# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 14:53:04 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: 3-(3,6-dihydroxy-9H-xanthen-9-yl)propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CC[C@H]1c2ccc(O)cc2Oc3cc(O)ccc13
#
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
 HXP  HXP  '3-(3,6-dihydroxy-9H-xanthen-9-yl)propanoic acid'  ligand  34  21  .  2021-08-11  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_HXP
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
 HXP  C1    C  CR16   0  -0.309  -1.2677   1.2340   1.8442
 HXP  C2    C  CR16   0  -0.343  -2.4938   0.9107   2.3976
 HXP  C3    C  CR6    0   0.356  -3.2744  -0.0794   1.8010
 HXP  O3    O  OH1    0  -0.634  -4.4611  -0.3717   2.3685
 HXP  C4    C  CR16   0  -0.485  -2.8255  -0.7111   0.6479
 HXP  C4A   C  CR6    0   0.344  -1.5906  -0.3594   0.1188
 HXP  O10   O  O2     0  -0.509  -1.2227  -0.9959  -1.0302
 HXP  C5A   C  C      0   0.343  -0.3154  -0.3772  -1.8389
 HXP  C5    C  C1     0  -0.483  -0.3184  -0.7566  -3.1750
 HXP  C6    C  C      0   0.355   0.5751  -0.1548  -4.0522
 HXP  O6    O  OH1    0  -0.634   0.6269  -0.4767  -5.3602
 HXP  C7    C  C1     0  -0.340   1.4480   0.8291  -3.5881
 HXP  C8    C  C1     0  -0.315   1.4253   1.1807  -2.2499
 HXP  C8A   C  C      0   0.061   0.5551   0.5832  -1.3438
 HXP  C9    C  CH1    0  -0.359   0.5866   0.8734   0.1319
 HXP  C9A   C  CR6    0   0.059  -0.7758   0.5983   0.7076
 HXP  C1'   C  CH2    0  -0.373   1.6928   0.0346   0.8052
 HXP  C2'   C  CH2    0  -0.596   1.8909   0.3378   2.2794
 HXP  C3'   C  C      0   0.417   3.0566  -0.4082   2.9547
 HXP  O1'   O  O      0  -0.608   3.5973  -1.3371   2.3231
 HXP  O2'   O  OC    -1  -0.631   3.3547  -0.0262   4.1059
 HXP  H1    H  HCR6   0   0.258  -0.6662   2.0036   2.3123
 HXP  H2    H  HCR6   0   0.261  -2.8479   1.4180   3.2858
 HXP  HO3   H  HOH1   0   0.475  -4.9194  -1.0525   1.8638
 HXP  H4    H  HCR6   0   0.279  -3.4313  -1.4599   0.1495
 HXP  H5    H  H      0   0.279  -1.0194  -1.5091  -3.5195
 HXP  HO6   H  HOH1   0   0.475  -0.0098  -1.1711  -5.5615
 HXP  H7    H  H      0   0.261   2.1386   1.3065  -4.2710
 HXP  H8    H  H      0   0.255   2.1134   1.9378  -1.8920
 HXP  H9    H  HCH1   0   0.256   0.8277   1.9314   0.2826
 HXP  H1'1  H  HCH2   0   0.222   2.6236   0.2263   0.2640
 HXP  H1'2  H  HCH2   0   0.212   1.4723  -1.0268   0.6614
 HXP  H2'1  H  HCH2   0   0.233   0.9805   0.0964   2.8389
 HXP  H2'2  H  HCH2   0   0.215   2.0355   1.4145   2.4227

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
 HXP  C1   C2    aromatic  1.384  0.020  1.384
 HXP  C1   C9A   aromatic  1.392  0.020  1.392
 HXP  C1   H1    single    0.930  0.020  1.080
 HXP  C2   C3    aromatic  1.395  0.020  1.395
 HXP  C2   H2    single    0.930  0.020  1.080
 HXP  C3   O3    single    1.348  0.020  1.348
 HXP  C3   C4    aromatic  1.389  0.020  1.389
 HXP  O3   HO3   single    0.850  0.020  0.980
