# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 04:05:10 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: 8-[4-[2-[4-(4-chlorophenyl)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: Clc1ccc(cc1)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
 5UO  5UO  8-[4-[2-[4-(4-chlorophenyl)piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one  ligand  54  31  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5UO
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
 5UO  C1   C   CR16  0   0.151  -6.7456   2.0575   0.9116
 5UO  N2   N   NR5   0  -0.370  -3.8443  -0.2994  -0.8183
 5UO  C3   C   CR6   0   0.441  -5.1080  -0.7925  -0.4609
 5UO  C4   C   CR15  0  -0.065  -2.4159   0.9416  -1.7306
 5UO  C5   C   CR5   0  -0.147  -1.6906  -0.1467  -1.1925
 5UO  C6   C   CH2   0  -0.543  -0.2126  -0.3544  -1.1977
 5UO  C9   C   CH2   0  -0.415   4.0684   0.5889  -1.0392
 5UO  C10  C   CH1   0  -0.350   4.7173   0.8376   0.3234
 5UO  C11  C   CR6   0   0.210   6.1762   0.4653   0.3411
 5UO  C12  C   CR16  0  -0.348   7.1526   1.4124   0.6341
 5UO  C13  C   CR16  0  -0.192   8.5015   1.0829   0.6570
 5UO  C18  C   CH2   0  -0.283   2.4413   0.4562   1.3252
 5UO  C19  C   CR15  0   0.030  -2.6579  -0.9297  -0.6198
 5UO  C20  C   CR16  0  -0.063  -6.4711  -2.6219  -0.3422
 5UO  C21  C   CR16  0  -0.356  -7.5242  -1.8913   0.1564
 5UO  N1   N   N     0  -0.429  -5.7985   1.3630   0.4000
 5UO  C2   C   CR66  0   0.155  -6.0855   0.0562   0.1080
 5UO  C7   C   CH2   0  -0.250   0.4574   0.3620  -0.0238
 5UO  C8   C   CH2   0  -0.289   2.5862   0.9267  -1.0092
 5UO  C14  C   CR6   0  -0.063   8.8789  -0.2201   0.3806
 5UO  N3   N   N     0  -0.267  -3.7058   0.8390  -1.5043
 5UO  C15  C   CR16  0  -0.194   7.9317  -1.1887   0.0845
 5UO  CL   CL  CL    0  -0.137  10.5607  -0.6492   0.4039
 5UO  C16  C   CR16  0  -0.326   6.5907  -0.8381   0.0672
 5UO  C17  C   CH2   0  -0.415   3.9180   0.1008   1.4004
 5UO  N4   N   NT    0  -0.424   1.8930   0.1629   0.0131
 5UO  N5   N   N     0  -0.400  -5.2955  -2.0724  -0.6569
 5UO  C22  C   CR66  0  -0.017  -7.3237  -0.5321   0.3876
 5UO  C    C   CR6   0   0.580  -8.3919   0.2980   0.9537
 5UO  O    O   O     0  -0.434  -9.5121  -0.0909   1.2125
 5UO  N    N   NR16  0  -0.658  -7.9946   1.5951   1.1721
 5UO  H1   H   HCR6  0   0.307  -6.5771   3.0945   1.1725
 5UO  H2   H   HCR5  0   0.262  -2.0259   1.7851  -2.2821
 5UO  H3   H   HCH2  0   0.243   0.0207  -1.4198  -1.1409
 5UO  H4   H   HCH2  0   0.248   0.1925   0.0051  -2.1464
 5UO  H5   H   HCH2  0   0.238   4.5621   1.1875  -1.8081
 5UO  H6   H   HCH2  0   0.221   4.1899  -0.4604  -1.3256
 5UO  H7   H   HCH1  0   0.239   4.6424   1.9115   0.5332
