# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 00:42:01 2022
#   Inital geometry file: a 76 line input string
#   Ligand name: 1,3,6,7-tetrahydroxy-9H-xanthen-9-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1cc(O)c2C(=O)c3cc(O)c(O)cc3Oc2c1
#
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
 NRA  NRA  1,3,6,7-tetrahydroxy-9H-xanthen-9-one  ligand  27  19  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NRA
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
 NRA  C10   C  CR16  0  -0.429  -2.3055  -1.1320   0.0168
 NRA  C13   C  CR6   0   0.323  -3.3937   1.0153  -0.0796
 NRA  C15   C  CR16  0  -0.442  -2.1679   1.6510  -0.0754
 NRA  C02   C  CR6   0   0.399   3.7132   1.0767   0.0833
 NRA  C03   C  CR16  0  -0.501   3.8167  -0.3147   0.1364
 NRA  C04   C  CR6   0   0.405   2.6676  -1.0856   0.1350
 NRA  O05   O  OH1   0  -0.627   2.7730  -2.4077   0.1866
 NRA  C06   C  CR66  0  -0.336   1.3923  -0.4700   0.0800
 NRA  C07   C  CR6   0   0.496   0.1834  -1.2562   0.0765
 NRA  O08   O  O     0  -0.494   0.2020  -2.4952   0.1180
 NRA  C09   C  CR66  0  -0.095  -1.0527  -0.4987   0.0222
 NRA  C11   C  CR6   0   0.282  -3.4615  -0.3980  -0.0322
 NRA  O12   O  OH1   0  -0.641  -4.7082  -0.9129  -0.0404
 NRA  O14   O  OH1   0  -0.611  -4.5038   1.7555  -0.1301
 NRA  C16   C  CR66  0   0.352  -1.0060   0.8904  -0.0247
 NRA  O17   O  O     0  -0.481   0.1592   1.5735  -0.0230
 NRA  C18   C  CR66  0   0.405   1.3391   0.9294   0.0293
 NRA  C19   C  CR16  0  -0.477   2.4751   1.7141   0.0299
 NRA  H10   H  HCR6  0   0.288  -2.3494  -2.2141   0.0521
 NRA  H15   H  HCR6  0   0.294  -2.1161   2.7317  -0.1110
 NRA  HO01  H  HOH1  0   0.484   5.6023   1.3343   0.1127
 NRA  H03   H  HCR6  0   0.285   4.7856  -0.7982   0.1794
 NRA  HO05  H  HOH1  0   0.479   1.8555  -2.7766   0.1750
 NRA  HO12  H  HOH1  0   0.488  -4.6890  -1.8762  -0.0131
 NRA  HO14  H  HOH1  0   0.483  -5.2921   1.1974  -0.1204
 NRA  H19   H  HCR6  0   0.285   2.4056   2.7928  -0.0095
 NRA  O01   O  OH1   0  -0.616   4.7946   1.8605   0.0817

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
 NRA  C10  C11   aromatic  1.370  0.020  1.370
 NRA  C10  C09   aromatic  1.404  0.020  1.404
 NRA  C10  H10   single    0.930  0.020  1.080
 NRA  C11  C13   aromatic  1.416  0.020  1.416
 NRA  C13  O14   single    1.335  0.020  1.335
 NRA  C13  C15   aromatic  1.381  0.020  1.381
 NRA  C16  C15   aromatic  1.390  0.020  1.390
 NRA  C15  H15   single    0.930  0.020  1.080
 NRA  C02  O01   single    1.336  0.020  1.336
 NRA  O01  HO01  single    0.850  0.020  0.980
 NRA  C03  C02   aromatic  1.396  0.020  1.396
 NRA  C02  C19   aromatic  1.394  0.020  1.394
 NRA  C04  C03   aromatic  1.384  0.020  1.384
 NRA  C03  H03   single    0.930  0.020  1.080
 NRA  O05  C04   single    1.327  0.020  1.327
 NRA  C04  C06   aromatic  1.417  0.020  1.417
 NRA  O05  HO05  single    0.850  0.020  0.980
 NRA  C07  C06   single    1.442  0.020  1.442
 NRA  C06  C18   aromatic  1.401  0.020  1.401
 NRA  O08  C07   double    1.240  0.020  1.240
 NRA  C07  C09   single    1.451  0.020  1.451
 NRA  C09  C16   aromatic  1.391  0.020  1.391
 NRA  O12  C11   single    1.349  0.020  1.349
 NRA  O12  HO12  single    0.850  0.020  0.980
 NRA  O14  HO14  single    0.850  0.020  0.980
 NRA  C16  O17   single    1.351  0.020  1.351
 NRA  C18  O17   single    1.345  0.020  1.345
 NRA  C18  C19   aromatic  1.381  0.020  1.381
 NRA  C19  H19   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
 NRA  H10   C10  C11  120.13  3.000
 NRA  H10   C10  C09  119.12  3.000
 NRA  C11   C10  C09  120.76  3.000
 NRA  O14   C13  C11  120.99  3.000
 NRA  O14   C13  C15  118.88  3.000
