# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 01:53:50 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: N-[2,2-dimethyl-6-(morpholin-4-yl)-2,3-dihydro-1-benzofuran-5-yl]pyrazolo[1,5-a]pyrimidine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(C)Cc2cc(NC(=O)c3cnn4cccnc34)c(cc2O1)N5CCOCC5
#
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
 LS7  LS7  N-[2,2-dimethyl-6-(morpholin-4-yl)-2,3-dihydro-1-benzofuran-5-yl]pyrazolo[1,5-a]pyrimidine-3-carboxamide  ligand  52  29  .  2021-08-12  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_LS7
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
 LS7  C4   C  CR56  0  -0.012   2.6813   1.9371  -0.2410
 LS7  C5   C  CR16  0  -0.400   1.3195   1.7116  -0.2611
 LS7  C6   C  CR6   0   0.318   0.8548   0.3949  -0.1936
 LS7  C7   C  CR6   0   0.225   1.7714  -0.6694  -0.1119
 LS7  C8   C  CR16  0  -0.403   3.1428  -0.4277  -0.0887
 LS7  C9   C  CR56  0   0.413   3.5757   0.8825  -0.1570
 LS7  C12  C  CH2   0  -0.307   1.8483  -2.9757  -0.8981
 LS7  C13  C  CH2   0  -0.191   1.0236  -4.2482  -0.8432
 LS7  C3   C  CH2   0  -0.496   3.4765   3.2011  -0.3490
 LS7  C2   C  CR5   0   0.188   4.8960   2.7220   0.0338
 LS7  O10  O  O     0  -0.503   4.8648   1.2758  -0.1470
 LS7  N11  N  NT    0  -0.541   1.2311  -1.9798  -0.0344
 LS7  O14  O  O2    0  -0.481   0.9159  -4.7340   0.4765
 LS7  C15  C  CH2   0  -0.187   0.3263  -3.7754   1.3248
 LS7  C16  C  CH2   0  -0.323   1.1099  -2.4770   1.3335
 LS7  N17  N  NH1   0  -0.762  -0.4896   0.0212  -0.2397
 LS7  C18  C  C     0   0.511  -1.5997   0.7747  -0.0563
 LS7  O19  O  O     0  -0.475  -1.5781   1.9775   0.1618
 LS7  C20  C  CR5   0  -0.370  -2.8585   0.0266  -0.1365
 LS7  C21  C  CR15  0  -0.031  -3.0959  -1.3297  -0.4164
 LS7  N22  N  N     0  -0.288  -4.3739  -1.6504  -0.3979
 LS7  N23  N  N     0  -0.361  -5.0004  -0.5079  -0.1046
 LS7  C24  C  CR56  0   0.633  -4.1359   0.5550   0.0663
 LS7  N25  N  N     0  -0.411  -4.5880   1.7778   0.3643
 LS7  C26  C  CR16  0  -0.043  -5.8814   1.9234   0.4846
 LS7  C27  C  CR16  0  -0.389  -6.8111   0.8726   0.3182
 LS7  C28  C  CR16  0   0.090  -6.3368  -0.3646   0.0180
 LS7  C29  C  CH3   0  -0.653   5.1880   2.9957   1.5017
 LS7  H1   H  HCR6  0   0.272   0.6311   2.5381  -0.3383
 LS7  H2   H  HCR6  0   0.263   3.8474  -1.2465  -0.0150
 LS7  H3   H  HCH2  0   0.216   2.8827  -3.2028  -0.6009
 LS7  H4   H  HCH2  0   0.256   1.8714  -2.6022  -1.9232
 LS7  H5   H  HCH2  0   0.204   0.0266  -4.0539  -1.2655
 LS7  H6   H  HCH2  0   0.243   1.4971  -5.0276  -1.4415
 LS7  H7   H  HCH2  0   0.265   3.4454   3.5962  -1.3689
 LS7  H8   H  HCH2  0   0.265   3.1272   3.9950   0.3131