 5UO  H8   H   HCR6  0   0.258   6.8609   2.4327   0.8523
 5UO  H9   H   HCR6  0   0.276   9.2441   1.8352   0.8871
 5UO  H10  H   HCH2  0   0.238   1.8926  -0.1220   2.0722
 5UO  H11  H   HCH2  0   0.187   2.3086   1.5207   1.5909
 5UO  H12  H   HCR5  0   0.292  -2.5939  -1.8630  -0.0845
 5UO  H13  H   HCR6  0   0.282  -6.5657  -3.6860  -0.5157
 5UO  H14  H   HCR6  0   0.286  -8.4728  -2.3612   0.3745
 5UO  H15  H   HCH2  0   0.195   0.1898   1.4328  -0.0457
 5UO  H16  H   HCH2  0   0.234   0.0340  -0.0383   0.9011
 5UO  H17  H   HCH2  0   0.189   2.4605   2.0130  -0.8469
 5UO  H18  H   HCH2  0   0.241   2.1547   0.7061  -1.9870
 5UO  H19  H   HCR6  0   0.276   8.2331  -2.2046  -0.1326
 5UO  H20  H   HCR6  0   0.256   5.8596  -1.6035  -0.1650
 5UO  H21  H   HCH2  0   0.221   4.0322  -0.9799   1.2750
 5UO  H22  H   HCH2  0   0.238   4.2998   0.3516   2.3928
 5UO  H24  H   HNR6  0   0.440  -8.6717   2.2370   1.5655

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
 5UO  CL   C14  single    1.736  0.020  1.736
 5UO  C14  C15  aromatic  1.387  0.020  1.387
 5UO  C14  C13  aromatic  1.384  0.020  1.384
 5UO  C15  C16  aromatic  1.386  0.020  1.386
 5UO  C13  C12  aromatic  1.389  0.020  1.389
 5UO  C16  C11  aromatic  1.395  0.020  1.395
 5UO  C12  C11  aromatic  1.391  0.020  1.391
 5UO  C11  C10  single    1.506  0.020  1.506
 5UO  C10  C17  single    1.530  0.020  1.530
 5UO  C10  C9   single    1.530  0.020  1.530
 5UO  C17  C18  single    1.521  0.020  1.521
 5UO  C9   C8   single    1.521  0.020  1.521
 5UO  C18  N4   single    1.452  0.020  1.452
 5UO  N4   C8   single    1.452  0.020  1.452
 5UO  N4   C7   single    1.450  0.020  1.450
 5UO  C7   C6   single    1.530  0.020  1.530
 5UO  C6   C5   single    1.492  0.020  1.492
 5UO  C5   C4   aromatic  1.414  0.020  1.414
 5UO  C5   C19  aromatic  1.370  0.020  1.370
 5UO  C4   N3   aromatic  1.314  0.020  1.314
 5UO  C19  N2   aromatic  1.358  0.020  1.358
 5UO  N3   N2   aromatic  1.336  0.020  1.336
 5UO  N2   C3   single    1.403  0.020  1.403
 5UO  N1   C1   double    1.281  0.020  1.281
 5UO  N1   C2   single    1.369  0.020  1.369
 5UO  C3   C2   aromatic  1.414  0.020  1.414
 5UO  C3   N5   aromatic  1.308  0.020  1.308
 5UO  C1   N    single    1.357  0.020  1.357
 5UO  C2   C22  aromatic  1.399  0.020  1.399
 5UO  N5   C20  aromatic  1.335  0.020  1.335
 5UO  N    C    single    1.374  0.020  1.374
 5UO  C22  C    single    1.466  0.020  1.466
 5UO  C22  C21  aromatic  1.393  0.020  1.393
 5UO  C20  C21  aromatic  1.375  0.020  1.375
 5UO  C    O    double    1.214  0.020  1.214
 5UO  C1   H1   single    0.930  0.020  1.080
 5UO  C4   H2   single    0.930  0.020  1.080
 5UO  C6   H3   single    0.970  0.020  1.090
