  0   0.438  -0.0265  -3.1089  -1.0575
 RP1  H1'   H  HCR5  0   0.310   1.1330  -1.0475  -2.1429
 RP1  H8    H  HCR5  0   0.272   1.0506   2.3289  -0.6822
 RP1  HN61  H  HNH2  0   0.420   6.5641   1.1197   1.8069
 RP1  HN62  H  HNH2  0   0.424   5.4063   2.3461   1.4710
 RP1  H2    H  HCR6  0   0.279   4.8746  -2.7192   0.2076

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
 RP1  P    S1P   double    1.907  0.020  1.907
 RP1  P    O2P   single    1.602  0.020  1.602
 RP1  P    O5'   single    1.608  0.020  1.608
 RP1  P    O3'   single    1.614  0.020  1.614
 RP1  O2P  HOP2  single    0.850  0.020  0.980
 RP1  O5'  C5'   single    1.440  0.020  1.440
 RP1  C5'  C4'   single    1.513  0.020  1.513
 RP1  C5'  H5'1  single    0.970  0.020  1.090
 RP1  C5'  H5'2  single    0.970  0.020  1.090
 RP1  C4'  O4'   single    1.411  0.020  1.411
 RP1  C4'  C3'   single    1.518  0.020  1.518
 RP1  C4'  H4'   single    0.970  0.020  1.090
 RP1  O4'  C1'   single    1.407  0.020  1.407
 RP1  C3'  O3'   single    1.416  0.020  1.416
 RP1  C3'  C2'   single    1.514  0.020  1.514
 RP1  C3'  H3'   single    0.970  0.020  1.090
 RP1  C2'  O2'   single    1.393  0.020  1.393
 RP1  C2'  C1'   single    1.556  0.020  1.556
 RP1  C2'  H2'   single    0.970  0.020  1.090
 RP1  O2'  HO2'  single    0.850  0.020  0.980
 RP1  C1'  N9    single    1.451  0.020  1.451
 RP1  C1'  H1'   single    0.970  0.020  1.090
 RP1  N9   C8    aromatic  1.370  0.020  1.370
 RP1  N9   C4    aromatic  1.364  0.020  1.364
 RP1  C8   N7    aromatic  1.300  0.020  1.300
 RP1  C8   H8    single    0.930  0.020  1.080
 RP1  N7   C5    aromatic  1.369  0.020  1.369
 RP1  C5   C6    aromatic  1.406  0.020  1.406
 RP1  C5   C4    aromatic  1.385  0.020  1.385
 RP1  C6   N6    single    1.335  0.020  1.335
 RP1  C6   N1    aromatic  1.337  0.020  1.337
 RP1  N6   HN61  single    0.860  0.020  1.020
 RP1  N6   HN62  single    0.860  0.020  1.020
 RP1  N1   C2    aromatic  1.330  0.020  1.330
 RP1  C2   N3    aromatic  1.321  0.020  1.321
 RP1  C2   H2    single    0.930  0.020  1.080
 RP1  N3   C4    aromatic  1.331  0.020  1.331

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
 RP1  O3'   P    O5'   105.10  3.000
 RP1  O3'   P    O2P    99.80  3.000
 RP1  O5'   P    O2P   105.76  3.000
 RP1  O3'   P    S1P   114.53  3.000
 RP1  O5'   P    S1P   112.60  3.000
 RP1  O2P   P    S1P   117.56  3.000
 RP1  HOP2  O2P  P     114.82  3.000
 RP1  C5'   O5'  P     122.20  3.000
 RP1  H5'2  C5'  H5'1  108.75  3.000
 RP1  H5'2  C5'  C4'   112.99  3.000
 RP1  H5'1  C5'  C4'   112.04  3.000
 RP1  H5'2  C5'  O5'   106.45  3.000
 RP1  H5'1  C5'  O5'   110.69  3.000
 RP1  C4'   C5'  O5'   105.76  3.000
 RP1  H4'   C4'  C3'   110.25  3.000
 RP1  H4'   C4'  O4'   110.44  3.000
 RP1  C3'   C4'  O4'   102.94  3.000
 RP1  H4'   C4'  C5'   108.31  3.000
 RP1  C3'   C4'  C5'   110.08  3.000
 RP1  O4'   C4'  C5'   114.73  3.000
 RP1  C1'   O4'  C4'   109.18  3.000
 RP1  H3'   C3'  C2'   107.19  3.000
 RP1  H3'   C3'  O3'   109.86  3.000
 RP1  C2'   C3'  O3'   116.84  3.000
 RP1  H3'   C3'  C4'   109.67  3.000
 RP1  C2'   C3'  C4'   101.23  3.000
 RP1  O3'   C3'  C4'   111.60  3.000
 RP1  C3'   O3'  P     114.39  3.000
 RP1  H2'   C2'  C1'   111.51  3.000
 RP1  H2'   C2'  O2'   112.59  3.000
 RP1  C1'   C2'  O2'   111.76  3.000
 RP1  H2'   C2'  C3'   113.01  3.000
 RP1  C1'   C2'  C3'    98.06  3.000
 RP1  O2'   C2'  C3'   109.05  3.000
 RP1  HO2'  O2'  C2'   109.16  3.000
