# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 02:23:07 2021
#   Inital geometry file: a 123 line input string
#   Ligand name: 5'-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]methyl}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[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
 G2P  G2P  5'-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]guanosine  ligand  50  32  .  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_G2P
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
 G2P  PG    P  P     0   1.473   4.9414  37.7119    2.2244
 G2P  O1G   O  OH1   0  -0.712   5.3722  38.2607    3.6380
 G2P  O2G   O  O     0  -0.686   4.5500  38.7620    1.2728
 G2P  O3G   O  OH1   0  -0.732   3.8762  36.5864    2.5719
 G2P  O3B   O  O2    0  -0.686   6.2690  36.8946    1.7382
 G2P  PB    P  P     0   1.381   6.3661  36.1951    0.2762
 G2P  O1B   O  OH1   0  -0.719   7.4591  35.1034    0.6544
 G2P  O2B   O  O     0  -0.683   5.0581  35.7292   -0.2332
 G2P  C3A   C  CH2   0  -1.054   7.1687  37.4336   -0.7609
 G2P  PA    P  P     0   1.399   7.2863  36.9240   -2.4952
 G2P  O1A   O  OH1   0  -0.745   7.8279  35.4281   -2.3181
 G2P  O2A   O  O     0  -0.684   6.0548  37.1145   -3.2886
 G2P  O5'   O  O2    0  -0.583   8.5839  37.6702   -3.0706
 G2P  C5'   C  CH2   0  -0.174   8.5113  39.0307   -3.5009
 G2P  C4'   C  CR15  0  -0.006   9.8593  39.4219   -4.0481
 G2P  O4'   O  O     0  -0.493  10.1592  38.6530   -5.2081
 G2P  C3'   C  CR15  0   0.006   9.9193  40.8754   -4.5118
 G2P  O3'   O  OH1   0  -0.654  10.1445  41.7160   -3.4255
 G2P  C2'   C  CR15  0  -0.066  11.0382  40.8131   -5.5562
 G2P  O2'   O  OH1   0  -0.655  12.2626  40.8171   -4.8814
 G2P  C1'   C  CR15  0   0.161  10.7620  39.4411   -6.1908
 G2P  N9    N  NR5   0  -0.531   9.8726  39.5386   -7.3395
 G2P  C8    C  CR15  0   0.088   8.5223  39.3016   -7.4124
 G2P  N7    N  N     0  -0.443   8.0411  39.4934   -8.6027
 G2P  C5    C  CR56  0  -0.085   9.1186  39.8755   -9.3572
 G2P  C6    C  CR6   0   0.505   9.2178  40.2085  -10.7392
 G2P  O6    O  OC    0  -0.472   8.3400  40.2372  -11.5850
 G2P  N1    N  NR16  0  -0.727  10.5404  40.5282  -11.0732
 G2P  C2    C  CR6   0   0.685  11.6114  40.5277  -10.2260
 G2P  N2    N  NH2   0  -0.831  12.7936  40.8967  -10.7407
 G2P  N3    N  N     0  -0.515  11.5155  40.2210   -8.9558
 G2P  C4    C  CR56  0   0.504  10.2655  39.9073   -8.5868
 G2P  H3A1  H  HCH2  0   0.350   8.1563  37.6628   -0.3553
 G2P  H3A2  H  HCH2  0   0.344   6.5704  38.3475   -0.7198
 G2P  H5'1  H  HCH2  0   0.256   8.2710  39.6870   -2.6588
 G2P  H5'2  H  HCH2  0   0.243   7.7318  39.1527   -4.2576
 G2P  H4'   H  HCR5  0   0.259  10.6254  39.2497   -3.2821
 G2P  H3'   H  HCR5  0   0.237   8.9833  41.1314   -5.0296
 G2P  HA    H  HOH1  0   0.464  10.0113  42.6270   -3.7052
 G2P  H2'   H  HCR5  0   0.270  10.9702  41.6180   -6.2967
 G2P  HB    H  HOH1  0   0.461  12.9726  40.8270   -5.5312
 G2P  H1'   H  HCR5  0   0.282  11.6848  38.9722   -6.5443
