# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 18:17:04 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: 4-amino-N-[(1S)-1-(4-chlorophenyl)-3-hydroxypropyl]-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidine-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1(CCN(CC1)c2ncnc3[nH]ccc23)C(=O)N[C@@H](CCO)c4ccc(Cl)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
 0XZ  0XZ  4-amino-N-[(1S)-1-(4-chlorophenyl)-3-hydroxypropyl]-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidine-4-carboxamide  ligand  55  30  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_0XZ
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
 0XZ  CL3  CL  CL    0  -0.133  -5.1973  -4.0043   1.3438
 0XZ  C27  C   CR6   0  -0.057  -4.5212  -2.4212   1.1278
 0XZ  C26  C   CR16  0  -0.196  -4.4804  -1.5443   2.1996
 0XZ  C25  C   CR16  0  -0.320  -3.9338  -0.2823   2.0145
 0XZ  C28  C   CR16  0  -0.197  -4.0275  -2.0551  -0.1151
 0XZ  C29  C   CR16  0  -0.312  -3.4879  -0.7885  -0.2800
 0XZ  C24  C   CR6   0   0.178  -3.4342   0.1114   0.7794
 0XZ  C20  C   CH1   0  -0.152  -2.8957   1.5120   0.5889
 0XZ  C21  C   CH2   0  -0.484  -3.9546   2.4119  -0.0480
 0XZ  C22  C   CH2   0  -0.135  -3.5290   3.8688  -0.1156
 0XZ  O23  O   OH1   0  -0.671  -4.6079   4.6176  -0.6296
 0XZ  N19  N   NH1   0  -0.648  -1.6930   1.5276  -0.2162
 0XZ  C17  C   C     0   0.584  -0.5119   1.0815   0.2370
 0XZ  O18  O   O     0  -0.491  -0.3655   0.6649   1.3777
 0XZ  C13  C   CT    0  -0.045   0.6654   1.1307  -0.7584
 0XZ  C12  C   CH2   0  -0.429   1.7681   2.0079  -0.1357
 0XZ  C11  C   CH2   0  -0.319   3.0864   1.8930  -0.8942
 0XZ  N16  N   NH2   0  -0.807   0.3596   1.6584  -2.0709
 0XZ  C14  C   CH2   0  -0.428   1.1876  -0.3085  -0.9330
 0XZ  C15  C   CH2   0  -0.336   2.5214  -0.3067  -1.6662
 0XZ  N10  N   NT    0  -0.469   3.4937   0.4983  -0.9583
 0XZ  C3   C   CR6   0   0.499   4.4210  -0.0038  -0.1123
 0XZ  N5   N   N     0  -0.494   5.2581   0.8764   0.4510
 0XZ  C6   C   CR16  0   0.037   6.2347   0.4543   1.2424
 0XZ  N4   N   N     0  -0.455   6.5198  -0.7838   1.5853
 0XZ  C1   C   CR56  0  -0.084   4.5836  -1.3802   0.2003
 0XZ  C9   C   CR15  0  -0.449   3.9369  -2.6376  -0.0500
 0XZ  C8   C   CR15  0  -0.014   4.6435  -3.5864   0.6251
 0XZ  N7   N   NR15  0  -0.656   5.6885  -2.9956   1.2823
 0XZ  C2   C   CR56  0   0.468   5.6679  -1.6635   1.0532
 0XZ  H1   H   HCR6  0   0.279  -4.8611  -1.8390   3.1681
 0XZ  H2   H   HCR6  0   0.261  -3.8969   0.4024   2.8535
 0XZ  H3   H   HCR6  0   0.279  -4.0620  -2.7463  -0.9463
 0XZ  H4   H   HCR6  0   0.254  -3.1016  -0.5087  -1.2526
 0XZ  H5   H   HCH1  0   0.264  -2.6503   1.9176   1.5753
 0XZ  H6   H   HCH2  0   0.242  -4.2001   2.0411  -1.0489
