# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 04:43:26 2020
#   Inital geometry file: a 143 line input string
#   Ligand name: 8-[4-[2-[4-[(4-chlorophenyl)methyl]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(CC2CCN(CC2)CCc3cnn(c3)c4nccc5C(=O)NC=Nc45)cc1
#
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
 5UL  5UL  8-[4-[2-[4-[(4-chlorophenyl)methyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one  ligand  57  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 OK
;

data_comp_5UL
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
 5UL  C1   C   CR16  0  -0.197  -8.2767   0.5123  -0.8798
 5UL  C2   C   CR16  0  -0.322  -7.3870  -0.5535  -0.8477
 5UL  N3   N   N     0  -0.400   5.0957   2.0199  -1.0284
 5UL  C4   C   CH2   0  -0.503  -5.8318  -2.1210   0.3789
 5UL  C7   C   CH2   0  -0.278  -2.0078  -2.3822   0.9390
 5UL  C9   C   CH2   0  -0.547   0.4177  -0.6710  -1.3705
 5UL  C10  C   CR5   0  -0.146   1.9059  -0.5884  -1.2969
 5UL  C11  C   CR15  0   0.029   2.6865   0.4466  -0.8536
 5UL  C12  C   CR15  0  -0.064   2.8404  -1.6027  -1.6103
 5UL  C13  C   CR6   0   0.441   5.1123   0.7822  -0.6055
 5UL  C14  C   CR16  0  -0.063   6.1429   2.8123  -0.7867
 5UL  C16  C   CR66  0  -0.017   7.2857   1.0657   0.3408
 5UL  C17  C   CR66  0   0.155   6.1816   0.2307   0.1379
 5UL  C18  C   CR16  0   0.151   7.1141  -1.4499   1.3179
 5UL  C20  C   CH2   0  -0.282  -2.4224  -0.3729  -0.2882
 5UL  C23  C   CR16  0  -0.197  -8.0610   0.7367   1.5114
 5UL  C19  C   CR6   0   0.580   8.4409   0.5479   1.0811
 5UL  C15  C   CR16  0  -0.356   7.2706   2.3765  -0.1311
 5UL  N5   N   NR16  0  -0.658   8.2507  -0.7381   1.5257
 5UL  N4   N   N     0  -0.429   6.0989  -1.0337   0.6570
 5UL  N1   N   NR5   0  -0.370   3.9747   0.0183  -0.9051
 5UL  N2   N   N     0  -0.267   4.0771  -1.2274  -1.3767
 5UL  N    N   NT    0  -0.421  -1.5799  -1.5505  -0.1717
 5UL  C6   C   CH2   0  -0.424  -3.4473  -2.8394   0.7652
 5UL  C21  C   CH2   0  -0.415  -3.8795  -0.7528  -0.5056
 5UL  C5   C   CH1   0  -0.238  -4.3920  -1.6519   0.6134
 5UL  C3   C   CR6   0   0.152  -6.8218  -0.9921   0.3458
 5UL  C22  C   CR16  0  -0.313  -7.1766  -0.3307   1.5206
 5UL  C    C   CR6   0  -0.060  -8.6047   1.1503   0.3046
 5UL  CL   CL  CL    0  -0.138  -9.7162   2.4835   0.2806
 5UL  H1   H   HCR6  0   0.276  -8.7064   0.8370  -1.8181
 5UL  H2   H   HCR6  0   0.257  -7.1334  -1.0505  -1.7764
 5UL  H3   H   HCH2  0   0.239  -5.8761  -2.6837  -0.5585
 5UL  H4   H   HCH2  0   0.247  -6.1032  -2.8225   1.1735
 5UL  H5   H   HCH2  0   0.233  -1.3496  -3.2527   0.9948
 5UL  H6   H   HCH2  0   0.182  -1.9119  -1.8509   1.9036
 5UL  H7   H   HCH2  0   0.250   0.0071   0.3153  -1.5933
 5UL  H8   H   HCH2  0   0.241   0.1255  -1.3275  -2.1940
 5UL  H9   H   HCR5  0   0.292   2.4289   1.4315  -0.4995
 5UL  H10  H   HCR5  0   0.262   2.6363  -2.5846  -2.0128
