# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 17 15:55:59 2020
#   Inital geometry file: a 144 line input string
#   Ligand name: (2~{R})-1-[6-methyl-5-(oxan-4-yl)-7-oxidanylidene-[1,3]thiazolo[5,4-d]pyrimidin-2-yl]-~{N}-(phenylmethyl)pyrrolidine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)c2nc(sc2N=C1C3CCOCC3)N4CCC[C@@H]4C(=O)NCc5ccccc5
#
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
 MVQ  MVQ  (2~{R})-1-[6-methyl-5-(oxan-4-yl)-7-oxidanylidene-[1,3]thiazolo[5,4-d]pyrimidin-2-yl]-~{N}-(phenylmethyl)pyrrolidine-2-carboxamide  ligand  59  32  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MVQ
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
 MVQ  C2   C  C     0   0.566  -2.9887   1.1046   0.1599
 MVQ  C4   C  CH2   0  -0.323  -4.2971  -0.7574   1.0759
 MVQ  C5   C  CR6   0   0.065  -5.3884  -1.6497   0.5513
 MVQ  C6   C  CR16  0  -0.303  -5.2820  -3.0325   0.6457
 MVQ  C7   C  CR16  0  -0.240  -6.2907  -3.8557   0.1586
 MVQ  C8   C  CR16  0  -0.265  -7.4153  -3.2993  -0.4333
 MVQ  C11  C  CH1   0  -0.258  -2.4557   1.7223  -1.1351
 MVQ  C12  C  CH2   0  -0.459  -3.4289   2.7752  -1.6862
 MVQ  C16  C  CR5   0   0.334  -0.0797   1.9496  -0.5936
 MVQ  C18  C  CR56  0   0.165   2.0368   1.7672  -0.1049
 MVQ  C19  C  CR56  0  -0.058   1.7716   0.4268  -0.1686
 MVQ  C21  C  CR6   0   0.556   3.8722  -0.2105   0.2717
 MVQ  N22  N  NR6   0  -0.561   4.2596   1.0991   0.3766
 MVQ  C23  C  CH3   0  -0.564   5.6477   1.4286   0.6986
 MVQ  C24  C  CR6   0   0.522   3.3765   2.1793   0.2057
 MVQ  O25  O  O     0  -0.472   3.7429   3.3373   0.3163
 MVQ  C27  C  CH2   0  -0.427   4.3527  -2.5851   0.9883
 MVQ  O29  O  O2    0  -0.482   5.9184  -3.9056  -0.3217
 MVQ  C30  C  CH2   0  -0.179   6.4819  -2.7547  -0.9080
 MVQ  C31  C  CH2   0  -0.445   5.4814  -1.6134  -1.0072
 MVQ  O1   O  O     0  -0.478  -2.8397   1.6540   1.2391
 MVQ  N3   N  NH1   0  -0.631  -3.6591  -0.0414  -0.0114
 MVQ  C9   C  CR16  0  -0.241  -7.5281  -1.9170  -0.5349
 MVQ  C10  C  CR16  0  -0.282  -6.5213  -1.0986  -0.0457
 MVQ  C13  C  CH2   0  -0.485  -2.9881   4.0671  -1.0037
 MVQ  C14  C  CH2   0  -0.258  -1.4719   3.9345  -0.9037
 MVQ  N15  N  NT    0  -0.483  -1.2624   2.4925  -0.8898
 MVQ  N17  N  N     0  -0.468   1.0013   2.6237  -0.3414
 MVQ  N20  N  N     0  -0.446   2.6519  -0.5654   0.0127
 MVQ  C26  C  CH1   0  -0.410   4.9076  -1.2964   0.3836
 MVQ  C28  C  CH2   0  -0.186   5.4347  -3.6532   0.9799
 MVQ  S32  S  S2    0   0.176   0.0903   0.1914  -0.5459
 MVQ  H1   H  HCH2  0   0.264  -4.7119  -0.0278   1.7730
 MVQ  H2   H  HCH2  0   0.259  -3.5628  -1.3492   1.6289
 MVQ  H3   H  HCR6  0   0.256  -4.4035  -3.4715   1.1033
 MVQ  H4   H  HCR6  0   0.257  -6.1944  -4.9306   0.2409
 MVQ  H5   H  HCR6  0   0.258  -8.2028  -3.9372  -0.8133
 MVQ  H6   H  HCH1  0   0.293  -2.2728   0.9412  -1.8822
