# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 20:43:30 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: 5-deoxy-5-(8-hydroxy-2,4-dioxo-3,4-dihydropyrimido[4,5-b]quinolin-10(2H)-yl)-D-xylitol
#   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
 HDF  HDF  5-deoxy-5-(8-hydroxy-2,4-dioxo-3,4-dihydropyrimido[4,5-b]quinolin-10(2H)-yl)-D-xylitol  ligand  43  26  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HDF
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
 HDF  N1    N  N     0  -0.627   2.0864   0.3514  -0.8860
 HDF  C2    C  CR6   0   0.597   3.2529   0.2392  -1.5752
 HDF  O2    O  OC    0  -0.473   4.3407   0.3363  -1.0409
 HDF  N3    N  NR16  0  -0.723   3.1865   0.0002  -2.9447
 HDF  C4    C  CR6   0   0.571   2.0515  -0.1689  -3.6847
 HDF  O4    O  OC    0  -0.444   2.0797  -0.3939  -4.8791
 HDF  C4A   C  CR66  0  -0.219   0.8205  -0.0538  -2.9026
 HDF  C5    C  CR16  0  -0.150  -0.4059  -0.2314  -3.4684
 HDF  C5A   C  CR66  0   0.026  -1.5666  -0.1576  -2.6849
 HDF  C6    C  CR16  0  -0.287  -2.8438  -0.3925  -3.2324
 HDF  C7    C  CR16  0  -0.340  -3.9671  -0.3460  -2.4611
 HDF  C8    C  CR6   0   0.418  -3.8395  -0.0623  -1.0872
 HDF  O8    O  OH1   0  -0.605  -4.9612  -0.0541  -0.3714
 HDF  C9    C  CR16  0  -0.473  -2.5996   0.1874  -0.5194
 HDF  C9A   C  CR66  0   0.444  -1.4499   0.1516  -1.3097
 HDF  N10   N  NR6   0  -0.609  -0.1999   0.4116  -0.7847
 HDF  C10   C  CR66  0   0.598   0.9395   0.2341  -1.5139
 HDF  C1'   C  CH2   0  -0.419  -0.0755   0.9584   0.5736
 HDF  C2'   C  CH1   0   0.020   0.1023  -0.0990   1.6630
 HDF  O2'   O  OH1   0  -0.688   1.3233  -0.7866   1.5322
 HDF  C3'   C  CH1   0  -0.012   0.0345   0.5844   3.0427
 HDF  O3'   O  OH1   0  -0.671   1.2495   1.2439   3.3133
 HDF  C4'   C  CH1   0  -0.021  -0.3794  -0.3810   4.1579
 HDF  O4'   O  OH1   0  -0.660   0.4605  -1.5058   4.2681
 HDF  C5'   C  CH2   0  -0.163  -0.5222   0.3586   5.4795
 HDF  O5'   O  OH1   0  -0.671  -1.0530  -0.5241   6.4401
 HDF  HN3   H  HNR6  0   0.421   4.0710  -0.0845  -3.4299
 HDF  H5    H  HCR6  0   0.296  -0.4911  -0.4498  -4.5260
 HDF  H6    H  HCR6  0   0.283  -2.9196  -0.6159  -4.2886
 HDF  H7    H  HCR6  0   0.287  -4.9456  -0.5320  -2.8826
 HDF  HO8   H  HOH1  0   0.488  -4.7859   0.1336   0.5592
 HDF  H9    H  HCR6  0   0.296  -2.5517   0.3826   0.5422
 HDF  H1'1  H  HCH2  0   0.297  -0.9610   1.5590   0.7686
 HDF  H1'2  H  HCH2  0   0.311   0.7666   1.6494   0.5728
 HDF  H2'   H  HCH1  0   0.234  -0.7262  -0.8160   1.5891
 HDF  HO2'  H  HOH1  0   0.468   1.8214  -0.4006   0.7857
 HDF  H3'   H  HCH1  0   0.238  -0.7423   1.3568   3.0046
 HDF  HO3'  H  HOH1  0   0.440   1.9588   0.6582   3.0176
 HDF  H4'   H  HCH1  0   0.232  -1.3644  -0.7734   3.8790
 HDF  HO4'  H  HOH1  0   0.440   1.3302  -1.2172   4.5638
