# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 30 22:05:07 2021
#   Inital geometry file: a 114 line input string
#   Ligand name: 5'-O-[(S)-hydroxy(phosphonomethyl)phosphoryl]guanosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@](O)(=O)C[P](O)(O)=O)[C@@H](O)[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
 GP2  GP2  5'-O-[(S)-hydroxy(phosphonomethyl)phosphoryl]guanosine  ligand  45  28  .  2021-08-10  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_GP2
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
 GP2  O6    O  O     0  -0.474  19.2353  -8.5478  48.8812
 GP2  C6    C  CR6   0   0.505  20.0930  -7.7873  48.4646
 GP2  C5    C  CR56  0  -0.098  20.3787  -6.4520  48.8705
 GP2  N7    N  N     0  -0.442  19.7869  -5.6621  49.8235
 GP2  C4    C  CR56  0   0.510  21.4144  -5.7777  48.2518
 GP2  N3    N  N     0  -0.514  22.2285  -6.2125  47.2823
 GP2  C2    C  CR6   0   0.696  21.9677  -7.4386  46.9000
 GP2  N1    N  NR16  0  -0.728  20.9681  -8.1905  47.4477
 GP2  N2    N  NH2   0  -0.833  22.6758  -7.9943  45.9096
 GP2  N9    N  NR5   0  -0.542  21.4459  -4.5501  48.8403
 GP2  C8    C  CR15  0   0.091  20.4405  -4.5438  49.7796
 GP2  C1'   C  CH1   0   0.209  22.3642  -3.4870  48.5308
 GP2  C2'   C  CH1   0  -0.008  21.6966  -2.2183  48.0055
 GP2  O2'   O  OH1   0  -0.653  21.4189  -2.3685  46.6502
 GP2  C3'   C  CH1   0  -0.056  22.7355  -1.1589  48.3759
 GP2  O3'   O  OH1   0  -0.667  23.7193  -1.1626  47.3744
 GP2  O4'   O  O2    0  -0.495  23.0465  -3.1097  49.6943
 GP2  C4'   C  CH1   0  -0.004  23.2757  -1.7017  49.7094
 GP2  C5'   C  CH2   0  -0.212  22.6779  -1.0929  50.9580
 GP2  O5'   O  O2    0  -0.588  21.2685  -1.3204  51.0133
 GP2  PA    P  P     0   1.389  20.2181  -0.1147  51.0854
 GP2  O1A   O  O     0  -0.687  20.4853   1.0355  50.1917
 GP2  O2A   O  OH1   0  -0.734  18.9194  -0.9952  50.7869
 GP2  C3A   C  CH2   0  -1.036  20.1451   0.3601  52.8320
 GP2  PB    P  P     0   1.377  19.0630   1.7723  53.1311
 GP2  O1B   O  O     0  -0.697  19.5576   3.1105  52.7374
 GP2  O3B   O  OH1   0  -0.736  18.7449   1.5984  54.6924
 GP2  O2B   O  OH1   0  -0.758  17.7447   1.2831  52.3425
 GP2  HN1   H  HNR6  0   0.425  20.8286  -9.1306  47.0994
 GP2  HN21  H  HNH2  0   0.416  22.6173  -8.9773  45.7069
 GP2  HN22  H  HNH2  0   0.414  23.4927  -7.5081  45.5817
 GP2  H8    H  HCR5  0   0.289  20.2497  -3.6852  50.4045
 GP2  H1'   H  HCH1  0   0.261  23.0473  -3.8875  47.7740
 GP2  H1    H  HCH1  0   0.241  20.7830  -2.0212  48.5795
 GP2  H2'   H  HOH1  0   0.464  20.8470  -1.6465  46.3719
