# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Oct  1 15:52:15 2022
#   Inital geometry file: a 123 line input string
#   Ligand name: 5'-O-[(S)-hydroxy{[(S)-hydroxy(thiophosphonooxy)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)O[P](O)(O)=S)[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
 GSP  GSP  "5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE"  ligand  48  32  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GSP
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
 GSP  PG    P  P     0   1.206  37.3302  -32.2663  12.1261
 GSP  O3B   O  O2    0  -0.667  37.1708  -30.8108  11.3979
 GSP  S1G   S  S1    0  -0.477  38.7429  -33.3714  11.4640
 GSP  O2G   O  OH1   0  -0.692  37.4394  -31.6861  13.5990
 GSP  O3G   O  OH1   0  -0.708  35.8562  -32.8673  12.0652
 GSP  PB    P  P     0   1.490  36.5353  -30.5311   9.9490
 GSP  O1B   O  O     0  -0.647  36.3162  -31.7148   9.1137
 GSP  O2B   O  OH1   0  -0.716  35.3027  -29.6343  10.3702
 GSP  PA    P  P     0   1.500  37.6382  -27.8878   9.2706
 GSP  O1A   O  O     0  -0.662  36.4702  -27.2769   8.6290
 GSP  O2A   O  OH1   0  -0.728  37.8368  -27.4201  10.7717
 GSP  O3A   O  O2    0  -0.685  37.6249  -29.5191   9.3286
 GSP  O5'   O  O2    0  -0.570  38.9571  -27.6274   8.4473
 GSP  C5'   C  CH2   0  -0.209  40.3133  -27.8320   8.8521
 GSP  C4'   C  CH1   0  -0.005  41.1534  -26.7019   8.3019
 GSP  O4'   O  O2    0  -0.485  41.0779  -26.6984   6.8808
 GSP  C3'   C  CH1   0  -0.038  40.7432  -25.3010   8.7646
 GSP  O3'   O  OH1   0  -0.662  41.9160  -24.5388   8.8900
 GSP  C2'   C  CH1   0  -0.033  39.8818  -24.8079   7.6031
 GSP  O2'   O  OH1   0  -0.655  39.8738  -23.4141   7.5437
 GSP  C1'   C  CH1   0   0.193  40.5824  -25.4720   6.4103
 GSP  N9    N  NR5   0  -0.547  39.7349  -25.7055   5.2727
 GSP  C8    C  CR15  0   0.094  38.4985  -26.3133   5.2466
 GSP  N7    N  N     0  -0.439  38.0293  -26.4490   4.0469
 GSP  C5    C  CR56  0  -0.096  38.9950  -25.9176   3.2301
 GSP  C6    C  CR6   0   0.502  39.0448  -25.7994   1.8111
 GSP  O6    O  O     0  -0.463  38.2195  -26.1490   0.9859
 GSP  N1    N  NR16  0  -0.728  40.2434  -25.1926   1.4097
 GSP  C2    C  CR6   0   0.693  41.2466  -24.7692   2.2345
 GSP  N2    N  NH2   0  -0.831  42.3340  -24.2418   1.6581
 GSP  N3    N  N     0  -0.513  41.1935  -24.8852   3.5391
 GSP  C4    C  CR56  0   0.509  40.0643  -25.4579   3.9728
 GSP  HOG2  H  HOH1  0   0.511  37.8715  -32.2848  14.2252
 GSP  HOG3  H  HOH1  0   0.508  35.7556  -33.6191  11.4643
 GSP  HOB2  H  HOH1  0   0.514  34.6748  -29.4230   9.6622
 GSP  HOA2  H  HOH1  0   0.508  38.4498  -27.9117  11.3380
 GSP  H5'1  H  HCH2  0   0.255  40.4190  -27.8576   9.9388
 GSP  H5'2  H  HCH2  0   0.276  40.6516  -28.7899   8.4549
 GSP  H4'   H  HCH1  0   0.272  42.1841  -26.8996   8.6166
 GSP  H3'   H  HCH1  0   0.254  40.1764  -25.3293   9.7044
 GSP  HO3'  H  HOH1  0   0.453  41.6683  -23.6135   8.9946
 GSP  H2'   H  HCH1  0   0.252  38.8688  -25.2061   7.7223
