# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 11:47:50 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: 5-chloranyl-4-imidazo[1,2-a]pyridin-3-yl-N-(3-methyl-1-piperidin-4-yl-pyrazol-4-yl)pyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nn(cc1Nc2ncc(Cl)c(n2)c3cnc4ccccn34)C5CCNCC5
#
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
 8LN  8LN  5-chloranyl-4-imidazo[1,2-a]pyridin-3-yl-N-(3-methyl-1-piperidin-4-yl-pyrazol-4-yl)pyrimidin-2-amine  ligand  50  29  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_8LN
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
 8LN  C1    C   CH3   0  -0.756  -2.7974   3.8233   0.6335
 8LN  C2    C   CR15  0   0.033  -2.9863   0.2023   0.0527
 8LN  C3    C   CR5   0   0.032  -2.2068   1.3370   0.1369
 8LN  C4    C   CR5   0   0.222  -3.1101   2.3814   0.4309
 8LN  N1    N   N     0  -0.295  -4.3401   1.9061   0.5191
 8LN  N2    N   NR5   0  -0.293  -4.2526   0.6026   0.2965
 8LN  C5    C   CH1   0  -0.082  -5.4458  -0.2253   0.2996
 8LN  C6    C   CH2   0  -0.424  -5.8780  -0.6157  -1.1113
 8LN  C7    C   CH2   0  -0.298  -7.1216  -1.4924  -1.0462
 8LN  N3    N   NH1   0  -0.595  -6.8586  -2.6652  -0.2328
 8LN  C8    C   CH2   0  -0.297  -6.5374  -2.3051   1.1357
 8LN  C9    C   CH2   0  -0.438  -5.2659  -1.4677   1.1660
 8LN  C10   C   CR6   0   0.590   0.1067   0.5824  -0.2218
 8LN  N5    N   N     0  -0.457  -0.2744  -0.6833  -0.4036
 8LN  C11   C   CR16  0   0.052   0.6835  -1.5516  -0.6670
 8LN  C12   C   CR6   0  -0.202   2.0176  -1.1905  -0.7307
 8LN  C13   C   CR6   0   0.299   2.3327   0.1465  -0.4638
 8LN  N6    N   N     0  -0.475   1.3684   1.0215  -0.2274
 8LN  C14   C   CR5   0   0.229   3.6908   0.6723  -0.4856
 8LN  C15   C   CR15  0  -0.205   4.1879   1.7621  -1.1638
 8LN  N7    N   N     0  -0.468   5.5096   1.9153  -0.9695
 8LN  C16   C   CR56  0   0.533   5.8614   0.9412  -0.1433
 8LN  N8    N   N     0  -0.556   4.7744   0.1492   0.1842
 8LN  C17   C   CR16  0   0.032   4.8663  -0.8687   1.0886
 8LN  C18   C   CR16  0  -0.391   6.0716  -1.1582   1.6399
 8LN  C19   C   CR16  0  -0.149   7.2183  -0.4022   1.2946
 8LN  C20   C   CR16  0  -0.403   7.1154   0.6403   0.4210
 8LN  CL    CL  CL    0  -0.098   3.2037  -2.3409  -1.2175
 8LN  H11C  H   HCH3  0   0.249  -2.3868   4.2795  -0.2695
 8LN  H12C  H   HCH3  0   0.260  -3.6969   4.3740   0.9028
 8LN  H13C  H   HCH3  0   0.248  -2.0671   3.9701   1.4318
 8LN  H2    H   HCR5  0   0.296  -2.7295  -0.8202  -0.1531
 8LN  H4    H   HNH1  0   0.413  -0.4856   2.4547   0.1436
 8LN  H5    H   HCH1  0   0.257  -6.2229   0.4003   0.7458
 8LN  H61C  H   HCH2  0   0.243  -6.0823   0.2785  -1.7039
 8LN  H62C  H   HCH2  0   0.227  -5.0720  -1.1667  -1.6045
 8LN  H91C  H   HCH2  0   0.227  -4.4348  -2.0707   0.7906
