# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 13:05:01 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: 1-(3-imidazol-1-ylpropyl)-5-(2-methylpropyl)-4-phenyl-imidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)Cc1n(CCCn2ccnc2)cnc1c3ccccc3
#
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
 B5B  B5B  1-(3-imidazol-1-ylpropyl)-5-(2-methylpropyl)-4-phenyl-imidazole  ligand  47  23  .  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_B5B
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
 B5B  C10  C  CH2   0  -0.329   1.4167   0.1296  -1.6235
 B5B  C15  C  CR15  0  -0.218   6.1582  -1.2862   1.3669
 B5B  C17  C  CR15  0   0.095   5.2391   0.6153   1.1244
 B5B  C20  C  CR16  0  -0.240  -5.5139  -1.4438   0.2094
 B5B  C21  C  CR16  0  -0.275  -5.6873  -0.8148   1.4360
 B5B  C22  C  CR16  0  -0.238  -4.6071  -0.1727   2.0261
 B5B  C01  C  CH3   0  -0.656  -1.3956   3.7161   0.7664
 B5B  C02  C  CH1   0  -0.229  -1.5888   2.5002  -0.1319
 B5B  C03  C  CH3   0  -0.658  -1.3846   2.8616  -1.5978
 B5B  C04  C  CH2   0  -0.554  -0.6341   1.3758   0.2983
 B5B  C05  C  CR5   0   0.321  -0.8322   0.1025  -0.4579
 B5B  C06  C  CR5   0   0.072  -1.8965  -0.7744  -0.5409
 B5B  N07  N  N     0  -0.461  -1.6275  -1.7489  -1.4665
 B5B  C08  C  CR15  0   0.084  -0.4390  -1.4837  -1.9272
 B5B  N09  N  NR5   0  -0.452   0.0849  -0.3751  -1.3609
 B5B  C11  C  CH2   0  -0.446   2.4103  -0.2779  -0.5437
 B5B  C12  C  CH2   0  -0.303   3.8070   0.2241  -0.8832
 B5B  N13  N  NR5   0  -0.399   4.7826  -0.1567   0.1160
 B5B  C14  C  CR15  0  -0.107   5.3608  -1.3863   0.2627
 B5B  N16  N  N     0  -0.457   6.0744  -0.0301   1.8977
 B5B  C18  C  CR6   0   0.037  -3.1856  -0.7688   0.1559
 B5B  C19  C  CR16  0  -0.305  -4.2796  -1.4222  -0.4211
 B5B  C23  C  CR16  0  -0.336  -3.3710  -0.1531   1.3964
 B5B  H1   H  HCH2  0   0.281   1.7270  -0.2655  -2.5913
 B5B  H2   H  HCH2  0   0.270   1.3769   1.2144  -1.7296
 B5B  H3   H  HCR5  0   0.250   6.7885  -2.0488   1.7980
 B5B  H4   H  HCR5  0   0.279   4.9307   1.6441   1.2399
 B5B  H5   H  HCR6  0   0.253  -6.3453  -1.9530  -0.2614
 B5B  H6   H  HCR6  0   0.253  -6.6518  -0.8267   1.9267
 B5B  H7   H  HCR6  0   0.254  -4.7228   0.3109   2.9876
 B5B  H8   H  HCH3  0   0.216  -0.3771   4.1044   0.6882
 B5B  H9   H  HCH3  0   0.231  -2.0768   4.5218   0.4885
 B5B  H10  H  HCH3  0   0.226  -1.5791   3.4722   1.8144
 B5B  H11  H  HCH1  0   0.231  -2.6168   2.1449  -0.0062
 B5B  H12  H  HCH3  0   0.232  -1.5729   2.0118  -2.2558
 B5B  H13  H  HCH3  0   0.233  -2.0573   3.6657  -1.8998
 B5B  H14  H  HCH3  0   0.215  -0.3611   3.2020  -1.7766
 B5B  H15  H  HCH2  0   0.256   0.3912   1.7333   0.1682
 B5B  H16  H  HCH2  0   0.265  -0.7358   1.1970   1.3713
 B5B  H17  H  HCR5  0   0.280   0.0991  -2.0548  -2.6695
 B5B  H18  H  HCH2  0   0.253   2.1028   0.1244   0.4246
 B5B  H19  H  HCH2  0   0.256   2.4166  -1.3668  -0.4544
