# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 12:33:32 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: (3S)-3-(2-fluorophenyl)-N-[(1R)-1-(2-oxidanylidene-1,3-dihydrobenzimidazol-5-yl)ethyl]butanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](CC(=O)N[C@H](C)c1ccc2NC(=O)Nc2c1)c3ccccc3F
#
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
 B2Z  B2Z  (3S)-3-(2-fluorophenyl)-N-[(1R)-1-(2-oxidanylidene-1,3-dihydrobenzimidazol-5-yl)ethyl]butanamide  ligand  45  25  .  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_B2Z
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
 B2Z  F     F  F     0  -0.316   5.4178  -1.4474   0.5986
 B2Z  C18   C  CR6   0   0.513   5.4323  -0.1046   0.4919
 B2Z  C17   C  CR16  0  -0.402   6.6492   0.5131   0.2820
 B2Z  C16   C  CR16  0  -0.256   6.6820   1.8952   0.1596
 B2Z  C15   C  CR16  0  -0.253   5.5040   2.6218   0.2508
 B2Z  C14   C  CR16  0  -0.302   4.2980   1.9678   0.4669
 B2Z  C13   C  CR6   0  -0.046   4.2290   0.5823   0.5961
 B2Z  C1    C  CH1   0  -0.312   2.9288  -0.1624   0.7959
 B2Z  C     C  CH3   0  -0.671   1.8917   0.6446   1.5701
 B2Z  C2    C  CH2   0  -0.545   2.3801  -0.6024  -0.5720
 B2Z  C3    C  C     0   0.543   1.1987  -1.5367  -0.4157
 B2Z  O     O  O     0  -0.506   1.3066  -2.6036   0.1770
 B2Z  N     N  NH1   0  -0.622   0.0464  -1.1063  -0.9514
 B2Z  C4    C  CH1   0  -0.180  -1.1983  -1.8589  -0.9074
 B2Z  C5    C  CH3   0  -0.647  -1.3766  -2.7113  -2.1597
 B2Z  C6    C  CR6   0   0.132  -2.3505  -0.9109  -0.6604
 B2Z  C11   C  CR16  0  -0.376  -2.9484  -0.8802   0.5996
 B2Z  C10   C  CR56  0   0.346  -3.9821   0.0110   0.8093
 B2Z  N1    N  NR15  0  -0.740  -4.7645   0.2743   1.9117
 B2Z  C12   C  CR5   0   0.608  -5.6784   1.2629   1.6400
 B2Z  O1    O  O     0  -0.498  -6.5128   1.7261   2.3960
 B2Z  N2    N  NR15  0  -0.736  -5.4483   1.6151   0.3329
 B2Z  C9    C  CR56  0   0.316  -4.4209   0.8699  -0.2028
 B2Z  C8    C  CR16  0  -0.295  -3.8354   0.8518  -1.4532
 B2Z  C7    C  CR16  0  -0.324  -2.7988  -0.0521  -1.6655
 B2Z  H17   H  HCR6  0   0.276   7.5529  -0.0791   0.2160
 B2Z  H16   H  HCR6  0   0.265   7.6261   2.3964  -0.0072
 B2Z  H15   H  HCR6  0   0.259   5.5202   3.6994   0.1577
 B2Z  H14   H  HCR6  0   0.258   3.3927   2.5564   0.5391
 B2Z  H1    H  HCH1  0   0.259   3.1419  -1.0664   1.3706
 B2Z  HC1   H  HCH3  0   0.245   2.2911   0.9872   2.5248
 B2Z  HC2   H  HCH3  0   0.227   1.5506   1.5179   1.0124
 B2Z  HC3   H  HCH3  0   0.245   1.0110   0.0376   1.7826
 B2Z  H21C  H  HCH2  0   0.255   2.1208   0.2789  -1.1641
 B2Z  H22C  H  HCH2  0   0.278   3.1511  -1.1427  -1.1272
 B2Z  H     H  HNH1  0   0.402   0.0429  -0.2227  -1.4367
 B2Z  H4    H  HCH1  0   0.265  -1.1260  -2.5292  -0.0501
 B2Z  H51C  H  HCH3  0   0.241  -0.5531  -3.4196  -2.2546
 B2Z  H52C  H  HCH3  0   0.236  -2.3060  -3.2786  -2.1065
