# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 02:09:48 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: ~{N}-[2-[(1~{S},2~{S})-2-(aminomethyl)cyclopropyl]-5-[[3-cyano-7-(cyclopropylamino)pyrazolo[1,5-a]pyrimidin-5-yl]amino]phenyl]ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)Nc1cc(Nc2cc(NC3CC3)n4ncc(C#N)c4n2)ccc1[C@H]5C[C@@H]5CN
#
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
 6XK  6XK  ~{N}-[2-[(1~{S},2~{S})-2-(aminomethyl)cyclopropyl]-5-[[3-cyano-7-(cyclopropylamino)pyrazolo[1,5-a]pyrimidin-5-yl]amino]phenyl]ethanamide  ligand  55  31  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_6XK
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
 6XK  C1   C  CH3   0  -0.787   5.1145   3.8319  -0.0149
 6XK  C2   C  C     0   0.517   3.7650   3.1627   0.0567
 6XK  C7   C  CR6   0   0.386   0.4581   0.2050   0.0725
 6XK  C8   C  CR16  0  -0.317   0.8324  -1.1321   0.1766
 6XK  C9   C  CR16  0  -0.309   2.1836  -1.4449   0.2300
 6XK  C10  C  CR6   0   0.049   3.1833  -0.4883   0.1816
 6XK  C11  C  CH1   0  -0.360   4.6201  -0.8595   0.3009
 6XK  C12  C  CH2   0  -0.489   5.1424  -2.1284  -0.2972
 6XK  C13  C  CH1   0  -0.256   5.5503  -0.8156  -0.8882
 6XK  C14  C  CH2   0  -0.281   6.9663  -0.3323  -0.7218
 6XK  C19  C  CR6   0   0.718  -4.4468   0.2073   0.0468
 6XK  C21  C  CR56  0   0.688  -3.2635  -1.8609   0.2073
 6XK  C24  C  CR15  0   0.032  -5.0817  -3.1500   0.3157
 6XK  N25  N  N     0  -0.304  -5.5389  -1.9277   0.2137
 6XK  C30  C  CH2   0  -0.506  -6.8579   2.8061  -0.8609
 6XK  C31  C  CH2   0  -0.486  -5.4237   2.9876  -1.2446
 6XK  O3   O  O     0  -0.469   2.7349   3.7986   0.1906
 6XK  N4   N  NH1   0  -0.747   3.8191   1.8059  -0.0087
 6XK  C5   C  CR6   0   0.351   2.7936   0.8596   0.0661
 6XK  C6   C  CR16  0  -0.457   1.4470   1.1935   0.0133
 6XK  N15  N  NH2   0  -0.797   7.8255  -0.9349  -1.7281
 6XK  C17  C  CR6   0   0.581  -2.0435   0.0219   0.0661
 6XK  C18  C  CR16  0  -0.568  -3.2132   0.8184   0.0128
 6XK  N20  N  N     0  -0.468  -4.4329  -1.1565   0.1483
 6XK  N22  N  N     0  -0.528  -2.0659  -1.2997   0.1631
 6XK  C23  C  CR5   0  -0.337  -3.6714  -3.1965   0.3179
 6XK  C26  C  CSP   0  -0.007  -2.8286  -4.3131   0.4106
 6XK  N27  N  NS    0  -0.270  -2.1320  -5.2315   0.4860
 6XK  C29  C  CH1   0  -0.108  -5.7833   2.2193  -0.0082
 6XK  H1   H  HCH3  0   0.279   5.4432   4.0861   0.9941
 6XK  H2   H  HCH3  0   0.248   5.8848   3.2121  -0.4709
 6XK  H3   H  HCH3  0   0.272   5.0347   4.7582  -0.5800
 6XK  H4   H  HCR6  0   0.287   0.0958  -1.9152   0.2204
 6XK  H5   H  HCR6  0   0.252   2.4659  -2.4865   0.3214
 6XK  H6   H  HCH1  0   0.283   5.0776  -0.5748   1.2472
 6XK  H7   H  HCH2  0   0.255   5.8785  -2.6817   0.2736
 6XK  H8   H  HCH2  0   0.256   4.4588  -2.7506  -0.8608
 6XK  H9   H  HCH1  0   0.265   5.0910  -0.5629  -1.8399
 6XK  H10  H  HCH2  0   0.218   7.0045   0.7544  -0.8546