 B5B  H20  H  HCH2  0   0.271   4.1317  -0.1661  -1.8486
 B5B  H21  H  HCH2  0   0.272   3.8157   1.3120  -0.9575
 B5B  H22  H  HCR5  0   0.288   5.1664  -2.1992  -0.4172
 B5B  H23  H  HCR6  0   0.244  -4.1574  -1.9154  -1.3764
 B5B  H24  H  HCR6  0   0.244  -2.5433   0.3324   1.8942

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
 B5B  C21  C20  aromatic  1.389  0.020  1.389
 B5B  C21  C22  aromatic  1.388  0.020  1.388
 B5B  C20  C19  aromatic  1.386  0.020  1.386
 B5B  C22  C23  aromatic  1.387  0.020  1.387
 B5B  C19  C18  aromatic  1.399  0.020  1.399
 B5B  C01  C02  single    1.524  0.020  1.524
 B5B  C23  C18  aromatic  1.397  0.020  1.397
 B5B  C18  C06  single    1.465  0.020  1.465
 B5B  C03  C02  single    1.524  0.020  1.524
 B5B  C02  C04  single    1.537  0.020  1.537
 B5B  C06  C05  aromatic  1.382  0.020  1.382
 B5B  C06  N07  aromatic  1.371  0.020  1.371
 B5B  C04  C05  single    1.494  0.020  1.494
 B5B  C05  N09  aromatic  1.373  0.020  1.373
 B5B  N07  C08  aromatic  1.302  0.020  1.302
 B5B  N09  C08  aromatic  1.351  0.020  1.351
 B5B  N09  C10  single    1.448  0.020  1.448
 B5B  C11  C10  single    1.523  0.020  1.523
 B5B  C11  C12  single    1.523  0.020  1.523
 B5B  C12  N13  single    1.447  0.020  1.447
 B5B  N13  C14  aromatic  1.367  0.020  1.367
 B5B  N13  C17  aromatic  1.350  0.020  1.350
 B5B  C14  C15  aromatic  1.366  0.020  1.366
 B5B  C17  N16  aromatic  1.309  0.020  1.309
 B5B  C15  N16  aromatic  1.366  0.020  1.366
 B5B  C10  H1   single    0.970  0.020  1.090
 B5B  C10  H2   single    0.970  0.020  1.090
 B5B  C15  H3   single    0.930  0.020  1.080
 B5B  C17  H4   single    0.930  0.020  1.080
 B5B  C20  H5   single    0.930  0.020  1.080
 B5B  C21  H6   single    0.930  0.020  1.080
 B5B  C22  H7   single    0.930  0.020  1.080
 B5B  C01  H8   single    0.970  0.020  1.090
 B5B  C01  H9   single    0.970  0.020  1.090
 B5B  C01  H10  single    0.970  0.020  1.090
 B5B  C02  H11  single    0.970  0.020  1.090
 B5B  C03  H12  single    0.970  0.020  1.090
 B5B  C03  H13  single    0.970  0.020  1.090
 B5B  C03  H14  single    0.970  0.020  1.090
 B5B  C04  H15  single    0.970  0.020  1.090
 B5B  C04  H16  single    0.970  0.020  1.090
 B5B  C08  H17  single    0.930  0.020  1.080
 B5B  C11  H18  single    0.970  0.020  1.090
 B5B  C11  H19  single    0.970  0.020  1.090
 B5B  C12  H20  single    0.970  0.020  1.090
 B5B  C12  H21  single    0.970  0.020  1.090
 B5B  C14  H22  single    0.930  0.020  1.080
 B5B  C19  H23  single    0.930  0.020  1.080
 B5B  C23  H24  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
 B5B  H2   C10  H1   106.52  3.000
 B5B  H2   C10  C11  111.03  3.000
 B5B  H1   C10  C11  110.29  3.000
 B5B  H2   C10  N09  109.31  3.000
 B5B  H1   C10  N09  107.24  3.000
 B5B  C11  C10  N09  112.22  3.000
 B5B  H3   C15  N16  122.02  3.000
 B5B  H3   C15  C14  127.75  3.000
 B5B  N16  C15  C14  110.23  3.000
