# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 19:06:02 2021
#   Inital geometry file: a 125 line input string
#   Ligand name: 2'-deoxy-5'-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]guanosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2n(cnc2C(=O)N1)[C@H]3C[C@H](O)[C@@H](CO[P](O)(=O)C[P](O)(=O)O[P](O)(O)=O)O3
#
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
 1GC  1GC  2'-deoxy-5'-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]guanosine  ligand  49  31  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_1GC
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
 1GC  N1    N  NR16  0  -0.726  31.8298  24.1117  18.0400
 1GC  C2    C  CR6   0   0.687  31.9591  24.6740  16.8023
 1GC  N2    N  NH2   0  -0.831  32.2857  23.8527  15.7927
 1GC  N3    N  N     0  -0.515  31.7447  25.9449  16.5703
 1GC  C4    C  CR56  0   0.505  31.3940  26.6287  17.6693
 1GC  C5    C  CR56  0  -0.091  31.2359  26.1592  18.9603
 1GC  C6    C  CR6   0   0.502  31.4645  24.7769  19.2174
 1GC  O6    O  O     0  -0.474  31.3794  24.1698  20.2718
 1GC  N7    N  N     0  -0.444  30.8799  27.1777  19.8044
 1GC  C8    C  CR15  0   0.087  30.8216  28.2298  19.0456
 1GC  N9    N  NR5   0  -0.525  31.1255  27.9592  17.7344
 1GC  PA    P  P     0   1.426  29.5311  32.5112  20.2507
 1GC  PB    P  P     0   1.428  26.7445  32.6039  19.1602
 1GC  PG    P  P     0   1.478  24.4150  31.0689  20.2414
 1GC  C1'   C  CH1   0   0.182  31.1392  28.8766  16.6033
 1GC  O1A   O  OH1   0  -0.725  30.1541  31.8704  21.5712
 1GC  O1B   O  O     0  -0.679  27.2884  32.6994  17.7839
 1GC  O1G   O  OH1   0  -0.735  24.6983  31.9064  21.5637
 1GC  C2'   C  CH2   0  -0.534  29.7668  29.0677  15.9594
 1GC  O2A   O  O     0  -0.692  29.6163  33.9776  20.0762
 1GC  O2B   O  OH1   0  -0.717  26.3154  33.9634  19.8518
 1GC  O2G   O  OH1   0  -0.726  25.1748  29.7065  20.5210
 1GC  C3'   C  CH1   0   0.010  29.2528  30.3321  16.6286
 1GC  O3'   O  OH1   0  -0.689  28.2851  30.9818  15.8621
 1GC  C3A   C  CH2   0  -1.070  27.8403  31.8651  20.3788
 1GC  O3B   O  O2    0  -0.685  25.4152  31.6760  19.1229
 1GC  O3G   O  O     0  -0.669  23.0281  31.0262  19.7590
 1GC  C4'   C  CH1   0   0.006  30.5614  31.1180  16.7726
 1GC  O4'   O  O2    0  -0.496  31.5498  30.1363  17.0622
 1GC  C5'   C  CH2   0  -0.201  30.5886  32.2071  17.8135
 1GC  O5'   O  O2    0  -0.600  30.2173  31.6578  19.0809
 1GC  HN1   H  HNR6  0   0.425  32.0010  23.1188  18.1356
 1GC  HN2   H  HNH2  0   0.412  32.5358  24.2776  14.9157
 1GC  HN2A  H  HNH2  0   0.414  32.6846  22.9471  15.9746
 1GC  H8    H  HCR5  0   0.282  30.5881  29.2262  19.3839
 1GC  H1'   H  HCH1  0   0.271  31.8631  28.4679  15.8950
 1GC  HO1A  H  HOH1  0   0.503  31.0837  32.0906  21.7291
