# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 10:06:55 2022
#   Inital geometry file: a 135 line input string
#   Ligand name: 2-(1~{H}-benzimidazol-2-yl)-~{N}-[[4-(2-ethylphenyl)-3-methyl-phenyl]methyl]ethanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1ccccc1c2ccc(CNCCc3[nH]c4ccccc4n3)cc2C
#
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
 B4Q  B4Q  2-(1~{H}-benzimidazol-2-yl)-~{N}-[[4-(2-ethylphenyl)-3-methyl-phenyl]methyl]ethanamine  ligand  55  28  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_B4Q
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
 B4Q  C1   C  CH2   0  -0.519  -5.1712   1.7758   1.3724
 B4Q  N1   N  NR15  0  -0.692   5.4112   0.4977  -1.0205
 B4Q  C2   C  CR6   0   0.096  -5.9764   0.9183   0.4335
 B4Q  N2   N  N     0  -0.473   5.5724   0.5315   1.1907
 B4Q  C3   C  CR16  0  -0.301  -7.3449   1.1458   0.2971
 B4Q  C4   C  CR16  0  -0.252  -8.1162   0.4137  -0.5937
 B4Q  C5   C  CR16  0  -0.262  -7.5212  -0.5694  -1.3717
 B4Q  C6   C  CR16  0  -0.276  -6.1609  -0.8090  -1.2449
 B4Q  C7   C  CR6   0   0.009  -5.3807  -0.0764  -0.3518
 B4Q  C8   C  CR6   0  -0.003  -3.9270  -0.3732  -0.2595
 B4Q  C9   C  CR16  0  -0.260  -3.0542   0.1599  -1.2055
 B4Q  C10  C  CR16  0  -0.303  -1.6979  -0.1198  -1.1695
 B4Q  C11  C  CR6   0   0.113  -1.1837  -0.9566  -0.1841
 B4Q  C12  C  CH2   0  -0.334   0.2836  -1.2856  -0.1477
 B4Q  C13  C  CH2   0  -0.254   2.5054  -0.3685   0.0194
 B4Q  C14  C  CH2   0  -0.555   3.3069   0.9151   0.2396
 B4Q  C15  C  CR5   0   0.429   4.7711   0.6653   0.1681
 B4Q  C16  C  CR56  0   0.333   6.7276   0.2379  -0.7503
 B4Q  C17  C  CR16  0  -0.309   7.8285  -0.0090  -1.5616
 B4Q  C18  C  CR16  0  -0.280   9.0346  -0.2368  -0.9205
 B4Q  C19  C  CR16  0  -0.272   9.1362  -0.2164   0.4787
 B4Q  C20  C  CR16  0  -0.337   8.0343   0.0326   1.2783
 B4Q  C21  C  CR56  0   0.133   6.8097   0.2629   0.6524
 B4Q  C22  C  CR16  0  -0.365  -2.0566  -1.4799   0.7618
 B4Q  C23  C  CR6   0   0.095  -3.4233  -1.2068   0.7447
 B4Q  C24  C  CH3   0  -0.744  -4.3275  -1.8158   1.7767
 B4Q  C    C  CH3   0  -0.654  -4.6545   3.0430   0.6936
 B4Q  N    N  NH1   0  -0.592   1.0848  -0.0914   0.0539
 B4Q  H1   H  HCH2  0   0.242  -5.7899   2.0546   2.2284
 B4Q  H2   H  HCH2  0   0.240  -4.3254   1.2135   1.7721
 B4Q  H5   H  HCR6  0   0.245  -7.8139   1.9134   0.9026
 B4Q  H6   H  HCR6  0   0.252  -9.1773   0.6105  -0.6786
 B4Q  H7   H  HCR6  0   0.253  -8.1117  -1.1474  -2.0706
 B4Q  H8   H  HCR6  0   0.245  -5.6919  -1.5799  -1.8447
 B4Q  H9   H  HCR6  0   0.243  -3.4482   0.7997  -1.9862
 B4Q  H10  H  HCR6  0   0.243  -1.0400   0.3087  -1.9157
 B4Q  H11  H  HCH2  0   0.215   0.4660  -2.0572   0.6153
 B4Q  H12  H  HCH2  0   0.238   0.5785  -1.7266  -1.1051
 B4Q  H13  H  HCH2  0   0.228   2.7464  -0.7845  -0.9632
 B4Q  H14  H  HCH2  0   0.208   2.8176  -1.1203   0.7604
