# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 15:14:21 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: 5-(4-cyclopropyl-1H-imidazol-1-yl)-2-fluoro-4-methyl-N-{6-[4-(propan-2-yl)-4H-1,2,4-triazol-3-yl]pyridin-2-yl}benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)n1cnnc1c2cccc(NC(=O)c3cc(n4cnc(c4)C5CC5)c(C)cc3F)n2
#
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
 NJV  NJV  5-(4-cyclopropyl-1H-imidazol-1-yl)-2-fluoro-4-methyl-N-{6-[4-(propan-2-yl)-4H-1,2,4-triazol-3-yl]pyridin-2-yl}benzamide  ligand  57  33  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_NJV
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
 NJV  C1   C  CR6   0   0.582  -1.2915  -2.7334   1.8326
 NJV  C6   C  CR16  0  -0.473  -2.5581  -3.2691   1.7316
 NJV  C11  C  CH1   0  -0.341  -6.2890   2.0718  -1.3599
 NJV  C12  C  CH2   0  -0.473  -5.6827   3.2245  -2.1151
 NJV  C16  C  CR6   0   0.201   3.6801   1.6730   0.8122
 NJV  N    N  NR5   0  -0.521  -4.1634  -0.7101  -0.3890
 NJV  CA   C  CR6   0   0.272  -3.2051  -1.4176   0.3729
 NJV  C    C  CR6   0   0.123  -3.5468  -2.6172   1.0020
 NJV  CB   C  CR16  0  -0.260  -1.9337  -0.8812   0.4973
 NJV  CG   C  CR6   0  -0.303  -0.9491  -1.5285   1.2352
 NJV  CD   C  C     0   0.547   0.4371  -0.9793   1.3284
 NJV  NE   N  NH1   0  -0.741   0.4642   0.3677   1.5477
 NJV  CZ   C  CR6   0   0.512   1.5971   1.1817   1.5948
 NJV  NH1  N  N     0  -0.440   2.6004   0.9001   0.7867
 NJV  C10  C  CR15  0  -0.144  -4.6371   0.5528  -0.1255
 NJV  C13  C  CH2   0  -0.492  -5.9317   3.3368  -0.6441
 NJV  C17  C  CR16  0  -0.320   3.7898   2.7882   1.6366
 NJV  C18  C  CR16  0  -0.142   2.7179   3.0911   2.4608
 NJV  C19  C  CR16  0  -0.383   1.5994   2.2785   2.4553
 NJV  C20  C  CR5   0   0.428   4.7741   1.3452  -0.1055
 NJV  C21  C  CR15  0   0.069   6.1069   0.3889  -1.4768
 NJV  C23  C  CH3   0  -0.641   3.1803  -1.0694  -1.8581
 NJV  C24  C  CH3   0  -0.676   5.1370  -2.2843  -0.8207
 NJV  C7   C  CH3   0  -0.732  -4.9250  -3.1975   0.9211
 NJV  C8   C  CR15  0   0.075  -4.7606  -1.1219  -1.5332
 NJV  C9   C  CR5   0   0.153  -5.5051   0.8431  -1.1391
 NJV  F1   F  F     0  -0.292  -0.3877  -3.3849   2.5669
 NJV  N2   N  N     0  -0.460  -5.5693  -0.2165  -2.0082
 NJV  N5   N  NR5   0  -0.462   4.9876   0.1688  -0.7550
 NJV  N6   N  N     0  -0.325   6.5546   1.5982  -1.2842
 NJV  N7   N  N     0  -0.331   5.7161   2.1993  -0.4207
 NJV  O1   O  O     0  -0.419   1.4162  -1.6834   1.2191
 NJV  H1   H  HCR6  0   0.288  -2.7839  -4.1969   2.2418
 NJV  H2   H  HCH1  0   0.265  -7.3466   1.9050  -1.5380
 NJV  H3   H  HCH2  0   0.247  -4.6584   3.1192  -2.4500
 NJV  H4   H  HCH2  0   0.252  -6.3222   3.7780  -2.7905
 NJV  H5   H  HCR6  0   0.296  -1.7033   0.0468  -0.0112
 NJV  H6   H  HNH1  0   0.429  -0.3938   0.7934   1.8653
 NJV  H7   H  HCR5  0   0.296  -4.3254   1.1040   0.7460
 NJV  H8   H  HCH2  0   0.256  -6.7417   3.9696  -0.3058
 NJV  H9   H  HCH2  0   0.251  -5.0743   3.3271   0.0169
 NJV  H10  H  HCR6  0   0.275   4.6823   3.3965   1.6297
