# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 17:22:57 2022
#   Inital geometry file: a 80 line input string
#   Ligand name: 8-oxoadenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2N([C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O)C(=O)Nc12
#
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
 8OX  8OX  '8-oxoadenosine           '  ligand  33  20  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8OX
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
 8OX  O50   O  OH1   0  -0.672   3.5317   2.2461   1.2422
 8OX  C50   C  CH2   0  -0.153   3.6353   1.3135   0.1936
 8OX  C40   C  CH1   0  -0.037   3.0933  -0.0153   0.6789
 8OX  O40   O  O2    0  -0.494   1.7176   0.0928   1.0539
 8OX  C30   C  CH1   0  -0.044   3.1493  -1.1083  -0.3918
 8OX  O30   O  OH1   0  -0.669   3.2087  -2.3973   0.1630
 8OX  C20   C  CH1   0  -0.028   1.7789  -0.9439  -1.0481
 8OX  O20   O  OH1   0  -0.658   1.2693  -2.0582  -1.7129
 8OX  C10   C  CH1   0   0.220   0.9124  -0.6424   0.1736
 8OX  N9    N  NR5   0  -0.625  -0.3080   0.0678  -0.1038
 8OX  C8    C  CR5   0   0.680  -0.4142   1.3035  -0.7400
 8OX  O8    O  O     0  -0.482   0.4895   1.9703  -1.2013
 8OX  N7    N  NR15  0  -0.752  -1.7475   1.6052  -0.7390
 8OX  C5    C  CR56  0   0.170  -2.4660   0.6020  -0.1189
 8OX  C6    C  CR6   0   0.472  -3.8108   0.3722   0.1613
 8OX  N6    N  NH2   0  -0.828  -4.7994   1.2314  -0.1451
 8OX  N1    N  N     0  -0.463  -4.1245  -0.7609   0.8075
 8OX  C2    C  CR16  0   0.047  -3.1606  -1.5987   1.1470
 8OX  N3    N  N     0  -0.457  -1.8585  -1.4733   0.9220
 8OX  C4    C  CR56  0   0.497  -1.5575  -0.3560   0.2835
 8OX  HO50  H  HOH1  0   0.456   3.8380   3.0968   0.9163
 8OX  H50   H  HCH2  0   0.209   3.0874   1.6411  -0.6964
 8OX  H50A  H  HCH2  0   0.200   4.6796   1.1554  -0.1070
 8OX  H40   H  HCH1  0   0.249   3.6646  -0.3193   1.5642
 8OX  H30   H  HCH1  0   0.247   3.9689  -0.9379  -1.1019
 8OX  HO30  H  HOH1  0   0.455   4.0263  -2.4733   0.6649
 8OX  H20   H  HCH1  0   0.255   1.8201  -0.0675  -1.7023
 8OX  HO20  H  HOH1  0   0.462   1.6984  -2.1255  -2.5711
 8OX  H10   H  HCH1  0   0.256   0.5940  -1.5863   0.6302
 8OX  HN7   H  HNR5  0   0.424  -2.1101   2.4529  -1.1445
 8OX  HN6   H  HNH2  0   0.405  -4.6466   1.9753  -0.8035
 8OX  HN6A  H  HNH2  0   0.402  -5.7480   0.9067  -0.0601
 8OX  H2    H  HCR6  0   0.257  -3.4722  -2.4965   1.6689

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
 8OX  O50  C50   single    1.407  0.020  1.407
 8OX  C50  C40   single    1.515  0.020  1.515
 8OX  C40  O40   single    1.430  0.020  1.430
 8OX  C40  C30   single    1.531  0.020  1.531
 8OX  O40  C10   single    1.401  0.020  1.401
 8OX  C30  O30   single    1.405  0.020  1.405
