# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 15:10:39 2021
#   Inital geometry file: a 125 line input string
#   Ligand name: 2'-deoxy-5'-O-[(R)-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]3C[C@H](O)[C@@H](CO[P@](O)(=O)O[P@@](O)(=O)C[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
 GGH  GGH  2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonomethyl)phosphoryl]oxy}phosphoryl]guanosine  ligand  49  31  .  2021-08-10  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GGH
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
 GGH  C2    C  CR6   0   0.691   8.3276   9.0395   7.5642
 GGH  C4    C  CR56  0   0.504   7.5105   8.1233   9.4038
 GGH  C5    C  CR56  0  -0.091   8.7393   7.8991   9.9970
 GGH  C6    C  CR6   0   0.502   9.9168   8.2869   9.2955
 GGH  P1    P  P     0   1.508   5.1598   5.0623  14.6979
 GGH  P2    P  P     0   1.387   4.3006   2.4101  13.4236
 GGH  O6    O  O     0  -0.474  11.0826   8.1761   9.6361
 GGH  O1A   O  OH1   0  -0.737   3.8487   4.9193  15.5803
 GGH  O2A   O  O     0  -0.669   6.4271   5.4002  15.3586
 GGH  O3A   O  O2    0  -0.707   5.2296   3.6229  13.9912
 GGH  O5'   O  O2    0  -0.585   4.8296   6.0840  13.5263
 GGH  O1B   O  O     0  -0.658   4.6549   2.0958  12.0296
 GGH  O2B   O  OH1   0  -0.759   2.7956   2.8510  13.6475
 GGH  C3B   C  CH2   0  -1.031   4.6257   1.0830  14.6098
 GGH  P3    P  P     0   1.396   3.9549   1.3934  16.2554
 GGH  O1G   O  OH1   0  -0.724   5.1048   2.2753  16.9200
 GGH  O2G   O  OH1   0  -0.718   3.8776   0.0089  17.0387
 GGH  O3G   O  O     0  -0.714   2.5943   2.0014  16.1736
 GGH  C5'   C  CH2   0  -0.218   3.5279   6.3496  12.9928
 GGH  C4'   C  CH1   0   0.008   3.6349   6.6493  11.5204
 GGH  O4'   O  O2    0  -0.495   4.5020   7.7486  11.2935
 GGH  C1'   C  CH1   0   0.189   5.1561   7.6180  10.0591
 GGH  N9    N  NR5   0  -0.527   6.5922   7.6559  10.2899
 GGH  N3    N  N     0  -0.516   7.2477   8.6739   8.2101
 GGH  N2    N  NH2   0  -0.833   8.2234   9.6453   6.3747
 GGH  N1    N  NR16  0  -0.728   9.5876   8.8597   8.0600
 GGH  N7    N  N     0  -0.444   8.5827   7.3054  11.2220
 GGH  C8    C  CR15  0   0.086   7.2990   7.1709  11.3623
 GGH  C2'   C  CH2   0  -0.546   4.6837   6.3048   9.4386
 GGH  C3'   C  CH1   0   0.002   4.1732   5.5169  10.6415
 GGH  O3'   O  OH1   0  -0.647   3.2328   4.5220  10.3695
 GGH  HO1A  H  HOH1  0   0.511   3.7608   5.5654  16.2953
 GGH  HO2B  H  HOH1  0   0.497   2.4713   2.6669  14.5685
 GGH  H3B1  H  HCH2  0   0.348   4.1309   0.1902  14.2169
 GGH  H3B2  H  HCH2  0   0.352   5.6968   0.8740  14.6381
 GGH  HO1G  H  HOH1  0   0.505   4.8795   2.6695  17.7753
 GGH  HO2G  H  HOH1  0   0.503   4.7229  -0.4062  17.2588
 GGH  H5'1  H  HCH2  0   0.274   3.1009   7.1957  13.5334