 0XZ  H7   H   HCH2  0   0.259  -4.8646   2.3351   0.5514
 0XZ  H8   H   HCH2  0   0.197  -3.2451   4.2051   0.8907
 0XZ  H9   H   HCH2  0   0.192  -2.6384   3.9762  -0.7469
 0XZ  H10  H   HOH1  0   0.455  -4.3323   5.5366  -0.6904
 0XZ  H11  H   HNH1  0   0.386  -1.7631   1.8060  -1.1809
 0XZ  H12  H   HCH2  0   0.249   1.4438   3.0531  -0.1260
 0XZ  H13  H   HCH2  0   0.246   1.9274   1.7115   0.9025
 0XZ  H14  H   HCH2  0   0.243   2.9724   2.2673  -1.9136
 0XZ  H15  H   HCH2  0   0.272   3.8578   2.4799  -0.4062
 0XZ  H16  H   HNH2  0   0.356  -0.2999   1.0952  -2.5912
 0XZ  H17  H   HNH2  0   0.355   0.0463   2.6195  -2.0545
 0XZ  H19  H   HCH2  0   0.249   1.3079  -0.7815   0.0434
 0XZ  H20  H   HCH2  0   0.248   0.4582  -0.9022  -1.4927
 0XZ  H21  H   HCH2  0   0.267   2.8941  -1.3118  -1.8280
 0XZ  H22  H   HCH2  0   0.263   2.3945   0.1302  -2.6586
 0XZ  H23  H   HCR6  0   0.242   6.8754   1.2298   1.6511
 0XZ  H24  H   HCR5  0   0.256   3.0570  -2.8457  -0.6334
 0XZ  H25  H   HCR5  0   0.287   4.4779  -4.6487   0.6932
 0XZ  H26  H   HNR5  0   0.412   6.3560  -3.4694   1.8693

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
 0XZ  N4   C2   aromatic  1.335  0.020  1.335
 0XZ  N4   C6   aromatic  1.316  0.020  1.316
 0XZ  N7   C2   aromatic  1.352  0.020  1.352
 0XZ  N7   C8   aromatic  1.369  0.020  1.369
 0XZ  C2   C1   aromatic  1.408  0.020  1.408
 0XZ  C6   N5   aromatic  1.326  0.020  1.326
 0XZ  C8   C9   aromatic  1.362  0.020  1.362
 0XZ  C1   C9   aromatic  1.436  0.020  1.436
 0XZ  C1   C3   aromatic  1.421  0.020  1.421
 0XZ  N5   C3   aromatic  1.339  0.020  1.339
 0XZ  C3   N10  single    1.352  0.020  1.352
 0XZ  N10  C11  single    1.454  0.020  1.454
 0XZ  N10  C15  single    1.447  0.020  1.447
 0XZ  C11  C12  single    1.525  0.020  1.525
 0XZ  CL3  C27  single    1.735  0.020  1.735
 0XZ  C15  C14  single    1.522  0.020  1.522
 0XZ  C27  C28  aromatic  1.387  0.020  1.387
 0XZ  C27  C26  aromatic  1.385  0.020  1.385
 0XZ  C12  C13  single    1.540  0.020  1.540
 0XZ  C14  C13  single    1.541  0.020  1.541
 0XZ  C28  C29  aromatic  1.387  0.020  1.387
 0XZ  C26  C25  aromatic  1.388  0.020  1.388
 0XZ  C13  C17  single    1.542  0.020  1.542
 0XZ  C13  N16  single    1.447  0.020  1.447
 0XZ  O18  C17  double    1.223  0.020  1.223
 0XZ  C29  C24  aromatic  1.391  0.020  1.391
 0XZ  C25  C24  aromatic  1.389  0.020  1.389
 0XZ  C17  N19  single    1.341  0.020  1.341
 0XZ  C24  C20  single    1.513  0.020  1.513
 0XZ  N19  C20  single    1.447  0.020  1.447
 0XZ  C20  C21  single    1.529  0.020  1.529
 0XZ  C21  C22  single    1.519  0.020  1.519
 0XZ  C22  O23  single    1.410  0.020  1.410
 0XZ  C26  H1   single    0.930  0.020  1.080
 0XZ  C25  H2   single    0.930  0.020  1.080
