# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 20:20:47 2021
#   Inital geometry file: a 150 line input string
#   Ligand name: 7-[5-(morpholin-4-yl)-7-oxo-7H-thieno[3,2-b]pyran-3-yl]-N-[(pyridin-3-yl)methyl]-2,3-dihydro-1,4-benzodioxine-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(NCc1cccnc1)c2cc(cc3OCCOc23)c4csc5C(=O)C=C(Oc45)N6CCOCC6
#
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
 KV9  KV9  7-[5-(morpholin-4-yl)-7-oxo-7H-thieno[3,2-b]pyran-3-yl]-N-[(pyridin-3-yl)methyl]-2,3-dihydro-1,4-benzodioxine-5-carboxamide  ligand  59  36  .  2022-07-25  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_KV9
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
 KV9  O01  O  O2    0  -0.479  -15.0436  -2.3263  25.5850
 KV9  O02  O  O2    0  -0.491  -15.9220  -3.1364  23.0458
 KV9  C03  C  CH2   0  -0.227  -14.7258  -2.3813  23.2135
 KV9  C04  C  CH2   0  -0.228  -14.1246  -2.6778  24.5621
 KV9  C05  C  CR6   0   0.367  -16.3144  -2.7331  25.3721
 KV9  C06  C  CR6   0   0.318  -16.7549  -3.1501  24.1074
 KV9  C07  C  CR6   0  -0.147  -18.0721  -3.5918  23.9507
 KV9  C08  C  CR16  0  -0.389  -18.9136  -3.6090  25.0587
 KV9  C09  C  CR6   0   0.140  -18.5070  -3.1300  26.2973
 KV9  C10  C  CR16  0  -0.434  -17.1907  -2.7005  26.4425
 KV9  C11  C  C     0   0.564  -18.7086  -4.0163  22.6567
 KV9  O12  O  O     0  -0.474  -19.7478  -4.6625  22.6648
 KV9  N13  N  NH1   0  -0.662  -18.1485  -3.6031  21.5092
 KV9  C14  C  CH2   0  -0.345  -18.7929  -3.8352  20.2411
 KV9  N15  N  N     0  -0.396  -21.2822  -1.0003  20.4298
 KV9  C16  C  CR16  0  -0.093  -20.2089  -1.7620  20.6075
 KV9  C17  C  CR6   0   0.024  -20.0466  -3.0201  20.0365
 KV9  C18  C  CR16  0  -0.202  -21.0766  -3.4898  19.2320
 KV9  C19  C  CR16  0  -0.305  -22.1996  -2.7027  19.0337
 KV9  C20  C  CR16  0  -0.087  -22.2571  -1.4651  19.6571
 KV9  O21  O  O     0  -0.471  -21.4292  -2.5034  26.1434
 KV9  C22  C  CR6   0   0.485  -22.9140  -2.3446  28.5671
 KV9  C23  C  CR16  0  -0.631  -23.4848  -2.1307  27.2702
 KV9  C24  C  CR6   0   0.698  -22.7443  -2.2374  26.1130
 KV9  S25  S  S2    0   0.278  -20.4515  -3.0182  29.8125
 KV9  C26  C  CR56  0  -0.434  -21.5021  -2.6830  28.5007
 KV9  C27  C  CR56  0   0.365  -20.8278  -2.7425  27.3200
 KV9  C28  C  CR5   0   0.164  -19.4430  -3.0585  27.4265
 KV9  C29  C  CR15  0  -0.574  -19.1272  -3.2325  28.7464
 KV9  C30  C  CH2   0  -0.408  -22.4108  -2.2335  23.6621
 KV9  C31  C  CH2   0  -0.138  -22.9704  -3.3585  22.8063
 KV9  O32  O  O2    0  -0.489  -24.3848  -3.3071  22.6978
 KV9  C33  C  CH2   0  -0.226  -24.9523  -2.1123  23.1741
 KV9  C34  C  CH2   0  -0.294  -24.6429  -1.9165  24.6503
 KV9  N35  N  NT    0  -0.511  -23.2138  -2.0989  24.8688
 KV9  H1   H  HCH2  0   0.270  -14.0505  -2.6789  22.4137
 KV9  H2   H  HCH2  0   0.256  -14.9438  -1.3143  23.1100
 KV9  H3   H  HCH2  0   0.251  -13.8582  -3.7368  24.6409
 KV9  H4   H  HCH2  0   0.268  -13.2268  -2.0824  24.7185
 KV9  H5   H  HCR6  0   0.262  -19.9081  -4.0061  24.9253
