# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 17:52:28 2020
#   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  42  28  .  2021-08-10  2021-08-10  
;
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  -0.979  -1.6815  -2.0689   5.1044
 GNH  PB    P  P      0   1.289  -1.3853  -0.3956   5.2103
 GNH  O1B   O  O      0  -0.813  -2.6105   0.4347   4.9545
 GNH  O2B   O  OP    -1  -0.811  -0.5559  -0.1685   6.4399
 GNH  O3A   O  O2     0  -0.745  -0.4086  -0.2820   3.8699
 GNH  PA    P  P      0   1.344  -0.2669   1.0569   2.9502
 GNH  O1A   O  O      0  -0.781  -1.2904   1.0645   1.8527
 GNH  O2A   O  OP    -1  -0.801  -0.0767   2.2772   3.7963
 GNH  O5'   O  O2     0  -0.620   1.1918   0.5969   2.3268
 GNH  C5'   C  CH2    0  -0.148   1.6530   1.2165   1.1507
 GNH  C4'   C  CH1    0   0.011   2.1768   0.1749   0.1890
 GNH  O4'   O  O2     0  -0.489   1.1497  -0.7458  -0.1803
 GNH  C3'   C  CH1    0  -0.049   2.6733   0.7796  -1.1224
 GNH  O3'   O  OH1    0  -0.658   4.0304   1.1131  -1.0205
 GNH  C2'   C  CH1    0  -0.039   2.3889  -0.3434  -2.1246
 GNH  O2'   O  OH1    0  -0.667   3.3605  -1.3499  -2.0390
 GNH  C1'   C  CH1    0   0.176   1.0906  -0.9145  -1.5599
 GNH  N9    N  NR5    0  -0.542  -0.0817  -0.2108  -2.0805
 GNH  C8    C  CR15   0   0.047  -1.0250   0.5001  -1.3750
 GNH  N7    N  N      0  -0.451  -1.9798   0.9493  -2.1347
 GNH  C5    C  CR56   0  -0.089  -1.6679   0.5076  -3.3929
 GNH  C6    C  CR6    0   0.498  -2.3480   0.6788  -4.6325
 GNH  O6    O  OC     0  -0.476  -3.3803   1.2875  -4.8621
 GNH  N1    N  NR16   0  -0.727  -1.6639   0.0240  -5.6646
 GNH  C2    C  CR6    0   0.683  -0.5077  -0.6919  -5.5384
 GNH  N2    N  NH2    0  -0.833  -0.0360  -1.2837  -6.6450
 GNH  N3    N  N      0  -0.515   0.1182  -0.8406  -4.3977
 GNH  C4    C  CR56   0   0.501  -0.4960  -0.2258  -3.3750
 GNH  HN31  H  HNH2   0   0.362  -2.4111  -2.3221   4.4510
 GNH  HN32  H  HNH2   0   0.366  -1.9049  -2.4748   6.0029
 GNH  H5'2  H  HCH2   0   0.206   0.8717   1.8066   0.6595
 GNH  H5'1  H  HCH2   0   0.226   2.4760   1.9039   1.3789
 GNH  H4'   H  HCH1   0   0.243   2.9891  -0.3869   0.6664
 GNH  H3'   H  HCH1   0   0.246   2.0676   1.6564  -1.3872
 GNH  HO3'  H  HOH1   0   0.468   4.2440   1.7521  -1.7081
 GNH  H2'   H  HCH1   0   0.260   2.2737   0.0245  -3.1501
 GNH  HO2'  H  HOH1   0   0.451   4.2141  -0.9208  -1.9016
 GNH  H1'   H  HCH1   0   0.282   0.9770  -1.9742  -1.8053
 GNH  H8    H  HCR5   0   0.322  -0.9710   0.6342  -0.3021
 GNH  HN1   H  HNR6   0   0.424  -2.0860   0.0955  -6.5815
 GNH  HN21  H  HNH2   0   0.412   0.8815  -1.6936  -6.6033
 GNH  HN22  H  HNH2   0   0.415  -0.3768  -1.0316  -7.5569

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    1.703  0.020  1.703
 GNH  N3B  HN31  single    0.890  0.020  1.040
 GNH  N3B  HN32  single    0.890  0.020  1.040
 GNH  PB   O1B   deloc     1.502  0.020  1.502
 GNH  PB   O2B   deloc     1.500  0.020  1.500
 GNH  PB   O3A   single    1.662  0.020  1.662
 GNH  O3A  PA    single    1.631  0.020  1.631
 GNH  PA   O1A   deloc     1.501  0.020  1.501
 GNH  PA   O2A   deloc     1.497  0.020  1.497
 GNH  PA   O5'   single    1.652  0.020  1.652
 GNH  O5'  C5'   single    1.407  0.020  1.407
 GNH  C5'  C4'   single    1.511  0.020  1.511
 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    1.428  0.020  1.428
 GNH  C4'  C3'   single    1.527  0.020  1.527
 GNH  C4'  H4'   single    0.970  0.020  1.090
 GNH  O4'  C1'   single    1.391  0.020  1.391
 GNH  C3'  O3'   single    1.401  0.020  1.401
 GNH  C3'  C2'   single    1.532  0.020  1.532
 GNH  C3'  H3'   single    0.970  0.020  1.090
 GNH  O3'  HO3'  single    0.850  0.020  0.980
 GNH  C2'  O2'   single    1.401  0.020  1.401
 GNH  C2'  C1'   single    1.527  0.020  1.527
 GNH  C2'  H2'   single    0.970  0.020  1.090
 GNH  O2'  HO2'  single    0.850  0.020  0.980
 GNH  C1'  N9    single    1.463  0.020  1.463
 GNH  C1'  H1'   single    0.970  0.020  1.090
 GNH  N9   C8    aromatic  1.376  0.020  1.376
 GNH  N9   C4    aromatic  1.359  0.020  1.359
 GNH  C8   N7    aromatic  1.300  0.020  1.300
 GNH  C8   H8    single    0.930  0.020  1.080
 GNH  N7   C5    aromatic  1.369  0.020  1.369
 GNH  C5   C6    aromatic  1.424  0.020  1.424
 GNH  C5   C4    aromatic  1.383  0.020  1.383
 GNH  C6   O6    double    1.220  0.020  1.220
 GNH  C6   N1    aromatic  1.401  0.020  1.401
 GNH  N1   C2    aromatic  1.366  0.020  1.366
 GNH  N1   HN1   single    0.860  0.020  1.020
 GNH  C2   N2    single    1.341  0.020  1.341
 GNH  C2   N3    aromatic  1.310  0.020  1.310
 GNH  N2   HN21  single    0.890  0.020  1.040
 GNH  N2   HN22  single    0.890  0.020  1.040
 GNH  N3   C4    aromatic  1.342  0.020  1.342

