# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 05:53:59 2022
#   Inital geometry file: a 136 line input string
#   Ligand name: 1-(3-fluorophenyl)-N-[trans-4-(2-hydroxypropan-2-yl)cyclohexyl]-1,4,6,7-tetrahydro-5H-pyrazolo[4,3-c]pyridine-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(O)[C@@H]1CC[C@H](CC1)NC(=O)N2CCc3n(ncc3C2)c4cccc(F)c4
#
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
 VH4  VH4  1-(3-fluorophenyl)-N-[trans-4-(2-hydroxypropan-2-yl)cyclohexyl]-1,4,6,7-tetrahydro-5H-pyrazolo[4,3-c]pyridine-5-carboxamide  ligand  58  29  .  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_VH4
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
 VH4  C17  C  CH2   0  -0.439  48.9688   0.9065   99.0317
 VH4  C20  C  CH1   0  -0.044  48.9175   2.0149  100.0746
 VH4  C22  C  CH2   0  -0.425  47.9261   1.6491  101.1745
 VH4  C05  C  CT    0   0.222  48.5837  -2.2137  101.3765
 VH4  C06  C  CH3   0  -0.679  48.5578  -3.2971  100.2947
 VH4  C12  C  CH1   0  -0.209  48.3091  -0.8215  100.7676
 VH4  C14  C  CH2   0  -0.437  49.3042  -0.4383   99.6674
 VH4  C25  C  CH2   0  -0.437  48.2593   0.3020  101.8089
 VH4  C33  C  CH2   0  -0.379  48.0277   5.5222   97.8921
 VH4  C36  C  CH2   0  -0.518  49.1207   5.2881   96.8441
 VH4  C39  C  CR5   0   0.430  50.2150   6.2537   97.1473
 VH4  C40  C  CR5   0  -0.198  50.3124   6.9839   98.3056
 VH4  C41  C  CH2   0  -0.371  49.3392   6.8245   99.4328
 VH4  C44  C  CR15  0  -0.078  51.4300   7.8146   98.1099
 VH4  C48  C  CR6   0   0.356  51.5637   6.2205   95.0535
 VH4  C49  C  CR16  0  -0.296  52.0056   7.1436   94.1111
 VH4  C51  C  CR16  0  -0.236  52.3255   6.7110   92.8344
 VH4  C53  C  CR16  0  -0.413  52.1976   5.3757   92.4753
 VH4  C55  C  CR6   0   0.539  51.7556   4.4878   93.4350
 VH4  C57  C  CR16  0  -0.456  51.4473   4.8754   94.7244
 VH4  F56  F  F     0  -0.311  51.6350   3.1907   93.1193
 VH4  N28  N  NH1   0  -0.686  48.5939   3.2740   99.4332
 VH4  N32  N  NT    0  -0.492  48.5856   5.5941   99.2349
 VH4  N46  N  N     0  -0.277  51.9813   7.6088   96.9328
 VH4  N47  N  NR5   0  -0.467  51.2420   6.6535   96.3527
 VH4  O10  O  OH1   0  -0.677  49.8724  -2.1548  101.9730
 VH4  O31  O  O     0  -0.530  49.8238   4.5448  100.8352
 VH4  H19  H  HCH2  0   0.214  47.9982   0.8404   98.5257
 VH4  H18  H  HCH2  0   0.235  49.7084   1.1531   98.2656
 VH4  H21  H  HCH1  0   0.234  49.9122   2.1153  100.5156
 VH4  H23  H  HCH2  0   0.231  47.9143   2.4296  101.9394
 VH4  H24  H  HCH2  0   0.209  46.9191   1.6126  100.7433
 VH4  H03  H  HCH3  0   0.227  47.6987  -3.5828  102.8060
 VH4  H04  H  HCH3  0   0.234  47.5618  -1.8960  103.2877
 VH4  H02  H  HCH3  0   0.221  46.5262  -2.5379  102.0114
 VH4  H09  H  HCH3  0   0.227  48.6706  -4.2870  100.7436