 GSP  HO2'  H  HOH1  0   0.467  39.1677  -23.1267   6.9563
 GSP  H1'   H  HCH1  0   0.257  41.3955  -24.8280   6.0597
 GSP  H8    H  HCR5  0   0.287  37.9958  -26.6316   6.1466
 GSP  HN1   H  HNR6  0   0.424  40.3561  -25.0748   0.4100
 GSP  HN21  H  HNH2  0   0.413  43.0212  -23.8117   2.2535
 GSP  HN22  H  HNH2  0   0.416  42.3459  -23.9823   0.6867

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
 GSP  PG   O3B   single    1.635  0.020  1.635
 GSP  PG   S1G   double    1.912  0.020  1.912
 GSP  PG   O2G   single    1.587  0.020  1.587
 GSP  PG   O3G   single    1.593  0.020  1.593
 GSP  O3B  PB    single    1.607  0.020  1.607
 GSP  O2G  HOG2  single    0.850  0.020  0.980
 GSP  O3G  HOG3  single    0.850  0.020  0.980
 GSP  PB   O1B   double    1.465  0.020  1.465
 GSP  PB   O2B   single    1.581  0.020  1.581
 GSP  PB   O3A   single    1.611  0.020  1.611
 GSP  O2B  HOB2  single    0.850  0.020  0.980
 GSP  PA   O1A   double    1.466  0.020  1.466
 GSP  PA   O2A   single    1.585  0.020  1.585
 GSP  PA   O3A   single    1.632  0.020  1.632
 GSP  PA   O5'   single    1.577  0.020  1.577
 GSP  O2A  HOA2  single    0.850  0.020  0.980
 GSP  O5'  C5'   single    1.430  0.020  1.430
 GSP  C5'  C4'   single    1.512  0.020  1.512
 GSP  C5'  H5'1  single    0.970  0.020  1.090
 GSP  C5'  H5'2  single    0.970  0.020  1.090
 GSP  C4'  O4'   single    1.423  0.020  1.423
 GSP  C4'  C3'   single    1.531  0.020  1.531
 GSP  C4'  H4'   single    0.970  0.020  1.090
 GSP  O4'  C1'   single    1.404  0.020  1.404
 GSP  C3'  O3'   single    1.404  0.020  1.404
 GSP  C3'  C2'   single    1.528  0.020  1.528
 GSP  C3'  H3'   single    0.970  0.020  1.090
 GSP  O3'  HO3'  single    0.850  0.020  0.980
 GSP  C2'  O2'   single    1.395  0.020  1.395
 GSP  C2'  C1'   single    1.535  0.020  1.535
 GSP  C2'  H2'   single    0.970  0.020  1.090
 GSP  O2'  HO2'  single    0.850  0.020  0.980
 GSP  C1'  N9    single    1.438  0.020  1.438
 GSP  C1'  H1'   single    0.970  0.020  1.090
 GSP  N9   C8    aromatic  1.378  0.020  1.378
 GSP  N9   C4    aromatic  1.364  0.020  1.364
 GSP  C8   N7    aromatic  1.295  0.020  1.295
 GSP  C8   H8    single    0.930  0.020  1.080
 GSP  N7   C5    aromatic  1.372  0.020  1.372
 GSP  C5   C6    single    1.425  0.020  1.425
 GSP  C5   C4    aromatic  1.381  0.020  1.381
 GSP  C6   O6    double    1.218  0.020  1.218
 GSP  C6   N1    single    1.402  0.020  1.402
 GSP  N1   C2    single    1.366  0.020  1.366
 GSP  N1   HN1   single    0.860  0.020  1.020
 GSP  C2   N2    single    1.339  0.020  1.339
 GSP  C2   N3    double    1.311  0.020  1.311
 GSP  N2   HN21  single    0.890  0.020  1.040
 GSP  N2   HN22  single    0.890  0.020  1.040
 GSP  N3   C4    single    1.338  0.020  1.338

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
 GSP  O3G   PG   O2G   103.72  3.000
 GSP  O3G   PG   S1G   116.90  3.000
 GSP  O2G   PG   S1G   118.82  3.000
 GSP  O3G   PG   O3B   103.21  3.000
 GSP  O2G   PG   O3B    95.43  3.000
 GSP  S1G   PG   O3B   115.61  3.000
