# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 20:16:09 2022
#   Inital geometry file: a 115 line input string
#   Ligand name: ~{N}-[(6-methylimidazo[1,2-a]pyridin-2-yl)methyl]-4-oxidanylidene-pyrido[1,2-a]pyrimidine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc2nc(CNC(=O)C3=CC(=O)N4C=CC=CC4=N3)cn2c1
#
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
 V0B  V0B  ~{N}-[(6-methylimidazo[1,2-a]pyridin-2-yl)methyl]-4-oxidanylidene-pyrido[1,2-a]pyrimidine-2-carboxamide  ligand  40  25  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_V0B
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
 V0B  C10  C  C     0   0.547  -41.4122  36.9586  27.0675
 V0B  C13  C  CR16  0  -0.480  -40.4750  39.2542  27.0664
 V0B  C17  C  CR16  0   0.052  -40.1788  41.6406  24.3283
 V0B  C20  C  CR16  0  -0.399  -41.3663  39.5310  23.0316
 V0B  C21  C  CR66  0   0.605  -41.0668  39.4191  24.4128
 V0B  C02  C  CR6   0  -0.053  -43.5521  30.6933  22.5500
 V0B  C03  C  CR16  0  -0.169  -43.9480  31.8617  21.8367
 V0B  C04  C  CR16  0  -0.393  -43.8563  33.1003  22.3960
 V0B  C05  C  CR56  0   0.528  -43.3590  33.2248  23.7089
 V0B  C07  C  CR5   0   0.094  -42.6662  33.8219  25.6337
 V0B  C08  C  CH2   0  -0.323  -42.3554  34.7345  26.7731
 V0B  C12  C  CR6   0   0.158  -41.0626  38.2440  26.3584
 V0B  C14  C  CR6   0   0.604  -40.1305  40.4709  26.4261
 V0B  C18  C  CR16  0  -0.374  -40.4617  41.7488  23.0110
 V0B  C19  C  CR16  0  -0.107  -41.0734  40.6637  22.3421
 V0B  C23  C  CR15  0  -0.128  -42.5288  32.4590  25.6084
 V0B  C25  C  CR16  0   0.001  -43.0732  30.8339  23.8136
 V0B  N06  N  N     0  -0.507  -43.1742  34.2912  24.4690
 V0B  N09  N  NH1   0  -0.655  -41.9155  36.0148  26.2734
 V0B  N16  N  N     0  -0.623  -40.4712  40.4987  25.0284
 V0B  N22  N  N     0  -0.522  -41.3578  38.3099  25.0587
 V0B  N24  N  N     0  -0.502  -42.9816  32.0763  24.3739
 V0B  O11  O  O     0  -0.475  -41.2298  36.8270  28.2688
 V0B  O15  O  O     0  -0.461  -39.5986  41.4425  26.9279
 V0B  H1   H  HCR6  0   0.280  -40.2561  39.1528  28.1190
 V0B  H3   H  HCR6  0   0.325  -39.7140  42.4295  24.8973
 V0B  H4   H  HCR6  0   0.296  -41.8336  38.6774  22.5621
 V0B  H5   H  HCH3  0   0.249  -43.0726  29.2923  20.9975
 V0B  H6   H  HCH3  0   0.248  -43.3233  28.5531  22.5782
 V0B  H7   H  HCH3  0   0.249  -44.6993  29.1263  21.6373
 V0B  H8   H  HCR6  0   0.264  -44.3298  31.7548  20.8291
 V0B  H9   H  HCR6  0   0.275  -44.1552  33.9922  21.8631
 V0B  H10  H  HCH2  0   0.261  -43.2431  34.8613  27.4030
 V0B  H11  H  HCH2  0   0.261  -41.5856  34.2885  27.4055
 V0B  H12  H  HCR6  0   0.294  -40.2171  42.6623  22.4898
 V0B  H13  H  HCR6  0   0.295  -41.3055  40.7379  21.2885
