# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Aug  1 08:55:06 2021
#   Inital geometry file: a 125 line input string
#   Ligand name: 5'-O-[(R)-{[(S)-[(S)-chloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2'-deoxyguanosine
#   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@@H](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
 G1C  G1C  5'-O-[(R)-{[(S)-[(S)-chloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2'-deoxyguanosine  ligand  49  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_G1C
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
 G1C  N1    N   NR16  0  -0.728   0.6509   3.6082   1.1255
 G1C  C2    C   CR6   0   0.699   0.2529   2.3078   1.2497
 G1C  N2    N   NH2   0  -0.832  -0.7761   1.9103   0.4948
 G1C  N3    N   N     0  -0.515   0.8495   1.4522   2.0452
 G1C  C4    C   CR56  0   0.514   1.8834   1.9827   2.7066
 G1C  C5    C   CR56  0  -0.095   2.3657   3.2752   2.6558
 G1C  C6    C   CR6   0   0.508   1.7210   4.2127   1.7980
 G1C  O6    O   O     0  -0.471   1.9891   5.3869   1.6101
 G1C  N7    N   N     0  -0.437   3.4408   3.4261   3.4951
 G1C  C8    C   CR15  0   0.103   3.6076   2.2616   4.0337
 G1C  N9    N   NR5   0  -0.549   2.6971   1.3292   3.5869
 G1C  PA    P   P     0   1.486   3.2901   2.1525   8.5575
 G1C  PB    P   P     0   1.427   0.6627   2.4724   9.7396
 G1C  PG    P   P     0   1.394  -0.7799   1.2903   7.2638
 G1C  C1'   C   CH1   0   0.234   2.5241  -0.0231   4.0373
 G1C  O1A   O   OH1   0  -0.713   3.9367   3.0249   7.4030
 G1C  O1B   O   OH1   0  -0.711   0.5598   3.7768  10.6419
 G1C  O1G   O   OH1   0  -0.765   0.2561   1.8316   6.2018
 G1C  C2'   C   CH2   0  -0.560   3.8093  -0.8336   4.1473
 G1C  O2A   O   O     0  -0.675   4.1004   1.9295   9.7631
 G1C  O2B   O   O     0  -0.659   0.8211   1.1743  10.4157
 G1C  O2G   O   OH1   0  -0.728  -2.1580   1.5916   6.5095
 G1C  C3'   C   CH1   0   0.004   3.5150  -1.7799   5.2993
 G1C  O3'   O   OH1   0  -0.665   2.7612  -2.8524   4.7974
 G1C  O3A   O   O2    0  -0.683   1.8939   2.9364   8.7975
 G1C  C3B   C   CH1   0  -0.822  -0.7574   2.5532   8.5999
 G1C  CL3B  CL  CL    0  -0.083  -0.8987   4.1877   7.9052
 G1C  O3G   O   O     0  -0.680  -0.5929  -0.0776   7.7923
 G1C  C4'   C   CH1   0  -0.037   2.6878  -0.8837   6.2254
 G1C  O4'   O   O2    0  -0.544   1.9691  -0.0175   5.3480
 G1C  C5'   C   CH2   0  -0.180   3.5655  -0.0838   7.1662
 G1C  O5'   O   O2    0  -0.586   2.7247   0.8799   7.7998
 G1C  HN1   H   HNR6  0   0.426   0.1481   4.2050   0.4807
 G1C  HN2   H   HNH2  0   0.415  -1.1508   0.9894   0.6447
 G1C  HN2A  H   HNH2  0   0.418  -1.3507   2.5645  -0.0073
 G1C  H8    H   HCR5  0   0.286   4.3719   2.0208   4.7562
 G1C  H1'   H   HCH1  0   0.284   1.8137  -0.4881   3.3526
