# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 23:05:42 2022
#   Inital geometry file: a 121 line input string
#   Ligand name: 5'-O-[(S)-hydroxy{[(R)-hydroxy(phosphonoamino)phosphoryl]oxy}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)O[P@@](O)(=O)N[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
 GNP  GNP  5'-O-[(S)-hydroxy{[(R)-hydroxy(phosphonoamino)phosphoryl]oxy}phosphoryl]guanosine  ligand  45  32  .  2017-07-21  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_GNP
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
 GNP  PG    P  P      0   1.180   5.1607  30.9390  21.4757
 GNP  O1G   O  O      0  -0.906   5.3486  30.3956  22.8945
 GNP  O2G   O  OP    -1  -0.902   4.4137  32.2697  21.4015
 GNP  O3G   O  OP    -1  -0.903   4.6753  29.8996  20.4610
 GNP  N3B   N  NH1    0  -0.985   6.8591  31.3333  21.0243
 GNP  PB    P  P      0   1.285   7.4099  31.3649  19.4361
 GNP  O1B   O  O      0  -0.815   7.8855  30.0216  18.9460
 GNP  O2B   O  OP    -1  -0.831   6.4900  32.1886  18.5758
 GNP  O3A   O  O2     0  -0.770   8.8453  32.2300  19.6262
 GNP  PA    P  P      0   1.362   9.0682  33.8171  19.3444
 GNP  O1A   O  O      0  -0.796   9.1929  34.0878  17.8781
 GNP  O2A   O  OP    -1  -0.810   8.1875  34.6538  20.2226
 GNP  O5'   O  O2     0  -0.621  10.6286  33.9140  19.9033
 GNP  C5'   C  CH2    0  -0.165  10.9099  33.8130  21.2740
 GNP  C4'   C  CH1    0  -0.015  12.3685  34.1273  21.5280
 GNP  O4'   O  O2     0  -0.494  13.2101  33.1270  20.9428
 GNP  C3'   C  CH1    0  -0.039  12.8445  35.4653  20.9609
 GNP  O3'   O  OH1    0  -0.667  13.8304  35.9753  21.8264
 GNP  C2'   C  CH1    0  -0.026  13.4427  35.0486  19.6213
 GNP  O2'   O  OH1    0  -0.659  14.3741  35.9829  19.1629
 GNP  C1'   C  CH1    0   0.201  14.0541  33.6880  19.9828
 GNP  N9    N  NR5    0  -0.539  14.1600  32.7843  18.8621
 GNP  C8    C  CR15   0   0.086  13.1307  32.1465  18.2115
 GNP  N7    N  N      0  -0.444  13.5381  31.4280  17.2106
 GNP  C5    C  CR5    0  -0.094  14.8987  31.6001  17.1876
 GNP  C6    C  C      0   0.499  15.8843  31.0786  16.3002
 GNP  O6    O  OC     0  -0.465  15.7380  30.3438  15.3390
 GNP  N1    N  NC1    0  -0.727  17.1614  31.5330  16.6609
 GNP  C2    C  C      0   0.686  17.4549  32.3718  17.6980
 GNP  N2    N  NH2    0  -0.831  18.7481  32.6726  17.8983
 GNP  N3    N  N      0  -0.512  16.5425  32.8557  18.5031
 GNP  C4    C  CR5    0   0.500  15.3024  32.4406  18.2080
 GNP  HNB3  H  HNH1   0   0.331   7.4959  30.8244  21.6260
 GNP  H5'2  H  HCH2   0   0.210  10.3097  34.5149  21.8642
 GNP  H5'1  H  HCH2   0   0.217  10.6938  32.8074  21.6565
 GNP  H4'   H  HCH1   0   0.254  12.5168  34.1161  22.6133
 GNP  H3'   H  HCH1   0   0.249  12.0148  36.1719  20.8348
