# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 21:27:57 2020
#   Inital geometry file: a 145 line input string
#   Ligand name: 2-[4-(aminomethyl)piperidin-1-yl]-N-(3-cyclohexyl-4-oxo-2,4-dihydroindeno[1,2-c]pyrazol-5-yl)acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCC1CCN(CC1)CC(=O)Nc2cccc3c4n[nH]c(C5CCCCC5)c4C(=O)c23
#
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
 D31  D31  2-[4-(aminomethyl)piperidin-1-yl]-N-(3-cyclohexyl-4-oxo-2,4-dihydroindeno[1,2-c]pyrazol-5-yl)acetamide  ligand  62  31  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_D31
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
 D31  N1    N  NH2   0  -0.807   -9.0592  -1.3517   1.7245
 D31  C2    C  CH2   0  -0.267   -8.5592  -1.4807   0.3629
 D31  C3    C  CH1   0  -0.238   -7.0385  -1.5556   0.3156
 D31  C6    C  CH2   0  -0.426   -6.5484  -1.8168  -1.1056
 D31  C7    C  CH2   0  -0.281   -5.0312  -1.8363  -1.1788
 D31  N8    N  NT    0  -0.410   -4.4690  -0.5928  -0.6787
 D31  C9    C  CH2   0  -0.281   -4.8582  -0.3609   0.7022
 D31  C10   C  CH2   0  -0.435   -6.3703  -0.2890   0.8433
 D31  C20   C  CH2   0  -0.417   -3.0446  -0.5535  -0.8503
 D31  C21   C  C     0   0.532   -2.4871   0.8605  -0.7878
 D31  N24   N  NH1   0  -0.766   -1.1506   0.8801  -0.5151
 D31  C25   C  CR6   0   0.400   -0.2804   1.9591  -0.4721
 D31  C26   C  CR16  0  -0.325   -0.6741   3.3065  -0.5781
 D31  C27   C  CR16  0  -0.238    0.2675   4.3182  -0.5135
 D31  C28   C  CR16  0  -0.334    1.6312   4.0647  -0.3459
 D31  C29   C  CR56  0   0.107    2.0157   2.7495  -0.2434
 D31  C30   C  CR56  0  -0.220    1.0779   1.7028  -0.3019
 D31  C31   C  CR55  0   0.206    3.3229   2.1130  -0.0753
 D31  C32   C  CR55  0  -0.283    3.1780   0.7174  -0.0310
 D31  C33   C  CR5   0   0.322    1.7671   0.3780  -0.1656
 D31  N34   N  NR15  0  -0.516    5.2333   1.3270   0.1516
 D31  C35   C  CR5   0   0.524    4.4575   0.2234   0.1185
 D31  C36   C  CH1   0  -0.367    4.9950  -1.1618   0.2259
 D31  C37   C  CH2   0  -0.417    5.9517  -1.4883  -0.9297
 D31  C38   C  CH2   0  -0.441    6.4771  -2.9150  -0.8172
 D31  C39   C  CH2   0  -0.430    7.1504  -3.1557   0.5299
 D31  C40   C  CH2   0  -0.441    6.2046  -2.8289   1.6802
 D31  C41   C  CH2   0  -0.416    5.6777  -1.4014   1.5812
 D31  O53   O  O     0  -0.444   -3.1585   1.8488  -0.9948
 D31  O54   O  O     0  -0.406    1.2294  -0.7134  -0.1687
 D31  N55   N  N     0  -0.268    4.5670   2.4931   0.0354
 D31  HN11  H  HNH2  0   0.342   -8.8626  -0.4225   2.0747
 D31  HN12  H  HNH2  0   0.347  -10.0684  -1.4248   1.7180
 D31  H21   H  HCH2  0   0.219   -8.9664  -2.4049  -0.0570
 D31  H22   H  HCH2  0   0.183   -8.8887  -0.6686  -0.3047
 D31  H3    H  HCH1  0   0.208   -6.7218  -2.3972   0.9460
 D31  H61   H  HCH2  0   0.230   -6.9357  -2.7707  -1.4734
 D31  H62   H  HCH2  0   0.213   -6.9297  -1.0376  -1.7743
 D31  H71   H  HCH2  0   0.188   -4.6527  -2.7077  -0.6150
 D31  H72   H  HCH2  0   0.237   -4.7134  -1.9706  -2.2156
 D31  H91   H  HCH2  0   0.189   -4.4698  -1.1601   1.3591
 D31  H92   H  HCH2  0   0.240   -4.4157   0.5742   1.0496