 B5B  H4   C17  N16  126.08  3.000
 B5B  H4   C17  N13  121.88  3.000
 B5B  N16  C17  N13  112.04  3.000
 B5B  H5   C20  C19  119.56  3.000
 B5B  H5   C20  C21  120.07  3.000
 B5B  C19  C20  C21  120.37  3.000
 B5B  H6   C21  C22  120.38  3.000
 B5B  H6   C21  C20  120.44  3.000
 B5B  C22  C21  C20  119.18  3.000
 B5B  H7   C22  C23  119.48  3.000
 B5B  H7   C22  C21  120.07  3.000
 B5B  C23  C22  C21  120.45  3.000
 B5B  H10  C01  H9   107.73  3.000
 B5B  H10  C01  H8   107.75  3.000
 B5B  H9   C01  H8   107.53  3.000
 B5B  H10  C01  C02  111.49  3.000
 B5B  H9   C01  C02  111.09  3.000
 B5B  H8   C01  C02  111.07  3.000
 B5B  H11  C02  C04  108.28  3.000
 B5B  H11  C02  C03  108.26  3.000
 B5B  C04  C02  C03  111.08  3.000
 B5B  H11  C02  C01  108.07  3.000
 B5B  C04  C02  C01  109.88  3.000
 B5B  C03  C02  C01  111.15  3.000
 B5B  H14  C03  H13  107.61  3.000
 B5B  H14  C03  H12  107.78  3.000
 B5B  H13  C03  H12  107.51  3.000
 B5B  H14  C03  C02  110.89  3.000
 B5B  H13  C03  C02  111.01  3.000
 B5B  H12  C03  C02  111.86  3.000
 B5B  H16  C04  H15  104.93  3.000
 B5B  H16  C04  C05  110.20  3.000
 B5B  H15  C04  C05  110.04  3.000
 B5B  H16  C04  C02  109.69  3.000
 B5B  H15  C04  C02  108.06  3.000
 B5B  C05  C04  C02  113.55  3.000
 B5B  N09  C05  C06  104.73  3.000
 B5B  N09  C05  C04  122.74  3.000
 B5B  C06  C05  C04  132.34  3.000
 B5B  C18  C06  N07  119.77  3.000
 B5B  N07  C06  C05  109.92  3.000
 B5B  C18  C06  C05  130.29  3.000
 B5B  C08  N07  C06  105.86  3.000
 B5B  H17  C08  N09  121.93  3.000
 B5B  H17  C08  N07  126.17  3.000
 B5B  N09  C08  N07  111.90  3.000
 B5B  C08  N09  C05  107.59  3.000
 B5B  C08  N09  C10  124.52  3.000
 B5B  C05  N09  C10  127.76  3.000
 B5B  H19  C11  H18  107.23  3.000
 B5B  H19  C11  C12  109.97  3.000
 B5B  H18  C11  C12  109.53  3.000
 B5B  H19  C11  C10  109.18  3.000
 B5B  H18  C11  C10  110.25  3.000
 B5B  C12  C11  C10  110.62  3.000
 B5B  H21  C12  H20  107.11  3.000
 B5B  H21  C12  N13  107.70  3.000
 B5B  H20  C12  N13  108.44  3.000
 B5B  H21  C12  C11  110.58  3.000
 B5B  H20  C12  C11  110.64  3.000
 B5B  N13  C12  C11  112.19  3.000
 B5B  C14  N13  C12  126.58  3.000
 B5B  C14  N13  C17  106.94  3.000
 B5B  C12  N13  C17  126.39  3.000
 B5B  H22  C14  N13  122.32  3.000
 B5B  H22  C14  C15  132.14  3.000
 B5B  N13  C14  C15  105.54  3.000
 B5B  C17  N16  C15  105.25  3.000
 B5B  C23  C18  C19  117.92  3.000
 B5B  C23  C18  C06  122.73  3.000
 B5B  C19  C18  C06  119.34  3.000
 B5B  H23  C19  C18  119.26  3.000
 B5B  H23  C19  C20  119.67  3.000
 B5B  C18  C19  C20  121.07  3.000
 B5B  H24  C23  C18  120.34  3.000
 B5B  H24  C23  C22  118.65  3.000
 B5B  C18  C23  C22  121.00  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
 B5B  CONST_01  C17  N13  C14  C15     0.00   0.0  0
 B5B  CONST_02  N13  C17  N16  C15     0.00   0.0  0
 B5B  CONST_03  C14  C15  N16  C17     0.00   0.0  0
 B5B  CONST_04  C23  C22  C21  C20     0.00   0.0  0