 B4Q  H15  H  HCH2  0   0.262   3.0147   1.6571  -0.5072
 B4Q  H16  H  HCH2  0   0.264   3.0807   1.3303   1.2229
 B4Q  H17  H  HCR6  0   0.265   7.7510  -0.0253  -2.6408
 B4Q  H18  H  HCR6  0   0.254   9.9184  -0.4369  -1.5121
 B4Q  H19  H  HCR6  0   0.251  10.0983  -0.4008   0.9387
 B4Q  H20  H  HCR6  0   0.252   8.1169   0.0476   2.3576
 B4Q  H21  H  HCR6  0   0.241  -1.6623  -2.1274   1.5384
 B4Q  H22  H  HCH3  0   0.246  -4.8588  -1.0577   2.3548
 B4Q  H23  H  HCH3  0   0.247  -5.0887  -2.4482   1.3167
 B4Q  H24  H  HCH3  0   0.248  -3.7636  -2.4281   2.4792
 B4Q  H25  H  HCH3  0   0.225  -5.4769   3.6409   0.2983
 B4Q  H26  H  HCH3  0   0.231  -4.0997   3.6620   1.3996
 B4Q  H27  H  HCH3  0   0.227  -3.9878   2.8044  -0.1359
 B4Q  H28  H  HNH1  0   0.345   0.8456   0.3092   0.9541
 B4Q  H3   H  HNR5  0   0.418   4.9920   0.5773  -1.9335

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
 B4Q  C    C1   single    1.528  0.020  1.528
 B4Q  C20  C19  aromatic  1.384  0.020  1.384
 B4Q  C20  C21  aromatic  1.394  0.020  1.394
 B4Q  N2   C21  aromatic  1.376  0.020  1.376
 B4Q  N2   C15  aromatic  1.306  0.020  1.306
 B4Q  C19  C18  aromatic  1.403  0.020  1.403
 B4Q  C21  C16  aromatic  1.405  0.020  1.405
 B4Q  C14  C15  single    1.487  0.020  1.487
 B4Q  C14  C13  single    1.529  0.020  1.529
 B4Q  C15  N1   aromatic  1.360  0.020  1.360
 B4Q  C1   C2   single    1.505  0.020  1.505
 B4Q  C18  C17  aromatic  1.385  0.020  1.385
 B4Q  C16  N1   aromatic  1.369  0.020  1.369
 B4Q  C16  C17  aromatic  1.390  0.020  1.390
 B4Q  C13  N    single    1.448  0.020  1.448
 B4Q  N    C12  single    1.452  0.020  1.452
 B4Q  C2   C3   aromatic  1.394  0.020  1.394
 B4Q  C2   C7   aromatic  1.400  0.020  1.400
 B4Q  C3   C4   aromatic  1.387  0.020  1.387
 B4Q  C12  C11  single    1.504  0.020  1.504
 B4Q  C22  C11  aromatic  1.389  0.020  1.389
 B4Q  C22  C23  aromatic  1.394  0.020  1.394
 B4Q  C11  C10  aromatic  1.391  0.020  1.391
 B4Q  C24  C23  single    1.501  0.020  1.501
 B4Q  C23  C8   aromatic  1.399  0.020  1.399
 B4Q  C10  C9   aromatic  1.385  0.020  1.385
 B4Q  C8   C9   aromatic  1.393  0.020  1.393
 B4Q  C8   C7   single    1.487  0.020  1.487
 B4Q  C7   C6   aromatic  1.394  0.020  1.394
 B4Q  C4   C5   aromatic  1.388  0.020  1.388
 B4Q  C6   C5   aromatic  1.387  0.020  1.387
 B4Q  C1   H1   single    0.970  0.020  1.090
 B4Q  C1   H2   single    0.970  0.020  1.090
 B4Q  N1   H3   single    0.860  0.020  1.020
 B4Q  C3   H5   single    0.930  0.020  1.080
 B4Q  C4   H6   single    0.930  0.020  1.080
 B4Q  C5   H7   single    0.930  0.020  1.080
 B4Q  C6   H8   single    0.930  0.020  1.080
 B4Q  C9   H9   single    0.930  0.020  1.080
 B4Q  C10  H10  single    0.930  0.020  1.080
 B4Q  C12  H11  single    0.970  0.020  1.090
 B4Q  C12  H12  single    0.970  0.020  1.090
 B4Q  C13  H13  single    0.970  0.020  1.090