 RP1  H1'   C1'  N9    107.86  3.000
 RP1  H1'   C1'  C2'   110.98  3.000
 RP1  N9    C1'  C2'   111.78  3.000
 RP1  H1'   C1'  O4'   110.50  3.000
 RP1  N9    C1'  O4'   108.18  3.000
 RP1  C2'   C1'  O4'   107.52  3.000
 RP1  C4    N9   C8    106.26  3.000
 RP1  C4    N9   C1'   124.63  3.000
 RP1  C8    N9   C1'   129.11  3.000
 RP1  H8    C8   N7    124.67  3.000
 RP1  H8    C8   N9    122.09  3.000
 RP1  N7    C8   N9    113.24  3.000
 RP1  C5    N7   C8    104.46  3.000
 RP1  C4    C5   C6    116.04  3.000
 RP1  C4    C5   N7    110.87  3.000
 RP1  C6    C5   N7    133.09  3.000
 RP1  N1    C6   N6    119.47  3.000
 RP1  N1    C6   C5    117.96  3.000
 RP1  N6    C6   C5    122.57  3.000
 RP1  HN62  N6   HN61  117.87  3.000
 RP1  HN62  N6   C6    120.86  3.000
 RP1  HN61  N6   C6    120.52  3.000
 RP1  C2    N1   C6    119.28  3.000
 RP1  H2    C2   N3    116.07  3.000
 RP1  H2    C2   N1    115.51  3.000
 RP1  N3    C2   N1    128.42  3.000
 RP1  C4    N3   C2    111.42  3.000
 RP1  N3    C4   C5    126.88  3.000
 RP1  N3    C4   N9    127.93  3.000
 RP1  C5    C4   N9    105.18  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
 RP1  CONST_01  C5    N7   C8   N9     0.00   0.0  0
 RP1  CONST_02  N7    C5   C4   N9     0.00   0.0  0
 RP1  CONST_03  C6    C5   C4   N9   180.00   0.0  0
 RP1  CONST_04  C2    N3   C4   N9   180.00   0.0  0
 RP1  CONST_05  C5    C4   N9   C8     0.00   0.0  0
 RP1  CONST_06  N3    C4   N9   C8   180.00   0.0  0
 RP1  CONST_07  C6    C5   N7   C8   180.00   0.0  0
 RP1  CONST_08  C4    C5   N7   C8     0.00   0.0  0
 RP1  CONST_09  C4    N9   C8   N7     0.00   0.0  0
 RP1  CONST_10  N1    C6   C5   N7   180.00   0.0  0
 RP1  CONST_11  N3    C4   C5   N7   180.00   0.0  0
 RP1  CONST_12  C2    N1   C6   C5     0.00   0.0  0
 RP1  CONST_13  C2    N3   C4   C5     0.00   0.0  0
 RP1  CONST_14  N3    C4   C5   C6     0.00   0.0  0
 RP1  CONST_15  N3    C2   N1   C6     0.00   0.0  0
 RP1  CONST_16  C4    C5   C6   N1     0.00   0.0  0
 RP1  CONST_17  C4    N3   C2   N1     0.00   0.0  0
 RP1  CONST_18  N7    C8   N9   C1'  180.00   0.0  0
 RP1  CONST_19  C5    C4   N9   C1'  180.00   0.0  0
 RP1  CONST_20  N3    C4   N9   C1'    0.00   0.0  0
 RP1  CONST_21  N6    C6   C5   N7     0.00   0.0  0
 RP1  CONST_22  C4    C5   C6   N6   180.00   0.0  0
 RP1  CONST_23  C2    N1   C6   N6   180.00   0.0  0
 RP1  CONST_24  H8    C8   N9   C1'    0.00   0.0  0
 RP1  CONST_25  H2    C2   N1   C6   180.00   0.0  0
 RP1  CONST_26  HN61  N6   C6   C5   180.00   0.0  0
 RP1  CONST_27  HN62  N6   C6   C5     0.00   0.0  0
 RP1  Var_01    C4'   C5'  O5'  P     52.30  30.0  1
 RP1  Var_02    O3'   P    O5'  C5'  -41.45  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
 RP1  chir_02  C4'  C5'  O4'  C3'  negativ
 RP1  chir_03  C3'  O3'  C4'  C2'  positiv
 RP1  chir_04  C2'  O2'  C3'  C1'  positiv
 RP1  chir_05  C1'  O4'  N9   C2'  negativ
 RP1  chir_06  P    O2P  O5'  O3'  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
 RP1  plan-1  C1'   0.020
 RP1  plan-1  N9    0.020
 RP1  plan-1  C8    0.020
 RP1  plan-1  N7    0.020
 RP1  plan-1  C5    0.020
 RP1  plan-1  C6    0.020
 RP1  plan-1  N6    0.020
 RP1  plan-1  N1    0.020
 RP1  plan-1  C2    0.020
 RP1  plan-1  N3    0.020
 RP1  plan-1  C4    0.020
 RP1  plan-1  H8    0.020
 RP1  plan-1  H2    0.020
 RP1  plan-2  C6    0.020
 RP1  plan-2  N6    0.020
 RP1  plan-2  HN61  0.020
 RP1  plan-2  HN62  0.020

