# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 15:31:09 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: 2-[(2~{S})-1-[3-cyano-7-[(2-oxidanylidene-3,4-dihydro-1~{H}-quinolin-6-yl)amino]pyrazolo[1,5-a]pyrimidin-5-yl]pyrrolidin-2-yl]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C[C@@H]1CCCN1c2cc(Nc3ccc4NC(=O)CCc4c3)n5ncc(C#N)c5n2
#
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
 8HN  8HN  '2-[(2~{S})-1-[3-cyano-7-[(2-oxidanylidene-3,4-dihydro-1~{H}-quinolin-6-yl)amino]pyrazolo[1,5-a]pyrimidin-5-yl]pyrrolidin-2-yl]ethanoic acid'  ligand  53  32  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_8HN
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
 8HN  C1   C  CR16  0  -0.321  -5.0004  -1.2614   1.1504
 8HN  C2   C  CR6   0   0.357  -5.1548  -0.4182   0.0573
 8HN  C3   C  CR6   0   0.069  -4.0392  -0.0041  -0.6719
 8HN  N6   N  NH1   0  -0.732  -6.4213   0.0371  -0.3156
 8HN  C7   C  CR16  0  -0.544   0.9755  -1.7256   0.5737
 8HN  C8   C  CR6   0   0.575   2.1741  -0.9692   0.4438
 8HN  C9   C  CR56  0   0.662   1.0800   0.9054   1.0770
 8HN  C10  C  CR15  0   0.028  -0.5676   2.1861   1.8637
 8HN  C11  C  CR5   0  -0.340   0.7815   2.2219   1.4521
 8HN  C12  C  CSP   0  -0.009   1.6670   3.3072   1.4349
 8HN  C13  C  CH2   0  -0.288   3.5286  -2.9920   0.0166
 8HN  C14  C  CH2   0  -0.462   5.0104  -3.1187   0.3349
 8HN  C15  C  CH2   0  -0.482   5.6121  -1.8921  -0.3385
 8HN  C16  C  CH1   0  -0.027   4.5500  -0.7961  -0.1768
 8HN  C19  C  CH2   0  -0.492  -4.2635   0.9367  -1.8171
 8HN  C20  C  CH2   0  -0.593  -5.5876   0.6316  -2.5051
 8HN  C21  C  C     0   0.506  -6.7374   0.5525  -1.5328
 8HN  O2   O  O     0  -0.470  -7.8760   0.8884  -1.8077
 8HN  C4   C  CR16  0  -0.344  -2.7854  -0.4597  -0.3042
 8HN  C5   C  CR6   0   0.322  -2.6216  -1.2819   0.8057
 8HN  C    C  CR16  0  -0.319  -3.7354  -1.6791   1.5320
 8HN  N    N  NH1   0  -0.764  -1.3490  -1.7642   1.1898
 8HN  C6   C  CR6   0   0.674  -0.1768  -1.1132   0.9927
 8HN  N2   N  N     0  -0.457  -0.0973   0.2232   1.2659
 8HN  N3   N  N     0  -0.277  -1.0932   0.9933   1.7611
 8HN  N4   N  NS    0  -0.275   2.3957   4.2040   1.4168
 8HN  N1   N  N     0  -0.522   2.2029   0.3438   0.6735
 8HN  N5   N  NT    0  -0.529   3.3154  -1.5524   0.0536
 8HN  O1   O  O     0  -0.443   6.5580   1.0880  -0.8552
 8HN  O    O  OH1   0  -0.595   5.6285   1.5193  -2.8348
 8HN  H1   H  HCR6  0   0.272  -5.8658  -1.5847   1.7154
 8HN  H2   H  HNH1  0   0.406  -7.1857  -0.1136   0.3288
 8HN  H3   H  HCR6  0   0.302   0.9322  -2.7684   0.2987
 8HN  H4   H  HCR5  0   0.290  -1.1556   3.0100   2.2386
 8HN  H5   H  HCH2  0   0.245   3.2913  -3.4015  -0.9703
 8HN  H6   H  HCH2  0   0.259   2.9043  -3.5002   0.7506
 8HN  H7   H  HCH2  0   0.242   5.1585  -3.0784   1.4157
