# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 16:56:33 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: (2S)-1-(dimethylamino)-3-(4-{[4-(2-methylimidazo[1,2-a]pyridin-3-yl)pyrimidin-2-yl]amino}phenoxy)propan-2-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)C[C@H](O)COc1ccc(Nc2nccc(n2)c3n4ccccc4nc3C)cc1
#
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
 HDY  HDY  (2S)-1-(dimethylamino)-3-(4-{[4-(2-methylimidazo[1,2-a]pyridin-3-yl)pyrimidin-2-yl]amino}phenoxy)propan-2-ol  ligand  57  31  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HDY
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
 HDY  C10   C  CH3   0  -0.753  -2.7407  -0.8407  -4.9690
 HDY  C9    C  CR5   0   0.113  -1.5414  -0.4467  -5.7576
 HDY  N8    N  N     0  -0.482  -1.6130  -0.3217  -7.0979
 HDY  C5    C  CR56  0   0.532  -0.3916  -0.0234  -7.5090
 HDY  C4    C  CR16  0  -0.407   0.0821   0.2403  -8.8075
 HDY  C3    C  CR16  0  -0.149   1.3937   0.5720  -8.9832
 HDY  C2    C  CR16  0  -0.392   2.2558   0.6657  -7.8647
 HDY  N6    N  N     0  -0.572   0.4893   0.0351  -6.4462
 HDY  C1    C  CR16  0   0.026   1.7916   0.4051  -6.6159
 HDY  C7    C  CR5   0   0.223  -0.2460  -0.2407  -5.3071
 HDY  C11   C  CR6   0   0.261   0.3221  -0.3739  -3.9746
 HDY  C12   C  CR16  0  -0.418   1.5748  -0.9566  -3.7473
 HDY  C13   C  CR16  0   0.009   1.9775  -1.0424  -2.4311
 HDY  N14   N  N     0  -0.470   1.2416  -0.6213  -1.4110
 HDY  N16   N  N     0  -0.492  -0.4247   0.0472  -2.9634
 HDY  C15   C  CR6   0   0.602   0.0560  -0.1055  -1.7258
 HDY  N17   N  NH1   0  -0.773  -0.7802   0.3305  -0.7496
 HDY  C18   C  CR6   0   0.340  -0.6566   0.3489   0.6397
 HDY  C19   C  CR16  0  -0.339  -1.7499   0.8545   1.3553
 HDY  C20   C  CR16  0  -0.335  -1.7391   0.9211   2.7321
 HDY  C23   C  CR16  0  -0.302   0.4497  -0.0864   1.3628
 HDY  C22   C  CR16  0  -0.369   0.4615  -0.0187   2.7538
 HDY  C21   C  CR6   0   0.369  -0.6278   0.4827   3.4540
 HDY  O24   O  O2    0  -0.480  -0.7037   0.5839   4.7987
 HDY  C25   C  CH2   0  -0.175   0.4086   0.1774   5.5705
 HDY  C26   C  CH1   0   0.003   0.0736   0.3795   7.0300
 HDY  O31   O  OH1   0  -0.681  -0.9719  -0.4824   7.4055
 HDY  C27   C  CH2   0  -0.308   1.3086   0.0912   7.8881
 HDY  N28   N  NT    0  -0.438   0.9209  -0.0340   9.2817
 HDY  C30   C  CH3   0  -0.515   1.8717  -0.8071  10.0546
 HDY  C29   C  CH3   0  -0.524   0.6635   1.2513   9.9027
 HDY  H101  H  HCH3  0   0.252  -2.9224  -1.9136  -5.0607
 HDY  H102  H  HCH3  0   0.257  -2.6291  -0.6051  -3.9153
 HDY  H103  H  HCH3  0   0.250  -3.6247  -0.3296  -5.3494
 HDY  H4    H  HCR6  0   0.282  -0.6121   0.1772  -9.6335
 HDY  H3    H  HCR6  0   0.277   1.7769   0.7771  -9.9729
 HDY  H2    H  HCR6  0   0.284   3.2899   0.9521  -7.9864
 HDY  H1    H  HCR6  0   0.317   2.4049   0.4913  -5.7335
 HDY  H12   H  HCR6  0   0.284   2.1876  -1.3604  -4.5392
 HDY  H13   H  HCR6  0   0.275   2.9368  -1.4816  -2.1813
 HDY  H17   H  HNH1  0   0.407  -1.6466   0.7025  -1.1085