 0XZ  C28  H3   single    0.930  0.020  1.080
 0XZ  C29  H4   single    0.930  0.020  1.080
 0XZ  C20  H5   single    0.970  0.020  1.090
 0XZ  C21  H6   single    0.970  0.020  1.090
 0XZ  C21  H7   single    0.970  0.020  1.090
 0XZ  C22  H8   single    0.970  0.020  1.090
 0XZ  C22  H9   single    0.970  0.020  1.090
 0XZ  O23  H10  single    0.850  0.020  0.980
 0XZ  N19  H11  single    0.860  0.020  1.020
 0XZ  C12  H12  single    0.970  0.020  1.090
 0XZ  C12  H13  single    0.970  0.020  1.090
 0XZ  C11  H14  single    0.970  0.020  1.090
 0XZ  C11  H15  single    0.970  0.020  1.090
 0XZ  N16  H16  single    0.890  0.020  1.040
 0XZ  N16  H17  single    0.890  0.020  1.040
 0XZ  C14  H19  single    0.970  0.020  1.090
 0XZ  C14  H20  single    0.970  0.020  1.090
 0XZ  C15  H21  single    0.970  0.020  1.090
 0XZ  C15  H22  single    0.970  0.020  1.090
 0XZ  C6   H23  single    0.930  0.020  1.080
 0XZ  C9   H24  single    0.930  0.020  1.080
 0XZ  C8   H25  single    0.930  0.020  1.080
 0XZ  N7   H26  single    0.860  0.020  1.020

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
 0XZ  C28  C27  C26  121.05  3.000
 0XZ  C26  C27  CL3  119.52  3.000
 0XZ  C28  C27  CL3  119.42  3.000
 0XZ  H1   C26  C25  120.39  3.000
 0XZ  H1   C26  C27  120.65  3.000
 0XZ  C25  C26  C27  118.95  3.000
 0XZ  H2   C25  C24  119.81  3.000
 0XZ  H2   C25  C26  119.00  3.000
 0XZ  C24  C25  C26  121.19  3.000
 0XZ  H3   C28  C29  120.32  3.000
 0XZ  H3   C28  C27  120.58  3.000
 0XZ  C29  C28  C27  119.10  3.000
 0XZ  H4   C29  C24  120.20  3.000
 0XZ  H4   C29  C28  118.78  3.000
 0XZ  C24  C29  C28  121.02  3.000
 0XZ  C20  C24  C29  121.12  3.000
 0XZ  C20  C24  C25  120.16  3.000
 0XZ  C29  C24  C25  118.68  3.000
 0XZ  H5   C20  N19  108.12  3.000
 0XZ  H5   C20  C21  108.22  3.000
 0XZ  N19  C20  C21  109.73  3.000
 0XZ  H5   C20  C24  108.02  3.000
 0XZ  C21  C20  C24  110.55  3.000
 0XZ  N19  C20  C24  112.08  3.000
 0XZ  H7   C21  H6   106.91  3.000
 0XZ  H7   C21  C22  108.98  3.000
 0XZ  H6   C21  C22  110.28  3.000
 0XZ  H7   C21  C20  107.88  3.000
 0XZ  H6   C21  C20  109.68  3.000
 0XZ  C22  C21  C20  112.90  3.000
 0XZ  H9   C22  H8   106.70  3.000
 0XZ  H9   C22  O23  111.06  3.000
 0XZ  H8   C22  O23  111.66  3.000
 0XZ  H9   C22  C21  110.30  3.000
 0XZ  H8   C22  C21  108.98  3.000
 0XZ  O23  C22  C21  108.13  3.000
 0XZ  H10  O23  C22  108.14  3.000
 0XZ  H11  N19  C17  118.50  3.000
 0XZ  H11  N19  C20  118.57  3.000
 0XZ  C17  N19  C20  122.70  3.000
 0XZ  C13  C17  O18  121.42  3.000
 0XZ  O18  C17  N19  122.25  3.000
 0XZ  C13  C17  N19  116.33  3.000
 0XZ  C14  C13  N16  108.02  3.000
 0XZ  N16  C13  C12  108.07  3.000
 0XZ  C14  C13  C12  109.57  3.000
