# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 09:52:05 2022
#   Inital geometry file: a 149 line input string
#   Ligand name: 1,5-dimethyl-6-(2-oxidanyl-6-oxidanylidene-cyclohexen-1-yl)carbonyl-3-(3-trimethylsilylprop-2-ynyl)quinazoline-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)N(CC#C[Si](C)(C)C)C(=O)c2c(C)c(ccc12)C(=O)C3=C(O)CCCC3=O
#
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
 NJX  NJX  1,5-dimethyl-6-(2-oxidanyl-6-oxidanylidene-cyclohexen-1-yl)carbonyl-3-(3-trimethylsilylprop-2-ynyl)quinazoline-2,4-dione  ligand  57  31  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NJX
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
 NJX  C13  C   CH2   0  -0.468   4.5673  -6.6682  84.3719
 NJX  C15  C   C     0   0.377   2.6210  -5.0805  84.1555
 NJX  C21  C   CR6   0   0.598  -1.9763  -2.0904  82.8512
 NJX  C26  C   CSP   0   0.184  -4.8264  -2.5320  84.0733
 NJX  C1   C   CR6   0  -0.011   1.7647  -2.3917  83.0218
 NJX  C2   C   CR16  0  -0.247   2.0621  -1.2879  83.8107
 NJX  C3   C   CR16  0  -0.361   1.0671  -0.4904  84.3282
 NJX  C4   C   CR66  0   0.443  -0.2654  -0.7746  84.0298
 NJX  C5   C   CR66  0  -0.155  -0.5705  -1.8546  83.1844
 NJX  C6   C   CR6   0   0.101   0.4511  -2.6882  82.6801
 NJX  C7   C   CH3   0  -0.730   0.1792  -3.8791  81.8044
 NJX  C8   C   C     0   0.352   2.9256  -3.1654  82.4889
 NJX  C9   C   C     0  -0.347   3.3339  -4.4391  83.0425
 NJX  C11  C   C     0   0.462   4.4402  -5.0650  82.4689
 NJX  C12  C   CH2   0  -0.548   4.9574  -6.3814  82.9334
 NJX  C14  C   CH2   0  -0.567   3.0736  -6.4652  84.5529
 NJX  C19  C   CR6   0   0.740  -2.6000  -0.2416  84.3637
 NJX  C27  C   CSP   0  -0.324  -5.2380  -3.3921  84.8181
 NJX  C29  C   CH3   0  -0.969  -5.9842  -6.3117  84.9951
 NJX  C30  C   CH3   0  -0.969  -7.4805  -4.1842  86.6726
 NJX  C31  C   CH3   0  -0.969  -4.5341  -4.8866  87.3254
 NJX  N18  N   NR6   0  -0.621  -1.2720   0.0036  84.5780
 NJX  N20  N   NR6   0  -0.596  -2.8923  -1.2367  83.4479
 NJX  O10  O   O     0  -0.468   3.5536  -2.6396  81.5585
 NJX  O16  O   OH1   0  -0.558   5.0860  -4.5427  81.4760
 NJX  O17  O   O     0  -0.411   1.6853  -4.5509  84.7237
 NJX  O22  O   O     0  -0.429  -2.3799  -2.9606  82.1082
 NJX  O23  O   O     0  -0.470  -3.4858   0.3744  84.9189
 NJX  SI   SI  SI    0   0.901  -5.8219  -4.7148  85.9693
 NJX  H1   H   HCH2  0   0.264   4.8443  -7.6893  84.6319
 NJX  H2   H   HCH2  0   0.249   5.1196  -6.0072  85.0439
 NJX  H3   H   HCH3  0   0.290  -1.8172   1.5984  85.8019
 NJX  H4   H   HCH3  0   0.262  -0.3855   0.7244  86.3462
 NJX  H5   H   HCH3  0   0.263  -0.2893   1.8207  84.9525
 NJX  H6   H   HCR6  0   0.274   3.0922  -1.0556  84.0506
