# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 21:16:23 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: 2-methoxy-4-(1-{2-[(2S)-1-methylpyrrolidin-2-yl]ethyl}-4-phenyl-1H-imidazol-5-yl)phenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(ccc1O)c2n(CC[C@@H]3CCCN3C)cnc2c4ccccc4
#
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
 VMC  VMC  2-methoxy-4-(1-{2-[(2S)-1-methylpyrrolidin-2-yl]ethyl}-4-phenyl-1H-imidazol-5-yl)phenol  ligand  55  28  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VMC
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
 VMC  O26  O  OH1   0  -0.622   0.3172   4.6084   0.0468
 VMC  C22  C  CR6   0   0.266   0.2952   3.2632   0.0948
 VMC  C21  C  CR16  0  -0.373  -0.7137   2.4900  -0.4508
 VMC  C20  C  CR16  0  -0.301  -0.6699   1.1020  -0.3789
 VMC  C23  C  CR6   0   0.343   1.3714   2.6303   0.7452
 VMC  O27  O  O2    0  -0.467   2.3166   3.4512   1.2427
 VMC  C28  C  CH3   0  -0.438   3.4603   2.8650   1.8296
 VMC  C24  C  CR16  0  -0.435   1.3914   1.2511   0.8394
 VMC  C19  C  CR6   0   0.018   0.3810   0.4663   0.2665
 VMC  C9   C  CR5   0   0.290   0.4850  -0.9921   0.3646
 VMC  C10  C  CR5   0   0.066   1.5546  -1.8398   0.1459
 VMC  C13  C  CR6   0   0.026   2.8914  -1.5395  -0.3748
 VMC  C18  C  CR16  0  -0.319   3.1148  -0.4980  -1.2788
 VMC  C17  C  CR16  0  -0.237   4.3869  -0.2423  -1.7676
 VMC  C16  C  CR16  0  -0.272   5.4622  -1.0288  -1.3737
 VMC  C15  C  CR16  0  -0.243   5.2498  -2.0769  -0.4873
 VMC  C14  C  CR16  0  -0.306   3.9782  -2.3302   0.0062
 VMC  N11  N  N     0  -0.456   1.2075  -3.1205   0.4729
 VMC  C12  C  CR15  0   0.085  -0.0372  -3.0619   0.8617
 VMC  N8   N  NR5   0  -0.455  -0.5261  -1.8062   0.8195
 VMC  C7   C  CH2   0  -0.320  -1.8961  -1.4448   1.1381
 VMC  C6   C  CH2   0  -0.435  -2.8654  -1.8309   0.0292
 VMC  C3   C  CR15  0  -0.084  -4.2314  -1.1813   0.2174
 VMC  N2   N  NR5   0  -0.398  -4.1255   0.2776   0.0730
 VMC  C25  C  CH3   0  -0.529  -4.7723   1.0159   1.1386
 VMC  C4   C  CH2   0  -0.466  -5.2506  -1.6699  -0.8447
 VMC  C5   C  CH2   0  -0.457  -5.8333  -0.3865  -1.4343
 VMC  C1   C  CH2   0  -0.310  -4.6734   0.5874  -1.2424
 VMC  H1   H  HOH1  0   0.476  -0.4713   4.9359  -0.4005
 VMC  H2   H  HCR6  0   0.270  -1.5468   2.9716  -0.9497
 VMC  H3   H  HCR6  0   0.266  -1.4742   0.5365  -0.8274
 VMC  H4   H  HCH3  0   0.261   4.1199   3.6835   2.1072
 VMC  H5   H  HCH3  0   0.228   3.2137   2.2941   2.7289
 VMC  H6   H  HCH3  0   0.225   3.9858   2.2086   1.1297
 VMC  H7   H  HCR6  0   0.278   2.1976   0.7532   1.3600
 VMC  H8   H  HCR6  0   0.251   2.2868   0.1132  -1.6130
 VMC  H9   H  HCR6  0   0.253   4.5348   0.5694  -2.4684
 VMC  H10  H  HCR6  0   0.252   6.4545  -0.8306  -1.7579