 GSP  PB    O3B  PG    126.52  3.000
 GSP  HOG2  O2G  PG    113.89  3.000
 GSP  HOG3  O3G  PG    114.40  3.000
 GSP  O3A   PB   O2B   105.87  3.000
 GSP  O3A   PB   O1B   112.90  3.000
 GSP  O2B   PB   O1B   119.57  3.000
 GSP  O3A   PB   O3B   100.90  3.000
 GSP  O2B   PB   O3B    99.60  3.000
 GSP  O1B   PB   O3B   115.63  3.000
 GSP  HOB2  O2B  PB    115.70  3.000
 GSP  O5'   PA   O3A   100.98  3.000
 GSP  O5'   PA   O2A   109.95  3.000
 GSP  O3A   PA   O2A   105.21  3.000
 GSP  O5'   PA   O1A   111.66  3.000
 GSP  O3A   PA   O1A   115.18  3.000
 GSP  O2A   PA   O1A   113.04  3.000
 GSP  HOA2  O2A  PA    118.90  3.000
 GSP  PA    O3A  PB    130.30  3.000
 GSP  C5'   O5'  PA    128.46  3.000
 GSP  H5'2  C5'  H5'1  108.16  3.000
 GSP  H5'2  C5'  C4'   110.58  3.000
 GSP  H5'1  C5'  C4'   109.02  3.000
 GSP  H5'2  C5'  O5'   108.47  3.000
 GSP  H5'1  C5'  O5'   112.14  3.000
 GSP  C4'   C5'  O5'   108.48  3.000
 GSP  H4'   C4'  C3'   109.28  3.000
 GSP  H4'   C4'  O4'   109.70  3.000
 GSP  C3'   C4'  O4'   106.57  3.000
 GSP  H4'   C4'  C5'   106.46  3.000
 GSP  C3'   C4'  C5'   115.15  3.000
 GSP  O4'   C4'  C5'   109.62  3.000
 GSP  C1'   O4'  C4'   110.83  3.000
 GSP  H3'   C3'  C2'   111.59  3.000
 GSP  H3'   C3'  O3'   111.64  3.000
 GSP  C2'   C3'  O3'   111.32  3.000
 GSP  H3'   C3'  C4'   111.92  3.000
 GSP  C2'   C3'  C4'   102.51  3.000
 GSP  O3'   C3'  C4'   107.44  3.000
 GSP  HO3'  O3'  C3'   108.43  3.000
 GSP  H2'   C2'  C1'   110.47  3.000
 GSP  H2'   C2'  O2'   111.26  3.000
 GSP  C1'   C2'  O2'   113.69  3.000
 GSP  H2'   C2'  C3'   108.75  3.000
 GSP  C1'   C2'  C3'   101.18  3.000
 GSP  O2'   C2'  C3'   110.98  3.000
 GSP  HO2'  O2'  C2'   109.19  3.000
 GSP  H1'   C1'  N9    106.26  3.000
 GSP  H1'   C1'  C2'   109.48  3.000
 GSP  N9    C1'  C2'   114.60  3.000
 GSP  H1'   C1'  O4'   111.04  3.000
 GSP  N9    C1'  O4'   109.35  3.000
 GSP  C2'   C1'  O4'   106.18  3.000
 GSP  C4    N9   C8    106.19  3.000
 GSP  C4    N9   C1'   125.62  3.000
 GSP  C8    N9   C1'   127.99  3.000
 GSP  H8    C8   N7    124.95  3.000
 GSP  H8    C8   N9    122.17  3.000
 GSP  N7    C8   N9    112.88  3.000
 GSP  C5    N7   C8    104.82  3.000
 GSP  C4    C5   C6    118.75  3.000
 GSP  C4    C5   N7    110.73  3.000
 GSP  C6    C5   N7    130.52  3.000
 GSP  N1    C6   O6    120.62  3.000
 GSP  N1    C6   C5    110.54  3.000
 GSP  O6    C6   C5    128.83  3.000
 GSP  HN1   N1   C2    118.56  3.000
 GSP  HN1   N1   C6    115.34  3.000
 GSP  C2    N1   C6    126.09  3.000
 GSP  N3    C2   N2    119.75  3.000
 GSP  N3    C2   N1    122.94  3.000
 GSP  N2    C2   N1    117.30  3.000
 GSP  HN22  N2   HN21  116.96  3.000
 GSP  HN22  N2   C2    121.81  3.000
 GSP  HN21  N2   C2    117.94  3.000
 GSP  C4    N3   C2    113.24  3.000
 GSP  N3    C4   C5    128.43  3.000
 GSP  N3    C4   N9    126.19  3.000
 GSP  C5    C4   N9    105.38  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
 GSP  CONST_01  C5    N7   C8   N9      0.00   0.0  0
