# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 01:15:22 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(2-phosphonopropan-2-yl)phosphoryl]oxy}phosphoryl]guanosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)([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
 G2M  G2M  2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(2-phosphonopropan-2-yl)phosphoryl]oxy}phosphoryl]guanosine  ligand  51  33  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_G2M
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
 G2M  N1    N  NR16   0  -0.569  -7.9969   1.5201  -0.4119
 G2M  C2    C  CR6    0   0.623  -7.4904   1.3713   0.8477
 G2M  N2    N  NH2    0  -0.785  -8.2622   1.7775   1.8658
 G2M  N3    N  N      0  -0.567  -6.3233   0.8276   1.0877
 G2M  C4    C  CR56   0   0.445  -5.6837   0.4410  -0.0254
 G2M  C5    C  CR56   0  -0.146  -6.1050   0.5420  -1.3388
 G2M  C6    C  CR6    0   0.497  -7.3744   1.1313  -1.6053
 G2M  O6    O  O      0  -0.480  -7.9250   1.3119  -2.6786
 G2M  N7    N  N      0  -0.341  -5.1584   0.0340  -2.1892
 G2M  C8    C  CR15   0   0.075  -4.1978  -0.3646  -1.4119
 G2M  N9    N  NR5    0  -0.490  -4.4580  -0.1420  -0.0832
 G2M  PA    P  P      0   1.372   1.7363  -0.7548  -1.0933
 G2M  PB    P  P      0   1.288   4.0233   1.0758  -0.7065
 G2M  PG    P  P      0   1.193   6.7245   1.0179   0.7058
 G2M  C1'   C  CR15   0   0.191  -3.6412  -0.5008   1.0698
 G2M  O1A   O  O      0  -0.865   1.2689  -0.3554  -2.4637
 G2M  O1B   O  OP    -1  -0.857   3.7745   2.5425  -0.9530
 G2M  O1G   O  OP    -1  -0.928   7.2362   1.1398   2.1527
 G2M  C2'   C  CH2    0  -0.544  -3.8234  -1.9522   1.5024
 G2M  O2A   O  OP    -1  -0.826   2.4258  -2.0743  -0.9123
 G2M  O2B   O  O      0  -0.830   4.5682   0.2271  -1.8244
 G2M  O2G   O  OP    -1  -0.944   7.2589  -0.2331   0.0004
 G2M  C3'   C  CR15   0  -0.032  -2.6716  -2.6592   0.7949
 G2M  O3'   O  OH1    0  -0.705  -2.2108  -3.8257   1.4167
 G2M  O3A   O  O2     0  -0.760   2.4777   0.4690  -0.3477
 G2M  C3B   C  CT     0  -0.525   4.8601   0.7831   0.8917
 G2M  C3B2  C  CH3    0  -0.688   4.3244   1.7807   1.9205
 G2M  C3B3  C  CH3    0  -0.667   4.6016  -0.6385   1.3892
 G2M  O3G   O  O      0  -0.964   6.9050   2.3075  -0.1060
 G2M  C4'   C  CR15   0  -0.027  -1.5910  -1.5836   0.8467
 G2M  O4'   O  O      0  -0.462  -2.2923  -0.3481   0.7272
 G2M  C5'   C  CH2    0  -0.142  -0.5540  -1.7057  -0.2415
 G2M  O5'   O  O2     0  -0.633   0.4249  -0.7156  -0.0668
 G2M  HN1   H  HNR6   0   0.453  -8.9071   1.9513  -0.5145
 G2M  HN2   H  HNH2   0   0.386  -9.0538   2.3771   1.7083
 G2M  HN2A  H  HNH2   0   0.378  -7.8452   1.8163   2.7803
 G2M  H8    H  HCR5   0   0.203  -3.2748  -0.8094  -1.7492
 G2M  H1'   H  HCR5   0   0.243  -3.9213   0.1969   1.8620
 G2M  H2'   H  HCH2   0   0.301  -3.6799  -2.0289   2.5826
 G2M  H2'A  H  HCH2   0   0.305  -4.8111  -2.3425   1.2596
 G2M  H3'   H  HCR5   0   0.270  -2.9422  -2.8571  -0.2530
