# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 17:14:36 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: (2S)-3-amino-2-(4-chlorobenzyl)-1-[4-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperazin-1-yl]propan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC[C@H](Cc1ccc(Cl)cc1)C(=O)N2CCN(CC2)c3ncnc4[nH]ccc34
#
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
 XM1  XM1  (2S)-3-amino-2-(4-chlorobenzyl)-1-[4-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperazin-1-yl]propan-1-one  ligand  51  28  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XM1
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
 XM1  C1    C   CR6   0   0.507   4.2993  -0.0501   0.0355
 XM1  CL1   CL  CL    0  -0.134  -7.2695   2.5814   0.1855
 XM1  C2    C   CR56  0  -0.077   4.5634   1.3397  -0.0639
 XM1  C3    C   CR15  0  -0.448   3.8453   2.5694  -0.2320
 XM1  C4    C   CR15  0  -0.010   4.7771   3.5613  -0.2974
 XM1  N5    N   NH2   0  -0.797  -2.1330  -2.7807   2.3270
 XM1  N6    N   NR15  0  -0.655   6.0293   3.0215  -0.1852
 XM1  C7    C   CR56  0   0.471   5.9291   1.6791  -0.0574
 XM1  N8    N   N     0  -0.495   5.3333  -0.8931   0.0868
 XM1  C9    C   CR16  0   0.038   6.5754  -0.4212   0.0723
 XM1  N10   N   N     0  -0.449   6.9601   0.8351   0.0188
 XM1  N11   N   NT    0  -0.499   3.0577  -0.5967   0.0478
 XM1  C12   C   CH2   0  -0.305   2.8731  -2.0355   0.0024
 XM1  C13   C   CH2   0  -0.308   1.6579  -2.3794  -0.8433
 XM1  N14   N   NT    0  -0.472   0.4750  -1.6826  -0.3669
 XM1  C15   C   CH2   0  -0.311   0.6690  -0.2463  -0.3109
 XM1  C16   C   CH2   0  -0.302   1.8812   0.0887   0.5416
 XM1  C17   C   C     0   0.596  -0.6944  -2.3493  -0.2069
 XM1  O18   O   O     0  -0.499  -0.7821  -3.5463  -0.4428
 XM1  C19   C   CH1   0  -0.415  -1.9271  -1.5635   0.2221
 XM1  C20   C   CH2   0  -0.522  -2.6393  -1.0652  -1.0513
 XM1  C21   C   CH2   0  -0.258  -2.8257  -2.4238   1.0986
 XM1  C22   C   CR6   0   0.148  -3.8007  -0.1568  -0.7604
 XM1  C23   C   CR16  0  -0.311  -3.5839   1.1465  -0.3185
 XM1  C24   C   CR16  0  -0.196  -4.6404   1.9940  -0.0241
 XM1  C25   C   CR6   0  -0.058  -5.9380   1.5302  -0.1784
 XM1  C26   C   CR16  0  -0.197  -6.1865   0.2424  -0.6227
 XM1  C27   C   CR16  0  -0.318  -5.1140  -0.5906  -0.9098
 XM1  H3    H   HCR5  0   0.257   2.7847   2.7316  -0.3177
 XM1  H4    H   HCR5  0   0.289   4.6440   4.6232  -0.4206
 XM1  HN5   H   HNH2  0   0.339  -2.0737  -1.9661   2.9258
 XM1  HN5A  H   HNH2  0   0.349  -2.6864  -3.4546   2.8401
 XM1  H9    H   HCR6  0   0.245   7.3611  -1.1682   0.1191
 XM1  H12   H   HCH2  0   0.275   3.7520  -2.5045  -0.4294