 D31  H101  H  HCH2  0   0.213   -6.7442   0.5798   0.2897
 D31  H102  H  HCH2  0   0.231   -6.6112  -0.1269   1.8966
 D31  H201  H  HCH2  0   0.230   -2.5052  -1.1991  -0.1358
 D31  H202  H  HCH2  0   0.292   -2.7933  -0.9373  -1.8455
 D31  H24   H  HNH1  0   0.422   -0.7083  -0.0196  -0.3685
 D31  H26   H  HCR6  0   0.291   -1.7110   3.5646  -0.7089
 D31  H27   H  HCR6  0   0.273   -0.0732   5.3420  -0.5972
 D31  H28   H  HCR6  0   0.264    2.3476   4.8732  -0.3000
 D31  H34   H  HNR5  0   0.425    6.2371   1.3556   0.2487
 D31  H36   H  HCH1  0   0.260    4.1351  -1.8360   0.1580
 D31  H371  H  HCH2  0   0.248    5.4427  -1.3431  -1.8852
 D31  H372  H  HCH2  0   0.219    6.7986  -0.7933  -0.9131
 D31  H381  H  HCH2  0   0.217    5.6465  -3.6181  -0.9411
 D31  H382  H  HCH2  0   0.235    7.1765  -3.1120  -1.6328
 D31  H391  H  HCH2  0   0.232    7.4908  -4.1912   0.6022
 D31  H392  H  HCH2  0   0.213    8.0442  -2.5266   0.6049
 D31  H401  H  HCH2  0   0.217    5.3591  -3.5249   1.6634
 D31  H402  H  HCH2  0   0.235    6.7056  -2.9687   2.6405
 D31  H411  H  HCH2  0   0.219    6.5079  -0.6976   1.7037
 D31  H412  H  HCH2  0   0.247    4.9712  -1.2001   2.3897

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
 D31  N1   C2    single    1.456  0.020  1.456
 D31  N1   HN11  single    0.890  0.020  1.040
 D31  N1   HN12  single    0.890  0.020  1.040
 D31  C2   C3    single    1.523  0.020  1.523
 D31  C2   H21   single    0.970  0.020  1.090
 D31  C2   H22   single    0.970  0.020  1.090
 D31  C3   C6    single    1.526  0.020  1.526
 D31  C3   C10   single    1.526  0.020  1.526
 D31  C3   H3    single    0.970  0.020  1.090
 D31  C6   C7    single    1.519  0.020  1.519
 D31  C6   H61   single    0.970  0.020  1.090
 D31  C6   H62   single    0.970  0.020  1.090
 D31  C7   N8    single    1.453  0.020  1.453
 D31  C7   H71   single    0.970  0.020  1.090
 D31  C7   H72   single    0.970  0.020  1.090
 D31  N8   C9    single    1.453  0.020  1.453
 D31  N8   C20   single    1.435  0.020  1.435
 D31  C9   C10   single    1.520  0.020  1.520
 D31  C9   H91   single    0.970  0.020  1.090
 D31  C9   H92   single    0.970  0.020  1.090
 D31  C10  H101  single    0.970  0.020  1.090
 D31  C10  H102  single    0.970  0.020  1.090
 D31  C20  C21   single    1.521  0.020  1.521
 D31  C20  H201  single    0.970  0.020  1.090
 D31  C20  H202  single    0.970  0.020  1.090
 D31  C21  N24   single    1.364  0.020  1.364
 D31  C21  O53   double    1.213  0.020  1.213
 D31  N24  C25   single    1.387  0.020  1.387
 D31  N24  H24   single    0.860  0.020  1.020
 D31  C25  C26   aromatic  1.408  0.020  1.408
 D31  C25  C30   aromatic  1.393  0.020  1.393
 D31  C26  C27   aromatic  1.384  0.020  1.384
 D31  C26  H26   single    0.930  0.020  1.080
 D31  C27  C28   aromatic  1.397  0.020  1.397
 D31  C27  H27   single    0.930  0.020  1.080
 D31  C28  C29   aromatic  1.374  0.020  1.374
 D31  C28  H28   single    0.930  0.020  1.080
 D31  C29  C30   aromatic  1.407  0.020  1.407
 D31  C29  C31   aromatic  1.464  0.020  1.464
