# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 23 05:58:20 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: 3-(6-{[(1S)-1-(4-fluorophenyl)ethyl]amino}pyrimidin-4-yl)pyrazolo[1,5-a]pyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](Nc1cc(ncn1)c2c(N)nn3cccnc23)c4ccc(F)cc4
#
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
 1P6  1P6  3-(6-{[(1S)-1-(4-fluorophenyl)ethyl]amino}pyrimidin-4-yl)pyrazolo[1,5-a]pyrimidin-2-amine  ligand  42  26  .  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_1P6
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
 1P6  C1    C  CH3   0  -0.649  -1.9494  -0.3375   2.1972
 1P6  C2    C  CH1   0  -0.187  -2.1407  -0.0344   0.7119
 1P6  N4    N  NH1   0  -0.655  -1.6674   1.2913   0.3551
 1P6  C5    C  CR6   0   0.540  -0.3856   1.6308   0.1360
 1P6  N6    N  N     0  -0.474  -0.1584   2.9321  -0.1159
 1P6  C7    C  CR16  0   0.055   1.0901   3.2727  -0.3597
 1P6  N8    N  N     0  -0.515   2.1530   2.4909  -0.3850
 1P6  C9    C  CR6   0   0.340   1.9415   1.1835  -0.1255
 1P6  C10   C  CR16  0  -0.489   0.6673   0.7061   0.1467
 1P6  C11   C  CR5   0  -0.308   3.1019   0.3248  -0.1525
 1P6  C12   C  CR56  0   0.571   3.1660  -1.0582   0.0286
 1P6  N13   N  N     0  -0.442   2.2426  -1.9830   0.2957
 1P6  C14   C  CR16  0  -0.031   2.6445  -3.2292   0.4027
 1P6  C15   C  CR16  0  -0.409   3.9815  -3.6287   0.2513
 1P6  C16   C  CR16  0   0.082   4.9136  -2.6659  -0.0227
 1P6  N17   N  N     0  -0.353   4.4965  -1.3981  -0.1305
 1P6  N18   N  N     0  -0.353   5.2808  -0.3434  -0.3942
 1P6  C19   C  CR5   0   0.472   4.4542   0.6983  -0.4057
 1P6  N20   N  NH2   0  -0.850   4.9218   1.9474  -0.5999
 1P6  C21   C  CR6   0   0.146  -3.5837  -0.1684   0.2828
 1P6  C22   C  CR16  0  -0.305  -3.9364  -1.0311  -0.7490
 1P6  C23   C  CR16  0  -0.394  -5.2548  -1.1552  -1.1661
 1P6  C24   C  CR6   0   0.516  -6.2183  -0.3932  -0.5365
 1P6  F25   F  F     0  -0.315  -7.4960  -0.4978  -0.9357
 1P6  C26   C  CR16  0  -0.395  -5.9082   0.4763   0.4919
 1P6  C27   C  CR16  0  -0.285  -4.5861   0.5785   0.8978
 1P6  H1    H  HCH3  0   0.232  -2.5260   0.3478   2.8190
 1P6  H1A   H  HCH3  0   0.239  -2.2715  -1.3545   2.4205
 1P6  H1B   H  HCH3  0   0.241  -0.9013  -0.2461   2.4853
 1P6  H2    H  HCH1  0   0.267  -1.5644  -0.7622   0.1350
 1P6  HN4   H  HNH1  0   0.393  -2.3256   2.0553   0.3755
 1P6  H7    H  HCR6  0   0.250   1.2662   4.3245  -0.5648
 1P6  H10   H  HCR6  0   0.277   0.5117  -0.3414   0.3529
 1P6  H14   H  HCR6  0   0.279   1.8828  -3.9684   0.6199
 1P6  H15   H  HCR6  0   0.295   4.2730  -4.6629   0.3464
 1P6  H16   H  HCR6  0   0.325   5.9691  -2.8486  -0.1621
 1P6  HN20  H  HNH2  0   0.403   4.2239   2.6499  -0.7940
 1P6  HN2A  H  HNH2  0   0.387   5.8211   2.0508  -1.0392
 1P6  H22   H  HCR6  0   0.267  -3.1735  -1.6233  -1.2392
 1P6  H23   H  HCR6  0   0.281  -5.5219  -1.8288  -1.9699
 1P6  H26   H  HCR6  0   0.282  -6.6818   1.0637   0.9688
 1P6  H27   H  HCR6  0   0.269  -4.3486   1.2566   1.7091

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
