# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 13:19:41 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: 4-(4-methyl-1~{H}-imidazol-5-yl)-~{N}-(4-morpholin-4-ylphenyl)pyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nc[nH]c1c2ccnc(Nc3ccc(cc3)N4CCOCC4)c2
#
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
 BGE  BGE  4-(4-methyl-1~{H}-imidazol-5-yl)-~{N}-(4-morpholin-4-ylphenyl)pyridin-2-amine  ligand  46  25  .  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_BGE
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
 BGE  C15  C  CR16  0  -0.313  -1.4645   0.7280  -0.1037
 BGE  C17  C  CR6   0   0.337  -3.7039  -0.2155   0.0980
 BGE  C21  C  CH2   0  -0.329  -5.6538   1.2398   0.0318
 BGE  C22  C  CH2   0  -0.183  -7.1329   1.2088   0.3690
 BGE  C24  C  CH2   0  -0.187  -7.3182  -0.9868  -0.3476
 BGE  C01  C  CR16  0  -0.454   3.7749   1.6334  -0.2852
 BGE  C02  C  CR16  0  -0.031   2.4815   2.0974  -0.3571
 BGE  N03  N  N     0  -0.483   1.3959   1.3400  -0.2138
 BGE  C04  C  CR6   0   0.571   1.5741   0.0455   0.0177
 BGE  C05  C  CR16  0  -0.510   2.8534  -0.5304   0.1215
 BGE  C06  C  CR6   0   0.184   3.9761   0.2655  -0.0337
 BGE  C07  C  CR5   0   0.284   5.3136  -0.2950   0.0529
 BGE  N08  N  NR15  0  -0.626   5.5787  -1.6249  -0.1636
 BGE  C09  C  CR15  0   0.091   6.8916  -1.8177   0.0178
 BGE  N10  N  N     0  -0.449   7.4996  -0.7055   0.3521
 BGE  C11  C  CR5   0   0.094   6.5360   0.2590   0.3784
 BGE  C12  C  CH3   0  -0.767   6.8682   1.6642   0.7482
 BGE  N13  N  NH1   0  -0.791   0.4916  -0.7746   0.1691
 BGE  C14  C  CR6   0   0.341  -0.8756  -0.5124   0.1309
 BGE  C16  C  CR16  0  -0.340  -2.8495   0.8622  -0.1272
 BGE  C18  C  CR16  0  -0.309  -3.1014  -1.4574   0.3408
 BGE  C19  C  CR16  0  -0.356  -1.7306  -1.6014   0.3496
 BGE  N20  N  NT    0  -0.518  -5.1000  -0.0961   0.1261
 BGE  O23  O  O2    0  -0.483  -7.8446   0.3164  -0.4572
 BGE  C25  C  CH2   0  -0.323  -5.8464  -1.0308  -0.7070
 BGE  H1   H  HCR6  0   0.281  -0.8505   1.5954  -0.2812
 BGE  H2   H  HCH2  0   0.213  -5.5086   1.6747  -0.9697
 BGE  H3   H  HCH2  0   0.254  -5.1581   1.8971   0.7487
 BGE  H4   H  HCH2  0   0.203  -7.2551   0.9342   1.4263
 BGE  H5   H  HCH2  0   0.240  -7.5621   2.2017   0.2272
 BGE  H6   H  HCH2  0   0.204  -7.4530  -1.3706   0.6736
 BGE  H7   H  HCH2  0   0.240  -7.8825  -1.6278  -1.0263
 BGE  H9   H  HCR6  0   0.259   2.2991   3.1488  -0.5507
 BGE  H10  H  HCR6  0   0.267   2.9411  -1.5882   0.3378
 BGE  H11  H  HNR5  0   0.424   4.9199  -2.3304  -0.4551
 BGE  H12  H  HCR5  0   0.282   7.3567  -2.7830  -0.1095
 BGE  H14  H  HCH3  0   0.249   6.9782   2.3036  -0.1304
 BGE  H15  H  HCH3  0   0.246   6.1027   2.1128   1.3816
 BGE  H16  H  HCH3  0   0.256   7.8127   1.6907   1.2896
 BGE  H17  H  HNH1  0   0.409   0.7200  -1.7395   0.3483
 BGE  H18  H  HCR6  0   0.264  -3.2468   1.8466  -0.3355
 BGE  H19  H  HCR6  0   0.261  -3.7108  -2.3288   0.5445
 BGE  H20  H  HCR6  0   0.262  -1.3106  -2.5813   0.5484