 8HN  H8   H  HCH2  0   0.254   5.4330  -4.0545  -0.0281
 8HN  H9   H  HCH2  0   0.262   6.5664  -1.5940   0.0902
 8HN  H10  H  HCH2  0   0.238   5.7788  -2.0972  -1.3995
 8HN  H11  H  HCH1  0   0.259   4.7564  -0.1802   0.7022
 8HN  H12  H  HCH2  0   0.264  -4.2752   1.9652  -1.4411
 8HN  H13  H  HCH2  0   0.270  -3.4452   0.8761  -2.5343
 8HN  H14  H  HCH2  0   0.279  -5.8212   1.3786  -3.2621
 8HN  H15  H  HCH2  0   0.282  -5.5292  -0.3352  -3.0176
 8HN  H16  H  HCR6  0   0.264  -1.9277  -0.1621  -0.8969
 8HN  H17  H  HCR6  0   0.271  -3.6191  -2.3202   2.3964
 8HN  H18  H  HNH1  0   0.419  -1.2572  -2.7697   1.2021
 8HN  H19  H  HCH2  0   0.279   4.2243  -0.5036  -2.2939
 8HN  H20  H  HCH2  0   0.308   3.5877   0.7862  -1.2941
 8HN  H21  H  HOH1  0   0.479   6.4138   2.0755  -2.9487
 8HN  C17  C  CH2   0  -0.606   4.4311   0.0990  -1.4053
 8HN  C18  C  C     0   0.555   5.6571   0.9335  -1.6423

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
 8HN  O2   C21  double    1.219  0.020  1.219
 8HN  C21  N6   single    1.359  0.020  1.359
 8HN  C21  C20  single    1.508  0.020  1.508
 8HN  N6   C2   single    1.397  0.020  1.397
 8HN  C1   C2   aromatic  1.389  0.020  1.389
 8HN  C1   C    aromatic  1.386  0.020  1.386
 8HN  C2   C3   aromatic  1.396  0.020  1.396
 8HN  C20  C19  single    1.523  0.020  1.523
 8HN  O1   C18  double    1.206  0.020  1.206
 8HN  C19  C3   single    1.499  0.020  1.499
 8HN  C    C5   aromatic  1.388  0.020  1.388
 8HN  C3   C4   aromatic  1.384  0.020  1.384
 8HN  C15  C16  single    1.535  0.020  1.535
 8HN  C15  C14  single    1.523  0.020  1.523
 8HN  C18  O    single    1.329  0.020  1.329
 8HN  C18  C17  single    1.502  0.020  1.502
 8HN  C5   C4   aromatic  1.391  0.020  1.391
 8HN  C5   N    single    1.414  0.020  1.414
 8HN  C16  C17  single    1.525  0.020  1.525
 8HN  C16  N5   single    1.466  0.020  1.466
 8HN  C14  C13  single    1.521  0.020  1.521
 8HN  C7   C6   aromatic  1.370  0.020  1.370
 8HN  C7   C8   aromatic  1.423  0.020  1.423
 8HN  N    C6   single    1.355  0.020  1.355
 8HN  N5   C8   single    1.340  0.020  1.340
 8HN  N5   C13  single    1.456  0.020  1.456
 8HN  C6   N2   aromatic  1.366  0.020  1.366
 8HN  C8   N1   aromatic  1.333  0.020  1.333
 8HN  N2   C9   aromatic  1.374  0.020  1.374
 8HN  N2   N3   aromatic  1.353  0.020  1.353
 8HN  N1   C9   aromatic  1.319  0.020  1.319
 8HN  C9   C11  aromatic  1.401  0.020  1.401
 8HN  N3   C10  aromatic  1.307  0.020  1.307
 8HN  C11  C10  aromatic  1.411  0.020  1.411
 8HN  C11  C12  single    1.401  0.020  1.401
 8HN  C12  N4   triple    1.156  0.020  1.156
 8HN  C1   H1   single    0.930  0.020  1.080
 8HN  N6   H2   single    0.860  0.020  1.020
 8HN  C7   H3   single    0.930  0.020  1.080
