# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 30 08:00:31 2022
#   Inital geometry file: a 113 line input string
#   Ligand name: (3R)-1-(2-{[1-(pyrimidin-5-yl)cyclopropyl]amino}pyrimidine-5-carbonyl)piperidine-3-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(N1CCC[C@H](C1)C#N)c2cnc(NC3(CC3)c4cncnc4)nc2
#
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
 9SS  9SS  "(3R)-1-(2-{[1-(pyrimidin-5-yl)cyclopropyl]amino}pyrimidine-5-carbonyl)piperidine-3-carbonitrile"
  ligand  45  26  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_9SS
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
 9SS  N3   N  NH1   0  -0.667  17.0881  -30.4701  -29.4781
 9SS  C4   C  CR6   0   0.612  17.6097  -30.1861  -28.2708
 9SS  N2   N  N     0  -0.447  16.7499  -30.1303  -27.2443
 9SS  C7   C  CH2   0  -0.488  17.4309  -31.4903  -31.7064
 9SS  C6   C  CH2   0  -0.476  18.7108  -31.6766  -30.9575
 9SS  C9   C  CR16  0  -0.037  17.3907  -28.2093  -31.6519
 9SS  C13  C  C     0  -0.307  19.1302  -28.3085  -22.3260
 9SS  C8   C  CR6   0  -0.013  18.2975  -29.1326  -31.1475
 9SS  N5   N  N     0  -0.391  19.9871  -27.4869  -31.4667
 9SS  C18  C  CSP   0   0.135  15.5422  -26.4330  -23.6001
 9SS  C16  C  CR16  0  -0.372  16.4914  -27.4612  -23.1967
 9SS  C1   C  CR16  0  -0.015  17.2552  -29.8278  -26.0672
 9SS  C2   C  CR6   0  -0.243  18.6106  -29.5790  -25.8614
 9SS  C3   C  CR16  0   0.012  19.4098  -29.7158  -26.9909
 9SS  N1   N  N     0  -0.443  18.9301  -29.9975  -28.1861
 9SS  C5   C  CT    0   0.105  17.8527  -30.4794  -30.6823
 9SS  N4   N  N     0  -0.389  17.7489  -26.9951  -32.0460
 9SS  C10  C  CR16  0   0.048  19.0346  -26.6946  -31.9317
 9SS  C11  C  CR16  0  -0.033  19.6120  -28.6987  -31.0733
 9SS  C12  C  C     0   0.528  19.2404  -29.3443  -24.5355
 9SS  O1   O  O     0  -0.471  20.2447  -29.9745  -24.2354
 9SS  N6   N  NR6   0  -0.467  18.6629  -28.4489  -23.6981
 9SS  C14  C  C     0  -0.447  17.9466  -28.3473  -21.3693
 9SS  C15  C  C     0  -0.431  16.8976  -27.3014  -21.7255
 9SS  C17  C  C     0  -0.295  17.7346  -27.4151  -24.0980
 9SS  N7   N  NS    0  -0.260  14.7943  -25.6213  -23.9241
 9SS  H3   H  HNH1  0   0.402  16.0835  -30.5272  -29.5389
 9SS  H7   H  HCH2  0   0.266  17.4793  -31.1945  -32.7463
 9SS  H6   H  HCH2  0   0.270  16.5927  -32.1296  -31.4583
 9SS  H5   H  HCH2  0   0.267  18.7501  -32.4415  -30.1931
 9SS  H4   H  HCH2  0   0.262  19.6422  -31.5260  -31.4879
 9SS  H12  H  H     0   0.272  19.8320  -29.1068  -22.1024
 9SS  H11  H  H     0   0.243  19.6672  -27.3586  -22.2258
 9SS  H17  H  HCR6  0   0.324  15.9916  -28.4262  -23.3318
 9SS  H1   H  HCR6  0   0.285  16.5530  -29.8036  -25.2391
 9SS  H2   H  HCR6  0   0.275  20.4838  -29.5749  -26.9234
 9SS  H9   H  HCR6  0   0.262  19.3349  -25.7031  -32.2527
 9SS  H10  H  HCR6  0   0.271  20.3860  -29.3527  -30.6882
