# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 00:43:06 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: (3S)-1-[6-(2-aminopyrazolo[1,5-a]pyrimidin-3-yl)pyrimidin-4-yl]-N,N-diethylpiperidine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN(CC)C(=O)[C@H]1CCCN(C1)c2cc(ncn2)c3c(N)nn4cccnc34
#
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
 1P5  1P5  (3S)-1-[6-(2-aminopyrazolo[1,5-a]pyrimidin-3-yl)pyrimidin-4-yl]-N,N-diethylpiperidine-3-carboxamide  ligand  55  29  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1P5
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
 1P5  N3    N  NT    0  -0.456  -4.6226  -0.6099  -0.6818
 1P5  C4    C  CH2   0  -0.335  -5.9328  -0.6348  -0.0454
 1P5  C5    C  CH3   0  -0.654  -6.7637   0.6184  -0.2777
 1P5  C6    C  C     0   0.596  -3.5017  -0.1245  -0.0974
 1P5  C8    C  CH1   0  -0.419  -3.5853   0.3186   1.3548
 1P5  C10   C  CH2   0  -0.443  -3.3940  -0.8852   2.2957
 1P5  C15   C  CR6   0   0.616  -0.2690   1.2602   0.8396
 1P5  C17   C  CR6   0   0.334   1.8437   1.0259  -0.2593
 1P5  C21   C  CR5   0  -0.306   3.1029   0.3629  -0.5204
 1P5  C22   C  CR56  0   0.569   3.5779  -0.8443  -0.0061
 1P5  C24   C  CR16  0  -0.032   3.7895  -2.7941   1.1262
 1P5  C26   C  CR16  0   0.081   5.5550  -2.1257  -0.3166
 1P5  C1    C  CH3   0  -0.664  -4.5623   0.0528  -3.1007
 1P5  C2    C  CH2   0  -0.301  -4.5351  -1.0624  -2.0652
 1P5  O7    O  O     0  -0.487  -2.4383  -0.0810  -0.7038
 1P5  C11   C  CH2   0  -0.430  -1.9434  -1.3505   2.3368
 1P5  C12   C  CH2   0  -0.329  -1.0414  -0.1760   2.6888
 1P5  N13   N  NT    0  -0.480  -1.2046   0.9139   1.7490
 1P5  C14   C  CH2   0  -0.311  -2.5622   1.4142   1.6838
 1P5  C16   C  CR16  0  -0.503   0.9296   0.5464   0.6648
 1P5  N18   N  N     0  -0.520   1.5929   2.1404  -0.9778
 1P5  C19   C  CR16  0   0.052   0.4329   2.7256  -0.7457
 1P5  N20   N  N     0  -0.483  -0.4998   2.3632   0.1071
 1P5  N23   N  N     0  -0.443   3.0700  -1.7293   0.8543
 1P5  C25   C  CR16  0  -0.411   5.0508  -3.0438   0.5630
 1P5  N27   N  N     0  -0.353   4.8166  -1.0429  -0.5896
 1P5  N28   N  N     0  -0.354   5.1661  -0.0572  -1.4279
 1P5  C29   C  CR5   0   0.470   4.1449   0.7944  -1.3918
 1P5  N30   N  NH2   0  -0.851   4.1814   1.9446  -2.0932
 1P5  H4    H  HCH2  0   0.255  -6.4652  -1.5040  -0.4337
 1P5  H4A   H  HCH2  0   0.257  -5.8251  -0.8174   1.0224
 1P5  H5    H  HCH3  0   0.227  -6.2607   1.5078   0.1038
 1P5  H5A   H  HCH3  0   0.233  -6.9709   0.7753  -1.3356
 1P5  H5B   H  HCH3  0   0.234  -7.7205   0.5293   0.2379
 1P5  H8    H  HCH1  0   0.276  -4.5636   0.7583   1.5582
 1P5  H10   H  HCH2  0   0.241  -3.6919  -0.5747   3.3022
 1P5  H10A  H  HCH2  0   0.249  -4.0561  -1.7078   2.0170
 1P5  H24   H  HCR6  0   0.278   3.3632  -3.5023   1.8266
 1P5  H26   H  HCR6  0   0.325   6.5113  -2.2066  -0.8123