 B5B  CONST_05  C23  C18  C19  C20     0.00   0.0  0
 B5B  CONST_06  C06  C18  C19  C20   180.00   0.0  0
 B5B  CONST_07  C18  C19  C20  C21     0.00   0.0  0
 B5B  CONST_08  C18  C23  C22  C21     0.00   0.0  0
 B5B  CONST_09  C19  C20  C21  C22     0.00   0.0  0
 B5B  CONST_10  C19  C18  C23  C22     0.00   0.0  0
 B5B  CONST_11  C06  C18  C23  C22   180.00   0.0  0
 B5B  CONST_14  C08  N07  C06  C05     0.00   0.0  0
 B5B  CONST_15  N07  C08  N09  C05     0.00   0.0  0
 B5B  CONST_16  C08  N09  C05  C06     0.00   0.0  0
 B5B  CONST_17  N09  C08  N07  C06     0.00   0.0  0
 B5B  CONST_20  N09  C05  C06  N07     0.00   0.0  0
 B5B  CONST_21  C18  C06  N07  C08   180.00   0.0  0
 B5B  CONST_22  C18  C06  C05  N09   180.00   0.0  0
 B5B  CONST_23  N16  C15  C14  N13     0.00   0.0  0
 B5B  CONST_24  N16  C17  N13  C14     0.00   0.0  0
 B5B  CONST_25  C06  C05  N09  C10   180.00   0.0  0
 B5B  CONST_26  N07  C08  N09  C10   180.00   0.0  0
 B5B  CONST_27  C12  N13  C14  C15   180.00   0.0  0
 B5B  CONST_28  C18  C06  C05  C04     0.00   0.0  0
 B5B  CONST_29  N07  C06  C05  C04   180.00   0.0  0
 B5B  CONST_30  C08  N09  C05  C04   180.00   0.0  0
 B5B  CONST_31  N16  C17  N13  C12   180.00   0.0  0
 B5B  CONST_32  H4   C17  N16  C15   180.00   0.0  0
 B5B  CONST_33  H22  C14  N13  C17   180.00   0.0  0
 B5B  CONST_34  H3   C15  N16  C17   180.00   0.0  0
 B5B  CONST_35  H7   C22  C21  C20   180.00   0.0  0
 B5B  CONST_36  H23  C19  C20  C21   180.00   0.0  0
 B5B  CONST_37  H24  C23  C22  C21   180.00   0.0  0
 B5B  CONST_38  H5   C20  C21  C22   180.00   0.0  0
 B5B  CONST_39  H17  C08  N09  C05   180.00   0.0  0
 B5B  CONST_40  H6   C21  C20  C19   180.00   0.0  0
 B5B  Var_01    C11  C12  N13  C17   -98.35  30.0  2
 B5B  Var_02    C06  C05  C04  C02   -63.71  30.0  2
 B5B  Var_03    C11  C10  N09  C05    76.65  30.0  2
 B5B  Var_04    N13  C12  C11  C10  -179.42  30.0  3
 B5B  Var_05    C05  C04  C02  C01   175.29  30.0  3
 B5B  Var_06    C12  C11  C10  N09   177.77  30.0  1
 B5B  Var_07    H12  C03  C02  C01  -176.93  30.0  3
 B5B  Var_08    H8   C01  C02  C03   -62.06  30.0  3

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
 B5B  plan-1  C10  0.020
 B5B  plan-1  C04  0.020
 B5B  plan-1  C05  0.020
 B5B  plan-1  C06  0.020
 B5B  plan-1  N07  0.020
 B5B  plan-1  C08  0.020
 B5B  plan-1  N09  0.020
 B5B  plan-1  C18  0.020
 B5B  plan-1  H17  0.020
 B5B  plan-2  C15  0.020
 B5B  plan-2  C17  0.020
 B5B  plan-2  C12  0.020
 B5B  plan-2  N13  0.020
 B5B  plan-2  C14  0.020
 B5B  plan-2  N16  0.020
 B5B  plan-2  H3   0.020
 B5B  plan-2  H4   0.020
 B5B  plan-2  H22  0.020
 B5B  plan-3  C20  0.020
 B5B  plan-3  C21  0.020
 B5B  plan-3  C22  0.020
 B5B  plan-3  C06  0.020
 B5B  plan-3  C18  0.020
 B5B  plan-3  C19  0.020
 B5B  plan-3  C23  0.020
 B5B  plan-3  H5   0.020
 B5B  plan-3  H6   0.020
 B5B  plan-3  H7   0.020
 B5B  plan-3  H23  0.020
 B5B  plan-3  H24  0.020