 HXP  C4   C4A   aromatic  1.389  0.020  1.389
 HXP  C4   H4    single    0.930  0.020  1.080
 HXP  C4A  O10   single    1.364  0.020  1.364
 HXP  C4A  C9A   aromatic  1.388  0.020  1.388
 HXP  O10  C5A   single    1.364  0.020  1.364
 HXP  C5A  C5    aromatic  1.389  0.020  1.389
 HXP  C5A  C8A   aromatic  1.388  0.020  1.388
 HXP  C5   C6    aromatic  1.389  0.020  1.389
 HXP  C5   H5    single    0.930  0.020  1.080
 HXP  C6   O6    single    1.348  0.020  1.348
 HXP  C6   C7    aromatic  1.395  0.020  1.395
 HXP  O6   HO6   single    0.850  0.020  0.980
 HXP  C7   C8    aromatic  1.384  0.020  1.384
 HXP  C7   H7    single    0.930  0.020  1.080
 HXP  C8   C8A   aromatic  1.391  0.020  1.391
 HXP  C8   H8    single    0.930  0.020  1.080
 HXP  C8A  C9    single    1.504  0.020  1.504
 HXP  C9   C9A   single    1.504  0.020  1.504
 HXP  C9   C1'   single    1.543  0.020  1.543
 HXP  C9   H9    single    0.970  0.020  1.090
 HXP  C1'  C2'   single    1.518  0.020  1.518
 HXP  C1'  H1'1  single    0.970  0.020  1.090
 HXP  C1'  H1'2  single    0.970  0.020  1.090
 HXP  C2'  C3'   single    1.540  0.020  1.540
 HXP  C2'  H2'1  single    0.970  0.020  1.090
 HXP  C2'  H2'2  single    0.970  0.020  1.090
 HXP  C3'  O1'   deloc     1.247  0.020  1.247
 HXP  C3'  O2'   deloc     1.249  0.020  1.249

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
 HXP  H1    C1   C9A   118.76  3.000
 HXP  H1    C1   C2    119.03  3.000
 HXP  C9A   C1   C2    122.21  3.000
 HXP  H2    C2   C3    120.03  3.000
 HXP  H2    C2   C1    120.57  3.000
 HXP  C3    C2   C1    119.39  3.000
 HXP  C4    C3   O3    122.37  3.000
 HXP  C4    C3   C2    119.80  3.000
 HXP  O3    C3   C2    117.83  3.000
 HXP  HO3   O3   C3    110.59  3.000
 HXP  H4    C4   C4A   119.77  3.000
 HXP  H4    C4   C3    120.99  3.000
 HXP  C4A   C4   C3    119.23  3.000
 HXP  C9A   C4A  O10   121.39  3.000
 HXP  C9A   C4A  C4    122.34  3.000
 HXP  O10   C4A  C4    116.27  3.000
 HXP  C5A   O10  C4A   117.85  3.000
 HXP  C8A   C5A  C5    122.25  3.000
 HXP  C8A   C5A  O10   121.32  3.000
 HXP  C5    C5A  O10   116.43  3.000
 HXP  H5    C5   C6    121.04  3.000
 HXP  H5    C5   C5A   119.77  3.000
 HXP  C6    C5   C5A   119.19  3.000
 HXP  C7    C6   O6    117.86  3.000
 HXP  C7    C6   C5    119.86  3.000
 HXP  O6    C6   C5    122.27  3.000
 HXP  HO6   O6   C6    110.46  3.000
 HXP  H7    C7   C8    120.58  3.000
 HXP  H7    C7   C6    120.03  3.000
 HXP  C8    C7   C6    119.39  3.000
 HXP  H8    C8   C8A   118.82  3.000
 HXP  H8    C8   C7    119.10  3.000
 HXP  C8A   C8   C7    122.07  3.000
 HXP  C9    C8A  C8    122.89  3.000
 HXP  C9    C8A  C5A   119.78  3.000
 HXP  C8    C8A  C5A   117.22  3.000
 HXP  H9    C9   C1'   107.89  3.000
 HXP  H9    C9   C9A   108.86  3.000
 HXP  C1'   C9   C9A   112.51  3.000
 HXP  H9    C9   C8A   109.01  3.000
 HXP  C1'   C9   C8A   109.77  3.000
 HXP  C9A   C9   C8A   108.73  3.000