 B4Q  C13  H14  single    0.970  0.020  1.090
 B4Q  C14  H15  single    0.970  0.020  1.090
 B4Q  C14  H16  single    0.970  0.020  1.090
 B4Q  C17  H17  single    0.930  0.020  1.080
 B4Q  C18  H18  single    0.930  0.020  1.080
 B4Q  C19  H19  single    0.930  0.020  1.080
 B4Q  C20  H20  single    0.930  0.020  1.080
 B4Q  C22  H21  single    0.930  0.020  1.080
 B4Q  C24  H22  single    0.970  0.020  1.090
 B4Q  C24  H23  single    0.970  0.020  1.090
 B4Q  C24  H24  single    0.970  0.020  1.090
 B4Q  C    H25  single    0.970  0.020  1.090
 B4Q  C    H26  single    0.970  0.020  1.090
 B4Q  C    H27  single    0.970  0.020  1.090
 B4Q  N    H28  single    0.890  0.020  1.040

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
 B4Q  H2   C1   H1   106.46  3.000
 B4Q  H2   C1   C    109.14  3.000
 B4Q  H1   C1   C    109.16  3.000
 B4Q  H2   C1   C2   110.46  3.000
 B4Q  H1   C1   C2   109.35  3.000
 B4Q  C    C1   C2   112.11  3.000
 B4Q  H3   N1   C16  126.43  3.000
 B4Q  H3   N1   C15  125.88  3.000
 B4Q  C16  N1   C15  107.67  3.000
 B4Q  C7   C2   C3   118.60  3.000
 B4Q  C7   C2   C1   121.80  3.000
 B4Q  C3   C2   C1   119.55  3.000
 B4Q  C21  N2   C15  105.39  3.000
 B4Q  H5   C3   C4   119.45  3.000
 B4Q  H5   C3   C2   119.05  3.000
 B4Q  C4   C3   C2   121.50  3.000
 B4Q  H6   C4   C5   120.33  3.000
 B4Q  H6   C4   C3   119.96  3.000
 B4Q  C5   C4   C3   119.70  3.000
 B4Q  H7   C5   C6   120.13  3.000
 B4Q  H7   C5   C4   120.43  3.000
 B4Q  C6   C5   C4   119.44  3.000
 B4Q  H8   C6   C7   119.10  3.000
 B4Q  H8   C6   C5   119.79  3.000
 B4Q  C7   C6   C5   121.11  3.000
 B4Q  C8   C7   C6   118.83  3.000
 B4Q  C6   C7   C2   119.64  3.000
 B4Q  C8   C7   C2   121.53  3.000
 B4Q  C23  C8   C9   119.34  3.000
 B4Q  C9   C8   C7   119.61  3.000
 B4Q  C23  C8   C7   121.04  3.000
 B4Q  H9   C9   C10  119.60  3.000
 B4Q  H9   C9   C8   119.17  3.000
 B4Q  C10  C9   C8   121.22  3.000
 B4Q  H10  C10  C11  120.09  3.000
 B4Q  H10  C10  C9   119.79  3.000
 B4Q  C11  C10  C9   120.12  3.000
 B4Q  C22  C11  C12  120.93  3.000
 B4Q  C22  C11  C10  118.46  3.000
 B4Q  C12  C11  C10  120.62  3.000
 B4Q  H12  C12  H11  106.22  3.000
 B4Q  H12  C12  N    107.70  3.000
 B4Q  H11  C12  N    112.89  3.000
 B4Q  H12  C12  C11  109.26  3.000
 B4Q  H11  C12  C11  109.38  3.000
 B4Q  N    C12  C11  111.20  3.000
 B4Q  H14  C13  H13  106.40  3.000
 B4Q  H14  C13  N    113.14  3.000
 B4Q  H13  C13  N    108.08  3.000
 B4Q  H14  C13  C14  109.13  3.000
 B4Q  H13  C13  C14  109.46  3.000
 B4Q  N    C13  C14  110.50  3.000
 B4Q  H16  C14  H15  107.58  3.000
 B4Q  H16  C14  C15  108.14  3.000
 B4Q  H15  C14  C15  110.16  3.000
 B4Q  H16  C14  C13  109.91  3.000
 B4Q  H15  C14  C13  109.36  3.000
 B4Q  C15  C14  C13  111.60  3.000
 B4Q  C14  C15  N2   125.71  3.000
 B4Q  C14  C15  N1   121.73  3.000
 B4Q  N2   C15  N1   112.50  3.000
