# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 11:10:34 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: 3-amino-6-[4-(2-hydroxyethyl)phenyl]-N-[4-(morpholin-4-yl)pyridin-3-yl]pyrazine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncc(nc1C(=O)Nc2cnccc2N3CCOCC3)c4ccc(CCO)cc4
#
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
 5L4  5L4  3-amino-6-[4-(2-hydroxyethyl)phenyl]-N-[4-(morpholin-4-yl)pyridin-3-yl]pyrazine-2-carboxamide  ligand  55  31  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5L4
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
 5L4  C13  C  CR16  0  -0.287   2.9818   1.3489  -0.5287
 5L4  C18  C  CR6   0   0.251  -3.4763  -0.2616  -0.6376
 5L4  C17  C  CH2   0  -0.539   5.1367   2.4922   0.1036
 5L4  C16  C  CR16  0  -0.303   3.5718  -0.8366   1.0576
 5L4  C15  C  CR16  0  -0.289   4.4518   0.2324   0.9850
 5L4  C19  C  CR16  0  -0.123  -4.6674  -0.8305  -1.0775
 5L4  C21  C  CR16  0  -0.083  -5.6417   1.2065  -1.3693
 5L4  C22  C  CR16  0  -0.383  -4.5074   1.8759  -0.9365
 5L4  C23  C  CR6   0   0.351  -3.3988   1.1422  -0.5373
 5L4  C24  C  CH2   0  -0.133   6.0635   2.3349  -1.0939
 5L4  C11  C  CR6   0   0.061   2.3805  -0.8278   0.3329
 5L4  C12  C  CR16  0  -0.277   2.1019   0.2824  -0.4656
 5L4  C27  C  CH2   0  -0.328  -1.9083   3.0679  -0.5138
 5L4  C1   C  CR16  0  -0.098   1.7878  -3.2508   0.7400
 5L4  C2   C  CR6   0   0.160   1.4189  -1.9368   0.4235
 5L4  N3   N  N     0  -0.423   0.1420  -1.6920   0.1853
 5L4  C4   C  CR6   0  -0.011  -0.7616  -2.6507   0.2687
 5L4  C5   C  CR6   0   0.483  -0.3783  -3.9722   0.6182
 5L4  N6   N  N     0  -0.410   0.9205  -4.2309   0.8340
 5L4  N7   N  NH2   0  -0.832  -1.2264  -4.9957   0.7375
 5L4  C8   C  C     0   0.554  -2.1748  -2.2687  -0.0019
 5L4  O9   O  O     0  -0.475  -3.0997  -3.0644   0.0992
 5L4  N10  N  NH1   0  -0.750  -2.3170  -0.9744  -0.3543
 5L4  C14  C  CR6   0   0.105   4.1719   1.3450   0.1968
 5L4  N20  N  N     0  -0.405  -5.7303  -0.1135  -1.4268
 5L4  O25  O  OH1   0  -0.670   6.9393   3.4390  -1.1298
 5L4  N26  N  NT    0  -0.527  -2.2076   1.7131  -0.0781
 5L4  C28  C  CH2   0  -0.189  -0.4686   3.3876  -0.1563
 5L4  O29  O  O2    0  -0.481  -0.2327   3.2532   1.2268
 5L4  C30  C  CH2   0  -0.192  -0.5379   1.9511   1.6732
 5L4  C31  C  CH2   0  -0.347  -1.9727   1.5752   1.3615
 5L4  H37  H  HCR6  0   0.248   2.7373   2.2009  -1.1529
 5L4  H41  H  HCH2  0   0.247   5.7347   2.5505   1.0165
 5L4  H40  H  HCH2  0   0.248   4.5896   3.4342   0.0131
 5L4  H39  H  HCR6  0   0.251   3.8129  -1.6672   1.7093
 5L4  H38  H  HCR6  0   0.252   5.3652   0.2065   1.5677
 5L4  H42  H  HCR6  0   0.276  -4.7619  -1.9032  -1.1665
 5L4  H43  H  HCR6  0   0.263  -6.5171   1.7696  -1.6730
 5L4  H44  H  HCR6  0   0.279  -4.5076   2.9565  -0.8991