 VH4  H07  H  HCH3  0   0.221  47.6109  -3.2911   99.7524
 VH4  H08  H  HCH3  0   0.234  49.3616  -3.1719   99.5702
 VH4  H13  H  HCH1  0   0.213  47.3143  -0.8848  100.3060
 VH4  H15  H  HCH2  0   0.235  49.3276  -1.1930   98.8799
 VH4  H16  H  HCH2  0   0.217  50.3148  -0.3937  100.0849
 VH4  H27  H  HCH2  0   0.216  49.2236   0.3712  102.3216
 VH4  H26  H  HCH2  0   0.233  47.5147   0.0883  102.5774
 VH4  H35  H  HCH2  0   0.279  47.5352   6.4764   97.6977
 VH4  H34  H  HCH2  0   0.274  47.2428   4.7712   97.8153
 VH4  H37  H  HCH2  0   0.277  48.7187   5.4379   95.8394
 VH4  H38  H  HCH2  0   0.266  49.4694   4.2534   96.8969
 VH4  H43  H  HCH2  0   0.274  49.8399   6.7993  100.3968
 VH4  H42  H  HCH2  0   0.260  48.6372   7.6631   99.4621
 VH4  H45  H  HCR5  0   0.262  51.8535   8.5429   98.7860
 VH4  H50  H  HCR6  0   0.275  52.0941   8.1882   94.3737
 VH4  H52  H  HCR6  0   0.275  52.6691   7.4276   92.1008
 VH4  H54  H  HCR6  0   0.284  52.4376   5.0365   91.4765
 VH4  H58  H  HCR6  0   0.297  51.1525   4.1328   95.4529
 VH4  H29  H  HNH1  0   0.394  47.8523   3.2364   98.7540
 VH4  H11  H  HOH1  0   0.440  50.0649  -3.0162  102.3577
 VH4  C01  C  CH3   0  -0.679  47.5328  -2.5696  102.4318
 VH4  C30  C  C     0   0.731  49.0486   4.4654   99.8886

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
 VH4  C53  C51  aromatic  1.389  0.020  1.389
 VH4  C53  C55  aromatic  1.380  0.020  1.380
 VH4  F56  C55  single    1.340  0.020  1.340
 VH4  C51  C49  aromatic  1.385  0.020  1.385
 VH4  C55  C57  aromatic  1.381  0.020  1.381
 VH4  C49  C48  aromatic  1.391  0.020  1.391
 VH4  C57  C48  aromatic  1.390  0.020  1.390
 VH4  C48  N47  single    1.407  0.020  1.407
 VH4  N47  N46  aromatic  1.340  0.020  1.340
 VH4  N47  C39  aromatic  1.359  0.020  1.359
 VH4  C36  C39  single    1.491  0.020  1.491
 VH4  C36  C33  single    1.532  0.020  1.532
 VH4  N46  C44  aromatic  1.316  0.020  1.316
 VH4  C39  C40  aromatic  1.373  0.020  1.373
 VH4  C33  N32  single    1.456  0.020  1.456
 VH4  C44  C40  aromatic  1.406  0.020  1.406
 VH4  C40  C41  single    1.498  0.020  1.498
 VH4  N32  C41  single    1.456  0.020  1.456
 VH4  N32  C30  single    1.384  0.020  1.384
 VH4  N28  C30  single    1.354  0.020  1.354
 VH4  N28  C20  single    1.450  0.020  1.450
 VH4  C17  C20  single    1.523  0.020  1.523
 VH4  C17  C14  single    1.525  0.020  1.525
 VH4  C30  O31  double    1.226  0.020  1.226
 VH4  C20  C22  single    1.525  0.020  1.525
 VH4  C14  C12  single    1.532  0.020  1.532
 VH4  C22  C25  single    1.526  0.020  1.526
 VH4  C12  C25  single    1.533  0.020  1.533
 VH4  C12  C05  single    1.544  0.020  1.544
 VH4  C06  C05  single    1.531  0.020  1.531