 8OX  C30  C20   single    1.528  0.020  1.528
 8OX  C20  O20   single    1.394  0.020  1.394
 8OX  C20  C10   single    1.528  0.020  1.528
 8OX  C10  N9    single    1.439  0.020  1.439
 8OX  N9   C8    single    1.394  0.020  1.394
 8OX  N9   C4    single    1.375  0.020  1.375
 8OX  C8   O8    double    1.214  0.020  1.214
 8OX  C8   N7    single    1.367  0.020  1.367
 8OX  N7   C5    single    1.381  0.020  1.381
 8OX  C5   C6    aromatic  1.393  0.020  1.393
 8OX  C5   C4    aromatic  1.380  0.020  1.380
 8OX  C6   N6    single    1.345  0.020  1.345
 8OX  C6   N1    aromatic  1.342  0.020  1.342
 8OX  N1   C2    aromatic  1.322  0.020  1.322
 8OX  C2   N3    aromatic  1.327  0.020  1.327
 8OX  N3   C4    aromatic  1.322  0.020  1.322
 8OX  O50  HO50  single    0.850  0.020  0.980
 8OX  C50  H50   single    0.970  0.020  1.090
 8OX  C50  H50A  single    0.970  0.020  1.090
 8OX  C40  H40   single    0.970  0.020  1.090
 8OX  C30  H30   single    0.970  0.020  1.090
 8OX  O30  HO30  single    0.850  0.020  0.980
 8OX  C20  H20   single    0.970  0.020  1.090
 8OX  O20  HO20  single    0.850  0.020  0.980
 8OX  C10  H10   single    0.970  0.020  1.090
 8OX  N7   HN7   single    0.860  0.020  1.020
 8OX  N6   HN6   single    0.890  0.020  1.040
 8OX  N6   HN6A  single    0.890  0.020  1.040
 8OX  C2   H2    single    0.930  0.020  1.080

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
 8OX  HO50  O50  C50  108.09  3.000
 8OX  H50A  C50  H50  107.24  3.000
 8OX  H50A  C50  C40  107.56  3.000
 8OX  H50   C50  C40  110.11  3.000
 8OX  H50A  C50  O50  111.67  3.000
 8OX  H50   C50  O50  111.74  3.000
 8OX  C40   C50  O50  108.43  3.000
 8OX  H40   C40  C30  110.34  3.000
 8OX  H40   C40  O40  108.09  3.000
 8OX  C30   C40  O40  105.82  3.000
 8OX  H40   C40  C50  108.38  3.000
 8OX  C30   C40  C50  112.89  3.000
 8OX  O40   C40  C50  111.22  3.000
 8OX  C10   O40  C40  110.39  3.000
 8OX  H30   C30  C20  112.02  3.000
 8OX  H30   C30  O30  111.50  3.000
 8OX  C20   C30  O30  107.83  3.000
 8OX  H30   C30  C40  111.64  3.000
 8OX  C20   C30  C40  100.99  3.000
 8OX  O30   C30  C40  112.37  3.000
 8OX  HO30  O30  C30  108.32  3.000
 8OX  H20   C20  C10  109.96  3.000
 8OX  H20   C20  O20  111.64  3.000
 8OX  C10   C20  O20  109.38  3.000
 8OX  H20   C20  C30  108.00  3.000
 8OX  C10   C20  C30  100.74  3.000
 8OX  O20   C20  C30  116.52  3.000
 8OX  HO20  O20  C20  108.57  3.000
 8OX  H10   C10  N9   105.01  3.000
 8OX  H10   C10  C20  109.15  3.000
 8OX  N9    C10  C20  115.10  3.000
 8OX  H10   C10  O40  110.93  3.000
 8OX  N9    C10  O40  110.45  3.000
 8OX  C20   C10  O40  106.26  3.000
 8OX  C4    N9   C8   109.42  3.000
 8OX  C4    N9   C10  124.35  3.000