 B2Z  H53C  H  HCH3  0   0.227  -1.4013  -2.1041  -3.0651
 B2Z  H11   H  HCR6  0   0.268  -2.6127  -1.5411   1.3894
 B2Z  H7    H  HCR6  0   0.254  -2.3366  -0.0801  -2.6443
 B2Z  HA    H  HNR5  0   0.420  -4.6968  -0.1812   2.8076
 B2Z  H2    H  HNR5  0   0.420  -5.9748   2.3276  -0.1464
 B2Z  H8    H  HCR6  0   0.270  -4.1688   1.5113  -2.2430

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
 B2Z  F    C18   single    1.347  0.020  1.347
 B2Z  C18  C17   aromatic  1.381  0.020  1.381
 B2Z  C18  C13   aromatic  1.390  0.020  1.390
 B2Z  C17  C16   aromatic  1.388  0.020  1.388
 B2Z  C16  C15   aromatic  1.387  0.020  1.387
 B2Z  C15  C14   aromatic  1.389  0.020  1.389
 B2Z  C14  C13   aromatic  1.393  0.020  1.393
 B2Z  C13  C1    single    1.512  0.020  1.512
 B2Z  C1   C     single    1.525  0.020  1.525
 B2Z  C1   C2    single    1.538  0.020  1.538
 B2Z  C2   C3    single    1.514  0.020  1.514
 B2Z  C3   O     double    1.225  0.020  1.225
 B2Z  C3   N     single    1.342  0.020  1.342
 B2Z  N    C4    single    1.455  0.020  1.455
 B2Z  C4   C5    single    1.525  0.020  1.525
 B2Z  C4   C6    single    1.512  0.020  1.512
 B2Z  C6   C11   aromatic  1.395  0.020  1.395
 B2Z  C6   C7    aromatic  1.396  0.020  1.396
 B2Z  C11  C10   aromatic  1.381  0.020  1.381
 B2Z  C10  N1    single    1.377  0.020  1.377
 B2Z  C10  C9    aromatic  1.398  0.020  1.398
 B2Z  N1   C12   single    1.373  0.020  1.373
 B2Z  C12  O1    double    1.218  0.020  1.218
 B2Z  C12  N2    single    1.373  0.020  1.373
 B2Z  N2   C9    single    1.378  0.020  1.378
 B2Z  C9   C8    aromatic  1.381  0.020  1.381
 B2Z  C8   C7    aromatic  1.392  0.020  1.392
 B2Z  C17  H17   single    0.930  0.020  1.080
 B2Z  C16  H16   single    0.930  0.020  1.080
 B2Z  C15  H15   single    0.930  0.020  1.080
 B2Z  C14  H14   single    0.930  0.020  1.080
 B2Z  C1   H1    single    0.970  0.020  1.090
 B2Z  C    HC1   single    0.970  0.020  1.090
 B2Z  C    HC2   single    0.970  0.020  1.090
 B2Z  C    HC3   single    0.970  0.020  1.090
 B2Z  C2   H21C  single    0.970  0.020  1.090
 B2Z  C2   H22C  single    0.970  0.020  1.090
 B2Z  N    H     single    0.860  0.020  1.020
 B2Z  C4   H4    single    0.970  0.020  1.090
 B2Z  C5   H51C  single    0.970  0.020  1.090
 B2Z  C5   H52C  single    0.970  0.020  1.090
 B2Z  C5   H53C  single    0.970  0.020  1.090
 B2Z  C11  H11   single    0.930  0.020  1.080
 B2Z  C7   H7    single    0.930  0.020  1.080
 B2Z  N1   HA    single    0.860  0.020  1.020
 B2Z  N2   H2    single    0.860  0.020  1.020
 B2Z  C8   H8    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
 B2Z  C13   C18  C17   123.60  3.000
 B2Z  C13   C18  F     118.52  3.000
 B2Z  C17   C18  F     117.88  3.000
 B2Z  H17   C17  C16   121.31  3.000
 B2Z  H17   C17  C18   120.01  3.000
 B2Z  C16   C17  C18   118.67  3.000
 B2Z  H16   C16  C15   120.57  3.000