 VH4  C05  C01  single    1.531  0.020  1.531
 VH4  C05  O10  single    1.421  0.020  1.421
 VH4  C17  H19  single    0.970  0.020  1.090
 VH4  C17  H18  single    0.970  0.020  1.090
 VH4  C20  H21  single    0.970  0.020  1.090
 VH4  C22  H23  single    0.970  0.020  1.090
 VH4  C22  H24  single    0.970  0.020  1.090
 VH4  C01  H03  single    0.970  0.020  1.090
 VH4  C01  H04  single    0.970  0.020  1.090
 VH4  C01  H02  single    0.970  0.020  1.090
 VH4  C06  H09  single    0.970  0.020  1.090
 VH4  C06  H07  single    0.970  0.020  1.090
 VH4  C06  H08  single    0.970  0.020  1.090
 VH4  C12  H13  single    0.970  0.020  1.090
 VH4  C14  H15  single    0.970  0.020  1.090
 VH4  C14  H16  single    0.970  0.020  1.090
 VH4  C25  H27  single    0.970  0.020  1.090
 VH4  C25  H26  single    0.970  0.020  1.090
 VH4  C33  H35  single    0.970  0.020  1.090
 VH4  C33  H34  single    0.970  0.020  1.090
 VH4  C36  H37  single    0.970  0.020  1.090
 VH4  C36  H38  single    0.970  0.020  1.090
 VH4  C41  H43  single    0.970  0.020  1.090
 VH4  C41  H42  single    0.970  0.020  1.090
 VH4  C44  H45  single    0.930  0.020  1.080
 VH4  C49  H50  single    0.930  0.020  1.080
 VH4  C51  H52  single    0.930  0.020  1.080
 VH4  C53  H54  single    0.930  0.020  1.080
 VH4  C57  H58  single    0.930  0.020  1.080
 VH4  N28  H29  single    0.860  0.020  1.020
 VH4  O10  H11  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
 VH4  H18  C17  H19  106.80  3.000
 VH4  H18  C17  C14  110.02  3.000
 VH4  H19  C17  C14  109.51  3.000
 VH4  H18  C17  C20  109.79  3.000
 VH4  H19  C17  C20  109.27  3.000
 VH4  C14  C17  C20  111.34  3.000
 VH4  H21  C20  N28  107.57  3.000
 VH4  H21  C20  C22  108.83  3.000
 VH4  N28  C20  C22  112.47  3.000
 VH4  H21  C20  C17  108.22  3.000
 VH4  C22  C20  C17  109.95  3.000
 VH4  N28  C20  C17  109.68  3.000
 VH4  H24  C22  H23  106.81  3.000
 VH4  H24  C22  C25  109.56  3.000
 VH4  H23  C22  C25  109.99  3.000
 VH4  H24  C22  C20  108.76  3.000
 VH4  H23  C22  C20  109.91  3.000
 VH4  C25  C22  C20  111.69  3.000
 VH4  O10  C05  C12  106.82  3.000
 VH4  O10  C05  C06  109.94  3.000
 VH4  C12  C05  C06  110.88  3.000
 VH4  O10  C05  C01  110.04  3.000
 VH4  C06  C05  C01  108.11  3.000
 VH4  C12  C05  C01  111.06  3.000
 VH4  H08  C06  H07  108.01  3.000
 VH4  H08  C06  H09  107.53  3.000
 VH4  H07  C06  H09  107.38  3.000
 VH4  H08  C06  C05  112.09  3.000
 VH4  H07  C06  C05  111.21  3.000
 VH4  H09  C06  C05  110.43  3.000
 VH4  H13  C12  C25  107.35  3.000
 VH4  H13  C12  C14  107.51  3.000
 VH4  C25  C12  C14  109.00  3.000
 VH4  H13  C12  C05  105.95  3.000
 VH4  C25  C12  C05  113.50  3.000
 VH4  C14  C12  C05  113.15  3.000
 VH4  H16  C14  H15  106.49  3.000