 MVQ  H7   H  HCH2  0   0.266  -3.2958   2.8445  -2.7668
 MVQ  H8   H  HCH2  0   0.267  -4.4708   2.5184  -1.4981
 MVQ  H9   H  HCH3  0   0.266   6.3261   0.9970  -0.0324
 MVQ  H10  H  HCH3  0   0.289   5.7630   2.5048   0.6793
 MVQ  H11  H  HCH3  0   0.272   5.9070   1.0681   1.6916
 MVQ  H12  H  HCH2  0   0.247   4.0212  -2.4178   2.0154
 MVQ  H13  H  HCH2  0   0.239   3.4885  -2.9289   0.4179
 MVQ  H14  H  HCH2  0   0.201   7.3580  -2.4210  -0.3322
 MVQ  H15  H  HCH2  0   0.242   6.8320  -3.0387  -1.9015
 MVQ  H16  H  HCH2  0   0.251   5.9780  -0.7440  -1.4447
 MVQ  H17  H  HCH2  0   0.244   4.6629  -1.8879  -1.6784
 MVQ  H18  H  HNH1  0   0.407  -3.6502  -0.4812  -0.9185
 MVQ  H19  H  HCR6  0   0.258  -8.4046  -1.4773  -0.9927
 MVQ  H20  H  HCR6  0   0.254  -6.6188  -0.0219  -0.1244
 MVQ  H21  H  HCH2  0   0.261  -3.2811   4.9525  -1.5656
 MVQ  H22  H  HCH2  0   0.250  -3.4266   4.1462  -0.0091
 MVQ  H23  H  HCH2  0   0.244  -0.9623   4.3793  -1.7624
 MVQ  H24  H  HCH2  0   0.254  -1.0682   4.3939  -0.0009
 MVQ  H25  H  HCH1  0   0.278   5.7292  -0.9650   1.0239
 MVQ  H26  H  HCH2  0   0.199   6.2605  -3.3483   1.6401
 MVQ  H27  H  HCH2  0   0.241   5.0416  -4.5963   1.3623

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
 MVQ  O29  C30  single    1.409  0.020  1.409
 MVQ  O29  C28  single    1.411  0.020  1.411
 MVQ  C30  C31  single    1.521  0.020  1.521
 MVQ  C28  C27  single    1.520  0.020  1.520
 MVQ  C31  C26  single    1.538  0.020  1.538
 MVQ  C27  C26  single    1.528  0.020  1.528
 MVQ  C26  C21  single    1.505  0.020  1.505
 MVQ  N20  C21  double    1.297  0.020  1.297
 MVQ  N20  C19  single    1.339  0.020  1.339
 MVQ  C21  N22  single    1.370  0.020  1.370
 MVQ  S32  C19  aromatic  1.739  0.020  1.739
 MVQ  S32  C16  aromatic  1.767  0.020  1.767
 MVQ  C19  C18  aromatic  1.368  0.020  1.368
 MVQ  N22  C23  single    1.462  0.020  1.462
 MVQ  N22  C24  single    1.406  0.020  1.406
 MVQ  C14  N15  single    1.457  0.020  1.457
 MVQ  C14  C13  single    1.525  0.020  1.525
 MVQ  C18  C24  single    1.436  0.020  1.436
 MVQ  C18  N17  aromatic  1.364  0.020  1.364
 MVQ  C16  N15  single    1.335  0.020  1.335
 MVQ  C16  N17  aromatic  1.299  0.020  1.299
 MVQ  C24  O25  double    1.220  0.020  1.220
 MVQ  N15  C11  single    1.441  0.020  1.441
 MVQ  C13  C12  single    1.526  0.020  1.526
 MVQ  N3   C4   single    1.450  0.020  1.450
 MVQ  N3   C2   single    1.339  0.020  1.339
 MVQ  C11  C12  single    1.536  0.020  1.536
 MVQ  C11  C2   single    1.531  0.020  1.531
 MVQ  C4   C5   single    1.504  0.020  1.504
 MVQ  C10  C5   aromatic  1.394  0.020  1.394
 MVQ  C10  C9   aromatic  1.387  0.020  1.387
 MVQ  C2   O1   double    1.220  0.020  1.220
 MVQ  C5   C6   aromatic  1.390  0.020  1.390
 MVQ  C9   C8   aromatic  1.391  0.020  1.391
 MVQ  C6   C7   aromatic  1.390  0.020  1.390
