# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 05:34:21 2021
#   Inital geometry file: a 108 line input string
#   Ligand name: 5'-O-[(S)-{[(R)-amino(hydroxy)phosphoryl]oxy}(hydroxy)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@@](N)(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
 GNH  GNH  5'-O-[(S)-{[(R)-amino(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]guanosine  ligand  44  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 PERFECT
;

data_comp_GNH
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
 GNH  N3B   N  NH2   0  -0.942  30.6862  62.4963  -20.2233
 GNH  PB    P  P     0   1.411  31.1704  62.6133  -18.6578
 GNH  O1B   O  O     0  -0.704  30.7718  61.6455  -17.6098
 GNH  O2B   O  OH1   0  -0.721  32.7376  62.8201  -18.8424
 GNH  O3A   O  O2    0  -0.686  30.5988  64.1033  -18.2909
 GNH  PA    P  P     0   1.472  29.7819  64.4519  -16.9428
 GNH  O1A   O  O     0  -0.685  28.4098  63.9235  -16.8895
 GNH  O2A   O  OH1   0  -0.731  30.7433  64.0679  -15.7336
 GNH  O5'   O  O2    0  -0.573  29.9548  66.0289  -17.0225
 GNH  C5'   C  CH2   0  -0.187  29.2148  66.8792  -16.1415
 GNH  C4'   C  CH1   0  -0.034  29.5670  68.3131  -16.5066
 GNH  O4'   O  O2    0  -0.492  28.7164  69.1750  -15.7519
 GNH  C3'   C  CH1   0  -0.030  30.9978  68.7078  -16.1571
 GNH  O3'   O  OH1   0  -0.666  31.3942  69.7275  -17.0363
 GNH  C2'   C  CH1   0  -0.034  30.8244  69.2294  -14.7327
 GNH  O2'   O  OH1   0  -0.656  31.8644  70.0789  -14.3603
 GNH  C1'   C  CH1   0   0.191  29.4643  69.9314  -14.8358
 GNH  N9    N  NR5   0  -0.540  28.7453  70.0058  -13.5917
 GNH  C8    C  CR15  0   0.094  28.2600  68.9511  -12.8542
 GNH  N7    N  N     0  -0.440  27.6428  69.3288  -11.7799
 GNH  C5    C  CR56  0  -0.098  27.7182  70.6982  -11.7974
 GNH  C6    C  CR6   0   0.506  27.2214  71.6634  -10.8749
 GNH  O6    O  OC    0  -0.473  26.6064  71.4839   -9.8374
 GNH  N1    N  NR16  0  -0.728  27.5319  72.9596  -11.3049
 GNH  C2    C  CR6   0   0.698  28.2091  73.2903  -12.4437
 GNH  N2    N  NH2   0  -0.833  28.3747  74.5937  -12.6961
 GNH  N3    N  N     0  -0.513  28.6665  72.3961  -13.2870
 GNH  C4    C  CR56  0   0.509  28.3955  71.1377  -12.9195
 GNH  HN31  H  HNH2  0   0.419  31.1202  61.7572  -20.7608
 GNH  HN32  H  HNH2  0   0.418  29.6869  62.5110  -20.3800
 GNH  HOB2  H  HOH1  0   0.503  33.2630  62.5034  -18.0950
 GNH  HOA2  H  HOH1  0   0.500  30.6142  63.1729  -15.3896
 GNH  H5'2  H  HCH2  0   0.274  28.1420  66.7226  -16.2713
 GNH  H5'1  H  HCH2  0   0.239  29.4715  66.6600  -15.1004
 GNH  H4'   H  HCH1  0   0.276  29.3735  68.4633  -17.5731
 GNH  H3'   H  HCH1  0   0.263  31.6813  67.8515  -16.1926
 GNH  HO3'  H  HOH1  0   0.457  32.2514  70.0623  -16.7516