 XM1  H12A  H   HCH2  0   0.236   2.7456  -2.4355   1.0158
 XM1  H13   H   HCH2  0   0.244   1.8487  -2.1023  -1.8860
 XM1  H13A  H   HCH2  0   0.272   1.4902  -3.4517  -0.8076
 XM1  H15   H   HCH2  0   0.252   0.8191   0.1414  -1.3245
 XM1  H15A  H   HCH2  0   0.270  -0.1964   0.2602   0.1044
 XM1  H16   H   HCH2  0   0.249   1.6888  -0.2197   1.5768
 XM1  H16A  H   HCH2  0   0.273   2.0212   1.1622   0.5512
 XM1  H19   H   HCH1  0   0.262  -1.6424  -0.6920   0.8172
 XM1  H20   H   HCH2  0   0.270  -1.9205  -0.5329  -1.6813
 XM1  H20A  H   HCH2  0   0.264  -2.9779  -1.9281  -1.6302
 XM1  H21   H   HCH2  0   0.223  -3.0921  -3.3370   0.5642
 XM1  H21A  H   HCH2  0   0.215  -3.7629  -1.8806   1.2731
 XM1  H23   H   HCR6  0   0.260  -2.5721   1.5180  -0.2046
 XM1  H24   H   HCR6  0   0.279  -4.4518   3.0030   0.3166
 XM1  H26   H   HCR6  0   0.279  -7.2006  -0.1123  -0.7464
 XM1  H27   H   HCR6  0   0.262  -5.3134  -1.5971  -1.2568
 XM1  HN6   H   HNR5  0   0.413   6.8943   3.5359  -0.2226

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
 XM1  C2   C1    aromatic  1.418  0.020  1.418
 XM1  N8   C1    aromatic  1.335  0.020  1.335
 XM1  C1   N11   single    1.357  0.020  1.357
 XM1  CL1  C25   single    1.735  0.020  1.735
 XM1  C7   C2    aromatic  1.407  0.020  1.407
 XM1  C3   C2    aromatic  1.434  0.020  1.434
 XM1  C4   C3    aromatic  1.363  0.020  1.363
 XM1  C3   H3    single    0.930  0.020  1.080
 XM1  N6   C4    aromatic  1.368  0.020  1.368
 XM1  C4   H4    single    0.930  0.020  1.080
 XM1  N5   C21   single    1.455  0.020  1.455
 XM1  N5   HN5   single    0.890  0.020  1.040
 XM1  N5   HN5A  single    0.890  0.020  1.040
 XM1  N6   C7    aromatic  1.352  0.020  1.352
 XM1  N10  C7    aromatic  1.335  0.020  1.335
 XM1  C9   N8    aromatic  1.329  0.020  1.329
 XM1  N10  C9    aromatic  1.315  0.020  1.315
 XM1  C9   H9    single    0.930  0.020  1.080
 XM1  N11  C12   single    1.451  0.020  1.451
 XM1  N11  C16   single    1.448  0.020  1.448
 XM1  C12  C13   single    1.520  0.020  1.520
 XM1  C12  H12   single    0.970  0.020  1.090
 XM1  C12  H12A  single    0.970  0.020  1.090
 XM1  C13  N14   single    1.453  0.020  1.453
 XM1  C13  H13   single    0.970  0.020  1.090
 XM1  C13  H13A  single    0.970  0.020  1.090
 XM1  C15  N14   single    1.450  0.020  1.450
 XM1  N14  C17   single    1.356  0.020  1.356
 XM1  C16  C15   single    1.519  0.020  1.519
 XM1  C15  H15   single    0.970  0.020  1.090
 XM1  C15  H15A  single    0.970  0.020  1.090
 XM1  C16  H16   single    0.970  0.020  1.090
 XM1  C16  H16A  single    0.970  0.020  1.090
 XM1  C17  O18   double    1.223  0.020  1.223
 XM1  C17  C19   single    1.524  0.020  1.524