 KV9  H6   H  HCR6  0   0.274  -16.8317  -2.3214  27.3919
 KV9  H7   H  HNH1  0   0.418  -17.2924  -3.0744  21.5263
 KV9  H8   H  HCH2  0   0.262  -19.0270  -4.8947  20.1199
 KV9  H9   H  HCH2  0   0.283  -18.0672  -3.5883  19.4650
 KV9  H10  H  HCR6  0   0.253  -19.4338  -1.3505  21.2456
 KV9  H11  H  HCR6  0   0.268  -21.0038  -4.4668  18.7685
 KV9  H12  H  HCR6  0   0.271  -23.0204  -3.0430  18.4173
 KV9  H13  H  HCR6  0   0.263  -23.1243  -0.8264  19.5314
 KV9  H14  H  HCR6  0   0.285  -24.5323  -1.8761  27.2094
 KV9  H15  H  HCR5  0   0.310  -18.1602  -3.4966  29.1478
 KV9  H16  H  HCH2  0   0.294  -21.3739  -2.4542  23.8933
 KV9  H17  H  HCH2  0   0.269  -22.4096  -1.2849  23.1202
 KV9  H18  H  HCH2  0   0.225  -22.7029  -4.3207  23.2507
 KV9  H19  H  HCH2  0   0.226  -22.5076  -3.3146  21.8159
 KV9  H20  H  HCH2  0   0.223  -24.6301  -1.2423  22.5893
 KV9  H21  H  HCH2  0   0.268  -26.0327  -2.1915  23.0531
 KV9  H22  H  HCH2  0   0.258  -24.9704  -0.9228  24.9714
 KV9  H23  H  HCH2  0   0.255  -25.1961  -2.6544  25.2370
 KV9  O36  O  O     0  -0.481  -23.5210  -2.2614  29.6350

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
 KV9  C19  C20  aromatic  1.387  0.020  1.387
 KV9  C19  C18  aromatic  1.386  0.020  1.386
 KV9  C20  N15  aromatic  1.328  0.020  1.328
 KV9  C18  C17  aromatic  1.389  0.020  1.389
 KV9  N15  C16  aromatic  1.328  0.020  1.328
 KV9  C17  C16  aromatic  1.391  0.020  1.391
 KV9  C17  C14  single    1.509  0.020  1.509
 KV9  C14  N13  single    1.441  0.020  1.441
 KV9  N13  C11  single    1.342  0.020  1.342
 KV9  O12  C11  double    1.224  0.020  1.224
 KV9  C11  C07  single    1.503  0.020  1.503
 KV9  O02  C03  single    1.425  0.020  1.425
 KV9  O02  C06  single    1.349  0.020  1.349
 KV9  C03  C04  single    1.506  0.020  1.506
 KV9  C31  O32  single    1.420  0.020  1.420
 KV9  C31  C30  single    1.520  0.020  1.520
 KV9  O32  C33  single    1.406  0.020  1.406
 KV9  C07  C06  aromatic  1.398  0.020  1.398
 KV9  C07  C08  aromatic  1.391  0.020  1.391
 KV9  C06  C05  aromatic  1.403  0.020  1.403
 KV9  C04  O01  single    1.419  0.020  1.419
 KV9  C30  N35  single    1.456  0.020  1.456
 KV9  C33  C34  single    1.521  0.020  1.521
 KV9  C08  C09  aromatic  1.389  0.020  1.389
 KV9  C05  O01  single    1.351  0.020  1.351
 KV9  C05  C10  aromatic  1.384  0.020  1.384
 KV9  N35  C34  single    1.457  0.020  1.457
 KV9  N35  C24  single    1.337  0.020  1.337
 KV9  C09  C10  aromatic  1.392  0.020  1.392
 KV9  C09  C28  single    1.468  0.020  1.468
 KV9  O21  C24  single    1.342  0.020  1.342
 KV9  O21  C27  single    1.343  0.020  1.343
 KV9  C24  C23  double    1.378  0.020  1.378
 KV9  C28  C27  aromatic  1.424  0.020  1.424
 KV9  C28  C29  aromatic  1.368  0.020  1.368
 KV9  C27  C26  aromatic  1.361  0.020  1.361
 KV9  C23  C22  single    1.433  0.020  1.433
 KV9  C29  S25  aromatic  1.714  0.020  1.714
 KV9  C26  C22  single    1.453  0.020  1.453
 KV9  C26  S25  aromatic  1.714  0.020  1.714
 KV9  C22  O36  double    1.231  0.020  1.231