 NJX  H7   H   HCR6  0   0.296   1.3418   0.3400  84.9593
 NJX  H8   H   HCH3  0   0.257  -0.4861  -4.5911  82.2883
 NJX  H9   H   HCH3  0   0.260  -0.2867  -3.5896  80.8647
 NJX  H10  H   HCH3  0   0.241   1.0981  -4.4066  81.5589
 NJX  H13  H   HCH2  0   0.290   4.5354  -7.1463  82.2702
 NJX  H14  H   HCH2  0   0.290   6.0388  -6.4094  82.7905
 NJX  H15  H   HCH2  0   0.272   2.7598  -6.6526  85.5799
 NJX  H16  H   HCH2  0   0.270   2.5291  -7.1754  83.9184
 NJX  H17  H   HCH2  0   0.309  -4.8676  -0.5770  83.2997
 NJX  H18  H   HCH2  0   0.306  -4.4123  -1.8126  82.1474
 NJX  H19  H   HCH3  0   0.246  -6.3165  -7.1244  85.6438
 NJX  H20  H   HCH3  0   0.250  -6.7109  -6.2140  84.1874
 NJX  H21  H   HCH3  0   0.250  -5.0308  -6.6068  84.5549
 NJX  H22  H   HCH3  0   0.246  -7.8554  -4.9297  87.3764
 NJX  H23  H   HCH3  0   0.250  -7.4031  -3.2349  87.2043
 NJX  H24  H   HCH3  0   0.250  -8.2269  -4.0665  85.8857
 NJX  H25  H   HCH3  0   0.246  -4.8310  -5.6537  88.0432
 NJX  H26  H   HCH3  0   0.250  -3.5638  -5.1718  86.9165
 NJX  H27  H   HCH3  0   0.250  -4.4049  -3.9520  87.8727
 NJX  H28  H   HOH1  0   0.492   4.6320  -3.6618  81.2605
 NJX  C25  C   CH2   0  -0.499  -4.3047  -1.5007  83.1847
 NJX  C24  C   CH3   0  -0.562  -0.9165   1.0976  85.4713

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
 NJX  O16  C11  single    1.295  0.020  1.295
 NJX  O10  C8   double    1.240  0.020  1.240
 NJX  C7   C6   single    1.503  0.020  1.503
 NJX  C11  C12  single    1.489  0.020  1.489
 NJX  C11  C9   double    1.394  0.020  1.394
 NJX  C8   C9   single    1.448  0.020  1.448
 NJX  C8   C1   single    1.493  0.020  1.493
 NJX  O22  C21  double    1.213  0.020  1.213
 NJX  C12  C13  single    1.518  0.020  1.518
 NJX  C9   C15  single    1.469  0.020  1.469
 NJX  C6   C1   aromatic  1.389  0.020  1.389
 NJX  C6   C5   aromatic  1.412  0.020  1.412
 NJX  C1   C2   aromatic  1.389  0.020  1.389
 NJX  C21  C5   single    1.464  0.020  1.464
 NJX  C21  N20  single    1.387  0.020  1.387
 NJX  C5   C4   aromatic  1.405  0.020  1.405
 NJX  C25  N20  single    1.461  0.020  1.461
 NJX  C25  C26  single    1.458  0.020  1.458
 NJX  C15  O17  double    1.216  0.020  1.216
 NJX  C15  C14  single    1.510  0.020  1.510
 NJX  C13  C14  single    1.518  0.020  1.518
 NJX  N20  C19  single    1.384  0.020  1.384
 NJX  C2   C3   aromatic  1.376  0.020  1.376
 NJX  C4   C3   aromatic  1.395  0.020  1.395
 NJX  C4   N18  single    1.385  0.020  1.385
 NJX  C26  C27  triple    1.210  0.020  1.210
 NJX  C19  N18  single    1.367  0.020  1.367
 NJX  C19  O23  double    1.213  0.020  1.213
 NJX  N18  C24  single    1.456  0.020  1.456