 9SS  H14  H  H     0   0.239  17.4985  -29.3442  -21.3915
 9SS  H13  H  H     0   0.256  18.3045  -28.1783  -20.3525
 9SS  H15  H  H     0   0.247  17.3029  -26.2971  -21.5729
 9SS  H16  H  H     0   0.268  16.0220  -27.3987  -21.0829
 9SS  H19  H  H     0   0.274  18.2183  -26.4382  -23.9844
 9SS  H18  H  H     0   0.296  17.4653  -27.5124  -25.1458
 9SS  H8   H  HCR6  0   0.274  16.3393  -28.4656  -31.7442

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
 9SS  C7   C6   single    1.495  0.020  1.495
 9SS  C7   C5   single    1.500  0.020  1.500
 9SS  C10  N5   aromatic  1.323  0.020  1.323
 9SS  C10  N4   aromatic  1.325  0.020  1.325
 9SS  N5   C11  aromatic  1.328  0.020  1.328
 9SS  N4   C9   aromatic  1.326  0.020  1.326
 9SS  C11  C8   aromatic  1.386  0.020  1.386
 9SS  C9   C8   aromatic  1.389  0.020  1.389
 9SS  C8   C5   single    1.493  0.020  1.493
 9SS  C6   C5   single    1.499  0.020  1.499
 9SS  C5   N3   single    1.426  0.020  1.426
 9SS  N3   C4   single    1.345  0.020  1.345
 9SS  C4   N1   aromatic  1.336  0.020  1.336
 9SS  C4   N2   aromatic  1.340  0.020  1.340
 9SS  N1   C3   aromatic  1.318  0.020  1.318
 9SS  N2   C1   aromatic  1.316  0.020  1.316
 9SS  C3   C2   aromatic  1.390  0.020  1.390
 9SS  C1   C2   aromatic  1.393  0.020  1.393
 9SS  C2   C12  single    1.487  0.020  1.487
 9SS  C12  O1   double    1.223  0.020  1.223
 9SS  C12  N6   single    1.355  0.020  1.355
 9SS  C17  N6   single    1.446  0.020  1.446
 9SS  C17  C16  single    1.536  0.020  1.536
 9SS  N7   C18  triple    1.150  0.020  1.150
 9SS  C18  C16  single    1.456  0.020  1.456
 9SS  N6   C13  single    1.456  0.020  1.456
 9SS  C16  C15  single    1.535  0.020  1.535
 9SS  C13  C14  single    1.522  0.020  1.522
 9SS  C15  C14  single    1.524  0.020  1.524
 9SS  N3   H3   single    0.860  0.020  1.020
 9SS  C7   H7   single    0.970  0.020  1.090
 9SS  C7   H6   single    0.970  0.020  1.090
 9SS  C6   H5   single    0.970  0.020  1.090
 9SS  C6   H4   single    0.970  0.020  1.090
 9SS  C9   H8   single    0.930  0.020  1.080
 9SS  C13  H12  single    0.970  0.020  1.090
 9SS  C13  H11  single    0.970  0.020  1.090
 9SS  C16  H17  single    0.970  0.020  1.090
 9SS  C1   H1   single    0.930  0.020  1.080
 9SS  C3   H2   single    0.930  0.020  1.080
 9SS  C10  H9   single    0.930  0.020  1.080
 9SS  C11  H10  single    0.930  0.020  1.080
 9SS  C14  H14  single    0.970  0.020  1.090
 9SS  C14  H13  single    0.970  0.020  1.090
 9SS  C15  H15  single    0.970  0.020  1.090
 9SS  C15  H16  single    0.970  0.020  1.090
 9SS  C17  H19  single    0.970  0.020  1.090
 9SS  C17  H18  single    0.970  0.020  1.090

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
 9SS  H3   N3   C5   118.88  3.000
 9SS  H3   N3   C4   116.90  3.000
 9SS  C5   N3   C4   123.44  3.000
