# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 02:57:30 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: [(1S)-1-{[(2-benzylphenyl)carbonyl]amino}ethyl](trihydroxy)borate(1-)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](NC(=O)c1ccccc1Cc2ccccc2)[B-](O)(O)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
 EWB  EWB  '[(1S)-1-{[(2-benzylphenyl)carbonyl]amino}ethyl](trihydroxy)borate(1-)'  ligand  41  22  .  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_EWB
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
 EWB  O6    O  O      0  -0.518   1.4612   0.7047   2.5327
 EWB  C5    C  C      0   0.456   1.2666   1.0164   1.3591
 EWB  N4    N  NH1    0  -0.595   2.0288   0.6562   0.3315
 EWB  C3    C  CH1    0  -0.290   3.0954  -0.3454   0.3594
 EWB  C16   C  CH3    0  -0.675   4.3415   0.2397  -0.2949
 EWB  B     B  B     -1   0.491   2.5630  -1.7543  -0.3389
 EWB  O1    O  OB     0  -0.753   2.2571  -1.5839  -1.7715
 EWB  O2    O  OB     0  -0.737   3.6167  -2.7799  -0.3230
 EWB  C7    C  CR6    0  -0.117   0.0964   1.8832   0.9885
 EWB  C8    C  CR6    0   0.123  -1.2067   1.3841   1.0533
 EWB  C11   C  CR16   0  -0.278  -2.2602   2.2507   0.7661
 EWB  C12   C  CR16   0  -0.244  -2.0346   3.5759   0.4276
 EWB  C13   C  CR16   0  -0.265  -0.7354   4.0605   0.3547
 EWB  C14   C  CR16   0  -0.257   0.3239   3.2107   0.6319
 EWB  C9    C  CH2    0  -0.619  -1.5013  -0.0599   1.4020
 EWB  C17   C  CR6    0   0.133  -2.3655  -0.7297   0.3654
 EWB  C22   C  CR16   0  -0.292  -1.8106  -1.1384  -0.8470
 EWB  C21   C  CR16   0  -0.244  -2.5959  -1.7346  -1.8221
 EWB  C20   C  CR16   0  -0.272  -3.9537  -1.9360  -1.5998
 EWB  C19   C  CR16   0  -0.242  -4.5147  -1.5415  -0.3937
 EWB  C18   C  CR16   0  -0.320  -3.7233  -0.9442   0.5810
 EWB  OXO   O  OB     0  -0.738   1.3637  -2.1424   0.4363
 EWB  H4    H  HNH1   0   0.377   1.7104   0.9429  -0.5817
 EWB  H3    H  HCH1   0   0.187   3.3170  -0.5138   1.4179
 EWB  H161  H  HCH3   0   0.210   5.1596  -0.4812  -0.2661
 EWB  H162  H  HCH3   0   0.200   4.1618   0.4770  -1.3465
 EWB  H163  H  HCH3   0   0.205   4.6840   1.1538   0.1981
 EWB  H1    H  H      0   0.420   1.4995  -1.0055  -1.8766
 EWB  H2    H  H      0   0.419   4.0223  -2.8036   0.5465
 EWB  H14   H  HCR6   0   0.255   1.3400   3.5826   0.5774
 EWB  H11   H  HCR6   0   0.250  -3.2778   1.8795   0.8023
 EWB  H91C  H  HCH2   0   0.286  -0.5755  -0.6255   1.5032
 EWB  H92C  H  HCH2   0   0.266  -2.0001  -0.0958   2.3740
 EWB  H12   H  HCR6   0   0.255  -2.8728   4.2276   0.2167
 EWB  H13   H  HCR6   0   0.256  -0.5479   5.0919   0.0860
 EWB  H22   H  HCR6   0   0.245  -0.7508  -0.9958  -1.0193
 EWB  H18   H  HCR6   0   0.248  -4.1691  -0.6433   1.5224
 EWB  H21   H  HCR6   0   0.252  -2.1484  -2.0499  -2.7562
 EWB  H20   H  HCR6   0   0.253  -4.5663  -2.4020  -2.3609
 EWB  H19   H  HCR6   0   0.252  -5.5692  -1.7004  -0.2070
 EWB  HX    H  H      0   0.419   0.8992  -2.8480  -0.0221

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
 EWB  O6   C5    double    1.230  0.020  1.230
 EWB  C5   N4    single    1.329  0.020  1.329
 EWB  C5   C7    single    1.503  0.020  1.503
 EWB  N4   C3    single    1.463  0.020  1.463
 EWB  C3   C16   single    1.524  0.020  1.524
 EWB  C3   B     single    1.660  0.020  1.660
 EWB  B    O1    single    1.475  0.020  1.475
 EWB  B    O2    single    1.470  0.020  1.470
 EWB  B    OXO   single    1.480  0.020  1.480