 5L4  H45  H  HCH2  0   0.197   6.6103   1.3868  -1.0037
 5L4  H46  H  HCH2  0   0.198   5.4612   2.2670  -2.0090
 5L4  H36  H  HCR6  0   0.254   1.1872   0.3067  -1.0439
 5L4  H48  H  HCH2  0   0.225  -2.5737   3.8101  -0.0494
 5L4  H32  H  HCR6  0   0.276   2.8269  -3.5126   0.9050
 5L4  H34  H  HNH2  0   0.417  -2.2158  -4.8613   0.6220
 5L4  H33  H  HNH2  0   0.400  -0.8712  -5.8962   1.0093
 5L4  H35  H  HNH1  0   0.423  -1.4607  -0.4292  -0.3719
 5L4  H47  H  HOH1  0   0.454   7.5017   3.3530  -1.9047
 5L4  H50  H  HCH2  0   0.207   0.1981   2.7282  -0.7284
 5L4  H51  H  HCH2  0   0.245  -0.2396   4.4183  -0.4298
 5L4  H53  H  HCH2  0   0.216   0.1377   1.2170   1.2128
 5L4  H52  H  HCH2  0   0.244  -0.3759   1.9285   2.7517
 5L4  H55  H  HCH2  0   0.241  -2.6647   2.2170   1.9247
 5L4  H54  H  HCH2  0   0.265  -2.1499   0.5483   1.6828
 5L4  H49  H  HCH2  0   0.263  -2.0317   3.1394  -1.5958

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
 5L4  O25  C24  single    1.410  0.020  1.410
 5L4  C24  C17  single    1.522  0.020  1.522
 5L4  C17  C14  single    1.502  0.020  1.502
 5L4  C14  C15  aromatic  1.392  0.020  1.392
 5L4  C14  C13  aromatic  1.394  0.020  1.394
 5L4  C15  C16  aromatic  1.387  0.020  1.387
 5L4  C13  C12  aromatic  1.384  0.020  1.384
 5L4  C16  C11  aromatic  1.394  0.020  1.394
 5L4  C12  C11  aromatic  1.396  0.020  1.396
 5L4  C30  O29  single    1.410  0.020  1.410
 5L4  C30  C31  single    1.516  0.020  1.516
 5L4  C11  C2   single    1.471  0.020  1.471
 5L4  O29  C28  single    1.409  0.020  1.409
 5L4  C31  N26  single    1.465  0.020  1.465
 5L4  C28  C27  single    1.517  0.020  1.517
 5L4  C2   C1   aromatic  1.401  0.020  1.401
 5L4  C2   N3   aromatic  1.322  0.020  1.322
 5L4  C1   N6   aromatic  1.312  0.020  1.312
 5L4  N3   C4   aromatic  1.320  0.020  1.320
 5L4  N26  C27  single    1.454  0.020  1.454
 5L4  N26  C23  single    1.398  0.020  1.398
 5L4  N6   C5   aromatic  1.342  0.020  1.342
 5L4  C23  C22  aromatic  1.388  0.020  1.388
 5L4  C23  C18  aromatic  1.409  0.020  1.409
 5L4  C4   C5   aromatic  1.420  0.020  1.420
 5L4  C4   C8   single    1.489  0.020  1.489
 5L4  N10  C18  single    1.390  0.020  1.390
 5L4  N10  C8   single    1.349  0.020  1.349
 5L4  C22  C21  aromatic  1.386  0.020  1.386
 5L4  C5   N7   single    1.335  0.020  1.335
 5L4  C18  C19  aromatic  1.391  0.020  1.391
 5L4  C8   O9   double    1.224  0.020  1.224
 5L4  C21  N20  aromatic  1.324  0.020  1.324
 5L4  C19  N20  aromatic  1.329  0.020  1.329
 5L4  C13  H37  single    0.930  0.020  1.080
 5L4  C17  H41  single    0.970  0.020  1.090
 5L4  C17  H40  single    0.970  0.020  1.090
 5L4  C16  H39  single    0.930  0.020  1.080
 5L4  C15  H38  single    0.930  0.020  1.080