 5UO  C6   H4   single    0.970  0.020  1.090
 5UO  C9   H5   single    0.970  0.020  1.090
 5UO  C9   H6   single    0.970  0.020  1.090
 5UO  C10  H7   single    0.970  0.020  1.090
 5UO  C12  H8   single    0.930  0.020  1.080
 5UO  C13  H9   single    0.930  0.020  1.080
 5UO  C18  H10  single    0.970  0.020  1.090
 5UO  C18  H11  single    0.970  0.020  1.090
 5UO  C19  H12  single    0.930  0.020  1.080
 5UO  C20  H13  single    0.930  0.020  1.080
 5UO  C21  H14  single    0.930  0.020  1.080
 5UO  C7   H15  single    0.970  0.020  1.090
 5UO  C7   H16  single    0.970  0.020  1.090
 5UO  C8   H17  single    0.970  0.020  1.090
 5UO  C8   H18  single    0.970  0.020  1.090
 5UO  C15  H19  single    0.930  0.020  1.080
 5UO  C16  H20  single    0.930  0.020  1.080
 5UO  C17  H21  single    0.970  0.020  1.090
 5UO  C17  H22  single    0.970  0.020  1.090
 5UO  N    H24  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
 5UO  H1   C1   N    115.05  3.000
 5UO  H1   C1   N1   120.04  3.000
 5UO  N    C1   N1   124.92  3.000
 5UO  N3   N2   C19  112.32  3.000
 5UO  N3   N2   C3   121.58  3.000
 5UO  C19  N2   C3   125.92  3.000
 5UO  N5   C3   C2   123.26  3.000
 5UO  N5   C3   N2   115.78  3.000
 5UO  C2   C3   N2   120.94  3.000
 5UO  H2   C4   N3   120.22  3.000
 5UO  H2   C4   C5   127.57  3.000
 5UO  N3   C4   C5   112.21  3.000
 5UO  C19  C5   C6   128.40  3.000
 5UO  C19  C5   C4   103.70  3.000
 5UO  C6   C5   C4   127.85  3.000
 5UO  H4   C6   H3   106.68  3.000
 5UO  H4   C6   C7   110.48  3.000
 5UO  H3   C6   C7   108.87  3.000
 5UO  H4   C6   C5   108.93  3.000
 5UO  H3   C6   C5   110.31  3.000
 5UO  C7   C6   C5   111.46  3.000
 5UO  H6   C9   H5   106.92  3.000
 5UO  H6   C9   C8   109.06  3.000
 5UO  H5   C9   C8   109.44  3.000
 5UO  H6   C9   C10  109.99  3.000
 5UO  H5   C9   C10  110.25  3.000
 5UO  C8   C9   C10  111.09  3.000
 5UO  H7   C10  C17  107.53  3.000
 5UO  H7   C10  C11  107.82  3.000
 5UO  C17  C10  C11  112.25  3.000
 5UO  H7   C10  C9   107.49  3.000
 5UO  C17  C10  C9   109.09  3.000
 5UO  C11  C10  C9   112.41  3.000
 5UO  C16  C11  C12  117.96  3.000
 5UO  C12  C11  C10  120.93  3.000
 5UO  C16  C11  C10  121.11  3.000
 5UO  H8   C12  C13  118.79  3.000
 5UO  H8   C12  C11  119.64  3.000
 5UO  C13  C12  C11  121.57  3.000
 5UO  H9   C13  C14  120.65  3.000
 5UO  H9   C13  C12  120.35  3.000
 5UO  C14  C13  C12  118.99  3.000
 5UO  H11  C18  H10  106.56  3.000
 5UO  H11  C18  N4   111.50  3.000
 5UO  H10  C18  N4   108.74  3.000
 5UO  H11  C18  C17  109.26  3.000
 5UO  H10  C18  C17  109.28  3.000
 5UO  N4   C18  C17  111.36  3.000
 5UO  H12  C19  C5   131.35  3.000
 5UO  H12  C19  N2   121.76  3.000
