# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 08:09:16 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: 1-{(3R)-3-[(7H-pyrrolo[2,3-d]pyrimidin-4-yl)amino]piperidin-1-yl}propan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)N1CCC[C@H](C1)Nc2ncnc3[nH]ccc23
#
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
 7KU  7KU  1-{(3R)-3-[(7H-pyrrolo[2,3-d]pyrimidin-4-yl)amino]piperidin-1-yl}propan-1-one  ligand  39  20  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7KU
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
 7KU  N3   N  NR15  0  -0.657   5.1313   0.4943  -0.2819
 7KU  C4   C  CH2   0  -0.324  -3.3434  -1.7108  -0.3388
 7KU  N2   N  NH1   0  -0.675   0.8148  -1.1330   0.0621
 7KU  C7   C  CH1   0  -0.059  -0.6017  -1.0220   0.3256
 7KU  C6   C  CH2   0  -0.463  -1.1644  -2.3866   0.7084
 7KU  C9   C  CR6   0   0.506   1.6958  -0.1255   0.1802
 7KU  C13  C  CR56  0   0.472   3.8657   0.8300   0.0612
 7KU  C8   C  CH2   0  -0.307  -1.3473  -0.4550  -0.8890
 7KU  N5   N  N     0  -0.488   1.2733   1.0587   0.6249
 7KU  C1   C  CH3   0  -0.650  -5.4822   2.1124   0.1174
 7KU  C2   C  CH2   0  -0.595  -4.8692   0.7336  -0.0497
 7KU  O1   O  O     0  -0.502  -2.8301   1.8479  -0.6063
 7KU  N1   N  NT    0  -0.458  -2.7720  -0.4062  -0.6250
 7KU  C5   C  CH2   0  -0.435  -2.6772  -2.3241   0.8861
 7KU  C10  C  CR56  0  -0.088   3.0600  -0.2959  -0.1373
 7KU  C11  C  CR15  0  -0.443   3.9018  -1.3421  -0.6206
 7KU  C12  C  CR15  0  -0.015   5.1579  -0.8142  -0.6933
 7KU  N4   N  N     0  -0.456   3.4528   2.0200   0.5120
 7KU  C14  C  CR16  0   0.034   2.1612   2.0433   0.7646
 7KU  H1   H  HNR5  0   0.412   5.9296   1.1064  -0.2310
 7KU  H2   H  HCH2  0   0.276  -4.4183  -1.6421  -0.2014
 7KU  H3   H  HCH2  0   0.245  -3.1785  -2.3553  -1.2085
 7KU  H4   H  HNH1  0   0.398   1.1456  -1.9971  -0.3366
 7KU  H5   H  HCH1  0   0.251  -0.7379  -0.3299   1.1596
 7KU  H6   H  HCH2  0   0.226  -0.9284  -3.1084  -0.0830
 7KU  H7   H  HCH2  0   0.254  -0.6828  -2.7436   1.6209
 7KU  H8   H  HCH2  0   0.270  -0.9813   0.5405  -1.1246
 7KU  H9   H  HCH2  0   0.237  -1.1684  -1.0998  -1.7569
 7KU  H10  H  HCH3  0   0.226  -4.9852   2.6841   0.9003
 7KU  H11  H  HCH3  0   0.226  -5.4352   2.6934  -0.8027
 7KU  H12  H  HCH3  0   0.230  -6.5318   2.0157   0.3944
 7KU  H13  H  HCH2  0   0.262  -4.9721   0.1705   0.8823
 7KU  H14  H  HCH2  0   0.266  -5.4294   0.1666  -0.7985
 7KU  H15  H  HCH2  0   0.231  -2.9323  -1.7324   1.7703
 7KU  H16  H  HCH2  0   0.246  -3.0744  -3.3276   1.0509
 7KU  H17  H  HCR5  0   0.254   3.6277  -2.3514  -0.8831
 7KU  H18  H  HCR5  0   0.287   6.0822  -1.2707  -1.0063
 7KU  H19  H  HCR6  0   0.243   1.7595   2.9822   1.1322
 7KU  C3   C  C     0   0.563  -3.4038   0.7786  -0.4459

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
 7KU  C1   C2   single    1.518  0.020  1.518
 7KU  C2   C3   single    1.519  0.020  1.519
 7KU  C4   N1   single    1.453  0.020  1.453
 7KU  C4   C5   single    1.523  0.020  1.523
 7KU  N1   C3   single    1.355  0.020  1.355
 7KU  N1   C8   single    1.450  0.020  1.450
 7KU  C3   O1   double    1.224  0.020  1.224
 7KU  C8   C7   single    1.534  0.020  1.534
 7KU  C5   C6   single    1.525  0.020  1.525
 7KU  C6   C7   single    1.525  0.020  1.525
 7KU  C7   N2   single    1.445  0.020  1.445