 6XK  H11  H  HCH2  0   0.200   7.2877  -0.5251   0.3123
 6XK  H12  H  HCR5  0   0.295  -5.7615  -3.9849   0.3873
 6XK  H14  H  HCH2  0   0.265  -7.4546   2.1240  -1.4528
 6XK  H15  H  HCH2  0   0.266  -5.0520   2.4262  -2.0919
 6XK  H16  H  HCH2  0   0.265  -4.9691   3.9601  -1.1093
 6XK  H17  H  HNH1  0   0.426   4.7404   1.4095  -0.1062
 6XK  H18  H  HCR6  0   0.290   1.1496   2.2270  -0.0774
 6XK  H19  H  HNH2  0   0.349   8.7720  -0.5958  -1.6116
 6XK  H20  H  HNH2  0   0.340   7.8702  -1.9342  -1.5685
 6XK  H23  H  HCR6  0   0.307  -3.1478   1.8941  -0.0545
 6XK  H25  H  HCH1  0   0.281  -5.5845   2.6963   0.9474
 6XK  N16  N  NH1   0  -0.800  -0.8543   0.6729   0.0173
 6XK  N28  N  NH1   0  -0.673  -5.6394   0.8016  -0.0143
 6XK  H13  H  HCH2  0   0.266  -7.4015   3.6524  -0.4629
 6XK  H22  H  HNH1  0   0.422  -0.9310   1.6756  -0.0574
 6XK  H24  H  HNH1  0   0.418  -6.4547   0.2270   0.1422

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
 6XK  C30  C31  single    1.496  0.020  1.496
 6XK  C30  C29  single    1.492  0.020  1.492
 6XK  C31  C29  single    1.499  0.020  1.499
 6XK  C29  N28  single    1.425  0.020  1.425
 6XK  C8   C9   aromatic  1.388  0.020  1.388
 6XK  C8   C7   aromatic  1.392  0.020  1.392
 6XK  N28  C19  single    1.334  0.020  1.334
 6XK  C9   C10  aromatic  1.384  0.020  1.384
 6XK  C18  C19  aromatic  1.377  0.020  1.377
 6XK  C18  C17  aromatic  1.416  0.020  1.416
 6XK  N16  C7   single    1.394  0.020  1.394
 6XK  N16  C17  single    1.357  0.020  1.357
 6XK  C7   C6   aromatic  1.400  0.020  1.400
 6XK  C19  N20  aromatic  1.368  0.020  1.368
 6XK  C13  C12  single    1.496  0.020  1.496
 6XK  C13  C14  single    1.505  0.020  1.505
 6XK  C13  C11  single    1.510  0.020  1.510
 6XK  C17  N22  aromatic  1.325  0.020  1.325
 6XK  C12  C11  single    1.497  0.020  1.497
 6XK  N15  C14  single    1.454  0.020  1.454
 6XK  C10  C11  single    1.489  0.020  1.489
 6XK  C10  C5   aromatic  1.408  0.020  1.408
 6XK  C6   C5   aromatic  1.388  0.020  1.388
 6XK  N20  C21  aromatic  1.366  0.020  1.366
 6XK  N20  N25  aromatic  1.350  0.020  1.350
 6XK  N22  C21  aromatic  1.323  0.020  1.323
 6XK  C5   N4   single    1.397  0.020  1.397
 6XK  C21  C23  aromatic  1.401  0.020  1.401
 6XK  N25  C24  aromatic  1.309  0.020  1.309
 6XK  N4   C2   single    1.359  0.020  1.359
 6XK  C24  C23  aromatic  1.411  0.020  1.411
 6XK  C23  C26  single    1.402  0.020  1.402
 6XK  C2   C1   single    1.508  0.020  1.508
 6XK  C2   O3   double    1.218  0.020  1.218
 6XK  C26  N27  triple    1.155  0.020  1.155
 6XK  C1   H1   single    0.970  0.020  1.090
 6XK  C1   H2   single    0.970  0.020  1.090
 6XK  C1   H3   single    0.970  0.020  1.090
 6XK  C8   H4   single    0.930  0.020  1.080
 6XK  C9   H5   single    0.930  0.020  1.080
 6XK  C11  H6   single    0.970  0.020  1.090
 6XK  C12  H7   single    0.970  0.020  1.090
 6XK  C12  H8   single    0.970  0.020  1.090