 5UO  C5   C19  N2   106.89  3.000
 5UO  H13  C20  N5   116.34  3.000
 5UO  H13  C20  C21  120.90  3.000
 5UO  N5   C20  C21  122.75  3.000
 5UO  H14  C21  C22  121.13  3.000
 5UO  H14  C21  C20  120.95  3.000
 5UO  C22  C21  C20  117.92  3.000
 5UO  C2   N1   C1   116.59  3.000
 5UO  C22  C2   N1   122.96  3.000
 5UO  C22  C2   C3   116.09  3.000
 5UO  N1   C2   C3   120.91  3.000
 5UO  H16  C7   H15  106.15  3.000
 5UO  H16  C7   N4   108.16  3.000
 5UO  H15  C7   N4   111.95  3.000
 5UO  H16  C7   C6   107.94  3.000
 5UO  H15  C7   C6   109.44  3.000
 5UO  N4   C7   C6   112.89  3.000
 5UO  H18  C8   H17  106.58  3.000
 5UO  H18  C8   N4   109.62  3.000
 5UO  H17  C8   N4   111.05  3.000
 5UO  H18  C8   C9   108.83  3.000
 5UO  H17  C8   C9   109.39  3.000
 5UO  N4   C8   C9   111.24  3.000
 5UO  CL   C14  C15  119.47  3.000
 5UO  C15  C14  C13  120.92  3.000
 5UO  CL   C14  C13  119.61  3.000
 5UO  C4   N3   N2   104.88  3.000
 5UO  H19  C15  C16  120.31  3.000
 5UO  H19  C15  C14  120.57  3.000
 5UO  C16  C15  C14  119.12  3.000
 5UO  H20  C16  C15  118.47  3.000
 5UO  H20  C16  C11  120.11  3.000
 5UO  C15  C16  C11  121.42  3.000
 5UO  H22  C17  H21  107.12  3.000
 5UO  H22  C17  C18  109.31  3.000
 5UO  H21  C17  C18  109.06  3.000
 5UO  H22  C17  C10  110.26  3.000
 5UO  H21  C17  C10  109.90  3.000
 5UO  C18  C17  C10  111.09  3.000
 5UO  C8   N4   C7   112.48  3.000
 5UO  C7   N4   C18  111.67  3.000
 5UO  C8   N4   C18  110.47  3.000
 5UO  C20  N5   C3   119.57  3.000
 5UO  C    C22  C2   118.93  3.000
 5UO  C    C22  C21  120.76  3.000
 5UO  C2   C22  C21  120.29  3.000
 5UO  N    C    O    122.37  3.000
 5UO  O    C    C22  124.98  3.000
 5UO  N    C    C22  112.65  3.000
 5UO  H24  N    C    117.83  3.000
 5UO  H24  N    C1   118.30  3.000
 5UO  C    N    C1   123.86  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
 5UO  CONST_01  C4   C5   C19  N2     0.00   0.0  0
 5UO  CONST_02  C5   C4   N3   N2     0.00   0.0  0
 5UO  CONST_03  C22  C2   C3   N2   180.00   0.0  0
 5UO  CONST_04  C20  N5   C3   N2   180.00   0.0  0
 5UO  CONST_05  C5   C19  N2   C3   180.00   0.0  0
 5UO  CONST_06  C4   N3   N2   C3   180.00   0.0  0
 5UO  CONST_07  C21  C22  C2   C3     0.00   0.0  0
 5UO  CONST_08  C21  C20  N5   C3     0.00   0.0  0
 5UO  CONST_09  C19  N2   N3   C4     0.00   0.0  0
 5UO  CONST_10  N3   N2   C19  C5     0.00   0.0  0
 5UO  CONST_11  C14  C15  C16  C11    0.00   0.0  0
 5UO  CONST_12  C14  C13  C12  C11    0.00   0.0  0
 5UO  CONST_13  C15  C14  C13  C12    0.00   0.0  0
 5UO  CONST_14  C15  C16  C11  C12    0.00   0.0  0
 5UO  CONST_15  C16  C15  C14  C13    0.00   0.0  0
 5UO  CONST_16  C16  C11  C12  C13    0.00   0.0  0
