# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 05:13:57 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: N-{7-[4-(aminomethyl)piperidin-1-yl]quinolin-6-yl}pyrazolo[1,5-a]pyrimidine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCC1CCN(CC1)c2cc3ncccc3cc2NC(=O)c4cnn5cccnc45
#
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
 LTY  LTY  N-{7-[4-(aminomethyl)piperidin-1-yl]quinolin-6-yl}pyrazolo[1,5-a]pyrimidine-3-carboxamide  ligand  53  30  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_LTY
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
 LTY  C4   C  CR16  0  -0.410  -0.5330   2.7724  -0.1617
 LTY  C14  C  CH1   0  -0.269  -2.5239  -3.4537   0.0986
 LTY  C5   C  CR6   0   0.354  -0.6377   1.4071  -0.2324
 LTY  C6   C  CR6   0   0.256  -1.9326   0.7855  -0.2883
 LTY  C7   C  CR16  0  -0.371  -3.0560   1.5625  -0.3372
 LTY  C8   C  CR66  0   0.210  -2.9714   2.9729  -0.2927
 LTY  C10  C  CR16  0  -0.088  -4.0279   4.9971  -0.2657
 LTY  C12  C  CH2   0  -0.308  -3.0184  -1.2557  -1.0641
 LTY  C13  C  CH2   0  -0.422  -2.7211  -2.7375  -1.2376
 LTY  C3   C  CR66  0   0.089  -1.6957   3.5747  -0.1822
 LTY  C1   C  CR16  0  -0.330  -2.8104   5.6969  -0.1561
 LTY  C2   C  CR16  0  -0.193  -1.6446   4.9829  -0.1144
 LTY  N9   N  N     0  -0.436  -4.1152   3.6933  -0.3329
 LTY  N11  N  NT    0  -0.529  -1.9498  -0.6225  -0.3036
 LTY  C15  C  CH2   0  -0.440  -1.4936  -2.6929   0.9332
 LTY  C16  C  CH2   0  -0.328  -1.8075  -1.2090   1.0324
 LTY  C17  C  CH2   0  -0.270  -3.8264  -3.6556   0.8750
 LTY  N18  N  NH2   0  -0.796  -4.7768  -4.4547   0.1182
 LTY  N19  N  NH1   0  -0.768   0.4247   0.5168  -0.3057
 LTY  C20  C  C     0   0.517   1.7368   0.7113  -0.0044
 LTY  O21  O  O     0  -0.463   2.1845   1.7694   0.4057
 LTY  C22  C  CR5   0  -0.377   2.5753  -0.4727  -0.2012
 LTY  C23  C  CR15  0  -0.033   2.2865  -1.6930  -0.8360
 LTY  N24  N  N     0  -0.287   3.2987  -2.5362  -0.8274
 LTY  N25  N  N     0  -0.360   4.2708  -1.8849  -0.1822
 LTY  C26  C  CR56  0   0.637   3.8981  -0.6195   0.2231
 LTY  N27  N  N     0  -0.412   4.7409   0.1756   0.8893
 LTY  C28  C  CR16  0  -0.042   5.9360  -0.2945   1.1348
 LTY  C29  C  CR16  0  -0.388   6.3729  -1.5785   0.7394
 LTY  C30  C  CR16  0   0.091   5.5026  -2.3765   0.0672
 LTY  H1   H  HCR6  0   0.276   0.4304   3.2563  -0.1160
 LTY  H2   H  HCH1  0   0.233  -2.1182  -4.4515  -0.1065
 LTY  H3   H  HCR6  0   0.264  -4.0396   1.1138  -0.3948
 LTY  H4   H  HCR6  0   0.260  -4.9606   5.5508  -0.2992
 LTY  H6   H  HCH2  0   0.214  -3.9984  -1.1238  -0.5826
 LTY  H7   H  HCH2  0   0.225  -1.8139  -2.8393  -1.8407
 LTY  H8   H  HCH2  0   0.237  -3.5334  -3.2017  -1.7988
 LTY  H9   H  HCR6  0   0.269  -2.8126   6.7769  -0.1074
 LTY  H10  H  HCR6  0   0.270  -0.6875   5.4833  -0.0294
 LTY  H11  H  HCH2  0   0.239  -1.4318  -3.1091   1.9422
