# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 16:15:00 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: 2-(1~{H}-benzimidazol-2-yl)-~{N}-[[4-(2-ethylphenyl)-3-(trifluoromethyl)phenyl]methyl]ethanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1ccccc1c2ccc(CNCCc3[nH]c4ccccc4n3)cc2C(F)(F)F
#
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
 B5E  B5E  2-(1~{H}-benzimidazol-2-yl)-~{N}-[[4-(2-ethylphenyl)-3-(trifluoromethyl)phenyl]methyl]ethanamine  ligand  55  31  .  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_B5E
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
 B5E  F2   F  F     0  -0.305  -2.4103  -2.8117  -0.6690
 B5E  C24  C  CT    0   1.062  -3.3116  -1.9367  -0.2064
 B5E  F    F  F     0  -0.305  -4.1326  -1.6633  -1.2252
 B5E  F1   F  F     0  -0.315  -4.0416  -2.5953   0.7090
 B5E  C23  C  CR6   0  -0.244  -2.6661  -0.7128   0.3757
 B5E  C8   C  CR6   0   0.069  -3.4070   0.4511   0.6207
 B5E  C7   C  CR6   0  -0.019  -4.8565   0.5901   0.3155
 B5E  C6   C  CR16  0  -0.267  -5.7804  -0.0256   1.1589
 B5E  C5   C  CR16  0  -0.261  -7.1434   0.1076   0.9468
 B5E  C4   C  CR16  0  -0.248  -7.5965   0.8678  -0.1221
 B5E  C3   C  CR16  0  -0.297  -6.6813   1.4946  -0.9527
 B5E  C2   C  CR6   0   0.108  -5.3064   1.3770  -0.7522
 B5E  C1   C  CH2   0  -0.525  -4.3783   2.0774  -1.7112
 B5E  C    C  CH3   0  -0.653  -4.1435   1.2826  -2.9950
 B5E  C22  C  CR16  0  -0.328  -1.3203  -0.7727   0.7160
 B5E  C11  C  CR6   0   0.118  -0.6791   0.3029   1.3186
 B5E  C10  C  CR16  0  -0.290  -1.4124   1.4550   1.5632
 B5E  C9   C  CR16  0  -0.268  -2.7531   1.5243   1.2169
 B5E  C12  C  CH2   0  -0.338   0.7850   0.2221   1.6479
 B5E  N    N  NH1   0  -0.594   1.5796   0.3785   0.4422
 B5E  C13  C  CH2   0  -0.251   3.0012   0.2558   0.6961
 B5E  C14  C  CH2   0  -0.572   3.7849   0.4447  -0.5979
 B5E  C15  C  CR5   0   0.473   5.2507   0.2805  -0.3954
 B5E  N2   N  NR15  0  -0.704   6.0144  -0.4641  -1.2366
 B5E  C21  C  CR56  0   0.325   7.3057  -0.4102  -0.7846
 B5E  C16  C  CR56  0   0.133   7.2418   0.4024   0.3601
 B5E  N1   N  N     0  -0.479   5.9475   0.8151   0.5721
 B5E  C20  C  CR16  0  -0.307   8.4919  -0.9737  -1.2390
 B5E  C19  C  CR16  0  -0.281   9.6330  -0.6968  -0.5046
 B5E  C18  C  CR16  0  -0.271   9.5892   0.1128   0.6402
 B5E  C17  C  CR16  0  -0.338   8.4027   0.6696   1.0851
 B5E  H1   H  HCR6  0   0.248  -5.4280  -0.5999   2.0063
 B5E  H2   H  HCR6  0   0.254  -7.8442  -0.3739   1.6162
 B5E  H3   H  HCR6  0   0.254  -8.6577   0.9821  -0.3024
 B5E  H4   H  HCR6  0   0.248  -7.0387   2.0976  -1.7799
 B5E  H5   H  HCH2  0   0.243  -4.8116   3.0468  -1.9682
 B5E  H6   H  HCH2  0   0.245  -3.4182   2.2884  -1.2399
 B5E  H7   H  HCH3  0   0.224  -5.0846   1.0653  -3.5021
 B5E  H8   H  HCH3  0   0.230  -3.5140   1.8452  -3.6851
 B5E  H9   H  HCH3  0   0.225  -3.6494   0.3346  -2.7896
