# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 24 05:40:38 2021
#   Inital geometry file: a 156 line input string
#   Ligand name: N-(4-tert-butylphenyl)-N-[(1R)-2-(cyclopentylamino)-2-oxo-1-(pyridin-3-yl)ethyl]-1H-imidazole-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)c1ccc(cc1)N([C@@H](C(=O)NC2CCCC2)c3cccnc3)C(=O)c4c[nH]cn4
#
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
 X47  X47  N-(4-tert-butylphenyl)-N-[(1R)-2-(cyclopentylamino)-2-oxo-1-(pyridin-3-yl)ethyl]-1H-imidazole-4-carboxamide  ligand  64  33  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_X47
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
 X47  C02   C  C     0   0.486  16.4784  -28.4826  25.2310
 X47  C04   C  CR6   0   0.165  17.5333  -27.6442  23.1929
 X47  C05   C  CR16  0  -0.215  18.8991  -27.7007  23.4458
 X47  C06   C  CR16  0  -0.308  19.7927  -27.8697  22.4053
 X47  C07   C  CR6   0   0.199  19.3598  -27.9623  21.0798
 X47  C08   C  CT    0  -0.176  20.3820  -28.1290  19.9625
 X47  C09   C  CH3   0  -0.630  21.1598  -29.4343  20.1785
 X47  C10   C  CH3   0  -0.666  19.7307  -28.1806  18.5808
 X47  C11   C  CH3   0  -0.632  21.3590  -26.9454  19.9927
 X47  C12   C  CR16  0  -0.335  17.9891  -27.8868  20.8455
 X47  C13   C  CR16  0  -0.221  17.0822  -27.7320  21.8866
 X47  C14   C  CH1   0  -0.286  16.1094  -26.1848  24.6466
 X47  C15   C  CR6   0   0.064  14.6167  -26.1749  24.8350
 X47  C16   C  CR16  0  -0.187  14.0396  -25.4435  25.8614
 X47  C17   C  CR16  0  -0.321  12.6585  -25.4062  25.9731
 X47  C18   C  CR16  0  -0.075  11.9035  -26.1104  25.0486
 X47  C20   C  CR16  0  -0.085  13.7653  -26.8447  23.9644
 X47  C21   C  C     0   0.550  16.4840  -25.1577  23.5642
 X47  C23   C  CH1   0  -0.113  18.1652  -23.5011  22.8954
 X47  C24   C  CH2   0  -0.464  19.0914  -22.5472  23.6438
 X47  C25   C  CH2   0  -0.465  20.3874  -23.3442  23.8117
 X47  C26   C  CH2   0  -0.450  20.4882  -24.2102  22.5388
 X47  C27   C  CH2   0  -0.445  19.0989  -24.1596  21.8697
 X47  C29   C  CR5   0   0.009  16.9286  -29.8604  24.9422
 X47  C30   C  CR15  0  -0.033  17.2535  -30.5092  23.7729
 X47  C32   C  CR15  0   0.096  17.3415  -31.8853  25.4706
 X47  N03   N  NT    0  -0.571  16.6185  -27.5106  24.2752
 X47  N19   N  N     0  -0.405  12.4430  -26.8207  24.0638
 X47  N22   N  NH1   0  -0.615  17.5993  -24.4690  23.8218
 X47  N31   N  NR15  0  -0.568  17.5055  -31.7885  24.1320
 X47  N33   N  N     0  -0.431  16.9889  -30.7445  25.9884
 X47  O01   O  O     0  -0.461  15.9559  -28.2265  26.3021
 X47  O28   O  O     0  -0.469  15.7888  -24.9906  22.5760
 X47  H051  H  HCR6  0   0.261  19.2610  -27.6280  24.4641
 X47  H061  H  HCR6  0   0.255  20.8491  -27.9210  22.6378
 X47  H093  H  HCH3  0   0.229  21.6885  -29.4428  21.1328
 X47  H091  H  HCH3  0   0.229  20.4945  -30.2993  20.1588
 X47  H092  H  HCH3  0   0.228  21.9057  -29.5647  19.3914
 X47  H101  H  HCH3  0   0.230  19.0387  -29.0192  18.4834
 X47  H102  H  HCH3  0   0.231  19.1858  -27.2633  18.3493
 X47  H103  H  HCH3  0   0.239  20.5013  -28.3040  17.8182
 X47  H112  H  HCH3  0   0.227  21.9226  -26.9048  20.9256
 X47  H113  H  HCH3  0   0.230  22.0777  -27.0328  19.1758
