# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 12:49:52 2022
#   Inital geometry file: a 90 line input string
#   Ligand name: 2-oxidanyl-4-(2-phenylimidazol-1-yl)benzaldehyde
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1cc(ccc1C=O)n2ccnc2c3ccccc3
#
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
 UPK  UPK  2-oxidanyl-4-(2-phenylimidazol-1-yl)benzaldehyde  ligand  32  20  .  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_UPK
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
 UPK  C02  C  C1    0   0.153  -21.2555  -21.1157  -3.7545
 UPK  C03  C  CR6   0  -0.154  -22.1778  -21.4765  -2.6919
 UPK  C04  C  CR6   0   0.385  -23.3807  -22.1521  -2.9747
 UPK  C06  C  CR16  0  -0.365  -24.2430  -22.4772  -1.9286
 UPK  C07  C  CR16  0  -0.275  -21.8715  -21.1399  -1.3705
 UPK  C08  C  CR16  0  -0.270  -22.7234  -21.4516  -0.3363
 UPK  C09  C  CR6   0   0.308  -23.9088  -22.1264  -0.6341
 UPK  C11  C  CR5   0   0.426  -24.5471  -23.0555   1.5974
 UPK  C12  C  CR6   0   0.024  -23.2745  -23.6919   1.9462
 UPK  C13  C  CR16  0  -0.282  -22.5402  -24.4304   1.0177
 UPK  C14  C  CR16  0  -0.238  -21.3541  -25.0432   1.3924
 UPK  C15  C  CR16  0  -0.256  -20.8899  -24.9337   2.6967
 UPK  C16  C  CR16  0  -0.240  -21.6239  -24.2121   3.6291
 UPK  C17  C  CR16  0  -0.282  -22.8089  -23.5960   3.2577
 UPK  C19  C  CR15  0  -0.213  -26.5857  -22.4078   1.6668
 UPK  C20  C  CR15  0  -0.111  -26.1213  -22.0279   0.4453
 UPK  N10  N  NR5   0  -0.556  -24.8111  -22.4386   0.4063
 UPK  N18  N  N     0  -0.442  -25.6051  -23.0455   2.3683
 UPK  O05  O  OH1   0  -0.609  -23.7266  -22.5057  -4.2067
 UPK  O1   O  O     0  -0.422  -21.4415  -21.3675  -4.9341
 UPK  H1   H  H     0   0.232  -20.3464  -20.5820  -3.4354
 UPK  H3   H  HCR6  0   0.292  -25.1597  -23.0147  -2.1361
 UPK  H4   H  HCR6  0   0.282  -20.9484  -20.6106  -1.1658
 UPK  H5   H  HCR6  0   0.283  -22.4906  -21.1705   0.6809
 UPK  H6   H  HCR6  0   0.263  -22.8985  -24.5505   0.0034
 UPK  H7   H  HCR6  0   0.260  -20.7963  -25.6163   0.6634
 UPK  H8   H  HCR6  0   0.259  -19.9635  -25.4122   2.9860
 UPK  H9   H  HCR6  0   0.259  -21.2708  -24.1239   4.6483
 UPK  H10  H  HCR6  0   0.254  -23.3739  -23.0277   3.9850
 UPK  H11  H  HCR5  0   0.257  -27.5733  -22.2568   2.0738
 UPK  H12  H  HCR5  0   0.301  -26.5746  -21.4905  -0.3708
 UPK  H13  H  HOH1  0   0.477  -23.0263  -22.2168  -4.8267

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
 UPK  O05  C04  single    1.328  0.020  1.328
 UPK  C02  C03  single    1.453  0.020  1.453
 UPK  C04  C03  aromatic  1.408  0.020  1.408
 UPK  C04  C06  aromatic  1.394  0.020  1.394
 UPK  C03  C07  aromatic  1.398  0.020  1.398
 UPK  C06  C09  aromatic  1.382  0.020  1.382
 UPK  C07  C08  aromatic  1.376  0.020  1.376
 UPK  C09  C08  aromatic  1.396  0.020  1.396
 UPK  C09  N10  single    1.412  0.020  1.412
 UPK  N10  C20  aromatic  1.374  0.020  1.374
 UPK  N10  C11  aromatic  1.367  0.020  1.367
 UPK  C20  C19  aromatic  1.361  0.020  1.361