 B5E  H10  H  HCR6  0   0.264  -0.7455  -1.6693   0.5235
 B5E  H11  H  HCR6  0   0.261  -0.9372   2.3083   2.0321
 B5E  H12  H  HCR6  0   0.263  -3.3109   2.4298   1.4205
 B5E  H13  H  HCH2  0   0.219   1.0278   0.9647   2.4222
 B5E  H14  H  HCH2  0   0.243   1.0100  -0.7586   2.0762
 B5E  H15  H  HNH1  0   0.345   1.3903   1.2939   0.0486
 B5E  H17  H  HCH2  0   0.208   3.3677   0.9637   1.4524
 B5E  H18  H  HCH2  0   0.232   3.1941  -0.7460   1.0903
 B5E  H19  H  HCH2  0   0.261   3.4324  -0.2650  -1.3484
 B5E  H20  H  HCH2  0   0.269   3.5936   1.4453  -0.9993
 B5E  H21  H  HNR5  0   0.417   5.6816  -0.9630  -2.0465
 B5E  H23  H  HCR6  0   0.265   8.5265  -1.5995  -2.1212
 B5E  H24  H  HCR6  0   0.254  10.5801  -1.1148  -0.8201
 B5E  H25  H  HCR6  0   0.251  10.5049   0.3026   1.1851
 B5E  H26  H  HCR6  0   0.251   8.3727   1.2937   1.9693

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
 B5E  C5   C4   aromatic  1.388  0.020  1.388
 B5E  C5   C6   aromatic  1.386  0.020  1.386
 B5E  C4   C3   aromatic  1.386  0.020  1.386
 B5E  C6   C7   aromatic  1.394  0.020  1.394
 B5E  C18  C17  aromatic  1.384  0.020  1.384
 B5E  C18  C19  aromatic  1.403  0.020  1.403
 B5E  C17  C16  aromatic  1.395  0.020  1.395
 B5E  C3   C2   aromatic  1.394  0.020  1.394
 B5E  F1   C24  single    1.343  0.020  1.343
 B5E  C19  C20  aromatic  1.385  0.020  1.385
 B5E  C7   C2   aromatic  1.401  0.020  1.401
 B5E  C7   C8   single    1.488  0.020  1.488
 B5E  C2   C1   single    1.507  0.020  1.507
 B5E  C16  N1   aromatic  1.375  0.020  1.375
 B5E  C16  C21  aromatic  1.405  0.020  1.405
 B5E  C24  F2   single    1.339  0.020  1.339
 B5E  C24  F    single    1.337  0.020  1.337
 B5E  C24  C23  single    1.501  0.020  1.501
 B5E  C20  C21  aromatic  1.390  0.020  1.390
 B5E  C8   C23  aromatic  1.401  0.020  1.401
 B5E  C8   C9   aromatic  1.391  0.020  1.391
 B5E  N1   C15  aromatic  1.307  0.020  1.307
 B5E  C21  N2   aromatic  1.369  0.020  1.369
 B5E  C23  C22  aromatic  1.389  0.020  1.389
 B5E  C1   C    single    1.528  0.020  1.528
 B5E  C9   C10  aromatic  1.386  0.020  1.386
 B5E  C15  N2   aromatic  1.358  0.020  1.358
 B5E  C15  C14  single    1.489  0.020  1.489
 B5E  C22  C11  aromatic  1.390  0.020  1.390
 B5E  C10  C11  aromatic  1.387  0.020  1.387
 B5E  C13  C14  single    1.525  0.020  1.525
 B5E  C13  N    single    1.449  0.020  1.449
 B5E  C11  C12  single    1.503  0.020  1.503
 B5E  N    C12  single    1.452  0.020  1.452
 B5E  C6   H1   single    0.930  0.020  1.080
 B5E  C5   H2   single    0.930  0.020  1.080
 B5E  C4   H3   single    0.930  0.020  1.080
 B5E  C3   H4   single    0.930  0.020  1.080
 B5E  C1   H5   single    0.970  0.020  1.090
 B5E  C1   H6   single    0.970  0.020  1.090
 B5E  C    H7   single    0.970  0.020  1.090
 B5E  C    H8   single    0.970  0.020  1.090
 B5E  C    H9   single    0.970  0.020  1.090