 GGH  H5'2  H  HCH2  0   0.253   2.8522   5.5003  13.1117
 GGH  H4'   H  HCH1  0   0.249   2.6159   6.8991  11.1873
 GGH  H1'   H  HCH1  0   0.271   4.9336   8.4705   9.4136
 GGH  HN21  H  HNH2  0   0.416   9.0235   9.7786   5.7808
 GGH  HN22  H  HNH2  0   0.413   7.3192   9.6758   5.9361
 GGH  HN1   H  HNR6  0   0.425  10.3720   9.1622   7.4958
 GGH  H8    H  HCR5  0   0.285   6.8087   6.7483  12.2235
 GGH  H2'1  H  HCH2  0   0.267   3.8588   6.5074   8.7499
 GGH  H2'2  H  HCH2  0   0.284   5.4682   5.7992   8.8773
 GGH  H3'   H  HCH1  0   0.249   5.0046   5.0105  11.1403
 GGH  HO3'  H  HOH1  0   0.445   2.5026   4.9129   9.8763

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
 GGH  C2   N2    single    1.339  0.020  1.339
 GGH  C2   N1    single    1.366  0.020  1.366
 GGH  C2   N3    double    1.310  0.020  1.310
 GGH  C4   N3    single    1.341  0.020  1.341
 GGH  C4   C5    aromatic  1.383  0.020  1.383
 GGH  C4   N9    aromatic  1.359  0.020  1.359
 GGH  C5   C6    single    1.424  0.020  1.424
 GGH  C5   N7    aromatic  1.370  0.020  1.370
 GGH  C6   N1    single    1.401  0.020  1.401
 GGH  C6   O6    double    1.220  0.020  1.220
 GGH  P1   O5'   single    1.589  0.020  1.589
 GGH  P1   O3A   single    1.605  0.020  1.605
 GGH  P1   O2A   double    1.469  0.020  1.469
 GGH  P1   O1A   single    1.587  0.020  1.587
 GGH  P2   O1B   double    1.472  0.020  1.472
 GGH  P2   O3A   single    1.630  0.020  1.630
 GGH  P2   O2B   single    1.584  0.020  1.584
 GGH  P2   C3B   single    1.809  0.020  1.809
 GGH  O1A  HO1A  single    0.850  0.020  0.980
 GGH  O5'  C5'   single    1.432  0.020  1.432
 GGH  O2B  HO2B  single    0.850  0.020  0.980
 GGH  C3B  P3    single    1.804  0.020  1.804
 GGH  C3B  H3B1  single    0.970  0.020  1.090
 GGH  C3B  H3B2  single    0.970  0.020  1.090
 GGH  P3   O3G   double    1.492  0.020  1.492
 GGH  P3   O1G   single    1.594  0.020  1.594
 GGH  P3   O2G   single    1.593  0.020  1.593
 GGH  O1G  HO1G  single    0.850  0.020  0.980
 GGH  O2G  HO2G  single    0.850  0.020  0.980
 GGH  C5'  C4'   single    1.506  0.020  1.506
 GGH  C5'  H5'1  single    0.970  0.020  1.090
 GGH  C5'  H5'2  single    0.970  0.020  1.090
 GGH  C4'  C3'   single    1.531  0.020  1.531
 GGH  C4'  O4'   single    1.418  0.020  1.418
 GGH  C4'  H4'   single    0.970  0.020  1.090
 GGH  O4'  C1'   single    1.403  0.020  1.403
 GGH  C1'  C2'   single    1.527  0.020  1.527
 GGH  C1'  N9    single    1.455  0.020  1.455
 GGH  C1'  H1'   single    0.970  0.020  1.090
 GGH  N9   C8    aromatic  1.373  0.020  1.373
 GGH  N2   HN21  single    0.890  0.020  1.040
 GGH  N2   HN22  single    0.890  0.020  1.040
 GGH  N1   HN1   single    0.860  0.020  1.020
 GGH  N7   C8    aromatic  1.298  0.020  1.298
 GGH  C8   H8    single    0.930  0.020  1.080