 G2P  H8    H  HCR5  0   0.288   7.9509  38.9757   -6.5584
 G2P  H1    H  HNR6  0   0.426  10.6975  40.7768  -12.0416
 G2P  H2N1  H  HNH2  0   0.412  13.6121  40.7399  -10.1771
 G2P  H2N2  H  HNH2  0   0.415  12.9380  40.9132  -11.7362
 G2P  HO1   H  HOH1  0   0.510   5.5898  37.6118    4.3220
 G2P  HO2   H  HOH1  0   0.502   3.4842  36.1433    1.8049
 G2P  HO3   H  HOH1  0   0.509   7.7573  34.8679   -3.1048
 G2P  HO4   H  HOH1  0   0.504   7.7738  34.5785   -0.0960

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
 G2P  PG   O1G   single    1.576  0.020  1.576
 G2P  PG   O2G   double    1.470  0.020  1.470
 G2P  PG   O3G   single    1.588  0.020  1.588
 G2P  PG   O3B   single    1.633  0.020  1.633
 G2P  O3B  PB    single    1.624  0.020  1.624
 G2P  PB   O1B   single    1.590  0.020  1.590
 G2P  PB   O2B   double    1.479  0.020  1.479
 G2P  PB   C3A   single    1.804  0.020  1.804
 G2P  C3A  PA    single    1.811  0.020  1.811
 G2P  C3A  H3A1  single    0.970  0.020  1.090
 G2P  C3A  H3A2  single    0.970  0.020  1.090
 G2P  PA   O1A   single    1.601  0.020  1.601
 G2P  PA   O2A   double    1.477  0.020  1.477
 G2P  PA   O5'   single    1.604  0.020  1.604
 G2P  O5'  C5'   single    1.429  0.020  1.429
 G2P  C5'  C4'   single    1.506  0.020  1.506
 G2P  C5'  H5'1  single    0.970  0.020  1.090
 G2P  C5'  H5'2  single    0.970  0.020  1.090
 G2P  C4'  O4'   single    1.424  0.020  1.424
 G2P  C4'  C3'   single    1.527  0.020  1.527
 G2P  C4'  H4'   single    0.970  0.020  1.090
 G2P  O4'  C1'   single    1.396  0.020  1.396
 G2P  C3'  O3'   single    1.392  0.020  1.392
 G2P  C3'  C2'   single    1.532  0.020  1.532
 G2P  C3'  H3'   single    0.970  0.020  1.090
 G2P  O3'  HA    single    0.850  0.020  0.980
 G2P  C2'  O2'   single    1.398  0.020  1.398
 G2P  C2'  C1'   single    1.537  0.020  1.537
 G2P  C2'  H2'   single    0.970  0.020  1.090
 G2P  O2'  HB    single    0.850  0.020  0.980
 G2P  C1'  N9    single    1.456  0.020  1.456
 G2P  C1'  H1'   single    0.970  0.020  1.090
 G2P  N9   C8    aromatic  1.373  0.020  1.373
 G2P  N9   C4    aromatic  1.359  0.020  1.359
 G2P  C8   N7    aromatic  1.298  0.020  1.298
 G2P  C8   H8    single    0.930  0.020  1.080
 G2P  N7   C5    aromatic  1.370  0.020  1.370
 G2P  C5   C6    aromatic  1.425  0.020  1.425
 G2P  C5   C4    aromatic  1.382  0.020  1.382
 G2P  C6   O6    double    1.219  0.020  1.219
 G2P  C6   N1    aromatic  1.401  0.020  1.401
 G2P  N1   C2    aromatic  1.366  0.020  1.366
 G2P  N1   H1    single    0.860  0.020  1.020
 G2P  C2   N2    single    1.341  0.020  1.341
 G2P  C2   N3    aromatic  1.310  0.020  1.310
 G2P  N2   H2N1  single    0.890  0.020  1.040
 G2P  N2   H2N2  single    0.890  0.020  1.040
 G2P  N3   C4    aromatic  1.341  0.020  1.341
 G2P  HO1  O1G   single    0.850  0.020  0.980
 G2P  HO2  O3G   single    0.850  0.020  0.980
 G2P  HO3  O1A   single    0.850  0.020  0.980
