# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 09:58:49 2020
#   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  45  32  .  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_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  -0.726  -7.2072   2.4702   0.1486
 G1C  C2    C   CR6    0   0.687  -7.0461   1.7080   1.2704
 G1C  N2    N   NH2    0  -0.832  -7.9730   1.8355   2.2319
 G1C  N3    N   N      0  -0.515  -6.0644   0.8540   1.4177
 G1C  C4    C   CR56   0   0.504  -5.2421   0.8091   0.3595
 G1C  C5    C   CR56   0  -0.090  -5.3158   1.5303  -0.8181
 G1C  C6    C   CR6    0   0.503  -6.3814   2.4613  -0.9832
 G1C  O6    O   O      0  -0.474  -6.6238   3.1869  -1.9330
 G1C  N7    N   N      0  -0.444  -4.2825   1.1962  -1.6535
 G1C  C8    C   CR15   0   0.090  -3.6082   0.2996  -0.9999
 G1C  N9    N   NR5    0  -0.523  -4.1405   0.0242   0.2342
 G1C  PA    P   P      0   1.338   1.9318  -1.9399  -0.0399
 G1C  PB    P   P      0   1.305   4.1737  -0.2175   0.7652
 G1C  PG    P   P      0   1.181   5.2688   2.0788  -1.0911
 G1C  C1'   C   CR15   0   0.177  -3.6804  -0.9467   1.2206
 G1C  O1A   O   OP    -1  -0.808   2.0041  -1.4856  -1.4677
 G1C  O1B   O   OP    -1  -0.806   5.0368  -1.2219   0.0568
 G1C  O1G   O   OP    -1  -0.894   5.8139   1.0908  -2.1220
 G1C  C2'   C   CH2    0  -0.540  -4.2062  -2.3545   0.9622
 G1C  O2A   O   O      0  -0.806   2.2838  -3.3569   0.3019
 G1C  O2B   O   O      0  -0.799   4.5392   0.2637   2.1377
 G1C  O2G   O   OP    -1  -0.901   4.6615   3.3389  -1.7103
 G1C  C3'   C   CR15   0   0.013  -3.0751  -2.9917   0.1614
 G1C  O3'   O   OH1    0  -0.661  -2.9685  -4.3833   0.2711
 G1C  O3A   O   O2     0  -0.746   2.6545  -0.9051   0.9777
 G1C  C3B   C   CH1    0  -0.776   3.7885   1.1593  -0.3691
 G1C  CL3B  CL  CL     0  -0.252   2.6874   2.3112   0.5120
 G1C  O3G   O   O      0  -0.895   6.2017   2.3451   0.0892
 G1C  C4'   C   CR15   0   0.001  -1.8531  -2.3290   0.7920
 G1C  O4'   O   O      0  -0.493  -2.2844  -1.0202   1.1578
 G1C  C5'   C   CH2    0  -0.148  -0.6601  -2.2495  -0.1290
 G1C  O5'   O   O2     0  -0.621   0.4094  -1.6275   0.5393
 G1C  HN1   H   HNR6   0   0.425  -7.9983   3.1002   0.1069
 G1C  HN2   H   HNH2   0   0.414  -8.5888   2.6304   2.2525
 G1C  HN2A  H   HNH2   0   0.412  -7.7823   1.3984   3.1177
 G1C  H8    H   HCR5   0   0.287  -2.7123  -0.1828  -1.3572
 G1C  H1'   H   HCR5   0   0.271  -4.0045  -0.5639   2.1906
 G1C  H2'   H   HCH2   0   0.266  -4.3162  -2.8794   1.9138
 G1C  H2'A  H   HCH2   0   0.279  -5.1712  -2.3558   0.4568
 G1C  H3'   H   HCR5   0   0.218  -3.1542  -2.6893  -0.8935
 G1C  HO3'  H   HOH1   0   0.461  -3.6748  -4.7850  -0.2437
 G1C  H3B   H   HCH1   0   0.268   3.1857   0.7609  -1.1861
 G1C  H4'   H   HCR5   0   0.236  -1.5756  -2.8869   1.6971