 D31  C30  C33   single    1.500  0.020  1.500
 D31  C31  C32   aromatic  1.404  0.020  1.404
 D31  C31  N55   aromatic  1.306  0.020  1.306
 D31  C32  C33   single    1.457  0.020  1.457
 D31  C32  C35   aromatic  1.380  0.020  1.380
 D31  C33  O54   double    1.217  0.020  1.217
 D31  N34  C35   aromatic  1.349  0.020  1.349
 D31  N34  N55   aromatic  1.348  0.020  1.348
 D31  N34  H34   single    0.860  0.020  1.020
 D31  C35  C36   single    1.490  0.020  1.490
 D31  C36  C37   single    1.535  0.020  1.535
 D31  C36  C41   single    1.536  0.020  1.536
 D31  C36  H36   single    0.970  0.020  1.090
 D31  C37  C38   single    1.525  0.020  1.525
 D31  C37  H371  single    0.970  0.020  1.090
 D31  C37  H372  single    0.970  0.020  1.090
 D31  C38  C39   single    1.525  0.020  1.525
 D31  C38  H381  single    0.970  0.020  1.090
 D31  C38  H382  single    0.970  0.020  1.090
 D31  C39  C40   single    1.525  0.020  1.525
 D31  C39  H391  single    0.970  0.020  1.090
 D31  C39  H392  single    0.970  0.020  1.090
 D31  C40  C41   single    1.525  0.020  1.525
 D31  C40  H401  single    0.970  0.020  1.090
 D31  C40  H402  single    0.970  0.020  1.090
 D31  C41  H411  single    0.970  0.020  1.090
 D31  C41  H412  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
 D31  HN12  N1   HN11  105.20  3.000
 D31  HN12  N1   C2    109.28  3.000
 D31  HN11  N1   C2    109.76  3.000
 D31  H22   C2   H21   106.19  3.000
 D31  H22   C2   C3    108.43  3.000
 D31  H21   C2   C3    108.55  3.000
 D31  H22   C2   N1    113.49  3.000
 D31  H21   C2   N1    107.81  3.000
 D31  C3    C2   N1    112.10  3.000
 D31  H3    C3   C10   108.13  3.000
 D31  H3    C3   C6    108.11  3.000
 D31  C10   C3   C6    108.87  3.000
 D31  H3    C3   C2    107.93  3.000
 D31  C10   C3   C2    112.68  3.000
 D31  C6    C3   C2    110.98  3.000
 D31  H62   C6   H61   106.98  3.000
 D31  H62   C6   C7    109.11  3.000
 D31  H61   C6   C7    109.05  3.000
 D31  H62   C6   C3    109.58  3.000
 D31  H61   C6   C3    110.42  3.000
 D31  C7    C6   C3    111.59  3.000
 D31  H72   C7   H71   106.71  3.000
 D31  H72   C7   N8    108.61  3.000
 D31  H71   C7   N8    111.52  3.000
 D31  H72   C7   C6    109.74  3.000
 D31  H71   C7   C6    109.13  3.000
 D31  N8    C7   C6    111.03  3.000
 D31  C20   N8   C9    112.03  3.000
 D31  C20   N8   C7    111.48  3.000
 D31  C9    N8   C7    111.09  3.000
 D31  H92   C9   H91   106.73  3.000
 D31  H92   C9   C10   109.46  3.000
 D31  H91   C9   C10   109.19  3.000
 D31  H92   C9   N8    109.30  3.000
 D31  H91   C9   N8    110.81  3.000
 D31  C10   C9   N8    111.23  3.000
 D31  H102  C10  H101  107.11  3.000
 D31  H102  C10  C9    108.41  3.000
 D31  H101  C10  C9    109.26  3.000
 D31  H102  C10  C3    111.09  3.000
 D31  H101  C10  C3    109.51  3.000
 D31  C9    C10  C3    111.35  3.000
 D31  H202  C20  H201  105.72  3.000
 D31  H202  C20  C21   106.20  3.000
 D31  H201  C20  C21   109.76  3.000
 D31  H202  C20  N8    109.06  3.000
 D31  H201  C20  N8    113.05  3.000
 D31  C21   C20  N8    112.60  3.000