 8HN  C10  H4   single    0.930  0.020  1.080
 8HN  C13  H5   single    0.970  0.020  1.090
 8HN  C13  H6   single    0.970  0.020  1.090
 8HN  C14  H7   single    0.970  0.020  1.090
 8HN  C14  H8   single    0.970  0.020  1.090
 8HN  C15  H9   single    0.970  0.020  1.090
 8HN  C15  H10  single    0.970  0.020  1.090
 8HN  C16  H11  single    0.970  0.020  1.090
 8HN  C19  H12  single    0.970  0.020  1.090
 8HN  C19  H13  single    0.970  0.020  1.090
 8HN  C20  H14  single    0.970  0.020  1.090
 8HN  C20  H15  single    0.970  0.020  1.090
 8HN  C4   H16  single    0.930  0.020  1.080
 8HN  C    H17  single    0.930  0.020  1.080
 8HN  N    H18  single    0.890  0.020  1.040
 8HN  C17  H19  single    0.970  0.020  1.090
 8HN  C17  H20  single    0.970  0.020  1.090
 8HN  O    H21  single    0.850  0.020  0.980

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
 8HN  H1   C1   C    119.72  3.000
 8HN  H1   C1   C2   120.20  3.000
 8HN  C    C1   C2   120.08  3.000
 8HN  N6   C2   C3   119.26  3.000
 8HN  C3   C2   C1   120.16  3.000
 8HN  N6   C2   C1   120.58  3.000
 8HN  C4   C3   C19  123.04  3.000
 8HN  C4   C3   C2   119.19  3.000
 8HN  C19  C3   C2   117.76  3.000
 8HN  H2   N6   C21  116.84  3.000
 8HN  H2   N6   C2   117.83  3.000
 8HN  C21  N6   C2   125.00  3.000
 8HN  H3   C7   C6   118.41  3.000
 8HN  H3   C7   C8   121.60  3.000
 8HN  C6   C7   C8   119.90  3.000
 8HN  N5   C8   N1   117.41  3.000
 8HN  N1   C8   C7   121.72  3.000
 8HN  N5   C8   C7   120.84  3.000
 8HN  N1   C9   N2   124.08  3.000
 8HN  N1   C9   C11  131.57  3.000
 8HN  N2   C9   C11  104.31  3.000
 8HN  H4   C10  N3   120.30  3.000
 8HN  H4   C10  C11  127.07  3.000
 8HN  N3   C10  C11  112.62  3.000
 8HN  C12  C11  C10  128.88  3.000
 8HN  C12  C11  C9   126.16  3.000
 8HN  C10  C11  C9   104.95  3.000
 8HN  N4   C12  C11  180.00  3.000
 8HN  H6   C13  H5   107.99  3.000
 8HN  H6   C13  N5   111.11  3.000
 8HN  H5   C13  N5   111.17  3.000
 8HN  H6   C13  C14  112.23  3.000
 8HN  H5   C13  C14  111.64  3.000
 8HN  N5   C13  C14  102.70  3.000
 8HN  H8   C14  H7   108.01  3.000
 8HN  H8   C14  C15  113.03  3.000
 8HN  H7   C14  C15  110.76  3.000
 8HN  H8   C14  C13  112.33  3.000
 8HN  H7   C14  C13  109.65  3.000
 8HN  C15  C14  C13  103.01  3.000
 8HN  H10  C15  H9   107.46  3.000
 8HN  H10  C15  C16  109.98  3.000
 8HN  H9   C15  C16  111.70  3.000
 8HN  H10  C15  C14  109.77  3.000
 8HN  H9   C15  C14  113.14  3.000
 8HN  C16  C15  C14  104.78  3.000
 8HN  H11  C16  C17  109.38  3.000
 8HN  H11  C16  N5   108.86  3.000
 8HN  C17  C16  N5   111.34  3.000
 8HN  H11  C16  C15  110.89  3.000
 8HN  N5   C16  C15  103.35  3.000
 8HN  C17  C16  C15  112.85  3.000
 8HN  H13  C19  H12  106.63  3.000
 8HN  H13  C19  C20  110.14  3.000
