# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 15:48:34 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: [6-(aminomethyl)-5-(2,4-dichlorophenyl)-7-methylimidazo[1,2-a]pyrimidin-2-yl](morpholin-4-yl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nc2nc(cn2c(c1CN)c3ccc(Cl)cc3Cl)C(=O)N4CCOCC4
#
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
 6A5  6A5  '[6-(aminomethyl)-5-(2,4-dichlorophenyl)-7-methylimidazo[1,2-a]pyrimidin-2-yl](morpholin-4-yl)methanone'  ligand  47  28  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6A5
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
 6A5  C1    C   CR6   0   0.430  -1.1965  -0.9463   0.5689
 6A5  C2    C   CR6   0  -0.099  -1.4992  -2.2457   0.8389
 6A5  C3    C   CR6   0   0.260  -0.4162  -3.1717   1.0164
 6A5  N4    N   N     0  -0.452   0.8374  -2.8103   0.9462
 6A5  N5    N   N     0  -0.539   0.1183  -0.5895   0.5072
 6A5  C6    C   CR56  0   0.571   1.1197  -1.5296   0.6941
 6A5  N7    N   N     0  -0.493   2.3053  -0.9777   0.5843
 6A5  C8    C   CR5   0  -0.005   2.0695   0.3355   0.3215
 6A5  C9    C   CR15  0  -0.060   0.7254   0.6097   0.2757
 6A5  C10   C   C     0   0.509   3.0915   1.4053   0.1854
 6A5  O11   O   O     0  -0.493   2.7583   2.5502   0.4753
 6A5  N12   N   NT    0  -0.474   4.3360   1.0966  -0.2278
 6A5  C13   C   CH3   0  -0.758  -0.6928  -4.6172   1.2851
 6A5  C14   C   CR6   0   0.083  -2.1931   0.1151   0.3357
 6A5  C15   C   CH2   0  -0.397  -2.9390  -2.6889   0.8503
 6A5  N16   N   NH2   0  -0.766  -3.4775  -2.6585  -0.5002
 6A5  C17   C   CR16  0  -0.287  -2.8432   0.7174   1.4059
 6A5  C18   C   CR16  0  -0.192  -3.7801   1.7177   1.2033
 6A5  C19   C   CR6   0  -0.050  -4.0593   2.1180  -0.0931
 6A5  C20   C   CR16  0  -0.159  -3.4228   1.5440  -1.1829
 6A5  C21   C   CR6   0  -0.056  -2.4940   0.5440  -0.9528
 6A5  CL22  CL  CL    0  -0.097  -1.6874  -0.1728  -2.2962
 6A5  CL23  CL  CL    0  -0.104  -5.2232   3.3637  -0.3682
 6A5  C24   C   CH2   0  -0.326   5.3720   2.1169  -0.2410
 6A5  C25   C   CH2   0  -0.183   6.6443   1.5464   0.3622
 6A5  O26   O   O2    0  -0.483   7.0600   0.3698  -0.2938
 6A5  C27   C   CH2   0  -0.181   6.0554  -0.6194  -0.2593
 6A5  C28   C   CH2   0  -0.330   4.7645  -0.1279  -0.8871
 6A5  H17   H   HCR6  0   0.287  -2.6132   0.4006   2.4148
 6A5  H18   H   HCR6  0   0.293  -4.2798   2.1757   2.0450
 6A5  H20   H   HCR6  0   0.307  -3.6469   1.8659  -2.1901
 6A5  H9    H   HCR5  0   0.314   0.1810   1.5220   0.1035
 6A5  H24   H   HCH2  0   0.245   5.5527   2.4468  -1.2699
 6A5  HN16  H   HNH2  0   0.343  -3.0054  -3.3473  -1.0728
 6A5  H24A  H   HCH2  0   0.270   5.0527   2.9827   0.3336
 6A5  HN1A  H   HNH2  0   0.354  -4.4507  -2.9358  -0.4730
 6A5  H28   H   HCH2  0   0.285   4.0080  -0.9001  -0.8111
 6A5  H28A  H   HCH2  0   0.245   4.9281   0.0864  -1.9492
 6A5  H25   H   HCH2  0   0.245   7.4513   2.2746   0.2716
 6A5  H25A  H   HCH2  0   0.208   6.4795   1.3555   1.4318
 6A5  H27   H   HCH2  0   0.244   6.4269  -1.4826  -0.8129
 6A5  H27A  H   HCH2  0   0.208   5.8572  -0.9374   0.7739
 6A5  H13   H   HCH3  0   0.259  -1.3527  -5.0448   0.5287
 6A5  H13A  H   HCH3  0   0.268   0.2372  -5.1799   1.2922
