# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 03:56:03 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: 8-[4-[2-[4-[3,5-bis(chloranyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cc(Cl)cc(c1)C2CCN(CC2)CCc3cnn(c3)c4nccc5C(=O)NC=Nc45
#
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
 5UJ  5UJ  8-[4-[2-[4-[3,5-bis(chloranyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one  ligand  54  32  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5UJ
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
 5UJ  C4   C   CR6   0  -0.022    7.9590  -1.1048  -0.2990
 5UJ  C5   C   CR16  0  -0.198    8.3774   0.2147  -0.3013
 5UJ  C6   C   CH1   0  -0.355    4.1872  -0.8124  -0.1423
 5UJ  C3   C   CR16  0  -0.293    6.6167  -1.4476  -0.2474
 5UJ  C2   C   CR6   0   0.190    5.6485  -0.4507  -0.1967
 5UJ  C1   C   CR16  0  -0.274    6.0508   0.8837  -0.1986
 5UJ  C    C   CR6   0  -0.024    7.3978   1.1949  -0.2500
 5UJ  C20  C   CR6   0   0.580   -8.9982  -0.5500  -0.8372
 5UJ  C17  C   CR66  0  -0.017   -7.9315   0.3676  -0.4237
 5UJ  C16  C   CR16  0  -0.357   -8.1570   1.7412  -0.3667
 5UJ  C15  C   CR16  0  -0.063   -7.1069   2.5511  -0.0028
 5UJ  N3   N   N     0  -0.402   -5.9108   2.0702   0.3445
 5UJ  N5   N   NR16  0  -0.659   -8.5793  -1.8572  -0.8951
 5UJ  C19  C   CR16  0   0.151   -7.3115  -2.2574  -0.6222
 5UJ  N4   N   N     0  -0.429   -6.3649  -1.4837  -0.2396
 5UJ  C18  C   CR66  0   0.155   -6.6721  -0.1555  -0.1105
 5UJ  C14  C   CR6   0   0.444   -5.6985   0.7795   0.3125
 5UJ  N1   N   NR5   0  -0.371   -4.4159   0.3649   0.6989
 5UJ  C12  C   CR15  0   0.027   -3.2518   1.0057   0.4150
 5UJ  N2   N   N     0  -0.267   -4.2331  -0.6836   1.5072
 5UJ  C13  C   CR15  0  -0.063   -2.9386  -0.7205   1.7254
 5UJ  C11  C   CR5   0  -0.145   -2.2543   0.3229   1.0580
 5UJ  C10  C   CH2   0  -0.544   -0.7844   0.5793   1.0299
 5UJ  N    N   NT    0  -0.423    1.3588  -0.1152  -0.0172
 5UJ  C8   C   CH2   0  -0.282    1.9386  -0.6328  -1.2444
 5UJ  C7   C   CH2   0  -0.417    3.4141  -0.2817  -1.3503
 5UJ  C21  C   CH2   0  -0.290    2.0348  -0.6721   1.1416
 5UJ  C22  C   CH2   0  -0.414    3.5147  -0.3226   1.1406
 5UJ  CL1  CL  CL    0  -0.117    9.1507  -2.3598  -0.3626
 5UJ  CL   CL  CL    0  -0.118    7.8835   2.8576  -0.2514
 5UJ  H1   H   HCR6  0   0.299    9.4267   0.4712  -0.3422
 5UJ  H2   H   HCH1  0   0.247    4.1131  -1.9061  -0.1566
 5UJ  H3   H   HCR6  0   0.277    6.3223  -2.4891  -0.2465
 5UJ  H4   H   HCR6  0   0.275    5.3191   1.6800  -0.1623
 5UJ  H6   H   HCR6  0   0.281   -7.2201   3.6269   0.0314
 5UJ  H7   H   HNR6  0   0.440   -9.2543  -2.5574  -1.1768
 5UJ  H8   H   HCR6  0   0.307   -7.1270  -3.3161  -0.7522
 5UJ  H9   H   HCR5  0   0.292   -3.2219   1.8739  -0.2230
