# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 00:57:29 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: 2'-deoxy-8-oxoguanosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC2=C(NC(=O)N2[C@H]3C[C@H](O)[C@@H](CO)O3)C(=O)N1
#
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
 8HG  8HG  '2'-deoxy-8-oxoguanosine  '  ligand  33  20  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8HG
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
 8HG  O6    O  O     0  -0.488   4.2170  -1.8566   0.3155
 8HG  C6    C  CR6   0   0.518   3.4415  -0.9124   0.2552
 8HG  N1    N  NR16  0  -0.724   3.8875   0.4016   0.4596
 8HG  C2    C  CR6   0   0.699   3.1150   1.5199   0.4121
 8HG  N2    N  NH2   0  -0.829   3.7099   2.6924   0.6649
 8HG  N3    N  N     0  -0.515   1.8260   1.4821   0.1610
 8HG  C4    C  CR56  0   0.513   1.3496   0.2518  -0.0386
 8HG  C5    C  CR56  0   0.073   2.0565  -0.9212  -0.0069
 8HG  N7    N  NR15  0  -0.737   1.1623  -1.9473  -0.2714
 8HG  C8    C  CR5   0   0.672  -0.0842  -1.4428  -0.4662
 8HG  O20   O  O     0  -0.496  -1.1097  -2.0522  -0.7116
 8HG  N9    N  NR5   0  -0.610   0.0459  -0.0598  -0.3302
 8HG  C1'   C  CH1   0   0.198  -1.0372   0.8942  -0.4010
 8HG  O4'   O  O2    0  -0.497  -1.9223   0.6698   0.6679
 8HG  C2'   C  CH2   0  -0.558  -1.8653   0.8508  -1.6880
 8HG  C3'   C  CH1   0   0.016  -3.2038   0.2473  -1.2677
 8HG  O3'   O  OH1   0  -0.669  -4.3264   0.7940  -1.9124
 8HG  C4'   C  CH1   0   0.024  -3.2661   0.5917   0.2198
 8HG  C5'   C  CH2   0  -0.161  -4.0213  -0.4351   1.0268
 8HG  O5'   O  OH1   0  -0.672  -4.1297   0.0056   2.3598
 8HG  HN1   H  HNR6  0   0.428   4.8761   0.5034   0.6516
 8HG  HN21  H  HNH2  0   0.417   4.7120   2.7783   0.6626
 8HG  HN22  H  HNH2  0   0.415   3.1849   3.5325   0.4910
 8HG  H1'   H  HCH1  0   0.262  -0.5553   1.8682  -0.2913
 8HG  H2'1  H  HCH2  0   0.265  -2.0282   1.8732  -2.0344
 8HG  H2'2  H  HCH2  0   0.272  -1.3712   0.3040  -2.4898
 8HG  H3'   H  HCH1  0   0.230  -3.1715  -0.8392  -1.3922
 8HG  H1    H  HOH1  0   0.457  -4.3691   0.4314  -2.8020
 8HG  H4'   H  HCH1  0   0.222  -3.7506   1.5735   0.3309
 8HG  H5'1  H  HCH2  0   0.202  -5.0060  -0.5669   0.5588
 8HG  H5'2  H  HCH2  0   0.200  -3.4964  -1.3967   0.9547
 8HG  H5'   H  HOH1  0   0.456  -4.6172  -0.6586   2.8550
 8HG  H13   H  HNR5  0   0.420   1.3774  -2.9305  -0.3102

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
 8HG  O6   C6    double  1.223  0.020  1.223
 8HG  C6   N1    single  1.403  0.020  1.403
 8HG  C6   C5    single  1.410  0.020  1.410
 8HG  N1   C2    single  1.360  0.020  1.360
 8HG  N1   HN1   single  0.860  0.020  1.020
 8HG  C2   N2    single  1.339  0.020  1.339
 8HG  C2   N3    double  1.314  0.020  1.314
