# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 06:11:47 2022
#   Inital geometry file: a 140 line input string
#   Ligand name: 3-[4-(2-{[4-(piperidin-4-yl)phenyl]amino}-6,7-dihydro-5H-pyrrolo[2,3-d]pyrimidin-4-yl)-1H-pyrazol-1-yl]propanenitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N#CCCn1cc(cn1)c2nc(Nc3ccc(cc3)C4CCNCC4)nc5NCCc25
#
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
 R5S  R5S  3-[4-(2-{[4-(piperidin-4-yl)phenyl]amino}-6,7-dihydro-5H-pyrrolo[2,3-d]pyrimidin-4-yl)-1H-pyrazol-1-yl]propanenitrile  ligand  57  31  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_R5S
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
 R5S  N12  N  NH1   0  -0.776  35.9506   1.2908  14.4271
 R5S  C13  C  CR6   0   0.343  37.1147   0.6726  13.9864
 R5S  C15  C  CR16  0  -0.309  39.5381   0.7296  13.9775
 R5S  C17  C  CH1   0  -0.342  40.9259  -1.0586  12.8368
 R5S  C21  C  CH2   0  -0.293  43.0475  -0.7827  11.5147
 R5S  C22  C  CH2   0  -0.405  41.7119  -0.1528  11.8830
 R5S  C24  C  CR16  0  -0.304  37.1696  -0.5099  13.2480
 R5S  C26  C  CR56  0   0.541  32.5293   1.7099  14.5123
 R5S  C28  C  CH2   0  -0.560  30.5484   0.8587  13.5409
 R5S  C02  C  CSP   0   0.128  30.5291  -4.8247  11.7709
 R5S  C03  C  CH2   0  -0.547  30.7825  -4.6848  10.3462
 R5S  C04  C  CH2   0  -0.308  30.7247  -3.2239   9.9007
 R5S  C07  C  CR15  0  -0.053  33.6011  -1.7513  11.1865
 R5S  C08  C  CR5   0  -0.195  32.6781  -1.0112  11.9574
 R5S  C09  C  CR6   0   0.269  32.9889   0.0051  12.9503
 R5S  C11  C  CR6   0   0.577  34.6364   1.0804  14.1186
 R5S  C14  C  CR16  0  -0.336  38.3253   1.2813  14.3434
 R5S  C16  C  CR6   0   0.182  39.6069  -0.4536  13.2413
 R5S  C18  C  CH2   0  -0.405  41.8028  -1.4202  14.0397
 R5S  C19  C  CH2   0  -0.293  43.1353  -1.9977  13.5840
 R5S  C23  C  CR16  0  -0.336  38.4007  -1.0470  12.8904
 R5S  C27  C  CR56  0  -0.127  32.0447   0.7735  13.5770
 R5S  C29  C  CH2   0  -0.258  30.2572   2.1245  14.3802
 R5S  C31  C  CR15  0   0.017  31.4481  -1.4836  11.5360
 R5S  N01  N  NS    0  -0.264  30.3294  -4.9138  12.9001
 R5S  N05  N  NR5   0  -0.278  31.6906  -2.4097  10.5960
 R5S  N06  N  N     0  -0.273  32.9933  -2.5876  10.3740
 R5S  N10  N  N     0  -0.541  34.3051   0.1686  13.2277
 R5S  N20  N  NH1   0  -0.594  43.8165  -1.0541  12.7160
 R5S  N25  N  N     0  -0.519  33.8018   1.8874  14.8002
 R5S  N30  N  NR15  0  -0.673  31.5105   2.3834  15.0760
 R5S  H1   H  HNH1  0   0.400  36.0856   2.0534  15.0732
 R5S  H2   H  HCR6  0   0.244  40.4475   1.2390  14.2748
 R5S  H3   H  HCH1  0   0.229  40.7100  -1.9904  12.2990
 R5S  H4   H  HCH2  0   0.184  42.8577  -1.6930  10.9208
 R5S  H5   H  HCH2  0   0.229  43.6160  -0.1029  10.8763
 R5S  H6   H  HCH2  0   0.216  41.8908   0.8175  12.3568
 R5S  H7   H  HCH2  0   0.229  41.1297   0.0344  10.9776
 R5S  H8   H  HCR6  0   0.285  36.2616  -1.0097  12.9534
