# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 01:40:43 2020
#   Inital geometry file: a 62 line input string
#   Ligand name: 4-bromanyl-1-oxidanyl-naphthalene-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cc(Br)c2ccccc2c1O
#
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
 H5B  H5B  '4-bromanyl-1-oxidanyl-naphthalene-2-carboxylic acid'  ligand  21  15  .  2021-08-11  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_H5B
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
 H5B  C2   C   C      0   0.508  -2.9740  -1.2511   0.0984
 H5B  C4   C   CR6    0  -0.314  -1.6823  -0.4869   0.0649
 H5B  C5   C   CR16   0  -0.270  -0.4498  -1.1634   0.0156
 H5B  C6   C   CR6    0  -0.235   0.7310  -0.4818  -0.0150
 H5B  C8   C   CR66   0   0.211   0.7671   0.9409  -0.0007
 H5B  C11  C   CR16   0  -0.261   0.6853   3.7567   0.0320
 H5B  C12  C   CR16   0  -0.274  -0.4840   3.0447   0.0640
 H5B  O1   O   OC    -1  -0.543  -2.9566  -2.4822   0.0751
 H5B  O3   O   O      0  -0.635  -4.0271  -0.5324   0.1513
 H5B  BR7  BR  BR     0  -0.072   2.3426  -1.4804  -0.0775
 H5B  C9   C   CR16   0  -0.328   1.9548   1.7071  -0.0324
 H5B  C10  C   CR16   0  -0.238   1.9137   3.0768  -0.0164
 H5B  C13  C   CR66   0  -0.029  -0.4742   1.6336   0.0487
 H5B  C14  C   CR6    0   0.340  -1.7017   0.9014   0.0832
 H5B  O15  O   OH1    0  -0.636  -2.8396   1.5655   0.1330
 H5B  H1   H   HCR6   0   0.270  -0.4662  -2.2456   0.0042
 H5B  H2   H   HCR6   0   0.259   0.6652   4.8381   0.0438
 H5B  H3   H   HCR6   0   0.259  -1.4297   3.5677   0.1016
 H5B  H5   H   HCR6   0   0.255   2.9166   1.2147  -0.0710
 H5B  H6   H   HCR6   0   0.263   2.8380   3.6391  -0.0419
 H5B  H7   H   HOH1   0   0.469  -3.5544   0.7953   0.1502

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
 H5B  O3   C2   deloc     1.276  0.020  1.276
 H5B  O15  C14  single    1.318  0.020  1.318
 H5B  C2   O1   deloc     1.231  0.020  1.231
 H5B  C2   C4   single    1.501  0.020  1.501
 H5B  C14  C4   aromatic  1.389  0.020  1.389
 H5B  C14  C13  aromatic  1.430  0.020  1.430
 H5B  C4   C5   aromatic  1.407  0.020  1.407
 H5B  C12  C13  aromatic  1.411  0.020  1.411
 H5B  C12  C11  aromatic  1.369  0.020  1.369
 H5B  C13  C8   aromatic  1.422  0.020  1.422
 H5B  C5   C6   aromatic  1.364  0.020  1.364
 H5B  C11  C10  aromatic  1.405  0.020  1.405
 H5B  C8   C6   aromatic  1.423  0.020  1.423
 H5B  C8   C9   aromatic  1.414  0.020  1.414
 H5B  C6   BR7  single    1.897  0.020  1.897
 H5B  C10  C9   aromatic  1.370  0.020  1.370
 H5B  C5   H1   single    0.930  0.020  1.080
 H5B  C11  H2   single    0.930  0.020  1.080
 H5B  C12  H3   single    0.930  0.020  1.080
 H5B  C9   H5   single    0.930  0.020  1.080
 H5B  C10  H6   single    0.930  0.020  1.080
 H5B  O15  H7   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
 H5B  O3   C2   O1   125.14  3.000
 H5B  O1   C2   C4   119.76  3.000
 H5B  O3   C2   C4   115.11  3.000
 H5B  C14  C4   C5   119.57  3.000
 H5B  C5   C4   C2   120.65  3.000
 H5B  C14  C4   C2   119.78  3.000
 H5B  H1   C5   C6   120.84  3.000
 H5B  H1   C5   C4   117.90  3.000
 H5B  C6   C5   C4   121.27  3.000
 H5B  BR7  C6   C8   120.33  3.000
