# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 05:57:38 2020
#   Inital geometry file: a 56 line input string
#   Ligand name: 2,3,5,6-tetrafluoro-4-methoxybenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1c(F)c(F)c(C(N)=O)c(F)c1F
#
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
 BEK  BEK  2,3,5,6-tetrafluoro-4-methoxybenzamide  ligand  20  15  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BEK
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
 BEK  C1   C  C     0   0.485   0.0168   0.0083  -2.7235
 BEK  O    O  O     0  -0.447   0.0262   1.0651  -3.3255
 BEK  N    N  NH2   0  -0.766   0.0153  -1.2010  -3.2797
 BEK  C2   C  CR6   0  -0.502   0.0088  -0.0061  -1.2149
 BEK  C3   C  CR6   0   0.460  -1.1795   0.0347  -0.5133
 BEK  C7   C  CR6   0   0.461   1.1906   0.0335  -0.5014
 BEK  F3   F  F     0  -0.288  -2.3330   0.0041  -1.1789
 BEK  F7   F  F     0  -0.288   2.3505   0.0031  -1.1558
 BEK  C4   C  CR6   0   0.363  -1.1938   0.0978   0.8665
 BEK  C6   C  CR6   0   0.368   1.1910   0.1004   0.8776
 BEK  C5   C  CR6   0   0.057  -0.0054   0.1419   1.5851
 BEK  F4   F  F     0  -0.289  -2.3530   0.1299   1.5170
 BEK  F6   F  F     0  -0.290   2.3435   0.1399   1.5401
 BEK  O5   O  O2    0  -0.477  -0.0158   0.2543   2.9239
 BEK  C8   C  CH3   0  -0.417   0.0509  -0.9868   3.6335
 BEK  HN1  H  HNH2  0   0.417   0.0126  -1.3035  -4.2828
 BEK  HN2  H  HNH2  0   0.424  -0.0032  -2.0406  -2.7252
 BEK  H81  H  HCH3  0   0.255   0.0550  -0.7385   4.6915
 BEK  H82  H  HCH3  0   0.238  -0.8146  -1.6154   3.4171
 BEK  H83  H  HCH3  0   0.237   0.9622  -1.5369   3.3937

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
 BEK  C1  O    double    1.216  0.020  1.216
 BEK  C1  N    single    1.331  0.020  1.331
 BEK  C1  C2   single    1.509  0.020  1.509
 BEK  N   HN1  single    0.860  0.020  1.020
 BEK  N   HN2  single    0.860  0.020  1.020
 BEK  C2  C3   aromatic  1.381  0.020  1.381
 BEK  C2  C7   aromatic  1.381  0.020  1.381
 BEK  C3  F3   single    1.332  0.020  1.332
 BEK  C3  C4   aromatic  1.381  0.020  1.381
 BEK  C7  F7   single    1.332  0.020  1.332
 BEK  C7  C6   aromatic  1.381  0.020  1.381
 BEK  C4  C5   aromatic  1.389  0.020  1.389
 BEK  C4  F4   single    1.330  0.020  1.330
 BEK  C6  C5   aromatic  1.390  0.020  1.390
 BEK  C6  F6   single    1.330  0.020  1.330
 BEK  C5  O5   single    1.344  0.020  1.344
 BEK  O5  C8   single    1.431  0.020  1.431
 BEK  C8  H81  single    0.970  0.020  1.090
 BEK  C8  H82  single    0.970  0.020  1.090
 BEK  C8  H83  single    0.970  0.020  1.090

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
 BEK  C2   C1  N    114.15  3.000