 9SS  N1   C4   N2   125.41  3.000
 9SS  N2   C4   N3   116.57  3.000
 9SS  N1   C4   N3   118.01  3.000
 9SS  C1   N2   C4   116.63  3.000
 9SS  H6   C7   H7   114.59  3.000
 9SS  H6   C7   C5   117.33  3.000
 9SS  H7   C7   C5   117.35  3.000
 9SS  H6   C7   C6   118.32  3.000
 9SS  H7   C7   C6   118.51  3.000
 9SS  C5   C7   C6    60.06  3.000
 9SS  H4   C6   H5   114.41  3.000
 9SS  H4   C6   C5   118.13  3.000
 9SS  H5   C6   C5   117.12  3.000
 9SS  H4   C6   C7   118.29  3.000
 9SS  H5   C6   C7   118.24  3.000
 9SS  C5   C6   C7    60.13  3.000
 9SS  H8   C9   N4   116.89  3.000
 9SS  H8   C9   C8   120.40  3.000
 9SS  N4   C9   C8   122.71  3.000
 9SS  H11  C13  H12  107.55  3.000
 9SS  H11  C13  C14  110.22  3.000
 9SS  H12  C13  C14  110.74  3.000
 9SS  H11  C13  N6   109.08  3.000
 9SS  H12  C13  N6   109.30  3.000
 9SS  C14  C13  N6   109.89  3.000
 9SS  C11  C8   C5   123.25  3.000
 9SS  C5   C8   C9   121.23  3.000
 9SS  C11  C8   C9   115.50  3.000
 9SS  C11  N5   C10  116.55  3.000
 9SS  N7   C18  C16  180.00  3.000
 9SS  H17  C16  C17  108.86  3.000
 9SS  H17  C16  C15  109.32  3.000
 9SS  C17  C16  C15  110.19  3.000
 9SS  H17  C16  C18  106.89  3.000
 9SS  C15  C16  C18  111.38  3.000
 9SS  C17  C16  C18  110.11  3.000
 9SS  H1   C1   C2   120.82  3.000
 9SS  H1   C1   N2   116.03  3.000
 9SS  C2   C1   N2   123.13  3.000
 9SS  C12  C2   C3   119.77  3.000
 9SS  C12  C2   C1   124.90  3.000
 9SS  C3   C2   C1   114.94  3.000
 9SS  H2   C3   N1   116.37  3.000
 9SS  H2   C3   C2   120.37  3.000
 9SS  N1   C3   C2   123.25  3.000
 9SS  C3   N1   C4   116.56  3.000
 9SS  C8   C5   C6   119.54  3.000
 9SS  C6   C5   C7    59.80  3.000
 9SS  C8   C5   C7   118.63  3.000
 9SS  C6   C5   N3   117.85  3.000
 9SS  C8   C5   N3   114.64  3.000
 9SS  C7   C5   N3   115.48  3.000
 9SS  C10  N4   C9   116.36  3.000
 9SS  H9   C10  N4   116.77  3.000
 9SS  H9   C10  N5   116.87  3.000
 9SS  N4   C10  N5   126.36  3.000
 9SS  H10  C11  N5   117.00  3.000
 9SS  H10  C11  C8   120.48  3.000
 9SS  N5   C11  C8   122.52  3.000
 9SS  N6   C12  O1   122.60  3.000
 9SS  N6   C12  C2   118.35  3.000
 9SS  O1   C12  C2   119.04  3.000
 9SS  C17  N6   C12  125.11  3.000
 9SS  C17  N6   C13  113.43  3.000
 9SS  C12  N6   C13  120.61  3.000
 9SS  H13  C14  H14  107.14  3.000
 9SS  H13  C14  C15  109.72  3.000
 9SS  H14  C14  C15  109.81  3.000
 9SS  H13  C14  C13  109.07  3.000
 9SS  H14  C14  C13  109.22  3.000
 9SS  C15  C14  C13  111.77  3.000
 9SS  H16  C15  H15  107.30  3.000
 9SS  H16  C15  C14  110.72  3.000
 9SS  H15  C15  C14  110.04  3.000
 9SS  H16  C15  C16  110.07  3.000
 9SS  H15  C15  C16  109.12  3.000
 9SS  C14  C15  C16  109.57  3.000
 9SS  H18  C17  H19  106.81  3.000
 9SS  H18  C17  N6   111.22  3.000
 9SS  H19  C17  N6   108.98  3.000
 9SS  H18  C17  C16  111.26  3.000
 9SS  H19  C17  C16  108.85  3.000