 KV9  C03  H1   single    0.970  0.020  1.090
 KV9  C03  H2   single    0.970  0.020  1.090
 KV9  C04  H3   single    0.970  0.020  1.090
 KV9  C04  H4   single    0.970  0.020  1.090
 KV9  C08  H5   single    0.930  0.020  1.080
 KV9  C10  H6   single    0.930  0.020  1.080
 KV9  N13  H7   single    0.860  0.020  1.020
 KV9  C14  H8   single    0.970  0.020  1.090
 KV9  C14  H9   single    0.970  0.020  1.090
 KV9  C16  H10  single    0.930  0.020  1.080
 KV9  C18  H11  single    0.930  0.020  1.080
 KV9  C19  H12  single    0.930  0.020  1.080
 KV9  C20  H13  single    0.930  0.020  1.080
 KV9  C23  H14  single    0.930  0.020  1.080
 KV9  C29  H15  single    0.930  0.020  1.080
 KV9  C30  H16  single    0.970  0.020  1.090
 KV9  C30  H17  single    0.970  0.020  1.090
 KV9  C31  H18  single    0.970  0.020  1.090
 KV9  C31  H19  single    0.970  0.020  1.090
 KV9  C33  H20  single    0.970  0.020  1.090
 KV9  C33  H21  single    0.970  0.020  1.090
 KV9  C34  H22  single    0.970  0.020  1.090
 KV9  C34  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
 KV9  C05  O01  C04  114.89  3.000
 KV9  C06  O02  C03  115.54  3.000
 KV9  H2   C03  H1   108.71  3.000
 KV9  H2   C03  C04  110.87  3.000
 KV9  H1   C03  C04  110.89  3.000
 KV9  H2   C03  O02  109.79  3.000
 KV9  H1   C03  O02  106.84  3.000
 KV9  C04  C03  O02  109.65  3.000
 KV9  H4   C04  H3   108.54  3.000
 KV9  H4   C04  C03  110.50  3.000
 KV9  H3   C04  C03  110.61  3.000
 KV9  H4   C04  O01  107.16  3.000
 KV9  H3   C04  O01  110.20  3.000
 KV9  C03  C04  O01  109.77  3.000
 KV9  C10  C05  C06  120.37  3.000
 KV9  C10  C05  O01  117.82  3.000
 KV9  C06  C05  O01  121.80  3.000
 KV9  C07  C06  C05  119.40  3.000
 KV9  C05  C06  O02  120.83  3.000
 KV9  C07  C06  O02  119.78  3.000
 KV9  C11  C07  C08  115.21  3.000
 KV9  C08  C07  C06  118.98  3.000
 KV9  C11  C07  C06  125.77  3.000
 KV9  H5   C08  C09  120.46  3.000
 KV9  H5   C08  C07  117.61  3.000
 KV9  C09  C08  C07  121.93  3.000
 KV9  C28  C09  C10  120.49  3.000
 KV9  C28  C09  C08  121.06  3.000
 KV9  C10  C09  C08  118.44  3.000
 KV9  H6   C10  C09  120.84  3.000
 KV9  H6   C10  C05  118.44  3.000
 KV9  C09  C10  C05  120.72  3.000
 KV9  N13  C11  O12  121.51  3.000
 KV9  O12  C11  C07  120.19  3.000
 KV9  N13  C11  C07  118.19  3.000
 KV9  H7   N13  C14  118.68  3.000
 KV9  H7   N13  C11  120.15  3.000
 KV9  C14  N13  C11  121.08  3.000
 KV9  H9   C14  H8   106.46  3.000
 KV9  H9   C14  C17  109.51  3.000
 KV9  H8   C14  C17  109.32  3.000
 KV9  H9   C14  N13  106.99  3.000
 KV9  H8   C14  N13  110.47  3.000
 KV9  C17  C14  N13  113.81  3.000
 KV9  C20  N15  C16  118.06  3.000
 KV9  H10  C16  C17  120.07  3.000
 KV9  H10  C16  N15  116.01  3.000
 KV9  C17  C16  N15  123.92  3.000
 KV9  C18  C17  C16  117.20  3.000
 KV9  C16  C17  C14  121.99  3.000
 KV9  C18  C17  C14  120.79  3.000
 KV9  H11  C18  C19  120.35  3.000
 KV9  H11  C18  C17  120.19  3.000
 KV9  C19  C18  C17  119.46  3.000
 KV9  H12  C19  C20  120.37  3.000
 KV9  H12  C19  C18  121.20  3.000