 X47  H111  H  HCH3  0   0.233  20.8337  -25.9951  19.8831
 X47  H121  H  HCR6  0   0.255  17.6016  -27.9539  19.8383
 X47  H131  H  HCR6  0   0.265  16.0215  -27.6962  21.6752
 X47  H141  H  HCH1  0   0.290  16.5760  -25.8793  25.5894
 X47  H161  H  HCR6  0   0.268  14.6622  -24.9126  26.5717
 X47  H171  H  HCR6  0   0.271  12.1750  -24.8502  26.7645
 X47  H181  H  HCR6  0   0.262  10.8207  -26.1047  25.1073
 X47  H201  H  HCR6  0   0.259  14.1722  -27.4432  23.1566
 X47  H231  H  HCH1  0   0.258  17.3367  -22.9806  22.4159
 X47  H242  H  HCH2  0   0.246  18.6673  -22.1910  24.5844
 X47  H251  H  HCH2  0   0.226  20.3376  -23.9726  24.7053
 X47  H252  H  HCH2  0   0.242  21.2523  -22.6939  23.9446
 X47  H261  H  HCH2  0   0.239  20.7669  -25.2351  22.7813
 X47  H262  H  HCH2  0   0.230  21.2538  -23.8273  21.8636
 X47  H271  H  HCH2  0   0.233  19.1259  -23.5364  20.9734
 X47  H272  H  HCH2  0   0.258  18.7430  -25.1462  21.5713
 X47  H301  H  HCR5  0   0.300  17.3212  -30.1912  22.7479
 X47  H321  H  HCR5  0   0.286  17.4968  -32.8090  26.0058
 X47  H221  H  HNH1  0   0.406  18.1157  -24.6900  24.6590
 X47  H1    H  HNR5  0   0.429  17.7726  -32.5334  23.5066
 X47  H241  H  HCH2  0   0.245  19.2673  -21.6737  23.0121

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
 X47  C10  C08   single    1.528  0.020  1.528
 X47  C11  C08   single    1.535  0.020  1.535
 X47  C08  C09   single    1.535  0.020  1.535
 X47  C08  C07   single    1.523  0.020  1.523
 X47  C12  C07   aromatic  1.393  0.020  1.393
 X47  C12  C13   aromatic  1.389  0.020  1.389
 X47  C07  C06   aromatic  1.397  0.020  1.397
 X47  C13  C04   aromatic  1.385  0.020  1.385
 X47  C27  C26   single    1.543  0.020  1.543
 X47  C27  C23   single    1.535  0.020  1.535
 X47  C26  C25   single    1.543  0.020  1.543
 X47  C06  C05   aromatic  1.382  0.020  1.382
 X47  O28  C21   double    1.220  0.020  1.220
 X47  C04  C05   aromatic  1.390  0.020  1.390
 X47  C04  N03   single    1.423  0.020  1.423
 X47  C23  C24   single    1.526  0.020  1.526
 X47  C23  N22   single    1.454  0.020  1.454
 X47  C25  C24   single    1.531  0.020  1.531
 X47  C21  N22   single    1.336  0.020  1.336
 X47  C21  C14   single    1.538  0.020  1.538
 X47  C20  N19   aromatic  1.326  0.020  1.326
 X47  C20  C15   aromatic  1.390  0.020  1.390
 X47  N19  C18   aromatic  1.329  0.020  1.329
 X47  C30  N31   aromatic  1.352  0.020  1.352
 X47  C30  C29   aromatic  1.376  0.020  1.376
 X47  N31  C32   aromatic  1.352  0.020  1.352
 X47  N03  C14   single    1.468  0.020  1.468
 X47  N03  C02   single    1.370  0.020  1.370
 X47  C14  C15   single    1.505  0.020  1.505
 X47  C15  C16   aromatic  1.386  0.020  1.386
 X47  C18  C17   aromatic  1.386  0.020  1.386
 X47  C29  C02   single    1.478  0.020  1.478
 X47  C29  N33   aromatic  1.371  0.020  1.371
 X47  C32  N33   aromatic  1.302  0.020  1.302
 X47  C02  O01   double    1.219  0.020  1.219
 X47  C16  C17   aromatic  1.386  0.020  1.386
 X47  C05  H051  single    0.930  0.020  1.080
 X47  C06  H061  single    0.930  0.020  1.080
 X47  C09  H093  single    0.970  0.020  1.090
 X47  C09  H091  single    0.970  0.020  1.090
 X47  C09  H092  single    0.970  0.020  1.090
