# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 12 03:03:33 2022
#   Inital geometry file: a 125 line input string
#   Ligand name: 5'-O-[(R)-{[(R)-[(R)-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
 GRC  GRC  5'-O-[(R)-{[(R)-[(R)-chloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2'-deoxyguanosine  ligand  45  32  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GRC
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
 GRC  N1   N   NR16   0  -0.725   9.7338  8.3323   8.5246
 GRC  C2   C   CR6    0   0.676   8.5598  8.3664   7.8281
 GRC  N2   N   NH2    0  -0.831   8.6437  8.5679   6.5017
 GRC  N3   N   N      0  -0.514   7.3884  8.2484   8.3995
 GRC  C4   C   CR56   0   0.496   7.4648  8.0923   9.7313
 GRC  C5   C   CR56   0  -0.087   8.5943  8.0404  10.5275
 GRC  C6   C   CR6    0   0.495   9.8720  8.1680   9.9103
 GRC  O6   O   O      0  -0.467  10.9788  8.1485  10.4215
 GRC  N7   N   N      0  -0.449   8.2494  7.8538  11.8401
 GRC  C8   C   CR15   0   0.070   6.9500  7.7926  11.8353
 GRC  N9   N   NR5    0  -0.524   6.4163  7.9363  10.5792
 GRC  PA   P   P      0   1.358   4.6733  5.5554  14.9281
 GRC  PB   P   P      0   1.334   3.8391  2.8825  13.6471
 GRC  PG   P   P      0   1.190   4.9718  1.1686  16.1773
 GRC  C1'  C   CH1    0   0.190   5.0101  7.8985  10.1682
 GRC  O1A  O   OP    -1  -0.797   3.4681  5.5829  15.8115
 GRC  O1B  O   O      0  -0.797   3.8988  2.8304  12.1252
 GRC  O1G  O   OP    -1  -0.873   5.0925  2.5571  16.8085
 GRC  C2'  C   CH2    0  -0.535   4.6172  6.5467   9.5865
 GRC  O2A  O   O      0  -0.786   6.0483  5.8382  15.4410
 GRC  O2B  O   OP    -1  -0.783   2.4853  2.9222  14.2882
 GRC  O2G  O   OP    -1  -0.892   6.2318  0.3107  16.3083
 GRC  C3'  C   CH1    0   0.024   4.1150  5.8003  10.8170
 GRC  O3'  O   OH1    0  -0.719   3.2702  4.7392  10.5203
 GRC  O3A  O   O2     0  -0.748   4.7685  4.1795  14.0508
 GRC  C3B  C   CH1    0  -0.773   4.9286  1.5601  14.3092
 GRC  CL1  CL  CL     0  -0.245   4.5415  0.0346  13.3792
 GRC  O3G  O   O      0  -0.884   3.6716  0.4332  16.4887
 GRC  C4'  C   CH1    0   0.016   3.4157  6.9433  11.5589
 GRC  O4'  O   O2     0  -0.499   4.2044  8.1047  11.2901
 GRC  C5'  C   CH2    0  -0.187   3.2207  6.7570  13.0449
 GRC  O5'  O   O2     0  -0.617   4.4585  6.6436  13.7020
 GRC  H1   H   HNR6   0   0.422  10.6001  8.4395   8.0119
 GRC  H2   H   HNH2   0   0.409   7.8055  8.4238   5.9638
 GRC  H3   H   HNH2   0   0.411   9.5105  8.4110   6.0147
 GRC  H4   H   HCR5   0   0.298   6.3290  7.6405  12.7033
 GRC  H5   H   HCH1   0   0.262   4.8793  8.7143   9.4528
 GRC  H8   H   HCH2   0   0.250   3.7955  6.6847   8.8783
 GRC  H9   H   HCH2   0   0.266   5.4367  6.0562   9.0622
 GRC  H12  H   HCH1   0   0.208   4.9799  5.4705  11.4089
 GRC  H13  H   HOH1   0   0.455   3.4642  3.9984  11.1628
 GRC  H14  H   HCH1   0   0.255   5.9443  1.8131  13.9957
 GRC  H15  H   HCH1   0   0.217   2.4169  7.0748  11.1172
 GRC  H16  H   HCH2   0   0.223   2.6551  7.6022  13.4538
 GRC  H17  H   HCH2   0   0.209   2.5858  5.8717  13.1718

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
 GRC  N2   C2   single    1.344  0.020  1.344
 GRC  C2   N1   single    1.366  0.020  1.366
 GRC  C2   N3   double    1.309  0.020  1.309
 GRC  N1   C6   single    1.402  0.020  1.402
 GRC  N3   C4   single    1.343  0.020  1.343