 VH4  H16  C14  C12  109.63  3.000
 VH4  H15  C14  C12  111.05  3.000
 VH4  H16  C14  C17  109.04  3.000
 VH4  H15  C14  C17  108.30  3.000
 VH4  C12  C14  C17  112.15  3.000
 VH4  H26  C25  H27  106.48  3.000
 VH4  H26  C25  C12  110.92  3.000
 VH4  H27  C25  C12  109.64  3.000
 VH4  H26  C25  C22  108.46  3.000
 VH4  H27  C25  C22  109.35  3.000
 VH4  C12  C25  C22  111.83  3.000
 VH4  H34  C33  H35  105.37  3.000
 VH4  H34  C33  N32  112.05  3.000
 VH4  H35  C33  N32  107.10  3.000
 VH4  H34  C33  C36  111.13  3.000
 VH4  H35  C33  C36  109.49  3.000
 VH4  N32  C33  C36  111.42  3.000
 VH4  H38  C36  H37  106.95  3.000
 VH4  H38  C36  C39  111.66  3.000
 VH4  H37  C36  C39  111.62  3.000
 VH4  H38  C36  C33  109.82  3.000
 VH4  H37  C36  C33  110.22  3.000
 VH4  C39  C36  C33  106.60  3.000
 VH4  N47  C39  C40  106.46  3.000
 VH4  C40  C39  C36  124.63  3.000
 VH4  N47  C39  C36  128.80  3.000
 VH4  C44  C40  C41  133.16  3.000
 VH4  C41  C40  C39  122.16  3.000
 VH4  C44  C40  C39  104.67  3.000
 VH4  H42  C41  H43  106.84  3.000
 VH4  H42  C41  N32  108.61  3.000
 VH4  H43  C41  N32  109.84  3.000
 VH4  H42  C41  C40  110.83  3.000
 VH4  H43  C41  C40  111.76  3.000
 VH4  N32  C41  C40  108.90  3.000
 VH4  H45  C44  N46  120.07  3.000
 VH4  H45  C44  C40  128.52  3.000
 VH4  N46  C44  C40  111.41  3.000
 VH4  N47  C48  C57  119.83  3.000
 VH4  N47  C48  C49  119.61  3.000
 VH4  C57  C48  C49  120.56  3.000
 VH4  H50  C49  C51  120.45  3.000
 VH4  H50  C49  C48  120.18  3.000
 VH4  C51  C49  C48  119.36  3.000
 VH4  H52  C51  C53  119.40  3.000
 VH4  H52  C51  C49  119.44  3.000
 VH4  C53  C51  C49  121.15  3.000
 VH4  H54  C53  C55  120.76  3.000
 VH4  H54  C53  C51  121.32  3.000
 VH4  C55  C53  C51  117.92  3.000
 VH4  F56  C55  C57  118.12  3.000
 VH4  C57  C55  C53  122.69  3.000
 VH4  F56  C55  C53  119.18  3.000
 VH4  H58  C57  C55  119.81  3.000
 VH4  H58  C57  C48  121.88  3.000
 VH4  C55  C57  C48  118.29  3.000
 VH4  H29  N28  C30  120.49  3.000
 VH4  H29  N28  C20  115.51  3.000
 VH4  C30  N28  C20  122.71  3.000
 VH4  C41  N32  C33  111.43  3.000
 VH4  C41  N32  C30  116.85  3.000
 VH4  C33  N32  C30  121.57  3.000
 VH4  N47  N46  C44  105.52  3.000
 VH4  N46  N47  C48  119.54  3.000
 VH4  N46  N47  C39  111.94  3.000
 VH4  C48  N47  C39  128.49  3.000
 VH4  H11  O10  C05  108.17  3.000
 VH4  H02  C01  H04  108.01  3.000
 VH4  H02  C01  H03  107.39  3.000
 VH4  H04  C01  H03  107.47  3.000
 VH4  H02  C01  C05  111.15  3.000
 VH4  H04  C01  C05  112.30  3.000
 VH4  H03  C01  C05  110.33  3.000
 VH4  O31  C30  N32  121.56  3.000
 VH4  O31  C30  N28  121.93  3.000
 VH4  N32  C30  N28  116.51  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