 6XK  C13  H9   single    0.970  0.020  1.090
 6XK  C14  H10  single    0.970  0.020  1.090
 6XK  C14  H11  single    0.970  0.020  1.090
 6XK  C24  H12  single    0.930  0.020  1.080
 6XK  C30  H13  single    0.970  0.020  1.090
 6XK  C30  H14  single    0.970  0.020  1.090
 6XK  C31  H15  single    0.970  0.020  1.090
 6XK  C31  H16  single    0.970  0.020  1.090
 6XK  N4   H17  single    0.860  0.020  1.020
 6XK  C6   H18  single    0.930  0.020  1.080
 6XK  N15  H19  single    0.890  0.020  1.040
 6XK  N15  H20  single    0.890  0.020  1.040
 6XK  N16  H22  single    0.860  0.020  1.020
 6XK  C18  H23  single    0.930  0.020  1.080
 6XK  N28  H24  single    0.860  0.020  1.020
 6XK  C29  H25  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
 6XK  H3   C1   H2   108.61  3.000
 6XK  H3   C1   H1   107.70  3.000
 6XK  H2   C1   H1   107.86  3.000
 6XK  H3   C1   C2   109.68  3.000
 6XK  H2   C1   C2   113.60  3.000
 6XK  H1   C1   C2   109.21  3.000
 6XK  N4   C2   O3   124.05  3.000
 6XK  O3   C2   C1   122.03  3.000
 6XK  N4   C2   C1   113.89  3.000
 6XK  N16  C7   C6   115.24  3.000
 6XK  C6   C7   C8   119.44  3.000
 6XK  N16  C7   C8   125.32  3.000
 6XK  H4   C8   C9   120.06  3.000
 6XK  H4   C8   C7   121.19  3.000
 6XK  C9   C8   C7   118.75  3.000
 6XK  H5   C9   C10  118.64  3.000
 6XK  H5   C9   C8   118.28  3.000
 6XK  C10  C9   C8   123.09  3.000
 6XK  C5   C10  C11  120.83  3.000
 6XK  C5   C10  C9   117.68  3.000
 6XK  C11  C10  C9   121.45  3.000
 6XK  H6   C11  C13  114.69  3.000
 6XK  H6   C11  C12  114.98  3.000
 6XK  C13  C11  C12   59.68  3.000
 6XK  H6   C11  C10  114.20  3.000
 6XK  C12  C11  C10  121.07  3.000
 6XK  C13  C11  C10  121.60  3.000
 6XK  H8   C12  H7   114.19  3.000
 6XK  H8   C12  C13  118.08  3.000
 6XK  H7   C12  C13  118.09  3.000
 6XK  H8   C12  C11  118.35  3.000
 6XK  H7   C12  C11  117.35  3.000
 6XK  C13  C12  C11   60.61  3.000
 6XK  H9   C13  C14  114.82  3.000
 6XK  H9   C13  C12  115.77  3.000
 6XK  C14  C13  C12  119.63  3.000
 6XK  H9   C13  C11  115.85  3.000
 6XK  C14  C13  C11  120.11  3.000
 6XK  C12  C13  C11   59.71  3.000
 6XK  H11  C14  H10  106.12  3.000
 6XK  H11  C14  N15  113.91  3.000
 6XK  H10  C14  N15  107.86  3.000
 6XK  H11  C14  C13  108.82  3.000
 6XK  H10  C14  C13  109.75  3.000
 6XK  N15  C14  C13  110.26  3.000
 6XK  N28  C19  N20  117.18  3.000
 6XK  N20  C19  C18  115.80  3.000
 6XK  N28  C19  C18  127.02  3.000
 6XK  C23  C21  N22  132.11  3.000
 6XK  C23  C21  N20  104.22  3.000
 6XK  N22  C21  N20  123.67  3.000
 6XK  H12  C24  C23  127.16  3.000
 6XK  H12  C24  N25  120.51  3.000
 6XK  C23  C24  N25  112.33  3.000
 6XK  N20  N25  C24  104.54  3.000
 6XK  H14  C30  H13  114.65  3.000
 6XK  H14  C30  C29  117.49  3.000
 6XK  H13  C30  C29  117.35  3.000
 6XK  H14  C30  C31  117.70  3.000
 6XK  H13  C30  C31  118.78  3.000
 6XK  C29  C30  C31   60.25  3.000
 6XK  H16  C31  H15  114.83  3.000