 MVQ  C8   C7   aromatic  1.387  0.020  1.387
 MVQ  C4   H1   single    0.970  0.020  1.090
 MVQ  C4   H2   single    0.970  0.020  1.090
 MVQ  C6   H3   single    0.930  0.020  1.080
 MVQ  C7   H4   single    0.930  0.020  1.080
 MVQ  C8   H5   single    0.930  0.020  1.080
 MVQ  C11  H6   single    0.970  0.020  1.090
 MVQ  C12  H7   single    0.970  0.020  1.090
 MVQ  C12  H8   single    0.970  0.020  1.090
 MVQ  C23  H9   single    0.970  0.020  1.090
 MVQ  C23  H10  single    0.970  0.020  1.090
 MVQ  C23  H11  single    0.970  0.020  1.090
 MVQ  C27  H12  single    0.970  0.020  1.090
 MVQ  C27  H13  single    0.970  0.020  1.090
 MVQ  C30  H14  single    0.970  0.020  1.090
 MVQ  C30  H15  single    0.970  0.020  1.090
 MVQ  C31  H16  single    0.970  0.020  1.090
 MVQ  C31  H17  single    0.970  0.020  1.090
 MVQ  N3   H18  single    0.860  0.020  1.020
 MVQ  C9   H19  single    0.930  0.020  1.080
 MVQ  C10  H20  single    0.930  0.020  1.080
 MVQ  C13  H21  single    0.970  0.020  1.090
 MVQ  C13  H22  single    0.970  0.020  1.090
 MVQ  C14  H23  single    0.970  0.020  1.090
 MVQ  C14  H24  single    0.970  0.020  1.090
 MVQ  C26  H25  single    0.970  0.020  1.090
 MVQ  C28  H26  single    0.970  0.020  1.090
 MVQ  C28  H27  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
 MVQ  N3   C2   O1   124.04  3.000
 MVQ  O1   C2   C11  121.61  3.000
 MVQ  N3   C2   C11  114.31  3.000
 MVQ  H2   C4   H1   107.11  3.000
 MVQ  H2   C4   N3   110.55  3.000
 MVQ  H1   C4   N3   108.44  3.000
 MVQ  H2   C4   C5   110.03  3.000
 MVQ  H1   C4   C5   110.10  3.000
 MVQ  N3   C4   C5   110.53  3.000
 MVQ  C10  C5   C6   118.98  3.000
 MVQ  C6   C5   C4   120.72  3.000
 MVQ  C10  C5   C4   120.29  3.000
 MVQ  H3   C6   C7   119.77  3.000
 MVQ  H3   C6   C5   119.59  3.000
 MVQ  C7   C6   C5   120.64  3.000
 MVQ  H4   C7   C8   120.19  3.000
 MVQ  H4   C7   C6   119.79  3.000
 MVQ  C8   C7   C6   120.02  3.000
 MVQ  H5   C8   C9   120.07  3.000
 MVQ  H5   C8   C7   120.22  3.000
 MVQ  C9   C8   C7   119.71  3.000
 MVQ  H6   C11  N15  111.01  3.000
 MVQ  H6   C11  C12  110.46  3.000
 MVQ  N15  C11  C12  102.67  3.000
 MVQ  H6   C11  C2   110.32  3.000
 MVQ  C12  C11  C2   111.07  3.000
 MVQ  N15  C11  C2   111.10  3.000
 MVQ  H8   C12  H7   107.62  3.000
 MVQ  H8   C12  C13  113.49  3.000
 MVQ  H7   C12  C13  110.73  3.000
 MVQ  H8   C12  C11  112.48  3.000
 MVQ  H7   C12  C11  108.76  3.000
 MVQ  C13  C12  C11  103.69  3.000
 MVQ  S32  C16  N17  115.54  3.000
 MVQ  N17  C16  N15  124.72  3.000
 MVQ  S32  C16  N15  119.73  3.000
 MVQ  N17  C18  C24  124.44  3.000
 MVQ  N17  C18  C19  117.38  3.000
 MVQ  C24  C18  C19  118.18  3.000
 MVQ  S32  C19  N20  124.39  3.000
 MVQ  S32  C19  C18  109.28  3.000
 MVQ  N20  C19  C18  126.33  3.000
 MVQ  C26  C21  N20  117.71  3.000
 MVQ  N20  C21  N22  122.89  3.000