 KV9  C20  C19  C18  118.43  3.000
 KV9  H13  C20  C19  120.44  3.000
 KV9  H13  C20  N15  116.64  3.000
 KV9  C19  C20  N15  122.92  3.000
 KV9  C27  O21  C24  119.60  3.000
 KV9  O36  C22  C26  122.30  3.000
 KV9  O36  C22  C23  125.35  3.000
 KV9  C26  C22  C23  112.35  3.000
 KV9  H14  C23  C24  119.49  3.000
 KV9  H14  C23  C22  118.20  3.000
 KV9  C24  C23  C22  122.31  3.000
 KV9  N35  C24  C23  125.79  3.000
 KV9  C23  C24  O21  121.53  3.000
 KV9  N35  C24  O21  112.68  3.000
 KV9  C29  S25  C26   91.26  3.000
 KV9  C27  C26  S25  110.60  3.000
 KV9  S25  C26  C22  127.31  3.000
 KV9  C27  C26  C22  122.08  3.000
 KV9  C28  C27  C26  115.24  3.000
 KV9  C26  C27  O21  122.04  3.000
 KV9  C28  C27  O21  122.71  3.000
 KV9  C29  C28  C27  108.95  3.000
 KV9  C29  C28  C09  126.05  3.000
 KV9  C27  C28  C09  124.96  3.000
 KV9  H15  C29  C28  126.61  3.000
 KV9  H15  C29  S25  119.43  3.000
 KV9  C28  C29  S25  113.95  3.000
 KV9  H17  C30  H16  106.33  3.000
 KV9  H17  C30  N35  109.36  3.000
 KV9  H16  C30  N35  111.68  3.000
 KV9  H17  C30  C31  111.33  3.000
 KV9  H16  C30  C31  108.73  3.000
 KV9  N35  C30  C31  109.39  3.000
 KV9  H19  C31  H18  107.45  3.000
 KV9  H19  C31  O32  110.54  3.000
 KV9  H18  C31  O32  107.86  3.000
 KV9  H19  C31  C30  108.92  3.000
 KV9  H18  C31  C30  109.42  3.000
 KV9  O32  C31  C30  112.51  3.000
 KV9  C33  O32  C31  114.02  3.000
 KV9  H21  C33  H20  106.83  3.000
 KV9  H21  C33  C34  108.59  3.000
 KV9  H20  C33  C34  110.84  3.000
 KV9  H21  C33  O32  107.50  3.000
 KV9  H20  C33  O32  112.02  3.000
 KV9  C34  C33  O32  110.86  3.000
 KV9  H23  C34  H22  107.69  3.000
 KV9  H23  C34  N35  109.35  3.000
 KV9  H22  C34  N35  111.29  3.000
 KV9  H23  C34  C33  109.34  3.000
 KV9  H22  C34  C33  109.93  3.000
 KV9  N35  C34  C33  109.20  3.000
 KV9  C34  N35  C30  115.36  3.000
 KV9  C34  N35  C24  119.79  3.000
 KV9  C30  N35  C24  124.62  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
 KV9  CONST_01  C08  C07  C06  C05     0.00   0.0  0
 KV9  CONST_02  C08  C09  C10  C05     0.00   0.0  0
 KV9  CONST_03  C28  C09  C10  C05   180.00   0.0  0
 KV9  CONST_04  C09  C08  C07  C06     0.00   0.0  0
 KV9  CONST_05  C09  C10  C05  C06     0.00   0.0  0
 KV9  CONST_06  C10  C05  C06  C07     0.00   0.0  0
 KV9  CONST_07  C10  C09  C08  C07     0.00   0.0  0
 KV9  CONST_08  C28  C09  C08  C07   180.00   0.0  0
 KV9  CONST_11  C26  C27  C28  C09   180.00   0.0  0
 KV9  CONST_12  S25  C29  C28  C09   180.00   0.0  0
 KV9  CONST_15  C18  C19  C20  N15     0.00   0.0  0
 KV9  CONST_16  C18  C17  C16  N15     0.00   0.0  0
 KV9  CONST_17  C19  C20  N15  C16     0.00   0.0  0
 KV9  CONST_18  C19  C18  C17  C16     0.00   0.0  0
 KV9  CONST_19  C20  C19  C18  C17     0.00   0.0  0
 KV9  CONST_20  C20  N15  C16  C17     0.00   0.0  0
 KV9  CONST_21  C27  C28  C29  S25     0.00   0.0  0
 KV9  CONST_22  C28  C27  C26  S25     0.00   0.0  0
 KV9  CONST_23  C29  C28  C27  C26     0.00   0.0  0
 KV9  CONST_24  C28  C29  S25  C26     0.00   0.0  0