 8OX  C8    N9   C10  126.17  3.000
 8OX  N7    C8   O8   127.22  3.000
 8OX  N7    C8   N9   105.65  3.000
 8OX  O8    C8   N9   127.13  3.000
 8OX  HN7   N7   C5   127.21  3.000
 8OX  HN7   N7   C8   122.46  3.000
 8OX  C5    N7   C8   110.33  3.000
 8OX  C4    C5   C6   117.55  3.000
 8OX  C4    C5   N7   107.01  3.000
 8OX  C6    C5   N7   135.44  3.000
 8OX  N1    C6   N6   118.51  3.000
 8OX  N1    C6   C5   117.52  3.000
 8OX  N6    C6   C5   123.95  3.000
 8OX  HN6A  N6   HN6  115.94  3.000
 8OX  HN6A  N6   C6   117.87  3.000
 8OX  HN6   N6   C6   120.68  3.000
 8OX  C2    N1   C6   119.25  3.000
 8OX  H2    C2   N3   116.22  3.000
 8OX  H2    C2   N1   116.04  3.000
 8OX  N3    C2   N1   127.75  3.000
 8OX  C4    N3   C2   112.66  3.000
 8OX  N3    C4   C5   125.28  3.000
 8OX  N3    C4   N9   127.13  3.000
 8OX  C5    C4   N9   107.59  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
 8OX  CONST_01  C2    N1  C6  C5     0.00  0.0  0
 8OX  CONST_02  C2    N3  C4  C5     0.00  0.0  0
 8OX  CONST_03  N3    C4  C5  C6     0.00  0.0  0
 8OX  CONST_04  N3    C2  N1  C6     0.00  0.0  0
 8OX  CONST_05  C4    C5  C6  N1     0.00  0.0  0
 8OX  CONST_06  C4    N3  C2  N1     0.00  0.0  0
 8OX  CONST_07  N7    C8  N9  C10  180.00  0.0  0
 8OX  CONST_08  C5    C4  N9  C10  180.00  0.0  0
 8OX  CONST_09  C5    N7  C8  N9     0.00  0.0  0
 8OX  CONST_10  N7    C5  C4  N9     0.00  0.0  0
 8OX  CONST_11  C5    C4  N9  C8     0.00  0.0  0
 8OX  CONST_12  C4    C5  N7  C8     0.00  0.0  0
 8OX  CONST_13  C4    N9  C8  N7     0.00  0.0  0
 8OX  CONST_14  N6    C6  C5  N7     0.00  0.0  0
 8OX  CONST_15  C4    C5  C6  N6   180.00  0.0  0
 8OX  CONST_16  C2    N1  C6  N6   180.00  0.0  0
 8OX  CONST_17  O8    C8  N9  C10    0.00  0.0  0
 8OX  CONST_18  C4    N9  C8  O8   180.00  0.0  0
 8OX  CONST_19  C5    N7  C8  O8   180.00  0.0  0
 8OX  CONST_20  H2    C2  N1  C6   180.00  0.0  0
 8OX  CONST_21  HN7   N7  C8  N9   180.00  0.0  0
 8OX  CONST_23  HN6A  N6  C6  C5   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
 8OX  chir_01  C40  C50  O40  C30  negativ
 8OX  chir_02  C30  O30  C40  C20  positiv
 8OX  chir_03  C20  O20  C30  C10  positiv
 8OX  chir_04  C10  O40  N9   C20  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
 8OX  plan-1  C10   0.020
 8OX  plan-1  N9    0.020
 8OX  plan-1  C8    0.020
 8OX  plan-1  O8    0.020
 8OX  plan-1  N7    0.020
 8OX  plan-1  C5    0.020
 8OX  plan-1  C6    0.020
 8OX  plan-1  N6    0.020
 8OX  plan-1  N1    0.020
 8OX  plan-1  C2    0.020
 8OX  plan-1  N3    0.020
 8OX  plan-1  C4    0.020
 8OX  plan-1  HN7   0.020
 8OX  plan-1  H2    0.020
 8OX  plan-2  C6    0.020
 8OX  plan-2  N6    0.020
 8OX  plan-2  HN6   0.020
 8OX  plan-2  HN6A  0.020

