# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 03:47:43 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: 2-[2-fluoro-4-[(2S)-piperidin-2-yl]phenyl]-3H-benzimidazole-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1cccc2nc([nH]c12)c3ccc(cc3F)[C@@H]4CCCCN4
#
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
 A92  A92  2-[2-fluoro-4-[(2S)-piperidin-2-yl]phenyl]-3H-benzimidazole-4-carboxamide  ligand  44  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 GRAND
;

data_comp_A92
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
 A92  F     F  F     0  -0.312   0.2343  -1.7476   0.0549
 A92  C1    C  CR16  0  -0.256  -5.5457   1.8444   0.1295
 A92  C2    C  CR16  0  -0.261   1.0019   1.7729   0.2161
 A92  C3    C  CR16  0  -0.331  -5.7035   0.4637  -0.0319
 A92  C4    C  CR16  0  -0.326   2.3825   1.7181   0.2084
 A92  C5    C  CR16  0  -0.337  -4.2933   2.4220   0.2372
 A92  C6    C  CR16  0  -0.466   2.2967  -0.6681   0.0911
 A92  C7    C  CR6   0  -0.242   0.2263   0.6118   0.1607
 A92  C8    C  CR6   0  -0.088  -4.6172  -0.4027  -0.0903
 A92  C9    C  CR6   0   0.208   3.0523   0.4985   0.1413
 A92  C10   C  CR56  0   0.332  -3.3586   0.1951   0.0269
 A92  C11   C  CR56  0   0.172  -3.1843   1.5814   0.1832
 A92  C12   C  CR6   0   0.572   0.9207  -0.5919   0.1054
 A92  C13   C  CR5   0   0.519  -1.2294   0.7319   0.1514
 A92  C15   C  CH2   0  -0.443   6.5557  -0.0425  -1.3663
 A92  C16   C  CH2   0  -0.439   7.1043  -0.9056  -0.2354
 A92  C17   C  CH2   0  -0.423   5.0319   0.0105  -1.3159
 A92  C18   C  CH2   0  -0.317   6.5536  -0.4360   1.1079
 A92  C19   C  CH1   0  -0.200   4.5565   0.4463   0.0776
 A92  N20   N  NR15  0  -0.726  -2.0943  -0.3107   0.0141
 A92  N21   N  N     0  -0.481  -1.8512   1.8790   0.2572
 A92  N22   N  NH1   0  -0.578   5.0982  -0.3729   1.1570
 A92  N23   N  NH2   0  -0.829  -5.9147  -2.4131  -0.4425
 A92  O24   O  O     0  -0.499  -3.6828  -2.5631  -0.2213
 A92  H1    H  HCR6  0   0.264  -6.4276   2.4690   0.1701
 A92  H2    H  HCR6  0   0.271   0.4990   2.7292   0.2639
 A92  H3    H  HCR6  0   0.249  -6.7152   0.0870  -0.1073
 A92  H4    H  HCR6  0   0.260   2.9512   2.6384   0.2511
 A92  H5    H  HCR6  0   0.265  -4.1763   3.4911   0.3571
 A92  H6    H  HCR6  0   0.273   2.7608  -1.6455   0.0273
 A92  H15   H  HCH2  0   0.216   6.9523   0.9743  -1.2719
 A92  H15A  H  HCH2  0   0.235   6.8885  -0.4172  -2.3365
 A92  H16   H  HCH2  0   0.215   6.8179  -1.9505  -0.3964
 A92  H16A  H  HCH2  0   0.228   8.1968  -0.8760  -0.2225
 A92  H17   H  HCH2  0   0.236   4.6456   0.7007  -2.0706
 A92  H17A  H  HCH2  0   0.220   4.6161  -0.9760  -1.5493
 A92  H18   H  HCH2  0   0.237   6.8946  -1.0887   1.9140
 A92  H18A  H  HCH2  0   0.217   6.9417   0.5641   1.3305
 A92  H19   H  HCH1  0   0.242   4.9278   1.4642   0.2475
 A92  HN20  H  HNR5  0   0.413  -1.8850  -1.2902  -0.0851
 A92  HN22  H  HNH1  0   0.343   4.7370  -1.3180   1.0815
 A92  HN23  H  HNH2  0   0.426  -6.7575  -1.8700  -0.5036
 A92  HN2A  H  HNH2  0   0.415  -6.0055  -3.4104  -0.5500