 8LN  H92C  H   HCH2  0   0.248  -5.0292  -1.1797   2.1921
 8LN  H71C  H   HCH2  0   0.192  -7.9604  -0.8904  -0.6586
 8LN  H72C  H   HCH2  0   0.239  -7.4000  -1.8109  -2.0522
 8LN  H3    H   HNH1  0   0.355  -7.6683  -3.2713  -0.2424
 8LN  H81C  H   HCH2  0   0.193  -7.3455  -1.7360   1.6243
 8LN  H82C  H   HCH2  0   0.240  -6.3914  -3.2152   1.7199
 8LN  H11   H   HCR6  0   0.295   0.3852  -2.5784  -0.8488
 8LN  H15   H   HCR5  0   0.273   3.6231   2.4188  -1.8089
 8LN  H20   H   HCR6  0   0.284   7.9645   1.2539   0.1544
 8LN  H17   H   HCR6  0   0.315   3.9581  -1.3898   1.3486
 8LN  H18   H   HCR6  0   0.285   6.1366  -1.9652   2.3544
 8LN  H19   H   HCR6  0   0.278   8.1723  -0.6448   1.7419
 8LN  N4    N   NH1   0  -0.759  -0.8368   1.5198   0.0035

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
 8LN  C1   C4    single    1.489  0.020  1.489
 8LN  C2   C3    aromatic  1.379  0.020  1.379
 8LN  C2   N2    aromatic  1.350  0.020  1.350
 8LN  C3   C4    aromatic  1.412  0.020  1.412
 8LN  C3   N4    single    1.389  0.020  1.389
 8LN  C4   N1    aromatic  1.322  0.020  1.322
 8LN  N1   N2    aromatic  1.325  0.020  1.325
 8LN  N2   C5    single    1.452  0.020  1.452
 8LN  C5   C6    single    1.526  0.020  1.526
 8LN  C5   C9    single    1.525  0.020  1.525
 8LN  C6   C7    single    1.523  0.020  1.523
 8LN  C7   N3    single    1.451  0.020  1.451
 8LN  N3   C8    single    1.451  0.020  1.451
 8LN  C8   C9    single    1.523  0.020  1.523
 8LN  N4   C10   single    1.349  0.020  1.349
 8LN  C10  N5    aromatic  1.334  0.020  1.334
 8LN  C10  N6    aromatic  1.336  0.020  1.336
 8LN  N5   C11   aromatic  1.319  0.020  1.319
 8LN  C11  C12   aromatic  1.384  0.020  1.384
 8LN  C12  C13   aromatic  1.399  0.020  1.399
 8LN  C12  CL    single    1.723  0.020  1.723
 8LN  C13  N6    aromatic  1.323  0.020  1.323
 8LN  C13  C14   single    1.456  0.020  1.456
 8LN  C14  C15   aromatic  1.377  0.020  1.377
 8LN  C14  N8    aromatic  1.377  0.020  1.377
 8LN  C15  N7    aromatic  1.345  0.020  1.345
 8LN  N7   C16   aromatic  1.325  0.020  1.325
 8LN  C16  N8    aromatic  1.384  0.020  1.384
 8LN  C16  C20   aromatic  1.408  0.020  1.408
 8LN  N8   C17   aromatic  1.365  0.020  1.365
 8LN  C17  C18   aromatic  1.357  0.020  1.357
 8LN  C18  C19   aromatic  1.416  0.020  1.416
 8LN  C19  C20   aromatic  1.364  0.020  1.364
 8LN  C1   H11C  single    0.970  0.020  1.090
 8LN  C1   H12C  single    0.970  0.020  1.090
 8LN  C1   H13C  single    0.970  0.020  1.090
 8LN  C2   H2    single    0.930  0.020  1.080
 8LN  N4   H4    single    0.860  0.020  1.020
 8LN  C5   H5    single    0.970  0.020  1.090
 8LN  C6   H61C  single    0.970  0.020  1.090
 8LN  C6   H62C  single    0.970  0.020  1.090
