# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 23:22:29 2020
#   Inital geometry file: a 144 line input string
#   Ligand name: 2-{4-[4-({4-[2-methyl-1-(1-methylethyl)-1H-imidazol-5-yl]pyrimidin-2-yl}amino)phenyl]piperazin-1-yl}-2-oxoethanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)n1c(C)ncc1c2ccnc(Nc3ccc(cc3)N4CCN(CC4)C(=O)CO)n2
#
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
 IM9  IM9  2-{4-[4-({4-[2-methyl-1-(1-methylethyl)-1H-imidazol-5-yl]pyrimidin-2-yl}amino)phenyl]piperazin-1-yl}-2-oxoethanol  ligand  61  32  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_IM9
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
 IM9  C1    C  CH3   0  -0.645   0.3715  28.4506  11.8867
 IM9  C2    C  CH1   0  -0.147  -0.0542  28.0250  10.4877
 IM9  C3    C  CH3   0  -0.674  -0.0744  26.5139  10.3044
 IM9  N4    N  NR5   0  -0.495  -1.3261  28.6570  10.1020
 IM9  C5    C  CR5   0   0.438  -2.5512  28.4137  10.6307
 IM9  C6    C  CH3   0  -0.768  -2.8929  27.3124  11.5708
 IM9  N7    N  N     0  -0.453  -3.4474  29.2737  10.1925
 IM9  C8    C  CR15  0  -0.235  -2.7842  30.1152   9.3689
 IM9  C9    C  CR5   0   0.262  -1.4601  29.7659   9.2864
 IM9  C10   C  CR6   0   0.285  -0.4481  30.3949   8.4502
 IM9  C11   C  CR16  0  -0.404  -0.5695  31.7437   8.1179
 IM9  C12   C  CR16  0  -0.019   0.3939  32.2539   7.2664
 IM9  N13   N  N     0  -0.466   1.4017  31.5383   6.7974
 IM9  C14   C  CR6   0   0.592   1.4436  30.2602   7.1913
 IM9  N15   N  NH1   0  -0.771   2.5046  29.5586   6.7149
 IM9  C16   C  CR6   0   0.338   2.9126  28.2454   6.9513
 IM9  C17   C  CR16  0  -0.293   2.0938  27.2236   7.4212
 IM9  C18   C  CR16  0  -0.341   2.5963  25.9393   7.5979
 IM9  C19   C  CR6   0   0.337   3.9248  25.6236   7.3200
 IM9  C20   C  CR16  0  -0.305   4.7393  26.6574   6.8426
 IM9  C21   C  CR16  0  -0.335   4.2453  27.9321   6.6601
 IM9  N22   N  NT    0  -0.520   4.4699  24.3461   7.5221
 IM9  C23   C  CH2   0  -0.299   3.6716  23.4012   8.2740
 IM9  C24   C  CH2   0  -0.327   4.5282  22.2213   8.7018
 IM9  N25   N  NT    0  -0.450   5.1545  21.6055   7.5477
 IM9  C26   C  CH2   0  -0.316   5.9389  22.5405   6.7625
 IM9  C27   C  CH2   0  -0.302   5.0833  23.7259   6.3546
 IM9  C28   C  C     0   0.492   4.9848  20.3315   7.1722
 IM9  O29   O  O     0  -0.510   5.5063  19.8422   6.1747
 IM9  C30   C  CH2   0  -0.250   4.0995  19.4336   8.0330
 IM9  O31   O  OH1   0  -0.670   4.0664  18.1442   7.5020
 IM9  N32   N  N     0  -0.507   0.5572  29.6607   7.9775
 IM9  H1C1  H  HCH3  0   0.243   1.3767  28.0782  12.0838
 IM9  H1C2  H  HCH3  0   0.242   0.3944  29.5368  11.9757
 IM9  H1C3  H  HCH3  0   0.228  -0.2820  28.0571  12.6650
 IM9  H2    H  HCH1  0   0.290   0.6765  28.4173   9.7869
 IM9  H3C1  H  HCH3  0   0.243  -0.4327  26.2389   9.3119
 IM9  H3C2  H  HCH3  0   0.245   0.9439  26.1388  10.4074
 IM9  H3C3  H  HCH3  0   0.244  -0.6866  26.0013  11.0442
 IM9  H6C1  H  HCH3  0   0.263  -2.9098  26.3446  11.0687
 IM9  H6C2  H  HCH3  0   0.256  -2.2035  27.2357  12.4097
 IM9  H6C3  H  HCH3  0   0.272  -3.8880  27.4972  11.9685
