# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 06:15:25 2021
#   Inital geometry file: a 123 line input string
#   Ligand name: 5'-O-[(S)-hydroxy{[(R)-hydroxy(phosphonomethyl)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)C[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
 GCP  GCP  5'-O-[(S)-hydroxy{[(R)-hydroxy(phosphonomethyl)phosphoryl]oxy}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 OK
;

data_comp_GCP
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
 GCP  PG    P  P     0   1.391  7.3329  22.3535  -17.5964
 GCP  O1G   O  O     0  -0.689  8.0392  21.2143  -16.9772
 GCP  O2G   O  OH1   0  -0.735  5.8410  21.9490  -18.0046
 GCP  O3G   O  OH1   0  -0.730  8.0909  22.8507  -18.9135
 GCP  C3B   C  CH2   0  -1.048  7.2076  23.8285  -16.5463
 GCP  PB    P  P     0   1.395  6.6874  23.5027  -14.8593
 GCP  O1B   O  O     0  -0.674  7.5458  22.6482  -14.0175
 GCP  O2B   O  OH1   0  -0.721  6.3747  24.9647  -14.3099
 GCP  O3A   O  O2    0  -0.703  5.2107  22.8505  -15.1257
 GCP  PA    P  P     0   1.502  4.3255  22.0564  -14.0307
 GCP  O1A   O  O     0  -0.679  4.2856  22.6513  -12.6876
 GCP  O2A   O  OH1   0  -0.724  2.9842  21.9960  -14.8781
 GCP  O5'   O  O2    0  -0.582  4.9287  20.5901  -13.9902
 GCP  C5'   C  CH2   0  -0.228  5.2274  19.8114  -15.1542
 GCP  C4'   C  CH1   0   0.003  4.9470  18.3601  -14.8742
 GCP  O4'   O  O2    0  -0.495  5.7463  17.9002  -13.7925
 GCP  C3'   C  CH1   0  -0.005  3.5121  18.0146  -14.4697
 GCP  O3'   O  OH1   0  -0.654  2.6058  17.9943  -15.5262
 GCP  C2'   C  CH1   0  -0.077  3.7233  16.6737  -13.7558
 GCP  O2'   O  OH1   0  -0.669  3.8584  15.6361  -14.6951
 GCP  C1'   C  CH1   0   0.184  5.0829  16.8952  -13.0789
 GCP  N9    N  NR5   0  -0.535  4.9544  17.3120  -11.6937
 GCP  C8    C  CR15  0   0.085  4.8365  18.5824  -11.1832
 GCP  N7    N  N     0  -0.444  4.7084  18.5938   -9.8915
 GCP  C5    C  CR56  0  -0.089  4.7380  17.2740   -9.5242
 GCP  C6    C  CR6   0   0.504  4.6496  16.6621   -8.2401
 GCP  O6    O  OC    0  -0.473  4.5148  17.1890   -7.1488
 GCP  N1    N  NR16  0  -0.727  4.7387  15.2684   -8.3527
 GCP  C2    C  CR6   0   0.688  4.8919  14.5598   -9.5098
 GCP  N2    N  NH2   0  -0.831  4.9267  13.2233   -9.4046
 GCP  N3    N  N     0  -0.515  4.9691  15.1269  -10.6881
 GCP  C4    C  CR56  0   0.505  4.8905  16.4636  -10.6333
 GCP  HOG2  H  HOH1  0   0.497  5.2487  22.6582  -18.2866
 GCP  HOG3  H  HOH1  0   0.498  7.6801  23.5670  -19.4157
 GCP  H3B1  H  HCH2  0   0.352  8.2031  24.2770  -16.4890
 GCP  H3B2  H  HCH2  0   0.348  6.5495  24.5717  -17.0037
 GCP  HOB2  H  HOH1  0   0.505  6.4806  25.0636  -13.3525
 GCP  HOA2  H  HOH1  0   0.510  2.1896  21.8172  -14.3562
 GCP  H5'2  H  HCH2  0   0.252  4.6235  20.1125  -16.0134
 GCP  H5'1  H  HCH2  0   0.275  6.2767  19.9634  -15.4117
 GCP  H4'   H  HCH1  0   0.256  5.2098  17.8168  -15.7932
 GCP  H3'   H  HCH1  0   0.258  3.1348  18.7463  -13.7489