 NJV  H11  H  HCR6  0   0.283   2.7595   3.9507   3.1158
 NJV  H12  H  HCR6  0   0.288   0.7565   2.4811   3.1026
 NJV  H13  H  HCR5  0   0.304   6.5611  -0.3473  -2.1196
 NJV  H14  H  HCH1  0   0.293   3.6853  -1.1031   0.2095
 NJV  H15  H  HCH3  0   0.236   2.5701  -1.9703  -1.7995
 NJV  H16  H  HCH3  0   0.244   2.5165  -0.2118  -1.7669
 NJV  H17  H  HCH3  0   0.224   3.6586  -1.0452  -2.8387
 NJV  H18  H  HCH3  0   0.249   5.8918  -2.2637  -0.0347
 NJV  H19  H  HCH3  0   0.254   4.5456  -3.1905  -0.6948
 NJV  H20  H  HCH3  0   0.233   5.6405  -2.3595  -1.7855
 NJV  H21  H  HCH3  0   0.261  -5.6911  -2.4323   1.0460
 NJV  H22  H  HCH3  0   0.263  -5.0987  -3.6778  -0.0424
 NJV  H23  H  HCH3  0   0.265  -5.0689  -3.9523   1.6915
 NJV  H24  H  HCR5  0   0.287  -4.5509  -2.0849  -1.9751
 NJV  C22  C  CH1   0  -0.129   4.2103  -1.0808  -0.7406

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
 NJV  N6   N7   aromatic  1.345  0.020  1.345
 NJV  N6   C21  aromatic  1.304  0.020  1.304
 NJV  N7   C20  aromatic  1.310  0.020  1.310
 NJV  C17  C18  aromatic  1.386  0.020  1.386
 NJV  C17  C16  aromatic  1.391  0.020  1.391
 NJV  C21  N5   aromatic  1.350  0.020  1.350
 NJV  C18  C19  aromatic  1.383  0.020  1.383
 NJV  C20  C16  single    1.465  0.020  1.465
 NJV  C20  N5   aromatic  1.361  0.020  1.361
 NJV  C16  NH1  aromatic  1.328  0.020  1.328
 NJV  N5   C22  single    1.472  0.020  1.472
 NJV  C19  CZ   aromatic  1.394  0.020  1.394
 NJV  NH1  CZ   aromatic  1.319  0.020  1.319
 NJV  CZ   NE   single    1.396  0.020  1.396
 NJV  C22  C23  single    1.520  0.020  1.520
 NJV  C22  C24  single    1.521  0.020  1.521
 NJV  NE   CD   single    1.365  0.020  1.365
 NJV  O1   CD   double    1.211  0.020  1.211
 NJV  CD   CG   single    1.494  0.020  1.494
 NJV  F1   C1   single    1.334  0.020  1.334
 NJV  CG   C1   aromatic  1.388  0.020  1.388
 NJV  CG   CB   aromatic  1.390  0.020  1.390
 NJV  C1   C6   aromatic  1.379  0.020  1.379
 NJV  CB   CA   aromatic  1.386  0.020  1.386
 NJV  C6   C    aromatic  1.391  0.020  1.391
 NJV  C8   N2   aromatic  1.304  0.020  1.304
 NJV  C8   N    aromatic  1.355  0.020  1.355
 NJV  CA   C    aromatic  1.397  0.020  1.397
 NJV  CA   N    single    1.414  0.020  1.414
 NJV  C    C7   single    1.498  0.020  1.498
 NJV  N2   C9   aromatic  1.372  0.020  1.372
 NJV  N    C10  aromatic  1.374  0.020  1.374
 NJV  C9   C10  aromatic  1.366  0.020  1.366
 NJV  C9   C11  single    1.474  0.020  1.474
 NJV  C13  C11  single    1.497  0.020  1.497
 NJV  C13  C12  single    1.496  0.020  1.496
 NJV  C11  C12  single    1.506  0.020  1.506
 NJV  C6   H1   single    0.930  0.020  1.080
 NJV  C11  H2   single    0.970  0.020  1.090
 NJV  C12  H3   single    0.970  0.020  1.090
 NJV  C12  H4   single    0.970  0.020  1.090
 NJV  CB   H5   single    0.930  0.020  1.080
 NJV  NE   H6   single    0.860  0.020  1.020
 NJV  C10  H7   single    0.930  0.020  1.080
 NJV  C13  H8   single    0.970  0.020  1.090