 HDY  H19   H  HCR6  0   0.269  -2.6263   1.2034   0.8217
 HDY  H20   H  HCR6  0   0.264  -2.5994   1.3174   3.2567
 HDY  H23   H  HCR6  0   0.287   1.3125  -0.4837   0.8547
 HDY  H22   H  HCR6  0   0.278   1.3465  -0.3725   3.2650
 HDY  H251  H  HCH2  0   0.225   1.2946   0.7708   5.3133
 HDY  H252  H  HCH2  0   0.223   0.6469  -0.8777   5.3877
 HDY  H26   H  HCH1  0   0.208  -0.2216   1.4314   7.1676
 HDY  H31   H  HOH1  0   0.438  -0.7992  -0.6768   8.3420
 HDY  H271  H  HCH2  0   0.220   2.0742   0.8647   7.7258
 HDY  H272  H  HCH2  0   0.241   1.7430  -0.8625   7.5731
 HDY  H301  H  HCH3  0   0.237   1.4809  -0.9763  11.0586
 HDY  H302  H  HCH3  0   0.238   2.0310  -1.7790   9.5876
 HDY  H303  H  HCH3  0   0.200   2.8496  -0.3150  10.1538
 HDY  H291  H  HCH3  0   0.240  -0.1269   1.7876   9.3771
 HDY  H292  H  HCH3  0   0.240   0.3306   1.1050  10.9304
 HDY  H293  H  HCH3  0   0.204   1.5538   1.8958   9.9210

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
 HDY  C10  C9    single    1.488  0.020  1.488
 HDY  C10  H101  single    0.970  0.020  1.090
 HDY  C10  H102  single    0.970  0.020  1.090
 HDY  C10  H103  single    0.970  0.020  1.090
 HDY  C9   N8    aromatic  1.348  0.020  1.348
 HDY  C9   C7    aromatic  1.387  0.020  1.387
 HDY  N8   C5    aromatic  1.323  0.020  1.323
 HDY  C5   C4    aromatic  1.407  0.020  1.407
 HDY  C5   N6    aromatic  1.382  0.020  1.382
 HDY  C4   C3    aromatic  1.364  0.020  1.364
 HDY  C4   H4    single    0.930  0.020  1.080
 HDY  C3   C2    aromatic  1.415  0.020  1.415
 HDY  C3   H3    single    0.930  0.020  1.080
 HDY  C2   C1    aromatic  1.358  0.020  1.358
 HDY  C2   H2    single    0.930  0.020  1.080
 HDY  N6   C1    aromatic  1.364  0.020  1.364
 HDY  N6   C7    aromatic  1.384  0.020  1.384
 HDY  C1   H1    single    0.930  0.020  1.080
 HDY  C7   C11   single    1.455  0.020  1.455
 HDY  C11  C12   aromatic  1.400  0.020  1.400
 HDY  C11  N16   aromatic  1.326  0.020  1.326
 HDY  C12  C13   aromatic  1.379  0.020  1.379
 HDY  C12  H12   single    0.930  0.020  1.080
 HDY  C13  N14   aromatic  1.326  0.020  1.326
 HDY  C13  H13   single    0.930  0.020  1.080
 HDY  N14  C15   aromatic  1.331  0.020  1.331
 HDY  N16  C15   aromatic  1.336  0.020  1.336
 HDY  C15  N17   single    1.357  0.020  1.357
 HDY  N17  C18   single    1.395  0.020  1.395
 HDY  N17  H17   single    0.860  0.020  1.020
 HDY  C18  C19   aromatic  1.401  0.020  1.401
 HDY  C18  C23   aromatic  1.392  0.020  1.392
 HDY  C19  C20   aromatic  1.378  0.020  1.378
 HDY  C19  H19   single    0.930  0.020  1.080
 HDY  C20  C21   aromatic  1.396  0.020  1.396
 HDY  C20  H20   single    0.930  0.020  1.080
 HDY  C23  C22   aromatic  1.393  0.020  1.393
 HDY  C23  H23   single    0.930  0.020  1.080
 HDY  C22  C21   aromatic  1.389  0.020  1.389
 HDY  C22  H22   single    0.930  0.020  1.080
 HDY  C21  O24   single    1.351  0.020  1.351
 HDY  O24  C25   single    1.414  0.020  1.414