 G1C  H2'   H   HCH2  0   0.301   4.0405  -1.3565   3.2209
 G1C  H2'A  H   HCH2  0   0.279   4.6663  -0.2023   4.3873
 G1C  H3'   H   HCH1  0   0.266   4.4325  -2.1213   5.7928
 G1C  HO3'  H   HOH1  0   0.459   2.5382  -3.4436   5.5241
 G1C  H3B   H   HCH1  0   0.375  -1.6436   2.3770   9.2187
 G1C  H4'   H   HCH1  0   0.287   1.9566  -1.4513   6.8078
 G1C  H5'   H   HCH2  0   0.273   4.0075  -0.7492   7.9103
 G1C  H5'A  H   HCH2  0   0.245   4.3796   0.4092   6.6272
 G1C  H14   H   HOH1  0   0.511   4.7246   3.5197   7.6674
 G1C  H15   H   HOH1  0   0.510  -0.0060   3.6828  11.4213
 G1C  H16   H   HOH1  0   0.513   0.9118   1.1549   5.8992
 G1C  H17   H   HOH1  0   0.499  -2.9427   1.2564   6.9640

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
 G1C  N1   C2    single    1.366  0.020  1.366
 G1C  N1   C6    single    1.401  0.020  1.401
 G1C  N1   HN1   single    0.860  0.020  1.020
 G1C  C2   N2    single    1.337  0.020  1.337
 G1C  C2   N3    double    1.312  0.020  1.312
 G1C  N2   HN2   single    0.860  0.020  1.020
 G1C  N2   HN2A  single    0.860  0.020  1.020
 G1C  N3   C4    single    1.337  0.020  1.337
 G1C  C4   C5    aromatic  1.380  0.020  1.380
 G1C  C4   N9    aromatic  1.365  0.020  1.365
 G1C  C5   C6    single    1.425  0.020  1.425
 G1C  C5   N7    aromatic  1.372  0.020  1.372
 G1C  C6   O6    double    1.219  0.020  1.219
 G1C  N7   C8    aromatic  1.294  0.020  1.294
 G1C  C8   N9    aromatic  1.378  0.020  1.378
 G1C  C8   H8    single    0.930  0.020  1.080
 G1C  N9   C1'   single    1.436  0.020  1.436
 G1C  PA   O1A   single    1.585  0.020  1.585
 G1C  PA   O2A   double    1.470  0.020  1.470
 G1C  PA   O3A   single    1.619  0.020  1.619
 G1C  PA   O5'   single    1.585  0.020  1.585
 G1C  PB   O1B   single    1.589  0.020  1.589
 G1C  PB   O2B   double    1.472  0.020  1.472
 G1C  PB   O3A   single    1.618  0.020  1.618
 G1C  PB   C3B   single    1.823  0.020  1.823
 G1C  PG   O1G   single    1.579  0.020  1.579
 G1C  PG   O2G   single    1.600  0.020  1.600
 G1C  PG   C3B   single    1.839  0.020  1.839
 G1C  PG   O3G   double    1.478  0.020  1.478
 G1C  C1'  C2'   single    1.523  0.020  1.523
 G1C  C1'  O4'   single    1.423  0.020  1.423
 G1C  C1'  H1'   single    0.970  0.020  1.090
 G1C  C2'  C3'   single    1.520  0.020  1.520
 G1C  C2'  H2'   single    0.970  0.020  1.090
 G1C  C2'  H2'A  single    0.970  0.020  1.090
 G1C  C3'  O3'   single    1.404  0.020  1.404
 G1C  C3'  C4'   single    1.531  0.020  1.531
 G1C  C3'  H3'   single    0.970  0.020  1.090
 G1C  O3'  HO3'  single    0.850  0.020  0.980
 G1C  C3B  CL3B  single    1.782  0.020  1.782
 G1C  C3B  H3B   single    0.970  0.020  1.090
 G1C  C4'  O4'   single    1.427  0.020  1.427
 G1C  C4'  C5'   single    1.515  0.020  1.515