 V0B  H14  H  HCR5  0   0.298  -42.1608  31.7530  26.3336
 V0B  H15  H  HCR6  0   0.298  -42.7493  30.0056  24.4281
 V0B  H16  H  HNH1  0   0.409  -42.0801  36.2377  25.3013
 V0B  C01  C  CH3   0  -0.721  -43.6659  29.3429  21.9116

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
 V0B  C01  C02  single    1.498  0.020  1.498
 V0B  C03  C02  aromatic  1.425  0.020  1.425
 V0B  C03  C04  aromatic  1.362  0.020  1.362
 V0B  C19  C20  double    1.358  0.020  1.358
 V0B  C19  C18  single    1.414  0.020  1.414
 V0B  C02  C25  aromatic  1.359  0.020  1.359
 V0B  C04  C05  aromatic  1.409  0.020  1.409
 V0B  C20  C21  single    1.418  0.020  1.418
 V0B  C18  C17  double    1.352  0.020  1.352
 V0B  C25  N24  aromatic  1.366  0.020  1.366
 V0B  C05  N24  aromatic  1.380  0.020  1.380
 V0B  C05  N06  aromatic  1.323  0.020  1.323
 V0B  C17  N16  single    1.371  0.020  1.371
 V0B  C21  N22  double    1.316  0.020  1.316
 V0B  C21  N16  single    1.378  0.020  1.378
 V0B  N24  C23  aromatic  1.369  0.020  1.369
 V0B  N06  C07  aromatic  1.355  0.020  1.355
 V0B  N22  C12  single    1.334  0.020  1.334
 V0B  N16  C14  single    1.439  0.020  1.439
 V0B  C23  C07  aromatic  1.370  0.020  1.370
 V0B  C07  C08  single    1.493  0.020  1.493
 V0B  N09  C08  single    1.443  0.020  1.443
 V0B  N09  C10  single    1.332  0.020  1.332
 V0B  C12  C10  single    1.509  0.020  1.509
 V0B  C12  C13  double    1.366  0.020  1.366
 V0B  C14  O15  double    1.216  0.020  1.216
 V0B  C14  C13  single    1.417  0.020  1.417
 V0B  C10  O11  double    1.222  0.020  1.222
 V0B  C13  H1   single    0.930  0.020  1.080
 V0B  C17  H3   single    0.930  0.020  1.080
 V0B  C20  H4   single    0.930  0.020  1.080
 V0B  C01  H5   single    0.970  0.020  1.090
 V0B  C01  H6   single    0.970  0.020  1.090
 V0B  C01  H7   single    0.970  0.020  1.090
 V0B  C03  H8   single    0.930  0.020  1.080
 V0B  C04  H9   single    0.930  0.020  1.080
 V0B  C08  H10  single    0.970  0.020  1.090
 V0B  C08  H11  single    0.970  0.020  1.090
 V0B  C18  H12  single    0.930  0.020  1.080
 V0B  C19  H13  single    0.930  0.020  1.080
 V0B  C23  H14  single    0.930  0.020  1.080
 V0B  C25  H15  single    0.930  0.020  1.080
 V0B  N09  H16  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
 V0B  O11  C10  N09  124.47  3.000
 V0B  O11  C10  C12  121.26  3.000
 V0B  N09  C10  C12  114.26  3.000
 V0B  H1   C13  C14  118.14  3.000
 V0B  H1   C13  C12  121.52  3.000
 V0B  C14  C13  C12  120.34  3.000
 V0B  H3   C17  N16  115.59  3.000
 V0B  H3   C17  C18  123.10  3.000
 V0B  N16  C17  C18  121.31  3.000
 V0B  H4   C20  C19  122.11  3.000
 V0B  H4   C20  C21  116.89  3.000
