# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 13:54:36 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: 3'-deoxyguanosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO)C[C@H]3O
#
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
 3DG  3DG  '3'-deoxyguanosine        '  ligand  32  19  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3DG
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
 3DG  N9    N  NR5   0  -0.531   0.2783  -0.1998  -0.3612
 3DG  C1'   C  CH1   0   0.181   1.2582   0.8641  -0.5566
 3DG  C2'   C  CH1   0  -0.017   1.5183   1.6251   0.7481
 3DG  C3'   C  CH2   0  -0.545   2.6684   0.8168   1.3301
 3DG  C4'   C  CH1   0   0.025   3.4589   0.4470   0.0846
 3DG  O4'   O  O2    0  -0.498   2.4722   0.3138  -0.9513
 3DG  C5'   C  CH2   0  -0.158   4.2593  -0.8233   0.2274
 3DG  O5'   O  OH1   0  -0.668   4.9785  -1.0528  -0.9590
 3DG  O2'   O  OH1   0  -0.666   1.9059   2.9248   0.3773
 3DG  C8    C  CR15  0   0.086   0.4871  -1.5438  -0.1795
 3DG  N7    N  N     0  -0.445  -0.6170  -2.2097  -0.0238
 3DG  C5    C  CR56  0  -0.088  -1.6070  -1.2662  -0.1056
 3DG  C6    C  CR6   0   0.502  -3.0233  -1.3905  -0.0138
 3DG  O6    O  O     0  -0.474  -3.6944  -2.3924   0.1695
 3DG  N1    N  NR16  0  -0.727  -3.6376  -0.1408  -0.1666
 3DG  C2    C  CR6   0   0.688  -3.0041   1.0515  -0.3748
 3DG  N2    N  NH2   0  -0.833  -3.7792   2.1319  -0.5326
 3DG  N3    N  N     0  -0.515  -1.7005   1.1621  -0.4512
 3DG  C4    C  CR56  0   0.501  -1.0663  -0.0113  -0.3164
 3DG  H1'   H  HCH1  0   0.277   0.8580   1.5227  -1.3326
 3DG  H2'   H  HCH1  0   0.258   0.6352   1.6324   1.3955
 3DG  H3'1  H  HCH2  0   0.253   2.2873  -0.0749   1.8369
 3DG  H3'2  H  HCH2  0   0.283   3.2592   1.3773   2.0552
 3DG  H4'   H  HCH1  0   0.240   4.1375   1.2631  -0.1894
 3DG  H5'1  H  HCH2  0   0.212   4.9238  -0.6946   1.0920
 3DG  H5'2  H  HCH2  0   0.198   3.5875  -1.6586   0.4670
 3DG  H5'   H  HOH1  0   0.458   5.4798  -1.8665  -0.8543
 3DG  H1    H  HOH1  0   0.459   2.2343   3.3789   1.1598
 3DG  H8    H  HCR5  0   0.291   1.4749  -1.9748  -0.1822
 3DG  HN1   H  HNR6  0   0.425  -4.6485  -0.1437  -0.1210
 3DG  HN21  H  HNH2  0   0.414  -3.3358   3.0344  -0.5514
 3DG  HN22  H  HNH2  0   0.416  -4.7596   2.1111  -0.3114

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
 3DG  N9   C1'   single    1.460  0.020  1.460
 3DG  N9   C8    aromatic  1.372  0.020  1.372
 3DG  N9   C4    aromatic  1.358  0.020  1.358
 3DG  C1'  C2'   single    1.533  0.020  1.533
 3DG  C1'  O4'   single    1.390  0.020  1.390
 3DG  C1'  H1'   single    0.970  0.020  1.090
 3DG  C2'  C3'   single    1.521  0.020  1.521
 3DG  C2'  O2'   single    1.406  0.020  1.406
 3DG  C2'  H2'   single    0.970  0.020  1.090
 3DG  C3'  C4'   single    1.521  0.020  1.521
 3DG  C3'  H3'1  single    0.970  0.020  1.090
 3DG  C3'  H3'2  single    0.970  0.020  1.090
 3DG  C4'  O4'   single    1.437  0.020  1.437
 3DG  C4'  C5'   single    1.508  0.020  1.508
 3DG  C4'  H4'   single    0.970  0.020  1.090
 3DG  C5'  O5'   single    1.406  0.020  1.406
 3DG  C5'  H5'1  single    0.970  0.020  1.090
 3DG  C5'  H5'2  single    0.970  0.020  1.090
 3DG  O5'  H5'   single    0.850  0.020  0.980
 3DG  O2'  H1    single    0.850  0.020  0.980
 3DG  C8   N7    aromatic  1.299  0.020  1.299
 3DG  C8   H8    single    0.930  0.020  1.080
 3DG  N7   C5    aromatic  1.370  0.020  1.370
 3DG  C5   C6    single    1.425  0.020  1.425
 3DG  C5   C4    aromatic  1.383  0.020  1.383
 3DG  C6   O6    double    1.220  0.020  1.220
 3DG  C6   N1    single    1.401  0.020  1.401
 3DG  N1   C2    single    1.366  0.020  1.366
 3DG  N1   HN1   single    0.860  0.020  1.020
 3DG  C2   N2    single    1.339  0.020  1.339
 3DG  C2   N3    double    1.311  0.020  1.311
 3DG  N2   HN21  single    0.890  0.020  1.040
 3DG  N2   HN22  single    0.890  0.020  1.040