 XM1  C19  C20   single    1.542  0.020  1.542
 XM1  C19  C21   single    1.522  0.020  1.522
 XM1  C19  H19   single    0.970  0.020  1.090
 XM1  C22  C20   single    1.503  0.020  1.503
 XM1  C20  H20   single    0.970  0.020  1.090
 XM1  C20  H20A  single    0.970  0.020  1.090
 XM1  C21  H21   single    0.970  0.020  1.090
 XM1  C21  H21A  single    0.970  0.020  1.090
 XM1  C23  C22   aromatic  1.393  0.020  1.393
 XM1  C27  C22   aromatic  1.391  0.020  1.391
 XM1  C24  C23   aromatic  1.386  0.020  1.386
 XM1  C23  H23   single    0.930  0.020  1.080
 XM1  C25  C24   aromatic  1.387  0.020  1.387
 XM1  C24  H24   single    0.930  0.020  1.080
 XM1  C25  C26   aromatic  1.385  0.020  1.385
 XM1  C26  C27   aromatic  1.388  0.020  1.388
 XM1  C26  H26   single    0.930  0.020  1.080
 XM1  C27  H27   single    0.930  0.020  1.080
 XM1  N6   HN6   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
 XM1  N11   C1   N8   117.00  3.000
 XM1  N11   C1   C2   124.47  3.000
 XM1  N8    C1   C2   118.50  3.000
 XM1  C7    C2   C3   106.24  3.000
 XM1  C3    C2   C1   139.06  3.000
 XM1  C7    C2   C1   114.63  3.000
 XM1  H3    C3   C4   124.08  3.000
 XM1  H3    C3   C2   129.20  3.000
 XM1  C4    C3   C2   106.71  3.000
 XM1  H4    C4   N6   120.76  3.000
 XM1  H4    C4   C3   129.69  3.000
 XM1  N6    C4   C3   109.55  3.000
 XM1  HN5A  N5   HN5  105.55  3.000
 XM1  HN5A  N5   C21  109.34  3.000
 XM1  HN5   N5   C21  109.26  3.000
 XM1  HN6   N6   C7   125.05  3.000
 XM1  HN6   N6   C4   125.56  3.000
 XM1  C7    N6   C4   109.36  3.000
 XM1  N10   C7   N6   125.16  3.000
 XM1  N10   C7   C2   126.69  3.000
 XM1  N6    C7   C2   108.12  3.000
 XM1  C9    N8   C1   119.95  3.000
 XM1  H9    C9   N10  116.59  3.000
 XM1  H9    C9   N8   115.59  3.000
 XM1  N10   C9   N8   127.82  3.000
 XM1  C9    N10  C7   112.36  3.000
 XM1  C16   N11  C12  112.12  3.000
 XM1  C16   N11  C1   123.77  3.000
 XM1  C12   N11  C1   121.04  3.000
 XM1  H12A  C12  H12  107.70  3.000
 XM1  H12A  C12  C13  109.79  3.000
 XM1  H12   C12  C13  109.16  3.000
 XM1  H12A  C12  N11  110.33  3.000
 XM1  H12   C12  N11  109.74  3.000
 XM1  C13   C12  N11  110.08  3.000
 XM1  H13A  C13  H13  107.93  3.000
 XM1  H13A  C13  N14  109.69  3.000
 XM1  H13   C13  N14  109.42  3.000
 XM1  H13A  C13  C12  109.18  3.000
 XM1  H13   C13  C12  109.46  3.000
 XM1  N14   C13  C12  111.10  3.000
 XM1  C17   N14  C15  126.72  3.000
 XM1  C17   N14  C13  120.34  3.000
 XM1  C15   N14  C13  112.24  3.000
 XM1  H15A  C15  H15  107.35  3.000
 XM1  H15A  C15  C16  108.57  3.000
 XM1  H15   C15  C16  109.38  3.000
 XM1  H15A  C15  N14  111.73  3.000
 XM1  H15   C15  N14  109.46  3.000
