# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 21:41:10 2021
#   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  55  33  .  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_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  -0.726   9.7949   8.7935   8.7963
 G2M  C2    C  CR6   0   0.687   8.7159   8.6302   7.9751
 G2M  N2    N  NH2   0  -0.832   8.8882   8.9246   6.6783
 G2M  N3    N  N     0  -0.516   7.5433   8.2383   8.4079
 G2M  C4    C  CR56  0   0.504   7.5157   8.0264   9.7317
 G2M  C5    C  CR56  0  -0.089   8.5450   8.1534  10.6460
 G2M  C6    C  CR6   0   0.501   9.8231   8.5757  10.1799
 G2M  O6    O  O     0  -0.474  10.8501   8.7519  10.8141
 G2M  N7    N  N     0  -0.445   8.1115   7.8382  11.9067
 G2M  C8    C  CR15  0   0.082   6.8590   7.5283  11.7582
 G2M  N9    N  NR5   0  -0.526   6.4371   7.6277  10.4554
 G2M  PA    P  P     0   1.491   4.2073   5.3079  14.6519
 G2M  PB    P  P     0   1.455   3.4167   2.4582  14.1725
 G2M  PG    P  P     0   1.416   5.0927   1.5166  16.4150
 G2M  C1'   C  CH1   0   0.186   5.1212   7.3434   9.8974
 G2M  O1A   O  O     0  -0.671   3.2627   5.4328  15.7701
 G2M  O1B   O  OH1   0  -0.746   3.0752   2.1259  12.6397
 G2M  O1G   O  OH1   0  -0.769   5.1670   3.1201  16.6173
 G2M  C2'   C  CH2   0  -0.536   4.9608   5.8936   9.4480
 G2M  O2A   O  OH1   0  -0.714   5.7536   5.5083  14.9275
 G2M  O2B   O  O     0  -0.655   2.2874   2.4523  15.1185
 G2M  O2G   O  OH1   0  -0.732   6.6079   1.0186  16.5244
 G2M  C3'   C  CH1   0   0.004   4.3082   5.2381  10.6547
 G2M  O3'   O  OH1   0  -0.668   3.6103   4.0824  10.2912
 G2M  O3A   O  O2    0  -0.717   4.1165   3.8884  13.8696
 G2M  C3B   C  CT    0  -0.644   4.8032   1.3512  14.6137
 G2M  C3B2  C  CH3   0  -0.657   6.0525   1.6740  13.7797
 G2M  C3B3  C  CH3   0  -0.686   4.3511  -0.0969  14.3440
 G2M  O3G   O  O     0  -0.689   4.1271   0.8408  17.3090
 G2M  C4'   C  CH1   0   0.015   3.4066   6.3846  11.1316
 G2M  O4'   O  O2    0  -0.494   4.1584   7.5669  10.8917
 G2M  C5'   C  CH2   0  -0.221   2.9461   6.3523  12.5672
 G2M  O5'   O  O2    0  -0.572   4.0778   6.3262  13.4443
 G2M  HN1   H  HNR6  0   0.425  10.6652   9.1081   8.3867
 G2M  HN2   H  HNH2  0   0.412   8.1585   8.6566   6.0398
 G2M  HN2A  H  HNH2  0   0.415   9.8102   9.0191   6.2876
 G2M  H8    H  HCR5  0   0.289   6.1933   7.2400  12.5545
 G2M  H1'   H  HCH1  0   0.274   4.9870   8.0413   9.0688
 G2M  H2'   H  HCH2  0   0.269   4.2748   5.8534   8.5983
 G2M  H2'A  H  HCH2  0   0.284   5.9044   5.4397   9.1488
 G2M  H3'   H  HCH1  0   0.228   5.0759   5.0244  11.4092
 G2M  HO3'  H  HOH1  0   0.453   3.4297   3.5507  11.0741
 G2M  HC3B  H  HCH3  0   0.270   6.8097   0.9087  13.9396
 G2M  HC3A  H  HCH3  0   0.258   5.8086   1.6651  12.7171
 G2M  HC3C  H  HCH3  0   0.256   6.4923   2.6410  14.0165
 G2M  HC3D  H  HCH3  0   0.272   5.1172  -0.7958  14.6803
 G2M  HC3E  H  HCH3  0   0.266   3.4212  -0.3504  14.8506
 G2M  HC3F  H  HCH3  0   0.267   4.2174  -0.2558  13.2745
 G2M  H4'   H  HCH1  0   0.251   2.4973   6.3837  10.5143
 G2M  H5'   H  HCH2  0   0.284   2.3537   7.2374  12.8019
 G2M  H5'A  H  HCH2  0   0.251   2.2973   5.4821  12.7002
 G2M  H19   H  HOH1  0   0.512   2.3489   1.4992  12.5116