 GNH  H2'   H  HCH1  0   0.250  30.7449  68.3715  -14.0519
 GNH  HO2'  H  HOH1  0   0.469  31.9588  70.0694  -13.4037
 GNH  H1'   H  HCH1  0   0.266  29.5999  70.9618  -15.1799
 GNH  H8    H  HCR5  0   0.291  28.3859  67.9269  -13.1712
 GNH  HN1   H  HNR6  0   0.426  27.2158  73.7076  -10.7007
 GNH  HN21  H  HNH2  0   0.415  28.9754  74.8576  -13.4581
 GNH  HN22  H  HNH2  0   0.417  28.1826  75.2949  -12.0015

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
 GNH  N3B  PB    single    1.643  0.020  1.643
 GNH  N3B  HN31  single    0.890  0.020  1.040
 GNH  N3B  HN32  single    0.890  0.020  1.040
 GNH  PB   O1B   double    1.481  0.020  1.481
 GNH  PB   O2B   single    1.592  0.020  1.592
 GNH  PB   O3A   single    1.638  0.020  1.638
 GNH  O2B  HOB2  single    0.850  0.020  0.980
 GNH  O3A  PA    single    1.614  0.020  1.614
 GNH  PA   O1A   double    1.471  0.020  1.471
 GNH  PA   O2A   single    1.592  0.020  1.592
 GNH  PA   O5'   single    1.588  0.020  1.588
 GNH  O2A  HOA2  single    0.850  0.020  0.980
 GNH  O5'  C5'   single    1.431  0.020  1.431
 GNH  C5'  C4'   single    1.521  0.020  1.521
 GNH  C5'  H5'2  single    0.970  0.020  1.090
 GNH  C5'  H5'1  single    0.970  0.020  1.090
 GNH  C4'  O4'   single    1.427  0.020  1.427
 GNH  C4'  C3'   single    1.525  0.020  1.525
 GNH  C4'  H4'   single    0.970  0.020  1.090
 GNH  O4'  C1'   single    1.404  0.020  1.404
 GNH  C3'  O3'   single    1.403  0.020  1.403
 GNH  C3'  C2'   single    1.527  0.020  1.527
 GNH  C3'  H3'   single    0.970  0.020  1.090
 GNH  O3'  HO3'  single    0.850  0.020  0.980
 GNH  C2'  O2'   single    1.394  0.020  1.394
 GNH  C2'  C1'   single    1.534  0.020  1.534
 GNH  C2'  H2'   single    0.970  0.020  1.090
 GNH  O2'  HO2'  single    0.850  0.020  0.980
 GNH  C1'  N9    single    1.439  0.020  1.439
 GNH  C1'  H1'   single    0.970  0.020  1.090
 GNH  N9   C8    aromatic  1.375  0.020  1.375
 GNH  N9   C4    aromatic  1.362  0.020  1.362
 GNH  C8   N7    aromatic  1.295  0.020  1.295
 GNH  C8   H8    single    0.930  0.020  1.080
 GNH  N7   C5    aromatic  1.372  0.020  1.372
 GNH  C5   C6    aromatic  1.425  0.020  1.425
 GNH  C5   C4    aromatic  1.382  0.020  1.382
 GNH  C6   O6    double    1.219  0.020  1.219
 GNH  C6   N1    aromatic  1.400  0.020  1.400
 GNH  N1   C2    aromatic  1.366  0.020  1.366
 GNH  N1   HN1   single    0.860  0.020  1.020
 GNH  C2   N2    single    1.338  0.020  1.338
 GNH  C2   N3    aromatic  1.312  0.020  1.312
 GNH  N2   HN21  single    0.860  0.020  1.020
 GNH  N2   HN22  single    0.860  0.020  1.020
 GNH  N3   C4    aromatic  1.339  0.020  1.339

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
 GNH  HN32  N3B  HN31  110.62  3.000
