# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 19:57:35 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: 2'-deoxy-5'-O-[(S)-{[(R)-[dichloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)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(Cl)(Cl)[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
 G2C  G2C  2'-deoxy-5'-O-[(S)-{[(R)-[dichloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]guanosine  ligand  45  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_G2C
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
 G2C  N1    N   NR16   0  -0.726  -7.7423   1.1930  -1.2052
 G2C  C2    C   CR6    0   0.681  -7.7378   0.6586   0.0512
 G2C  N2    N   NH2    0  -0.833  -8.9283   0.5229   0.6576
 G2C  N3    N   N      0  -0.515  -6.6413   0.3178   0.6785
 G2C  C4    C   CR6    0   0.503  -5.5270   0.5466  -0.0359
 G2C  C5    C   CR6    0  -0.090  -5.4237   1.0923  -1.3031
 G2C  C6    C   CR6    0   0.497  -6.6149   1.4607  -1.9915
 G2C  O6    O   O      0  -0.477  -6.7370   1.9466  -3.1042
 G2C  N7    N   N      0  -0.452  -4.1116   1.1918  -1.6806
 G2C  C8    C   C1     0   0.048  -3.4381   0.7193  -0.6733
 G2C  N9    N   N      0  -0.539  -4.2492   0.2926   0.3525
 G2C  PA    P   P      0   1.341   0.6943  -0.4789  -0.7023
 G2C  PB    P   P      0   1.332   3.2896   0.8419  -0.4376
 G2C  PG    P   P      0   1.210   6.4189   0.2855  -0.7634
 G2C  C1'   C   CR15   0   0.188  -3.8275  -0.2133   1.6675
 G2C  O1A   O   O      0  -0.791  -0.1097   0.7699  -0.9329
 G2C  O1B   O   O      0  -0.783   3.3582   2.0074   0.5009
 G2C  CL1B  CL  CL     0  -0.183   4.8100  -0.5539   1.6622
 G2C  O1G   O   OP    -1  -0.882   7.3974  -0.7104  -0.1540
 G2C  C2'   C   CH2    0  -0.544  -4.4279  -1.5712   1.9893
 G2C  O2A   O   OP    -1  -0.797   0.9132  -1.4320  -1.8346
 G2C  O2B   O   OP    -1  -0.789   3.1267   1.0463  -1.9117
 G2C  CL2B  CL  CL     0  -0.164   4.3455  -1.8955  -0.8550
 G2C  O2G   O   OP    -1  -0.874   6.2812   0.1966  -2.2759
 G2C  C3'   C   CR15   0   0.007  -3.4401  -2.5208   1.3216
 G2C  O3'   O   OH1    0  -0.664  -3.3541  -3.7967   1.8967
 G2C  O3A   O   O2     0  -0.740   2.0576  -0.1311   0.1133
 G2C  C3B   C   CT     0  -0.561   4.7159  -0.2976  -0.1217
 G2C  O3G   O   O      0  -0.879   6.5116   1.7020  -0.2081
 G2C  C4'   C   CR15   0   0.004  -2.1138  -1.7813   1.5026
 G2C  O4'   O   O      0  -0.490  -2.4475  -0.3999   1.6546
 G2C  C5'   C   CH2    0  -0.148  -1.1716  -1.9873   0.3397
 G2C  O5'   O   O2     0  -0.624   0.0418  -1.3130   0.5709
 G2C  HN1   H   HNR6   0   0.424  -8.6336   1.4267  -1.6237
 G2C  HN2   H   HNH2   0   0.413  -9.7821   0.5611   0.1271
 G2C  HN2A  H   HNH2   0   0.411  -8.9558  -0.0203   1.5038
 G2C  H8    H   H      0   0.318  -2.3580   0.6664  -0.6209
 G2C  H1'   H   HCR5   0   0.278  -4.0821   0.5488   2.4071
 G2C  H2'   H   HCH2   0   0.263  -4.3969  -1.7152   3.0721
 G2C  H2'A  H   HCH2   0   0.281  -5.4576  -1.6889   1.6589
 G2C  H3'   H   HCR5   0   0.224  -3.6732  -2.5961   0.2499
 G2C  HO3'  H   HOH1   0   0.459  -4.1059  -4.3145   1.5945
 G2C  H4'   H   HCR5   0   0.239  -1.6378  -2.1203   2.4313
 G2C  H5'   H   HCH2   0   0.222  -0.9964  -3.0646   0.2317
 G2C  H5'A  H   HCH2   0   0.202  -1.6687  -1.6585  -0.5808

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
 G2C  N1    C2    single    1.365  0.020  1.365
 G2C  N1    C6    single    1.400  0.020  1.400
 G2C  N1    HN1   single    0.860  0.020  1.020
 G2C  C2    N2    single    1.343  0.020  1.343