 R5S  H9   H  HCH2  0   0.262  30.1427   0.9546  12.5327
 R5S  H10  H  HCH2  0   0.263  30.0863  -0.0251  13.9898
 R5S  H11  H  HCH2  0   0.326  30.0347  -5.2594   9.7975
 R5S  H12  H  HCH2  0   0.320  31.7579  -5.1173  10.1192
 R5S  H13  H  HCH2  0   0.289  29.7370  -2.8062  10.0839
 R5S  H14  H  HCH2  0   0.302  30.9182  -3.1758   8.8302
 R5S  H15  H  HCR5  0   0.267  34.6780  -1.6851  11.2003
 R5S  H16  H  HCR6  0   0.258  38.3118   2.2031  14.9146
 R5S  H17  H  HCH2  0   0.216  41.9879  -0.5299  14.6487
 R5S  H18  H  HCH2  0   0.229  41.2875  -2.1433  14.6766
 R5S  H19  H  HCH2  0   0.184  42.9502  -2.9664  13.0894
 R5S  H20  H  HCH2  0   0.229  43.7677  -2.2026  14.4505
 R5S  H21  H  HCR6  0   0.240  38.4108  -1.9695  12.3203
 R5S  H22  H  HCH2  0   0.243  29.9907   2.9676  13.7377
 R5S  H23  H  HCR5  0   0.300  30.4396  -1.2421  11.8291
 R5S  H24  H  HNH1  0   0.349  44.7224  -1.4245  12.4597
 R5S  H26  H  HCH2  0   0.247  29.4422   1.9725  15.0867
 R5S  H25  H  HNR5  0   0.391  31.6620   3.2353  15.5912

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
 R5S  C04  N05  single    1.442  0.020  1.442
 R5S  C04  C03  single    1.528  0.020  1.528
 R5S  N06  N05  aromatic  1.333  0.020  1.333
 R5S  N06  C07  aromatic  1.315  0.020  1.315
 R5S  N05  C31  aromatic  1.342  0.020  1.342
 R5S  C03  C02  single    1.454  0.020  1.454
 R5S  C07  C08  aromatic  1.412  0.020  1.412
 R5S  C21  C22  single    1.522  0.020  1.522
 R5S  C21  N20  single    1.452  0.020  1.452
 R5S  C31  C08  aromatic  1.383  0.020  1.383
 R5S  C08  C09  single    1.454  0.020  1.454
 R5S  C22  C17  single    1.532  0.020  1.532
 R5S  C02  N01  triple    1.150  0.020  1.150
 R5S  N20  C19  single    1.452  0.020  1.452
 R5S  C23  C24  aromatic  1.390  0.020  1.390
 R5S  C23  C16  aromatic  1.389  0.020  1.389
 R5S  C09  N10  aromatic  1.355  0.020  1.355
 R5S  C09  C27  aromatic  1.369  0.020  1.369
 R5S  C17  C16  single    1.506  0.020  1.506
 R5S  C17  C18  single    1.532  0.020  1.532
 R5S  C28  C27  single    1.499  0.020  1.499
 R5S  C28  C29  single    1.546  0.020  1.546
 R5S  C24  C13  aromatic  1.395  0.020  1.395
 R5S  N10  C11  aromatic  1.317  0.020  1.317
 R5S  C19  C18  single    1.522  0.020  1.522
 R5S  C16  C15  aromatic  1.395  0.020  1.395
 R5S  C27  C26  aromatic  1.409  0.020  1.409
 R5S  C29  N30  single    1.457  0.020  1.457
 R5S  C13  N12  single    1.390  0.020  1.390
 R5S  C13  C14  aromatic  1.401  0.020  1.401
 R5S  C11  N12  single    1.366  0.020  1.366
 R5S  C11  N25  aromatic  1.346  0.020  1.346
 R5S  C15  C14  aromatic  1.382  0.020  1.382
 R5S  C26  N25  aromatic  1.317  0.020  1.317
 R5S  C26  N30  single    1.345  0.020  1.345
 R5S  N12  H1   single    0.860  0.020  1.020
 R5S  C15  H2   single    0.930  0.020  1.080
 R5S  C17  H3   single    0.970  0.020  1.090