 GNH  HN32  N3B  PB    115.96  3.000
 GNH  HN31  N3B  PB    115.58  3.000
 GNH  O3A   PB   O2B   104.57  3.000
 GNH  O3A   PB   O1B   110.00  3.000
 GNH  O2B   PB   O1B   115.59  3.000
 GNH  O3A   PB   N3B   100.11  3.000
 GNH  O2B   PB   N3B   100.90  3.000
 GNH  O1B   PB   N3B   123.25  3.000
 GNH  HOB2  O2B  PB    113.76  3.000
 GNH  PA    O3A  PB    124.07  3.000
 GNH  O5'   PA   O2A   102.23  3.000
 GNH  O5'   PA   O1A   117.38  3.000
 GNH  O2A   PA   O1A   116.69  3.000
 GNH  O5'   PA   O3A    96.74  3.000
 GNH  O2A   PA   O3A   106.06  3.000
 GNH  O1A   PA   O3A   115.13  3.000
 GNH  HOA2  O2A  PA    114.37  3.000
 GNH  C5'   O5'  PA    120.19  3.000
 GNH  H5'1  C5'  H5'2  108.35  3.000
 GNH  H5'1  C5'  C4'   111.28  3.000
 GNH  H5'2  C5'  C4'   109.52  3.000
 GNH  H5'1  C5'  O5'   110.21  3.000
 GNH  H5'2  C5'  O5'   110.47  3.000
 GNH  C4'   C5'  O5'   107.02  3.000
 GNH  H4'   C4'  C3'   110.72  3.000
 GNH  H4'   C4'  O4'   109.10  3.000
 GNH  C3'   C4'  O4'   106.37  3.000
 GNH  H4'   C4'  C5'   108.81  3.000
 GNH  C3'   C4'  C5'   113.97  3.000
 GNH  O4'   C4'  C5'   107.73  3.000
 GNH  C1'   O4'  C4'   110.67  3.000
 GNH  H3'   C3'  C2'   111.59  3.000
 GNH  H3'   C3'  O3'   111.79  3.000
 GNH  C2'   C3'  O3'   111.61  3.000
 GNH  H3'   C3'  C4'   112.05  3.000
 GNH  C2'   C3'  C4'   101.28  3.000
 GNH  O3'   C3'  C4'   108.03  3.000
 GNH  HO3'  O3'  C3'   108.58  3.000
 GNH  H2'   C2'  C1'   109.57  3.000
 GNH  H2'   C2'  O2'   111.38  3.000
 GNH  C1'   C2'  O2'   113.62  3.000
 GNH  H2'   C2'  C3'   108.65  3.000
 GNH  C1'   C2'  C3'   101.21  3.000
 GNH  O2'   C2'  C3'   111.89  3.000
 GNH  HO2'  O2'  C2'   109.46  3.000
 GNH  H1'   C1'  N9    106.56  3.000
 GNH  H1'   C1'  C2'   110.00  3.000
 GNH  N9    C1'  C2'   114.11  3.000
 GNH  H1'   C1'  O4'   111.59  3.000
 GNH  N9    C1'  O4'   109.02  3.000
 GNH  C2'   C1'  O4'   105.64  3.000
 GNH  C4    N9   C8    106.38  3.000
 GNH  C4    N9   C1'   126.73  3.000
 GNH  C8    N9   C1'   126.89  3.000
 GNH  H8    C8   N7    125.15  3.000
 GNH  H8    C8   N9    121.94  3.000
 GNH  N7    C8   N9    112.91  3.000
 GNH  C5    N7   C8    104.73  3.000
 GNH  C4    C5   C6    118.75  3.000
 GNH  C4    C5   N7    110.78  3.000
 GNH  C6    C5   N7    130.47  3.000
 GNH  N1    C6   O6    120.62  3.000
 GNH  N1    C6   C5    110.55  3.000
 GNH  O6    C6   C5    128.84  3.000
 GNH  HN1   N1   C2    118.27  3.000
 GNH  HN1   N1   C6    115.57  3.000
 GNH  C2    N1   C6    126.16  3.000
 GNH  N3    C2   N2    119.98  3.000
 GNH  N3    C2   N1    122.96  3.000
 GNH  N2    C2   N1    117.04  3.000
 GNH  HN22  N2   HN21  117.04  3.000
 GNH  HN22  N2   C2    121.69  3.000
 GNH  HN21  N2   C2    118.20  3.000