 VH4  CONST_03  C44  N46  N47  C39     0.00   0.0  0
 VH4  CONST_04  N46  C44  C40  C39     0.00   0.0  0
 VH4  CONST_05  C48  N47  C39  C40   180.00   0.0  0
 VH4  CONST_06  N46  N47  C39  C40     0.00   0.0  0
 VH4  CONST_07  N47  N46  C44  C40     0.00   0.0  0
 VH4  CONST_08  C48  N47  N46  C44   180.00   0.0  0
 VH4  CONST_09  N47  C39  C40  C44     0.00   0.0  0
 VH4  CONST_10  C53  C51  C49  C48     0.00   0.0  0
 VH4  CONST_11  C53  C55  C57  C48     0.00   0.0  0
 VH4  CONST_12  C55  C53  C51  C49     0.00   0.0  0
 VH4  CONST_13  C55  C57  C48  C49     0.00   0.0  0
 VH4  CONST_15  C57  C55  C53  C51     0.00   0.0  0
 VH4  CONST_16  C57  C48  C49  C51     0.00   0.0  0
 VH4  CONST_17  N47  C48  C49  C51   180.00   0.0  0
 VH4  CONST_18  N47  C48  C57  C55   180.00   0.0  0
 VH4  CONST_20  C48  N47  C39  C36     0.00   0.0  0
 VH4  CONST_21  F56  C55  C57  C48   180.00   0.0  0
 VH4  CONST_22  F56  C55  C53  C51   180.00   0.0  0
 VH4  CONST_23  H45  C44  C40  C39   180.00   0.0  0
 VH4  CONST_24  H52  C51  C49  C48   180.00   0.0  0
 VH4  CONST_25  H54  C53  C51  C49   180.00   0.0  0
 VH4  CONST_26  H58  C57  C48  C49   180.00   0.0  0
 VH4  CONST_27  H50  C49  C51  C53   180.00   0.0  0
 VH4  CONST_30  N32  C30  N28  C20   180.00   0.0  0
 VH4  CONST_33  O31  C30  N28  C20     0.00   0.0  0
 VH4  CONST_34  H29  N28  C30  N32     0.00   0.0  0
 VH4  Var_01    C12  C14  C17  C20    57.08  30.0  1
 VH4  Var_02    C12  C25  C22  C20   -56.77  30.0  1
 VH4  Var_03    N47  C39  C36  C33  -163.28  30.0  1
 VH4  Var_04    C40  C41  N32  C33   -50.66  30.0  1
 VH4  Var_05    C41  N32  C33  C36    71.11  30.0  1
 VH4  Var_06    N32  C33  C36  C39   -47.28  30.0  1
 VH4  Var_07    N32  C41  C40  C39    15.11  30.0  1
 VH4  Var_08    H09  C06  C05  C12  -175.34  30.0  3
 VH4  Var_09    H03  C01  C05  C12   176.20  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
 VH4  chir_01  C20  N28  C17  C22  positiv
 VH4  chir_02  C12  C14  C25  C05  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
 VH4  plan-1  C48  0.020
 VH4  plan-1  C49  0.020
 VH4  plan-1  C51  0.020
 VH4  plan-1  C53  0.020
 VH4  plan-1  C55  0.020
 VH4  plan-1  C57  0.020
 VH4  plan-1  F56  0.020
 VH4  plan-1  N47  0.020
 VH4  plan-1  H50  0.020
 VH4  plan-1  H52  0.020
 VH4  plan-1  H54  0.020
 VH4  plan-1  H58  0.020
 VH4  plan-2  C36  0.020
 VH4  plan-2  C39  0.020
 VH4  plan-2  C40  0.020
 VH4  plan-2  C41  0.020
 VH4  plan-2  C44  0.020
 VH4  plan-2  C48  0.020
 VH4  plan-2  N46  0.020
 VH4  plan-2  N47  0.020
 VH4  plan-2  H45  0.020
 VH4  plan-3  C20  0.020
 VH4  plan-3  C33  0.020
 VH4  plan-3  C41  0.020
 VH4  plan-3  N28  0.020
 VH4  plan-3  N32  0.020
 VH4  plan-3  O31  0.020
 VH4  plan-3  H29  0.020
 VH4  plan-3  C30  0.020