 3DG  N3   C4    single    1.341  0.020  1.341

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
 3DG  C4    N9   C8    106.39  3.000
 3DG  C4    N9   C1'   124.59  3.000
 3DG  C8    N9   C1'   129.02  3.000
 3DG  H1'   C1'  O4'   110.89  3.000
 3DG  H1'   C1'  C2'   111.54  3.000
 3DG  O4'   C1'  C2'   106.86  3.000
 3DG  H1'   C1'  N9    106.76  3.000
 3DG  O4'   C1'  N9    109.62  3.000
 3DG  C2'   C1'  N9    111.22  3.000
 3DG  H2'   C2'  O2'   111.84  3.000
 3DG  H2'   C2'  C3'   112.77  3.000
 3DG  O2'   C2'  C3'   112.55  3.000
 3DG  H2'   C2'  C1'   111.70  3.000
 3DG  O2'   C2'  C1'   106.34  3.000
 3DG  C3'   C2'  C1'   100.96  3.000
 3DG  H3'2  C3'  H3'1  107.43  3.000
 3DG  H3'2  C3'  C4'   112.83  3.000
 3DG  H3'1  C3'  C4'   111.23  3.000
 3DG  H3'2  C3'  C2'   113.01  3.000
 3DG  H3'1  C3'  C2'   110.29  3.000
 3DG  C4'   C3'  C2'   102.05  3.000
 3DG  H4'   C4'  C5'   108.80  3.000
 3DG  H4'   C4'  O4'   108.30  3.000
 3DG  C5'   C4'  O4'   110.77  3.000
 3DG  H4'   C4'  C3'   110.20  3.000
 3DG  C5'   C4'  C3'   113.78  3.000
 3DG  O4'   C4'  C3'   104.83  3.000
 3DG  C4'   O4'  C1'   111.00  3.000
 3DG  H5'2  C5'  H5'1  106.71  3.000
 3DG  H5'2  C5'  O5'   111.89  3.000
 3DG  H5'1  C5'  O5'   111.96  3.000
 3DG  H5'2  C5'  C4'   109.67  3.000
 3DG  H5'1  C5'  C4'   107.27  3.000
 3DG  O5'   C5'  C4'   109.21  3.000
 3DG  H5'   O5'  C5'   108.24  3.000
 3DG  H1    O2'  C2'   108.41  3.000
 3DG  H8    C8   N7    125.06  3.000
 3DG  H8    C8   N9    122.06  3.000
 3DG  N7    C8   N9    112.88  3.000
 3DG  C5    N7   C8    104.72  3.000
 3DG  C4    C5   C6    118.54  3.000
 3DG  C4    C5   N7    110.58  3.000
 3DG  C6    C5   N7    130.87  3.000
 3DG  N1    C6   O6    120.53  3.000
 3DG  N1    C6   C5    110.55  3.000
 3DG  O6    C6   C5    128.93  3.000
 3DG  HN1   N1   C2    118.21  3.000
 3DG  HN1   N1   C6    115.50  3.000
 3DG  C2    N1   C6    126.29  3.000
 3DG  N3    C2   N2    120.05  3.000
 3DG  N3    C2   N1    122.95  3.000
 3DG  N2    C2   N1    116.99  3.000
 3DG  HN22  N2   HN21  116.91  3.000
 3DG  HN22  N2   C2    121.46  3.000
 3DG  HN21  N2   C2    118.11  3.000
 3DG  C4    N3   C2    113.01  3.000
 3DG  N3    C4   C5    128.66  3.000
 3DG  N3    C4   N9    125.90  3.000
 3DG  C5    C4   N9    105.44  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
 3DG  CONST_01  C5    N7  C8  N9     0.00  0.0  0
 3DG  CONST_02  N7    C5  C4  N9     0.00  0.0  0
 3DG  CONST_03  C5    C4  N9  C8     0.00  0.0  0
 3DG  CONST_04  C4    C5  N7  C8     0.00  0.0  0
 3DG  CONST_05  C4    N9  C8  N7     0.00  0.0  0
 3DG  CONST_06  N7    C8  N9  C1'  180.00  0.0  0
 3DG  CONST_07  C5    C4  N9  C1'  180.00  0.0  0
 3DG  CONST_08  N3    C4  N9  C1'    0.00  0.0  0
 3DG  CONST_09  C2    N1  C6  C5     0.00  0.0  0
 3DG  CONST_10  N3    C2  N1  C6     0.00  0.0  0
 3DG  CONST_11  C4    N3  C2  N1     0.00  0.0  0
 3DG  CONST_12  N2    C2  N1  C6   180.00  0.0  0
 3DG  CONST_13  C2    N1  C6  O6   180.00  0.0  0
 3DG  CONST_14  C4    N3  C2  N2   180.00  0.0  0
 3DG  CONST_15  H8    C8  N9  C1'    0.00  0.0  0
 3DG  CONST_16  HN1   N1  C6  C5   180.00  0.0  0
 3DG  CONST_17  HN21  N2  C2  N1   180.00  0.0  0
 3DG  CONST_18  HN22  N2  C2  N1     0.00  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
 3DG  chir_01  C1'  N9   C2'  O4'  negativ
 3DG  chir_02  C2'  O2'  C1'  C3'  negativ
 3DG  chir_03  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
 3DG  plan-1  N9    0.020
 3DG  plan-1  C1'   0.020
 3DG  plan-1  C8    0.020
 3DG  plan-1  N7    0.020
 3DG  plan-1  C5    0.020
 3DG  plan-1  C6    0.020
 3DG  plan-1  O6    0.020
 3DG  plan-1  N1    0.020
 3DG  plan-1  C2    0.020
 3DG  plan-1  N2    0.020
 3DG  plan-1  N3    0.020
 3DG  plan-1  C4    0.020
 3DG  plan-1  H8    0.020
 3DG  plan-1  HN1   0.020
 3DG  plan-1  HN21  0.020
 3DG  plan-1  HN22  0.020

