# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 05:19:51 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: (E)-N~2~-({4-[(3-fluorobenzyl)oxy]phenyl}methylidene)-L-alaninamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](N=Cc1ccc(OCc2cccc(F)c2)cc1)C(N)=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
 SAG  SAG  (E)-N~2~-({4-[(3-fluorobenzyl)oxy]phenyl}methylidene)-L-alaninamide  ligand  39  22  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SAG
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
 SAG  F3    F  F     0  -0.315  -6.8229  -1.6092  -1.2522
 SAG  C3    C  CR6   0   0.541  -6.1945  -0.7246  -0.4611
 SAG  C2    C  CR16  0  -0.443  -4.8499  -0.9017  -0.2048
 SAG  C4    C  CR16  0  -0.414  -6.9177   0.3280   0.0670
 SAG  C5    C  CR16  0  -0.226  -6.2566   1.2337   0.8841
 SAG  C6    C  CR16  0  -0.305  -4.9036   1.0809   1.1559
 SAG  C1    C  CR6   0   0.113  -4.1961   0.0122   0.6163
 SAG  C7    C  CH2   0  -0.272  -2.7280  -0.1395   0.8772
 SAG  O8    O  O2    0  -0.462  -2.0472   0.4270  -0.2361
 SAG  C9    C  CR6   0   0.389  -0.7033   0.4281  -0.2427
 SAG  C10   C  CR16  0  -0.335  -0.0935   0.9908  -1.3659
 SAG  C11   C  CR16  0  -0.283   1.2837   1.0394  -1.4512
 SAG  C14   C  CR16  0  -0.364   0.0904  -0.0874   0.7848
 SAG  C13   C  CR16  0  -0.273   1.4697  -0.0305   0.6825
 SAG  C12   C  CR6   0   0.040   2.0898   0.5317  -0.4308
 SAG  C15   C  C1    0  -0.058   3.5452   0.6144  -0.5559
 SAG  N16   N  N     0  -0.333   4.3379   0.1744   0.3249
 SAG  C17   C  CH1   0  -0.245   5.7489   0.3467   0.1030
 SAG  C18   C  CH3   0  -0.646   6.3409   1.1609   1.2559
 SAG  C19   C  C     0   0.518   6.4231  -1.0237   0.0224
 SAG  O20   O  O     0  -0.480   5.8574  -2.0575   0.3358
 SAG  N21   N  NH2   0  -0.802   7.6917  -0.9829  -0.4127
 SAG  H2    H  HCR6  0   0.279  -4.3212  -1.7448  -0.6328
 SAG  H4    H  HCR6  0   0.283  -7.9715   0.4370  -0.1527
 SAG  H5    H  HCR6  0   0.272  -6.8036   2.0638   1.3103
 SAG  H6    H  HCR6  0   0.261  -4.3976   1.7948   1.7937
 SAG  H7C1  H  HCH2  0   0.251  -2.4504   0.3772   1.8011
 SAG  H7C2  H  HCH2  0   0.249  -2.4606  -1.1952   0.9888
 SAG  H10   H  HCR6  0   0.267  -0.7069   1.3900  -2.1638
 SAG  H14   H  HCR6  0   0.286  -0.3467  -0.5304   1.6688
 SAG  H11   H  HCR6  0   0.260   1.7425   1.4815  -2.3276
 SAG  H13   H  HCR6  0   0.259   2.0746  -0.4301   1.4862
 SAG  H15   H  H     0   0.222   3.9057   1.0926  -1.4753
 SAG  H17   H  HCH1  0   0.243   5.9549   0.8763  -0.8397
 SAG  H181  H  HCH3  0   0.236   6.1853   0.6525   2.2077
 SAG  H182  H  HCH3  0   0.235   7.4100   1.3238   1.1238
 SAG  H183  H  HCH3  0   0.244   5.8588   2.1368   1.3059
 SAG  H211  H  HNH2  0   0.407   8.1295  -0.1262  -0.7053
 SAG  H212  H  HNH2  0   0.402   8.2237  -1.8319  -0.5123

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
 SAG  F3   C3    single    1.343  0.020  1.343
 SAG  C3   C2    aromatic  1.380  0.020  1.380
 SAG  C3   C4    aromatic  1.382  0.020  1.382
 SAG  C2   C1    aromatic  1.392  0.020  1.392
 SAG  C2   H2    single    0.930  0.020  1.080
 SAG  C4   C5    aromatic  1.387  0.020  1.387
 SAG  C4   H4    single    0.930  0.020  1.080
 SAG  C5   C6    aromatic  1.388  0.020  1.388
 SAG  C5   H5    single    0.930  0.020  1.080
 SAG  C6   C1    aromatic  1.391  0.020  1.391
 SAG  C6   H6    single    0.930  0.020  1.080