 5L4  C19  H42  single    0.930  0.020  1.080
 5L4  C21  H43  single    0.930  0.020  1.080
 5L4  C22  H44  single    0.930  0.020  1.080
 5L4  C24  H45  single    0.970  0.020  1.090
 5L4  C24  H46  single    0.970  0.020  1.090
 5L4  C12  H36  single    0.930  0.020  1.080
 5L4  C27  H49  single    0.970  0.020  1.090
 5L4  C27  H48  single    0.970  0.020  1.090
 5L4  C1   H32  single    0.930  0.020  1.080
 5L4  N7   H34  single    0.860  0.020  1.020
 5L4  N7   H33  single    0.860  0.020  1.020
 5L4  N10  H35  single    0.860  0.020  1.020
 5L4  O25  H47  single    0.850  0.020  0.980
 5L4  C28  H50  single    0.970  0.020  1.090
 5L4  C28  H51  single    0.970  0.020  1.090
 5L4  C30  H53  single    0.970  0.020  1.090
 5L4  C30  H52  single    0.970  0.020  1.090
 5L4  C31  H55  single    0.970  0.020  1.090
 5L4  C31  H54  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
 5L4  H37  C13  C14  119.63  3.000
 5L4  H37  C13  C12  119.24  3.000
 5L4  C14  C13  C12  121.13  3.000
 5L4  N10  C18  C23  116.76  3.000
 5L4  N10  C18  C19  124.66  3.000
 5L4  C23  C18  C19  118.48  3.000
 5L4  H40  C17  H41  107.28  3.000
 5L4  H40  C17  C14  109.99  3.000
 5L4  H41  C17  C14  109.90  3.000
 5L4  H40  C17  C24  109.19  3.000
 5L4  H41  C17  C24  109.23  3.000
 5L4  C14  C17  C24  111.16  3.000
 5L4  H39  C16  C11  120.52  3.000
 5L4  H39  C16  C15  118.78  3.000
 5L4  C11  C16  C15  120.67  3.000
 5L4  H38  C15  C14  119.54  3.000
 5L4  H38  C15  C16  119.24  3.000
 5L4  C14  C15  C16  121.21  3.000
 5L4  H42  C19  N20  116.36  3.000
 5L4  H42  C19  C18  120.45  3.000
 5L4  N20  C19  C18  123.18  3.000
 5L4  H43  C21  N20  116.84  3.000
 5L4  H43  C21  C22  119.82  3.000
 5L4  N20  C21  C22  123.34  3.000
 5L4  H44  C22  C23  121.23  3.000
 5L4  H44  C22  C21  119.55  3.000
 5L4  C23  C22  C21  119.22  3.000
 5L4  N26  C23  C22  123.99  3.000
 5L4  C22  C23  C18  117.52  3.000
 5L4  N26  C23  C18  118.48  3.000
 5L4  H46  C24  H45  106.75  3.000
 5L4  H46  C24  O25  111.60  3.000
 5L4  H45  C24  O25  111.65  3.000
 5L4  H46  C24  C17  109.16  3.000
 5L4  H45  C24  C17  109.13  3.000
 5L4  O25  C24  C17  108.50  3.000
 5L4  C2   C11  C12  120.31  3.000
 5L4  C2   C11  C16  121.45  3.000
 5L4  C12  C11  C16  118.22  3.000
 5L4  H36  C12  C11  119.48  3.000
 5L4  H36  C12  C13  119.71  3.000
 5L4  C11  C12  C13  120.81  3.000
 5L4  H48  C27  H49  107.82  3.000
 5L4  H48  C27  C28  109.42  3.000
 5L4  H49  C27  C28  109.09  3.000
 5L4  H48  C27  N26  112.19  3.000
 5L4  H49  C27  N26  109.56  3.000
 5L4  C28  C27  N26  108.72  3.000
 5L4  H32  C1   N6   116.24  3.000
 5L4  H32  C1   C2   120.87  3.000
 5L4  N6   C1   C2   122.87  3.000
 5L4  N3   C2   C1   117.95  3.000
 5L4  N3   C2   C11  118.74  3.000
 5L4  C1   C2   C11  123.30  3.000
