# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 20:42:33 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: 1-[[4-(cyclopropylmethyl)-5-[2-(pyridin-4-ylamino)pyrimidin-4-yl]pyrimidin-2-yl]amino]-2-methyl-propan-2-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(O)CNc1ncc(c(CC2CC2)n1)c3ccnc(Nc4ccncc4)n3
#
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
 5QS  5QS  1-[[4-(cyclopropylmethyl)-5-[2-(pyridin-4-ylamino)pyrimidin-4-yl]pyrimidin-2-yl]amino]-2-methyl-propan-2-ol  ligand  54  29  .  2022-09-22  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_5QS
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
 5QS  C1   C  CT    0   0.146   6.8952  -0.0721  -0.4525
 5QS  C2   C  CH3   0  -0.653   6.7213  -0.9607  -1.6771
 5QS  C3   C  CH2   0  -0.249   5.6182   0.7296  -0.1682
 5QS  C11  C  CR6   0   0.454  -5.2597  -0.0240  -0.2989
 5QS  C12  C  CR16  0  -0.424  -5.9109  -1.1945  -0.7101
 5QS  C13  C  CR16  0  -0.066  -7.2868  -1.2073  -0.8035
 5QS  C14  C  CR16  0  -0.072  -7.4395   0.9429  -0.1365
 5QS  C15  C  CR16  0  -0.377  -6.0668   1.0784  -0.0045
 5QS  C16  C  CR6   0   0.327   1.1002  -0.3914   0.7612
 5QS  C17  C  CH2   0  -0.539   0.2119  -1.4751   1.3009
 5QS  C18  C  CH1   0  -0.232  -0.2335  -2.4207   0.2063
 5QS  C19  C  CH2   0  -0.497  -0.4313  -3.8732   0.5135
 5QS  C20  C  CH2   0  -0.479   0.7224  -3.4338  -0.3388
 5QS  O    O  OH1   0  -0.671   7.1669  -0.9453   0.6368
 5QS  C    C  CH3   0  -0.670   8.0506   0.9013  -0.6579
 5QS  N    N  NH1   0  -0.653   4.5311  -0.1511   0.1789
 5QS  C4   C  CR6   0   0.600   3.2434   0.2141   0.2307
 5QS  N6   N  N     0  -0.468   2.3839  -0.6949   0.7104
 5QS  C6   C  CR6   0  -0.117   0.6435   0.8747   0.3416
 5QS  C5   C  CR16  0  -0.020   1.6307   1.7397  -0.1242
 5QS  N1   N  N     0  -0.466   2.9107   1.4379  -0.1957
 5QS  C7   C  CR6   0   0.247  -0.7498   1.3299   0.3796
 5QS  N5   N  N     0  -0.484  -1.7086   0.4661   0.0770
 5QS  C10  C  CR6   0   0.611  -2.9681   0.8984   0.1061
 5QS  N2   N  N     0  -0.463  -3.3670   2.1275   0.3967
 5QS  C9   C  CR16  0   0.007  -2.4017   2.9904   0.6955
 5QS  C8   C  CR16  0  -0.396  -1.0661   2.6522   0.7121
 5QS  N3   N  NH1   0  -0.772  -3.8866  -0.0652  -0.2146
 5QS  N4   N  N     0  -0.424  -8.0631  -0.1625  -0.5252
 5QS  H1   H  HCH3  0   0.228   6.5283  -0.3547  -2.5622
 5QS  H2   H  HCH3  0   0.236   7.6269  -1.5406  -1.8612
 5QS  H3   H  HCH3  0   0.236   5.8905  -1.6570  -1.5599
 5QS  H4   H  HCH2  0   0.235   5.8096   1.4497   0.6387
 5QS  H5   H  HCH2  0   0.245   5.3502   1.3133  -1.0492
 5QS  H6   H  HCR6  0   0.280  -5.3465  -2.0851  -0.9572
 5QS  H7   H  HCR6  0   0.263  -7.7874  -2.1147  -1.1230
 5QS  H8   H  HCR6  0   0.261  -8.0694   1.7961   0.0926