 1P5  H1    H  HCH3  0   0.230  -4.4905  -0.3741  -4.1019
 1P5  H1A   H  HCH3  0   0.225  -5.4869   0.6275  -3.0539
 1P5  H1B   H  HCH3  0   0.233  -3.7269   0.7384  -2.9694
 1P5  H2    H  HCH2  0   0.242  -3.6263  -1.6525  -2.1862
 1P5  H2A   H  HCH2  0   0.238  -5.3696  -1.7433  -2.2357
 1P5  H11   H  HCH2  0   0.242  -1.8265  -2.1327   3.0894
 1P5  H11A  H  HCH2  0   0.234  -1.6392  -1.7787   1.3788
 1P5  H12   H  HCH2  0   0.245  -1.3169   0.1970   3.6822
 1P5  H12A  H  HCH2  0   0.262   0.0003  -0.4771   2.7567
 1P5  H14   H  HCH2  0   0.277  -2.6165   2.2300   0.9694
 1P5  H14A  H  HCH2  0   0.247  -2.8276   1.8231   2.6653
 1P5  H16   H  HCR6  0   0.272   1.1473  -0.3645   1.1990
 1P5  H19   H  HCR6  0   0.243   0.2257   3.6202  -1.3266
 1P5  H25   H  HCR6  0   0.294   5.6129  -3.9299   0.8129
 1P5  HN30  H  HNH2  0   0.403   3.2994   2.4244  -2.1927
 1P5  HN3A  H  HNH2  0   0.385   4.8422   2.0181  -2.8481

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
 1P5  N3   C4    single    1.457  0.020  1.457
 1P5  N3   C6    single    1.354  0.020  1.354
 1P5  N3   C2    single    1.458  0.020  1.458
 1P5  C4   C5    single    1.521  0.020  1.521
 1P5  C6   C8    single    1.521  0.020  1.521
 1P5  C6   O7    double    1.225  0.020  1.225
 1P5  C8   C10   single    1.540  0.020  1.540
 1P5  C8   C14   single    1.535  0.020  1.535
 1P5  C10  C11   single    1.524  0.020  1.524
 1P5  C15  N13   single    1.350  0.020  1.350
 1P5  C15  C16   aromatic  1.406  0.020  1.406
 1P5  C15  N20   aromatic  1.344  0.020  1.344
 1P5  C17  C21   single    1.447  0.020  1.447
 1P5  C17  C16   aromatic  1.385  0.020  1.385
 1P5  C17  N18   aromatic  1.350  0.020  1.350
 1P5  C21  C22   aromatic  1.396  0.020  1.396
 1P5  C21  C29   aromatic  1.425  0.020  1.425
 1P5  C22  N23   aromatic  1.335  0.020  1.335
 1P5  C22  N27   aromatic  1.384  0.020  1.384
 1P5  C24  N23   aromatic  1.314  0.020  1.314
 1P5  C24  C25   aromatic  1.404  0.020  1.404
 1P5  C26  C25   aromatic  1.368  0.020  1.368
 1P5  C26  N27   aromatic  1.339  0.020  1.339
 1P5  C1   C2    single    1.522  0.020  1.522
 1P5  C11  C12   single    1.522  0.020  1.522
 1P5  C12  N13   single    1.448  0.020  1.448
 1P5  N13  C14   single    1.448  0.020  1.448
 1P5  N18  C19   aromatic  1.320  0.020  1.320
 1P5  C19  N20   aromatic  1.315  0.020  1.315
 1P5  N27  N28   aromatic  1.340  0.020  1.340
 1P5  N28  C29   aromatic  1.330  0.020  1.330
 1P5  C29  N30   single    1.348  0.020  1.348
 1P5  C4   H4    single    0.970  0.020  1.090
 1P5  C4   H4A   single    0.970  0.020  1.090
 1P5  C5   H5    single    0.970  0.020  1.090
 1P5  C5   H5A   single    0.970  0.020  1.090
 1P5  C5   H5B   single    0.970  0.020  1.090
 1P5  C8   H8    single    0.970  0.020  1.090
 1P5  C10  H10   single    0.970  0.020  1.090
 1P5  C10  H10A  single    0.970  0.020  1.090
 1P5  C24  H24   single    0.930  0.020  1.080
