# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 03:53:19 2021
#   Inital geometry file: a 131 line input string
#   Ligand name: 2'-deoxy-5'-O-[(R)-hydroxy({(S)-hydroxy[(1R)-1-phosphonoethyl]phosphoryl}oxy)phosphoryl]guanosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]([P](O)(O)=O)[P](O)(=O)O[P](O)(=O)OC[C@H]1O[C@H](C[C@@H]1O)n2cnc3C(=O)NC(=Nc23)N
#
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
 G1M  G1M  2'-deoxy-5'-O-[(R)-hydroxy({(S)-hydroxy[(1R)-1-phosphonoethyl]phosphoryl}oxy)phosphoryl]guanosine  ligand  52  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 PERFECT
;

data_comp_G1M
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
 G1M  N1    N  NR16  0  -0.726   9.7259   9.3722   8.4191
 G1M  C2    C  CR6   0   0.688   8.5458   9.3043   7.7355
 G1M  N2    N  NH2   0  -0.831   8.5053   9.8939   6.5309
 G1M  N3    N  N     0  -0.515   7.4734   8.7287   8.2190
 G1M  C4    C  CR56  0   0.506   7.6551   8.2240   9.4476
 G1M  C5    C  CR56  0  -0.091   8.8028   8.2300  10.2182
 G1M  C6    C  CR6   0   0.503   9.9722   8.8555   9.6977
 G1M  O6    O  O     0  -0.474  11.0706   8.9748  10.2141
 G1M  N7    N  N     0  -0.444   8.5825   7.6043  11.4171
 G1M  C8    C  CR15  0   0.090   7.3407   7.2293  11.3713
 G1M  N9    N  NR5   0  -0.527   6.7207   7.5813  10.1975
 G1M  PA    P  P     0   1.503   4.9070   5.0771  14.5894
 G1M  PB    P  P     0   1.434   3.4822   2.5300  14.1504
 G1M  PG    P  P     0   1.398   4.3379   1.2389  16.7054
 G1M  C1'   C  CH1   0   0.181   5.3514   7.3173   9.7863
 G1M  O1A   O  OH1   0  -0.759   3.6672   5.3264  15.5350
 G1M  O1B   O  OH1   0  -0.724   3.2333   2.1966  12.6098
 G1M  O1G   O  OH1   0  -0.743   5.0008   2.6957  16.7887
 G1M  C2'   C  CH2   0  -0.537   5.1302   5.9048   9.2470
 G1M  O2A   O  O     0  -0.659   6.2341   5.2801  15.1766
 G1M  O2B   O  O     0  -0.695   2.3299   3.1263  14.8830
 G1M  O2G   O  OH1   0  -0.736   5.5091   0.1943  17.0288
 G1M  C3'   C  CH1   0   0.003   4.5662   5.1575  10.4454
 G1M  O3'   O  OH1   0  -0.663   3.7827   4.0688  10.0450
 G1M  O3A   O  O2    0  -0.701   4.7107   3.5654  13.9879
 G1M  C3B   C  CH1   0  -0.822   4.1908   1.0496  14.8997
 G1M  C3B2  C  CH3   0  -0.697   3.3474  -0.1922  14.5749
 G1M  O3G   O  O     0  -0.693   3.0958   1.0434  17.4848
 G1M  C4'   C  CH1   0   0.012   3.7634   6.2767  11.1200
 G1M  O4'   O  O2    0  -0.493   4.5189   7.4585  10.9073
 G1M  C5'   C  CH2   0  -0.232   3.4769   6.1127  12.5902
 G1M  O5'   O  O2    0  -0.572   4.7097   5.9874  13.3031
 G1M  HN1   H  HNR6  0   0.425  10.5056   9.8477   7.9827
 G1M  HN2   H  HNH2  0   0.412   7.6996   9.7126   5.9563
 G1M  HN2A  H  HNH2  0   0.414   9.3546  10.1200   6.0413
 G1M  H8    H  HCR5  0   0.284   6.8208   6.7151  12.1632
 G1M  H1'   H  HCH1  0   0.273   5.1165   8.0723   9.0330
 G1M  H2'   H  HCH2  0   0.270   4.3784   5.9375   8.4549
 G1M  H2'A  H  HCH2  0   0.285   6.0386   5.4668   8.8362
