# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 22:07:02 2022
#   Inital geometry file: a 118 line input string
#   Ligand name: 1-({3-[(3R,5R)-5-(4-fluorophenyl)oxolan-3-yl]-1,2,4-oxadiazol-5-yl}methyl)-7-methyl-1,7-dihydro-6H-purin-6-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cnc2N=CN(Cc3onc(n3)[C@@H]4CO[C@H](C4)c5ccc(F)cc5)C(=O)c12
#
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
 VKM  VKM  1-({3-[(3R,5R)-5-(4-fluorophenyl)oxolan-3-yl]-1,2,4-oxadiazol-5-yl}methyl)-7-methyl-1,7-dihydro-6H-purin-6-one  ligand  46  29  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_VKM
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
 VKM  C1   C  CH3   0  -0.521  58.2421  62.7975  83.4869
 VKM  C13  C  CR5   0   0.536  60.7741  60.6869  88.3232
 VKM  C15  C  CR5   0   0.347  62.2049  62.1050  88.8016
 VKM  C18  C  CH1   0  -0.429  62.7962  63.3941  89.2628
 VKM  C20  C  CH1   0   0.001  64.3023  64.1506  87.5904
 VKM  C23  C  CR6   0   0.115  65.5646  64.8932  87.2529
 VKM  C24  C  CR16  0  -0.281  65.8639  66.1045  87.8732
 VKM  C25  C  CR16  0  -0.396  67.0354  66.7846  87.5821
 VKM  C26  C  CR6   0   0.514  67.9077  66.2386  86.6580
 VKM  C28  C  CR16  0  -0.301  66.4651  64.3759  86.3299
 VKM  C6   C  CR56  0   0.132  57.6257  62.0020  85.8054
 VKM  C7   C  CR6   0   0.576  58.7334  61.2238  86.2340
 VKM  N9   N  NR6   0  -0.523  58.4978  60.7155  87.5194
 VKM  O21  O  O2    0  -0.493  63.2080  65.0485  87.5979
 VKM  C10  C  CR16  0   0.156  57.3698  60.9769  88.2453
 VKM  C12  C  CH2   0  -0.439  59.5434  59.8824  88.0790
 VKM  C19  C  CH2   0  -0.481  64.2910  63.5282  88.9838
 VKM  C22  C  CH2   0  -0.145  62.2124  64.6031  88.5027
 VKM  C27  C  CR16  0  -0.395  67.6472  65.0403  86.0261
 VKM  C3   C  CR15  0   0.114  56.1687  63.2435  84.8016
 VKM  C5   C  CR56  0   0.279  56.5125  62.2063  86.6023
 VKM  F29  F  F     0  -0.315  69.0401  66.8992  86.3660
 VKM  N11  N  N     0  -0.437  56.3756  61.6898  87.8508
 VKM  N14  N  N     0  -0.438  60.8539  61.9037  88.7332
 VKM  N16  N  N     0  -0.150  62.8990  61.0641  88.4614
 VKM  N2   N  NR5   0  -0.468  57.3817  62.6829  84.6461
 VKM  N4   N  N     0  -0.454  55.6093  62.9827  85.9628
 VKM  O17  O  O     0  -0.321  61.9539  60.1234  88.1421
 VKM  H31  H  HCH3  0   0.267  58.4598  61.8149  83.0762
 VKM  H30  H  HCH3  0   0.270  57.7280  63.3889  82.7350
 VKM  H32  H  HCH3  0   0.267  59.1735  63.2919  83.7515
 VKM  H37  H  HCH1  0   0.311  62.5802  63.4818  90.3303
 VKM  H40  H  HCH1  0   0.237  64.1455  63.3614  86.8404
 VKM  H43  H  HCR6  0   0.260  65.1782  66.5318  88.5939
 VKM  H44  H  HCR6  0   0.277  67.2658  67.7265  88.0630
 VKM  H46  H  HCR6  0   0.262  66.2453  63.4387  85.8329
 VKM  H34  H  HCR6  0   0.302  57.3451  60.5264  89.2300
 VKM  H36  H  HCH2  0   0.329  59.1916  59.4672  89.0249
 VKM  H35  H  HCH2  0   0.325  59.7634  59.0435  87.4191
 VKM  H38  H  HCH2  0   0.270  64.8439  62.5916  89.0290
 VKM  H39  H  HCH2  0   0.268  64.7364  64.2138  89.7075