 7KU  N2   C9   single    1.344  0.020  1.344
 7KU  C11  C12  aromatic  1.365  0.020  1.365
 7KU  C11  C10  aromatic  1.427  0.020  1.427
 7KU  C9   C10  aromatic  1.411  0.020  1.411
 7KU  C9   N5   aromatic  1.334  0.020  1.334
 7KU  C12  N3   aromatic  1.372  0.020  1.372
 7KU  C10  C13  aromatic  1.399  0.020  1.399
 7KU  N5   C14  aromatic  1.333  0.020  1.333
 7KU  N3   C13  aromatic  1.354  0.020  1.354
 7KU  C13  N4   aromatic  1.338  0.020  1.338
 7KU  C14  N4   aromatic  1.316  0.020  1.316
 7KU  N3   H1   single    0.860  0.020  1.020
 7KU  C4   H2   single    0.970  0.020  1.090
 7KU  C4   H3   single    0.970  0.020  1.090
 7KU  N2   H4   single    0.860  0.020  1.020
 7KU  C7   H5   single    0.970  0.020  1.090
 7KU  C6   H6   single    0.970  0.020  1.090
 7KU  C6   H7   single    0.970  0.020  1.090
 7KU  C8   H8   single    0.970  0.020  1.090
 7KU  C8   H9   single    0.970  0.020  1.090
 7KU  C1   H10  single    0.970  0.020  1.090
 7KU  C1   H11  single    0.970  0.020  1.090
 7KU  C1   H12  single    0.970  0.020  1.090
 7KU  C2   H13  single    0.970  0.020  1.090
 7KU  C2   H14  single    0.970  0.020  1.090
 7KU  C5   H15  single    0.970  0.020  1.090
 7KU  C5   H16  single    0.970  0.020  1.090
 7KU  C11  H17  single    0.930  0.020  1.080
 7KU  C12  H18  single    0.930  0.020  1.080
 7KU  C14  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
 7KU  H1   N3   C12  125.40  3.000
 7KU  H1   N3   C13  125.28  3.000
 7KU  C12  N3   C13  109.31  3.000
 7KU  H3   C4   H2   106.67  3.000
 7KU  H3   C4   C5   109.62  3.000
 7KU  H2   C4   C5   110.89  3.000
 7KU  H3   C4   N1   108.24  3.000
 7KU  H2   C4   N1   110.95  3.000
 7KU  C5   C4   N1   110.37  3.000
 7KU  H4   N2   C9   117.56  3.000
 7KU  H4   N2   C7   117.38  3.000
 7KU  C9   N2   C7   124.69  3.000
 7KU  H5   C7   C8   108.05  3.000
 7KU  H5   C7   C6   109.23  3.000
 7KU  C8   C7   C6   110.50  3.000
 7KU  H5   C7   N2   108.07  3.000
 7KU  C6   C7   N2   109.80  3.000
 7KU  C8   C7   N2   111.13  3.000
 7KU  H7   C6   H6   107.04  3.000
 7KU  H7   C6   C5   110.72  3.000
 7KU  H6   C6   C5   108.94  3.000
 7KU  H7   C6   C7   109.86  3.000
 7KU  H6   C6   C7   109.17  3.000
 7KU  C5   C6   C7   111.02  3.000
 7KU  C10  C9   N5   119.24  3.000
 7KU  N5   C9   N2   119.17  3.000
 7KU  C10  C9   N2   121.58  3.000
 7KU  N4   C13  C10  125.87  3.000
 7KU  N4   C13  N3   126.48  3.000
 7KU  C10  C13  N3   107.64  3.000
 7KU  H9   C8   H8   108.21  3.000
 7KU  H9   C8   N1   108.93  3.000
 7KU  H8   C8   N1   109.86  3.000
 7KU  H9   C8   C7   109.28  3.000
 7KU  H8   C8   C7   110.28  3.000
 7KU  N1   C8   C7   110.24  3.000
 7KU  C14  N5   C9   118.67  3.000
 7KU  H12  C1   H11  107.68  3.000
 7KU  H12  C1   H10  107.66  3.000
 7KU  H11  C1   H10  107.91  3.000
 7KU  H12  C1   C2   109.65  3.000
 7KU  H11  C1   C2   111.96  3.000
 7KU  H10  C1   C2   111.81  3.000
 7KU  H14  C2   H13  105.57  3.000
 7KU  H14  C2   C3   109.33  3.000
 7KU  H13  C2   C3   109.17  3.000
 7KU  H14  C2   C1   109.84  3.000
 7KU  H13  C2   C1   109.62  3.000
 7KU  C3   C2   C1   113.04  3.000
 7KU  C3   N1   C8   120.79  3.000
 7KU  C8   N1   C4   113.09  3.000
 7KU  C3   N1   C4   125.17  3.000
 7KU  H16  C5   H15  106.88  3.000
 7KU  H16  C5   C6   109.93  3.000
 7KU  H15  C5   C6   110.34  3.000
 7KU  H16  C5   C4   109.41  3.000