 NJV  C13  H9   single    0.970  0.020  1.090
 NJV  C17  H10  single    0.930  0.020  1.080
 NJV  C18  H11  single    0.930  0.020  1.080
 NJV  C19  H12  single    0.930  0.020  1.080
 NJV  C21  H13  single    0.930  0.020  1.080
 NJV  C22  H14  single    0.970  0.020  1.090
 NJV  C23  H15  single    0.970  0.020  1.090
 NJV  C23  H16  single    0.970  0.020  1.090
 NJV  C23  H17  single    0.970  0.020  1.090
 NJV  C24  H18  single    0.970  0.020  1.090
 NJV  C24  H19  single    0.970  0.020  1.090
 NJV  C24  H20  single    0.970  0.020  1.090
 NJV  C7   H21  single    0.970  0.020  1.090
 NJV  C7   H22  single    0.970  0.020  1.090
 NJV  C7   H23  single    0.970  0.020  1.090
 NJV  C8   H24  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
 NJV  F1   C1   CG   119.58  3.000
 NJV  CG   C1   C6   122.17  3.000
 NJV  F1   C1   C6   118.21  3.000
 NJV  H1   C6   C    120.04  3.000
 NJV  H1   C6   C1   119.34  3.000
 NJV  C    C6   C1   120.61  3.000
 NJV  H2   C11  C9   114.50  3.000
 NJV  H2   C11  C13  116.16  3.000
 NJV  C9   C11  C13  120.39  3.000
 NJV  H2   C11  C12  115.32  3.000
 NJV  C13  C11  C12   59.78  3.000
 NJV  C9   C11  C12  119.95  3.000
 NJV  H4   C12  H3   114.56  3.000
 NJV  H4   C12  C13  118.48  3.000
 NJV  H3   C12  C13  117.96  3.000
 NJV  H4   C12  C11  117.82  3.000
 NJV  H3   C12  C11  117.49  3.000
 NJV  C13  C12  C11   59.82  3.000
 NJV  C20  C16  C17  119.45  3.000
 NJV  C20  C16  NH1  117.70  3.000
 NJV  C17  C16  NH1  122.82  3.000
 NJV  C8   N    C10  106.82  3.000
 NJV  C10  N    CA   126.16  3.000
 NJV  C8   N    CA   126.99  3.000
 NJV  CB   CA   C    121.09  3.000
 NJV  C    CA   N    120.43  3.000
 NJV  CB   CA   N    118.46  3.000
 NJV  C7   C    CA   122.24  3.000
 NJV  C7   C    C6   120.06  3.000
 NJV  CA   C    C6   117.70  3.000
 NJV  H5   CB   CG   119.84  3.000
 NJV  H5   CB   CA   119.00  3.000
 NJV  CG   CB   CA   121.15  3.000
 NJV  CD   CG   CB   121.27  3.000
 NJV  CB   CG   C1   117.26  3.000
 NJV  CD   CG   C1   121.42  3.000
 NJV  O1   CD   NE   124.91  3.000
 NJV  O1   CD   CG   122.06  3.000
 NJV  NE   CD   CG   113.03  3.000
 NJV  H6   NE   CZ   115.69  3.000
 NJV  H6   NE   CD   116.75  3.000
 NJV  CZ   NE   CD   126.65  3.000
 NJV  C19  CZ   NH1  123.03  3.000
 NJV  NH1  CZ   NE   118.18  3.000
 NJV  C19  CZ   NE   118.75  3.000
 NJV  CZ   NH1  C16  118.85  3.000
 NJV  H7   C10  C9   132.50  3.000
 NJV  H7   C10  N    121.71  3.000
 NJV  C9   C10  N    105.79  3.000
 NJV  H9   C13  H8   114.03  3.000
 NJV  H9   C13  C12  117.89  3.000
 NJV  H8   C13  C12  118.41  3.000
 NJV  H9   C13  C11  118.26  3.000
 NJV  H8   C13  C11  117.71  3.000
 NJV  C12  C13  C11   60.40  3.000
 NJV  H10  C17  C18  121.33  3.000
 NJV  H10  C17  C16  120.86  3.000
 NJV  C18  C17  C16  117.82  3.000
 NJV  H11  C18  C19  120.05  3.000
 NJV  H11  C18  C17  120.28  3.000
 NJV  C19  C18  C17  119.67  3.000
 NJV  H12  C19  C18  121.19  3.000
 NJV  H12  C19  CZ   121.02  3.000
 NJV  C18  C19  CZ   117.79  3.000
 NJV  N7   C20  N5   109.63  3.000