 G2M  HO3'  H  HOH1   0   0.444  -2.8355  -4.5348   1.2365
 G2M  HC3B  H  HCH3   0   0.239   3.2361   1.7221   2.0222
 G2M  HC3A  H  HCH3   0   0.209   4.7597   1.5731   2.8991
 G2M  HC3C  H  HCH3   0   0.231   4.5807   2.8064   1.6547
 G2M  HC3D  H  HCH3   0   0.231   4.8201  -1.3803   0.6238
 G2M  HC3E  H  HCH3   0   0.269   5.2403  -0.8472   2.2512
 G2M  HC3F  H  HCH3   0   0.194   3.5640  -0.7821   1.6986
 G2M  H4'   H  HCR5   0   0.251  -1.0967  -1.6295   1.8275
 G2M  H5'   H  HCH2   0   0.244  -0.1253  -2.7138  -0.1808
 G2M  H5'A  H  HCH2   0   0.241  -1.0422  -1.6263  -1.2233

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
 G2M  N1    C2    single    1.366  0.020  1.366
 G2M  N1    C6    single    1.401  0.020  1.401
 G2M  N1    HN1   single    0.860  0.020  1.020
 G2M  C2    N2    single    1.341  0.020  1.341
 G2M  C2    N3    double    1.310  0.020  1.310
 G2M  N2    HN2   single    0.890  0.020  1.040
 G2M  N2    HN2A  single    0.890  0.020  1.040
 G2M  N3    C4    single    1.341  0.020  1.341
 G2M  C4    C5    aromatic  1.383  0.020  1.383
 G2M  C4    N9    aromatic  1.359  0.020  1.359
 G2M  C5    C6    single    1.425  0.020  1.425
 G2M  C5    N7    aromatic  1.370  0.020  1.370
 G2M  C6    O6    double    1.220  0.020  1.220
 G2M  N7    C8    aromatic  1.298  0.020  1.298
 G2M  C8    N9    aromatic  1.372  0.020  1.372
 G2M  C8    H8    single    0.930  0.020  1.080
 G2M  N9    C1'   single    1.458  0.020  1.458
 G2M  PA    O1A   deloc     1.502  0.020  1.502
 G2M  PA    O2A   deloc     1.500  0.020  1.500
 G2M  PA    O3A   single    1.613  0.020  1.613
 G2M  PA    O5'   single    1.666  0.020  1.666
 G2M  PB    O1B   deloc     1.508  0.020  1.508
 G2M  PB    O2B   deloc     1.506  0.020  1.506
 G2M  PB    O3A   single    1.699  0.020  1.699
 G2M  PB    C3B   single    1.828  0.020  1.828
 G2M  PG    O1G   deloc     1.540  0.020  1.540
 G2M  PG    O2G   deloc     1.532  0.020  1.532
 G2M  PG    C3B   single    1.888  0.020  1.888
 G2M  PG    O3G   deloc     1.535  0.020  1.535
 G2M  C1'   C2'   single    1.525  0.020  1.525
 G2M  C1'   O4'   single    1.400  0.020  1.400
 G2M  C1'   H1'   single    0.970  0.020  1.090
 G2M  C2'   C3'   single    1.525  0.020  1.525
 G2M  C2'   H2'   single    0.970  0.020  1.090
 G2M  C2'   H2'A  single    0.970  0.020  1.090
 G2M  C3'   O3'   single    1.400  0.020  1.400
 G2M  C3'   C4'   single    1.526  0.020  1.526
 G2M  C3'   H3'   single    0.970  0.020  1.090
 G2M  O3'   HO3'  single    0.850  0.020  0.980
 G2M  C3B   C3B2  single    1.530  0.020  1.530
 G2M  C3B   C3B3  single    1.528  0.020  1.528
 G2M  C3B2  HC3B  single    0.970  0.020  1.090
 G2M  C3B2  HC3A  single    0.970  0.020  1.090
 G2M  C3B2  HC3C  single    0.970  0.020  1.090
 G2M  C3B3  HC3D  single    0.970  0.020  1.090
 G2M  C3B3  HC3E  single    0.970  0.020  1.090
 G2M  C3B3  HC3F  single    0.970  0.020  1.090