 GGH  C2'  C3'   single    1.526  0.020  1.526
 GGH  C2'  H2'1  single    0.970  0.020  1.090
 GGH  C2'  H2'2  single    0.970  0.020  1.090
 GGH  C3'  O3'   single    1.396  0.020  1.396
 GGH  C3'  H3'   single    0.970  0.020  1.090
 GGH  O3'  HO3'  single    0.850  0.020  0.980

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
 GGH  N1    C2   N2    116.99  3.000
 GGH  N1    C2   N3    123.00  3.000
 GGH  N2    C2   N3    120.00  3.000
 GGH  N3    C4   N9    126.11  3.000
 GGH  N9    C4   C5    105.36  3.000
 GGH  N3    C4   C5    128.52  3.000
 GGH  N7    C5   C6    130.75  3.000
 GGH  N7    C5   C4    110.63  3.000
 GGH  C6    C5   C4    118.63  3.000
 GGH  N1    C6   O6    120.53  3.000
 GGH  O6    C6   C5    128.89  3.000
 GGH  N1    C6   C5    110.58  3.000
 GGH  O5'   P1   O3A   105.13  3.000
 GGH  O3A   P1   O2A   111.53  3.000
 GGH  O5'   P1   O2A   111.29  3.000
 GGH  O2A   P1   O1A   118.91  3.000
 GGH  O3A   P1   O1A   101.53  3.000
 GGH  O5'   P1   O1A   107.23  3.000
 GGH  C3B   P2   O2B   106.39  3.000
 GGH  C3B   P2   O1B   114.89  3.000
 GGH  O2B   P2   O1B   114.95  3.000
 GGH  C3B   P2   O3A   102.42  3.000
 GGH  O2B   P2   O3A   106.57  3.000
 GGH  O1B   P2   O3A   110.58  3.000
 GGH  HO1A  O1A  P1    115.20  3.000
 GGH  P2    O3A  P1    142.74  3.000
 GGH  C5'   O5'  P1    125.66  3.000
 GGH  HO2B  O2B  P2    112.92  3.000
 GGH  H3B2  C3B  H3B1  107.28  3.000
 GGH  H3B2  C3B  P3    111.97  3.000
 GGH  H3B1  C3B  P3    107.45  3.000
 GGH  H3B2  C3B  P2    109.49  3.000
 GGH  H3B1  C3B  P2    106.38  3.000
 GGH  P3    C3B  P2    113.89  3.000
 GGH  O3G   P3   O2G   109.68  3.000
 GGH  O2G   P3   O1G   108.11  3.000
 GGH  O3G   P3   O1G   117.07  3.000
 GGH  O2G   P3   C3B   108.48  3.000
 GGH  O1G   P3   C3B   101.96  3.000
 GGH  O3G   P3   C3B   111.04  3.000
 GGH  HO1G  O1G  P3    115.19  3.000
 GGH  HO2G  O2G  P3    116.27  3.000
 GGH  H5'2  C5'  H5'1  107.88  3.000
 GGH  H5'2  C5'  C4'   107.77  3.000
 GGH  H5'1  C5'  C4'   110.96  3.000
 GGH  H5'2  C5'  O5'   112.20  3.000
 GGH  H5'1  C5'  O5'   108.36  3.000
 GGH  C4'   C5'  O5'   109.67  3.000
 GGH  H4'   C4'  C3'   108.64  3.000
 GGH  H4'   C4'  O4'   109.98  3.000
 GGH  C3'   C4'  O4'   105.45  3.000
 GGH  H4'   C4'  C5'   105.97  3.000
 GGH  O4'   C4'  C5'   110.73  3.000
 GGH  C3'   C4'  C5'   116.03  3.000
 GGH  C1'   O4'  C4'   110.71  3.000
 GGH  H1'   C1'  C2'   111.59  3.000
 GGH  H1'   C1'  N9    105.93  3.000
 GGH  C2'   C1'  N9    113.09  3.000
 GGH  H1'   C1'  O4'   110.63  3.000
 GGH  N9    C1'  O4'   108.55  3.000
 GGH  C2'   C1'  O4'   107.06  3.000
 GGH  C8    N9   C1'   128.52  3.000
 GGH  C8    N9   C4    106.44  3.000
 GGH  C1'   N9   C4    124.92  3.000
 GGH  C4    N3   C2    113.08  3.000
 GGH  HN22  N2   HN21  117.00  3.000
 GGH  HN22  N2   C2    118.12  3.000