 A92  C14   C  C     0   0.528  -4.7039  -1.8796  -0.2571

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
 A92  F    C12   single    1.345  0.020  1.345
 A92  C1   C3    aromatic  1.399  0.020  1.399
 A92  C1   C5    aromatic  1.383  0.020  1.383
 A92  C2   C4    aromatic  1.382  0.020  1.382
 A92  C2   C7    aromatic  1.397  0.020  1.397
 A92  C3   C8    aromatic  1.391  0.020  1.391
 A92  C4   C9    aromatic  1.393  0.020  1.393
 A92  C5   C11   aromatic  1.393  0.020  1.393
 A92  C6   C9    aromatic  1.391  0.020  1.391
 A92  C6   C12   aromatic  1.378  0.020  1.378
 A92  C7   C12   aromatic  1.391  0.020  1.391
 A92  C7   C13   single    1.461  0.020  1.461
 A92  C8   C10   aromatic  1.398  0.020  1.398
 A92  C8   C14   single    1.489  0.020  1.489
 A92  C9   C19   single    1.507  0.020  1.507
 A92  C10  C11   aromatic  1.406  0.020  1.406
 A92  C10  N20   aromatic  1.362  0.020  1.362
 A92  C11  N21   aromatic  1.368  0.020  1.368
 A92  C13  N20   aromatic  1.362  0.020  1.362
 A92  C13  N21   aromatic  1.309  0.020  1.309
 A92  C14  N23   single    1.336  0.020  1.336
 A92  C14  O24   double    1.229  0.020  1.229
 A92  C15  C16   single    1.525  0.020  1.525
 A92  C15  C17   single    1.526  0.020  1.526
 A92  C16  C18   single    1.526  0.020  1.526
 A92  C17  C19   single    1.536  0.020  1.536
 A92  C18  N22   single    1.458  0.020  1.458
 A92  C19  N22   single    1.459  0.020  1.459
 A92  C1   H1    single    0.930  0.020  1.080
 A92  C2   H2    single    0.930  0.020  1.080
 A92  C3   H3    single    0.930  0.020  1.080
 A92  C4   H4    single    0.930  0.020  1.080
 A92  C5   H5    single    0.930  0.020  1.080
 A92  C6   H6    single    0.930  0.020  1.080
 A92  C15  H15   single    0.970  0.020  1.090
 A92  C15  H15A  single    0.970  0.020  1.090
 A92  C16  H16   single    0.970  0.020  1.090
 A92  C16  H16A  single    0.970  0.020  1.090
 A92  C17  H17   single    0.970  0.020  1.090
 A92  C17  H17A  single    0.970  0.020  1.090
 A92  C18  H18   single    0.970  0.020  1.090
 A92  C18  H18A  single    0.970  0.020  1.090
 A92  C19  H19   single    0.970  0.020  1.090
 A92  N20  HN20  single    0.860  0.020  1.020
 A92  N22  HN22  single    0.890  0.020  1.040
 A92  N23  HN23  single    0.860  0.020  1.020
 A92  N23  HN2A  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
 A92  H1    C1   C5    119.62  3.000
 A92  H1    C1   C3    118.84  3.000
 A92  C5    C1   C3    121.54  3.000
 A92  H2    C2   C7    118.58  3.000
 A92  H2    C2   C4    120.00  3.000
 A92  C7    C2   C4    121.42  3.000
 A92  H3    C3   C8    120.69  3.000
 A92  H3    C3   C1    117.20  3.000
 A92  C8    C3   C1    122.11  3.000
 A92  H4    C4   C9    119.57  3.000
 A92  H4    C4   C2    119.40  3.000
 A92  C9    C4   C2    121.03  3.000
 A92  H5    C5   C11   120.97  3.000
 A92  H5    C5   C1    121.26  3.000
 A92  C11   C5   C1    117.77  3.000
 A92  H6    C6   C12   118.56  3.000
 A92  H6    C6   C9    121.72  3.000
 A92  C12   C6   C9    119.72  3.000
 A92  C13   C7   C12   124.65  3.000
 A92  C13   C7   C2    119.01  3.000