 6A5  H13B  H   HCH3  0   0.265  -1.1838  -4.7524   2.2505
 6A5  H15   H   HCH2  0   0.239  -3.0169  -3.6625   1.3443
 6A5  H15A  H   HCH2  0   0.252  -3.5239  -2.0007   1.4631

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
 6A5  C1   C2    aromatic  1.361  0.020  1.361
 6A5  C1   N5    aromatic  1.364  0.020  1.364
 6A5  C1   C14   single    1.474  0.020  1.474
 6A5  C2   C3    aromatic  1.436  0.020  1.436
 6A5  C2   C15   single    1.507  0.020  1.507
 6A5  C3   N4    aromatic  1.306  0.020  1.306
 6A5  C3   C13   single    1.496  0.020  1.496
 6A5  N4   C6    aromatic  1.335  0.020  1.335
 6A5  N5   C6    aromatic  1.386  0.020  1.386
 6A5  N5   C9    aromatic  1.364  0.020  1.364
 6A5  C6   N7    aromatic  1.312  0.020  1.312
 6A5  N7   C8    aromatic  1.360  0.020  1.360
 6A5  C8   C9    aromatic  1.373  0.020  1.373
 6A5  C8   C10   single    1.486  0.020  1.486
 6A5  C9   H9    single    0.930  0.020  1.080
 6A5  C10  O11   double    1.227  0.020  1.227
 6A5  C10  N12   single    1.347  0.020  1.347
 6A5  N12  C24   single    1.454  0.020  1.454
 6A5  N12  C28   single    1.455  0.020  1.455
 6A5  C13  H13   single    0.970  0.020  1.090
 6A5  C13  H13A  single    0.970  0.020  1.090
 6A5  C13  H13B  single    0.970  0.020  1.090
 6A5  C14  C17   aromatic  1.390  0.020  1.390
 6A5  C14  C21   aromatic  1.391  0.020  1.391
 6A5  C15  N16   single    1.454  0.020  1.454
 6A5  C15  H15   single    0.970  0.020  1.090
 6A5  C15  H15A  single    0.970  0.020  1.090
 6A5  N16  HN16  single    0.890  0.020  1.040
 6A5  N16  HN1A  single    0.890  0.020  1.040
 6A5  C17  C18   aromatic  1.385  0.020  1.385
 6A5  C17  H17   single    0.930  0.020  1.080
 6A5  C18  C19   aromatic  1.385  0.020  1.385
 6A5  C18  H18   single    0.930  0.020  1.080
 6A5  C19  C20   aromatic  1.386  0.020  1.386
 6A5  C19  CL23  single    1.727  0.020  1.727
 6A5  C20  C21   aromatic  1.384  0.020  1.384
 6A5  C20  H20   single    0.930  0.020  1.080
 6A5  C21  CL22  single    1.723  0.020  1.723
 6A5  C24  C25   single    1.519  0.020  1.519
 6A5  C24  H24   single    0.970  0.020  1.090
 6A5  C24  H24A  single    0.970  0.020  1.090
 6A5  C25  O26   single    1.410  0.020  1.410
 6A5  C25  H25   single    0.970  0.020  1.090
 6A5  C25  H25A  single    0.970  0.020  1.090
 6A5  O26  C27   single    1.410  0.020  1.410
 6A5  C27  C28   single    1.517  0.020  1.517
 6A5  C27  H27   single    0.970  0.020  1.090
 6A5  C27  H27A  single    0.970  0.020  1.090
 6A5  C28  H28   single    0.970  0.020  1.090
 6A5  C28  H28A  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
 6A5  C14   C1   N5    117.14  3.000
 6A5  C14   C1   C2    124.63  3.000
 6A5  N5    C1   C2    118.24  3.000
 6A5  C15   C2   C3    122.02  3.000
 6A5  C15   C2   C1    119.66  3.000
 6A5  C3    C2   C1    118.19  3.000
 6A5  C13   C3   N4    117.02  3.000
 6A5  C13   C3   C2    120.38  3.000
 6A5  N4    C3   C2    122.59  3.000
 6A5  C6    N4   C3    118.57  3.000
 6A5  C9    N5   C6    107.32  3.000
 6A5  C9    N5   C1    131.82  3.000
 6A5  C6    N5   C1    120.86  3.000
 6A5  N7    C6   N5    110.86  3.000
 6A5  N7    C6   N4    127.59  3.000
 6A5  N5    C6   N4    121.55  3.000
 6A5  C8    N7   C6    105.40  3.000