 9SS  N6   C17  C16  109.62  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
 9SS  CONST_01  C2   C3   N1   C4      0.00   0.0  0
 9SS  CONST_02  C2   C1   N2   C4      0.00   0.0  0
 9SS  CONST_03  C3   N1   C4   N2      0.00   0.0  0
 9SS  CONST_04  C3   C2   C1   N2      0.00   0.0  0
 9SS  CONST_05  N5   C10  N4   C9      0.00   0.0  0
 9SS  CONST_06  N5   C11  C8   C9      0.00   0.0  0
 9SS  CONST_07  C10  N5   C11  C8      0.00   0.0  0
 9SS  CONST_08  C10  N4   C9   C8      0.00   0.0  0
 9SS  CONST_09  N1   C4   N2   C1      0.00   0.0  0
 9SS  CONST_10  N1   C3   C2   C1      0.00   0.0  0
 9SS  CONST_11  C11  N5   C10  N4      0.00   0.0  0
 9SS  CONST_12  C11  C8   C9   N4      0.00   0.0  0
 9SS  CONST_13  C5   C8   C11  N5    180.00   0.0  0
 9SS  CONST_14  N4   C9   C8   C5    180.00   0.0  0
 9SS  CONST_15  C3   N1   C4   N3    180.00   0.0  0
 9SS  CONST_16  C1   N2   C4   N3    180.00   0.0  0
 9SS  CONST_17  C12  C2   C1   N2    180.00   0.0  0
 9SS  CONST_18  C12  C2   C3   N1    180.00   0.0  0
 9SS  CONST_19  C2   C12  N6   C13   180.00   0.0  0
 9SS  CONST_21  C5   N3   C4   N2    180.00   0.0  0
 9SS  CONST_22  C5   N3   C4   N1      0.00   0.0  0
 9SS  CONST_23  H2   C3   N1   C4    180.00   0.0  0
 9SS  CONST_24  H1   C1   N2   C4    180.00   0.0  0
 9SS  CONST_25  H9   C10  N4   C9    180.00   0.0  0
 9SS  CONST_26  H10  C11  C8   C9    180.00   0.0  0
 9SS  CONST_27  H2   C3   C2   C1    180.00   0.0  0
 9SS  CONST_28  H1   C1   C2   C3    180.00   0.0  0
 9SS  CONST_29  H10  C11  C8   C5      0.00   0.0  0
 9SS  CONST_30  H8   C9   C8   C5      0.00   0.0  0
 9SS  CONST_31  H10  C11  N5   C10   180.00   0.0  0
 9SS  CONST_32  H8   C9   N4   C10   180.00   0.0  0
 9SS  CONST_33  H9   C10  N5   C11   180.00   0.0  0
 9SS  CONST_34  H8   C9   C8   C11   180.00   0.0  0
 9SS  CONST_35  O1   C12  N6   C13     0.00   0.0  0
 9SS  CONST_37  H3   N3   C4   N2      0.00   0.0  0
 9SS  CONST_38  H3   N3   C4   N1    180.00   0.0  0
 9SS  Var_01    C8   C5   C6   C7   -107.91  30.0  1
 9SS  Var_02    C11  C8   C5   C7   -110.04  30.0  2
 9SS  Var_03    C9   C8   C5   C7     72.00  30.0  2
 9SS  Var_04    C11  C8   C5   C6    -40.48  30.0  2
 9SS  Var_05    C9   C8   C5   C6    141.56  30.0  2
 9SS  Var_06    C16  C17  N6   C13   -60.63  30.0  1
 9SS  Var_07    C16  C15  C14  C13    53.68  30.0  1
 9SS  Var_08    C15  C14  C13  N6    -54.97  30.0  1
 9SS  Var_09    C17  N6   C13  C14    59.15  30.0  1
 9SS  Var_10    C6   C7   C5   N3   -108.75  30.0  1
 9SS  Var_11    C11  C8   C5   N3    107.81  30.0  2
 9SS  Var_12    C9   C8   C5   N3    -70.16  30.0  2
 9SS  Var_13    C7   C5   N3   C4    146.35  30.0  1
 9SS  Var_14    C8   C5   N3   C4    -70.27  30.0  1
 9SS  Var_15    C6   C5   N3   C4     78.58  30.0  1
 9SS  Var_16    C12  N6   C17  C16   129.92  30.0  1
