# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Oct  2 01:19:50 2022
#   Inital geometry file: a 123 line input string
#   Ligand name: guanosine 5'-(tetrahydrogen triphosphate)
#   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)=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
 GTP  GTP  "GUANOSINE-5'-TRIPHOSPHATE"  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_GTP
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
 GTP  PG    P  P     0   1.342   7.3586  29.9456  21.1794
 GTP  O1G   O  O     0  -0.706   7.5436  29.8029  22.6282
 GTP  O2G   O  OH1   0  -0.748   5.9704  30.4689  20.6335
 GTP  O3G   O  OH1   0  -0.648   7.4919  28.6674  20.2520
 GTP  O3B   O  O2    0  -0.702   8.4763  30.9989  20.6188
 GTP  PB    P  P     0   1.451   9.0502  31.3165  19.1593
 GTP  O1B   O  O     0  -0.619  10.1146  30.4291  18.6834
 GTP  O2B   O  OH1   0  -0.625   7.7307  31.4487  18.2942
 GTP  O3A   O  O2    0  -0.645   9.5832  32.8154  19.4067
 GTP  PA    P  P     0   1.490   8.8106  34.2390  19.4386
 GTP  O1A   O  O     0  -0.633   8.4840  34.8020  18.1235
 GTP  O2A   O  OH1   0  -0.676   7.6157  33.8704  20.4186
 GTP  O5'   O  O2    0  -0.603   9.8261  35.1480  20.2402
 GTP  C5'   C  CH2   0  -0.247  10.2834  34.8632  21.5691
 GTP  C4'   C  CH1   0   0.052  11.7940  34.8053  21.6116
 GTP  O4'   O  O2    0  -0.551  12.2614  33.7375  20.7933
 GTP  C3'   C  CH1   0  -0.016  12.5141  36.0702  21.1365
 GTP  O3'   O  OH1   0  -0.656  13.6571  36.2354  21.9366
 GTP  C2'   C  CH1   0  -0.023  12.8859  35.7108  19.7001
 GTP  O2'   O  OH1   0  -0.618  13.9715  36.4635  19.2542
 GTP  C1'   C  CH1   0   0.141  13.1846  34.2157  19.8485
 GTP  N9    N  NR5   0  -0.500  13.0736  33.4502  18.6379
 GTP  C8    C  CR15  0   0.011  12.2119  33.6189  17.5775
 GTP  N7    N  N     0  -0.451  12.3426  32.7056  16.6687
 GTP  C5    C  CR56  0   0.129  13.3313  31.8807  17.1408
 GTP  C6    C  CR6   0   0.362  13.9078  30.7066  16.5749
 GTP  O6    O  O     0  -0.492  13.6420  30.1547  15.5218
 GTP  N1    N  NR16  0  -0.624  14.9022  30.1923  17.4187
 GTP  C2    C  CR6   0   0.588  15.2905  30.7152  18.6191
 GTP  N2    N  NH2   0  -0.872  16.2936  30.0996  19.2595
 GTP  N3    N  N     0  -0.419  14.7467  31.7894  19.1373
 GTP  C4    C  CR56  0   0.479  13.7935  32.3237  18.3632
 GTP  HOG2  H  HOH1  0   0.444   5.6075  31.2311  21.1069
 GTP  HOG3  H  HOH1  0   0.533   8.1811  28.0427  20.5196
 GTP  HOB2  H  HOH1  0   0.551   7.8484  31.3174  17.3413
 GTP  HOA2  H  HOH1  0   0.524   6.8723  34.4908  20.4173
 GTP  H5'   H  HCH2  0   0.299   9.9285  35.6620  22.2213
 GTP  H5''  H  HCH2  0   0.270   9.8728  33.9223  21.9421
 GTP  H4'   H  HCH1  0   0.260  12.0600  34.6159  22.6578
 GTP  H3'   H  HCH1  0   0.175  11.8633  36.9524  21.1798
 GTP  HO3'  H  HOH1  0   0.447  14.1932  36.9422  21.5607
 GTP  H2'   H  HCH1  0   0.279  12.0007  35.8608  19.0737
 GTP  HO2'  H  HOH1  0   0.461  14.0215  36.4097  18.2947