 GRC  C6   O6   double    1.219  0.020  1.219
 GRC  C6   C5   single    1.425  0.020  1.425
 GRC  C4   C5   aromatic  1.383  0.020  1.383
 GRC  C4   N9   aromatic  1.357  0.020  1.357
 GRC  C2'  C1'  single    1.523  0.020  1.523
 GRC  C2'  C3'  single    1.524  0.020  1.524
 GRC  C1'  N9   single    1.466  0.020  1.466
 GRC  C1'  O4'  single    1.397  0.020  1.397
 GRC  C5   N7   aromatic  1.370  0.020  1.370
 GRC  N9   C8   aromatic  1.372  0.020  1.372
 GRC  O3'  C3'  single    1.388  0.020  1.388
 GRC  C3'  C4'  single    1.532  0.020  1.532
 GRC  O4'  C4'  single    1.429  0.020  1.429
 GRC  N7   C8   aromatic  1.301  0.020  1.301
 GRC  C4'  C5'  single    1.510  0.020  1.510
 GRC  O1B  PB   deloc     1.524  0.020  1.524
 GRC  C5'  O5'  single    1.406  0.020  1.406
 GRC  O5'  PA   single    1.653  0.020  1.653
 GRC  PB   O3A  single    1.646  0.020  1.646
 GRC  PB   O2B  deloc     1.498  0.020  1.498
 GRC  PB   C3B  single    1.837  0.020  1.837
 GRC  O3A  PA   single    1.635  0.020  1.635
 GRC  CL1  C3B  single    1.828  0.020  1.828
 GRC  PA   O2A  deloc     1.495  0.020  1.495
 GRC  PA   O1A  deloc     1.495  0.020  1.495
 GRC  C3B  PG   single    1.909  0.020  1.909
 GRC  O3G  PG   deloc     1.526  0.020  1.526
 GRC  PG   O1G  deloc     1.530  0.020  1.530
 GRC  PG   O2G  deloc     1.530  0.020  1.530
 GRC  N1   H1   single    0.860  0.020  1.020
 GRC  N2   H2   single    0.890  0.020  1.040
 GRC  N2   H3   single    0.890  0.020  1.040
 GRC  C8   H4   single    0.930  0.020  1.080
 GRC  C1'  H5   single    0.970  0.020  1.090
 GRC  C2'  H8   single    0.970  0.020  1.090
 GRC  C2'  H9   single    0.970  0.020  1.090
 GRC  C3'  H12  single    0.970  0.020  1.090
 GRC  O3'  H13  single    0.850  0.020  0.980
 GRC  C3B  H14  single    0.970  0.020  1.090
 GRC  C4'  H15  single    0.970  0.020  1.090
 GRC  C5'  H16  single    0.970  0.020  1.090
 GRC  C5'  H17  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
 GRC  H1   N1   C6   115.38  3.000
 GRC  H1   N1   C2   118.34  3.000
 GRC  C6   N1   C2   126.28  3.000
 GRC  N3   C2   N2   120.02  3.000
 GRC  N3   C2   N1   123.00  3.000
 GRC  N2   C2   N1   116.96  3.000
 GRC  H3   N2   H2   115.87  3.000
 GRC  H3   N2   C2   120.52  3.000
 GRC  H2   N2   C2   117.00  3.000
 GRC  C4   N3   C2   113.11  3.000
 GRC  N9   C4   C5   105.48  3.000
 GRC  N9   C4   N3   126.08  3.000
 GRC  C5   C4   N3   128.44  3.000
 GRC  N7   C5   C6   130.78  3.000
 GRC  N7   C5   C4   110.56  3.000
 GRC  C6   C5   C4   118.66  3.000
 GRC  O6   C6   C5   129.12  3.000
 GRC  C5   C6   N1   110.50  3.000
 GRC  O6   C6   N1   120.38  3.000
 GRC  C8   N7   C5   104.74  3.000
 GRC  H4   C8   N9   121.84  3.000
 GRC  H4   C8   N7   125.39  3.000
 GRC  N9   C8   N7   112.77  3.000
 GRC  C1'  N9   C8   128.85  3.000
 GRC  C8   N9   C4   106.46  3.000
 GRC  C1'  N9   C4   124.67  3.000
 GRC  O5'  PA   O3A   99.42  3.000
 GRC  O3A  PA   O2A  106.86  3.000
 GRC  O5'  PA   O2A  104.45  3.000
 GRC  O2A  PA   O1A  122.38  3.000
 GRC  O3A  PA   O1A  112.31  3.000
 GRC  O5'  PA   O1A  108.75  3.000
 GRC  C3B  PB   O3A   98.28  3.000
 GRC  C3B  PB   O2B  113.63  3.000
 GRC  O3A  PB   O2B  112.60  3.000
 GRC  C3B  PB   O1B  108.19  3.000
 GRC  O2B  PB   O1B  117.62  3.000
 GRC  O3A  PB   O1B  104.46  3.000
 GRC  O3G  PG   C3B  106.21  3.000