 1P5  C26  H26   single    0.930  0.020  1.080
 1P5  C1   H1    single    0.970  0.020  1.090
 1P5  C1   H1A   single    0.970  0.020  1.090
 1P5  C1   H1B   single    0.970  0.020  1.090
 1P5  C2   H2    single    0.970  0.020  1.090
 1P5  C2   H2A   single    0.970  0.020  1.090
 1P5  C11  H11   single    0.970  0.020  1.090
 1P5  C11  H11A  single    0.970  0.020  1.090
 1P5  C12  H12   single    0.970  0.020  1.090
 1P5  C12  H12A  single    0.970  0.020  1.090
 1P5  C14  H14   single    0.970  0.020  1.090
 1P5  C14  H14A  single    0.970  0.020  1.090
 1P5  C16  H16   single    0.930  0.020  1.080
 1P5  C19  H19   single    0.930  0.020  1.080
 1P5  C25  H25   single    0.930  0.020  1.080
 1P5  N30  HN30  single    0.890  0.020  1.040
 1P5  N30  HN3A  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
 1P5  C2    N3   C6    118.10  3.000
 1P5  C2    N3   C4    117.59  3.000
 1P5  C6    N3   C4    124.21  3.000
 1P5  H4A   C4   H4    105.30  3.000
 1P5  H4A   C4   C5    109.99  3.000
 1P5  H4    C4   C5    109.60  3.000
 1P5  H4A   C4   N3    110.02  3.000
 1P5  H4    C4   N3    107.28  3.000
 1P5  C5    C4   N3    114.23  3.000
 1P5  H5B   C5   H5A   107.70  3.000
 1P5  H5B   C5   H5    107.81  3.000
 1P5  H5A   C5   H5    108.05  3.000
 1P5  H5B   C5   C4    109.86  3.000
 1P5  H5A   C5   C4    111.77  3.000
 1P5  H5    C5   C4    111.50  3.000
 1P5  O7    C6   C8    120.67  3.000
 1P5  O7    C6   N3    121.18  3.000
 1P5  C8    C6   N3    118.10  3.000
 1P5  H8    C8   C14   105.66  3.000
 1P5  H8    C8   C10   108.20  3.000
 1P5  C14   C8   C10   110.14  3.000
 1P5  H8    C8   C6    110.16  3.000
 1P5  C14   C8   C6    112.09  3.000
 1P5  C10   C8   C6    110.42  3.000
 1P5  H10A  C10  H10   106.46  3.000
 1P5  H10A  C10  C11   110.73  3.000
 1P5  H10   C10  C11   108.72  3.000
 1P5  H10A  C10  C8    110.95  3.000
 1P5  H10   C10  C8    107.84  3.000
 1P5  C11   C10  C8    111.93  3.000
 1P5  N20   C15  C16   119.69  3.000
 1P5  N20   C15  N13   117.30  3.000
 1P5  C16   C15  N13   122.98  3.000
 1P5  N18   C17  C16   121.21  3.000
 1P5  N18   C17  C21   116.37  3.000
 1P5  C16   C17  C21   122.41  3.000
 1P5  C29   C21  C22   103.79  3.000
 1P5  C29   C21  C17   127.44  3.000
 1P5  C22   C21  C17   128.77  3.000
 1P5  N27   C22  N23   121.16  3.000
 1P5  N27   C22  C21   105.87  3.000
 1P5  N23   C22  C21   132.97  3.000
 1P5  H24   C24  C25   119.78  3.000
 1P5  H24   C24  N23   116.63  3.000
 1P5  C25   C24  N23   123.60  3.000
 1P5  H26   C26  N27   117.08  3.000
 1P5  H26   C26  C25   124.84  3.000
 1P5  N27   C26  C25   118.08  3.000
 1P5  H1B   C1   H1A   108.28  3.000
 1P5  H1B   C1   H1    107.86  3.000
 1P5  H1A   C1   H1    107.56  3.000
 1P5  H1B   C1   C2    111.45  3.000
 1P5  H1A   C1   C2    111.87  3.000
 1P5  H1    C1   C2    109.67  3.000
 1P5  H2A   C2   H2    106.42  3.000