 LS7  H9   H  HCH3  0   0.236   6.0101   4.3662  -0.7735
 LS7  H10  H  HCH3  0   0.238   6.9624   2.8950  -0.5904
 LS7  H11  H  HCH3  0   0.240   5.7916   3.0369  -1.9118
 LS7  H12  H  HCH2  0   0.197  -0.7082  -3.5706   1.0107
 LS7  H13  H  HCH2  0   0.245   0.2916  -4.2009   2.3286
 LS7  H14  H  HCH2  0   0.228   2.0983  -2.6338   1.7908
 LS7  H15  H  HCH2  0   0.258   0.5786  -1.7432   1.9433
 LS7  H16  H  HNH1  0   0.403  -0.5826  -0.9812  -0.3539
 LS7  H17  H  HCR5  0   0.265  -2.3780  -2.1050  -0.6448
 LS7  H18  H  HCR6  0   0.285  -6.2402   2.9172   0.7247
 LS7  H19  H  HCR6  0   0.303  -7.8708   1.0433   0.4258
 LS7  H20  H  HCR6  0   0.333  -6.9427  -1.2458  -0.1329
 LS7  H21  H  HCH3  0   0.236   4.4011   2.5975   2.1456
 LS7  H22  H  HCH3  0   0.238   6.1373   2.5510   1.8026
 LS7  H23  H  HCH3  0   0.234   5.2490   4.0706   1.6759
 LS7  C1   C  CH3   0  -0.672   5.9795   3.2801  -0.8654

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
 LS7  C28  N23  aromatic  1.350  0.020  1.350
 LS7  C28  C27  aromatic  1.359  0.020  1.359
 LS7  N22  N23  aromatic  1.336  0.020  1.336
 LS7  N22  C21  aromatic  1.318  0.020  1.318
 LS7  N23  C24  aromatic  1.381  0.020  1.381
 LS7  C27  C26  aromatic  1.413  0.020  1.413
 LS7  C21  C20  aromatic  1.405  0.020  1.405
 LS7  C24  C20  aromatic  1.397  0.020  1.397
 LS7  C24  N25  aromatic  1.337  0.020  1.337
 LS7  C26  N25  aromatic  1.307  0.020  1.307
 LS7  C20  C18  single    1.467  0.020  1.467
 LS7  C18  O19  double    1.223  0.020  1.223
 LS7  C18  N17  single    1.354  0.020  1.354
 LS7  N17  C6   single    1.396  0.020  1.396
 LS7  C15  C16  single    1.517  0.020  1.517
 LS7  C15  O14  single    1.409  0.020  1.409
 LS7  C16  N11  single    1.461  0.020  1.461
 LS7  O14  C13  single    1.410  0.020  1.410
 LS7  C6   C5   aromatic  1.398  0.020  1.398
 LS7  C6   C7   aromatic  1.407  0.020  1.407
 LS7  N11  C7   single    1.420  0.020  1.420
 LS7  N11  C12  single    1.456  0.020  1.456
 LS7  C5   C4   aromatic  1.381  0.020  1.381
 LS7  C13  C12  single    1.517  0.020  1.517
 LS7  C7   C8   aromatic  1.393  0.020  1.393
 LS7  C4   C9   aromatic  1.385  0.020  1.385
 LS7  C4   C3   single    1.497  0.020  1.497
 LS7  C8   C9   aromatic  1.382  0.020  1.382
 LS7  C9   O10  single    1.348  0.020  1.348
 LS7  C3   C2   single    1.546  0.020  1.546
 LS7  O10  C2   single    1.458  0.020  1.458
 LS7  C2   C29  single    1.521  0.020  1.521
 LS7  C2   C1   single    1.515  0.020  1.515
 LS7  C5   H1   single    0.930  0.020  1.080
 LS7  C8   H2   single    0.930  0.020  1.080
 LS7  C12  H3   single    0.970  0.020  1.090
 LS7  C12  H4   single    0.970  0.020  1.090
 LS7  C13  H5   single    0.970  0.020  1.090