 5UJ  H10  H   HCR5  0   0.262   -2.5166  -1.4837   2.3637
 5UJ  H11  H   HCH2  0   0.244   -0.5876   1.6197   0.7640
 5UJ  H12  H   HCH2  0   0.248   -0.3803   0.4289   2.0334
 5UJ  H16  H   HCH2  0   0.188    1.8201  -1.7290  -1.3193
 5UJ  H17  H   HCH2  0   0.239    1.4039  -0.2013  -2.0935
 5UJ  H18  H   HCH2  0   0.225    3.5205   0.8053  -1.4163
 5UJ  H19  H   HCH2  0   0.242    3.8215  -0.7001  -2.2734
 5UJ  H20  H   HCH2  0   0.243    1.5818  -0.2797   2.0536
 5UJ  H21  H   HCH2  0   0.190    1.9172  -1.7706   1.1818
 5UJ  H22  H   HCH2  0   0.242    3.9936  -0.7717   2.0135
 5UJ  H23  H   HCH2  0   0.224    3.6270   0.7614   1.2352
 5UJ  C9   C   CH2   0  -0.252   -0.0748  -0.3314   0.0262
 5UJ  H5   H   HCR6  0   0.286   -9.1223   2.1600  -0.6136
 5UJ  O    O   O     0  -0.434  -10.1348  -0.2191  -1.1057
 5UJ  H13  H   HCH2  0   0.197   -0.3244  -1.3844   0.2438
 5UJ  H14  H   HCH2  0   0.234   -0.4817  -0.1179  -0.9656

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
 5UJ  CL   C    single    1.732  0.020  1.732
 5UJ  C5   C    aromatic  1.387  0.020  1.387
 5UJ  C5   C4   aromatic  1.384  0.020  1.384
 5UJ  CL1  C4   single    1.732  0.020  1.732
 5UJ  C    C1   aromatic  1.383  0.020  1.383
 5UJ  C4   C3   aromatic  1.386  0.020  1.386
 5UJ  C1   C2   aromatic  1.394  0.020  1.394
 5UJ  C3   C2   aromatic  1.391  0.020  1.391
 5UJ  C2   C6   single    1.506  0.020  1.506
 5UJ  C6   C7   single    1.529  0.020  1.529
 5UJ  C6   C22  single    1.529  0.020  1.529
 5UJ  C7   C8   single    1.520  0.020  1.520
 5UJ  C22  C21  single    1.521  0.020  1.521
 5UJ  C8   N    single    1.453  0.020  1.453
 5UJ  C21  N    single    1.453  0.020  1.453
 5UJ  N    C9   single    1.450  0.020  1.450
 5UJ  C9   C10  single    1.530  0.020  1.530
 5UJ  C10  C11  single    1.492  0.020  1.492
 5UJ  C11  C13  aromatic  1.415  0.020  1.415
 5UJ  C11  C12  aromatic  1.369  0.020  1.369
 5UJ  C13  N2   aromatic  1.313  0.020  1.313
 5UJ  C12  N1   aromatic  1.359  0.020  1.359
 5UJ  N2   N1   aromatic  1.337  0.020  1.337
 5UJ  N1   C14  single    1.402  0.020  1.402
 5UJ  N4   C19  double    1.281  0.020  1.281
 5UJ  N4   C18  single    1.369  0.020  1.369
 5UJ  C14  C18  aromatic  1.415  0.020  1.415
 5UJ  C14  N3   aromatic  1.308  0.020  1.308
 5UJ  C19  N5   single    1.357  0.020  1.357
 5UJ  C18  C17  aromatic  1.399  0.020  1.399
 5UJ  N3   C15  aromatic  1.335  0.020  1.335
 5UJ  N5   C20  single    1.374  0.020  1.374
 5UJ  C17  C20  single    1.467  0.020  1.467
 5UJ  C17  C16  aromatic  1.393  0.020  1.393
 5UJ  C15  C16  aromatic  1.375  0.020  1.375
 5UJ  C20  O    double    1.214  0.020  1.214
 5UJ  C5   H1   single    0.930  0.020  1.080
 5UJ  C6   H2   single    0.970  0.020  1.090