 BEK  C2   C1  O    120.22  3.000
 BEK  N    C1  O    125.63  3.000
 BEK  HN2  N   HN1  117.61  3.000
 BEK  HN2  N   C1   121.86  3.000
 BEK  HN1  N   C1   120.52  3.000
 BEK  C7   C2  C3   118.24  3.000
 BEK  C7   C2  C1   120.78  3.000
 BEK  C3   C2  C1   120.83  3.000
 BEK  C4   C3  F3   119.42  3.000
 BEK  C4   C3  C2   121.19  3.000
 BEK  F3   C3  C2   119.39  3.000
 BEK  C6   C7  F7   119.44  3.000
 BEK  C6   C7  C2   121.17  3.000
 BEK  F7   C7  C2   119.39  3.000
 BEK  F4   C4  C5   119.46  3.000
 BEK  F4   C4  C3   119.92  3.000
 BEK  C5   C4  C3   120.61  3.000
 BEK  F6   C6  C5   119.42  3.000
 BEK  F6   C6  C7   119.95  3.000
 BEK  C5   C6  C7   120.63  3.000
 BEK  O5   C5  C6   121.08  3.000
 BEK  O5   C5  C4   120.75  3.000
 BEK  C6   C5  C4   118.15  3.000
 BEK  C8   O5  C5   114.91  3.000
 BEK  H83  C8  H82  109.17  3.000
 BEK  H83  C8  H81  109.02  3.000
 BEK  H82  C8  H81  109.12  3.000
 BEK  H83  C8  O5   111.54  3.000
 BEK  H82  C8  O5   111.36  3.000
 BEK  H81  C8  O5   106.54  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
 BEK  CONST_01  C5   C4  C3  C2    0.00   0.0  0
 BEK  CONST_02  C5   C6  C7  C2    0.00   0.0  0
 BEK  CONST_03  C6   C7  C2  C3    0.00   0.0  0
 BEK  CONST_04  C6   C5  C4  C3    0.00   0.0  0
 BEK  CONST_05  C4   C3  C2  C7    0.00   0.0  0
 BEK  CONST_06  C4   C5  C6  C7    0.00   0.0  0
 BEK  CONST_07  C4   C3  C2  C1  180.00   0.0  0
 BEK  CONST_08  C6   C7  C2  C1  180.00   0.0  0
 BEK  CONST_09  F4   C4  C3  C2  180.00   0.0  0
 BEK  CONST_10  F6   C6  C7  C2  180.00   0.0  0
 BEK  CONST_11  F7   C7  C2  C3  180.00   0.0  0
 BEK  CONST_12  O5   C5  C4  C3  180.00   0.0  0
 BEK  CONST_13  F3   C3  C2  C7  180.00   0.0  0
 BEK  CONST_14  O5   C5  C6  C7  180.00   0.0  0
 BEK  CONST_15  C5   C4  C3  F3  180.00   0.0  0
 BEK  CONST_16  C5   C6  C7  F7  180.00   0.0  0
 BEK  CONST_17  F6   C6  C5  C4  180.00   0.0  0
 BEK  CONST_18  F4   C4  C5  C6  180.00   0.0  0
 BEK  CONST_19  HN1  N   C1  C2  180.00   0.0  0
 BEK  CONST_20  HN2  N   C1  C2    0.00   0.0  0
 BEK  Var_01    C3   C2  C1  O    88.04  30.0  2
 BEK  Var_02    H81  C8  O5  C5  178.84  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
 BEK  plan-1  C1   0.020
 BEK  plan-1  C2   0.020
 BEK  plan-1  C3   0.020
 BEK  plan-1  C7   0.020
 BEK  plan-1  F3   0.020
 BEK  plan-1  F7   0.020
 BEK  plan-1  C4   0.020
 BEK  plan-1  C6   0.020
 BEK  plan-1  C5   0.020
 BEK  plan-1  F4   0.020
 BEK  plan-1  F6   0.020
 BEK  plan-1  O5   0.020
 BEK  plan-2  C1   0.020
 BEK  plan-2  O    0.020
 BEK  plan-2  N    0.020
 BEK  plan-2  C2   0.020
 BEK  plan-2  HN1  0.020
 BEK  plan-2  HN2  0.020