 G1M  H3'   H  HCH1  0   0.234   5.3880   4.8321  11.0959
 G1M  HO3'  H  HOH1  0   0.449   3.6750   3.4665  10.7879
 G1M  H3B   H  HCH1  0   0.360   5.1957   0.9238  14.4834
 G1M  HC3B  H  HCH3  0   0.278   3.7596  -1.0656  15.0771
 G1M  HC3A  H  HCH3  0   0.262   2.3129  -0.0790  14.8936
 G1M  HC3C  H  HCH3  0   0.274   3.3636  -0.3979  13.5069
 G1M  H4'   H  HCH1  0   0.252   2.7889   6.3521  10.6175
 G1M  H5'   H  HCH2  0   0.284   2.9318   6.9741  12.9795
 G1M  H5'A  H  HCH2  0   0.238   2.8307   5.2380  12.7124
 G1M  H17   H  HOH1  0   0.500   2.9441   4.6555  15.4821
 G1M  H18   H  HOH1  0   0.518   2.3532   1.8515  12.3971
 G1M  H19   H  HOH1  0   0.503   4.9774   3.1088  17.6637
 G1M  H20   H  HOH1  0   0.500   5.4164  -0.2452  17.8853

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
 G1M  N1    C2    single    1.366  0.020  1.366
 G1M  N1    C6    single    1.401  0.020  1.401
 G1M  N1    HN1   single    0.860  0.020  1.020
 G1M  C2    N2    single    1.342  0.020  1.342
 G1M  C2    N3    double    1.310  0.020  1.310
 G1M  N2    HN2   single    0.890  0.020  1.040
 G1M  N2    HN2A  single    0.890  0.020  1.040
 G1M  N3    C4    single    1.341  0.020  1.341
 G1M  C4    C5    aromatic  1.382  0.020  1.382
 G1M  C4    N9    aromatic  1.360  0.020  1.360
 G1M  C5    C6    single    1.425  0.020  1.425
 G1M  C5    N7    aromatic  1.370  0.020  1.370
 G1M  C6    O6    double    1.220  0.020  1.220
 G1M  N7    C8    aromatic  1.298  0.020  1.298
 G1M  C8    N9    aromatic  1.373  0.020  1.373
 G1M  C8    H8    single    0.930  0.020  1.080
 G1M  N9    C1'   single    1.454  0.020  1.454
 G1M  PA    O1A   single    1.579  0.020  1.579
 G1M  PA    O2A   double    1.465  0.020  1.465
 G1M  PA    O3A   single    1.639  0.020  1.639
 G1M  PA    O5'   single    1.588  0.020  1.588
 G1M  PB    O1B   single    1.596  0.020  1.596
 G1M  PB    O2B   double    1.490  0.020  1.490
 G1M  PB    O3A   single    1.615  0.020  1.615
 G1M  PB    C3B   single    1.804  0.020  1.804
 G1M  PG    O1G   single    1.603  0.020  1.603
 G1M  PG    O2G   single    1.602  0.020  1.602
 G1M  PG    C3B   single    1.822  0.020  1.822
 G1M  PG    O3G   double    1.479  0.020  1.479
 G1M  C1'   C2'   single    1.528  0.020  1.528
 G1M  C1'   O4'   single    1.403  0.020  1.403
 G1M  C1'   H1'   single    0.970  0.020  1.090
 G1M  C2'   C3'   single    1.521  0.020  1.521
 G1M  C2'   H2'   single    0.970  0.020  1.090
 G1M  C2'   H2'A  single    0.970  0.020  1.090
 G1M  C3'   O3'   single    1.400  0.020  1.400
 G1M  C3'   C4'   single    1.534  0.020  1.534
 G1M  C3'   H3'   single    0.970  0.020  1.090
 G1M  O3'   HO3'  single    0.850  0.020  0.980
 G1M  C3B   C3B2  single    1.536  0.020  1.536
 G1M  C3B   H3B   single    0.970  0.020  1.090
 G1M  C3B2  HC3B  single    0.970  0.020  1.090
 G1M  C3B2  HC3A  single    0.970  0.020  1.090
 G1M  C3B2  HC3C  single    0.970  0.020  1.090
 G1M  C4'   O4'   single    1.419  0.020  1.419