 G2M  C4'   O4'   single    1.426  0.020  1.426
 G2M  C4'   C5'   single    1.508  0.020  1.508
 G2M  C4'   H4'   single    0.970  0.020  1.090
 G2M  C5'   O5'   single    1.403  0.020  1.403
 G2M  C5'   H5'   single    0.970  0.020  1.090
 G2M  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
 G2M  HN1   N1    C6    115.55  3.000
 G2M  HN1   N1    C2    118.25  3.000
 G2M  C6    N1    C2    126.19  3.000
 G2M  N3    C2    N2    119.98  3.000
 G2M  N3    C2    N1    123.01  3.000
 G2M  N2    C2    N1    116.99  3.000
 G2M  HN2A  N2    HN2   116.48  3.000
 G2M  HN2A  N2    C2    117.61  3.000
 G2M  HN2   N2    C2    120.99  3.000
 G2M  C4    N3    C2    113.12  3.000
 G2M  N9    C4    C5    105.41  3.000
 G2M  N9    C4    N3    126.12  3.000
 G2M  C5    C4    N3    128.47  3.000
 G2M  N7    C5    C6    130.76  3.000
 G2M  N7    C5    C4    110.60  3.000
 G2M  C6    C5    C4    118.64  3.000
 G2M  O6    C6    C5    128.91  3.000
 G2M  O6    C6    N1    120.52  3.000
 G2M  C5    C6    N1    110.57  3.000
 G2M  C8    N7    C5    104.68  3.000
 G2M  H8    C8    N9    122.14  3.000
 G2M  H8    C8    N7    124.92  3.000
 G2M  N9    C8    N7    112.93  3.000
 G2M  C1'   N9    C8    128.30  3.000
 G2M  C1'   N9    C4    125.27  3.000
 G2M  C8    N9    C4    106.37  3.000
 G2M  O5'   PA    O3A    93.39  3.000
 G2M  O5'   PA    O2A   107.95  3.000
 G2M  O3A   PA    O2A   113.60  3.000
 G2M  O5'   PA    O1A   108.12  3.000
 G2M  O3A   PA    O1A   111.28  3.000
 G2M  O2A   PA    O1A   119.15  3.000
 G2M  C3B   PB    O3A   100.06  3.000
 G2M  C3B   PB    O2B   113.16  3.000
 G2M  O3A   PB    O2B   106.55  3.000
 G2M  C3B   PB    O1B   111.98  3.000
 G2M  O3A   PB    O1B   103.41  3.000
 G2M  O2B   PB    O1B   119.12  3.000
 G2M  O3G   PG    C3B   105.83  3.000
 G2M  O3G   PG    O2G   113.68  3.000
 G2M  C3B   PG    O2G   106.75  3.000
 G2M  O3G   PG    O1G   113.05  3.000
 G2M  C3B   PG    O1G   104.21  3.000
 G2M  O2G   PG    O1G   112.42  3.000
 G2M  H1'   C1'   O4'   110.79  3.000
 G2M  H1'   C1'   C2'   111.81  3.000
 G2M  O4'   C1'   C2'   106.75  3.000
 G2M  H1'   C1'   N9    105.83  3.000
 G2M  O4'   C1'   N9    108.63  3.000
 G2M  C2'   C1'   N9    113.05  3.000
 G2M  H2'A  C2'   H2'   108.31  3.000
 G2M  H2'A  C2'   C3'   114.53  3.000
 G2M  H2'   C2'   C3'   109.08  3.000
 G2M  H2'A  C2'   C1'   112.71  3.000
 G2M  H2'   C2'   C1'   109.37  3.000
 G2M  C3'   C2'   C1'   102.67  3.000
 G2M  H3'   C3'   C4'   109.48  3.000
 G2M  H3'   C3'   O3'   110.74  3.000
 G2M  C4'   C3'   O3'   109.83  3.000
 G2M  H3'   C3'   C2'   109.84  3.000
 G2M  C4'   C3'   C2'   101.09  3.000
 G2M  O3'   C3'   C2'   115.38  3.000
 G2M  HO3'  O3'   C3'   108.49  3.000
 G2M  PB    O3A   PA    126.26  3.000
 G2M  C3B3  C3B   C3B2  109.18  3.000
 G2M  C3B3  C3B   PG    108.35  3.000
 G2M  C3B2  C3B   PG    109.32  3.000
 G2M  C3B3  C3B   PB    110.86  3.000
 G2M  C3B2  C3B   PB    108.86  3.000