 1GC  HO1G  H  HOH1  0   0.509  24.1059  32.6574  21.7079
 1GC  H2'   H  HCH2  0   0.266  29.8927  29.2480  14.8890
 1GC  H2'A  H  HCH2  0   0.280  29.1194  28.2008  16.0841
 1GC  HO2B  H  HOH1  0   0.510  25.8546  34.5926  19.2773
 1GC  HO2G  H  HOH1  0   0.511  24.7031  29.0832  21.0916
 1GC  H3'   H  HCH1  0   0.214  28.8614  30.0805  17.6247
 1GC  HO3'  H  HOH1  0   0.460  27.8418  31.6257  16.4401
 1GC  H3A   H  HCH2  0   0.347  27.8448  30.7805  20.2481
 1GC  H3AA  H  HCH2  0   0.353  27.4624  32.0715  21.3828
 1GC  H4'   H  HCH1  0   0.245  30.7821  31.5995  15.8091
 1GC  H5'   H  HCH2  0   0.264  31.5884  32.6397  17.8883
 1GC  H5'A  H  HCH2  0   0.249  29.9050  32.9994  17.5046

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
 1GC  C2   N1    single    1.366  0.020  1.366
 1GC  N1   C6    single    1.401  0.020  1.401
 1GC  N1   HN1   single    0.860  0.020  1.020
 1GC  N2   C2    single    1.342  0.020  1.342
 1GC  N3   C2    double    1.310  0.020  1.310
 1GC  N2   HN2   single    0.890  0.020  1.040
 1GC  N2   HN2A  single    0.890  0.020  1.040
 1GC  N3   C4    single    1.341  0.020  1.341
 1GC  C4   N9    aromatic  1.359  0.020  1.359
 1GC  C4   C5    aromatic  1.383  0.020  1.383
 1GC  C5   C6    single    1.424  0.020  1.424
 1GC  C5   N7    aromatic  1.370  0.020  1.370
 1GC  C6   O6    double    1.220  0.020  1.220
 1GC  C8   N7    aromatic  1.298  0.020  1.298
 1GC  N9   C8    aromatic  1.373  0.020  1.373
 1GC  C8   H8    single    0.930  0.020  1.080
 1GC  C1'  N9    single    1.456  0.020  1.456
 1GC  O5'  PA    single    1.602  0.020  1.602
 1GC  C3A  PA    single    1.815  0.020  1.815
 1GC  PA   O2A   double    1.479  0.020  1.479
 1GC  PA   O1A   single    1.595  0.020  1.595
 1GC  O1B  PB    double    1.483  0.020  1.483
 1GC  O2B  PB    single    1.585  0.020  1.585
 1GC  PB   O3B   single    1.622  0.020  1.622
 1GC  PB   C3A   single    1.798  0.020  1.798
 1GC  O3B  PG    single    1.619  0.020  1.619
 1GC  O3G  PG    double    1.469  0.020  1.469
 1GC  PG   O1G   single    1.591  0.020  1.591
 1GC  PG   O2G   single    1.585  0.020  1.585
 1GC  C2'  C1'   single    1.528  0.020  1.528
 1GC  C1'  O4'   single    1.402  0.020  1.402
 1GC  C1'  H1'   single    0.970  0.020  1.090
 1GC  O1A  HO1A  single    0.850  0.020  0.980
 1GC  O1G  HO1G  single    0.850  0.020  0.980
 1GC  C2'  C3'   single    1.520  0.020  1.520
 1GC  C2'  H2'   single    0.970  0.020  1.090
 1GC  C2'  H2'A  single    0.970  0.020  1.090
 1GC  O2B  HO2B  single    0.850  0.020  0.980
 1GC  O2G  HO2G  single    0.850  0.020  0.980
 1GC  O3'  C3'   single    1.395  0.020  1.395
 1GC  C3'  C4'   single    1.533  0.020  1.533
 1GC  C3'  H3'   single    0.970  0.020  1.090
