# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 02:12:36 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: 1-deoxy-1-(8-hydroxy-2,4-dioxo-3,4-dihydropyrimido[4,5-b]quinolin-10(2H)-yl)-D-ribitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](O)[C@@H](O)[C@@H](O)CN1c2cc(O)ccc2C=C3C(=O)NC(=O)N=C13
#
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
 FO1  FO1  1-deoxy-1-(8-hydroxy-2,4-dioxo-3,4-dihydropyrimido[4,5-b]quinolin-10(2H)-yl)-D-ribitol  ligand  43  26  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_FO1
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
 FO1  N1    N  N     0  -0.539   0.9855  -2.0216   0.3308
 FO1  C1    C  CR6   0   0.563   1.7242  -3.1172   0.0336
 FO1  O1    O  O     0  -0.484   1.3018  -4.2525   0.1649
 FO1  N2    N  NR16  0  -0.722   3.0216  -2.9389  -0.4476
 FO1  C2    C  CR6   0   0.565   3.6504  -1.7455  -0.6450
 FO1  O2    O  O     0  -0.451   4.7909  -1.6698  -1.0641
 FO1  C3    C  CR66  0  -0.225   2.8238  -0.5875  -0.3055
 FO1  C4    C  CR16  0  -0.162   3.2982   0.6816  -0.4256
 FO1  C5    C  CR66  0   0.021   2.4822   1.7779  -0.1071
 FO1  C6    C  CR16  0  -0.288   2.9534   3.0985  -0.2308
 FO1  C7    C  CR16  0  -0.396   2.1573   4.1674   0.0626
 FO1  C9    C  CR6   0   0.392   0.8332   3.9321   0.4781
 FO1  O10   O  OH1   0  -0.607  -0.0014   4.9354   0.7556
 FO1  C11   C  CR16  0  -0.409   0.3372   2.6450   0.6062
 FO1  C12   C  CR66  0   0.441   1.1556   1.5478   0.3335
 FO1  N3    N  NR6   0  -0.608   0.7210   0.2471   0.4956
 FO1  C13   C  CR66  0   0.550   1.4998  -0.8286   0.1716
 FO1  C14   C  CH2   0  -0.354  -0.6059  -0.0354   1.0484
 FO1  C15   C  CH1   0   0.030  -1.6393  -0.3001  -0.0435
 FO1  O3    O  OH1   0  -0.677  -1.5562   0.7468  -0.9752
 FO1  C16   C  CH1   0  -0.029  -3.0412  -0.4239   0.5834
 FO1  O4    O  OH1   0  -0.657  -3.0215  -1.3016   1.6871
 FO1  C17   C  CH1   0  -0.028  -4.1029  -0.8740  -0.4380
 FO1  O5    O  OH1   0  -0.664  -4.1024  -0.0502  -1.5928
 FO1  C18   C  CH2   0  -0.166  -5.4844  -0.9389   0.1919
 FO1  O6    O  OH1   0  -0.668  -6.3942  -1.4247  -0.7662
 FO1  HN3   H  HNR6  0   0.416   3.5433  -3.7796  -0.6615
 FO1  HC6   H  HCR6  0   0.281   3.9708   3.2562  -0.5645
 FO1  HC82  H  HOH1  0   0.485   0.4317   5.7889   0.6353
 FO1  HC9   H  HCR6  0   0.284  -0.6976   2.5334   0.8868
 FO1  HC11  H  HCH2  0   0.299  -0.5120  -0.9047   1.6905
 FO1  HC12  H  HCH2  0   0.280  -0.9007   0.7973   1.6825
 FO1  HC2'  H  HCH1  0   0.219  -1.3869  -1.2643  -0.5117
 FO1  HO2'  H  HOH1  0   0.452  -2.2938   0.6305  -1.5908
 FO1  HC3'  H  HCH1  0   0.240  -3.3236   0.5579   0.9834
 FO1  HO3'  H  HOH1  0   0.448  -2.7837  -2.1843   1.3800
 FO1  HC4'  H  HCH1  0   0.237  -3.8270  -1.8747  -0.7936
 FO1  HO4'  H  HOH1  0   0.457  -4.5737   0.7673  -1.3915
 FO1  HC51  H  HCH2  0   0.216  -5.4454  -1.5807   1.0777
 FO1  HC52  H  HCH2  0   0.195  -5.7618   0.0682   0.5405
 FO1  HO5'  H  HOH1  0   0.458  -7.2608  -1.4732  -0.3530
 FO1  H21   H  HCR6  0   0.303   4.3098   0.8541  -0.7732
 FO1  HC7   H  HCR6  0   0.304   2.5308   5.1790  -0.0340

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
 FO1  N1   C1    single    1.354  0.020  1.354
 FO1  N1   C13   double    1.309  0.020  1.309
 FO1  C1   O1    double    1.218  0.020  1.218
 FO1  C1   N2    single    1.395  0.020  1.395
 FO1  N2   C2    single    1.363  0.020  1.363
