# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 08:55:53 2020
#   Inital geometry file: a 151 line input string
#   Ligand name: 4-[2-tert-butyl-5-(6-methoxynaphthalen-2-yl)-3H-imidazol-4-yl]pyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc2cc(ccc2c1)c3nc([nH]c3c4ccnc(N)c4)C(C)(C)C
#
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
 MXI  MXI  4-[2-tert-butyl-5-(6-methoxynaphthalen-2-yl)-3H-imidazol-4-yl]pyridin-2-amine  ligand  52  28  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MXI
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
 MXI  N26   N  NC2   0  -0.838  -4.3368   4.4950  -0.7982
 MXI  C8    C  CR6   0   0.466  -3.3376   3.7883  -0.2000
 MXI  N9    N  N     0  -0.462  -2.4594   4.4741   0.5288
 MXI  C10   C  CR16  0  -0.055  -1.4507   3.8041   1.0792
 MXI  C11   C  CR16  0  -0.418  -1.2515   2.4463   0.9505
 MXI  C7    C  CR16  0  -0.455  -3.2254   2.4015  -0.3983
 MXI  C6    C  CR6   0   0.122  -2.1701   1.7179   0.1820
 MXI  C5    C  CR5   0   0.310  -2.0423   0.2742   0.0237
 MXI  N1    N  NR15  0  -0.670  -3.1389  -0.5498   0.0184
 MXI  C2    C  CR5   0   0.528  -2.7174  -1.8292  -0.0772
 MXI  C22   C  CT    0  -0.227  -3.6566  -3.0032  -0.0808
 MXI  C24   C  CH3   0  -0.636  -4.6362  -2.8708  -1.2544
 MXI  C23   C  CH3   0  -0.630  -2.8563  -4.2948  -0.2328
 MXI  C25   C  CH3   0  -0.636  -4.4412  -3.0351   1.2382
 MXI  C4    C  CR5   0   0.084  -0.9672  -0.5796  -0.1037
 MXI  N3    N  N     0  -0.460  -1.4122  -1.8721  -0.1591
 MXI  C12   C  CR6   0   0.013   0.4631  -0.2861  -0.2122
 MXI  C21   C  CR16  0  -0.376   1.3852  -1.1714   0.2917
 MXI  C20   C  CR66  0   0.123   2.7725  -0.9289   0.1891
 MXI  C15   C  CR66  0   0.128   3.2338   0.2488  -0.4534
 MXI  C14   C  CR16  0  -0.307   2.2687   1.1405  -0.9852
 MXI  C13   C  CR16  0  -0.309   0.9339   0.8803  -0.8720
 MXI  C19   C  CR16  0  -0.303   3.7309  -1.8242   0.7100
 MXI  C18   C  CR16  0  -0.377   5.0733  -1.5745   0.6076
 MXI  C17   C  CR6   0   0.393   5.5281  -0.3963  -0.0311
 MXI  C16   C  CR16  0  -0.429   4.6158   0.4942  -0.5517
 MXI  O27   O  O2    0  -0.473   6.8309  -0.0830  -0.1646
 MXI  C28   C  CH3   0  -0.438   7.8071  -0.9650   0.3548
 MXI  H261  H  HNC2  0   0.383  -4.5213   5.4130  -0.4281
 MXI  H262  H  HNC2  0   0.391  -5.1574   3.9932  -1.0924
 MXI  H7    H  HCR6  0   0.264  -3.9527   1.8905  -1.0177
 MXI  H10   H  HCR6  0   0.258  -0.7603   4.3929   1.6735
 MXI  H11   H  HCR6  0   0.259  -0.4234   1.9652   1.4503
 MXI  H1    H  HNR5  0   0.415  -4.0916  -0.2447   0.1490
 MXI  H241  H  HCH3  0   0.237  -4.1083  -2.8348  -2.2084
 MXI  H242  H  HCH3  0   0.238  -5.3103  -3.7286  -1.2737
 MXI  H243  H  HCH3  0   0.227  -5.2533  -1.9740  -1.1761
 MXI  H231  H  HCH3  0   0.231  -2.1394  -4.4252   0.5781
 MXI  H232  H  HCH3  0   0.229  -3.5348  -5.1490  -0.2254