 GP2  H3'   H  HCH1  0   0.251  22.2901  -0.1645  48.4990
 GP2  H2    H  HOH1  0   0.457  24.4018  -0.5281  47.6155
 GP2  H4'   H  HCH1  0   0.265  24.3540  -1.5136  49.7727
 GP2  H5'1  H  HCH2  0   0.272  23.1190  -1.5501  51.8447
 GP2  H5'2  H  HCH2  0   0.251  22.9226  -0.0274  50.9766
 GP2  H2A   H  HOH1  0   0.497  18.0891  -0.5037  50.8618
 GP2  H3A1  H  HCH2  0   0.341  19.8309  -0.4977  53.4307
 GP2  H3A2  H  HCH2  0   0.338  21.1487   0.6397  53.1642
 GP2  H3B   H  HOH1  0   0.498  18.4705   2.4174  55.1280
 GP2  H2B   H  HOH1  0   0.501  17.1329   1.9934  52.1026

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
 GP2  O6   C6    double    1.220  0.020  1.220
 GP2  C6   C5    single    1.425  0.020  1.425
 GP2  C6   N1    single    1.401  0.020  1.401
 GP2  C5   N7    aromatic  1.372  0.020  1.372
 GP2  C5   C4    aromatic  1.382  0.020  1.382
 GP2  N7   C8    aromatic  1.296  0.020  1.296
 GP2  C4   N3    single    1.339  0.020  1.339
 GP2  C4   N9    aromatic  1.362  0.020  1.362
 GP2  N3   C2    double    1.311  0.020  1.311
 GP2  C2   N1    single    1.365  0.020  1.365
 GP2  C2   N2    single    1.338  0.020  1.338
 GP2  N1   HN1   single    0.860  0.020  1.020
 GP2  N2   HN21  single    0.890  0.020  1.040
 GP2  N2   HN22  single    0.890  0.020  1.040
 GP2  N9   C8    aromatic  1.376  0.020  1.376
 GP2  N9   C1'   single    1.438  0.020  1.438
 GP2  C8   H8    single    0.930  0.020  1.080
 GP2  C1'  C2'   single    1.527  0.020  1.527
 GP2  C1'  O4'   single    1.401  0.020  1.401
 GP2  C1'  H1'   single    0.970  0.020  1.090
 GP2  C2'  O2'   single    1.392  0.020  1.392
 GP2  C2'  C3'   single    1.529  0.020  1.529
 GP2  C2'  H1    single    0.970  0.020  1.090
 GP2  O2'  H2'   single    0.850  0.020  0.980
 GP2  C3'  O3'   single    1.404  0.020  1.404
 GP2  C3'  C4'   single    1.538  0.020  1.538
 GP2  C3'  H3'   single    0.970  0.020  1.090
 GP2  O3'  H2    single    0.850  0.020  0.980
 GP2  O4'  C4'   single    1.427  0.020  1.427
 GP2  C4'  C5'   single    1.512  0.020  1.512
 GP2  C4'  H4'   single    0.970  0.020  1.090
 GP2  C5'  O5'   single    1.429  0.020  1.429
 GP2  C5'  H5'1  single    0.970  0.020  1.090
 GP2  C5'  H5'2  single    0.970  0.020  1.090
 GP2  O5'  PA    single    1.601  0.020  1.601
 GP2  PA   O1A   double    1.481  0.020  1.481
 GP2  PA   O2A   single    1.597  0.020  1.597
 GP2  PA   C3A   single    1.811  0.020  1.811
 GP2  O2A  H2A   single    0.850  0.020  0.980
 GP2  C3A  PB    single    1.804  0.020  1.804
 GP2  C3A  H3A1  single    0.970  0.020  1.090
 GP2  C3A  H3A2  single    0.970  0.020  1.090