 UPK  C13  C14  aromatic  1.387  0.020  1.387
 UPK  C13  C12  aromatic  1.395  0.020  1.395
 UPK  C14  C15  aromatic  1.389  0.020  1.389
 UPK  C11  C12  single    1.465  0.020  1.465
 UPK  C11  N18  aromatic  1.309  0.020  1.309
 UPK  C19  N18  aromatic  1.364  0.020  1.364
 UPK  C12  C17  aromatic  1.395  0.020  1.395
 UPK  C15  C16  aromatic  1.389  0.020  1.389
 UPK  C17  C16  aromatic  1.386  0.020  1.386
 UPK  C02  O1   double    1.220  0.020  1.220
 UPK  C02  H1   single    0.930  0.020  1.080
 UPK  C06  H3   single    0.930  0.020  1.080
 UPK  C07  H4   single    0.930  0.020  1.080
 UPK  C08  H5   single    0.930  0.020  1.080
 UPK  C13  H6   single    0.930  0.020  1.080
 UPK  C14  H7   single    0.930  0.020  1.080
 UPK  C15  H8   single    0.930  0.020  1.080
 UPK  C16  H9   single    0.930  0.020  1.080
 UPK  C17  H10  single    0.930  0.020  1.080
 UPK  C19  H11  single    0.930  0.020  1.080
 UPK  C20  H12  single    0.930  0.020  1.080
 UPK  O05  H13  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
 UPK  H1   C02  O1   120.38  3.000
 UPK  H1   C02  C03  115.63  3.000
 UPK  O1   C02  C03  123.99  3.000
 UPK  C07  C03  C04  119.51  3.000
 UPK  C07  C03  C02  119.52  3.000
 UPK  C04  C03  C02  120.97  3.000
 UPK  O05  C04  C06  118.23  3.000
 UPK  C06  C04  C03  119.31  3.000
 UPK  O05  C04  C03  122.46  3.000
 UPK  H3   C06  C09  120.67  3.000
 UPK  H3   C06  C04  119.72  3.000
 UPK  C09  C06  C04  119.60  3.000
 UPK  H4   C07  C08  119.75  3.000
 UPK  H4   C07  C03  118.88  3.000
 UPK  C08  C07  C03  121.37  3.000
 UPK  H5   C08  C09  120.62  3.000
 UPK  H5   C08  C07  121.01  3.000
 UPK  C09  C08  C07  118.36  3.000
 UPK  N10  C09  C08  119.49  3.000
 UPK  N10  C09  C06  118.64  3.000
 UPK  C08  C09  C06  121.85  3.000
 UPK  N18  C11  N10  110.71  3.000
 UPK  N18  C11  C12  124.41  3.000
 UPK  N10  C11  C12  124.83  3.000
 UPK  C17  C12  C13  119.10  3.000
 UPK  C17  C12  C11  118.95  3.000
 UPK  C13  C12  C11  121.92  3.000
 UPK  H6   C13  C14  119.16  3.000
 UPK  H6   C13  C12  120.54  3.000
 UPK  C14  C13  C12  120.29  3.000
 UPK  H7   C14  C15  120.14  3.000
 UPK  H7   C14  C13  119.54  3.000
 UPK  C15  C14  C13  120.32  3.000
 UPK  H8   C15  C16  120.18  3.000
 UPK  H8   C15  C14  120.16  3.000
 UPK  C16  C15  C14  119.66  3.000
 UPK  H9   C16  C17  119.67  3.000
 UPK  H9   C16  C15  120.14  3.000
 UPK  C17  C16  C15  120.18  3.000
 UPK  H10  C17  C16  119.98  3.000
 UPK  H10  C17  C12  119.58  3.000
 UPK  C16  C17  C12  120.44  3.000
 UPK  H11  C19  N18  121.98  3.000
 UPK  H11  C19  C20  127.73  3.000
 UPK  N18  C19  C20  110.29  3.000
 UPK  H12  C20  N10  121.94  3.000
 UPK  H12  C20  C19  132.51  3.000
 UPK  N10  C20  C19  105.52  3.000
 UPK  C20  N10  C11  107.12  3.000
 UPK  C11  N10  C09  128.19  3.000
 UPK  C20  N10  C09  124.35  3.000
 UPK  C19  N18  C11  106.36  3.000
 UPK  H13  O05  C04  108.82  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
 UPK  CONST_01  C09  C06  C04  C03    0.00   0.0  0
 UPK  CONST_02  C09  C08  C07  C03    0.00   0.0  0