 G2C  C2    N3    double    1.308  0.020  1.308
 G2C  N2    HN2   single    0.890  0.020  1.040
 G2C  N2    HN2A  single    0.890  0.020  1.040
 G2C  N3    C4    single    1.343  0.020  1.343
 G2C  C4    C5    aromatic  1.384  0.020  1.384
 G2C  C4    N9    aromatic  1.360  0.020  1.360
 G2C  C5    C6    single    1.424  0.020  1.424
 G2C  C5    N7    aromatic  1.369  0.020  1.369
 G2C  C6    O6    double    1.220  0.020  1.220
 G2C  N7    C8    aromatic  1.301  0.020  1.301
 G2C  C8    N9    aromatic  1.376  0.020  1.376
 G2C  C8    H8    single    0.930  0.020  1.080
 G2C  N9    C1'   single    1.471  0.020  1.471
 G2C  PA    O1A   deloc     1.503  0.020  1.503
 G2C  PA    O2A   deloc     1.496  0.020  1.496
 G2C  PA    O3A   single    1.626  0.020  1.626
 G2C  PA    O5'   single    1.656  0.020  1.656
 G2C  PB    O1B   deloc     1.498  0.020  1.498
 G2C  PB    O2B   deloc     1.497  0.020  1.497
 G2C  PB    O3A   single    1.664  0.020  1.664
 G2C  PB    C3B   single    1.853  0.020  1.853
 G2C  PG    O1G   deloc     1.523  0.020  1.523
 G2C  PG    O2G   deloc     1.521  0.020  1.521
 G2C  PG    C3B   single    1.911  0.020  1.911
 G2C  PG    O3G   deloc     1.524  0.020  1.524
 G2C  C1'   C2'   single    1.519  0.020  1.519
 G2C  C1'   O4'   single    1.393  0.020  1.393
 G2C  C1'   H1'   single    0.970  0.020  1.090
 G2C  CL1B  C3B   single    1.805  0.020  1.805
 G2C  C2'   C3'   single    1.524  0.020  1.524
 G2C  C2'   H2'   single    0.970  0.020  1.090
 G2C  C2'   H2'A  single    0.970  0.020  1.090
 G2C  CL2B  C3B   single    1.797  0.020  1.797
 G2C  C3'   O3'   single    1.402  0.020  1.402
 G2C  C3'   C4'   single    1.529  0.020  1.529
 G2C  C3'   H3'   single    0.970  0.020  1.090
 G2C  O3'   HO3'  single    0.850  0.020  0.980
 G2C  C4'   O4'   single    1.429  0.020  1.429
 G2C  C4'   C5'   single    1.511  0.020  1.511
 G2C  C4'   H4'   single    0.970  0.020  1.090
 G2C  C5'   O5'   single    1.407  0.020  1.407
 G2C  C5'   H5'   single    0.970  0.020  1.090
 G2C  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
 G2C  HN1   N1   C6    115.64  3.000
 G2C  HN1   N1   C2    118.28  3.000
 G2C  C6    N1   C2    126.08  3.000
 G2C  N3    C2   N2    120.01  3.000
 G2C  N3    C2   N1    123.08  3.000
 G2C  N2    C2   N1    116.88  3.000
 G2C  HN2A  N2   HN2   116.16  3.000
 G2C  HN2A  N2   C2    117.30  3.000
 G2C  HN2   N2   C2    120.70  3.000
 G2C  C4    N3   C2    113.32  3.000
 G2C  N9    C4   C5    105.38  3.000
 G2C  N9    C4   N3    126.58  3.000
 G2C  C5    C4   N3    128.04  3.000
 G2C  N7    C5   C6    130.50  3.000
 G2C  N7    C5   C4    110.66  3.000
 G2C  C6    C5   C4    118.83  3.000
 G2C  O6    C6   C5    128.86  3.000
 G2C  O6    C6   N1    120.50  3.000
 G2C  C5    C6   N1    110.64  3.000
 G2C  C8    N7   C5    104.85  3.000
 G2C  H8    C8   N9    122.48  3.000
 G2C  H8    C8   N7    124.88  3.000
 G2C  N9    C8   N7    112.64  3.000
 G2C  C1'   N9   C8    127.19  3.000
 G2C  C1'   N9   C4    126.10  3.000
 G2C  C8    N9   C4    106.45  3.000
 G2C  O5'   PA   O3A    93.01  3.000
 G2C  O5'   PA   O2A   108.58  3.000
 G2C  O3A   PA   O2A   113.15  3.000
 G2C  O5'   PA   O1A   109.01  3.000
 G2C  O3A   PA   O1A   110.35  3.000
 G2C  O2A   PA   O1A   119.43  3.000
 G2C  C3B   PB   O3A    98.85  3.000
 G2C  C3B   PB   O2B   109.61  3.000
 G2C  O3A   PB   O2B   108.98  3.000
 G2C  C3B   PB   O1B   109.66  3.000
 G2C  O3A   PB   O1B   106.35  3.000
 G2C  O2B   PB   O1B   121.04  3.000