 8LN  C9   H91C  single    0.970  0.020  1.090
 8LN  C9   H92C  single    0.970  0.020  1.090
 8LN  C7   H71C  single    0.970  0.020  1.090
 8LN  C7   H72C  single    0.970  0.020  1.090
 8LN  N3   H3    single    0.890  0.020  1.040
 8LN  C8   H81C  single    0.970  0.020  1.090
 8LN  C8   H82C  single    0.970  0.020  1.090
 8LN  C11  H11   single    0.930  0.020  1.080
 8LN  C15  H15   single    0.930  0.020  1.080
 8LN  C20  H20   single    0.930  0.020  1.080
 8LN  C17  H17   single    0.930  0.020  1.080
 8LN  C18  H18   single    0.930  0.020  1.080
 8LN  C19  H19   single    0.930  0.020  1.080

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
 8LN  H13C  C1   H12C  107.68  3.000
 8LN  H13C  C1   H11C  107.28  3.000
 8LN  H12C  C1   H11C  107.69  3.000
 8LN  H13C  C1   C4    111.72  3.000
 8LN  H12C  C1   C4    110.48  3.000
 8LN  H11C  C1   C4    111.78  3.000
 8LN  H2    C2   N2    122.75  3.000
 8LN  H2    C2   C3    131.28  3.000
 8LN  N2    C2   C3    105.97  3.000
 8LN  N4    C3   C4    123.63  3.000
 8LN  N4    C3   C2    131.31  3.000
 8LN  C4    C3   C2    105.05  3.000
 8LN  N1    C4   C3    110.08  3.000
 8LN  N1    C4   C1    122.31  3.000
 8LN  C3    C4   C1    127.60  3.000
 8LN  N2    N1   C4    106.33  3.000
 8LN  C5    N2   N1    120.41  3.000
 8LN  C5    N2   C2    127.00  3.000
 8LN  N1    N2   C2    112.57  3.000
 8LN  H5    C5   C9    108.55  3.000
 8LN  H5    C5   C6    108.81  3.000
 8LN  C9    C5   C6    110.49  3.000
 8LN  H5    C5   N2    105.00  3.000
 8LN  C9    C5   N2    111.64  3.000
 8LN  C6    C5   N2    112.12  3.000
 8LN  H62C  C6   H61C  107.80  3.000
 8LN  H62C  C6   C7    109.33  3.000
 8LN  H61C  C6   C7    109.99  3.000
 8LN  H62C  C6   C5    109.69  3.000
 8LN  H61C  C6   C5    110.19  3.000
 8LN  C7    C6   C5    109.81  3.000
 8LN  H72C  C7   H71C  106.81  3.000
 8LN  H72C  C7   N3    109.08  3.000
 8LN  H71C  C7   N3    112.46  3.000
 8LN  H72C  C7   C6    109.69  3.000
 8LN  H71C  C7   C6    108.78  3.000
 8LN  N3    C7   C6    109.95  3.000
 8LN  H3    N3   C8    109.56  3.000
 8LN  H3    N3   C7    109.51  3.000
 8LN  C8    N3   C7    111.60  3.000
 8LN  H82C  C8   H81C  106.94  3.000
 8LN  H82C  C8   C9    109.65  3.000
 8LN  H81C  C8   C9    108.63  3.000
 8LN  H82C  C8   N3    109.12  3.000
 8LN  H81C  C8   N3    112.57  3.000
 8LN  C9    C8   N3    109.88  3.000
 8LN  H92C  C9   H91C  107.67  3.000
 8LN  H92C  C9   C8    110.16  3.000
 8LN  H91C  C9   C8    108.95  3.000
 8LN  H92C  C9   C5    110.15  3.000
 8LN  H91C  C9   C5    110.11  3.000
 8LN  C8    C9   C5    109.76  3.000
 8LN  N6    C10  N5    125.52  3.000
 8LN  N6    C10  N4    115.65  3.000
 8LN  N5    C10  N4    118.83  3.000
 8LN  C11   N5   C10   116.37  3.000