 5QS  H9   H  HCR6  0   0.293  -5.6478   2.0155   0.3197
 5QS  H10  H  HCH2  0   0.254   0.7862  -2.0309   2.0456
 5QS  H11  H  HCH2  0   0.254  -0.6605  -1.0593   1.8038
 5QS  H12  H  HCH1  0   0.262  -0.9253  -1.9777  -0.4999
 5QS  H13  H  HCH2  0   0.241  -0.2173  -4.2160   1.5191
 5QS  H14  H  HCH2  0   0.247  -1.2559  -4.3886   0.0377
 5QS  H15  H  HCH2  0   0.245   0.6901  -3.6504  -1.3990
 5QS  H16  H  HCH2  0   0.243   1.7157  -3.4688   0.0906
 5QS  H17  H  HOH1  0   0.448   7.3619  -0.4108   1.4147
 5QS  H18  H  HCH3  0   0.232   8.2041   1.5248   0.2265
 5QS  H19  H  HCH3  0   0.241   8.9772   0.3610  -0.8556
 5QS  H20  H  HCH3  0   0.231   7.8645   1.5666  -1.5017
 5QS  H21  H  HNH1  0   0.389   4.7663  -1.0156   0.6422
 5QS  H22  H  HCR6  0   0.269   1.3574   2.7284  -0.4805
 5QS  H23  H  HCR6  0   0.277  -2.7174   3.9973   0.9435
 5QS  H24  H  HCR6  0   0.278  -0.3133   3.3742   0.9912
 5QS  H25  H  HNH1  0   0.413  -3.4631  -0.9534  -0.4402

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
 5QS  C    C1   single    1.525  0.020  1.525
 5QS  C1   C3   single    1.534  0.020  1.534
 5QS  C1   O    single    1.422  0.020  1.422
 5QS  C1   C2   single    1.523  0.020  1.523
 5QS  C3   N    single    1.441  0.020  1.441
 5QS  C20  C19  single    1.500  0.020  1.500
 5QS  C20  C18  single    1.496  0.020  1.496
 5QS  C19  C18  single    1.498  0.020  1.498
 5QS  N    C4   single    1.339  0.020  1.339
 5QS  N6   C4   aromatic  1.340  0.020  1.340
 5QS  N6   C16  aromatic  1.320  0.020  1.320
 5QS  C18  C17  single    1.513  0.020  1.513
 5QS  C14  N4   aromatic  1.327  0.020  1.327
 5QS  C14  C15  aromatic  1.386  0.020  1.386
 5QS  N4   C13  aromatic  1.331  0.020  1.331
 5QS  C17  C16  single    1.502  0.020  1.502
 5QS  C4   N1   aromatic  1.338  0.020  1.338
 5QS  C16  C6   aromatic  1.410  0.020  1.410
 5QS  C15  C11  aromatic  1.398  0.020  1.398
 5QS  C13  C12  aromatic  1.379  0.020  1.379
 5QS  N1   C5   aromatic  1.317  0.020  1.317
 5QS  C6   C5   aromatic  1.393  0.020  1.393
 5QS  C6   C7   single    1.466  0.020  1.466
 5QS  C11  C12  aromatic  1.401  0.020  1.401
 5QS  C11  N3   single    1.376  0.020  1.376
 5QS  N5   C7   aromatic  1.326  0.020  1.326
 5QS  N5   C10  aromatic  1.332  0.020  1.332
 5QS  C7   C8   aromatic  1.400  0.020  1.400
 5QS  N3   C10  single    1.369  0.020  1.369
 5QS  C10  N2   aromatic  1.324  0.020  1.324
 5QS  C8   C9   aromatic  1.378  0.020  1.378
 5QS  N2   C9   aromatic  1.329  0.020  1.329
 5QS  C2   H1   single    0.970  0.020  1.090
 5QS  C2   H2   single    0.970  0.020  1.090
 5QS  C2   H3   single    0.970  0.020  1.090
 5QS  C3   H4   single    0.970  0.020  1.090
 5QS  C3   H5   single    0.970  0.020  1.090