 BGE  H21  H  HCH2  0   0.255  -5.4912  -2.0488  -0.5507
 BGE  H22  H  HCH2  0   0.217  -5.7149  -0.7965  -1.7746
 BGE  H8   H  HCR6  0   0.266   4.5981   2.3123  -0.4471

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
 BGE  C09  N10  aromatic  1.311  0.020  1.311
 BGE  C09  N08  aromatic  1.339  0.020  1.339
 BGE  N10  C11  aromatic  1.364  0.020  1.364
 BGE  C24  C25  single    1.516  0.020  1.516
 BGE  C24  O23  single    1.410  0.020  1.410
 BGE  N08  C07  aromatic  1.373  0.020  1.373
 BGE  C25  N20  single    1.458  0.020  1.458
 BGE  C11  C12  single    1.491  0.020  1.491
 BGE  C11  C07  aromatic  1.381  0.020  1.381
 BGE  O23  C22  single    1.409  0.020  1.409
 BGE  C07  C06  single    1.453  0.020  1.453
 BGE  C22  C21  single    1.517  0.020  1.517
 BGE  N20  C21  single    1.449  0.020  1.449
 BGE  N20  C17  single    1.402  0.020  1.402
 BGE  C16  C17  aromatic  1.394  0.020  1.394
 BGE  C16  C15  aromatic  1.392  0.020  1.392
 BGE  C06  C05  aromatic  1.385  0.020  1.385
 BGE  C06  C01  aromatic  1.405  0.020  1.405
 BGE  C17  C18  aromatic  1.402  0.020  1.402
 BGE  C15  C14  aromatic  1.393  0.020  1.393
 BGE  C05  C04  aromatic  1.407  0.020  1.407
 BGE  C01  C02  aromatic  1.376  0.020  1.376
 BGE  C18  C19  aromatic  1.378  0.020  1.378
 BGE  C14  C19  aromatic  1.402  0.020  1.402
 BGE  C14  N13  single    1.393  0.020  1.393
 BGE  C04  N13  single    1.367  0.020  1.367
 BGE  C04  N03  aromatic  1.327  0.020  1.327
 BGE  C02  N03  aromatic  1.331  0.020  1.331
 BGE  C15  H1   single    0.930  0.020  1.080
 BGE  C21  H2   single    0.970  0.020  1.090
 BGE  C21  H3   single    0.970  0.020  1.090
 BGE  C22  H4   single    0.970  0.020  1.090
 BGE  C22  H5   single    0.970  0.020  1.090
 BGE  C24  H6   single    0.970  0.020  1.090
 BGE  C24  H7   single    0.970  0.020  1.090
 BGE  C01  H8   single    0.930  0.020  1.080
 BGE  C02  H9   single    0.930  0.020  1.080
 BGE  C05  H10  single    0.930  0.020  1.080
 BGE  N08  H11  single    0.860  0.020  1.020
 BGE  C09  H12  single    0.930  0.020  1.080
 BGE  C12  H14  single    0.970  0.020  1.090
 BGE  C12  H15  single    0.970  0.020  1.090
 BGE  C12  H16  single    0.970  0.020  1.090
 BGE  N13  H17  single    0.860  0.020  1.020
 BGE  C16  H18  single    0.930  0.020  1.080
 BGE  C18  H19  single    0.930  0.020  1.080
 BGE  C19  H20  single    0.930  0.020  1.080
 BGE  C25  H21  single    0.970  0.020  1.090
 BGE  C25  H22  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
 BGE  H1   C15  C16  119.12  3.000
 BGE  H1   C15  C14  120.25  3.000
 BGE  C16  C15  C14  120.62  3.000
 BGE  N20  C17  C18  120.02  3.000
 BGE  C18  C17  C16  116.72  3.000
 BGE  N20  C17  C16  123.24  3.000
 BGE  H3   C21  H2   107.43  3.000
 BGE  H3   C21  N20  109.81  3.000
 BGE  H2   C21  N20  111.89  3.000
 BGE  H3   C21  C22  107.99  3.000
 BGE  H2   C21  C22  109.79  3.000
 BGE  N20  C21  C22  109.83  3.000
 BGE  H5   C22  H4   107.98  3.000