 5L4  C4   N3   C2   121.02  3.000
 5L4  C8   C4   C5   122.68  3.000
 5L4  C8   C4   N3   116.87  3.000
 5L4  C5   C4   N3   120.45  3.000
 5L4  N7   C5   N6   116.93  3.000
 5L4  N7   C5   C4   124.36  3.000
 5L4  N6   C5   C4   118.71  3.000
 5L4  C5   N6   C1   118.96  3.000
 5L4  H33  N7   H34  119.90  3.000
 5L4  H33  N7   C5   119.12  3.000
 5L4  H34  N7   C5   120.85  3.000
 5L4  N10  C8   O9   124.44  3.000
 5L4  O9   C8   C4   122.37  3.000
 5L4  N10  C8   C4   113.19  3.000
 5L4  H35  N10  C8   115.52  3.000
 5L4  H35  N10  C18  115.12  3.000
 5L4  C8   N10  C18  129.28  3.000
 5L4  C15  C14  C17  121.10  3.000
 5L4  C15  C14  C13  117.95  3.000
 5L4  C17  C14  C13  120.94  3.000
 5L4  C21  N20  C19  118.22  3.000
 5L4  H47  O25  C24  108.30  3.000
 5L4  C31  N26  C27  110.43  3.000
 5L4  C27  N26  C23  117.21  3.000
 5L4  C31  N26  C23  114.89  3.000
 5L4  H51  C28  H50  108.01  3.000
 5L4  H51  C28  O29  107.52  3.000
 5L4  H50  C28  O29  110.63  3.000
 5L4  H51  C28  C27  109.83  3.000
 5L4  H50  C28  C27  109.06  3.000
 5L4  O29  C28  C27  111.71  3.000
 5L4  C30  O29  C28  111.25  3.000
 5L4  H52  C30  H53  108.01  3.000
 5L4  H52  C30  C31  109.80  3.000
 5L4  H53  C30  C31  109.28  3.000
 5L4  H52  C30  O29  107.45  3.000
 5L4  H53  C30  O29  110.56  3.000
 5L4  C31  C30  O29  111.64  3.000
 5L4  H54  C31  H55  107.25  3.000
 5L4  H54  C31  C30  109.07  3.000
 5L4  H55  C31  C30  110.23  3.000
 5L4  H54  C31  N26  110.61  3.000
 5L4  H55  C31  N26  110.34  3.000
 5L4  C30  C31  N26  109.30  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
 5L4  CONST_01  C16  C15  C14  C13     0.00   0.0  0
 5L4  CONST_02  C16  C11  C12  C13     0.00   0.0  0
 5L4  CONST_03  C2   C11  C12  C13   180.00   0.0  0
 5L4  CONST_04  C21  C22  C23  C18     0.00   0.0  0
 5L4  CONST_05  C21  N20  C19  C18     0.00   0.0  0
 5L4  CONST_08  C12  C13  C14  C15     0.00   0.0  0
 5L4  CONST_09  C12  C11  C16  C15     0.00   0.0  0
 5L4  CONST_10  C2   C11  C16  C15   180.00   0.0  0
 5L4  CONST_11  C22  C23  C18  C19     0.00   0.0  0
 5L4  CONST_12  C22  C21  N20  C19     0.00   0.0  0
 5L4  CONST_13  N20  C21  C22  C23     0.00   0.0  0
 5L4  CONST_14  N20  C19  C18  C23     0.00   0.0  0
 5L4  CONST_15  C14  C15  C16  C11     0.00   0.0  0
 5L4  CONST_16  C14  C13  C12  C11     0.00   0.0  0
 5L4  CONST_17  N6   C1   C2   C11   180.00   0.0  0
 5L4  CONST_18  C4   N3   C2   C11   180.00   0.0  0
 5L4  CONST_21  C4   N3   C2   C1      0.00   0.0  0
 5L4  CONST_22  C4   C5   N6   C1      0.00   0.0  0
 5L4  CONST_23  C5   N6   C1   C2      0.00   0.0  0
 5L4  CONST_24  C5   C4   N3   C2      0.00   0.0  0
 5L4  CONST_25  N6   C1   C2   N3      0.00   0.0  0
 5L4  CONST_26  N6   C5   C4   N3      0.00   0.0  0