 H5B  BR7  C6   C5   118.25  3.000
 H5B  C8   C6   C5   121.42  3.000
 H5B  C13  C8   C9   118.03  3.000
 H5B  C9   C8   C6   124.26  3.000
 H5B  C13  C8   C6   117.71  3.000
 H5B  H2   C11  C10  120.04  3.000
 H5B  H2   C11  C12  120.24  3.000
 H5B  C10  C11  C12  119.72  3.000
 H5B  H3   C12  C13  119.34  3.000
 H5B  H3   C12  C11  119.75  3.000
 H5B  C13  C12  C11  120.91  3.000
 H5B  H5   C9   C10  118.83  3.000
 H5B  H5   C9   C8   120.09  3.000
 H5B  C10  C9   C8   121.08  3.000
 H5B  H6   C10  C9   119.57  3.000
 H5B  H6   C10  C11  119.74  3.000
 H5B  C9   C10  C11  120.69  3.000
 H5B  C14  C13  C12  120.39  3.000
 H5B  C12  C13  C8   119.57  3.000
 H5B  C14  C13  C8   120.04  3.000
 H5B  O15  C14  C13  118.94  3.000
 H5B  C13  C14  C4   119.99  3.000
 H5B  O15  C14  C4   121.07  3.000
 H5B  H7   O15  C14  102.62  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
 H5B  CONST_01  C12  C13  C14  C4   180.00   0.0  0
 H5B  CONST_02  C8   C13  C14  C4     0.00   0.0  0
 H5B  CONST_03  C8   C6   C5   C4     0.00   0.0  0
 H5B  CONST_04  C13  C14  C4   C5     0.00   0.0  0
 H5B  CONST_05  C13  C8   C6   C5     0.00   0.0  0
 H5B  CONST_06  C9   C8   C6   C5   180.00   0.0  0
 H5B  CONST_07  C14  C4   C5   C6     0.00   0.0  0
 H5B  CONST_08  C14  C13  C8   C6     0.00   0.0  0
 H5B  CONST_09  C12  C13  C8   C6   180.00   0.0  0
 H5B  CONST_10  C10  C9   C8   C6   180.00   0.0  0
 H5B  CONST_11  C11  C12  C13  C8     0.00   0.0  0
 H5B  CONST_12  C11  C10  C9   C8     0.00   0.0  0
 H5B  CONST_13  C14  C13  C12  C11  180.00   0.0  0
 H5B  CONST_14  C9   C8   C13  C12    0.00   0.0  0
 H5B  CONST_15  C9   C10  C11  C12    0.00   0.0  0
 H5B  CONST_16  C14  C13  C8   C9   180.00   0.0  0
 H5B  CONST_17  C13  C12  C11  C10    0.00   0.0  0
 H5B  CONST_18  C13  C8   C9   C10    0.00   0.0  0
 H5B  CONST_19  C13  C14  C4   C2   180.00   0.0  0
 H5B  CONST_20  C6   C5   C4   C2   180.00   0.0  0
 H5B  CONST_21  BR7  C6   C5   C4   180.00   0.0  0
 H5B  CONST_22  O15  C14  C4   C5   180.00   0.0  0
 H5B  CONST_23  O15  C14  C13  C8   180.00   0.0  0
 H5B  CONST_24  O15  C14  C13  C12    0.00   0.0  0
 H5B  CONST_25  C13  C8   C6   BR7  180.00   0.0  0
 H5B  CONST_26  C9   C8   C6   BR7    0.00   0.0  0
 H5B  CONST_27  H5   C9   C8   C6     0.00   0.0  0
 H5B  CONST_28  H3   C12  C13  C8   180.00   0.0  0
 H5B  CONST_29  H1   C5   C6   C8   180.00   0.0  0
 H5B  CONST_30  H6   C10  C9   C8   180.00   0.0  0
 H5B  CONST_31  H2   C11  C10  C9   180.00   0.0  0
 H5B  Var_01    O3   C2   C4   C5   179.55  30.0  3

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
 H5B  plan-1  C2   0.020
 H5B  plan-1  C4   0.020
 H5B  plan-1  C5   0.020
 H5B  plan-1  C6   0.020
 H5B  plan-1  C8   0.020
 H5B  plan-1  C11  0.020
 H5B  plan-1  C12  0.020
 H5B  plan-1  BR7  0.020
 H5B  plan-1  C9   0.020
 H5B  plan-1  C10  0.020
 H5B  plan-1  C13  0.020
 H5B  plan-1  C14  0.020
 H5B  plan-1  O15  0.020
 H5B  plan-1  H1   0.020
 H5B  plan-1  H2   0.020
 H5B  plan-1  H3   0.020
 H5B  plan-1  H5   0.020
 H5B  plan-1  H6   0.020
 H5B  plan-2  C2   0.020
 H5B  plan-2  C4   0.020
 H5B  plan-2  O1   0.020
 H5B  plan-2  O3   0.020