 GP2  PB   O1B   double    1.480  0.020  1.480
 GP2  PB   O3B   single    1.603  0.020  1.603
 GP2  PB   O2B   single    1.612  0.020  1.612
 GP2  O3B  H3B   single    0.850  0.020  0.980
 GP2  O2B  H2B   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
 GP2  N1    C6   C5    110.57  3.000
 GP2  N1    C6   O6    120.51  3.000
 GP2  C5    C6   O6    128.92  3.000
 GP2  C4    C5   N7    110.69  3.000
 GP2  C4    C5   C6    118.69  3.000
 GP2  N7    C5   C6    130.62  3.000
 GP2  C8    N7   C5    104.82  3.000
 GP2  N9    C4   N3    126.28  3.000
 GP2  N9    C4   C5    105.29  3.000
 GP2  N3    C4   C5    128.43  3.000
 GP2  C2    N3   C4    113.21  3.000
 GP2  N2    C2   N1    117.10  3.000
 GP2  N2    C2   N3    119.93  3.000
 GP2  N1    C2   N3    122.95  3.000
 GP2  HN1   N1   C2    118.31  3.000
 GP2  HN1   N1   C6    115.54  3.000
 GP2  C2    N1   C6    126.15  3.000
 GP2  HN22  N2   HN21  117.02  3.000
 GP2  HN22  N2   C2    118.06  3.000
 GP2  HN21  N2   C2    121.62  3.000
 GP2  C1'   N9   C8    127.59  3.000
 GP2  C1'   N9   C4    126.02  3.000
 GP2  C8    N9   C4    106.40  3.000
 GP2  H8    C8   N9    121.89  3.000
 GP2  H8    C8   N7    125.30  3.000
 GP2  N9    C8   N7    112.81  3.000
 GP2  H1'   C1'  O4'   111.63  3.000
 GP2  H1'   C1'  C2'   109.80  3.000
 GP2  O4'   C1'  C2'   105.96  3.000
 GP2  H1'   C1'  N9    106.05  3.000
 GP2  O4'   C1'  N9    109.35  3.000
 GP2  C2'   C1'  N9    114.14  3.000
 GP2  H1    C2'  C3'   108.34  3.000
 GP2  H1    C2'  O2'   111.27  3.000
 GP2  C3'   C2'  O2'   116.50  3.000
 GP2  H1    C2'  C1'   109.48  3.000
 GP2  C3'   C2'  C1'   101.26  3.000
 GP2  O2'   C2'  C1'   109.43  3.000
 GP2  H2'   O2'  C2'   108.62  3.000
 GP2  H3'   C3'  C4'   111.43  3.000
 GP2  H3'   C3'  O3'   111.54  3.000
 GP2  C4'   C3'  O3'   111.81  3.000
 GP2  H3'   C3'  C2'   112.30  3.000
 GP2  C4'   C3'  C2'   101.78  3.000
 GP2  O3'   C3'  C2'   107.55  3.000
 GP2  H2    O3'  C3'   108.46  3.000
 GP2  C4'   O4'  C1'   110.67  3.000
 GP2  H4'   C4'  C5'   105.79  3.000
 GP2  H4'   C4'  O4'   109.15  3.000
 GP2  C5'   C4'  O4'   110.03  3.000
 GP2  H4'   C4'  C3'   109.57  3.000
 GP2  C5'   C4'  C3'   115.79  3.000
 GP2  O4'   C4'  C3'   106.43  3.000
 GP2  H5'2  C5'  H5'1  107.71  3.000
 GP2  H5'2  C5'  O5'   112.04  3.000
 GP2  H5'1  C5'  O5'   107.50  3.000
 GP2  H5'2  C5'  C4'   108.53  3.000
 GP2  H5'1  C5'  C4'   110.03  3.000
 GP2  O5'   C5'  C4'   110.97  3.000
 GP2  PA    O5'  C5'   121.95  3.000
 GP2  C3A   PA   O2A   106.98  3.000
 GP2  C3A   PA   O1A   112.68  3.000
 GP2  O2A   PA   O1A   117.52  3.000