 8HG  N2   HN21  single  0.890  0.020  1.040
 8HG  N2   HN22  single  0.890  0.020  1.040
 8HG  N3   C4    single  1.334  0.020  1.334
 8HG  C4   C5    double  1.370  0.020  1.370
 8HG  C4   N9    single  1.372  0.020  1.372
 8HG  C5   N7    single  1.387  0.020  1.387
 8HG  N7   C8    single  1.359  0.020  1.359
 8HG  C8   O20   double  1.218  0.020  1.218
 8HG  C8   N9    single  1.396  0.020  1.396
 8HG  N9   C1'   single  1.445  0.020  1.445
 8HG  C1'  O4'   single  1.406  0.020  1.406
 8HG  C1'  C2'   single  1.531  0.020  1.531
 8HG  C1'  H1'   single  0.970  0.020  1.090
 8HG  O4'  C4'   single  1.419  0.020  1.419
 8HG  C2'  C3'   single  1.527  0.020  1.527
 8HG  C2'  H2'1  single  0.970  0.020  1.090
 8HG  C2'  H2'2  single  0.970  0.020  1.090
 8HG  C3'  O3'   single  1.405  0.020  1.405
 8HG  C3'  C4'   single  1.528  0.020  1.528
 8HG  C3'  H3'   single  0.970  0.020  1.090
 8HG  O3'  H1    single  0.850  0.020  0.980
 8HG  C4'  C5'   single  1.509  0.020  1.509
 8HG  C4'  H4'   single  0.970  0.020  1.090
 8HG  C5'  O5'   single  1.408  0.020  1.408
 8HG  C5'  H5'1  single  0.970  0.020  1.090
 8HG  C5'  H5'2  single  0.970  0.020  1.090
 8HG  O5'  H5'   single  0.850  0.020  0.980
 8HG  N7   H13   single  0.860  0.020  1.020

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
 8HG  C5    C6   N1    110.20  3.000
 8HG  C5    C6   O6    128.85  3.000
 8HG  N1    C6   O6    120.95  3.000
 8HG  HN1   N1   C2    118.60  3.000
 8HG  HN1   N1   C6    115.62  3.000
 8HG  C2    N1   C6    125.78  3.000
 8HG  N3    C2   N2    119.82  3.000
 8HG  N3    C2   N1    122.70  3.000
 8HG  N2    C2   N1    117.46  3.000
 8HG  HN22  N2   HN21  116.64  3.000
 8HG  HN22  N2   C2    117.83  3.000
 8HG  HN21  N2   C2    121.13  3.000
 8HG  C4    N3   C2    113.92  3.000
 8HG  N9    C4   C5    107.51  3.000
 8HG  N9    C4   N3    125.49  3.000
 8HG  C5    C4   N3    127.00  3.000
 8HG  N7    C5   C4    107.25  3.000
 8HG  N7    C5   C6    132.35  3.000
 8HG  C4    C5   C6    120.40  3.000
 8HG  H13   N7   C8    123.56  3.000
 8HG  H13   N7   C5    126.30  3.000
 8HG  C8    N7   C5    110.13  3.000
 8HG  N9    C8   O20   126.44  3.000
 8HG  N9    C8   N7    105.57  3.000
 8HG  O20   C8   N7    127.99  3.000
 8HG  C1'   N9   C8    125.41  3.000
 8HG  C1'   N9   C4    124.95  3.000
 8HG  C8    N9   C4    109.53  3.000
 8HG  H1'   C1'  C2'   110.39  3.000
 8HG  H1'   C1'  O4'   110.10  3.000
 8HG  C2'   C1'  O4'   107.11  3.000
 8HG  H1'   C1'  N9    104.66  3.000
 8HG  C2'   C1'  N9    115.34  3.000
 8HG  O4'   C1'  N9    109.22  3.000
 8HG  C4'   O4'  C1'   111.40  3.000
 8HG  H2'2  C2'  H2'1  107.72  3.000
 8HG  H2'2  C2'  C3'   113.69  3.000
 8HG  H2'1  C2'  C3'   109.06  3.000