 LTY  H12  H  HCH2  0   0.223  -0.5009  -2.8175   0.4892
 LTY  H13  H  HCH2  0   0.260  -1.0022  -0.7001   1.5661
 LTY  H14  H  HCH2  0   0.233  -2.7199  -1.0404   1.6221
 LTY  H15  H  HCH2  0   0.200  -3.5686  -4.0946   1.8503
 LTY  H16  H  HCH2  0   0.214  -4.2942  -2.6925   1.0964
 LTY  H17  H  HNH2  0   0.337  -4.4101  -5.3927   0.0101
 LTY  H18  H  HNH2  0   0.347  -5.6318  -4.5553   0.6496
 LTY  H20  H  HNH1  0   0.410   0.1111  -0.4100  -0.5695
 LTY  H21  H  HCR5  0   0.278   1.3713  -1.9914  -1.3280
 LTY  H22  H  HCR6  0   0.287   6.6146   0.3550   1.6748
 LTY  H23  H  HCR6  0   0.303   7.3708  -1.9208   0.9648
 LTY  H24  H  HCR6  0   0.334   5.7147  -3.3750  -0.2857
 LTY  H5   H  HCH2  0   0.252  -3.0804  -0.7736  -2.0412

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
 LTY  C10  N9   aromatic  1.308  0.020  1.308
 LTY  C10  C1   aromatic  1.409  0.020  1.409
 LTY  N9   C8   aromatic  1.352  0.020  1.352
 LTY  C1   C2   aromatic  1.368  0.020  1.368
 LTY  C8   C7   aromatic  1.414  0.020  1.414
 LTY  C8   C3   aromatic  1.415  0.020  1.415
 LTY  C2   C3   aromatic  1.411  0.020  1.411
 LTY  C7   C6   aromatic  1.367  0.020  1.367
 LTY  C3   C4   aromatic  1.413  0.020  1.413
 LTY  C12  N11  single    1.456  0.020  1.456
 LTY  C12  C13  single    1.521  0.020  1.521
 LTY  C6   N11  single    1.408  0.020  1.408
 LTY  C6   C5   aromatic  1.437  0.020  1.437
 LTY  C4   C5   aromatic  1.371  0.020  1.371
 LTY  N11  C16  single    1.466  0.020  1.466
 LTY  C17  N18  single    1.454  0.020  1.454
 LTY  C17  C14  single    1.530  0.020  1.530
 LTY  C5   N19  single    1.388  0.020  1.388
 LTY  C13  C14  single    1.529  0.020  1.529
 LTY  C16  C15  single    1.520  0.020  1.520
 LTY  C14  C15  single    1.529  0.020  1.529
 LTY  N19  C20  single    1.360  0.020  1.360
 LTY  O21  C20  double    1.220  0.020  1.220
 LTY  C20  C22  single    1.464  0.020  1.464
 LTY  N27  C26  aromatic  1.337  0.020  1.337
 LTY  N27  C28  aromatic  1.307  0.020  1.307
 LTY  C22  C26  aromatic  1.397  0.020  1.397
 LTY  C22  C23  aromatic  1.405  0.020  1.405
 LTY  C26  N25  aromatic  1.380  0.020  1.380
 LTY  C28  C29  aromatic  1.413  0.020  1.413
 LTY  C23  N24  aromatic  1.317  0.020  1.317
 LTY  N25  N24  aromatic  1.336  0.020  1.336
 LTY  N25  C30  aromatic  1.350  0.020  1.350
 LTY  C29  C30  aromatic  1.359  0.020  1.359
 LTY  C4   H1   single    0.930  0.020  1.080
 LTY  C14  H2   single    0.970  0.020  1.090
 LTY  C7   H3   single    0.930  0.020  1.080
 LTY  C10  H4   single    0.930  0.020  1.080
 LTY  C12  H5   single    0.970  0.020  1.090
 LTY  C12  H6   single    0.970  0.020  1.090
 LTY  C13  H7   single    0.970  0.020  1.090
 LTY  C13  H8   single    0.970  0.020  1.090
 LTY  C1   H9   single    0.930  0.020  1.080
 LTY  C2   H10  single    0.930  0.020  1.080
