# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 06:51:55 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: (2~{R},3~{R})-2-[(2~{S},3~{S})-3-bromanyl-1,4-bis(oxidanylidene)-2,3-dihydronaphthalen-2-yl]-3-oxidanyl-2,3-dihydronaphthalene-1,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1[C@@H]([C@@H]2[C@H](Br)C(=O)c3ccccc3C2=O)C(=O)c4ccccc4C1=O
#
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
 E6A  E6A  (2~{R},3~{R})-2-[(2~{S},3~{S})-3-bromanyl-1,4-bis(oxidanylidene)-2,3-dihydronaphthalen-2-yl]-3-oxidanyl-2,3-dihydronaphthalene-1,4-dione  ligand  39  26  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_E6A
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
 E6A  O40  O   O     0  -0.352  -0.2847  -1.5364  -1.8552
 E6A  C23  C   C     0   0.367  -0.8895  -0.7777  -1.1348
 E6A  C24  C   CR6   0   0.029  -2.2144  -1.1266  -0.5659
 E6A  C37  C   CR16  0  -0.275  -2.6718  -2.4370  -0.6522
 E6A  C36  C   CR16  0  -0.230  -3.8830  -2.7877  -0.0790
 E6A  C35  C   CR16  0  -0.235  -4.6470  -1.8324   0.5825
 E6A  C34  C   CR16  0  -0.267  -4.2009  -0.5239   0.6699
 E6A  C25  C   CR6   0  -0.016  -2.9873  -0.1639   0.0945
 E6A  C26  C   C     0   0.313  -2.5150   1.2372   0.1782
 E6A  O38  O   O     0  -0.361  -3.0099   2.0468   0.9282
 E6A  C27  C   CH1   0  -0.054  -1.3961   1.6102  -0.7871
 E6A  O41  O   OH1   0  -0.644  -1.8973   1.5661  -2.0992
 E6A  C22  C   CH1   0  -0.433  -0.2901   0.5609  -0.7251
 E6A  C6   C   CH1   0  -0.408   0.3855   0.5131   0.6812
 E6A  C5   C   CH1   0  -0.491   1.7742   1.1545   0.7020
 E6A  BR   BR  BR    0  -0.028   1.7432   3.0480   0.2815
 E6A  C4   C   C     0   0.381   2.7350   0.4114  -0.2059
 E6A  O20  O   O     0  -0.343   3.4869   0.9615  -0.9688
 E6A  C18  C   CR6   0  -0.005   2.7142  -1.0621  -0.0337
 E6A  C13  C   CR6   0   0.021   1.6852  -1.6936   0.6746
 E6A  C1   C   C     0   0.370   0.5351  -0.9181   1.1883
 E6A  O19  O   O     0  -0.344  -0.2807  -1.3938   1.9409
 E6A  C17  C   CR16  0  -0.264   3.7594  -1.8177  -0.5558
 E6A  C16  C   CR16  0  -0.231   3.7833  -3.1893  -0.3663
 E6A  C15  C   CR16  0  -0.228   2.7661  -3.8154   0.3461
 E6A  C14  C   CR16  0  -0.268   1.7207  -3.0712   0.8651
 E6A  H1   H   HCR6  0   0.276  -2.0747  -3.1857  -1.1553
 E6A  H2   H   HCR6  0   0.278  -4.2316  -3.8097  -0.1420
 E6A  H3   H   HCR6  0   0.278  -5.5926  -2.1103   1.0280
 E6A  H4   H   HCR6  0   0.276  -4.8009   0.2211   1.1749
 E6A  H5   H   HCH1  0   0.277  -1.0156   2.6006  -0.5204
 E6A  H6   H   HOH1  0   0.471  -2.5008   2.3045  -2.2366
 E6A  H7   H   HCH1  0   0.315   0.4606   0.8061  -1.4821
 E6A  H8   H   HCH1  0   0.333  -0.2393   1.0250   1.4169
 E6A  H9   H   HCH1  0   0.371   2.1689   1.0837   1.7219
 E6A  H10  H   HCR6  0   0.280   4.5599  -1.3314  -1.0961
 E6A  H11  H   HCR6  0   0.282   4.5989  -3.7726  -0.7715
 E6A  H12  H   HCR6  0   0.281   2.7883  -4.8869   0.4921
 E6A  H13  H   HCR6  0   0.280   0.9207  -3.5613   1.4030

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
 E6A  O41  C27  single    1.405  0.020  1.405
 E6A  O38  C26  double    1.209  0.020  1.209
 E6A  C16  C15  aromatic  1.391  0.020  1.391
 E6A  C16  C17  aromatic  1.385  0.020  1.385
 E6A  C15  C14  aromatic  1.384  0.020  1.384
 E6A  C27  C26  single    1.524  0.020  1.524
 E6A  C27  C22  single    1.526  0.020  1.526
 E6A  C17  C18  aromatic  1.391  0.020  1.391