 GCP  HO3'  H  HOH1  0   0.446  2.8691  17.2985  -16.1407
 GCP  H2'   H  HCH1  0   0.280  2.9430  16.4581  -13.0210
 GCP  HO2'  H  HOH1  0   0.471  3.0177  15.1767  -14.7746
 GCP  H1'   H  HCH1  0   0.278  5.6623  15.9676  -13.0735
 GCP  H8    H  HCR5  0   0.290  4.8686  19.4573  -11.8122
 GCP  HN1   H  HNR6  0   0.426  4.6756  14.7547   -7.4828
 GCP  HN21  H  HNH2  0   0.412  5.1944  12.7024  -10.2226
 GCP  HN22  H  HNH2  0   0.415  5.1069  12.7813   -8.5190

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
 GCP  PG   O1G   double    1.476  0.020  1.476
 GCP  PG   O2G   single    1.599  0.020  1.599
 GCP  PG   O3G   single    1.599  0.020  1.599
 GCP  PG   C3B   single    1.815  0.020  1.815
 GCP  O2G  HOG2  single    0.850  0.020  0.980
 GCP  O3G  HOG3  single    0.850  0.020  0.980
 GCP  C3B  PB    single    1.795  0.020  1.795
 GCP  C3B  H3B1  single    0.970  0.020  1.090
 GCP  C3B  H3B2  single    0.970  0.020  1.090
 GCP  PB   O1B   double    1.475  0.020  1.475
 GCP  PB   O2B   single    1.593  0.020  1.593
 GCP  PB   O3A   single    1.636  0.020  1.636
 GCP  O2B  HOB2  single    0.850  0.020  0.980
 GCP  O3A  PA    single    1.617  0.020  1.617
 GCP  PA   O1A   double    1.470  0.020  1.470
 GCP  PA   O2A   single    1.588  0.020  1.588
 GCP  PA   O5'   single    1.586  0.020  1.586
 GCP  O2A  HOA2  single    0.850  0.020  0.980
 GCP  O5'  C5'   single    1.432  0.020  1.432
 GCP  C5'  C4'   single    1.504  0.020  1.504
 GCP  C5'  H5'2  single    0.970  0.020  1.090
 GCP  C5'  H5'1  single    0.970  0.020  1.090
 GCP  C4'  O4'   single    1.421  0.020  1.421
 GCP  C4'  C3'   single    1.530  0.020  1.530
 GCP  C4'  H4'   single    0.970  0.020  1.090
 GCP  O4'  C1'   single    1.400  0.020  1.400
 GCP  C3'  O3'   single    1.392  0.020  1.392
 GCP  C3'  C2'   single    1.534  0.020  1.534
 GCP  C3'  H3'   single    0.970  0.020  1.090
 GCP  O3'  HO3'  single    0.850  0.020  0.980
 GCP  C2'  O2'   single    1.406  0.020  1.406
 GCP  C2'  C1'   single    1.535  0.020  1.535
 GCP  C2'  H2'   single    0.970  0.020  1.090
 GCP  O2'  HO2'  single    0.850  0.020  0.980
 GCP  C1'  N9    single    1.452  0.020  1.452
 GCP  C1'  H1'   single    0.970  0.020  1.090
 GCP  N9   C8    aromatic  1.374  0.020  1.374
 GCP  N9   C4    aromatic  1.360  0.020  1.360
 GCP  C8   N7    aromatic  1.298  0.020  1.298
 GCP  C8   H8    single    0.930  0.020  1.080
 GCP  N7   C5    aromatic  1.370  0.020  1.370
 GCP  C5   C6    aromatic  1.425  0.020  1.425
 GCP  C5   C4    aromatic  1.382  0.020  1.382
 GCP  C6   O6    double    1.219  0.020  1.219
 GCP  C6   N1    aromatic  1.401  0.020  1.401
 GCP  N1   C2    aromatic  1.365  0.020  1.365
 GCP  N1   HN1   single    0.860  0.020  1.020
 GCP  C2   N2    single    1.341  0.020  1.341
 GCP  C2   N3    aromatic  1.310  0.020  1.310
 GCP  N2   HN21  single    0.890  0.020  1.040
 GCP  N2   HN22  single    0.890  0.020  1.040
 GCP  N3   C4    aromatic  1.340  0.020  1.340