 V0B  C19  C20  C21  121.00  3.000
 V0B  N22  C21  N16  122.45  3.000
 V0B  N16  C21  C20  117.68  3.000
 V0B  N22  C21  C20  119.86  3.000
 V0B  C25  C02  C03  118.59  3.000
 V0B  C25  C02  C01  121.10  3.000
 V0B  C03  C02  C01  120.31  3.000
 V0B  H8   C03  C04  119.71  3.000
 V0B  H8   C03  C02  118.87  3.000
 V0B  C04  C03  C02  121.42  3.000
 V0B  H9   C04  C05  118.94  3.000
 V0B  H9   C04  C03  121.95  3.000
 V0B  C05  C04  C03  119.12  3.000
 V0B  N24  C05  N06  110.85  3.000
 V0B  N06  C05  C04  130.99  3.000
 V0B  N24  C05  C04  118.16  3.000
 V0B  N06  C07  C23  111.49  3.000
 V0B  C23  C07  C08  126.98  3.000
 V0B  N06  C07  C08  121.51  3.000
 V0B  H11  C08  H10  106.59  3.000
 V0B  H11  C08  N09  110.38  3.000
 V0B  H10  C08  N09  110.08  3.000
 V0B  H11  C08  C07  109.83  3.000
 V0B  H10  C08  C07  109.93  3.000
 V0B  N09  C08  C07  109.98  3.000
 V0B  N22  C12  C13  124.28  3.000
 V0B  C13  C12  C10  119.07  3.000
 V0B  N22  C12  C10  116.64  3.000
 V0B  O15  C14  N16  119.28  3.000
 V0B  O15  C14  C13  127.29  3.000
 V0B  N16  C14  C13  113.44  3.000
 V0B  H12  C18  C19  121.26  3.000
 V0B  H12  C18  C17  119.38  3.000
 V0B  C19  C18  C17  119.35  3.000
 V0B  H13  C19  C18  120.07  3.000
 V0B  H13  C19  C20  120.38  3.000
 V0B  C18  C19  C20  119.55  3.000
 V0B  H14  C23  N24  122.46  3.000
 V0B  H14  C23  C07  132.38  3.000
 V0B  N24  C23  C07  105.16  3.000
 V0B  H15  C25  N24  116.34  3.000
 V0B  H15  C25  C02  123.71  3.000
 V0B  N24  C25  C02  119.95  3.000
 V0B  C07  N06  C05  105.50  3.000
 V0B  H16  N09  C08  118.62  3.000
 V0B  H16  N09  C10  118.60  3.000
 V0B  C08  N09  C10  122.50  3.000
 V0B  C14  N16  C21  121.41  3.000
 V0B  C14  N16  C17  117.49  3.000
 V0B  C21  N16  C17  121.10  3.000
 V0B  C12  N22  C21  118.08  3.000
 V0B  C25  N24  C23  130.25  3.000
 V0B  C23  N24  C05  106.99  3.000
 V0B  C25  N24  C05  122.76  3.000
 V0B  H7   C01  H6   107.94  3.000
 V0B  H7   C01  H5   107.17  3.000
 V0B  H6   C01  H5   107.96  3.000
 V0B  H7   C01  C02  110.98  3.000
 V0B  H6   C01  C02  111.66  3.000
 V0B  H5   C01  C02  110.95  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
 V0B  CONST_01  C05  C04  C03  C02     0.00   0.0  0
 V0B  CONST_02  C05  N24  C25  C02     0.00   0.0  0
 V0B  CONST_03  C23  N24  C25  C02   180.00   0.0  0
 V0B  CONST_04  N24  C25  C02  C03     0.00   0.0  0
 V0B  CONST_05  N24  C05  C04  C03     0.00   0.0  0
 V0B  CONST_06  N06  C05  C04  C03   180.00   0.0  0
 V0B  CONST_07  C25  C02  C03  C04     0.00   0.0  0
 V0B  CONST_08  C25  N24  C05  C04     0.00   0.0  0
 V0B  CONST_09  C23  N24  C05  C04   180.00   0.0  0
 V0B  CONST_10  C07  N06  C05  C04   180.00   0.0  0