 E6A  C14  C13  aromatic  1.391  0.020  1.391
 E6A  C5   C6   single    1.530  0.020  1.530
 E6A  C5   C4   single    1.516  0.020  1.516
 E6A  C5   BR   single    1.940  0.020  1.940
 E6A  C26  C25  single    1.481  0.020  1.481
 E6A  C6   C22  single    1.561  0.020  1.561
 E6A  C6   C1   single    1.526  0.020  1.526
 E6A  C18  C13  aromatic  1.400  0.020  1.400
 E6A  C18  C4   single    1.484  0.020  1.484
 E6A  C13  C1   single    1.479  0.020  1.479
 E6A  C4   O20  double    1.204  0.020  1.204
 E6A  C22  C23  single    1.523  0.020  1.523
 E6A  C1   O19  double    1.208  0.020  1.208
 E6A  C25  C34  aromatic  1.391  0.020  1.391
 E6A  C25  C24  aromatic  1.400  0.020  1.400
 E6A  C34  C35  aromatic  1.385  0.020  1.385
 E6A  C23  C24  single    1.483  0.020  1.483
 E6A  C23  O40  double    1.208  0.020  1.208
 E6A  C24  C37  aromatic  1.391  0.020  1.391
 E6A  C35  C36  aromatic  1.391  0.020  1.391
 E6A  C37  C36  aromatic  1.385  0.020  1.385
 E6A  C37  H1   single    0.930  0.020  1.080
 E6A  C36  H2   single    0.930  0.020  1.080
 E6A  C35  H3   single    0.930  0.020  1.080
 E6A  C34  H4   single    0.930  0.020  1.080
 E6A  C27  H5   single    0.970  0.020  1.090
 E6A  O41  H6   single    0.850  0.020  0.980
 E6A  C22  H7   single    0.970  0.020  1.090
 E6A  C6   H8   single    0.970  0.020  1.090
 E6A  C5   H9   single    0.970  0.020  1.090
 E6A  C17  H10  single    0.930  0.020  1.080
 E6A  C16  H11  single    0.930  0.020  1.080
 E6A  C15  H12  single    0.930  0.020  1.080
 E6A  C14  H13  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
 E6A  C22  C23  C24  117.07  3.000
 E6A  C24  C23  O40  121.87  3.000
 E6A  C22  C23  O40  121.01  3.000
 E6A  C25  C24  C37  119.71  3.000
 E6A  C37  C24  C23  119.45  3.000
 E6A  C25  C24  C23  120.81  3.000
 E6A  H1   C37  C36  119.99  3.000
 E6A  H1   C37  C24  119.97  3.000
 E6A  C36  C37  C24  120.03  3.000
 E6A  H2   C36  C35  119.98  3.000
 E6A  H2   C36  C37  119.79  3.000
 E6A  C35  C36  C37  120.22  3.000
 E6A  H3   C35  C34  119.89  3.000
 E6A  H3   C35  C36  119.98  3.000
 E6A  C34  C35  C36  120.13  3.000
 E6A  H4   C34  C25  119.94  3.000
 E6A  H4   C34  C35  120.09  3.000
 E6A  C25  C34  C35  119.97  3.000
 E6A  C26  C25  C34  119.99  3.000
 E6A  C34  C25  C24  119.93  3.000
 E6A  C26  C25  C24  120.08  3.000
 E6A  C27  C26  O38  121.96  3.000
 E6A  C27  C26  C25  115.46  3.000
 E6A  O38  C26  C25  122.54  3.000
 E6A  H5   C27  C22  111.13  3.000
 E6A  H5   C27  O41  112.34  3.000
 E6A  C22  C27  O41  105.95  3.000
 E6A  H5   C27  C26  108.82  3.000
 E6A  C22  C27  C26  109.76  3.000
 E6A  O41  C27  C26  108.78  3.000
 E6A  H6   O41  C27  109.42  3.000
 E6A  H7   C22  C6   109.47  3.000
 E6A  H7   C22  C27  108.36  3.000
 E6A  C6   C22  C27  111.80  3.000
 E6A  H7   C22  C23  106.32  3.000
 E6A  C6   C22  C23  112.70  3.000
 E6A  C27  C22  C23  107.95  3.000
 E6A  H8   C6   C1   105.77  3.000
 E6A  H8   C6   C5   108.27  3.000
 E6A  C1   C6   C5   107.44  3.000
 E6A  H8   C6   C22  110.17  3.000
 E6A  C1   C6   C22  111.75  3.000
 E6A  C5   C6   C22  113.10  3.000
 E6A  H9   C5   C4   107.30  3.000
 E6A  H9   C5   BR   105.70  3.000
 E6A  C4   C5   BR   111.02  3.000
 E6A  H9   C5   C6   108.21  3.000
 E6A  BR   C5   C6   113.06  3.000
 E6A  C4   C5   C6   111.20  3.000
 E6A  C18  C4   O20  122.41  3.000
 E6A  O20  C4   C5   123.44  3.000