 G2P  HO4  O1B   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
 G2P  O3B   PG   O3G   104.82  3.000
 G2P  O3B   PG   O2G   112.41  3.000
 G2P  O3G   PG   O2G   117.98  3.000
 G2P  O3B   PG   O1G   102.65  3.000
 G2P  O3G   PG   O1G   103.52  3.000
 G2P  O2G   PG   O1G   113.86  3.000
 G2P  HO1   O1G  PG    117.51  3.000
 G2P  HO2   O3G  PG    114.99  3.000
 G2P  PB    O3B  PG    122.17  3.000
 G2P  C3A   PB   O2B   114.31  3.000
 G2P  C3A   PB   O1B   107.59  3.000
 G2P  O2B   PB   O1B   118.26  3.000
 G2P  C3A   PB   O3B   104.39  3.000
 G2P  O2B   PB   O3B   113.14  3.000
 G2P  O1B   PB   O3B    97.05  3.000
 G2P  HO4   O1B  PB    114.28  3.000
 G2P  H3A2  C3A  H3A1  107.80  3.000
 G2P  H3A2  C3A  PA    107.86  3.000
 G2P  H3A1  C3A  PA    110.85  3.000
 G2P  H3A2  C3A  PB    107.99  3.000
 G2P  H3A1  C3A  PB    109.45  3.000
 G2P  PA    C3A  PB    112.72  3.000
 G2P  O5'   PA   O2A   114.95  3.000
 G2P  O5'   PA   O1A   101.58  3.000
 G2P  O2A   PA   O1A   117.52  3.000
 G2P  O5'   PA   C3A   105.38  3.000
 G2P  O2A   PA   C3A   115.07  3.000
 G2P  O1A   PA   C3A   100.31  3.000
 G2P  HO3   O1A  PA    115.22  3.000
 G2P  C5'   O5'  PA    120.66  3.000
 G2P  H5'2  C5'  H5'1  108.00  3.000
 G2P  H5'2  C5'  C4'   110.96  3.000
 G2P  H5'1  C5'  C4'   108.68  3.000
 G2P  H5'2  C5'  O5'   110.55  3.000
 G2P  H5'1  C5'  O5'   110.51  3.000
 G2P  C4'   C5'  O5'   108.13  3.000
 G2P  H4'   C4'  C3'   109.51  3.000
 G2P  H4'   C4'  O4'   109.70  3.000
 G2P  C3'   C4'  O4'   104.97  3.000
 G2P  H4'   C4'  C5'   109.30  3.000
 G2P  C3'   C4'  C5'   113.12  3.000
 G2P  O4'   C4'  C5'   110.13  3.000
 G2P  C1'   O4'  C4'   111.07  3.000
 G2P  H3'   C3'  C2'   108.06  3.000
 G2P  H3'   C3'  O3'   111.38  3.000
 G2P  C2'   C3'  O3'   116.01  3.000
 G2P  H3'   C3'  C4'   109.33  3.000
 G2P  C2'   C3'  C4'   101.37  3.000
 G2P  O3'   C3'  C4'   110.14  3.000
 G2P  HA    O3'  C3'   108.82  3.000
 G2P  H2'   C2'  C1'   111.44  3.000
 G2P  H2'   C2'  O2'   112.23  3.000
 G2P  C1'   C2'  O2'   111.06  3.000
 G2P  H2'   C2'  C3'   112.68  3.000
 G2P  C1'   C2'  C3'   100.75  3.000
 G2P  O2'   C2'  C3'   108.09  3.000
 G2P  HB    O2'  C2'   108.68  3.000
 G2P  H1'   C1'  N9    106.80  3.000
 G2P  H1'   C1'  C2'   111.38  3.000
 G2P  N9    C1'  C2'   112.08  3.000
 G2P  H1'   C1'  O4'   110.46  3.000
 G2P  N9    C1'  O4'   109.22  3.000
 G2P  C2'   C1'  O4'   106.91  3.000
 G2P  C4    N9   C8    106.42  3.000
 G2P  C4    N9   C1'   124.45  3.000
 G2P  C8    N9   C1'   129.13  3.000
 G2P  H8    C8   N7    125.07  3.000
 G2P  H8    C8   N9    122.11  3.000
 G2P  N7    C8   N9    112.82  3.000
 G2P  C5    N7   C8    104.75  3.000
 G2P  C4    C5   C6    118.52  3.000
 G2P  C4    C5   N7    110.62  3.000
 G2P  C6    C5   N7    130.85  3.000
 G2P  N1    C6   O6    120.59  3.000
 G2P  N1    C6   C5    110.50  3.000
 G2P  O6    C6   C5    128.92  3.000
 G2P  H1    N1   C2    118.16  3.000
 G2P  H1    N1   C6    115.51  3.000
 G2P  C2    N1   C6    126.33  3.000