 G2C  O3G   PG   C3B   102.44  3.000
 G2C  O3G   PG   O2G   114.96  3.000
 G2C  C3B   PG   O2G   103.61  3.000
 G2C  O3G   PG   O1G   115.00  3.000
 G2C  C3B   PG   O1G   103.81  3.000
 G2C  O2G   PG   O1G   114.69  3.000
 G2C  H1'   C1'  O4'   109.32  3.000
 G2C  H1'   C1'  C2'   112.84  3.000
 G2C  O4'   C1'  C2'   105.89  3.000
 G2C  H1'   C1'  N9    107.38  3.000
 G2C  O4'   C1'  N9    108.78  3.000
 G2C  C2'   C1'  N9    112.55  3.000
 G2C  H2'A  C2'  H2'   108.27  3.000
 G2C  H2'A  C2'  C3'   114.39  3.000
 G2C  H2'   C2'  C3'   109.48  3.000
 G2C  H2'A  C2'  C1'   113.99  3.000
 G2C  H2'   C2'  C1'   108.45  3.000
 G2C  C3'   C2'  C1'   102.00  3.000
 G2C  H3'   C3'  C4'   109.42  3.000
 G2C  H3'   C3'  O3'   110.52  3.000
 G2C  C4'   C3'  O3'   109.77  3.000
 G2C  H3'   C3'  C2'   109.40  3.000
 G2C  C4'   C3'  C2'   102.06  3.000
 G2C  O3'   C3'  C2'   115.28  3.000
 G2C  HO3'  O3'  C3'   108.25  3.000
 G2C  PB    O3A  PA    125.44  3.000
 G2C  CL2B  C3B  CL1B  106.73  3.000
 G2C  CL2B  C3B  PG    108.54  3.000
 G2C  CL1B  C3B  PG    109.19  3.000
 G2C  CL2B  C3B  PB    108.58  3.000
 G2C  CL1B  C3B  PB    107.22  3.000
 G2C  PG    C3B  PB    116.18  3.000
 G2C  H4'   C4'  C5'   109.80  3.000
 G2C  H4'   C4'  O4'   108.05  3.000
 G2C  C5'   C4'  O4'   111.05  3.000
 G2C  H4'   C4'  C3'   109.09  3.000
 G2C  C5'   C4'  C3'   112.57  3.000
 G2C  O4'   C4'  C3'   106.11  3.000
 G2C  C4'   O4'  C1'   111.21  3.000
 G2C  H5'A  C5'  H5'   106.52  3.000
 G2C  H5'A  C5'  O5'   112.65  3.000
 G2C  H5'   C5'  O5'   110.44  3.000
 G2C  H5'A  C5'  C4'   108.81  3.000
 G2C  H5'   C5'  C4'   108.01  3.000
 G2C  O5'   C5'  C4'   110.24  3.000
 G2C  C5'   O5'  PA    117.05  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
 G2C  CONST_01  C8    N7   C5   C4     0.00   0.0  0
 G2C  CONST_02  N7    C8   N9   C4     0.00   0.0  0
 G2C  CONST_03  C8    N9   C4   C5     0.00   0.0  0
 G2C  CONST_04  N9    C8   N7   C5     0.00   0.0  0
 G2C  CONST_05  N9    C4   C5   N7     0.00   0.0  0
 G2C  CONST_06  C1'   N9   C4   N3     0.00   0.0  0
 G2C  CONST_07  C1'   N9   C4   C5   180.00   0.0  0
 G2C  CONST_08  C1'   N9   C8   N7   180.00   0.0  0
 G2C  CONST_09  C4    N3   C2   N1     0.00   0.0  0
 G2C  CONST_10  C5    C6   N1   C2     0.00   0.0  0
 G2C  CONST_11  C6    N1   C2   N3     0.00   0.0  0
 G2C  CONST_12  O6    C6   N1   C2   180.00   0.0  0
 G2C  CONST_13  C6    N1   C2   N2   180.00   0.0  0
 G2C  CONST_14  C4    N3   C2   N2   180.00   0.0  0
 G2C  CONST_15  H8    C8   N9   C4   180.00   0.0  0
 G2C  CONST_16  HN1   N1   C2   N3   180.00   0.0  0
 G2C  CONST_18  HN2A  N2   C2   N1   180.00   0.0  0
 G2C  Var_01    C4'   C5'  O5'  PA  -137.04  30.0  2
 G2C  Var_02    O1B   PB   O3A  PA   117.07  30.0  1
 G2C  Var_03    O1A   PA   O3A  PB   -63.39  30.0  1
 G2C  Var_04    O1G   PG   C3B  PB   170.48  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
 G2C  chir_03  C1'  N9   C2'  O4'  negativ
 G2C  chir_04  C3'  O3'  C4'  C2'  positiv
 G2C  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
 G2C  plan-1  N1    0.020
 G2C  plan-1  C2    0.020
 G2C  plan-1  N2    0.020
 G2C  plan-1  N3    0.020
 G2C  plan-1  C4    0.020
 G2C  plan-1  C5    0.020
 G2C  plan-1  C6    0.020
 G2C  plan-1  O6    0.020
 G2C  plan-1  N7    0.020
 G2C  plan-1  C8    0.020
 G2C  plan-1  N9    0.020
 G2C  plan-1  C1'   0.020
 G2C  plan-1  HN1   0.020
 G2C  plan-1  HN2   0.020
 G2C  plan-1  HN2A  0.020
 G2C  plan-1  H8    0.020