 VMC  H11  H  HCR6  0   0.252   6.0782  -2.7010  -0.1767
 VMC  H12  H  HCR6  0   0.244   3.8242  -3.1468   0.6996
 VMC  H13  H  HCR5  0   0.280  -0.6371  -3.8986   1.1882
 VMC  H14  H  HCH2  0   0.271  -2.1709  -1.9357   2.0731
 VMC  H15  H  HCH2  0   0.277  -1.9351  -0.3712   1.3109
 VMC  H16  H  HCH2  0   0.232  -2.4595  -1.5278  -0.9417
 VMC  H17  H  HCH2  0   0.242  -2.9751  -2.9188  -0.0050
 VMC  H18  H  HCR5  0   0.231  -4.5962  -1.4159   1.2229
 VMC  H20  H  HCH3  0   0.231  -4.3424   0.7302   2.0992
 VMC  H21  H  HCH3  0   0.230  -4.5915   2.0840   1.0098
 VMC  H22  H  HCH3  0   0.195  -5.8603   0.8666   1.2085
 VMC  H23  H  HCH2  0   0.229  -4.7359  -2.2405  -1.6227
 VMC  H24  H  HCH2  0   0.240  -6.0073  -2.3258  -0.4140
 VMC  H25  H  HCH2  0   0.233  -6.1401  -0.4944  -2.4753
 VMC  H26  H  HCH2  0   0.225  -6.7066  -0.0549  -0.8672
 VMC  H27  H  HCH2  0   0.235  -4.9544   1.6394  -1.3092
 VMC  H28  H  HCH2  0   0.223  -3.9123   0.4109  -2.0106

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
 VMC  O26  C22  single    1.346  0.020  1.346
 VMC  C21  C22  aromatic  1.383  0.020  1.383
 VMC  C21  C20  aromatic  1.391  0.020  1.391
 VMC  C22  C23  aromatic  1.408  0.020  1.408
 VMC  C20  C19  aromatic  1.387  0.020  1.387
 VMC  C28  O27  single    1.413  0.020  1.413
 VMC  C23  O27  single    1.347  0.020  1.347
 VMC  C23  C24  aromatic  1.383  0.020  1.383
 VMC  C19  C24  aromatic  1.402  0.020  1.402
 VMC  C19  C9   single    1.465  0.020  1.465
 VMC  C7   C6   single    1.523  0.020  1.523
 VMC  C7   N8   single    1.452  0.020  1.452
 VMC  C6   C3   single    1.524  0.020  1.524
 VMC  C9   N8   aromatic  1.375  0.020  1.375
 VMC  C9   C10  aromatic  1.382  0.020  1.382
 VMC  N8   C12  aromatic  1.348  0.020  1.348
 VMC  C25  N2   single    1.449  0.020  1.449
 VMC  C18  C17  aromatic  1.387  0.020  1.387
 VMC  C18  C13  aromatic  1.397  0.020  1.397
 VMC  C3   N2   single    1.470  0.020  1.470
 VMC  C3   C4   single    1.551  0.020  1.551
 VMC  N2   C1   single    1.458  0.020  1.458
 VMC  C12  N11  aromatic  1.305  0.020  1.305
 VMC  C10  C13  single    1.466  0.020  1.466
 VMC  C10  N11  aromatic  1.367  0.020  1.367
 VMC  C17  C16  aromatic  1.389  0.020  1.389
 VMC  C13  C14  aromatic  1.397  0.020  1.397
 VMC  C4   C5   single    1.528  0.020  1.528
 VMC  C1   C5   single    1.527  0.020  1.527
 VMC  C16  C15  aromatic  1.389  0.020  1.389
 VMC  C14  C15  aromatic  1.387  0.020  1.387
 VMC  O26  H1   single    0.850  0.020  0.980
 VMC  C21  H2   single    0.930  0.020  1.080
 VMC  C20  H3   single    0.930  0.020  1.080
 VMC  C28  H4   single    0.970  0.020  1.090
 VMC  C28  H5   single    0.970  0.020  1.090
 VMC  C28  H6   single    0.970  0.020  1.090