 G1C  H5'   H   HCH2   0   0.213  -0.4160  -3.2754  -0.4329
 G1C  H5'A  H   HCH2   0   0.205  -0.9292  -1.7009  -1.0414

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    1.342  0.020  1.342
 G1C  C2   N3    double    1.309  0.020  1.309
 G1C  N2   HN2   single    0.890  0.020  1.040
 G1C  N2   HN2A  single    0.890  0.020  1.040
 G1C  N3   C4    single    1.341  0.020  1.341
 G1C  C4   C5    aromatic  1.383  0.020  1.383
 G1C  C4   N9    aromatic  1.358  0.020  1.358
 G1C  C5   C6    single    1.425  0.020  1.425
 G1C  C5   N7    aromatic  1.370  0.020  1.370
 G1C  C6   O6    double    1.220  0.020  1.220
 G1C  N7   C8    aromatic  1.298  0.020  1.298
 G1C  C8   N9    aromatic  1.372  0.020  1.372
 G1C  C8   H8    single    0.930  0.020  1.080
 G1C  N9   C1'   single    1.459  0.020  1.459
 G1C  PA   O1A   deloc     1.500  0.020  1.500
 G1C  PA   O2A   deloc     1.500  0.020  1.500
 G1C  PA   O3A   single    1.621  0.020  1.621
 G1C  PA   O5'   single    1.659  0.020  1.659
 G1C  PB   O1B   deloc     1.502  0.020  1.502
 G1C  PB   O2B   deloc     1.500  0.020  1.500
 G1C  PB   O3A   single    1.681  0.020  1.681
 G1C  PB   C3B   single    1.825  0.020  1.825
 G1C  PG   O1G   deloc     1.528  0.020  1.528
 G1C  PG   O2G   deloc     1.530  0.020  1.530
 G1C  PG   C3B   single    1.886  0.020  1.886
 G1C  PG   O3G   deloc     1.528  0.020  1.528
 G1C  C1'  C2'   single    1.525  0.020  1.525
 G1C  C1'  O4'   single    1.399  0.020  1.399
 G1C  C1'  H1'   single    0.970  0.020  1.090
 G1C  C2'  C3'   single    1.525  0.020  1.525
 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    1.400  0.020  1.400
 G1C  C3'  C4'   single    1.526  0.020  1.526
 G1C  C3'  H3'   single    0.970  0.020  1.090
 G1C  O3'  HO3'  single    0.850  0.020  0.980
 G1C  C3B  CL3B  single    1.821  0.020  1.821
 G1C  C3B  H3B   single    0.970  0.020  1.090
 G1C  C4'  O4'   single    1.426  0.020  1.426
 G1C  C4'  C5'   single    1.509  0.020  1.509
 G1C  C4'  H4'   single    0.970  0.020  1.090
 G1C  C5'  O5'   single    1.406  0.020  1.406
 G1C  C5'  H5'   single    0.970  0.020  1.090
 G1C  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
 G1C  HN1   N1   C6    115.55  3.000
 G1C  HN1   N1   C2    118.26  3.000
 G1C  C6    N1   C2    126.19  3.000
 G1C  N3    C2   N2    119.95  3.000
 G1C  N3    C2   N1    123.01  3.000
 G1C  N2    C2   N1    117.01  3.000
 G1C  HN2A  N2   HN2   116.20  3.000
 G1C  HN2A  N2   C2    117.31  3.000
 G1C  HN2   N2   C2    120.85  3.000
 G1C  C4    N3   C2    113.13  3.000
 G1C  N9    C4   C5    105.42  3.000
 G1C  N9    C4   N3    126.12  3.000
 G1C  C5    C4   N3    128.45  3.000
 G1C  N7    C5   C6    130.75  3.000
 G1C  N7    C5   C4    110.60  3.000
 G1C  C6    C5   C4    118.64  3.000
 G1C  O6    C6   C5    128.88  3.000
 G1C  O6    C6   N1    120.55  3.000