 LS7  C13  H6   single    0.970  0.020  1.090
 LS7  C3   H7   single    0.970  0.020  1.090
 LS7  C3   H8   single    0.970  0.020  1.090
 LS7  C1   H9   single    0.970  0.020  1.090
 LS7  C1   H10  single    0.970  0.020  1.090
 LS7  C1   H11  single    0.970  0.020  1.090
 LS7  C15  H12  single    0.970  0.020  1.090
 LS7  C15  H13  single    0.970  0.020  1.090
 LS7  C16  H14  single    0.970  0.020  1.090
 LS7  C16  H15  single    0.970  0.020  1.090
 LS7  N17  H16  single    0.860  0.020  1.020
 LS7  C21  H17  single    0.930  0.020  1.080
 LS7  C26  H18  single    0.930  0.020  1.080
 LS7  C27  H19  single    0.930  0.020  1.080
 LS7  C28  H20  single    0.930  0.020  1.080
 LS7  C29  H21  single    0.970  0.020  1.090
 LS7  C29  H22  single    0.970  0.020  1.090
 LS7  C29  H23  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
 LS7  C3   C4   C9   107.71  3.000
 LS7  C3   C4   C5   131.36  3.000
 LS7  C9   C4   C5   120.89  3.000
 LS7  H1   C5   C6   120.87  3.000
 LS7  H1   C5   C4   120.37  3.000
 LS7  C6   C5   C4   118.75  3.000
 LS7  N17  C6   C7   115.26  3.000
 LS7  C7   C6   C5   119.92  3.000
 LS7  N17  C6   C5   124.79  3.000
 LS7  N11  C7   C8   122.28  3.000
 LS7  C8   C7   C6   120.74  3.000
 LS7  N11  C7   C6   116.97  3.000
 LS7  H2   C8   C9   121.11  3.000
 LS7  H2   C8   C7   120.71  3.000
 LS7  C9   C8   C7   118.18  3.000
 LS7  O10  C9   C8   125.17  3.000
 LS7  O10  C9   C4   113.32  3.000
 LS7  C8   C9   C4   121.51  3.000
 LS7  H4   C12  H3   107.73  3.000
 LS7  H4   C12  N11  109.40  3.000
 LS7  H3   C12  N11  112.31  3.000
 LS7  H4   C12  C13  109.43  3.000
 LS7  H3   C12  C13  109.16  3.000
 LS7  N11  C12  C13  108.77  3.000
 LS7  H6   C13  H5   108.00  3.000
 LS7  H6   C13  O14  107.48  3.000
 LS7  H5   C13  O14  110.54  3.000
 LS7  H6   C13  C12  110.09  3.000
 LS7  H5   C13  C12  109.30  3.000
 LS7  O14  C13  C12  111.36  3.000
 LS7  H8   C3   H7   107.08  3.000
 LS7  H8   C3   C2   111.66  3.000
 LS7  H7   C3   C2   111.64  3.000
 LS7  H8   C3   C4   113.61  3.000
 LS7  H7   C3   C4   110.91  3.000
 LS7  C2   C3   C4   102.01  3.000
 LS7  C29  C2   O10  107.59  3.000
 LS7  C29  C2   C1   111.67  3.000
 LS7  O10  C2   C1   107.89  3.000
 LS7  C1   C2   C3   113.30  3.000
 LS7  C29  C2   C3   111.05  3.000
 LS7  O10  C2   C3   104.90  3.000
 LS7  C2   O10  C9   108.11  3.000
 LS7  C16  N11  C12  110.98  3.000
 LS7  C12  N11  C7   115.96  3.000
 LS7  C16  N11  C7   113.39  3.000
 LS7  C15  O14  C13  111.16  3.000
 LS7  H13  C15  H12  107.78  3.000
 LS7  H13  C15  C16  110.19  3.000
 LS7  H12  C15  C16  109.15  3.000
 LS7  H13  C15  O14  107.57  3.000
 LS7  H12  C15  O14  110.37  3.000