 VKM  H41  H  HCH2  0   0.232  61.9718  65.4134  89.1940
 VKM  H42  H  HCH2  0   0.229  61.2977  64.3405  87.9647
 VKM  H45  H  HCR6  0   0.277  68.3440  64.6339  85.3047
 VKM  H33  H  HCR5  0   0.298  55.7274  63.8444  84.0196
 VKM  O8   O  O     0  -0.462  59.7748  60.9847  85.6468

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
 VKM  C1   N2   single    1.448  0.020  1.448
 VKM  N2   C3   aromatic  1.345  0.020  1.345
 VKM  N2   C6   aromatic  1.366  0.020  1.366
 VKM  C3   N4   aromatic  1.315  0.020  1.315
 VKM  O8   C7   double    1.219  0.020  1.219
 VKM  C6   C7   single    1.420  0.020  1.420
 VKM  C6   C5   aromatic  1.384  0.020  1.384
 VKM  C7   N9   single    1.402  0.020  1.402
 VKM  N4   C5   aromatic  1.352  0.020  1.352
 VKM  C5   N11  single    1.358  0.020  1.358
 VKM  F29  C26  single    1.343  0.020  1.343
 VKM  C25  C26  aromatic  1.383  0.020  1.383
 VKM  C25  C24  aromatic  1.386  0.020  1.386
 VKM  N9   C12  single    1.449  0.020  1.449
 VKM  N9   C10  single    1.367  0.020  1.367
 VKM  C26  C27  aromatic  1.380  0.020  1.380
 VKM  C24  C23  aromatic  1.393  0.020  1.393
 VKM  C12  C13  single    1.490  0.020  1.490
 VKM  C27  C28  aromatic  1.390  0.020  1.390
 VKM  C20  C23  single    1.503  0.020  1.503
 VKM  C20  O21  single    1.416  0.020  1.416
 VKM  C20  C19  single    1.526  0.020  1.526
 VKM  C23  C28  aromatic  1.389  0.020  1.389
 VKM  O17  C13  aromatic  1.320  0.020  1.320
 VKM  O17  N16  aromatic  1.371  0.020  1.371
 VKM  C13  N14  aromatic  1.287  0.020  1.287
 VKM  N11  C10  double    1.285  0.020  1.285
 VKM  N16  C15  aromatic  1.296  0.020  1.296
 VKM  N14  C15  aromatic  1.368  0.020  1.368
 VKM  O21  C22  single    1.417  0.020  1.417
 VKM  C22  C18  single    1.543  0.020  1.543
 VKM  C15  C18  single    1.491  0.020  1.491
 VKM  C19  C18  single    1.526  0.020  1.526
 VKM  C1   H31  single    0.970  0.020  1.090
 VKM  C1   H30  single    0.970  0.020  1.090
 VKM  C1   H32  single    0.970  0.020  1.090
 VKM  C18  H37  single    0.970  0.020  1.090
 VKM  C20  H40  single    0.970  0.020  1.090
 VKM  C24  H43  single    0.930  0.020  1.080
 VKM  C25  H44  single    0.930  0.020  1.080
 VKM  C28  H46  single    0.930  0.020  1.080
 VKM  C10  H34  single    0.930  0.020  1.080
 VKM  C12  H36  single    0.970  0.020  1.090
 VKM  C12  H35  single    0.970  0.020  1.090
 VKM  C19  H38  single    0.970  0.020  1.090
 VKM  C19  H39  single    0.970  0.020  1.090
 VKM  C22  H41  single    0.970  0.020  1.090
 VKM  C22  H42  single    0.970  0.020  1.090
 VKM  C27  H45  single    0.930  0.020  1.080
 VKM  C3   H33  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
 VKM  H32  C1   H30  109.05  3.000
 VKM  H32  C1   H31  109.36  3.000
 VKM  H30  C1   H31  108.99  3.000
 VKM  H32  C1   N2   110.50  3.000
 VKM  H30  C1   N2   108.42  3.000
 VKM  H31  C1   N2   110.48  3.000
 VKM  O17  C13  N14  113.08  3.000
 VKM  N14  C13  C12  127.88  3.000
 VKM  O17  C13  C12  119.02  3.000
 VKM  N16  C15  N14  113.42  3.000
 VKM  N14  C15  C18  122.30  3.000