 B5E  C22  H10  single    0.930  0.020  1.080
 B5E  C10  H11  single    0.930  0.020  1.080
 B5E  C9   H12  single    0.930  0.020  1.080
 B5E  C12  H13  single    0.970  0.020  1.090
 B5E  C12  H14  single    0.970  0.020  1.090
 B5E  N    H15  single    0.890  0.020  1.040
 B5E  C13  H17  single    0.970  0.020  1.090
 B5E  C13  H18  single    0.970  0.020  1.090
 B5E  C14  H19  single    0.970  0.020  1.090
 B5E  C14  H20  single    0.970  0.020  1.090
 B5E  N2   H21  single    0.860  0.020  1.020
 B5E  C20  H23  single    0.930  0.020  1.080
 B5E  C19  H24  single    0.930  0.020  1.080
 B5E  C18  H25  single    0.930  0.020  1.080
 B5E  C17  H26  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
 B5E  C23  C24  F1   111.66  3.000
 B5E  C23  C24  F    113.13  3.000
 B5E  F1   C24  F    106.61  3.000
 B5E  C23  C24  F2   112.17  3.000
 B5E  F    C24  F2   106.49  3.000
 B5E  F1   C24  F2   106.32  3.000
 B5E  C22  C23  C8   120.34  3.000
 B5E  C22  C23  C24  118.44  3.000
 B5E  C8   C23  C24  121.17  3.000
 B5E  C9   C8   C7   118.29  3.000
 B5E  C9   C8   C23  117.85  3.000
 B5E  C7   C8   C23  123.84  3.000
 B5E  C2   C7   C6   119.76  3.000
 B5E  C2   C7   C8   121.45  3.000
 B5E  C6   C7   C8   118.70  3.000
 B5E  H1   C6   C5   119.40  3.000
 B5E  H1   C6   C7   119.48  3.000
 B5E  C5   C6   C7   121.11  3.000
 B5E  H2   C5   C4   120.58  3.000
 B5E  H2   C5   C6   119.97  3.000
 B5E  C4   C5   C6   119.45  3.000
 B5E  H3   C4   C3   119.98  3.000
 B5E  H3   C4   C5   120.42  3.000
 B5E  C3   C4   C5   119.59  3.000
 B5E  H4   C3   C2   118.79  3.000
 B5E  H4   C3   C4   119.42  3.000
 B5E  C2   C3   C4   121.79  3.000
 B5E  C1   C2   C3   118.46  3.000
 B5E  C1   C2   C7   123.26  3.000
 B5E  C3   C2   C7   118.27  3.000
 B5E  H6   C1   H5   106.22  3.000
 B5E  H6   C1   C    109.18  3.000
 B5E  H5   C1   C    108.95  3.000
 B5E  H6   C1   C2   110.93  3.000
 B5E  H5   C1   C2   108.53  3.000
 B5E  C    C1   C2   112.80  3.000
 B5E  H9   C    H8   107.86  3.000
 B5E  H9   C    H7   107.80  3.000
 B5E  H8   C    H7   107.86  3.000
 B5E  H9   C    C1   111.36  3.000
 B5E  H8   C    C1   110.62  3.000
 B5E  H7   C    C1   111.20  3.000
 B5E  H10  C22  C11  118.25  3.000
 B5E  H10  C22  C23  120.44  3.000
 B5E  C11  C22  C23  121.31  3.000
 B5E  C12  C11  C10  121.40  3.000
 B5E  C12  C11  C22  120.19  3.000
 B5E  C10  C11  C22  118.38  3.000
 B5E  H11  C10  C9   119.53  3.000
 B5E  H11  C10  C11  119.90  3.000
 B5E  C9   C10  C11  120.57  3.000
 B5E  H12  C9   C10  119.54  3.000
 B5E  H12  C9   C8   118.92  3.000
 B5E  C10  C9   C8   121.54  3.000
 B5E  H14  C12  H13  106.52  3.000
 B5E  H14  C12  N    108.01  3.000
 B5E  H13  C12  N    113.00  3.000
 B5E  H14  C12  C11  109.55  3.000
 B5E  H13  C12  C11  109.45  3.000
 B5E  N    C12  C11  110.20  3.000
 B5E  H15  N    C13  109.12  3.000
 B5E  H15  N    C12  108.49  3.000