 MVQ  C26  C21  N22  119.32  3.000
 MVQ  C24  N22  C23  116.74  3.000
 MVQ  C24  N22  C21  123.21  3.000
 MVQ  C23  N22  C21  120.05  3.000
 MVQ  H11  C23  H10  108.68  3.000
 MVQ  H11  C23  H9   109.49  3.000
 MVQ  H10  C23  H9   108.44  3.000
 MVQ  H11  C23  N22  110.65  3.000
 MVQ  H10  C23  N22  108.73  3.000
 MVQ  H9   C23  N22  110.79  3.000
 MVQ  O25  C24  N22  122.00  3.000
 MVQ  O25  C24  C18  124.92  3.000
 MVQ  N22  C24  C18  113.08  3.000
 MVQ  H13  C27  H12  107.43  3.000
 MVQ  H13  C27  C28  109.85  3.000
 MVQ  H12  C27  C28  109.19  3.000
 MVQ  H13  C27  C26  110.28  3.000
 MVQ  H12  C27  C26  110.68  3.000
 MVQ  C28  C27  C26  109.38  3.000
 MVQ  C28  O29  C30  112.01  3.000
 MVQ  H15  C30  H14  107.46  3.000
 MVQ  H15  C30  C31  110.30  3.000
 MVQ  H14  C30  C31  109.29  3.000
 MVQ  H15  C30  O29  107.14  3.000
 MVQ  H14  C30  O29  110.39  3.000
 MVQ  C31  C30  O29  112.15  3.000
 MVQ  H17  C31  H16  107.11  3.000
 MVQ  H17  C31  C26  109.12  3.000
 MVQ  H16  C31  C26  111.58  3.000
 MVQ  H17  C31  C30  110.12  3.000
 MVQ  H16  C31  C30  108.92  3.000
 MVQ  C26  C31  C30  109.95  3.000
 MVQ  H18  N3   C4   117.60  3.000
 MVQ  H18  N3   C2   118.95  3.000
 MVQ  C4   N3   C2   123.17  3.000
 MVQ  H19  C9   C10  119.83  3.000
 MVQ  H19  C9   C8   120.03  3.000
 MVQ  C10  C9   C8   120.13  3.000
 MVQ  H20  C10  C9   119.69  3.000
 MVQ  H20  C10  C5   119.79  3.000
 MVQ  C9   C10  C5   120.51  3.000
 MVQ  H22  C13  H21  107.67  3.000
 MVQ  H22  C13  C14  110.27  3.000
 MVQ  H21  C13  C14  111.84  3.000
 MVQ  H22  C13  C12  110.69  3.000
 MVQ  H21  C13  C12  112.32  3.000
 MVQ  C14  C13  C12  104.06  3.000
 MVQ  H24  C14  H23  107.84  3.000
 MVQ  H24  C14  N15  110.84  3.000
 MVQ  H23  C14  N15  110.07  3.000
 MVQ  H24  C14  C13  112.69  3.000
 MVQ  H23  C14  C13  112.12  3.000
 MVQ  N15  C14  C13  103.27  3.000
 MVQ  C14  N15  C16  122.14  3.000
 MVQ  C16  N15  C11  123.65  3.000
 MVQ  C14  N15  C11  114.09  3.000
 MVQ  C18  N17  C16  109.85  3.000
 MVQ  C21  N20  C19  116.29  3.000
 MVQ  H25  C26  C31  108.17  3.000
 MVQ  H25  C26  C27  107.27  3.000
 MVQ  C31  C26  C27  108.64  3.000
 MVQ  H25  C26  C21  110.00  3.000
 MVQ  C27  C26  C21  112.84  3.000
 MVQ  C31  C26  C21  109.77  3.000
 MVQ  H27  C28  H26  107.43  3.000
 MVQ  H27  C28  O29  106.99  3.000
 MVQ  H26  C28  O29  110.22  3.000
 MVQ  H27  C28  C27  110.43  3.000
 MVQ  H26  C28  C27  109.64  3.000
 MVQ  O29  C28  C27  112.00  3.000
 MVQ  C19  S32  C16   87.95  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
 MVQ  CONST_01  C8   C9   C10  C5     0.00   0.0  0
 MVQ  CONST_02  C8   C7   C6   C5     0.00   0.0  0
 MVQ  CONST_03  C9   C10  C5   C6     0.00   0.0  0
 MVQ  CONST_04  C9   C8   C7   C6     0.00   0.0  0
 MVQ  CONST_05  C10  C5   C6   C7     0.00   0.0  0
 MVQ  CONST_06  C10  C9   C8   C7     0.00   0.0  0