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  108.31  3.000
 GNH  HN32  N3B  PB    112.20  3.000
 GNH  HN31  N3B  PB    114.31  3.000
 GNH  O3A   PB   O2B   109.01  3.000
 GNH  O3A   PB   O1B   107.71  3.000
 GNH  O2B   PB   O1B   120.45  3.000
 GNH  O3A   PB   N3B    96.85  3.000
 GNH  O2B   PB   N3B   107.21  3.000
 GNH  O1B   PB   N3B   113.00  3.000
 GNH  PA    O3A  PB    124.19  3.000
 GNH  O5'   PA   O2A   109.16  3.000
 GNH  O5'   PA   O1A   109.13  3.000
 GNH  O2A   PA   O1A   119.72  3.000
 GNH  O5'   PA   O3A    93.50  3.000
 GNH  O2A   PA   O3A   111.20  3.000
 GNH  O1A   PA   O3A   110.94  3.000
 GNH  C5'   O5'  PA    118.84  3.000
 GNH  H5'1  C5'  H5'2  106.92  3.000
 GNH  H5'1  C5'  C4'   107.72  3.000
 GNH  H5'2  C5'  C4'   109.46  3.000
 GNH  H5'1  C5'  O5'   110.37  3.000
 GNH  H5'2  C5'  O5'   112.23  3.000
 GNH  C4'   C5'  O5'   110.00  3.000
 GNH  H4'   C4'  C3'   109.62  3.000
 GNH  H4'   C4'  O4'   108.36  3.000
 GNH  C3'   C4'  O4'   105.49  3.000
 GNH  H4'   C4'  C5'   109.43  3.000
 GNH  C3'   C4'  C5'   112.72  3.000
 GNH  O4'   C4'  C5'   111.08  3.000
 GNH  C1'   O4'  C4'   111.43  3.000
 GNH  H3'   C3'  C2'   108.98  3.000
 GNH  H3'   C3'  O3'   111.20  3.000
 GNH  C2'   C3'  O3'   113.70  3.000
 GNH  H3'   C3'  C4'   110.12  3.000
 GNH  C2'   C3'  C4'   102.19  3.000
 GNH  O3'   C3'  C4'   110.29  3.000
 GNH  HO3'  O3'  C3'   108.72  3.000
 GNH  H2'   C2'  C1'   112.48  3.000
 GNH  H2'   C2'  O2'   111.79  3.000
 GNH  C1'   C2'  O2'   107.36  3.000
 GNH  H2'   C2'  C3'   112.69  3.000
 GNH  C1'   C2'  C3'   100.96  3.000
 GNH  O2'   C2'  C3'   110.97  3.000
 GNH  HO2'  O2'  C2'   107.61  3.000
 GNH  H1'   C1'  N9    107.64  3.000
 GNH  H1'   C1'  C2'   111.58  3.000
 GNH  N9    C1'  C2'   111.71  3.000
 GNH  H1'   C1'  O4'   110.15  3.000
 GNH  N9    C1'  O4'   109.18  3.000
 GNH  C2'   C1'  O4'   106.57  3.000
 GNH  C4    N9   C8    106.56  3.000
 GNH  C4    N9   C1'   125.30  3.000
 GNH  C8    N9   C1'   127.99  3.000
 GNH  H8    C8   N7    124.95  3.000
 GNH  H8    C8   N9    122.54  3.000
 GNH  N7    C8   N9    112.48  3.000
 GNH  C5    N7   C8    104.96  3.000
 GNH  C4    C5   C6    118.67  3.000
 GNH  C4    C5   N7    110.63  3.000
 GNH  C6    C5   N7    130.70  3.000
 GNH  N1    C6   O6    120.51  3.000
 GNH  N1    C6   C5    110.61  3.000
 GNH  O6    C6   C5    128.88  3.000
 GNH  HN1   N1   C2    118.29  3.000
 GNH  HN1   N1   C6    115.52  3.000
 GNH  C2    N1   C6    126.18  3.000
 GNH  N3    C2   N2    120.05  3.000
 GNH  N3    C2   N1    123.00  3.000
 GNH  N2    C2   N1    116.93  3.000
 GNH  HN22  N2   HN21  116.68  3.000
 GNH  HN22  N2   C2    121.24  3.000
 GNH  HN21  N2   C2    117.81  3.000
 GNH  C4    N3   C2    113.14  3.000
 GNH  N3    C4   C5    128.39  3.000
 GNH  N3    C4   N9    126.24  3.000
 GNH  C5    C4   N9    105.36  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   -134.14  30.0  3
 GNH  Var_02    O1A   PA   O3A  PB    -89.15  30.0  3
 GNH  Var_03    HN31  N3B  PB   O1B    30.77  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

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