 GNP  HO3'  H  HOH1   0   0.450  14.2670  36.7137  21.3879
 GNP  H2'   H  HCH1   0   0.251  12.6307  34.8975  18.9026
 GNP  HO2'  H  HOH1   0   0.464  14.5733  35.8015  18.2392
 GNP  H1'   H  HCH1   0   0.249  15.0728  33.8263  20.3632
 GNP  H8    H  HCR5   0   0.293  12.1056  32.2547  18.5323
 GNP  HN1   H  HNC1   0   0.424  17.9212  31.1927  16.0842
 GNP  HN21  H  HNH2   0   0.410  18.9523  33.4088  18.5532
 GNP  HN22  H  HNH2   0   0.413  19.4358  32.5140  17.1809

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
 GNP  PG   O1G   deloc     1.531  0.020  1.531
 GNP  PG   O2G   deloc     1.528  0.020  1.528
 GNP  PG   O3G   deloc     1.532  0.020  1.532
 GNP  PG   N3B   single    1.801  0.020  1.801
 GNP  N3B  PB    single    1.681  0.020  1.681
 GNP  N3B  HNB3  single    0.890  0.020  1.040
 GNP  PB   O1B   deloc     1.507  0.020  1.507
 GNP  PB   O2B   deloc     1.505  0.020  1.505
 GNP  PB   O3A   single    1.687  0.020  1.687
 GNP  O3A  PA    single    1.627  0.020  1.627
 GNP  PA   O1A   deloc     1.496  0.020  1.496
 GNP  PA   O2A   deloc     1.499  0.020  1.499
 GNP  PA   O5'   single    1.660  0.020  1.660
 GNP  O5'  C5'   single    1.403  0.020  1.403
 GNP  C5'  C4'   single    1.514  0.020  1.514
 GNP  C5'  H5'2  single    0.970  0.020  1.090
 GNP  C5'  H5'1  single    0.970  0.020  1.090
 GNP  C4'  O4'   single    1.432  0.020  1.432
 GNP  C4'  C3'   single    1.529  0.020  1.529
 GNP  C4'  H4'   single    0.970  0.020  1.090
 GNP  O4'  C1'   single    1.396  0.020  1.396
 GNP  C3'  O3'   single    1.408  0.020  1.408
 GNP  C3'  C2'   single    1.525  0.020  1.525
 GNP  C3'  H3'   single    0.970  0.020  1.090
 GNP  O3'  HO3'  single    0.850  0.020  0.980
 GNP  C2'  O2'   single    1.397  0.020  1.397
 GNP  C2'  C1'   single    1.535  0.020  1.535
 GNP  C2'  H2'   single    0.970  0.020  1.090
 GNP  O2'  HO2'  single    0.850  0.020  0.980
 GNP  C1'  N9    single    1.444  0.020  1.444
 GNP  C1'  H1'   single    0.970  0.020  1.090
 GNP  N9   C8    aromatic  1.375  0.020  1.375
 GNP  N9   C4    aromatic  1.361  0.020  1.361
 GNP  C8   N7    aromatic  1.298  0.020  1.298
 GNP  C8   H8    single    0.930  0.020  1.080
 GNP  N7   C5    aromatic  1.372  0.020  1.372
 GNP  C5   C6    aromatic  1.425  0.020  1.425
 GNP  C5   C4    aromatic  1.382  0.020  1.382
 GNP  C6   O6    double    1.219  0.020  1.219
 GNP  C6   N1    aromatic  1.403  0.020  1.403
 GNP  N1   C2    aromatic  1.366  0.020  1.366
 GNP  N1   HN1   single    0.860  0.020  1.020
 GNP  C2   N2    single    1.343  0.020  1.343
 GNP  C2   N3    aromatic  1.309  0.020  1.309
 GNP  N2   HN21  single    0.890  0.020  1.040
 GNP  N2   HN22  single    0.890  0.020  1.040
 GNP  N3   C4    aromatic  1.341  0.020  1.341

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