 LTY  C15  H11  single    0.970  0.020  1.090
 LTY  C15  H12  single    0.970  0.020  1.090
 LTY  C16  H13  single    0.970  0.020  1.090
 LTY  C16  H14  single    0.970  0.020  1.090
 LTY  C17  H15  single    0.970  0.020  1.090
 LTY  C17  H16  single    0.970  0.020  1.090
 LTY  N18  H17  single    0.890  0.020  1.040
 LTY  N18  H18  single    0.890  0.020  1.040
 LTY  N19  H20  single    0.860  0.020  1.020
 LTY  C23  H21  single    0.930  0.020  1.080
 LTY  C28  H22  single    0.930  0.020  1.080
 LTY  C29  H23  single    0.930  0.020  1.080
 LTY  C30  H24  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
 LTY  H1   C4   C3   118.73  3.000
 LTY  H1   C4   C5   121.13  3.000
 LTY  C3   C4   C5   120.13  3.000
 LTY  H2   C14  C17  106.85  3.000
 LTY  H2   C14  C15  107.80  3.000
 LTY  C17  C14  C15  111.25  3.000
 LTY  H2   C14  C13  108.09  3.000
 LTY  C15  C14  C13  109.33  3.000
 LTY  C17  C14  C13  113.30  3.000
 LTY  N19  C5   C6   114.21  3.000
 LTY  N19  C5   C4   125.66  3.000
 LTY  C6   C5   C4   120.09  3.000
 LTY  N11  C6   C7   123.92  3.000
 LTY  N11  C6   C5   116.34  3.000
 LTY  C7   C6   C5   119.74  3.000
 LTY  H3   C7   C8   118.01  3.000
 LTY  H3   C7   C6   120.86  3.000
 LTY  C8   C7   C6   121.12  3.000
 LTY  N9   C8   C3   122.57  3.000
 LTY  C3   C8   C7   118.74  3.000
 LTY  N9   C8   C7   118.68  3.000
 LTY  H4   C10  N9   116.71  3.000
 LTY  H4   C10  C1   119.46  3.000
 LTY  N9   C10  C1   123.83  3.000
 LTY  H6   C12  H5   106.77  3.000
 LTY  H6   C12  N11  111.91  3.000
 LTY  H5   C12  N11  108.49  3.000
 LTY  H6   C12  C13  109.93  3.000
 LTY  H5   C12  C13  109.83  3.000
 LTY  N11  C12  C13  109.85  3.000
 LTY  H8   C13  H7   107.11  3.000
 LTY  H8   C13  C12  109.13  3.000
 LTY  H7   C13  C12  108.40  3.000
 LTY  H8   C13  C14  110.26  3.000
 LTY  H7   C13  C14  109.34  3.000
 LTY  C12  C13  C14  112.45  3.000
 LTY  C2   C3   C8   117.45  3.000
 LTY  C2   C3   C4   122.44  3.000
 LTY  C8   C3   C4   120.11  3.000
 LTY  H9   C1   C2   121.46  3.000
 LTY  H9   C1   C10  119.87  3.000
 LTY  C2   C1   C10  118.67  3.000
 LTY  H10  C2   C1   120.95  3.000
 LTY  H10  C2   C3   119.79  3.000
 LTY  C1   C2   C3   119.26  3.000
 LTY  C10  N9   C8   118.22  3.000
 LTY  C16  N11  C12  111.91  3.000
 LTY  C16  N11  C6   112.89  3.000
 LTY  C12  N11  C6   116.70  3.000
 LTY  H12  C15  H11  106.25  3.000
 LTY  H12  C15  C16  108.96  3.000
 LTY  H11  C15  C16  108.85  3.000
 LTY  H12  C15  C14  109.46  3.000
 LTY  H11  C15  C14  110.64  3.000
 LTY  C16  C15  C14  112.48  3.000
 LTY  H14  C16  H13  106.17  3.000
 LTY  H14  C16  C15  110.86  3.000
 LTY  H13  C16  C15  109.55  3.000
 LTY  H14  C16  N11  110.30  3.000
 LTY  H13  C16  N11  109.31  3.000
 LTY  C15  C16  N11  110.56  3.000
 LTY  H16  C17  H15  105.80  3.000
 LTY  H16  C17  N18  108.05  3.000