 HDY  C25  C26   single    1.511  0.020  1.511
 HDY  C25  H251  single    0.970  0.020  1.090
 HDY  C25  H252  single    0.970  0.020  1.090
 HDY  C26  O31   single    1.406  0.020  1.406
 HDY  C26  C27   single    1.531  0.020  1.531
 HDY  C26  H26   single    0.970  0.020  1.090
 HDY  O31  H31   single    0.850  0.020  0.980
 HDY  C27  N28   single    1.452  0.020  1.452
 HDY  C27  H271  single    0.970  0.020  1.090
 HDY  C27  H272  single    0.970  0.020  1.090
 HDY  N28  C30   single    1.449  0.020  1.449
 HDY  N28  C29   single    1.450  0.020  1.450
 HDY  C30  H301  single    0.970  0.020  1.090
 HDY  C30  H302  single    0.970  0.020  1.090
 HDY  C30  H303  single    0.970  0.020  1.090
 HDY  C29  H291  single    0.970  0.020  1.090
 HDY  C29  H292  single    0.970  0.020  1.090
 HDY  C29  H293  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
 HDY  H103  C10  H102  108.69  3.000
 HDY  H103  C10  H101  107.25  3.000
 HDY  H102  C10  H101  108.17  3.000
 HDY  H103  C10  C9    110.16  3.000
 HDY  H102  C10  C9    111.96  3.000
 HDY  H101  C10  C9    110.47  3.000
 HDY  C7    C9   N8    111.03  3.000
 HDY  C7    C9   C10   128.30  3.000
 HDY  N8    C9   C10   120.56  3.000
 HDY  C5    N8   C9    106.31  3.000
 HDY  N6    C5   C4    119.16  3.000
 HDY  N6    C5   N8    111.05  3.000
 HDY  C4    C5   N8    129.79  3.000
 HDY  H4    C4   C3    122.22  3.000
 HDY  H4    C4   C5    118.56  3.000
 HDY  C3    C4   C5    119.21  3.000
 HDY  H3    C3   C2    119.67  3.000
 HDY  H3    C3   C4    120.33  3.000
 HDY  C2    C3   C4    120.00  3.000
 HDY  H2    C2   C1    118.82  3.000
 HDY  H2    C2   C3    120.79  3.000
 HDY  C1    C2   C3    120.39  3.000
 HDY  C7    N6   C1    131.58  3.000
 HDY  C7    N6   C5    106.62  3.000
 HDY  C1    N6   C5    121.63  3.000
 HDY  H1    C1   N6    117.58  3.000
 HDY  H1    C1   C2    122.89  3.000
 HDY  N6    C1   C2    119.53  3.000
 HDY  C11   C7   N6    124.39  3.000
 HDY  C11   C7   C9    130.45  3.000
 HDY  N6    C7   C9    104.98  3.000
 HDY  N16   C11  C12   120.82  3.000
 HDY  N16   C11  C7    116.72  3.000
 HDY  C12   C11  C7    122.43  3.000
 HDY  H12   C12  C13   120.73  3.000
 HDY  H12   C12  C11   122.98  3.000
 HDY  C13   C12  C11   116.23  3.000
 HDY  H13   C13  N14   116.25  3.000
 HDY  H13   C13  C12   120.23  3.000
 HDY  N14   C13  C12   123.52  3.000
 HDY  C15   N14  C13   115.81  3.000
 HDY  C15   N16  C11   117.86  3.000
 HDY  N17   C15  N16   114.06  3.000
 HDY  N17   C15  N14   120.22  3.000
 HDY  N16   C15  N14   125.72  3.000
 HDY  H17   N17  C18   115.18  3.000
 HDY  H17   N17  C15   113.06  3.000
 HDY  C18   N17  C15   131.76  3.000
 HDY  C23   C18  C19   117.90  3.000
 HDY  C23   C18  N17   125.72  3.000
 HDY  C19   C18  N17   116.38  3.000
 HDY  H19   C19  C20   118.85  3.000
 HDY  H19   C19  C18   119.71  3.000
 HDY  C20   C19  C18   121.43  3.000
 HDY  H20   C20  C21   119.79  3.000
 HDY  H20   C20  C19   119.70  3.000
 HDY  C21   C20  C19   120.51  3.000