 8HN  H12  C19  C20  109.51  3.000
 8HN  H13  C19  C3   110.83  3.000
 8HN  H12  C19  C3   109.20  3.000
 8HN  C20  C19  C3   110.45  3.000
 8HN  H15  C20  H14  106.95  3.000
 8HN  H15  C20  C21  107.21  3.000
 8HN  H14  C20  C21  108.70  3.000
 8HN  H15  C20  C19  109.99  3.000
 8HN  H14  C20  C19  111.29  3.000
 8HN  C21  C20  C19  112.47  3.000
 8HN  O2   C21  C20  123.55  3.000
 8HN  C20  C21  N6   114.84  3.000
 8HN  O2   C21  N6   121.59  3.000
 8HN  H16  C4   C5   120.35  3.000
 8HN  H16  C4   C3   118.76  3.000
 8HN  C5   C4   C3   120.89  3.000
 8HN  N    C5   C    118.85  3.000
 8HN  N    C5   C4   121.62  3.000
 8HN  C    C5   C4   119.49  3.000
 8HN  H17  C    C5   120.08  3.000
 8HN  H17  C    C1   119.77  3.000
 8HN  C5   C    C1   120.15  3.000
 8HN  H18  N    C6   113.67  3.000
 8HN  H18  N    C5   115.14  3.000
 8HN  C6   N    C5   125.11  3.000
 8HN  N2   C6   N    119.40  3.000
 8HN  N2   C6   C7   116.70  3.000
 8HN  N    C6   C7   123.86  3.000
 8HN  N3   N2   C6   125.96  3.000
 8HN  N3   N2   C9   113.49  3.000
 8HN  C6   N2   C9   120.53  3.000
 8HN  N2   N3   C10  104.60  3.000
 8HN  C9   N1   C8   116.98  3.000
 8HN  C16  N5   C13  112.51  3.000
 8HN  C13  N5   C8   124.24  3.000
 8HN  C16  N5   C8   122.59  3.000
 8HN  H21  O    C18  109.94  3.000
 8HN  H20  C17  H19  106.45  3.000
 8HN  H20  C17  C18  107.25  3.000
 8HN  H19  C17  C18  109.41  3.000
 8HN  H20  C17  C16  110.31  3.000
 8HN  H19  C17  C16  110.24  3.000
 8HN  C18  C17  C16  112.93  3.000
 8HN  O    C18  O1   123.04  3.000
 8HN  O    C18  C17  111.65  3.000
 8HN  O1   C18  C17  125.30  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
 8HN  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 8HN  CONST_02  C4   C5   C    C1      0.00   0.0  0
 8HN  CONST_03  C5   C    C1   C2      0.00   0.0  0
 8HN  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 8HN  CONST_05  C    C1   C2   C3      0.00   0.0  0
 8HN  CONST_06  C    C5   C4   C3      0.00   0.0  0
 8HN  CONST_07  C9   N2   C6   C7      0.00   0.0  0
 8HN  CONST_08  N3   N2   C6   C7    180.00   0.0  0
 8HN  CONST_09  C9   N1   C8   C7      0.00   0.0  0
 8HN  CONST_10  N2   C6   C7   C8      0.00   0.0  0
 8HN  CONST_11  N2   C9   N1   C8      0.00   0.0  0
 8HN  CONST_12  C11  C9   N1   C8    180.00   0.0  0
 8HN  CONST_13  C10  N3   N2   C9      0.00   0.0  0
 8HN  CONST_14  N3   C10  C11  C9      0.00   0.0  0
 8HN  CONST_15  C6   N2   N3   C10   180.00   0.0  0
 8HN  CONST_16  N2   C9   C11  C10     0.00   0.0  0
 8HN  CONST_17  N1   C9   C11  C10   180.00   0.0  0
 8HN  CONST_18  C6   N2   C9   C11   180.00   0.0  0
 8HN  CONST_19  N3   N2   C9   C11     0.00   0.0  0
 8HN  CONST_20  N2   N3   C10  C11     0.00   0.0  0
 8HN  CONST_21  N1   C8   C7   C6      0.00   0.0  0