 1P5  H2A   C2   C1    109.72  3.000
 1P5  H2    C2   C1    109.63  3.000
 1P5  H2A   C2   N3    107.23  3.000
 1P5  H2    C2   N3    108.86  3.000
 1P5  C1    C2   N3    114.65  3.000
 1P5  H11A  C11  H11   107.09  3.000
 1P5  H11A  C11  C12   109.89  3.000
 1P5  H11   C11  C12   109.27  3.000
 1P5  H11A  C11  C10   111.17  3.000
 1P5  H11   C11  C10   109.83  3.000
 1P5  C12   C11  C10   109.55  3.000
 1P5  H12A  C12  H12   106.17  3.000
 1P5  H12A  C12  N13   110.92  3.000
 1P5  H12   C12  N13   107.67  3.000
 1P5  H12A  C12  C11   111.64  3.000
 1P5  H12   C12  C11   108.86  3.000
 1P5  N13   C12  C11   111.34  3.000
 1P5  C14   N13  C12   113.25  3.000
 1P5  C14   N13  C15   122.05  3.000
 1P5  C12   N13  C15   123.51  3.000
 1P5  H14A  C14  H14   107.27  3.000
 1P5  H14A  C14  N13   108.40  3.000
 1P5  H14   C14  N13   109.64  3.000
 1P5  H14A  C14  C8    107.27  3.000
 1P5  H14   C14  C8    111.22  3.000
 1P5  N13   C14  C8    112.82  3.000
 1P5  H16   C16  C17   119.31  3.000
 1P5  H16   C16  C15   122.65  3.000
 1P5  C17   C16  C15   118.02  3.000
 1P5  C19   N18  C17   115.85  3.000
 1P5  H19   C19  N20   116.00  3.000
 1P5  H19   C19  N18   116.02  3.000
 1P5  N20   C19  N18   127.98  3.000
 1P5  C19   N20  C15   117.25  3.000
 1P5  C24   N23  C22   117.55  3.000
 1P5  H25   C25  C26   120.55  3.000
 1P5  H25   C25  C24   121.42  3.000
 1P5  C26   C25  C24   118.02  3.000
 1P5  N28   N27  C26   125.35  3.000
 1P5  N28   N27  C22   113.06  3.000
 1P5  C26   N27  C22   121.59  3.000
 1P5  C29   N28  N27   104.69  3.000
 1P5  N30   C29  N28   120.77  3.000
 1P5  N30   C29  C21   126.61  3.000
 1P5  N28   C29  C21   112.59  3.000
 1P5  HN3A  N30  HN30  117.75  3.000
 1P5  HN3A  N30  C29   118.08  3.000
 1P5  HN30  N30  C29   115.69  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
 1P5  CONST_01  C21  C17  C16  C15   180.00   0.0  0
 1P5  CONST_02  N18  C17  C16  C15     0.00   0.0  0
 1P5  CONST_03  N18  C19  N20  C15     0.00   0.0  0
 1P5  CONST_04  N23  C22  C21  C17     0.00   0.0  0
 1P5  CONST_05  N27  C22  C21  C17   180.00   0.0  0
 1P5  CONST_06  N28  C29  C21  C17   180.00   0.0  0
 1P5  CONST_07  N20  C15  C16  C17     0.00   0.0  0
 1P5  CONST_08  N20  C19  N18  C17     0.00   0.0  0
 1P5  CONST_09  C19  N18  C17  C21   180.00   0.0  0
 1P5  CONST_10  C24  N23  C22  C21   180.00   0.0  0
 1P5  CONST_11  C26  N27  C22  C21   180.00   0.0  0
 1P5  CONST_12  N28  N27  C22  C21     0.00   0.0  0
 1P5  CONST_13  N27  N28  C29  C21     0.00   0.0  0
 1P5  CONST_14  C16  C17  C21  C22     0.00   0.0  0
 1P5  CONST_15  N18  C17  C21  C22   180.00   0.0  0
 1P5  CONST_16  N28  C29  C21  C22     0.00   0.0  0
 1P5  CONST_17  C25  C24  N23  C22     0.00   0.0  0
 1P5  CONST_18  C25  C26  N27  C22     0.00   0.0  0
 1P5  CONST_19  C29  N28  N27  C22     0.00   0.0  0
 1P5  CONST_20  N27  C22  N23  C24     0.00   0.0  0