 1GC  O3'  HO3'  single    0.850  0.020  0.980
 1GC  C3A  H3A   single    0.970  0.020  1.090
 1GC  C3A  H3AA  single    0.970  0.020  1.090
 1GC  C4'  O4'   single    1.423  0.020  1.423
 1GC  C4'  C5'   single    1.507  0.020  1.507
 1GC  C4'  H4'   single    0.970  0.020  1.090
 1GC  C5'  O5'   single    1.430  0.020  1.430
 1GC  C5'  H5'   single    0.970  0.020  1.090
 1GC  C5'  H5'A  single    0.970  0.020  1.090

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
 1GC  HN1   N1   C6   115.50  3.000
 1GC  HN1   N1   C2   118.27  3.000
 1GC  C6    N1   C2   126.23  3.000
 1GC  N3    C2   N2   120.03  3.000
 1GC  N3    C2   N1   123.01  3.000
 1GC  N2    C2   N1   116.93  3.000
 1GC  HN2A  N2   HN2  116.06  3.000
 1GC  HN2A  N2   C2   120.76  3.000
 1GC  HN2   N2   C2   117.25  3.000
 1GC  C4    N3   C2   113.11  3.000
 1GC  N9    C4   C5   105.38  3.000
 1GC  C5    C4   N3   128.45  3.000
 1GC  N9    C4   N3   126.17  3.000
 1GC  N7    C5   C6   130.69  3.000
 1GC  N7    C5   C4   110.64  3.000
 1GC  C6    C5   C4   118.67  3.000
 1GC  O6    C6   C5   128.90  3.000
 1GC  O6    C6   N1   120.56  3.000
 1GC  C5    C6   N1   110.54  3.000
 1GC  C8    N7   C5   104.71  3.000
 1GC  H8    C8   N9   122.00  3.000
 1GC  H8    C8   N7   125.12  3.000
 1GC  N9    C8   N7   112.87  3.000
 1GC  C1'   N9   C8   128.29  3.000
 1GC  C1'   N9   C4   125.29  3.000
 1GC  C8    N9   C4   106.41  3.000
 1GC  O5'   PA   C3A  105.12  3.000
 1GC  C3A   PA   O2A  114.52  3.000
 1GC  O5'   PA   O2A  114.66  3.000
 1GC  O2A   PA   O1A  118.27  3.000
 1GC  C3A   PA   O1A   99.35  3.000
 1GC  O5'   PA   O1A  102.90  3.000
 1GC  O3B   PB   C3A  106.27  3.000
 1GC  C3A   PB   O2B  102.81  3.000
 1GC  O3B   PB   O2B  106.20  3.000
 1GC  C3A   PB   O1B  115.60  3.000
 1GC  O3B   PB   O1B  108.43  3.000
 1GC  O2B   PB   O1B  116.69  3.000
 1GC  O3G   PG   O3B  111.55  3.000
 1GC  O3G   PG   O2G  119.05  3.000
 1GC  O3B   PG   O2G   98.52  3.000
 1GC  O2G   PG   O1G  102.74  3.000
 1GC  O3G   PG   O1G  117.15  3.000
 1GC  O3B   PG   O1G  105.48  3.000
 1GC  H1'   C1'  O4'  110.75  3.000
 1GC  H1'   C1'  C2'  111.64  3.000
 1GC  O4'   C1'  C2'  106.78  3.000
 1GC  H1'   C1'  N9   105.92  3.000
 1GC  O4'   C1'  N9   108.33  3.000
 1GC  C2'   C1'  N9   113.43  3.000
 1GC  HO1A  O1A  PA   114.75  3.000
 1GC  HO1G  O1G  PG   115.06  3.000
 1GC  H2'A  C2'  H2'  108.18  3.000
 1GC  H2'A  C2'  C3'  114.25  3.000
 1GC  H2'   C2'  C3'  109.44  3.000
 1GC  H2'A  C2'  C1'  112.71  3.000
 1GC  H2'   C2'  C1'  109.27  3.000
 1GC  C3'   C2'  C1'  102.84  3.000
 1GC  HO2B  O2B  PB   115.29  3.000
 1GC  HO2G  O2G  PG   115.09  3.000
 1GC  H3'   C3'  C4'  109.64  3.000
 1GC  H3'   C3'  O3'  110.94  3.000
 1GC  C4'   C3'  O3'  113.89  3.000