 KV9  CONST_25  C29  S25  C26  C27     0.00   0.0  0
 KV9  CONST_26  O21  C27  C28  C09     0.00   0.0  0
 KV9  CONST_27  C11  C07  C06  O02     0.00   0.0  0
 KV9  CONST_28  C11  C07  C06  C05   180.00   0.0  0
 KV9  CONST_29  C11  C07  C08  C09   180.00   0.0  0
 KV9  CONST_30  C19  C18  C17  C14   180.00   0.0  0
 KV9  CONST_31  N15  C16  C17  C14   180.00   0.0  0
 KV9  CONST_32  H6   C10  C05  O01     0.00   0.0  0
 KV9  CONST_33  H5   C08  C07  C06   180.00   0.0  0
 KV9  CONST_34  H15  C29  C28  C09     0.00   0.0  0
 KV9  CONST_35  H12  C19  C20  N15   180.00   0.0  0
 KV9  CONST_36  H13  C20  N15  C16   180.00   0.0  0
 KV9  CONST_37  H11  C18  C17  C16   180.00   0.0  0
 KV9  CONST_38  H10  C16  C17  C18   180.00   0.0  0
 KV9  CONST_39  C14  N13  C11  C07   180.00   0.0  0
 KV9  CONST_40  H7   N13  C11  C07     0.00   0.0  0
 KV9  CONST_41  C14  N13  C11  O12     0.00   0.0  0
 KV9  Var_01    O02  C03  C04  O01   -60.14  30.0  1
 KV9  Var_02    C07  C06  O02  C03   165.35  30.0  1
 KV9  Var_03    C06  C05  O01  C04   -15.79  30.0  1
 KV9  Var_04    C30  N35  C24  O21     0.73  30.0  2
 KV9  Var_05    C22  C23  C24  O21    -2.39  30.0  1
 KV9  Var_06    C27  C26  C22  C23     1.70  30.0  1
 KV9  Var_07    C31  C30  N35  C24   119.97  30.0  1
 KV9  Var_08    C33  C34  N35  C24  -166.80  30.0  1
 KV9  Var_09    C28  C27  O21  C24   178.68  30.0  1
 KV9  Var_10    C26  C22  C23  C24    -0.25  30.0  1
 KV9  Var_11    C34  C33  O32  C31   -60.74  30.0  1
 KV9  Var_12    N35  C30  C31  O32    44.94  30.0  1
 KV9  Var_13    N35  C34  C33  O32    49.89  30.0  1
 KV9  Var_14    H18  C31  O32  C33   132.23  30.0  1
 KV9  Var_15    N13  C11  C07  C06   -20.28  30.0  2
 KV9  Var_16    C18  C17  C14  N13  -151.26  30.0  3
 KV9  Var_17    C17  C14  N13  C11    69.62  30.0  1

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
 KV9  plan-1  C14  0.020
 KV9  plan-1  N15  0.020
 KV9  plan-1  C16  0.020
 KV9  plan-1  C17  0.020
 KV9  plan-1  C18  0.020
 KV9  plan-1  C19  0.020
 KV9  plan-1  C20  0.020
 KV9  plan-1  H10  0.020
 KV9  plan-1  H11  0.020
 KV9  plan-1  H12  0.020
 KV9  plan-1  H13  0.020
 KV9  plan-2  C09  0.020
 KV9  plan-2  O21  0.020
 KV9  plan-2  C22  0.020
 KV9  plan-2  S25  0.020
 KV9  plan-2  C26  0.020
 KV9  plan-2  C27  0.020
 KV9  plan-2  C28  0.020
 KV9  plan-2  C29  0.020
 KV9  plan-2  H15  0.020
 KV9  plan-3  O01  0.020
 KV9  plan-3  O02  0.020
 KV9  plan-3  C05  0.020
 KV9  plan-3  C06  0.020
 KV9  plan-3  C07  0.020
 KV9  plan-3  C08  0.020
 KV9  plan-3  C09  0.020
 KV9  plan-3  C10  0.020
 KV9  plan-3  C11  0.020
 KV9  plan-3  C28  0.020
 KV9  plan-3  H5   0.020
 KV9  plan-3  H6   0.020
 KV9  plan-4  C07  0.020
 KV9  plan-4  C11  0.020
 KV9  plan-4  O12  0.020
 KV9  plan-4  N13  0.020
 KV9  plan-4  C14  0.020
 KV9  plan-4  H7   0.020
 KV9  plan-5  C22  0.020
 KV9  plan-5  C23  0.020
 KV9  plan-5  C26  0.020
 KV9  plan-5  O36  0.020
 KV9  plan-6  C24  0.020
 KV9  plan-6  C30  0.020
 KV9  plan-6  C34  0.020
 KV9  plan-6  N35  0.020