 IM9  H8    H  HCR5  0   0.264  -3.2846  30.9140   8.8419
 IM9  H11   H  HCR6  0   0.271  -1.3590  32.3671   8.5094
 IM9  H12   H  HCR6  0   0.275   0.3549  33.2931   6.9585
 IM9  H15   H  HNH1  0   0.406   3.1470  30.1226   6.1796
 IM9  H17   H  HCR6  0   0.277   1.0560  27.4115   7.6419
 IM9  H21   H  HCR6  0   0.266   4.9119  28.7077   6.2998
 IM9  H18   H  HCR6  0   0.263   1.9107  25.1799   7.9504
 IM9  H20   H  HCR6  0   0.263   5.7852  26.4720   6.6327
 IM9  H231  H  HCH2  0   0.260   3.2870  23.8846   9.1734
 IM9  H232  H  HCH2  0   0.220   2.8075  23.0323   7.6996
 IM9  H271  H  HCH2  0   0.224   4.3175  23.3933   5.6381
 IM9  H272  H  HCH2  0   0.264   5.7178  24.4446   5.8387
 IM9  H241  H  HCH2  0   0.258   5.3083  22.5659   9.3861
 IM9  H242  H  HCH2  0   0.280   3.9114  21.5106   9.2446
 IM9  H261  H  HCH2  0   0.252   6.7883  22.8829   7.3612
 IM9  H262  H  HCH2  0   0.273   6.3279  22.0443   5.8780
 IM9  H301  H  HCH2  0   0.241   4.4855  19.4182   9.0593
 IM9  H302  H  HCH2  0   0.236   3.0905  19.8630   8.0794
 IM9  H31   H  HOH1  0   0.443   4.5998  18.1732   6.6931

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
 IM9  C1   C2    single    1.523  0.020  1.523
 IM9  C2   C3    single    1.522  0.020  1.522
 IM9  C2   N4    single    1.472  0.020  1.472
 IM9  N4   C5    aromatic  1.356  0.020  1.356
 IM9  N4   C9    aromatic  1.383  0.020  1.383
 IM9  C5   C6    single    1.488  0.020  1.488
 IM9  C5   N7    aromatic  1.317  0.020  1.317
 IM9  N7   C8    aromatic  1.351  0.020  1.351
 IM9  C8   C9    aromatic  1.372  0.020  1.372
 IM9  C9   C10   single    1.456  0.020  1.456
 IM9  C10  C11   aromatic  1.394  0.020  1.394
 IM9  C10  N32   aromatic  1.332  0.020  1.332
 IM9  C11  C12   aromatic  1.383  0.020  1.383
 IM9  C12  N13   aromatic  1.322  0.020  1.322
 IM9  N13  C14   aromatic  1.338  0.020  1.338
 IM9  C14  N15   single    1.358  0.020  1.358
 IM9  C14  N32   aromatic  1.328  0.020  1.328
 IM9  N15  C16   single    1.395  0.020  1.395
 IM9  C16  C17   aromatic  1.391  0.020  1.391
 IM9  C16  C21   aromatic  1.400  0.020  1.400
 IM9  C17  C18   aromatic  1.390  0.020  1.390
 IM9  C18  C19   aromatic  1.393  0.020  1.393
 IM9  C19  C20   aromatic  1.400  0.020  1.400
 IM9  C19  N22   single    1.404  0.020  1.404
 IM9  C20  C21   aromatic  1.379  0.020  1.379
 IM9  N22  C23   single    1.448  0.020  1.448
 IM9  N22  C27   single    1.457  0.020  1.457
 IM9  C23  C24   single    1.519  0.020  1.519
 IM9  C24  N25   single    1.450  0.020  1.450
 IM9  N25  C26   single    1.451  0.020  1.451
 IM9  N25  C28   single    1.339  0.020  1.339
 IM9  C26  C27   single    1.518  0.020  1.518
 IM9  C28  O29   double    1.227  0.020  1.227
 IM9  C28  C30   single    1.527  0.020  1.527
 IM9  C30  O31   single    1.395  0.020  1.395
 IM9  C1   H1C1  single    0.970  0.020  1.090
 IM9  C1   H1C2  single    0.970  0.020  1.090
 IM9  C1   H1C3  single    0.970  0.020  1.090
 IM9  C2   H2    single    0.970  0.020  1.090
 IM9  C3   H3C1  single    0.970  0.020  1.090
 IM9  C3   H3C2  single    0.970  0.020  1.090
 IM9  C3   H3C3  single    0.970  0.020  1.090