 GGH  HN21  N2   C2    121.53  3.000
 GGH  HN1   N1   C6    115.57  3.000
 GGH  HN1   N1   C2    118.23  3.000
 GGH  C6    N1   C2    126.20  3.000
 GGH  C8    N7   C5    104.74  3.000
 GGH  H8    C8   N7    125.24  3.000
 GGH  H8    C8   N9    121.92  3.000
 GGH  N7    C8   N9    112.83  3.000
 GGH  H2'2  C2'  H2'1  107.75  3.000
 GGH  H2'2  C2'  C3'   114.05  3.000
 GGH  H2'1  C2'  C3'   109.86  3.000
 GGH  H2'2  C2'  C1'   112.69  3.000
 GGH  H2'1  C2'  C1'   109.27  3.000
 GGH  C3'   C2'  C1'   103.13  3.000
 GGH  H3'   C3'  O3'   105.72  3.000
 GGH  H3'   C3'  C2'   110.14  3.000
 GGH  O3'   C3'  C2'   116.09  3.000
 GGH  H3'   C3'  C4'   110.36  3.000
 GGH  O3'   C3'  C4'   113.71  3.000
 GGH  C2'   C3'  C4'   100.85  3.000
 GGH  HO3'  O3'  C3'   108.72  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
 GGH  CONST_01  C8    N7   C5   C4      0.00   0.0  0
 GGH  CONST_02  N7    C8   N9   C4      0.00   0.0  0
 GGH  CONST_03  C8    N9   C4   C5      0.00   0.0  0
 GGH  CONST_04  N9    C8   N7   C5      0.00   0.0  0
 GGH  CONST_05  N7    C5   C4   N9      0.00   0.0  0
 GGH  CONST_06  C1'   N9   C4   C5    180.00   0.0  0
 GGH  CONST_07  N3    C4   N9   C1'     0.00   0.0  0
 GGH  CONST_08  N7    C8   N9   C1'   180.00   0.0  0
 GGH  CONST_09  C5    C6   N1   C2      0.00   0.0  0
 GGH  CONST_10  N1    C2   N3   C4      0.00   0.0  0
 GGH  CONST_11  N3    C2   N1   C6      0.00   0.0  0
 GGH  CONST_12  O6    C6   N1   C2    180.00   0.0  0
 GGH  CONST_13  N2    C2   N3   C4    180.00   0.0  0
 GGH  CONST_14  N2    C2   N1   C6    180.00   0.0  0
 GGH  CONST_15  H8    C8   N9   C4    180.00   0.0  0
 GGH  CONST_16  HN1   N1   C6   C5    180.00   0.0  0
 GGH  CONST_17  HN21  N2   C2   N3    180.00   0.0  0
 GGH  CONST_18  HN22  N2   C2   N3      0.00   0.0  0
 GGH  Var_01    C4'   C5'  O5'  P1   -146.43  30.0  3
 GGH  Var_02    O1B   P2   O3A  P1    126.74  30.0  1
 GGH  Var_03    O5'   P1   O3A  P2    -79.70  30.0  2
 GGH  Var_04    O3G   P3   C3B  P2     41.01  30.0  3
 GGH  Var_05    P3    C3B  P2   O3A    68.94  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
 GGH  chir_03  C4'  C5'  C3'  O4'  positiv
 GGH  chir_04  C1'  O4'  N9   C2'  negativ
 GGH  chir_05  C3'  O3'  C4'  C2'  positiv
 GGH  chir_06  P1   O3A  O2A  O1A  both
 GGH  chir_07  P2   O3A  O2B  C3B  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
 GGH  plan-1  C2    0.020
 GGH  plan-1  C4    0.020
 GGH  plan-1  C5    0.020
 GGH  plan-1  C6    0.020
 GGH  plan-1  O6    0.020
 GGH  plan-1  C1'   0.020
 GGH  plan-1  N9    0.020
 GGH  plan-1  N3    0.020
 GGH  plan-1  N2    0.020
 GGH  plan-1  N1    0.020
 GGH  plan-1  N7    0.020
 GGH  plan-1  C8    0.020
 GGH  plan-1  HN21  0.020
 GGH  plan-1  HN22  0.020
 GGH  plan-1  HN1   0.020
 GGH  plan-1  H8    0.020