 8LN  H11   C11  C12   120.30  3.000
 8LN  H11   C11  N5    117.18  3.000
 8LN  C12   C11  N5    122.51  3.000
 8LN  CL    C12  C13   122.48  3.000
 8LN  CL    C12  C11   120.18  3.000
 8LN  C13   C12  C11   117.24  3.000
 8LN  C14   C13  N6    116.32  3.000
 8LN  C14   C13  C12   123.51  3.000
 8LN  N6    C13  C12   120.12  3.000
 8LN  C13   N6   C10   118.13  3.000
 8LN  N8    C14  C15   104.84  3.000
 8LN  N8    C14  C13   126.11  3.000
 8LN  C15   C14  C13   129.05  3.000
 8LN  H15   C15  N7    122.08  3.000
 8LN  H15   C15  C14   125.93  3.000
 8LN  N7    C15  C14   111.96  3.000
 8LN  C16   N7   C15   105.51  3.000
 8LN  C20   C16  N8    118.84  3.000
 8LN  C20   C16  N7    130.07  3.000
 8LN  N8    C16  N7    111.08  3.000
 8LN  C17   N8   C16   122.05  3.000
 8LN  C17   N8   C14   131.19  3.000
 8LN  C16   N8   C14   106.59  3.000
 8LN  H17   C17  C18   123.16  3.000
 8LN  H17   C17  N8    117.60  3.000
 8LN  C18   C17  N8    119.22  3.000
 8LN  H18   C18  C19   120.77  3.000
 8LN  H18   C18  C17   118.80  3.000
 8LN  C19   C18  C17   120.42  3.000
 8LN  H19   C19  C20   120.20  3.000
 8LN  H19   C19  C18   119.59  3.000
 8LN  C20   C19  C18   120.20  3.000
 8LN  H20   C20  C19   122.17  3.000
 8LN  H20   C20  C16   118.66  3.000
 8LN  C19   C20  C16   119.17  3.000
 8LN  H4    N4   C10   115.08  3.000
 8LN  H4    N4   C3    116.89  3.000
 8LN  C10   N4   C3    127.93  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
 8LN  CONST_01  N1    C4   C3   C2     0.00   0.0  0
 8LN  CONST_02  C4    N1   N2   C2     0.00   0.0  0
 8LN  CONST_03  N1    N2   C2   C3     0.00   0.0  0
 8LN  CONST_04  N2    N1   C4   C3     0.00   0.0  0
 8LN  CONST_05  N2    C2   C3   C4     0.00   0.0  0
 8LN  CONST_06  C12   C11  N5   C10    0.00   0.0  0
 8LN  CONST_07  C12   C13  N6   C10    0.00   0.0  0
 8LN  CONST_08  C14   C13  N6   C10  180.00   0.0  0
 8LN  CONST_09  C13   N6   C10  N5     0.00   0.0  0
 8LN  CONST_10  C13   C12  C11  N5     0.00   0.0  0
 8LN  CONST_11  N6    C10  N5   C11    0.00   0.0  0
 8LN  CONST_12  N6    C13  C12  C11    0.00   0.0  0
 8LN  CONST_13  C14   C13  C12  C11  180.00   0.0  0
 8LN  CONST_16  N7    C15  C14  C13  180.00   0.0  0
 8LN  CONST_17  C16   N8   C14  C13  180.00   0.0  0
 8LN  CONST_18  C17   N8   C14  C13    0.00   0.0  0
 8LN  CONST_21  C16   N7   C15  C14    0.00   0.0  0
 8LN  CONST_22  N7    C16  N8   C14    0.00   0.0  0
 8LN  CONST_23  C20   C16  N8   C14  180.00   0.0  0
 8LN  CONST_24  C18   C17  N8   C14  180.00   0.0  0
 8LN  CONST_25  C16   N8   C14  C15    0.00   0.0  0
 8LN  CONST_26  C17   N8   C14  C15  180.00   0.0  0
 8LN  CONST_27  N8    C16  N7   C15    0.00   0.0  0
 8LN  CONST_28  C20   C16  N7   C15  180.00   0.0  0
 8LN  CONST_29  N8    C14  C15  N7     0.00   0.0  0