 NJX  C27  SI   single    1.848  0.020  1.848
 NJX  C29  SI   single    1.878  0.020  1.878
 NJX  C30  SI   single    1.878  0.020  1.878
 NJX  SI   C31  single    1.878  0.020  1.878
 NJX  C13  H1   single    0.970  0.020  1.090
 NJX  C13  H2   single    0.970  0.020  1.090
 NJX  C24  H3   single    0.970  0.020  1.090
 NJX  C24  H4   single    0.970  0.020  1.090
 NJX  C24  H5   single    0.970  0.020  1.090
 NJX  C2   H6   single    0.930  0.020  1.080
 NJX  C3   H7   single    0.930  0.020  1.080
 NJX  C7   H8   single    0.970  0.020  1.090
 NJX  C7   H9   single    0.970  0.020  1.090
 NJX  C7   H10  single    0.970  0.020  1.090
 NJX  C12  H13  single    0.970  0.020  1.090
 NJX  C12  H14  single    0.970  0.020  1.090
 NJX  C14  H15  single    0.970  0.020  1.090
 NJX  C14  H16  single    0.970  0.020  1.090
 NJX  C25  H17  single    0.970  0.020  1.090
 NJX  C25  H18  single    0.970  0.020  1.090
 NJX  C29  H19  single    0.970  0.020  1.090
 NJX  C29  H20  single    0.970  0.020  1.090
 NJX  C29  H21  single    0.970  0.020  1.090
 NJX  C30  H22  single    0.970  0.020  1.090
 NJX  C30  H23  single    0.970  0.020  1.090
 NJX  C30  H24  single    0.970  0.020  1.090
 NJX  C31  H25  single    0.970  0.020  1.090
 NJX  C31  H26  single    0.970  0.020  1.090
 NJX  C31  H27  single    0.970  0.020  1.090
 NJX  O16  H28  single    0.850  0.020  0.980

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
 NJX  H2   C13  H1   106.96  3.000
 NJX  H2   C13  C14  110.07  3.000
 NJX  H1   C13  C14  110.30  3.000
 NJX  H2   C13  C12  109.80  3.000
 NJX  H1   C13  C12  109.75  3.000
 NJX  C14  C13  C12  109.91  3.000
 NJX  O17  C15  C14  120.46  3.000
 NJX  C14  C15  C9   117.02  3.000
 NJX  O17  C15  C9   122.49  3.000
 NJX  O22  C21  N20  119.03  3.000
 NJX  N20  C21  C5   115.92  3.000
 NJX  O22  C21  C5   125.05  3.000
 NJX  C27  C26  C25  180.00  3.000
 NJX  C8   C1   C6   122.45  3.000
 NJX  C6   C1   C2   120.78  3.000
 NJX  C8   C1   C2   116.61  3.000
 NJX  H6   C2   C3   118.69  3.000
 NJX  H6   C2   C1   120.00  3.000
 NJX  C3   C2   C1   121.29  3.000
 NJX  H7   C3   C4   121.69  3.000
 NJX  H7   C3   C2   118.82  3.000
 NJX  C4   C3   C2   119.48  3.000
 NJX  N18  C4   C5   120.80  3.000
 NJX  N18  C4   C3   119.67  3.000
 NJX  C5   C4   C3   119.53  3.000
 NJX  C6   C5   C4   120.77  3.000
 NJX  C4   C5   C21  117.99  3.000
 NJX  C6   C5   C21  121.24  3.000
 NJX  C7   C6   C5   123.03  3.000
 NJX  C5   C6   C1   118.06  3.000
 NJX  C7   C6   C1   118.92  3.000
 NJX  H10  C7   H9   107.21  3.000
 NJX  H10  C7   H8   107.43  3.000
 NJX  H9   C7   H8   107.24  3.000
 NJX  H10  C7   C6   111.28  3.000
 NJX  H9   C7   C6   111.71  3.000
