# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 06:11:25 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: 2'-deoxyguanosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)c2ncn([C@H]3C[C@H](O)[C@@H](CO)O3)c2N1
#
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
 GNG  GNG  '2'-deoxyguanosine        '  ligand  32  19  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_GNG
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
 GNG  O5'   O  OH1   0  -0.668  -1.4313   1.1663  -4.7233
 GNG  C5'   C  CH2   0  -0.155  -0.9861  -0.0321  -4.1387
 GNG  C4'   C  CH1   0   0.004   0.2796   0.2374  -3.3653
 GNG  O4'   O  O2    0  -0.494   0.0221   1.1416  -2.2883
 GNG  C1'   C  CH1   0   0.167   0.7329   0.7762  -1.1471
 GNG  N9    N  NR5   0  -0.519  -0.2283   0.3955  -0.1054
 GNG  C8    C  CR15  0   0.081  -1.5546   0.0589  -0.2451
 GNG  N7    N  N     0  -0.442  -2.1092  -0.2666   0.8834
 GNG  C5    C  CR56  0  -0.105  -1.1186  -0.1466   1.8217
 GNG  C4    C  CR56  0   0.630   0.0361   0.2631   1.2118
 GNG  N3    N  NR16  0  -0.739   1.1974   0.4640   1.8875
 GNG  C2    C  CR6   0   0.667   1.1542   0.2391   3.2361
 GNG  N1    N  N     0  -0.538   0.0871  -0.1593   3.8736
 GNG  C6    C  CR6   0   0.416  -1.1201  -0.3732   3.2501
 GNG  O6    O  O     0  -0.493  -2.1051  -0.7329   3.8840
 GNG  N2    N  NH2   0  -0.826   2.2870   0.4790   3.9108
 GNG  C2'   C  CH2   0  -0.547   1.6397  -0.3822  -1.5422
 GNG  C3'   C  CH1   0   0.018   0.8741  -1.0032  -2.7069
 GNG  O3'   O  OH1   0  -0.659   1.6518  -1.7069  -3.6318
 GNG  H5'   H  HOH1  0   0.459  -2.2351   0.9800  -5.2166
 GNG  H5'1  H  HCH2  0   0.214  -0.7541  -0.7964  -4.8913
 GNG  H5'2  H  HCH2  0   0.200  -1.7370  -0.4684  -3.4658
 GNG  H4'   H  HCH1  0   0.243   1.0294   0.6829  -4.0329
 GNG  H1'   H  HCH1  0   0.284   1.2901   1.6325  -0.7590
 GNG  H8    H  HCR5  0   0.295  -2.0504   0.0867  -1.2017
 GNG  HN3   H  HNR6  0   0.440   2.0274   0.8349   1.4476
 GNG  HN21  H  HNH2  0   0.412   2.3215   0.2009   4.8765
 GNG  HN22  H  HNH2  0   0.414   3.1686   0.5856   3.4382
 GNG  H2'1  H  HCH2  0   0.283   1.8364  -1.0739  -0.7231
 GNG  H2'2  H  HCH2  0   0.273   2.5949   0.0101  -1.8981
 GNG  H3'   H  HCH1  0   0.224   0.0602  -1.6308  -2.3162
 GNG  H1    H  HOH1  0   0.462   1.8781  -2.5623  -3.2545

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
 GNG  O5'  C5'   single    1.406  0.020  1.406
 GNG  O5'  H5'   single    0.850  0.020  0.980
 GNG  C5'  C4'   single    1.508  0.020  1.508
 GNG  C5'  H5'1  single    0.970  0.020  1.090
 GNG  C5'  H5'2  single    0.970  0.020  1.090
 GNG  C4'  O4'   single    1.430  0.020  1.430
 GNG  C4'  C3'   single    1.525  0.020  1.525
 GNG  C4'  H4'   single    0.970  0.020  1.090
 GNG  O4'  C1'   single    1.393  0.020  1.393
 GNG  C1'  N9    single    1.468  0.020  1.468
 GNG  C1'  C2'   single    1.523  0.020  1.523
 GNG  C1'  H1'   single    0.970  0.020  1.090
 GNG  N9   C8    aromatic  1.375  0.020  1.375
 GNG  N9   C4    aromatic  1.350  0.020  1.350
 GNG  C8   N7    aromatic  1.299  0.020  1.299
 GNG  C8   H8    single    0.930  0.020  1.080
 GNG  N7   C5    aromatic  1.370  0.020  1.370
 GNG  C5   C4    aromatic  1.369  0.020  1.369
 GNG  C5   C6    single    1.446  0.020  1.446
 GNG  C4   N3    single    1.359  0.020  1.359
 GNG  N3   C2    single    1.368  0.020  1.368
 GNG  N3   HN3   single    0.860  0.020  1.020
 GNG  C2   N1    double    1.305  0.020  1.305
 GNG  C2   N2    single    1.340  0.020  1.340
 GNG  N1   C6    single    1.375  0.020  1.375
 GNG  C6   O6    double    1.225  0.020  1.225
 GNG  N2   HN21  single    0.890  0.020  1.040
 GNG  N2   HN22  single    0.890  0.020  1.040
 GNG  C2'  C3'   single    1.526  0.020  1.526
 GNG  C2'  H2'1  single    0.970  0.020  1.090
 GNG  C2'  H2'2  single    0.970  0.020  1.090