 HDF  H5'1  H  HCH2  0   0.195  -1.1757   1.2282   5.3252
 HDF  H5'2  H  HCH2  0   0.199   0.4568   0.7483   5.7880
 HDF  HO5'  H  HOH1  0   0.455  -1.0496  -0.0745   7.2896

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
 HDF  N1   C2    aromatic  1.360  0.020  1.360
 HDF  N1   C10   aromatic  1.313  0.020  1.313
 HDF  C2   O2    double    1.216  0.020  1.216
 HDF  C2   N3    aromatic  1.392  0.020  1.392
 HDF  N3   C4    aromatic  1.365  0.020  1.365
 HDF  N3   HN3   single    0.860  0.020  1.020
 HDF  C4   O4    double    1.216  0.020  1.216
 HDF  C4   C4A   aromatic  1.463  0.020  1.463
 HDF  C4A  C5    aromatic  1.362  0.020  1.362
 HDF  C4A  C10   aromatic  1.423  0.020  1.423
 HDF  C5   C5A   aromatic  1.402  0.020  1.402
 HDF  C5   H5    single    0.930  0.020  1.080
 HDF  C5A  C6    aromatic  1.409  0.020  1.409
 HDF  C5A  C9A   aromatic  1.414  0.020  1.414
 HDF  C6   C7    aromatic  1.363  0.020  1.363
 HDF  C6   H6    single    0.930  0.020  1.080
 HDF  C7   C8    aromatic  1.409  0.020  1.409
 HDF  C7   H7    single    0.930  0.020  1.080
 HDF  C8   O8    single    1.331  0.020  1.331
 HDF  C8   C9    aromatic  1.386  0.020  1.386
 HDF  O8   HO8   single    0.850  0.020  0.980
 HDF  C9   C9A   aromatic  1.396  0.020  1.396
 HDF  C9   H9    single    0.930  0.020  1.080
 HDF  C9A  N10   aromatic  1.380  0.020  1.380
 HDF  N10  C10   aromatic  1.364  0.020  1.364
 HDF  N10  C1'   single    1.470  0.020  1.470
 HDF  C1'  C2'   single    1.528  0.020  1.528
 HDF  C1'  H1'1  single    0.970  0.020  1.090
 HDF  C1'  H1'2  single    0.970  0.020  1.090
 HDF  C2'  O2'   single    1.407  0.020  1.407
 HDF  C2'  C3'   single    1.541  0.020  1.541
 HDF  C2'  H2'   single    0.970  0.020  1.090
 HDF  O2'  HO2'  single    0.850  0.020  0.980
 HDF  C3'  O3'   single    1.409  0.020  1.409
 HDF  C3'  C4'   single    1.532  0.020  1.532
 HDF  C3'  H3'   single    0.970  0.020  1.090
 HDF  O3'  HO3'  single    0.850  0.020  0.980
 HDF  C4'  O4'   single    1.408  0.020  1.408
 HDF  C4'  C5'   single    1.521  0.020  1.521
 HDF  C4'  H4'   single    0.970  0.020  1.090
 HDF  O4'  HO4'  single    0.850  0.020  0.980
 HDF  C5'  O5'   single    1.408  0.020  1.408
 HDF  C5'  H5'1  single    0.970  0.020  1.090
 HDF  C5'  H5'2  single    0.970  0.020  1.090
 HDF  O5'  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
 HDF  C10   N1   C2    119.98  3.000
 HDF  N3    C2   O2    119.26  3.000
 HDF  N3    C2   N1    118.17  3.000
 HDF  O2    C2   N1    122.57  3.000
 HDF  HN3   N3   C4    117.14  3.000
 HDF  HN3   N3   C2    116.37  3.000
 HDF  C4    N3   C2    126.45  3.000
 HDF  C4A   C4   O4    124.01  3.000
 HDF  C4A   C4   N3    113.58  3.000
 HDF  O4    C4   N3    122.42  3.000
 HDF  C10   C4A  C5    120.46  3.000
 HDF  C10   C4A  C4    117.85  3.000