 7KU  H15  C5   C4   109.28  3.000
 7KU  C6   C5   C4   110.90  3.000
 7KU  C11  C10  C13  107.36  3.000
 7KU  C13  C10  C9   115.33  3.000
 7KU  C11  C10  C9   137.31  3.000
 7KU  H17  C11  C12  125.67  3.000
 7KU  H17  C11  C10  128.22  3.000
 7KU  C12  C11  C10  106.10  3.000
 7KU  H18  C12  C11  129.89  3.000
 7KU  H18  C12  N3   120.52  3.000
 7KU  C11  C12  N3   109.58  3.000
 7KU  C14  N4   C13  112.54  3.000
 7KU  H19  C14  N4   116.32  3.000
 7KU  H19  C14  N5   115.34  3.000
 7KU  N4   C14  N5   128.34  3.000
 7KU  N1   C3   O1   121.88  3.000
 7KU  O1   C3   C2   120.82  3.000
 7KU  N1   C3   C2   117.30  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
 7KU  CONST_01  C10  C11  C12  N3      0.00   0.0  0
 7KU  CONST_02  C11  C10  C13  N3      0.00   0.0  0
 7KU  CONST_03  C9   C10  C13  N3    180.00   0.0  0
 7KU  CONST_04  C14  N4   C13  N3    180.00   0.0  0
 7KU  CONST_05  C12  C11  C10  C9    180.00   0.0  0
 7KU  CONST_06  N4   C13  C10  C9      0.00   0.0  0
 7KU  CONST_07  N4   C14  N5   C9      0.00   0.0  0
 7KU  CONST_08  C12  C11  C10  C13     0.00   0.0  0
 7KU  CONST_09  N5   C9   C10  C13     0.00   0.0  0
 7KU  CONST_10  C11  C12  N3   C13     0.00   0.0  0
 7KU  CONST_11  N5   C14  N4   C13     0.00   0.0  0
 7KU  CONST_12  C11  C10  C9   N5    180.00   0.0  0
 7KU  CONST_13  C14  N5   C9   C10     0.00   0.0  0
 7KU  CONST_14  C12  N3   C13  C10     0.00   0.0  0
 7KU  CONST_15  C14  N4   C13  C10     0.00   0.0  0
 7KU  CONST_16  N4   C13  C10  C11   180.00   0.0  0
 7KU  CONST_17  N4   C13  N3   C12   180.00   0.0  0
 7KU  CONST_18  C11  C10  C9   N2      0.00   0.0  0
 7KU  CONST_19  C13  C10  C9   N2    180.00   0.0  0
 7KU  CONST_20  C14  N5   C9   N2    180.00   0.0  0
 7KU  CONST_21  C10  C9   N2   C7    180.00   0.0  0
 7KU  CONST_22  N5   C9   N2   C7      0.00   0.0  0
 7KU  CONST_23  H17  C11  C12  N3    180.00   0.0  0
 7KU  CONST_24  H19  C14  N5   C9    180.00   0.0  0
 7KU  CONST_25  H18  C12  N3   C13   180.00   0.0  0
 7KU  CONST_26  H1   N3   C13  C10   180.00   0.0  0
 7KU  CONST_27  C2   C3   N1   C4      0.00   0.0  0
 7KU  CONST_28  O1   C3   N1   C4    180.00   0.0  0
 7KU  CONST_29  C2   C3   N1   C8    180.00   0.0  0
 7KU  CONST_30  O1   C3   N1   C8      0.00   0.0  0
 7KU  CONST_31  H4   N2   C9   N5    180.00   0.0  0
 7KU  Var_01    C7   C8   N1   C4    -59.93  30.0  1
 7KU  Var_02    C7   C6   C5   C4     52.67  30.0  1
 7KU  Var_03    N1   C4   C5   C6    -55.14  30.0  1
 7KU  Var_04    C5   C4   N1   C8     59.84  30.0  1
 7KU  Var_05    N1   C3   C2   C1   -179.68  30.0  3
 7KU  Var_06    H10  C1   C2   C3    -61.03  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
 7KU  chir_01  C7  C8  C6  N2  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
 7KU  plan-1  N3   0.020
 7KU  plan-1  N2   0.020
 7KU  plan-1  C9   0.020
 7KU  plan-1  C13  0.020
 7KU  plan-1  N5   0.020
 7KU  plan-1  C10  0.020
 7KU  plan-1  C11  0.020
 7KU  plan-1  C12  0.020
 7KU  plan-1  N4   0.020
 7KU  plan-1  C14  0.020
 7KU  plan-1  H1   0.020
 7KU  plan-1  H17  0.020
 7KU  plan-1  H18  0.020
 7KU  plan-1  H19  0.020
 7KU  plan-2  N2   0.020
 7KU  plan-2  C7   0.020
 7KU  plan-2  C9   0.020
 7KU  plan-2  H4   0.020
 7KU  plan-3  C4   0.020
 7KU  plan-3  C8   0.020
 7KU  plan-3  C2   0.020
 7KU  plan-3  O1   0.020
 7KU  plan-3  N1   0.020
 7KU  plan-3  C3   0.020