 LS7  C16  C15  O14  111.69  3.000
 LS7  H15  C16  H14  107.51  3.000
 LS7  H15  C16  C15  109.09  3.000
 LS7  H14  C16  C15  110.15  3.000
 LS7  H15  C16  N11  109.54  3.000
 LS7  H14  C16  N11  111.30  3.000
 LS7  C15  C16  N11  109.21  3.000
 LS7  H16  N17  C18  119.37  3.000
 LS7  H16  N17  C6   110.92  3.000
 LS7  C18  N17  C6   129.49  3.000
 LS7  C20  C18  O19  121.79  3.000
 LS7  O19  C18  N17  123.85  3.000
 LS7  C20  C18  N17  114.36  3.000
 LS7  C24  C20  C21  103.86  3.000
 LS7  C24  C20  C18  125.73  3.000
 LS7  C21  C20  C18  130.42  3.000
 LS7  H17  C21  N22  118.19  3.000
 LS7  H17  C21  C20  128.47  3.000
 LS7  N22  C21  C20  113.33  3.000
 LS7  N23  N22  C21  104.46  3.000
 LS7  C28  N23  C24  121.81  3.000
 LS7  C24  N23  N22  113.08  3.000
 LS7  C28  N23  N22  125.12  3.000
 LS7  N25  C24  N23  121.32  3.000
 LS7  N25  C24  C20  133.41  3.000
 LS7  N23  C24  C20  105.27  3.000
 LS7  C26  N25  C24  117.19  3.000
 LS7  H18  C26  C27  119.36  3.000
 LS7  H18  C26  N25  116.76  3.000
 LS7  C27  C26  N25  123.88  3.000
 LS7  H19  C27  C28  120.61  3.000
 LS7  H19  C27  C26  121.13  3.000
 LS7  C28  C27  C26  118.27  3.000
 LS7  H20  C28  C27  125.31  3.000
 LS7  H20  C28  N23  117.14  3.000
 LS7  C27  C28  N23  117.55  3.000
 LS7  H23  C29  H22  108.00  3.000
 LS7  H23  C29  H21  107.79  3.000
 LS7  H22  C29  H21  108.41  3.000
 LS7  H23  C29  C2   110.01  3.000
 LS7  H22  C29  C2   111.09  3.000
 LS7  H21  C29  C2   111.41  3.000
 LS7  H11  C1   H10  108.57  3.000
 LS7  H11  C1   H9   107.92  3.000
 LS7  H10  C1   H9   107.77  3.000
 LS7  H11  C1   C2   111.36  3.000
 LS7  H10  C1   C2   111.40  3.000
 LS7  H9   C1   C2   109.70  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
 LS7  CONST_01  C7   C6   C5   C4      0.00   0.0  0
 LS7  CONST_02  C7   C8   C9   C4      0.00   0.0  0
 LS7  CONST_03  C8   C7   C6   C5      0.00   0.0  0
 LS7  CONST_04  C8   C9   C4   C5      0.00   0.0  0
 LS7  CONST_05  C9   C4   C5   C6      0.00   0.0  0
 LS7  CONST_06  C9   C8   C7   C6      0.00   0.0  0
 LS7  CONST_07  N23  N22  C21  C20     0.00   0.0  0
 LS7  CONST_08  C28  N23  C24  C20   180.00   0.0  0
 LS7  CONST_09  N22  N23  C24  C20     0.00   0.0  0
 LS7  CONST_10  C26  N25  C24  C20   180.00   0.0  0
 LS7  CONST_11  C28  N23  N22  C21   180.00   0.0  0
 LS7  CONST_12  C24  N23  N22  C21     0.00   0.0  0
 LS7  CONST_13  N23  C24  C20  C21     0.00   0.0  0
 LS7  CONST_14  N25  C24  C20  C21   180.00   0.0  0
 LS7  CONST_15  C27  C28  N23  N22   180.00   0.0  0
 LS7  CONST_16  N25  C24  N23  N22   180.00   0.0  0
 LS7  CONST_17  C24  C20  C21  N22     0.00   0.0  0
 LS7  CONST_18  C26  C27  C28  N23     0.00   0.0  0
