# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 18:30:12 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: 2,2-dimethyl-7-(2-oxidanylidene-3~{H}-imidazo[4,5-b]pyridin-1-yl)-1-(phenylmethyl)-3~{H}-quinazolin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(C)NC(=O)c2ccc(cc2N1Cc3ccccc3)N4C(=O)Nc5ncccc45
#
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
 5VS  5VS  2,2-dimethyl-7-(2-oxidanylidene-3~{H}-imidazo[4,5-b]pyridin-1-yl)-1-(phenylmethyl)-3~{H}-quinazolin-4-one  ligand  51  30  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5VS
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
 5VS  C5   C  C     0   0.529   3.4328   1.8672  -1.0566
 5VS  C7   C  CR6   0  -0.084   1.9812   1.5671  -0.9721
 5VS  C8   C  CR16  0  -0.304   1.0887   2.1952  -1.8342
 5VS  C10  C  CR6   0   0.346  -0.7171   0.9691  -0.8607
 5VS  C15  C  CR6   0   0.078   1.5878  -2.2750   0.2474
 5VS  C17  C  CR16  0  -0.240  -0.1601  -3.4235  -0.9590
 5VS  C20  C  CR16  0  -0.277   1.0399  -2.7336   1.4436
 5VS  C22  C  CR56  0   0.240  -2.8595   0.6165   0.3602
 5VS  C24  C  CR16  0  -0.336  -3.7147   0.7793   2.5438
 5VS  C2   C  CT    0   0.224   3.5397   0.8351   1.1859
 5VS  C3   C  CH3   0  -0.623   3.0013   1.9515   2.0868
 5VS  N4   N  NH1   0  -0.645   4.1518   1.4032  -0.0215
 5VS  O6   O  O     0  -0.483   3.9234   2.4673  -2.0048
 5VS  C9   C  CR16  0  -0.277  -0.2610   1.9043  -1.7847
 5VS  C11  C  CR16  0  -0.325   0.1598   0.3432   0.0120
 5VS  C12  C  CR6   0   0.308   1.5169   0.6367  -0.0383
 5VS  N13  N  NT    0  -0.501   2.4303  -0.0350   0.8078
 5VS  C14  C  CH2   0  -0.383   2.7815  -1.3622   0.2723
 5VS  C16  C  CR16  0  -0.276   0.9815  -2.6311  -0.9506
 5VS  C18  C  CR16  0  -0.261  -0.7059  -3.8667   0.2367
 5VS  C19  C  CR16  0  -0.246  -0.0998  -3.5227   1.4405
 5VS  N21  N  NR5   0  -0.710  -2.0891   0.6551  -0.7889
 5VS  C23  C  CR16  0  -0.200  -2.6332   0.9466   1.6752
 5VS  C25  C  CR16  0  -0.087  -4.9279   0.3130   2.0644
 5VS  N26  N  N     0  -0.419  -5.1529   0.0037   0.7813
 5VS  C27  C  CR56  0   0.456  -4.1297   0.1620  -0.0171
 5VS  N28  N  NR15  0  -0.730  -4.0851  -0.0673  -1.3692
 5VS  C30  C  CR5   0   0.664  -2.8420   0.2179  -1.8740
 5VS  O31  O  O     0  -0.470  -2.4636   0.1080  -3.0186
 5VS  H1   H  HCR6  0   0.268   1.4555   2.9220  -2.5464
 5VS  H2   H  HCR6  0   0.253  -0.6260  -3.6855  -1.9001
 5VS  H3   H  HCR6  0   0.248   1.5013  -2.4573   2.3848
 5VS  H4   H  HCR6  0   0.275  -3.6084   1.0134   3.5934
 5VS  H5   H  HCH3  0   0.257   5.1867  -0.6010   1.3148
 5VS  H6   H  HCH3  0   0.261   5.3319   0.8003   2.3685
 5VS  H7   H  HCH3  0   0.256   4.1897  -0.4743   2.7744
 5VS  H8   H  HCH3  0   0.238   3.8075   2.6394   2.3409