 5QS  C12  H6   single    0.930  0.020  1.080
 5QS  C13  H7   single    0.930  0.020  1.080
 5QS  C14  H8   single    0.930  0.020  1.080
 5QS  C15  H9   single    0.930  0.020  1.080
 5QS  C17  H10  single    0.970  0.020  1.090
 5QS  C17  H11  single    0.970  0.020  1.090
 5QS  C18  H12  single    0.970  0.020  1.090
 5QS  C19  H13  single    0.970  0.020  1.090
 5QS  C19  H14  single    0.970  0.020  1.090
 5QS  C20  H15  single    0.970  0.020  1.090
 5QS  C20  H16  single    0.970  0.020  1.090
 5QS  O    H17  single    0.850  0.020  0.980
 5QS  C    H18  single    0.970  0.020  1.090
 5QS  C    H19  single    0.970  0.020  1.090
 5QS  C    H20  single    0.970  0.020  1.090
 5QS  N    H21  single    0.860  0.020  1.020
 5QS  C5   H22  single    0.930  0.020  1.080
 5QS  C9   H23  single    0.930  0.020  1.080
 5QS  C8   H24  single    0.930  0.020  1.080
 5QS  N3   H25  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
 5QS  C    C1   O    110.51  3.000
 5QS  O    C1   C3   109.74  3.000
 5QS  C    C1   C3   108.79  3.000
 5QS  O    C1   C2   106.23  3.000
 5QS  C3   C1   C2   111.03  3.000
 5QS  C    C1   C2   110.53  3.000
 5QS  H3   C2   H2   108.13  3.000
 5QS  H3   C2   H1   107.91  3.000
 5QS  H2   C2   H1   107.79  3.000
 5QS  H3   C2   C1   111.91  3.000
 5QS  H2   C2   C1   110.55  3.000
 5QS  H1   C2   C1   110.41  3.000
 5QS  H5   C3   H4   106.59  3.000
 5QS  H5   C3   N    109.65  3.000
 5QS  H4   C3   N    110.80  3.000
 5QS  H5   C3   C1   109.54  3.000
 5QS  H4   C3   C1   109.49  3.000
 5QS  N    C3   C1   110.67  3.000
 5QS  N3   C11  C15  125.94  3.000
 5QS  N3   C11  C12  117.17  3.000
 5QS  C15  C11  C12  116.89  3.000
 5QS  H6   C12  C13  119.80  3.000
 5QS  H6   C12  C11  120.78  3.000
 5QS  C13  C12  C11  119.43  3.000
 5QS  H7   C13  N4   116.69  3.000
 5QS  H7   C13  C12  119.23  3.000
 5QS  N4   C13  C12  124.08  3.000
 5QS  H8   C14  N4   116.35  3.000
 5QS  H8   C14  C15  118.56  3.000
 5QS  N4   C14  C15  125.08  3.000
 5QS  H9   C15  C14  119.96  3.000
 5QS  H9   C15  C11  121.69  3.000
 5QS  C14  C15  C11  118.36  3.000
 5QS  C6   C16  N6   120.66  3.000
 5QS  C6   C16  C17  124.30  3.000
 5QS  N6   C16  C17  115.03  3.000
 5QS  H11  C17  H10  107.48  3.000
 5QS  H11  C17  C18  109.67  3.000
 5QS  H10  C17  C18  109.26  3.000
 5QS  H11  C17  C16  111.36  3.000
 5QS  H10  C17  C16  107.53  3.000
 5QS  C18  C17  C16  111.41  3.000
 5QS  H12  C18  C20  116.58  3.000
 5QS  H12  C18  C19  116.49  3.000
 5QS  C20  C18  C19   60.15  3.000
 5QS  H12  C18  C17  113.82  3.000
 5QS  C19  C18  C17  119.77  3.000
 5QS  C20  C18  C17  119.91  3.000
 5QS  H14  C19  H13  114.05  3.000
 5QS  H14  C19  C20  118.40  3.000
 5QS  H13  C19  C20  117.90  3.000