 BGE  H5   C22  O23  107.55  3.000
 BGE  H4   C22  O23  110.46  3.000
 BGE  H5   C22  C21  109.64  3.000
 BGE  H4   C22  C21  109.10  3.000
 BGE  O23  C22  C21  112.02  3.000
 BGE  H7   C24  H6   108.03  3.000
 BGE  H7   C24  C25  109.74  3.000
 BGE  H6   C24  C25  109.22  3.000
 BGE  H7   C24  O23  107.56  3.000
 BGE  H6   C24  O23  110.44  3.000
 BGE  C25  C24  O23  111.77  3.000
 BGE  H8   C01  C06  122.01  3.000
 BGE  H8   C01  C02  119.80  3.000
 BGE  C06  C01  C02  118.17  3.000
 BGE  H9   C02  N03  115.70  3.000
 BGE  H9   C02  C01  119.62  3.000
 BGE  N03  C02  C01  124.68  3.000
 BGE  C04  N03  C02  117.66  3.000
 BGE  N13  C04  C05  117.81  3.000
 BGE  N13  C04  N03  119.89  3.000
 BGE  C05  C04  N03  122.30  3.000
 BGE  H10  C05  C06  121.20  3.000
 BGE  H10  C05  C04  119.22  3.000
 BGE  C06  C05  C04  119.58  3.000
 BGE  C07  C06  C05  121.19  3.000
 BGE  C05  C06  C01  117.61  3.000
 BGE  C07  C06  C01  121.20  3.000
 BGE  C11  C07  N08  104.76  3.000
 BGE  C11  C07  C06  132.39  3.000
 BGE  N08  C07  C06  122.82  3.000
 BGE  H11  N08  C09  125.37  3.000
 BGE  H11  N08  C07  126.67  3.000
 BGE  C09  N08  C07  107.90  3.000
 BGE  H12  C09  N10  126.10  3.000
 BGE  H12  C09  N08  122.37  3.000
 BGE  N10  C09  N08  111.53  3.000
 BGE  C11  N10  C09  106.10  3.000
 BGE  C12  C11  N10  120.94  3.000
 BGE  C12  C11  C07  129.34  3.000
 BGE  N10  C11  C07  109.71  3.000
 BGE  H16  C12  H15  108.07  3.000
 BGE  H16  C12  H14  107.36  3.000
 BGE  H15  C12  H14  107.30  3.000
 BGE  H16  C12  C11  109.85  3.000
 BGE  H15  C12  C11  112.06  3.000
 BGE  H14  C12  C11  112.01  3.000
 BGE  H17  N13  C14  114.06  3.000
 BGE  H17  N13  C04  114.51  3.000
 BGE  C14  N13  C04  131.43  3.000
 BGE  C19  C14  N13  116.64  3.000
 BGE  N13  C14  C15  125.96  3.000
 BGE  C19  C14  C15  117.40  3.000
 BGE  H18  C16  C17  120.64  3.000
 BGE  H18  C16  C15  117.16  3.000
 BGE  C17  C16  C15  122.20  3.000
 BGE  H19  C18  C19  118.33  3.000
 BGE  H19  C18  C17  120.25  3.000
 BGE  C19  C18  C17  121.41  3.000
 BGE  H20  C19  C18  118.73  3.000
 BGE  H20  C19  C14  119.62  3.000
 BGE  C18  C19  C14  121.64  3.000
 BGE  C25  N20  C21  111.00  3.000
 BGE  C21  N20  C17  117.25  3.000
 BGE  C25  N20  C17  116.36  3.000
 BGE  C24  O23  C22  110.57  3.000
 BGE  H22  C25  H21  107.40  3.000
 BGE  H22  C25  N20  110.89  3.000
 BGE  H21  C25  N20  110.50  3.000
 BGE  H22  C25  C24  109.86  3.000
 BGE  H21  C25  C24  108.04  3.000
 BGE  N20  C25  C24  110.07  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
 BGE  CONST_01  C18  C17  C16  C15     0.00   0.0  0
 BGE  CONST_02  C18  C19  C14  C15     0.00   0.0  0
 BGE  CONST_03  C14  C15  C16  C17     0.00   0.0  0
 BGE  CONST_04  C14  C19  C18  C17     0.00   0.0  0
 BGE  CONST_07  C04  C05  C06  C01     0.00   0.0  0
 BGE  CONST_08  C04  N03  C02  C01     0.00   0.0  0
 BGE  CONST_09  C07  C06  C01  C02   180.00   0.0  0
 BGE  CONST_10  C05  C06  C01  C02     0.00   0.0  0
 BGE  CONST_11  C05  C04  N03  C02     0.00   0.0  0