 XM1  C16   C15  N14  110.28  3.000
 XM1  H16A  C16  H16  107.04  3.000
 XM1  H16A  C16  C15  109.07  3.000
 XM1  H16   C16  C15  109.12  3.000
 XM1  H16A  C16  N11  111.54  3.000
 XM1  H16   C16  N11  109.33  3.000
 XM1  C15   C16  N11  110.64  3.000
 XM1  C19   C17  O18  120.07  3.000
 XM1  C19   C17  N14  118.53  3.000
 XM1  O18   C17  N14  121.36  3.000
 XM1  H19   C19  C21  106.92  3.000
 XM1  H19   C19  C20  108.20  3.000
 XM1  C21   C19  C20  112.69  3.000
 XM1  H19   C19  C17  110.72  3.000
 XM1  C21   C19  C17  110.39  3.000
 XM1  C20   C19  C17  107.93  3.000
 XM1  H20A  C20  H20  106.43  3.000
 XM1  H20A  C20  C22  109.90  3.000
 XM1  H20   C20  C22  108.97  3.000
 XM1  H20A  C20  C19  108.99  3.000
 XM1  H20   C20  C19  109.23  3.000
 XM1  C22   C20  C19  113.11  3.000
 XM1  H21A  C21  H21  106.48  3.000
 XM1  H21A  C21  C19  108.43  3.000
 XM1  H21   C21  C19  109.58  3.000
 XM1  H21A  C21  N5   113.20  3.000
 XM1  H21   C21  N5   108.94  3.000
 XM1  C19   C21  N5   110.11  3.000
 XM1  C27   C22  C23  118.21  3.000
 XM1  C27   C22  C20  121.35  3.000
 XM1  C23   C22  C20  120.44  3.000
 XM1  H23   C23  C24  118.66  3.000
 XM1  H23   C23  C22  119.95  3.000
 XM1  C24   C23  C22  121.39  3.000
 XM1  H24   C24  C25  120.69  3.000
 XM1  H24   C24  C23  120.29  3.000
 XM1  C25   C24  C23  119.02  3.000
 XM1  C26   C25  C24  120.98  3.000
 XM1  C26   C25  CL1  119.54  3.000
 XM1  C24   C25  CL1  119.48  3.000
 XM1  H26   C26  C27  120.27  3.000
 XM1  H26   C26  C25  120.67  3.000
 XM1  C27   C26  C25  119.07  3.000
 XM1  H27   C27  C26  118.80  3.000
 XM1  H27   C27  C22  119.86  3.000
 XM1  C26   C27  C22  121.34  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
 XM1  CONST_01  N6   C7   C2   C1    180.00   0.0  0
 XM1  CONST_02  N10  C7   C2   C1      0.00   0.0  0
 XM1  CONST_03  C4   C3   C2   C1    180.00   0.0  0
 XM1  CONST_04  N10  C9   N8   C1      0.00   0.0  0
 XM1  CONST_05  C9   N8   C1   C2      0.00   0.0  0
 XM1  CONST_06  C4   N6   C7   C2      0.00   0.0  0
 XM1  CONST_07  C9   N10  C7   C2      0.00   0.0  0
 XM1  CONST_08  N6   C4   C3   C2      0.00   0.0  0
 XM1  CONST_09  N8   C1   C2   C3    180.00   0.0  0
 XM1  CONST_10  N6   C7   C2   C3      0.00   0.0  0
 XM1  CONST_11  N10  C7   C2   C3    180.00   0.0  0
 XM1  CONST_12  C7   N6   C4   C3      0.00   0.0  0
 XM1  CONST_13  C7   C2   C3   C4      0.00   0.0  0
 XM1  CONST_14  N10  C7   N6   C4    180.00   0.0  0
 XM1  CONST_15  C9   N10  C7   N6    180.00   0.0  0
 XM1  CONST_16  N8   C1   C2   C7      0.00   0.0  0
 XM1  CONST_17  N8   C9   N10  C7      0.00   0.0  0
 XM1  CONST_18  C25  C24  C23  C22     0.00   0.0  0