 D31  O53   C21  N24   124.40  3.000
 D31  O53   C21  C20   123.21  3.000
 D31  N24   C21  C20   112.37  3.000
 D31  H24   N24  C25   114.37  3.000
 D31  H24   N24  C21   116.35  3.000
 D31  C25   N24  C21   129.20  3.000
 D31  C30   C25  C26   117.27  3.000
 D31  C30   C25  N24   118.20  3.000
 D31  C26   C25  N24   124.54  3.000
 D31  H26   C26  C27   119.07  3.000
 D31  H26   C26  C25   120.53  3.000
 D31  C27   C26  C25   120.40  3.000
 D31  H27   C27  C28   119.22  3.000
 D31  H27   C27  C26   118.29  3.000
 D31  C28   C27  C26   122.49  3.000
 D31  H28   C28  C29   121.81  3.000
 D31  H28   C28  C27   121.07  3.000
 D31  C29   C28  C27   117.12  3.000
 D31  C31   C29  C30   106.06  3.000
 D31  C31   C29  C28   132.43  3.000
 D31  C30   C29  C28   121.51  3.000
 D31  C33   C30  C29   110.32  3.000
 D31  C33   C30  C25   128.46  3.000
 D31  C29   C30  C25   121.22  3.000
 D31  N55   C31  C32   112.65  3.000
 D31  N55   C31  C29   137.24  3.000
 D31  C32   C31  C29   110.10  3.000
 D31  C35   C32  C33   145.53  3.000
 D31  C35   C32  C31   105.29  3.000
 D31  C33   C32  C31   109.18  3.000
 D31  O54   C33  C32   129.57  3.000
 D31  O54   C33  C30   126.10  3.000
 D31  C32   C33  C30   104.34  3.000
 D31  H34   N34  N55   118.39  3.000
 D31  H34   N34  C35   126.70  3.000
 D31  N55   N34  C35   114.91  3.000
 D31  C36   C35  N34   123.45  3.000
 D31  C36   C35  C32   132.49  3.000
 D31  N34   C35  C32   104.06  3.000
 D31  H36   C36  C41   107.92  3.000
 D31  H36   C36  C37   108.17  3.000
 D31  C41   C36  C37   110.73  3.000
 D31  H36   C36  C35   106.54  3.000
 D31  C41   C36  C35   111.65  3.000
 D31  C37   C36  C35   111.61  3.000
 D31  H372  C37  H371  106.81  3.000
 D31  H372  C37  C38   109.04  3.000
 D31  H371  C37  C38   110.46  3.000
 D31  H372  C37  C36   109.59  3.000
 D31  H371  C37  C36   109.86  3.000
 D31  C38   C37  C36   110.99  3.000
 D31  H382  C38  H381  106.58  3.000
 D31  H382  C38  C39   110.39  3.000
 D31  H381  C38  C39   109.47  3.000
 D31  H382  C38  C37   109.53  3.000
 D31  H381  C38  C37   109.34  3.000
 D31  C39   C38  C37   111.41  3.000
 D31  H392  C39  H391  106.59  3.000
 D31  H392  C39  C40   109.35  3.000
 D31  H391  C39  C40   110.28  3.000
 D31  H392  C39  C38   109.27  3.000
 D31  H391  C39  C38   110.22  3.000
 D31  C40   C39  C38   111.02  3.000
 D31  H402  C40  H401  106.63  3.000
 D31  H402  C40  C41   109.60  3.000
 D31  H401  C40  C41   109.10  3.000
 D31  H402  C40  C39   110.58  3.000
 D31  H401  C40  C39   109.33  3.000
 D31  C41   C40  C39   111.47  3.000
 D31  H412  C41  H411  106.79  3.000
 D31  H412  C41  C40   110.36  3.000
 D31  H411  C41  C40   109.41  3.000
 D31  H412  C41  C36   109.68  3.000
 D31  H411  C41  C36   109.59  3.000
 D31  C40   C41  C36   110.91  3.000
 D31  N34   N55  C31   103.09  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
 D31  CONST_01  C28   C27  C26  C25    0.00   0.0  0
 D31  CONST_02  C28   C29  C30  C25    0.00   0.0  0
 D31  CONST_03  C31   C29  C30  C25  180.00   0.0  0
 D31  CONST_04  C29   C30  C25  C26    0.00   0.0  0