 R5S  C21  H4   single    0.970  0.020  1.090
 R5S  C21  H5   single    0.970  0.020  1.090
 R5S  C22  H6   single    0.970  0.020  1.090
 R5S  C22  H7   single    0.970  0.020  1.090
 R5S  C24  H8   single    0.930  0.020  1.080
 R5S  C28  H9   single    0.970  0.020  1.090
 R5S  C28  H10  single    0.970  0.020  1.090
 R5S  C03  H11  single    0.970  0.020  1.090
 R5S  C03  H12  single    0.970  0.020  1.090
 R5S  C04  H13  single    0.970  0.020  1.090
 R5S  C04  H14  single    0.970  0.020  1.090
 R5S  C07  H15  single    0.930  0.020  1.080
 R5S  C14  H16  single    0.930  0.020  1.080
 R5S  C18  H17  single    0.970  0.020  1.090
 R5S  C18  H18  single    0.970  0.020  1.090
 R5S  C19  H19  single    0.970  0.020  1.090
 R5S  C19  H20  single    0.970  0.020  1.090
 R5S  C23  H21  single    0.930  0.020  1.080
 R5S  C29  H22  single    0.970  0.020  1.090
 R5S  C31  H23  single    0.930  0.020  1.080
 R5S  N20  H24  single    0.890  0.020  1.040
 R5S  C29  H26  single    0.970  0.020  1.090
 R5S  N30  H25  single    0.890  0.020  1.040

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
 R5S  H1   N12  C11  112.94  3.000
 R5S  H1   N12  C13  115.30  3.000
 R5S  C11  N12  C13  131.73  3.000
 R5S  C14  C13  C24  117.97  3.000
 R5S  C14  C13  N12  116.71  3.000
 R5S  C24  C13  N12  125.30  3.000
 R5S  H2   C15  C16  120.13  3.000
 R5S  H2   C15  C14  118.43  3.000
 R5S  C16  C15  C14  121.44  3.000
 R5S  H3   C17  C18  107.28  3.000
 R5S  H3   C17  C16  107.48  3.000
 R5S  C18  C17  C16  112.66  3.000
 R5S  H3   C17  C22  107.32  3.000
 R5S  C18  C17  C22  109.55  3.000
 R5S  C16  C17  C22  112.26  3.000
 R5S  H5   C21  H4   106.76  3.000
 R5S  H5   C21  N20  108.92  3.000
 R5S  H4   C21  N20  112.47  3.000
 R5S  H5   C21  C22  109.92  3.000
 R5S  H4   C21  C22  108.71  3.000
 R5S  N20  C21  C22  110.00  3.000
 R5S  H7   C22  H6   107.09  3.000
 R5S  H7   C22  C21  109.76  3.000
 R5S  H6   C22  C21  109.16  3.000
 R5S  H7   C22  C17  110.11  3.000
 R5S  H6   C22  C17  109.78  3.000
 R5S  C21  C22  C17  110.86  3.000
 R5S  H8   C24  C23  119.79  3.000
 R5S  H8   C24  C13  120.31  3.000
 R5S  C23  C24  C13  119.90  3.000
 R5S  N30  C26  N25  124.95  3.000
 R5S  N30  C26  C27  110.51  3.000
 R5S  N25  C26  C27  124.54  3.000
 R5S  H10  C28  H9   107.06  3.000
 R5S  H10  C28  C29  111.05  3.000
 R5S  H9   C28  C29  111.07  3.000
 R5S  H10  C28  C27  111.46  3.000
 R5S  H9   C28  C27  113.47  3.000
 R5S  C29  C28  C27  102.79  3.000
 R5S  N01  C02  C03  180.00  3.000
 R5S  H12  C03  H11  107.43  3.000
 R5S  H12  C03  C04  110.62  3.000
 R5S  H11  C03  C04  109.33  3.000
 R5S  H12  C03  C02  108.75  3.000
 R5S  H11  C03  C02  108.83  3.000
 R5S  C04  C03  C02  111.78  3.000
 R5S  H14  C04  H13  108.05  3.000
 R5S  H14  C04  N05  109.28  3.000
 R5S  H13  C04  N05  108.07  3.000
 R5S  H14  C04  C03  108.78  3.000