 LTY  H15  C17  N18  113.28  3.000
 LTY  H16  C17  C14  110.54  3.000
 LTY  H15  C17  C14  107.64  3.000
 LTY  N18  C17  C14  111.40  3.000
 LTY  H18  N18  H17  105.66  3.000
 LTY  H18  N18  C17  109.49  3.000
 LTY  H17  N18  C17  109.14  3.000
 LTY  H20  N19  C20  119.14  3.000
 LTY  H20  N19  C5   111.32  3.000
 LTY  C20  N19  C5   129.42  3.000
 LTY  C22  C20  O21  122.44  3.000
 LTY  C22  C20  N19  114.02  3.000
 LTY  O21  C20  N19  123.53  3.000
 LTY  C26  C22  C23  103.92  3.000
 LTY  C23  C22  C20  130.18  3.000
 LTY  C26  C22  C20  125.90  3.000
 LTY  H21  C23  N24  118.47  3.000
 LTY  H21  C23  C22  128.26  3.000
 LTY  N24  C23  C22  113.26  3.000
 LTY  N25  N24  C23  104.49  3.000
 LTY  C30  N25  C26  121.75  3.000
 LTY  C30  N25  N24  125.15  3.000
 LTY  C26  N25  N24  113.10  3.000
 LTY  N27  C26  N25  121.44  3.000
 LTY  N25  C26  C22  105.24  3.000
 LTY  N27  C26  C22  133.32  3.000
 LTY  C28  N27  C26  117.14  3.000
 LTY  H22  C28  C29  119.38  3.000
 LTY  H22  C28  N27  116.78  3.000
 LTY  C29  C28  N27  123.84  3.000
 LTY  H23  C29  C30  120.63  3.000
 LTY  H23  C29  C28  121.07  3.000
 LTY  C30  C29  C28  118.31  3.000
 LTY  H24  C30  C29  125.37  3.000
 LTY  H24  C30  N25  117.10  3.000
 LTY  C29  C30  N25  117.52  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
 LTY  CONST_01  N9   C8   C3   C4    180.00   0.0  0
 LTY  CONST_02  C7   C8   C3   C4      0.00   0.0  0
 LTY  CONST_03  C1   C2   C3   C4    180.00   0.0  0
 LTY  CONST_04  C7   C6   C5   C4      0.00   0.0  0
 LTY  CONST_05  C8   C7   C6   C5      0.00   0.0  0
 LTY  CONST_06  C8   C3   C4   C5      0.00   0.0  0
 LTY  CONST_07  C2   C3   C4   C5    180.00   0.0  0
 LTY  CONST_08  N9   C8   C7   C6    180.00   0.0  0
 LTY  CONST_09  C3   C8   C7   C6      0.00   0.0  0
 LTY  CONST_10  C3   C4   C5   C6      0.00   0.0  0
 LTY  CONST_11  C10  N9   C8   C7    180.00   0.0  0
 LTY  CONST_12  C2   C3   C8   C7    180.00   0.0  0
 LTY  CONST_13  C1   C10  N9   C8      0.00   0.0  0
 LTY  CONST_14  C1   C2   C3   C8      0.00   0.0  0
 LTY  CONST_15  C3   C8   N9   C10     0.00   0.0  0
 LTY  CONST_16  C3   C2   C1   C10     0.00   0.0  0
 LTY  CONST_17  N9   C10  C1   C2      0.00   0.0  0
 LTY  CONST_18  N9   C8   C3   C2      0.00   0.0  0
 LTY  CONST_19  C28  N27  C26  C22   180.00   0.0  0
 LTY  CONST_20  N24  N25  C26  C22     0.00   0.0  0
 LTY  CONST_21  C30  N25  C26  C22   180.00   0.0  0
 LTY  CONST_22  N25  N24  C23  C22     0.00   0.0  0
 LTY  CONST_23  N27  C26  C22  C23   180.00   0.0  0
 LTY  CONST_24  N25  C26  C22  C23     0.00   0.0  0
 LTY  CONST_25  C26  N25  N24  C23     0.00   0.0  0
 LTY  CONST_26  C30  N25  N24  C23   180.00   0.0  0
 LTY  CONST_27  C26  C22  C23  N24     0.00   0.0  0
 LTY  CONST_28  N27  C26  N25  N24   180.00   0.0  0
 LTY  CONST_29  C29  C30  N25  N24   180.00   0.0  0