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
 GCP  C3B   PG   O3G   104.87  3.000
 GCP  C3B   PG   O2G   106.79  3.000
 GCP  O3G   PG   O2G   108.10  3.000
 GCP  C3B   PG   O1G   114.67  3.000
 GCP  O3G   PG   O1G   111.02  3.000
 GCP  O2G   PG   O1G   111.00  3.000
 GCP  HOG2  O2G  PG    117.45  3.000
 GCP  HOG3  O3G  PG    117.19  3.000
 GCP  H3B2  C3B  H3B1  106.93  3.000
 GCP  H3B2  C3B  PB    110.01  3.000
 GCP  H3B1  C3B  PB    106.80  3.000
 GCP  H3B2  C3B  PG    110.61  3.000
 GCP  H3B1  C3B  PG    107.50  3.000
 GCP  PB    C3B  PG    114.60  3.000
 GCP  O3A   PB   O2B   104.17  3.000
 GCP  O3A   PB   O1B   112.78  3.000
 GCP  O2B   PB   O1B   116.69  3.000
 GCP  O3A   PB   C3B   100.42  3.000
 GCP  O2B   PB   C3B   102.38  3.000
 GCP  O1B   PB   C3B   118.22  3.000
 GCP  HOB2  O2B  PB    114.42  3.000
 GCP  PA    O3A  PB    125.43  3.000
 GCP  O5'   PA   O2A   107.44  3.000
 GCP  O5'   PA   O1A   111.18  3.000
 GCP  O2A   PA   O1A   118.71  3.000
 GCP  O5'   PA   O3A   105.26  3.000
 GCP  O2A   PA   O3A    96.88  3.000
 GCP  O1A   PA   O3A   115.79  3.000
 GCP  HOA2  O2A  PA    114.40  3.000
 GCP  C5'   O5'  PA    124.15  3.000
 GCP  H5'1  C5'  H5'2  107.91  3.000
 GCP  H5'1  C5'  C4'   110.95  3.000
 GCP  H5'2  C5'  C4'   108.02  3.000
 GCP  H5'1  C5'  O5'   108.46  3.000
 GCP  H5'2  C5'  O5'   111.97  3.000
 GCP  C4'   C5'  O5'   109.54  3.000
 GCP  H4'   C4'  C3'   109.48  3.000
 GCP  H4'   C4'  O4'   109.99  3.000
 GCP  C3'   C4'  O4'   104.66  3.000
 GCP  H4'   C4'  C5'   106.05  3.000
 GCP  C3'   C4'  C5'   116.21  3.000
 GCP  O4'   C4'  C5'   110.42  3.000
 GCP  C1'   O4'  C4'   110.72  3.000
 GCP  H3'   C3'  C2'   109.00  3.000
 GCP  H3'   C3'  O3'   106.57  3.000
 GCP  C2'   C3'  O3'   115.47  3.000
 GCP  H3'   C3'  C4'   110.28  3.000
 GCP  C2'   C3'  C4'   101.03  3.000
 GCP  O3'   C3'  C4'   114.40  3.000
 GCP  HO3'  O3'  C3'   108.43  3.000
 GCP  H2'   C2'  C1'   111.37  3.000
 GCP  H2'   C2'  O2'   111.84  3.000
 GCP  C1'   C2'  O2'   108.42  3.000
 GCP  H2'   C2'  C3'   112.76  3.000
 GCP  C1'   C2'  C3'   101.60  3.000
 GCP  O2'   C2'  C3'   110.33  3.000
 GCP  HO2'  O2'  C2'   108.90  3.000
 GCP  H1'   C1'  N9    106.59  3.000
 GCP  H1'   C1'  C2'   110.43  3.000
 GCP  N9    C1'  C2'   112.56  3.000
 GCP  H1'   C1'  O4'   111.12  3.000
 GCP  N9    C1'  O4'   108.79  3.000
 GCP  C2'   C1'  O4'   107.38  3.000
 GCP  C4    N9   C8    106.44  3.000
 GCP  C4    N9   C1'   124.69  3.000
 GCP  C8    N9   C1'   128.85  3.000
 GCP  H8    C8   N7    125.20  3.000
 GCP  H8    C8   N9    122.07  3.000
 GCP  N7    C8   N9    112.72  3.000
 GCP  C5    N7   C8    104.84  3.000
 GCP  C4    C5   C6    118.57  3.000
 GCP  C4    C5   N7    110.61  3.000
 GCP  C6    C5   N7    130.81  3.000
 GCP  N1    C6   O6    120.58  3.000
 GCP  N1    C6   C5    110.53  3.000
 GCP  O6    C6   C5    128.89  3.000
 GCP  HN1   N1   C2    118.15  3.000
 GCP  HN1   N1   C6    115.59  3.000