 IM9  C6   H6C1  single    0.970  0.020  1.090
 IM9  C6   H6C2  single    0.970  0.020  1.090
 IM9  C6   H6C3  single    0.970  0.020  1.090
 IM9  C8   H8    single    0.930  0.020  1.080
 IM9  C11  H11   single    0.930  0.020  1.080
 IM9  C12  H12   single    0.930  0.020  1.080
 IM9  N15  H15   single    0.860  0.020  1.020
 IM9  C17  H17   single    0.930  0.020  1.080
 IM9  C21  H21   single    0.930  0.020  1.080
 IM9  C18  H18   single    0.930  0.020  1.080
 IM9  C20  H20   single    0.930  0.020  1.080
 IM9  C23  H231  single    0.970  0.020  1.090
 IM9  C23  H232  single    0.970  0.020  1.090
 IM9  C27  H271  single    0.970  0.020  1.090
 IM9  C27  H272  single    0.970  0.020  1.090
 IM9  C24  H241  single    0.970  0.020  1.090
 IM9  C24  H242  single    0.970  0.020  1.090
 IM9  C26  H261  single    0.970  0.020  1.090
 IM9  C26  H262  single    0.970  0.020  1.090
 IM9  C30  H301  single    0.970  0.020  1.090
 IM9  C30  H302  single    0.970  0.020  1.090
 IM9  O31  H31   single    0.850  0.020  0.980

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
 IM9  H1C3  C1   H1C2  108.30  3.000
 IM9  H1C3  C1   H1C1  107.49  3.000
 IM9  H1C2  C1   H1C1  107.83  3.000
 IM9  H1C3  C1   C2    112.80  3.000
 IM9  H1C2  C1   C2    111.06  3.000
 IM9  H1C1  C1   C2    109.18  3.000
 IM9  H2    C2   N4    104.91  3.000
 IM9  H2    C2   C3    106.85  3.000
 IM9  N4    C2   C3    112.54  3.000
 IM9  H2    C2   C1    107.68  3.000
 IM9  N4    C2   C1    111.24  3.000
 IM9  C3    C2   C1    113.06  3.000
 IM9  H3C3  C3   H3C2  107.41  3.000
 IM9  H3C3  C3   H3C1  108.36  3.000
 IM9  H3C2  C3   H3C1  107.83  3.000
 IM9  H3C3  C3   C2    113.14  3.000
 IM9  H3C2  C3   C2    108.53  3.000
 IM9  H3C1  C3   C2    111.36  3.000
 IM9  C9    N4   C5    106.63  3.000
 IM9  C9    N4   C2    125.63  3.000
 IM9  C5    N4   C2    126.97  3.000
 IM9  N7    C5   C6    122.50  3.000
 IM9  N7    C5   N4    111.58  3.000
 IM9  C6    C5   N4    125.92  3.000
 IM9  H6C3  C6   H6C2  108.03  3.000
 IM9  H6C3  C6   H6C1  107.76  3.000
 IM9  H6C2  C6   H6C1  107.58  3.000
 IM9  H6C3  C6   C5    108.39  3.000
 IM9  H6C2  C6   C5    113.19  3.000
 IM9  H6C1  C6   C5    111.69  3.000
 IM9  C8    N7   C5    105.98  3.000
 IM9  H8    C8   C9    127.32  3.000
 IM9  H8    C8   N7    122.04  3.000
 IM9  C9    C8   N7    110.60  3.000
 IM9  C10   C9   C8    126.55  3.000
 IM9  C10   C9   N4    128.16  3.000
 IM9  C8    C9   N4    105.20  3.000
 IM9  N32   C10  C11   120.97  3.000
 IM9  N32   C10  C9    119.38  3.000
 IM9  C11   C10  C9    119.62  3.000
 IM9  H11   C11  C12   121.31  3.000
 IM9  H11   C11  C10   122.41  3.000
 IM9  C12   C11  C10   116.28  3.000
 IM9  H12   C12  N13   116.44  3.000
 IM9  H12   C12  C11   120.20  3.000
 IM9  N13   C12  C11   123.35  3.000
 IM9  C14   N13  C12   115.88  3.000
 IM9  N32   C14  N15   119.73  3.000
 IM9  N32   C14  N13   125.77  3.000
 IM9  N15   C14  N13   114.50  3.000
 IM9  H15   N15  C16   115.47  3.000
 IM9  H15   N15  C14   113.25  3.000
 IM9  C16   N15  C14   130.93  3.000
 IM9  C21   C16  C17   117.79  3.000
 IM9  C21   C16  N15   116.99  3.000