 GTP  H1'   H  HCH1  0   0.284  14.2123  34.0870  20.2036
 GTP  H8    H  HCR5  0   0.349  11.5137  34.4394  17.5280
 GTP  HN1   H  HNR6  0   0.343  15.3678  29.3585  17.0826
 GTP  HN21  H  HNH2  0   0.403  16.4934  30.3885  20.2022
 GTP  HN22  H  HNH2  0   0.407  16.5976  29.1774  18.9957

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
 GTP  PG   O1G   double    1.468  0.020  1.468
 GTP  PG   O2G   single    1.581  0.020  1.581
 GTP  PG   O3G   single    1.585  0.020  1.585
 GTP  PG   O3B   single    1.635  0.020  1.635
 GTP  O2G  HOG2  single    0.850  0.020  0.980
 GTP  O3G  HOG3  single    0.850  0.020  0.980
 GTP  O3B  PB    single    1.600  0.020  1.600
 GTP  PB   O1B   double    1.465  0.020  1.465
 GTP  PB   O2B   single    1.583  0.020  1.583
 GTP  PB   O3A   single    1.610  0.020  1.610
 GTP  O2B  HOB2  single    0.850  0.020  0.980
 GTP  O3A  PA    single    1.620  0.020  1.620
 GTP  PA   O1A   double    1.467  0.020  1.467
 GTP  PA   O2A   single    1.589  0.020  1.589
 GTP  PA   O5'   single    1.581  0.020  1.581
 GTP  O2A  HOA2  single    0.850  0.020  0.980
 GTP  O5'  C5'   single    1.434  0.020  1.434
 GTP  C5'  C4'   single    1.512  0.020  1.512
 GTP  C5'  H5'   single    0.970  0.020  1.090
 GTP  C5'  H5''  single    0.970  0.020  1.090
 GTP  C4'  O4'   single    1.424  0.020  1.424
 GTP  C4'  C3'   single    1.531  0.020  1.531
 GTP  C4'  H4'   single    0.970  0.020  1.090
 GTP  O4'  C1'   single    1.405  0.020  1.405
 GTP  C3'  O3'   single    1.405  0.020  1.405
 GTP  C3'  C2'   single    1.527  0.020  1.527
 GTP  C3'  H3'   single    0.970  0.020  1.090
 GTP  O3'  HO3'  single    0.850  0.020  0.980
 GTP  C2'  O2'   single    1.394  0.020  1.394
 GTP  C2'  C1'   single    1.532  0.020  1.532
 GTP  C2'  H2'   single    0.970  0.020  1.090
 GTP  O2'  HO2'  single    0.850  0.020  0.980
 GTP  C1'  N9    single    1.437  0.020  1.437
 GTP  C1'  H1'   single    0.970  0.020  1.090
 GTP  N9   C8    aromatic  1.377  0.020  1.377
 GTP  N9   C4    aromatic  1.365  0.020  1.365
 GTP  C8   N7    aromatic  1.295  0.020  1.295
 GTP  C8   H8    single    0.930  0.020  1.080
 GTP  N7   C5    aromatic  1.371  0.020  1.371
 GTP  C5   C6    single    1.425  0.020  1.425
 GTP  C5   C4    aromatic  1.380  0.020  1.380
 GTP  C6   O6    double    1.218  0.020  1.218
 GTP  C6   N1    single    1.402  0.020  1.402
 GTP  N1   C2    single    1.366  0.020  1.366
 GTP  N1   HN1   single    0.860  0.020  1.020
 GTP  C2   N2    single    1.340  0.020  1.340
 GTP  C2   N3    double    1.311  0.020  1.311
 GTP  N2   HN21  single    0.890  0.020  1.040
 GTP  N2   HN22  single    0.890  0.020  1.040
 GTP  N3   C4    single    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
 GTP  O3B   PG   O3G   105.16  3.000
 GTP  O3B   PG   O2G   105.58  3.000
 GTP  O3G   PG   O2G    97.98  3.000
 GTP  O3B   PG   O1G   108.36  3.000
 GTP  O3G   PG   O1G   119.25  3.000
 GTP  O2G   PG   O1G   118.93  3.000
 GTP  HOG2  O2G  PG    114.90  3.000