 B4Q  C21  C16  C17  122.66  3.000
 B4Q  C17  C16  N1   132.88  3.000
 B4Q  C21  C16  N1   104.46  3.000
 B4Q  H17  C17  C18  121.44  3.000
 B4Q  H17  C17  C16  121.88  3.000
 B4Q  C18  C17  C16  116.68  3.000
 B4Q  H18  C18  C19  119.26  3.000
 B4Q  H18  C18  C17  119.25  3.000
 B4Q  C19  C18  C17  121.49  3.000
 B4Q  H19  C19  C20  119.52  3.000
 B4Q  H19  C19  C18  119.07  3.000
 B4Q  C20  C19  C18  121.41  3.000
 B4Q  H20  C20  C21  120.81  3.000
 B4Q  H20  C20  C19  121.18  3.000
 B4Q  C21  C20  C19  118.01  3.000
 B4Q  C20  C21  C16  119.76  3.000
 B4Q  C16  C21  N2   109.97  3.000
 B4Q  C20  C21  N2   130.27  3.000
 B4Q  H21  C22  C23  118.81  3.000
 B4Q  H21  C22  C11  118.92  3.000
 B4Q  C23  C22  C11  122.26  3.000
 B4Q  C24  C23  C22  120.18  3.000
 B4Q  C24  C23  C8   121.22  3.000
 B4Q  C22  C23  C8   118.60  3.000
 B4Q  H24  C24  H23  107.89  3.000
 B4Q  H24  C24  H22  107.51  3.000
 B4Q  H23  C24  H22  106.64  3.000
 B4Q  H24  C24  C23  111.07  3.000
 B4Q  H23  C24  C23  111.44  3.000
 B4Q  H22  C24  C23  112.06  3.000
 B4Q  H27  C    H26  107.79  3.000
 B4Q  H27  C    H25  107.77  3.000
 B4Q  H26  C    H25  107.88  3.000
 B4Q  H27  C    C1   111.30  3.000
 B4Q  H26  C    C1   110.81  3.000
 B4Q  H25  C    C1   111.14  3.000
 B4Q  H28  N    C13  109.16  3.000
 B4Q  H28  N    C12  108.54  3.000
 B4Q  C13  N    C12  112.37  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
 B4Q  CONST_01  C21  N2   C15  N1      0.00   0.0  0
 B4Q  CONST_02  C20  C21  C16  N1    180.00   0.0  0
 B4Q  CONST_03  N2   C21  C16  N1      0.00   0.0  0
 B4Q  CONST_04  C18  C17  C16  N1    180.00   0.0  0
 B4Q  CONST_05  C5   C4   C3   C2      0.00   0.0  0
 B4Q  CONST_08  C5   C6   C7   C2      0.00   0.0  0
 B4Q  CONST_09  C19  C20  C21  N2    180.00   0.0  0
 B4Q  CONST_10  C17  C16  C21  N2    180.00   0.0  0
 B4Q  CONST_11  C16  N1   C15  N2      0.00   0.0  0
 B4Q  CONST_12  C8   C7   C2   C3    180.00   0.0  0
 B4Q  CONST_13  C6   C7   C2   C3      0.00   0.0  0
 B4Q  CONST_14  C6   C5   C4   C3      0.00   0.0  0
 B4Q  CONST_15  C7   C2   C3   C4      0.00   0.0  0
 B4Q  CONST_16  C7   C6   C5   C4      0.00   0.0  0
 B4Q  CONST_17  C8   C7   C6   C5    180.00   0.0  0
 B4Q  CONST_20  C22  C23  C8   C7    180.00   0.0  0
 B4Q  CONST_21  C10  C9   C8   C7    180.00   0.0  0
 B4Q  CONST_22  C11  C22  C23  C8      0.00   0.0  0
 B4Q  CONST_23  C11  C10  C9   C8      0.00   0.0  0
 B4Q  CONST_24  C22  C11  C10  C9      0.00   0.0  0
 B4Q  CONST_25  C22  C23  C8   C9      0.00   0.0  0
 B4Q  CONST_26  C23  C22  C11  C10     0.00   0.0  0
 B4Q  CONST_27  C23  C8   C9   C10     0.00   0.0  0
 B4Q  CONST_28  C20  C21  N2   C15   180.00   0.0  0
 B4Q  CONST_29  C16  C21  N2   C15     0.00   0.0  0
 B4Q  CONST_30  C21  C16  N1   C15     0.00   0.0  0
 B4Q  CONST_31  C17  C16  N1   C15   180.00   0.0  0
 B4Q  CONST_32  C19  C20  C21  C16     0.00   0.0  0