 BGE  CONST_12  C06  C05  C04  N03     0.00   0.0  0
 BGE  CONST_13  C06  C01  C02  N03     0.00   0.0  0
 BGE  CONST_14  C07  C06  C05  C04   180.00   0.0  0
 BGE  CONST_17  C09  N08  C07  C06   180.00   0.0  0
 BGE  CONST_18  N10  C11  C07  C06   180.00   0.0  0
 BGE  CONST_19  N10  C09  N08  C07     0.00   0.0  0
 BGE  CONST_20  C09  N10  C11  C07     0.00   0.0  0
 BGE  CONST_21  C11  N10  C09  N08     0.00   0.0  0
 BGE  CONST_22  N10  C11  C07  N08     0.00   0.0  0
 BGE  CONST_23  C11  C07  N08  C09     0.00   0.0  0
 BGE  CONST_24  C19  C18  C17  C16     0.00   0.0  0
 BGE  CONST_25  C19  C14  C15  C16     0.00   0.0  0
 BGE  CONST_26  N20  C17  C16  C15   180.00   0.0  0
 BGE  CONST_27  N20  C17  C18  C19   180.00   0.0  0
 BGE  CONST_28  N13  C04  N03  C02   180.00   0.0  0
 BGE  CONST_29  C12  C11  C07  C06     0.00   0.0  0
 BGE  CONST_30  N13  C04  C05  C06   180.00   0.0  0
 BGE  CONST_31  C12  C11  C07  N08   180.00   0.0  0
 BGE  CONST_32  C12  C11  N10  C09   180.00   0.0  0
 BGE  CONST_33  C16  C15  C14  N13   180.00   0.0  0
 BGE  CONST_34  C18  C19  C14  N13   180.00   0.0  0
 BGE  CONST_35  H20  C19  C14  C15   180.00   0.0  0
 BGE  CONST_36  H1   C15  C16  C17   180.00   0.0  0
 BGE  CONST_37  H10  C05  C06  C01   180.00   0.0  0
 BGE  CONST_38  H8   C01  C02  N03   180.00   0.0  0
 BGE  CONST_39  H9   C02  N03  C04   180.00   0.0  0
 BGE  CONST_40  H11  N08  C07  C06     0.00   0.0  0
 BGE  CONST_41  H12  C09  N08  C07   180.00   0.0  0
 BGE  CONST_42  H18  C16  C15  C14   180.00   0.0  0
 BGE  CONST_43  H19  C18  C19  C14   180.00   0.0  0
 BGE  Var_01    C24  C25  N20  C17   167.66  30.0  1
 BGE  Var_02    C22  C21  N20  C17  -168.13  30.0  1
 BGE  Var_03    C16  C17  N20  C21    -5.59  30.0  2
 BGE  Var_04    C25  C24  O23  C22   -57.80  30.0  1
 BGE  Var_05    O23  C24  C25  N20    56.26  30.0  1
 BGE  Var_06    O23  C22  C21  N20   -56.62  30.0  1
 BGE  Var_07    C04  N13  C14  C15     0.94  30.0  2
 BGE  Var_08    C14  N13  C04  N03    -0.19  30.0  2
 BGE  Var_09    H4   C22  O23  C24   -63.82  30.0  1
 BGE  Var_10    H14  C12  C11  C07   -81.72  30.0  2

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
 BGE  plan-1  C06  0.020
 BGE  plan-1  C07  0.020
 BGE  plan-1  N08  0.020
 BGE  plan-1  C09  0.020
 BGE  plan-1  N10  0.020
 BGE  plan-1  C11  0.020
 BGE  plan-1  C12  0.020
 BGE  plan-1  H11  0.020
 BGE  plan-1  H12  0.020
 BGE  plan-2  C01  0.020
 BGE  plan-2  C02  0.020
 BGE  plan-2  N03  0.020
 BGE  plan-2  C04  0.020
 BGE  plan-2  C05  0.020
 BGE  plan-2  C06  0.020
 BGE  plan-2  C07  0.020
 BGE  plan-2  N13  0.020
 BGE  plan-2  H9   0.020
 BGE  plan-2  H10  0.020
 BGE  plan-2  H8   0.020
 BGE  plan-3  C15  0.020
 BGE  plan-3  C17  0.020
 BGE  plan-3  N13  0.020
 BGE  plan-3  C14  0.020
 BGE  plan-3  C16  0.020
 BGE  plan-3  C18  0.020
 BGE  plan-3  C19  0.020
 BGE  plan-3  N20  0.020
 BGE  plan-3  H1   0.020
 BGE  plan-3  H18  0.020
 BGE  plan-3  H19  0.020
 BGE  plan-3  H20  0.020