 EWB  C7   C8    aromatic  1.397  0.020  1.397
 EWB  C7   C14   aromatic  1.393  0.020  1.393
 EWB  C8   C11   aromatic  1.394  0.020  1.394
 EWB  C8   C9    single    1.514  0.020  1.514
 EWB  C11  C12   aromatic  1.386  0.020  1.386
 EWB  C12  C13   aromatic  1.389  0.020  1.389
 EWB  C13  C14   aromatic  1.386  0.020  1.386
 EWB  C9   C17   single    1.507  0.020  1.507
 EWB  C17  C22   aromatic  1.395  0.020  1.395
 EWB  C17  C18   aromatic  1.391  0.020  1.391
 EWB  C22  C21   aromatic  1.387  0.020  1.387
 EWB  C21  C20   aromatic  1.391  0.020  1.391
 EWB  C20  C19   aromatic  1.387  0.020  1.387
 EWB  C19  C18   aromatic  1.390  0.020  1.390
 EWB  N4   H4    single    0.860  0.020  1.020
 EWB  C3   H3    single    0.970  0.020  1.090
 EWB  C16  H161  single    0.970  0.020  1.090
 EWB  C16  H162  single    0.970  0.020  1.090
 EWB  C16  H163  single    0.970  0.020  1.090
 EWB  O1   H1    single    0.850  0.020  0.980
 EWB  O2   H2    single    0.850  0.020  0.980
 EWB  C14  H14   single    0.930  0.020  1.080
 EWB  C11  H11   single    0.930  0.020  1.080
 EWB  C9   H91C  single    0.970  0.020  1.090
 EWB  C9   H92C  single    0.970  0.020  1.090
 EWB  C12  H12   single    0.930  0.020  1.080
 EWB  C13  H13   single    0.930  0.020  1.080
 EWB  C22  H22   single    0.930  0.020  1.080
 EWB  C18  H18   single    0.930  0.020  1.080
 EWB  C21  H21   single    0.930  0.020  1.080
 EWB  C20  H20   single    0.930  0.020  1.080
 EWB  C19  H19   single    0.930  0.020  1.080
 EWB  OXO  HX    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
 EWB  C7    C5   N4    114.35  3.000
 EWB  C7    C5   O6    120.31  3.000
 EWB  N4    C5   O6    125.34  3.000
 EWB  H4    N4   C3    116.22  3.000
 EWB  H4    N4   C5    116.23  3.000
 EWB  C3    N4   C5    126.06  3.000
 EWB  H3    C3   B     109.95  3.000
 EWB  H3    C3   C16   107.98  3.000
 EWB  B     C3   C16   114.04  3.000
 EWB  H3    C3   N4    105.74  3.000
 EWB  B     C3   N4    109.82  3.000
 EWB  C16   C3   N4    108.97  3.000
 EWB  H163  C16  H162  107.68  3.000
 EWB  H163  C16  H161  107.79  3.000
 EWB  H162  C16  H161  106.99  3.000
 EWB  H163  C16  C3    112.55  3.000
 EWB  H162  C16  C3    111.22  3.000
 EWB  H161  C16  C3    110.38  3.000
 EWB  OXO   B    O2    113.09  3.000
 EWB  OXO   B    O1    111.78  3.000
 EWB  O2    B    O1    103.87  3.000
 EWB  OXO   B    C3    105.20  3.000
 EWB  O2    B    C3    110.95  3.000
 EWB  O1    B    C3    112.15  3.000
 EWB  H1    O1   B     109.88  3.000
 EWB  H2    O2   B     109.26  3.000
 EWB  C14   C7   C8    120.31  3.000
 EWB  C14   C7   C5    119.05  3.000
 EWB  C8    C7   C5    120.59  3.000
 EWB  C9    C8   C11   119.55  3.000
 EWB  C9    C8   C7    122.20  3.000
 EWB  C11   C8   C7    118.25  3.000
 EWB  H11   C11  C12   119.23  3.000
 EWB  H11   C11  C8    119.33  3.000
 EWB  C12   C11  C8    121.44  3.000
 EWB  H12   C12  C13   120.27  3.000
 EWB  H12   C12  C11   119.81  3.000
 EWB  C13   C12  C11   119.92  3.000
 EWB  H13   C13  C14   120.10  3.000
 EWB  H13   C13  C12   120.52  3.000
 EWB  C14   C13  C12   119.38  3.000
 EWB  H14   C14  C13   119.76  3.000
 EWB  H14   C14  C7    119.54  3.000
 EWB  C13   C14  C7    120.70  3.000
 EWB  H92C  C9   H91C  106.74  3.000
 EWB  H92C  C9   C17   109.60  3.000
 EWB  H91C  C9   C17   108.69  3.000
 EWB  H92C  C9   C8    108.96  3.000
 EWB  H91C  C9   C8    110.55  3.000