 B2Z  H16   C16  C17   119.71  3.000
 B2Z  C15   C16  C17   119.72  3.000
 B2Z  H15   C15  C14   119.70  3.000
 B2Z  H15   C15  C16   120.23  3.000
 B2Z  C14   C15  C16   120.07  3.000
 B2Z  H14   C14  C13   119.55  3.000
 B2Z  H14   C14  C15   118.73  3.000
 B2Z  C13   C14  C15   121.72  3.000
 B2Z  C1    C13  C14   123.01  3.000
 B2Z  C1    C13  C18   120.75  3.000
 B2Z  C14   C13  C18   116.22  3.000
 B2Z  H1    C1   C2    107.50  3.000
 B2Z  H1    C1   C     107.67  3.000
 B2Z  C2    C1   C     111.12  3.000
 B2Z  H1    C1   C13   108.02  3.000
 B2Z  C2    C1   C13   109.28  3.000
 B2Z  C     C1   C13   113.03  3.000
 B2Z  HC3   C    HC2   107.02  3.000
 B2Z  HC3   C    HC1   107.47  3.000
 B2Z  HC2   C    HC1   108.10  3.000
 B2Z  HC3   C    C1    110.70  3.000
 B2Z  HC2   C    C1    112.13  3.000
 B2Z  HC1   C    C1    111.21  3.000
 B2Z  H22C  C2   H21C  106.91  3.000
 B2Z  H22C  C2   C3    107.32  3.000
 B2Z  H21C  C2   C3    111.61  3.000
 B2Z  H22C  C2   C1    109.97  3.000
 B2Z  H21C  C2   C1    109.62  3.000
 B2Z  C3    C2   C1    111.28  3.000
 B2Z  N     C3   O     123.24  3.000
 B2Z  N     C3   C2    115.52  3.000
 B2Z  O     C3   C2    121.23  3.000
 B2Z  H     N    C4    117.70  3.000
 B2Z  H     N    C3    118.46  3.000
 B2Z  C4    N    C3    123.82  3.000
 B2Z  H4    C4   C6    107.90  3.000
 B2Z  H4    C4   C5    108.03  3.000
 B2Z  C6    C4   C5    113.29  3.000
 B2Z  H4    C4   N     106.55  3.000
 B2Z  C6    C4   N     109.42  3.000
 B2Z  C5    C4   N     111.36  3.000
 B2Z  H53C  C5   H52C  108.11  3.000
 B2Z  H53C  C5   H51C  107.85  3.000
 B2Z  H52C  C5   H51C  108.06  3.000
 B2Z  H53C  C5   C4    111.91  3.000
 B2Z  H52C  C5   C4    110.51  3.000
 B2Z  H51C  C5   C4    110.26  3.000
 B2Z  C7    C6   C11   119.94  3.000
 B2Z  C7    C6   C4    120.84  3.000
 B2Z  C11   C6   C4    119.20  3.000
 B2Z  H11   C11  C10   121.00  3.000
 B2Z  H11   C11  C6    120.82  3.000
 B2Z  C10   C11  C6    118.18  3.000
 B2Z  C9    C10  N1    106.48  3.000
 B2Z  C9    C10  C11   121.43  3.000
 B2Z  N1    C10  C11   132.09  3.000
 B2Z  HA    N1   C12   123.11  3.000
 B2Z  HA    N1   C10   125.96  3.000
 B2Z  C12   N1   C10   110.93  3.000
 B2Z  N2    C12  O1    127.47  3.000
 B2Z  N2    C12  N1    105.16  3.000
 B2Z  O1    C12  N1    127.37  3.000
 B2Z  H2    N2   C9    125.98  3.000
 B2Z  H2    N2   C12   123.15  3.000
 B2Z  C9    N2   C12   110.88  3.000
 B2Z  C8    C9   N2    132.49  3.000
 B2Z  C8    C9   C10   120.96  3.000
 B2Z  N2    C9   C10   106.55  3.000
 B2Z  H8    C8   C7    120.95  3.000
 B2Z  H8    C8   C9    121.50  3.000
 B2Z  C7    C8   C9    117.55  3.000
 B2Z  H7    C7   C8    118.21  3.000
 B2Z  H7    C7   C6    119.86  3.000
 B2Z  C8    C7   C6    121.94  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
 B2Z  CONST_01  C15  C16  C17  C18    0.00   0.0  0
 B2Z  CONST_02  C15  C14  C13  C18    0.00   0.0  0