 UPK  CONST_03  C08  C07  C03  C04    0.00   0.0  0
 UPK  CONST_04  C08  C09  C06  C04    0.00   0.0  0
 UPK  CONST_05  N10  C09  C06  C04  180.00   0.0  0
 UPK  CONST_06  C07  C03  C04  C06    0.00   0.0  0
 UPK  CONST_07  C07  C08  C09  C06    0.00   0.0  0
 UPK  CONST_10  N10  C09  C08  C07  180.00   0.0  0
 UPK  CONST_13  C19  C20  N10  C09  180.00   0.0  0
 UPK  CONST_14  C12  C11  N10  C09    0.00   0.0  0
 UPK  CONST_15  N18  C11  N10  C09  180.00   0.0  0
 UPK  CONST_16  C19  C20  N10  C11    0.00   0.0  0
 UPK  CONST_17  C14  C13  C12  C11  180.00   0.0  0
 UPK  CONST_18  C16  C17  C12  C11  180.00   0.0  0
 UPK  CONST_19  C20  C19  N18  C11    0.00   0.0  0
 UPK  CONST_20  C15  C14  C13  C12    0.00   0.0  0
 UPK  CONST_21  C20  N10  C11  C12  180.00   0.0  0
 UPK  CONST_22  C19  N18  C11  C12  180.00   0.0  0
 UPK  CONST_23  C15  C16  C17  C12    0.00   0.0  0
 UPK  CONST_24  C16  C15  C14  C13    0.00   0.0  0
 UPK  CONST_27  C16  C17  C12  C13    0.00   0.0  0
 UPK  CONST_28  C17  C12  C13  C14    0.00   0.0  0
 UPK  CONST_29  C17  C16  C15  C14    0.00   0.0  0
 UPK  CONST_32  N10  C11  N18  C19    0.00   0.0  0
 UPK  CONST_33  N18  C11  N10  C20    0.00   0.0  0
 UPK  CONST_34  N18  C19  C20  N10    0.00   0.0  0
 UPK  CONST_35  C06  C04  C03  C02  180.00   0.0  0
 UPK  CONST_36  C08  C07  C03  C02  180.00   0.0  0
 UPK  CONST_37  O05  C04  C03  C07  180.00   0.0  0
 UPK  CONST_38  O05  C04  C06  C09  180.00   0.0  0
 UPK  CONST_39  H3   C06  C04  C03  180.00   0.0  0
 UPK  CONST_40  H5   C08  C07  C03  180.00   0.0  0
 UPK  CONST_41  H4   C07  C03  C04  180.00   0.0  0
 UPK  CONST_42  H12  C20  N10  C09    0.00   0.0  0
 UPK  CONST_43  H6   C13  C12  C11    0.00   0.0  0
 UPK  CONST_44  H10  C17  C12  C11    0.00   0.0  0
 UPK  CONST_45  H11  C19  N18  C11  180.00   0.0  0
 UPK  CONST_46  H7   C14  C13  C12  180.00   0.0  0
 UPK  CONST_47  H9   C16  C17  C12  180.00   0.0  0
 UPK  CONST_48  H8   C15  C14  C13  180.00   0.0  0
 UPK  Var_01    O1   C02  C03  C04   -0.38  30.0  2

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
 UPK  plan-1  C09  0.020
 UPK  plan-1  C11  0.020
 UPK  plan-1  C12  0.020
 UPK  plan-1  C19  0.020
 UPK  plan-1  C20  0.020
 UPK  plan-1  N10  0.020
 UPK  plan-1  N18  0.020
 UPK  plan-1  H11  0.020
 UPK  plan-1  H12  0.020
 UPK  plan-2  C02  0.020
 UPK  plan-2  C03  0.020
 UPK  plan-2  C04  0.020
 UPK  plan-2  C06  0.020
 UPK  plan-2  C07  0.020
 UPK  plan-2  C08  0.020
 UPK  plan-2  C09  0.020
 UPK  plan-2  N10  0.020
 UPK  plan-2  O05  0.020
 UPK  plan-2  H3   0.020
 UPK  plan-2  H4   0.020
 UPK  plan-2  H5   0.020
 UPK  plan-3  C11  0.020
 UPK  plan-3  C12  0.020
 UPK  plan-3  C13  0.020
 UPK  plan-3  C14  0.020
 UPK  plan-3  C15  0.020
 UPK  plan-3  C16  0.020
 UPK  plan-3  C17  0.020
 UPK  plan-3  H6   0.020
 UPK  plan-3  H7   0.020
 UPK  plan-3  H8   0.020
 UPK  plan-3  H9   0.020
 UPK  plan-3  H10  0.020
 UPK  plan-4  C02  0.020
 UPK  plan-4  C03  0.020
 UPK  plan-4  O1   0.020
 UPK  plan-4  H1   0.020