 G2M  H20   H  HOH1  0   0.501   4.6650   3.4343  17.3826
 G2M  H21   H  HOH1  0   0.503   6.0682   5.0914  15.7424
 G2M  H22   H  HOH1  0   0.501   6.8912   0.8068  17.4253

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  1.299  0.020  1.299
 G2M  C8    N9    aromatic  1.373  0.020  1.373
 G2M  C8    H8    single    0.930  0.020  1.080
 G2M  N9    C1'   single    1.457  0.020  1.457
 G2M  PA    O1A   double    1.469  0.020  1.469
 G2M  PA    O2A   single    1.583  0.020  1.583
 G2M  PA    O3A   single    1.623  0.020  1.623
 G2M  PA    O5'   single    1.585  0.020  1.585
 G2M  PB    O1B   single    1.605  0.020  1.605
 G2M  PB    O2B   double    1.473  0.020  1.473
 G2M  PB    O3A   single    1.621  0.020  1.621
 G2M  PB    C3B   single    1.828  0.020  1.828
 G2M  PG    O1G   single    1.618  0.020  1.618
 G2M  PG    O2G   single    1.599  0.020  1.599
 G2M  PG    C3B   single    1.832  0.020  1.832
 G2M  PG    O3G   double    1.479  0.020  1.479
 G2M  C1'   C2'   single    1.526  0.020  1.526
 G2M  C1'   O4'   single    1.402  0.020  1.402
 G2M  C1'   H1'   single    0.970  0.020  1.090
 G2M  C2'   C3'   single    1.520  0.020  1.520
 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    1.398  0.020  1.398
 G2M  C3'   C4'   single    1.535  0.020  1.535
 G2M  C3'   H3'   single    0.970  0.020  1.090
 G2M  O3'   HO3'  single    0.850  0.020  0.980
 G2M  C3B   C3B2  single    1.536  0.020  1.536
 G2M  C3B   C3B3  single    1.541  0.020  1.541
 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    1.421  0.020  1.421
 G2M  C4'   C5'   single    1.508  0.020  1.508
 G2M  C4'   H4'   single    0.970  0.020  1.090
 G2M  C5'   O5'   single    1.432  0.020  1.432
 G2M  C5'   H5'   single    0.970  0.020  1.090
 G2M  C5'   H5'A  single    0.970  0.020  1.090
 G2M  O1B   H19   single    0.850  0.020  0.980
 G2M  O1G   H20   single    0.850  0.020  0.980
 G2M  O2A   H21   single    0.850  0.020  0.980
 G2M  O2G   H22   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
 G2M  HN1   N1    C6    115.51  3.000
 G2M  HN1   N1    C2    118.24  3.000
 G2M  C6    N1    C2    126.24  3.000
 G2M  N3    C2    N2    120.02  3.000
 G2M  N3    C2    N1    122.98  3.000
 G2M  N2    C2    N1    116.98  3.000
 G2M  HN2A  N2    HN2   116.32  3.000
 G2M  HN2A  N2    C2    120.94  3.000
 G2M  HN2   N2    C2    117.52  3.000
 G2M  C4    N3    C2    113.07  3.000
 G2M  N9    C4    C5    105.41  3.000
 G2M  N9    C4    N3    126.06  3.000
 G2M  C5    C4    N3    128.53  3.000
 G2M  N7    C5    C6    130.78  3.000
 G2M  N7    C5    C4    110.60  3.000
 G2M  C6    C5    C4    118.61  3.000
 G2M  O6    C6    C5    128.91  3.000
 G2M  O6    C6    N1    120.53  3.000
 G2M  C5    C6    N1    110.55  3.000
 G2M  C8    N7    C5    104.76  3.000
 G2M  H8    C8    N9    122.07  3.000
 G2M  H8    C8    N7    125.12  3.000
 G2M  N9    C8    N7    112.80  3.000
 G2M  C1'   N9    C8    128.80  3.000
 G2M  C1'   N9    C4    124.76  3.000
 G2M  C8    N9    C4    106.43  3.000
 G2M  O5'   PA    O3A   100.96  3.000
 G2M  O5'   PA    O2A    97.53  3.000
 G2M  O3A   PA    O2A   104.43  3.000
 G2M  O5'   PA    O1A   118.21  3.000
 G2M  O3A   PA    O1A   113.90  3.000
 G2M  O2A   PA    O1A   118.99  3.000