 A92  C12   C7   C2    116.34  3.000
 A92  C14   C8   C10   119.07  3.000
 A92  C14   C8   C3    125.26  3.000
 A92  C10   C8   C3    115.67  3.000
 A92  C19   C9   C6    120.79  3.000
 A92  C19   C9   C4    120.83  3.000
 A92  C6    C9   C4    118.35  3.000
 A92  N20   C10  C11   104.61  3.000
 A92  N20   C10  C8    132.54  3.000
 A92  C11   C10  C8    122.85  3.000
 A92  N21   C11  C10   109.96  3.000
 A92  N21   C11  C5    129.99  3.000
 A92  C10   C11  C5    120.05  3.000
 A92  C7    C12  C6    123.15  3.000
 A92  C7    C12  F     119.36  3.000
 A92  C6    C12  F     117.49  3.000
 A92  N21   C13  N20   112.17  3.000
 A92  N21   C13  C7    123.02  3.000
 A92  N20   C13  C7    124.80  3.000
 A92  H15A  C15  H15   106.55  3.000
 A92  H15A  C15  C17   110.22  3.000
 A92  H15   C15  C17   109.06  3.000
 A92  H15A  C15  C16   110.80  3.000
 A92  H15   C15  C16   109.34  3.000
 A92  C17   C15  C16   110.76  3.000
 A92  H16A  C16  H16   106.79  3.000
 A92  H16A  C16  C18   110.00  3.000
 A92  H16   C16  C18   109.18  3.000
 A92  H16A  C16  C15   110.68  3.000
 A92  H16   C16  C15   109.69  3.000
 A92  C18   C16  C15   110.42  3.000
 A92  H17A  C17  H17   106.70  3.000
 A92  H17A  C17  C19   109.35  3.000
 A92  H17   C17  C19   109.75  3.000
 A92  H17A  C17  C15   109.92  3.000
 A92  H17   C17  C15   110.61  3.000
 A92  C19   C17  C15   110.43  3.000
 A92  H18A  C18  H18   106.56  3.000
 A92  H18A  C18  N22   107.90  3.000
 A92  H18   C18  N22   108.23  3.000
 A92  H18A  C18  C16   109.39  3.000
 A92  H18   C18  C16   110.69  3.000
 A92  N22   C18  C16   113.79  3.000
 A92  H19   C19  N22   106.31  3.000
 A92  H19   C19  C17   107.41  3.000
 A92  N22   C19  C17   113.39  3.000
 A92  H19   C19  C9    107.41  3.000
 A92  N22   C19  C9    111.03  3.000
 A92  C17   C19  C9    110.93  3.000
 A92  HN20  N20  C13   128.54  3.000
 A92  HN20  N20  C10   123.74  3.000
 A92  C13   N20  C10   107.72  3.000
 A92  C13   N21  C11   105.54  3.000
 A92  HN22  N22  C19   109.62  3.000
 A92  HN22  N22  C18   108.22  3.000
 A92  C19   N22  C18   111.72  3.000
 A92  HN2A  N23  HN23  116.95  3.000
 A92  HN2A  N23  C14   119.47  3.000
 A92  HN23  N23  C14   123.57  3.000
 A92  O24   C14  N23   122.33  3.000
 A92  O24   C14  C8    120.00  3.000
 A92  N23   C14  C8    117.67  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
 A92  CONST_01  C10   C8   C3   C1     0.00   0.0  0
 A92  CONST_02  C10   C11  C5   C1     0.00   0.0  0
 A92  CONST_03  N21   C11  C5   C1   180.00   0.0  0
 A92  CONST_04  C6    C9   C4   C2     0.00   0.0  0
 A92  CONST_05  C6    C12  C7   C2     0.00   0.0  0
 A92  CONST_06  N20   C13  C7   C2   180.00   0.0  0
 A92  CONST_07  N21   C13  C7   C2     0.00   0.0  0
 A92  CONST_08  C11   C5   C1   C3     0.00   0.0  0
 A92  CONST_09  C11   C10  C8   C3     0.00   0.0  0
 A92  CONST_10  N20   C10  C8   C3   180.00   0.0  0
 A92  CONST_11  C12   C7   C2   C4     0.00   0.0  0
 A92  CONST_12  C13   C7   C2   C4   180.00   0.0  0
 A92  CONST_13  C12   C6   C9   C4     0.00   0.0  0
 A92  CONST_14  C8    C3   C1   C5     0.00   0.0  0