 5UL  H11  H   HCR6  0   0.282   6.0699   3.8289  -1.1515
 5UL  H12  H   HCR6  0   0.307   7.1038  -2.4366   1.7632
 5UL  H13  H   HCH2  0   0.183  -2.3402   0.2641   0.6116
 5UL  H14  H   HCH2  0   0.238  -2.0832   0.2327  -1.1299
 5UL  H15  H   HCR6  0   0.276  -8.3237   1.2369   2.4339
 5UL  H16  H   HCR6  0   0.286   8.1125   3.0363   0.0230
 5UL  H17  H   HNR6  0   0.440   8.9965  -1.1701   2.0567
 5UL  H21  H   HCH2  0   0.214  -3.5193  -3.4768  -0.1224
 5UL  H22  H   HCH2  0   0.230  -3.7367  -3.4513   1.6235
 5UL  H23  H   HCH2  0   0.233  -4.4803   0.1568  -0.5780
 5UL  H24  H   HCH2  0   0.211  -3.9734  -1.2747  -1.4643
 5UL  H25  H   HCH1  0   0.219  -4.3701  -1.0767   1.5494
 5UL  H26  H   HCR6  0   0.257  -6.7586  -0.6537   2.4669
 5UL  C8   C   CH2   0  -0.247  -0.1717  -1.2252  -0.0710
 5UL  O    O   O     0  -0.434   9.4638   1.1656   1.2946
 5UL  H18  H   HCH2  0   0.233   0.3645  -2.1445   0.1802
 5UL  H19  H   HCH2  0   0.191   0.0320  -0.5146   0.7493

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
 5UL  CL   C    single    1.736  0.020  1.736
 5UL  C23  C    aromatic  1.387  0.020  1.387
 5UL  C23  C22  aromatic  1.386  0.020  1.386
 5UL  C    C1   aromatic  1.385  0.020  1.385
 5UL  C22  C3   aromatic  1.394  0.020  1.394
 5UL  C1   C2   aromatic  1.389  0.020  1.389
 5UL  C3   C2   aromatic  1.392  0.020  1.392
 5UL  C3   C4   single    1.502  0.020  1.502
 5UL  C4   C5   single    1.532  0.020  1.532
 5UL  C5   C6   single    1.525  0.020  1.525
 5UL  C5   C21  single    1.524  0.020  1.524
 5UL  C6   C7   single    1.520  0.020  1.520
 5UL  C21  C20  single    1.521  0.020  1.521
 5UL  C7   N    single    1.452  0.020  1.452
 5UL  C20  N    single    1.453  0.020  1.453
 5UL  N    C8   single    1.449  0.020  1.449
 5UL  C8   C9   single    1.531  0.020  1.531
 5UL  C9   C10  single    1.492  0.020  1.492
 5UL  C10  C12  aromatic  1.414  0.020  1.414
 5UL  C10  C11  aromatic  1.370  0.020  1.370
 5UL  C12  N2   aromatic  1.313  0.020  1.313
 5UL  C11  N1   aromatic  1.359  0.020  1.359
 5UL  N2   N1   aromatic  1.336  0.020  1.336
 5UL  N1   C13  single    1.403  0.020  1.403
 5UL  N4   C17  single    1.369  0.020  1.369
 5UL  N4   C18  double    1.281  0.020  1.281
 5UL  C13  C17  aromatic  1.414  0.020  1.414
 5UL  C13  N3   aromatic  1.308  0.020  1.308
 5UL  C17  C16  aromatic  1.399  0.020  1.399
 5UL  N3   C14  aromatic  1.335  0.020  1.335
 5UL  C18  N5   single    1.357  0.020  1.357
 5UL  N5   C19  single    1.374  0.020  1.374
 5UL  C14  C15  aromatic  1.375  0.020  1.375
 5UL  C16  C15  aromatic  1.393  0.020  1.393
 5UL  C16  C19  single    1.467  0.020  1.467
 5UL  C19  O    double    1.214  0.020  1.214
 5UL  C1   H1   single    0.930  0.020  1.080
 5UL  C2   H2   single    0.930  0.020  1.080
 5UL  C4   H3   single    0.970  0.020  1.090