 1P6  C1   C2    single    1.528  0.020  1.528
 1P6  C2   N4    single    1.452  0.020  1.452
 1P6  C2   C21   single    1.511  0.020  1.511
 1P6  N4   C5    single    1.344  0.020  1.344
 1P6  C5   N6    aromatic  1.345  0.020  1.345
 1P6  C5   C10   aromatic  1.401  0.020  1.401
 1P6  N6   C7    aromatic  1.317  0.020  1.317
 1P6  C7   N8    aromatic  1.320  0.020  1.320
 1P6  N8   C9    aromatic  1.350  0.020  1.350
 1P6  C9   C10   aromatic  1.388  0.020  1.388
 1P6  C9   C11   single    1.444  0.020  1.444
 1P6  C11  C12   aromatic  1.396  0.020  1.396
 1P6  C11  C19   aromatic  1.426  0.020  1.426
 1P6  C12  N13   aromatic  1.334  0.020  1.334
 1P6  C12  N17   aromatic  1.382  0.020  1.382
 1P6  N13  C14   aromatic  1.314  0.020  1.314
 1P6  C14  C15   aromatic  1.404  0.020  1.404
 1P6  C15  C16   aromatic  1.368  0.020  1.368
 1P6  C16  N17   aromatic  1.339  0.020  1.339
 1P6  N17  N18   aromatic  1.341  0.020  1.341
 1P6  N18  C19   aromatic  1.330  0.020  1.330
 1P6  C19  N20   single    1.348  0.020  1.348
 1P6  C21  C22   aromatic  1.390  0.020  1.390
 1P6  C21  C27   aromatic  1.393  0.020  1.393
 1P6  C22  C23   aromatic  1.388  0.020  1.388
 1P6  C23  C24   aromatic  1.380  0.020  1.380
 1P6  C24  F25   single    1.343  0.020  1.343
 1P6  C24  C26   aromatic  1.382  0.020  1.382
 1P6  C26  C27   aromatic  1.387  0.020  1.387
 1P6  C1   H1    single    0.970  0.020  1.090
 1P6  C1   H1A   single    0.970  0.020  1.090
 1P6  C1   H1B   single    0.970  0.020  1.090
 1P6  C2   H2    single    0.970  0.020  1.090
 1P6  N4   HN4   single    0.860  0.020  1.020
 1P6  C7   H7    single    0.930  0.020  1.080
 1P6  C10  H10   single    0.930  0.020  1.080
 1P6  C14  H14   single    0.930  0.020  1.080
 1P6  C15  H15   single    0.930  0.020  1.080
 1P6  C16  H16   single    0.930  0.020  1.080
 1P6  N20  HN20  single    0.890  0.020  1.040
 1P6  N20  HN2A  single    0.890  0.020  1.040
 1P6  C22  H22   single    0.930  0.020  1.080
 1P6  C23  H23   single    0.930  0.020  1.080
 1P6  C26  H26   single    0.930  0.020  1.080
 1P6  C27  H27   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
 1P6  H1B   C1   H1A   107.94  3.000
 1P6  H1B   C1   H1    107.75  3.000
 1P6  H1A   C1   H1    108.27  3.000
 1P6  H1B   C1   C2    111.12  3.000
 1P6  H1A   C1   C2    110.32  3.000
 1P6  H1    C1   C2    111.32  3.000
 1P6  H2    C2   C21   107.13  3.000
 1P6  H2    C2   N4    107.84  3.000
 1P6  C21   C2   N4    108.80  3.000
 1P6  H2    C2   C1    108.36  3.000
 1P6  C21   C2   C1    112.20  3.000
 1P6  N4    C2   C1    112.28  3.000
 1P6  HN4   N4   C5    115.74  3.000
 1P6  HN4   N4   C2    118.29  3.000
 1P6  C5    N4   C2    125.55  3.000
 1P6  C10   C5   N6    120.86  3.000
 1P6  C10   C5   N4    123.28  3.000
 1P6  N6    C5   N4    115.85  3.000
 1P6  C7    N6   C5    116.43  3.000
 1P6  H7    C7   N8    116.07  3.000
 1P6  H7    C7   N6    116.05  3.000
 1P6  N8    C7   N6    127.87  3.000
 1P6  C9    N8   C7    116.36  3.000
 1P6  C11   C9   C10   122.48  3.000
 1P6  C11   C9   N8    116.52  3.000
 1P6  C10   C9   N8    120.99  3.000