 NRA  C11   C13  C15  120.13  3.000
 NRA  H15   C15  C16  120.51  3.000
 NRA  H15   C15  C13  120.13  3.000
 NRA  C16   C15  C13  119.37  3.000
 NRA  C19   C02  C03  121.54  3.000
 NRA  C19   C02  O01  116.80  3.000
 NRA  C03   C02  O01  121.66  3.000
 NRA  H03   C03  C04  119.61  3.000
 NRA  H03   C03  C02  120.82  3.000
 NRA  C04   C03  C02  119.58  3.000
 NRA  C06   C04  O05  120.38  3.000
 NRA  C06   C04  C03  120.36  3.000
 NRA  O05   C04  C03  119.27  3.000
 NRA  HO05  O05  C04  107.30  3.000
 NRA  C18   C06  C07  120.83  3.000
 NRA  C18   C06  C04  117.99  3.000
 NRA  C07   C06  C04  121.17  3.000
 NRA  C09   C07  O08  122.40  3.000
 NRA  C09   C07  C06  115.45  3.000
 NRA  O08   C07  C06  122.15  3.000
 NRA  C16   C09  C07  119.62  3.000
 NRA  C16   C09  C10  118.72  3.000
 NRA  C07   C09  C10  121.67  3.000
 NRA  O12   C11  C13  115.16  3.000
 NRA  O12   C11  C10  125.13  3.000
 NRA  C13   C11  C10  119.70  3.000
 NRA  HO12  O12  C11  111.28  3.000
 NRA  HO14  O14  C13  110.96  3.000
 NRA  O17   C16  C09  122.29  3.000
 NRA  O17   C16  C15  116.39  3.000
 NRA  C09   C16  C15  121.32  3.000
 NRA  C18   O17  C16  120.96  3.000
 NRA  C19   C18  O17  116.72  3.000
 NRA  C19   C18  C06  122.43  3.000
 NRA  O17   C18  C06  120.85  3.000
 NRA  H19   C19  C18  120.92  3.000
 NRA  H19   C19  C02  120.97  3.000
 NRA  C18   C19  C02  118.11  3.000
 NRA  HO01  O01  C02  110.97  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
 NRA  CONST_01  C15  C13  C11  C10     0.00   0.0  0
 NRA  CONST_02  C15  C16  C09  C10     0.00   0.0  0
 NRA  CONST_03  C09  C10  C11  C13     0.00   0.0  0
 NRA  CONST_04  C09  C16  C15  C13     0.00   0.0  0
 NRA  CONST_05  C06  C04  C03  C02     0.00   0.0  0
 NRA  CONST_06  C06  C18  C19  C02     0.00   0.0  0
 NRA  CONST_07  C18  C19  C02  C03     0.00   0.0  0
 NRA  CONST_08  C18  C06  C04  C03     0.00   0.0  0
 NRA  CONST_09  C19  C02  C03  C04     0.00   0.0  0
 NRA  CONST_10  C19  C18  C06  C04     0.00   0.0  0
 NRA  CONST_11  C16  C09  C10  C11     0.00   0.0  0
 NRA  CONST_12  C16  C15  C13  C11     0.00   0.0  0
 NRA  CONST_13  O14  C13  C11  C10   180.00   0.0  0
 NRA  CONST_14  O12  C11  C13  C15   180.00   0.0  0
 NRA  CONST_15  C04  C03  C02  O01   180.00   0.0  0
 NRA  CONST_16  C18  C19  C02  O01   180.00   0.0  0
 NRA  CONST_17  O05  C04  C03  C02   180.00   0.0  0
 NRA  CONST_18  C07  C06  C04  O05     0.00   0.0  0
 NRA  CONST_19  C18  C06  C04  O05   180.00   0.0  0
 NRA  CONST_20  O12  C11  C10  C09   180.00   0.0  0
 NRA  CONST_21  C16  C15  C13  O14   180.00   0.0  0
 NRA  CONST_22  H10  C10  C11  C13   180.00   0.0  0
 NRA  CONST_23  H19  C19  C02  C03   180.00   0.0  0
 NRA  CONST_24  H03  C03  C04  C06   180.00   0.0  0
 NRA  CONST_25  H15  C15  C16  C09   180.00   0.0  0
 NRA  Var_01    C06  C07  C09  C10  -179.80  30.0  1
 NRA  Var_02    C09  C07  C06  C04   179.79  30.0  1
 NRA  Var_03    C19  C18  O17  C16  -179.84  30.0  1

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
 NRA  plan-1  C06  0.020
 NRA  plan-1  C07  0.020
 NRA  plan-1  O08  0.020
 NRA  plan-1  C09  0.020
 NRA  plan-2  C10  0.020
 NRA  plan-2  C13  0.020
 NRA  plan-2  C15  0.020
 NRA  plan-2  C07  0.020
 NRA  plan-2  C09  0.020
 NRA  plan-2  C11  0.020
 NRA  plan-2  O12  0.020
 NRA  plan-2  O14  0.020
 NRA  plan-2  C16  0.020
 NRA  plan-2  O17  0.020
 NRA  plan-2  H10  0.020
 NRA  plan-2  H15  0.020
 NRA  plan-3  C02  0.020
 NRA  plan-3  C03  0.020
 NRA  plan-3  C04  0.020
 NRA  plan-3  O05  0.020
 NRA  plan-3  C06  0.020
 NRA  plan-3  C07  0.020
 NRA  plan-3  O17  0.020
 NRA  plan-3  C18  0.020
 NRA  plan-3  C19  0.020
 NRA  plan-3  H03  0.020
 NRA  plan-3  H19  0.020
 NRA  plan-3  O01  0.020