 FO1  N2   HN3   single    0.860  0.020  1.020
 FO1  C2   O2    double    1.217  0.020  1.217
 FO1  C2   C3    single    1.463  0.020  1.463
 FO1  C3   C4    double    1.360  0.020  1.360
 FO1  C3   C13   single    1.428  0.020  1.428
 FO1  C4   C5    single    1.403  0.020  1.403
 FO1  C4   H21   single    0.930  0.020  1.080
 FO1  C5   C6    aromatic  1.408  0.020  1.408
 FO1  C5   C12   aromatic  1.417  0.020  1.417
 FO1  C6   C7    aromatic  1.365  0.020  1.365
 FO1  C6   HC6   single    0.930  0.020  1.080
 FO1  C7   C9    aromatic  1.408  0.020  1.408
 FO1  C7   HC7   single    0.930  0.020  1.080
 FO1  C9   O10   single    1.334  0.020  1.334
 FO1  C9   C11   aromatic  1.385  0.020  1.385
 FO1  O10  HC82  single    0.850  0.020  0.980
 FO1  C11  C12   aromatic  1.396  0.020  1.396
 FO1  C11  HC9   single    0.930  0.020  1.080
 FO1  C12  N3    single    1.381  0.020  1.381
 FO1  N3   C13   single    1.367  0.020  1.367
 FO1  N3   C14   single    1.465  0.020  1.465
 FO1  C14  C15   single    1.526  0.020  1.526
 FO1  C14  HC11  single    0.970  0.020  1.090
 FO1  C14  HC12  single    0.970  0.020  1.090
 FO1  C15  O3    single    1.404  0.020  1.404
 FO1  C15  C16   single    1.541  0.020  1.541
 FO1  C15  HC2'  single    0.970  0.020  1.090
 FO1  O3   HO2'  single    0.850  0.020  0.980
 FO1  C16  O4    single    1.410  0.020  1.410
 FO1  C16  C17   single    1.540  0.020  1.540
 FO1  C16  HC3'  single    0.970  0.020  1.090
 FO1  O4   HO3'  single    0.850  0.020  0.980
 FO1  C17  O5    single    1.419  0.020  1.419
 FO1  C17  C18   single    1.520  0.020  1.520
 FO1  C17  HC4'  single    0.970  0.020  1.090
 FO1  O5   HO4'  single    0.850  0.020  0.980
 FO1  C18  O6    single    1.408  0.020  1.408
 FO1  C18  HC51  single    0.970  0.020  1.090
 FO1  C18  HC52  single    0.970  0.020  1.090
 FO1  O6   HO5'  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
 FO1  C13   N1   C1    119.76  3.000
 FO1  N2    C1   O1    118.60  3.000
 FO1  N2    C1   N1    118.65  3.000
 FO1  O1    C1   N1    122.75  3.000
 FO1  HN3   N2   C2    117.30  3.000
 FO1  HN3   N2   C1    116.48  3.000
 FO1  C2    N2   C1    126.21  3.000
 FO1  C3    C2   O2    124.06  3.000
 FO1  C3    C2   N2    113.50  3.000
 FO1  O2    C2   N2    122.44  3.000
 FO1  C13   C3   C4    120.70  3.000
 FO1  C13   C3   C2    117.89  3.000
 FO1  C4    C3   C2    121.41  3.000
 FO1  H21   C4   C5    119.43  3.000
 FO1  H21   C4   C3    120.16  3.000
 FO1  C5    C4   C3    120.41  3.000
 FO1  C12   C5   C6    119.55  3.000
 FO1  C12   C5   C4    119.22  3.000
 FO1  C6    C5   C4    121.23  3.000
 FO1  HC6   C6   C7    120.03  3.000
 FO1  HC6   C6   C5    118.59  3.000
 FO1  C7    C6   C5    121.37  3.000
 FO1  HC7   C7   C9    120.47  3.000
 FO1  HC7   C7   C6    120.76  3.000
 FO1  C9    C7   C6    118.77  3.000
 FO1  C11   C9   O10   117.10  3.000
 FO1  C11   C9   C7    121.29  3.000
 FO1  O10   C9   C7    121.61  3.000
 FO1  HC82  O10  C9    111.01  3.000
 FO1  HC9   C11  C12   122.16  3.000
 FO1  HC9   C11  C9    117.64  3.000
 FO1  C12   C11  C9    120.16  3.000
 FO1  N3    C12  C11   122.21  3.000
 FO1  N3    C12  C5    118.96  3.000
 FO1  C11   C12  C5    118.82  3.000
 FO1  C14   N3   C13   116.98  3.000
 FO1  C14   N3   C12   120.73  3.000
 FO1  C13   N3   C12   122.28  3.000
 FO1  N3    C13  C3    118.33  3.000