 R5S  H13  C04  C03  110.62  3.000
 R5S  N05  C04  C03  111.95  3.000
 R5S  H15  C07  N06  120.55  3.000
 R5S  H15  C07  C08  127.82  3.000
 R5S  N06  C07  C08  111.62  3.000
 R5S  C31  C08  C09  129.54  3.000
 R5S  C09  C08  C07  126.82  3.000
 R5S  C31  C08  C07  103.64  3.000
 R5S  N10  C09  C27  120.56  3.000
 R5S  C27  C09  C08  123.87  3.000
 R5S  N10  C09  C08  115.57  3.000
 R5S  N25  C11  N10  126.98  3.000
 R5S  N25  C11  N12  112.93  3.000
 R5S  N10  C11  N12  120.09  3.000
 R5S  H16  C14  C15  119.33  3.000
 R5S  H16  C14  C13  119.52  3.000
 R5S  C15  C14  C13  121.16  3.000
 R5S  C23  C16  C17  121.39  3.000
 R5S  C17  C16  C15  121.70  3.000
 R5S  C23  C16  C15  116.91  3.000
 R5S  H18  C18  H17  107.08  3.000
 R5S  H18  C18  C19  109.65  3.000
 R5S  H17  C18  C19  109.10  3.000
 R5S  H18  C18  C17  110.11  3.000
 R5S  H17  C18  C17  109.98  3.000
 R5S  C19  C18  C17  110.83  3.000
 R5S  H20  C19  H19  106.74  3.000
 R5S  H20  C19  N20  108.94  3.000
 R5S  H19  C19  N20  112.42  3.000
 R5S  H20  C19  C18  109.91  3.000
 R5S  H19  C19  C18  108.69  3.000
 R5S  N20  C19  C18  110.07  3.000
 R5S  H21  C23  C16  119.21  3.000
 R5S  H21  C23  C24  118.17  3.000
 R5S  C16  C23  C24  122.61  3.000
 R5S  C09  C27  C28  135.16  3.000
 R5S  C28  C27  C26  108.75  3.000
 R5S  C09  C27  C26  116.07  3.000
 R5S  H26  C29  H22  107.84  3.000
 R5S  H26  C29  N30  111.03  3.000
 R5S  H22  C29  N30  110.70  3.000
 R5S  H26  C29  C28  112.25  3.000
 R5S  H22  C29  C28  111.00  3.000
 R5S  N30  C29  C28  104.05  3.000
 R5S  H23  C31  N05  120.96  3.000
 R5S  H23  C31  C08  132.27  3.000
 R5S  N05  C31  C08  106.77  3.000
 R5S  N06  N05  C31  112.66  3.000
 R5S  C31  N05  C04  127.34  3.000
 R5S  N06  N05  C04  119.92  3.000
 R5S  N05  N06  C07  105.30  3.000
 R5S  C11  N10  C09  117.79  3.000
 R5S  H24  N20  C19  109.49  3.000
 R5S  H24  N20  C21  109.45  3.000
 R5S  C19  N20  C21  111.57  3.000
 R5S  C11  N25  C26  114.05  3.000
 R5S  H25  N30  C29  121.62  3.000
 R5S  H25  N30  C26  121.60  3.000
 R5S  C29  N30  C26  111.25  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
 R5S  CONST_01  C16  C23  C24  C13    0.00   0.0  0
 R5S  CONST_02  C16  C15  C14  C13    0.00   0.0  0
 R5S  CONST_03  C24  C23  C16  C15    0.00   0.0  0
 R5S  CONST_04  C24  C13  C14  C15    0.00   0.0  0
 R5S  CONST_05  C08  C09  C27  C26  180.00   0.0  0
 R5S  CONST_06  N10  C09  C27  C26    0.00   0.0  0
 R5S  CONST_07  N10  C11  N25  C26    0.00   0.0  0
 R5S  CONST_08  C31  N05  N06  C07    0.00   0.0  0
 R5S  CONST_09  N05  C31  C08  C07    0.00   0.0  0
 R5S  CONST_10  N10  C09  C08  C07    0.00   0.0  0
 R5S  CONST_11  C27  C09  C08  C07  180.00   0.0  0
 R5S  CONST_12  N05  N06  C07  C08    0.00   0.0  0
 R5S  CONST_13  N06  N05  C31  C08    0.00   0.0  0
 R5S  CONST_14  C11  N10  C09  C08  180.00   0.0  0
 R5S  CONST_15  N06  C07  C08  C09  180.00   0.0  0