 5QS  H14  C19  C18  118.17  3.000
 5QS  H13  C19  C18  118.10  3.000
 5QS  C20  C19  C18   59.86  3.000
 5QS  H16  C20  H15  114.17  3.000
 5QS  H16  C20  C19  118.08  3.000
 5QS  H15  C20  C19  118.35  3.000
 5QS  H16  C20  C18  117.62  3.000
 5QS  H15  C20  C18  118.25  3.000
 5QS  C19  C20  C18   59.99  3.000
 5QS  H17  O    C1   108.45  3.000
 5QS  H20  C    H19  107.87  3.000
 5QS  H20  C    H18  107.58  3.000
 5QS  H19  C    H18  108.06  3.000
 5QS  H20  C    C1   111.37  3.000
 5QS  H19  C    C1   110.61  3.000
 5QS  H18  C    C1   111.20  3.000
 5QS  H21  N    C4   116.11  3.000
 5QS  H21  N    C3   117.28  3.000
 5QS  C4   N    C3   124.59  3.000
 5QS  N1   C4   N6   125.10  3.000
 5QS  N1   C4   N    118.43  3.000
 5QS  N6   C4   N    116.46  3.000
 5QS  C4   N6   C16  118.79  3.000
 5QS  C7   C6   C5   119.30  3.000
 5QS  C7   C6   C16  125.37  3.000
 5QS  C5   C6   C16  115.32  3.000
 5QS  H22  C5   N1   115.81  3.000
 5QS  H22  C5   C6   119.79  3.000
 5QS  N1   C5   C6   124.39  3.000
 5QS  C5   N1   C4   115.72  3.000
 5QS  C8   C7   N5   120.42  3.000
 5QS  C8   C7   C6   120.94  3.000
 5QS  N5   C7   C6   118.63  3.000
 5QS  C10  N5   C7   117.87  3.000
 5QS  N3   C10  N2   120.16  3.000
 5QS  N2   C10  N5   126.21  3.000
 5QS  N3   C10  N5   113.63  3.000
 5QS  C9   N2   C10  115.67  3.000
 5QS  H23  C9   C8   120.50  3.000
 5QS  H23  C9   N2   116.30  3.000
 5QS  C8   C9   N2   123.19  3.000
 5QS  H24  C8   C9   120.98  3.000
 5QS  H24  C8   C7   122.38  3.000
 5QS  C9   C8   C7   116.62  3.000
 5QS  H25  N3   C10  112.96  3.000
 5QS  H25  N3   C11  115.55  3.000
 5QS  C10  N3   C11  131.49  3.000
 5QS  C14  N4   C13  116.16  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
 5QS  CONST_01  N4   C14  C15  C11     0.00   0.0  0
 5QS  CONST_02  N4   C13  C12  C11     0.00   0.0  0
 5QS  CONST_03  C14  N4   C13  C12     0.00   0.0  0
 5QS  CONST_04  C14  C15  C11  C12     0.00   0.0  0
 5QS  CONST_05  C15  C14  N4   C13     0.00   0.0  0
 5QS  CONST_06  C15  C11  C12  C13     0.00   0.0  0
 5QS  CONST_07  N1   C4   N6   C16     0.00   0.0  0
 5QS  CONST_08  N1   C5   C6   C16     0.00   0.0  0
 5QS  CONST_11  C6   C16  N6   C4      0.00   0.0  0
 5QS  CONST_12  C6   C5   N1   C4      0.00   0.0  0
 5QS  CONST_13  C5   N1   C4   N6      0.00   0.0  0
 5QS  CONST_14  C5   C6   C16  N6      0.00   0.0  0
 5QS  CONST_15  C7   C6   C16  N6    180.00   0.0  0
 5QS  CONST_16  C10  N5   C7   C6    180.00   0.0  0
 5QS  CONST_17  C9   C8   C7   C6    180.00   0.0  0
 5QS  CONST_20  C7   C6   C5   N1    180.00   0.0  0
 5QS  CONST_21  N2   C10  N5   C7      0.00   0.0  0
 5QS  CONST_22  N2   C9   C8   C7      0.00   0.0  0
 5QS  CONST_23  C9   C8   C7   N5      0.00   0.0  0