 G1C  C5    C6   N1    110.57  3.000
 G1C  C8    N7   C5    104.66  3.000
 G1C  H8    C8   N9    122.05  3.000
 G1C  H8    C8   N7    125.00  3.000
 G1C  N9    C8   N7    112.95  3.000
 G1C  C1'   N9   C8    128.28  3.000
 G1C  C1'   N9   C4    125.31  3.000
 G1C  C8    N9   C4    106.37  3.000
 G1C  O5'   PA   O3A    94.00  3.000
 G1C  O5'   PA   O2A   108.29  3.000
 G1C  O3A   PA   O2A   110.82  3.000
 G1C  O5'   PA   O1A   108.64  3.000
 G1C  O3A   PA   O1A   112.49  3.000
 G1C  O2A   PA   O1A   119.46  3.000
 G1C  C3B   PB   O3A   101.33  3.000
 G1C  C3B   PB   O2B   112.22  3.000
 G1C  O3A   PB   O2B   103.64  3.000
 G1C  C3B   PB   O1B   109.43  3.000
 G1C  O3A   PB   O1B   107.79  3.000
 G1C  O2B   PB   O1B   120.41  3.000
 G1C  O3G   PG   C3B   105.57  3.000
 G1C  O3G   PG   O2G   114.30  3.000
 G1C  C3B   PG   O2G   104.18  3.000
 G1C  O3G   PG   O1G   114.58  3.000
 G1C  C3B   PG   O1G   102.88  3.000
 G1C  O2G   PG   O1G   113.65  3.000
 G1C  H1'   C1'  O4'   110.76  3.000
 G1C  H1'   C1'  C2'   111.83  3.000
 G1C  O4'   C1'  C2'   106.74  3.000
 G1C  H1'   C1'  N9    105.89  3.000
 G1C  O4'   C1'  N9    108.62  3.000
 G1C  C2'   C1'  N9    113.03  3.000
 G1C  H2'A  C2'  H2'   108.33  3.000
 G1C  H2'A  C2'  C3'   114.38  3.000
 G1C  H2'   C2'  C3'   109.34  3.000
 G1C  H2'A  C2'  C1'   112.66  3.000
 G1C  H2'   C2'  C1'   109.32  3.000
 G1C  C3'   C2'  C1'   102.64  3.000
 G1C  H3'   C3'  C4'   109.53  3.000
 G1C  H3'   C3'  O3'   110.72  3.000
 G1C  C4'   C3'  O3'   109.77  3.000
 G1C  H3'   C3'  C2'   109.58  3.000
 G1C  C4'   C3'  C2'   101.27  3.000
 G1C  O3'   C3'  C2'   115.50  3.000
 G1C  HO3'  O3'  C3'   108.50  3.000
 G1C  PB    O3A  PA    125.77  3.000
 G1C  H3B   C3B  CL3B  105.03  3.000
 G1C  H3B   C3B  PG    108.97  3.000
 G1C  CL3B  C3B  PG    110.57  3.000
 G1C  H3B   C3B  PB    107.85  3.000
 G1C  CL3B  C3B  PB    107.70  3.000
 G1C  PG    C3B  PB    116.11  3.000
 G1C  H4'   C4'  C5'   109.25  3.000
 G1C  H4'   C4'  O4'   109.34  3.000
 G1C  C5'   C4'  O4'   110.32  3.000
 G1C  H4'   C4'  C3'   108.78  3.000
 G1C  C5'   C4'  C3'   113.80  3.000
 G1C  O4'   C4'  C3'   105.21  3.000
 G1C  C4'   O4'  C1'   111.19  3.000
 G1C  H5'A  C5'  H5'   106.94  3.000
 G1C  H5'A  C5'  O5'   111.12  3.000
 G1C  H5'   C5'  O5'   112.08  3.000
 G1C  H5'A  C5'  C4'   109.86  3.000
 G1C  H5'   C5'  C4'   107.19  3.000
 G1C  O5'   C5'  C4'   109.54  3.000
 G1C  C5'   O5'  PA    116.67  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_18  HN2A  N2   C2   N1  180.00   0.0  0
 G1C  Var_01    C4'   C5'  O5'  PA  157.61  30.0  2
 G1C  Var_02    O1B   PB   O3A  PA  -33.37  30.0  2
 G1C  Var_03    O1A   PA   O3A  PB  -46.98  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
 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

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