 GTP  HOG3  O3G  PG    114.75  3.000
 GTP  PB    O3B  PG    133.30  3.000
 GTP  O3A   PB   O2B   106.38  3.000
 GTP  O3A   PB   O1B   111.92  3.000
 GTP  O2B   PB   O1B   118.59  3.000
 GTP  O3A   PB   O3B    99.40  3.000
 GTP  O2B   PB   O3B   102.47  3.000
 GTP  O1B   PB   O3B   115.89  3.000
 GTP  HOB2  O2B  PB    115.13  3.000
 GTP  PA    O3A  PB    131.55  3.000
 GTP  O5'   PA   O2A   107.68  3.000
 GTP  O5'   PA   O1A   112.13  3.000
 GTP  O2A   PA   O1A   118.33  3.000
 GTP  O5'   PA   O3A   102.05  3.000
 GTP  O2A   PA   O3A    99.61  3.000
 GTP  O1A   PA   O3A   115.19  3.000
 GTP  HOA2  O2A  PA    115.34  3.000
 GTP  C5'   O5'  PA    124.09  3.000
 GTP  H5''  C5'  H5'   107.72  3.000
 GTP  H5''  C5'  C4'   109.44  3.000
 GTP  H5'   C5'  C4'   109.65  3.000
 GTP  H5''  C5'  O5'   111.58  3.000
 GTP  H5'   C5'  O5'   107.76  3.000
 GTP  C4'   C5'  O5'   110.62  3.000
 GTP  H4'   C4'  C3'   108.95  3.000
 GTP  H4'   C4'  O4'   109.84  3.000
 GTP  C3'   C4'  O4'   106.66  3.000
 GTP  H4'   C4'  C5'   106.02  3.000
 GTP  C3'   C4'  C5'   115.43  3.000
 GTP  O4'   C4'  C5'   109.90  3.000
 GTP  C1'   O4'  C4'   110.30  3.000
 GTP  H3'   C3'  C2'   111.77  3.000
 GTP  H3'   C3'  O3'   111.44  3.000
 GTP  C2'   C3'  O3'   111.43  3.000
 GTP  H3'   C3'  C4'   111.91  3.000
 GTP  C2'   C3'  C4'   102.24  3.000
 GTP  O3'   C3'  C4'   107.64  3.000
 GTP  HO3'  O3'  C3'   108.46  3.000
 GTP  H2'   C2'  C1'   110.29  3.000
 GTP  H2'   C2'  O2'   111.87  3.000
 GTP  C1'   C2'  O2'   113.95  3.000
 GTP  H2'   C2'  C3'   108.01  3.000
 GTP  C1'   C2'  C3'   100.73  3.000
 GTP  O2'   C2'  C3'   111.32  3.000
 GTP  HO2'  O2'  C2'   109.23  3.000
 GTP  H1'   C1'  N9    106.45  3.000
 GTP  H1'   C1'  C2'   109.22  3.000
 GTP  N9    C1'  C2'   115.05  3.000
 GTP  H1'   C1'  O4'   111.02  3.000
 GTP  N9    C1'  O4'   109.54  3.000
 GTP  C2'   C1'  O4'   105.62  3.000
 GTP  C4    N9   C8    106.04  3.000
 GTP  C4    N9   C1'   124.65  3.000
 GTP  C8    N9   C1'   129.21  3.000
 GTP  H8    C8   N7    124.72  3.000
 GTP  H8    C8   N9    122.26  3.000
 GTP  N7    C8   N9    113.01  3.000
 GTP  C5    N7   C8    104.80  3.000
 GTP  C4    C5   C6    118.74  3.000
 GTP  C4    C5   N7    110.69  3.000
 GTP  C6    C5   N7    130.58  3.000
 GTP  N1    C6   O6    120.58  3.000
 GTP  N1    C6   C5    110.50  3.000
 GTP  O6    C6   C5    128.92  3.000
 GTP  HN1   N1   C2    118.45  3.000
 GTP  HN1   N1   C6    115.38  3.000
 GTP  C2    N1   C6    126.17  3.000
 GTP  N3    C2   N2    119.88  3.000
 GTP  N3    C2   N1    122.91  3.000
 GTP  N2    C2   N1    117.20  3.000
 GTP  HN22  N2   HN21  116.67  3.000
 GTP  HN22  N2   C2    121.47  3.000
 GTP  HN21  N2   C2    117.69  3.000
 GTP  C4    N3   C2    113.19  3.000
 GTP  N3    C4   C5    128.49  3.000
 GTP  N3    C4   N9    126.05  3.000
 GTP  C5    C4   N9    105.46  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
 GTP  CONST_01  C5    N7   C8   N9      0.00   0.0  0
 GTP  CONST_02  N7    C5   C4   N9      0.00   0.0  0