 0XZ  N16  C13  C17  115.82  3.000
 0XZ  C14  C13  C17  107.58  3.000
 0XZ  C12  C13  C17  107.68  3.000
 0XZ  H13  C12  H12  107.11  3.000
 0XZ  H13  C12  C11  109.05  3.000
 0XZ  H12  C12  C11  109.42  3.000
 0XZ  H13  C12  C13  109.54  3.000
 0XZ  H12  C12  C13  109.59  3.000
 0XZ  C11  C12  C13  112.01  3.000
 0XZ  H15  C11  H14  107.98  3.000
 0XZ  H15  C11  N10  109.84  3.000
 0XZ  H14  C11  N10  108.47  3.000
 0XZ  H15  C11  C12  110.49  3.000
 0XZ  H14  C11  C12  110.38  3.000
 0XZ  N10  C11  C12  109.65  3.000
 0XZ  H17  N16  H16  109.61  3.000
 0XZ  H17  N16  C13  113.42  3.000
 0XZ  H16  N16  C13  113.66  3.000
 0XZ  H20  C14  H19  107.20  3.000
 0XZ  H20  C14  C15  109.78  3.000
 0XZ  H19  C14  C15  109.56  3.000
 0XZ  H20  C14  C13  109.80  3.000
 0XZ  H19  C14  C13  109.92  3.000
 0XZ  C15  C14  C13  110.52  3.000
 0XZ  H22  C15  H21  105.98  3.000
 0XZ  H22  C15  N10  107.46  3.000
 0XZ  H21  C15  N10  110.96  3.000
 0XZ  H22  C15  C14  109.66  3.000
 0XZ  H21  C15  C14  111.85  3.000
 0XZ  N10  C15  C14  110.72  3.000
 0XZ  C3   N10  C15  124.08  3.000
 0XZ  C15  N10  C11  111.52  3.000
 0XZ  C3   N10  C11  121.38  3.000
 0XZ  C1   C3   N5   118.21  3.000
 0XZ  N5   C3   N10  116.61  3.000
 0XZ  C1   C3   N10  125.17  3.000
 0XZ  C6   N5   C3   120.15  3.000
 0XZ  H23  C6   N4   116.49  3.000
 0XZ  H23  C6   N5   115.59  3.000
 0XZ  N4   C6   N5   127.92  3.000
 0XZ  C2   N4   C6   112.20  3.000
 0XZ  C2   C1   C9   106.03  3.000
 0XZ  C9   C1   C3   139.33  3.000
 0XZ  C2   C1   C3   114.60  3.000
 0XZ  H24  C9   C8   123.94  3.000
 0XZ  H24  C9   C1   129.20  3.000
 0XZ  C8   C9   C1   106.86  3.000
 0XZ  H25  C8   N7   120.84  3.000
 0XZ  H25  C8   C9   129.68  3.000
 0XZ  N7   C8   C9   109.48  3.000
 0XZ  H26  N7   C2   124.92  3.000
 0XZ  H26  N7   C8   125.65  3.000
 0XZ  C2   N7   C8   109.41  3.000
 0XZ  N7   C2   C1   108.22  3.000
 0XZ  C1   C2   N4   126.87  3.000
 0XZ  N7   C2   N4   124.89  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
 0XZ  CONST_01  C24  C29  C28  C27     0.00   0.0  0
 0XZ  CONST_02  C24  C25  C26  C27     0.00   0.0  0
 0XZ  CONST_03  C29  C28  C27  C26     0.00   0.0  0
 0XZ  CONST_04  C29  C24  C25  C26     0.00   0.0  0
 0XZ  CONST_05  C28  C27  C26  C25     0.00   0.0  0
 0XZ  CONST_06  C28  C29  C24  C25     0.00   0.0  0
 0XZ  CONST_07  N4   C2   C1   C3      0.00   0.0  0
 0XZ  CONST_08  N7   C2   C1   C3    180.00   0.0  0
 0XZ  CONST_09  C8   C9   C1   C3    180.00   0.0  0
 0XZ  CONST_10  N4   C6   N5   C3      0.00   0.0  0
 0XZ  CONST_11  C2   N4   C6   N5      0.00   0.0  0
 0XZ  CONST_12  C2   C1   C3   N5      0.00   0.0  0
 0XZ  CONST_13  C9   C1   C3   N5    180.00   0.0  0
 0XZ  CONST_14  N7   C2   N4   C6    180.00   0.0  0