 9SS  Var_17    N6   C12  C2   C1    -48.64  30.0  2
 9SS  Var_18    N6   C12  C2   C3    138.96  30.0  2
 9SS  Var_19    C14  C13  N6   C12  -130.87  30.0  1
 9SS  Var_20    H5   C6   C5   C7   -108.60  30.0  1
 9SS  Var_21    H4   C6   C5   C7    108.22  30.0  1
 9SS  Var_22    H7   C7   C5   C6   -108.80  30.0  1
 9SS  Var_23    H6   C7   C5   C6    108.58  30.0  1
 9SS  Var_24    H19  C17  N6   C13    58.41  30.0  1
 9SS  Var_25    H18  C17  N6   C13   175.90  30.0  1
 9SS  Var_26    H15  C15  C14  C13   -66.29  30.0  1
 9SS  Var_27    H16  C15  C14  C13   175.27  30.0  1
 9SS  Var_28    H7   C7   C5   C8      0.60  30.0  1
 9SS  Var_29    H6   C7   C5   C8   -142.02  30.0  1
 9SS  Var_30    H5   C6   C5   C8    143.49  30.0  1
 9SS  Var_31    H4   C6   C5   C8      0.31  30.0  1
 9SS  Var_32    H14  C14  C15  C16   -67.69  30.0  1
 9SS  Var_33    H13  C14  C15  C16   174.80  30.0  1
 9SS  Var_34    H14  C14  C13  N6     66.74  30.0  1
 9SS  Var_35    H13  C14  C13  N6   -176.47  30.0  1
 9SS  Var_36    H12  C13  C14  C15  -175.83  30.0  1
 9SS  Var_37    H11  C13  C14  C15    65.28  30.0  1
 9SS  Var_38    H12  C13  N6   C17  -179.13  30.0  1
 9SS  Var_39    H11  C13  N6   C17   -61.79  30.0  1
 9SS  Var_40    O1   C12  C2   C1    130.45  30.0  2
 9SS  Var_41    O1   C12  C2   C3    -41.95  30.0  2
 9SS  Var_42    H7   C7   C5   N3    142.45  30.0  1
 9SS  Var_43    H6   C7   C5   N3     -0.17  30.0  1
 9SS  Var_44    H5   C6   C5   N3     -3.80  30.0  1
 9SS  Var_45    H4   C6   C5   N3   -146.98  30.0  1
 9SS  Var_46    H3   N3   C5   C7    -44.13  30.0  3
 9SS  Var_47    H3   N3   C5   C6   -111.90  30.0  3
 9SS  Var_48    H3   N3   C5   C8     99.25  30.0  3
 9SS  Var_49    H19  C17  N6   C12  -111.04  30.0  1
 9SS  Var_50    H18  C17  N6   C12     6.45  30.0  1
 9SS  Var_51    H12  C13  N6   C12    -9.15  30.0  1
 9SS  Var_52    H11  C13  N6   C12   108.19  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
 9SS  chir_01  C16  C17  C18  C15  positiv
 9SS  chir_02  C5   C8   C6   N3   both

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
 9SS  plan-1  N3   0.020
 9SS  plan-1  C4   0.020
 9SS  plan-1  N2   0.020
 9SS  plan-1  C1   0.020
 9SS  plan-1  C2   0.020
 9SS  plan-1  C3   0.020
 9SS  plan-1  N1   0.020
 9SS  plan-1  C12  0.020
 9SS  plan-1  H1   0.020
 9SS  plan-1  H2   0.020
 9SS  plan-2  C9   0.020
 9SS  plan-2  C8   0.020
 9SS  plan-2  N5   0.020
 9SS  plan-2  C5   0.020
 9SS  plan-2  N4   0.020
 9SS  plan-2  C10  0.020
 9SS  plan-2  C11  0.020
 9SS  plan-2  H9   0.020
 9SS  plan-2  H10  0.020
 9SS  plan-2  H8   0.020
 9SS  plan-3  N3   0.020
 9SS  plan-3  C4   0.020
 9SS  plan-3  C5   0.020
 9SS  plan-3  H3   0.020
 9SS  plan-4  C13  0.020
 9SS  plan-4  C2   0.020
 9SS  plan-4  C12  0.020
 9SS  plan-4  O1   0.020
 9SS  plan-4  N6   0.020
 9SS  plan-4  C17  0.020