 X47  C10  H101  single    0.970  0.020  1.090
 X47  C10  H102  single    0.970  0.020  1.090
 X47  C10  H103  single    0.970  0.020  1.090
 X47  C11  H112  single    0.970  0.020  1.090
 X47  C11  H113  single    0.970  0.020  1.090
 X47  C11  H111  single    0.970  0.020  1.090
 X47  C12  H121  single    0.930  0.020  1.080
 X47  C13  H131  single    0.930  0.020  1.080
 X47  C14  H141  single    0.970  0.020  1.090
 X47  C16  H161  single    0.930  0.020  1.080
 X47  C17  H171  single    0.930  0.020  1.080
 X47  C18  H181  single    0.930  0.020  1.080
 X47  C20  H201  single    0.930  0.020  1.080
 X47  C23  H231  single    0.970  0.020  1.090
 X47  C24  H241  single    0.970  0.020  1.090
 X47  C24  H242  single    0.970  0.020  1.090
 X47  C25  H251  single    0.970  0.020  1.090
 X47  C25  H252  single    0.970  0.020  1.090
 X47  C26  H261  single    0.970  0.020  1.090
 X47  C26  H262  single    0.970  0.020  1.090
 X47  C27  H271  single    0.970  0.020  1.090
 X47  C27  H272  single    0.970  0.020  1.090
 X47  C30  H301  single    0.930  0.020  1.080
 X47  C32  H321  single    0.930  0.020  1.080
 X47  N22  H221  single    0.860  0.020  1.020
 X47  N31  H1    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
 X47  O01   C02  N03   120.51  3.000
 X47  O01   C02  C29   119.88  3.000
 X47  N03   C02  C29   119.59  3.000
 X47  N03   C04  C13   120.92  3.000
 X47  N03   C04  C05   119.80  3.000
 X47  C13   C04  C05   119.28  3.000
 X47  H051  C05  C06   120.00  3.000
 X47  H051  C05  C04   119.77  3.000
 X47  C06   C05  C04   120.22  3.000
 X47  H061  C06  C07   120.18  3.000
 X47  H061  C06  C05   118.35  3.000
 X47  C07   C06  C05   121.46  3.000
 X47  C12   C07  C08   122.88  3.000
 X47  C12   C07  C06   117.44  3.000
 X47  C08   C07  C06   119.67  3.000
 X47  C11   C08  C10   108.36  3.000
 X47  C11   C08  C09   109.29  3.000
 X47  C10   C08  C09   108.33  3.000
 X47  C09   C08  C07   109.26  3.000
 X47  C11   C08  C07   109.16  3.000
 X47  C10   C08  C07   112.38  3.000
 X47  H092  C09  H091  107.98  3.000
 X47  H092  C09  H093  107.37  3.000
 X47  H091  C09  H093  107.76  3.000
 X47  H092  C09  C08   110.26  3.000
 X47  H091  C09  C08   111.25  3.000
 X47  H093  C09  C08   112.05  3.000
 X47  H103  C10  H102  107.41  3.000
 X47  H103  C10  H101  107.37  3.000
 X47  H102  C10  H101  108.07  3.000
 X47  H103  C10  C08   109.55  3.000
 X47  H102  C10  C08   112.09  3.000
 X47  H101  C10  C08   112.13  3.000
 X47  H111  C11  H113  108.15  3.000
 X47  H111  C11  H112  107.59  3.000
 X47  H113  C11  H112  107.63  3.000
 X47  H111  C11  C08   111.29  3.000
 X47  H113  C11  C08   110.04  3.000
 X47  H112  C11  C08   111.99  3.000
 X47  H121  C12  C13   118.10  3.000
 X47  H121  C12  C07   120.40  3.000
 X47  C13   C12  C07   121.49  3.000
 X47  H131  C13  C12   119.81  3.000
 X47  H131  C13  C04   120.10  3.000
 X47  C12   C13  C04   120.09  3.000
 X47  H141  C14  N03   108.78  3.000
 X47  H141  C14  C21   108.40  3.000
 X47  N03   C14  C21   109.91  3.000
 X47  H141  C14  C15   108.24  3.000
 X47  N03   C14  C15   112.44  3.000
 X47  C21   C14  C15   108.98  3.000
 X47  C20   C15  C16   117.58  3.000
 X47  C16   C15  C14   120.61  3.000
 X47  C20   C15  C14   121.75  3.000