 0XZ  CONST_15  C1   C2   N4   C6      0.00   0.0  0
 0XZ  CONST_16  C1   C3   N5   C6      0.00   0.0  0
 0XZ  CONST_17  C8   N7   C2   N4    180.00   0.0  0
 0XZ  CONST_18  C9   C1   C2   N4    180.00   0.0  0
 0XZ  CONST_19  C8   N7   C2   C1      0.00   0.0  0
 0XZ  CONST_20  N7   C8   C9   C1      0.00   0.0  0
 0XZ  CONST_21  C2   N7   C8   C9      0.00   0.0  0
 0XZ  CONST_22  N7   C2   C1   C9      0.00   0.0  0
 0XZ  CONST_23  C2   C1   C9   C8      0.00   0.0  0
 0XZ  CONST_24  C2   C1   C3   N10   180.00   0.0  0
 0XZ  CONST_25  C9   C1   C3   N10     0.00   0.0  0
 0XZ  CONST_26  C6   N5   C3   N10   180.00   0.0  0
 0XZ  CONST_27  C29  C28  C27  CL3   180.00   0.0  0
 0XZ  CONST_28  C25  C26  C27  CL3   180.00   0.0  0
 0XZ  CONST_29  C20  C24  C25  C26   180.00   0.0  0
 0XZ  CONST_30  C20  C24  C29  C28   180.00   0.0  0
 0XZ  CONST_31  H4   C29  C28  C27   180.00   0.0  0
 0XZ  CONST_32  H2   C25  C26  C27   180.00   0.0  0
 0XZ  CONST_33  H3   C28  C27  C26   180.00   0.0  0
 0XZ  CONST_34  H1   C26  C27  C28   180.00   0.0  0
 0XZ  CONST_35  H24  C9   C1   C3      0.00   0.0  0
 0XZ  CONST_36  H23  C6   N5   C3    180.00   0.0  0
 0XZ  CONST_37  H26  N7   C2   N4      0.00   0.0  0
 0XZ  CONST_38  H25  C8   C9   C1    180.00   0.0  0
 0XZ  CONST_39  C13  C17  N19  C20   180.00   0.0  0
 0XZ  CONST_40  H11  N19  C17  C13     0.00   0.0  0
 0XZ  CONST_41  O18  C17  N19  C20     0.00   0.0  0
 0XZ  Var_01    N10  C11  C12  C13   -55.91  30.0  1
 0XZ  Var_02    N10  C15  C14  C13    57.45  30.0  1
 0XZ  Var_03    C3   N10  C11  C12   -99.64  30.0  1
 0XZ  Var_04    C1   C3   N10  C11   158.98  30.0  1
 0XZ  Var_05    C14  C15  N10  C11   -62.98  30.0  1
 0XZ  Var_06    O23  C22  C21  C20  -175.96  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
 0XZ  chir_01  C20  C24  N19  C21  negativ
 0XZ  chir_02  C13  C17  C14  C12  positiv

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
 0XZ  plan-1  CL3  0.020
 0XZ  plan-1  C27  0.020
 0XZ  plan-1  C26  0.020
 0XZ  plan-1  C25  0.020
 0XZ  plan-1  C28  0.020
 0XZ  plan-1  C29  0.020
 0XZ  plan-1  C24  0.020
 0XZ  plan-1  C20  0.020
 0XZ  plan-1  H1   0.020
 0XZ  plan-1  H2   0.020
 0XZ  plan-1  H3   0.020
 0XZ  plan-1  H4   0.020
 0XZ  plan-2  N10  0.020
 0XZ  plan-2  C3   0.020
 0XZ  plan-2  N5   0.020
 0XZ  plan-2  C6   0.020
 0XZ  plan-2  N4   0.020
 0XZ  plan-2  C1   0.020
 0XZ  plan-2  C9   0.020
 0XZ  plan-2  C8   0.020
 0XZ  plan-2  N7   0.020
 0XZ  plan-2  C2   0.020
 0XZ  plan-2  H23  0.020
 0XZ  plan-2  H24  0.020
 0XZ  plan-2  H25  0.020
 0XZ  plan-2  H26  0.020
 0XZ  plan-3  C20  0.020
 0XZ  plan-3  N19  0.020
 0XZ  plan-3  C17  0.020
 0XZ  plan-3  O18  0.020
 0XZ  plan-3  C13  0.020
 0XZ  plan-3  H11  0.020