 NJX  H8   C7   C6   111.72  3.000
 NJX  O10  C8   C9   121.15  3.000
 NJX  C9   C8   C1   122.60  3.000
 NJX  O10  C8   C1   116.22  3.000
 NJX  C11  C9   C8   117.48  3.000
 NJX  C8   C9   C15  122.48  3.000
 NJX  C11  C9   C15  120.04  3.000
 NJX  O16  C11  C12  115.01  3.000
 NJX  C12  C11  C9   122.97  3.000
 NJX  O16  C11  C9   122.02  3.000
 NJX  H14  C12  H13  106.52  3.000
 NJX  H14  C12  C11  109.03  3.000
 NJX  H13  C12  C11  107.12  3.000
 NJX  H14  C12  C13  111.97  3.000
 NJX  H13  C12  C13  110.02  3.000
 NJX  C11  C12  C13  111.93  3.000
 NJX  H16  C14  H15  106.91  3.000
 NJX  H16  C14  C15  107.02  3.000
 NJX  H15  C14  C15  108.62  3.000
 NJX  H16  C14  C13  109.44  3.000
 NJX  H15  C14  C13  111.87  3.000
 NJX  C15  C14  C13  112.71  3.000
 NJX  O23  C19  N20  120.91  3.000
 NJX  O23  C19  N18  123.11  3.000
 NJX  N20  C19  N18  115.97  3.000
 NJX  SI   C27  C26  180.00  3.000
 NJX  H21  C29  H20  107.92  3.000
 NJX  H21  C29  H19  107.73  3.000
 NJX  H20  C29  H19  107.69  3.000
 NJX  H21  C29  SI   111.34  3.000
 NJX  H20  C29  SI   111.44  3.000
 NJX  H19  C29  SI   110.56  3.000
 NJX  H24  C30  H23  107.83  3.000
 NJX  H24  C30  H22  107.68  3.000
 NJX  H23  C30  H22  107.72  3.000
 NJX  H24  C30  SI   111.39  3.000
 NJX  H23  C30  SI   111.45  3.000
 NJX  H22  C30  SI   110.60  3.000
 NJX  H27  C31  H26  107.86  3.000
 NJX  H27  C31  H25  107.72  3.000
 NJX  H26  C31  H25  107.74  3.000
 NJX  H27  C31  SI   111.42  3.000
 NJX  H26  C31  SI   111.29  3.000
 NJX  H25  C31  SI   110.65  3.000
 NJX  C19  N18  C4   122.88  3.000
 NJX  C19  N18  C24  117.90  3.000
 NJX  C4   N18  C24  119.16  3.000
 NJX  C25  N20  C19  116.97  3.000
 NJX  C19  N20  C21  126.01  3.000
 NJX  C25  N20  C21  116.73  3.000
 NJX  H28  O16  C11  106.86  3.000
 NJX  C31  SI   C30  111.16  3.000
 NJX  C31  SI   C29  110.87  3.000
 NJX  C30  SI   C29  110.99  3.000
 NJX  C31  SI   C27  107.38  3.000
 NJX  C30  SI   C27  108.06  3.000
 NJX  C29  SI   C27  108.23  3.000
 NJX  H18  C25  H17  107.03  3.000
 NJX  H18  C25  N20  108.61  3.000
 NJX  H17  C25  N20  109.13  3.000
 NJX  H18  C25  C26  110.04  3.000
 NJX  H17  C25  C26  110.56  3.000
 NJX  N20  C25  C26  111.35  3.000
 NJX  H5   C24  H4   109.23  3.000
 NJX  H5   C24  H3   108.52  3.000
 NJX  H4   C24  H3   108.59  3.000
 NJX  H5   C24  N18  110.32  3.000
 NJX  H4   C24  N18  110.75  3.000
 NJX  H3   C24  N18  109.38  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
 NJX  CONST_01  C4   C5   C6   C1      0.00   0.0  0
 NJX  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 NJX  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 NJX  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 NJX  CONST_05  C6   C1   C2   C3      0.00   0.0  0