 MXI  H233  H  HCH3  0   0.230  -2.3034  -4.3138  -1.1721
 MXI  H251  H  HCH3  0   0.227  -5.0673  -2.1495   1.3652
 MXI  H252  H  HCH3  0   0.238  -5.1014  -3.9039   1.2565
 MXI  H253  H  HCH3  0   0.237  -3.7737  -3.1017   2.0986
 MXI  H21   H  HCR6  0   0.246   1.0502  -2.0766   0.7843
 MXI  H13   H  HCR6  0   0.252   0.2238   1.5678  -1.3124
 MXI  H19   H  HCR6  0   0.260   3.3949  -2.7302   1.1998
 MXI  H14   H  HCR6  0   0.252   2.6030   2.0352  -1.4965
 MXI  H16   H  HCR6  0   0.258   4.9643   1.3972  -1.0394
 MXI  H18   H  HCR6  0   0.283   5.7718  -2.2890   1.0213
 MXI  H281  H  HCH3  0   0.261   8.7728  -0.5135   0.1408
 MXI  H282  H  HCH3  0   0.229   7.7117  -1.0908   1.4363
 MXI  H283  H  HCH3  0   0.230   7.7672  -1.9481  -0.1212

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
 MXI  N26  C8    aromatic  1.362  0.020  1.362
 MXI  C8   N9    aromatic  1.331  0.020  1.331
 MXI  C8   C7    aromatic  1.405  0.020  1.405
 MXI  N9   C10   aromatic  1.330  0.020  1.330
 MXI  C10  C11   aromatic  1.378  0.020  1.378
 MXI  C11  C6    aromatic  1.402  0.020  1.402
 MXI  C7   C6    aromatic  1.385  0.020  1.385
 MXI  C6   C5    single    1.458  0.020  1.458
 MXI  C5   N1    aromatic  1.372  0.020  1.372
 MXI  C5   C4    aromatic  1.379  0.020  1.379
 MXI  N1   C2    aromatic  1.350  0.020  1.350
 MXI  C2   C22   aromatic  1.503  0.020  1.503
 MXI  C2   N3    aromatic  1.308  0.020  1.308
 MXI  C22  C24   aromatic  1.534  0.020  1.534
 MXI  C22  C23   aromatic  1.527  0.020  1.527
 MXI  C22  C25   aromatic  1.535  0.020  1.535
 MXI  C4   N3    aromatic  1.368  0.020  1.368
 MXI  C4   C12   single    1.464  0.020  1.464
 MXI  C12  C21   aromatic  1.374  0.020  1.374
 MXI  C12  C13   aromatic  1.420  0.020  1.420
 MXI  C21  C20   aromatic  1.412  0.020  1.412
 MXI  C20  C15   aromatic  1.419  0.020  1.419
 MXI  C20  C19   aromatic  1.411  0.020  1.411
 MXI  C15  C14   aromatic  1.418  0.020  1.418
 MXI  C15  C16   aromatic  1.407  0.020  1.407
 MXI  C14  C13   aromatic  1.365  0.020  1.365
 MXI  C19  C18   aromatic  1.369  0.020  1.369
 MXI  C18  C17   aromatic  1.415  0.020  1.415
 MXI  C17  C16   aromatic  1.377  0.020  1.377
 MXI  C17  O27   single    1.347  0.020  1.347
 MXI  O27  C28   single    1.414  0.020  1.414
 MXI  N26  H261  aromatic  0.890  0.020  1.040
 MXI  N26  H262  single    0.890  0.020  1.040
 MXI  C7   H7    aromatic  0.930  0.020  1.080
 MXI  C10  H10   aromatic  0.930  0.020  1.080
 MXI  C11  H11   aromatic  0.930  0.020  1.080
 MXI  N1   H1    single    0.860  0.020  1.020
 MXI  C24  H241  aromatic  0.970  0.020  1.090
 MXI  C24  H242  aromatic  0.970  0.020  1.090
 MXI  C24  H243  aromatic  0.970  0.020  1.090
 MXI  C23  H231  aromatic  0.970  0.020  1.090
 MXI  C23  H232  aromatic  0.970  0.020  1.090
 MXI  C23  H233  single    0.970  0.020  1.090