 VKM  N16  C15  C18  124.25  3.000
 VKM  H37  C18  C22  110.09  3.000
 VKM  H37  C18  C19  111.41  3.000
 VKM  C22  C18  C19  102.22  3.000
 VKM  H37  C18  C15  107.05  3.000
 VKM  C19  C18  C15  114.06  3.000
 VKM  C22  C18  C15  112.02  3.000
 VKM  H40  C20  C19  109.20  3.000
 VKM  H40  C20  O21  110.40  3.000
 VKM  C19  C20  O21  104.37  3.000
 VKM  H40  C20  C23  108.73  3.000
 VKM  C19  C20  C23  114.38  3.000
 VKM  O21  C20  C23  109.70  3.000
 VKM  C28  C23  C24  118.69  3.000
 VKM  C28  C23  C20  120.64  3.000
 VKM  C24  C23  C20  120.66  3.000
 VKM  H43  C24  C25  118.79  3.000
 VKM  H43  C24  C23  120.23  3.000
 VKM  C25  C24  C23  120.99  3.000
 VKM  H44  C25  C26  120.41  3.000
 VKM  H44  C25  C24  120.92  3.000
 VKM  C26  C25  C24  118.67  3.000
 VKM  F29  C26  C27  119.14  3.000
 VKM  C27  C26  C25  122.00  3.000
 VKM  F29  C26  C25  118.86  3.000
 VKM  H46  C28  C27  119.07  3.000
 VKM  H46  C28  C23  119.69  3.000
 VKM  C27  C28  C23  121.24  3.000
 VKM  N2   C6   C5   105.74  3.000
 VKM  C5   C6   C7   122.31  3.000
 VKM  N2   C6   C7   131.94  3.000
 VKM  O8   C7   N9   120.93  3.000
 VKM  N9   C7   C6   110.14  3.000
 VKM  O8   C7   C6   128.93  3.000
 VKM  C12  N9   C10  120.02  3.000
 VKM  C10  N9   C7   123.80  3.000
 VKM  C12  N9   C7   116.18  3.000
 VKM  C22  O21  C20  110.31  3.000
 VKM  H34  C10  N11  119.48  3.000
 VKM  H34  C10  N9   114.97  3.000
 VKM  N11  C10  N9   125.55  3.000
 VKM  H35  C12  H36  107.28  3.000
 VKM  H35  C12  N9   110.75  3.000
 VKM  H36  C12  N9   108.71  3.000
 VKM  H35  C12  C13  110.37  3.000
 VKM  H36  C12  C13  109.24  3.000
 VKM  N9   C12  C13  110.41  3.000
 VKM  H39  C19  H38  107.79  3.000
 VKM  H39  C19  C20  110.24  3.000
 VKM  H38  C19  C20  112.65  3.000
 VKM  H39  C19  C18  109.48  3.000
 VKM  H38  C19  C18  114.47  3.000
 VKM  C20  C19  C18  102.12  3.000
 VKM  H42  C22  H41  107.78  3.000
 VKM  H42  C22  O21  110.44  3.000
 VKM  H41  C22  O21  109.02  3.000
 VKM  H42  C22  C18  111.76  3.000
 VKM  H41  C22  C18  110.67  3.000
 VKM  O21  C22  C18  107.16  3.000
 VKM  H45  C27  C28  120.93  3.000
 VKM  H45  C27  C26  120.66  3.000
 VKM  C28  C27  C26  118.41  3.000
 VKM  H33  C3   N4   125.14  3.000
 VKM  H33  C3   N2   121.09  3.000
 VKM  N4   C3   N2   113.77  3.000
 VKM  N4   C5   N11  125.87  3.000
 VKM  N11  C5   C6   123.66  3.000
 VKM  N4   C5   C6   110.47  3.000
 VKM  C5   N11  C10  114.52  3.000
 VKM  C15  N14  C13  102.50  3.000
 VKM  O17  N16  C15  104.06  3.000
 VKM  C3   N2   C6   105.69  3.000
 VKM  C6   N2   C1   127.77  3.000
 VKM  C3   N2   C1   126.54  3.000
 VKM  C5   N4   C3   104.32  3.000
 VKM  N16  O17  C13  106.93  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
 VKM  CONST_01  C15  N16  O17  C13     0.00   0.0  0
 VKM  CONST_02  N16  C15  N14  C13     0.00   0.0  0
 VKM  CONST_03  O17  C13  N14  C15     0.00   0.0  0
 VKM  CONST_04  C26  C25  C24  C23     0.00   0.0  0
 VKM  CONST_05  C26  C27  C28  C23     0.00   0.0  0
 VKM  CONST_06  C27  C26  C25  C24     0.00   0.0  0