 X47  H161  C16  C17   120.43  3.000
 X47  H161  C16  C15   120.31  3.000
 X47  C17   C16  C15   119.26  3.000
 X47  H171  C17  C18   120.39  3.000
 X47  H171  C17  C16   121.22  3.000
 X47  C18   C17  C16   118.38  3.000
 X47  H181  C18  N19   116.64  3.000
 X47  H181  C18  C17   120.34  3.000
 X47  N19   C18  C17   123.02  3.000
 X47  H201  C20  N19   116.10  3.000
 X47  H201  C20  C15   120.17  3.000
 X47  N19   C20  C15   123.72  3.000
 X47  O28   C21  N22   124.15  3.000
 X47  N22   C21  C14   114.32  3.000
 X47  O28   C21  C14   121.51  3.000
 X47  H231  C23  N22   107.60  3.000
 X47  H231  C23  C27   111.91  3.000
 X47  N22   C23  C27   112.13  3.000
 X47  H231  C23  C24   112.26  3.000
 X47  N22   C23  C24   109.87  3.000
 X47  C27   C23  C24   103.10  3.000
 X47  H242  C24  H241  107.45  3.000
 X47  H242  C24  C25   113.85  3.000
 X47  H241  C24  C25   110.09  3.000
 X47  H242  C24  C23   113.01  3.000
 X47  H241  C24  C23   108.31  3.000
 X47  C25   C24  C23   104.02  3.000
 X47  H252  C25  H251  106.21  3.000
 X47  H252  C25  C26   112.55  3.000
 X47  H251  C25  C26   110.77  3.000
 X47  H252  C25  C24   111.99  3.000
 X47  H251  C25  C24   110.51  3.000
 X47  C26   C25  C24   104.90  3.000
 X47  H262  C26  H261  106.78  3.000
 X47  H262  C26  C27   110.62  3.000
 X47  H261  C26  C27   110.96  3.000
 X47  H262  C26  C25   111.08  3.000
 X47  H261  C26  C25   111.17  3.000
 X47  C27   C26  C25   106.29  3.000
 X47  H272  C27  H271  107.44  3.000
 X47  H272  C27  C26   112.51  3.000
 X47  H271  C27  C26   110.64  3.000
 X47  H272  C27  C23   111.86  3.000
 X47  H271  C27  C23   108.58  3.000
 X47  C26   C27  C23   105.78  3.000
 X47  N33   C29  C30   109.51  3.000
 X47  N33   C29  C02   117.73  3.000
 X47  C30   C29  C02   132.65  3.000
 X47  H301  C30  N31   121.41  3.000
 X47  H301  C30  C29   133.26  3.000
 X47  N31   C30  C29   105.33  3.000
 X47  H321  C32  N33   126.30  3.000
 X47  H321  C32  N31   122.35  3.000
 X47  N33   C32  N31   111.35  3.000
 X47  C14   N03  C04   120.00  3.000
 X47  C14   N03  C02   115.38  3.000
 X47  C04   N03  C02   121.97  3.000
 X47  C20   N19  C18   118.04  3.000
 X47  H221  N22  C23   118.39  3.000
 X47  H221  N22  C21   118.34  3.000
 X47  C23   N22  C21   123.04  3.000
 X47  H1    N31  C32   126.37  3.000
 X47  H1    N31  C30   125.69  3.000
 X47  C32   N31  C30   107.94  3.000
 X47  C32   N33  C29   105.87  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
 X47  CONST_01  C07   C12  C13  C04     0.00   0.0  0
 X47  CONST_02  C07   C06  C05  C04     0.00   0.0  0
 X47  CONST_03  C12   C07  C06  C05     0.00   0.0  0
 X47  CONST_04  C12   C13  C04  C05     0.00   0.0  0
 X47  CONST_05  C13   C12  C07  C06     0.00   0.0  0
 X47  CONST_06  C13   C04  C05  C06     0.00   0.0  0
 X47  CONST_07  C18   N19  C20  C15     0.00   0.0  0
 X47  CONST_08  C18   C17  C16  C15     0.00   0.0  0
 X47  CONST_09  N19   C20  C15  C16     0.00   0.0  0
 X47  CONST_10  N19   C18  C17  C16     0.00   0.0  0
 X47  CONST_11  C20   N19  C18  C17     0.00   0.0  0
 X47  CONST_12  C20   C15  C16  C17     0.00   0.0  0
 X47  CONST_13  C32   N31  C30  C29     0.00   0.0  0
 X47  CONST_14  N31   C32  N33  C29     0.00   0.0  0