 VMC  C24  H7   single    0.930  0.020  1.080
 VMC  C18  H8   single    0.930  0.020  1.080
 VMC  C17  H9   single    0.930  0.020  1.080
 VMC  C16  H10  single    0.930  0.020  1.080
 VMC  C15  H11  single    0.930  0.020  1.080
 VMC  C14  H12  single    0.930  0.020  1.080
 VMC  C12  H13  single    0.930  0.020  1.080
 VMC  C7   H14  single    0.970  0.020  1.090
 VMC  C7   H15  single    0.970  0.020  1.090
 VMC  C6   H16  single    0.970  0.020  1.090
 VMC  C6   H17  single    0.970  0.020  1.090
 VMC  C3   H18  single    0.970  0.020  1.090
 VMC  C25  H20  single    0.970  0.020  1.090
 VMC  C25  H21  single    0.970  0.020  1.090
 VMC  C25  H22  single    0.970  0.020  1.090
 VMC  C4   H23  single    0.970  0.020  1.090
 VMC  C4   H24  single    0.970  0.020  1.090
 VMC  C5   H25  single    0.970  0.020  1.090
 VMC  C5   H26  single    0.970  0.020  1.090
 VMC  C1   H27  single    0.970  0.020  1.090
 VMC  C1   H28  single    0.970  0.020  1.090

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
 VMC  H1   O26  C22  110.04  3.000
 VMC  C23  C22  C21  119.24  3.000
 VMC  C23  C22  O26  116.95  3.000
 VMC  C21  C22  O26  123.81  3.000
 VMC  H2   C21  C20  119.44  3.000
 VMC  H2   C21  C22  119.59  3.000
 VMC  C20  C21  C22  120.97  3.000
 VMC  H3   C20  C19  121.13  3.000
 VMC  H3   C20  C21  118.52  3.000
 VMC  C19  C20  C21  120.35  3.000
 VMC  C24  C23  O27  124.93  3.000
 VMC  C24  C23  C22  119.41  3.000
 VMC  O27  C23  C22  115.67  3.000
 VMC  C28  O27  C23  117.94  3.000
 VMC  H6   C28  H5   108.74  3.000
 VMC  H6   C28  H4   108.89  3.000
 VMC  H5   C28  H4   108.66  3.000
 VMC  H6   C28  O27  111.84  3.000
 VMC  H5   C28  O27  112.07  3.000
 VMC  H4   C28  O27  106.55  3.000
 VMC  H7   C24  C19  118.46  3.000
 VMC  H7   C24  C23  120.19  3.000
 VMC  C19  C24  C23  121.35  3.000
 VMC  C9   C19  C24  118.60  3.000
 VMC  C9   C19  C20  122.74  3.000
 VMC  C24  C19  C20  118.65  3.000
 VMC  N8   C9   C10  104.96  3.000
 VMC  C10  C9   C19  130.90  3.000
 VMC  N8   C9   C19  123.99  3.000
 VMC  N11  C10  C13  120.57  3.000
 VMC  N11  C10  C9   109.90  3.000
 VMC  C13  C10  C9   129.52  3.000
 VMC  C14  C13  C18  118.29  3.000
 VMC  C14  C13  C10  119.79  3.000
 VMC  C18  C13  C10  121.90  3.000
 VMC  H8   C18  C17  119.28  3.000
 VMC  H8   C18  C13  119.90  3.000
 VMC  C17  C18  C13  120.82  3.000
 VMC  H9   C17  C16  120.16  3.000
 VMC  H9   C17  C18  119.46  3.000
 VMC  C16  C17  C18  120.38  3.000
 VMC  H10  C16  C15  120.32  3.000
 VMC  H10  C16  C17  120.35  3.000
 VMC  C15  C16  C17  119.33  3.000
 VMC  H11  C15  C14  119.60  3.000
 VMC  H11  C15  C16  120.07  3.000
 VMC  C14  C15  C16  120.33  3.000
 VMC  H12  C14  C15  119.74  3.000
 VMC  H12  C14  C13  119.41  3.000
 VMC  C15  C14  C13  120.85  3.000