 LTY  CONST_30  C28  N27  C26  N25     0.00   0.0  0
 LTY  CONST_31  C28  C29  C30  N25     0.00   0.0  0
 LTY  CONST_32  C29  C28  N27  C26     0.00   0.0  0
 LTY  CONST_33  C29  C30  N25  C26     0.00   0.0  0
 LTY  CONST_34  C30  N25  C26  N27     0.00   0.0  0
 LTY  CONST_35  C30  C29  C28  N27     0.00   0.0  0
 LTY  CONST_36  N11  C6   C5   C4    180.00   0.0  0
 LTY  CONST_37  N11  C6   C7   C8    180.00   0.0  0
 LTY  CONST_38  N19  C5   C6   C7    180.00   0.0  0
 LTY  CONST_39  N19  C5   C4   C3    180.00   0.0  0
 LTY  CONST_40  N19  C5   C6   N11     0.00   0.0  0
 LTY  CONST_41  N27  C26  C22  C20     0.00   0.0  0
 LTY  CONST_42  N25  C26  C22  C20   180.00   0.0  0
 LTY  CONST_43  N24  C23  C22  C20   180.00   0.0  0
 LTY  CONST_44  H10  C2   C3   C4      0.00   0.0  0
 LTY  CONST_45  H3   C7   C6   C5    180.00   0.0  0
 LTY  CONST_46  H1   C4   C5   C6    180.00   0.0  0
 LTY  CONST_47  H4   C10  N9   C8    180.00   0.0  0
 LTY  CONST_48  H9   C1   C2   C3    180.00   0.0  0
 LTY  CONST_49  H24  C30  N25  N24     0.00   0.0  0
 LTY  CONST_50  H21  C23  N24  N25   180.00   0.0  0
 LTY  CONST_51  H23  C29  C30  N25   180.00   0.0  0
 LTY  CONST_52  H22  C28  N27  C26   180.00   0.0  0
 LTY  CONST_53  C22  C20  N19  C5    180.00   0.0  0
 LTY  CONST_56  H20  N19  C5   C4    180.00   0.0  0
 LTY  CONST_57  O21  C20  N19  C5      0.00   0.0  0
 LTY  Var_01    N11  C12  C13  C14    56.72  30.0  1
 LTY  Var_02    N11  C16  C15  C14   -54.85  30.0  1
 LTY  Var_03    C12  N11  C6   C5   -146.80  30.0  2
 LTY  Var_04    C13  C12  N11  C6    167.44  30.0  1
 LTY  Var_05    C15  C16  N11  C6   -166.22  30.0  1
 LTY  Var_06    C26  C22  C20  N19  -169.30  30.0  2
 LTY  Var_07    H17  N18  C17  C14    65.85  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
 LTY  chir_01  C14  C17  C13  C15  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
 LTY  plan-1  C20  0.020
 LTY  plan-1  C22  0.020
 LTY  plan-1  C23  0.020
 LTY  plan-1  N24  0.020
 LTY  plan-1  N25  0.020
 LTY  plan-1  C26  0.020
 LTY  plan-1  N27  0.020
 LTY  plan-1  C28  0.020
 LTY  plan-1  C29  0.020
 LTY  plan-1  C30  0.020
 LTY  plan-1  H21  0.020
 LTY  plan-1  H22  0.020
 LTY  plan-1  H23  0.020
 LTY  plan-1  H24  0.020
 LTY  plan-2  C4   0.020
 LTY  plan-2  C5   0.020
 LTY  plan-2  C6   0.020
 LTY  plan-2  C7   0.020
 LTY  plan-2  C8   0.020
 LTY  plan-2  C10  0.020
 LTY  plan-2  C3   0.020
 LTY  plan-2  C1   0.020
 LTY  plan-2  C2   0.020
 LTY  plan-2  N9   0.020
 LTY  plan-2  N11  0.020
 LTY  plan-2  N19  0.020
 LTY  plan-2  H1   0.020
 LTY  plan-2  H3   0.020
 LTY  plan-2  H4   0.020
 LTY  plan-2  H9   0.020
 LTY  plan-2  H10  0.020
 LTY  plan-3  C5   0.020
 LTY  plan-3  N19  0.020
 LTY  plan-3  C20  0.020
 LTY  plan-3  O21  0.020
 LTY  plan-3  C22  0.020
 LTY  plan-3  H20  0.020