 1P6  H10   C10  C9    120.26  3.000
 1P6  H10   C10  C5    122.26  3.000
 1P6  C9    C10  C5    117.48  3.000
 1P6  C19   C11  C12   103.83  3.000
 1P6  C19   C11  C9    127.58  3.000
 1P6  C12   C11  C9    128.58  3.000
 1P6  N17   C12  N13   121.25  3.000
 1P6  N17   C12  C11   105.83  3.000
 1P6  N13   C12  C11   132.91  3.000
 1P6  C14   N13  C12   117.53  3.000
 1P6  H14   C14  C15   119.81  3.000
 1P6  H14   C14  N13   116.64  3.000
 1P6  C15   C14  N13   123.55  3.000
 1P6  H15   C15  C16   120.55  3.000
 1P6  H15   C15  C14   121.39  3.000
 1P6  C16   C15  C14   118.06  3.000
 1P6  H16   C16  N17   117.01  3.000
 1P6  H16   C16  C15   124.94  3.000
 1P6  N17   C16  C15   118.05  3.000
 1P6  N18   N17  C16   125.35  3.000
 1P6  N18   N17  C12   113.10  3.000
 1P6  C16   N17  C12   121.56  3.000
 1P6  C19   N18  N17   104.73  3.000
 1P6  N20   C19  N18   120.76  3.000
 1P6  N20   C19  C11   126.69  3.000
 1P6  N18   C19  C11   112.51  3.000
 1P6  HN2A  N20  HN20  117.56  3.000
 1P6  HN2A  N20  C19   117.92  3.000
 1P6  HN20  N20  C19   115.66  3.000
 1P6  C27   C21  C22   118.54  3.000
 1P6  C27   C21  C2    120.94  3.000
 1P6  C22   C21  C2    120.52  3.000
 1P6  H22   C22  C23   118.95  3.000
 1P6  H22   C22  C21   119.77  3.000
 1P6  C23   C22  C21   121.28  3.000
 1P6  H23   C23  C24   120.67  3.000
 1P6  H23   C23  C22   120.87  3.000
 1P6  C24   C23  C22   118.45  3.000
 1P6  C26   C24  F25   118.93  3.000
 1P6  C26   C24  C23   122.02  3.000
 1P6  F25   C24  C23   119.05  3.000
 1P6  H26   C26  C27   120.83  3.000
 1P6  H26   C26  C24   120.60  3.000
 1P6  C27   C26  C24   118.56  3.000
 1P6  H27   C27  C26   118.31  3.000
 1P6  H27   C27  C21   120.55  3.000
 1P6  C26   C27  C21   121.15  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
 1P6  CONST_01  N8    C7   N6   C5     0.00  0.0  0
 1P6  CONST_02  N8    C9   C10  C5     0.00  0.0  0
 1P6  CONST_03  C11   C9   C10  C5   180.00  0.0  0
 1P6  CONST_04  C9    C10  C5   N6     0.00  0.0  0
 1P6  CONST_05  C9    N8   C7   N6     0.00  0.0  0
 1P6  CONST_06  C10   C5   N6   C7     0.00  0.0  0
 1P6  CONST_07  C10   C9   N8   C7     0.00  0.0  0
 1P6  CONST_08  C11   C9   N8   C7   180.00  0.0  0
 1P6  CONST_09  C12   C11  C9   N8   180.00  0.0  0
 1P6  CONST_10  C19   C11  C9   N8     0.00  0.0  0
 1P6  CONST_11  N13   C12  C11  C9     0.00  0.0  0
 1P6  CONST_12  N17   C12  C11  C9   180.00  0.0  0
 1P6  CONST_13  N18   C19  C11  C9   180.00  0.0  0
 1P6  CONST_14  C12   C11  C9   C10    0.00  0.0  0
 1P6  CONST_15  C19   C11  C9   C10  180.00  0.0  0
 1P6  CONST_16  C14   N13  C12  C11  180.00  0.0  0
 1P6  CONST_17  C16   N17  C12  C11  180.00  0.0  0
 1P6  CONST_18  N18   N17  C12  C11    0.00  0.0  0
 1P6  CONST_19  N17   N18  C19  C11    0.00  0.0  0
 1P6  CONST_20  N18   C19  C11  C12    0.00  0.0  0
 1P6  CONST_21  C15   C14  N13  C12    0.00  0.0  0
 1P6  CONST_22  C15   C16  N17  C12    0.00  0.0  0
 1P6  CONST_23  C19   N18  N17  C12    0.00  0.0  0
 1P6  CONST_24  C19   C11  C12  N13  180.00  0.0  0
 1P6  CONST_25  C16   N17  C12  N13    0.00  0.0  0