 6XK  H16  C31  C29  117.27  3.000
 6XK  H15  C31  C29  117.53  3.000
 6XK  H16  C31  C30  118.67  3.000
 6XK  H15  C31  C30  117.86  3.000
 6XK  C29  C31  C30   59.76  3.000
 6XK  H17  N4   C5   114.18  3.000
 6XK  H17  N4   C2   115.70  3.000
 6XK  C5   N4   C2   130.10  3.000
 6XK  C6   C5   N4   123.15  3.000
 6XK  N4   C5   C10  116.72  3.000
 6XK  C6   C5   C10  120.12  3.000
 6XK  H18  C6   C5   120.06  3.000
 6XK  H18  C6   C7   119.02  3.000
 6XK  C5   C6   C7   120.92  3.000
 6XK  H20  N15  H19  105.73  3.000
 6XK  H20  N15  C14  109.02  3.000
 6XK  H19  N15  C14  109.52  3.000
 6XK  N22  C17  C18  123.34  3.000
 6XK  N22  C17  N16  119.73  3.000
 6XK  C18  C17  N16  116.92  3.000
 6XK  H23  C18  C17  120.84  3.000
 6XK  H23  C18  C19  119.86  3.000
 6XK  C17  C18  C19  119.30  3.000
 6XK  N25  N20  C21  113.86  3.000
 6XK  N25  N20  C19  124.40  3.000
 6XK  C21  N20  C19  121.73  3.000
 6XK  C17  N22  C21  116.15  3.000
 6XK  C26  C23  C24  128.84  3.000
 6XK  C26  C23  C21  126.12  3.000
 6XK  C24  C23  C21  105.04  3.000
 6XK  N27  C26  C23  180.00  3.000
 6XK  H25  C29  N28  114.97  3.000
 6XK  H25  C29  C31  117.16  3.000
 6XK  N28  C29  C31  118.81  3.000
 6XK  H25  C29  C30  117.50  3.000
 6XK  N28  C29  C30  117.49  3.000
 6XK  C31  C29  C30   59.99  3.000
 6XK  H22  N16  C17  114.40  3.000
 6XK  H22  N16  C7   114.09  3.000
 6XK  C17  N16  C7   131.50  3.000
 6XK  H24  N28  C29  118.94  3.000
 6XK  H24  N28  C19  117.47  3.000
 6XK  C29  N28  C19  122.24  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
 6XK  CONST_01  C10  C9   C8   C7      0.00   0.0  0
 6XK  CONST_02  C10  C5   C6   C7      0.00   0.0  0
 6XK  CONST_03  C5   C10  C9   C8      0.00   0.0  0
 6XK  CONST_04  C5   C6   C7   C8      0.00   0.0  0
 6XK  CONST_05  C6   C7   C8   C9      0.00   0.0  0
 6XK  CONST_06  C6   C5   C10  C9      0.00   0.0  0
 6XK  CONST_07  N22  C17  C18  C19     0.00   0.0  0
 6XK  CONST_08  N22  C21  N20  C19     0.00   0.0  0
 6XK  CONST_09  C23  C21  N20  C19   180.00   0.0  0
 6XK  CONST_10  C24  N25  N20  C19   180.00   0.0  0
 6XK  CONST_11  C18  C19  N20  C21     0.00   0.0  0
 6XK  CONST_12  C24  N25  N20  C21     0.00   0.0  0
 6XK  CONST_13  C18  C17  N22  C21     0.00   0.0  0
 6XK  CONST_14  N25  C24  C23  C21     0.00   0.0  0
 6XK  CONST_15  N20  C21  C23  C24     0.00   0.0  0
 6XK  CONST_16  N22  C21  C23  C24   180.00   0.0  0
 6XK  CONST_17  C18  C19  N20  N25   180.00   0.0  0
 6XK  CONST_18  N22  C21  N20  N25   180.00   0.0  0
 6XK  CONST_19  C23  C21  N20  N25     0.00   0.0  0
 6XK  CONST_20  N20  C19  C18  C17     0.00   0.0  0
 6XK  CONST_21  N20  C21  N22  C17     0.00   0.0  0
 6XK  CONST_22  C23  C21  N22  C17   180.00   0.0  0
 6XK  CONST_23  C23  C24  N25  N20     0.00   0.0  0
 6XK  CONST_24  C11  C10  C9   C8    180.00   0.0  0
 6XK  CONST_25  C6   C5   C10  C11   180.00   0.0  0
 6XK  CONST_26  N4   C5   C6   C7    180.00   0.0  0