 IM9  C17   C16  N15   125.20  3.000
 IM9  H17   C17  C18   118.89  3.000
 IM9  H17   C17  C16   120.53  3.000
 IM9  C18   C17  C16   120.58  3.000
 IM9  H18   C18  C19   120.66  3.000
 IM9  H18   C18  C17   117.43  3.000
 IM9  C19   C18  C17   121.91  3.000
 IM9  N22   C19  C20   119.69  3.000
 IM9  N22   C19  C18   123.21  3.000
 IM9  C20   C19  C18   117.09  3.000
 IM9  H20   C20  C21   118.59  3.000
 IM9  H20   C20  C19   120.10  3.000
 IM9  C21   C20  C19   121.28  3.000
 IM9  H21   C21  C20   119.01  3.000
 IM9  H21   C21  C16   119.63  3.000
 IM9  C20   C21  C16   121.36  3.000
 IM9  C27   N22  C23   111.74  3.000
 IM9  C27   N22  C19   115.82  3.000
 IM9  C23   N22  C19   117.05  3.000
 IM9  H232  C23  H231  107.56  3.000
 IM9  H232  C23  C24   109.22  3.000
 IM9  H231  C23  C24   108.10  3.000
 IM9  H232  C23  N22   112.36  3.000
 IM9  H231  C23  N22   109.47  3.000
 IM9  C24   C23  N22   110.01  3.000
 IM9  H242  C24  H241  107.37  3.000
 IM9  H242  C24  N25   111.40  3.000
 IM9  H241  C24  N25   108.89  3.000
 IM9  H242  C24  C23   109.18  3.000
 IM9  H241  C24  C23   109.49  3.000
 IM9  N25   C24  C23   110.44  3.000
 IM9  C28   N25  C26   121.99  3.000
 IM9  C28   N25  C24   124.93  3.000
 IM9  C26   N25  C24   112.98  3.000
 IM9  H262  C26  H261  108.09  3.000
 IM9  H262  C26  C27   109.86  3.000
 IM9  H261  C26  C27   109.90  3.000
 IM9  H262  C26  N25   109.86  3.000
 IM9  H261  C26  N25   108.98  3.000
 IM9  C27   C26  N25   110.12  3.000
 IM9  H272  C27  H271  107.26  3.000
 IM9  H272  C27  C26   108.32  3.000
 IM9  H271  C27  C26   109.35  3.000
 IM9  H272  C27  N22   110.12  3.000
 IM9  H271  C27  N22   110.94  3.000
 IM9  C26   C27  N22   110.75  3.000
 IM9  C30   C28  O29   118.04  3.000
 IM9  C30   C28  N25   118.35  3.000
 IM9  O29   C28  N25   123.60  3.000
 IM9  H302  C30  H301  106.83  3.000
 IM9  H302  C30  O31   110.85  3.000
 IM9  H301  C30  O31   110.59  3.000
 IM9  H302  C30  C28   109.08  3.000
 IM9  H301  C30  C28   109.38  3.000
 IM9  O31   C30  C28   110.05  3.000
 IM9  H31   O31  C30   106.08  3.000
 IM9  C14   N32  C10   117.72  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
 IM9  CONST_01  C8    N7   C5   N4      0.00   0.0  0
 IM9  CONST_02  N7    C8   C9   N4      0.00   0.0  0
 IM9  CONST_05  C8    C9   N4   C5      0.00   0.0  0
 IM9  CONST_06  C10   C9   N4   C5    180.00   0.0  0
 IM9  CONST_07  C9    C8   N7   C5      0.00   0.0  0
 IM9  CONST_08  C9    N4   C5   N7      0.00   0.0  0
 IM9  CONST_09  C10   C9   C8   N7    180.00   0.0  0
 IM9  CONST_12  C12   C11  C10  C9    180.00   0.0  0
 IM9  CONST_13  C14   N32  C10  C9    180.00   0.0  0
 IM9  CONST_14  N13   C12  C11  C10     0.00   0.0  0
 IM9  CONST_15  N13   C14  N32  C10     0.00   0.0  0
 IM9  CONST_16  C14   N32  C10  C11     0.00   0.0  0
 IM9  CONST_17  C14   N13  C12  C11     0.00   0.0  0
 IM9  CONST_18  N32   C10  C11  C12     0.00   0.0  0
 IM9  CONST_19  N32   C14  N13  C12     0.00   0.0  0
 IM9  CONST_20  C19   C18  C17  C16     0.00   0.0  0
 IM9  CONST_21  C19   C20  C21  C16     0.00   0.0  0