 A92  CONST_15  C8    C10  C11  C5     0.00   0.0  0
 A92  CONST_16  N20   C10  C11  C5   180.00   0.0  0
 A92  CONST_17  C13   N21  C11  C5   180.00   0.0  0
 A92  CONST_18  C13   C7   C12  C6   180.00   0.0  0
 A92  CONST_19  C9    C4   C2   C7     0.00   0.0  0
 A92  CONST_20  C9    C6   C12  C7     0.00   0.0  0
 A92  CONST_21  C10   N20  C13  C7   180.00   0.0  0
 A92  CONST_22  C11   N21  C13  C7   180.00   0.0  0
 A92  CONST_23  N21   C11  C10  C8   180.00   0.0  0
 A92  CONST_24  C13   N20  C10  C8   180.00   0.0  0
 A92  CONST_25  C13   N21  C11  C10    0.00   0.0  0
 A92  CONST_26  N21   C13  N20  C10    0.00   0.0  0
 A92  CONST_27  C13   N20  C10  C11    0.00   0.0  0
 A92  CONST_28  N20   C13  N21  C11    0.00   0.0  0
 A92  CONST_29  N20   C13  C7   C12    0.00   0.0  0
 A92  CONST_30  N21   C13  C7   C12  180.00   0.0  0
 A92  CONST_31  N21   C11  C10  N20    0.00   0.0  0
 A92  CONST_32  C19   C9   C4   C2   180.00   0.0  0
 A92  CONST_33  C19   C9   C6   C12  180.00   0.0  0
 A92  CONST_34  C9    C6   C12  F    180.00   0.0  0
 A92  CONST_35  C2    C7   C12  F    180.00   0.0  0
 A92  CONST_36  C13   C7   C12  F      0.00   0.0  0
 A92  CONST_37  C14   C8   C3   C1   180.00   0.0  0
 A92  CONST_38  C14   C8   C10  C11  180.00   0.0  0
 A92  CONST_39  N20   C10  C8   C14    0.00   0.0  0
 A92  CONST_40  H5    C5   C1   C3   180.00   0.0  0
 A92  CONST_41  H6    C6   C9   C4   180.00   0.0  0
 A92  CONST_42  H3    C3   C1   C5   180.00   0.0  0
 A92  CONST_43  H4    C4   C9   C6   180.00   0.0  0
 A92  CONST_44  HN20  N20  C13  C7     0.00   0.0  0
 A92  CONST_45  H1    C1   C3   C8   180.00   0.0  0
 A92  CONST_46  H2    C2   C4   C9   180.00   0.0  0
 A92  CONST_47  HN23  N23  C14  C8     0.00   0.0  0
 A92  CONST_48  HN2A  N23  C14  C8   180.00   0.0  0
 A92  Var_01    N22   C18  C16  C15   54.38  30.0  1
 A92  Var_02    C19   C17  C15  C16   53.20  30.0  1
 A92  Var_03    C19   N22  C18  C16  -54.50  30.0  1
 A92  Var_04    C18   C16  C15  C17  -53.28  30.0  1
 A92  Var_05    N23   C14  C8   C3     4.05  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
 A92  chir_01  C19  C9  C17  N22  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
 A92  plan-1  F     0.020
 A92  plan-1  C2    0.020
 A92  plan-1  C4    0.020
 A92  plan-1  C6    0.020
 A92  plan-1  C7    0.020
 A92  plan-1  C9    0.020
 A92  plan-1  C12   0.020
 A92  plan-1  C13   0.020
 A92  plan-1  C19   0.020
 A92  plan-1  H2    0.020
 A92  plan-1  H4    0.020
 A92  plan-1  H6    0.020
 A92  plan-2  C1    0.020
 A92  plan-2  C3    0.020
 A92  plan-2  C5    0.020
 A92  plan-2  C7    0.020
 A92  plan-2  C8    0.020
 A92  plan-2  C10   0.020
 A92  plan-2  C11   0.020
 A92  plan-2  C13   0.020
 A92  plan-2  N20   0.020
 A92  plan-2  N21   0.020
 A92  plan-2  H1    0.020
 A92  plan-2  H3    0.020
 A92  plan-2  H5    0.020
 A92  plan-2  HN20  0.020
 A92  plan-2  C14   0.020
 A92  plan-3  C8    0.020
 A92  plan-3  N23   0.020
 A92  plan-3  O24   0.020
 A92  plan-3  HN23  0.020
 A92  plan-3  HN2A  0.020
 A92  plan-3  C14   0.020