 GNP  N3B   PG   O3G   106.35  3.000
 GNP  N3B   PG   O2G   104.96  3.000
 GNP  O3G   PG   O2G   113.82  3.000
 GNP  N3B   PG   O1G   101.20  3.000
 GNP  O3G   PG   O1G   114.34  3.000
 GNP  O2G   PG   O1G   114.47  3.000
 GNP  HNB3  N3B  PB    111.38  3.000
 GNP  HNB3  N3B  PG    109.50  3.000
 GNP  PB    N3B  PG    123.35  3.000
 GNP  O3A   PB   O2B   107.69  3.000
 GNP  O3A   PB   O1B   103.02  3.000
 GNP  O2B   PB   O1B   119.66  3.000
 GNP  O3A   PB   N3B   100.48  3.000
 GNP  O2B   PB   N3B   110.49  3.000
 GNP  O1B   PB   N3B   113.20  3.000
 GNP  PA    O3A  PB    126.68  3.000
 GNP  O5'   PA   O2A   108.80  3.000
 GNP  O5'   PA   O1A   103.95  3.000
 GNP  O2A   PA   O1A   121.48  3.000
 GNP  O5'   PA   O3A    97.31  3.000
 GNP  O2A   PA   O3A   111.25  3.000
 GNP  O1A   PA   O3A   110.95  3.000
 GNP  C5'   O5'  PA    120.88  3.000
 GNP  H5'1  C5'  H5'2  106.93  3.000
 GNP  H5'1  C5'  C4'   108.75  3.000
 GNP  H5'2  C5'  C4'   107.72  3.000
 GNP  H5'1  C5'  O5'   111.53  3.000
 GNP  H5'2  C5'  O5'   111.73  3.000
 GNP  C4'   C5'  O5'   110.02  3.000
 GNP  H4'   C4'  C3'   109.52  3.000
 GNP  H4'   C4'  O4'   108.55  3.000
 GNP  C3'   C4'  O4'   106.06  3.000
 GNP  H4'   C4'  C5'   107.14  3.000
 GNP  C3'   C4'  C5'   114.80  3.000
 GNP  O4'   C4'  C5'   110.65  3.000
 GNP  C1'   O4'  C4'   110.83  3.000
 GNP  H3'   C3'  C2'   111.82  3.000
 GNP  H3'   C3'  O3'   111.53  3.000
 GNP  C2'   C3'  O3'   111.37  3.000
 GNP  H3'   C3'  C4'   111.76  3.000
 GNP  C2'   C3'  C4'   102.05  3.000
 GNP  O3'   C3'  C4'   107.88  3.000
 GNP  HO3'  O3'  C3'   108.38  3.000
 GNP  H2'   C2'  C1'   109.13  3.000
 GNP  H2'   C2'  O2'   111.81  3.000
 GNP  C1'   C2'  O2'   113.87  3.000
 GNP  H2'   C2'  C3'   108.87  3.000
 GNP  C1'   C2'  C3'   101.04  3.000
 GNP  O2'   C2'  C3'   111.54  3.000
 GNP  HO2'  O2'  C2'   109.09  3.000
 GNP  H1'   C1'  N9    106.27  3.000
 GNP  H1'   C1'  C2'   109.88  3.000
 GNP  N9    C1'  C2'   113.66  3.000
 GNP  H1'   C1'  O4'   111.96  3.000
 GNP  N9    C1'  O4'   109.06  3.000
 GNP  C2'   C1'  O4'   106.11  3.000
 GNP  C4    N9   C8    106.50  3.000
 GNP  C4    N9   C1'   126.37  3.000
 GNP  C8    N9   C1'   127.09  3.000
 GNP  H8    C8   N7    125.65  3.000
 GNP  H8    C8   N9    121.59  3.000
 GNP  N7    C8   N9    112.76  3.000
 GNP  C5    N7   C8    104.77  3.000
 GNP  C4    C5   C6    118.70  3.000
 GNP  C4    C5   N7    110.71  3.000
 GNP  C6    C5   N7    130.59  3.000
 GNP  N1    C6   O6    120.49  3.000
 GNP  N1    C6   C5    110.56  3.000
 GNP  O6    C6   C5    128.95  3.000
 GNP  HN1   N1   C2    118.53  3.000
 GNP  HN1   N1   C6    115.33  3.000
 GNP  C2    N1   C6    126.14  3.000
 GNP  N3    C2   N2    119.77  3.000
 GNP  N3    C2   N1    122.96  3.000
 GNP  N2    C2   N1    117.25  3.000