 1P6  CONST_26  N18   N17  C12  N13  180.00  0.0  0
 1P6  CONST_27  C16   C15  C14  N13    0.00  0.0  0
 1P6  CONST_28  N17   C12  N13  C14    0.00  0.0  0
 1P6  CONST_29  N17   C16  C15  C14    0.00  0.0  0
 1P6  CONST_30  N18   N17  C16  C15  180.00  0.0  0
 1P6  CONST_31  C19   N18  N17  C16  180.00  0.0  0
 1P6  CONST_32  C19   C11  C12  N17    0.00  0.0  0
 1P6  CONST_33  C24   C23  C22  C21    0.00  0.0  0
 1P6  CONST_34  C24   C26  C27  C21    0.00  0.0  0
 1P6  CONST_35  C26   C27  C21  C22    0.00  0.0  0
 1P6  CONST_36  C26   C24  C23  C22    0.00  0.0  0
 1P6  CONST_37  C27   C21  C22  C23    0.00  0.0  0
 1P6  CONST_38  C27   C26  C24  C23    0.00  0.0  0
 1P6  CONST_39  C23   C22  C21  C2   180.00  0.0  0
 1P6  CONST_40  C26   C27  C21  C2   180.00  0.0  0
 1P6  CONST_41  C7    N6   C5   N4   180.00  0.0  0
 1P6  CONST_42  C9    C10  C5   N4   180.00  0.0  0
 1P6  CONST_43  N20   C19  C11  C9     0.00  0.0  0
 1P6  CONST_44  N20   C19  C11  C12  180.00  0.0  0
 1P6  CONST_45  N20   C19  N18  N17  180.00  0.0  0
 1P6  CONST_46  F25   C24  C23  C22  180.00  0.0  0
 1P6  CONST_47  C27   C26  C24  F25  180.00  0.0  0
 1P6  CONST_48  H7    C7   N6   C5   180.00  0.0  0
 1P6  CONST_49  H10   C10  C5   N6   180.00  0.0  0
 1P6  CONST_50  H14   C14  N13  C12  180.00  0.0  0
 1P6  CONST_51  H16   C16  N17  C12  180.00  0.0  0
 1P6  CONST_52  H15   C15  C14  N13  180.00  0.0  0
 1P6  CONST_53  H23   C23  C22  C21  180.00  0.0  0
 1P6  CONST_54  H26   C26  C27  C21  180.00  0.0  0
 1P6  CONST_55  H27   C27  C21  C22  180.00  0.0  0
 1P6  CONST_56  H22   C22  C23  C24  180.00  0.0  0
 1P6  CONST_57  N6    C5   N4   C2   180.00  0.0  0
 1P6  CONST_58  C10   C5   N4   C2     0.00  0.0  0
 1P6  CONST_59  HN4   N4   C5   N6     0.00  0.0  0
 1P6  CONST_60  HN20  N20  C19  C11    0.00  0.0  0

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
 1P6  chir_01  C2  C1  N4  C21  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
 1P6  plan-1  N4    0.020
 1P6  plan-1  C5    0.020
 1P6  plan-1  N6    0.020
 1P6  plan-1  C7    0.020
 1P6  plan-1  N8    0.020
 1P6  plan-1  C9    0.020
 1P6  plan-1  C10   0.020
 1P6  plan-1  C11   0.020
 1P6  plan-1  H7    0.020
 1P6  plan-1  H10   0.020
 1P6  plan-2  C2    0.020
 1P6  plan-2  C21   0.020
 1P6  plan-2  C22   0.020
 1P6  plan-2  C23   0.020
 1P6  plan-2  C24   0.020
 1P6  plan-2  F25   0.020
 1P6  plan-2  C26   0.020
 1P6  plan-2  C27   0.020
 1P6  plan-2  H22   0.020
 1P6  plan-2  H23   0.020
 1P6  plan-2  H26   0.020
 1P6  plan-2  H27   0.020
 1P6  plan-3  C9    0.020
 1P6  plan-3  C11   0.020
 1P6  plan-3  C12   0.020
 1P6  plan-3  N13   0.020
 1P6  plan-3  C14   0.020
 1P6  plan-3  C15   0.020
 1P6  plan-3  C16   0.020
 1P6  plan-3  N17   0.020
 1P6  plan-3  N18   0.020
 1P6  plan-3  C19   0.020
 1P6  plan-3  N20   0.020
 1P6  plan-3  H14   0.020
 1P6  plan-3  H15   0.020
 1P6  plan-3  H16   0.020
 1P6  plan-4  C2    0.020
 1P6  plan-4  N4    0.020
 1P6  plan-4  C5    0.020
 1P6  plan-4  HN4   0.020
 1P6  plan-5  C19   0.020
 1P6  plan-5  N20   0.020
 1P6  plan-5  HN20  0.020
 1P6  plan-5  HN2A  0.020