 HDF  C5    C4A  C4    121.68  3.000
 HDF  H5    C5   C5A   119.41  3.000
 HDF  H5    C5   C4A   120.17  3.000
 HDF  C5A   C5   C4A   120.41  3.000
 HDF  C9A   C5A  C6    119.27  3.000
 HDF  C9A   C5A  C5    119.11  3.000
 HDF  C6    C5A  C5    121.62  3.000
 HDF  H6    C6   C7    120.10  3.000
 HDF  H6    C6   C5A   118.49  3.000
 HDF  C7    C6   C5A   121.41  3.000
 HDF  H7    C7   C8    119.78  3.000
 HDF  H7    C7   C6    121.27  3.000
 HDF  C8    C7   C6    118.95  3.000
 HDF  C9    C8   O8    122.17  3.000
 HDF  C9    C8   C7    121.11  3.000
 HDF  O8    C8   C7    116.71  3.000
 HDF  HO8   O8   C8    111.51  3.000
 HDF  H9    C9   C9A   121.64  3.000
 HDF  H9    C9   C8    118.33  3.000
 HDF  C9A   C9   C8    120.01  3.000
 HDF  N10   C9A  C9    121.72  3.000
 HDF  N10   C9A  C5A   119.05  3.000
 HDF  C9    C9A  C5A   119.23  3.000
 HDF  C1'   N10  C10   118.14  3.000
 HDF  C1'   N10  C9A   119.89  3.000
 HDF  C10   N10  C9A   121.90  3.000
 HDF  N10   C10  C4A   118.55  3.000
 HDF  N10   C10  N1    117.54  3.000
 HDF  C4A   C10  N1    123.91  3.000
 HDF  H1'2  C1'  H1'1  106.22  3.000
 HDF  H1'2  C1'  C2'   110.45  3.000
 HDF  H1'1  C1'  C2'   110.42  3.000
 HDF  H1'2  C1'  N10   107.51  3.000
 HDF  H1'1  C1'  N10   107.59  3.000
 HDF  C2'   C1'  N10   114.28  3.000
 HDF  H2'   C2'  C3'   108.45  3.000
 HDF  H2'   C2'  O2'   109.22  3.000
 HDF  C3'   C2'  O2'   109.75  3.000
 HDF  H2'   C2'  C1'   108.42  3.000
 HDF  C3'   C2'  C1'   109.04  3.000
 HDF  O2'   C2'  C1'   111.88  3.000
 HDF  HO2'  O2'  C2'   108.68  3.000
 HDF  H3'   C3'  C4'   106.13  3.000
 HDF  H3'   C3'  O3'   106.74  3.000
 HDF  C4'   C3'  O3'   112.85  3.000
 HDF  H3'   C3'  C2'   108.20  3.000
 HDF  C4'   C3'  C2'   112.59  3.000
 HDF  O3'   C3'  C2'   109.98  3.000
 HDF  HO3'  O3'  C3'   106.89  3.000
 HDF  H4'   C4'  C5'   108.10  3.000
 HDF  H4'   C4'  O4'   105.66  3.000
 HDF  C5'   C4'  O4'   112.11  3.000
 HDF  H4'   C4'  C3'   106.45  3.000
 HDF  C5'   C4'  C3'   110.57  3.000
 HDF  O4'   C4'  C3'   113.52  3.000
 HDF  HO4'  O4'  C4'   108.87  3.000
 HDF  H5'2  C5'  H5'1  106.79  3.000
 HDF  H5'2  C5'  O5'   111.52  3.000
 HDF  H5'1  C5'  O5'   111.58  3.000
 HDF  H5'2  C5'  C4'   109.45  3.000
 HDF  H5'1  C5'  C4'   108.58  3.000
 HDF  O5'   C5'  C4'   108.86  3.000
 HDF  HO5'  O5'  C5'   107.96  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
 HDF  CONST_01  C4   N3   C2   N1     0.00   0.0  0
 HDF  CONST_02  C4   C4A  C10  N1     0.00   0.0  0
 HDF  CONST_03  C5   C4A  C10  N1   180.00   0.0  0
 HDF  CONST_04  C9A  N10  C10  N1   180.00   0.0  0
 HDF  CONST_05  C4A  C10  N1   C2     0.00   0.0  0
 HDF  CONST_06  N10  C10  N1   C2   180.00   0.0  0
 HDF  CONST_07  C4A  C4   N3   C2     0.00   0.0  0
 HDF  CONST_08  C10  N1   C2   N3     0.00   0.0  0