 MXI  C25  H251  single    0.970  0.020  1.090
 MXI  C25  H252  aromatic  0.970  0.020  1.090
 MXI  C25  H253  single    0.970  0.020  1.090
 MXI  C21  H21   aromatic  0.930  0.020  1.080
 MXI  C13  H13   single    0.930  0.020  1.080
 MXI  C19  H19   aromatic  0.930  0.020  1.080
 MXI  C14  H14   single    0.930  0.020  1.080
 MXI  C16  H16   single    0.930  0.020  1.080
 MXI  C18  H18   single    0.930  0.020  1.080
 MXI  C28  H281  single    0.970  0.020  1.090
 MXI  C28  H282  single    0.970  0.020  1.090
 MXI  C28  H283  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
 MXI  H262  N26  H261  114.39  3.000
 MXI  H262  N26  C8    117.91  3.000
 MXI  H261  N26  C8    116.49  3.000
 MXI  C7    C8   N9    122.20  3.000
 MXI  C7    C8   N26   120.56  3.000
 MXI  N9    C8   N26   117.19  3.000
 MXI  C10   N9   C8    117.85  3.000
 MXI  H10   C10  C11   119.59  3.000
 MXI  H10   C10  N9    115.84  3.000
 MXI  C11   C10  N9    124.56  3.000
 MXI  H11   C11  C6    121.64  3.000
 MXI  H11   C11  C10   120.42  3.000
 MXI  C6    C11  C10   117.92  3.000
 MXI  H7    C7   C6    121.22  3.000
 MXI  H7    C7   C8    119.51  3.000
 MXI  C6    C7   C8    119.26  3.000
 MXI  C5    C6   C7    120.67  3.000
 MXI  C5    C6   C11   121.11  3.000
 MXI  C7    C6   C11   118.21  3.000
 MXI  C4    C5   N1    104.54  3.000
 MXI  C4    C5   C6    133.75  3.000
 MXI  N1    C5   C6    121.68  3.000
 MXI  H1    N1   C2    126.19  3.000
 MXI  H1    N1   C5    124.94  3.000
 MXI  C2    N1   C5    108.66  3.000
 MXI  N3    C2   C22   126.68  3.000
 MXI  N3    C2   N1    110.30  3.000
 MXI  C22   C2   N1    123.02  3.000
 MXI  C25   C22  C23   109.62  3.000
 MXI  C25   C22  C24   109.43  3.000
 MXI  C23   C22  C24   109.36  3.000
 MXI  C25   C22  C2    109.47  3.000
 MXI  C23   C22  C2    109.47  3.000
 MXI  C24   C22  C2    109.47  3.000
 MXI  H243  C24  H242  107.34  3.000
 MXI  H243  C24  H241  108.01  3.000
 MXI  H242  C24  H241  108.03  3.000
 MXI  H243  C24  C22   112.15  3.000
 MXI  H242  C24  C22   109.88  3.000
 MXI  H241  C24  C22   111.27  3.000
 MXI  H233  C23  H232  107.92  3.000
 MXI  H233  C23  H231  107.78  3.000
 MXI  H232  C23  H231  108.08  3.000
 MXI  H233  C23  C22   111.49  3.000
 MXI  H232  C23  C22   109.61  3.000
 MXI  H231  C23  C22   111.83  3.000
 MXI  H253  C25  H252  107.96  3.000
 MXI  H253  C25  H251  107.97  3.000
 MXI  H252  C25  H251  107.26  3.000
 MXI  H253  C25  C22   111.48  3.000
 MXI  H252  C25  C22   109.88  3.000
 MXI  H251  C25  C22   112.10  3.000
 MXI  C12   C4   N3    120.27  3.000
 MXI  C12   C4   C5    130.12  3.000
 MXI  N3    C4   C5    109.58  3.000
 MXI  C4    N3   C2    106.91  3.000
 MXI  C13   C12  C21   118.49  3.000
 MXI  C13   C12  C4    121.52  3.000
 MXI  C21   C12  C4    119.95  3.000
 MXI  H21   C21  C20   118.70  3.000
 MXI  H21   C21  C12   119.83  3.000