 1GC  H3'   C3'  C2'  109.20  3.000
 1GC  C4'   C3'  C2'  100.32  3.000
 1GC  O3'   C3'  C2'  112.33  3.000
 1GC  HO3'  O3'  C3'  107.34  3.000
 1GC  H3AA  C3A  H3A  107.39  3.000
 1GC  H3AA  C3A  PB   109.54  3.000
 1GC  H3A   C3A  PB   109.23  3.000
 1GC  H3AA  C3A  PA   108.66  3.000
 1GC  H3A   C3A  PA   109.95  3.000
 1GC  PB    C3A  PA   111.95  3.000
 1GC  PG    O3B  PB   134.85  3.000
 1GC  H4'   C4'  C5'  106.57  3.000
 1GC  H4'   C4'  O4'  109.94  3.000
 1GC  C5'   C4'  O4'  110.22  3.000
 1GC  H4'   C4'  C3'  108.27  3.000
 1GC  C5'   C4'  C3'  116.79  3.000
 1GC  O4'   C4'  C3'  104.97  3.000
 1GC  C4'   O4'  C1'  110.47  3.000
 1GC  H5'A  C5'  H5'  107.78  3.000
 1GC  H5'A  C5'  O5'  111.53  3.000
 1GC  H5'   C5'  O5'  109.22  3.000
 1GC  H5'A  C5'  C4'  108.54  3.000
 1GC  H5'   C5'  C4'  110.50  3.000
 1GC  O5'   C5'  C4'  109.26  3.000
 1GC  C5'   O5'  PA   123.61  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
 1GC  CONST_01  N7   C8   N9   C4     0.00   0.0  0
 1GC  CONST_02  C8   N7   C5   C4     0.00   0.0  0
 1GC  CONST_03  C8   N9   C4   C5     0.00   0.0  0
 1GC  CONST_04  N9   C8   N7   C5     0.00   0.0  0
 1GC  CONST_05  N9   C4   C5   N7     0.00   0.0  0
 1GC  CONST_06  C1'  N9   C4   N3     0.00   0.0  0
 1GC  CONST_07  C1'  N9   C4   C5   180.00   0.0  0
 1GC  CONST_08  C1'  N9   C8   N7   180.00   0.0  0
 1GC  CONST_09  C4   N3   C2   N1     0.00   0.0  0
 1GC  CONST_10  C5   C6   N1   C2     0.00   0.0  0
 1GC  CONST_11  C6   N1   C2   N3     0.00   0.0  0
 1GC  CONST_12  O6   C6   N1   C2   180.00   0.0  0
 1GC  CONST_13  C6   N1   C2   N2   180.00   0.0  0
 1GC  CONST_14  C4   N3   C2   N2   180.00   0.0  0
 1GC  CONST_15  H8   C8   N9   C4   180.00   0.0  0
 1GC  CONST_16  HN1  N1   C2   N3   180.00   0.0  0
 1GC  CONST_17  HN2  N2   C2   N1   180.00   0.0  0
 1GC  Var_01    C4'  C5'  O5'  PA  -152.75  30.0  2
 1GC  Var_02    O1B  PB   C3A  PA    44.98  30.0  1
 1GC  Var_03    O3G  PG   O3B  PB   144.84  30.0  3
 1GC  Var_04    O5'  PA   C3A  PB   -82.78  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
 1GC  chir_03  C1'  N9   C2'  O4'  negativ
 1GC  chir_04  C3'  O3'  C4'  C2'  positiv
 1GC  chir_05  C4'  O4'  C3'  C5'  negativ
 1GC  chir_06  PA   C3A  O2A  O1A  both
 1GC  chir_07  PB   O2B  O1B  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
 1GC  plan-1  N1    0.020
 1GC  plan-1  C2    0.020
 1GC  plan-1  N2    0.020
 1GC  plan-1  N3    0.020
 1GC  plan-1  C4    0.020
 1GC  plan-1  C5    0.020
 1GC  plan-1  C6    0.020
 1GC  plan-1  O6    0.020
 1GC  plan-1  N7    0.020
 1GC  plan-1  C8    0.020
 1GC  plan-1  N9    0.020
 1GC  plan-1  C1'   0.020
 1GC  plan-1  HN1   0.020
 1GC  plan-1  HN2   0.020
 1GC  plan-1  HN2A  0.020
 1GC  plan-1  H8    0.020