 XM1  CONST_19  C25  C26  C27  C22     0.00   0.0  0
 XM1  CONST_20  C26  C27  C22  C23     0.00   0.0  0
 XM1  CONST_21  C26  C25  C24  C23     0.00   0.0  0
 XM1  CONST_22  C27  C22  C23  C24     0.00   0.0  0
 XM1  CONST_23  C27  C26  C25  C24     0.00   0.0  0
 XM1  CONST_24  N11  C1   C2   C3      0.00   0.0  0
 XM1  CONST_25  N11  C1   C2   C7    180.00   0.0  0
 XM1  CONST_26  N11  C1   N8   C9    180.00   0.0  0
 XM1  CONST_27  C23  C24  C25  CL1   180.00   0.0  0
 XM1  CONST_28  C27  C26  C25  CL1   180.00   0.0  0
 XM1  CONST_29  C24  C23  C22  C20   180.00   0.0  0
 XM1  CONST_30  C26  C27  C22  C20   180.00   0.0  0
 XM1  CONST_31  H3   C3   C2   C1      0.00   0.0  0
 XM1  CONST_32  H9   C9   N8   C1    180.00   0.0  0
 XM1  CONST_33  HN6  N6   C7   C2    180.00   0.0  0
 XM1  CONST_34  H4   C4   C3   C2    180.00   0.0  0
 XM1  CONST_35  H24  C24  C23  C22   180.00   0.0  0
 XM1  CONST_36  H26  C26  C27  C22   180.00   0.0  0
 XM1  CONST_37  H27  C27  C22  C23   180.00   0.0  0
 XM1  CONST_38  H23  C23  C24  C25   180.00   0.0  0
 XM1  CONST_39  O18  C17  N14  C13     0.00   0.0  0
 XM1  CONST_40  C19  C17  N14  C13   180.00   0.0  0
 XM1  CONST_41  O18  C17  N14  C15   180.00   0.0  0
 XM1  CONST_42  C19  C17  N14  C15     0.00   0.0  0
 XM1  Var_01    C13  C12  N11  C1   -142.77  30.0  1
 XM1  Var_02    C15  C16  N11  C1    142.60  30.0  1
 XM1  Var_03    C12  N11  C1   C2    173.07  30.0  2
 XM1  Var_04    N14  C13  C12  N11   -54.76  30.0  1
 XM1  Var_05    N14  C15  C16  N11    55.65  30.0  1
 XM1  Var_06    C15  N14  C13  C12    55.53  30.0  1
 XM1  Var_07    C16  C15  N14  C13   -55.56  30.0  1
 XM1  Var_08    C23  C22  C20  C19    73.12  30.0  2
 XM1  Var_09    HN5  N5   C21  C19    72.80  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
 XM1  chir_01  C19  C17  C20  C21  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
 XM1  plan-1  CL1  0.020
 XM1  plan-1  C20  0.020
 XM1  plan-1  C22  0.020
 XM1  plan-1  C23  0.020
 XM1  plan-1  C24  0.020
 XM1  plan-1  C25  0.020
 XM1  plan-1  C26  0.020
 XM1  plan-1  C27  0.020
 XM1  plan-1  H23  0.020
 XM1  plan-1  H24  0.020
 XM1  plan-1  H26  0.020
 XM1  plan-1  H27  0.020
 XM1  plan-2  C1   0.020
 XM1  plan-2  C2   0.020
 XM1  plan-2  C3   0.020
 XM1  plan-2  C4   0.020
 XM1  plan-2  N6   0.020
 XM1  plan-2  C7   0.020
 XM1  plan-2  N8   0.020
 XM1  plan-2  C9   0.020
 XM1  plan-2  N10  0.020
 XM1  plan-2  N11  0.020
 XM1  plan-2  H3   0.020
 XM1  plan-2  H4   0.020
 XM1  plan-2  H9   0.020
 XM1  plan-2  HN6  0.020
 XM1  plan-3  C13  0.020
 XM1  plan-3  N14  0.020
 XM1  plan-3  C15  0.020
 XM1  plan-3  C17  0.020
 XM1  plan-3  O18  0.020
 XM1  plan-3  C19  0.020

