# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Aug  1 03:18:35 2021
#   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  49  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 OK
;

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  -0.731   2.0642   3.3806   0.8616
 G2C  C2    C   CR6   0   0.721   2.7019   2.1949   0.6221
 G2C  N2    N   NH2   0  -0.825   3.4915   2.1343  -0.4450
 G2C  N3    N   N     0  -0.510   2.5550   1.1341   1.3876
 G2C  C4    C   CR56  0   0.506   1.7331   1.3303   2.4157
 G2C  C5    C   CR56  0   0.087   1.0419   2.4802   2.7212
 G2C  C6    C   CR6   0   0.550   1.1846   3.6436   1.9106
 G2C  O6    O   O     0  -0.446   0.6540   4.7264   2.0540
 G2C  N7    N   N     0  -0.634   0.2909   2.2252   3.8367
 G2C  C8    C   CR15  0   0.224   0.5195   0.9928   4.2145
 G2C  N9    N   NR5   0  -0.546   1.4039   0.4156   3.3890
 G2C  PA    P   P     0   1.477   2.2660   2.2979   7.0558
 G2C  PB    P   P     0   1.390  -0.6740   2.5467   7.2030
 G2C  PG    P   P     0   1.398  -3.3410   3.0438   8.4977
 G2C  C1'   C   CR15  0   0.222   1.8804  -0.9759   3.5704
 G2C  O1A   O   O     0  -0.682   2.5200   3.1324   5.8695
 G2C  O1B   O   O     0  -0.739  -1.2115   1.1420   7.1853
 G2C  CL1B  CL  CL    0  -0.031  -0.9327   2.6727  10.1647
 G2C  O1G   O   OH1   0  -0.719  -3.9618   3.4806   9.8952
 G2C  C2'   C   CH2   0  -0.575   3.3859  -1.1347   3.3108
 G2C  O2A   O   OH1   0  -0.718   3.3031   2.4163   8.2527
 G2C  O2B   O   OH1   0  -0.713  -0.7466   3.4201   5.9913
 G2C  CL2B  CL  CL    0  -0.034  -1.2484   5.1187   8.6302
 G2C  O2G   O   OH1   0  -0.750  -3.4194   1.4664   8.6260
 G2C  C3'   C   CR15  0   0.035   3.9022  -1.7898   4.5903
 G2C  O3'   O   OH1   0  -0.665   3.8385  -3.1831   4.4368
 G2C  O3A   O   O2    0  -0.687   0.8650   2.5199   7.7945
 G2C  C3B   C   CT    0  -0.611  -1.5182   3.3710   8.6413
 G2C  O3G   O   O     0  -0.675  -3.8911   3.6856   7.2871
 G2C  C4'   C   CR15  0  -0.081   2.8878  -1.2793   5.6149
 G2C  O4'   O   O     0  -0.477   1.6570  -1.3080   4.9019
 G2C  C5'   C   CH2   0  -0.204   3.2912   0.1088   6.0877
 G2C  O5'   O   O2    0  -0.589   2.2086   0.7208   6.7952
 G2C  HN1   H   HNR6  0   0.439   2.2314   4.1519   0.2266
 G2C  HN2   H   HNH2  0   0.424   4.0232   1.2967  -0.6103
 G2C  HN2A  H   HNH2  0   0.427   3.6932   2.9382  -1.0147
 G2C  H8    H   HCR5  0   0.351   0.0514   0.5154   5.0587
 G2C  H1'   H   HCR5  0   0.308   1.2654  -1.6098   2.9318
 G2C  H2'   H   HCH2  0   0.298   3.5764  -1.7542   2.4367
 G2C  H2'A  H   HCH2  0   0.291   3.8812  -0.1812   3.1392
 G2C  H3'   H   HCR5  0   0.255   4.9192  -1.4539   4.8249
 G2C  HO3'  H   HOH1  0   0.458   4.1674  -3.5966   5.2417
 G2C  H4'   H   HCR5  0   0.289   2.7746  -1.9454   6.4731
 G2C  H5'   H   HCH2  0   0.278   4.1550   0.0051   6.7488
 G2C  H5'A  H   HCH2  0   0.246   3.5965   0.7401   5.2479
 G2C  H13   H   HOH1  0   0.506  -4.3956   4.3445   9.8801
 G2C  H14   H   HOH1  0   0.507   3.7590   3.2675   8.3067
 G2C  H15   H   HOH1  0   0.460  -0.2375   2.8750   4.4510
 G2C  H16   H   HOH1  0   0.494  -2.7036   1.0473   8.0815