 NJX  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 NJX  CONST_07  N18  C19  N20  C21     0.00   0.0  0
 NJX  CONST_08  N20  C19  N18  C4      0.00   0.0  0
 NJX  CONST_09  C19  N20  C21  C5      0.00   0.0  0
 NJX  CONST_10  C7   C6   C5   C21     0.00   0.0  0
 NJX  CONST_11  C7   C6   C1   C2    180.00   0.0  0
 NJX  CONST_12  C8   C1   C2   C3    180.00   0.0  0
 NJX  CONST_13  C7   C6   C5   C4    180.00   0.0  0
 NJX  CONST_14  C8   C1   C6   C5    180.00   0.0  0
 NJX  CONST_15  O23  C19  N20  C21   180.00   0.0  0
 NJX  CONST_16  N20  C19  N18  C24   180.00   0.0  0
 NJX  CONST_17  O23  C19  N18  C4    180.00   0.0  0
 NJX  CONST_18  C25  N20  C21  C5    180.00   0.0  0
 NJX  CONST_19  O22  C21  N20  C19   180.00   0.0  0
 NJX  CONST_20  N18  C19  N20  C25   180.00   0.0  0
 NJX  CONST_21  H7   C3   C2   C1    180.00   0.0  0
 NJX  CONST_22  H6   C2   C3   C4    180.00   0.0  0
 NJX  CONST_23  O23  C19  N18  C24     0.00   0.0  0
 NJX  CONST_24  O22  C21  N20  C25     0.00   0.0  0
 NJX  CONST_25  O23  C19  N20  C25     0.00   0.0  0
 NJX  Var_01    C9   C11  C12  C13   -23.78  30.0  1
 NJX  Var_02    C9   C15  C14  C13    33.57  30.0  1
 NJX  Var_03    C12  C11  C9   C15    -0.13  30.0  1
 NJX  Var_04    C12  C13  C14  C15   -56.63  30.0  1
 NJX  Var_05    C14  C13  C12  C11    50.90  30.0  1
 NJX  Var_06    C14  C15  C9   C11    -4.75  30.0  1
 NJX  Var_07    C1   C8   C9   C15     1.19  30.0  2
 NJX  Var_08    C9   C8   C1   C2    103.85  30.0  2
 NJX  Var_09    C26  C25  N20  C21    83.05  30.0  2
 NJX  Var_10    H8   C7   C6   C1    121.88  30.0  2
 NJX  Var_11    H3   C24  N18  C4    179.80  30.0  3
 NJX  Var_12    N20  C25  C26  C27    -8.47  30.0  2
 NJX  Var_13    C29  SI   C27  C26   -94.25  30.0  3
 NJX  Var_14    H19  C29  SI   C27   179.31  30.0  3
 NJX  Var_15    H22  C30  SI   C27  -178.86  30.0  3
 NJX  Var_16    H25  C31  SI   C27   179.60  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
 NJX  plan-1  C21  0.020
 NJX  plan-1  C1   0.020
 NJX  plan-1  C2   0.020
 NJX  plan-1  C3   0.020
 NJX  plan-1  C4   0.020
 NJX  plan-1  C5   0.020
 NJX  plan-1  C6   0.020
 NJX  plan-1  C7   0.020
 NJX  plan-1  C8   0.020
 NJX  plan-1  C19  0.020
 NJX  plan-1  N18  0.020
 NJX  plan-1  N20  0.020
 NJX  plan-1  O22  0.020
 NJX  plan-1  O23  0.020
 NJX  plan-1  H6   0.020
 NJX  plan-1  H7   0.020
 NJX  plan-1  C25  0.020
 NJX  plan-1  C24  0.020
 NJX  plan-2  C1   0.020
 NJX  plan-2  C8   0.020
 NJX  plan-2  C9   0.020
 NJX  plan-2  O10  0.020
 NJX  plan-3  C15  0.020
 NJX  plan-3  C9   0.020
 NJX  plan-3  C14  0.020
 NJX  plan-3  O17  0.020