 5VS  H9   H  HCH3  0   0.240   2.2096   2.5312   1.6121
 5VS  H10  H  HCH3  0   0.239   2.6056   1.5290   3.0104
 5VS  H11  H  HNH1  0   0.398   5.1421   1.6030  -0.0176
 5VS  H12  H  HCR6  0   0.275  -0.9519   2.4090  -2.4447
 5VS  H13  H  HCR6  0   0.283  -0.2078  -0.3781   0.7288
 5VS  H14  H  HCH2  0   0.276   3.5373  -1.7996   0.9210
 5VS  H15  H  HCH2  0   0.243   3.2184  -1.2921  -0.7326
 5VS  H16  H  HCR6  0   0.249   1.3932  -2.2716  -1.8863
 5VS  H17  H  HCR6  0   0.254  -1.5981  -4.4793   0.2337
 5VS  H18  H  HCR6  0   0.255  -0.5190  -3.8681   2.3768
 5VS  H19  H  HCR6  0   0.289  -1.6796   1.3140   2.0291
 5VS  H20  H  HCR6  0   0.265  -5.7638   0.1820   2.7402
 5VS  H21  H  HNR5  0   0.426  -4.8504  -0.4005  -1.9358
 5VS  C1   C  CH3   0  -0.718   4.6254   0.0852   1.9473

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
 5VS  O6   C5   double    1.225  0.020  1.225
 5VS  C3   C2   single    1.532  0.020  1.532
 5VS  N4   C5   single    1.343  0.020  1.343
 5VS  N4   C2   single    1.468  0.020  1.468
 5VS  C5   C7   single    1.485  0.020  1.485
 5VS  C2   C1   single    1.523  0.020  1.523
 5VS  C2   N13  single    1.460  0.020  1.460
 5VS  C20  C19  aromatic  1.386  0.020  1.386
 5VS  C20  C15  aromatic  1.393  0.020  1.393
 5VS  C19  C18  aromatic  1.391  0.020  1.391
 5VS  C7   C8   aromatic  1.391  0.020  1.391
 5VS  C7   C12  aromatic  1.398  0.020  1.398
 5VS  N13  C14  single    1.474  0.020  1.474
 5VS  N13  C12  single    1.415  0.020  1.415
 5VS  C8   C9   aromatic  1.382  0.020  1.382
 5VS  C15  C14  single    1.503  0.020  1.503
 5VS  C15  C16  aromatic  1.389  0.020  1.389
 5VS  C18  C17  aromatic  1.387  0.020  1.387
 5VS  C12  C11  aromatic  1.389  0.020  1.389
 5VS  C16  C17  aromatic  1.390  0.020  1.390
 5VS  C9   C10  aromatic  1.392  0.020  1.392
 5VS  C11  C10  aromatic  1.386  0.020  1.386
 5VS  C10  N21  single    1.409  0.020  1.409
 5VS  C23  C22  aromatic  1.375  0.020  1.375
 5VS  C23  C24  aromatic  1.397  0.020  1.397
 5VS  N21  C22  single    1.384  0.020  1.384
 5VS  N21  C30  single    1.391  0.020  1.391
 5VS  C22  C27  aromatic  1.401  0.020  1.401
 5VS  C24  C25  aromatic  1.385  0.020  1.385
 5VS  O31  C30  double    1.211  0.020  1.211
 5VS  C30  N28  single    1.372  0.020  1.372
 5VS  C27  N28  single    1.372  0.020  1.372
 5VS  C27  N26  aromatic  1.307  0.020  1.307
 5VS  C25  N26  aromatic  1.339  0.020  1.339
 5VS  C8   H1   single    0.930  0.020  1.080
 5VS  C17  H2   single    0.930  0.020  1.080
 5VS  C20  H3   single    0.930  0.020  1.080
 5VS  C24  H4   single    0.930  0.020  1.080
 5VS  C1   H5   single    0.970  0.020  1.090
 5VS  C1   H6   single    0.970  0.020  1.090