 MXI  C20   C21  C12   121.47  3.000
 MXI  C19   C20  C15   118.23  3.000
 MXI  C19   C20  C21   122.11  3.000
 MXI  C15   C20  C21   119.67  3.000
 MXI  C16   C15  C14   122.19  3.000
 MXI  C16   C15  C20   119.73  3.000
 MXI  C14   C15  C20   118.08  3.000
 MXI  H14   C14  C13   119.90  3.000
 MXI  H14   C14  C15   119.11  3.000
 MXI  C13   C14  C15   120.99  3.000
 MXI  H13   C13  C14   119.15  3.000
 MXI  H13   C13  C12   119.56  3.000
 MXI  C14   C13  C12   121.28  3.000
 MXI  H19   C19  C18   119.37  3.000
 MXI  H19   C19  C20   119.13  3.000
 MXI  C18   C19  C20   121.50  3.000
 MXI  H18   C18  C17   121.01  3.000
 MXI  H18   C18  C19   118.95  3.000
 MXI  C17   C18  C19   120.04  3.000
 MXI  O27   C17  C16   116.94  3.000
 MXI  O27   C17  C18   123.32  3.000
 MXI  C16   C17  C18   119.74  3.000
 MXI  H16   C16  C17   119.73  3.000
 MXI  H16   C16  C15   119.51  3.000
 MXI  C17   C16  C15   120.76  3.000
 MXI  C28   O27  C17   119.10  3.000
 MXI  H283  C28  H282  108.91  3.000
 MXI  H283  C28  H281  108.68  3.000
 MXI  H282  C28  H281  108.67  3.000
 MXI  H283  C28  O27   112.07  3.000
 MXI  H282  C28  O27   112.01  3.000
 MXI  H281  C28  O27   106.37  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
 MXI  CONST_01  C11   C10  N9   C8      0.00   0.0  0
 MXI  CONST_02  C11   C6   C7   C8      0.00   0.0  0
 MXI  CONST_03  C5    C6   C7   C8    180.00   0.0  0
 MXI  CONST_04  C6    C7   C8   N9      0.00   0.0  0
 MXI  CONST_05  C6    C11  C10  N9      0.00   0.0  0
 MXI  CONST_06  C7    C8   N9   C10     0.00   0.0  0
 MXI  CONST_07  C7    C6   C11  C10     0.00   0.0  0
 MXI  CONST_08  C5    C6   C11  C10   180.00   0.0  0
 MXI  CONST_13  C2    N1   C5   C6    180.00   0.0  0
 MXI  CONST_14  N3    C4   C5   C6    180.00   0.0  0
 MXI  CONST_15  C12   C4   C5   C6      0.00   0.0  0
 MXI  CONST_16  N3    C2   N1   C5      0.00   0.0  0
 MXI  CONST_17  C2    N3   C4   C5      0.00   0.0  0
 MXI  CONST_20  N3    C4   C5   N1      0.00   0.0  0
 MXI  CONST_21  C12   C4   C5   N1    180.00   0.0  0
 MXI  CONST_22  C4    N3   C2   N1      0.00   0.0  0
 MXI  CONST_23  C4    C5   N1   C2      0.00   0.0  0
 MXI  CONST_24  C12   C4   N3   C2    180.00   0.0  0
 MXI  CONST_25  C20   C21  C12  C4    180.00   0.0  0
 MXI  CONST_26  C14   C13  C12  C4    180.00   0.0  0
 MXI  CONST_29  C15   C20  C21  C12     0.00   0.0  0
 MXI  CONST_30  C19   C20  C21  C12   180.00   0.0  0
 MXI  CONST_31  C15   C14  C13  C12     0.00   0.0  0
 MXI  CONST_32  C14   C13  C12  C21     0.00   0.0  0
 MXI  CONST_33  C14   C15  C20  C21     0.00   0.0  0
 MXI  CONST_34  C16   C15  C20  C21   180.00   0.0  0
 MXI  CONST_35  C18   C19  C20  C21   180.00   0.0  0
 MXI  CONST_36  C13   C12  C21  C20     0.00   0.0  0
 MXI  CONST_37  C13   C14  C15  C20     0.00   0.0  0
 MXI  CONST_38  C17   C16  C15  C20     0.00   0.0  0