 NJV  N5   C20  C16  127.56  3.000
 NJV  N7   C20  C16  122.81  3.000
 NJV  H13  C21  N6   125.23  3.000
 NJV  H13  C21  N5   123.85  3.000
 NJV  N6   C21  N5   110.91  3.000
 NJV  H17  C23  H16  108.98  3.000
 NJV  H17  C23  H15  108.18  3.000
 NJV  H16  C23  H15  107.79  3.000
 NJV  H17  C23  C22  111.33  3.000
 NJV  H16  C23  C22  110.96  3.000
 NJV  H15  C23  C22  109.49  3.000
 NJV  H20  C24  H19  107.18  3.000
 NJV  H20  C24  H18  108.64  3.000
 NJV  H19  C24  H18  107.96  3.000
 NJV  H20  C24  C22  112.48  3.000
 NJV  H19  C24  C22  108.74  3.000
 NJV  H18  C24  C22  111.65  3.000
 NJV  H23  C7   H22  107.39  3.000
 NJV  H23  C7   H21  108.23  3.000
 NJV  H22  C7   H21  107.37  3.000
 NJV  H23  C7   C    110.63  3.000
 NJV  H22  C7   C    111.41  3.000
 NJV  H21  C7   C    111.63  3.000
 NJV  H24  C8   N2   126.20  3.000
 NJV  H24  C8   N    122.07  3.000
 NJV  N2   C8   N    111.72  3.000
 NJV  N2   C9   C10  109.62  3.000
 NJV  C10  C9   C11  128.78  3.000
 NJV  N2   C9   C11  121.60  3.000
 NJV  C9   N2   C8   106.05  3.000
 NJV  C22  N5   C21  125.56  3.000
 NJV  C22  N5   C20  130.28  3.000
 NJV  C21  N5   C20  104.15  3.000
 NJV  N7   N6   C21  107.17  3.000
 NJV  N6   N7   C20  108.13  3.000
 NJV  H14  C22  N5   106.34  3.000
 NJV  H14  C22  C24  108.93  3.000
 NJV  N5   C22  C24  110.46  3.000
 NJV  H14  C22  C23  108.41  3.000
 NJV  C24  C22  C23  112.34  3.000
 NJV  N5   C22  C23  110.14  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
 NJV  CONST_01  CA   CB   CG   C1      0.00   0.0  0
 NJV  CONST_02  CA   C    C6   C1      0.00   0.0  0
 NJV  CONST_03  CB   CG   C1   C6      0.00   0.0  0
 NJV  CONST_04  CB   CA   C    C6      0.00   0.0  0
 NJV  CONST_05  N    CA   C    C6    180.00   0.0  0
 NJV  CONST_06  C19  C18  C17  C16     0.00   0.0  0
 NJV  CONST_07  N6   N7   C20  C16   180.00   0.0  0
 NJV  CONST_08  C21  N5   C20  C16   180.00   0.0  0
 NJV  CONST_09  C19  CZ   NH1  C16     0.00   0.0  0
 NJV  CONST_10  C9   N2   C8   N       0.00   0.0  0
 NJV  CONST_11  CG   CB   CA   N     180.00   0.0  0
 NJV  CONST_12  N2   C9   C10  N       0.00   0.0  0
 NJV  CONST_13  N2   C8   N    CA    180.00   0.0  0
 NJV  CONST_14  C9   C10  N    CA    180.00   0.0  0
 NJV  CONST_15  CG   C1   C6   C       0.00   0.0  0
 NJV  CONST_16  CG   CB   CA   C       0.00   0.0  0
 NJV  CONST_21  C17  C18  C19  CZ      0.00   0.0  0
 NJV  CONST_22  C17  C16  NH1  CZ      0.00   0.0  0
 NJV  CONST_23  C20  C16  NH1  CZ    180.00   0.0  0
 NJV  CONST_24  C18  C17  C16  NH1     0.00   0.0  0
 NJV  CONST_27  C18  C19  CZ   NH1     0.00   0.0  0
 NJV  CONST_28  N2   C8   N    C10     0.00   0.0  0
 NJV  CONST_29  C8   N2   C9   C10     0.00   0.0  0
 NJV  CONST_32  C20  C16  C17  C18   180.00   0.0  0
 NJV  CONST_33  C21  N6   N7   C20     0.00   0.0  0
 NJV  CONST_34  N6   C21  N5   C20     0.00   0.0  0
 NJV  CONST_35  N7   C20  N5   C21     0.00   0.0  0
 NJV  CONST_36  C9   C10  N    C8      0.00   0.0  0
 NJV  CONST_37  N7   N6   C21  N5      0.00   0.0  0