 G1M  C4'   C5'   single    1.507  0.020  1.507
 G1M  C4'   H4'   single    0.970  0.020  1.090
 G1M  C5'   O5'   single    1.430  0.020  1.430
 G1M  C5'   H5'   single    0.970  0.020  1.090
 G1M  C5'   H5'A  single    0.970  0.020  1.090
 G1M  O1A   H17   single    0.850  0.020  0.980
 G1M  O1B   H18   single    0.850  0.020  0.980
 G1M  O1G   H19   single    0.850  0.020  0.980
 G1M  O2G   H20   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
 G1M  HN1   N1    C6    115.55  3.000
 G1M  HN1   N1    C2    118.25  3.000
 G1M  C6    N1    C2    126.19  3.000
 G1M  N3    C2    N2    119.99  3.000
 G1M  N3    C2    N1    123.01  3.000
 G1M  N2    C2    N1    116.97  3.000
 G1M  HN2A  N2    HN2   116.01  3.000
 G1M  HN2A  N2    C2    120.68  3.000
 G1M  HN2   N2    C2    117.24  3.000
 G1M  C4    N3    C2    113.13  3.000
 G1M  N9    C4    C5    105.38  3.000
 G1M  N9    C4    N3    126.18  3.000
 G1M  C5    C4    N3    128.44  3.000
 G1M  N7    C5    C6    130.70  3.000
 G1M  N7    C5    C4    110.62  3.000
 G1M  C6    C5    C4    118.67  3.000
 G1M  O6    C6    C5    128.87  3.000
 G1M  O6    C6    N1    120.58  3.000
 G1M  C5    C6    N1    110.56  3.000
 G1M  C8    N7    C5    104.76  3.000
 G1M  H8    C8    N9    122.17  3.000
 G1M  H8    C8    N7    124.98  3.000
 G1M  N9    C8    N7    112.83  3.000
 G1M  C1'   N9    C8    128.34  3.000
 G1M  C1'   N9    C4    125.25  3.000
 G1M  C8    N9    C4    106.39  3.000
 G1M  O5'   PA    O3A   102.51  3.000
 G1M  O5'   PA    O2A   110.96  3.000
 G1M  O3A   PA    O2A   112.54  3.000
 G1M  O5'   PA    O1A   107.28  3.000
 G1M  O3A   PA    O1A   105.75  3.000
 G1M  O2A   PA    O1A   116.70  3.000
 G1M  C3B   PB    O3A   105.61  3.000
 G1M  C3B   PB    O2B   115.33  3.000
 G1M  O3A   PB    O2B   112.41  3.000
 G1M  C3B   PB    O1B   106.90  3.000
 G1M  O3A   PB    O1B    98.94  3.000
 G1M  O2B   PB    O1B   115.96  3.000
 G1M  O3G   PG    C3B   116.15  3.000
 G1M  O3G   PG    O2G   114.91  3.000
 G1M  C3B   PG    O2G   101.03  3.000
 G1M  O3G   PG    O1G   116.11  3.000
 G1M  C3B   PG    O1G   100.34  3.000
 G1M  O2G   PG    O1G   106.25  3.000
 G1M  H1'   C1'   O4'   110.72  3.000
 G1M  H1'   C1'   C2'   111.37  3.000
 G1M  O4'   C1'   C2'   106.80  3.000
 G1M  H1'   C1'   N9    105.79  3.000
 G1M  O4'   C1'   N9    108.33  3.000
 G1M  C2'   C1'   N9    113.83  3.000
 G1M  H17   O1A   PA    115.82  3.000
 G1M  H18   O1B   PB    115.34  3.000
 G1M  H19   O1G   PG    115.15  3.000
 G1M  H2'A  C2'   H2'   108.21  3.000
 G1M  H2'A  C2'   C3'   114.14  3.000
 G1M  H2'   C2'   C3'   109.32  3.000
 G1M  H2'A  C2'   C1'   112.59  3.000
 G1M  H2'   C2'   C1'   109.14  3.000
 G1M  C3'   C2'   C1'   103.29  3.000
 G1M  H20   O2G   PG    113.89  3.000
 G1M  H3'   C3'   C4'   110.34  3.000
 G1M  H3'   C3'   O3'   110.98  3.000
 G1M  C4'   C3'   O3'   113.60  3.000
 G1M  H3'   C3'   C2'   109.58  3.000
 G1M  C4'   C3'   C2'   100.49  3.000