 G2M  C3B   PB    O3A   104.60  3.000
 G2M  C3B   PB    O2B   115.09  3.000
 G2M  O3A   PB    O2B   117.03  3.000
 G2M  C3B   PB    O1B   105.45  3.000
 G2M  O3A   PB    O1B    95.51  3.000
 G2M  O2B   PB    O1B   116.70  3.000
 G2M  O3G   PG    C3B   116.73  3.000
 G2M  O3G   PG    O2G   115.78  3.000
 G2M  C3B   PG    O2G   100.89  3.000
 G2M  O3G   PG    O1G   114.03  3.000
 G2M  C3B   PG    O1G   102.70  3.000
 G2M  O2G   PG    O1G   104.87  3.000
 G2M  H1'   C1'   O4'   110.61  3.000
 G2M  H1'   C1'   C2'   111.77  3.000
 G2M  O4'   C1'   C2'   106.74  3.000
 G2M  H1'   C1'   N9    106.07  3.000
 G2M  O4'   C1'   N9    108.51  3.000
 G2M  C2'   C1'   N9    113.14  3.000
 G2M  H19   O1B   PB    114.84  3.000
 G2M  H20   O1G   PG    113.39  3.000
 G2M  H2'A  C2'   H2'   108.36  3.000
 G2M  H2'A  C2'   C3'   114.22  3.000
 G2M  H2'   C2'   C3'   109.38  3.000
 G2M  H2'A  C2'   C1'   112.69  3.000
 G2M  H2'   C2'   C1'   109.26  3.000
 G2M  C3'   C2'   C1'   102.76  3.000
 G2M  H21   O2A   PA    114.17  3.000
 G2M  H22   O2G   PG    114.16  3.000
 G2M  H3'   C3'   C4'   110.05  3.000
 G2M  H3'   C3'   O3'   111.53  3.000
 G2M  C4'   C3'   O3'   113.90  3.000
 G2M  H3'   C3'   C2'   109.23  3.000
 G2M  C4'   C3'   C2'   100.18  3.000
 G2M  O3'   C3'   C2'   111.36  3.000
 G2M  HO3'  O3'   C3'   109.78  3.000
 G2M  PB    O3A   PA    134.89  3.000
 G2M  C3B3  C3B   C3B2  109.94  3.000
 G2M  C3B3  C3B   PG    107.66  3.000
 G2M  C3B2  C3B   PG    112.72  3.000
 G2M  C3B3  C3B   PB    107.72  3.000
 G2M  C3B2  C3B   PB    111.01  3.000
 G2M  PG    C3B   PB    107.60  3.000
 G2M  HC3C  C3B2  HC3A  108.03  3.000
 G2M  HC3C  C3B2  HC3B  108.16  3.000
 G2M  HC3A  C3B2  HC3B  107.04  3.000
 G2M  HC3C  C3B2  C3B   113.40  3.000
 G2M  HC3A  C3B2  C3B   110.20  3.000
 G2M  HC3B  C3B2  C3B   109.77  3.000
 G2M  HC3F  C3B3  HC3E  108.54  3.000
 G2M  HC3F  C3B3  HC3D  107.20  3.000
 G2M  HC3E  C3B3  HC3D  107.90  3.000
 G2M  HC3F  C3B3  C3B   110.17  3.000
 G2M  HC3E  C3B3  C3B   112.82  3.000
 G2M  HC3D  C3B3  C3B   110.02  3.000
 G2M  H4'   C4'   C5'   106.38  3.000
 G2M  H4'   C4'   O4'   110.09  3.000
 G2M  C5'   C4'   O4'   109.88  3.000
 G2M  H4'   C4'   C3'   108.12  3.000
 G2M  C5'   C4'   C3'   117.34  3.000
 G2M  O4'   C4'   C3'   104.97  3.000
 G2M  C4'   O4'   C1'   110.50  3.000
 G2M  H5'A  C5'   H5'   107.31  3.000
 G2M  H5'A  C5'   O5'   112.32  3.000
 G2M  H5'   C5'   O5'   108.19  3.000
 G2M  H5'A  C5'   C4'   108.30  3.000
 G2M  H5'   C5'   C4'   110.69  3.000
 G2M  O5'   C5'   C4'   110.01  3.000
 G2M  C5'   O5'   PA    122.89  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_17  HN2   N2    C2   N1   180.00   0.0  0
 G2M  Var_01    C4'   C5'   O5'  PA  -132.04  30.0  1
 G2M  Var_02    O1B   PB    O3A  PA   146.10  30.0  1
 G2M  Var_03    O1A   PA    O3A  PB   -13.15  30.0  2
 G2M  Var_04    O1G   PG    C3B  PB   -49.69  30.0  3
 G2M  Var_05    HC3B  C3B2  C3B  PB  -170.94  30.0  3
 G2M  Var_06    HC3D  C3B3  C3B  PB  -174.83  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
 G2M  chir_06  PA   O2A  O3A  O5'  both
 G2M  chir_07  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
 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