 B5E  C13  N    C12  112.46  3.000
 B5E  H18  C13  H17  106.45  3.000
 B5E  H18  C13  C14  109.19  3.000
 B5E  H17  C13  C14  109.44  3.000
 B5E  H18  C13  N    108.29  3.000
 B5E  H17  C13  N    113.15  3.000
 B5E  C14  C13  N    110.18  3.000
 B5E  H20  C14  H19  106.60  3.000
 B5E  H20  C14  C15  108.83  3.000
 B5E  H19  C14  C15  109.86  3.000
 B5E  H20  C14  C13  109.55  3.000
 B5E  H19  C14  C13  109.69  3.000
 B5E  C15  C14  C13  112.15  3.000
 B5E  N1   C15  N2   112.52  3.000
 B5E  N2   C15  C14  121.98  3.000
 B5E  N1   C15  C14  125.49  3.000
 B5E  H21  N2   C21  126.60  3.000
 B5E  H21  N2   C15  125.69  3.000
 B5E  C21  N2   C15  107.71  3.000
 B5E  C20  C21  C16  122.66  3.000
 B5E  C20  C21  N2   132.93  3.000
 B5E  C16  C21  N2   104.41  3.000
 B5E  C17  C16  N1   130.24  3.000
 B5E  N1   C16  C21  110.00  3.000
 B5E  C17  C16  C21  119.76  3.000
 B5E  C16  N1   C15  105.37  3.000
 B5E  H23  C20  C19  121.43  3.000
 B5E  H23  C20  C21  121.90  3.000
 B5E  C19  C20  C21  116.67  3.000
 B5E  H24  C19  C18  119.22  3.000
 B5E  H24  C19  C20  119.29  3.000
 B5E  C18  C19  C20  121.49  3.000
 B5E  H25  C18  C17  119.53  3.000
 B5E  H25  C18  C19  119.05  3.000
 B5E  C17  C18  C19  121.42  3.000
 B5E  H26  C17  C18  121.21  3.000
 B5E  H26  C17  C16  120.79  3.000
 B5E  C18  C17  C16  118.00  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
 B5E  CONST_03  C10  C9   C8   C23     0.00   0.0  0
 B5E  CONST_04  C10  C11  C22  C23     0.00   0.0  0
 B5E  CONST_05  C5   C6   C7   C8    180.00   0.0  0
 B5E  CONST_06  C3   C2   C7   C8    180.00   0.0  0
 B5E  CONST_07  C11  C22  C23  C8      0.00   0.0  0
 B5E  CONST_08  C11  C10  C9   C8      0.00   0.0  0
 B5E  CONST_09  C4   C5   C6   C7      0.00   0.0  0
 B5E  CONST_10  C4   C3   C2   C7      0.00   0.0  0
 B5E  CONST_11  C22  C23  C8   C7    180.00   0.0  0
 B5E  CONST_12  C10  C9   C8   C7    180.00   0.0  0
 B5E  CONST_13  C3   C4   C5   C6      0.00   0.0  0
 B5E  CONST_14  C3   C2   C7   C6      0.00   0.0  0
 B5E  CONST_16  C2   C3   C4   C5      0.00   0.0  0
 B5E  CONST_17  C2   C7   C6   C5      0.00   0.0  0
 B5E  CONST_19  C9   C8   C23  C22     0.00   0.0  0
 B5E  CONST_20  C9   C10  C11  C22     0.00   0.0  0
 B5E  CONST_21  C17  C16  N1   C15   180.00   0.0  0
 B5E  CONST_22  C21  C16  N1   C15     0.00   0.0  0
 B5E  CONST_23  C16  C21  N2   C15     0.00   0.0  0
 B5E  CONST_24  C20  C21  N2   C15   180.00   0.0  0
 B5E  CONST_25  C17  C16  C21  N2    180.00   0.0  0
 B5E  CONST_26  N1   C16  C21  N2      0.00   0.0  0
 B5E  CONST_27  C19  C20  C21  N2    180.00   0.0  0
 B5E  CONST_28  C16  N1   C15  N2      0.00   0.0  0
 B5E  CONST_29  C18  C17  C16  C21     0.00   0.0  0
 B5E  CONST_30  C18  C19  C20  C21     0.00   0.0  0
 B5E  CONST_31  N1   C15  N2   C21     0.00   0.0  0
 B5E  CONST_32  C19  C18  C17  C16     0.00   0.0  0