 8HN  CONST_22  N1   C9   N2   C6      0.00   0.0  0
 8HN  CONST_23  N1   C9   N2   N3    180.00   0.0  0
 8HN  CONST_24  N5   C8   N1   C9    180.00   0.0  0
 8HN  CONST_25  N5   C8   C7   C6    180.00   0.0  0
 8HN  CONST_26  C20  C21  N6   C2      0.00   0.0  0
 8HN  CONST_27  N    C5   C    C1    180.00   0.0  0
 8HN  CONST_28  N    C5   C4   C3    180.00   0.0  0
 8HN  CONST_29  N    C6   C7   C8    180.00   0.0  0
 8HN  CONST_30  N    C6   N2   C9    180.00   0.0  0
 8HN  CONST_31  N2   C9   C11  C12   180.00   0.0  0
 8HN  CONST_32  N1   C9   C11  C12     0.00   0.0  0
 8HN  CONST_33  N3   C10  C11  C12   180.00   0.0  0
 8HN  CONST_34  N3   N2   C6   N       0.00   0.0  0
 8HN  CONST_35  O2   C21  N6   C2    180.00   0.0  0
 8HN  CONST_36  H17  C    C1   C2    180.00   0.0  0
 8HN  CONST_37  H16  C4   C3   C2    180.00   0.0  0
 8HN  CONST_38  H1   C1   C2   C3    180.00   0.0  0
 8HN  CONST_39  H4   C10  C11  C9    180.00   0.0  0
 8HN  CONST_40  H3   C7   C6   N2    180.00   0.0  0
 8HN  CONST_41  H2   N6   C21  C20   180.00   0.0  0
 8HN  CONST_42  H21  O    C18  C17   180.00   0.0  0
 8HN  Var_01    C21  N6   C2   C1   -161.55  30.0  1
 8HN  Var_02    C20  C19  C3   C2    -34.76  30.0  1
 8HN  Var_03    C21  C20  C19  C3     50.99  30.0  1
 8HN  Var_04    C19  C20  C21  N6    -34.48  30.0  1
 8HN  Var_05    C16  N5   C8   C7    175.93  30.0  1
 8HN  Var_06    C14  C13  N5   C8   -147.69  30.0  1
 8HN  Var_07    C16  C15  C14  C13    35.27  30.0  1
 8HN  Var_08    N5   C13  C14  C15   -35.20  30.0  1
 8HN  Var_09    C5   N    C6   C7   -138.09  30.0  3
 8HN  Var_10    C6   N    C5   C4     30.60  30.0  2
 8HN  Var_11    O1   C18  C17  C16   -12.42  30.0  2

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
 8HN  chir_01  C16  C15  C17  N5  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
 8HN  plan-1  C7   0.020
 8HN  plan-1  C8   0.020
 8HN  plan-1  C9   0.020
 8HN  plan-1  C10  0.020
 8HN  plan-1  C11  0.020
 8HN  plan-1  C12  0.020
 8HN  plan-1  N    0.020
 8HN  plan-1  C6   0.020
 8HN  plan-1  N2   0.020
 8HN  plan-1  N3   0.020
 8HN  plan-1  N4   0.020
 8HN  plan-1  N1   0.020
 8HN  plan-1  N5   0.020
 8HN  plan-1  H3   0.020
 8HN  plan-1  H4   0.020
 8HN  plan-2  C1   0.020
 8HN  plan-2  C2   0.020
 8HN  plan-2  C3   0.020
 8HN  plan-2  N6   0.020
 8HN  plan-2  C19  0.020
 8HN  plan-2  C4   0.020
 8HN  plan-2  C5   0.020
 8HN  plan-2  C    0.020
 8HN  plan-2  N    0.020
 8HN  plan-2  H1   0.020
 8HN  plan-2  H16  0.020
 8HN  plan-2  H17  0.020
 8HN  plan-3  C2   0.020
 8HN  plan-3  N6   0.020
 8HN  plan-3  C20  0.020
 8HN  plan-3  C21  0.020
 8HN  plan-3  O2   0.020
 8HN  plan-3  H2   0.020
 8HN  plan-4  O1   0.020
 8HN  plan-4  O    0.020
 8HN  plan-4  H21  0.020
 8HN  plan-4  C17  0.020
 8HN  plan-4  C18  0.020