 5UJ  C3   H3   single    0.930  0.020  1.080
 5UJ  C1   H4   single    0.930  0.020  1.080
 5UJ  C16  H5   single    0.930  0.020  1.080
 5UJ  C15  H6   single    0.930  0.020  1.080
 5UJ  N5   H7   single    0.860  0.020  1.020
 5UJ  C19  H8   single    0.930  0.020  1.080
 5UJ  C12  H9   single    0.930  0.020  1.080
 5UJ  C13  H10  single    0.930  0.020  1.080
 5UJ  C10  H11  single    0.970  0.020  1.090
 5UJ  C10  H12  single    0.970  0.020  1.090
 5UJ  C9   H13  single    0.970  0.020  1.090
 5UJ  C9   H14  single    0.970  0.020  1.090
 5UJ  C8   H16  single    0.970  0.020  1.090
 5UJ  C8   H17  single    0.970  0.020  1.090
 5UJ  C7   H18  single    0.970  0.020  1.090
 5UJ  C7   H19  single    0.970  0.020  1.090
 5UJ  C21  H20  single    0.970  0.020  1.090
 5UJ  C21  H21  single    0.970  0.020  1.090
 5UJ  C22  H22  single    0.970  0.020  1.090
 5UJ  C22  H23  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
 5UJ  CL1  C4   C3   119.24  3.000
 5UJ  C3   C4   C5   121.90  3.000
 5UJ  CL1  C4   C5   118.86  3.000
 5UJ  H1   C5   C    121.28  3.000
 5UJ  H1   C5   C4   121.31  3.000
 5UJ  C    C5   C4   117.40  3.000
 5UJ  H2   C6   C22  107.50  3.000
 5UJ  H2   C6   C7   107.56  3.000
 5UJ  C22  C6   C7   109.22  3.000
 5UJ  H2   C6   C2   107.74  3.000
 5UJ  C22  C6   C2   112.33  3.000
 5UJ  C7   C6   C2   112.24  3.000
 5UJ  H3   C3   C2   120.03  3.000
 5UJ  H3   C3   C4   120.09  3.000
 5UJ  C2   C3   C4   119.88  3.000
 5UJ  C1   C2   C3   119.04  3.000
 5UJ  C3   C2   C6   120.30  3.000
 5UJ  C1   C2   C6   120.66  3.000
 5UJ  H4   C1   C    119.61  3.000
 5UJ  H4   C1   C2   120.63  3.000
 5UJ  C    C1   C2   119.77  3.000
 5UJ  CL   C    C1   119.27  3.000
 5UJ  C1   C    C5   122.02  3.000
 5UJ  CL   C    C5   118.71  3.000
 5UJ  N5   C20  C17  112.67  3.000
 5UJ  C17  C20  O    124.96  3.000
 5UJ  N5   C20  O    122.37  3.000
 5UJ  C18  C17  C16  120.34  3.000
 5UJ  C16  C17  C20  120.71  3.000
 5UJ  C18  C17  C20  118.94  3.000
 5UJ  H5   C16  C15  120.95  3.000
 5UJ  H5   C16  C17  121.15  3.000
 5UJ  C15  C16  C17  117.90  3.000
 5UJ  H6   C15  N3   116.33  3.000
 5UJ  H6   C15  C16  120.92  3.000
 5UJ  N3   C15  C16  122.74  3.000
 5UJ  C14  N3   C15  119.62  3.000
 5UJ  H7   N5   C19  118.34  3.000
 5UJ  H7   N5   C20  117.81  3.000
 5UJ  C19  N5   C20  123.84  3.000
 5UJ  H8   C19  N4   120.04  3.000
 5UJ  H8   C19  N5   115.05  3.000
 5UJ  N4   C19  N5   124.91  3.000
 5UJ  C18  N4   C19  116.63  3.000
 5UJ  C14  C18  N4   120.99  3.000
 5UJ  C14  C18  C17  116.06  3.000
 5UJ  N4   C18  C17  122.92  3.000
 5UJ  N1   C14  C18  121.10  3.000
 5UJ  C18  C14  N3   123.20  3.000
 5UJ  N1   C14  N3   115.68  3.000
 5UJ  N2   N1   C12  112.28  3.000
 5UJ  N2   N1   C14  121.58  3.000