 SAG  C1   C7    single    1.499  0.020  1.499
 SAG  C7   O8    single    1.423  0.020  1.423
 SAG  C7   H7C1  single    0.970  0.020  1.090
 SAG  C7   H7C2  single    0.970  0.020  1.090
 SAG  O8   C9    single    1.344  0.020  1.344
 SAG  C9   C10   aromatic  1.396  0.020  1.396
 SAG  C9   C14   aromatic  1.397  0.020  1.397
 SAG  C10  C11   aromatic  1.381  0.020  1.381
 SAG  C10  H10   single    0.930  0.020  1.080
 SAG  C11  C12   aromatic  1.396  0.020  1.396
 SAG  C11  H11   single    0.930  0.020  1.080
 SAG  C14  C13   aromatic  1.384  0.020  1.384
 SAG  C14  H14   single    0.930  0.020  1.080
 SAG  C13  C12   aromatic  1.393  0.020  1.393
 SAG  C13  H13   single    0.930  0.020  1.080
 SAG  C12  C15   single    1.463  0.020  1.463
 SAG  C15  N16   double    1.264  0.020  1.264
 SAG  C15  H15   single    0.930  0.020  1.080
 SAG  N16  C17   single    1.439  0.020  1.439
 SAG  C17  C18   single    1.531  0.020  1.531
 SAG  C17  C19   single    1.529  0.020  1.529
 SAG  C17  H17   single    0.970  0.020  1.090
 SAG  C18  H181  single    0.970  0.020  1.090
 SAG  C18  H182  single    0.970  0.020  1.090
 SAG  C18  H183  single    0.970  0.020  1.090
 SAG  C19  O20   double    1.219  0.020  1.219
 SAG  C19  N21   single    1.342  0.020  1.342
 SAG  N21  H211  single    0.860  0.020  1.020
 SAG  N21  H212  single    0.860  0.020  1.020

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
 SAG  C4    C3   C2    122.45  3.000
 SAG  C4    C3   F3    118.82  3.000
 SAG  C2    C3   F3    118.73  3.000
 SAG  H2    C2   C1    120.99  3.000
 SAG  H2    C2   C3    120.13  3.000
 SAG  C1    C2   C3    118.87  3.000
 SAG  H4    C4   C5    121.19  3.000
 SAG  H4    C4   C3    120.59  3.000
 SAG  C5    C4   C3    118.22  3.000
 SAG  H5    C5   C6    120.01  3.000
 SAG  H5    C5   C4    119.47  3.000
 SAG  C6    C5   C4    120.52  3.000
 SAG  H6    C6   C1    119.84  3.000
 SAG  H6    C6   C5    119.87  3.000
 SAG  C1    C6   C5    120.29  3.000
 SAG  C7    C1   C6    120.57  3.000
 SAG  C7    C1   C2    119.76  3.000
 SAG  C6    C1   C2    119.65  3.000
 SAG  H7C2  C7   H7C1  107.89  3.000
 SAG  H7C2  C7   O8    110.30  3.000
 SAG  H7C1  C7   O8    110.56  3.000
 SAG  H7C2  C7   C1    110.77  3.000
 SAG  H7C1  C7   C1    110.34  3.000
 SAG  O8    C7   C1    106.99  3.000
 SAG  C9    O8   C7    118.86  3.000
 SAG  C14   C9   C10   119.48  3.000
 SAG  C14   C9   O8    124.35  3.000
 SAG  C10   C9   O8    116.16  3.000
 SAG  H10   C10  C11   120.44  3.000
 SAG  H10   C10  C9    119.60  3.000
 SAG  C11   C10  C9    119.96  3.000
 SAG  H11   C11  C12   119.67  3.000
 SAG  H11   C11  C10   119.12  3.000
 SAG  C12   C11  C10   121.20  3.000
 SAG  H14   C14  C13   118.69  3.000
 SAG  H14   C14  C9    121.53  3.000
 SAG  C13   C14  C9    119.78  3.000
 SAG  H13   C13  C12   119.59  3.000
 SAG  H13   C13  C14   119.13  3.000
 SAG  C12   C13  C14   121.28  3.000
 SAG  C15   C12  C13   122.28  3.000
 SAG  C15   C12  C11   119.43  3.000
 SAG  C13   C12  C11   118.29  3.000
 SAG  H15   C15  N16   121.97  3.000
 SAG  H15   C15  C12   115.04  3.000
 SAG  N16   C15  C12   122.99  3.000
 SAG  C17   N16  C15   117.77  3.000
 SAG  H17   C17  C19   107.66  3.000
 SAG  H17   C17  C18   108.46  3.000
 SAG  C19   C17  C18   110.23  3.000
 SAG  H17   C17  N16   111.92  3.000
 SAG  C19   C17  N16   109.47  3.000