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    1.367  0.020  1.367
 G2C  N1    C6    single    1.394  0.020  1.394
 G2C  N1    HN1   single    0.860  0.020  1.020
 G2C  C2    N2    single    1.329  0.020  1.329
 G2C  C2    N3    double    1.316  0.020  1.316
 G2C  N2    HN2   single    0.860  0.020  1.020
 G2C  N2    HN2A  single    0.860  0.020  1.020
 G2C  N3    C4    single    1.331  0.020  1.331
 G2C  C4    C5    aromatic  1.376  0.020  1.376
 G2C  C4    N9    aromatic  1.376  0.020  1.376
 G2C  C5    C6    single    1.425  0.020  1.425
 G2C  C5    N7    aromatic  1.369  0.020  1.369
 G2C  C6    O6    double    1.214  0.020  1.214
 G2C  N7    C8    aromatic  1.309  0.020  1.309
 G2C  C8    N9    aromatic  1.340  0.020  1.340
 G2C  C8    H8    single    0.930  0.020  1.080
 G2C  N9    C1'   single    1.482  0.020  1.482
 G2C  PA    O1A   double    1.473  0.020  1.473
 G2C  PA    O2A   single    1.588  0.020  1.588
 G2C  PA    O3A   single    1.599  0.020  1.599
 G2C  PA    O5'   single    1.599  0.020  1.599
 G2C  PB    O1B   double    1.504  0.020  1.504
 G2C  PB    O2B   single    1.495  0.020  1.495
 G2C  PB    O3A   single    1.649  0.020  1.649
 G2C  PB    C3B   single    1.860  0.020  1.860
 G2C  PG    O1G   single    1.590  0.020  1.590
 G2C  PG    O2G   single    1.585  0.020  1.585
 G2C  PG    C3B   single    1.857  0.020  1.857
 G2C  PG    O3G   double    1.477  0.020  1.477
 G2C  C1'   C2'   single    1.536  0.020  1.536
 G2C  C1'   O4'   single    1.390  0.020  1.390
 G2C  C1'   H1'   single    0.970  0.020  1.090
 G2C  CL1B  C3B   single    1.775  0.020  1.775
 G2C  C2'   C3'   single    1.527  0.020  1.527
 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    1.768  0.020  1.768
 G2C  C3'   O3'   single    1.403  0.020  1.403
 G2C  C3'   C4'   single    1.530  0.020  1.530
 G2C  C3'   H3'   single    0.970  0.020  1.090
 G2C  O3'   HO3'  single    0.850  0.020  0.980
 G2C  C4'   O4'   single    1.423  0.020  1.423
 G2C  C4'   C5'   single    1.521  0.020  1.521
 G2C  C4'   H4'   single    0.970  0.020  1.090
 G2C  C5'   O5'   single    1.431  0.020  1.431
 G2C  C5'   H5'   single    0.970  0.020  1.090
 G2C  C5'   H5'A  single    0.970  0.020  1.090
 G2C  O1G   H13   single    0.850  0.020  0.980
 G2C  O2A   H14   single    0.850  0.020  0.980
 G2C  O2B   H15   single    0.850  0.020  0.980
 G2C  O2G   H16   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
 G2C  HN1   N1   C6    115.61  3.000
 G2C  HN1   N1   C2    118.26  3.000
 G2C  C6    N1   C2    126.13  3.000
 G2C  N3    C2   N2    119.77  3.000
 G2C  N3    C2   N1    123.01  3.000
 G2C  N2    C2   N1    117.21  3.000
 G2C  HN2A  N2   HN2   117.81  3.000
 G2C  HN2A  N2   C2    122.52  3.000
 G2C  HN2   N2   C2    118.95  3.000
 G2C  C4    N3   C2    113.54  3.000
 G2C  N9    C4   C5    106.17  3.000
 G2C  N9    C4   N3    126.61  3.000
 G2C  C5    C4   N3    127.23  3.000
 G2C  N7    C5   C6    132.12  3.000
 G2C  N7    C5   C4    107.51  3.000
 G2C  C6    C5   C4    120.37  3.000
 G2C  O6    C6   C5    128.10  3.000
 G2C  O6    C6   N1    122.19  3.000
 G2C  C5    C6   N1    109.71  3.000