 G2M  PG    C3B   PB    110.25  3.000
 G2M  HC3C  C3B2  HC3A  107.69  3.000
 G2M  HC3C  C3B2  HC3B  107.86  3.000
 G2M  HC3A  C3B2  HC3B  107.65  3.000
 G2M  HC3C  C3B2  C3B   111.55  3.000
 G2M  HC3A  C3B2  C3B   109.84  3.000
 G2M  HC3B  C3B2  C3B   112.07  3.000
 G2M  HC3F  C3B3  HC3E  107.85  3.000
 G2M  HC3F  C3B3  HC3D  107.48  3.000
 G2M  HC3E  C3B3  HC3D  107.89  3.000
 G2M  HC3F  C3B3  C3B   112.04  3.000
 G2M  HC3E  C3B3  C3B   109.60  3.000
 G2M  HC3D  C3B3  C3B   111.79  3.000
 G2M  H4'   C4'   C5'   109.34  3.000
 G2M  H4'   C4'   O4'   109.40  3.000
 G2M  C5'   C4'   O4'   110.36  3.000
 G2M  H4'   C4'   C3'   108.62  3.000
 G2M  C5'   C4'   C3'   113.92  3.000
 G2M  O4'   C4'   C3'   105.05  3.000
 G2M  C4'   O4'   C1'   111.03  3.000
 G2M  H5'A  C5'   H5'   106.82  3.000
 G2M  H5'A  C5'   O5'   111.72  3.000
 G2M  H5'   C5'   O5'   111.64  3.000
 G2M  H5'A  C5'   C4'   109.46  3.000
 G2M  H5'   C5'   C4'   107.64  3.000
 G2M  O5'   C5'   C4'   109.43  3.000
 G2M  C5'   O5'   PA    117.12  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
 G2M  CONST_01  C8    N7    C5   C4    0.00   0.0  0
 G2M  CONST_02  N7    C8    N9   C4    0.00   0.0  0
 G2M  CONST_03  C8    N9    C4   C5    0.00   0.0  0
 G2M  CONST_04  N9    C8    N7   C5    0.00   0.0  0
 G2M  CONST_05  N9    C4    C5   N7    0.00   0.0  0
 G2M  CONST_06  C1'   N9    C4   N3    0.00   0.0  0
 G2M  CONST_07  C1'   N9    C4   C5  180.00   0.0  0
 G2M  CONST_08  C1'   N9    C8   N7  180.00   0.0  0
 G2M  CONST_09  C4    N3    C2   N1    0.00   0.0  0
 G2M  CONST_10  C5    C6    N1   C2    0.00   0.0  0
 G2M  CONST_11  C6    N1    C2   N3    0.00   0.0  0
 G2M  CONST_12  O6    C6    N1   C2  180.00   0.0  0
 G2M  CONST_13  C6    N1    C2   N2  180.00   0.0  0
 G2M  CONST_14  C4    N3    C2   N2  180.00   0.0  0
 G2M  CONST_15  H8    C8    N9   C4  180.00   0.0  0
 G2M  CONST_16  HN1   N1    C2   N3  180.00   0.0  0
 G2M  CONST_18  HN2A  N2    C2   N1  180.00   0.0  0
 G2M  Var_01    C4'   C5'   O5'  PA  175.01  30.0  1
 G2M  Var_02    O1B   PB    O3A  PA  124.95  30.0  1
 G2M  Var_03    O1A   PA    O3A  PB  -73.04  30.0  1
 G2M  Var_04    O1G   PG    C3B  PB  164.49  30.0  2
 G2M  Var_05    HC3B  C3B2  C3B  PB   56.27  30.0  3
 G2M  Var_06    HC3D  C3B3  C3B  PB   50.98  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
 G2M  chir_03  C1'  N9   C2'  O4'  negativ
 G2M  chir_04  C3'  O3'  C4'  C2'  positiv
 G2M  chir_05  C4'  O4'  C3'  C5'  negativ

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
 G2M  plan-1  N1    0.020
 G2M  plan-1  C2    0.020
 G2M  plan-1  N2    0.020
 G2M  plan-1  N3    0.020
 G2M  plan-1  C4    0.020
 G2M  plan-1  C5    0.020
 G2M  plan-1  C6    0.020
 G2M  plan-1  O6    0.020
 G2M  plan-1  N7    0.020
 G2M  plan-1  C8    0.020
 G2M  plan-1  N9    0.020
 G2M  plan-1  C1'   0.020
 G2M  plan-1  HN1   0.020
 G2M  plan-1  HN2   0.020
 G2M  plan-1  HN2A  0.020
 G2M  plan-1  H8    0.020