 6A5  C10   C8   C9    121.78  3.000
 6A5  C10   C8   N7    126.42  3.000
 6A5  C9    C8   N7    111.67  3.000
 6A5  H9    C9   C8    132.07  3.000
 6A5  H9    C9   N5    123.18  3.000
 6A5  C8    C9   N5    104.75  3.000
 6A5  N12   C10  O11   122.49  3.000
 6A5  N12   C10  C8    119.90  3.000
 6A5  O11   C10  C8    117.61  3.000
 6A5  C28   N12  C24   112.11  3.000
 6A5  C28   N12  C10   127.14  3.000
 6A5  C24   N12  C10   120.01  3.000
 6A5  H13B  C13  H13A  108.36  3.000
 6A5  H13B  C13  H13   107.02  3.000
 6A5  H13A  C13  H13   108.61  3.000
 6A5  H13B  C13  C3    111.21  3.000
 6A5  H13A  C13  C3    110.06  3.000
 6A5  H13   C13  C3    111.47  3.000
 6A5  C21   C14  C17   118.59  3.000
 6A5  C21   C14  C1    120.98  3.000
 6A5  C17   C14  C1    120.43  3.000
 6A5  H15A  C15  H15   105.62  3.000
 6A5  H15A  C15  N16   108.05  3.000
 6A5  H15   C15  N16   114.29  3.000
 6A5  H15A  C15  C2    109.33  3.000
 6A5  H15   C15  C2    109.45  3.000
 6A5  N16   C15  C2    109.92  3.000
 6A5  HN1A  N16  HN16  106.08  3.000
 6A5  HN1A  N16  C15   108.98  3.000
 6A5  HN16  N16  C15   109.78  3.000
 6A5  H17   C17  C18   119.43  3.000
 6A5  H17   C17  C14   119.45  3.000
 6A5  C18   C17  C14   121.12  3.000
 6A5  H18   C18  C19   120.88  3.000
 6A5  H18   C18  C17   120.32  3.000
 6A5  C19   C18  C17   118.80  3.000
 6A5  CL23  C19  C20   118.87  3.000
 6A5  CL23  C19  C18   119.56  3.000
 6A5  C20   C19  C18   121.56  3.000
 6A5  H20   C20  C21   120.62  3.000
 6A5  H20   C20  C19   120.92  3.000
 6A5  C21   C20  C19   118.46  3.000
 6A5  CL22  C21  C20   119.02  3.000
 6A5  CL22  C21  C14   119.52  3.000
 6A5  C20   C21  C14   121.47  3.000
 6A5  H24A  C24  H24   107.76  3.000
 6A5  H24A  C24  C25   109.59  3.000
 6A5  H24   C24  C25   110.36  3.000
 6A5  H24A  C24  N12   110.16  3.000
 6A5  H24   C24  N12   109.71  3.000
 6A5  C25   C24  N12   109.25  3.000
 6A5  H25A  C25  H25   107.92  3.000
 6A5  H25A  C25  O26   110.62  3.000
 6A5  H25   C25  O26   107.48  3.000
 6A5  H25A  C25  C24   109.03  3.000
 6A5  H25   C25  C24   109.63  3.000
 6A5  O26   C25  C24   112.06  3.000
 6A5  C27   O26  C25   111.34  3.000
 6A5  H27A  C27  H27   108.04  3.000
 6A5  H27A  C27  C28   109.23  3.000
 6A5  H27   C27  C28   109.64  3.000
 6A5  H27A  C27  O26   110.75  3.000
 6A5  H27   C27  O26   107.46  3.000
 6A5  C28   C27  O26   111.63  3.000
 6A5  H28A  C28  H28   108.15  3.000
 6A5  H28A  C28  C27   109.72  3.000
 6A5  H28   C28  C27   109.52  3.000
 6A5  H28A  C28  N12   108.57  3.000
 6A5  H28   C28  N12   111.24  3.000
 6A5  C27   C28  N12   109.61  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
 6A5  CONST_01  N4    C3   C2   C1     0.00   0.0  0
 6A5  CONST_02  N4    C6   N5   C1     0.00   0.0  0
 6A5  CONST_03  N7    C6   N5   C1   180.00   0.0  0
 6A5  CONST_04  C8    C9   N5   C1   180.00   0.0  0
 6A5  CONST_05  C18   C17  C14  C1   180.00   0.0  0
 6A5  CONST_06  C20   C21  C14  C1   180.00   0.0  0
 6A5  CONST_07  C6    N5   C1   C2     0.00   0.0  0
 6A5  CONST_08  C9    N5   C1   C2   180.00   0.0  0
 6A5  CONST_11  C6    N4   C3   C2     0.00   0.0  0
 6A5  CONST_12  N5    C1   C2   C3     0.00   0.0  0
 6A5  CONST_13  C14   C1   C2   C3   180.00   0.0  0