 GRC  O3G  PG   O2G  114.46  3.000
 GRC  C3B  PG   O2G  102.55  3.000
 GRC  O2G  PG   O1G  114.12  3.000
 GRC  O3G  PG   O1G  114.86  3.000
 GRC  C3B  PG   O1G  102.67  3.000
 GRC  H5   C1'  O4'  110.28  3.000
 GRC  H5   C1'  C2'  112.43  3.000
 GRC  O4'  C1'  C2'  106.80  3.000
 GRC  H5   C1'  N9   106.21  3.000
 GRC  O4'  C1'  N9   108.93  3.000
 GRC  C2'  C1'  N9   112.18  3.000
 GRC  H9   C2'  H8   108.08  3.000
 GRC  H9   C2'  C3'  114.58  3.000
 GRC  H8   C2'  C3'  109.70  3.000
 GRC  H9   C2'  C1'  112.91  3.000
 GRC  H8   C2'  C1'  109.22  3.000
 GRC  C3'  C2'  C1'  102.19  3.000
 GRC  H12  C3'  C4'  108.81  3.000
 GRC  H12  C3'  O3'  111.39  3.000
 GRC  C4'  C3'  O3'  113.33  3.000
 GRC  H12  C3'  C2'  108.81  3.000
 GRC  C4'  C3'  C2'  100.14  3.000
 GRC  O3'  C3'  C2'  113.72  3.000
 GRC  H13  O3'  C3'  108.12  3.000
 GRC  PB   O3A  PA   139.65  3.000
 GRC  H14  C3B  CL1  104.13  3.000
 GRC  H14  C3B  PG   107.89  3.000
 GRC  CL1  C3B  PG   109.36  3.000
 GRC  H14  C3B  PB   106.34  3.000
 GRC  PG   C3B  PB   120.91  3.000
 GRC  CL1  C3B  PB   106.96  3.000
 GRC  H15  C4'  C5'  107.01  3.000
 GRC  H15  C4'  O4'  109.17  3.000
 GRC  C5'  C4'  O4'  110.89  3.000
 GRC  H15  C4'  C3'  108.01  3.000
 GRC  C5'  C4'  C3'  116.33  3.000
 GRC  O4'  C4'  C3'  105.27  3.000
 GRC  C4'  O4'  C1'  110.45  3.000
 GRC  H17  C5'  H16  106.30  3.000
 GRC  H17  C5'  O5'  112.98  3.000
 GRC  H16  C5'  O5'  110.00  3.000
 GRC  H17  C5'  C4'  106.75  3.000
 GRC  H16  C5'  C4'  109.79  3.000
 GRC  O5'  C5'  C4'  110.86  3.000
 GRC  C5'  O5'  PA   120.94  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
 GRC  CONST_01  C8   N7   C5   C4     0.00   0.0  0
 GRC  CONST_02  N7   C8   N9   C4     0.00   0.0  0
 GRC  CONST_03  C8   N9   C4   C5     0.00   0.0  0
 GRC  CONST_04  N9   C8   N7   C5     0.00   0.0  0
 GRC  CONST_05  N9   C4   C5   N7     0.00   0.0  0
 GRC  CONST_06  C1'  N9   C4   N3     0.00   0.0  0
 GRC  CONST_07  C1'  N9   C4   C5   180.00   0.0  0
 GRC  CONST_08  C1'  N9   C8   N7   180.00   0.0  0
 GRC  CONST_09  C4   N3   C2   N1     0.00   0.0  0
 GRC  CONST_10  C5   C6   N1   C2     0.00   0.0  0
 GRC  CONST_11  C6   N1   C2   N3     0.00   0.0  0
 GRC  CONST_12  O6   C6   N1   C2   180.00   0.0  0
 GRC  CONST_13  C6   N1   C2   N2   180.00   0.0  0
 GRC  CONST_14  C4   N3   C2   N2   180.00   0.0  0
 GRC  CONST_15  H4   C8   N9   C4   180.00   0.0  0
 GRC  CONST_16  H1   N1   C2   N3   180.00   0.0  0
 GRC  CONST_17  H2   N2   C2   N1   180.00   0.0  0
 GRC  Var_01    C4'  C5'  O5'  PA  -139.66  30.0  1
 GRC  Var_02    O1B  PB   O3A  PA   126.93  30.0  1
 GRC  Var_03    O5'  PA   O3A  PB  -102.55  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
 GRC  chir_03  C1'  C2'  N9   O4'  positiv
 GRC  chir_04  C3'  O3'  C4'  C2'  positiv
 GRC  chir_05  C3B  PB   CL1  PG   positiv
 GRC  chir_06  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
 GRC  plan-1  N1   0.020
 GRC  plan-1  C2   0.020
 GRC  plan-1  N2   0.020
 GRC  plan-1  N3   0.020
 GRC  plan-1  C4   0.020
 GRC  plan-1  C5   0.020
 GRC  plan-1  C6   0.020
 GRC  plan-1  O6   0.020
 GRC  plan-1  N7   0.020
 GRC  plan-1  C8   0.020
 GRC  plan-1  N9   0.020
 GRC  plan-1  C1'  0.020
 GRC  plan-1  H1   0.020
 GRC  plan-1  H2   0.020
 GRC  plan-1  H3   0.020
 GRC  plan-1  H4   0.020