 MVQ  CONST_07  C18  C19  S32  C16    0.00   0.0  0
 MVQ  CONST_08  C19  C18  N17  C16    0.00   0.0  0
 MVQ  CONST_09  S32  C16  N17  C18    0.00   0.0  0
 MVQ  CONST_10  N17  C16  S32  C19    0.00   0.0  0
 MVQ  CONST_11  S32  C19  C18  N17    0.00   0.0  0
 MVQ  CONST_12  N15  C16  N17  C18  180.00   0.0  0
 MVQ  CONST_13  N15  C16  S32  C19  180.00   0.0  0
 MVQ  CONST_14  C21  N22  C24  C18    0.00   0.0  0
 MVQ  CONST_15  C26  C21  N20  C19  180.00   0.0  0
 MVQ  CONST_16  N22  C21  N20  C19    0.00   0.0  0
 MVQ  CONST_17  C26  C21  N22  C24  180.00   0.0  0
 MVQ  CONST_18  N20  C21  N22  C24    0.00   0.0  0
 MVQ  CONST_19  C9   C10  C5   C4   180.00   0.0  0
 MVQ  CONST_20  C7   C6   C5   C4   180.00   0.0  0
 MVQ  CONST_21  C23  N22  C24  C18  180.00   0.0  0
 MVQ  CONST_22  O25  C24  N22  C21  180.00   0.0  0
 MVQ  CONST_23  C26  C21  N22  C23    0.00   0.0  0
 MVQ  CONST_24  N20  C21  N22  C23  180.00   0.0  0
 MVQ  CONST_25  H19  C9   C10  C5   180.00   0.0  0
 MVQ  CONST_26  H4   C7   C6   C5   180.00   0.0  0
 MVQ  CONST_27  H20  C10  C5   C6   180.00   0.0  0
 MVQ  CONST_28  H5   C8   C7   C6   180.00   0.0  0
 MVQ  CONST_29  H3   C6   C7   C8   180.00   0.0  0
 MVQ  CONST_30  O25  C24  N22  C23    0.00   0.0  0
 MVQ  CONST_31  C11  C2   N3   C4   180.00   0.0  0
 MVQ  CONST_32  H18  N3   C2   C11    0.00   0.0  0
 MVQ  CONST_33  O1   C2   N3   C4     0.00   0.0  0
 MVQ  Var_01    C13  C14  N15  C11    7.26  30.0  1
 MVQ  Var_02    S32  C16  N15  C11    2.29  30.0  1
 MVQ  Var_03    C14  C13  C12  C11   35.17  30.0  1
 MVQ  Var_04    N15  C14  C13  C12  -26.14  30.0  1
 MVQ  Var_05    C26  C31  C30  O29   56.08  30.0  1
 MVQ  Var_06    C26  C27  C28  O29  -58.04  30.0  1
 MVQ  Var_07    H26  C28  O29  C30  -62.16  30.0  1
 MVQ  Var_08    N3   C4   C5   C6   114.15  30.0  3
 MVQ  Var_09    H9   C23  N22  C21   57.70  30.0  3
 MVQ  Var_10    C5   C4   N3   C2   157.45  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
 MVQ  chir_01  C11  N15  C12  C2   positiv
 MVQ  chir_02  C26  C31  C27  C21  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
 MVQ  plan-1  C4   0.020
 MVQ  plan-1  C5   0.020
 MVQ  plan-1  C6   0.020
 MVQ  plan-1  C7   0.020
 MVQ  plan-1  C8   0.020
 MVQ  plan-1  C9   0.020
 MVQ  plan-1  C10  0.020
 MVQ  plan-1  H3   0.020
 MVQ  plan-1  H4   0.020
 MVQ  plan-1  H5   0.020
 MVQ  plan-1  H19  0.020
 MVQ  plan-1  H20  0.020
 MVQ  plan-2  C16  0.020
 MVQ  plan-2  C18  0.020
 MVQ  plan-2  C19  0.020
 MVQ  plan-2  C21  0.020
 MVQ  plan-2  N22  0.020
 MVQ  plan-2  C23  0.020
 MVQ  plan-2  C24  0.020
 MVQ  plan-2  O25  0.020
 MVQ  plan-2  N15  0.020
 MVQ  plan-2  N17  0.020
 MVQ  plan-2  N20  0.020
 MVQ  plan-2  C26  0.020
 MVQ  plan-2  S32  0.020
 MVQ  plan-3  C2   0.020
 MVQ  plan-3  C4   0.020
 MVQ  plan-3  C11  0.020
 MVQ  plan-3  O1   0.020
 MVQ  plan-3  N3   0.020
 MVQ  plan-3  H18  0.020