 X47  CONST_15  N33   C32  N31  C30     0.00   0.0  0
 X47  CONST_16  C32   N33  C29  C30     0.00   0.0  0
 X47  CONST_17  N33   C29  C30  N31     0.00   0.0  0
 X47  CONST_18  N31   C30  C29  C02   180.00   0.0  0
 X47  CONST_19  C32   N33  C29  C02   180.00   0.0  0
 X47  CONST_20  C08   C07  C06  C05   180.00   0.0  0
 X47  CONST_21  N03   C04  C05  C06   180.00   0.0  0
 X47  CONST_22  C13   C12  C07  C08   180.00   0.0  0
 X47  CONST_23  N03   C04  C13  C12   180.00   0.0  0
 X47  CONST_24  N19   C20  C15  C14   180.00   0.0  0
 X47  CONST_25  C17   C16  C15  C14   180.00   0.0  0
 X47  CONST_26  H121  C12  C13  C04   180.00   0.0  0
 X47  CONST_27  H061  C06  C05  C04   180.00   0.0  0
 X47  CONST_28  H131  C13  C04  C05   180.00   0.0  0
 X47  CONST_29  H051  C05  C06  C07   180.00   0.0  0
 X47  CONST_30  H171  C17  C16  C15   180.00   0.0  0
 X47  CONST_31  H201  C20  C15  C16   180.00   0.0  0
 X47  CONST_32  H181  C18  C17  C16   180.00   0.0  0
 X47  CONST_33  H161  C16  C17  C18   180.00   0.0  0
 X47  CONST_34  H1    N31  C30  C29   180.00   0.0  0
 X47  CONST_35  H321  C32  N33  C29   180.00   0.0  0
 X47  CONST_36  H301  C30  N31  C32   180.00   0.0  0
 X47  CONST_43  C23   N22  C21  C14   180.00   0.0  0
 X47  CONST_44  C29   C02  N03  C14   180.00   0.0  0
 X47  CONST_45  O28   C21  N22  C23     0.00   0.0  0
 X47  CONST_46  O01   C02  N03  C14     0.00   0.0  0
 X47  CONST_47  H221  N22  C21  C14     0.00   0.0  0
 X47  Var_01    C25   C26  C27  C23   -10.60  30.0  1
 X47  Var_02    C26   C25  C24  C23    33.90  30.0  1
 X47  Var_03    C27   C26  C25  C24   -14.21  30.0  1
 X47  Var_04    C10   C08  C07  C06  -178.71  30.0  2
 X47  Var_05    N03   C02  C29  C30   -15.32  30.0  2
 X47  Var_06    H101  C10  C08  C07   -60.69  30.0  3
 X47  Var_07    H112  C11  C08  C07    62.27  30.0  3
 X47  Var_08    H093  C09  C08  C07   -59.86  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
 X47  chir_01  C14  C21  N03  C15  positiv
 X47  chir_02  C23  N22  C27  C24  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
 X47  plan-1  C02   0.020
 X47  plan-1  C29   0.020
 X47  plan-1  C30   0.020
 X47  plan-1  C32   0.020
 X47  plan-1  N31   0.020
 X47  plan-1  N33   0.020
 X47  plan-1  H301  0.020
 X47  plan-1  H321  0.020
 X47  plan-1  H1    0.020
 X47  plan-2  C04   0.020
 X47  plan-2  C05   0.020
 X47  plan-2  C06   0.020
 X47  plan-2  C07   0.020
 X47  plan-2  C08   0.020
 X47  plan-2  C12   0.020
 X47  plan-2  C13   0.020
 X47  plan-2  N03   0.020
 X47  plan-2  H051  0.020
 X47  plan-2  H061  0.020
 X47  plan-2  H121  0.020
 X47  plan-2  H131  0.020
 X47  plan-3  C14   0.020
 X47  plan-3  C15   0.020
 X47  plan-3  C16   0.020
 X47  plan-3  C17   0.020
 X47  plan-3  C18   0.020
 X47  plan-3  C20   0.020
 X47  plan-3  N19   0.020
 X47  plan-3  H161  0.020
 X47  plan-3  H171  0.020
 X47  plan-3  H181  0.020
 X47  plan-3  H201  0.020
 X47  plan-4  C14   0.020
 X47  plan-4  C21   0.020
 X47  plan-4  C23   0.020
 X47  plan-4  N22   0.020
 X47  plan-4  O28   0.020
 X47  plan-4  H221  0.020
 X47  plan-5  C02   0.020
 X47  plan-5  C04   0.020
 X47  plan-5  C14   0.020
 X47  plan-5  C29   0.020
 X47  plan-5  N03   0.020
 X47  plan-5  O01   0.020