 B2Z  CONST_03  C14  C13  C18  C17    0.00   0.0  0
 B2Z  CONST_04  C14  C15  C16  C17    0.00   0.0  0
 B2Z  CONST_05  C13  C18  C17  C16    0.00   0.0  0
 B2Z  CONST_06  C13  C14  C15  C16    0.00   0.0  0
 B2Z  CONST_07  C9   C10  C11  C6     0.00   0.0  0
 B2Z  CONST_08  C9   C8   C7   C6     0.00   0.0  0
 B2Z  CONST_09  C8   C7   C6   C11    0.00   0.0  0
 B2Z  CONST_10  C8   C9   C10  C11    0.00   0.0  0
 B2Z  CONST_11  C7   C6   C11  C10    0.00   0.0  0
 B2Z  CONST_12  C7   C8   C9   C10    0.00   0.0  0
 B2Z  CONST_13  N2   C12  N1   C10    0.00   0.0  0
 B2Z  CONST_14  C12  N2   C9   C10    0.00   0.0  0
 B2Z  CONST_15  N2   C9   C10  N1     0.00   0.0  0
 B2Z  CONST_16  C9   N2   C12  N1     0.00   0.0  0
 B2Z  CONST_17  C9   C10  N1   C12    0.00   0.0  0
 B2Z  CONST_18  C16  C17  C18  F    180.00   0.0  0
 B2Z  CONST_19  C14  C13  C18  F    180.00   0.0  0
 B2Z  CONST_20  C1   C13  C18  C17  180.00   0.0  0
 B2Z  CONST_21  C1   C13  C14  C15  180.00   0.0  0
 B2Z  CONST_22  C10  C11  C6   C4   180.00   0.0  0
 B2Z  CONST_23  C8   C7   C6   C4   180.00   0.0  0
 B2Z  CONST_24  O1   C12  N1   C10  180.00   0.0  0
 B2Z  CONST_25  C9   N2   C12  O1   180.00   0.0  0
 B2Z  CONST_26  H16  C16  C17  C18  180.00   0.0  0
 B2Z  CONST_27  H14  C14  C13  C18  180.00   0.0  0
 B2Z  CONST_28  H15  C15  C16  C17  180.00   0.0  0
 B2Z  CONST_29  H17  C17  C16  C15  180.00   0.0  0
 B2Z  CONST_30  H8   C8   C7   C6   180.00   0.0  0
 B2Z  CONST_31  H7   C7   C6   C11  180.00   0.0  0
 B2Z  CONST_32  H11  C11  C10  N1     0.00   0.0  0
 B2Z  CONST_33  H2   N2   C9   C10  180.00   0.0  0
 B2Z  CONST_34  HA   N1   C12  N2   180.00   0.0  0
 B2Z  CONST_35  C4   N    C3   C2   180.00   0.0  0
 B2Z  CONST_36  C4   N    C3   O      0.00   0.0  0
 B2Z  CONST_37  H    N    C3   C2     0.00   0.0  0
 B2Z  Var_01    O    C3   C2   C1   -59.80  30.0  3

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
 B2Z  chir_01  C1  C13  C   C2  negativ
 B2Z  chir_02  C4  N    C5  C6  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
 B2Z  plan-1  F    0.020
 B2Z  plan-1  C18  0.020
 B2Z  plan-1  C17  0.020
 B2Z  plan-1  C16  0.020
 B2Z  plan-1  C15  0.020
 B2Z  plan-1  C14  0.020
 B2Z  plan-1  C13  0.020
 B2Z  plan-1  C1   0.020
 B2Z  plan-1  H17  0.020
 B2Z  plan-1  H16  0.020
 B2Z  plan-1  H15  0.020
 B2Z  plan-1  H14  0.020
 B2Z  plan-2  C4   0.020
 B2Z  plan-2  C6   0.020
 B2Z  plan-2  C11  0.020
 B2Z  plan-2  C10  0.020
 B2Z  plan-2  N1   0.020
 B2Z  plan-2  C12  0.020
 B2Z  plan-2  O1   0.020
 B2Z  plan-2  N2   0.020
 B2Z  plan-2  C9   0.020
 B2Z  plan-2  C8   0.020
 B2Z  plan-2  C7   0.020
 B2Z  plan-2  H11  0.020
 B2Z  plan-2  H7   0.020
 B2Z  plan-2  HA   0.020
 B2Z  plan-2  H2   0.020
 B2Z  plan-2  H8   0.020
 B2Z  plan-3  C2   0.020
 B2Z  plan-3  C3   0.020
 B2Z  plan-3  O    0.020
 B2Z  plan-3  N    0.020
 B2Z  plan-3  C4   0.020
 B2Z  plan-3  H    0.020