 SAG  C18   C17  N16   109.08  3.000
 SAG  H183  C18  H182  107.80  3.000
 SAG  H183  C18  H181  108.32  3.000
 SAG  H182  C18  H181  108.40  3.000
 SAG  H183  C18  C17   109.87  3.000
 SAG  H182  C18  C17   111.58  3.000
 SAG  H181  C18  C17   110.75  3.000
 SAG  N21   C19  O20   123.22  3.000
 SAG  N21   C19  C17   113.99  3.000
 SAG  O20   C19  C17   122.79  3.000
 SAG  H212  N21  H211  117.36  3.000
 SAG  H212  N21  C19   120.40  3.000
 SAG  H211  N21  C19   122.13  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
 SAG  CONST_01  C6    C1   C2   C3      0.00   0.0  0
 SAG  CONST_02  C6    C5   C4   C3      0.00   0.0  0
 SAG  CONST_03  C5    C4   C3   C2      0.00   0.0  0
 SAG  CONST_04  C5    C6   C1   C2      0.00   0.0  0
 SAG  CONST_05  C1    C2   C3   C4      0.00   0.0  0
 SAG  CONST_06  C1    C6   C5   C4      0.00   0.0  0
 SAG  CONST_07  C12   C11  C10  C9      0.00   0.0  0
 SAG  CONST_08  C12   C13  C14  C9      0.00   0.0  0
 SAG  CONST_09  C13   C14  C9   C10     0.00   0.0  0
 SAG  CONST_10  C13   C12  C11  C10     0.00   0.0  0
 SAG  CONST_11  C14   C9   C10  C11     0.00   0.0  0
 SAG  CONST_12  C14   C13  C12  C11     0.00   0.0  0
 SAG  CONST_13  C1    C2   C3   F3    180.00   0.0  0
 SAG  CONST_14  C5    C4   C3   F3    180.00   0.0  0
 SAG  CONST_15  C7    C1   C2   C3    180.00   0.0  0
 SAG  CONST_16  C7    C1   C6   C5    180.00   0.0  0
 SAG  CONST_17  C11   C10  C9   O8    180.00   0.0  0
 SAG  CONST_18  C13   C14  C9   O8    180.00   0.0  0
 SAG  CONST_19  C15   C12  C11  C10   180.00   0.0  0
 SAG  CONST_20  C15   C12  C13  C14   180.00   0.0  0
 SAG  CONST_21  H5    C5   C4   C3    180.00   0.0  0
 SAG  CONST_22  H4    C4   C3   C2    180.00   0.0  0
 SAG  CONST_23  H6    C6   C1   C2    180.00   0.0  0
 SAG  CONST_24  H2    C2   C3   C4    180.00   0.0  0
 SAG  CONST_25  H11   C11  C10  C9    180.00   0.0  0
 SAG  CONST_26  H13   C13  C14  C9    180.00   0.0  0
 SAG  CONST_27  H14   C14  C9   C10   180.00   0.0  0
 SAG  CONST_28  H10   C10  C9   C14   180.00   0.0  0
 SAG  CONST_29  H211  N21  C19  C17     0.00   0.0  0
 SAG  CONST_30  H212  N21  C19  C17   180.00   0.0  0
 SAG  Var_01    O8    C7   C1   C2     81.66  30.0  2
 SAG  Var_02    C10   C9   O8   C7    179.63  30.0  2
 SAG  Var_03    N16   C15  C12  C11  -179.86  30.0  2

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
 SAG  chir_01  C17  N16  C18  C19  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
 SAG  plan-1  F3    0.020
 SAG  plan-1  C3    0.020
 SAG  plan-1  C2    0.020
 SAG  plan-1  C4    0.020
 SAG  plan-1  C5    0.020
 SAG  plan-1  C6    0.020
 SAG  plan-1  C1    0.020
 SAG  plan-1  C7    0.020
 SAG  plan-1  H2    0.020
 SAG  plan-1  H4    0.020
 SAG  plan-1  H5    0.020
 SAG  plan-1  H6    0.020
 SAG  plan-2  O8    0.020
 SAG  plan-2  C9    0.020
 SAG  plan-2  C10   0.020
 SAG  plan-2  C11   0.020
 SAG  plan-2  C14   0.020
 SAG  plan-2  C13   0.020
 SAG  plan-2  C12   0.020
 SAG  plan-2  C15   0.020
 SAG  plan-2  H10   0.020
 SAG  plan-2  H14   0.020
 SAG  plan-2  H11   0.020
 SAG  plan-2  H13   0.020
 SAG  plan-3  C17   0.020
 SAG  plan-3  C19   0.020
 SAG  plan-3  O20   0.020
 SAG  plan-3  N21   0.020
 SAG  plan-3  H211  0.020
 SAG  plan-3  H212  0.020
 SAG  plan-4  C12   0.020
 SAG  plan-4  C15   0.020
 SAG  plan-4  N16   0.020
 SAG  plan-4  C17   0.020
 SAG  plan-4  H15   0.020