 VMC  C12  N11  C10  105.75  3.000
 VMC  H13  C12  N8   121.98  3.000
 VMC  H13  C12  N11  125.79  3.000
 VMC  N8   C12  N11  112.23  3.000
 VMC  C7   N8   C12  124.54  3.000
 VMC  C12  N8   C9   107.16  3.000
 VMC  C7   N8   C9   128.22  3.000
 VMC  H15  C7   H14  107.38  3.000
 VMC  H15  C7   C6   110.06  3.000
 VMC  H14  C7   C6   110.47  3.000
 VMC  H15  C7   N8   108.31  3.000
 VMC  H14  C7   N8   108.27  3.000
 VMC  C6   C7   N8   112.19  3.000
 VMC  H17  C6   H16  106.54  3.000
 VMC  H17  C6   C3   109.74  3.000
 VMC  H16  C6   C3   108.89  3.000
 VMC  H17  C6   C7   109.80  3.000
 VMC  H16  C6   C7   109.85  3.000
 VMC  C3   C6   C7   111.88  3.000
 VMC  H18  C3   C4   110.02  3.000
 VMC  H18  C3   N2   109.08  3.000
 VMC  C4   C3   N2   107.02  3.000
 VMC  H18  C3   C6   108.70  3.000
 VMC  C4   C3   C6   111.72  3.000
 VMC  N2   C3   C6   110.26  3.000
 VMC  C1   N2   C25  112.80  3.000
 VMC  C1   N2   C3   105.81  3.000
 VMC  C25  N2   C3   113.66  3.000
 VMC  H22  C25  H21  107.71  3.000
 VMC  H22  C25  H20  107.35  3.000
 VMC  H21  C25  H20  107.17  3.000
 VMC  H22  C25  N2   114.77  3.000
 VMC  H21  C25  N2   109.76  3.000
 VMC  H20  C25  N2   109.78  3.000
 VMC  H24  C4   H23  107.09  3.000
 VMC  H24  C4   C5   113.15  3.000
 VMC  H23  C4   C5   110.07  3.000
 VMC  H24  C4   C3   112.04  3.000
 VMC  H23  C4   C3   110.02  3.000
 VMC  C5   C4   C3   104.49  3.000
 VMC  H26  C5   H25  107.49  3.000
 VMC  H26  C5   C1   110.38  3.000
 VMC  H25  C5   C1   113.38  3.000
 VMC  H26  C5   C4   111.06  3.000
 VMC  H25  C5   C4   113.12  3.000
 VMC  C1   C5   C4   101.39  3.000
 VMC  H28  C1   H27  106.94  3.000
 VMC  H28  C1   C5   109.69  3.000
 VMC  H27  C1   C5   114.32  3.000
 VMC  H28  C1   N2   109.70  3.000
 VMC  H27  C1   N2   110.91  3.000
 VMC  C5   C1   N2   105.27  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
 VMC  CONST_01  C19  C20  C21  C22     0.00   0.0  0
 VMC  CONST_02  C19  C24  C23  C22     0.00   0.0  0
 VMC  CONST_03  C24  C23  C22  C21     0.00   0.0  0
 VMC  CONST_04  C24  C19  C20  C21     0.00   0.0  0
 VMC  CONST_05  C9   C19  C20  C21   180.00   0.0  0
 VMC  CONST_06  C23  C22  C21  C20     0.00   0.0  0
 VMC  CONST_07  C23  C24  C19  C20     0.00   0.0  0
 VMC  CONST_10  C9   C19  C24  C23   180.00   0.0  0
 VMC  CONST_13  C12  N8   C9   C19   180.00   0.0  0
 VMC  CONST_14  C13  C10  C9   C19     0.00   0.0  0
 VMC  CONST_15  N11  C10  C9   C19   180.00   0.0  0
 VMC  CONST_16  N11  C12  N8   C9      0.00   0.0  0
 VMC  CONST_19  C12  N11  C10  C9      0.00   0.0  0
 VMC  CONST_20  C12  N8   C9   C10     0.00   0.0  0
 VMC  CONST_21  C17  C18  C13  C10   180.00   0.0  0
 VMC  CONST_22  C15  C14  C13  C10   180.00   0.0  0