 GCP  C2    N1   C6    126.26  3.000
 GCP  N3    C2   N2    120.03  3.000
 GCP  N3    C2   N1    122.97  3.000
 GCP  N2    C2   N1    116.98  3.000
 GCP  HN22  N2   HN21  116.14  3.000
 GCP  HN22  N2   C2    120.77  3.000
 GCP  HN21  N2   C2    117.33  3.000
 GCP  C4    N3   C2    113.05  3.000
 GCP  N3    C4   C5    128.62  3.000
 GCP  N3    C4   N9    125.99  3.000
 GCP  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
 GCP  CONST_01  C5    N7   C8   N9      0.00   0.0  0
 GCP  CONST_02  N7    C5   C4   N9      0.00   0.0  0
 GCP  CONST_03  C6    C5   C4   N9    180.00   0.0  0
 GCP  CONST_04  C2    N3   C4   N9    180.00   0.0  0
 GCP  CONST_05  C5    C4   N9   C8      0.00   0.0  0
 GCP  CONST_06  N3    C4   N9   C8    180.00   0.0  0
 GCP  CONST_07  C6    C5   N7   C8    180.00   0.0  0
 GCP  CONST_08  C4    C5   N7   C8      0.00   0.0  0
 GCP  CONST_09  C4    N9   C8   N7      0.00   0.0  0
 GCP  CONST_10  N1    C6   C5   N7    180.00   0.0  0
 GCP  CONST_11  N3    C4   C5   N7    180.00   0.0  0
 GCP  CONST_12  C2    N1   C6   C5      0.00   0.0  0
 GCP  CONST_13  C2    N3   C4   C5      0.00   0.0  0
 GCP  CONST_14  N3    C4   C5   C6      0.00   0.0  0
 GCP  CONST_15  N3    C2   N1   C6      0.00   0.0  0
 GCP  CONST_16  C4    C5   C6   N1      0.00   0.0  0
 GCP  CONST_17  C4    N3   C2   N1      0.00   0.0  0
 GCP  CONST_18  N7    C8   N9   C1'   180.00   0.0  0
 GCP  CONST_19  C5    C4   N9   C1'   180.00   0.0  0
 GCP  CONST_20  N3    C4   N9   C1'     0.00   0.0  0
 GCP  CONST_21  O6    C6   C5   N7      0.00   0.0  0
 GCP  CONST_22  N2    C2   N1   C6    180.00   0.0  0
 GCP  CONST_23  C4    C5   C6   O6    180.00   0.0  0
 GCP  CONST_24  C2    N1   C6   O6    180.00   0.0  0
 GCP  CONST_25  C4    N3   C2   N2    180.00   0.0  0
 GCP  CONST_26  H8    C8   N9   C1'     0.00   0.0  0
 GCP  CONST_27  HN1   N1   C6   C5    180.00   0.0  0
 GCP  CONST_28  HN21  N2   C2   N1    180.00   0.0  0
 GCP  Var_01    C4'   C5'  O5'  PA   -144.88  30.0  3
 GCP  Var_02    O1B   PB   C3B  PG     61.88  30.0  3
 GCP  Var_03    PB    C3B  PG   O1G   -46.45  30.0  3
 GCP  Var_04    O1A   PA   O3A  PB     42.84  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
 GCP  chir_03  C4'  C5'  O4'  C3'  negativ
 GCP  chir_04  C3'  O3'  C4'  C2'  positiv
 GCP  chir_05  C2'  O2'  C3'  C1'  positiv
 GCP  chir_06  C1'  O4'  N9   C2'  negativ
 GCP  chir_07  PB   O1B  O2B  O3A  both
 GCP  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
 GCP  plan-1  C1'   0.020
 GCP  plan-1  N9    0.020
 GCP  plan-1  C8    0.020
 GCP  plan-1  N7    0.020
 GCP  plan-1  C5    0.020
 GCP  plan-1  C6    0.020
 GCP  plan-1  O6    0.020
 GCP  plan-1  N1    0.020
 GCP  plan-1  C2    0.020
 GCP  plan-1  N2    0.020
 GCP  plan-1  N3    0.020
 GCP  plan-1  C4    0.020
 GCP  plan-1  H8    0.020
 GCP  plan-1  HN1   0.020
 GCP  plan-2  C2    0.020
 GCP  plan-2  N2    0.020
 GCP  plan-2  HN21  0.020
 GCP  plan-2  HN22  0.020