 LS7  CONST_19  C26  N25  C24  N23     0.00   0.0  0
 LS7  CONST_20  C27  C28  N23  C24     0.00   0.0  0
 LS7  CONST_21  C27  C26  N25  C24     0.00   0.0  0
 LS7  CONST_22  C28  N23  C24  N25     0.00   0.0  0
 LS7  CONST_23  C28  C27  C26  N25     0.00   0.0  0
 LS7  CONST_24  N11  C7   C6   C5    180.00   0.0  0
 LS7  CONST_25  N11  C7   C8   C9    180.00   0.0  0
 LS7  CONST_26  N17  C6   C5   C4    180.00   0.0  0
 LS7  CONST_27  N17  C6   C7   C8    180.00   0.0  0
 LS7  CONST_28  N17  C6   C7   N11     0.00   0.0  0
 LS7  CONST_29  N22  C21  C20  C18   180.00   0.0  0
 LS7  CONST_30  N23  C24  C20  C18   180.00   0.0  0
 LS7  CONST_31  N25  C24  C20  C18     0.00   0.0  0
 LS7  CONST_32  H2   C8   C9   C4    180.00   0.0  0
 LS7  CONST_33  H1   C5   C6   C7    180.00   0.0  0
 LS7  CONST_34  H20  C28  N23  N22     0.00   0.0  0
 LS7  CONST_35  H19  C27  C28  N23   180.00   0.0  0
 LS7  CONST_36  H17  C21  N22  N23   180.00   0.0  0
 LS7  CONST_37  H18  C26  N25  C24   180.00   0.0  0
 LS7  CONST_38  C20  C18  N17  C6    180.00   0.0  0
 LS7  CONST_40  C18  N17  C6   C7    180.00   0.0  0
 LS7  CONST_41  H16  N17  C6   C5    180.00   0.0  0
 LS7  CONST_42  O19  C18  N17  C6      0.00   0.0  0
 LS7  Var_01    O10  C2   C3   C4     19.06  30.0  1
 LS7  Var_02    C2   C3   C4   C5    169.16  30.0  1
 LS7  Var_03    C16  N11  C7   C6    -95.46  30.0  2
 LS7  Var_04    C15  C16  N11  C7    171.01  30.0  1
 LS7  Var_05    C13  C12  N11  C7   -171.60  30.0  1
 LS7  Var_06    C3   C2   O10  C9    -18.83  30.0  1
 LS7  Var_07    C16  C15  O14  C13   -57.75  30.0  1
 LS7  Var_08    O14  C15  C16  N11    56.17  30.0  1
 LS7  Var_09    O14  C13  C12  N11   -57.85  30.0  1
 LS7  Var_10    C21  C20  C18  N17    -2.44  30.0  2
 LS7  Var_11    H21  C29  C2   C3     52.11  30.0  3
 LS7  Var_12    H9   C1   C2   C3     62.79  30.0  3

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
 LS7  plan-1  C4   0.020
 LS7  plan-1  C5   0.020
 LS7  plan-1  C6   0.020
 LS7  plan-1  C7   0.020
 LS7  plan-1  C8   0.020
 LS7  plan-1  C9   0.020
 LS7  plan-1  C3   0.020
 LS7  plan-1  O10  0.020
 LS7  plan-1  N11  0.020
 LS7  plan-1  N17  0.020
 LS7  plan-1  H1   0.020
 LS7  plan-1  H2   0.020
 LS7  plan-2  C18  0.020
 LS7  plan-2  C20  0.020
 LS7  plan-2  C21  0.020
 LS7  plan-2  N22  0.020
 LS7  plan-2  N23  0.020
 LS7  plan-2  C24  0.020
 LS7  plan-2  N25  0.020
 LS7  plan-2  C26  0.020
 LS7  plan-2  C27  0.020
 LS7  plan-2  C28  0.020
 LS7  plan-2  H17  0.020
 LS7  plan-2  H18  0.020
 LS7  plan-2  H19  0.020
 LS7  plan-2  H20  0.020
 LS7  plan-3  C6   0.020
 LS7  plan-3  N17  0.020
 LS7  plan-3  C18  0.020
 LS7  plan-3  O19  0.020
 LS7  plan-3  C20  0.020
 LS7  plan-3  H16  0.020