 E6A  C18  C4   C5   114.10  3.000
 E6A  C17  C18  C13  119.80  3.000
 E6A  C13  C18  C4   121.14  3.000
 E6A  C17  C18  C4   119.03  3.000
 E6A  C14  C13  C1   119.43  3.000
 E6A  C1   C13  C18  120.71  3.000
 E6A  C14  C13  C18  119.82  3.000
 E6A  O19  C1   C13  122.36  3.000
 E6A  O19  C1   C6   120.69  3.000
 E6A  C13  C1   C6   116.91  3.000
 E6A  H10  C17  C16  120.07  3.000
 E6A  H10  C17  C18  119.95  3.000
 E6A  C16  C17  C18  119.97  3.000
 E6A  H11  C16  C15  120.04  3.000
 E6A  H11  C16  C17  119.73  3.000
 E6A  C15  C16  C17  120.22  3.000
 E6A  H12  C15  C14  119.83  3.000
 E6A  H12  C15  C16  120.01  3.000
 E6A  C14  C15  C16  120.16  3.000
 E6A  H13  C14  C15  120.10  3.000
 E6A  H13  C14  C13  119.87  3.000
 E6A  C15  C14  C13  120.02  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
 E6A  CONST_01  C35  C34  C25  C24     0.00   0.0  0
 E6A  CONST_02  C35  C36  C37  C24     0.00   0.0  0
 E6A  CONST_03  C34  C25  C24  C37     0.00   0.0  0
 E6A  CONST_04  C34  C35  C36  C37     0.00   0.0  0
 E6A  CONST_05  C25  C34  C35  C36     0.00   0.0  0
 E6A  CONST_06  C25  C24  C37  C36     0.00   0.0  0
 E6A  CONST_07  C15  C16  C17  C18     0.00   0.0  0
 E6A  CONST_08  C15  C14  C13  C18     0.00   0.0  0
 E6A  CONST_09  C16  C15  C14  C13     0.00   0.0  0
 E6A  CONST_10  C16  C17  C18  C13     0.00   0.0  0
 E6A  CONST_11  C14  C15  C16  C17     0.00   0.0  0
 E6A  CONST_12  C14  C13  C18  C17     0.00   0.0  0
 E6A  CONST_13  H1   C37  C24  C23     0.00   0.0  0
 E6A  CONST_14  H4   C34  C25  C24   180.00   0.0  0
 E6A  CONST_15  H2   C36  C37  C24   180.00   0.0  0
 E6A  CONST_16  H3   C35  C36  C37   180.00   0.0  0
 E6A  CONST_17  H10  C17  C18  C4      0.00   0.0  0
 E6A  CONST_18  H11  C16  C17  C18   180.00   0.0  0
 E6A  CONST_19  H13  C14  C13  C18   180.00   0.0  0
 E6A  CONST_20  H12  C15  C14  C13   180.00   0.0  0
 E6A  Var_01    C27  C26  C25  C24    15.98  30.0  1
 E6A  Var_02    C22  C23  C24  C37  -165.51  30.0  1
 E6A  Var_03    C14  C13  C1   C6   -166.29  30.0  1
 E6A  Var_04    C17  C18  C4   C5   -164.35  30.0  1

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
 E6A  chir_01  C27  O41  C26  C22  negativ
 E6A  chir_02  C22  C23  C6   C27  positiv
 E6A  chir_03  C6   C5   C22  C1   negativ
 E6A  chir_04  C5   BR   C6   C4   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
 E6A  plan-1  C23  0.020
 E6A  plan-1  C24  0.020
 E6A  plan-1  C37  0.020
 E6A  plan-1  C36  0.020
 E6A  plan-1  C35  0.020
 E6A  plan-1  C34  0.020
 E6A  plan-1  C25  0.020
 E6A  plan-1  C26  0.020
 E6A  plan-1  H1   0.020
 E6A  plan-1  H2   0.020
 E6A  plan-1  H3   0.020
 E6A  plan-1  H4   0.020
 E6A  plan-2  C4   0.020
 E6A  plan-2  C18  0.020
 E6A  plan-2  C13  0.020
 E6A  plan-2  C1   0.020
 E6A  plan-2  C17  0.020
 E6A  plan-2  C16  0.020
 E6A  plan-2  C15  0.020
 E6A  plan-2  C14  0.020
 E6A  plan-2  H10  0.020
 E6A  plan-2  H11  0.020
 E6A  plan-2  H12  0.020
 E6A  plan-2  H13  0.020
 E6A  plan-3  O40  0.020
 E6A  plan-3  C23  0.020
 E6A  plan-3  C24  0.020
 E6A  plan-3  C22  0.020
 E6A  plan-4  C25  0.020
 E6A  plan-4  C26  0.020
 E6A  plan-4  O38  0.020
 E6A  plan-4  C27  0.020
 E6A  plan-5  C5   0.020
 E6A  plan-5  C4   0.020
 E6A  plan-5  O20  0.020
 E6A  plan-5  C18  0.020
 E6A  plan-6  C6   0.020
 E6A  plan-6  C13  0.020
 E6A  plan-6  C1   0.020
 E6A  plan-6  O19  0.020