 GNG  C3'  O3'   single    1.398  0.020  1.398
 GNG  C3'  H3'   single    0.970  0.020  1.090
 GNG  O3'  H1    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
 GNG  H5'   O5'  C5'   108.24  3.000
 GNG  H5'2  C5'  H5'1  106.73  3.000
 GNG  H5'2  C5'  C4'   109.31  3.000
 GNG  H5'1  C5'  C4'   107.39  3.000
 GNG  H5'2  C5'  O5'   112.14  3.000
 GNG  H5'1  C5'  O5'   112.05  3.000
 GNG  C4'   C5'  O5'   109.08  3.000
 GNG  H4'   C4'  C3'   109.04  3.000
 GNG  H4'   C4'  O4'   108.93  3.000
 GNG  C3'   C4'  O4'   105.04  3.000
 GNG  H4'   C4'  C5'   109.50  3.000
 GNG  C3'   C4'  C5'   113.79  3.000
 GNG  O4'   C4'  C5'   110.38  3.000
 GNG  C1'   O4'  C4'   111.06  3.000
 GNG  H1'   C1'  C2'   112.61  3.000
 GNG  H1'   C1'  N9    106.56  3.000
 GNG  C2'   C1'  N9    112.13  3.000
 GNG  H1'   C1'  O4'   110.21  3.000
 GNG  C2'   C1'  O4'   106.90  3.000
 GNG  N9    C1'  O4'   108.38  3.000
 GNG  C4    N9   C8    105.30  3.000
 GNG  C4    N9   C1'   126.14  3.000
 GNG  C8    N9   C1'   128.53  3.000
 GNG  H8    C8   N7    125.54  3.000
 GNG  H8    C8   N9    121.82  3.000
 GNG  N7    C8   N9    112.63  3.000
 GNG  C5    N7   C8    105.33  3.000
 GNG  C6    C5   C4    119.20  3.000
 GNG  C6    C5   N7    131.46  3.000
 GNG  C4    C5   N7    109.34  3.000
 GNG  N3    C4   C5    122.94  3.000
 GNG  N3    C4   N9    129.66  3.000
 GNG  C5    C4   N9    107.40  3.000
 GNG  HN3   N3   C2    121.05  3.000
 GNG  HN3   N3   C4    122.69  3.000
 GNG  C2    N3   C4    116.04  3.000
 GNG  N2    C2   N1    119.99  3.000
 GNG  N2    C2   N3    116.12  3.000
 GNG  N1    C2   N3    123.88  3.000
 GNG  C6    N1   C2    122.93  3.000
 GNG  O6    C6   N1    121.11  3.000
 GNG  O6    C6   C5    123.90  3.000
 GNG  N1    C6   C5    114.99  3.000
 GNG  HN22  N2   HN21  116.78  3.000
 GNG  HN22  N2   C2    121.55  3.000
 GNG  HN21  N2   C2    117.58  3.000
 GNG  H2'2  C2'  H2'1  108.36  3.000
 GNG  H2'2  C2'  C3'   109.65  3.000
 GNG  H2'1  C2'  C3'   113.94  3.000
 GNG  H2'2  C2'  C1'   109.39  3.000
 GNG  H2'1  C2'  C1'   113.27  3.000
 GNG  C3'   C2'  C1'   102.05  3.000
 GNG  H3'   C3'  O3'   111.07  3.000
 GNG  H3'   C3'  C2'   109.42  3.000
 GNG  O3'   C3'  C2'   115.51  3.000
 GNG  H3'   C3'  C4'   109.21  3.000
 GNG  O3'   C3'  C4'   109.91  3.000
 GNG  C2'   C3'  C4'   101.19  3.000
 GNG  H1    O3'  C3'   108.60  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
 GNG  CONST_01  C5    N7  C8  N9     0.00  0.0  0
 GNG  CONST_02  N7    C5  C4  N9     0.00  0.0  0
 GNG  CONST_03  C5    C4  N9  C8     0.00  0.0  0
 GNG  CONST_04  C4    C5  N7  C8     0.00  0.0  0
 GNG  CONST_05  C4    N9  C8  N7     0.00  0.0  0
 GNG  CONST_06  N7    C8  N9  C1'  180.00  0.0  0
 GNG  CONST_07  C5    C4  N9  C1'  180.00  0.0  0
 GNG  CONST_08  N3    C4  N9  C1'    0.00  0.0  0
 GNG  CONST_09  N1    C2  N3  C4     0.00  0.0  0
 GNG  CONST_10  C6    N1  C2  N3     0.00  0.0  0
 GNG  CONST_11  N2    C2  N3  C4   180.00  0.0  0
 GNG  CONST_12  N2    C2  N1  C6   180.00  0.0  0
 GNG  CONST_13  H8    C8  N9  C1'    0.00  0.0  0
 GNG  CONST_14  HN3   N3  C2  N1   180.00  0.0  0
 GNG  CONST_15  HN21  N2  C2  N3   180.00  0.0  0

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
 GNG  chir_01  C4'  C5'  O4'  C3'  negativ
 GNG  chir_02  C1'  O4'  N9   C2'  negativ
 GNG  chir_03  C3'  O3'  C4'  C2'  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
 GNG  plan-1  C1'   0.020
 GNG  plan-1  N9    0.020
 GNG  plan-1  C8    0.020
 GNG  plan-1  N7    0.020
 GNG  plan-1  C5    0.020
 GNG  plan-1  C4    0.020
 GNG  plan-1  N3    0.020
 GNG  plan-1  C2    0.020
 GNG  plan-1  N1    0.020
 GNG  plan-1  C6    0.020
 GNG  plan-1  O6    0.020
 GNG  plan-1  N2    0.020
 GNG  plan-1  H8    0.020
 GNG  plan-1  HN3   0.020
 GNG  plan-1  HN21  0.020
 GNG  plan-1  HN22  0.020