 5UJ  C12  N1   C14  125.92  3.000
 5UJ  H9   C12  C11  131.26  3.000
 5UJ  H9   C12  N1   121.82  3.000
 5UJ  C11  C12  N1   106.91  3.000
 5UJ  C13  N2   N1   104.91  3.000
 5UJ  H10  C13  C11  127.62  3.000
 5UJ  H10  C13  N2   120.19  3.000
 5UJ  C11  C13  N2   112.19  3.000
 5UJ  C10  C11  C13  127.73  3.000
 5UJ  C13  C11  C12  103.70  3.000
 5UJ  C10  C11  C12  128.54  3.000
 5UJ  H12  C10  H11  106.76  3.000
 5UJ  H12  C10  C9   110.44  3.000
 5UJ  H11  C10  C9   108.90  3.000
 5UJ  H12  C10  C11  108.87  3.000
 5UJ  H11  C10  C11  110.24  3.000
 5UJ  C9   C10  C11  111.53  3.000
 5UJ  C21  N    C8   110.59  3.000
 5UJ  C21  N    C9   112.27  3.000
 5UJ  C8   N    C9   111.51  3.000
 5UJ  H17  C8   H16  106.65  3.000
 5UJ  H17  C8   C7   109.25  3.000
 5UJ  H16  C8   C7   109.17  3.000
 5UJ  H17  C8   N    108.70  3.000
 5UJ  H16  C8   N    111.59  3.000
 5UJ  C7   C8   N    111.34  3.000
 5UJ  H19  C7   H18  107.06  3.000
 5UJ  H19  C7   C8   109.41  3.000
 5UJ  H18  C7   C8   109.15  3.000
 5UJ  H19  C7   C6   110.24  3.000
 5UJ  H18  C7   C6   110.08  3.000
 5UJ  C8   C7   C6   110.82  3.000
 5UJ  H21  C21  H20  106.42  3.000
 5UJ  H21  C21  C22  109.39  3.000
 5UJ  H20  C21  C22  108.78  3.000
 5UJ  H21  C21  N    111.13  3.000
 5UJ  H20  C21  N    109.61  3.000
 5UJ  C22  C21  N    111.36  3.000
 5UJ  H23  C22  H22  107.06  3.000
 5UJ  H23  C22  C21  109.13  3.000
 5UJ  H22  C22  C21  109.37  3.000
 5UJ  H23  C22  C6   110.17  3.000
 5UJ  H22  C22  C6   110.24  3.000
 5UJ  C21  C22  C6   110.79  3.000
 5UJ  H14  C9   H13  106.32  3.000
 5UJ  H14  C9   N    108.15  3.000
 5UJ  H13  C9   N    111.81  3.000
 5UJ  H14  C9   C10  107.84  3.000
 5UJ  H13  C9   C10  109.50  3.000
 5UJ  N    C9   C10  112.92  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
 5UJ  CONST_01  C1   C    C5   C4      0.00   0.0  0
 5UJ  CONST_02  C1   C2   C3   C4      0.00   0.0  0
 5UJ  CONST_03  C2   C1   C    C5      0.00   0.0  0
 5UJ  CONST_04  C2   C3   C4   C5      0.00   0.0  0
 5UJ  CONST_05  C    C5   C4   C3      0.00   0.0  0
 5UJ  CONST_06  C    C1   C2   C3      0.00   0.0  0
 5UJ  CONST_07  N1   C14  C18  C17   180.00   0.0  0
 5UJ  CONST_08  N3   C14  C18  C17     0.00   0.0  0
 5UJ  CONST_09  N3   C15  C16  C17     0.00   0.0  0
 5UJ  CONST_10  C14  C18  C17  C16     0.00   0.0  0
 5UJ  CONST_11  C14  N3   C15  C16     0.00   0.0  0
 5UJ  CONST_12  N1   C14  N3   C15   180.00   0.0  0
 5UJ  CONST_13  C18  C14  N3   C15     0.00   0.0  0
 5UJ  CONST_14  C18  C17  C16  C15     0.00   0.0  0
 5UJ  CONST_19  C11  C12  N1   C14   180.00   0.0  0
 5UJ  CONST_20  C13  N2   N1   C14   180.00   0.0  0
 5UJ  CONST_21  C13  C11  C12  N1      0.00   0.0  0
 5UJ  CONST_22  C11  C13  N2   N1      0.00   0.0  0