 8LN  CONST_30  C17   N8   C16  N7   180.00   0.0  0
 8LN  CONST_31  C19   C20  C16  N7   180.00   0.0  0
 8LN  CONST_32  C18   C17  N8   C16    0.00   0.0  0
 8LN  CONST_33  C18   C19  C20  C16    0.00   0.0  0
 8LN  CONST_34  C19   C20  C16  N8     0.00   0.0  0
 8LN  CONST_35  C19   C18  C17  N8     0.00   0.0  0
 8LN  CONST_36  C20   C16  N8   C17    0.00   0.0  0
 8LN  CONST_37  C20   C19  C18  C17    0.00   0.0  0
 8LN  CONST_38  C5    N2   C2   C3   180.00   0.0  0
 8LN  CONST_39  C5    N2   N1   C4   180.00   0.0  0
 8LN  CONST_40  C2    C3   C4   C1   180.00   0.0  0
 8LN  CONST_41  N2    N1   C4   C1   180.00   0.0  0
 8LN  CONST_42  N4    C3   C4   N1   180.00   0.0  0
 8LN  CONST_43  N4    C3   C2   N2   180.00   0.0  0
 8LN  CONST_44  C11   N5   C10  N4   180.00   0.0  0
 8LN  CONST_45  C13   N6   C10  N4   180.00   0.0  0
 8LN  CONST_46  CL    C12  C11  N5   180.00   0.0  0
 8LN  CONST_47  CL    C12  C13  N6   180.00   0.0  0
 8LN  CONST_48  CL    C12  C13  C14    0.00   0.0  0
 8LN  CONST_49  H2    C2   C3   C4   180.00   0.0  0
 8LN  CONST_50  H11   C11  N5   C10  180.00   0.0  0
 8LN  CONST_51  H15   C15  C14  C13    0.00   0.0  0
 8LN  CONST_52  H17   C17  N8   C14    0.00   0.0  0
 8LN  CONST_53  H20   C20  C16  N7     0.00   0.0  0
 8LN  CONST_54  H19   C19  C20  C16  180.00   0.0  0
 8LN  CONST_55  H18   C18  C17  N8   180.00   0.0  0
 8LN  Var_01    N3    C7   C6   C5   -57.26  30.0  1
 8LN  Var_02    N3    C8   C9   C5    57.57  30.0  1
 8LN  Var_03    C8    N3   C7   C6    62.11  30.0  1
 8LN  Var_04    C9    C8   N3   C7   -62.25  30.0  1
 8LN  Var_05    C10   N4   C3   C2    -1.68  30.0  2
 8LN  Var_06    N5    C10  N4   C3     3.22  30.0  2
 8LN  Var_07    H11C  C1   C4   C3    63.34  30.0  2

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
 8LN  chir_01  C5  N2  C6  C9  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
 8LN  plan-1  C1   0.020
 8LN  plan-1  C2   0.020
 8LN  plan-1  C3   0.020
 8LN  plan-1  C4   0.020
 8LN  plan-1  N1   0.020
 8LN  plan-1  N2   0.020
 8LN  plan-1  C5   0.020
 8LN  plan-1  H2   0.020
 8LN  plan-1  N4   0.020
 8LN  plan-2  C10  0.020
 8LN  plan-2  N5   0.020
 8LN  plan-2  C11  0.020
 8LN  plan-2  C12  0.020
 8LN  plan-2  C13  0.020
 8LN  plan-2  N6   0.020
 8LN  plan-2  C14  0.020
 8LN  plan-2  CL   0.020
 8LN  plan-2  H11  0.020
 8LN  plan-2  N4   0.020
 8LN  plan-3  C13  0.020
 8LN  plan-3  C14  0.020
 8LN  plan-3  C15  0.020
 8LN  plan-3  N7   0.020
 8LN  plan-3  C16  0.020
 8LN  plan-3  N8   0.020
 8LN  plan-3  C17  0.020
 8LN  plan-3  C18  0.020
 8LN  plan-3  C19  0.020
 8LN  plan-3  C20  0.020
 8LN  plan-3  H15  0.020
 8LN  plan-3  H20  0.020
 8LN  plan-3  H17  0.020
 8LN  plan-3  H18  0.020
 8LN  plan-3  H19  0.020