 B4Q  CONST_33  C19  C18  C17  C16     0.00   0.0  0
 B4Q  CONST_34  C20  C19  C18  C17     0.00   0.0  0
 B4Q  CONST_35  C20  C21  C16  C17     0.00   0.0  0
 B4Q  CONST_36  C21  C20  C19  C18     0.00   0.0  0
 B4Q  CONST_37  C21  C16  C17  C18     0.00   0.0  0
 B4Q  CONST_38  C4   C3   C2   C1    180.00   0.0  0
 B4Q  CONST_39  C8   C7   C2   C1      0.00   0.0  0
 B4Q  CONST_40  C6   C7   C2   C1    180.00   0.0  0
 B4Q  CONST_41  C24  C23  C8   C7      0.00   0.0  0
 B4Q  CONST_42  C12  C11  C10  C9    180.00   0.0  0
 B4Q  CONST_43  C24  C23  C8   C9    180.00   0.0  0
 B4Q  CONST_44  C24  C23  C22  C11   180.00   0.0  0
 B4Q  CONST_45  C23  C22  C11  C12   180.00   0.0  0
 B4Q  CONST_46  C21  N2   C15  C14   180.00   0.0  0
 B4Q  CONST_47  C16  N1   C15  C14   180.00   0.0  0
 B4Q  CONST_48  H17  C17  C16  N1      0.00   0.0  0
 B4Q  CONST_49  H6   C4   C3   C2    180.00   0.0  0
 B4Q  CONST_50  H8   C6   C7   C2    180.00   0.0  0
 B4Q  CONST_51  H20  C20  C21  N2      0.00   0.0  0
 B4Q  CONST_52  H3   N1   C15  N2    180.00   0.0  0
 B4Q  CONST_53  H7   C5   C4   C3    180.00   0.0  0
 B4Q  CONST_54  H5   C3   C4   C5    180.00   0.0  0
 B4Q  CONST_55  H9   C9   C8   C7      0.00   0.0  0
 B4Q  CONST_56  H21  C22  C23  C8    180.00   0.0  0
 B4Q  CONST_57  H10  C10  C9   C8    180.00   0.0  0
 B4Q  CONST_58  H18  C18  C17  C16   180.00   0.0  0
 B4Q  CONST_59  H19  C19  C18  C17   180.00   0.0  0
 B4Q  Var_01    C13  C14  C15  N1     77.12  30.0  1
 B4Q  Var_02    C    C1   C2   C3    -87.70  30.0  2
 B4Q  Var_03    N    C12  C11  C10    62.01  30.0  2
 B4Q  Var_04    H22  C24  C23  C8    -59.39  30.0  2
 B4Q  Var_05    C13  N    C12  C11  -176.81  30.0  1
 B4Q  Var_06    N    C13  C14  C15  -178.29  30.0  3
 B4Q  Var_07    H25  C    C1   C2     58.40  30.0  3
 B4Q  Var_08    C14  C13  N    C12  -179.84  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
 B4Q  plan-1  C1   0.020
 B4Q  plan-1  C2   0.020
 B4Q  plan-1  C3   0.020
 B4Q  plan-1  C4   0.020
 B4Q  plan-1  C5   0.020
 B4Q  plan-1  C6   0.020
 B4Q  plan-1  C7   0.020
 B4Q  plan-1  C8   0.020
 B4Q  plan-1  H5   0.020
 B4Q  plan-1  H6   0.020
 B4Q  plan-1  H7   0.020
 B4Q  plan-1  H8   0.020
 B4Q  plan-2  C7   0.020
 B4Q  plan-2  C8   0.020
 B4Q  plan-2  C9   0.020
 B4Q  plan-2  C10  0.020
 B4Q  plan-2  C11  0.020
 B4Q  plan-2  C12  0.020
 B4Q  plan-2  C22  0.020
 B4Q  plan-2  C23  0.020
 B4Q  plan-2  C24  0.020
 B4Q  plan-2  H9   0.020
 B4Q  plan-2  H10  0.020
 B4Q  plan-2  H21  0.020
 B4Q  plan-3  N1   0.020
 B4Q  plan-3  N2   0.020
 B4Q  plan-3  C14  0.020
 B4Q  plan-3  C15  0.020
 B4Q  plan-3  C16  0.020
 B4Q  plan-3  C17  0.020
 B4Q  plan-3  C18  0.020
 B4Q  plan-3  C19  0.020
 B4Q  plan-3  C20  0.020
 B4Q  plan-3  C21  0.020
 B4Q  plan-3  H17  0.020
 B4Q  plan-3  H18  0.020
 B4Q  plan-3  H19  0.020
 B4Q  plan-3  H20  0.020
 B4Q  plan-3  H3   0.020