 G2C  C8    N7   C5    108.35  3.000
 G2C  H8    C8   N9    125.36  3.000
 G2C  H8    C8   N7    124.59  3.000
 G2C  N9    C8   N7    110.05  3.000
 G2C  C1'   N9   C8    122.76  3.000
 G2C  C1'   N9   C4    129.35  3.000
 G2C  C8    N9   C4    107.89  3.000
 G2C  O5'   PA   O3A   100.41  3.000
 G2C  O5'   PA   O2A   102.70  3.000
 G2C  O3A   PA   O2A   102.33  3.000
 G2C  O5'   PA   O1A   115.70  3.000
 G2C  O3A   PA   O1A   116.39  3.000
 G2C  O2A   PA   O1A   116.89  3.000
 G2C  C3B   PB   O3A    98.82  3.000
 G2C  C3B   PB   O2B   110.22  3.000
 G2C  O3A   PB   O2B   110.21  3.000
 G2C  C3B   PB   O1B   105.11  3.000
 G2C  O3A   PB   O1B   108.82  3.000
 G2C  O2B   PB   O1B   121.24  3.000
 G2C  O3G   PG   C3B   110.63  3.000
 G2C  O3G   PG   O2G   118.73  3.000
 G2C  C3B   PG   O2G   102.57  3.000
 G2C  O3G   PG   O1G   117.11  3.000
 G2C  C3B   PG   O1G   105.47  3.000
 G2C  O2G   PG   O1G   100.54  3.000
 G2C  H1'   C1'  O4'   109.37  3.000
 G2C  H1'   C1'  C2'   113.20  3.000
 G2C  O4'   C1'  C2'   107.14  3.000
 G2C  H1'   C1'  N9    107.03  3.000
 G2C  O4'   C1'  N9    106.85  3.000
 G2C  C2'   C1'  N9    113.05  3.000
 G2C  H13   O1G  PG    114.01  3.000
 G2C  H2'A  C2'  H2'   107.01  3.000
 G2C  H2'A  C2'  C3'   110.73  3.000
 G2C  H2'   C2'  C3'   111.69  3.000
 G2C  H2'A  C2'  C1'   112.47  3.000
 G2C  H2'   C2'  C1'   111.48  3.000
 G2C  C3'   C2'  C1'   103.54  3.000
 G2C  H14   O2A  PA    114.55  3.000
 G2C  H15   O2B  PB    121.93  3.000
 G2C  H16   O2G  PG    109.90  3.000
 G2C  H3'   C3'  C4'   111.69  3.000
 G2C  H3'   C3'  O3'   111.70  3.000
 G2C  C4'   C3'  O3'   112.00  3.000
 G2C  H3'   C3'  C2'   111.19  3.000
 G2C  C4'   C3'  C2'   101.18  3.000
 G2C  O3'   C3'  C2'   108.59  3.000
 G2C  HO3'  O3'  C3'   108.62  3.000
 G2C  PB    O3A  PA    130.85  3.000
 G2C  CL2B  C3B  CL1B  110.11  3.000
 G2C  CL2B  C3B  PG    108.86  3.000
 G2C  CL1B  C3B  PG    108.71  3.000
 G2C  CL2B  C3B  PB    111.33  3.000
 G2C  CL1B  C3B  PB    109.85  3.000
 G2C  PG    C3B  PB    107.91  3.000
 G2C  H4'   C4'  C5'   109.87  3.000
 G2C  H4'   C4'  O4'   106.96  3.000
 G2C  C5'   C4'  O4'   113.81  3.000
 G2C  H4'   C4'  C3'   113.05  3.000
 G2C  C5'   C4'  C3'   109.69  3.000
 G2C  O4'   C4'  C3'   103.37  3.000
 G2C  C4'   O4'  C1'   109.64  3.000
 G2C  H5'A  C5'  H5'   107.37  3.000
 G2C  H5'A  C5'  O5'   110.11  3.000
 G2C  H5'   C5'  O5'   109.85  3.000
 G2C  H5'A  C5'  C4'   111.23  3.000
 G2C  H5'   C5'  C4'   108.13  3.000
 G2C  O5'   C5'  C4'   110.09  3.000
 G2C  C5'   O5'  PA    118.37  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_17  HN2   N2   C2   N1   180.00   0.0  0
 G2C  CONST_18  HN2A  N2   C2   N1     0.00   0.0  0
 G2C  Var_01    C4'   C5'  O5'  PA  -164.65  30.0  2
 G2C  Var_02    O1B   PB   O3A  PA    87.36  30.0  1
 G2C  Var_03    O1A   PA   O3A  PB    50.82  30.0  2
 G2C  Var_04    O1G   PG   C3B  PB   167.75  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
 G2C  chir_06  PA   O2A  O3A  O5'  both
 G2C  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
 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