 5L4  CONST_27  N26  C23  C18  C19   180.00   0.0  0
 5L4  CONST_28  N26  C23  C22  C21   180.00   0.0  0
 5L4  CONST_29  C16  C15  C14  C17   180.00   0.0  0
 5L4  CONST_30  C12  C13  C14  C17   180.00   0.0  0
 5L4  CONST_31  N10  C18  C23  C22   180.00   0.0  0
 5L4  CONST_32  N7   C5   N6   C1    180.00   0.0  0
 5L4  CONST_33  C8   C4   N3   C2    180.00   0.0  0
 5L4  CONST_34  N7   C5   C4   N3    180.00   0.0  0
 5L4  CONST_35  C8   C4   C5   N6    180.00   0.0  0
 5L4  CONST_36  N26  C23  C18  N10     0.00   0.0  0
 5L4  CONST_37  N20  C19  C18  N10   180.00   0.0  0
 5L4  CONST_38  H38  C15  C14  C13   180.00   0.0  0
 5L4  CONST_39  H44  C22  C23  C18   180.00   0.0  0
 5L4  CONST_40  H36  C12  C11  C16   180.00   0.0  0
 5L4  CONST_41  H37  C13  C14  C15   180.00   0.0  0
 5L4  CONST_42  H43  C21  N20  C19   180.00   0.0  0
 5L4  CONST_43  H42  C19  N20  C21   180.00   0.0  0
 5L4  CONST_44  H32  C1   C2   C11     0.00   0.0  0
 5L4  CONST_45  H39  C16  C11  C12   180.00   0.0  0
 5L4  CONST_46  C4   C8   N10  C18   180.00   0.0  0
 5L4  CONST_50  H34  N7   C5   C4      0.00   0.0  0
 5L4  CONST_51  H33  N7   C5   C4    180.00   0.0  0
 5L4  CONST_52  O9   C8   N10  C18     0.00   0.0  0
 5L4  Var_01    C31  N26  C23  C18   -74.31  30.0  2
 5L4  Var_02    C30  C31  N26  C23   167.55  30.0  1
 5L4  Var_03    C28  C27  N26  C23  -168.28  30.0  1
 5L4  Var_04    O29  C30  C31  N26    56.42  30.0  1
 5L4  Var_05    O29  C28  C27  N26   -57.94  30.0  1
 5L4  Var_06    C31  C30  O29  C28   -57.12  30.0  1
 5L4  Var_07    C24  C17  C14  C13   -84.63  30.0  2
 5L4  Var_08    N10  C8   C4   N3      2.57  30.0  2
 5L4  Var_09    O25  C24  C17  C14   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
 5L4  plan-1  C18  0.020
 5L4  plan-1  C19  0.020
 5L4  plan-1  C21  0.020
 5L4  plan-1  C22  0.020
 5L4  plan-1  C23  0.020
 5L4  plan-1  N10  0.020
 5L4  plan-1  N20  0.020
 5L4  plan-1  N26  0.020
 5L4  plan-1  H42  0.020
 5L4  plan-1  H43  0.020
 5L4  plan-1  H44  0.020
 5L4  plan-2  C11  0.020
 5L4  plan-2  C1   0.020
 5L4  plan-2  C2   0.020
 5L4  plan-2  N3   0.020
 5L4  plan-2  C4   0.020
 5L4  plan-2  C5   0.020
 5L4  plan-2  N6   0.020
 5L4  plan-2  N7   0.020
 5L4  plan-2  C8   0.020
 5L4  plan-2  H32  0.020
 5L4  plan-3  C13  0.020
 5L4  plan-3  C17  0.020
 5L4  plan-3  C16  0.020
 5L4  plan-3  C15  0.020
 5L4  plan-3  C11  0.020
 5L4  plan-3  C12  0.020
 5L4  plan-3  C2   0.020
 5L4  plan-3  C14  0.020
 5L4  plan-3  H37  0.020
 5L4  plan-3  H39  0.020
 5L4  plan-3  H38  0.020
 5L4  plan-3  H36  0.020
 5L4  plan-4  C18  0.020
 5L4  plan-4  C4   0.020
 5L4  plan-4  C8   0.020
 5L4  plan-4  O9   0.020
 5L4  plan-4  N10  0.020
 5L4  plan-4  H35  0.020
 5L4  plan-5  C5   0.020
 5L4  plan-5  N7   0.020
 5L4  plan-5  H34  0.020
 5L4  plan-5  H33  0.020