 IM9  CONST_22  C20   C21  C16  C17     0.00   0.0  0
 IM9  CONST_23  C20   C19  C18  C17     0.00   0.0  0
 IM9  CONST_24  C21   C16  C17  C18     0.00   0.0  0
 IM9  CONST_25  C21   C20  C19  C18     0.00   0.0  0
 IM9  CONST_26  N22   C19  C18  C17   180.00   0.0  0
 IM9  CONST_27  N22   C19  C20  C21   180.00   0.0  0
 IM9  CONST_28  N7    C5   N4   C2    180.00   0.0  0
 IM9  CONST_29  C8    C9   N4   C2    180.00   0.0  0
 IM9  CONST_30  C10   C9   N4   C2      0.00   0.0  0
 IM9  CONST_31  C9    N4   C5   C6    180.00   0.0  0
 IM9  CONST_32  C8    N7   C5   C6    180.00   0.0  0
 IM9  CONST_33  N15   C14  N32  C10   180.00   0.0  0
 IM9  CONST_34  N15   C14  N13  C12   180.00   0.0  0
 IM9  CONST_35  C18   C17  C16  N15   180.00   0.0  0
 IM9  CONST_36  C20   C21  C16  N15   180.00   0.0  0
 IM9  CONST_37  H8    C8   C9   N4    180.00   0.0  0
 IM9  CONST_38  H11   C11  C10  C9      0.00   0.0  0
 IM9  CONST_39  H12   C12  C11  C10   180.00   0.0  0
 IM9  CONST_40  H18   C18  C17  C16   180.00   0.0  0
 IM9  CONST_41  H20   C20  C21  C16   180.00   0.0  0
 IM9  CONST_42  H21   C21  C16  C17   180.00   0.0  0
 IM9  CONST_43  H17   C17  C18  C19   180.00   0.0  0
 IM9  CONST_44  O29   C28  N25  C24   180.00   0.0  0
 IM9  CONST_45  C30   C28  N25  C24     0.00   0.0  0
 IM9  CONST_46  O29   C28  N25  C26     0.00   0.0  0
 IM9  CONST_47  C30   C28  N25  C26   180.00   0.0  0
 IM9  Var_01    C23   N22  C19  C18   -11.36  30.0  2
 IM9  Var_02    C24   C23  N22  C19  -165.61  30.0  1
 IM9  Var_03    C26   C27  N22  C19   165.29  30.0  1
 IM9  Var_04    N25   C24  C23  N22   -55.89  30.0  1
 IM9  Var_05    N25   C26  C27  N22    54.61  30.0  1
 IM9  Var_06    C26   N25  C24  C23    55.86  30.0  1
 IM9  Var_07    C27   C26  N25  C24   -55.03  30.0  1
 IM9  Var_08    C16   N15  C14  N13   176.72  30.0  2
 IM9  Var_09    C17   C16  N15  C14    20.98  30.0  2
 IM9  Var_10    C5    N4   C2   C1    -68.47  30.0  2
 IM9  Var_11    H6C1  C6   C5   N4    -72.76  30.0  2
 IM9  Var_12    O31   C30  C28  N25  -178.75  30.0  3
 IM9  Var_13    H1C1  C1   C2   N4   -172.18  30.0  3
 IM9  Var_14    H3C1  C3   C2   N4     49.92  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
 IM9  plan-1  C2   0.020
 IM9  plan-1  N4   0.020
 IM9  plan-1  C5   0.020
 IM9  plan-1  C6   0.020
 IM9  plan-1  N7   0.020
 IM9  plan-1  C8   0.020
 IM9  plan-1  C9   0.020
 IM9  plan-1  C10  0.020
 IM9  plan-1  H8   0.020
 IM9  plan-2  C9   0.020
 IM9  plan-2  C10  0.020
 IM9  plan-2  C11  0.020
 IM9  plan-2  C12  0.020
 IM9  plan-2  N13  0.020
 IM9  plan-2  C14  0.020
 IM9  plan-2  N15  0.020
 IM9  plan-2  N32  0.020
 IM9  plan-2  H11  0.020
 IM9  plan-2  H12  0.020
 IM9  plan-3  N15  0.020
 IM9  plan-3  C16  0.020
 IM9  plan-3  C17  0.020
 IM9  plan-3  C18  0.020
 IM9  plan-3  C19  0.020
 IM9  plan-3  C20  0.020
 IM9  plan-3  C21  0.020
 IM9  plan-3  N22  0.020
 IM9  plan-3  H17  0.020
 IM9  plan-3  H21  0.020
 IM9  plan-3  H18  0.020
 IM9  plan-3  H20  0.020
 IM9  plan-4  C24  0.020
 IM9  plan-4  N25  0.020
 IM9  plan-4  C26  0.020
 IM9  plan-4  C28  0.020
 IM9  plan-4  O29  0.020
 IM9  plan-4  C30  0.020