 5UO  CONST_17  N3   C4   C5   C19    0.00   0.0  0
 5UO  CONST_20  C2   C3   N5   C20    0.00   0.0  0
 5UO  CONST_21  C2   C22  C21  C20    0.00   0.0  0
 5UO  CONST_24  C22  C2   C3   N5     0.00   0.0  0
 5UO  CONST_25  C22  C21  C20  N5     0.00   0.0  0
 5UO  CONST_26  N1   C2   C3   N2     0.00   0.0  0
 5UO  CONST_27  C15  C16  C11  C10  180.00   0.0  0
 5UO  CONST_28  C13  C12  C11  C10  180.00   0.0  0
 5UO  CONST_29  C22  C    N    C1     0.00   0.0  0
 5UO  CONST_30  C    N    C1   N1     0.00   0.0  0
 5UO  CONST_31  N    C1   N1   C2     0.00   0.0  0
 5UO  CONST_32  C6   C5   C19  N2   180.00   0.0  0
 5UO  CONST_33  N3   C4   C5   C6   180.00   0.0  0
 5UO  CONST_34  CL   C14  C13  C12  180.00   0.0  0
 5UO  CONST_35  C16  C15  C14  CL   180.00   0.0  0
 5UO  CONST_36  O    C    N    C1   180.00   0.0  0
 5UO  CONST_37  H2   C4   N3   N2   180.00   0.0  0
 5UO  CONST_38  H12  C19  N2   C3     0.00   0.0  0
 5UO  CONST_39  H13  C20  N5   C3   180.00   0.0  0
 5UO  CONST_40  H20  C16  C11  C10    0.00   0.0  0
 5UO  CONST_41  H8   C12  C11  C10    0.00   0.0  0
 5UO  CONST_42  H19  C15  C16  C11  180.00   0.0  0
 5UO  CONST_43  H9   C13  C12  C11  180.00   0.0  0
 5UO  CONST_44  H14  C21  C22  C2   180.00   0.0  0
 5UO  CONST_45  H24  N    C1   N1   180.00   0.0  0
 5UO  CONST_46  H1   C1   N1   C2   180.00   0.0  0
 5UO  Var_01    C18  N4   C8   C9    60.35  30.0  1
 5UO  Var_02    N4   C18  C17  C10   57.06  30.0  1
 5UO  Var_03    N4   C8   C9   C10  -57.33  30.0  1
 5UO  Var_04    C17  C18  N4   C8   -60.25  30.0  1
 5UO  Var_05    C7   C6   C5   C4    84.67  30.0  2
 5UO  Var_06    N4   C7   C6   C5   179.07  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
 5UO  chir_01  C10  C11  C17  C9  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
 5UO  plan-1  N2   0.020
 5UO  plan-1  C3   0.020
 5UO  plan-1  C4   0.020
 5UO  plan-1  C5   0.020
 5UO  plan-1  C6   0.020
 5UO  plan-1  C19  0.020
 5UO  plan-1  N3   0.020
 5UO  plan-1  H2   0.020
 5UO  plan-1  H12  0.020
 5UO  plan-2  C10  0.020
 5UO  plan-2  C11  0.020
 5UO  plan-2  C12  0.020
 5UO  plan-2  C13  0.020
 5UO  plan-2  C14  0.020
 5UO  plan-2  C15  0.020
 5UO  plan-2  CL   0.020
 5UO  plan-2  C16  0.020
 5UO  plan-2  H8   0.020
 5UO  plan-2  H9   0.020
 5UO  plan-2  H19  0.020
 5UO  plan-2  H20  0.020
 5UO  plan-3  C1   0.020
 5UO  plan-3  N2   0.020
 5UO  plan-3  C3   0.020
 5UO  plan-3  C20  0.020
 5UO  plan-3  C21  0.020
 5UO  plan-3  N1   0.020
 5UO  plan-3  C2   0.020
 5UO  plan-3  N5   0.020
 5UO  plan-3  C22  0.020
 5UO  plan-3  C    0.020
 5UO  plan-3  O    0.020
 5UO  plan-3  N    0.020
 5UO  plan-3  H1   0.020
 5UO  plan-3  H13  0.020
 5UO  plan-3  H14  0.020
 5UO  plan-3  H24  0.020