 G1M  O3'   C3'   C2'   111.37  3.000
 G1M  HO3'  O3'   C3'   109.18  3.000
 G1M  PB    O3A   PA    130.21  3.000
 G1M  H3B   C3B   C3B2  109.31  3.000
 G1M  H3B   C3B   PG    108.34  3.000
 G1M  C3B2  C3B   PG    109.76  3.000
 G1M  H3B   C3B   PB    107.27  3.000
 G1M  C3B2  C3B   PB    111.10  3.000
 G1M  PG    C3B   PB    110.99  3.000
 G1M  HC3C  C3B2  HC3A  108.74  3.000
 G1M  HC3C  C3B2  HC3B  107.19  3.000
 G1M  HC3A  C3B2  HC3B  107.96  3.000
 G1M  HC3C  C3B2  C3B   110.63  3.000
 G1M  HC3A  C3B2  C3B   112.08  3.000
 G1M  HC3B  C3B2  C3B   110.07  3.000
 G1M  H4'   C4'   C5'   106.56  3.000
 G1M  H4'   C4'   O4'   110.27  3.000
 G1M  C5'   C4'   O4'   109.77  3.000
 G1M  H4'   C4'   C3'   108.24  3.000
 G1M  C5'   C4'   C3'   116.70  3.000
 G1M  O4'   C4'   C3'   105.26  3.000
 G1M  C4'   O4'   C1'   110.60  3.000
 G1M  H5'A  C5'   H5'   107.22  3.000
 G1M  H5'A  C5'   O5'   112.54  3.000
 G1M  H5'   C5'   O5'   108.79  3.000
 G1M  H5'A  C5'   C4'   107.95  3.000
 G1M  H5'   C5'   C4'   110.93  3.000
 G1M  O5'   C5'   C4'   109.40  3.000
 G1M  C5'   O5'   PA    124.15  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
 G1M  CONST_01  C8   N7   C5   C4     0.00   0.0  0
 G1M  CONST_02  N7   C8   N9   C4     0.00   0.0  0
 G1M  CONST_03  C8   N9   C4   C5     0.00   0.0  0
 G1M  CONST_04  N9   C8   N7   C5     0.00   0.0  0
 G1M  CONST_05  N9   C4   C5   N7     0.00   0.0  0
 G1M  CONST_06  C1'  N9   C4   N3     0.00   0.0  0
 G1M  CONST_07  C1'  N9   C4   C5   180.00   0.0  0
 G1M  CONST_08  C1'  N9   C8   N7   180.00   0.0  0
 G1M  CONST_09  C4   N3   C2   N1     0.00   0.0  0
 G1M  CONST_10  C5   C6   N1   C2     0.00   0.0  0
 G1M  CONST_11  C6   N1   C2   N3     0.00   0.0  0
 G1M  CONST_12  O6   C6   N1   C2   180.00   0.0  0
 G1M  CONST_13  C6   N1   C2   N2   180.00   0.0  0
 G1M  CONST_14  C4   N3   C2   N2   180.00   0.0  0
 G1M  CONST_15  H8   C8   N9   C4   180.00   0.0  0
 G1M  CONST_16  HN1  N1   C2   N3   180.00   0.0  0
 G1M  CONST_17  HN2  N2   C2   N1   180.00   0.0  0
 G1M  Var_01    C4'  C5'  O5'  PA  -145.41  30.0  2
 G1M  Var_02    O1B  PB   O3A  PA   128.09  30.0  1
 G1M  Var_03    O1A  PA   O3A  PB     5.51  30.0  2

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
 G1M  chir_03  C1'  N9   C2'  O4'   negativ
 G1M  chir_04  C3'  O3'  C4'  C2'   positiv
 G1M  chir_05  C3B  PB   PG   C3B2  negativ
 G1M  chir_06  C4'  O4'  C5'  C3'   positiv
 G1M  chir_07  PA   O2A  O3A  O5'   both
 G1M  chir_08  PB   O2B  O3A  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
 G1M  plan-1  N1    0.020
 G1M  plan-1  C2    0.020
 G1M  plan-1  N2    0.020
 G1M  plan-1  N3    0.020
 G1M  plan-1  C4    0.020
 G1M  plan-1  C5    0.020
 G1M  plan-1  C6    0.020
 G1M  plan-1  O6    0.020
 G1M  plan-1  N7    0.020
 G1M  plan-1  C8    0.020
 G1M  plan-1  N9    0.020
 G1M  plan-1  C1'   0.020
 G1M  plan-1  HN1   0.020
 G1M  plan-1  HN2   0.020
 G1M  plan-1  HN2A  0.020
 G1M  plan-1  H8    0.020