 HDY  H23   C23  C22   118.83  3.000
 HDY  H23   C23  C18   120.47  3.000
 HDY  C22   C23  C18   120.70  3.000
 HDY  H22   C22  C21   121.45  3.000
 HDY  H22   C22  C23   117.58  3.000
 HDY  C21   C22  C23   120.97  3.000
 HDY  O24   C21  C22   124.97  3.000
 HDY  O24   C21  C20   116.53  3.000
 HDY  C22   C21  C20   118.50  3.000
 HDY  C25   O24  C21   118.55  3.000
 HDY  H252  C25  H251  107.80  3.000
 HDY  H252  C25  C26   109.74  3.000
 HDY  H251  C25  C26   109.46  3.000
 HDY  H252  C25  O24   110.88  3.000
 HDY  H251  C25  O24   110.61  3.000
 HDY  C26   C25  O24   108.33  3.000
 HDY  H26   C26  C27   109.03  3.000
 HDY  H26   C26  O31   110.66  3.000
 HDY  C27   C26  O31   109.55  3.000
 HDY  H26   C26  C25   107.93  3.000
 HDY  C27   C26  C25   109.71  3.000
 HDY  O31   C26  C25   109.93  3.000
 HDY  H31   O31  C26   104.35  3.000
 HDY  H272  C27  H271  107.10  3.000
 HDY  H272  C27  N28   107.89  3.000
 HDY  H271  C27  N28   112.83  3.000
 HDY  H272  C27  C26   108.84  3.000
 HDY  H271  C27  C26   110.25  3.000
 HDY  N28   C27  C26   109.80  3.000
 HDY  C29   N28  C30   111.16  3.000
 HDY  C29   N28  C27   112.45  3.000
 HDY  C30   N28  C27   112.51  3.000
 HDY  H303  C30  H302  107.94  3.000
 HDY  H303  C30  H301  107.76  3.000
 HDY  H302  C30  H301  107.97  3.000
 HDY  H303  C30  N28   113.15  3.000
 HDY  H302  C30  N28   110.07  3.000
 HDY  H301  C30  N28   109.80  3.000
 HDY  H293  C29  H292  108.08  3.000
 HDY  H293  C29  H291  107.86  3.000
 HDY  H292  C29  H291  107.41  3.000
 HDY  H293  C29  N28   112.52  3.000
 HDY  H292  C29  N28   109.81  3.000
 HDY  H291  C29  N28   110.99  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
 HDY  CONST_01  C4    C5   N8   C9    180.00   0.0  0
 HDY  CONST_02  N6    C5   N8   C9      0.00   0.0  0
 HDY  CONST_03  C5    N6   C7   C9      0.00   0.0  0
 HDY  CONST_04  C1    N6   C7   C9    180.00   0.0  0
 HDY  CONST_07  N6    C7   C9   N8      0.00   0.0  0
 HDY  CONST_08  C11   C7   C9   N8    180.00   0.0  0
 HDY  CONST_09  C3    C4   C5   N8    180.00   0.0  0
 HDY  CONST_10  C1    N6   C5   N8    180.00   0.0  0
 HDY  CONST_11  C7    N6   C5   N8      0.00   0.0  0
 HDY  CONST_12  C7    C9   N8   C5      0.00   0.0  0
 HDY  CONST_13  C2    C3   C4   C5      0.00   0.0  0
 HDY  CONST_14  C2    C1   N6   C5      0.00   0.0  0
 HDY  CONST_15  C11   C7   N6   C5    180.00   0.0  0
 HDY  CONST_16  C1    N6   C5   C4      0.00   0.0  0
 HDY  CONST_17  C7    N6   C5   C4    180.00   0.0  0
 HDY  CONST_18  C1    C2   C3   C4      0.00   0.0  0
 HDY  CONST_19  N6    C5   C4   C3      0.00   0.0  0
 HDY  CONST_20  N6    C1   C2   C3      0.00   0.0  0
 HDY  CONST_21  C7    N6   C1   C2    180.00   0.0  0
 HDY  CONST_24  C11   C7   N6   C1      0.00   0.0  0
 HDY  CONST_25  C13   C12  C11  C7    180.00   0.0  0
 HDY  CONST_26  C15   N16  C11  C7    180.00   0.0  0
 HDY  CONST_27  N14   C13  C12  C11     0.00   0.0  0
 HDY  CONST_28  N14   C15  N16  C11     0.00   0.0  0
 HDY  CONST_29  C15   N16  C11  C12     0.00   0.0  0