 G1C  C4'  H4'   single    0.970  0.020  1.090
 G1C  C5'  O5'   single    1.427  0.020  1.427
 G1C  C5'  H5'   single    0.970  0.020  1.090
 G1C  C5'  H5'A  single    0.970  0.020  1.090
 G1C  O1A  H14   single    0.850  0.020  0.980
 G1C  O1B  H15   single    0.850  0.020  0.980
 G1C  O1G  H16   single    0.850  0.020  0.980
 G1C  O2G  H17   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
 G1C  HN1   N1   C6    115.52  3.000
 G1C  HN1   N1   C2    118.33  3.000
 G1C  C6    N1   C2    126.15  3.000
 G1C  N3    C2   N2    119.91  3.000
 G1C  N3    C2   N1    122.93  3.000
 G1C  N2    C2   N1    117.14  3.000
 G1C  HN2A  N2   HN2   117.23  3.000
 G1C  HN2A  N2   C2    121.92  3.000
 G1C  HN2   N2   C2    118.36  3.000
 G1C  C4    N3   C2    113.14  3.000
 G1C  N9    C4   C5    105.29  3.000
 G1C  N9    C4   N3    126.15  3.000
 G1C  C5    C4   N3    128.56  3.000
 G1C  N7    C5   C6    130.57  3.000
 G1C  N7    C5   C4    110.74  3.000
 G1C  C6    C5   C4    118.69  3.000
 G1C  O6    C6   C5    128.83  3.000
 G1C  O6    C6   N1    120.64  3.000
 G1C  C5    C6   N1    110.52  3.000
 G1C  C8    N7   C5    104.87  3.000
 G1C  H8    C8   N9    122.30  3.000
 G1C  H8    C8   N7    124.81  3.000
 G1C  N9    C8   N7    112.89  3.000
 G1C  C1'   N9   C8    127.98  3.000
 G1C  C1'   N9   C4    125.54  3.000
 G1C  C8    N9   C4    106.20  3.000
 G1C  O5'   PA   O3A    98.74  3.000
 G1C  O5'   PA   O2A   117.83  3.000
 G1C  O3A   PA   O2A   115.30  3.000
 G1C  O5'   PA   O1A   103.84  3.000
 G1C  O3A   PA   O1A   101.14  3.000
 G1C  O2A   PA   O1A   117.14  3.000
 G1C  C3B   PB   O3A   102.48  3.000
 G1C  C3B   PB   O2B   114.21  3.000
 G1C  O3A   PB   O2B   116.00  3.000
 G1C  C3B   PB   O1B   105.56  3.000
 G1C  O3A   PB   O1B    98.31  3.000
 G1C  O2B   PB   O1B   118.03  3.000
 G1C  O3G   PG   C3B   111.98  3.000
 G1C  O3G   PG   O2G   116.86  3.000
 G1C  C3B   PG   O2G   102.93  3.000
 G1C  O3G   PG   O1G   118.33  3.000
 G1C  C3B   PG   O1G   104.20  3.000
 G1C  O2G   PG   O1G   100.58  3.000
 G1C  H1'   C1'  O4'   109.01  3.000
 G1C  H1'   C1'  C2'   111.59  3.000
 G1C  O4'   C1'  C2'   105.34  3.000
 G1C  H1'   C1'  N9    106.45  3.000
 G1C  O4'   C1'  N9    109.40  3.000
 G1C  C2'   C1'  N9    114.97  3.000
 G1C  H14   O1A  PA    114.51  3.000
 G1C  H15   O1B  PB    114.55  3.000
 G1C  H16   O1G  PG    113.95  3.000
 G1C  H2'A  C2'  H2'   107.36  3.000
 G1C  H2'A  C2'  C3'   110.23  3.000
 G1C  H2'   C2'  C3'   112.77  3.000
 G1C  H2'A  C2'  C1'   111.76  3.000
 G1C  H2'   C2'  C1'   111.92  3.000
 G1C  C3'   C2'  C1'   102.87  3.000
 G1C  H17   O2G  PG    114.35  3.000
 G1C  H3'   C3'  C4'   111.23  3.000
 G1C  H3'   C3'  O3'   111.87  3.000
 G1C  C4'   C3'  O3'   111.92  3.000
 G1C  H3'   C3'  C2'   111.90  3.000