 6XK  CONST_27  N16  C7   C8   C9    180.00   0.0  0
 6XK  CONST_28  N4   C5   C10  C9    180.00   0.0  0
 6XK  CONST_29  N4   C5   C10  C11     0.00   0.0  0
 6XK  CONST_30  N16  C17  C18  C19   180.00   0.0  0
 6XK  CONST_31  N28  C19  N20  C21   180.00   0.0  0
 6XK  CONST_32  N16  C17  N22  C21   180.00   0.0  0
 6XK  CONST_33  N28  C19  N20  N25     0.00   0.0  0
 6XK  CONST_34  C26  C23  C24  N25   180.00   0.0  0
 6XK  CONST_35  N16  C7   C6   C5    180.00   0.0  0
 6XK  CONST_36  N28  C19  C18  C17   180.00   0.0  0
 6XK  CONST_37  C26  C23  C21  N20   180.00   0.0  0
 6XK  CONST_38  C26  C23  C21  N22     0.00   0.0  0
 6XK  CONST_39  C29  N28  C19  C18     0.00   0.0  0
 6XK  CONST_40  C29  N28  C19  N20   180.00   0.0  0
 6XK  CONST_41  H5   C9   C8   C7    180.00   0.0  0
 6XK  CONST_42  H18  C6   C7   C8    180.00   0.0  0
 6XK  CONST_43  H4   C8   C9   C10   180.00   0.0  0
 6XK  CONST_44  H12  C24  C23  C21   180.00   0.0  0
 6XK  CONST_45  H23  C18  C19  N20   180.00   0.0  0
 6XK  CONST_46  C10  C5   N4   C2    180.00   0.0  0
 6XK  CONST_47  C6   C5   N4   C2      0.00   0.0  0
 6XK  CONST_48  H17  N4   C5   C10     0.00   0.0  0
 6XK  CONST_49  H24  N28  C19  C18   180.00   0.0  0
 6XK  CONST_50  C5   N4   C2   C1    180.00   0.0  0
 6XK  CONST_51  C5   N4   C2   O3      0.00   0.0  0
 6XK  Var_01    C13  C11  C10  C9    107.54  30.0  2
 6XK  Var_02    C12  C13  C11  C10  -110.01  30.0  1
 6XK  Var_03    C18  C17  N16  C7    178.61  30.0  2
 6XK  Var_04    C17  N16  C7   C8      1.11  30.0  2
 6XK  Var_05    C30  C29  N28  C19   142.99  30.0  1
 6XK  Var_06    N28  C29  C31  C30   106.90  30.0  1
 6XK  Var_07    N15  C14  C13  C11   153.00  30.0  3
 6XK  Var_08    H19  N15  C14  C13   179.46  30.0  3
 6XK  Var_09    H1   C1   C2   O3     79.71  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
 6XK  chir_01  C11  C13  C12  C10  both
 6XK  chir_02  C13  C11  C14  C12  both
 6XK  chir_03  C29  C30  C31  N28  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
 6XK  plan-1  C7   0.020
 6XK  plan-1  C8   0.020
 6XK  plan-1  C9   0.020
 6XK  plan-1  C10  0.020
 6XK  plan-1  C11  0.020
 6XK  plan-1  N4   0.020
 6XK  plan-1  C5   0.020
 6XK  plan-1  C6   0.020
 6XK  plan-1  H4   0.020
 6XK  plan-1  H5   0.020
 6XK  plan-1  H18  0.020
 6XK  plan-1  N16  0.020
 6XK  plan-2  C19  0.020
 6XK  plan-2  C21  0.020
 6XK  plan-2  C24  0.020
 6XK  plan-2  N25  0.020
 6XK  plan-2  C17  0.020
 6XK  plan-2  C18  0.020
 6XK  plan-2  N20  0.020
 6XK  plan-2  N22  0.020
 6XK  plan-2  C23  0.020
 6XK  plan-2  C26  0.020
 6XK  plan-2  N27  0.020
 6XK  plan-2  H12  0.020
 6XK  plan-2  H23  0.020
 6XK  plan-2  N16  0.020
 6XK  plan-2  N28  0.020
 6XK  plan-3  C19  0.020
 6XK  plan-3  C29  0.020
 6XK  plan-3  N28  0.020
 6XK  plan-3  H24  0.020
 6XK  plan-4  C1   0.020
 6XK  plan-4  C2   0.020
 6XK  plan-4  O3   0.020
 6XK  plan-4  N4   0.020
 6XK  plan-4  C5   0.020
 6XK  plan-4  H17  0.020