 D31  CONST_05  C29   C28  C27  C26    0.00   0.0  0
 D31  CONST_06  C30   C25  C26  C27    0.00   0.0  0
 D31  CONST_07  C30   C29  C28  C27    0.00   0.0  0
 D31  CONST_08  C31   C29  C28  C27  180.00   0.0  0
 D31  CONST_09  C32   C31  C29  C28  180.00   0.0  0
 D31  CONST_10  N55   C31  C29  C28    0.00   0.0  0
 D31  CONST_11  C35   C32  C31  C29  180.00   0.0  0
 D31  CONST_12  N34   N55  C31  C29  180.00   0.0  0
 D31  CONST_13  C32   C31  C29  C30    0.00   0.0  0
 D31  CONST_14  N55   C31  C29  C30  180.00   0.0  0
 D31  CONST_15  N34   C35  C32  C31    0.00   0.0  0
 D31  CONST_16  C35   N34  N55  C31    0.00   0.0  0
 D31  CONST_17  N34   N55  C31  C32    0.00   0.0  0
 D31  CONST_18  N55   N34  C35  C32    0.00   0.0  0
 D31  CONST_19  N55   C31  C32  C35    0.00   0.0  0
 D31  CONST_20  C36   C35  C32  C31  180.00   0.0  0
 D31  CONST_21  C36   C35  C32  C33    0.00   0.0  0
 D31  CONST_22  N55   N34  C35  C36  180.00   0.0  0
 D31  CONST_23  C27   C26  C25  N24  180.00   0.0  0
 D31  CONST_24  C29   C30  C25  N24  180.00   0.0  0
 D31  CONST_25  C33   C30  C25  N24    0.00   0.0  0
 D31  CONST_26  H27   C27  C26  C25  180.00   0.0  0
 D31  CONST_27  H28   C28  C27  C26  180.00   0.0  0
 D31  CONST_28  H26   C26  C27  C28  180.00   0.0  0
 D31  CONST_29  H34   N34  N55  C31  180.00   0.0  0
 D31  CONST_30  C26   C25  N24  C21    0.00   0.0  0
 D31  CONST_31  C30   C25  N24  C21  180.00   0.0  0
 D31  CONST_32  H24   N24  C25  C26  180.00   0.0  0
 D31  CONST_33  C25   N24  C21  C20  180.00   0.0  0
 D31  CONST_34  O53   C21  N24  C25    0.00   0.0  0
 D31  Var_01    N8    C7   C6   C3   -56.85  30.0  1
 D31  Var_02    N8    C9   C10  C3    56.79  30.0  1
 D31  Var_03    C9    N8   C7   C6    59.31  30.0  1
 D31  Var_04    C10   C9   N8   C7   -59.41  30.0  1
 D31  Var_05    C39   C38  C37  C36  -55.94  30.0  1
 D31  Var_06    C39   C40  C41  C36   55.92  30.0  1
 D31  Var_07    C40   C39  C38  C37   55.71  30.0  1
 D31  Var_08    C41   C40  C39  C38  -55.74  30.0  1
 D31  Var_09    O54   C33  C30  C25   -0.83  30.0  1
 D31  Var_10    C21   C20  N8   C7   160.63  30.0  3
 D31  Var_11    N24   C21  C20  N8   160.06  30.0  3
 D31  Var_12    HN11  N1   C2   C3    72.30  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
 D31  chir_01  C3   C2   C6   C10  negativ
 D31  chir_02  C36  C35  C37  C41  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
 D31  plan-1  C20  0.020
 D31  plan-1  C21  0.020
 D31  plan-1  N24  0.020
 D31  plan-1  C25  0.020
 D31  plan-1  O53  0.020
 D31  plan-1  H24  0.020
 D31  plan-2  N24  0.020
 D31  plan-2  C25  0.020
 D31  plan-2  C26  0.020
 D31  plan-2  C27  0.020
 D31  plan-2  C28  0.020
 D31  plan-2  C29  0.020
 D31  plan-2  C30  0.020
 D31  plan-2  C31  0.020
 D31  plan-2  C32  0.020
 D31  plan-2  C33  0.020
 D31  plan-2  N34  0.020
 D31  plan-2  C35  0.020
 D31  plan-2  C36  0.020
 D31  plan-2  N55  0.020
 D31  plan-2  H26  0.020
 D31  plan-2  H27  0.020
 D31  plan-2  H28  0.020
 D31  plan-2  H34  0.020
 D31  plan-3  C30  0.020
 D31  plan-3  C32  0.020
 D31  plan-3  C33  0.020
 D31  plan-3  O54  0.020