 6A5  CONST_14  N5    C6   N4   C3     0.00   0.0  0
 6A5  CONST_15  N7    C6   N4   C3   180.00   0.0  0
 6A5  CONST_16  C9    N5   C6   N4   180.00   0.0  0
 6A5  CONST_17  C8    N7   C6   N4   180.00   0.0  0
 6A5  CONST_20  C8    N7   C6   N5     0.00   0.0  0
 6A5  CONST_21  N7    C8   C9   N5     0.00   0.0  0
 6A5  CONST_22  C14   C1   N5   C6   180.00   0.0  0
 6A5  CONST_23  C8    C9   N5   C6     0.00   0.0  0
 6A5  CONST_24  C9    C8   N7   C6     0.00   0.0  0
 6A5  CONST_25  C9    N5   C6   N7     0.00   0.0  0
 6A5  CONST_26  C14   C1   N5   C9     0.00   0.0  0
 6A5  CONST_27  C19   C18  C17  C14    0.00   0.0  0
 6A5  CONST_28  C19   C20  C21  C14    0.00   0.0  0
 6A5  CONST_29  C20   C21  C14  C17    0.00   0.0  0
 6A5  CONST_30  C20   C19  C18  C17    0.00   0.0  0
 6A5  CONST_31  C21   C14  C17  C18    0.00   0.0  0
 6A5  CONST_32  C21   C20  C19  C18    0.00   0.0  0
 6A5  CONST_33  C13   C3   C2   C1   180.00   0.0  0
 6A5  CONST_34  CL22  C21  C14  C1     0.00   0.0  0
 6A5  CONST_35  C15   C2   C3   N4   180.00   0.0  0
 6A5  CONST_36  C15   C2   C1   N5   180.00   0.0  0
 6A5  CONST_37  C10   C8   C9   N5   180.00   0.0  0
 6A5  CONST_38  C13   C3   N4   C6   180.00   0.0  0
 6A5  CONST_39  C10   C8   N7   C6   180.00   0.0  0
 6A5  CONST_40  C15   C2   C1   C14    0.00   0.0  0
 6A5  CONST_41  CL22  C21  C14  C17  180.00   0.0  0
 6A5  CONST_42  CL23  C19  C18  C17  180.00   0.0  0
 6A5  CONST_43  CL22  C21  C20  C19  180.00   0.0  0
 6A5  CONST_44  CL23  C19  C20  C21  180.00   0.0  0
 6A5  CONST_45  C24   N12  C10  C8   180.00   0.0  0
 6A5  CONST_47  H9    C9   N5   C1     0.00   0.0  0
 6A5  CONST_48  H17   C17  C14  C1     0.00   0.0  0
 6A5  CONST_49  H18   C18  C17  C14  180.00   0.0  0
 6A5  CONST_50  H20   C20  C21  C14  180.00   0.0  0
 6A5  CONST_51  C24   N12  C10  O11    0.00   0.0  0
 6A5  Var_01    O26   C25  C24  N12   55.54  30.0  1
 6A5  Var_02    O26   C27  C28  N12  -55.73  30.0  1
 6A5  Var_03    C27   C28  N12  C24   54.93  30.0  1
 6A5  Var_04    C28   N12  C24  C25  -54.59  30.0  1
 6A5  Var_05    C28   C27  O26  C25   57.68  30.0  1
 6A5  Var_06    N12   C10  C8   N7    27.59  30.0  2
 6A5  Var_07    N16   C15  C2   C1    69.18  30.0  2
 6A5  Var_08    H13   C13  C3   C2    53.79  30.0  2
 6A5  Var_09    HN16  N16  C15  C2    65.63  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
 6A5  plan-1  C1    0.020
 6A5  plan-1  C14   0.020
 6A5  plan-1  C17   0.020
 6A5  plan-1  C18   0.020
 6A5  plan-1  C19   0.020
 6A5  plan-1  C20   0.020
 6A5  plan-1  C21   0.020
 6A5  plan-1  CL22  0.020
 6A5  plan-1  CL23  0.020
 6A5  plan-1  H17   0.020
 6A5  plan-1  H18   0.020
 6A5  plan-1  H20   0.020
 6A5  plan-2  C1    0.020
 6A5  plan-2  C2    0.020
 6A5  plan-2  C3    0.020
 6A5  plan-2  N4    0.020
 6A5  plan-2  N5    0.020
 6A5  plan-2  C6    0.020
 6A5  plan-2  N7    0.020
 6A5  plan-2  C8    0.020
 6A5  plan-2  C9    0.020
 6A5  plan-2  C10   0.020
 6A5  plan-2  C13   0.020
 6A5  plan-2  C14   0.020
 6A5  plan-2  C15   0.020
 6A5  plan-2  H9    0.020
 6A5  plan-3  C8    0.020
 6A5  plan-3  C10   0.020
 6A5  plan-3  O11   0.020
 6A5  plan-3  N12   0.020
 6A5  plan-3  C24   0.020
 6A5  plan-3  C28   0.020