 GTP  CONST_03  C5    C4   N9   C8      0.00   0.0  0
 GTP  CONST_04  C4    C5   N7   C8      0.00   0.0  0
 GTP  CONST_05  C4    N9   C8   N7      0.00   0.0  0
 GTP  CONST_06  N7    C8   N9   C1'   180.00   0.0  0
 GTP  CONST_07  C5    C4   N9   C1'   180.00   0.0  0
 GTP  CONST_08  N3    C4   N9   C1'     0.00   0.0  0
 GTP  CONST_09  C2    N1   C6   C5      0.00   0.0  0
 GTP  CONST_10  N3    C2   N1   C6      0.00   0.0  0
 GTP  CONST_11  C4    N3   C2   N1      0.00   0.0  0
 GTP  CONST_12  N2    C2   N1   C6    180.00   0.0  0
 GTP  CONST_13  C2    N1   C6   O6    180.00   0.0  0
 GTP  CONST_14  C4    N3   C2   N2    180.00   0.0  0
 GTP  CONST_15  H8    C8   N9   C1'     0.00   0.0  0
 GTP  CONST_16  H8    C8   N7   C5    180.00   0.0  0
 GTP  CONST_17  H8    C8   N9   C4    180.00   0.0  0
 GTP  CONST_18  HN1   N1   C6   C5    180.00   0.0  0
 GTP  CONST_19  HN1   N1   C2   N3    180.00   0.0  0
 GTP  CONST_20  HN1   N1   C6   O6      0.00   0.0  0
 GTP  CONST_21  HN21  N2   C2   N1    180.00   0.0  0
 GTP  CONST_22  HN22  N2   C2   N1      0.00   0.0  0
 GTP  CONST_23  HN1   N1   C2   N2      0.00   0.0  0
 GTP  CONST_24  HN21  N2   C2   N3      0.00   0.0  0
 GTP  CONST_25  HN22  N2   C2   N3    180.00   0.0  0
 GTP  Var_01    C4'   C5'  O5'  PA    124.27  30.0  3
 GTP  Var_02    O1B   PB   O3B  PG    -82.84  30.0  3
 GTP  Var_03    O2B   PB   O3B  PG     47.87  30.0  3
 GTP  Var_04    O3A   PB   O3B  PG    157.10  30.0  3
 GTP  Var_05    PB    O3B  PG   O1G   162.44  30.0  3
 GTP  Var_06    PB    O3B  PG   O2G   -69.11  30.0  3
 GTP  Var_07    PB    O3B  PG   O3G    33.88  30.0  3
 GTP  Var_08    PA    O3A  PB   O3B   -80.41  30.0  3
 GTP  Var_09    O1A   PA   O3A  PB    -78.37  30.0  3
 GTP  Var_10    O2A   PA   O3A  PB     49.32  30.0  3
 GTP  Var_11    O5'   PA   O3A  PB    159.88  30.0  3
 GTP  Var_12    PA    O3A  PB   O1B   156.66  30.0  3
 GTP  Var_13    PA    O3A  PB   O2B    25.66  30.0  3
 GTP  Var_14    C5'   O5'  PA   O3A   -58.32  30.0  3
 GTP  Var_15    C5'   O5'  PA   O1A   177.86  30.0  3
 GTP  Var_16    C5'   O5'  PA   O2A    46.00  30.0  3
 GTP  Var_17    H5'   C5'  O5'  PA   -115.88  30.0  3
 GTP  Var_18    H5''  C5'  O5'  PA      2.17  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
 GTP  chir_03  C4'  C5'  O4'  C3'  negativ
 GTP  chir_04  C3'  O3'  C4'  C2'  positiv
 GTP  chir_05  C2'  O2'  C3'  C1'  positiv
 GTP  chir_06  C1'  O4'  N9   C2'  negativ
 GTP  chir_07  PB   O1B  O2B  O3A  both
 GTP  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
 GTP  plan-1  C1'   0.020
 GTP  plan-1  N9    0.020
 GTP  plan-1  C8    0.020
 GTP  plan-1  N7    0.020
 GTP  plan-1  C5    0.020
 GTP  plan-1  C6    0.020
 GTP  plan-1  O6    0.020
 GTP  plan-1  N1    0.020
 GTP  plan-1  C2    0.020
 GTP  plan-1  N2    0.020
 GTP  plan-1  N3    0.020
 GTP  plan-1  C4    0.020
 GTP  plan-1  H8    0.020
 GTP  plan-1  HN1   0.020
 GTP  plan-1  HN21  0.020
 GTP  plan-1  HN22  0.020