 5VS  C1   H7   single    0.970  0.020  1.090
 5VS  C3   H8   single    0.970  0.020  1.090
 5VS  C3   H9   single    0.970  0.020  1.090
 5VS  C3   H10  single    0.970  0.020  1.090
 5VS  N4   H11  single    0.860  0.020  1.020
 5VS  C9   H12  single    0.930  0.020  1.080
 5VS  C11  H13  single    0.930  0.020  1.080
 5VS  C14  H14  single    0.970  0.020  1.090
 5VS  C14  H15  single    0.970  0.020  1.090
 5VS  C16  H16  single    0.930  0.020  1.080
 5VS  C18  H17  single    0.930  0.020  1.080
 5VS  C19  H18  single    0.930  0.020  1.080
 5VS  C23  H19  single    0.930  0.020  1.080
 5VS  C25  H20  single    0.930  0.020  1.080
 5VS  N28  H21  single    0.860  0.020  1.020

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
 5VS  O6   C5   N4   123.48  3.000
 5VS  N4   C5   C7   114.19  3.000
 5VS  O6   C5   C7   122.32  3.000
 5VS  C12  C7   C8   120.11  3.000
 5VS  C12  C7   C5   119.83  3.000
 5VS  C8   C7   C5   120.06  3.000
 5VS  H1   C8   C9   119.76  3.000
 5VS  H1   C8   C7   119.60  3.000
 5VS  C9   C8   C7   120.64  3.000
 5VS  N21  C10  C11  118.89  3.000
 5VS  N21  C10  C9   120.17  3.000
 5VS  C11  C10  C9   120.94  3.000
 5VS  C16  C15  C14  121.11  3.000
 5VS  C16  C15  C20  118.98  3.000
 5VS  C14  C15  C20  119.86  3.000
 5VS  H2   C17  C18  120.19  3.000
 5VS  H2   C17  C16  119.80  3.000
 5VS  C18  C17  C16  120.02  3.000
 5VS  H3   C20  C19  119.80  3.000
 5VS  H3   C20  C15  119.61  3.000
 5VS  C19  C20  C15  120.57  3.000
 5VS  C27  C22  C23  119.00  3.000
 5VS  C27  C22  N21  106.87  3.000
 5VS  C23  C22  N21  134.10  3.000
 5VS  H4   C24  C25  119.68  3.000
 5VS  H4   C24  C23  120.12  3.000
 5VS  C25  C24  C23  120.20  3.000
 5VS  N13  C2   N4   109.54  3.000
 5VS  N13  C2   C3   108.63  3.000
 5VS  N4   C2   C3   110.37  3.000
 5VS  N13  C2   C1   112.19  3.000
 5VS  N4   C2   C1   107.72  3.000
 5VS  C3   C2   C1   108.37  3.000
 5VS  H10  C3   H9   108.14  3.000
 5VS  H10  C3   H8   108.40  3.000
 5VS  H9   C3   H8   107.65  3.000
 5VS  H10  C3   C2   110.08  3.000
 5VS  H9   C3   C2   112.75  3.000
 5VS  H8   C3   C2   109.70  3.000
 5VS  H11  N4   C2   118.82  3.000
 5VS  H11  N4   C5   117.35  3.000
 5VS  C2   N4   C5   122.98  3.000
 5VS  H12  C9   C10  120.66  3.000
 5VS  H12  C9   C8   120.29  3.000
 5VS  C10  C9   C8   119.04  3.000
 5VS  H13  C11  C12  119.80  3.000
 5VS  H13  C11  C10  120.22  3.000
 5VS  C12  C11  C10  119.97  3.000
 5VS  N13  C12  C11  120.58  3.000
 5VS  C11  C12  C7   119.30  3.000
 5VS  N13  C12  C7   120.08  3.000
 5VS  C14  N13  C12  111.35  3.000
 5VS  C12  N13  C2   111.26  3.000
 5VS  C14  N13  C2   116.73  3.000
 5VS  H15  C14  H14  107.15  3.000
 5VS  H15  C14  N13  111.71  3.000
 5VS  H14  C14  N13  108.12  3.000