 5UL  C4   H4   single    0.970  0.020  1.090
 5UL  C7   H5   single    0.970  0.020  1.090
 5UL  C7   H6   single    0.970  0.020  1.090
 5UL  C9   H7   single    0.970  0.020  1.090
 5UL  C9   H8   single    0.970  0.020  1.090
 5UL  C11  H9   single    0.930  0.020  1.080
 5UL  C12  H10  single    0.930  0.020  1.080
 5UL  C14  H11  single    0.930  0.020  1.080
 5UL  C18  H12  single    0.930  0.020  1.080
 5UL  C20  H13  single    0.970  0.020  1.090
 5UL  C20  H14  single    0.970  0.020  1.090
 5UL  C23  H15  single    0.930  0.020  1.080
 5UL  C15  H16  single    0.930  0.020  1.080
 5UL  N5   H17  single    0.860  0.020  1.020
 5UL  C8   H18  single    0.970  0.020  1.090
 5UL  C8   H19  single    0.970  0.020  1.090
 5UL  C6   H21  single    0.970  0.020  1.090
 5UL  C6   H22  single    0.970  0.020  1.090
 5UL  C21  H23  single    0.970  0.020  1.090
 5UL  C21  H24  single    0.970  0.020  1.090
 5UL  C5   H25  single    0.970  0.020  1.090
 5UL  C22  H26  single    0.930  0.020  1.080

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
 5UL  H1   C1   C    120.63  3.000
 5UL  H1   C1   C2   120.32  3.000
 5UL  C    C1   C2   119.05  3.000
 5UL  H2   C2   C3   119.71  3.000
 5UL  H2   C2   C1   118.83  3.000
 5UL  C3   C2   C1   121.46  3.000
 5UL  C14  N3   C13  119.54  3.000
 5UL  H4   C4   H3   106.40  3.000
 5UL  H4   C4   C3   109.54  3.000
 5UL  H3   C4   C3   109.94  3.000
 5UL  H4   C4   C5   108.56  3.000
 5UL  H3   C4   C5   109.06  3.000
 5UL  C3   C4   C5   113.12  3.000
 5UL  H6   C7   H5   106.63  3.000
 5UL  H6   C7   C6   109.05  3.000
 5UL  H5   C7   C6   109.67  3.000
 5UL  H6   C7   N    111.50  3.000
 5UL  H5   C7   N    108.53  3.000
 5UL  C6   C7   N    111.34  3.000
 5UL  H8   C9   H7   106.76  3.000
 5UL  H8   C9   C8   108.61  3.000
 5UL  H7   C9   C8   110.83  3.000
 5UL  H8   C9   C10  109.70  3.000
 5UL  H7   C9   C10  109.59  3.000
 5UL  C8   C9   C10  111.24  3.000
 5UL  C12  C10  C11  103.71  3.000
 5UL  C11  C10  C9   128.75  3.000
 5UL  C12  C10  C9   127.47  3.000
 5UL  H9   C11  N1   121.81  3.000
 5UL  H9   C11  C10  131.34  3.000
 5UL  N1   C11  C10  106.85  3.000
 5UL  H10  C12  N2   120.25  3.000
 5UL  H10  C12  C10  127.54  3.000
 5UL  N2   C12  C10  112.20  3.000
 5UL  N1   C13  C17  120.87  3.000
 5UL  C17  C13  N3   123.26  3.000
 5UL  N1   C13  N3   115.85  3.000
 5UL  H11  C14  C15  120.90  3.000
 5UL  H11  C14  N3   116.32  3.000
 5UL  C15  C14  N3   122.77  3.000
 5UL  C15  C16  C19  120.78  3.000
 5UL  C19  C16  C17  118.95  3.000
 5UL  C15  C16  C17  120.26  3.000
 5UL  N4   C17  C16  122.94  3.000
 5UL  C16  C17  C13  116.11  3.000
 5UL  N4   C17  C13  120.91  3.000
 5UL  H12  C18  N4   120.06  3.000
 5UL  H12  C18  N5   115.02  3.000
 5UL  N4   C18  N5   124.92  3.000
 5UL  H14  C20  H13  106.56  3.000
 5UL  H14  C20  C21  109.04  3.000
 5UL  H13  C20  C21  109.35  3.000