 GSP  CONST_02  N7    C5   C4   N9      0.00   0.0  0
 GSP  CONST_03  C5    C4   N9   C8      0.00   0.0  0
 GSP  CONST_04  C4    C5   N7   C8      0.00   0.0  0
 GSP  CONST_05  C4    N9   C8   N7      0.00   0.0  0
 GSP  CONST_06  N7    C8   N9   C1'   180.00   0.0  0
 GSP  CONST_07  C5    C4   N9   C1'   180.00   0.0  0
 GSP  CONST_08  N3    C4   N9   C1'     0.00   0.0  0
 GSP  CONST_09  C2    N1   C6   C5      0.00   0.0  0
 GSP  CONST_10  N3    C2   N1   C6      0.00   0.0  0
 GSP  CONST_11  C4    N3   C2   N1      0.00   0.0  0
 GSP  CONST_12  N2    C2   N1   C6    180.00   0.0  0
 GSP  CONST_13  C2    N1   C6   O6    180.00   0.0  0
 GSP  CONST_14  C4    N3   C2   N2    180.00   0.0  0
 GSP  CONST_15  H8    C8   N9   C1'     0.00   0.0  0
 GSP  CONST_16  H8    C8   N7   C5    180.00   0.0  0
 GSP  CONST_17  H8    C8   N9   C4    180.00   0.0  0
 GSP  CONST_18  HN1   N1   C6   C5    180.00   0.0  0
 GSP  CONST_19  HN1   N1   C2   N3    180.00   0.0  0
 GSP  CONST_20  HN1   N1   C6   O6      0.00   0.0  0
 GSP  CONST_21  HN21  N2   C2   N1    180.00   0.0  0
 GSP  CONST_22  HN22  N2   C2   N1      0.00   0.0  0
 GSP  CONST_23  HN1   N1   C2   N2      0.00   0.0  0
 GSP  CONST_24  HN21  N2   C2   N3      0.00   0.0  0
 GSP  CONST_25  HN22  N2   C2   N3    180.00   0.0  0
 GSP  Var_01    C4'   C5'  O5'  PA   -141.51  30.0  3
 GSP  Var_02    O1B   PB   O3B  PG    -12.26  30.0  3
 GSP  Var_03    O2B   PB   O3B  PG    117.25  30.0  3
 GSP  Var_04    O3A   PB   O3B  PG   -134.39  30.0  3
 GSP  Var_05    PA    O3A  PB   O3B   -96.17  30.0  3
 GSP  Var_06    PB    O3B  PG   S1G    75.89  30.0  3
 GSP  Var_07    PB    O3B  PG   O2G  -158.49  30.0  3
 GSP  Var_08    PB    O3B  PG   O3G   -53.01  30.0  3
 GSP  Var_09    O1A   PA   O3A  PB    -56.21  30.0  1
 GSP  Var_10    O2A   PA   O3A  PB     68.96  30.0  1
 GSP  Var_11    O5'   PA   O3A  PB   -176.66  30.0  1
 GSP  Var_12    PA    O3A  PB   O1B   139.81  30.0  3
 GSP  Var_13    PA    O3A  PB   O2B     7.20  30.0  3
 GSP  Var_14    C5'   O5'  PA   O1A   167.15  30.0  3
 GSP  Var_15    C5'   O5'  PA   O2A    40.84  30.0  3
 GSP  Var_16    C5'   O5'  PA   O3A   -69.93  30.0  3
 GSP  Var_17    H5'1  C5'  O5'  PA    -21.05  30.0  3
 GSP  Var_18    H5'2  C5'  O5'  PA     98.33  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
 GSP  chir_03  C4'  C5'  O4'  C3'  negativ
 GSP  chir_04  C3'  O3'  C4'  C2'  positiv
 GSP  chir_05  C2'  O2'  C3'  C1'  positiv
 GSP  chir_06  C1'  O4'  N9   C2'  negativ
 GSP  chir_07  PB   O1B  O2B  O3A  both
 GSP  chir_08  PA   O2A  O3A  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
 GSP  plan-1  C1'   0.020
 GSP  plan-1  N9    0.020
 GSP  plan-1  C8    0.020
 GSP  plan-1  N7    0.020
 GSP  plan-1  C5    0.020
 GSP  plan-1  C6    0.020
 GSP  plan-1  O6    0.020
 GSP  plan-1  N1    0.020
 GSP  plan-1  C2    0.020
 GSP  plan-1  N2    0.020
 GSP  plan-1  N3    0.020
 GSP  plan-1  C4    0.020
 GSP  plan-1  H8    0.020
 GSP  plan-1  HN1   0.020
 GSP  plan-1  HN21  0.020
 GSP  plan-1  HN22  0.020