 5VS  H15  C14  C15  109.85  3.000
 5VS  H14  C14  C15  108.51  3.000
 5VS  N13  C14  C15  111.33  3.000
 5VS  H16  C16  C17  119.74  3.000
 5VS  H16  C16  C15  119.60  3.000
 5VS  C17  C16  C15  120.66  3.000
 5VS  H17  C18  C19  120.10  3.000
 5VS  H17  C18  C17  120.19  3.000
 5VS  C19  C18  C17  119.70  3.000
 5VS  H18  C19  C18  120.06  3.000
 5VS  H18  C19  C20  119.87  3.000
 5VS  C18  C19  C20  120.07  3.000
 5VS  C30  N21  C22  109.73  3.000
 5VS  C30  N21  C10  123.86  3.000
 5VS  C22  N21  C10  126.19  3.000
 5VS  H19  C23  C24  121.32  3.000
 5VS  H19  C23  C22  122.67  3.000
 5VS  C24  C23  C22  116.01  3.000
 5VS  H20  C25  N26  116.13  3.000
 5VS  H20  C25  C24  120.05  3.000
 5VS  N26  C25  C24  123.82  3.000
 5VS  C27  N26  C25  115.19  3.000
 5VS  N28  C27  N26  127.37  3.000
 5VS  N26  C27  C22  125.76  3.000
 5VS  N28  C27  C22  106.87  3.000
 5VS  H21  N28  C30  123.33  3.000
 5VS  H21  N28  C27  125.73  3.000
 5VS  C30  N28  C27  110.94  3.000
 5VS  O31  C30  N28  127.77  3.000
 5VS  N28  C30  N21  105.59  3.000
 5VS  O31  C30  N21  126.64  3.000
 5VS  H7   C1   H6   107.63  3.000
 5VS  H7   C1   H5   108.87  3.000
 5VS  H6   C1   H5   107.69  3.000
 5VS  H7   C1   C2   110.31  3.000
 5VS  H6   C1   C2   109.40  3.000
 5VS  H5   C1   C2   112.78  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
 5VS  CONST_01  C10  C9   C8   C7      0.00   0.0  0
 5VS  CONST_02  C10  C11  C12  C7      0.00   0.0  0
 5VS  CONST_03  C11  C12  C7   C8      0.00   0.0  0
 5VS  CONST_04  C11  C10  C9   C8      0.00   0.0  0
 5VS  CONST_05  C18  C19  C20  C15     0.00   0.0  0
 5VS  CONST_06  C18  C17  C16  C15     0.00   0.0  0
 5VS  CONST_07  C20  C19  C18  C17     0.00   0.0  0
 5VS  CONST_08  C20  C15  C16  C17     0.00   0.0  0
 5VS  CONST_09  C25  C24  C23  C22     0.00   0.0  0
 5VS  CONST_10  C25  N26  C27  C22     0.00   0.0  0
 5VS  CONST_11  C27  C22  C23  C24     0.00   0.0  0
 5VS  CONST_12  C27  N26  C25  C24     0.00   0.0  0
 5VS  CONST_13  C12  C7   C8   C9      0.00   0.0  0
 5VS  CONST_14  C12  C11  C10  C9      0.00   0.0  0
 5VS  CONST_15  C19  C20  C15  C16     0.00   0.0  0
 5VS  CONST_16  C19  C18  C17  C16     0.00   0.0  0
 5VS  CONST_17  N26  C27  C22  C23     0.00   0.0  0
 5VS  CONST_18  N26  C25  C24  C23     0.00   0.0  0
 5VS  CONST_19  N21  C10  C9   C8    180.00   0.0  0
 5VS  CONST_20  N21  C10  C11  C12   180.00   0.0  0
 5VS  CONST_21  C2   N4   C5   C7      0.00   0.0  0
 5VS  CONST_22  C27  C22  N21  C10   180.00   0.0  0
 5VS  CONST_23  N28  C30  N21  C10   180.00   0.0  0
 5VS  CONST_24  N28  C30  N21  C22     0.00   0.0  0
 5VS  CONST_25  C30  N28  C27  C22     0.00   0.0  0
 5VS  CONST_26  N28  C27  C22  N21     0.00   0.0  0