 EWB  C17   C9   C8    112.15  3.000
 EWB  C18   C17  C22   118.54  3.000
 EWB  C18   C17  C9    121.44  3.000
 EWB  C22   C17  C9    120.02  3.000
 EWB  H22   C22  C21   119.92  3.000
 EWB  H22   C22  C17   119.27  3.000
 EWB  C21   C22  C17   120.80  3.000
 EWB  H21   C21  C20   119.95  3.000
 EWB  H21   C21  C22   119.86  3.000
 EWB  C20   C21  C22   120.19  3.000
 EWB  H20   C20  C19   120.32  3.000
 EWB  H20   C20  C21   120.17  3.000
 EWB  C19   C20  C21   119.51  3.000
 EWB  H19   C19  C18   119.77  3.000
 EWB  H19   C19  C20   120.13  3.000
 EWB  C18   C19  C20   120.09  3.000
 EWB  H18   C18  C19   119.60  3.000
 EWB  H18   C18  C17   119.54  3.000
 EWB  C19   C18  C17   120.86  3.000
 EWB  HX    OXO  B     109.54  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
 EWB  CONST_01  C12  C11  C8   C7      0.00   0.0  0
 EWB  CONST_02  C12  C13  C14  C7      0.00   0.0  0
 EWB  CONST_03  C13  C14  C7   C8      0.00   0.0  0
 EWB  CONST_04  C13  C12  C11  C8      0.00   0.0  0
 EWB  CONST_05  C14  C7   C8   C11     0.00   0.0  0
 EWB  CONST_06  C14  C13  C12  C11     0.00   0.0  0
 EWB  CONST_07  C20  C21  C22  C17     0.00   0.0  0
 EWB  CONST_08  C20  C19  C18  C17     0.00   0.0  0
 EWB  CONST_09  C19  C18  C17  C22     0.00   0.0  0
 EWB  CONST_10  C19  C20  C21  C22     0.00   0.0  0
 EWB  CONST_11  C18  C17  C22  C21     0.00   0.0  0
 EWB  CONST_12  C18  C19  C20  C21     0.00   0.0  0
 EWB  CONST_13  C11  C8   C7   C5    180.00   0.0  0
 EWB  CONST_14  C13  C14  C7   C5    180.00   0.0  0
 EWB  CONST_15  C9   C8   C11  C12   180.00   0.0  0
 EWB  CONST_16  C9   C8   C7   C14   180.00   0.0  0
 EWB  CONST_17  C21  C22  C17  C9    180.00   0.0  0
 EWB  CONST_18  C19  C18  C17  C9    180.00   0.0  0
 EWB  CONST_19  H11  C11  C8   C7    180.00   0.0  0
 EWB  CONST_20  H13  C13  C14  C7    180.00   0.0  0
 EWB  CONST_21  H14  C14  C7   C8    180.00   0.0  0
 EWB  CONST_22  H12  C12  C11  C8    180.00   0.0  0
 EWB  CONST_23  H21  C21  C22  C17   180.00   0.0  0
 EWB  CONST_24  H19  C19  C18  C17   180.00   0.0  0
 EWB  CONST_25  H18  C18  C17  C22   180.00   0.0  0
 EWB  CONST_26  H20  C20  C21  C22   180.00   0.0  0
 EWB  CONST_27  H22  C22  C21  C20   180.00   0.0  0
 EWB  CONST_28  C7   C5   N4   C3    180.00   0.0  0
 EWB  CONST_29  H4   N4   C5   C7      0.00   0.0  0
 EWB  CONST_30  C3   N4   C5   O6      0.00   0.0  0
 EWB  Var_01    C17  C9   C8   C7   -126.03  30.0  2
 EWB  Var_02    C22  C17  C9   C8     76.53  30.0  2
 EWB  Var_03    C8   C7   C5   O6    -70.83  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
 EWB  chir_01  C3  N4  C16  B  positiv

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
 EWB  plan-1  C5   0.020
 EWB  plan-1  C7   0.020
 EWB  plan-1  C8   0.020
 EWB  plan-1  C11  0.020
 EWB  plan-1  C12  0.020
 EWB  plan-1  C13  0.020
 EWB  plan-1  C14  0.020
 EWB  plan-1  C9   0.020
 EWB  plan-1  H14  0.020
 EWB  plan-1  H11  0.020
 EWB  plan-1  H12  0.020
 EWB  plan-1  H13  0.020
 EWB  plan-2  C9   0.020
 EWB  plan-2  C17  0.020
 EWB  plan-2  C22  0.020
 EWB  plan-2  C21  0.020
 EWB  plan-2  C20  0.020
 EWB  plan-2  C19  0.020
 EWB  plan-2  C18  0.020
 EWB  plan-2  H22  0.020
 EWB  plan-2  H18  0.020
 EWB  plan-2  H21  0.020
 EWB  plan-2  H20  0.020
 EWB  plan-2  H19  0.020
 EWB  plan-3  O6   0.020
 EWB  plan-3  C5   0.020
 EWB  plan-3  N4   0.020
 EWB  plan-3  C3   0.020
 EWB  plan-3  C7   0.020
 EWB  plan-3  H4   0.020