 G2P  N3    C2   N2    120.06  3.000
 G2P  N3    C2   N1    122.96  3.000
 G2P  N2    C2   N1    116.95  3.000
 G2P  H2N2  N2   H2N1  116.11  3.000
 G2P  H2N2  N2   C2    120.72  3.000
 G2P  H2N1  N2   C2    117.34  3.000
 G2P  C4    N3   C2    112.95  3.000
 G2P  N3    C4   C5    128.74  3.000
 G2P  N3    C4   N9    125.87  3.000
 G2P  C5    C4   N9    105.39  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
 G2P  CONST_01  C5    N7   C8   N9      0.00   0.0  0
 G2P  CONST_02  N7    C5   C4   N9      0.00   0.0  0
 G2P  CONST_03  C6    C5   C4   N9    180.00   0.0  0
 G2P  CONST_04  C2    N3   C4   N9    180.00   0.0  0
 G2P  CONST_05  C5    C4   N9   C8      0.00   0.0  0
 G2P  CONST_06  N3    C4   N9   C8    180.00   0.0  0
 G2P  CONST_07  C6    C5   N7   C8    180.00   0.0  0
 G2P  CONST_08  C4    C5   N7   C8      0.00   0.0  0
 G2P  CONST_09  C4    N9   C8   N7      0.00   0.0  0
 G2P  CONST_10  N1    C6   C5   N7    180.00   0.0  0
 G2P  CONST_11  N3    C4   C5   N7    180.00   0.0  0
 G2P  CONST_12  C2    N1   C6   C5      0.00   0.0  0
 G2P  CONST_13  C2    N3   C4   C5      0.00   0.0  0
 G2P  CONST_14  N3    C4   C5   C6      0.00   0.0  0
 G2P  CONST_15  N3    C2   N1   C6      0.00   0.0  0
 G2P  CONST_16  C4    C5   C6   N1      0.00   0.0  0
 G2P  CONST_17  C4    N3   C2   N1      0.00   0.0  0
 G2P  CONST_18  N7    C8   N9   C1'   180.00   0.0  0
 G2P  CONST_19  C5    C4   N9   C1'   180.00   0.0  0
 G2P  CONST_20  N3    C4   N9   C1'     0.00   0.0  0
 G2P  CONST_21  O6    C6   C5   N7      0.00   0.0  0
 G2P  CONST_22  N2    C2   N1   C6    180.00   0.0  0
 G2P  CONST_23  C4    C5   C6   O6    180.00   0.0  0
 G2P  CONST_24  C2    N1   C6   O6    180.00   0.0  0
 G2P  CONST_25  C4    N3   C2   N2    180.00   0.0  0
 G2P  CONST_26  H8    C8   N9   C1'     0.00   0.0  0
 G2P  CONST_27  H1    N1   C6   C5    180.00   0.0  0
 G2P  CONST_28  H2N1  N2   C2   N1    180.00   0.0  0
 G2P  Var_01    C4'   C5'  O5'  PA   -177.19  30.0  3
 G2P  Var_02    O1B   PB   O3B  PG   -155.76  30.0  3
 G2P  Var_03    PA    C3A  PB   O3B  -175.92  30.0  3
 G2P  Var_04    O1A   PA   C3A  PB    -46.58  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
 G2P  chir_03  C4'  C5'  O4'  C3'  negativ
 G2P  chir_04  C3'  O3'  C4'  C2'  positiv
 G2P  chir_05  C2'  O2'  C3'  C1'  positiv
 G2P  chir_06  C1'  O4'  N9   C2'  negativ
 G2P  chir_07  PB   O1B  O2B  C3A  both
 G2P  chir_08  PA   O2A  O5'  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
 G2P  plan-1  C1'   0.020
 G2P  plan-1  N9    0.020
 G2P  plan-1  C8    0.020
 G2P  plan-1  N7    0.020
 G2P  plan-1  C5    0.020
 G2P  plan-1  C6    0.020
 G2P  plan-1  O6    0.020
 G2P  plan-1  N1    0.020
 G2P  plan-1  C2    0.020
 G2P  plan-1  N2    0.020
 G2P  plan-1  N3    0.020
 G2P  plan-1  C4    0.020
 G2P  plan-1  H8    0.020
 G2P  plan-1  H1    0.020
 G2P  plan-2  C2    0.020
 G2P  plan-2  N2    0.020
 G2P  plan-2  H2N1  0.020
 G2P  plan-2  H2N2  0.020