 NJV  CONST_38  N6   N7   C20  N5      0.00   0.0  0
 NJV  CONST_39  C8   N2   C9   C11   180.00   0.0  0
 NJV  CONST_40  N    C10  C9   C11   180.00   0.0  0
 NJV  CONST_41  C7   C    C6   C1    180.00   0.0  0
 NJV  CONST_42  CD   CG   C1   C6    180.00   0.0  0
 NJV  CONST_43  C22  N5   C20  C16     0.00   0.0  0
 NJV  CONST_44  NE   CZ   NH1  C16   180.00   0.0  0
 NJV  CONST_45  C7   C    CA   N       0.00   0.0  0
 NJV  CONST_46  CD   CG   CB   CA    180.00   0.0  0
 NJV  CONST_47  F1   C1   C6   C     180.00   0.0  0
 NJV  CONST_48  F1   C1   CG   CB    180.00   0.0  0
 NJV  CONST_49  C7   C    CA   CB    180.00   0.0  0
 NJV  CONST_50  C18  C19  CZ   NE    180.00   0.0  0
 NJV  CONST_51  N6   C21  N5   C22   180.00   0.0  0
 NJV  CONST_52  N7   C20  N5   C22   180.00   0.0  0
 NJV  CONST_53  H5   CB   CG   C1    180.00   0.0  0
 NJV  CONST_54  H7   C10  C9   C11     0.00   0.0  0
 NJV  CONST_55  H11  C18  C17  C16   180.00   0.0  0
 NJV  CONST_56  H1   C6   C    CA    180.00   0.0  0
 NJV  CONST_57  H24  C8   N    CA      0.00   0.0  0
 NJV  CONST_58  H10  C17  C16  NH1   180.00   0.0  0
 NJV  CONST_59  H12  C19  CZ   NH1   180.00   0.0  0
 NJV  CONST_60  H13  C21  N5   C20   180.00   0.0  0
 NJV  CONST_61  CZ   NE   CD   CG    180.00   0.0  0
 NJV  CONST_65  O1   CD   NE   CZ      0.00   0.0  0
 NJV  Var_01    C9   C11  C13  C12   109.15  30.0  1
 NJV  Var_02    N2   C9   C11  C12   -92.40  30.0  1
 NJV  Var_03    H3   C12  C13  C11  -107.21  30.0  1
 NJV  Var_04    NE   CD   CG   C1   -138.54  30.0  2
 NJV  Var_05    C23  C22  N5   C20    91.24  30.0  2
 NJV  Var_06    H21  C7   C    C6    136.52  30.0  2
 NJV  Var_07    H15  C23  C22  N5   -176.49  30.0  3
 NJV  Var_08    H18  C24  C22  N5     54.66  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
 NJV  chir_01  C11  C9  C13  C12  both

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
 NJV  plan-1  C11  0.020
 NJV  plan-1  N    0.020
 NJV  plan-1  CA   0.020
 NJV  plan-1  C10  0.020
 NJV  plan-1  C8   0.020
 NJV  plan-1  C9   0.020
 NJV  plan-1  N2   0.020
 NJV  plan-1  H7   0.020
 NJV  plan-1  H24  0.020
 NJV  plan-2  C16  0.020
 NJV  plan-2  C20  0.020
 NJV  plan-2  C21  0.020
 NJV  plan-2  N5   0.020
 NJV  plan-2  N6   0.020
 NJV  plan-2  N7   0.020
 NJV  plan-2  H13  0.020
 NJV  plan-2  C22  0.020
 NJV  plan-3  C1   0.020
 NJV  plan-3  C6   0.020
 NJV  plan-3  N    0.020
 NJV  plan-3  CA   0.020
 NJV  plan-3  C    0.020
 NJV  plan-3  CB   0.020
 NJV  plan-3  CG   0.020
 NJV  plan-3  CD   0.020
 NJV  plan-3  C7   0.020
 NJV  plan-3  F1   0.020
 NJV  plan-3  H1   0.020
 NJV  plan-3  H5   0.020
 NJV  plan-4  C16  0.020
 NJV  plan-4  NE   0.020
 NJV  plan-4  CZ   0.020
 NJV  plan-4  NH1  0.020
 NJV  plan-4  C17  0.020
 NJV  plan-4  C18  0.020
 NJV  plan-4  C19  0.020
 NJV  plan-4  C20  0.020
 NJV  plan-4  H10  0.020
 NJV  plan-4  H11  0.020
 NJV  plan-4  H12  0.020
 NJV  plan-5  CG   0.020
 NJV  plan-5  CD   0.020
 NJV  plan-5  NE   0.020
 NJV  plan-5  CZ   0.020
 NJV  plan-5  O1   0.020
 NJV  plan-5  H6   0.020