 VKM  CONST_07  C27  C28  C23  C24     0.00   0.0  0
 VKM  CONST_08  C28  C27  C26  C25     0.00   0.0  0
 VKM  CONST_09  C28  C23  C24  C25     0.00   0.0  0
 VKM  CONST_10  N4   C3   N2   C6      0.00   0.0  0
 VKM  CONST_11  C3   N4   C5   C6      0.00   0.0  0
 VKM  CONST_12  C5   C6   N2   C3      0.00   0.0  0
 VKM  CONST_13  N2   C3   N4   C5      0.00   0.0  0
 VKM  CONST_14  N16  O17  C13  N14     0.00   0.0  0
 VKM  CONST_15  O17  N16  C15  N14     0.00   0.0  0
 VKM  CONST_16  N4   C5   C6   N2      0.00   0.0  0
 VKM  CONST_17  C18  C15  N14  C13   180.00   0.0  0
 VKM  CONST_18  O17  N16  C15  C18   180.00   0.0  0
 VKM  CONST_19  C25  C24  C23  C20   180.00   0.0  0
 VKM  CONST_20  C27  C28  C23  C20   180.00   0.0  0
 VKM  CONST_21  C10  N9   C7   C6      0.00   0.0  0
 VKM  CONST_22  N11  C10  N9   C7      0.00   0.0  0
 VKM  CONST_23  C5   N11  C10  N9      0.00   0.0  0
 VKM  CONST_24  N4   C3   N2   C1    180.00   0.0  0
 VKM  CONST_25  C7   C6   N2   C1      0.00   0.0  0
 VKM  CONST_26  C5   C6   N2   C1    180.00   0.0  0
 VKM  CONST_27  C12  C13  N14  C15   180.00   0.0  0
 VKM  CONST_28  F29  C26  C25  C24   180.00   0.0  0
 VKM  CONST_29  F29  C26  C27  C28   180.00   0.0  0
 VKM  CONST_30  N16  O17  C13  C12   180.00   0.0  0
 VKM  CONST_31  C12  N9   C7   C6    180.00   0.0  0
 VKM  CONST_32  O8   C7   N9   C10   180.00   0.0  0
 VKM  CONST_33  N11  C10  N9   C12   180.00   0.0  0
 VKM  CONST_34  H43  C24  C23  C20     0.00   0.0  0
 VKM  CONST_35  H46  C28  C23  C20     0.00   0.0  0
 VKM  CONST_36  H44  C25  C24  C23   180.00   0.0  0
 VKM  CONST_37  H45  C27  C28  C23   180.00   0.0  0
 VKM  CONST_38  H33  C3   N2   C6    180.00   0.0  0
 VKM  CONST_39  H34  C10  N9   C7    180.00   0.0  0
 VKM  CONST_40  O8   C7   N9   C12     0.00   0.0  0
 VKM  Var_01    C7   N9   C12  C13    66.30  30.0  2
 VKM  Var_02    O17  C13  C12  N9   -144.61  30.0  2
 VKM  Var_03    H41  C22  O21  C20   126.81  30.0  1
 VKM  Var_04    H31  C1   N2   C6     59.13  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
 VKM  chir_01  C18  C22  C15  C19  negativ
 VKM  chir_02  C20  O21  C19  C23  positiv

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
 VKM  plan-1  C13  0.020
 VKM  plan-1  C15  0.020
 VKM  plan-1  C18  0.020
 VKM  plan-1  C12  0.020
 VKM  plan-1  N14  0.020
 VKM  plan-1  N16  0.020
 VKM  plan-1  O17  0.020
 VKM  plan-2  C20  0.020
 VKM  plan-2  C23  0.020
 VKM  plan-2  C24  0.020
 VKM  plan-2  C25  0.020
 VKM  plan-2  C26  0.020
 VKM  plan-2  C28  0.020
 VKM  plan-2  C27  0.020
 VKM  plan-2  F29  0.020
 VKM  plan-2  H43  0.020
 VKM  plan-2  H44  0.020
 VKM  plan-2  H46  0.020
 VKM  plan-2  H45  0.020
 VKM  plan-3  C1   0.020
 VKM  plan-3  C6   0.020
 VKM  plan-3  C7   0.020
 VKM  plan-3  N9   0.020
 VKM  plan-3  C10  0.020
 VKM  plan-3  C12  0.020
 VKM  plan-3  C3   0.020
 VKM  plan-3  C5   0.020
 VKM  plan-3  N11  0.020
 VKM  plan-3  N2   0.020
 VKM  plan-3  N4   0.020
 VKM  plan-3  H34  0.020
 VKM  plan-3  H33  0.020
 VKM  plan-3  O8   0.020