 B5E  CONST_33  C19  C20  C21  C16     0.00   0.0  0
 B5E  CONST_34  C18  C17  C16  N1    180.00   0.0  0
 B5E  CONST_35  C20  C21  C16  N1    180.00   0.0  0
 B5E  CONST_36  C17  C18  C19  C20     0.00   0.0  0
 B5E  CONST_37  C17  C16  C21  C20     0.00   0.0  0
 B5E  CONST_38  C7   C8   C23  C24     0.00   0.0  0
 B5E  CONST_39  C9   C8   C23  C24   180.00   0.0  0
 B5E  CONST_40  C11  C22  C23  C24   180.00   0.0  0
 B5E  CONST_41  C12  C11  C22  C23   180.00   0.0  0
 B5E  CONST_42  C1   C2   C7   C8      0.00   0.0  0
 B5E  CONST_43  C1   C2   C7   C6    180.00   0.0  0
 B5E  CONST_44  C1   C2   C3   C4    180.00   0.0  0
 B5E  CONST_45  C12  C11  C10  C9    180.00   0.0  0
 B5E  CONST_46  C16  N1   C15  C14   180.00   0.0  0
 B5E  CONST_47  C21  N2   C15  C14   180.00   0.0  0
 B5E  CONST_48  H12  C9   C8   C23   180.00   0.0  0
 B5E  CONST_49  H1   C6   C7   C8      0.00   0.0  0
 B5E  CONST_50  H10  C22  C23  C8    180.00   0.0  0
 B5E  CONST_51  H11  C10  C9   C8    180.00   0.0  0
 B5E  CONST_52  H2   C5   C6   C7    180.00   0.0  0
 B5E  CONST_53  H4   C3   C2   C7    180.00   0.0  0
 B5E  CONST_54  H3   C4   C5   C6    180.00   0.0  0
 B5E  CONST_55  H23  C20  C21  N2      0.00   0.0  0
 B5E  CONST_56  H26  C17  C16  C21   180.00   0.0  0
 B5E  CONST_57  H24  C19  C20  C21   180.00   0.0  0
 B5E  CONST_58  H25  C18  C17  C16   180.00   0.0  0
 B5E  CONST_59  H21  N2   C21  C16   180.00   0.0  0
 B5E  Var_01    C8   C23  C24  F2    164.62  30.0  2
 B5E  Var_02    C    C1   C2   C7     96.44  30.0  2
 B5E  Var_03    N    C12  C11  C22    75.88  30.0  2
 B5E  Var_04    N1   C15  C14  C13   -46.15  30.0  2
 B5E  Var_05    C13  N    C12  C11  -177.72  30.0  1
 B5E  Var_06    C15  C14  C13  N    -178.03  30.0  3
 B5E  Var_07    H7   C    C1   C2     57.00  30.0  3
 B5E  Var_08    C14  C13  N    C12  -179.32  30.0  1

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
 B5E  plan-1  C24  0.020
 B5E  plan-1  C23  0.020
 B5E  plan-1  C8   0.020
 B5E  plan-1  C7   0.020
 B5E  plan-1  C22  0.020
 B5E  plan-1  C11  0.020
 B5E  plan-1  C10  0.020
 B5E  plan-1  C9   0.020
 B5E  plan-1  C12  0.020
 B5E  plan-1  H10  0.020
 B5E  plan-1  H11  0.020
 B5E  plan-1  H12  0.020
 B5E  plan-2  C8   0.020
 B5E  plan-2  C7   0.020
 B5E  plan-2  C6   0.020
 B5E  plan-2  C5   0.020
 B5E  plan-2  C4   0.020
 B5E  plan-2  C3   0.020
 B5E  plan-2  C2   0.020
 B5E  plan-2  C1   0.020
 B5E  plan-2  H1   0.020
 B5E  plan-2  H2   0.020
 B5E  plan-2  H3   0.020
 B5E  plan-2  H4   0.020
 B5E  plan-3  C14  0.020
 B5E  plan-3  C15  0.020
 B5E  plan-3  N2   0.020
 B5E  plan-3  C21  0.020
 B5E  plan-3  C16  0.020
 B5E  plan-3  N1   0.020
 B5E  plan-3  C20  0.020
 B5E  plan-3  C19  0.020
 B5E  plan-3  C18  0.020
 B5E  plan-3  C17  0.020
 B5E  plan-3  H21  0.020
 B5E  plan-3  H23  0.020
 B5E  plan-3  H24  0.020
 B5E  plan-3  H25  0.020
 B5E  plan-3  H26  0.020