 5QS  CONST_24  C9   N2   C10  N5      0.00   0.0  0
 5QS  CONST_25  C8   C7   N5   C10     0.00   0.0  0
 5QS  CONST_26  C8   C9   N2   C10     0.00   0.0  0
 5QS  CONST_27  N3   C11  C12  C13   180.00   0.0  0
 5QS  CONST_28  N3   C11  C15  C14   180.00   0.0  0
 5QS  CONST_29  N    C4   N6   C16   180.00   0.0  0
 5QS  CONST_30  C4   N6   C16  C17   180.00   0.0  0
 5QS  CONST_31  C5   C6   C16  C17   180.00   0.0  0
 5QS  CONST_32  C7   C6   C16  C17     0.00   0.0  0
 5QS  CONST_33  C5   N1   C4   N     180.00   0.0  0
 5QS  CONST_34  N3   C10  N5   C7    180.00   0.0  0
 5QS  CONST_35  N3   C10  N2   C9    180.00   0.0  0
 5QS  CONST_36  H8   C14  C15  C11   180.00   0.0  0
 5QS  CONST_37  H7   C13  C12  C11   180.00   0.0  0
 5QS  CONST_38  H9   C15  C11  C12   180.00   0.0  0
 5QS  CONST_39  H6   C12  C11  C15   180.00   0.0  0
 5QS  CONST_40  H22  C5   C6   C16   180.00   0.0  0
 5QS  CONST_41  H24  C8   C7   C6      0.00   0.0  0
 5QS  CONST_42  H23  C9   C8   C7    180.00   0.0  0
 5QS  CONST_43  N6   C4   N    C3    180.00   0.0  0
 5QS  CONST_44  N1   C4   N    C3      0.00   0.0  0
 5QS  CONST_45  H21  N    C4   N6      0.00   0.0  0
 5QS  Var_01    N5   C10  N3   C11  -179.95  30.0  2
 5QS  Var_02    C10  N3   C11  C12   177.61  30.0  2
 5QS  Var_03    C20  C18  C17  C16    75.48  30.0  1
 5QS  Var_04    C19  C20  C18  C17   109.29  30.0  1
 5QS  Var_05    N6   C16  C17  C18   -87.30  30.0  2
 5QS  Var_06    H13  C19  C20  C18  -107.99  30.0  1
 5QS  Var_07    C4   N    C3   C1   -166.61  30.0  3
 5QS  Var_08    N    C3   C1   C2     64.52  30.0  3
 5QS  Var_09    H18  C    C1   C2   -178.33  30.0  3
 5QS  Var_10    H1   C2   C1   C3     61.86  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
 5QS  chir_01  C18  C20  C19  C17  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
 5QS  plan-1  C11  0.020
 5QS  plan-1  C12  0.020
 5QS  plan-1  C13  0.020
 5QS  plan-1  C14  0.020
 5QS  plan-1  C15  0.020
 5QS  plan-1  N3   0.020
 5QS  plan-1  N4   0.020
 5QS  plan-1  H6   0.020
 5QS  plan-1  H7   0.020
 5QS  plan-1  H8   0.020
 5QS  plan-1  H9   0.020
 5QS  plan-2  C16  0.020
 5QS  plan-2  C17  0.020
 5QS  plan-2  N    0.020
 5QS  plan-2  C4   0.020
 5QS  plan-2  N6   0.020
 5QS  plan-2  C6   0.020
 5QS  plan-2  C5   0.020
 5QS  plan-2  N1   0.020
 5QS  plan-2  C7   0.020
 5QS  plan-2  H22  0.020
 5QS  plan-3  C6   0.020
 5QS  plan-3  C7   0.020
 5QS  plan-3  N5   0.020
 5QS  plan-3  C10  0.020
 5QS  plan-3  N2   0.020
 5QS  plan-3  C9   0.020
 5QS  plan-3  C8   0.020
 5QS  plan-3  N3   0.020
 5QS  plan-3  H23  0.020
 5QS  plan-3  H24  0.020
 5QS  plan-4  C3   0.020
 5QS  plan-4  N    0.020
 5QS  plan-4  C4   0.020
 5QS  plan-4  H21  0.020