 GNH  C4    N3   C2    113.19  3.000
 GNH  N3    C4   C5    128.38  3.000
 GNH  N3    C4   N9    126.41  3.000
 GNH  C5    C4   N9    105.20  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
 GNH  CONST_01  C5    N7   C8   N9      0.00   0.0  0
 GNH  CONST_02  N7    C5   C4   N9      0.00   0.0  0
 GNH  CONST_03  C6    C5   C4   N9    180.00   0.0  0
 GNH  CONST_04  C2    N3   C4   N9    180.00   0.0  0
 GNH  CONST_05  C5    C4   N9   C8      0.00   0.0  0
 GNH  CONST_06  N3    C4   N9   C8    180.00   0.0  0
 GNH  CONST_07  C6    C5   N7   C8    180.00   0.0  0
 GNH  CONST_08  C4    C5   N7   C8      0.00   0.0  0
 GNH  CONST_09  C4    N9   C8   N7      0.00   0.0  0
 GNH  CONST_10  N1    C6   C5   N7    180.00   0.0  0
 GNH  CONST_11  N3    C4   C5   N7    180.00   0.0  0
 GNH  CONST_12  C2    N1   C6   C5      0.00   0.0  0
 GNH  CONST_13  C2    N3   C4   C5      0.00   0.0  0
 GNH  CONST_14  N3    C4   C5   C6      0.00   0.0  0
 GNH  CONST_15  N3    C2   N1   C6      0.00   0.0  0
 GNH  CONST_16  C4    C5   C6   N1      0.00   0.0  0
 GNH  CONST_17  C4    N3   C2   N1      0.00   0.0  0
 GNH  CONST_18  N7    C8   N9   C1'   180.00   0.0  0
 GNH  CONST_19  C5    C4   N9   C1'   180.00   0.0  0
 GNH  CONST_20  N3    C4   N9   C1'     0.00   0.0  0
 GNH  CONST_21  O6    C6   C5   N7      0.00   0.0  0
 GNH  CONST_22  N2    C2   N1   C6    180.00   0.0  0
 GNH  CONST_23  C4    C5   C6   O6    180.00   0.0  0
 GNH  CONST_24  C2    N1   C6   O6    180.00   0.0  0
 GNH  CONST_25  C4    N3   C2   N2    180.00   0.0  0
 GNH  CONST_26  H8    C8   N9   C1'     0.00   0.0  0
 GNH  CONST_27  HN1   N1   C6   C5    180.00   0.0  0
 GNH  CONST_28  HN21  N2   C2   N1    180.00   0.0  0
 GNH  CONST_29  HN22  N2   C2   N1      0.00   0.0  0
 GNH  Var_01    C4'   C5'  O5'  PA   -177.98  30.0  3
 GNH  Var_02    O1A   PA   O3A  PB    -72.05  30.0  3
 GNH  Var_03    HN31  N3B  PB   O1B   -72.82  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
 GNH  chir_03  C4'  C5'  O4'  C3'  negativ
 GNH  chir_04  C3'  O3'  C4'  C2'  positiv
 GNH  chir_05  C2'  O2'  C3'  C1'  positiv
 GNH  chir_06  C1'  O4'  N9   C2'  negativ
 GNH  chir_07  PB   O1B  O2B  O3A  both
 GNH  chir_08  PA   O1A  O2A  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
 GNH  plan-1  C1'   0.020
 GNH  plan-1  N9    0.020
 GNH  plan-1  C8    0.020
 GNH  plan-1  N7    0.020
 GNH  plan-1  C5    0.020
 GNH  plan-1  C6    0.020
 GNH  plan-1  O6    0.020
 GNH  plan-1  N1    0.020
 GNH  plan-1  C2    0.020
 GNH  plan-1  N2    0.020
 GNH  plan-1  N3    0.020
 GNH  plan-1  C4    0.020
 GNH  plan-1  H8    0.020
 GNH  plan-1  HN1   0.020
 GNH  plan-2  C2    0.020
 GNH  plan-2  N2    0.020
 GNH  plan-2  HN21  0.020
 GNH  plan-2  HN22  0.020