 HDF  CONST_09  C5   C4A  C4   N3   180.00   0.0  0
 HDF  CONST_10  C10  C4A  C4   N3     0.00   0.0  0
 HDF  CONST_11  C5A  C5   C4A  C4   180.00   0.0  0
 HDF  CONST_12  N10  C10  C4A  C4   180.00   0.0  0
 HDF  CONST_13  C6   C5A  C5   C4A  180.00   0.0  0
 HDF  CONST_14  C9A  C5A  C5   C4A    0.00   0.0  0
 HDF  CONST_15  C9A  N10  C10  C4A    0.00   0.0  0
 HDF  CONST_16  N10  C10  C4A  C5     0.00   0.0  0
 HDF  CONST_17  C7   C6   C5A  C5   180.00   0.0  0
 HDF  CONST_18  C9   C9A  C5A  C5   180.00   0.0  0
 HDF  CONST_19  N10  C9A  C5A  C5     0.00   0.0  0
 HDF  CONST_20  C10  C4A  C5   C5A    0.00   0.0  0
 HDF  CONST_21  C8   C7   C6   C5A    0.00   0.0  0
 HDF  CONST_22  C8   C9   C9A  C5A    0.00   0.0  0
 HDF  CONST_23  C10  N10  C9A  C5A    0.00   0.0  0
 HDF  CONST_24  C9   C9A  C5A  C6     0.00   0.0  0
 HDF  CONST_25  N10  C9A  C5A  C6   180.00   0.0  0
 HDF  CONST_26  C9   C8   C7   C6     0.00   0.0  0
 HDF  CONST_27  C9A  C5A  C6   C7     0.00   0.0  0
 HDF  CONST_28  C9A  C9   C8   C7     0.00   0.0  0
 HDF  CONST_29  N10  C9A  C9   C8   180.00   0.0  0
 HDF  CONST_30  C10  N10  C9A  C9   180.00   0.0  0
 HDF  CONST_31  C1'  N10  C10  N1     0.00   0.0  0
 HDF  CONST_32  O4   C4   N3   C2   180.00   0.0  0
 HDF  CONST_33  C10  N1   C2   O2   180.00   0.0  0
 HDF  CONST_34  C4   N3   C2   O2   180.00   0.0  0
 HDF  CONST_35  C5   C4A  C4   O4     0.00   0.0  0
 HDF  CONST_36  C10  C4A  C4   O4   180.00   0.0  0
 HDF  CONST_37  C1'  N10  C10  C4A  180.00   0.0  0
 HDF  CONST_38  C1'  N10  C9A  C5A  180.00   0.0  0
 HDF  CONST_39  O8   C8   C7   C6   180.00   0.0  0
 HDF  CONST_40  C9A  C9   C8   O8   180.00   0.0  0
 HDF  CONST_41  C1'  N10  C9A  C9     0.00   0.0  0
 HDF  CONST_42  HN3  N3   C2   N1   180.00   0.0  0
 HDF  CONST_43  H5   C5   C4A  C4     0.00   0.0  0
 HDF  CONST_44  H6   C6   C5A  C5     0.00   0.0  0
 HDF  CONST_45  H7   C7   C6   C5A  180.00   0.0  0
 HDF  CONST_46  H9   C9   C9A  C5A  180.00   0.0  0
 HDF  Var_01    C2'  C1'  N10  C9A   92.99  30.0  2

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
 HDF  chir_01  C2'  C1'  O2'  C3'  negativ
 HDF  chir_02  C3'  O3'  C2'  C4'  negativ
 HDF  chir_03  C4'  O4'  C3'  C5'  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
 HDF  plan-1  N1   0.020
 HDF  plan-1  C2   0.020
 HDF  plan-1  O2   0.020
 HDF  plan-1  N3   0.020
 HDF  plan-1  C4   0.020
 HDF  plan-1  O4   0.020
 HDF  plan-1  C4A  0.020
 HDF  plan-1  C5   0.020
 HDF  plan-1  C5A  0.020
 HDF  plan-1  C6   0.020
 HDF  plan-1  C7   0.020
 HDF  plan-1  C8   0.020
 HDF  plan-1  O8   0.020
 HDF  plan-1  C9   0.020
 HDF  plan-1  C9A  0.020
 HDF  plan-1  N10  0.020
 HDF  plan-1  C10  0.020
 HDF  plan-1  C1'  0.020
 HDF  plan-1  HN3  0.020
 HDF  plan-1  H5   0.020
 HDF  plan-1  H6   0.020
 HDF  plan-1  H7   0.020
 HDF  plan-1  H9   0.020