 HXP  C9    C9A  C4A   119.69  3.000
 HXP  C9    C9A  C1    123.29  3.000
 HXP  C4A   C9A  C1    116.99  3.000
 HXP  H1'2  C1'  H1'1  106.06  3.000
 HXP  H1'2  C1'  C2'   110.36  3.000
 HXP  H1'1  C1'  C2'   109.54  3.000
 HXP  H1'2  C1'  C9    109.01  3.000
 HXP  H1'1  C1'  C9    107.40  3.000
 HXP  C2'   C1'  C9    114.13  3.000
 HXP  H2'2  C2'  H2'1  105.03  3.000
 HXP  H2'2  C2'  C3'   108.59  3.000
 HXP  H2'1  C2'  C3'   107.36  3.000
 HXP  H2'2  C2'  C1'   109.91  3.000
 HXP  H2'1  C2'  C1'   110.09  3.000
 HXP  C3'   C2'  C1'   115.33  3.000
 HXP  O2'   C3'  O1'   126.25  3.000
 HXP  O2'   C3'  C2'   115.89  3.000
 HXP  O1'   C3'  C2'   117.85  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
 HXP  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 HXP  CONST_02  C4   C4A  C9A  C1      0.00   0.0  0
 HXP  CONST_03  C4A  C9A  C1   C2      0.00   0.0  0
 HXP  CONST_04  C4A  C4   C3   C2      0.00   0.0  0
 HXP  CONST_05  C9A  C1   C2   C3      0.00   0.0  0
 HXP  CONST_06  C9A  C4A  C4   C3      0.00   0.0  0
 HXP  CONST_07  C7   C6   C5   C5A     0.00   0.0  0
 HXP  CONST_08  C7   C8   C8A  C5A     0.00   0.0  0
 HXP  CONST_09  C8   C8A  C5A  C5      0.00   0.0  0
 HXP  CONST_10  C8   C7   C6   C5      0.00   0.0  0
 HXP  CONST_11  C8A  C5A  C5   C6      0.00   0.0  0
 HXP  CONST_12  C8A  C8   C7   C6      0.00   0.0  0
 HXP  CONST_13  O3   C3   C2   C1    180.00   0.0  0
 HXP  CONST_14  C4A  C4   C3   O3    180.00   0.0  0
 HXP  CONST_15  O6   C6   C5   C5A   180.00   0.0  0
 HXP  CONST_16  C8   C7   C6   O6    180.00   0.0  0
 HXP  CONST_17  H4   C4   C3   C2    180.00   0.0  0
 HXP  CONST_18  H1   C1   C2   C3    180.00   0.0  0
 HXP  CONST_19  H2   C2   C3   C4    180.00   0.0  0
 HXP  CONST_20  H5   C5   C5A  O10     0.00   0.0  0
 HXP  CONST_21  H8   C8   C8A  C5A   180.00   0.0  0
 HXP  CONST_22  H7   C7   C6   C5    180.00   0.0  0
 HXP  Var_01    C5   C5A  O10  C4A  -157.08  30.0  1
 HXP  Var_02    C9A  C4A  O10  C5A   -22.92  30.0  1
 HXP  Var_03    C3'  C2'  C1'  C9   -175.69  30.0  3
 HXP  Var_04    O1'  C3'  C2'  C1'   -11.14  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
 HXP  chir_01  C9  C8A  C9A  C1'  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
 HXP  plan-1  C2'  0.020
 HXP  plan-1  C3'  0.020
 HXP  plan-1  O1'  0.020
 HXP  plan-1  O2'  0.020
 HXP  plan-2  C1   0.020
 HXP  plan-2  C2   0.020
 HXP  plan-2  C3   0.020
 HXP  plan-2  O3   0.020
 HXP  plan-2  C4   0.020
 HXP  plan-2  C4A  0.020
 HXP  plan-2  O10  0.020
 HXP  plan-2  C9   0.020
 HXP  plan-2  C9A  0.020
 HXP  plan-2  H1   0.020
 HXP  plan-2  H2   0.020
 HXP  plan-2  H4   0.020
 HXP  plan-3  O10  0.020
 HXP  plan-3  C5A  0.020
 HXP  plan-3  C5   0.020
 HXP  plan-3  C6   0.020
 HXP  plan-3  O6   0.020
 HXP  plan-3  C7   0.020
 HXP  plan-3  C8   0.020
 HXP  plan-3  C8A  0.020
 HXP  plan-3  C9   0.020
 HXP  plan-3  H5   0.020
 HXP  plan-3  H7   0.020
 HXP  plan-3  H8   0.020