 MXI  CONST_39  C17   C18  C19  C20     0.00   0.0  0
 MXI  CONST_40  C18   C19  C20  C15     0.00   0.0  0
 MXI  CONST_41  C18   C17  C16  C15     0.00   0.0  0
 MXI  CONST_42  C19   C20  C15  C14   180.00   0.0  0
 MXI  CONST_43  C17   C16  C15  C14   180.00   0.0  0
 MXI  CONST_44  C16   C15  C14  C13   180.00   0.0  0
 MXI  CONST_45  C16   C15  C20  C19     0.00   0.0  0
 MXI  CONST_46  C16   C17  C18  C19     0.00   0.0  0
 MXI  CONST_47  C10   N9   C8   N26   180.00   0.0  0
 MXI  CONST_48  C6    C7   C8   N26   180.00   0.0  0
 MXI  CONST_49  C22   C2   N1   C5    180.00   0.0  0
 MXI  CONST_50  C4    N3   C2   C22   180.00   0.0  0
 MXI  CONST_51  O27   C17  C16  C15   180.00   0.0  0
 MXI  CONST_52  O27   C17  C18  C19   180.00   0.0  0
 MXI  CONST_53  H10   C10  N9   C8    180.00   0.0  0
 MXI  CONST_54  H7    C7   C8   N9    180.00   0.0  0
 MXI  CONST_55  H11   C11  C10  N9    180.00   0.0  0
 MXI  CONST_56  H21   C21  C12  C4      0.00   0.0  0
 MXI  CONST_57  H19   C19  C20  C21     0.00   0.0  0
 MXI  CONST_58  H1    N1   C5   C6      0.00   0.0  0
 MXI  CONST_59  H13   C13  C12  C4      0.00   0.0  0
 MXI  CONST_60  H14   C14  C13  C12   180.00   0.0  0
 MXI  CONST_61  H16   C16  C15  C20   180.00   0.0  0
 MXI  CONST_62  H18   C18  C19  C20   180.00   0.0  0
 MXI  CONST_64  C23   C22  C2   N1    180.00   0.0  0
 MXI  CONST_67  N3    C2   C22  C23     0.00   0.0  0
 MXI  CONST_72  H242  C24  C22  C2    180.00   0.0  0
 MXI  CONST_75  H232  C23  C22  C2    180.00   0.0  0
 MXI  CONST_76  H252  C25  C22  C2    180.00   0.0  0
 MXI  Var_01    H251  C25  C22  C2     62.69  30.0  1
 MXI  Var_02    H281  C28  O27  C17  -179.68  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
 MXI  plan-1  C6    0.020
 MXI  plan-1  C5    0.020
 MXI  plan-1  N1    0.020
 MXI  plan-1  C2    0.020
 MXI  plan-1  C22   0.020
 MXI  plan-1  C4    0.020
 MXI  plan-1  N3    0.020
 MXI  plan-1  C12   0.020
 MXI  plan-1  H1    0.020
 MXI  plan-2  N26   0.020
 MXI  plan-2  C8    0.020
 MXI  plan-2  N9    0.020
 MXI  plan-2  C10   0.020
 MXI  plan-2  C11   0.020
 MXI  plan-2  C7    0.020
 MXI  plan-2  C6    0.020
 MXI  plan-2  C5    0.020
 MXI  plan-2  H7    0.020
 MXI  plan-2  H10   0.020
 MXI  plan-2  H11   0.020
 MXI  plan-3  C4    0.020
 MXI  plan-3  C12   0.020
 MXI  plan-3  C21   0.020
 MXI  plan-3  C20   0.020
 MXI  plan-3  C15   0.020
 MXI  plan-3  C14   0.020
 MXI  plan-3  C13   0.020
 MXI  plan-3  C19   0.020
 MXI  plan-3  C18   0.020
 MXI  plan-3  C17   0.020
 MXI  plan-3  C16   0.020
 MXI  plan-3  O27   0.020
 MXI  plan-3  H21   0.020
 MXI  plan-3  H13   0.020
 MXI  plan-3  H19   0.020
 MXI  plan-3  H14   0.020
 MXI  plan-3  H16   0.020
 MXI  plan-3  H18   0.020
 MXI  plan-4  N26   0.020
 MXI  plan-4  C8    0.020
 MXI  plan-4  H261  0.020
 MXI  plan-4  H262  0.020