 5UJ  CONST_23  N2   C13  C11  C12     0.00   0.0  0
 5UJ  CONST_24  C13  N2   N1   C12     0.00   0.0  0
 5UJ  CONST_25  C11  C12  N1   N2      0.00   0.0  0
 5UJ  CONST_26  C6   C2   C3   C4    180.00   0.0  0
 5UJ  CONST_27  C    C1   C2   C6    180.00   0.0  0
 5UJ  CONST_28  N1   C14  C18  N4      0.00   0.0  0
 5UJ  CONST_29  N4   C19  N5   C20     0.00   0.0  0
 5UJ  CONST_30  C19  N5   C20  C17     0.00   0.0  0
 5UJ  CONST_31  C18  N4   C19  N5      0.00   0.0  0
 5UJ  CONST_32  CL   C    C5   C4    180.00   0.0  0
 5UJ  CONST_33  CL   C    C1   C2    180.00   0.0  0
 5UJ  CONST_34  CL1  C4   C3   C2    180.00   0.0  0
 5UJ  CONST_35  CL1  C4   C5   C     180.00   0.0  0
 5UJ  CONST_36  C10  C11  C12  N1    180.00   0.0  0
 5UJ  CONST_37  C10  C11  C13  N2    180.00   0.0  0
 5UJ  CONST_38  C19  N5   C20  O     180.00   0.0  0
 5UJ  CONST_39  H4   C1   C    C5    180.00   0.0  0
 5UJ  CONST_40  H3   C3   C4   C5    180.00   0.0  0
 5UJ  CONST_41  H1   C5   C4   C3    180.00   0.0  0
 5UJ  CONST_42  H5   C16  C17  C20     0.00   0.0  0
 5UJ  CONST_43  H6   C15  C16  C17   180.00   0.0  0
 5UJ  CONST_44  H9   C12  N1   C14     0.00   0.0  0
 5UJ  CONST_45  H10  C13  N2   N1    180.00   0.0  0
 5UJ  CONST_46  H8   C19  N5   C20   180.00   0.0  0
 5UJ  CONST_47  H7   N5   C20  C17   180.00   0.0  0
 5UJ  Var_01    N    C8   C7   C6     57.23  30.0  1
 5UJ  Var_02    N    C21  C22  C6    -57.23  30.0  1
 5UJ  Var_03    C22  C21  N    C8     60.05  30.0  1
 5UJ  Var_04    C21  N    C8   C7    -60.04  30.0  1
 5UJ  Var_05    C9   C10  C11  C12   -97.75  30.0  1
 5UJ  Var_06    N    C9   C10  C11  -179.49  30.0  1
 5UJ  Var_07    C8   N    C9   C10  -160.70  30.0  1

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
 5UJ  chir_01  C6  C2  C7  C22  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
 5UJ  plan-1  C14  0.020
 5UJ  plan-1  N1   0.020
 5UJ  plan-1  C12  0.020
 5UJ  plan-1  N2   0.020
 5UJ  plan-1  C13  0.020
 5UJ  plan-1  C11  0.020
 5UJ  plan-1  C10  0.020
 5UJ  plan-1  H9   0.020
 5UJ  plan-1  H10  0.020
 5UJ  plan-2  C4   0.020
 5UJ  plan-2  C5   0.020
 5UJ  plan-2  C6   0.020
 5UJ  plan-2  C3   0.020
 5UJ  plan-2  C2   0.020
 5UJ  plan-2  C1   0.020
 5UJ  plan-2  C    0.020
 5UJ  plan-2  CL1  0.020
 5UJ  plan-2  CL   0.020
 5UJ  plan-2  H1   0.020
 5UJ  plan-2  H3   0.020
 5UJ  plan-2  H4   0.020
 5UJ  plan-3  C20  0.020
 5UJ  plan-3  C17  0.020
 5UJ  plan-3  C16  0.020
 5UJ  plan-3  C15  0.020
 5UJ  plan-3  N3   0.020
 5UJ  plan-3  N5   0.020
 5UJ  plan-3  C19  0.020
 5UJ  plan-3  N4   0.020
 5UJ  plan-3  C18  0.020
 5UJ  plan-3  C14  0.020
 5UJ  plan-3  N1   0.020
 5UJ  plan-3  H6   0.020
 5UJ  plan-3  H7   0.020
 5UJ  plan-3  H8   0.020
 5UJ  plan-3  H5   0.020
 5UJ  plan-3  O    0.020