 8HG  H2'2  C2'  C1'   112.81  3.000
 8HG  H2'1  C2'  C1'   108.71  3.000
 8HG  C3'   C2'  C1'   104.71  3.000
 8HG  H3'   C3'  C4'   109.62  3.000
 8HG  H3'   C3'  O3'   110.96  3.000
 8HG  C4'   C3'  O3'   109.05  3.000
 8HG  H3'   C3'  C2'   109.59  3.000
 8HG  C4'   C3'  C2'   102.39  3.000
 8HG  O3'   C3'  C2'   114.84  3.000
 8HG  H1    O3'  C3'   108.25  3.000
 8HG  H4'   C4'  C5'   109.44  3.000
 8HG  H4'   C4'  C3'   108.50  3.000
 8HG  C5'   C4'  C3'   112.81  3.000
 8HG  H4'   C4'  O4'   109.64  3.000
 8HG  C5'   C4'  O4'   110.04  3.000
 8HG  C3'   C4'  O4'   106.34  3.000
 8HG  H5'2  C5'  H5'1  107.20  3.000
 8HG  H5'2  C5'  O5'   111.91  3.000
 8HG  H5'1  C5'  O5'   111.83  3.000
 8HG  H5'2  C5'  C4'   108.76  3.000
 8HG  H5'1  C5'  C4'   107.61  3.000
 8HG  O5'   C5'  C4'   109.39  3.000
 8HG  H5'   O5'  C5'   108.09  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
 8HG  CONST_01  N3    C2  N1  C6     0.00  0.0  0
 8HG  CONST_02  C4    N3  C2  N1     0.00  0.0  0
 8HG  CONST_03  C5    C6  N1  C2     0.00  0.0  0
 8HG  CONST_04  C5    C4  N3  C2     0.00  0.0  0
 8HG  CONST_05  N9    C4  N3  C2   180.00  0.0  0
 8HG  CONST_06  C8    N9  C4  N3   180.00  0.0  0
 8HG  CONST_07  C1'   N9  C4  N3     0.00  0.0  0
 8HG  CONST_08  C8    N7  C5  C4     0.00  0.0  0
 8HG  CONST_09  N7    C8  N9  C4     0.00  0.0  0
 8HG  CONST_10  C8    N9  C4  C5     0.00  0.0  0
 8HG  CONST_11  C1'   N9  C4  C5   180.00  0.0  0
 8HG  CONST_12  N9    C8  N7  C5     0.00  0.0  0
 8HG  CONST_13  N9    C4  C5  N7     0.00  0.0  0
 8HG  CONST_14  C1'   N9  C8  N7   180.00  0.0  0
 8HG  CONST_15  C2    N1  C6  O6   180.00  0.0  0
 8HG  CONST_16  N2    C2  N1  C6   180.00  0.0  0
 8HG  CONST_17  C4    N3  C2  N2   180.00  0.0  0
 8HG  CONST_18  O20   C8  N9  C4   180.00  0.0  0
 8HG  CONST_19  O20   C8  N7  C5   180.00  0.0  0
 8HG  CONST_20  C1'   N9  C8  O20    0.00  0.0  0
 8HG  CONST_21  HN1   N1  C2  N3   180.00  0.0  0
 8HG  CONST_22  H13   N7  C5  C4   180.00  0.0  0
 8HG  CONST_23  HN21  N2  C2  N1     0.00  0.0  0
 8HG  CONST_24  HN22  N2  C2  N1   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
 8HG  chir_01  C1'  N9   O4'  C2'  positiv
 8HG  chir_02  C3'  O3'  C4'  C2'  positiv
 8HG  chir_03  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
 8HG  plan-1  O6    0.020
 8HG  plan-1  C6    0.020
 8HG  plan-1  N1    0.020
 8HG  plan-1  C2    0.020
 8HG  plan-1  N2    0.020
 8HG  plan-1  N3    0.020
 8HG  plan-1  C4    0.020
 8HG  plan-1  C5    0.020
 8HG  plan-1  N7    0.020
 8HG  plan-1  C8    0.020
 8HG  plan-1  O20   0.020
 8HG  plan-1  N9    0.020
 8HG  plan-1  C1'   0.020
 8HG  plan-1  HN1   0.020
 8HG  plan-1  HN21  0.020
 8HG  plan-1  HN22  0.020
 8HG  plan-1  H13   0.020