 5UL  H14  C20  N    109.36  3.000
 5UL  H13  C20  N    111.02  3.000
 5UL  C21  C20  N    111.37  3.000
 5UL  H15  C23  C    120.60  3.000
 5UL  H15  C23  C22  120.35  3.000
 5UL  C    C23  C22  119.05  3.000
 5UL  N5   C19  O    122.41  3.000
 5UL  O    C19  C16  124.95  3.000
 5UL  N5   C19  C16  112.63  3.000
 5UL  H16  C15  C16  121.18  3.000
 5UL  H16  C15  C14  120.88  3.000
 5UL  C16  C15  C14  117.94  3.000
 5UL  H17  N5   C19  117.86  3.000
 5UL  H17  N5   C18  118.26  3.000
 5UL  C19  N5   C18  123.87  3.000
 5UL  C18  N4   C17  116.60  3.000
 5UL  N2   N1   C13  121.41  3.000
 5UL  C13  N1   C11  126.10  3.000
 5UL  N2   N1   C11  112.33  3.000
 5UL  N1   N2   C12  104.90  3.000
 5UL  C8   N    C20  112.78  3.000
 5UL  C8   N    C7   111.22  3.000
 5UL  C20  N    C7   110.78  3.000
 5UL  H22  C6   H21  107.05  3.000
 5UL  H22  C6   C5   110.49  3.000
 5UL  H21  C6   C5   109.38  3.000
 5UL  H22  C6   C7   109.23  3.000
 5UL  H21  C6   C7   109.26  3.000
 5UL  C5   C6   C7   111.33  3.000
 5UL  H24  C21  H23  106.95  3.000
 5UL  H24  C21  C5   109.43  3.000
 5UL  H23  C21  C5   110.78  3.000
 5UL  H24  C21  C20  109.03  3.000
 5UL  H23  C21  C20  109.16  3.000
 5UL  C5   C21  C20  111.37  3.000
 5UL  H25  C5   C21  108.06  3.000
 5UL  H25  C5   C6   108.09  3.000
 5UL  C21  C5   C6   108.91  3.000
 5UL  H25  C5   C4   108.01  3.000
 5UL  C21  C5   C4   112.59  3.000
 5UL  C6   C5   C4   111.03  3.000
 5UL  C22  C3   C4   120.39  3.000
 5UL  C4   C3   C2   121.57  3.000
 5UL  C22  C3   C2   118.02  3.000
 5UL  H26  C22  C3   119.75  3.000
 5UL  H26  C22  C23  118.77  3.000
 5UL  C3   C22  C23  121.48  3.000
 5UL  CL   C    C23  119.48  3.000
 5UL  C23  C    C1   120.93  3.000
 5UL  CL   C    C1   119.58  3.000
 5UL  H19  C8   H18  106.25  3.000
 5UL  H19  C8   N    112.05  3.000
 5UL  H18  C8   N    107.69  3.000
 5UL  H19  C8   C9   109.06  3.000
 5UL  H18  C8   C9   108.09  3.000
 5UL  N    C8   C9   113.37  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
 5UL  CONST_01  C22  C23  C    C1      0.00   0.0  0
 5UL  CONST_02  C22  C3   C2   C1      0.00   0.0  0
 5UL  CONST_03  C23  C    C1   C2      0.00   0.0  0
 5UL  CONST_04  C23  C22  C3   C2      0.00   0.0  0
 5UL  CONST_07  C16  C17  C13  N3      0.00   0.0  0
 5UL  CONST_08  C16  C15  C14  N3      0.00   0.0  0
 5UL  CONST_09  N1   N2   C12  C10     0.00   0.0  0
 5UL  CONST_10  N2   N1   C11  C10     0.00   0.0  0
 5UL  CONST_11  C13  N1   C11  C10   180.00   0.0  0
 5UL  CONST_12  N2   C12  C10  C11     0.00   0.0  0
 5UL  CONST_13  C12  N2   N1   C11     0.00   0.0  0
 5UL  CONST_15  N1   C11  C10  C12     0.00   0.0  0
 5UL  CONST_16  C13  N1   N2   C12   180.00   0.0  0
 5UL  CONST_17  C15  C16  C17  C13     0.00   0.0  0
 5UL  CONST_18  C15  C14  N3   C13     0.00   0.0  0
 5UL  CONST_19  N1   C13  N3   C14   180.00   0.0  0