 R5S  CONST_16  N05  C31  C08  C09  180.00   0.0  0
 R5S  CONST_17  N25  C11  N10  C09    0.00   0.0  0
 R5S  CONST_18  N25  C26  C27  C09    0.00   0.0  0
 R5S  CONST_19  C27  C09  N10  C11    0.00   0.0  0
 R5S  CONST_20  C27  C26  N25  C11    0.00   0.0  0
 R5S  CONST_21  C23  C24  C13  C14    0.00   0.0  0
 R5S  CONST_22  C23  C16  C15  C14    0.00   0.0  0
 R5S  CONST_23  C31  C08  C09  C27    0.00   0.0  0
 R5S  CONST_24  N06  C07  C08  C31    0.00   0.0  0
 R5S  CONST_25  N10  C09  C08  C31  180.00   0.0  0
 R5S  CONST_26  C24  C23  C16  C17  180.00   0.0  0
 R5S  CONST_27  C14  C15  C16  C17  180.00   0.0  0
 R5S  CONST_28  C08  C09  C27  C28    0.00   0.0  0
 R5S  CONST_29  C23  C24  C13  N12  180.00   0.0  0
 R5S  CONST_30  C15  C14  C13  N12  180.00   0.0  0
 R5S  CONST_31  C09  N10  C11  N12  180.00   0.0  0
 R5S  CONST_32  C26  N25  C11  N12  180.00   0.0  0
 R5S  CONST_33  C07  N06  N05  C04  180.00   0.0  0
 R5S  CONST_34  C08  C31  N05  C04  180.00   0.0  0
 R5S  CONST_35  H21  C23  C24  C13  180.00   0.0  0
 R5S  CONST_36  H2   C15  C14  C13  180.00   0.0  0
 R5S  CONST_37  H16  C14  C13  C24  180.00   0.0  0
 R5S  CONST_38  H23  C31  C08  C07  180.00   0.0  0
 R5S  CONST_39  H15  C07  C08  C09    0.00   0.0  0
 R5S  CONST_40  H8   C24  C13  C14  180.00   0.0  0
 R5S  Var_01    N20  C21  C22  C17  -57.21  30.0  1
 R5S  Var_02    N20  C19  C18  C17   57.14  30.0  1
 R5S  Var_03    C18  C19  N20  C21  -61.78  30.0  1
 R5S  Var_04    C19  N20  C21  C22   61.79  30.0  1
 R5S  Var_05    C29  C28  C27  C26    9.65  30.0  1
 R5S  Var_06    C28  C29  N30  C26   16.28  30.0  1
 R5S  Var_07    N30  C29  C28  C27  -14.98  30.0  1
 R5S  Var_08    C29  N30  C26  C27  -10.65  30.0  1
 R5S  Var_09    N10  C11  N12  C13   -1.92  30.0  2
 R5S  Var_10    C11  N12  C13  C24  -11.56  30.0  2
 R5S  Var_11    N06  N05  C04  C03   67.90  30.0  2
 R5S  Var_12    N05  C04  C03  C02   59.26  30.0  1

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
 R5S  chir_01  C17  C22  C16  C18  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
 R5S  plan-1  C04  0.020
 R5S  plan-1  C07  0.020
 R5S  plan-1  C08  0.020
 R5S  plan-1  C09  0.020
 R5S  plan-1  C31  0.020
 R5S  plan-1  N05  0.020
 R5S  plan-1  N06  0.020
 R5S  plan-1  H15  0.020
 R5S  plan-1  H23  0.020
 R5S  plan-2  N12  0.020
 R5S  plan-2  C26  0.020
 R5S  plan-2  C28  0.020
 R5S  plan-2  C08  0.020
 R5S  plan-2  C09  0.020
 R5S  plan-2  C11  0.020
 R5S  plan-2  C27  0.020
 R5S  plan-2  N10  0.020
 R5S  plan-2  N25  0.020
 R5S  plan-2  N30  0.020
 R5S  plan-3  N12  0.020
 R5S  plan-3  C13  0.020
 R5S  plan-3  C15  0.020
 R5S  plan-3  C17  0.020
 R5S  plan-3  C24  0.020
 R5S  plan-3  C14  0.020
 R5S  plan-3  C16  0.020
 R5S  plan-3  C23  0.020
 R5S  plan-3  H2   0.020
 R5S  plan-3  H8   0.020
 R5S  plan-3  H16  0.020
 R5S  plan-3  H21  0.020