 VMC  CONST_23  N8   C12  N11  C10     0.00   0.0  0
 VMC  CONST_24  C16  C17  C18  C13     0.00   0.0  0
 VMC  CONST_25  N8   C9   C10  C13   180.00   0.0  0
 VMC  CONST_26  C12  N11  C10  C13   180.00   0.0  0
 VMC  CONST_27  C16  C15  C14  C13     0.00   0.0  0
 VMC  CONST_28  C15  C16  C17  C18     0.00   0.0  0
 VMC  CONST_30  C15  C14  C13  C18     0.00   0.0  0
 VMC  CONST_31  C14  C13  C18  C17     0.00   0.0  0
 VMC  CONST_32  C14  C15  C16  C17     0.00   0.0  0
 VMC  CONST_34  N8   C9   C10  N11     0.00   0.0  0
 VMC  CONST_35  C20  C21  C22  O26   180.00   0.0  0
 VMC  CONST_36  C24  C23  C22  O26   180.00   0.0  0
 VMC  CONST_37  O27  C23  C22  C21   180.00   0.0  0
 VMC  CONST_38  C19  C24  C23  O27   180.00   0.0  0
 VMC  CONST_39  C7   N8   C9   C19     0.00   0.0  0
 VMC  CONST_40  C7   N8   C9   C10   180.00   0.0  0
 VMC  CONST_41  C7   N8   C12  N11   180.00   0.0  0
 VMC  CONST_42  H3   C20  C21  C22   180.00   0.0  0
 VMC  CONST_43  H7   C24  C23  C22   180.00   0.0  0
 VMC  CONST_44  H2   C21  C22  C23   180.00   0.0  0
 VMC  CONST_45  H13  C12  N8   C9    180.00   0.0  0
 VMC  CONST_46  H8   C18  C13  C10     0.00   0.0  0
 VMC  CONST_47  H12  C14  C13  C10     0.00   0.0  0
 VMC  CONST_48  H9   C17  C18  C13   180.00   0.0  0
 VMC  CONST_49  H11  C15  C14  C13   180.00   0.0  0
 VMC  CONST_50  H10  C16  C17  C18   180.00   0.0  0
 VMC  Var_01    C5   C1   N2   C3     36.38  30.0  1
 VMC  Var_02    C1   C5   C4   C3     28.28  30.0  1
 VMC  Var_03    C4   C5   C1   N2    -40.24  30.0  1
 VMC  Var_04    C24  C23  O27  C28     4.36  30.0  2
 VMC  Var_05    C6   C7   N8   C9    101.37  30.0  2
 VMC  Var_06    C3   C6   C7   N8   -167.18  30.0  3
 VMC  Var_07    H20  C25  N2   C3     58.21  30.0  3
 VMC  Var_08    H4   C28  O27  C23   176.49  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
 VMC  chir_01  C3  C6  N2  C4  negativ

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
 VMC  plan-1  C19  0.020
 VMC  plan-1  C9   0.020
 VMC  plan-1  C10  0.020
 VMC  plan-1  C13  0.020
 VMC  plan-1  N11  0.020
 VMC  plan-1  C12  0.020
 VMC  plan-1  N8   0.020
 VMC  plan-1  C7   0.020
 VMC  plan-1  H13  0.020
 VMC  plan-2  O26  0.020
 VMC  plan-2  C22  0.020
 VMC  plan-2  C21  0.020
 VMC  plan-2  C20  0.020
 VMC  plan-2  C23  0.020
 VMC  plan-2  O27  0.020
 VMC  plan-2  C24  0.020
 VMC  plan-2  C19  0.020
 VMC  plan-2  C9   0.020
 VMC  plan-2  H2   0.020
 VMC  plan-2  H3   0.020
 VMC  plan-2  H7   0.020
 VMC  plan-3  C10  0.020
 VMC  plan-3  C13  0.020
 VMC  plan-3  C18  0.020
 VMC  plan-3  C17  0.020
 VMC  plan-3  C16  0.020
 VMC  plan-3  C15  0.020
 VMC  plan-3  C14  0.020
 VMC  plan-3  H8   0.020
 VMC  plan-3  H9   0.020
 VMC  plan-3  H10  0.020
 VMC  plan-3  H11  0.020
 VMC  plan-3  H12  0.020