 G1C  C4'   C3'  C2'   101.45  3.000
 G1C  O3'   C3'  C2'   107.98  3.000
 G1C  HO3'  O3'  C3'   108.88  3.000
 G1C  PB    O3A  PA    127.13  3.000
 G1C  H3B   C3B  CL3B  107.68  3.000
 G1C  H3B   C3B  PG    106.87  3.000
 G1C  CL3B  C3B  PG    110.23  3.000
 G1C  H3B   C3B  PB    105.67  3.000
 G1C  CL3B  C3B  PB    110.26  3.000
 G1C  PG    C3B  PB    115.69  3.000
 G1C  H4'   C4'  C5'   109.31  3.000
 G1C  H4'   C4'  O4'   107.80  3.000
 G1C  C5'   C4'  O4'   110.67  3.000
 G1C  H4'   C4'  C3'   112.30  3.000
 G1C  C5'   C4'  C3'   111.81  3.000
 G1C  O4'   C4'  C3'   104.80  3.000
 G1C  C4'   O4'  C1'   111.55  3.000
 G1C  H5'A  C5'  H5'   108.01  3.000
 G1C  H5'A  C5'  O5'   110.67  3.000
 G1C  H5'   C5'  O5'   110.34  3.000
 G1C  H5'A  C5'  C4'   111.30  3.000
 G1C  H5'   C5'  C4'   109.63  3.000
 G1C  O5'   C5'  C4'   106.91  3.000
 G1C  C5'   O5'  PA    122.96  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
 G1C  CONST_01  C8    N7   C5   C4     0.00   0.0  0
 G1C  CONST_02  N7    C8   N9   C4     0.00   0.0  0
 G1C  CONST_03  C8    N9   C4   C5     0.00   0.0  0
 G1C  CONST_04  N9    C8   N7   C5     0.00   0.0  0
 G1C  CONST_05  N9    C4   C5   N7     0.00   0.0  0
 G1C  CONST_06  C1'   N9   C4   N3     0.00   0.0  0
 G1C  CONST_07  C1'   N9   C4   C5   180.00   0.0  0
 G1C  CONST_08  C1'   N9   C8   N7   180.00   0.0  0
 G1C  CONST_09  C4    N3   C2   N1     0.00   0.0  0
 G1C  CONST_10  C5    C6   N1   C2     0.00   0.0  0
 G1C  CONST_11  C6    N1   C2   N3     0.00   0.0  0
 G1C  CONST_12  O6    C6   N1   C2   180.00   0.0  0
 G1C  CONST_13  C6    N1   C2   N2   180.00   0.0  0
 G1C  CONST_14  C4    N3   C2   N2   180.00   0.0  0
 G1C  CONST_15  H8    C8   N9   C4   180.00   0.0  0
 G1C  CONST_16  HN1   N1   C2   N3   180.00   0.0  0
 G1C  CONST_17  HN2   N2   C2   N1   180.00   0.0  0
 G1C  CONST_18  HN2A  N2   C2   N1     0.00   0.0  0
 G1C  Var_01    C4'   C5'  O5'  PA  -163.32  30.0  2
 G1C  Var_02    O1B   PB   O3A  PA   124.79  30.0  1
 G1C  Var_03    O1A   PA   O3A  PB   172.52  30.0  1

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
 G1C  chir_03  C1'  N9   C2'  O4'   negativ
 G1C  chir_04  C3'  O3'  C4'  C2'   positiv
 G1C  chir_05  C3B  PB   PG   CL3B  positiv
 G1C  chir_06  C4'  O4'  C5'  C3'   positiv
 G1C  chir_07  PA   O2A  O3A  O5'   both
 G1C  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
 G1C  plan-1  N1    0.020
 G1C  plan-1  C2    0.020
 G1C  plan-1  N2    0.020
 G1C  plan-1  N3    0.020
 G1C  plan-1  C4    0.020
 G1C  plan-1  C5    0.020
 G1C  plan-1  C6    0.020
 G1C  plan-1  O6    0.020
 G1C  plan-1  N7    0.020
 G1C  plan-1  C8    0.020
 G1C  plan-1  N9    0.020
 G1C  plan-1  C1'   0.020
 G1C  plan-1  HN1   0.020
 G1C  plan-1  HN2   0.020
 G1C  plan-1  HN2A  0.020
 G1C  plan-1  H8    0.020