 GNP  HN22  N2   HN21  116.14  3.000
 GNP  HN22  N2   C2    121.09  3.000
 GNP  HN21  N2   C2    117.16  3.000
 GNP  C4    N3   C2    113.25  3.000
 GNP  N3    C4   C5    128.38  3.000
 GNP  N3    C4   N9    126.35  3.000
 GNP  C5    C4   N9    105.26  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
 GNP  CONST_01  C5    N7   C8   N9      0.00   0.0  0
 GNP  CONST_02  N7    C5   C4   N9      0.00   0.0  0
 GNP  CONST_03  C6    C5   C4   N9    180.00   0.0  0
 GNP  CONST_04  C2    N3   C4   N9    180.00   0.0  0
 GNP  CONST_05  C5    C4   N9   C8      0.00   0.0  0
 GNP  CONST_06  N3    C4   N9   C8    180.00   0.0  0
 GNP  CONST_07  C6    C5   N7   C8    180.00   0.0  0
 GNP  CONST_08  C4    C5   N7   C8      0.00   0.0  0
 GNP  CONST_09  C4    N9   C8   N7      0.00   0.0  0
 GNP  CONST_10  N1    C6   C5   N7    180.00   0.0  0
 GNP  CONST_11  N3    C4   C5   N7    180.00   0.0  0
 GNP  CONST_12  C2    N1   C6   C5      0.00   0.0  0
 GNP  CONST_13  C2    N3   C4   C5      0.00   0.0  0
 GNP  CONST_14  N3    C4   C5   C6      0.00   0.0  0
 GNP  CONST_15  N3    C2   N1   C6      0.00   0.0  0
 GNP  CONST_16  C4    C5   C6   N1      0.00   0.0  0
 GNP  CONST_17  C4    N3   C2   N1      0.00   0.0  0
 GNP  CONST_18  N7    C8   N9   C1'   180.00   0.0  0
 GNP  CONST_19  C5    C4   N9   C1'   180.00   0.0  0
 GNP  CONST_20  N3    C4   N9   C1'     0.00   0.0  0
 GNP  CONST_21  O6    C6   C5   N7      0.00   0.0  0
 GNP  CONST_22  N2    C2   N1   C6    180.00   0.0  0
 GNP  CONST_23  C4    C5   C6   O6    180.00   0.0  0
 GNP  CONST_24  C2    N1   C6   O6    180.00   0.0  0
 GNP  CONST_25  C4    N3   C2   N2    180.00   0.0  0
 GNP  CONST_26  H8    C8   N9   C1'     0.00   0.0  0
 GNP  CONST_27  HN1   N1   C6   C5    180.00   0.0  0
 GNP  CONST_28  HN21  N2   C2   N1    180.00   0.0  0
 GNP  Var_01    C4'   C5'  O5'  PA   -172.04  30.0  3
 GNP  Var_02    O1B   PB   N3B  PG    -87.57  30.0  3
 GNP  Var_03    PB    N3B  PG   O1G   153.79  30.0  3
 GNP  Var_04    O1A   PA   O3A  PB    -77.64  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
 GNP  chir_03  C4'  C5'  O4'  C3'  negativ
 GNP  chir_04  C3'  O3'  C4'  C2'  positiv
 GNP  chir_05  C2'  O2'  C3'  C1'  positiv
 GNP  chir_06  C1'  O4'  N9   C2'  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
 GNP  plan-1  C1'   0.020
 GNP  plan-1  N9    0.020
 GNP  plan-1  C8    0.020
 GNP  plan-1  N7    0.020
 GNP  plan-1  C5    0.020
 GNP  plan-1  C6    0.020
 GNP  plan-1  O6    0.020
 GNP  plan-1  N1    0.020
 GNP  plan-1  C2    0.020
 GNP  plan-1  N2    0.020
 GNP  plan-1  N3    0.020
 GNP  plan-1  C4    0.020
 GNP  plan-1  H8    0.020
 GNP  plan-1  HN1   0.020
 GNP  plan-2  C2    0.020
 GNP  plan-2  N2    0.020
 GNP  plan-2  HN21  0.020
 GNP  plan-2  HN22  0.020