 5UL  CONST_20  C17  C13  N3   C14     0.00   0.0  0
 5UL  CONST_21  C17  C16  C15  C14     0.00   0.0  0
 5UL  CONST_22  N1   C13  C17  C16   180.00   0.0  0
 5UL  CONST_24  C    C23  C22  C3      0.00   0.0  0
 5UL  CONST_25  C    C1   C2   C3      0.00   0.0  0
 5UL  CONST_26  N1   C13  C17  N4      0.00   0.0  0
 5UL  CONST_27  C18  N5   C19  C16     0.00   0.0  0
 5UL  CONST_28  N5   C18  N4   C17     0.00   0.0  0
 5UL  CONST_29  N4   C18  N5   C19     0.00   0.0  0
 5UL  CONST_30  C4   C3   C2   C1    180.00   0.0  0
 5UL  CONST_31  CL   C    C1   C2    180.00   0.0  0
 5UL  CONST_32  C23  C22  C3   C4    180.00   0.0  0
 5UL  CONST_33  N2   C12  C10  C9    180.00   0.0  0
 5UL  CONST_34  N1   C11  C10  C9    180.00   0.0  0
 5UL  CONST_35  CL   C    C23  C22   180.00   0.0  0
 5UL  CONST_36  O    C19  N5   C18   180.00   0.0  0
 5UL  CONST_37  H15  C23  C    C1    180.00   0.0  0
 5UL  CONST_38  H26  C22  C3   C2    180.00   0.0  0
 5UL  CONST_39  H16  C15  C14  N3    180.00   0.0  0
 5UL  CONST_40  H10  C12  C10  C11   180.00   0.0  0
 5UL  CONST_41  H9   C11  C10  C12   180.00   0.0  0
 5UL  CONST_42  H11  C14  N3   C13   180.00   0.0  0
 5UL  CONST_43  H1   C1   C    C23   180.00   0.0  0
 5UL  CONST_44  H2   C2   C3   C22   180.00   0.0  0
 5UL  CONST_45  H17  N5   C19  C16   180.00   0.0  0
 5UL  CONST_46  H12  C18  N4   C17   180.00   0.0  0
 5UL  Var_01    C21  C20  N    C7    -59.24  30.0  1
 5UL  Var_02    C6   C7   N    C20    59.38  30.0  1
 5UL  Var_03    C5   C6   C7   N     -57.05  30.0  1
 5UL  Var_04    C5   C21  C20  N      56.79  30.0  1
 5UL  Var_05    C5   C4   C3   C2    105.61  30.0  2
 5UL  Var_06    C9   C8   N    C7    165.01  30.0  3
 5UL  Var_07    N    C8   C9   C10  -169.57  30.0  1
 5UL  Var_08    C8   C9   C10  C11   -89.33  30.0  3

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
 5UL  chir_01  C5  C4  C6  C21  negativ

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
 5UL  plan-1  C9   0.020
 5UL  plan-1  C10  0.020
 5UL  plan-1  C11  0.020
 5UL  plan-1  C12  0.020
 5UL  plan-1  C13  0.020
 5UL  plan-1  N1   0.020
 5UL  plan-1  N2   0.020
 5UL  plan-1  H9   0.020
 5UL  plan-1  H10  0.020
 5UL  plan-2  C1   0.020
 5UL  plan-2  C2   0.020
 5UL  plan-2  C4   0.020
 5UL  plan-2  C23  0.020
 5UL  plan-2  C3   0.020
 5UL  plan-2  C22  0.020
 5UL  plan-2  C    0.020
 5UL  plan-2  CL   0.020
 5UL  plan-2  H1   0.020
 5UL  plan-2  H2   0.020
 5UL  plan-2  H15  0.020
 5UL  plan-2  H26  0.020
 5UL  plan-3  N3   0.020
 5UL  plan-3  C13  0.020
 5UL  plan-3  C14  0.020
 5UL  plan-3  C16  0.020
 5UL  plan-3  C17  0.020
 5UL  plan-3  C18  0.020
 5UL  plan-3  C19  0.020
 5UL  plan-3  C15  0.020
 5UL  plan-3  N5   0.020
 5UL  plan-3  N4   0.020
 5UL  plan-3  N1   0.020
 5UL  plan-3  H11  0.020
 5UL  plan-3  H12  0.020
 5UL  plan-3  H16  0.020
 5UL  plan-3  H17  0.020
 5UL  plan-3  O    0.020