 GP2  C3A   PA   O5'   105.50  3.000
 GP2  O2A   PA   O5'    96.31  3.000
 GP2  O1A   PA   O5'   116.07  3.000
 GP2  H2A   O2A  PA    113.78  3.000
 GP2  H3A2  C3A  H3A1  107.36  3.000
 GP2  H3A2  C3A  PB    107.46  3.000
 GP2  H3A1  C3A  PB    110.57  3.000
 GP2  H3A2  C3A  PA    108.84  3.000
 GP2  H3A1  C3A  PA    109.53  3.000
 GP2  PB    C3A  PA    112.90  3.000
 GP2  O2B   PB   O3B   106.34  3.000
 GP2  O2B   PB   O1B   114.68  3.000
 GP2  O3B   PB   O1B   115.06  3.000
 GP2  O2B   PB   C3A    99.90  3.000
 GP2  O3B   PB   C3A   101.28  3.000
 GP2  O1B   PB   C3A   117.59  3.000
 GP2  H3B   O3B  PB    113.77  3.000
 GP2  H2B   O2B  PB    114.55  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
 GP2  CONST_01  N9    C8   N7   C5     0.00   0.0  0
 GP2  CONST_02  C8    N9   C4   C5     0.00   0.0  0
 GP2  CONST_03  N9    C4   C5   N7     0.00   0.0  0
 GP2  CONST_04  C4    N9   C8   N7     0.00   0.0  0
 GP2  CONST_05  C8    N7   C5   C4     0.00   0.0  0
 GP2  CONST_06  C1'   N9   C4   C5   180.00   0.0  0
 GP2  CONST_07  C1'   N9   C8   N7   180.00   0.0  0
 GP2  CONST_08  C1'   N9   C4   N3     0.00   0.0  0
 GP2  CONST_09  N3    C2   N1   C6     0.00   0.0  0
 GP2  CONST_10  C2    N1   C6   C5     0.00   0.0  0
 GP2  CONST_11  N1    C2   N3   C4     0.00   0.0  0
 GP2  CONST_12  C2    N1   C6   O6   180.00   0.0  0
 GP2  CONST_13  N2    C2   N1   C6   180.00   0.0  0
 GP2  CONST_14  N2    C2   N3   C4   180.00   0.0  0
 GP2  CONST_15  H8    C8   N7   C5   180.00   0.0  0
 GP2  CONST_16  HN1   N1   C6   C5   180.00   0.0  0
 GP2  CONST_17  HN21  N2   C2   N3   180.00   0.0  0
 GP2  CONST_18  HN22  N2   C2   N3     0.00   0.0  0
 GP2  Var_01    O1A   PA   O5'  C5'   42.99  30.0  3
 GP2  Var_02    PB    C3A  PA   O5'  177.30  30.0  3
 GP2  Var_03    O1B   PB   C3A  PA   -74.86  30.0  3
 GP2  Var_04    H5'1  C5'  O5'  PA   118.44  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
 GP2  chir_01  C1'  N9   C2'  O4'  negativ
 GP2  chir_02  C2'  O2'  C3'  C1'  positiv
 GP2  chir_03  C3'  O3'  C4'  C2'  positiv
 GP2  chir_04  C4'  O4'  C3'  C5'  negativ
 GP2  chir_05  PA   O1A  O2A  C3A  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
 GP2  plan-1  O6    0.020
 GP2  plan-1  C6    0.020
 GP2  plan-1  C5    0.020
 GP2  plan-1  N7    0.020
 GP2  plan-1  C4    0.020
 GP2  plan-1  N3    0.020
 GP2  plan-1  C2    0.020
 GP2  plan-1  N1    0.020
 GP2  plan-1  N2    0.020
 GP2  plan-1  N9    0.020
 GP2  plan-1  C8    0.020
 GP2  plan-1  C1'   0.020
 GP2  plan-1  HN1   0.020
 GP2  plan-1  HN21  0.020
 GP2  plan-1  HN22  0.020
 GP2  plan-1  H8    0.020