 1P5  CONST_21  N27  C26  C25  C24     0.00   0.0  0
 1P5  CONST_22  N23  C24  C25  C26     0.00   0.0  0
 1P5  CONST_23  N23  C22  N27  C26     0.00   0.0  0
 1P5  CONST_24  C29  N28  N27  C26   180.00   0.0  0
 1P5  CONST_25  C19  N20  C15  C16     0.00   0.0  0
 1P5  CONST_26  C29  C21  C17  C16   180.00   0.0  0
 1P5  CONST_27  C19  N18  C17  C16     0.00   0.0  0
 1P5  CONST_28  C29  C21  C17  N18     0.00   0.0  0
 1P5  CONST_29  C29  C21  C22  N23   180.00   0.0  0
 1P5  CONST_30  N28  N27  C22  N23   180.00   0.0  0
 1P5  CONST_31  N28  N27  C26  C25   180.00   0.0  0
 1P5  CONST_32  C29  C21  C22  N27     0.00   0.0  0
 1P5  CONST_33  N13  C15  C16  C17   180.00   0.0  0
 1P5  CONST_34  C19  N20  C15  N13   180.00   0.0  0
 1P5  CONST_35  N30  C29  C21  C17     0.00   0.0  0
 1P5  CONST_36  N30  C29  C21  C22   180.00   0.0  0
 1P5  CONST_37  N30  C29  N28  N27   180.00   0.0  0
 1P5  CONST_38  H19  C19  N20  C15   180.00   0.0  0
 1P5  CONST_39  H16  C16  C17  C21     0.00   0.0  0
 1P5  CONST_40  H24  C24  N23  C22   180.00   0.0  0
 1P5  CONST_41  H26  C26  N27  C22   180.00   0.0  0
 1P5  CONST_42  H25  C25  C24  N23   180.00   0.0  0
 1P5  CONST_45  C8   C6   N3   C4      0.00   0.0  0
 1P5  CONST_46  C2   N3   C6   C8    180.00   0.0  0
 1P5  CONST_47  O7   C6   N3   C4    180.00   0.0  0
 1P5  CONST_48  O7   C6   N3   C2      0.00   0.0  0
 1P5  Var_01    C12  C11  C10  C8     54.05  30.0  1
 1P5  Var_02    C15  N13  C14  C8    112.18  30.0  1
 1P5  Var_03    N13  C12  C11  C10   -57.14  30.0  1
 1P5  Var_04    C11  C12  N13  C15  -108.93  30.0  1
 1P5  Var_05    C16  C15  N13  C12     3.69  30.0  2
 1P5  Var_06    C1   C2   N3   C4     97.17  30.0  3
 1P5  Var_07    C6   N3   C4   C5     89.39  30.0  2
 1P5  Var_08    H5   C5   C4   N3    -59.84  30.0  3
 1P5  Var_09    H1   C1   C2   N3    179.88  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
 1P5  chir_01  C8  C6  C10  C14  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
 1P5  plan-1  C15   0.020
 1P5  plan-1  C17   0.020
 1P5  plan-1  C21   0.020
 1P5  plan-1  N13   0.020
 1P5  plan-1  C16   0.020
 1P5  plan-1  N18   0.020
 1P5  plan-1  C19   0.020
 1P5  plan-1  N20   0.020
 1P5  plan-1  H16   0.020
 1P5  plan-1  H19   0.020
 1P5  plan-2  C17   0.020
 1P5  plan-2  C21   0.020
 1P5  plan-2  C22   0.020
 1P5  plan-2  C24   0.020
 1P5  plan-2  C26   0.020
 1P5  plan-2  N23   0.020
 1P5  plan-2  C25   0.020
 1P5  plan-2  N27   0.020
 1P5  plan-2  N28   0.020
 1P5  plan-2  C29   0.020
 1P5  plan-2  N30   0.020
 1P5  plan-2  H24   0.020
 1P5  plan-2  H26   0.020
 1P5  plan-2  H25   0.020
 1P5  plan-3  C29   0.020
 1P5  plan-3  N30   0.020
 1P5  plan-3  HN30  0.020
 1P5  plan-3  HN3A  0.020
 1P5  plan-4  N3    0.020
 1P5  plan-4  C4    0.020
 1P5  plan-4  C6    0.020
 1P5  plan-4  C8    0.020
 1P5  plan-4  C2    0.020
 1P5  plan-4  O7    0.020