 V0B  CONST_11  C07  C23  N24  C05     0.00   0.0  0
 V0B  CONST_12  C23  C07  N06  C05     0.00   0.0  0
 V0B  CONST_13  N24  C05  N06  C07     0.00   0.0  0
 V0B  CONST_14  C25  N24  C23  C07   180.00   0.0  0
 V0B  CONST_15  N06  C05  N24  C23     0.00   0.0  0
 V0B  CONST_16  N06  C05  N24  C25   180.00   0.0  0
 V0B  CONST_17  N24  C23  C07  N06     0.00   0.0  0
 V0B  CONST_18  C17  N16  C14  C13   180.00   0.0  0
 V0B  CONST_19  C21  N16  C14  C13     0.00   0.0  0
 V0B  CONST_20  C20  C21  N16  C17     0.00   0.0  0
 V0B  CONST_21  N22  C21  N16  C17   180.00   0.0  0
 V0B  CONST_22  C12  N22  C21  C20   180.00   0.0  0
 V0B  CONST_23  C14  N16  C21  C20   180.00   0.0  0
 V0B  CONST_24  N16  C21  N22  C12     0.00   0.0  0
 V0B  CONST_25  N22  C21  N16  C14     0.00   0.0  0
 V0B  CONST_26  C04  C03  C02  C01   180.00   0.0  0
 V0B  CONST_27  N24  C25  C02  C01   180.00   0.0  0
 V0B  CONST_28  C08  C07  N06  C05   180.00   0.0  0
 V0B  CONST_29  N24  C23  C07  C08   180.00   0.0  0
 V0B  CONST_30  O15  C14  N16  C17     0.00   0.0  0
 V0B  CONST_31  O15  C14  N16  C21   180.00   0.0  0
 V0B  CONST_32  H9   C04  C03  C02   180.00   0.0  0
 V0B  CONST_33  H15  C25  C02  C03   180.00   0.0  0
 V0B  CONST_34  H8   C03  C04  C05   180.00   0.0  0
 V0B  CONST_35  H14  C23  N24  C05   180.00   0.0  0
 V0B  CONST_36  C12  C10  N09  C08   180.00   0.0  0
 V0B  CONST_37  H16  N09  C10  C12     0.00   0.0  0
 V0B  CONST_38  O11  C10  N09  C08     0.00   0.0  0
 V0B  Var_01    N09  C10  C12  C13  -176.66  30.0  2
 V0B  Var_02    N09  C08  C07  C23   148.49  30.0  2
 V0B  Var_03    H5   C01  C02  C03    59.37  30.0  2
 V0B  Var_04    C07  C08  N09  C10  -171.23  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
 V0B  plan-1  C02  0.020
 V0B  plan-1  C03  0.020
 V0B  plan-1  C04  0.020
 V0B  plan-1  C05  0.020
 V0B  plan-1  C07  0.020
 V0B  plan-1  C08  0.020
 V0B  plan-1  C23  0.020
 V0B  plan-1  C25  0.020
 V0B  plan-1  N06  0.020
 V0B  plan-1  N24  0.020
 V0B  plan-1  H8   0.020
 V0B  plan-1  H9   0.020
 V0B  plan-1  H14  0.020
 V0B  plan-1  H15  0.020
 V0B  plan-1  C01  0.020
 V0B  plan-2  C10  0.020
 V0B  plan-2  C13  0.020
 V0B  plan-2  C17  0.020
 V0B  plan-2  C20  0.020
 V0B  plan-2  C21  0.020
 V0B  plan-2  C12  0.020
 V0B  plan-2  C14  0.020
 V0B  plan-2  C18  0.020
 V0B  plan-2  C19  0.020
 V0B  plan-2  N16  0.020
 V0B  plan-2  N22  0.020
 V0B  plan-2  O15  0.020
 V0B  plan-2  H1   0.020
 V0B  plan-2  H3   0.020
 V0B  plan-2  H4   0.020
 V0B  plan-2  H12  0.020
 V0B  plan-2  H13  0.020
 V0B  plan-3  C10  0.020
 V0B  plan-3  C08  0.020
 V0B  plan-3  C12  0.020
 V0B  plan-3  N09  0.020
 V0B  plan-3  O11  0.020
 V0B  plan-3  H16  0.020