 HDY  CONST_30  C15   N14  C13  C12     0.00   0.0  0
 HDY  CONST_31  N16   C11  C12  C13     0.00   0.0  0
 HDY  CONST_32  N16   C15  N14  C13     0.00   0.0  0
 HDY  CONST_33  C21   C20  C19  C18     0.00   0.0  0
 HDY  CONST_34  C21   C22  C23  C18     0.00   0.0  0
 HDY  CONST_35  C22   C23  C18  C19     0.00   0.0  0
 HDY  CONST_36  C22   C21  C20  C19     0.00   0.0  0
 HDY  CONST_37  C23   C18  C19  C20     0.00   0.0  0
 HDY  CONST_38  C23   C22  C21  C20     0.00   0.0  0
 HDY  CONST_39  C5    N8   C9   C10   180.00   0.0  0
 HDY  CONST_40  N6    C7   C9   C10   180.00   0.0  0
 HDY  CONST_41  C11   C7   C9   C10     0.00   0.0  0
 HDY  CONST_42  N17   C15  N16  C11   180.00   0.0  0
 HDY  CONST_43  N17   C15  N14  C13   180.00   0.0  0
 HDY  CONST_44  C20   C19  C18  N17   180.00   0.0  0
 HDY  CONST_45  C22   C23  C18  N17   180.00   0.0  0
 HDY  CONST_46  O24   C21  C20  C19   180.00   0.0  0
 HDY  CONST_47  O24   C21  C22  C23   180.00   0.0  0
 HDY  CONST_48  H4    C4   C5   N8      0.00   0.0  0
 HDY  CONST_49  H3    C3   C4   C5    180.00   0.0  0
 HDY  CONST_50  H1    C1   N6   C5    180.00   0.0  0
 HDY  CONST_51  H2    C2   C3   C4    180.00   0.0  0
 HDY  CONST_52  H12   C12  C11  C7      0.00   0.0  0
 HDY  CONST_53  H13   C13  C12  C11   180.00   0.0  0
 HDY  CONST_54  H20   C20  C19  C18   180.00   0.0  0
 HDY  CONST_55  H22   C22  C23  C18   180.00   0.0  0
 HDY  CONST_56  H23   C23  C18  C19   180.00   0.0  0
 HDY  CONST_57  H19   C19  C18  C23   180.00   0.0  0
 HDY  Var_01    C18   N17  C15  N14    -0.49  30.0  2
 HDY  Var_02    C19   C18  N17  C15  -178.58  30.0  2
 HDY  Var_03    H101  C10  C9   N8     77.18  30.0  2
 HDY  Var_04    C26   C25  O24  C21  -179.66  30.0  3
 HDY  Var_05    C30   N28  C27  C26   156.82  30.0  3
 HDY  Var_06    H301  C30  N28  C27  -173.16  30.0  3
 HDY  Var_07    H291  C29  N28  C27    58.69  30.0  3

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
 HDY  chir_01  C26  C25  O31  C27  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
 HDY  plan-1  C7   0.020
 HDY  plan-1  C11  0.020
 HDY  plan-1  C12  0.020
 HDY  plan-1  C13  0.020
 HDY  plan-1  N14  0.020
 HDY  plan-1  N16  0.020
 HDY  plan-1  C15  0.020
 HDY  plan-1  N17  0.020
 HDY  plan-1  H12  0.020
 HDY  plan-1  H13  0.020
 HDY  plan-2  N17  0.020
 HDY  plan-2  C18  0.020
 HDY  plan-2  C19  0.020
 HDY  plan-2  C20  0.020
 HDY  plan-2  C23  0.020
 HDY  plan-2  C22  0.020
 HDY  plan-2  C21  0.020
 HDY  plan-2  O24  0.020
 HDY  plan-2  H19  0.020
 HDY  plan-2  H20  0.020
 HDY  plan-2  H23  0.020
 HDY  plan-2  H22  0.020
 HDY  plan-3  C10  0.020
 HDY  plan-3  C9   0.020
 HDY  plan-3  N8   0.020
 HDY  plan-3  C5   0.020
 HDY  plan-3  C4   0.020
 HDY  plan-3  C3   0.020
 HDY  plan-3  C2   0.020
 HDY  plan-3  N6   0.020
 HDY  plan-3  C1   0.020
 HDY  plan-3  C7   0.020
 HDY  plan-3  C11  0.020
 HDY  plan-3  H4   0.020
 HDY  plan-3  H3   0.020
 HDY  plan-3  H2   0.020
 HDY  plan-3  H1   0.020