 5VS  CONST_27  C27  N28  C30  N21     0.00   0.0  0
 5VS  CONST_28  C30  N21  C22  C27     0.00   0.0  0
 5VS  CONST_29  C14  C15  C16  C17   180.00   0.0  0
 5VS  CONST_30  C19  C20  C15  C14   180.00   0.0  0
 5VS  CONST_31  O31  C30  N21  C10     0.00   0.0  0
 5VS  CONST_32  O31  C30  N21  C22   180.00   0.0  0
 5VS  CONST_33  O6   C5   N4   C2    180.00   0.0  0
 5VS  CONST_34  O31  C30  N28  C27   180.00   0.0  0
 5VS  CONST_35  H1   C8   C7   C5      0.00   0.0  0
 5VS  CONST_36  H12  C9   C8   C7    180.00   0.0  0
 5VS  CONST_37  H13  C11  C12  C7    180.00   0.0  0
 5VS  CONST_38  H18  C19  C20  C15   180.00   0.0  0
 5VS  CONST_39  H2   C17  C16  C15   180.00   0.0  0
 5VS  CONST_40  H17  C18  C19  C20   180.00   0.0  0
 5VS  CONST_41  H16  C16  C15  C20   180.00   0.0  0
 5VS  CONST_42  H4   C24  C23  C22   180.00   0.0  0
 5VS  CONST_43  H3   C20  C15  C16   180.00   0.0  0
 5VS  CONST_44  H19  C23  C22  N21     0.00   0.0  0
 5VS  CONST_45  H20  C25  C24  C23   180.00   0.0  0
 5VS  CONST_46  H11  N4   C5   C7    180.00   0.0  0
 5VS  CONST_47  H21  N28  C27  C22   180.00   0.0  0
 5VS  Var_01    N13  C2   N4   C5     42.52  30.0  1
 5VS  Var_02    C2   N13  C12  C7     35.32  30.0  1
 5VS  Var_03    N4   C5   C7   C8    167.94  30.0  1
 5VS  Var_04    C9   C10  N21  C22  -130.78  30.0  2
 5VS  Var_05    C12  N13  C2   N4    -53.07  30.0  1
 5VS  Var_06    N13  C14  C15  C20   -68.92  30.0  2
 5VS  Var_07    H8   C3   C2   N4    -57.19  30.0  3
 5VS  Var_08    H5   C1   C2   N4    -49.83  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
 5VS  plan-1  C15  0.020
 5VS  plan-1  C17  0.020
 5VS  plan-1  C20  0.020
 5VS  plan-1  C14  0.020
 5VS  plan-1  C16  0.020
 5VS  plan-1  C18  0.020
 5VS  plan-1  C19  0.020
 5VS  plan-1  H2   0.020
 5VS  plan-1  H3   0.020
 5VS  plan-1  H16  0.020
 5VS  plan-1  H17  0.020
 5VS  plan-1  H18  0.020
 5VS  plan-2  C10  0.020
 5VS  plan-2  C22  0.020
 5VS  plan-2  C24  0.020
 5VS  plan-2  N21  0.020
 5VS  plan-2  C23  0.020
 5VS  plan-2  C25  0.020
 5VS  plan-2  N26  0.020
 5VS  plan-2  C27  0.020
 5VS  plan-2  N28  0.020
 5VS  plan-2  C30  0.020
 5VS  plan-2  O31  0.020
 5VS  plan-2  H4   0.020
 5VS  plan-2  H19  0.020
 5VS  plan-2  H20  0.020
 5VS  plan-2  H21  0.020
 5VS  plan-3  C5   0.020
 5VS  plan-3  C7   0.020
 5VS  plan-3  C8   0.020
 5VS  plan-3  C10  0.020
 5VS  plan-3  C9   0.020
 5VS  plan-3  C11  0.020
 5VS  plan-3  C12  0.020
 5VS  plan-3  N13  0.020
 5VS  plan-3  N21  0.020
 5VS  plan-3  H1   0.020
 5VS  plan-3  H12  0.020
 5VS  plan-3  H13  0.020
 5VS  plan-4  C5   0.020
 5VS  plan-4  C7   0.020
 5VS  plan-4  C2   0.020
 5VS  plan-4  N4   0.020
 5VS  plan-4  O6   0.020
 5VS  plan-4  H11  0.020