 FO1  N3    C13  N1    117.68  3.000
 FO1  C3    C13  N1    123.99  3.000
 FO1  HC12  C14  HC11  106.98  3.000
 FO1  HC12  C14  C15   111.49  3.000
 FO1  HC11  C14  C15   110.06  3.000
 FO1  HC12  C14  N3    108.54  3.000
 FO1  HC11  C14  N3    107.43  3.000
 FO1  C15   C14  N3    112.13  3.000
 FO1  HC2'  C15  C16   108.13  3.000
 FO1  HC2'  C15  O3    110.92  3.000
 FO1  C16   C15  O3    112.57  3.000
 FO1  HC2'  C15  C14   107.50  3.000
 FO1  C16   C15  C14   109.81  3.000
 FO1  O3    C15  C14   107.78  3.000
 FO1  HO2'  O3   C15   106.71  3.000
 FO1  HC3'  C16  C17   109.02  3.000
 FO1  HC3'  C16  O4    105.97  3.000
 FO1  C17   C16  O4    110.29  3.000
 FO1  HC3'  C16  C15   108.10  3.000
 FO1  C17   C16  C15   112.39  3.000
 FO1  O4    C16  C15   110.84  3.000
 FO1  HO3'  O4   C16   108.90  3.000
 FO1  HC4'  C17  C18   108.90  3.000
 FO1  HC4'  C17  O5    105.41  3.000
 FO1  C18   C17  O5    111.26  3.000
 FO1  HC4'  C17  C16   107.94  3.000
 FO1  C18   C17  C16   111.36  3.000
 FO1  O5    C17  C16   111.71  3.000
 FO1  HO4'  O5   C17   108.78  3.000
 FO1  HC52  C18  HC51  106.80  3.000
 FO1  HC52  C18  O6    111.60  3.000
 FO1  HC51  C18  O6    111.81  3.000
 FO1  HC52  C18  C17   108.73  3.000
 FO1  HC51  C18  C17   109.15  3.000
 FO1  O6    C18  C17   108.68  3.000
 FO1  HO5'  O6   C18   107.91  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
 FO1  CONST_01  C9   C7   C6   C5     0.00   0.0  0
 FO1  CONST_02  C9   C11  C12  C5     0.00   0.0  0
 FO1  CONST_03  C11  C12  C5   C6     0.00   0.0  0
 FO1  CONST_04  C11  C9   C7   C6     0.00   0.0  0
 FO1  CONST_05  C12  C5   C6   C7     0.00   0.0  0
 FO1  CONST_06  C12  C11  C9   C7     0.00   0.0  0
 FO1  CONST_07  C2   N2   C1   N1     0.00   0.0  0
 FO1  CONST_08  C12  N3   C13  N1   180.00   0.0  0
 FO1  CONST_09  C3   C13  N1   C1     0.00   0.0  0
 FO1  CONST_10  N3   C13  N1   C1   180.00   0.0  0
 FO1  CONST_11  C13  N1   C1   N2     0.00   0.0  0
 FO1  CONST_12  C12  N3   C13  C3     0.00   0.0  0
 FO1  CONST_13  O10  C9   C7   C6   180.00   0.0  0
 FO1  CONST_14  C12  C11  C9   O10  180.00   0.0  0
 FO1  CONST_15  C14  N3   C13  N1     0.00   0.0  0
 FO1  CONST_16  C13  N1   C1   O1   180.00   0.0  0
 FO1  CONST_17  C2   N2   C1   O1   180.00   0.0  0
 FO1  CONST_18  C14  N3   C13  C3   180.00   0.0  0
 FO1  CONST_19  HC6  C6   C5   C4     0.00   0.0  0
 FO1  CONST_20  HC7  C7   C6   C5   180.00   0.0  0
 FO1  CONST_21  HC9  C11  C12  C5   180.00   0.0  0
 FO1  CONST_22  HN3  N2   C1   N1   180.00   0.0  0
 FO1  Var_01    C15  C14  N3   C12   97.21  30.0  3

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
 FO1  chir_01  C15  C14  O3   C16  positiv
 FO1  chir_02  C16  O4   C15  C17  negativ
 FO1  chir_03  C17  O5   C16  C18  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
 FO1  plan-1  N1   0.020
 FO1  plan-1  C1   0.020
 FO1  plan-1  O1   0.020
 FO1  plan-1  N2   0.020
 FO1  plan-1  C2   0.020
 FO1  plan-1  O2   0.020
 FO1  plan-1  C3   0.020
 FO1  plan-1  C4   0.020
 FO1  plan-1  C5   0.020
 FO1  plan-1  C6   0.020
 FO1  plan-1  C7   0.020
 FO1  plan-1  C9   0.020
 FO1  plan-1  O10  0.020
 FO1  plan-1  C11  0.020
 FO1  plan-1  C12  0.020
 FO1  plan-1  N3   0.020
 FO1  plan-1  C13  0.020
 FO1  plan-1  C14  0.020
 FO1  plan-1  HN3  0.020
 FO1  plan-1  HC6  0.020
 FO1  plan-1  HC9  0.020
 FO1  plan-1  H21  0.020
 FO1  plan-1  HC7  0.020

